# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Microsporidia/Encephalitozoon_romaleae_SJ-2008-ASM28003v2/GCA_000280035.2_ASM28003v2_genomic.fixed.ORF.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Microsporidia/Encephalitozoon_romaleae_SJ-2008-ASM28003v2/GCA_000280035.2_ASM28003v2_genomic.fixed.ORF.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Microsporidia/Encephalitozoon_romaleae_SJ-2008-ASM28003v2/GCA_000280035.2_ASM28003v2_genomic.fixed.ORF.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gene0|gene0|rna0|rna0  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1515.37
//
Query:       gene1|gene1|rna1|rna1  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.6e-09   35.7   0.0    1.7e-08   34.6   0.0    1.6  1  UBX         UBX domain
  ------ inclusion threshold ------
      0.014   15.0   0.7      0.057   13.0   0.1    2.1  2  Ndc80_HEC   HEC/Ndc80p family
      0.014   14.6   2.5      0.019   14.2   2.5    1.2  1  RE_HindIII  HindIII restriction endonuclease
      0.031   14.3   2.1      0.031   14.3   2.1    1.6  2  YcbB        YcbB domain
      0.035   14.2   0.0        2.6    8.2   0.0    2.8  2  UBA_2       Ubiquitin associated domain (UBA)


Domain annotation for each model (and alignments):
>> UBX  UBX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   4.6e-12   1.7e-08       1      81 []     125     203 .]     125     203 .] 0.93

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 4.6e-12
                            XTTSSEEEEEEEETTSTEEEEEEESSSBHHHHHHHHHHHCCCCCTSEEEEETTTTEEGGCCCCSBCCCC.TTTSCEEEEEEE CS
                    UBX   1 seaedatrlqiRlpdGsrlvrrFkksdtlesvyeyVdsklfekeepFqLltsfPrreltksdkktLsdl.gllpnstlvlee 81 
                            se+ +++++++ l dG++    F+k+dt+e++++ +++ l++k  +F+L ++   +++++++ k++s++ gl+p+++l++ee
  gene1|gene1|rna1|rna1 125 SEDTSDCKIKLWLGDGTSSILGFSKDDTIEDLFKKIETRLNKK--RFSLFKMNHVKPIERNT-KKISEIpGLYPRGVLFIEE 203
                            58899******************************99988654..59**************8.****************985 PP

>> Ndc80_HEC  HEC/Ndc80p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.6e-05     0.057      34      92 ..       3      62 ..       1      91 [. 0.81
   2 ?    0.6   0.3      0.11   3.9e+02      24      52 ..      78     106 ..      57     129 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
              Ndc80_HEC 34 dksfqseliqellefLkennfehsisaktlksPsqkdfssifkfLykrldpsyefq.kki 92
                           +++  + +  e++++L +++f+++  ++++k+  +kd+  +++f+++  + + +   k+ 
  gene1|gene1|rna1|rna1  3 ERNKTEVSDGEVISYLVQSGFTKEEVQNAIKETGSKDIDLLVNFIISSTQDKIHKGvKQT 62
                           56666777789**********************************998766654443444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
              Ndc80_HEC  24 sverDprplrdksfqseliqellefLken 52 
                            +++r    ++++ ++++li+++ + ++e+
  gene1|gene1|rna1|rna1  78 EKKRREEIMKERIYREQLINQIKADMAEK 106
                            33333345788888888888876655554 PP

>> RE_HindIII  HindIII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.5   5.2e-06     0.019     176     276 ..      32     162 ..      14     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-06
             RE_HindIII 176 skespteaerlLke..yakivaaldpaklkeakaYWskinqtilklaettkellreeklaasellkeakqeelarleaek........ 253
                             ke  +++  lL +  ++ + ++++ +  + +k+Y +++ ++ ++l+++ +e++ +e   +++l+++ k +  ++le +k        
  gene1|gene1|rna1|rna1  32 IKETGSKDIDLLVNfiISSTQDKIHKGVKQTKKEYNNTMPKEAAELEKKRREEIMKERIYREQLINQIKADMAEKLERDKlederlms 119
                            5555666667776633577888888888679***********************************9999999999999888877777 PP

             RE_HindIII 254 ......................erirglsdeealkelivekKlea 276
                                                  ++i g s+++ +++l   kK+e+
  gene1|gene1|rna1|rna1 120 stveksedtsdckiklwlgdgtSSILGFSKDDTIEDLF--KKIET 162
                            77777777777777777777777777777777777764..45555 PP

>> YcbB  YcbB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.1   8.8e-06     0.031      12      74 ..      32      93 ..      28     115 .. 0.86
   2 ?   -2.9   0.0       1.9   6.7e+03      48     126 ..     159     164 ..     144     181 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.8e-06
                   YcbB 12 igeaGskdllkiveyleekekeetekklpslkeiyeelaekkeaseeeiekevkaieqRiRRa 74
                           i e+Gskd+  +v++++++ +++ +k   + k+ y++ + k++a e e+++  + ++ Ri R 
  gene1|gene1|rna1|rna1 32 IKETGSKDIDLLVNFIISSTQDKIHKGVKQTKKEYNNTMPKEAA-ELEKKRREEIMKERIYRE 93
                           789***************877766999*************9855.7888888899*****985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                   YcbB  48 elaekkeaseeeiekevkaieqRiRRaikkalknlAslGledysnpkfeeYasklFdfkevrkkmkelekksesskgki 126
                            ++                                                                          +++
  gene1|gene1|rna1|rna1 159 KIE-------------------------------------------------------------------------TRL 164
                            222.........................................................................222 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00072       2.6       4      27 ..      13      35 ..      11      53 .. 0.83
   2 ?    2.8   0.0     0.036   1.3e+02      11      29 ..     143     161 ..     141     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00072
                  UBA_2  4 dvvsaLsktMGYdkdeIieaLeka 27
                           +v+s L ++ G+ k+e+++a+++ 
  gene1|gene1|rna1|rna1 13 EVISYLVQS-GFTKEEVQNAIKET 35
                           677777666.***********975 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.036
                  UBA_2  11 ktMGYdkdeIieaLekaek 29 
                            + +G++kd+ ie L k+ +
  gene1|gene1|rna1|rna1 143 SILGFSKDDTIEDLFKKIE 161
                            678******9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2319  (0.129344); expected 358.6 (0.02)
Passed bias filter:                      746  (0.0416086); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1292.78
//
Query:       gene10|gene10|rna10|rna10  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-14   51.0   1.7    9.3e-14   50.8   1.7    1.2  1  Mpp10     Mpp10 protein


Domain annotation for each model (and alignments):
>> Mpp10  Mpp10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   1.7   5.2e-18   9.3e-14     329     409 ..       1      81 [.       1     113 [. 0.89

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 5.2e-18
                      Mpp10 329 lqekIkkLEeealaeKpWqLkGEvtAkdRPenSLLe.edleFdrtarpaPviTeettetLEdiIkqRIkdkafDDveRkvkp 409
                                ++e I+++E+ +++ K+W+  GEv  k+RP+nSLLe e+++F ++    P   +++  ++E+i  qRI++ +fD+ e  +k+
  gene10|gene10|rna10|rna10   1 MNESIEEIEKLLVKPKEWKYAGEVDIKKRPKNSLLErEEIDFKQGPPLIPFS-SKQDSEVESITLQRIREGTFDNHEYNIKE 81 
                                799********************************9559******9999975.566778***************97766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 901.58
//
Query:       gene100|gene100|rna100|rna100  [L=383]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   38.3   0.0    6.5e-08   32.7   0.0    2.6  2  Rad17           Rad17 P-loop domain
    2.5e-08   34.4   0.1    1.1e-07   32.3   0.0    2.1  2  AAA             ATPase family associated with various cellula
    0.00015   22.0   0.0    0.00035   20.9   0.0    1.7  1  AAA_assoc_2     AAA C-terminal domain
    0.00017   21.4   0.0    0.00034   20.4   0.0    1.5  1  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
    0.00028   20.7   0.0    0.00052   19.8   0.0    1.3  1  DNA_pol3_delta  DNA polymerase III, delta subunit
    0.00075   19.8   0.2       0.22   11.8   0.0    2.6  2  AAA_22          AAA domain
     0.0013   18.6   0.1     0.0041   17.0   0.0    1.8  2  AAA_11          AAA domain
     0.0034   17.4   0.0     0.0078   16.2   0.0    1.7  1  AAA_14          AAA domain
     0.0037   17.8   0.8      0.012   16.1   0.0    2.3  3  AAA_18          AAA domain
     0.0043   17.5   0.0      0.014   15.8   0.0    1.8  1  AAA_16          AAA ATPase domain
     0.0058   16.6   0.1      0.047   13.7   0.1    2.3  1  AAA_5           AAA domain (dynein-related subfamily)
     0.0079   15.4   0.4      0.046   12.9   0.0    2.0  2  TIP49           TIP49 P-loop domain
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.099   12.2   0.0    2.1  1  AAA_7           P-loop containing dynein motor region
      0.028   14.1   0.0       0.23   11.1   0.0    2.1  2  AAA_30          AAA domain
      0.054   13.4   0.1       0.41   10.5   0.0    2.3  2  NACHT           NACHT domain
      0.056   14.0   0.9       0.42   11.1   0.0    2.6  3  ABC_tran        ABC transporter
      0.067   13.1   0.1       0.58   10.1   0.0    2.4  3  RsgA_GTPase     RsgA GTPase
      0.073   12.9   0.1        1.1    9.1   0.0    2.5  3  AAA_3           ATPase family associated with various cellula
      0.094   11.8   0.0       0.23   10.5   0.0    1.6  1  T2SSE           Type II/IV secretion system protein
      0.094   12.5   0.0       0.19   11.5   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
       0.12   12.8   0.0       0.24   11.9   0.0    1.5  1  AAA_23          AAA domain
       0.14   12.5   0.0       0.49   10.7   0.0    1.8  2  AAA_19          AAA domain


Domain annotation for each model (and alignments):
>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     8e-11   6.5e-08       8      76 ..       5      70 ..       2      78 .. 0.84
   2 ?    2.6   0.1      0.14   1.1e+02     128     152 ..      88     112 ..      78     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 8e-11
                          Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew 76
                                    W eky+P+k  +l       +e  +wl+    +++  riLLi GP+G gk+  v++Ls  +g +l+e+
  gene100|gene100|rna100|rna100  5 VWAEKYRPQKYTDLVFKGGVHHEALKWLRDY--PNH-GRILLINGPPGTGKTSLVHILSSVFGLNLIEF 70
                                   6*************76666667778888754..554.67**************************9996 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                          Rad17 128 dlrtdkklilvedlPnkfyrdsdal 152
                                     ++++k+lil++++ +    d+++l
  gene100|gene100|rna100|rna100  88 TVNGKKNLILIDEIDSLPSVDVETL 112
                                    5789********9987777666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   1.4e-10   1.1e-07       1      72 [.      42     106 ..      42     134 .. 0.82
   2 ?   -1.8   0.0       4.8   3.9e+03      23      52 ..     156     184 ..     144     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.4e-10
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalak 72 
                                    +l+ GppGtGKT+l++ + + +g +++e+++s+          +ki ++  ++  k  +  ++iDEid+l +
  gene100|gene100|rna100|rna100  42 LLINGPPGTGKTSLVHILSSVFGLNLIEFNASNGS-----GCVDKILNVYGTVNGK--KNLILIDEIDSLPS 106
                                    5899*************************999888.....3345555555555444..49*********955 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.8
                                    THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                            AAA  23 gvefleisgsellskyvgesekkirelfke 52 
                                    + e+++++ s l  ++v++s  ++r++++ 
  gene100|gene100|rna100|rna100 156 KEEMVNVDNSALS-QLVEDSDGDFRAIINY 184
                                    4467777777776.7788888888887765 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.3e-07   0.00035       3      66 ..     158     226 ..     156     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.3e-07
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak.....egkieitledleealqrkalryDkag 66 
                                    + ++++++al++l+e +dGD R+++n+L++  +   ++      +++ it++ + e++  k++r    +
  gene100|gene100|rna100|rna100 158 EMVNVDNSALSQLVEDSDGDFRAIINYLQIHKQGLTNSkdlriGKSVPITRHRAVELILTKHVRWKTYE 226
                                    56899************************9888877667888888888999999999988888876554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.1e-07   0.00034      36     106 ..      42     114 ..      16     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.1e-07
                         RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsg....Pvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                                    +l+ GpPG Gkt+l +i+++ +g +l    +      ++k  ++ + ++   +k++++idei  l ++  e l s
  gene100|gene100|rna100|rna100  42 LLINGPPGTGKTSLVHILSSVFGLNLIEFNAsngsGCVDKILNVYGTVN--GKKNLILIDEIDSLPSVDVETLIS 114
                                    6889*****************9998754333000134555555555444..478999*******99877676655 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   6.4e-07   0.00052     120     170 ..     136     186 ..     129     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.4e-07
                                    EEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                 DNA_pol3_delta 120 vveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsaikqele 170
                                     +e+k++  ee++k i+++++e+ ++ ++ al++L+e + ++++ai + l+
  gene100|gene100|rna100|rna100 136 TMEIKRPGIEEVRKCIERVCKEEMVNVDNSALSQLVEDSDGDFRAIINYLQ 186
                                    579999****************************************99886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00027      0.22       4      24 ..      38      58 ..      33      82 .. 0.86
   2 ?    5.5   0.0     0.024        20      89     114 ..      92     114 ..      71     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                         AAA_22  4 tagilvvtGesGtGKTtllrr 24
                                   + +il++ G++GtGKT l+  
  gene100|gene100|rna100|rna100 38 HGRILLINGPPGTGKTSLVHI 58
                                   789*************99865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                         AAA_22  89 ravielliiDEaqhlrseealeeLrs 114
                                    +  + l++iDE++ l +   +e+L s
  gene100|gene100|rna100|rna100  92 K--KNLILIDEIDSL-PSVDVETLIS 114
                                    2..47**********.9888888844 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     5e-06    0.0041       8      37 ..      30      59 ..      24      98 .. 0.76
   2 ?   -1.2   0.1       1.8   1.4e+03      83     110 ..     279     306 ..     179     360 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5e-06
                         AAA_11  8 eaiksalseseitliqGPPGtgKTktivel 37
                                   ++++   ++  i li GPPGtgKT+ +  l
  gene100|gene100|rna100|rna100 30 KWLRDYPNHGRILLINGPPGTGKTSLVHIL 59
                                   566777788889************654333 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                         AAA_11  83 gekykpkivRvgneeeriseavksvsle 110
                                    ++++k +i Rv +  e i++ +k+  l 
  gene100|gene100|rna100|rna100 279 CNSRKADIHRVEHYREPIHDLAKERILP 306
                                    3444445555555553333333333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.6e-06    0.0078       2      79 ..      39     107 ..      38     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.6e-06
                         AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpew 79 
                                    ++il+i G+  +GKT l++ l +       + +++n  + +       +k+l+++   +++ kk+++++DEi  +p++
  gene100|gene100|rna100|rna100  39 GRILLINGPPGTGKTSLVHILSSVFG---LNLIEFNASNGSG--C--VDKILNVYGT-VNG-KKNLILIDEIDSLPSV 107
                                    689**************966643333...4444444444333..2..2335666666.456.99*********99765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-05     0.012       2      31 ..      43      70 ..      42     115 .. 0.80
   2 ?   -1.7   0.0       4.9     4e+03      50      84 ..     178     211 ..     145     227 .. 0.49
   3 ?   -2.3   0.0       7.2   5.9e+03      24      39 ..     279     307 ..     258     345 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-05
                         AAA_18  2 lltGtpGvGKttlakeLskrlgfgvnlrdv 31
                                   l++G+pG+GKt+l + Ls+    g nl++ 
  gene100|gene100|rna100|rna100 43 LINGPPGTGKTSLVHILSSVF--GLNLIEF 70
                                   79***************9987..7776654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.9
                         AAA_18  50 krldedkldklldaleenssaleegknlvidghla 84 
                                     r+ +++l+ + ++l ++  +l+ gk++ i  h+a
  gene100|gene100|rna100|rna100 178 FRAIINYLQIHKQGLTNSK-DLRIGKSVPITRHRA 211
                                    2333333333333333333.355555555555554 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 7.2
                         AAA_18  24 f.............gvnlrdvakenglll 39 
                                    +              + + d+ake+ l +
  gene100|gene100|rna100|rna100 279 CnsrkadihrvehyREPIHDLAKERILPY 307
                                    14444444444444445555555555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-05     0.014      24      42 ..      39      57 ..      26      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                         AAA_16 24 pelvllsGesGvGKsslvr 42
                                   ++++l+ G++G+GK+slv 
  gene100|gene100|rna100|rna100 39 GRILLINGPPGTGKTSLVH 57
                                   399**************96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   5.7e-05     0.047       2      27 ..      42      67 ..      41     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                                   EEEE--SSSSHHHHHHHGGGGBS--E CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnrev 27
                                   +l+ GppGtgK++l+  l+++++ ++
  gene100|gene100|rna100|rna100 42 LLINGPPGTGKTSLVHILSSVFGLNL 67
                                   6889***************9987665 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   5.7e-05     0.046      49      86 ..      38      76 ..      28      98 .. 0.88
   2 ?    0.1   0.2      0.45   3.7e+02      85     162 ..     131     204 ..     116     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                          TIP49 49 aGravLlaGpsgtGktalaiaiskelg.edvpfvalsgs 86
                                    Gr +L+ Gp+gtGkt+l   +s  +g + + f+a +gs
  gene100|gene100|rna100|rna100 38 HGRILLINGPPGTGKTSLVHILSSVFGlNLIEFNASNGS 76
                                   69*****************99999999777899888887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.45
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHH CS
                          TIP49  85 gsevyslevkktevltqalrksigvrikeekevleGevveleveeaenplskekkikevkitlktakeekklklgski 162
                                      +vy++e+k+  +  +++rk i    kee   ++    +  ve+++ ++     i++ +i  +   ++k l++g+++
  gene100|gene100|rna100|rna100 131 LEDVYTMEIKRPGI--EEVRKCIERVCKEEMVNVDNSALSQLVEDSDGDFR--AIINYLQIHKQGLTNSKDLRIGKSV 204
                                    46789999988774..88999999888887655555554444555555544..8888888888888888888888776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012     0.099      28     110 ..      34     102 ..      26     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                          AAA_7  28 lllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvD 107
                                     + ++++ +l+ Gp GtGKt++++ l +      +  + i+f+a+  +  + +i+         +vyg  +gkk ++ +D
  gene100|gene100|rna100|rna100  34 DYPNHGRILLINGPPGTGKTSLVHILSSV-----FGLNLIEFNASNGSGCVDKIL---------NVYGTVNGKKNLILID 99 
                                    556788999************99866544.....458889999988887777666.........6888888888888888 PP

                          AAA_7 108 Dln 110
                                    +++
  gene100|gene100|rna100|rna100 100 EID 102
                                    885 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00029      0.23      18      39 ..      39      60 ..      29      65 .. 0.83
   2 ?    0.2   0.0      0.65   5.3e+02      87     112 ..      91     116 ..      69     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                         AAA_30 18 drvavltGpAGtGKttalkalr 39
                                    r+ +++Gp+GtGKt ++  l 
  gene100|gene100|rna100|rna100 39 GRILLINGPPGTGKTSLVHILS 60
                                   46999***********998765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.65
                         AAA_30  87 epgtllivDEagmvdtkqlaallkaa 112
                                     +++l+++DE+  + + ++++l+++ 
  gene100|gene100|rna100|rna100  91 GKKNLILIDEIDSLPSVDVETLISST 116
                                    3569*******999999999998765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0005      0.41       1      20 [.      40      59 ..      40      64 .. 0.88
   2 ?   -0.7   0.0       1.5   1.2e+03      82      99 ..      93     110 ..      87     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                   SCEEEEC-TTTCHHHHHHHH CS
                          NACHT  1 rlvilqGeaGsGKTtLlqkl 20
                                   r+++++G++G GKT L++ l
  gene100|gene100|rna100|rna100 40 RILLINGPPGTGKTSLVHIL 59
                                   6799************9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.5
                                    CEEEEEE-STT-SS-TCH CS
                          NACHT  82 rlLlilDglDelvtdlgq 99 
                                    + L+++D +D l++ + +
  gene100|gene100|rna100|rna100  93 KNLILIDEIDSLPSVDVE 110
                                    6699*******9997655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00052      0.42       9      33 ..      37      61 ..      35      65 .. 0.91
   2 ?   -1.1   0.0         3   2.4e+03     123     134 ..      89     100 ..      70     197 .. 0.64
   3 ?   -0.3   0.0       1.8   1.5e+03      54     114 ..     289     353 ..     245     356 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00052
                                   ETTSEEEEEESTTSSHHHHHHHHTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  9 kegekvaivGenGaGKStLlkllag 33
                                   ++g+++ i G+ G+GK++L+ +l+ 
  gene100|gene100|rna100|rna100 37 NHGRILLINGPPGTGKTSLVHILSS 61
                                   57999****************9985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                                    HHHTSSEEEEES CS
                                    xxxxxxxxxxxx RF
                       ABC_tran 123 llkkpkllllDE 134
                                    +  k++l+l+DE
  gene100|gene100|rna100|rna100  89 VNGKKNLILIDE 100
                                    334444444444 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.8
                                    HHHCCHCEEEE-SS--S-TTSBHHHH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  54 leslrkeigvlpqepqlfpeltvren....esdeeiekalsklglkelkdtvvksspssLSgGqk 114
                                     e++r+ i  l +e  l +  +   n     s ++++++++ ++++++k +  ++   s+S+G +
  gene100|gene100|rna100|rna100 289 VEHYREPIHDLAKERILPYFRKYDLNrtdrRSLSHLKEIMEMYSITDVKLKEEDRMEDSISKGSR 353
                                    55555555555555222222222222323344444777777777777666666666688888877 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00071      0.58      70     133 ..       8      73 ..       3      79 .. 0.71
   2 ?   -0.2   0.0         1   8.3e+02      35      86 ..      79     129 ..      71     138 .. 0.74
   3 ?   -3.4   0.0       9.6   7.8e+03      53      81 ..     308     335 ..     303     348 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00071
                                    HHHHHTTSEEEE--.TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                    RsgA_GTPase  70 eelealgyevllvs.aktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevsek 133
                                    e+++   y+ l+ +   ++e+l+ l+++ ++ ++ ++ G+ G GK++L+  l +   l+  e  ++
  gene100|gene100|rna100|rna100   8 EKYRPQKYTDLVFKgGVHHEALKWLRDYPNHgRILLINGPPGTGKTSLVHILSSVFGLNLIEFNAS 73 
                                    55666665544333044578888899888877999***************9988766666555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1
                                    HHHHHHHHHH.TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTT CS
                    RsgA_GTPase  35 ldrfLvlaee.kgiepvivlnKiDlleeeeeleelkeelealgyevllvsakt 86 
                                    +d++L ++ + +g + +i++  iD l + + +e+l + ++ + y+v+++s++ 
  gene100|gene100|rna100|rna100  79 VDKILNVYGTvNGKKNLILIDEIDSLPSVD-VETLISSTKLI-YPVVMISNEM 129
                                    566665544314557899999999999999.99888888777.9999998873 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 9.6
                                    EE-GGG--HHH.HHHHHHHHHHHTTSEEEE CS
                    RsgA_GTPase  53 lnKiDlleeee.eleelkeelealgyevll 81 
                                    + K Dl  +++ +l++lke +e   y+++ 
  gene100|gene100|rna100|rna100 308 FRKYDLNRTDRrSLSHLKEIMEM--YSITD 335
                                    66777776666323333333322..33333 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0013       1.1       2      27 ..      42      67 ..      41      73 .. 0.89
   2 ?   -3.0   0.0       7.3   5.9e+03      64      75 ..      94     105 ..      90     134 .. 0.80
   3 ?    0.4   0.0      0.66   5.4e+02      70      93 ..     312     335 ..     307     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                          AAA_3  2 vllegvPGlaktllvkalakaldlef 27
                                   +l++g PG++kt lv+ l+++++l++
  gene100|gene100|rna100|rna100 42 LLINGPPGTGKTSLVHILSSVFGLNL 67
                                   689****************9998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.3
                          AAA_3  64 nllladeinrap 75 
                                    nl+l dei+  p
  gene100|gene100|rna100|rna100  94 NLILIDEIDSLP 105
                                    789999997655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.66
                          AAA_3  70 einrappktqsalleameerqvtv 93 
                                    ++nr+  ++ s l e+me   +t 
  gene100|gene100|rna100|rna100 312 DLNRTDRRSLSHLKEIMEMYSITD 335
                                    68****************998885 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00028      0.23     104     151 ..      14      61 ..       2      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                          T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                    ++ dl++++ ++++  + lr   ++  ++l+ G+ g+GKt l+ +l +
  gene100|gene100|rna100|rna100  14 KYTDLVFKGGVHHEALKWLRDYPNHGRILLINGPPGTGKTSLVHILSS 61 
                                    68899999999999999**998677778899*********99987765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.19      22      58 ..      38      74 ..      30      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                         AAA_29 22 kg.atlltGpsGsGKSTllDAiqalLvpakkvrfNkaa 58
                                   +g + l+ Gp G+GK++l+  ++ ++  +  ++fN++ 
  gene100|gene100|rna100|rna100 38 HGrILLINGPPGTGKTSLVHILSSVFGLNL-IEFNASN 74
                                   56689**************88888887777.9999875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.24      21     154 ..      41     246 ..      35     350 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                         AAA_23  21 ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese............gkvkayvelt..fenkdgry 86 
                                    + lI Gp G+GKT+++  +  +++    +++ ++g+g+++   ++                +  ++v+++  +++++ +y
  gene100|gene100|rna100|rna100  41 ILLINGPPGTGKTSLVHILSSVFGLNLIEFNASNGSGCVDKILNVYGTvngkknlilideIDSLPSVDVEtlISSTKLIY 120
                                    679*******************9999988888885555544444333232233344444433444433333254444444 PP

                         AAA_23  87 ...............trsier.erelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkd 150
                                                   t++i+r  +e+ +k  +++ k++  +++ ++l q+++++ g + +i+n++++++q+ ++ ++l  
  gene100|gene100|rna100|rna100 121 pvvmisnemhledvyTMEIKRpGIEEVRKCIERVCKEEMVNVDNSALSQLVEDSDGDFRAIINYLQIHKQGLTNSKDL-- 198
                                    777777777777755555555444555566677778888888889999999998778888999999999999633322.. PP

                         AAA_23 151 kke..............................................r 154
                                                                                      
  gene100|gene100|rna100|rna100 199 --RigksvpitrhraveliltkhvrwktyedvystdvlslchssfpyntS 246
                                    ..122234444555555555555544444455555555555555555551 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0006      0.49      10      29 ..      39      58 ..      35      70 .. 0.81
   2 ?   -2.4   0.0       6.5   5.3e+03     103     115 ..      93     105 ..      82     117 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0006
                         AAA_19 10 ekvllvtaGpGtGKTrvlkh 29
                                    ++ll+ ++pGtGKT +++ 
  gene100|gene100|rna100|rna100 39 GRILLINGPPGTGKTSLVHI 58
                                   578999*********97754 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                         AAA_19 103 eellivDEfqdvd 115
                                    ++l+++DE+  + 
  gene100|gene100|rna100|rna100  93 KNLILIDEIDSLP 105
                                    3489999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2189.29
//
Query:       gene1001|gene1001|rna1000|rna1000  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-25   88.2  13.3    2.9e-24   86.1  13.3    1.7  1  MIP       Major intrinsic protein


Domain annotation for each model (and alignments):
>> MIP  Major intrinsic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1  13.3   1.6e-28   2.9e-24       4     226 ..       5     240 ..       2     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 1.6e-28
                                        CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSCSSSSTTSSHHHHHHHHHHHHHHHHHHHHHHHCHT-S-SHHHHH CS
                                MIP   4 svkflravlAEflatlllvfigvgsalnvkkkvsslaslvsvtleavalafglalavlvylaagiSGaHlNPavTl 79 
                                        ++k l++++ E++a++++ f++  ++l+   +++s+        + v l+ g++ +  +y ++++  aH+NPa+Tl
  gene1001|gene1001|rna1000|rna1000   5 TLKTLQSMFGEMVASFVFGFAVYSAVLGSTVSQQSA------ARVIVGLTVGFSAIGIIYSFGDVTIAHFNPAITL 74 
                                        678899***************999999887777773......3466888889999999****************** PP

                                        HHHHTTSSSHHHHHHHHHHHHHHHHHHHHHHHHHCH.HHHHHTTTTSSSSST.TSSHHHHHHHHHHHHHHHHHHHH CS
                                MIP  80 allvarkisllrailYivaQllGaivaaallklltk.glesraglfanslkp.glsagqalvvEiiltfvLvlvvf 153
                                         +++++ki +++++ Yi aQ +G ++a+  l  +   g++++ +  + ++++ g   ++ ++ E++lt+++v +vf
  gene1001|gene1001|rna1000|rna1000  75 TAILTGKIGIFHGLGYILAQYVGFMLAVCALIPCSPiGYKETLNIIRPAPSSfGGDNLNVFFTEFFLTAIFVHIVF 150
                                        ***********************9999666655554044344444444443324467899**************** PP

                                        HHCSTT...SSSSTCH..............GHHHHHHHHHHHHHHHHHHHHST-SSHHHHHHHHHHHTHSTTTTHH CS
                                MIP 154 altddk...rkvslge..............laplaigllvaliilvgipltGaamNpArslgpavvlnkfedhwvy 212
                                        a++ ++   +  ++g+               apl+igl++    ++g + +G a Np   ++p +++n+++++w y
  gene1001|gene1001|rna1000|rna1000 151 AVAVNPykpKVDTDGKfvdpdekepvdrriTAPLSIGLTLGFLAFLGLASSGGAFNPGLTFAPVIMSNTWTHFWLY 226
                                        *986541113334455999999999999989********************************************* PP

                                        HHHHHHHHHHHHHH CS
                                MIP 213 lvGPliGailgalv 226
                                        + G  +G+ +g+l+
  gene1001|gene1001|rna1000|rna1000 227 FGGQYLGGFVGGLL 240
                                        ***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1770.08
//
Query:       gene1002|gene1002|rna1001|rna1001  [L=384]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-26   91.8   0.3    2.5e-25   88.5   0.1    2.5  2  CAF1C_H4-bd  Histone-binding protein RBBP4 or subunit C of CA
    1.6e-22   79.3  13.5    7.4e-05   23.4   0.6    6.0  6  WD40         WD domain, G-beta repeat
    0.00047   19.2   0.0      0.084   11.8   0.0    3.2  3  Ge1_WD40     WD40 region of Ge1, enhancer of mRNA-decapping p
     0.0015   18.8   0.3        5.1    7.5   0.1    3.8  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain


Domain annotation for each model (and alignments):
>> CAF1C_H4-bd  Histone-binding protein RBBP4 or subunit C of CAF1 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.1   5.6e-29   2.5e-25       1      66 [.      13      82 ..      13      83 .. 0.90
   2 ?    0.6   0.0      0.16   7.1e+02      42      65 ..     342     382 ..     296     384 .] 0.61

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 5.6e-29
                                       HHHHHHHHHHHHHEEEEEEEE-SS--S-EEE-S-.....B---.EEEEEEEE----TTSS-EEEEEEEEEEE CS
                        CAF1C_H4-bd  1 eeylewkknapfLYdmlhshslewPsLsfdwlPd.....tvss.lskqrllvGtqtsgkeqnylyvakvslp 66
                                       eey++wkkn+p+LYd+++sh+l+wPsLs++w+Pd     +     ++qrll++t+tsg+e++y+++ +v+ p
  gene1002|gene1002|rna1001|rna1001 13 EEYKVWKKNVPYLYDLMFSHTLQWPSLSVQWFPDvrrdeD--IgRTTQRLLLSTHTSGSEDEYIMIVNVEFP 82
                                       7********************************9766431..34779*********************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.16
                                        EEEEE----TT.................SS-EEEEEEEEEE CS
                        CAF1C_H4-bd  42 qrllvGtqtsg.................keqnylyvakvsl 65 
                                         r+l G +ts+                 +e+n l+++++ +
  gene1002|gene1002|rna1001|rna1001 342 MRFLHGGHTSTvcdiswnpaepfeiasvSEDNILQIWQMPQ 382
                                        35666666655555555555555555557888888887755 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.93   4.2e+03      25      36 ..      65      76 ..      39      78 .. 0.75
   2 !    8.0   0.0    0.0013       5.7       6      38 .]     153     187 ..     149     187 .. 0.76
   3 !   14.4   0.1   1.2e-05     0.053       4      38 .]     198     234 ..     196     234 .. 0.76
   4 !   23.4   0.6   1.7e-08   7.4e-05       2      38 .]     239     278 ..     238     278 .. 0.85
   5 !   22.1   0.3   4.2e-08   0.00019       2      38 .]     284     322 ..     283     322 .. 0.89
   6 !   15.7   0.0   4.6e-06     0.021       8      37 ..     347     378 ..     340     379 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.93
                                       EEEEETTSEEEE CS
                               WD40 25 lasGsdDgtvri 36
                                       ++sGs+D  ++i
  gene1002|gene1002|rna1001|rna1001 65 HTSGSEDEYIMI 76
                                       468999988887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0013
                                        EEESS.SS.EEEEEEETTSSE.......EEEEETTSEEEEEE CS
                               WD40   6 tltGH.ss.vtslafspdgaw.......lasGsdDgtvriWd 38 
                                        +l+GH s+   +l      +w       +as+++Dg+v ++d
  gene1002|gene1002|rna1001|rna1001 153 VLRGHeSGgF-GL------SWnnlspgeVASCGEDGNVCVFD 187
                                        7889974445.77......66666666899*********998 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 1.2e-05
                                        EEEEESS.SSEEEEE.EETTSSEEEEEETTSEEEEEE CS
                               WD40   4 lrtltGH.ssvtsla.fspdgawlasGsdDgtvriWd 38 
                                        + tl+ H   v++++    d+ +l+s +dDg +++Wd
  gene1002|gene1002|rna1001|rna1001 198 MVTLSRHkAAVNDCSfGFFDKELLSSVGDDGILMFWD 234
                                        668999*656****966666666655599*******9 PP

  == domain 4  score: 23.4 bits;  conditional E-value: 1.7e-08
                                        EEEEEEE.SS.SSEEEEE.EETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtlt.GH.ssvtsla.fspdgawlasGsdDgtvriWd 38 
                                        +c++  + +H s+v s++  s dg+ +a++s+D++v+iWd
  gene1002|gene1002|rna1001|rna1001 239 DCIHLVEeAHsSDVLSVSfSSLDGNVVATSSEDKSVKIWD 278
                                        677777559*88899999888899999************9 PP

  == domain 5  score: 22.1 bits;  conditional E-value: 4.2e-08
                                        EEEEEEESS.SSEEEEEEETTSSE.EEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgaw.lasGsdDgtvriWd 38 
                                        q+ +++ GH ++v  + +sp+ +  lasGs D+ v +Wd
  gene1002|gene1002|rna1001|rna1001 284 QPFQVFLGHsKDVLNVEWSPHDSGvLASGSADRRVIVWD 322
                                        7889999**999*****9999999447999********9 PP

  == domain 6  score: 15.7 bits;  conditional E-value: 4.6e-06
                                        ESS.SSEEEEEEETTSSE.EEEEETTSEEEEE CS
                               WD40   8 tGH.ssvtslafspdgaw.lasGsdDgtvriW 37 
                                         GH s v++++++p  ++ +as s+D+ + iW
  gene1002|gene1002|rna1001|rna1001 347 GGHtSTVCDISWNPAEPFeIASVSEDNILQIW 378
                                        49*777************99988********* PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.1   0.0    0.0082        37      62      97 ..     202     237 ..     174     245 .. 0.83
   2 !   11.8   0.0   1.9e-05     0.084     185     238 ..     247     309 ..     236     312 .. 0.66
   3 ?   -0.6   0.0      0.12   5.2e+02      56      96 ..     341     381 ..     337     384 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0082
                           Ge1_WD40  62 kglkgevldlafahvsskillavdekgslfvykvee 97 
                                           k++v+d +f + +++ l +v + g l+ ++ ++
  gene1002|gene1002|rna1001|rna1001 202 SRHKAAVNDCSFGFFDKELLSSVGDDGILMFWDTRT 237
                                        456889*********************999998765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.9e-05
                           Ge1_WD40 185 eehsliveaafsp.dGtalatasedGevkffqvylede........eeprCLheWkPhdGksl 238
                                         + s + + +fs+ dG ++at+sed  vk +      +        +++    eW Phd   l
  gene1002|gene1002|rna1001|rna1001 247 AHSSDVLSVSFSSlDGNVVATSSEDKSVKIWDRRNLSQpfqvflghSKDVLNVEWSPHDSGVL 309
                                        34457888888766***************9743332222334444133334459999997655 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.12
                           Ge1_WD40  56 eeraLlkglkgevldlafahvsskillavdekgslfvykve 96 
                                        e+r L  g +++v d+++   +   +++v e   l+++++ 
  gene1002|gene1002|rna1001|rna1001 341 EMRFLHGGHTSTVCDISWNPAEPFEIASVSEDNILQIWQMP 381
                                        57788888999999999999999999999999999999875 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   7.1e+03      51      68 ..     122     139 ..     107     148 .. 0.70
   2 !    6.0   0.0    0.0032        14      49      90 ..     217     258 ..     174     260 .. 0.83
   3 !    7.5   0.1    0.0011       5.1      34      90 ..     245     302 ..     217     304 .. 0.73
   4 !    7.2   0.1    0.0014       6.2      10      69 ..     265     325 ..     261     361 .. 0.75
   5 ?    1.0   0.0      0.12   5.4e+02      36      65 ..     348     378 ..     341     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                        ANAPC4_WD40  51 klLavaysdgevrlldae 68 
                                        ++Lav  + + v+++d  
  gene1002|gene1002|rna1001|rna1001 122 NILAVRSDISDVHIYDYT 139
                                        678888877888888865 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0032
                        ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                        d +lL  + +dg + + d  +g+++h ++ ++++ v +++++
  gene1002|gene1002|rna1001|rna1001 217 DKELLSSVGDDGILMFWDTRTGDCIHLVEEAHSSDVLSVSFS 258
                                        6678999999******************99999889888875 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0011
                        ANAPC4_WD40  34 edkedsevrsLaWkp.dgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                        e++++s v s++++  dg++ a + +d +v++ d  +     ++  +++k v  ++W+
  gene1002|gene1002|rna1001|rna1001 245 EEAHSSDVLSVSFSSlDGNVVATSSEDKSVKIWDRRNLSQPFQVFLGHSKDVLNVEWS 302
                                        5677778888888643888888888888888888888777777777777778888875 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0014
                        ANAPC4_WD40  10 iAlatedgellv.fRlngqrvwtleedkedsevrsLaWkpdgk.lLavaysdgevrlldaes 69 
                                        +A  +ed+++ +  R n  + +++   ++++ v +++W+p ++ +La + +d +v + d++ 
  gene1002|gene1002|rna1001|rna1001 265 VATSSEDKSVKIwDRRNLSQPFQV-FLGHSKDVLNVEWSPHDSgVLASGSADRRVIVWDMNR 325
                                        778888888877458899888888.678899999****98664499****999999988765 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.12
                        ANAPC4_WD40  36 kedsevrsLaWkpdgkl.Lavaysdgevrll 65 
                                        ++ s+v +++W+p + + +a + +d+ +++ 
  gene1002|gene1002|rna1001|rna1001 348 GHTSTVCDISWNPAEPFeIASVSEDNILQIW 378
                                        57789999*****999868888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2328.19
//
Query:       gene1003|gene1003|rna1002|rna1002  [L=398]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-26   91.4   0.4      8e-26   90.9   0.4    1.2  1  DnaJ_C          DnaJ C terminal domain
      3e-09   37.1  21.1    6.6e-09   36.0  21.1    1.6  1  DnaJ_CXXCXGXG   DnaJ central domain
    3.3e-08   33.5   2.8    9.9e-08   32.0   2.8    1.8  1  DnaJ            DnaJ domain
  ------ inclusion threshold ------
      0.081   13.6   0.3       0.16   12.6   0.3    1.4  1  Cytochrom_B562  Cytochrome b562
       0.18   10.7   0.1       0.24   10.3   0.1    1.2  1  Baculo_p48      Baculovirus P48 protein
       0.51   10.4  10.9        1.6    8.8  11.1    1.8  1  DZR             Double zinc ribbon
          1    9.4  18.6          2    8.5   2.5    2.7  2  Anti-TRAP       Tryptophan RNA-binding attenuator protein inh


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.4   3.1e-29     8e-26       3     145 ..     127     334 ..     125     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 3.1e-29
                                        EEEEE-HHHHHH-.EEE.EEEE...................................................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                             DnaJ_C   3 veleisleelykGktkkikikrnvi................................................... 27 
                                        + ++isl+e + Gk  k++++ ++i                                                   
  gene1003|gene1003|rna1002|rna1002 127 YVITISLRESFVGKVSKFNVRTEKIcptcdgkggkdveackkcngsgvcttrrnlggfvtlaetrcdscggsgnki 202
                                        7799****************88888*************************************************** PP

                                        .................TEEEEEE-TT--TT-EEEETT-SSSS...S---EEEEEEE---SS-EEETTEEEEEEEE CS
                                        .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaJ_C  28 .............kkekktlevkipaGikdgqkirlegeGdeeg.gepGDlivtikvkphpvFkrkgndlyvevei 89 
                                                     +++k+ +ev+i++G+++g+ki++eg+Gd++    pGD+i++i+v+++++F+r+gndl+ +++i
  gene1003|gene1003|rna1002|rna1002 203 kgkacsacnggeyIQDKTMFEVNIKPGVRKGEKIVFEGMGDQRRnHVPGDVIFIIDVQEDSRFERRGNDLIGKIDI 278
                                        ************9888889**********************7777**************************9999* PP

                                        EHHHHHHTEEEEEE-SS-EE.EEEE...--TT-EEEETT-S-EET...TEE--EEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxx.xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaJ_C  90 slaeallGgklevptldgkv.klki...tqpgevlrikgkGmpklkkpgkrGdlyvevkv 145
                                        +l +a+ Gg      +dg+  ++++      ++vlri+++G++ +    k G+l+++ ++
  gene1003|gene1003|rna1002|rna1002 279 PLCTAIGGGVAYFTHIDGRLlEINVnpfKTFDTVLRIRNEGFKGN----KVGNLVLRPNI 334
                                        ********7776655655431455577556677*********755....79999888766 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0  21.1   2.6e-12   6.6e-09       1      65 [.     152     212 ..     152     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.6e-12
                      DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkG 65 
                                        C++C+G+g   ++++ Ck+C+GsGv +++++ lg fv+  +++C++C+G+G+ ik k  C++C+G
  gene1003|gene1003|rna1002|rna1002 152 CPTCDGKGG--KDVEACKKCNGSGVCTTRRN-LGGFVTLAETRCDSCGGSGNKIKGK-ACSACNG 212
                                        ********8..56899********7666664.788888999*************655.8*****9 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   2.8   3.9e-11   9.9e-08       2      63 .]       8      85 ..       7      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 3.9e-11
                                       HHHHHTSSTTG-HHHHHHHHHHHHHHHSTT........TS.....CCHHHHHH........HHHHHHHHHHHHTSHHH CS
                               DnaJ  2 yYeiLgvskdasedeIkkaYrklalkyHPD........kn.....pkdpeaee........kFkeineAyevLsdpek 58
                                       yY+iL++s+ as +e+++aY ++  kyH D        kn     +     +e        +  ++n A +vL d++k
  gene1003|gene1003|rna1002|rna1002  8 YYKILELSPGASISEVRRAYSRQQAKYHLDspfmkdklKNaandeE-----REkikkecgeMSAKLNSAKSVLFDEKK 80
                                       9***************************997777555444433321.....22344556658889************* PP

                                       HHHHH CS
                               DnaJ 59 RkqYD 63
                                       +k+YD
  gene1003|gene1003|rna1002|rna1002 81 KKEYD 85
                                       ****9 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   6.2e-05      0.16       9      63 ..      41      90 ..      39      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                     Cytochrom_B562  9 mkkalkqvakaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldk 63
                                       mk++lk++a+ ++ e++kk+  e+ a  ++ak+  +     d+++ k+Y+ G  +
  gene1003|gene1003|rna1002|rna1002 41 MKDKLKNAANDEEREKIKKECGEMSAKLNSAKSVLF-----DEKKKKEYDSGVGE 90
                                       99**********************************.....*********99765 PP

>> Baculo_p48  Baculovirus P48 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   9.4e-05      0.24      66     122 ..     117     190 ..     102     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.4e-05
                         Baculo_p48  66 qktdseanvkqilalflrkefisqvpsfrvikqilqkyykpveapnveyivCqkCa...................p 122
                                        q+t+ +   k ++++ lr+ f+++v++f+v  + + +  +   + +ve+  C+kC                     
  gene1003|gene1003|rna1002|rna1002 117 QRTNKVNSTKYVITISLRESFVGKVSKFNVRTEKICPTCDGKGGKDVEA--CKKCNgsgvcttrrnlggfvtlaeT 190
                                        6799999999***************************************..****866666665555555555550 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  11.1   0.00063       1.6       1      48 [.     152     210 ..     152     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00063
                                DZR   1 CpqCgeelppdarfCseCgtk.lkavaa.........edrCpsCgek.vdpearfCpeC 48 
                                        Cp+C  +  +d + C++C+ + +  + +         e+rC+sCg + ++ + + C +C
  gene1003|gene1003|rna1002|rna1002 152 CPTCDGKGGKDVEACKKCNGSgVCTTRRnlggfvtlaETRCDSCGGSgNKIKGKACSAC 210
                                        ******************88856544449999***************9*********** PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.4    0.0061        16      10      45 ..     149     178 ..     146     181 .. 0.92
   2 ?    8.5   2.5   0.00077         2      10      42 ..     189     216 ..     185     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0061
                                        EEE-TTTTTTSEETTE......E-TTTTTSSEEE-H CS
                          Anti-TRAP  10 EtkCdaCngsGkiepeeprasleCPkCsGkglipTa 45 
                                        E+ C++C+g G  + e       C kC+G g+  T 
  gene1003|gene1003|rna1002|rna1002 149 EKICPTCDGKGGKDVE------ACKKCNGSGVCTTR 178
                                        889*************......9*********9885 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00077
                                        EEE-TTTTTTSE.ETTE......E-TTTTTSSEE CS
                          Anti-TRAP  10 EtkCdaCngsGk.iepeeprasleCPkCsGkgli 42 
                                        Et Cd C gsG+ i+++       C +C+G   i
  gene1003|gene1003|rna1002|rna1002 189 ETRCDSCGGSGNkIKGK------ACSACNGGEYI 216
                                        99*********625666......99999997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2335.53
//
Query:       gene1004|gene1004|rna1003|rna1003  [L=505]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-44  151.2   0.0    7.3e-44  150.4   0.0    1.5  1  NPL4      NPL4 family
    2.9e-29  102.1   4.3    9.5e-29  100.4   4.3    1.8  1  zf-NPL4   NPL4 family, putative zinc binding region
    0.00027   20.2  10.0    0.00038   19.7   3.7    2.6  2  zf-RanBP  Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> NPL4  NPL4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.4   0.0   1.2e-47   7.3e-44       1     222 [.     202     402 ..     202     474 .. 0.85

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 1.2e-47
                               NPL4   1 RlgylyGryekydevPlGikavveaiyEPpqedeldgltlledeeekevdeiakklglekvGviftDlldagakdg 76 
                                        R+g+l Gry  +d +PlG+kavv  i+EP+qed  dg  ++      ++de     g+  vG+i+tD+l +   +g
  gene1004|gene1004|rna1003|rna1003 202 RFGFLVGRYMDHDMIPLGMKAVVSGIWEPEQEDYPDGFVITG-----SIDEPFGGTGFGIVGMIYTDILME---KG 269
                                        9*************************************9975.....799999***************965...68 PP

                               NPL4  77 tvlckRhkdsyflsslEvilaaklqlkhpnvtkys.etgkfsskFvtvvvsgdeegeieiesyqvsneaealvrad 151
                                         v+  + +  yflsslE+ + ak+ql hp++ k   ++ +f+s+Fvt++ + +++g i ++ yqvsn+++alv+ +
  gene1004|gene1004|rna1003|rna1003 270 GVTSDKLIRDYFLSSLEIEFMAKMQLMHPHTLKDGgHEVEFGSRFVTIIATVEKDGSIGLQEYQVSNQCMALVKGN 345
                                        8888889999********************9998647899************************************ PP

                               NPL4 152 iiepstdPslayvresseerYvpevfYkkkneyglevkenakPalPveyLlvslthgfpkepkplFkkkak 222
                                         i p+ +P++ + r+        ++ Y++k +   e   +a P lP e+ lv+lthg   +  plF k+++
  gene1004|gene1004|rna1003|rna1003 346 WILPTENPKVFLARR--------DILYRTKAK---ESMIKADPYLPGEFFLVKLTHGCKAN--PLF-KNTE 402
                                        **************9........*****9976...556789****************8765..567.2333 PP

>> zf-NPL4  NPL4 family, putative zinc binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   4.3   1.6e-32   9.5e-29      10     145 .]      78     199 ..      69     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 1.6e-32
                            zf-NPL4  10 lekqdGkikrkrdeklcrhgekgmceycsplepydeeylkekkikhlsfhaylrklnekknkkesssskiapLeel 85 
                                         +  d +ikr rd+ lc+h +++mc++c+pl+p+de+y k++ ik+lsf +y   +++kk++          L   
  gene1004|gene1004|rna1003|rna1003  78 RQDGDKTIKRGRDRMLCQHDSNAMCSNCAPLDPWDEKYYKDNMIKYLSFGSYHEMMKSKKKE----------LYVD 143
                                        4445668*********************************************8777766554..........6677 PP

                            zf-NPL4  86 sykvkkecksghapwPkgicskcqPsaitlqrqkfRmvDhvefesseivdkfldaWRktg 145
                                        +y+v   c++ h +  +  c +cq + i l+ q fRmvDhvef+ +++v++f+  WR++g
  gene1004|gene1004|rna1003|rna1003 144 DYSVVV-CSD-HGS--NTRCNRCQEKNIILTPQVFRMVDHVEFDGQHLVENFIRNWRESG 199
                                        788764.777.765..677***************************************98 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.4    0.0072        43      18      25 ..     156     163 ..     154     165 .. 0.88
   2 !   19.7   3.7   6.3e-08   0.00038       5      29 ..     481     505 .]     480     505 .] 0.95

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0072
                                        SSB-TTT- CS
                           zf-RanBP  18 stkCvaCq 25 
                                        +t+C++Cq
  gene1004|gene1004|rna1003|rna1003 156 NTRCNRCQ 163
                                        79*****8 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 6.3e-08
                                        EE-SSS--EEESSSSB-TTT--BTS CS
                           zf-RanBP   5 WdCskClvqNfawstkCvaCqapkp 29 
                                        W+C +C++ N+  +++C++C ++++
  gene1004|gene1004|rna1003|rna1003 481 WECRACTFVNERNTSACEMCNGKRE 505
                                        ********************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.37s 00:00:01.08 Elapsed: 00:00:00.58
# Mc/sec: 2620.32
//
Query:       gene1005|gene1005|rna1004|rna1004  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-13   48.8   0.1    5.6e-13   48.8   0.1    1.8  2  DnaJ         DnaJ domain
      0.008   16.1   0.1      0.056   13.3   0.0    2.0  2  Sigma70_ner  Sigma-70, non-essential region
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.063   13.3   0.0    1.9  2  DUF5444      Family of unknown function (DUF5444)
       0.02   14.4   1.2      0.025   14.0   1.2    1.2  1  DIT1_PvcA    Pyoverdine/dityrosine biosynthesis protein
       0.11   12.3   0.0        0.3   10.8   0.0    1.8  1  SPOB_a       Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   1.6e-16   5.6e-13       1      53 [.       6      55 ..       6      60 .. 0.91
   2 ?   -2.5   0.3       1.6   5.8e+03      19      37 ..     126     144 ..     126     156 .. 0.57

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.6e-16
                                       HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHH CS
                               DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevL 53
                                       d+Y+iLgv++++++ e+k+aYr+l + +HPD +   + ++e+++ei +Aye  
  gene1005|gene1005|rna1004|rna1004  6 DPYKILGVERTSTDMEVKRAYRRLQRAHHPDSK---TGNRERYEEICRAYEEI 55
                                       78*****************************99...566699********965 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                        HHHHHHHHHHSTTTSCCHH CS
                               DnaJ  19 kaYrklalkyHPDknpkdp 37 
                                        k+Y k ++k+  D  +k++
  gene1005|gene1005|rna1004|rna1004 126 KKYNKYCKKVCEDAMRKKR 144
                                        5777777777666443333 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.12   4.4e+02      73      90 ..      41      69 ..      26     104 .. 0.67
   2 !   13.3   0.0   1.6e-05     0.056      17      71 ..     107     176 ..      96     194 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                        Sigma70_ner 73 alekfeelreqyeklrk...........a 90
                                        +e++ee+  +ye+++k           +
  gene1005|gene1005|rna1004|rna1004 41 NRERYEEICRAYEEIQKrptveiipvddV 69
                                       57888888888888887666665555552 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.6e-05
                        Sigma70_ner  17 ageirLrdiidGflD...................eeeeeeeeeeeedeeeeeee......edddeeeseseaadee 67 
                                        ++e rLr+iidG+++                              ++++++ee+      ++ + + ++ +++ ++
  gene1005|gene1005|rna1004|rna1004 107 RDESRLREIIDGLIEcgalkkynkyckkvcedamR----------KKRKAREEKmarkiaDEMGIDIDAPLEELLG 172
                                        6899***************9998887654422210..........1111111111223323333444455555555 PP

                        Sigma70_ner  68 elke 71 
                                          +e
  gene1005|gene1005|rna1004|rna1004 173 RRRE 176
                                        5555 PP

>> DUF5444  Family of unknown function (DUF5444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.8e-05     0.063      16      53 ..      23      57 ..      10      59 .. 0.90
   2 ?   -0.6   0.0      0.38   1.4e+03       3      18 ..      63      78 ..      61      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                            DUF5444 16 nrelnkLyeasfPdteeGlkeayeWaseiavGWhdiqe 53
                                        r + +L  a  Pd++ G++e ye   ei+  +++iq+
  gene1005|gene1005|rna1004|rna1004 23 KRAYRRLQRAHHPDSKTGNRERYE---EICRAYEEIQK 57
                                       58999******************7...89999999996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.38
                            DUF5444  3 ivPvnGiilvqqGnre 18
                                       i+Pv+ ++ v +G++e
  gene1005|gene1005|rna1004|rna1004 63 IIPVDDVMKVYKGSKE 78
                                       99****9999999875 PP

>> DIT1_PvcA  Pyoverdine/dityrosine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.2     7e-06     0.025      83     200 ..      44     159 ..      17     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7e-06
                                        HHHHHHHHHHHHCT-TTEEEE-GGG-GGGGGG...............TT-HHHHHHHHHHHH---HHHHHHHHT.. CS
                          DIT1_PvcA  83 aYgeeLrelakekglediefvrlkdlleseeeaeeeseells.eeeyleeaeklrkeLlksfgedeeelrkeik.. 155
                                        +Y+e  r+  + ++   +e++ ++d+++  + ++ee ++++   ++y  ++ k+ ++Ll s ++de++lr+ i+  
  gene1005|gene1005|rna1004|rna1004  44 RYEEICRAYEEIQKRPTVEIIPVDDVMKVYKGSKEEVDDIIAlYNRYKGKMAKIVDNLLLSDDRDESRLREIIDgl 119
                                        5655555554444555599999999998766655555555555999****************************99 PP

                                        TSHHHHHHHHHHHHHHHHHH..--TT--S-HHHHHHHHHHHHHHH CS
                          DIT1_PvcA 156 ededtlalYrgfskflleDlaslpeakklskkklkkevkkvakem 200
                                         +  +l+ Y++++k + eD  + ++ k+++    +k ++k+a em
  gene1005|gene1005|rna1004|rna1004 120 IECGALKKYNKYCKKVCEDA-MRKKRKARE----EKMARKIADEM 159
                                        8999***************9.333333333....34444444444 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.3e-05       0.3      29      57 ..     115     143 ..     114     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.3e-05
                             SPOB_a  29 vIsGylqLgkydkaeeyieevvkelkees 57 
                                        +I+G+++ g + k ++y+++v++++++ +
  gene1005|gene1005|rna1004|rna1004 115 IIDGLIECGALKKYNKYCKKVCEDAMRKK 143
                                        79**********************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1376  (0.0767472); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.37s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1060.65
//
Query:       gene1006|gene1006|rna1005|rna1005  [L=487]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.3e-19   67.3   4.0    1.4e-18   66.7   3.3    1.5  1  Sec3_C       Exocyst complex component Sec3
  ------ inclusion threshold ------
       0.01   16.3   1.0       0.01   16.3   1.0    2.3  2  LsmAD        LsmAD domain
      0.016   15.6   1.9        3.9    7.9   0.1    2.4  2  CCDC53       Subunit CCDC53 of WASH complex
       0.43   11.1  11.5       0.13   12.8   3.1    2.9  2  APG6_N       Apg6 coiled-coil region
        1.3    9.4   6.8       0.78   10.1   3.4    2.5  2  DUF5517      Family of unknown function (DUF5517)


Domain annotation for each model (and alignments):
>> Sec3_C  Exocyst complex component Sec3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   3.3     4e-22   1.4e-18      16     258 ..      21     239 ..      15     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 4e-22
                             Sec3_C  16 kleaanikrllesdkkveelkkdidkalkecdeldalltlysveLstlsedieyIEsqnngLQvksaNqklLykeL 91 
                                        k++++ i+ l     ++ ++ + ++++ + c e+d  l+ly+ +L++l +++++IE+ n +L+ + + q   y+ L
  gene1006|gene1006|rna1005|rna1005  21 KVDQDKINMLERCMGEIPKIYPNLEQVRTKCKEIDLSLSLYTIKLESLAKEMKEIERENTKLENEIRYQTSIYEHL 96 
                                        788889999999999999********************************************************** PP

                             Sec3_C  92 eellstvslsesdleaLkeaelssanglealeealeaLfkAltaIdsdlkdlesdlgemravkerrerYekvsssF 167
                                        +ell  v++ e++  aL++++++s +g+ ++e+ale L    +           ++ ++r+v+e++er     + F
  gene1006|gene1006|rna1005|rna1005  97 KELLINVEIKEDHFIALESESFDSIDGVCRIEKALEVLDSFCVD----------EY-DIRIVREKKERINDALRGF 161
                                        ************************************99665554..........56.78***************** PP

                             Sec3_C 168 lrrlveflekkfksaekelgkdldsatkkklslekhlevlnlLliYsgLilflKevdaekfeallqqYnasiskvY 243
                                         +r++++l           g+++      + +l+ h+ ++    +++++i   K   ++ ++ ++++Y+a+++k+Y
  gene1006|gene1006|rna1005|rna1005 162 YKRFITYLGGFM------VGSES------SGELKVHKGLYGAIKRFKKIIQHSKRY-RDYYIVICSIYMARSKKLY 224
                                        ********9987......33333......4678899******************97.789**************** PP

                             Sec3_C 244 ereikeffeslkksl 258
                                        ere+   ++++ + l
  gene1006|gene1006|rna1005|rna1005 225 EREFGFHLKTVLRLL 239
                                        ***977766655555 PP

>> LsmAD  LsmAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   1.0   2.9e-06      0.01      10      49 ..      59      98 ..      55     108 .. 0.93
   2 ?   -2.5   0.1       2.2   7.9e+03      21      40 ..     404     423 ..     399     430 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.9e-06
                              LsmAD 10 nlYTtkldksspeykereaeAeriArEIessastnahvae 49
                                       +lYT kl++ ++e+ke e+e  ++++EI  ++s   h++e
  gene1006|gene1006|rna1005|rna1005 59 SLYTIKLESLAKEMKEIERENTKLENEIRYQTSIYEHLKE 98
                                       58*****************************999999876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.2
                              LsmAD  21 peykereaeAeriArEIess 40 
                                        + ++er +e e  +r +es+
  gene1006|gene1006|rna1005|rna1005 404 NVCSERISEVEDAERKVESE 423
                                        55667777777777777665 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0025       8.9      23      63 ..      44      85 ..      37     153 .. 0.86
   2 ?    7.9   0.1    0.0011       3.9      10      36 ..     397     423 ..     391     425 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0025
                             CCDC53 23 LvevekrlqrleitlalLEakLsSip.gleeveaeaaeasts 63
                                       L +v +++++++++l+l   kL+S   +++e+e e+++ +++
  gene1006|gene1006|rna1005|rna1005 44 LEQVRTKCKEIDLSLSLYTIKLESLAkEMKEIERENTKLENE 85
                                       78999*******************876888888887665555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0011
                             CCDC53  10 qfLNrFatecEekLvevekrlqrleit 36 
                                        ++LN++ ++c e++ eve+   ++e +
  gene1006|gene1006|rna1005|rna1005 397 RLLNHMKNVCSERISEVEDAERKVESE 423
                                        89*****************99999975 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.1   3.5e-05      0.13      28      96 ..      30      98 ..      21     119 .. 0.83
   2 ?    2.0   1.3     0.077   2.7e+02      44      85 ..     339     425 ..     304     427 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                             APG6_N 28 YeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                       +e+++ ++ k  ++ e+ +++++e++ +l+    + e+l +e+ke+e+e+ +le+e++ +++  e+l+e
  gene1006|gene1006|rna1005|rna1005 30 LERCMGEIPKIYPNLEQVRTKCKEIDLSLSLYTIKLESLAKEMKEIERENTKLENEIRYQTSIYEHLKE 98
                                       555555555555666667899*************************************99999888887 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.077
                             APG6_N  44 k.............................................qdeeleeleeeleklekeeeelleeLkele 74 
                                        +                                             ++ +l+++  + + l+  ++   e + e+e
  gene1006|gene1006|rna1005|rna1005 339 SgylkkkmgrkengvgkleevlrkssneevkrkavvlgvqrvmeeeDRGDLKRTIGRWRLLNHMKNVCSERISEVE 414
                                        3555555554444444433333333333333444777777776443344444444445557777777777777777 PP

                             APG6_N  75 kereeleaela 85 
                                        ++++++e+e +
  gene1006|gene1006|rna1005|rna1005 415 DAERKVESEFE 425
                                        77777777765 PP

>> DUF5517  Family of unknown function (DUF5517)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.4   0.00022      0.78      38      76 ..      63     101 ..      52     135 .. 0.76
   2 ?   -2.7   0.1       2.1   7.4e+03      14      31 ..     335     352 ..     326     391 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                        EEETTTEEEEEEEESTT--HHHHHHHHHHHHHHHTT--S CS
                            DUF5517  38 ieldedeklekeiyadniklenelrqlkrlyevyqsvei 76 
                                        i+l+   k  kei  +n klene+r    +ye  + + i
  gene1006|gene1006|rna1005|rna1005  63 IKLESLAKEMKEIERENTKLENEIRYQTSIYEHLKELLI 101
                                        6677778889***************99999987664333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                                        EEEEEEEEEEEEEEETTE CS
                            DUF5517  14 ekqnsvfylltlgrkpyg 31 
                                        ek +s +    +grk  g
  gene1006|gene1006|rna1005|rna1005 335 EKLESGYLKKKMGRKENG 352
                                        555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1335  (0.0744604); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2926.34
//
Query:       gene1007|gene1007|rna1006|rna1006  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-58  196.3   0.0    3.2e-58  195.8   0.0    1.2  1  Gp_dh_C       Glyceraldehyde 3-phosphate dehydrogenase, C-ter
    7.6e-26   90.4   0.0    2.9e-25   88.5   0.0    2.0  2  Gp_dh_N       Glyceraldehyde 3-phosphate dehydrogenase, NAD b
    0.00057   19.3   0.0      0.003   16.9   0.0    2.0  2  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.0   5.3e-62   3.2e-58       1     158 []     149     304 ..     149     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 5.3e-62
                                        HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEE CS
                            Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeniiptstgaakavglVlpelkgkldglA 76 
                                        Lapl+kv++d+fgi++glmttvha+t++Qk++Dg   k  rr+r+  +niip+stgaa+ vg+V+p+l++kl+g+A
  gene1007|gene1007|rna1006|rna1006 149 LAPLVKVIDDNFGIVEGLMTTVHAVTATQKIVDGIG-KSSRRGRSGLSNIIPASTGAATSVGRVIPSLANKLNGMA 223
                                        8********************************997.9************************************** PP

                                        EEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHHTTTTTTEEEEHSHHHGGGGTTGCSSEEEEGGGCEEETTTEE CS
                            Gp_dh_C  77 vrVPtpnvsvvdlvvelekevtveevnaalkeaaegalkgilsyteeelvssDlvgdphssifdaketivveenlv 152
                                        +rVP+ nvsvvdlv++++ke++ ee+ +a+++ + ++ +gi+++t +++vssD++gdp+ss+ d +++i + +n++
  gene1007|gene1007|rna1006|rna1006 224 MRVPVSNVSVVDLVCRTRKETSIEEIVKAIEKFS-ENNEGIIGTTRDPVVSSDFIGDPRSSVLDINASISMGSNFF 298
                                        **********************************.6667************************************* PP

                                        EEEEEE CS
                            Gp_dh_C 153 kvvawy 158
                                        k+++wy
  gene1007|gene1007|rna1006|rna1006 299 KLISWY 304
                                        *****9 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.0   4.9e-29   2.9e-25       1      99 [.       1      98 [.       1     100 [. 0.95
   2 ?   -1.6   0.0       0.6   3.6e+03      23      49 ..     107     130 ..     101     150 .. 0.57

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 4.9e-29
                                       CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE--SS CS
                            Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaind.ltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvlaekd 77
                                       +kv+inG+GRIG+lv+++l  e+ +ev  +nd   ++e++ayllkyDsv+g++k e+++e++++v  gkk  +++  +
  gene1007|gene1007|rna1006|rna1006  1 MKVGINGLGRIGKLVYKVLR-ERGVEVPLVNDpHLKPEQVAYLLKYDSVFGKCK-ECQVEGDKIVYRGKKTCLSSFDK 76
                                       79**************9876.559********99******************96.68899****************** PP

                                       GGGS-CHHHTSSEEEE-SSS-- CS
                            Gp_dh_N 78 peelpwkelgvdlVvestGvft 99
                                       pe++pw+++gvd V+e++Gvft
  gene1007|gene1007|rna1006|rna1006 77 PESIPWTKYGVDAVIEASGVFT 98
                                       *********************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.6
                                        TTCEEEEEE-.TS-HHHHHHHHHEETTT CS
                            Gp_dh_N  23 kelevvaind.ltdletlayllkyDsvh 49 
                                        k++++v i   + d+ +++y +     h
  gene1007|gene1007|rna1006|rna1006 107 KDVKIVVITApSKDAPMFVYGV----NH 130
                                        5777777776555555555443....33 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     5e-07     0.003      38      77 ..       2      40 ..       1      57 [. 0.72
   2 ?   -0.2   0.0     0.089   5.3e+02      42      70 ..     206     234 ..     167     258 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-07
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEE.SSSHHHHHCHHH CS
                       2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviay.drskkkeeeeee 77
                                       +vGi GlGrIG+ v k+l++ g++v  + d++ k+e+   +
  gene1007|gene1007|rna1006|rna1006  2 KVGINGLGRIGKLVYKVLRERGVEVPLVnDPHLKPEQ--VA 40
                                       89***********************665155555444..33 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.089
                                        ES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                       2-Hacid_dh_C  42 iGlGrIGqavakrlkafgmkviaydrskk 70 
                                          +Gr+  ++a++l+++ m+v + ++s  
  gene1007|gene1007|rna1006|rna1006 206 TSVGRVIPSLANKLNGMAMRVPVSNVSVV 234
                                        56788888999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2098.54
//
Query:       gene1008|gene1008|rna1007|rna1007  [L=338]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2470.14
//
Query:       gene1009|gene1009|rna1008|rna1008  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-21   75.7   0.0      4e-21   74.8   0.0    1.5  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    2.2e-20   72.6   0.1    4.4e-20   71.7   0.1    1.4  1  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   4.4e-25     4e-21       1      71 []     120     189 ..     120     189 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 4.4e-25
                       RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                        A++G+iA++dv++ ++ ++++P+++ + ++ lg+ tk++kGk+++ + y+v +kG++++++qa+lL +L+i
  gene1009|gene1009|rna1008|rna1008 120 AKVGNIAQKDVWVDSCITGMTPDKT-SYFQVLGIATKITKGKVEIISPYKVLSKGDKVGPSQANLLGMLNI 189
                                        9************************.*******************************************98 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.1   4.9e-24   4.4e-20       3      98 ..      18     114 ..      16     115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 4.9e-24
                                        CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS..S.SCGCCS CS
                      Ribosomal_L10   3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeee.k.lkellk 76 
                                        ke+Ke  +++ k+l+ +y+ +++v +e++ ++ql+++++++ +n +e+ ++Kn+ ++rA+++ g+ e + + +l+k
  gene1009|gene1009|rna1008|rna1008  18 KERKELTYEKAKKLFGTYSRFALVGIENVESTQLKDIKRQWGNN-VEFLMGKNSAIKRAIADLGKPElSrVLDLIK 92 
                                        89****************************************99.********************8754788**** PP

                                        SSEEEEEESS-TCHHHHCCCCC CS
                      Ribosomal_L10  77 gpvalvftnedpvalakvleef 98 
                                        g+v++vf ++d+ +++k+++e+
  gene1009|gene1009|rna1008|rna1008  93 GDVCFVFFKGDARDIKKTIDEN 114
                                        *******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1882.26
//
Query:       gene1010|gene1010|rna1009|rna1009  [L=1059]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-24   85.4   0.0    1.1e-23   83.9   0.0    1.8  1  DEAD            DEAD/DEAH box helicase
    6.7e-21   74.6   0.2    1.1e-20   73.9   0.2    1.4  1  Sec63           Sec63 Brl domain
      1e-10   41.9   0.0    3.2e-10   40.3   0.0    1.8  2  ResIII          Type III restriction enzyme, res subunit
    7.1e-09   36.0   0.1    3.5e-07   30.5   0.0    2.8  2  Helicase_C      Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.013   15.4   0.4      0.029   14.3   0.4    1.5  1  GerD            Spore germination GerD central core domain
      0.037   14.3   0.0      0.085   13.1   0.0    1.6  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
      0.065   12.3   0.0       0.15   11.1   0.0    1.5  1  T2SSE           Type II/IV secretion system protein
      0.085   13.0   0.0       0.17   12.1   0.0    1.5  1  Pirin_C_2       Quercetinase C-terminal cupin domain
       0.11   12.7   0.2        0.5   10.6   0.0    2.1  3  Helicase_PWI    N-terminal helicase PWI domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   5.4e-27   1.1e-23       2     172 ..     108     268 ..     107     272 .. 0.83

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 5.4e-27
                                        HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                        xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                        ++Q++++++++ g+g++lv+a+T sGKT ++l+ vl+++      +g k+++++P+r+La +++++++k +     
  gene1010|gene1010|rna1009|rna1009 108 RVQSKVFKAAYrGDGNLLVCAPTSSGKTDVALLCVLRAL-----GKGDKVIYIVPMRALATEIASKYRKKLGG--Q 176
                                        79*********4447*********************999.....5677*******************999995..4 PP

                                        EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                        rv+  ++g+++ + ++++  ++d+vv+tp+++d ++ +++ n    ++ +++lDE++ l+d+ +++ +++i+ ++ 
  gene1010|gene1010|rna1009|rna1009 177 RVV-EYTGDTEMR-VEDM-VRYDVVVSTPEKFDVVT-RKQYNvfQGRIGLVILDEIHILQDE-RGPVVEAIVCRMF 247
                                        565.566666644.4444.48***********9866.4555633566789***********9.9999999999998 PP

                                        HHCTTSTTTSEEEEEESSBSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 151 qitcdgklqrqvivlSATlpkd 172
                                        +  +  + + +++ lSATlp +
  gene1010|gene1010|rna1009|rna1009 248 RHVELWQRHIRIVGLSATLP-N 268
                                        88888887888********9.3 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.2   5.7e-24   1.1e-20       1     208 [.     572     778 ..     572     817 .. 0.76

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 5.7e-24
                                        ECHHHHHHHHHT--HHHHHHHHHHS-TT--HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHTSSS--SSSTTSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              Sec63   1 ptelGriaShYyisyetiklfneslkpnttlkdlLeilssasEFeeipvReeEkkelkkLlekvpikvkediespe 76 
                                        +te+GriaS Yy+ +et++   ++++ + +++ +L++  +++E +++  Ree+++++k++ +++ +       s  
  gene1010|gene1010|rna1009|rna1009 572 STEYGRIASMYYLPHETVEGWLKEISDTHDEDAILRLCFESKELSSLGYREEDEETIKEICSELGVMY---EMSMG 644
                                        69***********************************************************9965554...23678 PP

                                        HHHHHHHHHHHTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTS-.TTS--EEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                              Sec63  77 aKvniLlqayisrlklegsdlvsDlkyilqnairilralveillskgwlslalslleLskmveqrlw.dslPklei 151
                                         K + L++a+i r ++  ++lv D++ +++n  r+l  l +i++ +g+  ++ ++  L k +e+++  +   + + 
  gene1010|gene1010|rna1009|rna1009 645 CKLMALVKAHIRRYPITRFSLVCDTEHVVKNLRRVLMGLSQIFMFQGKHLAVSRCCILLKRIERQRErPWNCNNNA 720
                                        8**************************************************************9875333333333 PP

                                        EEEECEBTTSEEEEEEEEEESSSS-SCTSSS-CH......TSBEEEEEEEEETTTTEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxx RF
                              Sec63 152 eaevqpitrsklrvevtiereeeeskpdfpwdkk......gksekfwlvvedsendellaikr 208
                                        +++++  +++ +++e++++++ e     f+wd +        ++   l++++++   +l i+ 
  gene1010|gene1010|rna1009|rna1009 721 AVSLS-RANEMVKIEISLKDKGE--YWVFVWDGDflvhsgLFKQRANLFIKSES--DVLRIEI 778
                                        33444.55666667777772222..12344444333333355556666665444..3555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   1.6e-13   3.2e-10      18     170 ..     112     267 ..      96     268 .. 0.86
   2 ?   -3.3   0.0       3.8   7.6e+03      43      71 ..     649     677 ..     647     688 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.6e-13
                                        ........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEES CS
                             ResIII  18 klks...krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvs 90 
                                        k+ +   ++d ++l+ ++T +GKT va+  + r l kg+  k++ +vp ++l     ++++k l  +      +++
  gene1010|gene1010|rna1009|rna1009 112 KVFKaayRGDGNLLVCAPTSSGKTDVALLCVLRALGKGD--KVIYIVPMRALATEIASKYRKKLGGQ---RVVEYT 182
                                        33335557788999**********************988..************************99...6899** PP

                                        SS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T..........TTHHHHHT CS
                             ResIII  91 gdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk..........swreilek 156
                                        gd++++  +d    +++v+t +++d       +++    ++r+ ++i DE H l+++            +r++   
  gene1010|gene1010|rna1009|rna1009 183 GDTEMR-VEDMVRYDVVVSTPEKFDVVT----RKQYNVFQGRIGLVILDEIHILQDERgpvveaivcrMFRHVELW 253
                                        *****9.99******************9....9999********************83554455566688888777 PP

                                        ---SEEEEEESS-S CS
                             ResIII 157 fkeavllglTATpe 170
                                         ++  ++gl+AT++
  gene1010|gene1010|rna1009|rna1009 254 QRHIRIVGLSATLP 267
                                        7889********86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.8
                                        HHHHHH-S.....-EEEEESSHHHHHHHH CS
                             ResIII  43 klierllkkgkeekflflvprkslleqtl 71 
                                        +l+++  + +++ +f ++++++++++ ++
  gene1010|gene1010|rna1009|rna1009 649 ALVKAHIRRYPITRFSLVCDTEHVVKNLR 677
                                        56666777788889********9999876 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.8e-10   3.5e-07       9     109 ..     320     446 ..     312     448 .. 0.78
   2 ?    2.1   0.0      0.12   2.4e+02      24      89 ..     805     874 ..     790     886 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.8e-10
                                        HHHHTTTTSEEEEEESSHHHHHH.HHHH..................HHHTTSTEEEESTTSTHHHHHHHHHHHHTT CS
                         Helicase_C   9 llkleeeggkilifvntidrlek.vkll..................lekkgikvavlhgelpqnereeileqfnkg 65 
                                        +l    +g+++l+fv+++ +  k +kll                  le     v ++h+ lp + r+ + ++f+ +
  gene1010|gene1010|rna1009|rna1009 320 YL---DDGKQVLVFVHSRGETTKtAKLLsdedvkrevkdgvvggalLELVRRGVGIHHAGLPRRIRLYMEDEFKMK 392
                                        45...7899**********7777566666666655544544444443334899999******************** PP

                                        SSSEEEESGGGTSSSTSTTESEEE....ESSSSSSH......HHHHHHHTTSSS CS
                         Helicase_C  66 esdvLiatdvaerGidipkvnlVi....nfdlprnv......tsyiqriGRtgR 109
                                        ++++L++t+ ++ G+++p   ++i    ++d  +++       ++ q  GR+gR
  gene1010|gene1010|rna1009|rna1009 393 RIKILVTTSTLAWGVNLPAYAVIIkgtrFYDSSKGMfsdigiLDVLQIFGRAGR 446
                                        ***********************966665666644356666699*********9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                        SSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEE CS
                         Helicase_C  24 ntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVi 89 
                                        n + ++++  +++ ek+   +++v+   ++l +   e il+   + e ++L+ t+    ++d++k + V+
  gene1010|gene1010|rna1009|rna1009 805 NGVHECSQkWSIVGEKQgcaHFNVINTFSDLLKATHEWILNHGSASELKILLLTNKRIDSLDLKKERRVH 874
                                        555555545666667776767999999999*************************999999999888776 PP

>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   1.5e-05     0.029      44      94 ..      17      66 ..      14      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                               GerD 44 kenekllkdLmkDpeYqkmlleilkdpemekqllellkskeyrkqlekviq 94
                                       ke  +++ + ++Dp+Yq+ l+eil   em+++++ + k +ey +  +kv+ 
  gene1010|gene1010|rna1009|rna1009 17 KETMDMVSQALRDPSYQERLVEILGY-EMMDEIEMICKNQEYFTSQDKVVD 66
                                       6778899999**************85.8999**********9888888775 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-05     0.085      11     107 ..     130     230 ..     121     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                     CobA_CobO_BtuR  11 dGKGKttAAlGlalRalgaglkvlvvqFlKg.ekesgElaalkkl.eielerlg.kegfvkmeeeekeedaaaake 83 
                                        +  GKt  Al  +lRalg+g kv+++  ++  + +    +  kkl + +++++  +++    e+  + +    + e
  gene1010|gene1010|rna1009|rna1009 130 TSSGKTDVALLCVLRALGKGDKVIYIVPMRAlA-TEIASKYRKKLgGQRVVEYTgDTEMR-VEDMVRYDVVVSTPE 203
                                        567***************************933.23334455777634444444133333.444455555555555 PP

                     CobA_CobO_BtuR  84 alekakea...laseeydlvvlDEiny 107
                                         ++ ++++   + ++++ lv+lDEi +
  gene1010|gene1010|rna1009|rna1009 204 KFDVVTRKqynVFQGRIGLVILDEIHI 230
                                        555555442225668999******986 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   7.4e-05      0.15     110     161 ..     102     154 ..      88     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.4e-05
                              T2SSE 110 aeealkekiaevlrkavrerglilvsGgTgsGKt.tllyallkeinksderiv 161
                                          ++++  +++v ++a r  g++lv  +T+sGKt + l  +l  + k d+ i 
  gene1010|gene1010|rna1009|rna1009 102 DYKTFNRVQSKVFKAAYRGDGNLLVCAPTSSGKTdVALLCVLRALGKGDKVIY 154
                                        5567778888999999999***************5556778888888765554 PP

>> Pirin_C_2  Quercetinase C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.5e-05      0.17      12      70 ..     714     772 ..     707     785 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.5e-05
                          Pirin_C_2  12 lkinQdarlyaakldegesleyelaagrkaYlqvieGevevngeslaagDGlaiedess 70 
                                         + n +a +++++ +e  ++e++l+++ +++++v +G + v+    +++  l i++es+
  gene1010|gene1010|rna1009|rna1009 714 WNCNNNAAVSLSRANEMVKIEISLKDKGEYWVFVWDGDFLVHSGLFKQRANLFIKSESD 772
                                        56688999**********************************99999999999988875 PP

>> Helicase_PWI  N-terminal helicase PWI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025       0.5      34      74 ..      17      56 ..       9      59 .. 0.87
   2 ?   -3.8   0.0       7.5   1.5e+04      14      29 ..     312     327 ..     308     355 .. 0.65
   3 ?   -2.4   0.0       2.7   5.4e+03      37      57 ..     468     484 ..     460     486 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                       Helicase_PWI 34 eevleiLkseadelrelEnkLvelldydkfdliklllknre 74
                                       +e++++++++  +    +++Lve+l+y+ +d i++++kn+e
  gene1010|gene1010|rna1009|rna1009 17 KETMDMVSQALRD-PSYQERLVEILGYEMMDEIEMICKNQE 56
                                       5778888888766.78999********************86 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.5
                       Helicase_PWI  14 WLqrelkkiykDaeea 29 
                                        +L r++k++++D +++
  gene1010|gene1010|rna1009|rna1009 312 FLRRKVKEYLDDGKQV 327
                                        6888888888876643 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.7
                       Helicase_PWI  37 leiLkseadelrelEnkLvel 57 
                                        +++Lk++    r++E++L++ 
  gene1010|gene1010|rna1009|rna1009 468 VSLLKNS----RDVESRLLQH 484
                                        5566666....99****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1059 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.90u 0.33s 00:00:01.23 Elapsed: 00:00:00.55
# Mc/sec: 5768.32
//
Query:       gene101|gene101|rna101|rna101  [L=374]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.7   0.1       0.19   11.9   0.0    1.9  2  DUF4372   Domain of unknown function (DUF4372)


Domain annotation for each model (and alignments):
>> DUF4372  Domain of unknown function (DUF4372)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2      0.52   9.3e+03      31      45 ..      95     109 ..      91     110 .. 0.82
   2 ?   11.9   0.0   1.1e-05      0.19      42      56 ..     118     132 ..     114     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.52
                        DUF4372  31 vkkfttwdqlvamlf 45 
                                    + +f++ d +v+ +f
  gene101|gene101|rna101|rna101  95 MTNFSCHDRTVLYMF 109
                                    568999999999988 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.1e-05
                        DUF4372  42 amlfaqLtgreSLRd 56 
                                    +m +aq++g++SLRd
  gene101|gene101|rna101|rna101 118 SMYYAQFSGCHSLRD 132
                                    69************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 2084.03
//
Query:       gene1011|gene1011|rna1010|rna1010  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-18   65.3   0.0    5.4e-15   55.8   0.0    2.0  1  RNA_pol_Rpb8  RNA polymerase Rpb8
    0.00011   22.3   0.0    0.00012   22.1   0.0    1.1  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb8  RNA polymerase Rpb8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0     6e-19   5.4e-15       2     128 ..       6     108 ..       5     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 6e-19
                                        EEEEEEEEE-..TT-SSEEEEEEEESS-S-EEEEEEETTTS---SS-EEEEEEES------------------GGS CS
                       RNA_pol_Rpb8   2 diFevkdvdkdgkkfdrVsRieaeseslemeltlDintelyplkegdkltlvlasslsldgskdeeeakkswegek 77 
                                        d F+++d+dk+gk + +VsRi+ +s   ++++ lD+nt+l +l+ g  +++ + + ++++                
  gene1011|gene1011|rna1010|rna1010   6 DNFKITDIDKEGKLYTKVSRIYMQSP--TISIALDYNTTLCKLQMGHAVEVRIFRGIHEN---------------- 63 
                                        89***********************9..6999***********************99988................ PP

                                        -CGGGSSEEEBEEEEEEEE-ST..T-EEEEEEBTTBEEEEEBSHHTTTSGS CS
                       RNA_pol_Rpb8  78 sladkydYvmyGkvYkieeeeskeekvkvyvSfGGLlmaLegdakklskle 128
                                            ++ Y  yG++Y +e +++   +v++ +SfGGLl+ ++++++ ++ + 
  gene1011|gene1011|rna1010|rna1010  64 --I-DCFYLAYGRIYSVEPRDN---RVSITASFGGLLLIMDAPQEAVKGVG 108
                                        ..2.456***********9995...9******************9998875 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.4e-08   0.00012       5      96 ..       7      99 ..       3     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.4e-08
                       RNA_pol_RpbG  5 eckvksiekskl..kdlkivkikcqneeielDiiselnifkeedkveviisrekPeyldgkdFcghGylvtekeeenk 80
                                       + k+++i+k+     ++  + +++    i lD    l +++ +  vev i r   e++d   + + G + + + ++n+
  gene1011|gene1011|rna1010|rna1010  7 NFKITDIDKEGKlyTKVSRIYMQSPTISIALDYNTTLCKLQMGHAVEVRIFRGIHENID-CFYLAYGRIYSVEPRDNR 83
                                       67899999875402445555566666699******************************.889*************** PP

                       RNA_pol_RpbG 81 iitliSlfGllvkiss 96
                                       + ++ S+ Gll+++ +
  gene1011|gene1011|rna1010|rna1010 84 VSITASFGGLLLIMDA 99
                                       ***********99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 809.27
//
Query:       gene1012|gene1012|rna1011|rna1011  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 681.65
//
Query:       gene1013|gene1013|rna1012|rna1012  [L=742]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-38  131.5  14.8    4.8e-37  127.9  14.8    2.3  1  Cullin        Cullin family
    0.00022   21.2   0.3    0.00065   19.7   0.0    2.0  2  Cullin_Nedd8  Cullin protein neddylation domain
  ------ inclusion threshold ------
      0.028   14.4   0.1       0.15   12.1   0.0    2.2  2  Bromo_TP      Bromodomain associated


Domain annotation for each model (and alignments):
>> Cullin  Cullin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9  14.8   8.1e-41   4.8e-37      20     600 ..      34     643 ..      17     659 .. 0.79

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 8.1e-41
                             Cullin  20 sfeelYravynlvlskekkqgekLydklkelieehlkellkellkeesdeelLkalkkeWedhktsmkmirdifmy 95 
                                        s  e+Y+++y +++s++ +  +kLy k+ +++  + +e+++e+    ++ +++++++k ++++k+ +  i++++  
  gene1013|gene1013|rna1012|rna1012  34 SALEIYNSIYVICTSSTPRLESKLYWKIGDFVYMKAREIRREI---FEARDWIEEYNKGFRKFKVMVFAIDELCDF 106
                                        45689***********999**********************87...88888************************* PP

                             Cullin  96 ldrvyvkklpsvydlglelfrdhvfriklkdrlieallkliekeRegevidrsllksviemlvelgedsedkk... 168
                                        l++ +  k  +++dlg+ l++++v++++ k + ++  ++l+++eR       +++k++ie++  +  d +  k   
  gene1013|gene1013|rna1012|rna1012 107 LNECV--KGRTMRDLGFLLWERCVLQQTTKYKHTTLGFELVNQER------IEVVKEAIESFRLIVPDLK--Kpml 172
                                        ***99..7889**************8798999999999*******......3489999999986644443..3457 PP

                             Cullin 169 vYeeeFekafleateefYraeaeellaensvaseYlkkaeerleeEeervekyldsstkkkllevleeelikkhl. 243
                                        +Y++ +e+  l+++ + Y +e ++  +e   +++Y  +++e++  E++  ek++ +++ +k+ evlee++i ++  
  gene1013|gene1013|rna1012|rna1012 173 YYTQRYEQFALQKIGSKYMEEIKSACSE---VERYSFYVKEKIWYEKSIREKIFLEESWEKVEEVLEEVFILNKKd 245
                                        **********************999996...56***************999988899******************6 PP

                             Cullin 244 ............................................eelleee.lkklledekledLkrlykllsrvd 274
                                                                                     el+ ee  kk   d  l +++ ly+ ls  +
  gene1013|gene1013|rna1012|rna1012 246 ylfneiygimsmyklpveilgkvfrgadhdkhsfdsggyrtndfYELQGEEgAKKSHGDVFLRKMSVLYRNLSGLK 321
                                        6666666666666666666666666666666666666655533322222222221111112333333333333332 PP

                             Cullin 275 .gleeLrkaleeyikeegkaivkdakekektedakkyveklLelkdkfdklvkeafnndkefekaldeafeefvnk 349
                                           e +r+++ +yi+e+ ++           +  +k +e+l  ++  + ++v+  f +d+e+ k l++ f+  + +
  gene1013|gene1013|rna1012|rna1012 322 sAYEIFREVFTRYIREMSEK---------YMDIYSKSIETLYIFHCMLRHVVDIGFLGDQEYFKILKKEFSASCMR 388
                                        24455555555555544433.........44567899**********************************99985 PP

                             Cullin 350 nkv..nsksael..........lakYiDelLkkg.lkgl....................seeeleekldkv.lvlf 391
                                         k   + ++ e+          + k++ e + ++ +kg                       e  +  l++v  +l 
  gene1013|gene1013|rna1012|rna1012 389 LKPslEARILEFsecivgdnsnVFKFLGEEFERStAKGSlglpflgsgdacedgselgrRFEGKNGFLRQVfGTLY 464
                                        554774444444444444444477888877776436666899**********9998888666667888888779** PP

                             Cullin 392 ryiedKDvFekyYkkhLakRLllgksasddaEksmiskLkeecGseftskLegMfkDiklskdlnkefkeyleeek 467
                                        + +e+K vF + Y   L kRLl + s +  +E+++is ++ +  ++f++k e M+ Di++s   nk+  +      
  gene1013|gene1013|rna1012|rna1012 465 KMVENKHVFYELYLLGLGKRLLEK-SPNLCEERKLISLMRRKGNQDFIKKAEAMVADISISLSYNKDRDR------ 533
                                        *********************975.666689*********99999****************966655444...... PP

                             Cullin 468 kkkkkvdlsvkVLtagaWpterskesevsvklpeeledlieeFeefYkskhsgrkLtWlhslgsaelkatfpkkky 543
                                                 v +Lt+++Wp   ++e     +l  ++   +e  ++ Y  k++++kL+W ++lgs+ +++    +  
  gene1013|gene1013|rna1012|rna1012 534 --------FVWILTQAYWP--LQTE-----NLFIQIPGPLEMIRKVYDLKFNKKKLHWAWHLGSVCVEV----GGV 590
                                        ........577********..4534.....6888888888899********************999988....446 PP

                             Cullin 544 elqvstfqmvvLllFndeeeklsyeeiqeatglpekeLkrtLqsLavakkarvLlke 600
                                        e+q+++ q  v+ lFn+  e++ +e i +++++  k  +  L sL+   + ++L+++
  gene1013|gene1013|rna1012|rna1012 591 EIQMNVPQYSVINLFNKY-EQVDLETILSSVKMGAKVANDVLRSLV---EGNLLVCS 643
                                        8***************65.9*************************8...45677765 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.4   8.4e+03      21      49 ..     136     158 ..     130     160 .. 0.58
   2 !   19.7   0.0   1.1e-07   0.00065       1      59 [.     675     733 ..     675     737 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                       Cullin_Nedd8  21 shneLvsevieqlskrftpsiadikkrIe 49 
                                        +h++L +e ++q       +i+ +k+ Ie
  gene1013|gene1013|rna1012|rna1012 136 KHTTLGFELVNQE------RIEVVKEAIE 158
                                        6666666666653......3445555555 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.1e-07
                       Cullin_Nedd8   1 dRklaiqaaIVRiMKsrktlshneLvsevieqlskrftpsiadikkrIesLiekeYleR 59 
                                        d++++ q+++ R++K+rk++  +e+ +e++++  +rf+ + a + + I  L +k+ +e 
  gene1013|gene1013|rna1012|rna1012 675 DKNVYYQSLVSRLLKKRKRIGLEEIAKEILSEHTERFEYDEAIFLEGIRTLGDKGIIED 733
                                        5778999********************************************99998885 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.88   5.3e+03      18      39 ..     139     160 ..     137     162 .. 0.83
   2 ?   12.1   0.0   2.4e-05      0.15      26      65 ..     321     357 ..     318     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.88
                                        HHT-SEE-HHHHHHHHHHHHHH CS
                           Bromo_TP  18 eaGfdsaeesaLEtLteiaqkY 39 
                                        + Gf+ ++++ +E  +e ++++
  gene1013|gene1013|rna1012|rna1012 139 TLGFELVNQERIEVVKEAIESF 160
                                        7899999999999988887776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.4e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHH CS
                           Bromo_TP  26 esaLEtLteiaqkYirelgeqaksfaehagRseptlkDvv 65 
                                        +sa E ++e++++Yire++e+   +++++ +s  tl ++ 
  gene1013|gene1013|rna1012|rna1012 321 KSAYEIFREVFTRYIREMSEK---YMDIYSKSIETLYIFH 357
                                        7899****************9...*******999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 4342.24
//
Query:       gene1014|gene1014|rna1013|rna1013  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00035   20.4   3.5    0.00067   19.5   3.5    1.4  1  Nop52      Nucleolar protein,Nop52
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.24   11.0   0.0    1.3  1  RanGAP1_C  RanGAP1 C-terminal domain


Domain annotation for each model (and alignments):
>> Nop52  Nucleolar protein,Nop52
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.5   7.4e-08   0.00067      33     114 ..      31     104 ..       5     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.4e-08
                              Nop52  33 klselellkLwkGLFycmWmsDkplvQqelaeeLaelvkslkskeaalkFlkafwetmsreWkgiDklRlDKfllL 108
                                         l+e+++ +L   + y++W   k + Q+++  +L + +++           + ++  +  +W++i  +R+DKf++ 
  gene1014|gene1014|rna1013|rna1013  31 LLKEEDIVRLTPSIAYYLWKLPKFVAQKQFVLDLLSHTDQRL--------RHSMFMYLIDKWSEIQLVRMDKFYYI 98 
                                        478888888888899999999999999999888765554433........3567778999**************** PP

                              Nop52 109 vRrvlr 114
                                        ++r+l+
  gene1014|gene1014|rna1013|rna1013  99 MKRILE 104
                                        ***997 PP

>> RanGAP1_C  RanGAP1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.7e-05      0.24      84     145 ..       3      60 ..       2      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.7e-05
                          RanGAP1_C  84 vletiDallkkafsseefqsesfissllvhlGllKsEdKikpvkvvsGhLlaleHvvkqdyf 145
                                        v++tiDa+ ++ +++    +++ i ++  + GllK Ed ++   +++  L  l   v q+ f
  gene1014|gene1014|rna1013|rna1013   3 VQKTIDAIRSNDIET----NKAAIETIYANYGLLKEEDIVRLTPSIAYYLWKLPKFVAQKQF 60 
                                        566677666555544....45679999******************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.37s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1041.80
//
Query:       gene1015|gene1015|rna1014|rna1014  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-17   64.2  13.2      8e-14   51.8   8.7    3.0  2  Tfb4      Transcription factor Tfb4


Domain annotation for each model (and alignments):
>> Tfb4  Transcription factor Tfb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   9.5e-06      0.17       5      60 ..       4      50 ..       1      71 [. 0.76
   2 !   51.8   8.7   4.5e-18     8e-14     147     276 .]      89     203 ..      77     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.5e-06
                               Tfb4  5 tvvldtnpkawaeleekltlsevlasllvflNahLalnaaNkvaviashsqkakfl 60
                                        +++d + + w+ +       +++++++vflNa+   +++N+  v++      ++l
  gene1015|gene1015|rna1014|rna1014  4 FLLIDLKNENWELT-----TRDLFNDIIVFLNAYHKSSRSNRFIVVSG----KNIL 50
                                       56666666666554.....47899********************9974....3445 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 4.5e-18
                               Tfb4 147 RilvvsaskdsalqyipimNviFaaqklkipidvvklggkdsafLqQasdaTkGvylkvkepkgllqyLltaflid 222
                                         i++ +  ++++ +y+ ++ ++Faaq+l + i +++l + ++++L Q + +T+G y + +  +  l++Ll+ + + 
  gene1015|gene1015|rna1014|rna1014  89 QIVIFTLGRERKDEYLRYLKCMFAAQRLGVRISAFSLFE-NKTIL-QCCVSTGGDYSTSE--DRCLRFLLSLLGTG 160
                                        6888888889999************************66.66666.799*******8654..45688888888777 PP

                               Tfb4 223 qssRsllvlptrvsVdfRasCfchrkvvdiGfvCSvCLsilceispenkCktCe 276
                                         s+         +   f a+C+ch++ + +G vC +CLs++c++ p   Ck C+
  gene1015|gene1015|rna1014|rna1014 161 GSQ---------KPLGFPATCYCHNRQILLGLVCPICLSVFCKFIPV--CKKCK 203
                                        665.........446899**************************885..99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1275.32
//
Query:       gene1017|gene1017|rna1016|rna1016  [L=408]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-29  101.8   0.5    6.4e-29  100.7   0.5    1.6  1  NIF        NLI interacting factor-like phosphatase
    1.1e-08   35.4   0.0    2.7e-08   34.1   0.0    1.7  1  BRCT_2     BRCT domain, a BRCA1 C-terminus domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.068   13.6   0.0    2.1  1  BRCT       BRCA1 C Terminus (BRCT) domain
      0.025   14.3   0.4        3.7    7.4   0.0    2.7  2  zf-CCHC_4  Zinc knuckle
       0.13   11.9   0.1       0.21   11.2   0.1    1.3  1  Pentaxin   Pentaxin family


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.5   1.8e-32   6.4e-29       2     143 ..      62     206 ..      61     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.8e-32
                                NIF   2 tLVLDLDetLvhskleks.k..klkvegekvevsvlkRpgldefLkelsklyevvifTasseeyaeavidildpek 74 
                                        +LVLDLD+t +h+ +  s +   ++++   +++sv++Rp l+ +L+++s+lye+ ++T++++ yae++++i+dp++
  gene1017|gene1017|rna1016|rna1016  62 ILVLDLDQTVLHTAYGASsEkgIVRFTMDGCKYSVKLRPNLKRMLRKVSRLYEIHVYTMGTRPYAERIVRIIDPTR 137
                                        8*************855544675566666688******************************************** PP

                                NIF  75 kllshr.lyrescvkkkgeyvKdLsllgr.dlsrvvivDdspdsfelqpengipiksf..fsdkkDneLlkll 143
                                        k++++r ++r++    +g  vK Ls l   +++++vi+Dd++d++    en++ ik+f  f++ + n+ l+l 
  gene1017|gene1017|rna1016|rna1016 138 KYFHDRiITRDEN---QGVLVKRLSRLFPyNHKNIVILDDRADVWDY-CENLVLIKPFwyFNRVDINDPLRLK 206
                                        ******7788888...9**********877***************86.89*******8755755555444444 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   7.5e-12   2.7e-08       2      79 ..     308     383 ..     307     389 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7.5e-12
                             BRCT_2   2 sklFeglrFYindaepspsreklkklIeknGGevvetitsavyiviaesneee..laekrkrrvvspkyIkdCikk 75 
                                        +k+F+g rFY+      ++r  l k+Ie +GG ++   + +v +++++  ee   la+k +  vvspk+I dC+ +
  gene1017|gene1017|rna1016|rna1016 308 KKIFDGDRFYV---VGPTNRVWLMKVIEMHGGIISGLGN-EVDFIVSSCLEEAreLAQKIECVVVSPKWISDCVYS 379
                                        79*********...4458****************99886.6666677776666799******************88 PP

                             BRCT_2  76 gkll 79 
                                         k +
  gene1017|gene1017|rna1016|rna1016 380 LKRV 383
                                        7766 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.068       4      79 .]     309     377 ..     307     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                        TTTTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHHH CS
                               BRCT   4 llfhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldci 79 
                                        ++f+g  f++      ++r  l ++i++hGG + + + ++++++v +   ++  ++ +++++   +v+++w+ dc+
  gene1017|gene1017|rna1016|rna1016 309 KIFDGDRFYV---VGPTNRVWLMKVIEMHGGII-SGLGNEVDFIVSSCL-EEARELAQKIECV--VVSPKWISDCV 377
                                        7999999999...88899999************.888888888885444.6666666666664..79********5 PP

>> zf-CCHC_4  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2    0.0097        35      29      39 ..       9      19 ..       9      20 .. 0.95
   2 ?    7.4   0.0     0.001       3.7       1      21 [.     197     217 ..     197     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0097
                          zf-CCHC_4 29 rLrsfCyiCgv 39
                                       rL+++C +Cg+
  gene1017|gene1017|rna1016|rna1016  9 RLGTLCGVCGM 19
                                       8*********8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.001
                          zf-CCHC_4   1 iDvtkpLrafmkikkesGeea 21 
                                        +D+ +pLr ++ki+kes e+ 
  gene1017|gene1017|rna1016|rna1016 197 VDINDPLRLKRKIEKESEECK 217
                                        79***************9985 PP

>> Pentaxin  Pentaxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   5.9e-05      0.21      20     111 ..       4      97 ..       1     109 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.9e-05
                                        S-S-BSEEEEEEEEEESGCS-EEEEEEEETTECCCEEEEEECTTEEEEEETTEEEEEE...-SS-SSSEEEEEEEE CS
                           Pentaxin  20 lekPLkeltlClrfytdLsrslslfsyatkkkdnelLifkekqgeyslyvggaevlvk...vseekvepvhvCasW 92 
                                         ++P++  tlC     ++++  +lf  a  + dn  +++ke +  y  +++  e+ +k   v +   +  h+    
  gene1017|gene1017|rna1016|rna1016   4 CDHPIRLGTLCGVCGMEIQKDSHLFC-ALYNTDNVKITHKEAVSIYKEKIKTLEMQMKlilVLDLDQTVLHTAYGA 78 
                                        56789999****************97.6677788888888888888777776665544111667778999****** PP

                                        ETTTTEEEEEETTEEEEEE CS
                           Pentaxin  93 esssGivelwvdGkplvkk 111
                                        +s +Giv + +dG  +  k
  gene1017|gene1017|rna1016|rna1016  79 SSEKGIVRFTMDGCKYSVK 97 
                                        *************776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1133  (0.0631937); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2501.49
//
Query:       gene1018|gene1018|rna1017|rna1017  [L=369]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-11   43.3   0.3    1.3e-05   24.9   0.2    2.4  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.2e-06   28.0   0.0    2.9e-06   26.7   0.0    1.6  1  Hydrolase_4    Serine aminopeptidase, S33
     0.0019   18.9   0.0      0.031   14.9   0.0    2.6  2  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.023   14.6   0.0      0.037   13.9   0.0    1.3  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      0.072   13.5   0.0       0.12   12.7   0.0    1.3  1  AAA_16         AAA ATPase domain
        0.3   10.8   0.0       0.46   10.2   0.0    1.2  1  AAA_30         AAA domain


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2   4.5e-09   1.3e-05       4      42 ..     114     152 ..     114     256 .. 0.79
   2 !   16.2   0.0   2.1e-06    0.0061     174     255 ..     270     350 ..     225     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.5e-09
                                        EEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTT CS
                      Abhydrolase_1   4 vilhGlpgssdvwaerglapaLakdgfdvillDlrGvgy 42 
                                        +++hG+ gs+d+ + rgla +L+++g++v++++ rG  +
  gene1018|gene1018|rna1017|rna1017 114 LLVHGFNGSGDSTYMRGLAGHLSREGYRVFCFNARGIKS 152
                                        79**********************************876 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.1e-06
                                        HHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTSEEEEEEETC CS
                      Abhydrolase_1 174 gsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvpp.kaledlaqllpkkrlvvisda 248
                                        + ++  +++t+ +++i+  +++++++++ ++ e  ++++p ++i + +Dp++p  +   +++   ++ +lv+  ++
  gene1018|gene1018|rna1017|rna1017 270 SVQQIDMMVTTKIFDIKDVNEYYKNQSCVNYIE--KINVPFIIINTYDDPIIPAfSIDKEMCMRNKNILLVIAHKG 343
                                        5678899**************************..9999***************8888888888888999999999 PP

                                        SSSHHHH CS
                      Abhydrolase_1 249 gHlafle 255
                                        gHl fl 
  gene1018|gene1018|rna1017|rna1017 344 GHLGFLS 350
                                        9999985 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   9.6e-10   2.9e-06       8     206 ..     114     320 ..     110     345 .. 0.69

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.6e-10
                        Hydrolase_4   8 vlvHGlaehsgr.yae.laeaLaaqGfavyalDhrGhGrsegkrghvpsfdd..yvdDlaafvekvkeehpelplf 79 
                                        +lvHG++ + +  y + la +L ++G+ v+++++rG  +s   + + p f +  ++ Dl+a  e + +++p++ l 
  gene1018|gene1018|rna1017|rna1017 114 LLVHGFNGSGDStYMRgLAGHLSREGYRVFCFNARGI-KS---KLDSPVFFHigWTVDLKATAEFILRNYPGT-LE 184
                                        799***98865314445*******************9.55...34444444322799***************9.99 PP

                        Hydrolase_4  80 llGhSmGGliallyl...lrypdkvaglilsaPa..lkikaklkappllklllkllgkllpklqvsnnlkadslsr 150
                                        ++G SmG+ ++++++   +  p+ v+g  ++ P+  +ki  ++  +p+ ++++kll+  + k+   n+  ++s   
  gene1018|gene1018|rna1017|rna1017 185 IFGFSMGASWVTKFFgeeKLDPRIVKGGAVCLPFdfFKIGIHFLKNPYTRFFNKLLAINFVKYMNRNKEVFKSAGY 260
                                        ***************7766666677777777775224444443355666666666665555555566666666666 PP

                        Hydrolase_4 151 dpevvaayeadplvhgkitvrll.....lelldamkrleeraakitlPllllhGeaDkvvd 206
                                        d++ ++++ + + +  ++t++++     +e ++  +++++  +ki++P++++   +D++++
  gene1018|gene1018|rna1017|rna1017 261 DTDIIKKCSSVQQIDMMVTTKIFdikdvNEYYK-NQSCVNYIEKINVPFIIINTYDDPIIP 320
                                        666666666666655555555542211023332.355666777777888888888888775 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.29   8.7e+02     185     211 ..      74     101 ..      35     109 .. 0.78
   2 !   14.9   0.0   1.1e-05     0.031       2      87 ..     114     208 ..     113     359 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.29
                                        HCHHCCCHSTTEEET..CE...SSS-HHH CS
                      Abhydrolase_6 185 rllerllaqagarlp..vvlpgaGHlphl 211
                                        +l++r  + +  r+   v++p++GH +++
  gene1018|gene1018|rna1017|rna1017  74 QLFRRSIV-PPGRISlrVEVPHNGHILLD 101
                                        55666667.6666656799******6554 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.1e-05
                                        EEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTS...TS-GGCS--HHHCHHHHHHHCCTT.....TTSEEEE CS
                      Abhydrolase_6   2 lllHGagssassWlvapLaallaag.vhvlapDlpGh...Grsdpppldledladlaalldelaa...gggpvvlv 70 
                                        ll+HG+ +s++s +++ La  l++  ++v+++ ++G      ++p  ++    +dl a+++ +     g+ ++  +
  gene1018|gene1018|rna1017|rna1017 114 LLVHGFNGSGDSTYMRGLAGHLSREgYRVFCFNARGIkskL-DSPVFFHIGWTVDLKATAEFILRnypGTLEI--F 186
                                        8****8888777778899777777779**********6542.4555566666899988888888876666666..* PP

                                        EETCHHHHHHHHHHCC...... CS
                      Abhydrolase_6  71 GHSlGGalalaaapla.....l 87 
                                        G S+G++ ++ ++        +
  gene1018|gene1018|rna1017|rna1017 187 GFSMGASWVTKFFGEEkldprI 208
                                        *****99777733333455533 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.037      62     141 ..     245     331 ..     225     346 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                        EEEETTE..EE----B-GGG-EE....-TTS-EE-TT-B--TTTG..GGCCCB--.GGG--SEEEEEEETT-SSS- CS
                             BAAT_C  62 klvykdeskvlpelklsmeklkv....nknglldivdvlallkek..laekalip.vekakgpillvvgedDknwp 130
                                         ++++ +++v++  + +++ +k+    ++ ++++++++++  + +   +++++++ +ek++ p+++++ +dD ++p
  gene1018|gene1018|rna1017|rna1017 245 VKYMNRNKEVFKSAGYDTDIIKKcssvQQIDMMVTTKIFDIKDVNeyYKNQSCVNyIEKINVPFIIINTYDDPIIP 320
                                        455555566677777777666666666555566666655544433114556666448******************* PP

                                        HHHHHHHHHHH CS
                             BAAT_C 131 Skesaekaser 141
                                        + +  +++++r
  gene1018|gene1018|rna1017|rna1017 321 AFSIDKEMCMR 331
                                        **999999987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.2e-05      0.12      12      62 ..      99     151 ..      96     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.2e-05
                             AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekdg.gif.lrgkcdq 62 
                                        Ll+++e+ r+ + +++l++G  G+G s+ +r l+ +l+++g  +f ++++  +
  gene1018|gene1018|rna1017|rna1017  99 LLDLVETDRMAGKNALLVHGFNGSGDSTYMRGLAGHLSREGyRVFcFNARGIK 151
                                        7999999999999***************************6333345555544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00015      0.46      17      52 ..     110     145 ..     101     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                             AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrvigl 52 
                                        g+   +++G  G+G +t +++l+ ++ ++g+rv+ +
  gene1018|gene1018|rna1017|rna1017 110 GKNALLVHGFNGSGDSTYMRGLAGHLSREGYRVFCF 145
                                        4557899**************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2291.24
//
Query:       gene1019|gene1019|rna1018|rna1018  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00014   21.4   0.9      0.029   13.8   0.4    2.2  2  KTI12     Chromatin associated protein KTI12
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.17   11.9   0.0    1.2  1  Sad1_UNC  Sad1 / UNC-like C-terminal
       0.15   12.3   0.0       0.27   11.5   0.0    1.4  1  DUF333    Domain of unknown function (DUF333)


Domain annotation for each model (and alignments):
>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.4   4.8e-06     0.029      82     103 ..      62      83 ..      53      86 .. 0.91
   2 !    5.9   0.0    0.0013       7.8     142     205 ..      89     146 ..      85     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.8e-06
                                        SHHHHHHHHHHHHHTT-EEEEE CS
                              KTI12  82 ikgfRYeLyciakaakttlcvv 103
                                        +k  RYe+yc+ak  +t +c++
  gene1019|gene1019|rna1018|rna1018  62 MKPQRYEIYCLAKRNETSYCIL 83 
                                        5788****************96 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0013
                                        SS-GGGS-SEEEE.TTS---HHHHHHHHHHHHTS--SSSTT-------HHHHHHHHHHHHHHHH CS
                              KTI12 142 sknrWDsPlftvlsaeeklpldeilkaliekkklkpnqatlskplaeanflqeLdketseivke 205
                                        s+ + D P+f ++   e lp++eil++l  k + +      +k+    n+l +L+k+++++ +e
  gene1019|gene1019|rna1018|rna1018  89 SSSKHDTPVFHIK---ERLPTKEILDCLEFKLNCS---VAHKKKVVGPNYLMHLKKIINQVNDE 146
                                        57899*******9...9**********94333222...22334445668888888888887766 PP

>> Sad1_UNC  Sad1 / UNC-like C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.17      23     112 ..      23     118 ..       4     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                                        EEESS-EEEEEEEEEEEEEEEEEEE---GGGSG....-TTSB-EEEEEEESSTT----EEEEEEE--TTS-SEEEE CS
                           Sad1_UNC  23 sfkgsrgfvvieLseeiiveavtlehveksvap....isSapKdfevsgskrypekkwvllgefsydedgknaqtF 94 
                                        s++ s  f v++L++e  +   +l +++   a+     + +p+++e++ + + +e+++  l++ ++++ + ++  F
  gene1019|gene1019|rna1018|rna1018  23 STYLSAHFRVVHLDDEFRIIRSKLSNMDPGTAYiienCEMKPQRYEIYCLAKRNETSYCILADGELSSSKHDTPVF 98 
                                        6666788999******************999999888899************************************ PP

                                        E--TT---..-EEEEEEEE- CS
                           Sad1_UNC  95 eleeskdi..lvkyvkleil 112
                                        +++e+     ++++++++++
  gene1019|gene1019|rna1018|rna1018  99 HIKERLPTkeILDCLEFKLN 118
                                        ****9433358899988876 PP

>> DUF333  Domain of unknown function (DUF333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.5e-05      0.27       8      37 ..      58      87 ..      57      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                             DUF333  8 vyCvkqGGkleiakdadGgqvgyCqlpdGk 37
                                       ++C+++  ++ei   a+ +++ yC+l+dG+
  gene1019|gene1019|rna1018|rna1018 58 ENCEMKPQRYEIYCLAKRNETSYCILADGE 87
                                       589999999999999999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1401.51
//
Query:       gene1020|gene1020|rna1019|rna1019  [L=310]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2198.45
//
Query:       gene102|gene102|rna102|rna102  [L=376]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-15   58.0   1.9    2.6e-15   56.8   1.9    1.7  1  SAS-6_N          Centriolar protein SAS N-terminal
    1.1e-06   28.6  36.5    4.5e-05   23.4  23.6    2.5  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      1e-05   24.8  33.1    0.00048   19.3  33.1    2.2  1  CCDC144C         CCDC144C protein coiled-coil region
    1.4e-05   25.0  41.6      0.094   12.8   1.8    6.2  6  bZIP_1           bZIP transcription factor
    2.3e-05   24.7  29.6      0.058   13.6   9.7    3.0  2  ATG16            Autophagy protein 16 (ATG16)
    4.3e-05   23.3  34.0     0.0014   18.4  18.2    2.3  2  Lebercilin       Ciliary protein causing Leber congenital ama
    6.3e-05   23.2  28.2       0.11   12.9   1.7    4.6  4  Csm1_N           Csm1 N-terminal domain
    0.00065   19.7  36.9      0.076   13.0  23.4    2.5  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0014   18.2  28.7      0.059   12.9   9.8    2.5  2  Filament         Intermediate filament protein
     0.0015   19.3   9.2     0.0015   19.3   9.2    3.2  3  DUF4472          Domain of unknown function (DUF4472)
     0.0015   17.3  28.3     0.0036   16.0  27.9    1.6  1  AAA_13           AAA domain
     0.0016   16.9  26.4     0.0026   16.2  26.4    1.3  1  MAD              Mitotic checkpoint protein
     0.0016   17.7  30.3      0.024   13.8   8.2    2.2  2  HAP1_N           HAP1 N-terminal conserved region
      0.002   18.4  26.4       0.05   13.9   9.7    2.7  2  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0037   17.4  29.5       0.45   10.6  13.4    2.6  2  ADIP             Afadin- and alpha -actinin-Binding
     0.0045   17.0  11.7     0.0045   17.0  11.7    3.1  3  BRE1             BRE1 E3 ubiquitin ligase
     0.0048   18.0   6.4     0.0048   18.0   6.4    3.7  3  SOGA             Protein SOGA
     0.0056   17.0  32.2      0.018   15.3   1.9    6.5  6  TSC22            TSC-22/dip/bun family
     0.0065   15.9  24.3       0.12   11.8   4.6    2.3  2  DUF4618          Domain of unknown function (DUF4618)
     0.0075   16.9  32.2       0.92   10.2   4.6    4.5  5  YabA             Initiation control protein YabA
      0.008   16.0  30.5       0.21   11.3   7.0    2.3  2  ERM              Ezrin/radixin/moesin family
     0.0096   15.5  21.4       0.16   11.5   2.3    2.9  2  MscS_porin       Mechanosensitive ion channel porin domain
  ------ inclusion threshold ------
      0.019   14.5  25.8      0.052   13.1  11.1    2.3  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
      0.022   14.9  37.3       0.12   12.6   9.1    2.8  3  Tropomyosin_1    Tropomyosin like
      0.034   13.5  38.5       0.19   11.0  15.3    3.0  3  GAS              Growth-arrest specific micro-tubule binding
      0.047   13.1  28.1       0.06   12.7   5.2    2.3  2  Cluap1           Clusterin-associated protein-1
      0.051   12.9  20.0      0.043   13.1   7.9    2.3  2  DUF3450          Protein of unknown function (DUF3450)
      0.064   11.4  31.1      0.015   13.5   1.8    3.0  3  FPP              Filament-like plant protein, long coiled-coi
      0.072   12.9  28.1      0.034   14.0  10.2    2.6  4  DUF724           Protein of unknown function (DUF724)
      0.087   13.5  16.2        4.6    7.9   1.1    5.1  5  SlyX             SlyX
        0.1   11.4  31.7      0.039   12.9  22.8    2.2  2  Spc7             Spc7 kinetochore protein
       0.11   11.8  23.3       0.27   10.4  11.4    2.2  2  TMPIT            TMPIT-like protein
       0.15   12.1  34.0        1.2    9.2   7.8    3.0  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.15   12.1  14.0       0.33   11.0   6.0    2.6  2  DUF1664          Protein of unknown function (DUF1664)
       0.16   12.1  30.6       0.97    9.5  16.2    3.4  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        0.2   11.9  32.4       0.28   11.4   0.9    5.1  6  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.26   11.8  34.6       0.33   11.5  14.0    3.1  3  APG6_N           Apg6 coiled-coil region
       0.28   10.9   6.4       0.58    9.8   6.4    1.4  1  DUF745           Protein of unknown function (DUF745)
       0.32   10.9  27.7        0.4   10.5  12.9    2.3  2  CEP63            Centrosomal protein of 63 kDa
       0.38   10.8  16.2       0.13   12.4   0.8    2.8  3  Nup54            Nucleoporin complex subunit 54
        0.5   10.5  24.4       0.21   11.7  10.3    2.5  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.62   10.5  29.9        3.7    8.0   5.9    4.2  4  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
       0.68    9.5  27.4          1    9.0  27.4    1.2  1  DUF4795          Domain of unknown function (DUF4795)
       0.79   10.6  34.6       0.69   10.9  15.6    3.6  3  PRKG1_interact   cGMP-dependent protein kinase interacting do
        0.9    8.9  36.3        2.3    7.6  36.3    1.6  1  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.93    9.9  38.2        7.2    7.0  10.7    3.0  2  DUF4200          Domain of unknown function (DUF4200)
          1    9.6  32.7        5.4    7.2  17.5    2.5  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        1.1    8.6  18.9         15    4.8  18.8    2.0  1  DUF4407          Domain of unknown function (DUF4407)
        1.1    9.6  33.4        2.2    8.5   8.4    3.3  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        1.1    9.7  29.2        1.9    8.9  13.8    2.3  2  Fez1             Fez1
        1.1    9.2  28.2       0.98    9.4  11.0    2.9  3  Rootletin        Ciliary rootlet component, centrosome cohesi
        1.2    8.8  27.3      0.045   13.4  11.5    2.5  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
        1.2    9.6  35.5        4.1    7.9   4.5    4.3  3  ZapB             Cell division protein ZapB
        1.2    8.7  23.9       0.75    9.3  14.2    2.9  2  PspA_IM30        PspA/IM30 family
        1.4    7.4  30.5         10    4.5  30.5    1.9  1  Macoilin         Macoilin family
        1.5    9.2  27.6        3.1    8.2   5.7    4.1  3  Tup_N            Tup N-terminal
        1.5    9.4  19.3        2.4    8.8   7.6    3.1  2  Syntaxin-6_N     Syntaxin 6, N-terminal
        1.6    8.9  24.9       0.75   10.0  13.5    2.5  2  Fib_alpha        Fibrinogen alpha/beta chain family
        2.4    8.0  39.3       0.95    9.3   2.1    6.5  7  DivIC            Septum formation initiator
        2.4    8.7  18.7       0.68   10.5   5.9    3.1  3  Spectrin         Spectrin repeat
        2.5    8.7  24.6       0.36   11.4   8.9    3.6  3  BST2             Bone marrow stromal antigen 2
        3.1    8.1   6.8         27    5.1   0.1    3.0  3  DUF948           Bacterial protein of unknown function (DUF94
        3.8    7.5  21.4          2    8.4   9.6    2.3  2  Laminin_II       Laminin Domain II
          4    8.0   8.5        3.4    8.2   0.7    3.1  2  NPV_P10          Nucleopolyhedrovirus P10 protein
        4.9    6.6  32.2        3.9    6.9  19.6    2.3  2  Leu_zip          Leucine zipper
        5.6    7.0  27.7        4.1    7.5  13.8    3.3  2  CtIP_N           Tumour-suppressor protein CtIP N-terminal do
        5.8    7.7  15.9        1.7    9.4   5.3    2.5  2  DUF2203          Uncharacterized conserved protein (DUF2203)
        6.5    7.1  22.9       0.22   11.8   5.6    3.4  3  DUF4164          Domain of unknown function (DUF4164)
        9.6    5.4  15.5         13    4.9   6.3    2.5  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
        9.6    5.8  19.4      0.097   12.3   2.2    3.7  4  DUF4988          Domain of unknown function


Domain annotation for each model (and alignments):
>> SAS-6_N  Centriolar protein SAS N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   1.9     1e-17   2.6e-15       1      92 []      34     118 ..      34     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1e-17
                                    EEEEEEETTEEEEEEEEEEEHHHHHHHHHHCTB-S-CCCHHHHHHHHHHHHHHS...SSEEEECCTTTSSEEEEEEEEE- CS
                        SAS-6_N   1 lrieltdenDlfflytleiseedFeelkeeqnLlvdFaeFpsklikllnscqkpekkkylavlslekdegqakLsivetn 80 
                                    ++i+l+d+ D+f++y ++is  dF  +k+eq++ vd+++F+s l+k+++s ++    k+   +s    ++++k+ +ve+ 
  gene102|gene102|rna102|rna102  34 VEIRLIDTRDIFTFYFSTISPGDFYVMKREQDIIVDYEKFVSILVKMFHSLHSG---KLRGLFS----KETSKFLFVEKD 106
                                    589************************************************764...4443344....669********* PP

                                    SSBEEEEEEEEE CS
                        SAS-6_N  81 eFkqlehLslef 92 
                                    eF+++  L+l+f
  gene102|gene102|rna102|rna102 107 EFRNIVRLELKF 118
                                    **********97 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  10.0   8.4e-06    0.0021      30     123 ..     133     227 ..     124     233 .. 0.91
   2 !   23.4  23.6   1.7e-07   4.5e-05       8     146 ..     206     344 ..     204     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.4e-06
                       KASH_CCD  30 avetaeetnakLteeieeLkkklkstQqalq.kaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLq 108
                                     +  +e  n +L+ e+  L+ k k + + l  + + leeE    ++ +++l   ++ l+ + +    e + L++ki +L+
  gene102|gene102|rna102|rna102 133 MIGRMEADNVRLIKENGMLRDKCKNGEKELRdRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLE 212
                                    57789********************998876268*************************99999999************* PP

                       KASH_CCD 109 eenikllaekdelkk 123
                                     en +l+ e d+lk 
  gene102|gene102|rna102|rna102 213 KENGRLQYELDKLKL 227
                                    ***********9986 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.7e-07
                       KASH_CCD   8 stvadLqlnNkkLaeenskLk.kavetae..etnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkra 84 
                                    s + dL+  N +L+ e  kLk + v ++   e  +k+ +e++ Lk+ l      + k    ++E+ ++k+ ++  e+  +
  gene102|gene102|rna102|rna102 206 SKIYDLEKENGRLQYELDKLKlQDVKNSGlvERAQKIEDENKMLKEELSTANEIIRK---YNDEITQMKNAINGNEDATK 282
                                    5799****************9445776534499***************987766665...589***************** PP

                       KASH_CCD  85 rlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleell 146
                                     l  +nk+ + e + L+++++ ++e+++k++ e  + +++lk+L +e+  L k+l +++++ 
  gene102|gene102|rna102|rna102 283 DLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQNVY 344
                                    ****************************************************9999988876 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3  33.1   1.9e-06   0.00048      27     242 ..     142     342 ..     135     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-06
                       CCDC144C  27 kkyledieilkeknddlqkslKlneetltktvfqyngqLnvlkaentmlnskLekekqnkerleaevesyrsrLaaAiqd 106
                                     ++++++ +l++k+++ +k+l+     l +  + +++++n+l  +n++l+ k ++++++ e           rL++ i d
  gene102|gene102|rna102|rna102 142 VRLIKENGMLRDKCKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIE-----------RLNSKIYD 210
                                    5789*******************************************99866655544443...........67777788 PP

                       CCDC144C 107 heqsqtskrdlelalqrerdewlrlqdklnf.dvsnlkdknevLsqqLskaeskansLenelhetrdaLrektlllesvq 185
                                    +e++     + el   + +d    +++   +  + ++ d+n++L+++Ls+a+  +++ ++e+ ++++a+  +  +   + 
  gene102|gene102|rna102|rna102 211 LEKENGR-LQYELDKLKLQD----VKNSGLVeRAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLR 285
                                    8754433.344444444445....33333330345789****************************************** PP

                       CCDC144C 186 rdlsqaqcqikeleqmyqneeekvnkyiakqesleerlaqlqsenmlLrqqLedaqn 242
                                     + ++ +++i +l++  +  eek++k  ++ ++ e rl+ l+ enm L + Le+aqn
  gene102|gene102|rna102|rna102 286 LNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQN 342
                                    ********************************************************9 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.15        37      37      60 ..     136     159 ..     126     163 .. 0.78
   2 ?    1.4   2.1       1.4   3.6e+02      25      59 ..     156     190 ..     150     195 .. 0.78
   3 !   12.8   1.8   0.00037     0.094      25      53 ..     198     226 ..     195     232 .. 0.94
   4 !   12.0   2.8   0.00068      0.17      31      61 ..     235     265 ..     226     275 .. 0.87
   5 !    8.7   2.8     0.007       1.8      35      63 ..     281     309 ..     277     311 .. 0.86
   6 ?    7.9   3.2     0.012       3.2      25      58 ..     313     346 ..     310     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  37 aLekeNksLkseleelkkevekLk 60 
                                     +e+ N  L++e++ l++++++ +
  gene102|gene102|rna102|rna102 136 RMEADNVRLIKENGMLRDKCKNGE 159
                                    578899999999999999998655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                    +   +eL +r   Le+e ++ ++++++l  ++e L
  gene102|gene102|rna102|rna102 156 KNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVL 190
                                    55668999999999999999999999987777655 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00037
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelk 53 
                                    ++eie+L ++   LekeN  L+ el++lk
  gene102|gene102|rna102|rna102 198 REEIERLNSKIYDLEKENGRLQYELDKLK 226
                                    79*************************98 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00068
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  31 LerrvkaLekeNksLkseleelkkevekLks 61 
                                    L +r++++e eNk+Lk+el++ ++ + k  +
  gene102|gene102|rna102|rna102 235 LVERAQKIEDENKMLKEELSTANEIIRKYND 265
                                    889*****************99999887655 PP

  == domain 5  score: 8.7 bits;  conditional E-value: 0.007
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  35 vkaLekeNksLkseleelkkevekLkskv 63 
                                     k L   Nk++kse+e lkk v+ +++k 
  gene102|gene102|rna102|rna102 281 TKDLRLNNKKYKSEIEDLKKRVKGMEEKM 309
                                    6788899***************9998775 PP

  == domain 6  score: 7.9 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevek 58 
                                    ++e ++ e+r k Le+eN+ L + le+ ++ ++ 
  gene102|gene102|rna102|rna102 313 KEELKAKETRLKDLETENMGLVKNLENAQNVYSH 346
                                    7889999*******************99887765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   9.7   0.00023     0.058      72     184 ..     123     249 ..      95     249 .. 0.71
   2 !   13.1  15.0   0.00033     0.085     103     180 ..     238     315 ..     229     337 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00023
                          ATG16  72 qsakiqsleqklaqlreelaelyksrgelaqrllelneelqk....leeklkedeerlaeleaeraaletklkdreeelr 147
                                    ++++   l + + ++ ++   l k++g l ++ ++ ++el++    lee++++ ++++++l +++++l++k ++++ee++
  gene102|gene102|rna102|rna102 123 ETHYKMYLGDMIGRMEADNVRLIKENGMLRDKCKNGEKELRDriryLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIE 202
                                    5555555666677777788888888888888888877777653333899************************9999999 PP

                          ATG16 148 ekeklvqdlqDElsaLqlqlnqaEeklr..........klekENkeL 184
                                     ++  + dl  E   Lq +l ++  +            k+e+ENk L
  gene102|gene102|rna102|rna102 203 RLNSKIYDLEKENGRLQYELDKLKLQDVknsglveraqKIEDENKML 249
                                    99888886655555555555543322222223333333888888765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00033
                          ATG16 103 rllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekE 180
                                    r ++ ++e + l+e+l++ +e +++ ++e+++++ +++ +e++ ++++  +++ + E++ L+ +++ +Eek +k+++E
  gene102|gene102|rna102|rna102 238 RAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEE 315
                                    445555555555555555555555555555555555555555555555555555555555555555555555544444 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   9.3    0.0033      0.85     118     184 ..     158     227 ..     140     233 .. 0.84
   2 !   18.4  18.2   5.3e-06    0.0014      23     130 ..     235     341 ..     226     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0033
                     Lebercilin 118 ereeLqkkLeeleakleekeekikeLerklelee...ksfrrqlaaekkktkeaqeevkalqeeierlkq 184
                                      +eL  +++ le++  ++++k+++L r  e+++   +s+r ++++ ++k+ ++++e+ +lq e+++lk 
  gene102|gene102|rna102|rna102 158 GEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSekgNSQREEIERLNSKIYDLEKENGRLQYELDKLKL 227
                                    56899***********************9887652225778889999*******************9984 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 5.3e-06
                     Lebercilin  23 lqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkd 102
                                    l ++ ++++ Enk+Lk+     ++ ++ky+d+  ++ + ++  ++ ++ lr + +k + + ++l+k++k  e++++++k+
  gene102|gene102|rna102|rna102 235 LVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKE 314
                                    667899************************************************************************** PP

                     Lebercilin 103 klkklkkLsedknLaereeLqkkLeele 130
                                    +lk+ +   +d +  e   L k Le+++
  gene102|gene102|rna102|rna102 315 ELKAKETRLKDLET-ENMGLVKNLENAQ 341
                                    ****9996666554.5666666666666 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2      0.01       2.6      24      66 ..     143     182 ..     138     184 .. 0.87
   2 !   12.9   1.7   0.00042      0.11      23      63 ..     181     221 ..     179     228 .. 0.89
   3 ?    8.3   2.1     0.012         3      24      66 ..     241     283 ..     235     287 .. 0.90
   4 !    9.1   4.8    0.0062       1.6      35      67 ..     287     319 ..     278     327 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.01
                         Csm1_N  24 klvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                    +l++EN +L+ k ++ ++e   L+ ++  lee+   ++++ +k
  gene102|gene102|rna102|rna102 143 RLIKENGMLRDKCKNGEKE---LRDRIRYLEEETMASQKKMNK 182
                                    79***********999987...789999999998888887765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00042
                         Csm1_N  23 sklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleer 63 
                                    +kl   N vLs+k +++ +eie+L  ++  le+++ +l+ +
  gene102|gene102|rna102|rna102 181 NKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYE 221
                                    79999***************************998887765 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.012
                         Csm1_N  24 klvhENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                    k+  EN +L+++l+t ++ i +   ++ ++++ ++  e+ +k+
  gene102|gene102|rna102|rna102 241 KIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKD 283
                                    6778****************************99999988876 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0062
                         Csm1_N  35 kletkdqeiesLkeqlaeleekvkeleerrkkq 67 
                                    ++++++ eie Lk++++ +eek+k+++e+ k++
  gene102|gene102|rna102|rna102 287 NNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAK 319
                                    4567789******************99988765 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   8.8   0.00047      0.12      18      79 ..     158     226 ..     145     229 .. 0.73
   2 !   13.0  23.4    0.0003     0.076       8     128 ..     221     341 ..     214     349 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00047
                 CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaE.......tskaevetlkeeieelaeelreleldLvalr 79 
                                     +  L+d++  Le e   s+++ +k+ ++ E       ++++e+e l+++i  l++e  +l+ +L++l+
  gene102|gene102|rna102|rna102 158 GEKELRDRIRYLEEETMASQKKMNKLYRDNEvlsekgnSQREEIERLNSKIYDLEKENGRLQYELDKLK 226
                                    4568**********************9999933333334566666677777666666666666666654 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.0003
                 CENP-F_leu_zip   8 vlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLek 87 
                                     l+kLK    k++ L ++++++e e +m++e+++ +     +   e+ ++k+ i+  +  +++l+l+ ++ +se e+L+k
  gene102|gene102|rna102|rna102 221 ELDKLKLQDVKNSGLVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKK 300
                                    5789**************************************************************************** PP

                 CENP-F_leu_zip  88 elqkkqervseLeslnsslenlleekEqekvqmkeeskaav 128
                                     ++ + e+++  ++     e  l+++E e++ + ++ ++a 
  gene102|gene102|rna102|rna102 301 RVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQ 341
                                    *****************************988877777765 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   9.8   0.00023     0.059      18     103 ..     164     246 ..     162     248 .. 0.86
   2 !    8.6  14.8     0.005       1.3      17     114 ..     236     325 ..     231     353 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00023
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  18 dkVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnk 97 
                                    d++r LE+e  + + k+++l+   ++  s+  +   +e+e l +++ +l+ke+ rlq eld+l+  l+d++++   e ++
  gene102|gene102|rna102|rna102 164 DRIRYLEEETMASQKKMNKLYRD-NEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLK--LQDVKNSGLVERAQ 240
                                    89********************9.556666899999*************************987..57777777777777 PP

                                    XXXXXX CS
                       Filament  98 reevEa 103
                                    + e E+
  gene102|gene102|rna102|rna102 241 KIEDEN 246
                                    666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.005
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  17 idkVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekeln 96 
                                    +++ +++E enk+L+ +++  +e          + y++e+++++++++  + + + l+l+ ++ + e+edl+k+++   +
  gene102|gene102|rna102|rna102 236 VERAQKIEDENKMLKEELSTANEI--------IRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEE 307
                                    455666666666666665555444........345667777777777777777777777777777777777766654333 PP

                                    XXXXXXXXXXXXXXXXXX CS
                       Filament  97 kreevEaelkalrkdlde 114
                                    k +++ +elka    l++
  gene102|gene102|rna102|rna102 308 KMKKIKEELKAKETRLKD 325
                                    333333333333322222 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   3.4      0.64   1.6e+02      53     107 .]     166     222 ..     134     222 .. 0.71
   2 ?    3.7   3.8      0.39        99      28      82 ..     199     256 ..     193     259 .. 0.66
   3 !   19.3   9.2   5.7e-06    0.0015      19     101 ..     256     338 ..     254     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.64
                        DUF4472  53 k..aaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqelsleL 107
                                       ++ee  + ++++++l ++++ l+e++ + ++++  l+ +  + +k++ +l+ eL
  gene102|gene102|rna102|rna102 166 IryLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYEL 222
                                    144666777778888888888888888888888888888888888888888888776 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.39
                        DUF4472  28 aekfelknkvlalenrvlelelerek...aaeeiqslrerlaeleeekkeleeeyvvl 82 
                                    +e+  l++k+  le++   l+ e +k      +++ l er +++e+e+k l+ee+++ 
  gene102|gene102|rna102|rna102 199 EEIERLNSKIYDLEKENGRLQYELDKlklQDVKNSGLVERAQKIEDENKMLKEELSTA 256
                                    4555677888777666555555555533333456678999999999999999998875 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 5.7e-06
                        DUF4472  19 tnklreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekk 98 
                                     n++ ++++ e+ ++kn +   e    +l l+++k ++ei++l++r++++ee+ k+++ee+++ ++++++le+e +  +k
  gene102|gene102|rna102|rna102 256 ANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVK 335
                                    789999*****************************************************************999887766 PP

                        DUF4472  99 kqq 101
                                      +
  gene102|gene102|rna102|rna102 336 NLE 338
                                    655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  27.9   1.4e-05    0.0036     285     456 ..     159     340 ..     150     347 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                         AAA_13 285 qerLekliekveskkselleklkavsde....asensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesv 360
                                     ++L ++i  +e+++   ++k++++  +    +++ +  +e++e l++++  le++   lq +l++ + + +k+  l + 
  gene102|gene102|rna102|rna102 159 EKELRDRIRYLEEETMASQKKMNKLYRDnevlSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVER 238
                                    56677777777666666666666666652232444444566677788888888888777777777644444454555444 PP

                         AAA_13 361 kaki....esikklvaeineliakhNekvanleeeke...eakkklelhlveeleseldeykkkykklekaieklekelk 433
                                    ++ki    + +k++++++ne+i+k+N  +++++++ +   +a+k+l+l   ++++se++ +kk +k++e++++k ++elk
  gene102|gene102|rna102|rna102 239 AQKIedenKMLKEELSTANEIIRKYNDEITQMKNAINgneDATKDLRL-NNKKYKSEIEDLKKRVKGMEEKMKKIKEELK 317
                                    444433336899*****************9999986522267777777.5588*************************** PP

                         AAA_13 434 eeeaelkkleeeikeLekqlrde 456
                                    ++e++lk le e   L k+l++ 
  gene102|gene102|rna102|rna102 318 AKETRLKDLETENMGLVKNLENA 340
                                    ***********955555555544 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  26.4     1e-05    0.0026     408     572 ..     146     321 ..     125     345 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                            MAD 408 eevggykqqastlerelqalrqqesladassskeevdslkkkleeLelerqrLreqkeelElele...rreLqgdydlkk 484
                                    +e g  +++++  e+el  + +   +++   s+  +++l++++e L  + ++ re++e l +++    +++ + +y+l k
  gene102|gene102|rna102|rna102 146 KENGMLRDKCKNGEKELRDRIRYL-EEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYdleKENGRLQYELDK 224
                                    455666777777777765443322.2222235677777777777777777777777777776654444666666777777 PP

                            MAD 485 tkVlhlseNPaakakqqkkeqlekLqaEierlkellkkleedkekkvaslpes.....sltlafk....evleLrkeles 555
                                     k   +++    +  q+ +++ ++L++E++   e+++k +++  +  ++++ +      l+l++k    e+ +L+k ++ 
  gene102|gene102|rna102|rna102 225 LKLQDVKNSGLVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNedatkDLRLNNKkyksEIEDLKKRVKG 304
                                    77666666666666666666667777777777777777776666656666555556666666665222345677777777 PP

                            MAD 556 aelkiqrlKevFkakiq 572
                                     e k++++Ke  kak +
  gene102|gene102|rna102|rna102 305 MEEKMKKIKEELKAKET 321
                                    77777777776666643 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   8.2   9.4e-05     0.024     168     266 ..     130     228 ..     104     232 .. 0.90
   2 !    9.4  14.4    0.0022      0.55     102     206 ..     232     336 ..     229     347 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-05
                         HAP1_N 168 LqeklreLeeeNekLreeasqLktetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeissLlaqiv 247
                                    L + + ++e +N +L +e   L+++ ++ E++ +  +  + e+   +++++++l  + +  +e+ + q+eei++L ++i 
  gene102|gene102|rna102|rna102 130 LGDMIGRMEADNVRLIKENGMLRDKCKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIY 209
                                    66667789**************99999999999999******************************************** PP

                         HAP1_N 248 dlqqklkelgveneelkqh 266
                                    dl++   +l+ e ++lk +
  gene102|gene102|rna102|rna102 210 DLEKENGRLQYELDKLKLQ 228
                                    ********99999999865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0022
                         HAP1_N 102 nekLeeqLesareeiaqlrhelslkddLLqlysdseeeseeeseeseelreeesleslqklvqldlLqeklreLeeeNek 181
                                    n+ L e+ +++++e + l+ els  +++++ y d+  + +++ + +e   ++  l+ ++   +++ L+++++ +ee  +k
  gene102|gene102|rna102|rna102 232 NSGLVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKK 311
                                    66667777778888888888888888888888888777777777777777777777777888888888888888888888 PP

                         HAP1_N 182 LreeasqLktetdtlEekEqqLvld 206
                                    ++ee +  +t  ++lE +   Lv++
  gene102|gene102|rna102|rna102 312 IKEELKAKETRLKDLETENMGLVKN 336
                                    8888777777777777777777665 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   9.7   0.00019      0.05       6      93 ..     164     251 ..     159     254 .. 0.93
   2 !    9.8  11.5    0.0037      0.94      10      95 ..     241     323 ..     236     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00019
                        BLOC1_2   6 kvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLD 85 
                                    +  +yle+e+ a++++++ L + Ne+ sek ++ +++++ l++k+ +l++++  lq  l++++  + + + L e +++++
  gene102|gene102|rna102|rna102 164 DRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVERAQKIE 243
                                    5679**********************************************************************999999 PP

                        BLOC1_2  86 eyskeLEa 93 
                                       k L++
  gene102|gene102|rna102|rna102 244 DENKMLKE 251
                                    88888765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0037
                        BLOC1_2  10 yleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeysk 89 
                                     +e e ++ +e++++ +++ ++ + +++++k+++++ e+  ++l+    + ++y+++i++++k+v+ +ee  +++ e  k
  gene102|gene102|rna102|rna102 241 KIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRL---NNKKYKSEIEDLKKRVKGMEEKMKKIKEELK 317
                                    5788999999***********************************9...999********************99998888 PP

                        BLOC1_2  90 eLEakf 95 
                                    + E ++
  gene102|gene102|rna102|rna102 318 AKETRL 323
                                    777766 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5  12.1    0.0039         1      50     150 ..     154     253 ..     150     255 .. 0.88
   2 !   10.6  13.4    0.0018      0.45      53     131 ..     251     329 ..     240     338 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0039
                           ADIP  50 rdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqik 129
                                    + ++ +++l ++ir le e    q+k+++l + +e l  +  ++ ++   l+ k+ +le+ + +++ el +lk  lq++k
  gene102|gene102|rna102|rna102 154 KCKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLK--LQDVK 231
                                    556778999************************************************************9986..89999 PP

                           ADIP 130 tqyahelkkk.dreiekLkekl 150
                                    ++  +e  +k + e + Lke l
  gene102|gene102|rna102|rna102 232 NSGLVERAQKiEDENKMLKEEL 253
                                    9999997766477777788777 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0018
                           ADIP  53 eqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktq 131
                                    e+  + ne irk + ei++++++i+  ++ +++l+  ++ ++++  +l+k++k  e+k+k+ keel+  ++ l++++t 
  gene102|gene102|rna102|rna102 251 EELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETE 329
                                    34445678899********************************************************999999999886 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       4.3   1.1e+03      68      95 .]     145     172 ..     137     172 .. 0.80
   2 !   17.0  11.7   1.8e-05    0.0045       7      88 ..     168     249 ..     162     253 .. 0.92
   3 ?    4.5  17.2      0.14        36       1      94 [.     249     339 ..     249     342 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 4.3
                           BRE1  68 lsKsselieqLkelekefvrklkeleke 95 
                                    ++ +  l ++ k+ eke++ ++  le+e
  gene102|gene102|rna102|rna102 145 IKENGMLRDKCKNGEKELRDRIRYLEEE 172
                                    5556667788999999999999999976 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.8e-05
                           BRE1   7 klekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefv 86 
                                     le++  + +++++k++ + + l ek +    e+++   k+++++++   l+ el kL+ +  K+s l+e+ + +e e++
  gene102|gene102|rna102|rna102 168 YLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVERAQKIEDENK 247
                                    578899999*****************************************************************999987 PP

                           BRE1  87 rk 88 
                                     +
  gene102|gene102|rna102|rna102 248 ML 249
                                    65 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.14
                           BRE1   1 lqkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLke 80 
                                    l+ EL   ++ +++ ++++ ++++ +   e+  + l  + +k + ++ ++++  + +e ++kk+++ l+ +    ++Lk+
  gene102|gene102|rna102|rna102 249 LKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKE---TRLKD 325
                                    578999999999******************************************************997554...57888 PP

                           BRE1  81 lekefvrklkelek 94 
                                    le+e+  ++k+le+
  gene102|gene102|rna102|rna102 326 LETENMGLVKNLEN 339
                                    88888888888875 PP

>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.2      0.05        13       3      35 ..     160     192 ..     158     198 .. 0.92
   2 !   18.0   6.4   1.9e-05    0.0048      13      89 ..     198     271 ..     195     276 .. 0.87
   3 ?    1.6  15.0       2.4   6.1e+02      12      92 ..     242     330 ..     237     343 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.05
                           SOGA   3 aeLrrhLqfveeEaeLlrrslseleeenkqlte 35 
                                    +eLr ++++ eeE+    +++ +l ++n+ l e
  gene102|gene102|rna102|rna102 160 KELRDRIRYLEEETMASQKKMNKLYRDNEVLSE 192
                                    79**************************99976 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.9e-05
                           SOGA  13 eeEaeLlrrslseleeenkqlteeLnkyksklgeeessleeeeeassdsskeaelkeeLklarlqineLsgkvvkLq 89 
                                     eE e l  ++ +le+en +l+ eL k+k +  ++++ +e+   a++ + ++++lkeeL +a + i++ +  + +++
  gene102|gene102|rna102|rna102 198 REEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVER---AQKIEDENKMLKEELSTANEIIRKYNDEITQMK 271
                                    5899999*************************999999977...4444456899**********9999988888775 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 2.4
                           SOGA  12 veeEaeLlrrslseleeenkqlteeLnkyksklgeeessleeee........eassdsskeaelkeeLklarlqineLsg 83 
                                    +e+E ++l+ +ls  +e  ++ + e++++k   + +e ++++          e ++ +++ + ++e++k  +++ +  + 
  gene102|gene102|rna102|rna102 242 IEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRlnnkkyksEIEDLKKRVKGMEEKMKKIKEELKAKET 321
                                    45666666666666666666666666666665555555544433444444432222233444455555555555555555 PP

                           SOGA  84 kvvkLqven 92 
                                    +++ L+ en
  gene102|gene102|rna102|rna102 322 RLKDLETEN 330
                                    556666665 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.76     2e+02      23      45 ..     134     156 ..     129     160 .. 0.83
   2 ?    2.8   1.0      0.57   1.5e+02      18      42 ..     161     186 ..     156     197 .. 0.68
   3 !   15.3   1.9   7.2e-05     0.018      13      41 ..     198     226 ..     195     233 .. 0.93
   4 ?    8.2   0.5     0.012       3.1      26      46 ..     235     255 ..     230     267 .. 0.84
   5 ?    1.9   0.3       1.1   2.9e+02      13      44 ..     264     295 ..     263     297 .. 0.90
   6 ?    3.9   3.4      0.26        66      14      36 ..     293     315 ..     291     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.76
                          TSC22  23 IkeLeernseleeENslLkalas 45 
                                    I  +e++n +l +EN +L+  + 
  gene102|gene102|rna102|rna102 134 IGRMEADNVRLIKENGMLRDKCK 156
                                    6667889999*********9996 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.57
                          TSC22  18 vLkekIkeLeer.nseleeENslLka 42 
                                    +L+++I+ Lee+ ++  ++ N+l++ 
  gene102|gene102|rna102|rna102 161 ELRDRIRYLEEEtMASQKKMNKLYRD 186
                                    58888888876514444556788874 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 7.2e-05
                          TSC22  13 rEeVevLkekIkeLeernseleeENslLk 41 
                                    rEe+e L +kI +Le++n +l++E   Lk
  gene102|gene102|rna102|rna102 198 REEIERLNSKIYDLEKENGRLQYELDKLK 226
                                    9***********************98887 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.012
                          TSC22  26 LeernseleeENslLkalasp 46 
                                    L+er +++e EN++Lk+ +s 
  gene102|gene102|rna102|rna102 235 LVERAQKIEDENKMLKEELST 255
                                    99**************98774 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 1.1
                          TSC22  13 rEeVevLkekIkeLeernseleeENslLkala 44 
                                    ++e+ ++k+ I   e+  + l+  N+ +k+ +
  gene102|gene102|rna102|rna102 264 NDEITQMKNAINGNEDATKDLRLNNKKYKSEI 295
                                    5899999*********************9876 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.26
                          TSC22  14 EeVevLkekIkeLeernseleeE 36 
                                     e+e Lk+++k +ee++++++eE
  gene102|gene102|rna102|rna102 293 SEIEDLKKRVKGMEEKMKKIKEE 315
                                    58999999999999999999988 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   4.6   0.00046      0.12     151     224 ..     148     223 ..     135     232 .. 0.79
   2 !    8.7  13.1    0.0041       1.1     136     221 ..     238     321 ..     222     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                        DUF4618 151 leklskkiqkkkekllksl..aektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqae 224
                                      +l +k ++ +++l + +   e+  +a q+ + +  ++n+vl+++ + +re+ie+l+ +i +L++e  +Lq +  
  gene102|gene102|rna102|rna102 148 NGMLRDKCKNGEKELRDRIryLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELD 223
                                    4567777777777776654223555666799************************************999997765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0041
                        DUF4618 136 qqdeldeleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkae 215
                                    + + +++ ++++ke+l + ++ i+k ++++++   +++++ +++a ++  l+n++ k+eie  ++ ++ +ee+++++k+e
  gene102|gene102|rna102|rna102 238 RAQKIEDENKMLKEELSTANEIIRKYNDEITQM--KNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEE 315
                                    345678889999999999999999999999875..699999999999999999999999999999999999999999999 PP

                        DUF4618 216 veqLqa 221
                                    +++ + 
  gene102|gene102|rna102|rna102 316 LKAKET 321
                                    987555 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.3      0.04        10      27      79 ..     130     186 ..     103     188 .. 0.70
   2 !   10.2   4.6    0.0036      0.92       5      52 ..     182     229 ..     179     249 .. 0.76
   3 ?    2.9   2.3      0.67   1.7e+02      33      66 ..     234     267 ..     226     283 .. 0.58
   4 ?    6.1   2.7     0.066        17       3      52 ..     246     295 ..     244     297 .. 0.90
   5 !    9.6   7.0    0.0055       1.4       3      57 ..     288     342 ..     286     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.04
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH....XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           YabA  27 lkeelaelleenaeLeleneklrerl....eeeekkekekkkelsegkenLarlYee 79 
                                    l + + ++  +n +L  en  lr++     +e +++ +  ++e+  +++++++lY++
  gene102|gene102|rna102|rna102 130 LGDMIGRMEADNVRLIKENGMLRDKCkngeKELRDRIRYLEEETMASQKKMNKLYRD 186
                                    556778888999999999999999995443333333344466777788889999975 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0036
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                    +l++  e l+e+ ++  ee+e+l++++++l +en +L+ e +kl+ + 
  gene102|gene102|rna102|rna102 182 KLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQD 229
                                    5777778899999999*************************9998654 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.67
                                    HHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXX CS
                           YabA  33 elleenaeLeleneklrerleeeekkekekkkel 66 
                                     l+e+ +++e en+ l+e+l+++++  ++ + e+
  gene102|gene102|rna102|rna102 234 GLVERAQKIEDENKMLKEELSTANEIIRKYNDEI 267
                                    4677777777777777777744433333333333 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.066
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                    +k l ++l++ +e +++ ++e++++k++++   +  ++L+l+n+k ++++
  gene102|gene102|rna102|rna102 246 NKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEI 295
                                    56678899999*********************************998876 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.0055
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXX CS
                           YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeek 57 
                                    +k+  +++e+l+++++ + e+++++keel++   + ++Le+en  l ++le++++
  gene102|gene102|rna102|rna102 288 NKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQN 342
                                    6677789999*********************************999999955443 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   7.0   0.00084      0.21       7      69 ..     159     221 ..     153     226 .. 0.93
   2 !   10.3  15.5    0.0018      0.46      10     134 ..     235     352 ..     227     372 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00084
                            ERM   7 kreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkes 69 
                                    ++el++r++ l+ee+ + q+++++  +  e L ek    +ee e+L+ k  ++e+e+ rl+ +
  gene102|gene102|rna102|rna102 159 EKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYE 221
                                    789********************************************************9865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0018
                            ERM  10 leerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreael 89 
                                    l er +++++e ++ +e+L+ ++e +++++ +  +++++        +  e +++ l+ +++k ++e e+l+++++ +e+
  gene102|gene102|rna102|rna102 235 LVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAI-------NGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEE 307
                                    6788888999999999999999988888887777776655.......667778888888888888888888888888888 PP

                            ERM  90 eaarleeeserkeeeaerLkeeleeareaeeeakekllealstps 134
                                    ++++++ee ++ke   + L++e +   +++e+a++   ++ s++ 
  gene102|gene102|rna102|rna102 308 KMKKIKEELKAKETRLKDLETENMGLVKNLENAQNVYSHFYSKNI 352
                                    888888888888888888888888888888888887777777774 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  12.5     0.011       2.9       6     131 ..     170     283 ..     165     286 .. 0.76
   2 !   11.5   2.3   0.00062      0.16      25      63 ..     281     319 ..     279     341 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.011
                     MscS_porin   6 ekakldeaeqkallqdLeqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeq 85 
                                    e+++   a+qk++ + +++   l +k + +++++e l+ +i d  ke   lq el++l         ++ ++  l e  q
  gene102|gene102|rna102|rna102 170 EEET--MASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKL-------KLQDVKNSGLVERAQ 240
                                    5555..99**************************************************.......445555555555555 PP

                     MscS_porin  86 rllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqe 131
                                    ++++++     l+e+l+++n+ ++++++ +++  +++  +  ++++
  gene102|gene102|rna102|rna102 241 KIEDENKM---LKEELSTANEIIRKYNDEITQMKNAINGNEDATKD 283
                                    55555444...45567777777777777777777777777666665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00062
                     MscS_porin  25 alnlLdkidkskkkaeelqkaiddaPkelrelqqeleal 63 
                                    + +l  + +k+k+++e+l+k+++   ++++++++el+a 
  gene102|gene102|rna102|rna102 281 TKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAK 319
                                    667777889****************************98 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  11.1    0.0002     0.052      44     145 ..     169     269 ..     155     276 .. 0.80
   2 ?    6.5   7.4     0.021       5.3      70     135 ..     278     343 ..     268     350 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                   HAUS-augmin3  44 LegeaLeeaLktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslq...qelrklee 120
                                    Le+e+++ + k+++   + ++d+e l++  + ++e +e L++++ +L+ke+ +++ +l+kL++q  +++   ++ +k e+
  gene102|gene102|rna102|rna102 169 LEEETMASQ-KKMN---KLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSglvERAQKIED 244
                                    555555444.3333...4558999999999999****************************9887665522278899999 PP

                   HAUS-augmin3 121 eekeakkklkeaqeelraenaetna 145
                                    e+k  k++l  a+e +r+ n e+++
  gene102|gene102|rna102|rna102 245 ENKMLKEELSTANEIIRKYNDEITQ 269
                                    9999**********99999988876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.021
                   HAUS-augmin3  70 evileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqee 135
                                    e  +++++ + +++++e+++L+k  +  +++++k++    + + +l++le+e+    k+l++aq+ 
  gene102|gene102|rna102|rna102 278 EDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQNV 343
                                    56678899999***************************************************9975 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5      0.23        60      73      97 ..     157     181 ..     140     184 .. 0.74
   2 ?    8.5  18.6    0.0083       2.1       4     120 ..     168     284 ..     165     291 .. 0.90
   3 ?   12.6   9.1   0.00045      0.12       5      59 ..     291     345 ..     285     366 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.23
                  Tropomyosin_1  73 tnnealtrkiqlLEeeleesdkkLk 97 
                                        +l  +i+ LEee   s+kk++
  gene102|gene102|rna102|rna102 157 NGEKELRDRIRYLEEETMASQKKMN 181
                                    3334788899999999999999886 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0083
                  Tropomyosin_1   4 sLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiq 83 
                                     L  e+ ++q+k+++l  ++  l ++  ++ +ei+ L+ k+  le+e  +l+ +l + k +  +++ +   + +++  ++
  gene102|gene102|rna102|rna102 168 YLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVERAQKIEDENK 247
                                    56677888999************9**999*************************************************** PP

                  Tropomyosin_1  84 lLEeeleesdkkLkettekLretdvkaeelERkvkaL 120
                                    +L eel  +++ +++ ++ ++++  + +  E ++k+L
  gene102|gene102|rna102|rna102 248 MLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDL 284
                                    ******************9999988877777777766 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00045
                  Tropomyosin_1   5 LkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklk 59 
                                     k e e+ +++++ +eek+K+  +e ++ke  +k+L++ n  l +++e++++  +
  gene102|gene102|rna102|rna102 291 YKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQNVYS 345
                                    58999********************************************998655 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  18.3     0.086        22      29     127 ..     160     258 ..     159     271 .. 0.80
   2 ?    4.1  17.0       0.1        26      47     121 ..     237     315 ..     216     316 .. 0.72
   3 ?   11.0  15.3   0.00075      0.19       2      82 ..     259     342 ..     258     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.086
                            GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkweh 108
                                    k+l++ i  l+++  + +k+++++  +n+ l+e+ + ++ee+e+L+ ++ + ek+  +l+    +lk ++ + + l + +
  gene102|gene102|rna102|rna102 160 KELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVERA 239
                                    78999999999999999999999999999999999999999999999999999999999888888888888888888888 PP

                            GAS 109 evleqrfekvekerdelyk 127
                                    +  e++ + +++e  + ++
  gene102|gene102|rna102|rna102 240 QKIEDENKMLKEELSTANE 258
                                    8888888888777655444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                            GAS  47 kelseisqenkrlkepLkkaeeeveeLrkqlknyek....dkqslknlkarlkelekelkdlkwehevleqrfekveke 121
                                     + ++i+ enk lke+L +a+e + + + ++ + ++       + k l+ ++k+ ++e++dlk   + +e++++k+++e
  gene102|gene102|rna102|rna102 237 ERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNaingNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEE 315
                                    3456788899999999999999998888877666651112456888999999999999999999999999999999987 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00075
                            GAS   2 LmknHekafneiknYYn...ditrnNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlk 78 
                                    ++++++++++++kn  n   d t++     k++K+eie+lkk+ + +e ++++i++e k  +  Lk +e e+  L k+l+
  gene102|gene102|rna102|rna102 259 IIRKYNDEITQMKNAINgneDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLE 338
                                    66667777777776665333455555445577777777777777777777777777777777777777777777777777 PP

                            GAS  79 nyek 82 
                                    n ++
  gene102|gene102|rna102|rna102 339 NAQN 342
                                    7654 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   5.2   0.00023      0.06     165     221 ..     157     213 ..     142     225 .. 0.93
   2 ?    5.2  15.7     0.048        12     129     240 ..     239     347 ..     214     365 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
                         Cluap1 165 eiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqs 221
                                    + ek+l+++i+ ++ee+  ++k++++l +d++ L++k + +++e+er + ++  l++
  gene102|gene102|rna102|rna102 157 NGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEK 213
                                    5699********************************************999988875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.048
                         Cluap1 129 aseitekgasLydlLekevelreartkalsrqleleeiekalk...eaikkvkeelektkkalenlesdeanLeakiekk 205
                                    a++i ++   L + L++ +e       + + + e++++++a++   +a+k+++ + +k+k+++e+l++  + +e+k++k 
  gene102|gene102|rna102|rna102 239 AQKIEDENKMLKEELSTANE------IIRKYNDEITQMKNAINgneDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKI 312
                                    33333333333333333333......2223455666666666422267888999999*********************** PP

                         Cluap1 206 kqeleraqkrLqslqsvrPafmdeyekleeeLqel 240
                                    k+el  +++rL+ l++      ++ e++++  ++ 
  gene102|gene102|rna102|rna102 313 KEELKAKETRLKDLETENMGLVKNLENAQNVYSHF 347
                                    *************9976655555555555555555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   4.2     0.043        11      30      87 ..     171     228 ..     159     238 .. 0.77
   2 ?   13.1   7.9   0.00017     0.043      15     114 ..     250     349 ..     233     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
                        DUF3450  30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeq 87 
                                    ++  +sqkk++kl ++ + l+++ ++ +ee+e+l+ +   le+    ++ e+++l+ q
  gene102|gene102|rna102|rna102 171 EETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQ 228
                                    5556788888888888888888888888888888888888888888888888887755 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00017
                        DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                    +++l++a++  +k +++  q+ + i+  +d +++l  + ++ k+e+e+l++  + +e+ +++ ++e++  e++++++e  
  gene102|gene102|rna102|rna102 250 KEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETE 329
                                    56777888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                        DUF3450  95 erelvpllekmidrLeqfve 114
                                    +++lv  le+  + +  f+ 
  gene102|gene102|rna102|rna102 330 NMGLVKNLENAQNVYSHFYS 349
                                    88888888888777777765 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   5.9      0.13        33     687     743 ..     170     226 ..     117     231 .. 0.68
   2 ?   13.5   1.8   5.8e-05     0.015     264     290 ..     231     257 ..     223     262 .. 0.87
   3 ?    6.1  10.0      0.01       2.6     733     814 ..     261     342 ..     255     362 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.13
                            FPP 687 keenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslk 743
                                    +ee+  +++++++l  + e l  + +s+ e++e l++++ + E+    l+ eL++lk
  gene102|gene102|rna102|rna102 170 EEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLK 226
                                    556666666777777777777777777777777777777777777777777776665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.8e-05
                            FPP 264 enefLterLlameeEtkmLKEaLakrn 290
                                    +n+ L+er  ++e+E+kmLKE L+  n
  gene102|gene102|rna102|rna102 231 KNSGLVERAQKIEDENKMLKEELSTAN 257
                                    6788*******************9876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.01
                            FPP 733 aelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLeeekksheeleakckelqeqlerv 812
                                     + + e++++k++ +  e+  k   + +++  +  ++l++ ++ +++k++++++eL+ +++  ++le++ + l + le +
  gene102|gene102|rna102|rna102 261 RKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENA 340
                                    45555666666666666666666666666666666666666666666666666666666666666666666666666665 PP

                            FPP 813 ek 814
                                    ++
  gene102|gene102|rna102|rna102 341 QN 342
                                    54 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.2     0.013       3.2     111     183 ..     155     224 ..     136     229 .. 0.72
   2 ?    3.1   9.9      0.28        72      99     181 ..     171     253 ..     157     262 .. 0.52
   3 ?    9.1  14.7    0.0041       1.1     102     184 ..     237     319 ..     225     329 .. 0.84
   4 ?   14.0  10.2   0.00013     0.034      99     183 ..     262     346 ..     253     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.013
                         DUF724 111 rkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFea 183
                                     k+ ek+++   ++ r leee    +kk+ +l r +++l ek +++ +ei rl+s+  +le+e  + + e ++
  gene102|gene102|rna102|rna102 155 CKNGEKELR---DRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDK 224
                                    333333333...4445678888889999999999999999999999999999999988888887776666555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.28
                         DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk...ekkeaadkeiarlkseaekleeele 175
                                    +     +k+++++ + ++ ++e+ ++     eei+ l++ki +le+++ +l+    k + +d + + l   a+k+e+e +
  gene102|gene102|rna102|rna102 171 EETMASQKKMNKLYRDNEVLSEKGNS---QREEIERLNSKIYDLEKENGRLQyelDKLKLQDVKNSGLVERAQKIEDENK 247
                                    22222233333333322222333322...236666777777777777777777765555555666666666666666655 PP

                         DUF724 176 dveqeF 181
                                      ++e 
  gene102|gene102|rna102|rna102 248 MLKEEL 253
                                    555554 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0041
                         DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181
                                    ++ +k+++e k l+++++++++  rk+++ei +++++i   e   + l+ ++++ ++ei +lk+ ++ +ee+++++++e 
  gene102|gene102|rna102|rna102 237 ERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEEL 316
                                    56788999999999999999999999999999999999999999999998888888888888888888888888888887 PP

                         DUF724 182 eav 184
                                    +a 
  gene102|gene102|rna102|rna102 317 KAK 319
                                    764 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 0.00013
                         DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledve 178
                                    + +de t++++++++ e  +++ + +++k+++ei++l+k+++ +e++ + +ke+ +a++ ++++l++e+  l ++le+++
  gene102|gene102|rna102|rna102 262 KYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQ 341
                                    678999************************************************************************99 PP

                         DUF724 179 qeFea 183
                                    + +++
  gene102|gene102|rna102|rna102 342 NVYSH 346
                                    87665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1       1.1   2.8e+02      22      56 ..     130     164 ..     109     178 .. 0.67
   2 ?    3.2   0.4      0.56   1.4e+02      17      49 ..     164     196 ..     160     200 .. 0.78
   3 ?    7.9   1.1     0.018       4.6      14      45 ..     196     227 ..     188     247 .. 0.82
   4 ?    1.6   0.4       1.7   4.4e+02      15      41 ..     249     275 ..     235     290 .. 0.53
   5 ?    7.4   1.2     0.027       6.9      19      52 ..     295     328 ..     278     341 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                           SlyX  22 Lndvvaeqqqqidrlqrqlrllaerlkeleessga 56 
                                    L d++ + + +  rl ++  +l+++ k+ e++ ++
  gene102|gene102|rna102|rna102 130 LGDMIGRMEADNVRLIKENGMLRDKCKNGEKELRD 164
                                    56777788888888888888888888877776654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.56
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XX CS
                           SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlke 49 
                                    d i  L ++ ++ q+++ +l r  + l e+ ++
  gene102|gene102|rna102|rna102 164 DRIRYLEEETMASQKKMNKLYRDNEVLSEKGNS 196
                                    667788888899999999999999999888655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.018
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX  14 fqedtieeLndvvaeqqqqidrlqrqlrllae 45 
                                     q + ie+Ln  +++ +++  rlq +l++l+ 
  gene102|gene102|rna102|rna102 196 SQREEIERLNSKIYDLEKENGRLQYELDKLKL 227
                                    58899***********************9974 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX  15 qedtieeLndvvaeqqqqidrlqrqlr 41 
                                    + + + + n+++ + +++i++++  ++
  gene102|gene102|rna102|rna102 249 LKEELSTANEIIRKYNDEITQMKNAIN 275
                                    334444445555555555555555444 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.027
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                           SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                    ie+L + v   ++++++++++l++ + rlk+le+
  gene102|gene102|rna102|rna102 295 IEDLKKRVKGMEEKMKKIKEELKAKETRLKDLET 328
                                    5555555555555555555555555555555555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  22.8   0.00015     0.039     142     282 ..     174     309 ..     164     311 .. 0.77
   2 ?    9.8  19.4    0.0012      0.32     142     257 ..     233     344 ..     224     354 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                           Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelree.laelkaeieekkk 220
                                       ++++++l +d+e+L+++ +   e  ++l+++  +le+e  +lq       ++dk +L+ ++++ l+e  ++ie   +
  gene102|gene102|rna102|rna102 174 MASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQY------ELDKLKLQDVKNSgLVERAQKIE---D 244
                                    44577777788888888888888888888888888888888888877......5899******986699******9...7 PP

                           Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaervlee...ckgwsesevsrlkeevkaleelt 282
                                    e + l+e+l + +e i + ++++++++++i+  e+ ++    + +  +se++ lk++vk +ee+ 
  gene102|gene102|rna102|rna102 245 ENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDlrlNNKKYKSEIEDLKKRVKGMEEKM 309
                                    7777888999999999999999999999998766666650005555679*************986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                           Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                    +gl e+ +++e+++++L+++ + ++e+  +++ e +++++ ++  ++a ++l      + +++++e+++lk+ ++  +++
  gene102|gene102|rna102|rna102 233 SGLVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRL----NNKKYKSEIEDLKKRVKGMEEK 308
                                    466667777777777777777777777777666666666666666664444322....2234666777777777777777 PP

                           Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervl 257
                                    +++ +e+l+++e+++++l+++   l +++++a++v+
  gene102|gene102|rna102|rna102 309 MKKIKEELKAKETRLKDLETENMGLVKNLENAQNVY 344
                                    777777777777777777777777777777777665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   8.0     0.041        10       5      89 ..     160     249 ..     156     255 .. 0.78
   2 ?   10.4  11.4    0.0011      0.27       3      84 ..     245     325 ..     232     336 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.041
                          TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk....eeeeeeveelkee.lkerk 79 
                                    +el+++++ lee+    ++k+++l + ++ +s++ ++q++++++l+s++ +l+k+ +    e ++ +++++k++ l er 
  gene102|gene102|rna102|rna102 160 KELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGrlqyELDKLKLQDVKNSgLVERA 239
                                    68999999*********************************************996655555555566666554255555 PP

                          TMPIT  80 kvlkevesll 89 
                                    + +++ +++l
  gene102|gene102|rna102|rna102 240 QKIEDENKML 249
                                    5666655555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                          TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                    e + l++e+ + +e  ++y+ ++ ++++ ++    ++k  + + k+ ks++++lkk+v +  ee+++++keelk +++ l
  gene102|gene102|rna102|rna102 245 ENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRV-KGMEEKMKKIKEELKAKETRL 323
                                    3344445555555555555555555555555555555555555555555555555554.344555555555555555555 PP

                          TMPIT  83 ke 84 
                                    k+
  gene102|gene102|rna102|rna102 324 KD 325
                                    55 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  23.8       1.1   2.7e+02      70     176 ..     176     285 ..      93     303 .. 0.73
   2 ?    9.2   7.8    0.0049       1.2      82     136 ..     293     347 ..     278     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.1
                        UPF0242  70 leekeaklteld....eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLa 145
                                     ++k +kl   +    e+ + ++e++e l+++  +L++e    + el +lk ++ + +  l + a+ +e+  + l+e+L 
  gene102|gene102|rna102|rna102 176 SQKKMNKLYRDNevlsEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNS-GLVERAQKIEDENKMLKEELS 254
                                    2233333333333444444777778888888888888887777777776665555433.333334467777777788889 PP

                        UPF0242 146 ekqellqeyqetieeqrsvlekrqdqieqLe 176
                                      +e + +y+ +i++ ++ ++  +d  ++L 
  gene102|gene102|rna102|rna102 255 TANEIIRKYNDEITQMKNAINGNEDATKDLR 285
                                    9999999999999999998888887777764 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0049
                        UPF0242  82 eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeel 136
                                     +++  ++ ++ ++e+ ++ keel+ake+ l+ l+ en  L + le++++ ++++
  gene102|gene102|rna102|rna102 293 SEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENAQNVYSHF 347
                                    45677788999999*********************************99877654 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.8     0.068        17      56     120 ..     154     218 ..     142     222 .. 0.75
   2 ?   11.0   6.0    0.0013      0.33      59     122 ..     248     314 ..     226     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.068
                        DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                    + ++  ++L +ri  ++++  ++++  +++ ++ + ++e+ ++ +e++e +++ + +le++  r+
  gene102|gene102|rna102|rna102 154 KCKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRL 218
                                    55666788888888888877777777777777777888888888888888888888888766555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0013
                        DUF1664  59 atkrhLs...sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                      k++Ls   + i + ++++ ++k++++  ++  +++r + ++ ++++e +k+ v+g+e+k+++i+e
  gene102|gene102|rna102|rna102 248 MLKEELStanEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKE 314
                                    33444431114577788888888888888899999999999**********************9975 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   6.2      0.16        40      67     128 ..     160     224 ..     151     225 .. 0.73
   2 ?    9.5  16.2    0.0038      0.97      22     128 ..     237     339 ..     226     340 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.16
                     TPR_MLP1_2  67 nelkaeiaelkaeaesakae...leeseesweeqkeelekelselekriedlneqNklLhdQlEs 128
                                    +el+++i+ l++e  + +++   l +  e ++e+ ++ ++e++ l+++i dl++ N  L   l++
  gene102|gene102|rna102|rna102 160 KELRDRIRYLEEETMASQKKmnkLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDK 224
                                    67777888888776665554111555677778888888999999999999999999999887776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0038
                     TPR_MLP1_2  22 aklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleesees...weeqk 98 
                                    +++qk++++ +  +e++++a++     ++ + +  +e++++++ +n  ++  ++l+ ++++ k+e+e  ++    +ee+ 
  gene102|gene102|rna102|rna102 237 ERAQKIEDENKMLKEELSTANE-----IIRKYN--DEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRvkgMEEKM 309
                                    4455555555555555555544.....222221..356666666666666666666666666666655555411156777 PP

                     TPR_MLP1_2  99 eelekelselekriedlneqNklLhdQlEs 128
                                    +++++el+  e+r++dl++ N  L + lE+
  gene102|gene102|rna102|rna102 310 KKIKEELKAKETRLKDLETENMGLVKNLEN 339
                                    778889999999999999999999999997 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4       1.2   3.2e+02      44      69 ..     150     172 ..     132     174 .. 0.68
   2 ?   11.4   0.9    0.0011      0.28      34      69 ..     179     214 ..     177     216 .. 0.94
   3 ?    8.7   5.0    0.0077         2      24      67 ..     227     271 ..     213     275 .. 0.80
   4 ?    5.1   5.7       0.1        26      14      71 .]     264     317 ..     264     317 .. 0.85
   5 ?    3.9   4.7      0.24        62      34      69 ..     294     329 ..     293     331 .. 0.85
   6 ?   -0.3   0.1       4.8   1.2e+03      34      60 ..     322     348 ..     320     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.2
                       JIP_LZII  44 iLreEleslqkakerlesrikelEee 69 
                                    +Lr   +++++  ++l++ri+ lEee
  gene102|gene102|rna102|rna102 150 MLR---DKCKNGEKELRDRIRYLEEE 172
                                    444...35667778888888888888 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0011
                       JIP_LZII  34 rvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                    +  +L  ++e+L+e  +s +++ erl+s+i +lE+e
  gene102|gene102|rna102|rna102 179 KMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKE 214
                                    778999****************************98 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0077
                       JIP_LZII  24 Lnvvkd.dLIarvdeLtsereiLreEleslqkakerlesrikelE 67 
                                    L  vk+  L++r  ++  e+++L+eEl++ +++ ++ +++i+++ 
  gene102|gene102|rna102|rna102 227 LQDVKNsGLVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMK 271
                                    444554169********************************9986 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.1
                       JIP_LZII  14 NteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeelk 71 
                                    N e  ++kna+n   d     + +L  +++  ++E+e l+k  + +e+++k++ eelk
  gene102|gene102|rna102|rna102 264 NDEITQMKNAINGNEDA----TKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELK 317
                                    66777778888777665....67889999999************************98 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.24
                       JIP_LZII  34 rvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                    ++++L+++ + ++e ++++++++++ e+r+k+lE e
  gene102|gene102|rna102|rna102 294 EIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETE 329
                                    578899999999999999999999999999999987 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 4.8
                       JIP_LZII  34 rvdeLtsereiLreEleslqkakerle 60 
                                    r+ +L +e+  L + le+ q++ +  +
  gene102|gene102|rna102|rna102 322 RLKDLETENMGLVKNLENAQNVYSHFY 348
                                    667777888888888877777766655 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   9.9     0.077        20      46     114 ..     156     224 ..     106     233 .. 0.61
   2 ?    9.7  14.8    0.0046       1.2      11     122 ..     201     312 ..     201     313 .. 0.96
   3 ?   11.5  14.0    0.0013      0.33      14     110 ..     249     342 ..     246     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.077
                         APG6_N  46 deeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelle 114
                                    ++ ++el+++++ le+e  + ++++++l + +e l ++ ++++ee e+l+ +     +e   lq el +
  gene102|gene102|rna102|rna102 156 KNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDK 224
                                    333344444455688888888888888888888888888777777777776655555555555554443 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0046
                         APG6_N  11 leeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleee 90 
                                    +e+l++++ ++eke   ++  l+klk ++++++   e  +++e+e + l++e +++ e +++  +e  +++++++  e  
  gene102|gene102|rna102|rna102 201 IERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDA 280
                                    689999*************************98899999***************************************** PP

                         APG6_N  91 lealeeeeerfwreynelqlelleleeeldsl 122
                                    +++l  +++++ +e  +l+  ++ +ee+++++
  gene102|gene102|rna102|rna102 281 TKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKI 312
                                    **********************9999999876 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0013
                         APG6_N  14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                                    l+++l++a++ +++Y++   ++k+  + +e   + +++l+   +k ++e e+l +  k +e++ +++++el+a e  l++
  gene102|gene102|rna102|rna102 249 LKEELSTANEIIRKYNDEITQMKNAINGNE---DATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKD 325
                                    789999999999999999999999977755...788999999999*********************************** PP

                         APG6_N  94 leeeeerfwreynelql 110
                                    le e+   ++   + q 
  gene102|gene102|rna102|rna102 326 LETENMGLVKNLENAQN 342
                                    **999999888877665 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.4    0.0023      0.58      67     162 ..     249     344 ..     244     350 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0023
                         DUF745  67 leqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk 146
                                    l++el+ a++++++ ++++++ +++++  ++a k+ + + +  k+ ++  k++++ +e+  ++ ++el++k++ l++ ++
  gene102|gene102|rna102|rna102 249 LKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLET 328
                                    899************************************************************************99999 PP

                         DUF745 147 RveeLkkqlkearkdl 162
                                        L k+l++a++ +
  gene102|gene102|rna102|rna102 329 ENMGLVKNLENAQNVY 344
                                    9999999999999866 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  12.9    0.0016       0.4     152     266 ..     135     254 ..      59     258 .. 0.81
   2 ?    5.3   7.2     0.064        16     194     265 ..     266     337 ..     255     342 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0016
                          CEP63 152 asleaqrkaLaekleliqs..aaykvqlekrkqkLesveldsqseiqrLrskleraqdtleaqelelerLrllveelgks 229
                                      +ea++  L+ +  +++   +  +++l +r   Le+  ++sq ++++L  + e   ++ ++q  e+erL++   +l k+
  gene102|gene102|rna102|rna102 135 GRMEADNVRLIKENGMLRDkcKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKE 214
                                    357888887777777777755566779999999*********************************************** PP

                          CEP63 230 krvlleekqele.eelrese..kqlqvleeekselkqtlq 266
                                    +  l+ e  +l+ +++++s   ++ q++e+e++ lk++l+
  gene102|gene102|rna102|rna102 215 NGRLQYELDKLKlQDVKNSGlvERAQKIEDENKMLKEELS 254
                                    *9999888877625677776225778999******99996 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.064
                          CEP63 194 eiqrLrskleraqdtleaqelelerLrllveelgkskrvlleekqeleeelresekqlqvleeekselkqtl 265
                                    ei +++  ++ ++d  +   l+ ++ ++  e+l k+ + ++e+ ++ +eel+++e +l+ le e++ l ++l
  gene102|gene102|rna102|rna102 266 EITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNL 337
                                    566666666666666666666666777777777777777777777777777777777777777777666665 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   8.4      0.79     2e+02      31     131 ..     159     261 ..     156     275 .. 0.64
   2 ?   -0.0   0.2       3.4   8.7e+02      41      61 ..     249     269 ..     233     288 .. 0.51
   3 ?   12.4   0.8   0.00051      0.13      32      79 ..     296     342 ..     294     352 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.79
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...TT-SS---S CS
                          Nup54  31 FedLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleil...rsrgyalda 107
                                     ++L++R +  ++e+ + +++++++  + e l+ ++  +  +++e++ ++   l++   rl   l+ l     ++++l +
  gene102|gene102|rna102|rna102 159 EKELRDRIRYLEEETMASQKKMNKLYRDNEVLS-EKGNSQREEIERLNSKIYDLEKENGRLQYELDKLklqDVKNSGLVE 237
                                    578888888888888888888888887777777.6666667777777777777777666665555533233555666666 PP

                                    SHHHHHHHHHHHHHHHS-HHH.HH CS
                          Nup54 108 eEeelrarletleaqlndpaqlkg 131
                                      ++++ + + l+++l+  +++ +
  gene102|gene102|rna102|rna102 238 RAQKIEDENKMLKEELSTANEIIR 261
                                    666666666666666665444433 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 3.4
                                    HHHHHHHHHHHHHHHHHHHHH CS
                          Nup54  41 Qqkevaqhrerlkeisdrlee 61 
                                     ++e++ ++e + + +d++++
  gene102|gene102|rna102|rna102 249 LKEELSTANEIIRKYNDEITQ 269
                                    233333333333333333333 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00051
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Nup54  32 edLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakk 79 
                                    edL+kRvk  ++++++ +e lk+ ++rl++le  ++  + + le+a++
  gene102|gene102|rna102|rna102 296 EDLKKRVKGMEEKMKKIKEELKAKETRLKDLE-TENMGLVKNLENAQN 342
                                    89******************************.999999999999987 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   6.1      0.15        39      15      81 ..     159     226 ..     148     240 .. 0.86
   2 ?   11.7  10.3   0.00084      0.21      10      88 ..     247     327 ..     239     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                          Mod_r  15 eeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeeke 81 
                                    e+ l+ ++  l +e+ + +++  +l   ne l ek  s+++e+e l s++ +  +e  +l+ e+++++
  gene102|gene102|rna102|rna102 159 EKELRDRIRYLeEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLK 226
                                    45677777777677999999999*************************99999999999988888876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00084
                          Mod_r  10 ellede.eklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldel 87 
                                    ++l++e +  ++++ +  +e+ q+k++    ++++++l  +n + + e+e+l+++++   e++k++++e+++ke++l++l
  gene102|gene102|rna102|rna102 247 KMLKEElSTANEIIRKYnDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDL 326
                                    67777778899999999899******************9999999********************************987 PP

                          Mod_r  88 l 88 
                                     
  gene102|gene102|rna102|rna102 327 E 327
                                    5 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.9      0.58   1.5e+02      12      45 ..     154     188 ..     144     195 .. 0.76
   2 ?    6.9   2.1     0.032       8.2       7      49 ..     192     234 ..     186     243 .. 0.83
   3 ?    7.7   2.5     0.017       4.4      12      49 ..     241     279 ..     231     288 .. 0.83
   4 ?    8.0   5.9     0.015       3.7       9      65 ..     288     345 ..     280     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.58
                         CC2-LZ  12 k.keeieeLkaqlqaaeealaakqeeidelkeeik 45 
                                    k k+  +eL  ++   ee   a+q+++++l+ +++
  gene102|gene102|rna102|rna102 154 KcKNGEKELRDRIRYLEEETMASQKKMNKLYRDNE 188
                                    44566678999999999999999999999987665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.032
                         CC2-LZ   7 eaekvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkee 49 
                                    e  + ++eeie+L+ ++++ e+   + q e+d+lk ++ k++ 
  gene102|gene102|rna102|rna102 192 EKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSG 234
                                    4556679****************************99888765 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.017
                         CC2-LZ  12 k.keeieeLkaqlqaaeealaakqeeidelkeeikkkee 49 
                                    k ++e + Lk++l++a+e +++ ++ei ++k+ i+ +e+
  gene102|gene102|rna102|rna102 241 KiEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNED 279
                                    33889999***********************99987765 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.015
                         CC2-LZ   9 ekvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkee.eletisvlkaQaevYr 65 
                                    +k++k+eie+Lk++++  ee++++ +ee++  ++ +k  e+ ++  ++ l    +vY+
  gene102|gene102|rna102|rna102 288 NKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETeNMGLVKNLENAQNVYS 345
                                    56779999****9999999999999999998888888776635668888888778886 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  27.4    0.0039         1      10     160 ..     160     328 ..     146     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0039
                        DUF4795  10 kklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq.... 85 
                                    k+l++ i+ l+ee    ++k+++l  + e +++k ++ +++ie+l+++  d e+ +  l++  dk +L+ + +       
  gene102|gene102|rna102|rna102 160 KELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLvera 239
                                    67888899999999999999999999999999999999999999999999999999999999999999877654445555 PP

                        DUF4795  86 ..fDeakkeLekmleellekleeqeealkkaldtLq........eelkekldrlelepLkeqle...erlkelqkelqea 152
                                      ++   k L++ l+ + e + +  ++++++ + ++          l++k  + e+e+Lk++++   e++k++++el+ +
  gene102|gene102|rna102|rna102 240 qkIEDENKMLKEELSTANEIIRKYNDEITQMKNAINgnedatkdLRLNNKKYKSEIEDLKKRVKgmeEKMKKIKEELKAK 319
                                    5899999999999977777777777777777777777778774334556666**********99999***********77 PP

                        DUF4795 153 mekedk.ed 160
                                       +++ e+
  gene102|gene102|rna102|rna102 320 ETRLKDlET 328
                                    666655544 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       3.2   8.1e+02      75      93 ..     133     151 ..      94     152 .. 0.77
   2 ?    2.5  12.9       1.1   2.7e+02       9      90 ..     155     246 ..     143     247 .. 0.59
   3 ?   10.9  15.6    0.0027      0.69       9      94 ..     242     334 ..     237     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 3.2
                 PRKG1_interact  75 eleeLraenqrLkdEngAL 93 
                                     + ++ a+n rL +Eng L
  gene102|gene102|rna102|rna102 133 MIGRMEADNVRLIKENGML 151
                                    6788999*********966 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.1
                 PRKG1_interact   9 ekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeel....keleeLr.... 80 
                                     k+ +++L+++++ le+e+  ++++++kl +     ++  s+  + +++e + l+ ki +le+e+     el++L+    
  gene102|gene102|rna102|rna102 155 CKNGEKELRDRIRYLEEETMASQKKMNKLYRD----NEVLSEKGNSQREEIERLNSKIYDLEKENgrlqYELDKLKlqdv 230
                                    44555667777777777777777777776633....22233333445566666777777888777655544555555555 PP

                 PRKG1_interact  81 ......aenqrLkdEn 90 
                                          +  q++ dEn
  gene102|gene102|rna102|rna102 231 knsglvERAQKIEDEN 246
                                    5666667777777777 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0027
                 PRKG1_interact   9 ekeenerLkreLeelekelselkseleklkqq...rqesvskrssllelekrerrslerkiseleeelkele.eLraenq 84 
                                     ++en+ Lk+eL+++++ +++ + e++++k+    +++ +++     +  k+e + l+++++ +ee++k+++ eL+a+  
  gene102|gene102|rna102|rna102 242 IEDENKMLKEELSTANEIIRKYNDEITQMKNAingNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKeELKAKET 321
                                    5789************************997764333334444444445778889999**********998537****** PP

                 PRKG1_interact  85 rLkd...EngALi 94 
                                    rLkd   En  L+
  gene102|gene102|rna102|rna102 322 RLKDletENMGLV 334
                                    **98555666665 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  36.3     0.009       2.3     129     329 ..     134     331 ..     123     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.009
                         HMMR_N 129 vasLekqlaelkranelLksKvsedgt..kKklnsLsleLmklrnkleakekevsvkQedmeaklqvtqknLeeskakva 206
                                    +  +e  ++ l + n +L+ K+ +  +  + +++ L  e m  ++k++   +      e +  k ++  +++e+  +k+ 
  gene102|gene102|rna102|rna102 134 IGRMEADNVRLIKENGMLRDKCKNGEKelRDRIRYLEEETMASQKKMNKLYRDN----EVLSEKGNSQREEIERLNSKIY 209
                                    566889999999******99997655544899*********9999998887777....5555556666677777799999 PP

                         HMMR_N 207 qLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdln 286
                                     L+  +  l+ e  + k +  k    +e+ +++ ++  + k+++  ++e++ + ndei ++k++++ +e+   k  +  n
  gene102|gene102|rna102|rna102 210 DLEKENGRLQYELDKLKLQDVKNSGLVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNED-ATKDLRLNN 288
                                    9999999998888888888877777777777777777777****************************99.777777777 PP

                         HMMR_N 287 ekckllekekeelvreeeekeqtlsaEleelkeklklkeqeaq 329
                                    +k+k   +++++ v+  eek ++++ El+  + +lk  e e+ 
  gene102|gene102|rna102|rna102 289 KKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENM 331
                                    7777666667778999999999999999999999998888765 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  10.7     0.028       7.2      24     100 ..     150     226 ..     133     232 .. 0.80
   2 ?    6.8  20.1     0.033       8.4      29     107 ..     235     313 ..     228     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.028
                        DUF4200  24 rleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekle 100
                                    +l +++k+ e+el+++ ++lee+    +k +++  +  +   +k +++r+++++ +++i +l++e  +l+ e++kl+
  gene102|gene102|rna102|rna102 150 MLRDKCKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLK 226
                                    56677888888888888888888888888888888888888888888888888888888888888888888888876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.033
                        DUF4200  29 lkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekleeyk 107
                                    l +r +++e+++++l+e+l   ++ +++ +++ ++    ++  ++++k+     kk k+eie+lk++ + +eek+++ k
  gene102|gene102|rna102|rna102 235 LVERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIK 313
                                    568999*********************************************************************9987 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  17.5     0.021       5.4      47     155 ..     154     271 ..     133     272 .. 0.83
   2 ?    5.5  15.3     0.072        18      47     133 ..     245     330 ..     234     354 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.021
                  Jnk-SapK_ap_N  47 eeeaeleelreeleqLeteyerekelrk...raeeeleeiedqweeerkelqekveqleeenrele...lkaknaadqls 120
                                    + +  ++elr+ +  Le+e +  +++ +   r +e l e+ ++ +ee + l++k+ +le+en +l+    k+k ++ + s
  gene102|gene102|rna102|rna102 154 KCKNGEKELRDRIRYLEEETMASQKKMNklyRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQyelDKLKLQDVKNS 233
                                    556667899999999999876554444311155588999999***********************966657777888889 PP

                  Jnk-SapK_ap_N 121 rleekeaelkkeysklhe...retellkklkelverqr 155
                                     l e+ ++ + e++ l+e   + +e+++k+ + + +++
  gene102|gene102|rna102|rna102 234 GLVERAQKIEDENKMLKEelsTANEIIRKYNDEITQMK 271
                                    9999999999999999999999*********9998887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.072
                  Jnk-SapK_ap_N  47 eeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleeke 126
                                    e++   eel+ ++e +  +y++e  + k+a +  e + + ++ ++k++++++e+l+++++ +e k+k+++++l++ e + 
  gene102|gene102|rna102|rna102 245 ENKMLKEELSTANE-IIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRL 323
                                    33333333333333.34446666666666665555555555555555555555555555555544444444444444444 PP

                  Jnk-SapK_ap_N 127 aelkkey 133
                                    ++l++e+
  gene102|gene102|rna102|rna102 324 KDLETEN 330
                                    4443333 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  18.8     0.058        15     130     234 ..     215     338 ..     159     351 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.058
                        DUF4407 130 a...................ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekka 190
                                    +                   l ++ +++e++++ l++e+++a++ +++ ++e +    +      ++++G+++a+k  + 
  gene102|gene102|rna102|rna102 215 NgrlqyeldklklqdvknsgLVERAQKIEDENKMLKEELSTANEIIRKYNDEIT----Q----MKNAINGNEDATKDLRL 286
                                    044333333444444444446666667777777777777777666655444444....3....22358899999999999 PP

                        DUF4407 191 qldaaqaelaelkakld........atarlaalraelaeleaerakeraasq 234
                                    ++++++ e+++lk++++         +++l+a++++l++le+e    +++ +
  gene102|gene102|rna102|rna102 287 NNKKYKSEIEDLKKRVKgmeekmkkIKEELKAKETRLKDLETENMGLVKNLE 338
                                    9999999999999997776666666555555555555555555544444444 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.5      0.39        99      62     101 ..     145     184 ..     137     186 .. 0.80
   2 ?    8.1  10.7     0.012       3.1       8      98 ..     185     275 ..     181     277 .. 0.85
   3 ?    8.5   8.4    0.0088       2.2      51      96 ..     287     329 ..     277     340 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.39
                                    CCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  62 akkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                    +k+++  ++++++  kel +++  le+e  + +++++kl 
  gene102|gene102|rna102|rna102 145 IKENGMLRDKCKNGEKELRDRIRYLEEETMASQKKMNKLY 184
                                    5677788889999999999999999999999999998875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.012
                                    HH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHH CS
                   Seryl_tRNA_N   8 renpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkale 87 
                                    r+n  + ++   +R+e + +  ++++l+++  +lq el++l+ +  + s  +++a k +++ + l++e ++ +e + +++
  gene102|gene102|rna102|rna102 185 RDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVERAQKIEDENKMLKEELSTANEIIRKYN 264
                                    55555555556678889999999********************************9999999999999999999999999 PP

                                    HHHHHHHHHHH CS
                   Seryl_tRNA_N  88 aelkeleaele 98 
                                    +e ++++++++
  gene102|gene102|rna102|rna102 265 DEITQMKNAIN 275
                                    99999998875 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0088
                                    HHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  51 erNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleae 96 
                                    + ++   eI+ +kk+    + + +++k++keelka+e++lk+le+e
  gene102|gene102|rna102|rna102 287 NNKKYKSEIEDLKKR---VKGMEEKMKKIKEELKAKETRLKDLETE 329
                                    444455555555543...3445555566666666666666665555 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  13.8    0.0073       1.9      51     161 ..     156     266 ..     138     269 .. 0.81
   2 ?    4.4  13.8      0.17        44      38     105 ..     258     325 ..     240     363 .. 0.36

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0073
                           Fez1  51 eeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeaeel 130
                                     +  kel+++++  ++e    ++++++   ++e+l+ek ++  ee+++l +++ +l++e+ + ++e d+ k q  +++ l
  gene102|gene102|rna102|rna102 156 KNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGL 235
                                    45567788888888888888888888888899999999999999999999999998888888889999999998888888 PP

                           Fez1 131 eelkreverlraeLkeerqkkeeqassFeqE 161
                                     e  +++e  ++ Lkee  + +e   ++++E
  gene102|gene102|rna102|rna102 236 VERAQKIEDENKMLKEELSTANEIIRKYNDE 266
                                    8888889999999999988888888888877 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.17
                           Fez1  38 aqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelse 105
                                      +r  + ++++  ++i+  e+++++  l+++++++e++  k++++ ++ek++k++eelk   ++l++
  gene102|gene102|rna102|rna102 258 EIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKD 325
                                    11222222222222222222222222222222222222222222222222222222222222222222 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   8.3      0.12        32      28     126 ..     126     223 ..     120     233 .. 0.72
   2 ?    9.4  11.0    0.0038      0.98      81     169 ..     237     328 ..     234     330 .. 0.88
   3 ?    2.1   1.2      0.66   1.7e+02      68     101 ..     308     341 ..     300     348 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.12
                      Rootletin  28 YkkrcseleqrllektselektkltlllssareleeeesadleealakLeeE....rqrseklaqvnslLreqleearqa 103
                                    Yk   +++ +r+++++ +l k+++     + r   ++ +++l   ++ LeeE    +++ +kl + n++L e+ + +r++
  gene102|gene102|rna102|rna102 126 YKMYLGDMIGRMEADNVRLIKENG-----MLRDKCKNGEKELRDRIRYLEEEtmasQKKMNKLYRDNEVLSEKGNSQREE 200
                                    666666677777777766666665.....334455566778889999999996665677888888888888888888888 PP

                      Rootletin 104 neaLtedlqkltkdwerlreele 126
                                     e+L++ +  l+k+  rl+ el+
  gene102|gene102|rna102|rna102 201 IERLNSKIYDLEKENGRLQYELD 223
                                    88888888888888777777765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0038
                      Rootletin  81 qrseklaqvnslLreqleearqaneaLtedlqkltkdw...erlreeleqkekewreeeeafneylssehsrllsLWrev 157
                                    +r++k++++n++L+e+l  a++  ++ +++++++++ +   e ++++l+ ++k++++e e +++ ++  ++++ ++  e+
  gene102|gene102|rna102|rna102 237 ERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAIngnEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEEL 316
                                    599********************************9983335789999*************************9998888 PP

                      Rootletin 158 vavrrqfselks 169
                                    +a    +++l +
  gene102|gene102|rna102|rna102 317 KAKETRLKDLET 328
                                    877777776665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.66
                      Rootletin  68 dleealakLeeErqrseklaqvnslLreqleear 101
                                    +++++ ++L+    r ++l+ +n  L ++le+a+
  gene102|gene102|rna102|rna102 308 KMKKIKEELKAKETRLKDLETENMGLVKNLENAQ 341
                                    3334444455555566666666666666666665 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   8.3       1.9     5e+02      80     142 ..     163     225 ..     142     240 .. 0.73
   2 ?   13.4  11.5   0.00017     0.045      59     126 ..     244     331 ..     236     344 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.9
                  PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdky 142
                                    +  i+ l+e     ++++++l    e L+e+ ++q ee   l+ +i+ l  e  +Lq + dk+
  gene102|gene102|rna102|rna102 163 RDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKL 225
                                    344666777777888888888888888888888888888888888888888888888777765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00017
                  PI3K_P85_iSH2  59 eaikmFeeqiklqekfskeaq....................ehEieklqenleqlksrlkelhsskekLeedlkqqkeee 118
                                    + +km++e++ + ++++++++                    + +++k ++ +e+lk+r+k ++++++k++e+lk++ ++ 
  gene102|gene102|rna102|rna102 244 DENKMLKEELSTANEIIRKYNdeitqmknaingnedatkdlRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRL 323
                                    45789999999999999988556666666777777777777999999******************************999 PP

                  PI3K_P85_iSH2 119 releRein 126
                                    + le e  
  gene102|gene102|rna102|rna102 324 KDLETENM 331
                                    99997755 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.5     0.016       4.1      22      65 ..     161     204 ..     157     208 .. 0.90
   2 ?    6.4  11.5     0.047        12       4      64 ..     199     262 ..     196     275 .. 0.78
   3 ?    4.5   8.8      0.19        49      21      65 ..     282     326 ..     265     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.016
                           ZapB  22 lLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    +L+ +i+ L+ee  + ++++++l + ne l e  ++++e ++ L
  gene102|gene102|rna102|rna102 161 ELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERL 204
                                    7999***************************9999999999987 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.047
                           ZapB   4 elLeqLEskiqkaidtitlLqmeieeLke...eneelkeenreleeeneqlkeereawqerlkk 64 
                                    e  e+L ski  +  +  +Lq e+++Lk    +n+ l e+++++e en+ lkee +  +e ++k
  gene102|gene102|rna102|rna102 199 EEIERLNSKIYDLEKENGRLQYELDKLKLqdvKNSGLVERAQKIEDENKMLKEELSTANEIIRK 262
                                    566778888888888888888888888752224688888888888********99998887776 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.19
                           ZapB  21 tlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    + L+  +++ k e e lk++ + +ee+ ++ kee +a + rlk L
  gene102|gene102|rna102|rna102 282 KDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDL 326
                                    567777777777777777777777788888888888888888765 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.6      0.36        92      19      73 ..     153     207 ..     150     213 .. 0.91
   2 ?    9.3  14.2    0.0029      0.75      51     146 ..     244     341 ..     235     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.36
                      PspA_IM30  19 dkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekk 73 
                                    dk  + ek l+  ir +++e  ++++++ ++  ++  l +k ++q+e++++l +k
  gene102|gene102|rna102|rna102 153 DKCKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSK 207
                                    7888899999999************************************999877 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0029
                      PspA_IM30  51 arqkqlerkleeqkeqakklekkAkaALtkg...eeeLArealaeikslekqaealetqlaqqrsaveqlrkqlealetk 127
                                     ++k l+++l +++e ++k+ ++ ++  +++   +e++ + +    k++++++e+l++ ++ +++ +++++++l+a et+
  gene102|gene102|rna102|rna102 244 DENKMLKEELSTANEIIRKYNDEITQM-KNAingNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETR 322
                                    567889***************998874.333344********************************************** PP

                      PspA_IM30 128 ieelkakkellkarekaak 146
                                    +++l+++   l  +++ a+
  gene102|gene102|rna102|rna102 323 LKDLETENMGLVKNLENAQ 341
                                    ******9988877777665 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  30.5     0.039        10     388     564 ..     156     341 ..      82     347 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.039
                       Macoilin 388 pnnqlskkdalvrLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhelvsakqkd... 464
                                     n++   +d +  Le++    + ++++  + ++ l +k +s  +e   l s++  l+ken  lq  l++l  +  k+   
  gene102|gene102|rna102|rna102 156 KNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNsgl 235
                                    444445556677788888888888888888888899999999998899****************9888876555443112 PP

                       Macoilin 465 ...kqtlqqlekrLkeekearaslekqLaeekkrkkee...eetaaravalaaasrsecteslkskkreleaeikkLeke 538
                                        q+++  +k Lkee ++ +++ ++ ++e  + k++   +e a +   l   + +   e lk++ + +e  +kk+++e
  gene102|gene102|rna102|rna102 236 verAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAingNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEE 315
                                    21247777778888888888888888888887777665222344444444444444666788999999999999999999 PP

                       Macoilin 539 lklkeeqirelelkvqelrkykesek 564
                                    lk ke ++++le++   l k  e+++
  gene102|gene102|rna102|rna102 316 LKAKETRLKDLETENMGLVKNLENAQ 341
                                    99999999999988888887766665 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.7     0.012       3.1      11      63 ..     171     221 ..     160     233 .. 0.74
   2 ?    4.0   1.4      0.25        63      54      74 ..     255     275 ..     238     278 .. 0.75
   3 ?    7.5   8.2     0.019         5      10      71 ..     264     325 ..     256     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.012
                          Tup_N  11 qEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYE 63 
                                    +E  a ++++++l   ++ +  k +sq +E++++ +++y+Le++  ++  qYE
  gene102|gene102|rna102|rna102 171 EETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRL--QYE 221
                                    45555566677777777778999*******************987755..454 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.25
                          Tup_N  54 ahrkikqqYEeeiarLkaeLe 74 
                                    + ++i ++Y++ei+++k+ ++
  gene102|gene102|rna102|rna102 255 TANEIIRKYNDEITQMKNAIN 275
                                    556788899999999999876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.019
                          Tup_N  10 kqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEeeiarLka 71 
                                      E+ ++++ ++  +  ++++ l  ++  +E++ +++ ++ +ee+ +kik++     +rLk 
  gene102|gene102|rna102|rna102 264 NDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKD 325
                                    46888888888889999999999999***************************999999985 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.6    0.0093       2.4       7      99 .]     170     271 ..     167     271 .. 0.81
   2 ?    7.9   8.1     0.018       4.6      11      84 ..     250     322 ..     244     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0093
                   Syntaxin-6_N   7 keeVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLe.etv...riveknp...skfkid 77 
                                    +ee   s +k+++lyr  e l e+++s  ++ e l++   +L+k+ + ++++l+ L+ + v   + ve+ +   ++ k+ 
  gene102|gene102|rna102|rna102 170 EEETMASQKKMNKLYRDNEVLSEKGNSqrEEIERLNSKIYDLEKENGRLQYELDKLKlQDVknsGLVERAQkieDENKML 249
                                    577888999********999999999854477888888899*************9974344344345443334277**** PP

                   Syntaxin-6_N  78 ekelsrrrafveevreevkemk 99 
                                    ++els+ ++++++ ++e+ +mk
  gene102|gene102|rna102|rna102 250 KEELSTANEIIRKYNDEITQMK 271
                                    *********************8 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.018
                   Syntaxin-6_N  11 qkslnkaeslyrrwe.rlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrr 84 
                                    +++l++a++++r+++ ++ + +++   +  ++++++Lr + ++ + ++edL++ v+ +e++ +k k + k+ ++r
  gene102|gene102|rna102|rna102 250 KEELSTANEIIRKYNdEITQMKNA--INGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETR 322
                                    68899*********7577777665..6788999**********************99988777766555554444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   3.2      0.18        47      79     130 ..     162     213 ..     136     216 .. 0.66
   2 ?   10.0  13.5    0.0029      0.75      28     124 ..     237     329 ..     226     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  79 ikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqker 130
                                    +++  + leee +  ++++++  +  +vL +  +s++++i++L+++i  +e+
  gene102|gene102|rna102|rna102 162 LRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEK 213
                                    3333344555555556666666666677888888999999999999987765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0029
                                    CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                      Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                    +  ++++++ + l++el+++++  ++ ++ ++++k+ ++ ++  +kd     kk+++e+e    +lk++++  e++++++
  gene102|gene102|rna102|rna102 237 ERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIE----DLKKRVKGMEEKMKKI 312
                                    445555556666677777777777777777777777777777777666666666666666....9*************** PP

                                    HHHHHHHHHHHHHHHHH CS
                      Fib_alpha 108 qnvlesneqkiqkLeqd 124
                                    ++ l+++e ++++Le++
  gene102|gene102|rna102|rna102 313 KEELKAKETRLKDLETE 329
                                    **************986 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.029       7.3      55      76 ..     106     127 ..      97     129 .. 0.85
   2 ?   -1.0   0.1       5.8   1.5e+03      31      49 ..     139     157 ..     134     173 .. 0.46
   3 ?    1.0   0.4       1.4   3.6e+02      21      44 ..     168     191 ..     155     196 .. 0.54
   4 ?    9.3   2.1    0.0037      0.95      21      51 ..     196     226 ..     193     232 .. 0.88
   5 ?    3.1   2.7      0.32        82      18      52 ..     238     272 ..     232     280 .. 0.86
   6 ?    6.6   2.5     0.026       6.7      20      53 ..     268     301 ..     266     308 .. 0.85
   7 ?    4.2   2.4      0.14        36      18      51 ..     308     341 ..     302     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.029
                                    XXXXXXXXXXXXXXXXXXXXXX CS
                          DivIC  55 dyieerARselglvkpgEtvyr 76 
                                    d  + + R el ++kp+Et y+
  gene102|gene102|rna102|rna102 106 DEFRNIVRLELKFSKPDETHYK 127
                                    5566789************998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.8
                                    HHHHHHHHHHHHHHHHHCC CS
                          DivIC  31 aelaklkaeneeLeaevkd 49 
                                    a++++l +en  L ++ k+
  gene102|gene102|rna102|rna102 139 ADNVRLIKENGMLRDKCKN 157
                                    4444444444444443333 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC  21 qlkqeiaalqaelaklkaeneeLe 44 
                                     l++e  a q++++kl  +ne L 
  gene102|gene102|rna102|rna102 168 YLEEETMASQKKMNKLYRDNEVLS 191
                                    344455555555555555555444 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0037
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                    ++++ei++l+ ++  l +en +L+ e+++Lk
  gene102|gene102|rna102|rna102 196 SQREEIERLNSKIYDLEKENGRLQYELDKLK 226
                                    78999*******************9999995 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                          DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                    + ++++ e + l++el + ++ +++ ++e+ ++k+
  gene102|gene102|rna102|rna102 238 RAQKIEDENKMLKEELSTANEIIRKYNDEITQMKN 272
                                    678999999*********************99975 PP

  == domain 6  score: 6.6 bits;  conditional E-value: 0.026
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                          DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                                     q+k+ i+  ++  + l+  n++ ++e++dLk+ 
  gene102|gene102|rna102|rna102 268 TQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKR 301
                                    5788899999999999**************9864 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                    ++k++k+e++a++  l+ l  en+ L +++++ +
  gene102|gene102|rna102|rna102 308 KMKKIKEELKAKETRLKDLETENMGLVKNLENAQ 341
                                    678999*****************99999888874 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.0      0.31        80      38      80 ..     161     203 ..     156     219 .. 0.84
   2 ?    8.5   9.3      0.01       2.7      42     104 ..     259     324 ..     221     325 .. 0.87
   3 ?   10.5   5.9    0.0026      0.68      48     104 ..     265     324 ..     262     354 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHH CS
                       Spectrin  38 allkkhkaleaelaaqqervkalnelaeklldeghsaseeiee 80 
                                    +l ++ + le+e  a q+++++l    e l ++g s+ eeie 
  gene102|gene102|rna102|rna102 161 ELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIER 203
                                    5677888899999999999999999999999999999988876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.01
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  42 khkaleaelaaqqervkalnelaekl.ldeghsas..eeieerleelnerWeeLkelaaerkqkLe 104
                                      + + +e++++++ ++  ++  ++l l++++++s  e++++r+++++e+ +++ke +++++ +L+
  gene102|gene102|rna102|rna102 259 IIRKYNDEITQMKNAINGNEDATKDLrLNNKKYKSeiEDLKKRVKGMEEKMKKIKEELKAKETRLK 324
                                    55778899***********************8888779*************************997 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0026
                                    HHHHHHHHHHHHHHHHHHHH.HHTTHTTH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  48 aelaaqqervkalnelaekl.ldeghsas..eeieerleelnerWeeLkelaaerkqkLe 104
                                    +e++++++ ++  ++  ++l l++++++s  e++++r+++++e+ +++ke +++++ +L+
  gene102|gene102|rna102|rna102 265 DEITQMKNAINGNEDATKDLrLNNKKYKSeiEDLKKRVKGMEEKMKKIKEELKAKETRLK 324
                                    567777777777777777777777755555567777777777777777777777777765 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   4.3      0.54   1.4e+02      23      81 ..     163     214 ..     147     232 .. 0.49
   2 ?   11.4   8.9    0.0014      0.36      13      90 ..     240     317 ..     232     325 .. 0.80
   3 ?    1.2   0.6       2.2   5.6e+02      63      86 ..     318     341 ..     314     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.54
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  23 erqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqk 81 
                                              +r  e + ++ ++ + +L  + e    +++ q+++++ l+ +i +L+++
  gene102|gene102|rna102|rna102 163 RD-------RIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKE 214
                                    33.......33333344444444444454555555555555555555555555444443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0014
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                           BST2  13 qecrnvtrlLerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                    q++++ +++L+++L  a+e +r+ +++++  ++ +   +++ +  + +++k ++++++l++ +k +++k+++ ++e++
  gene102|gene102|rna102|rna102 240 QKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELK 317
                                    788999*****************9999999988887777777777777777777777777777777777777777765 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  63 kqqakvqelqgeikkLnqkLqdae 86 
                                     +++++++l+ e+  L ++L++a+
  gene102|gene102|rna102|rna102 318 AKETRLKDLETENMGLVKNLENAQ 341
                                    467899**************9986 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1      0.11        27      29      82 ..     160     213 ..     153     219 .. 0.89
   2 ?    1.7   1.7       1.2   3.1e+02      34      77 ..     266     309 ..     235     315 .. 0.46
   3 ?    4.3   0.5      0.18        47      23      55 ..     290     322 ..     284     344 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.11
                         DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                    +e++++i+ le+++ +  k++++l +  ++l e  n++ e++++l +++ dl +
  gene102|gene102|rna102|rna102 160 KELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEK 213
                                    6899999*********************99999999999999999998888776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.2
                         DUF948  34 tieelekqvdpilkevedllakvnelledvneklekvdplteav 77 
                                     i+++++ +++  + ++dl  + ++  +++++  ++v+ + e++
  gene102|gene102|rna102|rna102 266 EITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKM 309
                                    33333333333333333333333333333333333333333333 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.18
                         DUF948  23 klkktldeaaatieelekqvdpilkevedllak 55 
                                    k k+ ++ ++++++++e+++++i +e+++  + 
  gene102|gene102|rna102|rna102 290 KYKSEIEDLKKRVKGMEEKMKKIKEELKAKETR 322
                                    566778888999999999999999988765554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.8     0.093        24      17      92 ..     164     239 ..     153     245 .. 0.86
   2 ?    8.4   9.6    0.0079         2       2      94 ..     250     339 ..     249     346 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.093
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHH CS
                     Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdni 92 
                                    + +  l++++   ++k++++ r+ e   ek ++  + i+  ++++ +Lek+  +L   l +lk + +++s l +  
  gene102|gene102|rna102|rna102 164 DRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKNSGLVERA 239
                                    55667888899999*********99999999********************************9999977665554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0079
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                     Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                    ke ++ ane++ +  + ++++++ ++  ++  + ++ + ++ + +++d++k ++  ++++kk+++++   + +lk l++ 
  gene102|gene102|rna102|rna102 250 KEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETE 329
                                    788999*****************************99999*********************************9999998 PP

                                    HHH...HHHHHHH CS
                     Laminin_II  82 eeassslsdnise 94 
                                    + +   l +n+++
  gene102|gene102|rna102|rna102 330 NMG---LVKNLEN 339
                                    887...7777766 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   4.5         2   5.1e+02      14      63 ..     261     314 ..     160     318 .. 0.66
   2 ?    8.2   0.7     0.013       3.4      17      60 ..     292     339 ..     284     356 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 2
                        NPV_P10  14 kavddkVdalqqqv.......ddvqenlpdvtelnekLdaqsaqLaeletkvenIqd 63 
                                    ++ +d ++ +++++       +d++ n ++    +++++++ + ++ +e+k+++I++
  gene102|gene102|rna102|rna102 261 RKYNDEITQMKNAIngnedatKDLRLNNKK---YKSEIEDLKKRVKGMEEKMKKIKE 314
                                    344444444444442221111333333333...345566666666666666666665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.013
                        NPV_P10  17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet.......kven 60 
                                    ++ ++ l+++v+ ++e++++   ++e+L a  + L++let       ++en
  gene102|gene102|rna102|rna102 292 KSEIEDLKKRVKGMEEKMKK---IKEELKAKETRLKDLETenmglvkNLEN 339
                                    56778889999999998888...7799999999999999966664444444 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9  19.8      0.51   1.3e+02     139     272 ..     156     286 ..     137     290 .. 0.64
   2 ?    6.9  19.6     0.015       3.9     116     223 ..     224     327 ..     221     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.51
                        Leu_zip 139 keenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlektleektasaks 217
                                    k+  + L++r++ lE++ + + ++ +kl ++ + l ++ +++++e e  +++i +le++   l+++l+k +  +  +++ 
  gene102|gene102|rna102|rna102 156 KNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIErLNSKIYDLEKENGRLQYELDKLK-LQDVKNSG 234
                                    45556677777777777777777777777776666655555544444366777778888777777777644.34445555 PP

                        Leu_zip 218 leedlastkhelLkvqeqLelaekeLekkfqqtaayknlkemltkkneqikelRk 272
                                    l e  ++   e   ++e+L++a+ e+ +k+++  +   +k+ ++   +  k+lR 
  gene102|gene102|rna102|rna102 235 LVERAQKIEDENKMLKEELSTAN-EIIRKYND--EITQMKNAINGNEDATKDLRL 286
                                    66666666666667778887775.55555554..334567777777777777774 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.015
                        Leu_zip 116 kkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskle 194
                                    k kL+ ++++G +       +++++en+ Lke l + ++ + +  +e +++++a++  +++ ++ + +++  ++ei++l+
  gene102|gene102|rna102|rna102 224 KLKLQDVKNSGLV----ERAQKIEDENKMLKEELSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKkYKSEIEDLK 299
                                    5677777777644....4568999********************************999999998655543789999999 PP

                        Leu_zip 195 eklaelkldlektleektasaksleedla 223
                                    ++++ ++ +++k +ee +a++ +l+ dl 
  gene102|gene102|rna102|rna102 300 KRVKGMEEKMKKIKEELKAKETRLK-DLE 327
                                    9999999999998888887777764.444 PP

>> CtIP_N  Tumour-suppressor protein CtIP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  13.8     0.016       4.1      10     119 ..     153     253 ..     144     258 .. 0.80
   2 ?    3.3   5.8      0.31        81      21      73 ..     279     331 ..     263     365 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.016
                         CtIP_N  10 eiHekevqglqekvlelkkercldaqrleelfsknqqlreqqkalkenikvlenrLraglCdrCavtqelakkkqqefes 89 
                                    +  ++  ++l+++++ l++e +   +++++l+  n+ l e+ + ++e+i++l++++           ++   + q e+++
  gene102|gene102|rna102|rna102 153 DKCKNGEKELRDRIRYLEEETMASQKKMNKLYRDNEVLSEKGNSQREEIERLNSKIYDL--------EKENGRLQYELDK 224
                                    55556668999***************************************999988654........4444556667777 PP

                         CtIP_N  90 sklqslqlitiLtnEmntLkeenkkLkeel 119
                                     klq+++  + L +  +++++enk Lkeel
  gene102|gene102|rna102|rna102 225 LKLQDVKN-SGLVERAQKIEDENKMLKEEL 253
                                    77777766.567777777777777777776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.31
                         CtIP_N  21 ekvlelkkercldaqrleelfsknqqlreqqkalkenikvlenrLraglCdrC 73 
                                    +  ++l+ +     +++e+l ++ + ++e+ k  ke++k  e rL+  + +  
  gene102|gene102|rna102|rna102 279 DATKDLRLNNKKYKSEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENM 331
                                    44444444444445667777777777777777777777777777765444433 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   3.4      0.59   1.5e+02      12      94 ..     166     246 ..     157     252 .. 0.62
   2 ?    9.4   5.3    0.0065       1.7       5      81 ..     253     328 ..     247     345 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.59
                        DUF2203  12 LpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGve.vkdleaglvDFpakl 90 
                                    +  l+e + + +++ ++l +  e l+e+ ++ +++e ++l++++  le+e  +l  e+++l+ + vk+   glv+   k+
  gene102|gene102|rna102|rna102 166 IRYLEEETMASQKKMNKLYRDNEVLSEKGNS-QREEIERLNSKIYDLEKENGRLQYELDKLKLQdVKNS--GLVERAQKI 242
                                    3344444444444444444444444444444.3445889999999999999999999998887535555..777776666 PP

                        DUF2203  91 dgee 94 
                                    ++e+
  gene102|gene102|rna102|rna102 243 EDEN 246
                                    6665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0065
                        DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdlea 81 
                                    l +An+++ + ++ +++++++ +  e++ ++l+ ++++++ se + l+++++ +e++++++ ee+++    +kdle 
  gene102|gene102|rna102|rna102 253 LSTANEIIRKYNDEITQMKNAINGNEDATKDLRLNNKKYK-SEIEDLKKRVKGMEEKMKKIKEELKAKETRLKDLET 328
                                    5678888888888888888888888888888887777754.558999999999999999999999999999999875 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.9       5.8   1.5e+03      48      75 ..     165     193 ..     133     206 .. 0.58
   2 ?    1.3   6.8       1.7   4.4e+02      24      84 ..     190     261 ..     173     266 .. 0.70
   3 ?   11.8   5.6   0.00086      0.22      11      79 ..     268     340 ..     262     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5.8
                        DUF4164  48 rsR.LaeeLdqaearaarleevnrEvsrr 75 
                                    r R L+ee ++++ + ++l + n+ +s++
  gene102|gene102|rna102|rna102 165 RIRyLEEETMASQKKMNKLYRDNEVLSEK 193
                                    22225555555555555555544444444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.7
                        DUF4164  24 vdrrleaerkr.deleaeiealgedrsRLaeeLdqae..........araarleevnrEvsrrLkaaietir 84 
                                    + ++ +++r++ + l+++i  l+++  RL  eLd+ +           ra+++e+ n+ ++++L +a+e ir
  gene102|gene102|rna102|rna102 190 LSEKGNSQREEiERLNSKIYDLEKENGRLQYELDKLKlqdvknsglvERAQKIEDENKMLKEELSTANEIIR 261
                                    555666666655888889999999999999999975422222222335777777777777777777777777 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00086
                        DUF4164  11 trLeaaldsLEkav.drrleaerkr...deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaa 79 
                                    t++++a++  E+a  d rl++++ +   ++l+++++ ++e  +++ eeL ++e r++ le  n  + ++L+ a
  gene102|gene102|rna102|rna102 268 TQMKNAINGNEDATkDLRLNNKKYKseiEDLKKRVKGMEEKMKKIKEELKAKETRLKDLETENMGLVKNLENA 340
                                    55666777777665255777777666679999*****************************999999988876 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.7     0.075        19      38     106 ..     160     232 ..     147     240 .. 0.74
   2 ?    4.9   6.3     0.051        13      48     102 ..     257     308 ..     231     350 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.075
                           HemX  38 aelqqqlaaleqqlaq....veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkd 106
                                    +el++++  le+++ +    ++++ ++++ l+e+ + + e++e+l++++ +l+k+  +lq +l k++ ++ k+
  gene102|gene102|rna102|rna102 160 KELRDRIRYLEEETMAsqkkMNKLYRDNEVLSEKGNSQREEIERLNSKIYDLEKENGRLQYELDKLKLQDVKN 232
                                    5555555555554433333366788889999999999999999999999999999999999999998776655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.051
                           HemX  48 eqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                    ++    +++ + + ++++++++ +++++++l+ +++++++++e l+++++ ++ +
  gene102|gene102|rna102|rna102 257 NEI---IRKYNDEITQMKNAINGNEDATKDLRLNNKKYKSEIEDLKKRVKGMEEK 308
                                    222...3335556666666666666666666666666666666666666655443 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4       1.1   2.7e+02       7      40 ..     161     191 ..     156     217 .. 0.66
   2 ?    0.2   1.3         2     5e+02       2      50 ..     198     247 ..     197     259 .. 0.74
   3 ?    1.2   2.7      0.99   2.5e+02       8      56 ..     235     288 ..     227     292 .. 0.71
   4 ?   12.3   2.2   0.00038     0.097       2      52 ..     292     346 ..     291     372 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.1
                        DUF4988   7 dlkdrvaaleeqvkelndniealkklleegkvit 40 
                                    +l+dr+  lee++ + ++++++l   +++++v++
  gene102|gene102|rna102|rna102 161 ELRDRIRYLEEETMASQKKMNKL---YRDNEVLS 191
                                    67888888888777766666555...44444444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2
                        DUF4988   2 eddvndlkdrvaaleeqvkelndniealkkll..eegkviteveensdgsy 50 
                                    +++++ l++++  le++   l+ ++++lk     +++ ++   ++ +d ++
  gene102|gene102|rna102|rna102 198 REEIERLNSKIYDLEKENGRLQYELDKLKL-QdvKNSGLVERAQKIEDENK 247
                                    578999**************9999999954.32455556666666666544 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.99
                        DUF4988   8 lkdrvaaleeqvkelndniealkkll.eegkviteveensdg....syvltlsd 56 
                                    l +r + +e + k l++++++ ++++ + +  it+++++ +g    +++l l++
  gene102|gene102|rna102|rna102 235 LVERAQKIEDENKMLKEELSTANEIIrKYNDEITQMKNAINGnedaTKDLRLNN 288
                                    667888888888888888888888886777888888777666444456666665 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00038
                        DUF4988   2 eddvndlkdrvaaleeqvkelndniea....lkklleegkviteveensdgsyvl 52 
                                    +++++dlk+rv+ +ee++k+++++++a    lk l +e+  +++  en+++ y  
  gene102|gene102|rna102|rna102 292 KSEIEDLKKRVKGMEEKMKKIKEELKAketrLKDLETENMGLVKNLENAQNVYSH 346
                                    579*****************99998764444778876666555555556664443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2603  (0.145184); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                       191  (0.0106531); expected 17.9 (0.001)
Passed Fwd filter:                       133  (0.00741815); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              70  [number of targets reported over threshold]
# CPU time: 1.75u 0.41s 00:00:02.16 Elapsed: 00:00:00.64
# Mc/sec: 1778.29
//
Query:       gene1021|gene1021|rna1020|rna1020  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-14   53.3   0.2    4.9e-14   52.3   0.1    1.5  2  Ribosomal_L24e  Ribosomal protein L24e
  ------ inclusion threshold ------
      0.072   12.8   0.1       0.13   11.9   0.1    1.5  1  DUF5053         Domain of unknown function (DUF5053)


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.1   5.4e-18   4.9e-14       8      63 ..       8      63 ..       4      66 .. 0.96
   2 ?   -0.5   0.0      0.17   1.5e+03      35      58 ..      61      84 ..      59      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 5.4e-18
                                       TT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXXXX CS
                     Ribosomal_L24e  8 FsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkkel 63
                                       Fsg++i +G G+  v nDg+++   s+K +kl+++k+nPr+++WT++ R+  +ke 
  gene1021|gene1021|rna1020|rna1020  8 FSGHNIPKGSGIYRVMNDGRTVLTASNKERKLIQRKINPRDIRWTTTSREFFGKES 63
                                       **************************************************999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                                       HHHHHHHTT--GGGSTTSTTT-XX CS
                     Ribosomal_L24e 35 KceklfkqkrnPrklkWTkayRra 58
                                       K  +++ +k n +k+k  + +R++
  gene1021|gene1021|rna1020|rna1020 61 KESQYVVEKMNVQKVKIVRGFRHI 84
                                       666777888899998888877776 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.4e-05      0.13       6      33 ..      48      75 ..      46      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                            DUF5053  6 ivslsyiAkkYFgKsksWlyqrlnGidv 33
                                        + +   ++++FgK ++    ++n  +v
  gene1021|gene1021|rna1020|rna1020 48 DIRWTTTSREFFGKESQYVVEKMNVQKV 75
                                       589*********************8777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 605.93
//
Query:       gene1022|gene1022|rna1021|rna1021  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-27   96.2   0.2    3.5e-27   95.3   0.2    1.4  2  TLD       TLD
     0.0061   16.6   0.1      0.014   15.4   0.1    1.5  1  DUF5338   Family of unknown function (DUF5338)


Domain annotation for each model (and alignments):
>> TLD  TLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.3   1.2e+04     104     122 ..      21      39 ..      20      48 .. 0.72
   2 !   95.3   0.2     4e-31   3.5e-27       1     138 [.      61     209 ..      61     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
                                TLD 104 lekgtsrhsetfengllsg 122
                                        l ++++++ + + n++lsg
  gene1022|gene1022|rna1021|rna1021  21 LRFSMIHNGKEYRNSILSG 39 
                                        5566777778888888774 PP

  == domain 2  score: 95.3 bits;  conditional E-value: 4e-31
                                TLD   1 llyssskdgsslstllekie.nkgptlllikdekkyifGaflsqpwkssnkkfygdsesflfsl............ 63 
                                        ll+s+ +dg+s++t+le++e +  p++l++k++++ ++Gaf +++++ s    yg+ ++flf+             
  gene1022|gene1022|rna1021|rna1021  61 LLFSTFEDGFSYRTFLESFEeDGWPFVLACKTREGELLGAFFEDRIRISRA-VYGKPSTFLFTTaknkavqpedis 135
                                        79******************555************************9999.************999999888888 PP

                                TLD  64 .spkfkvykstgknkaylntssdglgfGggqpkfsLwidsslekgtsrhsetfengllsgaseerfkikdiEVWgl 138
                                         ++++ +++ +++++a +++  d+l+fG++ +kf+L i++sl +g++ + etf+n++l+  s+++f+i+ iE+W +
  gene1022|gene1022|rna1021|rna1021 136 tDNELMIFTMSKNKEANIYCCPDFLAFGCSGEKFGLLINKSLLDGETYPIETFGNHPLA--SKSHFRISYIELWLI 209
                                        88888888888888999999999************************************..9************76 PP

>> DUF5338  Family of unknown function (DUF5338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.6e-06     0.014      22      64 ..      33      77 ..      25      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                            DUF5338 22 rvaFL..avrkdikealkaGyalktiwehLheegkitisYeTFlr 64
                                       r  +L   v +   eal++ y++ t w++L ++ +  +sY+TFl+
  gene1022|gene1022|rna1021|rna1021 33 RNSILsgKVVTGLREALEDRYKYSTTWKLLFSTFEDGFSYRTFLE 77
                                       55555444677789*****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1182.98
//
Query:       gene1023|gene1023|rna1022|rna1022  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-07   31.8   0.2    1.7e-07   31.5   0.2    1.1  1  Rep_fac-A_3  Replication factor A protein 3
  ------ inclusion threshold ------
      0.092   12.1   0.0          3    7.2   0.0    2.2  2  Slp          Outer membrane lipoprotein Slp family


Domain annotation for each model (and alignments):
>> Rep_fac-A_3  Replication factor A protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.2   1.9e-11   1.7e-07      14     105 .]      17     104 .]      11     104 .] 0.88

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.9e-11
                                        GGGTTSEEEEEEEEEEETTSSEEEEE-TTS-EEEEEESS--SS---SEEEEEEEE-TTS-EEEEEEEE------HH CS
                        Rep_fac-A_3  14 sqfvgrtvrivgkvesvpsgktlilqstdggsvtvrlsedstleiskwvEvvGkvsddlgirldsvvefgedlDld 89 
                                        +++ g+ v+i+g+ esv +   +il++  +++++vr  + +  + +++v v G+v+++  ++ +sv  +g+++D++
  gene1023|gene1023|rna1022|rna1022  17 ENYEGQDVTIIGRFESV-EDGVVILKCM-DKEIQVRHRSIESYK-TGIVRVNGIVENGV-VVENSVFPIGNEFDME 88 
                                        799**************.**********.688999998876665.89999999998643.477899999******* PP

                                        HHHHHHHHHHHSGGGS CS
                        Rep_fac-A_3  90 lynklvqlthkfpely 105
                                        +y   v +++k+++l+
  gene1023|gene1023|rna1022|rna1022  89 TYGRFVAVAAKYQDLF 104
                                        ************9988 PP

>> Slp  Outer membrane lipoprotein Slp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00033         3      85     109 ..      14      37 ..      11      42 .. 0.90
   2 ?    2.8   0.0    0.0076        68      70      86 ..      86     102 ..      74     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00033
                                Slp  85 lDPaiykkgrlvTvvGtlkgsetgk 109
                                        lD ++y +g+ vT++G+++++e+g 
  gene1023|gene1023|rna1022|rna1022  14 LDVENY-EGQDVTIIGRFESVEDGV 37 
                                        78999*.************999875 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0076
                                Slp  70 sdeseGRflarvegFlD 86 
                                        ++e+ GRf+a  +++ D
  gene1023|gene1023|rna1022|rna1022  86 DMETYGRFVAVAAKYQD 102
                                        68899*****9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 634.87
//
Query:       gene1024|gene1024|rna1023|rna1023  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-27   95.0   0.0    3.2e-27   94.2   0.0    1.4  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
    1.7e-05   25.3   0.0    3.4e-05   24.3   0.0    1.5  1  RNA_pol_Rpb5_N  RNA polymerase Rpb5, N-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.0   3.5e-31   3.2e-27       1      73 []     135     207 ..     135     207 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 3.5e-31
                                        ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                     RNA_pol_Rpb5_C   1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73 
                                        +n tkH+ vP h++ls+eek+++lk lk+ + +LP+i+ksD +ary+g+k+Gdv++I+r+s+tage+++YR+V
  gene1024|gene1024|rna1023|rna1023 135 FNKTKHSWVPPHRILSREEKENVLKALKLGPGDLPRILKSDVIARYYGAKRGDVMEIVRRSRTAGESIYYRIV 207
                                        688*********************************************************************9 PP

>> RNA_pol_Rpb5_N  RNA polymerase Rpb5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.8e-09   3.4e-05      10      80 ..      21      84 ..      13      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.8e-09
                                       HHCCCCCCCCCCCEE--CCCCT--CHHHHCCSB-SSSSB-GCCT-EEEESS.SS--EEEEEE-SSTTE-TC CS
                     RNA_pol_Rpb5_N 10 irrTvleMlkdRgYlvaeeelnisleeFkekygdepkevdrekltisaskkddpseqilVfFpeekkvgvk 80
                                        r T +eM+kdRgY+ ++e   +sle+F e+y       +r+ l++++   d p   + + F +++k+g k
  gene1024|gene1024|rna1023|rna1023 21 SRNTTIEMIKDRGYTTTQEV--QSLESFHERYPFAL--TKRSTLNFVCVDVDRP---VGIHFGDDEKMGKK 84
                                       689***********988876..799*******8764..58********987776...77788888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1295.18
//
Query:       gene1025|gene1025|rna1024|rna1024  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.031   13.1   0.1      0.036   12.9   0.1    1.0  1  MtmB          Monomethylamine methyltransferase MtmB
      0.033   14.4   1.1      0.039   14.2   1.1    1.1  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
       0.13   12.4   0.6          2    8.6   0.6    2.3  1  UBA_2         Ubiquitin associated domain (UBA)
       0.14   12.4   4.0       0.65   10.3   0.1    2.6  3  Tup_N         Tup N-terminal


Domain annotation for each model (and alignments):
>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   8.1e-06     0.036     133     183 ..      15      65 ..      12      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-06
                               MtmB 133 vfleviqsyaqeplvdtivsGvletvegkeaktksPfeikatlaearlvke 183
                                        ++ + +qs+ + + v+++vs +l++++     +k+  ei+a +ae  + k+
  gene1025|gene1025|rna1024|rna1024  15 ILAKTMQSSYRKKQVEELVSRILQKIQCIIGPAKTHEEIEALKAEFMALKQ 65 
                                        5678899999***********************************998876 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.1   8.6e-06     0.039      19      84 ..       3      68 ..       2      73 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.6e-06
                                       CCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHH CS
                       Seryl_tRNA_N 19 kkRgedkadvdelleldekrrelqveleelqaer.NelskeIgkakkkkedaeeliaevkelkeelk 84
                                       k+R+++++++ ++l+   +    ++++eel ++   +++  Ig ak   e++e+l+ae  +lk+e  
  gene1025|gene1025|rna1024|rna1024  3 KARKAYELEITKILAKTMQSSYRKKQVEELVSRIlQKIQCIIGPAKTH-EEIEALKAEFMALKQEAY 68
                                       57999***************************9835667777777765.8*************9975 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.6   0.00045         2       4      31 ..      11      48 ..       9      73 .] 0.70

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00045
                              UBA_2  4 dvvsaLsktM..GYdkdeIieaLekaeks........k 31
                                       ++ ++L+ktM   Y k  + e   +  ++        k
  gene1025|gene1025|rna1024|rna1024 11 EITKILAKTMqsSYRKKQVEELVSRILQKiqciigpaK 48
                                       57899*****999*****99988877666666666663 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.033   1.5e+02      57      69 ..       3      15 ..       1      23 [. 0.81
   2 ?    0.4   0.2      0.18   8.1e+02      24      39 ..      23      38 ..      11      43 .. 0.44
   3 ?   10.3   0.1   0.00014      0.65       3      23 ..      50      70 ..      48      73 .] 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.033
                              Tup_N 57 kikqqYEeeiarL 69
                                       k +++YE ei+++
  gene1025|gene1025|rna1024|rna1024  3 KARKAYELEITKI 15
                                       78999****9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.18
                              Tup_N 24 kaqkdeyelkiqsqiq 39
                                         +k+ +e  ++  +q
  gene1025|gene1025|rna1024|rna1024 23 SYRKKQVEELVSRILQ 38
                                       3333333333333333 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00014
                              Tup_N  3 nelLdavkqEfdalsqeassl 23
                                       +e ++a+k+Ef al+qea sl
  gene1025|gene1025|rna1024|rna1024 50 HEEIEALKAEFMALKQEAYSL 70
                                       6889*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1455  (0.0811534); expected 358.6 (0.02)
Passed bias filter:                      700  (0.0390429); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 489.95
//
Query:       gene1026|gene1026|rna1025|rna1025  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-95  320.1   0.0      2e-95  319.8   0.0    1.1  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.8   0.0   1.1e-99     2e-95       1     291 [.      43     325 ..      43     335 .. 0.95

  Alignments for each domain:
  == domain 1  score: 319.8 bits;  conditional E-value: 1.1e-99
                    Diphthamide_syn   1 fPegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd..rlpvlYvfveie 73 
                                        fP+gll++s  i+di+ + ++ae+vil D++YG Ccvd+ +   +++dllvHyGhscl+pv   + +vlYvfv+i+
  gene1026|gene1026|rna1025|rna1025  43 FPDGLLKYSFVIIDIIeKYTDAECVILNDVVYGGCCVDDES---IDSDLLVHYGHSCLVPVGemNTKVLYVFVDIR 115
                                        9***************5556*******************65...666*************9999************ PP

                    Diphthamide_syn  74 ldvehlvetlkknfkekkkivlvstiqyahaleevkeeleee..gyevvkvpqsekplspgevlgctspklkeeee 147
                                        +d++h +e++++nf  + ki++++tiqy+++++++++ l+ee  g+e +  pq+ +pls gevlgctsp+++    
  gene1026|gene1026|rna1025|rna1025 116 IDIDHAAEMIRRNF--EGKIAVIGTIQYNSSINKLRRVLSEEkdGVECI-LPQV-RPLSSGEVLGCTSPRIE---- 183
                                        **************..778*********************887778888.9999.****************5.... PP

                    Diphthamide_syn 148 evdailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgr 223
                                         v+a++ igdgrfhl+++m+ np+l++y+y+p+++++t+esyd+  +++ R++ai +a + +++G+i+g+lg+qg+
  gene1026|gene1026|rna1025|rna1025 184 GVSAVVSIGDGRFHLEGAMIRNPHLKFYKYCPFNRRMTQESYDYHTMISARRSAIGRALNGRSFGVILGSLGRQGN 259
                                        89************************************************************************** PP

                    Diphthamide_syn 224 lelverlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElev 291
                                         ++++++ ++lk+  +++yl++++e++p+kL+ ++ id fV+++Cprlsid+g+ F+kP+l+p+E+++
  gene1026|gene1026|rna1025|rna1025 260 RSILRSVVDKLKK--YDIYLLMLDEISPKKLERYDFIDSFVQISCPRLSIDWGTLFKKPLLSPFEVFY 325
                                        ***********96..68*****************77*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.59
# Mc/sec: 1772.26
//
Query:       gene1027|gene1027|rna1026|rna1026  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.025   14.8   0.0    1.6  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.4e-06     0.025      38      90 ..     103     153 ..      88     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-06
                                        GEEEEE..TTSEEEETT.TTEEEEESSSSTTSBEEEEETTTTSGGGCEEEETTTT CS
                     Ricin_B_lectin  38 Qlwtlt..kdgeirskaqselCldvsstaegakvvlakChkgkgnqrWefdkdgt 90 
                                         +w+++  ++g + +ka++++Cl v   a ++++ ++kC  +++ q + f+k+++
  gene1027|gene1027|rna1026|rna1026 103 KYWEYRevGNGGYILKAKKNKCLGV---AGNNTLGVFKCR-NEEGQVFIFEKKNS 153
                                        5666665555555555666666666...466666666666.55566666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2206.82
//
Query:       gene1028|gene1028|rna1027|rna1027  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.068   13.3   0.1    1.7  2  DUF3630   Protein of unknown function (DUF3630)


Domain annotation for each model (and alignments):
>> DUF3630  Protein of unknown function (DUF3630)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.8e-06     0.068      57      79 ..      72      94 ..      68     107 .. 0.85
   2 ?   -2.5   0.0      0.31   5.6e+03      46      59 ..     146     159 ..     137     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-06
                            DUF3630 57 egsrllLkyEhYsesvWlesesa 79
                                       e++ + LkyE +s+ +Wle +++
  gene1028|gene1028|rna1027|rna1027 72 ENQIFDLKYESFSKKIWLELKKE 94
                                       8899***************7765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.31
                            DUF3630  46 gaDrhswlldfegs 59 
                                         a ++ w l f ++
  gene1028|gene1028|rna1027|rna1027 146 YAGVRGWALSFTDC 159
                                        57789999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1250.23
//
Query:       gene1029|gene1029|rna1028|rna1028  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-32  110.7   6.2    2.9e-32  110.6   6.2    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0046   17.1   0.2     0.0063   16.6   0.2    1.2  1  zf-RING_13       RING/Ubox like zinc-binding domain
  ------ inclusion threshold ------
       0.02   14.9   0.1      0.024   14.7   0.1    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.043   13.6   0.6      0.061   13.1   0.6    1.3  1  Rep_fac-A_C      Replication factor-A C terminal domain
      0.044   13.9   2.8       0.16   12.1   2.8    1.8  1  Mut7-C           Mut7-C RNAse domain
      0.051   13.5   1.3      0.074   12.9   1.3    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.062   13.4   0.6        1.5    9.0   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
      0.097   13.0   2.0       0.23   11.8   1.9    1.6  2  C1_2             C1 domain
       0.12   12.8   4.9       0.22   12.0   0.1    2.2  2  zf-IS66          zinc-finger binding domain of transposase IS
       0.22   11.5   7.1       0.65   10.0   7.1    1.8  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
        1.6    8.8   5.2        4.2    7.5   0.4    2.3  2  zf-BED           BED zinc finger
        1.7    8.5   7.1         18    5.2   7.1    2.1  1  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   6.2   1.9e-35   2.9e-32       2      82 ..       5      85 ..       4      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.9e-35
                                       XXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH- CS
                    Ribosomal_L37ae  2 tkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsaktvksa 79
                                       tkkvgiaG +g+rYG++lrkr+k + ++q+aky C+ cgk++v+R+avgiwkC++c++ +aGg+y+ +t+++k++ ++
  gene1029|gene1029|rna1028|rna1028  5 TKKVGIAGSFGARYGSTLRKRMKAVLETQRAKYSCEACGKKRVRREAVGIWKCRSCRRIFAGGSYVTSTPAGKIFINM 82
                                       9************************************************************************99888 PP

                                       XXX CS
                    Ribosomal_L37ae 80 irr 82
                                       +++
  gene1029|gene1029|rna1028|rna1028 83 VKQ 85
                                       876 PP

>> zf-RING_13  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   4.2e-06    0.0063       4      38 ..      39      73 ..      36      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.2e-06
                                       -TTTSS--SEEETTS-EE-TTTHHHTTTSS-EEES CS
                         zf-RING_13  4 ctvcgaapvaksacggwfcgncvpyhaghchttsl 38
                                       c  cg   v + a g w c  c    ag  + ts 
  gene1029|gene1029|rna1028|rna1028 39 CEACGKKRVRREAVGIWKCRSCRRIFAGGSYVTST 73
                                       99***************************999996 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.6e-05     0.024      54      94 ..      20      62 ..       6      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                       C.TTTT-EEEEEEE--EEEETTTS-EEECHHH..HHS-TTTSS CS
                               HypA 54 gtvlegaeLeieevpvkvrCreCgkefeleek..alrCpkCgs 94
                                       +t+ ++ +  +e++++k+ C+ Cgk+   +e+    +C +C +
  gene1029|gene1029|rna1028|rna1028 20 STLRKRMKAVLETQRAKYSCEACGKKRVRREAvgIWKCRSCRR 62
                                       55667778889*************8877555334569***975 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   4.1e-05     0.061      15      47 ..      34      64 ..      21      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-05
                                       TTEEEB--STT---B-EEE.TTTEEEETTTTEEE CS
                        Rep_fac-A_C 15 nlvYkACpsedCnkKvvee.edgewrCekCdkev 47
                                       ++ Y +C+   C kK v++ + g w+C  C + +
  gene1029|gene1029|rna1028|rna1028 34 RAKY-SCE--ACGKKRVRReAVGIWKCRSCRRIF 64
                                       4455.588..999998888466********9866 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.8   0.00011      0.16     113     140 ..      44      71 ..      20      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                             Mut7-C 113 pekvyeeadeftrCekCrkvfWkGshwe 140
                                        +++v++ea  +++C++Cr++f +Gs  +
  gene1029|gene1029|rna1028|rna1028  44 KKRVRREAVGIWKCRSCRRIFAGGSYVT 71 
                                        4556666666************999765 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.3     5e-05     0.074       9      37 ..      34      63 ..      27      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5e-05
                                       SS--B-TTT-SB--S.SSS-EEEETTT--E CS
                               C1_1  9 kqptfCkhCgeflwg.kekqglkCswCkll 37
                                       + +  C+ Cg+   + ++  ++kC+ C+++
  gene1029|gene1029|rna1028|rna1028 34 RAKYSCEACGKKRVRrEAVGIWKCRSCRRI 63
                                       56779*****998777999********987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1     0.001       1.5      27      38 ..      36      49 ..      19      51 .. 0.74
   2 ?    2.9   0.0      0.08   1.2e+02       7      15 ..      56      64 ..      54      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                        Zn-ribbon_8 27 ta.CPeCgs.evrr 38
                                       +  C +Cg+ +vrr
  gene1029|gene1029|rna1028|rna1028 36 KYsCEACGKkRVRR 49
                                       34488888888877 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.08
                        Zn-ribbon_8  7 rCeeCghef 15
                                       +C++C + f
  gene1029|gene1029|rna1028|rna1028 56 KCRSCRRIF 64
                                       8****9988 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.9   0.00015      0.23      14      39 ..      32      61 ..      24      65 .. 0.79
   2 ?    3.5   0.1     0.059        89      17      30 ..      53      66 ..      47      70 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                               C1_2 14 dssesfnCsaCgrk.idgff...YsCseCd 39
                                       ++ ++++C+aCg+k +  +     +C  C+
  gene1029|gene1029|rna1028|rna1028 32 TQRAKYSCEACGKKrVRREAvgiWKCRSCR 61
                                       67889*********854444789***9996 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.059
                               C1_2 17 esfnCsaCgrkidg 30
                                       + ++C+ C+r   g
  gene1029|gene1029|rna1028|rna1028 53 GIWKCRSCRRIFAG 66
                                       6789****997444 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015      0.22      32      46 .]      29      43 ..      28      43 .. 0.94
   2 ?    2.2   1.4      0.16   2.4e+02      31      45 ..      46      60 ..      44      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                            zf-IS66 32 ViehirpkyaCpcCe 46
                                       V e++r ky+C +C+
  gene1029|gene1029|rna1028|rna1028 29 VLETQRAKYSCEACG 43
                                       89************7 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.16
                            zf-IS66 31 rViehirpkyaCpcC 45
                                       rV +     ++C++C
  gene1029|gene1029|rna1028|rna1028 46 RVRREAVGIWKCRSC 60
                                       5667777799***** PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.1   0.00043      0.65      19      45 ..      37      62 ..      27      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00043
                      Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                         C +Cg+++++r +  g ++C++Cr+
  gene1029|gene1029|rna1028|rna1028 37 YSCEACGKKRVRREAV-GIWKCRSCRR 62
                                       5699***998888885.********97 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4     0.038        57      11      29 ..      31      49 ..      26      54 .. 0.81
   2 ?    7.5   0.4    0.0028       4.2      16      30 ..      54      68 ..      49      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.038
                                       -GGSS--EETTTTEE---- CS
                             zf-BED 11 slkeqkavCryCgkilsrg 29
                                       ++++ k  C  Cgk+  r+
  gene1029|gene1029|rna1028|rna1028 31 ETQRAKYSCEACGKKRVRR 49
                                       56788999******97775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                                       --EETTTTEE----S CS
                             zf-BED 16 kavCryCgkilsrgg 30
                                        ++Cr C +i+++g+
  gene1029|gene1029|rna1028|rna1028 54 IWKCRSCRRIFAGGS 68
                                       69**********993 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   7.1     0.012        18       1      21 [.      37      61 ..      37      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.012
                       Rubredoxin_2  1 YvCsqCGfesakw....fGrCpsCg 21
                                       Y+C++CG +  +      ++C+sC+
  gene1029|gene1029|rna1028|rna1028 37 YSCEACGKKRVRReavgIWKCRSCR 61
                                       99*****87655533338******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 655.24
//
Query:       gene1030|gene1030|rna1029|rna1029  [L=424]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-19   67.7   1.1    3.4e-16   59.4   0.0    3.3  3  Rtt106         Histone chaperone Rttp106-like
    8.6e-08   32.5   0.3    0.00011   22.5   0.1    3.0  3  POB3_N         POB3-like N-terminal PH domain
  ------ inclusion threshold ------
      0.072   13.2   1.2         17    5.5   0.1    3.3  3  gp45-slide_C   gp45 sliding clamp, C terminal
       0.13   12.3   1.1         19    5.3   0.1    2.5  2  BBS2_Mid       Ciliary BBSome complex subunit 2, middle regio
       0.16   12.2   0.2          1    9.6   0.0    2.3  2  Enterotoxin_b  Heat-labile enterotoxin beta chain


Domain annotation for each model (and alignments):
>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.03   1.1e+02      59      79 ..      63      83 ..      12     100 .. 0.81
   2 ?    1.8   0.2     0.091   3.3e+02      26      63 ..     120     157 ..     112     176 .. 0.68
   3 !   59.4   0.0   9.5e-20   3.4e-16       2      88 ..     305     391 ..     304     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.03
                             Rtt106 59 kkeeveFsmidqeelegidef 79
                                        ++ +e++++dq++++++++ 
  gene1030|gene1030|rna1029|rna1029 63 GNAVYEINNVDQNYIDELKRM 83
                                       35899***********99964 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.091
                             Rtt106  26 kkPllfiplediesvsfeRvsvtsrtfdlvvelkkeev 63 
                                         k ++ +p+ediesv   R + +    d+++++ +++ 
  gene1030|gene1030|rna1029|rna1029 120 TKTIFEVPVEDIESVVDIRNELSISLKDVEIRFVSNKK 157
                                        677888999*****999999555555555555533333 PP

  == domain 3  score: 59.4 bits;  conditional E-value: 9.5e-20
                             Rtt106   2 gVkasrkakeGlLyflekgllfgfkkPllfiplediesvsfeRv...svtsrtfdlvvelkkeeveFsmidqeele 74 
                                        + ++  ka eG+Ly+le+++lf ++k ++ + l++i+ v+f+R+   s++ +tfd+++ + + +++F+ ++++e++
  gene1030|gene1030|rna1029|rna1029 305 CLRCAIKAYEGQLYPLEDCVLF-LPK-AIRLGLNEISLVEFSRInlsSMQAKTFDMTLFC-EGSYTFNGLSKDEFG 377
                                        67899*****************.888.899******************************.69************* PP

                             Rtt106  75 gidefvkskgikik 88 
                                         ++++++skg+k +
  gene1030|gene1030|rna1029|rna1029 378 MLEQYFHSKGVKAR 391
                                        ***********987 PP

>> POB3_N  POB3-like N-terminal PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   3.1e-08   0.00011      16      91 ..      20      92 ..       6      94 .. 0.92
   2 ?   -0.4   0.0      0.45   1.6e+03      15      46 ..     105     135 ..     101     151 .. 0.74
   3 !    5.9   0.0    0.0047        17      40      85 ..     336     385 ..     328     389 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3.1e-08
                             POB3_N 16 klrlsesglgwknsktgkvvqikasdissaqWvrvargyqLrillkdgkvvrfdGFkeedfdkLskllkknfniel 91
                                        +++s++g+++k++++ +v+++++++++ a+  + +r++++ri+   + v++ +  +++ +d+L+++++++f+i+l
  gene1030|gene1030|rna1029|rna1029 20 TVKISRDGIAIKAEGG-EVYTMEKNEVKDAELFHGSRKMAIRIF--GNAVYEINNVDQNYIDELKRMFSEYFKISL 92
                                       5799********9888.5**************************..89**************************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.45
                             POB3_N  15 Gklrls.esglgwknsktgkvvqikasdissaq 46 
                                        G+l ++ ++ l ++++kt   ++++ +di+s+ 
  gene1030|gene1030|rna1029|rna1029 105 GELGINgQKALEFRSTKT--IFEVPVEDIESVV 135
                                        555555567788888888..7999999999985 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0047
                             POB3_N  40 sdissaqWvrva.rgyqLrill...kdgkvvrfdGFkeedfdkLskllkk 85 
                                        ++is ++++r++  ++q + +      ++ ++f+G+++++f  L++++++
  gene1030|gene1030|rna1029|rna1029 336 NEISLVEFSRINlSSMQAKTFDmtlFCEGSYTFNGLSKDEFGMLEQYFHS 385
                                        788889999998878877765322246799*****************986 PP

>> gp45-slide_C  gp45 sliding clamp, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0048        17      13      48 ..      17      52 ..      11      98 .. 0.77
   2 ?    3.0   0.1      0.03   1.1e+02       1      90 [.     123     215 ..     123     229 .. 0.70
   3 ?    1.4   0.0      0.09   3.2e+02      74     104 ..     350     380 ..     339     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0048
                                       HHHHHHHT--EEEEEEETTEEEEEEE-TTTSSSS-S CS
                       gp45-slide_C 13 krasrtlsidtiaitveeGkivinGfnkvtdadlvr 48
                                       k+a+  +s d iai++e G++     n v+da+l +
  gene1030|gene1030|rna1029|rna1029 17 KKATVKISRDGIAIKAEGGEVYTMEKNEVKDAELFH 52
                                       57777888899************8888888888764 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.03
                                        EEEE-HHHHHHHHHHHHHHT--..EEEEEEETTEEEEEEE-TTTSSSS-S-SEEEE.EEE--SS--EEEEEEGGG- CS
                       gp45-slide_C   1 vfdikaedlqklkrasrtlsid..tiaitveeGkivinGfnkvtdadlvrvkysle.vgdydgeaefnflvnmanl 73 
                                        +f++  ed++ +  +   lsi+  ++ i+    k +i+  +    +++ +  +++e ++ +    +fn+++  + l
  gene1030|gene1030|rna1029|rna1029 123 IFEVPVEDIESVVDIRNELSISlkDVEIRFVSNKKAIEEIKEGCSSSVDDEIFKMEgLSLAYPRGKFNLIFFRDYL 198
                                        5888899999998777766553339999999999999666555555555666666534555667789999888888 PP

                                        ---SS-EEEEEEEEEEE CS
                       gp45-slide_C  74 kildddykvlisakGaa 90 
                                        +++   y   ++ k + 
  gene1030|gene1030|rna1029|rna1029 199 RLVGSSYDHKVYYKSVR 215
                                        88888887776666555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.09
                                        ---SS-EEEEEEEEEEEEEEESSEEEEEEBB CS
                       gp45-slide_C  74 kildddykvlisakGaakfeGksaeyvvale 104
                                         ++ + + ++++ +G   f+G+s + ++ le
  gene1030|gene1030|rna1029|rna1029 350 SMQAKTFDMTLFCEGSYTFNGLSKDEFGMLE 380
                                        4788899999************999998887 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1    0.0053        19      10      57 ..      45      92 ..      37      94 .. 0.83
   2 ?    5.2   0.1     0.006        22      12      39 ..     138     165 ..     130     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0053
                           BBS2_Mid 10 dgeneLvvgsddfeirvfkeeelvaeitetekvvslarlekerfayal 57
                                         ++eL+ gs  + ir+f +     +   ++ +  l+r+ +e f ++l
  gene1030|gene1030|rna1029|rna1029 45 VKDAELFHGSRKMAIRIFGNAVYEINNVDQNYIDELKRMFSEYFKISL 92
                                       45689*************998888888888889999999999988876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.006
                           BBS2_Mid  12 eneLvvgsddfeirvfkeeelvaeitet 39 
                                        +neL ++ +d eir  ++++++ ei+e 
  gene1030|gene1030|rna1029|rna1029 138 RNELSISLKDVEIRFVSNKKAIEEIKEG 165
                                        689**********************985 PP

>> Enterotoxin_b  Heat-labile enterotoxin beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00028         1      15      75 ..      35      95 ..      26     108 .. 0.81
   2 ?   -1.1   0.0      0.59   2.1e+03      59      71 ..     153     165 ..     145     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                                       EEEEEEEEEESEEEEEESTTBEEEEEEETTS-EEEEXXSSTTSXTTHHHHH.HHHHHHHHHH CS
                      Enterotoxin_b 15 tqiytlndkifsyteslagkremaiitfkngaifqvevpgsqhidsqkkai.ermkdtlria 75
                                        ++yt++ + +  +e + g r+mai  f n a+++++    ++id  k+   e +k +l + 
  gene1030|gene1030|rna1029|rna1029 35 GEVYTMEKNEVKDAELFHGSRKMAIRIFGN-AVYEINNVDQNYIDELKRMFsEYFKISLYVK 95
                                       5799**99999*****************98.79999999999***99986525556655555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.59
                                        TTHHHHHHHHHHH CS
                      Enterotoxin_b  59 dsqkkaiermkdt 71 
                                         s+kkaie +k+ 
  gene1030|gene1030|rna1029|rna1029 153 VSNKKAIEEIKEG 165
                                        5899****99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2669.66
//
Query:       gene103|gene103|rna103|rna103  [L=593]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-41  141.6   0.3    6.1e-41  140.3   0.1    1.8  2  Dynamin_N    Dynamin family
    5.8e-34  117.6   0.2    2.3e-33  115.7   0.2    2.0  1  Dynamin_M    Dynamin central region
      8e-14   51.6   0.6    1.7e-13   50.5   0.1    1.9  2  GED          Dynamin GTPase effector domain
    5.9e-07   29.6   0.1    1.1e-05   25.4   0.1    2.5  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0088   15.7   0.1      0.015   15.0   0.1    1.3  1  zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
  ------ inclusion threshold ------
      0.043   13.6   0.1        1.9    8.2   0.0    2.5  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati


Domain annotation for each model (and alignments):
>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.3   0.1     2e-44   6.1e-41       1     168 []      31     205 ..      31     205 .. 0.96
   2 ?   -1.7   0.0      0.86   2.6e+03     120     143 ..     400     424 ..     391     527 .. 0.59

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 2e-44
                                    EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEET-EB--CHHHHHHHHHHHHHHH CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkekekkledfsevreeieketekia 80 
                                    i+ +GsqSsGKSSvl+++++++ilprg+n++Tr+p++l+l++  +   +a+++ +   +   +df++ r  i+k++ +i 
  gene103|gene103|rna103|rna103  31 IIAIGSQSSGKSSVLEQIIRREILPRGTNLVTRCPVVLHLRRCRD---EAESVVFDHLANPVYDFTAARSIITKRMVEIC 107
                                    789***************************************777...4566655555999******************* PP

                                    TSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTS.........HHHHHHH.STTEEEEEEEETTS-CCC-CHHHH CS
                      Dynamin_N  81 gankgiskkvillkilsllvkgltlvDlPGldsvnkrdq.........elvkeyi.kkadiilavtsanhdlsnsealfl 150
                                    g nkgis+++i+  +   +  ++tlvDlPGl++v+ ++q         +++ +y+ k+++iila+ +an d++++eal++
  gene103|gene103|rna103|rna103 108 GDNKGISSTPITAFVNLEDTLDMTLVDLPGLIKVPIGEQpedievqieNMALNYAeKESSIILALINANADIATNEALKV 187
                                    ******************************************************************************** PP

                                    HHHHSTTBTTEEEEEE-C CS
                      Dynamin_N 151 arevdpkgkrtivvltkl 168
                                    ar++dp+ krt++v+tk+
  gene103|gene103|rna103|rna103 188 ARKADPQLKRTLGVVTKI 205
                                    ****************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.86
                                    HHHHHHH.STTEEEEEEEETTS-CC CS
                      Dynamin_N 120 elvkeyi.kkadiilavtsanhdls 143
                                    +++++y+ k ++++ ++ +   ++s
  gene103|gene103|rna103|rna103 400 KMTETYLeKTNTAVRLLIEEIWSIS 424
                                    4555555554544444433333333 PP

>> Dynamin_M  Dynamin central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.2   7.6e-37   2.3e-33       2     279 ..     215     475 ..     214     479 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 7.6e-37
                      Dynamin_M   2 vdilenkvipLklGYvgVvnRsqkdInkkksieealkkEkaFFeshpayrkladkaGtpyLakkLnqiLvehIrkslPel 81 
                                    ++il n+   L lGYvgV+nR+ +dI+k++s++ea+ kE+++F++ p y k+  + G +yL kkLn+i +++  +s+P++
  gene103|gene103|rna103|rna103 215 LNILCNRNPRLALGYVGVINRGYQDISKGVSVHEAILKESMYFKESPLYGKVYPNIGSNYLMKKLNEIFYKMAVESIPGI 294
                                    689***************************************************************************** PP

                      Dynamin_M  82 kkkineklqklekeleelgeskpsdeektklllqlitkfkedfkklieGesevstkelsggarireiFnetlekslekid 161
                                    k+ i+++l+   ++l+elg +  ++ ++++l+l   + +   fk++   +        ++++r ++ F + l++++e+ +
  gene103|gene103|rna103|rna103 295 KTAIRNQLNGKAERLHELGLGSAMK-SERSLVLAYHQVVLGIFKNIKPSS--------RVFSRGSSNFLSDLKETFERDE 365
                                    *******************887765.888899999999999999998775........7899999999999999999966 PP

                      Dynamin_M 162 pleelsdeeirtairnsrGrelplfvpekaFealvkkqikkleepalkcvelVyeelekiveklekelkrFpnLreeike 241
                                    +l     e+ +  +r+s+     +f++e++F  +v++ i+k+ e  l+  + +   l++ + ++  +++rF  L ++++ 
  gene103|gene103|rna103|rna103 366 FLPS--FEDLSSRLRKSS----YIFISEAVFYDVVRENIRKMTETYLEKTNTAVRLLIEEIWSI--SSTRFGDLSKKLNA 437
                                    6665..455555566665....89*******************999999977766666666663..889*********** PP

                      Dynamin_M 242 vvedllreqeeptkemienliemelayintnhpdfiga 279
                                    v+ ++++ q+++  + i+ + +++ +yin  hpdf ++
  gene103|gene103|rna103|rna103 438 VTCECMEGQRNRLLDNIDMYSSIQSSYINVDHPDFDKS 475
                                    ***********************************765 PP

>> GED  Dynamin GTPase effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       4.9   1.5e+04       7      21 ..     396     410 ..     391     417 .. 0.58
   2 !   50.5   0.1   5.8e-17   1.7e-13       3      91 ..     508     592 ..     506     593 .] 0.89

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.9
                                    THHHHHHHHHHHHHH CS
                            GED   7 eeirslvksYfnivr 21 
                                    e+ir++ + Y++ ++
  gene103|gene103|rna103|rna103 396 ENIRKMTETYLEKTN 410
                                    445555555555544 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 5.8e-17
                                    XXXTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHCCCCCHHHCCTTSGGGHHHHT---SCHCCCCHHHHHHHHHH CS
                            GED   3 eseveeirslvksYfnivrktiadqiPkaimhllvneakeslqkellakLykkedldeLLkEdeeiaekRkelkkrleal 82 
                                    + ev++i++l  sY+ iv+k++++ + kai + l +++ ++l +     L + e  d+ L+E++ei+++R+ l+k +e+l
  gene103|gene103|rna103|rna103 508 AFEVRVIKELAGSYLGIVNKEMRNYVFKAIHYYLFEHIDSKLLN----TLTELEIEDSVLAECPEIIHERDGLAKDIEVL 583
                                    6799******************************9988877766....45555555689********************* PP

                                    HHHCCCCCH CS
                            GED  83 kkAreilse 91 
                                    k+A ++l++
  gene103|gene103|rna103|rna103 584 KNALSVLDN 592
                                    ******987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   3.8e-09   1.1e-05       2     103 ..      31     190 ..      30     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.8e-09
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.................................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.................................. 47 
                                    ++ +G   +GKS+++ ++++++     ++ +Tr ++  +++  ++e                                  
  gene103|gene103|rna103|rna103  31 IIAIGSQSSGKSSVLEQIIRREILPRGTNLVTRCPVVLHLRRCRDEaesvvfdhlanpvydftaarsiitkrmveicgdn 110
                                    7789*****************9999**********999998333235688888899999999999999999999999999 PP

                                    ...................EEEEECGGCSS......HHHHHH..HHHHHHHH..HHCTSEEEEEEETTTTCSHHHHHHHH CS
                       MMR_HSR1  48 ...................ielvDtpGlie......gaseek..glgkafla..leeadlillvvdaseeklkpldeele 98 
                                                       ++lvD+pGli+         e+   ++++  l+   +e+++il +++a+ + ++   +e  
  gene103|gene103|rna103|rna103 111 kgisstpitafvnledtldMTLVDLPGLIKvpigeqP--EDIevQIENMALNyaEKESSIILALINANAD-IA--TNEAL 185
                                    9999999999999999999********9844443221..2222333333333223458********8833.43..33444 PP

                                    HHHHH CS
                       MMR_HSR1  99 ellee 103
                                    ++ ++
  gene103|gene103|rna103|rna103 186 KVARK 190
                                    44443 PP

>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   5.1e-06     0.015       8     105 ..     351     440 ..     345     459 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.1e-06
                    zf-SNAP50_C   8 sqtLteLrdkisClsdseeleekkekleelakkkfkssfffiedtfynDlrnpeaidysepilewlkkkekslgefkvks 87 
                                    s++L++L+++++  +         ++ e+l+++  kss++fi + +++D   ++ ++++e+ le  +++  +l   ++ s
  gene103|gene103|rna103|rna103 351 SNFLSDLKETFERDE-------FLPSFEDLSSRLRKSSYIFISEAVFYDVVRENIRKMTETYLEKTNTA-VRLLIEEIWS 422
                                    666777777765333.......3455789999************9999**9999999999999999999.78888899** PP

                    zf-SNAP50_C  88 meetrfedLelrlgqpyl 105
                                    +++trf dL+ +l++  +
  gene103|gene103|rna103|rna103 423 ISSTRFGDLSKKLNAVTC 440
                                    **********99998666 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.037   1.1e+02       1      26 [.      28      53 ..      28      67 .. 0.79
   2 ?    8.2   0.0   0.00065       1.9      55     104 ..     157     210 ..     145     219 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.037
                      PduV-EutP  1 mkkilliGkvgsGKttLtqalkgeel 26
                                   m +i+ iG+  sGK ++ +++  +e+
  gene103|gene103|rna103|rna103 28 MPQIIAIGSQSSGKSSVLEQIIRREI 53
                                   6789***********98777766666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00065
                      PduV-EutP  55 salivtsaeadvialvqdate....eesvfppgfasvfnkeviGiitkidlaed 104
                                     al+ +  e+++i  + +a++    +e +  +  a    k ++G++tkidl+++
  gene103|gene103|rna103|rna103 157 MALNYAEKESSIILALINANAdiatNEALKVARKADPQLKRTLGVVTKIDLMDE 210
                                    56777777777777766655411113344445667778899**********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 3868.60
//
Query:       gene1031|gene1031|rna1030|rna1030  [L=401]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-05   24.7   0.0        5.8    7.3   0.0    4.3  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    0.00097   19.9   6.4        3.1    8.8   0.1    5.3  6  WD40         WD domain, G-beta repeat
     0.0044   15.7   0.0     0.0074   15.0   0.0    1.3  1  Nup160       Nucleoporin Nup120/160


Domain annotation for each model (and alignments):
>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.033     2e+02      37      81 ..     115     159 ..      96     169 .. 0.85
   2 !    6.8   0.0    0.0014       8.1      29      80 ..     184     241 ..     178     254 .. 0.80
   3 ?    2.2   0.0     0.037   2.2e+02      48      76 ..     261     289 ..     247     296 .. 0.86
   4 !    7.3   0.0   0.00097       5.8      43      90 ..     336     381 ..     319     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.033
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                        ++  v+s++     klL  +  dg+  l++   g++v ++  +s+
  gene1031|gene1031|rna1030|rna1030 115 HKDMVSSVSLFRRHKLLLTSGLDGKAYLYNLRAGDLVTTYMGHSK 159
                                        566788888888999**********************99977766 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0014
                        ANAPC4_WD40  29 vwtl......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvks 80 
                                        vw++      ++ + +   ++ ++k+ gk   ++  dg++r +d  + k ++  + +s
  gene1031|gene1031|rna1030|rna1030 184 VWDIetgrcnAKIDLECPLTCQSFKELGKAVFIGGLDGRIRTVDTRNRKALNGAKEES 241
                                        66665555444445566678899*************************9998777665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.037
                        ANAPC4_WD40  48 pdgklLavaysdgevrlldaesgkvvhsl 76 
                                        +++++L++  ++g+++ ld  + ++v++ 
  gene1031|gene1031|rna1030|rna1030 261 EQDNFLVFTRKKGSLHYLDLRNDRIVKTH 289
                                        6899*******************999865 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.00097
                        ANAPC4_WD40  43 sLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                         ++ +pdg++L+++  +g v+++  +s+k  +  s+++    t+++W 
  gene1031|gene1031|rna1030|rna1030 336 RVKASPDGSMLCFGDTNGLVNFIARSSTKETSLGSTSEA--LTTIDWI 381
                                        566789*****************9999998877776666..7888885 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0037        22       7      38 .]     112     144 ..     107     144 .. 0.81
   2 !    8.8   0.1   0.00052       3.1       2      38 .]     149     186 ..     148     186 .. 0.77
   3 ?   -0.1   0.0      0.35   2.1e+03      13      35 ..     202     224 ..     196     225 .. 0.80
   4 ?   -1.5   0.0      0.92   5.5e+03       5      31 ..     284     311 ..     281     316 .. 0.54
   5 ?   -0.6   0.0      0.48   2.9e+03      14      29 ..     335     350 ..     331     357 .. 0.75
   6 ?    2.2   0.2     0.062   3.7e+02      14      37 ..     376     400 ..     363     401 .] 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0037
                                        EESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   7 ltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                        +  H++ v+s++  + +++l++++ Dg+ ++++
  gene1031|gene1031|rna1030|rna1030 112 FHDHKDmVSSVSLFRRHKLLLTSGLDGKAYLYN 144
                                        5568889*****8888888888888**999987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00052
                                        EEEEEEESS.SSEEEEEEETTSSEEEEE.ETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasG.sdDgtvriWd 38 
                                        ++++t+ GH ++v+s   s   + ++   s Dg +++Wd
  gene1031|gene1031|rna1030|rna1030 149 DLVTTYMGHsKGVSSATLSECESKFS-TiSFDGFLKVWD 186
                                        6789999**999*9997666666664.3355*******9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.35
                                        EEEEEEETTSSEEEEEETTSEEE CS
                               WD40  13 vtslafspdgawlasGsdDgtvr 35 
                                         t+++f   g+ ++ G+ Dg +r
  gene1031|gene1031|rna1030|rna1030 202 LTCQSFKELGKAVFIGGLDGRIR 224
                                        588877777777888999**998 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.92
                                        EEEESS.SS...EEEEEEETTSSEE.EEEETT CS
                               WD40   5 rtltGH.ss...vtslafspdgawl.asGsdD 31 
                                        r+ ++H +s   + +l  +p+ + l +++s D
  gene1031|gene1031|rna1030|rna1030 284 RIVKTHnGScsfI-GL--NPEENTLmITAS-D 311
                                        5566774333345.55..555555425777.6 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.48
                                        EEEEEETTSSEEEEEE CS
                               WD40  14 tslafspdgawlasGs 29 
                                        t ++ spdg++l+ G+
  gene1031|gene1031|rna1030|rna1030 335 TRVKASPDGSMLCFGD 350
                                        568889****995454 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.062
                                        EEEE.EETTSSEEEEEETTSEEEEE CS
                               WD40  14 tsla.fspdgawlasGsdDgtvriW 37 
                                        t ++  + +++ l+sG+  g++++W
  gene1031|gene1031|rna1030|rna1030 376 TTIDwIDGSSSSLVSGDVLGNIKVW 400
                                        666333444444899999******* PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-06    0.0074     235     259 ..     175     199 ..     149     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-06
                                        EEETT-EEEEEETTTTEEEEEEE-- CS
                             Nup160 235 alsrdgkLrvWnlltgkclatidll 259
                                        ++s dg+L+vW+++tg+c a idl 
  gene1031|gene1031|rna1030|rna1030 175 TISFDGFLKVWDIETGRCNAKIDLE 199
                                        899********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2577.62
//
Query:       gene1032|gene1032|rna1031|rna1031  [L=295]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.028   14.1   9.2      0.037   13.7   9.2    1.1  1  Use1            Membrane fusion protein Use1
       0.32   10.8  12.1       0.48   10.2  12.1    1.3  1  SpoIIIAH        SpoIIIAH-like protein
        1.4    8.9   5.9        1.8    8.6   5.9    1.2  1  Neur_chan_memb  Neurotransmitter-gated ion-channel transmembr
        7.9    5.3  10.0         10    4.9  10.0    1.2  1  XRN_M           Xrn1 helical domain
        8.2    4.6  20.0         12    4.0  20.0    1.3  1  CDC45           CDC45-like protein
        9.8    5.0   9.3         15    4.4   9.3    1.2  1  DUF913          Domain of Unknown Function (DUF913)


Domain annotation for each model (and alignments):
>> Use1  Membrane fusion protein Use1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   9.2   1.2e-05     0.037      65     191 ..     149     287 ..     127     290 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                               Use1  65 kllleaeklssteekalanqllapg.................eeskeekeeskereeaskelrqkekakyqkel.r 122
                                        k+   + ++s ++ +a  + +   +                  +++eek +s++++ + ++ +q+ +++ +ke+  
  gene1032|gene1032|rna1031|rna1031 149 KDRCGYLEKS-KKVRAEGEDK---SshpeddtkgkdegggpkMNQDEEKISSETTDYSEPGCHQNVEKEDKKEDeE 220
                                        5555554444.1112211111...1122455555555556544555566666666777789998866665555404 PP

                               Use1 123 kellgkndsssspekekeskkkksdedldavlkkhenlqEklaeemlsLarnLKenslaasqiikkDte 191
                                        ke+ +k+d++++++k+k++ k + de+l+ +++k + ++  +   m  L  +LK +  +a+ i+k D++
  gene1032|gene1032|rna1031|rna1031 221 KEDKEKEDKEKEEKKKKSHAKGNDDESLEDIIEKVRFKRPRIKKKMKRLGSSLKRK--LAKAILKVDKK 287
                                        5555555555555555555566********************************85..78889998886 PP

>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  12.1   0.00016      0.48      30     118 ..     186     267 ..     152     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXX--HHHH CS
                           SpoIIIAH  30 aetaeteqeesekaeigddkekdessaasaeaesssetesesseksdiassdedeadeltsetasaaasasdyfae 105
                                        + ++++e+ +se++++++        ++ +++++++++e+e++ek+d+++++++++   + +++++++s +d++++
  gene1032|gene1032|rna1031|rna1031 186 KMNQDEEKISSETTDYSE----PGCHQNVEKEDKKEDEEKEDKEKEDKEKEEKKKK---SHAKGNDDESLEDIIEK 254
                                        222333333333333333....2333344444445555555555555555555544...56666677899****** PP

                                        HHHHHHHHHHHHH CS
                           SpoIIIAH 106 akleReqkrsknk 118
                                        ++ +R ++  k+k
  gene1032|gene1032|rna1031|rna1031 255 VRFKRPRIKKKMK 267
                                        ******9999987 PP

>> Neur_chan_memb  Neurotransmitter-gated ion-channel transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.9    0.0006       1.8     122     203 ..     171     267 ..     127     286 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0006
                                        ..............-------------------..-------------------SS---TTGGG--........-- CS
                     Neur_chan_memb 122 l.............ssgasseaeelilskskse..skkaklseeqgsekastckckckegeeaspstqlsk...ee 179
                                                      +   +++++e + s++ ++   + ++++ e++++k++++k +++++ + ++++++++    +
  gene1032|gene1032|rna1031|rna1031 171 HpeddtkgkdegggP---KMNQDEEKISSETTDysEPGCHQNVEKEDKKEDEEKEDKEKEDKEKEEKKKKShakGN 243
                                        123333333332221...2222222222222222367788888877777777777766555555544444456566 PP

                                        ---TTTTTHHHHHHHHHHHHHHHH CS
                     Neur_chan_memb 180 lspelkkavegvkyiadhlraede 203
                                          ++l++++e+v++ + +++++ +
  gene1032|gene1032|rna1031|rna1031 244 DDESLEDIIEKVRFKRPRIKKKMK 267
                                        6678999******99999888765 PP

>> XRN_M  Xrn1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9  10.0    0.0035        10      98     172 ..     186     260 ..     142     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0035
                              XRN_M  98 eeaskedaaneeaavaeeklseskvaksaeaeaeaeaeaeaeakaekekrekaekeleeseeeeeeeDkvrLgee 172
                                        +++++e++ ++e++   e+  +++v+k++++e e+++  e+e k+++ek++k +++ +++e+ e+  +kvr   +
  gene1032|gene1032|rna1031|rna1031 186 KMNQDEEKISSETTDYSEPGCHQNVEKEDKKEDEEKEDKEKEDKEKEEKKKKSHAKGNDDESLEDIIEKVRFKRP 260
                                        334444444455555555555666666888888888888888888888899999999999999999999998766 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  20.0    0.0042        12     137     213 ..     192     278 ..     140     293 .. 0.37

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0042
                              CDC45 137 e...............eeeeeddddeeeeeeeeedeedeeedeeeskkkrksksdeeee...sddddersrkrrrs 194
                                        e               ++ e++d   ++e+ee+ed+e+  ed+e+++kk+ks+++ +++   +d  ++ + kr r 
  gene1032|gene1032|rna1031|rna1031 192 EkissettdysepgchQNVEKED---KKEDEEKEDKEK--EDKEKEEKKKKSHAKGNDDeslEDIIEKVRFKRPRI 262
                                        01111111222222211111111...111111111112..222222222222222222212333333333333333 PP

                              CDC45 195 epsakklrrqlkkerrkye 213
                                        +   kk++r   +++rk  
  gene1032|gene1032|rna1031|rna1031 263 K---KKMKRLGSSLKRKLA 278
                                        3...344444333333333 PP

>> DUF913  Domain of Unknown Function (DUF913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   9.3     0.005        15     247     328 ..     159     253 ..     149     257 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.005
                             DUF913 247 arvvelgkekaakllved.............assasskseasssssssetkeeek..................sse 291
                                        ++v++ g++k+    +ed             +                 ++ee+                   +++
  gene1032|gene1032|rna1031|rna1031 159 KKVRAEGEDKS--SHPEDdtkgkdegggpkmN-----------------QDEEKIssettdysepgchqnvekEDK 215
                                        56777777777..2222234433333332220.................111111333334444556666655555 PP

                             DUF913 292 dedvemedaeeetesesdeseeseee.keknslldyil 328
                                        +ed+e+ed+e+e++++++++++s+++ ++++sl d i 
  gene1032|gene1032|rna1031|rna1031 216 KEDEEKEDKEKEDKEKEEKKKKSHAKgNDDESLEDIIE 253
                                        55556666655555555555555555455555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2385  (0.133025); expected 358.6 (0.02)
Passed bias filter:                      870  (0.0485247); expected 358.6 (0.02)
Passed Vit filter:                       209  (0.0116571); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.82u 0.35s 00:00:01.17 Elapsed: 00:00:00.53
# Mc/sec: 1673.05
//
Query:       gene1033|gene1033|rna1032|rna1032  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-21   75.5   0.0    5.2e-21   75.0   0.0    1.2  1  Proteasome      Proteasome subunit
    1.1e-09   37.7   0.2    1.9e-09   37.0   0.2    1.4  1  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   5.7e-25   5.2e-21      23     164 ..      47     184 ..      27     202 .. 0.86

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 5.7e-25
                                        EEEETTEEEESSSSTSEEEEETT..EEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHH CS
                         Proteasome  23 ratagskllskstveKifkiddh..igvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqayt 96 
                                        r + g+kl  ++  eK+f +++   i+++++G  +Da  +++ ar+ + +y++++g++i +++l++++++++q+yt
  gene1033|gene1033|rna1032|rna1032  47 RKS-GNKLFLEE--EKVFLLNEAqcIWMSYSGFKPDAYLVMNVARMMCLSYKISTGEDIAIDQLARKLSEYKQRYT 119
                                        333.68997777..8*****6543399************************************************* PP

                                        HHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHH CS
                         Proteasome  97 qrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeav 164
                                          +++rpfgv++++ g+    +p  y i+p+G++ e   + aiG++s+ + ++lek+ kedl +  ++
  gene1033|gene1033|rna1032|rna1032 120 VVYHQRPFGVRTVLFGLE--PRPVAYVIEPDGNFSEF-FCGAIGQKSQRVCEYLEKKEKEDLVKLTIL 184
                                        *****************9..5699*************.7*****99***********97776554444 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.2   2.1e-13   1.9e-09       4      23 .]       6      25 ..       3      25 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.1e-13
                     Proteasome_A_N  4 slttFSPdGRLfQVEYAmkA 23
                                        l +FSPdGRL QVEYA++A
  gene1033|gene1033|rna1032|rna1032  6 QLAVFSPDGRLIQVEYAQQA 25
                                       588***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1453.07
//
Query:       gene1034|gene1034|rna1033|rna1033  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.6e-13   48.5   0.5    4.7e-12   45.7   0.5    1.9  1  NAD_kinase  ATP-NAD kinase
     0.0025   17.4   0.0      0.004   16.8   0.0    1.3  1  DAGK_cat    Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.095   12.9   0.0        8.6    6.6   0.0    2.8  2  PK_C        Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.5   7.8e-16   4.7e-12      79     266 ..      35     202 ..      13     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 7.8e-16
                                        SSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEETTE. CS
                         NAD_kinase  79 vdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrskge 154
                                         d iiv+GGDGT+l+     ++  + v +vn+G++gfl  ++  a++el+ +l +g  r+e+ ev +  ++ sk+ 
  gene1034|gene1034|rna1033|rna1033  35 YDGIIVLGGDGTVLRTIASYRN-PPAVYAVNRGRVGFLCPIPHTAIDELIGRLRNG-KRIELVEVKR--LCLSKK- 105
                                        588***************9996.777***************************993.3555555544..555666. PP

                                        .....EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEE CS
                         NAD_kinase 155 ediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailiv 230
                                                 ++ ln+ vi + ++  l ++++ +d+  l +++ d +iv+t tGs ay  s +gpl+  +     + 
  gene1034|gene1034|rna1033|rna1033 106 ---------HYFLNDAVIRPSSIG-LGTFKIFIDDISL-VLRGDAVIVATKTGSSAYNASLNGPLLLNEGMV--VN 168
                                        .........567999998776654.667*****99776.79************************9988777..67 PP

                                        EESESSS----EEE-TT-EEEEEE-SS--EEEEETT CS
                         NAD_kinase 231 picPhslssrpiVvssssklrirvasrseallaldG 266
                                         + P   +++piV     ++r++v  +++a ++ldG
  gene1034|gene1034|rna1033|rna1033 169 VVAPNNCRFKPIVCGIGTRVRVEV--DRDAQIILDG 202
                                        77899*************999775..5555555565 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.7e-07     0.004      39      71 ..       8      50 ..       3      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.7e-07
                                       -STTHHHHHHHHHHHC..........C-SEEEEEESHHHHHHH CS
                           DAGK_cat 39 eepgdakelakeakee..........gvdlivvaGGDGtvsev 71
                                       +++g   el+++++++          ++d+i+v+GGDGtv   
  gene1034|gene1034|rna1033|rna1033  8 TKNGNDAELVEKIRHSldchtldqgiEYDGIIVLGGDGTVLRT 50
                                       4456667888888887777777777899***********9655 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.02   1.2e+02      15      46 ..      34      65 ..       3     107 .. 0.77
   2 ?    6.6   0.0    0.0014       8.6      16      33 ..     137     154 ..     130     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.02
                                       T-SEEEEE-SSSHHHHHHHHT-TSSEEEEEES CS
                               PK_C 15 gakaIvvltesGetArliskyrpkvpiiavtp 46
                                       + + I+vl   G+  r i+ yr    ++av +
  gene1034|gene1034|rna1033|rna1033 34 EYDGIIVLGGDGTVLRTIASYRNPPAVYAVNR 65
                                       44567888888888888888888777777755 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0014
                                        -SEEEEE-SSSHHHHHHH CS
                               PK_C  16 akaIvvltesGetArlis 33 
                                         +a++v+t++G++A  +s
  gene1034|gene1034|rna1033|rna1033 137 GDAVIVATKTGSSAYNAS 154
                                        579***********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1543.31
//
Query:       gene1035|gene1035|rna1034|rna1034  [L=416]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-22   79.7   0.0      5e-22   78.5   0.0    1.5  1  DEAD        DEAD/DEAH box helicase
    4.9e-13   49.4   0.1    1.6e-11   44.6   0.0    2.9  3  Helicase_C  Helicase conserved C-terminal domain
     0.0023   18.0   0.0      0.004   17.2   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
     0.0038   17.0   0.0     0.0081   15.9   0.0    1.5  1  NIF         NLI interacting factor-like phosphatase
  ------ inclusion threshold ------
      0.025   14.5   0.1      0.061   13.3   0.0    1.6  2  Flavi_DEAD  Flavivirus DEAD domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   1.4e-25     5e-22       3     173 ..      51     230 ..      50     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.4e-25
                                        HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                        +Q+ +ip +l++ +v+v+a TGsGKTl +++p+++      +k+    +i++P ++L++q+++ ++++k++ +l+v
  gene1035|gene1035|rna1034|rna1034  51 VQRIVIPYFLKKTNVVVQAFTGSGKTLSYCLPLVEMA----RKESLFGMILVPGKALVRQVYRVVNEIKHE-GLEV 121
                                        799*******************************777....89***************************5.3444 PP

                                        EEEETT......................SSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHH CS
                                        xxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  79 lliigg......................vaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadr 132
                                        ++ + +                       ++++  ++++++++i++gtp   + l+      +++++ lV+DEad 
  gene1035|gene1035|rna1034|rna1034 122 VAGYRDgeedflieedekgglaergvdcRSKEKIERAFQSDAKILIGTPLSALGLMPMSG--TRSITHLVIDEADL 195
                                        43333223333333344445666666555666666666788**********999996566..899*********** PP

                                        HHHTTTHHHHHHHHHHSHHHCTTST.TTSEEEEEESSBSHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                               DEAD 133 lldqgfsdfinrilnqlpqitcdgk.lqrqvivlSATlpkdv 173
                                        l + g  +   +il+++       + ++ ++ ++SAT+++ v
  gene1035|gene1035|rna1034|rna1034 196 LINPGTVEVFGSILREI-------EvENAHIGCFSATMNEYV 230
                                        *****************.......224455********9776 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.55     2e+03      55      82 ..     118     149 ..     106     153 .. 0.84
   2 ?    0.6   0.0      0.19     7e+02      53      80 ..     150     176 ..     144     177 .. 0.83
   3 !   44.6   0.0   4.3e-15   1.6e-11      56     109 ..     311     364 ..     261     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.55
                                        HHHHHHHHHTTSSSEEEESGG....GTSSSTS CS
                         Helicase_C  55 reeileqfnkgesdvLiatdv....aerGidi 82 
                                         +e+++ +++ge d+Li  d     aerG+d 
  gene1035|gene1035|rna1034|rna1034 118 GLEVVAGYRDGEEDFLIEEDEkgglAERGVDC 149
                                        56888889999999999999888889999985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                                        HHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                         Helicase_C  53 nereeileqfnkgesdvLiatdvaerGi 80 
                                        +++e+i ++f + + ++Li t   + G+
  gene1035|gene1035|rna1034|rna1034 150 RSKEKIERAF-QSDAKILIGTPLSALGL 176
                                        578999999*.7799*****98877775 PP

  == domain 3  score: 44.6 bits;  conditional E-value: 4.3e-15
                                        HHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                         Helicase_C  56 eeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                         e+l++f+ +++ +L  td ++rG+d+ +++ +in+dlp++ t++++r+GR+ R
  gene1035|gene1035|rna1034|rna1034 311 GEVLDAFRLKKIWYLFGTDSLSRGVDFYNIRSIINYDLPDTKTQFVHRVGRINR 364
                                        589*****99*****************************************999 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06     0.004      23     111 ..      61     170 ..       9     204 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                                        TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG............GEEEES CS
                             ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke........igkkvs 90 
                                        +++++++++ TG+GKTl ++    ++++k++    ++lvp+k+l+ q ++ ++++++e  +         +     
  gene1035|gene1035|rna1034|rna1034  61 KKTNVVVQAFTGSGKTLSYCLPLVEMARKESL-FGMILVPGKALVRQVYRVVNEIKHEGLEVvagyrdgeE----- 130
                                        577899*************6666666665443.55789***********7776655555443222332220..... PP

                                        SS-B--.............................-SEEEEEH CS
                             ResIII  91 gdkkka......................kekdstnkkilvtti 111
                                           +                        ++ +++++kil+ t 
  gene1035|gene1035|rna1034|rna1034 131 ---DFLieedekgglaergvdcrskekiERAFQSDAKILIGTP 170
                                        ...2111122222222223333333334466777777777665 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.3e-06    0.0081      47     101 ..     214     275 ..     204     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-06
                                NIF  47 sklyevvifTasseeyaeavidil.dpekkl.lshrlyrescvkkkgeyvKdLsll.....g 101
                                        ++++ ++ f+a+++ey+ +vi+ + d +k + +s+rl  ++ v+ +++ +K Lsll     g
  gene1035|gene1035|rna1034|rna1034 214 VENAHIGCFSATMNEYVGEVIETVkDITKVYvMSKRLIDHEFVFGTSKKIKHLSLLqiiadG 275
                                        578999******************99999998889999999987799*******99444432 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.7e-05     0.061       3      55 ..      61     113 ..      59     123 .. 0.91
   2 ?   -3.0   0.0       1.8   6.5e+03      97     135 ..     186     225 ..     175     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                        X--EEEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTT CS
                         Flavi_DEAD   3 kkkltvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkg 55 
                                        kk+  v++++ G+Gkt  +   lv+ a ++ l  ++L+P +  ++ +++ +++
  gene1035|gene1035|rna1034|rna1034  61 KKTNVVVQAFTGSGKTLSYCLPLVEMARKESLFGMILVPGKALVRQVYRVVNE 113
                                        788899************************************99999988776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                                        SEEEEETTT-.-SHHHHHHHHHHHHHHHTTS-EEEEEESS CS
                         Flavi_DEAD  97 eliimDeahf.lDPasiaarGyletkaeegeaalilltat 135
                                        + +++Dea   ++P  + + G + ++ e ++a +  ++at
  gene1035|gene1035|rna1034|rna1034 186 THLVIDEADLlINPGTVEVFGSILREIEVENAHIGCFSAT 225
                                        4567888875268888888888888777777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2520.59
//
Query:       gene1036|gene1036|rna1035|rna1035  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1078.76
//
Query:       gene1037|gene1037|rna1036|rna1036  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0069   16.6   0.1      0.011   15.9   0.1    1.3  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
  ------ inclusion threshold ------
      0.042   14.4   1.3       0.07   13.7   1.3    1.3  1  Rotamase_3      PPIC-type PPIASE domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.3e-06     0.011      28      85 ..      90     142 ..      79     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                                        EEE-TSCCGGGEEEEETTSEEEETT.TTEEEEESSSSTTSBEEEEETTTTSGGGCEEE CS
                     Ricin_B_lectin  28 lydChgskgkQlwtltkdgeirskaqselCldvsstaegakvvlakChkgkgnqrWef 85 
                                        l +C ++ + ++w++t+ g+  + +q+++Cl++   + +++++l++C++ + + ++ f
  gene1037|gene1037|rna1036|rna1036  90 LSKCADN-T-DFWEITRSGDGFTISQEGYCLST---EGKGRLILERCNGRSRSHLFLF 142
                                        5666666.4.67777755544444457777754...5667777777775444666555 PP

>> Rotamase_3  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.3   7.8e-06      0.07      15      65 ..     164     212 ..     156     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-06
                         Rotamase_3  15 svkvshIlistkgkesrseeeakakadsllaalkegadFaalAkeySdDpa 65 
                                        + kv+++ ++   k ++ +++ +aka+++ ++l+e++dF++ Ak++  D +
  gene1037|gene1037|rna1036|rna1036 164 AEKVKQLKLKK--KLDDLKKKDRAKAEKIKKKLEEKNDFEKYAKKNLPDLT 212
                                        55677776665..557788899**********************9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1851  (0.103241); expected 358.6 (0.02)
Passed bias filter:                      896  (0.0499749); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1651.44
//
Query:       gene1038|gene1038|rna1037|rna1037  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.18   10.7   0.0        2.1    7.2   0.0    2.1  2  Transketolase_N  Transketolase, thiamine diphosphate binding 


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00012       2.1      22      61 ..      34      73 ..      27      80 .. 0.90
   2 ?    1.6   0.0     0.006   1.1e+02     174     198 ..      75      99 ..      73     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00012
                                       -S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEES CS
                    Transketolase_N 22 sGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLs 61
                                       s +P  +lg+ +   vl ++ + +nP++ k+i R R v s
  gene1038|gene1038|rna1037|rna1037 34 SSYPAQVLGMEENNGVLVSHSKYVNPSKYKFITRARLVRS 73
                                       7789*********************************988 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.006
                                        TTEEEEEEESSEETTEEGGGT--S- CS
                    Transketolase_N 174 gkLivlyDdnkisidGeteisfted 198
                                        +k +v++ +n+i+ dG+  i  +e+
  gene1038|gene1038|rna1037|rna1037  75 DKYVVIFGENNICKDGNSVIKCKEE 99 
                                        6899************998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1933.65
//
Query:       gene1039|gene1039|rna1038|rna1038  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00037   20.5   0.1     0.0005   20.1   0.1    1.2  1  SNAPc_SNAP43  Small nuclear RNA activating complex (SNAPc), s
  ------ inclusion threshold ------
      0.074   12.0   0.0      0.088   11.8   0.0    1.2  1  DUF2434       Protein of unknown function (DUF2434)


Domain annotation for each model (and alignments):
>> SNAPc_SNAP43  Small nuclear RNA activating complex (SNAPc), subunit SNAP43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   5.5e-08    0.0005      31     151 ..      38     163 ..      32     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.5e-08
                       SNAPc_SNAP43  31 kfslifegrqnaaeliefteellqvalkymls...prslqeRigglYlLYslYntQptkpkvkIrlslkewrellk 103
                                        +++ +f   +n +++  f++ +++ + + +l+   ++ ++e +  + +LY ++ +Q     + +++sl++++++ +
  gene1039|gene1039|rna1038|rna1038  38 NLEGLFGIYKNPEQQVVFMRTIYKQITREILKflsSKCISEAMVSICILYEMFKSQR--GYIDVEMSLEDVECINQ 111
                                        67889999999*************9988665433388*******************9..78*************** PP

                       SNAPc_SNAP43 104 flqelkeekhldvaa....ilkkLlkekaFrftafeltedpatlkryekeee 151
                                        ++ +l +++++d++     +   L ++ka+r++ + +  d ++l + eke e
  gene1039|gene1039|rna1038|rna1038 112 YVYSLGKKENTDIIWegvrAWGCLKRKKAIRICMMPFPDDEQSLMVIEKELE 163
                                        *****9999998754222267779999******9988888888877777665 PP

>> DUF2434  Protein of unknown function (DUF2434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.8e-06     0.088     121     161 ..     108     148 ..      60     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.8e-06
                            DUF2434 121 vltsffwylllpatlavvWeavrhwGswqerqlidqdpfal 161
                                        ++++ +++l       ++We vr wG +++++ i    + +
  gene1039|gene1039|rna1038|rna1038 108 CINQYVYSLGKKENTDIIWEGVRAWGCLKRKKAIRICMMPF 148
                                        6778889999999999**************99987655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1194.32
//
Query:       gene1040|gene1040|rna1039|rna1039  [L=422]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.4   5.1      0.095   12.6   0.8    2.4  3  PIP49_N   N-term cysteine-rich ER, FAM69


Domain annotation for each model (and alignments):
>> PIP49_N  N-term cysteine-rich ER, FAM69
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.021   3.7e+02      15      32 ..     198     215 ..     174     225 .. 0.86
   2 ?   -3.7   0.0      0.52   9.3e+03      44      54 ..     295     305 ..     268     310 .. 0.66
   3 ?   12.6   0.8   5.3e-06     0.095      23      77 ..     330     387 ..     321     420 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.021
                            PIP49_N  15 llavavlswvvYvqyssy 32 
                                        +++++v s +vY++y  y
  gene1040|gene1040|rna1039|rna1039 198 MVVIVVTSGIVYMEYGGY 215
                                        578889999999999888 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.52
                            PIP49_N  44 kvnkiCdkyrk 54 
                                        k +++C  yrk
  gene1040|gene1040|rna1039|rna1039 295 KEMILCRLYRK 305
                                        34667777766 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 5.3e-06
                            PIP49_N  23 wvvY..vqyssyselCrgleverkvnkiCdkyrkgiisGslCeeLCeketlselk.Cl 77 
                                        +++Y   +   y  +C + + e +++ i ++yr  ++  ++C+ L  ++ l+ ++ C+
  gene1040|gene1040|rna1039|rna1039 330 VIIYfpEEMERYIRMCIEEKREYEIEEIIEHYRGSEMIERICQILLRNNCLYLFSlCM 387
                                        55665545568*****************************************655153 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2988.06
//
Query:       gene104|gene104|rna104|rna104  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-40  136.6   0.3    8.7e-40  136.3   0.3    1.0  1  Guanylate_kin    Guanylate kinase
      7e-07   29.5   0.3      0.039   14.1   0.1    2.6  2  AAA_33           AAA domain
    1.9e-06   28.5   0.5      5e-06   27.1   0.4    1.7  1  AAA_18           AAA domain
    0.00012   22.5   0.4     0.0037   17.7   0.2    2.6  2  AAA_17           AAA domain
    0.00029   20.9   0.1    0.00052   20.1   0.1    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
    0.00057   19.6   0.2     0.0012   18.6   0.2    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0011   18.7   0.4       0.22   11.2   0.4    2.2  1  Thymidylate_kin  Thymidylate kinase
     0.0022   18.2   0.2      0.014   15.6   0.2    2.1  1  AAA_22           AAA domain
     0.0026   17.7   0.0     0.0046   16.9   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0031   17.0   0.0     0.0062   16.1   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0042   17.5   0.1     0.0071   16.8   0.1    1.7  1  AAA_16           AAA ATPase domain
     0.0061   17.1   0.9     0.0088   16.6   0.9    1.7  1  ABC_tran         ABC transporter
     0.0069   16.3   0.2      0.012   15.6   0.0    1.6  2  NTPase_1         NTPase
     0.0095   15.9   0.0      0.077   13.0   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.026   14.9   0.4      0.095   13.1   0.0    2.0  2  RNA_helicase     RNA helicase
      0.028   13.7   0.0        5.2    6.3   0.0    2.2  2  Zeta_toxin       Zeta toxin
      0.032   14.0   0.5       0.41   10.3   0.1    2.3  2  AAA_24           AAA domain
      0.032   14.1   0.1       0.38   10.6   0.0    2.1  2  APS_kinase       Adenylylsulphate kinase
      0.035   13.7   0.0      0.069   12.7   0.0    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.035   14.0   0.0      0.067   13.1   0.0    1.5  1  Rad17            Rad17 P-loop domain
      0.036   13.9   0.0      0.052   13.3   0.0    1.3  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.037   13.9   3.8       0.68    9.8   0.9    2.3  2  dNK              Deoxynucleoside kinase
      0.039   14.4   0.1       0.25   11.8   0.0    2.0  2  AAA              ATPase family associated with various cellul
      0.042   13.6   1.4      0.098   12.4   0.2    1.9  2  Endotoxin_N      delta endotoxin, N-terminal domain
       0.05   13.6   1.4        1.1    9.3   0.0    2.3  2  AAA_14           AAA domain
      0.051   13.6   0.6       0.13   12.3   0.1    1.9  2  ThiS-like        ThiS-like ubiquitin
      0.058   12.6   0.0       0.12   11.6   0.0    1.4  1  NB-ARC           NB-ARC domain
       0.06   12.4   0.0      0.083   11.9   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.074   13.1   1.5       0.16   12.0   1.5    1.7  1  Dynamin_N        Dynamin family
      0.082   12.6   0.0          2    8.1   0.0    2.1  2  CoaE             Dephospho-CoA kinase
       0.11   13.0   5.8        0.3   11.6   5.8    1.8  1  AAA_23           AAA domain
       0.13   12.4   0.0       0.34   11.1   0.0    1.7  1  Thioredoxin_7    Thioredoxin-like
       0.15   12.3   0.0       0.35   11.1   0.0    1.7  2  AAA_28           AAA domain


Domain annotation for each model (and alignments):
>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3   0.3   1.6e-42   8.7e-40       5     181 ..       7     180 ..       4     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 1.6e-42
                                    EEEESTTTSSHHHHHHHHHHHSTTTEEE--EEESS---TTS-TTTSEEE--HHHHHHHHHTTTEEEEEEETTEEEEEEHH CS
                  Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekfgvsvshtTrdprkgevdGkdYyFvskeemekdiskneflEaaefsgnlygtsve 84 
                                    +v  gpsg Gks++++++ls++p  f++svshtTr+prkgev+GkdY+Fvs++e+e+++ ++eflE+ +++gn+ygt v+
  gene104|gene104|rna104|rna104   7 LVFTGPSGSGKSTIISHILSKFP--FKFSVSHTTRAPRKGEVNGKDYHFVSTKEFEEMVRNQEFLEYVQYNGNYYGTGVS 84 
                                    7999******************9..6679***********************************************9765 PP

                                    HHHHHHHTTSEEEEE--CHHHHHHHHTTTTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHGGG.CSSEEE CS
                  Guanylate_kin  85 aieevlekgkiviLDvdiqavkqlrkaelspiivFikppslkelqrrlksrgkeqeeklakrlaaaekelqey.efdvvi 163
                                       +  +++k+v+LD + ++v   +k  ++ +i++i+   + + +r+ k++g+++e+ ++ r++  e+  +     d+vi
  gene104|gene104|rna104|rna104  85 ---QLKNSQKTVLLDLEYEGVLYCKKNYPNFVILYIHCDKNVARERLEKRMGNKSEKDIEARMSLYEAFNSIKdKCDYVI 161
                                    ...6667999**************************9999999999999**************998877666644***** PP

                                    EE.SSHHHHHHHHHHHHHH CS
                  Guanylate_kin 164 vn.ddleealkklkellea 181
                                    +n  +le++  +++e++++
  gene104|gene104|rna104|rna104 162 DNtHSLEKSKGEVEEIISK 180
                                    *9458**********9986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   7.2e-05     0.039       3      25 ..       8      30 ..       7      90 .. 0.83
   2 !   13.1   0.0   0.00014     0.078      99     132 ..     112     146 ..     100     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.2e-05
                         AAA_33  3 llvGlpGsGKstlaerllkklga 25
                                   ++ G++GsGKst + ++l k ++
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSKFPF 30
                                   799************99988774 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00014
                         AAA_33  99 vrivvvetdeetlkeRlakRaang.ddrsevpeea 132
                                    + i+++++d  +++eRl+kR+ n+ ++++e+ ++ 
  gene104|gene104|rna104|rna104 112 FVILYIHCDKNVARERLEKRMGNKsEKDIEARMSL 146
                                    689*******************9756666666654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.4   9.2e-09     5e-06       3     121 ..       9     139 ..       7     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 9.2e-09
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf..............gvnlrdvakenglllevdpealdeskrldedkldklldaleens 68 
                                     tG++G+GK+t+  ++ ++  f               vn +d+++ +  ++e+     +e+++ ++ + ++  +++ +  
  gene104|gene104|rna104|rna104   9 FTGPSGSGKSTIISHILSKFPFkfsvshttraprkgEVNGKDYHFVSTKEFEEMVR-NQEFLEYVQYNGNYYGTGVSQLK 87 
                                    79*************98887667777777777777766666666664444443333.55677777777777777777765 PP

                         AAA_18  69 saleegknlvidghlaeleseaakdikk.....vvLtaspeelleRlekRgyeeakik 121
                                    +   ++k++++d   +  ++ +     +      ++++++++ +eRlekR  ++ ++ 
  gene104|gene104|rna104|rna104  88 N---SQKTVLLDLEYEGVLYCKKN---YpnfviLYIHCDKNVARERLEKRMGNKSEKD 139
                                    4...55665665555554444333...1345889****************98776643 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   6.7e-06    0.0037       1     128 [.      10     139 ..      10     147 .. 0.63
   2 ?   -0.6   0.0         3   1.6e+03      61      94 ..     149     179 ..     133     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.7e-06
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghp 80 
                                    +G+ GsGK+t+++++  k+ f++ s +   r+  k +  +k+ + +++ + ee     +e  e ++    ++++  +g  
  gene104|gene104|rna104|rna104  10 TGPSGSGKSTIISHILSKFPFKF-SVSHTTRAPRKGEVNGKDYHFVSTKEFEEMV-RNQEFLEYVQY---NGNYYGTGVS 84 
                                    69*******************96.6699999986555434444444333333333.34445555554...6788888888 PP

                                    EEEETTEE.EESSHHHH...HHHH..SE.EEEEE--HHHHHHHHHHH..TTST-T CS
                         AAA_17  81 rikeqagf.ldglpkev...leelkpda.iilleadpeeilerrlkd..rtrgrd 128
                                     +k++++  l +l+ e    +++  p++ i+++++d+ + +er+ k+   +++ d
  gene104|gene104|rna104|rna104  85 QLKNSQKTvLLDLEYEGvlyCKKNYPNFvILYIHCDKNVARERLEKRmgNKSEKD 139
                                    7776655435666644434446666766255699999988888888843334444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3
                                    HHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHH CS
                         AAA_17  61 aaekiaeeakkkgvlvdghprikeqagfldglpk 94 
                                    a ++i+   +k ++++d   ++++++g+++++ +
  gene104|gene104|rna104|rna104 149 AFNSIK---DKCDYVIDNTHSLEKSKGEVEEIIS 179
                                    333444...4456888888888888888777655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   9.6e-07   0.00052       2      53 ..       7      56 ..       6     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.6e-07
                                   EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEEC CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDt 53
                                    ++ G + +GKSt+i+ ++ +     +   tTr +++g+v+  gk++++v t
  gene104|gene104|rna104|rna104  7 LVFTGPSGSGKSTIISHILSKFPFKFSVSHTTRAPRKGEVN--GKDYHFVST 56
                                   5799*****************777778899**********9..778877755 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   2.1e-06    0.0012      25      39 ..       7      21 ..       1      26 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                         AAA_29 25 tlltGpsGsGKSTll 39
                                    ++tGpsGsGKST++
  gene104|gene104|rna104|rna104  7 LVFTGPSGSGKSTII 21
                                   679***********9 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.4    0.0004      0.22       3     180 ..      11     169 ..       9     174 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                                    ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH...TCS---HHHHHHHHHHHHHHTTHHHHHHHHHT CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelll...keeeleeqteallfaadriehleekikpalkq 79 
                                    G  G+GK+t++  + ++++ +    ++tr p+++e+  k  + ++   +ee + +q ++ +   +  +  + + + +++ 
  gene104|gene104|rna104|rna104  11 GPSGSGKSTIISHILSKFPFKFSVSHTTRAPRKGEVNGKDYHFVStkeFEEMVRNQEFLEYVQYNGNYYGTGVSQLKNS- 89 
                                    5566777777777777776666446666666666665555555553322333333333333333332222222222222. PP

                                    T-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SE.EEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHH CS
                Thymidylate_kin  80 gktvivdRylfSslaYqgakegvdldlvlslnedvllkPdl.tflldvdpevalkRlakrdeldeeeeeqldflrkvrer 158
                                    +ktv +d      l Y+g         vl  +++    P + ++++ +d++va +Rl+kr    ++ e++++   ++ e 
  gene104|gene104|rna104|rna104  90 QKTVLLD------LEYEG---------VLYCKKN---YPNFvILYIHCDKNVARERLEKRMG--NKSEKDIEARMSLYEA 149
                                    2444444......22222.........2222222...2343045677888888888888888..6667777777777776 PP

                                    HHHHHHTTSTEEEEETTS-HHH CS
                Thymidylate_kin 159 ylelakederiliidasksiee 180
                                    ++++   d+  ++id ++s+e+
  gene104|gene104|rna104|rna104 150 FNSIK--DKCDYVIDNTHSLEK 169
                                    66666..444455666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   2.6e-05     0.014       7      30 ..       6      29 ..       3     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                   +lv tG+sG+GK+t +  +l++++
  gene104|gene104|rna104|rna104  6 HLVFTGPSGSGKSTIISHILSKFP 29
                                   7899*************9999986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.4e-06    0.0046     101     123 ..       6      28 ..       1      63 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.4e-06
                                    EEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinallpel 123
                                      v+ G+SG GKSt+i ++l++ 
  gene104|gene104|rna104|rna104   6 HLVFTGPSGSGKSTIISHILSKF 28 
                                    579****************9974 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05    0.0062      34      61 ..       5      31 ..       1      41 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldkek 61
                                    +++++Gp+G+GK++ii+++l+k++  k
  gene104|gene104|rna104|rna104  5 VHLVFTGPSGSGKSTIISHILSKFP-FK 31
                                   6899******************998.44 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.3e-05    0.0071      26      49 ..       6      29 ..       3     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                         AAA_16 26 lvllsGesGvGKsslvrellrale 49
                                    ++++G+sG+GKs+++ ++l  + 
  gene104|gene104|rna104|rna104  6 HLVFTGPSGSGKSTIISHILSKFP 29
                                   6899**************997554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.9   1.6e-05    0.0088      14      35 ..       7      28 ..       4     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-05
                                   EEEEESTTSSHHHHHHHHTTSS CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagll 35
                                   ++++G++G+GKSt+++ ++ + 
  gene104|gene104|rna104|rna104  7 LVFTGPSGSGKSTIISHILSKF 28
                                   6789************998765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.2e-05     0.012       1      64 [.       6      66 ..       6      98 .. 0.72
   2 ?   -2.7   0.0       8.7   4.8e+03      95     118 ..     156     178 ..     126     182 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-05
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarve 64
                                   +++ TGp+G+GK+T+++ +l++     +k +   t +  ++g+  g ++  ++++e +++ r++
  gene104|gene104|rna104|rna104  6 HLVFTGPSGSGKSTIISHILSKF---PFKFSVSHTTRAPRKGEVNGKDYHFVSTKEFEEMVRNQ 66
                                   6789***************9998...45555556777777777777777777666666666665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.7
                                    HH-EEEE---STTGGG-HHHHHHH CS
                       NTPase_1  95 eadviviDEiGkmElkskkfkeav 118
                                    ++d +viD   ++E +  +++e +
  gene104|gene104|rna104|rna104 156 KCD-YVIDNTHSLEKSKGEVEEII 178
                                    333.45666666666655555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00014     0.077       1      31 [.       6      36 ..       6      53 .. 0.83
   2 ?    0.6   0.0      0.93   5.1e+02      24      64 ..     111     151 ..     102     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                   EEEEE--SSSSHHHHHHHGGGGBS--EEEEE CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaalnreveyvq 31
                                   +++  Gp+G+gKs+++ ++++ +  ++ +  
  gene104|gene104|rna104|rna104  6 HLVFTGPSGSGKSTIISHILSKFPFKFSVSH 36
                                   68999***************99977776655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.93
                                    S--EEEEE--TT--HHHHH--B--.........-------- CS
                          AAA_5  24 nreveyvqltrdtteedlkgrreikngttslvdsplvraar 64 
                                    n  ++y+ + ++  +e l  r+  k+++      +l++a++
  gene104|gene104|rna104|rna104 111 NFVILYIHCDKNVARERLEKRMGNKSEKDIEARMSLYEAFN 151
                                    67789999999999999999998764444444444554544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00017     0.095       2      26 ..       8      32 ..       7      71 .. 0.76
   2 ?   -0.8   0.0       3.7     2e+03      22      64 ..     128     170 ..     118     181 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                   +++Gpsg GKSt++ ++ +++  k+
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSKFPFKF 32
                                   799*************777765444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.7
                   RNA_helicase  22 llkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                    l+k++++k+++++ +r +  + +++ +++   vid   + +++
  gene104|gene104|rna104|rna104 128 LEKRMGNKSEKDIEARMSLYEAFNSIKDKCDYVIDNTHSLEKS 170
                                    5566666666666666666666666666666666665555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.019        10      20      39 ..       8      27 ..       4      34 .. 0.83
   2 ?    6.3   0.0    0.0096       5.2     125     167 ..     113     158 ..     103     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.019
                     Zeta_toxin 20 llgGqpGAGKselaellkde 39
                                   +  G +G+GKs++++ +  +
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSK 27
                                   557999********998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0096
                     Zeta_toxin 125 evvvvavkkelSrlgvldRyeeevae...gRlvpkeehdeafeglr 167
                                     ++++ ++k+++r+++++R  +++++   +R+   e ++ + ++  
  gene104|gene104|rna104|rna104 113 VILYIHCDKNVARERLEKRMGNKSEKdieARMSLYEAFNSIKDKCD 158
                                    6889*****************9966567779988888777666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00075      0.41       5      23 ..       7      26 ..       4      97 .. 0.67
   2 ?    1.7   0.0      0.35   1.9e+02     147     172 ..     141     165 ..     105     181 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00075
                         AAA_24  5 iliyGpsgiGKTtlakel.g 23
                                   ++ +Gpsg+GK+t+++++  
  gene104|gene104|rna104|rna104  7 LVFTGPSGSGKSTIISHIlS 26
                                   6789************9942 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.35
                         AAA_24 147 rlepklgkktanelkeevDlvlranl 172
                                      +++l + ++n +k ++D+v++ + 
  gene104|gene104|rna104|rna104 141 EARMSLYE-AFNSIKDKCDYVIDNTH 165
                                    22222222.28888888888887554 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00071      0.38       3      22 ..       5      24 ..       3      36 .. 0.81
   2 ?    1.5   0.0      0.46   2.5e+02     101     128 ..     111     138 ..     102     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00071
                                   EEEEEESSTTSSHHHHHHHH CS
                     APS_kinase  3 vvvwltGlsgsGKstianal 22
                                   v + +tG sgsGKsti  ++
  gene104|gene104|rna104|rna104  5 VHLVFTGPSGSGKSTIISHI 24
                                   5678***********96654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.46
                                    EEEEEEEE--HHHHHHHTTTSHHHHHHT CS
                     APS_kinase 101 kfievfvdtplevceerDpkglYkkare 128
                                    +f+ ++++++ +v++er  k + +k+++
  gene104|gene104|rna104|rna104 111 NFVILYIHCDKNVARERLEKRMGNKSEK 138
                                    6999999999999999999888777765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00013     0.069       3      23 ..       7      27 ..       5      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                                   EEEEESTTCCHHHHHHHHHCT CS
                           cobW  3 tvltGflGsGKTtLlnhllen 23
                                   +v+tG+ GsGK+t+++h+l++
  gene104|gene104|rna104|rna104  7 LVFTGPSGSGKSTIISHILSK 27
                                   689***************964 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00012     0.067      48      68 ..       7      28 ..       3      99 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                          Rad17 48 LLisGPsGCgkstvv.kvLske 68
                                   L+ +GPsG gkst++ ++Lsk 
  gene104|gene104|rna104|rna104  7 LVFTGPSGSGKSTIIsHILSKF 28
                                   789***********94478885 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.6e-05     0.052       3      57 ..       8      62 ..       7      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.6e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeip 57
                                   v++Gp gsGKS+++  +   + +  +v ++t  +++g  ++k+ ++  ++++e+ 
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSKFPFKFSVSHTTRAPRKGEVNGKDYHFVSTKEFEEM 62
                                   89*************9955444488888888888888888888888888877765 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.035        19       2      25 ..       8      31 ..       7      65 .. 0.83
   2 ?    9.8   0.9    0.0012      0.68     125     154 ..     113     143 ..      68     183 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.035
                                   EEEESTTSSHHHHHHHHHCCSTCE CS
                            dNK  2 vveGnIgaGKstlvklLskklgvk 25
                                   v  G+ g+GKst+++ +  k+++k
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSKFPFK 31
                                   567999*******99555555555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                                    EEEEEE--HHHHHHHHHHC.TTCCCTTS-HH CS
                            dNK 125 lliYLkasletclerikkR.greeekkield 154
                                    ++ Y++++ ++  er++kR g++ ek ie +
  gene104|gene104|rna104|rna104 113 VILYIHCDKNVARERLEKRmGNKSEKDIEAR 143
                                    577***************9567788888765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00046      0.25       2      26 ..       8      32 ..       7      95 .. 0.75
   2 ?    0.8   0.0       1.1   6.2e+02      38      74 ..     132     171 ..     105     182 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
                                   EEESSTTSSHHHHHHHHHHHHTHEE CS
                            AAA  2 llyGppGtGKTllakavakelgvef 26
                                   +++Gp G GK+++++ + +++ ++f
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSKFPFKF 32
                                   799***************9975544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                                    STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                            AAA  38 yvgesekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                    +  +sek+i++ ++  ++ +   +++  +iD+ ++l ks+
  gene104|gene104|rna104|rna104 132 MGNKSEKDIEARMSLYEAFNsikDKCDYVIDNTHSLEKSK 171
                                    3344555555555444433344333555666666665555 PP

>> Endotoxin_N  delta endotoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00018     0.098     139     188 ..      42      90 ..      36     120 .. 0.76
   2 ?   -0.1   0.1       1.2   6.5e+02      30      52 ..     142     164 ..     139     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                    Endotoxin_N 139 keaivkgkewgisdskvkifidkf.kksivdyaeycktayekGlakikkee 188
                                    + + v+gk++++   + k f++   ++++ +y++y    y +G+ ++k+++
  gene104|gene104|rna104|rna104  42 RKGEVNGKDYHFV--STKEFEEMVrNQEFLEYVQYNGNYYGTGVSQLKNSQ 90 
                                    56889*******9..55666666526889******************8633 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                    Endotoxin_N  30 edksiaelvnsyrkeiqdlidns 52 
                                       s +e +ns ++++  +idn 
  gene104|gene104|rna104|rna104 142 ARMSLYEAFNSIKDKCDYVIDNT 164
                                    567899999*******9999985 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0     0.002       1.1       5      43 ..       7      53 ..       4      97 .. 0.61
   2 ?    3.5   0.6      0.12        66      24      88 ..     106     179 ..      86     184 .] 0.55

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.002
                         AAA_14  5 lvitGaRrvGKTtllkqlikell........vkkesilyinldderd 43
                                   lv tG+  +GK+t++ +++++          +++ +  ++n +d ++
  gene104|gene104|rna104|rna104  7 LVFTGPSGSGKSTIISHILSKFPfkfsvshtTRAPRKGEVNGKDYHF 53
                                   6889**************98876666666653333333344444333 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                         AAA_14  24 kellvkkesilyinldderdkkladpe.............kllelileklke....ekktylflDEiqevpewekalksl 86 
                                    k++  ++  ilyi +d++  +++ +++             +l+e       +    ++k   ++D  + +++ +  + ++
  gene104|gene104|rna104|rna104 106 KKN-YPNFVILYIHCDKNVARERLEKRmgnksekdiearmSLYE-------AfnsiKDKCDYVIDNTHSLEKSKGEVEEI 177
                                    333.4777899999999766443322122222222222222222.......13344445558999999988877777777 PP

                         AAA_14  87 vd 88 
                                    + 
  gene104|gene104|rna104|rna104 178 IS 179
                                    65 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.2   3.4e+03       5      19 ..      46      60 ..      45      70 .. 0.70
   2 ?   12.3   0.1   0.00025      0.13       6      41 ..     134     169 ..     133     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.2
                      ThiS-like  5 lNekeveveegttle 19
                                   +N+k + + + +  e
  gene104|gene104|rna104|rna104 46 VNGKDYHFVSTKEFE 60
                                   899999876655444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00025
                      ThiS-like   6 NekeveveegttlealkekikpdaDvvIlNGFpike 41 
                                    N  e ++e+  +l++  ++ik+++D+vI N +++++
  gene104|gene104|rna104|rna104 134 NKSEKDIEARMSLYEAFNSIKDKCDYVIDNTHSLEK 169
                                    667889999*********************998776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.12      21      44 ..       5      28 ..       2      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                   EEEEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnks 44
                                   + + + G  G+GK+t++++il+k+
  gene104|gene104|rna104|rna104  5 VHLVFTGPSGSGKSTIISHILSKF 28
                                   567899***************997 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015     0.083     131     154 ..       6      29 ..       1      64 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                          T2SSE 131 lilvsGgTgsGKttllyallkein 154
                                     ++++G+ gsGK+t++  +l++++
  gene104|gene104|rna104|rna104   6 HLVFTGPSGSGKSTIISHILSKFP 29 
                                    6899*************9999876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.5   0.00029      0.16       2      58 ..       8      62 ..       7     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                                   EEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEE CS
                      Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkek 58
                                   ++ G   sGKS+++ ++l +  +  +  +tTr+p + + + + + +   +++e++e 
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSKFPFKFSVSHTTRAPRKGEVNGKDY-H-FVSTKEFEEM 62
                                   78999***************9999**********9877755555.2.1222223333 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.18     1e+02       5      19 ..       9      23 ..       5      37 .. 0.80
   2 ?    8.1   0.0    0.0037         2     124     177 ..     113     167 ..     100     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.18
                                   EEESTTSSHHHHHHH CS
                           CoaE  5 ltGgiasGKstvanl 19
                                    tG  +sGKst+ + 
  gene104|gene104|rna104|rna104  9 FTGPSGSGKSTIISH 23
                                   7999******98554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                                    EEEEEE--HHHHHHHHHHCC.TSTHHHHHHHHHHS--HHHHHHH-SEEEE-.SSH CS
                           CoaE 124 rvlvvdvelelqveRlvard.gvseeevkaiiaaQlseeerlaladvvldNdssl 177
                                    ++l ++++++   eRl +r  + se++++a+++   + +  +   d+v+dN  sl
  gene104|gene104|rna104|rna104 113 VILYIHCDKNVARERLEKRMgNKSEKDIEARMSLYEAFNSIKDKCDYVIDNTHSL 167
                                    47889999999999*****9567899*******9999999999********7765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.8   0.00054       0.3      23      67 ..       8      55 ..       6     181 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00054
                         AAA_23 23 lItGpNGaGKTTildAiklaL.yget..prlsrksgrgfeksdveies 67
                                   ++tGp G+GK+Ti+  i   + + ++  ++++  +++  +  d+++ s
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHILSKFpFKFSvsHTTRAPRKGEVNGKDYHFVS 55
                                   79************9987555333222122222223344444444333 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00063      0.34       5      39 ..      78     112 ..      74     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00063
                                    SHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHH CS
                  Thioredoxin_7   5 dldealakaaergkpvlvffgaswcftCqalerdf 39 
                                     + +++++++ ++k+vl++++ ++  +C+++  +f
  gene104|gene104|rna104|rna104  78 YYGTGVSQLKNSQKTVLLDLEYEGVLYCKKNYPNF 112
                                    5667899***********************98766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00064      0.35       3      20 ..       8      25 ..       6      75 .. 0.87
   2 ?   -1.3   0.0       4.2   2.3e+03     121     141 ..     128     150 ..      83     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00064
                         AAA_28  3 vitGgestGKTtlleaLa 20
                                   v+tG++++GK+t+++++ 
  gene104|gene104|rna104|rna104  8 VFTGPSGSGKSTIISHIL 25
                                   9*************9875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.2
                         AAA_28 121 i.dddgeR.redleereaiderl 141
                                    + ++ g+  ++d e+r+ ++e++
  gene104|gene104|rna104|rna104 128 LeKRMGNKsEKDIEARMSLYEAF 150
                                    12222222123445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 1065.13
//
Query:       gene1041|gene1041|rna1040|rna1040  [L=765]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-23   81.9   0.1    1.1e-19   70.9   0.0    3.2  3  Helicase_C       Helicase conserved C-terminal domain
    3.2e-21   75.9   0.0    2.1e-20   73.2   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
    1.9e-17   63.8   5.3    1.9e-17   63.8   5.3    2.7  3  RecQ_Zn_bind     RecQ zinc-binding
    3.6e-16   58.9   0.5    8.4e-16   57.8   0.5    1.6  1  RQC              RQC domain
  ------ inclusion threshold ------
      0.054   13.9   0.5        4.8    7.6   0.1    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0018       6.4      14      66 ..     274     326 ..     264     339 .. 0.76
   2 !   70.9   0.0   2.9e-23   1.1e-19      20     110 ..     460     549 ..     445     550 .. 0.93
   3 ?   -1.8   0.0       1.1   3.9e+03      15      31 ..     587     603 ..     563     661 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                                        TTTSEEEEEESSHHHHHH..HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTS CS
                         Helicase_C  14 eeggkilifvntidrlek..vklllekkgikvavlhgelpqnereeileqfnkge 66 
                                        + +g ++++++  + +++   +ll  +k+i +++++++l+ ner  ++e+ +++e
  gene1041|gene1041|rna1040|rna1040 274 VYEGITIVVSPLLSLVQDqiRNLL--QKDILALPINSNLSRNERSLVFEALRSDE 326
                                        556667888888886655534455..667********************998765 PP

  == domain 2  score: 70.9 bits;  conditional E-value: 2.9e-23
                                        EEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS CS
                         Helicase_C  20 lifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp 94 
                                        +i++++++++e+  + l  kk +k+a +h+ l++ner+ + e++nkge++v++at + ++Gid ++v++Vi++ +p
  gene1041|gene1041|rna1040|rna1040 460 IIYCTSKKECEMiSDKL--KKYMKTAFYHAGLSKNERNSVQEKWNKGEFKVIVATIAFGMGIDKKDVRFVIHYCIP 533
                                        9*********8776777..7789***************************************************** PP

                                        SSHHHHHHHHTTSSST CS
                         Helicase_C  95 rnvtsyiqriGRtgRa 110
                                        ++++ y q  GR+gR 
  gene1041|gene1041|rna1040|rna1040 534 KSLEGYYQETGRAGRD 549
                                        ***************6 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.1
                                        TTSEEEEEESSHHHHHH CS
                         Helicase_C  15 eggkilifvntidrlek 31 
                                        + + ++ f+++++++ +
  gene1041|gene1041|rna1040|rna1040 587 DLEAVIQFCENKTDCRR 603
                                        34455666666665544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   5.9e-24   2.1e-20       3     174 ..     240     407 ..     238     408 .. 0.86
   2 ?   -0.6   0.0      0.26   9.4e+02      50     105 ..     459     513 ..     438     526 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 5.9e-24
                                        HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                         Q+e+i+++l+g+dv+v ++TG GK+ ++++p+l  vye        +++v+P+ +L++++++nl +    + l +
  gene1041|gene1041|rna1040|rna1040 240 NQREVIQACLSGKDVFVLMPTGGGKSICYQLPAL--VYE------GITIVVSPLLSLVQDQIRNLLQKDI-LALPI 306
                                        59********************************..876......689*****************88766.67899 PP

                                        EEEETTSSHHHHHHHHHTT...CSEEEEEH......HHHHHHHHCTSSHCTTEEEEEEETHHHHHHT..TTHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx...xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                               DEAD  79 lliiggvaardqlskldng...vdivvgtp......grlddllstgklnlsqvrflVlDEadrlldq..gfsdfin 143
                                        ++ ++ ++++   ++l+++   ++i++ tp      g ++d++s + ++  +++ +V+DEa++++++  +f+++++
  gene1041|gene1041|rna1040|rna1040 307 NSNLSRNERSLVFEALRSDeliCKIFYVTPeliaksGHFHDVVS-ELVRRGRLKRFVIDEAHCVSQWghDFRPDYK 381
                                        9999999*********866789********44444444444443.5667899999************999****** PP

                                        HHHHHSHHHCTTSTTTSEEEEEESSBSHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 144 rilnqlpqitcdgklqrqvivlSATlpkdvk 174
                                        + l +++  + + +    +i+l+AT++k+v+
  gene1041|gene1041|rna1040|rna1040 382 E-LGSIRIRYPSVP----IIALTATATKKVE 407
                                        *.999977777777....********98875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.26
                                        EEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEEH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                               DEAD  50 alivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgtp 105
                                         +i + +++ +e + ++lkk++k++   +++ ++++++++ ++k ++g  +++v+t 
  gene1041|gene1041|rna1040|rna1040 459 GIIYCTSKKECEMISDKLKKYMKTA--FYHAGLSKNERNSVQEKWNKGeFKVIVATI 513
                                        5777778888899999999999963..456678888888888888666799999885 PP

>> RecQ_Zn_bind  RecQ zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.93   3.3e+03      28      48 ..     169     189 ..     157     197 .. 0.77
   2 ?   -3.7   0.3         5   1.8e+04      34      41 ..     462     469 ..     460     470 .. 0.88
   3 !   63.8   5.3   5.2e-21   1.9e-17       2      66 .]     562     627 ..     561     627 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.93
                       RecQ_Zn_bind  28 leamlaycentteCrrkllle 48 
                                        +e+  + c+ +++C r  +l+
  gene1041|gene1041|rna1040|rna1040 169 VEKFSDSCSLNNDCIRTTFLR 189
                                        5666667888899***99997 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5
                       RecQ_Zn_bind  34 ycentteC 41 
                                        yc++++eC
  gene1041|gene1041|rna1040|rna1040 462 YCTSKKEC 469
                                        9*****99 PP

  == domain 3  score: 63.8 bits;  conditional E-value: 5.2e-21
                       RecQ_Zn_bind   2 qDvsrlrrlieqseesekekeaelekleamlaycentteCrrkllleyFgeeaaeeeC.gnCDnCl 66 
                                        +D ++++++ie+++++ ++k++++e lea++++cen+t+Crr ++l +Fge+++ + C ++CDnC+
  gene1041|gene1041|rna1040|rna1040 562 GDKKKISFMIEKGDGGYEQKQRQREDLEAVIQFCENKTDCRRMQVLGHFGEKFDPQMCrKTCDNCR 627
                                        799*************************************************9999**666****5 PP

>> RQC  RQC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.5   2.3e-19   8.4e-16       4      85 ..     633     715 ..     630     740 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 2.3e-19
                                        EEE-HHHHHHHHHHHHHTTS-SBHHHHHHHHHT---CCCCCTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEE CS
                                RQC   4 tvDvteeaqkilscvyrtgqrfgaghivdvLrGsktkkirqlghdklstfGigkdlskkewrrlirqLiaegyLee 79 
                                        ++D t+ea++++ +vy   +r+++ + vdv++G ++kk r++   + +++G+gk l+k++++r++r Li++g+++e
  gene1041|gene1041|rna1040|rna1040 633 KKDYTKEARDLILLVYTS-NRITLCQAVDVYKGLSNKKSREY--SESEYYGKGKSLKKTTIERILRSLISQGCIQE 705
                                        78**************99.6*********************8..******************************** PP

                                        E......SSS CS
                                RQC  80 dve....eyg 85 
                                         +e    +++
  gene1041|gene1041|rna1040|rna1040 706 RIEfmerRFS 715
                                        9996666444 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0013       4.8      27      61 ..     452     504 ..     425     505 .. 0.80
   2 ?    3.7   0.0     0.022        79       4      36 ..     621     658 ..     620     678 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0013
                    Lar_restr_allev  27 q.......cvyCad...Cga........stpwfkiaedeaeaekeaieaWNrR 61 
                                        +        +yC+    C++        +++ f++a+  +++++ + e+WN++
  gene1041|gene1041|rna1040|rna1040 452 ThfpdccgIIYCTSkkeCEMisdklkkyMKTAFYHAGLSKNERNSVQEKWNKG 504
                                        14555555899*54557***********99*********************95 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.022
                    Lar_restr_allev   4 kpCPfCggravlersqrvvaeigq.cvyCad....Cga 36 
                                        k C+ C  +a +++++ + a      vy  +    C a
  gene1041|gene1041|rna1040|rna1040 621 KTCDNCRREAMVKKDYTKEARDLIlLVYTSNritlCQA 658
                                        78*************99887544454444444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (765 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 5156.45
//
Query:       gene1042|gene1042|rna1041|rna1041  [L=375]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-22   79.8   0.2    9.1e-22   77.7   0.1    2.0  2  DUF3449         Domain of unknown function (DUF3449)
    3.5e-05   24.2   4.3    3.6e-05   24.2   2.6    1.9  2  SF3A3           Pre-mRNA-splicing factor SF3A3, of SF3a compl
     0.0001   22.6   1.4       0.64   10.4   2.0    3.2  2  zf-C2H2_2       C2H2 type zinc-finger (2 copies)
  ------ inclusion threshold ------
      0.053   13.7   1.7        4.2    7.5   0.1    2.4  2  Importin_rep_6  Importin repeat 6
       0.13   11.9   3.1       0.19   11.3   0.1    2.5  3  Sgf11           Sgf11 (transcriptional regulation protein)


Domain annotation for each model (and alignments):
>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.58   2.1e+03       2      29 ..     242     269 ..     241     273 .. 0.85
   2 !   77.7   0.1   2.5e-25   9.1e-22      76     184 .]     274     374 ..     264     374 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.58
                                        HHHHHHHHHHTHHHHHHHHHHHHHHHT- CS
                            DUF3449   2 elkikklaellskeieetkenverkqal 29 
                                        e  ikk +e+l++e++ ++++++rk+++
  gene1042|gene1042|rna1041|rna1041 242 EGLIKKALEILDRERRYSISRLSRKKKR 269
                                        66799999************99999865 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 2.5e-25
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DUF3449  76 ipyWLykLhgLgkeykCeiCgnavYkGrkaFekHFseerHaeglkcLgientklfkeitkiedaleLweklkkekk 151
                                        +p WLyk ++L+++++C+iCg   Y Gr  F++HF e  H + + + gi+ + + k+it++   +++ ++++++  
  gene1042|gene1042|rna1041|rna1041 274 VPKWLYKREELDISFECDICGYSGY-GRDGFDRHFGEDSHRKSVARYGIKYSPALKGITRVGILMKMKDRVEES-- 346
                                        89*******************8888.**********************************99888777777665.. PP

                                        XXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DUF3449 152 kekakeeeeveveDeeGnvmskkvYedLkkqgl 184
                                             e+ ++e+eD +Gnv+ +++YedLk+++l
  gene1042|gene1042|rna1041|rna1041 347 -----ESYTEEFEDGDGNVFDRRTYEDLKRNNL 374
                                        .....45678*******************9876 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8   6.5e+03      53      55 ..      48      50 ..      14      74 .. 0.63
   2 !   24.2   2.6     1e-08   3.6e-05       2      70 ..      98     161 ..      97     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                              SF3A3 53 eYk 55
                                       +Y+
  gene1042|gene1042|rna1041|rna1041 48 RYT 50
                                       332 PP

  == domain 2  score: 24.2 bits;  conditional E-value: 1e-08
                              SF3A3   2 FsgeEqyGkylDLnelyeeylnlk.eikldYlqYLesfdkfseipkkqkkskeYkeYlkeLleYLesfik 70 
                                        F++   yG  l+L +++++y +++ +   dY ++L+s+ k+    + +k   +Y eYl+eL+eYL+  ik
  gene1042|gene1042|rna1041|rna1041  98 FKDSRLYGAGLELDKIFKKYTDVHlC--DDYKKFLKSICKL----NVDKSRFRYLEYLNELKEYLSGVIK 161
                                        778888****************9952..5******999888....45566679************98765 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   2.0   0.00018      0.64      47      80 ..     196     228 ..     113     234 .. 0.77
   2 !    7.2   0.0    0.0018       6.4      42      77 ..     279     314 ..     249     322 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                          zf-C2H2_2  47 ieekleClyCekefkslealreHmkkkgHckine 80 
                                        +  k+ C+ C++e  s++ +  H+k k+Hck + 
  gene1042|gene1042|rna1041|rna1041 196 VFPKVYCVKCSREI-SRSVFGYHLKGKRHCKKER 228
                                        344899****9996.99999**********9644 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                          zf-C2H2_2  42 ylrekieekleClyCekefkslealreHmkkkgHck 77 
                                        y re+++ ++eC +C++++  ++ +  H  + +H+k
  gene1042|gene1042|rna1041|rna1041 279 YKREELDISFECDICGYSGYGRDGFDRHFGEDSHRK 314
                                        668999999*********99**************98 PP

>> Importin_rep_6  Importin repeat 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0012       4.2      58     100 ..     110     156 ..     104     162 .. 0.75
   2 ?    4.9   0.2    0.0079        28      40      62 ..     335     357 ..     322     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                     Importin_rep_6  58 vdddyddytdedlldeinkslaailkak....kseylpalqtllpli 100
                                        +d+ +++ytd  l d+ +k l +i k +    + +yl+ l++l + +
  gene1042|gene1042|rna1041|rna1041 110 LDKIFKKYTDVHLCDDYKKFLKSICKLNvdksRFRYLEYLNELKEYL 156
                                        6777899*****************99652211446777777776655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0079
                     Importin_rep_6  40 vyervkereneddeynedvdddy 62 
                                        +  ++k+r +e + y+e+ +d  
  gene1042|gene1042|rna1041|rna1041 335 ILMKMKDRVEESESYTEEFEDGD 357
                                        6779**************98853 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.77   2.7e+03       9      19 ..     133     143 ..     132     143 .. 0.89
   2 ?   11.3   0.1   5.2e-05      0.19       4      23 ..     199     218 ..     198     219 .. 0.90
   3 ?   -0.5   0.1      0.27   9.6e+02       5      11 ..     288     294 ..     286     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.77
                                        TTSSEEEGGGH CS
                              Sgf11   9 nCgRqiaasRF 19 
                                        +C+ ++  sRF
  gene1042|gene1042|rna1041|rna1041 133 ICKLNVDKSRF 143
                                        69999*****9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.2e-05
                                        EEE-TTTSSEEEGGGHHHHH CS
                              Sgf11   4 yvtCpnCgRqiaasRFApHL 23 
                                         v C  C+R+i+ s F  HL
  gene1042|gene1042|rna1041|rna1041 199 KVYCVKCSREISRSVFGYHL 218
                                        689***********999998 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.27
                                        EE-TTTS CS
                              Sgf11   5 vtCpnCg 11 
                                        ++C++Cg
  gene1042|gene1042|rna1041|rna1041 288 FECDICG 294
                                        89****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2119.26
//
Query:       gene1043|gene1043|rna1042|rna1042  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.017   15.2   0.1    1.3  1  FANCI_S1-cap  FANCI solenoid 1 cap


Domain annotation for each model (and alignments):
>> FANCI_S1-cap  FANCI solenoid 1 cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   9.7e-07     0.017      23      46 ..      46      69 ..      39      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.7e-07
                       FANCI_S1-cap 23 tLkedeLtelitnsAlKGkevGal 46
                                       + +e++L e++++ AlKGk++++l
  gene1043|gene1043|rna1042|rna1042 46 CTSEGDLLEILKSLALKGKDIAIL 69
                                       6789*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 706.52
//
Query:       gene1044|gene1044|rna1043|rna1043  [L=446]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-44  151.0   0.0    5.3e-44  150.6   0.0    1.1  1  Dus       Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.6   0.0     3e-48   5.3e-44       2     285 ..     108     400 ..     107     409 .. 0.87

  Alignments for each domain:
  == domain 1  score: 150.6 bits;  conditional E-value: 3e-48
                                        E---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHH CS
                                Dus   2 laPmagvtdlpfRelvrefgataLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaAklvad 77 
                                        laPm+gvt+ ++R+++r  ++t+ ++tem+ ++ +++  + ++++ +  e + +++vQ+ggsdp ++ ea+++ + 
  gene1044|gene1044|rna1043|rna1043 108 LAPMMGVTTPHYRRFIRLTSETTVLFTEMIVSNTVIHIPRDKLKE-KLGEYDDKTVVQIGGSDPVQIIEAVRIIQS 182
                                        9******************************99999974444443.33333347********************** PP

                                        TT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESS..TTTC.HHHHHHHHHHCT CS
                                Dus  78 lgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigid..deeenalelakiveaaG 151
                                        lg++  +lN+GCPs +v++g +Ga L+ +++lva+i++ v k ++  +++kir+g+d  d   ++  ++  + ++ 
  gene1044|gene1044|rna1043|rna1043 183 LGYKMFNLNCGCPSSRVKKGSFGAVLMLNKELVAEIINRVYKETGEVLSLKIRTGVDdeDGIGFLSGFVGYIRKNT 258
                                        *********************************************************6555678888888776655 PP

                                        .-SEEEEESS.......ECCCTT-C.G--CHHHHHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                                Dus 152 .aqaltvHgR.......traqnyeg.tadweaIkevkqavs.ipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                            + +H+R       ++ qn++  ++d+++++e+k+  + + +i NG I +     +  + +G dg migr+a 
  gene1044|gene1044|rna1043|rna1043 259 pNRTFYIHARkcwleglSPGQNRKLpPLDYDSVYEIKKLYPeLKIILNGSISEN----NLDRVSGLDGAMIGREAI 330
                                        4999***********************************************874....455679************ PP

                                        CSTTHHHH.HHHHHHSC------.HHHH..HHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHH CS
                                Dus 218 gnPwlfae.stavktgeaepapp.laee..aeiveehlkkleeelgedkglrkirkhlawylkglkkaaelr 285
                                        +n ++f    ++++ g+  ++++  +e   ++   +++++   e ++ k+++ki   +++y++g+  + +l+
  gene1044|gene1044|rna1043|rna1043 331 RNAFVFWDiDQQLHGGQGVEMWNgSKETcpLDSSMRRIECN--EDHKSKRVQKIHSVVKQYFEGFSPSIQLK 400
                                        *******9999999999999999555553334444444444..44557999*************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2786.07
//
Query:       gene1045|gene1045|rna1044|rna1044  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.053   13.3   1.0      0.071   12.9   0.2    1.7  2  PI31_Prot_N   PI31 proteasome regulator N-terminal
       0.82   10.3   6.6        4.1    8.0   5.3    2.4  2  Syntaxin-6_N  Syntaxin 6, N-terminal
        3.2    7.7   7.5        1.6    8.7   3.2    2.3  2  RF-1          RF-1 domain
        4.1    5.9   8.3        5.2    5.6   8.3    1.3  1  FapA          Flagellar Assembly Protein A


Domain annotation for each model (and alignments):
>> PI31_Prot_N  PI31 proteasome regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.89     4e+03     138     154 ..       7      23 ..       4      31 .. 0.69
   2 ?   12.9   0.2   1.6e-05     0.071      24      71 ..      42      91 ..      33      99 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.89
                        PI31_Prot_N 138 eerladLisllkvsivq 154
                                        e+r ++L +++k+++++
  gene1045|gene1045|rna1044|rna1044   7 ETRFNELPQQIKQKLIN 23 
                                        56777777777777775 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.6e-05
                        PI31_Prot_N 24 gFrlvglgedkkieeses...ksecqslaprLpaeWnassdsysFrYaheq 71
                                       +F+l+  + ++    + +   k    + a++L + Wn ++d+  FrY he+
  gene1045|gene1045|rna1044|rna1044 42 KFNLLYSQTQDLQTRNLQknfK-LLVESAEKLKRMWNLNKDEADFRYLHEN 91
                                       5666654444333322223221.22344566******************87 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.3   0.00092       4.1      16      73 ..      54     112 ..      10     122 .. 0.75
   2 ?    5.2   0.4     0.007        31      52      73 ..      91     112 ..      85     137 .. 0.44

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00092
                       Syntaxin-6_N  16 kaeslyrrwerlledtss.stseeldetrteLrkalrsiewdledLeetvriveknpsk 73 
                                        ++++l ++++ l e++++ ++ ++l++ + ++r   +++++ le+L+e v   +kn+++
  gene1045|gene1045|rna1044|rna1044  54 QTRNLQKNFKLLVESAEKlKRMWNLNKDEADFRYLHENLKKALEELKEEVMLYKKNEEN 112
                                        345555555555555555559999999999******************99888888765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.007
                       Syntaxin-6_N  52 siewdledLeetvriveknpsk 73 
                                        ++++ le+L+e v   +kn+++
  gene1045|gene1045|rna1044|rna1044  91 NLKKALEELKEEVMLYKKNEEN 112
                                        3444444444444444444332 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3     0.075   3.4e+02      40      71 ..      40      71 ..      22      84 .. 0.70
   2 ?    8.7   3.2   0.00036       1.6      50      80 ..      84     114 ..      66     139 .] 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.075
                                       TTTEEEEEEECSSSHHHHHHHHHHHHHHHHHH CS
                               RF-1 40 ptgvivvecqeeRsqekNrekAlerLkaklke 71
                                       pt+  +  +q++  q +N +k +++L +  ++
  gene1045|gene1045|rna1044|rna1044 40 PTKFNLLYSQTQDLQTRNLQKNFKLLVESAEK 71
                                       55545666777778888888888888776543 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00036
                                        CSSSHHHHHHHHHHHHHHHHHHHHHHHCCCC CS
                               RF-1  50 eeRsqekNrekAlerLkaklkekeleeekee 80 
                                        + R  ++N +kAle Lk++++ ++++ee++e
  gene1045|gene1045|rna1044|rna1044  84 DFRYLHENLKKALEELKEEVMLYKKNEENRE 114
                                        67999***************77755555544 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.3    0.0012       5.2     317     406 ..      34     128 ..       3     139 .] 0.59

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0012
                               FapA 317 Gselgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletk..... 387
                                          e+ + t+ ++  + ++ + ++++l+++ + l e+ eklk++ +++++++    l ++ k+ l++l+e+      
  gene1045|gene1045|rna1044|rna1044  34 SMEMLKPTKFNLLYS-QTQDLQTRNLQKNFKLLVESAEKLKRMWNLNKDEADFRYLHENLKKALEELKEEVmlykk 108
                                        556666677777666.666667788888888888888888888888888555444444444444444444444333 PP

                               FapA 388 .eklkeeleeleeelkelke 406
                                         e+ +e l e++  ++ l +
  gene1045|gene1045|rna1044|rna1044 109 nEENREFLDEITMTYAMLRN 128
                                        33333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2062  (0.115009); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 870.30
//
Query:       gene1046|gene1046|rna1045|rna1045  [L=441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-67  225.4   0.0    1.5e-66  224.4   0.0    1.5  2  Tubulin          Tubulin/FtsZ family, GTPase domain
    4.5e-49  165.8   0.1      7e-49  165.2   0.1    1.3  1  Tubulin_C        Tubulin C-terminal domain
    0.00019   21.1   0.0    0.00042   20.1   0.0    1.6  1  Tubulin_3        Tubulin domain
  ------ inclusion threshold ------
      0.052   13.8   0.0        0.1   12.9   0.0    1.5  1  Misat_Tub_SegII  Misato Segment II tubulin-like domain


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.4   0.0   3.3e-70   1.5e-66       1     196 [.       3     210 ..       3     211 .. 0.99
   2 ?   -3.4   0.0       2.1   9.3e+03     150     190 ..     337     377 ..     326     380 .. 0.75

  Alignments for each domain:
  == domain 1  score: 224.4 bits;  conditional E-value: 3.3e-70
                                        EEEEEEEHHHHHHHHHHHHH...HHHCH.............HHHT.....TTEEEEE....EEESBHHHHHTS-GS CS
                            Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdg.........dslesfFsesgkveyiprsvaidtdpqvlneikag 67 
                                        eii +++Gq+G+qign++wel++kehgi +dg         +s esfFs+++ ++y+pr++++d++p vl++ik+g
  gene1046|gene1046|rna1045|rna1045   3 EIISLHIGQAGVQIGNACWELYCKEHGILPDGrldqnrmddESAESFFSQTSVGTYVPRTLMVDLEPGVLESIKTG 78 
                                        79***************************999******************************************** PP

                                        ........EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHH CS
                            Tubulin  68 s..elfnpnklllgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevl 141
                                        +  el++p +l++gke+a+nn+a+g+++vgke++e ++e+ir+++++cd lqgf+i++s+gGGTGSG++++++++l
  gene1046|gene1046|rna1045|rna1045  79 KyrELYHPGQLISGKEDAANNYARGHYTVGKEIIEPVMEQIRRMADNCDGLQGFLIYHSFGGGTGSGFASLMMDRL 154
                                        **************************************************************************** PP

                                        HHTSTTSEEEEEEEE--.GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                            Tubulin 142 keeypkalvvtvvvlPs.efsevvvepynailalkelieesdavividNdaLlkil 196
                                          e+ k+ ++ ++v+P  ++ + vvepyn+il++++  ++sd+ +++dN+a+++++
  gene1046|gene1046|rna1045|rna1045 155 AAEFGKKSKLEFSVYPApKIATAVVEPYNSILTTHTTLDYSDCSFLVDNEAIYDMC 210
                                        ******************************************************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.1
                                        EEEEEEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHH CS
                            Tubulin 150 vvtvvvlPsefsevvvepynailalkelieesdavividNd 190
                                         + v  +P +f+ ++ + + ++l  +++ e s av  ++N 
  gene1046|gene1046|rna1045|rna1045 337 NQFVEWCPTGFKVGINSRKPTVLDGEAMAEVSRAVCALSNT 377
                                        44455678888889999999999999999999999988886 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.2   0.1   1.6e-52     7e-49       1     125 [.     259     388 ..     259     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 165.2 bits;  conditional E-value: 1.6e-52
                                        TTC-EEEEEEESSSCTTTTTCS-HHHHHHHHHTCSGGGBSSSTSTTTSSEEEEEEEEEESSSHHHHHHHHHHHHHT CS
                          Tubulin_C   1 PrlhFlltsyaPlvsaekaavektsvqdvtrallepknimvkvdprkgkylaiallirGdvepkevnkavqrikek 76 
                                        Pr+hF+l++y+P++s+ekaa+ek+svq++t+a++ep+++mv++d+rkgky+a++ll+rGdv+pke+n+a +++k+k
  gene1046|gene1046|rna1045|rna1045 259 PRIHFPLVAYSPMLSKEKAAHEKLSVQEITNACFEPQSQMVRCDTRKGKYMACCLLFRGDVNPKEANNATANVKAK 334
                                        9*************************************************************************** PP

                                        TTS-BSTTSTTTEEEEEEECECT-TTTS.....SCEEEEEEEEGGGHHHHHHHH CS
                          Tubulin_C  77 kkaqfveWiptgikvalnkkspyvkkqs.....kvsvlmlaNttsiaelfkrll 125
                                        +++qfveW+ptg+kv++n+++p+v +++     +++v+ l+Ntt+i+e++krl+
  gene1046|gene1046|rna1045|rna1045 335 RTNQFVEWCPTGFKVGINSRKPTVLDGEamaevSRAVCALSNTTAISEAWKRLN 388
                                        **************************9999*999******************97 PP

>> Tubulin_3  Tubulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   9.3e-08   0.00042      63     107 ..     118     163 ..      82     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.3e-08
                          Tubulin_3  63 dlrpfaeecdqlrglqvftgvddaWG.Gfaakylerlrdeygkksi 107
                                         +r +a++cd l+g+ ++ +     G Gfa+  ++rl  e+gkks 
  gene1046|gene1046|rna1045|rna1045 118 QIRRMADNCDGLQGFLIYHSFGGGTGsGFASLMMDRLAAEFGKKSK 163
                                        689*****************99887769***************985 PP

>> Misat_Tub_SegII  Misato Segment II tubulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.2e-05       0.1       1      80 [.       2      82 ..       2     118 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.2e-05
                    Misat_Tub_SegII  1 rEivtlqlGnyaNyvgtHfWNt..Qesyftydeeeeesev..dhdvlfregetkqgqvtytPRllivDlkgslgslrk 74
                                       rEi++l +G+    +g   W +  +e+ +  d + +++ +  ++  +f++   ++   ty+PR+l+vDl+ ++ +  k
  gene1046|gene1046|rna1045|rna1045  2 REIISLHIGQAGVQIGNACWELycKEHGILPDGRLDQNRMddESAESFFS---QTSVGTYVPRTLMVDLEPGVLESIK 76
                                       78888888888888888888753366666555555544452122223333...55678***********987766555 PP

                    Misat_Tub_SegII 75 egelye 80
                                       +g+  e
  gene1046|gene1046|rna1045|rna1045 77 TGKYRE 82
                                       555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3115.63
//
Query:       gene1047|gene1047|rna1046|rna1046  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 797.18
//
Query:       gene1048|gene1048|rna1047|rna1047  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.34s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 648.35
//
Query:       gene1049|gene1049|rna1048|rna1048  [L=680]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-33  115.0   2.8    4.3e-33  115.0   2.8    2.4  2  FH2         Formin Homology 2 Domain
    3.9e-05   23.3   0.4    3.9e-05   23.3   0.4    2.2  2  Drf_GBD     Diaphanous GTPase-binding Domain
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.061   13.7   0.0    2.2  2  Cyclin_C_2  Cyclin C-terminal domain
      0.062   13.6   1.5       0.39   11.1   0.3    2.6  2  P22_AR_N    P22_AR N-terminal domain
       0.28   11.5   0.1       0.28   11.5   0.1    2.7  3  DapH_N      Tetrahydrodipicolinate succinyltransferase N-term
        0.4   11.1   8.9        1.9    8.9   0.0    4.4  3  FlaC_arch   Flagella accessory protein C (FlaC)
       0.68   10.3   3.2         27    5.1   0.5    2.8  2  KORA        TrfB plasmid transcriptional repressor


Domain annotation for each model (and alignments):
>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3      0.84   2.2e+03     158     187 ..      38      67 ..      27      77 .. 0.73
   2 !  115.0   2.8   1.7e-36   4.3e-33       3     352 ..     344     658 ..     342     665 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.84
                                        THHHHHHHHHHHHTHHHHHHHHHHHHHHHH CS
                                FH2 158 rlekRleallfkstfeeeveelkrsleale 187
                                        +l+k++++++ ++t+ee+ +++k+ + +l+
  gene1049|gene1049|rna1048|rna1048  38 NLSKKIRTITSMQTLEERKKKIKEYVIKLK 67 
                                        567778888888888887777777666665 PP

  == domain 2  score: 115.0 bits;  conditional E-value: 1.7e-36
                                        XX---SS-B------EESSGGCTTSCCCCTCCHHHHCTSHHHHHHHHTBSC--HCCH......HCSCCTTCCESSS CS
                                FH2   3 kkikpkkkLkplhWdkvkpsqdrstvWdklkeesfekeldlseleelFsakekkkkkkksekskkskkkkkkvklL 78 
                                        k+  p+k+  +++W+k+ +  +   vW++++ e+ e+  + +e+ ++F++k +k+k+       +   +k + ++ 
  gene1049|gene1049|rna1048|rna1048 344 KSTAPSKRYIQVKWTKMGKGNS---VWNRIRIEEMESAFKAEEF-DGFEMKGEKPKA------LSTGIEKRRPSVF 409
                                        677899999*******988776...9*****9988866666666.578888887665......6788899999*** PP

                                        -HHHHHHHHHHHHHHTS-HHHHHHHHHTTTTCCCTHHHHHHHHHHCGGHHHHHHHHCTCTSGTTB-HHHHHHHHHT CS
                                FH2  79 dpkrsqniaIlLkklkltaeeiveaileldeealdlellenLlkmaPtkeelkklkeykgevseLseaeqFllelv 154
                                        ++k+  +i+I L ++k +  e+++ail++ e  l+++l+++Ll ++Pt+ee+++l+   g     ++ae F++e +
  gene1049|gene1049|rna1048|rna1048 410 SEKKNYAINIALGRVKESNCELKSAILNMQE-DLNENLVKQLLFYFPTDEEIEQLQ---GTDHVFGRAEEFFKESI 481
                                        ******************************9.9**********************8...55567************ PP

                                        TSTTHHHH.HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHSTCSTTCS-SEE-GGG CS
                                FH2 155 kiprlekR.leallfkstfeeeveelkrslealeaaseeLknskkfkklLeliLalGNymNdgtrrgqAkGFkLss 229
                                        +  ++ kR l  l f+++f ++  ++ ++l  le+  + L +sk+++++L + L +GNy+N+g+  g+A GF ++s
  gene1049|gene1049|rna1048|rna1048 482 EEAEVMKRcLYYLYFMISFRNQ--NVCKNLGILERYYTMLLESKELRRFLGITLVAGNYLNKGSFLGSAEGFTMES 555
                                        *88888885688999****985..99************************************************** PP

                                        GGGCCCSB-STTTSBHHHHHHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTT CS
                                FH2 230 LlkLsdvKstdnkttLLHylvkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekk 305
                                        + k+ +vK++    +LL +l k i+      + + ++L+ v +a+ +n+e+l  e+++l+k+         +s + 
  gene1049|gene1049|rna1048|rna1048 556 IPKILEVKNNG--NSLLGLLKKKID-----CKLLLEDLSVVYDASGINFEALCIEIEELKKNYIS------ASGS- 617
                                        ********865..59*****99986.....55699*****************9999999987643......3333. PP

                                        SSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--T CS
                                FH2 306 eepsdkflevlkeflkeaeeklkkleeelkeakelvkelveYfgedk 352
                                                 +++e +++ +ek++++ ++++++ +l  ++ eYfge+ 
  gene1049|gene1049|rna1048|rna1048 618 ------PFPKIQERIERIQEKYEDICSLYDKVSKLHRDCREYFGEKV 658
                                        ......35667888899999999999999999999999999998864 PP

>> Drf_GBD  Diaphanous GTPase-binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.4   1.5e-08   3.9e-05       5     123 ..       8     112 ..       5     117 .. 0.85
   2 ?   -3.5   0.6       2.5   6.5e+03      36      77 ..     318     343 ..     294     356 .. 0.45

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.5e-08
                            Drf_GBD   5 deeeidklFeelleelnlpeekrealla.lpiekKwqlvvqdkkkkakkeeklsksksksneeespesyvkklkdd 79 
                                        + e i+  F +++e + ++eek+++l+a l+ +kK   +++ +  ++ k+              + ++yv klkd 
  gene1049|gene1049|rna1048|rna1048   8 SLEHINIQFRSIMEGMGIDEEKQHKLAAkLNLSKKIRTITSMQTLEERKK--------------KIKEYVIKLKDR 69 
                                        56789******************988751688888888887777555444..............8999******** PP

                            Drf_GBD  80 slkekqlesLrVaLrtqplsWvkrFieleGlvaLlnvLskinek 123
                                        ++    l sL+V+L t p    + F + +G+ +L+  +++++e+
  gene1049|gene1049|rna1048|rna1048  70 NSV-LNLLSLSVSLETGPRVLYEIFSGEGGHDVLVRCMRRMDEE 112
                                        *99.66779***************************99999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.5
                            Drf_GBD  36 ekKwqlvvqdkkkkakkeeklsksksksneeespesyvkklk 77 
                                         kK+  v + +                 n+ + p+  +kk+ 
  gene1049|gene1049|rna1048|rna1048 318 AKKKDVVKKAE----------------VNKVKGPKKIIKKVA 343
                                        33333333333................333333344443333 PP

>> Cyclin_C_2  Cyclin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.8   1.2e+04      84     101 ..     180     197 ..     156     198 .. 0.63
   2 ?   13.7   0.0   2.4e-05     0.061       8      95 ..     550     646 ..     547     654 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.8
                         Cyclin_C_2  84 aksellekllktiescrk 101
                                        ++++ l+k+++ i++++ 
  gene1049|gene1049|rna1048|rna1048 180 VCNSYLSKIIEYIKRISR 197
                                        455668888888888875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.4e-05
                         Cyclin_C_2   8 Gflld.LkalgkslekriekaykrareilkssalltDayflytPsqIalaallladeklaerYleeklgk.....e 77 
                                        Gf ++ + ++ ++ +++ +++    ++ ++ + ll D+  +y  s I + al ++ e+l+++Y++ + +      e
  gene1049|gene1049|rna1048|rna1048 550 GFTMEsIPKILEV-KNNGNSLLGLLKKKIDCKLLLEDLSVVYDASGINFEALCIEIEELKKNYISASGSPfpkiqE 624
                                        6666533333333.34778888889999999*********************************998766433320 PP

                         Cyclin_C_2  78 esseks..........aksellekllkt 95 
                                             +          ++ +l++k+ k 
  gene1049|gene1049|rna1048|rna1048 625 -----RieriqekyedIC-SLYDKVSKL 646
                                        .....1232222222222.334444444 PP

>> P22_AR_N  P22_AR N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00015      0.39      21      77 ..      14      73 ..       7      79 .. 0.74
   2 ?    0.0   0.0      0.41     1e+03      53     101 ..     587     634 ..     573     642 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                           P22_AR_N 21 vamkpivealGldwssQve...KlkedeklssvvieitvpsdgktremlclplrklpgwL 77
                                       +  ++i+e++G+d ++Q++   Kl+ ++k+++++   t+++  k+ + ++++l+  +  L
  gene1049|gene1049|rna1048|rna1048 14 IQFRSIMEGMGIDEEKQHKlaaKLNLSKKIRTITSMQTLEERKKKIKEYVIKLKDRNSVL 73
                                       6789*************9533366666666666666567778888888888888766665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.41
                           P22_AR_N  53 eitvpsdgktremlclplrklpgwLakInpnkvkpelrekviaYqeeca 101
                                        ++++ ++g + e+lc++++ l+   ++ + +   p+++e++++ qe+ +
  gene1049|gene1049|rna1048|rna1048 587 SVVYDASGINFEALCIEIEELKKNYISASGS-PFPKIQERIERIQEKYE 634
                                        4457778888999*****9999877776533.23555555555555544 PP

>> DapH_N  Tetrahydrodipicolinate succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00011      0.28      58      84 ..      50      76 ..      45      78 .. 0.90
   2 ?   -3.3   0.0       4.2   1.1e+04      49      56 ..     289     296 ..     280     324 .. 0.53
   3 ?   -1.3   0.4         1   2.7e+03       8      27 ..     337     357 ..     335     366 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                       HHHHHTTTTEEEEEEEE--BSB-S-B- CS
                             DapH_N 58 evleenkdkiedyevendrRnSAiPll 84
                                       + lee+k+ki++y++  + RnS + ll
  gene1049|gene1049|rna1048|rna1048 50 QTLEERKKKIKEYVIKLKDRNSVLNLL 76
                                       689*******************99987 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                                        EEEEHHHH CS
                             DapH_N  49 vfGdwkei 56 
                                        vfGd+ e 
  gene1049|gene1049|rna1048|rna1048 289 VFGDLREN 296
                                        45554432 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1
                                        HHHHH---B-.EEEEEEEE-. CS
                             DapH_N   8 kyIkeakKkT.pvkvYvkgel 27 
                                        k+Ik+  K+T p k Y++ + 
  gene1049|gene1049|rna1048|rna1048 337 KIIKKVAKSTaPSKRYIQVKW 357
                                        567887787768999999875 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.1     0.092   2.4e+02      14      43 ..      47      78 ..      37      78 .. 0.77
   2 ?    1.2   0.4      0.19   4.9e+02      12      37 ..     417     442 ..     411     451 .. 0.77
   3 ?    8.9   0.0   0.00075       1.9      25      49 ..     621     645 ..     601     647 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.092
                          FlaC_arch 14 teletvkkeneelsksveelken..VkdllsL 43
                                       t+++t+++  +++++ v +lk++  V +llsL
  gene1049|gene1049|rna1048|rna1048 47 TSMQTLEERKKKIKEYVIKLKDRnsVLNLLSL 78
                                       699*****************985226666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                          FlaC_arch  12 lsteletvkkeneelsksveelkenV 37 
                                        + + l+ vk++n el++ + +++e+ 
  gene1049|gene1049|rna1048|rna1048 417 INIALGRVKESNCELKSAILNMQEDL 442
                                        67789999**********99999887 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00075
                          FlaC_arch  25 elsksveelkenVkdllsLYEvVsn 49 
                                        ++++ +e+++e+ +d+ sLY+ Vs+
  gene1049|gene1049|rna1048|rna1048 621 KIQERIERIQEKYEDICSLYDKVSK 645
                                        799********************96 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.016        42      11      46 ..       7      42 ..       4      70 .. 0.90
   2 ?    5.1   0.5     0.011        27      11      55 ..     298     342 ..     291     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                               KORA 11 kgleelaeqtveiargvLVegkkqadvatelgltkq 46
                                       k le++  q + i  g+ ++++kq ++a++l l+k+
  gene1049|gene1049|rna1048|rna1048  7 KSLEHINIQFRSIMEGMGIDEEKQHKLAAKLNLSKK 42
                                       678888899999999999****************97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                               KORA  11 kgleelaeqtveiargvLVegkkqadvatelgltkqa.vsqavkrv 55 
                                        +++ ++ e+  e+  +v Ve  k++dv+++  + k +  ++++k+v
  gene1049|gene1049|rna1048|rna1048 298 EKM-KISEEGSEVTGEVVVEAAKKKDVVKKAEVNKVKgPKKIIKKV 342
                                        678.899999*******************99888744134555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1392  (0.0776396); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 4147.61
//
Query:       gene1050|gene1050|rna1049|rna1049  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-05   25.2   0.9     0.0001   22.1   0.2    2.5  3  EF-hand_8  EF-hand domain pair
     0.0001   22.7   1.6    0.00068   20.0   0.1    2.3  2  EF-hand_7  EF-hand domain pair
    0.00023   20.8   0.8      0.083   12.9   0.0    3.4  3  EF-hand_6  EF-hand domain
     0.0029   17.0   4.7      0.012   15.1   0.1    3.7  4  EF-hand_1  EF hand
  ------ inclusion threshold ------
       0.12   12.7   0.0        6.8    7.1   0.0    2.2  2  EF-hand_9  EF-hand domain


Domain annotation for each model (and alignments):
>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.84     3e+03       2      11 ..      13      22 ..      12      32 .. 0.59
   2 ?    0.7   0.0      0.14   4.9e+02       6      31 ..      42      65 ..      42      69 .. 0.58
   3 !   22.1   0.2   2.9e-08    0.0001       2      53 ..      72     120 ..      71     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.84
                          EF-hand_8  2 kgkItreelr 11
                                       +gk+t+e+ +
  gene1050|gene1050|rna1049|rna1049 13 TGKLTKETTK 22
                                       5666665533 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                          EF-hand_8  6 treelrrilrilglkkglseeevdil 31
                                       t+ee++  ++++  +  + +ee++ +
  gene1050|gene1050|rna1049|rna1049 42 TFEEFSQLASTIPPP--IPKEEMRRM 65
                                       677777765555333..666666555 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 2.9e-08
                          EF-hand_8   2 kgkItreelrrilrilglkkglseeevdilfrefDtdgdGkisfeEFcvlle 53 
                                        ++ I+r +l + +++ g   +l+eee+ +lfr   +d++G i+ +E +++l 
  gene1050|gene1050|rna1049|rna1049  72 GMHISRKNLGKYMTM-GD--KLNEEEMSELFRSCPFDRNGEITINELLDFLY 120
                                        677888888886655.55..5**************************99986 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.11   3.8e+02      12      29 ..       9      26 ..       4      50 .. 0.69
   2 !   20.0   0.1   1.9e-07   0.00068      19      69 ..      57     118 ..      57     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                          EF-hand_7 12 Dtdgdgyldkeellrllr 29
                                       D  ++g+l+ke  ++llr
  gene1050|gene1050|rna1049|rna1049  9 DAFDTGKLTKETTKDLLR 26
                                       556778888888888877 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.9e-07
                          EF-hand_7  19 ldkeellrllrkifqga...........gegsklsdeelellfkefDtdkdGvisfdEFlkl 69 
                                        + kee++r+++ +++g              g+kl +ee+ +lf+    d++G+i+ +E+l +
  gene1050|gene1050|rna1049|rna1049  57 IPKEEMRRMVQMFIHGMhisrknlgkymTMGDKLNEEEMSELFRSCPFDRNGEITINELLDF 118
                                        56899*********999*****************************************9987 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.013        46       9      29 ..       8      27 ..       4      29 .. 0.81
   2 ?   -0.2   0.0      0.36   1.3e+03      16      27 ..      74      85 ..      57      91 .. 0.64
   3 !   12.9   0.0   2.3e-05     0.083       4      26 ..      97     119 ..      94     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                          EF-hand_6  9 fDkdgdGkidaeElrkalrka 29
                                       +D  ++Gk+++e  +++lr +
  gene1050|gene1050|rna1049|rna1049  8 WDAFDTGKLTKETTKDLLR-L 27
                                       576789******9999999.4 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.36
                          EF-hand_6 16 kidaeElrkalr 27
                                       +i+++ l k ++
  gene1050|gene1050|rna1049|rna1049 74 HISRKNLGKYMT 85
                                       456666666665 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 2.3e-05
                          EF-hand_6   4 eaFklfDkdgdGkidaeElrkal 26 
                                        e+F+   +d++G+i+++El ++l
  gene1050|gene1050|rna1049|rna1049  97 ELFRSCPFDRNGEITINELLDFL 119
                                        66666668************998 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.59   2.1e+03       3      11 ..       5      13 ..       3      19 .. 0.72
   2 ?    0.6   0.0      0.15   5.3e+02      18      26 ..      42      50 ..      42      53 .. 0.80
   3 ?   -0.1   0.1      0.24   8.5e+02      19      28 ..      59      68 ..      57      69 .. 0.77
   4 !   15.1   0.1   3.4e-06     0.012       1      26 [.      94     119 ..      89     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.59
                                       HHHHHHHTT CS
                          EF-hand_1  3 keiFrefDk 11
                                       ke ++ fD+
  gene1050|gene1050|rna1049|rna1049  5 KEQWDAFDT 13
                                       677788885 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                                       EHHHHHHHH CS
                          EF-hand_1 18 dfeEfkell 26
                                       +feEf +l 
  gene1050|gene1050|rna1049|rna1049 42 TFEEFSQLA 50
                                       79***9876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.24
                                       HHHHHHHHHH CS
                          EF-hand_1 19 feEfkellkk 28
                                       +eE+++++++
  gene1050|gene1050|rna1049|rna1049 59 KEEMRRMVQM 68
                                       7999999876 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 3.4e-06
                                        HHHHHHHHHTTTSSSEEEHHHHHHHH CS
                          EF-hand_1   1 elkeiFrefDkDgdGkIdfeEfkell 26 
                                        e+ e+Fr    D++G I+++E++++l
  gene1050|gene1050|rna1049|rna1049  94 EMSELFRSCPFDRNGEITINELLDFL 119
                                        56799******************998 PP

>> EF-hand_9  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.023        83       8      36 ..       9      36 ..       5      48 .. 0.82
   2 ?    7.1   0.0    0.0019       6.8       3      24 ..      98     119 ..      96     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.023
                          EF-hand_9  8 DtqktGrVpvsrlidyLravtaqdpeese 36
                                       D   tG+ +    +d+Lr ++  +p e +
  gene1050|gene1050|rna1049|rna1049  9 DAFDTGKLTKETTKDLLRLCGF-TPRERD 36
                                       44557999999999******99.999875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0019
                          EF-hand_9   3 vFevcDtqktGrVpvsrlidyL 24 
                                        +F+ c  ++ G++++ +l+d+L
  gene1050|gene1050|rna1049|rna1049  98 LFRSCPFDRNGEITINELLDFL 119
                                        7999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 833.07
//
Query:       gene105|gene105|rna105|rna105  [L=780]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-99  329.6   0.0    2.8e-48  163.7   0.0    2.4  2  AAA              ATPase family associated with various cellul
    6.2e-24   83.5   2.1    1.8e-12   46.8   0.3    2.6  2  AAA_lid_3        AAA+ lid domain
      2e-15   56.9   0.0    7.5e-07   29.0   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.9e-13   50.9   0.0    7.7e-06   26.1   0.0    2.7  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.2e-12   47.7   0.1      0.002   18.5   0.0    4.2  3  AAA_16           AAA ATPase domain
    1.2e-10   41.6   0.2    9.3e-05   22.4   0.0    3.6  2  AAA_5            AAA domain (dynein-related subfamily)
    2.1e-10   41.0   1.6      0.049   13.9   0.0    4.8  4  AAA_22           AAA domain
    7.7e-10   39.1   0.0    0.00031   20.9   0.0    2.6  2  AAA_33           AAA domain
    4.4e-09   36.0   0.0     0.0021   17.3   0.0    2.4  2  TIP49            TIP49 P-loop domain
    1.8e-08   34.5   0.0      0.003   17.6   0.0    2.6  2  AAA_14           AAA domain
      1e-07   31.9   0.6      0.021   14.5   0.0    3.7  4  IstB_IS21        IstB-like ATP binding protein
      2e-07   31.6   0.0     0.0071   16.9   0.0    2.7  2  AAA_18           AAA domain
    2.4e-07   31.1   0.0      0.014   15.8   0.0    2.8  2  RNA_helicase     RNA helicase
    3.6e-07   29.8   0.3      0.029   13.7   0.0    2.6  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      2e-06   28.3   0.0       0.16   12.5   0.0    3.6  2  ABC_tran         ABC transporter
    2.3e-06   27.3   2.4       0.72    9.4   0.0    4.0  4  AAA_25           AAA domain
    3.2e-06   26.7   1.8          1    8.7   0.0    4.1  4  ATPase           KaiC
    4.3e-06   26.0   0.3      0.021   13.9   0.0    2.5  2  Parvo_NS1        Parvovirus non-structural protein NS1
    8.3e-06   25.4   0.0       0.15   11.6   0.0    2.8  2  AAA_7            P-loop containing dynein motor region
    9.7e-06   25.4   0.0      0.018   14.7   0.0    2.6  2  AAA_24           AAA domain
      1e-05   25.5   0.0      0.013   15.3   0.0    2.9  2  Bac_DnaA         Bacterial dnaA  protein
      1e-05   25.9   0.0       0.17   12.1   0.0    3.1  3  AAA_28           AAA domain
    1.6e-05   24.8   0.2    0.00085   19.3   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
    2.8e-05   23.9   0.1       0.21   11.3   0.0    3.6  2  Sigma54_activat  Sigma-54 interaction domain
    3.5e-05   23.1   0.0      0.031   13.4   0.0    2.4  2  DUF815           Protein of unknown function (DUF815)
    4.6e-05   23.5   0.0     0.0042   17.1   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
    4.9e-05   23.8   0.0       0.45   10.9   0.0    2.8  2  AAA_17           AAA domain
    5.8e-05   23.1   0.0       0.49   10.4   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    6.4e-05   23.1   0.0    0.00015   21.8   0.0    1.7  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    0.00017   21.6   0.1       0.94    9.3   0.0    2.9  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00022   21.4   0.0       0.22   11.7   0.0    2.7  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00025   21.0   0.5       0.44   10.5   0.0    3.3  4  NACHT            NACHT domain
     0.0003   20.1   0.1       0.84    8.9   0.1    2.9  2  Zeta_toxin       Zeta toxin
    0.00036   20.4   0.0        0.7    9.8   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    0.00064   19.0   0.0       0.76    8.9   0.0    2.7  2  NB-ARC           NB-ARC domain
    0.00069   19.4   0.0      0.091   12.5   0.0    2.4  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00091   18.7   1.0        1.1    8.7   0.1    2.4  2  PhoH             PhoH-like protein
     0.0017   17.7   0.0       0.29   10.3   0.0    2.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0023   17.8   0.9       0.87    9.3   0.3    3.1  2  AAA_11           AAA domain
     0.0057   16.6   0.0        3.3    7.6   0.0    3.0  2  Rad17            Rad17 P-loop domain
     0.0062   16.9   1.1          2    8.8   0.1    2.8  2  AAA_19           AAA domain
     0.0069   16.3   1.2          6    6.7   0.0    4.0  4  NTPase_1         NTPase
  ------ inclusion threshold ------
      0.048   13.8   0.0        5.2    7.2   0.0    2.7  2  Cytidylate_kin2  Cytidylate kinase-like family
      0.061   13.1   0.6         14    5.4   0.0    3.8  4  DEAD             DEAD/DEAH box helicase
      0.074   12.8   0.2         14    5.3   0.0    3.1  3  Cytidylate_kin   Cytidylate kinase
      0.075   12.7   1.2        3.8    7.2   0.1    2.4  2  AAA_30           AAA domain
       0.11   11.9   0.0         11    5.4   0.0    3.2  3  TniB             Bacterial TniB protein
       0.13   11.6   0.0       0.69    9.2   0.0    2.2  2  Nrap_D4          Nrap protein nucleotidyltransferase domain 4
       0.27   11.2   0.8       0.61   10.1   0.1    2.0  1  DUF2388          Protein of unknown function (DUF2388)
       0.48   10.9   2.5         29    5.1   0.1    3.2  3  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.6   0.0     8e-51   2.9e-48       1     131 [.     245     374 ..     245     375 .. 0.98
   2 !  163.7   0.0   7.9e-51   2.8e-48       1     132 []     518     650 ..     518     650 .. 0.97

  Alignments for each domain:
  == domain 1  score: 163.6 bits;  conditional E-value: 8e-51
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +llyGppGtGKTl+a+a+a+e+g+ ++ i+g+e++sk+ gese+++r+ f+ea+++a psi+fiDEidala++r++s+ e
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGAFLFLINGPEIMSKMAGESESNLRKAFEEAEKNA-PSIIFIDEIDALAPKREKSQGE 323
                                    69******************************************************9.********************** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +e+r+v+qLlt +dg+k + s+viv+gatnrp+++d+al+r gRfdr+iei+
  gene105|gene105|rna105|rna105 324 VERRIVSQLLTLMDGMKAR-SNVIVLGATNRPNSIDSALRRyGRFDREIEIG 374
                                    ******************7.66***************************996 PP

  == domain 2  score: 163.7 bits;  conditional E-value: 7.9e-51
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgse 78 
                                    vl+yGppG+GKTllakava+e++++f++i+g+ells++vgese++ir+lf++a+  a p++lf+DEid++ak+r  ++++
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKANFISIKGPELLSMWVGESESNIRDLFARARGAA-PCVLFFDEIDSIAKARsgNDAS 596
                                    79****************************************************999.****************877889 PP

                                    CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                            AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                    s++++r++nqLl+e+dg + k++ v+vigatnrpd+ld+al+r gR+d+ ++i+l
  gene105|gene105|rna105|rna105 597 SGVTDRMLNQLLSEMDGINLKKN-VFVIGATNRPDQLDSALMRpGRLDQLVYIPL 650
                                    *******************9755.**************************99985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   1.7e-11   5.9e-09       1      43 [.     397     439 ..     397     442 .. 0.95
   2 !   46.8   0.3     5e-15   1.8e-12       1      42 [.     672     714 ..     672     723 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.7e-11
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedf 43 
                                    dvdl ++ ++ +G++G Dla+lc eAal  +r+++++i+ +d 
  gene105|gene105|rna105|rna105 397 DVDLVAINKELHGFTGSDLASLCSEAALQQIREKLPQIDLDDE 439
                                    9************************************998886 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 5e-15
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.eitmed 42 
                                    d+dl +LAe+T+ +SGADl+++c++A  lA+r++i+ e++++ 
  gene105|gene105|rna105|rna105 672 DIDLRQLAEATDKFSGADLSEICQRACKLAIRETIEyELEQKK 714
                                    89*********************************95588874 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   2.1e-09   7.5e-07      35     103 ..     244     320 ..     231     370 .. 0.68
   2 !   24.7   0.0   4.4e-08   1.6e-05      34     100 ..     516     590 ..     488     642 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.1e-09
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                     +llyGpPG Gkt +a+ ia+e g+ l    gP +      e +++l   + + e++   ++fidei  l+++ e  
  gene105|gene105|rna105|rna105 244 GILLYGPPGTGKTLIARAIANETGAFLFLINGPEImskmagESESNLRKAFEEAEKNapSIIFIDEIDALAPKREKS 320
                                    69*******************************883322222334565555555544337**********9987765 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 4.4e-08
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideihrlsrav 100
                                      vl+yGpPG Gkt lak +a+e ++++ +  gP l      e ++++  l+++ +     vlf dei  +++a 
  gene105|gene105|rna105|rna105 516 KGVLFYGPPGCGKTLLAKAVATECKANFISIKGPELlsmwvgESESNIRDLFARARGAApcVLFFDEIDSIAKAR 590
                                    569*******************************87444444556667666666554323399999999887764 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.2e-08   7.7e-06       6     108 ..     245     341 ..     240     356 .. 0.86
   2 !   21.8   0.0   4.5e-07   0.00016       6     100 ..     518     604 ..     513     624 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.2e-08
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt++a+a+a+   +     l  ++  e++     +   +++   +++  +ae++   i+++DEid  +pk
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGA----FLFLINGPEIMS----KMAGESESNLRKAFEEAEKNApsIIFIDEIDALAPK 316
                                    8999****************9995....9999********....88888888888888888888889************* PP

                                    .---------HHHHHHHHHHHH--EE CS
                          AAA_2  84 .essgadvSregVqrdLLqileggtl 108
                                     e+s+ +v r  ++  LL +++g ++
  gene105|gene105|rna105|rna105 317 rEKSQGEVERR-IVSQLLTLMDGMKA 341
                                    76677777665.66779999999766 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 4.5e-07
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKihpk 83 
                                    +l+ gp g+Gkt+laka+a   ++    ++i +   ell     e+e+ +  l   + g        ++++DEid i++ 
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKA----NFISIKGPELLSmwVGESESNIRDLFARARGAA----PCVLFFDEIDSIAK- 588
                                    799*******************95....9****9999999554555555555555554443....44************. PP

                                    ---------HHHHHHHH CS
                          AAA_2  84 essgadvSregVqrdLL 100
                                     +sg+d S+ gV + +L
  gene105|gene105|rna105|rna105 589 ARSGNDASS-GVTDRML 604
                                    999999997.4444333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   5.8e-06    0.0021      24      52 ..     242     267 ..     215     348 .. 0.60
   2 !   18.5   0.0   5.6e-06     0.002      25      63 ..     516     551 ..     509     560 .. 0.84
   3 ?    4.0   0.0      0.17        60     124     161 ..     564     610 ..     557     623 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.8e-06
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdg 52 
                                    p  +ll+G++G+GK+ ++r++++   ++g
  gene105|gene105|rna105|rna105 242 PKGILLYGPPGTGKTLIARAIAN---ETG 267
                                    489******************96...333 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 5.6e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                      vl++G++G+GK+ l+++++++ +++   f++ k  +l
  gene105|gene105|rna105|rna105 516 KGVLFYGPPGCGKTLLAKAVATECKAN---FISIKGPEL 551
                                    689******************999988...777776665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.17
                         AAA_16 124 krllallsrderplvlvlDdlq.........wadeaslql.laaLlrl 161
                                    ++l+a+++  + p vl++D+++         +a ++  +  l +Ll++
  gene105|gene105|rna105|rna105 564 RDLFARARG-AAPCVLFFDEIDsiakarsgnDASSGVTDRmLNQLLSE 610
                                    556677776.889*********77766665544444444445555555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.6e-07   9.3e-05       2     136 ..     245     363 ..     244     364 .. 0.67
   2 !   14.6   0.0     7e-05     0.025       2      80 ..     518     589 ..     517     638 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.6e-07
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.....G-SEEEEESGGG CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.....egeilvlDEver 76 
                                    +lL GppGtgK+ +a+ +a  +++ ++ +++++ +++     + ++             +a++      ++i+++DE++ 
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGAFLFLINGPEIMSKMAGESESNL------------RKAFEeaeknAPSIIFIDEIDA 312
                                    89*******************************9987554444444............3333333367899********9 PP

                                    --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                          AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                    + ++  +s   + e+r ++  ++ +l++  +  + +++ v++++n+++    ++++alr+
  gene105|gene105|rna105|rna105 313 LAPKREKSQGEV-ERRIVS--QLLTLMDGMK--ARSNVIVLGATNRPN----SIDSALRR 363
                                    888766666333.333333..4444443333..122266666666666....77777765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 7e-05
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HH CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraese 80 
                                    vl  GppG+gK+ la+ +a   ++++  + +++      l+  +   +++   +d  +   +  +++l++DE++ + ++
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKANFISIKGPE------LLSMWV-GESESNIRDLFARARGAAPCVLFFDEIDSIAKA 589
                                    899***************999999988888876......555555.355555566666655568888888888877744 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00014     0.049       8      29 ..     245     266 ..     240     281 .. 0.86
   2 ?    6.4   0.0     0.029        10      73     118 ..     285     338 ..     277     354 .. 0.72
   3 !   13.4   0.0    0.0002     0.073       8      44 ..     518     553 ..     512     570 .. 0.69
   4 ?    2.7   0.0       0.4   1.4e+02      89     117 ..     570     612 ..     557     632 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G++GtGKT+ +r ++++ 
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANET 266
                                    89***************99976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.029
                         AAA_22  73 lsseellealeqalraravielliiDEaqhlr.....s.....eealeeLrsllnl 118
                                     s++ l++a+e+a +++    ++ iDE++ l      s      +++++L +l++ 
  gene105|gene105|rna105|rna105 285 ESESNLRKAFEEAEKNAPS--IIFIDEIDALApkrekSqgeveRRIVSQLLTLMDG 338
                                    5788888999999888888..**********8875541666667777777777774 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.0002
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvf 44 
                                    ++ +G++G+GKT+l++ ++ +  +++++  ++pe+++
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATEC-KANFISIKGPELLS 553
                                    6789**************9985.33344335555555 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.4
                         AAA_22  89 rav..ielliiDEaqhlr...s.........eealeeLrslln 117
                                    ++   + +l  DE++ +    s         +++l++L s ++
  gene105|gene105|rna105|rna105 570 ARGaaPCVLFFDEIDSIAkarSgndassgvtDRMLNQLLSEMD 612
                                    2224668*********988872555667888999999976665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   8.8e-07   0.00031       2      80 ..     245     353 ..     245     380 .. 0.69
   2 !   15.6   0.0   3.9e-05     0.014       2      45 ..     518     563 ..     518     628 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.8e-07
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrv 51 
                                    +ll G+pG+GK+  a+ +++++g   +l++ ++++++++g+ + +++                             + +v
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGafLFLINGPEIMSKMAGESESNLRkafeeaeknapsiifideidalapkrekSQGEV 324
                                    6789*******************98889*****99999996555555555566666666667766666666665545556 PP

                         AAA_33  52 ldrlyqilnelarkalsagrnvil.datnl 80 
                                    + r+  +l  l +  ++a+ nvi+  atn+
  gene105|gene105|rna105|rna105 325 ERRIVSQLLTLMD-GMKARSNVIVlGATNR 353
                                    6666666655553.4444444443255554 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.9e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsk 45 
                                    vl+ G+pG+GK+ la+ ++ + +  ++ +  ++l+++ +g+ + ++
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKanFISIKGPELLSMWVGESESNI 563
                                    799******************9977777777777777666555444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.8e-06    0.0021      51     105 ..     243     292 ..     235     344 .. 0.80
   2 !   16.0   0.0   1.5e-05    0.0052      42      98 ..     507     561 ..     502     572 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.8e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrk 105
                                    +++Ll Gp+gtGkt +a ai++e g+      ++g e+ s     +e    +lrk
  gene105|gene105|rna105|rna105 243 KGILLYGPPGTGKTLIARAIANETGA--FLFLINGPEIMSKMAGESES---NLRK 292
                                    89*********************993..44578999999988777763...4444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  42 likekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                    +ik +    ++vL+ Gp+g Gkt la a++ e      f++++g e+ s+ v  +e 
  gene105|gene105|rna105|rna105 507 FIKFGMTPAKGVLFYGPPGCGKTLLAKAVATECK--ANFISIKGPELLSMWVGESES 561
                                    5677777789*********************986..78**********998888775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.3e-06     0.003       5     104 ..     245     354 ..     242     373 .. 0.76
   2 !   14.1   0.0    0.0001     0.036       5      80 ..     518     590 ..     515     650 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.3e-06
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev....... 76 
                                    +++ G+  +GKT +++ +++e        + in  +   k++ ++e +l +++ e  +++  +++f+DEi  +       
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETG---AFLFLINGPEIMSKMAGESEsNLRKAFEEA-EKNAPSIIFIDEIDALapkreks 320
                                    7899***************9988...778888988888877776662444555554.45599*********999999999 PP

                         AAA_14  77 .....pewekalkslvd.egknldvivtGSnskl 104
                                         +++ + l  l+d  + + +viv G  +  
  gene105|gene105|rna105|rna105 321 qgeveRRIVSQLLTLMDgMKARSNVIVLGATNRP 354
                                    8888888888888888853367788888877655 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.0001
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe 80 
                                    ++  G+  +GKT l+k ++ e      +++ i+  +       ++e++++ +++++++    +lf+DEi  + +++
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECK---ANFISIKGPELLSMWVGESESNIRDLFARARGAAPCVLFFDEIDSIAKAR 590
                                    5678999********99997766...7777777777666555555545555555555568899******9995543 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     6e-05     0.021      47      71 ..     242     266 ..     228     321 .. 0.72
   2 ?   -1.0   0.0       3.6   1.3e+03      27      56 ..     321     351 ..     318     353 .. 0.81
   3 !   12.3   0.1   0.00029       0.1      47      71 ..     515     539 ..     508     547 .. 0.84
   4 ?   -1.5   0.0       4.8   1.7e+03      77      98 ..     725     746 ..     716     760 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                     ++i+l Gp+G+GK+ +a a++ e+
  gene105|gene105|rna105|rna105 242 PKGILLYGPPGTGKTLIARAIANET 266
                                    5789*****************9863 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                      IstB_IS21  27 arsldkrkvkeLat.lsfiekkenivllGps 56 
                                    + ++++r+v++L t ++ ++++ n+++lG +
  gene105|gene105|rna105|rna105 321 QGEVERRIVSQLLTlMDGMKARSNVIVLGAT 351
                                    55789999998866258999********986 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00029
                      IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                    ++++++ Gp+G GK+ la a+++e 
  gene105|gene105|rna105|rna105 515 AKGVLFYGPPGCGKTLLAKAVATEC 539
                                    57899***************99875 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 4.8
                      IstB_IS21  77 svlfvrvedLveelkrarrdgk 98 
                                     v ++r + Lv+ lk+arr  +
  gene105|gene105|rna105|rna105 725 PVPYLRPDHLVQALKTARRSVS 746
                                    6889999**********99765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-05    0.0071       1      25 [.     245     287 ..     245     371 .. 0.62
   2 !   12.1   0.0   0.00061      0.22       1      30 [.     518     565 ..     518     625 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                    Ill G+pG+GKt +a+++++++ +f                  
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETgAFlflingpeimskmagesE 287
                                    99******************99666877776444444443331 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00061
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrd 30 
                                    +l  G+pG+GKt lak+++ ++ ++                   n+rd
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECkANfisikgpellsmwvgesESNIRD 565
                                    6789**************999854456666665555555555444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00043      0.15       1      29 [.     245     273 ..     245     290 .. 0.78
   2 !   15.8   0.0   3.8e-05     0.014       1      40 [.     518     560 ..     518     621 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00043
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklk 29 
                                    i+lyGp+g+GK+++a+ +a++    l l+
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGAFLFLI 273
                                    789**************999877665555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.8e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsvysrnpe 40 
                                    +++yGp+g+GK++lak +a++   ++   k ++  s++++++e
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKANFisiKGPELLSMWVGESE 560
                                    689**************99998866644444444444445555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00011      0.04      24      43 ..     244     263 ..     233     270 .. 0.89
   2 !   13.7   0.0   8.1e-05     0.029      24      43 ..     517     536 ..     505     540 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                     +ll+GppG+GKt++a++++
  gene105|gene105|rna105|rna105 244 GILLYGPPGTGKTLIARAIA 263
                                    589*************9985 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.1e-05
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                     +l++GppG+GKt+lak+++
  gene105|gene105|rna105|rna105 517 GVLFYGPPGCGKTLLAKAVA 536
                                    589*************9875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0019      0.68       8      80 ..     239     379 ..     235     449 .. 0.57
   2 !   12.5   0.0   0.00044      0.16       4      49 ..     508     551 ..     506     620 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0019
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--....SEE.EE...........................EETTCEGGGB-HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.xx...........................xxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp....teG.ei...........................lldgkdlkeqele 55 
                                    +k+ + + + G+ G+GK+ +++++a+++       +G ei                            +d+ d    ++e
  gene105|gene105|rna105|rna105 239 VKPPKGILLYGPPGTGKTLIARAIANETGAflflINGpEImskmagesesnlrkafeeaeknapsiiFIDEIDALAPKRE 318
                                    677778899****************9987655552221335555666666666666655555555553443333333333 PP

                                    HCCHCE..EEE-SS--S-TTSBHHHH..................................H CS
                                    xxxxxx..xxxxxxxxxxxxxxxxxx..................................x RF
                       ABC_tran  56 slrkei..gvlpqepqlfpeltvren..................................e 80 
                                    +++ e+  ++++q  +l +++++r+n                                   
  gene105|gene105|rna105|rna105 319 KSQGEVerRIVSQLLTLMDGMKARSNvivlgatnrpnsidsalrrygrfdreieigvpdeM 379
                                    3333331156666677777776666677776665555555555555555555555555550 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00044
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdl 49 
                                    +++ + + + v + G+ G+GK+ L+k++a + k     i ++g +l
  gene105|gene105|rna105|rna105 508 IKFGMTPAKGVLFYGPPGCGKTLLAKAVATECKA--NFISIKGPEL 551
                                    67889999999*****************998764..4555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0077       2.8      36      53 ..     245     262 ..     241     266 .. 0.86
   2 ?    6.6   0.0     0.014       5.1     130     177 ..     290     337 ..     265     349 .. 0.79
   3 !    9.4   0.0     0.002      0.72      22      55 ..     504     537 ..     491     545 .. 0.78
   4 ?   -0.5   0.0       2.2   7.9e+02     130     172 ..     563     607 ..     554     625 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0077
                         AAA_25  36 allaGapgtGKttlaldl 53 
                                    +ll+G+pgtGKt +a  +
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAI 262
                                    69**********998665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                         AAA_25 130 vdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                    +++  +++e+ + +  + iD ++++ +  e+s+ +v +++v++l  + +
  gene105|gene105|rna105|rna105 290 LRKAFEEAEK-NAPSIIFIDEIDALAPKREKSQGEVeRRIVSQLLTLMD 337
                                    4445566666.55**********************99999999987765 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.002
                         AAA_25  22 rrwlvk.gllpagelallaGapgtGKttlaldlal 55 
                                    +++ +k g+ pa++ +l++G+pg+GKt la  +a 
  gene105|gene105|rna105|rna105 504 PEKFIKfGMTPAKG-VLFYGPPGCGKTLLAKAVAT 537
                                    55666667777555.589***********987775 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.2
                         AAA_25 130 vdaleaaieevegvrlvviDplsralgg.densnsd.v.galveal 172
                                    +++l a+++  + + ++ +D ++++  + + n++s  v ++++++l
  gene105|gene105|rna105|rna105 563 IRDLFARARG-AAPCVLFFDEIDSIAKArSGNDASSgVtDRMLNQL 607
                                    5667777777.45888888888887777677777664346666665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0068       2.4      19      37 ..     242     260 ..     232     268 .. 0.83
   2 ?    6.7   0.0     0.011       4.1     109     161 ..     288     347 ..     273     364 .. 0.70
   3 ?   -1.6   0.0       3.8   1.4e+03      59      98 ..     423     461 ..     417     475 .. 0.66
   4 !    8.7   0.0    0.0028         1       9      38 ..     505     534 ..     497     543 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0068
                         ATPase  19 grvvlitGepGtGKtifal 37 
                                     + +l++G pGtGKt++a 
  gene105|gene105|rna105|rna105 242 PKGILLYGPPGTGKTLIAR 260
                                    56799***********985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                         ATPase 109 eelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlkklgv.Tailv 161
                                    ++l++a +e +    + + iD i++l    ++++ +v R+i+ ql++ + +++   +++v
  gene105|gene105|rna105|rna105 288 SNLRKAFEEAEKnapSIIFIDEIDALapkREKSQGEVERRIVSQLLTLMDGMKArSNVIV 347
                                    5566666555443358899*******752344455679***********77654145555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.8
                         ATPase  59 paedlrenakslGwdlekleeegklaiidasesaeesaee 98 
                                      +++re+  +++ d ek+e++  la + +++++ ++a e
  gene105|gene105|rna105|rna105 423 ALQQIREKLPQIDLDDEKIEAK-VLASLKVTNENFRYAIE 461
                                    4489999999999999999999.55666665555555443 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0028
                         ATPase   9 DeilkgGipegrvvlitGepGtGKtifalq 38 
                                    ++++k G+  ++ vl +G pG+GKt++a+ 
  gene105|gene105|rna105|rna105 505 EKFIKFGMTPAKGVLFYGPPGCGKTLLAKA 534
                                    5667889999999**************975 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.8e-05     0.021     117     141 ..     245     269 ..     239     275 .. 0.88
   2 !    9.5   0.0    0.0013      0.48     117     137 ..     518     538 ..     511     542 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                    +++yGp+ tGkt +a+aIa+ +  +
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGAF 269
                                    89*****************987665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                      Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                    v+fyGp+ +Gkt la+a a+ 
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATE 538
                                    89***************9976 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00079      0.28      30      57 ..     239     266 ..     229     326 .. 0.84
   2 !   11.6   0.0   0.00042      0.15      26      62 ..     508     543 ..     501     549 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00079
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkl 57 
                                    +k  k +ll+Gp GtGKt+i++ + ++ 
  gene105|gene105|rna105|rna105 239 VKPPKGILLYGPPGTGKTLIARAIANET 266
                                    5666889*************99987765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00042
                          AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                    ++  ++  k vl++Gp G+GKt+++k + ++++  ++
  gene105|gene105|rna105|rna105 508 IKFGMTPAKGVLFYGPPGCGKTLLAKAVATECK-ANF 543
                                    5566777899****************9988887.444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.1e-05     0.018       5      77 ..     245     313 ..     242     323 .. 0.73
   2 !    7.7   0.1    0.0073       2.6       5      22 ..     518     535 ..     515     551 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-05
                         AAA_24   5 iliyGpsgiGKTtlakel.gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77 
                                    il+yGp+g+GKT +a+ +  ++ +f+ + +G   +    ++   s  +++++++e +++ +  ++++iD id l
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIaNETGAFLFLINGPEIMSKMAGE---SESNLRKAFEEAEKNAP--SIIFIDEIDAL 313
                                    89**************9984445555555555555555554...66777888877766666..78888888876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0073
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +l yGp+g GKT lak  
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAV 535
                                    789************977 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.7e-05     0.013      37     189 ..     245     397 ..     234     420 .. 0.75
   2 ?    6.6   0.0     0.017       6.1      37      63 ..     518     544 ..     510     553 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-05
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT-.HH CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk.ek 114
                                    +++yg+ G Gkt + +ai+ne+      + +  +++ e +++++   +++  ++f e  +++  ++ iD+i  la k ek
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANET-----GAFLFLINGPEIMSKMAGESESNLRKAFEEAEKNApSIIFIDEIDALAPKrEK 319
                                    79************99999875.....5678999**********************99986527899*******977345 PP

                                    HHHH........HHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT--- CS
                       Bac_DnaA 115 tqee........lfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklev 186
                                    +q e        l+++++ +   ++ +vl +   P+++++   r   rf++   ++i  pd+  rl+il+ + ++ k+  
  gene105|gene105|rna105|rna105 320 SQGEverrivsqLLTLMDGMKARSNVIVLGATNRPNSIDSALRR-YGRFDRE--IEIGVPDEMGRLEILRIHTKNMKM-- 394
                                    5544222211114455555555667899*******988775544.4688775..667779999*****9866554444.. PP

                                    -TT CS
                       Bac_DnaA 187 pee 189
                                     e+
  gene105|gene105|rna105|rna105 395 SED 397
                                    333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.017
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                    +++yg+ G Gkt L ka++ e ++n+ 
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKANFI 544
                                    89*****************99988765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       7.6   2.7e+03      68      95 ..      16      43 ..       8     100 .. 0.72
   2 !   12.1   0.0   0.00047      0.17       2      43 ..     245     291 ..     244     338 .. 0.66
   3 !   10.0   0.0    0.0021      0.76       2      23 ..     518     542 ..     517     585 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 7.6
                         AAA_28 68 aaaaankvlfcDrglldtlaYaraygge 95
                                   ++ ++n +++cD ++    +Y   ++ +
  gene105|gene105|rna105|rna105 16 ESKTKNTLIVCDKDCNKLRTYQVGLHPT 43
                                   4557899999999988888776555544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00047
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakge 43 
                                    i + G+++tGKT +++a+a++ g   +    pE++ ++  e   + +
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANEtGAFLFlingPEIMSKMAGESESNLR 291
                                    7899***************7655443323566666666555444333 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0021
                         AAA_28   2 ivitGgestGKTtlleaLaar...g 23 
                                    + + G++++GKT l++a a +   +
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATEckaN 542
                                    6799**************9554332 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.43   1.5e+02      18      44 ..     440     466 ..     419     475 .. 0.75
   2 !   19.3   0.0   2.4e-06   0.00085      27      58 ..     727     758 ..     711     760 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.43
                         Vps4_C  18 dipsdkllePpvtlkDflkalkkarpt 44 
                                    +i+++ l   +vt + f  a++++ p+
  gene105|gene105|rna105|rna105 440 KIEAKVLASLKVTNENFRYAIEHTDPS 466
                                    3556666667**************998 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.4e-06
                         Vps4_C  27 PpvtlkDflkalkkarptVskeDLekheeFTk 58 
                                    P ++ +++++alk+ar++Vs++++e++e F +
  gene105|gene105|rna105|rna105 727 PYLRPDHLVQALKTARRSVSEKEVERYEAFAR 758
                                    6778899***********************87 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00057      0.21      22      46 ..     242     266 ..     228     363 .. 0.75
   2 ?    7.3   0.0      0.01       3.6      23      47 ..     516     540 ..     500     590 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00057
                                    SS-EEEECSTTSSHHHHHHHHHHHS CS
                Sigma54_activat  22 dlsvlitGesGtGKellaraiheas 46 
                                    +  +l+ G  GtGK+l+arai +++
  gene105|gene105|rna105|rna105 242 PKGILLYGPPGTGKTLIARAIANET 266
                                    4679****************98754 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.01
                                    S-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                      vl  G  G+GK+lla+a+ ++ k
  gene105|gene105|rna105|rna105 516 KGVLFYGPPGCGKTLLAKAVATECK 540
                                    569****************987665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0072       2.6      52      85 ..     241     273 ..     216     363 .. 0.73
   2 !   13.4   0.0   8.7e-05     0.031      16      81 ..     469     543 ..     452     554 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0072
                         DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli 85 
                                    p + +LL+G  GtGK  + +a+ ne+ +  L li
  gene105|gene105|rna105|rna105 241 PPKGILLYGPPGTGKTLIARAIANETGA-FLFLI 273
                                    66789****************9998754.44444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.7e-05
                         DUF815  16 lepveevdevklddLvgidkqkealvent.......eqfle..glpannvLLwGarGtGKSslvkallneyaeeg 81 
                                     e+v +  +vk++d+ g+++ k++l e +       e+f++   +pa+ vL++G  G+GK  l ka+ +e++++ 
  gene105|gene105|rna105|rna105 469 RETVIQSPNVKWSDIGGLKQVKQELRETVqypveypEKFIKfgMTPAKGVLFYGPPGCGKTLLAKAVATECKANF 543
                                    5678888899999999999999999887622222224677643479**********************9998765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-05    0.0042      22      85 ..     240     306 ..     212     436 .. 0.67
   2 ?    3.6   0.0      0.16        59      22      50 ..     513     541 ..     483     547 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-05
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.............G CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke.........i 85 
                                    k  k +l+  + GtGKTl+a +++ +         flfl+++ ++++++  e ++ l +a++e          
  gene105|gene105|rna105|rna105 240 KPPKGILLYGPPGTGKTLIARAIANETG------AFLFLINGPEIMSKMAGESESNLRKAFEEaeknapsiiF 306
                                    677889999*********9988887766......59**************87777777776653333333330 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.16
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllk 50 
                                    +  k +l+  + G+GKTl+a +++ +++ 
  gene105|gene105|rna105|rna105 513 TPAKGVLFYGPPGCGKTLLAKAVATECKA 541
                                    5667889999**********888887765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0    0.0013      0.45       1      53 [.     248     301 ..     248     334 .. 0.67
   2 !    9.9   0.0    0.0026      0.92       1      26 [.     521     546 ..     521     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0013
                                    EE-TTSSHHHHHHHHHHHHT.EEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklvekyg.fthlsaGdllreeakrgglakardemrklplee 53 
                                    +G+PG GK+ +++ ++ + g f +l  G  +++ ++ ++ ++ r+++++++++ 
  gene105|gene105|rna105|rna105 248 YGPPGTGKTLIARAIANETGaFLFLINGPEIMSKMAGESESNLRKAFEEAEKNA 301
                                    7***************99964666666666655554443335556665544443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0026
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                    +G+PG+GK+ +++ ++ + +  ++s 
  gene105|gene105|rna105|rna105 521 YGPPGCGKTLLAKAVATECKANFISI 546
                                    7**************99887777765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0014      0.49      19      44 ..     242     267 ..     216     277 .. 0.77
   2 !   10.0   0.0    0.0018      0.64      19      51 ..     515     549 ..     487     552 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                                    TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                     + ilL+G+ G+GKT ++r++a++ g
  gene105|gene105|rna105|rna105 242 PKGILLYGPPGTGKTLIARAIANETG 267
                                    3459******************9887 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0018
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                    ++ +l++G+ G+GKT l++++a +++ +  ++k P
  gene105|gene105|rna105|rna105 515 AKGVLFYGPPGCGKTLLAKAVATECKANfiSIKGP 549
                                    3359******************9998876666655 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   4.3e-07   0.00015      13      83 ..      34     104 ..      22     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.3e-07
                                    STTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTST.TTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                        CDC48_N  13 grgivridpedmeelglepgdvveiegkrkTvaivwpaepede.gkgiIrmdgvtRknagvsiGdkVtVrka 83 
                                     +  v ++p +++el+l++ d+v+i gk+k+  i  + +  ++  + +I + +  R n++v+i d+V+  ++
  gene105|gene105|rna105|rna105  34 RTYQVGLHPTTLNELELFESDYVRILGKKKAELIFSTVA-LESvPPRHISVVRDGRFNLRVRITDTVKLYRV 104
                                    5567889********************886555555555.55559**********************98776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0035       1.3      19      76 ..     241     292 ..     231     348 .. 0.65
   2 !    9.3   0.0    0.0026      0.94      22      44 ..     517     539 ..     510     546 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0035
                       ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekk 76 
                                    p + +++YGp g GKt + + i+++        +++i+  e+ ++ + e+  e++ +k
  gene105|gene105|rna105|rna105 241 PPKGILLYGPPGTGKTLIARAIANETG----AFLFLINGPEIMSKMAGES--ESNLRK 292
                                    5666899*********99998888873....4677777777777777666..222222 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0026
                       ATPase_2  22 iyfiYGpegsGKtaLlkeiienl 44 
                                     ++ YGp g+GKt L k ++++ 
  gene105|gene105|rna105|rna105 517 GVLFYGPPGCGKTLLAKAVATEC 539
                                    5778************9998765 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0006      0.22      24      85 ..     245     317 ..     236     350 .. 0.73
   2 ?    6.6   0.0     0.022       7.9      24      84 ..     518     589 ..     510     592 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0006
                                    EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHH.H-H..........HHHHHHTTTSEEEEEE-TT--HHH CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverla.klp..........ldlleqakggtLylkdiadlskae 85 
                                    ++l G++G+gk+l+Ar+++++ g  l + +  + + k+            +  e+  + ++++ +i+ l ++ 
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGAFLFLINGPEIMsKMAgesesnlrkaFEEAEKNAPSIIFIDEIDALAPKR 317
                                    799******************9997655443222212223334444333333344488899999999987765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.022
                                    EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H..........HHHHHH...TTTSEEEEEE-TT--HH CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp..........ldlleq...akggtLylkdiadlska 84 
                                    v+  G++G+gk+l A++ + +   + ++i+  e l               dl+++   a + +L++ +i+++ ka
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKANfISIKGPELL---SmwvgesesniRDLFARargAAPCVLFFDEIDSIAKA 589
                                    8999************9986543320233222222...1234444455588888833446778999999988775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.016       5.6       3      23 ..     245     265 ..     243     268 .. 0.90
   2 ?   -1.8   0.0       7.1   2.6e+03      66     113 ..     287     336 ..     278     363 .. 0.58
   3 !   10.5   0.0    0.0012      0.44       3      25 ..     518     540 ..     516     547 .. 0.89
   4 ?   -2.2   0.0       9.3   3.3e+03      77     115 ..     570     610 ..     549     631 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.016
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    ++l G++G GKT  ++ +a +
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANE 265
                                    7899*************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.1
                                    -SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHH CS
                          NACHT  66 aapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLseli 113
                                    +++ ++ +++  +++ ++ + +D +D l+ + ++     e++ v +lL +l+
  gene105|gene105|rna105|rna105 287 ESNLRKAFEEAEKNAPSIIF-IDEIDALAPKREKsqgeVERRIVSQLL-TLM 336
                                    55555555555566666655.588888887666644432333333333.444 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0012
                                    EEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                    v+  G++G+GKT L++ +a++ +
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECK 540
                                    6789**************99876 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 9.3
                                    CCSCCCEEEEEE-STT-SS-TCH...........HHHHHCT CS
                          NACHT  77 lelperlLlilDglDelvtdlgq..kekqpvrtlLselirk 115
                                    ++ +   +l +D +D +++  +   +    ++++L++l+++
  gene105|gene105|rna105|rna105 570 ARGAAPCVLFFDEIDSIAKARSGndASSGVTDRMLNQLLSE 610
                                    45556677889999988876655555555667777777665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0024      0.84      14      40 ..     240     266 ..     231     273 .. 0.89
   2 !    7.8   0.0    0.0049       1.8      19      51 ..     518     548 ..     511     554 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0024
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdel 40 
                                    + Pk ill G pG GK+ +a+++++e+
  gene105|gene105|rna105|rna105 240 KPPKGILLYGPPGTGKTLIARAIANET 266
                                    6799*******************9996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0049
                     Zeta_toxin  19 illgGqpGAGKselaellkdelerqgnvvrldp 51 
                                    +l  G pG+GK+ la+++++e   + n++ +++
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATEC--KANFISIKG 548
                                    566799***************9..899998876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0067       2.4       2      26 ..     245     269 ..     244     356 .. 0.74
   2 !    9.8   0.0    0.0019       0.7       2      71 ..     518     583 ..     517     644 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0067
                          AAA_3   2 vllegvPGlaktllvkalakaldle 26 
                                    +ll g PG++ktl+++a+a+  ++ 
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGAF 269
                                    7999***************988764 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0019
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladei 71 
                                    vl+ g PG +ktll+ka+a+  +++f  i+  p+ll    +G +  +  +  f   +G+    +l+ dei
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKANFISIK-GPELLSMW-VGESESNI-RDLFARARGAA-PCVLFFDEI 583
                                    788999*******************99987.57777554.34443332.23344444443.334445555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0079       2.8      23      43 ..     245     265 ..     237     269 .. 0.90
   2 !    8.9   0.0    0.0021      0.76      23      44 ..     518     539 ..     508     631 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0079
                                    EEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                    + l+G +G GKt +a+ i n+
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANE 265
                                    679***************997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0021
                                    EEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                    v ++G +G+GKt lak +  + 
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATEC 539
                                    678*************998773 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.073        26       4      73 ..     248     312 ..     245     316 .. 0.69
   2 !   12.5   0.0   0.00025     0.091       5      71 ..     522     583 ..     518     588 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.073
                Viral_helicase1   4 hGvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEyll 73 
                                     G pG GK+ + r ++++     + +n p  e+ ++ + +++++  + ++++++++       i+++DE+ +
  gene105|gene105|rna105|rna105 248 YGPPGTGKTLIARAIANETgaFLFLINGP--EIMSKMAGESESNLRKAFEEAEKNAP-----SIIFIDEIDA 312
                                    588**************998644444444..56666665666665666666666653.....5999999865 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00025
                Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                    G pGcGK+ l + ++ ++  ++ +++   ell++++ +++++    +  +  a+ +     +l++DE+
  gene105|gene105|rna105|rna105 522 GPPGCGKTLLAKAVATECkANFISIKG-PELLSMWVGESESNIRDLFARARGAAPC-----VLFFDEI 583
                                    78***************9*99999999.9*******99999988888888888765.....7999997 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1    0.0044       1.6      23      40 ..     246     263 ..     231     268 .. 0.86
   2 !    8.7   0.1    0.0031       1.1      22      42 ..     518     538 ..     506     544 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0044
                                    EEE--TTSSTTHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavala 40 
                                       Gp GtGKt++a a+a
  gene105|gene105|rna105|rna105 246 LLYGPPGTGKTLIARAIA 263
                                    678***********9988 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0031
                                    EEEE--TTSSTTHHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalave 42 
                                    v   Gp G+GKt+la a+a e
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATE 538
                                    6779*************9976 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00082      0.29       4      25 ..     245     266 ..     242     331 .. 0.68
   2 ?    5.0   0.0     0.034        12       5      25 ..     519     539 ..     516     593 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00082
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    +l  G +GtGKt+++ ++++e 
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANET 266
                                    6789**************9998 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.034
                        DUF2075   5 lVtGvaGtGKtvvllnllael 25 
                                    l  G +G GKt+++ ++++e+
  gene105|gene105|rna105|rna105 519 LFYGPPGCGKTLLAKAVATEC 539
                                    5679**************999 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3    0.0024      0.87      20      43 ..     245     285 ..     230     499 .. 0.69
   2 ?    5.2   0.0     0.043        16      19      37 ..     517     535 ..     501     578 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                         AAA_11  20 tliqGPPGtgKTktivellsqll.................s 43 
                                     l+ GPPGtgKT    ++ ++                   +
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGaflflingpeimskmagE 285
                                    6899********88888877765555555555555544440 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.043
                         AAA_11  19 itliqGPPGtgKTktivel 37 
                                     +l+ GPPG+gKT    ++
  gene105|gene105|rna105|rna105 517 GVLFYGPPGCGKTLLAKAV 535
                                    47999********544444 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.049        17      48      79 ..     245     275 ..     224     323 .. 0.70
   2 !    7.6   0.0    0.0091       3.3      48      77 ..     518     547 ..     510     589 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.049
                          Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                    +L+ GP+G gk+ + + ++ e g  l   +n+
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIANETGAFLF-LING 275
                                    6789***************99997654.3444 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0091
                          Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewl 77 
                                    +L  GP+GCgk+   k ++ e   +++   
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATECKANFISIK 547
                                    6889********999999988777766555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0055         2      11      32 ..     243     264 ..     237     293 .. 0.87
   2 ?    5.2   0.0     0.071        26       9      35 ..     514     540 ..     507     554 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0055
                         AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                    k +l+ ++pGtGKT + ++i +
  gene105|gene105|rna105|rna105 243 KGILLYGPPGTGKTLIARAIAN 264
                                    56899*********99988876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.071
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallv 35 
                                    ++k +l  ++pG+GKT + k++ ++++
  gene105|gene105|rna105|rna105 514 PAKGVLFYGPPGCGKTLLAKAVATECK 540
                                    56778999********98887776655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.22        77       2      21 ..     245     264 ..     244     269 .. 0.85
   2 ?    1.7   0.1      0.58   2.1e+02      85     121 ..     290     327 ..     280     348 .. 0.71
   3 ?   -1.9   0.0       7.5   2.7e+03      90     109 ..     365     384 ..     351     392 .. 0.77
   4 ?    6.7   0.0     0.017         6       6      32 ..     522     548 ..     518     553 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.22
                                    EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvle 21 
                                    +++ GppG+GKt + + +++
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIAN 264
                                    6788********99888876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.58
                                    HHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHH CS
                       NTPase_1  85 alealrkal.seadviviDEiGkmElkskkfkeaveev 121
                                      +a+++a  + + +i iDEi  +  k +k + +ve+ 
  gene105|gene105|rna105|rna105 290 LRKAFEEAEkNAPSIIFIDEIDALAPKREKSQGEVERR 327
                                    44455555534455*******98877777777777665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.5
                                    HHHHHHH-EEEE---STTGG CS
                       NTPase_1  90 rkalseadviviDEiGkmEl 109
                                     + ++e ++ v DE G++E 
  gene105|gene105|rna105|rna105 365 GRFDREIEIGVPDEMGRLEI 384
                                    455578889999******96 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.017
                                    --TTSSHHHHHHHHHHHH...GGGEEE CS
                       NTPase_1   6 GppGvGKtTlvkkvlellkssgvkvgG 32 
                                    GppG GKt l k v+ ++k + ++++G
  gene105|gene105|rna105|rna105 522 GPPGCGKTLLAKAVATECKANFISIKG 548
                                    9*****************999888887 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.015       5.2       8     102 ..     251     349 ..     245     351 .. 0.73
   2 ?    3.6   0.0      0.18        65       8      47 ..     524     563 ..     521     614 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
                Cytidylate_kin2   8 yGsgGetigeaLAekLg..lpfydr.eiieevakelglseeev.eevdersrlssflskllaarvagdtldeklddelfe 83 
                                     G+g++ i++a+A++ g  l +++  ei+ ++a e++ +  ++ ee+++++++  f++++ a   + ++ + + + +++ 
  gene105|gene105|rna105|rna105 251 PGTGKTLIARAIANETGafLFLINGpEIMSKMAGESESNLRKAfEEAEKNAPSIIFIDEIDALAPKREKSQGEVERRIVS 330
                                    69*************99333445667999999999999998888999888888888888877765555556666666666 PP

                Cytidylate_kin2  84 aqervirelaaeesvVivG 102
                                       +++  + a ++v+++G
  gene105|gene105|rna105|rna105 331 QLLTLMDGMKARSNVIVLG 349
                                    6666666665554777776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.18
                Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev 47 
                                     G+g++ +++a+A++ + +f++ + +e ++   g se+ +
  gene105|gene105|rna105|rna105 524 PGCGKTLLAKAVATECKANFISIKGPELLSMWVGESESNI 563
                                    59****************9998776666666555555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.1   7.6e+02      17      32 ..     245     260 ..     236     267 .. 0.82
   2 ?    5.4   0.0     0.039        14     121     170 ..     301     353 ..     271     359 .. 0.78
   3 ?   -0.5   0.1       2.5   8.9e+02      15      33 ..     516     534 ..     505     550 .. 0.82
   4 ?    1.7   0.0      0.53   1.9e+02     125     170 ..     578     628 ..     560     635 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.1
                                    EEEEESTTSSHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                           DEAD  17 vlvaaeTGsGKTlafl 32 
                                    +l+ ++ G+GKTl++ 
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIAR 260
                                    7888999*****9875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                                    TEEEEEEETHHHHHHT...TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 121 qvrflVlDEadrlldq...gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                      +++ +DE+d l  +   ++++  +ri++ql +  +  k+ ++vivl AT  
  gene105|gene105|rna105|rna105 301 APSIIFIDEIDALAPKrekSQGEVERRIVSQLLTLMDGMKARSNVIVLGATNR 353
                                    5577889******98877788888999*****888888888888*******65 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.5
                                    CEEEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                           DEAD  15 gdvlvaaeTGsGKTlafli 33 
                                    + vl  ++ G GKTl +  
  gene105|gene105|rna105|rna105 516 KGVLFYGPPGCGKTLLAKA 534
                                    6689999*******98765 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.53
                                    EEEETHHHHHHT.....TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 125 lVlDEadrlldq.....gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                    l +DE+d + +        s   +r+lnql +  +  +l+++v v+ AT  
  gene105|gene105|rna105|rna105 578 LFFDEIDSIAKArsgndASSGVTDRMLNQLLSEMDGINLKKNVFVIGATNR 628
                                    6689999998885555456667789*****888888889999**9999976 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.039        14       3      24 ..     247     268 ..     245     275 .. 0.86
   2 ?   -1.9   0.0       6.2   2.2e+03      43      78 ..     426     467 ..     399     504 .. 0.60
   3 ?    3.6   0.0      0.13        46       5      28 ..     522     545 ..     518     547 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.039
                                    EE-STTSSHHHHHHHHHHHHT- CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklgl 24 
                                    + GP g+GK  +ara+a++ g+
  gene105|gene105|rna105|rna105 247 LYGPPGTGKTLIARAIANETGA 268
                                    67***************99886 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.2
                                    T......T--TT-HHHHHHHHHT--EEEEEEEEEETTEE-TT CS
                 Cytidylate_kin  43 r......kvdlldeaalvelakevelsfeaekvllngedvee 78 
                                    +      ++dl de+  +++++++++  e+ ++ ++ +d ++
  gene105|gene105|rna105|rna105 426 QireklpQIDLDDEKIEAKVLASLKVTNENFRYAIEHTDPSS 467
                                    233344466667777777777777777777777776666543 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.13
                                    -STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                    GP g GK  +a+a+a++ ++++++
  gene105|gene105|rna105|rna105 522 GPPGCGKTLLAKAVATECKANFIS 545
                                    9****************9999985 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.011       3.8      22      40 ..     246     264 ..     234     268 .. 0.87
   2 ?    3.8   0.1      0.12        42      21      41 ..     518     538 ..     508     548 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                         AAA_30  22 vltGpAGtGKttalkalre 40 
                                    +l Gp+GtGKt + +a+++
  gene105|gene105|rna105|rna105 246 LLYGPPGTGKTLIARAIAN 264
                                    688**********999965 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                         AAA_30  21 avltGpAGtGKttalkalrea 41 
                                    ++  Gp+G GKt + ka++  
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAVATE 538
                                    6778**********9999765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.03        11      26      56 ..     233     263 ..     224     268 .. 0.81
   2 ?   -1.2   0.0       3.1   1.1e+03     116     142 ..     298     324 ..     279     368 .. 0.73
   3 ?    1.8   0.0      0.39   1.4e+02      36      58 ..     516     538 ..     486     550 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.03
                           TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFa 56 
                                    L+++   k ++ +ll+G++ +GKt i++  a
  gene105|gene105|rna105|rna105 233 LYSKIGVKPPKGILLYGPPGTGKTLIARAIA 263
                                    666666677889**************98766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                           TniB 116 relkvrvLiiDEihnllagsarkqref 142
                                    ++  + ++ iDEi+ l   + ++q e+
  gene105|gene105|rna105|rna105 298 EKNAPSIIFIDEIDALAPKREKSQGEV 324
                                    555678999999999887666666544 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.39
                           TniB  36 pnlllvGdsnnGKtmivekFarl 58 
                                    + +l++G++ +GKt +++  a +
  gene105|gene105|rna105|rna105 516 KGVLFYGPPGCGKTLLAKAVATE 538
                                    6799***********99877665 PP

>> Nrap_D4  Nrap protein nucleotidyltransferase domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0019      0.69      29      73 ..     129     178 ..     121     202 .. 0.82
   2 ?   -2.0   0.0       5.4   1.9e+03     132     180 ..     434     479 ..     422     500 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                                    HHHHHHHHHHHT-.--SS-EEEEEE-SGGGGT--SS---TT......... CS
                        Nrap_D4  29 kaFdeLekdlrsLedLPLsirsvqpaspalRytsvfppvpvkls.....p 73 
                                    + Fde+++   + + +PL++ s++++s+ l   ++++ + ++++      
  gene105|gene105|rna105|rna105 129 NIFDEFVRPFLDFNFMPLTVGSIYGVSSGLGRVEFKVTKMIDAQdmeikH 178
                                    68******************************999999998776655540 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.4
                                    EEE-------...EEEEEE-TTS-EEEEEEE-TTHHHHHHHHH...HHS CS
                        Nrap_D4 132 vgldnssekianqayLdvlkesgfaFrlrilherEltllerqlkdkgla 180
                                    + ld+++ + +  a L+v+ e    Fr  i h +  +l e  +++ +++
  gene105|gene105|rna105|rna105 434 IDLDDEKIEAKVLASLKVTNE---NFRYAIEHTDPSSLRETVIQSPNVK 479
                                    666776555555777777776...7888998888888888777655544 PP

>> DUF2388  Protein of unknown function (DUF2388)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0017      0.61      44      67 ..     421     444 ..     412     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                        DUF2388  44 EaaLqelRsenpelqasDleLAea 67 
                                    EaaLq++R++ p+ + +D++    
  gene105|gene105|rna105|rna105 421 EAALQQIREKLPQIDLDDEKIEAK 444
                                    9*****************987555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1      0.08        29      22      40 ..     245     263 ..     239     269 .. 0.92
   2 ?   -1.5   0.1       8.6   3.1e+03     182     182 ..     421     421 ..     280     496 .. 0.61
   3 ?    3.9   0.0      0.18        66      22      39 ..     518     535 ..     503     537 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.08
                         AAA_23  22 tlItGpNGaGKTTildAik 40 
                                     l++Gp G+GKT i +Ai 
  gene105|gene105|rna105|rna105 245 ILLYGPPGTGKTLIARAIA 263
                                    489**************95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 8.6
                         AAA_23 182 e 182
                                    e
  gene105|gene105|rna105|rna105 421 E 421
                                    2 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.18
                         AAA_23  22 tlItGpNGaGKTTildAi 39 
                                    +l++Gp G+GKT +  A+
  gene105|gene105|rna105|rna105 518 VLFYGPPGCGKTLLAKAV 535
                                    49**********998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (780 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        50  (0.00278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              50  [number of targets reported over threshold]
# CPU time: 0.92u 0.33s 00:00:01.25 Elapsed: 00:00:00.51
# Mc/sec: 4646.24
//
Query:       gene1051|gene1051|rna1050|rna1050  [L=78]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 443.19
//
Query:       gene1052|gene1052|rna1051|rna1051  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   12.0   9.5       0.69    8.7   3.7    2.5  3  EcsB      Bacterial ABC transporter protein EcsB


Domain annotation for each model (and alignments):
>> EcsB  Bacterial ABC transporter protein EcsB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0002       3.6     331     379 ..      45      93 ..      39      97 .. 0.87
   2 ?    0.2   0.6     0.015   2.7e+02      27      59 ..     101     134 ..      99     139 .. 0.64
   3 ?    8.7   3.7   3.9e-05      0.69     106     186 ..     129     211 ..     119     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0002
                               EcsB 331 wvrlYPisekqkkkafkkllrillliqalllslvvliltgsllalllll 379
                                         ++lY+i+ ++ +++++ +l+++ l+ + ++++ ++++ ++ ++ +   
  gene1052|gene1052|rna1051|rna1051  45 AFKLYHIDMENVRESIVPVLTYAGLLTIQIFGFLCIVSWAEDMGGISST 93 
                                        579*********************************9998887777665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.015
                               EcsB  27 fvlallfllgalglyYsewlkelpssfp.lklll 59 
                                        f  +++f++ga+  y   + k  ++s   +  ++
  gene1052|gene1052|rna1051|rna1051 101 FCAMIMFFFGAGYIYRGTLGKGTDTSYIsYVYVV 134
                                        6667888888888887777777766666333333 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 3.9e-05
                               EcsB 106 qllllllvllillPlllettglsiaelllllllllllkllnlllkweelrlqgkkkrridr...lirlllnallly 178
                                          ++++ ++++ +P+l+   gl   +++++l+++++ +++++l++  +lr+++ + +r  +   +i ++l+  + +
  gene1052|gene1052|rna1051|rna1051 129 SYVYVVALSVVHYPYLM-FVGLLTKGIWMFLCMMAITSISQFLIRTSMLRNHSFENHRDGFmfdIITFILQCGFCF 203
                                        4456677889999*999.889999**************************99988888766555667777666666 PP

                               EcsB 179 lllalapl 186
                                         +l+l++l
  gene1052|gene1052|rna1051|rna1051 204 GSLSLFSL 211
                                        66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1377.14
//
Query:       gene1053|gene1053|rna1052|rna1052  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-17   61.5   0.3    3.9e-16   58.7   0.1    2.0  2  GDA1_CD39  GDA1/CD39 (nucleoside phosphatase) family
    5.6e-08   32.6   0.0    8.1e-08   32.0   0.0    1.2  1  Ppx-GppA   Ppx/GppA phosphatase family
  ------ inclusion threshold ------
      0.045   12.7   0.0      0.071   12.1   0.0    1.3  1  DDR        Diol dehydratase reactivase ATPase-like domain


Domain annotation for each model (and alignments):
>> GDA1_CD39  GDA1/CD39 (nucleoside phosphatase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.1   6.6e-20   3.9e-16       8     182 ..      30     183 ..      23     201 .. 0.82
   2 ?    0.8   0.0     0.025   1.5e+02     342     410 ..     257     321 ..     229     326 .] 0.77

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 6.6e-20
                          GDA1_CD39   8 ekygiviDAGSsgsrlhvykwkdekesllqivklieevkklePGlSsfekkpeeaaeylkpllelaeeviPeekrs 83 
                                          y+ viDAG +g+rl +y +       l+ +   + ++    Gl + e + ee+ +++k+l+  a+ +  +++ +
  gene1053|gene1053|rna1052|rna1052  30 MTYSGVIDAGTTGTRLNIYGF-------LDGEIRHQGLFTNASGLANAE-NDEEIRNSIKELFTHAKPF--YSNIK 95 
                                        67999****************.......222333344777889**9865.5589*************87..78999 PP

                          GDA1_CD39  84 etpvlikATAGlRLlkeekkekilkalrnklkklsefkvedqgiriidGeeEGiYgWiaiNYllGkfnkeapevsk 159
                                        + p+    TAG+R l + ++++il+ ++n+lk+   ++   +++++i G+ EG  + +a+  +l + +++    s 
  gene1053|gene1053|rna1052|rna1052  96 KIPIGFYGTAGFRTLDKPRSDHILEIIKNELKD---YNL--KEAEVISGSDEGKLALMAL--VLSNKGAD----SG 160
                                        *****************************9985...444..56789*********99997..67776666....79 PP

                          GDA1_CD39 160 qetvgvlDlGGaStQiafepqee 182
                                        ++ +g++D+GG+StQi f  ++ 
  gene1053|gene1053|rna1052|rna1052 161 HKSMGIIDMGGGSTQISFLEKNG 183
                                        9*****************87733 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.025
                          GDA1_CD39 342 kknweeikaeskkskeksiseeeaCfkgayvlslLhdGfdldktveelqsvekiaekelgWtLGamlnl 410
                                        k++  eik+++ ++    +s  + C  + y +s       +d++ + ++ +++ ++ +++W+ G   +l
  gene1053|gene1053|rna1052|rna1052 257 KTTIREIKDKFYGKCSLLES--NECRRLFYLIS-FIRNLGIDDS-KPIRQIDTNNGINVSWASGKGYEL 321
                                        45667777777777666666..99********9.5667899999.999999999999****99876555 PP

>> Ppx-GppA  Ppx/GppA phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   1.4e-11   8.1e-08      29     147 ..      65     197 ..      57     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.4e-11
                                        CSSC-HHHHHHHHHHHHHHHHHCCCTTG....CCEEEEEEHHHH..HSTTHHHHHHHHCCCCS....S-EEEE-HH CS
                           Ppx-GppA  29 sgrlqeeaiertisaLkefaellqkfkv....envrvVATsalR..davNadeFlarvkkevg....lkveiisge 94 
                                        sg  + e  e+ ++++ke+   ++ f +      +   +T+  R  d + +d  l+++k+e+      ++e+isg 
  gene1053|gene1053|rna1052|rna1052  65 SGLANAENDEEIRNSIKELFTHAKPFYSnikkIPIGFYGTAGFRtlDKPRSDHILEIIKNELKdynlKEAEVISGS 140
                                        555555556666666666555555554434112334467777774456788999999999998888789******* PP

                                        HHHHHHHHHHHHHT.---...SSEEEEEEETTEEEEEEEETTEEEEEEEES--CCHH CS
                           Ppx-GppA  95 eEarliylgvvssl.lek...grglviDiGGGStElvlgeekevsklvSlplGavrl 147
                                        +E++l+ +++v s   ++    ++ +iD+GGGSt++++ e++    ++S +lG+  l
  gene1053|gene1053|rna1052|rna1052 141 DEGKLALMALVLSNkGADsghKSMGIIDMGGGSTQISFLEKNGKIVSESIDLGITAL 197
                                        *********98776433311134567***************99999*******9765 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.2e-05     0.071     132     158 ..     161     187 ..     114     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                                DDR 132 ekplailDlGaGstDaalieeegevka 158
                                        +k + i+D+G+Gst  +++e++g++ +
  gene1053|gene1053|rna1052|rna1052 161 HKSMGIIDMGGGSTQISFLEKNGKIVS 187
                                        46788******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2210.06
//
Query:       gene1054|gene1054|rna1053|rna1053  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-56  190.4   0.0    4.3e-56  190.2   0.0    1.0  1  Pkinase         Protein kinase domain
    5.7e-26   91.3   0.0    8.8e-26   90.7   0.0    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
    0.00021   20.7   0.0    0.00035   20.0   0.0    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0007   19.3   0.1      0.039   13.6   0.0    2.2  2  FTA2            Kinetochore Sim4 complex subunit FTA2
     0.0007   18.6   0.0    0.00098   18.2   0.0    1.2  1  Haspin_kinase   Haspin like kinase domain
     0.0056   16.0   0.0      0.019   14.3   0.0    1.8  2  Kinase-like     Kinase-like
  ------ inclusion threshold ------
      0.011   14.6   0.0      0.029   13.2   0.0    1.5  2  Pkinase_fungal  Fungal protein kinase
      0.026   14.4   0.0      0.039   13.9   0.0    1.2  1  APH             Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.2   0.0   1.9e-59   4.3e-56       1     264 []      40     313 ..      40     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: 190.2 bits;  conditional E-value: 1.9e-59
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE.....SS CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee.....kd 71 
                                        y+ +e +G+GsfG+V+k++ +++++ +A+K++ ++++ +       rE+ il +++hpniv+l+++f++       
  gene1054|gene1054|rna1053|rna1053  40 YKYVEMIGKGSFGVVVKIM-DDRCNFFALKRVYQDRRYH------NRELGILMEIDHPNIVKLISYFHTdktpsGM 108
                                        677899*************.69***********998887......479********************97775555 PP

                                        EEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEE CS
                            Pkinase  72 elylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlake 147
                                        +l ++++++  + l+++++ ++s++ +++++i kqilegl+ylH+kgi+HrD+Kp+NiLi  +g +Ki+D+G ak 
  gene1054|gene1054|rna1053|rna1053 109 YLNIITDFAGIN-LEEYIKSNRSVEVRTIRSIYKQILEGLRYLHEKGICHRDIKPSNILIGPNGLVKICDLGSAKV 183
                                        666999999866.*************************************************************** PP

                                        SSSSCSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT. CS
                            Pkinase 148 lessskltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg. 221
                                        + ++++  ++++++ Y+APE l +++ey+ k+DvWs+G++++e+    p+f+g ++ ++ +k+l+ + ++l+ l  
  gene1054|gene1054|rna1053|rna1053 184 IVRGERNITYICSRFYRAPENLlDYKEYDFKIDVWSAGCVIAEFRHPGPMFKGGTSGSTLNKILEIVRTSLEDLIe 259
                                        ********************998*****************************777777555555553222222211 PP

                                        ..SHH...HHHTTS..................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 222 ..etkeklpeasei..................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                                 +                      + +++d+l++ l+  p kR ta+ell++p++
  gene1054|gene1054|rna1053|rna1053 260 lgY------Q---KsdykpglgvrkylekffdDTDLLDVLERSLTFSPCKRSTASELLSKPFF 313
                                        221......1...12234566779999**********************************98 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   3.9e-29   8.8e-26       3     202 ..      42     231 ..      23     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 3.9e-29
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEE.SSSS.. CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvct.keep.. 75 
                                        + + +G+G+fG Vv+   +     ++   a+K + ++ +        +e+ i+++++hpnivkl+     ++ p  
  gene1054|gene1054|rna1053|rna1053  42 YVEMIGKGSFGVVVKIMDD-----RCNFFALKRVYQDRRY-----HNRELGILMEIDHPNIVKLISYFHtDKTPsg 107
                                        5688999****99987666.....8899999999554444.....479******************9985333367 PP

                                        ..EEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTT CS
                        Pkinase_Tyr  76 ..llivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGL 149
                                          l i+t+++   +L+++++++  ++++++++ s+  q+ +G++yL++k + Hrd+   N+L+  n +vki+D G 
  gene1054|gene1054|rna1053|rna1053 108 myLNIITDFAG-INLEEYIKSN--RSVEVRTIRSIYKQILEGLRYLHEKGICHRDIKPSNILIGPNGLVKICDLGS 180
                                        66888999865.59*******9..9*************************************************** PP

                                        HEETTTSSEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTS CS
                        Pkinase_Tyr 150 ardiekddeyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlg 202
                                        a+ i + +   ++ +  ++  + apE l + k +  k DvWs G ++ E    g
  gene1054|gene1054|rna1053|rna1053 181 AKVIVRGE---RNITYICSRFYRAPENLLDYKeYDFKIDVWSAGCVIAEFRHPG 231
                                        ****3333...333445556677***8765544**************9986654 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.6e-07   0.00035     103     175 ..     119     187 ..     112     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.6e-07
                                Kdo 103 qdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlra 175
                                        ++Le+++++ ++++++  r ++k++    + lh+ g++H+d+ + nil+  ++     + + Dl  a+  +r+
  gene1054|gene1054|rna1053|rna1053 119 INLEEYIKSNRSVEVRTIRSIYKQILEGLRYLHEKGICHRDIKPSNILIGPNG----LVKICDLGSAKVIVRG 187
                                        579999999899*************************************9888....6666666666665555 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.018        40      22      59 ..      38      74 ..      31     104 .. 0.66
   2 !   13.6   0.0   1.7e-05     0.039     173     214 ..     135     181 ..     102     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.018
                               FTA2 22 kdiefleyLgkglhsiVlkvkirgk.eYALKlFrfleae 59
                                        +++++e++gkg  ++V+k+  ++   +ALK  r ++++
  gene1054|gene1054|rna1053|rna1053 38 VQYKYVEMIGKGSFGVVVKIMDDRCnFFALK--RVYQDR 74
                                       57899**************987654388999..444333 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.7e-05
                               FTA2 173 levsqlpkllrdlkklhklgIvvrDlkeenyidg.....kLvDlsaa 214
                                        ++ s+ +++l+ l+ lh+ gI +rD+k++n++ g     k++Dl++a
  gene1054|gene1054|rna1053|rna1053 135 TIRSIYKQILEGLRYLHEKGICHRDIKPSNILIGpnglvKICDLGSA 181
                                        344667899999******************99665556678888776 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.4e-07   0.00098     182     264 ..     106     192 ..      83     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.4e-07
                      Haspin_kinase 182 qqlflvlllkdkGtdLeev....klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlkl 253
                                          ++l ++ +++G +Lee     +  +++++ si+ qi++ L    +k    HRd++  niL+  n+ v ++dl  
  gene1054|gene1054|rna1053|rna1053 106 SGMYLNIITDFAGINLEEYiksnRSVEVRTIRSIYKQILEGLRYLHEK-GICHRDIKPSNILIGPNGLVKICDLGS 180
                                        56788889999999999987765667799************9777665.689**********************99 PP

                      Haspin_kinase 254 sRle.ssegkvl 264
                                        +++  + e ++ 
  gene1054|gene1054|rna1053|rna1053 181 AKVIvRGERNIT 192
                                        988754444444 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.53   1.2e+03      13      43 ..      39      68 ..      30      81 .. 0.79
   2 !   14.3   0.0   8.6e-06     0.019     155     240 ..     145     224 ..     110     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.53
                        Kinase-like 13 tlvrgellkkgdrsvvfevkdqetgeplavk 43
                                       +++ +e+++kg ++vv+++ d    + +a+k
  gene1054|gene1054|rna1053|rna1053 39 QYKYVEMIGKGSFGVVVKIMDDR-CNFFALK 68
                                       678899************99987.5555555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.6e-06
                        Kinase-like 155 rlaanLqakglvhgkftvdnllldekgglmlggfta..Lvragtkvvlseve.kgfaPpEllgsrggytrknktkm 227
                                            +L++kg+ h ++++ n+l  ++g +++ ++++   +  g++     ++ + +  pE l     y++     +
  gene1054|gene1054|rna1053|rna1053 145 EGLRYLHEKGICHRDIKPSNILIGPNGLVKICDLGSakVIVRGERNI-TYICsRFYRAPENLLD---YKE-----Y 211
                                        55679*************************99986522445566665.4444388888887777...444.....8 PP

                        Kinase-like 228 thkldaWqlGlvi 240
                                         +k+d+W  G vi
  gene1054|gene1054|rna1053|rna1053 212 DFKIDVWSAGCVI 224
                                        8999999999998 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.62   1.4e+03     172     210 ..      64     103 ..      43     141 .. 0.75
   2 ?   13.2   0.0   1.3e-05     0.029     315     341 ..     143     168 ..     134     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.62
                     Pkinase_fungal 172 eyvvKdsWrdaerk.sEaelLkkaeergvegvarlvahed 210
                                         + +K + +d++ + +E  +L ++ + ++  +  +++  +
  gene1054|gene1054|rna1053|rna1053  64 FFALKRVYQDRRYHnRELGILMEIDHPNIVKLISYFHTDK 103
                                        5778888888877779999999998888888888777655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                     Pkinase_fungal 315 aIkghrsLflkagiLHrDiSenNilit 341
                                         ++g+r L+ ++gi HrDi   Nili 
  gene1054|gene1054|rna1053|rna1053 143 ILEGLRYLH-EKGICHRDIKPSNILIG 168
                                        57899****.***************97 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.039     163     196 ..     150     181 ..     120     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                        SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                                APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                          +++++H+D++p N+l+   ++ ++ + D++ a
  gene1054|gene1054|rna1053|rna1053 150 LHEKGICHRDIKPSNILIG--PNGLVKICDLGSA 181
                                        5689**************9..5555446666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1986.49
//
Query:       gene1055|gene1055|rna1054|rna1054  [L=698]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-56  188.4   0.0    1.2e-31  109.2   0.0    2.4  2  SIS       SIS domain
    9.6e-18   64.7   0.0    2.1e-17   63.6   0.0    1.5  1  GATase_6  Glutamine amidotransferase domain
    2.8e-11   43.4   0.0    7.8e-11   42.0   0.0    1.7  1  GATase_7  Glutamine amidotransferase domain
    3.2e-06   26.3   0.0      6e-06   25.3   0.0    1.4  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.2   0.0   2.7e-35   1.2e-31       2     129 ..     380     506 ..     379     508 .. 0.98
   2 !   76.9   0.0   2.8e-25   1.2e-21       6     130 ..     556     680 ..     551     681 .. 0.91

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 2.7e-35
                                        HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHH CS
                                SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelak 77 
                                        ++ ++ri+++++Gtsy++ +  ++ lee+ + +v+ve as++ ++  ++i + d+v+++s+sget+d+v++++++ 
  gene1055|gene1055|rna1054|rna1054 380 IRRSQRIIFVACGTSYHASLANRPLLEELLETPVSVEIASDFLDR-NPPILRSDCVFFVSQSGETADSVMVLRYCL 454
                                        78899****************************************.****************************** PP

                                        HTTSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
                                SIS  78 ergakiiaITdskgsplareadlalyinaepetlvastksltaqlaaldala 129
                                        +rga +++IT+  gs+++re+++ ++ina+pe++vastk++t+q++a+ ++a
  gene1055|gene1055|rna1054|rna1054 455 SRGALCVGITNTVGSTISRETTCGVHINAGPEIGVASTKAYTSQYVAIVLVA 506
                                        ***********************************************99876 PP

  == domain 2  score: 76.9 bits;  conditional E-value: 2.8e-25
                                        SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTT CS
                                SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakerg 80 
                                         +++++G+G++y++++e+alk++ei++i++e+ +a+elkhg++al+de+  +i+i + +   d++++a  + ++rg
  gene1055|gene1055|rna1054|rna1054 556 TNLLLIGRGYQYPTCLEGALKIKEITYIHSEGLAAGELKHGPIALVDENFKIIFIITKDLLYDKARNAMeQISARG 631
                                        5799************************************************************************ PP

                                        SEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                                SIS  81 akiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                        +++i+I+ ++ s  ++  d +++i++    l+++++ +++ql++++++++
  gene1055|gene1055|rna1054|rna1054 632 GRPIIICTEDISKDYEGHD-VFIIPKTVDCLQGILSIIPLQLLSYYLAVI 680
                                        *******999888888774.45555555559****************997 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   4.6e-21   2.1e-17       6     112 ..      74     197 ..      69     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 4.6e-21
                           GATase_6   6 laslvedevalaHvRlaivglaeeegaqPf.psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllal 80 
                                        la+ v+++v +aH+R+a++g +  e ++P+ + +++++l+vhNG i nyk+l+  l + kg +f+s++Dte  ++l
  gene1055|gene1055|rna1054|rna1054  74 LARKVSNHVSIAHTRWATHGQPSVENCHPLsSDKNDNFLVVHNGIITNYKDLKTYLGK-KGFSFESNTDTECAAKL 148
                                        67788999**************88888***8889999*********************.**************996 PP

                           GATase_6  81 l.......eelG.........eevlerlrGmfafaiwdk.rentlilar 112
                                        +       e+ G         ++v++ ++G+faf++++   +n+l+++r
  gene1055|gene1055|rna1054|rna1054 149 AlhfykemESNGekpdfvsivKKVAKNCEGAFAFVFASPlFPNELVTIR 197
                                        6699987744447778999999999***********9999999998886 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   1.7e-14   7.8e-11      10      83 ..      97     185 ..      86     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1.7e-14
                           GATase_7  10 eagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea...............ewgeea 70 
                                         ++  P++s++++++ +v+nG i+Nyk+l+  L +kg++f++++Dte  ++l  +                 ++++
  gene1055|gene1055|rna1054|rna1054  97 VENCHPLSSDKNDNFLVVHNGIITNYKDLKTYLGKKGFSFESNTDTECAAKLALHfykemesngekpdfvSIVKKV 172
                                        566789*9999999*********************************987776667777***********99**** PP

                           GATase_7  71 lerlnGmfAfaiw 83 
                                         ++++G fAf+  
  gene1055|gene1055|rna1054|rna1054 173 AKNCEGAFAFVFA 185
                                        **********975 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.3e-09     6e-06      69     177 ..      78     185 ..      66     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.3e-09
                           GATase_4  69 iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCellee 140
                                        +  ++ +aH R at+G+ + en+hp + + ++++++  HnG +++yk+      ++ f+   +TD+E a    l+ 
  gene1055|gene1055|rna1054|rna1054  78 VSNHVSIAHTRWATHGQPSVENCHPLSSD-KNDNFLVVHNGIITNYKDLKtylgKKGFSFESNTDTECAAKLALHF 152
                                        556788*******************9866.788999*******9998876677888899999*****987655554 PP

                           GATase_4 141 lasrfekaepsaeeleralaelakeiaelGvfnllls 177
                                         ++    ++ ++ +  ++++++ak+   +G f ++++
  gene1055|gene1055|rna1054|rna1054 153 YKEME--SNGEKPDFVSIVKKVAKNC--EGAFAFVFA 185
                                        44433..3445555556666666543..466666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.51
# Mc/sec: 4102.87
//
Query:       gene1056|gene1056|rna1055|rna1055  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.1   0.0      0.043   13.5   0.0    1.2  1  ITI_HC_C  Inter-alpha-trypsin inhibitor heavy chain C-terminu
      0.059   13.4   0.4         14    5.8   0.0    2.4  2  DUF5640   Family of unknown function (DUF5640)


Domain annotation for each model (and alignments):
>> ITI_HC_C  Inter-alpha-trypsin inhibitor heavy chain C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.8e-06     0.043      26      80 ..      11      67 ..       3      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.8e-06
                           ITI_HC_C 26 Yfgklgivvkkkrvkievttekitlk.dgekrlvlswsdta.slkkkglevsvskes 80
                                       + g l+i +kk+++k ev++ +i+++  g+++  l+++d + +++ ++l+++v++++
  gene1056|gene1056|rna1055|rna1055 11 FRGMLSIFNKKDDIKFEVKQGTISISsYGQSNFYLTMNDDVfMVNGDDLTFTVKAQH 67
                                       44789********************989*********98862678999****99875 PP

>> DUF5640  Family of unknown function (DUF5640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.002        18      33      72 ..      20      62 ..      12      69 .. 0.59
   2 ?    5.8   0.0    0.0015        14      38      60 ..     135     158 ..     121     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.002
                                       TTEEEEEE-SSSSEEEEEESS--...--EEE-EEESSSEEEE- CS
                            DUF5640 33 aaykftYtieedqLkidfeaekk...edceyefsvngntLtLt 72
                                        + + ++++++++++i ++++++   +  +  f vng+ Lt t
  gene1056|gene1056|rna1055|rna1055 20 KKDDIKFEVKQGTISISSYGQSNfylTMNDDVFMVNGDDLTFT 62
                                       4566899*********777733200011222355555555544 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0015
                                        EEE-SSSSEEE.EEESS----EEE CS
                            DUF5640  38 tYtieedqLki.dfeaekkedcey 60 
                                        tY+ieed+L i + +a+  e+ e+
  gene1056|gene1056|rna1055|rna1055 135 TYEIEEDRLFIrKAGADLLEEIEF 158
                                        9**********7666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1427.74
//
Query:       gene1057|gene1057|rna1056|rna1056  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.034   14.2   0.2       0.14   12.3   0.2    2.0  1  DUF2750   Protein of unknown function (DUF2750)
      0.039   14.2   0.0      0.065   13.5   0.0    1.3  1  AHSA1     Activator of Hsp90 ATPase homolog 1-like protein


Domain annotation for each model (and alignments):
>> DUF2750  Protein of unknown function (DUF2750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   1.5e-05      0.14      46      80 ..     192     226 ..     191     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                            DUF2750  46 awakeewadykpkeisleeFleewlpgLeedgvlv 80 
                                        +w+ +ew++++ ++i+leeFl++   +L++++v +
  gene1057|gene1057|rna1056|rna1056 192 KWKLKEWSNFTEVRIQLEEFLNSSKITLKQKNVPI 226
                                        68899************************999865 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.3e-06     0.065      49     104 ..     175     229 ..     150     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-06
                                        EEEEEEEE.ETTTEEEEEEEEETSETEEEEEEEEEEEEETTEEEEEEEEEEEEHCHH CS
                              AHSA1  49 negeylev.vpperlvytwrledepeeeestvtieleeegggTrltlthtglprkqk 104
                                         +++++e+ +++  ++++w+l+++++  +++v+i+lee  +  ++tl+++++p k++
  gene1057|gene1057|rna1056|rna1056 175 DNVIIRELkEKNGGIEMKWKLKEWSN--FTEVRIQLEEFLNSSKITLKQKNVPIKEE 229
                                        45557777245678*********994..8********************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1469.27
//
Query:       gene1058|gene1058|rna1057|rna1057  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-24   84.2   6.0    1.1e-23   84.0   6.0    1.1  1  FAM72     FAM72 protein


Domain annotation for each model (and alignments):
>> FAM72  FAM72 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   6.0   6.1e-28   1.1e-23       9     118 ..      10     120 ..       2     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 6.1e-28
                              FAM72   9 vsvleckfcekvlcsrgmkavlladtevelystdippeetvdfvgslystesckcklkdiaclkcGnvvGyhvvap 84 
                                          v+ c  c +v+c+r+ +++ll+   +++yst++p +e+v+ +g+ y++ sckc + di c+ c  ++Gyhv++ 
  gene1058|gene1058|rna1057|rna1057  10 RYVIRCFGCGNVICRRAARSLLLSSLRIKVYSTNVP-TENVKCIGNSYMAYSCKCIVADIECRLCRLILGYHVLQL 84 
                                        45789*****************************95.778************************************ PP

                              FAM72  85 ckscllscnnGhfwmfhskavsa..vnrldssgvnl 118
                                        c+ c     nG  w+f +++v +  ++r +++  n+
  gene1058|gene1058|rna1057|rna1057  85 CELCAGEGKNGRTWIFDASSVIStiIKRCSKACLNM 120
                                        *****************9998753368888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 925.45
//
Query:       gene1059|gene1059|rna1058|rna1058  [L=336]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-49  167.3   0.1    4.7e-49  166.9   0.1    1.2  1  DUF155    Uncharacterised ACR, YagE family COG1723


Domain annotation for each model (and alignments):
>> DUF155  Uncharacterised ACR, YagE family COG1723
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.9   0.1   2.6e-53   4.7e-49       1     176 []     112     281 ..     112     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 2.6e-53
                             DUF155   1 vfiFknGsvVfwgldeeeeknflnkllkflneeselpreeeqeteeleyvydeqsessrikgdvivlksksllekl 76 
                                        +f++++G+vV+wg++e +e+ +++ ++k+ +e+    + +e e e ++y ++    ++ i +dvi+l+s+++ +k+
  gene1059|gene1059|rna1058|rna1058 112 CFFYEYGVVVCWGMSETQESMIVKLVEKY-EENG--HEPSEVEIESFKYGITG---NPFIINDVIYLNSENHFTKM 181
                                        79*************99998888866665.4443..33344446899998865...689***************** PP

                             DUF155  77 aiShalaqSvkLdvlEesldellestekipkelakkgklklsrkellkktgellslrinlnlkselldtPdffWee 152
                                        +iS a+aqSvkLd++E+++d+++e ++++p+e++++gk++ s+ke+lk +g+l++lr nlnl s++ld+P+f+W++
  gene1059|gene1059|rna1058|rna1058 182 VISIAIAQSVKLDYFENLVDNTIEAVKEFPEEVEREGKVSKSKKEILKMIGKLHRLRFNLNLGSNILDEPEFVWDY 257
                                        *************************************99999********************************** PP

                             DUF155 153 peleslyeavseyleikeRikiLn 176
                                        p + slye +++yl+ik+R ++Ln
  gene1059|gene1059|rna1058|rna1058 258 PAFSSLYETCKRYLDIKPRADLLN 281
                                        ***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2196.55
//
Query:       gene1060|gene1060|rna1059|rna1059  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-31  107.7   0.1    6.6e-31  106.6   0.0    1.6  2  eIF-5_eIF-2B  Domain found in IF2B/IF5
  ------ inclusion threshold ------
       0.16   11.5   3.2       0.36   10.4   3.2    1.6  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   7.3e-35   6.6e-31       3     116 ..       7     121 ..       5     122 .. 0.95
   2 ?   -3.0   0.0      0.72   6.5e+03      30      41 ..     233     244 ..     224     265 .. 0.54

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 7.3e-35
                                        CCCSSSS--SSTT--EEEETT....EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCH CS
                       eIF-5_eIF-2B   3 ekedkkerykmpklqvkvegkk...ktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakk 75 
                                        +++d  +rykmp++ vk egk    +tvivN+eei ++L+r+p ++lk++++el+t+ ++  +gr+ +ng++++++
  gene1060|gene1060|rna1059|rna1059   7 TNNDFYYRYKMPRAVVKLEGKAgntRTVIVNLEEIGSSLKRPPLYILKFMSYELATRIDV-VKGRYAVNGRYDSSR 81 
                                        566889***************9999*********************************99.999************ PP

                                        HHHHHHHHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                       eIF-5_eIF-2B  76 leklldkyieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                        +++l++++i+++V+C+ C++pet  + ++ l+ ++C aCg+
  gene1060|gene1060|rna1059|rna1059  82 VQDLIYDFIDRFVMCPFCNNPETFYVNNDGLS-MECLACGK 121
                                        ***********************999999999.*******8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.72
                                        THHHHHHHHTTS CS
                       eIF-5_eIF-2B  30 NfeeiakaLnrd 41 
                                        N++e  ++L+ +
  gene1060|gene1060|rna1059|rna1059 233 NIQEYLRMLEEE 244
                                        555555555443 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.2   4.1e-05      0.36       2      26 ..      95     120 ..      94     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.1e-05
                                        EETTTTCEE.CHEETSTTCEEESSSS CS
                       TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdCG 26 
                                        +CP C++++ ++++++   + C +CG
  gene1060|gene1060|rna1059|rna1059  95 MCPFCNNPEtFYVNNDGLSMECLACG 120
                                        8******998***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1679.50
//
Query:       gene106|gene106|rna106|rna106  [L=575]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-13   48.8   0.3    6.1e-13   48.8   0.3    2.2  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.6     0.039   6.9e+02      25      42 ..       5      22 ..       3      33 .. 0.87
   2 !   48.8   0.3   3.4e-17   6.1e-13      53     152 ..     402     500 ..     394     536 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.039
                                   CCHHHHHHHHHHHHHHHH CS
                     MS_channel 25 sallavlGalglalglal 42
                                   s+ll++l++++l lg+ l
  gene106|gene106|rna106|rna106  5 SSLLSSLALAALLLGFIL 22
                                   79**************87 PP

  == domain 2  score: 48.8 bits;  conditional E-value: 3.4e-17
                                    HHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-... CS
                     MS_channel  53 iillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkk 132
                                    +++++++p++ GD+v i +    V+ i+l++t ++t+dg +++iPn  + +++i N +r s +++ k+s  +  +++  k
  gene106|gene106|rna106|rna106 402 LFIIYTHPYDPGDRVHIDGENMVVRRISLFSTVLETWDGMETIIPNLVIREKAILNIRR-SRQQQWKLSLLISSNTPARK 480
                                    79*********************************************************.999***************** PP

                                    HHHHHHHHHHHHHH-TTB-T CS
                     MS_channel 133 lekvleelkealkekpevlk 152
                                    +e ++e +k+++k+++  ++
  gene106|gene106|rna106|rna106 481 IELLREAIKRFVKHDKSYIT 500
                                    *************9987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (575 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 4030.33
//
Query:       gene1061|gene1061|rna1060|rna1060  [L=551]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-51  175.4   0.0      2e-51  174.6   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    2.3e-18   66.5   8.7    2.3e-18   66.5   8.7    2.6  2  DUF3381          Domain of unknown function (DUF3381)
     0.0025   17.5  31.0      0.013   15.1  19.1    3.9  3  Spb1_C           Spb1 C-terminal domain
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.052   13.2   0.0    1.8  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
        3.1    8.1  13.8       0.24   11.7   4.6    2.5  2  RSB_motif        RNSP1-SAP18 binding (RSB) motif


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   0.0   5.6e-55     2e-51       1     177 []      24     200 ..      24     200 .. 0.99

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 5.6e-55
                                        CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHH CS
                               FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpeti 76 
                                        yr+Rsa+KLl+++ k+ ++k+ +  +Dl+aaPG+wsqv++q++  + k+vavDl p++ +  v ti  dit+ e +
  gene1061|gene1061|rna1060|rna1060  24 YRARSAFKLLQMNRKYAFLKNAHVLIDLCAAPGSWSQVAAQEMPLRRKIVAVDLEPIKFIGDVDTIVEDITSDECR 99 
                                        9****************99************************999****************************** PP

                                        HHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCE CS
                               FtsJ  77 ekikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfF 152
                                         k++e l+ +k+d+v++Dgap+v   ++ d+++q  L+l +++la++ lk+gg+f++k+fr+++  +l + l+++F
  gene1061|gene1061|rna1060|rna1060 100 LKLREILGAQKADVVLHDGAPNVGTSWENDAFNQNLLALHSTKLASEFLKRGGVFITKVFRSQDYFSLHNILSQLF 175
                                        ***************************************************************9999********* PP

                                        EEEEEEE-SS--CCG-EEEEEEEEC CS
                               FtsJ 153 ekvsvvkPkssrsesseeflvcrgf 177
                                        e+v+  kP ssrs+s+e+flvc+gf
  gene1061|gene1061|rna1060|rna1060 176 ETVETSKPLSSRSQSAEIFLVCLGF 200
                                        ***********************98 PP

>> DUF3381  Domain of unknown function (DUF3381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   8.7   6.5e-22   2.3e-18       5     156 ..     220     357 ..     218     364 .. 0.84
   2 ?   -6.3   6.8         5   1.8e+04     143     162 ..     459     478 ..     414     489 .. 0.69

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 6.5e-22
                                        XXXXXXXXXXXXXX--EEEHHHHHT-----...HHHHH-SEEE--SHHHHH.HHSSSSS-SSHHHHHH-SSS--HH CS
                            DUF3381   5 krkreGYeegdytlykelsvseFiksedpi...elLgkaneitfdkeelkekilkhpktteEikelckDLkVLGkk 77 
                                         + + GY++  +++ k+l+++eF+k++dp    e+L+k++ei +d +e k   +  +  ++E++++++DL++LGk+
  gene1061|gene1061|rna1060|rna1060 220 TKDAGGYDD--FNFCKKLKFTEFLKEDDPDvlsEMLSKYSEIMVDIDE-K---DIPKVLEPEFLDMFRDLQLLGKG 289
                                        57899****..788**************96677************533.2...3467899**************** PP

                                        HHHHHHHHHHHHHHH-XXXX.................XXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DUF3381  78 dlkkLLkWrkklrkelgleekkekeekeeeeeedeeeeeeeeeeaeeeeldeeeeiekeleelkeeekkkkKrekk 153
                                        d++k L+ r ++ + +++   +  + +  +++e+           ee el +e++ e++++e+++  +k+k+++++
  gene1061|gene1061|rna1060|rna1060 290 DIRKVLRKRRRIIQDVQKGVIEVPDLDFLRDNENV----------EEAEL-KEKSSEEKIKEIQMLIEKRKRKNER 354
                                        *****************999988888887776543..........23444.447889999******9999999999 PP

                                        XXX CS
                            DUF3381 154 kan 156
                                        k+ 
  gene1061|gene1061|rna1060|rna1060 355 KES 357
                                        976 PP

  == domain 2  score: -6.3 bits;  conditional E-value: 5
                                        XXXXXXXXXXXXXXXXXXXX CS
                            DUF3381 143 eekkkkKrekkkankkkqke 162
                                        ee++  K+ek   n++k++ 
  gene1061|gene1061|rna1060|rna1060 459 EERRLTKKEKEALNRRKTRA 478
                                        33333344444444444433 PP

>> Spb1_C  Spb1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.17   6.2e+02      90     116 ..     248     274 ..     241     293 .. 0.82
   2 ?    1.4   5.0      0.06   2.1e+02     140     168 ..     328     356 ..     320     362 .. 0.83
   3 !   15.1  19.1   3.7e-06     0.013      98     205 ..     444     548 ..     375     551 .] 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.17
                             Spb1_C  90 itkeavaaikeklralnarpiKKVaEA 116
                                        +  e+++++ e + +++++ i KV+E 
  gene1061|gene1061|rna1060|rna1060 248 VLSEMLSKYSEIMVDIDEKDIPKVLEP 274
                                        66799999****************996 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.06
                             Spb1_C 140 ededlsekeKakqieklmkkaakkkkkkk 168
                                        e ++ s +eK+k+i+ l++k ++k+++k+
  gene1061|gene1061|rna1060|rna1060 328 ELKEKSSEEKIKEIQMLIEKRKRKNERKE 356
                                        56789999*************98866554 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 3.7e-06
                             Spb1_C  98 ikeklralnarpiKKVaEAkaRKklkaa..kkleklkkkaeliaededlsekeKakqieklmkkaakkkkkkkvkv 171
                                        ++e ++ + +rp  KV E +  Kk k+a  ++  +++++ae+ +++  + ++e    ++k + k + kk+k k ++
  gene1061|gene1061|rna1060|rna1060 444 LREDQESFYSRPP-KVEERRLTKKEKEAlnRRKTRAERRAEMFMKNVVIDDSEEEGVVAKKIYKSSFKKTKSKPRI 518
                                        5666666666775.5777777777766433566677778888888888888888888876666666666999**** PP

                             Spb1_C 172 vvakkankglsgrpkgvkgkykmVDkrmKkdlRa 205
                                        v+ kk+     g p+g kg+    DkrmKkd+R+
  gene1061|gene1061|rna1060|rna1060 519 VFPKKGRC---GIPRG-KGRIVALDKRMKKDKRK 548
                                        **998755...58997.9***************8 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.052       7      43 ..      43      79 ..      40     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSC CS
                    Methyltr_RsmB-F  7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdank 43
                                       ++   ++DlcaaPG+     a+ m  + ++vAvd + 
  gene1061|gene1061|rna1060|rna1060 43 KNAHVLIDLCAAPGSWSQVAAQEMPLRRKIVAVDLEP 79
                                       5777899***************************876 PP

>> RSB_motif  RNSP1-SAP18 binding (RSB) motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.8      0.13   4.5e+02      17      53 ..     330     355 ..     314     370 .. 0.37
   2 ?   11.7   4.6   6.8e-05      0.24      14      79 ..     451     518 ..     442     521 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                          RSB_motif  17 eekerkrkrsrseekarerrrerskskekrreskask 53 
                                        +ek+ ++k ++ +   ++r+r           ++++k
  gene1061|gene1061|rna1060|rna1060 330 KEKSSEEKIKEIQMLIEKRKR-----------KNERK 355
                                        222222222222211111111...........11111 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.8e-05
                          RSB_motif  14 v.ereekerkrkrsrseekarerrrerskskekrreskaskekkkeeepp.akllDdlFrkTkatPci 79 
                                        + +r+ k ++r+  ++e++a +rr++r++++ +   ++   +  +ee    +k+    F+kTk++P i
  gene1061|gene1061|rna1060|rna1060 451 FySRPPKVEERRLTKKEKEALNRRKTRAERRAEMFMKNVVIDDSEEEGVVaKKIYKSSFKKTKSKPRI 518
                                        337777778888888888888888877777766666665555555555544999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3466.60
//
Query:       gene1062|gene1062|rna1061|rna1061  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-09   37.8  17.7    1.3e-06   28.6   4.2    2.1  2  ATP-synt_C  ATP synthase subunit C
  ------ inclusion threshold ------
       0.07   11.3   1.3        1.3    7.2   0.1    2.0  2  BIV_Env     Bovine immunodeficiency virus surface protein (SU
       0.13   11.1   2.4       0.15   10.8   2.4    1.1  1  Otopetrin   Otopetrin
        4.3    6.4   6.6         13    4.9   4.7    2.3  2  RELT        Tumour necrosis factor receptor superfamily membe


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   5.6   4.5e-06      0.02       1      59 [.      15      72 ..      15      73 .. 0.95
   2 !   28.6   4.2   2.9e-10   1.3e-06       2      59 ..      89     146 ..      88     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.5e-06
                                       HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59
                                       lg gl++ lsa+g G+g  +ags gi   a+n   +t sl++++f+ a  +y +i  ++
  gene1062|gene1062|rna1061|rna1061 15 LGPGLMISLSAIGGGLGF-IAGSEGICKAAENVVNTTYSLVPIIFITAPTMYSVILYFM 72
                                       789**************9.***********************************99886 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 2.9e-10
                                        HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         ATP-synt_C   2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59 
                                         a++  G+s   +G+ iG  +++++   +++ k  + +++il+f e+++l+gL++a+ 
  gene1062|gene1062|rna1061|rna1061  89 SACVVNGVSSGVAGYSIGHSAKVACVTRSQQKKFNSIFFLILIFGEVVGLLGLVCAMA 146
                                        6888899*************************************************85 PP

>> BIV_Env  Bovine immunodeficiency virus surface protein (SU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.003        13     196     226 ..      53      85 ..      19      98 .. 0.76
   2 ?    7.2   0.1   0.00028       1.3     128     171 ..     107     150 ..      85     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.003
                            BIV_Env 196 tvpiilisspl..agilgyfvmeryskilkgGc 226
                                         vpii+i++p   + il ++v ++  + l++G 
  gene1062|gene1062|rna1061|rna1061  53 LVPIIFITAPTmySVILYFMVYDKKIESLRDGL 85 
                                        48*******962134555668899999999997 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00028
                            BIV_Env 128 rssvienitkkdikdtdpyilillglvvilGllGviialrrsns 171
                                        +s+ +  +t+ + k  + + +++l++  ++GllG++ a+  s s
  gene1062|gene1062|rna1061|rna1061 107 HSAKVACVTRSQQKKFNSIFFLILIFGEVVGLLGLVCAMAISSS 150
                                        4566778999999999999999999*************988765 PP

>> Otopetrin  Otopetrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.4   3.4e-05      0.15     239     338 ..      45     144 ..      36     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.4e-05
                          Otopetrin 239 dcsgsskGLflglLllvltiislilFfvlvrkpklsslailladlselvllalaiiaviigf.irvrklkfrreeq 313
                                        ++++++  L+  +++   t+ s+il+f++++k+ ++sl   l+ ls +v+ +++     +++   ++   ++r++q
  gene1062|gene1062|rna1061|rna1061  45 NVVNTTYSLVPIIFITAPTMYSVILYFMVYDKK-IESLRDGLLVLSACVVNGVSSGVAGYSIgHSAKVACVTRSQQ 119
                                        566777777878888999************966.999999999999999999988777666625667777888899 PP

                          Otopetrin 314 leLddiLllisafGlfvysvfsiia 338
                                         ++++i  li +fG +v  +  + a
  gene1062|gene1062|rna1061|rna1061 120 KKFNSIFFLILIFGEVVGLLGLVCA 144
                                        9*************98755544444 PP

>> RELT  Tumour necrosis factor receptor superfamily member 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.067     3e+02       4      13 ..      51      60 ..      48      61 .. 0.85
   2 ?    4.9   4.7    0.0028        13       3      21 ..     125     143 ..     123     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.067
                               RELT  4 fvLVpvFflm 13
                                       + LVp+ f++
  gene1062|gene1062|rna1061|rna1061 51 YSLVPIIFIT 60
                                       88******97 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0028
                               RELT   3 vfvLVpvFf.lmGLlGvLiC 21 
                                        +f+L+++F  ++GLlG+ +C
  gene1062|gene1062|rna1061|rna1061 125 IFFLILIFGeVVGLLGL-VC 143
                                        8*******659*****5.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 856.18
//
Query:       gene1063|gene1063|rna1062|rna1062  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00079   19.6   0.1     0.0017   18.5   0.1    1.5  1  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t


Domain annotation for each model (and alignments):
>> tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   9.7e-08    0.0017      27      66 ..      25      61 ..       9      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.7e-08
                    tRNA_int_end_N2 27 vvvespkarGkhfktmGvsrarrgrlwLlpeEaLYLvErG 66
                                       + v++ +++ ++ + +G++  +++ l+L  eE+LYL +r 
  gene1063|gene1063|rna1062|rna1062 25 MFVPK-DQSQNWCRHFGMR--KNKVLYLCEEEVLYLYDRE 61
                                       44553.4799*******66..9**************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.37s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 860.28
//
Query:       gene1064|gene1064|rna1063|rna1063  [L=253]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-06   25.5   1.0    9.3e-05   22.2   0.2    2.5  2  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom
  ------ inclusion threshold ------
       0.07   11.8   0.0      0.093   11.3   0.0    1.1  1  Hanta_G2  Hantavirus glycoprotein G2


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.033   2.9e+02       2      62 ..      17      73 ..      16      80 .. 0.69
   2 !   22.2   0.2     1e-08   9.3e-05       4      67 ..     108     165 ..     107     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.033
                                       EEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTE CS
                              RRM_1  2 fVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngk 62
                                       +V++++    +ee+k+  +k  +ik+i  + +      ++  + F +++ A++A++ l g 
  gene1064|gene1064|rna1063|rna1063 17 IVTGFNDQKHQEEVKDRIKKKFEIKEIYTIQN----DYRVLCILFYDERRAREAISYLKGS 73
                                       56677777777888888877666666666664....4555556688888899999888775 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1e-08
                                        ESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTE CS
                              RRM_1   4 gnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggr 67 
                                        +nL+ +v+++e +e  skfG++k+i+ v++          VeF ++++A +A   +n+ k+++ 
  gene1064|gene1064|rna1063|rna1063 108 KNLTGSVDDKEFSEEVSKFGEVKDIRYVKT------HQRCVEFYDSRNAIAAFHGMNELKFMDG 165
                                        79***************************5......5556******************999875 PP

>> Hanta_G2  Hantavirus glycoprotein G2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     1e-05     0.093     194     297 ..     100     203 ..      75     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1e-05
                           Hanta_G2 194 gdtllflgpleeggiifkqwctstcvfgdpgdimstkegelkcpefagsfrkkcafattpvcey.dgntvsgykrv 268
                                          tllf      g++  k++     +fg+  di   k++  +c ef  s + + af  +   ++ dg + + +   
  gene1064|gene1064|rna1063|rna1063 100 QSTLLFTFKNLTGSVDDKEFSEEVSKFGEVKDIRYVKTH-QRCVEFYDSRNAIAAFHGMNELKFmDGVIQAKWVWD 174
                                        578999888889999******************999988.89***************9999887478888899999 PP

                           Hanta_G2 269 latkdsfqsfnvtelhltserlewvdpds 297
                                        l+tk  +  + +t+ +l++ +le + p  
  gene1064|gene1064|rna1063|rna1063 175 LSTKTRWELIRLTDSILKECKLEIKTPAK 203
                                        ***********************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1414.94
//
Query:       gene1065|gene1065|rna1064|rna1064  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-08   34.3   0.0      2e-08   33.8   0.0    1.2  1  ubiquitin       Ubiquitin family
    5.9e-08   32.5   8.1    1.3e-07   31.4   8.1    1.5  1  Ribosomal_L40e  Ribosomal L40e family
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.15   11.9   0.0    1.3  1  Rad60-SLD       Ubiquitin-2 like Rad60 SUMO-like
       0.22   11.6   2.9       0.26   11.3   2.9    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   4.5e-12     2e-08       1      68 [.       3      69 ..       1      72 [. 0.94

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.5e-12
                                       EEEEETTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEE CS
                          ubiquitin  1 itvktldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlv 68
                                       i v+ + gk+  ++ e+s+ +++lK  +     +  + + L ++ k Led++t+++ygi++ +t++++
  gene1065|gene1065|rna1064|rna1064  3 ISVR-FGGKTSFIQAEPSQLILSLKTLVGNACSLDSSMMALQHNSKALEDSKTVASYGIRNFDTIVMY 69
                                       4455.89**********************************************************986 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   8.1   2.8e-11   1.3e-07       7      48 ..      85     123 ..      84     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.8e-11
                     Ribosomal_L40e   7 qLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKK 48 
                                        ++A K + d  iCr+CYAr  + A++Cr  kC+ s++lrpKK
  gene1065|gene1065|rna1064|rna1064  85 AMAMKEKNDCLICRRCYARSGKSAQKCR--KCD-SKDLRPKK 123
                                        6899************************..9*8.99*****9 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.4e-05      0.15      10      68 ..       9      66 ..       1      69 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                                       S--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEEE CS
                          Rad60-SLD 10 gkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdti 68
                                       gk+ +i+ +p+  +  L++   ++ +++  + + L+ + + L++ +tv++++i++ dti
  gene1065|gene1065|rna1064|rna1064  9 GKTSFIQAEPSQLILSLKTLVGNACSLDS-SMMALQHNSKALEDSKTVASYGIRNFDTI 66
                                       77888999999999999999999999999.99************************998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.9   5.8e-05      0.26      59      98 ..      83     120 ..       5     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.8e-05
                                        T-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                               HypA  59 gaeLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                                        +  ++++e++  + Cr+C ++  +++   +C kC+s+d++
  gene1065|gene1065|rna1064|rna1064  83 DGAMAMKEKNDCLICRRCYARSGKSA--QKCRKCDSKDLR 120
                                        55678889999999****99888664..58******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 728.18
//
Query:       gene1066|gene1066|rna1065|rna1065  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 378.54
//
Query:       gene1067|gene1067|rna1066|rna1066  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-36  122.4   0.5    1.1e-35  121.9   0.5    1.3  1  Ribosomal_L22  Ribosomal protein L22p/L17e
  ------ inclusion threshold ------
       0.18   11.7   0.5          2    8.4   0.1    2.3  2  zf-CCCH_6      Chromatin remodeling factor Mit1 C-terminal Zn


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   0.5   1.3e-39   1.1e-35       2     101 ..      19     170 ..      18     172 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1.3e-39
                                        EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST..................................... CS
                      Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf..skkk..................................... 38 
                                        k++n++vsfkk+re++ ++r++kv +A++yLk+  +k++                                     
  gene1067|gene1067|rna1066|rna1066  19 KIDNAKVSFKKTRETCSTLRKRKVVDAIEYLKNviNKTEcvpfrrynrgcgqthqarkfsipkreivkangekvik 94 
                                        5789*****************************955555************************************* PP

                                        .............THHHHHHHHHHHHHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEE CS
                      Ribosomal_L22  39 .............aakfvlklLknaeanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievv 101
                                                     +a+fv+ lL+n ++ ae+k+ldv++lvI++iqv+k+pk+ +rt+rA+Gr+np++kspchi+ v
  gene1067|gene1067|rna1066|rna1066  95 rghvqtrgrwpkkSAEFVITLLENLKESAETKNLDVENLVITHIQVSKAPKIFGRTFRAHGRVNPFNKSPCHIQAV 170
                                        *************************************************************************987 PP

>> zf-CCCH_6  Chromatin remodeling factor Mit1 C-terminal Zn finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.049   4.4e+02      14      29 ..      31      46 ..      27      59 .. 0.68
   2 ?    8.4   0.1   0.00022         2      22      42 ..     108     128 ..     106     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.049
                                       SS--GGGSSHHHHHHH CS
                          zf-CCCH_6 14 krtCPhlksetqvrrm 29
                                       ++tC  l+ ++ v ++
  gene1067|gene1067|rna1066|rna1066 31 RETCSTLRKRKVVDAI 46
                                       5788888877666553 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00022
                                        SHHHHHHHHHHHHT--S-HHH CS
                          zf-CCCH_6  22 setqvrrmleaLkeStEprel 42 
                                        s + v ++le LkeS+E ++l
  gene1067|gene1067|rna1066|rna1066 108 SAEFVITLLENLKESAETKNL 128
                                        778899***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1199.85
//
Query:       gene1068|gene1068|rna1067|rna1067  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.5e-30  103.5   0.0    1.2e-29  103.2   0.0    1.1  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
        0.1   12.3   0.0       0.25   11.0   0.0    1.6  1  PGM_PMM_I   Phosphoglucomutase/phosphomannomutase, alpha/beta


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   1.3e-33   1.2e-29       3     190 .]      88     274 ..      86     274 .. 0.93

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.3e-33
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        + +tvv+++ +d++v+++d+r++ +++++++++++Kif+i d ++++ +G +aD   +  ++ +e+++y+   +  
  gene1068|gene1068|rna1067|rna1067  88 NSGTVVCLRQDDFIVIGGDTRHS-SDMIINSREMTKIFQIGD-LFLTGTGFYADSHEVYVKMAYEIRQYE--VEGS 159
                                        678********************.666678888*******65.8999***********************..6777 PP

                                        TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        i+v+    ++a++l++ ++++++ p++  +++ g+  +g+p++y+ dp Gs+ +   +++ Gsg+ +++++l++ +
  gene1068|gene1068|rna1067|rna1067 160 INVH----SAANLLSKILYSKRFFPYYSYCVLSGFE-NGRPYVYSYDPVGSFESV-TCICNGSGRSMIQPLLDSFV 229
                                        7777....99*************************9.999***************.5***************9988 PP

                                        .........STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                         Proteasome 155 .........kedltleeavelavkalkealerdklsgknievavi 190
                                                 +  l++e++v+l+ ka ++a+erd+ +++n+ev+v+
  gene1068|gene1068|rna1067|rna1067 230 skknwnnagQAQLSQEDCVRLITKAFNAAAERDVKTKDNLEVYVV 274
                                        877778888888*******************************97 PP

>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.8e-05      0.25      40      59 ..      98     117 ..      89     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.8e-05
                                        S-EEEEEE-S-TTHHHHHHH CS
                          PGM_PMM_I  40 kkkvvvGrDtRvssrelaea 59 
                                        +  +v+G+DtR+ss++++++
  gene1068|gene1068|rna1067|rna1067  98 DDFIVIGGDTRHSSDMIINS 117
                                        5679************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1929.95
//
Query:       gene1069|gene1069|rna1068|rna1068  [L=604]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1446  (0.0806515); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 3948.44
//
Query:       gene1070|gene1070|rna1069|rna1069  [L=1562]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-69  234.6   4.8    1.4e-69  234.6   4.8    3.1  3  Dopey_N   Dopey, N-terminal
     0.0072   16.3   0.8       0.17   11.9   0.1    2.7  2  PX        PX domain


Domain annotation for each model (and alignments):
>> Dopey_N  Dopey, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.6   4.8   1.5e-73   1.4e-69       2     305 ..       3     278 ..       2     280 .. 0.95
   2 ?   -2.7   0.3      0.28   2.5e+03     132     182 ..     323     372 ..     304     438 .. 0.64
   3 ?   -2.4   0.3      0.23     2e+03     102     141 ..    1381    1421 ..    1377    1446 .. 0.82

  Alignments for each domain:
  == domain 1  score: 234.6 bits;  conditional E-value: 1.5e-73
                            Dopey_N   2 kkykkykkevekaLksfekveeWaDlisfLgkLlkaLqssnskfevipekllvakrLaqCLnpalPsgVHqkaLev 77 
                                        +++++y++e++k L  f++ +eW+D+is+L+ L  ++++   +++ ip+k l+ krL qCLnp lP+g+H+k+Le+
  gene1070|gene1070|rna1069|rna1069   3 ESRERYEAEMTKKLDAFKTAKEWSDFISLLSSLDSTIKK--FSISEIPKKKLLFKRLNQCLNPVLPAGIHNKTLET 76 
                                        6789**********************************5..7899******************************* PP

                            Dopey_N  78 YelifenigseslskdlslylpGLlpllsyaslsvkpqlleliekyllpLgekLrpalkglilslLpGLeeensev 153
                                        Y+l+fe+i++e+l k++   ++GL+ + +++ + v   +l+lie+y++pLg+++++ + +++++lLp +e e+ e+
  gene1070|gene1070|rna1069|rna1069  77 YSLVFERISKENLLKEFDFLTLGLFTFSAHCRILVINSFLDLIERYIVPLGKDVEMYCTSILIGLLPPMEFESGEH 152
                                        **************************************************************************** PP

                            Dopey_N 154 fertlklleklkekvgekyfyqclwlaiirspsrRlgalkylskklpklkeveeeeekkeklsklseeaeallspe 229
                                        + r+  +++++k+ v++ +fy+++w ++++ ++ R++++++ ++                       e+++++  +
  gene1070|gene1070|rna1069|rna1069 153 YGRARLIITEFKSLVSPVVFYSSMWSILLNDERLRTSVVNFTLSMS--------------------WEESMVV--N 206
                                        **************************************99876555....................2344555..6 PP

                            Dopey_N 230 pgllvrallatledenllvqRgiLDlLlshlpldsdvlqeklskedkellveaalklllrkDmSlnRRlwaWLlgp 305
                                         +l+ ral+++l +e++lv R++LDlL+  +p +s+v+ e    + ++ l+ea++kl++++D+Sln+R++ WL+ +
  gene1070|gene1070|rna1069|rna1069 207 TKLVTRALCEGLGSESTLVVRNCLDLLIFIFPDKSHVCYE----DILDNLIEAVIKLFVKRDLSLNKRIYGWLCMT 278
                                        79********************************997655....99***************************976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.28
                            Dopey_N 132 rpalkglilslLpGLeeensevfertlklleklkekvge........kyfyqclwlaii 182
                                        + +++ l+  +L  L+  +++  +++++  + ++e++ge        k        a++
  gene1070|gene1070|rna1069|rna1069 323 EKIMENLLFNVLGCLQKHEKNSAKEIMQ-QDAFEESLGEsidiekiaK--------AFL 372
                                        4567888888888888777777777776.4777777777444444441........333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.23
                            Dopey_N  102 lpllsyaslsvkpqlleliekyllpLg.ekLrpalkglils 141 
                                         + l++y s +v+ +++ l +  +l+++ +kL+++ + l+  
  gene1070|gene1070|rna1069|rna1069 1381 AALINYPSSKVRKEVFFLSKMLILKIShDKLINLYPILLYD 1421
                                         67899999************99****999999988877765 PP

>> PX  PX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   1.9e-05      0.17      24      70 ..       8      54 ..       6      90 .. 0.89
   2 ?    1.6   0.1     0.029   2.6e+02      35      71 ..     520     558 ..     494     585 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.9e-05
                                       EEEEETTSSSEEEEEEEHHHHHHHHHHHHHHHTTSTSTSSSTSGSSS CS
                                 PX 24 yevelktgakewtvkRrYsdFeeLhskLlrkfprvkiPplPkkvlfg 70
                                       ye e++ +   +++ +  sdF++L s L ++ ++ +i ++Pkk+l+ 
  gene1070|gene1070|rna1069|rna1069  8 YEAEMTKKLDAFKTAKEWSDFISLLSSLDSTIKKFSISEIPKKKLLF 54
                                       67788888899*********************************975 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.029
                                        EEEEEEHHHHHHHHHHHHHHHT..TSTSTSSSTSGSSSS CS
                                 PX  35 wtvkRrYsdFeeLhskLlrkfp..rvkiPplPkkvlfgs 71 
                                        ++v+   sdF  + s++l+ f   +vk+ ++ +k++ g 
  gene1070|gene1070|rna1069|rna1069 520 FLVHLVLSDFLLFDSQILFSFLdfSVKVMKFKEKQVEGG 558
                                        55666689**********999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.92u 0.30s 00:00:01.22 Elapsed: 00:00:00.50
# Mc/sec: 9308.36
//
Query:       gene107|gene107|rna107|rna107  [L=1018]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-23   82.1   0.3    3.1e-10   40.3   0.0    5.3  5  C2        C2 domain
  ------ inclusion threshold ------
      0.012   15.1   0.5        1.8    8.0   0.5    2.7  1  SMP_LBD   Synaptotagmin-like mitochondrial-lipid-binding doma


Domain annotation for each model (and alignments):
>> C2  C2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0022        20      23      74 ..     353     402 ..     334     431 .. 0.69
   2 !   25.4   0.1   1.4e-09   1.3e-05      39      94 ..     565     617 ..     557     625 .. 0.82
   3 ?    3.3   0.0     0.011        97      60      90 ..     701     730 ..     683     741 .. 0.82
   4 ?   -1.1   0.0      0.26   2.3e+03      50      93 ..     809     848 ..     806     855 .. 0.74
   5 !   40.3   0.0   3.4e-14   3.1e-10       1      93 [.     879     969 ..     879     983 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0022
                                    EEEEEEEEECEEEEEE-SCSSSSSSEEEEEEEEEESCHTTSEEEEEEEEECS CS
                             C2  23 dpyvkvsldgkqkakTrviknslnPvWnekftfevaeleeakLeveVfdndr 74 
                                       v++++dg + ++Tr  + +   v+ne+f++++++  ++++ +++ +++r
  gene107|gene107|rna107|rna107 353 RLAVEIDVDGRVGYQTRYGEGK-GIVYNEHFYMPIEN-VDSRIGLSLRSESR 402
                                    45799999999******54444.46************.99999998888666 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.4e-09
                                    -SCSSSSSSEEEEEEEEEESCHTTSEEEEEEEEECSSSTEEEEEEEEEEGHHHHTT CS
                             C2  39 rviknslnPvWnekftfevaeleeakLeveVfdndrlskddfiGkveiplstllsg 94 
                                    + i  + +P++ne+ftf +++ + +++ + V+++++   +++iG+v+ip+++++ +
  gene107|gene107|rna107|rna107 565 KRIFGTNSPIYNENFTFFCRDIQVDVVSICVMNDKT---NEVIGRVSIPVRDIHFN 617
                                    44666746************************9877...99**********95443 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.011
                                    HTTSEEEEEEEEECSSSTEEEEEEEEEEGHH CS
                             C2  60 leeakLeveVfdndrlskddfiGkveiplst 90 
                                    +++++L+++++ +   ++d fiG+ +i+ + 
  gene107|gene107|rna107|rna107 701 QSQDTLRFRLYKETI-NGDVFIGEDRISCRP 730
                                    5699*******9888.********9999876 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.26
                                    EEEEEEEESCHTTSEEEEEEEEECSSSTEEEEEEEEEEGHHHHT CS
                             C2  50 nekftfevaeleeakLeveVfdndrlskddfiGkveiplstlls 93 
                                    n +ftf ++   ++++   V++ d+ + +  +G++ ip + l++
  gene107|gene107|rna107|rna107 809 NDTFTF-IS--GSEEIYAVVKSGDQ-TVNLTLGQCIIPKRALKE 848
                                    666777.33..36788899999999.88889******9877554 PP

  == domain 5  score: 40.3 bits;  conditional E-value: 3.4e-14
                                    TEEEEEEEEEESSSSSSTTSSCEEEEEEEEECEEEEEE-SCSSSSSSEEEEEEEEEESCHTTSEEEEEEEEECSSSTEEE CS
                             C2   1 gklevtvieAknLpnkdkkgssdpyvkvsldgkqkakTrviknslnPvWnekftfevaeleeakLeveVfdndrlskddf 80 
                                    g+lev++++A  +    +++ +d+y+k+ +++++++ T+ ++++ +Pv+ne+f +e+++  +++  +++ d+++ +++++
  gene107|gene107|rna107|rna107 879 GYLEVYIKNASSIRSA-IQSPIDTYCKILVNETKVYTTKPVRKNNDPVFNESFIMEIDK-TKDVFGIQICDYNVSERNSL 956
                                    689**********888.8999******************6666638*************.**************9***** PP

                                    EEEEEEEGHHHHT CS
                             C2  81 iGkveiplstlls 93 
                                    +  +e++l +l +
  gene107|gene107|rna107|rna107 957 LCYTEFSLHNLSE 969
                                    *999999998554 PP

>> SMP_LBD  Synaptotagmin-like mitochondrial-lipid-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.5    0.0002       1.8       3      96 ..     124     215 ..     122     326 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0002
                                    B--HHHHHHHHHHHHHHHHHHH.HHHHHTHHHHHHTT-GGGTTEEEEEEE--SS--EEEEEEEE-TT--TTSEEEEEEEE CS
                        SMP_LBD   3 eraewlnktvkhmwpficqfie.klfretiepavrganthlstfsftkvdvgqqplringvkvytenvdkrqiildlqis 81 
                                    e  ewln  vk++w +   +i  +++++  +  ++ + ++l+ + +t+  +g +   i+g+      +d   + ++++++
  gene107|gene107|rna107|rna107 124 ETVEWLNYVVKKFWEVAEPVISaEIYQQVNNELLKVTPPFLNGLRLTEFTLGSRSPFIEGISYI--SMDGNTLAIEIEVA 201
                                    6788999999999988887776246666666777888888888999998888888888888654..35666666677777 PP

                                    EEEEEEEEEEECCCT CS
                        SMP_LBD  82 fvgnceidleikryf 96 
                                    fv   ei  ++  y+
  gene107|gene107|rna107|rna107 202 FVP-LEISRDVVNYL 215
                                    764.45555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1018 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.88u 0.37s 00:00:01.25 Elapsed: 00:00:00.58
# Mc/sec: 5294.58
//
Query:       gene1071|gene1071|rna1070|rna1070  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.8   0.1       0.23   11.0   0.1    1.3  1  DUF2674   Protein of unknown function (DUF2674)


Domain annotation for each model (and alignments):
>> DUF2674  Protein of unknown function (DUF2674)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.3e-05      0.23      27      52 ..      78     103 ..      75     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.3e-05
                            DUF2674  27 eGWvIvnlvPyedaFlcvLEKsieae 52 
                                        +GW+I+ l   +d F+ ++ K ie e
  gene1071|gene1071|rna1070|rna1070  78 NGWMISSLSGIDDVFIILISKRIEME 103
                                        7********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 839.81
//
Query:       gene1072|gene1072|rna1071|rna1071  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-17   64.0  10.9    1.2e-17   63.8  10.1    1.5  2  Ribosomal_L37e  Ribosomal protein L37e
      0.006   16.6   3.2      0.009   16.0   3.2    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.032   14.3   0.4      0.035   14.2   0.4    1.1  1  SelR            SelR domain
      0.081   12.9   0.0       0.12   12.4   0.0    1.2  1  PUA             PUA domain
      0.097   12.7   1.2       0.13   12.3   1.2    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.19   11.5   4.7       0.71    9.7   3.7    2.2  2  zinc_ribbon_2   zinc-ribbon domain
        0.2   11.5   4.1       0.43   10.5   4.1    1.5  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
          4    7.7   6.1         77    3.7   6.1    2.1  1  Fer4_2          4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8  10.1   5.3e-21   1.2e-17       1      46 [.       2      46 ..       2      53 .. 0.92
   2 ?   -2.5   0.0       2.6   5.9e+03      24      39 ..      62      77 ..      59      85 .. 0.62

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 5.3e-21
                     Ribosomal_L37e  1 tkGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGypsaklrk 46
                                       +kGt+sfGk++k+    +CrrCg++syh qk++C+scGyp++k+r+
  gene1072|gene1072|rna1071|rna1071  2 SKGTASFGKKNKR-NTEMCRRCGRQSYHKQKNSCSSCGYPNSKMRN 46
                                       69********666.7789***************************6 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.6
                     Ribosomal_L37e 24 krsyhvqkktCascGy 39
                                       +  y  ++ + a  G+
  gene1072|gene1072|rna1071|rna1071 62 RMRYMKRELRAARNGH 77
                                       5555555555555554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.2     4e-06     0.009       6      40 ..      10      43 ..       7      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4e-06
                                DZR  6 eelppdarfCseCgtklkavaaedrCpsCgekvdp 40
                                       ++++ + ++C +Cg +    ++++ C+sCg+++++
  gene1072|gene1072|rna1071|rna1071 10 KKNKRNTEMCRRCGRQSY-HKQKNSCSSCGYPNSK 43
                                       678888899999999974.5668999999998765 PP

>> SelR  SelR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   1.5e-05     0.035      25      86 ..       6      66 ..       2      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                       SSTSS--SSCEEEETTTS-EEEECCCCE-STTSSSEESS-STTTTEEEEEEECTTSEEEEEE CS
                               SelR 25 geyekekekGvyecavcgepLfssetkfdsgcGwpsFaeaikeeavkekkdtslgmertevv 86
                                        ++ k++++ +  c+ cg + ++ ++   s cG+p  +   ++ ++k ++ +++g+ r+  +
  gene1072|gene1072|rna1071|rna1071  6 ASFGKKNKRNTEMCRRCGRQSYHKQKNSCSSCGYPNSKMRNPG-SIKARRRRTVGTGRMRYM 66
                                       5667778888889**********************97766666.999999998887776544 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.2e-05      0.12      39      66 ..      50      77 ..      49      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                                       EEETTSCEEEEEEESS-HHHHHHHCTSE CS
                                PUA 39 ivdedgelvavGlanysseelakikggk 66
                                       i+++ +++v+ G+++y+  el+ +  g+
  gene1072|gene1072|rna1071|rna1071 50 IKARRRRTVGTGRMRYMKRELRAARNGH 77
                                       778889****************999777 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.2   5.6e-05      0.13      70      99 ..      16      44 ..       4      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                                       EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                               HypA 70 kvrCreCgkefeleekalrCpkCgsadvei 99
                                       + +Cr+Cg++  +++k  +C +Cg  + ++
  gene1072|gene1072|rna1071|rna1071 16 TEMCRRCGRQSYHKQK-NSCSSCGYPNSKM 44
                                       568*****99887754.68*****988766 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.011        25      15      20 ..      18      23 ..       9      25 .. 0.52
   2 ?    9.7   3.7   0.00032      0.71       2      22 ..      19      40 ..      18      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
                      zinc_ribbon_2 15 FCpyCG 20
                                        C +CG
  gene1072|gene1072|rna1071|rna1071 18 MCRRCG 23
                                       566665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00032
                      zinc_ribbon_2  2 CpnCGaelq.dnakFCpyCGtp 22
                                       C +CG++   +  + C+ CG+p
  gene1072|gene1072|rna1071|rna1071 19 CRRCGRQSYhKQKNSCSSCGYP 40
                                       9*******7588888******9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.1   0.00019      0.43      14      32 ..      19      38 ..      19      40 .. 0.98

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                            DUF35_N 14 CpdCGtvqfPPr.avCphCg 32
                                       C+ CG+  + ++ ++C+ Cg
  gene1072|gene1072|rna1071|rna1071 19 CRRCGRQSYHKQkNSCSSCG 38
                                       *******************8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   6.1     0.034        77       6      16 ..      15      34 ..      11      37 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.034
                             Fer4_2  6 dtdrCigCg.........aC 16
                                       +t++C +Cg         +C
  gene1072|gene1072|rna1071|rna1071 15 NTEMCRRCGrqsyhkqknSC 34
                                       99******955555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 560.31
//
Query:       gene1073|gene1073|rna1072|rna1072  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1507.26
//
Query:       gene1075|gene1075|rna1074|rna1074  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1459.93
//
Query:       gene1077|gene1077|rna1076|rna1076  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0072   16.3   0.1      0.017   15.1   0.1    1.5  1  DUF3557         Domain of unknown function (DUF3557)
  ------ inclusion threshold ------
      0.018   14.9   0.7       0.23   11.4   0.2    2.8  3  GIT_CC          GIT coiled-coil Rho guanine nucleotide exchan
       0.06   12.7  12.0      0.095   12.0  12.0    1.3  1  GAS             Growth-arrest specific micro-tubule binding
      0.062   12.6   9.9      0.042   13.2   7.8    1.6  2  DUF4763         Domain of unknown function (DUF4763)
      0.086   12.6   7.9        1.9    8.3   0.1    3.1  3  TRAF_BIRC3_bd   TNF receptor-associated factor BIRC3 binding 
       0.12   12.4  13.9       0.35   11.0  13.9    1.7  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.15   11.6   4.7        0.3   10.7   0.2    2.1  2  DUF1280         Protein of unknown function (DUF1280)
       0.25   11.4  18.9       0.47   10.5  14.1    2.2  3  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.38   10.2   6.9       0.21   11.1   4.5    1.7  2  FAP206          Domain of unknown function
       0.65    9.8  17.0        3.5    7.4   8.3    2.2  2  TACC_C          Transforming acidic coiled-coil-containing pr
        7.6    6.6  14.9        1.6    8.8   6.7    2.8  3  DHR10           Designed helical repeat protein 10 domain


Domain annotation for each model (and alignments):
>> DUF3557  Domain of unknown function (DUF3557)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     1e-05     0.017      65     137 ..      32     101 ..      17     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                            DUF3557  65 ldesslplkslevedtkvsnldhpivqnaklLilngeytnprnslllalknkrvhieadevsieelvelidnW 137
                                        ++ess pl+s++++++ ++  +    ++ +  ++  ++   +++ l  l ++rv ie  +   ee+ ++++n+
  gene1077|gene1077|rna1076|rna1076  32 VEESSVPLSSINMSEK-TQDCESIANHSDEETVIVKKSD--HEKSLFELTSSRVVIEDLKRREEEYSRMLKNY 101
                                        789*************.8888888888888888888865..459***********************999986 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.86   1.4e+03      42      59 ..      10      27 ..       8      30 .. 0.86
   2 ?   -0.1   0.0      0.51   8.4e+02      49      62 ..     124     137 ..      76     141 .. 0.64
   3 ?   11.4   0.2   0.00014      0.23      21      44 ..     145     168 ..     137     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.86
                             GIT_CC 42 lsdelrlLQskvqkLqae 59
                                       lsd ++ L s+v ++ ++
  gene1077|gene1077|rna1076|rna1076 10 LSDSIASLGSMVMSMSPN 27
                                       8999********999776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.51
                             GIT_CC  49 LQskvqkLqaeNaq 62 
                                        + +++++L++++  
  gene1077|gene1077|rna1076|rna1076 124 MNEEIERLKSNEYR 137
                                        44555555555544 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00014
                             GIT_CC  21 lKkalaaseakiqqLlkvNtslsd 44 
                                        lK+ l ase ki+ L+++N++  +
  gene1077|gene1077|rna1076|rna1076 145 LKRDLFASEDKIESLQRANNERME 168
                                        9******************98655 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  12.0   5.8e-05     0.095      35     170 ..      84     214 ..      67     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-05
                                GAS  35 ieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                        ie+lk++ee+ ++ l+++ +    l+  L++ e+e++ L+  + n e   ++lk+ + rlk+  + lk+    +e 
  gene1077|gene1077|rna1076|rna1076  84 IEDLKRREEEYSRMLKNYDA---TLTYVLERNEKEKALLEGVVMNEEI--ERLKSNEYRLKSYIQALKRDLFASED 154
                                        77788888888777777765...5788888888888888887776655..78899999999999999999999999 PP

                                GAS 111 leqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevla 170
                                        + + ++++ +er e+ +k+ + i+ + ++ + k  +L kkl++l+++  ++  ++ e+++
  gene1077|gene1077|rna1076|rna1076 155 KIESLQRANNERMEFLAKQVEEIRGMYEEEKGKVSCLSKKLSELENAFGARCNEMVELVE 214
                                        9999999999***********************************999988888888776 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   7.8   2.5e-05     0.042      16     146 ..      47     172 ..      21     180 .. 0.77
   2 ?    0.4   0.1       0.2   3.2e+02     127     155 ..     171     199 ..     163     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                            DUF4763  16 klsqvsqseqldveeeisseselpaeqe.eeeeeldLdeiydelekiKqrvlelrskLalnvpecPeidecvdedl 90 
                                        k +++      +   + s+e++   +++  e++ ++L++    +e +K+r +e+ + L+   +      e  ++++
  gene1077|gene1077|rna1076|rna1076  47 KTQDC------ESIANHSDEETVIVKKSdHEKSLFELTSSRVVIEDLKRREEEYSRMLKNYDATLTYVLERNEKEK 116
                                        44444......3445666666666677779*****************************66444555566666666 PP

                            DUF4763  91 elelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrk 146
                                         l +   ++ ei  L+ n+ +L+  ++ l++ l as+++++ l++   + +++l+k
  gene1077|gene1077|rna1076|rna1076 117 ALLEGVVMNEEIERLKSNEYRLKSYIQALKRDLFASEDKIESLQRANNERMEFLAK 172
                                        6666677*********************************9999887777777665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.2
                            DUF4763 127 rkslkelreslcqekkrlrklqkrlneld 155
                                         k+++e+r ++ +ek  +  l+k+l el+
  gene1077|gene1077|rna1076|rna1076 171 AKQVEEIRGMYEEEKGKVSCLSKKLSELE 199
                                        58899999999999999999999999987 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.6   5.9e+03      29      42 ..      79      92 ..      76      98 .. 0.64
   2 ?    7.2   1.6    0.0026       4.3      19      53 ..     122     161 ..     105     166 .. 0.73
   3 ?    8.3   0.1    0.0012       1.9      30      62 ..     170     202 ..     163     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                      TRAF_BIRC3_bd 29 rssttieaverqrr 42
                                       +s + ie+++r ++
  gene1077|gene1077|rna1076|rna1076 79 SSRVVIEDLKRREE 92
                                       56667777777654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0026
                      TRAF_BIRC3_bd  19 IVsVLnrEversstt.......ieaverqrrldqekieaLek 53 
                                        +  V+n E+er +++       i+a++r   + ++kie+L++
  gene1077|gene1077|rna1076|rna1076 122 V--VMNEEIERLKSNeyrlksyIQALKRDLFASEDKIESLQR 161
                                        4..689999987653222223399999999999999999975 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0012
                      TRAF_BIRC3_bd  30 ssttieaverqrrldqekieaLekKvrqLerti 62 
                                         + ++e+++   ++++ k+  L+kK+ +Le  +
  gene1077|gene1077|rna1076|rna1076 170 LAKQVEEIRGMYEEEKGKVSCLSKKLSELENAF 202
                                        577999999999*****************9776 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0  13.9   0.00021      0.35      71     182 ..      71     198 ..       9     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                            UPF0242  71 eekeaklteld...eglktkee..............aleelqeeeeeLkeeldakeeelerlkeenqqLqekleai 129
                                        e+    lt+ +   e+lk  ee               + e++e+e+ L e +  ++ee+erlk ++  L++  +a 
  gene1077|gene1077|rna1076|rna1076  71 EKSLFELTSSRvviEDLKRREEeysrmlknydatltYVLERNEKEKALLEGV-VMNEEIERLKSNEYRLKSYIQAL 145
                                        3333333333355544444444455555555555556777777777776655.79********************* PP

                            UPF0242 130 aedfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDl 182
                                        ++d  ++  ++e+  +  +e+++ +++++ee r + e+ + +++ L  k + l
  gene1077|gene1077|rna1076|rna1076 146 KRDLFASEDKIESLQRANNERMEFLAKQVEEIRGMYEEEKGKVSCLSKKLSEL 198
                                        **************9***************************99999998876 PP

>> DUF1280  Protein of unknown function (DUF1280)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.9     0.056        91      56      98 ..      51      93 ..      36     137 .. 0.72
   2 ?   10.7   0.2   0.00018       0.3      74     142 ..     141     209 ..     132     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.056
                            DUF1280 56 lkvklkLsdsqlkelKkflkeklgfdvfpsrkkikelekkvss 98
                                       + + ++ sd++   +Kk  +ek  f++ +sr  i++l+++ + 
  gene1077|gene1077|rna1076|rna1076 51 CESIANHSDEETVIVKKSDHEKSLFELTSSRVVIEDLKRREEE 93
                                       5666778888888999999999999999999999999887643 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                            DUF1280  74 lkeklgfdvfpsrkkikelekkvsskelYeisvekvekktksgrevkkkvvvvqlkdvekllsrRleeL 142
                                        + + l  d+f+s +ki++l++  + + ++  ++++  + + ++++ k+++   +l ++e+    R +e+
  gene1077|gene1077|rna1076|rna1076 141 YIQALKRDLFASEDKIESLQRANNERMEFLAKQVEEIRGMYEEEKGKVSCLSKKLSELENAFGARCNEM 209
                                        4567889*******************************99999999***99999999999999998887 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   4.4      0.19   3.2e+02      38      78 ..      68     108 ..      10     120 .. 0.59
   2 ?    2.5   6.6     0.084   1.4e+02      37     110 ..      67     142 ..      56     143 .. 0.72
   3 ?   10.5  14.1   0.00029      0.47      40     139 ..     105     199 ..      87     200 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                     CENP-F_leu_zip  38 enqekvileaEtskaevetlkeeieelaeelreleldLval 78 
                                        ++ ek   e  +s+  +e lk   ee ++ l++  + L+ +
  gene1077|gene1077|rna1076|rna1076  68 SDHEKSLFELTSSRVVIEDLKRREEEYSRMLKNYDATLTYV 108
                                        23333344444444444444444444444444444444333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.084
                     CENP-F_leu_zip  37 eenqekvileaEtskaevetlkeeieelaeelreleldLval..rsekeeLekelqkkqervseLeslnsslenll 110
                                        +++ ek   e  +s+  +e lk   ee ++ l++  + L+ +  r+eke+   e   ++e+++ L+s +  l++ +
  gene1077|gene1077|rna1076|rna1076  67 KSDHEKSLFELTSSRVVIEDLKRREEEYSRMLKNYDATLTYVleRNEKEKALLEGVVMNEEIERLKSNEYRLKSYI 142
                                        4567777888888888888888888888888888888887663356666666666678888888887777766655 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00029
                     CENP-F_leu_zip  40 qekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEq 115
                                        ++ v    E++ka +e+       ++ee ++l+++   l+s  + L+++l  + +++++L+++n +  ++l ++ +
  gene1077|gene1077|rna1076|rna1076 105 LTYVLERNEKEKALLEG-----VVMNEEIERLKSNEYRLKSYIQALKRDLFASEDKIESLQRANNERMEFLAKQVE 175
                                        44555555555555555.....34666677777777778888889999**************************** PP

                     CENP-F_leu_zip 116 ekvqmkeeskaaveeLqtqlkeln 139
                                        e + m+ee k +v+ L++ l el+
  gene1077|gene1077|rna1076|rna1076 176 EIRGMYEEEKGKVSCLSKKLSELE 199
                                        ********************9986 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.74   1.2e+03     130     157 ..       9      57 ..       3      86 .. 0.44
   2 ?   11.1   4.5   0.00013      0.21      10      97 ..      84     175 ..      78     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.74
                             FAP206 130 vlsnllesLqqfl.....................asqeklfeeeelesl 157
                                        +ls  ++sL +++                     ++ ek+ + e + ++
  gene1077|gene1077|rna1076|rna1076   9 YLSDSIASLGSMVmsmspnsrapveessvplssiNMSEKTQDCESIANH 57 
                                        5555666666666333332233333332222222222222222222222 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                             FAP206  10 reaiekeleeaqelasrytallekl....veeseaevaeeqlerlkqalinvrqyeaylrilledveksaeeveel 81 
                                         e+++   ee+ ++ ++y a+l ++    ++e++  +     e ++    n   +++y+++l++d+  s+ ++e+l
  gene1077|gene1077|rna1076|rna1076  84 IEDLKRREEEYSRMLKNYDATLTYVlernEKEKALLEGVVMNEEIERLKSNEYRLKSYIQALKRDLFASEDKIESL 159
                                        5677788899999999999999999766433333333334455566666788899********************* PP

                             FAP206  82 lkrfeaeleklketvk 97 
                                        +   ++++e l + v+
  gene1077|gene1077|rna1076|rna1076 160 QRANNERMEFLAKQVE 175
                                        *********9998886 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.2    0.0045       7.4      75     129 ..      58     108 ..      39     121 .. 0.62
   2 ?    7.4   8.3    0.0021       3.5     101     171 ..     124     194 ..     108     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0045
                             TACC_C  75 eekeqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkke 129
                                        +++e ++ + +++eks+ +l      ++ v+e++k+ ee + +  ++y a+++  
  gene1077|gene1077|rna1076|rna1076  58 SDEETVIVKKSDHEKSLFELT----SSRVVIEDLKRREEEYSRMLKNYDATLTYV 108
                                        555666666667777777754....356677777777777777777777766544 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                             TACC_C 101 qkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeekLekAneeiaqvrskakaetaalqasLrk 171
                                        + e +e +k+ne +lk+ ++ ++  +   e + ++L+   +e++e   ++++++r  +++e  ++    +k
  gene1077|gene1077|rna1076|rna1076 124 MNEEIERLKSNEYRLKSYIQALKRDLFASEDKIESLQRANNERMEFLAKQVEEIRGMYEEEKGKVSCLSKK 194
                                        6788********************************************************99998776555 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.6      0.15   2.5e+02      66     104 ..      77     115 ..      44     121 .. 0.74
   2 ?    8.8   6.7   0.00096       1.6      62     116 ..     124     178 ..     108     179 .. 0.88
   3 ?    0.5   0.2      0.38   6.2e+02      44      71 ..     173     200 ..     170     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.15
                              DHR10  66 leekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                        l++ +   ++l+r+ee   r l+n    l+ + e+ e++
  gene1077|gene1077|rna1076|rna1076  77 LTSSRVVIEDLKRREEEYSRMLKNYDATLTYVLERNEKE 115
                                        555556678999999999999999888887666665555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00096
                              DHR10  62 lrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleelr 116
                                         ++++e ++ +   l++ ++ l+r l   e+k+e l++  +e++e   +++ee+r
  gene1077|gene1077|rna1076|rna1076 124 MNEEIERLKSNEYRLKSYIQALKRDLFASEDKIESLQRANNERMEFLAKQVEEIR 178
                                        5799*********************************************999987 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.38
                              DHR10  44 eieaelakleeakkklkelrdaleekei 71 
                                        ++e+    +ee+k k++ l+++l+e+e+
  gene1077|gene1077|rna1076|rna1076 173 QVEEIRGMYEEEKGKVSCLSKKLSELEN 200
                                        5555556666777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1391  (0.0775838); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1491.87
//
Query:       gene1079|gene1079|rna1078|rna1078  [L=1142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-19   69.0   3.5    5.2e-17   61.9   0.0    3.6  2  E1-E2_ATPase   E1-E2 ATPase
    5.6e-11   43.1   2.4     0.0031   17.8   0.0    3.6  4  Hydrolase      haloacid dehalogenase-like hydrolase
    3.6e-08   33.6   0.3    1.8e-07   31.3   0.0    2.3  2  P5-ATPase      P5-type ATPase cation transporter
    0.00022   21.2   0.0    0.00062   19.8   0.0    1.7  1  Cation_ATPase  Cation transport ATPase (P-type)
  ------ inclusion threshold ------
      0.057   13.4   1.2       0.19   11.7   1.2    1.9  1  LRR_5          BspA type Leucine rich repeat region (6 copies
       0.21   11.3   4.4        1.2    8.9   0.1    3.0  3  Hydrolase_3    haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   1.8e-20   5.2e-17       4     177 ..     231     447 ..     228     451 .. 0.87
   2 ?    0.4   1.5      0.14   4.1e+02     110     172 ..    1055    1116 ..    1040    1124 .. 0.61

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.8e-20
                                        --EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-............... CS
                       E1-E2_ATPase   4 pptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvek............... 64 
                                        +++++++r+g+ +++d++e+ pG i  +++ +  p+D+ ++ g a  +e +LTGE++p++k               
  gene1079|gene1079|rna1078|rna1078 231 KRMVRILRGGRFVKVDSREIYPGNIMYIEPCKEFPCDALVIRGDAITNECLLTGEAVPIYKnadqpstvysgtdvl 306
                                        6789999******************************************************998888888888888 PP

                                        ............................G-TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHH CS
                       E1-E2_ATPase  65 ............................ekgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplq 112
                                                                    ++++ + +++ + +  a++ V++tg +t  g+i + + ++k+   ++ 
  gene1079|gene1079|rna1078|rna1078 307 ksintvptftnprnenlcrvksltskskQRTTGMVGSMHIPENFAIGMVLRTGFQTARGQILKNMVNSKPVHNRFI 382
                                        8888888888888888888888888775555555555566669999****************************** PP

                                        HHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHH CS
                       E1-E2_ATPase 113 kkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLplavplalalgarr 177
                                        k+++ ++  ++ +++++++ ++ ++ ++g ++++ l+  l+l+     +aLp+ + l   l  ++
  gene1079|gene1079|rna1078|rna1078 383 KEAEAIIFGIAGIGMIVSVGMAYVFKMMGFDARTNLVYNLDLFFTLANPALPTYLRLGAQLCYKK 447
                                        *******************************9999999999999999889988777666555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                                         HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.....HHHHHHHHHHHHHS-TTHHHHHHHHHH CS
                       E1-E2_ATPase  110 plqkkldklgkvlvpvvlliallvflialllgksla.....eallralallvaaiPcaLplavplala 172 
                                         ++  k+  +++ l+ ++lli++++f  +             + ++r+ ++ v+ + + + l+++++++
  gene1079|gene1079|rna1078|rna1078 1055 NVLFKAFIFFALLTSIALLIVVYIFPEWT------SlwlkeYKFVRTSGFEVGLVFISMFLIATVVFI 1116
                                         33444444555555555555555555553......333445677777777777777777777776665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.1    0.0011       3.2       1      15 [.     467     482 ..     467     514 .. 0.79
   2 ?   -1.4   0.0      0.81   2.4e+03     170     187 ..     652     671 ..     621     684 .. 0.71
   3 !   13.5   0.0   2.2e-05     0.066     103     156 ..     701     758 ..     637     777 .. 0.78
   4 !   17.8   0.0     1e-06    0.0031     166     210 .]     832     880 ..     804     880 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                        SSEEEEESBTTTB.CH CS
                                        xxxxxxxxxxxxx.xx RF
                          Hydrolase   1 iktvvfDkdGTLt.tg 15 
                                        ++t vfDk+GTLt +g
  gene1079|gene1079|rna1078|rna1078 467 VDTAVFDKTGTLTcDG 482
                                        689**********544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.81
                                        S..STTTSHHHHHHHHHHHT CS
                                        x..xxxxxxxxxxxxxxxxx RF
                          Hydrolase 170 t..vakpspegkvaaireLq 187
                                        +  + k spe  ++++re+ 
  gene1079|gene1079|rna1078|rna1078 652 KyvFTKGSPESIQQILRECP 671
                                        24589999999999999994 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 2.2e-05
                                        H......TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                        x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 103 l......qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                        +      + + la++ ++++  +k   + ++++L+ a+i+ +++tgdn  ta ++ +++ 
  gene1079|gene1079|rna1078|rna1078 701 DrivdehEMEFLALIVFSNK--LKANSKRTIEELNGANIRNIMCTGDNILTAISVGKECK 758
                                        044444477999******99..******************************99998887 PP

  == domain 4  score: 17.8 bits;  conditional E-value: 1e-06
                                        HHCES....STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                        xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 166 sdiet....vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        + i +    +a  +p +k+a+i+ L++ ++ +++ GDg+nD+ al  A+
  gene1079|gene1079|rna1078|rna1078 832 QFILEkgaiFARFNPGQKKALIENLRAIGKITMFCGDGANDSGALSSAD 880
                                        3344446789999*************55555**************9997 PP

>> P5-ATPase  P5-type ATPase cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   5.9e-11   1.8e-07      11      74 ..      17      80 ..      12     105 .. 0.87
   2 ?   -2.0   0.3       1.2   3.5e+03      16      44 ..    1057    1085 ..    1047    1091 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.9e-11
                          P5-ATPase 11 rtsrwrlalyilgciltlGlllLlfrWlPewrvkltgkpcpLkeadvvliedefgelsvkkvrk 74
                                       r++r+ + +y ++c+l+lG +++++r lP+++  l  +pc+L+ead+ +i+++ g+    +v  
  gene1079|gene1079|rna1078|rna1078 17 RKRRISTRFYNALCVLSLGGVYMVCRYLPSVKHFLLSSPCSLSEADCAIITSQNGKREFINVLF 80
                                       567888999******************************************9998877777655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                          P5-ATPase   16 rlalyilgciltlGlllLlfrWlPewrvk 44  
                                          + ++i++ +lt   ll++++ +Pew   
  gene1079|gene1079|rna1078|rna1078 1057 LFKAFIFFALLTSIALLIVVYIFPEWTSL 1085
                                         45567888899999999999*9***9755 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.1e-07   0.00062      47      85 ..     628     664 ..     587     671 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.1e-07
                      Cation_ATPase  47 kkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiil 85 
                                         +v++++F+s+ +rmsvv+     ++  +++KG+pe+i 
  gene1079|gene1079|rna1078|rna1078 628 MIVKTYEFDSNIRRMSVVVDV--GSRKYVFTKGSPESIQ 664
                                        589*****************6..599999*******984 PP

>> LRR_5  BspA type Leucine rich repeat region (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   6.2e-05      0.19      43      87 ..     145     187 ..     127     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                              LRR_5  43 sslteigsyaFsncssltsitipssltsigeyaFsncsslkeitl 87 
                                        ++ ++i++++F++  ++t++ ips  + i +++Fs ++ l+++ +
  gene1079|gene1079|rna1078|rna1078 145 ENAESIQRNIFYGK-NITNLPIPSIPEIILKNVFS-ITFLSNMIC 187
                                        57889999999999.99999999999999999999.888888765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3      0.38   1.1e+03      96     188 ..     597     698 ..     553     700 .. 0.61
   2 ?    2.4   0.0     0.038   1.1e+02      14      55 ..     719     760 ..     714     774 .. 0.86
   3 ?    8.9   0.1   0.00039       1.2     194     236 ..     851     893 ..     848     899 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.38
                                        CEEEEEESSEEEESTT........THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEE.EES-HHHHHHHHHHHHH CS
                        Hydrolase_3  96 veillytedkvyvlnk.......eksekkkkeeektkkkkeeidseeeledeeiakil.ilkdkekldelekelks 163
                                         + ++ + d+v ++n+       ++++ ++ ++ kt++++ +i+  +   d    k + +  ++e+++++  e+++
  gene1079|gene1079|rna1078|rna1078 597 TSPVILNIDGVHGHNNlnegykdDQDDVINAMIVKTYEFDSNIRRMSVVVDVGSRKYVfTKGSPESIQQILRECPK 672
                                        4444455555555555555555455555555555566666666666666666666655667777778888888777 PP

                                        HCTTTEEEEEESTT.EEEEEETT-SH CS
                        Hydrolase_3 164 klnklltitssskg.yleimpkgvsK 188
                                         ++++++++s +++ ++ +  k++sK
  gene1079|gene1079|rna1078|rna1078 673 GYEEKAKVYSLGGYrVISLSYKEISK 698
                                        77777766666655234466666666 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.038
                                        S---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCC CS
                        Hydrolase_3  14 kkisektkeaikklkekgikvviATGRslravlpvleelgld 55 
                                        +k++ ++k++i++l  ++i  + +TG ++ ++++v +e ++ 
  gene1079|gene1079|rna1078|rna1078 719 NKLKANSKRTIEELNGANIRNIMCTGDNILTAISVGKECKIV 760
                                        5678899************************99999998865 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00039
                                        HHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHH CS
                        Hydrolase_3 194 klakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevk 236
                                        +l+++l+   + ++  GDg ND   L+ a++g A+++ + ++ 
  gene1079|gene1079|rna1078|rna1078 851 ALIENLRAIGKITMFCGDGANDSGALSSADVGLALAQNEASLA 893
                                        678888888899**********************998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.85u 0.31s 00:00:01.15 Elapsed: 00:00:00.49
# Mc/sec: 6974.70
//
Query:       gene1080|gene1080|rna1079|rna1079  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 503.51
//
Query:       gene108|gene108|rna108|rna108  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-05   22.6   1.3     0.0034   17.2   0.0    3.1  4  EF-hand_6      EF-hand domain
    0.00028   21.3   1.4     0.0029   18.0   0.8    2.4  2  EF-hand_7      EF-hand domain pair
  ------ inclusion threshold ------
      0.014   14.9   0.2      0.094   12.3   0.0    2.5  3  EF-hand_1      EF hand
      0.085   13.2   0.0         13    6.2   0.0    3.0  3  Nif11          Nif11 domain
       0.11   13.1   0.0        2.5    8.8   0.0    2.5  3  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         1   3.6e+03      13      26 ..      16      29 ..       9      31 .. 0.69
   2 ?    2.6   0.0     0.045   1.6e+02      15      27 ..      50      62 ..      49      67 .. 0.87
   3 !   17.2   0.0   9.5e-07    0.0034       4      31 .]      73      99 ..      71      99 .. 0.93
   4 ?   -2.4   0.0       1.8   6.5e+03      18      26 ..     120     128 ..     115     130 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                      EF-hand_6 13 gdGkidaeElrkal 26
                                   + G+ + e lr+++
  gene108|gene108|rna108|rna108 16 NGGEMTLEALRQFI 29
                                   55777877777765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.045
                      EF-hand_6 15 GkidaeElrkalr 27
                                   ++++++++ ++l 
  gene108|gene108|rna108|rna108 50 NTVTRDDFNAVLD 62
                                   589*******997 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 9.5e-07
                      EF-hand_6  4 eaFklfDkdgdGkidaeElrkalrkalg 31
                                   ++F+ +Dk   G+id++++  +l+ ++g
  gene108|gene108|rna108|rna108 73 DIFNSWDKGQKGYIDKSDVETILK-SYG 99
                                   79*********************9.765 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.8
                      EF-hand_6  18 daeElrkal 26 
                                     ++++ +++
  gene108|gene108|rna108|rna108 120 KFDDFNRLY 128
                                    456666655 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.08   2.9e+02      27      53 ..      24      64 ..      16      74 .. 0.57
   2 !   18.0   0.8   8.2e-07    0.0029       6      71 .]      73     129 ..      68     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.08
                      EF-hand_7 27 llrkifqga..............gegsklsdeelellfkef 53
                                   +lr++++                + g+ ++++   ++++ +
  gene108|gene108|rna108|rna108 24 ALRQFIDIVflgvnpqqvsqltqSLGNTVTRDDFNAVLDAL 64
                                   45555444444556666666666666666666666666555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 8.2e-07
                      EF-hand_7   6 eaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisfdEFlklyr 71 
                                    ++F++ D+ + gy+dk++++ +l+      + g ++ +  +++++      kd ++ fd+F +ly+
  gene108|gene108|rna108|rna108  73 DIFNSWDKGQKGYIDKSDVETILK------SYGLSFKESYVDTMV---GIFKDKRMKFDDFNRLYK 129
                                    68******************8888......999998885555555...558999*******99986 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.54   1.9e+03      16      27 ..      51      62 ..      50      64 .. 0.78
   2 ?   12.3   0.0   2.6e-05     0.094       4      28 ..      73      97 ..      70      98 .. 0.92
   3 ?   -2.4   0.1       1.3   4.8e+03      17      25 ..     119     127 ..     115     130 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.54
                                   EEEHHHHHHHHH CS
                      EF-hand_1 16 kIdfeEfkellk 27
                                   ++++++f ++l 
  gene108|gene108|rna108|rna108 51 TVTRDDFNAVLD 62
                                   689999988875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.6e-05
                                   HHHHHHTTTSSSEEEHHHHHHHHHH CS
                      EF-hand_1  4 eiFrefDkDgdGkIdfeEfkellkk 28
                                   +iF+  Dk + G+Id+++  ++lk+
  gene108|gene108|rna108|rna108 73 DIFNSWDKGQKGYIDKSDVETILKS 97
                                   89******************99996 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.3
                                    EEHHHHHHH CS
                      EF-hand_1  17 IdfeEfkel 25 
                                    + f++f +l
  gene108|gene108|rna108|rna108 119 MKFDDFNRL 127
                                    557787766 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.07   2.5e+02       1      11 [.      20      30 ..      20      32 .. 0.91
   2 ?    6.2   0.0    0.0036        13      28      48 .]      37      57 ..      33      57 .. 0.93
   3 ?    1.0   0.0      0.15   5.5e+02      28      45 ..      87     104 ..      83     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.07
                          Nif11  1 MSeeqlkaFle 11
                                   M++e l++F++
  gene108|gene108|rna108|rna108 20 MTLEALRQFID 30
                                   99*******97 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0036
                          Nif11 28 dheevvalAkeaGyefteeel 48
                                   ++++v +l +++G ++t++++
  gene108|gene108|rna108|rna108 37 NPQQVSQLTQSLGNTVTRDDF 57
                                   89****************996 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                          Nif11  28 dheevvalAkeaGyefte 45 
                                    d+ +v  + k++G +f e
  gene108|gene108|rna108|rna108  87 DKSDVETILKSYGLSFKE 104
                                    6789999*******9975 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.27   9.6e+02      28      45 ..       3      20 ..       1      27 [. 0.81
   2 ?   -0.6   0.0      0.57   2.1e+03       3      30 ..      37      64 ..      35      69 .. 0.80
   3 ?    8.8   0.0   0.00069       2.5       2      35 ..      86     119 ..      85     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.27
                                   XXXXXXXXXXXXXXXXXX CS
                  Ribosomal_60s 28 kalegkdieellangaak 45
                                   + +e  +i +l++ng++ 
  gene108|gene108|rna108|rna108  3 EKIESDTIYDLITNGGEM 20
                                   5678999*******9876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.57
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Ribosomal_60s  3 taenikkvlkaagveveaarvkllvkal 30
                                   + +++ +++++ g +v     +++++al
  gene108|gene108|rna108|rna108 37 NPQQVSQLTQSLGNTVTRDDFNAVLDAL 64
                                   5678899999999999999998888887 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00069
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdi 35 
                                    +++++++++lk+ g   +++ v++ v  +++k +
  gene108|gene108|rna108|rna108  86 IDKSDVETILKSYGLSFKESYVDTMVGIFKDKRM 119
                                    8899*************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 976.11
//
Query:       gene1082|gene1082|rna1081|rna1081  [L=795]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4418  (0.246416); expected 358.6 (0.02)
Passed bias filter:                     1002  (0.0558871); expected 358.6 (0.02)
Passed Vit filter:                       757  (0.0422221); expected 17.9 (0.001)
Passed Fwd filter:                       169  (0.00942607); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 3.26u 0.46s 00:00:03.72 Elapsed: 00:00:00.85
# Mc/sec: 2815.25
//
Query:       gene1083|gene1083|rna1082|rna1082  [L=525]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1978  (0.110324); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 1.17u 0.45s 00:00:01.62 Elapsed: 00:00:00.65
# Mc/sec: 2426.74
//
Query:       gene1084|gene1084|rna1083|rna1083  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 772.03
//
Query:       gene1085|gene1085|rna1084|rna1084  [L=178]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   13.0   0.1       0.15   12.5   0.1    1.2  1  AAA_17    AAA domain


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.5e-06      0.15      15      77 ..      56     124 ..      53     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-06
                                        HHHHH....TEEEEEHHHHHHHHH.HTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEEEEE CS
                             AAA_17  15 lveky....gfthlsaGdllreea.krgglakardemrklpleekkelqkeaaekiaeea..kkkgvlvd 77 
                                        lv++     g+++ s+Gd+l +   +r g + +++++ +++ +e+  ++k++  +ia+e+  + ++v+ +
  gene1085|gene1085|rna1084|rna1084  56 LVDETgyfeGIKVNSFGDMLTQGRmTRTGFV-QKKDIGENEVNENLITMKLLLSEIAKEKntSIHNVINE 124
                                        55554446689**********7551555665.6777999******************9983333455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1282.88
//
Query:       gene1086|gene1086|rna1085|rna1085  [L=646]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-39  134.2   0.2    1.1e-38  133.1   0.0    1.6  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    2.4e-09   37.2   0.0    6.5e-09   35.8   0.0    1.8  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad
      3e-09   36.9   0.5    7.3e-09   35.7   0.5    1.7  1  HGTP_anticodon  Anticodon binding domain
     0.0071   15.5   0.0      0.012   14.8   0.0    1.2  1  Njmu-R1         Mjmu-R1-like protein family
  ------ inclusion threshold ------
      0.072   13.2   0.0       0.23   11.6   0.0    1.8  1  UPF0767         UPF0767 family


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       2.5   9.1e+03      79     105 ..     118     143 ..     112     168 .. 0.63
   2 !  133.1   0.0   2.9e-42   1.1e-38       8     178 ..     320     523 ..     313     524 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                                        HHHHHHHHHHHHHHHTT.SCEEEEEEG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b  79 slrdlikaisriferlglefraiielm 105
                                         ++++++++ ri ++   +f ++i++ 
  gene1086|gene1086|rna1085|rna1085 118 DYKKIEMEMTRIMKKNY-KFEKVIKSK 143
                                        56677777777777766.444444443 PP

  == domain 2  score: 133.1 bits;  conditional E-value: 2.9e-42
                                        SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslr 81 
                                        +++++LkP+n+++++ +++ +   s ++LPl++++++ ++R+E s  + GL+Rvr F+q+d+++f+++++++++++
  gene1086|gene1086|rna1085|rna1085 320 GDDFALKPMNCPGHCVMFKHQ-DHSfRDLPLRFADFGVLHRNELSgTLTGLTRVRRFQQDDAHIFCTKDQVKSEIK 394
                                        69*****************88.999888****************98888*************************** PP

                                        HHHHHHHHHHHHTT.SCEEEEEEGTTSC.................................BTTSEEEEEEEEETT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................xxxxxxxxxxxxxxx RF
                       tRNA-synt_2b  82 dlikaisriferlglefraiielmsaks.................................adykdkkefeavses 124
                                         +++  s ++  +g++f  ++   + ++                                 a+y++k ++++ +  
  gene1086|gene1086|rna1085|rna1085 395 GCLEFLSFVYGVFGFKFELVLST-RPEKylgsveewdraekalaeamdesgltfkinegdgAFYGPKIDITLHDA- 468
                                        ***************98755555.4444567788999999**********************************9. PP

                                        TSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxx RF
                       tRNA-synt_2b 125 ltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaileq 178
                                        l++ i+++tiq + ++l++r+++++ d++++ +++++i++a +g +eR++++ile+
  gene1086|gene1086|rna1085|rna1085 469 LDRRIQCATIQLD-FQLPQRFELKYRDSDGQCRTPVIIHRAiLGsIERMIAIILES 523
                                        *************.****************************9***********97 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   1.8e-12   6.5e-09       2      44 .]     169     217 ..     168     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.8e-12
                                        EEEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                           tRNA_SAD   2 rvvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                        +v++ G+ + ++C G+Hv++Tg ++a+k+l         + + k l+RIy
  gene1086|gene1086|rna1085|rna1085 169 SVYRNGE-FFDMCLGPHVRSTGVVKAVKVLknssayfLNDPSLKSLQRIY 217
                                        79****8.**********************88888888888899999998 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.5     2e-12   7.3e-09       1      74 [.     536     602 ..     536     626 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2e-12
                                        SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET CS
                     HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr 74 
                                        qv+++++++      +y++k+++ L    +rv++ d++++++k+ir a++ g+ ++ vvGe+e++ ++v++r  
  gene1086|gene1086|rna1085|rna1085 536 QVAIVNIGN-----FDYVEKIKSVLG--RFRVDVIDDSNTLNKRIRIAETSGYALVCVVGEREAKANEVNIRLS 602
                                        788999998.....79*********8..578*********************************99*****955 PP

>> Njmu-R1  Mjmu-R1-like protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.3e-06     0.012     278     335 ..     551     607 ..     538     615 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.3e-06
                            Njmu-R1 278 lrqilenfklkaiqdtnnlkrfirqaemshyalfkcylflkncGsgdillkivkveha 335
                                        ++ +l  f++  i d n l + ir ae+s yal  c++  ++  + ++ ++  kve +
  gene1086|gene1086|rna1085|rna1085 551 IKSVLGRFRVDVIDDSNTLNKRIRIAETSGYALV-CVVGEREAKANEVNIRLSKVEKS 607
                                        58899***************************96.99999999999999999999975 PP

>> UPF0767  UPF0767 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.3e-05      0.23      21      60 ..     401     441 ..     399     449 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.3e-05
                            UPF0767  21 aavvGviGynlEsllsdkytpyeksise.kReeRlleeeln 60 
                                        ++v Gv G++ E +ls ++++y  s++e  R+e+ l+e + 
  gene1086|gene1086|rna1085|rna1085 401 SFVYGVFGFKFELVLSTRPEKYLGSVEEwDRAEKALAEAMD 441
                                        6899***********************96799999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4052.48
//
Query:       gene1087|gene1087|rna1086|rna1086  [L=396]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00019   21.8   0.0    0.00049   20.5   0.0    1.7  1  Telomere_reg-2  Telomere length regulation protein


Domain annotation for each model (and alignments):
>> Telomere_reg-2  Telomere length regulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.8e-08   0.00049       1     101 [.     234     329 ..     234     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.8e-08
                     Telomere_reg-2   1 pvYlkdllelLrdkddyekieaaLksaeeLirrkad.eveenaveLataLltledkfdienfeelrlnalvallva 75 
                                        p++l++ ++++++++d+ek+ea+++  + L+r++++  ++  +++ +++L++       + +ee +  a+ +l+  
  gene1087|gene1087|rna1086|rna1086 234 PKFLQEAINAIEEERDAEKVEASFRWFPDLVRSATErTLKYKSKKALEVLMNY------DGYEEHKVDAISSLIQR 303
                                        89******************************888858888888888887654......899************** PP

                     Telomere_reg-2  76 tpekvaeylteeffsnqyslqqRidi 101
                                        + +  ++  ++ ff++++ l+++i +
  gene1087|gene1087|rna1086|rna1086 304 SHKFLIDDTIDDFFNGKLCLRHKIIL 329
                                        ********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2623.58
//
Query:       gene1088|gene1088|rna1087|rna1087  [L=946]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0065   16.5   0.4     0.0065   16.5   0.4    2.8  3  Rsbr_N    Rsbr N terminal
  ------ inclusion threshold ------
       0.22   11.9   1.2         40    4.6   1.1    3.3  2  FAM25     FAM25 family


Domain annotation for each model (and alignments):
>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.13   1.2e+03      25      56 ..     417     448 ..     403     462 .. 0.77
   2 ?   -2.7   0.2      0.67     6e+03      52      52 ..     529     529 ..     498     561 .. 0.50
   3 !   16.5   0.4   7.3e-07    0.0065       3      76 ..     713     787 ..     711     808 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.13
                                        S-.--HHHHHHHHHHHHHHHHH-SS.-SSTTH CS
                             Rsbr_N  25 lqtisdevyektskefvdlilssveegneele 56 
                                        ++  +++ y+   +e++  i+  ++++ + +e
  gene1088|gene1088|rna1087|rna1087 417 IKGSNNSYYDDYTRELIRSIFDMLKGSTTTSE 448
                                        5556889999************9997666554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.67
                                        S CS
                             Rsbr_N  52 n 52 
                                        +
  gene1088|gene1088|rna1087|rna1087 529 E 529
                                        1 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 7.3e-07
                                        HTHHHHHHHHHHHHHHHHTTSSS-.--HHHHHHHHHH.HHHHHHH-SS.-SSTTHHHHHHHHHHHHHTT--HHHH CS
                             Rsbr_N   3 enkdellkewlkelkelrkeeslqtisdevyektske.fvdlilssveegneeleekleefaerlvqlGwpLkyl 76 
                                        +n+de+  + ++  k++  +++++ti  +v    ++  ++  + s vee  + le+kl+ef++r+vq+G  L  l
  gene1088|gene1088|rna1087|rna1087 713 DNRDEIYSRMMDVEKDTGCKTITDTIRTTVIRDFNSSvHLSAVSSIVEERMKGLERKLNEFSDRVVQIGNRLLML 787
                                        57778887777777777777777777777777766551345555566788999****************988766 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.1    0.0045        40      37      53 ..     458     474 ..     453     477 .. 0.88
   2 ?    3.2   0.0     0.012   1.1e+02       7      29 ..     717     739 ..     711     742 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0045
                              FAM25  37 kvvKevtekvtntvtna 53 
                                         +vKe t +vt+t t a
  gene1088|gene1088|rna1087|rna1087 458 TIVKETTTTVTKTTTRA 474
                                        58***********9976 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.012
                              FAM25   7 evvkevveHaKeaGEKAiadalK 29 
                                        e+ + +++  K++G K i+d+++
  gene1088|gene1088|rna1087|rna1087 717 EIYSRMMDVEKDTGCKTITDTIR 739
                                        6667789999**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (946 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 5485.48
//
Query:       gene1089|gene1089|rna1088|rna1088  [L=407]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00087   19.4   0.6     0.0015   18.6   0.6    1.3  1  COG2             COG (conserved oligomeric Golgi) complex com
     0.0012   18.8   0.5      0.002   18.1   0.5    1.4  1  SPATA24          Spermatogenesis-associated protein 24
     0.0088   15.4   0.0      0.015   14.7   0.0    1.3  1  Lectin_leg-like  Legume-like lectin family
  ------ inclusion threshold ------
      0.014   13.6   0.7      0.018   13.2   0.7    1.1  1  EzrA             Septation ring formation regulator, EzrA
      0.025   14.2   0.1      0.042   13.5   0.1    1.3  1  ISPD_C           D-ribitol-5-phosphate cytidylyltransferase C
      0.074   12.6   0.7       0.11   12.1   0.7    1.2  1  TMCO5            TMCO5 family


Domain annotation for each model (and alignments):
>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   5.2e-07    0.0015      31      96 ..     307     374 ..     296     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.2e-07
                               COG2  31 lrrdLeaylkllekellelvnedyad..FvslSghLvglqeeleevesplaaarkkvesvreklsere 96 
                                        l+++L++++k +e+++ +  n+   +  F++lS+++ g++ +l+++++++a +   v+s+++  s+ +
  gene1089|gene1089|rna1088|rna1088 307 LSEQLKTHMKNIEDAITSAKNKGGSEmkFMNLSEKMNGIDIKLQRIQKSFADLEHVVNSLKNDYSRSS 374
                                        899*******************999999********************************99988766 PP

>> SPATA24  Spermatogenesis-associated protein 24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5   6.7e-07     0.002      79     147 ..     304     371 ..     269     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.7e-07
                            SPATA24  79 ievLskqlerekkafekalgsvkekaarEskkadqLkekCseveseierqeDilnakeneikeLkqrls 147
                                        + vLs+ql+   k+ e+a+ s k+k   E+k   +L ek + ++++++r + ++   e  +++Lk+  s
  gene1089|gene1089|rna1088|rna1088 304 VYVLSEQLKTHMKNIEDAITSAKNKGGSEMKF-MNLSEKMNGIDIKLQRIQKSFADLEHVVNSLKNDYS 371
                                        779**************************865.67*****************************99765 PP

>> Lectin_leg-like  Legume-like lectin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.9e-06     0.015      48     137 ..      69     149 ..      49     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.9e-06
                                        EEEEESS-BEESSEEEEEEEEEESS--SS-S-EEEEEEESSSSSCCSBTTB-SS-EEEEEEEE-S-TSCTTTSS-S CS
                    Lectin_leg-like  48 GslwtkspvaleswevevsFrvtgseselegdglaiwytsergkegpvFgskdkfdGlailldtydndngpdkknk 123
                                        G +    p   e+w  + +F         + +g+ +wyts+ +++g   g++d f+G+   l+     +g+    +
  gene1089|gene1089|rna1088|rna1088  69 GLVVFLAPNPYEEWSFSYTFTNAKL-RFPHIGGVYLWYTSDIQDQGVYRGGHDMFEGIMAGLEF----RGS----Q 135
                                        5555556667788988888876555.5568899*************999***********9995....544....7 PP

                                        SEEEEEEEESSC-- CS
                    Lectin_leg-like 124 ptisamlndgsley 137
                                        p i++ +ndg++++
  gene1089|gene1089|rna1088|rna1088 136 PEIVMAINDGKTSL 149
                                        9999*****99875 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   6.2e-06     0.018      60     136 ..     298     375 ..     271     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-06
                                        HHHHHHHHHHHHHHHHHTHHHHHT-GGGT--.S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTT CS
                               EzrA  60 ekfeewkkkwdeiktkklpeieellfeaeel.ldkykfkkakkklaeleeeldeveekikkileelkelteseekn 134
                                        ++f+++     e  ++++++ie+ ++ a++   +++kf+++ +k++ ++ +l++++++ +++ + ++ l++  +++
  gene1089|gene1089|rna1088|rna1088 298 SSFDKVVYVLSEQLKTHMKNIEDAITSAKNKgGSEMKFMNLSEKMNGIDIKLQRIQKSFADLEHVVNSLKNDYSRS 373
                                        56666666667777789***********98725789********************************99988877 PP

                                        HH CS
                               EzrA 135 re 136
                                        ++
  gene1089|gene1089|rna1088|rna1088 374 SN 375
                                        65 PP

>> ISPD_C  D-ribitol-5-phosphate cytidylyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.4e-05     0.042      14      91 ..     301     381 ..     291     395 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.4e-05
                             ISPD_C  14 eevghlLeevLkaelkkvkvt.stsllkagsdlqniileqcynficvnvk..esdfeetqklvklLeesnlsllyP 86 
                                         +v+ +L e Lk+++k+++   +++  k gs+++ + l++ +n i ++ +  + +f +++++v+ L++        
  gene1089|gene1089|rna1088|rna1088 301 DKVVYVLSEQLKTHMKNIEDAiTSAKNKGGSEMKFMNLSEKMNGIDIKLQriQKSFADLEHVVNSLKNDYSRSSNI 376
                                        68999***********998650555566789999999**********9961256799*********9865555544 PP

                             ISPD_C  87 vVvis 91 
                                        +V i+
  gene1089|gene1089|rna1088|rna1088 377 LVYII 381
                                        55554 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   3.5e-05      0.11      81     142 ..     309     371 ..     267     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                              TMCO5  81 eiLlkevveLqkkisrkeskqd.dleketlkqkleelkvklqkseescaeqekelakveedyq 142
                                        e L   + +++  i+ +++k   +++  +l++k++++ +klq+ ++s a+ e  ++++++dy 
  gene1089|gene1089|rna1088|rna1088 309 EQLKTHMKNIEDAITSAKNKGGsEMKFMNLSEKMNGIDIKLQRIQKSFADLEHVVNSLKNDYS 371
                                        66788888999999999987776677799*********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      735  (0.040995); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2371.34
//
Query:       gene1090|gene1090|rna1089|rna1089  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-69  232.2   0.0    8.2e-69  232.0   0.0    1.1  1  Dus       Dihydrouridine synthase (Dus)
     0.0016   17.7   0.0     0.0062   15.8   0.0    1.8  1  DHO_dh    Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
       0.12   12.1   0.0        5.9    6.6   0.0    2.3  2  SOR_SNZ   SOR/SNZ family


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.0   0.0   1.4e-72   8.2e-69       2     257 ..      15     276 ..      14     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 232.0 bits;  conditional E-value: 1.4e-72
                                        E---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---..HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHH CS
                                Dus   2 laPmagvtdlpfRelvrefgataLvvtemvtakaivre..ekvrirmlseeeeetplavQlggsdpallaeaAklv 75 
                                        +aPm+g ++ ++R+l++++ga+ + +t+mv+ + ++r   + vr + ++++ee++pl++Q++g++p+ ++eaA + 
  gene1090|gene1090|rna1089|rna1089  15 VAPMVGNSEEAWRRLSKRYGAN-MFYTQMVHCESFLRGprNPVRNQWYTTSEEDRPLIIQICGNSPEAMLEAALIM 89 
                                        89********************.*************962255666678999999********************** PP

                                        HHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT CS
                                Dus  76 adlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelakiveaaG 151
                                        +d  +d+Id+N+GCP+  + +gg+Ga L +++dl ++ivk++  +++iPv  kir++     e+++e+ +++e+aG
  gene1090|gene1090|rna1089|rna1089  90 QD-HCDAIDINFGCPQRVARKGGYGAYLQENWDLTEKIVKTLSTNLSIPVFCKIRVFES--IEKTVEYTRMIEKAG 162
                                        **.*****************************************************955..8999*********** PP

                                        -SEEEEESSECCCTT-C..G--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH CS
                                Dus 152 aqaltvHgRtraqnyeg..tadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae 225
                                        +  l+vHgRtr q+ ++   a w++Ik+vk++++ipv+ NG+I   +d+ ++le+t +dgvm+g+  l+nP +f  
  gene1090|gene1090|rna1089|rna1089 163 CSLLAVHGRTRDQKGKAmgFASWDHIKAVKESLTIPVLSNGNIMVHSDIWRCLEYTKCDGVMVGETHLYNPLIFTG 238
                                        ***************99999******************************************************97 PP

                                        .HHHHHHSC------HHHH......HHHHHHHHHHCHHT CS
                                Dus 226 .stavktgeaepapplaee......aeiveehlkkleee 257
                                         s+ + + ++++   ++ e      +  +++h+ kl+++
  gene1090|gene1090|rna1089|rna1089 239 eSKPCLE-IIREYLDICMEfpgsadVGHMKSHIFKLLYN 276
                                        5555554.5555444333336655555555555555555 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-06    0.0062      96     170 ..      67     143 ..      53     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-06
                                        CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTC...C..TSCCCGCHHHHHHHHHHHHHHHHSSEEE CS
                             DHO_dh  96 elginlskakktenavddyvevvrkigpfadilelNvSsPnt...p..glrdlqekeelkaillkvvkevskvpvl 166
                                        + + ++ + +++    +   e +  ++   d++ +N  +P     +  +++ lqe+ +l+++++k ++++ ++pv+
  gene1090|gene1090|rna1089|rna1089  67 DRPLIIQICGNS---PEAMLEAALIMQDHCDAIDINFGCPQRvarKggYGAYLQENWDLTEKIVKTLSTNLSIPVF 139
                                        556677777776...777888888999*************842223445789************************ PP

                                        EEE- CS
                             DHO_dh 167 vKla 170
                                         K+ 
  gene1090|gene1090|rna1089|rna1089 140 CKIR 143
                                        **96 PP

>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.009        54      60      84 ..     125     149 ..     120     154 .. 0.85
   2 ?    6.6   0.0   0.00099       5.9      22      79 ..     151     205 ..     147     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.009
                                        HHHHHHHHH-SS-EEEEEETT-HHH CS
                            SOR_SNZ  60 klikeikeavsipvmakvriGhfve 84 
                                        k++k + + +sipv  k+r+   +e
  gene1090|gene1090|rna1089|rna1089 125 KIVKTLSTNLSIPVFCKIRVFESIE 149
                                        7899999************987776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00099
                                        SHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                            SOR_SNZ  22 naeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                        ++e  ++ e+aG ++++a++  + d  ++g+    ++ + ik +ke+++ipv++   i
  gene1090|gene1090|rna1089|rna1089 151 TVEYTRMIEKAG-CSLLAVHGRTRD--QKGKAMGFASWDHIKAVKESLTIPVLSNGNI 205
                                        567788889998.566666655554..6788889999***************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2128.13
//
Query:       gene109|gene109|rna109|rna109  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.068   13.7   0.8       0.19   12.2   0.3    1.9  2  UCR_TM    Ubiquinol cytochrome reductase transmembrane region


Domain annotation for each model (and alignments):
>> UCR_TM  Ubiquinol cytochrome reductase transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.34   6.1e+03      35      49 ..       7      24 ..       3      32 .. 0.50
   2 ?   12.2   0.3   1.1e-05      0.19      17      48 ..     172     203 ..     169     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.34
                         UCR_TM 35 tylvlag...gavvgaya 49
                                     l +ag    +++g+y+
  gene109|gene109|rna109|rna109  7 YILAVAGvgiIRAGGLYI 24
                                   445555533345555555 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.1e-05
                         UCR_TM  17 vkDpskssretedeRkaftylvlaggavvgay 48 
                                    ++D sk++ ++++++k+   l+++g++v++a 
  gene109|gene109|rna109|rna109 172 TGDKSKNNTSSSKKKKGAKSLMAFGAVVTTAL 203
                                    89**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1292.53
//
Query:       gene1091|gene1091|rna1090|rna1090  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00057   20.1   0.5     0.0015   18.8   0.5    1.7  1  V-SNARE_C   Snare region anchored in the vesicle membrane C-t
     0.0042   17.1   1.9     0.0042   17.1   1.9    1.6  2  DHR10       Designed helical repeat protein 10 domain
  ------ inclusion threshold ------
      0.068   12.6   0.3      0.074   12.5   0.3    1.1  1  MSC         Man1-Src1p-C-terminal domain
       0.11   12.5   2.9       0.12   12.3   0.3    2.2  3  Sec20       Sec20
       0.14   10.4   1.0       0.16   10.3   1.0    1.0  1  Birna_RdRp  Birnavirus RNA dependent RNA polymerase (VP1)


Domain annotation for each model (and alignments):
>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5     4e-07    0.0015      12      65 ..     115     168 ..     110     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4e-07
                          V-SNARE_C  12 nShrivdetisiGaailedLhsQretLkrarsklhnvanrlgksnsiLrsikrR 65 
                                        +S+  +++++  ++  +e+ ++Q+  ++r+ ++++   +++g+s++++  i++R
  gene1091|gene1091|rna1090|rna1090 115 SSTKRINDVLMNAMDAFETVKRQNVYINRTSERIRASLSQIGLSKQLIDQIDKR 168
                                        788999*********************************************999 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.9   1.2e-06    0.0042      31     116 ..       2      90 ..       1      91 [. 0.90
   2 ?   -2.8   0.0       1.7   6.2e+03      97     100 ..     134     137 ..     117     155 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                              DHR10  31 vekdlrsciklleeieaelakleeakkklkelrdaleekeielrel...erkeerlqrqlenaeeklerlreqaee 103
                                        +ekd+ s+i+  + i +el+ +ee  +++ +l  ++++ ++ ++ l   e + erl +q +   + + rl +q+++
  gene1091|gene1091|rna1090|rna1090   2 AEKDVPSLIEEENAIRKELKVCEEDLENIGALAIRIQSFSRSVSNLdpsEPEAERLSKQADLFSKSILRLGNQRSK 77 
                                        69*******************************99999888888872225667*********************** PP

                              DHR10 104 kreaakarleelr 116
                                        kr ++++++++ +
  gene1091|gene1091|rna1090|rna1090  78 KRSEMREEMTKSK 90 
                                        *********9876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                              DHR10  97 lreq 100
                                        +++q
  gene1091|gene1091|rna1090|rna1090 134 VKRQ 137
                                        2222 PP

>> MSC  Man1-Src1p-C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   2.1e-05     0.074      93     239 ..      52     190 ..      17     194 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                                MSC  93 pdsekerkvkevakkalelLreknakvecgeskdde.ek..akksglseeeLkeslsekksksiskeefeelwkea 165
                                        p+ e+  k +++ +k++  L ++++k + + +++ + +k  ++k  ++++++ + +s+    s s++ +++++ +a
  gene1091|gene1091|rna1090|rna1090  52 PEAERLSKQADLFSKSILRLGNQRSKKRSEMREEMTkSKanTEKEYMENTNIPQPISDDDFFSSSTKRINDVLMNA 127
                                        5556666666667777777777777766666655553224566667777777777777666666777777777777 PP

                                MSC 166 lkeLkke..eeivvredseseseksskekkkllrstslaklslkcrlrrsvretlaryrllllglllllllilylr 239
                                        ++ +++   ++++++            ++++++r +sl++++l+++l  ++ + + + r+l++g ++ll+++++l 
  gene1091|gene1091|rna1090|rna1090 128 MDAFETVkrQNVYIN------------RTSERIR-ASLSQIGLSKQLIDQIDKRYLSDRVLFMGGIVLLVIMFFLL 190
                                        666654311444333............3345555.589***********************999988877776654 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.76   2.7e+03      29      29 ..      55      55 ..      18      88 .. 0.61
   2 ?    0.3   0.3      0.19   6.9e+02      14      39 ..      79     105 ..      64     140 .. 0.57
   3 ?   12.3   0.3   3.4e-05      0.12      26      83 ..     129     186 ..     113     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.76
                              Sec20 29 e 29
                                       e
  gene1091|gene1091|rna1090|rna1090 55 E 55
                                       2 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                              Sec20  14 sqllsqevqqSeenle.eldastksle 39 
                                        +  + +e+ +S+ n e e  ++t+  +
  gene1091|gene1091|rna1090|rna1090  79 RSEMREEMTKSKANTEkEYMENTNIPQ 105
                                        455666666666555413444444433 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.4e-05
                              Sec20  26 enleeldastkslekleeeykqvedvlsrskklvkklerrdktdkllvflalglflac 83 
                                         + e+++ +   +++++e      + +  sk+l+ ++++r ++d++l + ++ l++++
  gene1091|gene1091|rna1090|rna1090 129 DAFETVKRQNVYINRTSERIRASLSQIGLSKQLIDQIDKRYLSDRVLFMGGIVLLVIM 186
                                        45677888888999999*****************************999988887765 PP

>> Birna_RdRp  Birnavirus RNA dependent RNA polymerase (VP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.0   4.4e-05      0.16     674     792 ..      26     137 ..       5     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.4e-05
                                        TSTT--SSS--..-HHHHHHHH--SS---GGGS-B-SSS--HHHHHHHHHTTTTSS-SSHHHHHHHHHTTB-GGGH CS
                         Birna_RdRp 674 alegltideklevtseslaelnlpveskdpnvnkqvlrskglkevssalksGayrneksvaglvllaraksrvska 749
                                        +le++     l +  +s+ +   ++++ +p++++  +++  +    s l+ G+ r +k    +  ++++ks+ ++ 
  gene1091|gene1091|rna1090|rna1090  26 DLENI---GALAIRIQSFSRSVSNLDPSEPEAERLSKQADLFS--KSILRLGNQRSKKRSEMR--EEMTKSKANTE 94 
                                        34433...34666777777777778888888888777773333..356788988888876555..68899999999 PP

                                        H...HHHHHHHHHHHT-THHHHHHHHHHHHTTSGGG....B-- CS
                         Birna_RdRp 750 kkvldeaeklkpksesadwaerseeladllmkannlaskvaks 792
                                        k+ +++ +  +p s+++ ++  ++ ++d lm a + +  v + 
  gene1091|gene1091|rna1090|rna1090  95 KEYMENTNIPQPISDDDFFSSSTKRINDVLMNAMDAFETVKRQ 137
                                        9999999888998888779999999********9987666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1656  (0.0923643); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1328.50
//
Query:       gene1092|gene1092|rna1091|rna1091  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   51.2   0.6    3.1e-13   49.8   0.0    1.9  2  DCP2      Dcp2, box A domain
    1.5e-09   37.9   0.0    3.7e-09   36.7   0.0    1.6  2  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> DCP2  Dcp2, box A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   3.5e-17   3.1e-13       1      83 []       5      78 ..       5      78 .. 0.93
   2 ?   -1.7   0.1      0.43   3.9e+03       2      17 ..     149     164 ..     148     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.5e-17
                                       HHHHHHHHHHTTTS-HHHHTSHHHHHHHHHHHHHHHHHTHHHHTTTS----HHHHHHHHHCCSCCCHHCCCHCHHHHH CS
                               DCP2  1 eiLddlavrFilnlpeeeleslerlffqleeAhWfYeDfvreknpklpslklkeFaeklfekcpllkklkedvdeile 78
                                       +iLd +a+rF++ l ++e++ +erlff +eeAhWf +D+++ ++     l++ +F+++l+ ++ +    k +++e+ +
  gene1092|gene1092|rna1091|rna1091  5 DILDSIASRFLVGLGNQERNAAERLFFAVEEAHWFLMDNYKISD-----LSFADFSRELLGHVGI----KMNIEEAHK 73
                                       79**************************************9966.....99***********977....678888888 PP

                                       HHHHH CS
                               DCP2 79 efkeY 83
                                       +f +Y
  gene1092|gene1092|rna1091|rna1091 74 SFVRY 78
                                       88887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.43
                                        HHHHHHHHHTTTS-HH CS
                               DCP2   2 iLddlavrFilnlpee 17 
                                        i+d+++  F+ n+ ++
  gene1092|gene1092|rna1091|rna1091 149 IFDKITLYFVFNVKQS 164
                                        6677888888888765 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       0.7   6.3e+03     104     115 ..      33      44 ..      16      59 .. 0.57
   2 !   36.7   0.0   4.1e-13   3.7e-09       7     116 ..      86     187 ..      81     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.7
                                        EEEEEEEEHHHH CS
                              NUDIX 104 vsevrwvpleel 115
                                        v+e+ w+ ++  
  gene1092|gene1092|rna1091|rna1091  33 VEEAHWFLMDNY 44 
                                        555666666655 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 4.1e-13
                                        EEEEEETT.SEEEEEEESSSSTTTEESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEEEEEEEEEEEEEEEEEEEE CS
                              NUDIX   7 gvvllnek.gevLlvrrskkpfpgWelPgGkvepgEtpeeAArREleEEtGlea.ellellgrlhylapydgpygd 80 
                                        g++l ++   +vL v+++ k+++++++P+Gk  ++E+   +A+RE+ EEtG+++ + +  l          ++++ 
  gene1092|gene1092|rna1091|rna1091  86 GAILVDPSiSHVLAVKEK-KKTKNYSFPKGKKCMDEDGTSCAIREVYEETGYDVqNKICNLP--------ITIFD- 151
                                        66777777445*******.7777779**********999*************9977777776........22333. PP

                                        EEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHH CS
                              NUDIX  81 eheilyvfleevegelepndenevsevrwvpleell 116
                                        +  +++vf  +     e +  +e++e++w++  +l 
  gene1092|gene1092|rna1091|rna1091 152 KITLYFVFNVKQSFPFEAQTIKEIEEIKWLSTRKLS 187
                                        333334444555555555588999******999883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1558.78
//
Query:       gene1093|gene1093|rna1092|rna1092  [L=424]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-40  136.4   0.0    1.6e-39  135.3   0.0    1.6  1  AAA             ATPase family associated with various cellula
    1.3e-12   47.2   0.1    2.6e-12   46.3   0.1    1.5  1  AAA_lid_3       AAA+ lid domain
    3.5e-07   30.1   0.0    7.7e-07   29.0   0.0    1.6  1  Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
    2.2e-05   24.6   0.0    6.2e-05   23.2   0.0    1.7  1  AAA_2           AAA domain (Cdc48 subfamily)
    2.4e-05   24.6   0.4      0.013   15.8   0.4    2.5  1  AAA_22          AAA domain
    3.5e-05   23.1   0.0    5.6e-05   22.4   0.0    1.2  1  DUF815          Protein of unknown function (DUF815)
    0.00027   20.9   0.3     0.0022   18.0   0.2    2.6  2  AAA_5           AAA domain (dynein-related subfamily)
     0.0016   18.2   0.0     0.0035   17.1   0.0    1.5  1  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
     0.0025   18.2   0.2      0.015   15.7   0.2    2.0  2  AAA_16          AAA ATPase domain
     0.0058   16.8   0.0      0.012   15.8   0.0    1.5  1  AAA_33          AAA domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.025   14.4   0.0    1.6  1  AAA_3           ATPase family associated with various cellula
      0.019   14.7   0.0      0.034   13.9   0.0    1.4  1  IstB_IS21       IstB-like ATP binding protein
      0.019   14.1   0.1       0.76    8.9   0.0    2.4  2  NB-ARC          NB-ARC domain
      0.026   14.8   0.0      0.045   14.0   0.0    1.4  1  AAA_28          AAA domain
      0.029   14.9   0.0      0.066   13.8   0.0    1.7  1  AAA_18          AAA domain
      0.042   13.9   0.0       0.12   12.4   0.0    1.8  1  AAA_14          AAA domain
      0.074   12.7   0.1       0.22   11.2   0.0    1.9  2  Prot_ATP_OB_N   Proteasomal ATPase OB N-terminal domain
       0.15   11.4   0.1       0.31   10.4   0.1    1.4  1  Mg_chelatase    Magnesium chelatase, subunit ChlI
       0.17   11.6   0.1       0.48   10.1   0.1    1.7  1  AAA_30          AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   0.0   1.7e-42   1.6e-39       1     131 [.     206     338 ..     206     339 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 1.7e-42
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.. CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.. 74 
                                        v+lyG pGtGKTllakava++++++fl++ g+el+++y+ge++k +relf+ a  +a psi+fiDEida++++r  
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTSATFLRVVGTELIQEYLGEGPKLVRELFRVADMHA-PSIIFIDEIDAIGGRRyn 280
                                        79******************************************************9.****************98 PP

                                        .TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                                AAA  75 .sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                         s++ ++e +r++ +Ll++ldg++++ +++ vi+atn+++ ldpal+r gR+drkie++
  gene1093|gene1093|rna1092|rna1092 281 tSSGGRREVQRTMLELLNQLDGFDTR-NDIKVIMATNKIEALDPALIRpGRIDRKIEFG 338
                                        777788889999999**********7.66***************************996 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.1   2.8e-15   2.6e-12       1      44 [.     361     404 ..     361     405 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.8e-15
                          AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                        +v+++ L    e  SGAD++a+c eA++ Alr+ +k++tm+df+
  gene1093|gene1093|rna1092|rna1092 361 SVNIESLITSKEDLSGADIKAICTEAGMIALRERRKTVTMKDFI 404
                                        5889999999999******************************6 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   8.1e-10   7.7e-07       1      56 [.      93     147 ..      93     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8.1e-10
                                        EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE CS
                     Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkL 56 
                                        V+t+ E++dd ++ i++t  + e++v++ + v+++ L pg +V+++ + + ++ +L
  gene1093|gene1093|rna1092|rna1092  93 VGTLEEFIDD-HHGIITTGVGLEYYVNIMSFVDKDLLEPGCTVLLNYKDNSVVGVL 147
                                        9*********.************************************999998877 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   6.6e-08   6.2e-05       7     104 ..     207     298 ..     202     317 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.6e-08
                                        EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                              AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                        +l g  g+Gkt+laka+a+  ++    ++ r+  +el++    e  +lv +l   +++        i+++DEid i
  gene1093|gene1093|rna1092|rna1092 207 ILYGLPGTGKTLLAKAVANQTSA----TFLRVVGTELIQeyLGEGPKLVRELFRVADMH----APSIIFIDEIDAI 274
                                        4567889************9996....99999999999922223444444444444333....345********** PP

                                        ------------HHHHHHHHHHHH CS
                              AAA_2  81 hpkessgadvSregVqrdLLqile 104
                                          ++ +++   r +Vqr +L +l 
  gene1093|gene1093|rna1092|rna1092 275 GGRRYNTSSGGRREVQRTMLELLN 298
                                        *********************996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   1.3e-05     0.013       8      30 ..     206     228 ..     200     321 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                             AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                        ++++G +GtGKT+l++ +++q  
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTS 228
                                        689*****************973 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   5.9e-08   5.6e-05      51     115 ..     201     270 ..     156     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.9e-08
                             DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDD 115
                                        +p + v+L+G  GtGK  l ka+ n+++++ Lr++  e+ +e l e pklv++l    +++   i+f+D 
  gene1093|gene1093|rna1092|rna1092 201 KPPKGVILYGLPGTGKTLLAKAVANQTSATFLRVVgtELIQEYLGEGPKLVRELFrvaDMHAPSIIFIDE 270
                                        67789*****************************9778889*********99864222778889***997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         3   2.9e+03      34      64 ..      12      42 ..      10      62 .. 0.78
   2 !   18.0   0.2   2.3e-06    0.0022       1      77 [.     205     274 ..     205     327 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3
                                       TT--HHHHH--B--.........-------- CS
                              AAA_5 34 rdtteedlkgrreikngttslvdsplvraar 64
                                       +dtt+ +lk r ++k+++t+ ++  ++ +++
  gene1093|gene1093|rna1092|rna1092 12 QDTTTINLKRRKRVKESKTASKPPQVYPQMK 42
                                       6899999999999999999888888887777 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.3e-06
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                        +v+L G pGtgK+ la+ +a  + ++++ v +t+      l++++   +g +  ++   v  +  ++i+++DE++ 
  gene1093|gene1093|rna1092|rna1092 205 GVILYGLPGTGKTLLAKAVANQTSATFLRVVGTE------LIQEYLG-EGPKLVRELFRVADMHAPSIIFIDEIDA 273
                                        59****************************9997......7777774.4444444555555777999999999986 PP

                                        - CS
                              AAA_5  77 a 77 
                                        +
  gene1093|gene1093|rna1092|rna1092 274 I 274
                                        5 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.7e-06    0.0035      35      94 ..     205     272 ..     179     278 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvkl.kitsgPvleka.g...dlaall...tnleekdvlfideih 94 
                                         v+lyG PG Gkt lak +a++  +++ ++  +  +++  g    l+  l   +++++  ++fidei 
  gene1093|gene1093|rna1092|rna1092 205 GVILYGLPGTGKTLLAKAVANQTSATFlRVVGTELIQEYlGegpKLVRELfrvADMHAPSIIFIDEID 272
                                        69********************9988615555555554223111455443111456777899999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.6e-05     0.015      24      55 ..     203     231 ..     193     261 .. 0.80
   2 ?   -0.1   0.0       1.1   1.1e+03     123     146 ..     251     273 ..     238     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                             AAA_16  24 pelvllsGesGvGKsslvrellralekdggif 55 
                                        p  v+l+G +G+GK+ l+++++++ +++   f
  gene1093|gene1093|rna1092|rna1092 203 PKGVILYGLPGTGKTLLAKAVANQTSAT---F 231
                                        589******************9876655...4 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                             AAA_16 123 lkrllallsrderplvlvlDdlqw 146
                                        +++l++ +   + p ++++D+++ 
  gene1093|gene1093|rna1092|rna1092 251 VRELFRVADM-HAPSIIFIDEIDA 273
                                        5566666666.66899****9994 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-05     0.012       2      29 ..     206     233 ..     206     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                             AAA_33   2 vllvGlpGsGKstlaerllkklgavlls 29 
                                        v+l GlpG+GK+ la+ +++++ a++l+
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTSATFLR 233
                                        7899***************999966665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-05     0.025       2      33 ..     206     237 ..     205     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqft 33 
                                        v+l g+PG++ktll+ka+a++ +++f r+  t
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTSATFLRVVGT 237
                                        7899***********************99655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.6e-05     0.034      44      77 ..     200     233 ..     174     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                          IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavragls 77 
                                        i+  ++++l G +G+GK+ la a++ ++ ++ l+
  gene1093|gene1093|rna1092|rna1092 200 IKPPKGVILYGLPGTGKTLLAKAVANQTSATFLR 233
                                        6667899*****************9987665555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.067        63     183     208 ..      75     100 ..      30     106 .. 0.72
   2 ?    8.9   0.0    0.0008      0.76      23      45 ..     206     228 ..     196     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.067
                                        CHHHHHHHHHHCTT-HHHHHHHHHHH CS
                             NB-ARC 183 leevakeivekckGlPlalkvlggll 208
                                          +  k++ve+ +G+Pl++ +l +++
  gene1093|gene1093|rna1092|rna1092  75 GSNSQKHVVEQLRGSPLSVGTLEEFI 100
                                        4566789************9998776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0008
                                        EEEEESTTSSHHHHHHHHCCSHC CS
                             NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                        v l+G +G GKt lak + n+ +
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTS 228
                                        789***************99854 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-05     0.045       2      37 ..     206     246 ..     205     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-05
                             AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareilee 37 
                                        +++ G ++tGKT l++a a++      +vv +E   e+l e
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQtsatFLRVVgTELIQEYLGE 246
                                        7899***************7755555556667777666654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     7e-05     0.066       1      25 [.     206     236 ..     206     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-05
                             AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.....g 25 
                                        ++l G pG+GKt lak++++ + +      g
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTsATflrvvG 236
                                        79****************9986322565552 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.12       5      76 ..     206     274 ..     203     315 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla.dpekllelilek.lkeekktylflDEiqev 76 
                                        +++ G+  +GKT l+k ++++       +l +   +  ++ l   p kl +++++   + +  +++f+DEi  +
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTS---ATFLRVVGTELIQEYLGeGP-KLVRELFRVaDM-HAPSIIFIDEIDAI 274
                                        8999**************98877...55555544333222222134.455555444234.4899*******887 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.22      21      57 ..     112     149 ..      92     152 .. 0.76
   2 ?   -3.4   0.1       8.5     8e+03       2       9 ..     228     235 ..     227     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                      Prot_ATP_OB_N  21 grrmrVavsPlvdaeeLrpGqeVlLn.EalvvVealgy 57 
                                        g ++ V++   vd + L+pG +VlLn   + vV++l+ 
  gene1093|gene1093|rna1092|rna1092 112 GLEYYVNIMSFVDKDLLEPGCTVLLNyKDNSVVGVLEG 149
                                        66899*********************445778888775 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.5
                      Prot_ATP_OB_N   2 yGtflavn 9  
                                         +tfl+v+
  gene1093|gene1093|rna1092|rna1092 228 SATFLRVV 235
                                        699**997 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00033      0.31      25      43 ..     206     224 ..     199     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00033
                       Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                        ++l+G pG+GKt+lak+++
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVA 224
                                        79*************9975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00051      0.48      21      51 ..     206     236 ..     194     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                             AAA_30  21 avltGpAGtGKttalkalreaweaaggrvig 51 
                                        ++l G +GtGKt + ka+++   a   rv+g
  gene1093|gene1093|rna1092|rna1092 206 VILYGLPGTGKTLLAKAVANQTSATFLRVVG 236
                                        6899**************9998888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2672.50
//
Query:       gene1094|gene1094|rna1093|rna1093  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-05   23.2   0.8    0.00014   21.7   0.8    1.8  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.8   7.8e-09   0.00014       9      73 ..      89     145 ..      81     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.8e-09
                                        SS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCC CS
                            UPF0086   9 hGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsq 73 
                                        +Ga++++v        g +Gi+v+E  n + +v ++++vkt  K+ + F+++ +  +e+   Gs+
  gene1094|gene1094|rna1093|rna1093  89 TGAKIKIV-------GGRTGIIVEERANSIIVVLEDDSVKTYLKKTTDFTVTHE-GIEYVFIGSE 145
                                        45555444.......5899********************************994.5666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1032.63
//
Query:       gene1095|gene1095|rna1094|rna1094  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-88  295.4   0.2    6.4e-88  294.4   0.0    1.6  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    1.7e-09   37.8   0.3      4e-09   36.6   0.3    1.6  1  PheRS_DBD3       PheRS DNA binding domain 3
    5.8e-08   32.4   0.0    2.3e-06   27.2   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0034   16.5   0.0      0.014   14.5   0.0    2.0  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.59   2.6e+03      17      44 ..     108     135 ..      99     138 .. 0.81
   2 !  294.4   0.0   1.4e-91   6.4e-88       2     242 ..     187     463 ..     186     466 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.59
                                        SHHHHHHHHHHHHHHCTTCEESSTTSEE CS
                       tRNA-synt_2d  17 hpltkvleeikeiflelgfeevegpeve 44 
                                        + ++kv + i+++ ++++  +++++e+e
  gene1095|gene1095|rna1094|rna1094 108 RSVEKVEDMIRNMVINMKRGKATDEEIE 135
                                        5678889999999999999999998887 PP

  == domain 2  score: 294.4 bits;  conditional E-value: 1.4e-91
                                        .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESS.TTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS- CS
                       tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeeve.gpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka 76 
                                        ++++++g+  + g++hpl+k++e++k+if+elgf+e+  +++ves+f+nfd+L++pq+hp Rd++dtF+l +pe +
  gene1095|gene1095|rna1094|rna1094 187 YNFDAKGNIPQCGSIHPLMKIREDFKRIFIELGFSEMPtDQYVESSFWNFDVLFQPQNHPSRDAHDTFFLLNPELS 262
                                        8999999999***************************99*******************************999888 PP

                                        ................................ECESEEE-SSTHHHHHHHH....TTS-SSEEEEEEEEEEBSST- CS
                       tRNA-synt_2d  77 ................................veekllLRthttavqirtl....ekkkppikiisigrvfRrdav 116
                                                                        +++k++LRthtt+v++r l    ++  +p+k++si++vfR+++v
  gene1095|gene1095|rna1094|rna1094 263 lnfpkdylnevkethcggkygslgymnnwdikEAQKNILRTHTTSVSARNLyklaKEGFKPVKLFSIDKVFRNESV 338
                                        9*******************************999*****************9999999***************** PP

                                        SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEE CS
                       tRNA-synt_2d 117 DathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllga 192
                                        DathlaeFhqvegl++++++++++l+g+l+e++++l g+  ++rf+p+++p+tePs+ev+ y+ +  ++w+E++++
  gene1095|gene1095|rna1094|rna1094 339 DATHLAEFHQVEGLIAGKGLNITHLMGILQEFFNRL-GMC-DIRFKPAFNPYTEPSMEVFGYH-KGMNRWMEVGNS 411
                                        ************************************.997.**********************.9*********** PP

                                        EEE-HHHHHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT...HHHH CS
                       tRNA-synt_2d 193 GmvrpevleavgideevsgfafGlGveRlamlkygieDiRelven..dlrfl 242
                                        G++rpe+l ++g+d++vs++a+Gl++eR am+kyg+++iRelv +  d++f 
  gene1095|gene1095|rna1094|rna1094 412 GIFRPEMLGPMGFDSDVSVIAWGLSLERPAMIKYGLKNIRELVGHkvDIEFS 463
                                        *******************************************995666665 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.3   8.9e-13     4e-09       1      59 []      64     113 ..      64     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8.9e-13
                         PheRS_DBD3   1 ShEarvfaavppeggisqkelkklggdpvakiGfskAmknkWikkdkgdgkvvrkvdsi 59 
                                        S+E+  f+++ + +gi  +el+k        +G  +A+knkW+k  k++ k++r v+++
  gene1095|gene1095|rna1094|rna1094  64 SPEYLFFKSIGK-DGIDSDELSK------HEVGKMNAFKNKWVKR-KDG-KIFRSVEKV 113
                                        9*********55.66******44......579*************.766.49**99986 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.016        72      15      43 ..     201     229 ..     195     261 .. 0.77
   2 !   27.2   0.0     5e-10   2.3e-06      70     209 ..     297     430 ..     293     432 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.016
                    tRNA_synthFbeta  15 lnkeqklrrklrdllagaGlnEvitysfv 43 
                                         ++  k+r+  +++ +++G++E+ t   v
  gene1095|gene1095|rna1094|rna1094 201 IHPLMKIREDFKRIFIELGFSEMPTDQYV 229
                                        578899****************9885544 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 5e-10
                    tRNA_synthFbeta  70 dqsvlRtsLlpglLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfy 144
                                        ++++lRt  ++    +l +  + g + v+lF i kvf+++  + +  +e +++ ++++gk             +  
  gene1095|gene1095|rna1094|rna1094 297 QKNILRTHTTSVSARNLYKLAKEGFKPVKLFSIDKVFRNEsVDATHLAEFHQVEGLIAGKG-----------LNIT 361
                                        567899999999999999999*******************888899***************...........**** PP

                    tRNA_synthFbeta 145 dlkgivealleslgiekvefepaehpalhpgrsAeikvdgk....evGvlGelhpevleafdlkqrvyv 209
                                        +l gi+++++++lg+ +++f+pa +p+ +p      + +g     evG  G + pe+l  ++++  v+v
  gene1095|gene1095|rna1094|rna1094 362 HLMGILQEFFNRLGMCDIRFKPAFNPYTEPSMEVFGYHKGMnrwmEVGNSGIFRPEMLGPMGFDSDVSV 430
                                        ******************************766555555547888999999999999988888777765 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     3e-06     0.014      93     120 ..     325     351 ..     308     405 .. 0.83
   2 ?   -1.9   0.0      0.31   1.4e+03     287     307 ..     433     453 ..     432     455 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                                        EEEEEEEEE--S--BTTB-S-CEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqiea 120
                                        + f+i ++FR+E+++++ hlaEF q+e 
  gene1095|gene1095|rna1094|rna1094 325 KLFSIDKVFRNESVDAT-HLAEFHQVEG 351
                                        78*************77.566*****95 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.31
                                        EEEEHHHHHHHHCT-SSGGGC CS
                                        xxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                        +gl+l+R  m+  g+++Ir++
  gene1095|gene1095|rna1094|rna1094 433 WGLSLERPAMIKYGLKNIREL 453
                                        699****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2722.81
//
Query:       gene1096|gene1096|rna1095|rna1095  [L=933]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-05   21.7   0.9    0.00016   20.4   0.4    1.8  2  MMS1_N    Mono-functional DNA-alkylating methyl methanesulfon
     0.0016   17.1   0.0     0.0036   16.0   0.0    1.5  1  Nup160    Nucleoporin Nup120/160
     0.0048   17.3   1.1         23    5.7   0.0    5.1  6  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> MMS1_N  Mono-functional DNA-alkylating methyl methanesulfonate N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.13   7.7e+02     409     459 ..      20      70 ..      17      81 .. 0.72
   2 !   20.4   0.4   2.7e-08   0.00016      25     292 ..      80     326 ..      63     337 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.13
                             MMS1_N 409 nlgdgslvQVtpngirliradkrvsewkppngksiiaaaangeqllvalsg 459
                                        +l++  +vQ ++ +i  i+  k v + k +  + i +a++ ++ +lv+ sg
  gene1096|gene1096|rna1095|rna1095  20 SLSNIYFVQTSSITIYNISHRKLVYTRKMEFFDVIKSASIVEDEILVVFSG 70 
                                        556666777777777666666655443444457999*****9999999986 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.7e-08
                             MMS1_N  25 etvhshetlgksgsrrsqpGqylavDPkgraiavsayekvflvyslkkkeilnrealllssplearksegvilsmv 100
                                        +    ++++g+ +++  q+G y+a   ++ ++a      +f  +        +   ++l+ p+e+   e v++++ 
  gene1096|gene1096|rna1095|rna1095  80 NERA-RHRFGRCSIDYRQVGAYVAHGKSSMCLASYFGNMIFYFF--------E---DKLQIPIEHSVGESVVIDLK 143
                                        4455.666777777777777777665555444444444444333........2...23347888777777777777 PP

                             MMS1_N 101 FldpgykeednpiialleqdrrgkteltlyewdlglnlvrkisktsepkknldsganlLiplpkpggvlVcgetii 176
                                         ++ +         +ll+ +++g + +++ye +l    + k+++         +g  +++pl+  + v+++++ + 
  gene1096|gene1096|rna1095|rna1095 144 VMEGTR------RYLLLVRNQNG-VSVRIYEHKLEMIEMLKEEN--------VPGGYIVVPLKD-SFVVFSPDRVF 203
                                        775555......34666677887.99999999995543344322........34667*****99.77888888888 PP

                             MMS1_N 177 tykdildqedirkkswarPrrekatn...................fv.aweklds..fffllatedGdLylleiek 230
                                        + +++ d  +i++ ++++  +e  t                    f+  ++ +d+     l+ +e+G++++l++  
  gene1096|gene1096|rna1095|rna1095 204 FFRNN-D--KIEVYKISLGSSE--TLtlieassrceckdisetkiFTcYTSHYDGkcLLTLIVNEEGEIFSLKF-- 272
                                        88888.3..2443223333333..223466666777777888887775556666699999**************.. PP

                             MMS1_N 231 dedsgkvvtsislkyfdtvsvasalvilksgfLfvasefGdgqlyqieargeddknleliqt 292
                                               ++ ++l+ ++ +++ + + i  sg ++  +  +++++y+i+ + e   +lel++ 
  gene1096|gene1096|rna1095|rna1095 273 -------TDRLKLEHIGRINPSKDIEIHSSGLMVSVGYNSNNCMYYIKREDEMV-SLELVDV 326
                                        .......3479**************************************85433.6666554 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     6e-07    0.0036     173     253 ..     443     523 ..     434     529 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6e-07
                                        EEEETTEEEEEEEEE-------B--TTTT.TSS--SS---TT-ECEEEEET.....TTTEEEEEETT-EEEEEETT CS
                             Nup160 173 lkrdedggawkesvfepksfllslsgllglladpsrrksgasvalsldvavavveigqtylfalsrdgkLrvWnll 248
                                        ++ +++  + k+s++ ++ +  s++ +lg ++++++ +s++s+ +++ +++++ e+++ ylf l+  ++Lrv  ++
  gene1096|gene1096|rna1095|rna1095 443 ISSENNLTTNKHSIDYDSFSANSQYVFLGYKNRITKLDSSSSENIEIEFTIKEMEVNERYLFILTGKRVLRVYRID 518
                                        4447888888999999999999999************************************************999 PP

                                        TTEEE CS
                             Nup160 249 tgkcl 253
                                        +gk++
  gene1096|gene1096|rna1095|rna1095 519 DGKLV 523
                                        99987 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.2   7.4e+03      18      29 ..     338     351 ..     332     355 .. 0.68
   2 ?   -2.6   0.0       1.5   8.8e+03      19      33 ..     517     522 ..     498     543 .. 0.58
   3 ?   -1.1   0.1      0.49   2.9e+03      18      31 ..     603     616 ..     593     620 .. 0.82
   4 ?    3.4   0.0      0.02   1.2e+02      18      37 ..     724     742 ..     708     744 .. 0.82
   5 !    5.7   0.0    0.0038        23       6      30 ..     753     784 ..     750     791 .. 0.76
   6 ?    1.2   0.0     0.098   5.9e+02      19      34 ..     803     818 ..     797     819 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                              PQQ_3  18 avdgg..lvyvgtg 29 
                                         +++g  +vyv++g
  gene1096|gene1096|rna1095|rna1095 338 ITADGiyHVYVSDG 351
                                        56777555888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                              PQQ_3  19 vdgglvyvgtgdGtl 33 
                                        +d         dG+l
  gene1096|gene1096|rna1095|rna1095 517 ID---------DGKL 522
                                        23.........3333 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.49
                              PQQ_3  18 avdgglvyvgtgdG 31 
                                        a++g+ v++g+  G
  gene1096|gene1096|rna1095|rna1095 603 ALSGDMVVIGGRCG 616
                                        899*******9765 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.02
                              PQQ_3  18 avdgglvyvgtgdGtlyAlD 37 
                                        a+ g  vy+gt+ ++ly+++
  gene1096|gene1096|rna1095|rna1095 724 AMNGKEVYCGTE-NSLYCYE 742
                                        778888*****9.*****97 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0038
                              PQQ_3   6 svqlpgpvnsspavdgglvyvgtg........d 30 
                                        +v++p+++ + + v++g++++gt+        d
  gene1096|gene1096|rna1095|rna1095 753 KVKFPSKI-TRMCVGEGKLFAGTEkdsvfmvkD 784
                                        57889999.67************9655555555 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.098
                              PQQ_3  19 vdgglvyvgtgdGtly 34 
                                        +++g ++vg+  G+++
  gene1096|gene1096|rna1095|rna1095 803 TSDGNLVVGDRAGNIV 818
                                        589********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 5672.31
//
Query:       gene1097|gene1097|rna1096|rna1096  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-07   29.4   0.0    9.1e-07   29.1   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.7e-06   28.0   0.1    2.1e-06   27.7   0.1    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
      3e-06   27.6   0.1    3.9e-06   27.2   0.1    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.8e-05   22.6   0.0    0.00011   22.0   0.0    1.3  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     2e-10   9.1e-07      52     117 .]      70     135 ..      15     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2e-10
                                        EEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                     Acetyltransf_1  52 kipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                                +a+i  + V+p+yr++  G++ +  +e+     +++   l+v+e n  ai++Y+klG+
  gene1097|gene1097|rna1096|rna1096  70 LEEKDGFINAHISAVSVAPSYRKNRFGRLCMSVIEKSGDVYNAHFADLYVREGNITAIEFYKKLGY 135
                                        4444455679999******************999996666699888***************88**8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   4.7e-10   2.1e-06      49     113 ..      73     142 ..      51     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 4.7e-10
                    Acetyltransf_10  49 rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavgeeq 113
                                        +dg    his + V+p+yr++  g+  +  +e+  +  + +  +l v++ + +a++fY+klG+ +  +++
  gene1097|gene1097|rna1096|rna1096  73 KDGFinaHISAVSVAPSYRKNRFGRLCMSVIEKSGDVYNAHFaDLYVREGNiTAIEFYKKLGYAVYRKVF 142
                                        4444666*******************99999999877777779********************9997665 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   8.7e-10   3.9e-06      24      75 ..      72     136 ..      32     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 8.7e-10
                                        S......TCTEEEEE-GGGTTSSHHHHHHHHTT.SE..EEEE..EEEETHH..HHHHHHHHTTEE CS
                     Acetyltransf_7  24 d......aeitrlaVdpeyrgkGiGraLleaae.kg..iile..qlelnae..kaikfYeklGFe 75 
                                        +      a+i  + V+p+yr++  Gr  + ++e +g  ++ +   l++++   +ai+fY+klG+ 
  gene1097|gene1097|rna1096|rna1096  72 EkdgfinAHISAVSVAPSYRKNRFGRLCMSVIEkSGdvYNAHfaDLYVREGniTAIEFYKKLGYA 136
                                        133334345556******************7334554222222444553324799********95 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.6e-08   0.00011      22      82 ..      79     140 ..      59     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-08
                                        SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                               FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfekiee 82 
                                          ++a+ v p+ r+  +g++  + + k     + + + l+v+++N ++i++y+klG+ ++++
  gene1097|gene1097|rna1096|rna1096  79 AHISAVSVAPSYRKNRFGRLCMSVIEKSGDVyNAHFADLYVREGNITAIEFYKKLGYAVYRK 140
                                        6799**************98888888777666778889*******************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1288.65
//
Query:       gene1098|gene1098|rna1097|rna1097  [L=893]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-23   82.6   2.2    2.6e-23   82.6   2.2    2.0  2  SH2_2         SH2 domain
    0.00051   20.9   0.0     0.0018   19.1   0.0    2.0  1  HHH_9         HHH domain
  ------ inclusion threshold ------
      0.025   14.4   0.2        2.8    7.7   0.0    3.3  4  YqgF          Holliday-junction resolvase-like of SPT6
        2.9    8.4   4.6        4.8    7.7   0.4    3.2  3  CW_binding_1  Putative cell wall binding repeat


Domain annotation for each model (and alignments):
>> SH2_2  SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.42   1.9e+03      27      42 ..     233     248 ..     227     251 .. 0.82
   2 !   82.6   2.2   5.7e-27   2.6e-23      23     213 ..     720     890 ..     711     893 .] 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.42
                              SH2_2  27 kyvkRvikHpnFknvs 42 
                                        ++v+R+  Hp Fkn  
  gene1098|gene1098|rna1097|rna1097 233 ELVRRISLHPVFKNAL 248
                                        5789999*******75 PP

  == domain 2  score: 82.6 bits;  conditional E-value: 5.7e-27
                              SH2_2  23 kkrkkyvkRvikHpnFknvsaeeaeellaskerGdvviRPSskgedhLtvtwkvadgvyqhidvlEedkenefslg 98 
                                        +k+k   +R ++Hp+Fk++++ee e++l++++  ++++R S++      v ++v+ ++y hi+++E++k       
  gene1098|gene1098|rna1097|rna1097 720 EKKKPHHSRFMTHPLFKDLNSEESERYLKDNS-SSMLLRRSRRD-GSPVVVLRVSGDIYVHIKIQEAEKY------ 787
                                        45566689********************9865.68999999995.5556889***************997...... PP

                              SH2_2  99 ktLiigkeeyeDLDeliarhvepmakkveellahekfkkgskeeveelLreekkanpkrsvYafslskkkpgkflL 174
                                           + ++++yeDLDe i r  ++m ++ +++ +h+++ +      ee L e+ ++  + + Y f++skk+pgk+++
  gene1098|gene1098|rna1097|rna1097 788 ---YYKGNSYEDLDEFISRTAKKMLTNFKNIKNHKYYFED-----EEKLLEYLNQGGSYIRYGFCFSKKYPGKLCM 855
                                        ...67899******************************53.....445566888999******************* PP

                              SH2_2 175 sflankkarveheyvkvipegfklrkqefddvkaLlnwF 213
                                         +    +    +ey++v  + + +++++f ++++ +++ 
  gene1098|gene1098|rna1097|rna1097 856 IYRDGYNR---KEYITVD-DHLVYEGKNFGSLDEFVRYK 890
                                        **999997...5***985.77999********9998875 PP

>> HHH_9  HHH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     4e-07    0.0018       1      45 [.     557     602 ..     557     613 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4e-07
                              HHH_9   1 npLDnTavHPEsYalakkllkklgldlkelige..eallkkldkkkl 45 
                                        ++LD TavHP +Y +a kl+++l  + +++ g+  +   k+ld++k 
  gene1098|gene1098|rna1097|rna1097 557 EILDCTAVHPKNYTIATKLCTNLC-SKESINGKtiDPIRKALDNEKE 602
                                        68******************9963.3333333311445666666655 PP

>> YqgF  Holliday-junction resolvase-like of SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.27   1.2e+03      43     103 ..     319     374 ..     296     378 .. 0.54
   2 ?    7.7   0.0   0.00063       2.8      18      82 ..     355     410 ..     342     413 .. 0.79
   3 ?    2.7   0.0     0.022     1e+02     131     149 ..     434     452 ..     429     453 .. 0.90
   4 ?   -2.7   0.0         1   4.5e+03      29      67 ..     772     809 ..     761     834 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.27
                                        T-SS-SHHHHHHHHHHHHHH--SEEEE--SSTHHHHHHHHHHHHHHHTTB-TTS-B--EEE CS
                               YqgF  43 edrekkakfvetlkkfllskkPdvigvsGenrdaqkliedvkevlhekeqdsrlstvgvil 103
                                         +  kk  f+e+++++++      ig+ Ge +    ++++ k+ l+   ++ +++ v+ i 
  gene1098|gene1098|rna1097|rna1097 319 LEERKKGVFIEAIDRIVNG----SIGIKGEGTYVCGVTKE-KKYLKAAIVNFEGDLVDCIT 374
                                        4555666667766666653....35555555544444443.33344444444444444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00063
                                        TS-EEEEEE-TTS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEEEE--SSTHHHHHHHH CS
                               YqgF  18 ddaiicvlvngeGevvdslklaareedrekkakfvetlkkfllskkPdvigvsGenrdaqklied 82 
                                        ++ + +++vn eG++vd + +         k++ +e+l kf+ +  P   ++sG +++ + l++ 
  gene1098|gene1098|rna1097|rna1097 355 KKYLKAAIVNFEGDLVDCITV---------KEEEEEELLKFIGKFDPCCTAISGYSTSIRYLMKS 410
                                        455667889999999998888.........4555677999*****************99999986 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.022
                                        HHHHHHHHHH-HHHHHHCS CS
                               YqgF 131 yavalaRkiqdPLleyaql 149
                                        ++  +aR iq P +ey+++
  gene1098|gene1098|rna1097|rna1097 434 FCCNIARVIQCPEIEYSDM 452
                                        799*************987 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1
                                        TS-EEEEEEE-S-TT-SS-SHHHHHHHHHHHHHH--SEE CS
                               YqgF  29 eGevvdslklaareedrekkakfvetlkkfllskkPdvi 67 
                                         G++  ++k+ +  e    k +  e l++f+ ++  +++
  gene1098|gene1098|rna1097|rna1097 772 SGDIYVHIKIQEA-EKYYYKGNSYEDLDEFISRTAKKML 809
                                        5777777777333.3334445555669999877655544 PP

>> CW_binding_1  Putative cell wall binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.17   7.6e+02       8      15 ..     666     674 ..     661     675 .. 0.74
   2 ?   -2.7   0.2       2.1   9.6e+03       9      13 ..     786     790 ..     781     793 .. 0.56
   3 ?    7.7   0.4    0.0011       4.8       2      14 ..     811     823 ..     810     827 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                                        TEEEEE.TT CS
                       CW_binding_1   8 gnWYYf.ds 15 
                                        g+ YY+ +s
  gene1098|gene1098|rna1097|rna1097 666 GTTYYLlNS 674
                                        889**9666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                                        EEEEE CS
                       CW_binding_1   9 nWYYf 13 
                                        + YY 
  gene1098|gene1098|rna1097|rna1097 786 KYYYK 790
                                        56664 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0011
                                        EEEEETTEEEEET CS
                       CW_binding_1   2 gWvkdngnWYYfd 14 
                                         +++++++ YYf 
  gene1098|gene1098|rna1097|rna1097 811 NFKNIKNHKYYFE 823
                                        59**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (893 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 5540.27
//
Query:       gene1099|gene1099|rna1098|rna1098  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-25   87.0   4.4    1.2e-24   86.0   4.4    1.5  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    1.3e-20   72.7   0.0    2.1e-20   71.9   0.0    1.4  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   4.4   1.4e-28   1.2e-24       2      65 .]      64     127 ..      63     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.4e-28
                                        EEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                       Ribosomal_S5   2 kekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                        ke+vl+ik+vqk+t++G++t+++a+vvvGd+nG+vG+G++ +ke a Air+Ai +Ak  + pv+
  gene1099|gene1099|rna1098|rna1098  64 KEEVLSIKSVQKQTRAGQKTRIKAVVVVGDENGHVGIGTKASKEAASAIRGAIARAKCAIRPVR 127
                                        89************************************************************96 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   2.4e-24   2.1e-20       2      66 ..     147     212 ..     146     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.4e-24
                                        EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                     Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                        gk+g + v+++paprGtGii+g + ++++elaGikD+++ s g ++++ n++kA + AL++++s+ 
  gene1099|gene1099|rna1098|rna1098 147 GKCGTSIVRVIPAPRGTGIISGSVNKKIFELAGIKDLYTISSGaTSTTENFAKASIAALEATSSMI 212
                                        9************************************************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1506.04
//
Query:       gene1100|gene1100|rna1099|rna1099  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-28   98.7   0.1    6.7e-28   97.0   0.1    1.9  1  VPS9      Vacuolar sorting protein 9 (VPS9) domain


Domain annotation for each model (and alignments):
>> VPS9  Vacuolar sorting protein 9 (VPS9) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.1   3.7e-32   6.7e-28       1     103 [.     110     232 ..     110     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 3.7e-32
                               VPS9   1 leqaseeLkklseaksPreKlkcllrtieeiteavskseegeslgaDdlLPiliyviikssppnlysnvqfikrF. 75 
                                        le++s+ Lk+l ++++P+eK++c++ ++e +++++     g+++g+D++LP++iy+iikss+p++y+++ f+  + 
  gene1100|gene1100|rna1099|rna1099 110 LEDISKVLKSLPFLQTPTEKISCVMDVMERLCNSI-----GRNEGQDKILPSIIYCIIKSSVPDIYLETRFMVLYr 180
                                        5899*******************************.....************************************ PP

                               VPS9  76 ........................rsktllegeegYylttleaavefiesle 103
                                                                 +kt+ e+e +Yylt+++aav+fi+++e
  gene1100|gene1100|rna1099|rna1099 181 rkngerckekcnhelnikadcecfFNKTYDEKEVSYYLTSVQAAVDFIRKME 232
                                        **********************966*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1684.28
//
Query:       gene11|gene11|rna11|rna11  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-11   41.7   0.2    1.2e-10   41.4   0.2    1.1  1  NIF       NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.2   6.7e-15   1.2e-10      31     149 ..      12     142 ..       4     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.7e-15
                        NIF  31 vsvlkRpgldefLkelskl.yevvifTasseeyaeavidildpekkllshr.lyre.scv..kkkg.......eyvKdLsllgr 102
                                + v+ Rp ld ++k l  +    v++T +++++a + i++l   +   ++  +y + +c+  k           +vKdL+++ r
  gene11|gene11|rna11|rna11  12 YLVYNRPNLDLLIKFLKTHdTSYVLWTTGMRRNATNLINHLSHVGF-NEYLgWYSQlDCKagK--VkldsecnLWVKDLNVVAR 92 
                                789************9877688899****************88874.3333655441564441..13345677888******77 PP

                        NIF 103 ....dlsrvvivDdspdsfelqpengipiksffsdkkDneLlkllpllkel 149
                                    d +r ++vDds d+   + +n i +++++   +D+ ++ + ++l++ 
  gene11|gene11|rna11|rna11  93 nhnvDVERCILVDDSIDKSV-HTQNFICCPEYIPGTEDDGIKYICKHLDDF 142
                                7777999**********986.79**********999999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 905.28
//
Query:       gene110|gene110|rna110|rna110  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.8e-38  130.4   0.2    6.5e-38  130.3   0.2    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.2   3.6e-42   6.5e-38       1     227 [.      43     290 ..      43     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 3.6e-42
                                    CEEEEESSH.....HHHHHHHHHEEEEEEEEEE.....TTEEEEEEEETTEEEEEEE--.....SSHHHHHHHHHHHHHH CS
                      PNP_UDP_1   1 kiaiivgsp.....gevellaespleetpfgre....grgfkfvtGtlkgkpvvivstG.....iGkpnaavvaeirllk 66 
                                    k++ii+gs+     +e+   +e +++++p+++     g+ +k+vtG++ g++ vi+++G     +G+p + +  ++r++k
  gene110|gene110|rna110|rna110  43 KVGIICGSGmgaipEELTEKIEIEYKDIPHFPIstvqGHDGKLVTGKM-GRVGVICMQGrfhyyEGYPLSTCSMPVRMMK 121
                                    689******98888888888888*************************.9999*************************** PP

                                    HC--SEEEEEEEEEESSTTT-TT-EEEEEEEEE...SSSCCGCCTHHCC..TCCCCTTSSEE--HHHHHHHHHCHHTTT. CS
                      PNP_UDP_1  67 efgvkaiiriGtaGglnpdlkvGDvvipddain...fdgrsplygpkee..gqyfpdsydapadpelrallkeaaealg. 140
                                      g+ +ii +++aGg+np++++GD++i++d+in   + g +pl g  +e  g++f++++++ +++e r+++k aa++lg 
  gene110|gene110|rna110|rna110 122 LCGITHIIISNAAGGINPEYNIGDIMIIKDHINflgYGGVNPLVGAHDErwGPRFVPVNKI-YSEEVREKAKIAAQRLGi 200
                                    *********************************999******999999999**********.*****************6 PP

                                    .TTEEEEEEEEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTB.....ETTCTCH.HCC CS
                      PNP_UDP_1 141 .ikvhrGvvatadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaag.....gadaeatheev 214
                                       +++Gv   ++g+ +et+ae+r+l++lgadav+M+   +a+ A ++g+ + ++++++    +       d e +h ev
  gene110|gene110|rna110|rna110 201 eSFLREGVLSITGGPCYETVAESRMLHKLGADAVGMSVIGEAITACQAGLTVFGFSLIAG---KcpmeySVDSEISHSEV 277
                                    555677****************************************************44...44445555666666777 PP

                                    CHHHHHHHHHHHH CS
                      PNP_UDP_1 215 eefaqeaaknaaa 227
                                     e+aq+ +  + +
  gene110|gene110|rna110|rna110 278 VECAQKREILIRK 290
                                    7776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2048.22
//
Query:       gene1101|gene1101|rna1100|rna1100  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-20   71.8   0.1    1.4e-09   37.6   0.0    2.1  2  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom
  ------ inclusion threshold ------
       0.13   12.4   1.4          1    9.6   0.1    2.4  2  RRM_7     RNA recognition motif


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.6e-13   1.4e-09       1      69 [.      12      75 ..      12      76 .. 0.95
   2 !   32.5   0.0   6.1e-12   5.5e-08       1      65 [.      86     143 ..      86     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.6e-13
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69
                                       lf++n+p+ + ++ ++el+ ++ +i+++    d     kg++fV +e++e+ +   + l+g kl g++l
  gene1101|gene1101|rna1100|rna1100 12 LFITNIPTKTRKQLVYELLTQVSKISNLYYNQD-----KGYCFVSYETHEELDYTYKVLQGVKLYGKRL 75
                                       8************************88888887.....**************************99987 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 6.1e-12
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEET CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklg 65 
                                        ++V+n+ ++++e  L ++FskfGp  ++++  d      g ++V +  k++A kA++++n+k +g
  gene1101|gene1101|rna1100|rna1100  86 VVVRNIGQEIDEVFLWDVFSKFGPC-HVEIDGD------GLGIVVYRRKDSAIKAVDTVNRKIIG 143
                                        78***********************.7877776......***********************997 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.03   2.7e+02      46      62 ..      41      57 ..       9      82 .. 0.65
   2 ?    9.6   0.1   0.00011         1       4      35 ..      86     117 ..      83     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.03
                              RRM_7 46 skaakgyvflvfedeks 62
                                        ++ kgy f+ +e+++ 
  gene1101|gene1101|rna1100|rna1100 41 YNQDKGYCFVSYETHEE 57
                                       34567888888877654 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00011
                              RRM_7   4 vFvGGlPiDiteeelkatfkefgkvlvdwPkk 35 
                                        v v  +  +i+e  l++ f++fg++ v+  + 
  gene1101|gene1101|rna1100|rna1100  86 VVVRNIGQEIDEVFLWDVFSKFGPCHVEIDGD 117
                                        667777889******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1049.83
//
Query:       gene1102|gene1102|rna1101|rna1101  [L=787]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-07   31.5   0.8    2.6e-07   30.6   0.8    1.6  1  KIX_2     KIX domain


Domain annotation for each model (and alignments):
>> KIX_2  KIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.8   1.4e-11   2.6e-07       8      80 ..       2      73 ..       1      75 [. 0.90

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.4e-11
                              KIX_2  8 lspeeRqkivnkiletLkk.hlpvsgpeglnelkkiAvrFEekiFskAtskedYlrkislKmlqmetksqnaas 80
                                       ls+eeR++++ k+  +Lk+ + ++ g  +  ++k+ A r E++i+++++ske+Ylr + ++ + +e+  +n+++
  gene1102|gene1102|rna1101|rna1101  2 LSQEERKQMILKLFIALKEsN-IFPG-YTPVQIKEAAIRAEQRIYEESNSKEEYLRGMGERFQRIERVVSNRNR 73
                                       799****************55.6666.567899*********************************99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 5000.16
//
Query:       gene1103|gene1103|rna1102|rna1102  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-19   66.9   0.3    1.3e-18   66.2   0.3    1.3  1  SRF-TF    SRF-type transcription factor (DNA-binding and dime


Domain annotation for each model (and alignments):
>> SRF-TF  SRF-type transcription factor (DNA-binding and dimerisation domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.3     7e-23   1.3e-18       2      48 .]     105     151 ..     104     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 7e-23
                             SRF-TF   2 IeneraRqvtFsKRrnGLfKKAsELsvLcgvevavvvfspngklytf 48 
                                        I+ +++R+v+FsKR+ G++KKA+EL vL+g+e+ ++v s++g+++tf
  gene1103|gene1103|rna1102|rna1102 105 ISGKNKRSVCFSKRKRGIMKKAYELNVLTGTEILLLVASESGHVFTF 151
                                        7889******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1520.20
//
Query:       gene1104|gene1104|rna1103|rna1103  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-11   42.1   0.0    1.5e-10   41.3   0.0    1.5  1  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    1.2e-08   35.1   0.1    2.6e-08   34.1   0.1    1.5  1  S1           S1 RNA binding domain


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   1.7e-14   1.5e-10       3      68 ..      10      73 ..       8      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.7e-14
                                       EEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEE CS
                        SHS2_Rpb7-N  3 tvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfral 68
                                       ++ l Psylg+++++ ++e+ll+k+eg ++ s G++v vl i e+se++++   G + ++V+++al
  gene1104|gene1104|rna1103|rna1103 10 NIHLSPSYLGPNIQTLIEEYLLSKVEGSCSSS-GYVVMVLSIDEVSESRIILT-GETIFTVKYKAL 73
                                       789****************************9.*****************988.**********98 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   2.9e-12   2.6e-08       1      66 [.      76     136 ..      76     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.9e-12
                                        HSTTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETT CS
                                 S1   1 kpekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkd 66 
                                        kp+kge+++++V++ +k+G+f  +g + ++f++ +++++       + +++++ ++++k+++++ d
  gene1104|gene1104|rna1103|rna1103  76 KPFKGEIIDANVVETNKMGVFASVG-PLTVFISNHQIPNF----LLENEITKDIMIRLKIIGTKID 136
                                        79***********************.************75....5788888999999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 961.43
//
Query:       gene1105|gene1105|rna1104|rna1104  [L=205]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-13   48.8   0.1    9.4e-13   48.4   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.8e-09   36.5   0.1      8e-09   35.8   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    6.2e-07   29.4   0.0    8.9e-07   28.9   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.045   13.8   0.0      0.062   13.4   0.0    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.072   13.1   0.0        0.1   12.5   0.0    1.4  1  BRCA-2_OB1       BRCA2, oligonucleotide/oligosaccharide-bindi


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.1   2.6e-16   9.4e-13      19     116 ..      93     193 ..      78     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 2.6e-16
                                        HHHHHHHHHHHSTTCEEEEEEET...TEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHH CS
                     Acetyltransf_1  19 aseeefeesfsleaegllvaeed...geliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeer 88 
                                        +++ee++ s+ ++ ++ +v+ +d   +++iG  +l++          +++ie+++V +e rgkG+G+  le+l+ +
  gene1105|gene1105|rna1104|rna1104  93 KQFEERYLSLCKDGCYKIVVAYDpkdEKVIGSGTLFIEKKfirGCAAKGHIEDVVVLKEKRGKGIGKDILETLIWI 168
                                        4444555556667774444444444499***************77899**************************** PP

                                        HHHTTESEEEEEEETTEHHHHHHHHHTT CS
                     Acetyltransf_1  89 areegikkivlaveedndaairlYeklG 116
                                         ++ g++k  l ++  n   i++Y+k+G
  gene1105|gene1105|rna1104|rna1104 169 SKKMGCYKTALVCDLKN---IEFYKKCG 193
                                        ******88788666666...****88*9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   2.2e-12     8e-09       5      73 ..     110     193 ..     104     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.2e-12
                                        EEEEEET..TEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH.....TTSEEEEE..EEEETH CS
                     Acetyltransf_7   5 vfVaedd..gkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea.....aekgiile..qlelna 62 
                                        + Va+d   +k++G   l +++         ++i+ ++V++e rgkGiG+ +le      ++ g+  +  +  l  
  gene1105|gene1105|rna1104|rna1104 110 IVVAYDPkdEKVIGSGTLFIEKkfirgcaakGHIEDVVVLKEKRGKGIGKDILETliwisKKMGCYKTalVCDL-- 183
                                        667766677888887777777788888877677788******************64554322777533222333.. PP

                                        HHHHHHHHHTT CS
                     Acetyltransf_7  63 ekaikfYeklG 73 
                                         k+i+fY+k+G
  gene1105|gene1105|rna1104|rna1104 184 -KNIEFYKKCG 193
                                        .67*******9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.5e-10   8.9e-07      19     112 ..      96     200 ..      80     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.5e-10
                    Acetyltransf_10  19 pealrerieegealllvaeeg..gkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaek 82 
                                        +e++ + +++g ++++va++   +k++G ++l  +++         hi+ ++V +e rg+Gigk +le+++   +k
  gene1105|gene1105|rna1104|rna1104  96 EERYLSLCKDGCYKIVVAYDPkdEKVIGSGTLfIEKKfirgcaakgHIEDVVVLKEKRGKGIGKDILETLIWISKK 171
                                        2666677889999999999744489999999988888899999999****************************99 PP

                    Acetyltransf_10  83 dgikleltvnaspyavpfYeklGFkavgee 112
                                        +g   ++ +  + + ++fY+k+G k+ ++e
  gene1105|gene1105|rna1104|rna1104 172 MGCY-KTALVCDLKNIEFYKKCGLKEKERE 200
                                        9887.8999999999********9987665 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.062      30     124 ..      94     193 ..      67     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                        HHHHHHHHHHTTS..EEEEEEE..TTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHH CS
                     Acetyltransf_9  30 eireyfrkllees..rvlgaed..ngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaralee 101
                                        +++e++  l++++  ++++a+d  +++++g+ +l+  +  ++G   k + + +V v  e+rg+g+ +++l++++  
  gene1105|gene1105|rna1104|rna1104  94 QFEERYLSLCKDGcyKIVVAYDpkDEKVIGSGTLFIEKKFIRGCAAK-GHIEDVVVLKEKRGKGIGKDILETLIWI 168
                                        45566666666667789999999999999999999999999997766.79***********************999 PP

                                        HHHTT--EEEE--..SSHHHHHTTT CS
                     Acetyltransf_9 102 mreegqplsllfP..ssipiYrrfG 124
                                         +++g   + l+    +i++Y++ G
  gene1105|gene1105|rna1104|rna1104 169 SKKMGCYKTALVCdlKNIEFYKKCG 193
                                        9999988888877776678887776 PP

>> BRCA-2_OB1  BRCA2, oligonucleotide/oligosaccharide-binding, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05       0.1      38      92 ..      93     146 ..      39     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                                        --------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEES--EEES--S-- CS
                         BRCA-2_OB1  38 keksekaeleltDGWYsikavlDaalsrllkrgkikvGqKlvvagaelvgseeav 92 
                                        k+ +e++   + DG Y+i ++ D++ ++++ +g++++ +K +  +a+  g+ e+v
  gene1105|gene1105|rna1104|rna1104  93 KQFEERYLSLCKDGCYKIVVAYDPKDEKVIGSGTLFIEKKFIRGCAAK-GHIEDV 146
                                        334455555677**************************9988877776.555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1416.17
//
Query:       gene1106|gene1106|rna1105|rna1105  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1217.25
//
Query:       gene1107|gene1107|rna1106|rna1106  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.8   0.1      0.086   13.3   0.1    1.4  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   4.8e-06     0.086      55      84 ..      55      80 ..       7     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-06
                                       HHHHHHHT.HCHHHHHHHHHHHHHHHHHHH CS
                               Sld5 55 vkllelardldelkrllrdllevRlakirk 84
                                       v+ lel+r    +k+ ++++++vRl+k+  
  gene1107|gene1107|rna1106|rna1106 55 VYELELER----VKFFIKEYIRVRLKKLST 80
                                       55566666....8**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1112.91
//
Query:       gene1108|gene1108|rna1107|rna1107  [L=315]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-90  301.4   0.0    1.1e-89  301.2   0.0    1.0  1  UPF0160   Uncharacterised protein family (UPF0160)


Domain annotation for each model (and alignments):
>> UPF0160  Uncharacterised protein family (UPF0160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.2   0.0   6.2e-94   1.1e-89       2     315 ..       3     299 ..       2     301 .. 0.97

  Alignments for each domain:
  == domain 1  score: 301.2 bits;  conditional E-value: 6.2e-94
                            UPF0160   2 igTHngkFhaDevlAvalLrllpeykdaelvRtrdpevleecdivvDVggvyDpakkryDHHqrefnetfsekakt 77 
                                        ++TH+ kFh+DevlA+a+L ++  y+d+e++Rtr+p+v++  di++DVggv+Dp+++ryDHHq++fnetfs+++k+
  gene1108|gene1108|rna1107|rna1107   3 LVTHDRKFHLDEVLATAVLLKI--YPDSEIIRTRNPAVVQGGDIIYDVGGVFDPKTNRYDHHQESFNETFSSNHKI 76 
                                        68********************..**************************************************** PP

                            UPF0160  78 klSSaGLvYkhfgkeiikkllkleldeeevellyeklyeefveaiDaiDnGisvyeevekkykiktslssrvgrln 153
                                        klSS+GL+Yk++g+++++ +  ++ ++e ++  +e++ye+++ + DaiDnG +++ e+ ++     sls++v+++n
  gene1108|gene1108|rna1107|rna1107  77 KLSSSGLIYKYYGERFLEVY-GITRTDEYFHKALEEIYETYFMSADAIDNGYEIFGEIVPR-----SLSHIVESFN 146
                                        ******************99.77889*****************************988888.....9********* PP

                            UPF0160 154 pewneeekeedederFekAselvgeeflekvkylakswlpareivkealekrkevdesgrilvleesvpwkehlle 229
                                            + ++++++++rF +A+++v++++++ +++++ sw+p  ++  + ++        g+il++++ + + + + e
  gene1108|gene1108|rna1107|rna1107 147 ILSFSGNENDEQNRRFLEAVRIVSRDLDNFMHTMIGSWIPNYKYLDKLISG-----VVGDILCVDRYC-FIDVVPE 216
                                        9888889999*****************************************.....69*******996.6789999 PP

                            UPF0160 230 lekelkiekkvlyvlyedeeekwrvqavpvskesfesrkpLpeeWrGlrdeeLsevsgiegavFvHasgFiggnkt 305
                                        +ek++k  k++++vl e +e+++++ avp+++++f+s++pL++eWrGl  ++L+++sgieg+ FvHasgF+g+nkt
  gene1108|gene1108|rna1107|rna1107 217 IEKKYK--KDIKFVLNE-RENSVTILAVPKERKHFKSKIPLKKEWRGLTGSKLETISGIEGCNFVHASGFVGSNKT 289
                                        **9999..9*******5.9********************************************************* PP

                            UPF0160 306 kegalemAkk 315
                                         egalem++ 
  gene1108|gene1108|rna1107|rna1107 290 IEGALEMCRV 299
                                        ********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2163.02
//
Query:       gene1109|gene1109|rna1108|rna1108  [L=473]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-35  122.1   2.9    3.8e-35  121.4   2.9    1.3  1  DUF1686        Protein of unknown function (DUF1686)
  ------ inclusion threshold ------
       0.25   11.2   3.5        2.7    8.0   0.4    3.2  3  A1_Propeptide  A1 Propeptide
       0.29   11.3   2.1       0.27   11.4   0.4    1.7  2  Colipase-like  Colipase-like
       0.61   10.1   4.1        1.2    9.1   1.9    2.4  2  ArAE_1_C       Putative aromatic acid exporter C-terminal dom
        1.4    9.3   5.7        1.7    9.1   1.9    2.2  2  Syntaxin_2     Syntaxin-like protein
        1.5    9.0   5.6        1.1    9.4   3.0    2.0  2  Med9           RNA polymerase II transcription mediator compl


Domain annotation for each model (and alignments):
>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   2.9   1.3e-38   3.8e-35       7     179 ..     283     471 ..     277     472 .. 0.86

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 1.3e-38
                            DUF1686   7 ntalyvlavaGtiiyqiwvLakeyrdkgveevlreeWsvvgcmvPmlvgl.....lnagvirssvysv.tvagigi 76 
                                         ++ y +++ G+i+++ w+L++e ++ g+ evl ++W+v+g+m+Pml  l     +++   ++sv+s  +++g+++
  gene1109|gene1109|rna1108|rna1108 283 KKVAYTISILGPILHGRWILTNEDYNRGIVEVLSKNWNVIGSMFPMLLVLkkdslRKTFEGKASVESYgAMVGMSV 358
                                        6889**********************************************54444222223456666557999*** PP

                            DUF1686  77 vmlyvQslvkk..kmsrrqvcvvvlgnillasaclagdklllpgvedrsslvcvglvvfaallllvsyveegg..k 148
                                        +m++ Q   k+  k+  rq+ v+v+gnil++ a++    +++ ++   ++lv  g ++f ++l+ + ++e g+  +
  gene1109|gene1109|rna1108|rna1108 359 IMMCSQTFSKRdrKIHGRQMNVFVIGNILMGMAYVN--NFIALSARSGHNLVLFGHIIFGLILCFMIIIEGGDrmE 432
                                        *******999888***********************..677778999999********************765335 PP

                            DUF1686 149 kakaeevgevvks........vvlvlsvlvltvvsyvkg 179
                                        ++k++++++ v          v+++ ++l+   + y k+
  gene1109|gene1109|rna1108|rna1108 433 DTKSKGMEWTVIFqwimswifVIFGFQNLESCYFHYTKN 471
                                        678999999887778889999999999999999988765 PP

>> A1_Propeptide  A1 Propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4   0.00089       2.7      10      24 ..      58      73 ..      57      75 .. 0.91
   2 ?   -0.1   0.3      0.29   8.7e+02       5      12 ..     208     215 ..     208     215 .. 0.92
   3 ?    1.3   0.0      0.11   3.3e+02      11      25 ..     336     350 ..     335     352 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00089
                                       --HHHHHHH.TT-HHH CS
                      A1_Propeptide 10 KSmRetLrE.kglLee 24
                                       KS+R+ ++E k lLe+
  gene1109|gene1109|rna1108|rna1108 58 KSIRNLMKEaKELLES 73
                                       9*************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.29
                                        EEEE---H CS
                      A1_Propeptide   5 PLkKvKSm 12 
                                        PLk+ KS+
  gene1109|gene1109|rna1108|rna1108 208 PLKRKKSA 215
                                        9*****95 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.11
                                        -HHHHHHHTT-HHHH CS
                      A1_Propeptide  11 SmRetLrEkglLeeF 25 
                                        S+R+t+ +k  +e++
  gene1109|gene1109|rna1108|rna1108 336 SLRKTFEGKASVESY 350
                                        99*******999987 PP

>> Colipase-like  Colipase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4     9e-05      0.27      35      64 ..     113     142 ..      87     151 .. 0.83
   2 ?   -2.7   0.1       2.3   6.7e+03      48      65 ..     185     202 ..     175     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                      Colipase-like  35 slekfCkpksliflqClklrkpagevCqsh 64 
                                         ++++C+ k+++ + C+ +rk     C+s 
  gene1109|gene1109|rna1108|rna1108 113 DSKHYCQGKTKVGVSCVDQRKQIASTCLSV 142
                                        4789***********************875 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                      Colipase-like  48 lqClklrkpagevCqshk 65 
                                        ++  +l k + ++C s  
  gene1109|gene1109|rna1108|rna1108 185 QHNSSLSKTEPTYCISEG 202
                                        444445555555555544 PP

>> ArAE_1_C  Putative aromatic acid exporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.3   8.9e+02       2      33 ..       5      36 ..       4      46 .. 0.65
   2 ?    9.1   1.9    0.0004       1.2       1      63 [.      39     111 ..      39     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHH.HHHHHHHSTS--S CS
                           ArAE_1_C  2 kklkelqeeieeelkkils.emaeylrekekei 33
                                       k+++ + ++ie++l +i s e ++ l + ++e+
  gene1109|gene1109|rna1108|rna1108  5 KDITDYIQNIEKKLGEIVSsEASKKLLS-AEEW 36
                                       6789999999999999986134444444.4444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0004
                                        .HHHHHHHHHHHHHHHHHHH..........HHHHHHHSTS--SHHHHHH.HHHHHHHHHHHHHHHCCCCS-HH CS
                           ArAE_1_C   1 ekklkelqeeieeelkkils..........emaeylrekekeidekelleeleellkeakklayrnleNtlls 63 
                                        e+k+k+ q++++ +++k+++          e+ e++r++e + + k+++++ ++++k+ k+   ++ +N    
  gene1109|gene1109|rna1108|rna1108  39 ERKIKTDQRNVDGQFSKVIKsirnlmkeakELLESIRNGEFSLYRKDIFNKYNKEIKKVKNALETYKDNICSY 111
                                        678999999999999888761111111111445677788889999999***********99999888886544 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.9   0.00057       1.7      38      99 ..       3      66 ..       1      68 [. 0.87
   2 ?   -0.0   0.1      0.39   1.2e+03       8      28 ..      87     107 ..      83     132 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00057
                         Syntaxin_2 38 lieeinelikktnellkklsqldnsssds..qqklqkekLkkdfkealqeFqkiqrqyaekekq 99
                                       ++++i++ i++++++l ++ + + s++     + + + k+k+d +++  +F k+ +++++ +k+
  gene1109|gene1109|rna1108|rna1108  3 TQKDITDYIQNIEKKLGEIVSSEASKKLLsaEEWFRERKIKTDQRNVDGQFSKVIKSIRNLMKE 66
                                       68899999*****9999999988777433779999*************************9997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.39
                         Syntaxin_2   8 insnvstleklvkqLgtkkdt 28 
                                        +n+ +++++k  + L+t kd+
  gene1109|gene1109|rna1108|rna1108  87 FNKYNKEIKKVKNALETYKDN 107
                                        456667777777777777763 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.94   2.8e+03      21      35 ..       4      18 ..       2      26 .. 0.69
   2 ?    9.4   3.0   0.00036       1.1      11      79 ..      40     107 ..      38     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.94
                               Med9 21 skdletktgelrhkL 35
                                       +kd+   ++++ +kL
  gene1109|gene1109|rna1108|rna1108  4 QKDITDYIQNIEKKL 18
                                       566666777777766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00036
                               Med9  11 ksiekdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkyknr 79 
                                        ++i+ d+++   ++++ + ++r+  k+a+el++++ + + s  ++++  ++++++++k ++ L+ yk+ 
  gene1109|gene1109|rna1108|rna1108  40 RKIKTDQRNVDGQFSKVIKSIRNLMKEAKELLESIRNGEFSL-YRKDIFNKYNKEIKKVKNALETYKDN 107
                                        578889999999*****************************8.7999*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 2742.86
//
Query:       gene1110|gene1110|rna1109|rna1109  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1351.16
//
Query:       gene111|gene111|rna111|rna111  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.8e-12   46.7   0.2    7.3e-12   46.1   0.2    1.3  1  CS          CS domain
  ------ inclusion threshold ------
      0.061   12.7   0.1      0.099   12.0   0.1    1.3  1  DUF3387     Domain of unknown function (DUF3387)
       0.13   12.2   0.2       0.67   10.0   0.0    1.9  2  Neuralized  Neuralized


Domain annotation for each model (and alignments):
>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.2   1.2e-15   7.3e-12       2      76 .]       6      78 ..       5      78 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.2e-15
                                   SCEEEEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETSCEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                             CS  2 kydWyQtldeVvvtiyvkkvnikkkdvkvefkerslkvkigkeklliegeLfgpIdpeesswtieskkveitLkK 76
                                   ky+W+Q+l+e+++++++ + + ++++vk++   +++ +k+ +e+++++ge+++++d ++ +w i +++v+i ++K
  gene111|gene111|rna111|rna111  6 KYTWDQELNEINIRFPMAE-GADSNSVKISVVGKKVLMKM-QEEVIMDGEFLHEVDSSSLWWVIDGDSVDINITK 78
                                   8******************.9******************9.77999*************************9998 PP

>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.7e-05     0.099     132     168 ..      88     124 ..      70     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                        DUF3387 132 iaseevvdifaaaglekpdisiLseefleevkkmkek 168
                                    ++ +e vd+ ++a+ ++ dis+L+ e  e v+km ++
  gene111|gene111|rna111|rna111  88 LVGSESVDVQKLAEDKHADISMLDPEAREVVEKMMHN 124
                                    566899**************************99886 PP

>> Neuralized  Neuralized
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.046   2.8e+02     121     138 ..      51      68 ..       8      71 .. 0.71
   2 ?   10.0   0.0   0.00011      0.67      37      73 ..      68     107 ..      66     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.046
                     Neuralized 121 g.valsgvpdsqplwavvd 138
                                       +l +v ds++lw v+d
  gene111|gene111|rna111|rna111  51 DgEFLHEV-DSSSLWWVID 68 
                                    33688899.6668999998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                     Neuralized  37 igelfevriekledkwsgsLevGvtsvdPatl.ep..esl 73 
                                    +g+ + ++i+k+ ++w  sL vG  svd ++l e+  +++
  gene111|gene111|rna111|rna111  68 DGDSVDINITKKRNEWWDSLLVGSESVDVQKLaEDkhADI 107
                                    577899**************************42212233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 878.46
//
Query:       gene1111|gene1111|rna1110|rna1110  [L=651]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   70.9   0.0    2.3e-19   70.3   0.0    1.3  1  ABC_tran  ABC transporter
  ------ inclusion threshold ------
      0.011   15.5   0.7        3.3    7.4   0.0    2.4  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   2.5e-23   2.3e-19       3     137 .]      32     177 ..      30     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.5e-23
                                        EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpelt 75 
                                         +s ++  g+++a++G +G+ K+++l+ll+g+++    t+G i++dg++ k     ++ ++ ++l+q + + ++lt
  gene1111|gene1111|rna1110|rna1110  32 GISGEVVSGRLTAVMGGSGSSKTSFLNLLMGKVDSdalTSGIITFDGEQRKV---YKWIERTSYLEQFDIFTSGLT 104
                                        6889999***************************9999********988776...7888999************** PP

                                        HHHH...............HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                        xxxx...............xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  76 vren...............esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                        v+e+               +       ++++++ lgl+ l+ + v    ss+SgG+++rv+la  l+ +p++++lD
  gene1111|gene1111|rna1110|rna1110 105 VEESiryslifrgreikdsN---IpsmVDDIIKDLGLERLRGSLV----SSISGGERRRVMLAVELVIDPEVIFLD 173
                                        **********9999754433...1666******************....*************************** PP

                                        STTT CS
                                        xxxx RF
                           ABC_tran 134 Epta 137
                                        Ept+
  gene1111|gene1111|rna1110|rna1110 174 EPTS 177
                                        **96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1   0.00086       7.7       1      77 [.      42     116 ..      42     122 .. 0.95
   2 ?    7.4   0.0   0.00037       3.3     238     297 ..     150     207 ..     140     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00086
                             AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryrygl 76 
                                        l+++ G  gs K+++L +l  +  +d+d+  ++++  +g + +++ +  ++ + e+ + f+  +++++++ry+ ++
  gene1111|gene1111|rna1110|rna1110  42 LTAVMGGSGSSKTSFLNLL--MGKVDSDALTSGIITFDGEQRKVYKWIERTSYLEQFDIFTSGLTVEESIRYSLIF 115
                                        68999**************..7778************************************************999 PP

                             AAA_21  77 r 77 
                                        r
  gene1111|gene1111|rna1110|rna1110 116 R 116
                                        8 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00037
                             AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTH 297
                                        S G +r   l++ l  ++    ++++DEp +gL+ +l    +++l++ ++ + ++ ++t H
  gene1111|gene1111|rna1110|rna1110 150 SGGERRRVMLAVELVIDP---EVIFLDEPTSGLDSRLALDTVRILRRYAESKNKIvLMTVH 207
                                        555555555555556555...9************977755556663333334444366555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.55
# Mc/sec: 3583.82
//
Query:       gene1112|gene1112|rna1111|rna1111  [L=430]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-09   38.2  18.2    3.6e-06   27.0   3.2    2.8  3  zf-B_box    B-box zinc finger
     0.0082   16.5   0.2      0.019   15.3   0.2    1.6  1  Muted       Organelle biogenesis, Muted-like protein
  ------ inclusion threshold ------
      0.034   13.9   1.6      0.089   12.5   1.6    1.7  1  DUF4364     Domain of unknown function (DUF4364)
       0.58   10.4  12.5       0.81   10.0   2.5    2.6  2  IBR         IBR domain, a half RING-finger domain
        8.4    6.7  15.6        6.6    7.1   4.6    2.7  3  CEBP_ZZ     Cytoplasmic polyadenylation element-binding prote


Domain annotation for each model (and alignments):
>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   4.5e+03      11      20 ..      41      50 ..      40      50 .. 0.81
   2 !   18.2   4.7   5.7e-07     0.002       5      38 ..     158     191 ..     155     195 .. 0.93
   3 !   27.0   3.2     1e-09   3.6e-06       5      39 ..     210     250 ..     206     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                           zf-B_box 11 nkpatlfCed 20
                                       +k+++ fC++
  gene1112|gene1112|rna1111|rna1111 41 TKRIKAFCTE 50
                                       589999**85 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 5.7e-07
                           zf-B_box   5 kCpeHknkpatlfCedCqqplCeeCstgeHrgHe 38 
                                        +C+++  ++ t fC   ++ +C+eC+++ H+ H 
  gene1112|gene1112|rna1111|rna1111 158 ICDRCRISQSTSFCPAERASFCKECDEEVHNDHF 191
                                        7******************************995 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 1e-09
                           zf-B_box   5 kCpeHknkpatlfCedCqqplCeeC.stgeHr.....gHev 39 
                                        +C+ H +    +fCe+C  p+C +C  +g+H+      H++
  gene1112|gene1112|rna1111|rna1111 210 YCTSHMDTMVDYFCEECFIPVCTKCkISGNHSelpngSHNL 250
                                        7*******************************999855887 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   5.4e-06     0.019      76     137 ..     255     316 ..     222     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                              Muted  76 aalekverllqkeleeekrkseqlqekeeerkaeweeflkelqekkeevDeefeekveelke 137
                                        +a +k ++ll+  + +  +++++l+e+    k+++e f +++++ + +++ e+++ ++el++
  gene1112|gene1112|rna1111|rna1111 255 EACDKLQDLLKAGELRLVEEEKRLKENIGDFKKNVEVFQNNISDVRGKIESEYRNSMNELHA 316
                                        2334444444454445556788*************************************986 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.6   2.5e-05     0.089      28     120 ..     248     338 ..     245     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                            DUF4364  28 neytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfenripksirekideylkenkeelkkesevk 103
                                        ++++nY++ ++ l++L+++g ++  e e+k l +   + k+++e f+n+i++ +r ki++  ++ ++el+  ++ +
  gene1112|gene1112|rna1111|rna1111 248 HNLLNYVEACDKLQDLLKAGELRLVE-EEKRLKENIGDFKKNVEVFQNNISD-VRGKIESEYRNSMNELHAFEKRE 321
                                        799********************977.777888888889***********85.78888888888888877777777 PP

                            DUF4364 104 adyykkengeytVklki 120
                                        ++++++   +y ++l  
  gene1112|gene1112|rna1111|rna1111 322 FQVINTHYISYLIRLAE 338
                                        77777777777776665 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.5   0.00023      0.81      34      58 ..     166     188 ..     143     191 .. 0.78
   2 ?    5.1   2.6    0.0072        26      39      55 ..     221     237 ..     193     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                                IBR  34 egcksvtCskCgfefCfnCkkewHe 58 
                                        ++  ++ C+  + +fC +C +e H+
  gene1112|gene1112|rna1111|rna1111 166 QS--TSFCPAERASFCKECDEEVHN 188
                                        22..356*****************7 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0072
                                IBR  39 vtCskCgfefCfnCkke 55 
                                          C++C    C++Ck +
  gene1112|gene1112|rna1111|rna1111 221 YFCEECFIPVCTKCKIS 237
                                        46*************65 PP

>> CEBP_ZZ  Cytoplasmic polyadenylation element-binding protein ZZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.5   1.3e+04      25      37 ..      45      57 ..      40      57 .. 0.75
   2 ?    7.1   4.6    0.0018       6.6      13      55 ..     158     195 ..     154     201 .. 0.82
   3 ?    6.1   1.6    0.0036        13      24      56 ..     219     241 ..     204     252 .. 0.52

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.5
                            CEBP_ZZ 25 pyfCrdlaCfkYy 37
                                       + fC++    +Y+
  gene1112|gene1112|rna1111|rna1111 45 KAFCTEIGSTTYF 57
                                       5799998887776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0018
                            CEBP_ZZ  13 eCeiCekakargpyfCrdlaCfkYyCetCwqrrHsaeskeaaH 55 
                                         C+ C+  +  +  fC+  +    +C++C +++H+ +   ++H
  gene1112|gene1112|rna1111|rna1111 158 ICDRCRISQ--STSFCPAER--ASFCKECDEEVHNDHF-LKRH 195
                                        7******99..9****9887..469*********8874.4445 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0036
                            CEBP_ZZ  24 gpyfCrdlaCfkYyCetCwqrrHsaeskeaaHr 56 
                                          yfC+  +Cf   C++C            +H 
  gene1112|gene1112|rna1111|rna1111 219 VDYFCE--ECFIPVCTKCKIS--------GNHS 241
                                        445555..4555555555433........3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2390.95
//
Query:       gene1113|gene1113|rna1112|rna1112  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1219.27
//
Query:       gene1114|gene1114|rna1113|rna1113  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-13   49.1   1.0    3.9e-13   48.9   1.0    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   1.0   2.2e-17   3.9e-13       2      63 ..       8      68 ..       7      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 2.2e-17
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEE CS
                                LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnniv 63
                                        lkk + k+v++++ n+++++G+L++fD ++N +L+d   +++++ e++ +g+vli+G +i+
  gene1114|gene1114|rna1113|rna1113  8 ILKKNRSKNVRIITLNNKTYKGVLENFDMHVNTHLKDSYLRVDGE-EETYIGEVLINGGTIA 68
                                       599***************************************999.************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 487.34
//
Query:       gene1115|gene1115|rna1114|rna1114  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.11   12.8   0.1       0.24   11.7   0.1    1.6  1  zf-RING_2  Ring finger domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.4e-05      0.24      19      44 .]      97     124 ..      82     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                          zf-RING_2  19 l.pCgHvfhreClerwlrssst...CPlCr 44 
                                          pC +vf  eC ++    s     CP+C+
  gene1115|gene1115|rna1114|rna1114  97 NgPC-YVFEDECYKEVSSGS-GykrCPFCN 124
                                        3589.9*********54333.2479****5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1735.67
//
Query:       gene1116|gene1116|rna1115|rna1115  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-15   55.6   6.7    5.6e-15   55.5   6.7    1.0  1  Clat_adaptor_s  Clathrin adaptor complex small chain
  ------ inclusion threshold ------
      0.096   12.4   0.0       0.12   12.0   0.0    1.1  1  HAUS2           HAUS augmin-like complex subunit 2


Domain annotation for each model (and alignments):
>> Clat_adaptor_s  Clathrin adaptor complex small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   6.7   6.2e-19   5.6e-15      45     134 ..       6      93 ..       1      98 [] 0.91

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 6.2e-19
                                        SS-SEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCTS-SHHHHHHCHHHHHHHHHCCEET CS
                     Clat_adaptor_s  45 klsniveledlkviYkryasLYFvvivdeqeneliilelihlfvesLdkyfgnVceldlvfnfekvylildEivsg 120
                                        k  ni++ ++ ++++ ++ +L+  ++v e+ene+ +l+li+++v   d++f++Vcel  ++nf++ + ild  +  
  gene1116|gene1116|rna1115|rna1115   6 KERNIIDGNE-TIVFNKFGNLFIAFVV-ENENEMYVLSLINNLVSIYDRFFTKVCELHFIYNFKETHIILDNYIVN 79 
                                        4568999888.9*********888777.579********************************************* PP

                                        TEES---HHHHHHC CS
                     Clat_adaptor_s 121 Geiletskkevlkr 134
                                        G+ +e ++ ev+k+
  gene1116|gene1116|rna1115|rna1115  80 GKCIENDPFEVMKH 93 
                                        **********9987 PP

>> HAUS2  HAUS augmin-like complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.4e-05      0.12     116     163 ..      29      76 ..      26      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                              HAUS2 116 lpveaeYhrqvselLekaasdlealeahledlqWsesvkeppslldev 163
                                         +ve e + +v  l+++++s ++++ +++ +l++  ++ke+  +ld+ 
  gene1116|gene1116|rna1115|rna1115  29 FVVENENEMYVLSLINNLVSIYDRFFTKVCELHFIYNFKETHIILDNY 76 
                                        589999999*********************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 623.44
//
Query:       gene1117|gene1117|rna1116|rna1116  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-14   53.8   6.0    7.4e-09   35.9   0.6    2.5  2  EF-hand_7  EF-hand domain pair
    7.9e-12   44.1   0.7     0.0045   16.8   0.0    3.7  3  EF-hand_6  EF-hand domain
    3.7e-09   35.5   0.9      0.072   12.7   0.1    4.1  3  EF-hand_1  EF hand
    1.9e-06   27.6   2.4       0.11   12.4   0.0    3.5  3  EF-hand_8  EF-hand domain pair
     0.0063   16.0   4.0     0.0078   15.7   0.1    3.2  4  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.6   2.1e-12   7.4e-09       2      61 ..      29     116 ..      28     122 .. 0.84
   2 !   27.5   0.5   9.2e-10   3.3e-06       2      71 .]      99     162 ..      98     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 2.1e-12
                          EF-hand_7   2 eklkeaFkelDtdgdgyldkeellr............llrkifqga.................gegsklsdeelel 48 
                                        e l+e+F+ lD+  +gyl+++el +            ++++i  ++                 +e+ +  ++ +++
  gene1117|gene1117|rna1116|rna1116  29 EHLYERFQFLDRESRGYLTYNELNNipefqsnpfshlIMKSIEKMTdyekmtfphfleflgifSEKAS-KKKRVRY 103
                                        789*********************99999888888875555555558889999999999998755555.5567*** PP

                          EF-hand_7  49 lfkefDtdkdGvi 61 
                                        lf+ fD+++dG++
  gene1117|gene1117|rna1116|rna1116 104 LFDIFDLNGDGRL 116
                                        ***********98 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 9.2e-10
                          EF-hand_7   2 eklkeaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisfdEFlklyr 71 
                                        +++++ F+ +D +gdg+l+++ l r+ +        g +   ee+e l++  D  + G+++ ++F k+y+
  gene1117|gene1117|rna1116|rna1116  99 KRVRYLFDIFDLNGDGRLCRNVLIRVNK------MMGQDGKMEEVENLLNIYDEGGKGYLDISDFTKFYE 162
                                        67899*****************887777......6677777889************************95 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   7.6e-05      0.27       2      25 ..      31      54 ..      30      56 .. 0.91
   2 !   16.8   0.0   1.3e-06    0.0045       2      24 ..     101     123 ..     100     129 .. 0.84
   3 !   12.3   0.1   3.6e-05      0.13       4      27 ..     139     162 ..     136     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                          EF-hand_6  2 lreaFklfDkdgdGkidaeElrka 25
                                       l+e F+ +D++  G+++++El ++
  gene1117|gene1117|rna1116|rna1116 31 LYERFQFLDRESRGYLTYNELNNI 54
                                       7899*****************876 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.3e-06
                          EF-hand_6   2 lreaFklfDkdgdGkidaeElrk 24 
                                        +r++F++fD +gdG + ++ l++
  gene1117|gene1117|rna1116|rna1116 101 VRYLFDIFDLNGDGRLCRNVLIR 123
                                        79*************99887766 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.6e-05
                          EF-hand_6   4 eaFklfDkdgdGkidaeElrkalr 27 
                                         + +++D  g G++d++++ k++ 
  gene1117|gene1117|rna1116|rna1116 139 NLLNIYDEGGKGYLDISDFTKFYE 162
                                        56789**************99986 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00051       1.8       3      23 ..      32      52 ..      30      55 .. 0.88
   2 !   12.7   0.1     2e-05     0.072       2      18 ..     101     117 ..     100     119 .. 0.86
   3 !   10.3   0.2   0.00011      0.41       1      25 [.     136     160 ..     136     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00051
                                       HHHHHHHTTTSSSEEEHHHHH CS
                          EF-hand_1  3 keiFrefDkDgdGkIdfeEfk 23
                                        e F+ +D+   G+++++E+ 
  gene1117|gene1117|rna1116|rna1116 32 YERFQFLDRESRGYLTYNELN 52
                                       678****************96 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2e-05
                                        HHHHHHHHTTTSSSEEE CS
                          EF-hand_1   2 lkeiFrefDkDgdGkId 18 
                                        ++ +F++fD +gdG++ 
  gene1117|gene1117|rna1116|rna1116 101 VRYLFDIFDLNGDGRLC 117
                                        6789**********985 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00011
                                        HHHHHHHHHTTTSSSEEEHHHHHHH CS
                          EF-hand_1   1 elkeiFrefDkDgdGkIdfeEfkel 25 
                                        e++++ +++D  g G++d+++f ++
  gene1117|gene1117|rna1116|rna1116 136 EVENLLNIYDEGGKGYLDISDFTKF 160
                                        688999****************987 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.013        47      32      47 ..      35      50 ..      15      52 .. 0.85
   2 !   12.4   0.0     3e-05      0.11      20      43 ..      94     116 ..      75     119 .. 0.77
   3 !    9.5   0.2   0.00024      0.85      22      52 ..     131     161 ..     121     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.013
                          EF-hand_8 32 frefDtdgdGkisfeE 47
                                       f  +D++  G+++++E
  gene1117|gene1117|rna1116|rna1116 35 FQFLDRESRGYLTYNE 50
                                       8899***********9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3e-05
                          EF-hand_8  20 kkglseee.vdilfrefDtdgdGki 43 
                                        k   s+++ v+ lf+ fD++gdG++
  gene1117|gene1117|rna1116|rna1116  94 K--ASKKKrVRYLFDIFDLNGDGRL 116
                                        4..677777**************87 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00024
                          EF-hand_8  22 glseeevdilfrefDtdgdGkisfeEFcvll 52 
                                        +   eev+ l++  D+ g+G+++  +F  ++
  gene1117|gene1117|rna1116|rna1116 131 DGKMEEVENLLNIYDEGGKGYLDISDFTKFY 161
                                        37779*********************97766 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.4   5.1e+03      18      23 ..      14      19 ..      13      20 .. 0.78
   2 ?   -1.9   0.0      0.77   2.8e+03      14      21 ..      44      51 ..      33      54 .. 0.54
   3 !   15.7   0.1   2.2e-06    0.0078       4      18 ..     104     118 ..     101     119 .. 0.89
   4 ?   -1.0   0.0      0.42   1.5e+03      12      24 ..     148     160 ..     139     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.4
                                       HHHHHH CS
                          EF-hand_5 18 keELkt 23
                                       +eELk+
  gene1117|gene1117|rna1116|rna1116 14 IEELKN 19
                                       69*996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.77
                                       SCE-HHHH CS
                          EF-hand_5 14 GkIskeEL 21
                                       G+++  EL
  gene1117|gene1117|rna1116|rna1116 44 GYLTYNEL 51
                                       55666666 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.2e-06
                                        HHHHH-SS-SSCE-H CS
                          EF-hand_5   4 tFqaiDlNgDGkIsk 18 
                                        +F+ +DlNgDG++ +
  gene1117|gene1117|rna1116|rna1116 104 LFDIFDLNGDGRLCR 118
                                        6***********976 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.42
                                        -SSCE-HHHHHHH CS
                          EF-hand_5  12 gDGkIskeELktl 24 
                                        g G+++++ + ++
  gene1117|gene1117|rna1116|rna1116 148 GKGYLDISDFTKF 160
                                        67999*9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1211.04
//
Query:       gene1118|gene1118|rna1117|rna1117  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2818.99
//
Query:       gene1119|gene1119|rna1118|rna1118  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-21   76.0   0.0    3.1e-21   75.7   0.0    1.1  1  DUF1749        Protein of unknown function (DUF1749)
    0.00057   19.8   0.0    0.00091   19.1   0.0    1.3  1  Ser_hydrolase  Serine hydrolase
     0.0011   19.6   0.0     0.0022   18.6   0.0    1.4  1  Abhydrolase_6  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> DUF1749  Protein of unknown function (DUF1749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0   5.3e-25   3.1e-21      17     247 ..      19     223 ..       1     243 [. 0.81

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 5.3e-25
                            DUF1749  17 lvafeyetsgelkskallFigGLgdGlltvpyvkelanaldeagwsvvelqlsssyggwGtgsLkrDaeeieklve 92 
                                        l+a+  + ++      ++++gGLg  l     +  l +   e g++++ ++l  sy  +G  +++ D+e+++ l++
  gene1119|gene1119|rna1118|rna1118  19 LIAYSNQVKS---DTKIIYVGGLGSRLPICLPTTMLNEHCFENGYELIIPELR-SYPNYGLFTIDDDVEDLSCLLH 90 
                                        3444333333...3559*********98888899999999***********98.5*****************9988 PP

                            DUF1749  93 YlkktksGeekkekvvlmGHstGsqdvlyYltssnerdrekvdgailqapvsDReailkvleerkklkelvalakk 168
                                         l+ +         +vl+G stG+qd+++Yl  +++   ++++ a+l ++vsD e+  +   ++k l e++ +ak+
  gene1119|gene1119|rna1118|rna1118  91 QLRGN---------IVLIGNSTGCQDIIHYLNTTRD---KRIKLAVLLGAVSDVEFEEH---KNKDLPETLRWAKE 151
                                        77766.........*****************99976...89**************9988...3467********** PP

                            DUF1749 169 lvdkgkaeeilprelaekvgletpvsarRflsLasvdgdDDfFssDlsdeklektfGkvkepllillsekDefvpe 244
                                        +  +++ e++     ++ +g ++ ++ rR+l++ s  g +D+Fss l d ++     +  + ll+++s+kDe+   
  gene1119|gene1119|rna1118|rna1118 152 M--TDRKEDVA----IKYCGTDSYLTPRRILDIFSRYGKEDMFSSYLED-RFYMELNRGDTRLLFVVSGKDEYSIR 220
                                        *..55566663....345556778999*******************986.566666777789**********9765 PP

                            DUF1749 245 svd 247
                                         ++
  gene1119|gene1119|rna1118|rna1118 221 DIE 223
                                        553 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-07   0.00091      40     100 ..      79     140 ..      73     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-07
                                        HHHHHHHHHHHHC-STTEEEEEETCHHHHHHHHHHHTTSSSEE.EEEEET--SGGS..TT.G CS
                      Ser_hydrolase  40 edWvaaleaaveaaeekvvlvAHSlgclavlhaaelqlakkva.galLVapadveeeaakla 100
                                        +d v+ l+  ++++++++vl+  S gc  ++h+++ ++ k+++ ++lL a+ dve e++k++
  gene1119|gene1119|rna1118|rna1118  79 DDDVEDLSCLLHQLRGNIVLIGNSTGCQDIIHYLNTTRDKRIKlAVLLGAVSDVEFEEHKNK 140
                                        6668899999*************************999999*93456678899984444433 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.7e-07    0.0022      27     208 ..      60     243 ..      47     252 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.7e-07
                                        CEEEEE--TTSTS-GGCS--HHH.CHHHHHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC....EE....EEES- CS
                      Abhydrolase_6  27 vhvlapDlpGhGrsdpppldled.ladlaalldelaagggpvvlvGHSlGGalalaaapla..lvvg....vlldp 95 
                                        ++ ++p l+++  +    ++ +d ++dl+ ll+ l   +g++vl+G+S G+    +++  +     +    vll +
  gene1119|gene1119|rna1118|rna1118  60 YELIIPELRSY--PNYGLFTIDDdVEDLSCLLHQL---RGNIVLIGNSTGCQDIIHYLNTTrdK--RiklaVLLGA 128
                                        55578999988..67777888887899999*****...7*****************55555663..3336799999 PP

                                        ..----TTT...S----TTHHHHHHTT-C............CCCHCCHS-HSCCCCHHHCCCCHCHCCCGHHHHCC CS
                      Abhydrolase_6  96 pptalpagl...laaalelllallallrl............lawlsreplprlfladedadaawrarlarlaalla 156
                                           + +  +    +  l+  l++ +  ++            + +l+               ++  + ++r  + ++
  gene1119|gene1119|rna1118|rna1118 129 ---VSDVEFeehKNKDLPETLRWAKEMTDrkedvaikycgtDSYLT--------------PRRILDIFSRYGKEDM 187
                                        ...3333333443333333333333222211111111222222221..............2444444444443333 PP

                                        ...HHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH.STTEEETCE...SSS- CS
                      Abhydrolase_6 157 ...glgllpaaawadlpvpllvl.ggeDplvprllerlla.qagarlpvvlpgaGHl 208
                                           +l+ + + ++ +  ++ll +  g+D+   r +e+ l+ ++  r+ + +p + H+
  gene1119|gene1119|rna1118|rna1118 188 fssYLEDRFYMELNRGDTRLLFVvSGKDEYSIRDIEAKLRlVRNSRV-EKIPEGTHV 243
                                        21122233355666666666433378888666677777778788888.888888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1607.11
//
Query:       gene1120|gene1120|rna1119|rna1119  [L=418]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-18   67.8  15.0    3.5e-12   46.7   5.3    2.3  2  POP1      Ribonucleases P/MRP protein subunit POP1
    1.7e-12   47.5   0.0    4.3e-12   46.2   0.0    1.6  1  POPLD     POPLD (NUC188) domain


Domain annotation for each model (and alignments):
>> POP1  Ribonucleases P/MRP protein subunit POP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   8.6   3.1e-09   2.8e-05       1      55 [.      11      62 ..      11      66 .. 0.82
   2 !   46.7   5.3     4e-16   3.5e-12     135     201 ..      55     120 ..      51     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.1e-09
                               POP1  1 FvksrefEIkaleealkkskkasstraFQslPrklRRRtaSHnvkRvPkrlrara 55
                                       Fv+ r++EI+ +e+a+++++k+  + +FQ+lP  lRRR  SH+ kR+ ++   r 
  gene1120|gene1120|rna1119|rna1119 11 FVEERAKEIQFIETAIESNRKK--SMMFQRLPFYLRRRLRSHE-KRIKRKKHMRK 62
                                       8999*************99665..569***************8.67766654443 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 4e-16
                               POP1 135 kikylkrqkektWLpTHvwhaKRakmikrwgfaiplsptqKcyrlthRaaksrgavawDtSYmstie 201
                                        k+k + r+k+   L THvw+aKR++m k w+++ipl++  K+ ++++++++srg+v  D+SY +++ 
  gene1120|gene1120|rna1119|rna1119  55 KRKKHMRKKDRHGLRTHVWYAKRFEMLKVWNTSIPLRRRMKSSKFIYKSQNSRGFVF-DESYKDVVV 120
                                        5566667788899***********************************888888775.****98765 PP

>> POPLD  POPLD (NUC188) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   4.8e-16   4.3e-12       4      79 ..     240     315 ..     237     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 4.8e-16
                              POPLD   4 lilPwgwglpfwlsLvrvgvrvgGlrerrqlalesgkpyfPddypdtkagekeekeeeeeaeekwerkPpskRvny 79 
                                        ++l +++++++w+ ++  g+ +++++e ++lale+  + +P+dyp ++ +++ e  + e  ++k+er+P+sk+++ 
  gene1120|gene1120|rna1119|rna1119 240 ILLKRNMVMNLWQDIINAGIVPVCVEELQRLALENDYMVYPFDYPTSRLYRDFERSHVEPIKRKYERTPKSKKMEL 315
                                        8999*********************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2569.18
//
Query:       gene112|gene112|rna112|rna112  [L=971]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-33  114.0   9.0    1.1e-08   35.5   0.1    7.0  6  WD40           WD domain, G-beta repeat
    9.3e-30  104.0   0.0    2.1e-29  102.8   0.0    1.5  1  Coatomer_WDAD  Coatomer WD associated region
    1.2e-11   44.0   0.0    2.2e-11   43.2   0.0    1.3  1  COPI_C         Coatomer (COPI) alpha subunit C-terminus
    2.3e-06   27.8   0.0       0.13   12.6   0.0    4.2  4  ANAPC4_WD40    Anaphase-promoting complex subunit 4 WD40 doma


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     7e-06     0.031      12      38 .]      16      42 ..       8      42 .. 0.91
   2 !   31.1   0.5   6.5e-11   2.9e-07       1      38 []      46      84 ..      46      84 .. 0.94
   3 !   35.5   0.1   2.6e-12   1.1e-08       5      38 .]      92     126 ..      88     126 .. 0.92
   4 !   15.5   0.0   5.5e-06     0.025       2      38 .]     131     167 ..     130     167 .. 0.83
   5 !   11.8   0.2   7.7e-05      0.35       6      37 ..     189     219 ..     185     220 .. 0.75
   6 ?    3.7   0.0     0.029   1.3e+02      10      38 .]     235     262 ..     228     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7e-06
                                   SEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40 12 svtslafspdgawlasGsdDgtvriWd 38
                                    v sl+f+p+++ ++sG+  g++r Wd
  gene112|gene112|rna112|rna112 16 RVKSLSFHPNKPVVISGHHSGSIRAWD 42
                                   489**************99*******9 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 6.5e-11
                                   TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38
                                   g c++++  H +sv+++ f+p g++++sG+dD+ +r+W+
  gene112|gene112|rna112|rna112 46 GVCIHEFLDHdGSVRAVLFHPRGDFFVSGGDDKIIRVWS 84
                                   579*******888*************************5 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 2.6e-12
                                    EEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                     +l+GH ++v+sl+f+p ++w++s+sdD+t+++W+
  gene112|gene112|rna112|rna112  92 NKLKGHeDFVRSLDFHPTKPWILSASDDQTIMVWN 126
                                    5799**888*************************8 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 5.5e-06
                                    EEEEEEESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                    ++l t +GH++ v + +f  + + + sGs D+++riWd
  gene112|gene112|rna112|rna112 131 KLLATARGHCHyVMAARFLGEESIV-SGSLDQSIRIWD 167
                                    6788889**667****888887775.8**********9 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 7.7e-05
                                    EEESS.SSEEEEEEETTSSE....EEEEETTSEEEEE CS
                           WD40   6 tltGH.ssvtslafspdgaw....lasGsdDgtvriW 37 
                                    + +GH  +++s+      a     ++sG+dD+ ++ W
  gene112|gene112|rna112|rna112 189 IVDGHdRGINSI------AVkdeiFVSGGDDRDIKCW 219
                                    678**6559999......333333689********** PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.029
                                    S.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  10 H.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    H ++vt+l    d ++++s+++Dg   i++
  gene112|gene112|rna112|rna112 235 HqGPVTGL--LCDRKYILSSGEDGLFSIYN 262
                                    87779999..888999999999**999987 PP

>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.0   4.8e-33   2.1e-29     175     410 ..     473     681 ..     440     690 .. 0.88

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 4.8e-33
                                    X.............XXXXXXX.XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX CS
                  Coatomer_WDAD 175 eaveeedeeegvedafevlhelsesiksgaWvgdvfiYttsnnrlkylvngevgiikhldktlyilgykgkenklylldk 254
                                    +              +++++e  +s+ +g + +d+fiY t + +lky    ++g++k+++k++     +g  +++y l  
  gene112|gene112|rna112|rna112 473 N-------------PVNSVNE-IVSVVDGFFCEDIFIYATYR-HLKYAF-EDSGVLKSVEKPIVPFALEG-GKTVYFLSD 535
                                    4.............6889999.899*****************.****54.689****************9.666666654 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXX-GGGSS-HHHHHHHHHHTT CS
                  Coatomer_WDAD 255 dgnvvsleidlselefktavlrkdleevlkiiaasnllpeipkeegqkiirfLekkgypelAlqlvqDpetkFdLAlelg 334
                                    d  ++   +d +e++fk+avl +   +v ++i++  +        g +  ++L k+    lAl  ++D +++F+L l+  
  gene112|gene112|rna112|rna112 536 D-GIECTDVDFTEIRFKKAVLTGG--DVTSLIEEGMMP-------GLAPLSYLVKQKKGALALPYIKDGKQRFELCLSDM 605
                                    4.3677789************997..566899966666.......*********************************** PP

                                    -HHHHHHHHHHH--HHHHHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHHHT-HHHHHHHHHHHHHTT-HHHH CS
                  Coatomer_WDAD 335 nLelAlelakelddeekWkkLgdaAlsqgniklaeeayqkakdfdkLllLylstgnkekLkkLakiaekkgdynia 410
                                    +L++++e + ++ d ++ ++L+daA++++++++ae++++ +k+++ L++Ly++++n ek+k+L++++ +  + +i+
  gene112|gene112|rna112|rna112 606 RLDECMEYCMQEGDADMNRRLADAAIRECRVDIAEKCLESIKEWNMLFMLYVCSKNDEKVKRLVDKVDSVTKNMIM 681
                                    *****************************************************************99988888775 PP

>> COPI_C  Coatomer (COPI) alpha subunit C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0     5e-15   2.2e-11     187     317 ..     789     915 ..     746     928 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 5e-15
                                    HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHGGG----SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-SSHHHHHHHHH CS
                         COPI_C 187 leerLkaaYklttegkfseavekfrsillsipllvvdskqevdevkeLieicreYivgLrmEikRkelkksddqkrqaEl 266
                                    l   + ++  lttegkf  a+e fr+ + +i+  +  ++   + v+e  +i   Y+ gL +E  R++++    + ++  +
  gene112|gene112|rna112|rna112 789 LGRIIEKGLSLTTEGKFGKAIEAFRAGIVKIATYICGNNAGEAFVEERRKIG-SYLSGLGVERIRRKTE---SPLKNIMM 864
                                    5556678889****************99999999999999989999999986.7***********9887...899***** PP

                                    HHHHHHS---HHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHH---HHHH CS
                         COPI_C 267 aAYfthcnlqpvHliLaLrsAlnlffKlknfktaasfarrLLelgpkeeva 317
                                    a Yf+   l++ H iLa  +A+ +f K  n+k a+++a  L   g +++v 
  gene112|gene112|rna112|rna112 865 AKYFSELPLEKEHHILASSTAIMVFRKNGNLKQAKELALLLKKEGGNSKVI 915
                                    *************************************98776666666665 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   2.8e-05      0.13      35      76 ..      11      52 ..       3      57 .. 0.90
   2 !    9.2   0.0   0.00032       1.4      37      89 ..      55     106 ..      52     109 .. 0.90
   3 ?    2.5   0.0      0.04   1.8e+02      38      76 ..      98     136 ..      95     146 .. 0.87
   4 ?   -1.7   0.0       0.8   3.6e+03      49      74 ..     245     270 ..     211     281 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                    ANAPC4_WD40 35 dkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76
                                   +ke s+v+sL+++p+  +   +++ g++r  d + g ++h++
  gene112|gene112|rna112|rna112 11 EKETSRVKSLSFHPNKPVVISGHHSGSIRAWDYQMGVCIHEF 52
                                   67999***********************************97 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00032
                    ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                    +d++vr++ ++p g +++ + +d  +r+ +  + ++ ++l+ +++  v +l++
  gene112|gene112|rna112|rna112  55 HDGSVRAVLFHPRGDFFVSGGDDKIIRVWSYTERRITNKLKGHED-FVRSLDF 106
                                    7899**********************************9999888.4777765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.04
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76 
                                    +  vrsL ++p    +  a +d ++ + ++ +gk++ + 
  gene112|gene112|rna112|rna112  98 EDFVRSLDFHPTKPWILSASDDQTIMVWNMLTGKLLATA 136
                                    5669******************************99876 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.8
                    ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvh 74 
                                    d k +  + +dg  ++++ es k ++
  gene112|gene112|rna112|rna112 245 DRKYILSSGEDGLFSIYNTESRKSIE 270
                                    55667777777877777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (971 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.50
# Mc/sec: 5877.23
//
Query:       gene1121|gene1121|rna1120|rna1120  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1515.29
//
Query:       gene1122|gene1122|rna1121|rna1121  [L=952]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-08   34.8   1.2      0.014   15.6   0.2    4.8  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    3.8e-05   22.2   0.0    6.5e-05   21.4   0.0    1.3  1  Frtz         WD repeat-containing and planar cell polarity ef
     0.0094   16.8   7.4        3.4    8.7   0.1    4.3  4  WD40         WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.087   12.7   0.0       0.51   10.3   0.0    2.3  2  BBS2_N       Ciliary BBSome complex subunit 2, N-terminal


Domain annotation for each model (and alignments):
>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0012       5.6      36      66 ..      52      84 ..      42      93 .. 0.81
   2 !   11.8   0.0   5.1e-05      0.23      38      91 ..     103     156 ..      93     157 .. 0.87
   3 !   15.6   0.2   3.2e-06     0.014      10      78 ..     118     187 ..     110     201 .. 0.67
   4 ?    0.9   0.0      0.13   5.8e+02      27      52 ..     179     204 ..     166     227 .. 0.60
   5 ?    3.5   0.0      0.02        90      55      79 ..     247     271 ..     236     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                        ANAPC4_WD40 36 kedsevrsLaWkp..dgklLavaysdgevrlld 66
                                       ++d++  +L+W +  dg++La + +dg+v l+ 
  gene1122|gene1122|rna1121|rna1121 52 QTDNKFYKLKWCNwgDGEILATGNEDGKVTLYT 84
                                       56788889999754499*************986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.1e-05
                        ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWge 91 
                                        ++ v +L ++ +  +La + s+g++ + + ++ +   ++++  ++++tcl+W++
  gene1122|gene1122|rna1121|rna1121 103 EGDVLGLDFNASKGVLAAGSSNGKIIFWNLNKLDSQYTSDIPLTSNITCLSWNK 156
                                        578999**********************999988777777777777******86 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 3.2e-06
                        ANAPC4_WD40  10 iAlatedgellvfRlngqrvwtleedkedsevrsLaWkpd.gklLavaysdgevrlldaesgkvvhslsv 78 
                                        +A ++++g+++   ln      +++    s++++L+W+++  ++L+ +++dg++ +lda  ++v  +l  
  gene1122|gene1122|rna1121|rna1121 118 LAAGSSNGKIIFWNLNKLDSQYTSDIPLTSNITCLSWNKKvSRILCAGTDDGKILILDARAKNVAMTLGG 187
                                        5555555555544444322222234467899******876489*****************9999887755 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.13
                        ANAPC4_WD40  27 qrvwtleedkedsevrsLaWkpdgkl 52 
                                        ++v  +   +   +v++++W+p+g+ 
  gene1122|gene1122|rna1121|rna1121 179 KNVAMTLGGDGIVSVSDVMWHPNGST 204
                                        44544444555567889999999964 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.02
                        ANAPC4_WD40  55 vaysdgevrlldaesgkvvhslsvk 79 
                                         a s++++ ++++ +gk+v +++v+
  gene1122|gene1122|rna1121|rna1121 247 AASSKNQIDIIEVGDGKIVDTIPVD 271
                                        57899**************999875 PP

>> Frtz  WD repeat-containing and planar cell polarity effector protein Fritz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.4e-08   6.5e-05     246     329 ..     133     221 ..     121     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-08
                               Frtz 246 nklqrvavtsiPlraqvislafnpdedkLl.lGceDssviLydeerkitklv...kaevvPsliswhpdsai.llv 316
                                        nkl       iPl +++ +l+ n++  ++l  G+ D+++++ d+  k   ++      v  s + whp+++  +l 
  gene1122|gene1122|rna1121|rna1121 133 NKLDSQYTSDIPLTSNITCLSWNKKVSRILcAGTDDGKILILDARAKNVAMTlggDGIVSVSDVMWHPNGSTsILA 208
                                        7888888899*************99888652799*********98886666644366788899*****98652777 PP

                               Frtz 317 asergelqifDla 329
                                        a + g lq+f+l+
  gene1122|gene1122|rna1121|rna1121 209 ATNLGGLQCFNLS 221
                                        8899******986 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.24   1.1e+03      21      36 ..      67      82 ..      60      84 .. 0.84
   2 !    8.7   0.1   0.00076       3.4      12      38 .]     105     131 ..      96     131 .. 0.88
   3 !    7.8   0.1    0.0015       6.5      12      36 ..     148     173 ..     137     175 .. 0.72
   4 ?   -0.3   0.1      0.54   2.4e+03      12      24 ..     192     204 ..     181     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.24
                                       TSSEEEEEETTSEEEE CS
                               WD40 21 dgawlasGsdDgtvri 36
                                       dg  la+G +Dg+v +
  gene1122|gene1122|rna1121|rna1121 67 DGEILATGNEDGKVTL 82
                                       7888****99**9976 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00076
                                        SEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  12 svtslafspdgawlasGsdDgtvriWd 38 
                                        +v +l+f+ ++  la+Gs +g++ +W+
  gene1122|gene1122|rna1121|rna1121 105 DVLGLDFNASKGVLAAGSSNGKIIFWN 131
                                        489999***********99*******8 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0015
                                        SEEEEEEETTSSE.......EEEEETTSEEEE CS
                               WD40  12 svtslafspdgaw.......lasGsdDgtvri 36 
                                        ++t+l+      w       l++G+dDg++ i
  gene1122|gene1122|rna1121|rna1121 148 NITCLS------WnkkvsriLCAGTDDGKILI 173
                                        39***5......44444555568899***987 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.54
                                        SEEEEEEETTSSE CS
                               WD40  12 svtslafspdgaw 24 
                                        sv+++ ++p+g+ 
  gene1122|gene1122|rna1121|rna1121 192 SVSDVMWHPNGST 204
                                        2555559999987 PP

>> BBS2_N  Ciliary BBSome complex subunit 2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.65   2.9e+03      11      31 ..      70      90 ..      66      98 .. 0.80
   2 ?   10.3   0.0   0.00011      0.51       5      62 ..     111     166 ..     107     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.65
                             BBS2_N 11 claaattagkvlihnphekeq 31
                                        la + + gkv +++p  +++
  gene1122|gene1122|rna1121|rna1121 70 ILATGNEDGKVTLYTPAPEKN 90
                                       58999999*******977664 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                             BBS2_N   5 fdgshpclaaattagkvlihnphekeqklkserlsas..esevslLninkevtalaagkl 62 
                                        f+ s+  laa+++ gk++ +n ++ +++ +s   +    +s+++ L+ nk+v+ + ++  
  gene1122|gene1122|rna1121|rna1121 111 FNASKGVLAAGSSNGKIIFWNLNKLDSQYTS---D-IplTSNITCLSWNKKVSRILCAGT 166
                                        899999***************8655433332...2.2579*************9988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (952 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.32s 00:00:01.13 Elapsed: 00:00:00.54
# Mc/sec: 5344.12
//
Query:       gene1124|gene1124|rna1123|rna1123  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-65  221.6   0.0    1.4e-65  221.3   0.0    1.0  1  Pkinase         Protein kinase domain
    3.4e-40  138.0   0.0    4.3e-40  137.6   0.0    1.0  1  Pkinase_Tyr     Protein tyrosine kinase
    7.4e-08   32.0   0.0    6.7e-06   25.6   0.0    2.3  2  Kinase-like     Kinase-like
    4.1e-05   22.7   0.0      0.015   14.3   0.0    2.1  2  Haspin_kinase   Haspin like kinase domain
    6.3e-05   22.6   0.1    0.00011   21.9   0.1    1.3  1  RIO1            RIO1 family
     0.0028   17.0   0.1     0.0088   15.4   0.0    1.8  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0035   17.3   0.0      0.024   14.6   0.0    1.9  2  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.062   12.9   0.2       0.13   11.8   0.1    1.5  1  Choline_kinase  Choline/ethanolamine kinase
      0.077   13.3   0.1       0.26   11.6   0.0    1.9  2  FOP_dimer       FOP N terminal dimerisation domain
      0.099   11.4   0.2       0.17   10.6   0.0    1.4  2  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.3   0.0   7.5e-69   1.4e-65       4     259 ..       7     255 ..       4     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 221.3 bits;  conditional E-value: 7.5e-69
                                        EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                            Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                           +G+G++G+Vy+a+++et+++vA+K+ik ++++ +   ++lrEi+ilkkl+h+ni+ l++++++++ l++v+ +
  gene1124|gene1124|rna1123|rna1123   7 GGVIGSGTYGEVYEAIDTETKEKVALKRIKLNEKEGM-PGTALREISILKKLNHRNIISLVSTIHTDTLLTMVFPF 81 
                                        578****************************987765.57************************************ PP

                                        -TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS.B CS
                            Pkinase  80 veggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk.l 154
                                        ++  el++++e   + + +++ ++++q++ g++ylH+++++HrDlKp+NiL+ ++g+lKi+DFGl++ le + + +
  gene1124|gene1124|rna1123|rna1123  82 IDY-ELKKYIE---MNTGRNIMELINQLICGVHYLHRMNVVHRDLKPQNILVTSDGVLKIADFGLSRSLEIRVPpY 153
                                        **5.5*****8...47889999************************************************99988* PP

                                        CTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HH CS
                            Pkinase 155 tsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpe 229
                                        +s+v+t +Y++PE+l ++++y   vD+WslG+i+ye++t +p+f+ge+++++ + + ++   +++     k+ +++
  gene1124|gene1124|rna1123|rna1123 154 SSEVVTLWYRSPELLmGSTSYRFYVDIWSLGCIIYEMITLEPLFPGESKENQLTLIRRK-AGTRR---SLKNVVEQ 225
                                        ***************999***************************88888866666666.33333...33445556 PP

                                        HTTS-HHHHHHHHHHT-SSGCCSTTHHHHH CS
                            Pkinase 230 aseiseeakdllkkllkkdpkkRltaeell 259
                                            ++ +++++ ++l+ + ++R+ta+e++
  gene1124|gene1124|rna1123|rna1123 226 SLAAPKFLIEIILRCLDLNYNQRITADEII 255
                                        66669999******************9985 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6   0.0   2.4e-43   4.3e-40       5     257 ..       8     256 ..       5     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 2.4e-43
                                        EEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEE CS
                        Pkinase_Tyr   5 kklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivt 80 
                                          +G+G++G+V+e+  +    ++++kVa+K +k + +e      l+e++i+kkl+h+ni++l+  +  +  l +v+
  gene1124|gene1124|rna1123|rna1123   8 GVIGSGTYGEVYEAIDT----ETKEKVALKRIKLNEKEGMPGTALREISILKKLNHRNIISLVSTIHTDTLLTMVF 79 
                                        679***********999....999**************99************************************ PP

                                        E--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTS CS
                        Pkinase_Tyr  81 eyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekd 156
                                         ++++ +L+k+++ +     t +++++++ q+ +G++yL+++++vHrdl  +N+L++++ v ki+DfGL+r++  +
  gene1124|gene1124|rna1123|rna1123  80 PFIDY-ELKKYIEMN-----TGRNIMELINQLICGVHYLHRMNVVHRDLKPQNILVTSDGVLKIADFGLSRSL--E 147
                                        ****9.8*******9.....8889999**********************************************..4 PP

                                        SEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH..HTTEE...... CS
                        Pkinase_Tyr 157 deyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypglkneevlekl..kegkr...... 223
                                         +    +++ + + + +pE l+ ++ +    D+Ws G +++E++tl e  +pg ++e+ l+ +  k+g+r      
  gene1124|gene1124|rna1123|rna1123 148 IRVPPYSSEVVTLWYRSPELLMGSTsYRFYVDIWSLGCIIYEMITL-EPLFPGESKENQLTLIrrKAGTRrslknv 222
                                        5555556667777778****998766*******************5.44455555555455443255555444444 PP

                                        S-BBTTSBHHHHHHHHHHT-SSGGGS--HHHHHH CS
                        Pkinase_Tyr 224 lekpekcpeelyelmkkcweedpeeRptfselve 257
                                        +e+   +p+ l e++ +c++ + ++R t  e++ 
  gene1124|gene1124|rna1123|rna1123 223 VEQSLAAPKFLIEIILRCLDLNYNQRITADEIIG 256
                                        7888899999******************999976 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.014        26      14      50 ..       4      40 ..       2      49 .. 0.89
   2 !   25.6   0.0   3.8e-09   6.7e-06     150     246 ..     102     193 ..      60     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.014
                        Kinase-like 14 lvrgellkkgdrsvvfevkdqetgeplavkvfllpse 50
                                       ++ g +++ g  + v+e+ d et+e++a+k   l+++
  gene1124|gene1124|rna1123|rna1123  4 YILGGVIGSGTYGEVYEAIDTETKEKVALKRIKLNEK 40
                                       57788999*********************99887775 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 3.8e-09
                        Kinase-like 150 TlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvl..seve.kgfaPpEllgsrggytrk 222
                                          qli  + +L+   +vh +++++n+l   +g l++ +f+  +    +v+   sev    +  pEll         
  gene1124|gene1124|rna1123|rna1123 102 INQLICGVHYLHRMNVVHRDLKPQNILVTSDGVLKIADFGLSRSLEIRVPPysSEVVtLWYRSPELLMG------- 170
                                        3589999********************************988888889886634443356899999866....... PP

                        Kinase-like 223 nktkmthkldaWqlGlviyriwcl 246
                                          t + + +d W lG  iy +  l
  gene1124|gene1124|rna1123|rna1123 171 -STSYRFYVDIWSLGCIIYEMITL 193
                                        .588999************99876 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.1     0.002       3.6     110     175 ..      12      94 ..       6     111 .. 0.83
   2 !   14.3   0.0   8.2e-06     0.015     229     282 ..     118     176 ..     106     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                      Haspin_kinase 110 eklssevyqtke..kdkevvlKvipl..............evledvtiskelsl.kelkslklvkgtypglllllq 168
                                         + ++evy++ +  ++++v+lK i l               +l+ +++ +++sl    ++  l++ ++p + + l+
  gene1124|gene1124|rna1123|rna1123  12 SGTYGEVYEAIDteTKEKVALKRIKLnekegmpgtalreiSILKKLNHRNIISLvSTIHTDTLLTMVFPFIDYELK 87 
                                        567899**9988778999****************888888888888888888886677888888888998988888 PP

                      Haspin_kinase 169 dkvlkek 175
                                        +++ ++ 
  gene1124|gene1124|rna1123|rna1123  88 KYIEMNT 94 
                                        8888776 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.2e-06
                      Haspin_kinase 229 EHRdLhldniLvdknlnvtlidlklsRle.....ssegkvlytrlddpllFqGggDyqf 282
                                         HRdL+ +niLv + +   + d+ lsR         +++v+      p+l  G   y+f
  gene1124|gene1124|rna1123|rna1123 118 VHRDLKPQNILVTSDGVLKIADFGLSRSLeirvpPYSSEVVTLWYRSPELLMGSTSYRF 176
                                        5**************************87788873344444444557888888888888 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   5.9e-08   0.00011      28     149 ..      22     140 ..      14     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.9e-08
                                        HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEE..EEE--EETTEEGGBHHHC CS
                               RIO1  28 rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvl..vmefigedgvaapklkdv 101
                                        ++  ++++     ++ k n ++ +  +a +E+++Lk+l+++++       + +  l  v  fi+   ++++k  ++
  gene1124|gene1124|rna1123|rna1123  22 IDTETKEKVA--LKRIKLNEKEGMPGTALREISILKKLNHRNIISLVSTIHTDTLLtmVFPFID---YELKKYIEM 92 
                                        5555555555..557799**********************995433333334444411556787...888888888 PP

                                        G-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--G CS
                               RIO1 102 eeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDv 149
                                        ++ +++ el ++++  ++ l  ++++vH DL   N+lv++d  + i D+
  gene1124|gene1124|rna1123|rna1123  93 NTGRNIMELINQLICGVHYLH-RMNVVHRDLKPQNILVTSDgVLKIADF 140
                                        87779999******9888776.*******************44455566 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   2.8e+03      57      73 ..      46      62 ..      40      66 .. 0.84
   2 !   15.4   0.0   4.9e-06    0.0088     123     155 ..     101     133 ..      83     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                                Kdo 57 ravrEfrllkrLeeagv 73
                                       +a rE+++lk+L+++ +
  gene1124|gene1124|rna1123|rna1123 46 TALREISILKKLNHRNI 62
                                       78999999999998877 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.9e-06
                                Kdo 123 llkavgrliaklhragvnHadlyaknillqqee 155
                                        l++++   ++ lhr++v H+dl ++nil+  ++
  gene1124|gene1124|rna1123|rna1123 101 LINQLICGVHYLHRMNVVHRDLKPQNILVTSDG 133
                                        45555556899******************9887 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.25   4.4e+02       5      66 ..      10      74 ..       8     110 .. 0.73
   2 !   14.6   0.0   1.3e-05     0.024     165     195 ..     114     142 ..      93     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.25
                                       E--.SSCEEEEEEETT.-.-EEEEEE-TT...S-HHHHHHHHHHHHHHHHTT-.B--B-CTTBS-EEE CS
                                APH  5 lsggasnrtylvttpa.g.ryvlrrnppa...raaeeirrevallrlLakagv.pvPevlagdtddee 66
                                       +++g++  +y+  +++ + +++l+r+        + ++ re  +l+ L+ +++ +    ++    d+ 
  gene1124|gene1124|rna1123|rna1123 10 IGSGTYGEVYEAIDTEtKeKVALKRIKLNekeGMPGTALREISILKKLNHRNIiSLVSTIH---TDTL 74
                                       7899999999999888536999999665533467777779999999998888876556666...3444 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.3e-05
                                        -EEEE-SS-SGGGEEEC..TTEEEEE---TT CS
                                APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfed 195
                                        ++ ++H+Dl+p+N+lv+  dg +  + Df++
  gene1124|gene1124|rna1123|rna1123 114 RMNVVHRDLKPQNILVT-SDGVL-KIADFGL 142
                                        66689************.44554.5777776 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.2e-05      0.13     120     171 ..      88     140 ..      82     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                                        CCCTHHHHHHHHHTHHHHHHCHGG-..EEEE-S--SGGGEEE.-CTTEEEE--G CS
                     Choline_kinase 120 klinledlekelekleklleelesp..vvfcHnDlqegNillnkeekklvlIDF 171
                                        k+i++++ ++ +e +++l+   ++   ++  H Dl ++Nil+ ++++ l + DF
  gene1124|gene1124|rna1123|rna1123  88 KYIEMNTGRNIMELINQLICGVHYLhrMNVVHRDLKPQNILV-TSDGVLKIADF 140
                                        567788888889999999954333335***************.999*******9 PP

>> FOP_dimer  FOP N terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         4   7.1e+03      44      58 ..      50      64 ..      49      72 .. 0.78
   2 ?   11.6   0.0   0.00014      0.26       3      27 ..      80     104 ..      78     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4
                          FOP_dimer 44 EanlseelddReals 58
                                       E+++  +l+ R+++s
  gene1124|gene1124|rna1123|rna1123 50 EISILKKLNHRNIIS 64
                                       788888999999887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                          FOP_dimer   3 PlvneNLkkvlsikeGrlvaeLire 27 
                                        P+++  Lkk ++++ Gr + eLi++
  gene1124|gene1124|rna1123|rna1123  80 PFIDYELKKYIEMNTGRNIMELINQ 104
                                        9999*******************87 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.3   2.4e+03     186     209 ..      49      72 ..      27      78 .. 0.81
   2 ?   10.6   0.0   9.5e-05      0.17     302     342 ..      92     131 ..      84     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                     Pkinase_fungal 186 sEaelLkkaeergvegvarlvahe 209
                                        +E  +Lkk ++r++  ++  ++  
  gene1124|gene1124|rna1123|rna1123  49 REISILKKLNHRNIISLVSTIHTD 72 
                                        688899999888888887777665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9.5e-05
                     Pkinase_fungal 302 aespkellealrDaIkghrsLflkagiLHrDiSenNilitd 342
                                        +++ ++++e + + I g   L+   +++HrD   +Nil+t 
  gene1124|gene1124|rna1123|rna1123  92 MNTGRNIMELINQLICGVHYLH-RMNVVHRDLKPQNILVTS 131
                                        6777899999************.***************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1859.81
//
Query:       gene1125|gene1125|rna1124|rna1124  [L=378]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-16   60.6   0.1    3.4e-15   56.1   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
    1.7e-08   34.5   0.0    4.6e-08   33.1   0.0    1.7  2  RsgA_GTPase  RsgA GTPase
    1.7e-07   30.9   0.0     0.0005   19.6   0.0    2.3  2  FeoB_N       Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.027   13.8   0.0      0.046   13.1   0.0    1.4  1  AIG1         AIG1 family
      0.033   13.2   0.2       0.24   10.3   0.0    2.3  3  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.095   12.8   0.2       0.27   11.3   0.0    1.9  2  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.071   2.1e+02      71     113 ..     130     169 ..      97     173 .. 0.68
   2 !   56.1   0.0   1.1e-18   3.4e-15       2      62 ..     208     266 ..     207     297 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.071
                                        HHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                           MMR_HSR1  71 laleeadlillvvdaseeklkpldeeleelleeakkplilvln 113
                                           e++d+i+ +vda++ ++  l+ ++ +l    +k+ i+++n
  gene1125|gene1125|rna1124|rna1124 130 ITCERSDVIVQIVDARNPEF-FLNDDIRKLY--PRKEHIILIN 169
                                        456789********882222.2334444443..2344455555 PP

  == domain 2  score: 56.1 bits;  conditional E-value: 1.1e-18
                                        EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHH CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGliegase 62 
                                        +++vG+pNvGKS+ in+++++ +++vs++pg+Tr+i++++++  +    l+D+pGl+   ++
  gene1125|gene1125|rna1124|rna1124 208 IGFVGYPNVGKSSTINSIVNSkRVRVSQTPGKTRHIQTIHIE--E-GPCLLDCPGLVFPRHD 266
                                        89******************9799*****************9..3.359******8632222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.8   8.4e+03      74     101 ..      19      46 ..      12      51 .. 0.71
   2 !   33.1   0.0   1.5e-11   4.6e-08      49     161 ..     164     260 ..     119     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.8
                                        HTTSEEEE--TTTHTTHHHHHHHCTTSE CS
                        RsgA_GTPase  74 algyevllvsaktkegleelkellkdkt 101
                                        ++ ++v   s+++  g+e+l+e+l+ k 
  gene1125|gene1125|rna1124|rna1124  19 KAKTRVQRASVTEYGGVEKLSEELAMKN 46 
                                        5556677778888888888888887765 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.5e-11
                                        EEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                        RsgA_GTPase  49 pvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpele 124
                                         +i++nK+Dl +++          e  +y++++ sa ++++l +   + k+k++ +vG   vGKS+ in+++++++
  gene1125|gene1125|rna1124|rna1124 164 HIILINKADLSSSRV---------EIKEYRCFYYSALERNSLLKFILEYKGKVIGFVGYPNVGKSSTINSIVNSKR 230
                                        578888888877766.........44568899999999999999999**************************977 PP

                                        ---S--------------SEEEEEETTTEEEESS-SS CS
                        RsgA_GTPase 125 lktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                        ++++++       k  T++ + ++++eg +l D PG+
  gene1125|gene1125|rna1124|rna1124 231 VRVSQTPG-----K--TRHIQTIHIEEGPCLLDCPGL 260
                                        66665554.....4..9*******************7 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00029      0.88      73     119 ..     129     175 ..      86     184 .. 0.78
   2 !   19.6   0.0   1.7e-07    0.0005       3      56 ..     208     259 ..     206     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00029
                                        HHHCTSSSEEEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHH CS
                             FeoB_N  73 flleeepdvvvnvvdatnlernLyLtlqllelgvpvvlalnmideae 119
                                         ++ e+ dv+v++vda n e  L   ++ l  +++ ++ +n+ d  +
  gene1125|gene1125|rna1124|rna1124 129 WITCERSDVIVQIVDARNPEFFLNDDIRKLYPRKEHIILINKADLSS 175
                                        4667999************9888888888888899999999999754 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.7e-07
                                        EEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE--- CS
                             FeoB_N   3 valvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPG 56 
                                        + +vG pnvGk++ +n++ ++k  +v+  pG+t   ++ +++   +   ++D PG
  gene1125|gene1125|rna1124|rna1124 208 IGFVGYPNVGKSSTINSIVNSKrVRVSQTPGKTRHIQTIHIE---EGPCLLDCPG 259
                                        779***************9986479********999999888...6677888888 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.046       5      41 ..     210     245 ..     206     280 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                                        EESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EE CS
                               AIG1   5 lvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqk 41 
                                         vG   +GkS+T+Nsi+++k  + + ++ + t++ q+
  gene1125|gene1125|rna1124|rna1124 210 FVGYPNVGKSSTINSIVNSKRVRVS-QTPGKTRHIQT 245
                                        589999************9987766.45555555554 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.32   9.7e+02     200     235 ..      17      52 ..       6      80 .. 0.64
   2 ?   -1.2   0.0      0.27   8.1e+02     171     190 ..     165     184 ..     163     193 .. 0.77
   3 ?   10.3   0.0   8.1e-05      0.24      16      51 ..     194     227 ..     187     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.32
                                        BTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHT CS
                               MeaB 200 ekeWrpkvlktsavegeGidelvdaieehrevlkkt 235
                                        +++ +++v ++s +e  G+++l +++    + ++  
  gene1125|gene1125|rna1124|rna1124  17 KQKAKTRVQRASVTEYGGVEKLSEELAMKNKKITGG 52 
                                        666778899999999999999999887766666543 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.27
                                        EEEEE---HHHHHHHHHHHH CS
                               MeaB 171 iivvnkaDkkeaekaarelr 190
                                        ii +nkaD++ ++   +e+r
  gene1125|gene1125|rna1124|rna1124 165 IILINKADLSSSRVEIKEYR 184
                                        899*****888777666665 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 8.1e-05
                                        HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHH CS
                               MeaB  16 kellerllakaGraqvvGltGvPGaGkstlvealgl 51 
                                        ++ll+ +l++ G  +v+G+ G P +Gks +++ ++ 
  gene1125|gene1125|rna1124|rna1124 194 NSLLKFILEYKG--KVIGFVGYPNVGKSSTINSIVN 227
                                        568888888877..59**************998865 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.8   5.5e+03      64      81 ..      34      51 ..      11     101 .. 0.63
   2 ?   11.3   0.0   9.2e-05      0.27       1      42 [.     208     250 ..     208     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                                       -CHHHHHHHHHHHHHHHT CS
                          Dynamin_N 64 dfsevreeieketekiag 81
                                        ++++ ee+ ++++ki+g
  gene1125|gene1125|rna1124|rna1124 34 GVEKLSEELAMKNKKITG 51
                                       444555555555555554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.2e-05
                                        EEEEEBTTTTHHHHHHHHHTS--S---SSS.---S-EEEEECC CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnp.tTrrplelqlge 42 
                                        i +vG  + GKSS +n+++ ++   ++++p  Tr + +++ +e
  gene1125|gene1125|rna1124|rna1124 208 IGFVGYPNVGKSSTINSIVNSKRVRVSQTPgKTRHIQTIHIEE 250
                                        7799999************988777666652788888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2528.28
//
Query:       gene1126|gene1126|rna1125|rna1125  [L=375]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-29  101.6   2.0    2.7e-29  101.6   2.0    2.4  2  V-ATPase_H_C  V-ATPase subunit H
    4.3e-12   46.0   0.5    4.3e-12   46.0   0.5    1.8  2  V-ATPase_H_N  V-ATPase subunit H
  ------ inclusion threshold ------
       0.01   15.4   0.2      0.017   14.7   0.2    1.3  1  TMEM101       TMEM101 protein family
      0.069   13.6   0.0        3.5    8.1   0.0    3.2  4  HEAT_2        HEAT repeats
       0.56   10.0   2.8        0.4   10.5   0.3    2.0  2  CdvA          CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.1      0.28     1e+03       7      56 ..      76     129 ..      72     164 .. 0.57
   2 !  101.6   2.0   7.5e-33   2.7e-29       7     117 .]     265     374 ..     261     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.28
                       V-ATPase_H_C   7 eYlaElesgkLewspvHkse..kFWkenaekl..eeknfkllkkLikll..eeskd 56 
                                        +Y++     kL  +  H++e  +F+k+ ++     +++  ll+ Li++l  +  ++
  gene1126|gene1126|rna1125|rna1125  76 RYKSAEMLTKLYENKSHRKEyfSFFKQMLKDStsYDESNYLLSLLIDFLscK--SN 129
                                        5665555667888888887633456666655432344466777778877431..22 PP

  == domain 2  score: 101.6 bits;  conditional E-value: 7.5e-33
                       V-ATPase_H_C   7 eYlaElesgkLewspvHksekFWkenaekleeknfkllkkLiklleeskdktvlavalnDigelvkllpegkkvle 82 
                                        +Yl+El sg++e s +H++e+FW++n++ l +++++++k L+k+l +s++++++++a++Di +lvk+lpe ++vl+
  gene1126|gene1126|rna1125|rna1125 265 NYLNELFSGRFEDSEYHHKEDFWNNNLDMLMKNKVEIVKVLKKYL-KSSNPSWVCLACSDIFQLVKVLPEINAVLN 339
                                        8********************************************.6999************************** PP

                       V-ATPase_H_C  83 klkaKekimellehedeevkyeALkavqkllvqnw 117
                                        k+++Ke++++l+++++++++++A++++ ++++++w
  gene1126|gene1126|rna1125|rna1125 340 KYQVKEVLFNLINSDNDDIRFHAIQTLYTCISSEW 374
                                        *********************************99 PP

>> V-ATPase_H_N  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.5   1.2e-15   4.3e-12     120     312 ..      75     251 ..      44     254 .. 0.88
   2 ?   -1.6   0.1      0.36   1.3e+03     100     114 ..     338     352 ..     276     372 .. 0.50

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.2e-15
                       V-ATPase_H_N 120 ivllalrllakllvqgkkksnklvesaLnrllqlLssqlssstnevieiavrllqellrtkeyRelfveadgvstl 195
                                           +++ +l+kl  +++k++ k   + + ++ q+L++++s +++   +  + ll   l+ k+   + ve+ +v ++
  gene1126|gene1126|rna1125|rna1125  75 SRYKSAEMLTKL--YENKSHRK---EYFSFFKQMLKDSTSYDES---NYLLSLLIDFLSCKSNSNFDVEKRKVALV 142
                                        555666666665..45556666...8999999999999999888...66999999999999999999**9999999 PP

                       V-ATPase_H_N 196 isilrstvanstrvgiQlqYqvllclWlLsFekkiaeelvkkkelipllvdilrdsvKEKvtRvilatlrNlleka 271
                                         + ++ ++  ++     +qY++l+++ + s++ + ++++     li  +v i+++ ++EK+ Rv+  ++ N+le+ 
  gene1126|gene1126|rna1125|rna1125 143 TNKMFMEILHTSVFVKEVQYNTLMVILIFSYSTECVGKM--GT-LIDDVVIIVKEKAREKILRVCYGIIANVLESG 215
                                        998889999999999***********************9..67.9******************************9 PP

                       V-ATPase_H_N 272 eksskelaavmvqvkllkllenLeerkfsDeditedleyLk 312
                                              +     ++++ k +  L e  ++De++++dl+++ 
  gene1126|gene1126|rna1125|rna1125 216 Y-----VFSPGRLNDISKCTDLLLEGGYGDEELEQDLKKVR 251
                                        9.....88888899************************997 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.36
                       V-ATPase_H_N 100 keeqdpwkpflklln 114
                                         +++++ +++++l+n
  gene1126|gene1126|rna1125|rna1125 338 LNKYQVKEVLFNLIN 352
                                        222333334444444 PP

>> TMEM101  TMEM101 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   4.6e-06     0.017      56     136 ..     121     202 ..      93     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.6e-06
                            TMEM101  56 vavl.casamsldvkrrtfalaaalqla.islylslsgekaeyadwlkvrvlsralaiiggylvlasglgesyRrk 129
                                        + +l c s   +dv++r +al++   ++ i    s   ++++y+  + + ++s +   +g   +l   +  ++++k
  gene1126|gene1126|rna1125|rna1125 121 IDFLsCKSNSNFDVEKRKVALVTNKMFMeILH-TSVFVKEVQYNTLMVILIFSYSTECVGKMGTLIDDVVIIVKEK 195
                                        4444399999************9876664444.44566789********************999999999999999 PP

                            TMEM101 130 prsrslq 136
                                        +r++ l+
  gene1126|gene1126|rna1125|rna1125 196 AREKILR 202
                                        9998876 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.16   5.8e+02      34      62 ..      62      90 ..      47     114 .. 0.67
   2 ?   -2.5   0.0       1.9     7e+03      14      37 ..     248     271 ..     242     280 .. 0.72
   3 ?   -1.0   0.0      0.66   2.4e+03      31      46 ..     300     315 ..     291     324 .. 0.72
   4 ?    8.1   0.0   0.00098       3.5      31      55 ..     342     366 ..     302     372 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.16
                             HEAT_2 34 paLvellededpavRraaaeaLgaigdpe 62
                                       + L++ll ++d + R+  ae L ++ +++
  gene1126|gene1126|rna1125|rna1125 62 DELIDLLFCSDIYSRYKSAEMLTKLYENK 90
                                       67888888888888888888888875432 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                             HEAT_2  14 pevrraairaLgrignpealpaLv 37 
                                        ++vr++++++  r+  + +l+ L+
  gene1126|gene1126|rna1125|rna1125 248 KKVRARIAQNAKRFCLRNYLNELF 271
                                        468888888777777666666665 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.66
                             HEAT_2  31 ealpaLvellededpa 46 
                                        e+++ L ++l++++p 
  gene1126|gene1126|rna1125|rna1125 300 EIVKVLKKYLKSSNPS 315
                                        7788888888888874 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.00098
                             HEAT_2  31 ealpaLvellededpavRraaaeaL 55 
                                        ++ + L++l+++++ ++R +a+++L
  gene1126|gene1126|rna1125|rna1125 342 QVKEVLFNLINSDNDDIRFHAIQTL 366
                                        77899*****************998 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.1     4e+03       4      27 ..      81     104 ..      76     109 .. 0.58
   2 ?   10.5   0.3   0.00011       0.4      43     107 ..     241     307 ..     240     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                               CdvA   4 kALeeLvsegdipkstyeeikekl 27 
                                          L +L++++   k+ ++ +k+ l
  gene1126|gene1126|rna1125|rna1125  81 EMLTKLYENKSHRKEYFSFFKQML 104
                                        445666666666666665555554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00011
                               CdvA  43 eklkkrlkeledqiksleka..lanlkisyasGEidEeaYksaieairellesaleekeeikkllek 107
                                        e+l++ lk+++  i++ +k   l n   + +sG  ++++Y++  +  +++l+++++ k ei k+l+k
  gene1126|gene1126|rna1125|rna1125 241 EELEQDLKKVRARIAQNAKRfcLRNYLNELFSGRFEDSEYHHKEDFWNNNLDMLMKNKVEIVKVLKK 307
                                        678888888888887766554677788899*********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2253.59
//
Query:       gene1127|gene1127|rna1126|rna1126  [L=300]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-33  115.6   0.3      8e-33  112.9   0.0    2.1  2  Cyclin_N  Cyclin, N-terminal domain
    1.6e-25   89.5   0.5    3.5e-25   88.4   0.5    1.6  1  Cyclin_C  Cyclin, C-terminal domain


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   0.0   8.9e-37     8e-33      23     126 ..      73     176 ..      57     177 .. 0.93
   2 ?    0.4   0.0     0.055   4.9e+02      34      68 ..     205     239 ..     183     260 .. 0.64

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 8.9e-37
                                        TSSS-HHHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHH CS
                           Cyclin_N  23 qpelnpemRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledl 98 
                                        ++ ++++mR+ l+dw+++++ k+ l ++tlfla+n++dRfls +s+p +klqlvg+++L++A+K+ee+ +p l+ +
  gene1127|gene1127|rna1126|rna1126  73 NDGVSWKMRSLLVDWIIDIHDKLGLCHDTLFLAINLIDRFLSMRSIPGSKLQLVGISALMIACKYEEVVCPALQTF 148
                                        456899********************************************************************** PP

                                        HHHTTTSS-HHHHHHHHHHHHHHTTT-- CS
                           Cyclin_N  99 vyitdeafteeeilemErliLetLnfdl 126
                                        v +t+++ t e++ ++E+++L tLn+dl
  gene1127|gene1127|rna1126|rna1126 149 VLLTEKTLTGEDVRKAEKYMLHTLNYDL 176
                                        ***************************9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.055
                                        HHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS-- CS
                           Cyclin_N  34 lidwlvevaekfkltpetlflavnyldRflskksv 68 
                                        l++ ++  +e ++++ ++ + a+ yl R ++++++
  gene1127|gene1127|rna1126|rna1126 205 LLELMTLYQEFLRFKGSVRAAAAMYLSRKMTSQDH 239
                                        44455555555555555556666666655555444 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.5   3.9e-29   3.5e-25       1     117 [.     179     291 ..     179     293 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 3.9e-29
                                        --HHHHHHHHHCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---H CS
                           Cyclin_C   1 ptplsFlrrflkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgysk 76 
                                        + pl+Flrr++ka+++  ++  r++ kyllel++l  +fl+++ S+ Aaaa++l+r++ ++ ++++ +  y+g  k
  gene1127|gene1127|rna1126|rna1126 179 VSPLNFLRRCSKANNY--EISSRAVGKYLLELMTLYQEFLRFKGSVRAAAAMYLSRKMTSQDHCKNLFLMYSGHMK 252
                                        679**********888..7789****************************************************** PP

                                        HHHHHHHHHHHHHHHHHHGSS--HHCCCCTCGGGCCCGGS- CS
                           Cyclin_C  77 edlkpcvelilellssapssklqavrrkyssskfhkvstls 117
                                        +d+k+c ++++  +  ++s  ++++++ky+++kf +vs+++
  gene1127|gene1127|rna1126|rna1126 253 DDIKECFNALVRII--SESIPFENIQNKYNTPKFLHVSSFV 291
                                        **************..778899****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1859.15
//
Query:       gene1128|gene1128|rna1127|rna1127  [L=393]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-06   27.7   0.0      3e-06   26.9   0.0    1.4  1  MIF4G_like_2  MIF4G like


Domain annotation for each model (and alignments):
>> MIF4G_like_2  MIF4G like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   1.7e-10     3e-06      54     129 ..     310     382 ..     266     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 1.7e-10
                       MIF4G_like_2  54 lsidvfvqtllhvGskSlSHvlsaierykevLkelaeseearaqileavmrfWknnpqmaiiivdkLlnyqivepa 129
                                          +++f++  +++Gs S+SH+l ++e yke++     ++e +   +++ +++++  + ++ i+++k+ +++i++pa
  gene1128|gene1128|rna1127|rna1127 310 KDREAFFKNFCFLGSPSISHFLTYLEIYKERFVL---NKEDQKLFISIFFEIFEGLESFCRIVTEKMVRFGIIDPA 382
                                        66899*************************9964...67788899******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.83
# Mc/sec: 1425.08
//
Query:       gene1129|gene1129|rna1128|rna1128  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-33  115.4   0.1    2.6e-33  115.1   0.1    1.0  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
       0.08   13.0   0.0       0.22   11.6   0.0    1.9  2  DUF5072     Domain of unknown function (DUF5072)
       0.13   11.0   0.0       0.14   10.9   0.0    1.1  1  Prd1-P2     Bacteriophage Prd1, adsorption protein P2


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.1   4.4e-37   2.6e-33       6     190 .]       3     181 ..       2     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 4.4e-37
                                        EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                         Proteasome   6 tvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                        +++Gikg++++++aad+r++  s ll k++ eK   i+d+++++++G+++Da   +  +++ a+ +++++g +i++
  gene1129|gene1129|rna1128|rna1128   3 SSIGIKGSNFAMVAADTRVS-RSFLLVKEDYEKFQVIKDKVVMSVVGDQGDAFRTMLNVSESARYEEIQNGIEISP 77 
                                        789*****************.6666677779********************************************* PP

                                        HHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTT CS
                         Proteasome  82 erlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyked 157
                                        ++l++ + +k+++ + r+  r++ +s++iag   eg + L+++d  G++ +  +++a G+++++++++l++ey+e+
  gene1129|gene1129|rna1128|rna1128  78 SVLAHMIQNKVHESL-RK--RQLDASTIIAGKGPEG-YDLWSVDRYGAISSV-PFCASGYAAYFVYGILDREYSEN 148
                                        *55555555555544.44..699**********999.9**************.6********************** PP

                                        BSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                         Proteasome 158 ltleeavelavkalkealerdklsgknievavi 190
                                        +t ++a+++++k+++ + er  ++ +++ + ++
  gene1129|gene1129|rna1128|rna1128 149 ITIDDALKIIQKCINLLKERLIINLEGFMIKIV 181
                                        ***********************9999998876 PP

>> DUF5072  Domain of unknown function (DUF5072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.6e-05      0.22      73      92 ..     106     125 ..      38     130 .. 0.75
   2 ?   -2.3   0.0      0.75   4.5e+03      58      86 ..     155     184 ..     143     195 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                            DUF5072  73 rlPeGykliavvesGkislv 92 
                                        + PeGy+l++v ++G is v
  gene1129|gene1129|rna1128|rna1128 106 KGPEGYDLWSVDRYGAISSV 125
                                        67**************9976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.75
                            DUF5072  58 lanvekvdellteyirlP.eGykliavves 86 
                                        l+ ++k  +ll+e + +  eG+ +  v + 
  gene1129|gene1129|rna1128|rna1128 155 LKIIQKCINLLKERLIINlEGFMIKIVTDD 184
                                        555666666666554432256555555555 PP

>> Prd1-P2  Bacteriophage Prd1, adsorption protein P2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   2.3e-05      0.14     429     479 ..      90     141 ..      38     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.3e-05
                                        EEEEHHHHH-..S--S--TTTT-EEEETT-TTS-TT---EEEEETTEEEEEEE CS
                            Prd1-P2 429 leiprrqlea..inpqdgpgqydlfilddsgayasfssfigypeaayyvagaa 479
                                          + +rql+a  i    gp  ydl+ +d  ga +s+  f     aay+v g  
  gene1129|gene1129|rna1128|rna1128  90 ESLRKRQLDAstIIAGKGPEGYDLWSVDRYGAISSV-PFCASGYAAYFVYGIL 141
                                        45678999974467889999************9886.68888889****9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1242.14
//
Query:       gene1130|gene1130|rna1129|rna1129  [L=688]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-91  303.4   0.2    1.1e-90  302.6   0.2    1.4  1  MCM              MCM P-loop domain
    1.7e-27   95.7   0.1    1.7e-26   92.5   0.0    2.4  2  MCM_OB           MCM OB domain
    5.2e-23   81.3   1.0    1.1e-22   80.3   1.0    1.6  1  MCM_lid          MCM AAA-lid domain
    8.9e-08   31.8   0.0    1.1e-06   28.2   0.0    2.5  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.5e-07   31.2   0.4    9.5e-07   29.4   0.0    2.1  2  MCM_N            MCM N-terminal domain
    0.00019   21.3   0.1    0.00062   19.6   0.0    2.0  2  AAA_3            ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.051   13.3   0.0    1.9  2  Sigma54_activat  Sigma-54 interaction domain
      0.014   15.3   0.0       0.04   13.9   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
       0.16   11.8   0.0         16    5.4   0.0    2.5  2  Crust_neurohorm  Crustacean CHH/MIH/GIH neurohormone family
       0.19   11.6   0.0       0.58   10.1   0.0    1.8  1  Pput2613-deam    Pput_2613-like deaminase
        0.2   11.0   0.0       0.32   10.3   0.0    1.2  1  OprB             Carbohydrate-selective porin, OprB family


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.6   0.2   6.8e-94   1.1e-90      13     224 .]     268     479 ..     255     479 .. 0.97

  Alignments for each domain:
  == domain 1  score: 302.6 bits;  conditional E-value: 6.8e-94
                                        THHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEE CS
                                MCM  13 diieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravyts 88 
                                        + ++++ +siapsi+gh+ +kk+i+l+l+gg++  +++++k+rgdin+llvgdp+taKsqlL+yv + a+ +v t+
  gene1130|gene1130|rna1129|rna1129 268 SRMKNIHHSIAPSIFGHDIIKKCIALLLVGGNEVIMRNGSKIRGDINILLVGDPSTAKSQLLRYVLNAAQLSVATT 343
                                        567899********************************************************************** PP

                                        SSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE-- CS
                                MCM  89 gkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnar 164
                                        gkgss++gLtaavv d++tge  leaGa+vlad+Gv+ciDefdkm++ dr+a+hE+mEqqt++iaKaGi++tLnar
  gene1130|gene1130|rna1129|rna1129 344 GKGSSGVGLTAAVVLDRDTGEKRLEAGAMVLADRGVVCIDEFDKMSDGDRVAIHEVMEQQTVTIAKAGIHTTLNAR 419
                                        **************************************************************************** PP

                                        EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                                MCM 165 tsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                        +svlaAanp++g+y+++++ ++n++l+++lL+rFDlifv lDk++++ D+ ++eh++++h
  gene1130|gene1130|rna1129|rna1129 420 CSVLAAANPVWGQYKESRPPQDNVRLPESLLTRFDLIFVTLDKSNADVDQLISEHVLRMH 479
                                        *********************************************************998 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   1.1e-29   1.7e-26       3     124 ..      96     226 ..      92     228 .. 0.86
   2 ?   -0.0   0.0      0.45   7.3e+02     103     119 ..     577     593 ..     568     597 .. 0.73

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 1.1e-29
                                        GG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES---.......-SB-..TTT-HHH-EEE-GG. CS
                             MCM_OB   3 RdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvevelee.......PrkCeekeCeskdpfklete. 70 
                                        R+l+s +igk+v++eGivt++s ++pk+ ++v++ ++ +   + e+++       P + +    +  d   l+te 
  gene1130|gene1130|rna1129|rna1129  96 RTLSSVYIGKMVCIEGIVTSCSICRPKVMRSVHYNPSKNVFYSKEYRDatmvtklPVTNTVYPTRDVDGTLLMTEf 171
                                        9*********************************999887666556556666778664433333445677777777 PP

                                        .GSEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                             MCM_OB  71 .kskfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                          s++ d+q++ lQE+pe++p+G+lPrs+ev+l+ dlvdk+kPGdr +v Giy++
  gene1130|gene1130|rna1129|rna1129 172 gLSEYFDYQTVILQEMPEKAPPGQLPRSVEVVLTFDLVDKLKPGDRAKVYGIYKS 226
                                        79***************************************************86 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.45
                                        EGGGTT---TT-EEEEE CS
                             MCM_OB 103 eddlvdkvkPGdrvevt 119
                                        +    + vkPG+r++++
  gene1130|gene1130|rna1129|rna1129 577 DSLFQKVVKPGKRIKIV 593
                                        44445678*******98 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   1.0   6.6e-26   1.1e-22       1      87 []     495     579 ..     495     579 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 6.6e-26
                                        HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHH CS
                            MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedv 76 
                                        e++r+Yi+y+r + kP ls ea+  +s+ Y  lR+++ d+k++ ++it+R+Le++iRL++A Aklrls+vv+ +d+
  gene1130|gene1130|rna1129|rna1129 495 EVFRAYIQYCR-QKKPALSREAAGLISKEYTLLRQTK-DKKEQIVSITPRMLETMIRLATANAKLRLSDVVEYDDA 568
                                        579********.***********************99.56799********************************* PP

                                        HHHHHHHHHHH CS
                            MCM_lid  77 eeairllkesl 87 
                                        e a++l+k+sl
  gene1130|gene1130|rna1129|rna1129 569 ECAVNLIKDSL 579
                                        *******9985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5   4.1e+03     144     162 ..     232     250 ..     230     271 .. 0.65
   2 ?   -0.2   0.0      0.32   5.3e+02      21      40 ..     311     330 ..     307     338 .. 0.85
   3 !   28.2   0.0   6.5e-10   1.1e-06      93     165 ..     363     434 ..     355     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                       Mg_chelatase 144 vefparfqlvaamNpcpcg 162
                                         +fp+rf+ v+ +N     
  gene1130|gene1130|rna1129|rna1129 232 QQFPSRFKTVVIANNIEKT 250
                                        6899999988777765443 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.32
                       Mg_chelatase  21 GgHnlllvGppGsGKtmlak 40 
                                        G  n+llvG p + K+ l +
  gene1130|gene1130|rna1129|rna1129 311 GDINILLVGDPSTAKSQLLR 330
                                        888************98865 PP

  == domain 3  score: 28.2 bits;  conditional E-value: 6.5e-10
                       Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklk 165
                                        g ++ + G++ la +Gv+ +DE+ +++     ++ e +e+++vti++a  +++  ar+ ++aa+Np    ++k
  gene1130|gene1130|rna1129|rna1129 363 GEKRLEAGAMVLADRGVVCIDEFDKMSDGDRVAIHEVMEQQTVTIAKAGIHTTLNARCSVLAAANPVWG-QYK 434
                                        5678899***********************************************************754.443 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   5.8e-10   9.5e-07       2      73 ..       7      73 ..       6      80 .. 0.93
   2 ?   -1.8   0.1       2.8   4.6e+03      26      55 ..     542     572 ..     518     583 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 5.8e-10
                              MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealk 73
                                       e F++F+e++     +++++k   + + ++  ++++++ ++++d++afd++L++ i+e+p   +p+ e+ l 
  gene1130|gene1130|rna1129|rna1129  7 ELFKSFIESY-----RTSQDKDIAEIITKLPYEDHQRIILNINDMRAFDKTLSKGIMEEPATLIPFAEDELS 73
                                       67********.....78889**********************************************998666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.8
                              MCM_N  26 dqlqemaerekttLevdlddLaafde.eLae 55 
                                        ++l++m++    +  + l+d+ ++d+ e a 
  gene1130|gene1130|rna1129|rna1129 542 RMLETMIRLATANAKLRLSDVVEYDDaECAV 572
                                        5788888888888889999999998754444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         3   4.9e+03      62      89 ..     238     265 ..     231     278 .. 0.72
   2 !   19.6   0.0   3.8e-07   0.00062       2     114 ..     315     430 ..     314     455 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3
                              AAA_3  62 fanllladeinrappktqsalleameer 89 
                                        f+ +++a++i++++   ++ ++  +e +
  gene1130|gene1130|rna1129|rna1129 238 FKTVVIANNIEKTKEEEECKVVSEIEFE 265
                                        7889999999998887776666655555 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 3.8e-07
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvf.an..llladeinra 74 
                                        +ll g P +ak +l + + +a +l++      +      ++ + v+++++ e ++++G+++ a+  ++  de ++ 
  gene1130|gene1130|rna1129|rna1129 315 ILLVGDPSTAKSQLLRYVLNAAQLSVATTGKGS--SGVGLTAAVVLDRDTGEKRLEAGAMVlADrgVVCIDEFDKM 388
                                        677778888888887777777666665544333..3456889999*************976233459********* PP

                              AAA_3  75 ppktqsalleameerqvtvege..thklpepflvlatqnPie 114
                                        +   + a+ e+me+++vt++++   ++l+    vla+ nP+ 
  gene1130|gene1130|rna1129|rna1129 389 SDGDRVAIHEVMEQQTVTIAKAgiHTTLNARCSVLAAANPVW 430
                                        ******************9875226789************94 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.8   2.9e+03      19      44 ..     309     334 ..     300     350 .. 0.79
   2 ?   13.3   0.0   3.1e-05     0.051      79     142 ..     362     427 ..     361     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.8
                                        CTSSS-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat  19 aktdlsvlitGesGtGKellaraihe 44 
                                        ++ d+++l++G+  t K+ l r + +
  gene1130|gene1130|rna1129|rna1129 309 IRGDINILLVGDPSTAKSQLLRYVLN 334
                                        56789999999999999988877765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.1e-05
                                        TTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEES CS
                    Sigma54_activat  79 tGAekekkGlfekadgGtlfLDeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatn 142
                                        tG ++ ++G++  ad G++ +De  +++    + + +v+++++v   + G +++ ++ + ++aa+n
  gene1130|gene1130|rna1129|rna1129 362 TGEKRLEAGAMVLADRGVVCIDEFDKMSDGDRVAIHEVMEQQTVtiAKAGIHTTLNARCSVLAAAN 427
                                        67788889*******************************9997522699*************9987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.4e-05      0.04       1     126 [.     314     432 ..     314     442 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEv 74 
                                        ++lLvG+p t+Ks+l ++++ a + +v +    ++ +   l+  + ++   g+++l+ +++v       ++++DE+
  gene1130|gene1130|rna1129|rna1129 314 NILLVGDPSTAKSQLLRYVLNAAQLSVATT--GKGSSGVGLTAAVVLDrdTGEKRLEAGAMV--LADRGVVCIDEF 385
                                        689*******************97776654..344444444444444444699999999999..6667899***** PP

                                        GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.- CS
                              AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrs 126
                                        +++++    + + ++e++++ +++ g  +  ++       +v+a+anp+ ++
  gene1130|gene1130|rna1129|rna1129 386 DKMSDGDRVAIHEVMEQQTVTIAKAGIHTTLNAR-----CSVLAAANPVWGQ 432
                                        ****99999999*********9999988888775.....9999999998754 PP

>> Crust_neurohorm  Crustacean CHH/MIH/GIH neurohormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.01        16      31      64 ..     219     252 ..     216     255 .. 0.88
   2 ?    3.7   0.0     0.034        56      26      56 ..     267     297 ..     264     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                    Crust_neurohorm  31 qlhrlCkkeCFtteyFkkCleallledekeklqe 64 
                                        +++ + k+ CF ++ F    +++++ ++ ek +e
  gene1130|gene1130|rna1129|rna1129 219 KVYGIYKSLCFGNQQFPSRFKTVVIANNIEKTKE 252
                                        6788899******************999998875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.034
                    Crust_neurohorm  26 LyrepqlhrlCkkeCFtteyFkkCleallle 56 
                                        L r +++h+    + F  ++ kkC++ ll+ 
  gene1130|gene1130|rna1129|rna1129 267 LSRMKNIHHSIAPSIFGHDIIKKCIALLLVG 297
                                        66888999999999************99985 PP

>> Pput2613-deam  Pput_2613-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00036      0.58      65     104 ..     103     143 ..      93     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00036
                      Pput2613-deam  65 lGdvlvidGqyaPCssCkGk.mrvaseetgakvqYtweegg 104
                                        +G+++ i+G+ + Cs C+ k mr    +   +v Y  e  +
  gene1130|gene1130|rna1129|rna1129 103 IGKMVCIEGIVTSCSICRPKvMRSVHYNPSKNVFYSKEYRD 143
                                        59****************86488888888888988877664 PP

>> OprB  Carbohydrate-selective porin, OprB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002      0.32      28     101 ..     400     474 ..     394     492 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                               OprB  28 leartsalerqgfslttkltgevlfavtevfggkk.....qnrvrLtelsftqkffddrLdirlgrgnvndefyya 98 
                                         e +t ++   g  +t +++ +vl a+++v+g  k     q+ vrL+e  +t     d + ++l + n++ +  + 
  gene1130|gene1130|rna1129|rna1129 400 MEQQTVTIAKAGIHTTLNARCSVLAAANPVWGQYKesrppQDNVRLPESLLTRF---DLIFVTLDKSNADVDQ-LI 471
                                        68999*************************************************...************9998.44 PP

                               OprB  99 spt 101
                                        s+ 
  gene1130|gene1130|rna1129|rna1129 472 SEH 474
                                        444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 4496.33
//
Query:       gene113|gene113|rna113|rna113  [L=408]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-28   98.4  14.8    6.7e-06   26.7   0.2    7.5  7  WD40         WD domain, G-beta repeat
    1.2e-09   38.0   2.7    5.2e-06   26.0   0.1    3.7  4  WD40_like    WD40-like domain
    6.7e-06   26.3   0.2       0.16   12.3   0.0    4.2  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
     0.0029   17.6   0.2          4    7.5   0.0    3.4  4  BBS2_Mid     Ciliary BBSome complex subunit 2, middle region
     0.0032   16.2   6.3        7.8    5.0   0.0    4.4  4  Nup160       Nucleoporin Nup120/160
  ------ inclusion threshold ------
      0.024   14.5   0.1        7.4    6.5   0.0    2.8  2  DUF4934      Domain of unknown function (DUF4934)


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0069        21      23      37 ..     111     125 ..      93     125 .. 0.79
   2 !   26.7   0.2   2.3e-09   6.7e-06       1      38 []     129     165 ..     129     165 .. 0.91
   3 !   20.0   0.1   3.1e-07   0.00092       3      38 .]     171     205 ..     169     205 .. 0.84
   4 !   25.9   0.1     4e-09   1.2e-05       1      38 []     208     244 ..     208     244 .. 0.94
   5 !    9.4   0.1   0.00069       2.1       1      36 [.     248     282 ..     248     282 .. 0.82
   6 !   10.0   0.2   0.00044       1.3       2      38 .]     288     325 ..     287     325 .. 0.82
   7 ?    4.1   0.0     0.031        93       9      38 .]     339     363 ..     330     363 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0069
                                    SEEEEEETTSEEEEE CS
                           WD40  23 awlasGsdDgtvriW 37 
                                    + ++++sdD+t++i+
  gene113|gene113|rna113|rna113 111 DRIICSSDDQTIKIF 125
                                    45778999*****96 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 2.3e-09
                                    TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    g+++rt+ GH ++v+ +    ++++l+sGs D+t riWd
  gene113|gene113|rna113|rna113 129 GRLIRTFIGHkGGVWTF--MFNSKYLVSGSTDKTARIWD 165
                                    5789******777**88..99*****************9 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 3.1e-07
                                    EEEEEESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   3 clrtltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                    +l +l GH+s v+sl    + +++a+Gs+D  +r+W+
  gene113|gene113|rna113|rna113 171 TLCVLVGHKSvVRSL--KIYEDYIATGSRDSEIRVWN 205
                                    567899**8856*99..557788*************8 PP

  == domain 4  score: 25.9 bits;  conditional E-value: 4e-09
                                    TEEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   1 gqclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    g+cl +l+GH  sv+++  + d ++l+sGs+Dg+v +Wd
  gene113|gene113|rna113|rna113 208 GTCLNVLKGHtMSVRCM--DMDESYLVSGSYDGSVALWD 244
                                    68********888****..999999*************9 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.00069
                                    TEEEEEEESSSS..EEEEEEETTSSEEEEEETTSEEEE CS
                           WD40   1 gqclrtltGHss..vtslafspdgawlasGsdDgtvri 36 
                                    g++lr ++ H s  v+s+  s + +++asGs D +v+i
  gene113|gene113|rna113|rna113 248 GKLLRYFKSH-SlrVYSV--SLSPSYVASGSLDSSVHI 282
                                    57889999**.5569999..66677899*******997 PP

  == domain 6  score: 10.0 bits;  conditional E-value: 0.00044
                                    EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    ++l +++ H s v  l+f  +g++l+s++ Dg +  Wd
  gene113|gene113|rna113|rna113 288 RLLCSYKIHrSLVIWLKFVGNGRYLLSSGADGILCKWD 325
                                    56778888844467899********99888*****998 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.031
                                    SS.SS...EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   9 GH.ss...vtslafspdgawlasGsdDgtvriWd 38 
                                    GH +    v +l        l+ G+ ++ v+i++
  gene113|gene113|rna113|rna113 339 GHiTAqavVEDL--------LIVGT-KREVKIYN 363
                                    886444556788........999**.******97 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.013        39      71     133 ..      89     151 ..      79     159 .. 0.80
   2 !    4.7   0.1    0.0054        16      10      65 ..     147     201 ..     142     240 .. 0.67
   3 !    6.0   0.0    0.0021       6.3     204     282 ..     187     263 ..     174     266 .. 0.66
   4 !   26.0   0.1   1.8e-09   5.2e-06       3     130 ..     261     386 ..     259     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
                      WD40_like  71 eneeevenekieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennk 133
                                    +ne +++ e  + d+++++++ d+++  ++  +i +f  +  l  +++g++  +     ++ +
  gene113|gene113|rna113|rna113  89 KNERSIDFETNQSDLTFMQIDRDRIICSSDDQTIKIFGMNGRLIRTFIGHKGGVWTFMFNSKY 151
                                    678899999999999999999999999999999999999989999999998776666555555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0054
                      WD40_like  10 kkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGti 65 
                                    +++++++ G+ d+++++ +l ++++  ++ + + Sv+ +  + +d i  ++ D  i
  gene113|gene113|rna113|rna113 147 FNSKYLVSGSTDKTARIWDLWTGCTLCVLVGHK-SVVRSLKIYEDYIATGSRDSEI 201
                                    688888888888888888888888888777755.5555555666677777777666 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0021
                      WD40_like 204 lvddylivGgsfkyllliNiklnvntfklrl.evegiskikkisefvvafsTlcgkvgigDiRdketfkllesgvGviyd 282
                                    + +dy+  G   + + + N++    + ++   ++  ++ +   +++ v    ++g v++ D R+++ +++ +s+   +y+
  gene113|gene113|rna113|rna113 187 IYEDYIATGSRDSEIRVWNFR--GTCLNVLKgHTMSVRCMDMDESYLVS-GSYDGSVALWDYRKGKLLRYFKSHSLRVYS 263
                                    566777777777777777777..33333333256666666666666654.558888888888888888888887777776 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 1.8e-09
                      WD40_like   3 iYsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvt.lDGtillslleneeeveneki 81 
                                    +Ys+ +    s+++ G+ d  + +  l+   +  + +  +  vi+ k++ +  +l  +  DG + + ++ ++  v + + 
  gene113|gene113|rna113|rna113 261 VYSVSL--SPSYVASGSLDSSVHISALDGR-LLCSYKIHRSLVIWLKFVGNGRYLLSSgADGILCKWDVLENALVYKIEE 337
                                    899999..5679************999865.56667888999*********977665439****9988888888999999 PP

                      WD40_like  82 eedistvkviddklliGtnk.GsiyvfskdlqleevllgqsseIkeikie 130
                                    +  i+   v++d l++Gt++  +iy +s   q+  +l + ss I +++++
  gene113|gene113|rna113|rna113 338 NGHITAQAVVEDLLIVGTKReVKIYNLSSG-QFIRTLFSASSLISKVEVS 386
                                    99****************972589999999.8888888999999998765 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.11   3.4e+02      13      76 ..     116     175 ..     108     187 .. 0.72
   2 !   12.3   0.0   5.2e-05      0.16       8      84 ..     190     261 ..     188     267 .. 0.74
   3 ?    4.8   0.0     0.012        35      13      78 ..     274     337 ..     269     347 .. 0.82
   4 ?    1.8   0.0     0.099     3e+02      52      86 ..     350     382 ..     344     388 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                    ANAPC4_WD40  13 atedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76 
                                     ++d+ + +f +ng+ + t+   ++++ v  +++  + k L+ +  d + r+ d  +g ++  l
  gene113|gene113|rna113|rna113 116 SSDDQTIKIFGMNGRLIRTF--IGHKGGVWTFMF--NSKYLVSGSTDKTARIWDLWTGCTLCVL 175
                                    56777777777777777777..566666665554..6789999999999999999988777655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.2e-05
                    ANAPC4_WD40   8 DLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekav 84 
                                    D iA ++ d+e++v  + g  +  l  +++  +vr++   +d++ L+ +  dg+v l d  +gk+++ ++ +s + v
  gene113|gene113|rna113|rna113 190 DYIATGSRDSEIRVWNFRGTCLNVL--KGHTMSVRCM--DMDESYLVSGSYDGSVALWDYRKGKLLRYFKSHSLR-V 261
                                    5566666666666654444444444..4577778776..589***************************999873.5 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.012
                    ANAPC4_WD40  13 atedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsv 78 
                                    ++ d++++++ l+g+ + +   + + s v  L++  +g+ L  + +dg +   d+ +  +v +++ 
  gene113|gene113|rna113|rna113 274 GSLDSSVHISALDGRLLCSY--KIHRSLVIWLKFVGNGRYLLSSGADGILCKWDVLENALVYKIEE 337
                                    56677888888888888888..788899999*****************999999988888887765 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.099
                    ANAPC4_WD40  52 lLavaysdgevrlldaesgkvvhslsvksekavtc 86 
                                    lL v++ + ev++++ +sg+ +++l  +s+  +++
  gene113|gene113|rna113|rna113 350 LLIVGT-KREVKIYNLSSGQFIRTLFSASSL-ISK 382
                                    555555.579***********9998776664.555 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0058        17       2      29 ..     103     127 ..     102     140 .. 0.79
   2 ?   -0.8   0.0      0.51   1.5e+03      11      27 ..     148     164 ..     142     166 .. 0.84
   3 !    7.5   0.0    0.0013         4      12      68 ..     189     246 ..     181     266 .. 0.83
   4 ?   -2.2   0.0       1.4   4.3e+03      14      41 ..     350     378 ..     342     393 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0058
                       BBS2_Mid   2 laladvdgdgeneLvvgsddfeirvfke 29 
                                    l+++++d+d    ++ +sdd++i++f  
  gene113|gene113|rna113|rna113 103 LTFMQIDRD---RIICSSDDQTIKIFGM 127
                                    567777777...9************964 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.51
                       BBS2_Mid  11 geneLvvgsddfeirvf 27 
                                    ++++Lv gs+d + r++
  gene113|gene113|rna113|rna113 148 NSKYLVSGSTDKTARIW 164
                                    4689*******999886 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0013
                       BBS2_Mid  12 eneLvvgsddfeirvfkee.elvaeitetekvvslarlekerfayaleNGtvgvyekk 68 
                                    e+++  gs d eirv++   + ++ ++ +   v  ++++++ ++ +   G+v++++ +
  gene113|gene113|rna113|rna113 189 EDYIATGSRDSEIRVWNFRgTCLNVLKGHTMSVRCMDMDESYLVSGSYDGSVALWDYR 246
                                    468899*********996537788888888899999*****************98754 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.4
                       BBS2_Mid  14 eLvvgsd.dfeirvfkeeelvaeitetek 41 
                                     L+vg++ + +i  ++ ++ ++++  ++ 
  gene113|gene113|rna113|rna113 350 LLIVGTKrEVKIYNLSSGQFIRTLFSASS 378
                                    46666642445554555555555555555 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.016        47      35      81 ..      43      96 ..      36     123 .. 0.71
   2 !    4.2   0.3    0.0047        14     229     253 ..     148     172 ..     141     176 .. 0.86
   3 !    5.0   0.0    0.0026       7.8     228     248 ..     184     207 ..     178     213 .. 0.80
   4 !    4.4   0.0    0.0039        12     221     281 ..     219     280 ..     212     310 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.016
                                   CEESSEEEEESSSSEEEEEE.EETTEEE....EEE---S......SSS--EEEEEE- CS
                         Nup160 35 agvvyfrksnsynrfilWrvltdgktLe....lvelslk......ssllnnnlrldF 81
                                   ++ +y+   +++n+f lWr++t+g+  +    + e++ k       s  +n+ ++dF
  gene113|gene113|rna113|rna113 43 NSLLYI---KLRNDFSLWRFFTSGRHSSiagyIEEIKNKytlmrnISRSKNERSIDF 96
                                   566777...899**********99976655866666666555544444455555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0047
                                    TTTEEEEEETT-EEEEEETTTTEEE CS
                         Nup160 229 gqtylfalsrdgkLrvWnlltgkcl 253
                                    +++yl++ s d++ r+W+l tg++l
  gene113|gene113|rna113|rna113 148 NSKYLVSGSTDKTARIWDLWTGCTL 172
                                    78999****************9875 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0026
                                    ....TTTEEEEEETT-EEEEEETT CS
                         Nup160 228 i...gqtylfalsrdgkLrvWnll 248
                                    +    ++y+++ srd ++rvWn +
  gene113|gene113|rna113|rna113 184 SlkiYEDYIATGSRDSEIRVWNFR 207
                                    4444789***************86 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.0039
                                    EET.....TTTEEEEEETT-EEEEEETTTTEEEEEEE--...-SSSTTS--SSEESEEESSSS CS
                         Nup160 221 vavavveigqtylfalsrdgkLrvWnlltgkclatidll..rdeeaqdessskstldpaessl 281
                                    ++v++ +++++yl++ s dg + +W+++ gk+l+ +     r +++ + s s+  ++  +ss 
  gene113|gene113|rna113|rna113 219 MSVRCMDMDESYLVSGSYDGSVALWDYRKGKLLRYFKSHslR-VYSVSLSPSYVASGSLDSSV 280
                                    67889999*************************995544444.77777777775544444443 PP

>> DUF4934  Domain of unknown function (DUF4934)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0025       7.4      11      63 ..      92     141 ..      84     154 .. 0.83
   2 ?    4.8   0.0    0.0088        26      28      57 ..     343     372 ..     327     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0025
                        DUF4934  11 ryvpLettdsvLvGnspkikllkdkivvsskkqCllfdketGkflas.vGhiGe 63 
                                    r + +et++s L    + +++  d+i+ ss++q +     +G+ +++ +Gh+G 
  gene113|gene113|rna113|rna113  92 RSIDFETNQSDL----TFMQIDRDRIICSSDDQTIKIFGMNGRLIRTfIGHKGG 141
                                    566777777755....4678999*******99999988999****8659**995 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0088
                        DUF4934  28 kikllkdkivvsskkqCllfdketGkflas 57 
                                      ++++d ++v +k +  +++ ++G+f+++
  gene113|gene113|rna113|rna113 343 AQAVVEDLLIVGTKREVKIYNLSSGQFIRT 372
                                    457899**********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 2204.94
//
Query:       gene1131|gene1131|rna1130|rna1130  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-14   55.1   0.0    1.4e-14   54.8   0.0    1.1  1  PIG-L     GlcNAc-PI de-N-acetylase


Domain annotation for each model (and alignments):
>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   8.1e-19   1.4e-14       1     128 [.      38     149 ..      38     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 8.1e-19
                                        EEEESSTTHHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH-HHHHHHHHHHHHHHHHCTE..EEEEEC CS
                              PIG-L   1 llvlAHpDDellfaggtiaklvaagvevkivcltaGdagsplatleekeelaeiRekEaraaakhlgvadedvffl 76 
                                        ll++AHpDDe++f+++ +++l+    ++ i+cl++G+++          + ++ Re+E+r++  ++g+   +v+++
  gene1131|gene1131|rna1130|rna1130  38 LLLIAHPDDESMFFAPSLLNLKG---NIDILCLSNGNKE----------GKGKEREEELRKVGYYIGA---NVTIT 97 
                                        789******************99...8**********99..........9******************...99999 PP

                                        C.CBTT-STTS-CHHHHHHHHHHHHHH--SEEEEE-TTTT.H-HHHHHHHHHHH CS
                              PIG-L  77 d.fpDgslesydedellddlaklieryrPdvvltldpegd.dhpDHtavasaav 128
                                          f Dg+  + + + +l+ l +++ r   dv++t+d+ g  +h++H +++++a+
  gene1131|gene1131|rna1130|rna1130  98 TlFSDGKDWD-PLKVYLRLLWAYMSRP-FDVLMTFDERGVsGHKNHISCYKGAT 149
                                        9677777777.9999999999999776.5*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1426.61
//
Query:       gene1132|gene1132|rna1131|rna1131  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1759.93
//
Query:       gene1133|gene1133|rna1132|rna1132  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-12   44.8   0.0    1.2e-11   44.3   0.0    1.2  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   6.7e-16   1.2e-11       5      49 .]      40      89 ..      36      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 6.7e-16
                                       SS--HHHHHHHHHHHHHHH.......HT...SS-SSSSTTCHHHHTT-S-- CS
                       RNA_pol_Rpb6  5 kvltrYelvriaakRArQieeg.e..sl...etqkpvviAlrEiaegkipi 49
                                       + +t+Ye++++++ RA Q+++g +       e ++p+ iA  E+ e+kip+
  gene1133|gene1133|rna1132|rna1132 40 PRMTKYEKAHVIGVRASQLSAGaPpfVDignE-SNPLNIANMELNEKKIPF 89
                                       779****************6666556225433.6****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 647.89
//
Query:       gene1134|gene1134|rna1133|rna1133  [L=313]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.6   0.2       0.99    8.9   0.0    2.1  2  FeoB_N    Ferrous iron transport protein B


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   5.5e-05      0.99      76     123 ..      94     143 ..      76     158 .. 0.82
   2 ?    0.2   0.0     0.027   4.8e+02       2      23 ..     173     194 ..     172     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 5.5e-05
                                        CTSSSEEEEEEEGGGH..HHHHHHHHHHHHTTSSEEEEEETHHHHHHTTE CS
                             FeoB_N  76 eeepdvvvnvvdatnl..ernLyLtlqllelgvpvvlalnmideaekkgi 123
                                         ++ dvv++v+da      rn  +   +++ g++++++ln +  + ++ i
  gene1134|gene1134|rna1133|rna1133  94 VSKSDVVIEVIDARDPdsSRNGEVEKVVFDYGKKLIMVLNYTQYVPRDTI 143
                                        5789*********9752279999999**************9998877665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.027
                                        EEEEEESTTSSHHHHHHHHHTT CS
                             FeoB_N   2 tvalvGnpnvGkttlfnaltga 23 
                                        ++ + Gn  +Gk  ++ ++t+a
  gene1134|gene1134|rna1133|rna1133 173 RIGIFGNSKSGKNFVLRSITKA 194
                                        67899***********999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1817.11
//
Query:       gene1135|gene1135|rna1134|rna1134  [L=420]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-07   29.5   2.7    1.8e-06   27.5   2.7    1.8  1  Adap_comp_sub  Adaptor complexes medium subunit family


Domain annotation for each model (and alignments):
>> Adap_comp_sub  Adaptor complexes medium subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   2.7     1e-10   1.8e-06       6     206 ..     190     372 ..     186     382 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1e-10
                                        XXXXXXX-EEEEEEEEEEEEEE-TTS-EEEEEEEEEEEEEE---TT-EEEEEE-SS-EE--SSEESEEEEETT-B- CS
                      Adap_comp_sub   6 kgikykkneiyldviErvsvlvdkkGkilksevqGtiacksklsgmpelklgLndklnkekkielddvsfHqcVnl 81 
                                        ++   +  ++++   Er+++++dk+++i + evqG++ ++++ ++  +++++L + ++           +++++nl
  gene1135|gene1135|rna1134|rna1134 190 RELETSMSSVFILFKERLKMVIDKENNIKSGEVQGDMSITIREEEYKDIEIKLGNVDKD----------MKFSPNL 255
                                        556677788999999**************************************988777..........8889999 PP

                                        TT.HHHH-EEEE...---SEEEEEEEEEES--SS--SEEEEEEEEE.-TTTSEEEEEEEEEE-S-TT-EEEEEEEE CS
                      Adap_comp_sub  82 dk.feservisF...iPpdgeftLmrYrlsannvklPfsvkpkvkl.sgdevrveielklkenfkkkltlenvkis 152
                                        dk  ++e ++      P + ++ L++++  ++  ++P++ + ++++ s +  ++ +e+++++n+k      ++++ 
  gene1135|gene1135|rna1134|rna1134 256 DKsVSNEGILRCekgFPIEKNVALVKWKG-SDIREPPITFTFWPSEtSLNVYQIMFEYTAECNMK------DLNVF 324
                                        99888889997633359999*********.**************997777888888888888775......55555 PP

                                        EE--TT-EEEEEEESSTT-EEEEETTEEEEEE--EETT-EE..EEEEEEE---- CS
                      Adap_comp_sub 153 iplpkevsnlaiktskGkakynpeenaleWtikklpggnesslsgeleleaese 206
                                        +      s+++i++ k++ + +++++ +eW+i+ +++g++ +l+ + +++++se
  gene1135|gene1135|rna1134|rna1134 325 F------SKANISNIKINGTAKERDSHIEWSIGDVEKGTSDTLEFSCTCTDPSE 372
                                        4......45566666666678889999999999999999998988888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1231  (0.0686597); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2840.75
//
Query:       gene1136|gene1136|rna1135|rna1135  [L=158]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-22   78.4   0.0    4.7e-22   77.7   0.0    1.3  1  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.0   2.6e-26   4.7e-22       1      81 []      55     141 ..      55     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 2.6e-26
                                        .HHHSS.TTCCCHHHHHHHHHH.....TS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCG CS
                      Ribosomal_S19   1 rslkkg.pfvqesllkkvrkak.....aekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLg 70 
                                        r++++g + ++ +l+k++ ++k     +++k+e+++t++R+ +I P m+g  vgV+ G+ + p+eik++mvG kL 
  gene1136|gene1136|rna1135|rna1135  55 RKVRRGlSSREVQLIKDCIATKaactfNTEKPEMVRTQARSAIIWPVMIGALVGVHVGNGYLPIEIKPDMVGFKLS 130
                                        678899999999****99877765665556********************************************** PP

                                        GGT-SS----S CS
                      Ribosomal_S19  71 EFspTrkpvkh 81 
                                        EF+pTr + kh
  gene1136|gene1136|rna1135|rna1135 131 EFAPTRVIPKH 141
                                        *******9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1082.40
//
Query:       gene1137|gene1137|rna1136|rna1136  [L=366]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.023   14.0   0.8       0.85    9.0   0.0    3.2  3  LVIVD      LVIVD repeat
       0.58   10.2   5.1        1.1    9.3   5.1    1.5  1  DSS1_SEM1  DSS1/SEM1 family


Domain annotation for each model (and alignments):
>> LVIVD  LVIVD repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.023   2.1e+02      20      30 ..     114     125 ..     112     126 .. 0.79
   2 ?   -1.4   0.1      0.17   1.5e+03      12      18 ..     147     153 ..     145     154 .. 0.87
   3 ?    9.0   0.0   9.5e-05      0.85       2      25 ..     217     240 ..     216     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.023
                              LVIVD  20 dngLvIvDI.SN 30 
                                        + +Lv+vD  SN
  gene1137|gene1137|rna1136|rna1136 114 GEYLVVVDTySN 125
                                        689*****7776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.17
                              LVIVD  12 nYaYvAd 18 
                                        +++Y++d
  gene1137|gene1137|rna1136|rna1136 147 DFVYIGD 153
                                        89****8 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 9.5e-05
                              LVIVD   2 GdaqdvavsGnYaYvAdqdngLvI 25 
                                        G  +d+avs+ Y+Y   + ++ +I
  gene1137|gene1137|rna1136|rna1136 217 GRFMDIAVSEEYVYAMSFSGEIII 240
                                        6779**********7777666666 PP

>> DSS1_SEM1  DSS1/SEM1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.1   0.00013       1.1       8      50 ..      23      69 ..      17      72 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00013
                                       HHHH.TTSTTHHHHH--...--------..---BESSTTTSCGGCHH CS
                          DSS1_SEM1  8 lLee.DDEFEeFpvedw...deeeeeakeekklWednWDDddveddF 50
                                       +Le   +E Ee++ e +   +ee +  +e+   Wed+ DD+++ +++
  gene1137|gene1137|rna1136|rna1136 23 SLETiSEEIEEYEREYFgdvSEEGSSRSEDVAAWEDSDDDEKIRENY 69
                                       566556899******6633355555556699***********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 2132.87
//
Query:       gene1138|gene1138|rna1137|rna1137  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-26   90.6   0.0    9.1e-26   90.1   0.0    1.2  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    2.8e-06   27.1   2.4    4.3e-06   26.5   2.4    1.3  1  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0     1e-29   9.1e-26       1      82 []       9     122 ..       9     122 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 1e-29
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................x RF
                      Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................g 44 
                                        +ssrrkqrKahf ++  ++r   sa+Ls+eLr+kyg+r++p+r                                g
  gene1138|gene1138|rna1137|rna1137   9 TSSRRKQRKAHFACNDGEKRIRSSARLSRELRKKYGFRTFPLRtgdtvvvkggkfdgkegtiskinyrdykvyveG 84 
                                        89************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Ribosomal_L26  45 vtrekangttvpvgihpSkvvItklklDkdrkkiLerk 82 
                                        + ++k+ngt+  v+i pS ++It++ l++ r++ Lerk
  gene1138|gene1138|rna1137|rna1137  85 CFVTKNNGTNALVPIYPSRLTITNFFLENGREQQLERK 122
                                        *************************************8 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   2.4   4.8e-10   4.3e-06       2      32 .]      53      83 ..      52      83 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4.8e-10
                                       TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                                KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                       Gd+V V +G++ Gk+G++ k+++  ++V+v+
  gene1138|gene1138|rna1137|rna1137 53 GDTVVVKGGKFDGKEGTISKINYRDYKVYVE 83
                                       9****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.51
# Mc/sec: 843.85
//
Query:       gene1139|gene1139|rna1138|rna1138  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-16   60.5   0.2    3.1e-16   59.6   0.2    1.5  1  CSTF2_hinge  Hinge domain of cleavage stimulation factor subu
    3.3e-14   52.4   0.0    6.3e-14   51.5   0.0    1.5  1  RRM_1        RNA recognition motif. (a.k.a. RRM, RBD, or RNP 


Domain annotation for each model (and alignments):
>> CSTF2_hinge  Hinge domain of cleavage stimulation factor subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.2   3.4e-20   3.1e-16       3      81 .]      85     164 ..      83     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3.4e-20
                        CSTF2_hinge   3 Pqgvqlpp.glsapdaIsktLsslppeqllellsqlKalaqqnpsqarelLkqnpqLayAllqalllmglvdpdvv 77 
                                        P++++ p  ++  +d+  ++L+ +++++l+e+l +l++la ++ps +relL++n  L+yA+++a+l ++l dp vv
  gene1139|gene1139|rna1138|rna1138  85 PAKTKEPDsQIPEIDNLINVLDGMDKDNLKEVLFYLRKLALDQPSYLRELLNKNSSLVYAIIHAILKLKLADPGVV 160
                                        777777777999**************************************************************** PP

                        CSTF2_hinge  78 tkvl 81 
                                         ++l
  gene1139|gene1139|rna1138|rna1138 161 DEIL 164
                                        9986 PP

>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   7.1e-18   6.3e-14       1      67 [.       7      73 ..       7      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 7.1e-18
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklggr 67
                                       +fVgn+ ++v ee + e ++ +G+++s+++v+d  tgks+gf+f+e+es+   ekAl++l    ++gr
  gene1139|gene1139|rna1138|rna1138  7 IFVGNIDFEVPEERIIEELGAVGRVVSFRMVYDkTTGKSRGFGFCEYESPLIVEKALQNLK-ISFNGR 73
                                       8*********************************************************773.555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1580.81
//
Query:       gene1140|gene1140|rna1139|rna1139  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-17   63.3   0.7      4e-17   62.7   0.7    1.2  1  HIT       HIT domain
    6.4e-10   39.5   0.9    9.4e-10   39.0   0.9    1.3  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    3.2e-06   27.0   0.8    4.4e-06   26.6   0.7    1.3  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.7   6.8e-21     4e-17       6      94 ..      14      96 ..      10      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 6.8e-21
                                       CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT- CS
                                HIT  6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagq 83
                                       ++++ye+ +++++ d  p ++gh+Lvipk+h + +h+ ++eel+++l +++++ ++++     + ++++ nng h  q
  gene1140|gene1140|rna1139|rna1139 14 NNIIYETAKAFVLMDRYPLSRGHFLVIPKAHHAYFHEYEPEELSDILGTINHLIQKFGI----EKYNILQNNGNH--Q 85
                                       689*******************************************************9....78********97..9 PP

                                       SSSS-EEEEEE CS
                                HIT 84 svahlHiHvip 94
                                        v+h+H+H+ip
  gene1140|gene1140|rna1139|rna1139 86 AVFHVHFHLIP 96
                                       9*********8 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.9   1.6e-13   9.4e-10       1     108 [.       3     103 ..       3     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.6e-13
                                        T-HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TT.TTTHHHHHHHHHHHHHHHTT- CS
                             DcpS_C   1 kwvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtke.hlpllkemrekakkvieekyn 75 
                                        k++f+ ++++   ++++ye+ k+ vl D +p ++ h+lvipk++ +  ++ ++e   ++l ++++ ++k   ekyn
  gene1140|gene1140|rna1139|rna1139   3 KCIFCTMYQK--GNNIIYETAKAFVLMDRYPLSRGHFLVIPKAHHAYFHEYEPEeLSDILGTINHLIQKFGIEKYN 76 
                                        6999997777..56*************************************8872568999999999999999996 PP

                                        T-EEEEE--SCCCT--S-S--EEEEE....... CS
                             DcpS_C  76 evdaeelrvgvhyqPsvyhlHlHvisldfespg 108
                                         +     + g h  + v+h+H+H+i   ++s++
  gene1140|gene1140|rna1139|rna1139  77 IL----QNNGNH--QAVFHVHFHLIPFVSSSER 103
                                        52....233444..5677777777765555555 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.7   7.4e-10   4.4e-06      12     113 ..       2     101 ..       1     109 [. 0.90

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 7.4e-10
                                        HH-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHHHHHTT- CS
                           CwfJ_C_1  12 dsClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalvkmykkqdk 87 
                                        ++C fC  ++k   ++i+    k+++ + + pLs gH l+ip +H +   + + e+l++i    + l++ +  ++ 
  gene1140|gene1140|rna1139|rna1139   2 EKCIFCTMYQK--GNNIIYETAKAFVLMDRYPLSRGHFLVIPKAHHAYFHEYEPEELSDILGTINHLIQKFGIEKY 75 
                                        79****87765..678999****************************************************99999 PP

                                        -EEEEEE-SSS-----EEEEE--HHH CS
                           CwfJ_C_1  88 davvfEissersvHlaiqvipvpksi 113
                                        +++    +++   H++ ++ip  +s+
  gene1140|gene1140|rna1139|rna1139  76 NILQNNGNHQAVFHVHFHLIPFVSSS 101
                                        99999998999**********76655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 894.22
//
Query:       gene114|gene114|rna114|rna114  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-22   77.7   0.3    7.8e-22   77.4   0.3    1.1  1  Frataxin_Cyay  Frataxin-like domain
  ------ inclusion threshold ------
      0.017   15.3   0.1      0.056   13.6   0.0    1.8  2  P22_AR_C       P22AR C-terminal domain


Domain annotation for each model (and alignments):
>> Frataxin_Cyay  Frataxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.3   8.7e-26   7.8e-22       3     103 ..      13     108 ..      11     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 8.7e-26
                                    HHHHHHHHHHHHHHHHHHH.HHHHH--CTS.SEEEETTEEEEEETTS-EEEEEEEGGGTEEEEEES.SEEEEEEEET.TE CS
                  Frataxin_Cyay   3 deeyhkladelldsleekleelaeeaeedeldveyssgvLtiefekkgtyvinkqppnkqIWlsspisgpkrfdydekge 82 
                                    +  yh+lade+l +l+e+le+   +       ++y++  L++++e+ g+y++nkqp++ qIW sspi gp +fd   + e
  gene114|gene114|rna114|rna114  13 KPLYHRLADEALANLSEHLENELYD----G-YADYKGDNLQVKVENVGEYMFNKQPASMQIWTSSPITGPRKFDIYRSYE 87 
                                    567****************443333....2.589*****************************************99999 PP

                                    EEETTTT-BHHHHHHHHHHHH CS
                  Frataxin_Cyay  83 WiskrdgseLkelLeeelska 103
                                    Wi+++++ +L + +eeel+k+
  gene114|gene114|rna114|rna114  88 WIDTKNNISLSKYVEEELKKI 108
                                    ******************986 PP

>> P22_AR_C  P22AR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.27   2.4e+03      35      55 ..      23      43 ..      17      49 .. 0.80
   2 ?   13.6   0.0   6.2e-06     0.056      18      50 ..      87     119 ..      85     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                       P22_AR_C 35 aLraigsnlapkaYsiakEYs 55
                                   aL ++  +l+ + Y+  + Y+
  gene114|gene114|rna114|rna114 23 ALANLSEHLENELYDGYADYK 43
                                   678888889999998877775 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.2e-06
                       P22_AR_C  18 lWfalvrsvellrelepaLraigsnlapkaYsi 50 
                                     W++ ++ ++l +++e  L++i+s+l+ ka  +
  gene114|gene114|rna114|rna114  87 EWIDTKNNISLSKYVEEELKKIQSKLNRKANNM 119
                                    6*************************9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 817.64
//
Query:       gene1141|gene1141|rna1140|rna1140  [L=515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-34  116.9   0.0    1.2e-32  113.2   0.0    2.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00046   20.3   0.0     0.0008   19.6   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.0   1.3e-36   1.2e-32       2     200 .]     107     341 ..     106     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 1.3e-36
                                        HHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC CS
                    Methyltr_RsmB-F   2 llLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlgg 77 
                                        ll++++e+ +++D+caaPG+KT  i+e+  ++g v+A+dan +Rlk +++ + + +  ++iv++ Da+ ++k+   
  gene1141|gene1141|rna1140|rna1140 107 LLMELKEDSKVIDMCAAPGSKTKQILEV-VTNGLVIANDANGKRLKVLVSETAKRPNGSLIVTKHDATAFPKIYEC 181
                                        678999**********************.6789**************999999999999***********997644 PP

                                        .....EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHH CS
                    Methyltr_RsmB-F  78 ...elfDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevi 150
                                           + fDr+  D+ Cs+ g++r+ p +  + k +  + l   q ++l     l+ + G + YsTCs+++ Ene v+
  gene1141|gene1141|rna1140|rna1140 182 gsqIRFDRVFCDVVCSSDGTVRKSPGLLDEWKVSRSTGLFDTQLKILRRGCSLVAERGLVSYSTCSLNPIENECVV 257
                                        45699*********************98777778888999************************************ PP

                                        HHHHHH-TTEEEESSBSTTSTTSSECEEC.....................................TSEEE-TTTT CS
                    Methyltr_RsmB-F 151 eeaLkkredvelvetelsepkglklgeea.....................................gtlrllPhte 189
                                        +++L +  + elv+++      l    e+                                     + +rl+Ph +
  gene1141|gene1141|rna1140|rna1140 258 QKILLEG-EFELVDFRSDPRLSLFP--EYgdgtkiifreglkkwatdnqvfknpsyrpsgldlgleKCIRLYPHDQ 330
                                        ****998.89999995544333322..22246699999**************************9999******** PP

                                        SS-SEEEEEEE CS
                    Methyltr_RsmB-F 190 nkdgffiaklk 200
                                        ++ gffia lk
  gene1141|gene1141|rna1140|rna1140 331 DTGGFFIAILK 341
                                        ********885 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   8.9e-08    0.0008      22     102 ..     106     201 ..      68     267 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.9e-08
                                        T........-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHHTTEEEE..CS-CCCSSHHHH CS
                               FtsJ  22 g........ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvtti..qgditdpetiek 78 
                                        +         +v+D +aaPG+ ++ +l+ +++ g v+a D +           a++p+ ++i  + d t   +i +
  gene1141|gene1141|rna1140|rna1140 106 VllmelkedSKVIDMCAAPGSKTKQILEVVTN-GLVIANDANGKrlkvlvsetAKRPNGSLIvtKHDATAFPKIYE 180
                                        04444333377******************986.********66658989888755565555557999999987776 PP

                                        HCHCHHHSSEEEEEE--S-SS-CH CS
                               FtsJ  79 ikealserkvdlvvsDgapdvsgv 102
                                              + ++d v +D++ +  g+
  gene1141|gene1141|rna1140|rna1140 181 CGS---QIRFDRVFCDVVCSSDGT 201
                                        665...558*******99766664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3505.14
//
Query:       gene1142|gene1142|rna1141|rna1141  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-07   31.1   0.0    3.6e-07   30.6   0.0    1.3  1  Histone        Core histone H2A/H2B/H3/H4
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.033   14.6   0.0    1.2  1  CENP-S         CENP-S protein
       0.04   14.2   0.0      0.079   13.3   0.0    1.5  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     6e-11   3.6e-07      42     129 ..      17     102 ..       3     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 6e-11
                                        XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXS CS
                            Histone  42 rpgtvalkeirkyqkstdlliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRv 117
                                         +g  ++k ++k+++++   ++k  ++R+ re+ +  ++++++++ ++++l  ++ ++   ++ +A+ la++  ++
  gene1142|gene1142|rna1141|rna1141  17 LDGGDKKKTKKKSSSMCVGGMFKSAVKRISREVSP--DNNIMLTSNSIQVLCGISFDFVDTVADLAGELARKVGKQ 90 
                                        566678999**************************..*************************************** PP

                                        EEXHHHHHHHHH CS
                            Histone 118 TitpkDiqlArr 129
                                        T+ + Di +A  
  gene1142|gene1142|rna1141|rna1141  91 TVGSDDIISAFE 102
                                        *******99976 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.5e-06     0.033       9      67 ..      40      98 ..      36     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                             CENP-S  9 ysvgkiveeeaaekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvl 67
                                        +v++i++e + ++++  t++ i+ l  + ++ ++++a+     a+  +++t+  dD++
  gene1142|gene1142|rna1141|rna1141 40 SAVKRISREVSPDNNIMLTSNSIQVLCGISFDFVDTVADLAGELARKVGKQTVGSDDII 98
                                       5899*********************************988889**************86 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.3e-05     0.079       6      64 ..      40     100 ..      38     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                        HHHHHHHHCC.TTXS-.B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                      CBFD_NFYB_HMF   6 arvkkImksd.pdark.iakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64 
                                        ++vk+I ++  pd++  +++ + +++  +   f+  +a+ A e++ k ++ t+  ++i +A
  gene1142|gene1142|rna1141|rna1141  40 SAVKRISREVsPDNNImLTSNSIQVLCGISFDFVDTVADLAGELARKVGKQTVGSDDIISA 100
                                        67999999997776645788888899999999**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 865.69
//
Query:       gene1143|gene1143|rna1142|rna1142  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0042   17.1   1.0     0.0042   17.1   1.0    3.3  2  TolA_bind_tri  TolA binding protein trimerisation
     0.0044   17.4   4.0     0.0044   17.4   4.0    4.3  4  CENP-H         Centromere protein H (CENP-H)
  ------ inclusion threshold ------
      0.036   14.7   2.4      0.036   14.7   2.4    3.9  4  SlyX           SlyX
      0.037   13.6   0.5      0.037   13.6   0.5    3.7  3  Trimer_CC      Trimerisation motif
      0.055   13.0  20.6       0.22   11.1   6.6    2.3  2  HAUS-augmin3   HAUS augmin-like complex subunit 3
       0.13   12.3  28.1        1.4    9.0  12.9    2.9  2  ADIP           Afadin- and alpha -actinin-Binding
       0.14   12.6  43.9          1    9.9  13.7    3.5  4  APG6_N         Apg6 coiled-coil region
       0.87    9.6  39.0        1.2    9.1  10.3    4.1  3  TMF_DNA_bd     TATA element modulatory factor 1 DNA binding
        1.2    9.2   6.9        3.4    7.7   0.7    3.0  2  Noelin-1       Neurogenesis glycoprotein
        1.2    6.9  22.2      0.055   11.4   8.2    2.1  2  V_ATPase_I     V-type ATPase 116kDa subunit family
        2.7    7.2  23.0        1.3    8.2   4.7    2.7  3  TMPIT          TMPIT-like protein
          4    7.3  21.2        3.8    7.4   3.7    3.8  3  Sec34          Sec34-like family
        5.5    6.9  14.6        1.3    8.9   3.5    3.0  2  CHASE3         CHASE3 domain
        6.2    7.2  27.5        2.9    8.2   8.2    3.5  3  BLOC1_2        Biogenesis of lysosome-related organelles comp
        7.2    7.0  12.2        6.3    7.1   1.8    3.2  4  DUF948         Bacterial protein of unknown function (DUF948)
        8.3    5.9  16.7        0.8    9.3   2.1    2.5  3  Phage_GPO      Phage capsid scaffolding protein (GPO) serine 
        9.5    5.0  45.3      0.055   12.3  13.3    2.6  3  Spc7           Spc7 kinetochore protein


Domain annotation for each model (and alignments):
>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   1.2      0.17   1.8e+02      27      70 ..      73     116 ..      61     131 .. 0.67
   2 !   17.1   1.0     4e-06    0.0042       8      64 ..     152     205 ..     145     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.17
                      TolA_bind_tri  27 lealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkle 70 
                                        +++l++ +++L+ ++ + + ++++l e  ++l   + e+ +k++
  gene1143|gene1143|rna1142|rna1142  73 INDLKTMIDKLNQDNAKKEDDIRRLTEENKNLMSTVQELEKKSK 116
                                        55666666666666666666666666666666655555554444 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4e-06
                      TolA_bind_tri   8 rLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDe 64 
                                        ++ ri+++   l  elq++l++lq+e  + RG++E+++ ++e+l+ r  d  ++++e
  gene1143|gene1143|rna1142|rna1142 152 EIHRIAKS---LEGELQSNLSKLQEECIRYRGDTERMASEIEKLKLRNADNIEKINE 205
                                        44455554...889*******************************999988777765 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.7   7.1e+03      14      40 ..      14      40 ..      12      45 .. 0.76
   2 !   17.4   4.0   4.2e-06    0.0044       9      73 ..      67     131 ..      59     144 .. 0.85
   3 ?   -1.4  15.8       2.9     3e+03      26      80 ..     165     225 ..     145     271 .. 0.51
   4 ?    0.0   0.2         1   1.1e+03      21      75 ..     307     366 ..     300     385 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.7
                             CENP-H 14 ellklsqelrelqeeltevekenlrlk 40
                                       e+ ++s ++r+l+ + t++    lrl+
  gene1143|gene1143|rna1142|rna1142 14 EYFQISDKTRTLEHQYTDLLTRKLRLE 40
                                       566788888999999988888887776 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.2e-06
                             CENP-H   9 delssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeeleklea 73 
                                        d   +++ +l++ + +l+++ ++ e +++rl+++n++l+++++el+k++++e+ + +++++  ++
  gene1143|gene1143|rna1142|rna1142  67 DSYKKHINDLKTMIDKLNQDNAKKEDDIRRLTEENKNLMSTVQELEKKSKEESRQGERKIKGGKK 131
                                        556678999999******************************99999999999666667766555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.9
                             CENP-H  26 qeeltevekenlrlkrknrelaaellelakekesek......eklkeelekleaelkksrq 80 
                                        q++l+++++e +r +  ++ +a+e+++l+  ++         +++k+ +e+  + l+++ +
  gene1143|gene1143|rna1142|rna1142 165 QSNLSKLQEECIRYRGDTERMASEIEKLKLRNADNIekineiKENKADIEEKLKRLEEENA 225
                                        5555555555555555555555555333333333322343332233333333333333332 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1
                             CENP-H  21 elrelqeeltevekenlrlkrknrelaaellelakekesek.....eklkeelekleael 75 
                                        e+++++e  ++v  +++++ rk+ e +a+ ++++++ ++ek     +k+  ++ek ++++
  gene1143|gene1143|rna1142|rna1142 307 ECNAMEEFWNDVPIKSKATMRKKPEGVASARRKTNAPKAEKirrilPKAVTSIEKTKSDI 366
                                        666667777777777777777777878777766666666666677766777777766665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.4   3.4e-05     0.036      16      58 ..      77     119 ..      72     125 .. 0.88
   2 ?    2.1   0.3      0.29     3e+02      18      48 ..     167     197 ..     162     216 .. 0.68
   3 ?    1.5   1.8      0.45   4.8e+02       4      45 ..     188     229 ..     185     246 .. 0.67
   4 ?    1.5   1.7      0.45   4.8e+02       2      47 ..     214     262 ..     213     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.4e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                               SlyX  16 edtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                                          +i++Ln+  a+ +++i rl+++ + l+  ++ele++s+++ 
  gene1143|gene1143|rna1142|rna1142  77 KTMIDKLNQDNAKKEDDIRRLTEENKNLMSTVQELEKKSKEES 119
                                        578*********************************9988554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.29
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                               SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlk 48 
                                         + +L+++ ++ + + +r+  ++++l+ r +
  gene1143|gene1143|rna1142|rna1142 167 NLSKLQEECIRYRGDTERMASEIEKLKLRNA 197
                                        5677888888888888888888888876653 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.45
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllae 45 
                                         +e+L  + a   + i+e  +  a+ +++++rl+++ ++la+
  gene1143|gene1143|rna1142|rna1142 188 EIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENARLAK 229
                                        566666666666666666666667777777777777666654 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.45
                                        HHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                               SlyX   2 eerleeLEi...klafqedtieeLndvvaeqqqqidrlqrqlrllaerl 47 
                                        ee+l++LE+   +la      +eL + + e ++ i++l++ +++  e +
  gene1143|gene1143|rna1142|rna1142 214 EEKLKRLEEenaRLAKEKICSDELRRSINEKDEIISALKENMKQKSELI 262
                                        6777777762224555556679999999999999999999998876666 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   3.5e-05     0.037      17      40 ..      90     113 ..      84     117 .. 0.89
   2 ?   -0.3   0.3      0.77   8.1e+02      19      27 ..     215     223 ..     205     228 .. 0.72
   3 ?    0.7   0.8      0.36   3.8e+02      17      42 ..     244     268 ..     236     268 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                                        XXXX--HHHHHHHHHHHHHHHHHH CS
                          Trimer_CC  17 ssdavSRLEEelrkLqatVQelQk 40 
                                        ++d + RL Ee ++L  tVQel k
  gene1143|gene1143|rna1142|rna1142  90 KEDDIRRLTEENKNLMSTVQELEK 113
                                        678999****************88 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.77
                                        XX--HHHHH CS
                          Trimer_CC  19 davSRLEEe 27 
                                        + + RLEEe
  gene1143|gene1143|rna1142|rna1142 215 EKLKRLEEE 223
                                        556688888 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.36
                                        XXXX--HHHHHHHHHHHHHHHHHHHH CS
                          Trimer_CC  17 ssdavSRLEEelrkLqatVQelQkRL 42 
                                        + + +S L E++++      e Q+R+
  gene1143|gene1143|rna1142|rna1142 244 KDEIISALKENMKQKSE-LIEIQRRM 268
                                        56899*******99444.44677775 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.6   0.00021      0.22      72     167 ..      18     114 ..       6     123 .. 0.86
   2 ?    7.7   6.0    0.0023       2.4      60     165 ..     163     266 ..     130     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00021
                       HAUS-augmin3  72 ileeeeesleaLeqel.qeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetnav 146
                                        i ++ ++ ++++ ++l ++L+ e  l ++ +n+L v+ ++l ++ r+ e++ k+  ++lk   ++l++ na+ +  
  gene1143|gene1143|rna1142|rna1142  18 ISDKTRTLEHQYTDLLtRKLRLETLLVEEDYNNLLVMHSELVSKARDSEDSYKKHINDLKTMIDKLNQDNAKKEDD 93 
                                        55556666677777662468888888999*********************************************** PP

                       HAUS-augmin3 147 Lqqlteeakqlaeyfeeaekg 167
                                          +ltee k+l++  +e ek+
  gene1143|gene1143|rna1142|rna1142  94 IRRLTEENKNLMSTVQELEKK 114
                                        *************99998874 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                       HAUS-augmin3  60 dlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqee 135
                                        +l+ ++ ++l++++   + ++e  ++e+++L+  +a  +++ n+++   a+++++l++leee+   +k+ k   +e
  gene1143|gene1143|rna1142|rna1142 163 ELQ-SNLSKLQEECIRYRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENARLAKE-KICSDE 236
                                        222.4666677777777999999******************************9999999998887776.677889 PP

                       HAUS-augmin3 136 lraenaetnavLqqlteeakqlaeyfeeae 165
                                        lr+ ++e ++  + l e+ kq +e  e ++
  gene1143|gene1143|rna1142|rna1142 237 LRRSINEKDEIISALKENMKQKSELIEIQR 266
                                        999999999999999999998888777665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.2    0.0025       2.6      89     142 ..      72     125 ..      17     137 .. 0.54
   2 ?    9.0  12.9    0.0013       1.4      58     117 ..     171     230 ..     150     265 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                               ADIP  89 elalvqakerqlekklktleqklknekeelqrlknalqqiktqyahelkkkdre 142
                                         +  ++    +l++++++ e+ +++++ee++ l +++q+++++ + e ++ +r+
  gene1143|gene1143|rna1142|rna1142  72 HINDLKTMIDKLNQDNAKKEDDIRRLTEENKNLMSTVQELEKKSKEESRQGERK 125
                                        222333333344444444444444444444444444444444444444444444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                               ADIP  58 lnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekee 117
                                        l+e+  + + + er+ s+ie+lk ++++   ++   +++++++e klk+le+ + +++ e
  gene1143|gene1143|rna1142|rna1142 171 LQEECIRYRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENARLAKE 230
                                        56666778899***************************************9998776533 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  13.7   0.00097         1       7     103 ..      30     127 ..      29     140 .. 0.83
   2 ?    7.6  19.9    0.0048       5.1      20      98 ..     156     231 ..     145     261 .. 0.75
   3 ?    0.6   0.7      0.72   7.6e+02      16      59 ..     235     295 ..     231     314 .. 0.61
   4 ?   -2.4   0.0       6.2   6.6e+03      23      43 ..     306     326 ..     296     370 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00097
                             APG6_N   7 tdlLleeldkqleqaekerdaYeeflkklkkekkeeek.qdeeleeleeeleklekeeeelleeLkelekereele 81 
                                        tdlL  +l  +   +e++ ++++   ++l ++++++e+  ++ +++l+  ++kl+++ ++++  +++l +e+++l 
  gene1143|gene1143|rna1142|rna1142  30 TDLLTRKLRLETLLVEEDYNNLLVMHSELVSKARDSEDsYKKHINDLKTMIDKLNQDNAKKEDDIRRLTEENKNLM 105
                                        7889999999999999999999999999987766665557888889999999999999999999999999999999 PP

                             APG6_N  82 aelaaleeelealeeeeerfwr 103
                                        + +++le+++++  ++ er+++
  gene1143|gene1143|rna1142|rna1142 106 STVQELEKKSKEESRQGERKIK 127
                                        9999999999998888888776 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0048
                             APG6_N  20 qaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleale 95 
                                         a++   ++++ l+kl++e       + ++e+   e+ekl+   ++ +e+++e++++++++e++l+ leee ++l 
  gene1143|gene1143|rna1142|rna1142 156 IAKSLEGELQSNLSKLQEECIR---YRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENARLA 228
                                        4455555556666666666444...457888999999999999999999999999999999999999999999998 PP

                             APG6_N  96 eee 98 
                                        +e+
  gene1143|gene1143|rna1142|rna1142 229 KEK 231
                                        875 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.72
                             APG6_N  16 kqleqaekerdaYeeflkklkkekkeeek...................qdeeleeleeelekl 59 
                                         +l+++ +e+d+  + lk+  k+k+e                      +d+ ++  +ee+ k 
  gene1143|gene1143|rna1142|rna1142 235 DELRRSINEKDEIISALKENMKQKSE--LieiqrrmigggpqesrvilNDDVCNVFDEEILKA 295
                                        56667777777777777776666444..22356666666666666666555555555555554 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 6.2
                             APG6_N  23 kerdaYeeflkklkkekkeee 43 
                                        +e++a+eef + +  ++k + 
  gene1143|gene1143|rna1142|rna1142 306 DECNAMEEFWNDVPIKSKATM 326
                                        677777777776654433322 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.3    0.0012       1.2      25      72 ..      70     117 ..      57     121 .. 0.92
   2 ?    4.4  10.9     0.035        37      15      70 ..     169     224 ..     159     228 .. 0.91
   3 ?    6.8   2.2    0.0062       6.5       2      22 ..     236     256 ..     235     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                         TMF_DNA_bd  25 skkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                        +k  ++l++ i+kL+++n++ e +i++l++++++l + ++ele++ ke
  gene1143|gene1143|rna1142|rna1142  70 KKHINDLKTMIDKLNQDNAKKEDDIRRLTEENKNLMSTVQELEKKSKE 117
                                        677889999**********************************99886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.035
                         TMF_DNA_bd  15 aqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                         +L+eE  +++    +    i kL+  n+++ ++i+e k+ +++ e++l++lee+ 
  gene1143|gene1143|rna1142|rna1142 169 SKLQEECIRYRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEEN 224
                                        6789999999999999999**********************************985 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0062
                         TMF_DNA_bd   2 slekklkeKDeqIaqLmeEGe 22 
                                        +l+  ++eKDe+I +L+e+ +
  gene1143|gene1143|rna1142|rna1142 236 ELRRSINEKDEIISALKENMK 256
                                        567889**********98765 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4     0.055        58      36      63 ..      89     116 ..      60     128 .. 0.69
   2 ?    7.7   0.7    0.0032       3.4      50      95 ..     184     229 ..     172     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.055
                           Noelin-1  36 arsrqlrqllekvqnlsqsievldlRts 63 
                                         ++  +r+l+e+ +nl  +++ l+++ +
  gene1143|gene1143|rna1142|rna1142  89 KKEDDIRRLTEENKNLMSTVQELEKKSK 116
                                        3455678888888888777777777655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0032
                           Noelin-1  50 nlsqsievldlRtsrdlqyvrktetllktlesklkvveedrkelsa 95 
                                         ++ +ie l+lR + +++ +++ ++   ++e+klk +ee++ +l +
  gene1143|gene1143|rna1142|rna1142 184 RMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENARLAK 229
                                        68899********************************998877655 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   6.0      0.04        42      37     120 ..      49     115 ..      11     141 .. 0.51
   2 ?   11.4   8.2   5.2e-05     0.055      27     139 ..     145     256 ..     142     391 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.04
                         V_ATPase_I  37 rklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavleka 112
                                        ++l +++                 ++l ++ +++ d++++++++l++ + +ln+ + k +++ ++l+e+++ l ++
  gene1143|gene1143|rna1142|rna1142  49 NNLLVMH-----------------SELVSKARDSEDSYKKHINDLKTMIDKLNQDNAKKEDDIRRLTEENKNLMST 107
                                        2223333.................3333444444445555555555555555555555555555555544444444 PP

                         V_ATPase_I 113 kefleeee 120
                                         + le+++
  gene1143|gene1143|rna1142|rna1142 108 VQELEKKS 115
                                        44443332 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.2e-05
                         V_ATPase_I  27 kevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnel 102
                                        + ++++de++r  + le e++++ ++ ++e    +  +++ ++e+++l+ +  +  e+++e++en+ +++++l++l
  gene1143|gene1143|rna1142|rna1142 145 EGLKKMDEIHRIAKSLEGELQSNLSKLQEECIRYRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRL 220
                                        5689****************99554444444445555555566666666666666666666666666666666666 PP

                         V_ATPase_I 103 velkavlekakefleeeeeeeeeeeseeeeee.keeee 139
                                        +e++a l k k + +e +++ +e+   e  ++ ke+ +
  gene1143|gene1143|rna1142|rna1142 221 EEENARLAKEKICSDELRRSINEKD--EIISAlKENMK 256
                                        6666666555444433221111111..11111111111 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.7    0.0012       1.3      20      88 ..      47     114 ..      32     128 .. 0.77
   2 ?    7.8   6.5    0.0016       1.7       6      92 ..     170     258 ..     145     278 .. 0.59
   3 ?   -2.7   0.1       2.5   2.6e+03      38      63 ..     344     369 ..     309     411 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                              TMPIT  20 eykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesl 88 
                                         y++ l   s+l sk + ++++ kk++++lk++++kl+++ ++++e+ +++l+ee k+  ++++e+e+ 
  gene1143|gene1143|rna1142|rna1142  47 DYNNLLVMHSELVSKARDSEDSYKKHINDLKTMIDKLNQD-NAKKEDDIRRLTEENKNLMSTVQELEKK 114
                                        5666666777888888888899999999999999998887.5677888888888888888877777765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0016
                              TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerk 79 
                                        +l++e+ + +   +++ +++e+l+  + +  ++i++ k++  +++++lk+l+++    ++e+   +el+++++e++
  gene1143|gene1143|rna1142|rna1142 170 KLQEECIRYRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENArlAKEKICSDELRRSINEKD 245
                                        4444444444444444444555555555555566666666666666666666654444333334455555555555 PP

                              TMPIT  80 kvlkevesllpkk 92 
                                        ++++ +++ + +k
  gene1143|gene1143|rna1142|rna1142 246 EIISALKENMKQK 258
                                        5555555554444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.5
                              TMPIT  38 eikkqkkrlkelksslkklkksvkee 63 
                                        +++k ++ l +  +s++k+k++++++
  gene1143|gene1143|rna1142|rna1142 344 KAEKIRRILPKAVTSIEKTKSDINTK 369
                                        33344444444444444444443322 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.011        12      31      60 ..      13      42 ..      10      46 .. 0.91
   2 ?    2.9   3.7     0.085        89      10      60 ..      64     114 ..      48     120 .. 0.60
   3 ?    7.4   3.7    0.0036       3.8       7      72 ..     184     249 ..     178     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                              Sec34 31 ekfksvsektsslheaceqlleeqkrleel 60
                                       e++ ++s+kt++l+++  +ll+ + rle+l
  gene1143|gene1143|rna1142|rna1142 13 EEYFQISDKTRTLEHQYTDLLTRKLRLETL 42
                                       67899*******************999987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.085
                              Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleel 60 
                                        ++ d+  ++++++++ +++l+++  + +++ ++l e+ ++l++  ++le+ 
  gene1143|gene1143|rna1142|rna1142  64 DSEDSYKKHINDLKTMIDKLNQDNAKKEDDIRRLTEENKNLMSTVQELEKK 114
                                        344444555666666666666666666666666666666666666666655 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0036
                              Sec34   7 skeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFe 72 
                                        +  +e+++l  +  +  e+++e++e+  +++ek ++l+e+  +l +e+   +el ++i+ek ++ +
  gene1143|gene1143|rna1142|rna1142 184 RMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENARLAKEKICSDELRRSINEKDEIIS 249
                                        5667778887777888899****************************************9866555 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.5    0.0013       1.3      56     137 ..      92     173 ..      51     174 .. 0.90
   2 ?    2.5   3.4      0.12   1.2e+02      44      95 ..     178     230 ..     177     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                             CHASE3  56 eelreltadnpeqqerldrlealieqklaeleetialrreggleaalalvrsdegkelmdeiraliaemrdeerrl 131
                                        +++r+lt++n++  + +++le+  ++   + e+ i+  + g  + +++ +   eg + mdei ++++ ++ e +  
  gene1143|gene1143|rna1142|rna1142  92 DDIRRLTEENKNLMSTVQELEKKSKEESRQGERKIKGGKKGAGDLEEDEIWEVEGLKKMDEIHRIAKSLEGELQSN 167
                                        67899999999999999999999999999999999999999999999999999*****************999999 PP

                             CHASE3 132 laqrea 137
                                        l++ ++
  gene1143|gene1143|rna1142|rna1142 168 LSKLQE 173
                                        998776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                             CHASE3  44 yeqaraeiqealeelreltadnpeqqerldrlealieqklaeleet.ialrre 95 
                                        y+   +++  ++e+l+   adn e    +++ +a ie+kl+ lee+  +l++e
  gene1143|gene1143|rna1142|rna1142 178 YRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEEnARLAKE 230
                                        77778899999999999999999999999999999999997777662444444 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   9.0     0.039        41       9      90 ..      35     117 ..      13     121 .. 0.83
   2 ?    0.9   0.1      0.52   5.5e+02      35      77 ..     149     192 ..     145     193 .. 0.67
   3 ?    8.2   8.2    0.0028       2.9      13      89 ..     180     256 ..     173     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                            BLOC1_2   9 kyleaeleatvedyklLeklNeaasekykklkdvaaslekklekl.nekyeelqpylqqidqiekqvteLeeavse 83 
                                        + l+ e+  + edy+ L  ++ +  +k  + +d+ ++  ++l+ + +++++  +++ + i ++ ++ + L ++v+e
  gene1143|gene1143|rna1142|rna1142  35 RKLRLETLLVEEDYNNLLVMHSELVSKARDSEDSYKKHINDLKTMiDKLNQDNAKKEDDIRRLTEENKNLMSTVQE 110
                                        557778888999999999999999999988887777666666655133344899999******************* PP

                            BLOC1_2  84 LDeyske 90 
                                        L++ ske
  gene1143|gene1143|rna1142|rna1142 111 LEKKSKE 117
                                        **99986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.52
                            BLOC1_2  35 kykklkdvaaslekkle.klnekyeelqpylqqidqiekqvteL 77 
                                        k +++ ++a+sle +l+ +l++++ee   y    +++  ++++L
  gene1143|gene1143|rna1142|rna1142 149 KMDEIHRIAKSLEGELQsNLSKLQEECIRYRGDTERMASEIEKL 192
                                        67777888888887775256777777777776666666666665 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0028
                            BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                        +++e  +++++ L+  N   +ek++++k++ a++e+kl++l+e+++ l++ +   d++ ++++e  e++s+L e +
  gene1143|gene1143|rna1142|rna1142 180 GDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLEEENARLAKEKICSDELRRSINEKDEIISALKENM 255
                                        6788889999***************************************999999999999999999999987766 PP

                            BLOC1_2  89 k 89 
                                        k
  gene1143|gene1143|rna1142|rna1142 256 K 256
                                        5 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.8     0.006       6.3      39      88 ..      66     112 ..      49     118 .. 0.67
   2 ?    6.1   0.2     0.013        14      30      88 ..     163     221 ..     148     222 .. 0.89
   3 ?   -3.0   0.0       8.6   9.1e+03      25      43 ..     238     256 ..     234     262 .. 0.43
   4 ?   -2.1   0.0       4.7   4.9e+03      30      65 ..     354     368 ..     340     385 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.006
                             DUF948  39 ekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        e+  ++ +++++++++k n+   d  +k +++ +lte+ ++l  +v+el+
  gene1143|gene1143|rna1142|rna1142  66 EDSYKKHINDLKTMIDKLNQ---DNAKKEDDIRRLTEENKNLMSTVQELE 112
                                        44555555555555555555...777788888888888888877777775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                             DUF948  30 eaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        e+++ + +l+++   +  ++e++ +++++l     + +ek++++ e+ ad+ e+++ l+
  gene1143|gene1143|rna1142|rna1142 163 ELQSNLSKLQEECIRYRGDTERMASEIEKLKLRNADNIEKINEIKENKADIEEKLKRLE 221
                                        7788899999999999999**********9999999****************9999885 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.6
                             DUF948  25 kktldeaaatieelekqvd 43 
                                        ++ ++e  + i  l+++++
  gene1143|gene1143|rna1142|rna1142 238 RRSINEKDEIISALKENMK 256
                                        3333333333333333333 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.7
                             DUF948  30 eaaatieelekqvdpilkevedllakvnelledvne 65 
                                        +a ++ie++++                     d+n 
  gene1143|gene1143|rna1142|rna1142 354 KAVTSIEKTKS---------------------DINT 368
                                        33333333333.....................4444 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   3.1      0.01        11     156     240 ..      30     117 ..      13     138 .. 0.60
   2 ?    9.3   2.1   0.00076       0.8     177     267 ..     185     275 ..     147     282 .. 0.80
   3 ?   -3.6   0.1       6.4   6.8e+03     180     199 ..     347     366 ..     310     389 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.01
                          Phage_GPO 156 taavetalefeeeeeeeegeslferikallskkkksdd...arfadveeavelvAeevkelsekveallaleaela 228
                                        t+    +l +e+   ee+ ++l+    +l+sk + s+d   ++++d++  ++++ +  ++ ++++++l++++++l+
  gene1143|gene1143|rna1142|rna1142  30 TDLLTRKLRLETLLVEEDYNNLLVMHSELVSKARDSEDsykKHINDLKTMIDKLNQDNAKKEDDIRRLTEENKNLM 105
                                        5555556666666666666677777777777777777523255666666666666666666666665555555555 PP

                          Phage_GPO 229 alkkeveklkae 240
                                        +  +e+ek+++e
  gene1143|gene1143|rna1142|rna1142 106 STVQELEKKSKE 117
                                        444444444433 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00076
                          Phage_GPO 177 lferikallskkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsktd 252
                                        ++++i++l + +++++ +++++++e   ++ e++k+l+e+ ++l++++    +l+++++++++ ++aLke+++++ 
  gene1143|gene1143|rna1142|rna1142 185 MASEIEKL-KLRNADNIEKINEIKENKADIEEKLKRLEEENARLAKEKICSDELRRSINEKDEIISALKENMKQKS 259
                                        44455443.44455556889999999999999999999999999899999999*********************99 PP

                          Phage_GPO 253 a.kekqrpeatGeege 267
                                        +  e qr  + G+ +e
  gene1143|gene1143|rna1142|rna1142 260 ElIEIQRRMIGGGPQE 275
                                        9888999998885543 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.4
                          Phage_GPO 180 rikallskkkksddarfadv 199
                                        +i+++l k  +s +++ +d+
  gene1143|gene1143|rna1142|rna1142 347 KIRRILPKAVTSIEKTKSDI 366
                                        23333333333222222222 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  13.3   5.2e-05     0.055     162     290 ..      22     148 ..      11     153 .. 0.78
   2 ?    3.4  19.1     0.027        28     146     260 ..     152     265 ..     144     269 .. 0.45
   3 ?   -3.4   0.3       3.3   3.5e+03     234     245 ..     354     365 ..     323     389 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.2e-05
                               Spc7 162 eeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                           l+  + +l ++k +le  l   +e +++l  + +e + ++r++ ++ k+ i+ +k+++++l+++ +++e++i 
  gene1143|gene1143|rna1142|rna1142  22 TRTLEHQYTDLLTRKLRLETLLV--EEDYNNLLVMHSELVSKARDSEDSYKKHINDLKTMIDKLNQDNAKKEDDIR 95 
                                        44444444444444444444333..33556677789999999********************************** PP

                               Spc7 238 elkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivsls 290
                                         l+e+ ++l++ ++e e+  +e+ +  e  ++  k+   +lee   w++ +l+
  gene1143|gene1143|rna1142|rna1142  96 RLTEENKNLMSTVQELEKKSKEESRQGERKIKGGKKGAGDLEEDEIWEVEGLK 148
                                        *****************999999999999999999999999999999887765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                               Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid.keeLeelreelaelkaeieekkk 220
                                        e+  + ++ + +L+++ ++l+e   +++   +++ +e+ekl+ ++++  +i+  +e++e + +++e  + +ee ++
  gene1143|gene1143|rna1142|rna1142 152 EIHRIAKSLEGELQSNLSKLQEECIRYRGDTERMASEIEKLKLRNAD--NIEkINEIKENKADIEEKLKRLEEENA 225
                                        33333333344455555555555555555555555555555553322..332223344444444444444444444 PP

                               Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                                        +la+ +   +el+ +i+e +e +s l+e+++++ +++e +
  gene1143|gene1143|rna1142|rna1142 226 RLAKEKICSDELRRSINEKDEIISALKENMKQKSELIEIQ 265
                                        4444444445555555555555555555555555555555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.3
                               Spc7 234 ekieelkeqkse 245
                                        ++++++++ ks+
  gene1143|gene1143|rna1142|rna1142 354 KAVTSIEKTKSD 365
                                        222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2976  (0.165988); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                       128  (0.00713927); expected 17.9 (0.001)
Passed Fwd filter:                        62  (0.00345808); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 1.22u 0.36s 00:00:01.58 Elapsed: 00:00:00.55
# Mc/sec: 2320.00
//
Query:       gene1144|gene1144|rna1143|rna1143  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   12.3   0.2      0.076   12.3   0.2    2.8  3  SLATT_5   SMODS and SLOG-associating 2TM effector domain fami
       0.25   11.8   8.3       0.32   11.5   1.1    2.4  2  MerC      MerC mercury resistance protein
       0.43   11.0   2.8        2.1    8.8   0.0    3.0  3  DUF202    Domain of unknown function (DUF202)
       0.81    9.8   8.0       0.07   13.2   1.6    2.3  2  TMEM169   TMEM169 protein family
       0.84   10.1   7.1          2    8.9   0.1    2.6  2  DUF4231   Protein of unknown function (DUF4231)


Domain annotation for each model (and alignments):
>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   2.1e-05     0.076       2      82 ..       8      92 ..       7     109 .. 0.75
   2 ?   -0.6   0.1       0.2   7.2e+02     125     168 ..      94     137 ..      88     163 .. 0.51
   3 ?   -1.4   2.6      0.33   1.2e+03      28      76 ..     172     217 ..     167     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                            SLATT_5  2 keeleelkrkiwvTkkaRfnAaeRlrrknklstfsls......llSvylivlsllsnkssestinenlldflsiilSi 73
                                        + +e+lk+  ++T +a+ + +eR+++++k ++++ +      +lS+ li+ ++++   s+  +n++++  ++ i++ 
  gene1144|gene1144|rna1143|rna1143  8 AKAKENLKDLHEKTNEACKRIKERIKENHKSINICGIeidssdVLSLILIFTPIVP---SILGFNNSYVPTTISIIGY 82
                                       678999***99***********************7643333338999999999999...7777777777666666665 PP

                            SLATT_5 74 lv.lvislle 82
                                       lv +++sl+ 
  gene1144|gene1144|rna1143|rna1143 83 LVaIIFSLYQ 92
                                       5414555554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.2
                            SLATT_5 125 iskeYeeiLdkyeNHdeiDyklfraknakkseelekskklkwfl 168
                                        i k Y++ ++ +e H+      fr  +   +  +++   l++++
  gene1144|gene1144|rna1143|rna1143  94 ITKLYNSYVKYKETHSIWELLGFRNLMLLFQVAFGMFLSLHLLH 137
                                        55555555555555555555555555444444444444444444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.33
                            SLATT_5  28 rknklstfslsllSvylivlsllsnkssestinenlldflsiilSilvl 76 
                                        +k+++++f++ l++++li+l+           + +++ +++++ S+++l
  gene1144|gene1144|rna1143|rna1143 172 KKDDFYQFLILLIGLVLILLATSI---AWKEVTTSYIVVSALLSSMMIL 217
                                        578888888888888888888777...6666666777777777777766 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.3     0.026        94      17      85 ..      58     136 ..      51     165 .. 0.54
   2 ?   11.5   1.1     9e-05      0.32      25      91 ..     161     229 ..     151     255 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.026
                               MerC  17 llPvllallpllglsf.la.sellhqvllilvvaigllalvvgyrrhrktsvl.vlgalGllillvalflg..... 84 
                                         +P++ ++l   +  + ++ s +   v++i+++  g+  l+ +y + ++t+ +  l+ +  l+ll+ + +g     
  gene1144|gene1144|rna1143|rna1143  58 FTPIVPSILGFNNSYVpTTiSIIGYLVAIIFSLYQGITKLYNSYVKYKETHSIwELLGFRNLMLLFQVAFGmflsl 133
                                        4666666666666555555555577888888888899999999965555554403333333444433333323333 PP

                               MerC  85 ..t 85 
                                           
  gene1144|gene1144|rna1143|rna1143 134 hlL 136
                                        330 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9e-05
                               MerC  25 lpllglsf..la.sellhqvllilvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetl 91 
                                          ++ ls   ++ +   + ++l++++++ lla+ +++++ +  +++v ++l+ +++l  ++ +    e+l
  gene1144|gene1144|rna1143|rna1143 161 KLAWKLSNfsIKkDDFYQFLILLIGLVLILLATSIAWKEVTTSYIVVSALLSSMMILSDHIGE-PITEKL 229
                                        45555554222323336667778899999***********************99999999998.444444 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.42   1.5e+03      42      55 ..      76      89 ..      45     110 .. 0.62
   2 ?    0.3   0.5      0.27   9.5e+02      23      23 ..     159     159 ..     116     193 .. 0.41
   3 ?    8.8   0.0    0.0006       2.1       9      64 ..     193     256 ..     192     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.42
                             DUF202 42 ilglilivlgiltl 55
                                        +++i  +++i++ 
  gene1144|gene1144|rna1143|rna1143 76 TISIIGYLVAIIFS 89
                                       23333333333333 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                             DUF202  23 l 23 
                                        +
  gene1144|gene1144|rna1143|rna1143 159 I 159
                                        1 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0006
                             DUF202   9 TfLaWlRtslalialglallrffl.........tgepsal..gkilglilivlgiltllvglvrylr 64 
                                        T +aW  ++++ i+++++l              t+    l  + +l++i+++l i+t+++++ + ++
  gene1144|gene1144|rna1143|rna1143 193 TSIAWKEVTTSYIVVSALLSSMMIlsdhigepiTEK---LdeTEPLSAIAALLPIFTVIYVTANTIQ 256
                                        889****************98544556555554222...133699***************9988776 PP

>> TMEM169  TMEM169 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.6     2e-05      0.07      26      76 ..      82     132 ..      65     144 .. 0.84
   2 ?   -0.4   0.4      0.32   1.2e+03      63      77 ..     179     193 ..     147     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                            TMEM169  26 fvvsavvsfylGtltWyniflvyneersllhkillcPllillyPllivlvt 76 
                                         +v+++ s y G+   yn ++ y+e++s+++ + +  l++l+   + ++++
  gene1144|gene1144|rna1143|rna1143  82 YLVAIIFSLYQGITKLYNSYVKYKETHSIWELLGFRNLMLLFQVAFGMFLS 132
                                        68999***************************9999999887655555554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.32
                            TMEM169  63 llillyPllivlvtl 77 
                                        +lill  l+++l++ 
  gene1144|gene1144|rna1143|rna1143 179 FLILLIGLVLILLAT 193
                                        333333333333333 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00056         2      21      80 ..      53     108 ..      45     119 .. 0.68
   2 ?    1.8   3.8     0.091   3.3e+02       8      59 ..     167     217 ..     160     259 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00056
                            DUF4231  21 rlitivlgallpilvssklgagvsvlkiltallsalvai.laaleeffrykerWrryRsta 80 
                                        +li+i++ ++ +il       + s  + ++++++ lvai  + ++++ +  +++ +y++t+
  gene1144|gene1144|rna1143|rna1143  53 SLILIFTPIVPSILGF-----NNSYVPTTISIIGYLVAIiFSLYQGITKLYNSYVKYKETH 108
                                        5555555555555555.....5566666666665555553777888999999999999986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.091
                            DUF4231   8 kkasrakrrfrllrlitivlgallpilvssklgagvsvlkiltallsalvai 59 
                                        +  s+ k  f+ + +++i l+ +l +++   ++ + +   +++alls++ ++
  gene1144|gene1144|rna1143|rna1143 167 SNFSIKKDDFYQFLILLIGLVLILLATSI-AWKEVTTSYIVVSALLSSMMIL 217
                                        55566677788666666666666666666.2333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2004  (0.111774); expected 358.6 (0.02)
Passed bias filter:                     1164  (0.0649228); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 1650.14
//
Query:       gene1145|gene1145|rna1144|rna1144  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-11   42.7   0.2      9e-11   41.6   0.2    1.6  1  Med26     TFIIS helical bundle-like domain


Domain annotation for each model (and alignments):
>> Med26  TFIIS helical bundle-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.2     5e-15     9e-11       2      51 ..     125     174 ..     124     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 5e-15
                                        HHHHS---....HHHHHHSHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHH CS
                              Med26   2 iLaqLeklpittetLkstgIGkvVnalrkhkhetaevktlAksLvekWkk 51 
                                        +L+ L+ ++i +e+L  +g+Gk+V +++ +++et+ev+++Ak Lv+kW +
  gene1145|gene1145|rna1144|rna1144 125 LLDVLKSMKIHKEHLIVSGVGKIVYFYSINPKETKEVRSMAKTLVQKWTN 174
                                        7999************************99******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1075.90
//
Query:       gene1146|gene1146|rna1145|rna1145  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.023   14.7   0.0    1.4  1  Swi3      Replication Fork Protection Component Swi3
      0.024   14.9   0.5        4.1    7.7   0.1    2.1  2  Flu_B_M2  Influenza B matrix protein 2 (BM2)


Domain annotation for each model (and alignments):
>> Swi3  Replication Fork Protection Component Swi3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.5e-06     0.023       7      74 ..      25     101 ..      16     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-06
                               Swi3   7 LlsekGlpaLrknf......kklkfkgkgheaedlkkllqfyqlWahrL....fPkakfkdflekveklgkkkevk 72 
                                        L+s+kG+++L  ++      ++++ ++k    +++++l+ +y  W ++L      +++  +fl+ +e++++k+ v 
  gene1146|gene1146|rna1145|rna1145  25 LVSSKGISFLVDHVnressnEDVRPNKKSI-EKEVSNLIDYYFAWINGLpirkNMTMSKYEFLKYLEDFCRKNDVS 99 
                                        9999******99987433333444444444.589**************9332223455569999999999999987 PP

                               Swi3  73 ty 74 
                                        + 
  gene1146|gene1146|rna1145|rna1145 100 NL 101
                                        76 PP

>> Flu_B_M2  Influenza B matrix protein 2 (BM2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00045       4.1      58      89 ..       9      42 ..       3      48 .. 0.79
   2 ?    6.2   0.1    0.0013        12      43      67 ..      48      72 ..      43      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00045
                           Flu_B_M2 58 hnyqkeiqaketmkkil..sdnmevlgdhivveg 89
                                        n q+  + ket+kk l  s  +  l dh+  e 
  gene1146|gene1146|rna1145|rna1145  9 RNKQRRYNEKETIKKFLvsSKGISFLVDHVNRES 42
                                       689999*********8844567889999998775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0013
                           Flu_B_M2 43 npnkeainrevsilrhnyqkeiqak 67
                                        pnk++i++evs l   y   i+  
  gene1146|gene1146|rna1145|rna1145 48 RPNKKSIEKEVSNLIDYYFAWINGL 72
                                       59***********999998777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 669.26
//
Query:       gene1147|gene1147|rna1146|rna1146  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0035   16.8   2.1       0.33   10.3   0.3    2.9  2  ThiF      ThiF family


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.3   1.9e-05      0.33       1      47 [.       9      66 ..       9      69 .. 0.76
   2 !    3.5   0.1    0.0022        40     126     214 ..      79     173 ..      73     180 .] 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.9e-05
                                       THHHHHHHHHHHHHHHHTSEEEEE.-..........-SHHHHHHHHHHHHHTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.x..........xxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF  1 ysrqlallgedgqekLrdskvllv.G..........aGglGsellknLalsGvgkltl 47
                                       y+rq++l+g+d q+ +++s+v+++ G          +  +G e+lknL+l+Gv+++t+
  gene1147|gene1147|rna1146|rna1146  9 YDRQIRLFGKDTQKLIEESHVAIIqGppyvlgrekrINDVGGEILKNLVLLGVERVTV 66
                                       8999999999999999998887654333331144444579*************99997 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0022
                                        HHHHHH...HHT-EEEE..EEEETTEEEEEEE.EE........CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE- CS
                                        xxxxxx...xxxxxxxx..xxxxxxxxxxxxx.xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF 126 vnracv...kkgiplie..agtlgfegqvvvi.ip........gktgcyeCldpsstedptekkvplctsiagnip 187
                                        vn++     k ++ +i+   + ++++g++ vi i+        g   c +C+        +  k  lc + ++n  
  gene1147|gene1147|rna1146|rna1146  79 VNEITKineKIRVAVIDeqQTEEAWNGYTLVIlIDckgqttcpGIYVCSRCM-----GFHPLGKRHLC-RECSN-- 146
                                        5555554444555566654567778888888864344333233555666666.....57888888888.77773.. PP

                                        B-HHH.HHHHHHHHHHHHHHHHTTBCGG CS
                                        xxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF 188 aiatt.tavvaglaalellkllsgkekl 214
                                         i+ +   +++ ++++e +k l++k+  
  gene1147|gene1147|rna1146|rna1146 147 -ISVVhDCLLGAIIVQEWVKRLQKKPFV 173
                                        .333325678889999999998766644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1243.06
//
Query:       gene1148|gene1148|rna1147|rna1147  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-47  162.1   0.1    1.5e-47  161.8   0.1    1.1  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   0.1   8.6e-52   1.5e-47       8     157 ..      28     178 ..      21     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 8.6e-52
                      Pro_isomerase   8 s..kGrivieLfadkaPktvenFlklvkeg...fYdgttFhRvikgfmvqgGdptgktsageqekkggesi..rai 76 
                                        +  +Griv++Lf+d +P t++nF++l+k+     Y+g++FhR+i+gfmvqgGd+t++  +g+    ggesi   ++
  gene1148|gene1148|rna1147|rna1147  28 EerLGRIVMKLFDDVVPRTARNFRELCKRPeraGYKGSIFHRIIPGFMVQGGDYTAH--NGT----GGESIygDRF 97 
                                        3348***********************976777********************8887..344....333333369* PP

                      Pro_isomerase  77 pdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiek.vetde.erpkk 149
                                        +dE+ ++lkh k+G+l+ma+ g  ++++gsqFfItl+++p+ldgk++vFG+V+eGm vv +i+k +++++  +   
  gene1148|gene1148|rna1147|rna1147  98 DDEN-FNLKHsKEGILSMANCG--KHTNGSQFFITLEKTPWLDGKHVVFGEVIEGMSVVHRIAKyGSQNGqVARGY 170
                                        ****.89999899*******98..6***************************************544444433334 PP

                      Pro_isomerase 150 nvkivsae 157
                                        +v i++++
  gene1148|gene1148|rna1147|rna1147 171 KVEIRDCG 178
                                        48888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1328.28
//
Query:       gene1149|gene1149|rna1148|rna1148  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1368.97
//
Query:       gene1150|gene1150|rna1149|rna1149  [L=482]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   5.8e-115  383.8   0.7   5.8e-115  383.8   0.7    1.5  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    9.4e-15   54.2   2.4    2.7e-08   33.0   0.3    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    0.00046   19.2   0.3       0.16   10.9   0.1    2.4  2  tRNA-synt_1f  tRNA synthetases class I (K)
    0.00063   18.1   0.1      0.011   14.1   0.0    2.3  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
       0.05   13.4   1.8        4.4    7.0   0.0    2.4  2  TACC_C        Transforming acidic coiled-coil-containing prot
       0.08   13.1   0.4        1.2    9.3   0.5    2.4  2  FliG_C        FliG C-terminal domain
      0.093   13.3   0.0        1.6    9.3   0.0    2.6  1  DUF1801       Domain of unknown function (DU1801)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.8   0.7  2.3e-118  5.8e-115       2     299 ..      20     317 ..      19     319 .. 0.93
   2 ?   -3.0   0.1       1.4   3.6e+03     107     112 ..     381     386 ..     346     429 .. 0.55

  Alignments for each domain:
  == domain 1  score: 383.8 bits;  conditional E-value: 2.3e-118
                                        ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHH.TT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHH CS
                       tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqa.lgYdvqfvqnvtDidDkiikrareeeksvkela 76 
                                        ++p++ ++v++Y+CGptvyd  h+GhaR++v+fD++rr+l + l Ydv+fv n+tDidDkii ra+ ++ s++e++
  gene1150|gene1150|rna1149|rna1149  20 FVPSRGNEVKMYICGPTVYDSPHIGHARTYVMFDVMRRVLSDyLKYDVRFVMNITDIDDKIISRANVSGASTEEIT 95 
                                        5678889*********************************998********************************* PP

                                        HHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT.--HHHHH CS
                       tRNA-synt_1e  77 ekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklsk.qnleele 151
                                         k+ eef++d+eaLnv++p++ + v+ +vd+i++++ekl  +g+aY++  g vyfd +k++e  +    ++++ ++
  gene1150|gene1150|rna1149|rna1149  96 RKYTEEFFEDMEALNVRQPSFVTFVTSYVDKIVKFIEKLETNGFAYESG-GSVYFDLEKYQEKHNYPLfKSKDGIN 170
                                        ************************************************9.******98766554443303334344 PP

                                        HT----S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHH CS
                       tRNA-synt_1e 152 lgaegevseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenela 227
                                        +  eg+ +++k+ + Df+LWk+ske+ep+++s wg GRPGWhieCsvm+s++lg ++dih+GGiDLafPhhene+a
  gene1150|gene1150|rna1149|rna1149 171 S--EGAENKDKRGSWDFVLWKKSKENEPRYKSKWGYGRPGWHIECSVMSSDILGGDLDIHAGGIDLAFPHHENEIA 244
                                        3..3444578****************************************************************** PP

                                        HHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHH CS
                       tRNA-synt_1e 228 qseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleea 299
                                        q +a+f  +++v++flh+ghl+i+g kmsksLknf+tik++l+  +prqlR+l+l +++++ + ++ e+l+ a
  gene1150|gene1150|rna1149|rna1149 245 QCQAYFMkEPWVRWFLHTGHLNIDGLKMSKSLKNFTTIKEALEMISPRQLRVLFLYHQWNKDMSYEREHLKFA 317
                                        *****99789**********************************************************99866 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                        HHHHHH CS
                       tRNA-synt_1e 107 eiielv 112
                                        e+i++ 
  gene1150|gene1150|rna1149|rna1149 381 EMINFT 386
                                        333222 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.3   1.1e-11   2.7e-08      12     126 ..      39     153 ..      30     160 .. 0.90
   2 !   21.0   0.1   4.5e-08   0.00011     317     371 ..     261     314 ..     244     330 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.1e-11
                                        S---HHHHHHHHHHHHHHHHHHHT.T-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---S CS
                       tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlr.geevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfd 86 
                                        +++H+Gh+++++  D++ R      +++v fv        +i  +A+ +g + ee+++k++ee+ e+++ ln+ + 
  gene1150|gene1150|rna1149|rna1149  39 DSPHIGHARTYVMFDVMRRVLSDYlKYDVRFVMNITDIDDKIISRANVSGASTEEITRKYTEEFFEDMEALNVRQP 114
                                        689****************9876559*******999999************************************* PP

                                        EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTT CS
                       tRNA-synt_1g  87 kygrttseehkelvqeifkklkekgliyekeieqlycpkd 126
                                        ++ +  ++   ++v ++++kl+++g+ ye+  +++++ ++
  gene1150|gene1150|rna1149|rna1149 115 SFVTFVTSYVDKIV-KFIEKLETNGFAYESGGSVYFDLEK 153
                                        **998888888887.699***********99999998765 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4.5e-08
                                        EE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
                       tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedf 371
                                         +++l+++g K+SkS +++ ++keale +++ +lR  ++++ + +kD++++ e++
  gene1150|gene1150|rna1149|rna1149 261 HTGHLNIDGLKMSKSLKNFTTIKEALEMISPRQLRVLFLYH-QWNKDMSYEREHL 314
                                        689********************************777665.5678898887754 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0017       4.5      30      73 ..      34      78 ..      13     136 .. 0.85
   2 !   10.9   0.1   6.2e-05      0.16     280     318 ..     270     308 ..     240     339 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0017
                       tRNA-synt_1f 30 GispSGliHiGnlrevltadlvaralrkrgee.vrlilisDdmDg 73
                                       G ++  ++HiG +r  +  d+++r l++  +  vr+++ + d+D 
  gene1150|gene1150|rna1149|rna1149 34 GPTVYDSPHIGHARTYVMFDVMRRVLSDYLKYdVRFVMNITDIDD 78
                                       55555689*******************995545*********996 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.2e-05
                       tRNA-synt_1f 280 ekmssSkGnvltledwlevaepevlrflilrrkPkkakk 318
                                         kms+S  n+ t++++le+++p  lr l+l ++ +k ++
  gene1150|gene1150|rna1149|rna1149 270 LKMSKSLKNFTTIKEALEMISPRQLRVLFLYHQWNKDMS 308
                                        39************************9999888777665 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.037        94      27      55 ..      30      58 ..      14      70 .. 0.85
   2 !   14.1   0.0   4.2e-06     0.011     518     600 ..     226     308 ..     223     310 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.037
                        tRNA-synt_1 27 lvdgPPyvtGslHiGhalaktlkdiviry 55
                                       +++  P v  s+HiGha + ++ d++ r+
  gene1150|gene1150|rna1149|rna1149 30 MYICGPTVYDSPHIGHARTYVMFDVMRRV 58
                                       6777899999**************99886 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.2e-06
                        tRNA-synt_1 518 dmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlils 593
                                        d+ + G+D  +   ++ i +  a + +eP+ + ++h   ++ +G KmSKsl+N    ++ ++  +   lR   ++ 
  gene1150|gene1150|rna1149|rna1149 226 DIHAGGIDLAFPHHENEIAQCQAYFMKEPWVRWFLHTGHLNIDGLKMSKSLKNFTTIKEALEMISPRQLRVLFLYH 301
                                        56678999999999999999***********************************999999999999999999888 PP

                        tRNA-synt_1 594 dvgrdin 600
                                        +  +d++
  gene1150|gene1150|rna1149|rna1149 302 QWNKDMS 308
                                        8888875 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5    0.0074        19      35     124 ..     266     357 ..     235     362 .. 0.74
   2 ?    7.0   0.0    0.0017       4.4      44     109 ..     400     467 ..     397     476 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0074
                             TACC_C  35 kkenqemkkivaefekt..iaqlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqkevlegy 108
                                        + + ++m+k +++f ++    ++i+ +q +     ++ +k ++ + + l+  +s+ek++ + ++  e +++ + g+
  gene1150|gene1150|rna1149|rna1149 266 NIDGLKMSKSLKNFTTIkeALEMISPRQLRVLFLYHQWNKDMSYEREHLKFAESIEKKIFNFMSIAESMRKNTLGF 341
                                        55667777777777653112345555555555556666666655555666678*********************** PP

                             TACC_C 109 kkneeslkkcaeeyla 124
                                        k+ e++ +++ ee+++
  gene1150|gene1150|rna1149|rna1149 342 KTLEDVDREVLEELKD 357
                                        ******9999998764 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0017
                             TACC_C  44 ivaefektiaqli..eekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqkevlegyk 109
                                        +v+++ k i ++   +e ++q+++++  ++++l++  + +  +   +  +s+ f++++  +e++++y 
  gene1150|gene1150|rna1149|rna1149 400 VVKDYIKEIMEMFglSEGEAQASSKEDLVAQMLSDFRESIRGMARRKEPYSNFFQKCDWVREAIKDYG 467
                                        899999*****962267778888888889************************************995 PP

>> FliG_C  FliG C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.23   5.9e+02      67     104 ..      98     138 ..      85     139 .. 0.71
   2 ?    9.3   0.5   0.00047       1.2       6      63 ..     312     370 ..     308     394 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.23
                                        HHHHHHHHHHHC...-S--HHHHHHHHHHHHHHHHHHHCTT CS
                             FliG_C  67 aaemlreeleal...gpvrlsdveeaqkeivaiirrleeeG 104
                                          e++ e++eal   +p  +  v  + ++iv+ i +le +G
  gene1150|gene1150|rna1149|rna1149  98 YTEEFFEDMEALnvrQPSFVTFVTSYVDKIVKFIEKLETNG 138
                                        55666677777622244445567888899999999999988 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00047
                                        H-HHHHHHHHHHHS-GGGG.GGS-HHHHH.HHHTTS-HHHHHHHHCTS-HHHHHHHHTTS CS
                             FliG_C   6 edpelaeeirkkmftfedl.vrlddraiq.rllrevdkedLalaLkgaseelrekilsnm 63 
                                        e  ++ae+i+kk+f+f  +   + ++++  + l++vd e+L   Lk  +e + ++il+n+
  gene1150|gene1150|rna1149|rna1149 312 EHLKFAESIEKKIFNFMSIaESMRKNTLGfKTLEDVDREVLE-ELKDVQESIHAAILDNI 370
                                        56689**************77788888864678888888775.69999999999999998 PP

>> DUF1801  Domain of unknown function (DU1801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00062       1.6      34      79 ..     311     355 ..     189     357 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00062
                                        SSEEEE......HHTHHHHHH.........-EEESSEEEEETTS---HHHHHHH CS
                            DUF1801  34 kkhvslffkGakedpkglleg........kkgkgkrcirfkslddideelleel 79 
                                         +h+++         ++ +e+         +++ k ++ fk+l+d+d e+leel
  gene1150|gene1150|rna1149|rna1149 311 REHLKF---------AESIEKkifnfmsiAESMRKNTLGFKTLEDVDREVLEEL 355
                                        333333.........33344444445556678*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 3024.19
//
Query:       gene115|gene115|rna115|rna115  [L=863]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-50  170.2   0.0    5.6e-50  170.2   0.0    3.0  4  Pkinase         Protein kinase domain
    1.5e-22   80.1   0.1    9.6e-22   77.5   0.0    2.2  2  Pkinase_Tyr     Protein tyrosine kinase
    1.2e-10   41.1   0.6    2.6e-10   40.0   0.6    1.5  1  C1_1            Phorbol esters/diacylglycerol binding domain 
    8.7e-08   31.8   0.0    1.7e-07   30.8   0.0    1.5  1  Kinase-like     Kinase-like
    1.9e-06   27.9   6.9    1.9e-06   27.9   6.9    3.2  3  HR1             Hr1 repeat
     0.0019   18.1   0.3     0.0071   16.3   0.3    1.9  2  APH             Phosphotransferase enzyme family
     0.0066   16.0   2.4      0.017   14.7   2.4    1.6  1  PHD_2           PHD-finger
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.032   13.6   0.0    1.6  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.017   15.1   1.3      0.017   15.1   1.3    2.5  3  zf-RING_9       Putative zinc-RING and/or ribbon
      0.067   12.8  32.6        0.2   11.2   7.7    3.2  3  Filament        Intermediate filament protein
        0.1   12.5   0.1        0.3   11.0   0.1    1.9  1  DUF4478         Pyrimidine/purine nucleotide 5'-monophosphate
       0.16   12.3   2.2       0.37   11.1   2.2    1.6  1  C1_2            C1 domain
       0.23   11.4   3.5       0.54   10.2   3.5    1.6  1  PHD             PHD-finger
        9.8    6.6   6.1        3.5    8.0   3.0    1.9  2  zf-RING-like    RING-like domain


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   0.0   4.4e-53   5.6e-50       1     264 []      45     298 ..      45     298 .. 0.92
   2 ?   -1.7   0.8       1.2   1.5e+03     204     246 ..     404     443 ..     379     448 .. 0.57
   3 ?   -1.6   0.3         1   1.3e+03      30      79 ..     459     508 ..     449     535 .. 0.81
   4 ?   -2.2   0.1       1.7   2.1e+03      21     111 ..     712     805 ..     707     807 .. 0.65

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 4.4e-53
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEEEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklk.hpnivrlyevfeekdelylvle 78 
                                    ye ++++ +G++G+V+ ++   +gki+A+K+++ke    + +   +++E + +  +  ++ +v    +++++++ly +++
  gene115|gene115|rna115|rna115  45 YEIVKNVAKGGYGEVFLVR---KGKIYAMKRVSKELVLRQPHtALFMAEKEAMVDCIgSEWLVCAHMTMQDEEYLYYLMD 121
                                    67889999**********9...7************99998886788999999888777********************** PP

                                    --TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS.BCTT CS
                        Pkinase  79 yveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk.ltsf 157
                                    +++gg+++ ll+++ +l+e+ ++++a++i+++l+ lH+ g iHrDlKp+NiLi ++g++K++DFG + +++ ++   +  
  gene115|gene115|rna115|rna115 122 FIPGGDFMGLLSKEDVLEEDWVRFYAAEIVAALDELHKLGWIHRDLKPDNILIGSDGHVKLADFGSCIKMKDGKArSSIT 201
                                    ************************************************************************99956668 PP

                                    TSCGGGS-HHHH....TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS CS
                        Pkinase 158 vgtseYlAPEvl....keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeasei 233
                                    vgt++Y++P vl    +e ey++ vD W+lGvi+ye+++g++pf++++  e     +++          tk ++  + ++
  gene115|gene115|rna115|rna115 202 VGTPDYVSPDVLcsvnEECEYGEDVDFWTLGVIIYEMVYGTTPFYSDTLME----TYRK---------ITKAEFGFPFKV 268
                                    9************999999**************************333333....3333.........3456899999** PP

                                    -HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 234 seeakdllkkllkkdpkkRltaeellqhpyl 264
                                    s+e+++l+++l++  + kR+ +e++++h+++
  gene115|gene115|rna115|rna115 269 SPELTSLIESLITT-KDKRIKIEDIKSHRFF 298
                                    **********9975.689***********98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT- CS
                        Pkinase 204 ekvekeldqlekilkilgetkeklpeaseiseeakdllkkllk 246
                                    ++   + ++le+++k   e + + +e ++ ++e+kd+l++ll 
  gene115|gene115|rna115|rna115 404 QELMGMKMELESTRK---ELEDSKNEVQHRQKELKDVLSQLLF 443
                                    212222222222222...4455666667779999999999885 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1
                                    EEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase  30 KkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                    K+  k+ +++ ++k++l+E   +++ +++ni ++  + e+ +++ l+ e+
  gene115|gene115|rna115|rna115 459 KTWLKDVTEEVNNKALLSEEYSIAEKESMNISKFSASTERLEKRALFKEL 508
                                    66777778888889999999999999999999999999987777776665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.7
                                    TTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEB....HHHHHHHHSS-- CS
                        Pkinase  21 ketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyvegge....ladllerkgsls 96 
                                    ++ + ++A+K+  ++ +    + k+l+E ++  + + ++i +l+  +e++++ ++v ++ e       ++++l + ++l+
  gene115|gene115|rna115|rna115 712 EDLNTEIAIKEGIEKIRA-LLQGKTLEEANMQLEGSNRKISQLKAEIERSRKSTIVENIPEDPVkiyeFNNHLFAVKTLP 790
                                    556677777776554433.3445788999999999999999999888888888877665443223333666666666677 PP

                                    HHHHHHHHHHHHHHH CS
                        Pkinase  97 eeeakkiakqilegl 111
                                    +  + ++++++l gl
  gene115|gene115|rna115|rna115 791 QGSLCDFCNEVLYGL 805
                                    777777777776665 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.0   7.5e-25   9.6e-22       4     256 ..      48     293 ..      45     295 .. 0.83
   2 ?   -1.1   0.1      0.71   9.1e+02      23      80 ..     710     767 ..     699     782 .. 0.86

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 7.5e-25
                                    EEEEEEESSEEEEEEEEETTTTSSEEEEEEEEEST..TSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEEEEE CS
                    Pkinase_Tyr   4 gkklGeGafGkVvegtlkgekekkevkVavKtlke..eateeekeelleeakimkkl.khpnivkllgvctkeepllivt 80 
                                     k++++G +G+V+  +            a+K +++    ++ +++ ++ e + m ++   + +v  +  + +ee l+ ++
  gene115|gene115|rna115|rna115  48 VKNVAKGGYGEVFLVRKG-------KIYAMKRVSKelVLRQPHTALFMAEKEAMVDCiGSEWLVCAHMTMQDEEYLYYLM 120
                                    577788888888765544.......3345555533113455667899*********999999999999999********* PP

                                    E--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEE CS
                    Pkinase_Tyr  81 eyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyv 160
                                    ++++gGd+   L k+  + l+ +++  +a+++ ++++ L++   +Hrdl   N+L+ ++ +vk++DfG + ++  +d   
  gene115|gene115|rna115|rna115 121 DFIPGGDFMGLLSKE--DVLEEDWVRFYAAEIVAALDELHKLGWIHRDLKPDNILIGSDGHVKLADFGSCIKM--KDGKA 196
                                    ************998..9999999999*******************************************999..55556 PP

                                    ETTSSTSGGGGS-HHHHHHSE....EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBHHHHH CS
                    Pkinase_Tyr 161 kkeeaklpvkWmapEslkekk....ftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcpeelye 236
                                    +++ +     +++p +l + +    + +  D W  Gv+++E++  g +p+ + + +e+++k+++  +   p k+++el++
  gene115|gene115|rna115|rna115 197 RSSITVGTPDYVSPDVLCSVNeeceYGEDVDFWTLGVIIYEMVY-GTTPFYSDTLMETYRKITKA-EFGFPFKVSPELTS 274
                                    6777888889*****9855444445*****************98.******99999*99999764.57889999999999 PP

                                    HHHHHT-SSGGGS--HHHHH CS
                    Pkinase_Tyr 237 lmkkcweedpeeRptfselv 256
                                    l+++  + ++++R +++++ 
  gene115|gene115|rna115|rna115 275 LIESLIT-TKDKRIKIEDIK 293
                                    9987665.556787777765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.71
                                    TTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEE CS
                    Pkinase_Tyr  23 ekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivt 80 
                                     +e+ ++++a+K   e+ ++  + + leea++  + ++++i +l + + ++++  iv 
  gene115|gene115|rna115|rna115 710 LEEDLNTEIAIKEGIEKIRALLQGKTLEEANMQLEGSNRKISQLKAEIERSRKSTIVE 767
                                    56777899******999999999********99999999**99999999888877775 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.6     2e-13   2.6e-10       1      51 [.     782     832 ..     782     833 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2e-13
                                    --EEEE--SS--B-TTT-SB--SSSS-EEEETTT--EE-CCCCTTS-SBTT CS
                           C1_1   1 HhwvhrnfkqptfCkhCgeflwgkekqglkCswCkllvHkkChekvpkecg 51 
                                    H ++++++ q + C+ C+e l+g+  qg+ C++Ck++vH +C+ + +++c+
  gene115|gene115|rna115|rna115 782 HLFAVKTLPQGSLCDFCNEVLYGLVDQGFECRDCKMIVHRSCYVLGDISCE 832
                                    99****************************************988888886 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   1.4e-10   1.7e-07     151     281 ..     148     280 ..     120     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.4e-10
                    Kinase-like 151 lqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlsevekg...faPpEllgsrggytrknktkm 227
                                    ++++    +L+++g +h ++++dn+l   +g ++l +f++ ++ ++    s++ +g   +  p++l s      +++ ++
  gene115|gene115|rna115|rna115 148 AEIVAALDELHKLGWIHRDLKPDNILIGSDGHVKLADFGSCIKMKDGKARSSITVGtpdYVSPDVLCS-----VNEECEY 222
                                    677777889**********************************9986665777754122444444444.....5689*** PP

                    Kinase-like 228 thkldaWqlGlviyriwclklPltlateeakeew......kfklckkipekvkaLlkkfL 281
                                       +d W+lG+ iy +   + P+  +t      +      +f    k++ ++  L++ ++
  gene115|gene115|rna115|rna115 223 GEDVDFWTLGVIIYEMVYGTTPFYSDTLME--TYrkitkaEFGFPFKVSPELTSLIESLI 280
                                    ******************999997655221..1111122255555566666666666655 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       5.8   7.5e+03      38      53 ..     365     380 ..     363     395 .. 0.83
   2 ?   -2.2   1.4       3.6   4.6e+03      18      55 ..     579     619 ..     573     630 .. 0.57
   3 !   27.9   6.9   1.5e-09   1.9e-06       2      66 ..     707     765 ..     706     768 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.8
                            HR1  38 qeaeselsesnskiel 53 
                                    ++a+s+ s  +ski++
  gene115|gene115|rna115|rna115 365 EKADSTCSRKDSKIRE 380
                                    7899999999999875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.6
                            HR1  18 GAenllraleskktqnkkvrqeaeselsesns...kielLr 55 
                                    G  +l r+l  k    k++ q+ ++e+ + +s   ++++L+
  gene115|gene115|rna115|rna115 579 GLDSLKRQLRLKTAEVKEYEQKLNQEILFRKSmeeELSFLK 619
                                    55555555543323333366666666666655555555555 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 1.5e-09
                            HR1   2 leelekklekElkireGAenllraleskktqnkkvrqeaeselsesnskielLreqLeelqasvq 66 
                                    l +le  l+ E +i+eG+e+++ +l+       k ++ea+ +l+ sn+ki++L+ ++e+ ++s  
  gene115|gene115|rna115|rna115 707 LKSLEEDLNTEIAIKEGIEKIRALLQ------GKTLEEANMQLEGSNRKISQLKAEIERSRKSTI 765
                                    679********************755......789************************998765 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.95   1.2e+03      65      84 ..     111     130 ..      76     158 .. 0.76
   2 !   16.3   0.3   5.6e-06    0.0071     154     193 ..     148     185 ..     105     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.95
                                    EETTEEEEEEE----EE-SS CS
                            APH  65 eeigllfalieyvpgrsllr 84 
                                    +++++l++l+ ++pg ++  
  gene115|gene115|rna115|rna115 111 QDEEYLYYLMDFIPGGDFMG 130
                                    567789*********99988 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 5.6e-06
                                    HHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                            APH 154 aalaallpgelptvllHgDlhpgNllvdpddgrvtGviDf 193
                                    a++ a l+   + +++H+Dl+p+N+l+   dg+v  + Df
  gene115|gene115|rna115|rna115 148 AEIVAALDELHKLGWIHRDLKPDNILIG-SDGHV-KLADF 185
                                    2222222225579***************.55655.35555 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.4   1.3e-05     0.017       7      21 ..     812     826 ..     810     832 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                          PHD_2   7 CdkCsvaVHasCYGv 21 
                                    C  C+++VH+sCY +
  gene115|gene115|rna115|rna115 812 CRDCKMIVHRSCYVL 826
                                    *************65 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.5e-05     0.032     125     169 ..     148     188 ..     127     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                            Kdo 125 kavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldka 169
                                     ++ ++  +lh++g+ H+dl + nil+  ++    ++ l D+  +
  gene115|gene115|rna115|rna115 148 AEIVAALDELHKLGWIHRDLKPDNILIGSDG----HVKLADFGSC 188
                                    567788999*******************999....8889998766 PP

>> zf-RING_9  Putative zinc-RING and/or ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.7       1.8   2.3e+03      57     105 ..     382     430 ..     364     521 .. 0.63
   2 ?   -3.1   0.3       5.1   6.5e+03      61      62 ..     573     574 ..     529     634 .. 0.52
   3 ?   15.1   1.3   1.3e-05     0.017     154     192 ..     791     826 ..     776     838 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.8
                      zf-RING_9  57 eelnpelykkvkelkkvke.lrkqlkllkeylktCrsaeaekllkllklr 105
                                    ee++++l++k++e k + e  +++l+ +k  l++ r++ + + ++++++r
  gene115|gene115|rna115|rna115 382 EEAHKNLLTKISENKGILEsQKQELMGMKMELESTRKELE-DSKNEVQHR 430
                                    5555666666665555544144456666666665555522.222222222 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                      zf-RING_9  61 pe 62 
                                    ++
  gene115|gene115|rna115|rna115 573 EK 574
                                    22 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.3e-05
                      zf-RING_9 154 kgfiCelCkseellfpfqlktverCekCkavfHkeClkk 192
                                    +g +C +C+  e+l+    + +e C++Ck+++H++C+  
  gene115|gene115|rna115|rna115 791 QGSLCDFCN--EVLYGLVDQGFE-CRDCKMIVHRSCYVL 826
                                    7899****9..79***7777776.************954 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.8    0.0015       1.9     195     275 ..     383     463 ..     367     480 .. 0.69
   2 ?   11.2   7.7   0.00016       0.2      16     111 ..     529     621 ..     506     639 .. 0.67
   3 ?    4.0   0.6     0.025        32      81     138 ..     704     762 ..     666     769 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0015
                                    XXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 195 skleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaei 274
                                    +  ++l +++++n+  l+s k+e++ ++++++s + ele+ k++ +  +++l+++  +l  e e+l+++  ele+  + +
  gene115|gene115|rna115|rna115 383 EAHKNLLTKISENKGILESQKQELMGMKMELESTRKELEDSKNEVQHRQKELKDVLSQLLFEKEELEDAKGELERYKTWL 462
                                    44566777777888888888888888888888888888888888888888888887777666666666666665544444 PP

                                    H CS
                       Filament 275 r 275
                                    +
  gene115|gene115|rna115|rna115 463 K 463
                                    4 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00016
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  16 YidkVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekel 95 
                                    + +    L  enk L++++e  +ek  +ev ++k++ e e ++l ++l +   +  + ql l++  +e++++ +k+++e+
  gene115|gene115|rna115|rna115 529 FQESMNNLSVENKGLKSEVEICKEK-FQEVLRIKAMVEYENKSLSEKLRSEGLDSLKRQLRLKT--AEVKEYEQKLNQEI 605
                                    4455556666777777777777777.66666677777777777777777777766666666654..45677777777777 PP

                                    XXXXXXXXXXXXXXXX CS
                       Filament  96 nkreevEaelkalrkd 111
                                      r+++E+el  l+k+
  gene115|gene115|rna115|rna115 606 LFRKSMEEELSFLKKE 621
                                    7777777777777765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.025
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  81 reeledlrkkyekelnkreevEaelkalr.kdldeatlarvdLekkvesLkeelaflkk 138
                                    r +l+ l + +++e++ +e +E+  + l+ k l+ea+++    ++k+ +Lk e++  +k
  gene115|gene115|rna115|rna115 704 RRSLKSLEEDLNTEIAIKEGIEKIRALLQgKTLEEANMQLEGSNRKISQLKAEIERSRK 762
                                    44555556666666666666665544444678888888888888888888888877665 PP

>> DUF4478  Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00024       0.3      17      75 ..     489     548 ..     475     576 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                    HHTTSTSSSC.HHHHHHHHHHHHHHTTT----SSSTTCGTTTT-EEEEEEETTEEEEEEE CS
                        DUF4478  17 verlkdsses.elyelfRncalavLnsgsetDdskellekykdFdikvlqkerGiklelk 75 
                                    +++++ s+e+ e   lf++ +la+ ++g+e ++  ++++ +++   ++  +++G+k e++
  gene115|gene115|rna115|rna115 489 ISKFSASTERlEKRALFKELSLAIHAAGKEVEEIMSIFQGFQESMNNLSVENKGLKSEVE 548
                                    555555544336678****************************************98775 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.2   0.00029      0.37      19      46 ..     793     823 ..     782     824 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                           C1_2  19 fnCsaCgrkidgff...YsCseCdfslhvrC 46 
                                      C+ C +   g     ++C  C+ ++h +C
  gene115|gene115|rna115|rna115 793 SLCDFCNEVLYGLVdqgFECRDCKMIVHRSC 823
                                    67*******65555667************** PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.5   0.00042      0.54       2      33 ..     795     827 ..     794     835 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                                    BTTTTS.TTSTTSCEEEETTTSCEEETTTSSST CS
                            PHD   2 CavCkk.ksdeeeelvqCdgCkrwfHqkClkpp 33 
                                    C++C++      ++   C +Ck  +H +C+ + 
  gene115|gene115|rna115|rna115 795 CDFCNEvLYGLVDQGFECRDCKMIVHRSCYVLG 827
                                    99****7666789999*************9765 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       8.4   1.1e+04      13      27 ..     370     384 ..     369     394 .. 0.74
   2 ?    8.0   3.0    0.0027       3.5       1      28 [.     795     824 ..     795     825 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.4
                   zf-RING-like  13 rCsnesCnvrlHvdC 27 
                                     Cs+++ ++r H++ 
  gene115|gene115|rna115|rna115 370 TCSRKDSKIREHEEA 384
                                    599999999999865 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0027
                   zf-RING-like   1 CeaCkei....vtqGvrCsnesCnvrlHvdCf 28 
                                    C  C+e+    v qG  C   +C++++H  C+
  gene115|gene115|rna115|rna115 795 CDFCNEVlyglVDQGFECR--DCKMIVHRSCY 824
                                    8889986333366******..**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (863 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1566  (0.0873445); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.98u 0.37s 00:00:01.35 Elapsed: 00:00:00.52
# Mc/sec: 4970.67
//
Query:       gene1151|gene1151|rna1150|rna1150  [L=243]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0048   16.7   0.0      0.029   14.2   0.0    2.2  2  DUF1421   UBA-like domain (DUF1421)


Domain annotation for each model (and alignments):
>> DUF1421  UBA-like domain (DUF1421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0     0.082   1.5e+03      10      17 ..     146     153 ..     143     160 .. 0.80
   2 !   14.2   0.0   1.6e-06     0.029       2      20 ..     192     211 ..     191     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.082
                            DUF1421  10 sMGfrrDq 17 
                                         +Gf +D+
  gene1151|gene1151|rna1150|rna1150 146 EIGFDGDH 153
                                        68*****9 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.6e-06
                            DUF1421   2 ddlidkvasMGfrrDq.Vrs 20 
                                        +++++k+  MGfr+D  Vr+
  gene1151|gene1151|rna1150|rna1150 192 EEVFEKLEEMGFRGDLlVRN 211
                                        79*************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1638.85
//
Query:       gene1152|gene1152|rna1151|rna1151  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 784.87
//
Query:       gene1153|gene1153|rna1152|rna1152  [L=411]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-37  124.7   2.7    1.9e-10   40.4   0.1    4.7  5  RRM_1         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
    1.1e-07   31.9   3.1     0.0022   18.1   0.0    4.7  5  RRM_7         RNA recognition motif
    0.00011   22.0   0.4        2.1    8.2   0.0    4.1  5  RRM_occluded  Occluded RNA-recognition motif
      0.008   16.0   0.1        7.4    6.3   0.0    3.6  4  RRM_Rrp7      Rrp7 RRM-like N-terminal domain
  ------ inclusion threshold ------
      0.029   14.4   7.5       0.13   12.3   0.1    3.6  4  RRM_3         RNA binding motif


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   5.4e-14   1.9e-10       1      70 []       3      72 ..       3      72 .. 0.97
   2 !   28.9   0.0   2.1e-10   7.6e-07       1      59 [.      97     152 ..      97     161 .. 0.91
   3 !   12.8   0.0   2.3e-05     0.081      31      69 ..     269     304 ..     261     305 .. 0.85
   4 ?   -3.2   0.0       2.2   7.8e+03       4      13 ..     312     321 ..     311     325 .. 0.81
   5 !   39.4   0.0   1.1e-13   3.9e-10       1      68 [.     336     403 ..     336     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.4e-14
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrelk 70
                                       ++V++Lp ++t+ee+++ Fsk G+i+++ + r+ +g+ ++++f+ +  + +  +A++  ng  +++++++
  gene1153|gene1153|rna1152|rna1152  3 IVVKDLPLSTTKEEIEKEFSKHGRITDVFMARNGQGRFRRICFIGYMEEKEGVEAIKYRNGSLFKNQKIR 72
                                       79*********************************************99999999999********9986 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 2.1e-10
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHH CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAleal 59 
                                        +f++n+p +v+e+ +++ F+++G+i+++ l      k  + a+V+F   e A +A +++
  gene1153|gene1153|rna1152|rna1152  97 IFIRNVPMEVSEQIIHDTFKEYGEIEEVGLLDL---KEGKGAYVKFSEGECAVEAYRSV 152
                                        8*******************************8...88888***********9999854 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 2.3e-05
                                        EEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1  31 vrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        +     +sk+ a  +Fe +e+A+k+ ++l  k ++ +++
  gene1153|gene1153|rna1152|rna1152 269 SI---APSKCLALLKFEEEEEARKCYKKLSLKRMKEKVI 304
                                        44...489*********************9998888876 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 2.2
                                        ESETTTSSHH CS
                              RRM_1   4 gnLppdvtee 13 
                                         n+p+d++ee
  gene1153|gene1153|rna1152|rna1152 312 CNIPKDTKEE 321
                                        5999999998 PP

  == domain 5  score: 39.4 bits;  conditional E-value: 1.1e-13
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTT.EEETTEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealng.kklggre 68 
                                        l V+n+p+ ++e+e++++F  f  + +++++ ++ g+s+gf+fV+  s+++ ++A++++   + l gr+
  gene1153|gene1153|rna1152|rna1152 336 LLVRNVPFQASEKEIRKIFDSFHVV-DVRIPIKREGTSRGFCFVTLGSPDEVDAAIRHFGSsTHLYGRR 403
                                        68********************988.******************************9987766666666 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.052   1.9e+02       4      29 ..       3      28 ..       1      42 [. 0.87
   2 !   18.1   0.0     6e-07    0.0022       1      28 [.      94     121 ..      94     149 .. 0.95
   3 ?   -1.8   0.0      0.95   3.4e+03      45      66 ..     170     191 ..     131     200 .. 0.70
   4 ?    0.8   0.2      0.15   5.4e+02      71      90 ..     284     303 ..     273     306 .. 0.76
   5 !    7.0   0.0    0.0018       6.3       3      38 ..     335     370 ..     333     394 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.052
                              RRM_7  4 vFvGGlPiDiteeelkatfkefgkvl 29
                                       + v  lP   t+ee+++ f+++g+++
  gene1153|gene1153|rna1152|rna1152  3 IVVKDLPLSTTKEEIEKEFSKHGRIT 28
                                       667789****************9875 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6e-07
                              RRM_7   1 srkvFvGGlPiDiteeelkatfkefgkv 28 
                                        srk+F+  +P++++e+ +++tfke+g++
  gene1153|gene1153|rna1152|rna1152  94 SRKIFIRNVPMEVSEQIIHDTFKEYGEI 121
                                        8*************************86 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.95
                              RRM_7  45 nskaakgyvflvfedeksvkaL 66 
                                        ++++ + y  l f+ e+ vk++
  gene1153|gene1153|rna1152|rna1152 170 EKSQYEHYNTLFFSFESVVKRI 191
                                        3334566777888888877766 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.15
                              RRM_7  71 teeeeelylklssrrlkske 90 
                                        +ee +++y kls +r+k+k 
  gene1153|gene1153|rna1152|rna1152 284 EEEARKCYKKLSLKRMKEKV 303
                                        45569************996 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0018
                              RRM_7   3 kvFvGGlPiDiteeelkatfkefgkvlvdwPkkaes 38 
                                        k+ v  +P   +e+e+ + f +f  v v  P k e 
  gene1153|gene1153|rna1152|rna1152 335 KLLVRNVPFQASEKEIRKIFDSFHVVDVRIPIKREG 370
                                        788999***********************9998664 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0     0.004        14       8      72 ..       7      75 ..       2      78 .. 0.85
   2 !    8.2   0.0    0.0006       2.1       3      51 ..      96     145 ..      94     149 .. 0.83
   3 ?   -2.8   0.0       1.7     6e+03      45      60 ..     192     207 ..     181     217 .. 0.63
   4 ?    3.1   0.0     0.025        89      31      70 ..     267     306 ..     256     308 .. 0.91
   5 ?   -3.6   0.0         3   1.1e+04       9      25 ..     341     357 ..     335     364 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.004
                       RRM_occluded  8 plsDtvnkariralveekegeikkivLvpdheG.....AivefkdekiagkasLaLdgsefegkklrcGt 72
                                       +l+   +k++i++ ++++ g+i+++++  + +G     +++ + +ek    a+   +gs f+++k+rc  
  gene1153|gene1153|rna1152|rna1152  7 DLPLSTTKEEIEKEFSKH-GRITDVFMARNGQGrfrriCFIGYMEEKEGVEAIKYRNGSLFKNQKIRCEA 75
                                       5666789999********.********9999998888888999999999999999999999999999965 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0006
                       RRM_occluded   3 tisllplsDtvnkariralveekegeikkivLv..pdheGAivefkdekia 51 
                                         i + +++  v+++ i + ++e+ gei+++ L    + +GA v+f++ + a
  gene1153|gene1153|rna1152|rna1152  96 KIFIRNVPMEVSEQIIHDTFKEY-GEIEEVGLLdlKEGKGAYVKFSEGECA 145
                                        6778899****************.******997225667899999887655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.7
                       RRM_occluded  45 fkdekiagkasLaLdg 60 
                                        +++e+ia+k +  ++ 
  gene1153|gene1153|rna1152|rna1152 192 CESERIAAKDLVDIND 207
                                        5566666665555544 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.025
                       RRM_occluded  31 kivLvpdheGAivefkdekiagkasLaLdgsefegkklrc 70 
                                        ki + p++  A+++f++e+ a k+  +L  +++++k++ c
  gene1153|gene1153|rna1152|rna1152 267 KISIAPSKCLALLKFEEEEEARKCYKKLSLKRMKEKVIYC 306
                                        7889999999**************9999999999998876 PP

  == domain 5  score: -3.6 bits;  conditional E-value: 3
                       RRM_occluded   9 lsDtvnkariralveek 25 
                                        ++ + ++++ir+++ + 
  gene1153|gene1153|rna1152|rna1152 341 VPFQASEKEIRKIFDSF 357
                                        55556778888887766 PP

>> RRM_Rrp7  Rrp7 RRM-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.69   2.5e+03      48      65 ..       7      24 ..       3      33 .. 0.82
   2 !    6.3   0.0    0.0021       7.4      36      65 ..      89     118 ..      81     129 .. 0.80
   3 ?    2.0   0.0     0.044   1.6e+02      68     138 ..     214     300 ..     200     309 .. 0.76
   4 ?    2.5   0.0     0.031   1.1e+02      39      65 ..     331     357 ..     317     366 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.69
                           RRM_Rrp7 48 NlPiettletlkkffqkv 65
                                        lP+ tt e++ k f k+
  gene1153|gene1153|rna1152|rna1152  7 DLPLSTTKEEIEKEFSKH 24
                                       69*******999999886 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0021
                           RRM_Rrp7  36 ndeessrslFlvNlPiettletlkkffqkv 65 
                                        +  + sr +F+ N+P+e + + ++  f++ 
  gene1153|gene1153|rna1152|rna1152  89 RMVKYSRKIFIRNVPMEVSEQIIHDTFKEY 118
                                        4445799**************999999875 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.044
                           RRM_Rrp7  68 gatiesvvsslltdeqedvsidltkltsdlelkdeekdeeeakl................Pknt.glvkfvDkssv 126
                                         a ie+     +++  e++ i l +lt ++++++    +   +l                P ++ +l+kf  ++ +
  gene1153|gene1153|rna1152|rna1152 214 MALIETHLVQETKEFLENNGIYLDNLTGEIDKRTLIIRNM--ELmkcldlvdsgckisiaPSKClALLKFEEEEEA 287
                                        577888888888888999999999***9999933322222..2224669999999999998877689999999999 PP

                           RRM_Rrp7 127 elafnalk.Klsk 138
                                          ++++l  K++k
  gene1153|gene1153|rna1152|rna1152 288 RKCYKKLSlKRMK 300
                                        9999987535555 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.031
                           RRM_Rrp7  39 essrslFlvNlPiettletlkkffqkv 65 
                                        +  + l + N+P +++ ++++k f+  
  gene1153|gene1153|rna1152|rna1152 331 RAINKLLVRNVPFQASEKEIRKIFDSF 357
                                        34678999***************9876 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4     0.076   2.7e+02      13      81 ..      12      89 ..       3     101 .. 0.61
   2 ?   12.3   0.1   3.6e-05      0.13      11      60 ..     104     155 ..      96     176 .. 0.75
   3 ?   -3.6   0.0       3.3   1.2e+04      61      81 ..     226     246 ..     215     248 .. 0.68
   4 ?    2.7   0.0     0.035   1.2e+02      41      66 ..     278     301 ..     272     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.076
                                       --HHHHHHHCHCCS-ECEEEE-TTSSE.....EEEEESSHHHHHHHHHHHHHC...-B-CCTSSEEEEE--.HHHHHH CS
                              RRM_3 13 lsredikellsklgevayvdyekgdke.....gevrFkedeeakkalekatea...klkikdaevtlelLe.GeeEke 81
                                       +++e+i + +sk+g +  v ++++ +      + + + e++e+ +a++ +  +   + ki+ + ++ ++++ Ge Ek+
  gene1153|gene1153|rna1152|rna1152 12 TTKEEIEKEFSKHGRITDVFMARNGQGrfrriCFIGYMEEKEGVEAIKYRNGSlfkNQKIRCEALKEDIVQmGESEKR 89
                                       678999999999998876655544332111225566667777777776666654444444444555555433666665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.6e-05
                                        SS--HHHHHHHCHCCS...-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC CS
                              RRM_3  11 kelsredikellsklg...evayvdyekgdkegevrFkedeeakkalekatea 60 
                                         e+s + i+++++++g   ev+  d+++  k ++v+F e e a +a  + + +
  gene1153|gene1153|rna1152|rna1152 104 MEVSEQIIHDTFKEYGeieEVGLLDLKE-GKGAYVKFSEGECAVEAYRSVKTI 155
                                        5788999*********444455555555.5789******99999998887766 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.3
                                        -B-CCTSSEEEEE--HHHHHH CS
                              RRM_3  61 klkikdaevtlelLeGeeEke 81 
                                        k  ++++ + l+ L+Ge  k+
  gene1153|gene1153|rna1152|rna1152 226 KEFLENNGIYLDNLTGEIDKR 246
                                        444677777788888887776 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.035
                                        EEEESSHHHHHHHHHHHHHC-B-CCT CS
                              RRM_3  41 evrFkedeeakkalekateaklkikd 66 
                                         ++F+e+eea+k  +k+  +  ++k+
  gene1153|gene1153|rna1152|rna1152 278 LLKFEEEEEARKCYKKLSLK--RMKE 301
                                        579***********999887..2333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2729.47
//
Query:       gene1154|gene1154|rna1153|rna1153  [L=543]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-15   54.9  21.6    2.7e-14   52.7  21.6    2.0  1  Sulfate_transp  Sulfate permease family


Domain annotation for each model (and alignments):
>> Sulfate_transp  Sulfate permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7  21.6   1.5e-18   2.7e-14      27     378 ..      50     392 ..      43     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.5e-18
                     Sulfate_transp  27 glppiygLyssvvpqlvyalfGtsrqlavGpvavlslivgeiiakv......aeeepekgieiattltllaGviqv 96 
                                        ++ +++ Lys++ +q+v+ +f +   ++ G+       + +i + +      + ee  +  +  +++t+l  ++++
  gene1154|gene1154|rna1153|rna1153  50 NVSATMFLYSTIAAQFVFGMFSGLGGVCAGAIFEAQKDTRKIHKLCfkmsssLGEEISTTYACIFLSTVLFALFSY 125
                                        66777889*****************99999887775555554444444455446667788888999999999**** PP

                     Sulfate_transp  97 llGllRLgflveflseavlsGfiaGaaivillsqikvllglervskkeslvsvlsslftnlekvnlakvvlgllll 172
                                        +l  +R+g   ++++ ++l G +++++i+      +   g+e      +++++ +++++ +     +++ l+ll++
  gene1154|gene1154|rna1153|rna1153 126 ILKRFRIGNSLRYIPVSALYGVMVSIGIM------SIECGYE------EVYTMTWEYVNGCLV---VTIGLALLAV 186
                                        **************************985......3357776......9***********954...5566666666 PP

                     Sulfate_transp 173 vvLlvtkellkklkkllvipapaelvavivatlvsaifelkreagvk.i......vgeipsg.lpelslp...kvd 237
                                        ++ ++   +       l+ip+    +   ++++++++ +  +   +  +      + +i+ + + +l+l    +++
  gene1154|gene1154|rna1153|rna1153 187 ALDIMFPAY------FLMIPMLSFGIFAAFYIVFAVAGKDTE---WMrSvglipkAEDINLDsFATLKLLrmeNIN 253
                                        666666665......389999999999999999999994333...3322122334566666555555555444788 PP

                     Sulfate_transp 238 wsllsallpdalaialvglleaiavsksldkkkgykvdsnkELvAlGfsNilsslfgglpatgafsrsavnikaGa 313
                                        + +++a l ++l + l+ l++      s+++  g k d nkEL  ++++Ni+s++f g+p++   s s  + k+G+
  gene1154|gene1154|rna1153|rna1153 254 VGAIKANLMNILGLSLFNLVHIAVNVPSFAESFGLKADLNKELGVQSVANIVSAFF-GYPIYFICSTSIYFNKSGG 328
                                        888888888888888888776444456899999*********************99.6****************** PP

                     Sulfate_transp 314 ktqlsglvsalvvllvllvltplleyiPkavLaaiiivagkglLvelkelkk.lwklskldflill 378
                                        +++l +l+ a+v+ ++l+v++++ e iP    + i +++g g L +   l+  + kls +d+++l+
  gene1154|gene1154|rna1153|rna1153 329 RSRLHSLMGAVVISSLLVVGGRIRESIPLILSGTIPMFIGFGFLYS--YLWLpIFKLSWMDLVTLM 392
                                        *****************************99999*9******9988..444314457777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 3294.32
//
Query:       gene1155|gene1155|rna1154|rna1154  [L=319]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.37s 00:00:01.01 Elapsed: 00:00:00.58
# Mc/sec: 1663.10
//
Query:       gene1156|gene1156|rna1155|rna1155  [L=79]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-15   54.9   0.2    5.8e-15   54.7   0.2    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.2   3.2e-19   5.8e-15       2      65 ..       4      71 ..       3      73 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 3.2e-19
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET....EEEEEEEEEEEGGGEEEE CS
                                LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk....ekrklglvliRGnnivli 65
                                        l+k++n++v  ++++gr  +Gt+ ++D   N+vL+d+ee++k k     + r lglv+iRG+ i+ i
  gene1156|gene1156|rna1155|rna1155  4 NLEKYVNYRVKARMRDGRWMEGTMLAVDGDTNAVLDDTEEFRKIKGskeaRRRILGLVVIRGDFIMDI 71
                                       699***************************************9998999999999**********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 564.25
//
Query:       gene1157|gene1157|rna1156|rna1156  [L=563]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-76  256.8   4.3      4e-76  256.2   4.3    1.2  1  tRNA-synt_1d  tRNA synthetases class I (R)
    1.1e-25   90.1   0.2      3e-25   88.7   0.2    1.8  1  DALR_1        DALR anticodon binding domain
  ------ inclusion threshold ------
      0.024   15.1   0.8       0.12   12.9   0.1    2.7  3  eRF1_3        eRF1 domain 3
      0.089   12.1   0.0       0.17   11.1   0.0    1.4  1  DUF1786       Putative pyruvate format-lyase activating enzym
      0.093   12.1   0.7       0.27   10.5   0.1    2.1  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.2   4.3   1.1e-79     4e-76      14     348 ..     106     430 ..      94     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: 256.2 bits;  conditional E-value: 1.1e-79
                                        ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTT CS
                       tRNA-synt_1d  14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekll 89 
                                        +  ++ k++vvd+ssPniak +h+GhLr+ti+G+++++ll + Gy+ + +n+ GDWG+qfG+++ ++ k++dek l
  gene1157|gene1157|rna1156|rna1156 106 NDIGKGKRIVVDYSSPNIAKVFHMGHLRTTILGQFIVNLLKASGYETTSINYFGDWGKQFGFVLLGYGKYGDEKEL 181
                                        5667889********************************************************************* PP

                                        S-----SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHC.T-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--C CS
                       tRNA-synt_1d  90 qeqelqdLeafykeakkdydeeeifaerarnyvvkLqs.gdedirklwkllvditrtelqklydrldvtlie.rGe 163
                                        ++ +l++L ++y+++  d  e+  +  +a++ + k+++ +de +  lwk+  +++ ++++ ly++l+v      Ge
  gene1157|gene1157|rna1156|rna1156 182 ERDPLKHLLNVYVKISSDAKENPDVDSEAKDLFRKMEEeKDEWCISLWKKFRELSIERYKTLYEKLNVRFDVySGE 257
                                        ***********************************97527788999*********9999999999999763349** PP

                                        CCCCCCHHHHHHHHHCTT-EE.ECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEE CS
                       tRNA-synt_1d 164 slykeslneivkelkkkglvk.esdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvi 238
                                        s+y+e+ ++iv+  +   lv+ + dG +v +l    kr  v+v k+DG++ly t+Diaaa+er e+   +k++yv+
  gene1157|gene1157|rna1156|rna1156 258 SMYNEKGKKIVETCE---LVRtDADGSKVFDLG---KRGKVLVMKNDGTTLYITRDIAAAIERVEDYSPEKIIYVV 327
                                        **********98765...665167*****9997...666789********************************** PP

                                        ECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCT. CS
                       tRNA-synt_1d 239 dsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdk. 313
                                        +s+q++h++ +f +l  +gy  +  +  h ++G+v      +++tr+G + +L+d+++e+ +  ++ ++  +++k 
  gene1157|gene1157|rna1156|rna1156 328 SSEQNKHFEDLFKVLGVLGY--DEDKFLHVSYGLV-----AGMSTRAGRVQFLEDIIQESTDVMKK-VMLSDTNKs 395
                                        ********************..777899*******.....89******************997655.555555541 PP

                                        S-CCCCHCHHHHHHHHHHHHCCCCTS-TTS-EE-- CS
                       tRNA-synt_1d 314 vlqadelekvaeavgvgaikyaDlsknrindyifd 348
                                          +  e++k ae ++++++ + D+  +r++ y+fd
  gene1157|gene1157|rna1156|rna1156 396 SFTMAEMDKTAEILAISTLLVMDFTARRVKGYEFD 430
                                        57899*****************************8 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.2   8.4e-29     3e-25       1     119 []     445     563 .]     445     563 .] 0.95

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 8.4e-29
                                        HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SH.HHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHH CS
                             DALR_1   1 vqyahaRiksilrkaeeegekleeealalleee.eekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkf 75 
                                        +qyah+R+ksi  k+ + ++++ ++ +++l +  e  +L+ +l+ f+ ++e+++e++ep+++++yl++La+t+++ 
  gene1157|gene1157|rna1156|rna1156 445 LQYAHCRLKSIEVKNSKIDYSDISTIDFTLIHVpEVTNLVYKLLWFEHIVEKCLEDYEPSRIVTYLQDLASTINAA 520
                                        6**************9999999999999855555****************************************** PP

                                        HHHCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                             DALR_1  76 YnkervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                         n+ +vl+ e+e   +aRL  ++++r vL+ngL++LG ++++km
  gene1157|gene1157|rna1156|rna1156 521 INSLKVLGVEKELA-RARLLVLSSARIVLHNGLKILGATPLNKM 563
                                        ***********976.****************************9 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.94   3.4e+03       9      34 ..       3      29 ..       1      31 [. 0.75
   2 ?   -1.9   0.0       1.3   4.7e+03      59      84 ..     296     321 ..     236     347 .. 0.63
   3 ?   12.9   0.1   3.3e-05      0.12      13      50 ..     386     423 ..     374     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.94
                                       HHHHHHHHCTCSSE.EESHHHHHHHHH CS
                             eRF1_3  9 eefleelakdtgka.vYGveevlkale 34
                                       +ef++++  +  k+  ++ eev++++e
  gene1157|gene1157|rna1156|rna1156  3 NEFFKKIVDQISKVsKFTPEEVERCME 29
                                       789999887655541699999999988 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                                        -HHH-HHHHHHHHHHHHHHHHHTT-E CS
                             eRF1_3  59 ketgeelelvelieelvenveesgak 84 
                                        k++g++l +   i   +e ve++  +
  gene1157|gene1157|rna1156|rna1156 296 KNDGTTLYITRDIAAAIERVEDYSPE 321
                                        33444444444455555555555444 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3.3e-05
                                        HHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTS CS
                             eRF1_3  13 eelakdtgkavYGveevlkalemgAvetLLvseelers 50 
                                        + +  dt+k  +++ e  k +e+ A++tLLv++   r 
  gene1157|gene1157|rna1156|rna1156 386 KVMLSDTNKSSFTMAEMDKTAEILAISTLLVMDFTARR 423
                                        34455***************************977665 PP

>> DUF1786  Putative pyruvate format-lyase activating enzyme (DUF1786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.9e-05      0.17      87     164 ..     357     436 ..     314     443 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                            DUF1786  87 HGyspgesnrkfRfelleelleeggkleelvfeee.vpeeftRlkavaeslkeeg..kvvvmDtgaaavlGalldp 159
                                         G   g+s r  R ++le++++e+ ++ + v+ ++  +++ft ++++ ++++  +  + +vmD  a  v G  +d 
  gene1157|gene1157|rna1156|rna1156 357 YGLVAGMSTRAGRVQFLEDIIQESTDVMKKVMLSDtNKSSFT-MAEMDKTAEILAisTLLVMDFTARRVKGYEFDI 431
                                        588999***************988887766665552444444.666666665444559*****9999999999988 PP

                            DUF1786 160 evekl 164
                                        e +++
  gene1157|gene1157|rna1156|rna1156 432 EKRAR 436
                                        77665 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   7.5e-05      0.27      16      56 ..     120     160 ..     107     272 .. 0.78
   2 ?   -3.4   0.0       1.3   4.6e+03      52      72 ..     378     398 ..     370     482 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.5e-05
                                        EEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB- CS
                       tRNA-synt_1e  16 GptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtD 56 
                                         p +    h+Gh R+++    + ++l+a+gY+ + ++ + D
  gene1157|gene1157|rna1156|rna1156 120 SPNIAKVFHMGHLRTTILGQFIVNLLKASGYETTSINYFGD 160
                                        57778899************************999988887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                                        EEBB--SHHHHHHHHHTTS-H CS
                       tRNA-synt_1e  52 qnvtDidDkiikrareeeksv 72 
                                        q  tD+  k+++  +++++++
  gene1157|gene1157|rna1156|rna1156 378 QESTDVMKKVMLSDTNKSSFT 398
                                        555666655555444433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3742.82
//
Query:       gene1159|gene1159|rna1158|rna1158  [L=295]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-08   32.4  13.8    0.00057   20.2   2.6    2.9  2  zf-C2H2      Zinc finger, C2H2 type
    2.2e-05   24.7  18.8    0.00012   22.3   4.6    3.8  3  zf-H2C2_2    Zinc-finger double domain
     0.0049   17.5   2.5        0.1   13.2   0.2    2.8  3  FOXP-CC      FOXP coiled-coil domain
     0.0086   16.8  14.9        0.1   13.5   2.2    3.4  3  zf-C2H2_4    C2H2-type zinc finger
  ------ inclusion threshold ------
      0.012   15.9   3.6        1.6    9.1   0.2    3.6  4  zf-C2H2_8    C2H2-type zinc ribbon
      0.025   14.2   1.0      0.025   14.2   1.0    2.2  2  zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   3.6   2.2e-06    0.0066       1      23 []     219     243 ..     219     243 .. 0.95
   2 !   20.2   2.6   1.9e-07   0.00057       1      23 []     249     273 ..     249     273 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                                        EEET..TTTEEESSHHHHHHHHHCC CS
                            zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                        ++C+  +C++ Fkr ++LkrH  +H
  gene1159|gene1159|rna1158|rna1158 219 FVCTynECKRAFKRYEHLKRHNLMH 243
                                        89*******************9888 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.9e-07
                                        EEET..TTTEEESSHHHHHHHHHCC CS
                            zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                        +kC+  +C+k F+r++nL +H+++H
  gene1159|gene1159|rna1158|rna1158 249 HKCKfpGCSKAFSRSDNLSQHYKVH 273
                                        79*********************99 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.8    0.0036        11       4      26 .]     206     232 ..     206     232 .. 0.79
   2 !   22.3   4.6   4.2e-08   0.00012       1      25 [.     235     261 ..     235     262 .. 0.91
   3 ?    4.1   0.5     0.023        68       1      10 [.     265     274 ..     265     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0036
                          zf-H2C2_2   4 rHir.k.HtgekpyeCp..lCdkaFkt 26 
                                        rH++ +   +++p+ C   +C+ aFk+
  gene1159|gene1159|rna1158|rna1158 206 RHMKySgSLKDRPFVCTynECKRAFKR 232
                                        677734444889*****999*****96 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 4.2e-08
                          zf-H2C2_2   1 nLrrHirkHtgekpyeCp..lCdkaFk 25 
                                        +L+rH   Htge+p++C+   C+kaF+
  gene1159|gene1159|rna1158|rna1158 235 HLKRHNLMHTGERPHKCKfpGCSKAFS 261
                                        79****************666*****8 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.023
                          zf-H2C2_2   1 nLrrHirkHt 10 
                                        nL++H ++Ht
  gene1159|gene1159|rna1158|rna1158 265 NLSQHYKVHT 274
                                        8********9 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.6   1.4e+04      14      32 ..     106     124 ..     105     126 .. 0.76
   2 ?    3.3   0.2     0.042   1.3e+02       6      25 ..     220     239 ..     218     249 .. 0.88
   3 !   13.2   0.2   3.4e-05       0.1       6      31 ..     250     274 ..     247     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.6
                            FOXP-CC  14 kvledveeflkhlnseHal 32 
                                        kvle++e+f+   ++ H+l
  gene1159|gene1159|rna1158|rna1158 106 KVLESMESFMYDGKRPHQL 124
                                        6788889998888888876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.042
                            FOXP-CC   6 vCkWPgCekvledveeflkh 25 
                                        vC   +C+++++ +e++ +h
  gene1159|gene1159|rna1158|rna1158 220 VCTYNECKRAFKRYEHLKRH 239
                                        79999************999 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 3.4e-05
                            FOXP-CC   6 vCkWPgCekvledveeflkhlnseHa 31 
                                         Ck PgC+k+++ ++++ +h +  H+
  gene1159|gene1159|rna1158|rna1158 250 KCKFPGCSKAFSRSDNLSQHYKV-HT 274
                                        7*******************875.43 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       2.4   7.2e+03       6      21 ..      60      75 ..      58      76 .. 0.78
   2 !   10.0   2.0   0.00045       1.3       1      19 [.     219     239 ..     219     243 .. 0.92
   3 !   13.5   2.2   3.4e-05       0.1       1      23 [.     249     273 ..     249     274 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                          zf-C2H2_4  6 CgksFsskkaLlrHlk 21
                                       C +++ s+++++  ++
  gene1159|gene1159|rna1158|rna1158 60 CFGVCASPSQIREYMR 75
                                       8889999998877776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00045
                          zf-C2H2_4   1 fkCpi..CgksFsskkaLlrH 19 
                                        f C++  C++ F+++++L+rH
  gene1159|gene1159|rna1158|rna1158 219 FVCTYneCKRAFKRYEHLKRH 239
                                        78******************* PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3.4e-05
                          zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlkth 23 
                                        +kC++  C+k Fs++++L++H k h
  gene1159|gene1159|rna1158|rna1158 249 HKCKFpgCSKAFSRSDNLSQHYKVH 273
                                        6899999***************999 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.27   7.9e+02      66      94 ..      41      69 ..      16      72 .. 0.80
   2 ?   -1.4   0.0      0.99     3e+03      32      57 ..      93     118 ..      79     123 .. 0.79
   3 ?    5.4   0.3    0.0072        22      24      69 ..     207     251 ..     193     253 .. 0.83
   4 ?    9.1   0.2   0.00052       1.6       2      29 ..     251     278 ..     248     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.27
                          zf-C2H2_8 66 yfkcencllrfrthrslfkhlhvcsdqsh 94
                                       +f    +l+ +    s+fk + vc+  s+
  gene1159|gene1159|rna1158|rna1158 41 FFVNGRVLFNLSDLASVFKCFGVCASPSQ 69
                                       55555667777788899*******98775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.99
                          zf-C2H2_8  32 egklfrcstascaetfpsmqelvaht 57 
                                        +g    cs a  ++ + sm+ ++   
  gene1159|gene1159|rna1158|rna1158  93 QGLEVVCSDAINTKVLESMESFMYDG 118
                                        56778899999999999999888665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0072
                          zf-C2H2_8  24 hlsptqslegklfrcstascaetfpsmqelvahtklhykpnryfkc 69 
                                        h++ + sl+ + f c+   c  +f   + l  h  +h   +r  kc
  gene1159|gene1159|rna1158|rna1158 207 HMKYSGSLKDRPFVCTYNECKRAFKRYEHLKRHNLMHT-GERPHKC 251
                                        555667899999***************99999988875.5666677 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00052
                          zf-C2H2_8   2 cssygcrlafpnvrelaqhlrvhlsptq 29 
                                        c  +gc  af  + +l qh++vh + t+
  gene1159|gene1159|rna1158|rna1158 251 CKFPGCSKAFSRSDNLSQHYKVHTTTTE 278
                                        8899******************988764 PP

>> zf_C2H2_ZHX  Zinc-fingers and homeoboxes C2H2 finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0   8.4e-06     0.025       3      32 ..     217     247 ..     215     253 .. 0.85
   2 ?    0.7   0.4      0.14   4.1e+02      10      33 ..     256     278 ..     255     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.4e-06
                        zf_C2H2_ZHX   3 PsFvCv..eCsfsakkfegLalHNarsHpget 32 
                                          FvC+  eC+   k++e L+ HN  +H+ge 
  gene1159|gene1159|rna1158|rna1158 217 RPFVCTynECKRAFKRYEHLKRHNL-MHTGER 247
                                        569**8779***************8.688875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                        zf_C2H2_ZHX  10 CsfsakkfegLalHNarsHpgetn 33 
                                        Cs    + ++L++H  ++H+ +t+
  gene1159|gene1159|rna1158|rna1158 256 CSKAFSRSDNLSQH-YKVHTTTTE 278
                                        88888999******.578887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1782.90
//
Query:       gene1160|gene1160|rna1159|rna1159  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-29  101.9   1.9    5.8e-29  101.8   1.9    1.0  1  DUF572           Family of unknown function (DUF572)
  ------ inclusion threshold ------
      0.011   15.8   5.6        1.1    9.4   1.0    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.014   15.3   0.2        2.3    8.2   0.0    2.5  2  DUF951           Bacterial protein of unknown function (DUF95
       0.05   14.0   0.4          2    8.9   0.0    2.3  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.06   12.4   0.1        0.1   11.6   0.1    1.4  1  Tmemb_55A        Transmembrane protein 55A
       0.13   12.6   1.4        0.2   12.1   0.7    1.6  1  DUF3795          Protein of unknown function (DUF3795)


Domain annotation for each model (and alignments):
>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   1.9   1.9e-32   5.8e-29      14     135 ..       5     125 ..       1     138 [. 0.86

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 1.9e-32
                             DUF572  14 alrekarlknrqlvvRlmaPfnmrCktCgeyIykGvkFNarKekVgnetYlgipIfrFyikCtrClneitfkTDPk 89 
                                        a r+k + k +    Rl +Pf+++C +Cg+yIyk ++ Na ++  ++ +Ylg+   rFyikCt C+++++++TDPk
  gene1160|gene1160|rna1159|rna1159   5 ANRKKES-KSKGAATRLATPFTIKCLSCGAYIYKNKRHNATRQVAQGKDYLGVESHRFYIKCTGCNETLSIRTDPK 79 
                                        5688888.9999999************************************************************* PP

                             DUF572  90 ntdYvveeGatRnfkaek.leeeeakreekekeeeeaedamkklEkr 135
                                        n  Y  e+G+ R  + e   +++ ++++ + k+e +++d + kl  +
  gene1160|gene1160|rna1159|rna1159  80 NGIYITENGCVR-IDGEDnIQDKIEDSSIQLKKESDMKDEIIKLRMQ 125
                                        ************.5444415555557777888888999998887655 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0   0.00037       1.1       2      14 ..      26      38 ..      26      39 .. 0.93
   2 ?    8.5   0.3   0.00071       2.1       2      11 ..      63      72 ..      62      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00037
                             zf-ACC  2 tKCpsCgemlykk 14
                                       +KC sCg+ +yk+
  gene1160|gene1160|rna1159|rna1159 26 IKCLSCGAYIYKN 38
                                       8**********96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00071
                             zf-ACC  2 tKCpsCgeml 11
                                       +KC++C+e+l
  gene1160|gene1160|rna1159|rna1159 63 IKCTGCNETL 72
                                       8*******97 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00077       2.3      24      51 ..      19      47 ..      16      49 .. 0.79
   2 ?    4.5   0.1     0.011        33      29      40 ..      61      72 ..      59      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00077
                             DUF951 24 RvGadiklkClgcgrevm.lpRskfekki 51
                                       R+ + + +kCl+cg  +   +R+++ +++
  gene1160|gene1160|rna1159|rna1159 19 RLATPFTIKCLSCGAYIYkNKRHNATRQV 47
                                       5566799********99977787777766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.011
                             DUF951 29 iklkClgcgrev 40
                                       + +kC+gc++ +
  gene1160|gene1160|rna1159|rna1159 61 FYIKCTGCNETL 72
                                       679*****9876 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00066         2      27      48 ..      14      48 ..       2      54 .. 0.61
   2 ?    4.5   0.1     0.015        45      17      36 ..      51      70 ..      39      87 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00066
                    Lar_restr_allev 27 q..........cvyCadCga...stpwfkiaedea 48
                                       +          ++ C  Cga    ++  + + ++a
  gene1160|gene1160|rna1159|rna1159 14 KgaatrlatpfTIKCLSCGAyiyKNKRHNATRQVA 48
                                       133556677889********665444444444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                    Lar_restr_allev 17 rsqrvvaeigq....cvyCadCga 36
                                       +++++v    +    ++ C+ C+ 
  gene1160|gene1160|rna1159|rna1159 51 KDYLGV----EshrfYIKCTGCNE 70
                                       334444....14455*******98 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.5e-05       0.1      72     100 ..      56      84 ..      37      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                          Tmemb_55A  72 gkleqhvvkCevCneatpiknapagkkyv 100
                                           ++  +kC+ Cne   i+  p++  y+
  gene1160|gene1160|rna1159|rna1159  56 VESHRFYIKCTGCNETLSIRTDPKNGIYI 84 
                                        5578999****************998887 PP

>> DUF3795  Protein of unknown function (DUF3795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.7   6.8e-05       0.2       7      49 ..      26      71 ..      20      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
                            DUF3795  7 ldCeeCeayeakekeekkkkkk...eafeelllaleeikCeGCree 49
                                       ++C +C ay  k+k+++++++    + +  ++++   ikC+GC+e+
  gene1160|gene1160|rna1159|rna1159 26 IKCLSCGAYIYKNKRHNATRQVaqgKDYLGVESHRFYIKCTGCNET 71
                                       79*******99877776666665555566666777789*****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 852.28
//
Query:       gene116|gene116|rna116|rna116  [L=272]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-11   43.1   0.1    2.2e-08   34.0   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
      2e-09   37.1   0.2    4.1e-08   32.8   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    2.3e-07   31.6   0.0    2.4e-07   31.6   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
      8e-06   25.5   0.1    0.00011   21.7   0.1    2.4  1  Peptidase_S9   Prolyl oligopeptidase family
    0.00071   19.3   0.0     0.0016   18.1   0.0    1.6  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
      0.001   18.5   0.0       0.25   10.6   0.0    2.3  2  LIP            Secretory lipase
      0.002   17.1   0.0      0.003   16.5   0.0    1.3  1  Say1_Mug180    Steryl acetyl hydrolase
  ------ inclusion threshold ------
      0.027   13.8   0.0      0.044   13.1   0.0    1.3  1  DUF915         Alpha/beta hydrolase of unknown function (DUF9


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0     1e-11   2.2e-08      26      92 ..      80     143 ..      56     191 .. 0.84
   2 !    7.4   0.0    0.0014       3.1     202     251 ..     196     247 ..     161     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1e-11
                                    HHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHH CS
                  Abhydrolase_1  26 akdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaa 92 
                                      +g++v+++D rG++ S+   +   + + + +v ++++++  +++ +++++vGhS+G+ i+++y+ 
  gene116|gene116|rna116|rna116  80 VSKGYCVLIPDYRGFADSEGEFD---VSMVNLDVMACFEYLISRFNAEEVHMVGHSLGTGIMAEYCG 143
                                    344******************99...99*************************************86 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                                    HHHHCTHHHHS....EEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                  Abhydrolase_1 202 lrlrelknvla....ptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                      ++ lkn+      ++++++g++D ++p++++  l ++     +v++sd gH 
  gene116|gene116|rna116|rna116 196 MGYDTLKNMEHvngeDIFLYHGMKDDIIPYHHSIMLSKKYGA--KVRLSDHGHG 247
                                    333447888888888***************999999988655..8888888885 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.8e-11   4.1e-08       3     114 ..      53     169 ..      51     207 .. 0.78
   2 ?    3.0   0.0     0.023        51     194     219 ..     212     237 ..     185     251 .. 0.62

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.8e-11
                    Hydrolase_4   3 pkavvvlvHGlaehsgryae..laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfl 80 
                                    p++ +v +HG + + + y     ++ L+ +G+ v++ D+rG+  seg+      ++ +  D+ a +e + ++ + +++ +
  gene116|gene116|rna116|rna116  53 PEGFIVALHGKGCSREDYVSssKVDILVSKGYCVLIPDYRGFADSEGEFD----VSMVNLDVMACFEYLISRFNAEEVHM 128
                                    78899***********9987557899*******************99986....999999******************** PP

                    Hydrolase_4  81 lGhSmGGliallyl.........lrypdkvaglilsaPalkik 114
                                    +GhS+G  i ++y+         +ry  + +++ +++++ +i 
  gene116|gene116|rna116|rna116 129 VGHSLGTGIMAEYCgyieknslgTRY--RPQKMFMISAFTSIT 169
                                    *************9765444422222..335666666665555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.023
                    Hydrolase_4 194 llllhGeaDkvvdpeasrelyerlgs 219
                                    ++l+hG +D ++++  s  l ++ g+
  gene116|gene116|rna116|rna116 212 IFLYHGMKDDIIPYHHSIMLSKKYGA 237
                                    57777777777777777666666554 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.1e-10   2.4e-07       1      87 [.      57     155 ..      57     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.1e-10
                                    EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHC.HHH....HHHHCCTT..TTSEEEEEETC CS
                  Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldledl.adl....aalldelaagggpvvlvGHSl 74 
                                    ++ lHG g+s++++   + +  l ++g++vl+pD++G+  ++   +d++ + +d+    + l+ ++   + +v+ vGHSl
  gene116|gene116|rna116|rna116  57 IVALHGKGCSREDYVsSSKVDILVSKGYCVLIPDYRGFA-DSEGEFDVSMVnLDVmacfEYLISRFN--AEEVHMVGHSL 133
                                    7899**99******6688********************5.677777776644555455677888885..9********** PP

                                    HHHHHHHHHHCC............. CS
                  Abhydrolase_6  75 GGalalaaapla............l 87 
                                    G+ ++++   ++            +
  gene116|gene116|rna116|rna116 134 GTGIMAE---YCgyieknslgtryR 155
                                    *999999...554335555554441 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1     5e-08   0.00011       5     167 ..      74     233 ..      70     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5e-08
                                    HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHH........HH CS
                   Peptidase_S9   5 selqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyG........Gy 76 
                                    s++ +l ++Gy v+++++rG ++   +f  ++          D++a+ e+l++++  ++e++ + G+S G        Gy
  gene116|gene116|rna116|rna116  74 SKVDILVSKGYCVLIPDYRGFADSEGEFDVSM-------VNLDVMACFEYLISRF--NAEEVHMVGHSLGtgimaeycGY 144
                                    7788899***************8888887743.......3459*********997..5599999******7333333333 PP

                                    HHHHHHH..H-GGG-SEEEEESE---CCCHHCSTTS...THHHCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEE CS
                   Peptidase_S9  77 ltgaaln..qrpdlFkaavaevpvvdvlrydsdtdl...lteeymewgnpeeneegykelspyspldnvkaypplLlihG 151
                                         l+   rp++  ++ a  +++dv +     ++   l ++  e      +e gy++l+++++++      +++l hG
  gene116|gene116|rna116|rna116 145 IEKNSLGtrYRPQKMFMISAFTSITDVAMESVACRIisfLFPWIKEKLS---KEMGYDTLKNMEHVNG----EDIFLYHG 217
                                    3333344233455555555566666666666665555533335555443...4666666666666655....9******* PP

                                    TT-SSS-THHHHHHHH CS
                   Peptidase_S9 152 laDdrvppaealklva 167
                                    ++Dd +p+ ++++l +
  gene116|gene116|rna116|rna116 218 MKDDIIPYHHSIMLSK 233
                                    ***********98866 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   7.3e-07    0.0016      52      78 ..      71     104 ..      15     134 .. 0.79
   2 ?   -2.1   0.0         1   2.3e+03     228     247 ..     209     229 ..     189     240 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.3e-07
                                    H.......HHHTT-EEEEEE-TTSTTS-S---TT CS
                  Peptidase_S15  52 v.......fvarGYavVvqdvrGtggSeGeftvg 78 
                                    v       +v++GY v++ d rG+++SeGef+v 
  gene116|gene116|rna116|rna116  71 VssskvdiLVSKGYCVLIPDYRGFADSEGEFDVS 104
                                    044444459**********************994 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1
                                    -S-EEEEEECCSSTTC.CHHH CS
                  Peptidase_S15 228 kapvllvgGwnDwnvk.ngai 247
                                    + +++l++G+ D++   +++i
  gene116|gene116|rna116|rna116 209 GEDIFLYHGMKDDIIPyHHSI 229
                                    557899999999887766655 PP

>> LIP  Secretory lipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0034       7.5      21      37 ..      78      94 ..      71     138 .. 0.86
   2 !   10.6   0.0   0.00011      0.25     197     244 ..     190     238 ..     167     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0034
                            LIP 21 plLkeGyyVvvpDyeGp 37
                                    l ++Gy V +pDy G 
  gene116|gene116|rna116|rna116 78 ILVSKGYCVLIPDYRGF 94
                                   5789***********96 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                            LIP 197 etikkvlednkl.sksavPqiPvlvyhgvidelipikdakklaknwcdk 244
                                    e+++k +  + l + ++v +  +++yhg+ d++ip++ +  l k++ +k
  gene116|gene116|rna116|rna116 190 EKLSKEMGYDTLkNMEHVNGEDIFLYHGMKDDIIPYHHSIMLSKKYGAK 238
                                    56777778888888999**********************9999999776 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.4e-06     0.003     156     241 ..      85     172 ..      47     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-06
                    Say1_Mug180 156 ailvsDYtvtaakdqskkYplqvleslavydylvkskgfknvvvlGdSaGGnlvLslllklsk..lnkvvlPkkaiaiSP 233
                                     +l++DY   a  +   +  + +l+++a ++yl+      +v ++G S G  ++     +++k  l+    P+k  +iS 
  gene116|gene116|rna116|rna116  85 CVLIPDYRGFADSEGEFDVSMVNLDVMACFEYLISRFNAEEVHMVGHSLGTGIMAEYCGYIEKnsLGTRYRPQKMFMISA 164
                                    699********999999**********************************99999999988822345678999999999 PP

                    Say1_Mug180 234 Wlnltild 241
                                    +  +t++ 
  gene116|gene116|rna116|rna116 165 FTSITDVA 172
                                    98888765 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05     0.044      92     123 ..     113     144 ..      94     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                         DUF915  92 vlseLkkkYnikkfnavGhSmGglaltsYlee 123
                                      ++L +++n +++ +vGhS G   ++ Y   
  gene116|gene116|rna116|rna116 113 CFEYLISRFNAEEVHMVGHSLGTGIMAEYCGY 144
                                    5689********************99999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1632.98
//
Query:       gene1162|gene1162|rna1161|rna1161  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.02   14.7   0.0    1.4  1  DUF1652   Protein of unknown function (DUF1652)
      0.024   14.7   0.6      0.038   14.1   0.6    1.5  1  YcgR_2    Flagellar protein YcgR


Domain annotation for each model (and alignments):
>> DUF1652  Protein of unknown function (DUF1652)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.2e-06      0.02      26      65 ..      78     117 ..      75     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-06
                            DUF1652  26 mtvrlfdpasgevdLlvtGiplrelnssrdisrLieelra 65 
                                        +t+rl  pa ++v + v+G + +++ ss  i r ie +++
  gene1162|gene1162|rna1161|rna1161  78 FTLRLINPARDRVVIIVNGTKIKTIVSSKYIIRFIETIEN 117
                                        79**********************************9986 PP

>> YcgR_2  Flagellar protein YcgR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   4.2e-06     0.038      40      84 ..      87     130 ..      41     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-06
                                        T-SB----TT-EEEEEEE-TSSEEEEEEEEEEEEETTCEEEEEE- CS
                             YcgR_2  40 egrlvplregtevevrfiseggvyaFrsrvlgrikdpipllvlsy 84 
                                        ++r+v++ +gt+++   +s++ +++F  ++ +r k+p++ ++lsy
  gene1162|gene1162|rna1161|rna1161  87 RDRVVIIVNGTKIKT-IVSSKYIIRFIETIENRDKSPFYFIFLSY 130
                                        479999999***998.66778**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1115.67
//
Query:       gene1163|gene1163|rna1162|rna1162  [L=583]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-13   48.6   0.2    5.7e-13   48.6   0.2    2.9  3  RINT1_TIP1    RINT-1 / TIP-1 family
  ------ inclusion threshold ------
       0.39   10.2   8.4       0.83    9.2   8.4    1.6  1  Exonuc_VII_L  Exonuclease VII, large subunit
        2.2    7.3  13.6       0.14   11.2   8.3    1.7  2  Atg14         Vacuolar sorting 38 and autophagy-related subun


Domain annotation for each model (and alignments):
>> RINT1_TIP1  RINT-1 / TIP-1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.8      0.19   1.1e+03     274     341 ..      56     154 ..       9     157 .. 0.62
   2 !   48.6   0.2   9.6e-17   5.7e-13       6     115 ..     186     297 ..     183     333 .. 0.84
   3 ?    0.1   0.1     0.048   2.9e+02     379     412 ..     491     524 ..     381     530 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.19
                         RINT1_TIP1 274 edwsdevfFieLweelqerakknee..........................stavgse..........eegalFde 313
                                        + +++ + F+ L++e+ + +k+  e                          s     +           e  +F +
  gene1163|gene1163|rna1162|rna1162  56 TLLEKREKFVCLKDEVSKYKKRALEkarnefeglyreifeeasrirpsatfS-----TfgeftkikglIERNIFRN 126
                                        4456667788888887655555544566666666666666665555544432.....0222233445566677777 PP

                         RINT1_TIP1 314 tiaaydrlrkraeelivealkkeikeal 341
                                        + ++++r  ++ +e++ +++ ++++++l
  gene1163|gene1163|rna1162|rna1162 127 LGRRLTRFYSEEKEKLRKHILSQMEKKL 154
                                        7666666666666666666666665555 PP

  == domain 2  score: 48.6 bits;  conditional E-value: 9.6e-17
                         RINT1_TIP1   6 lvkplekrFrYHFsgdkqTnklskpewflefilklleknldflrenvqpilakkfrekidav.sefitaLlplvre 80 
                                        l + +   F+YHF +d++ n+l+kpewfl+fil  l++ + ++  +++   ++ ++ + d   +e++  +  l+r 
  gene1163|gene1163|rna1162|rna1162 186 LYEKISRGFEYHFLSDRDSNRLDKPEWFLDFILAKLKESKVVFDIYLDLNKKDVEEGEFDGRfEELVSRVCGLIRT 261
                                        67788889********************************99988888755555555577767************* PP

                         RINT1_TIP1  81 Kvasvleevl.sdpalLshlisellsfdkeLrekyk 115
                                        K++++    + ++ +l+ hl  e+l+f  e+ ++y 
  gene1163|gene1163|rna1162|rna1162 262 KIEEISGCSSkQKRNLMLHLGMEILKFRYEVCHDYG 297
                                        ****98764444556************999888876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.048
                         RINT1_TIP1 379 dfLekalskalfrriwrelleklqdllweevllr 412
                                        ++L+ +    ++  i+r++ e+++ +l+ee++l+
  gene1163|gene1163|rna1162|rna1162 491 RYLDDYKECLSYDAIKRDVKERIDGVLLEEIILK 524
                                        3444555555667777888888888888888876 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   8.4   0.00014      0.83     137     258 ..       3     163 ..       1     192 [. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00014
                       Exonuc_VII_L 137 lvvpdkaeleeqleelerrlekaikrll......eekkqrleklasrlkspeellerkrqrldeleerleralkkq 206
                                        +++++k++le+ql++++++ ++ i+++       +ek++ +e++++++++ e  l +kr+++  l++++++  k++
  gene1163|gene1163|rna1162|rna1162   3 ILLRRKNHLEHQLQQFKQKESDRIEHRNhlarqaKEKREAIEAVKKEIHEMELTLLEKREKFVCLKDEVSKYKKRA 78 
                                        567789999******99976666654333333339999***********999999999****************** PP

                       Exonuc_VII_L 207 lkkkrerleelkerl.k....ekleekk...........................erl....kklkerle..llee 244
                                        l+k+r+++e l +++ +          +                           +rl    ++ ke+l+  +l++
  gene1163|gene1163|rna1162|rna1162  79 LEKARNEFEGLYREIfEeasrI-----RpsatfstfgeftkikgliernifrnlgRRLtrfySEEKEKLRkhILSQ 149
                                        ***********98885555330.....2333555555555555555554444444222221222222222444555 PP

                       Exonuc_VII_L 245 kkerleeleeklea 258
                                         +++le   +  ea
  gene1163|gene1163|rna1162|rna1162 150 MEKKLEDDRRMHEA 163
                                        55555555555554 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   8.3   2.4e-05      0.14      61     139 ..       7      85 ..       2     108 .. 0.90
   2 ?   -3.5   0.2      0.71   4.2e+03      36      53 ..     137     154 ..     129     164 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.4e-05
                              Atg14  61 kiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiakl 136
                                        +  ++  +l++ k++ +d  e+ + l  + ++ +++ie+ kk++ ++  +l ++r++   l++e+++++k+ ++k 
  gene1163|gene1163|rna1162|rna1162   7 RKNHLEHQLQQFKQKESDRIEHRNHLARQAKEKREAIEAVKKEIHEMELTLLEKREKFVCLKDEVSKYKKRALEKA 82 
                                        56677889****************************************************************9998 PP

                              Atg14 137 qda 139
                                         ++
  gene1163|gene1163|rna1162|rna1162  83 RNE 85 
                                        776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.71
                              Atg14  36 sekeslkkkiekalegke 53 
                                        +eke l+k+i   +e+k 
  gene1163|gene1163|rna1162|rna1162 137 EEKEKLRKHILSQMEKKL 154
                                        467777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1628  (0.0908026); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.35s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 3352.24
//
Query:       gene1164|gene1164|rna1163|rna1163  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-32  110.0   0.1    9.2e-32  109.7   0.1    1.1  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
  ------ inclusion threshold ------
      0.076   13.5   0.0       0.15   12.5   0.0    1.5  1  Na_Ca_ex_C      C-terminal extension of sodium/calcium exchan
      0.078   13.2   0.1       0.15   12.3   0.0    1.5  2  DNA_pol_B_3     DNA polymerase family B viral insert


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.1   1.5e-35   9.2e-32       2     121 .]       7     129 ..       6     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 1.5e-35
                                        EEEEEEEEEEET................................................................ CS
                     Ribosomal_L18A   2 keYeVvGrklpsekepepkvyrmrifapnevvak...wyflkklkkvkkanGeilavkkieekkptkvknygiwlr 74 
                                        keY+++G+++p+e +p p+++  +if +n+v ak   + +l+k  k+k ++G i+++++i e + ++v+nygi   
  gene1164|gene1164|rna1163|rna1163   7 KEYRIHGSAMPTEGDPRPQIFVATIFTKNHVFAKakfFKILEKKYKIKASKGLIINCERIPEPSFKEVQNYGIRFI 82 
                                        89*********************************9999************************************* PP

                                        ....TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEEE CS
                     Ribosomal_L18A  75 ydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekve 121
                                        y+srsg hn yke r++++ gav+ v +el++rh++krs + I++ve
  gene1164|gene1164|rna1163|rna1163  83 YRSRSGVHNAYKECRAISRCGAVDHVLRELAGRHKLKRSAVDIISVE 129
                                        ********************************************996 PP

>> Na_Ca_ex_C  C-terminal extension of sodium/calcium exchanger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.15       5      38 ..      43      76 ..      40     127 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                         Na_Ca_ex_C  5 fykylskryradkrrgvivetegeleekeegvel 38
                                       f+k+l+k+y+ + ++g+i++ e   e++ ++v+ 
  gene1164|gene1164|rna1163|rna1163 43 FFKILEKKYKIKASKGLIINCERIPEPSFKEVQN 76
                                       89********************955555444443 PP

>> DNA_pol_B_3  DNA polymerase family B viral insert
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      27      69 ..      18      63 ..       3      94 .. 0.75
   2 ?   -2.8   0.0       1.2     7e+03      29      42 ..     147     160 ..     136     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                        DNA_pol_B_3 27 kdakdkisiFsevlstgnYvtiddnvlkilekkin...ekkFtvkv 69
                                       ++ + + +iF   + t n+v+ + + +kilekk +   +k+  ++ 
  gene1164|gene1164|rna1163|rna1163 18 TEGDPRPQIFVATIFTKNHVFAKAKFFKILEKKYKikaSKGLIINC 63
                                       56667889************************98753344444443 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                        DNA_pol_B_3  29 akdkisiFsevlst 42 
                                         + +  +F+++l+t
  gene1164|gene1164|rna1163|rna1163 147 ENVEFPVFTKILNT 160
                                        44456688888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 1049.40
//
Query:       gene1165|gene1165|rna1164|rna1164  [L=726]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00056   20.0   6.1     0.0037   17.3   0.3    3.6  4  Cnd1      non-SMC mitotic condensation complex subunit 1
  ------ inclusion threshold ------
      0.015   14.7   0.0      0.025   13.9   0.0    1.3  1  DUF1442   Protein of unknown function (DUF1442)
      0.016   15.7   0.3        4.8    7.8   0.1    3.2  3  RPAP3_C   Potential Monad-binding region of RPAP3
      0.097   13.1   0.0       0.66   10.4   0.0    2.4  2  HEAT_2    HEAT repeats


Domain annotation for each model (and alignments):
>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.32   1.4e+03      79     128 ..      13      59 ..      10      77 .. 0.76
   2 !   17.3   0.3   8.2e-07    0.0037       5      84 ..     110     192 ..     104     242 .. 0.78
   3 ?    3.5   0.0     0.015        67     110     143 ..     373     408 ..     328     447 .. 0.74
   4 ?   -2.9   0.0       1.3   5.9e+03      71     105 ..     577     611 ..     550     618 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                               Cnd1  79 laalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyip 128
                                        +++++ei+  ++++  ++l+++i  l  + + +  ++++ il+++l++ +
  gene1165|gene1165|rna1164|rna1164  13 QLMFNEIQLCDTKKYSESLKEVIEMLIGQ-DLF--EEFCRILNVVLTCRK 59 
                                        57899999999999999999999999843.333..347777777777665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 8.2e-07
                               Cnd1   5 lairtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselakll.eDenprVvan 77 
                                        l+i  l+  +++ +++ e ++ ++ +rL D++  VRk a+ +++   ++++ ++ ++++ +++++  D+n++V+++
  gene1165|gene1165|rna1164|rna1164 110 LCILKLAmdVVQPESIDEGVLGKISERLFDKEKSVRKEALRLLSGYQEMGLNRNVKVVNLFKDIVrYDPNDEVRTL 185
                                        5566666778999999999**************************9999999999999999999999********* PP

                               Cnd1  78 alaalte 84 
                                        al++++ 
  gene1165|gene1165|rna1164|rna1164 186 ALSLISV 192
                                        *987654 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.015
                               Cnd1 110 e....csewgqitilefLlsyipkdkqeaeslveklcp 143
                                             ++e ++++il+++ +  +k++   e++ve  ++
  gene1165|gene1165|rna1164|rna1164 373 RfydfFNETSRKYILSTVYKLLAKNSV--EEVVEEAMQ 408
                                        133348999999999999999999988..777776555 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.3
                               Cnd1  71 nprVvanalaalteiseksenaiynllpdiiskls 105
                                        ++   + + +++ e+ +++++++++++ +++  l+
  gene1165|gene1165|rna1164|rna1164 577 DDHLKQYCSILFFELFSEDSTPLISVFCEVLETLV 611
                                        55566778888888888888999999988888877 PP

>> DUF1442  Protein of unknown function (DUF1442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.6e-06     0.025      95     167 ..     388     461 ..     372     483 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-06
                            DUF1442  95 selpevivaeevektmeklqGvdflvvdskrkefvanal.rlaklskrGavlvcknalrrsisgfkwkkvlrdr 167
                                        s + + +  ++ve+++e+   +  lv d + ++f+ +++ ++ak s r  ++vck+ +++  +  ++++++ + 
  gene1165|gene1165|rna1164|rna1164 388 STVYKLLAKNSVEEVVEEAMQMASLVCDDDLNNFIGSIIkKNAKASPRVCLMVCKQVMKHIRPLGRLHEAIVEE 461
                                        55666777999************************98873689**************99877777777766555 PP

>> RPAP3_C  Potential Monad-binding region of RPAP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0011       4.8      31      76 ..      28      73 ..       7      98 .. 0.87
   2 ?    4.1   0.0     0.015        67       8      82 ..     295     374 ..     293     378 .. 0.76
   3 ?   -2.4   0.0       1.6   7.1e+03      43      60 ..     519     536 ..     517     543 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                            RPAP3_C 31 pkqlpkiFknsledeilsdildalnerlqeekaedsslvleiLdrL 76
                                       +++l+++++ ++  ++++++ ++ln  l   k + +s++ ++L+r+
  gene1165|gene1165|rna1164|rna1164 28 SESLKEVIEMLIGQDLFEEFCRILNVVLTCRKPNIPSRISNFLRRI 73
                                       389*************************999988888888888875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                            RPAP3_C   8 FeklwrklkredkdlkavllqinpkqlpkiFk.nsledeilsdildalnerlqeekaeds....slvleiLdrLsk 78 
                                        +ek+++ l ++ ++ + +l +i+ + ++++F+ ++l    l++++ ++ +++ +  ++       + +ei+++L +
  gene1165|gene1165|rna1164|rna1164 295 YEKEFEYLLSNPSEENTFLSRIELSYIEELFGrDDLGLPSLESFVSVMYQSCLSVVESLDaperGAQVEIMKNLFR 370
                                        577888885555666667777**********9999**********9777666554322224455788999999999 PP

                            RPAP3_C  79 vkRF 82 
                                        + RF
  gene1165|gene1165|rna1164|rna1164 371 IARF 374
                                        9999 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.6
                            RPAP3_C  43 edeilsdildalnerlqe 60 
                                        ++e+ls +l++l+++l+ 
  gene1165|gene1165|rna1164|rna1164 519 DPELLSHVLRYLEKELEC 536
                                        68999999*999998765 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00015      0.66      30      84 ..     127     187 ..      94     191 .. 0.75
   2 ?   -1.6   0.0      0.83   3.7e+03      30      56 ..     504     531 ..     483     538 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                             HEAT_2  30 pealpaLvellededpavRraaaeaLg...aigd...pealpaLkellddddddvvReaAa 84 
                                        + +l  + e l d++  vR++a + L+   ++g+    +++++ k++++ d++d+vR+ A+
  gene1165|gene1165|rna1164|rna1164 127 EGVLGKISERLFDKEKSVRKEALRLLSgyqEMGLnrnVKVVNLFKDIVRYDPNDEVRTLAL 187
                                        4567777888889999999999999975556664222668899999999999999998765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.83
                             HEAT_2  30 pealpaLvell.ededpavRraaaeaLg 56 
                                         ++++++v+l+  ++dp+   ++ ++L 
  gene1165|gene1165|rna1164|rna1164 504 SKVFEMCVDLAlCSDDPELLSHVLRYLE 531
                                        4678888887768888998888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.54
# Mc/sec: 4059.18
//
Query:       gene1166|gene1166|rna1165|rna1165  [L=596]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3530.32
//
Query:       gene1167|gene1167|rna1166|rna1166  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-40  138.7   1.3    6.7e-40  137.0   1.3    1.8  1  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   1.3   3.7e-44   6.7e-40       1     176 [.      91     242 ..      91     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 3.7e-44
                                        EEEEEETTT-...TT--HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHH CS
                      DNA_primase_S   1 FDiDmddydd..cseatvcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraai 74 
                                        FD+D++dy+   cs++++c+kc+  ++vavk+ld +l++++gfk++ +vfsgrrG+Hcwv d++a +l+d+er +i
  gene1167|gene1167|rna1166|rna1166  91 FDVDLTDYPRecCSKKLICNKCLVLIKVAVKILDYSLKQELGFKNVGFVFSGRRGVHCWVFDDTALELSDIERGEI 166
                                        9*************************************************************************** PP

                                        HHH..................................HCHHHHCT--------..................----- CS
                      DNA_primase_S  75 vnylnlyrplhpflsrsmlkivkpvveeiileeqdpfeikkllrllpdkslrekkkweakedivlvllyprldeqv 150
                                        v+y+ ++       +++          ++  ee      k l++  p  ++       + e++ ++++y+r+d++v
  gene1167|gene1167|rna1166|rna1166 167 VRYYDCV-------AKR----------KMYSEE----YSKILREYSPFFESEG-----LEESVLFERMYIRIDKEV 216
                                        **88885.......222..........222222....4444444444444444.....6679************** PP

                                        ------------....---------. CS
                      DNA_primase_S 151 tkgikhllkapfcihgktgnvcvpld 176
                                        t++ khl+k+pf++h++t   +vp+d
  gene1167|gene1167|rna1166|rna1166 217 TQKSKHLIKMPFSVHPSTEIISVPID 242
                                        ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2005.92
//
Query:       gene1168|gene1168|rna1167|rna1167  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0059   16.8  12.6     0.0059   16.8  12.6    3.3  3  EamA         EamA-like transporter family
  ------ inclusion threshold ------
      0.014   15.5   0.6      0.014   15.5   0.6    3.1  3  Insulin_TMD  Insulin receptor trans-membrane segment


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  12.6   6.6e-07    0.0059      33     134 ..      34     131 ..       9     134 .. 0.72
   2 ?    3.1   6.0     0.011     1e+02      39     109 ..     147     220 ..     132     239 .. 0.77
   3 !    4.8   0.2    0.0033        30      12      53 ..     247     287 ..     242     293 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.6e-07
                               EamA  33 ltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnaslitslePvftlil 108
                                        + ++ +l+++++ ++i+ l+ +++  ++ k     ++++ l+++ ++l +++   k s+   ++ + l+ +ft+++
  gene1168|gene1168|rna1167|rna1167  34 AGGLLMLVSSFAKMMISYLNIQSF-DFKMKY---AFIIAGLSFIGGYLGMVSYYYKASSISYVISSDLQYLFTALI 105
                                        344667777777788888888888.555555...5555555555555556666666777777888899999***** PP

                               EamA 109 svlllgekltlkqllgivlillGvll 134
                                        + ++ g + +++q +gi++il G ++
  gene1168|gene1168|rna1167|rna1167 106 ATAWNGTRYSSTQCVGILMILGGFFI 131
                                        **********************9875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                               EamA  39 l..iagillliiallkegklaklslkdwlll.lllgllgtvlafllffyalkktsasnasli.tslePvftlils 109
                                        +  ++g++ +i ++++e+k+ k+ l d+  +  ++ +  ++l+f+ +fya +++ + +  ++ +  +P++ +++ 
  gene1168|gene1168|rna1167|rna1167 147 IgtLSGLFNSISLAIFESKI-KPALVDFRRFwCYMTTYTFFLTFFSLFYAAEEVFSKKSNYVkIISSPIIYIVFL 220
                                        334889999999********.999999888889999999999999999999999888766665556666666654 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0033
                               EamA  12 lfwaiyfvlskil.lrkvspltltfvrfliagillliiallke 53 
                                        ++ +i++v+s++  +r+++ +++++++f++ g+   i+ ++++
  gene1168|gene1168|rna1167|rna1167 247 VVTGISAVVSDVYlSREIDVQRFLAFSFTAIGVQ--IFNFFWK 287
                                        6789999999555388999999999888755544..4444444 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   1.2     0.047   4.2e+02      18      32 ..      15      29 ..       5      34 .. 0.53
   2 ?   15.5   0.6   1.5e-06     0.014       3      33 ..     193     225 ..     191     229 .. 0.83
   3 ?   -3.4   0.0       1.2   1.1e+04      30      41 ..     276     287 ..     274     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.047
                        Insulin_TMD 18 vigPviciillllvi 32
                                       +++ vi+++l ++v 
  gene1168|gene1168|rna1167|rna1167 15 IVAAVILSVLKVVVL 29
                                       334455555444443 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.5e-06
                        Insulin_TMD   3 FYvad..yldpsnivkIvigPviciillllvig 33 
                                        FY a+   +  sn vkI+  P+i i++l+ v  
  gene1168|gene1168|rna1167|rna1167 193 FYAAEevFSKKSNYVKIISSPIIYIVFLIEVLT 225
                                        777776667889****************98865 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.2
                        Insulin_TMD  30 lvigavfvvvkK 41 
                                         +++ +f ++ K
  gene1168|gene1168|rna1167|rna1167 276 AIGVQIFNFFWK 287
                                        588999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1958.70
//
Query:       gene1169|gene1169|rna1168|rna1168  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-11   43.5   0.8    3.9e-08   33.6   0.0    2.5  2  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
    0.00036   20.8   0.6    0.00059   20.2   0.6    1.3  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25


Domain annotation for each model (and alignments):
>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   4.3e-12   3.9e-08       2      71 ..      77     151 ..      77     159 .. 0.86
   2 !    8.1   0.3   0.00034         3     111     129 .]     158     176 ..     152     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 4.3e-12
                                        STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTT......EEEECCCTCEEEEESSSEEEEE-TTSEEEEEE CS
                      RNA_pol_Rbc25   2 fvgevltgkiksstregikvslgffddifvpkelLfep......sefdeeeqawvweveeeeelyldvgeeirfrv 71 
                                        f+ ev+ g+i +++++gik+ + ff+ +fv k  L++       s   e++ awvw +   ++ly+  +  +rfrv
  gene1169|gene1169|rna1168|rna1168  77 FKYEVVCGTILEQNEDGIKLGVPFFSSLFVKKGDLPDMtekvhvSDCGENQLAWVWIY-RGNKLYFRRNACVRFRV 151
                                        6679****************************99986511121155678899******.9***************9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00034
                                        SCEEEEEB-STTTCECGCC CS
                      RNA_pol_Rbc25 111 pyevlgsiqedGlGlvsWw 129
                                        +  vl s+ e+GlG++ Ww
  gene1169|gene1169|rna1168|rna1168 158 SSLVLCSLGEAGLGPLEWW 176
                                        556899************* PP

>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.6   6.6e-08   0.00059      16      70 .]      22      74 ..       9      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.6e-08
                                       HHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                        SHS2_Rpb7-N 16 edallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                       e+ + e+l++ky+g+v+++  ++v v  +a++ e kv ++  +   rV+f+al F
  gene1169|gene1169|rna1168|rna1168 22 EREVFEELKRKYVGRVLEDGSICVLVVRVANVHEYKVCDE--FLVARVEFEALLF 74
                                       67899**************99****************999..***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1169.20
//
Query:       gene1170|gene1170|rna1169|rna1169  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2189.24
//
Query:       gene117|gene117|rna117|rna117  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-37  126.6   0.0    5.8e-37  126.5   0.0    1.0  1  TFIID-31kDa  Transcription initiation factor IID, 31kD subuni
    8.8e-08   32.4   0.1    1.3e-07   31.9   0.1    1.2  1  CENP-S       CENP-S protein
    1.5e-05   24.9   0.0    2.6e-05   24.2   0.0    1.3  1  Bromo_TP     Bromodomain associated
    0.00034   21.0   0.1    0.00047   20.5   0.1    1.2  1  Histone      Core histone H2A/H2B/H3/H4
     0.0021   18.2   0.0     0.0033   17.5   0.0    1.3  1  TAF          TATA box binding protein associated factor (TAF)
  ------ inclusion threshold ------
      0.049   13.6   0.0       0.17   11.8   0.0    1.9  2  TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa s
      0.096   12.8   0.0       0.14   12.3   0.0    1.3  1  CENP-T_C     Centromere kinetochore component CENP-T histone 


Domain annotation for each model (and alignments):
>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0   2.3e-40   5.8e-37       3     121 ..       7     125 ..       5     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 2.3e-40
                    TFIID-31kDa   3 krPrdarlihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqsrlekqfkepppke 82 
                                      Prda++i+ iL+slg++e+e++V+ qLl+fay+yt++vLedA+++a+ha++ ++ ++dv+lA+q+++  +f +ppp++
  gene117|gene117|rna117|rna117   7 LAPRDAKVISVILRSLGIEECEPKVIIQLLEFAYKYTTDVLEDALLFAKHADRVHIITNDVKLALQTKVGRHFVPPPPRQ 86 
                                    57****************************************************************************** PP

                    TFIID-31kDa  83 lLlelAaerNkipLpkvkeklgirLPperycltavnyql 121
                                    +L ++Aa +N++pL   + +  i++Pp +  l++ +y++
  gene117|gene117|rna117|rna117  87 YLSDIAAMVNSKPLSIPDGENLIKVPPSSSALLNLDYEV 125
                                    *****************99999**************985 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   5.1e-11   1.3e-07      25      70 ..      26      71 ..      13      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.1e-11
                         CENP-S 25 eatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLla 70
                                   e+ +++i  l e  yk + ++ +D  +FakHA R  i t+Dv+L +
  gene117|gene117|rna117|rna117 26 ECEPKVIIQLLEFAYKYTTDVLEDALLFAKHADRVHIITNDVKLAL 71
                                   5789***************************************986 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     1e-08   2.6e-05       9      69 ..      12      72 ..       7      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1e-08
                                   HHHHHHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHH CS
                       Bromo_TP  9 kvvvsqileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLq 69
                                    +v+s il++ G+++ e+ ++  L e+a kY + + e+a  fa ha R      Dv l+Lq
  gene117|gene117|rna117|rna117 12 AKVISVILRSLGIEECEPKVIIQLLEFAYKYTTDVLEDALLFAKHADRVHIITNDVKLALQ 72
                                   589*******************************************************998 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.8e-07   0.00047      92     129 ..      35      72 ..      27      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                                    HHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                        Histone  92 lqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                    l e++  ++++++e+A l akha Rv i   D++lA++
  gene117|gene117|rna117|rna117  35 LLEFAYKYTTDVLEDALLFAKHADRVHIITNDVKLALQ 72 
                                    5677889*****************************97 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06    0.0033       9      65 ..      15      71 ..       7      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                                   HHHHHHHTT---B-HHHH.HHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH CS
                            TAF  9 vkviAeslGitnLsdeaa.alLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsAL 65
                                   + vi  slGi++ +  +  +lL++  +y    + ++a+ f +h+ R  + ++Dv  AL
  gene117|gene117|rna117|rna117 15 ISVILRSLGIEECEPKVIiQLLEFAYKYT-TDVLEDALLFAKHADRVHIITNDVKLAL 71
                                   778999********998637777777775.79***********************998 PP

>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.8e-05      0.17       6      48 ..      13      55 ..      12      57 .. 0.84
   2 ?   -1.8   0.0       1.3   3.2e+03      34      41 ..      86      93 ..      85      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.8e-05
                    TFIID_30kDa  6 avtayyLekaGle.tsDprlarlvsLaaqKFisdiaadAyqysk 48
                                   +v+  +L++ G+e ++ + +++l+   a K+ +d+++dA+ ++k
  gene117|gene117|rna117|rna117 13 KVISVILRSLGIEeCEPKVIIQLLEF-AYKYTTDVLEDALLFAK 55
                                   589999******94577778899886.57***********9998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                    TFIID_30kDa 34 KFisdiaa 41
                                   +++sdiaa
  gene117|gene117|rna117|rna117 86 QYLSDIAA 93
                                   689***96 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.3e-05      0.14      36      75 ..      33      72 ..      13      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                       CENP-T_C 36 kalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75
                                    +l +   k+   v eD   +akHa R  i ++Dv l ++
  gene117|gene117|rna117|rna117 33 IQLLEFAYKYTTDVLEDALLFAKHADRVHIITNDVKLALQ 72
                                   456667779999***********************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 851.37
//
Query:       gene1172|gene1172|rna1171|rna1171  [L=434]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-67  226.2   0.1    6.7e-67  225.5   0.1    1.3  1  Tubulin          Tubulin/FtsZ family, GTPase domain
    1.9e-18   66.8   0.0    3.6e-18   65.9   0.0    1.4  1  Tubulin_C        Tubulin C-terminal domain
    7.9e-05   22.4   0.0    0.00013   21.7   0.0    1.4  1  Tubulin_3        Tubulin domain
    0.00026   21.3   0.0    0.00051   20.3   0.0    1.5  1  Misat_Tub_SegII  Misato Segment II tubulin-like domain
     0.0071   15.6   0.0      0.011   14.9   0.0    1.3  1  Tubulin_2        Tubulin like
  ------ inclusion threshold ------
       0.15   12.2   2.1        0.3   11.2   2.1    1.5  1  Bombesin         Bombesin-like peptide


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.5   0.1   2.2e-70   6.7e-67       1     193 [.       3     204 ..       3     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 2.2e-70
                                        EEEEEEEHHHHHHHHHHHHH...HHHCH.............HHHT.....TTEEEEE....EEESBHHHHHTS-GS CS
                            Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdg.........dslesfFsesgkveyiprsvaidtdpqvlneikag 67 
                                        e+i++++GqcGnq+g e+w++l+kehgi++ g         d++++fF++ +++ ++pr++++d++p+v+++  + 
  gene1172|gene1172|rna1171|rna1171   3 EVITLQIGQCGNQMGGEFWKVLCKEHGISNCGtlqddrdlgDRKDVFFYQADDNVFVPRAILVDLEPRVISQASSF 78 
                                        79**************************76669**************************************98888 PP

                                        ......EEEE--CCC..CTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHH CS
                            Tubulin  68 selfnpnklllgkeg..agnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevl 141
                                           fn+++++l++eg  agnn+a+gy+  gk + +++ ++i++e+e+cdsl+ ff+++s++GGTGSG+g+++le++
  gene1172|gene1172|rna1171|rna1171  79 ---FNQENIFLSNEGggAGNNWAHGYYM-GKTMGNDVVDMIQREAEGCDSLETFFLLHSIAGGTGSGFGSLLLERI 150
                                        ...***********999**********9.*********************************************** PP

                                        HHTSTTSEEEEEEEE--..GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHH CS
                            Tubulin 142 keeypkalvvtvvvlPs..efsevvvepynailalkelieesdavividNdaLl 193
                                        +ee+pk++++t++++P+  e s+vvv+pyn+ilal++lie+sd++i +dN +L 
  gene1172|gene1172|rna1171|rna1171 151 REEFPKKIIQTYSIFPNndESSDVVVQPYNSILALQRLIENSDCIIAMDNSSLG 204
                                        *****************99999*****************************996 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   1.2e-21   3.6e-18       3     125 ..     259     383 ..     258     384 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.2e-21
                                        C-EEEEEEESSSCTT.TTTCS-HHHHHHHHHTCSGGGBSSSTSTTT.SSEEEEEEEEEESSSHHHHHHHHHHHHHT CS
                          Tubulin_C   3 lhFlltsyaPlvsae.kaavektsvqdvtrallepknimvkvdprk.gkylaiallirGdvepkevnkavqrikek 76 
                                        l F++ sy+P++ +e +  v+kt+ +d++r+ll pk  +++ d++k +  +++++++ G  ++ ev+++v r  +k
  gene1172|gene1172|rna1171|rna1171 259 LKFIVPSYTPFLCDEmSRIVRKTTCSDIMRRLLLPKTRLASYDQSKaQSVVSMLNIFHGVEDSGEVSRTVMRFLDK 334
                                        68**********9998999************************99868899999********************** PP

                                        TTS-BSTTSTTTEEEEEEECECT-TTTSSCEEEEEEEEGGGHHHHHHHH CS
                          Tubulin_C  77 kkaqfveWiptgikvalnkkspyvkkqskvsvlmlaNttsiaelfkrll 125
                                          ++fv+W+p ++ +al ++    ++ ++ s+l l N+t+i++++++++
  gene1172|gene1172|rna1171|rna1171 335 GMVNFVPWMPPSFNIALGRRIINNTSPNRISGLSLTNSTGISSILSKIS 383
                                        *************************999****************99985 PP

>> Tubulin_3  Tubulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.4e-08   0.00013      57     152 ..     109     198 ..      67     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.4e-08
                          Tubulin_3  57 hdlldrdlrpfaeecdqlrglqvftgvddaWG.GfaakylerlrdeygkksilvWvlaleeklkkkkkaklerklk 131
                                        +d++d   r  ae cd+l+++ ++ ++    G Gf++  ler+r+e++kk i ++ +  ++++++      +  ++
  gene1172|gene1172|rna1171|rna1171 109 NDVVDMIQR-EAEGCDSLETFFLLHSIAGGTGsGFGSLLLERIREEFPKKIIQTYSIFPNNDESS------DVVVQ 177
                                        466665444.48**************99887769****************998886644333322......22355 PP

                          Tubulin_3 132 klnkarslkelseqaslyvPi 152
                                          n++ +l++l e++  ++ +
  gene1172|gene1172|rna1171|rna1171 178 PYNSILALQRLIENSDCIIAM 198
                                        566666777666666665555 PP

>> Misat_Tub_SegII  Misato Segment II tubulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.7e-07   0.00051       1      68 [.       2      70 ..       2      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.7e-07
                    Misat_Tub_SegII  1 rEivtlqlGnyaNyvgtHfWNt..Qesyftydeeeee.sev.dhdvlfregetkqgqvtytPRllivDlkgs 68
                                       rE++tlq+G+  N +g  fW +  +e+ ++   + ++  ++ d++  f+    +  + +++PR+++vDl+  
  gene1172|gene1172|rna1171|rna1171  2 REVITLQIGQCGNQMGGEFWKVlcKEHGISNCGTLQDdRDLgDRKDVFFY---QADDNVFVPRAILVDLEPR 70
                                       8*******************964477777444433332555444333333...467899*********9765 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.7e-06     0.011     142     188 ..     111     158 ..      70     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-06
                          Tubulin_2 142 aikrlrgsage.eeglnvfVvgSLaGGTGSGiflDvayllrkilkeek 188
                                        +++ ++++a++ +++ ++f++ S+aGGTGSG    ++  +r++++++ 
  gene1172|gene1172|rna1171|rna1171 111 VVDMIQREAEGcDSLETFFLLHSIAGGTGSGFGSLLLERIREEFPKKI 158
                                        55666666666667789**************99999999999998875 PP

>> Bombesin  Bombesin-like peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.1    0.0001       0.3       1      12 [.      94     105 ..      94     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                           Bombesin   1 GNlWAvGHlMGK 12 
                                        GN WA G +MGK
  gene1172|gene1172|rna1171|rna1171  94 GNNWAHGYYMGK 105
                                        9**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2764.24
//
Query:       gene1173|gene1173|rna1172|rna1172  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.3   2.0       0.64    9.8   0.5    2.3  2  NTF-like  Nucleotidyltransferase-like
       0.05   13.7   0.0       0.11   12.6   0.0    1.5  1  YrhC      YrhC-like protein
       0.12   12.1   0.0       0.59    9.9   0.0    1.9  2  DUF3481   C-terminal domain of neuropilin glycoprotein


Domain annotation for each model (and alignments):
>> NTF-like  Nucleotidyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00011      0.64      37      89 ..       4      55 ..       1      63 [. 0.87
   2 ?    5.7   0.1     0.002        12      36      79 ..      57     100 ..      54     136 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                                       SSEEEEEEE--TT-SEEEEEEEETTEEEEEEEEEHHHHHHHHHHT--HHHHHH CS
                           NTF-like 37 fdvvllvivkeseeeltvkhyeveekkaalhvvseeqLeewlllgsnrrlvdw 89
                                       fdv  lv+v+ +  e+  k + ++e+ +a ++v++++ ++ ++  s+ r+v +
  gene1173|gene1173|rna1172|rna1172  4 FDVEGLVVVDVQ-GEILYKRIFSKEEDIAAKIVEKSTKDRDIISVSHERIVMC 55
                                       888888887655.568889999*****************************88 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.002
                                        TSSEEEEEEE--TT-SEEEEEEEETTEEEEEEEEEHHHHHHHHH CS
                           NTF-like  36 dfdvvllvivkeseeeltvkhyeveekkaalhvvseeqLeewll 79 
                                        ++d +llvi++  e +      +++e ++a  +v ++  +e + 
  gene1173|gene1173|rna1172|rna1172  57 KLDEILLVIYSPLEVNEAFIGQVFDEFTTAFVSVIKTPTRERVW 100
                                        68999999999999999888888888888888777666665553 PP

>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05      0.11      10      33 ..     100     123 ..      97     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                               YrhC  10 YkrFafvLLalsaFLyiGlviPse 33 
                                        +k++ ++ L +s+FLy G+v+  +
  gene1173|gene1173|rna1172|rna1172 100 WKKYDQIVLLVSTFLYEGIVMVGK 123
                                        699*****************9765 PP

>> DUF3481  C-terminal domain of neuropilin glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.19   1.1e+03       8      21 ..      53      66 ..      47      79 .. 0.79
   2 ?    9.9   0.0   9.8e-05      0.59      38      70 ..     114     146 ..     107     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.19
                            DUF3481  8 sllktldPilitii 21
                                        + k ld il+ i 
  gene1173|gene1173|rna1172|rna1172 53 VMCKKLDEILLVIY 66
                                       578999**999875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 9.8e-05
                            DUF3481  38 lycacsqaslsdrnlsalenynfelvdGvklkk 70 
                                        ly      + sd  l  l   nfe vdG+k+ k
  gene1173|gene1173|rna1172|rna1172 114 LYEGIVMVGKSDEMLNRLPKRNFEGVDGIKVPK 146
                                        6777777888999999**************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 953.76
//
Query:       gene1174|gene1174|rna1173|rna1173  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-05   22.5   0.0    0.00034   20.5   0.1    2.1  2  BBS2_N    Ciliary BBSome complex subunit 2, N-terminal
     0.0071   17.2   0.1         17    6.5   0.0    4.5  5  WD40      WD domain, G-beta repeat
  ------ inclusion threshold ------
        5.2    7.7   6.2         22    5.7   0.2    4.0  5  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> BBS2_N  Ciliary BBSome complex subunit 2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.4   8.1e+03      77      95 ..      59      77 ..      56      83 .. 0.74
   2 !   20.5   0.1   5.6e-08   0.00034      67     101 ..     132     166 ..     105     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.4
                             BBS2_N 77 tnllaYdveeNsdlFykev 95
                                       + ++a d+e N  ++ + +
  gene1174|gene1174|rna1173|rna1173 59 EAVIAGDIEGNVRIYDRRL 77
                                       5677888888888887766 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 5.6e-08
                             BBS2_N  67 ekdiLligtqtnllaYdveeNsdlFykevpDGvnv 101
                                          diLl+g+q++++aYd  +N++ F ++++  v++
  gene1174|gene1174|rna1173|rna1173 132 IGDILLVGQQEHVVAYDLRTNASFFNRKFNMVVRS 166
                                        579***********************998766655 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.022   1.3e+02      12      37 ..      12      34 ..       2      35 .. 0.78
   2 ?    0.2   0.0      0.27   1.6e+03      26      38 .]      62      74 ..      50      74 .. 0.84
   3 ?   -1.1   0.0      0.69   4.1e+03      15      34 ..      99     109 ..      90     113 .. 0.67
   4 ?   -2.0   0.0       1.3     8e+03      25      34 ..     174     183 ..     153     184 .. 0.63
   5 !    6.5   0.0    0.0028        17       7      37 ..     197     234 ..     191     235 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.022
                                       SEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40 12 svtslafspdgawlasGsdDgtvriW 37
                                        +ts+  s ++++l+ +s+ g v+++
  gene1174|gene1174|rna1173|rna1173 12 TITSI--SYNKDLLV-SSWSGEVMLY 34
                                       38999..99999998.7999999987 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
                                       EEEETTSEEEEEE CS
                               WD40 26 asGsdDgtvriWd 38
                                       ++G+  g+vri+d
  gene1174|gene1174|rna1173|rna1173 62 IAGDIEGNVRIYD 74
                                       468889*****98 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.69
                                        EEEEETTSSEEEEEETTSEE CS
                               WD40  15 slafspdgawlasGsdDgtv 34 
                                        +         +++G++++++
  gene1174|gene1174|rna1173|rna1173  99 C---------VVAGGWNKKI 109
                                        3.........4568888776 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.3
                                        EEEEETTSEE CS
                               WD40  25 lasGsdDgtv 34 
                                        +++G+ Dg +
  gene1174|gene1174|rna1173|rna1173 174 FFAGTTDGRI 183
                                        2346668876 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.0028
                                        EESS...SS.......EEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   7 ltGH...ss.......vtslafspdgawlasGsdDgtvriW 37 
                                        + +H   s+       v+sl   + g++l+sG+ Dg v  W
  gene1174|gene1174|rna1173|rna1173 197 FNAHysiSGdskvfypVNSL---RMGKYLLSGGSDGRVLRW 234
                                        55664332245556667777...5578899*988**99877 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   6.6e+03      22      33 ..      98     109 ..      93     114 .. 0.74
   2 ?    1.9   0.0     0.056   3.4e+02      23      40 .]     135     151 ..     119     151 .. 0.77
   3 ?    5.7   0.2    0.0036        22      14      34 ..     164     184 ..     162     185 .. 0.87
   4 ?   -2.3   0.1       1.2   7.1e+03      23      33 ..     221     231 ..     213     234 .. 0.78
   5 ?   -0.7   0.2      0.38   2.3e+03      13      27 ..     251     265 ..     229     287 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                              PQQ_3  22 glvyvgtgdGtl 33 
                                        g v++g+++ ++
  gene1174|gene1174|rna1173|rna1173  98 GCVVAGGWNKKI 109
                                        567888888776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.056
                              PQQ_3  23 lvyvgtgdGtlyAlDaet 40 
                                        ++  ++ + +++A+D +t
  gene1174|gene1174|rna1173|rna1173 135 ILL-VGQQEHVVAYDLRT 151
                                        343.44579******998 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0036
                              PQQ_3  14 nsspavdgglvyvgtgdGtly 34 
                                        ++s+++ g   ++gt+dG++y
  gene1174|gene1174|rna1173|rna1173 164 VRSLVLTGKGFFAGTTDGRIY 184
                                        57888899999*********9 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.2
                              PQQ_3  23 lvyvgtgdGtl 33 
                                        ++  g++dG++
  gene1174|gene1174|rna1173|rna1173 221 YLLSGGSDGRV 231
                                        56668889987 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 0.38
                              PQQ_3  13 vnsspavdgglvyvg 27 
                                        ++ss+ v+g +v vg
  gene1174|gene1174|rna1173|rna1173 251 GVSSLCVAGERVAVG 265
                                        348888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1827.09
//
Query:       gene1175|gene1175|rna1174|rna1174  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-52  176.0   6.1    5.8e-52  175.9   6.1    1.0  1  Rer1      Rer1 family


Domain annotation for each model (and alignments):
>> Rer1  Rer1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.9   6.1   3.2e-56   5.8e-52       6     171 .]       3     165 ..       1     165 [. 0.95

  Alignments for each domain:
  == domain 1  score: 175.9 bits;  conditional E-value: 3.2e-56
                               Rer1   6 lkrkyqklldkltpytleRWiatlvllllfllriillqgfyivaYalgiylLnlllafltPkfdpsleeeaaeeea 81 
                                        lk+  q +ld+l+p    RW +t ++++l+++ri+++ +fy+++Y+lgiylL+ l+ fltPk ++   +    e++
  gene1175|gene1175|rna1174|rna1174   3 LKTLKQIYLDRLAPRPDVRWGITGAMFVLYCVRIWTTGAFYLITYCLGIYLLHALILFLTPKGEMI-PD--PFENI 75 
                                        677889*******************************************************99554.33..46789 PP

                               Rer1  82 eegaelptkkdeefrPfirrlpEfkfWlsatkailialvltffevfdvpVfwpiLlvyfivlfvltmrrqikhmik 157
                                        e++  +p++ d+ef+Pfir+lpEf+fW+ +tk + +a++ t+f+++d+pV+ piL++yfi+++  t +r i hm+k
  gene1175|gene1175|rna1174|rna1174  76 EDDDYIPETIDNEFKPFIRNLPEFDFWMFVTKIVGMAFIGTYFDILDIPVYTPILVIYFIFMVGYTTKRLIAHMKK 151
                                        99999*********************************************************************** PP

                               Rer1 158 ykyvpfdlgKkkyk 171
                                        y+y pf  +K+ yk
  gene1175|gene1175|rna1174|rna1174 152 YNYNPFLQSKEYYK 165
                                        **********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1034.70
//
Query:       gene1176|gene1176|rna1175|rna1175  [L=795]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4997.31
//
Query:       gene1177|gene1177|rna1176|rna1176  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-62  210.2   4.0    3.3e-62  209.2   4.0    1.5  1  DUF5092   Domain of unknown function (DUF5092)
     0.0069   15.9   0.2      0.032   13.8   0.2    2.1  1  HTH_Bact  Helix-turn-helix bacterial domain


Domain annotation for each model (and alignments):
>> DUF5092  Domain of unknown function (DUF5092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.2   4.0   3.6e-66   3.3e-62       1     163 []      44     258 ..      44     258 .. 0.99

  Alignments for each domain:
  == domain 1  score: 209.2 bits;  conditional E-value: 3.6e-66
                            DUF5092   1 vEtftleefrklilesrkkkkdfilArVttkdpedqsslynvyYdAeelnkvlFevvieserrllhrkkvkdPlnn 76 
                                        vEtftleef+ ++l++r+k+kdfilArVtt+dp+dqs +yn+yY+A+eln++lF++  es+rrllhr+kv++Plnn
  gene1177|gene1177|rna1176|rna1176  44 VETFTLEEFKAIVLDCRSKNKDFILARVTTPDPDDQSIIYNFYYAASELNRILFRF--ESDRRLLHRMKVRNPLNN 117
                                        59******************************************************..****************** PP

                            DUF5092  77 mkI.kqvyyYkltveeldralveyffkeaksks........................................... 108
                                        m+I +qvyyYk++++e+dral eyff e+k +                                            
  gene1177|gene1177|rna1176|rna1176 118 MYIlGQVYYYKIPPQEVDRALIEYFFIETKVEGkvtkkafsqvfrhkieeasedgkrchksrdsldandrslkins 193
                                        *****************************999999***************************************** PP

                            DUF5092 109 ..........evkedsiaaveelakekklilkaeyfasdddFLeksevreyfkenaldaddnFlF 163
                                                  +++++ i+++++++ e+++ ++a+yfasdddFL++ evreyf++n+ldadd+FlF
  gene1177|gene1177|rna1176|rna1176 194 veenpreiieKIQKGIISIPKAIPPERSVLYSANYFASDDDFLMQPEVREYFRRNTLDADDDFLF 258
                                        **********9*****************************************************9 PP

>> HTH_Bact  Helix-turn-helix bacterial domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.2   3.6e-06     0.032      19      32 ..     115     128 ..     110     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-06
                                        TTB-TTHHHHHHHH CS
                           HTH_Bact  19 insMsLlGQLyYqk 32 
                                         n+M +lGQ yY+k
  gene1177|gene1177|rna1176|rna1176 115 LNNMYILGQVYYYK 128
                                        59***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2506.38
//
Query:       gene1178|gene1178|rna1177|rna1177  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.8e-57  191.2   0.2      1e-56  191.0   0.2    1.0  1  Ras          Ras family
    1.2e-31  109.4   0.0      2e-31  108.7   0.0    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    2.2e-12   46.8   0.0    2.7e-12   46.5   0.0    1.1  1  Arf          ADP-ribosylation factor family
      2e-05   24.6   0.0    2.6e-05   24.3   0.0    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    0.00021   20.7   0.0    0.00029   20.3   0.0    1.3  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
  ------ inclusion threshold ------
      0.016   15.1   0.1       0.96    9.3   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
       0.07   13.2   0.7        0.1   12.7   0.7    1.6  1  Dynamin_N    Dynamin family
      0.079   12.5   0.0       0.33   10.5   0.0    2.0  1  GTP_EFTU     Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.0   0.2   4.6e-60     1e-56       1     160 [.      14     173 ..      14     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 4.6e-60
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegil 76 
                                        K+v++G  +vGK+sl+l++vk++F+ + esTig+ f+tk+i +++ ++k+eiwDTAGqe+++sl ++yyr+a+++l
  gene1178|gene1178|rna1177|rna1177  14 KVVVLGYYSVGKSSLVLKYVKGEFNPNEESTIGASFLTKTIFTQEGSIKFEIWDTAGQERYNSLIPMYYRGAQVAL 89 
                                        9*************************************************************************** PP

                                        EEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHH CS
                                Ras  77 lvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenveea 152
                                        + ydits esfe++k+wvee++  +++++  vL+GnK+Dle++r+v++++g+e+a++++l f+e SAkt +n+ e+
  gene1178|gene1178|rna1177|rna1177  90 IAYDITSMESFETAKRWVEELSFEKPKEFIKVLIGNKSDLESDRKVEYQKGKEYADSQNLLFFESSAKTGKNIAEI 165
                                        **************************************************************************** PP

                                        HHHHHHHH CS
                                Ras 153 feellrei 160
                                        f+++++++
  gene1178|gene1178|rna1177|rna1177 166 FNAIAERV 173
                                        ****9987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.0   9.1e-35     2e-31       1     119 [.      14     128 ..      14     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 9.1e-35
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        Kvv++G  +vGK+sl+ ++v+++f+++e+stig++fltk++ + +         ++k++iWDtaGqer++sl p+y
  gene1178|gene1178|rna1177|rna1177  14 KVVVLGYYSVGKSSLVLKYVKGEFNPNEESTIGASFLTKTIFTQE--------GSIKFEIWDTAGQERYNSLIPMY 81 
                                        9**************************************985322........3699******************* PP

                                        HCTSCEEEEEEE...GHHHHCHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                                Roc  77 lreaalailvyd...srssenlkeWlkelkkvagks.pvilvgnkiD 119
                                        +r+a++a++ yd    +s+e++k+W++el+ + +k+ + +l+gnk D
  gene1178|gene1178|rna1177|rna1177  82 YRGAQVALIAYDitsMESFETAKRWVEELSFEKPKEfIKVLIGNKSD 128
                                        ************65444678999*******9999883569*****99 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.0   1.2e-15   2.7e-12      12     173 ..      10     171 ..       3     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.2e-15
                                        TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSS..EEEEEEEE..TTEEEEEEEE-SSGGGGGGGGGGCTTE CS
                                Arf  12 kkelrilllGLDnaGKtTilkklkleelvt.tvPTig..fnveelei..knlkftvwDvGGqeklRplWknYfekt 82 
                                        +  +++++lG  + GK+ ++ k+ ++e++     Tig  f ++++ +    +kf++wD  Gqe+  +l   Y++  
  gene1178|gene1178|rna1177|rna1177  10 TYTFKVVVLGYYSVGKSSLVLKYVKGEFNPnEESTIGasFLTKTIFTqeGSIKFEIWDTAGQERYNSLIPMYYRGA 85 
                                        4679*******************9999975378899833445666544478************************* PP

                                        SEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBT CS
                                Arf  83 davifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsa 158
                                        ++ +   D +  e +e+ak+ +++l  e+  + +++ +++NK Dl+++   ++++ + g e    +++l  +++sa
  gene1178|gene1178|rna1177|rna1177  86 QVALIAYDITSMESFETAKRWVEELSFEKPKEFIKV-LIGNKSDLESD---RKVEYQKGKEYAD-SQNLLFFESSA 156
                                        ************************977766655555.569*****865...5667777777666.88999****** PP

                                        TTTBTHHHHHHHHHH CS
                                Arf 159 vkgeglkeglewlse 173
                                         +g+++ e ++ ++e
  gene1178|gene1178|rna1177|rna1177 157 KTGKNIAEIFNAIAE 171
                                        ********9998876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.2e-08   2.6e-05       1      86 [.      14      95 ..      14     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-08
                                       EEEEEESTTSSHHHHHHHHHT......S.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHH CS
                           MMR_HSR1  1 evaivGrpNvGKStLinaltg......e.kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkafl 71
                                       +v+++G+  vGKS+L+ + ++      e   i +++  +T+ ++eg +k     +e++Dt+G  e   + ++l   + 
  gene1178|gene1178|rna1177|rna1177 14 KVVVLGYYSVGKSSLVLKYVKgefnpnEeSTIGASFLTKTIFTQEGSIK-----FEIWDTAG-QE---RYNSLIPMYY 82
                                       699****************975555543244557888888888888886.....9*******.33...2224444444 PP

                                       HHHCTSEEEEEEETT CS
                           MMR_HSR1 72 aleeadlillvvdas 86
                                       +    +++l+  d++
  gene1178|gene1178|rna1177|rna1177 83 RGA--QVALIAYDIT 95
                                       333..3333333333 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.3e-07   0.00029       1     132 [.      14     137 ..      14     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                          Gtr1_RagA   1 kvLLmGksgsGKtsm.rsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifr 75 
                                        kv+ +G  + GK+s+  + +  ++ +++  ++ga+   +k+ +   g +++++wD  Gqe++            +r
  gene1178|gene1178|rna1177|rna1177  14 KVVVLGYYSVGKSSLvLKYVKGEFNPNEESTIGASFL-TKTIFTQEGSIKFEIWDTAGQERYNSLI-----PMYYR 83 
                                        79999*********7359999************9985.5666778***************997764.....55566 PP

                          Gtr1_RagA  76 nvgvliyVfDvesreleedletlkeilealrqyspeakvfvli.hKmDliqedereei 132
                                          +v +   D++     e++et k+ +e+l+  +p+  ++vli +K Dl +++ + e 
  gene1178|gene1178|rna1177|rna1177  84 GAQVALIAYDIT---SMESFETAKRWVEELSFEKPKEFIKVLIgNKSDLESDR-KVEY 137
                                        666666677999...56789999999*****************6788887544.3333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.02        44     102     119 ..      15      32 ..       2      49 .. 0.78
   2 ?    9.3   0.0   0.00043      0.96      48     100 ..     119     172 ..      72     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.02
                                        EEEECSTTSSHHHHHHHH CS
                        RsgA_GTPase 102 svlvGqSGvGKStLinal 119
                                        +v++G   vGKS+L+ + 
  gene1178|gene1178|rna1177|rna1177  15 VVVLGYYSVGKSSLVLKY 32 
                                        68899999******9665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00043
                                        EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTS CS
                        RsgA_GTPase  48 epvivlnKiDlleeee.eleelkeelealgyevllvsaktkegleelkellkdk 100
                                          v++ nK Dl ++++ e+++ ke   + ++ ++  sakt+++++e+ ++++++
  gene1178|gene1178|rna1177|rna1177 119 IKVLIGNKSDLESDRKvEYQKGKEYADSQNLLFFESSAKTGKNIAEIFNAIAER 172
                                        345667********99888899999999999****************9999876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   4.5e-05       0.1       1      40 [.      15      54 ..      15     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE CS
                          Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql 40
                                       ++v+G +S GKSS++ + ++ +++p+++  + + +l+ + 
  gene1178|gene1178|rna1177|rna1177 15 VVVLGYYSVGKSSLVLKYVKGEFNPNEESTIGASFLTKTI 54
                                       79***********************999888777766555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00015      0.33      49     193 ..      42     174 ..      12     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                        HHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE CS
                           GTP_EFTU  49 ErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp 124
                                        E   g +  +++i ++  + + ++ + Dt G + +++ +   +r + +a++  d+++     t + +   l+ + p
  gene1178|gene1178|rna1177|rna1177  42 ESTIGASFLTKTIFTQ--EGSIKFEIWDTAGQERYNSLIPMYYRGAQVALIAYDITSMESFETAKRWVEELSFEKP 115
                                        4445555555555555..8889999999999999999999999999999999999876666666666555555555 PP

                                        ....EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                           GTP_EFTU 125 ....iivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                             +++ NK D   + +++ ++ + + +                ++  ++  Sa++g+++ ++++a+ e +p
  gene1178|gene1178|rna1177|rna1177 116 kefiKVLIGNKSDLEsDRKVEYQKGKEYADS---------------QNLLFFESSAKTGKNIAEIFNAIAERVP 174
                                        5665667779999875444444444444333...............3577888999999999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1202.94
//
Query:       gene1179|gene1179|rna1178|rna1178  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-59  201.2   0.0      2e-59  201.0   0.0    1.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    5.8e-09   36.1   0.0      1e-08   35.3   0.0    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.8e-09   35.9   0.1    2.5e-08   34.0   0.1    1.8  1  AAA_31       AAA domain
    7.2e-08   32.0   0.3    1.8e-05   24.1   0.1    2.2  2  ArsA_ATPase  Anion-transporting ATPase
     0.0018   18.2   0.0       0.12   12.1   0.0    2.1  2  AAA_26       AAA domain
  ------ inclusion threshold ------
      0.047   13.1   0.1        0.1   12.0   0.1    1.5  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
       0.22   10.8   0.0       0.26   10.5   0.0    1.1  1  MipZ         ATPase MipZ


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.0   0.0   7.8e-63     2e-59       5     228 ..       3     219 ..       1     237 [. 0.89

  Alignments for each domain:
  == domain 1  score: 201.0 bits;  conditional E-value: 7.8e-63
                               ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSig 79 
                                        +iav+SgKGGVGKS++++ l+++++++  k+ llD D++Gpsi + +g++e+ + + ek+liP ++ +++ ++S++
  gene1179|gene1179|rna1178|rna1178   3 MIAVMSGKGGVGKSSISIMLSTMMSER-RKTLLLDFDLCGPSITSGFGIREN-IFKGEKGLIPAKVtESLYILSMA 76 
                                        79*******************999766.6788******************97.6677779*****9899******* PP

                               ParA  80 fllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltva.qklplagaviVttpqevaladvk 154
                                        +l++ +d++v+wrGp+k+++++ ++++++      ++iD+PPG + e+  ++ + +    ++iVttpq+++l+d +
  gene1179|gene1179|rna1178|rna1178  77 LLMK-DDDSVIWRGPKKMSVLSMFYESID--GFSNVVIDMPPGISEEHGFLIgKDI---STLIVTTPQNISLEDSS 146
                                        ***9.9*******************9986..67789***********966550445...689************** PP

                               ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlk 228
                                        +ai+++++  +++lG++eNmsg++c+ cg+ t+ifg++gge+la+e+g+p+++++p+dp ++ea deg   ++k
  gene1179|gene1179|rna1178|rna1178 147 RAIDFCTSNGIEILGLIENMSGYCCECCGSFTNIFGSKGGERLAKEMGIPFVCRLPVDPLLCEALDEGGF-TEK 219
                                        *******************************************************************983.333 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.9e-12     1e-08       1      55 [.       4     155 ..       4     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.9e-12
                                        EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH...................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                               CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep...................... 54 
                                        ia++s+kGGvGK+++++ L + +++ ++++ll+D+D  +++ ++ +g +++i +                      
  gene1179|gene1179|rna1178|rna1178   4 IAVMSGKGGVGKSSISIMLSTMMSE-RRKTLLLDFDLCGPSITSGFGIRENIFKgekglipakvteslyilsmall 78 
                                        89***********************.***************99866666666557777777888888888888888 PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                               CbiA  55 ............................................................................ 54 
                                                                                                                    
  gene1179|gene1179|rna1178|rna1178  79 mkdddsviwrgpkkmsvlsmfyesidgfsnvvidmppgiseehgfligkdistlivttpqnisledssraidfcts 154
                                        8888888888888888888888866666666666666666666666666555555555555555544444444444 PP

                                        C CS
                                        x RF
                               CbiA  55 d 55 
                                        +
  gene1179|gene1179|rna1178|rna1178 155 N 155
                                        1 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   9.7e-12   2.5e-08       3     158 ..       3     146 ..       1     156 [. 0.72

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 9.7e-12
                             AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekneiektlyevlieeknikeaiiktk 77 
                                        +Ia++  KGGvGK+  s++l+ +++++  k+Ll D+D  + + t+g+gi      +++++        ++ +i +k
  gene1179|gene1179|rna1178|rna1178   3 MIAVMSGKGGVGKSSISIMLSTMMSER-RKTLLLDFDLCGpSITSGFGI-----RENIFKG-------EKGLIPAK 65 
                                        79*******************998876.6899*****877367889996.....4566666.......33444444 PP

                             AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeaya 153
                                        v++   i s   L++ +++++    k+  + +++ +  d +  ++iD+pP ++      +    s +i++ +++ +
  gene1179|gene1179|rna1178|rna1178  66 VTESLYILSMALLMKDDDSVIWRGPKKMSVLSMFYESIDGFSNVVIDMPPGISEEHGFLIGKDISTLIVTTPQNIS 141
                                        4444445566777777777777777777777777777789999999999988765544444444677777777777 PP

                             AAA_31 154 leGle 158
                                        le  +
  gene1179|gene1179|rna1178|rna1178 142 LEDSS 146
                                        77655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   7.2e-09   1.8e-05       4      65 ..       5      73 ..       2     124 .. 0.69
   2 !    6.6   0.0    0.0015       3.8     201     243 ..     124     165 ..      90     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.2e-09
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S.TTTHHHHHHTS.......--BSS-EEETSSEEEE CS
                        ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD.PAhslsDsfdq.......klgkeptkvkeNLsav 65
                                        +++GKGGVGK+++s  +++ +se + k+ll+  D   +s+   f         + g  p kv+e L++ 
  gene1179|gene1179|rna1178|rna1178  5 AVMSGKGGVGKSSISIMLSTMMSERR-KTLLLDFDlCGPSITSGFGIrenifkgEKGLIPAKVTESLYIL 73
                                       579********************976.5677777633466665555544444445555666666666665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0015
                                        HTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                        ArsA_ATPase 201 ltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                        l+ +++ s  +V++p ++sl+++ Rai   ++ gi++  +i N
  gene1179|gene1179|rna1178|rna1178 124 LIGKDI-STLIVTTPQNISLEDSSRAIDFCTSNGIEILGLIEN 165
                                        566666.5568******************99999999888876 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.019        49       5      28 ..       6      29 ..       3      33 .. 0.80
   2 !   12.1   0.0   4.9e-05      0.12     128     194 ..     128     207 ..     124     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.019
                             AAA_26  5 vtgtdtgvGKTvvslgLvralkrk 28
                                       v +   gvGK+++s +L  +++++
  gene1179|gene1179|rna1178|rna1178  6 VMSGKGGVGKSSISIMLSTMMSER 29
                                       6666779**********9999765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.9e-05
                             AAA_26 128 gapvilVargglgtinqllltiealrqknvrvlGvilNkvrnp..............envetlekksgipvlGvvP 189
                                        ++ +++V+++++ ++++   +i+++ ++++++lG+i N                   +  e l k  gip ++++P
  gene1179|gene1179|rna1178|rna1178 128 DISTLIVTTPQNISLEDSSRAIDFCTSNGIEILGLIENMS-GYcceccgsftnifgsKGGERLAKEMGIPFVCRLP 202
                                        6899**********************************84.333655665555554448888888889******99 PP

                             AAA_26 190 ylpdl 194
                                         +p l
  gene1179|gene1179|rna1178|rna1178 203 VDPLL 207
                                        99987 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     4e-05       0.1       4      33 ..       6      35 ..       3      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4e-05
                          Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvli 33
                                        + GkGG+Gks  s  ls++++e+ k +l+
  gene1179|gene1179|rna1178|rna1178  6 VMSGKGGVGKSSISIMLSTMMSERRKTLLL 35
                                       457********************9998875 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0001      0.26       3     108 ..       4     114 ..       2     151 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                        EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHHHHHHHT------EEE-SSS-HHHHT CS
                               MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraataerkglsLplpealalseaeeaev 78 
                                        i +   kGG Gks +++ + + ++++  +   +d+dl   +++  ++ r ++ + ++  +p   + +l   ++a +
  gene1179|gene1179|rna1178|rna1178   4 IAVMSGKGGVGKSSISIMLSTMMSER-RKTLLLDFDLCGPSITSGFGIRENIFKGEKGLIPAKVTESLYILSMALL 78 
                                        777889***********999877766.566789**99999999999999988776554455444434433333333 PP

                                        TS-HHH......HHHHHHHHHHHHHHH-SEEEEE-- CS
                               MipZ  79 eeeeea......evaeleelvadleaeldfividtP 108
                                         ++++       + +++  ++ +    +  +vid P
  gene1179|gene1179|rna1178|rna1178  79 MKDDDSviwrgpKKMSVLSMFYESIDGFSNVVIDMP 114
                                        333322011110111222233333334445677765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1437.20
//
Query:       gene1180|gene1180|rna1179|rna1179  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.36s 00:00:00.91 Elapsed: 00:00:00.55
# Mc/sec: 1115.08
//
Query:       gene118|gene118|rna118|rna118  [L=365]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2249.87
//
Query:       gene1181|gene1181|rna1180|rna1180  [L=768]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-14   54.9   0.0    3.4e-14   53.3   0.0    1.9  1  ERCC4     ERCC4 domain


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   1.9e-18   3.4e-14       1     154 [.     549     675 ..     549     677 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.9e-18
                                        EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHH CS
                              ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrl 76 
                                        iDsrel+ +++ + l + g ++ ++tl igdy l+   +++               +++erks+ d+++s+  grl
  gene1181|gene1181|rna1180|rna1180 549 IDSRELRAELPFF-LFKAGNKICVSTLAIGDY-LI---SPT---------------ICIERKSIPDFTSSLGTGRL 604
                                        8******999999.899999************.**...***...............******************** PP

                                        HHHHHHHHH.H-SEEEEEEES..-GGGTT................THHH.HHHHHHHHHHHH.S-EEEEESSHHHH CS
                              ERCC4  77 eeqvsrlkrngykkpillveg..ldqykrknknsrnkqykakvrqinrktiesaLvqlqldf.gvsilttesanet 149
                                        + q+s +    y+ pill+e     +++    +++ ++         +++i ++L+ l  +f  ++i+++es+  +
  gene1181|gene1181|rna1180|rna1180 605 YLQASMMCH-RYPSPILLLEFdgRPCLSD--HYRYDQD-------TFKNSIAAKLALLLFNFgTLRIIWSESRLFS 670
                                        *********.*********9965444444..4555555.......33445***********************999 PP

                                        HHHHH CS
                              ERCC4 150 aewla 154
                                        a+++ 
  gene1181|gene1181|rna1180|rna1180 671 AKVIR 675
                                        98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (768 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 4596.77
//
Query:       gene1182|gene1182|rna1181|rna1181  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-12   47.5   0.0    2.3e-12   47.3   0.0    1.2  1  RNA_pol_Rpb4  RNA polymerase Rpb4


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   1.3e-16   2.3e-12       5     114 ..       3      95 ..       1     104 [] 0.81

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.3e-16
                                        HHHHHHHHHHHHHHHCHHHHHTCCCCCHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHH CS
                       RNA_pol_Rpb4   5 sEvllvlkeeleerknkdkkeseddkisekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeLtka 80 
                                        sE++ +l+   +er +               +   n++ki++ tl yl++ f+r k+++ ++ l+++++  ++ + 
  gene1182|gene1182|rna1181|rna1181   3 SEARYLLE-GQKERFRA--------------DFRSNASKIFRSTLGYLDE-FCRIKDKSVAEDLRTTFSGLGFSEL 62 
                                        66666666.33333344..............44689*************9.************************* PP

                                        HHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHH CS
                       RNA_pol_Rpb4  81 EklqlvnlkPesavelktlieeleerfedeqlee 114
                                        E++ l++l P+s++e+ktli++l+++ +d  + +
  gene1182|gene1182|rna1181|rna1181  63 EIALLGSLFPQSVEEAKTLIPSLASKSDD-AIGQ 95 
                                        ************************99766.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 682.03
//
Query:       gene1183|gene1183|rna1182|rna1182  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-12   48.0   0.0    2.3e-12   47.1   0.0    1.4  1  OGG_N           8-oxoguanine DNA glycosylase, N-terminal doma
    1.7e-09   38.1   0.0      3e-09   37.3   0.0    1.4  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
  ------ inclusion threshold ------
       0.22   11.5   0.0       0.34   10.8   0.0    1.2  1  Tir_receptor_C  Translocated intimin receptor (Tir) C-terminu


Domain annotation for each model (and alignments):
>> OGG_N  8-oxoguanine DNA glycosylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   3.8e-16   2.3e-12       4     114 ..      10     105 ..       9     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3.8e-16
                                        ES-SS--HHHHHCSSS-SSEEE-TTS-EEEEETTEEEEEEEETTEEEEET--.............HHHHHHTHHHH CS
                              OGG_N   4 vskeeldlkktLkcGQsFrWkktekteyvgvlgdrvveLkqeeddllyrtlesesstkasseeakeeeteeilrdY 79 
                                        +++e++dl+ktL++GQ F++++t+++ey+gvlg  +v++ q+ + +ly++l+          + +++e e  ++ +
  gene1183|gene1183|rna1182|rna1182  10 CTEETVDLEKTLHSGQVFSFRQTDEKEYTGVLGTCLVSFLQDGNRVLYKVLN---------GDKTSKEIELEITSF 76 
                                        67889******************9999*************************.........56788999999**** PP

                                        TTTTS-HHHHHHHHTT.SHHHHHHHCCTTT----- CS
                              OGG_N  80 fnLdvdleelykewskkdplfkksadkftGiRllr 114
                                        f+Ldv+l  l ++w+  dp      +  +G+R lr
  gene1183|gene1183|rna1182|rna1182  77 FTLDVKLCPLLRRWRL-DP-----NNLLVGLRALR 105
                                        **************87.43.....34445556555 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   5.1e-13     3e-09       2      97 ..     114     249 ..     113     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 5.1e-13
                                        HHHHHTTS-HHHHHHHHHHHHHHHS.............HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HhH-GPD   2 sailsqqtsderanriierlferfg.............fptpedladadeekLrelirelGfyrrKakyikelAri 64 
                                        s+i+s++++++r++r++  l+++ g             fp++e+l d++ e+L++     Gf+ ++ +yi ++A+ 
  gene1183|gene1183|rna1182|rna1182 114 SFICSSNNNIARITRMVGFLYSK-GefimkyknadfyhFPDLEKLVDIE-EELKSN----GFG-YRSSYICNAAKY 182
                                        89*********************.5599*****************9995.689999....***.************ PP

                                        HH...................................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHH CS
                                        xx...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HhH-GPD  65 lv...................................gkpdvlivvDvhvrrilkrlrsikekktkkk 97 
                                        l+                                   g  d +++vD+h+ +  k++++i+ek   +k
  gene1183|gene1183|rna1182|rna1182 183 LLknrldhqqasriremmvsikgigykiadcilligtGNLD-VVPVDTHIFKHSKKMFGINEKVLSQK 249
                                        ***********************************998788.7778**************99854444 PP

>> Tir_receptor_C  Translocated intimin receptor (Tir) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.8e-05      0.34       9      41 ..     186     219 ..     179     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.8e-05
                     Tir_receptor_C   9 kryddqqakrqeelnvs.sGiGyGlsgalilgGG 41 
                                        +r d qqa r +e+ vs  GiGy ++  ++l G 
  gene1183|gene1183|rna1182|rna1182 186 NRLDHQQASRIREMMVSiKGIGYKIADCILLIGT 219
                                        799*************966******988766553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1675.85
//
Query:       gene1184|gene1184|rna1183|rna1183  [L=271]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1599.47
//
Query:       gene1185|gene1185|rna1184|rna1184  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-34  117.6   2.3    5.1e-33  114.3   2.3    2.0  1  DUF5092    Domain of unknown function (DUF5092)
  ------ inclusion threshold ------
       0.16   12.1   0.3       0.87    9.7   0.1    2.2  2  PHB_acc_N  PHB/PHA accumulation regulator DNA-binding domain


Domain annotation for each model (and alignments):
>> DUF5092  Domain of unknown function (DUF5092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   2.3   5.7e-37   5.1e-33       1     161 [.      35     172 ..      35     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 5.7e-37
                            DUF5092   1 vEtftleefrklilesrkkkkdfilArVttkdpedqsslynvyYdAeelnkvlFevvieserrllhrkkvkdPlnn 76 
                                        vE+ftle+f++li+++ k++kdfi+A+Vtt+dp ++s +++ yY+A eln++lF+v  e +++ l r+  ++P+nn
  gene1185|gene1185|rna1184|rna1184  35 VEVFTLEKFKDLIVSHIKEGKDFIIAEVTTRDPLTES-VFRSYYSAIELNRILFCV--EGNNNPLYRVTARNPINN 107
                                        599****************************998887.8899**************..****************** PP

                            DUF5092  77 mkI.kqvyyYkltveeldralveyffkeaksksevkedsiaaveelakekklilkaeyfasdddFLeksevreyfk 151
                                          I ++v+yYk+t ++l+ ++++                     e+a ++++ +ka+yfa+d+d L + ++r yf 
  gene1185|gene1185|rna1184|rna1184 108 LRItGKVFYYKITWRTLSDVVKS--------------------RECACDNEMLIKANYFANDEDLLFDPSIRGYFA 163
                                        ****************7766554....................58999**************************** PP

                            DUF5092 152 enaldaddnF 161
                                        +n +++  +F
  gene1185|gene1185|rna1184|rna1184 164 KNLIEEG-YF 172
                                        **99986.66 PP

>> PHB_acc_N  PHB/PHA accumulation regulator DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.21   1.9e+03      23      41 ..       4      22 ..       3      24 .. 0.86
   2 ?    9.7   0.1   9.8e-05      0.87      12      50 ..      31      73 ..      30      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.21
                          PHB_acc_N 23 diaelvregeevkVvDakt 41
                                       d+ e+v +g +  V+D++ 
  gene1185|gene1185|rna1184|rna1184  4 DVLEMVLKGCSRVVFDSDR 22
                                       8899******999999876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 9.8e-05
                          PHB_acc_N 12 dtetssYitlediael....vregeevkVvDaktgeDiTrsil 50
                                       dtet +  tle+ ++l    ++eg+++ + + +t + +T+s++
  gene1185|gene1185|rna1184|rna1184 31 DTETVEVFTLEKFKDLivshIKEGKDFIIAEVTTRDPLTESVF 73
                                       899999999999887722225899****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1559.34
//
Query:       gene1186|gene1186|rna1185|rna1185  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-19   69.6   1.9    1.1e-18   68.0   1.9    1.8  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   1.9   5.9e-23   1.1e-18       1      67 [.       7      89 ..       7     137 .] 0.83

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 5.9e-23
                                       EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCCEEEEEC-............ CS
                              SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanpGrVrvkl............ 66
                                       ++YP+++ds+++ +eGR+ +ke +v++P ++ei++al++l++e+v e++k++P d++n Gr r+k+            
  gene1186|gene1186|rna1185|rna1185  7 CLYPIHMDSRRSLSEGRKYKKEICVQRPRYHEIKNALEKLEIEHVDEASKRHPNDFFNGGRFRIKKeygkvlviegvs 84
                                       89***************************************************************9666666666655 PP

                                       ..... CS
                              SRP19 67 ....k 67
                                           +
  gene1186|gene1186|rna1185|rna1185 85 qtiaE 89
                                       55541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 844.97
//
Query:       gene1187|gene1187|rna1186|rna1186  [L=435]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2658.28
//
Query:       gene1188|gene1188|rna1187|rna1187  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-39  135.1   0.5      3e-39  134.7   0.5    1.2  1  Ribosomal_L4     Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.059   13.4   0.0    2.0  2  Ribos_L4_asso_C  60S ribosomal protein L4 C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.5   3.4e-43     3e-39       3     191 ..      21     258 ..      19     259 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 3.4e-43
                                        E-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT............ST CS
                       Ribosomal_L4   3 LspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir............sp 65 
                                        L p+vF++p+r+dl+ + +  y+ + rq++a +k a++++s+  +++++  G++ ARv++++            ++
  gene1188|gene1188|rna1187|rna1187  21 L-PEVFSTPVRQDLVLKTYSLYRMKTRQPYAVSKyAGMQHSA--ESWGT--GRAIARVPRVKgggtrragqgafAN 91 
                                        7.9***************************************..6****..************************* PP

                                        TSTT---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES....---.-S............S--HHHH CS
                       Ribosomal_L4  66 iargGgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd....nleple............esktkel 125
                                        ++r+G++ah++k++r++++k+ +  ++ A ++a++a a+ +l+++++    ++   +             +ktk++
  gene1188|gene1188|rna1187|rna1187  92 FCRKGRMAHPTKTHRRWARKVVENTKKIAEAMAVAASAQTSLVEARGhrisDV---KmlpiivsddlskVKKTKDA 164
                                        ***********************************************866644...234577899999999***** PP

                                        HHHHHHTT-..........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHH CS
                       Ribosomal_L4 126 vellkklgl..........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllk 175
                                         ++lk+l++                          ++k++Liv +e  +  +la+rn+ gv+ ++++sl++++l++
  gene1188|gene1188|rna1187|rna1187 165 LQILKNLNMkeelkrvensrgvrcgkgkmrnrrytQRKGILIVHGE--SSELLAFRNIRGVDQMSIDSLDLLELAP 238
                                        ******9998899999999999999999999999999*******97..7899************************ PP

                                        SSE....EEEEHHHHHHHHH CS
                       Ribosomal_L4 176 adk....vvitksaveklee 191
                                        +      +++t+sa+ekl++
  gene1188|gene1188|rna1187|rna1187 239 GGMagrlIIWTESAFEKLDK 258
                                        **99**************86 PP

>> Ribos_L4_asso_C  60S ribosomal protein L4 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.39   3.5e+03      13      34 ..     153     174 ..     147     200 .. 0.58
   2 ?   13.4   0.0   6.6e-06     0.059       2      31 ..     272     301 ..     271     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.39
                    Ribos_L4_asso_C  13 aDlsRiinSdeiqsvlrpakke 34 
                                         Dls++ + ++  ++l++ +++
  gene1188|gene1188|rna1187|rna1187 153 DDLSKVKKTKDALQILKNLNMK 174
                                        4444444444444444444443 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.6e-06
                    Ribos_L4_asso_C   2 gynLPrpkmtnaDlsRiinSdeiqsvlrpa 31 
                                        g++LP++++t  Dl+ +  Sd +q++l ++
  gene1188|gene1188|rna1187|rna1187 272 GFKLPNKIVTHDDLEELFYSDAVQAILDEP 301
                                        8************************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2207.41
//
Query:       gene1189|gene1189|rna1188|rna1188  [L=803]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-07   28.9   1.7      0.034   14.3   0.1    5.1  4  TPR_8     Tetratricopeptide repeat
    6.6e-06   25.7   0.4       0.12   12.1   0.0    3.4  3  TPR_11    TPR repeat
    4.1e-05   23.4   9.7     0.0042   17.1   0.2    5.5  6  TPR_2     Tetratricopeptide repeat
    0.00039   20.1  12.5     0.0049   16.6   0.3    4.5  5  TPR_1     Tetratricopeptide repeat
    0.00073   19.8   0.1       0.81   10.0   0.0    3.6  3  TPR_12    Tetratricopeptide repeat
     0.0051   16.1   0.0      0.031   13.5   0.0    2.2  2  TPR_15    Tetratricopeptide repeat
     0.0066   16.9   0.0        0.3   11.6   0.0    3.0  3  TPR_19    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.67   1.7e+03       4      16 ..      70      82 ..      67      86 .. 0.87
   2 !   14.3   0.1   1.3e-05     0.034       3      33 ..     314     344 ..     314     345 .. 0.94
   3 ?    4.9   0.1     0.015        38      10      23 ..     355     368 ..     354     368 .. 0.94
   4 ?    3.9   0.1     0.031        78       5      29 ..     727     751 ..     723     754 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHTT- CS
                              TPR_8  4 yynlgsiylklgd 16
                                       y+ lg+i +++g+
  gene1189|gene1189|rna1188|rna1188 70 YFTLGLIFEEKGE 82
                                       9*********997 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.3e-05
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        +y++lg+ ++ +++y+eA  yy+ +le +p 
  gene1189|gene1189|rna1188|rna1188 314 VYWKLGKMLDAKERYDEALLYYKLVLETNPG 344
                                        699************************9996 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.015
                                        HHHHTT-HHHHHHH CS
                              TPR_8  10 iylklgdyeeAkey 23 
                                        iy k+g++e Ak+y
  gene1189|gene1189|rna1188|rna1188 355 IYTKQGNHELAKKY 368
                                        9***********98 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.031
                                        HHHHHHHHHTT-HHHHHHHHHHHHH CS
                              TPR_8   5 ynlgsiylklgdyeeAkeyyekale 29 
                                        yn+g++y+  g    A+ +y++al 
  gene1189|gene1189|rna1188|rna1188 727 YNIGKAYQFFGFPGLAENFYMEALG 751
                                        9**********************95 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   4.6e-05      0.12       4      42 .]      43      81 ..      40      81 .. 0.89
   2 !    8.7   0.1   0.00052       1.3       3      42 .]     321     360 ..     315     360 .. 0.92
   3 ?    0.8   0.1      0.16   4.1e+02      29      39 ..     724     734 ..     720     734 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.6e-05
                             TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                       +y ++++ + +e +k+A+ l P n+  y+ LGl++ ++G
  gene1189|gene1189|rna1188|rna1188 43 LYVRNELGKCVEILKEAICLMPRNPHPYFTLGLIFEEKG 81
                                       67788888889999*********************9998 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00052
                             TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                        ++ ++ +y+eA+  Yk  l+ +P n ++ + ++l+y kqG
  gene1189|gene1189|rna1188|rna1188 321 MLDAKERYDEALLYYKLVLETNPGNDDVKSRIHLIYTKQG 360
                                        555789********************************99 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.16
                             TPR_11  29 eayynLGlayy 39 
                                         + yn+G+ay+
  gene1189|gene1189|rna1188|rna1188 724 AISYNIGKAYQ 734
                                        588*******6 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.095   2.4e+02       2      33 ..      34      65 ..      33      66 .. 0.86
   2 ?    3.8   0.0     0.029        75       4      24 ..      70      90 ..      67     100 .. 0.91
   3 ?   -0.3   0.0      0.59   1.5e+03      10      23 ..     247     260 ..     246     262 .. 0.88
   4 !   17.1   0.2   1.7e-06    0.0042       3      34 .]     314     345 ..     312     345 .. 0.95
   5 ?    1.3   0.1      0.19   4.8e+02      10      23 ..     355     368 ..     354     368 .. 0.91
   6 ?   -2.5   0.1         3   7.6e+03       5      28 ..     727     750 ..     725     750 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.095
                              TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                       + l ++++ +y ++++ +++e +++A+ l P+
  gene1189|gene1189|rna1188|rna1188 34 KNLIAIANNLYVRNELGKCVEILKEAICLMPR 65
                                       568899********************966665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.029
                              TPR_2  4 lynlGlayyklgdyeeAleaf 24
                                       ++ lGl+ +++g+  +A  +f
  gene1189|gene1189|rna1188|rna1188 70 YFTLGLIFEEKGEIPKAYYCF 90
                                       89***************9998 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.59
                              TPR_2  10 ayyklgdyeeAlea 23 
                                        a++++g+  eA+e+
  gene1189|gene1189|rna1188|rna1188 247 ACLYSGNDGEAKEC 260
                                        8999********99 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 1.7e-06
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +++ lG+ + ++ +y+eAl +++ +le +P+n
  gene1189|gene1189|rna1188|rna1188 314 VYWKLGKMLDAKERYDEALLYYKLVLETNPGN 345
                                        7999**************************87 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.19
                              TPR_2  10 ayyklgdyeeAlea 23 
                                        +y k+g++e A+++
  gene1189|gene1189|rna1188|rna1188 355 IYTKQGNHELAKKY 368
                                        799********997 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 3
                              TPR_2   5 ynlGlayyklgdyeeAleafekAl 28 
                                        yn+G+ay   g +  A++++ +Al
  gene1189|gene1189|rna1188|rna1188 727 YNIGKAYQFFGFPGLAENFYMEAL 750
                                        899999987777777777777776 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.5   8.9e+03      11      33 ..      43      65 ..      38      66 .. 0.72
   2 ?    4.8   0.1      0.01        26       4      24 ..      70      90 ..      69     100 .. 0.91
   3 !   16.6   0.3   1.9e-06    0.0049       7      34 .]     318     345 ..     317     345 .. 0.94
   4 ?    4.7   0.1     0.011        28       9      23 ..     354     368 ..     354     368 .. 0.92
   5 ?   -1.3   0.1       0.9   2.3e+03       5      12 ..     727     734 ..     724     750 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.5
                                       HHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1 11 yfklgkydeAleyyekALelnPn 33
                                       ++  +++ +++e  ++A+ l P 
  gene1189|gene1189|rna1188|rna1188 43 LYVRNELGKCVEILKEAICLMPR 65
                                       66677788888888999887776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHTT-HHHHHHHH CS
                              TPR_1  4 lynlGnayfklgkydeAleyy 24
                                       ++ lG+++ ++g+  +A  ++
  gene1189|gene1189|rna1188|rna1188 70 YFTLGLIFEEKGEIPKAYYCF 90
                                       788***************998 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.9e-06
                                        HHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1   7 lGnayfklgkydeAleyyekALelnPnn 34 
                                        lG ++  +++ydeAl yy+ +Le nP n
  gene1189|gene1189|rna1188|rna1188 318 LGKMLDAKERYDEALLYYKLVLETNPGN 345
                                        899999********************87 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.011
                                        HHHHHTT-HHHHHHH CS
                              TPR_1   9 nayfklgkydeAley 23 
                                        ++y k+g+++ A +y
  gene1189|gene1189|rna1188|rna1188 354 LIYTKQGNHELAKKY 368
                                        58**********997 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 0.9
                                        HHHHHHHH CS
                              TPR_1   5 ynlGnayf 12 
                                        yn+G ay+
  gene1189|gene1189|rna1188|rna1188 727 YNIGKAYQ 734
                                        89999997 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00032      0.81      47      73 ..     314     340 ..     300     343 .. 0.84
   2 ?    0.5   0.0       0.3   7.7e+02      10      25 ..     353     368 ..     347     369 .. 0.77
   3 ?    4.1   0.0     0.023        59      36      72 ..     717     750 ..     705     753 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00032
                             TPR_12  47 tlrnLgrlyralgryeeAlelleeala 73 
                                        ++  Lg +++a +ry+eAl +++ +l+
  gene1189|gene1189|rna1188|rna1188 314 VYWKLGKMLDAKERYDEALLYYKLVLE 340
                                        577899999999999999999987776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                             TPR_12  10 aavlrrlgrydeAlel 25 
                                         ++++++g+++ A ++
  gene1189|gene1189|rna1188|rna1188 353 HLIYTKQGNHELAKKY 368
                                        5788999999988765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.023
                             TPR_12  36 llGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                        + G+d+++   + +n+g +y+ +g +  A++++ eal
  gene1189|gene1189|rna1188|rna1188 717 SKGEDSYA---ISYNIGKAYQFFGFPGLAENFYMEAL 750
                                        45666533...56789999999999999999999887 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.23   5.8e+02      17      87 ..      76     144 ..      28     158 .. 0.65
   2 !   13.5   0.0   1.2e-05     0.031     104     201 ..     271     367 ..     247     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.23
                             TPR_15  17 llykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliel 87 
                                        ++ ++g++ kA+      a++  ++++   Wr l d +++l   +e +   ++L + g+ r+   e++ ++
  gene1189|gene1189|rna1188|rna1188  76 IFEEKGEIPKAYYCF-FVAAHL-QKNNYGLWRKLYDYSRQLGYNRERIYFIEVLQRKGNKREMVVEKMSLY 144
                                        444555666666666.445555.356666677777777777777777777777777777777777777666 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.2e-05
                             TPR_15 104 wrrfrsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapds 179
                                        w    + +lL+  ++ll ++  +d++ +ll ++++  + +++  ++  ++++  ++ + d+Al  y+ +l+ +p++
  gene1189|gene1189|rna1188|rna1188 271 WSEITDIDLLKHLVDLLIESDMVDEVTKLLGRIKNSFNGQREFVYW-KLGKMLDAKERYDEALLYYKLVLETNPGN 345
                                        88888999************************88777776666666.56999999********************* PP

                             TPR_15 180 selraallWlliDlgrraeLre 201
                                        +++++++  ++   g+ + +++
  gene1189|gene1189|rna1188|rna1188 346 DDVKSRIHLIYTKQGNHELAKK 367
                                        *****99888887777776554 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   8.1e+03      12      44 ..      54      86 ..      49      86 .. 0.80
   2 ?    1.4   0.0      0.19   4.7e+02      25      56 ..     277     308 ..     262     317 .. 0.87
   3 !   11.6   0.0   0.00012       0.3       5      46 ..     326     367 ..     322     368 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                             TPR_19 12 alleqalqedpknaearllLAeallalgqldeA 44
                                       ++l++a+   p n+     L  +  + g++ +A
  gene1189|gene1189|rna1188|rna1188 54 EILKEAICLMPRNPHPYFTLGLIFEEKGEIPKA 86
                                       799999999999998888887777777777666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.19
                             TPR_19  25 aearllLAeallalgqldeAealLdalpeedp 56 
                                         +++  L+++l+++  +de  +lL ++ +++ 
  gene1189|gene1189|rna1188|rna1188 277 IDLLKHLVDLLIESDMVDEVTKLLGRIKNSFN 308
                                        5778899******************9998875 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00012
                             TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                        ++y+eAl +++ +l+ +p+n++++ +   ++ ++g+ + A++
  gene1189|gene1189|rna1188|rna1188 326 ERYDEALLYYKLVLETNPGNDDVKSRIHLIYTKQGNHELAKK 367
                                        79**********************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (803 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 5207.59
//
Query:       gene1190|gene1190|rna1189|rna1189  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   67.5   2.6    6.7e-10   38.6   0.0    2.6  2  CAF1      CAF1 family ribonuclease


Domain annotation for each model (and alignments):
>> CAF1  CAF1 family ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   3.7e-14   6.7e-10       1     125 [.       9     125 ..       9     130 .. 0.83
   2 !   27.6   0.9   8.6e-11   1.5e-06     209     319 .]     147     232 ..     128     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.7e-14
                                        E-GGGHHHHHHHHHHHHHH-SEEEEEEEES-SS-----------HH.HHHHHHHHHTTTB-EEEEEEEEEEEETTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1   1 VtrsNfkellpeilkaikeasFvAiDlEftGlsegerkesladsle.erYeklkqaaesfsilqlGlscfsedkek 75 
                                        V ++N+++ +++i + +++ +++++D+Ef G+    ++   ++s+    Y++l+ ++   +i+qlG+s+  ++ ++
  gene1190|gene1190|rna1189|rna1189   9 VWKDNLRSEMRRISQLVNTYNYISMDTEFPGV--VAKPIGSFKSPSsFAYQQLRCNVDILNIIQLGISLSDSQGNR 82 
                                        789****************************9..567777777777369*********************555555 PP

                                        TE..EEEEEEEEEB----SS---EEEEEHHHHHHHHHTT--HHHHHTT-B CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1  76 kekeykvqpynfylfpkeedldrefsvspsslqFLakngfdfnkliseGi 125
                                              +++++f    +     +  ++  +s++ L + ++df +  + Gi
  gene1190|gene1190|rna1189|rna1189  83 P---CPISTWQFNFAFSL----ETDMYAQESIDLLIQARIDFKEHERRGI 125
                                        4...45555555444443....567888999************9999998 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8.6e-11
                                        EEESSTHHHHHHHHHHH.T----SSHHHHHHHHHHH-SSEEEHHHHHTSTTTTTT-S--SHHHHHHHTTSTTS--. CS
                                        xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1 209 iVgHNgllDllflyqtf.yaeLPesleeFkaklselFPgiiDtKylakneelearleassLeelfeklkkensksk 283
                                         V + + +D+ +l++ + +++LPe+ e+F + l  lFP  +D K+l+   +     ++++L++  ++++++ +   
  gene1190|gene1190|rna1189|rna1189 147 WVSFHSAYDFGYLIKILtCNPLPEREEDFYRFLAALFPDFYDIKFLV---Q-----NSKYLKKGLQEISNDLGL-- 212
                                        47888999********96778**************************...3.....566777777777333332.. PP

                                        ......--EEE-TTS---------HHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CAF1 284 dassseekkesekkkaaseesaHeAGyDafmTGlvf 319
                                                        + ++ +H+AG Da++T  +f
  gene1190|gene1190|rna1189|rna1189 213 ----------------VRDGIQHQAGSDALLTSHAF 232
                                        ................23456899999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1595.80
//
Query:       gene119|gene119|rna119|rna119  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-05   25.1   0.6    1.8e-05   25.1   0.6    2.3  2  ICMT        Isoprenylcysteine carboxyl methyltransferase (ICM
    0.00027   21.3   2.1    0.00032   21.1   0.3    2.0  2  PEMT        Phospholipid methyltransferase
     0.0069   16.4   0.2      0.012   15.6   0.2    1.4  1  Steroid_dh  3-oxo-5-alpha-steroid 4-dehydrogenase
  ------ inclusion threshold ------
      0.032   13.8   0.1      0.052   13.0   0.1    1.6  1  NnrU        NnrU protein
      0.044   13.3   0.5       0.09   12.3   0.5    1.6  1  DUF1295     Protein of unknown function (DUF1295)
       0.12   12.8   1.5        0.4   11.1   1.5    2.0  1  DUF1211     Protein of unknown function (DUF1211)


Domain annotation for each model (and alignments):
>> ICMT  Isoprenylcysteine carboxyl methyltransferase (ICMT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.1   3.2e+03      55      82 ..      11      38 ..       4      52 .. 0.52
   2 !   25.1   0.6   6.1e-09   1.8e-05      33      93 ..     116     175 ..      86     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                           ICMT 55 lelatllLlcnakltalvllalvalllf 82
                                    +l +l + ++  ++al +++ + ll+f
  gene119|gene119|rna119|rna119 11 GSLFMLGISHSSCYLALHIVSSTSLLIF 38
                                   4444444455555555544444433333 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 6.1e-09
                           ICMT  33 hklvksglykylrHPnYllf.vilelatllLlcnakltalvllalvalllfvRikeEekaLa 93 
                                     ++ +sg+y+++rHP Y    ++++  t+ L c      +++l +v  +++ Rike e+ ++
  gene119|gene119|rna119|rna119 116 RRIQRSGPYRFVRHPLYSSLiLYWASCTIYLSCFV--SLAIFLWFVSSRIIPRIKECEREMV 175
                                    567799***********864157888888888877..44556667999999****9999986 PP

>> PEMT  Phospholipid methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1         1   3.1e+03      70      94 ..      19      43 ..       5      45 .. 0.59
   2 !   21.1   0.3   1.1e-07   0.00032      40      91 ..     112     166 ..      85     178 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                           PEMT 70 tgsaaglllallvllvylialkfvE 94
                                   ++s   l+l +++ +  li+l   E
  gene119|gene119|rna119|rna119 19 SHSSCYLALHIVSSTSLLIFLHSRE 43
                                   3444456666666666666666555 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.1e-07
                           PEMT  40 d....klvtsGiYrylnnPeyvgstlgflGlaLitgsaaglllallvllvylialk 91 
                                    +    ++ +sG+Yr++++P y  s++ +++   i+ s+ + l+++l+++   i+ +
  gene119|gene119|rna119|rna119 112 KtggrRIQRSGPYRFVRHPLYS-SLILYWASCTIYLSCFVSLAIFLWFVSSRIIPR 166
                                    256668889***********96.778899999999999999999999998777644 PP

>> Steroid_dh  3-oxo-5-alpha-steroid 4-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2     4e-06     0.012      62     145 ..     104     188 ..      83     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                     Steroid_dh  62 iLrelrkegetkykiprgglFelvsapnyfgEilewigyalvtkslaala.FalftvlnltvraaahhkwykkkfekYpk 140
                                    +Lr++  ++  +++i r g + +v  p y   il w + ++    + +la F  f+++ + +r ++  +    +  +Y +
  gene119|gene119|rna119|rna119 104 TLRHMPDNKTGGRRIQRSGPYRFVRHPLYSSLILYWASCTIYLSCFVSLAiFLWFVSSRIIPRIKECEREMVSTSSEYME 183
                                    678888889999*****************************9999988762777************************** PP

                     Steroid_dh 141 sRkil 145
                                     Rk++
  gene119|gene119|rna119|rna119 184 YRKAV 188
                                    **997 PP

>> NnrU  NnrU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.8e-05     0.052      73     124 ..      92     141 ..      60     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                           NnrU  73 alllmlvafillaaallpgnplsvglkadlaetgivritrHPmllgvai.WAl 124
                                      l+  + f+++   ++p n+   ++ ++ ++ g +r +rHP+  ++++ WA 
  gene119|gene119|rna119|rna119  92 CGLVFSITFFFVTLRHMPDNK---TGGRRIQRSGPYRFVRHPLYSSLILyWAS 141
                                    335556677777777888886...67779***************998875764 PP

>> DUF1295  Protein of unknown function (DUF1295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5     3e-05      0.09     146     195 ..     106     159 ..      88     188 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                        DUF1295 146 kkdpank..gk.vldsGLwrysRHPNYfgealiWwglfli.alealeglealai 195
                                    ++ p+nk  g+ + +sG +r+ RHP Y   +l W +  +  ++ ++  +  + +
  gene119|gene119|rna119|rna119 106 RHMPDNKtgGRrIQRSGPYRFVRHPLYSSLILYWASCTIYlSCFVSLAIFLWFV 159
                                    667777732446999*******************98765303323222233333 PP

>> DUF1211  Protein of unknown function (DUF1211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.5   0.00013       0.4      25      72 ..     128     176 ..      62     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHTHHHHHHHHHHHHHHHHH.HHHHHHHHHH-----HHHHH CS
                        DUF1211  25 eeellaallellpsllayllsFlvvasf.Wlnhhrlfrrikkvderllw 72 
                                     + l ++l+  + s  +yl +F+ +a+f W+  +r++ rik++++ ++ 
  gene119|gene119|rna119|rna119 128 RHPLYSSLILYWASCTIYLSCFVSLAIFlWFVSSRIIPRIKECEREMVS 176
                                    45577888899*************99866**************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1120.95
//
Query:       gene1191|gene1191|rna1190|rna1190  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-37  128.1   0.1    2.2e-37  127.8   0.1    1.1  1  UQ_con    Ubiquitin-conjugating enzyme
  ------ inclusion threshold ------
      0.025   14.9   0.1       0.05   13.9   0.1    1.8  1  RWD       RWD domain
      0.034   14.0   0.1       0.06   13.2   0.1    1.5  1  UEV       UEV domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.8   0.1   3.7e-41   2.2e-37       8     139 ..      11     142 ..       5     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 127.8 bits;  conditional E-value: 3.7e-41
                                        HHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE.TTSBB- CS
                             UQ_con   8 elakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd.ksGevc 82 
                                        e++k  + ++++ +++  + ++++vli+gped+pY g+ + +++ +p++YP+k+P++ f+t+ifHPnvd +sG++c
  gene1191|gene1191|rna1190|rna1190  11 EIQKLYNANYEVRMIEG-RHTQMEVLINGPEDSPYSGAKYIINILLPDNYPFKSPSIGFTTRIFHPNVDeASGSIC 85 
                                        44566778888888886.99******************************************************** PP

                                        CGGGSTTT--TTSHHHHHHH.HHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHHH CS
                             UQ_con  83 ldiLkeekWspaltlesvll.siqsLlaepnpesplnkeaakllkkdreeykkkvkey 139
                                        ld+L+ + Wsp ++l +++   + +Ll+ pn  +pln ea++++ ++re+y++ v+ y
  gene1191|gene1191|rna1190|rna1190  86 LDVLN-QIWSPIYDLLNIVDiLLPQLLSYPNAADPLNCEAGSMYLTNREKYNEIVRSY 142
                                        *****.55***********87899*******************************987 PP

>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.4e-06      0.05      24      97 ..      28      94 ..      10     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.4e-06
                                       --EE--S-EEEEEEECECCCC....TT-CEEEEEEEEE-SSTTSS--EEEEEECC...SS-HHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                                RWD 24 enysikleikikldededeedsefeekkkpslkleiklpeeYPeeaPiislsste...nlpkeqvksleekleelae 97
                                       ++ +    +++ ++ +ed+        +  ++ ++i lp +YP + P i +++     n++++  + + + l+++++
  gene1191|gene1191|rna1190|rna1190 28 RHTQ----MEVLINGPEDSP------YSGAKYIINILLPDNYPFKSPSIGFTTRIfhpNVDEASGSICLDVLNQIWS 94
                                       3333....666666665543......5688999****************9999887787777777777788887776 PP

>> UEV  UEV domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     1e-05      0.06      33     112 ..      34     107 ..      10     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1e-05
                                        EEEEEEEE-SSSTTS-EEEEEEE--TTTTTS--EEEE-GCC--TSGGGGGB-TTSBB--HHHHS--TTT--HHHHH CS
                                UEV  33 lnlkGtipvkykgatyniPiliwvlesyPveaPivyvkptksmvikknenvdaqGlvylpyLeeWkreksnlvslv 108
                                        + ++G     y+ga y i   i ++++yP++ P +  + +    i + +  +a+G + l++L++ +++ ++l+++v
  gene1191|gene1191|rna1190|rna1190  34 VLINGPEDSPYSGAKYII--NILLPDNYPFKSPSIGFTTR----IFHPNVDEASGSICLDVLNQIWSPIYDLLNIV 103
                                        556666666777777765..5668*********9876544....5455555689********99777799999999 PP

                                        HHHH CS
                                UEV 109 qela 112
                                        + l 
  gene1191|gene1191|rna1190|rna1190 104 DILL 107
                                        8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1077.03
//
Query:       gene1192|gene1192|rna1191|rna1191  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-22   77.5   0.1    1.1e-21   76.5   0.1    1.6  1  Ribosomal_S4e  Ribosomal family S4e
    6.5e-15   55.0   0.9    6.5e-15   55.0   0.9    1.8  2  RS4NT          RS4NT (NUC023) domain
    1.1e-06   28.2   0.0    2.2e-06   27.2   0.0    1.6  1  40S_S4_C       40S ribosomal protein S4 C-terminus
  ------ inclusion threshold ------
       0.01   15.5   0.2      0.024   14.3   0.2    1.6  1  S4             S4 domain
      0.054   13.8   0.1       0.22   11.8   0.0    2.0  2  DUF3912        Protein of unknown function (DUF3912)


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.1   3.1e-25   1.1e-21       1      75 []      95     168 ..      95     168 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 3.1e-25
                                        TTEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                      Ribosomal_S4e   1 tgenyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                        tge++r+ly+t+++f+lhkI+s+ea y+L K++kk+t + gip++v ++G  ir+ dp i+   t+ki+ e+ k+
  gene1192|gene1192|rna1191|rna1191  95 TGEHFRVLYNTHKKFHLHKISSQEAGYRLAKVTKKYTSR-GIPYVVSSCGLSIRFCDPAIEQEYTIKISNETSKV 168
                                        89*********************************9987.9*******************************997 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.9   1.8e-18   6.5e-15       2      36 ..       4      38 ..       3      39 .. 0.96
   2 ?   -3.2   0.0       2.6   9.5e+03      17      28 ..     122     133 ..     121     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.8e-18
                                       S----EETTTS-TTS---SSSSSEE----SSSS-T CS
                              RS4NT  2 GpkkHLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                       G++ HLKr +AP +W+ldk++g+fa++P +GPH +
  gene1192|gene1192|rna1191|rna1191  4 GHRDHLKRKTAPESWMLDKQGGTFALMPASGPHRK 38
                                       99*******************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.6
                                        ---SSSSSEE-- CS
                              RS4NT  17 pldkkegvfavk 28 
                                         l+k +++++ +
  gene1192|gene1192|rna1191|rna1191 122 RLAKVTKKYTSR 133
                                        588999999865 PP

>> 40S_S4_C  40S ribosomal protein S4 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   6.2e-10   2.2e-06       1      43 [.     210     253 ..     210     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.2e-10
                                        -SSS-EEEEEGGGEEE--.STTS-SS---SS-S----HHHHHHH CS
                           40S_S4_C   1 DaaGntFATRlsNvFvIG.kgnkpwvsLPkgkGiklsiaeerdk 43 
                                        D aGntF+   +   +IG  +++ w++LPk++Gi+ls +e+ ++
  gene1192|gene1192|rna1191|rna1191 210 DFAGNTFSCTSKSCIIIGeSSENIWITLPKENGIRLSELEKINA 253
                                        789***************667789*************9998766 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   6.8e-06     0.024      26      48 .]      68      90 ..      66      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.8e-06
                                       TTEEETTEEE--TT-EE-TTCEE CS
                                 S4 26 GrVlVNGkvvkdpsyrVkpgDvi 48
                                       + ++VNGkv+++  ++V+  Dvi
  gene1192|gene1192|rna1191|rna1191 68 KNIKVNGKVRTNSHFPVGLFDVI 90
                                       579***************99997 PP

>> DUF3912  Protein of unknown function (DUF3912)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.5   8.9e+03      36      47 ..      62      73 ..      56      76 .. 0.76
   2 ?   11.8   0.0     6e-05      0.22       9      53 ..     179     225 ..     176     233 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                            DUF3912 36 tvviddqdidve 47
                                        +v+++++i+v+
  gene1192|gene1192|rna1191|rna1191 62 GIVLGGKNIKVN 73
                                       588999999886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6e-05
                            DUF3912   9 kvyvkdGPyrnklGvvkkkeqe.dddhftvv.iddqdidvelkdill 53 
                                         v+v +G  r+++Gv+  ++ + ++  ++++ + +       k  ++
  gene1192|gene1192|rna1191|rna1191 179 VVFVSRGKARGRIGVINTIDVQgKETVYVMTdFAGNTFSCTSKSCII 225
                                        59****************98551566676667766666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.57
# Mc/sec: 1408.18
//
Query:       gene1193|gene1193|rna1192|rna1192  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-20   72.4   0.1    7.4e-20   71.4   0.0    1.5  2  HhH-GPD          HhH-GPD superfamily base excision DNA repair
    0.00027   20.7   0.1     0.0032   17.2   0.0    2.5  2  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.017   15.6   0.1       0.03   14.8   0.1    1.4  1  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_
      0.022   15.3   0.0        1.3    9.7   0.0    2.5  2  HHH_5            Helix-hairpin-helix domain
      0.031   14.3   0.5       0.85    9.6   0.0    2.3  2  DUF2400          Protein of unknown function (DUF2400)
      0.057   13.8  11.2      0.097   13.0  11.2    1.4  1  EndIII_4Fe-2S    Iron-sulfur binding domain of endonuclease I


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   2.5e-23   7.4e-20       1     107 [.      53     198 ..      53     199 .. 0.96
   2 ?   -3.5   0.0       4.8   1.4e+04      48      60 ..     235     247 ..     226     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 2.5e-23
                                        HHHHHHTTS-HHHHHHHHHHHHHHHS...........HCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HhH-GPD   1 vsailsqqtsderanriierlferfg...........fptpedladadeekLrelirelGfyrrKakyikelAril 65 
                                        vs +ls+qt+de++ +++erl+e+             ++t e + + + ++++e+i+ +Gf+++Ka+++k++A+il
  gene1193|gene1193|rna1192|rna1192  53 VSLLLSSQTKDEVTHEAMERLRELLPenaaiddnirrGLTIENIVNSSVDHINECIKRVGFHNKKAENLKKIAEIL 128
                                        799*********************99************************************************** PP

                                        H..............................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHHH CS
                                        x..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            HhH-GPD  66 v..............................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleelle 107
                                                                       gk  v+i vD+hv+ri +r++++k++ + + +++ le++++
  gene1193|gene1193|rna1192|rna1192 129 KkkglpkrmedltslpgignkmailymnhacGK-VVGISVDTHVHRISNRIGLVKTR-DVEDTREGLEKIIP 198
                                        *****************************9985.48999*****************6.99999999988876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.8
                                        STTHHHHHHHHHH CS
                                        xxxxxxxxxxxxx RF
                            HhH-GPD  48 lGfyrrKakyike 60 
                                          +++rKa+ +ke
  gene1193|gene1193|rna1192|rna1192 235 SSLFNRKASALKE 247
                                        5678899998876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.1e-06    0.0032       6      24 ..     133     151 ..     129     153 .. 0.88
   2 ?    0.2   0.0      0.27   8.1e+02       5      16 ..     185     196 ..     184     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                                        HTSSHHHHHTSTT-SHHHH CS
                                HHH   6 ipasreeLlalPGVGpktA 24 
                                         p  +e+L++lPG+G k+A
  gene1193|gene1193|rna1192|rna1192 133 LPKRMEDLTSLPGIGNKMA 151
                                        68899*************9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.27
                                        HHTSSHHHHHTS CS
                                HHH   5 lipasreeLlal 16 
                                        +++++re L+++
  gene1193|gene1193|rna1192|rna1192 185 DVEDTREGLEKI 196
                                        6899*****995 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   9.9e-06      0.03      38      89 ..      91     141 ..      65     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.9e-06
                    Phage_holin_6_1  38 kkiaeiaknaVkaveqvakedakgeeKkeeAleklkellkekgisitddele 89 
                                         +i++i++++V   ++ +k+ +    Kk+e l+k+ e+lk+kg+   +++l+
  gene1193|gene1193|rna1192|rna1192  91 LTIENIVNSSVDHINECIKR-VGFHNKKAENLKKIAEILKKKGLPKRMEDLT 141
                                        6899****************.***********************77777766 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.065   1.9e+02      21      52 ..      90     122 ..      85     129 .. 0.72
   2 ?    9.7   0.0   0.00042       1.3       2      16 ..     138     152 ..     137     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.065
                                        TT--SHHHHHHS-HHHHHT.S..TTS-HHHHHHHH CS
                              HHH_5  21 aGiesvedlaaadveeLak.i..pGiGkktAerii 52 
                                        +   ++e +++ +v+ + + i   G+ +k+Ae+++
  gene1193|gene1193|rna1192|rna1192  90 G--LTIENIVNSSVDHINEcIkrVGFHNKKAENLK 122
                                        4..69999999998885553322478899999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00042
                                        HHHHTSTT--HHHHH CS
                              HHH_5   2 eeLlsvsGiGpktAl 16 
                                        e+L+s++GiG k+A+
  gene1193|gene1193|rna1192|rna1192 138 EDLTSLPGIGNKMAI 152
                                        688999999999886 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.037   1.1e+02      89     144 ..      61     136 ..      17     138 .. 0.46
   2 ?    9.6   0.0   0.00029      0.85     173     193 ..     165     185 ..     157     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.037
                            DUF2400  89 eksgsLeeaflk.................aeeeeeeleealeafreafle...kekrtrkleflipspekksacKR 144
                                        +k +  +ea+ +                   + e+ +++++++++e + +   ++k+ ++l+++    +kk+  KR
  gene1193|gene1193|rna1192|rna1192  61 TKDEVTHEAMERlrellpenaaiddnirrGLTIENIVNSSVDHINECIKRvgfHNKKAENLKKIAEILKKKGLPKR 136
                                        4444333333333333333333322222222222223333333333333344344444444444444455555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00029
                            DUF2400 173 iPlDvHvarvarklgllkrkq 193
                                        i +D+Hv+r+++++gl+k+++
  gene1193|gene1193|rna1192|rna1192 165 ISVDTHVHRISNRIGLVKTRD 185
                                        789*************98554 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  11.2   3.3e-05     0.097       1      17 []     217     233 ..     217     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.3e-05
                      EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                        C AR+P+Ce+C ++  C
  gene1193|gene1193|rna1192|rna1192 217 CVARRPRCEECCIRSRC 233
                                        **************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      837  (0.0466841); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.56
# Mc/sec: 1433.07
//
Query:       gene1194|gene1194|rna1193|rna1193  [L=448]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-85  285.7   4.0    6.1e-85  285.1   4.0    1.2  1  Kinesin      Kinesin motor domain
      2e-23   83.0   0.1    4.4e-23   81.9   0.1    1.6  1  Microtub_bd  Microtubule binding
     0.0086   15.8   1.8       0.02   14.7   1.8    1.6  1  DivIC        Septum formation initiator
  ------ inclusion threshold ------
      0.028   14.4   3.1      0.059   13.4   3.1    1.4  1  DUF1664      Protein of unknown function (DUF1664)
      0.095   13.1   2.2       0.23   11.9   2.2    1.7  1  CENP-H       Centromere protein H (CENP-H)
       0.16   12.2   3.0        0.4   10.9   3.0    1.6  1  Fib_alpha    Fibrinogen alpha/beta chain family
       0.21   11.8   5.1       0.17   12.1   1.9    2.3  2  Cnn_1N       Centrosomin N-terminal motif 1


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.1   4.0   2.4e-88   6.1e-85      41     333 .]      58     324 ..      44     324 .. 0.94

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 2.4e-88
                                        EEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBCTTTSBSHHHHHHHHHHHHHHH CS
                            Kinesin  41 kkfkFdkvfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyTmegkeeeeeGiipraleelFesikk 116
                                        +kf+Fd++f   +tq+ev++e++k+l+ ++++Gyn+t+faYGqtgsGKTyT++g+  ++ Gi++r+l+ l +++  
  gene1194|gene1194|rna1193|rna1193  58 NKFSFDRIFRG-STQQEVFQEVSKSLLVECMQGYNCTLFAYGQTGSGKTYTIQGN-AHNIGIVQRSLSLLHRNT-- 129
                                        79*******96.67889*************************************8.999*********998877.. PP

                                        CTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EEESSHHHHHHHHHHHHHHH CS
                            Kinesin 117 ekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkgltevevksaeevlellekgeknr 192
                                               ++++++s++EiYne + DL++++      +l+ired+  g v+v++l++ve +s+e+ +e+ ++g + r
  gene1194|gene1194|rna1193|rna1193 130 -------DLKISLSFVEIYNEMMLDLFDPE-----ASLSIREDPLCG-VVVDNLSTVESDSYEKSMEMYSRGIRTR 192
                                        .......4689*****************99.....469*******98.**************************** PP

                                        TSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSSTCHHHHHHHHHHHHHHHHHH CS
                            Kinesin 193 kvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktgaaegerlkEaaniNkSLlaLg 268
                                        ++++t +n+eSSRSH++f + l++++        +k+s+l++vDLAGsEr+++++  e++++kEaaniNkSLl+Lg
  gene1194|gene1194|rna1193|rna1193 193 RTSSTCMNKESSRSHSIFIVYLKSNSGVM-----SKSSRLCFVDLAGSERLREREI-EETKMKEAANINKSLLCLG 262
                                        ***********************998553.....368***************9995.7888*************** PP

                                        HHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHHCTT CS
                            Kinesin 269 rvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaerakei 333
                                        +vi++L++  ++ hi YR+SkLT lL+dsLgGn+k ++i +vs +  + ++t++t++f +r k i
  gene1194|gene1194|rna1193|rna1193 263 KVINKLSNG-EDGHIGYRESKLTFLLKDSLGGNCKLTVIGNVSLE--SRSDTVNTMNFLQRSKMI 324
                                        ********9.**********************************7..559**********99876 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.1   1.7e-26   4.4e-23      21     148 ..      30     148 ..      27     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.7e-26
                                        B-EEEEEEECCCS-T.EEEETTT...TTTEEEE-SEEEECTTHCCCCCCCC.HHHHHHHHTT--EEEEEEES.... CS
                        Microtub_bd  21 niRvfarvrpelesekakikfpeeekkkkkefsFdrvfeseseqeevfeei.sqlvqsaldgynvcifaygqTGsG 95 
                                        n+R++ r++p+   e++ +  + ++    ++fsFdr+f  ++ q+evf+e+ + l+  +++gyn+++faygqTGsG
  gene1194|gene1194|rna1193|rna1193  30 NVRTYLRIKPQAIPEDIVVGGD-SIVVDGNKFSFDRIFRGST-QQEVFQEVsKSLLVECMQGYNCTLFAYGQTGSG 103
                                        89************96555555.6688999********8765.56677776257999******************* PP

                                        ............ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEET CS
                        Microtub_bd  96 KtyTmegeeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDl 148
                                        KtyT++g+ ++ g ++r+++ + +          + +i+l+fveiyne + Dl
  gene1194|gene1194|rna1193|rna1193 104 KTYTIQGNAHNIGIVQRSLSLLHRN--------TDLKISLSFVEIYNEMMLDL 148
                                        *******877777777776655443........5667*************998 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.8   7.6e-06      0.02      13      52 ..     325     363 ..     318     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
                                        XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                              DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                        k+  +  ++++ e+++ +++l++l  en++L+a+++++ +
  gene1194|gene1194|rna1193|rna1193 325 KNLAVVNSDVNGELEEVKNKLKALDSENQSLKARIALM-D 363
                                        5666677899**************************99.3 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.1   2.3e-05     0.059      37     112 ..     325     403 ..     319     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                            DUF1664  37 rslsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                        ++l+ + ++v  +le+v+   ++l +  + L++ri+ +d++++e +++  + + +++++++ ++++ + + +++++
  gene1194|gene1194|rna1193|rna1193 325 KNLAVVNSDVNGELEEVKnklKALDSENQSLKARIALMDTQMQEESKVLPSYHYDIKRMKSVVDDTMNTLLELETV 400
                                        688888899999999999333445578899******************************9999999999999888 PP

                            DUF1664 110 veg 112
                                        +++
  gene1194|gene1194|rna1193|rna1193 401 IKK 403
                                        876 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.2   9.2e-05      0.23      11      80 ..     320     392 ..     314     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.2e-05
                             CENP-H  11 lssellklsqelrelqeeltevekenlrlkrknrelaael.lelakekesek..eklkeelekleaelkksrq 80 
                                         s+ +++l+   ++++ el+ev+ + ++l  +n++l a++ l+ ++ +e+ k  + +   ++++++ +++  +
  gene1194|gene1194|rna1193|rna1193 320 RSKMIKNLAVVNSDVNGELEEVKNKLKALDSENQSLKARIaLMDTQMQEESKvlPSYHYDIKRMKSVVDDTMN 392
                                        688999999999****************************778888888888998888899999888877655 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.0   0.00016       0.4      25      93 ..     326     394 ..     322     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                        CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH CS
                          Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrl 93 
                                         l  +++dv+ +le+++n+l+ + +++++ +  +  ++++++e+ k  +     ik++++ +++ +++l
  gene1194|gene1194|rna1193|rna1193 326 NLAVVNSDVNGELEEVKNKLKALDSENQSLKARIALMDTQMQEESKVLPSYHYDIKRMKSVVDDTMNTL 394
                                        56678999****************************************988888888888888554443 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.75   1.9e+03      16      27 ..     128     139 ..     121     148 .. 0.79
   2 ?   12.1   1.9   6.5e-05      0.17       4      53 ..     340     402 ..     338     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.75
                             Cnn_1N  16 NFdLKLriyfLe 27 
                                        N dLK+ + f e
  gene1194|gene1194|rna1193|rna1193 128 NTDLKISLSFVE 139
                                        889999998887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.5e-05
                             Cnn_1N   4 EqeeqidkLkKENFdLKLriyfLeerleklse.............eqkeellkenielkveve 53 
                                        E  +++++L+ EN +LK ri+ ++ ++++ s+             + ++++++++ el++ ++
  gene1194|gene1194|rna1193|rna1193 340 EVKNKLKALDSENQSLKARIALMDTQMQEESKvlpsyhydikrmkSVVDDTMNTLLELETVIK 402
                                        8899*************************9999988888886666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2637.32
//
Query:       gene1195|gene1195|rna1194|rna1194  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-30  105.3   0.6      3e-30  105.1   0.6    1.1  1  IF4E      Eukaryotic initiation factor 4E


Domain annotation for each model (and alignments):
>> IF4E  Eukaryotic initiation factor 4E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.6   1.7e-34     3e-30       2     150 ..       3     145 ..       2     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 1.7e-34
                                        EEEEEEEEEE-TTT--SS-SGGG-EEEEEEEEHHHHHHHHHHS--GGGB-SSEEEEEEETT--SSTTSHHHHS-EE CS
                               IF4E   2 LkskWtlwfdsksksksenyeeslkkvatfstveeFwslynnlkkpsklkvksdyhlFkkgikPmWEdpankkGGk 77 
                                        L s+W+lw +++++s+++++ ++l+ v+++st+ eF+ l +++ +   + + ++++lFkkg+kPmWEd+an +GG+
  gene1195|gene1195|rna1194|rna1194   3 LASQWVLWQNNNDESNAKSWGDDLVAVGEVSTIPEFLYLCDEISN-AGIGKLCTMNLFKKGVKPMWEDEANIDGGR 77 
                                        889******87777999***************************9.89999************************* PP

                                        EEEEE--..---HHHHHHHHHHHHHTT-SS--.-SEEEEEEEE-SSEEEEEEEES-TT-HHHHHHHHHHHHHT-- CS
                               IF4E  78 wvirlkk..kekldrlWeelllaligeqleeeedeicGvvvsvRkkedrisiWtrdasdeekvekigeklkevle 150
                                        +++ +    ++++ +lW++++  +i++ +    d++cG+v+s ++++++++iW+ ++    ++++i+e ++e+le
  gene1195|gene1195|rna1194|rna1194  78 IIMDVPVvgRDNIGELWKKTMAFCISNVV----DNVCGCVLSEKQSFYKLAIWFGKDY---NQDTIKEMWQETLE 145
                                        ****95544678***************99....689********************94...56667777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 967.13
//
Query:       gene1196|gene1196|rna1195|rna1195  [L=291]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   13.8   0.0      0.078   12.8   0.0    1.5  1  GYF_2     GYF domain 2
      0.048   13.3   0.0       0.16   11.7   0.0    1.9  2  GYF       GYF domain
      0.053   13.6   0.1        0.8    9.8   0.0    2.5  3  DUF2314   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> GYF_2  GYF domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05     0.078       1      28 [.     104     131 ..     104     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                              GYF_2   1 WyyadngqqqGPfsleeLkelaasgeit 28 
                                        W ++++g  +GPf+  e+ke+++s e++
  gene1196|gene1196|rna1195|rna1195 104 WLVKKEGSIYGPFTGREMKEKVNSEELK 131
                                        9999******************999886 PP

>> GYF  GYF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.7e-05      0.16       6      21 ..     108     123 ..     104     145 .. 0.85
   2 ?   -3.1   0.0       1.1   6.7e+03      26      37 ..     164     175 ..     163     183 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                                GYF   6 pqgevqGPFsseeMqk 21 
                                         +g ++GPF++ eM++
  gene1196|gene1196|rna1195|rna1195 108 KEGSIYGPFTGREMKE 123
                                        4899**********86 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                                GYF  26 gYFkdgllvrrv 37 
                                         YF++   +++ 
  gene1196|gene1196|rna1195|rna1195 164 EYFEMHAAIKKP 175
                                        589888888875 PP

>> DUF2314  Uncharacterized protein conserved in bacteria (DUF2314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.48   2.8e+03      21      62 ..      36      78 ..      25      86 .. 0.56
   2 ?    9.8   0.0   0.00013       0.8      98     129 ..     103     134 ..      90     140 .. 0.87
   3 ?    0.2   0.0      0.13   7.5e+02       3      24 ..     167     188 ..     166     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.48
                            DUF2314 21 elswekrRiipgldlaav...KiaftdekkgeeepkvEhmWiedv 62
                                       e s+e++  i +  + av   K   +++k++    + E mW  d+
  gene1196|gene1196|rna1195|rna1195 36 EYSKEEKACILKKRILAVagrKGGWPQKKAS--RRESESMWDVDL 78
                                       5555555555444444443334445555554..346788885555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00013
                            DUF2314  98 DWlyvedgktyGgyTikalrsemskeerkehd 129
                                         Wl+ ++g++yG +T + + +++++ee k  +
  gene1196|gene1196|rna1195|rna1195 103 SWLVKKEGSIYGPFTGREMKEKVNSEELKGTE 134
                                        6*************************998655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.13
                            DUF2314   3 emkeAiekAretfkyFlrelsw 24 
                                        em++Ai+k  e+ ++F++ ls+
  gene1196|gene1196|rna1195|rna1195 167 EMHAAIKKPLEKSQEFFEDLSS 188
                                        699*************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2104.66
//
Query:       gene1197|gene1197|rna1196|rna1196  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 946.96
//
Query:       gene1198|gene1198|rna1197|rna1197  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-16   59.8   0.1    4.4e-16   58.7   0.0    1.5  2  cNMP_binding  Cyclic nucleotide-binding domain
  ------ inclusion threshold ------
       0.13   12.0   0.1       0.29   10.9   0.1    1.6  1  Cupin_2       Cupin domain


Domain annotation for each model (and alignments):
>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.2   1.1e+04      14      29 ..      41      57 ..      40      69 .. 0.62
   2 !   58.7   0.0   4.9e-20   4.4e-16       3      85 ..     137     214 ..     135     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.2
                                       TSB-SEE.EEEEES-EE CS
                       cNMP_binding 14 Gdpadsl.yivlsGevr 29
                                       Gdp++ +  +v+ G++ 
  gene1198|gene1198|rna1197|rna1197 41 GDPGKLIeMLVEDGTLM 57
                                       67776666677777754 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 4.9e-20
                                        EE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEE CS
                       cNMP_binding   3 sfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalp 78 
                                        ++k g+++ ++ d + ++yiv+sGe++v+     g    l+ l++G++fGe+all++ prtatv A++d ++++++
  gene1198|gene1198|rna1197|rna1197 137 EIKCGTFVMHEEDVGSQMYIVESGEFEVT----RGGC-FLRKLSRGSFFGEIALLHNIPRTATVKAISDGKVWVVE 207
                                        67889***********************3....4544.9************************************* PP

                                        HHHHHHH CS
                       cNMP_binding  79 rddflel 85 
                                        + +f  +
  gene1198|gene1198|rna1197|rna1197 208 QTSFSGI 214
                                        **99876 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   3.3e-05      0.29      14      47 ..     146     180 ..     134     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.3e-05
                                        EC.SSSEEEEEEEEESEEEEEECTE.EEEEETTEEE CS
                            Cupin_2  14 hr.HpgedeffyVleGegeltvdge.eveleaGdsv 47 
                                        h    g+ ++++V +Ge+e+t +g    +l++G ++
  gene1198|gene1198|rna1197|rna1197 146 HEeDVGS-QMYIVESGEFEVTRGGCfLRKLSRGSFF 180
                                        5523345.****************988889998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1311.64
//
Query:       gene1199|gene1199|rna1198|rna1198  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 731.04
//
Query:       gene12|gene12|rna12|rna12  [L=1245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-58  198.8   0.8    3.1e-58  197.2   0.3    1.9  2  SNF2_N      SNF2 family N-terminal domain
    4.4e-20   72.1   0.5    8.6e-19   67.9   0.0    3.1  3  Helicase_C  Helicase conserved C-terminal domain
    9.5e-15   54.3   6.0    3.6e-10   39.6   0.8    3.3  2  Chromo      Chromo (CHRromatin Organisation MOdifier) domain
      4e-12   46.5   0.0    1.2e-11   44.9   0.0    1.9  1  ResIII      Type III restriction enzyme, res subunit
    5.9e-05   22.9   0.0    0.00013   21.8   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.037   13.3   0.0       0.12   11.6   0.0    1.8  1  DUF2075     Uncharacterized conserved protein (DUF2075)
      0.046   13.6   4.3       0.12   12.3   4.3    1.8  1  AT_hook     AT hook motif
       0.12   12.8   4.3       0.69   10.4   4.3    2.3  1  IBB         Importin beta binding domain


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.18   3.9e+02       1      13 [.     301     313 ..     301     318 .. 0.88
   2 !  197.2   0.3   1.4e-61   3.1e-58      56     350 .]     317     583 ..     313     583 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
                                HHHHHHHHH.... CS
                                xxxxxxxxxxxxx RF
                     SNF2_N   1 yQkeavkwmlkRe 13 
                                yQ e+++w+l+R 
  gene12|gene12|rna12|rna12 301 YQLEGLNWLLNRW 313
                                9********9995 PP

  == domain 2  score: 197.2 bits;  conditional E-value: 1.4e-61
                                --EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH..... CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                     SNF2_N  56 rGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkk..... 134
                                + +i+aDemGLGKTvq++++i ++ +          k     p+L+v P s++ +We+e+e+++    lrvl y++++      
  gene12|gene12|rna12|rna12 317 QSCIMADEMGLGKTVQSVTFINTLFT----------KYDYCAPVLVVTPLSIIPHWEREFEAWTD---LRVLKYHENRPgrali 387
                                57********************5544..........3334579********************96...5678888876688887 PP

                                ......-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE- CS
                                ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SNF2_N 135 ......mkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwilt 212
                                       kk      +   + +dv+ittYd++  e+      ++l+q +    + DE+h+lkn +skaa+++++L+ +++++l+
  gene12|gene12|rna12|rna12 388 aeyefvLKK-----NNLEIRLFDVLITTYDTVMAEQ------EHLSQFHFSVGIFDEAHRLKNAKSKAATVLRTLKFNHKVLLS 460
                                554432111.....12235679***********888......9***************************************** PP

                                S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHHHHHHHHHHHHHTT-STTEE---GGGT--S---EEEEEEEEE--HHH CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SNF2_N 213 GTPiqnsledlygLlkfLreepfgekqtfdkllqrpieaqaekgrsrLlqllqrlmlrrakkdveknlPpkteeiiflklskve 296
                                GTP+qn+ ++l++Ll+f+ +  f++   f   ++ +      + +++L  ll++lmlrr+k+dvek++P k+e ii + l+  +
  gene12|gene12|rna12|rna12 461 GTPLQNNISELWSLLNFIDPARFSSLPHFLGEFKMENI----NDVEKLQGLLRPLMLRRMKEDVEKSIPTKEETIIEVALTMIQ 540
                                *****************************999998887....99**************************************** PP

                                HHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH---XX CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     SNF2_N 297 rksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnhpqlv 350
                                +++Y            a l k+ e+ +k +++s  ++l+ ++elr++c hp+l+
  gene12|gene12|rna12|rna12 541 KRFYR-----------AILEKNIEFLTKGGKESAPNLLNVMMELRKCCIHPYLI 583
                                *****...........45555555666666655688***************985 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0   3.9e-22   8.6e-19       3     111 .]     646     757 ..     644     757 .. 0.87
   2 ?   -0.4   0.0      0.63   1.4e+03      49      77 ..     802     830 ..     771     871 .. 0.86
   3 ?   -0.9   0.1      0.89     2e+03      17      60 ..    1098    1137 ..    1081    1144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.9e-22
                                HHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS...EEEESGGGTSSSTS CS
                 Helicase_C   3 leallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesd...vLiatdvaerGidi 82 
                                l  l +ll + ++g+k+lif++ ++ l+  +++l + +++k+ +++g   +++r++++++f +++sd   +L++t++++ Gi++
  gene12|gene12|rna12|rna12 646 LVLLDKLLGKLKDGHKVLIFSQMTRCLDLlAEYL-TYRKYKYERIDGGARTENRQAAIDRFSDKTSDvfvFLLSTRAGGVGINL 728
                                556777777789*************997767777.5557**********************95554421478************ PP

                                TTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                 Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtgRag 111
                                + +++Vi+fd ++n+++  q+  R++R+g
  gene12|gene12|rna12|rna12 729 TAADTVIIFDSDWNPQNDLQAQARCHRIG 757
                                ***************************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.63
                                TSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                 Helicase_C  49 elpqnereeileqfnkgesdvLiatdvae 77 
                                + +++++++i +  +kg + vL+ td+a+
  gene12|gene12|rna12|rna12 802 SEKTRKKDAIETLLRKGAYGVLMETDDAS 830
                                445667778888899***********997 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.89
                                 SEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHH CS
                 Helicase_C   17 gkilifvntidrlek.vklllekkgikvavlhgelpqnereeile 60  
                                 +ki+  + +++++ +  +l+      k++++ g+++ ++re i+e
  gene12|gene12|rna12|rna12 1098 RKIVSTLSRKKEVREdDNLF-----HKAIMMFGRITDDNRESIIE 1137
                                 44444444455554333333.....88999999999999999997 PP

>> Chromo  Chromo (CHRromatin Organisation MOdifier) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   5.1e-06     0.011      12      41 ..     161     188 ..     148     201 .. 0.81
   2 !   39.6   0.8   1.6e-13   3.6e-10       2      54 .]     213     264 ..     212     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                                ETTEECEEEEEEETTSTGGGTEEEEGGGCS CS
                     Chromo  12 dkdgleleYlVKWkglpysentWEpeenle 41 
                                d ++  + Y+VK k  +y ++ W p+e++ 
  gene12|gene12|rna12|rna12 161 DSEN--ERYFVKFKYKSYLHCDWVPKEEIM 188
                                3333..69*****************99996 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 1.6e-13
                                EEEEEEEEEEETTEECEEEEEEETTSTGGGTEEEEGGGCSSH..SHHHHHHHHHH CS
                     Chromo   2 eVerIidhrtdkdgleleYlVKWkglpysentWEpeenlekc..fqelideFkkr 54 
                                +V+rI+++ +d ++    +lVKWk+ py+ +t+E++e + kc  f+e ++++++r
  gene12|gene12|rna12|rna12 213 KVDRILHEDYDGEKV---FLVKWKSQPYELSTFETAESVTKCegFEEELKKYRDR 264
                                69*************...**************************9999****997 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   5.5e-15   1.2e-11       4     169 ..     298     463 ..     296     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 5.5e-15
                                E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEE CS
                     ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigk 87 
                                lreyQ e ++ ll+ +  + ++  +++ + G GKT+ ++ +i  l++k+++   +++v  +s++  +++ef+ +++  + +  +
  gene12|gene12|rna12|rna12 298 LREYQLEGLNWLLNRW--YYRQSCIMADEMGLGKTVQSVTFINTLFTKYDYCAPVLVVTPLSIIPHWEREFEAWTDLRVLKYHE 379
                                89********999999..6899999999************************99999999***********9999999888777 PP

                                EESSS-B--...............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.TTHHHHHT---SEE CS
                     ResIII  88 kvsgdkkka........kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.swreilekfkeavl 162
                                +  g+  +a        ++ ++   ++l+tt++++ a++       e+l++ +f v i+DEaHrl+ +k +   +l+ +k + +
  gene12|gene12|rna12|rna12 380 NRPGRALIAeyefvlkkNNLEIRLFDVLITTYDTVMAEQ-------EHLSQFHFSVGIFDEAHRLKNAKsKAATVLRTLKFNHK 456
                                7666666666666665555668889999*******9999.......999999*************9975366669999999999 PP

                                EEEESS- CS
                     ResIII 163 lglTATp 169
                                + l++Tp
  gene12|gene12|rna12|rna12 457 VLLSGTP 463
                                9999*99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.7e-08   0.00013       4     170 ..     302     464 ..     299     471 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.7e-08
                                HHHHHHHHH....TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                xxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DEAD   4 Qaeaiplil....gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                Q e ++++l      +++++a e G GKT   +   ++++++ k +    +l+v+P+  ++    ++++ +++   lrvl   +
  gene12|gene12|rna12|rna12 302 QLEGLNWLLnrwyYRQSCIMADEMGLGKTVQSVTF-INTLFT-KYDYCAPVLVVTPLS-IIPHWEREFEAWTD---LRVLKYHE 379
                                66666666644445699************985555.555554.788888999999985.67888888888888...55554444 PP

                                ...TSSHHHHHHHH..HTT.....CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                ...xxxxxxxxxxx..xxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DEAD  84 ...gvaardqlskl..dng.....vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgk 157
                                   g a   +++ +  +n+      d++++t + ++   ++++l+  ++++ ++DEa+rl +   + +  ++l++l       k
  gene12|gene12|rna12|rna12 380 nrpGRALIAEYEFVlkKNNleirlFDVLITTYDTVMA--EQEHLSQFHFSVGIFDEAHRLKNA--KSKAATVLRTL-------K 452
                                2224444444444343222556689*******99988..88997777778899*******998..77888888888.......3 PP

                                .TTSEEEEEESSBS CS
                                .xxxxxxxxxxxxx RF
                       DEAD 158 .lqrqvivlSATlp 170
                                 ++   ++lS T+ 
  gene12|gene12|rna12|rna12 453 fNH--KVLLSGTPL 464
                                223..677887776 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.4e-05      0.12      65     106 ..     402     443 ..     382     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.4e-05
                    DUF2075  65 eklssfinnlsefkkaeekkeepkedvvivDEAhrlltksdq 106
                                + ++ +i+++++   ++e+ ++ ++ v i+DEAhrl + +++
  gene12|gene12|rna12|rna12 402 RLFDVLITTYDTVMAEQEHLSQFHFSVGIFDEAHRLKNAKSK 443
                                55678899999889999999****************995444 PP

>> AT_hook  AT hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.3   5.3e-05      0.12       1      12 [.      25      36 ..      25      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.3e-05
                    AT_hook  1 kRkRGRPrKaat 12
                               +RkRGRPrK+++
  gene12|gene12|rna12|rna12 25 PRKRGRPRKNES 36
                               7********986 PP

>> IBB  Importin beta binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.3   0.00031      0.69      11      55 ..     104     150 ..     101     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                                XXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXX........ CS
                        IBB  11 daeelRrrReeeqvel..RKqkreeqllKrRnvaaeaaaeeeadsee 55 
                                +++  R r ee +v +  R+qkr+ ++ Kr +v  ++++++e ++e+
  gene12|gene12|rna12|rna12 104 ETNGYRERNEERNVYIpeRRQKRNAAMVKRASVPESESSTNEYNEES 150
                                56778***********99***************55222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.81u 0.30s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 7751.60
//
Query:       gene120|gene120|rna120|rna120  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-16   60.7   3.6      3e-16   59.6   0.1    2.0  2  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   1.7e-20     3e-16      11     145 ..       7     127 ..       2     136 .. 0.79
   2 !    1.9   1.0    0.0092   1.7e+02     115     152 ..     140     174 ..     131     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.7e-20
                                    T----TTS-EEEEEEEEEEETTEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHH CS
                           Gar1  11 dieigppeevleiGtvssivenevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaks 90 
                                    + ++++++e+ e+G+v  +++++ v+k +++   ++++ ns++ +   ++iGkVdEi+G++ +++ +++l++ ++     
  gene120|gene120|rna120|rna120   7 NKKVQKSTETMELGKVLYMCQGQPVVKLMAK---DIPYPNSPVLDLSSRVIGKVDEILGRLDDVHATIRLENPSGTL--- 80 
                                    456778899********************44...9************************************665555... PP

                                    TTTTSE.EEEE-X...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Gar1  91 fkvgdk.vyiapd.lplerfllteelkkkkgpdasnendeElpeeevefsdDekeae 145
                                     k g++ + ++ +  p +rfl  ee++k         ++eE + ++ +f +D++ ++
  gene120|gene120|rna120|rna120  81 -KRGETlLSYVDKfIPKKRFLPREEVEK---------KKEETDRKKSKFRKDQRAER 127
                                    .5666615666669*******4333333.........45677777778887766544 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.0092
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Gar1 115 kkkkgpdasnendeElpeeevefsdDekeaeakkkkkg 152
                                    +  + +++++++ ++   +++ef +D++ +++ +++ +
  gene120|gene120|rna120|rna120 140 HG-RKTNNKWASRQNG--KKQEFGKDNRRRKWDSSRSN 174
                                    33.3367777766555..578*******9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1045.55
//
Query:       gene1202|gene1202|rna1201|rna1201  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1252  (0.069831); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 829.20
//
Query:       gene1203|gene1203|rna1202|rna1202  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0071   16.1   0.1     0.0071   16.1   0.1    2.4  3  T_cell_tran_alt  T-cell leukemia translocation-altered
  ------ inclusion threshold ------
        2.7    7.4   5.6        1.3    8.4   0.3    2.1  2  GPI2             Phosphatidylinositol N-acetylglucosaminyltra


Domain annotation for each model (and alignments):
>> T_cell_tran_alt  T-cell leukemia translocation-altered
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.79   7.1e+03      32      44 ..      18      30 ..      14      40 .. 0.74
   2 !   16.1   0.1   7.9e-07    0.0071       8      64 ..      89     146 ..      82     162 .. 0.82
   3 ?   -0.5   0.2      0.12   1.1e+03       8      39 ..     204     236 ..     197     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.79
                    T_cell_tran_alt 32 lswlvlslvaihl 44
                                       + +l+l l++i +
  gene1203|gene1203|rna1202|rna1202 18 FLYLILRLIVIGI 30
                                       5678888888765 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 7.9e-07
                    T_cell_tran_alt   8 lsflsefvddweandmrvaifklllswlvl.slvaihlawkvyGstvndlyyrqglgG 64 
                                         s++ e + ++  ndm v+ f l++  l l  ++ +h+  k +G+  + +y+++g   
  gene1203|gene1203|rna1202|rna1202  89 ASVVVETIFKFGDNDMEVIFFSLVYLGLCLcEFIRVHFICKEFGDMFEWIYFKHGGAN 146
                                        577889999999**********98666655279*******************987543 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.12
                    T_cell_tran_alt   8 lsflsefvddwean.dmrvaifklllswlvlsl 39 
                                        ++f   fv++ e n + r+ +  ++l  ++ s+
  gene1203|gene1203|rna1202|rna1202 204 ITFFLMFVRQNEENeEQRMLLIMIVLLNILYSV 236
                                        456667777665541566666677766666654 PP

>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.9     0.023   2.1e+02     197     244 ..      52     107 ..      44     135 .. 0.56
   2 ?    8.4   0.3   0.00015       1.3      42      91 ..     193     241 ..     181     276 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.023
                               GPI2 197 lllfsievfglfPvfrrslrhrswrlhvvltvllvllagagvgiilk........l 244
                                        l l  i +f+++    ++ +  + ++++v++v+  l a+++v +i k        +
  gene1203|gene1203|rna1202|rna1202  52 LSLTNIYMFIYLDNAISRKNLEQCKAYWVIIVMASLEASVVVETIFKfgdndmevI 107
                                        44445555555544444444445556666666666777777777776655444431 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00015
                               GPI2  42 stvivqhvcsviifvlvFvgiyqervspvsvvllssiltvlgwllwelwa 91 
                                        +  i+ h++ vi f+l+Fv   +e+ ++++++++ ++l +l  + + + +
  gene1203|gene1203|rna1202|rna1202 193 IYIIIDHLLEVITFFLMFVRQNEENEEQRMLLIMIVLLNILYSVHL-VDK 241
                                        56799***************99999888777766555555544333.222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1883.10
//
Query:       gene1204|gene1204|rna1203|rna1203  [L=300]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-05   24.5   0.0    2.3e-05   23.6   0.0    1.5  1  Rad21_Rec8    Conserved region of Rad21 / Rec8 like protein
    5.9e-05   23.2   0.6    0.00011   22.3   0.6    1.4  1  Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein


Domain annotation for each model (and alignments):
>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.5e-09   2.3e-05      17      50 ..     263     296 ..     251     300 .] 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.5e-09
                                        -HHHHHHHHHHHHHHHHTSEEEEESSTT--EEEE CS
                         Rad21_Rec8  17 RkeAArlFyelLvLatkgvIkvkQeaPYgdIlit 50 
                                        R+  Ar Fy +L+L+++g++   Q+++Yg+I++t
  gene1204|gene1204|rna1203|rna1203 263 RRRRARIFYLMLELSSRGAFVPVQKQAYGEIVLT 296
                                        55568**************************997 PP

>> Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.6   1.2e-08   0.00011      28      90 ..      34      96 ..      23     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-08
                       Rad21_Rec8_N 28 skkeilevniekaveeIlnpeaplaLrlsgqLllGvvriyskkvkyllsDceealekikkafk 90
                                       +k  i  v i+k ve I+n+     Lr+s+ L   +vr y+ kv++ l +++++++ ++ + +
  gene1204|gene1204|rna1203|rna1203 34 KKGPIARVRISKVVEIIMNSVPVYNLRISSVLFRVIVRAYEAKVRVYLLEIQSLVKILSITKR 96
                                       4556999************97789****************************99988876444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2380.57
//
Query:       gene1205|gene1205|rna1204|rna1204  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-26   92.8   2.0    2.9e-26   91.9   2.0    1.4  1  HSF_DNA-bind  HSF-type DNA-binding


Domain annotation for each model (and alignments):
>> HSF_DNA-bind  HSF-type DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   2.0   1.6e-30   2.9e-26       1      96 []       9     106 ..       9     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.6e-30
                                        HHHHHHHHHCT...TTTSEESSSSSEEEES-HHHHHHHTHHHHSTT--HHHHHHHHHHTTEEE---SSBTTB--TT CS
                       HSF_DNA-bind   1 FlkkLyklled...eelisWsedgksfvvkdkeefakevlpkyfkhsnfssFvrqLnlYgFrkvkrkeekkkkksk 73 
                                        F+ kL+++le+     +isW  dg+sf++++ + f++ vl+k+f+h+n+ssFvrqLn Y+F kv+r+e ++  ++ 
  gene1205|gene1205|rna1204|rna1204   9 FVVKLFQILEEpenYPYISWALDGRSFIISNIQGFSEFVLEKHFRHKNWSSFVRQLNKYDFYKVRRDE-ERIGERG 83 
                                        99*******87644666**********************************************99766.5555558 PP

                                        SEEEEESS--XXXXXXXXXXXXX CS
                       HSF_DNA-bind  74 vweFshenFkrgkpelLkkikrk 96 
                                        +we+++++F+rg+pelL+ki+rk
  gene1205|gene1205|rna1204|rna1204  84 QWEYKNKYFQRGRPELLDKIRRK 106
                                        9********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2007.06
//
Query:       gene1206|gene1206|rna1205|rna1205  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.9   0.5     0.0024   18.3   0.0    1.6  2  GLTSCR1   Conserved region of unknown function on GLTSCR prot


Domain annotation for each model (and alignments):
>> GLTSCR1  Conserved region of unknown function on GLTSCR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-07    0.0024       6      73 ..     100     161 ..      95     186 .. 0.70
   2 ?   -3.5   0.2      0.82   1.5e+04      58      71 ..     192     205 ..     190     210 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-07
                            GLTSCR1   6 lnpdvktPFasveDavkRLlPYHvfqepkedeedlekadeefekvaeellkrfqklenkfrklllkea 73 
                                         +pd++  F +v++a++ LlPYH+f     ++  +       +k+a  + ++++++ + ++ +++ e+
  gene1206|gene1206|rna1205|rna1205 100 GRPDLR-RFMNVNHAYECLLPYHIFGFDLYEDMLFM-----SSKEAGGISSEIDEMIELMKDAVVLES 161
                                        579997.9****************988888776665.....455566666666666666666655555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.82
                            GLTSCR1  58 fqklenkfrklllk 71 
                                        +qk  +++r+ l k
  gene1206|gene1206|rna1205|rna1205 192 KQKAQRRYRQQLNK 205
                                        55666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1442.85
//
Query:       gene1207|gene1207|rna1206|rna1206  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-14   53.2  15.9    3.2e-14   53.0  15.9    1.0  1  PHF5      PHF5-like protein


Domain annotation for each model (and alignments):
>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0  15.9   1.8e-18   3.2e-14      10      89 ..       8      89 ..       2      90 .] 0.92

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.8e-18
                               PHF5 10 lcrkqpGtaigklcekcdgkcpicdslv.kpatkvricdecsfgkleekciicgs.kgvsdayyclecvrlekdrdGc 85
                                        c k +  +++++c+kc g+c ic     ++ +++ ic  c  + ++++ci+c      ++ay c ec  l+k++d c
  gene1207|gene1207|rna1206|rna1206  8 RCGKISTGSVAMMCDKCSGRCYICGLDAgTSSRRIYICSVCFHSMYKDRCIVCKLkDPRNNAYCCRECWLLQKNHDRC 85
                                       69999999****************9988577899********************967899****************** PP

                               PHF5 86 prii 89
                                       p +i
  gene1207|gene1207|rna1206|rna1206 86 PVLI 89
                                       *876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 585.20
//
Query:       gene1208|gene1208|rna1207|rna1207  [L=369]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2562.36
//
Query:       gene1209|gene1209|rna1208|rna1208  [L=681]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.4   3.1       0.38   11.1   3.1    1.7  1  PRP1_N    PRP1 splicing factor, N-terminal


Domain annotation for each model (and alignments):
>> PRP1_N  PRP1 splicing factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.1   2.1e-05      0.38      66     108 ..      12      54 ..       6      92 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.1e-05
                                        --------------------HHHHHHHHHHHHHHTT------- CS
                             PRP1_N  66 glfakaeydedDeeAdriyeeiderlderrkkrreakekeele 108
                                        +lf +++  e D+e d++y++i+++ +++  + +e+  +++  
  gene1209|gene1209|rna1208|rna1208  12 NLFGESTVSEYDKEEDEVYRAIEKKRKKKSAEVEERILSRKDV 54 
                                        789999999***************9888877776665544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4578.60
//
Query:       gene1210|gene1210|rna1209|rna1209  [L=614]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-13   49.0  26.3    7.5e-12   44.8  26.3    2.1  1  Spc7             Spc7 kinetochore protein
     0.0045   15.9  26.8     0.0077   15.1  26.8    1.2  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
  ------ inclusion threshold ------
      0.028   13.1  16.2      0.047   12.3  16.2    1.3  1  AAA_13           AAA domain
       0.38   10.8  14.9         19    5.3   0.0    3.7  5  DUF1664          Protein of unknown function (DUF1664)
        1.9    9.1  10.1         14    6.3   3.7    4.1  3  SlyX             SlyX
          2    8.6   5.7        3.6    7.7   2.6    3.0  2  YojJ             Bacterial membrane-spanning protein N-termin
        3.5    6.8  11.8        2.6    7.3   0.4    2.4  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
        9.1    6.1  10.0       0.91    9.3   1.5    2.8  3  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8  26.3   3.3e-15   7.5e-12       4     297 ..     191     469 ..     188     477 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 3.3e-15
                               Spc7   4 episLqdFLnmtgIrFmdl..tttkrrstiaptaeekeeeekisledyvvAaactvPlLeLYqhscreLkkyiseg 77 
                                        e +++++ L   gIrF+d   +++ rr t+  +  e       + e++++++    P    +   ++eL++++s++
  gene1210|gene1210|rna1209|rna1209 191 EVVNVSELLVSKGIRFLDSlvVSNTRRDTMSKSLNE----VHPRQEKFYESFL--EPRTRFFLEFSSELEERMSKQ 260
                                        5677788888999***99668888899998776544....5888999999999..899999999999********* PP

                               Spc7  78 rkiireieeetleenPpLfreYmeadpdvkalmdnqfklvKtnarlqakkdWYeWRmqllegLkegleenleglee 153
                                         k+ +e+e+++            + +  ++ + ++q++ +Kt +r++ak +WYe R +   +   +++++ + l e
  gene1210|gene1210|rna1209|rna1209 261 EKVNNELERDFNI----------SGTVFEREDASSQLRSLKTECRMRAKIEWYELRKEKEVEFNREVTDRRNRLAE 326
                                        *****99999864..........45566799********************************************* PP

                               Spc7 154 dkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                        +++ ++ + +e++e +++  +  +++ee++ ++++++    + +  ++ el+  ++e+++ ie+ kke++ l+e++
  gene1210|gene1210|rna1209|rna1209 327 EYNDISGRLKEVSEDVEAKGKSNERMEEQISRIRNRVGGDGEEKDRKISELKLVISEQENAIENIKKEVKGLEEEK 402
                                        ***********************************99987888899****************************** PP

                               Spc7 230 eeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsgstlelt 297
                                         +++++   lke  +++e+e++  e+ l+  ++++e +++++++e+++++ + g++i +++ s++ l+
  gene1210|gene1210|rna1209|rna1209 403 IRKQAEKRVLKEALKKIEDEVKDLEKALK-VQNVTEGQLKEIRQEFRTICAIFGMEISRVDTSEIRLK 469
                                        ***************************98.7899***************************9998876 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  26.8   3.4e-06    0.0077      42     240 ..     252     444 ..     245     453 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                           CALCOCO1  42 eraeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeek 117
                                        e +e + +qe +n++ e++   ++   + ++r  ++ +s++  lk+e  ++r k+e  e +++++ +++ e+++++
  gene1210|gene1210|rna1209|rna1209 252 ELEERMSKQEKVNNELERD---FNISGTVFER--EDASSQLRSLKTEC-RMRAKIEWYELRKEKEVEFNREVTDRR 321
                                        6777788889999999888...6666677765..5778999******5.5788888888888888889999***** PP

                           CALCOCO1 118 salleakeesearirELEeDiktltqralekEteLeRlkerakkalaqrkeeeaerkqlqakleqseeel..rsls 191
                                        ++l+e+ ++ + r++E+ eD+++ ++     E ++ R+++r+         ee++rk ++ kl  se+e+  +++ 
  gene1210|gene1210|rna1209|rna1209 322 NRLAEEYNDISGRLKEVSEDVEAKGKSNERMEEQISRIRNRVGG-----DGEEKDRKISELKLVISEQENaiENIK 392
                                        ***********************999999999999999998853.....45788999999999999999633699* PP

                           CALCOCO1 192 kelqelrnslaerdtqvlqLqdtittltqk...LttAqrkeaenEallkelr 240
                                        ke++ l + + +++++   L++ + +++++   L++A + +  +E  lke+r
  gene1210|gene1210|rna1209|rna1209 393 KEVKGLEEEKIRKQAEKRVLKEALKKIEDEvkdLEKALKVQNVTEGQLKEIR 444
                                        **********************999998761114445444444555555554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  16.2   2.1e-05     0.047     318     457 ..     297     434 ..     231     459 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.1e-05
                             AAA_13 318 afeedkeelkaea.ealeeqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeek 392
                                        +++ +  el++e+  +++ + +  +++l +  ++++    l++v++++e+  k+ ++++e+i++  ++v    eek
  gene1210|gene1210|rna1209|rna1209 297 RAKIEWYELRKEKeVEFNREVTDRRNRLAEEYNDISG--RLKEVSEDVEAKGKSNERMEEQISRIRNRVGGDGEEK 370
                                        1222222222222123344444444444444444444..4667777777777777888888888877777777788 PP

                             AAA_13 393 eeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdek 457
                                         +  ++l+l +++e e+++++ kk++k+le++    ++e++  +++lkk+e+e+k+Lek l+ ++
  gene1210|gene1210|rna1209|rna1209 371 DRKISELKL-VISEQENAIENIKKEVKGLEEEKIRKQAEKRVLKEALKKIEDEVKDLEKALKVQN 434
                                        888888888.7788899999999999999999999999999999999999999999999987554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0084        19      24      88 ..     202     270 ..     191     304 .. 0.79
   2 ?    5.1   0.4    0.0098        22      55      93 ..     322     360 ..     278     369 .. 0.58
   3 ?    4.3   3.4     0.018        40      54     121 ..     321     392 ..     307     394 .. 0.73
   4 ?    3.8   8.1     0.026        57      45     122 ..     351     428 ..     347     430 .. 0.90
   5 ?    2.8   5.4     0.052   1.2e+02      40     103 ..     385     454 ..     382     473 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0084
                            DUF1664  24 kGwklsdlmfv..Tkr.slsdavesvskqleqvseslaatkrhLssri.drvdkkldeqkeiskeikee 88 
                                        kG+++ d + v  T+r  +s+ +++v  + e+++es  + + ++  +   ++++++ +q+++ +e++++
  gene1210|gene1210|rna1209|rna1209 202 KGIRFLDSLVVsnTRRdTMSKSLNEVHPRQEKFYESFLEPRTRFFLEFsSELEERMSKQEKVNNELERD 270
                                        9****9999886677746******************999999887665245777777777777776665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0098
                            DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevr 93 
                                        + la+  +++s r+++v + +++  +  + ++e+++++r
  gene1210|gene1210|rna1209|rna1209 322 NRLAEEYNDISGRLKEVSEDVEAKGKSNERMEEQISRIR 360
                                        333344444444444444444444444444444444444 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.018
                            DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredl....seigedvesvkeaveglesklerie 121
                                         + la+  +++s r+++v + +++  +  + ++e+++++r+ +    +e +++++++k ++++ e+ +e+i+
  gene1210|gene1210|rna1209|rna1209 321 RNRLAEEYNDISGRLKEVSEDVEAKGKSNERMEEQISRIRNRVggdgEEKDRKISELKLVISEQENAIENIK 392
                                        566777778888899999999999999999999999888876522225566667777778888887777775 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.026
                            DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        ++ +q+ ++ + +    ++  ++i ++   + eq++++++ik+ev+ ++e+  + + + + +kea +++e +++++
  gene1210|gene1210|rna1209|rna1209 351 RMEEQISRIRNRVGGDGEEKDRKISELKLVISEQENAIENIKKEVKGLEEEKIRKQAEKRVLKEALKKIEDEVKDL 426
                                        67778888888888888888999***************************9999999999**************99 PP

                            DUF1664 121 ee 122
                                        e+
  gene1210|gene1210|rna1209|rna1209 427 EK 428
                                        86 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.052
                            DUF1664  40 sdavesvskqleqvs.eslaat..krhLssridrvdk...kldeqkeiskeikeevtevredlseigedv 103
                                        ++a+e++ k+++ +  e+++++  kr L++ ++++++    l++  ++++ ++ +++e+r++ ++i   +
  gene1210|gene1210|rna1209|rna1209 385 ENAIENIKKEVKGLEeEKIRKQaeKRVLKEALKKIEDevkDLEKALKVQNVTEGQLKEIRQEFRTICAIF 454
                                        4677777777777763445443227777776666654111567777788888888888888887776655 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.14   3.1e+02       7      23 ..     252     268 ..     250     295 .. 0.89
   2 ?    0.3   0.1       0.5   1.1e+03      34      62 ..     322     350 ..     315     355 .. 0.81
   3 ?    6.3   3.7    0.0064        14       4      53 ..     373     422 ..     369     439 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
                                        HHHHHHHHHHHHHHHHH CS
                               SlyX   7 eLEiklafqedtieeLn 23 
                                        eLE++++ qe++ +eL 
  gene1210|gene1210|rna1209|rna1209 252 ELEERMSKQEKVNNELE 268
                                        89********9999986 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.5
                                        HHHHHHHHHHHHT-XXXXXXXXXXXXXXX CS
                               SlyX  34 drlqrqlrllaerlkeleessgaseaeee 62 
                                         rl ++ + +  rlke++e+ +a+++ +e
  gene1210|gene1210|rna1209|rna1209 322 NRLAEEYNDISGRLKEVSEDVEAKGKSNE 350
                                        689999999999**999999987776544 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0064
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                               SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                        ++ eL   ++ qe++ie   ++v   +++  r q++ r l+e lk++e++
  gene1210|gene1210|rna1209|rna1209 373 KISELKLVISEQENAIENIKKEVKGLEEEKIRKQAEKRVLKEALKKIEDE 422
                                        45555556666666666666666666666666666666666666555555 PP

>> YojJ  Bacterial membrane-spanning protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.72   1.6e+03      11      33 ..     321     343 ..     313     360 .. 0.80
   2 ?    7.7   2.6    0.0016       3.6       3      53 ..     401     450 ..     399     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.72
                               YojJ  11 keklkeeLeqiekeleevlkald 33 
                                        ++ l+ee ++i+++l+ev +  +
  gene1210|gene1210|rna1209|rna1209 321 RNRLAEEYNDISGRLKEVSEDVE 343
                                        77888999999999999877655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                               YojJ   3 ekcleeelkeklkeeLeqiekeleevlkaldeedeClLcelesirekfael 53 
                                        ek+ +++ k+ lke L++ie e+++  kal+ ++    ++l++ir++f ++
  gene1210|gene1210|rna1209|rna1209 401 EKIRKQAEKRVLKEALKKIEDEVKDLEKALKVQNV-TEGQLKEIRQEFRTI 450
                                        67777888999*******************98875.468888888888765 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4    0.0011       2.6      55     111 ..     315     376 ..     275     382 .. 0.79
   2 ?    3.3   5.3     0.018        41      32      99 ..     383     450 ..     374     457 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                               HemX  55 eaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga.....erkdWlLae 111
                                        ++   + ++l+e++++ +++l++ ++ +e++ k+ e++++q+s++ ++     e+kd++++e
  gene1210|gene1210|rna1209|rna1209 315 REVTDRRNRLAEEYNDISGRLKEVSEDVEAKGKSNERMEEQISRIRNRvggdgEEKDRKISE 376
                                        44456788999999******************************999988888888888887 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.018
                               HemX  32 eltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskv 99 
                                        e++  +++++++++ le+++ + +aek+  +e  +++++  ++le++ k ++ ++ ql+e++q++ ++
  gene1210|gene1210|rna1209|rna1209 383 EQENAIENIKKEVKGLEEEKIRKQAEKRVLKEALKKIEDEVKDLEKALKVQNVTEGQLKEIRQEFRTI 450
                                        44555688888888888887777888888888888888888888888888888899999999988876 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.18     4e+02      24      51 ..     160     188 ..     158     193 .. 0.86
   2 ?    9.3   1.5   0.00041      0.91     102     172 ..     330     400 ..     324     406 .. 0.92
   3 ?   -0.3   0.6      0.35   7.9e+02      94     122 ..     402     431 ..     400     449 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                       Bacillus_HBL  24 Yanlilkqpdvnleei.knkellsklnqh 51 
                                        + ++++ +  +n+eei + ++l++ ++q 
  gene1210|gene1210|rna1209|rna1209 160 FEDTLISNETINVEEIiNTQDLRKMIPQA 188
                                        67899***********9999999999885 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00041
                       Bacillus_HBL 102 ellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqg 172
                                        +++ +l++ +e++  + k+ ++  +++++ ++++  d ++ + +++el+ +++ ++  i+++++e++ l++
  gene1210|gene1210|rna1209|rna1209 330 DISGRLKEVSEDVEAKGKSNERMEEQISRIRNRVGGDGEEKDRKISELKLVISEQENAIENIKKEVKGLEE 400
                                        677789999*********************************************************98865 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.35
                       Bacillus_HBL  94 av.dkkdkaellellekLqeeiqqnqkevk 122
                                        ++ ++ +k  l+e+l+k+++e+   +k+ k
  gene1210|gene1210|rna1209|rna1209 402 KIrKQAEKRVLKEALKKIEDEVKDLEKALK 431
                                        564566778888899999998888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2018  (0.112555); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.87u 0.35s 00:00:01.22 Elapsed: 00:00:00.52
# Mc/sec: 3520.33
//
Query:       gene121|gene121|rna121|rna121  [L=367]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-59  201.4   0.7    3.2e-59  200.5   0.7    1.4  1  Septin       Septin
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.085   12.6   0.0    2.1  2  AAA_24       AAA domain
      0.015   15.8   0.1      0.097   13.2   0.0    2.2  2  ABC_tran     ABC transporter
      0.025   14.5   0.1       0.17   11.8   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
      0.034   14.2   0.4       0.24   11.5   0.1    2.5  3  MMR_HSR1     50S ribosome-binding GTPase
      0.041   13.2   0.3       0.24   10.7   0.0    2.3  3  AIG1         AIG1 family
      0.058   13.6   0.0       0.25   11.6   0.0    2.1  2  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.066   12.7   0.0       0.17   11.4   0.0    1.6  1  AAA_7        P-loop containing dynein motor region
      0.081   13.0   5.7      0.048   13.7   1.1    2.6  2  Dynamin_N    Dynamin family
       0.09   12.6   8.0       0.13   12.0   6.5    1.9  2  CdvA         CdvA-like coiled-coil domain
       0.16   12.1   0.0       0.41   10.8   0.0    1.7  1  AAA_33       AAA domain
       0.21   10.8   1.5       0.32   10.2   1.5    1.2  1  TMPIT        TMPIT-like protein


Domain annotation for each model (and alignments):
>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.5   0.7   2.2e-62   3.2e-59       2     275 ..      23     308 ..      22     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: 200.5 bits;  conditional E-value: 2.2e-62
                                    EEEEEEEEEEBTTSSCCCCCCTTSSSS----........................--------------S-EEEEEEEEE CS
                         Septin   2 gieftlmvvGesglGkttlintlfetdliee........................ekleeasekkkktveikkkkvviee 57 
                                    gi+f++m+vG++glGkt++in ++ +++ ++                        e++e++  + ++ ++i+ +k  + e
  gene121|gene121|rna121|rna121  23 GIDFNIMLVGSNGLGKTSFINQMLGDSVLSSdpflkpddeqqsndstkvsdkdgcEEQEDKYFHRNSLINIQISKFFVME 102
                                    99***********************9999999******************99877656666667888999********** PP

                                    TTCEEEEEEEE---BSSSSSHHCCCHHHHHHHHHHHHHHHHHCTSS--SS-----EEEEEEEE-TTSSSS-HHHHHHHHH CS
                         Septin  58 dgvklnltviDtpgfGdavdnskswepiveyideqfeeylreesklkRkkivDkRvHaclyfisPtghglkpldvelmkk 137
                                    ++++ ++t+ + +g Gd+v n+++w piv+ i+++f++yl++e++  R  i+DkR H+clyf++P+  ++k +d+++mk+
  gene121|gene121|rna121|rna121 103 KDFQTRITIAEIDGVGDNVCNHECWVPIVDLIQDNFKDYLEQERRNVRPLIKDKRFHVCLYFLEPNPSHVKLVDIKTMKE 182
                                    ******************************************************************************** PP

                                    HTTTS-EEEEESSGGGS-HHHHHHHHHHHHHHHHHTT--------SSSS-SCCHHHHHHHHHHC-SEEB-SSSSEEEESS CS
                         Septin 138 lsekvnliPviaKaDtltkeElkefKkkireeleeeeikiyklpdeeededeeakelseklkeslPfaivgsneliekkg 217
                                    +s+ +nliPv++K+D l + E +e  ++i e l +e+i++++  d  ++e        +  k+++Pf +++ +++ e++ 
  gene121|gene121|rna121|rna121 183 ISKMCNLIPVVGKSDLLSDIERQECSNRIAEALYRESIDVFH-LDVPDKE--------RIGKSEYPFFVIAKSTIPEDNN 253
                                    ******************************************.5555444........556899******9999988855 PP

                                    SEEEEEEETTEEEETT-TTT-SCCHHHHHHHHHCHHHHHHHHHHTHHHHHHHHHH-XX CS
                         Septin 218 kkvrgRkypWGvvevenekhsdFlkLrklllkthledLkevteellYetyRseklskl 275
                                     +  +R+ypWG++ +e    +dF  L ++l++++l  L e te ++Y+ y+++++ ++
  gene121|gene121|rna121|rna121 254 GC--SREYPWGTMILEKVVSNDFYLLVDILIAKNLIKLVEATE-IFYDDYKTKEIGRS 308
                                    54..79***********************************96.6*******998765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.7e-05     0.085       4      27 ..      27      51 ..      25      78 .. 0.87
   2 ?   -0.7   0.0      0.68     1e+03     126     171 ..     241     285 ..     232     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.7e-05
                         AAA_24  4 kiliyGpsgiGKTtlakel.gpkpl 27
                                   +i+++G++g GKT++++++ g+++l
  gene121|gene121|rna121|rna121 27 NIMLVGSNGLGKTSFINQMlGDSVL 51
                                   79*****************766655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.68
                         AAA_24 126 ifiahektrkdedpegeakytrlepklgkktanelkeevDlvlran 171
                                     +ia++++ +d ++ ++ +y + ++ l+k ++n +   vD+++  n
  gene121|gene121|rna121|rna121 241 FVIAKSTIPEDNNGCSR-EYPWGTMILEKVVSNDFYLLVDILIAKN 285
                                    57888888888888777.9999999999999999999999988655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.5e-05     0.097      14      73 ..      28      87 ..      25     158 .. 0.77
   2 ?   -0.3   0.2      0.92   1.4e+03      41      93 ..     294     346 ..     281     362 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                                   EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpe 73
                                   + +vG+nG GK+++++ ++g +   ++  l  +++ ++++ ++++ + g+ +qe++ f +
  gene121|gene121|rna121|rna121 28 IMLVGSNGLGKTSFINQMLGDSVLSSDPFLKPDDEQQSNDSTKVSDKDGCEEQEDKYFHR 87
                                   689*****************9988877773335555556666777777777777665555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.92
                                    EEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHHHHHTCHHHHHHHST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  41 eilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvrenesdeeiekalsklg 93 
                                    ei +d+ ++ke+ +++  +++g l ++ ++l +e++ + +e+++ i+++++kl 
  gene121|gene121|rna121|rna121 294 EIFYDDYKTKEIGRSI-TNKSGALGEDdKRLTREIQKKIKEDEKTIAEIRQKLI 346
                                    5556655566644444.4444444444366666665444466666777777664 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.17     102     124 ..      28      50 ..      19      76 .. 0.83
   2 ?   -0.6   0.0      0.75   1.1e+03      50      70 ..     190     209 ..     168     235 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                    EEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpele 124
                                    ++lvG+ G GK+++in++l++  
  gene121|gene121|rna121|rna121  28 IMLVGSNGLGKTSFINQMLGDSV 50 
                                    589***************99854 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.75
                                    EEEEE-GGG--HHHHHHHHHH CS
                    RsgA_GTPase  50 vivlnKiDlleeeeeleelke 70 
                                    + v+ K Dll++ e  +e ++
  gene121|gene121|rna121|rna121 190 IPVVGKSDLLSDIE-RQECSN 209
                                    55666777777666.222222 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00016      0.24       1      27 [.      27      53 ..      27      80 .. 0.85
   2 ?   -1.6   0.0       1.9   2.8e+03       9      21 ..     192     204 ..     190     215 .. 0.76
   3 ?   -2.4   0.0       3.3     5e+03      35      97 ..     326     338 ..     306     353 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                   EEEEEESTTSSHHHHHHHHHTSTEEES CS
                       MMR_HSR1  1 evaivGrpNvGKStLinaltgekaivs 27
                                   ++++vG    GK+++in+++g+ +  s
  gene121|gene121|rna121|rna121 27 NIMLVGSNGLGKTSFINQMLGDSVLSS 53
                                   589*****************9755444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                                    TSSHHHHHHHHHT CS
                       MMR_HSR1   9 NvGKStLinaltg 21 
                                     vGKS L++ + +
  gene121|gene121|rna121|rna121 192 VVGKSDLLSDIER 204
                                    59****9988755 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.3
                                    SEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH CS
                       MMR_HSR1  35 dinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeel 97 
                                    +i++                                                  k+k++++++
  gene121|gene121|rna121|rna121 326 EIQK--------------------------------------------------KIKEDEKTI 338
                                    3332..................................................233333333 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.24       2      29 ..      27      54 ..      26      75 .. 0.86
   2 ?   -1.0   0.0      0.59   8.9e+02     128     154 ..     132     157 ..     130     172 .. 0.76
   3 ?   -3.2   0.0       2.8   4.2e+03     190     206 ..     320     336 ..     288     343 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                   EEEEESSTTSSHHHHHHHHHTS--SS-- CS
                           AIG1  2 tivlvGktgnGkSaTgNsilgkkaFesk 29
                                   +i+lvG  g Gk + +N +lg+++ +s 
  gene121|gene121|rna121|rna121 27 NIMLVGSNGLGKTSFINQMLGDSVLSSD 54
                                   89********************998886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                                    GGTTCCHHHHHHHHH-HHHHHHHHHTT CS
                           AIG1 128 dleddsledylsksspeaLkevlkecg 154
                                    dl +d+++dyl+++  ++++ ++k  +
  gene121|gene121|rna121|rna121 132 DLIQDNFKDYLEQER-RNVRPLIKDKR 157
                                    577899******665.66888887544 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                                    TT--B-HHHHHHHHCCH CS
                           AIG1 190 gkpytnelyekikeeae 206
                                    +k++t e+++kike ++
  gene121|gene121|rna121|rna121 320 DKRLTREIQKKIKEDEK 336
                                    44445555555555444 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.25       2      24 ..      28      50 ..      27      77 .. 0.90
   2 ?   -2.1   0.0       2.8   4.2e+03      10      26 ..     193     209 ..     191     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                   EEEESSTTSSHHHHHHCHCT-CC CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkf 24
                                   ++lvG +g GKts++++++ d++
  gene121|gene121|rna121|rna121 28 IMLVGSNGLGKTSFINQMLGDSV 50
                                   89***************998765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                                    SSHHHHHHCHCT-CCC- CS
                            Roc  10 vGKtsllkrfvedkfse 26 
                                    vGK+ ll+ + +++ s+
  gene121|gene121|rna121|rna121 193 VGKSDLLSDIERQECSN 209
                                    8****999988877765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.17      22      54 ..      16      46 ..       3      54 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                          AAA_7 22 ysyllelllknkkpvllvGptGtGKtviikdll 54
                                   y+ +++  +  + +++lvG+ G GKt+ i+++l
  gene121|gene121|rna121|rna121 16 YRSFCKAGI--DFNIMLVGSNGLGKTSFINQML 46
                                   555555433..5789***************987 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   3.2e-05     0.048       1      28 [.      28      55 ..      28     177 .. 0.94
   2 ?    1.0   0.2      0.26   3.8e+02      50      79 ..     323     352 ..     265     364 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                                   EEEEEBTTTTHHHHHHHHHTS--S---S CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgp 28
                                   i++vGs   GK+S++n++lg+ +l ++p
  gene121|gene121|rna121|rna121 28 IMLVGSNGLGKTSFINQMLGDSVLSSDP 55
                                   799********************98876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                                    ...SSEEEET-EB--CHHHHHHHHHHHHHH CS
                      Dynamin_N  50 avkeelkekekkledfsevreeieketeki 79 
                                      +e +k+ +++++ + e+r+++ ++++  
  gene121|gene121|rna121|rna121 323 LTREIQKKIKEDEKTIAEIRQKLIEKKKYY 352
                                    222222233455555555555555544444 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   1.7e+03      65      87 ..     201     223 ..     196     226 .. 0.79
   2 ?   12.0   6.5     9e-05      0.13       4      72 ..     284     354 ..     283     358 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                           CdvA  65 nlkisyasGEidEeaYksaieai 87 
                                    +++ +  s+ i E  Y+++i+ +
  gene121|gene121|rna121|rna121 201 DIERQECSNRIAEALYRESIDVF 223
                                    6666778999******9999865 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9e-05
                           CdvA   4 kALeeLvsegdipkstye..eikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyas 72 
                                    k L +Lv+  +i+ ++y+  ei + +++++ +l e+ k l  +++k++ke e+ i+++ + l+  k  y+s
  gene121|gene121|rna121|rna121 284 KNLIKLVEATEIFYDDYKtkEIGRSITNKSGALGEDDKRLTREIQKKIKEDEKTIAEIRQKLIEKKKYYES 354
                                    67999********99995449*****************************************998888876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00027      0.41       2      50 ..      28      70 ..      28     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                         AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytr 50
                                   ++lvG +G GK+ ++ ++l   g  +lssd +++   ++d+q+ +d+t+
  gene121|gene121|rna121|rna121 28 IMLVGSNGLGKTSFINQML---GDSVLSSDPFLK---PDDEQQSNDSTK 70
                                   79**************988...999999998654...334444444444 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   0.00021      0.32      43     106 ..     299     361 ..     285     367 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                          TMPIT  43 kkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpkknglylklvlGnvnv 106
                                     ++ ke+ +s+++ + +++e++++ ++e+++++ke +k+++e+ + l +k+ +y + +l +++v
  gene121|gene121|rna121|rna121 299 DYKTKEIGRSITNKSGALGEDDKRLTREIQKKIKEDEKTIAEIRQKLIEKKKYYESKLL-EISV 361
                                    6788999999999999999*******************************999866555.4455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1207  (0.0673211); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2106.21
//
Query:       gene1211|gene1211|rna1210|rna1210  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 856.87
//
Query:       gene1212|gene1212|rna1211|rna1211  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.53   10.7   6.0        4.5    7.8   2.8    2.8  2  MerC      MerC mercury resistance protein


Domain annotation for each model (and alignments):
>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.15   2.7e+03      62      79 ..      42      59 ..      15      99 .. 0.51
   2 ?    7.8   2.8   0.00025       4.5      45     110 ..     178     238 ..     156     279 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.15
                               MerC 62 rktsvlvlgalGllillv 79
                                       r+t+ + ++++ l i ++
  gene1212|gene1212|rna1211|rna1211 42 RETRTFKVFVIFLDITNI 59
                                       333333333333333333 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00025
                               MerC  45 lvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetllfgslwqvltvlGaalLai 110
                                        ++++  ++++ +g + h++ + +v g   +++++ + fl+   ee +  ++    l+v G++ L+ 
  gene1212|gene1212|rna1211|rna1211 178 IFLCGEVATFNMGIKDHQDLYFFVAGTQIFVLVISSIFLN---EEYI--NQRRFLLIVSGLCTLIG 238
                                        4555556666666666666666666666666666666666...2222..22222233333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1812.85
//
Query:       gene1213|gene1213|rna1212|rna1212  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-24   86.2   3.6    1.8e-24   85.8   3.6    1.0  1  Ribosomal_S25  S25 ribosomal protein
     0.0037   17.6   0.3      0.059   13.7   0.1    2.0  2  Rrf2           Transcriptional regulator


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   3.6     2e-28   1.8e-24       3      99 ..       6     102 ..       2     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 2e-28
                      Ribosomal_S25   3 kkakkakaaaakaggkakkKKwskgkvkdklnnavlfdketydkllkevpkyklitpsvvserlkingslArraLr 78 
                                        +++k++ka +a++g ++ kKKw +gk+k+++++ v++++++++k+ k+v +++++t+++v +r ++n+ +A+++Lr
  gene1213|gene1213|rna1212|rna1212   6 QESKEKKALKAMSGTRKDKKKWGDGKKKEEVHKIVTVSEDLLSKVRKDVGRASVVTRYMVGSRHNLNLGVAENILR 81 
                                        678899999999999999********************************************************** PP

                      Ribosomal_S25  79 eleekgliklvskhraqviYt 99 
                                        +l e+g+i++v  +++++ Y+
  gene1213|gene1213|rna1212|rna1212  82 HLSEEGVIERVRGNSRMTMYA 102
                                        *******************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.018   1.6e+02      26      56 ..      31      61 ..       7      64 .. 0.78
   2 !   13.7   0.1   6.6e-06     0.059      31      61 ..      65      95 ..      57      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                               Rrf2 26 vsseeiaerqnispsylekilakLrkaglvk 56
                                        + ee+++ + +s+  l+k+ +   +a +v+
  gene1213|gene1213|rna1212|rna1212 31 KKKEEVHKIVTVSEDLLSKVRKDVGRASVVT 61
                                       5678999999**********99999999886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.6e-06
                                       HHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                               Rrf2 31 iaerqnispsylekilakLrkaglvksvrGk 61
                                       + +r+n++  ++e il++L+++g+++ vrG+
  gene1213|gene1213|rna1212|rna1212 65 VGSRHNLNLGVAENILRHLSEEGVIERVRGN 95
                                       56799*************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 683.90
//
Query:       gene1214|gene1214|rna1213|rna1213  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.23   10.4   0.2        0.3   10.0   0.2    1.1  1  AAA_6        Hydrolytic ATP binding site of dynein motor regi
        2.6    8.0   6.6       0.49   10.4   1.7    1.9  2  Dzip-like_N  Iguana/Dzip1-like DAZ-interacting protein N-term


Domain annotation for each model (and alignments):
>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   3.3e-05       0.3     230     294 ..      39     104 ..      18     116 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.3e-05
                              AAA_6 230 epeese.eelllralrdvnlpklvaeDvplfkglisdlFpgvelpesdyeeleeaieevlkekklq 294
                                        ++e+++ + l+ + l +v + k+++eD + +++ i+dlF +   +e  ++++ + +e+ ++ ++l+
  gene1214|gene1214|rna1213|rna1213  39 QREKEDnTALIKKILDNVDVDKIIEEDSESMEDAIDDLFFNDYSNEDCSDDIIDLCESDYAGESLS 104
                                        444444055555677889*********************997777777777777777766666665 PP

>> Dzip-like_N  Iguana/Dzip1-like DAZ-interacting protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.5     0.075   6.8e+02      74     110 ..      13      49 ..       5      55 .. 0.58
   2 ?   10.4   1.7   5.5e-05      0.49      13      51 ..      51      88 ..      45      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.075
                        Dzip-like_N  74 sqelLakslekleerlqeaqaeaeelekelakqeeel 110
                                         ++lL++++++   +l ++++e+e  ++e + +   +
  gene1214|gene1214|rna1213|rna1213  13 KKRLLSEEEADKLMQLIAQSMEIEDGQREKEDNTALI 49 
                                        3455566666666667777777777666666555444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.5e-05
                        Dzip-like_N 13 rklasvDvdrvakeldvdtLqenienitFcnlereeaak 51
                                       + l +vDvd++++e d +++++ i ++ F +  +e++  
  gene1214|gene1214|rna1213|rna1213 51 KILDNVDVDKIIEE-DSESMEDAIDDLFFNDYSNEDCSD 88
                                       56899******987.99********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1541.69
//
Query:       gene1215|gene1215|rna1214|rna1214  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-21   75.1   0.1    4.9e-21   74.5   0.1    1.3  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    6.2e-08   32.7   0.1    8.6e-08   32.3   0.1    1.2  1  Ribosomal_S15    Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.1   5.4e-25   4.9e-21       1      60 []       1      60 [.       1      60 [. 1.00

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 5.4e-25
                                       X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                    Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                       Ma+mhs+g+G+SgS++Py +  p+Wl+ s +e++  +v++ +kG++   IG  LRD+yGv
  gene1215|gene1215|rna1214|rna1214  1 MAKMHSSGRGRSGSVKPYDTAFPTWLTKSVDEIKADVVQMGNKGIPAPDIGKRLRDEYGV 60
                                       ***********************************************************8 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   9.6e-12   8.6e-08      17      68 ..      83     134 ..      71     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 9.6e-12
                                        SHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H CS
                      Ribosomal_S15  17 spevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv 68 
                                        +++ ++  l++r+n+l++hl+  +kD++++ +L+++ s+  ++ +Y+kr+ +
  gene1215|gene1215|rna1214|rna1214  83 KIPFDLESLVRRANTLRSHLNIYRKDNSAKYRLILVSSRMYRVARYYKRTMK 134
                                        67889999*****************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1069.47
//
Query:       gene1216|gene1216|rna1215|rna1215  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-24   86.2   3.6    1.8e-24   85.8   3.6    1.0  1  Ribosomal_S25  S25 ribosomal protein
     0.0037   17.6   0.3      0.059   13.7   0.1    2.0  2  Rrf2           Transcriptional regulator


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   3.6     2e-28   1.8e-24       3      99 ..       6     102 ..       2     103 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 2e-28
                      Ribosomal_S25   3 kkakkakaaaakaggkakkKKwskgkvkdklnnavlfdketydkllkevpkyklitpsvvserlkingslArraLr 78 
                                        +++k++ka +a++g ++ kKKw +gk+k+++++ v++++++++k+ k+v +++++t+++v +r ++n+ +A+++Lr
  gene1216|gene1216|rna1215|rna1215   6 QESKEKKALKAMSGTRKDKKKWGDGKKKEEVHKIVTVSEDLLSKVRKDVGRASVVTRYMVGSRHNLNLGVAENILR 81 
                                        678899999999999999********************************************************** PP

                      Ribosomal_S25  79 eleekgliklvskhraqviYt 99 
                                        +l e+g+i++v  +++++ Y+
  gene1216|gene1216|rna1215|rna1215  82 HLSEEGVIERVRGNSRMTMYA 102
                                        *******************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.018   1.6e+02      26      56 ..      31      61 ..       7      64 .. 0.78
   2 !   13.7   0.1   6.6e-06     0.059      31      61 ..      65      95 ..      57      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                               Rrf2 26 vsseeiaerqnispsylekilakLrkaglvk 56
                                        + ee+++ + +s+  l+k+ +   +a +v+
  gene1216|gene1216|rna1215|rna1215 31 KKKEEVHKIVTVSEDLLSKVRKDVGRASVVT 61
                                       5678999999**********99999999886 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.6e-06
                                       HHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                               Rrf2 31 iaerqnispsylekilakLrkaglvksvrGk 61
                                       + +r+n++  ++e il++L+++g+++ vrG+
  gene1216|gene1216|rna1215|rna1215 65 VGSRHNLNLGVAENILRHLSEEGVIERVRGN 95
                                       56799*************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 701.04
//
Query:       gene1217|gene1217|rna1216|rna1216  [L=493]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-46  156.2   0.0    1.2e-45  155.4   0.0    1.4  1  DEAD           DEAD/DEAH box helicase
    3.9e-33  114.1   0.0    1.1e-31  109.5   0.0    2.8  3  Helicase_C     Helicase conserved C-terminal domain
    0.00031   20.0   0.0    0.00049   19.4   0.0    1.2  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    0.00071   19.6   0.0     0.0015   18.5   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.79   10.0   0.0    2.4  3  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   0.0   3.4e-49   1.2e-45       1     174 [.     111     280 ..     111     282 .. 0.96

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 3.4e-49
                                        -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet...kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                        t+iQa+ +p +l+g+d+++ a+TGsGKTl f++p+l +  ++   ++ +gp +l+++PtreL+ q+ + + +f++ 
  gene1217|gene1217|rna1216|rna1216 111 TPIQAQGWPMALSGRDMVGIAQTGSGKTLSFILPALVHAKDQpplRRGDGPIVLVLAPTRELVMQIKKVADEFCEM 186
                                        89**********************************888777**99****************************** PP

                                        STSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  74 idlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                         dlr  +++gg + + q+++l++g+++v++tpgrl+dl ++g+  l +v+flVlDEadr+ld+gf++++++i+ ++
  gene1217|gene1217|rna1216|rna1216 187 FDLRSTAVYGGASSQPQIRALHEGAEVVIATPGRLIDLHEQGHAPLGRVTFLVLDEADRMLDMGFEPQLRKIIPKT 262
                                        ***********************************************************************99999 PP

                                        HHHCTTSTTTSEEEEEESSBSHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 150 pqitcdgklqrqvivlSATlpkdvk 174
                                               + +rq+++ SAT+pk+v+
  gene1217|gene1217|rna1216|rna1216 263 -------NPNRQTLMWSATWPKEVR 280
                                        .......56788*********8875 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.34   1.2e+03      19      61 ..     163     209 ..     154     217 .. 0.74
   2 ?    0.3   0.0      0.24   8.6e+02      12      59 ..     261     309 ..     253     323 .. 0.62
   3 !  109.5   0.0     3e-35   1.1e-31       4     111 .]     320     426 ..     317     426 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.34
                                        EEEEESSHH...HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHH CS
                         Helicase_C  19 ilifvntid...rlek.vklllekkgikvavlhgelpqnereeileq 61 
                                        +l+ ++t++   +++k ++ ++e +++++++++g  +++ ++++l++
  gene1217|gene1217|rna1216|rna1216 163 VLVLAPTRElvmQIKKvADEFCEMFDLRSTAVYGGASSQPQIRALHE 209
                                        68888888865555557788889999999999999888888777765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.24
                                        HTTTTSEEEEEESSHH.HHHH..HHHHHHHTTSTEEEESTTSTHHHHHHHH CS
                         Helicase_C  12 leeeggkilifvntid.rlek..vklllekkgikvavlhgelpqnereeil 59 
                                        +++ ++++l+ + t+  ++     +++  +  i+v++ + el++n++++ +
  gene1217|gene1217|rna1216|rna1216 261 KTNPNRQTLMWSATWPkEVRGlaESYM--NDYIQVVIGNEELKTNSKIKQV 309
                                        566777777777777754432433444..5568888888888888877543 PP

  == domain 3  score: 109.5 bits;  conditional E-value: 3e-35
                                        HHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                         Helicase_C   4 eallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                        ++ll  l  + +g++i++f+n ++++++++++l+++g+ +a+lhg+ +qn r+++l++f++g++ +Liat va+rG
  gene1217|gene1217|rna1216|rna1216 320 DKLLGVL-DKFKGDRIIVFCNMKRTCDDLEYVLNRSGYGAAALHGDKSQNIRDKVLDDFRSGRRPILIATEVAGRG 394
                                        5666666.67899*************************************************************** PP

                                        STSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        +d+++++lVinfd+p + ++y++riGRt+R++
  gene1217|gene1217|rna1216|rna1216 395 LDVNDIKLVINFDFPGSCEDYVHRIGRTARGN 426
                                        ******************************85 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.4e-07   0.00049      27     165 ..     299     436 ..     290     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-07
                      ERCC3_RAD25_C  27 ylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkk.....pyiyGetseaerlki 97 
                                         lk++sk k+++ v+n +  +  + L  + + +gD+iivf++   +  ++   l++     + ++G+ s++ r k+
  gene1217|gene1217|rna1216|rna1216 299 ELKTNSKIKQVIEVCNGRD-KEDKLLGVLDKFKGDRIIVFCNMKRTCDDLEYVLNRsgygaAALHGDKSQNIRDKV 373
                                        5788888899999999876.4456666778889********98888777777776522222679************ PP

                      ERCC3_RAD25_C  98 lqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffY 165
                                        l++f++  +   ++   v+   +D+ + + +i  ++  gs      r+Gr  r  +k   e+    f+
  gene1217|gene1217|rna1216|rna1216 374 LDDFRSGRR-PILIATEVAGRGLDVNDIKLVINFDFP-GSCEDYVHRIGRTARGNTK---EGISHTFF 436
                                        *****8855.5677789***************99875.899999******9998766...44444444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.3e-07    0.0015      31     168 ..     131     274 ..     124     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.3e-07
                                        ESTTSTHHHHHHHHHHHH-S............-EEEEESSHHHHHHHH...HHGGGGTGG....GEEEESSS-B-- CS
                             ResIII  31 maTGtGKTlvaaklierllkkgkee.......kflflvprkslleqtl...eefkkflseaykeigkkvsgdkkka 96 
                                        + TG+GKTl  + l + ++ k +          +l+l+p+++l+ q +   +ef ++++      + ++ g + ++
  gene1217|gene1217|rna1216|rna1216 131 AQTGSGKTLSFI-LPALVHAKDQPPlrrgdgpIVLVLAPTRELVMQIKkvaDEFCEMFDLRS---TAVYGGASSQP 202
                                        57******8653.3344444333336689999****************66666655555554...44444444443 PP

                                        ........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---.SEEEEEES CS
                             ResIII  97 .kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfke.avllglTA 167
                                          +   + ++++++t  +l         e+ ++  +r  +++ DEa r+ ++    + r+i+ k ++    l  +A
  gene1217|gene1217|rna1216|rna1216 203 qIRALHEGAEVVIATPGRLIDLH-----EQGHAPLGRVTFLVLDEADRMLDMgfePQLRKIIPKTNPnRQTLMWSA 273
                                        33357788999999999999988.....99999999999**********999665599998666554145566677 PP

                                        S CS
                             ResIII 168 T 168
                                        T
  gene1217|gene1217|rna1216|rna1216 274 T 274
                                        7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00022      0.79      11     111 ..     130     257 ..     127     271 .. 0.63
   2 ?   -3.7   0.0       3.8   1.4e+04      72      96 ..     363     386 ..     344     390 .. 0.63
   3 ?   -1.7   0.0      0.89   3.2e+03      40      76 ..     431     463 ..     411     479 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00022
                             AAA_22  11 tGesGtGKTtl..lrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka........... 70 
                                        ++++G+GKT++  l  l++ +d+ +  +  +p v +v +p  +     k+++ e+++ ++l+  a           
  gene1217|gene1217|rna1216|rna1216 130 IAQTGSGKTLSfiLPALVHAKDQPPLRRGDGPIV-LVLAPTRElvmQIKKVADEFCEMFDLRSTAvyggassqpqi 204
                                        6789999998722456666666555555555554.55555555588999999999999999999999999866666 PP

                             AAA_22  71 .........erlsseellealeqalrarav..............ielliiDEaqh.lr.s.eealee 111
                                                                + + ++              + +l++DEa++ l+   e +l++
  gene1217|gene1217|rna1216|rna1216 205 ralhegaevV--------------IATPGRlidlheqghaplgrVTFLVLDEADRmLDmGfEPQLRK 257
                                        6665433331..............22222233333334446667899********663424555544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.8
                             AAA_22  72 rlsseellealeqalraravielli 96 
                                        +++s+ +++++ + +r+ ++ ++li
  gene1217|gene1217|rna1216|rna1216 363 GDKSQNIRDKVLDDFRSGRR-PILI 386
                                        34555666666666666666.5555 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.89
                             AAA_22  40 pevvfvtlpsstsskdllrellralglelkaerlsse 76 
                                         +  f+t++ +++ ++l r+l +a ++  ++    +e
  gene1217|gene1217|rna1216|rna1216 431 ISHTFFTINDKGNARELIRMLKEAKQVVPSD----LE 463
                                        4445888888899999999998888875555....44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3565.01
//
Query:       gene1218|gene1218|rna1217|rna1217  [L=560]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-32  110.4   0.0      8e-32  109.1   0.0    1.8  1  Radical_SAM_C    Radical_SAM C-terminal domain
    5.3e-18   66.0   0.2    1.4e-16   61.4   0.0    2.8  3  Radical_SAM      Radical SAM superfamily
    4.8e-09   36.5   0.2    1.4e-08   35.0   0.2    1.9  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-05   24.4   0.1    5.7e-05   23.1   0.1    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0057   17.0   0.1      0.012   16.0   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.0   2.2e-35     8e-32       2      81 ..     301     380 ..     300     381 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 2.2e-35
                      Radical_SAM_C   2 dgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                        dg+K+yp+lvikgT+L el+k+++yk +s++e+vd++a+il+++pp++rv+R+++dip+ l+++g++h+n+rel++
  gene1218|gene1218|rna1217|rna1217 301 DGLKIYPTLVIKGTGLFELWKNNKYKNYSPDELVDILARILSFVPPWMRVYRVQRDIPMTLVSSGVEHGNIRELAL 376
                                        8*************************************************************************** PP

                      Radical_SAM_C  78 krlk 81 
                                        +r++
  gene1218|gene1218|rna1217|rna1217 377 ARMR 380
                                        **96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   3.8e-20   1.4e-16       9     158 ..      95     283 ..      84     292 .. 0.86
   2 ?    0.4   0.0      0.21   7.4e+02      74     101 ..     344     383 ..     306     425 .. 0.73
   3 ?   -0.8   0.0      0.49   1.8e+03      31      64 ..     514     546 ..     503     550 .. 0.76

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 3.8e-20
                                        S--TTTSCCTT...................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHH CS
                                        xxxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM   9 lrCsfCarpet...................vrregrgrslsveeileevkelkaekgvkevilgggepllypdfve 65 
                                        + C++C+ + +                     r ++  + + +e l+++k l ++ ++ e i++gg+ +  p+ ++
  gene1218|gene1218|rna1217|rna1217  95 NICVYCPGGPDsdfeystqsytgyeptsmrAIRSRYDPFDQARERLKQLKGLGHSIDKVEYIIMGGTFMSLPESYR 170
                                        34*************************7776667777777777777777777788887777777777888888888 PP

                                        HHHHHHHTC..................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHH CS
                                        xxxxxxxxx..................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM  66 llerlakla..................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlkl 120
                                        + +  +  +                  +  ++++ +t +t+pd   + +l ++le+g++r+++g++++ ++ v   
  gene1218|gene1218|rna1217|rna1217 171 DSFISKLHDalsghtsssveeairvgaEGRLKCVGITIETRPDfciRPHLSKMLEYGCTRIEIGVQSVYED-VAMD 245
                                        7777777778899999999999999999*******************************************.**** PP

                                        HTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM 121 mnrghtfeevlealeklreagikrvvdrivglpGende 158
                                        +nrght+  v e++ + ++ag+k v ++++ lp++ ++
  gene1218|gene1218|rna1217|rna1217 246 TNRGHTVGSVCESFGLSKDAGFKIVAHMMPNLPNVPMK 283
                                        ********************************998875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                                        C.........CCTEEEEEEECSSCHG...HHHHHHHHHTT CS
                                        x.........xxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                        Radical_SAM  74 a.........vpgiritvetngtlpd...eeklerllelg 101
                                                   ++i +t++++g+ +    e  l+r++++ 
  gene1218|gene1218|rna1217|rna1217 344 VppwmrvyrvQRDIPMTLVSSGVEHGnirELALARMRDYK 383
                                        1555555555578888888888888788777778888877 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.49
                                        HHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Radical_SAM  31 veeileevkelkaekgvkevilgggepllypdfv 64 
                                        + e +++++e + +  +  +i+g g+ ++y++f 
  gene1218|gene1218|rna1217|rna1217 514 IAEAERIAREEH-KSKKIAIISGVGTRNYYARFG 546
                                        567777787775.444999999999999999886 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   3.9e-12   1.4e-08       2     117 .]     387     547 ..     386     547 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.9e-12
                                        HHHHHHHHHHTHHHHHHHHHHH...HHHHHHSTTC...EEEEEEET...TEEEEEEEEEEEET............. CS
                     Acetyltransf_1   2 rdlvellvesffppnedaseee...feesfsleae...gllvaeed...geliGfisllkipd............. 55 
                                        rd+++ +v ++ ++++  +ee+   ++++    a+   ++++ +ed   + liG ++l+k                
  gene1218|gene1218|rna1217|rna1217 387 RDIRTREVGIKNIHESILPEEIelvRRDY---VANkgwETFLSYEDvkqDILIGLLRLRKCSVdtfrkelkdvdll 459
                                        67777788888888888888887767777...44411344443333333449999988888888888888888888 PP

                                        .................TSTTEEEEEEEEE...........SGGGTTSSHHHHHHHHHHHHHHHT.TESEEEEEEE CS
                     Acetyltransf_1  56 .................ekggvayieslaV...........speyrgkGlGsaLlealeeraree.gikkivlave 102
                                                          +g+  +i++l+V            ++y+++G+G++L+ ++e++aree   kki +   
  gene1218|gene1218|rna1217|rna1217 460 sgreeaklqeskyhpgvVNGNASIIRELHVygsavginksdGKKYQHQGYGTLLIAEAERIAREEhKSKKIAI--- 532
                                        88888888888888888788999999999999999******************************66699977... PP

                                        TTEHHHHHHHHHTTE CS
                     Acetyltransf_1 103 edndaairlYeklGF 117
                                         + ++++++Y ++G+
  gene1218|gene1218|rna1217|rna1217 533 ISGVGTRNYYARFGY 547
                                        699*******99**8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.6e-08   5.7e-05      61     111 ..     502     552 ..     479     557 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.6e-08
                    Acetyltransf_10  61 peyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavge 111
                                        ++y++qG+g+ L+ ++e+ a++++ ++++ + +    +++Y ++G++  g+
  gene1218|gene1218|rna1217|rna1217 502 KKYQHQGYGTLLIAEAERIAREEHKSKKIAIISGVGTRNYYARFGYVLEGP 552
                                        79*****************98887777*******************98765 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   3.4e-06     0.012      34      75 ..     502     548 ..     476     549 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.4e-06
                                        GGGTTSSHHHHHHHH......TT...SEEEEEEEEETHH..HHHHHHHHTTEE CS
                     Acetyltransf_7  34 peyrgkGiGraLlea......ae...kgiileqlelnae..kaikfYeklGFe 75 
                                        ++y+ +G+G+ L++       +e   k+i ++      +   ++++Y+++G++
  gene1218|gene1218|rna1217|rna1217 502 KKYQHQGYGTLLIAEaeriarEEhksKKIAII------SgvGTRNYYARFGYV 548
                                        58***********8534433211222222222......0235588******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3908.61
//
Query:       gene1219|gene1219|rna1218|rna1218  [L=819]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-25   88.3   0.4    1.5e-24   86.5   0.1    2.0  2  Adaptin_N        Adaptin N terminal region
    5.6e-21   74.9   0.0    1.4e-20   73.6   0.0    1.7  1  Coatamer_beta_C  Coatomer beta C-terminal region
      4e-19   68.9   0.2    1.1e-18   67.4   0.2    1.8  1  Coatomer_b_Cpla  Coatomer beta subunit appendage platform
    0.00072   19.6   0.6      0.014   15.5   0.0    3.0  3  Cnd1             non-SMC mitotic condensation complex subunit
     0.0017   18.7   0.0      0.011   16.1   0.0    2.4  2  HEAT_2           HEAT repeats
      0.004   17.5   0.0       0.01   16.2   0.0    1.7  1  AP4E_app_platf   Adaptin AP4 complex epsilon appendage platfo
      0.004   17.3   0.0      0.048   13.9   0.0    2.8  3  HEAT             HEAT repeat
     0.0059   16.7   0.2      0.023   14.8   0.1    2.1  1  Coatomer_g_Cpla  Coatomer subunit gamma-1 C-terminal appendag


Domain annotation for each model (and alignments):
>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.1   6.6e-28   1.5e-24       4     175 ..      13     186 ..      10     202 .. 0.90
   2 ?   -2.7   0.0      0.73   1.6e+03     203     227 ..     512     536 ..     479     626 .. 0.65

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 6.6e-28
                                        HCCHHHHHHCCSSS-SCHHHHHHHHHHHHHHHCT---GHHHHHHHCCCC.SS-CHHHHHHHHHHHHHCTTSCC... CS
                          Adaptin_N   4 riqqelaeilnsnkdddekkkeavkkliylialGedvsflffevvklva.skdfelKrlvYlylellaeesed... 75 
                                        ++++e+++ l sn  + + k+e +k  i+++ +Ged+  l  +++k +   k  elKrl Y ylell++++     
  gene1219|gene1219|rna1218|rna1218  13 MRKDEIMQKLRSN--SEQDKIEGMKQMIAQMSQGEDFGALTHKITKEILvVKSNELKRLFYYYLELLPKSRGTqsf 86 
                                        6677888888888..*******************************99889*****************98765566 PP

                                        .HHCCCCHHHHHHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCC CS
                          Adaptin_N  76 .lalLvtnslqkDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllr 150
                                         ++lL+ n+++kDl++pn+++rg+ +r++s++ +++l+  +++ ik+  +++++yvr++A  ++  +++k      
  gene1219|gene1219|rna1218|rna1218  87 eEMLLLSNQVRKDLEHPNEYVRGFVMRFVSTLDDQDLVGNFYKLIKDNFSHPNSYVRRNAYFCLGEIFSKMDTY-- 160
                                        69********************************************************************7777.. PP

                                        CCHHHHH..HHCTT-SSHHHHHHHHHH CS
                          Adaptin_N 151 kqlveei..kellsdkdpgvvlaAval 175
                                        k+ v+++  + ll d dp +++ A+  
  gene1219|gene1219|rna1218|rna1218 161 KE-VPDLlyHALLRDLDPNCLREAFVS 186
                                        55.555422567799999999999865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.73
                                        CS-HHHHHHHHHHHCC---SSHHHH CS
                          Adaptin_N 203 eldpwlqvkiiklltrlarqepeer 227
                                        ++d   +++i++++++l+ ++p+++
  gene1219|gene1219|rna1218|rna1218 512 SMDASSHLTIVSCIRSLISSNPQSE 536
                                        4444444555555555555555555 PP

>> Coatamer_beta_C  Coatomer beta C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   6.5e-24   1.4e-20      26     138 ..     563     675 ..     557     677 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 6.5e-24
                    Coatamer_beta_C  26 eedlsqatgakkkeeefasklkkvvqLtGfsDpvYaEayvkvnqfDivLdvlivNqtketLqnltvelatlgdlkl 101
                                        e++l++  +  +++e+ + ++k+v+qLtG+sDp+Y+Ea+ + +++++v+dvl++Nqt+++Lqn+ ++++t   +  
  gene1219|gene1219|rna1218|rna1218 563 ERNLNKLHEFLSRDESGEAEMKNVTQLTGLSDPIYVEATTSYTRYEVVMDVLLINQTSSYLQNVLLDFVTSQGFSA 638
                                        56677777777778889999******************************************************** PP

                    Coatamer_beta_C 102 vekpqsvtlaphdfakikatvkvsstetGvifGnivY 138
                                        +   +++ l  +++++ + t ++    +G i G+i++
  gene1219|gene1219|rna1218|rna1218 639 IFINTPFSLSSRSVVTKRFTFRIVDGSNGFISGSITF 675
                                        ***********************************98 PP

>> Coatomer_b_Cpla  Coatomer beta subunit appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.2     5e-22   1.1e-18       4     125 ..     690     806 ..     687     809 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 5e-22
                    Coatomer_b_Cpla   4 vvilndikidimdyikpakiseeeFremWaefeWEnkiavktkltd.lkeyleelvkktnmklltpeeeleeeaef 78 
                                        +++l+++k ++  +++p+k++++ FremW+e+eWEn++++k  ++  l+e++ e++k++n ++++    +e ++++
  gene1219|gene1219|rna1218|rna1218 690 TINLSEVKTSVSKFLEPKKMDSDGFREMWKELEWENTYTLKFATRRtLEEIFGEVCKTLNGEVVD----IECDESY 761
                                        699**************************************987655*****************8....5667789 PP

                    Coatomer_b_Cpla  79 lsanlyaksvfgedalanvsiekeeegkisgvvRiRsktqgialslg 125
                                         + n+   ++++  +l+nv++ + e   ++   RiRs+++gi++s+ 
  gene1219|gene1219|rna1218|rna1218 762 GVGNIACSTLQNVCVLINVCLRRGE--YVHFESRIRSRKEGIVKSVS 806
                                        99*******************9988..9***************9975 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       1.6   3.5e+03     100     149 ..      18      62 ..       6      68 .. 0.71
   2 !   15.5   0.0   6.2e-06     0.014      24     105 ..      94     171 ..      87     189 .. 0.72
   3 ?    0.2   0.0       0.3   6.8e+02      62     142 ..     369     450 ..     347     457 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                               Cnd1 100 iisklsdalnecsewgqitilefLlsyipkdkqeaeslveklcprlqhan 149
                                        i++kl     + se++ i+ ++ ++ ++++ +     l+ k+++++  ++
  gene1219|gene1219|rna1218|rna1218  18 IMQKLR----SNSEQDKIEGMKQMIAQMSQGED-FGALTHKITKEILVVK 62 
                                        444444....67888888888888888888887.7788888887776655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 6.2e-06
                               Cnd1  24 epLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllpd 99 
                                        +++rk L+ +++yVR   +  v+ L ++d+v   +f + +++  + +n+ V+ na ++l ei +k    +y+ +pd
  gene1219|gene1219|rna1218|rna1218  94 NQVRKDLEHPNEYVRGFVMRFVSTLDDQDLVG--NFYKLIKDNFSHPNSYVRRNAYFCLGEIFSKM--DTYKEVPD 165
                                        66778888888888888888888887777764..57777788888888888888888888888774..47777777 PP

                               Cnd1 100 iiskls 105
                                        ++++ +
  gene1219|gene1219|rna1218|rna1218 166 LLYHAL 171
                                        777655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.3
                               Cnd1  62 elaklleDenprVvanalaalteisek...senaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqea 134
                                        e ++ +  enp+ +  +l++l+ ++e    s ++  +   +++ +l +  n+++e +  +il++ +s   k +   
  gene1219|gene1219|rna1218|rna1218 369 EALEGIVSENPEMSYGSLTFLSSCLEVmrkSFEPGTEGGMEYVGYLEKLVNKINEVKYGKILRCCFSLLRKHAT-- 442
                                        5555566667777777777777666663223344556667888899999999***********99999999887.. PP

                               Cnd1 135 eslveklc 142
                                         +++ +++
  gene1219|gene1219|rna1218|rna1218 443 RDIFLRVV 450
                                        77776665 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.8e-06     0.011       7      78 ..      99     178 ..      93     188 .. 0.78
   2 ?   -3.4   0.0         6   1.3e+04      29      45 ..     562     579 ..     557     594 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                             HEAT_2   7 alendpdpevrraairaLgrignpealpaLvelled....edpavRraaaeaLgai....gd.pealpaLkelldd 73 
                                         l ++p+++vr  + r   ++++++++  + +l++d    ++++vRr+a   Lg+i    ++ +e+ ++L ++l++
  gene1219|gene1219|rna1218|rna1218  99 DL-EHPNEYVRGFVMRFVSTLDDQDLVGNFYKLIKDnfshPNSYVRRNAYFCLGEIfskmDTyKEVPDLLYHALLR 173
                                        57.89*********************999999996656558899**********8855443358888888888888 PP

                             HEAT_2  74 ddddv 78 
                                        d d+ 
  gene1219|gene1219|rna1218|rna1218 174 DLDPN 178
                                        87654 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6
                             HEAT_2  29 npealpaLvell.ededp 45 
                                        +++ l+ L+e+l +de+ 
  gene1219|gene1219|rna1218|rna1218 562 DERNLNKLHEFLsRDESG 579
                                        555566666666555554 PP

>> AP4E_app_platf  Adaptin AP4 complex epsilon appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.5e-06      0.01       3      81 ..     708     791 ..     706     811 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.5e-06
                     AP4E_app_platf   3 tisteeFgklWlslsserkqklkssqvstlsel.kalleklslhvVevignEgi....aAcqllssskvcllhvkv 73 
                                        ++  + F ++W++l+ e  ++lk    +tl+e+   ++++l+ +vV++  +E      +Ac +l++  ++l+ v++
  gene1219|gene1219|rna1218|rna1218 708 KMDSDGFREMWKELEWENTYTLKFATRRTLEEIfGEVCKTLNGEVVDIECDESYgvgnIACSTLQNV-CVLINVCL 782
                                        6667889****************55556666655**************9988542233799999999.99999999 PP

                     AP4E_app_platf  74 .sagvldvt 81 
                                          ++ +++ 
  gene1219|gene1219|rna1218|rna1218 783 rRGEYVHFE 791
                                        755555553 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0         8   1.8e+04       9      17 ..     100     108 ..      96     110 .. 0.85
   2 !   13.9   0.0   2.1e-05     0.048       4      29 ..     130     155 ..     127     157 .. 0.87
   3 ?   -1.1   0.0       1.5   3.3e+03       5      19 ..     184     199 ..     180     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 8
                                        HT-SSHHHH CS
                               HEAT   9 lsDpspeVR 17 
                                        l++p+  VR
  gene1219|gene1219|rna1218|rna1218 100 LEHPNEYVR 108
                                        7899*9999 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.1e-05
                                        HHHHHHT-SSHHHHHHHHHHHHHHHH CS
                               HEAT   4 lllkllsDpspeVReaAakaLgalae 29 
                                        l+  + s+p++ VR++A  +Lg++ +
  gene1219|gene1219|rna1218|rna1218 130 LIKDNFSHPNSYVRRNAYFCLGEIFS 155
                                        6677899****************987 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.5
                                        HHHH.HT-SSHHHHHH CS
                               HEAT   5 llkl.lsDpspeVRea 19 
                                        +++l lsDps   R+a
  gene1219|gene1219|rna1218|rna1218 184 FVSLhLSDPSLALRYA 199
                                        556659****999998 PP

>> Coatomer_g_Cpla  Coatomer subunit gamma-1 C-terminal appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     1e-05     0.023       6     114 ..     708     808 ..     701     809 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                                        E---S-HHHHHHHH-STT-EEEEEEESS---HHHHHHHHHHHHT-EE-TTTT---SS-SEEEEEEEEEETTS-EEE CS
                    Coatomer_g_Cpla   6 pvavsnFeaaWeeleseaeavetfaLssvksleeavdkliellgmqplegsdkvpenassHtLklaGkfvggekvl 81 
                                        +++   F+++W ele   e++ t ++++  +lee   +++++l+ ++++       ++s  + ++a  ++   +v 
  gene1219|gene1219|rna1218|rna1218 708 KMDSDGFREMWKELEW--ENTYTLKFATRRTLEEIFGEVCKTLNGEVVDIEC----DESYGVGNIACSTLQ--NVC 775
                                        455568**********..99999999********************999987....444334445554444..566 PP

                                        EEEEEEE..SS.EEEEEEEEESSHHHHHHHHHH CS
                    Coatomer_g_Cpla  82 vrarlalssskgvtlkltvRsedeevaelvlsa 114
                                        v +++ l  ++ v  +  +Rs +e +++ v ++
  gene1219|gene1219|rna1218|rna1218 776 VLINVCLRRGEYVHFESRIRSRKEGIVKSVSAV 808
                                        666666666789************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (819 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 4809.25
//
Query:       gene1220|gene1220|rna1219|rna1219  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-25   86.8   5.0    9.4e-06   26.3   0.1    7.1  7  WD40         WD domain, G-beta repeat
      1e-17   64.2   0.9     0.0001   22.6   0.0    4.7  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    1.6e-05   24.9   0.1    8.5e-05   22.5   0.1    2.1  2  eIF2A        Eukaryotic translation initiation factor eIF2A
     0.0067   15.8   1.7       0.41    9.9   0.1    2.6  2  WD40_like    WD40-like domain
  ------ inclusion threshold ------
      0.028   13.1   0.0       0.17   10.5   0.0    2.1  2  Nup160       Nucleoporin Nup120/160
       0.04   13.4   0.0       0.11   12.0   0.0    1.6  1  DsbC_N       Disulfide bond isomerase protein N-terminus


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0028       8.5       7      38 .]      12      46 ..       6      46 .. 0.69
   2 !   21.0   0.0   1.5e-07   0.00045       6      38 .]      61      95 ..      56      95 .. 0.81
   3 !   17.7   0.0   1.6e-06    0.0047       5      38 .]     102     136 ..      98     136 .. 0.87
   4 !   26.3   0.1   3.1e-09   9.4e-06      10      38 .]     153     183 ..     149     183 .. 0.88
   5 ?    5.0   0.0     0.017        51      11      26 ..     218     233 ..     209     245 .. 0.78
   6 ?    2.3   0.0      0.12   3.5e+02       3      37 ..     251     284 ..     249     285 .. 0.66
   7 ?    1.8   0.0      0.17     5e+02       9      28 ..     301     319 ..     289     327 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0028
                                       EESSSS.EEEEE.EETTSSE.EEEEETTSEEEEEE CS
                               WD40  7 ltGHss.vtsla.fspdgaw.lasGsdDgtvriWd 38
                                       l GH++ v +l+ +  +g+  l s+s+D++v  Wd
  gene1220|gene1220|rna1219|rna1219 12 LNGHKDeVKGLKiVRVSGREiLYSSSKDKKVFSWD 46
                                       5799555888854222333335699*********9 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.5e-07
                                       EEE.SS.SSEEEEEEETTSSEEEE.EETTSEEEEEE CS
                               WD40  6 tlt.GH.ssvtslafspdgawlas.GsdDgtvriWd 38
                                        ++ GH + +++l++s+dg+++++ Gs Dg  riWd
  gene1220|gene1220|rna1219|rna1219 61 LYEgGHsKRINGLDVSKDGRMMVTvGS-DGIGRIWD 95
                                       4545**888************885277.*******9 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 1.6e-06
                                        EEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        + l+GH  +v +++ +++ + ++sGs D+t  +++
  gene1220|gene1220|rna1219|rna1219 102 KRLEGHtRDVLCVSINSNDTKIVSGSVDRTMNLYN 136
                                        6699**777*****999999999*******99987 PP

  == domain 4  score: 26.3 bits;  conditional E-value: 3.1e-09
                                        S.SSEEEEEEETTSSE.EEEEETTSEEEEEE CS
                               WD40  10 H.ssvtslafspdgaw.lasGsdDgtvriWd 38 
                                        H ++++++af+p     lasGs Dgtv+iWd
  gene1220|gene1220|rna1219|rna1219 153 HrGWINCVAFHPIEENvLASGSTDGTVKIWD 183
                                        8788*****99999994479999*******9 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.017
                                        SSEEEEEEETTSSEEE CS
                               WD40  11 ssvtslafspdgawla 26 
                                        +svt++afs+dg+ l+
  gene1220|gene1220|rna1219|rna1219 218 KSVTAMAFSKDGSILT 233
                                        67***********985 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.12
                                        EEEEEESSSSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   3 clrtltGHssvtslafspdgawlasGsdDgtvriW 37 
                                        c+++l++ ++v+s+a+    + +a G+ D +v iW
  gene1220|gene1220|rna1219|rna1219 251 CIQSLDAITPVRSIAVGEAEPVIALGT-DDSVIIW 284
                                        556665335677886666666665588.******* PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.17
                                        SSSSEEEEEEETTSSEEEEE CS
                               WD40   9 GHssvtslafspdgawlasG 28 
                                        G  +v++l+   +g+ l +G
  gene1220|gene1220|rna1219|rna1219 301 GN-GVRCLSLAFSGNALYCG 319
                                        33.69999855555554444 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   7.2e-05      0.21      28      72 ..      57     101 ..      16     119 .. 0.83
   2 ?   -0.4   0.0      0.48   1.4e+03      51      79 ..     110     138 ..     103     150 .. 0.69
   3 !   12.3   0.0   5.3e-05      0.16      19      75 ..     132     192 ..     123     196 .. 0.78
   4 !   22.6   0.0   3.4e-08    0.0001      20      81 ..     200     260 ..     195     269 .. 0.89
   5 !   12.5   0.0   4.4e-05      0.13       9      68 ..     272     331 ..     265     334 .] 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-05
                        ANAPC4_WD40  28 rvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkv 72 
                                        ++ +l e ++++++++L  ++dg++++ + sdg  r+ d e +k 
  gene1220|gene1220|rna1219|rna1219  57 KILKLYEGGHSKRINGLDVSKDGRMMVTVGSDGIGRIWDTEVKKS 101
                                        5666788899*****************************997765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.48
                        ANAPC4_WD40  51 klLavaysdgevrlldaesgkvvhslsvk 79 
                                         +L+v+++ +  ++++ +  ++++ +++ 
  gene1220|gene1220|rna1219|rna1219 110 DVLCVSINSNDTKIVSGSVDRTMNLYNTR 138
                                        47888888888888877766666666554 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 5.3e-05
                        ANAPC4_WD40  19 llvfRlngqrvwtl...eedkedsevrsLaWkp.dgklLavaysdgevrlldaesgkvvhs 75 
                                        ++++ + g+ + ++   +e+ + + ++++a++p ++++La +  dg+v++ d  s++ +++
  gene1220|gene1220|rna1219|rna1219 132 MNLYNTRGELIAKMgkdTEKMHRGWINCVAFHPiEENVLASGSTDGTVKIWDLDSQEHMQT 192
                                        55555666666666665667778889*****985689****************99987765 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 3.4e-08
                        ANAPC4_WD40  20 lvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                           R + ++v  + + +e+++v+++a+++dg++L  + + g+v l++  ++++++sl++ + 
  gene1220|gene1220|rna1219|rna1219 200 DYERAKEKKVLPV-DYDESKSVTAMAFSKDGSILTYGEKSGKVYLVNLDTKECIQSLDAITP 260
                                        5679999999999.788999***********************************9987655 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 4.4e-05
                        ANAPC4_WD40   9 LiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldae 68 
                                         iAl+t+d+ ++   +n + + + + ++ ++ vr+L+   +g+ L  + s g++ ll+  
  gene1220|gene1220|rna1219|rna1219 272 VIALGTDDSVIIWETINSRVIASHNLKEIGNGVRCLSLAFSGNALYCGLSTGSIILLELR 331
                                        69**********************99****************************999875 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.8e-08   8.5e-05      68     141 ..     115     193 ..      90     208 .. 0.81
   2 ?   -0.9   0.0      0.42   1.2e+03     105     143 ..     222     257 ..     199     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.8e-08
                                        -TTSS-EEEEESSSSCEEEEEECSCEEEEEEEEES-.......-EEEE-TTSSEEEEE-TTSSS-EEEEEETTTTE CS
                              eIF2A  68 spkskefaviyGkmpakvslfdlkvkviskleeqkr.......NtiffspkgklvllaGfgnlaGeleiwdvkkkk 136
                                        s +s++  ++ G ++++++l+++++++i+k++++ +       N++ f+p ++ vl +G  ++ G+++iwd ++ +
  gene1220|gene1220|rna1219|rna1219 115 SINSNDTKIVSGSVDRTMNLYNTRGELIAKMGKDTEkmhrgwiNCVAFHPIEENVLASG--STDGTVKIWDLDSQE 188
                                        67888899***************97777777665422333444************9986..889**********99 PP

                                        EEEEE CS
                              eIF2A 137 kiaka 141
                                        +++++
  gene1220|gene1220|rna1219|rna1219 189 HMQTY 193
                                        99886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.42
                                        EEEE-TTSSEEEEE-TTSSS-EEEEEETTTTEEEEEEE- CS
                              eIF2A 105 tiffspkgklvllaGfgnlaGeleiwdvkkkkkiakaea 143
                                        ++ fs+ g ++    +g+ +G++ +++ ++k++i++++a
  gene1220|gene1220|rna1219|rna1219 222 AMAFSKDGSILT---YGEKSGKVYLVNLDTKECIQSLDA 257
                                        455555555543...566677777777777777776665 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.2    0.0056        17       5     110 ..      72     185 ..      68     195 .. 0.54
   2 !    9.9   0.1   0.00014      0.41       5     106 ..     222     327 ..     218     332 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0056
                          WD40_like   5 sidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillsllenee....e 75 
                                         +d+sk+g +++  g d   ++ ++e ++s+ ++ + +d v+ v + ++d +i+ +++D t+ l+  + e      
  gene1220|gene1220|rna1219|rna1219  72 GLDVSKDGRMMVTVGSDGIGRIWDTEVKKSKRLEGHTRD-VLCVSINSNDtKIVSGSVDRTMNLYNTRGELiakmG 146
                                        578888888888888888888888888887776555554.555555555546777788877755443333211111 PP

                          WD40_like  76 venekie....edistvkviddklliGtnkGsiyvfskd 110
                                         ++ek++    + +++  + ++ l+ G++ G++ +++ d
  gene1220|gene1220|rna1219|rna1219 147 KDTEKMHrgwiNCVAFHPIEENVLASGSTDGTVKIWDLD 185
                                        122222211113334444445555566666666666665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00014
                          WD40_like   5 sidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillslleneeevene 79 
                                        ++ +sk+gs++ yG k+ k+ +++l+++e +++++ ++  v  + + + + +i  +t D  i+     n+ ++ ++
  gene1220|gene1220|rna1219|rna1219 222 AMAFSKDGSILTYGEKSGKVYLVNLDTKECIQSLDAITP-VRSIAVGEAEpVIALGTDDSVII-WETINSRVIASH 295
                                        6789****************************9998874.33333333343666667666664.444455555555 PP

                          WD40_like  80 kiee...distvk..viddklliGtnkGsiyv 106
                                        +++e    + + +    ++ l+ G ++Gsi +
  gene1220|gene1220|rna1219|rna1219 296 NLKEignGVRCLSlaFSGNALYCGLSTGSIIL 327
                                        44431115555431145777777777777765 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.092   2.8e+02     226     268 ..      25      67 ..      22     129 .. 0.74
   2 ?   10.5   0.0   5.6e-05      0.17     229     255 ..     166     192 ..     139     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.092
                                        ....TTTEEEEEETT-EEEEEETTTTEEEEEEE--.-SSSTTS- CS
                             Nup160 226 vei.gqtylfalsrdgkLrvWnlltgkclatidllrdeeaqdes 268
                                        v++ g+ +l++ s d+k+  W+l ++   + + +l ++++   s
  gene1220|gene1220|rna1219|rna1219  25 VRVsGREILYSSSKDKKVFSWDLHSKIESEFGKIL-KLYEGGHS 67 
                                        55568888888888998888888888777766666.34444444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.6e-05
                                        TTTEEEEEETT-EEEEEETTTTEEEEE CS
                             Nup160 229 gqtylfalsrdgkLrvWnlltgkclat 255
                                        ++++l++ s dg++++W+l+++ ++ t
  gene1220|gene1220|rna1219|rna1219 166 EENVLASGSTDGTVKIWDLDSQEHMQT 192
                                        79********************99987 PP

>> DsbC_N  Disulfide bond isomerase protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.5e-05      0.11      19      44 ..      17      43 ..      15      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                                       -SSTTEE--EE.TTEE-EEESSSS-EE CS
                             DsbC_N 19 spipGLyEVvi.ggqvlYtdadgkyli 44
                                        +++GL+ V++ g+++lY +++ k+++
  gene1220|gene1220|rna1219|rna1219 17 DEVKGLKIVRVsGREILYSSSKDKKVF 43
                                       689******99999********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 1963.57
//
Query:       gene122|gene122|rna122|rna122  [L=431]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-41  140.4   0.0    1.4e-40  139.7   0.0    1.3  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.033   13.8   0.0    1.7  1  PI-PLC-X  Phosphatidylinositol-specific phospholipase C, X do


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   0.0   1.5e-44   1.4e-40       1     258 [.     169     421 ..     169     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 1.5e-44
                                    TTTTTTTSS......TTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECC CS
                           GDPD   1 HRGasgnlp......EnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkia 74 
                                    HRG++ n        EnT+ sf++A+ +G + +E+DvqlT+D+vpV++HDf ++      g   ++++tl+e+ +l   +
  gene122|gene122|rna122|rna122 169 HRGCGTNGHpstrmmENTVSSFKEAYRRGLKWVEMDVQLTRDEVPVIFHDFVIQSGASRIG---INEITLKEFLHLV--G 243
                                    9****9987799*************************************************...*************..3 PP

                                    TTCCCCSCCCSSGCCB...BHHHHHHH.HHHCCSEEEEEEECCCCCCCHHHH..HHTCHHHCCCCCSCHHTT..STTCSC CS
                           GDPD  75 kenkaqlsenrvrlefpfptleevlkk.pqnvglnieikipmlseakeeeel..qivkeilksvdeilkkvlkkadkrkv 151
                                    ++      ++ ++     +tl+ +l+  + ++g+nieik+p  se ++ +++    + ++++ v     ++++ ++k++v
  gene122|gene122|rna122|rna122 244 NQD---EENHSLP-----CTLSRFLEQiDDEHGVNIEIKYPLPSEEGRYKLKdlVPAERVVEKVV----EMVQRSRKQRV 311
                                    333...4455555.....9********************************53322233333333....45689****** PP

                                    EEEESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E...EECHCCCCCCCTCCCCHHCCCHC.CCEB.CHHHHHHHTT-EE CS
                           GDPD 152 ifssfnpdilkllrekqpklpllflteggteaead..ssleraakfakadallgevsavae.glgdpdlVkraksrglvv 228
                                    ifssf+p il +++ ++p+ ++++lte +    ++  ++l  a+ f+++ +l g+v   +  ++++ d Vk +ks  l+ 
  gene122|gene122|rna122|rna122 312 IFSSFHPYILLMVKLRLPNFNIFMLTEAKGGEGNPytNTLYDALYFCTKLGLDGVVLDWSCmAINPIDIVKIFKSFDLKT 391
                                    ***************************99999888888999999999999999998775541444679************ PP

                                    EEBSB-THSHHHHHHHHCCC-SEEEES-HH CS
                           GDPD 229 hvytvnnedeeemkrlleagvdgvitDfpd 258
                                    +vy+   +d++ + +l+eag +g+i D+ +
  gene122|gene122|rna122|rna122 392 FVYGDEINDKNIISILKEAGAHGIIIDDLE 421
                                    ***************************875 PP

>> PI-PLC-X  Phosphatidylinositol-specific phospholipase C, X domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.7e-06     0.033      26      91 ..     184     257 ..     179     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.7e-06
                                    ---SS-HHHHHHTT--EEEEEE-...TT.SEEEETTEEE.........EEEHHHHHHHHHHHHHHSTT--EEEE CS
                       PI-PLC-X  26 essveayrnaLlrGcRcvEidvwdgedeepvvlhgytlt........kkikfrdvleaikdyafktselPvivs 91 
                                    e +v+++++a +rG + vE+dv+  +de pv++h   +         ++i+++++l+ + +   ++ +lP  +s
  gene122|gene122|rna122|rna122 184 ENTVSSFKEAYRRGLKWVEMDVQLTRDEVPVIFHDFVIQsgasrigiNEITLKEFLHLVGNQDEENHSLPCTLS 257
                                    56788999**************************8777666666677899999999988888888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2721.43
//
Query:       gene1221|gene1221|rna1220|rna1220  [L=617]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-40  137.5   2.7      4e-40  137.3   1.3    1.8  2  DEAD_2        DEAD_2
    2.6e-34  118.9   0.1    8.1e-34  117.2   0.0    1.8  2  Helicase_C_2  Helicase C-terminal domain
    3.4e-07   30.4   0.0    2.4e-06   27.6   0.0    2.2  1  ResIII        Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.024   14.4   0.0        1.3    8.7   0.0    2.4  2  DEAD          DEAD/DEAH box helicase
      0.037   13.9   0.0       0.12   12.3   0.0    1.9  1  SWIB          SWIB/MDM2 domain
      0.073   12.5   0.3         16    4.9   0.0    2.9  3  PhoH          PhoH-like protein
      0.098   12.8   0.0        9.8    6.4   0.0    2.8  2  Trans_coact   Phage late-transcription coactivator
       0.11   11.2   0.0       0.94    8.1   0.0    2.0  1  SNF2_N        SNF2 family N-terminal domain
       0.12   11.9   0.0       0.48   10.0   0.0    1.9  2  AAA_25        AAA domain


Domain annotation for each model (and alignments):
>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.3   1.3     2e-43     4e-40       1     171 [.      77     228 ..      77     233 .. 0.94
   2 ?   -2.2   0.0       1.4   2.8e+03      27      54 ..     486     513 ..     477     525 .. 0.67

  Alignments for each domain:
  == domain 1  score: 137.3 bits;  conditional E-value: 2e-43
                                        EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTTTTT CS
                             DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeekeekCsf 76 
                                        yc+RTh ql+q+++elk+l +++      ++v+LgSRk +C+ne++++ k+++a+ne Ck+ +k+        C f
  gene1221|gene1221|rna1220|rna1220  77 YCTRTHTQLAQAINELKRL-DVR-----CNAVVLGSRKIYCLNEKILQYKNSDAMNEGCKQIVKEG------LCAF 140
                                        9*****************9.455.....59**********************************99......7*** PP

                                        -SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEE CS
                             DEAD_2  77 fenleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslkgislknsivi 152
                                        ++  e       +   +v+d+edl+ +g++++lCPYy+s+   +++di++lpYq+L+ ++ r+s++ i+++ sivi
  gene1221|gene1221|rna1220|rna1220 141 YDGGE------LFDGCGVLDVEDLTLIGKEQRLCPYYASKIYSHQCDIVFLPYQLLFTREGRRSVD-IDVRGSIVI 209
                                        *8884......34579*************************************************9.********* PP

                                        ECTCCCHHHHHHHCC-EEE CS
                             DEAD_2 153 lDEAhNiedvceeaasvei 171
                                        +DEAhNi d +++++ + i
  gene1221|gene1221|rna1220|rna1220 210 VDEAHNICDSVIQMNTSTI 228
                                        ************9998766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                                        S---EEEE--CCCC-SCHHCCCHHCCCC CS
                             DEAD_2  27 ekvkvviLgSRknlCineevkkekkeka 54 
                                        ++++  +L  +k+ Ci  +v+  + ++ 
  gene1221|gene1221|rna1220|rna1220 486 TNFQEYVLEVKKEACILFAVMGGRLSEG 513
                                        4677788999999999999987554333 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.9   3.8e+03     104     135 ..      57      89 ..      44      93 .. 0.72
   2 !  117.2   0.0   4.1e-37   8.1e-34       2     170 ..     443     595 ..     442     596 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                       Helicase_C_2 104 eakreylde.kgkknsgkewylpealravnQai 135
                                        + + ++l++  +++n+g  +y+ ++ +++ Qai
  gene1221|gene1221|rna1220|rna1220  57 NHRNRVLEQaLFQRNGGTVFYCTRTHTQLAQAI 89 
                                        445555554234467899999999999999997 PP

  == domain 2  score: 117.2 bits;  conditional E-value: 4.1e-37
                       Helicase_C_2   2 lellevvp.ggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsE 76 
                                        l+++++v+ gg+++f pS ++l+ ++e+  +     +++ + e +  ++++ + e+k+   + +il+av++G+lsE
  gene1221|gene1221|rna1220|rna1220 443 LNFSNAVRdGGMVCFLPSKAYLKILREVCGDMIG--RKKALYE-DLTNFQEYVLEVKK---EACILFAVMGGRLSE 512
                                        56666666599******************99874..4455666.67888888888888...9************** PP

                       Helicase_C_2  77 GidfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllD 152
                                        G++f+d+l+r++++vg+P+p+  d e++++ +         +g+ + +  a+r vnQ +GR++RhkdDy+++vllD
  gene1221|gene1221|rna1220|rna1220 513 GMNFNDKLCRLLMVVGVPYPSQ-DLELKERIK--------HNGRGYTTSIAMRIVNQTLGRALRHKDDYAVLVLLD 579
                                        *******************986.676655544........3567899***************************** PP

                       Helicase_C_2 153 eRfakeeireklpkwlre 170
                                        +R+a+  +++ +++w+re
  gene1221|gene1221|rna1220|rna1220 580 RRYAQ--LSKLISSWIRE 595
                                        ****9..5599****997 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.2e-09   2.4e-06       2     147 ..       4     219 ..       3     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                                        -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH..HHG. CS
                             ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl..eef. 74 
                                        +el+e Q++ i++ ++ +  +++  g++  +TGtGKT+ +++++  +    +    + l +r+ +leq+l  +   
  gene1221|gene1221|rna1220|rna1220   4 IELYEGQKQFIKDAKKIV--DGEAVGIFSSPTGTGKTMSLLSAVVDYIDVDG----VELNHRNRVLEQALfqR-Ng 72 
                                        7899**********8655..7********************99999999866....55666666666666431.12 PP

                                        .....................................................GGGTGG....GEEEESSS-B--. CS
                             ResIII  75 .....................................................kkflseaykeigkkvsgdkkka. 96 
                                                                                             +                    + 
  gene1221|gene1221|rna1220|rna1220  73 gtvfyctrthtqlaqainelkrldvrcnavvlgsrkiyclnekilqyknsdamN--------------------Eg 128
                                        333455555555555555557777777777777777777665554333333220....................03 PP

                                        ...................................................-SEEEEEHHHHHHTH........HH CS
                             ResIII  97 ............................................kekdstnkkilvttiqsldadseeeeeeseel 128
                                                                                    +++ s++++i++  +q l  ++      +   
  gene1221|gene1221|rna1220|rna1220 129 ckqivkeglcafydggelfdgcgvldvedltligkeqrlcpyyaSKIYSHQCDIVFLPYQLLFTRE----GRRSVD 200
                                        33333333444445555555888888888888889999999*9999*******************9....777778 PP

                                        HTTT-SEEEEETGGGTTS. CS
                             ResIII 129 lrdrfdviiiDEaHrlgak 147
                                         + r  ++i+DEaH++ ++
  gene1221|gene1221|rna1220|rna1220 201 IDVRGSIVIVDEAHNICDS 219
                                        888888********99885 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00066       1.3      12      65 ..      18      90 ..       7     126 .. 0.66
   2 ?    3.2   0.0     0.033        65     123     144 ..     206     227 ..     158     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00066
                                       H...TTCEE.EEEESTTSSHHHHHHHHHHHHHHHS...............TTSTS-EEEEEESSHHHHHHHHH CS
                                       x...xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 12 l...gggdv.lvaaeTGsGKTlaflipvlqivyet...............kgktgpkalivePtreLaeqtln 65
                                           +g+ v + + +TG+GKT+  l +v++ +  +                +++g  +++ + t+    q +n
  gene1221|gene1221|rna1220|rna1220 18 KkivDGEAVgIFSSPTGTGKTMSLLSAVVDYIDVDgvelnhrnrvleqalFQRNGGTVFYCTRTHTQLAQAIN 90
                                       43335554427899***********999988733366555555555555544455555555555555555555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.033
                                        EEEEEETHHHHHHTTTHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 123 rflVlDEadrlldqgfsdfinr 144
                                        +++++DEa+++ d+  +   ++
  gene1221|gene1221|rna1220|rna1220 206 SIVIVDEAHNICDSVIQMNTST 227
                                        689*******999866665555 PP

>> SWIB  SWIB/MDM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.1e-05      0.12      24      67 ..     230     273 ..     217     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
                               SWIB  24 vkklweYIkennLqdpedkreilcDekLkklfggkdrvkffemp 67 
                                         + + +YIk+++++++   + ++ D  L+++++   r++ f ++
  gene1221|gene1221|rna1220|rna1220 230 FMTISKYIKAMEMYKERYSERVRRDGVLERILEVLRRIEAFGLM 273
                                        67899***************************999999999875 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0081        16       8      42 ..       9      47 ..       5      56 .. 0.69
   2 ?   -1.7   0.0      0.81   1.6e+03     135     156 ..      87     108 ..      82     134 .. 0.77
   3 ?    4.3   0.0     0.012        25     121     141 ..     206     226 ..     202     279 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0081
                                       HHHHHHHHHH....H-SEEEEE--TTSSTTHHHHHHHHH CS
                               PhoH  8 eQkeylealk....kndivfaiGpaGtGKtylavalave 42
                                       +Qk++++  k     + + +   p+GtGKt+  +++ v+
  gene1221|gene1221|rna1220|rna1220  9 GQKQFIKDAKkivdGEAVGIFSSPTGTGKTMSLLSAVVD 47
                                       56666665554443566888899*******866665555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.81
                                        HHHHHHTTB-TT-EEEEEE--- CS
                               PhoH 135 qmkmfltRlGenskvvvtGdvt 156
                                        q    l Rl+  + +vv+G+ +
  gene1221|gene1221|rna1220|rna1220  87 QAINELKRLDVRCNAVVLGSRK 108
                                        5556689**********99876 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.012
                                        EEEEE-SGGG--HHHHHHHHT CS
                               PhoH 121 afvilDEAQnttkeqmkmflt 141
                                        ++vi+DEA n+  + ++m  +
  gene1221|gene1221|rna1220|rna1220 206 SIVIVDEAHNICDSVIQMNTS 226
                                        89*********9999998655 PP

>> Trans_coact  Phage late-transcription coactivator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0049       9.8      15      46 ..      37      68 ..      33      70 .. 0.90
   2 ?    3.1   0.0     0.052     1e+02      34      61 ..     582     609 ..     577     614 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0049
                        Trans_coact 15 eglsYlEAvlewceendieeeqvpklIskpLk 46
                                       + +s+l Av+++++  ++e ++ ++ + ++L 
  gene1221|gene1221|rna1220|rna1220 37 KTMSLLSAVVDYIDVDGVELNHRNRVLEQALF 68
                                       469***********************999986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.052
                        Trans_coact  34 eeqvpklIskpLkeKikaEAielnllkp 61 
                                        ++q +klIs+ ++e+i      + llk+
  gene1221|gene1221|rna1220|rna1220 582 YAQLSKLISSWIRERIACCSFGDGLLKA 609
                                        6899************866666666665 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00047      0.94     142     192 ..     172     219 ..      13     242 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00047
                                        ----------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 142 vapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns 192
                                         ++ + ++ d+v+  Y+ l ++     +rsv  +v+   v++DE+h++  s
  gene1221|gene1221|rna1220|rna1220 172 ASKIYSHQCDIVFLPYQLLFTRE---GRRSVDIDVRGSIVIVDEAHNICDS 219
                                        45556778899999999999777...688888999***********99776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00024      0.48      29      63 ..      20      56 ..      10      77 .. 0.82
   2 ?   -2.2   0.1       1.3   2.5e+03     163     184 ..      83     104 ..      80     105 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00024
                             AAA_25 29 llpagelallaGapgtGKttlaldlalava..tGkpw 63
                                       ++  ++++++  ++gtGKt+ +l+ ++++    G ++
  gene1221|gene1221|rna1220|rna1220 20 IVDGEAVGIFSSPTGTGKTMSLLSAVVDYIdvDGVEL 56
                                       5667899*******************99985555554 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                             AAA_25 163 sdvgalvealeriarrtgaavl 184
                                        ++ +++++ l+r+  r++a vl
  gene1221|gene1221|rna1220|rna1220  83 TQLAQAINELKRLDVRCNAVVL 104
                                        5678999******99**99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.54
# Mc/sec: 3430.68
//
Query:       gene1222|gene1222|rna1221|rna1221  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-16   60.2   0.4    3.5e-16   59.9   0.4    1.1  1  Brix           Brix domain
  ------ inclusion threshold ------
      0.031   13.0   0.9      0.045   12.5   0.9    1.2  1  Peptidase_C57  Vaccinia virus I7 processing peptidase


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.4   3.9e-20   3.5e-16       3     193 .]      13     170 ..      11     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 3.9e-20
                                        T--HHHHHHHHHHHHHCTTSEEEEEEECT-TTTHHHHHHH...-HHHHHHHHHCTCSEEEEEE..SSTTEEEEEEE CS
                               Brix   3 ktssrlrqllkdlrslmkphtasflkrnsnklkdlvelag...vthlellsekndcslfvfelskkrPngptlefk 75 
                                        k+++r +q++  +r++++p+ +s+l+ +++ +++++ +a     +h++l+    d   + +++   rP+gpt+ f+
  gene1222|gene1222|rna1221|rna1221  13 KPTKRSKQMCMHIRRMLEPNVTSKLRDKNTTVRSYLDVADileLSHFILVDAR-D---IKIGV---RPKGPTYVFN 81 
                                        788999*****************999555599998888886545555554443.4...44566...8********* PP

                                        EECECTGGGSTTTSTS-TT---EEEEES.HHHHHHHHHHHHHH..SEEEG..-B-GG-SEEEEEEES.CCTTTECE CS
                               Brix  76 venyslmkdlkkakktefgsrPllvfngkenfkllksllqdlFrvpkislkspklsglrrvvlftaaenqetdkti 151
                                        v +y +   + ++    ++  P++ f+   + + +k+l+++l ++p         + ++r + f        d  i
  gene1222|gene1222|rna1221|rna1221  82 VIDYNPKYVMVGS--EYYKDDPCITFT---GESDTKELFMSLSSQP---------KTFKRNLHFYFDG----D-LI 138
                                        ******9999876..9999********...98999******99333.........689*******443....5.8* PP

                                        EEEEEEEEEE..STTTTECT..T..EEEEEEESEEEEEEEEE CS
                               Brix 152 sfRhYaiklkksgkklpnlekekkerveLeEiGPrfdLklrk 193
                                        ++RhYai++k+          e++ +v  +EiGPr+++kl+k
  gene1222|gene1222|rna1221|rna1221 139 HVRHYAIVTKE----------EEDIKVGFNEIGPRITMKLIK 170
                                        *******7322..........23568**************97 PP

>> Peptidase_C57  Vaccinia virus I7 processing peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9     5e-06     0.045     232     279 ..      86     133 ..      77     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-06
                      Peptidase_C57 232 kkryvmfgfiYlshwkcvvfdkekklvlFydsgGniPeefkhyknfyF 279
                                        + +yvm+g  Y +   c+ f  e+++   + s  ++P+ fk++ +fyF
  gene1222|gene1222|rna1221|rna1221  86 NPKYVMVGSEYYKDDPCITFTGESDTKELFMSLSSQPKTFKRNLHFYF 133
                                        569********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1026.61
//
Query:       gene1223|gene1223|rna1222|rna1222  [L=314]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.066   13.2   0.1       0.19   11.7   0.1    1.8  1  SNARE     SNARE domain
       0.09   12.4   0.6       0.29   10.8   0.1    1.9  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.1e-05      0.19      26      49 ..      39      62 ..      38      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                                       HHHHHHCTXXXXXXXXXXXXXXXX CS
                              SNARE 26 kavkyqksnRklkciillilviil 49
                                       ++ ++ ks+Rk+ +i++l+++i+ 
  gene1223|gene1223|rna1222|rna1222 39 RYIEKIKSTRKKGMIFFLLALIFT 62
                                       688999****************95 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.2e-05      0.29       8      62 ..       9      81 ..       3      98 .. 0.61
   2 ?   -0.6   0.1       0.1   9.2e+02      13      60 ..     179     244 ..     170     259 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                            DUF4131  8 vllalllllllllllllrr..................rprrrvllllllllllallgfalrapqpnandlsql 62
                                       vlla++l+l ++l+ l                      +r++ ++++ll+l++ +++++++++++ + + ++l
  gene1223|gene1223|rna1222|rna1222  9 VLLAIMLILGATLVNLIALrannkaepagtryiekikSTRKKGMIFFLLALIFTTVYYFFYTQNHLEGRTPPL 81
                                       3333333333333222222456999999999999988555555666666666666666666666655555555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.1
                            DUF4131  13 llllllllllllrr.....................rprrrvllllllllllallgfalrapqpnandls 60 
                                        l  llll  +   +                     r ++++++++++l+l +++g+a  ++   a d+s
  gene1223|gene1223|rna1222|rna1222 179 LYSLLLLKMC---KvhdvlsytqvitkfeieevldRVKPKIIGIIGYLCLDGASGVARMTAMFFAGDYS 244
                                        3333333333...24457777777777788888888899999999999998888887776666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2034.52
//
Query:       gene1224|gene1224|rna1223|rna1223  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-28   97.1   0.1    1.3e-27   96.5   0.1    1.2  1  adh_short        short chain dehydrogenase
    4.4e-14   52.6   0.1    8.7e-14   51.6   0.1    1.4  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.1e-06   28.1   0.0    1.4e-06   27.7   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      1e-05   25.1   0.0    1.4e-05   24.7   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0011   19.5   0.0     0.0019   18.8   0.0    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0012   18.8   0.0     0.0017   18.2   0.0    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
     0.0016   18.4   0.3     0.0035   17.3   0.3    1.7  1  KR               KR domain
     0.0019   18.4   0.0     0.0034   17.7   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0021   18.2   0.1     0.0037   17.3   0.1    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0034   17.3   0.1     0.0056   16.6   0.1    1.4  1  NAD_binding_10   NAD(P)H-binding
     0.0037   16.4   0.0     0.0057   15.8   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
  ------ inclusion threshold ------
      0.023   14.0   0.0      0.039   13.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.061   13.4   0.9       0.13   12.3   0.2    2.0  2  RcnB             Nickel/cobalt transporter regulator
      0.092   12.6   0.0       0.13   12.0   0.0    1.2  1  DFP              DNA / pantothenate metabolism flavoprotein


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.1   1.1e-30   1.3e-27       1     185 [.      41     217 ..      41     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 1.1e-30
                                        SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                          adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                        k vl+ Ga++ +Gr +ak++a++G+k+++v+rse++l ++++++++  ++ ++  vD + +     +v+k      
  gene1224|gene1224|rna1223|rna1223  41 KYVLINGATGKVGRGLAKKFAEKGMKILLVGRSESRLTRLHAKIERM-TECHMHIVDYKRSP-NISFVDKY----- 109
                                        679******************************************95.56666677766444.44566666..... PP

                                        SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                          adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152
                                         + +Lvn+A+  +++p+  + e+ +e++++ Nl+gv++ltr vl +m++   G ++nv+S  g+ + + ++a+++s
  gene1224|gene1224|rna1223|rna1223 110 DIGILVNCASAMKDSPA-YFVEQSVEEIMNANLVGVMSLTRYVLVNMMDCGYGYVINVGSLMGEASTPLYSAFGCS 184
                                        8**********777666.455677**************************************************** PP

                                        HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSH CS
                          adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTd 185
                                        K a+++l++sl  el+ ++++v  +  G v+++
  gene1224|gene1224|rna1223|rna1223 185 KQALKALSDSLYYELEGYNVNVEYMGVGSVSSG 217
                                        *************************99999865 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.1   6.8e-17   8.7e-14       1     168 [.      47     208 ..      47     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 6.8e-17
                                        TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTT.SEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                       adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelg.aevlecDVtdeeqvealveevvekfgklDilvn 75 
                                        Ga   +Gr++Ak++ae+G++++l+ ++e++  r+++  e++   ++  +D ++  ++       v+k+  + ilvn
  gene1224|gene1224|rna1223|rna1223  47 GATGKVGRGLAKKFAEKGMKILLVGRSESRLTRLHAKIERMTeCHMHIVDYKRSPNI-----SFVDKY-DIGILVN 116
                                        566668***********************9333333333333133555555555555.....345555.799**** PP

                                        -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                       adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaale 149
                                        +a  +++  +p + + +++++++++ nl ++++l++++l  +m  g g ++n+ s+ +e ++p y+a g +K al+
  gene1224|gene1224|rna1223|rna1223 117 CASAMKD--SP-AYFVEQSVEEIMNANLVGVMSLTRYVLVnMMDCGyGYVINVGSLMGEASTPLYSAFGCSKQALK 189
                                        ***9999..44.55667889999***************99999999****************************** PP

                                        HHHHHHHHHHGGGTEEEEE CS
                       adh_short_C2 150 altrylAvelgpkgiRvNa 168
                                        al+ +l +el  +++ v  
  gene1224|gene1224|rna1223|rna1223 190 ALSDSLYYELEGYNVNVEY 208
                                        *************999965 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.1e-09   1.4e-06       1     114 [.      43     150 ..      43     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.1e-09
                                        EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                    Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76 
                                        vl+ Ga+G +G+ l +++++k + ki+l+ r+E +l +++ ++e ++++      +++ i d + + +++  ++++
  gene1224|gene1224|rna1223|rna1223  43 VLINGATGKVGRGLAKKFAEKGM-KILLVGRSESRLTRLHAKIE-RMTE------CHMHIVDYKRSPNIS-FVDKY 109
                                        89****************98876.7999*************984.3333......334599999999986.56669 PP

                                        T-SEEEE--.----HHH..HHHSHHHHHHHHHHHHHHHHHH CS
                    Polysacc_synt_2  77 kvdvvfhaA.AlKhVPl..veenpleaiktNvlgtenviea 114
                                        ++ +++++A A+K  P+  ve+ + e ++ N +g +++ + 
  gene1224|gene1224|rna1223|rna1223 110 DIGILVNCAsAMKDSPAyfVEQSVEEIMNANLVGVMSLTRY 150
                                        99988775549*****6448**************8877654 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.1e-08   1.4e-05       1     104 [.      43     153 ..      43     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.1e-08
                                        EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                          Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavih 70 
                                        +l+ GatG +G+ l+k+++ekg +++ + r +s+  t +++++      +++ +d++ +     +++++++ + ++
  gene1224|gene1224|rna1223|rna1223  43 VLINGATGKVGRGLAKKFAEKGMKILLVGRSESR-LTRLHAKIermtecHMHIVDYKRSP-NISFVDKYDIGILVN 116
                                        6999******************999999998333.333333337889999*****99777.56789999******* PP

                                        --S.---HHHHHHSH..HHHHHHHTHHHHHHHHHHHH CS
                          Epimerase  71 lAa.vggvaassedp..adfieknlqgtlnlleaark 104
                                        +A   ++ +a++ ++  ++++++nl+g++ l  ++  
  gene1224|gene1224|rna1223|rna1223 117 CASaMKDSPAYFVEQsvEEIMNANLVGVMSLTRYVLV 153
                                        *998999999875442278899999999999888763 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-06    0.0019       6      67 ..      48     114 ..      41     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                                        TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE CS
                      F420_oxidored   6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvl 67 
                                        ++G++g++la++++++g    +i+++  r++++++ l+++++         v+ + ++n   +++ d+ +l
  gene1224|gene1224|rna1223|rna1223  48 ATGKVGRGLAKKFAEKG---MKILLV-GRSESRLTRLHAKIErmtechmhiVDYKRSPNISFVDKYDIGIL 114
                                        58***************...****88.*************9987777777777777777777777776555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.4e-06    0.0017       6      47 ..      47      89 ..      42     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                                       --.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                            3HCDH_N  6 Ga.GtmGagiaavfasagleVvlvdiseealekalekieksle 47
                                       Ga G +G+g+a+ fa++g+++ lv +se++l++ ++kie+ +e
  gene1224|gene1224|rna1223|rna1223 47 GAtGKVGRGLAKKFAEKGMKILLVGRSESRLTRLHAKIERMTE 89
                                       6669**********************************98654 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   2.7e-06    0.0035       3      55 ..      43      94 ..      42     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EE CS
                                 KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaev 55
                                       +li G++G++G+ la+  aekg  +++l++Rs++   + +a+i+++++  +++
  gene1224|gene1224|rna1223|rna1223 43 VLINGATGKVGRGLAKKFAEKGM-KILLVGRSESRLTRLHAKIERMTECHMHI 94
                                       69********************7.5889****766666666666666554444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   2.6e-06    0.0034       1      80 [.      43     121 ..      43     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-06
                                        EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.TTTCEEEEE--TTTHHHHHHHHHTTS..SE CS
                    Sacchrp_dh_NADP   1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka.lgvrfeaialdaenyeavLaallkeg..dl 72 
                                        vli Ga G+vG+++a++ a+++    +i +++rs+++l +l ak+ + ++++ + +d +  +    + + ++  ++
  gene1224|gene1224|rna1223|rna1223  43 VLINGAtGKVGRGLAKKFAEKGM---KILLVGRSESRLTRLHAKIeRMTECHMHIVDYKRSPN--ISFVDKYdiGI 113
                                        7889****************985...7***************998777888888888888887..55677777888 PP

                                        EEE-SSGG CS
                    Sacchrp_dh_NADP  73 vvnlsppi 80 
                                        +vn++  +
  gene1224|gene1224|rna1223|rna1223 114 LVNCASAM 121
                                        99998766 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   2.9e-06    0.0037       7      59 ..      35      87 ..      30     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-06
                                       HS..TT-EEEEES-.SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                       Shikimate_DH  7 leslkekkvlliGa.GemaelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                        e +++k vl+ Ga G++++ +ak++++kg+k ++ ++R+ +r  +l  +++  
  gene1224|gene1224|rna1223|rna1223 35 WEGIRKKYVLINGAtGKVGRGLAKKFAEKGMK-ILLVGRSESRLTRLHAKIERM 87
                                       566788999999*88*****************.**************9999655 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.4e-06    0.0056       1      40 [.      47      83 ..      47     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.4e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTT CS
                     NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeg 40
                                       GAtGkvGr l+k+ +++ g+++ ++ R++++l++l a  +
  gene1224|gene1224|rna1223|rna1223 47 GATGKVGRGLAKKFAEK-GMKILLVGRSESRLTRLHA--K 83
                                       9****************.5*************99863..3 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.4e-06    0.0057       3      49 ..      43      89 ..      41     151 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.4e-06
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHH CS
                      RmlD_sub_bind  3 ilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellke 49
                                       +l+ Ga+G++G+ Lak++ae+g+++l ++r+e  lt+ +a  e + e
  gene1224|gene1224|rna1223|rna1223 43 VLINGATGKVGRGLAKKFAEKGMKILLVGRSESRLTRLHAKIERMTE 89
                                       79****************************96665554433333322 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.1e-05     0.039      28      77 ..      32      79 ..      16     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                                       CGSBS-GTTSEEEEES.-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                       2-Hacid_dh_C 28 allgkelsgktvGiiG.lGrIGqavakrlkafgmkviaydrskkkeeeeee 77
                                       +   + +++k v i G +G++G+ +ak++++ gmk++ + rs+++ +   +
  gene1224|gene1224|rna1223|rna1223 32 HQVWEGIRKKYVLINGaTGKVGRGLAKKFAEKGMKILLVGRSESRLT---R 79
                                       555677899999999967***********************987544...3 PP

>> RcnB  Nickel/cobalt transporter regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2    0.0001      0.13      21      50 ..      24      53 ..      16      54 .. 0.84
   2 ?   -2.7   0.0       5.1   6.5e+03      38      43 ..     149     154 ..     148     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                               RcnB 21 yhLpaPprGyrWvriggdyvLvaiatGvIa 50
                                       y  ++   ++ W  i  +yvL++ atG++ 
  gene1224|gene1224|rna1223|rna1223 24 YIYSKCRNHQVWEGIRKKYVLINGATGKVG 53
                                       55666678999*****************95 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                               RcnB  38 dyvLva 43 
                                         yvLv+
  gene1224|gene1224|rna1223|rna1223 149 RYVLVN 154
                                        69**99 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.13      23      56 ..      44      78 ..      36     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                       EEE----HHHHHHHHHHHHTT-EEEEEE-S.-SS- CS
                                DFP 23 isNrSSGkmGyalAeaaaarGaeVtlvsgp.vsle 56
                                       + N ++Gk G  lA+++a++G+++ lv  + ++l+
  gene1224|gene1224|rna1223|rna1223 44 LINGATGKVGRGLAKKFAEKGMKILLVGRSeSRLT 78
                                       6799**********************976523443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1800.91
//
Query:       gene1225|gene1225|rna1224|rna1224  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-37  127.4   0.0      4e-37  127.0   0.0    1.1  1  Ribosomal_L14  Ribosomal protein L14p/L23e


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.0   0.0   2.3e-41     4e-37       2     121 ..      26     145 ..      25     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 2.3e-41
                                        .CSS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TT CS
                      Ribosomal_L14   2 iqlktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkd 73 
                                        +q+++ lk+aDNsgak ++ci v +++    + +aa  Gdi+vvsvkk+kp   + +++v++a+++r+kk +rr+d
  gene1225|gene1225|rna1224|rna1224  26 VQVESLLKCADNSGAKILRCIGVKRYRgrlnRLPAAAPGDICVVSVKKGKP---ELRKKVHYAILIRQKKIWRRTD 98 
                                        6999********************998655455******************...899******************* PP

                                        S-EEEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                      Ribosomal_L14  74 GsvirfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                        Gs+i f+dnaaVl+n+kge++G +i gpv+re+++  ++ki s A+++
  gene1225|gene1225|rna1224|rna1224  99 GSHIMFEDNAAVLINNKGELRGAQIAGPVPREVADM-WPKISSQASSI 145
                                        ***********************************9.********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1014.02
//
Query:       gene1226|gene1226|rna1225|rna1225  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-07   29.6   0.8    2.3e-06   28.1   0.8    1.9  1  Trm112p   Trm112p-like protein


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.8   1.3e-10   2.3e-06      41      66 ..      74     110 ..       2     112 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.3e-10
                                        S...........CHHTTEECCCCEEEETTTTEEEEEE CS
                            Trm112p  41 y...........ellleldieegeLvCpncgraYpIk 66 
                                                    ell+ +d++eg+L C  cg++YpI+
  gene1226|gene1226|rna1225|rna1225  74 FvenpdhderikELLFGVDVVEGSLRCDTCGLIYPIR 110
                                        144444447889************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 788.82
//
Query:       gene1227|gene1227|rna1226|rna1226  [L=928]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-09   38.8  13.7     0.0002   22.1   0.0    6.1  7  WD40         WD domain, G-beta repeat
    1.4e-06   28.5   0.0      0.015   15.6   0.0    4.8  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
      0.024   14.7   0.0      0.059   13.5   0.0    1.6  1  Bromodomain  Bromodomain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.4e-08    0.0002       6      38 .]      87     120 ..      82     120 .. 0.87
   2 !   16.6   1.2   1.8e-06     0.011       3      29 ..     126     153 ..     124     162 .. 0.87
   3 ?    1.6   0.1     0.098   5.8e+02      13      30 ..     227     244 ..     221     262 .. 0.74
   4 ?   -0.3   0.0       0.4   2.4e+03      12      37 ..     268     292 ..     256     293 .. 0.83
   5 ?   -0.1   0.0      0.35   2.1e+03       6      37 ..     313     356 ..     309     356 .. 0.71
   6 ?   -0.0   0.0      0.33   1.9e+03      12      35 ..     406     429 ..     400     431 .. 0.78
   7 ?   -3.0   0.1       2.8   1.7e+04       7      16 ..     910     921 ..     908     924 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.4e-08
                                        EEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +l GH + v  ++f++ +++++sG+ Dg +++Wd
  gene1227|gene1227|rna1226|rna1226  87 ELLGHsGQVDRICFDQGNRFFMSGGSDGMIKLWD 120
                                        5679*555****************88*******9 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.8e-06
                                        EEEEEESS.SSEEEEEEETTSSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGs 29 
                                        +++++ GH ++v++l+ s+dg+ l+s++
  gene1227|gene1227|rna1226|rna1226 126 LVHSFIGHrNFVSDLCISSDGKILVSCD 153
                                        689**********************884 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.098
                                        EEEEEEETTSSEEEEEET CS
                               WD40  13 vtslafspdgawlasGsd 30 
                                        + +l+f + g++l+++++
  gene1227|gene1227|rna1226|rna1226 227 IKGLCFTDGGRFLLCSGW 244
                                        7899**********9887 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.4
                                        SEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40  12 svtslafspdgawlasGsdDgtvriW 37 
                                        +v+ ++  + g  +a+++ D  v  W
  gene1227|gene1227|rna1226|rna1226 268 PVNTICGAKKGLKIAAAC-DTQVFQW 292
                                        488888888999999999.****999 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.35
                                        EEESS.SS............EEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   6 tltGH.ss............vtslafspdgawlasGsdDgtvriW 37 
                                        +l GH +             v  +++ +d+ +++ ++ D ++ri+
  gene1227|gene1227|rna1226|rna1226 313 SLQGHwKRsiikidisegelVERICYLRDNFLVCICT-DLKIRIY 356
                                        5778865566666666666667777888888888889.9999986 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 0.33
                                        SEEEEEEETTSSEEEEEETTSEEE CS
                               WD40  12 svtslafspdgawlasGsdDgtvr 35 
                                        ++++ +fs dg +++ G++ g vr
  gene1227|gene1227|rna1226|rna1226 406 GINDAQFSNDGEFFVFGDERGVVR 429
                                        489999*******87676555555 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 2.8
                                        EESS.SS.EEEE CS
                               WD40   7 ltGH.ss.vtsl 16 
                                        l GH +  v+++
  gene1227|gene1227|rna1226|rna1226 910 LHGHcQQvVNGI 921
                                        679965556887 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.5e-06     0.015      36      79 ..      90     133 ..      58     138 .. 0.85
   2 ?    3.7   0.0     0.013        76      40      79 ..     136     175 ..     131     183 .. 0.88
   3 ?   -0.5   0.0      0.26   1.6e+03      35      53 ..     221     239 ..     193     243 .. 0.50
   4 ?   -0.7   0.0      0.29   1.7e+03      36      66 ..     328     357 ..     315     368 .. 0.75
   5 ?    2.0   0.0     0.044   2.6e+02      41      67 ..     407     433 ..     392     435 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                        ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                        +++++v  +++ + +++++ + sdg ++l d++sg +vhs+  +
  gene1227|gene1227|rna1226|rna1226  90 GHSGQVDRICFDQGNRFFMSGGSDGMIKLWDVYSGLLVHSFIGH 133
                                        56789**********************************99765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.013
                        ANAPC4_WD40  40 evrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                         v++L+ + dgk+L+   s g ++  + e  +v+ +l+ +
  gene1227|gene1227|rna1226|rna1226 136 FVSDLCISSDGKILVSCDSHGLLSAWSLERFEVLFQLELG 175
                                        6899**********************99999999988765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.26
                        ANAPC4_WD40  35 dkedsevrsLaWkpdgklL 53 
                                        +  d+ +++L++   g++L
  gene1227|gene1227|rna1226|rna1226 221 CLLDEAIKGLCFTDGGRFL 239
                                        3445666666666666666 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.29
                        ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlld 66 
                                        +e++ v+ +++   +++L+  + d ++r++ 
  gene1227|gene1227|rna1226|rna1226 328 SEGELVERICYLR-DNFLVCICTDLKIRIYA 357
                                        6777888888865.57899999999999986 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.044
                        ANAPC4_WD40  41 vrsLaWkpdgklLavaysdgevrllda 67 
                                        +++ ++++dg++++++ + g vr++++
  gene1227|gene1227|rna1226|rna1226 407 INDAQFSNDGEFFVFGDERGVVRVISM 433
                                        667789*****************9986 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.8e-06     0.059      22      70 ..     857     905 ..     838     915 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-06
                                        -GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHH CS
                        Bromodomain  22 dpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNark 70 
                                         +e++  yy+ +   ++L  I++k+++  Y+++  +e dl   +sN+++
  gene1227|gene1227|rna1226|rna1226 857 RRESNGSYYENVASTVNLGVIEEKIQNDLYRTVGGLEFDLDIAISNSMY 905
                                        6889999***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (928 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.82u 0.34s 00:00:01.15 Elapsed: 00:00:00.54
# Mc/sec: 5176.62
//
Query:       gene1228|gene1228|rna1227|rna1227  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-35  121.4   0.0    4.5e-35  121.1   0.0    1.1  1  RNase_P_p30    RNase P subunit p30
  ------ inclusion threshold ------
      0.077   12.9   0.4       0.38   10.7   0.1    2.1  2  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.0     5e-39   4.5e-35       1     213 [.       3     198 ..       3     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 5e-39
                                        EEEEE-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH...HHSSEEEEEE CS
                        RNase_P_p30   1 ydlnipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsg.lkllsRvtlvvs 75 
                                        yd+ni  +  ++      +k+l+e +y+g ++n ++++ +       e    +++ +  e+ g    +sRv++v++
  gene1228|gene1228|rna1227|rna1227   3 YDVNISLDYLKQ-----DMKELEENEYEGFCVNRIIKPRD------LE----KIRYEPVEFLGaKPCYSRVEVVFE 63 
                                        688888887774.....7899****************333......33....122333355554779********* PP

                                        ES-H.HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTT.SSS-S--HHHHHHHHHHT-EEEEESHHHH CS
                        RNase_P_p30  76 dpsklqrlskvrqkfdllavrPttekalraacenldvDiisidlts.rlpfglkhktiraAvergvafEinyspll 150
                                        ++++++  +k + k+dl +vr    +++   +   + D+i++++ s  lpf  k  ++r A++++++fE+ + ++l
  gene1228|gene1228|rna1227|rna1227  64 EKEEVGYDAKKSMKYDLFVVRLNGVAGMDRLI-RCQPDMITFNYGSqILPF--KCGLVRTAIKENIFFEVPLRESL 136
                                        ********************************.55*********9955666..*********************** PP

                                        HS-HHHHHHHHHHHHHHHHHHHH--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTTT CS
                        RNase_P_p30 151 rdsglaRrnfisnarkllrltrgkgvviSSgAesplelRnpydiinLlktlGLeedrakeavs 213
                                        ++ + + + +++n+rkll +t+gk+vv+SSgA++++e++ p+di+++l+++GL+++ra+e++ 
  gene1228|gene1228|rna1227|rna1227 137 YGGT-SSIMWMRNVRKLLFITNGKNVVFSSGARCSTEIKRPRDITKMLEMFGLKKKRASEVML 198
                                        ****.*******************************************************986 PP

>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.14   1.2e+03       1      13 [.      80      92 ..      80      96 .. 0.83
   2 ?   10.7   0.1   4.3e-05      0.38      10      35 ..     173     198 ..     168     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                                       EEEEE-S-STTS- CS
                      Ribosomal_L30  1 lfVtrirsiigvp 13
                                       lfV+r  +++g+ 
  gene1228|gene1228|rna1227|rna1227 80 LFVVRLNGVAGMD 92
                                       79*****999986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.3e-05
                                        TTS-HHHHHHHHHTT-SSTTEEEE-- CS
                      Ribosomal_L30  10 igvppkvrktLqlLgLrkingtvvkl 35 
                                        i++p ++ k L+++gL+k  ++ v l
  gene1228|gene1228|rna1227|rna1227 173 IKRPRDITKMLEMFGLKKKRASEVML 198
                                        89****************98554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1466.26
//
Query:       gene1229|gene1229|rna1228|rna1228  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-26   91.7   0.0    5.1e-26   91.5   0.0    1.1  1  RNase_P_p30  RNase P subunit p30
  ------ inclusion threshold ------
      0.061   13.1   0.2       0.13   12.0   0.2    1.6  1  QRPTase_C    Quinolinate phosphoribosyl transferase, C-termin


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   5.7e-30   5.1e-26       1     212 [.       3     196 ..       3     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 5.7e-30
                                        EEEEE-SH.........HHHHHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH.....HHSSEEEE CS
                        RNase_P_p30   1 ydlnipwpsddskkksrtiktlaelgytgvainftveaekekkpnasepikeelkelkkelsg...lkllsRvtlv 73 
                                        +d+n+     ++    +++  l++lg +g+++n  ve   +kk +++             + g    +++ Rv++ 
  gene1229|gene1229|rna1228|rna1228   3 FDMNVSSRCLGP----ELMDVLRQLGHDGICVNTVVELDIVKKYKKPS------------FDGwkdRRIYERVEIK 62 
                                        578888888884....48999****************87777777777............33333379******** PP

                                        EEES-H.HHHHHHHHH--EEEEE--SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHH CS
                        RNase_P_p30  74 vsdpsklqrlskvrqkfdllavrPttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspl 149
                                        ++d +    ++k     d++avr   +k ++ ++e+ + D+i++d+t+   f l + +   A++r+++fEi +   
  gene1229|gene1229|rna1228|rna1228  63 YKDCEDWDDVRK-DIDPDVVAVRLEGMKDFKKVLEM-RPDVITFDYTK--SFCLGRDEFIEATKRNIFFEIPLVCG 134
                                        *****7333333.33457****************77.*********87..************************** PP

                                        HHS-HHHHHHHHHHHHHHHHHHHH--EEEE--BSSGGG---HHHHHHHHHHHT--HHHHHHTT CS
                        RNase_P_p30 150 lrdsglaRrnfisnarkllrltrgkgvviSSgAesplelRnpydiinLlktlGLeedrakeav 212
                                         +++  +++ +++nar+ll++t g +vv+ SgA++ +e+R+ +dii++l  lG++ed+ ++++
  gene1229|gene1229|rna1228|rna1228 135 MYSQR-SKAMWMRNARRLLNVTGGVNVVVGSGATCLTEMRGGQDIIKILWGLGMSEDNGRKVL 196
                                        *****.*****************************************************9987 PP

>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.5e-05      0.13      70     110 ..      69     124 ..      63     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                                        HHHHHHHHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES-................- CS
                          QRPTase_C  70 vksvreavdkevkievevesleeleevleaeadiimLDnf................s 110
                                        ++ vr+ +d  v + v  e ++++++vle+++d+i +D                  +
  gene1229|gene1229|rna1228|rna1228  69 WDDVRKDIDPDV-VAVRLEGMKDFKKVLEMRPDVITFDYTksfclgrdefieatkrN 124
                                        788999999998.9************************9844555444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1185.10
//
Query:       gene1230|gene1230|rna1229|rna1229  [L=446]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2589.38
//
Query:       gene123|gene123|rna123|rna123  [L=816]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.7e-203  676.4  11.8   7.6e-104  348.2   0.7    2.1  2  Chitin_synth_2   Chitin synthase
    1.5e-15   57.6   0.8    6.8e-15   55.5   0.8    2.2  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    7.1e-15   55.5   0.0    1.1e-12   48.4   0.0    2.7  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.9e-07   31.0   0.1     0.0044   16.9   0.0    2.4  2  Glycos_transf_2  Glycosyl transferase family 2
      9e-05   22.0   0.0    0.00085   18.8   0.0    2.1  2  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.2   0.7  2.1e-107  7.6e-104      27     295 ..     279     557 ..     263     567 .. 0.94
   2 !  332.7   4.5    1e-102   3.7e-99     293     525 ..     585     811 ..     572     813 .. 0.95

  Alignments for each domain:
  == domain 1  score: 348.2 bits;  conditional E-value: 2.1e-107
                 Chitin_synth_2  27 ticlvtaysegeeglrttldslastdyddkrklllvvcdGlikGsGndkstPeivldllkdavspkedveplsyvavaeG 106
                                     i+lvt+yseg++g+++tldsl++ dy    k+++v+cdG i+GsGn+ stP+ivl+l +       ++ep sy ++++G
  gene123|gene123|rna123|rna123 279 CILLVTCYSEGKDGIKNTLDSLCKQDYGYDYKMIVVICDGEIIGSGNEMSTPDIVLSLSD----VDRNAEPKSYISLTHG 354
                                    689******************************************************998....45688999******** PP

                 Chitin_synth_2 107 skrhnkakvyaGfyeyed...............dstvpeekqqrvPlivvvkvGtpseasekkPGnrGkrdsqiilmsfl 171
                                     krhn+akvyaG+y++++               ++ + e ++ ++ ++++ k+G+p+e+   k GnrGkrdsq+ilmsf+
  gene123|gene123|rna123|rna123 355 AKRHNRAKVYAGYYHVKEeikstrhrcwpcfgrQEDTTEVRNYKTRILIINKCGNPEETF--KAGNRGKRDSQVILMSFF 432
                                    ****************999999999**99999977788889999**************99..9***************** PP

                 Chitin_synth_2 172 ekvtfdermteleyelfkkikkviG.vspdfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvt 250
                                    +++++ +rmtel++e+++k+k ++  ++p+ +e +lmvdadt v pd+l+ +v+ + +d++++g+cGet i nk eswvt
  gene123|gene123|rna123|rna123 433 SRLIYGDRMTELDFEIYQKMKLLMPhMDPEDFECILMVDADTIVKPDALSIMVNVFETDQKVIGICGETMILNKFESWVT 512
                                    *********************99962679*************************************************** PP

                 Chitin_synth_2 251 aiqvfeyyishhlskafesvfGsvtclPGcfslyrikaakgadgk 295
                                    +iqvfeyyishhl kafesvfG+vtclPGcf++yrik   +++g+
  gene123|gene123|rna123|rna123 513 MIQVFEYYISHHLNKAFESVFGGVTCLPGCFCMYRIKIVTNQQGQ 557
                                    *************************************98887765 PP

  == domain 2  score: 332.7 bits;  conditional E-value: 1e-102
                 Chitin_synth_2 293 dgkwvPilvspeiveeysenvvdtlhkknllllGedrylttlllktfpkrktvfvpqakcktvaPdtfkvllsqrrrwin 372
                                    +    Pil++p i+++ys  + +tlh+knll+lGedrylttlllk+f +rk vf+p akc+t +P +f vllsqrrrwin
  gene123|gene123|rna123|rna123 585 KSLCLPILANPAIINAYSVLEAKTLHQKNLLHLGEDRYLTTLLLKNFYRRKLVFIPAAKCETYVPGEFGVLLSQRRRWIN 664
                                    56678*************************************************************************** PP

                 Chitin_synth_2 373 stvhnllelvlvrdlcGtfcfsmrfvvfieligtvvlPvaiaftlylivasilksklvpviplvllaivlGlpailivlt 452
                                    st+hnl+elv+v++lcG fcfsm++vv +el gt+vlP+ai+ft+ +i  sil       +pl++l  ++Glpaili++t
  gene123|gene123|rna123|rna123 665 STIHNLFELVQVNNLCGAFCFSMQLVVVMELFGTLVLPAAIIFTFVMIAVSILI--EPAWVPLIMLVGIFGLPAILILIT 742
                                    ************************************************999998..56789******************* PP

                 Chitin_synth_2 453 arkleyvawllvyllalPifnfvlPlyafwhlddfswGetrvveGekkkkaageaegefdsskivlkrfeefe 525
                                    + +++yv w l+y+l++Pi+n+vlP+yafwh+ddf+wG+tr+v+Gek     ++++g fd++k+++++  ef 
  gene123|gene123|rna123|rna123 743 TMEVQYVFWCLIYILSIPIWNLVLPTYAFWHFDDFTWGDTRKVDGEK----GEDEDGVFDHTKVKMRELGEFL 811
                                    **********************************************9....56789************99995 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.8   1.9e-18   6.8e-15       2     194 ..     467     732 ..     466     772 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.9e-18
                Glyco_trans_2_3   2 illlDaDtvlppdclreiaaela.spevaivqgpvlvmnv.anwleelaalffaedhgkdilvrealgrvvpsvGsgafl 79 
                                    il++DaDt + pd l   ++ ++ +++v  ++g +++ n+  +w++ ++++++ ++h     + + +g+v+ ++G  ++ 
  gene123|gene123|rna123|rna123 467 ILMVDADTIVKPDALSIMVNVFEtDQKVIGICGETMILNKfESWVTMIQVFEYYISHHLNKAFESVFGGVTCLPGCFCMY 546
                                    89*********************669********999876599999*******99999999******************* PP

                Glyco_trans_2_3  80 rrsalq............................evg..........................gwdgdessvsEDfdmgl 105
                                    r++ ++                            + +                            + +  +++ED ++  
  gene123|gene123|rna123|rna123 547 RIKIVTnqqgqllsgpsksrigaqrfnnvksilsS-SlekslclpilanpaiinaysvleaktLHQKNLLHLGEDRYLTT 625
                                    ******88888888888886666555555555540.0455555555555555555555555544444556********99 PP

                Glyco_trans_2_3 106 rlqrkGyrv..rfvpeslvkekspltlraalrQrkRwayGc.....eleklil...............lvrllgylgsll 163
                                     l+++ yr   +f+p++ + +++p ++   l Qr+Rw+        e     l               lv+ + ++g+l+
  gene123|gene123|rna123|rna123 626 LLLKNFYRRklVFIPAAKCETYVPGEFGVLLSQRRRWINSTihnlfE-----LvqvnnlcgafcfsmqLVVVMELFGTLV 700
                                    998777654339****************************7654331.....0334444555555666888889999998 PP

                Glyco_trans_2_3 164 wsalplhlallllfs.llalalvlllllllaa 194
                                    + a  +  ++++  s l+  a+v+l++l++++
  gene123|gene123|rna123|rna123 701 LPAAIIFTFVMIAVSiLIEPAWVPLIMLVGIF 732
                                    86655444555555515669999999988876 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.012        44       4      37 ..     279     314 ..     277     333 .. 0.83
   2 !   48.4   0.0   2.9e-16   1.1e-12      87     228 ..     463     663 ..     446     665 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqey.prvevvvv 37 
                                    +++lV+++ e +  + ++l+sl +q+y  +++ +vv
  gene123|gene123|rna123|rna123 279 CILLVTCYSEGKdGIKNTLDSLCKQDYgYDYKMIVV 314
                                    789********967888*********9555776665 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 2.9e-16
                Glyco_tranf_2_3  87 ksdlvllvDdDtvvePdtlkrllqff.ltpkv.gavgtpvfllnrstlvsalgalefaerhlrflaarralg.vltlnGs 163
                                    +++ +l+vD+Dt+v Pd+l  ++++f  ++kv g+ g  + l+  +++v++ + +e+++ h+ + a+   +g v++l G 
  gene123|gene123|rna123|rna123 463 DFECILMVDADTIVKPDALSIMVNVFeTDQKViGICGETMILNKFESWVTMIQVFEYYISHHLNKAFESVFGgVTCLPGC 542
                                    4889**********************744444044445555567**************************9869****** PP

                Glyco_tranf_2_3 164 gslirrevlkele.....................................................gldp.lflltdDye 189
                                    ++++r +++++ +                                                     ++++ l +l++D  
  gene123|gene123|rna123|rna123 543 FCMYRIKIVTNQQgqllsgpsksrigaqrfnnvksilssslekslclpilanpaiinaysvleaktLHQKnLLHLGEDRY 622
                                    ****************************************************************97777799******87 PP

                Glyco_tranf_2_3 190 lglrlrr..agfrtayvpgaavrevfpsslkayikqrnRwv 228
                                    l+  l +  ++ + ++ p a ++++ p ++  +  qr+Rw+
  gene123|gene123|rna123|rna123 623 LTTLLLKnfYRRKLVFIPAAKCETYVPGEFGVLLSQRRRWI 663
                                    776666659999999*************************7 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   4.9e-05      0.17       3      34 ..     282     314 ..     280     321 .. 0.89
   2 !   16.9   0.0   1.2e-06    0.0044      81     166 ..     465     551 ..     460     553 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                                    EEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEE CS
                Glycos_transf_2   3 viptyNe.ektlletlesllaqdpypdfeiivv 34 
                                     +++y e ++ +++tl+sl++qd+ +d+++ivv
  gene123|gene123|rna123|rna123 282 LVTCYSEgKDGIKNTLDSLCKQDYGYDYKMIVV 314
                                    699*******************88888888887 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.2e-06
                                    SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..EEEECCHCCCCHC.CCCCCSTTCSTC CS
                Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv..generlyfkerkr.slkgnlsfeigs 157
                                    ++il +DaD++++pd l+ +v+ +e d++  v+g    +   +++ ++ + +  +e ++  +  + + s +g++++  g+
  gene123|gene123|rna123|rna123 465 ECILMVDADTIVKPDALSIMVNVFETDQK--VIGICGETMILNKFESWVTMIqvFEYYISHHLNKAFeSVFGGVTCLPGC 542
                                    59************************877..4444333333333333333333444444444444331567789999999 PP

                                    CCEEEEHHH CS
                Glycos_transf_2 158 aallrreal 166
                                    ++++r +++
  gene123|gene123|rna123|rna123 543 FCMYRIKIV 551
                                    999998875 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.4e-07   0.00085      16     113 ..     449     551 ..     440     557 .. 0.84
   2 ?    0.5   0.0       0.1   3.7e+02     125     172 ..     616     663 ..     602     664 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.4e-07
                Glyco_transf_21  16 npKvnnllqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakglaaaleaafl.ntlagvlqa 93 
                                     +K+  l++ ++    + +++ D+d++vkpd+L  +++ +e+ +kv  +++  +  ++   + ++ ++f  ++ + + +a
  gene123|gene123|rna123|rna123 449 YQKMKLLMPHMDPEDFECILMVDADTIVKPDALSIMVNVFETdQKVIGICGETMILNKFESWVTMIQVFEyYISHHLNKA 528
                                    567777999999999*************************87699999***99999999999999999986555555555 PP

                Glyco_transf_21  94 ...klsglgfavGksmalrreaL 113
                                        ++g+ +  G ++++r +++
  gene123|gene123|rna123|rna123 529 fesVFGGVTCLPGCFCMYRIKIV 551
                                    443669**********9997766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.1
                Glyco_transf_21 125 eLAeDyalgkllraa..GlkvvlspapiaqtsvprrsslrallaRqlrWa 172
                                    +L eD  l++ll ++    k+v+ pa+ ++t vp    +  ll++  rW 
  gene123|gene123|rna123|rna123 616 HLGEDRYLTTLLLKNfyRRKLVFIPAAKCETYVPG--EFGVLLSQRRRWI 663
                                    89************966667777777777888873..6899999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (816 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 5240.91
//
Query:       gene1231|gene1231|rna1230|rna1230  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-35  118.8   7.3      1e-34  118.6   7.3    1.0  1  DUF5101   Domain of unknown function (DUF5101)


Domain annotation for each model (and alignments):
>> DUF5101  Domain of unknown function (DUF5101)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.6   7.3   5.6e-39     1e-34       1      98 [.       3      99 ..       3     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 5.6e-39
                            DUF5101  1 mrlkleektneekkevkkkkkkklsdkekvleylkevkaktkdysLkYDlskCiEileGkEnqevvelkealeevleE 78
                                       mr  l+e+tn++k++  k+k++ +sdke+vl +lk+++ kt+d+sL+YDl+kC+Ei+eGkEnqe+++l++alee+l+E
  gene1231|gene1231|rna1230|rna1230  3 MRPVLNETTNATKRSDSKGKEI-ESDKERVLCFLKNTYMKTRDHSLRYDLKKCLEIIEGKENQEITDLRNALEEALVE 79
                                       8999************999999.9****************************************************** PP

                            DUF5101 79 nEklvkekvdLiaeleilke 98
                                       nE l++ek++L+++le++k+
  gene1231|gene1231|rna1230|rna1230 80 NEALFAEKCELAVTLECMKA 99
                                       ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 728.66
//
Query:       gene1232|gene1232|rna1231|rna1231  [L=83]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      176  (0.0098165); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 588.51
//
Query:       gene1233|gene1233|rna1232|rna1232  [L=421]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3138.62
//
Query:       gene1234|gene1234|rna1233|rna1233  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1816.28
//
Query:       gene1235|gene1235|rna1234|rna1234  [L=721]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-41  140.5   2.3    5.8e-40  137.7   0.1    2.7  3  Coatomer_WDAD  Coatomer WD associated region
    2.5e-28   97.7  20.5    4.9e-06   27.2   0.1    8.6  8  WD40           WD domain, G-beta repeat
    0.00015   22.0   0.2        5.7    7.3   0.0    4.6  6  ANAPC4_WD40    Anaphase-promoting complex subunit 4 WD40 doma
     0.0008   17.8   0.4      0.039   12.3   0.0    2.8  3  Frtz           WD repeat-containing and planar cell polarity 
  ------ inclusion threshold ------
       0.54   10.5   7.1         11    6.4   0.1    4.1  4  TPR_2          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.14   5.1e+02      93     146 ..       7      55 ..       4     141 .. 0.82
   2 ?    1.2   0.0     0.043   1.5e+02      72     173 ..     144     253 ..      87     278 .. 0.75
   3 !  137.7   0.1   1.6e-43   5.8e-40      24     434 ..     324     713 ..     296     720 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                                        X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD  93 ifknfkekktksikleyqvdkifgGalLgvksegsvsfYDweqgklvrridvkk 146
                                        i k f ++k+ksi+++  ++ i   a++g+ s + v ++D+++ ++v++i+v++
  gene1235|gene1235|rna1234|rna1234   7 IQKTFGSSKVKSIQMH-PTKAI---AIIGLFSGD-VQVWDIDKMSMVSNIHVSN 55 
                                        5566666666666666.35555...578888888.9999999999999999986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.043
                                        XXXXXXX..XXXXXXXXXXXXXXX.XXX.XXXXXXXXX.XXXXXXXXXX..XXXXXXXXXX..XXXXXXXXXXXXX CS
                      Coatomer_WDAD  72 ldfvwvs..snrfavlessksvkifknf.kekktksik.leyqvdkifg..GalLgvkseg.svsfYDweqgklvr 140
                                        +d+++++  s++f+     +++k+  n+ +++ +k++  +   +++i    G  L+   ++ ++ ++D ++ + + 
  gene1235|gene1235|rna1234|rna1234 144 MDVCFYPndSGKFVSCSLDSTIKV-WNVgQSHCVKTFRgHASGINSICFlsGDYLVSGADDlVLKVWDFQTTQCIT 218
                                        788999988899************.66637777777762445577777799999999988856779*********9 PP

                                        XXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD 141 rid..vkkvknVvwsddgelvalvskdtvyilsyn 173
                                         ++   +++++V+   +  l+a + +d  + l  n
  gene1235|gene1235|rna1234|rna1234 219 TLSghTNNINKVYLFTSFPLFASCGEDGSIRLWNN 253
                                        99854557999999988888888877765555554 PP

  == domain 3  score: 137.7 bits;  conditional E-value: 1.6e-43
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                      Coatomer_WDAD  24 qlkelgsieiypqslshnpngrfvlVcgdgeyiiytalalrnkaygkgldfvwvssnrfavlessksvkifknfke 99 
                                         +kel ++ +yp  l+ +p+g+ ++V  +ge++i ++l++r+k  g+g df +++  +f++++   +v+ +k+ + 
  gene1235|gene1235|rna1234|rna1234 324 ASKELCNVGFYPDELEVSPSGKTIAVGSEGEFHIFSSLGFRKKFNGTGRDFHFINDDEFVARN-GDDVSFYKKTEV 398
                                        6799*********************************************************99.778999898887 PP

                                        XXXXXXXXXXXXXXXXX..XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD 100 kktksikleyqvdkifg..GalLgvksegsvsfYDweqgklvrridvkkvknVvwsddgelvalvskdtvyilsyn 173
                                            si+++  ++k+f    +l+g +  +   +Y    g+++ +id  +  +     d  lva    + v i++ n
  gene1235|gene1235|rna1234|rna1234 399 VR--SISIKG-ISKLFClsPTLIGCNICDQTRIYSYS-GEFILSIDHAS-DHLAIVGD-FLVACG--TLVRIYRVN 466
                                        77..999985.9****999999999888878888875.99******887.66666655.355555..455555555 PP

                                        XX...................XXXXXXX.XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Coatomer_WDAD 174 leavee......edeeegvedafevlhelsesiksgaWvgdvfiYttsnnrlkylvngevgiikhldktlyilgyk 243
                                         e+++       e++eeg+ da+  l +   s+ s +  ++vf+++++n + +yl+ g+   + h+++   ++   
  gene1235|gene1235|rna1234|rna1234 467 YEVIDGfieqgiEVPEEGISDALVHLGTEYYSVSSWCASEEVFYFVSNN-KGYYLILGDKPYVHHFSSINGVVAGI 541
                                        5544556779*************99999899****999999******99.****************9988877777 PP

                                        X..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXX-GGG CS
                      Coatomer_WDAD 244 gkenklylldkdgnvvsleidlselefktavlrkdleevlkiiaasnllpeipkeegqkiirfLekkgypelAlql 319
                                        +  + +yl dk  +++s +id++ lef+ +v+ ++  +        + +       ++k i+f+e+++  e Al+l
  gene1235|gene1235|rna1234|rna1234 542 EDGTLFYLHDK--EIESKKIDMEFLEFQRSVMLEKEYK------MTEGI-------RSKAIAFFESLEMHEKALEL 602
                                        64555666666..57899*************9877555......34556.......7999**************** PP

                                        SS-HHHHHHHHHHTT-HHHHHHHHHHH--HHHHHHHHHHHHHTT-HHHHHHHHHHTT-HHHHHHHHHHHT-HHHHH CS
                      Coatomer_WDAD 320 vqDpetkFdLAlelgnLelAlelakelddeekWkkLgdaAlsqgniklaeeayqkakdfdkLllLylstgnkekLk 395
                                        ++D+++kF++ l+l + ++A++ a+      k++kLg+  l+ g+++ a e++ ++k++  Ll L+ ++  k++L+
  gene1235|gene1235|rna1234|rna1234 603 CTDDNQKFEILLKLDRYDEAFSKANSI---VKYDKLGRYFLKAGELSKASECFLRSKNWVCLL-LADILSGKKNLN 674
                                        ********************9988655...5****************************9775.6666666789** PP

                                        HHHHHHHHTT-HHHHHHHHHHHT-HHHHHHHHHHTT-HH CS
                      Coatomer_WDAD 396 kLakiaekkgdyniafqaalllgdvekcvdlLiksgrlp 434
                                          + +++k+g++n af a+l  g++++c++lL ++  lp
  gene1235|gene1235|rna1234|rna1234 675 VAGAECRKEGRLNHAFFAYLKDGQYAECAKLLESTPFLP 713
                                        ********************************9987665 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.23   8.4e+02       5      38 .]       9      41 ..       5      41 .. 0.79
   2 !    8.1   0.0    0.0015       5.2      15      37 ..      61      82 ..      49      83 .. 0.69
   3 !   18.3   0.0   8.8e-07    0.0032       3      37 ..      89     124 ..      87     125 .. 0.92
   4 !   22.7   0.3   3.6e-08   0.00013       5      38 .]     134     169 ..     130     169 .. 0.77
   5 !   24.6   0.9   8.7e-09   3.1e-05       2      38 .]     174     210 ..     173     210 .. 0.86
   6 !   27.2   0.1   1.4e-09   4.9e-06       2      38 .]     215     252 ..     214     252 .. 0.88
   7 ?    1.5   0.0      0.17   6.2e+02      17      36 ..     339     357 ..     307     359 .. 0.79
   8 ?   -0.2   0.1      0.61   2.2e+03       7      34 ..     527     546 ..     524     547 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                                       EEEESSSSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  5 rtltGHssvtslafspdgawlasGsdDgtvriWd 38
                                       +t+ G s v s++ +p +a  + G   g v +Wd
  gene1235|gene1235|rna1234|rna1234  9 KTF-GSSKVKSIQMHPTKAIAIIGLFSGDVQVWD 41
                                       555.4545999999******889955999*9*98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                                       EEEEETTSSEEEEEETTSEEEEE CS
                               WD40 15 slafspdgawlasGsdDgtvriW 37
                                       ++   +  +wl+ GsdDg+v ++
  gene1235|gene1235|rna1234|rna1234 61 CV-ILSRMDWLLVGSDDGNVNVY 82
                                       44.3333499999*******997 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 8.8e-07
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                        +++t+ +H ++++ +  +p  ++++++sdD t+++W
  gene1235|gene1235|rna1234|rna1234  89 KIKTFYAHdDFIRKIEGHPQDSLFLTASDDTTLKMW 124
                                        6899****777************************* PP

  == domain 4  score: 22.7 bits;  conditional E-value: 3.6e-08
                                        EEEESSSS.EEEEE..EETTSSEEEEEETTSEEEEEE CS
                               WD40   5 rtltGHss.vtsla..fspdgawlasGsdDgtvriWd 38 
                                         ++tGH++ v +++   +++g++ +s+s D t+++W+
  gene1235|gene1235|rna1234|rna1234 134 MVYTGHTHfVMDVCfyPNDSGKF-VSCSLDSTIKVWN 169
                                        6799**55599999656666666.58999*******8 PP

  == domain 5  score: 24.6 bits;  conditional E-value: 8.7e-09
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                         c++t++GH s+++s++f  +g++l+sG dD  +++Wd
  gene1235|gene1235|rna1234|rna1234 174 HCVKTFRGHaSGINSICFL-SGDYLVSGADDLVLKVWD 210
                                        59*******9889999776.5566689**********9 PP

  == domain 6  score: 27.2 bits;  conditional E-value: 1.4e-09
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        qc++tl+GH ++++ +    + +++as+++Dg++r+W+
  gene1235|gene1235|rna1234|rna1234 215 QCITTLSGHtNNINKVYLFTSFPLFASCGEDGSIRLWN 252
                                        8********9888888766666999************8 PP

  == domain 7  score: 1.5 bits;  conditional E-value: 0.17
                                        EEETTSSEEEEEETTSEEEE CS
                               WD40  17 afspdgawlasGsdDgtvri 36 
                                         +sp+g+ +a Gs  g  +i
  gene1235|gene1235|rna1234|rna1234 339 EVSPSGKTIAVGS-EGEFHI 357
                                        48**********9.777766 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 0.61
                                        EESS.SSEEEEEEETTSSEEEEE.ETTSEE CS
                               WD40   7 ltGH.ssvtslafspdgawlasG.sdDgtv 34 
                                        +  H ss++++        +a G   Dgt+
  gene1235|gene1235|rna1234|rna1234 527 YVHHfSSINGV--------VA-GiE-DGTL 546
                                        5567788****........85.766.7775 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0016       5.7      34      85 ..       9      60 ..       3      66 .. 0.87
   2 !    6.2   0.0    0.0036        13       6      76 ..      66     134 ..      63     146 .. 0.85
   3 ?    0.5   0.0      0.22   7.8e+02      37      86 ..     139     188 ..     129     193 .. 0.74
   4 ?    2.0   0.0     0.072   2.6e+02      28      85 ..     166     228 ..     143     234 .. 0.71
   5 ?   -3.1   0.0       2.8     1e+04      24      40 ..     264     278 ..     260     283 .. 0.68
   6 ?   -1.8   0.0       1.1   3.9e+03      44      66 ..     338     359 ..     334     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0016
                        ANAPC4_WD40 34 edkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavt 85
                                       ++  +s+v+s++ +p   +  ++   g v++ d+ +  +v++++v++e   t
  gene1235|gene1235|rna1234|rna1234  9 KTFGSSKVKSIQMHPTKAIAIIGLFSGDVQVWDIDKMSMVSNIHVSNEPIRT 60
                                       456789**************************************99986444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0036
                        ANAPC4_WD40   6 tmDLiAlatedgellvfRl.ngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76 
                                         mD + ++++dg+++v+ l + +++ t+   ++d  +r+++ +p+++l+  a +d+++++  +++g++ +++
  gene1235|gene1235|rna1234|rna1234  66 RMDWLLVGSDDGNVNVYELgKYRKIKTF--YAHDDFIRKIEGHPQDSLFLTASDDTTLKMW-VYEGEISQKM 134
                                        6999999***********9677888888..8999******************999999976.6677766655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.22
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavays.dgevrlldaesgkvvhslsvksekavtc 86 
                                        + + v ++++ p+++   v++s d+++++ ++ + ++v++++ +++  +++
  gene1235|gene1235|rna1234|rna1234 139 HTHFVMDVCFYPNDSGKFVSCSlDSTIKVWNVGQSHCVKTFRGHASG-INS 188
                                        5667888888888877667766589*************999887763.555 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.072
                        ANAPC4_WD40  28 rvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavt 85 
                                        +vw++       +  ++ s ++s+++  +g  L+ + +d  +++ d ++++++ +ls ++++ ++
  gene1235|gene1235|rna1234|rna1234 166 KVWNVgqshcvkTFRGHASGINSICF-LSGDYLVSGADDLVLKVWDFQTTQCITTLSGHTNN-IN 228
                                        56666555555545666777888887.46888999999999999999999999988877663.55 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 2.8
                        ANAPC4_WD40  24 lngqrvwtleedkedse 40 
                                        l+g rvw++  +++d++
  gene1235|gene1235|rna1234|rna1234 264 LQGGRVWDV--KEKDGK 278
                                        567899999..444444 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 1.1
                        ANAPC4_WD40  44 LaWkpdgklLavaysdgevrlld 66 
                                        L+ +p+gk +av+ s+ge ++++
  gene1235|gene1235|rna1234|rna1234 338 LEVSPSGKTIAVG-SEGEFHIFS 359
                                        777899*****99.567777776 PP

>> Frtz  WD repeat-containing and planar cell polarity effector protein Fritz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.01        37     304     333 ..      18      48 ..      14      57 .. 0.80
   2 !   12.3   0.0   1.1e-05     0.039     260     325 ..      56     123 ..      43     127 .. 0.73
   3 ?   -0.9   0.1      0.11   3.9e+02     501     525 ..     610     634 ..     594     650 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.01
                               Frtz 304 liswhpdsaillvasergelqifDla.Lspi 333
                                         i++hp +ai +++   g++q++D+  +s +
  gene1235|gene1235|rna1234|rna1234  18 SIQMHPTKAIAIIGLFSGDVQVWDIDkMSMV 48 
                                        6899********************9624444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.1e-05
                               Frtz 260 aqvislafnpdedkLllGceDssviLydee..rki.tklvkaevvPsliswhpdsaillvasergelqi 325
                                         ++ ++ + +  d Ll+G+ D++v +y+    rki t +++ +++  +i+ hp+++++l as+ + l++
  gene1235|gene1235|rna1234|rna1234  56 EPIRTCVILSRMDWLLVGSDDGNVNVYELGkyRKIkTFYAHDDFI-RKIEGHPQDSLFLTASDDTTLKM 123
                                        3445556667889**************975337873455566665.789**************999886 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.11
                               Frtz 501 fhfLLrkkrfekafllavDigakDL 525
                                        f  LL+ +r+++af+ a  i ++D 
  gene1235|gene1235|rna1234|rna1234 610 FEILLKLDRYDEAFSKANSIVKYDK 634
                                        6789**************9999984 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.9   1.4e+04      25      31 ..     597     603 ..     593     605 .. 0.67
   2 ?    2.0   0.1      0.08   2.9e+02      10      22 ..     612     624 ..     611     634 .. 0.79
   3 ?    6.4   0.1    0.0032        11       4      26 ..     632     654 ..     629     656 .. 0.91
   4 ?    3.6   0.3     0.024        87      10      25 ..     692     707 ..     691     708 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.9
                              TPR_2  25 ekAleld 31 
                                        ekAlel+
  gene1235|gene1235|rna1234|rna1234 597 EKALELC 603
                                        5666664 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.08
                              TPR_2  10 ayyklgdyeeAle 22 
                                        +++kl++y+eA  
  gene1235|gene1235|rna1234|rna1234 612 ILLKLDRYDEAFS 624
                                        799********65 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0032
                              TPR_2   4 lynlGlayyklgdyeeAleafek 26 
                                        +  lG+  +k+g++ +A e+f +
  gene1235|gene1235|rna1234|rna1234 632 YDKLGRYFLKAGELSKASECFLR 654
                                        5689*****************87 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.024
                              TPR_2  10 ayyklgdyeeAleafe 25 
                                        ay+k g+y+e+++++e
  gene1235|gene1235|rna1234|rna1234 692 AYLKDGQYAECAKLLE 707
                                        8***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4542.59
//
Query:       gene1236|gene1236|rna1235|rna1235  [L=361]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-09   37.0  11.1     0.0034   18.2   0.4    5.5  6  WD40      WD domain, G-beta repeat
     0.0035   16.9   0.0        2.1    7.8   0.0    3.4  3  HPS3_N    Hermansky-Pudlak syndrome 3


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     9e-06     0.081       4      37 ..      14      47 ..      11      48 .. 0.80
   2 !   18.2   0.4   3.8e-07    0.0034       6      38 .]      76     107 ..      72     107 .. 0.88
   3 ?   -3.8   0.0         2   1.8e+04      14      36 ..     127     143 ..     122     145 .. 0.58
   4 ?    4.0   0.1     0.011     1e+02       3      33 ..     188     219 ..     186     221 .. 0.79
   5 ?    3.6   0.0     0.016   1.4e+02      14      34 ..     252     273 ..     239     276 .. 0.71
   6 ?   -0.6   0.1      0.33     3e+03       6      25 ..     334     346 ..     318     354 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                                       EEEEESS..SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40  4 lrtltGH..ssvtslafspdgawlasGsdDgtvriW 37
                                       ++ l  H   s+  +  + + +++a+G+ D+ +r+W
  gene1236|gene1236|rna1235|rna1235 14 THNLHFHeeASIFTM--HGNEKFIATGGGDKDIRLW 47
                                       566677765558888..99********88******* PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.8e-07
                                        EEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +l+GH  sv+++    +g+ las+sd g v +W+
  gene1236|gene1236|rna1235|rna1235  76 VLSGHhRSVNCV--RFNGDILASCSDGGEVILWK 107
                                        699**777****..669********9**999995 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2
                                        EEEEEETTSSEEEEE.ETTSEEEE CS
                               WD40  14 tslafspdgawlasG.sdDgtvri 36 
                                        +++      + l+ G s  g++ +
  gene1236|gene1236|rna1235|rna1235 127 WGC------RHLFVGfS-SGNILV 143
                                        455......44555633.666665 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.011
                                        EEEEEESSSS.EEEEEEETTSSEEEEE.ETTSE CS
                               WD40   3 clrtltGHss.vtslafspdgawlasG.sdDgt 33 
                                        ++++++ H + + +laf+++ + l+ + s+D+t
  gene1236|gene1236|rna1235|rna1235 188 LVQKIKCHEDiIQGLAFNHHFNVLT-SlSKDCT 219
                                        6788899*5548****999999985.5588886 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.016
                                        EEEEEETTSSEE..EEEETTSEE CS
                               WD40  14 tslafspdgawl..asGsdDgtv 34 
                                        + l++spdg++l  +++ + ++v
  gene1236|gene1236|rna1235|rna1235 252 RRLSYSPDGKLLylVCC-RSNSV 273
                                        5789*******632555.35544 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.33
                                        EEESS.SS.EEEEEEETTSSEE CS
                               WD40   6 tltGH.ss.vtslafspdgawl 25 
                                        + +GH ++ v ++        l
  gene1236|gene1236|rna1235|rna1235 334 ITDGHvFDgV-CF--------L 346
                                        4468873346.44........3 PP

>> HPS3_N  Hermansky-Pudlak syndrome 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.026   2.3e+02      18      67 ..      21      74 ..      13      80 .. 0.76
   2 !    3.4   0.0    0.0053        47      28      69 ..     130     167 ..     114     172 .. 0.73
   3 !    7.8   0.0   0.00024       2.1       6      58 ..     278     334 ..     273     339 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.026
                             HPS3_N 18 qeptavcaagdkLlvatesgc..vevydleeeeckv..lcrfstvdkvlkiays 67
                                       +e   ++++g++ ++at +g   +  + +e++ ck   +c  +++d  +ki+y 
  gene1236|gene1236|rna1235|rna1235 21 EEASIFTMHGNEKFIATGGGDkdIRLWRVEKDTCKGidFCYTTAIDSSIKIKYH 74
                                       56667777778899***988557******9999985225777778888888886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0053
                             HPS3_N  28 dkLlvatesgcvevydleeeeckvlcrfstvdkvlkiayses 69 
                                         +L+v+ +sg + vy++++++ +    + t d++++ +++e+
  gene1236|gene1236|rna1235|rna1235 130 RHLFVGFSSGNILVYQVTSDN-N---FLDTADAINEGEFNEA 167
                                        36**************98433.3...3567777777666665 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00024
                             HPS3_N   6 HnFksqevv....sveqeptavcaagdkLlvatesgcvevydleeeeckvlcrfstv 58 
                                        ++F+  +v     + + ep +v++++d+++++t++    v +++   c    +f+t+
  gene1236|gene1236|rna1235|rna1235 278 YPFRMEHVYatigPFDSEPLKVVCGEDRVFITTKKSLYMVAHNKPALCVDNISFMTI 334
                                        55665555411115678*****************99877777777778777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2390.85
//
Query:       gene1237|gene1237|rna1236|rna1236  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-37  127.2   1.4    4.6e-37  126.3   1.4    1.5  1  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
    1.5e-19   70.2   0.0    3.4e-19   69.0   0.0    1.6  1  MMR_HSR1        50S ribosome-binding GTPase
    3.1e-19   68.8   0.0    6.1e-19   67.8   0.0    1.5  1  TGS             TGS domain
    3.9e-12   46.0   0.0    6.7e-12   45.2   0.0    1.4  1  FeoB_N          Ferrous iron transport protein B
     0.0017   17.7   0.0     0.0032   16.8   0.0    1.4  1  AIG1            AIG1 family
     0.0078   15.2   0.0       0.03   13.3   0.0    1.9  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
  ------ inclusion threshold ------
      0.011   15.8   0.2        1.1    9.2   0.0    2.5  2  Dynamin_N       Dynamin family
      0.036   14.0   0.0      0.064   13.2   0.0    1.4  1  Ploopntkinase3  P-loop Nucleotide Kinase3
       0.04   14.1   0.0       0.15   12.3   0.0    2.0  1  Roc             Ras of Complex, Roc, domain of DAPkinase
      0.041   14.3   0.0       0.07   13.5   0.0    1.4  1  AAA_16          AAA ATPase domain
      0.047   14.0   0.0       0.18   12.0   0.0    2.0  3  AAA_22          AAA domain
      0.065   13.5   0.1       0.18   12.0   0.1    1.8  1  AAA_28          AAA domain
      0.072   12.2   0.0       0.17   11.0   0.0    1.5  1  MCM             MCM P-loop domain
      0.077   12.2   0.0       0.32   10.1   0.0    2.0  2  NB-ARC          NB-ARC domain
      0.083   13.4   0.0       0.18   12.3   0.0    1.7  1  ABC_tran        ABC transporter
      0.086   12.1   0.1         12    5.1   0.1    2.2  2  6PF2K           6-phosphofructo-2-kinase


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   1.4   4.1e-40   4.6e-37       2     106 .]     183     287 ..     182     287 .. 0.99

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 4.1e-40
                       MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldela 77 
                                        gGi+i  t++ltk++eet+k+il+eyki+n+++ +redv  Dd+id ++g+ vY+ clyv+NKiD++sle+++++a
  gene1237|gene1237|rna1236|rna1236 183 GGINIGVTCQLTKTTEETIKAILREYKINNCQMFVREDVCDDDIIDLVSGSSVYVDCLYVYNKIDELSLEDFNKVA 258
                                        9*************************************************************************** PP

                       MMR_HSR1_Xtn  78 repnsvviSaekelnldeLkekiweeLnL 106
                                        + p+s+ iS++ke+n+d L+e+iw++L+L
  gene1237|gene1237|rna1236|rna1236 259 EYPDSTLISCQKEWNIDMLLEDIWNKLGL 287
                                        ***************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   0.0     3e-22   3.4e-19       1     104 [.      63     170 ..      63     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 3e-22
                                        EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC. CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee. 75 
                                        +va++G p vGKStL++++t++ ++++++ +tT++ + g++ l+g+ i+++D+pG+++gas+++g g+++ ++ + 
  gene1237|gene1237|rna1236|rna1236  63 RVALIGFPSVGKSTLLSKITNTYSRAAEHEFTTLECISGKMYLNGTWIQVLDLPGIVSGASQNRGRGRQVISIARt 138
                                        69*****************************************************999**************9997 PP

                                        TSEEEEEEETT.TTCSHHHHHHHHHHHHH..T CS
                           MMR_HSR1  76 adlillvvdas.eeklkpldeeleellee..a 104
                                        adlil+v+d + +e+ + l++el+e+  +  +
  gene1237|gene1237|rna1236|rna1236 139 ADLILMVLDPRrHEDKRTLENELHEMGIRlnK 170
                                        8********66422223333444444333433 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   5.4e-22   6.1e-19       2      59 ..     289     360 ..     288     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 5.4e-22
                                        EEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                                TGS   2 rvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                        r+yt ++G  p+      +++g tv+D++ +Ih+++  +f++AlV+G       q+vgl h+Led+dvv+I+
  gene1237|gene1237|rna1236|rna1236 289 RIYTkKKGVFPTlddpvvIREGGTVKDLCAHIHKDFLLSFKHALVWGtsakhspQKVGLGHTLEDEDVVQIF 360
                                        9***99999999***********************************************************7 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.0     6e-15   6.7e-12       2     107 ..      63     167 ..      62     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 6e-15
                                        EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.C CS
                             FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.e 76 
                                        +val+G p vGk+tl+ ++t+++++ + +  +t e  +gk+ l+g+ ++++DlPGi   s  s++    r+++   
  gene1237|gene1237|rna1236|rna1236  63 RVALIGFPSVGKSTLLSKITNTYSRAAEHEFTTLECISGKMYLNGTWIQVLDLPGIV--SGASQNRGRGRQVISiA 136
                                        69*****************************************************96..57888889999999648 PP

                                        TSSSEEEEEEEGGGHHHHHHHHHHHHHTTSS CS
                             FeoB_N  77 eepdvvvnvvdatnlernLyLtlqllelgvp 107
                                        +++d+++ v+d  + e + +L  +l e+g++
  gene1237|gene1237|rna1236|rna1236 137 RTADLILMVLDPRRHEDKRTLENELHEMGIR 167
                                        899*************************986 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.8e-06    0.0032       2     104 ..      63     157 ..      62     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                                        EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHH CS
                               AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcl 77 
                                        ++ l+G   +GkS+    i   + ++  ++++  t +c + +   +g+ i+V D Pg+++  +++    ++++   
  gene1237|gene1237|rna1236|rna1236  63 RVALIGFPSVGKSTLLSKIT--NTYSRAAEHEFTTLECISGKMYLNGTWIQVLDLPGIVSGASQNRGRGRQVIS-- 134
                                        67789999999998887774..45666667889999*****************************999999984.. PP

                                        HHCTT-ESEEEEEEETTB-SHHHHHHH CS
                               AIG1  78 llseegihalllvlslgrfteedekal 104
                                         ++++  + +l+vl+ +r +  d+ +l
  gene1237|gene1237|rna1236|rna1236 135 -IART-ADLILMVLDPRRHE--DKRTL 157
                                        .6666.89******999865..55554 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   2.7e-05      0.03      24      56 ..      57      88 ..      40      93 .. 0.85
   2 ?   -2.1   0.0       1.3   1.5e+03     170     219 ..     239     288 ..     211     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                                       GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCT CS
                               MeaB 24 akaGraqvvGltGvPGaGkstlvealglelrrr 56
                                       +k+G a +v l G+P +Gkstl+++++ ++ r+
  gene1237|gene1237|rna1236|rna1236 57 SKSGDA-RVALIGFPSVGKSTLLSKITNTYSRA 88
                                       566766.789****************9988776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                        SEEEEE---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHH CS
                               MeaB 170 DiivvnkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGid 219
                                         ++v nk D+   e  ++  ++  + + + +keW+  +l     ++ G+ 
  gene1237|gene1237|rna1236|rna1236 239 CLYVYNKIDELSLEDFNKVAEYPDSTLISCQKEWNIDMLLEDIWNKLGLT 288
                                        57899999977777777777777777777777787776655555555555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.04        45       1      19 [.      64      82 ..      64     100 .. 0.87
   2 ?    9.2   0.0     0.001       1.1     103     140 ..     110     150 ..      90     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.04
                                       EEEEEBTTTTHHHHHHHHH CS
                          Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                       +a++G  S GKS++l +++
  gene1237|gene1237|rna1236|rna1236 64 VALIGFPSVGKSTLLSKIT 82
                                       7999***********9886 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.001
                                        EEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS CS
                          Dynamin_N 103 ltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanh 140
                                        + ++DlPG+ s + ++    + v ++++ ad+il+v++   
  gene1237|gene1237|rna1236|rna1236 110 IQVLDLPGIVSGASQNRgrgRQVISIARTADLILMVLDPRR 150
                                        7789*******9999999999999999*********97554 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.8e-05     0.064       7      33 ..      65      91 ..      61     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
                     Ploopntkinase3  7 ylvGqPGaGkstlmaeltkgfdrskve 33
                                        l+G P  Gkstl++++t++++r   +
  gene1237|gene1237|rna1236|rna1236 65 ALIGFPSVGKSTLLSKITNTYSRAAEH 91
                                       69********************98766 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.15       1      92 [.      63     151 ..      63     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEE.EEEEE-SGGCTTTT-H. CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvkl.niWDtaGqerfrslhp. 74 
                                        +v l+G  +vGK++ll+++++   +  e++ + ++ ++ ++  ++g+     ++ + l  i   a q+r r  +  
  gene1237|gene1237|rna1236|rna1236  63 RVALIGFPSVGKSTLLSKITNTYSRAAEHEFTTLECISGKMY-LNGT----WIQVLDLpGIVSGASQNRGRGRQVi 133
                                        589*****************8888887877777777776653.4432....2333333344445556666654431 PP

                                        HHHCTSCEEEEEEEGHHH CS
                                Roc  75 lylreaalailvydsrss 92 
                                        +  r a+l+++v+d r++
  gene1237|gene1237|rna1236|rna1236 134 SIARTADLILMVLDPRRH 151
                                        334566666666665544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.3e-05      0.07      25      76 ..      62     113 ..      54     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                             AAA_16  25 elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysalaqal 76 
                                          v l+G + vGKs+l+ ++ + ++++         +++gk   +       +++q+l
  gene1237|gene1237|rna1236|rna1236  62 ARVALIGFPSVGKSTLLSKITNTYSRAaeheftTLECISGKMYLN------GTWIQVL 113
                                        5688*****************999888433222111133333333......3355555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.18       8      37 ..      64      93 ..      58     147 .. 0.82
   2 ?   -1.8   0.0         3   3.4e+03      44      70 ..     188     214 ..     154     278 .. 0.66
   3 ?   -1.9   0.0       3.3   3.7e+03      57      67 ..     278     288 ..     194     329 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                             AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee 37
                                       ++++G + +GK+tll ++++++ ++a++e 
  gene1237|gene1237|rna1236|rna1236 64 VALIGFPSVGKSTLLSKITNTYSRAAEHEF 93
                                       589*******************98888775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                             AAA_22  44 fvtlpsstsskdllrellralglelka 70 
                                         vt++  ++ ++  +++lr+++ ++  
  gene1237|gene1237|rna1236|rna1236 188 GVTCQLTKTTEETIKAILREYKINNCQ 214
                                        566666666666666666666655544 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.3
                             AAA_22  57 lrellralgle 67 
                                        l+++ ++lgl 
  gene1237|gene1237|rna1236|rna1236 278 LEDIWNKLGLT 288
                                        44444444433 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00016      0.18       1      28 [.      63      91 ..      63     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                             AAA_28  1 kivitGgestGKTtlleaLaargypvv.p 28
                                       +++++G +s GK+tll++++++  +   +
  gene1237|gene1237|rna1236|rna1236 63 RVALIGFPSVGKSTLLSKITNTYSRAAeH 91
                                       799***************99875544434 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00015      0.17      52      84 ..      56      88 ..      44     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00015
                                       SBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                                MCM 52 tklrgdinvllvgdpgtaKsqlLkyveklapra 84
                                       ++  gd  v l+g p+++Ks+lL +++++ +ra
  gene1237|gene1237|rna1236|rna1236 56 VSKSGDARVALIGFPSVGKSTLLSKITNTYSRA 88
                                       456799********************9998887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00029      0.32      21      51 ..      62      93 ..      54     161 .. 0.86
   2 ?   -1.2   0.0      0.82   9.1e+02      63     120 ..     272     289 ..     248     296 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                       EEEEEEESTTSSHHHHHHHHCCSHCCCCC.CB CS
                             NB-ARC 21 lvvalvGmgGvGKttlakqilnksdeveg.rF 51
                                         val G + vGK+tl+++i n ++   + +F
  gene1237|gene1237|rna1236|rna1236 62 ARVALIGFPSVGKSTLLSKITNTYSRAAEhEF 93
                                       3499*****************99776543266 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.82
                                        XHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEEEEEE-SHHHH.. CS
                             NB-ARC  63 dkseeiletilkeLslseddleekeeveslkrklvrlLltkrfllvlDDVweeedwdk 120
                                         ++                                          +l D+w++  + +
  gene1237|gene1237|rna1236|rna1236 272 WNIDM----------------------------------------LLEDIWNKLGLTR 289
                                        44444........................................5555555544444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.18      11      50 ..      61     111 ..      52     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                        TSEEEEEESTTSSHHHHHHHHTTSS--...........SEEEEEETTCEGG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxx RF
                           ABC_tran  11 gekvaivGenGaGKStLlkllagllkp...........teGeilldgkdlk 50 
                                        + +va++G    GKStLl+ +++ ++             +G++ l+g+ ++
  gene1237|gene1237|rna1236|rna1236  61 DARVALIGFPSVGKSTLLSKITNTYSRaaehefttlecISGKMYLNGTWIQ 111
                                        679********************9998555555555555555555555555 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.013        15      14      35 ..      62      83 ..      51      97 .. 0.83
   2 ?    5.1   0.1     0.011        12     105     138 ..     194     227 ..     180     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
                                       EEEEEESSTTSSHHHHHHHHHH CS
                              6PF2K 14 lvivlvGLpargKtyiskkltr 35
                                         + l+G p  gK+++ +k+t 
  gene1237|gene1237|rna1236|rna1236 62 ARVALIGFPSVGKSTLLSKITN 83
                                       5688************999986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                                        ---SHHHHHHHHHHHHHTT-EEEEEEEE--HHHH CS
                              6PF2K 105 tNttrerRklilefveennlkvlflesicsdeei 138
                                        t tt e  k il++ + nn+++++ e +c+d  i
  gene1237|gene1237|rna1236|rna1236 194 TKTTEETIKAILREYKINNCQMFVREDVCDDDII 227
                                        78999999*********************99744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2472.03
//
Query:       gene1238|gene1238|rna1237|rna1237  [L=455]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3155.18
//
Query:       gene1239|gene1239|rna1238|rna1238  [L=319]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  139.8   7.4    4.3e-11   42.4   0.0    6.0  6  Prenyltrans      Prenyltransferase and squalene oxidase repea
  ------ inclusion threshold ------
      0.046   12.8   0.0        3.6    6.6   0.0    2.8  3  SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
      0.068   12.8   0.1       0.13   11.9   0.1    1.4  1  Pardaxin         Pardaxin


Domain annotation for each model (and alignments):
>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.05     3e+02      34      44 .]      35      45 ..      33      45 .. 0.92
   2 !   29.5   0.0   7.4e-11   4.4e-07       3      42 ..      53      93 ..      51      95 .. 0.93
   3 !    4.0   0.0    0.0071        43       8      43 ..     105     140 ..     101     141 .. 0.85
   4 !   29.1   0.1   9.7e-11   5.8e-07       1      44 []     167     210 ..     167     210 .. 0.93
   5 !   32.8   0.0   6.9e-12   4.1e-08       1      44 []     215     258 ..     215     258 .. 0.94
   6 !   42.4   0.0   7.1e-15   4.3e-11       2      44 .]     264     306 ..     263     306 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.05
                                       HHHHHHHHHCT CS
                        Prenyltrans 34 ywalaaLallG 44
                                       yw +++L++lG
  gene1239|gene1239|rna1238|rna1238 35 YWSVNSLSMLG 45
                                       9********98 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 7.4e-11
                                       HHHHHHHHHHHSH.TTS-BBSSTTSSBBHHHHHHHHHHHHH CS
                        Prenyltrans  3 vekavefLlscQn.edGGwggrpgsesdtyytywalaaLal 42
                                       + ++++++++c n +dGG+gg+ g+ s    t+ al++L++
  gene1239|gene1239|rna1238|rna1238 53 KGRVIDYVMRCKNdDDGGFGGCEGYSSNITSTFNALQILYI 93
                                       56789**********************************98 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0071
                                        HHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHC CS
                        Prenyltrans   8 efLlscQnedGGwggrpgsesdtyytywalaaLall 43 
                                         f+ +  +++G +  +  +e+dt+  ++++++L+ll
  gene1239|gene1239|rna1238|rna1238 105 SFISKLLQPEGYFFNDSYGEVDTRINCCGVLGLHLL 140
                                        67888888888888888999**************98 PP

  == domain 4  score: 29.1 bits;  conditional E-value: 9.7e-11
                                        HHHHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHCT CS
                        Prenyltrans   1 idvekavefLlscQnedGGwggrpgsesdtyytywalaaLallG 44 
                                        id++++v +  +c n dGG+g   g es++++ +++l++L  lG
  gene1239|gene1239|rna1238|rna1238 167 IDIKTIVSYTQKCYNLDGGFGAVEGAESHAAQVFCCLSTLRSLG 210
                                        68888999999*****************************9876 PP

  == domain 5  score: 32.8 bits;  conditional E-value: 6.9e-12
                                        HHHHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHCT CS
                        Prenyltrans   1 idvekavefLlscQnedGGwggrpgsesdtyytywalaaLallG 44 
                                        idve +++f+  +Q+ +GG++gr  +  d++y++wa+++L l+G
  gene1239|gene1239|rna1238|rna1238 215 IDVEGVTRFVAMKQMVSGGLSGRVSKKEDVCYSFWAYSSLVLIG 258
                                        799********************88855*************998 PP

  == domain 6  score: 42.4 bits;  conditional E-value: 7.1e-15
                                        HHHHHHHHHHHHSHTTS-BBSSTTSSBBHHHHHHHHHHHHHCT CS
                        Prenyltrans   2 dvekavefLlscQnedGGwggrpgsesdtyytywalaaLallG 44 
                                        + +++v f+l cQ   GG+++rpg e+d+y+ ++ala+L+llG
  gene1239|gene1239|rna1238|rna1238 264 NQKELVKFILACQGRYGGFSDRPGNEADLYHLMFALAGLSLLG 306
                                        789***************************************8 PP

>> SQHop_cyclase_N  Squalene-hopene cyclase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.018   1.1e+02      41      80 ..      47      87 ..      38      92 .. 0.77
   2 ?    2.3   0.0     0.013        76      47      90 ..     217     260 ..     195     265 .. 0.87
   3 ?    6.6   0.0   0.00061       3.6      40      90 ..     258     308 ..     253     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.018
                    SQHop_cyclase_N 41 eddeeeeekiakylrsqqr.edGgWelypggpgdlsttvea 80
                                       e+ ee + ++  y+++ ++ +dGg++ + g ++++  t +a
  gene1239|gene1239|rna1238|rna1238 47 EEIEEMKGRVIDYVMRCKNdDDGGFGGCEGYSSNITSTFNA 87
                                       4445666677778777777699*************999876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.013
                    SQHop_cyclase_N  47 eekiakylrsqqredGgWelypggpgdlsttveaYlALkllGds 90 
                                         e +++++  +q   Gg +    ++ d+  +  aY  L l+G +
  gene1239|gene1239|rna1238|rna1238 217 VEGVTRFVAMKQMVSGGLSGRVSKKEDVCYSFWAYSSLVLIGRE 260
                                        567788999999******************************76 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00061
                    SQHop_cyclase_N  40 geddeeeeekiakylrsqqredGgWelypggpgdlsttveaYlALkllGds 90 
                                        g++++ ++++++k++++ q   Gg++  pg+++dl     a  +L llG++
  gene1239|gene1239|rna1238|rna1238 258 GRESRVNQKELVKFILACQGRYGGFSDRPGNEADLYHLMFALAGLSLLGYK 308
                                        667778999**************************************9986 PP

>> Pardaxin  Pardaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.2e-05      0.13       7      23 ..     150     166 ..     147     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                           Pardaxin   7 PKIISSPlFKTLLSAVG 23 
                                        PK +SSP+ K  LS VG
  gene1239|gene1239|rna1238|rna1238 150 PKSLSSPICKVFLSEVG 166
                                        9***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2095.37
//
Query:       gene1240|gene1240|rna1239|rna1239  [L=559]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-46  156.7  30.1      1e-45  156.4  30.1    1.0  1  TLC       TLC ATP/ADP transporter


Domain annotation for each model (and alignments):
>> TLC  TLC ATP/ADP transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.4  30.1   5.7e-50     1e-45      15     491 .]      35     527 ..      20     527 .. 0.83

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 5.7e-50
                                TLC  15 lwpverlelkkllplllllflilfnysilrdlKDslvvtasesgAEvipFlKvwgvlPsAilftliyaklsnklsk 90 
                                         + v r+e  k+ +l l++ +i f+ys +r lKD  v++ +     +i F+K++ +lP+ + ++++   +  + + 
  gene1240|gene1240|rna1239|rna1239  35 YFRVARVEYTKFAILGLMFGIIGFIYSFMRILKDMFVMVRQ--EPTTILFIKIFYILPVSMALVFLIQYMLGTKTV 108
                                        48899********************************9999..7889*************999999999******* PP

                                TLC  91 ekvFyiivsfflvffllFafvlyPlrellhleaeadkle......si.lppglkglialvrnWsyalfYvlaELWg 159
                                         ++F i+   f + f++ ++v+  ++e + +++   ++       s+   + +k +   +++   ++ ++ aE+Wg
  gene1240|gene1240|rna1239|rna1239 109 SRIFSIFCGGFASLFFVCGVVFL-IEEQVSPSKFLFRDMfidgkmSTrGLNVFKSMFLTLNEPLATIVFIAAEMWG 183
                                        ***************99987765.555555554444333000000330345567777778888899********** PP

                                TLC 160 svvlsllfWgfaneitkveeakrFYsllglvanlalivaGevlillsnirkklasavdsweeslkvlvlivvilgl 235
                                        s+vls lf  f ne  ++++  rF + l +++n++l ++ +v+ ++ ++r+kla  +++ + +l+ + +   +l +
  gene1240|gene1240|rna1239|rna1239 184 SLVLSYLFLSFLNESCTIKQFSRFIPPLIIITNVSLFLSATVAGAFFKLREKLA--FQQNQFLLSGIFISQGFLVV 257
                                        ********************************************9999777765..55556667777766677777 PP

                                TLC 236 iilllyrllnkkvltderlylaekkkkkkkkkklslkesfklllrskyllliavlviayglsinlvEvvWKaqik. 310
                                        ++++l  +l++  ++ + + +++ ++ kk+k+++s+ e ++++ +sk ll ++++v+ +++s n++E ++K  +k 
  gene1240|gene1240|rna1239|rna1239 258 LVIFLKIYLERVTMKRPLFIVSSGSRRKKAKANVSFSEGLEIMSQSKLLLAMSLIVLFFNISYNMIESTFKVGVKv 333
                                        78888889***************************************************************97762 PP

                                TLC 311 .elypt..pneynafmgklt.sltGvvtilim.llssnilrkfgWtvaAlitPlillvtgvlFFslilfekelae. 380
                                         + y +  + +y+   ++l   lt vv+i++     s+ +  +g++   +itP++ l+   lF +  l++ +++e 
  gene1240|gene1240|rna1239|rna1239 334 aAEYFNeeKGKYSGKFNRLDqYLTSVVVICLNlSPFSSYVETKGFLLVGVITPIVTLLAITLFLGSALYNTSMEEs 409
                                        2345430134577655555414567777777633457889999*********************999988877652 PP

                                TLC 381 ...liasll.gtspll.lavvvGaiqnilsksaKyslfDatkemayipldeeskvkgkaaidvvgarlGKSggsli 451
                                           +++ l+   +pl+ l  + G i   l k +Kys fD +ke   + +++  + + k++ d++  +lGKS gs+ 
  gene1240|gene1240|rna1239|rna1239 410 gigIVNGLFpSGKPLYiLENYSGIIFMSLLKITKYSAFDICKEKLGMRINPTYRARFKSVYDGIFGKLGKSIGSIY 485
                                        1114555442346776156788999**************************************************9 PP

                                TLC 452 qqllliif..atlasispllavvlllvilvwiiavkklekqf 491
                                          l++ ++    l + +p+ a+++++ +++wi a+  l++ +
  gene1240|gene1240|rna1239|rna1239 486 GLLMFEALdtEDLRKATPITAAIIFIFVVMWIKAIIYLSRSY 527
                                        999999996677999********************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3474.36
//
Query:       gene124|gene124|rna124|rna124  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-05   24.3   0.2     0.0096   15.1   0.0    2.1  2  NAP       Nucleosome assembly protein (NAP)
  ------ inclusion threshold ------
      0.088   12.7   0.0       0.11   12.4   0.0    1.2  1  BOP1NT    BOP1NT (NUC169) domain


Domain annotation for each model (and alignments):
>> NAP  Nucleosome assembly protein (NAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2   0.00027       2.5       5      48 ..       9      52 ..       6      56 .. 0.92
   2 !   15.1   0.0   1.1e-06    0.0096      90     157 ..      57     123 ..      53     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00027
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                            NAP  5 aLkklqkelskleaefqeevlelekkyaalykplyekrseIing 48
                                    L+++q e+++  +ef ++ +e +  +++ +kpl+ +r + i++
  gene124|gene124|rna124|rna124  9 DLEEIQWEIDRKYEEFSKKDFECKLDHHKMIKPLLIRRDQAIAK 52
                                   6999**********************************998875 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-06
                                    THHHHHHHTSHHHHTT--HHHHHHH...TTEEEEEEEE-------EEEEEEEE-S-SSB--SEEEEEEEE- CS
                            NAP  90 eFWltvlknvellaeliqerDepiL...khLkdirveyllskekegFtleFeFdeNpyFtnevLtktyilk 157
                                    ++W +vl   e ++e+i +rD+  L     ++ ++v+yl +     +++e e +eN++  n++L k+ +l 
  gene124|gene124|rna124|rna124  57 SYWGRVLDRYE-IGEMILPRDSSNLintGWMRSLSVDYL-D--GYAYRVEMEVNENEFVANKTLMKKAYLL 123
                                    69*****9887.89********99976567999999995.3..478*****************99875554 PP

>> BOP1NT  BOP1NT (NUC169) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05      0.11      26     101 ..      47     120 ..      19     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                         BOP1NT  26 dkllekiddpkawrtvkDkktgkevkLsdeelelikrlqkgelpdeeydpyedvvelftseeeihplseapepkrr 101
                                    d+ ++k+d+ ++w +v D+++  e+ L +++ +li+    ++l  + +d y+  ve++ +e  ++ +++++  k+ 
  gene124|gene124|rna124|rna124  47 DQAIAKMDSGSYWGRVLDRYEIGEMILPRDSSNLINTGWMRSLSVDYLDGYAYRVEMEVNE--NEFVANKTLMKKA 120
                                    899**********************************9999999999**********9994..4445555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 985.84
//
Query:       gene1241|gene1241|rna1240|rna1240  [L=88]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.023   14.8   0.1    1.4  1  COX6C     Cytochrome c oxidase subunit VIc


Domain annotation for each model (and alignments):
>> COX6C  Cytochrome c oxidase subunit VIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.3e-06     0.023      13      63 ..      36      86 ..      25      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-06
                              COX6C 13 krlkrhlvvafvlslgvaaaykfavaepRKkayadFYknYDaekefeemrk 63
                                       + l+  l++ fvls+ ++ a+ +   ++  k y +    YDa ++  +m++
  gene1241|gene1241|rna1240|rna1240 36 AVLQCALAGLFVLSTSIYGAFRIRNGDKENKSYMERIARYDALDASRKMEN 86
                                       56788899*************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 544.30
//
Query:       gene1242|gene1242|rna1241|rna1241  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-15   54.2   7.5    2.5e-14   52.8   2.7    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
     0.0092   16.0   2.6      0.018   15.0   2.6    1.6  1  CpXC             CpXC protein
  ------ inclusion threshold ------
      0.019   14.4   0.6          3    7.3   0.1    2.5  2  Mu-like_Com      Mu-like prophage protein Com
       0.07   12.0   2.1       0.17   10.8   0.6    1.9  2  tRNA-synt_1f     tRNA synthetases class I (K)
        0.1   12.6   5.8      0.043   13.8   2.5    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.11   12.3  11.9       0.26   11.1   0.1    3.6  3  zf-RING_4        RING/Ubox like zinc-binding domain
       0.11   12.4   8.8        3.2    7.7   0.0    3.3  3  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.28   11.0   4.5        0.3   10.9   4.5    1.1  1  PIP49_N          N-term cysteine-rich ER, FAM69
       0.36   10.6   6.1        2.6    7.8   0.4    2.1  2  UPF0167          Uncharacterised protein family (UPF0167)
       0.79   10.0  10.5        4.7    7.5   1.4    2.3  2  IBR              IBR domain, a half RING-finger domain
       0.88    9.5   6.5        4.5    7.3   0.1    3.1  3  zinc_ribbon_4    zinc-ribbon domain
        2.1    8.8   7.2       0.53   10.7   1.2    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar
        2.6    7.6   7.8        1.9    8.0   0.6    3.5  4  zf-ribbon_3      zinc-ribbon domain
        3.9    7.8   8.3        3.3    8.1   0.4    2.6  3  zf-LITAF-like    LITAF-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.039        50      27      36 ..      16      25 ..      13      29 .. 0.73
   2 !   52.8   2.7   1.9e-17   2.5e-14       1      39 []      59      96 ..      59      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.039
                            TFIIS_C 27 vfykCtkCgh 36
                                       + ++C+ C++
  gene1242|gene1242|rna1241|rna1241 16 TKVECLRCKK 25
                                       5678888886 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 1.9e-17
                            TFIIS_C  1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                       ++Cp Cg +e+++ ++Q Rs DE++tvfy C +Cg++++
  gene1242|gene1242|rna1241|rna1241 59 HRCPACGAEEMMYNTVQVRSTDEGQTVFYSC-ECGYKFT 96
                                       58*****************************.*****96 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.6   1.4e-05     0.018       1      68 [.      18      89 ..      18      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                               CpXC  1 ltCpaCgkefeaeiwtsidadedpe...lkekl.ldgslfeatCpkCgatakleapllyhdpekellillvp 68
                                       ++C +C+ke ++++ + i ++ + +     e++ ++g   +++Cp+Cga+ ++   + +   ++ + +++  
  gene1242|gene1242|rna1241|rna1241 18 VECLRCKKENSVDMIRPIYTEVEIKgdsCIEAIdVSGAKIKHRCPACGAEEMMYNTVQVRSTDEGQTVFYSC 89
                                       68********99876666555544311134444599****************99999988888888887765 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0024         3      30      48 ..       5      23 ..       3      28 .. 0.85
   2 ?    5.4   0.0    0.0099        13      23      32 ..      57      66 ..      38      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0024
                        Mu-like_Com 30 CGtLnHlkaesldaegrRe 48
                                       CGtL  +k++s + e  R 
  gene1242|gene1242|rna1241|rna1241  5 CGTLIYVKSNSTKVECLRC 23
                                       ***********99987665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0099
                        Mu-like_Com 23 ltiKCPRCGt 32
                                       ++ +CP CG 
  gene1242|gene1242|rna1241|rna1241 57 IKHRCPACGA 66
                                       6678*****6 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.016        20     169     210 ..      28      69 ..      17      72 .. 0.74
   2 ?   10.8   0.6   0.00013      0.17     177     212 ..      61      98 ..      53      99 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.016
                       tRNA-synt_1f 169 tyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeee 210
                                        +   + p+ ++ +      ++++d+++ +i+++c +cG ee 
  gene1242|gene1242|rna1241|rna1241  28 SVDMIRPIYTEVEIKGDSCIEAIDVSGAKIKHRCPACGAEEM 69 
                                        55556666666665566678889999************9875 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                       tRNA-synt_1f 177 cekcg...rv.dttevvevdaeeeeieYkceecGeeeevd 212
                                        c++cg    + +t++v ++d e++++ Y+c ecG++ +v+
  gene1242|gene1242|rna1241|rna1241  61 CPACGaeeMMyNTVQVRSTD-EGQTVFYSC-ECGYKFTVQ 98 
                                        55554221332678899998.*********.****99875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   2.5   3.3e-05     0.043      62      99 ..       9      71 ..       3      81 .. 0.84
   2 ?   -1.2   0.1       1.6     2e+03      70      82 ..      86      97 ..      75      99 .] 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                                       EEEEEE--EEEETTTS-EEECHH.HHH.........................S-TTTSSS-EEE CS
                               HypA 62 LeieevpvkvrCreCgkefelee.kal.........................rCpkCgsadvei 99
                                       + +++ + kv+C +C+ke +++  +                           rCp+Cg++++  
  gene1242|gene1242|rna1241|rna1241  9 IYVKSNSTKVECLRCKKENSVDMiR-PiyteveikgdscieaidvsgakikhRCPACGAEEMMY 71
                                       55789999*********99988643.14577899*************************98755 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                                       EEEETTTS-EEEC CS
                               HypA 70 kvrCreCgkefel 82
                                        + C eCg++f++
  gene1242|gene1242|rna1241|rna1241 86 FYSC-ECGYKFTV 97
                                       4567.58888875 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.8      0.13   1.7e+02      34      46 ..      14      26 ..       1      28 [. 0.60
   2 ?    4.5   1.3     0.024        31      36      43 ..      57      64 ..      44      67 .. 0.66
   3 ?   11.1   0.1    0.0002      0.26       8      24 ..      79      95 ..      74      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                          zf-RING_4 34 eeeegrCPaCree 46
                                       ++++  C  C++e
  gene1242|gene1242|rna1241|rna1241 14 NSTKVECLRCKKE 26
                                       3467889999986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.024
                          zf-RING_4 36 eegrCPaC 43
                                        + rCPaC
  gene1242|gene1242|rna1241|rna1241 57 IKHRCPAC 64
                                       47899999 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0002
                          zf-RING_4  8 ldetdkdlkpCeCgyqi 24
                                        de  + ++ CeCgy++
  gene1242|gene1242|rna1241|rna1241 79 TDEGQTVFYSCECGYKF 95
                                       57888899*******97 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.1      0.42   5.3e+02      10      28 ..       5      24 ..       2      27 .. 0.61
   2 ?    7.7   0.0    0.0025       3.2       2      12 ..      56      66 ..      55      69 .. 0.83
   3 ?    7.2   0.7    0.0038       4.9       5      18 ..      87      99 .]      87      99 .] 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.42
                     Zn_ribbon_SprT 10 Cgreythhlsi.rrhnYrCr 28
                                       Cg+ +++ + + + +  rC+
  gene1242|gene1242|rna1241|rna1241  5 CGTLIYVKSNStKVECLRCK 24
                                       66666666666666656666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                     Zn_ribbon_SprT  2 kyvYrCtgCgr 12
                                       k ++rC+ Cg 
  gene1242|gene1242|rna1241|rna1241 56 KIKHRCPACGA 66
                                       6799*****96 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0038
                     Zn_ribbon_SprT  5 YrCtgCgreythhl 18
                                       Y+C  Cg ++t+++
  gene1242|gene1242|rna1241|rna1241 87 YSC-ECGYKFTVQS 99
                                       9**.***9999875 PP

>> PIP49_N  N-term cysteine-rich ER, FAM69
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.5   0.00024       0.3      20      89 ..       4      74 ..       1      90 [. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                            PIP49_N 20 vlswvvYvqyssyselCrgleverkvnkiCdkyrkgiisGslCeeLCeketls.elkClsakpkeqvfsak 89
                                       +   ++Yv+++s    C   + e++v +i   y + +i+G  C e  + +    +++C +  ++e ++ + 
  gene1242|gene1242|rna1241|rna1241  4 ICGTLIYVKSNSTKVECLRCKKENSVDMIRPIYTEVEIKGDSCIEAIDVSGAKiKHRCPACGAEEMMYNTV 74
                                       667899*******9**********************************999888999*8888888888765 PP

>> UPF0167  Uncharacterised protein family (UPF0167)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4     0.002       2.6      19      52 ..      16      50 ..       9      60 .. 0.83
   2 ?    6.5   0.7    0.0051       6.5      20      51 ..      58      89 ..      51      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.002
                            UPF0167 19 eeekCqcCgkereliyespfysvedv.ealCpwCi 52
                                        +++C  C+ke+++ +  p+y++ ++    C + i
  gene1242|gene1242|rna1241|rna1241 16 TKVECLRCKKENSVDMIRPIYTEVEIkGDSCIEAI 50
                                       6799*******************999767787776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0051
                            UPF0167 20 eekCqcCgkereliyespfysvedvealCpwC 51
                                       ++ C  Cg e+ ++ + ++ s+++ +++   C
  gene1242|gene1242|rna1241|rna1241 58 KHRCPACGAEEMMYNTVQVRSTDEGQTVFYSC 89
                                       579*********************99887777 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.4    0.0037       4.7      21      47 ..       3      26 ..       1      30 [. 0.89
   2 ?    7.4   2.2    0.0039         5      18      48 ..      58      95 ..      43      98 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0037
                                IBR 21 CprpdCeaiieksegcksvtCskCgfe 47
                                       C    C+++i  ++++++v+C +C++e
  gene1242|gene1242|rna1241|rna1241  3 CI---CGTLIYVKSNSTKVECLRCKKE 26
                                       76...*****99999999******986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0039
                                IBR 18 lkwCprpdCeaiiekseg..cks.......vtCskCgfef 48
                                       +  Cp+ + e ++ ++ +  + +        +C+ Cg++f
  gene1242|gene1242|rna1241|rna1241 58 KHRCPACGAEEMMYNTVQvrS-TdegqtvfYSCE-CGYKF 95
                                       678**8888899955555431.1334455577**.***99 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.021        27      25      32 ..      17      24 ..      11      31 .. 0.61
   2 ?    7.3   0.1    0.0035       4.5      19      33 ..      52      66 ..      47      67 .. 0.73
   3 ?   -0.9   0.2       1.3   1.6e+03       8      14 ..      91      97 ..      89      99 .] 0.59

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.021
                      zinc_ribbon_4 25 kvrCskCg 32
                                       kv C +C+
  gene1242|gene1242|rna1241|rna1241 17 KVECLRCK 24
                                       55555554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0035
                      zinc_ribbon_4 19 lpakgvkvrCskCgh 33
                                       +++++ k rC++Cg+
  gene1242|gene1242|rna1241|rna1241 52 VSGAKIKHRCPACGA 66
                                       566677888999985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                      zinc_ribbon_4  8 Ckakyei 14
                                       C+ k+++
  gene1242|gene1242|rna1241|rna1241 91 CGYKFTV 97
                                       6666655 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.5      0.26   3.3e+02      19      36 ..      12      25 ..       2      50 .. 0.65
   2 ?   10.7   1.2   0.00041      0.53       5      36 ..      60      93 ..      57      99 .] 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.26
                    Lar_restr_allev 19 qrvvaeigqcvyCadCga 36
                                       ++++      v+C  C+ 
  gene1242|gene1242|rna1241|rna1241 12 KSNST----KVECLRCKK 25
                                       33333....688888877 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00041
                    Lar_restr_allev  5 pCPfCggravlersqrvvaeigq..cvyCadCga 36
                                        CP Cg ++ + ++ +v++  +   ++y  +Cg+
  gene1242|gene1242|rna1241|rna1241 60 RCPACGAEEMMYNTVQVRSTDEGqtVFYSCECGY 93
                                       6*********999988887655578666668999 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   1.5e+03       8      10 ..       5       7 ..       4      13 .. 0.63
   2 ?    1.5   0.0      0.16   2.1e+02       2      16 ..      17      31 ..      16      32 .. 0.80
   3 ?    8.0   0.6    0.0015       1.9       4      10 ..      60      66 ..      58      67 .. 0.85
   4 ?   -0.8   0.1      0.91   1.2e+03      22      25 ..      91      94 ..      90      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                        zf-ribbon_3  8 CGa 10
                                       CG+
  gene1242|gene1242|rna1241|rna1241  5 CGT 7 
                                       555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                        zf-ribbon_3  2 tvrCPnCGa.plssdd 16
                                       +v+C +C++ + s d+
  gene1242|gene1242|rna1241|rna1241 17 KVECLRCKKeN-SVDM 31
                                       589999**999.7776 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0015
                        zf-ribbon_3  4 rCPnCGa 10
                                       rCP+CGa
  gene1242|gene1242|rna1241|rna1241 60 RCPACGA 66
                                       8999997 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.91
                        zf-ribbon_3 22 CGtk 25
                                       CG+k
  gene1242|gene1242|rna1241|rna1241 91 CGYK 94
                                       9998 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.2      0.12   1.5e+02      47      64 ..       8      25 ..       1      29 [. 0.57
   2 ?    3.9   0.3     0.052        67       3      15 ..      15      27 ..      13      50 .. 0.70
   3 ?    8.1   0.4    0.0026       3.3      54      65 ..      56      67 ..      45      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                      zf-LITAF-like 47 fcvdslkdvehyCpnCga 64
                                       +++ + + ++  C +C++
  gene1242|gene1242|rna1241|rna1241  8 LIYVKSNSTKVECLRCKK 25
                                       445566667777777776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.052
                      zf-LITAF-like  3 ptqvdCpaCqqrv 15
                                       +t+v+C +C+++ 
  gene1242|gene1242|rna1241|rna1241 15 STKVECLRCKKEN 27
                                       7899999999986 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0026
                      zf-LITAF-like 54 dvehyCpnCgal 65
                                       +++h+Cp Cga 
  gene1242|gene1242|rna1241|rna1241 56 KIKHRCPACGAE 67
                                       689******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 618.11
//
Query:       gene1243|gene1243|rna1242|rna1242  [L=409]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-13   49.9   0.8    0.00057   19.8   0.0    6.9  8  TPR_2     Tetratricopeptide repeat
    3.4e-12   45.6   3.6    0.00011   21.9   0.0    6.4  7  TPR_1     Tetratricopeptide repeat
    3.2e-11   42.5   5.4    0.00041   20.3   0.0    6.5  7  TPR_8     Tetratricopeptide repeat
    1.2e-07   31.6   3.4     0.0054   17.0   0.3    6.0  6  TPR_17    Tetratricopeptide repeat
    6.1e-07   29.9   0.0      0.074   13.6   0.1    4.3  4  TPR_19    Tetratricopeptide repeat
    2.3e-06   27.9   0.7        8.7    7.2   0.0    5.9  6  TPR_6     Tetratricopeptide repeat
    1.9e-05   25.2   0.0        2.3    9.0   0.0    4.1  4  TPR_16    Tetratricopeptide repeat
    2.7e-05   24.4   0.3        6.6    7.1   0.1    5.2  4  TPR_12    Tetratricopeptide repeat
      7e-05   23.3   0.0        3.6    8.7   0.0    4.8  5  TPR_14    Tetratricopeptide repeat
     0.0007   19.8   0.9       0.69   10.2   0.0    4.1  4  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
  ------ inclusion threshold ------
      0.015   15.1   0.0       0.13   11.9   0.0    2.1  2  TPR_21    Tetratricopeptide repeat-like domain
      0.035   13.8   0.0         16    5.3   0.0    3.5  2  TPR_11    TPR repeat
      0.056   13.8   0.1         18    5.8   0.0    2.6  2  TPR_20    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.6   2.3e+03      21      32 ..      37      48 ..      32      48 .. 0.83
   2 !   12.7   0.0   7.7e-05      0.11       2      33 ..      52      83 ..      51      84 .. 0.95
   3 ?   -0.7   0.0       1.5     2e+03       5      21 ..     124     140 ..     122     143 .. 0.79
   4 ?    4.2   0.0     0.041        57       2      24 ..     158     180 ..     157     182 .. 0.89
   5 ?    0.8   0.0      0.51   7.1e+02       3      24 ..     196     217 ..     194     218 .. 0.85
   6 ?   -2.2   0.0       4.7   6.5e+03       7      25 ..     234     252 ..     232     253 .. 0.81
   7 ?    2.0   0.0      0.21   2.9e+02       2      26 ..     262     286 ..     261     292 .. 0.84
   8 !   19.8   0.0   4.1e-07   0.00057       3      33 ..     297     327 ..     296     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                              TPR_2 21 leafekAleldP 32
                                       ++++e Al+ +P
  gene1243|gene1243|rna1242|rna1242 37 VACCEDALKANP 48
                                       6899*****998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.7e-05
                              TPR_2  2 ealynlGlayyklgdyeeAleafekAleldPn 33
                                       ealy lG+ ++++++ +eA+    +  el+P+
  gene1243|gene1243|rna1242|rna1242 52 EALYSLGKYHIENKNIDEAEIIATRLFELEPE 83
                                       89**************************9997 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.5
                              TPR_2   5 ynlGlayyklgdyeeAl 21 
                                        y + l y++ gdy  A+
  gene1243|gene1243|rna1242|rna1242 124 YGISLFYEAIGDYTSAR 140
                                        56677899999999998 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.041
                              TPR_2   2 ealynlGlayyklgdyeeAleaf 24 
                                        e l++ G ++ k++++++ ++ f
  gene1243|gene1243|rna1242|rna1242 158 ETLFRTGVCLKKMNRLQDSINIF 180
                                        689***************99877 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.51
                              TPR_2   3 alynlGlayyklgdyeeAleaf 24 
                                        +  +++ +y+ + ++e A+e +
  gene1243|gene1243|rna1242|rna1242 196 VQIQMAHLYEMQSKHELAIEVL 217
                                        667899************9976 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 4.7
                              TPR_2   7 lGlayyklgdyeeAleafe 25 
                                         +++ +k g++   +++++
  gene1243|gene1243|rna1242|rna1242 234 YAWIDFKIGNFRGVKKWYR 252
                                        5788899999998888886 PP

  == domain 7  score: 2.0 bits;  conditional E-value: 0.21
                              TPR_2   2 ealynlGlayyklgdyeeAleafek 26 
                                        ++ly  G++ y   +y  Al+ + +
  gene1243|gene1243|rna1242|rna1242 262 YLLYLVGRIRYMERNYMAALRKYMR 286
                                        689*************999998866 PP

  == domain 8  score: 19.8 bits;  conditional E-value: 4.1e-07
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        +++ +G++y+++g++  A+ af  Ale++P+
  gene1243|gene1243|rna1242|rna1242 297 VHNSIGCIYLRQGRFLLAKTAFMNALEINPK 327
                                        58899*************************7 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.19   2.6e+02      17      32 ..      33      48 ..      32      48 .. 0.85
   2 ?    5.6   0.0     0.011        15       2      21 ..      52      71 ..      51      73 .. 0.94
   3 ?   -3.4   0.0       7.6     1e+04      18      25 ..     130     137 ..     129     139 .. 0.57
   4 ?    4.1   0.0     0.032        45       2      21 ..     158     177 ..     157     181 .. 0.86
   5 !    6.1   0.0    0.0078        11       3      22 ..     196     215 ..     194     218 .. 0.86
   6 ?    0.1   0.0      0.59   8.1e+02       3      31 ..     263     291 ..     261     292 .. 0.82
   7 !   21.9   0.0   7.9e-08   0.00011       3      33 ..     297     327 ..     296     328 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHST CS
                              TPR_1 17 ydeAleyyekALelnP 32
                                       ++  ++++e AL+ nP
  gene1243|gene1243|rna1242|rna1242 33 LEAVVACCEDALKANP 48
                                       667789*******999 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHTT-HHHHH CS
                              TPR_1  2 kalynlGnayfklgkydeAl 21
                                       +aly lG  + ++++ deA+
  gene1243|gene1243|rna1242|rna1242 52 EALYSLGKYHIENKNIDEAE 71
                                       79*****************6 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.6
                                        HHHHHHHH CS
                              TPR_1  18 deAleyye 25 
                                         eA+ +y 
  gene1243|gene1243|rna1242|rna1242 130 YEAIGDYT 137
                                        46776665 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.032
                                        HHHHHHHHHHHHTT-HHHHH CS
                              TPR_1   2 kalynlGnayfklgkydeAl 21 
                                        ++l++ G+++ k++++++ +
  gene1243|gene1243|rna1242|rna1242 158 ETLFRTGVCLKKMNRLQDSI 177
                                        688999**********9987 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0078
                                        HHHHHHHHHHHTT-HHHHHH CS
                              TPR_1   3 alynlGnayfklgkydeAle 22 
                                        +  +++++y  + k++ A+e
  gene1243|gene1243|rna1242|rna1242 196 VQIQMAHLYEMQSKHELAIE 215
                                        55689**************8 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 0.59
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                         ly  G + +   +y  Al  y + ++++
  gene1243|gene1243|rna1242|rna1242 263 LLYLVGRIRYMERNYMAALRKYMRTVQVD 291
                                        6788899999999******9888877766 PP

  == domain 7  score: 21.9 bits;  conditional E-value: 7.9e-08
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                        +++ +G +y+++g++  A  ++  ALe+nP+
  gene1243|gene1243|rna1242|rna1242 297 VHNSIGCIYLRQGRFLLAKTAFMNALEINPK 327
                                        6899**************************7 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.61   8.5e+02      16      32 ..      32      48 ..      32      48 .. 0.86
   2 !   11.6   0.0   0.00019      0.26       2      33 ..      52      83 ..      51      84 .. 0.94
   3 ?   -2.2   0.5       5.1   7.1e+03      17      27 ..     105     115 ..     103     117 .. 0.81
   4 ?    2.7   0.0      0.13   1.8e+02       5      23 ..     124     142 ..     122     146 .. 0.86
   5 ?   -0.1   0.0       1.1   1.5e+03       2      25 ..     158     181 ..     157     181 .. 0.84
   6 ?    2.0   0.0      0.23   3.2e+02       4      24 ..     197     217 ..     194     219 .. 0.86
   7 !   20.3   0.0     3e-07   0.00041       4      33 ..     298     327 ..     297     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.61
                                       -HHHHHHHHHHHHHHHH CS
                              TPR_8 16 dyeeAkeyyekaleldp 32
                                       d+e+ ++++e al+++p
  gene1243|gene1243|rna1242|rna1242 32 DLEAVVACCEDALKANP 48
                                       5677799*******998 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00019
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                       ea+y lg+ +++ ++++eA+    +  el+p+
  gene1243|gene1243|rna1242|rna1242 52 EALYSLGKYHIENKNIDEAEIIATRLFELEPE 83
                                       79**************************9996 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5.1
                                        HHHHHHHHHHH CS
                              TPR_8  17 yeeAkeyyeka 27 
                                        ye+ +++y ka
  gene1243|gene1243|rna1242|rna1242 105 YENFVKAYYKA 115
                                        88889999887 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.13
                                        HHHHHHHHHTT-HHHHHHH CS
                              TPR_8   5 ynlgsiylklgdyeeAkey 23 
                                        y +++ y+  gdy +A  +
  gene1243|gene1243|rna1242|rna1242 124 YGISLFYEAIGDYTSARPW 142
                                        678999*********9865 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 1.1
                                        CHHHHHHHHHHHTT-HHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyye 25 
                                        e +++ g +++k+++++ ++  ++
  gene1243|gene1243|rna1242|rna1242 158 ETLFRTGVCLKKMNRLQDSINIFR 181
                                        567778999********9999886 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.23
                                        HHHHHHHHHHTT-HHHHHHHH CS
                              TPR_8   4 yynlgsiylklgdyeeAkeyy 24 
                                          +++++y+ + ++e A+e++
  gene1243|gene1243|rna1242|rna1242 197 QIQMAHLYEMQSKHELAIEVL 217
                                        6789**************987 PP

  == domain 7  score: 20.3 bits;  conditional E-value: 3e-07
                                        HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        ++ +g+iyl +g++  Ak +++ ale++p+
  gene1243|gene1243|rna1242|rna1242 298 HNSIGCIYLRQGRFLLAKTAFMNALEINPK 327
                                        5789*************************7 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   3.9e-06    0.0054       1      33 [.      39      71 ..      39      72 .. 0.96
   2 ?   -1.3   0.0       2.7   3.7e+03      13      31 ..     157     175 ..     155     177 .. 0.81
   3 ?    2.3   0.0       0.2   2.8e+02       8      34 .]     185     215 ..     181     215 .. 0.79
   4 ?   -0.7   0.0       1.8   2.5e+03      11      33 ..     259     281 ..     256     282 .. 0.86
   5 ?    1.8   0.0      0.27   3.8e+02      14      32 ..     296     314 ..     284     316 .. 0.81
   6 ?    4.3   0.0     0.046        63       2      18 ..     318     334 ..     317     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.9e-06
                             TPR_17  1 lylkaleldPnnadaynnLAelllknGdlmtAr 33
                                       +++ al+ +P n +a++ L++++ +n++ ++A+
  gene1243|gene1243|rna1242|rna1242 39 CCEDALKANPCNTEALYSLGKYHIENKNIDEAE 71
                                       79****************************997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.7
                             TPR_17  13 adaynnLAelllknGdlmt 31 
                                         + ++  +++l+k ++l++
  gene1243|gene1243|rna1242|rna1242 157 YETLFRTGVCLKKMNRLQD 175
                                        67789999*****999986 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.2
                             TPR_17   8 ldPnn....adaynnLAelllknGdlmtArq 34 
                                        +dP n    +d+  ++A l++++ +++ A++
  gene1243|gene1243|rna1242|rna1242 185 YDPLNniynPDVQIQMAHLYEMQSKHELAIE 215
                                        56665566699***********999999875 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.8
                             TPR_17  11 nnadaynnLAelllknGdlmtAr 33 
                                        n+++++++ +++ ++  ++m A+
  gene1243|gene1243|rna1242|rna1242 259 NDPYLLYLVGRIRYMERNYMAAL 281
                                        89999999999999999999885 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.27
                             TPR_17  14 daynnLAelllknGdlmtA 32 
                                         ++n  + ++l++G++  A
  gene1243|gene1243|rna1242|rna1242 296 MVHNSIGCIYLRQGRFLLA 314
                                        6899**********97555 PP

  == domain 6  score: 4.3 bits;  conditional E-value: 0.046
                             TPR_17   2 ylkaleldPnnadaynn 18 
                                        + +ale++P+ ++a  n
  gene1243|gene1243|rna1242|rna1242 318 FMNALEINPKLSEASMN 334
                                        789*******9998655 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   5.3e-05     0.074       9      57 ..      35      83 ..      29      86 .. 0.86
   2 ?    1.8   0.0      0.26   3.5e+02       5      51 ..     134     183 ..     132     189 .. 0.78
   3 ?    6.0   0.0     0.013        17      24      55 ..     193     224 ..     185     237 .. 0.87
   4 ?    2.6   0.0      0.14     2e+02       2      31 ..     306     335 ..     305     337 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.3e-05
                             TPR_19  9 eAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57
                                       + +a  e al+++p n ea++ L + +++++++deAe +  +l e +p 
  gene1243|gene1243|rna1242|rna1242 35 AVVACCEDALKANPCNTEALYSLGKYHIENKNIDEAEIIATRLFELEPE 83
                                       55666799*****************************998888777775 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                             TPR_19   5 gdyaeA...lalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                        gdy++A   l ll ++  e+ k+ e + +   +l ++++l++ +++   +
  gene1243|gene1243|rna1242|rna1242 134 GDYTSArpwLVLLNKLGVEKYKSYETLFRTGVCLKKMNRLQDSINIFRVI 183
                                        78888877788888876556666677777999*********999887665 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.013
                             TPR_19  24 naearllLAeallalgqldeAealLdalpeed 55 
                                        n+++++++A ++  +   + A+++L+ + + +
  gene1243|gene1243|rna1242|rna1242 193 NPDVQIQMAHLYEMQSKHELAIEVLNGIEKPN 224
                                        89************************997765 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.14
                             TPR_19   2 laegdyaeAlalleqalqedpknaearllL 31 
                                        l +g++  A  ++ +al+ +pk +ea ++L
  gene1243|gene1243|rna1242|rna1242 306 LRQGRFLLAKTAFMNALEINPKLSEASMNL 335
                                        67999999999**********999888765 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.02        28       1      33 []      52      84 ..      52      84 .. 0.93
   2 ?   -1.6   0.0       4.2   5.8e+03       4      20 ..     124     140 ..     122     141 .. 0.77
   3 !    7.2   0.0    0.0063       8.7       2      27 ..     159     184 ..     158     186 .. 0.91
   4 ?    1.5   0.0      0.42   5.8e+02       3      24 ..     197     218 ..     195     220 .. 0.85
   5 ?    1.4   0.9      0.45   6.2e+02       2      25 ..     263     286 ..     262     289 .. 0.83
   6 ?    3.0   0.0      0.14     2e+02       6      32 ..     301     327 ..     301     327 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                              TPR_6  1 dAlyklalsyrklgdtdkAlealerlikeYPdS 33
                                       +Aly l++ +++ ++ d+A  +  rl +  P+S
  gene1243|gene1243|rna1242|rna1242 52 EALYSLGKYHIENKNIDEAEIIATRLFELEPES 84
                                       7***********99********99999988887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.2
                                        HHHHHHHHHHHHHHHHH CS
                              TPR_6   4 yklalsyrklgdtdkAl 20 
                                        y + l y++ gd++ A+
  gene1243|gene1243|rna1242|rna1242 124 YGISLFYEAIGDYTSAR 140
                                        66777788878999886 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0063
                                        HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   2 AlyklalsyrklgdtdkAlealerli 27 
                                         l++ + +++k+++ ++++ +++ ++
  gene1243|gene1243|rna1242|rna1242 159 TLFRTGVCLKKMNRLQDSINIFRVIV 184
                                        59********************9876 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.42
                                        HHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   3 lyklalsyrklgdtdkAleale 24 
                                        + ++a +y+++ +++ A+e l+
  gene1243|gene1243|rna1242|rna1242 197 QIQMAHLYEMQSKHELAIEVLN 218
                                        568999****99******9885 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.45
                                        HHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   2 AlyklalsyrklgdtdkAlealer 25 
                                         ly+ ++ +++  ++ +Al+ + r
  gene1243|gene1243|rna1242|rna1242 263 LLYLVGRIRYMERNYMAALRKYMR 286
                                        59********977*****998866 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.14
                                        HHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                              TPR_6   6 lalsyrklgdtdkAlealerlikeYPd 32 
                                        ++  y+++g+   A++a+ + ++  P+
  gene1243|gene1243|rna1242|rna1242 301 IGCIYLRQGRFLLAKTAFMNALEINPK 327
                                        577899*99**********99998885 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0018       2.5      21      56 ..      41      74 ..      37      86 .. 0.88
   2 ?   -2.4   0.0       5.9   8.2e+03      44      58 ..     204     218 ..     199     224 .. 0.58
   3 ?    1.6   0.0      0.32   4.4e+02      26      58 ..     253     286 ..     251     292 .. 0.77
   4 !    9.0   0.0    0.0016       2.3       4      40 ..     302     335 ..     300     339 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                             TPR_16 21 eaalkrdpssPdaaeAllllgdaalrqgrlaeAa.al 56
                                       e alk++   P + eAl+ lg  + ++++ +eA+  +
  gene1243|gene1243|rna1242|rna1242 41 EDALKAN---PCNTEALYSLGKYHIENKNIDEAEiIA 74
                                       689****...***********************9554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                             TPR_16  44 alrqgrlaeAaalyr 58 
                                        +  q+ +++A+++++
  gene1243|gene1243|rna1242|rna1242 204 YEMQSKHELAIEVLN 218
                                        445556666665554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.32
                             TPR_16  26 rdpssPdaaeAllllgdaalrqgrlaeAa.alyr 58 
                                        +d+ ++ ++  l+l g++++   ++ +A+  + r
  gene1243|gene1243|rna1242|rna1242 253 ADSTTSNDPYLLYLVGRIRYMERNYMAALrKYMR 286
                                        5666677888899999999999999999877766 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0016
                             TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllll 40 
                                        + ++lr+g++  A  a+  al+ +   P   eA+++l
  gene1243|gene1243|rna1242|rna1242 302 GCIYLRQGRFLLAKTAFMNALEIN---PKLSEASMNL 335
                                        789*********************...9999999876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.036        50      28      72 ..      35      78 ..      28      83 .. 0.73
   2 ?    2.3   0.0      0.15   2.1e+02      40      68 ..     152     180 ..     120     182 .. 0.63
   3 ?    3.0   0.0     0.088   1.2e+02      49      68 ..     198     217 ..     192     219 .. 0.77
   4 !    7.1   0.1    0.0048       6.6      47      74 ..     297     324 ..     262     327 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.036
                             TPR_12 28 kaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72
                                       ++++ ++ +l + +p+  ++l+ Lg ++ + ++ +eA+ + ++  
  gene1243|gene1243|rna1242|rna1242 35 AVVACCEDAL-KANPCNTEALYSLGKYHIENKNIDEAEIIATRLF 78
                                       5555555554.3467777899999999999999999998887755 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                             TPR_12  40 dhpltattlrnLgrlyralgryeeAlell 68 
                                        +++   +tl+  g ++ +++r+++ ++++
  gene1243|gene1243|rna1242|rna1242 152 EKYKSYETLFRTGVCLKKMNRLQDSINIF 180
                                        44444567777778888888888777776 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.088
                             TPR_12  49 rnLgrlyralgryeeAlell 68 
                                        + ++ ly+++ ++e A+e l
  gene1243|gene1243|rna1242|rna1242 198 IQMAHLYEMQSKHELAIEVL 217
                                        56788888888888888876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0048
                             TPR_12  47 tlrnLgrlyralgryeeAlelleealai 74 
                                        + + +g +y+++gr+  A  ++  al+i
  gene1243|gene1243|rna1242|rna1242 297 VHNSIGCIYLRQGRFLLAKTAFMNALEI 324
                                        5555566666666666655555555555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0088        12      15      42 ..      31      58 ..      27      59 .. 0.87
   2 !    8.7   0.0    0.0026       3.6       2      36 ..      52      86 ..      51      93 .. 0.91
   3 ?   -2.0   0.0       7.1   9.8e+03       9      23 ..     128     142 ..     123     143 .. 0.80
   4 ?    2.6   0.0      0.23   3.2e+02       2      25 ..     195     218 ..     194     226 .. 0.88
   5 ?    2.5   0.0      0.25   3.4e+02      11      37 ..     305     331 ..     304     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0088
                             TPR_14 15 GdpdeAiallrralalaPddaeawllla 42
                                        d+++ +a++++al+++P + ea++ l+
  gene1243|gene1243|rna1242|rna1242 31 PDLEAVVACCEDALKANPCNTEALYSLG 58
                                       5889999***************998776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                             TPR_14  2 eallalaeallalGdpdeAiallrralalaPddae 36
                                       eal+ l++++ ++ + deA+ ++ r+ +l P++ e
  gene1243|gene1243|rna1242|rna1242 52 EALYSLGKYHIENKNIDEAEIIATRLFELEPESYE 86
                                       799****************************9865 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.1
                             TPR_14   9 eallalGdpdeAial 23 
                                         +++a Gd+  A+  
  gene1243|gene1243|rna1242|rna1242 128 LFYEAIGDYTSARPW 142
                                        579999999999865 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.23
                             TPR_14   2 eallalaeallalGdpdeAiallr 25 
                                        +++ ++a++++ + +++ Ai++l+
  gene1243|gene1243|rna1242|rna1242 195 DVQIQMAHLYEMQSKHELAIEVLN 218
                                        67789*****************97 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.25
                             TPR_14  11 llalGdpdeAiallrralalaPddaea 37 
                                        +l++G++  A +++  al+ +P+  ea
  gene1243|gene1243|rna1242|rna1242 305 YLRQGRFLLAKTAFMNALEINPKLSEA 331
                                        89********************97776 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0005      0.69       9      55 ..      37      84 ..      32      95 .. 0.85
   2 ?    0.3   0.0      0.62   8.6e+02      54      79 ..     155     180 ..     110     183 .. 0.72
   3 ?    4.0   0.0     0.042        58      26      71 ..     197     243 ..     184     246 .. 0.82
   4 ?   -1.5   0.1       2.2   3.1e+03      21      45 ..     259     283 ..     248     308 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                                       HHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC- CS
                             ANAPC3  9 iflaerllaaetespedayllAlclylngqykrAyellrka.klnsks 55
                                       + ++e +l+a++ + e++y l++ + +n++ ++A  ++ ++ +l+++s
  gene1243|gene1243|rna1242|rna1242 37 VACCEDALKANPCNTEALYSLGKYHIENKNIDEAEIIATRLfELEPES 84
                                       56899999999********************99999988887777666 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.62
                                        C-HHHHHHHHHHHHHTT-HHHHHHHH CS
                             ANAPC3  54 kslgcrylfAqcllkLkkyeeAiaaL 79 
                                        ks + ++ ++ cl k++++++ i+++
  gene1243|gene1243|rna1242|rna1242 155 KSYETLFRTGVCLKKMNRLQDSINIF 180
                                        44456666778888999999999887 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.042
                                        HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT- CS
                             ANAPC3  26 ayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkk 71 
                                            A  +  +++++ A+e+l+   k n ++l +  l+A   +k+++
  gene1243|gene1243|rna1242|rna1242 197 QIQMAHLYEMQSKHELAIEVLNGIeKPNRHHLIISRLYAWIDFKIGN 243
                                        5566899999**************99999999999998877777765 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 2.2
                                        --HHHHHHHHHHHHHTT-HHHHHHH CS
                             ANAPC3  21 espedayllAlclylngqykrAyel 45 
                                        ++p+ +yl +   y   +y  A++ 
  gene1243|gene1243|rna1242|rna1242 259 NDPYLLYLVGRIRYMERNYMAALRK 283
                                        4444455556666666666666654 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.33   4.5e+02      72     141 ..     152     222 ..     143     226 .. 0.73
   2 ?   11.9   0.0   9.6e-05      0.13     121     188 ..     269     337 ..     264     341 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.33
                             TPR_21  72 taYaalaaLllAkaavea.gdlaaAkaqLewvlekakdeelkalarlRLarvllaekkydeAlktLeakke 141
                                         +Y ++ +L+ + +  ++ + l+++ + ++ ++ +  ++ ++  +++++a ++  + k++ A++ L++ ++
  gene1243|gene1243|rna1242|rna1242 152 EKYKSYETLFRTGVCLKKmNRLQDSINIFRVIVYDPLNNIYNPDVQIQMAHLYEMQSKHELAIEVLNGIEK 222
                                        556666666666665554255666777777777777777777889999***************99998765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.6e-05
                             TPR_21 121 rvllaekkydeAlkt.LeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleekarellqlKl 188
                                        r+   e +y +Al++ + +++ ++ +++v +  G i+++qg++  A++a+ +Al+ + + +++ ++lKl
  gene1243|gene1243|rna1242|rna1242 269 RIRYMERNYMAALRKyMRTVQVDSIEGMVHNSIGCIYLRQGRFLLAKTAFMNALEINPKLSEASMNLKL 337
                                        6777889999999652799999********************************999888877777776 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.025        35      20      36 ..      43      59 ..      33      64 .. 0.88
   2 ?    5.3   0.0     0.012        16       3      33 ..     304     334 ..     297     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.025
                             TPR_11 20 AlkldPdnaeayynLGl 36
                                       Alk +P n ea+y LG+
  gene1243|gene1243|rna1242|rna1242 43 ALKANPCNTEALYSLGK 59
                                       9999************8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                             TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayyn 33 
                                        +y  qG++  A +a+ +Al+++P+  ea  n
  gene1243|gene1243|rna1242|rna1242 304 IYLRQGRFLLAKTAFMNALEINPKLSEASMN 334
                                        8999999999*************98887666 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.013        18      10      41 ..      39      70 ..      30      80 .. 0.88
   2 ?    5.1   0.0     0.021        30      21      50 ..     193     222 ..     188     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                             TPR_20 10 eleaalaanpddldarldlAlallaagryeeA 41
                                         e+al+anp + +a + l +  +++++ +eA
  gene1243|gene1243|rna1242|rna1242 39 CCEDALKANPCNTEALYSLGKYHIENKNIDEA 70
                                       56899*******************99999998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                             TPR_20  21 dldarldlAlallaagryeeAleqLleilk 50 
                                        + d ++++A ++ +++++e A+e L  i k
  gene1243|gene1243|rna1242|rna1242 193 NPDVQIQMAHLYEMQSKHELAIEVLNGIEK 222
                                        7899*******************9977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2699.08
//
Query:       gene1244|gene1244|rna1243|rna1243  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-33  114.7  28.5    4.4e-33  114.7  28.5    1.4  2  TRAM_LAG1_CLN8  TLC domain


Domain annotation for each model (and alignments):
>> TRAM_LAG1_CLN8  TLC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.26   4.7e+03     177     184 ..      29      36 ..      16      46 .. 0.48
   2 !  114.7  28.5   2.4e-37   4.4e-33       1     198 []      68     260 ..      68     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.26
                     TRAM_LAG1_CLN8 177 iflilllv 184
                                        +++++ll+
  gene1244|gene1244|rna1243|rna1243  29 VMVFCLLI 36 
                                        11122222 PP

  == domain 2  score: 114.7 bits;  conditional E-value: 2.4e-37
                     TRAM_LAG1_CLN8   1 kfdervvslvqyllstvfglivlsssp...elwegy...perilgathfllkayyllalgYfiydllvlllyekkr 70 
                                        kf+++++++++y++ +++g+ +++s+p       ++       l + +f +++yy l+ +Y++ +l++l+ ++ + 
  gene1244|gene1244|rna1243|rna1243  68 KFSVSLWKAMFYSFTSIYGYLIIRSEPlayT---MKnlsGTWGLHNIPFKVLFYYYLEFAYYFVELFYLFNEH-MY 139
                                        79*************************6663...3333444445556779******************99966.55 PP

                     TRAM_LAG1_CLN8  71 kdfvemliHhiitlvllvlsyvrnlgrvglvvlllhelsdpflnlrkilsylkkkskssklvlfngllfllsFfvc 146
                                        kdf +m++Hhi+t+ ll+lsy r l+r g++++ +h++sdpfl+++k+ +y++ k  s+++ +f  ++f+ +F+v 
  gene1244|gene1244|rna1243|rna1243 140 KDFLQMVTHHIVTIMLLTLSYHRDLLRPGVIIIAVHDISDPFLEISKLTNYIHYK--SLAKGIF--MCFAGVFVVS 211
                                        69**************************************************555..667789*..********** PP

                     TRAM_LAG1_CLN8 147 Rlvllpylillsildvaklslstaplwlpliflilllv.LqllnlyWfylivk 198
                                        Rlv++ + i l+i    ++      + l+l+++  ll  L +++++W ++i+k
  gene1244|gene1244|rna1243|rna1243 212 RLVIYAFFISLPISISIWRYT----FDLYLFLISILLQgLTVMHIIWSSMIMK 260
                                        ******998888876655443....45555555444445***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1982.07
//
Query:       gene1245|gene1245|rna1244|rna1244  [L=249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-60  201.8   1.3    9.8e-60  201.6   1.3    1.0  1  Acetyltransf_15  Putative acetyl-transferase
    0.00059   20.2   0.0     0.0012   19.2   0.0    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0018   18.5   0.0     0.0031   17.8   0.0    1.4  1  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
       0.02   15.0   0.4        3.1    8.0   0.0    2.9  3  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.07   13.1   0.0       0.13   12.3   0.0    1.5  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.6   1.3   2.7e-63   9.8e-60       1     210 []      27     236 ..      27     236 .. 0.99

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 2.7e-63
                    Acetyltransf_15   1 qpiksidqlkdilkevkkeFrnkrdeeeaitknenkydivqykkkeeLvasvfivkkkyyslvssilieknvleiY 76 
                                        q+ik+ +q++d+++e   eF +k+   ++i++  +++di+qyk  eeLvasvf+ + ++y++v+  ++++ ++ +Y
  gene1245|gene1245|rna1244|rna1244  27 QGIKMAEQIVDDYNEAEGEFGTKAMTFDHIFHGGSRMDIFQYKIGEELVASVFLCRTTFYGMVDGNIVNRSAVFVY 102
                                        78************************************************************************** PP

                    Acetyltransf_15  77 tlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkglfvksgPeelkkr 152
                                        t+yvs+k+rg+G++k++L +s+++l+ +Y ++ ++ll+LHlnp DksM+++f++Yy+l+Fr+g+ ++ gP e ++ 
  gene1245|gene1245|rna1244|rna1244 103 TMYVSKKHRGRGYSKRILRDSTDSLNSHYGMNGDFLLVLHLNPRDKSMELAFSIYYNLNFRNGGLTMIGPGEKQYF 178
                                        **************************************************************************** PP

                    Acetyltransf_15 153 lekiltfkdlvkvikkekrseekgkylamfckvndflnkkkiraeemkelgekLrkiL 210
                                        le++l ++++++vi++ ++++++g y++mfc+++++  ++k+r+++++ +g++Lr+iL
  gene1245|gene1245|rna1244|rna1244 179 LEELLDYRNPCDVIDEYDEERDRGMYMVMFCEYSKLFICEKERYSKLMSYGSRLRSIL 236
                                        *******************************************************998 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.3e-07    0.0012      19      49 ..      90     129 ..      65     164 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.3e-07
                                        EEEEES...TCTEE.EEE-GGGTTSSHHHHHHH.H.....T CS
                     Acetyltransf_7  19 alslld...aeitr.laVdpeyrgkGiGraLle.a.....a 49 
                                           +++       + ++V++++rg+G+ +++l+        
  gene1245|gene1245|rna1244|rna1244  90 DGNIVNrsaVFV-YtMYVSKKHRGRGYSKRILRdStdslnS 129
                                        333333332223.25*****************842343321 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   8.5e-07    0.0031      43      94 ..      84     133 ..      30     153 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.5e-07
                                        EEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TE CS
                     Acetyltransf_1  43 eliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gi 94 
                                        +  G++ +++++      ++++ ++Vs+++rg+G+ ++ l++  + + ++ g 
  gene1245|gene1245|rna1244|rna1244  84 TFYGMVDGNIVNR---SAVFVYTMYVSKKHRGRGYSKRILRDSTDSLNSHyGM 133
                                        3445555555555...8999*********************998888777655 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.8   2.9e+03      12      29 ..      41      55 ..      16      57 .. 0.53
   2 ?    8.0   0.0   0.00086       3.1      24      52 ..      98     126 ..      69     131 .. 0.83
   3 ?    4.0   0.1     0.015        54      51      79 ..     196     224 ..     194     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.8
                    Acetyltransf_CG 12 vafleYevrkegvldfth 29
                                       +a+ e+   +++ ++f+h
  gene1245|gene1245|rna1244|rna1244 41 EAEGEF---GTKAMTFDH 55
                                       233333...234566666 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00086
                    Acetyltransf_CG  24 vldfthTeVpeelrGkGiAkkLvkaaldd 52 
                                         + ++  +V++++rG+G+ k++ +   d 
  gene1245|gene1245|rna1244|rna1244  98 AVFVYTMYVSKKHRGRGYSKRILRDSTDS 126
                                        56678889************999877765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.015
                    Acetyltransf_CG  51 ddareeglkvvptCsyvaaylekhpeyad 79 
                                        d+ r++g+ +v+ C+y + ++ +++ y++
  gene1245|gene1245|rna1244|rna1244 196 DEERDRGMYMVMFCEYSKLFICEKERYSK 224
                                        667999***************99888876 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05      0.13      15      51 ..      92     128 ..      78     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                                        EEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHH CS
                               FR47  15 wilrkdggelgalqvlpehrrrGlgsrlvkalakeia 51 
                                         i+++   +++ ++v ++hr+rG+ +r+ +  +  + 
  gene1245|gene1245|rna1244|rna1244  92 NIVNRSAVFVYTMYVSKKHRGRGYSKRILRDSTDSLN 128
                                        3555556899****************99887666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1619.38
//
Query:       gene1246|gene1246|rna1245|rna1245  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-11   43.4   0.2    3.8e-11   43.0   0.2    1.2  1  Glutaredoxin     Glutaredoxin
    0.00039   20.8   0.0     0.0005   20.4   0.0    1.2  1  GST_N_3          Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.022   15.2   0.0    1.2  1  DUF836           Glutaredoxin-like domain (DUF836)
       0.17   12.6   0.0       0.22   12.2   0.0    1.2  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.2   8.4e-15   3.8e-11       2      60 .]      31      87 ..      30      87 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 8.4e-15
                                       EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                       Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                       ++f+k+ Cpy+  a++lL+++g++ ++i+vd  +e+ +  k++  +rt+P+ f ++ ++
  gene1246|gene1246|rna1245|rna1245 31 TMFVKRFCPYSIEARKLLHKRGISCKVIEVDYSPEAHDFAKRY--QRTFPVFFLNDTLI 87
                                       79*****************************************..8*********9876 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.1e-07    0.0005       2      62 ..      33      92 ..      32     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-07
                                       ES-TTSHHHHHHHHHHHHHT--EEEE---TTTTHHHHHHH-TT--SSEEETTS-EEESHHH CS
                            GST_N_3  2 ygfpaSpyarrvrlaLnekglpvevvevtpgehdeellaknplgkvPvLeddgealtdSla 62
                                       +  +++py+ ++r +L+ +g++++v ev++    ++  ak+ ++++Pv+  +++ + +  +
  gene1246|gene1246|rna1245|rna1245 33 FVKRFCPYSIEARKLLHKRGISCKVIEVDYSPE-AHDFAKRYQRTFPVFFLNDTLIKGGYE 92
                                       5679*********************99976665.4467899999****9888877766555 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   4.8e-06     0.022       1      57 [.      29      84 ..      29     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.8e-06
                                       -EEEEE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETT...T-CCCHCCCCTTTTEEEECT CS
                             DUF836  1 kltLyskpgChlCeqakekLkelkleegleleviDIa...kdeeleakYgleipvlaleg 57
                                       k+t+++k+ C+   +a ++L++     g++ +vi ++   +  ++ ++Y+ + pv +l++
  gene1246|gene1246|rna1245|rna1245 29 KCTMFVKRFCPYSIEARKLLHK----RGISCKVIEVDyspEAHDFAKRYQRTFPVFFLND 84
                                       5899*****************4....567777888885555555*************998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.8e-05      0.22      12      57 ..      46      96 ..      38     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                                       HHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCTSS CS
                    Methyltransf_11 12 ealakrg..arvvgvDlskemlklakekaseegl...kvefvvadaeklpf 57
                                       + l+krg  ++v+ vD+s+e+++ ak+ +++ ++   + +++++  ekl++
  gene1246|gene1246|rna1245|rna1245 46 KLLHKRGisCKVIEVDYSPEAHDFAKRYQRTFPVfflNDTLIKGGYEKLKY 96
                                       456688999****************99999988788877788888888854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 811.41
//
Query:       gene1247|gene1247|rna1246|rna1246  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   13.9   0.0      0.083   13.4   0.0    1.2  1  DUF3293   Protein of unknown function (DUF3293)


Domain annotation for each model (and alignments):
>> DUF3293  Protein of unknown function (DUF3293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.6e-06     0.083      13      42 ..      75     104 ..      70     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-06
                            DUF3293  13 aeeNaaaqeqLleelkklglpvlpavgade 42 
                                         eeN+ + +qL+++lk+lg+p+ p +++++
  gene1247|gene1247|rna1246|rna1246  75 LEENCSHARQLENKLKELGVPYKPLYAEEN 104
                                        59********************99987554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1077.69
//
Query:       gene1248|gene1248|rna1247|rna1247  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-17   62.7   4.3      3e-17   61.9   4.3    1.5  1  GATA           GATA zinc finger
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.015   14.9   0.0    1.1  1  Lant_dehydr_C  Lantibiotic biosynthesis dehydratase C-term
      0.019   14.4   0.9      0.019   14.4   0.9    1.9  2  TF_Zn_Ribbon   TFIIB zinc-binding
       0.22   11.2   1.2       0.42   10.3   1.2    1.4  1  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB


Domain annotation for each model (and alignments):
>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   4.3   6.8e-21     3e-17       1      36 []       8      42 ..       8      42 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 6.8e-21
                               GATA  1 CsnCgttkTplWRrgpdgnksLCnaCGlyykkkglk 36
                                       CsnC+tt TplWRr++dg++ LCnaCGlyyk +g+k
  gene1248|gene1248|rna1247|rna1247  8 CSNCNTTATPLWRRAEDGSY-LCNACGLYYKIHGRK 42
                                       ********************.************985 PP

>> Lant_dehydr_C  Lantibiotic biosynthesis dehydratase C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.3e-06     0.015     171     260 ..     130     211 ..     116     220 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.3e-06
                                        SSSS-HHHHH..HHHHHHHHHHHHTSTTHHH.HHHHHHHHHHHTHHHHHHHHHHHHHHHH-SSS-SS.....HHHH CS
                      Lant_dehydr_C 171 lstfgldleekvdlleryaeaflaefsdtkkalrealdrkyraqrealearlravlaaaaepesegesadlppfla 246
                                          +fg++   + ++le  ++ ++++++ +   +++ ++r+++++  ++ ++++ +++ ++++e+e+e++  +    
  gene1248|gene1248|rna1247|rna1247 130 YEGFGMSEYGRNTILEDKRD-YRRHTNVA---TKSLIRRHFDKRPGRIPPFMSEIESKETSNEKEPEKSTSE---- 197
                                        578999999999*****999.99999998...88**************************999999966666.... PP

                                        HHHHHHHHHHHHHH CS
                      Lant_dehydr_C 247 ewaerlrelrrrle 260
                                        +w+++ +e++++le
  gene1248|gene1248|rna1247|rna1247 198 PWIKANEEHETDLE 211
                                        77777777776665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.9   4.3e-06     0.019       3      27 ..       8      34 ..       6      37 .. 0.87
   2 ?   -2.8   0.1         1   4.6e+03      31      41 ..     184     194 ..     182     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-06
                                       ETTTTC.EE.CHEETSTTCEEESSSSB CS
                       TF_Zn_Ribbon  3 CPnCgs.tn.lveDpergelvCtdCGl 27
                                       C nC++  + l + +e g ++C +CGl
  gene1248|gene1248|rna1247|rna1247  8 CSNCNTtATpLWRRAEDGSYLCNACGL 34
                                       ******54457999************8 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                        ECCCCCCCHHH CS
                       TF_Zn_Ribbon  31 dnsidegpewr 41 
                                        + s++++pe+ 
  gene1248|gene1248|rna1247|rna1247 184 ETSNEKEPEKS 194
                                        67899999986 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.2   9.4e-05      0.42       7      28 ..       8      33 ..       4      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.4e-05
                            zf-RRN7  7 CgvCgc..r.sftl.ddGfyyCrrCh 28
                                       C  C+   + +++  +dG y C+ C+
  gene1248|gene1248|rna1247|rna1247  8 CSNCNTtaTpLWRRaEDGSYLCNACG 33
                                       9999999988***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1602.51
//
Query:       gene1249|gene1249|rna1248|rna1248  [L=249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-15   55.2   6.5    1.1e-14   54.4   6.5    1.4  1  zf-RING_2       Ring finger domain
    1.7e-10   41.0   5.1    3.2e-10   40.1   5.1    1.5  1  zf-rbx1         RING-H2 zinc finger domain
    2.8e-10   39.8   4.7    5.2e-10   39.0   4.7    1.5  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
    8.4e-10   38.5   0.8    8.4e-10   38.5   0.8    1.7  2  zf-RING_UBOX    RING-type zinc-finger
    1.6e-09   37.3   4.1    1.6e-09   37.3   4.1    1.8  2  zf-RING_11      RING-like zinc finger
    2.8e-08   33.5   4.7      5e-08   32.7   4.7    1.4  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
    5.8e-07   29.4   5.0    9.5e-07   28.7   5.0    1.4  1  zf-RING_5       zinc-RING finger domain
    9.4e-06   25.4   4.8    1.6e-05   24.7   4.8    1.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    0.00016   21.5   4.1     0.0004   20.2   4.1    1.7  1  Prok-RING_4     Prokaryotic RING finger family 4
    0.00046   19.9   2.6     0.0013   18.5   2.6    1.8  1  zf-Nse          Zinc-finger of the MIZ type in Nse subunit
    0.00089   19.3   4.3     0.0022   18.0   4.3    1.6  1  zf-ANAPC11      Anaphase-promoting complex subunit 11 RING-H2
     0.0012   19.0   2.6     0.0033   17.5   2.6    1.8  1  zf-C3HC4_4      zinc finger of C3HC4-type, RING
     0.0013   18.3   6.1     0.0022   17.5   6.1    1.4  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
  ------ inclusion threshold ------
      0.052   13.5   1.5      0.052   13.5   1.5    1.7  2  Baculo_RING     Baculovirus U-box/Ring-like domain
      0.056   13.7   3.6      0.091   13.0   1.2    2.1  2  zinc_ribbon_16  Zinc-ribbon like family
      0.069   13.2   0.8       0.24   11.5   0.8    2.0  1  XPA_N           XPA protein N-terminal
       0.11   12.6   1.0       0.29   11.2   1.0    1.7  1  zf-C3H2C3       Zinc-finger
       0.12   12.5   5.3       0.24   11.5   5.3    1.5  1  RINGv           RING-variant domain
       0.18   11.7   5.7       0.33   10.9   5.7    1.4  1  PHD             PHD-finger
        0.2   11.9   0.1        0.2   11.9   0.1    1.8  1  Carb_bind       Carbohydrate binding
       0.21   11.8   6.9       0.63   10.3   5.8    2.4  1  FANCL_C         FANCL C-terminal domain
        0.4   10.7   8.0       0.25   11.3   2.4    2.3  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.69    9.7   6.1        1.4    8.8   6.1    1.6  1  zf-RING_4       RING/Ubox like zinc-binding domain
        1.6    9.1   6.0        2.8    8.3   6.0    1.5  1  zf-RING-like    RING-like domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   6.5   1.5e-17   1.1e-14       3      44 .]     188     229 ..     186     229 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.5e-17
                          zf-RING_2   3 CpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                        C ICle+++++ +v+ l CgHvfhreC+++wlr++  CP+Cr
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGGCVRNLGCGHVFHRECIDKWLRKNFVCPVCR 229
                                        *****************************************9 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   5.1   4.3e-13   3.2e-10      10      55 .]     184     229 ..     175     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 4.3e-13
                            zf-rbx1  10 leeacieckapgdee.cpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55 
                                        +++ ci c ++ ++  c+  l  CgH+FH +Ci+kWl+++ vCP+cr
  gene1249|gene1249|rna1248|rna1248 184 ISRGCIICLEDFEDGgCVRNL-GCGHVFHRECIDKWLRKNFVCPVCR 229
                                        557799998888887899999.6***********************8 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   4.7     7e-13   5.2e-10       2      40 .]     188     228 ..     187     228 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 7e-13
                         zf-C3HC4_2   2 CpiCldmlkdpsvvt..pCgHvfCqkCilrsLeekneCPlC 40 
                                        C iCl+ ++d+  v    CgHvf+++Ci+++L+++  CP+C
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGGCVRnlGCGHVFHRECIDKWLRKNFVCPVC 228
                                        **********98888779*********************** PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.8   1.1e-12   8.4e-10       1      39 []     188     226 ..     188     226 .. 0.90
   2 ?    2.6   0.5      0.19   1.4e+02       1       9 [.     225     233 ..     225     237 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.1e-12
                       zf-RING_UBOX   1 CpIClelftdP..lv.lpCGHtFCreClwelskslegafkCP 39 
                                        C ICle+f+d   +  l+CGH+F+reC+   +k+l+++f CP
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGgcVRnLGCGHVFHRECI---DKWLRKNFVCP 226
                                        99******9667555669**********...9*********9 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
                       zf-RING_UBOX   1 CpIClelft 9  
                                        Cp+C++ +t
  gene1249|gene1249|rna1248|rna1248 225 CPVCRSRMT 233
                                        *****9883 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   4.1   2.1e-12   1.6e-09       2      29 .]     188     215 ..     187     215 .. 0.99
   2 ?   -2.6   0.5       6.6   4.9e+03       2      10 ..     225     233 ..     225     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.1e-12
                         zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                        C ICLe+f++g +++ l C+H+FH +CI
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGGCVRNLGCGHVFHRECI 215
                                        ***************************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.6
                         zf-RING_11   2 CsICLeefk 10 
                                        C +C + ++
  gene1249|gene1249|rna1248|rna1248 225 CPVCRSRMT 233
                                        778866554 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   4.7   6.6e-11     5e-08       1      41 []     188     228 ..     188     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6.6e-11
                                        -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C+iCle +++    + l C+H f+++Ci+k+l+  k++ CP+C
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGGcvRNLGCGHVFHRECIDKWLR--KNFVCPVC 228
                                        **********99999******************..9999**** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   5.0   1.3e-09   9.5e-07       2      43 ..     188     229 ..     187     230 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.3e-09
                          zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43 
                                        C +C e +++   +  + CgH+f+ +C++k l k++vCp+Cr
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGGCVRNLGCGHVFHRECIDKWLRKNFVCPVCR 229
                                        99******777778899************************9 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   4.8   2.1e-08   1.6e-05       4      47 ..     187     232 ..     184     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-08
                                        B-TTTSSSBS-EEETT...EEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                         zf-C3HC4_3   4 eCviClerprnvvllp...CgHlvlCeeCaekllkrkkkCpiCrrpi 47 
                                         C+iCle  ++  +++   CgH+ +  eC +k+l+++  Cp+Cr+ +
  gene1249|gene1249|rna1248|rna1248 187 GCIICLEDFEDGGCVRnlgCGHV-FHRECIDKWLRKNFVCPVCRSRM 232
                                        6*******99988886677****.********************875 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   4.1   5.3e-07    0.0004       1      40 [.     188     232 ..     188     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.3e-07
                        Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk..dls.sCPlCqrri 40 
                                        C++C e    +  ++   CgH++ +eC d++  + +  CP+C++r+
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDfedGGCVRNLGCGHVFHRECIDKWlrK-NfVCPVCRSRM 232
                                        778877765555566678*************743.369*****996 PP

>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   2.6   1.7e-06    0.0013       7      56 ..     181     228 ..     171     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                                        SSBXXSB-TTTSSB-SS..EEEESSS--EEEHHHHHHHCTTTS-EE-SCCC- CS
                             zf-Nse   7 eerislkCPltlqpfee..PvtskkCpHvFEreaIlelikrkktvkCPvagC 56 
                                        +e is  C + l+ fe+   v++  C HvF re I + +  +k   CPv  C
  gene1249|gene1249|rna1248|rna1248 181 QEFISRGCIICLEDFEDggCVRNLGCGHVFHRECIDKWL--RKNFVCPV--C 228
                                        577889999999999984459999***************..88899***..7 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.3     3e-06    0.0022      50      82 ..     203     233 ..     176     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3e-06
                                        BT.TS-EEEHHHHHHHHHHHSTSSB-TTTSSB-- CS
                         zf-ANAPC11  50 Gk.ckhnfhlhcilkwletetskglcpmcrqtfk 82 
                                           c h+fh  ci kwl ++     cp+cr  ++
  gene1249|gene1249|rna1248|rna1248 203 NLgCGHVFHRECIDKWLRKNF---VCPVCRSRMT 233
                                        333**************9875...7*****9887 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.6   4.5e-06    0.0033       1      42 []     188     228 ..     188     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-06
                         zf-C3HC4_4   1 CPiCldYLekPv...sleCGhsfClsCisslqkepdgeqllCplC 42 
                                        C iCl+ +e+      l CGh+f  +Ci+++  ++    + Cp+C
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGGcvrNLGCGHVFHRECIDKWLRKN----FVCPVC 228
                                        778888888864112578**************999....****** PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   6.1     3e-06    0.0022       5      50 ..     186     237 ..     182     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3e-06
                       Zn_ribbon_17   5 ksCayCelavk.grvvlcgvCeHvlHasCarewfendd.laeCps....GCG 50 
                                        + C +C    + g +v    C+Hv H +C+++w+ ++   ++C s    GCG
  gene1249|gene1249|rna1248|rna1248 186 RGCIICLEDFEdGGCVRNLGCGHVFHRECIDKWLRKNFvCPVCRSrmtlGCG 237
                                        56777766654267788889**************999966777655556777 PP

>> Baculo_RING  Baculovirus U-box/Ring-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.9   2.9e+03     103     122 ..      73      95 ..      51     103 .. 0.60
   2 ?   13.5   1.5     7e-05     0.052      26      72 ..     185     225 ..     178     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.9
                        Baculo_RING 103 v...Gdeeiievykkvlkrvtse 122
                                            G ee++++  +v k v  +
  gene1249|gene1249|rna1248|rna1248  73 YkieGKEEVDRLNGRVSKDVIFG 95 
                                        23468888888888888877655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7e-05
                        Baculo_RING  26 atecaiclediddnrGvvaitdtGlldlekvlhkecikrfrreekrd 72 
                                        +  c icled +d + v  + ++      +v+h+eci ++ r++   
  gene1249|gene1249|rna1248|rna1248 185 SRGCIICLEDFEDGGCVRNLGCG------HVFHRECIDKWLRKNFVC 225
                                        567**********9999999987......69*********9987655 PP

>> zinc_ribbon_16  Zinc-ribbon like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.92   6.9e+02      28      55 ..     163     192 ..     156     203 .. 0.74
   2 ?   13.0   1.2   0.00012     0.091      92     117 ..     204     229 ..     199     236 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.92
                     zinc_ribbon_16  28 Ggakfldksksslcprcskplpk..cavcg 55 
                                        Gg    +++k  lcp  s+++    c +c+
  gene1249|gene1249|rna1248|rna1248 163 GGLSEKEIEKIPLCPYSSQEFISrgCIICL 192
                                        555666788999****99986432377775 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                     zinc_ribbon_16  92 lscghgahashakewfsthsicpvad 117
                                        l cgh+ h +   +w+ +  +cpv  
  gene1249|gene1249|rna1248|rna1248 204 LGCGHVFHRECIDKWLRKNFVCPVCR 229
                                        78*********************965 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   0.00032      0.24      12      26 ..     215     229 ..     206     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                              XPA_N  12 ldSyLldnFdysVCD 26 
                                         d +L +nF ++VC 
  gene1249|gene1249|rna1248|rna1248 215 IDKWLRKNFVCPVCR 229
                                        578***********6 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   0.00039      0.29      17      34 ..     206     228 ..     201     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                          zf-C3H2C3  17 CkHlvHakCade.....evCPkC 34 
                                        C H++H++C d+      vCP C
  gene1249|gene1249|rna1248|rna1248 206 CGHVFHRECIDKwlrknFVCPVC 228
                                        *********98522222699999 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.3   0.00032      0.24       1      48 []     188     228 ..     188     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                                        ETTTTEE-SSSS--B-SS--STCCCSB-HHHHHHHHHHTCT-SB-TTT CS
                              RINGv   1 CriCleeeeeseplispCkCrGslklvHesClekWldekeantqCeiC 48 
                                        C iCle+ e+    +++  C    +++H++C++kWl++   n  C +C
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGG-CVRNLGC---GHVFHRECIDKWLRK---NFVCPVC 228
                                        777777766655.5555555...379**********99...8889999 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.7   0.00044      0.33       2      51 ..     188     230 ..     187     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00044
                                        BTTTTSTTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTHT CS
                                PHD   2 CavCkkksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCke 51 
                                        C +C + + e++  v   gC++ fH +C++  l+      ++++C+ C++
  gene1249|gene1249|rna1248|rna1248 188 CIICLE-DFEDGGCVRNLGCGHVFHRECIDKWLR------KNFVCPVCRS 230
                                        999***.9999999999*************9988......369*****86 PP

>> Carb_bind  Carbohydrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00027       0.2      18      39 ..     222     243 ..     211     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                          Carb_bind  18 kvLCPivngvalqaCggaCYsp 39 
                                        ++ CP+  +  ++ Cg++ Y++
  gene1249|gene1249|rna1248|rna1248 222 NFVCPVCRSRMTLGCGKQGYER 243
                                        59****************9986 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.8   0.00084      0.63       5      44 ..     188     222 ..     184     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00084
                                        -SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHH CS
                            FANCL_C   5 CgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrsl 44 
                                        C iC+  + d g v      n  C++ fH++C+  Wlr++
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDFEDGGCV-----RNLGCGHVFHRECIDKWLRKN 222
                                        77777777755544.....57889*************975 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.4   0.00034      0.25       5      37 ..     186     217 ..     182     220 .. 0.88
   2 ?    2.5   0.3      0.19   1.4e+02       4      15 ..     222     233 ..     219     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                        Prok-RING_1   5 kkCpvCgkelkeedDiVvCpeCgtpyHraCyek 37 
                                          C +C + ++++   V    Cg ++Hr+C +k
  gene1249|gene1249|rna1248|rna1248 186 RGCIICLEDFEDG-GCVRNLGCGHVFHRECIDK 217
                                        67*********99.789999**********876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                        Prok-RING_1   4 gkkCpvCgkelk 15 
                                        +  CpvC+ +++
  gene1249|gene1249|rna1248|rna1248 222 NFVCPVCRSRMT 233
                                        567888888765 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.1    0.0019       1.4       1      45 [.     188     230 ..     188     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                          zf-RING_4   1 cplCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCre 45 
                                        c +C e++ e++  ++   Cg+ + + C ++ l+ ++++CP Cr+
  gene1249|gene1249|rna1248|rna1248 188 CIICLEDF-EDGGCVRNLGCGHVFHRECIDKWLR-KNFVCPVCRS 230
                                        55677766.3444566668**************6.7********8 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.0    0.0038       2.8      15      43 .]     202     228 ..     188     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0038
                       zf-RING-like  15 snesCnvrlHvdCfqhyirthsskkCpkC 43 
                                         n  C   +H +C+++ +  +++  Cp C
  gene1249|gene1249|rna1248|rna1248 202 RNLGCGHVFHRECIDKWL--RKNFVCPVC 228
                                        5779************99..66778***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1744.44
//
Query:       gene1250|gene1250|rna1249|rna1249  [L=453]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-42  146.2   1.3    8.9e-40  136.9   1.3    2.2  1  Syja_N    SacI homology domain
  ------ inclusion threshold ------
      0.024   14.2   0.0      0.058   13.0   0.0    1.6  1  SHQ1      SHQ1 protein


Domain annotation for each model (and alignments):
>> Syja_N  SacI homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   1.3     1e-43   8.9e-40       2     320 .]      43     316 ..      42     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 1e-43
                             Syja_N   2 gilGlirlls....gsyllvitkreevgtlkgkkeiykitevellplsseeeaekalkslkaktekkkeekeleek 73 
                                        +ilG++r+++    + +l+++tk++ vg + +  e+yki+++++l+++ +                       +++
  gene1250|gene1250|rna1249|rna1249  43 TILGILRVERnkhhEEFLACVTKSTLVGMYDAV-EVYKIDKIRFLNIKGP-------------------G--RADE 96 
                                        69*****99445679**************9776.**********998544...................2..2456 PP

                             Syja_N  74 llklleklfessgsfYFsydlDltrslqrqlekssesskslplweraderFvWNrhllkpli.............. 135
                                        +++++ k f +s++fY+ +      sl                   ++++FvWN+h+  +l+              
  gene1250|gene1250|rna1249|rna1249  97 VMSQV-KGFVQSHDFYYFFG-----SLF------------------IEDEFVWNKHMKANLLkyfgpssymwvlsh 148
                                        88889.88889******881.....221..................245588888888886655555444444443 PP

                             Syja_N 136 ...eaeldswllpviqGfveqsklklsksqkekekkevtltlisRrsrkraGtRylrRGiddeGnvANfvEtEqil 208
                                            + l+  +  + +Gf+  +++k s       ++ +++ l+s  s++r GtRyl RG+d+eGn++ fv t    
  gene1250|gene1250|rna1249|rna1249 149 rpgREPLNLNISTLFCGFFAAEAFKAS-------GDFYHMKLLSLISSNRVGTRYLCRGVDSEGNASLFVKTHFQT 217
                                        332224555666699999977777654.......56799*********************************9988 PP

                             Syja_N 209 evessekeskilSfvqiRGSiPlfWsqeptlkykpkirierseeenleafkkHfekllkrYgkvvvvnLlekkgrE 284
                                              +++ i+ f+ iRGS+P+fWsq+    ++ ki+i+ ++e+ +eaf+kHf+kl ++Ygkv+v+nLl +k+ E
  gene1250|gene1250|rna1249|rna1249 218 KR----NNNTIFDFTTIRGSVPIFWSQTE-HGISTKINIYGDDESVREAFTKHFKKLRREYGKVHVINLLGEKKYE 288
                                        84....4579*****************88.588*******9*****************************99**** PP

                             Syja_N 285 kkLgeayekavkklnklekekkklkyveFDfhkeck 320
                                        k+L+ +++++++         +++ y++FD  +++k
  gene1250|gene1250|rna1249|rna1249 289 KQLTLHFNRLLNL--------ENIPYTTFDLDAHVK 316
                                        **********653........4799*****988775 PP

>> SHQ1  SHQ1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.4e-06     0.058     124     161 ..      98     135 ..      83     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.4e-06
                               SHQ1 124 LldikelfrehdvyyvlnklyldDycvwiqsakeevlr 161
                                        + ++k  ++ hd+yy + +l+++D  vw  + k + l+
  gene1250|gene1250|rna1249|rna1249  98 MSQVKGFVQSHDFYYFFGSLFIEDEFVWNKHMKANLLK 135
                                        56789999*********************999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2870.02
//
Query:       gene125|gene125|rna125|rna125  [L=606]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.6e-30  104.6   0.0    8.8e-30  104.0   0.0    1.3  1  ABC_tran      ABC transporter
    1.4e-07   31.5   5.9      2e-07   30.9   5.9    1.2  1  ABC_membrane  ABC transporter transmembrane region
    0.00023   20.7   0.1       0.19   11.2   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00088   19.5   0.3      0.018   15.3   0.3    2.5  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0024   18.2   0.0     0.0096   16.2   0.0    2.0  1  AAA_22        AAA domain
     0.0026   17.6   0.0      0.004   17.0   0.0    1.2  1  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0041   16.8   0.3     0.0083   15.8   0.3    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0044   16.0   0.0      0.007   15.4   0.0    1.2  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0083   15.4   0.0      0.014   14.7   0.0    1.3  1  Zeta_toxin    Zeta toxin
  ------ inclusion threshold ------
      0.043   13.0   0.0      0.068   12.3   0.0    1.2  1  G-alpha       G-protein alpha subunit
       0.06   13.4   0.1       0.16   12.0   0.1    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
      0.067   13.3   0.1       0.13   12.4   0.1    1.4  1  DUF87         Helicase HerA, central domain
       0.08   12.7   0.0        9.2    6.0   0.0    2.3  2  IstB_IS21     IstB-like ATP binding protein
       0.13   11.9   0.0       0.21   11.2   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.14   12.7   0.0       0.22   12.0   0.0    1.3  1  AAA_23        AAA domain
       0.16   11.9   0.2       0.67    9.8   0.0    2.0  2  RsgA_GTPase   RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   7.9e-33   8.8e-30       1     137 []     395     537 ..     395     537 .. 0.91

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 7.9e-33
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    lk +s+ + +ge+v+i+G++G+GKSt+l+l++ l+    G+i++dg+++++++ + lr+ ig++ q++ +f+e+ +  n 
  gene125|gene125|rna125|rna125 395 LKGLSFRIMRGERVGIIGRSGSGKSTILRLILMLHG-HTGTIRVDGTEIRKISPKALRRTIGCILQDTLFFDES-ILYNv 472
                                    7899****************************9975.89****************************8888888.66666 PP

                                    ...HHHTCHHHHHHHSTTGG....TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...esdeeiekalsklglke....lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       + + +++++l+   + +    + ++ ++s+++ LSgG+ q+v++ar+l+k+ +++llDE+t+
  gene125|gene125|rna125|rna125 473 rygNPSGRMDEILKGCMDAGlwevISKKGLDSRMKDLSGGEAQMVCIARCLAKDCEVMLLDEATS 537
                                    9998888899999988888866677888888888*****************************96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   5.9   1.8e-10     2e-07       2     268 ..      29     297 ..      23     303 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.8e-10
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpet...ealnvysllllllglaqfilallqsyllnvtgerlskrlrr 78 
                                    i++ l+++l+++l+++     g i++ l ++++ ++     +   +++++++  +++++   +  l++v+  r++ ++ +
  gene125|gene125|rna125|rna125  29 IALALCIFLGKWLDVASIKERGIIINGLRSTKEVSDgnvPSMCSGAVTFFIFRTLSSVFIESKGILFSVITNRIVEDMTS 108
                                    44455555555555555555555555555555555544444555555555555566666666666666666666666666 PP

                                    HHHHHHHCSTHHHHHH..SCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH.HSHHHHHHHHHHHHHHH CS
                   ABC_membrane  79 klfkkilrqpmsffdt..nsvGellsrltndvsklrdglgeklglffqslltfvgglivmfy.lgwkltlvllailplii 155
                                     +f+  ++       +  +++ +l+  + +   k++ +lg  l + +  + +++ ++  +   +g +  + +l +++ + 
  gene125|gene125|rna125|rna125 109 HVFRLAIHS----AHSceKKPTSLNRVVERGNKKICKVLGKVLTIGVPTFYNLILLFKEIHMmFGFRYLFPVLLTVIAYT 184
                                    666655554....3334688888999999999************************9877666999999*********** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 156 lvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllg 235
                                    + + v  +i + ++k+ ++a + as+ + E + +i  Vka + ee ++++     + + +  ++  ++ gl++  ++ l+
  gene125|gene125|rna125|rna125 185 VYTHVTLRIRSLYRKRINDADNLASRRIHECIANIDLVKACCCEEMEESRLAAIMRIMWSLKLSDKKCVGLINFGQRTLF 264
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHH CS
                   ABC_membrane 236 llsyalalwfGttlvisgelsvgdlvvflslfa 268
                                    +++++ + + G+t   ++ + +gdl+++ s+  
  gene125|gene125|rna125|rna125 265 TVLFVHVVFKGSTDAAASRMAIGDLTTLFSFVL 297
                                    ************************888887764 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0026       2.9      28      50 ..     409     431 ..     400     452 .. 0.81
   2 !   11.2   0.0   0.00017      0.19     135     211 ..     507     578 ..     462     582 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0026
                                    EEEESTTSSHHHHHHHHHHHCTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnlldAilFvLGe 50 
                                     i+G+ GSGKs +l  il + G+
  gene125|gene125|rna125|rna125 409 GIIGRSGSGKSTILRLILMLHGH 431
                                    69************999776663 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00017
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                    + LSgGe ++v +a  +A    k   ++llDe  ++LD    k+v ell   +    +++i ++  m+e +dk++ v
  gene125|gene125|rna125|rna125 507 KDLSGGEAQMVCIARCLA----KDCEVMLLDEATSKLDGCAEKRVFELLMGLEG-KTIVMILHNLWMTEYMDKIIVV 578
                                    57***********99988....566789*********************98883.3455556666777778887765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   1.6e-05     0.018      23      88 ..     499     551 ..     493     553 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                        SbcCD_C  23 ekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    +k l+++++ lSGGe+q   ++++a      +       +++++++LDEA sklD+   ++++ell
  gene125|gene125|rna125|rna125 499 KKGLDSRMKDLSGGEAQ---MVCIA----RCL------AKDCEVMLLDEATSKLDGCAEKRVFELL 551
                                    45689999999999994...34444....222......34699*************9999999987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.5e-06    0.0096      10      71 ..     410     471 ..     405     564 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelka......e 71 
                                    ++G sG+GK+t lr +l+ +         + ++++v+ ++    s+k l+r +  +l++ l        +
  gene125|gene125|rna125|rna125 410 IIGRSGSGKSTILRLILMLHG--------HTGTIRVDGTEIRkiSPKALRRTIGCILQDTLFFdesilyN 471
                                    89*****************97........9*********99999*******9999999887775555540 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.6e-06     0.004       3      44 ..     409     444 ..     408     474 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44 
                                    ++iG+ gsGKS++L+++ +l++      ++++++ +g +irk
  gene125|gene125|rna125|rna125 409 GIIGRSGSGKSTILRLILMLHG------HTGTIRVDGTEIRK 444
                                    69***************99975......44444444444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   7.4e-06    0.0083      17      39 ..     400     422 ..     394     434 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.4e-06
                         AAA_29  17 ieidlkgatlltGpsGsGKSTll 39 
                                    ++i + + + ++G+sGsGKST+l
  gene125|gene125|rna125|rna125 400 FRIMRGERVGIIGRSGSGKSTIL 422
                                    5555444788************9 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.2e-06     0.007      11      55 ..     387     431 ..     377     467 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                                    -SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHC CS
                           MeaB  11 erpeakellerllakaGraqvvGltGvPGaGkstlvealglelrr 55 
                                    ++p++ ++l+ l+ +  r ++vG+ G  G+Gkst++  + +   +
  gene125|gene125|rna125|rna125 387 SYPQSVDVLKGLSFRIMRGERVGIIGRSGSGKSTILRLILMLHGH 431
                                    689*******************************98765554444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.3e-05     0.014      23      61 ..     412     449 ..     407     453 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                     Zeta_toxin  23 GqpGAGKselaellkdelerqgnvvrldpDdlRelhPey 61 
                                    G +G+GKs++++l+   ++ + + +r+d++++R+  P++
  gene125|gene125|rna125|rna125 412 GRSGSGKSTILRLILMLHG-HTGTIRVDGTEIRKISPKA 449
                                    899*************996.99*************9985 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     6e-05     0.068      26      82 ..     408     465 ..     399     519 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                                    EEEEESTTSSHHHHHHHHHHHCS--..--HHHH.HCCHHHHHHHHHHHHHHHHHHHHHTT CS
                        G-alpha  26 llllGqseSGKsTilkqlkllykkg..fseeel.atwraviqlnivrsiktilealesle 82 
                                    + ++G s+SGKsTil+ + +l++++  +  +    ++r++  + + r i  il+   +++
  gene125|gene125|rna125|rna125 408 VGIIGRSGSGKSTILRLILMLHGHTgtI--RVDgTEIRKISPKALRRTIGCILQDTLFFD 465
                                    5689******************888442..322133566666666666666666665555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       8.9     1e+04       5      20 ..     253     268 ..     252     282 .. 0.79
   2 ?   12.0   0.1   0.00015      0.16       1      20 [.     407     426 ..     407     454 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 8.9
                                    EESTTSSHHHHHHHHH CS
                       MMR_HSR1   5 vGrpNvGKStLinalt 20 
                                    vG  N G  tL+  l+
  gene125|gene125|rna125|rna125 253 VGLINFGQRTLFTVLF 268
                                    8999999999998886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00015
                                    EEEEEESTTSSHHHHHHHHH CS
                       MMR_HSR1   1 evaivGrpNvGKStLinalt 20 
                                    +v+i+Gr+ +GKSt+++ ++
  gene125|gene125|rna125|rna125 407 RVGIIGRSGSGKSTILRLIL 426
                                    69**************9886 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00011      0.13      24      44 ..     406     426 ..     398     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                          DUF87  24 rHlAilgsTGsGKSntvavLl 44 
                                    ++++i+g++GsGKS+  +++l
  gene125|gene125|rna125|rna125 406 ERVGIIGRSGSGKSTILRLIL 426
                                    689****************98 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0082       9.2      22      63 ..     379     421 ..     372     432 .. 0.87
   2 ?    4.2   0.0     0.028        31     109     157 ..     527     574 ..     509     579 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0082
                      IstB_IS21  22 idfraarsldkrkvkeLatlsf.iekkenivllGpsGvGKshl 63 
                                    i+f++   + ++ v+ L +lsf i + e + ++G sG GKs +
  gene125|gene125|rna125|rna125 379 IEFENVGFSYPQSVDVLKGLSFrIMRGERVGIIGRSGSGKSTI 421
                                    6677777777889999*****9899***************965 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.028
                      IstB_IS21 109 vdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewdev 157
                                    +++++lD+ ++ +ld  +++ +fe++    +++ ++i  nl + e+ + 
  gene125|gene125|rna125|rna125 527 CEVMLLDE-ATSKLDGCAEKRVFELLMGLEGKTIVMILHNLWMTEYMDK 574
                                    58999999.5789***************************999998765 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00019      0.21       9      40 ..     400     431 ..     392     582 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                                    S-EBTT-EEEEEESTTSSHHHHHHHHHHHSST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   9 fpivqGqrtlipgafgvGktvisqslskqsns 40 
                                    f i++G+r++i+g +g Gk++i++ ++  + +
  gene125|gene125|rna125|rna125 400 FRIMRGERVGIIGRSGSGKSTILRLILMLHGH 431
                                    6799******************9888766544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.22      23      40 ..     409     426 ..     380     449 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                         AAA_23  23 lItGpNGaGKTTildAik 40 
                                     I+G  G+GK+Til+ i 
  gene125|gene125|rna125|rna125 409 GIIGRSGSGKSTILRLIL 426
                                    69************9885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.5   1.7e+03      12      43 ..     205     246 ..     190     257 .. 0.71
   2 ?    9.8   0.0   0.00059      0.67      97     121 ..     403     427 ..     376     444 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.5
                                    T..........EES--EEEEEEESTTTT--HHHHHHHHHHHH CS
                    RsgA_GTPase  12 k..........vaNvdqllivvslkepelslnlldrfLvlae 43 
                                    +          +aN+d +  ++  + +e +l  + r++  ++
  gene125|gene125|rna125|rna125 205 DnlasrrihecIANIDLVKACCCEEMEESRLAAIMRIMWSLK 246
                                    055555566779999999998888888888888888877665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00059
                                    CTTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                    ++++ + ++G SG GKSt++  +l 
  gene125|gene125|rna125|rna125 403 MRGERVGIIGRSGSGKSTILRLILM 427
                                    45578889***********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 3736.21
//
Query:       gene1251|gene1251|rna1250|rna1250  [L=264]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-27   95.0  16.5    3.8e-27   95.0  16.5    1.7  2  DHHC      DHHC palmitoyltransferase
  ------ inclusion threshold ------
       0.36   11.1   5.4       0.93    9.8   5.4    1.7  1  TrbE      Conjugal transfer protein TrbE


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.6      0.56     5e+03      71      71 ..      34      34 ..      12      63 .. 0.50
   2 !   95.0  16.5   4.2e-31   3.8e-27       2     133 ..     109     234 ..     108     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.56
                               DHHC 71 i 71
                                        
  gene1251|gene1251|rna1250|rna1250 34 L 34
                                       1 PP

  == domain 2  score: 95.0 bits;  conditional E-value: 4.2e-31
                               DHHC   2 ekelkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvklv 77 
                                        e+++k+C +cn ++ + ++Hcr+Cnrcvl++DHhC+w++nciG++N +yF ++l +l++++++++ +++++lv ++
  gene1251|gene1251|rna1250|rna1250 109 EYQEKYCLECNLFRINGMSHCRECNRCVLDMDHHCIWFGNCIGRNNIRYFHIYLYTLSIVTFINA-AFMYGLVIIC 183
                                        5799**********************************************555555555444444.4444454444 PP

                               DHHC  78 eeekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtieamkk 133
                                         ++++  +la+++l    +  + +l +lf+++++l+++f++y +l+  T+++++k+
  gene1251|gene1251|rna1250|rna1250 184 -SRNTLLMLALRIL----AAAFGALYTLFFCIIFLFTMFNIYVALNSSTSRDFIKN 234
                                        .4555556666554....467777778888888888999999999******99986 PP

>> TrbE  Conjugal transfer protein TrbE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.4    0.0001      0.93      35      60 ..     189     215 ..     163     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0001
                               TrbE  35 imlavlii.aayGlmftllfcfvnvlt 60 
                                        +mla+ i+ aa+G ++tl+fc + ++t
  gene1251|gene1251|rna1250|rna1250 189 LMLALRILaAAFGALYTLFFCIIFLFT 215
                                        79999887257**********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1847.70
//
Query:       gene1252|gene1252|rna1251|rna1251  [L=633]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-50  172.8  36.8    1.5e-50  172.4  36.8    1.1  1  EXS       EXS family
    2.9e-10   40.6  15.6    0.00036   20.6  13.5    2.8  2  SPX       SPX domain
  ------ inclusion threshold ------
       0.16   11.1   0.9       0.22   10.7   0.9    1.2  1  CitMHS    Citrate transporter


Domain annotation for each model (and alignments):
>> EXS  EXS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.4  36.8   2.6e-54   1.5e-50       6     331 .]     305     590 ..     302     590 .. 0.90

  Alignments for each domain:
  == domain 1  score: 172.4 bits;  conditional E-value: 2.6e-54
                                EXS   6 rvlllvvlglllwalnlhvlsklginyalifeldprsslsyrqlyelaalllllllllllllllsaevdalellpl 81 
                                          + l+ +g +l+++ l v+++++iny++if++d  ssls  +++ l +l +++ ++  +++++       +l p 
  gene1252|gene1252|rna1251|rna1251 305 FSMALLQYGAFLFGISLVVFKRFHINYKFIFNFDVCSSLSSDKYLFLISLSVFANVVGTWINIS-----FIHLNPY 375
                                        5678999****************************99999999995555555555556566554.....3557799 PP

                                EXS  82 llllllllllllplnilyrssrrrflrtllrillaplapvefadfllaDiltSlakvlgDlaltvclyasswseed 157
                                        llll+ l++l++p+++ly++sr+++l +++ri++ p++ v+f++f +aDi  Sl+ ++  ++++ + +  +w+   
  gene1252|gene1252|rna1251|rna1251 376 LLLLGHLFVLVVPFKVLYHESRFYLLLVVFRIIVFPMSFVRFRHFYFADIGQSLTFCFKRIFFCGIKL--NWRI-- 447
                                        ************************************************************99999888..8887.. PP

                                EXS 158 rkcgsssvvvplllslPyliRfrQclreyrdtkkr.phllNalKYatafpvivlsalqrlsksdesestlrvlwll 232
                                        + c         + s+ ++iRf+Qclr+y+dt+ + ph++NalKY++++++ ++  +++++k+      l+++ ++
  gene1252|gene1252|rna1251|rna1251 448 EGC---------INSFFAMIRFLQCLRRYKDTRLKfPHIANALKYSFSILAGFAVPFYKSNKTW----DLFIYKIM 510
                                        556.........44455679*************99******************99999977776....9******* PP

                                EXS 233 aalvnslysfiWDvtmDWgLlkllksknwflRdellypkkwvYylaivldlvlRftWslklsshlhsiqeselgvf 308
                                        ++ ++s+ys++WD++mDWg++          Rd+l+yp+   Y + ++++l+ Rf+W+l   ++        +  f
  gene1252|gene1252|rna1251|rna1251 511 VISISSIYSSAWDIFMDWGIF----------RDKLTYPR-YTYTCGVAFNLMCRFFWVLAYWFK--------ISPF 567
                                        *********************..........899****9.8********************944........6789 PP

                                EXS 309 llellEvlRRwvWvffRvEnEhv 331
                                        +++++E+ RR+vW++fRvE Eh+
  gene1252|gene1252|rna1251|rna1251 568 WMAFVEISRRFVWTIFRVEFEHL 590
                                        *********************96 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-07    0.0011       1      26 [.       1      26 [.       1      31 [. 0.95
   2 !   20.6  13.5   6.1e-08   0.00036     183     370 ..      33     208 ..      27     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-07
                                SPX  1 MKFakeLeenlvpEWrdaYldYkqLK 26
                                       M+F+ +L +n v EW++ Y+ Y  LK
  gene1252|gene1252|rna1251|rna1251  1 MRFSNTLRANQVDEWKENYVSYEILK 26
                                       9**********************999 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.1e-08
                                SPX 183 ekeFferLdseLnkvetFykakeeefterlesLrkqleal.rprrikeaeerksdlyrwreifglksveaqvfess 257
                                         keF ++ dseL k+++F+   e++++ + e++  +      + r++ +++     +++r+++g   +++    ++
  gene1252|gene1252|rna1251|rna1251  33 RKEFKTLIDSELRKINDFFFLLEKKAVIEKEEIFVDAGVSpED-RPS-NDSG-VRIRDSRKKAGCL-SDDYGLGRD 104
                                        689******************9999999999776665555233.333.2222.2233344444444.666666666 PP

                                SPX 258 reldrgelseeardkevseelekngwikptksklekkrneralekvk....pektlkafldsvrrdylrk...enr 326
                                        +++dr + +  +  +e+           +++ ++e++r+++++e+ +    +   l  ++  +++++        +
  gene1252|gene1252|rna1251|rna1251 105 DQKDRLRIKT-DGKDEF-----------DEEGDDEDSRSTNTSEEGEsgrfK--YLVSKAAKGTDEK--GfggLFK 164
                                        6666655221.111111...........111122222233333332211111..2222222222222..1335577 PP

                                SPX 327 vklkkakkklkkafvelYrgLelLKsYqeLNrtAFrKIlKKfDK 370
                                         + +  ++k  k ++e+ ++   +K ++eLN t+  K+ KK+DK
  gene1252|gene1252|rna1251|rna1251 165 ISRRFERRKREKNIQEFLHAVISIKRFRELNYTGLMKLSKKYDK 208
                                        7777777777889******************************* PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.9   3.7e-05      0.22     104     181 ..     338     406 ..     335     560 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             CitMHS 104 slakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnllllalllvgllplvllfmfgvalalpvn 179
                                        +++ +l+ ++ l+li l+++an+ g+ + i  +            p+llll+ l+v+++p+ +l+  ++++ l+v 
  gene1252|gene1252|rna1251|rna1251 338 DVCSSLSSDKYLFLISLSVFANVVGTWINISFI---------HLNPYLLLLGHLFVLVVPFKVLYHESRFYLLLVV 404
                                        789999999999*************87777777.........88899***99999999999999977777777776 PP

                                        xx RF
                             CitMHS 180 ap 181
                                        + 
  gene1252|gene1252|rna1251|rna1251 405 FR 406
                                        64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4194.02
//
Query:       gene1253|gene1253|rna1252|rna1252  [L=432]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-91  306.9   0.7    3.1e-91  306.4   0.7    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    2.3e-05   24.2   0.1    6.5e-05   22.8   0.1    1.7  1  Methyltransf_31  Methyltransferase domain
    0.00075   19.1   0.0     0.0016   18.0   0.0    1.5  1  MTS              Methyltransferase small domain
     0.0087   15.8   0.0      0.016   15.0   0.0    1.4  1  Methyltransf_16  Lysine methyltransferase
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.061   13.1   0.0    2.1  1  Met_10           Met-10+ like-protein
      0.018   14.7   0.3      0.038   13.6   0.3    1.5  1  zf-PHD-like      PHD/FYVE-zinc-finger like domain
      0.024   14.2   0.0      0.056   13.0   0.0    1.6  1  DUF2067          Uncharacterized protein conserved in archaea
      0.046   14.4   0.0        0.1   13.3   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
       0.09   12.6   0.1       0.45   10.3   0.0    2.1  2  COR              C-terminal of Roc, COR, domain


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.4   0.7   1.5e-94   3.1e-91       8     375 ..      13     382 ..       4     383 .. 0.90

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 1.5e-94
                                        ----SS--TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S- CS
                                TRM   8 edkevtvskkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDis 83 
                                        e++ ++++k+e  F+NP+q+ nRD+sv +i+  e++k k  + i++lda+sa+GlR+iR+++E+++ ++v++NDis
  gene1253|gene1253|rna1252|rna1252  13 EES-TVITKNEWTFFNPAQKLNRDISVELIK--EYFKDK--ATIRILDAMSATGLRGIRYLKEISN-STVYLNDIS 82 
                                        333.67899999*****************66..555555..589*******************776.6899***** PP

                                        HHHHHHHHHHHHHTT--.................GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHH CS
                                TRM  84 ekAvelikeNvklneve.................eivvineddAnvllaekkkrfdviDlDPfGspapfldsavqs 142
                                        +  +e+ik Nv ln +e                  +v+i ++d nvl+ +    fdviD+DPfGs ++++d+a+++
  gene1253|gene1253|rna1252|rna1252  83 QSSIETIKSNVLLNGIEdmeyfesnlqeirtsgnTRVNIIKSDCNVLMGSLPCFFDVIDIDPFGSCSEYIDNALRA 158
                                        **********9999999999999999999999955899999*********************************** PP

                                        EEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEE CS
                                TRM 143 vkekglLlvTaTDtavLaGaspekclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrv 218
                                        +k++g++++TaTD  vL+ + ++kcl kY++  ++   + E+ lR ++++v r+a+k+   vep++sls+dfYvr+
  gene1253|gene1253|rna1252|rna1252 159 IKHRGIICLTATDKGVLCSN-ERKCLIKYSTAIMRGVGMNETPLRTIVSLVSRQASKFGCSVEPVMSLSIDFYVRI 233
                                        ******************87.578**************************************************** PP

                                        EEEEEE-HHHHHHHHTTEEEEEEETTT--E.EEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHC CS
                                TRM 219 fvkvktgaakvkkvleklglvlhCsgClse.ekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeae 293
                                        f+++ + + ++  v+e+  +vl C +C +  e  +  +++ ++c++cg +++l GP+w   l+d+ ++++vl++++
  gene1253|gene1253|rna1252|rna1252 234 FLRIVRRNPRS--VIERNSFVLMC-RCHNItEISNVQKEIDNRCSNCGGRMKLCGPFWNRALNDTSVIKNVLNNTS 306
                                        ****9887665..67777777775.56554134444455669******************************9988 PP

                                        T..-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HH CS
                                TRM 294 kekeeelkkrvkklLklikeElldaplyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnaple 369
                                               +kr+ ++L+ +++E l + +yy++ +l+s+l +s+ +++k+++al ++g+ vs tH + +aikTnap++
  gene1253|gene1253|rna1252|rna1252 307 R-----DNKRLIGILRYLEQE-LPNMFYYEIPRLCSILGISTIKQSKLMHALANMGYLVSYTHSELNAIKTNAPID 376
                                        8.....4899***********.7789************************************************** PP

                                        HHHHHH CS
                                TRM 370 avvevl 375
                                         + +vl
  gene1253|gene1253|rna1252|rna1252 377 SINKVL 382
                                        **9986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   3.2e-08   6.5e-05       3     113 ..      49     171 ..      47     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.2e-08
                    Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                         ++r+lD+ ++tG  +++   + +++++v++ Dis+ +ie  ++n   +g++ +e  +++ +e+ ++    ++++i
  gene1253|gene1253|rna1252|rna1252  49 ATIRILDAMSATGLRGIRYL-KEISNSTVYLNDISQSSIETIKSNVLLNGIEDMEYFESNLQEIRTS-GNTRVNII 122
                                        6789****************.7799****************************************97.5578**** PP

                    Methyltransf_31  79 lsnevl..............naladpdkileeiervlkpggilliedpr 113
                                         s++ +              + + ++ +++ ++ r++k  gi++++  +
  gene1253|gene1253|rna1252|rna1252 123 KSDCNVlmgslpcffdvidiDPFGSCSEYIDNALRAIKHRGIICLTATD 171
                                        999555566666777888*9***********************998776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.8e-07    0.0016      17      92 ..      35     111 ..      29     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.8e-07
                                        -HHHHHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT CS
                                MTS  17 DkGsklLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvle 91 
                                        D+  +l+ e+++++++ ++lD  + +G+ g+  +ke ++ +v l d++  ++e  k n+  n++e +e+++s++ e
  gene1253|gene1253|rna1252|rna1252  35 DISVELIKEYFKDKATIRILDAMSATGLRGIRYLKEISNSTVYLNDISQSSIETIKSNVLLNGIEdMEYFESNLQE 110
                                        788889999999999999***********************************************9******9976 PP

                                        T CS
                                MTS  92 e 92 
                                         
  gene1253|gene1253|rna1252|rna1252 111 I 111
                                        5 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     8e-06     0.016      43     142 ..      46     139 ..      28     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-06
                    Methyltransf_16  43 nelsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvkvevLdWgeeleedlle 117
                                        ++ +++++l+  s tGl G+   + +++  v+l D+++  +e +k+n+ ln+  ++++  + + +  +e+    ++
  gene1253|gene1253|rna1252|rna1252  46 KDKATIRILDAMSATGLRGIRYLKEISNSTVYLNDISQsSIETIKSNVLLNG--IEDMEYF-ESNL-QEI---RTS 114
                                        566788999999*********99999**********9989**********77..4433222.2222.223...222 PP

                    Methyltransf_16 118 keevDlilaaDcvYledslelLvkv 142
                                         ++   i+ +Dc  l+ sl++  +v
  gene1253|gene1253|rna1252|rna1252 115 GNTRVNIIKSDCNVLMGSLPCFFDV 139
                                        2233346777777777777777666 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.061     104     198 ..      53     166 ..      37     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                                        EEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EE......... CS
                             Met_10 104 VvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqlad......... 170
                                        ++d +   G   i   k   +++v+ +d+  +s++ +k+n+ lN +e++ + +++  +e+ ++  +          
  gene1253|gene1253|rna1252|rna1252  53 ILDAMSATGLRGIRYLKEISNSTVYLNDISQSSIETIKSNVLLNGIEDM-EYFESNLQEIRTSGNTRvniiksdcn 127
                                        56777777777777778888899***********************985.58899999987754444668999999 PP

                                        ..........EEE.E--TTTGGGGHHHHHHHEEEEEEEE CS
                             Met_10 171 ..........rvv.mnlpksaieFldkvlaalkdggvih 198
                                                   v+ ++   s+ e++d++l+a+k++g+i+
  gene1253|gene1253|rna1252|rna1252 128 vlmgslpcffDVIdIDPFGSCSEYIDNALRAIKHRGIIC 166
                                        99999999985552677799*****************99 PP

>> zf-PHD-like  PHD/FYVE-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.9e-05     0.038      33      89 ..     236     291 ..     231     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                        zf-PHD-like  33 RsaRehlvtkvgedsFvlqCrrCiglakkkdklapkldvCqeCkeegksckpfrekk 89 
                                        R  R    + ++++sFvl Cr C ++++  + +    ++C++C  + k c pf ++ 
  gene1253|gene1253|rna1252|rna1252 236 RIVRRNPRSVIERNSFVLMCR-CHNITEISNVQKEIDNRCSNCGGRMKLCGPFWNRA 291
                                        5556666677999*******7.9******************************8876 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.8e-05     0.056      61     121 ..     319     382 ..     296     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                            DUF2067  61 lkkekrglfkyslsdllreag.apvppdvLvdaLkllGykaelre..envlktnapleevvela 121
                                        l++e   +f y++ +l++ +g  ++    L  aL  +Gy +++     n++ktnap++ +++++
  gene1253|gene1253|rna1252|rna1252 319 LEQELPNMFYYEIPRLCSILGiSTIKQSKLMHALANMGYLVSYTHseLNAIKTNAPIDSINKVL 382
                                        67777899***********************************987569**********99975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     5e-05       0.1       1      63 [.      53     116 ..      53     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTT CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedg 63 
                                        +Ld+   tG   ++ +k++++++v+  Dis++ +e++++++  +g+ ++e+ + +++++    +
  gene1253|gene1253|rna1252|rna1252  53 ILDAMSATGLRGIRYLKEISNSTVYLNDISQSSIETIKSNVLLNGIeDMEYFESNLQEIRTSGN 116
                                        899999***999999999988********************99999********9999876544 PP

>> COR  C-terminal of Roc, COR, domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.65   1.3e+03      15      39 ..     240     264 ..     230     271 .. 0.80
   2 ?   10.3   0.0   0.00022      0.45      16      65 ..     321     368 ..     310     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.65
                                COR  15 kkkekyisleeykeickekglkdee 39 
                                        ++ +++i+ + +  +c+ +++++ +
  gene1253|gene1253|rna1252|rna1252 240 RNPRSVIERNSFVLMCRCHNITEIS 264
                                        678899**************99865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00022
                                COR  16 kkekyisleeykeickekglkdeeeqetllefLhdlGvvlyFqddeglrd 65 
                                        ++ + + + e+ ++c+  g+++ + q++l++ L ++G ++ ++++ +l+ 
  gene1253|gene1253|rna1252|rna1252 321 QELPNMFYYEIPRLCSILGISTIK-QSKLMHALANMGYLVSYTHS-ELNA 368
                                        566778888999************.******************97.5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2591.49
//
Query:       gene1254|gene1254|rna1253|rna1253  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.7   4.1      0.015   15.7   4.1    1.4  1  DUF2262   Uncharacterized protein conserved in bacteria (DUF2
      0.028   14.2   0.2       0.04   13.7   0.2    1.3  1  TadF      Putative tight adherence pilin protein F


Domain annotation for each model (and alignments):
>> DUF2262  Uncharacterized protein conserved in bacteria (DUF2262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   4.1   1.7e-06     0.015      67     136 ..      41     110 ..      10     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                            DUF2262  67 kelldlandWleddeedeelkaeeiteedFikrieldsisieeegeftlyfddgdlFaghsiivsgning 136
                                        +el++ a++W e++++ + +   ++++e++++  ++ds +i+ +++ +l   d+  ++ +++++s n ++
  gene1254|gene1254|rna1253|rna1253  41 RELVKKAQEWDEKKAQRHVMFSSKMSDEEYTNLWKVDSYIIDGNDKEKLKNLDQRTVFNNIMWLSRNVEK 110
                                        799**********999999999********************************55559****9999876 PP

>> TadF  Putative tight adherence pilin protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   4.5e-06      0.04      39      90 ..      10      57 ..       4     108 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                               TadF 39 gkLdrlSYSLvnvlkertqlydgqeaitekeadqleklAkrllrggesddkk 90
                                         L r+S+  +nvlkert +    e it+++ + + +l k+  + +e+ +++
  gene1254|gene1254|rna1253|rna1253 10 QALHRMSWKFLNVLKERTGM----ESITKEQIKGIRELVKKAQEWDEKKAQR 57
                                       5699*************965....5788888888888887776444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1461  (0.0814881); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1153.62
//
Query:       gene1255|gene1255|rna1254|rna1254  [L=470]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-62  208.7   0.0    1.3e-61  208.3   0.0    1.2  1  Pkinase        Protein kinase domain
    1.2e-31  110.0   0.0    1.7e-31  109.5   0.0    1.1  1  Pkinase_Tyr    Protein tyrosine kinase
    1.5e-05   24.5   0.0      3e-05   23.5   0.0    1.5  1  Kinase-like    Kinase-like
     0.0018   18.3   0.0     0.0026   17.7   0.0    1.3  1  APH            Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.016   14.7   0.1      0.034   13.7   0.1    1.5  1  YrbL-PhoP_reg  PhoP regulatory network protein YrbL
      0.033   13.1   0.3      0.054   12.4   0.3    1.3  1  Haspin_kinase  Haspin like kinase domain
       0.07   12.5   0.1       0.13   11.6   0.1    1.3  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
      0.078   12.6   0.1       0.14   11.7   0.1    1.5  1  RIO1           RIO1 family
       0.28   12.0   1.3        2.5    9.0   0.4    2.3  2  FliT           Flagellar protein FliT


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.3   0.0   6.5e-65   1.3e-61       3     264 .]      12     256 ..      10     256 .. 0.93

  Alignments for each domain:
  == domain 1  score: 208.3 bits;  conditional E-value: 6.5e-65
                                        EEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE CS
                            Pkinase   3 kleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvle 78 
                                            lG+Gs+G V++a+++ tg  vA+K i+k+ ++ k+      E+ki + l+h+ +++ly+ ++++++l+lvle
  gene1255|gene1255|rna1254|rna1254  12 ITGLLGSGSYGDVVSATDNITGMRVAMKFIRKDVDRWKHS----LELKIQRLLNHRSVCKLYGHVNTSRNLVLVLE 83 
                                        5678*****************************9999775....8******************************* PP

                                        --TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSB CS
                            Pkinase  79 yveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskl 154
                                        +++g +l+++++r+g l+e  a+ ++ q+l+g++ylH ++i+HrDlK eNi++d  + +Ki+DFGl++ +++ss l
  gene1255|gene1255|rna1254|rna1254  84 LARGIDLHKYIRRNGRLEEGYARTLFVQMLHGVDYLHTHSIVHRDLKLENIIVD-GETVKICDFGLSTFYDRSSVL 158
                                        ******************************************************.888****************** PP

                                        CTTTSCGGGS-HHHHTTSCB.SHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HH CS
                            Pkinase 155 tsfvgtseYlAPEvlkeney.skkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpe 229
                                        ++++gt++  +PE++++ +y ++++D+W lG+ily ++ g+ pf+   ++e   +  +               +  
  gene1255|gene1255|rna1254|rna1254 159 RDYCGTPQCAPPEIMRGIPYvGPEIDIWCLGIILYAMVHGRLPFE---EEEIGLSSRHA----------IISRMSV 221
                                        *****************9999************************...44433333333..........2345788 PP

                                        HTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 230 aseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                        ++++s+e+kdl++++++ d++ R+ +++l++hp++
  gene1255|gene1255|rna1254|rna1254 222 DESLSNELKDLIRRIIEPDKSIRIEMDDLMRHPWV 256
                                        99********************************6 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.5   0.0   8.3e-35   1.7e-31       5     257 ..      14     252 ..      10     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.5 bits;  conditional E-value: 8.3e-35
                                        EEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEE CS
                        Pkinase_Tyr   5 kklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivt 80 
                                          lG+G++G+Vv++t +     + ++Va+K ++++ ++    +   e+ki + l+h+ + kl+g +  +++l++v+
  gene1255|gene1255|rna1254|rna1254  14 GLLGSGSYGDVVSATDN----ITGMRVAMKFIRKDVDRW---KHSLELKIQRLLNHRSVCKLYGHVNTSRNLVLVL 82 
                                        579***********999....899********8888877...45569***9************************* PP

                                        E--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTS CS
                        Pkinase_Tyr  81 eyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekd 156
                                        e+++g dL+k++r++   +l+      + +q+ +G++yL+++++vHrdl   N++++ +++vki+DfGL+     d
  gene1255|gene1255|rna1254|rna1254  83 ELARGIDLHKYIRRN--GRLEEGYARTLFVQMLHGVDYLHTHSIVHRDLKLENIIVD-GETVKICDFGLSTFY--D 153
                                        **************9..9999999999*****************************9.99***********99..4 PP

                                        SEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSB CS
                        Pkinase_Tyr 157 deyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcp 231
                                         + v ++ + +p +  +pE+++    +  + D+W+ G++l+ ++  g+ p+++  +  + ++     r++  e+ +
  gene1255|gene1255|rna1254|rna1254 154 RSSVLRDYCGTP-QCAPPEIMRGIPyVGPEIDIWCLGIILYAMVH-GRLPFEEE-EIGLSSRHAIISRMSVDESLS 226
                                        455555555555.558999999988346799***********999.*****875.4455666667789******** PP

                                        HHHHHHHHHHT-SSGGGS--HHHHHH CS
                        Pkinase_Tyr 232 eelyelmkkcweedpeeRptfselve 257
                                        +el++l+++  e d++ R ++ +l++
  gene1255|gene1255|rna1254|rna1254 227 NELKDLIRRIIEPDKSIRIEMDDLMR 252
                                        *********************99976 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.5e-08     3e-05     141     286 ..     101     242 ..      82     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.5e-08
                        Kinase-like 141 letiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve..kgfaPpEllg 214
                                        +e  ar l  +q++  + +L+ + +vh +++ +n++ d +  +++ +f+    +  + vl   +     aPpE++ 
  gene1255|gene1255|rna1254|rna1254 101 EEGYARTLF-VQMLHGVDYLHTHSIVHRDLKLENIIVDGE-TVKICDFGLSTFYDRSSVLRDYCgtPQCAPPEIMR 174
                                        445666666.***************************987.69*****9888888888888888555689***986 PP

                        Kinase-like 215 srggytrknktkmthkldaWqlGlviyriwclklPltlateeakeew....kfklckkipekvkaLlkkfLqlsqe 286
                                                    +  ++d W lG+  y +    lP+++ + + ++ +     ++  +  ++++k L+++++++++ 
  gene1255|gene1255|rna1254|rna1254 175 G--I------PYVGPEIDIWCLGIILYAMVHGRLPFEEEEIGLSSRHaiisRMSVDESLSNELKDLIRRIIEPDKS 242
                                        6..3......346689***********************9999999876533343448999999999999998876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.3e-06    0.0026     154     205 ..     106     154 ..      37     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.3e-06
                                        HHHHHH--S....SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHH CS
                                APH 154 aalaallpg....elptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDl 205
                                        ++l   ++        ++++H+Dl++ N++vd +++    + Df++++      D 
  gene1255|gene1255|rna1254|rna1254 106 RTLFVQMLHgvdyLHTHSIVHRDLKLENIIVD-GETVK--ICDFGLSTFY----DR 154
                                        444444444566677899**************.66776..9****99987....44 PP

>> YrbL-PhoP_reg  PhoP regulatory network protein YrbL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.7e-05     0.034      71     153 ..      56     137 ..      36     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                      YrbL-PhoP_reg  71 lreeidnsplarilGlvqTdlGlGlvvekirdadGnvaktLedlvk.keeltaelkeaLdefleelldnhivtndl 145
                                         ++  +   + +++G v+T++ l lv e+ r+ d  + k +++  + +e+++  l  ++ + +++l    iv +dl
  gene1255|gene1255|rna1254|rna1254  56 IQRLLNHRSVCKLYGHVNTSRNLVLVLELARGID--LHKYIRRNGRlEEGYARTLFVQMLHGVDYLHTHSIVHRDL 129
                                        46667777889***********************..4444444443134455567777788899************ PP

                      YrbL-PhoP_reg 146 sakNivvk 153
                                        + +Ni+v 
  gene1255|gene1255|rna1254|rna1254 130 KLENIIVD 137
                                        *****986 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.7e-05     0.054     228     257 ..     124     152 ..      59     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                      Haspin_kinase 228 FEHRdLhldniLvdknlnvtlidlklsRle 257
                                          HRdL+l+ni+vd + +v ++d+ ls + 
  gene1255|gene1255|rna1254|rna1254 124 IVHRDLKLENIIVDGE-TVKICDFGLSTFY 152
                                        56***********986.8*******99876 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.4e-05      0.13      91     155 ..      76     140 ..      61     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.4e-05
                                Kdo  91 rAlllterlegaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqee 155
                                        r l+l+ +l+  +dL +++++  +l+e   r+l+ +    +  lh   + H+dl   ni ++ e 
  gene1255|gene1255|rna1254|rna1254  76 RNLVLVLELARGIDLHKYIRRNGRLEEGYARTLFVQMLHGVDYLHTHSIVHRDLKLENIIVDGET 140
                                        556777789999********9888************************************99875 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.1e-05      0.14      80     150 ..      77     147 ..      34     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.1e-05
                                        TTEEEEE--EETTEEGGBHHHCG.-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                               RIO1  80 rhvlvmefigedgvaapklkdve.e..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                        + vlv+e+    g+ + k    + +  e  a++l+ ++l+ +  l  ++ +vH DL   N++vd + v i D++
  gene1255|gene1255|rna1254|rna1254  77 NLVLVLELAR--GIDLHKYIRRNgRleEGYARTLFVQMLHGVDYLH-THSIVHRDLKLENIIVDGETVKICDFG 147
                                        4577788777..6666665444433347789999999999877666.9************************97 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.34   6.8e+02      56      85 .]      40      69 ..      35      69 .. 0.91
   2 ?    9.0   0.4    0.0013       2.5      35      65 ..     221     251 ..     209     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHHHHCHTHHHHHHHHHH CS
                               FliT 56 eirallqprldelqkllgalrrqrkannaY 85
                                        ir+ +++++ +l+ ++++l + r++ + Y
  gene1255|gene1255|rna1254|rna1254 40 FIRKDVDRWKHSLELKIQRLLNHRSVCKLY 69
                                       5999****************9999998877 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                                        --HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FliT  35 lspaereekrellrrilandaeirallqprl 65 
                                         ++++++e+ +l+rri++ d+ ir  ++  +
  gene1255|gene1255|rna1254|rna1254 221 VDESLSNELKDLIRRIIEPDKSIRIEMDDLM 251
                                        677999******************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3234.88
//
Query:       gene1256|gene1256|rna1255|rna1255  [L=379]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2844.19
//
Query:       gene1257|gene1257|rna1256|rna1256  [L=215]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-13   51.3   9.0    1.2e-13   51.3   9.0    3.2  3  DHHC      DHHC palmitoyltransferase
  ------ inclusion threshold ------
        6.2    6.9   7.8        5.8    7.0   0.2    2.7  2  zf-A20    A20-like zinc finger


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   5.0       1.1     1e+04      67      67 ..      37      37 ..       5      63 .. 0.48
   2 !   51.3   9.0   1.4e-17   1.2e-13       6      66 ..      74     134 ..      69     146 .. 0.80
   3 !    4.2   1.1    0.0047        42     104     131 ..     149     176 ..     138     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                               DHHC 67 v 67
                                        
  gene1257|gene1257|rna1256|rna1256 37 S 37
                                       1 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 1.4e-17
                               DHHC   6 kfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilal 66 
                                         +C++cn+++  ++ Hc++Cn+c ++ DHhCp+++ c+   N k  +l + ++ + ++ a+
  gene1257|gene1257|rna1256|rna1256  74 GICKKCNRIVGTKTVHCEICNKCYYKRDHHCPIIGRCVASSNIKDLYLAVSFMGFHSLAAI 134
                                        68*****************************************876555555554444444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.0047
                               DHHC 104 llfllllgllllfhlylilrnlTtieam 131
                                          ++++ +++ +  ++lil+++Tt+e +
  gene1257|gene1257|rna1256|rna1256 149 RYLFIMSSAFACWLTFLILTGKTTRELI 176
                                        4567788888888999999999999976 PP

>> zf-A20  A20-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2   0.00064       5.8      10      22 ..      67      79 ..      67      79 .. 0.98
   2 ?    2.0   2.6     0.024   2.1e+02      19      23 ..      93      97 ..      88      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00064
                             zf-A20 10 yGnpatnglCSkC 22
                                       +Gn++ +g C kC
  gene1257|gene1257|rna1256|rna1256 67 FGNANVKGICKKC 79
                                       9************ PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.024
                             zf-A20 19 CSkCY 23
                                       C+kCY
  gene1257|gene1257|rna1256|rna1256 93 CNKCY 97
                                       ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1516.13
//
Query:       gene1258|gene1258|rna1257|rna1257  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-27   94.7   1.2    6.2e-27   94.4   1.2    1.0  1  RRS1      Ribosome biogenesis regulatory protein (RRS1)


Domain annotation for each model (and alignments):
>> RRS1  Ribosome biogenesis regulatory protein (RRS1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   1.2   3.5e-31   6.2e-27      25     162 .]      16     144 ..       2     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 3.5e-31
                                        HHHHHHHHHHHHHHHHHHHHHHS-EEEE.TEEEEE-----S----SS-S---XXXXXXXXXXXXXXXXXXXXXXXX CS
                               RRS1  25 keeelkelardnvqlLinqllslptesteegvlakLpepttkLPRekplPkpkplTkWekFAkkKGikkkkekrsk 100
                                         ++++++ + + ++ +++++ ++++++  ++++  Lpept+ LPR++   k+  +T+We+FA++KGikkk  k+s+
  gene1258|gene1258|rna1257|rna1257  16 GRSDINQETSNLLKGIVKEIKACQSSRRGSDLVFALPEPTMILPRQHL--KEHTETRWERFARSKGIKKK--KKSQ 87 
                                        568999***************************************997..9****************444..59** PP

                                        XXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               RRS1 101 lvyDeetkeWvprwGykgankekekdwlvevkddeeedpfekkrkekkervaknekqelkNk 162
                                        +vyD+e +++vpr+G ++++++       ++  +e e   ++ r++kk++++kne ++l+N+
  gene1258|gene1258|rna1257|rna1257  88 IVYDKEIGDYVPRYGPHSKKNRI-----LKAAVKEGEVTLSALRRQKKNNIEKNEANRLANI 144
                                        ****************9988853.....33333457889********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 973.14
//
Query:       gene1259|gene1259|rna1258|rna1258  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-38  133.2  15.9      2e-38  132.8  15.9    1.1  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
       0.01   15.4   0.9       0.01   15.4   0.9    1.7  2  MICSWaP         Spore wall protein
      0.015   15.3   8.6       0.06   13.3   3.0    3.0  3  LRR_5           BspA type Leucine rich repeat region (6 copie
      0.046   13.8   0.3       0.21   11.7   0.1    2.1  2  Pro_3_hydrox_C  L-proline 3-hydroxylase, C-terminal


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8  15.9   4.4e-42     2e-38       5     333 ..      18     323 ..      14     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 4.4e-42
                                        HHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H.HH CS
                     vATP-synt_AC39   5 vramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgpsr 80 
                                        + ++r ++L+eedy+ L +cesle+v+  L++t Y+   ++e    ++  ++ k+l e+l ++f++  +  ++  r
  gene1259|gene1259|rna1258|rna1258  18 INGKREEMLKEEDYNALKRCESLEEVAIKLSKT-YRG--LSEGI-AYTKPELKKKLLESLKADFDYYHDAEDKGIR 89 
                                        7899**************************987.***..56665.5899********************9999989 PP

                                        HHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.S..S.SS-HHHHHHHHHSSSHHHHHHHHH.T-HHHHHH CS
                     vATP-synt_AC39  81 efldyllyrydidNvklllrgklsgdldleeleeklhpl..g.elsaldldklieaksveelyeall.gtpyakyl 152
                                        ++ldy++  + i+N  +ll+ kl  d +le+  ek+ ++  +  l+++++     +++++++ +++  ++ ++k+ 
  gene1259|gene1259|rna1258|rna1258  90 TILDYYMDFHKIQNFFYLLQCKLQ-DPNLEKSFEKI-EIgdFsALRTIKF-----SNDMDDVQRYCMeNSFLKKFE 158
                                        ************************.66556555555.3434556666666.....************666666666 PP

                                        HHH..HCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T. CS
                     vATP-synt_AC39 153 eea..ldeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrk 226
                                        +++   +e++  ++++ +++   k  +e+ ++  +    ++ e+++eil+ e D+  i i+++++++++l  ++r 
  gene1259|gene1259|rna1258|rna1258 159 KRVrfKKEFSA-NNFQVLQTLFFKFHIEETYRNLN----DDMEYMKEILRLEGDRQIIEITVNTLNSKDLVGKKRM 229
                                        65666777777.899******************76....34478***************************999** PP

                                        ..--SS-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHTTTSSSTSTHH CS
                     vATP-synt_AC39 227 kllipggslypeglealaeaedveellaalkyteygelleealeeagslksledaldealvkllkkafrqqfsvgv 302
                                        +l+++++s++ +  e l+ +e++e+++++l+++ y             ++++   l +a++++++++f     + +
  gene1259|gene1259|rna1258|rna1258 230 SLFPDVHSMSLNARELLSHVENLEDMKSILSEA-YNF-----------DTDISNVLIKAELQKYQESFSMYGDLSC 293
                                        *****************************7443.322...........5789999********************* PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHT--SHHH CS
                     vATP-synt_AC39 303 fyaYlklkeqEirnlrwIaegiaqglpkekI 333
                                        +y+Y+k keqEi+n+ w+ae+i q+  ++ +
  gene1259|gene1259|rna1258|rna1258 294 VYSYFKMKEQEIKNILWVAECIVQN-RRDAM 323
                                        *************************.88876 PP

>> MICSWaP  Spore wall protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.5   6.8e+03      89     102 ..     100     113 ..      88     127 .. 0.63
   2 ?   15.4   0.9   2.2e-06      0.01      31     110 ..     208     287 ..     178     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                            MICSWaP  89 satsiIllltCese 102
                                        + +++ +ll+C+++
  gene1259|gene1259|rna1258|rna1258 100 KIQNFFYLLQCKLQ 113
                                        55677888888765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.2e-06
                            MICSWaP  31 aeelekalNks.lkksnkeiriefdievsleipneieldkCgksvselaslLnnvnnadsatsiIllltCeselye 105
                                        ++ +e ++N   +k +  ++r+++ + v+++ +n  el    +++++++s+L++++n d++ s +l+ + e+++y+
  gene1259|gene1259|rna1258|rna1258 208 RQIIEITVNTLnSKDLVGKKRMSLFPDVHSMSLNARELLSHVENLEDMKSILSEAYNFDTDISNVLI-KAELQKYQ 282
                                        67788999999899999**********************************************9865.77999999 PP

                            MICSWaP 106 evfis 110
                                        e f+ 
  gene1259|gene1259|rna1258|rna1258 283 ESFSM 287
                                        99975 PP

>> LRR_5  BspA type Leucine rich repeat region (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.086   3.9e+02      72      88 ..      30      46 ..      14      65 .. 0.63
   2 ?   13.3   3.0   1.3e-05      0.06      10      67 ..     109     162 ..      99     220 .. 0.69
   3 ?    2.4   0.1     0.031   1.4e+02      60      96 ..     247     283 ..     232     307 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.086
                              LRR_5 72 geyaFsncsslkeitlp 88
                                       + +a + c+sl+e+ ++
  gene1259|gene1259|rna1258|rna1258 30 DYNALKRCESLEEVAIK 46
                                       33444444444444443 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.3e-05
                              LRR_5  10 ncnltsitipssvtsIgeyaFsnctslksitlpsslteigsyaFsncssltsitipss 67 
                                        +c+l++ ++++s ++I+   Fs     ++i++++ +  +++y+ +n+  l++++    
  gene1259|gene1259|rna1258|rna1258 109 QCKLQDPNLEKSFEKIEIGDFSAL---RTIKFSNDMDDVQRYCMENS-FLKKFEKRVR 162
                                        478888888888888888888766...88888888888888888888.7877766543 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.031
                              LRR_5  60 tsitipssltsigeyaFsncsslkeitlpsnlttigs 96 
                                        ++++  ++++si ++a++  + ++++ ++ +l++ ++
  gene1259|gene1259|rna1258|rna1258 247 SHVENLEDMKSILSEAYNFDTDISNVLIKAELQKYQE 283
                                        3333344455555555555555555555555544433 PP

>> Pro_3_hydrox_C  L-proline 3-hydroxylase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.7e-05      0.21      35      86 ..     162     214 ..     138     228 .. 0.85
   2 ?   -0.9   0.0      0.39   1.8e+03      31      67 ..     250     288 ..     219     294 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-05
                                        GGGGT--TTTHHHHHHHHHHHCCTBSS.-TTHHHHHHHHHHHHH--HHHHHHH CS
                     Pro_3_hydrox_C  35 alsevvsranykdivflLaklhffekv.pieasydWLkeicrrrGdpaLieka 86 
                                        ++ +  s +n++ + +l+ k h +e   + ++  +++kei r +Gd ++ie +
  gene1259|gene1259|rna1258|rna1258 162 RFKKEFSANNFQVLQTLFFKFHIEETYrNLNDDMEYMKEILRLEGDRQIIEIT 214
                                        566777999**************98762678999****************976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.39
                                        HHHHGGGGT--TT.TH.HHHHHHHHHHCCTBSS-TTHHH CS
                     Pro_3_hydrox_C  31 erllalsevvsra.ny.kdivflLaklhffekvpieasy 67 
                                        e+l  +  ++s+a n+  di  +L k   ++  +  ++y
  gene1259|gene1259|rna1258|rna1258 250 ENLEDMKSILSEAyNFdTDISNVLIKAELQKYQESFSMY 288
                                        344445555555434433566666666555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1868.83
//
Query:       gene1260|gene1260|rna1259|rna1259  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1294.58
//
Query:       gene126|gene126|rna126|rna126  [L=460]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.4e-162  539.0   0.0   6.3e-162  538.7   0.0    1.0  1  SHMT      Serine hydroxymethyltransferase


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.7   0.0  3.5e-166  6.3e-162       2     399 .]      15     406 ..      14     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 538.7 bits;  conditional E-value: 3.5e-166
                                    HHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT- CS
                           SHMT   2 eesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkl 81 
                                    e+sdpe+  +i+ e+erqk++i+liasen++ ++v+ea Gs+ltnky+eG  G+ryyGG++++d++e l+q+ra+elf+l
  gene126|gene126|rna126|rna126  15 ETSDPELHALINGETERQKKTINLIASENYVHQSVMEANGSILTNKYSEGRVGERYYGGTHWIDRIEALCQKRALELFSL 94 
                                    689***************************************************************************** PP

                                    STTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHH CS
                           SHMT  82 dpakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydel 161
                                    dp+ wgvnvq++sGs+an+avyt l+ pg++i+gldl+ GGhlthG+k+ ++kisa+s++f+s +yk+  ++glidy  l
  gene126|gene126|rna126|rna126  95 DPDVWGVNVQAYSGSPANFAVYTGLVPPGGKIMGLDLPSGGHLTHGYKTRTRKISATSVYFDSRSYKIG-SDGLIDYSGL 173
                                    ********************************************************************9.99******** PP

                                    HHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EE CS
                           SHMT 162 ekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprggl 241
                                    e++  ef P+l+++G saysr idy+rl  ia++ +a+l+ d++hi+ l+a+g++ sPf+y+dvv ttthk lrGprg+l
  gene126|gene126|rna126|rna126 174 EESFMEFLPHLLICGYSAYSRDIDYKRLSMIANKNNAFLFGDISHISPLIASGLMESPFKYCDVVMTTTHKGLRGPRGAL 253
                                    ******************************************************************************** PP

                                    EEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           SHMT 242 illrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekgy 321
                                    i++r+ v+    +g+e   +le kin+avfP lqGGP+nh+ia++a  l +a +p f +y+++v++n+k+l ++l + gy
  gene126|gene126|rna126|rna126 254 IFYRRSVR----KGEE-VVDLETKINFAVFPMLQGGPHNHTIAGIASMLLHAKSPSFVEYARRVVENSKTLCNHLLSLGY 328
                                    ****6654....5777.689************************************************************ PP

                                    EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTSSTTTT-SEEEEESHHHHHTT--HHHHHHHHHHH CS
                           SHMT 322 klvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgdksalvtsGlrlGtpaltsrgfkeedlekvakfi 399
                                    k+ +gGtdnh++lvdlr kg+dG+ +e+++++++i++n+ntv gd s+l +sG+r+Gt a+t+rgf+ +++++v+++i
  gene126|gene126|rna126|rna126 329 KVPTGGTDNHMFLVDLRGKGVDGSIVEHMCDALEISVNRNTVVGDTSPLNPSGIRVGTYAVTARGFGADEMKEVGDII 406
                                    **************************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2613.27
//
Query:       gene1261|gene1261|rna1260|rna1260  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 805.69
//
Query:       gene1262|gene1262|rna1261|rna1261  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0062   16.4   1.1     0.0071   16.2   1.1    1.2  1  Mei5      Double-strand recombination repair protein
  ------ inclusion threshold ------
      0.056   13.4   0.6        3.2    7.7   0.1    2.2  2  GerD      Spore germination GerD central core domain


Domain annotation for each model (and alignments):
>> Mei5  Double-strand recombination repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.1   7.9e-07    0.0071      34     102 ..      23      92 ..       5     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.9e-07
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXX......XXXXXXXXXXXXXXXXXXX CS
                               Mei5  34 trssfnsdtnvvkrlkveneennetssekatsskeenql.qqsikildseeeeskllkstiknrdvckse 102
                                        +     ++ +v+kr+   n+en+ +s++  t +   +++ +++i+++ +e + + +lk+ i++rd +  +
  gene1262|gene1262|rna1261|rna1261  23 KLKDGEACKSVKKRILSMNDENEDNSKQIRTNPHYRKNVgASTIQDTLGEGKRNDVLKQAIRKRDLSYIN 92 
                                        444557899*************************999999************************988766 PP

>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00036       3.2      27      63 ..      22      61 ..       9      63 .. 0.76
   2 ?    4.1   0.0    0.0048        43      10      74 ..      64     130 ..      60     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00036
                               GerD 27 klfkdpkfaealak...smkkenekllkdLmkDpeYqkml 63
                                       + +kd +  +++ k   sm++ene+  k++ ++p+Y+k++
  gene1262|gene1262|rna1261|rna1261 22 EKLKDGEACKSVKKrilSMNDENEDNSKQIRTNPHYRKNV 61
                                       556666666666555559*******************975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0048
                               GerD  10 kaiektltsekgkkfwkklfkdpkfaealaksmkkenekllkdLmkDpe..Yqkmlleilkdpemek 74 
                                        ++i++tl + k ++++k+++ + + +      ++k++  llk+L  D +    +mlle++ +p  ++
  gene1262|gene1262|rna1261|rna1261  64 STIQDTLGEGKRNDVLKQAIRKRDLSYINEFLVRKDRGMLLKTLSYDDKevLGEMLLEFVDQPVRSE 130
                                        699***************9988777666666788888888888876643234566666666664444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1125.00
//
Query:       gene1263|gene1263|rna1262|rna1262  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.015   15.8   0.5      0.019   15.4   0.5    1.1  1  DUF3357      Domain of unknown function (DUF3357)
       0.12   12.3   0.1       0.12   12.3   0.1    1.8  2  ODV-E18      Occlusion-derived virus envelope protein ODV-E18
       0.47   10.8   3.1       0.87    9.9   3.1    1.4  1  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> DUF3357  Domain of unknown function (DUF3357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.5   3.1e-06     0.019      13      94 ..      14      94 ..       3     106 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.1e-06
                            DUF3357 13 aaaaararrpllaavliasalvvlvvlvalagv.....rlagqaslvapgevavsetaesvsaaveetaSRGveaGVS 85
                                       + + +r +r  ++++ i+++++v+ +l+a+a+       ++g +s+ + g  a+    ++ s + +e +  G ++G S
  gene1263|gene1263|rna1262|rna1262 14 SNGNNRTKR--NTIITIVVVVLVVTLLLAVASKkgwfgGNKGGSSTKVGGDPAS----KPPSLKSSEESGKGGNKGNS 85
                                       334555555..3333344444444444445544566663444434433333232....3334555689999******* PP

                            DUF3357 86 eKssgaala 94
                                        K s + + 
  gene1263|gene1263|rna1262|rna1262 86 MKGSPSSNK 94
                                       999998873 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.9e-05      0.12      16      56 ..      14      55 ..       3      61 .. 0.61
   2 ?   -2.8   1.3         1   6.1e+03      49      60 ..      87      98 ..      75     107 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                            ODV-E18 16 trrlarlePsllltilvvlviiillvllv.qssstGsdssss 56
                                        +  +r + + ++ti+vv++++ ll+ +  +    G +  +s
  gene1263|gene1263|rna1262|rna1262 14 SNGNNRTKRNTIITIVVVVLVVTLLLAVAsKKGWFGGNKGGS 55
                                       444567777999999988877777654430333345554444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                            ODV-E18 49 tGsdssssnann 60
                                        Gs ss  + +n
  gene1263|gene1263|rna1262|rna1262 87 KGSPSSNKEEEN 98
                                       455555555444 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.1   0.00014      0.87       5      30 ..      18      43 ..      17      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                        Sigma_reg_N  5 kkakrksilrivlislivlllifvil 30
                                       +++kr +i++iv+++l+v+ll+ v +
  gene1263|gene1263|rna1262|rna1262 18 NRTKRNTIITIVVVVLVVTLLLAVAS 43
                                       689******************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 735.93
//
Query:       gene1264|gene1264|rna1263|rna1263  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-16   60.4   0.2    2.1e-16   59.8   0.2    1.3  1  Bromodomain    Bromodomain
      1e-05   25.7   2.1    1.7e-05   24.9   0.1    2.1  2  Bromo_TP_like  Histone-fold protein


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.2   2.3e-20   2.1e-16       3      74 ..      37     106 ..      35     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.3e-20
                                        HHHHHBHTTTCGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHT CS
                        Bromodomain   3 kilsellehklaepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkynge 74 
                                        +il+ ++  + +++Fl+ v ++  p+yy++ik+P+dLs ++kk+  +kYks+++f+ dl l+++N+ k+n +
  gene1264|gene1264|rna1263|rna1263  37 RILTAIKAFEQSKIFLSRVLKKDAPNYYEIIKRPMDLSIVQKKI--GKYKSFEEFKGDLDLIWDNCLKFNHS 106
                                        577778888899*******************************9..79**********************74 PP

>> Bromo_TP_like  Histone-fold protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2     0.087   7.8e+02      44      77 ..      75     122 ..      33     132 .. 0.65
   2 !   24.9   0.1   1.9e-09   1.7e-05       3      45 ..     157     199 ..     155     203 .] 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.087
                      Bromo_TP_like  44 k..............evdkdlleeilikllleeslgedsYkrnELlsF 77 
                                                       + d dl+ +  +k+   +   ++ +k +E++s 
  gene1264|gene1264|rna1263|rna1263  75 IvqkkigkyksfeefKGDLDLIWDNCLKFNHSKYHRDCAFKMKEVVST 122
                                        033444445555555667777777777777777777788888887775 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.9e-09
                      Bromo_TP_like   3 lklvivEillQvGferiseqslniltdllkyyiekillkikke 45 
                                        +k  i+E+ll +G+   se +l ++ d+++y i ki +kik e
  gene1264|gene1264|rna1263|rna1263 157 VKKIISEVLLSSGYGFASETALGVFCDVFQYRILKIIKKIKAE 199
                                        5778************************************983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1341.15
//
Query:       gene1265|gene1265|rna1264|rna1264  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-37  128.5   0.1    2.3e-37  128.0   0.1    1.2  1  Ribosomal_L16  Ribosomal protein L16p/L10e
  ------ inclusion threshold ------
       0.14   12.3   0.0          5    7.3   0.0    2.7  2  CRF            Corticotropin-releasing factor family


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.1   2.5e-41   2.3e-37       2     131 ..      13     165 ..      12     166 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 2.5e-41
                                        XSSXXBSSSXXSSTSXX.XSXXXXXESX...........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...E CS
                      Ribosomal_L16   2 krkkyrKsrkryirgvs.tkgtklefgd...........ygLvalekgqltaealeaariainrylkkkrgk...k 62 
                                        ++k+y+Ksr  ++rgv+ +k++++++g+           ++ +++e++ l+aealeaari++n+y++k+ gk   +
  gene1265|gene1265|rna1264|rna1264  13 SKKAYPKSR--FNRGVPdSKIQIFDLGRrkagvlefpllVNCISNERENLSAEALEAARICANKYMVKHAGKdnfH 86 
                                        5799*****..************************************************************9**** PP

                                        EXXSXXXXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSX CS
                      Ribosomal_L16  63 lwirvfphhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpik 128
                                        l++rv+p+h+++++     ag+dR+++G+    Gkp+g +arv  +q+i++i  ++  +++a ealrra++K+p++
  gene1265|gene1265|rna1264|rna1264  87 LRVRVYPFHVLRINkmlscAGADRLQTGMrgsfGKPYGRAARVVFNQPILSIrTKESFKDVAVEALRRAKNKFPGH 162
                                        ****************************************************63335899***************9 PP

                                        EEE CS
                      Ribosomal_L16 129 tki 131
                                        ++i
  gene1265|gene1265|rna1264|rna1264 163 QEI 165
                                        987 PP

>> CRF  Corticotropin-releasing factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00056         5       7      19 ..      92     106 ..      91     113 .. 0.83
   2 ?    2.0   0.0     0.025   2.2e+02       8      31 ..     196     219 .]     196     219 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00056
                                        HHHHHHHH..HHHHH CS
                                CRF   7 lpfhvLRq..lleiA 19 
                                         pfhvLR+  +l  A
  gene1265|gene1265|rna1264|rna1264  92 YPFHVLRInkMLSCA 106
                                        59******9999877 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.025
                                        HHHHHHH..HHHHHHHHHHHHHHHHH CS
                                CRF   8 pfhvLRq..lleiARaksqreqaaaN 31 
                                        +f+v+R+   +++ ++  + eqaa+N
  gene1265|gene1265|rna1264|rna1264 196 SFSVIREkgSIDNFKR--NLEQAANN 219
                                        6999999999999999..89999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1342.93
//
Query:       gene1266|gene1266|rna1265|rna1265  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-35  122.4   0.0    1.7e-35  122.2   0.0    1.1  1  Proteasome      Proteasome subunit
  ------ inclusion threshold ------
      0.034   13.8   0.0        0.8    9.5   0.0    2.4  2  Proteasome_A_N  Proteasome subunit A N-terminal signature
       0.17   11.9   0.0       0.31   11.0   0.0    1.4  1  E2              Bacteriophage E2-like protein


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.0   2.8e-39   1.7e-35       3     164 ..      30     183 ..      28     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 2.8e-39
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        +G+ ++G  + dgvvl++ + ++    +++++ v+K+fki d+ig++++Gl++D+r+ v++  + a++y   ygr 
  gene1266|gene1266|rna1265|rna1265  30 NGSLSIGASAADGVVLMSFRDVP--PLVIKEE-VKKVFKICDTIGCTYSGLQPDCRIQVNIGCQIAEEYYDVYGRY 102
                                        79999******************..8886666.******************************************* PP

                                        TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        + v++ +a++++ +q+ytq+sg rpfg  +++ag   +g p+Lyq+dpsGsy   + +++ G g  +ak ++++++
  gene1266|gene1266|rna1265|rna1265 103 PDVDVFTAHFSSVVQEYTQKSGYRPFGTLMIFAGPV-KGVPRLYQVDPSGSYQTAD-VCTSGIGYSEAKKFIKRRL 176
                                        ************************************.899***************6.******9*********999 PP

                                        STTBSHHHHH CS
                         Proteasome 155 kedltleeav 164
                                            +l++ +
  gene1266|gene1266|rna1265|rna1265 177 ---ESLDDNM 183
                                        ...3444444 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00013       0.8       5      23 .]       9      27 ..       8      27 .. 0.92
   2 ?    1.7   0.1     0.035   2.1e+02      13      18 ..     143     148 ..     143     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00013
                     Proteasome_A_N  5 lttFSPdGRLfQVEYAmkA 23
                                       +t FS +G L Q + A+ A
  gene1266|gene1266|rna1265|rna1265  9 VTLFSSEGNLGQCDNALRA 27
                                       79**********9999887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.035
                     Proteasome_A_N  13 RLfQVE 18 
                                        RL+QV+
  gene1266|gene1266|rna1265|rna1265 143 RLYQVD 148
                                        9****7 PP

>> E2  Bacteriophage E2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.1e-05      0.31       7      25 ..     165     185 ..     160     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                                 E2   7 YsRFGKFiKRRL..LiDnFsn 25 
                                        Ys   KFiKRRL  L Dn  n
  gene1266|gene1266|rna1265|rna1265 165 YSEAKKFIKRRLesLDDNMVN 185
                                        99999******9777788766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1666.03
//
Query:       gene1267|gene1267|rna1266|rna1266  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-05   24.5   0.6       0.12   12.6   0.1    3.7  3  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    0.00089   19.2   3.9       0.14   12.3   0.0    4.2  5  TPR_2       Tetratricopeptide repeat
     0.0012   19.3   0.3       0.27   11.9   0.1    3.0  2  TPR_6       Tetratricopeptide repeat
     0.0022   18.5   0.1        2.9    8.5   0.0    3.1  2  TPR_19      Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.01   16.0   0.2         13    6.3   0.0    3.6  3  TPR_8       Tetratricopeptide repeat
       0.01   16.1   0.0       0.15   12.4   0.0    2.7  2  TPR_12      Tetratricopeptide repeat
      0.051   13.7   0.0      0.094   12.8   0.0    1.4  1  MoaC        MoaC family
      0.055   14.0   0.3        1.2    9.6   0.1    2.6  2  DUF1474     Protein of unknown function (DUF1474)
      0.058   13.0   0.0         12    5.6   0.0    2.4  2  HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
       0.15   12.0   0.7         25    4.9   0.0    3.7  4  TPR_10      Tetratricopeptide repeat
       0.16   12.7   0.0        3.9    8.2   0.0    2.9  2  TPR_16      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   7.3e-05      0.12      26      72 ..      37      85 ..      14      95 .. 0.85
   2 ?    2.4   0.0      0.11   1.8e+02      27      55 ..     133     161 ..     115     171 .. 0.78
   3 ?    5.6   0.0     0.012        19      21      60 ..     171     214 ..     161     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.3e-05
                                       HHHH.HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-H CS
                             ANAPC3 26 ayll.AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkky 72
                                       +y + ++ lyl+++y++  ++lr++ ++ ++s+++   +  +ll+L+ +
  gene1267|gene1267|rna1266|rna1266 37 IYPYkGQILYLQKRYEESATFLRRLmESFPQSIKAKRFLYLSLLALGDF 85
                                       555559*************************************999865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                                        HHHHHHHHHTT-HHHHHHHHHCTSHHHC- CS
                             ANAPC3  27 yllAlclylngqykrAyellrkaklnsks 55 
                                        +ll+ ++  +g+ +rA e+ ++ +  s++
  gene1267|gene1267|rna1266|rna1266 133 LLLSMAYIYSGKLDRAVEIMKTIEDSSNT 161
                                        678899999************99333333 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.012
                                        --HHHHHHHHHHHHHTT-.HHHHHHHHHCT.S..HHHC-HHHHH CS
                             ANAPC3  21 espedayllAlclylngq.ykrAyellrka.k..lnskslgcry 60 
                                         + +++y+l ++ yln++ + +A++ l+k+ +  ++ ++lgc y
  gene1267|gene1267|rna1266|rna1266 171 VRTKSIYMLDYVRYLNEDiFVTAINCLEKKqRvfEKIENLGCKY 214
                                        57899*************9********99854113344447766 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         3   4.9e+03      24      30 ..      17      23 ..      16      24 .. 0.75
   2 !   12.3   0.0   8.7e-05      0.14       7      33 ..      41      67 ..      40      68 .. 0.92
   3 ?   -3.1   0.0       7.6   1.2e+04       6      18 ..      90     102 ..      88     103 .. 0.74
   4 ?    4.9   0.0      0.02        33       7      22 ..     135     150 ..     133     154 .. 0.87
   5 ?   -2.5   0.1         5   8.1e+03      11      23 ..     334     346 ..     333     346 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3
                              TPR_2 24 fekAlel 30
                                       +e+Al++
  gene1267|gene1267|rna1266|rna1266 17 YEEALQI 23
                                       8888875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.7e-05
                              TPR_2  7 lGlayyklgdyeeAleafekAleldPn 33
                                        G+++y +++yee + ++++  e  P+
  gene1267|gene1267|rna1266|rna1266 41 KGQILYLQKRYEESATFLRRLMESFPQ 67
                                       79******************9998886 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 7.6
                              TPR_2   6 nlGlayyklgdye 18 
                                         +++ ++k gdy 
  gene1267|gene1267|rna1266|rna1266  90 TIAKECWKDGDYR 102
                                        6777788888885 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.02
                              TPR_2   7 lGlayyklgdyeeAle 22 
                                        l +ay+++g++++A+e
  gene1267|gene1267|rna1266|rna1266 135 LSMAYIYSGKLDRAVE 150
                                        889***********98 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 5
                              TPR_2  11 yyklgdyeeAlea 23 
                                        y+  g+ e+A ++
  gene1267|gene1267|rna1266|rna1266 334 YLDHGKKEDACHY 346
                                        88999***99876 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00017      0.27       7      33 .]      42      68 ..      40      68 .. 0.92
   2 ?    4.3   0.0     0.045        73       5      25 ..     134     154 ..     133     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                              TPR_6  7 alsyrklgdtdkAlealerlikeYPdS 33
                                       ++ ++ +++++++ + l+rl +++P+S
  gene1267|gene1267|rna1266|rna1266 42 GQILYLQKRYEESATFLRRLMESFPQS 68
                                       78889999*****************98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.045
                                        HHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   5 klalsyrklgdtdkAlealer 25 
                                        +l ++y+  g+ d+A+e+++ 
  gene1267|gene1267|rna1266|rna1266 134 LLSMAYIYSGKLDRAVEIMKT 154
                                        6889999977*******9986 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.011        17      32      58 ..      42      68 ..      16      82 .. 0.81
   2 !    8.5   0.0    0.0018       2.9      21      55 ..     126     159 ..     119     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                             TPR_19 32 AeallalgqldeAealLdalpeedpdd 58
                                        ++l+ +++++e    L +l+e++p++
  gene1267|gene1267|rna1266|rna1266 42 GQILYLQKRYEESATFLRRLMESFPQS 68
                                       6889999****************9994 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
                             TPR_19  21 dpknaearllLAeallalgqldeAealLdalpeed 55 
                                        d++ +e +l L  a++ +g ld A ++++++ ++ 
  gene1267|gene1267|rna1266|rna1266 126 DAHCDEPLL-LSMAYIYSGKLDRAVEIMKTIEDSS 159
                                        666666666.99******************98875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.016        26       7      32 ..      41      66 ..      41      68 .. 0.88
   2 ?   -2.1   0.0       3.8   6.2e+03       4      17 ..      88     101 ..      80     104 .. 0.72
   3 ?    6.3   0.0    0.0082        13       6      25 ..     134     153 ..     133     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                                       HHHHHHHTT-HHHHHHHHHHHHHHHH CS
                              TPR_8  7 lgsiylklgdyeeAkeyyekaleldp 32
                                       +g+i+  +++yee+  ++++  e  p
  gene1267|gene1267|rna1266|rna1266 41 KGQILYLQKRYEESATFLRRLMESFP 66
                                       699****************9988766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.8
                                        HHHHHHHHHHTT-H CS
                              TPR_8   4 yynlgsiylklgdy 17 
                                         + +++ ++k gdy
  gene1267|gene1267|rna1266|rna1266  88 SFTIAKECWKDGDY 101
                                        46778888888887 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0082
                                        HHHHHHHHTT-HHHHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkeyye 25 
                                        +l+++y+  g+++ A+e ++
  gene1267|gene1267|rna1266|rna1266 134 LLSMAYIYSGKLDRAVEIMK 153
                                        799**************987 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.3e-05      0.15      25      74 ..      16      64 ..      15      67 .. 0.90
   2 ?    0.2   0.0      0.57   9.3e+02      51      68 ..     135     152 ..     133     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.3e-05
                             TPR_12 25 llekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74
                                       l+e+al+i+ +++  +++  ++++   g+++++++ryee   +l++ ++ 
  gene1267|gene1267|rna1266|rna1266 16 LYEEALQIIDSTPL-TYESGINIYPYKGQILYLQKRYEESATFLRRLMES 64
                                       69*******99975.6889**************************98876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.57
                             TPR_12  51 LgrlyralgryeeAlell 68 
                                        L+++y ++g+++ A+e+ 
  gene1267|gene1267|rna1266|rna1266 135 LSMAYIYSGKLDRAVEIM 152
                                        778888999999998875 PP

>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.8e-05     0.094      79     134 ..     145     200 ..     102     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                                        TTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT-EEEEEEEEEEE CS
                               MoaC  79 eeesveieatvktegktGvemEALtavsvaaltvyDmvKavdkemvieevrlveKs 134
                                         +++vei  t++ +++t + ++AL +v + ++ + D v+ +++++ ++ ++ +eK+
  gene1267|gene1267|rna1266|rna1266 145 LDRAVEIMKTIEDSSNTKMYLDALISVRTKSIYMLDYVRYLNEDIFVTAINCLEKK 200
                                        57899**********************************************99997 PP

>> DUF1474  Protein of unknown function (DUF1474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00077       1.2      59      92 ..     127     162 ..      89     167 .. 0.74
   2 ?    1.7   0.0      0.24   3.9e+02      40      60 ..     200     220 ..     178     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00077
                            DUF1474  59 iyieq..lidllymylkeldkkldefkdiekassak 92 
                                         ++++  l+ + y+y ++ld+ ++ +k ie +s +k
  gene1267|gene1267|rna1266|rna1266 127 AHCDEplLLSMAYIYSGKLDRAVEIMKTIEDSSNTK 162
                                        5665422567899******************99987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.24
                            DUF1474  40 rlkskeevlkyGykynehriy 60 
                                        +++  e++ + G+ky e +i 
  gene1267|gene1267|rna1266|rna1266 200 KQRVFEKIENLGCKYVEIKIM 220
                                        45567889999****998763 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.013        21      50     120 ..      40     110 ..      34     113 .. 0.81
   2 ?    5.6   0.0    0.0072        12      53      86 ..     137     170 ..     128     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.013
                         HrpB1_HrpK  50 legvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalrDeeWr.ayAeevlesdadpdalaLvkaL 120
                                        + g++l  ++r+ee +  Lr + ++ ++   ak  l l L al+D      +A+e+ + d+d  + +L++ L
  gene1267|gene1267|rna1266|rna1266  40 YKGQILYLQKRYEESATFLRRLMESFPQSIKAKRFLYLSLLALGDFRSSfTIAKECWK-DGDYRRSTLIRIL 110
                                        568899999*********************************9995433156777776.7777777777666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0072
                         HrpB1_HrpK  53 vlliergrweeAlrlLreveaeasgtpyakaLlA 86 
                                        + +i  g+++ A+ +++++e++++   y  aL++
  gene1267|gene1267|rna1266|rna1266 137 MAYIYSGKLDRAVEIMKTIEDSSNTKMYLDALIS 170
                                        668999*************************987 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.8   2.9e+03      24      31 ..      16      23 ..      15      24 .. 0.81
   2 ?    2.7   0.1     0.074   1.2e+02       9      28 ..      42      61 ..      41      64 .. 0.86
   3 ?    4.9   0.0     0.016        25       8      26 ..     135     153 ..     134     155 .. 0.92
   4 ?   -3.7   0.0         8   1.3e+04      30      39 ..     221     230 ..     218     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                             TPR_10 24 lleealai 31
                                       l+eeal+i
  gene1267|gene1267|rna1266|rna1266 16 LYEEALQI 23
                                       68999987 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.074
                             TPR_10  9 analrqrgrydeAealleea 28
                                       + +l+ ++ry+e+  +l++ 
  gene1267|gene1267|rna1266|rna1266 42 GQILYLQKRYEESATFLRRL 61
                                       67899********9999985 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.016
                             TPR_10   8 LanalrqrgrydeAealle 26 
                                        L++a+   g++d+A+++++
  gene1267|gene1267|rna1266|rna1266 135 LSMAYIYSGKLDRAVEIMK 153
                                        89**************986 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 8
                             TPR_10  30 airrrllGpd 39 
                                         i +++lG++
  gene1267|gene1267|rna1266|rna1266 221 HIAKKTLGRN 230
                                        5889999986 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0024       3.9      40      67 ..      41      68 ..      40      87 .. 0.75
   2 ?    0.8   0.0       0.5   8.2e+02       3      18 ..     135     150 ..     133     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                             TPR_16 40 lgdaalrqgrlaeAaalyraalraapda 67
                                       +g++++ q+r++e a ++r++ +  p++
  gene1267|gene1267|rna1266|rna1266 41 KGQILYLQKRYEESATFLRRLMESFPQS 68
                                       5788888888888888888876666654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.5
                             TPR_16   3 laraalragdyddAaa 18 
                                        l +a++++g+ d+A++
  gene1267|gene1267|rna1266|rna1266 135 LSMAYIYSGKLDRAVE 150
                                        6789**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2326.36
//
Query:       gene1268|gene1268|rna1267|rna1267  [L=526]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3193.90
//
Query:       gene1269|gene1269|rna1268|rna1268  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-23   81.9   0.2    1.1e-22   79.9   0.0    2.0  2  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
  ------ inclusion threshold ------
      0.021   13.9   0.1      0.024   13.7   0.1    1.1  1  BPL_N     Biotin-protein ligase, N terminal
       0.23   12.0   2.4        3.1    8.3   0.1    2.8  3  Pox_D5    Poxvirus D5 protein-like


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   1.8e-26   1.1e-22       1      87 [.      12      96 ..      12      97 .. 0.96
   2 ?   -0.1   0.1      0.17     1e+03      29      48 ..     122     142 ..      96     183 .. 0.63

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.8e-26
                                       T-EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHS CS
                               SBDS  1 nvsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkG 78
                                       nvsiv++kk+++r+e+ vy+nkl+eyr+g  ++L+e+l +++i++++skGe a +++l+ + ++++  ei++eIL++G
  gene1269|gene1269|rna1268|rna1268 12 NVSIVALKKFGRRYELGVYPNKLYEYRNGMATPLNEILLTDTIYRSVSKGEIAGQDDLDLFCKSHE--EIVREILNNG 87
                                       89**********************************************************977665..9********* PP

                                       EEE--HHHH CS
                               SBDS 79 eiqvsaeer 87
                                        +q+++ +r
  gene1269|gene1269|rna1268|rna1268 88 YEQKNEATR 96
                                       *****9866 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                                        TT---HHHHB.SSSS-EEETT CS
                               SBDS  29 gkeidLsevl.qsekiFtnas 48 
                                         +e +L+e + ++++i+  +s
  gene1269|gene1269|rna1268|rna1268 122 LNEASLKEAIgKVHNIYIGNS 142
                                        334444433323445554443 PP

>> BPL_N  Biotin-protein ligase, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     4e-06     0.024     213     325 ..      71     180 ..      34     221 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4e-06
                              BPL_N 213 lLtgvhpEfalanlkkqeaeekeykkvveeleadekaRleflkalLtklgLevneeeeetevpslsplllsslske 288
                                        l++  h E+  + l++   e+k++++ + e e++e++ +efl++  tk g ++ne++ +++  +++++++ +++k+
  gene1269|gene1269|rna1268|rna1268  71 LFCKSHEEIVREILNNG-YEQKNEATRIYEQEKTEREIIEFLRNKVTKGGRHLNEASLKEAIGKVHNIYIGNSKKQ 145
                                        56778999999999766.5666777789999***********************999889**********999888 PP

                              BPL_N 289 eveelleslkeklaaekeeeeevikdend.tfrleked 325
                                        + +e+l +l++    +   + +v  d nd  ++++k++
  gene1269|gene1269|rna1268|rna1268 146 S-QEILGKLEKMGFDRV--GIKVSVDMNDkVMEFAKKN 180
                                        7.79*****99555543..2344444444145666665 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.033     2e+02      54      84 ..      81     111 ..      69     113 .. 0.79
   2 ?   -1.5   0.0      0.63   3.8e+03      44      75 ..     122     152 ..     115     161 .. 0.57
   3 ?    8.3   0.1   0.00052       3.1       3      37 ..     170     204 ..     168     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.033
                             Pox_D5  54 kkileegfekkkkkkgqqpneyleyifiedl 84 
                                         +il++g+e+k+  +  + +e+ e + ie l
  gene1269|gene1269|rna1268|rna1268  81 REILNNGYEQKNEATRIYEQEKTEREIIEFL 111
                                        4688889*****9988888888888877766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.63
                             Pox_D5  44 lskrtFqkrlkkileegfekkkkkkgqqpney 75 
                                        l++ ++++ ++k+ +  ++ + kk+ q    +
  gene1269|gene1269|rna1268|rna1268 122 LNEASLKEAIGKVHNI-YIGNSKKQSQEILGK 152
                                        5555555555555444.777777655555444 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00052
                             Pox_D5   3 nDpvldFveelfeeekstrvpsdvlYeaYkafcek 37 
                                        nD+v++F+ +  e +++ +++++  ++++k+ ce 
  gene1269|gene1269|rna1268|rna1268 170 NDKVMEFAKKNGEVYDGYVIIRSECFPKFKEVCEG 204
                                        9********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1333.10
//
Query:       gene1270|gene1270|rna1269|rna1269  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-38  131.7   0.1    8.9e-38  130.1   0.1    1.7  1  Pkinase      Protein kinase domain
    2.3e-24   86.1   0.0      3e-24   85.7   0.0    1.2  1  Pkinase_Tyr  Protein tyrosine kinase
  ------ inclusion threshold ------
      0.034   13.5   0.0      0.072   12.4   0.0    1.4  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.1   0.1   1.5e-41   8.9e-38      24     198 ..     123     317 ..     116     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 1.5e-41
                                        TEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHH.....HHSS CS
                            Pkinase  24 gkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladlle.....rkgs 94 
                                         +  +vKk kk+   + ++k+ +rEi++lk++ ++++vr+y+++e+  +l++ ley++ g+l d+++     rk++
  gene1270|gene1270|rna1269|rna1269 123 ADYTVVKKSKKRISGELDRKSRMREIEMLKRVGSDHVVRYYDFWESRGYLFIELEYCNIGTLRDYIHevyflRKSK 198
                                        566789**********999*****************************************************99** PP

                                        --HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEET..................TTE...EEE-SGTTSEESS CS
                            Pkinase  95 lseeeakkiakqilegleylHskgiiHrDlKpeNiLide..................kge...lKitDFGlakele 149
                                        +s+e ++k+++++++gle +Hs +i+H DlKpeNiL+++                        +Ki+DF +++   
  gene1270|gene1270|rna1269|rna1269 199 FSPEITRKMMYELAKGLEAIHSCNIVHLDLKPENILMKSivskekcsgrcqcmfptdP-GsfvFKISDFNISRYEG 273
                                        **************************************88888888877777776651.0566**********988 PP

                                        SSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STT CS
                            Pkinase 150 ssskltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfs 198
                                        ++    ++ g+++Y+APEvl +   +k++D++slG+i +e++++  +++
  gene1270|gene1270|rna1269|rna1269 274 EDI---DEDGDKRYMAPEVL-RDVCTKASDIYSLGLIYLEIIAE-IILP 317
                                        876...99************.5678***************9765.4444 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.0   4.9e-28     3e-24      29     201 ..     125     313 ..      82     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 4.9e-28
                                        EEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHT...CTTTSB CS
                        Pkinase_Tyr  29 vkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkk...ekeklt 101
                                        ++V+ K+ k+ + e ++++ ++e++++k++  +++v+++ +  +++ l+i +ey++ G+L++++++    +k+k++
  gene1270|gene1270|rna1269|rna1269 125 YTVVKKSKKRISGELDRKSRMREIEMLKRVGSDHVVRYYDFWESRGYLFIELEYCNIGTLRDYIHEVyflRKSKFS 200
                                        455555556666777899************************************************98989***** PP

                                        HHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE....................TTEEEE-STTTHEETTTSS CS
                        Pkinase_Tyr 102 lkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse....................nkvvkisDfGLardiekdd 157
                                         + + ++++++AkG+e ++s ++vH dl   N+L+++                    + v kisDf ++r      
  gene1270|gene1270|rna1269|rna1269 201 PEITRKMMYELAKGLEAIHSCNIVHLDLKPENILMKSivskekcsgrcqcmfptdpgSFVFKISDFNISRYE---- 272
                                        *******************************************************988899*********87.... PP

                                        EEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTT CS
                        Pkinase_Tyr 158 eyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftl 201
                                           ++ +++   ++mapE+l++ ++t++sD++s G +  Ei+  
  gene1270|gene1270|rna1269|rna1269 273 --GEDIDEDGDKRYMAPEVLRD-VCTKASDIYSLGLIYLEIIAE 313
                                        ..44445555679******987.789***************975 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05     0.072     112     153 ..     196     237 ..     185     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                Kdo 112 waelaeelkrallkavgrliaklhragvnHadlyaknillqq 153
                                         ++++ e +r+++ ++++  + +h+ ++ H dl + nil++ 
  gene1270|gene1270|rna1269|rna1269 196 KSKFSPEITRKMMYELAKGLEAIHSCNIVHLDLKPENILMKS 237
                                        3568999********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2126.24
//
Query:       gene127|gene127|rna127|rna127  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.5e-114  379.0   0.0   1.1e-113  378.9   0.0    1.0  1  Thymidylat_synt  Thymidylate synthase


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.9   0.0    6e-118  1.1e-113       2     268 .]      11     294 .]      10     294 .] 0.95

  Alignments for each domain:
  == domain 1  score: 378.9 bits;  conditional E-value: 6e-118
                                    HHHHHHHHHHHH-EEEE-TTSSEEEEEEEEEEEEEGGGCB----SSST--HHHHHHHHHHHHTT--BTHHHHTTT--TTH CS
                Thymidylat_synt   2 qYldlvrkileeGeekedRtgtgtisvfgaqlrfdlsegefPllTtkkvflksvieEllWflsgetnvkeLqekgvkiWd 81 
                                    qYldlv++ile+G+++ dRtgtgt+svfga++rf+l++++fPllTtk+vf+k v+eEll+fl+g+t+ k L+ekg++iW+
  gene127|gene127|rna127|rna127  11 QYLDLVQHILENGVKRADRTGTGTLSVFGATMRFSLEDNTFPLLTTKRVFYKGVVEELLFFLRGQTDSKILEEKGIRIWE 90 
                                    9******************************************************************************* PP

                                    HH...........HHHTTB-SSSHHHHHHHBTST........TTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSS CS
                Thymidylat_synt  82 ew...........adeegdlgpvYGkqwrkfkae........egkkidqlakvidqlkenpdsRriivsawnpaeldkma 142
                                    +             +eegdlgp+YG+qwr+f+ae        egk++dq+++vid++k+np+sRr++v+awnp+ l +ma
  gene127|gene127|rna127|rna127  91 KNgskqflqsigiDREEGDLGPIYGFQWRHFGAEyrtsgssyEGKGVDQIKDVIDTIKKNPNSRRMVVCAWNPTALGEMA 170
                                    66333334444435666***************999*****************************************99** PP

                                    S--SEEEEEEEE..SEETEEEEEEEEEEEETTTHHHHHHHHHHHHHHHHHHHHT-EEEEEEEEEEEEEEEGGGHHHHHHH CS
                Thymidylat_synt 143 LppChvlfqfyvkdkkegkLslqlyqRSaDvflGvpFNiasyalLthmlaqvtglkpgelihtigdaHiYsnhveqvkeq 222
                                    LppChvlfqf+v    +gkL++ +yqRS D++lGvpFNiasy+lLt ++a+ tgl+pge++h +gd+HiY +hv+ ++ q
  gene127|gene127|rna127|rna127 171 LPPCHVLFQFNV---MDGKLNCAMYQRSGDMGLGVPFNIASYSLLTIIVAHLTGLQPGEFVHFLGDTHIYLDHVDSLRLQ 247
                                    ************...4567************************************************************* PP

                                    HTS---S--EEEE--SSTH.SGGG--GGGEEEES----SXXXXXXX. CS
                Thymidylat_synt 223 lereprelpklelnkekkv.siedfeledfelenYkphpkikakvav 268
                                    l+r pr++pkl +n+++k+ ++edf++edf+l++Y+php ik++++v
  gene127|gene127|rna127|rna127 248 LQRAPRPFPKLFVNPKEKRgKVEDFQYEDFSLVGYDPHPPIKMDMSV 294
                                    **************999999*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2072.13
//
Query:       gene1271|gene1271|rna1270|rna1270  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-07   30.5   3.4    3.9e-07   29.7   3.4    1.4  1  zf-CCCH_4  CCCH-type zinc finger
    8.3e-07   28.9   6.3      2e-06   27.6   6.3    1.7  1  zf_CCCH_4  Zinc finger domain
    1.1e-05   25.2   2.9      2e-05   24.4   2.9    1.5  1  zf-CCCH    Zinc finger C-x8-C-x5-C-x3-H type (and similar)
  ------ inclusion threshold ------
      0.025   15.3   1.3       0.06   14.0   1.3    1.6  1  Torus      Torus domain
      0.074   13.5   5.5       0.13   12.8   5.5    1.4  1  zf-CCCH_2  RNA-binding, Nab2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   3.4   1.1e-10   3.9e-07       2      21 ..       4      23 ..       3      24 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.1e-10
                          zf-CCCH_4  2 lCpyfakGsCrfGdnCrFsH 21
                                       +C++f++G+C+fG++C++ H
  gene1271|gene1271|rna1270|rna1270  4 VCRFFIEGKCKFGSKCKYDH 23
                                       8*****************99 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   6.3   5.7e-10     2e-06       1      19 []       5      23 ..       5      23 .. 0.99

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.7e-10
                          zf_CCCH_4  1 CkfflqGtCkkGdkCrFaH 19
                                       C+ff++G+Ck+G+kC++ H
  gene1271|gene1271|rna1270|rna1270  5 CRFFIEGKCKFGSKCKYDH 23
                                       *****************99 PP

>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   2.9   5.5e-09     2e-05       5      26 ..       4      24 ..       2      25 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.5e-09
                                       CBCHHHHHS--TTGGG-SSBSC CS
                            zf-CCCH  5 lCrffmrtGyCkyGdrCkFaHg 26
                                        Crff + G Ck+G++Ck+ H+
  gene1271|gene1271|rna1270|rna1270  4 VCRFFIE-GKCKFGSKCKYDHV 24
                                       6997777.*************7 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.3   1.7e-05      0.06      71      91 ..       3      23 ..       1      28 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                       -B-HHHHHT--SSGGG-SSB- CS
                              Torus 71 yfClfFarGlCakGkkCeylH 91
                                        +C fF  G C+ G+kC+y H
  gene1271|gene1271|rna1270|rna1270  3 NVCRFFIEGKCKFGSKCKYDH 23
                                       68*****************99 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.5   3.7e-05      0.13       2      17 ..       5      23 ..       5      23 .. 0.99

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                          zf-CCCH_2  2 Crffpn..C.tnpkCpFaH 17
                                       Crff+   C ++ kC++ H
  gene1271|gene1271|rna1270|rna1270  5 CRFFIEgkCkFGSKCKYDH 23
                                       ******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2195.90
//
Query:       gene1272|gene1272|rna1271|rna1271  [L=370]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-51  170.5   0.1    2.6e-24   85.1   0.0    2.8  3  Bromodomain  Bromodomain
    6.8e-08   32.6   0.1    1.5e-07   31.5   0.1    1.6  1  BET          Bromodomain extra-terminal - transcription regul
  ------ inclusion threshold ------
      0.048   13.8   1.0        0.1   12.7   0.3    1.9  2  DUF3461      Protein of unknown function (DUF3461)
       0.07   12.4   0.8       0.13   11.5   0.8    1.4  1  MPS2         Monopolar spindle protein 2


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0   5.8e-28   2.6e-24       1      81 [.      20     102 ..      20     105 .. 0.94
   2 !   82.3   0.0   4.2e-27   1.9e-23       1      83 [.     157     242 ..     157     243 .. 0.94
   3 ?   -1.8   0.0      0.78   3.5e+03       7      34 ..     332     359 ..     326     360 .. 0.82

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 5.8e-28
                                        HHHHHHHBHTTTCGGGGCSTT..-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHT CS
                        Bromodomain   1 lekilsellehklaepFlepv..dpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkynge 74 
                                        ++++l+ +++++ a pFlepv   +   pdy+++ik+P+dLstI+kkl+ ++Y+ ++ f +d+kl+f+N+++yn++
  gene1272|gene1272|rna1271|rna1271  20 CSQVLTRIKRNSNAPPFLEPVdpVKLGIPDYPEKIKNPMDLSTIRKKLDAKEYSGPEGFDDDMKLMFNNCYTYNPP 95 
                                        99*******************6556668************************************************ PP

                                        TSHHHHH CS
                        Bromodomain  75 gsviyel 81 
                                        g+ ++++
  gene1272|gene1272|rna1271|rna1271  96 GTIVHDM 102
                                        **99875 PP

  == domain 2  score: 82.3 bits;  conditional E-value: 4.2e-27
                                        HHHHHHHBHTTT...CGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSH CS
                        Bromodomain   1 lekilsellehk...laepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyng 73 
                                        ++++ls+l++ k    + pFlepvd++ +p yy+vik+P+d++t+k+kl+++kY+s+++f  dl+l+++N++k+n 
  gene1272|gene1272|rna1271|rna1271 157 CSEVLSDLVKPKhksYNWPFLEPVDGDLVPGYYSVIKEPMDIQTMKNKLDQRKYHSVEEFGRDLELIVENCKKFNA 232
                                        8999998888886657789********************************************************* PP

                                        TTSHHHHHHH CS
                        Bromodomain  74 egsviyelae 83 
                                        +g+++y++ +
  gene1272|gene1272|rna1271|rna1271 233 PGTEVYACGQ 242
                                        *******976 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.78
                                        HBHTTTCGGGGCSTT-GCCSTTHHHH.S CS
                        Bromodomain   7 ellehklaepFlepvdpeefpdyyavik 34 
                                        e++e+++ e+ ++++++ ++++ + +ik
  gene1272|gene1272|rna1271|rna1271 332 EFVENDEIEVDMRTIPDHVVEEIDMYIK 359
                                        6889999999999999999998887775 PP

>> BET  Bromodomain extra-terminal - transcription regulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   3.3e-11   1.5e-07       3      64 .]     299     360 ..     297     360 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.3e-11
                                BET   3 tyeeKkeLseeInkLpgeklgrvveIIqerepelqsdedEiElDidaldddtLreLekyvkk 64 
                                        +  e+ +++++I +++ e+ ++v +I+ ++ + +  ++dEiE+D+ +++d+++ e+  y+k+
  gene1272|gene1272|rna1271|rna1271 299 SLSERVSIGNAILNMTKEQTENVAKIVLKNGAGEFVENDEIEVDMRTIPDHVVEEIDMYIKS 360
                                        678999*************************66569**********************9985 PP

>> DUF3461  Protein of unknown function (DUF3461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   2.3e-05       0.1      55     122 ..     199     271 ..     190     274 .. 0.87
   2 ?   -2.5   0.0       1.2   5.2e+03      25      42 ..     317     334 ..     311     359 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                            DUF3461  55 kkvlvdsgseeykevseisavlrkvleeLdkltekkkeekdikekllkdlk.hlekv....vnskikeierkl 122
                                        ++++   ++++y++v+e  + l+ ++e+ +k     +e  +  ++  k +k h+ek     +++ki+e++rk+
  gene1272|gene1272|rna1271|rna1271 199 QTMKNKLDQRKYHSVEEFGRDLELIVENCKKFNAPGTEVYACGQEFEKAVKaHMEKTspvdIKNKISELKRKV 271
                                        667777799*************************99999999999999997799996554689********97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                            DUF3461  25 gekDiLkiYfkkekgell 42 
                                         ++++ ki  k   ge++
  gene1272|gene1272|rna1271|rna1271 317 QTENVAKIVLKNGAGEFV 334
                                        445555555555555444 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.8   2.8e-05      0.13     168     288 ..     200     318 ..     195     328 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                               MPS2 168 slkdELeakd.evlrekeRelleLkkrlseyk....ekYellqrefslykarrveksqnslktaikheviisElkr 238
                                         +k+ L++++ + ++e  R+l  + ++ ++++    e Y+   +ef+  ka + + ++ s    ++ +  isElkr
  gene1272|gene1272|rna1271|rna1271 200 TMKNKLDQRKyHSVEEFGRDLELIVENCKKFNapgtEVYA-CGQEFE--KAVKAHMEKTS---PVDIKNKISELKR 269
                                        5666665543145566666666666666666521113333.345566..77777777777...55666669***** PP

                               MPS2 239 klqeqteiisilkeqiqreeGasqskr.krlhddgigstknlilalpknlv 288
                                        k+   t+ i++l  ++  + G + s r   l +    s+ n il+++k+ +
  gene1272|gene1272|rna1271|rna1271 270 KVMSYTREIRMLESKLVEQTGEAPSSRaYSLSERV--SIGNAILNMTKEQT 318
                                        ****************9999997777745555444..77777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2221.98
//
Query:       gene1273|gene1273|rna1272|rna1272  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        2.1    7.5   7.7       0.25   10.5   0.5    2.1  2  Bac_export_2  FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> Bac_export_2  FlhB HrpN YscU SpaS Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5   1.4e-05      0.25     105     202 ..      91     192 ..       9     195 .. 0.75
   2 ?    0.5   1.5     0.016   2.8e+02      36      85 ..     235     294 ..     224     314 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.4e-05
                                        XXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXX CS
                       Bac_export_2 105 kpklsklnplkglkrifslrsl...vellksllkvvlvgavaylvlkseleellalaeldle.aalelllslllkl 176
                                        + k + +  lkgl+++f +++l   ++++ +ll +++++++++ + k   + + ++ +++ e     l++s++++ 
  gene1273|gene1273|rna1272|rna1272  91 TYKEKTIRYLKGLRKFFIKNKLsavIDFFGALLMIFAISVMIISMCKVGGRVINSINATPNEnGGRGLVTSVVFSS 166
                                        4566789999******9888774436777777777777777777776655555444444444244559999***** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Bac_export_2 177 lllvllallviallDlllqrwefekk 202
                                          l+ l+ l+ +l  l++q +++++ 
  gene1273|gene1273|rna1272|rna1272 167 SGLYSLLSLLYSLYNLVMQGYQYISG 192
                                        **********************9875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.016
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........XXXXXXX CS
                       Bac_export_2  36 glllllllgpslveelaellrevlsalelllelllallllllp..........lllvlll 85 
                                        ++++l++++   ++    +++++++   +++++++a+l+ ++p          +ll +++
  gene1273|gene1273|rna1272|rna1272 235 VIFMLIFIIWGTLKGGFGYVKQAFALSFIVQKIVTATLQYMAPffrhsgsknvILLPIIF 294
                                        333333333333333334444455555566677777777777722222222222333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2063.32
//
Query:       gene1274|gene1274|rna1273|rna1273  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-29  101.2   0.1    3.2e-29  100.8   0.1    1.1  1  Spt4      Spt4/RpoE2 zinc finger


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.1   1.8e-33   3.2e-29       1      76 [.      13      88 ..      13      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.8e-33
                               Spt4  1 lrACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkv 76
                                       lrACl C+ +kt + F+++gC+nC +l +kg+  +v+ects++f+G+va+l+p++Sw++kwqr++++++glYA+ +
  gene1274|gene1274|rna1273|rna1273 13 LRACLGCSQIKTLNGFRKDGCENCPMLGMKGNIANVNECTSSNFKGVVALLQPSNSWIGKWQRIGEFKKGLYAMVI 88
                                       69***********************************************************************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 780.93
//
Query:       gene1275|gene1275|rna1274|rna1274  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.15   12.2   2.8       0.18   11.9   1.4    1.7  2  DUF1877        Domain of unknown function (DUF1877)
        1.2    9.0   7.9        1.4    8.8   7.9    1.1  1  Auxin_canalis  Auxin canalisation


Domain annotation for each model (and alignments):
>> DUF1877  Domain of unknown function (DUF1877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.4     2e-05      0.18      79     148 ..       7      71 ..       1      73 [. 0.72
   2 ?    0.9   0.2     0.047   4.2e+02      95     126 ..      59      90 ..      54     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                            DUF1877  79 edegygparlltpeqVkevaeaLaeldfeelrerfdaeeleea.eiYpniweeeeeededleylleyfeel 148
                                        ed+++ ++r  ++  Vk+++++L++l+f++  e++d e ++++ ei  +    e+++ +  e +++ ++e+
  gene1275|gene1275|rna1274|rna1274   7 EDVDDAILR--EKLFVKAASKFLKTLEFKKVEEEYDGELMRSQkEIEQG----EKDARRKAEKMMKRHNEM 71 
                                        566666666..7778**********************999865144433....566777777777666665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.047
                            DUF1877  95 kevaeaLaeldfeelrerfdaeeleeaeiYpn 126
                                        +++ + +++ ++ +l+++ +++e+++ ++ p+
  gene1275|gene1275|rna1274|rna1274  59 RKAEKMMKRHNEMRLKRKSKMSEMDSDDLEPE 90 
                                        56778899999999999999999999987665 PP

>> Auxin_canalis  Auxin canalisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.9   0.00015       1.4      54     132 ..      44     127 ..      12     130 .] 0.60

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00015
                      Auxin_canalis  54 iesqsaaeskevsplts.erlshssgp...tdsppispsesddvk..yiraqnalkpelnllrggksktvgrwlkd 123
                                        + sq+++e+ e+ ++ + e++++++++   ++++++s  +sdd++   + a   ++ e+   ++++++ v++ lk 
  gene1275|gene1275|rna1274|rna1274  44 MRSQKEIEQGEKDARRKaEKMMKRHNEmrlKRKSKMSEMDSDDLEpeSFIAPMLSNRET-RKKNKGKHPVNKSLKR 118
                                        23334444444533333367777666667789999999999999954222222222222.33477899******** PP

                      Auxin_canalis 124 rkekkkeea 132
                                        rk kk+++ 
  gene1275|gene1275|rna1274|rna1274 119 RKMKKRQKR 127
                                        ***999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2376  (0.132523); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 819.26
//
Query:       gene1276|gene1276|rna1275|rna1275  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00024   20.9   0.0    0.00043   20.0   0.0    1.4  1  Cyclin_N        Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.038   13.3   0.2      0.051   12.8   0.2    1.2  1  Pox_RNA_pol_35  Poxvirus DNA-directed RNA polymerase, 35 kD s
      0.049   14.0   0.0      0.068   13.5   0.0    1.3  1  Cyclin          Cyclin
      0.057   13.5   0.0        2.1    8.4   0.0    2.2  2  SIR2_2          SIR2-like domain
      0.092   11.7   0.0        0.1   11.5   0.0    1.1  1  Fucokinase      L-fucokinase
       0.13   12.3   1.7       0.22   11.6   0.2    2.0  2  HTH_7           Helix-turn-helix domain of resolvase
       0.15   11.9   0.0       0.32   10.8   0.0    1.6  1  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.7e-07   0.00043      59     127 .]      79     150 ..      75     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.7e-07
                                        HHHHHHHS---CC.....CHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT--- CS
                           Cyclin_N  59 ldRflskksvpkd.....klqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfdls 127
                                        +d+f+s++  ++      +  l++++c ++++K+  + + +   ++ ++ + +  ++i+ +Er+iL++L++d++
  gene1276|gene1276|rna1275|rna1275  79 VDKFMSNRRKKELekilgNEYLLFIGCTIISSKIYMDLSYTNFSWIEVCHHGV--DQINVAERQILQVLDYDVN 150
                                        68999944333324579999**************9999999999999998766..9***************986 PP

>> Pox_RNA_pol_35  Poxvirus DNA-directed RNA polymerase, 35 kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     2e-05     0.051     151     220 ..      72     143 ..      56     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                     Pox_RNA_pol_35 151 eklsfLdvevf..nreyenvkvileeefrsivpfiviapeGkltlfvekysWldlkkhlkdildflerklva 220
                                        ek s+ dv+ f  nr  + +  il +e+   +  ++i+++  + l  +++sW++  +h  d +++ er++++
  gene1276|gene1276|rna1275|rna1275  72 EKGSLSDVDKFmsNRRKKELEKILGNEYLLFIGCTIISSKIYMDLSYTNFSWIEVCHHGVDQINVAERQILQ 143
                                        5556777777766899****************************************************9986 PP

>> Cyclin  Cyclin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.7e-05     0.068     109     161 .]      97     149 ..      66     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                        THHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHHHHHHHHHTTT-- CS
                             Cyclin 109 nihRllivallvatKflvDlsysnekfakvggislkELnkLEidFlflvdFdl 161
                                        n + l i  + +++K++ Dlsy+n  + +v    +  +n  E + l ++d+d+
  gene1276|gene1276|rna1275|rna1275  97 NEYLLFIGCTIISSKIYMDLSYTNFSWIEVCHHGVDQINVAERQILQVLDYDV 149
                                        77889999999****************************************95 PP

>> SIR2_2  SIR2-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00084       2.1      92     125 ..      22      53 ..      10      70 .. 0.85
   2 ?    3.1   0.0     0.037        94      69      96 ..      81     106 ..      62     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00084
                             SIR2_2  92 flGySfsDpnirelleellkesgnarrhyaflpe 125
                                        flG+S++D + r+ ++++lk+s++  + y +l  
  gene1276|gene1276|rna1275|rna1275  22 FLGTSINDGYTRHRICKSLKRSRT--SLYTILTA 53 
                                        9*********************99..77777665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.037
                             SIR2_2  69 ellarktpiptllkallrskslLflGyS 96 
                                        +++  ++  ++ l+++l +  lLf+G+ 
  gene1276|gene1276|rna1275|rna1275  81 KFM--SNRRKKELEKILGNEYLLFIGCT 106
                                        344..677888999***999******95 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.1e-05       0.1     208     324 ..      33     156 ..      25     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                         Fucokinase 208 reelwnlLkgtpLnvillnnskFyHlgttaeylehltkdaslkeelsltstafsaiknkkekk.......kesavv 276
                                        r+++++ Lk++  +++++ ++k + +  t+ y+  + +++++ +   +++ ++++ k++ ek+         ++++
  gene1276|gene1276|rna1275|rna1275  33 RHRICKSLKRSRTSLYTILTAK-ILFDKTKRYFPSYIEKIEKGSLSDVDKFMSNRRKKELEKIlgneyllFIGCTI 107
                                        7778888887775555555555.3356777777777777777777777777777776666666999999999**** PP

                         Fucokinase 277 inSvlessvsvgegsviehsslk.gnvsigsnsivsglelesseeslel 324
                                        i+S++  ++s  + s ie ++ + +++++ ++ i+  l+++ + + +el
  gene1276|gene1276|rna1275|rna1275 108 ISSKIYMDLSYTNFSWIEVCHHGvDQINVAERQILQVLDYDVNLQWIEL 156
                                        ***********************************99988877764444 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   8.6e-05      0.22      19      44 ..      28      53 ..      24      54 .. 0.92
   2 ?   -1.2   0.1      0.87   2.2e+03       6      20 ..     147     162 ..     145     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.6e-05
                                       TTT--STTTSSSS---SSSS--SS-- CS
                              HTH_7 19 eeGisiskIAkevnisRsTvYRylad 44
                                       ++G+++  I+k ++ sR+++Y +l++
  gene1276|gene1276|rna1275|rna1275 28 NDGYTRHRICKSLKRSRTSLYTILTA 53
                                       78*******************99987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.87
                                        S-HH.HHGGGGSSTTT CS
                              HTH_7   6 lskn.dinrvvkLlee 20 
                                        ++ n ++ +++++++e
  gene1276|gene1276|rna1275|rna1275 147 YDVNlQWIELKRMYDE 162
                                        5666689999****97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.32      16      38 ..      29      51 ..      16      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                             HTH_23 16 eGlsvreIAreLgvsrrTvyrwl 38
                                       +G+++++I++ L +sr  +y +l
  gene1276|gene1276|rna1275|rna1275 29 DGYTRHRICKSLKRSRTSLYTIL 51
                                       4*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1308.09
//
Query:       gene1277|gene1277|rna1276|rna1276  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-23   81.5   0.8    4.7e-23   81.5   0.8    2.1  2  ArfGap    Putative GTPase activating protein for Arf
  ------ inclusion threshold ------
       0.14   12.5   0.1        1.6    9.1   0.0    2.1  2  DUF1890   Domain of unknown function (DUF1890)
       0.99    9.2   3.9         10    5.9   3.9    2.1  1  zf-RRN7   Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn


Domain annotation for each model (and alignments):
>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.8   7.8e-27   4.7e-23       3      79 ..      15      91 ..      13     123 .. 0.90
   2 ?   -0.1   0.1      0.16   9.6e+02      52      87 ..     144     181 ..     134     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 7.8e-27
                                       HHHHHCCSCCCCB-TTT-SBS--EEETTTTEEE-HHHHHHHCCS.TTT--EEETTTS---HHHHHHHHHTCHHHHHH CS
                             ArfGap  3 alkellkepenkvCaDCgakeptWaslnlgvflCieCsgvHrslgvhiskvrsltldkwedeelellkalgNkkane 79
                                       ++k ++ +++nk+CaDC++ +p W+++++g f+C+eC++ Hr+lgv+i+kv+s+ ld+w+ +el+ +   gN++a +
  gene1277|gene1277|rna1276|rna1276 15 FFKYIRMQSNNKRCADCNNLSPIWVTVTYGFFICTECASKHRELGVRITKVKSTILDTWSLSELRRVYVSGNSNAPK 91
                                       677888999***************************************************************99866 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                                        -EEETTTS---HHHHHHHH..HTCHHHHHHHHTTTC-T CS
                             ArfGap  52 kvrsltldkwedeelellk..algNkkaneileaklpk 87 
                                        k+++ ++ k++d++ + ++  ++ N+k  + l++++ k
  gene1277|gene1277|rna1276|rna1276 144 KIEERRMPKFSDSDAKYVEekSITNEKQSDELKETKIK 181
                                        55556666667776666664456666666666665544 PP

>> DUF1890  Domain of unknown function (DUF1890)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00027       1.6      29      55 ..      80     106 ..      67     130 .. 0.81
   2 ?    1.1   0.1     0.079   4.7e+02      42      69 ..     151     181 ..     146     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                                        EEEEEE-HHHHHHHHHHSTT-SS-SEE CS
                            DUF1890  29 evvvagnpaalkLlkvaDpekhYvkel 55 
                                        +v+v+gn  a kL kv+D  + Y+k  
  gene1277|gene1277|rna1276|rna1276  80 RVYVSGNSNAPKLGKVSDLRTKYTKAE 106
                                        799********************9864 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.079
                                        HHHHSTT-SS-SEE.EEHHHHHHH--TT..S CS
                            DUF1890  42 lkvaDpekhYvkel.vdldkaleeieek..d 69 
                                         k +D +  Yv+e  ++ +k  +e++e   +
  gene1277|gene1277|rna1276|rna1276 151 PKFSDSDAKYVEEKsITNEKQSDELKETkiK 181
                                        5789999999999867777777777766333 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.9    0.0018        10       4      29 ..      25      53 ..      23      55 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0018
                            zf-RRN7  4 gppCgvCgc.....rsftlddGfyyCrrCht 29
                                       +++C+ C++     +++t   Gf++C++C +
  gene1277|gene1277|rna1276|rna1276 25 NKRCADCNNlspiwVTVTY--GFFICTECAS 53
                                       5778888887654444444..********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1418.24
//
Query:       gene1278|gene1278|rna1277|rna1277  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-06   27.3   0.1     0.0056   17.4   0.0    1.8  3  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
      0.004   17.4   0.0     0.0066   16.7   0.0    1.3  1  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain
  ------ inclusion threshold ------
      0.024   14.2   0.1      0.031   13.8   0.1    1.2  1  CDtoxinA         Cytolethal distending toxin A/C domain
       0.13   12.4   0.0       0.44   10.7   0.0    1.9  1  BNR_6            BNR-Asp box repeat
       0.36   10.0   2.0       0.43    9.8   2.0    1.2  1  Zip              ZIP Zinc transporter
        1.5    8.1  17.5        1.1    8.7  15.1    1.8  2  SelP_N           Selenoprotein P, N terminal region


Domain annotation for each model (and alignments):
>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.73   2.2e+03      45      76 ..      50      82 ..      18      92 .. 0.71
   2 !   17.4   0.0   1.9e-06    0.0056      17      80 ..      70     132 ..      57     141 .. 0.84
   3 !   15.0   0.0     1e-05     0.031       3      59 ..     102     153 ..     100     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.73
                                       T.T-GGCEEEEECCESSEEEEEETTTTEEEEEC CS
                    RicinB_lectin_2 45 s.gaanqqWrledtgdgtyrivnkasgkvLdva 76
                                       s +++ +++r e+++ g   ++ + ++ vLd+ 
  gene1278|gene1278|rna1277|rna1277 50 StSGTPTEFRSEELSPGIKILKEVGTSDVLDLH 82
                                       336667777777777777777778888888876 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.9e-06
                                        EECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESSEEEEEETTTTEEEEECGCS- CS
                    RicinB_lectin_2  17 iknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtgdgtyrivnkasgkvLdvaggst 80 
                                        +k v++  vLd +  +   ++++   + +++  q++ +e + ++ y+++nk+ +++L+ ++ ++
  gene1278|gene1278|rna1277|rna1277  70 LKEVGTSDVLDLHHPKSG-QTKLIFHSRNNGLTQKFGIEGNENDGYTLKNKNKDLCLEYDDDGN 132
                                        577888889988888887.6889999999*************99*************9986665 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1e-05
                                        GEEEECETTTTEEEEECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCES CS
                    RicinB_lectin_2   3 QqWtlgsggdgyytiknvasgkvLdvaggstanganvqqwtcsgaanqqWrledtgd 59 
                                        Q++ ++ ++++ yt+kn+++ ++L+ +++++         tcs +  q++ ++ t++
  gene1278|gene1278|rna1277|rna1277 102 QKFGIEGNENDGYTLKNKNKDLCLEYDDDGNI-----YGTTCSENSRQKFDVVYTPE 153
                                        8888843445559***********88888776.....56778899999998876665 PP

>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.2e-06    0.0066       7      85 ..      72     150 ..      68     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-06
                                        ETTTGEEEEETTCTTSTEBEEEEE-TSCCGGGEEEEE...TT.SEEEETT.TTEEEEESSSSTTSBEEEEETTTTS CS
                     Ricin_B_lectin   7 nvasgkCLdvegeskagapvglydChgskgkQlwtlt...kd.geirskaqselCldvsstaegakvvlakChkgk 78 
                                         v +   Ld  + ++++++++  + +++ + Q++ ++   +d  ++++k +++lCl+    ++++++  ++C+ ++
  gene1278|gene1278|rna1277|rna1277  72 EVGTSDVLDLHHPKSGQTKLIFHSRNNGLT-QKFGIEgneNDgYTLKNK-NKDLCLEY---DDDGNIYGTTCS-EN 141
                                        556677788888888788888888888877.****99654443455554.6*****97...79999******9.99 PP

                                        GGGCEE..E CS
                     Ricin_B_lectin  79 gnqrWe..f 85 
                                        ++q+++  +
  gene1278|gene1278|rna1277|rna1277 142 SRQKFDvvY 150
                                        999998433 PP

>> CDtoxinA  Cytolethal distending toxin A/C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.1e-05     0.031      46      91 ..     106     150 ..      70     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                        EE-SSTT-EEEEETTT--EEEEETTEEEEE-.--TT-GGG-EEEEE CS
                           CDtoxinA  46 ldkknaglvqfknvdegtClaayenGvialkkCdeddketvFslip 91 
                                        +++++ +   +kn +++ Cl+ + +G i  ++C+e++ ++ F ++ 
  gene1278|gene1278|rna1277|rna1277 106 IEGNENDGYTLKNKNKDLCLEYDDDGNIYGTTCSENS-RQKFDVVY 150
                                        44555577789********************9**998.88888765 PP

>> BNR_6  BNR-Asp box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.44       2      11 ..      35      44 ..      35      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                              BNR_6  2 yrSeDfGknf 11
                                       +rS D+G+n+
  gene1278|gene1278|rna1277|rna1277 35 WRSPDYGINY 44
                                       9********9 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.0   0.00014      0.43     143     174 ..     186     217 ..     140     231 .] 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                                Zip 143 aeadtdadskeelrngkqeksesekeqaseee 174
                                        ++ + ++ sk+++r+g+++k++++++++ +e+
  gene1278|gene1278|rna1277|rna1277 186 ESPENNHGSKHKHRRGHSHKHHHHHHHSPHES 217
                                        455678999999**********9999977444 PP

>> SelP_N  Selenoprotein P, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.3   8.9e+02      95     119 ..     107     131 ..      82     134 .. 0.77
   2 ?    8.7  15.1   0.00036       1.1     178     209 ..     186     217 ..     178     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.3
                             SelP_N  95 eekqeDvWqilngnkDDFliYDRCG 119
                                        e +++D +++ n nkD  l YD  G
  gene1278|gene1278|rna1277|rna1277 107 EGNENDGYTLKNKNKDLCLEYDDDG 131
                                        6678888999999999988888666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00036
                             SelP_N 178 aeektehehahshkqghkhhekhghhHkekee 209
                                        ++++++h ++h+h++gh h+++h+hhH ++e+
  gene1278|gene1278|rna1277|rna1277 186 ESPENNHGSKHKHRRGHSHKHHHHHHHSPHES 217
                                        457788999999999***99999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1399.26
//
Query:       gene1279|gene1279|rna1278|rna1278  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00031   21.4   0.0     0.0059   17.3   0.0    2.5  3  RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like


Domain annotation for each model (and alignments):
>> RicinB_lectin_2  Ricin-type beta-trefoil lectin domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.17   3.1e+03      69      75 ..      38      44 ..       5      58 .. 0.54
   2 !   17.3   0.0   3.3e-07    0.0059      15      66 ..      53     101 ..      42     107 .. 0.80
   3 ?    0.9   0.0     0.042   7.5e+02      31      60 ..     109     135 ..     103     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.17
                                       TTEEEEE CS
                    RicinB_lectin_2 69 sgkvLdv 75
                                        gk++d 
  gene1279|gene1279|rna1278|rna1278 38 EGKAVDF 44
                                       2234444 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.3e-07
                                        EEE.ECTSSSEEEECGCCTBCTTEEEEEE-TTT-GGCEEEEECCESSEEEEEE CS
                    RicinB_lectin_2  15 yti.knvasgkvLdvaggstanganvqqwtcsgaanqqWrledtgdgtyrivn 66 
                                        ++i + ++++kvLd++g+ t+    +  ++ +g+anq++ l ++ ++ y+i++
  gene1279|gene1279|rna1278|rna1278  53 VKIfTDKSNNKVLDIEGSRTN----LIFYARHGGANQRFSLIKDEGSGYYIKS 101
                                        566355667*********998....999999*********9777767888876 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.042
                                        CTBCTTEEEEEE-TTT-GGCEEEEECCESS CS
                    RicinB_lectin_2  31 gstanganvqqwtcsgaanqqWrledtgdg 60 
                                        gst    n+   tcs++++q++ ++ t+++
  gene1279|gene1279|rna1278|rna1278 109 GSTG---NLYRTTCSSKPQQKFDVVYTPED 135
                                        5666...6788899999***9999777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1429.23
//
Query:       gene1280|gene1280|rna1279|rna1279  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1118.89
//
Query:       gene128|gene128|rna128|rna128  [L=205]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-32  112.5   0.0    5.5e-24   84.7   0.0    2.1  2  DHFR_1    Dihydrofolate reductase


Domain annotation for each model (and alignments):
>> DHFR_1  Dihydrofolate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   3.6e-10   6.5e-06       1      41 [.       1      43 [.       1      46 [. 0.89
   2 !   84.7   0.0   3.1e-28   5.5e-24      38     140 ..      56     162 ..      53     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.6e-10
                                   EEEEEEEEETT-EEEBTTB-SS-..-HHHHHHHHHHHTTCEEE CS
                         DHFR_1  1 kislivAvaengvIGkdnklpwh..lpeDlkrFkklTtgkpvi 41
                                   +++livA a+n+ IG+ n+lpw+  l++D+ +F++l++  p+i
  gene128|gene128|rna128|rna128  1 MFALIVALARNKGIGRANRLPWSrpLRTDMSWFRTLSQSIPLI 43
                                   5789******************855679*******99988877 PP

  == domain 2  score: 84.7 bits;  conditional E-value: 3.1e-28
                                    CEEEEEHHHHHCC-...S--TTCEEEEE-S-TT---TTEEEESSHHHHCCCCTTS.SEEEEEE-HHHHHHCGG..G-SEE CS
                         DHFR_1  38 kpvimGrkTfeslg..krpLpnrkniVltrnedlkvegvevvssleealalakeekeevfviGGaeiYkqalp..ladkl 113
                                    ++v+mGrkT+es++  +rpLpnr niVl+r++ +k+e++ ++ ++e++ +l    ++ +fviGG +iY+ a++   a+ +
  gene128|gene128|rna128|rna128  56 NAVVMGRKTWESIPpkFRPLPNRMNIVLSRRPGAKTENAFFIPTFEDLSHLDIPPSSMIFVIGGHDIYNLAIQngKAQIM 135
                                    78***********99899******************************9877666789*************984458899 PP

                                    EEEEESS----SEE-----CCCEEEEE CS
                         DHFR_1 114 ylTeidaefegdtffpeideeewelve 140
                                     +Te+ +++++d+ffp++d+e++e+ +
  gene128|gene128|rna128|rna128 136 FVTEVFESPDCDVFFPHVDWESYEKRD 162
                                    **********************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1270.97
//
Query:       gene1281|gene1281|rna1280|rna1280  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.024   14.0   1.7      0.029   13.6   1.7    1.2  1  CcmF_C     Cytochrome c-type biogenesis protein CcmF C-termin
       0.12   12.7   0.7       0.22   11.9   0.7    1.4  1  zf-CCCH_7  Chromatin remodeling factor Mit1 C-terminal Zn fin


Domain annotation for each model (and alignments):
>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.7   3.3e-06     0.029      39      68 ..      14      43 ..       8      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.3e-06
                             CcmF_C 39 lnNllLvvaaavVllGTLyPlvldalglgk 68
                                       l+N++Lv+ + +V+lGT+yP ++  + l +
  gene1281|gene1281|rna1280|rna1280 14 LSNIILVAKVGLVILGTVYPCLYGLVALIS 43
                                       78******************9988776655 PP

>> zf-CCCH_7  Chromatin remodeling factor Mit1 C-terminal Zn finger 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   2.4e-05      0.22      23      75 ..      95     145 ..      73     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                                        ---------...B-----S--S-----EESS---HHHHHHHHHTT--SSS-B-TTT CS
                          zf-CCCH_7  23 seyvrelek...DdpvfsykviekehrLvansvsklvldnflalysvddsvrCrcC 75 
                                        +++  ++     Dd +f+ +v +k+++++++++ +  l       +  d+ rCr+C
  gene1281|gene1281|rna1280|rna1280  95 ADEFSSSSEhfiDDKIFPSEV-KKNENIIGHRLEESNL----SHLQNRDDARCRFC 145
                                        333333333477999999997.6777789999988655....55678899****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1004.47
//
Query:       gene1282|gene1282|rna1281|rna1281  [L=481]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3180.00
//
Query:       gene1283|gene1283|rna1282|rna1282  [L=338]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-18   66.3   0.0      8e-18   65.6   0.0    1.3  1  Tau95     RNA polymerase III transcription factor (TF)IIIC su


Domain annotation for each model (and alignments):
>> Tau95  RNA polymerase III transcription factor (TF)IIIC subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   4.4e-22     8e-18      45     140 .]     156     269 ..     118     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 4.4e-22
                                        E-.......--S--TT-----........HHHHHHHHHHHHHHHH-SEEEHHHHHTTS-GGGT........TTHHH CS
                              Tau95  45 lk.......Ptepeeelvkelkek.....kelqkaveelkklfeerPiwtrraLknklekker........kklkl 100
                                        ++       P++p + l+++l++      ++lq++    ++lf  +Pi   +++   ++++er        +k+k+
  gene1283|gene1283|rna1282|rna1282 156 IHvgyeddtPEGPVPGLPERLEKLhgedvMKLQED--LFNHLFATHPILRISNIIRMFKSDERaaemgfsdWKIKK 229
                                        23446667889999999988885455333222222..3369******************88888************ PP

                                        HGGGTEEEE-SSTTTTEEEETT--TTS-GGGGGG-EEE-- CS
                              Tau95 101 alpyvaYyfksGPWrdlwvrfGyDPrkdpeariYQtldfr 140
                                        +lp+ aY + sGPWr +wv+fG+DP++d++  +YQ+ d r
  gene1283|gene1283|rna1282|rna1282 230 LLPLHAYFIDSGPWRGCWVKFGVDPKQDQSNFKYQIYDSR 269
                                        ***********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2259.87
//
Query:       gene1284|gene1284|rna1283|rna1283  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-10   41.7   1.1    0.00017   22.1   0.0    2.2  2  Ribosomal_L6e  Ribosomal protein L6e
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.25   11.6   0.0    1.5  1  Thr_synth_N    Threonine synthase N terminus


Domain annotation for each model (and alignments):
>> Ribosomal_L6e  Ribosomal protein L6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.9e-08   0.00017       1      32 [.      80     110 ..      80     121 .. 0.79
   2 !   19.3   0.9   1.4e-07    0.0013      52     111 .]     110     171 .]     104     171 .] 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.9e-08
                      Ribosomal_L6e   1 lNgvPLrRvnqryVIatstkvdls.gvdekipe 32 
                                        +NgvPL ++++ry++atst +d++ +v   i+e
  gene1284|gene1284|rna1283|rna1283  80 INGVPLFKIDERYLLATSTVLDINvNV--DIDE 110
                                        7*********************96244..4554 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.4e-07
                      Ribosomal_L6e  52 eeelfeekkek..kelseerkadqkavDkallaaikkekllkkYLkskFsLrkgdyphelkF 111
                                        e++++ +k+++    ++ e +   k++D+++ +  k+ k++k+YL++ F + ++  +  lk+
  gene1284|gene1284|rna1283|rna1283 110 EKDIILTKRDDytAPMDVEMTDAEKKIDEEIAKVAKEIKFMKSYLSEPFEIDTTRNFYSLKY 171
                                        666765555552245677888999***************************99998888876 PP

>> Thr_synth_N  Threonine synthase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.8e-05      0.25      24      40 ..      11      27 ..       6      36 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                        Thr_synth_N 24 eDgGLyvPeeiPklsae 40
                                       +D GLy+P+ iPk+ ++
  gene1284|gene1284|rna1283|rna1283 11 DDAGLYMPDDIPKFVEK 27
                                       79***********9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1235.35
//
Query:       gene1285|gene1285|rna1284|rna1284  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-58  198.5   0.0    1.5e-58  198.3   0.0    1.0  1  Pkinase        Protein kinase domain
    2.4e-29  102.4   0.0      3e-29  102.1   0.0    1.1  1  Pkinase_Tyr    Protein tyrosine kinase
    7.3e-10   38.6   0.0    1.2e-09   37.9   0.0    1.3  1  Kinase-like    Kinase-like
    8.5e-06   25.3   0.0    1.3e-05   24.6   0.0    1.2  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0012   17.9   0.0     0.0059   15.6   0.0    2.1  2  Haspin_kinase  Haspin like kinase domain
      0.003   16.7   0.1     0.0061   15.6   0.1    1.4  1  Seadorna_VP7   Seadornavirus VP7
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.29   11.0   0.0    1.3  1  APH            Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.3   0.0   5.8e-62   1.5e-58       1     256 [.       4     272 ..       4     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 198.3 bits;  conditional E-value: 5.8e-62
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylv 76 
                                        ye+++++GeG+fG+Vyk +++++g  +A+Kk+ +++++     +++rEik+ k++  ++i++l e++ ++  +++v
  gene1285|gene1285|rna1284|rna1284   4 YENIKQVGEGAFGQVYKSRRTSDGTVFAIKKMPVDRETGF-PFTAIREIKLCKSVINKHIIKLDEIVFDEGFIFVV 78 
                                        7899*******************************99875.569******************************** PP

                                        EE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSC CS
                            Pkinase  77 leyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesss 152
                                        ley++ + l+ ll     ls +++++i++q++e+++ +H+ g++HrD+Kp+NiL+d++g+lK+tDFGl +e++   
  gene1285|gene1285|rna1284|rna1284  79 LEYMPYD-LTGLLASGARLSTDHTRSIISQLVEAVSSMHELGLVHRDIKPSNILMDHRGMLKLTDFGLTREISGM- 152
                                        *****77.*****99899******************************************************995. PP

                                        SBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH... CS
                            Pkinase 153 kltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkekl 227
                                         +t++v+t +Y+APE+l +e++y  kvD Ws+G+i++e+  g+pp++   g++    e+ q++ i++ lg  + k+
  gene1285|gene1285|rna1284|rna1284 153 -MTNRVCTLWYRAPELLlGETSYNFKVDAWSVGCIMLEMRLGRPPYR---GND----EVSQIKLIFEELGVPQDKY 220
                                        .7***************9*****************************...444....5666666666677333343 PP

                                        HHHTTS.......................-HHHHHHHHHHT-SSGCCSTTHH CS
                            Pkinase 228 peasei.......................seeakdllkkllkkdpkkRltae 256
                                        ++ + +                       +ee +++l+  l+ + ++Rl++ 
  gene1285|gene1285|rna1284|rna1284 221 KWSDLLdvgvyskdkdaqeiiteryrslfDEEELKVLSGFLCLTSRRRLSVV 272
                                        3333335588888888888899999999999999999999999999999975 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.1   0.0   1.2e-32     3e-29       3     236 ..       6     227 ..       4     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.1 bits;  conditional E-value: 1.2e-32
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEE CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeeplli 78 
                                          k++GeGafG+V++ + +    ++ +  a+K++  + +       ++e+k+ k++ +++i+kl  ++ +e+ +++
  gene1285|gene1285|rna1284|rna1284   6 NIKQVGEGAFGQVYKSRRT----SDGTVFAIKKMPVDRETGFPFTAIREIKLCKSVINKHIIKLDEIVFDEGFIFV 77 
                                        5789************999....788899*****8888888889999***************************** PP

                                        EEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETT CS
                        Pkinase_Tyr  79 vteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardie 154
                                        v+ey+++ dL   L +   ++l+++++ s++ q+ ++++ +++  lvHrd+   N+L++++ + k++DfGL+r+i 
  gene1285|gene1285|rna1284|rna1284  78 VLEYMPY-DLTGLLASG--ARLSTDHTRSIISQLVEAVSSMHELGLVHRDIKPSNILMDHRGMLKLTDFGLTREI- 149
                                        ******9.899999986..9*******************************************************. PP

                                        TSSEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTT CS
                        Pkinase_Tyr 155 kddeyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpek 229
                                              + +++ + + + apE l  ++ ++ k D Ws G ++ E+   g+ py+g ++ + ++ + e+  +++ ++
  gene1285|gene1285|rna1284|rna1284 150 ----SGMMTNRVCTLWYRAPELLLGETsYNFKVDAWSVGCIMLEMRL-GRPPYRGNDEVSQIKLIFEELGVPQDKY 220
                                        ....45555666666667***9875544****************865.********99999999988888888887 PP

                                        SBHHHHH CS
                        Pkinase_Tyr 230 cpeelye 236
                                         +++l +
  gene1285|gene1285|rna1284|rna1284 221 KWSDLLD 227
                                        7777665 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   4.8e-13   1.2e-09     142     255 ..      98     202 ..      75     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.8e-13
                        Kinase-like 142 etiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve.kgfaPpEllgsr 216
                                         ++ r ++  ql+  + +++++glvh ++++ n+l+d++g l+l++f+ L r    +  + v+   +  pEll   
  gene1285|gene1285|rna1284|rna1284  98 TDHTRSII-SQLVEAVSSMHELGLVHRDIKPSNILMDHRGMLKLTDFG-LTREISGMMTNRVCtLWYRAPELLLG- 170
                                        57889999.89************************************8.66666666669999567899999876. PP

                        Kinase-like 217 ggytrknktkmthkldaWqlGlviyriwclklPltlate 255
                                               +t + +k+daW +G  ++ +     P     e
  gene1285|gene1285|rna1284|rna1284 171 -------ETSYNFKVDAWSVGCIMLEMRLGRPPYRGNDE 202
                                        .......5899***********99988766666655555 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.2e-09   1.3e-05     104     166 ..      85     143 ..      78     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.2e-09
                                Kdo 104 dLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                        dL+ lla++a+l+   +r ++ ++  +++ +h++g+ H+d+ + nil++ ++     + l D+
  gene1285|gene1285|rna1284|rna1284  85 DLTGLLASGARLSTDHTRSIISQLVEAVSSMHELGLVHRDIKPSNILMDHRG----MLKLTDF 143
                                        8999*********************************************998....6666666 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.3e-06    0.0059     109     284 ..      11     178 ..       1     180 [. 0.70
   2 ?   -2.7   0.0      0.81   2.1e+03     138     181 ..     253     295 ..     203     300 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-06
                      Haspin_kinase 109 seklssevyqtke..kdkevvlKviplevledvtiskelslkelkslklvkgtypglllllqdkvlkekpdfyseq 182
                                        +e+ +++vy+ +   + +  ++K++p++    +  +        +++kl+k + +++++ l + v  e        
  gene1285|gene1285|rna1284|rna1284  11 GEGAFGQVYKSRRtsDGTVFAIKKMPVDRETGFPFT------AIREIKLCKSVINKHIIKLDEIVFDEG------- 73 
                                        677777777776643444455677777555544444......445556666665555555555444444....... PP

                      Haspin_kinase 183 qlflvlllkdkGtdLeev....klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlkls 254
                                          f+ ++l+++  dL+ +       s ++  si  q v+ ++    ++ + HRd++  niL+d+ +   l d+ l 
  gene1285|gene1285|rna1284|rna1284  74 --FIFVVLEYMPYDLTGLlasgARLSTDHTRSIISQLVEAVSSM-HELGLVHRDIKPSNILMDHRGMLKLTDFGLT 146
                                        ..777777888888777655445567888999999999998866.57999************************** PP

                      Haspin_kinase 255 Rle..ssegkvlytrlddpllFqGggDyqfei 284
                                        R      ++ v+      p+l  G+  y+f +
  gene1285|gene1285|rna1284|rna1284 147 REIsgMMTNRVCTLWYRAPELLLGETSYNFKV 178
                                        *8767666666666667899999999999976 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.81
                      Haspin_kinase 138 dvtis.kelslkelkslklvkgtypglllllqdkvlkekpdfyse 181
                                        ++++   +l+l   + l +v+  + +++   +d ++  +  f+++
  gene1285|gene1285|rna1284|rna1284 253 ELKVLsGFLCLTSRRRLSVVNSRHFSIISAYKDTYIPLN--FEES 295
                                        333322556666666666666666666666666666655..5555 PP

>> Seadorna_VP7  Seadornavirus VP7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.4e-06    0.0061     146     188 ..     104     144 ..      95     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-06
                       Seadorna_VP7 146 iivaglkdLmdfhsestnllhGDcnpenlmcDknGylklvDPv 188
                                        ii   ++++  +h  + +l+h D++p+n++ D+ G+lkl D +
  gene1285|gene1285|rna1284|rna1284 104 IISQLVEAVSSMH--ELGLVHRDIKPSNILMDHRGMLKLTDFG 144
                                        5555566777788..7899********************9965 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.29     165     184 ..     117     135 ..      76     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                        -EEEE-SS-SGGGEEEC..T CS
                                APH 165 ptvllHgDlhpgNllvdpdd 184
                                        + +l+H+D++p N+l+d + 
  gene1285|gene1285|rna1284|rna1284 117 ELGLVHRDIKPSNILMD-HR 135
                                        689**************.32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1961.81
//
Query:       gene1286|gene1286|rna1285|rna1285  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1648  (0.0919181); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.82u 0.36s 00:00:01.18 Elapsed: 00:00:00.51
# Mc/sec: 1356.18
//
Query:       gene1287|gene1287|rna1286|rna1286  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-15   56.9   0.0    3.5e-15   56.0   0.0    1.5  1  Nse4_C    Nse4 C-terminal


Domain annotation for each model (and alignments):
>> Nse4_C  Nse4 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0     2e-19   3.5e-15       2      90 ..     177     258 ..     176     259 .] 0.88

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2e-19
                             Nse4_C   2 islfkfvinpksFaqtVeNlFylSfLvkdgkvkieldedglpvleeteeeeeekakeeeakkkqavlsldmetWke 77 
                                        +++f++vinp+sF++t+eN+FylS  ++ g + ie d+d++ +++       +k++ ++ +  ++ ++++++++  
  gene1287|gene1287|rna1286|rna1286 177 VEYFRLVINPQSFSKTIENIFYLSLSLRSGLIYIEWDDDEILYVT-------SKNSGRKGDLGHLAIEMTYDEYLA 245
                                        89*************************************998884.......12222344578999********** PP

                             Nse4_C  78 lieafdikeplip 90 
                                        ++e+  i+e li+
  gene1287|gene1287|rna1286|rna1286 246 IVEKAGISETLIE 258
                                        *********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1655.09
//
Query:       gene1288|gene1288|rna1287|rna1287  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-12   47.1   3.4    2.9e-12   46.4   3.4    1.4  1  TBCC            Tubulin binding cofactor C
     0.0095   15.9   0.2      0.082   12.9   0.1    2.2  2  RuBisCO_small   Ribulose bisphosphate carboxylase, small chai
  ------ inclusion threshold ------
       0.18   11.8   3.3        3.5    7.7   0.6    2.6  2  Viral_cys_rich  Viral cysteine rich


Domain annotation for each model (and alignments):
>> TBCC  Tubulin binding cofactor C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   3.4   4.9e-16   2.9e-12       6      99 ..      86     178 ..      81     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 4.9e-16
                                        E-S-BS-EEEE-S--S-EEEES-BS-EEE----SS-EEEES-BS-EEE---SEEEEES-BS-EEE---SSEEEEES CS
                               TBCC   6 isnlsdctiylldplssvtiddcknctivlgpvsgsvfiedcenctivvacrqlrihdctnvdvylltksrPiied 81 
                                        +++++++ + + +++++v i++c+n  +    +++sv ++++++c+++++ +q+r++ c+nv++ ++t +   +++
  gene1288|gene1288|rna1287|rna1287  86 VKDVNNSIVTI-EDCTEVVIENCHNTVFPHFSCEKSVVLNNIKDCRVSCSGHQIRMNGCQNVELEVYTLTGVFLQS 160
                                        56777777777.8899************************************************************ PP

                                        -BSEEEE------TTSHH CS
                               TBCC  82 skgirfapynlsypelee 99 
                                        skgi + +y ++ ++  e
  gene1288|gene1288|rna1287|rna1287 161 SKGIVVKKYGTKENNKFE 178
                                        *******99887666555 PP

>> RuBisCO_small  Ribulose bisphosphate carboxylase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.11   6.7e+02      57      81 ..      17      41 ..      10      53 .. 0.79
   2 !   12.9   0.1   1.4e-05     0.082      50      85 ..     113     147 ..      89     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHSTTSEEEEEEE CS
                      RuBisCO_small 57 aaevlaeleecrkaypeeyvrligf 81
                                       a++ + ++e c ++ p+ y r + +
  gene1288|gene1288|rna1287|rna1287 17 ARQTILNIEGCIREEPSLYNRKVLL 41
                                       6778889*********999886655 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.4e-05
                                        --TT---HHHHHHHHHHHHHHSTTSEEEEEEEETTT CS
                      RuBisCO_small  50 pmfdlkdaaevlaeleecrkaypeeyvrligfDnkk 85 
                                        p f ++ ++ vl+++++cr + +++ +r++g  n++
  gene1288|gene1288|rna1287|rna1287 113 PHFSCE-KSVVLNNIKDCRVSCSGHQIRMNGCQNVE 147
                                        777776.578*********************99986 PP

>> Viral_cys_rich  Viral cysteine rich
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1    0.0035        21      32      64 ..      46      74 ..      18      78 .. 0.70
   2 ?    7.7   0.6   0.00059       3.5       2      32 ..      76     106 ..      75     131 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0035
                     Viral_cys_rich 32 rkeficdrllgGicaPLsvinnatLyaeLskql 64
                                       r ++i++ + + + +P++  +n tL+++   q 
  gene1288|gene1288|rna1287|rna1287 46 RLKDIYNTY-NVVETPIIPFKNHTLFKK---QK 74
                                       566777654.5689************97...44 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00059
                     Viral_cys_rich   2 epdcidnykpCiestkpcCrledrtlvqfGr 32 
                                        e+d i+n ++ ++++++   +ed t v +  
  gene1288|gene1288|rna1287|rna1287  76 ETDGIKNKRYVKDVNNSIVTIEDCTEVVIEN 106
                                        89***********************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1216.80
//
Query:       gene1289|gene1289|rna1288|rna1288  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-38  133.0   0.2      2e-38  132.1   0.2    1.4  1  Diphthami_syn_2  Diphthamide synthase
      0.001   18.8   0.0      0.016   15.1   0.0    2.3  2  UvrD_C_2         UvrD-like helicase C-terminal domain
  ------ inclusion threshold ------
      0.017   13.9   0.0      0.023   13.5   0.0    1.2  1  tRNA_Me_trans    tRNA methyl transferase


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.1   0.2   3.4e-42     2e-38       1     206 [.       1     221 [.       1     230 [. 0.84

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 3.4e-42
                    Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke..sevesLvsvisen.kesymfhvvnvhlvellaesvGiplikletaG..... 68 
                                        m+  +l sGGkDs +a++   +e    v  L    s++ ++s+m+ +v  ++ ++l e + ip+   +t+      
  gene1289|gene1289|rna1288|rna1288   1 MRFLALASGGKDSLYAIHCLQQEghRAVGLLHMRCSDGyQDSFMYQTVGSEVADVLGECLNIPVFIYQTKCrsinq 76 
                                        7899****************999844566665556665489**********************9766655322222 PP

                    Diphthami_syn_2  69 ......eeekevedLkgtlkkld....veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveek 134
                                              ee +evedL   + + +     e+v +Gai s yqksr+e+vC +l lk + PLW+ d + ll+ +++++
  gene1289|gene1289|rna1288|rna1288  77 sleynrEEGDEVEDLYTAISRAKekvyFEGVSSGAILSRYQKSRVENVCSRLFLKCLSPLWEMDQKRLLLDMISNG 152
                                        22222266799****9999776656559************************************************ PP

                    Diphthami_syn_2 135 fevivvavkaegldeslLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwd 206
                                        ++ ++v ++   l+++ +  rid  + + l+    k  ++ +gegGe+et+vlD P+fkkr++++e+e   +
  gene1289|gene1289|rna1288|rna1288 153 MDGRIVKIASSILGKECINMRIDE-IYEYLEAA--KEEVNFCGEGGEYETIVLDCPMFKKRINIDEYEVISH 221
                                        **********99999999999984.55666655..778*****************************98655 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-06     0.016      36      50 ..      89     103 ..      78     104 .. 0.82
   2 ?    1.2   0.0     0.056   3.3e+02      12      27 ..     194     209 ..     193     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                           UvrD_C_2  36 rlLYtavTRArekli 50 
                                        + LYta++RA+ek++
  gene1289|gene1289|rna1288|rna1288  89 EDLYTAISRAKEKVY 103
                                        559**********98 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.056
                           UvrD_C_2  12 GsefpaVivfdpdlaa 27 
                                        G+e+++++++ p +  
  gene1289|gene1289|rna1288|rna1288 194 GGEYETIVLDCPMFKK 209
                                        99*******9998765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.9e-06     0.023       4      67 ..       4      66 ..       1      84 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.9e-06
                      tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqgyevigv.flklwee.edeegkeccaeedlkdaervaeklgiplev 67
                                       +++ SgG DS +a + l+++g+  +g+ ++++++  +d+     +  ++++d+    e l+ip+ +
  gene1289|gene1289|rna1288|rna1288  4 LALASGGKDSLYAIHCLQQEGHRAVGLlHMRCSDGyQDSFM-YQTVGSEVADVL--GECLNIPVFI 66
                                       6778******************9999538999998445544.666666666665..4556665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1421.93
//
Query:       gene1290|gene1290|rna1289|rna1289  [L=433]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-39  134.0   0.0    9.7e-39  133.3   0.0    1.3  1  G6PD_C    Glucose-6-phosphate dehydrogenase, C-terminal domai
    1.8e-17   64.5   0.0    4.5e-17   63.3   0.0    1.7  1  G6PD_N    Glucose-6-phosphate dehydrogenase, NAD binding doma


Domain annotation for each model (and alignments):
>> G6PD_C  Glucose-6-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.0   1.1e-42   9.7e-39       9     284 ..     156     429 ..     151     433 .] 0.85

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 1.1e-42
                                        TTSTTSSTTTEEEEEEEEEESS--TTTHHHHTTTHHHHHTTTTHHHHHHHHHH----SSSSHHHHHHHHHHHHTTB CS
                             G6PD_C   9 lfeplwnrnyidhvqitvketlgvegrggYydeaGalrDvvqnHllqllalvamepPasldaedirdekvkvLksl 84 
                                         +++++++++++ v+i  ke lg egr +Y+d+ G+++D+vq H+ +ll ++a +  +    +   +e++kv+k+ 
  gene1290|gene1290|rna1289|rna1289 156 ALQEVMDNKHVKTVEIISKEVLGGEGR-SYFDKNGIIKDIVQGHMAELLGVIASDVTEPS-RTMEASERLKVFKEC 229
                                        68899*********************9.6************************8765543.334457999999987 PP

                                        ----G...GG.EEEEEE.....E--TGS-STTSTTS-TT----SEEEEEEEB-STTTTT-EEEEEEESSBSS-EEE CS
                             G6PD_C  85 rplkleevekkvvrGqYaagavkgkevkgYreeegvakdSkteTfvalkleidnerwagVPfylrtGKrLnekkte 160
                                        + ++   +ek ++ GqY            Y++e  +++dS+teTf+++ ++i++ rw+ VPf++ +GK +nek+te
  gene1290|gene1290|rna1289|rna1289 230 T-ID---IEK-CLYGQY----------DDYNKE--IHRDSSTETFCMIPINISSPRWSKVPFIIVAGKGMNEKRTE 288
                                        5.44...466.9*****..........788765..689************************************** PP

                                        EEEEE---....SS-SS..---.............--EEEEEEESS-EEEEEEEEE-SSS.E.....EEEEEEHHH CS
                             G6PD_C 161 iriqfkkv....psdlf..kkke............rneLviriqpdeaislklnakkpgl.eleleeveldlsyke 217
                                        i+i+f++       dlf  +  +            + +Lv++i p+ ++ l++ + +    ++  ++ +++  +++
  gene1290|gene1290|rna1289|rna1289 289 IVIEFRRDafakCIDLFcgD--QpsgrtvhtneieAVRLVFNIYPECEVFLEVLVGSDPIrHVLHDKKNINDLMHD 362
                                        ******95332234555542..1458999988898889**************998765542555667888877888 PP

                                        HTT---HHHHHHHHHHHT-GTTSB-HHHHHHHHHHHHHHHHHHHH---EEEETTSSS-HHHHHHHHH CS
                             G6PD_C 218 rfklpeaYerLlldvlkgdqtlFvrsdeveaaWkivdpileaweeeklekYeagsrgPeeadellek 284
                                        +    + Ye ++  ++++++   v+s e e  W+++d+il+  + + l  Y+ g   P+ea+e+++k
  gene1290|gene1290|rna1289|rna1289 363 SHGEYHDYEIIFDSLIRDKEFSSVSSHEAEVLWNVFDSILSIDKGDVLFYYSKGIDMPKEAEEMIRK 429
                                        7778899*********************************988668899***************987 PP

>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0     5e-21   4.5e-17       1     175 [.       4     144 ..       4     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 5e-21
                             G6PD_N   1 vifGasGdLakrkllPaLyelaregllpeevrivgvarsklsdeefrekvkealkkekekeeldeekleeflkrle 76 
                                        vifG+sGdLakrkl+PaL ++       e+v++vg+ar+k++  ef e ++e             +   efl+r+ 
  gene1290|gene1290|rna1289|rna1289   4 VIFGSSGDLAKRKLFPALSRINL-----EDVEVVGYARTKFDI-EFSEVLEEVG-----------NYSPEFLSRVA 62 
                                        8*****************98864.....679*********985.5888776654...........24579****** PP

                             G6PD_N  77 yvsgdleeeeeyekLkekleeleanrlfYlavppslfeevaeklkkaglakeeewkrvvvEKPfGkdlesarelne 152
                                        y++g++++    +kL++ +++   +++ Y++vpps+++ + ++++k       + k v +EKP+G+  es ++++e
  gene1290|gene1290|rna1289|rna1289  63 YIRGSYDDL---SKLRDIVDS---ETVLYFSVPPSVYTCLFREISKL------DYKVVGIEKPYGETKESFEKIKE 126
                                        ****99887...899999998...99********************6......345677**************976 PP

                             G6PD_N 153 elkkvfkeeqiyrIDhYLGketv 175
                                             f+ ++   IDhYL k  v
  gene1290|gene1290|rna1289|rna1289 127 -----FDLSRAKFIDHYLLKPLV 144
                                        .....666667779999988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2717.79
//
Query:       gene129|gene129|rna129|rna129  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-42  144.8   0.0    3.9e-42  144.6   0.0    1.0  1  Peptidase_M1_N  Peptidase M1 N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   0.0   2.2e-46   3.9e-42       1     186 []      36     214 ..      36     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 2.2e-46
                                    EEEEEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEE CS
                 Peptidase_M1_N   1 vpehYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkesl 80 
                                    vp+hYdl++k+  +   f+Gsv i+++++e+++eiv++ak+l+i ++ ++   k  + ++    ++k++e++++++++  
  gene129|gene129|rna129|rna129  36 VPSHYDLHVKVMDA--GFCGSVGIQVDISEPVDEIVMNAKELEIWDAGIVVGDKRIDGEVVVGDYEKEYEVVRLRFPSRI 113
                                    69********9988..7***************************777777555555556777778999999******966 PP

                                    ETTCEEEEEEEEEEE-BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSE CS
                 Peptidase_M1_N  81 qqtskytLeieyegelndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmp 160
                                      +++  +  e++g++n  l G+yk     +g+   +++T+fe+tdAR++fPCfD+P++KAtf+is+ ap++ ++lSn p
  gene129|gene129|rna129|rna129 114 P-KGEGYIVAEFCGDYNSGLVGFYK-----SGGDSKIYSTHFEPTDARRVFPCFDQPDMKATFSISLDAPANLVVLSNSP 187
                                    6.9999999****************.....888999******************************************** PP

                                    CCCEEEETTCEE.EEEEEEEESBEGGG CS
                 Peptidase_M1_N 161 eeeseklengqk.iteFeqtpkmstYL 186
                                       s+++e g + i+ Fe+t kmstYL
  gene129|gene129|rna129|rna129 188 AVGSSRKEYGDRaIEYFEKTSKMSTYL 214
                                    *999999988888*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1347.73
//
Query:       gene1291|gene1291|rna1290|rna1290  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-11   43.0   0.0    2.6e-10   40.9   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
      7e-10   38.7   0.0    8.7e-10   38.4   0.0    1.2  1  MTS              Methyltransferase small domain
    3.9e-06   26.8   0.0    5.3e-06   26.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    4.8e-06   27.1   0.0    9.6e-06   26.2   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0001   22.1   0.0     0.0051   16.5   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
    0.00012   21.5   0.0    0.00025   20.4   0.0    1.5  1  N6_Mtase         N-6 DNA Methylase
    0.00033   20.1   0.0    0.00073   18.9   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00035   20.1   0.0    0.00052   19.5   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00055   19.9   0.0    0.00089   19.3   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
     0.0098   15.5   0.0      0.016   14.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.041   13.7   0.0      0.044   13.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.045   14.5   0.0      0.082   13.7   0.0    1.5  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.9   2.8e+03      25      41 ..      28      44 ..      15      49 .. 0.76
   2 !   40.9   0.0   1.8e-13   2.6e-10       1      84 [.      52     138 ..      52     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.9
                                       EEEESSHHHHHHHHHHH CS
                    Methyltransf_25 25 tgvDiseemleaarera 41
                                       t  Di+++m+  a++ +
  gene1291|gene1291|rna1290|rna1290 28 TPPDIAASMVSVAHSTY 44
                                       55699999999998877 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1.8e-13
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE...EST CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs...sga 73 
                                        +Ldl+cGtG l++a+   ++ + ++g+D+ +++le+ r ++ e g+n+++v+++++dl f +g+fD  ++   +g+
  gene1291|gene1291|rna1290|rna1290  52 ILDLCCGTGMLSFACGY-FSPSYILGIDLCPSALETFRLNNLEFGINIDLVRCSIDDLTFIEGRFDTAIVnppFGT 126
                                        8***********99984.467********************9999***********************99333333 PP

                                        .GGGSSHHHHHH CS
                    Methyltransf_25  74 .lhhlsdedlek 84 
                                         + h + + ++k
  gene1291|gene1291|rna1290|rna1290 127 kIKHADIKAVDK 138
                                        344444444444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   5.8e-13   8.7e-10      31     112 ..      48     129 ..      31     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 5.8e-13
                                        TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEEEEE-- CS
                                MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdlivsNP 105
                                        + +++lDl+cG+G+l+ a+  +sp+  +  +d    Ale  + n  + ++++++v +++ + +  e++fd+ + NP
  gene1291|gene1291|rna1290|rna1290  48 EGRSILDLCCGTGMLSFACGYFSPS-YILGIDLCPSALETFRLNNLEFGINIDLVRCSIDDLTFiEGRFDTAIVNP 122
                                        6778*********************.5999*********************999999998865558********** PP

                                        -STTTCH CS
                                MTS 106 Pfhagka 112
                                        Pf ++ +
  gene1291|gene1291|rna1290|rna1290 123 PFGTKIK 129
                                        **88765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.5e-09   5.3e-06       5      97 ..      50     146 ..      47     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.5e-09
                    Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                         ++lDl CGtG l+f+     ++ + + GiD  + a+e  r n  +l++  n+ + +++i +l   + + +fD  +
  gene1291|gene1291|rna1290|rna1290  50 RSILDLCCGTGMLSFACG--YFSPSYILGIDLCPSALETFRLN--NLEFGiNIDLVRCSIDDLT--FIEGRFDTAI 119
                                        579**************9..456799************99887..788877***********99..888******* PP

                    Methyltransf_31  80 snevl......naladpdkile...ei 97 
                                         n ++      +++++ dk+le    +
  gene1291|gene1291|rna1290|rna1290 120 VNPPFgtkikhADIKAVDKALEicnVV 146
                                        **7778778898888888888866522 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   6.4e-09   9.6e-06       1      68 [.      53     121 ..      53     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6.4e-09
                                        EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
                    Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68 
                                        Ld+ cGtG l+ a+     + ++g+Dl++ +l++ + ++ e g+++++v++++ +l f ++ fD  +++
  gene1291|gene1291|rna1290|rna1290  53 LDLCCGTGMLSFACGYFSpSYILGIDLCPSALETFRLNNLEFGINIDLVRCSIDDLTFIEGRFDTAIVN 121
                                        89*************5559******************9999999********************98876 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.4e-06    0.0051      52     138 ..      72     131 ..      27     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.4e-06
                                        T--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE CS
                            UPF0020  52 niapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivt 127
                                        +                          + g+Dl ++++++ r N  + g+   i+++   + +L+  eg +d+ + 
  gene1291|gene1291|rna1290|rna1290  72 SY-------------------------ILGIDLCPSALETFRLNNLEFGI--NIDLVRCSIDDLTFIEGRFDTAIV 120
                                        33.........................58***********9999777666..688888899999988999****** PP

                                        ----------H CS
                            UPF0020 128 npPYGerlgsk 138
                                        npP+G +++++
  gene1291|gene1291|rna1290|rna1290 121 NPPFGTKIKHA 131
                                        *******9876 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.7e-07   0.00025      27     144 ..      25     132 ..      13     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.7e-07
                           N6_Mtase  27 effTPrevsklivell....epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNll 98 
                                        ++ TP ++   +v+++    ++ +g+s++D +cG+g +l  a  ++       +   i G ++ +++ +  ++N l
  gene1291|gene1291|rna1290|rna1290  25 QYMTPPDIAASMVSVAhstyDDIEGRSILDLCCGTG-MLSFACGYF-------SPSYILGIDLCPSALETFRLNNL 92 
                                        89*************99999899999********97.666666665.......577899***************** PP

                           N6_Mtase  99 lhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqkewkekt 144
                                          gi+ + v+  ++d      f  + +fd+ + Nppf++k  k+++
  gene1291|gene1291|rna1290|rna1290  93 EFGINIDLVRCSIDD----LTFI-EGRFDTAIVNPPFGTK-IKHAD 132
                                        *******87777766....3455.78999*********99.44433 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.9e-07   0.00073      45     126 ..      46     126 ..      34     146 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.9e-07
                                        S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                    Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                        + +g+++lD+++Gtg l+f+      +   + ++D+ ++ L++ +    e g ini+++  +  +L f ++ fD+ 
  gene1291|gene1291|rna1290|rna1290  46 DIEGRSILDLCCGTGMLSFACGYF--SPSYILGIDLCPSALETFRLNNLEFG-INIDLVRCSIDDLTFIEGRFDTA 118
                                        67899***********99987654..455799**********9877666666.59*******************98 PP

                                        EEE..S-G CS
                    Ubie_methyltran 121 tvs..fGl 126
                                         v   fG 
  gene1291|gene1291|rna1290|rna1290 119 IVNppFGT 126
                                        77433665 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.5e-07   0.00052     161     206 ..      48      93 ..      37     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.5e-07
                               PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNael 206
                                        eg+++lD+ +G+G+L+ a   +  + ++++D+ + A++  + N   
  gene1291|gene1291|rna1290|rna1290  48 EGRSILDLCCGTGMLSFACGYFSPSYILGIDLCPSALETFRLNNLE 93 
                                        5789********************************9988777554 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.9e-07   0.00089      15      75 ..      39      95 ..      31     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.9e-07
                    Methyltransf_32 15 kllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                         ++++ ++ +  +++D+++G g Lsf+  +     + +++gid++ +  e+ +  + ++g
  gene1291|gene1291|rna1290|rna1290 39 V-AHSTYDDIEGRSILDLCCGTGMLSFACGY---FSPSYILGIDLCPSALETFRLNNLEFG 95
                                       3.333356677899*****************...88***********99998877776666 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.016      39     152 ..      46     150 ..      34     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                        CHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                      Cons_hypoth95  39 eiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                        +ieg ++LDl++G+G l++ +     + ++ ++  ++a+++ + n  e++++     +  d+l  +      +++f
  gene1291|gene1291|rna1290|rna1290  46 DIEGRSILDLCCGTGMLSFACGYFSPSYILGIDLCPSALETFRLNNLEFGINIDLVRCSIDDLTFI------EGRF 115
                                        49999**************999999999999**************999998854444444444444......456* PP

                                        EEEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEEEEEE CS
                      Cons_hypoth95 115 divflDPPyakellieevlelleekkllkenalvvvet 152
                                        d   ++PP+ ++   ++ ++++   k+l+   +v+  +
  gene1291|gene1291|rna1290|rna1290 116 DTAIVNPPFGTKIK-HADIKAVD--KALEICNVVYSLH 150
                                        ***********976.88899988..5666555555433 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.9e-05     0.044      22      62 ..      48     100 ..      26     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                    Methyltransf_23  22 aggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae...........k 62 
                                        +g ++Ld+ cGtG l+  + ++    + g+Dl+p a e  +            
  gene1291|gene1291|rna1290|rna1290  48 EGRSILDLCCGTGMLSFACGYFSPsYILGIDLCPSALETFRlnnlefginidL 100
                                        6789*********888877888773466*****99888776777777666662 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.5e-05     0.082       1      72 [.      53     120 ..      53     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-05
                    Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvva 72 
                                        L++ cGtG l++a+   ++++ ++g+D+ psa+    e ++ ++ ++  n++l  ++++dl    + fD+ ++
  gene1291|gene1291|rna1290|rna1290  53 LDLCCGTGMLSFACGY-FSPSYILGIDLCPSAL----ETFRLNNLEFGINIDLVRCSIDDLTFIeGRFDTAIV 120
                                        899*****99999955.5999999*********....444444444455666666666655554568998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1312.70
//
Query:       gene1293|gene1293|rna1292|rna1292  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-44  151.5   1.3    2.4e-44  151.1   1.3    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   1.3   1.3e-48   2.4e-44       3     189 ..      30     209 ..      29     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 1.3e-48
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        +Gtt++++ +k+g+v+a+d+rat+gs++ +++tv+K+++i+++++ ++aG aaD+  + + +   a++y+l++gr+
  gene1293|gene1293|rna1292|rna1292  30 HGTTTLAFVFKEGMVIAVDSRATSGSYI-ASQTVNKVIEINRNLLGTMAGGAADCFFWEKLMGLYAKNYELTNGRR 104
                                        8***************************.7777******************************************* PP

                                        TCHHHHHHHHHHHHHHHHHHCTT.TTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgr.rpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktaleke 153
                                        i+       +a++ +++  ++++   + ++++i+g+d    p++y++d +G+ ++  + +++Gsgs++a+++l ++
  gene1293|gene1293|rna1292|rna1292 105 ITAA-----AASMYLSNCVYRYKgYGLSMGTMICGYD-GSIPSIYYVDDDGKRVKG-NLFSVGSGSTVAYGILSSS 173
                                        ****.....66666666666655155579********.555***************.7****************** PP

                                        HSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                         Proteasome 154 ykedltleeavelavkalkealerdklsgknievav 189
                                        y+ d++++ea+el ++a+ +a++rd++sg+ i++++
  gene1293|gene1293|rna1292|rna1292 174 YRFDMSKQEALELGREAIFHAAHRDAYSGGSINLYY 209
                                        ********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1643.79
//
Query:       gene1294|gene1294|rna1293|rna1293  [L=781]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   5.1e-149  497.0  14.3   7.9e-149  496.3  14.3    1.3  1  HTH_micro    HTH-like
    9.8e-05   22.2   4.4       0.04   13.8   0.1    3.7  3  TFIIE_alpha  TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.3  14.3  8.8e-153  7.9e-149       2     454 .]       4     455 ..       3     455 .. 0.97

  Alignments for each domain:
  == domain 1  score: 496.3 bits;  conditional E-value: 8.8e-153
                          HTH_micro   2 lkekilefGiYGkkisnltkeEieelikkpwveilskaevdelennftaskltkledkniienll..dLyvRmnls 75 
                                        lkeki++fGiYG+k+  l k+Eie++i++pw ei++++ v+el +nft+++l+ +++k+++ n+   dLyvRm++ 
  gene1294|gene1294|rna1293|rna1293   4 LKEKIFQFGIYGAKLKRLSKDEIEMAIEEPWTEIVKAETVEELRRNFTTDCLRVETNKFMVNNYNwdDLYVRMGTL 79 
                                        799************************************************************8799********* PP

                          HTH_micro  76 awkeyLtsgkfkftskeyykivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeak...ivi 148
                                        awk++Lt g f+ftskey+ i+++l++ k+yv+++elr kl +dpKk++Y+i++La+kg+ie+kt+ee +   +++
  gene1294|gene1294|rna1293|rna1293  80 AWKDHLTAGAFNFTSKEYFLIMNLLIETKEYVDNVELR-KLCLDPKKTHYCINRLARKGFIEYKTSEEVEkksFIY 154
                                        **************************************.**************************98866667*** PP

                          HTH_micro 149 kink..DesgsvvkkldkeklleinkedtitlpekiipmeylieiplidqikkkienteeGitskdlkdkfGislk 222
                                        k+++  De+g+v +++++++ l+ n++       k  ++ey+i+i+l+d+++ +i n++ Gi+++dlk+k+G+s+k
  gene1294|gene1294|rna1293|rna1293 155 KVRAiiDEKGFVTRRVEHQQ-LDLNRAG---SGGKGWMFEYRIDIGLYDNVRSMILNSKGGIITEDLKKKLGVSSK 226
                                        *****************999.9999999...899****************************************** PP

                          HTH_micro 223 qglklLnklieeeedsiktkeefegkikrlkfytvenleklnerkkkrliegddleekeliTsedriealkqllkk 298
                                        +g+klLnk+++ee++ +k ++efeg+++r++++ v      +         g + +  ++iTse+r+ a+++l++ 
  gene1294|gene1294|rna1293|rna1293 227 IGYKLLNKVFNEEKNVLKGVKEFEGRVRRYRYHVVGRGTSNE--------VGRGEKDGGYITSEERVMAIRKLMSM 294
                                        *********************************998877666........45666899****************** PP

                          HTH_micro 299 kkafvlsketfeklseilgvkYtldrktlistaikaglkvyklkdtkeg..skyviarkdvdesdivlnnyvnkke 372
                                        +++++l+k+t+ekl+e++g+kY++dr+t+i++ai ag+k+yk+k++ eg  s+y+i+r++++esd+ +++++n+++
  gene1294|gene1294|rna1293|rna1293 295 SPILQLDKRTYEKLQELTGWKYEFDRRTIIRAAILAGFKIYKQKRGREGkcSRYMIMRNEMVESDVKALDVSNCNA 370
                                        ************************************************999************************* PP

                          HTH_micro 373 aekenkfqkkvkkkfvnnskfieiDNgyekkeeerikilyefl...vknskeeslqfskevllemslklllslvpf 445
                                        +e++++fq+k++++fvn++k++e+DNgy++ +eer+k++y+fl   + + + es++f++e++ +m l llls+vpf
  gene1294|gene1294|rna1293|rna1293 371 QENMSEFQRKIYNIFVNSPKLVEMDNGYIPLREERLKLFYKFLiehMDSEEAESVRFDWEIIGKMGLDLLLSIVPF 446
                                        *******************************************88888888999********************** PP

                          HTH_micro 446 krikflekL 454
                                        +ri f+e+L
  gene1294|gene1294|rna1293|rna1293 447 SRIGFRESL 455
                                        *****9987 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   4.4e-06      0.04       8      68 ..      90     150 ..      85     167 .. 0.88
   2 !    7.1   0.0   0.00052       4.7      20      75 ..     204     259 ..     201     268 .. 0.85
   3 ?   -0.5   0.2      0.12   1.1e+03      37      64 ..     511     538 ..     506     548 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                                        HHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTE CS
                        TFIIE_alpha   8 rkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeeks 68 
                                        ++f  +e +l+++ L+e  e  ++   ++l +d+++    +nrL  +++++yk + + ek+
  gene1294|gene1294|rna1293|rna1293  90 FNFTSKEYFLIMNLLIETKEYVDNVELRKLCLDPKKTHYCINRLARKGFIEYKTSEEVEKK 150
                                        6788899*************999999999*************************9995544 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00052
                                        HHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEE CS
                        TFIIE_alpha  20 dvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywr 75 
                                        ++L +kg +  edl+k+l++  ++  klLn+ +++     k  ++ e  +++y + 
  gene1294|gene1294|rna1293|rna1293 204 MILNSKGGIITEDLKKKLGVSSKIGYKLLNKVFNEEKNVLKGVKEFEGRVRRYRYH 259
                                        578899999**********************9988777777777777777777776 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.12
                                        HTS-HHHHHHHHHHHHHCTSEEEEEEEE CS
                        TFIIE_alpha  37 lkidlnelrklLnrLyearlvkykrrrd 64 
                                        lk+   +  +lL +L + r+ ++ ++ +
  gene1294|gene1294|rna1293|rna1293 511 LKVAVGNFASLLRQLNDLRVLDIEMSSE 538
                                        66667777899************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (781 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5322.14
//
Query:       gene1295|gene1295|rna1294|rna1294  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.1   0.1      0.095   12.8   0.1    1.3  1  Spo0A_C   Sporulation initiation factor Spo0A C terminal
      0.091   12.2   3.2       0.12   11.8   3.2    1.2  1  DUF4349   Domain of unknown function (DUF4349)


Domain annotation for each model (and alignments):
>> Spo0A_C  Sporulation initiation factor Spo0A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.1e-05     0.095      23      65 ..      11      53 ..       5      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                            Spo0A_C 23 aielvledpellesitkelypevAkkykttpsrVeraIrhaIe 65
                                        i+ + +d+el ++i  ++ +ev k+++ t+sr+ +++r+  e
  gene1295|gene1295|rna1294|rna1294 11 GIHAISSDEELKDAIRATIKEEVTKEMHDTVSRITNDMREDLE 53
                                       6888999********************************8666 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.2   1.3e-05      0.12      77     133 ..      26      83 ..      12      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                            DUF4349  77 rstsaeDVTeqyvDleaRlka.leasedrllallekaksvedlleiereLsevqaeie 133
                                        r t  e+VT+++ D+ +R+++  ++  ++  ++l   k++e+ ++ie+ ++++++e e
  gene1295|gene1295|rna1294|rna1294  26 RATIKEEVTKEMHDTVSRITNdMREDLEKRIDYLISGKEAEEEIAIETPVQDTEEEGE 83 
                                        567789*************984456666677777788999999********9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1253  (0.0698868); expected 358.6 (0.02)
Passed bias filter:                      781  (0.0435607); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 833.29
//
Query:       gene1296|gene1296|rna1295|rna1295  [L=2818]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.9e-108  357.0   0.2    1.9e-28   99.2   0.0    7.8  7  AAA_5            AAA domain (dynein-related subfamily)
      2e-24   85.9   0.0    1.8e-07   31.0   0.0    5.2  4  AAA_3            ATPase family associated with various cellul
    5.1e-20   72.3   0.2     0.0008   19.8   0.0    6.8  6  AAA              ATPase family associated with various cellul
    7.7e-17   61.5   0.0      0.011   15.8   0.0    5.9  5  Dynein_heavy     Dynein heavy chain region D6 P-loop domain
    9.1e-16   57.9   0.0     0.0019   17.8   0.0    5.3  5  AAA_7            P-loop containing dynein motor region
    5.8e-14   52.8   4.7      0.058   13.8   0.0    6.3  5  AAA_16           AAA ATPase domain
    5.6e-13   48.5   0.0     0.0012   18.0   0.0    5.2  5  MCM              MCM P-loop domain
    1.3e-12   47.4   0.1      0.001   18.1   0.0    5.3  4  AAA_6            Hydrolytic ATP binding site of dynein motor 
    3.7e-11   43.5   0.3        0.4   10.9   0.0    6.2  5  AAA_22           AAA domain
    4.2e-11   42.9   0.1    1.5e-10   41.1   0.1    2.1  1  AAA_lid_5        Midasin AAA lid domain
    2.7e-08   33.7   0.7       0.98    9.1   0.1    7.0  6  Sigma54_activat  Sigma-54 interaction domain
      2e-07   30.9   1.8        2.5    7.8   0.0    5.9  4  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.8e-07   30.3   0.0    1.5e-06   28.4   0.0    2.1  1  AAA_lid_7        Midasin AAA lid domain
    4.7e-07   29.8   2.5      0.069   13.2   0.0    5.3  5  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.8e-06   27.3   0.8        4.9    6.2   0.0    4.9  4  DUF815           Protein of unknown function (DUF815)
    3.7e-06   27.5   4.2        2.8    8.5   0.0    6.1  5  AAA_18           AAA domain
    2.6e-05   24.6   0.2         11    6.5   0.0    5.5  5  RNA_helicase     RNA helicase
    3.1e-05   23.9   0.5       0.14   12.1   0.0    4.4  4  NACHT            NACHT domain
      9e-05   22.7   4.0        1.4    9.1   0.0    5.4  5  Roc              Ras of Complex, Roc, domain of DAPkinase
    0.00041   20.1   0.6         12    5.6   0.0    4.9  5  AAA_24           AAA domain
    0.00094   19.0   0.1         15    5.3   0.0    4.1  4  IstB_IS21        IstB-like ATP binding protein
      0.001   18.7   6.2     0.0027   17.4   0.2    3.8  4  AAA_29           P-loop containing region of AAA domain
     0.0011   18.1   1.2        0.1   11.6   0.0    3.2  3  T2SSE            Type II/IV secretion system protein
     0.0011   19.5   2.6        3.8    8.0   0.0    5.0  5  ABC_tran         ABC transporter
      0.002   17.4   0.0        1.5    8.0   0.1    2.8  2  TIP49            TIP49 P-loop domain
     0.0035   17.3   5.6       0.66    9.9   0.0    5.8  7  RsgA_GTPase      RsgA GTPase
     0.0097   15.3   0.2         40    3.6   0.0    4.6  5  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.015   14.6   0.1        4.6    6.5   0.0    3.9  4  Zeta_toxin       Zeta toxin
      0.039   13.3   4.0        2.3    7.4   0.1    3.4  3  AAA_8            P-loop containing dynein motor region D4
      0.047   13.4   0.1         54    3.4   0.0    4.5  4  AAA_30           AAA domain
       0.16   11.5   0.0         45    3.5   0.0    3.7  4  AAA_25           AAA domain
       0.17   12.2   7.0         49    4.2   0.3    5.3  5  AAA_19           AAA domain
       0.23   11.2   2.4        7.4    6.3   0.0    3.9  4  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.26   11.1   0.5         34    4.2   0.1    4.0  3  DEAD             DEAD/DEAH box helicase
       0.27   10.9   0.8        0.6    9.8   0.1    1.9  1  LRR_12           Leucine-rich repeat
        5.8    6.4   6.7         12    5.4   1.4    3.3  3  Hpr_kinase_C     HPr Serine kinase C-terminal domain
        7.8    6.4   8.2        9.1    6.2   0.1    4.6  5  NTPase_1         NTPase


Domain annotation for each model (and alignments):
>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   5.6e-07   0.00027      10     123 ..      39     148 ..      36     155 .. 0.91
   2 !   15.8   0.0   2.2e-05     0.011       1      47 [.     310     362 ..     310     373 .. 0.86
   3 !   16.4   0.0   1.4e-05    0.0068      40     124 ..     417     497 ..     414     505 .. 0.82
   4 !   79.5   0.0   4.8e-25   2.3e-22       1     138 []     658     791 ..     658     791 .. 0.95
   5 !   99.2   0.0   3.9e-31   1.9e-28       2     138 .]     951    1084 ..     950    1084 .. 0.93
   6 !   70.3   0.0   3.3e-22   1.6e-19       1     138 []    1228    1361 ..    1228    1361 .. 0.97
   7 !   44.1   0.0   3.9e-14   1.9e-11       9     138 .]    1463    1587 ..    1461    1587 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.6e-07
                                        SSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHHH CS
                              AAA_5  10 tgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevl 82 
                                        +gK++l+ +l + l   + +++++  ++ t +++l g + ik+g+ ++v++ l +++++g+ +++  +++ +   l
  gene1296|gene1296|rna1295|rna1295  39 VGKTSLVSKLHSELcdeEGRLVEIDSREITDARTLGGFYAIKGGDVEYVKGLLIESMKSGDWVLFKRIDK-NHGLL 113
                                        79********9999999999999999999****************************************5.56799 PP

                                        HHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS- CS
                              AAA_5  83 nsLlslleerrllleeggelvkaknddllerfrviatanpl 123
                                        + L +++  rrll ++g e+  ++n      fr+++t++++
  gene1296|gene1296|rna1295|rna1295 114 QYLFTVIKYRRLLGNNGEEVLAHDN------FRLFFTSEDR 148
                                        9************888877777777......******9986 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.2e-05
                                        EEEEE--SSSSHHHHHHHGGGGB......S--EEEEE--TT--HHHHH--B-- CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaal......nreveyvqltrdtteedlkgrrei 47 
                                        + lL+G++G+gK++++++l+         ++++ +v++++d   +dl+g++ +
  gene1296|gene1296|rna1295|rna1295 310 HTLLIGDTGVGKTSMIQYLSLKShfflgrQTRLRIVNMSADFDGTDLIGGYGT 362
                                        679***************985555569*99*******************9865 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.4e-05
                                        HHH--B--.........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-E CS
                              AAA_5  40 dlkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfr 115
                                        dl+  +e k+ + ++++++l++ + +ge l+lDE++  + e+ln    +l +r++ll e+g +   +   + + f+
  gene1296|gene1296|rna1295|rna1295 417 DLVKLLE-KKVHFVYKKGILTECMINGEWLLLDEINLSSEETLNLIDGVLGKREILLYESGDVKPLR---IHPGFM 488
                                        5555556.578899******************************************87777665443...4566** PP

                                        EEEEESS-- CS
                              AAA_5 116 viatanpld 124
                                        +++ +np  
  gene1296|gene1296|rna1295|rna1295 489 LFGCMNPGG 497
                                        ******987 PP

  == domain 4  score: 79.5 bits;  conditional E-value: 4.8e-25
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                        ++lL+G++ tgK++++  l++ +nr+v  +++++ t+++d +g+   ++ + ++++++lv+a+r+g+ +vlDE++ 
  gene1296|gene1296|rna1295|rna1295 658 PLLLQGDTSTGKTSMVLFLSREMNRRVIRINNHEHTEASDYIGSFTSTSNGIEFREGALVKAMRRGDWVVLDELNL 733
                                        589*******************************************99**************************** PP

                                        --HHHHHHHHHHHHS.SEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                              AAA_5  77 aesevlnsLlsllee.rrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                        a+s+vl++L++ll++ r+++++e +e +   ++     fr++at n  +++++ ls+a+r Rf
  gene1296|gene1296|rna1295|rna1295 734 ASSDVLEVLNRLLDDnRQIYIPETDEIITPHKN-----FRIFATQNIGYGGRKGLSKAFRNRF 791
                                        *************86266888888888888777.....************************9 PP

  == domain 5  score: 99.2 bits;  conditional E-value: 3.9e-31
                                         EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGG CS
                              AAA_5    2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEve 75  
                                         +l+vG++G+gK+++ e + +++++++++  ++++++++d++g   ++n++ +++d+plv+a+++g+ +++DE++
  gene1296|gene1296|rna1295|rna1295  951 ILIVGETGIGKTRVCEIVGSLFETKIVTLSMHKGIESSDFIGNFVFENSKVVWRDGPLVKAMKNGDAFLIDEIN 1024
                                         79************************************************************************ PP

                                         G--HHHHHHHHHHHHS.SEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                              AAA_5   76 raesevlnsLlsllee.rrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138 
                                          ae++vl++L+s+le  r+l+++e g++v a ++     fr++at+np   +++ elspal+ Rf
  gene1296|gene1296|rna1295|rna1295 1025 LAEDSVLERLNSVLESqRTLYIAETGKEVVAHEK-----FRILATMNPGGdFGKRELSPALKNRF 1084
                                         **************97155666666667666665.....*************************9 PP

  == domain 6  score: 70.3 bits;  conditional E-value: 3.3e-22
                                         EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESG CS
                              AAA_5    1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEv 74  
                                         +v+L G+pG+gK+++++ +a+ ++r+   ++l+++t+  dl+g++ + +g+ ++ +s+l  + r g  ++lDE+
  gene1296|gene1296|rna1295|rna1295 1228 GVMLEGDPGIGKTSIIQGIARKIGRKCIRINLSEQTELCDLVGSYLPIDGEIRFIESELLHSLRDGGWIILDEI 1301
                                         599*********************************************************************** PP

                                         GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--...-TT-TTHHHHTT- CS
                              AAA_5   75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld..rslnelspalrsRf 138 
                                         + + ++v++ L+s+l+ rr l+ +  ++  ++       +r++at np +  ++++ l  ++++Rf
  gene1296|gene1296|rna1295|rna1295 1302 NLCTQSVIEGLNSVLDYRRKLFIPEATVNVHRD------TRIFATLNPYNsvNGRKVLPRSFLDRF 1361
                                         *********************999999998877......9**********9999***********9 PP

  == domain 7  score: 44.1 bits;  conditional E-value: 3.9e-14
                                         SSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGGG--HHH CS
                              AAA_5    9 GtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEveraesev 81  
                                         G+gK +l + +++++++e+ + ++++dt   dl+g+++ + ng  ++ ds +v  +++g i+v+ +ve +e++v
  gene1296|gene1296|rna1295|rna1295 1463 GIGKDSLLRFISSVIGQEIMIFNCHKDTDVCDLLGQYQKMqNGMFEWCDSTVVCGIKKGMIVVFTGVEFVEKSV 1536
                                         99***********************************9778********************************* PP

                                         HHHHHHHHHSSEEE..-SSSEEE---.......-EEEEEESS--.-TT-TTHHHHTT- CS
                              AAA_5   82 lnsLlslleerrllleeggelvkakndd.llerfrviatanpldrslnelspalrsRf 138 
                                         +++L+sl+e +r l    ++    + +    + +r+i  a +++     lspal++R+
  gene1296|gene1296|rna1295|rna1295 1537 FDRLNSLFESERTLNVYERG---IDTNVvVNPSTRLILMAKEPN----MLSPALLDRC 1587
                                         ********988877333333...223222223378887777777....7999999995 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.55   2.6e+02       1      42 [.     310     357 ..     310     369 .. 0.65
   2 !   17.5   0.0   5.9e-06    0.0029       2     130 ..     659     792 ..     658     793 .. 0.83
   3 !   28.9   0.0   1.8e-09   8.6e-07       2     129 ..     951    1084 ..     950    1086 .. 0.85
   4 !   31.0   0.0   3.8e-10   1.8e-07       2     130 ..    1229    1362 ..    1228    1363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.55
                              AAA_3   1 hvllegvPGlaktllvkalakal......dlefkriqftpdllPsdil 42 
                                        h ll g  G++kt +++ l+ +       +++++ + + +d+  +d++
  gene1296|gene1296|rna1295|rna1295 310 HTLLIGDTGVGKTSMIQYLSLKShfflgrQTRLRIVNMSADFDGTDLI 357
                                        8999*************9985540111112233334555555555555 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.9e-06
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanl.....lladein 72 
                                        +ll+g   ++kt +v  l++ ++ ++ ri        sd +G+  f+++++ +ef++G++++ +     ++ de+n
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMVLFLSREMNRRVIRINNHEHTEASDYIGS--FTSTSNGIEFREGALVKAMrrgdwVVLDELN 732
                                        58999999**********************************7..7788899999****9986544444999**** PP

                              AAA_3  73 rappktqsalleamee.rqvtveget..hklpepflvlatqnPieqeGtyplpeaqldrfl 130
                                         a++ +   l   +++ rq+ + ++    + +++f ++atqn i + G   l +a  +rf+
  gene1296|gene1296|rna1295|rna1295 733 LASSDVLEVLNRLLDDnRQIYIPETDeiITPHKNFRIFATQN-IGYGGRKGLSKAFRNRFV 792
                                        ****999988888765256666554400455789*******9.888999999999999885 PP

  == domain 3  score: 28.9 bits;  conditional E-value: 1.8e-09
                              AAA_3    2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanl.....llade 70  
                                         +l+ g  G++kt++ + +++ +++++  + +   +  sd +G  vfe++  ++  + Gp+++ +     +l de
  gene1296|gene1296|rna1295|rna1295  951 ILIVGETGIGKTRVCEIVGSLFETKIVTLSMHKGIESSDFIGNFVFENS--KVVWRDGPLVKAMkngdaFLIDE 1022
                                         789999***************************************9875..6778899998754333339**** PP

                              AAA_3   71 inrappktqs...alleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrf 129 
                                         in a+  +     ++le+ +   ++ +g+    +e+f +lat nP    G  +l  a  +rf
  gene1296|gene1296|rna1295|rna1295 1023 INLAEDSVLErlnSVLESQRTLYIAETGKEVVAHEKFRILATMNPGGDFGKRELSPALKNRF 1084
                                         ****998876111556666666688888999999*********************9999999 PP

  == domain 4  score: 31.0 bits;  conditional E-value: 3.8e-10
                              AAA_3    2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanl.....llade 70  
                                         v+leg PG++kt +++ +a++++ +  ri +       d++G+ +    + e++f +  ++++l     ++ de
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKIGRKCIRINLSEQTELCDLVGSYL--PIDGEIRFIESELLHSLrdggwIILDE 1300
                                         79****************************************966..4556777777777776555555999** PP

                              AAA_3   71 inrappktqsalleame.erqvtvegethklpepflvlatqnPieq.eGtyplpeaqldrfl 130 
                                         in ++  +   l  +++  r++ + ++t ++++   ++at nP ++ +G   lp + ldrf+
  gene1296|gene1296|rna1295|rna1295 1301 INLCTQSVIEGLNSVLDyRRKLFIPEATVNVHRDTRIFATLNPYNSvNGRKVLPRSFLDRFI 1362
                                         ************99998346899********************9853899***********7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.97   4.7e+02       9      36 ..      39      69 ..      34     103 .. 0.84
   2 ?    4.8   0.0     0.072        35       2      22 ..     312     332 ..     311     376 .. 0.78
   3 !   14.7   0.0   6.6e-05     0.032       1     124 [.     659     791 ..     659     799 .. 0.62
   4 !   11.4   0.0   0.00065      0.31       1     126 [.     951    1086 ..     951    1090 .. 0.65
   5 !   19.8   0.0   1.6e-06    0.0008       1      35 [.    1229    1263 ..    1229    1319 .. 0.86
   6 !   10.4   0.0    0.0013      0.65       8     125 ..    1463    1588 ..    1460    1592 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.97
                                       SSHHHHHHHHHHHH...THEEEEEETTTCSS CS
                                AAA  9 tGKTllakavakel...gvefleisgsells 36
                                       +GKT+l++ + +el   + +++ei+  e+++
  gene1296|gene1296|rna1295|rna1295 39 VGKTSLVSKLHSELcdeEGRLVEIDSREITD 69
                                       8************976668899999999884 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.072
                                        EEESSTTSSHHHHHHHHHHHH CS
                                AAA   2 llyGppGtGKTllakavakel 22 
                                        ll+G  G+GKT++++ +  ++
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQYLSLKS 332
                                        89***********99887664 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 6.6e-05
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS..SSSTTHHHHHHHHH.HHH.HHHTS..TSEEEEEETGGGH CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsell..skyvgesekkirel.fke.akeka..kpsilfiDEidal 70 
                                        +ll G   tGKT+++  + +e+++++++i+ +e +  s+y+g   +  +++ f+e a  ka  +   +++DE+   
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMVLFLSREMNRRVIRINNHEHTeaSDYIGSFTSTSNGIeFREgALVKAmrRGDWVVLDELNLA 734
                                        5899*****************************9955558887666655552222233333534477888888655 PP

                                        HHHHTTCCCHHHHHHHHHHHHHHHHTTTS...........SSTEEEEEEESS....GGGSTHHHHSTTS CS
                                AAA  71 aksrsgseseeeervvnqLlteldgvkkk...........eskvivigatnr....pdkldpallrgRf 124
                                         ++           v+++L + ld+ ++            ++++ + ++ n      + l++a++ +Rf
  gene1296|gene1296|rna1295|rna1295 735 SSD-----------VLEVLNRLLDDNRQIyipetdeiitpHKNFRIFATQNIgyggRKGLSKAFR-NRF 791
                                        333...........366666666655554555555555544444444444445555555555555.555 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00065
                                         EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS......STTHHHHHH.HHHHHHHHHTSTSEEEEEETG CS
                                AAA    1 vllyGppGtGKTllakavakelgvefleisgsellsk......yvgesekki.relfkeakekakpsilfiDEi 67  
                                         +l++G  G+GKT +++ v + ++++++++s+++ +++      +v e++k + r+    +k++++   ++iDEi
  gene1296|gene1296|rna1295|rna1295  951 ILIVGETGIGKTRVCEIVGSLFETKIVTLSMHKGIESsdfignFVFENSKVVwRDGP-LVKAMKNGDAFLIDEI 1023
                                         699**********************99999999884446555544444443313322.3344443489999999 PP

                                         GGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...........SSTEEEEEEESS.....GGGSTHHHHSTTSS CS
                                AAA   68 dalaksrsgseseeeervvnqLlteldgvkkk...........eskvivigatnr.....pdkldpallrgRfd 125 
                                              s           v++ L ++l+ +++            ++k+ ++++ n       ++l+pal  +Rf+
  gene1296|gene1296|rna1295|rna1295 1024 NLAEDS-----------VLERLNSVLESQRTLyiaetgkevvaHEKFRILATMNPggdfgKRELSPALK-NRFT 1085
                                         766433...........3555555555555555555555555656666666666666666777777777.7776 PP

                                         E CS
                                AAA  126 r 126 
                                         +
  gene1296|gene1296|rna1295|rna1295 1086 E 1086
                                         5 PP

  == domain 5  score: 19.8 bits;  conditional E-value: 1.6e-06
                                         EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                                AAA    1 vllyGppGtGKTllakavakelgvefleisgsell 35  
                                         v+l G pG+GKT++++ +a+++g+++++i++se +
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKIGRKCIRINLSEQT 1263
                                         6899***************************9977 PP

  == domain 6  score: 10.4 bits;  conditional E-value: 0.0013
                                         TSSHHHHHHHHHHHHTHEEEEEETTTCSSS..STTHHHHHHHHHHHHHHHTS....TS.EEEEEETGGGHHHHH CS
                                AAA    8 GtGKTllakavakelgvefleisgsellsk..yvgesekkirelfkeakeka....kp.silfiDEidalaksr 74  
                                         G+GK +l + + + +g+e++ +++++ ++   ++g+ +k  +++f+ + +      k+  i+++  ++ + ks 
  gene1296|gene1296|rna1295|rna1295 1463 GIGKDSLLRFISSVIGQEIMIFNCHKDTDVcdLLGQYQKMQNGMFEWCDSTVvcgiKKgMIVVFTGVEFVEKSV 1536
                                         89****************999999999854669*************9988779999555999999999998887 PP

                                         ..TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSS CS
                                AAA   75 ..sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfd 125 
                                           + ++  e+er++n+  + +d     +  + +i+++++p++l+pall +R+ 
  gene1296|gene1296|rna1295|rna1295 1537 fdRLNSLFESERTLNVYERGIDTNVVVNPSTRLILMAKEPNMLSPALL-DRCM 1588
                                         866678888899999999999999998999******************.9995 PP

>> Dynein_heavy  Dynein heavy chain region D6 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00028      0.14      42      97 ..      85     148 ..      72     165 .. 0.83
   2 ?    3.1   0.0       0.2        98      47      67 ..     434     454 ..     422     499 .. 0.83
   3 !   15.8   0.0   2.3e-05     0.011      44      94 ..     712     773 ..     668     776 .. 0.77
   4 !    8.1   0.0    0.0056       2.7      48     108 ..    1008    1079 ..    1003    1085 .. 0.86
   5 !   13.5   0.0   0.00012     0.058      46     114 ..    1284    1367 ..    1276    1371 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
                                        HHHHHHHHHHHHHT-EEEEE-GGG-CCCHHHHHHH...............HHTT-EEEEEEES- CS
                       Dynein_heavy  42 eeaekalekaakegsWvlLqNchlapswlkeLekileel........eeklhssfRlwltseps 97 
                                        e ++ +l +++k+g+Wvl++ +      l+ L ++++          e  +h++fRl++tse  
  gene1296|gene1296|rna1295|rna1295  85 EYVKGLLIESMKSGDWVLFKRIDKNHGLLQYLFTVIKYRrllgnngeEVLAHDNFRLFFTSEDR 148
                                        567788999***********999888888888888763356788887778899********965 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.2
                                        HHHHHHHHT-EEEEE-GGG-C CS
                       Dynein_heavy  47 alekaakegsWvlLqNchlap 67 
                                        +l++++ +g+W+lL ++ l+ 
  gene1296|gene1296|rna1295|rna1295 434 ILTECMINGEWLLLDEINLSS 454
                                        7899*************9985 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 2.3e-05
                                        HHHHHHHHHHHT-EEEEE-GGG-.CCCHHHHHHH.................HHTT-EEEEEE CS
                       Dynein_heavy  44 aekalekaakegsWvlLqNchla.pswlkeLekileel..........eeklhssfRlwlts 94 
                                         e al ka+++g+Wv+L +  la  + l+ L+++l++             + h++fR++ t 
  gene1296|gene1296|rna1295|rna1295 712 REGALVKAMRRGDWVVLDELNLAsSDVLEVLNRLLDDNrqiyipetdeIITPHKNFRIFATQ 773
                                        467899*****************566799*****88666778888766456689*****986 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0056
                                         HHHHHHHT-EEEEE-GGG-.CCCHHHHHHH.................HHTT-EEEEEEES-TTS-HHHHHTS CS
                       Dynein_heavy   48 lekaakegsWvlLqNchla.pswlkeLekileel..........eeklhssfRlwltsepspkfPislLqss 108 
                                         l ka+k+g+  l+ ++ la  s l++L+++le++          e  +h++fR+  t++p  +f ++ L  +
  gene1296|gene1296|rna1295|rna1295 1008 LVKAMKNGDAFLIDEINLAeDSVLERLNSVLESQrtlyiaetgkEVVAHEKFRILATMNPGGDFGKRELSPA 1079
                                         579****************677899*****99888999999998788899*********9998877666555 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 0.00012
                                         HHHHHHHHHT-EEEEE-GGG-.CCCHHHHHHH...............HHTT-EEEEEEES-T.....T.S-HHH CS
                       Dynein_heavy   46 kalekaakegsWvlLqNchla.pswlkeLekileel........eeklhssfRlwltsepsp.....k.fPisl 104 
                                         + l ++ ++g+W++L ++ l+ +s ++ L+++l+          + ++h++ R++ t +p +     k +P s+
  gene1296|gene1296|rna1295|rna1295 1284 SELLHSLRDGGWIILDEINLCtQSVIEGLNSVLDYRrklfipeaTVNVHRDTRIFATLNPYNsvngrKvLPRSF 1357
                                         556678899************5566889****7743567888879999**********9999777774488888 PP

                                         HHTSEEEEE- CS
                       Dynein_heavy  105 Lqssikvtne 114 
                                         L + i++ ++
  gene1296|gene1296|rna1295|rna1295 1358 LDRFIRIKMD 1367
                                         8888887765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.3   1.6e+03      29      74 ..      26      69 ..      19      74 .. 0.75
   2 !   13.9   0.0     6e-05     0.029      30      55 ..     305     331 ..     294     356 .. 0.73
   3 !   17.8   0.0   3.9e-06    0.0019       5      76 ..     628     696 ..     624     746 .. 0.77
   4 !    8.7   0.0    0.0023       1.1      25      58 ..     940     973 ..     926    1025 .. 0.81
   5 !    9.9   0.0     0.001       0.5      34      74 ..    1227    1264 ..    1213    1269 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.3
                              AAA_7 29 llknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqts 74
                                        ++ +  v ++G++  GKt+++++l ++l +e+   + i     t+
  gene1296|gene1296|rna1295|rna1295 26 AVRLRVAVAVYGEV--GKTSLVSKLHSELCDEEGRLVEIDSREITD 69
                                       56667778888887..9*******9999988887777776666555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6e-05
                              AAA_7  30 lknkkpvllvGptGtGKtviikd.llk 55 
                                        ++++ ++ll+G+tG+GKt++i+   lk
  gene1296|gene1296|rna1295|rna1295 305 ISHRDHTLLIGDTGVGKTSMIQYlSLK 331
                                        7899*****************984444 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.9e-06
                              AAA_7   5 eeakfseilVptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsan 76 
                                        e++++++ +V t     y  ++el + +++p+ll G+t tGKt+++  l ++++++   ++ in + +t+a+
  gene1296|gene1296|rna1295|rna1295 628 EKTRVKDGFVLTRRIQTYLRIMELAIISNYPLLLQGDTSTGKTSMVLFLSREMNRR---VIRINNHEHTEAS 696
                                        67788999999************************************999999944...4455555555554 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0023
                              AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkld 58 
                                        l+ l   +k p+l+vG+tG GKt +++ + + ++
  gene1296|gene1296|rna1295|rna1295 940 LVVLAWGSKEPILIVGETGIGKTRVCEIVGSLFE 973
                                        5556667899*************99875554444 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.001
                              AAA_7   34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqts 74  
                                           v+l G+ G GKt+ii+ + +k+     +++ in+s qt+
  gene1296|gene1296|rna1295|rna1295 1227 IGVMLEGDPGIGKTSIIQGIARKIG---RKCIRINLSEQTE 1264
                                         679********************99...5677889998886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.022        10      27      64 ..      33      68 ..      15      90 .. 0.76
   2 !    8.0   0.0    0.0073       3.6      26      45 ..     310     329 ..     300     470 .. 0.78
   3 !    9.5   0.2    0.0024       1.2      27      73 ..     659     703 ..     639     749 .. 0.79
   4 !    9.6   0.0    0.0023       1.1      22      45 ..     946     969 ..     932     995 .. 0.80
   5 !   13.8   0.0   0.00012     0.058      25      61 ..    1227    1264 ..    1214    1308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.022
                             AAA_16 27 vllsGesGvGKsslvrellralekdggiflrgkcdqle 64
                                       v ++Ge  vGK+slv +l+ +l++++g +++ + ++ +
  gene1296|gene1296|rna1295|rna1295 33 VAVYGE--VGKTSLVSKLHSELCDEEGRLVEIDSREIT 68
                                       445554..9****************8888877776664 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0073
                             AAA_16  26 lvllsGesGvGKsslvrell 45 
                                         +ll+G+ GvGK+s+++ l 
  gene1296|gene1296|rna1295|rna1295 310 HTLLIGDTGVGKTSMIQYLS 329
                                        689*************8776 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0024
                             AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.la 73 
                                        +ll G+  +GK+s+v  l r+++++   ++r +++++++a  y+  ++
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMVLFLSREMNRR---VIRINNHEHTEASDYIGsFT 703
                                        89*********************99...89999999988877755444 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0023
                             AAA_16  22 grpelvllsGesGvGKsslvrell 45 
                                        g+ e +l++Ge G+GK+++ + + 
  gene1296|gene1296|rna1295|rna1295 946 GSKEPILIVGETGIGKTRVCEIVG 969
                                        56688**************97665 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 0.00012
                             AAA_16   25 elvllsGesGvGKsslvrellralekdggif.lrgkcd 61  
                                           v+l G++G+GK+s+++ ++r + ++ +   l+++++
  gene1296|gene1296|rna1295|rna1295 1227 IGVMLEGDPGIGKTSIIQGIARKIGRKCIRInLSEQTE 1264
                                         4699*********************9943333444444 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.02       9.9      58      78 ..     309     329 ..     302     340 .. 0.85
   2 !    6.7   0.0    0.0072       3.5      30     137 ..     630     738 ..     608     754 .. 0.69
   3 !   18.0   0.0   2.5e-06    0.0012      60     174 ..     951    1068 ..     944    1084 .. 0.84
   4 !   10.5   0.0   0.00047      0.23      58     175 ..    1227    1345 ..    1218    1361 .. 0.78
   5 ?   -0.5   0.0       1.1   5.6e+02      56      86 ..    1452    1482 ..    1435    1523 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.02
                                        -EEEEEESSTSTHHHHHHHHH CS
                                MCM  58 invllvgdpgtaKsqlLkyve 78 
                                         + ll+gd g++K+ +++y++
  gene1296|gene1296|rna1295|rna1295 309 DHTLLIGDTGVGKTSMIQYLS 329
                                        589***************987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0072
                                        HHHHHHHHHH.HH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEE..ESSSSSSSHSSSEEE CS
                                MCM  30 edvkkaillq.lfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravyt..sgkgssaagLtaavv 102
                                        + vk + +l+  + ++ + + +   ++++  +ll gd +t+K+ ++ ++++ ++r v    + +++ a++   + +
  gene1296|gene1296|rna1295|rna1295 630 TRVKDGFVLTrRIQTYLRIM-E-LAIISNYPLLLQGDTSTGKTSMVLFLSREMNRRVIRinNHEHTEASDYIGSFT 703
                                        55666655541344444433.3.58999999***************999998888776411334445555566655 PP

                                        EESSSSSEEEEETHHHHTT..TSEEEEESGGGSTCHH CS
                                MCM 103 rdeetgefvleaGalvlad..kGvcciDefdkmkeed 137
                                          ++++ + +  Galv a   +  +++De++  +++ 
  gene1296|gene1296|rna1295|rna1295 704 --STSNGIEFREGALVKAMrrGDWVVLDELNLASSDV 738
                                        ..55566778999999885214478899998777654 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.5e-06
                                         EEEEESSTSTHHHHHHHHHHHSSSEEEE..ESSSSSSSHSSSEEEEESSSSSEEEEETHHHHT.TTS.EEEEES CS
                                MCM   60 vllvgdpgtaKsqlLkyveklapravyt..sgkgssaagLtaavvrdeetgefvleaGalvla.dkG.vcciDe 129 
                                         +l+vg+ g++K+++ + v +l+++ + t    kg  +++     v +  ++++v   G lv a  +G   +iDe
  gene1296|gene1296|rna1295|rna1295  951 ILIVGETGIGKTRVCEIVGSLFETKIVTlsMHKGIESSDFIGNFVFE--NSKVVWRDGPLVKAmKNGdAFLIDE 1022
                                         9********************99988872245778888888777754..5678999*****9843453789*** PP

                                         GGGSTCHHHHHHHHHHHHS.EEEEESSSCEEEEE--EEEEEEE--S CS
                                MCM  130 fdkmkeedrsalhEamEqq.tisiaKaGivatLnartsvlaAanpk 174 
                                         ++  +++  + l  ++E+q t+ ia  G  ++ + +  +la +np 
  gene1296|gene1296|rna1295|rna1295 1023 INLAEDSVLERLNSVLESQrTLYIAETGKEVVAHEKFRILATMNPG 1068
                                         *****************76589******99999************6 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00047
                                         -EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEE.ESSSSS.EEEEETHHH.HTTTSEEEEE CS
                                MCM   58 invllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaavvr.deetge.fvleaGalv.ladkGvcciD 128 
                                         i v+l gdpg++K+ +++ +++ + r   + ++ s +++L   v    +  ge  ++e+  l  l+d+G +++D
  gene1296|gene1296|rna1295|rna1295 1227 IGVMLEGDPGIGKTSIIQGIARKIGRKC-IRINLSEQTELCDLVGSyLPIDGEiRFIESELLHsLRDGGWIILD 1299
                                         789*****************98887764.6677788888876665414677774567777764489******** PP

                                         SGGGSTCHHHHHHHHHHH.HSEEEEESSSCEEEEE--EEEEEEE--SS CS
                                MCM  129 efdkmkeedrsalhEamE.qqtisiaKaGivatLnartsvlaAanpka 175 
                                         e++  +++  + l  +++ + ++ i  a +++  +  t ++a  np +
  gene1296|gene1296|rna1295|rna1295 1300 EINLCTQSVIEGLNSVLDyRRKLFIPEATVNV--HRDTRIFATLNPYN 1345
                                         *****999999999999845688899988655..45555778777765 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1.1
                                         SS-EEEEEESSTSTHHHHHHHHHHHSSSEEE CS
                                MCM   56 gdinvllvgdpgtaKsqlLkyveklapravy 86  
                                          +in+ +v   g++K  lL+++++++ + ++
  gene1296|gene1296|rna1295|rna1295 1452 MEINIPVVISGGIGKDSLLRFISSVIGQEIM 1482
                                         589999999*************999866554 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.1e-06     0.003      27     197 ..     651     827 ..     627     836 .. 0.70
   2 ?    3.5   0.0     0.058        28     119     162 ..    1041    1087 ..    1026    1104 .. 0.78
   3 !   18.1   0.0   2.1e-06     0.001      25     173 ..    1219    1378 ..    1210    1397 .. 0.76
   4 ?    0.7   0.0      0.42     2e+02      42      73 ..    1463    1494 ..    1446    1509 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.1e-06
                              AAA_6  27 qAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldyk....slgkifkGl..........aqsGaWg 88 
                                         A+  ++   ++G + tGKt  v  L++++ + v+ +n +++ +++    s + + +G+          ++ G W+
  gene1296|gene1296|rna1295|rna1295 651 LAIISNYPLLLQGDTSTGKTSMVLFLSREMNRRVIRINNHEHTEASdyigSFTSTSNGIefregalvkaMRRGDWV 726
                                        466666677789**************************99988765211234444556532222222224567788 PP

                              AAA_6  89 CfdeFnrielevLSvvaqqiktiqqalkekkkkfvf..egkeiklnksvgifitmnpgyagrteLPdnLkalfRpv 162
                                         +de+n  + +vL v  + +         +++++ +  +++ i+ +k+++if t n gy gr+ L   ++  f ++
  gene1296|gene1296|rna1295|rna1295 727 VLDELNLASSDVLEVLNRLLD--------DNRQIYIpeTDEIITPHKNFRIFATQNIGYGGRKGLSKAFRNRFVEM 794
                                        888888777777766655554........44444443234457789999**********************99999 PP

                              AAA_6 163 ammvPdlelIaeimLfseGfkeakelakklvtlyk 197
                                          +    e I ei   ++  k  k+  kk+v++y 
  gene1296|gene1296|rna1295|rna1295 795 FFCESSEEEILEILHGAS--KLPKSFCKKMVEVYG 827
                                        999999999999864443..445778888888885 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.058
                              AAA_6  119 kkkfvf..egkeiklnksvgifitmnp.gyagrteLPdnLkalfRpv 162 
                                         ++++ +  +gke+  +++++i  tmnp g  g+ eL   Lk  f ++
  gene1296|gene1296|rna1295|rna1295 1041 QRTLYIaeTGKEVVAHEKFRILATMNPgGDFGKRELSPALKNRFTEI 1087
                                         44444433689999*************5678***********99877 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 2.1e-06
                              AAA_6   25 ltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldykslgkif...kG...laqsGaWgCfde 92  
                                         +++A+ l +g  ++G  g GKt  ++ +a+++++ ++ +n s+q +   l   +    G   +++s     + +
  gene1296|gene1296|rna1295|rna1295 1219 ILRAMGLGIGVMLEGDPGIGKTSIIQGIARKIGRKCIRINLSEQTELCDLVGSYlpiDGeirFIESELLHSLRD 1292
                                         6789****************************************998766544412233222334444444444 PP

                              AAA_6   93 FnrielevLSvvaqqiktiqqalkekkkkfvfegkeiklnksvgifitmnp..gyagrteLPdnLkalfRpvam 164 
                                            i l+ +  ++q + + ++++ + ++k+ + + +++++++++if t+np  + +gr+ LP ++   f  + m
  gene1296|gene1296|rna1295|rna1295 1293 GGWIILDEINLCTQSVIEGLNSVLDYRRKLFIPEATVNVHRDTRIFATLNPynSVNGRKVLPRSFLDRFIRIKM 1366
                                         44444444456667777777888889999999*******************77789********9999999998 PP

                              AAA_6  165 ...mvPdlelIa 173 
                                            ++ d++ I 
  gene1296|gene1296|rna1295|rna1295 1367 dkyTIKDITHIL 1378
                                         333344555555 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.42
                              AAA_6   42 gtGKtEtvkdLakalakqvvvfncsdqldyks 73  
                                         g GK    + +++ +++ +++fnc+++ d+  
  gene1296|gene1296|rna1295|rna1295 1463 GIGKDSLLRFISSVIGQEIMIFNCHKDTDVCD 1494
                                         78999999999***************999755 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0011      0.51       4      29 ..     307     332 ..     304     461 .. 0.83
   2 ?    3.5   0.0      0.17        83       8     117 ..     659     747 ..     655     758 .. 0.71
   3 !   10.9   0.0   0.00083       0.4       6      29 ..     949     972 ..     946     999 .. 0.80
   4 ?    5.6   0.0     0.038        18       9      57 ..    1230    1269 ..    1228    1317 .. 0.88
   5 ?    3.9   0.0      0.12        60      91     133 ..    2660    2706 ..    2602    2709 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleql 29 
                                        ++ +++++G +G+GKT  ++ l  + 
  gene1296|gene1296|rna1295|rna1295 307 HRDHTLLIGDTGVGKTSMIQYLSLKS 332
                                        7899****************998775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.17
                             AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                        l++ G + tGKT  +  l ++          +++v++++  + t+ +d    + +  +           e++e   
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMVLFLSREM---------NRRVIRINNHEHTEASDYIGSFTSTSNG---------IEFREGAL 716
                                        7888999*********999998.........9********9999999987777766663.........33443333 PP

                             AAA_22  84 qalraravielliiDEaqhlrseealeeLrslln 117
                                          + +r++   +++DE     s ++le L +ll+
  gene1296|gene1296|rna1295|rna1295 717 VKAMRRGD--WVVLDELNLA-SSDVLEVLNRLLD 747
                                        33333444..5777777776.6666666655555 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00083
                             AAA_22   6 gilvvtGesGtGKTtllrrlleql 29 
                                          ++++Ge+G+GKT++++ + + +
  gene1296|gene1296|rna1295|rna1295 949 EPILIVGETGIGKTRVCEIVGSLF 972
                                        5699*************9887776 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.038
                             AAA_22    9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdll 57  
                                         ++ G +G+GKT  ++ ++++          ++++++++l+++t++ dl 
  gene1296|gene1296|rna1295|rna1295 1230 MLEGDPGIGKTSIIQGIARKI---------GRKCIRINLSEQTELCDLV 1269
                                         678*****************9.........999*****99999766665 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.12
                             AAA_22   91 v.....ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp.el 133 
                                               i  l iD+   + ++e++ +L sl+   + ++++ L G p e+
  gene1296|gene1296|rna1295|rna1295 2660 NdkkdyILRLFIDNSKSMYNQEMVDTLLSLYS--KINISFSLLGIPvEV 2706
                                         144556788999*****867************..**********99776 PP

>> AAA_lid_5  Midasin AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   3.2e-13   1.5e-10       1     104 [.     523     621 ..     523     623 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.2e-13
                          AAA_lid_5   1 DLellvknyLkevsltdqalvtdvvefYlelkklaerkeltdgagqkphfSlRtlsraLsyartilklaglrraly 76 
                                        D+ l++++ L    +++  +  ++ ef+lelk++  ++el++    +p +S R+l+r+L+++r+     +++r +y
  gene1296|gene1296|rna1295|rna1295 523 DISLVIHSVLGYEVSEE--KKGKIGEFFLELKNKVLKNELSN--VVEPLISGRSLVRVLNFIRKK-SEEEFERGVY 593
                                        88899999999887776..7899*************9***97..558*****************9.889******* PP

                          AAA_lid_5  77 eGfsmsFltqLdsesrkkveklirkill 104
                                        e+f ++ +tqLd+ sr++  +l++k++ 
  gene1296|gene1296|rna1295|rna1295 594 EAFDLFVFTQLDFVSRSIATTLLSKYFT 621
                                        ***********************99985 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.94   4.6e+02      15      62 ..      23      68 ..      16      79 .. 0.85
   2 ?    3.4   0.0      0.12        56      22      44 ..     308     330 ..     300     350 .. 0.79
   3 ?    6.2   0.0     0.016       7.6       7     121 ..     641     750 ..     637     776 .. 0.66
   4 !    9.1   0.1     0.002      0.98       7      42 ..     933     968 ..     929    1067 .. 0.82
   5 ?    3.4   0.0      0.12        57      13      59 ..    1217    1260 ..    1207    1365 .. 0.69
   6 ?   -1.4   0.0       3.5   1.7e+03      10      45 ..    1443    1476 ..    1438    1490 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.94
                                       HHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS- CS
                    Sigma54_activat 15 ikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaip 62
                                       ++++++ ++ v + Ge  +GK+ l +++h++   +e+++v+++  +i+
  gene1296|gene1296|rna1295|rna1295 23 ATEAVRLRVAVAVYGE--VGKTSLVSKLHSELCDEEGRLVEIDSREIT 68
                                       5677888899999999..78**********999999999999987765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                                        SS-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat  22 dlsvlitGesGtGKellaraihe 44 
                                        + ++l+ G++G+GK+ + + +  
  gene1296|gene1296|rna1295|rna1295 308 RDHTLLIGDTGVGKTSMIQYLSL 330
                                        56899**********99887755 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.016
                                        HHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTS CS
                    Sigma54_activat   7 alkelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAe 82 
                                        ++++ l+ ++ ++ ++ ++l++G++ tGK+ +   + ++    +++++++n  + +e   +s+  G    +  G e
  gene1296|gene1296|rna1295|rna1295 641 RIQTYLRIMELAIISNYPLLLQGDTSTGKTSMVLFLSRE---MNRRVIRINNHEHTE---ASDYIGSFTSTSNGIE 710
                                        5777888888999999*************9887666554...456677777665554...3554444444433333 PP

                                        S-BEHHHHHT..TTSEEEEETGGGS-HHHHHHHHHHHHHSE CS
                    Sigma54_activat  83 kekkGlfeka..dgGtlfLDeigelplelQekLlrvlqege 121
                                          ++G++ ka   g  + LDe++  + ++ e L r+l++++
  gene1296|gene1296|rna1295|rna1295 711 -FREGALVKAmrRGDWVVLDELNLASSDVLEVLNRLLDDNR 750
                                        .3455555552234567777777777777777777777655 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.002
                                        HHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                    Sigma54_activat   7 alkelleqikkvaktdlsvlitGesGtGKellarai 42 
                                        ++k+l++ +  +  ++ ++li+Ge+G GK+ + + +
  gene1296|gene1296|rna1295|rna1295 933 TFKKLINLVVLAWGSKEPILIVGETGIGKTRVCEIV 968
                                        6788888888899999**************998876 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.12
                                         HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT CS
                    Sigma54_activat   13 eqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavnca 59  
                                         ++i +++   + v+++G+ G GK+ + + i ++  rk    +++n +
  gene1296|gene1296|rna1295|rna1295 1217 RRILRAMGLGIGVMLEGDPGIGKTSIIQGIARKIGRK---CIRINLS 1260
                                         5566666777889999999999999988887766543...4455554 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 3.5
                                         HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                    Sigma54_activat   10 elleqikkvaktdlsvlitGesGtGKellaraihea 45  
                                         +++e i k+++ +++v+i G  G GK+ l r i + 
  gene1296|gene1296|rna1295|rna1295 1443 QQIEVIMKCMEINIPVVISG--GIGKDSLLRFISSV 1476
                                         5678889999999*****99..99999998887554 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.015       7.5      32      53 ..     307     328 ..     304     348 .. 0.88
   2 ?    2.7   0.0      0.19        92      36      64 ..     659     687 ..     642     795 .. 0.57
   3 ?    6.5   0.2     0.014       6.6      34     120 ..     949    1050 ..     926    1086 .. 0.68
   4 !    7.8   0.0    0.0051       2.5      36      61 ..    1229    1254 ..    1225    1328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.015
                             RuvB_N  32 aldhvllyGpPGlGkttlakii 53 
                                        + dh+ll+G  G+Gkt++ + +
  gene1296|gene1296|rna1295|rna1295 307 HRDHTLLIGDTGVGKTSMIQYL 328
                                        57***************98766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.19
                             RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkit 64 
                                        +ll+G    Gkt++   +++e++ ++   
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMVLFLSREMNRRVIRI 687
                                        57888888888888888888888654322 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.014
                             RuvB_N   34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaa...............lltnleekdvlfide 92  
                                         + +l++G  G+Gkt +++i+ + +++k+ + s     +++d+++               l++ ++++d ++ide
  gene1296|gene1296|rna1295|rna1295  949 EPILIVGETGIGKTRVCEIVGSLFETKIVTLSMHKGIESSDFIGnfvfenskvvwrdgpLVKAMKNGDAFLIDE 1022
                                         458999***********999998888876655432222222221111111111112222667788888888888 PP

                             RuvB_N   93 ihrlsraveevlysamedfrldivigkG 120 
                                         i   + +v e l s +e  r   + ++G
  gene1296|gene1296|rna1295|rna1295 1023 INLAEDSVLERLNSVLESQRTLYIAETG 1050
                                         8888888888888888876655555555 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0051
                             RuvB_N   36 vllyGpPGlGkttlakiiakelgvkl 61  
                                         v+l G PG+Gkt++ + ia+++g k+
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKIGRKC 1254
                                         89******************999775 PP

>> AAA_lid_7  Midasin AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     3e-09   1.5e-06       1     104 [.     803     888 ..     803     889 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3e-09
                          AAA_lid_7   1 eLeeilqskfpllasvadklievyeelrseqsssrsfsgspreislRDLlkWcrRlsalldrsgflspsvreeifl 76 
                                        e+ eil++  +l++s+++k++evy  lrs +s +         ++lRDL+kW  R+ ++            +e+  
  gene1296|gene1296|rna1295|rna1295 803 EILEILHGASKLPKSFCKKMVEVYGGLRSKRSIN-------ALVTLRDLFKWSGRVPRT-----------LDEVCF 860
                                        799****************************999.......9**************998...........556777 PP

                          AAA_lid_7  77 eavdvFaaslstqedrlrvaeviaehlg 104
                                         ++ +  ++ +++ dr+ v +++ e +g
  gene1296|gene1296|rna1295|rna1295 861 LGMGIVYERQREPRDRRWVYQIFSESFG 888
                                        7888888999999999999999998886 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.044        21      19      39 ..     308     328 ..     287     334 .. 0.82
   2 ?    4.1   0.0     0.088        42      21      44 ..     654     681 ..     634     693 .. 0.74
   3 ?    1.9   0.1      0.45   2.2e+02      18      43 ..     943     972 ..     929     981 .. 0.67
   4 !   13.2   0.0   0.00014     0.069       8      46 ..    1214    1253 ..    1207    1259 .. 0.73
   5 ?   -2.5   0.0       9.8   4.7e+03      71     104 ..    2706    2737 ..    2704    2745 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.044
                                        TEEEEEEESTTSSHHHHHHHH CS
                               TsaE  19 gdvilLeGdLGaGKTtlvrgl 39 
                                        +d  lL Gd G+GKT +++ l
  gene1296|gene1296|rna1295|rna1295 308 RDHTLLIGDTGVGKTSMIQYL 328
                                        56789************9987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.088
                                        E....EEEEESTTSSHHHHHHHHHHHTT CS
                               TsaE  21 v....ilLeGdLGaGKTtlvrglakalg 44 
                                        +    +lL+Gd  +GKT +v  l ++++
  gene1296|gene1296|rna1295|rna1295 654 IsnypLLLQGDTSTGKTSMVLFLSREMN 681
                                        133459*************998888875 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.45
                                        H....TEEEEEEESTTSSHHHHHHHHHHHT CS
                               TsaE  18 l....gdvilLeGdLGaGKTtlvrglakal 43 
                                        l    ++ il+ G+ G GKT  +  + + +
  gene1296|gene1296|rna1295|rna1295 943 LawgsKEPILIVGETGIGKTRVCEIVGSLF 972
                                        034334459***********9988776655 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00014
                                         HHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE    8 ealgkklakal..gdvilLeGdLGaGKTtlvrglakalgve 46  
                                          +l + l + +  g  ++LeGd G GKT +++g+a+++g +
  gene1296|gene1296|rna1295|rna1295 1214 LNLRRILRA-MglGIGVMLEGDPGIGKTSIIQGIARKIGRK 1253
                                         555555544.334556********************99865 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 9.8
                                         -TT-SSTHHHHHCTTCCC.CSTSCEEEEETGGGGC CS
                               TsaE   71 lYRledeeeleelgleey.leeeavvlvEWpekle 104 
                                         +YR+   e le++ +e++ + +++ +++ W ++++
  gene1296|gene1296|rna1295|rna1295 2706 VYRFG--EVLERCSVEDMkF-NDSKTMIDWIDEFN 2737
                                         79995..5678899999855.556899***99865 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0      0.01       4.9      64      95 ..      39      70 ..      18      79 .. 0.90
   2 ?    6.0   0.0     0.012       5.8      52      77 ..     307     332 ..     261     351 .. 0.66
   3 ?    3.2   0.0     0.083        40      56      84 ..     659     687 ..     651     699 .. 0.88
   4 ?    5.4   0.0     0.018       8.7      55      84 ..    1228    1257 ..    1195    1271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                             DUF815 64 tGKSslvkallneyaeegLrlievekedlkel 95
                                       +GK slv  l++e+++e+ rl+e++ +++++ 
  gene1296|gene1296|rna1295|rna1295 39 VGKTSLVSKLHSELCDEEGRLVEIDSREITDA 70
                                       69************************999875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                             DUF815  52 pannvLLwGarGtGKSslvkallney 77 
                                        +  + LL+G+ G+GK s+++ l  + 
  gene1296|gene1296|rna1295|rna1295 307 HRDHTLLIGDTGVGKTSMIQYLSLKS 332
                                        55799**************9876543 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.083
                             DUF815  56 vLLwGarGtGKSslvkallneyaeegLrl 84 
                                        +LL G+  tGK s+v +l +e++++ +r+
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMVLFLSREMNRRVIRI 687
                                        69*********************998887 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.018
                             DUF815   55 nvLLwGarGtGKSslvkallneyaeegLrl 84  
                                          v+L G+ G GK s+++ + +++ ++ +r+
  gene1296|gene1296|rna1295|rna1295 1228 GVMLEGDPGIGKTSIIQGIARKIGRKCIRI 1257
                                         69*********************9999887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.018       8.8       2      22 ..     312     332 ..     312     368 .. 0.82
   2 ?    1.5   0.0      0.83     4e+02       3      25 ..     661     692 ..     659     761 .. 0.73
   3 ?    5.4   0.1     0.052        25       1      68 [.     951    1016 ..     951    1058 .. 0.56
   4 !    8.5   0.0    0.0057       2.8       1      81 [.    1229    1300 ..    1229    1348 .. 0.73
   5 ?   -1.1   0.0       5.5   2.7e+03      79     121 ..    2162    2202 ..    2077    2209 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.018
                             AAA_18   2 lltGtpGvGKttlakeLskrl 22 
                                        ll G  GvGKt++ ++Ls + 
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQYLSLKS 332
                                        589**************8664 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.83
                             AAA_18   3 ltGtpGvGKttlakeLskrlgf.........g 25 
                                        l G   +GKt++   Ls++++          +
  gene1296|gene1296|rna1295|rna1295 661 LQGDTSTGKTSMVLFLSREMNRrvirinnheH 692
                                        678899***********998656654444442 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.052
                             AAA_18    1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe..aldeskrldedkldklldaleens 68  
                                         Il+ G  G GKt +++ + ++    +++  +  ++g++ +++     +++sk++ +d    l++a+++ +
  gene1296|gene1296|rna1295|rna1295  951 ILIVGETGIGKTRVCEIVGSLF--ETKIVTLSMHKGIESSDFIGnfVFENSKVVWRDG--PLVKAMKNGD 1016
                                         89****************9986..5555555555555555544444444444444444..3333333333 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0057
                             AAA_18    1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleeg 74  
                                         ++l G pG GKt++ + ++++   g++++ +   ++++l++      +++ +d + +   +++l+  ++    g
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKI--GRKCIRINLSEQTELCDLVG---SYLPIDGEIRFIESELLHSLRD----G 1293
                                         789******************8..77777777777777777666...6666666666666666666544....4 PP

                             AAA_18   75 knlvidg 81  
                                         +++++d 
  gene1296|gene1296|rna1295|rna1295 1294 GWIILDE 1300
                                         4444443 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 5.5
                             AAA_18   79 idghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik 121 
                                         +  +l  +++ ++ ++  ++L++s  e  +R++   ++  k k
  gene1296|gene1296|rna1295|rna1295 2162 FLYLLLTPFDFEMAER--YFLDCSVYEFVDRVRHAQEMAIKNK 2202
                                         3334444443333332..7999999999999999988777654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.6   1.8e+03       8      26 ..      38      56 ..      33      86 .. 0.85
   2 ?    3.8   0.0      0.15        73       2      19 ..     312     329 ..     311     351 .. 0.82
   3 ?    0.9   0.0       1.2   5.7e+02       2      26 ..     660     684 ..     659     706 .. 0.78
   4 ?    4.9   0.0     0.068        33       1      26 [.     951     976 ..     951    1024 .. 0.76
   5 ?    6.5   0.0     0.022        11       1      26 [.    1229    1254 ..    1229    1267 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.6
                       RNA_helicase  8 geGKStlakeLakallkkl 26
                                        +GK++l+ +L ++l+++ 
  gene1296|gene1296|rna1295|rna1295 38 EVGKTSLVSKLHSELCDEE 56
                                       48*************9764 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.15
                       RNA_helicase   2 wlyGpsgeGKStlakeLa 19 
                                        +l G++g+GK++++++L+
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQYLS 329
                                        588************975 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.2
                       RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl 26 
                                        +l+G++ +GK++++  L++++ +++
  gene1296|gene1296|rna1295|rna1295 660 LLQGDTSTGKTSMVLFLSREMNRRV 684
                                        689****************999776 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.068
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                        i+++G++g+GK+++++ + + +++k+
  gene1296|gene1296|rna1295|rna1295 951 ILIVGETGIGKTRVCEIVGSLFETKI 976
                                        689************99888777776 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.022
                       RNA_helicase    1 iwlyGpsgeGKStlakeLakallkkl 26  
                                         ++l G++g+GK+++++ +a+++ +k 
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKIGRKC 1254
                                         6799****************998765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.6   2.7e+03      11      25 ..      39      53 ..      33      59 .. 0.83
   2 ?    3.7   0.0      0.11        52       3      21 ..     311     329 ..     309     333 .. 0.86
   3 ?    2.4   0.0      0.26   1.3e+02       2      15 ..     950     963 ..     949     975 .. 0.86
   4 !   12.1   0.0   0.00028      0.14       3      28 ..    1229    1254 ..    1228    1316 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.6
                                       TCHHHHHHHHHHHHC CS
                              NACHT 11 sGKTtLlqklalawa 25
                                       +GKT L+ kl++++ 
  gene1296|gene1296|rna1295|rna1295 39 VGKTSLVSKLHSELC 53
                                       69********99885 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                        EEEEC-TTTCHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                         +l G+ G+GKT ++q l 
  gene1296|gene1296|rna1295|rna1295 311 TLLIGDTGVGKTSMIQYLS 329
                                        5899**********99886 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.26
                                        CEEEEC-TTTCHHH CS
                              NACHT   2 lvilqGeaGsGKTt 15 
                                        ++++ Ge G+GKT 
  gene1296|gene1296|rna1295|rna1295 950 PILIVGETGIGKTR 963
                                        689*********95 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00028
                                         EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                              NACHT    3 vilqGeaGsGKTtLlqklalawaegk 28  
                                         v+l+G++G+GKT  +q++a+++ +++
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKIGRKC 1254
                                         789*****************998876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.61     3e+02       9      26 ..      38      55 ..      34      72 .. 0.78
   2 !    9.1   0.0     0.003       1.4       3      19 ..     312     328 ..     310     344 .. 0.87
   3 ?    1.9   0.0      0.49   2.4e+02       3      19 ..     660     676 ..     659     703 .. 0.82
   4 ?    1.2   0.1      0.82     4e+02       2      16 ..     951     965 ..     950     979 .. 0.87
   5 ?    4.0   0.1      0.11        54       2      20 ..    1229    1247 ..    1228    1256 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.61
                                       TSSHHHHHHCHCT-CCC- CS
                                Roc  9 gvGKtsllkrfvedkfse 26
                                       +vGKtsl++++ ++  +e
  gene1296|gene1296|rna1295|rna1295 38 EVGKTSLVSKLHSELCDE 55
                                       79********98776654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.003
                                        EEESSTTSSHHHHHHCH CS
                                Roc   3 vlvGdsgvGKtsllkrf 19 
                                        +l+Gd+gvGKts+++ +
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQYL 328
                                        79************976 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.49
                                        EEESSTTSSHHHHHHCH CS
                                Roc   3 vlvGdsgvGKtsllkrf 19 
                                        +l Gd+++GKts++  +
  gene1296|gene1296|rna1295|rna1295 660 LLQGDTSTGKTSMVLFL 676
                                        678*********98654 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.82
                                        EEEESSTTSSHHHHH CS
                                Roc   2 vvlvGdsgvGKtsll 16 
                                        +++vG++g+GKt  +
  gene1296|gene1296|rna1295|rna1295 951 ILIVGETGIGKTRVC 965
                                        799*********876 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.11
                                         EEEESSTTSSHHHHHHCHC CS
                                Roc    2 vvlvGdsgvGKtsllkrfv 20  
                                         v+l Gd g+GKts+++ + 
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIA 1247
                                         6888***********9765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.47   2.3e+02       5      52 ..      33      76 ..      28      81 .. 0.77
   2 ?    3.5   0.0      0.11        52       6      29 ..     312     336 ..     309     364 .. 0.82
   3 ?   -1.5   0.0       3.7   1.8e+03       4      22 ..     658     676 ..     655     744 .. 0.69
   4 ?    5.6   0.0     0.025        12       5      40 ..     951     990 ..     947    1039 .. 0.80
   5 ?    2.6   0.1      0.19        94       5      21 ..    1229    1245 ..    1225    1259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.47
                             AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedf 52
                                       +++yG  ++GKT+l+++l  +  ++d e+ l ++d +++ d++++  f
  gene1296|gene1296|rna1295|rna1295 33 VAVYG--EVGKTSLVSKL--HSELCDEEGRLVEIDSREITDARTLGGF 76
                                       34444..69*********..7777899999999999988888766555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                             AAA_24   6 liyGpsgiGKTtlakel.gpkplfi 29 
                                        l++G+ g+GKT+++  l  ++ +f+
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQYLsLKSHFFL 336
                                        89***********999875665555 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 3.7
                             AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                         +l+ G+  +GKT++++ l
  gene1296|gene1296|rna1295|rna1295 658 PLLLQGDTSTGKTSMVLFL 676
                                        5677788888888877655 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.025
                             AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtekGlkslda 40 
                                        ili+G+ giGKT ++       + k++ + + kG  s d+
  gene1296|gene1296|rna1295|rna1295 951 ILIVGETGIGKTRVCEIVgslfETKIVTLSMHKGIESSDF 990
                                        89***********999887777888888888888777665 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.19
                             AAA_24    5 iliyGpsgiGKTtlake 21  
                                         +++ G++giGKT+++  
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQG 1245
                                         7889*********9875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.17        81      44      64 ..     305     325 ..     286     333 .. 0.83
   2 ?   -1.4   0.0       3.4   1.6e+03      48     119 ..     657     733 ..     625     748 .. 0.67
   3 ?    5.3   0.0      0.03        15      35      65 ..     937     966 ..     919     973 .. 0.80
   4 ?    4.7   0.0     0.047        23      49     119 ..    1228    1303 ..    1195    1319 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                          IstB_IS21  44 iekkenivllGpsGvGKshla 64 
                                        i++++  +l+G +GvGK+ + 
  gene1296|gene1296|rna1295|rna1295 305 ISHRDHTLLIGDTGVGKTSMI 325
                                        7788999***********875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                          IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvl...fvrvedLveelkrarrdgkla..ralkrllkvdllilDdlg 118
                                          ++l G + +GK+ +   l++e  r+ +++    ++ ++d + +     +  ++     +k++ + d ++lD+l 
  gene1296|gene1296|rna1295|rna1295 657 YPLLLQGDTSTGKTSMVLFLSREMNRRVIRINnheHTEASDYIGSFTSTSNGIEFRegALVKAMRRGDWVVLDELN 732
                                        5578999999999999999888888877777422245555555555554443333311344555555666666665 PP

                          IstB_IS21 119 l 119
                                        l
  gene1296|gene1296|rna1295|rna1295 733 L 733
                                        5 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.03
                          IstB_IS21  35 vkeLatlsfiekkenivllGpsGvGKshlai 65 
                                        + +L+ l++  +ke i+++G +G+GK+ +  
  gene1296|gene1296|rna1295|rna1295 937 LINLVVLAW-GSKEPILIVGETGIGKTRVCE 966
                                        445666777.56899************8765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.047
                          IstB_IS21   49 nivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkra...rrdgkl.ar.alkrllkvdllilDdl 117 
                                         +++l G +G+GK+ +   ++++  r+ +++     ++L   +      +++ ++ ++  l++l     +ilD++
  gene1296|gene1296|rna1295|rna1295 1228 GVMLEGDPGIGKTSIIQGIARKIGRKCIRINLSEQTELCDLVGSYlpiDGEIRFiESeLLHSLRDGGWIILDEI 1301
                                         68999*********999999999999888887777666655533210023333212213444444566777776 PP

                          IstB_IS21  118 gl 119 
                                          l
  gene1296|gene1296|rna1295|rna1295 1302 NL 1303
                                         65 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   5.6e-06    0.0027       4      39 ..     291     325 ..     288     330 .. 0.89
   2 ?   -0.8   0.0       2.8   1.3e+03      25      39 ..     659     673 ..     650     674 .. 0.86
   3 ?   -0.3   0.0       1.9   9.3e+02      24      36 ..     950     962 ..     941     965 .. 0.84
   4 ?    0.6   0.2         1     5e+02      25      42 ..    1229    1246 ..    1221    1249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.6e-06
                             AAA_29   4 lqlvNWgtfdghtieidlkgatlltGpsGsGKSTll 39 
                                         + v+Wg f+   ++i+ ++ tll+G++G+GK++++
  gene1296|gene1296|rna1295|rna1295 291 TSCVEWGIFNL-LWNISHRDHTLLIGDTGVGKTSMI 325
                                        56799****98.69999999*************998 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.8
                             AAA_29  25 tlltGpsGsGKSTll 39 
                                         ll G++ +GK++++
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMV 673
                                        699********9986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.9
                             AAA_29  24 atlltGpsGsGKS 36 
                                         +l++G++G GK+
  gene1296|gene1296|rna1295|rna1295 950 PILIVGETGIGKT 962
                                        589*********7 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1
                             AAA_29   25 tlltGpsGsGKSTllDAi 42  
                                         ++l G+ G GK++++  i
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGI 1246
                                         7899**********9665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         2   9.7e+02     126     147 ..     305     326 ..     287     333 .. 0.82
   2 !   11.6   0.0   0.00022       0.1      94     161 ..     621     688 ..     582     722 .. 0.82
   3 ?    3.1   0.0     0.084        41     107     156 ..     927     975 ..     901     980 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2
                              T2SSE 126 vrerglilvsGgTgsGKttlly 147
                                        +++r   l+ G Tg GKt ++ 
  gene1296|gene1296|rna1295|rna1295 305 ISHRDHTLLIGDTGVGKTSMIQ 326
                                        5778888999********8874 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00022
                              T2SSE  94 viRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                        ++  +s ++ +++d  +  +  +++ ++++ a+ +++ +l+ G T++GKt ++  l  e+n +  ri 
  gene1296|gene1296|rna1295|rna1295 621 TVQAESMEKTRVKDGFVLTRRIQTYLRIMELAIISNYPLLLQGDTSTGKTSMVLFLSREMNRRVIRIN 688
                                        44444455555555555555559999***************************999999998866665 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.084
                              T2SSE 107 dlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                        +++ + ++k+ i+ v+ +   ++  il+ G Tg GKt +  ++ + ++++
  gene1296|gene1296|rna1295|rna1295 927 NFVLTDTFKKLINLVVLA-WGSKEPILIVGETGIGKTRVCEIVGSLFETK 975
                                        333344444444333332.267899************9887776666555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       4.4   2.1e+03      22      51 ..      39      69 ..      31      78 .. 0.83
   2 !    8.0   0.0    0.0078       3.8       4      33 ..     301     330 ..     298     347 .. 0.88
   3 ?   -1.2   0.0       5.4   2.6e+03      15      49 ..     660     692 ..     648     719 .. 0.78
   4 ?    3.7   0.1      0.17        84      12      32 ..     949     969 ..     940     997 .. 0.85
   5 ?    2.1   0.1      0.52   2.5e+02      14      36 ..    1229    1251 ..    1222    1285 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.4
                                       SSHHHHHHHHTTSS--SEEEE.EETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                           ABC_tran 22 aGKStLlkllagllkpteGei.lldgkdlke 51
                                        GK++L++ l  +l ++eG++ ++d++++++
  gene1296|gene1296|rna1295|rna1295 39 VGKTSLVSKLHSELCDEEGRLvEIDSREITD 69
                                       59*****************963777887776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0078
                                        EEEEEETTSEEEEEESTTSSHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   4 vslklkegekvaivGenGaGKStLlkllag 33 
                                        + +++++   + ++G++G GK+++++ l+ 
  gene1296|gene1296|rna1295|rna1295 301 LLWNISHRDHTLLIGDTGVGKTSMIQYLSL 330
                                        6678999999***************99975 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 5.4
                                        EEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  15 aivGenGaGKStLlkllagllkpteGeilldgkdl 49 
                                         + G++ +GK++++  l+++++     i++++++ 
  gene1296|gene1296|rna1295|rna1295 660 LLQGDTSTGKTSMVLFLSREMNRR--VIRINNHEH 692
                                        6789999***********998754..444455554 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.17
                                        SEEEEEESTTSSHHHHHHHHT CS
                                        xxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  12 ekvaivGenGaGKStLlklla 32 
                                        e + ivGe+G GK+ +++++ 
  gene1296|gene1296|rna1295|rna1295 949 EPILIVGETGIGKTRVCEIVG 969
                                        6789**********9988765 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.52
                                         EEEEESTTSSHHHHHHHHTTSS- CS
                                         xxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   14 vaivGenGaGKStLlkllagllk 36  
                                         v + G+ G GK+++++ +a++  
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKIG 1251
                                         6788************9999765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.013       6.1      48      78 ..     654     684 ..     628     694 .. 0.86
   2 !    8.0   0.1     0.003       1.5      50      78 ..    1226    1254 ..    1214    1266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  48 laGravLlaGpsgtGktalaiaiskelgedv 78 
                                        ++   +Ll+G+++tGkt++ + +s+e+++ v
  gene1296|gene1296|rna1295|rna1295 654 ISNYPLLLQGDTSTGKTSMVLFLSREMNRRV 684
                                        666779*********************9765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                                         XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49   50 GravLlaGpsgtGktalaiaiskelgedv 78  
                                         G +v+l G++g Gkt++  +i++++g++ 
  gene1296|gene1296|rna1295|rna1295 1226 GIGVMLEGDPGIGKTSIIQGIARKIGRKC 1254
                                         6789**********************875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       3.2   1.6e+03     110     123 ..      39      52 ..      24      70 .. 0.81
   2 !    9.9   0.0    0.0014      0.66      97     121 ..     305     330 ..     282     346 .. 0.79
   3 ?    0.2   0.0       1.3   6.4e+02     101     134 ..     658     691 ..     616     709 .. 0.85
   4 ?    0.2   0.0       1.3   6.1e+02      99     121 ..     948     970 ..     927     986 .. 0.74
   5 ?    1.0   0.0      0.74   3.6e+02     102     123 ..    1229    1250 ..    1207    1263 .. 0.79
   6 ?   -0.9   0.0       2.7   1.3e+03      79     122 ..    1435    1476 ..    1414    1485 .. 0.73
   7 ?   -1.3   0.0       3.6   1.8e+03       3      42 ..    1538    1591 ..    1536    1599 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.2
                                        SSHHHHHHHHCTT- CS
                        RsgA_GTPase 110 vGKStLinallpel 123
                                        vGK++L+ +l++el
  gene1296|gene1296|rna1295|rna1295  39 VGKTSLVSKLHSEL 52 
                                        9*********9986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                        CTT.SEEEEECSTTSSHHHHHHHHCT CS
                        RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallp 121
                                        +++ + ++l+G +GvGK+++i  l  
  gene1296|gene1296|rna1295|rna1295 305 ISHrDHTLLIGDTGVGKTSMIQYLSL 330
                                        44438899*************99865 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.3
                                        EEEEECSTTSSHHHHHHHHCTT-----S------ CS
                        RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelktgevsekl 134
                                          +l G +  GK++++  l  e++ ++  + ++ 
  gene1296|gene1296|rna1295|rna1295 658 PLLLQGDTSTGKTSMVLFLSREMNRRVIRINNHE 691
                                        56789******************99999988765 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.3
                                        TSEEEEECSTTSSHHHHHHHHCT CS
                        RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                        ++ +++vG++G+GK+ + + + +
  gene1296|gene1296|rna1295|rna1295 948 KEPILIVGETGIGKTRVCEIVGS 970
                                        566789********987765555 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.74
                                         EEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase  102 svlvGqSGvGKStLinallpel 123 
                                         ++l G  G+GK+++i  ++ + 
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKI 1250
                                         5678***********9988765 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 2.7
                                         EEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase   79 vllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpe 122 
                                         ++l++++  +++e + + ++ ++ v++ + G+GK +L+  + + 
  gene1296|gene1296|rna1295|rna1295 1435 FVLIHSQ-LQQIEVIMKCMEINIPVVI-SGGIGKDSLLRFISSV 1476
                                         4444333.5778888888888777766.679******9988775 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 3.6
                                         --S-EETTTT..............EES--EEEEEEESTTTT--HHHHHHHHHHH CS
                        RsgA_GTPase    3 eRknelvrpk..............vaNvdqllivvslkepelslnlldrfLvla 42  
                                         +R n+l +++              v N  + li+++ + + ls+ lldr++ + 
  gene1296|gene1296|rna1295|rna1295 1538 DRLNSLFESErtlnvyergidtnvVVNPSTRLILMAKEPNMLSPALLDRCMHVG 1591
                                         566666666566666666677777999999********9999*******99765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0       0.1        50      36      54 ..     309     327 ..     301     349 .. 0.80
   2 ?   -3.1   0.0       9.2   4.4e+03     145     171 ..     368     395 ..     365     402 .. 0.82
   3 ?   -1.3   0.0       2.4   1.2e+03      38      52 ..     659     673 ..     654     690 .. 0.86
   4 ?    3.6   0.0     0.082        40      25      53 ..     939     966 ..     930     970 .. 0.74
   5 ?    1.4   0.0      0.36   1.8e+02      38      58 ..    1229    1249 ..    1226    1292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.1
                               TniB  36 pnlllvGdsnnGKtmivek 54 
                                         + ll+Gd+ +GKt++++ 
  gene1296|gene1296|rna1295|rna1295 309 DHTLLIGDTGVGKTSMIQY 327
                                        6789***********9975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.2
                               TniB 145 alksLgnelkipi.vlvGteealralrt 171
                                        a+ +L+ne ki++ v+ G ++ l+ lr+
  gene1296|gene1296|rna1295|rna1295 368 AIERLCNEEKITVpVCYGNRQKLEYLRH 395
                                        7889*******9769****999998876 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.4
                               TniB  38 lllvGdsnnGKtmiv 52 
                                        lll Gd+ +GKt++v
  gene1296|gene1296|rna1295|rna1295 659 LLLQGDTSTGKTSMV 673
                                        799*********987 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.082
                               TniB  25 eLleypkrkrmpnlllvGdsnnGKtmive 53 
                                        +L+  +  ++ + +l+vG++ +GKt ++e
  gene1296|gene1296|rna1295|rna1295 939 NLVVLAWGSK-EPILIVGETGIGKTRVCE 966
                                        5555555555.568***********9987 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.36
                               TniB   38 lllvGdsnnGKtmivekFarl 58  
                                         ++l Gd+ +GKt+i++  ar+
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARK 1249
                                         6899***********987776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.3     3e+03      20      37 ..     312     329 ..     308     340 .. 0.85
   2 ?    1.4   0.0      0.34   1.6e+02      20      51 ..     660     689 ..     655     698 .. 0.91
   3 ?    0.5   0.0      0.65   3.1e+02      19      38 ..     951     970 ..     944     981 .. 0.79
   4 ?    6.5   0.0    0.0094       4.6      19      51 ..    1229    1259 ..    1227    1265 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.3
                         Zeta_toxin  20 llgGqpGAGKselaellk 37 
                                        ll G +G GK++++++l 
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQYLS 329
                                        7889********999876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.34
                         Zeta_toxin  20 llgGqpGAGKselaellkdelerqgnvvrldp 51 
                                        ll G +  GK+++   l +e+  +++v+r++ 
  gene1296|gene1296|rna1295|rna1295 660 LLQGDTSTGKTSMVLFLSREM--NRRVIRINN 689
                                        78899****************..9******96 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.65
                         Zeta_toxin  19 illgGqpGAGKselaellkd 38 
                                        il++G +G GK+++ e +  
  gene1296|gene1296|rna1295|rna1295 951 ILIVGETGIGKTRVCEIVGS 970
                                        899***********987755 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0094
                         Zeta_toxin   19 illgGqpGAGKselaellkdelerqgnvvrldp 51  
                                         ++l G pG GK+++++ +++++  +++++r++ 
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKI--GRKCIRINL 1259
                                         6788******************..9*****986 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.82     4e+02      24      42 ..     308     326 ..     305     332 .. 0.88
   2 ?    7.4   0.1    0.0048       2.3      27     108 ..     951    1040 ..     935    1066 .. 0.80
   3 ?    4.2   0.3     0.047        23      13     116 ..    1442    1554 ..    1433    1569 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.82
                              AAA_8  24 rghaLlvGvgGsGrqsltk 42 
                                        r h+Ll+G  G G+ s+++
  gene1296|gene1296|rna1295|rna1295 308 RDHTLLIGDTGVGKTSMIQ 326
                                        77**************875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0048
                              AAA_8   27 aLlvGvgGsGrqsltkLAafiaelelfqievtkkykekefredlkkllkkag........ikqkevvfllsdnq 92  
                                         +L+vG  G G+  ++++  ++ e ++++++++k  + ++f  +      k++          ++   fl+++ +
  gene1296|gene1296|rna1295|rna1295  951 ILIVGETGIGKTRVCEIVGSLFETKIVTLSMHKGIESSDFIGNFVFENSKVVwrdgplvkAMKNGDAFLIDEIN 1024
                                         799************************************98766544444441222332222335689999999 PP

                              AAA_8   93 iieesfledinnlLnt 108 
                                         ++e+s+le +n++L++
  gene1296|gene1296|rna1295|rna1295 1025 LAEDSVLERLNSVLES 1040
                                         99999***99999987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.047
                              AAA_8   13 larilRvlrqprghaLlvGvgGsGrqsltkLAafiaelelfqievtkkykekefredlkkllk..........k 76  
                                         l +i  +++  + ++ +v  gG G+ sl +  +++ ++e++ ++++k+ ++ +   + +k+ +           
  gene1296|gene1296|rna1295|rna1295 1442 LQQIEVIMKCMEINIPVVISGGIGKDSLLRFISSVIGQEIMIFNCHKDTDVCDLLGQYQKMQNgmfewcdstvV 1515
                                         44555556666667778889***************************999887555544443311111111113 PP

                              AAA_8   77 agikqkevvfllsdnqiieesfledinnlLntGevpnLfs 116 
                                         +gik k ++ +++  +++e+s+++ +n+l+++    n+++
  gene1296|gene1296|rna1295|rna1295 1516 CGIK-KGMIVVFTGVEFVEKSVFDRLNSLFESERTLNVYE 1554
                                         4444.57888999999999999999999998866666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.84   4.1e+02      18      38 ..     308     328 ..     304     333 .. 0.83
   2 ?    1.8   0.0      0.35   1.7e+02      65     114 ..     698     748 ..     648     754 .. 0.62
   3 ?   -0.3   0.0       1.5   7.5e+02      81     112 ..     999    1038 ..     940    1046 .. 0.52
   4 ?    3.4   0.0      0.11        54      22      43 ..    1230    1251 ..    1221    1310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.84
                             AAA_30  18 drvavltGpAGtGKttalkal 38 
                                        +  ++l G  G GKt +++ l
  gene1296|gene1296|rna1295|rna1295 308 RDHTLLIGDTGVGKTSMIQYL 328
                                        447899***********9865 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.35
                             AAA_30  65 elgieastiakllkrlk.grarlepgtllivDEagmvdtkqlaallkaaek 114
                                         +g  +st + +  r +   +++++g+ ++ DE  +++++ l+ l + +++
  gene1296|gene1296|rna1295|rna1295 698 YIGSFTSTSNGIEFREGaLVKAMRRGDWVVLDELNLASSDVLEVLNRLLDD 748
                                        33444444444444444523467778************9999988887766 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.5
                             AAA_30   81 k........grarlepgtllivDEagmvdtkqlaallkaa 112 
                                                    +++++g+ +++DE+ ++  + l++l + +
  gene1296|gene1296|rna1295|rna1295  999 SkvvwrdgpLVKAMKNGDAFLIDEINLAEDSVLERLNSVL 1038
                                         2333333342234555577777777777777777766655 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.11
                             AAA_30   22 vltGpAGtGKttalkalreawe 43  
                                         +l+G +G GKt +++++++ + 
  gene1296|gene1296|rna1295|rna1295 1230 MLEGDPGIGKTSIIQGIARKIG 1251
                                         799*************987665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.092        45      33      55 ..     308     330 ..     278     345 .. 0.82
   2 ?    1.1   0.0      0.53   2.6e+02      24      57 ..     647     680 ..     623     738 .. 0.78
   3 ?   -2.1   0.0       4.9   2.4e+03      33      49 ..     948     964 ..     939     965 .. 0.84
   4 ?    1.0   0.0      0.57   2.8e+02      31      56 ..    1224    1249 ..    1198    1254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.092
                             AAA_25  33 gelallaGapgtGKttlaldlal 55 
                                         + +ll+G++g+GKt +   l+l
  gene1296|gene1296|rna1295|rna1295 308 RDHTLLIGDTGVGKTSMIQYLSL 330
                                        5679************9988887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.53
                             AAA_25  24 wlvkgllpagelallaGapgtGKttlaldlalav 57 
                                         +++  ++ +   ll G++ tGKt ++l l+ ++
  gene1296|gene1296|rna1295|rna1295 647 RIMELAIISNYPLLLQGDTSTGKTSMVLFLSREM 680
                                        56666677888899************99988776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.9
                             AAA_25  33 gelallaGapgtGKttl 49 
                                        +e +l++G +g GKt +
  gene1296|gene1296|rna1295|rna1295 948 KEPILIVGETGIGKTRV 964
                                        6889***********75 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.57
                             AAA_25   31 pagelallaGapgtGKttlaldlala 56  
                                          +g  ++l G+pg GKt +   +a +
  gene1296|gene1296|rna1295|rna1295 1224 GLGIGVMLEGDPGIGKTSIIQGIARK 1249
                                         45556789*********999888765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.38   1.9e+02       9      29 ..     307     327 ..     302     339 .. 0.88
   2 ?    0.4   0.0       1.6   7.7e+02      97     133 ..     436     471 ..     366     479 .. 0.73
   3 ?   -1.3   0.0         5   2.4e+03      97     132 ..     717     752 ..     678     754 .. 0.78
   4 ?    2.9   0.1      0.27   1.3e+02      10      30 ..     948     968 ..     942     980 .. 0.82
   5 ?    4.2   0.3       0.1        49      13      34 ..    1229    1250 ..    1222    1258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.38
                             AAA_19   9 kekvllvtaGpGtGKTrvlkh 29 
                                        ++++ l+++  G GKT +++ 
  gene1296|gene1296|rna1295|rna1295 307 HRDHTLLIGDTGVGKTSMIQY 327
                                        67889************9975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.6
                             AAA_19  97 ekklqeeellivDEfqdvdelqyrLlkallgekkkll 133
                                        ++ + ++e+l+ DE+   +e   +L++ +lg+++ +l
  gene1296|gene1296|rna1295|rna1295 436 TECMINGEWLLLDEINLSSEETLNLIDGVLGKRE-IL 471
                                        34444899********999*********998886.43 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5
                             AAA_19  97 ekklqeeellivDEfqdvdelqyrLlkallgekkkl 132
                                         k ++++++++ DE    +    ++l++ll+++ ++
  gene1296|gene1296|rna1295|rna1295 717 VKAMRRGDWVVLDELNLASSDVLEVLNRLLDDNRQI 752
                                        46777889******9888888888888888666555 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.27
                             AAA_19  10 ekvllvtaGpGtGKTrvlkhi 30 
                                        ++++l+++  G GKTrv + +
  gene1296|gene1296|rna1295|rna1295 948 KEPILIVGETGIGKTRVCEIV 968
                                        6799************97654 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.1
                             AAA_19   13 llvtaGpGtGKTrvlkhivall 34  
                                         +++ + pG GKT ++++i + +
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKI 1250
                                         578899**********998765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.015       7.4       4      23 ..     311     330 ..     308     346 .. 0.88
   2 ?   -2.5   0.0       7.9   3.8e+03       5      22 ..     660     677 ..     658     684 .. 0.82
   3 ?    0.9   0.1      0.71   3.5e+02       4      20 ..     951     967 ..     948     977 .. 0.87
   4 ?   -0.3   0.0       1.6     8e+02       4      23 ..    1229    1248 ..    1228    1276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.015
                          PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                         lliG +g+GKt++ q l+ 
  gene1296|gene1296|rna1295|rna1295 311 TLLIGDTGVGKTSMIQYLSL 330
                                        79**************9975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.9
                          PduV-EutP   5 lliGkvgsGKttLtqalk 22 
                                        ll G + +GKt++   l+
  gene1296|gene1296|rna1295|rna1295 660 LLQGDTSTGKTSMVLFLS 677
                                        789*********976665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.71
                          PduV-EutP   4 illiGkvgsGKttLtqa 20 
                                        il++G++g GKt +++ 
  gene1296|gene1296|rna1295|rna1295 951 ILIVGETGIGKTRVCEI 967
                                        89**********99975 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.6
                          PduV-EutP    4 illiGkvgsGKttLtqalkg 23  
                                         ++l G  g GKt++ q +  
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIAR 1248
                                         8999***********99875 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.63     3e+02      13      35 ..     307     329 ..     300     345 .. 0.80
   2 ?   -0.9   0.0       2.5   1.2e+03      12      32 ..     654     674 ..     646     690 .. 0.83
   3 ?    4.2   0.1     0.069        34      12      33 ..     942     967 ..     931     985 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.63
                                        TTCEEEEEESTTSSHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  13 gggdvlvaaeTGsGKTlaflipv 35 
                                        + ++ l+ ++TG GKT + +   
  gene1296|gene1296|rna1295|rna1295 307 HRDHTLLIGDTGVGKTSMIQYLS 329
                                        556789999*******9877655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                                        HTTCEEEEEESTTSSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  12 lgggdvlvaaeTGsGKTlafl 32 
                                        +++  +l++++T +GKT + l
  gene1296|gene1296|rna1295|rna1295 654 ISNYPLLLQGDTSTGKTSMVL 674
                                        46667899*********9865 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.069
                                        H....TTCEEEEEESTTSSHHHHHHH CS
                                        x....xxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  12 l....gggdvlvaaeTGsGKTlafli 33 
                                        +    +++ +l+ +eTG GKT +  i
  gene1296|gene1296|rna1295|rna1295 942 VlawgSKEPILIVGETGIGKTRVCEI 967
                                        44454677899**********98765 PP

>> LRR_12  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1    0.0012       0.6      10      24 ..    1725    1739 ..    1723    1739 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                             LRR_12   10 FInqAqLsiFgaFps 24  
                                         FI+ A+Ls+F  F s
  gene1296|gene1296|rna1295|rna1295 1725 FIKSADLSVFNRFHS 1739
                                         *************76 PP

>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.1     1e+03      22      43 ..     312     333 ..     310     338 .. 0.79
   2 ?    1.0   0.1      0.54   2.6e+02      21      34 ..     951     964 ..     943     968 .. 0.89
   3 ?    5.4   1.4     0.024        12      17      34 ..    1225    1242 ..    1223    1251 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.1
                                        EEEESTCHHHHHHHHHHHTTT- CS
                       Hpr_kinase_C  22 LitGesgvGKselaleLikrgh 43 
                                        L++G+ gvGK+ +   L  + h
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQYLSLKSH 333
                                        89********998766666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.54
                                        EEEEESTCHHHHHH CS
                       Hpr_kinase_C  21 vLitGesgvGKsel 34 
                                        +Li+Ge g+GK+ +
  gene1296|gene1296|rna1295|rna1295 951 ILIVGETGIGKTRV 964
                                        8**********975 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.024
                                         TTEEEEEEESTCHHHHHH CS
                       Hpr_kinase_C   17 ygvGvLitGesgvGKsel 34  
                                         +g+Gv++ G+ g+GK+ +
  gene1296|gene1296|rna1295|rna1295 1225 LGIGVMLEGDPGIGKTSI 1242
                                         59*************976 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.2   1.1e+03       9      29 ..      38      58 ..      30      80 .. 0.73
   2 ?   -1.1   0.1       3.2   1.6e+03       3      18 ..     312     327 ..     310     331 .. 0.83
   3 ?    0.5   0.3         1     5e+02       2      23 ..     951     972 ..     950     980 .. 0.81
   4 ?   -2.7   0.0       9.8   4.7e+03      89     123 ..    1008    1039 ..     981    1047 .. 0.72
   5 ?    6.2   0.1     0.019       9.1       2      26 ..    1229    1253 ..    1228    1258 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.2
                                       TSSHHHHHHHHHHHH...GGG CS
                           NTPase_1  9 GvGKtTlvkkvlellkssgvk 29
                                        vGKt lv+k+ ++l +++ +
  gene1296|gene1296|rna1295|rna1295 38 EVGKTSLVSKLHSELCDEEGR 58
                                       59*********9998776555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.2
                                        EEE--TTSSHHHHHHH CS
                           NTPase_1   3 fiTGppGvGKtTlvkk 18 
                                        ++ G  GvGKt +++ 
  gene1296|gene1296|rna1295|rna1295 312 LLIGDTGVGKTSMIQY 327
                                        6789********9985 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1
                                        EEEE--TTSSHHHHHHHHHHHH CS
                           NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                        ++i G+ G+GKt +++ v +l 
  gene1296|gene1296|rna1295|rna1295 951 ILIVGETGIGKTRVCEIVGSLF 972
                                        7899*********999876655 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 9.8
                                         HHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                           NTPase_1   89 lrkalseadviviDEiGkmElkskkfkeaveevLk 123 
                                         l ka+++ d ++iDEi    l   ++ e ++ vL+
  gene1296|gene1296|rna1295|rna1295 1008 LVKAMKNGDAFLIDEIN---LAEDSVLERLNSVLE 1039
                                         456889999******95...444455555555555 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.019
                                         EEEE--TTSSHHHHHHHHHHHH... CS
                           NTPase_1    2 vfiTGppGvGKtTlvkkvlellkss 26  
                                         v++ G pG+GKt +++ +++++ ++
  gene1296|gene1296|rna1295|rna1295 1229 VMLEGDPGIGKTSIIQGIARKIGRK 1253
                                         6899***************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2818 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 1.45u 0.35s 00:00:01.79 Elapsed: 00:00:00.56
# Mc/sec: 15045.73
//
Query:       gene1297|gene1297|rna1296|rna1296  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-15   57.4   2.2    2.7e-15   56.5   2.2    1.4  1  Ribosomal_L23  Ribosomal protein L23


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   2.2   1.5e-19   2.7e-15       1      64 [.      25      89 ..      25      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.5e-19
                                       SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSS CS
                      Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrk 64
                                       d+il  + tEk+ + +++ n++vF V+k+++K+eikka+ +l+g kV+kVntl+ k  kk + r+
  gene1297|gene1297|rna1296|rna1296 25 DIILYALTTEKAARCMDQfNTLVFYVEKTSTKPEIKKAITELYGFKVKKVNTLINKHGKKAYVRF 89
                                       79999*************99*********************************999888854443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 649.58
//
Query:       gene1299|gene1299|rna1298|rna1298  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-76  254.8   0.0    9.6e-76  254.6   0.0    1.0  1  Pkinase        Protein kinase domain
    3.9e-33  114.8   0.0    4.7e-33  114.6   0.0    1.2  1  Pkinase_Tyr    Protein tyrosine kinase
    4.7e-07   29.1   0.1    2.6e-06   26.6   0.1    1.9  1  Haspin_kinase  Haspin like kinase domain
    0.00013   21.4   0.0    0.00055   19.3   0.0    1.8  2  Kinase-like    Kinase-like
     0.0019   17.6   0.0     0.0032   16.8   0.0    1.3  1  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.058   13.3   0.0       0.09   12.7   0.0    1.3  1  APH            Phosphotransferase enzyme family
       0.06   13.0   0.4      0.096   12.3   0.1    1.5  2  DUF2713        Protein of unknown function (DUF2713)


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.6   0.0   3.7e-79   9.6e-76       1     264 []       5     288 ..       5     288 .. 0.94

  Alignments for each domain:
  == domain 1  score: 254.6 bits;  conditional E-value: 3.7e-79
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylv 76 
                                        ++klek+GeG++G+Vyka+e++t++ivA+Kki+ e++++    +++rEi +lk+lkh+ iv+l +v+++++++ylv
  gene1299|gene1299|rna1298|rna1298   5 FQKLEKIGEGTYGVVYKARERNTDRIVALKKIRLENENEGIPATTIREILLLKNLKHSTIVELSDVIYNNNKMYLV 80 
                                        6899************************************************************************ PP

                                        EE--TTEBHHHHHH....HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEES CS
                            Pkinase  77 leyveggeladlle....rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakel 148
                                        +eyve + l ++l     + +  +e  +kk+ +q+l+++ey+Hs++i+HrDlKp+NiLid k+++K++DFGl + +
  gene1299|gene1299|rna1298|rna1298  81 FEYVELD-LRRYLDkmndEGRLADEGFVKKMSHQLLTAMEYCHSRNIFHRDLKPQNILIDPKENIKLADFGLGRAA 155
                                        *****88.6666666663545588889***********************************************99 PP

                                        SSSCS.BCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT. CS
                            Pkinase 149 esssk.ltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg. 221
                                            + +t++v+t +Y++PE+l + + y+++vDvWs+++i++e++  kp f+   g++    e+dql++i+k+lg 
  gene1299|gene1299|rna1298|rna1298 156 GVPLRtYTTEVVTLWYRPPELLlGCKYYDASVDVWSAACIMAEVVLMKPFFP---GDS----EIDQLFRIFKVLGt 224
                                        887667****************888999************************...666....9************8 PP

                                        SHH...HHHTTS.....................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 222 etkeklpeasei.....................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                        +++  + + +++                     +++++dl++k+l++dpk R+ta++ l+h+y+
  gene1299|gene1299|rna1298|rna1298 225 PSNSRWSNVENFpnykvefpiwdpvdlktilkaDSDFIDLISKMLEYDPKLRMTAKSGLSHRYF 288
                                        7777788888889999**********************************************98 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   0.0   1.8e-36   4.7e-33       3     200 ..       7     201 ..       5     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 1.8e-36
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH.HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEE CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee.keelleeakimkklkhpnivkllgvctkeepll 77 
                                          +k+GeG++G V++++ +    +++  Va+K+++ e+++e   +  ++e+ ++k+lkh  iv+l  v++++++++
  gene1299|gene1299|rna1298|rna1298   7 KLEKIGEGTYGVVYKARER----NTDRIVALKKIRLENENEGiPATTIREILLLKNLKHSTIVELSDVIYNNNKMY 78 
                                        5789*************99....999********86666655378899**************************** PP

                                        EEEE--TTEBHHHHHHHT.CTTTSBHHH.HHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHE CS
                        Pkinase_Tyr  78 ivteyvkgGdLlkfLrkk.ekekltlkd.llsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLar 151
                                        +v+eyv+  dL+ +L k  ++ +l  +  + ++++q+  +mey +s+++ Hrdl  +N+L++ ++ +k++DfGL r
  gene1299|gene1299|rna1298|rna1298  79 LVFEYVEL-DLRRYLDKMnDEGRLADEGfVKKMSHQLLTAMEYCHSRNIFHRDLKPQNILIDPKENIKLADFGLGR 153
                                        ******98.9*****998233344444435689******************************************* PP

                                        ETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHH.HHHHHHHHHHHHHT CS
                        Pkinase_Tyr 152 diekddeyvkkeeaklpvkWmapEslkekkftsks.DvWsfGvllwEift 200
                                        +       ++ +++ + + + +pE l  +k+  +s DvWs + ++ E++ 
  gene1299|gene1299|rna1298|rna1298 154 AA--GVPLRTYTTEVVTLWYRPPELLLGCKYYDASvDVWSAACIMAEVVL 201
                                        99..55566667777888888*******99665555***********986 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1     1e-09   2.6e-06     104     257 ..       7     155 ..       1     181 [. 0.73

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1e-09
                      Haspin_kinase 104 sllndseklssevyqtke..kdkevvlKvipl....evledvtiskelslkelkslklvkgtypglllllqdkvlk 173
                                        +l + +e+ ++ vy+++e  +d+ v+lK+i l    e ++  ti ++l lk+lk   +v+ +  ++++  ++ +l 
  gene1299|gene1299|rna1298|rna1298   7 KLEKIGEGTYGVVYKARErnTDRIVALKKIRLenenEGIPATTIREILLLKNLKHSTIVELS--DVIYNNNKMYLV 80 
                                        33444999999****99976777899******655555556677777777888888888777..444444444444 PP

                      Haspin_kinase 174 ekpdfyseqqlflvl.llkdkGtdLeevklkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtl 248
                                         +   y e +l  +l  ++d+G      +l +   ++++ +q ++ +    ++  F HRdL+ +niL+d + n+ l
  gene1299|gene1299|rna1298|rna1298  81 FE---YVELDLRRYLdKMNDEG------RLADEGFVKKMSHQLLTAMEYCHSRNIF-HRDLKPQNILIDPKENIKL 146
                                        44...33333333331233333......7888889999************999888.******************* PP

                      Haspin_kinase 249 idlklsRle 257
                                         d+ l+R+ 
  gene1299|gene1299|rna1298|rna1298 147 ADFGLGRAA 155
                                        *******97 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.35   9.1e+02      18      52 ..       9      43 ..       4      61 .. 0.81
   2 !   19.3   0.0   2.1e-07   0.00055     112     213 ..      76     177 ..      63     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.35
                        Kinase-like 18 ellkkgdrsvvfevkdqetgeplavkvfllpseas 52
                                       e +++g  +vv+++++ +t   +a+k   l++e+ 
  gene1299|gene1299|rna1298|rna1298  9 EKIGEGTYGVVYKARERNTDRIVALKKIRLENENE 43
                                       5688899999********99999999988888775 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.1e-07
                        Kinase-like 112 nallllpaasvdleilnkvlqkrset..hkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglml 185
                                         ++l+   +++dl +  + ++ +     +   ++++++llT+       + +++ ++h +++++n+l d+k  ++l
  gene1299|gene1299|rna1298|rna1298  76 KMYLVFEYVELDLRRYLDKMNDEGRLadEGFVKKMSHQLLTA-----MEYCHSRNIFHRDLKPQNILIDPKENIKL 146
                                        456777888889988888888776665455667788888888.....99*************************** PP

                        Kinase-like 186 ggftaLvragtkvvlseve...kgfaPpEll 213
                                         +f+  + ag   +  ++e     + PpEll
  gene1299|gene1299|rna1298|rna1298 147 ADFGLGRAAGVPLRTYTTEvvtLWYRPPELL 177
                                        ***9888888776654433333679999986 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-06    0.0032     104     166 ..      87     149 ..      42     157 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                                Kdo 104 dLedllakwae....laeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                        dL  +l k ++     +e   +++ +++ ++++  h++++ H+dl ++nil++ +e    +i l D+
  gene1299|gene1299|rna1298|rna1298  87 DLRRYLDKMNDegrlADEGFVKKMSHQLLTAMEYCHSRNIFHRDLKPQNILIDPKE----NIKLADF 149
                                        4555555544444445677888999999999***********************99....6667776 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.5e-05      0.09     123     185 ..      86     143 ..      59     155 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                        CCHHHHHHCHHHCCCGCCTCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TT CS
                                APH 123 lellrqlesatarllaselldlleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddg 185
                                        l+l r+l++ +  ++ ++ +  + ++ +q+l a++        + + H+Dl+p+N+l+dp ++
  gene1299|gene1299|rna1298|rna1298  86 LDLRRYLDKMNDEGRLADEGF-VKKMSHQLLTAMEYCHS----RNIFHRDLKPQNILIDPKEN 143
                                        555555555555333333333.46666666666665544....7899************6655 PP

>> DUF2713  Protein of unknown function (DUF2713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.8e-05     0.096     118     180 ..      60     114 ..      47     141 .. 0.77
   2 ?   -3.5   0.0       2.6   6.8e+03     188     206 ..     263     281 ..     258     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                            DUF2713 118 yssayadlsetvyinennesylkaqfeklsqrdmkkylgemkrladggemnfdgyldkmshlv 180
                                          s+  +ls+ +y  +nn+ yl  ++ +    d+++yl +m    d g +  +g++ kmsh +
  gene1299|gene1299|rna1298|rna1298  60 KHSTIVELSDVIY--NNNKMYLVFEYVE---LDLRRYLDKM---NDEGRLADEGFVKKMSHQL 114
                                        4567789999888..6799999866655...5999**9877...6999************964 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                            DUF2713 188 dilskmrdaapqlisfaks 206
                                        d++skm +  p+l   aks
  gene1299|gene1299|rna1298|rna1298 263 DLISKMLEYDPKLRMTAKS 281
                                        7899999999999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1808.08
//
Query:       gene1300|gene1300|rna1299|rna1299  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-41  140.1   0.0    5.7e-41  139.9   0.0    1.1  1  Arf          ADP-ribosylation factor family
    2.3e-12   47.2   0.0    3.6e-12   46.6   0.0    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    1.7e-11   44.0   0.0    2.2e-11   43.6   0.0    1.1  1  Ras          Ras family
    1.7e-10   40.6   0.0      2e-10   40.4   0.0    1.2  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    2.2e-08   33.7   0.0    2.7e-08   33.4   0.0    1.2  1  SRPRB        Signal recognition particle receptor beta subuni
      4e-06   26.2   3.2      4e-05   22.9   0.5    2.8  2  G-alpha      G-protein alpha subunit
    1.1e-05   25.1   0.0    0.00016   21.3   0.0    2.0  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00076   19.3   0.0       0.24   11.2   0.0    2.2  2  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0026   17.7   0.3       0.98    9.3   0.1    2.1  2  RsgA_GTPase  RsgA GTPase
     0.0027   17.3   0.0        1.9    8.0   0.0    2.2  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.003   17.6   0.0     0.0049   16.9   0.0    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.059   13.6   0.2       0.13   12.5   0.2    1.8  1  AAA_22       AAA domain
       0.15   12.6   0.8       0.22   12.0   0.8    1.7  1  ABC_tran     ABC transporter
       0.18   11.7   0.1       0.43   10.5   0.0    1.6  2  NTPase_1     NTPase


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   4.5e-44   5.7e-41       5     159 ..      16     171 ..      12     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 4.5e-44
                                        HHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCT CS
                                Arf   5 laklklkkkelrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfe 80 
                                        l+ +++ k e  i ++GLD+aGKtT+l  l+++e+++tvPT+gfn e+++  n+kf+vwD+GGq++  ++W++Y +
  gene1300|gene1300|rna1299|rna1299  16 LRGIFSGKTERSITMIGLDGAGKTTLLLYLQTGEVHQTVPTLGFNCENVNLGNMKFQVWDIGGQNSFMRFWHQYIN 91 
                                        556677788999**************************************************************** PP

                                        TESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTT.GGGSS.SSSSEEEE CS
                                Arf  81 ktdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellg.leelk.gkrkleiq 154
                                        +  ++i++vD+ad +R+ +++eeL ++l+  +    +llvlaNK+Dl +  +++e+ +++    +l+  + + +i+
  gene1300|gene1300|rna1299|rna1299  92 DGCGIIYMVDCADPQRFGKSSEELWRILNILNT-PRPLLVLANKIDLLKEHERSEVIKSIRnEFNLEkYNGPSQIV 166
                                        *****************************9765.569**********99999988655443033343322333333 PP

                                        EEBTT CS
                                Arf 155 kcsav 159
                                          s++
  gene1300|gene1300|rna1299|rna1299 167 PISVL 171
                                        33333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   2.8e-15   3.6e-12       2     120 .]      28     137 ..      27     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.8e-15
                                        EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHH CS
                                Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplyl 77 
                                        + ++G  g+GKt+ll  +++++++ ++ +t+g +  + ++             ++k+++WD++Gq+ f    + y+
  gene1300|gene1300|rna1299|rna1299  28 ITMIGLDGAGKTTLLLYLQTGEVH-QTVPTLGFNCENVNL------------GNMKFQVWDIGGQNSFMRFWHQYI 90 
                                        689******************996.5589***99854332............3578******************** PP

                                        CTSCEEEEEEE...GHHH.HCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                                Roc  78 reaalailvyd...srss.enlkeWlkelkkvagkspvilvgnkiDl 120
                                        ++   +i+++d    +++ ++ +e  + l+  ++  p+++++nkiDl
  gene1300|gene1300|rna1299|rna1299  91 NDGCGIIYMVDcadPQRFgKSSEELWRILNILNTPRPLLVLANKIDL 137
                                        *********997653344256667777888888899*********95 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   1.8e-14   2.2e-11       3     120 ..      29     141 ..      27     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.8e-14
                                        EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEE CS
                                Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillv 78 
                                         ++G  + GKt+lll   +++ + +  +T+g++    +  v+  ++k+++wD  Gq+ f ++ ++y++d+ gi+ +
  gene1300|gene1300|rna1299|rna1299  29 TMIGLDGAGKTTLLLYLQTGEVH-QTVPTLGFNCE--N--VNLGNMKFQVWDIGGQNSFMRFWHQYINDGCGIIYM 99 
                                        689***********988888865.669***87665..3..4446799***************************** PP

                                        EETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG- CS
                                Ras  79 yditsresfenvkkwveeikrvaeenvpivLvGnKvDleekr 120
                                         d  + + f + ++ +  i ++ ++  p+++++nK+Dl +++
  gene1300|gene1300|rna1299|rna1299 100 VDCADPQRFGKSSEELWRILNILNTPRPLLVLANKIDLLKEH 141
                                        *************88889999999999**********98743 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.6e-13     2e-10       4     141 ..      30     155 ..      27     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.6e-13
                          Gtr1_RagA   4 LmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                        ++G  g+GKt++       ++  ++ +   t   + ++v +lgn+++++wD+gGq++f+       +++i   +g 
  gene1300|gene1300|rna1299|rna1299  30 MIGLDGAGKTTLLL----YLQTGEVHQTVPTLGFNCENV-NLGNMKFQVWDIGGQNSFMRFW----HQYINDGCG- 95 
                                        78999999999854....457778888889999999999.79*****************875....678888887. PP

                          Gtr1_RagA  80 liyVfDvesre.leedletlkeilealrqyspeakvfvlihKmDliqedereeifeerkeeir 141
                                        +iy++D+ + + + ++ e+l +il+ l +  p   + vl +K+Dl++e+er+e+++++++e +
  gene1300|gene1300|rna1299|rna1299  96 IIYMVDCADPQrFGKSSEELWRILNILNTPRP---LLVLANKIDLLKEHERSEVIKSIRNEFN 155
                                        79******876699999999999988877776...78*******************9998865 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   2.1e-11   2.7e-08       3     141 ..      25     154 ..      23     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.1e-11
                                        --EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEE CS
                              SRPRB   3 kpavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPGheklrqklleklkaksslk 77 
                                        ++++ ++Gl  +GKT+l+  L t++v++tv  +  ++   ++    + k+++ D+ G++++   + ++  + +   
  gene1300|gene1300|rna1299|rna1299  25 ERSITMIGLDGAGKTTLLLYLQTGEVHQTVPTLgFNCENVNL---GNMKFQVWDIGGQNSFMR-FWHQ--YINDGC 94 
                                        68999**************************99778777777...999************975.5555..456678 PP

                                        EEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHHHHHH CS
                              SRPRB  78 glvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflakspklikdaLEkEl 141
                                        g++++vD  +dp++  +  E l  il i        ++l+  nK +l   ++ + + +++ +E 
  gene1300|gene1300|rna1299|rna1299  95 GIIYMVDC-ADPQRFGKSSEELWRILNILN---TPRPLLVLANKIDLLKEHERSEVIKSIRNEF 154
                                        *******7.6999999999*******9988...6778999999999988777766666666665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.095   1.2e+02      21      44 ..      23      46 ..       6      52 .. 0.80
   2 !   22.9   0.5   3.1e-08     4e-05     183     240 ..      51     107 ..      44     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.095
                                       ..EEEEEEEESTTSSHHHHHHHHH CS
                            G-alpha 21 krevkllllGqseSGKsTilkqlk 44
                                       k+e ++ ++G ++ GK+T+l  l+
  gene1300|gene1300|rna1299|rna1299 23 KTERSITMIGLDGAGKTTLLLYLQ 46
                                       4456899***********986655 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 3.1e-08
                                        CS-----SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT- CS
                            G-alpha 183 karlktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvslsefdq 240
                                        +  ++t+G++  +++++ +++f+++d+gGq+s  + W ++++d   ii++v +++ + 
  gene1300|gene1300|rna1299|rna1299  51 HQTVPTLGFNCENVNLG-NMKFQVWDIGGQNSFMRFWHQYINDGCGIIYMVDCADPQR 107
                                        55689***********9.*********************************9887544 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2       0.1   1.3e+02       4      21 ..      26      43 ..      23      57 .. 0.74
   2 !   21.3   0.0   1.2e-07   0.00016      70     178 ..      69     173 ..      52     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.1
                                       EEEEEEESTTSSHHHHHH CS
                           GTP_EFTU  4 rnigiighvDhGKtTLtd 21
                                       r i++ig   +GKtTL+ 
  gene1300|gene1300|rna1299|rna1299 26 RSITMIGLDGAGKTTLLL 43
                                       7788899999******84 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.2e-07
                                        EEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB..STHHHHHHHHHHHHTTTE..EEEEEESCGST.HHHHH CS
                           GTP_EFTU  70 ylinliDtPGHvdFskevirglrvlDgavlvvdaveG..vepqteevlrlalkegvp..iivfiNKmDrl.kaelk 140
                                         ++++ D  G  +F++   + ++   g + +vd+++       +ee++r+++ +++p  + v+ NK+D l ++e +
  gene1300|gene1300|rna1299|rna1299  69 MKFQVWDIGGQNSFMRFWHQYINDGCGIIYMVDCADPqrFGKSSEELWRILNILNTPrpLLVLANKIDLLkEHERS 144
                                        5667777777777777777777777799999***966558999**************9999999******999*** PP

                                        HHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTT CS
                           GTP_EFTU 141 eiveevkqklsrkeeklekygekgekevpvvfgSalkg 178
                                        e+++ +++++     +leky   +    ++v++S l++
  gene1300|gene1300|rna1299|rna1299 145 EVIKSIRNEF-----NLEKYNGPS----QIVPISVLQA 173
                                        **********.....666665544....4555555554 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0047         6       2      32 ..      31      66 ..      30      73 .. 0.84
   2 !   11.2   0.0   0.00019      0.24      94     180 ..      72     150 ..      67     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0047
                         ATP_bind_1  2 vGpaGsGKttf.....vgalseilelrgrsvavvNL 32
                                       +G  G+GKtt+     +g++ +++++ g +++ vNL
  gene1300|gene1300|rna1299|rna1299 31 IGLDGAGKTTLllylqTGEVHQTVPTLGFNCENVNL 66
                                       8999******9444445889999***********99 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00019
                         ATP_bind_1  94 llfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDll 169
                                         + D+ GQ  +  ++ +          +   +++y+vD+   +   k  ++ l  +  +l++  P +v  nk+Dll
  gene1300|gene1300|rna1299|rna1299  72 QVWDIGGQNSFMRFWHQYI--------NDGCGIIYMVDCADPQRFGKSSEE-LWRILNILNTPRPLLVLANKIDLL 138
                                        5677778888888888888........778899999999888887776666.888888999*************** PP

                         ATP_bind_1 170 kek.lekeleff 180
                                        ke+ + + ++ +
  gene1300|gene1300|rna1299|rna1299 139 KEHeRSEVIKSI 150
                                        *88644444433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00076      0.98      97     126 ..      23      52 ..       2      58 .. 0.74
   2 !    6.5   0.0    0.0056       7.1      48      76 ..     127     155 ..     106     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00076
                                        CTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                        RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpelelk 126
                                         +++ ++++G  G+GK+tL+  l+  +  +
  gene1300|gene1300|rna1299|rna1299  23 KTERSITMIGLDGAGKTTLLLYLQTGEVHQ 52 
                                        4567889*************9999865444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0056
                                        EEEEEEE-GGG--HHHHHHHHHHHHHHTT CS
                        RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealg 76 
                                        +++++ nKiDll+e+e+ e +k+  ++++
  gene1300|gene1300|rna1299|rna1299 127 PLLVLANKIDLLKEHERSEVIKSIRNEFN 155
                                        566777**********7777766666665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.2    0.0032         4       6      21 ..      31      46 ..      27      56 .. 0.78
   2 !    8.0   0.0    0.0015       1.9     101     170 ..      85     155 ..      77     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0032
                                       EESTTCCHHHHHHHHH CS
                               cobW  6 tGflGsGKTtLlnhll 21
                                        G  G+GKTtLl  l 
  gene1300|gene1300|rna1299|rna1299 31 IGLDGAGKTTLLLYLQ 46
                                       6788********8875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0015
                                        TTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSS.EEEEE-HHHHCHC..HHHHHHHHHHHH CS
                               cobW 101 fteeelksdltldavvavvDaknleaeeekieekaedqlaaad.llvlnKtDlldeeallekleerlrqln 170
                                        f+++ +++ + +  +v + D +++ +++e+  + ++   +    l++ nK+Dll+e++  e+++++ +++n
  gene1300|gene1300|rna1299|rna1299  85 FWHQYINDGCGIIYMVDCADPQRFGKSSEELWRILNILNTPRPlLVLANKIDLLKEHERSEVIKSIRNEFN 155
                                        556667777777777777777777666666666665544444415667*********88677766666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.8e-06    0.0049       2     114 .]      28     134 ..      27     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-06
                                        EEEEESTTSSHHHHHHHH.HTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC. CS
                           MMR_HSR1   2 vaivGrpNvGKStLinal.tgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee. 75 
                                        +  +G   +GK+tL+  l tge+    ++   T+  n ++v+l++ +++++D+ G       ++++ + +++ ++ 
  gene1300|gene1300|rna1299|rna1299  28 ITMIGLDGAGKTTLLLYLqTGEV----HQTVPTLGFNCENVNLGNMKFQVWDIGG-------QNSFMRFWHQYINd 92 
                                        6789************9944443....33456777888888888888********.......34677777776663 PP

                                        TSEEEEEEETT..TTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                           MMR_HSR1  76 adlillvvdas..eeklkpldeeleellee..akkplilvlnk 114
                                           i+++vd++  +  + +  eel ++l+   + +pl++++nk
  gene1300|gene1300|rna1299|rna1299  93 GCGIIYMVDCAdpQ-RFGKSSEELWRILNIlnTPRPLLVLANK 134
                                        57799****99752.3444555555554333356677777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2    0.0001      0.13       4      42 ..      24      56 ..      21     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                             AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpev 42
                                       t+++++ +G  G+GKTtll  l+   + +       +++
  gene1300|gene1300|rna1299|rna1299 24 TERSITMIGLDGAGKTTLLLYLQTGEVHQ------TVPT 56
                                       78999**************9999886543......4444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   0.00017      0.22      11      36 ..      25      51 ..      20     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                       TSEEEEEESTTSSHHHHHHHH.TTSS- CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                           ABC_tran 11 gekvaivGenGaGKStLlkll.agllk 36
                                        + + ++G  GaGK+tLl  l +g+++
  gene1300|gene1300|rna1299|rna1299 25 ERSITMIGLDGAGKTTLLLYLqTGEVH 51
                                       567899***********9877234444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00034      0.43       4      52 ..      30      76 ..      27      93 .. 0.82
   2 ?   -2.2   0.0       2.7   3.4e+03     132     147 ..     138     153 ..     116     160 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET CS
                           NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdl 52
                                       + G  G GKtTl+  +     ++ v+  Gf +e+v  g+  + F++ d+
  gene1300|gene1300|rna1299|rna1299 30 MIGLDGAGKTTLLLYLQTGEVHQTVPTLGFNCENVNLGN--MKFQVWDI 76
                                       56889**********999888999***********8776..45777777 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                                        --SS--SHHHHHHHT- CS
                           NTPase_1 132 ihrrkdlalveeirer 147
                                        ++++++++++++ir++
  gene1300|gene1300|rna1299|rna1299 138 LKEHERSEVIKSIRNE 153
                                        2233345555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1285.27
//
Query:       gene13|gene13|rna13|rna13  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-15   55.6   0.1    8.8e-15   55.3   0.1    1.1  1  Brix      Brix domain


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.1   4.9e-19   8.8e-15       2     192 ..       9     169 ..       8     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 4.9e-19
                                TT--HHHHHHHHHHHHHCTTSEEEEEE..ECT-TTTHHHHHHH-HHHHHHHH.HCTCSEEEEEE..SSTTEEEEEEEEECECTG CS
                       Brix   2 rktssrlrqllkdlrslmkphtasflk..rnsnklkdlvelagvthlellse.kndcslfvfelskkrPngptlefkvenyslm 82 
                                r++++++r+l+kd+ +l k +  ++    ++ ++lk+l+e+++  +++++ + k+++ l +  l     ng ++ f+ +n+ +m
  gene13|gene13|rna13|rna13   9 RGATAKIRHLMKDISKLVKVEEEQKWDmgKDYRELKNLIEMNECDSMLFFRStKRSDDLWIGIL-----NGMSVLFRMHNVFTM 87 
                                678999************8755554446555589999999999777777777577778888777.....*************** PP

                                GGSTTTSTS-TT---EEEEES.....HHHHHHHHHHHHHH..SEEEG..-B-GG-SEEEEEEES.CCTTTECEEEEEEEEEEE. CS
                       Brix  83 kdlkkakktefgsrPllvfng....kenfkllksllqdlFrvpkislkspklsglrrvvlftaaenqetdktisfRhYaiklkk 162
                                kd +   ++      +l+f++     e+++ +k+++ ++F  ++           ++ ++f + +    + +i++R Y+i    
  gene13|gene13|rna13|rna13  88 KDCNFPVNSFRDCGYVLMFSKefdeIEHLRCAKNVIDHVF--QSNEI-------KDKALCFFYLD----G-FIWVRCYKI---- 153
                                ***98855555555577888677766777***********..54433.......35778888787....5.9********.... PP

                                .STTTTECT..T..EEEEEEESEEEEEEEE CS
                       Brix 163 sgkklpnlekekkerveLeEiGPrfdLklr 192
                                                +LeEiGPrf+L++ 
  gene13|gene13|rna13|rna13 154 --------------GKKLEEIGPRFVLEVL 169
                                ..............348**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1194.43
//
Query:       gene130|gene130|rna130|rna130  [L=584]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-68  229.7   0.5    4.4e-68  229.1   0.5    1.3  1  Peptidase_M1  Peptidase family M1 domain
    5.2e-18   65.7   0.0      7e-18   65.2   0.0    1.1  1  ERAP1_C       ERAP1-like C-terminal domain
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.37   10.8   0.0    1.6  2  WLM           WLM domain


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.1   0.5   7.4e-72   4.4e-68      28     218 .]       1     194 [.       1     194 [. 0.99

  Alignments for each domain:
  == domain 1  score: 229.1 bits;  conditional E-value: 7.4e-72
                                    EEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBTTTEEESSGGGGHHHHHHHHHHHHHHH CS
                   Peptidase_M1  28 lvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfGnlVtmkwWddlwLnEGfatyleylil 107
                                    +v +p+f  gAMEnwglit+r+e+llv  ++ss +dk+++ae+++HEl H+WfGnlVtm wWddlwLnEGfat+++++++
  gene130|gene130|rna130|rna130   1 MVGIPNFGSGAMENWGLITFRKESLLVVDGKSSVEDKKNIAETVCHELGHMWFGNLVTMTWWDDLWLNEGFATWISFKGM 80 
                                    6899**************************************************************************** PP

                                    HHHSC...CCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHH CS
                   Peptidase_M1 108 dklep...ewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKGasllrmlekllgeevFqkglks 184
                                    +++     +w+v+ +++ ++v + + +d l++sh+i++ev++  e+ e+Fd+i+Y+KGas++rm+e+++ge+vF++g+++
  gene130|gene130|rna130|rna130  81 ENVGReyvDWDVEGEFVQWNVIRGMVDDGLGKSHKIRMEVSSGGEVGEIFDTISYSKGASIIRMIERYVGESVFMDGIRR 160
                                    ***99888899********************************************************************* PP

                                    HHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                   Peptidase_M1 185 Ylkefkyknaetedlwdaleealnkdisevmdtw 218
                                    Y+ke++y+n ++ +lw+a+ e+++ dis++++ w
  gene130|gene130|rna130|rna130 161 YIKEHMYGNGNAGSLWRAIGESYGRDISSMVEGW 194
                                    ********************************99 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   1.2e-21     7e-18       2     314 ..     262     564 ..     261     564 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 1.2e-21
                                    EEESGGG-SSSEEEE-HHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHHHHHH CS
                        ERAP1_C   2 vllNdddtGyyrVnYdeeslaalleqllskklspldRaglisdafalaragelsaadlldlllgylanEtdylvwsqals 81 
                                    +++N+   G+yrV Y e+ l++l e  +++ ls +dR+ +i+d+f l +  +  +++ l  +  y    + y+v +++l+
  gene130|gene130|rna130|rna130 262 YKVNSSYGGFYRVEYCEAGLRRLEE-RMEG-LSNVDRVNIIEDVFGLGFGLYGGITEGLRKIGVY--YTSTYSVGRSVLE 337
                                    79***********************.8888.*******************************844..4789********* PP

                                    HHHHHHHHHTTST.THHHHHHHHHHHHHHHHHHHHH.T.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHC.ST CS
                        ERAP1_C  82 qlatlksllsadp.lyaalkaflrklleplaeklgw.epgeshldaqlrslllsaacaagdpevveearklfkawle.gd 158
                                     l ++ks++ +d+ + +a+++ +++l+e  ++++   + g s  +  + + +ls     g++++ +++ +l+++++e g 
  gene130|gene130|rna130|rna130 338 KLLRIKSVFYDDAeIVSAIDRRVLELIEERVNEVDVsSMGGSVEKISMDKYVLSVGIEVGSESAMRKVGELWRRHIEeG- 416
                                    *******9986556999*****************88546678899999999999999******************8734. PP

                                    T-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHH CS
                        ERAP1_C 159 dlippdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvlesdevrnqdlrallag 238
                                     +   ++rw vy  ++    ++ ++ lle+y++  +p  ++ +++  + ++  e  e + + +   + ++ +d+  ++a 
  gene130|gene130|rna130|rna130 417 -EELGEFRWIVYKGVV----DDNIEYLLEKYRKGETPGARREVMSGFSGIKRDENFELIVKTL---PRLNVEDIGVVIAI 488
                                    .57789*********9....778********88777788999999998888888888777777...56788999999999 PP

                                    H.HSTTHHHHHHHHHHHCHCCHHHHTSSTSCHHHHHHHHHTT--SHHHHHHHHHHHCHTT--GGGHHHHHHHHHHH CS
                        ERAP1_C 239 lannpegrellwefvkenwdalakrwsggeildrivkgllpgftseeelaeieaffadkdtpglrrtlkqaletvr 314
                                    + +  + r+ + e+v e+ ++l+++  ++ +l +i+ ++l   + ++ ++++  f++  +++g++ ++++ ++ ++
  gene130|gene130|rna130|rna130 489 ICRGGRFRDKMVEYVVEHGAELYSMVHKNVMLYNIIIMSLRYVSRDSMVEKVVGFLDGIKHSGSNLSIEKVRDEIE 564
                                    966699999999*************9986799************************99999**********99985 PP

>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.3e-05      0.37      80      98 ..      37      55 ..      29      61 .. 0.89
   2 ?   -3.6   0.0       1.7     1e+04     118     143 ..     539     564 ..     532     574 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.3e-05
                            WLM 80 yesimgtllHELaHnvygp 98
                                    ++i +t +HEL H+++g+
  gene130|gene130|rna130|rna130 37 KKNIAETVCHELGHMWFGN 55
                                   579**************95 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                            WLM 118 kakGlkegflkeGkrlggkevrnksa 143
                                    k+ G+ +g +++G +l+ ++vr++ +
  gene130|gene130|rna130|rna130 539 KVVGFLDGIKHSGSNLSIEKVRDEIE 564
                                    45688899999999999999887644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3915.59
//
Query:       gene1301|gene1301|rna1300|rna1300  [L=378]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        0.3    9.8   2.5       0.42    9.3   2.5    1.2  1  Presenilin  Presenilin
       0.39   11.2   8.9       0.72   10.3   8.9    1.4  1  DUF4692     Regulator of human erythroid cell expansion (RHEX


Domain annotation for each model (and alignments):
>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.5   4.6e-05      0.42     249     332 ..     257     359 ..     216     360 .. 0.35

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 4.6e-05
                         Presenilin 249 sesskeeeseeesseksaqsseseeeseeesseaessaeesseekeseessesseeeeeeeeeeeeses....... 317
                                           s+++++ +++  ks++++es+++++++++++++++++s+e+++                   +se+       
  gene1301|gene1301|rna1300|rna1300 257 CVPSSQSTKGSSKVVKSNKNTESDKDTQRAQKRDSEDSSSSQESSS-------------------SSEKggkplym 313
                                        1111111111111111111111111111111111111111111111...................11112223333 PP

                         Presenilin 318 ...............................eergvkLGLGDFiFY 332
                                                                       e++  +L +GD + Y
  gene1301|gene1301|rna1300|rna1300 314 lksarlgrkrpkkresfidcylrgnpsectaENSEGRLDIGDAVIY 359
                                        3333344444444555666666666666665555667777776666 PP

>> DUF4692  Regulator of human erythroid cell expansion (RHEX)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.9     8e-05      0.72      44      94 ..     255     306 ..     228     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8e-05
                            DUF4692  44 lqa..pepspahksppaakelketraerstsvsepryrhdsdtssdssdssds 94 
                                        + a  p++++++ s+ ++k+ k+t+++++t+  + r ++ds +s +ss ss++
  gene1301|gene1301|rna1300|rna1300 255 T-AcvPSSQSTKGSSKVVKSNKNTESDKDTQRAQKRDSEDSSSSQESSSSSEK 306
                                        2.2359999999999***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1496  (0.0834402); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2644.85
//
Query:       gene1302|gene1302|rna1301|rna1301  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-48  164.1   0.0    1.6e-47  162.1   0.0    1.9  1  Pkinase         Protein kinase domain
    7.5e-19   68.0   0.0    3.1e-14   52.9   0.0    2.1  2  Pkinase_Tyr     Protein tyrosine kinase
    9.5e-06   25.7   0.0    0.00011   22.2   0.0    2.1  2  APH             Phosphotransferase enzyme family
      5e-05   22.8   0.0        2.1    7.6   0.0    3.1  3  Kinase-like     Kinase-like
    0.00055   18.8   0.0    0.00072   18.4   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase
     0.0027   17.3   0.1     0.0041   16.7   0.1    1.2  1  Choline_kinase  Choline/ethanolamine kinase
     0.0088   15.4   0.1      0.014   14.7   0.1    1.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.0   6.1e-51   1.6e-47       1     264 []       4     324 ..       4     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 6.1e-51
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyevfeekdelyl 75 
                                        y+ +ek+GeGsf++Vyka+++e+g+ vA+K i + +       ++l+E+ +lk l+  +n + l++vf+++d+++ 
  gene1302|gene1302|rna1301|rna1301   4 YTPIEKIGEGSFSVVYKALDAESGRYVALKAITRTSSP----ARILEELMFLKALEgKRNCMGLLGVFRNEDQVVA 75 
                                        67789***************************988655....4799**********9******************* PP

                                        EEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTEEEE-SGTTSEESSS CS
                            Pkinase  76 vleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekgelKitDFGlakeles 150
                                        v+ y +  ++ +++++      +++k++++++l +++++Hs+giiHrDlKp N+L++ e g  +++DFGla+  + 
  gene1302|gene1302|rna1301|rna1301  76 VFPYFKPVDFREFISN---AGLADIKQYLYNLLVAIDHVHSNGIIHRDLKPGNFLYNkEAGRGMLIDFGLAQYEDC 148
                                        **************95...7889**********************************88899*********98777 PP

                                        SCS.....................................BCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHH CS
                            Pkinase 151 ssk.....................................ltsfvgtseYlAPEvl.keneyskkvDvWslGvily 188
                                        +++                                     +  + gt+ ++APEvl ++++ ++++D+Ws+Gvi++
  gene1302|gene1302|rna1301|rna1301 149 KEDqarddssksstpllffnsivskakppgyyerdgrpqmKAPRAGTRGFRAPEVLfRHQRQTRAIDMWSIGVIFL 224
                                        6668899*******************************9888899***********999999************** PP

                                        HHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT......SHH...HHHTTS......................... CS
                            Pkinase 189 elltgkppfsgekgkekvekeldqlekilkilg......etkeklpeasei......................... 233
                                        ++lt + pf  +++      ++d +++i+ i+g        +        +                         
  gene1302|gene1302|rna1301|rna1301 225 TILTAQYPFFYSSD------DVDSIVEIATIFGhaemrkAAR--------Fygrlwrsnidtipeeripferives 286
                                        *********95555......4555555566665321111111........12234555567778888899999999 PP

                                        .......-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 234 .......seeakdllkkllkkdpkkRltaeellqhpyl 264
                                                 e  dll ++l+   ++R+ta+++l+hp++
  gene1302|gene1302|rna1301|rna1301 287 lnpwaevGAEGYDLLYRMLDLCSSSRITASDALSHPFF 324
                                        9999999******************************8 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   1.2e-17   3.1e-14       5     166 ..       8     159 ..       5     171 .. 0.87
   2 !   13.2   0.0   1.5e-05      0.04     171     259 .]     198     287 ..     179     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.2e-17
                                        EEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEEEE CS
                        Pkinase_Tyr   5 kklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl.khpnivkllgvctkeeplliv 79 
                                        +k+GeG+f+ V+++       ++   Va+K ++++++    +++lee+ ++k+l  ++n + llgv  +e++++ v
  gene1302|gene1302|rna1301|rna1301   8 EKIGEGSFSVVYKALDA----ESGRYVALKAITRTSS---PARILEELMFLKALeGKRNCMGLLGVFRNEDQVVAV 76 
                                        89************988....88999******55554...469***********999******************* PP

                                        EE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETT.EEEE-STTTHEETT CS
                        Pkinase_Tyr  80 teyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenk.vvkisDfGLardie 154
                                        + y k  d+++f+ +       l d+ ++ +++  ++++++s+ ++Hrdl   N L +++     + DfGLa+   
  gene1302|gene1302|rna1301|rna1301  77 FPYFKPVDFREFISNA-----GLADIKQYLYNLLVAIDHVHSNGIIHRDLKPGNFLYNKEAgRGMLIDFGLAQYED 147
                                        *************998.....8999999*****************************9865488999*****9985 PP

                                        TSSEEEETTSST CS
                        Pkinase_Tyr 155 kddeyvkkeeak 166
                                         ++++ +++++k
  gene1302|gene1302|rna1301|rna1301 148 CKEDQARDDSSK 159
                                        555554444433 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.5e-05
                                        GS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGT.TTTSHHHHHHHHHHTTEES-BBTTSBHHHHHHHHHHT-S CS
                        Pkinase_Tyr 171 WmapEslkekk.ftsksDvWsfGvllwEiftlgesp.ypglkneevleklkegkrlekpekcpeelyelmkkcwee 244
                                        + apE+l++++  t + D+Ws Gv+   i+t ++ p + + ++ + +  + +    ++ +k+ +   +l ++  ++
  gene1302|gene1302|rna1301|rna1301 198 FRAPEVLFRHQrQTRAIDMWSIGVIFLTILT-AQYPfFYSSDDVDSIVEIATIFGHAEMRKAARFYGRLWRSNIDT 272
                                        78****98776478889**************.55551445577777777777777788888888888999999999 PP

                                        SGGGS--HHHHHHHH CS
                        Pkinase_Tyr 245 dpeeRptfselvekl 259
                                         peeR  f+++ve l
  gene1302|gene1302|rna1301|rna1301 273 IPEERIPFERIVESL 287
                                        999999999999876 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.097   2.5e+02       6      50 ..      11      57 ..       7     113 .. 0.67
   2 !   22.2   0.0   4.4e-08   0.00011     159     200 ..     110     147 ..     101     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.097
                                       --.SSCEEEEEEETT.--EE.EEEE-TTS-HHHHHHHHHHHHHHHHT CS
                                APH  6 sggasnrtylvttpa.gryv.lrrnpparaaeeirrevallrlLaka 50
                                       + g  + +y+  +++ gryv l+ +    ++++i +e+ +l++L++ 
  gene1302|gene1302|rna1301|rna1301 11 GEGSFSVVYKALDAEsGRYVaLKAITRTSSPARILEELMFLKALEGK 57
                                       55555558888888889999888888888999********9999965 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 4.4e-08
                                        H--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEE CS
                                APH 159 llpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgp 200
                                        +++   + +++H+Dl+pgN+l +++ gr   +iDf++a + +
  gene1302|gene1302|rna1301|rna1301 110 HVH---SNGIIHRDLKPGNFLYNKEAGRG-MLIDFGLAQYED 147
                                        556...689**************555554.5*******9976 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0031       7.9      18      53 ..       8      43 ..       1      55 [. 0.87
   2 !    7.6   0.0   0.00084       2.1     154     189 ..     105     141 ..      84     151 .. 0.80
   3 !    5.9   0.0    0.0026       6.7     207     251 ..     198     234 ..     183     256 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0031
                        Kinase-like 18 ellkkgdrsvvfevkdqetgeplavkvfllpseask 53
                                       e +++g +svv+++ d e g ++a+k  + +s +++
  gene1302|gene1302|rna1301|rna1301  8 EKIGEGSFSVVYKALDAESGRYVALKAITRTSSPAR 43
                                       668999************************999987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00084
                        Kinase-like 154 irlaanLqakglvhgkftvdnllldek.gglmlggft 189
                                        +  + + +++g++h ++++ n+l++++ g+ ml +f+
  gene1302|gene1302|rna1301|rna1301 105 LVAIDHVHSNGIIHRDLKPGNFLYNKEaGRGMLIDFG 141
                                        4456799*****************7652777888885 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0026
                        Kinase-like 207 faPpEllgsrggytrknktkmthkldaWqlGlviyriwclklPlt 251
                                        f  pE+l +        + + t ++d W +G+  + i  ++ P+ 
  gene1302|gene1302|rna1301|rna1301 198 FRAPEVLFR--------HQRQTRAIDMWSIGVIFLTILTAQYPFF 234
                                        555555444........3356889****************99985 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.8e-07   0.00072     323     392 ..     112     208 ..      98     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.8e-07
                     Pkinase_fungal 323 flkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgare......................... 373
                                        +   gi+HrD   +N l +    ++  +g+LiD+ la  ++ ++ ++   +                         
  gene1302|gene1302|rna1301|rna1301 112 H-SNGIIHRDLKPGNFLYN----KEAGRGMLIDFGLAQYEDCKEDQAR--Ddssksstpllffnsivskakppgyy 180
                                        4.78*************99....55789*********98886444443..22466788999999999999999999 PP

                     Pkinase_fungal 374 ...........rtGTleFmaievlkgeeHs 392
                                                   r GT+ F a evl    H+
  gene1302|gene1302|rna1301|rna1301 181 erdgrpqmkapRAGTRGFRAPEVLF--RHQ 208
                                        99999999999*******9999997..444 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.6e-06    0.0041     127     179 ..      97     148 ..      79     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                                        HHHHHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEH CS
                     Choline_kinase 127 lekelekleklleelespvvfcHnDlqegNillnkeekklvlIDFEYagynyr 179
                                        +++ l +l   +++ +s+    H Dl +gN+l+nke ++ +lIDF  a+y  +
  gene1302|gene1302|rna1301|rna1301  97 IKQYLYNLLVAIDHVHSN-GIIHRDLKPGNFLYNKEAGRGMLIDFGLAQYEDC 148
                                        444444444444333333.345***********************99999766 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   5.7e-06     0.014     129     173 ..     106     147 ..      96     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                                Kdo 129 rliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrl 173
                                         +i   h+ g+ H+dl + n+l ++e+    + +liD+  a+   
  gene1302|gene1302|rna1301|rna1301 106 VAIDHVHSNGIIHRDLKPGNFLYNKEA---GRGMLIDFGLAQYED 147
                                        57999******************9998...89******8877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1910.05
//
Query:       gene1303|gene1303|rna1302|rna1302  [L=398]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-46  158.4   0.0    2.6e-46  157.3   0.0    1.6  1  AAA              ATPase family associated with various cellul
    7.3e-10   38.6   0.2    2.5e-09   37.0   0.0    2.0  2  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    8.5e-09   35.1   0.1    1.7e-08   34.1   0.1    1.5  1  AAA_lid_3        AAA+ lid domain
      4e-08   33.3   0.1    1.1e-07   31.9   0.1    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
      6e-08   33.0   0.1    1.7e-07   31.5   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
      4e-07   30.6   0.0    4.5e-05   23.9   0.0    2.4  2  AAA_16           AAA ATPase domain
    9.1e-06   25.7   0.3     0.0003   20.8   0.0    2.6  3  NTPase_1         NTPase
    3.6e-05   24.1   1.2     0.0047   17.2   1.2    2.4  1  AAA_22           AAA domain
    6.9e-05   23.4   0.0    0.00015   22.3   0.0    1.6  1  AAA_18           AAA domain
    7.8e-05   22.0   0.0    0.00014   21.2   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
    0.00012   21.9   0.0    0.00029   20.6   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00043   20.3   0.0    0.00072   19.6   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.001   18.9   0.0     0.0036   17.0   0.0    2.0  1  AAA_30           AAA domain
     0.0013   18.8   0.0     0.0023   18.0   0.0    1.4  1  AAA_14           AAA domain
     0.0017   18.7   0.0     0.0034   17.7   0.0    1.5  1  RNA_helicase     RNA helicase
     0.0025   18.1   0.0     0.0044   17.3   0.0    1.5  1  AAA_28           AAA domain
     0.0031   16.8   0.0       0.01   15.1   0.0    1.9  2  TIP49            TIP49 P-loop domain
     0.0034   16.8   0.2       0.17   11.3   0.0    2.7  3  TniB             Bacterial TniB protein
     0.0038   16.7   0.3      0.021   14.2   0.1    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0038   17.0   0.0      0.007   16.1   0.0    1.5  1  AAA_24           AAA domain
     0.0039   16.9   1.2      0.066   12.9   0.0    3.1  3  Sigma54_activat  Sigma-54 interaction domain
     0.0053   16.3   0.1      0.015   14.8   0.1    1.7  1  AAA_7            P-loop containing dynein motor region
     0.0074   16.5   0.0      0.015   15.5   0.0    1.6  1  AAA_33           AAA domain
     0.0088   16.0   0.2       0.21   11.4   0.0    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.037   13.8   0.0    1.9  2  IstB_IS21        IstB-like ATP binding protein
      0.016   15.1   0.1      0.091   12.7   0.0    2.1  2  NACHT            NACHT domain
      0.017   15.0   0.0      0.052   13.4   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
      0.027   14.8   0.1      0.076   13.3   0.1    1.7  1  AAA_19           AAA domain
      0.045   13.3   0.9       0.35   10.4   0.9    2.1  1  AAA_25           AAA domain
      0.047   14.2   0.0       0.13   12.7   0.0    1.8  1  ABC_tran         ABC transporter
      0.048   13.4   0.2       0.09   12.5   0.0    1.6  1  AAA_11           AAA domain
      0.065   13.1   0.0       0.12   12.2   0.0    1.5  1  Bac_DnaA         Bacterial dnaA  protein
      0.073   12.4   0.7        1.5    8.1   0.1    2.3  2  ATPase           KaiC


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.3   0.0   4.7e-49   2.6e-46       1     132 []     182     315 ..     182     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 4.7e-49
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.. CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.. 74 
                                        vllyGppGtGKT+l+kava++++++f++++gse+++ky+ge+++ +r++f+ a+eka psi+fiDE+d++a++r  
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTKATFIKVNGSEFVQKYLGEGPRMVRDVFRLAREKA-PSIVFIDEVDSIATKRfd 256
                                        79******************************************************9.*****************9 PP

                                        .TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                                AAA  75 .sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                         s+s+++e +rv+ +Ll+++dg+++  ++v vi+atnr d++dpallr gR+drkie++l
  gene1303|gene1303|rna1302|rna1302 257 aSTSADREVQRVLIELLNQMDGFDQT-ANVKVIMATNRADTIDPALLRpGRLDRKIEFPL 315
                                        9999999******************6.66****************************985 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   4.6e-12   2.5e-09       3      57 .]      71     124 ..      69     124 .. 0.95
   2 ?   -1.9   0.0       6.1   3.3e+03      28      41 ..     293     306 ..     289     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 4.6e-12
                                        EEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                     Prot_ATP_ID_OB   3 tVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                        +  E +d    aiV ++++ ++vv++ + v+re Lrp+++Va+++++ +i+++LP
  gene1303|gene1303|rna1302|rna1302  71 QFLEPIDN-STAIVGSTAGSNFVVRILSTVDRELLRPNTTVALHRHSSAIVDVLP 124
                                        66788999.9********************************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6.1
                                        E-GGGSSST--TTE CS
                     Prot_ATP_ID_OB  28 lagavpremLrpgD 41 
                                        +a+ ++++ Lrpg 
  gene1303|gene1303|rna1302|rna1302 293 RADTIDPALLRPGR 306
                                        788999999***96 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   3.1e-11   1.7e-08       2      45 .]     338     381 ..     337     381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.1e-11
                          AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                        vd++ L+ r e  S AD+ ++c+eA++lA+r ++  +t++dfee
  gene1303|gene1303|rna1302|rna1302 338 VDIESLVCRPERISCADINSICQEAGMLAVRASRYMVTQKDFEE 381
                                        9*****************************************97 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   2.1e-10   1.1e-07       1     136 [.     181     303 ..     181     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.1e-10
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEv 74 
                                        +vlL GppGtgK++l++ +a  +++++  v+++++ ++    g+r +           + r ar   ++i+++DEv
  gene1303|gene1303|rna1302|rna1302 181 GVLLYGPPGTGKTMLVKAVANHTKATFIKVNGSEFVQKYLGEGPRMV---------RDVFRLARekAPSIVFIDEV 247
                                        59*****************************9998888877788777.........6666677756889******* PP

                                        GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                              AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                        + + ++ +++  s   e ++ l e+ ++++     ++ ++ vi+++n++d     ++pal++
  gene1303|gene1303|rna1302|rna1302 248 DSIATKRFDASTSADREVQRVLIELLNQMDGFD--QTANVKVIMATNRAD----TIDPALLR 303
                                        ********9999998888888888877776544..3455***********....88888875 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   3.2e-10   1.7e-07       6     105 ..     182     275 ..     177     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.2e-10
                                        EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                              AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        +ll gp g+Gkt+l ka+a++ ++    ++i ++ se+ +    + l +     ++    a e+   iv++DE+d 
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTKA----TFIKVNGSEFVQ----KYLGEGPRMVRDVFRLAREKApsIVFIDEVDS 249
                                        6899******************96....************....99999999999999999999899********* PP

                                        -------------HHHHHHHHHHHH- CS
                              AAA_2  80 ihpkessgadvSregVqrdLLqileg 105
                                        i+ k+   +     +Vqr+L  +l +
  gene1303|gene1303|rna1302|rna1302 250 IATKRFDASTSADREVQRVLIELLNQ 275
                                        ***74444444567999999999865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   8.2e-08   4.5e-05      14      59 ..     169     211 ..     160     223 .. 0.76
   2 ?    4.1   0.0       0.1        55     126     156 ..     230     270 ..     224     288 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.2e-08
                             AAA_16  14 salervrsgrpelvllsGesGvGKsslvrellralekdggiflrgk 59 
                                        ++++++  + p+ vll+G++G+GK+ lv++++++ +++   f++ +
  gene1303|gene1303|rna1302|rna1302 169 DLYRQIGIDPPQGVLLYGPPGTGKTMLVKAVANHTKAT---FIKVN 211
                                        566666666679********************866655...55444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                             AAA_16 126 llallsrderplvlvlDdlq...........wadeaslqlla 156
                                         ++l+++ + p ++++D+++            ad + + +l 
  gene1303|gene1303|rna1302|rna1302 230 VFRLARE-KAPSIVFIDEVDsiatkrfdastSADREVQRVLI 270
                                        4467777.778*********8888866665555555555533 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.2   2.3e+03      84     119 ..     129     162 ..      89     169 .. 0.59
   2 !   20.8   0.0   5.5e-07    0.0003       2      93 ..     182     277 ..     181     288 .. 0.79
   3 ?    1.8   0.0      0.38     2e+02      65      93 ..     363     391 ..     352     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.2
                                        HHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHH CS
                           NTPase_1  84 lalealrkalseadviviDEiGkmElkskkfkeave 119
                                         +++++ +  +++dv   D +G + ++ ++++e+ve
  gene1303|gene1303|rna1302|rna1302 129 STIPVMGE-EEKPDVTYAD-VGGLDVQKQEIRETVE 162
                                        34566655.3777887777.8888888888888876 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 5.5e-07
                                        EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE CS
                           NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasgeegiLarveakreprvgkyvv 76 
                                        v++ GppG+GKt lvk v++  k   +kv+G   ++++  +g r+  ++  la ++   +   ++  ++  +++  
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTKATFIKVNGSeFVQKYLGEGPRMVRDVFRLAREKAPSIVFIDEVDSIATKRFDA 257
                                        6788***************************74689999*************999999999888777777777766 PP

                                        -HHH...HHHHHHHHHHHHH CS
                           NTPase_1  77 dves...feelalealrkal 93 
                                         + +   ++++ +e l++++
  gene1303|gene1303|rna1302|rna1302 258 STSAdreVQRVLIELLNQMD 277
                                        65443347777777777665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.38
                                        ---SSEETTEEE-HHHHHHHHHHHHHHHH CS
                           NTPase_1  65 akreprvgkyvvdvesfeelalealrkal 93 
                                        +   +r ++y+v+ ++fee  ++++++++
  gene1303|gene1303|rna1302|rna1302 363 GMLAVRASRYMVTQKDFEEAYSKVVERSD 391
                                        55678999**************9999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.2   8.6e-06    0.0047       8      47 ..     182     212 ..     177     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.6e-06
                             AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtl 47 
                                        ++++G++GtGKT+l++ +++           ++++++v+ 
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHT---------KATFIKVNG 212
                                        689*****************98.........666665554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.7e-07   0.00015       1      83 [.     182     293 ..     182     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.7e-07
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......alde 48 
                                        +ll G+pG+GKt l k+++++++                      ++ +  +a+e+ +++ + +e        +d 
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTKAtfikvngsefvqkylgegprmVRDVFRLAREKAPSIVFIDEvdsiatkRFDA 257
                                        799******************84458999999999**********999**************999*****999999 PP

                             AAA_18  49 skrldedkldklldaleenss.aleegknlvidghl 83 
                                        s  +d++++ +l+++l++ +  +++ +  +++   +
  gene1303|gene1303|rna1302|rna1302 258 STSADREVQRVLIELLNQMDGfDQTANVKVIMATNR 293
                                        9999****9999999999988855555555555444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.5e-07   0.00014      51     116 ..     177     247 ..     129     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.5e-07
                             DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrl..ievekedlkelpklvellr...erperfilfvDDL 116
                                         p + vLL+G  GtGK  lvka+ n+++++ +++   e  ++ l e p++v+ +    +++   i+f+D +
  gene1303|gene1303|rna1302|rna1302 177 DPPQGVLLYGPPGTGKTMLVKAVANHTKATFIKVngSEFVQKYLGEGPRMVRDVFrlaREKAPSIVFIDEV 247
                                        57789*************************98874358889999999999987642226677789999976 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.3e-07   0.00029      33      97 ..     179     251 ..     151     266 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.3e-07
                             RuvB_N  33 ldhvllyGpPGlGkttlakiiakelgvkl.kitsgPvleka.gd...laal...ltnleekdvlfideihrls 97 
                                           vllyGpPG Gkt l k +a+  ++++ k+  +  ++k  g+   ++     l++ ++  ++fide+  ++
  gene1303|gene1303|rna1302|rna1302 179 PQGVLLYGPPGTGKTMLVKAVANHTKATFiKVNGSEFVQKYlGEgprMVRDvfrLAREKAPSIVFIDEVDSIA 251
                                        3469********************9988615555555655322211122220112333455788888887665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-06   0.00072      19      81 ..     179     239 ..     155     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-06
                                        TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEEE..SSEEEEE-TT-SSTHHHH CS
                               TsaE  19 gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYelekeglyHfDlYRledeeele 81 
                                         + +lL+G+ G+GKT+lv+++a++ + + +k      v++Y  e    +  D++Rl++e+   
  gene1303|gene1303|rna1302|rna1302 179 PQGVLLYGPPGTGKTMLVKAVANHTKATFIKVNGSEFVQKYLGEGP-RMVRDVFRLAREKA-P 239
                                        3459*********************99955555566699**66444.55589***965433.2 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.7e-06    0.0036       6      46 ..     167     207 ..     163     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.7e-06
                             AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaag 46 
                                        Q+++ +++  ++ + ++l Gp+GtGKt+++ka++++ +a  
  gene1303|gene1303|rna1302|rna1302 167 QSDLYRQIGIDPPQGVLLYGPPGTGKTMLVKAVANHTKATF 207
                                        8888899999999999*****************99988765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.2e-06    0.0023       5      77 ..     182     263 ..     179     291 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.2e-06
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev.... 76 
                                        +++ G+  +GKT+l+k ++++       ++ +n  +  +k l +  ++ + ++++++e+  +++f+DE+  +    
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTK---ATFIKVNGSEFVQKYLGEGPRMVRDVFRLAREKAPSIVFIDEVDSIatkr 254
                                        6899**************97777...999999998876665554334555555554555889*******9985555 PP

                             AAA_14  77 ........p 77 
                                                +
  gene1303|gene1303|rna1302|rna1302 255 fdastsadR 263
                                        555544444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.3e-06    0.0034       1      68 [.     182     240 ..     182     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.3e-06
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenps 68 
                                        ++lyGp+g+GK++l+k            ++++ ++++ + ++f+++Y g+   ++ D+ +   e+ ps
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKA---------VANHTKATFIKVNGSEFVQKYLGEGPRMVRDVFRLAREKAPS 240
                                        689**************.........345667788899999999999999999999998887765555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   8.2e-06    0.0044       2      44 ..     182     225 ..     181     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.2e-06
                             AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakged 44 
                                        + + G+++tGKT l++a a++ + + ++  + e++++ l +g +
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHtKATFIKVNGSEFVQKYLGEGPR 225
                                        6799***************9975555565555555555444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.9e-05      0.01      51     147 ..     180     272 ..     150     296 .. 0.78
   2 ?   -1.5   0.0       2.1   1.1e+03     166     207 ..     345     387 ..     310     391 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX-S-EEEEEEEEE CS
                              TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt.evltqalrksigvrikeekevleGevvel 125
                                        ++vLl Gp+gtGkt l  a++++  ++  f++++gse+ +  +     ++ + +r +   r k  + v+  ev ++
  gene1303|gene1303|rna1302|rna1302 180 QGVLLYGPPGTGKTMLVKAVANH--TKATFIKVNGSEFVQKYLGEGpRMVRDVFRLA---REKAPSIVFIDEVDSI 250
                                        689*****************997..5689********98887766514555556644...5666777777777777 PP

                                        EE...-SSS-..TTS--EEEEE CS
                              TIP49 126 eveeaenplskekkikevkitl 147
                                         +++++ ++s +++++ v i l
  gene1303|gene1303|rna1302|rna1302 251 ATKRFDASTSADREVQRVLIEL 272
                                        7777777777666666666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                                        HHHHT--TT-EEEEETTT--EE.E-SSS-SS------S----- CS
                              TIP49 166 llkekvkegDviviekesGkvk.klGrsearakefDiekdefv 207
                                        +  e+++  D+  i +e+G +  +  r +  +k+f+   +++v
  gene1303|gene1303|rna1302|rna1302 345 CRPERISCADINSICQEAGMLAvRASRYMVTQKDFEEAYSKVV 387
                                        3468999999999999999875377888888888887777766 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         4   2.2e+03       5      24 ..      16      35 ..      15      44 .. 0.82
   2 !   11.3   0.0   0.00032      0.17      26      61 ..     170     205 ..     162     216 .. 0.81
   3 ?    2.4   0.0      0.17        93     107     151 ..     226     274 ..     217     277 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4
                               TniB  5 iradrwigyprakeilerLe 24
                                       ++ad +++y+++++ l+ Le
  gene1303|gene1303|rna1302|rna1302 16 LKADLFVRYKQMERKLKLLE 35
                                       5789999****999999887 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00032
                               TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlhpp 61 
                                        L++    + ++ +ll+G++ +GKtm+v+  a++ ++
  gene1303|gene1303|rna1302|rna1302 170 LYRQIGIDPPQGVLLYGPPGTGKTMLVKAVANHTKA 205
                                        555566667899****************98877665 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.17
                               TniB 107 leqqvlrllrelkvrvLiiDEihnlla....gsarkqreflnalksLgn 151
                                        + ++v rl re  + ++ iDE++++ +    +s ++ re+  +l  L n
  gene1303|gene1303|rna1302|rna1302 226 MVRDVFRLAREKAPSIVFIDEVDSIATkrfdASTSADREVQRVLIELLN 274
                                        5577889999999***********9862222344555566555555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   3.9e-05     0.021      25      43 ..     182     200 ..     178     207 .. 0.90
   2 ?   -0.6   0.0       1.3   7.2e+02     109     159 ..     241     294 ..     221     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                       Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                        +ll+GppG+GKtml k+++
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVA 200
                                        79************99875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                       Mg_chelatase 109 vLfLDElpefkrkvlevLR.ePledgevtisrakakvef..parfqlvaamNpc 159
                                        ++f+DE+  + +k +++      e ++v i+  ++   f   a++++++a+N +
  gene1303|gene1303|rna1302|rna1302 241 IVFIDEVDSIATKRFDASTsADREVQRVLIELLNQMDGFdqTANVKVIMATNRA 294
                                        788999988888877764414566667766665555444116899999999965 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.3e-05     0.007       5      34 ..     182     213 ..     179     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                             AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekG 34 
                                        +l+yGp+g+GKT+l+k      k+ fi ++++
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVanHTKATFIKVNGS 213
                                        89**************9988788888877763 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.8     1e+03      99     146 ..      59     104 ..      52     114 .. 0.75
   2 !   12.9   0.0   0.00012     0.066      23      63 ..     180     217 ..     166     222 .. 0.82
   3 ?   -0.0   0.1       1.1   6.1e+02     130     143 ..     280     293 ..     235     299 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.8
                                        EETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                    Sigma54_activat  99 LDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                        LD ++++pl +  ++l+ +++     vGs++  ++ vri+++ +++l 
  gene1303|gene1303|rna1302|rna1302  59 LDRVKSVPLIMG-QFLEPIDNS-TAIVGSTAGSNFVVRILSTVDRELL 104
                                        566666666553.456666654.4679*************99999875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                                        S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-T CS
                    Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipe 63 
                                          vl+ G  GtGK++l +a+ +++k   + f++vn +++ +
  gene1303|gene1303|rna1302|rna1302 180 QGVLLYGPPGTGKTMLVKAVANHTK---ATFIKVNGSEFVQ 217
                                        679***************9987665...8899999887655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.1
                                        EEE--EEEEEEESS CS
                    Sigma54_activat 130 eikvdvriiaatne 143
                                         ++++v++i+atn+
  gene1303|gene1303|rna1302|rna1302 280 DQTANVKVIMATNR 293
                                        45678888999886 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   2.8e-05     0.015      34      62 ..     180     208 ..     170     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                              AAA_7  34 kpvllvGptGtGKtviikdllkkldkeky 62 
                                        + vll+Gp GtGKt+++k + ++ + + +
  gene1303|gene1303|rna1302|rna1302 180 QGVLLYGPPGTGKTMLVKAVANHTKATFI 208
                                        569****************9998884433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.8e-05     0.015       2      31 ..     182     211 ..     182     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-05
                             AAA_33   2 vllvGlpGsGKstlaerllkklgavllssd 31 
                                        vll G+pG+GK+ l++ ++++++a+++  +
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTKATFIKVN 211
                                        7899**************988886665543 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0    0.0004      0.21      21      45 ..     180     204 ..     169     222 .. 0.84
   2 ?    2.0   0.1       0.3   1.6e+02     115     150 ..     235     277 ..     207     298 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                           ATPase_2  21 eiyfiYGpegsGKtaLlkeiienle 45 
                                        + +++YGp g GKt L+k +++  +
  gene1303|gene1303|rna1302|rna1302 180 QGVLLYGPPGTGKTMLVKAVANHTK 204
                                        55789**************999875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.3
                           ATPase_2 115 kkgkkiiiiiDelqklidlgln.......gaellvkeLlnlie 150
                                        +++   i++iDe+  +    ++       + + ++ eLln ++
  gene1303|gene1303|rna1302|rna1302 235 REKAPSIVFIDEVDSIATKRFDastsadrEVQRVLIELLNQMD 277
                                        3333367777777777755555555555544444445555444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.9   3.8e+03      17      45 ..      46      74 ..      19      88 .. 0.49
   2 ?   13.8   0.0   6.7e-05     0.037      44      71 ..     176     203 ..     155     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.9
                          IstB_IS21 17 ktledidfraarsldkrkvkeLatlsfie 45
                                       +tl+  + +  ++ld+ k   L+ ++f+e
  gene1303|gene1303|rna1302|rna1302 46 ETLKREERHGREELDRVKSVPLIMGQFLE 74
                                       23333333334445555555555555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.7e-05
                          IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                        i+  ++++l Gp+G+GK+ l  a++ ++
  gene1303|gene1303|rna1302|rna1302 176 IDPPQGVLLYGPPGTGKTMLVKAVANHT 203
                                        666799**************99998765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017     0.091       3      24 ..     182     203 ..     180     216 .. 0.88
   2 ?   -0.7   0.0       2.2   1.2e+03      68     114 ..     226     274 ..     213     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                        EEEEC-TTTCHHHHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqklalaw 24 
                                        v+l G++G GKT+L++ +a   
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHT 203
                                        799*************999765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                                        SS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                              NACHT  68 pvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                         v+ v+ +  e + ++++ +D +D ++t+      +  ++v+++L el++
  gene1303|gene1303|rna1302|rna1302 226 MVRDVFRLAREKAPSIVF-IDEVDSIATKRFDastSADREVQRVLIELLN 274
                                        556666666677777777.5999998885444677777778888878876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.6e-05     0.052       2      30 ..     182     210 ..     181     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.6e-05
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                        vll g PG++kt+lvka+a++ +++f ++
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTKATFIKV 210
                                        7999*******************999877 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00014     0.076      12      36 ..     181     205 ..     175     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                             AAA_19  12 vllvtaGpGtGKTrvlkhivallve 36 
                                         +l+ ++pGtGKT ++k++ ++ ++
  gene1303|gene1303|rna1302|rna1302 181 GVLLYGPPGTGKTMLVKAVANHTKA 205
                                        5899**************9999876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.9   0.00064      0.35      36      56 ..     182     202 ..     178     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00064
                             AAA_25  36 allaGapgtGKttlaldlala 56 
                                        +ll+G+pgtGKt+l+  +a +
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANH 202
                                        69************9777755 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00024      0.13       8      46 ..     176     212 ..     173     301 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00024
                                        EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldg 46 
                                        + + + v + G+ G+GK+ L+k++a+++k t   i+++g
  gene1303|gene1303|rna1302|rna1302 176 IDPPQGVLLYGPPGTGKTMLVKAVANHTKATF--IKVNG 212
                                        55667789*****************9998754..33344 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017      0.09      20      42 ..     182     204 ..     163     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                             AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                        +l+ GPPGtgKT  + ++ ++  
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTK 204
                                        699*********99998888874 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022      0.12      37      78 ..     182     218 ..     176     294 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                                        EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHH CS
                           Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlne 78 
                                        +++yg+ G Gkt L+ka++n++++++ +     +++ eF+++
  gene1303|gene1303|rna1302|rna1302 182 VLLYGPPGTGKTMLVKAVANHTKATFIK-----VNGSEFVQK 218
                                        79*****************998766533.....345555555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0027       1.5      15      37 ..     175     197 ..     168     206 .. 0.84
   2 ?    2.0   0.1       0.2   1.1e+02     113     158 ..     232     283 ..     221     294 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0027
                             ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                        Gi   + vl++G pGtGKt++++
  gene1303|gene1303|rna1302|rna1302 175 GIDPPQGVLLYGPPGTGKTMLVK 197
                                        66666789***********9976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                             ATPase 113 eaikeikakrvviDsitgl.ay.....eekeavaReilrqlvrvlkklgvTa 158
                                        +  +e+  + v iD ++++ ++     ++ + ++ + l +l++++ + ++Ta
  gene1303|gene1303|rna1302|rna1302 232 RLAREKAPSIVFIDEVDSIaTKrfdasTSADREVQRVLIELLNQMDGFDQTA 283
                                        5567777788888888888332111113344456667777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.76u 0.35s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 2283.01
//
Query:       gene1304|gene1304|rna1303|rna1303  [L=253]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.93    9.5   2.9         34    4.6   0.1    2.7  2  LisH      LisH


Domain annotation for each model (and alignments):
>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0019        34       2      17 ..       2      17 ..       2      22 .. 0.90
   2 ?    4.1   0.6    0.0026        47       5      12 ..     165     172 ..     165     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHCT-H CS
                               LisH  2 eLNrLIydYLvkeGye 17
                                       ++N LI+  L+ e y+
  gene1304|gene1304|rna1303|rna1303  2 DINILILSLLMQESYS 17
                                       79**********9996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0026
                                        HHHHHHHH CS
                               LisH   5 rLIydYLv 12 
                                        r+I+dYL+
  gene1304|gene1304|rna1303|rna1303 165 RYILDYLM 172
                                        79*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1706.59
//
Query:       gene1305|gene1305|rna1304|rna1304  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-05   24.8   6.1    1.6e-05   24.8   6.1    1.8  1  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
     0.0046   16.8   5.1     0.0073   16.1   5.1    1.3  1  Mer2            Mer2
      0.008   16.5   0.5        2.8    8.4   0.1    2.4  2  LPP             Lipoprotein leucine-zipper
  ------ inclusion threshold ------
      0.011   14.7   1.5       0.01   14.8   1.5    1.1  1  LMBR1           LMBR1-like membrane protein
      0.011   14.9   7.9      0.013   14.6   7.9    1.2  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
      0.018   15.5   3.3      0.018   15.5   3.3    1.9  2  DUF16           Protein of unknown function DUF16
      0.023   15.0   7.1      0.031   14.6   6.4    1.7  2  TBCA            Tubulin binding cofactor A
      0.026   14.4   6.0      0.034   14.0   6.0    1.4  1  KASH_CCD        Coiled-coil region of CCDC155 or KASH
      0.027   14.7   4.7      0.033   14.3   1.5    2.4  2  JIP_LZII        JNK-interacting protein  leucine zipper II
      0.029   14.5   2.3        4.8    7.4   0.2    2.2  2  COG5            Golgi transport complex subunit 5
      0.033   14.2   8.0      0.076   13.0   8.0    1.7  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
      0.039   14.6   1.1        8.6    7.1   0.5    2.6  2  SlyX            SlyX
      0.043   14.3   1.7      0.073   13.6   1.4    1.5  1  Spectrin        Spectrin repeat
      0.057   12.0   6.0      0.063   11.8   6.0    1.1  1  Macoilin        Macoilin family
      0.077   13.3   5.2       0.14   12.5   5.2    1.7  1  OmpH            Outer membrane protein (OmpH-like)
       0.08   13.2   3.8      0.083   13.2   3.8    1.1  1  zf-C4H2         Zinc finger-containing protein
      0.092   13.3   2.7       0.22   12.2   2.7    1.7  1  ING             Inhibitor of growth proteins N-terminal histo
      0.098   12.9   0.3       0.38   11.0   0.3    2.0  2  DUF948          Bacterial protein of unknown function (DUF948
       0.14   11.5   1.1       0.22   10.8   1.1    1.4  1  DUF4407         Domain of unknown function (DUF4407)
       0.16   12.1   5.6       0.23   11.5   5.6    1.4  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.16   12.7   2.3       0.28   11.9   2.3    1.4  1  DUF2203         Uncharacterized conserved protein (DUF2203)
       0.17   12.1   6.8       0.32   11.2   6.4    1.7  1  ATG16           Autophagy protein 16 (ATG16)
        0.2   11.6   1.5       0.25   11.2   1.5    1.1  1  GvpL_GvpF       Gas vesicle synthesis protein GvpL/GvpF
       0.29   11.3   4.7       0.29   11.3   4.7    1.3  1  CENP-Q          CENP-Q, a CENPA-CAD centromere complex subuni
        0.6   10.5   6.9        3.8    7.9   2.2    2.6  2  Csm1_N          Csm1 N-terminal domain
       0.77    9.4   6.6       0.33   10.6   1.7    2.2  2  GrpE            GrpE
       0.86    8.8   3.4       0.97    8.6   3.4    1.1  1  TMPIT           TMPIT-like protein
       0.88    9.6   7.1       0.13   12.2   2.4    1.9  2  FlxA            FlxA-like protein
       0.92    9.3   5.9        4.7    7.0   1.8    2.5  2  DivIC           Septum formation initiator
        4.6    6.5   9.9        2.9    7.2   6.6    1.8  2  FAM76           FAM76 protein
        4.8    7.6   7.7          3    8.3   0.4    3.3  4  FlaC_arch       Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   6.1   2.7e-08   1.6e-05      13      73 ..       7      67 ..       5      68 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.7e-08
                         TMF_DNA_bd 13 qIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkea 73
                                       +I+ L  E  +Lsk+ +k  + ikkLr+  +e+ + i + ++++++l++ +++l++r +e+
  gene1305|gene1305|rna1304|rna1304  7 KIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEK 67
                                       7999*****************************************************9886 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   5.1   1.3e-05    0.0073      41     127 ..       3      92 ..       2     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.3e-05
                               Mer2  41 dLrEksskLinvlkenskeLlkvisklne...llidlkeeesd.nskekeikdlikdLsvkienqlskvskavldk 112
                                        dL+ k ++L++++++ skeL k  +++++   ++ + ke+ ++  s+++e+   i +L+ +i+++ ++v +  +  
  gene1305|gene1305|rna1304|rna1304   3 DLKVKIDSLTREVRNLSKELQKGYEEIKKlraRTREQKEGIMQrDSRIDELNMCISKLKKRIDEKTKDVGSREKAI 78 
                                        89******************98666555500056566666554157889999999999999999888887665544 PP

                               Mer2 113 lkvkkhksntdtksn 127
                                        ++ +++++++ ++++
  gene1305|gene1305|rna1304|rna1304  79 IN-ESRRKELFNEKV 92 
                                        44.444444444444 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0048       2.8      12      36 ..       4      28 ..       1      41 [. 0.59
   2 ?    6.2   0.0     0.023        14       2      30 ..      50      78 ..      49      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0048
                                LPP 12 LkskvdqlssdvnsakaaaqaakeE 36
                                       Lk k+d+l+ +v ++++++q+ +eE
  gene1305|gene1305|rna1304|rna1304  4 LKVKIDSLTREVRNLSKELQKGYEE 28
                                       5556666666666666666655555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.023
                                LPP  2 ldeLssqVsqLkskvdqlssdvnsakaaa 30
                                       +deL+  +s+Lk+ +d+ ++dv s ++a+
  gene1305|gene1305|rna1304|rna1304 50 IDELNMCISKLKKRIDEKTKDVGSREKAI 78
                                       89**************9999998877765 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.5   1.8e-05      0.01     197     301 ..       3     109 ..       1     159 [. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                              LMBR1 197 dldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks.....nen 267
                                        dl+ ++++l  e+ +l++e+++  +e+++l  + +++++ i + d + + l+++++k  + i ek+k      +  
  gene1305|gene1305|rna1304|rna1304   3 DLKVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDvgsreK-- 76 
                                        566778888888888888888888888888888888888888888788*****************888775431.. PP

                              LMBR1 268 k..teeslaklekqlikalqkrertekqwkrlleka 301
                                        +  +e++ ++l     +++  + r++ +++  le  
  gene1305|gene1305|rna1304|rna1304  77 AiiNESRRKELF---NEKVLGSSRSQGEYYISLEMK 109
                                        122444444443...556666666666666655544 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   7.9   2.2e-05     0.013      34     123 ..       4      90 ..       1     119 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                              Atg14  34 lksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsd 109
                                        lk + +sl +++  + ++ +   +  ++ik+++a+ +e+k  i +  +r+ el++++s+lkk+i+ek k + ++ +
  gene1305|gene1305|rna1304|rna1304   4 LKVKIDSLTREVRNLSKELQ---KGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVGSREK 76 
                                        55555666666653333333...5569999*************************************999988888 PP

                              Atg14 110 klk..kRrsdleslqn 123
                                        ++    Rr++  + ++
  gene1305|gene1305|rna1304|rna1304  77 AIIneSRRKE--LFNE 90 
                                        8763333333..5554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   3.3   3.1e-05     0.018      39     101 ..       4      66 ..       1      69 [. 0.94
   2 ?    6.7   0.3     0.017       9.8      45      81 ..      45      81 ..      41     131 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-05
                                        HHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHH CS
                              DUF16  39 ieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDs 101
                                        ++ k+d+l  ++ +l ++ +k  e+ik+l+++   q+e + + d+ ++ +   + k++kR+D+
  gene1305|gene1305|rna1304|rna1304   4 LKVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDE 66 
                                        567999*******************************************************96 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                                       ...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..... CS
                              DUF16 45 klgeqinkleqkvekqgekikelkveqkaqgeelnkv 81
                                       +++ +i++l+  ++k+ ++i+e ++++  +++++ + 
  gene1305|gene1305|rna1304|rna1304 45 QRDSRIDELNMCISKLKKRIDEKTKDVGSREKAIINE 81
                                       4555666666666666666666666666655554422 PP

>> TBCA  Tubulin binding cofactor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   6.4   5.4e-05     0.031      11      71 ..      11      71 ..       4      91 .. 0.87
   2 ?   -1.5   0.0       5.7   3.3e+03      46      46 ..     107     107 ..      69     147 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.4e-05
                               TBCA 11 lvKEeasYekEleeqearleklkadgdedeydlkkqeevleetkamipdlkkrlekavekL 71
                                       l +E     kEl++  ++++kl+a   e +  + +    ++e ++ i++lkkr+++  ++ 
  gene1305|gene1305|rna1304|rna1304 11 LTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDV 71
                                       556888899***************98777999***********************998875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.7
                               TBCA  46 q 46 
                                        +
  gene1305|gene1305|rna1304|rna1304 107 E 107
                                        2 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   6.0   5.9e-05     0.034      85     162 ..      10      87 ..       1     118 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                           KASH_CCD  85 rlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqi 160
                                        +l  + ++l ke q   ++i++L  + +  +  + +  +++ eL + +++Lkk+++e  + ++++e+++++  ++ 
  gene1305|gene1305|rna1304|rna1304  10 SLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVGSREKAIINESRRK 85 
                                        4555566777777777777777777777777777777788888888888899999888888888888887777766 PP

                           KASH_CCD 161 ee 162
                                        e 
  gene1305|gene1305|rna1304|rna1304  86 EL 87 
                                        55 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.5   5.7e-05     0.033      29      66 ..       2      39 ..       1      43 [. 0.93
   2 ?    0.4   0.1       1.3   7.2e+02      54      65 ..      55      66 ..      46      78 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.7e-05
                           JIP_LZII 29 ddLIarvdeLtsereiLreEleslqkakerlesrikel 66
                                       ddL  ++d Lt e   L++El++  ++ ++l+ r++e 
  gene1305|gene1305|rna1304|rna1304  2 DDLKVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQ 39
                                       79999******************************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                           JIP_LZII 54 kakerlesrike 65
                                       +  ++l++ri e
  gene1305|gene1305|rna1304|rna1304 55 MCISKLKKRIDE 66
                                       222233333222 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0083       4.8      75     109 ..       2      36 ..       1      41 [. 0.91
   2 ?    6.9   0.2     0.012       6.7      78     109 ..      47      78 ..      35      92 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0083
                                        XXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHH CS
                               COG5  75 selksslesLsasyerlkskvlepyeeaeklqsal 109
                                        ++lk +++sL+  ++ l++++ + yee++kl+++ 
  gene1305|gene1305|rna1304|rna1304   2 DDLKVKIDSLTREVRNLSKELQKGYEEIKKLRART 36 
                                        67999*************************99875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                                        XXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHH CS
                               COG5  78 ksslesLsasyerlkskvlepyeeaeklqsal 109
                                        +s++++L++ +++lk+ + e+ +++ ++++a+
  gene1305|gene1305|rna1304|rna1304  47 DSRIDELNMCISKLKKRIDEKTKDVGSREKAI 78 
                                        56666777777777777777766666666554 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   8.0   0.00013     0.076      51     116 ..       5      70 ..       1      91 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                     CENP-F_leu_zip  51 kaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqe 116
                                        k ++ +l  e+++l++el++   ++++lr    e ++ + +  +r++eL+++ s+l++ + ek ++
  gene1305|gene1305|rna1304|rna1304   5 KVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKD 70 
                                        566777778888888888888888888887777777888888899***************999877 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5     0.015       8.6      19      49 ..       8      38 ..       1      48 [. 0.47
   2 ?    5.9   0.1     0.034        19      15      40 ..      46      71 ..      38      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XX CS
                               SlyX 19 ieeLndvvaeqqqqidrlqrqlrllaerlke 49
                                       i++L ++v +  +++++  +++++l+ r +e
  gene1305|gene1305|rna1304|rna1304  8 IDSLTREVRNLSKELQKGYEEIKKLRARTRE 38
                                       3444444444444444444444444444443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               SlyX 15 qedtieeLndvvaeqqqqidrlqrql 40
                                        +  i+eLn  + +  ++id+ ++ +
  gene1305|gene1305|rna1304|rna1304 46 RDSRIDELNMCISKLKKRIDEKTKDV 71
                                       56678899999998888888877665 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.4   0.00013     0.073      25      85 ..      18      78 ..       1      87 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                                       CCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHH CS
                           Spectrin 25 ssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleel 85
                                        s++l k +ee+++l  + ++ ++ + +++ r+++ln   +kl ++ +++++++ +r +++
  gene1305|gene1305|rna1304|rna1304 18 LSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVGSREKAI 78
                                       589999*************************************999999999999998876 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.0   0.00011     0.063     421     503 ..       3      92 ..       1     132 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                           Macoilin 421 elrskissltseerslkselqqlkkendllqtklhelvsa.kqkdkq......tlqqlekrLkeekearaslekqL 489
                                        +l+ ki+slt e r+l +elq+  +e  +l+++ +e  +   q+d +       +++l kr++e  +   s ek +
  gene1305|gene1305|rna1304|rna1304   3 DLKVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGiMQRDSRidelnmCISKLKKRIDEKTKDVGSREKAI 78 
                                        89*****************************99987654314444322222225799******************* PP

                           Macoilin 490 aeekkrkkeeeeta 503
                                         +e +rk   +e+ 
  gene1305|gene1305|rna1304|rna1304  79 INESRRKELFNEKV 92 
                                        *****998876654 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.2   0.00024      0.14      22     104 ..       2      81 ..       1     157 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqe.lqkkeqelqqkqqqkaqelqkkqqellkpil 95 
                                        ++l+ k+ +l  e++++ kelqk +ee++    kl +++++++e ++++  ++ + ++    +l+k+  e +k + 
  gene1305|gene1305|rna1304|rna1304   2 DDLKVKIDSLTREVRNLSKELQKGYEEIK----KLrARTREQKEgIMQRDSRIDE-LNMCISKLKKRIDEKTKDVG 72 
                                        56888889999999999999999999996....3323555555588888888888.88777888888888777777 PP

                                        HHHHHHHHH CS
                               OmpH  96 dkinkaike 104
                                         + +++i+e
  gene1305|gene1305|rna1304|rna1304  73 SREKAIINE 81 
                                        766666665 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.8   0.00014     0.083      36     131 ..       4     110 ..       1     171 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                            zf-C4H2  36 ykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrselglekle.d 110
                                         k +++ L++E ++ + eL++  + i++l   ++e +e  +++ +++ +l   ++klk++++e  +++g ++    
  gene1305|gene1305|rna1304|rna1304   4 LKVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVGSREKAiI 79 
                                        5678999************************************************************998744303 PP

                            zf-C4H2 111 leeeeeellkeeifekqklk..........a 131
                                        +e+  +el++e+++ ++ ++           
  gene1305|gene1305|rna1304|rna1304  80 NESRRKELFNEKVLGSSRSQgeyyislemkI 110
                                        4455566777777666655555555555550 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.7   0.00037      0.22       5      77 ..      11      92 ..       8     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00037
                                       HHTSGGGHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHH.....TS..S-HHHHHHHHH.HHHHHHHHHHHHH CS
                                ING  5 yldsvenLPlelqrnltelreiDakvqellkei...dskiekfl.....kngslqknekeeels.riqeelkeaqell 73
                                       ++  v nL +elq+ ++e++++ a+++e+++ i   ds+i+++       ++++++++k+   + +   + ++ +el 
  gene1305|gene1305|rna1304|rna1304 11 LTREVRNLSKELQKGYEEIKKLRARTREQKEGImqrDSRIDELNmciskLKKRIDEKTKDVGSReKAIINESRRKELF 88
                                       67789****************************999999999988888833444444444444342222223445666 PP

                                       HHHH CS
                                ING 74 deKi 77
                                       +eK+
  gene1305|gene1305|rna1304|rna1304 89 NEKV 92
                                       6665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00066      0.38      25      82 ..       5      62 ..       1      69 [. 0.79
   2 ?    2.2   0.0      0.38   2.2e+02      26      49 ..      48      71 ..      42      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00066
                             DUF948 25 kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82
                                       k  +d++++ +++l k++++  +e+++l a ++e  e++ ++  ++d+l   + +l +
  gene1305|gene1305|rna1304|rna1304  5 KVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKK 62
                                       5567899999999999999999999999999999999999999999888666666655 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.38
                             DUF948 26 ktldeaaatieelekqvdpilkev 49
                                       + +de++  i +l+k++d+ +k+v
  gene1305|gene1305|rna1304|rna1304 48 SRIDELNMCISKLKKRIDEKTKDV 71
                                       568888999999999998888776 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1   0.00038      0.22     140     228 ..       6      80 ..       1     107 [. 0.39

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                            DUF4407 140 aqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldatarlaal 215
                                         +i++l +e+++++++l++ ++e +k    t+  + +g++ +       ++ +d+++  + +lk++      ++++
  gene1305|gene1305|rna1304|rna1304   6 VKIDSLTREVRNLSKELQKGYEEIKKLRARTRE-QKEGIMQR-------DSRIDELNMCISKLKKR------IDEK 67 
                                        334444444444444444444444433333221.11222223.......33333333333333333......2222 PP

                            DUF4407 216 raelaeleaerak 228
                                         +   + e+++++
  gene1305|gene1305|rna1304|rna1304  68 TKDVGSREKAIIN 80 
                                        2222222222222 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.6    0.0004      0.23     109     173 ..       5      72 ..       1      92 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                            UPF0242 109 eeelerlkeenqqLqekleaiaedfeelk...leleeqLaekqellqeyqetieeqrsvlekrqdqie 173
                                        + ++  l++e  +L+++l++  e++++l+   +e +e + ++  +++e++  i+++++ ++++ + ++
  gene1305|gene1305|rna1304|rna1304   5 KVKIDSLTREVRNLSKELQKGYEEIKKLRartREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVG 72 
                                        667889999999999999999999998873335778889***********************988766 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.3   0.00048      0.28      14      73 ..       7      68 ..       3      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00048
                            DUF2203 14 llkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelG 73
                                       ++++l++e+r+l kel++ +ee+++ +a++++++   +++ ++++el++ i++l ++i+e  
  gene1305|gene1305|rna1304|rna1304  7 KIDSLTREVRNLSKELQKGYEEIKKLRARTREQKegIMQRDSRIDELNMCISKLKKRIDEKT 68
                                       67889999999999999999999999999887777888999999999999999999988765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   6.4   0.00055      0.32      80     151 ..       5      76 ..       1      89 [. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00055
                              ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                        + k+ +l  e+ +l k+ ++  + +++l +  ++++e ++++++r++el+  +++l+++++++++ +  +ek
  gene1305|gene1305|rna1304|rna1304   5 KVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVGSREK 76 
                                        456666777777777777777777777778888888888888888888888888888777777666543333 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.5   0.00043      0.25     123     197 ..      16      90 ..       4     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                          GvpL_GvpF 123 ealleelleedpelrelreeieaasesgtayllrkrlgqrleealeerreelaeeleeaLaplaeevrerepqde 197
                                        ++l +el +  +e+++lr+++++++e+ ++  +r++   +  ++l++r +e ++++ ++ +++  e+r++e  +e
  gene1305|gene1305|rna1304|rna1304  16 RNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVGSREKAIINESRRKELFNE 90 
                                        67889999******************9999*****************************9999999999988774 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.7   0.00049      0.29      47     115 ..       7      76 ..       1     168 [. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                             CENP-Q  47 slelLeaeiekeeralerdyeaLreLeknakaeare.rke.klkkehvllqesdseelslleassdevlge 115
                                        +++ L +e++ + ++l++ ye++++L + ++ +++   ++  +  e+++   s+ ++++++++++   +++
  gene1305|gene1305|rna1304|rna1304   7 KIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGiMQRdSRIDELNMCI-SKLKKRIDEKTKDVGSREK 76 
                                        6899******************************99755545455566664.4444444444444433333 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.2    0.0067       3.8      33      69 ..       5      41 ..       2      42 .. 0.83
   2 ?    4.4   0.1     0.081        47      38      63 ..      45      70 ..      42      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0067
                             Csm1_N 33 sqkletkdqeiesLkeqlaeleekvkeleerrkkqeE 69
                                       + k+++ ++e+ +L ++l++  e++k+l  r+++q+E
  gene1305|gene1305|rna1304|rna1304  5 KVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKE 41
                                       5577788889999999999999999999999999888 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.081
                             Csm1_N 38 tkdqeiesLkeqlaeleekvkeleer 63
                                       ++d +i +L   + +l+++++e  ++
  gene1305|gene1305|rna1304|rna1304 45 QRDSRIDELNMCISKLKKRIDEKTKD 70
                                       68889999999999999988887665 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.7   0.00056      0.33      16      57 ..       3      44 ..       1      48 [. 0.91
   2 ?    1.1   0.3      0.48   2.8e+02      19      52 ..      48      81 ..      43      93 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                                       CCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHH CS
                               GrpE 16 eleeeleelekevkelkekllrllaefenlrkrtekekeeak 57
                                       +l+ ++++l +ev++l+++l++  +e+++lr rt+++ke + 
  gene1305|gene1305|rna1304|rna1304  3 DLKVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIM 44
                                       678899********************************9765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.48
                                       CCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHH CS
                               GrpE 19 eeleelekevkelkekllrllaefenlrkrteke 52
                                       ++++el+  + +lk++++++ +++   +k   +e
  gene1305|gene1305|rna1304|rna1304 48 SRIDELNMCISKLKKRIDEKTKDVGSREKAIINE 81
                                       4555555555556665555555555444444433 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.4    0.0017      0.97       6      69 ..      10      73 ..       1     117 [. 0.45

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                              TMPIT  6 elekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeve 69
                                       +l++e+++l+++ ++  +++++l +   + ++ i +   r+ el+  ++klkk+++e++++  +
  gene1305|gene1305|rna1304|rna1304 10 SLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKKRIDEKTKDVGS 73
                                       3444444444444444444444444444444444444444444444444444443322222211 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.4   0.00023      0.13      18      85 ..       7      77 ..       2      92 .. 0.74
   2 ?   -1.4   0.2       3.9   2.3e+03      37      49 ..     159     170 ..     154     172 .] 0.52

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                               FlxA 18 qiasLqkQiknlqkqLkelses.deltkeekkkqqqliq..aQIqqlqaQIaqlqqqqaekaqekqqseke 85
                                       +i sL++++ nl+k+L++  e+ ++l +  +++++  +q  + I+ l++ I +l++  +ek+++  ++ek 
  gene1305|gene1305|rna1304|rna1304  7 KIDSLTREVRNLSKELQKGYEEiKKLRARTREQKEGIMQrdSRIDELNMCISKLKKRIDEKTKDVGSREKA 77
                                       79999999999999999988888666666555666666622579999999999999999988887666655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.9
                               FlxA  37 sesdeltkeekkk 49 
                                        s + +++ +ekk+
  gene1305|gene1305|rna1304|rna1304 159 SPN-KQSSQEKKE 170
                                        444.455555554 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.8    0.0082       4.7      21      51 ..       3      33 ..       1      41 [. 0.76
   2 ?    4.8   2.3     0.041        24      14      57 ..      24      64 ..      22      88 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0082
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                              DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdLk 51
                                       +lk +i+ l++e+ +l++e ++  +e+k+L+
  gene1305|gene1305|rna1304|rna1304  3 DLKVKIDSLTREVRNLSKELQKGYEEIKKLR 33
                                       6777888888888888888888888888886 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.041
                                       XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
                              DivIC 14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyi 57
                                       kg+  +k+l++   ++++ + +   +++eL+  +++Lk+   +i
  gene1305|gene1305|rna1304|rna1304 24 KGYEEIKKLRARTREQKEGIMQRDSRIDELNMCISKLKK---RI 64
                                       667777777777777777777777777777777777764...23 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.6    0.0051       2.9     222     297 ..       2      76 ..       1      78 [. 0.89
   2 ?    5.6   5.9     0.015       8.8     220     263 ..      49      93 ..      27     128 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0051
                              FAM76 222 tqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirellkevaelsk 297
                                         +Lk +i sl +++++  +el +   +i +l+a + e+++ ++++ + +  e ++ i+kl+k+i e +k+v +++k
  gene1305|gene1305|rna1304|rna1304   2 DDLKVKIDSLTREVRNLSKELQKGYEEIKKLRARTREQKEGIMQRDS-RIDELNMCISKLKKRIDEKTKDVGSREK 76 
                                        6899999**************9999*********9999999999865.56789999*************9999887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                              FAM76 220 avtqLkeeiaslkkqleqkdqellekdkki.telkaellekekel 263
                                         + +L+  i +lkk++++k +++ +++k i  e + ++l +ek l
  gene1305|gene1305|rna1304|rna1304  49 RIDELNMCISKLKKRIDEKTKDVGSREKAIiNESRRKELFNEKVL 93 
                                        244555555555555555555555555543134444444445544 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.4    0.0052         3       9      40 ..       1      32 [.       1      38 [. 0.83
   2 ?    2.2   0.1      0.42   2.4e+02       1      25 [.      49      66 ..      35      80 .. 0.59
   3 ?   -0.8   0.0       3.7   2.1e+03       8      28 ..     107     127 ..     104     129 .. 0.78
   4 ?   -2.1   0.0       9.2   5.3e+03      26      38 ..     135     147 ..     134     150 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0052
                          FlaC_arch  9 lsklsteletvkkeneelsksveelkenVkdl 40
                                       +++l+++++++ +e  +lsk++++  e++k+l
  gene1305|gene1305|rna1304|rna1304  1 MDDLKVKIDSLTREVRNLSKELQKGYEEIKKL 32
                                       67888899999999999999998888888776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.42
                          FlaC_arch  1 ridelEnklsklsteletvkkenee 25
                                       ridel        + ++ +kk ++e
  gene1305|gene1305|rna1304|rna1304 49 RIDEL-------NMCISKLKKRIDE 66
                                       33333.......3333333333333 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 3.7
                          FlaC_arch   8 klsklsteletvkkeneelsk 28 
                                        +++ l t+le +++ + e+sk
  gene1305|gene1305|rna1304|rna1304 107 EMKILNTRLEIMRRFILEISK 127
                                        577788899999988888887 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 9.2
                          FlaC_arch  26 lsksveelkenVk 38 
                                        + ++++++ en+ 
  gene1305|gene1305|rna1304|rna1304 135 VFDELTKISENFD 147
                                        5577888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1531  (0.0853924); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 980.19
//
Query:       gene1306|gene1306|rna1305|rna1305  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-18   66.9   0.8    2.5e-18   66.3   0.8    1.3  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
    2.8e-15   55.9   0.1    5.6e-15   54.9   0.1    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.8   2.8e-22   2.5e-18       2      70 .]      74     144 ..      73     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 2.8e-22
                                        --SHHHHHHHHHTXSSXXSSTTTSXX..EEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                      Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketv..GtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                        +P+ ++l++ka++++++++k++k++   G++++ +++eIA+i +s+++ +++l +avk++lgt++s+G+kV
  gene1306|gene1306|rna1305|rna1305  74 QPSIATLIIKALKEPPRDRKKEKNILhnGSLKMTEIVEIARIARSSRSYSKTLAGAVKEVLGTCKSIGCKV 144
                                        7***********************8899******************99555*******************9 PP

>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.1   6.2e-19   5.6e-15       4      64 ..      10      68 ..       4      69 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 6.2e-19
                    Ribosomal_L11_N  4 vvkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrs 64
                                        +k++kl+v +G+  p+  l++ +GplGl+ k +++++ kaT d+k l++ V++ + +dr+
  gene1306|gene1306|rna1305|rna1305 10 DTKYIKLQVVGGEL-PGATLAQRVGPLGLSSKVVGEDIRKATTDYKSLKVHVELAI-KDRK 68
                                       589***********.*****************************************.9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1179.61
//
Query:       gene1307|gene1307|rna1306|rna1306  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.012   15.9   0.6      0.078   13.2   0.3    1.9  2  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.036   6.4e+02      65     102 ..      39      79 ..      17      87 .. 0.55
   2 ?   13.2   0.3   4.4e-06     0.078      28      86 ..      85     148 ..      70     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.036
                                        TTSBEEEEETTT...TSGGGCEEEETTTTEEEETTTSEEEE CS
                     Ricin_B_lectin  65 egakvvlakChk...gkgnqrWefdkdgtqirhkksgkCLd 102
                                         +++v++ + ++   ++++  ++++k  t++ + +s++C +
  gene1307|gene1307|rna1306|rna1306  39 GKGSVRMLSTKEnrkMEQQGTFKINKGMTEVSQGESKLCKN 79 
                                        33445555555533233344566666666677777877755 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.4e-06
                                        EEE-TSCCGG.GEEEEE.TTSEEEETT.TTEEEEES...SSSTTSBEEEEETTTTSGGGCEEEE CS
                     Ricin_B_lectin  28 lydChgskgk.Qlwtlt.kdgeirskaqselCldvs...staegakvvlakChkgkgnqrWefd 86 
                                        +  C+gs++   +w+l  +dg +r k +++ Cl++    s + g +++ ++C+ ++++q+++++
  gene1307|gene1307|rna1306|rna1306  85 IDVCTGSDELySKWRLVsEDGGVRFKTENDICLETVedqSVSGGVRLAGRECKLNTKSQLFDLK 148
                                        567999966699999776999****999*****9988544444445555689877779988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1645.11
//
Query:       gene1308|gene1308|rna1307|rna1307  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0014   18.2   0.8     0.0018   17.9   0.8    1.2  1  CDtoxinA        Cytolethal distending toxin A/C domain
     0.0058   16.9   0.2      0.011   16.0   0.2    1.6  1  Ricin_B_lectin  Ricin-type beta-trefoil lectin domain


Domain annotation for each model (and alignments):
>> CDtoxinA  Cytolethal distending toxin A/C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.8     2e-07    0.0018      69     132 ..      76     140 ..      39     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-07
                                        TTEEEEE-.--TT-GGG-EEEEEBTTS-EEEEETTT--EEEE-SS-SS..S-B-EEEE-----EE CS
                           CDtoxinA  69 enGvialkkCdeddketvFsliptttgavqikslssgeCitanflsrl.piaktltlekCdlake 132
                                        + G+ ++ +C +++k+ ++ +i  ++  v +k  +++ Citan  +        l l+kCd+   
  gene1308|gene1308|rna1307|rna1307  76 KYGFSKVMSCINENKNSMWGVIIDSSKFVSFKMNEEEDCITANGPDSAdILGDVLSLNKCDKNSD 140
                                        559999999*********************************99888844677799****76542 PP

>> Ricin_B_lectin  Ricin-type beta-trefoil lectin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.2e-06     0.011      71     127 .]      82     144 ..      37     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-06
                                        EEETTTTSGGGCEEEETTTTEEEETT...TSEEEEESTTSSTTT...BEEEEEE.TSSGGGBE CS
                     Ricin_B_lectin  71 lakChkgkgnqrWefdkdgtqirhkk...sgkCLdvkgasksne...klilkkcdsgsdsQkW 127
                                        +++C ++++n +W +  d++++++ k   ++ C++++g + ++     l l+kcd++sdsQk+
  gene1308|gene1308|rna1307|rna1307  82 VMSCINENKNSMWGVIIDSSKFVSFKmneEEDCITANGPDSADIlgdVLSLNKCDKNSDSQKF 144
                                        678**9999*****888888866555444777******998887998889999********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1158.78
//
Query:       gene1309|gene1309|rna1308|rna1308  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 673.19
//
Query:       gene1310|gene1310|rna1309|rna1309  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-66  223.2  24.7    4.1e-66  222.9  24.7    1.1  1  DUF2463          Protein of unknown function (DUF2463)
  ------ inclusion threshold ------
        6.1    6.4  10.1        2.2    7.8   6.9    1.9  2  Pox_P21          Poxvirus P21 membrane protein


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.9  24.7   4.6e-70   4.1e-66       1     207 [.      35     241 ..      35     243 .. 0.99

  Alignments for each domain:
  == domain 1  score: 222.9 bits;  conditional E-value: 4.6e-70
                            DUF2463   1 fpvlmyfifekdsfeeslllrfitlllpfsysavqyllllhtnwkssnkpesilhkilyyllnllllaFaiisilS 76 
                                        +p+l+y+if++++f+ ++ll+f t+l p+sysav+y+ l+++nw s+ k+  il+++ y+++n+l+ +F+i+si+S
  gene1310|gene1310|rna1309|rna1309  35 LPMLIYYIFKEHEFDGNPLLKFLTVLPPLSYSAVEYFTLFRDNWYSDWKSLTILQRMFYFIFNILFAMFSIVSIFS 110
                                        69************************************************************************** PP

                            DUF2463  77 iialtidkwesdddlliysiilPslvvpltyLlstscnlvpgqisftdtginilidlliLlllivslvllleesey 152
                                         i++++ +w+++d +l  s++lPsl+vpl yLl tsc+l+p+ isf+dtg++i idl+iL+l+ivsl+ll + +e+
  gene1310|gene1310|rna1309|rna1309 111 AIIFPFAEWDDNDGVLANSVFLPSLFVPLPYLLCTSCSLTPELISFIDTGTTICIDLVILSLSIVSLILLSKGPEH 186
                                        **************************************************************************** PP

                            DUF2463 153 llyfaiissiliLvrllkekylpskksslptakwrvaifvliLilavliYvflal 207
                                        ++y+   s+i+iLvr+lke ++ps k  + +++wr++if++i++  v+iYv+++l
  gene1310|gene1310|rna1309|rna1309 187 YIYIPTSSLIFILVRSLKEYIFPSSKYLEYIITWRTLIFIVIFLTNVFIYVSVGL 241
                                        ***************************************************9875 PP

>> Pox_P21  Poxvirus P21 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.32   2.8e+03     145     161 ..      88     104 ..      83     110 .. 0.70
   2 ?    7.8   6.9   0.00024       2.2      88     155 ..     129     198 ..      94     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.32
                            Pox_P21 145 lktisyivLavlfciYv 161
                                        l+++ y +  +lf+++ 
  gene1310|gene1310|rna1309|rna1309  88 LQRMFYFIFNILFAMFS 104
                                        56677788888887764 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00024
                            Pox_P21  88 miaiaslllPlpsLviaYClal.qilnpsn.antvgmsivcvllsivtivvnsvsvsktlktisyivLav 155
                                         +++ sl++Plp L+ + C  + +++ + + ++t+ + +v++ lsiv +++ s    + +++ +  ++++
  gene1310|gene1310|rna1309|rna1309 129 SVFLPSLFVPLPYLLCTSCSLTpELISFIDtGTTICIDLVILSLSIVSLILLSKGPEHYIYIPTSSLIFI 198
                                        57899**************655377777663789999999999****99998444444444433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1711.62
//
Query:       gene131|gene131|rna131|rna131  [L=420]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-24   84.6   7.3    6.8e-24   84.6   7.3    2.8  4  DUF3654   Protein of unknown function (DUF3654)
    4.8e-05   23.0   2.7    4.8e-05   23.0   2.7    2.5  2  DUF1609   Protein of unknown function (DUF1609)
  ------ inclusion threshold ------
       0.47   11.0   5.5        1.6    9.3   2.1    2.6  2  LsmAD     LsmAD domain
       0.98    9.9   5.5       0.36   11.3   0.3    2.4  2  ParB      ParB family


Domain annotation for each model (and alignments):
>> DUF3654  Protein of unknown function (DUF3654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.41   1.8e+03      44      61 ..     168     184 ..     167     187 .. 0.80
   2 !   84.6   7.3   1.5e-27   6.8e-24       6     138 .]     184     311 ..     177     311 .. 0.86
   3 ?   -1.5   0.5      0.58   2.6e+03       7      26 ..     313     333 ..     307     341 .. 0.58
   4 ?   -4.5   0.5         4   1.8e+04       9      21 ..     364     376 ..     362     378 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.41
                        DUF3654  44 kivcdaCkeiwerleedr 61 
                                    ++v ++C +i +  +edr
  gene131|gene131|rna131|rna131 168 EVVKNVCSKIKSL-KEDR 184
                                    688999**99665.9999 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 1.5e-27
                        DUF3654   6 selseeekkkeeevlqkikeygesLctkekqeeiveaqkivcdaCkeiwerleedrksfllelyaeglmlkalkakldee 85 
                                     +++e+ekk+e  vl++i++ygesL+t+ k++ei++aq+ivc++ k+ wer eed++     +  + ++l++l+   ++ 
  gene131|gene131|rna131|rna131 184 RNMNEKEKKEEMMVLEDIRKYGESLQTRWKKDEILKAQEIVCEVFKYFWER-EEDKR-----IITTIMYLRVLSYGGGKI 257
                                    5799***********************************************.99994.....445555556666555443 PP

                        DUF3654  86 eve.epllavvdhelLidahkeykidvvkELvkqvllegkeIddesinkvveev 138
                                    + e  pl+++++h++L++++++y+i  ++ L+kqvl+++++ ++e+ +k+ +ev
  gene131|gene131|rna131|rna131 258 KKEvFPLIHYINHSVLVKTYNRYGIRAAGMLIKQVLIKDNDCNEEYAEKIGKEV 311
                                    33314788**************************************99987765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.58
                        DUF3654   7 elseeekkkeeev.lqkikey 26 
                                    ++++ee++ eee    + ke 
  gene131|gene131|rna131|rna131 313 KMESEERRMEEEKkRMESKES 333
                                    566666665554303445555 PP

  == domain 4  score: -4.5 bits;  conditional E-value: 4
                        DUF3654   9 seeekkkeeevlq 21 
                                     ++ek+ e+++++
  gene131|gene131|rna131|rna131 364 RKKEKRSERRMME 376
                                    5778888888876 PP

>> DUF1609  Protein of unknown function (DUF1609)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   2.7      0.34   1.5e+03       6      43 ..     335     372 ..     328     378 .. 0.68
   2 !   23.0   2.7   1.1e-08   4.8e-05       7      53 ..     374     419 ..     365     420 .] 0.73

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.34
                        DUF1609   6 eeaevssvevgGarkkkkkkkkskgerkrykihkrvlr 43 
                                     e ev     gG+ k+k  ++++kg r   k  kr  r
  gene131|gene131|rna131|rna131 335 CEFEVLEGLEGGSSKRKGGERRRKGRRGVRKKEKRSER 372
                                    45555544467777888889999999988888888766 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.1e-08
                        DUF1609   7 eaevssvevgGarkkkkkkkkskgerkrykihkrvlrWrksaekikk 53 
                                     +e +    +Ga  +k+  + ++g  + y ihkrvlrW+k++ ki+k
  gene131|gene131|rna131|rna131 374 MMEEACSGREGATSSKEPCD-KQGSVHFYNIHKRVLRWKKDPKKIRK 419
                                    34444445678886665555.47899*******************97 PP

>> LsmAD  LsmAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.082   3.7e+02      33      64 ..     165     195 ..     149     197 .. 0.69
   2 ?    9.3   2.1   0.00036       1.6      25      55 ..     299     328 ..     293     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.082
                          LsmAD  33 iArEIess.astnahvaeerglkvddsgldEEd 64 
                                      rE+ ++  s+ + ++e+r++  +++++ EE+
  gene131|gene131|rna131|rna131 165 FGREVVKNvCSKIKSLKEDRNM--NEKEKKEEM 195
                                    5688888855566778888888..555666765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                          LsmAD  25 ereaeAeriArEIessastnahvaeerglkv 55 
                                     +e++Ae+i +E+++ +s++ +++ee+++ +
  gene131|gene131|rna131|rna131 299 CNEEYAEKIGKEVQKMESEERRMEEEKKR-M 328
                                    5799*********************9988.3 PP

>> ParB  ParB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3     8e-05      0.36      30      81 ..     167     221 ..     149     268 .. 0.73
   2 ?   -0.0   0.8      0.26   1.2e+03      29      55 ..     300     326 ..     287     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8e-05
                           ParB  30 seliekvkeeiekvqsdtelaedeqkseil..klikkeskrlkkpkkkdka.vve 81 
                                     e++++v ++i+ +++d + +e e+k+e++  + i+k  ++l++  kkd   +++
  gene131|gene131|rna131|rna131 167 REVVKNVCSKIKSLKEDRNMNEKEKKEEMMvlEDIRKYGESLQTRWKKDEIlKAQ 221
                                    589***********************99762256999999999888887653333 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.26
                           ParB  29 lseliekvkeeiekvqsdtelaedeqk 55 
                                     +e  ek+ +e++k++s++ + e+e+k
  gene131|gene131|rna131|rna131 300 NEEYAEKIGKEVQKMESEERRMEEEKK 326
                                    467889999999998888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1885  (0.105137); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2922.73
//
Query:       gene1311|gene1311|rna1310|rna1310  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-45  154.9  13.5    2.7e-45  154.5  13.5    1.1  1  DUF1686    Protein of unknown function (DUF1686)
  ------ inclusion threshold ------
      0.085   12.9   5.0       0.15   12.1   5.0    1.4  1  HisKA_7TM  N-terminal 7TM region of histidine kinase
      0.092   12.9  10.3        2.2    8.5   0.6    3.2  3  DUF3397    Protein of unknown function (DUF3397)
          3    7.6   9.9         32    4.3   9.9    2.4  1  Bax1-I     Inhibitor of apoptosis-promoting Bax1
        4.4    6.6  16.4        3.5    6.9   3.6    2.2  2  TssN       Type VI secretion system, TssN


Domain annotation for each model (and alignments):
>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5  13.5   7.5e-49   2.7e-45       3     177 ..      95     262 ..      93     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 7.5e-49
                            DUF1686   3 kvswntalyvlavaGtiiyqiwvLakeyrdkgveevlreeWsvvgcmvPmlvgllnagvirssvysvtvagigivm 78 
                                        +  ++ +l++++vaG+i+y++w+L++ey d+g+e+v++++W++vg+m+P+++g+ln+ v     y +++ag+gi+m
  gene1311|gene1311|rna1310|rna1310  95 EMGIDVLLFLVSVAGPIMYGMWILMNEYNDNGIENVIKNNWNIVGSMIPIIIGILNGKV--TRRYRIMMAGLGIIM 168
                                        55677889***************************************************..779************ PP

                            DUF1686  79 lyvQslvkkkmsrrqvcvvvlgnillasaclagdklllpgvedrss.lvcvglvvfaallllvsyveeggkkakae 153
                                        +yvQ+ v++k+ + q+  +++gn+++ s++l   kl+ +g ed ++ ++c+ ++v+a+ l+++++ e   +k++ +
  gene1311|gene1311|rna1310|rna1310 169 IYVQKIVQEKIHKGQLLTLIIGNAVMISVYLI--KLVNEGFEDEYEiVICIVPIVIAIGLIVIDMLE---EKKEGS 239
                                        ********************************..*****998877626799****************...9999** PP

                            DUF1686 154 evgevvksvvlvlsvlvltvvsyv 177
                                        ev++ +k++v+v+s++v+t++ + 
  gene1311|gene1311|rna1310|rna1310 240 EVNSEMKNIVCVMSWIVGTIG-WY 262
                                        *******************99.54 PP

>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   5.0   4.2e-05      0.15      53     205 ..      58     224 ..      48     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                          HisKA_7TM  53 akllwaklqylgivfipvlwllfaleytgk...rrwltrrrlallllvpvltli....lvltnplhh.....lf.. 114
                                          ++  ++ ++  +++ +++l+f+    g    ++++ + + +ll+lv v+  i     +l n+++      ++  
  gene1311|gene1311|rna1310|rna1310  58 INPFNRNFFFILYCLTTLGLLFFSCIVKGSvqsNKKMEMGIDVLLFLVSVAGPImygmWILMNEYNDngienVIkn 133
                                        5667778889999999999999999999963444445555555566666555542222345566544222222333 PP

                          HisKA_7TM 115 .yvsagsfvvlefehGplf.wvhlaysyllliagvvlliralirssglyrrqalllligllvPwlanllyllglsp 188
                                         +  +   +++ +  G+l   v   y +++  +g++++  + i + ++++ q l+l+ig +v + ++l+ l++ ++
  gene1311|gene1311|rna1310|rna1310 134 nW--NIVGSMIPIIIGILNgKVTRRYRIMMAGLGIIMIYVQKIVQEKIHKGQLLTLIIGNAVMISVYLIKLVNEGF 207
                                        33..2223344448899996666666666666666666666667778********************999975444 PP

                          HisKA_7TM 189 lpgidltplafaltgll 205
                                           ++++++ + +  ++
  gene1311|gene1311|rna1310|rna1310 208 EDEYEIVICIVPIVIAI 224
                                        33455444444444333 PP

>> DUF3397  Protein of unknown function (DUF3397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6   0.00062       2.2      60     102 ..      65     107 ..      52     117 .. 0.86
   2 ?    7.0   1.1    0.0018       6.6      48     105 ..     144     199 ..     137     205 .. 0.77
   3 ?    2.9   0.2     0.033   1.2e+02      48      81 ..     202     235 ..     192     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00062
                            DUF3397  60 llllvllllaillliiqarkkgeisykrffklfwRllfLltfl 102
                                        +++++++l ++ ll+++ + kg+++  + + + + +l +l ++
  gene1311|gene1311|rna1310|rna1310  65 FFFILYCLTTLGLLFFSCIVKGSVQSNKKMEMGIDVLLFLVSV 107
                                        489***************************9999988777665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0018
                            DUF3397  48 lseelfgksflpllllvllllaillliiqarkkgeisykrffklfwRllfLltfllYl 105
                                        ++  +++ ++   + +++  l+i+++++q + +++i+ +++++l++  +  +++ +Yl
  gene1311|gene1311|rna1310|rna1310 144 IIIGILNGKVTRRYRIMMAGLGIIMIYVQKIVQEKIHKGQLLTLII--GNAVMISVYL 199
                                        5556667777777889*********************999998874..5555555565 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.033
                            DUF3397  48 lseelfgksflpllllvllllaillliiqarkkg 81 
                                        l++e f+ ++  ++++v +++ai l++i++  ++
  gene1311|gene1311|rna1310|rna1310 202 LVNEGFEDEYEIVICIVPIVIAIGLIVIDMLEEK 235
                                        5788889999999999999999999999988766 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   9.9    0.0089        32       6     183 ..      68     244 ..      61     263 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0089
                             Bax1-I   6 kvYgllalgllltalvaavvlsspaqlflslhivlflvvilaplalvflslsaarlkkkssalalallllftlleG 81 
                                          Y l++lgll+  ++  + ++s++++ +  ++ lflv++ +p++  +++l+ +  +++       ++     + G
  gene1311|gene1311|rna1310|rna1310  68 ILYCLTTLGLLFFSCIVKGSVQSNKKMEMGIDVLLFLVSVAGPIMYGMWILMNE-YNDNGIE--N-VIKNNWNIVG 139
                                        457777777777766666666666677777777777777777777775444442.3222222..1.2222222345 PP

                             Bax1-I  82 lslspillvytgaiilqaflltaaifgglslyalttkrdls..glggflf..agligliiaslvn.lFlpssalel 152
                                         ++ +i+ + +g++  +  ++ a++ +++  +    ++++   +l  +++  a++i + ++ lvn  F      e+
  gene1311|gene1311|rna1310|rna1310 140 SMIPIIIGILNGKVTRRYRIMMAGLGIIMIYVQKIVQEKIHkgQLLTLIIgnAVMISVYLIKLVNeGF--EDEYEI 213
                                        55555555554555444444444444444444222233333214444443667777777777777677..678999 PP

                             Bax1-I 153 aisylgvllfsglilyDtqkiierageygee 183
                                        +i+++ +++  gli++D+   +++  e+++e
  gene1311|gene1311|rna1310|rna1310 214 VICIVPIVIAIGLIVIDMLEEKKEGSEVNSE 244
                                        *****************98777766666555 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.6   0.00097       3.5      56     116 ..      59     123 ..      53     158 .. 0.74
   2 ?    5.8   4.8    0.0022         8       9     107 ..     159     260 ..     154     264 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00097
                               TssN  56 efvpygyillqilylllGilhlylllkkffkelkekkilfeilltliv....illglvlfvlvfn 116
                                        +    +++++  + + lG+l+   ++k   + +k++++++++ll+l++    i++g+++ +  +n
  gene1311|gene1311|rna1310|rna1310  59 NPFNRNFFFILYCLTTLGLLFFSCIVKGSVQSNKKMEMGIDVLLFLVSvagpIMYGMWILMNEYN 123
                                        555678999999********************************999833334677777776665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0022
                               TssN   9 llavilllilsliakknkllkkkkliiyiLlaglvlalpgllgflknefvpygy..illqilylllGilhlylllk 82 
                                        ++++ l++i+++++k  + + +k  ++++++   v+  + l+ +++  f       i ++ +++ +G++ +  +l+
  gene1311|gene1311|rna1310|rna1310 159 IMMAGLGIIMIYVQKIVQEKIHKGQLLTLIIGNAVMISVYLIKLVNEGFEDEYEivICIVPIVIAIGLIVID-MLE 233
                                        566778899999999988888888888888888888888899998888874433004444466778888888.555 PP

                               TssN  83 kffkelkekk..ilfeilltlivillg 107
                                        + ++  + ++    + ++++ iv+ +g
  gene1311|gene1311|rna1310|rna1310 234 EKKEGSEVNSemKNIVCVMSWIVGTIG 260
                                        544444444412333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1613.03
//
Query:       gene1312|gene1312|rna1311|rna1311  [L=263]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-06   27.2   3.5    0.00019   21.0   0.1    2.1  2  DUF1129   Protein of unknown function (DUF1129)
  ------ inclusion threshold ------
      0.033   13.9   0.1      0.033   13.9   0.1    2.8  3  MatE      MatE
       0.16   12.5   5.9       0.12   12.8   0.7    2.6  2  DUF2231   Predicted membrane protein (DUF2231)
        9.3    4.8   8.5        1.2    7.7   0.0    2.6  3  Ndc1_Nup  Nucleoporin protein Ndc1-Nup


Domain annotation for each model (and alignments):
>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   4.3e-08   0.00019      67     168 ..      12     119 ..       2     129 .. 0.71
   2 !    6.9   0.8   0.00085       3.8     111     169 ..     189     248 ..     153     261 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.3e-08
                            DUF1129  67 kkakkesk........enpwlmalDnsLlllalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrll 134
                                        k++ +++k        ++ w    D+ L    +++l++gi+ +f ++  t+   + + ++  +  G +++++++ l
  gene1312|gene1312|rna1311|rna1311  12 KNERQKHKeptdslpkSKSWKDFPDTWLS--LILTLMTGIMVFFRSSFRTKVENIFSQIIGWFNLGRLIYFTAKRL 85 
                                        33333333344566645555555665444..3789***********9999889********************999 PP

                            DUF1129 135 trekkkkkrpplwkrllilllllvvwlvlftlva 168
                                        + + + +k+ +   +++i+ lll +++++f++ +
  gene1312|gene1312|rna1311|rna1311  86 YFRIEGSKKLKGNDVAMIVCLLLHLLMLAFLVCS 119
                                        9887777777777777777777777777776654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00085
                            DUF1129 111 iGlitlllvalvgGlamvlvyrlltre.kkkkkrp.plwkrllilllllvvwlvlftlval 169
                                          l t l++++ +G+++ +v +++  + +  +kr+   ++ ++ ++++l+  +  + ++++
  gene1312|gene1312|rna1311|rna1311 189 KNLWTRLFISIFVGVMLWIVEDWIVDSlN-ISKRNvRKIRNFMKIVVALIYTIGGYCIMNM 248
                                        36888899999999999999999998742.3333213344444444445555555555555 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.4      0.65   2.9e+03     114     130 ..      65      81 ..      37     114 .. 0.52
   2 ?   -0.1   2.3      0.14   6.4e+02      75     129 ..     101     154 ..      90     157 .. 0.68
   3 ?   13.9   0.1   7.3e-06     0.033      76     141 ..     191     256 ..     184     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.65
                               MatE 114 ylrililgipalalqlv 130
                                        + +i++++ ++ +++++
  gene1312|gene1312|rna1311|rna1311  65 FSQIIGWFNLGRLIYFT 81 
                                        34444444444444444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.14
                               MatE  75 glilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalql 129
                                        ++i+ lll l++ ++ l++s++i+  ++ ++  ++l ++ + i + +i++l  ql
  gene1312|gene1312|rna1311|rna1311 101 AMIVCLLLHLLMLAF-LVCSNFIFPGIGIHKMATALERNPIGIFFASIFFLNAQL 154
                                        445555666666666.777888877777777777777777777777777776665 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 7.3e-06
                               MatE  76 lilllllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagkt 141
                                        l++ l++s+++ +++++  ++i+  ++ ++  + +++++++i++  i  ++ +++ + i+  a++t
  gene1312|gene1312|rna1311|rna1311 191 LWTRLFISIFVGVMLWIVEDWIVDSLNISKRNVRKIRNFMKIVVALIYTIGGYCIMNMIFLNASNT 256
                                        78899****************************************************999988887 PP

>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.073   3.3e+02      21      86 ..      46     109 ..      37     121 .. 0.63
   2 ?   12.8   0.7   2.6e-05      0.12      35      89 ..     151     207 ..     117     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.073
                            DUF2231  21 laGlvelllaepsirakktallHavggvlllalivaltvWrfvlrlreeeqvsplylalslvvvvl 86 
                                        ++G++ ++    s r+k   ++  ++g++ l+ ++++t+ r++ r + +++++   +a+ + +++ 
  gene1312|gene1312|rna1311|rna1311  46 MTGIMVFFRS--SFRTKVENIFSQIIGWFNLGRLIYFTAKRLYFRIEGSKKLKGNDVAMIVCLLLH 109
                                        5555444433..555555666667888888888888888888888888877766655554444433 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.6e-05
                            DUF2231  35 rakktallHavggvlllalivaltvW..rfvlrlreeeqvsplylalslvvvvlllv 89 
                                        +a+ ++  H +  vl+++l ++lt+W  + +   ++  +  ++ l++s++v v+l +
  gene1312|gene1312|rna1311|rna1311 151 NAQLVMEPHNTYSVLVVGLEAILTAWdvEGFDYEKDVIKNLWTRLFISIFVGVMLWI 207
                                        788899********************855555555555999999**99998777654 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00027       1.2     446     502 ..      13      69 ..       4      74 .. 0.67
   2 ?   -0.3   0.2     0.073   3.3e+02     211     254 ..      78     121 ..      68     127 .. 0.77
   3 ?    0.4   0.8     0.046   2.1e+02     180     253 ..     187     247 ..     181     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00027
                           Ndc1_Nup 446 ksrllskeqkealsestikkkvekelaq.llk.spligylFrqslrrrlealvsnpqli 502
                                        ++r++ ke + +l++s++ k + +  +  +l  +++i+++Fr s+r+++e+++s  q+i
  gene1312|gene1312|rna1311|rna1311  13 NERQKHKEPTDSLPKSKSWKDFPDTWLSlILTlMTGIMVFFRSSFRTKVENIFS--QII 69 
                                        334444555556665555555555555547777889****************95..554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.073
                           Ndc1_Nup 211 alillrlfl.nlprsaapppldslpfnlsLllrtlllgflllllw 254
                                        ++++++ ++  +  s++++ +d+  + + Lll++l+l+fl+++++
  gene1312|gene1312|rna1311|rna1311  78 IYFTAKRLYfRIEGSKKLKGNDVAMI-VCLLLHLLMLAFLVCSNF 121
                                        45566666668888888888888876.889999999999999886 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.046
                           Ndc1_Nup 180 ilkkslilslvlllvspiiyylllrsfiwslalillrlflnlprsaapppldslpfnlsLllrtlllgflllll 253
                                        ++k+  ++++++++v++++  +++  +i           ln+++++ ++   ++++ + L++     g  ++++
  gene1312|gene1312|rna1311|rna1311 187 VIKNLWTRLFISIFVGVML--WIVEDWIVDS--------LNISKRNVRKIRNFMKIVVALIYT---IGGYCIMN 247
                                        6777779999999998877..8889999983........389998888888888888888876...44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 1722.58
//
Query:       gene1313|gene1313|rna1312|rna1312  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-14   52.2  23.9    1.5e-07   31.0   5.0    4.2  4  LRR_8     Leucine rich repeat
    7.4e-14   51.6  27.9    2.7e-06   27.6   1.5    4.8  6  LRR_4     Leucine Rich repeats (2 copies)
    5.6e-05   23.1  24.2        1.4    9.7   0.2    7.4  8  LRR_1     Leucine Rich Repeat
     0.0035   16.9   3.7     0.0035   16.9   3.7    2.2  2  LRR_9     Leucine-rich repeat
     0.0084   16.4   0.1       0.11   12.9   0.0    2.6  3  YcgL      YcgL domain
  ------ inclusion threshold ------
       0.14   12.3  26.0         12    6.2   0.1    7.1  7  LRR_6     Leucine Rich repeat


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   5.0   5.1e-11   1.5e-07       5      61 .]      55     109 ..      51     109 .. 0.94
   2 !   28.6   6.8     3e-10   9.1e-07       3      61 .]      99     155 ..      98     155 .. 0.98
   3 !    9.8   0.1   0.00022      0.66      23      42 ..     164     183 ..     159     200 .. 0.69
   4 ?    1.2   0.8      0.11   3.3e+02      21      39 ..     213     232 ..     189     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.1e-11
                                        EEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   5 sLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        +L++s N++++l+   F++ls +kvLd snN+l++ls  +++g+p L sL+L++N+L
  gene1313|gene1313|rna1312|rna1312  55 ELNISGNKINVLP-AYFENLSFMKVLDVSNNELKFLS-SSIAGMPFLVSLNLNSNDL 109
                                        79*********97.57899*****************8.*****************98 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 3e-10
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        L sL+L++N lt l+ e  + l+ L+ L++++N+l+ l p+ +++ +sL  LdL +N+L
  gene1313|gene1313|rna1312|rna1312  99 LVSLNLNSNDLTFLPEEITE-LKYLENLSIRDNQLQEL-PEKMDDIASLVNLDLANNKL 155
                                        789****************9.*****************.9*****************98 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00022
                                        T-TT--EEE--SS---GGGG CS
                              LRR_8  23 glsnLkvLdLsnNllttlsp 42 
                                        g++nLk LdL  Nl +tl p
  gene1313|gene1313|rna1312|rna1312 164 GVENLKRLDLEGNLFDTLPP 183
                                        67888888888888888844 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.11
                                        STT-TT--EEE--SS.---G CS
                              LRR_8  21 FkglsnLkvLdLsnN.lltt 39 
                                          + + L  Ld++nN +l+ 
  gene1313|gene1313|rna1312|rna1312 213 LANSKTLLLLDMRNNnRLRE 232
                                        34556788888888856655 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.9   1.3e-07    0.0004       3      39 ..      53      89 ..      51      94 .. 0.84
   2 !   21.5   2.7   7.8e-08   0.00023       4      43 ..      77     113 ..      75     120 .. 0.91
   3 !   14.0   4.1   1.7e-05     0.051       3      40 ..      99     136 ..      97     144 .. 0.84
   4 !   17.3   2.9   1.6e-06    0.0048       3      39 ..     122     158 ..     120     159 .. 0.87
   5 !   27.6   1.5   8.9e-10   2.7e-06       2      41 ..     144     183 ..     143     190 .. 0.87
   6 ?    3.6   1.1     0.032        96       4      37 ..     192     231 ..     189     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                                       --EEE--SS---E-S-.HHH-TT--EEE-.-S-----G CS
                              LRR_4  3 LevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdl 39
                                        ++L++s+N++  +p  +e+l  +k+Ld+s+N  ++ l
  gene1313|gene1313|rna1312|rna1312 53 IIELNISGNKINVLPAyFENLSFMKVLDVSNN-ELKFL 89
                                       689**************999*********666.55444 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 7.8e-08
                                        -EEE--SS---E-S-.HHH-TT--EEE-.-S-----GGGGX CS
                              LRR_4   4 evLdLsnNqltdipl.leklpnLkeLdLsgNnlitdldeLk 43 
                                        +vLd snN l+ +++ ++++p L +L+L++N    dl+ L+
  gene1313|gene1313|rna1312|rna1312  77 KVLDVSNNELKFLSSsIAGMPFLVSLNLNSN----DLTFLP 113
                                        79*************7778*********99*....999886 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.7e-05
                                        --EEE--SS---E-S-.HHH-TT--EEE-.-S-----GG CS
                              LRR_4   3 LevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdld 40 
                                        L +L+L++N lt +p  +  l+ L+ L++ + n+++ l+
  gene1313|gene1313|rna1312|rna1312  99 LVSLNLNSNDLTFLPEeITELKYLENLSI-RDNQLQELP 136
                                        678*************6556*********.655887774 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 1.6e-06
                                        --EEE--SS---E-S-..HHH-TT--EEE-.-S-----G CS
                              LRR_4   3 LevLdLsnNqltdipl..leklpnLkeLdLsgNnlitdl 39 
                                        Le+L++++Nql+++p      + +L  LdL  Nn+++dl
  gene1313|gene1313|rna1312|rna1312 122 LENLSIRDNQLQELPEkmDD-IASLVNLDL-ANNKLEDL 158
                                        89***********9996444.999******.77799998 PP

  == domain 5  score: 27.6 bits;  conditional E-value: 8.9e-10
                                        S--EEE--SS---E-S-.HHH-TT--EEE-.-S-----GGG CS
                              LRR_4   2 nLevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdlde 41 
                                        +L +LdL+nN+l d+p+ +++  nLk LdL gN l ++l++
  gene1313|gene1313|rna1312|rna1312 144 SLVNLDLANNKLEDLPFgIGGVENLKRLDLEGN-LFDTLPP 183
                                        6889*************8778*********999.6666654 PP

  == domain 6  score: 3.6 bits;  conditional E-value: 0.032
                                        -EEE--SS.---E-S-.....HHH-TT--EEE-.-S---- CS
                              LRR_4   4 evLdLsnN.qltdipl.....leklpnLkeLdLsgNnlit 37 
                                        e++ +  N +l +ip      l++ + L  Ld+ +Nn+++
  gene1313|gene1313|rna1312|rna1312 192 EEIIFTKNrRLGEIPRklvqmLANSKTLLLLDMRNNNRLR 231
                                        56666666567777777333333455599****8888885 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0026       7.9       3      23 .]      54      73 ..      52      73 .. 0.89
   2 !    5.7   0.0    0.0098        29       3      21 ..      77      94 ..      76      96 .. 0.82
   3 ?    4.9   0.5     0.019        56       2      18 ..      99     114 ..      98     119 .. 0.77
   4 ?    1.9   0.2      0.18   5.4e+02       2      16 ..     122     135 ..     118     138 .. 0.78
   5 ?    4.3   0.1     0.028        85       2      16 ..     145     159 ..     144     162 .. 0.85
   6 !    9.7   0.2   0.00047       1.4       1      17 [.     167     183 ..     167     188 .. 0.86
   7 ?   -3.1   0.0         6   1.8e+04       2      18 ..     191     207 ..     190     209 .. 0.70
   8 ?    1.4   0.2      0.27     8e+02       4      14 ..     221     231 ..     218     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0026
                              LRR_1  3 rhLdLsnnpllglppnsfqnL 23
                                        +L++s+n + + +p++f+nL
  gene1313|gene1313|rna1312|rna1312 54 IELNISGNKI-NVLPAYFENL 73
                                       58********.8999999997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0098
                              LRR_1  3 rhLdLsnnpllglppnsfq 21
                                       ++Ld+snn l  ++++s+ 
  gene1313|gene1313|rna1312|rna1312 77 KVLDVSNNEL-KFLSSSIA 94
                                       79********.78888775 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.019
                              LRR_1   2 LrhLdLsnnpllglppn 18 
                                        L +L+L++n l+ ++p+
  gene1313|gene1313|rna1312|rna1312  99 LVSLNLNSNDLT-FLPE 114
                                        779********4.6555 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.18
                              LRR_1   2 LrhLdLsnnpllglp 16 
                                        L+ L +++n+l + +
  gene1313|gene1313|rna1312|rna1312 122 LENLSIRDNQL-QEL 135
                                        78889****99.444 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.028
                              LRR_1   2 LrhLdLsnnpllglp 16 
                                        L  LdL nn l++lp
  gene1313|gene1313|rna1312|rna1312 145 LVNLDLANNKLEDLP 159
                                        677********9987 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.00047
                              LRR_1   1 nLrhLdLsnnpllglpp 17 
                                        nL++LdL++n ++ lpp
  gene1313|gene1313|rna1312|rna1312 167 NLKRLDLEGNLFDTLPP 183
                                        8**********976665 PP

  == domain 7  score: -3.1 bits;  conditional E-value: 6
                              LRR_1   2 LrhLdLsnnpllglppn 18 
                                         +++  + n+ lg +p+
  gene1313|gene1313|rna1312|rna1312 191 IEEIIFTKNRRLGEIPR 207
                                        56677778888787776 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 0.27
                              LRR_1   4 hLdLsnnpllg 14 
                                         Ld++nn+ l+
  gene1313|gene1313|rna1312|rna1312 221 LLDMRNNNRLR 231
                                        69****99765 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.7   1.2e-06    0.0035      22     116 ..      54     149 ..      45     155 .. 0.86
   2 ?    3.6   1.2     0.014        42      63     117 ..     165     221 ..     148     247 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                              LRR_9  22 reldlrgykipvienlGatldqfdtidlsdndirkld.gfPllkrlktlllnnnrivriaegleevlPnleelvlt 96 
                                         el++ g+ki v+      l  +  +d+s+n+++ l  ++  +  l +l ln+n ++ + e++ e l  le+l + 
  gene1313|gene1313|rna1312|rna1312  54 IELNISGNKINVLPAYFENLSFMKVLDVSNNELKFLSsSIAGMPFLVSLNLNSNDLTFLPEEITE-LKYLENLSIR 128
                                        5999**********99999**************99862466777788999************987.789******* PP

                              LRR_9  97 nnelqelad.ldPlaslkkle 116
                                        +n+lqel + +d +asl +l+
  gene1313|gene1313|rna1312|rna1312 129 DNQLQELPEkMDDIASLVNLD 149
                                        *******75378888888776 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                              LRR_9  63 lkrlktlllnnnrivriaegleevlPnleelvltnne.lqelad..ldPlaslkklel 117
                                        ++ lk l l+ n    + + +  +l n+ee+++t+n+ l e+    ++ la+ k l l
  gene1313|gene1313|rna1312|rna1312 165 VENLKRLDLEGNLFDTLPP-ILGYLENIEEIIFTKNRrLGEIPRklVQMLANSKTLLL 221
                                        5666666666665544444.34467777777777775455543311222333333333 PP

>> YcgL  YcgL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.76   2.3e+03      23      47 ..      37      61 ..      34      63 .. 0.88
   2 ?   -1.8   0.0       1.4   4.2e+03      19      29 ..     129     139 ..     121     154 .. 0.72
   3 !   12.9   0.0   3.6e-05      0.11      17      55 ..     197     235 ..     191     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.76
                               YcgL 23 sevPeeLlesfGkpefvmeleLske 47
                                       ++vP e+ +s+ +   ++el++s +
  gene1313|gene1313|rna1312|rna1312 37 KQVPREVFDSMMRGDRIIELNISGN 61
                                       589********99999999999876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                               YcgL  19 kddfsevPeeL 29 
                                         ++++e+Pe++
  gene1313|gene1313|rna1312|rna1312 129 DNQLQELPEKM 139
                                        56788888876 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3.6e-05
                               YcgL  17 ekkddfsevPeeLlesfGkpefvmeleLskerkLarada 55 
                                        +k+ +++e+P +L++++ + +  + l+++++++L ++++
  gene1313|gene1313|rna1312|rna1312 197 TKNRRLGEIPRKLVQMLANSKTLLLLDMRNNNRLREEST 235
                                        57789*****************************98875 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.018        54       7      16 ..      55      64 ..      53      65 .. 0.89
   2 ?    4.4   0.1     0.015        46       3      15 ..      74      86 ..      72      87 .. 0.85
   3 ?    6.2   0.1     0.004        12       3      16 ..      97     110 ..      95     110 .. 0.88
   4 ?    3.0   0.1     0.043   1.3e+02       4      15 ..     121     132 ..     118     133 .. 0.87
   5 ?    4.3   0.3     0.016        49       4      17 ..     144     157 ..     143     158 .. 0.89
   6 ?    3.7   0.1     0.026        79       4      15 ..     167     178 ..     166     180 .. 0.86
   7 ?    0.6   0.6      0.26   7.7e+02       2      14 ..     216     228 ..     215     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                              LRR_6  7 eLdLsgNdIg 16
                                       eL++sgN+I+
  gene1313|gene1313|rna1312|rna1312 55 ELNISGNKIN 64
                                       7*******95 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.015
                              LRR_6  3 thLteLdLsgNdI 15
                                       + ++ Ld+s N++
  gene1313|gene1313|rna1312|rna1312 74 SFMKVLDVSNNEL 86
                                       6799*******87 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.004
                              LRR_6   3 thLteLdLsgNdIg 16 
                                        + L +L+L++Nd++
  gene1313|gene1313|rna1312|rna1312  97 PFLVSLNLNSNDLT 110
                                        5799********97 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.043
                              LRR_6   4 hLteLdLsgNdI 15 
                                        +L+ L++++N++
  gene1313|gene1313|rna1312|rna1312 121 YLENLSIRDNQL 132
                                        799*******98 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.016
                              LRR_6   4 hLteLdLsgNdIgD 17 
                                        +L  LdL+ N++ D
  gene1313|gene1313|rna1312|rna1312 144 SLVNLDLANNKLED 157
                                        6889*******988 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.026
                              LRR_6   4 hLteLdLsgNdI 15 
                                        +L+ LdL gN +
  gene1313|gene1313|rna1312|rna1312 167 NLKRLDLEGNLF 178
                                        79********76 PP

  == domain 7  score: 0.6 bits;  conditional E-value: 0.26
                              LRR_6   2 nthLteLdLsgNd 14 
                                        + +L  Ld++ N+
  gene1313|gene1313|rna1312|rna1312 216 SKTLLLLDMRNNN 228
                                        678999******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1618.27
//
Query:       gene1314|gene1314|rna1313|rna1313  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.014   15.3   5.3       0.31   10.9   0.5    2.2  2  DUF2463        Protein of unknown function (DUF2463)
      0.038   13.2  13.0      0.062   12.5  13.0    1.3  1  MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
          3    8.0   7.5        1.1    9.4   0.2    2.7  2  DUF4229        Protein of unknown function (DUF4229)


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   5.2e-05      0.31      13      68 ..      32      87 ..      17      94 .. 0.88
   2 ?    6.9   0.5   0.00086       5.2      70     138 ..     145     213 ..     123     226 .] 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.2e-05
                            DUF2463 13 sfeeslllrfitlllpfsysavqyllllhtnwkssnkpesilhkilyyllnlllla 68
                                       s  e+++lrf+  +++ ++ ++  +  +  nw+ +       +++ly+++ +l l+
  gene1314|gene1314|rna1313|rna1313 32 SAGENHVLRFVSAVSSSLFTIFMLSYWIIRNWRMNVSGGYSKESVLYLVFIVLCLT 87
                                       566899**********************************************9986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00086
                            DUF2463  70 aiisilSiialtidkwesdddlliysiilPslvvpltyLlstscnlvpgqisftdtginilidlliLll 138
                                        +++ il + a+ti+ ++++  ++++s++l+  v+ +  L+  +     ++i  +  +   ++dl+ L+l
  gene1314|gene1314|rna1313|rna1313 145 IAAIILITCAITINAKTNNMFVVLWSFVLSGAVMASISLAEEIALPKKKNIWDVSKNHLGFFDLIRLIL 213
                                        334455566677777777766666666666655555555555444444444444444444455555444 PP

>> MIG-14_Wnt-bd  Wnt-binding factor required for Wnt secretion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5  13.0     1e-05     0.062     114     290 ..      36     221 ..      13     223 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                      MIG-14_Wnt-bd 114 swflllldiifqsiFlsvLllFwlvffeslrdeqnrrktlsfylpklllvll.lwlvllvlalyerleqlkdpfys 188
                                        + +l +++++  s+F++++l++w++   +++ +    k+  +yl  ++l+l+ l+ ++  ++ly  +++  d  ++
  gene1314|gene1314|rna1313|rna1313  36 NHVLRFVSAVSSSLFTIFMLSYWIIRNWRMNVSGGYSKESVLYLVFIVLCLTgLFTCIGETFLYGLGNDRLDI-LK 110
                                        77899**************************998888888888888888866344444455555555555553.33 PP

                      MIG-14_Wnt-bd 189 iwss.....al............ilkilaiilavlyflyLlylifrsfseirskrvkegdiRfkflilltllvlav 247
                                        i+++     +             + + +++ la + +++L+ + +++  ++++  +      f   ++l ++vl  
  gene1314|gene1314|rna1313|rna1313 111 IFATfssinYIrfkclgllprpvYRSSGIGNLASIAAIILITCAITINAKTNN--M------F---VVLWSFVLSG 175
                                        44443333311333445556664444444444555555555444433333333..4......3...3344444444 PP

                      MIG-14_Wnt-bd 248 lvifiilglvse.....lsptsdssaqflgvygllNlyvytlaylYaP 290
                                        +v++ i+++ +e      ++ +d s + lg++ l+ l ++ lay Y+P
  gene1314|gene1314|rna1313|rna1313 176 AVMASISLA-EEialpkKKNIWDVSKNHLGFFDLIRLILFSLAY-YWP 221
                                        444444444.33555666667788******************98.566 PP

>> DUF4229  Protein of unknown function (DUF4229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00019       1.1      13      58 ..      21      68 ..      15      73 .. 0.81
   2 ?    0.2   2.7      0.14   8.3e+02      15      44 ..     147     176 ..     141     183 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00019
                            DUF4229 13 vltavillvarliglp..vpllvaallAlvvalplSmvllkklRdrat 58
                                       v+  +i+l+ r +g +  ++++ a+  +l   ++lS+++ +++R +++
  gene1314|gene1314|rna1313|rna1313 21 VIPTAIYLFDRSAGENhvLRFVSAVSSSLFTIFMLSYWIIRNWRMNVS 68
                                       55566778887777778888888888899999*************998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                            DUF4229  15 tavillvarliglpvpllvaallAlvvalp 44 
                                        +++++  a +i ++ + + ++l ++v++++
  gene1314|gene1314|rna1313|rna1313 147 AIILITCAITINAKTNNMFVVLWSFVLSGA 176
                                        222233333344447777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1577.11
//
Query:       gene1315|gene1315|rna1314|rna1314  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00062   19.6   3.9      0.011   15.6   0.2    2.8  2  DUF1514      Protein of unknown function (DUF1514)
  ------ inclusion threshold ------
      0.016   14.6   6.8      0.025   13.9   6.6    1.4  1  EpsG         EpsG family
      0.037   13.8  16.4       0.16   11.8   9.9    2.6  2  Bax1-I       Inhibitor of apoptosis-promoting Bax1
      0.043   13.4  10.2       0.39   10.3   9.6    2.1  1  TauE         Sulfite exporter TauE/SafE
      0.051   12.9   1.3       0.11   11.7   1.4    1.6  1  SUa-2TM      SMODS- and Ubiquitin system-associated 2TM effec
       0.13   11.2   3.3      0.079   11.9   1.1    1.7  1  DUF3488      Domain of unknown function (DUF3488)
       0.63   10.2   9.6        0.1   12.7   3.7    1.9  2  DUF63        Membrane protein of unknown function DUF63
        1.1    9.6   5.5       0.31   11.4   0.5    2.5  2  DUF3981      Domain of unknown function (DUF3981)
        1.8    8.6   9.4       0.22   11.6   0.5    2.9  3  DUF389       Domain of unknown function (DUF389)
        7.3    6.8   8.2       0.44   10.7   0.3    3.1  3  Insulin_TMD  Insulin receptor trans-membrane segment


Domain annotation for each model (and alignments):
>> DUF1514  Protein of unknown function (DUF1514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   5.9e-06     0.011       6      38 ..     119     151 ..     117     156 .. 0.93
   2 ?    4.0   0.5     0.025        45       3      23 ..     173     193 ..     172     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.9e-06
                            DUF1514   6 sivlailLLvllsiisdkakeieaLeYmndYLl 38 
                                        +iv ai+LLv  s i +   +ie  ++mn  L+
  gene1315|gene1315|rna1314|rna1314 119 TIVAAIFLLVQTSKIIKTKNTIERRDFMNGLLM 151
                                        8****************************9886 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.025
                            DUF1514   3 ivisivlailLLvllsiisdk 23 
                                        i+i + l + LL+l+s++ + 
  gene1315|gene1315|rna1314|rna1314 173 IIICLALVVALLLLVSSNNKE 193
                                        566666777777778887654 PP

>> EpsG  EpsG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   6.6   1.4e-05     0.025     175     315 ..      74     217 ..      42     224 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                               EpsG 175 llllllldlilsllslllliseryesYlesdeysggtig......gvqlaillfilfllllkkileekkkeklklf 244
                                         ++++++  +++ll  +    + +++ ++ ++ +++++g      g+  +i+++i++l+   ki+++k + + + f
  gene1315|gene1315|rna1314|rna1314  74 AVASSVFLSVIGLLQAIC---SVVNMKSDRGKLFYSKEGkrliagGY-ATIVAAIFLLVQTSKIIKTKNTIERRDF 145
                                        333333333333333332...35555555555555555555556444.4444444444555555555544444777 PP

                               EpsG 245 lnllliglallllllsls.vilsRlslyflifqiillppllkklfkrkkrrlilliliillflflfvkllas 315
                                         n ll+++a  + ++ ++ +    ls++ +++ +++ + ll++  +++++++   +++ +l++ ++ +++as
  gene1315|gene1315|rna1314|rna1314 146 MNGLLMMVAATVYFFLADdIDQEQLSSIIICLALVVALLLLVSSNNKEENKVPNKGILSYLMASYIGWFIAS 217
                                        777777776666666666699999*9999999998999999999999*****999********999999965 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   9.9   8.7e-05      0.16      80     201 ..      16     161 ..      13     165 .. 0.73
   2 ?    3.9   5.3     0.024        43      15      89 ..     149     220 ..     145     241 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.7e-05
                             Bax1-I  80 eGlslspillvyt.......gaiilqaflltaaifgglslyalttkr...dlsglggflfagligliiaslvnlF. 144
                                        e+l+l  ++l+ +       +++  q f l a++f+++ +++   +    d++ lg++++a  + l +++l++ + 
  gene1315|gene1315|rna1314|rna1314  16 ESLILIGVVLAEMrlnriesSGVGFQIFSLGAVAFFVVRVLVTISNVelgDVNTLGSIAVASSVFLSVIGLLQAIc 91 
                                        5556666665555666666666666777777777777766655555556699999999999999998888888776 PP

                             Bax1-I 145 ............lpssalelai.sylgvllfsglilyDtqkiierageygeedailaalsLyldfinlFl 201
                                                    + s+  + +i +  ++++ ++++l++t+kii++ ++ +  d +++ l++ +  +  Fl
  gene1315|gene1315|rna1314|rna1314  92 svvnmksdrgklFYSKEGKRLIaGGYATIVAAIFLLVQTSKIIKTKNTIERRDFMNGLLMMVAATVYFFL 161
                                        7766666666644466666666567789***************998888888999999999998888886 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.024
                             Bax1-I  15 lllt.alvaavvlsspa..qlflslhivlflvvilaplalvflslsaarlkkkssalalallllftlleGlslspi 87 
                                        ll++ a++ +++l+     q         ++++ la +++++l++s + +++++ + + +l +l++  +G ++++ 
  gene1315|gene1315|rna1314|rna1314 149 LLMMvAATVYFFLAD-DidQE-----QLSSIIICLALVVALLLLVSSNNKEENKVPNKGILSYLMASYIGWFIASA 218
                                        433313333333222.12322.....22233333333333322333444444555555777777777777777765 PP

                             Bax1-I  88 ll 89 
                                        l 
  gene1315|gene1315|rna1314|rna1314 219 LG 220
                                        54 PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   9.6   0.00022      0.39      35     144 ..     113     221 ..      35     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                               TauE  35 vavatsllavvatslsgalahrrr.gnvdwrlllllllgsliGallGallllllpsellkllfgvlllllallmll 109
                                        +a +++++++++  l+++ + ++  ++++ r ++  +l ++++a + ++l+  +++e l+ ++ +l l++all+l+
  gene1315|gene1315|rna1314|rna1314 113 IAGGYATIVAAIFLLVQTSKIIKTkNTIERRDFMN-GLLMMVAATVYFFLADDIDQEQLSSIIICLALVVALLLLV 187
                                        46677777777778888888888745777777774.5555666666699999999999****************99 PP

                               TauE 110 rkkrsrakgrerrptaillvligglvG.llsGllGi 144
                                        +++ ++++ ++ + + il+ l++  +G ++++ lGi
  gene1315|gene1315|rna1314|rna1314 188 SSN-NKEE-NKVPNKGILSYLMASYIGwFIASALGI 221
                                        886.3333.466666666666655555377777777 PP

>> SUa-2TM  SMODS- and Ubiquitin system-associated 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   6.4e-05      0.11      60     133 ..     167     236 ..     117     247 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                            SUa-2TM  60 lkgylsvillilvlvalilFiRKvnmekekilnikgnvYhnypyiffkfcskllgynkinlvlvPiqlqfkLvv 133
                                        +++++s+i+ + ++val+l +  +n+e +k+ n     Y + +yi + + s  lg   i++++  + +  kLv 
  gene1315|gene1315|rna1314|rna1314 167 QEQLSSIIICLALVVALLLLVSSNNKEENKVPNKGILSYLMASYIGWFIAS-ALG---IQVMGDKVKMVEKLVA 236
                                        45668999999999***********99999999555789*****9855554.555...4555666666666665 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   4.4e-05     0.079      82     143 ..     131     196 ..     110     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.4e-05
                            DUF3488  82 llalKllElrsrRDalvllllgffllatsflfs...qsllfalylllalllllaalvalh.asasa 143
                                          ++K+ ++ +rRD++  ll+ + +++  fl +   q+ l  ++++lal+++l+ lv+ + +++++
  gene1315|gene1315|rna1314|rna1314 131 SKIIKTKNTIERRDFMNGLLMMVAATVYFFLADdidQEQLSSIIICLALVVALLLLVSSNnKEENK 196
                                        33577778889****************999976222566666666666666666666555222222 PP

>> DUF63  Membrane protein of unknown function DUF63
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.3      0.22     4e+02     118     167 ..      41      91 ..      15     108 .. 0.48
   2 ?   12.7   3.7   5.8e-05       0.1      93     199 ..     120     225 ..     111     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.22
                              DUF63 118 lyaavGvvlvlvvlllLl.lteevvnlevlllvlllaavltalvllllrkl 167
                                         ++ +G+v+++vv +l++ ++ e  ++ +l  ++++ +v+ +++ ll    
  gene1315|gene1315|rna1314|rna1314  41 QIFSLGAVAFFVVRVLVTiSNVELGDVNTLGSIAVASSVFLSVIGLLQAIC 91 
                                        344455555444444333244455555555555555555444444443333 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.8e-05
                              DUF63  93 vflitlavlliskklekklkkdykklyaavGvvlvlvvlllLllteevvnlevlllvlllaavltalvllllrklk 168
                                        + + +++ + +sk    k+k++ ++  ++ G++++++++++++l+ ++ + ++  +++ la+v+++l+l+ +++ +
  gene1315|gene1315|rna1314|rna1314 120 IVAAIFLLVQTSKI--IKTKNTIERRDFMNGLLMMVAATVYFFLADDIDQEQLSSIIICLALVVALLLLVSSNNKE 193
                                        33333333333333..46889999999****************888888888888888888888877777777777 PP

                              DUF63 169 .lellsdklnlllllahllDasatfvgidllg 199
                                          ++ ++ +  +l+ + +    a+ +gi+++g
  gene1315|gene1315|rna1314|rna1314 194 eNKVPNKGILSYLMASYIGWFIASALGIQVMG 225
                                        45555666666666666667789999999975 PP

>> DUF3981  Domain of unknown function (DUF3981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.91   1.6e+03      67      97 ..      18      47 ..      12      64 .. 0.71
   2 ?   11.4   0.5   0.00017      0.31      40     102 ..     151     214 ..     128     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.91
                            DUF3981 67 ailiglvlfsqdqigklegtlkgllmfvlla 97
                                        ilig+vl ++ ++ ++e +  g+ +f l a
  gene1315|gene1315|rna1314|rna1314 18 LILIGVVL-AEMRLNRIESSGVGFQIFSLGA 47
                                       58899877.4567888888888888877654 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00017
                            DUF3981  40 igiaiyeyfwliddrvdsilthysvavailiglvl.fsqdqigklegtlkgllmfvllasygyf 102
                                        + +a   yf+l dd  +  l+   +++a+++ l+l +s ++  + +   kg+l +++ +  g+f
  gene1315|gene1315|rna1314|rna1314 151 MMVAATVYFFLADDIDQEQLSSIIICLALVVALLLlVSSNNKEENKVPNKGILSYLMASYIGWF 214
                                        45677889*******999**********999987615667777777788999999765555776 PP

>> DUF389  Domain of unknown function (DUF389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.1      0.27   4.8e+02      15      82 ..      21      92 ..      17      98 .. 0.58
   2 ?    0.4   0.1      0.34   6.1e+02       9      28 ..     119     138 ..      96     172 .. 0.48
   3 ?   11.6   0.5   0.00012      0.22      36      87 ..     173     224 ..     150     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                             DUF389 15 fglvigdrkllrrglknlliglllallvgflfg.lllplk..vlg.eeelptsemlsrtepnlvdllvAlas 82
                                       +g+v+ + +l r     + ++++   +v+f+++ +l+ ++  +lg  ++l +  ++s + +++++ll A++s
  gene1315|gene1315|rna1314|rna1314 21 IGVVLAEMRLNRIESSGVGFQIFSLGAVAFFVVrVLVTISnvELGdVNTLGSIAVASSVFLSVIGLLQAICS 92
                                       566666666666555556666666666666666433333334445555555556666666667788777776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                             DUF389   9 pilaiafglvigdrkllrrg 28 
                                         i+a+ f lv  ++ + ++ 
  gene1315|gene1315|rna1314|rna1314 119 TIVAAIFLLVQTSKIIKTKN 138
                                        33333333333222222221 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00012
                             DUF389  36 lllallvgflfglllplkvlg.eeelptsemlsrtepnlvdllvAlasGaaga 87 
                                        ++++l++ +++ ll+   + + e+++p++ +ls   +++++ ++A a G+ ++
  gene1315|gene1315|rna1314|rna1314 173 IIICLALVVALLLLVSS-NNKeENKVPNKGILSYLMASYIGWFIASALGIQVM 224
                                        33333333333332333.3444999************************9987 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.7       4.4   7.9e+03      30      40 ..      44      54 ..      40      57 .. 0.66
   2 ?   -1.5   0.1       1.6   2.8e+03      31      39 ..     120     128 ..     117     132 .. 0.58
   3 ?   10.7   0.3   0.00024      0.44       2      31 ..     158     187 ..     157     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.4
                        Insulin_TMD 30 lvigavfvvvk 40
                                        +++++f vv+
  gene1315|gene1315|rna1314|rna1314 44 SLGAVAFFVVR 54
                                       45666677765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                        Insulin_TMD  31 vigavfvvv 39 
                                        +++a+f++v
  gene1315|gene1315|rna1314|rna1314 120 IVAAIFLLV 128
                                        455555554 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00024
                        Insulin_TMD   2 YFYvadyldpsnivkIvigPviciillllv 31 
                                        YF++ad  d +++  I+i    ++ llllv
  gene1315|gene1315|rna1314|rna1314 158 YFFLADDIDQEQLSSIIICLALVVALLLLV 187
                                        ******99*99*****99977777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1176  (0.0655921); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 1609.78
//
Query:       gene1316|gene1316|rna1315|rna1315  [L=436]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.7    7.7  14.1        1.6    8.8   9.2    2.9  2  GWT1      GWT1


Domain annotation for each model (and alignments):
>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.17     3e+03      57      57 ..      55      55 ..       9      93 .. 0.63
   2 ?    8.8   9.2     9e-05       1.6      56     147 ..     299     380 ..     267     381 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.17
                               GWT1 57 l 57
                                       l
  gene1316|gene1316|rna1315|rna1315 55 L 55
                                       1 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 9e-05
                               GWT1  56 kllllsilllllllllelyvefvSRrlaNlpYvlwvvalnltllllflliellfvekeeekerkekatstvleain 131
                                         +++l  ++++++ll + + ++++Rr+ Nl ++++++ l +t+ +++ + +++f          + ++ ++ +  +
  gene1316|gene1316|rna1315|rna1315 299 GIIVLYNIFFVTILLGTRMYSMSCRRIHNLYFCMVIMLLHTTQGIACGASNKIF----------KIRDLKIHRFTS 364
                                        33333334444444555566678*******************999998887755..........788999999999 PP

                               GWT1 132 rngLlvFLlaNlltGl 147
                                        +  L++ + +Nll+G+
  gene1316|gene1316|rna1315|rna1315 365 KYLLFILIWSNLLVGI 380
                                        9999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2657.00
//
Query:       gene1317|gene1317|rna1316|rna1316  [L=662]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-33  116.4   0.0    5.4e-32  110.9   0.0    2.7  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.3e-16   60.6   0.3      5e-16   58.7   0.3    2.0  1  IF-2         Translation-initiation factor 2
    2.8e-15   56.0   0.8    1.2e-14   54.0   0.1    2.4  2  GTP_EFTU_D4  Elongation factor Tu domain 4
    9.2e-12   45.2   7.1    3.1e-09   37.1   0.2    3.4  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    3.8e-07   30.2   0.1    2.5e-06   27.5   0.0    2.4  2  MMR_HSR1     50S ribosome-binding GTPase
    0.00013   22.1   0.0    0.00036   20.7   0.0    1.7  1  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0096   15.4   0.1      0.036   13.5   0.0    2.1  2  SRPRB        Signal recognition particle receptor beta subuni
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.065   13.0   0.0    1.8  1  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.065   12.8   0.0       0.23   11.1   0.0    2.0  1  Ras          Ras family
       0.15   12.4   0.2       0.72   10.1   0.2    2.2  1  AAA_22       AAA domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0     3e-35   5.4e-32       5     191 ..      76     278 ..      73     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 3e-35
                                        EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..........TTCSSE CS
                           GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..........ketkky 70 
                                         ++i+ghvD+GKt L+d+L +                   + + E++ giT ++ a+ +           k++k  
  gene1317|gene1317|rna1316|rna1316  76 ICCILGHVDTGKTKLLDKLRE------------------SNVQGEEAGGITQQIGATFFPvselfkkcgkKDSKLP 133
                                        69*****************92..................245679999***********9******999669999* PP

                                        EEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST........... CS
                           GTP_EFTU  71 linliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl........... 135
                                         i +iDtPGH++F +  +rg + +++a+lvvd+v+G e+qt e ++l++++++p++v++NK+Drl           
  gene1317|gene1317|rna1316|rna1316 134 GILVIDTPGHESFANLRTRGSSLCNLAILVVDIVHGLEAQTLESIELLRRRRTPFVVALNKIDRLygwkstsfggv 209
                                        *****************************************************************99997777777 PP

                                        HHHHHHHHHHHHHHHHHH.............HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                           GTP_EFTU 136 kaelkeiveevkqklsrk.............eeklekygekgekevpvvfgSalkgegvktllealvel 191
                                        k++lk++ ++  ++++r+             ++kl    ++++++v++v++Sa++geg+ +l++ + el
  gene1317|gene1317|rna1316|rna1316 210 KNTLKKQSRATIDDFKRRvnntivafaeiglNAKLFCENTDQKRFVSLVPTSAMSGEGIPDLISLILEL 278
                                        66666666666666655588889999999987777777777779******************9999875 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.3   2.8e-19     5e-16       4     103 ..     405     503 ..     402     505 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.8e-19
                                        HHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH...ST...EEEEEES CS
                               IF-2   4 lfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa...sn...aiiigFn 73 
                                        +f++++   ++ +v + +++ GsleAl ++L++      +v++  +++G++ ++D   +s+   ++   a+i++F+
  gene1317|gene1317|rna1316|rna1316 405 VFSSME--LHQEGVHVVSSTLGSLEALVSFLKTS-----NVPIAGVSIGTVRKKDMIIVSSmakRHkeyAVILCFD 473
                                        555555..356689999****************8.....5***************99998765511568******* PP

                                        SSCTHHHHHCCCCCTSEEEEESSHHHHHHH CS
                               IF-2  74 vkvskkakklaekegvkirlynvIYklidd 103
                                        v ++k+++++a++ gvki+++++IY+l+d 
  gene1317|gene1317|rna1316|rna1316 474 VVLDKEIRDMASSMGVKIFEAKIIYHLLDS 503
                                        ****************************97 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   2.1e+03       9      31 ..     354     376 ..     347     394 .. 0.76
   2 !   54.0   0.1   6.5e-18   1.2e-14       2      86 .]     526     619 ..     525     619 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                        EEEEEETCCCEEEEEEEEEEEEE CS
                        GTP_EFTU_D4   9 pgvvfrrsdpaivGvevlgGvik 31 
                                        ++++ ++   a  G+++ +G ++
  gene1317|gene1317|rna1316|rna1316 354 NQYIIVKEAKASLGIKIAAGGLE 376
                                        56788888888888888888765 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 6.5e-18
                                        -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEE...ETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS. CS
                        GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvkli...kedGrevGeilqiqdkgkkleeakaGqevaisiegk. 73 
                                        P++++i+p+++f ++ p ++Gv+v +G++k g +l    +++  ++G++++i+++++ ++ea++ q+vai ie k 
  gene1317|gene1317|rna1316|rna1316 526 PVQMSIVPKCIFNSRSPLVIGVHVREGILKIGTPLCvfkEDQVVRLGTVTSIENNKEVVKEATKDQKVAIKIEAKh 601
                                        999*******************************963324556789**************************9863 PP

                                        .....-TTTS--TT-EEE CS
                        GTP_EFTU_D4  74 .....ivGrqikegdily 86 
                                             + Gr+++++di+y
  gene1317|gene1317|rna1316|rna1316 602 nlpprMFGRHFDQEDIIY 619
                                        34333579***9999998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.2   1.7e-12   3.1e-09       1      71 [.     307     382 ..     307     385 .. 0.95
   2 ?   -1.0   0.0       1.4   2.4e+03      11      28 ..     446     463 ..     440     486 .. 0.77
   3 !    9.3   1.2    0.0008       1.4       3      60 ..     544     599 ..     543     601 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.7e-12
                                        EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE..........ETTSEEEEEEEESSCCS CS
                        GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea..........vaganaGvivaikgled 65 
                                        G++ ++++ +G+lk+Gd++ ++g n+    +i+t+i++l+++ ++++e+          +a a  G+++a+ gle+
  gene1317|gene1317|rna1316|rna1316 307 GVTLDAILSNGVLKEGDRIGVCGfNG----PIITTIKALLMP-QPLKELrmknqyiivkEAKASLGIKIAAGGLEK 377
                                        77889999***************999....9***********.88******************************* PP

                                        GSSTTC CS
                        GTP_EFTU_D2  66 aiivGd 71 
                                        a i+G+
  gene1317|gene1317|rna1316|rna1316 378 A-IAGS 382
                                        8.9986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                        SEEETTEEEEEECTCTTS CS
                        GTP_EFTU_D2  11 GtlkkGdevrilgndtsk 28 
                                        Gt++k d + + ++ +  
  gene1317|gene1317|rna1316|rna1316 446 GTVRKKDMIIVSSMAKRH 463
                                        999999999996655433 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0008
                                        EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEE CS
                        GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivai 60 
                                        v+++ v +G+lk G  + +   + ++   +++++s+e ++e ++ea + + + +++ +
  gene1317|gene1317|rna1316|rna1316 544 VIGVHVREGILKIGTPLCV--FKEDQVVRLGTVTSIENNKEVVKEATKDQKVAIKIEA 599
                                        7899999************..666566899***********99999999999988866 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.4e-09   2.5e-06       2     114 .]      77     194 ..      76     194 .. 0.73
   2 ?   -1.3   0.0       1.2   2.2e+03      73      86 ..     491     504 ..     440     528 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.4e-09
                                        EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSE..EEEEEE.......ETTEE......EEEEECGGCSSHHHH CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdi..negrvk.......lkgke......ielvDtpGliegase 62 
                                        ++i+G+  +GK+ L+ +l +++++ ++  g T++i  +++ v+       +   +      i ++DtpG  e    
  gene1317|gene1317|rna1316|rna1316  77 CCILGHVDTGKTKLLDKLRESNVQGEEAGGITQQIgaTFFPVSelfkkcgK---KdsklpgILVIDTPG-HE---- 144
                                        689****************98777777777777774333344344334441...1344555********.44.... PP

                                        HHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                           MMR_HSR1  63 ekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                          ++++   +  + ++l++lvvd+  ++l+++  e  ell++++ p++++lnk
  gene1317|gene1317|rna1316|rna1316 145 --SFANLRTRGSSlCNLAILVVDIV-HGLEAQTLESIELLRRRRTPFVVALNK 194
                                        ..33333333333489*******99.66999999999999999********98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                        HHCTSEEEEEEETT CS
                           MMR_HSR1  73 leeadlillvvdas 86 
                                        + ea++i +++d+ 
  gene1317|gene1317|rna1316|rna1316 491 IFEAKIIYHLLDSY 504
                                        33567777777733 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     2e-07   0.00036       3     119 ..      78     196 ..      77     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2e-07
                                        EEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-H CS
                                Roc   3 vlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhp 74 
                                        +++G   +GKt+ll+++ e++++ +e    ++ ig++f+  + + +k++  +k+ k   + + Dt G+e f +l++
  gene1317|gene1317|rna1316|rna1316  78 CILGHVDTGKTKLLDKLRESNVQGEEaggiTQQIGATFFPVS-ELFKKCG-KKDSKLPGILVIDTPGHESFANLRT 151
                                        699*****************9998762333578888887743.2244443.34445567899************** PP

                                        HHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                                Roc  75 lylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiD 119
                                           +  +lailv+d  +  ++ + l++++  ++ ++p+++  nkiD
  gene1317|gene1317|rna1316|rna1316 152 RGSSLCNLAILVVDIVHGLEA-QTLESIELLRRrRTPFVVALNKID 196
                                        **************7655444.447888876551568888899999 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     2e-05     0.036       3      64 ..      74     148 ..      72     167 .. 0.65
   2 ?   -4.1   0.0       5.1   9.1e+03     129     146 ..     390     407 ..     385     411 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                                        --EEEEE-STTSSHHHHHHHHHHS..........S---B---SS-EEETTG...............GGTT-SEEEE CS
                              SRPRB   3 kpavllvGlsdsGKTslftrLttd..........svkktvtSqessaalkv............ksekgskltliDf 56 
                                        +p+  ++G  d+GKT l+ +L +           +         +++ + +            k++k   + +iD 
  gene1317|gene1317|rna1316|rna1316  74 SPICCILGHVDTGKTKLLDKLRESnvqgeeaggiT---------QQIGATFfpvselfkkcgkKDSKLPGILVIDT 140
                                        577889***************99855554444331.........33333323333444442333334445679*** PP

                                        TT-GCCSH CS
                              SRPRB  57 PGheklrq 64 
                                        PGhe++++
  gene1317|gene1317|rna1316|rna1316 141 PGHESFAN 148
                                        ****9874 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 5.1
                                        -HHHHHHHHHHHHHHHHH CS
                              SRPRB 129 spklikdaLEkElnkiie 146
                                        ++  +k+ LE +l+ ++ 
  gene1317|gene1317|rna1316|rna1316 390 NEDEVKNTLEADLESVFS 407
                                        567799999999998875 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.6e-05     0.065      92     237 ..     134     277 ..     110     281 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                         ATP_bind_1  92 dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfD 167
                                          l++DtPG   + +++  ++        +    ++ +vD     ++ ++      ++  + r ++P+vv+lnk+D
  gene1317|gene1317|rna1316|rna1316 134 GILVIDTPGHESFANLRTRGS--------SLCNLAILVVDIVHGLEAQTLE-----SIELLRRRRTPFVVALNKID 196
                                        578999999999999999999........4444566666665555544433.....3577888************* PP

                         ATP_bind_1 168 llkeklekeleffedvealslllekee............ekykklaeaiaelleefalvlrflplssekeesiedl 231
                                         l   +   +  ++++ + +  ++ ++                 +a+  +e  ++   v +++p s+ ++e+i dl
  gene1317|gene1317|rna1316|rna1316 197 RLYGWKSTSFGGVKNTLKKQSRATIDDfkrrvnntivafAEIGLNAKLFCENTDQKRFV-SLVPTSAMSGEGIPDL 271
                                        98744444443333333333333333333344444466433333444445555555555.7778888888888888 PP

                         ATP_bind_1 232 lslide 237
                                        +sli e
  gene1317|gene1317|rna1316|rna1316 272 ISLILE 277
                                        877765 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.23       4      84 ..      79     169 ..      77     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                        EEESTTSSHHHHHHHHHHSSCSSSCTTTSSEE....EEEEEEEET......TEEEEEEEEEETTSGGGHHHHHHHH CS
                                Ras   4 lvGdsavGKtslllrfvkdkFkeeyesTigvd....fytkeievd......gkevkleiwDTAGqeefkslrelyy 69 
                                        ++G   +GKt ll +  +++ + e    i  +    f+  +  ++      +k   + + DT G e f +lr+   
  gene1317|gene1317|rna1316|rna1316  79 ILGHVDTGKTKLLDKLRESNVQGEEAGGITQQigatFFPVSELFKkcgkkdSKLPGILVIDTPGHESFANLRTRGS 154
                                        88999999999999998888877765554333222233222222235422244445679***************** PP

                                        TTESEEEEEEETTBH CS
                                Ras  70 rdaegillvyditsr 84 
                                        + ++ ++lv di + 
  gene1317|gene1317|rna1316|rna1316 155 SLCNLAILVVDIVHG 169
                                        ***********9853 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0004      0.72       7      38 ..      76     109 ..      71     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                             AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..e 38 
                                        i+++ G++ tGKT ll +l+e++++ ++a    +
  gene1317|gene1317|rna1316|rna1316  76 ICCILGHVDTGKTKLLDKLRESNVQGEEAGGitQ 109
                                        7899*******************99998877773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.80u 0.35s 00:00:01.14 Elapsed: 00:00:00.54
# Mc/sec: 3693.42
//
Query:       gene1318|gene1318|rna1317|rna1317  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 835.05
//
Query:       gene1319|gene1319|rna1318|rna1318  [L=1131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 6810.01
//
Query:       gene1320|gene1320|rna1319|rna1319  [L=526]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-08   33.5  12.1      6e-08   32.4  12.1    1.5  1  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
    1.6e-05   24.6  12.8    4.7e-05   23.2  12.8    1.9  1  zf-C3HC4_2       Zinc finger, C3HC4 type (RING finger)
    2.4e-05   24.1  14.5    7.5e-05   22.5  14.5    1.9  1  zf-C3HC4         Zinc finger, C3HC4 type (RING finger)
    0.00012   22.4  13.6    0.00033   20.9  13.6    1.8  1  zf-RING_2        Ring finger domain
    0.00026   20.9   8.1     0.0008   19.4   7.6    2.2  2  zf-RING_UBOX     RING-type zinc-finger
    0.00034   21.1  12.9      0.069   13.6   0.6    3.6  4  T3SSipB          Type III cell invasion protein SipB
    0.00056   19.7  13.0    0.00056   19.7  13.0    5.5  3  DUF4201          Domain of unknown function (DUF4201)
    0.00078   19.3   5.2     0.0021   17.9   5.2    1.7  1  zf-RING_6        zf-RING of BARD1-type protein
     0.0019   18.1   1.6     0.0019   18.1   1.6    4.8  5  Sec34            Sec34-like family
     0.0022   17.8  11.6     0.0049   16.7  11.6    1.6  1  Prok-RING_4      Prokaryotic RING finger family 4
  ------ inclusion threshold ------
       0.01   15.8  13.6      0.024   14.6  13.6    1.7  1  zf-RING_5        zinc-RING finger domain
      0.013   16.1   8.4      0.013   16.1   8.4    4.6  2  APG6_N           Apg6 coiled-coil region
      0.036   14.3   7.4       0.14   12.5   7.4    2.1  1  zf-rbx1          RING-H2 zinc finger domain
       0.28   11.4  11.6       0.83    9.9  11.3    2.0  1  zf-C3HC4_4       zinc finger of C3HC4-type, RING
       0.38   10.8  30.5        0.4   10.7   3.7    4.8  5  DUF1664          Protein of unknown function (DUF1664)
       0.76   10.4  53.0       0.22   12.2   5.3    6.6  6  YabA             Initiation control protein YabA
        0.8    9.5  12.0       0.08   12.8   0.6    3.3  4  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
        1.3    9.2  44.9       0.61   10.3   6.8    4.2  3  ATG16            Autophagy protein 16 (ATG16)
        1.5    8.2  18.2       0.89    9.0   2.8    3.4  3  DUF4349          Domain of unknown function (DUF4349)
        3.2    7.4  43.6        2.8    7.6   6.0    4.3  4  Laminin_I        Laminin Domain I
        3.6    7.9  12.6        1.3    9.4   0.2    3.7  3  HrpB7            Bacterial type III secretion protein (HrpB7)
        3.7    6.8  59.2      0.099   12.0  10.4    5.3  6  GAS              Growth-arrest specific micro-tubule binding
        5.4    6.9  11.3         15    5.5  11.3    1.8  1  zf-RING_4        RING/Ubox like zinc-binding domain
        9.7    7.2   7.6        1.6    9.7   0.5    3.1  2  Rotamase         PPIC-type PPIASE domain


Domain annotation for each model (and alignments):
>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4  12.1   8.1e-11     6e-08       4      47 ..     473     516 ..     471     518 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 8.1e-11
                                        B-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH.TT-B-TTT--B- CS
                         zf-C3HC4_3   4 eCviClerprnvvllpCgHlvlCeeCaekllk.rkkkCpiCrrpi 47 
                                         C++C +r +n+++++C+H+ +CeeC ++  + r++kCp C++p 
  gene1320|gene1320|rna1319|rna1319 473 RCSLCDTRFKNTAIVKCMHC-FCEECISSRIRmRDRKCPSCNEPF 516
                                        6*******************.*****9988888*********986 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  12.8   6.2e-08   4.7e-05       1      40 []     473     512 ..     473     512 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.2e-08
                         zf-C3HC4_2   1 kCpiCldmlkdpsvvtpCgHvfCqkCilrsLeekn.eCPlC 40 
                                        +C +C  ++k++  + +C H fC++Ci   ++  + +CP C
  gene1320|gene1320|rna1319|rna1319 473 RCSLCDTRFKNT-AIVKCMHCFCEECISSRIRMRDrKCPSC 512
                                        6**********7.999*************9999999***** PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5  14.5     1e-07   7.5e-05       1      41 []     474     512 ..     474     512 .. 0.98

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1e-07
                                        -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41 
                                        C++C + +k++  + +C+H fC++Ci++ ++  + +kCP C
  gene1320|gene1320|rna1319|rna1319 474 CSLCDTRFKNTA-IVKCMHCFCEECISSRIR-MRDRKCPSC 512
                                        ************.******************.9999***** PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  13.6   4.4e-07   0.00033       2      44 .]     473     513 ..     472     513 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.4e-07
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssst.CPlCr 44 
                                         C++C  +++++  v   +C H+f++eC++  +r + + CP C+
  gene1320|gene1320|rna1319|rna1319 473 RCSLCDTRFKNTAIV---KCMHCFCEECISSRIRMRDRkCPSCN 513
                                        6****9899754443...4**********8888888888****5 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   7.6   1.1e-06    0.0008       1      39 []     474     510 ..     474     512 .. 0.89
   2 ?    1.3   0.3      0.47   3.5e+02       1       9 [.     509     517 ..     509     522 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                       zf-RING_UBOX   1 CpIClelftdP.lvlpCGHtFCreClwelskslegafkCP 39 
                                        C+ C   f++  +v +C H+FC+eC+  +s+ + + +kCP
  gene1320|gene1320|rna1319|rna1319 474 CSLCDTRFKNTaIV-KCMHCFCEECI--SSRIRMRDRKCP 510
                                        999******88555.8**********..799999999998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.47
                       zf-RING_UBOX   1 CpIClelft 9  
                                        Cp C+e+f+
  gene1320|gene1320|rna1319|rna1319 509 CPSCNEPFS 517
                                        ********6 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.6   9.2e-05     0.069       7      93 ..      16     107 ..      14     169 .. 0.67
   2 ?   -1.2   0.0       3.5   2.6e+03      39      63 ..     181     205 ..     178     209 .. 0.83
   3 !   12.4   0.9   0.00022      0.16      19     142 ..     203     325 ..     199     336 .. 0.87
   4 ?    1.6   0.2      0.48   3.6e+02      60     109 ..     368     418 ..     346     455 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                                        HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                            T3SSipB   7 llGnlikllgnkSLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaat.. 80 
                                        ++G+l k++  k + +L+++  ++  m++ + +++++l  + +++++e +++t  le + e++++a+   +a +  
  gene1320|gene1320|rna1319|rna1319  16 VVGQLWKVIDRKEI-NLHQKCSIFLEMIECK-KMNEELTRKNNELIEENAALTSILETQKENTNNAGCLDEAPKfd 89 
                                        67999999999987.6*************86.6999*****************************98654433310 PP

                                        ..HHHHHHHH...HHTT- CS
                            T3SSipB  81 ..kkvdeaqk...rlkeL 93 
                                           k++       rl+++
  gene1320|gene1320|rna1319|rna1319  90 vgSKISSLNYeirRLNSI 107
                                        113444443333344444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.5
                                        TTT----STHHHHHHHHHHHHHHHH CS
                            T3SSipB  39 eaasklSdelqtalseakgatddle 63 
                                        ++  klS el++ + ++k+a + l 
  gene1320|gene1320|rna1319|rna1319 181 QKIFKLSRELNEITLNTKDAEERLR 205
                                        677899*******999999998775 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 0.00022
                                        CHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                            T3SSipB  19 SLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLa 94 
                                         L +L+   + wk m +  +e+ +++S e+ + +++a+ + + +++ i  +d     +++ +   +e  k +++  
  gene1320|gene1320|rna1319|rna1319 203 RLRALKIENEKWKEMLQRLNEKEINISGEIDQCIQKAESLDRSMQNIISGVDLWVRRIEQTNTEKEELYKVIENH- 277
                                        5889999999***************************************************99999999999988. PP

                                        -------CHHHHH.HHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            T3SSipB  95 PdePekakleaae.qQagaaadalqadealqKkldaasklsekakakek 142
                                          + eka+ + ++ +Q     + ++  e l+K ld  ++l  k  a +k
  gene1320|gene1320|rna1319|rna1319 278 -KSYEKARNRGNNgEQGSLEEEIANLIESLDKSLDENKALVMKLEAIHK 325
                                        .7888888775442777777999999999*********99887666555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.48
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--------.-CHHHHHHH CS
                            T3SSipB  60 ddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePek.akleaaeqQ 109
                                        +d e++  k+++++  + +  k +++ +krl +++ ++ e  + le  ++Q
  gene1320|gene1320|rna1319|rna1319 368 EDPEDKTLKIKKLENSITESSKLITDYKKRLYSISREKEETeKMLESIKKQ 418
                                        666777778888888888888888888888888855444331333444444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   7.3       9.3   6.9e+03      49     106 ..      42     114 ..      39     139 .. 0.70
   2 ?    0.6   9.7      0.55   4.1e+02      55     130 ..     173     248 ..     169     252 .. 0.90
   3 !   19.7  13.0   7.5e-07   0.00056      52     132 ..     364     444 ..     361     451 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.3
                            DUF4201  49 ienqalnkkIeernkeLkrlkkkttktvhalthlkeklh...............mleselselkkelkekeer 106
                                        ie +++n+++ ++n+eL +     t+ + + +++ +++                 l+ e ++l++++ e++++
  gene1320|gene1320|rna1319|rna1319  42 IECKKMNEELTRKNNELIEENAALTSILETQKENTNNAGcldeapkfdvgskisSLNYEIRRLNSIICEMQKK 114
                                        7889999999999999999999999998888888888885555555544444444444444444444444444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.55
                            DUF4201  55 nkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnek 130
                                        ++++ er++++ +l++  +     +++  e+l +l+ e+++ k+ l++++e++  +  e+ ++ ++ + l++  ++
  gene1320|gene1320|rna1319|rna1319 173 SEELCERDQKIFKLSRELNEITLNTKDAEERLRALKIENEKWKEMLQRLNEKEINISGEIDQCIQKAESLDRSMQN 248
                                        67888999****************************************9999999999999999999998887766 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 7.5e-07
                            DUF4201  52 qalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkq 127
                                        ++l +  e+++ ++k+l +++t +++ +t++k++l  +++e +e +k l++++++ +++r e+++   e ++++++
  gene1320|gene1320|rna1319|rna1319 364 TSLLEDPEDKTLKIKKLENSITESSKLITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAE 439
                                        56778889******************************************************************** PP

                            DUF4201 128 neklk 132
                                        n++l+
  gene1320|gene1320|rna1319|rna1319 440 NKRLN 444
                                        **997 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.2   2.8e-06    0.0021       2      56 ..     466     522 ..     465     525 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                          zf-RING_6   2 arlekllrcsrctdilrepvclggcehifcsncisdcf...gsgcpvcytpawiqdvk 56 
                                         r   llrcs c   +++   +  c h fc +cis  +      cp c  p   +dvk
  gene1320|gene1320|rna1319|rna1319 466 ERYRGLLRCSLCDTRFKNT-AIVKCMHCFCEECISSRIrmrDRKCPSCNEPFSPNDVK 522
                                        57888*******8777765.6778***********976222578*****999999987 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.4         3   2.3e+03      38      59 ..      46      67 ..      19      78 .. 0.56
   2 ?    3.7   2.1     0.069        51       9     103 ..     134     223 ..     126     224 .. 0.78
   3 ?    1.3   0.4      0.38   2.8e+02       5      62 ..     218     275 ..     215     283 .. 0.81
   4 ?    3.1   1.7      0.11        80      10      63 ..     297     350 ..     291     384 .. 0.66
   5 !   18.1   1.6   2.5e-06    0.0019       5      66 ..     391     452 ..     387     453 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3
                              Sec34 38 ektsslheaceqlleeqkrlee 59
                                       +  ++l ++ ++l+ee+  l++
  gene1320|gene1320|rna1319|rna1319 46 KMNEELTRKNNELIEENAALTS 67
                                       3333444444444444444444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.069
                              Sec34   9 eeecdelleqtdealeqLeeleekfksvsektsslhe.aceqlleeqkrleelaeeieekLkyFeeldpitrkLns 83 
                                         e+ ++++++   a+e  +++ e++ + ++k+  l++ ++e+l e  +++ +l++e++e      + + ++++L++
  gene1320|gene1320|rna1319|rna1319 134 GEKKHNVVDDSMVANEIYRKIAEEYGDLKAKMAGLESkHSEELCERDQKIFKLSRELNEITL---NTKDAEERLRA 206
                                        56677888999999999999999999999999999752689999999999999999998764...45556666766 PP

                              Sec34  84 pgsslvksesFlemLkklDe 103
                                         + +   +e+++emL++l+e
  gene1320|gene1320|rna1319|rna1319 207 LKIE---NEKWKEMLQRLNE 223
                                        6655...8888888888875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.38
                              Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelae 62 
                                        L++ +e+  ++  ++d++ ++ e+l  +++++ +      ++ eq  +e+++l ++ e
  gene1320|gene1320|rna1319|rna1319 218 LQRLNEKEINISGEIDQCIQKAESLDRSMQNIISGVDLWVRRIEQTNTEKEELYKVIE 275
                                        5566666677889999999999999999999999999999999999999988887766 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.11
                              Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                        ee+ +l+e++d+ l++ + l  k +++++k ++l+ +  +l  ++++l+  + +
  gene1320|gene1320|rna1319|rna1319 297 EEIANLIESLDKSLDENKALVMKLEAIHKKNRELEGEVISLKMSTSDLNCKNAK 350
                                        566666666666666666666666666666666666665555555555544444 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 2.5e-06
                              Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                        ++++++++ ++ ++ +e+++ Le+++++ +++ +++s+++++c q+ +e+krl+ l ++i++
  gene1320|gene1320|rna1319|rna1319 391 ITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAENKRLNGLLKAIQN 452
                                        567889999999**********************************************9986 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7  11.6   6.6e-06    0.0049       1      43 [.     474     519 ..     474     521 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.6e-06
                        Prok-RING_4   1 CvlCgeqekkailepCgHlvCkeCfdsk.dls..sCPlCqrrisks 43 
                                        C lC ++ k+ +++ C H +C+eC +s   +    CP C++ +s++
  gene1320|gene1320|rna1319|rna1319 474 CSLCDTRFKNTAIVKCMHCFCEECISSRiRMRdrKCPSCNEPFSPN 519
                                        **************************996333569****9987765 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6  13.6   3.2e-05     0.024       1      43 [.     473     513 ..     473     514 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-05
                          zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkll.ekeavCpiCr 43 
                                        +C+ C +++   ++  +++C H fCe+C++ +   ++++Cp C+
  gene1320|gene1320|rna1319|rna1319 473 RCSLCDTRF---KNTAIVKCMHCFCEECISSRIrMRDRKCPSCN 513
                                        6999*****...9999*****************99********7 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   8.4   1.7e-05     0.013      16     101 ..     258     351 ..     252     368 .. 0.83
   2 ?   11.7   8.4   0.00038      0.29      34     100 ..     379     442 ..     359     462 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                             APG6_N  16 kqleqaekerdaYeeflkklkkekkeeek........qdeeleeleeeleklekeeeelleeLkelekereeleae 83 
                                        +++eq++ e++++ +  ++ k+++k  ++         +ee+++l e+l+k  +e ++l+ +L+++ k+++ele e
  gene1320|gene1320|rna1319|rna1319 258 RRIEQTNTEKEELYKVIENHKSYEKARNRgnngeqgsLEEEIANLIESLDKSLDENKALVMKLEAIHKKNRELEGE 333
                                        677888888888888888888886666558888888899************************************* PP

                             APG6_N  84 laaleeelealeeeeerf 101
                                        + +l+  +++l+ ++++ 
  gene1320|gene1320|rna1319|rna1319 334 VISLKMSTSDLNCKNAKL 351
                                        *****9999998777665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00038
                             APG6_N  34 klkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeer 100
                                        kl+++ +e++   + + + +++l  +++e+ee ++ L+ ++k+++e+++e++ +++e++++++e++r
  gene1320|gene1320|rna1319|rna1319 379 KLENSITESS---KLITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAENKR 442
                                        4444433333...456666777777888888888888888888888888888888888888877765 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   7.4   0.00019      0.14      19      55 .]     479     513 ..     470     513 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                            zf-rbx1  19 apgdeecpvvlGeCgHaFHlhCiskWlkt.rkvCPlcr 55 
                                        +  ++    ++ +C H+F  +Cis+ ++   ++CP c+
  gene1320|gene1320|rna1319|rna1319 479 TRFKN---TAIVKCMHCFCEECISSRIRMrDRKCPSCN 513
                                        44444...56779***************95677****7 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  11.3    0.0011      0.83       1      42 []     474     512 ..     474     512 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                         zf-C3HC4_4   1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                        C  C   +++ + ++C h fC +Ciss     d +   Cp C
  gene1320|gene1320|rna1319|rna1319 474 CSLCDTRFKNTAIVKCMHCFCEECISSRIRMRDRK---CPSC 512
                                        999999**********************9999886...9999 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6     0.012         9      52     119 ..      46     117 ..      30     120 .. 0.73
   2 ?    1.0   1.7      0.55   4.1e+02      70     121 ..     178     222 ..     129     237 .. 0.48
   3 ?    2.0   2.5      0.27     2e+02      62     112 ..     198     248 ..     180     276 .. 0.57
   4 ?    7.4   0.9    0.0057       4.2      63     121 ..     294     352 ..     288     354 .. 0.90
   5 ?   10.7   3.7   0.00054       0.4      49     121 ..     379     451 ..     371     453 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                            DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeik..ee..vtevredlseigedvesvkeavegleskler 119
                                        ++ e+l++  ++L ++ + + + l+ qke +++    +e    +v +++s+++ +++ ++++++++++k++r
  gene1320|gene1320|rna1319|rna1319  46 KMNEELTRKNNELIEENAALTSILETQKENTNNAGclDEapKFDVGSKISSLNYEIRRLNSIICEMQKKIAR 117
                                        55667777777777777777777777777666543112211356889**********************987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.55
                            DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        + d+k+ + +       +e++e+  ++++ +e ++++k   e++++ l+r++
  gene1320|gene1320|rna1319|rna1319 178 ERDQKIFKLS-------RELNEITLNTKDAEERLRALKIENEKWKEMLQRLN 222
                                        2233333333.......33333333333333333333333333333333332 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.27
                            DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                        ++ ++r+  +  + ++ ke+ + ++e+  ++++++++  ++ es+++ +++
  gene1320|gene1320|rna1319|rna1319 198 KDAEERLRALKIENEKWKEMLQRLNEKEINISGEIDQCIQKAESLDRSMQN 248
                                        444556666666666666666666666666666666555555443332222 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0057
                            DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                         L+++i+++ ++ld++ +  k++  ++++++++ +e++ +v s+k   ++l+ k +++e
  gene1320|gene1320|rna1319|rna1319 294 SLEEEIANLIESLDKSLDENKALVMKLEAIHKKNRELEGEVISLKMSTSDLNCKNAKLE 352
                                        68999999999999999999**************************9999998877776 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00054
                            DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                        +le+  ++ ++   + ++r+ ++ ++ +e++++ ++ik++  e+r+++s+i+++ +++++  + l++ l+ i+
  gene1320|gene1320|rna1319|rna1319 379 KLENSITESSKLITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAENKRLNGLLKAIQ 451
                                        3444444444444555677778899999999999999999999999999999999999998888888888776 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   3.7      0.04        30      21      61 ..      38      78 ..      23      90 .. 0.77
   2 ?   -0.5   0.1       2.6   1.9e+03       9      42 ..      93     129 ..      85     158 .. 0.56
   3 ?    7.7   5.5    0.0074       5.6       9      67 ..     175     233 ..     168     242 .. 0.82
   4 ?    2.1   0.9       0.4     3e+02       9      64 ..     231     286 ..     226     308 .. 0.65
   5 ?   12.2   5.3    0.0003      0.22       3      55 ..     313     373 ..     310     404 .. 0.76
   6 ?    8.5   3.6     0.004         3      11      65 ..     406     460 ..     395     493 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXX CS
                               YabA 21 leeleelkeelaelleenaeLeleneklrerleeeekkeke 61
                                         e+ e k+  +el+ +n+eL  en  l + le++++++++
  gene1320|gene1320|rna1319|rna1319 38 FLEMIECKKMNEELTRKNNELIEENAALTSILETQKENTNN 78
                                       345667899999********************655555443 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.6
                                        HHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHH CS
                               YabA   9 kleeleeqleelleeleelkeelae...lleenaeLe 42 
                                        k+++l+ ++++l++ + e+++++a+    +e +++L+
  gene1320|gene1320|rna1319|rna1319  93 KISSLNYEIRRLNSIICEMQKKIARneiFVETEEALQ 129
                                        5555566666666655555555543111233333333 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0074
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXX CS
                               YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkels 67 
                                        +l e ++++ +l++el+e+  ++++  e+ ++L++enek +e+l++ ++ke + + e++
  gene1320|gene1320|rna1319|rna1319 175 ELCERDQKIFKLSRELNEITLNTKDAEERLRALKIENEKWKEMLQRLNEKEINISGEID 233
                                        5666789999**********************************877777766555555 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.4
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXX CS
                               YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkk 64 
                                        ++++  ++ e+l ++++++ + +   + + ++ ++e+e+l + +e++++ ek++++
  gene1320|gene1320|rna1319|rna1319 231 EIDQCIQKAESLDRSMQNIISGVDLWVRRIEQTNTEKEELYKVIENHKSYEKARNR 286
                                        56666677777788888888888888888888888888888888444433333322 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.0003
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........XXX CS
                               YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl........eee 55 
                                        +k l+ kle+++++ +el  e+ +lk+++++l  +na+Lel+ ++lr +         e++
  gene1320|gene1320|rna1319|rna1319 313 NKALVMKLEAIHKKNRELEGEVISLKMSTSDLNCKNAKLELDIKHLRMERrtslledpEDK 373
                                        68899******************************************88755555544222 PP

  == domain 6  score: 8.5 bits;  conditional E-value: 0.004
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXX CS
                               YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkke 65 
                                        ee e+ le+++++ +e+++e++++  e +++ +en++l  +l+  ++ ++e +++
  gene1320|gene1320|rna1319|rna1319 406 EETEKMLESIKKQNREIRNEMSRISRECSQIDAENKRLNGLLKAIQNGDSEGDSD 460
                                        677889999999999***********************99997666666555554 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.6   1.2e+03      98     148 ..     120     169 ..      89     194 .. 0.50
   2 ?    2.6   1.1      0.14   1.1e+02      81     125 ..     222     262 ..     142     279 .. 0.60
   3 ?    2.5   0.4      0.15   1.1e+02      80     133 ..     221     270 ..     214     308 .. 0.68
   4 ?   12.8   0.6   0.00011      0.08      95     163 ..     377     445 ..     365     452 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                                        ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH CS
                          MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeia 148
                                        i  e+++++++ ++  ++ ++ ++    ++e  ++i+e+ +++++ +  + 
  gene1320|gene1320|rna1319|rna1319 120 IFVETEEALQTKDS-GEKKHNVVDDSMVANEIYRKIAEEYGDLKAKMAGLE 169
                                        33333333333222.222223333333455555666666666666666654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.14
                                        HHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHH CS
                          MCPsignal  81 Aersaqaakeiealiieiqkeindsvesleetrqrveegselvee 125
                                         e+  + + ei++ i    ++ ++  +s+++  + v+  +  +e+
  gene1320|gene1320|rna1319|rna1319 222 NEKEINISGEIDQCI----QKAESLDRSMQNIISGVDLWVRRIEQ 262
                                        233333333333333....33333333333333333333333333 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.15
                                        HHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHH CS
                          MCPsignal  80 LAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkei 133
                                        L e+  + + ei++ i    ++ ++  +s+++  + v+  +  +e+t+++ +e+
  gene1320|gene1320|rna1319|rna1319 221 LNEKEINISGEIDQCI----QKAESLDRSMQNIISGVDLWVRRIEQTNTEKEEL 270
                                        5555555556666666....5555666666666666666666666665544444 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00011
                                        H..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          MCPsignal  95 iieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnq 163
                                        i+++++ i +s + +++ ++r  + s + eet++ l++i ++  e+ ++++ i++  +++ a  +  n 
  gene1320|gene1320|rna1319|rna1319 377 IKKLENSITESSKLITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAENKRLNG 445
                                        667778889999999999****999**************************999999998777766665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  15.5      0.39   2.9e+02      15     183 ..      46     213 ..      33     224 .. 0.57
   2 ?    6.4   6.5     0.012       9.2      30     146 ..     259     362 ..     231     372 .. 0.75
   3 ?   10.3   6.8   0.00082      0.61     108     177 ..     374     443 ..     364     445 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.39
                              ATG16  15 kafaeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreel 90 
                                        k+++el +  n+L++  +al +  ++ +++           +++   +++a +   +  +ki+sl+ ++ +l++  
  gene1320|gene1320|rna1319|rna1319  46 KMNEELTRKNNELIEENAALTSILETQKEN-----------TNNAGCLDEAPK--FDVGSKISSLNYEIRRLNSII 108
                                        445555555555555555554443333222...........233333333333..456666666666666666666 PP

                              ATG16  91 aelyksrgelaqrllelneelqklee.........klkedeerlaeleaeraaletkl....kdreeelrekeklv 153
                                         e++k+ + ++   +e++e+lq++++          ++  +e  +++ +e  +l+ k+    +++ eel e+++ +
  gene1320|gene1320|rna1319|rna1319 109 CEMQKKIARNEIF-VETEEALQTKDSgekkhnvvdDSMVANEIYRKIAEEYGDLKAKMagleSKHSEELCERDQKI 183
                                        6666666666543.34555555555422211111122222333444444444444444111124778899999999 PP

                              ATG16 154 qdlqDElsaLqlqlnqaEeklrklekENke 183
                                         +l  El+  +l  + aEe+lr l+ EN++
  gene1320|gene1320|rna1319|rna1319 184 FKLSRELNEITLNTKDAEERLRALKIENEK 213
                                        9***************************53 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                              ATG16  30 rtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrll 105
                                        r+++ ++e+++l k +++          ++ ++a+    n  ++ +  sle+++a l e l +++ ++  l  +l 
  gene1320|gene1320|rna1319|rna1319 259 RIEQTNTEKEELYKVIEN---------HKSYEKAR----NRGNNGEQGSLEEEIANLIESLDKSLDENKALVMKLE 321
                                        555555666666333332.........22333333....3346777789999999999999999999999999999 PP

                              ATG16 106 elneelqkleeklkedeerlaeleaeraaletklkdreeel 146
                                        +  ++ ++le +  + + +  +l+ ++a+le  +k +++e 
  gene1320|gene1320|rna1319|rna1319 322 AIHKKNRELEGEVISLKMSTSDLNCKNAKLELDIKHLRMER 362
                                        99999999999999999999999999999999999888775 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00082
                              ATG16 108 neelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkl 177
                                        + +++kle++++e ++ + + +++  +++++ ++ e+ l+  +k + +++ E+s    +++q+++++++l
  gene1320|gene1320|rna1319|rna1319 374 TLKIKKLENSITESSKLITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAENKRL 443
                                        5578999999999999999999999999999999999999999999999999999999999999999988 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.047        35     121     168 ..      90     137 ..      82     168 .. 0.86
   2 ?    9.0   2.8    0.0012      0.89      74     147 ..     183     254 ..     155     270 .. 0.85
   3 ?    2.7   4.0       0.1        75      21     142 ..     321     446 ..     301     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.047
                            DUF4349 121 iereLsevqaeieslegqlryLdnqvaystvtvtlrepeaeteaeeee 168
                                        + +++s+ ++ei +l + + ++++++a   + v+ +e  ++++++e++
  gene1320|gene1320|rna1319|rna1319  90 VGSKISSLNYEIRRLNSIICEMQKKIARNEIFVETEEALQTKDSGEKK 137
                                        668999*****************************9999988888776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                            DUF4349  74 vtsrstsaeDVTeqyvDleaRlkaleasedrllallekaksvedlleiereLsevqaeieslegqlryLdnqva 147
                                        + + s +  ++T +  D e Rl+al+ + ++ +++l++ ++ e  ++i+ e+ +  +  esl ++++++ + v+
  gene1320|gene1320|rna1319|rna1319 183 IFKLSRELNEITLNTKDAEERLRALKIENEKWKEMLQRLNEKE--INISGEIDQCIQKAESLDRSMQNIISGVD 254
                                        44567788899***************************88655..99999999999999999999998777666 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.1
                            DUF4349  21 aairelveeagGyvesssersgtegdersasltlRvPaarldafldela....elgkvtsrstsaeDVTeqyvDle 92 
                                        +ai ++ +e++G v s +  s+++ + ++a+l+l + + r++   + l+    +  k+++ + s ++ ++ ++D +
  gene1320|gene1320|rna1319|rna1319 321 EAIHKKNRELEGEVISLK-MSTSDLNCKNAKLELDIKHLRMERRTSLLEdpedKTLKIKKLENSITESSKLITDYK 395
                                        566777778888888888.8888888899999999999666665555553324446666889999999999***** PP

                            DUF4349  93 aRlkaleasedrllallek.aksvedlleiereLsevqaeieslegqlryL 142
                                         Rl +   + +  +++le  +k+  ++ +  +++s+  ++i++  ++l+ L
  gene1320|gene1320|rna1319|rna1319 396 KRLYSISREKEETEKMLESiKKQNREIRNEMSRISRECSQIDAENKRLNGL 446
                                        *****************8867888888888888888888888888888877 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  14.4    0.0044       3.3      74     236 ..      69     230 ..      36     237 .. 0.77
   2 ?    7.6   6.0    0.0037       2.8      29     115 ..     187     270 ..     185     277 .. 0.87
   3 ?    5.1   4.3     0.021        15      14     109 ..     260     352 ..     250     358 .. 0.76
   4 ?    5.2   6.8      0.02        15      17     101 ..     366     450 ..     357     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0044
                          Laminin_I  74 naesertlnnakeLaekik.kladnikeilekvatlne....neealpssklseelaeaqrlLeelrsRdftkqle 144
                                         +  ++ +nna  L+e+ k ++  +i+ ++  + +ln      +++ + +++  e +ea      l+ +d ++++ 
  gene1320|gene1320|rna1319|rna1319  69 LETQKENTNNAGCLDEAPKfDVGSKISSLNYEIRRLNSiiceMQKKIARNEIFVETEEA------LQTKDSGEKKH 138
                                        44444555666666666654666777777777777777766566667777776666665......999******** PP

                          Laminin_I 145 eaeaelkaAqkLLsrvqtllqklqeenkaLkealrdsLaeyeakLsDlrelleeAaaktrdanrlnlanqanlrei 220
                                        ++ ++ + A++ + ++ + +  l+++  +L+ + +++L e ++k   l   l+e +  t+da+++++a +   ++ 
  gene1320|gene1320|rna1319|rna1319 139 NVVDDSMVANEIYRKIAEEYGDLKAKMAGLESKHSEELCERDQKIFKLSRELNEITLNTKDAEERLRALKIENEKW 214
                                        ******************************************************************9988888877 PP

                          Laminin_I 221 ekkkeevseeknqlee 236
                                        ++  ++++e++  ++ 
  gene1320|gene1320|rna1319|rna1319 215 KEMLQRLNEKEINISG 230
                                        7777777777666665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0037
                          Laminin_I  29 qeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilek 104
                                        ++ l+++  + +++   e+ l  L+ e e+  + +++  +k  ++  e+++ +++a++L+   ++++  +   + +
  gene1320|gene1320|rna1319|rna1319 187 SRELNEITLNTKDA---EERLRALKIENEKWKEMLQRLNEKEINISGEIDQCIQKAESLDRSMQNIISGVDLWVRR 259
                                        55555555555555...555******************************************************** PP

                          Laminin_I 105 vatlneneeal 115
                                        ++++n ++e+l
  gene1320|gene1320|rna1319|rna1319 260 IEQTNTEKEEL 270
                                        *****987765 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.021
                          Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLae 89 
                                        +++ n++ e+l k +++  s e+a++    + ++e  sL++e+ +L + + + l++ + +  + e++ ++  eL+ 
  gene1320|gene1320|rna1319|rna1319 260 IEQTNTEKEELYKVIENHKSYEKARN---RGNNGEQGSLEEEIANLIESLDKSLDENKALVMKLEAIHKKNRELEG 332
                                        44444444444444444444444444...444455899************************************** PP

                          Laminin_I  90 kikkladnikeilekvatln 109
                                        ++  l+++ + ++ k a+l+
  gene1320|gene1320|rna1319|rna1319 333 EVISLKMSTSDLNCKNAKLE 352
                                        *******9999999887775 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.02
                          Laminin_I  17 inanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekik 92 
                                        +++  ed t ++++ ++ + + +++i   +k l s+  e ee  k ++   ++  ++++e++r++ + ++ +++ k
  gene1320|gene1320|rna1319|rna1319 366 LLEDPEDKTLKIKKLENSITESSKLITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAENK 441
                                        66667888889999999999**************************************************999999 PP

                          Laminin_I  93 kladnikei 101
                                        +l+  +k+i
  gene1320|gene1320|rna1319|rna1319 442 RLNGLLKAI 450
                                        988777766 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       5.3   3.9e+03     112     132 ..      97     117 ..      92     130 .. 0.61
   2 ?    5.4   0.8      0.03        23      84     138 ..     193     247 ..     180     250 .. 0.88
   3 ?    9.4   0.2    0.0018       1.3      94     139 ..     407     452 ..     380     460 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                              HrpB7 112 tarkiaRndaqidacrerier 132
                                         + +i+R+++ i  ++++i+r
  gene1320|gene1320|rna1319|rna1319  97 LNYEIRRLNSIICEMQKKIAR 117
                                        555666666666666666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.03
                              HrpB7  84 legrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraae 138
                                        ++ + + ae++l+a++ + ++ ++ +++ ++k     ++id+c +++e l+r ++
  gene1320|gene1320|rna1319|rna1319 193 ITLNTKDAEERLRALKIENEKWKEMLQRLNEKEINISGEIDQCIQKAESLDRSMQ 247
                                        555678899********************999999*****************987 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0018
                              HrpB7  94 elaaarqaldaaedavaatarkiaRndaqidacrerierlrraaer 139
                                        e+++  + +++++++++    +i+R  +qida ++r++ l +a + 
  gene1320|gene1320|rna1319|rna1319 407 ETEKMLESIKKQNREIRNEMSRISRECSQIDAENKRLNGLLKAIQN 452
                                        55666678899**************************999988876 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.0      0.15   1.1e+02      34      71 ..      40      77 ..      28      81 .. 0.87
   2 ?   -0.3   0.7      0.76   5.7e+02      32      48 ..     105     121 ..      92     174 .. 0.48
   3 ?    2.1  14.9      0.14     1e+02      29     128 ..     170     273 ..     148     286 .. 0.68
   4 ?    2.6   0.7       0.1        74      34      86 ..     231     283 ..     228     302 .. 0.75
   5 ?    5.6  10.9     0.012       8.7      29     133 ..     264     366 ..     254     376 .. 0.74
   6 ?   12.0  10.4   0.00013     0.099      27     104 ..     376     453 ..     371     460 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
                                GAS 34 eieelkkkeernekelseisqenkrlkepLkkaeeeve 71
                                       e+ e kk +e+ +++ +e+ +en  l+  L++++e+ +
  gene1320|gene1320|rna1319|rna1319 40 EMIECKKMNEELTRKNNELIEENAALTSILETQKENTN 77
                                       67789999999999999999999999999999998776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.76
                                GAS  32 Keeieelkkkeerneke 48 
                                         + i+e++kk +rne  
  gene1320|gene1320|rna1319|rna1319 105 NSIICEMQKKIARNEIF 121
                                        44444444444444322 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.14
                                GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkq....slknlkarlkeleke 100
                                         +  ee++e ++k  + ++el+ei+ + k+ +e L++++ e+e+ ++ l++ +++      ++++  ++ ++l++ 
  gene1320|gene1320|rna1319|rna1319 170 SKHSEELCERDQKIFKLSRELNEITLNTKDAEERLRALKIENEKWKEMLQRLNEKEInisgEIDQCIQKAESLDRS 245
                                        5566778888888888888888888888888888888888887777777766554431111456666777777777 PP

                                GAS 101 lkdlkwehevleqrfekvekerdelykk 128
                                        ++++    +    r+e+   e++elyk 
  gene1320|gene1320|rna1319|rna1319 246 MQNIISGVDLWVRRIEQTNTEKEELYKV 273
                                        7777777777777777777777777765 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.1
                                GAS  34 eieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqs 86 
                                        ei +  +k+e+ ++ +++i +     +  +++ + e+eeL k ++n+++  ++
  gene1320|gene1320|rna1319|rna1319 231 EIDQCIQKAESLDRSMQNIISGVDLWVRRIEQTNTEKEELYKVIENHKSYEKA 283
                                        67777789999999999999999999999************999998764333 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.012
                                GAS  29 kslKeeieelkkkeernekelseisq.enkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                        ++ Kee+ +  ++ ++ ek  +  ++ e  +l+e++    + +e L k l + +   ++l++++++++ele e+ +
  gene1320|gene1320|rna1319|rna1319 264 NTEKEELYKVIENHKSYEKARNRGNNgEQGSLEEEI---ANLIESLDKSLDENKALVMKLEAIHKKNRELEGEVIS 336
                                        455555555555555555554443331333344433...44578999***************************** PP

                                GAS 104 lkwehevleqrfekvekerdelykkfeaai 133
                                        lk++   l+ + +k+e +++ l+ + ++++
  gene1320|gene1320|rna1319|rna1319 337 LKMSTSDLNCKNAKLELDIKHLRMERRTSL 366
                                        ********************9998877665 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00013
                                GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                        +Ik+l + i+e  k  +  +k+l+ is e+++ ++ L+  ++++ e r+++ + +++ +++++ ++rl+ l k ++
  gene1320|gene1320|rna1319|rna1319 376 KIKKLENSITESSKLITDYKKRLYSISREKEETEKMLESIKKQNREIRNEMSRISRECSQIDAENKRLNGLLKAIQ 451
                                        69******************************************************************99999998 PP

                                GAS 103 dl 104
                                        + 
  gene1320|gene1320|rna1319|rna1319 452 NG 453
                                        75 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  11.3      0.02        15       3      47 ..     476     516 ..     473     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.02
                          zf-RING_4   3 lCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCreeY 47 
                                        lCd+++    k+    +C + +C  C +  ++  + +CP C e++
  gene1320|gene1320|rna1319|rna1319 476 LCDTRF----KNTAIVKCMHCFCEECISSRIRMRDRKCPSCNEPF 516
                                        444444....55666789999******9988899*********98 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       2.7     2e+03      47      76 ..     280     307 ..     258     336 .. 0.63
   2 ?    9.7   0.5    0.0022       1.6      10      63 ..     400     454 ..     383     466 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.7
                                        CHHHCCTTEEECEETTTS-CCCHHHHCCS- CS
                           Rotamase  47 knsakngGdlgwvekgqlppefekaafslk 76 
                                        +++a+n+G+ g  e+g l++e+++ ++sl+
  gene1320|gene1320|rna1319|rna1319 280 YEKARNRGNNG--EQGSLEEEIANLIESLD 307
                                        44455555555..55555555555555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                                        E----HHHHHHHHHHHHCCTCCCHHHHHHHHCCC-..-CHHHCCTTEEECEETTT CS
                           Rotamase  10 asekeraeakakaeeileqlksgedtFeelArkySd.dknsakngGdlgwvekgq 63 
                                        ++++e++e+++ +e+i++q ++  ++++++ r+ S+ d ++++ +G l  ++ g+
  gene1320|gene1320|rna1319|rna1319 400 SISREKEETEKMLESIKKQNREIRNEMSRISRECSQiDAENKRLNGLLKAIQNGD 454
                                        5789*******************************75666677788888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2831  (0.157901); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                       128  (0.00713927); expected 17.9 (0.001)
Passed Fwd filter:                        74  (0.00412739); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 1.52u 0.34s 00:00:01.86 Elapsed: 00:00:00.57
# Mc/sec: 2785.75
//
Query:       gene132|gene132|rna132|rna132  [L=687]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-96  321.5   0.8      1e-95  321.2   0.8    1.1  1  HSP70     Hsp70 protein
  ------ inclusion threshold ------
      0.011   16.1   0.2        2.6    8.5   0.1    3.1  2  FtsA      Cell division protein FtsA
      0.014   15.4   0.2          8    6.5   0.0    2.7  2  PUA       PUA domain
       0.71   10.1   6.0       0.25   11.5   1.7    2.4  2  DUF3091   Protein of unknown function (DUF3091)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.2   0.8   2.3e-99     1e-95       1     594 [.      32     671 ..      32     676 .. 0.84

  Alignments for each domain:
  == domain 1  score: 321.2 bits;  conditional E-value: 2.3e-99
                                    EEEEEEXSSEEEEEEEET..TEEEEEXXTTSXSSEESEEEEXTTSEEETHHHHHCTTT............TGGGEEEXGG CS
                          HSP70   1 viGiDLGttnsvvavmeg..gkievianeegnrttPsvvaFtkkerlvGeaAkrqavt............npkntvfsvK 66 
                                    ++GiDLGtt+s+++v     ++++ +    g+ t Psvv F+k     G+++k +a+             n++  ++++K
  gene132|gene132|rna132|rna132  32 AVGIDLGTTYSCISVYSPslKDTKFVLSPSGEETYPSVVYFKKLPEGDGNKSKYEAIAgwpglqmynaegNANTYFYAFK 111
                                    59*************9753379999****************9987777777777765322222233222255566899** PP

                                    GTTTXB...TTSHHHHHHHTTXSSEE.EEETTSBEEEEEEETTE......EEEHHHHHHHHHHHHHHHHHHHHTSBEEEE CS
                          HSP70  67 rliGrk...fsdpevqkeikelpykv.vkkengkavveveaage......kftpeqisamvLkklketaeaylgkkvtda 136
                                    r +G +     d++v+  +++ ++ + v++  gk  v  +++++      + tpe++s+ vL+ lk++     + +++ +
  gene132|gene132|rna132|rna132 112 RGMGIEdlaNIDKKVEDIKRNASVPIfVESVGGKKRVAYKIQENdlgsyeSVTPEELSSHVLRMLKDQILR--EYRIQGI 189
                                    ****742213355666555444444324555777777777776666667789**************97643..34699** PP

                                    EEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHH..HHTCCSS.......SCEEEEEEEEXSSXEEEEEEEEET CS
                          HSP70 137 vitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaala..YGldkkd.......kernvlvyDlGggtfdvSilelek 207
                                     itvPaYf+ +q  at  A+++AGL    i  ep Aaa a  Y l +k        ++ n+ v+DlGggtfdvSi+e + 
  gene132|gene132|rna132|rna132 190 TITVPAYFDLNQVAATVKAAEMAGLPTPMIWKEPSAAAFAhtYDLIRKGittkeevDDMNICVFDLGGGTFDVSIVESSG 269
                                    **************************************99555555554666668999********************** PP

                                    TEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCS....EEEEEE.EEE CS
                          HSP70 208 GvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqt....einlei.etv 282
                                    G + v +  g++ lGGe++ ++l++++++++k+++g d+ +++++  rl++ +e++K+++ ++ ++    ++n +i +++
  gene132|gene132|rna132|rna132 270 GFMMVPNYGGNNFLGGENVNDNLTQYFASHIKSSTGFDVMENQNVKLRLRNLVEEMKRDICDEVRKspgrKANSSIsKSF 349
                                    ***********************************************************988654311113444432456 PP

                                    ETTT.EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHH.....HCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTT..CHH CS
                          HSP70 283 dedg.kdlseklsRakfeelvedllertlepvekalk.....daklkkeeidevvlvGGstRiPkvqelvkelfg..kep 354
                                      dg k ++ +l+ +kf++l+ed+ +++ + +  +l+     + +++k+ i+ v+lvGGstRiPkv ++v+e+fg  k  
  gene132|gene132|rna132|rna132 350 IYDGeKSITLELTNEKFNKLNEDFYSKIRKTMDLLLSgdgkeNKGYDKNLINRVLLVGGSTRIPKVIDIVEEIFGadKIY 429
                                    66677******************************964221134567899*************************87888 PP

                                    BSSSHTTTHHHHHHHHH.HHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEE CS
                          HSP70 355 sktvnpDeavaiGAAvq.agvlsgeeevkdllllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtavei 433
                                     ++vn+D +va+GAA+  a+ ls  +e ++++  D +pLslgi t+ + ++ +i++   +p+  ++ f+ta+dnq +v+i
  gene132|gene132|rna132|rna132 430 YEGVNADTIVARGAALYtANELSMLSESEQIVTADSVPLSLGICTEEDHFEAIISKGALLPATGTKEFTTAQDNQVKVRI 509
                                    9**************972567888899***************************************************** PP

                                    EEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSS.SBHHHHHHHHH CS
                          HSP70 434 evlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseg.lseeeiekmvk 512
                                    +v qg  e  kdn  +g  eld    +prGvp+i Vt++id +G + v+a d +++k+++   ++    +++eeie+ ++
  gene132|gene132|rna132|rna132 510 RVAQGGLESFKDNIYIGDIELDLPGNQPRGVPRIGVTLEIDTHGKIYVKAVDLQNDKTADAYFSSVVAnMTSEEIERFEE 589
                                    **********************999*********************************999998877769*******988 PP

                                    HHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..GGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHH CS
                          HSP70 513 daeesaeedkkkkeaieakneaeelvyslekkleee..aekvseaekekvesaieeLkeeleeeekeeieakteelkkvv 590
                                      ++ ++++  kk   e  +++e  + ++e+    e   e++++++ e v+++  +L+++ e + + +ie+k++e+++ +
  gene132|gene132|rna132|rna132 590 RVHSEENQELVKK--REVVKKLEYALSQAENPKFAEiiPENIKKDALEYVQKTRLWLEKHKEIAPRIHIEEKLQEFDNGI 667
                                    7766655555444..467777888888887755544479999*9999*************99999999****99999887 PP

                                    HHHH CS
                          HSP70 591 ekia 594
                                    +++ 
  gene132|gene132|rna132|rna132 668 KEFL 671
                                    7765 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.011        51       1      20 [.      33      51 ..      33      64 .. 0.83
   2 ?    8.5   0.1   0.00058       2.6       2      87 ..     252     427 ..     251     625 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
                                   EEEEE-SSSEEEEEEETTEE CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                           FtsA  1 alvDiGagktdvavaedgal 20
                                   +++D+G++ ++++v++  +l
  gene132|gene132|rna132|rna132 33 VGIDLGTTYSCISVYSP-SL 51
                                   68*************87.45 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00058
                                    EEEE-SSSEEEEEEETTEEEEEEEES-.......-HHHHHHH........HHHHHT--HHHHHHHHHHH--S--...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxx...... RF
                           FtsA   2 lvDiGagktdvavaedgalvhlrvigv.......ggngitkd........iakalrtaveeAerikikyGsala...... 60 
                                    + D+G+g+ dv+++e ++   + +++        gg+++++         i+ + +  v e +++k       +      
  gene132|gene132|rna132|rna132 252 VFDLGGGTFDVSIVESSG--GFMMVPNyggnnflGGENVNDNltqyfashIKSSTGFDVMENQNVKL------Rlrnlve 323
                                    77*************942..34444444444445555555556666666655555555566666663......1334433 PP

                                    ..............EEEEEHHHHH........................................................ CS
                                    ..............xxxxxxxxxx........................................................ RF
                           FtsA  61 ..............ekeigrkels........................................................ 70 
                                                                                                                    
  gene132|gene132|rna132|rna132 324 emkrdicdevrkspG--------Rkanssisksfiydgeksitleltnekfnklnedfyskirktmdlllsgdgkenkgy 395
                                    555555555544441........044445556666677777777777888889999999999999999999999999999 PP

                                    ............GGGGSTTHHHHHHHHH...T CS
                                    ............xxxxxxxxxxxxxxxx...x RF
                           FtsA  71 ............ggsalpnleelaeral...s 87 
                                                g++ +p++++++e+++   +
  gene132|gene132|rna132|rna132 396 dknlinrvllvgGSTRIPKVIDIVEEIFgadK 427
                                    99999999999999999999999999984430 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0028        12      29      60 ..     408     452 ..     399     460 .. 0.67
   2 ?    6.5   0.0    0.0018         8      50      71 ..     575     597 ..     564     600 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0028
                                    TT--TTSEEEEEET............T.SCEEEEEEESS-HHHHH CS
                            PUA  29 gdfeegdvVaivde............d.gelvavGlanysseela 60 
                                    g+ +   v++iv e            + +++va+G a+y+++el 
  gene132|gene132|rna132|rna132 408 GSTRIPKVIDIVEEifgadkiyyegvNaDTIVARGAALYTANELS 452
                                    555555566666665555444444443369*************96 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                                    EEESS-HHHHHHHC.TSEEEEEE CS
                            PUA  50 Glanysseelakik.ggksveie 71 
                                    ++an++see+++++ + +s+e+ 
  gene132|gene132|rna132|rna132 575 VVANMTSEEIERFEeRVHSEENQ 597
                                    68************778888876 PP

>> DUF3091  Protein of unknown function (DUF3091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.87   3.9e+03      73      91 ..     363     381 ..     355     384 .. 0.74
   2 ?   11.5   1.7   5.5e-05      0.25       6      63 ..     582     640 ..     578     660 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.87
                        DUF3091  73 alnvfklkkkyllkvkenl 91 
                                    + ++ kl++++++k+ + +
  gene132|gene132|rna132|rna132 363 NEKFNKLNEDFYSKIRKTM 381
                                    4567788888888888776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.5e-05
                        DUF3091   6 eeiek.dYpnfsrevleeikrlkeklkqlfdelqSkkenmtCnkPenidekdlenLenl 63 
                                    eeie+ + + +s+e  e +k++++  k+ +  +q+++ +     Peni+++ le+ ++ 
  gene132|gene132|rna132|rna132 582 EEIERfEERVHSEENQELVKKREVVKKLEYALSQAENPKFAEIIPENIKKDALEYVQKT 640
                                    566653456799*****************************************999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (687 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.36s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 3900.61
//
Query:       gene1321|gene1321|rna1320|rna1320  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0028   17.2   1.8     0.0035   16.9   1.2    1.5  1  HtrL_YibB  Bacterial protein of unknown function (HtrL_YibB)
  ------ inclusion threshold ------
       0.02   15.0   2.3      0.034   14.3   1.0    2.0  2  DUF150_C   RimP C-terminal SH3 domain
      0.028   14.1   0.1      0.042   13.5   0.1    1.4  1  DUF4085    Protein of unknown function (DUF4085)
      0.042   13.8   0.1      0.086   12.8   0.0    1.6  2  CHAD       CHAD domain


Domain annotation for each model (and alignments):
>> HtrL_YibB  Bacterial protein of unknown function (HtrL_YibB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.2   7.7e-07    0.0035      22      87 ..      19      82 ..      11     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.7e-07
                          HtrL_YibB 22 efreklarsldtyfeylekLltLenelvvftsdelkdrvkkirtkkktkvikidlnklprkilnei 87
                                       +  e+  rs ++y ++++++  Lenel     +++k +v+ ++ +++ +   +d++++ ++ ++e 
  gene1321|gene1321|rna1320|rna1320 19 KRVEEKKRSAEIYKDFVKRMYELENELDFISAEDQKSMVESTKRRRRSTT--LDVDEILYTAVDET 82
                                       4456778**********************************988866654..56666666666654 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.63   2.8e+03      37      61 ..      51      74 ..      47      80 .. 0.67
   2 ?   14.3   1.0   7.5e-06     0.034      25      63 ..     123     158 ..     113     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.63
                           DUF150_C 37 deetitlevdgkkrkkettipladi 61
                                       ++++  +e ++  r++ tt+ +++i
  gene1321|gene1321|rna1320|rna1320 51 EDQKSMVESTKR-RRRSTTLDVDEI 74
                                       555566776666.666777777766 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.5e-06
                           DUF150_C  25 grkkftGkivevdeetitlevdgkkrkkettipladidk 63 
                                        +r++f+G iv++ ee+i+l  ++    k+++i l+di+ 
  gene1321|gene1321|rna1320|rna1320 123 KREEFVGAIVSIGEEDIVLKTKEY---KRLKILLDDIRS 158
                                        599*****************6666...6899*****986 PP

>> DUF4085  Protein of unknown function (DUF4085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.5e-06     0.042       6      71 ..      38     106 ..      33     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.5e-06
                            DUF4085   6 efeelq.sellsfeetkkdweeelaeekeegedleellkeeleelKedLLkfLP..keilpyiqditln 71 
                                         +e  +  +++s e++k+ +e++ +  ++ + d++e+l   ++e  +dL ++L   k +   i++  ln
  gene1321|gene1321|rna1320|rna1320  38 MYELENeLDFISAEDQKSMVESTKRRRRSTTLDVDEILYTAVDETAKDLRRILGgeKDLDVFIENNALN 106
                                        565444589******************************************996224455566666666 PP

>> CHAD  CHAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.43   1.9e+03     121     127 ..      31      37 ..       9      73 .. 0.47
   2 ?   12.8   0.0   1.9e-05     0.086      41      84 ..      70     125 ..      59     165 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.43
                                        HHHHHHH CS
                               CHAD 121 yqallda 127
                                        y++++++
  gene1321|gene1321|rna1320|rna1320  31 YKDFVKR 37 
                                        2222222 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.9e-05
                                        HTTTSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH.................H CS
                               CHAD  41 lfapvldkeeaaalekelrwlaraLGeaRDldVllerllsrle................e 84 
                                         ++++l    + a+++  ++l r+LG   DldV++e  + +++                e
  gene1321|gene1321|rna1320|rna1320  70 DVDEIL----YTAVDETAKDLRRILGGEKDLDVFIENNALNIKgcvftkgdkikarikrE 125
                                        444444....8899999******************8766555555555444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1171.89
//
Query:       gene1322|gene1322|rna1321|rna1321  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1229.61
//
Query:       gene1323|gene1323|rna1322|rna1322  [L=474]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-56  190.4  14.1    6.1e-56  189.9  14.1    1.2  1  SecY             SecY translocase
    2.5e-15   56.0   0.1      6e-15   54.8   0.1    1.7  1  Plug_translocon  Plug domain of Sec61p


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.9  14.1   6.9e-60   6.1e-56       1     305 [.      75     455 ..      75     456 .. 0.84

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 6.9e-60
                                        BTTSSTCHHHHHHHHHHHHHHHHSSSSSSTS.-S.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC......... CS
                               SecY   1 sifaLGImPyitasIilqLltvvipkleelk.ke.geegrkkinqitryltvvlalvqalgialslg......... 65 
                                        +++ LG +P++t+s+i+q+lt+     e+lk +   +e++++ n ++r++++++++ qa++ +++ g         
  gene1323|gene1323|rna1322|rna1322  75 TLMDLGTSPVVTSSLIMQFLTM----SEILKvDWsIKEDKNLHNATQRLISLIMTVGQAFVQVYT-Gfygspkslg 145
                                        89******************88....466665445999**********************97643.56799***** PP

                                        .HH.HHHHHHHHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHC.CHSS.................-HHHH. CS
                               SecY  66 .lalllivlqltagtvllmwLgEqite.kGiGnGisllifagivarlp.kals.................gliel. 120
                                         + +ll+v+ql++ +v++++L+E++++ +G+GnG+ l+i+++++++++ ka+s                     l 
  gene1323|gene1323|rna1322|rna1322 146 tIYCLLLVMQLIFSGVIIILLDELLQKgYGLGNGVNLFIATNVCESIVwKAFSpkvlftgrgiefegsviA---Lf 218
                                        *89**************************************************988888888877765551...24 PP

                                        ...........SS........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S-EEEEETTCCCS CS
                               SecY 121 ...........ale......gilallllllvtllvillvvyveeaerripvqya.krgrkggqssylPlklnyagv 178
                                                   a        + l++l+ ll t+l+++lv+y++ +++++p +++  r    g+  ++P+kl+y++ 
  gene1323|gene1323|rna1322|rna1322 219 hllvvrknkfaA-IyeaffrQNLPNLFSLLSTVLLFTLVIYLQGIRVELPTESSqVR----GHVAKFPIKLLYTST 289
                                        444444443331.0344556669******************************9667....99************* PP

                                        CHHHHHHHHHHHHHCCCCS.........................................TCCCS..THHHHHHHH CS
                               SecY 179 iPiIfassllalpstiaqfl........................................lalls..psvlyvvly 212
                                        +PiI +  ++   s+i +fl                                        l   +   ++l+++ y
  gene1323|gene1323|rna1322|rna1322 290 MPIIAQNYIVGHISSISSFLyrrwpqnlvvkilgvwntskggrympvsgisyyitspesiL---EglRDPLRFFAY 362
                                        ***********99999888899999888888888888888888877777665555543222...145334555555 PP

                                        HHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSSCTTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                               SecY 213 vlliif....Fayfyteit.fnpkevaenlkksggfipgirpgketakyLekvlsritliGalflaliavlpdllg 283
                                        + ++++    ++  + e+  ++p++ a++lk+s + ++g+r+  +ta++L++++++++++G+++ +++++l++l++
  gene1323|gene1323|rna1322|rna1322 363 LSIMLLtsaiLSTSWLELNeLSPEKAAQKLKESRMRLKGVRE-ASTATVLSRYIPTAAFLGGILTSMVVILSNLFD 437
                                        5555544555*******************************7.8******************************** PP

                                        TS.TT.TTHHHHHHHHHHHHHH CS
                               SecY 284 asligafggtslLivVgvalet 305
                                        a  ig  +gt + ++ +++ ++
  gene1323|gene1323|rna1322|rna1322 438 A--IG--SGTNIFLATSIVNQY 455
                                        *..88..9*********99887 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.1   6.7e-19     6e-15       1      35 []      40      74 ..      40      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 6.7e-19
                                       HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                    Plug_translocon  1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35
                                       l+Ylv sq+PL+Gi s++ +Dp++w+Ra++AsnrG
  gene1323|gene1323|rna1322|rna1322 40 LIYLVSSQVPLFGIISNDAADPLQWMRAMMASNRG 74
                                       7*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3040.67
//
Query:       gene1324|gene1324|rna1323|rna1323  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-82  276.4   0.0    3.5e-82  276.1   0.0    1.0  1  Peptidase_M22   Glycoprotease family
  ------ inclusion threshold ------
       0.05   13.2   0.0       0.97    9.0   0.0    2.1  2  Carbam_trans_N  Carbamoyltransferase N-terminus


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.1   0.0     4e-86   3.5e-82       2     271 .]      20     293 ..      19     293 .. 0.95

  Alignments for each domain:
  == domain 1  score: 276.1 bits;  conditional E-value: 4e-86
                                        CEXEEEEEEEEE....S.SSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHH CS
                      Peptidase_M22   2 vlanvvasqkelhakyG.GvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkgl 76 
                                        +lan+  +++   +++G G++P +++++H+ ++l li+  l++a + l+d+d+ ++tkgPG++ +L v++++A++l
  gene1324|gene1324|rna1323|rna1323  20 ILANERFTYA---PPPGeGFIPAKTAEHHRSKILDLIAISLEKAAICLSDVDVFCYTKGPGMGLPLAVVATVARTL 92 
                                        5666666665...89999********************************************************** PP

                                        HHHCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..S CS
                      Peptidase_M22  77 alalnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpy 152
                                        +l +nkPl++Vnh++ah++++r+ +k e+Pvvl+ sGg+tq+++++++ry+i+getld+a+g+++d++ar+l+lp+
  gene1324|gene1324|rna1323|rna1323  93 SLYCNKPLIPVNHCIAHIEMGRFMTKAENPVVLYASGGNTQIIAYHNKRYRIFGETLDIAVGNCIDRFARALRLPN 168
                                        **********************998889*****************99***************************** PP

                                        ..SCCHHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHH.ST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Peptidase_M22 153 ..pggpkieklakeg.kkiefprplkgldfsfsGlktavlkel.ek.e.vedlaasfqeavvdhlvekteralklp 222
                                           +g+ +e++ak g ++ie+p+++kg+d+sfsG+ +++ +++ e+ + + dl++s+qe++++ lve+tera++  
  gene1324|gene1324|rna1323|rna1323 169 fpAPGLSVERYAKLGkNYIELPYVVKGMDVSFSGILSNIKSKIvENdQmKYDLCYSLQETIFSALVEVTERAMAFS 244
                                        654667*********888*************************766548*************************** PP

                                        TBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                      Peptidase_M22 223 kakelvilGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                        ++ke++i+GGv++n rL+e+++ +a+e+g   +  ++++c dn+ mia+
  gene1324|gene1324|rna1323|rna1323 245 NSKEVLIVGGVGCNLRLQEMMSIMAKERGGISYGMDERFCIDNGLMIAY 293
                                        **************************9*999999*************97 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.017   1.5e+02      43      70 ..      48      75 ..      39      92 .. 0.83
   2 ?    9.0   0.0   0.00011      0.97     259     308 ..     212     261 ..     190     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.017
                     Carbam_trans_N 43 pklkaidyaleeagvelsdiDqivfdei 70
                                       + l+ i++ le+a + lsd+D++ + + 
  gene1324|gene1324|rna1323|rna1323 48 KILDLIAISLEKAAICLSDVDVFCYTKG 75
                                       44678999***************99875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00011
                     Carbam_trans_N 259 kearekdedlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNikl 308
                                         e+ + + dl  s+q+ +   +vev++ +++  +++   + GGv+ N+ l
  gene1324|gene1324|rna1323|rna1323 212 VENDQMKYDLCYSLQETIFSALVEVTERAMAFSNSKEVLIVGGVGCNLRL 261
                                        333333459**************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1970.64
//
Query:       gene1325|gene1325|rna1324|rna1324  [L=798]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-15   55.4   0.0    1.5e-14   54.2   0.0    1.7  1  HA2             Helicase associated domain (HA2)
    2.4e-12   47.0   0.1      6e-12   45.8   0.1    1.7  1  OB_NTP_bind     Oligonucleotide/oligosaccharide-binding (OB)-
    8.9e-11   42.1   0.4    3.4e-10   40.2   0.0    2.3  2  Helicase_C      Helicase conserved C-terminal domain
    1.4e-05   25.3   0.1    3.2e-05   24.2   0.1    1.6  1  AAA_22          AAA domain
    0.00053   19.8   0.7     0.0021   17.9   0.5    2.1  2  DEAD            DEAD/DEAH box helicase
     0.0018   18.0   0.0      0.003   17.3   0.0    1.3  1  AAA_30          AAA domain
     0.0028   17.7   0.0     0.0051   16.8   0.0    1.4  1  Flavi_DEAD      Flavivirus DEAD domain
  ------ inclusion threshold ------
      0.022   15.2   0.2       0.28   11.7   0.1    2.5  2  ABC_tran        ABC transporter
      0.023   14.4   0.0      0.074   12.8   0.0    1.8  2  AAA_29          P-loop containing region of AAA domain
      0.023   14.1   0.1      0.052   12.9   0.1    1.6  1  ATPase          KaiC
      0.054   13.5   0.0       0.13   12.2   0.0    1.6  1  ResIII          Type III restriction enzyme, res subunit
      0.095   12.4   0.0        2.3    7.9   0.0    2.3  2  AAA_24          AAA domain
       0.13   11.4   0.2         15    4.6   0.0    2.2  2  Nuc_sug_transp  Nucleotide-sugar transporter


Domain annotation for each model (and alignments):
>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   1.1e-17   1.5e-14       1      74 [.     498     569 ..     498     620 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.1e-17
                                HA2   1 AlelLvalgALdeegnlTelGrkmaelPlsprlakmLlaaaeleegcldevitivAalsveeifleeneeekee 74 
                                        Al lL++lgA+ ++g lT+ G++m+el l+p la+m l + ++  g++de++tiv++lsv ++f e  ++++  
  gene1325|gene1325|rna1324|rna1324 498 ALLLLYRLGAVCRKGLLTKDGKEMSELRLEPPLARMVLNSPRY--GVVDEIATIVSMLSVYNVFFEGFDKSSPL 569
                                        7889************************************666..*******************9877655444 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.1   4.3e-15     6e-12       1      83 []     636     712 ..     636     712 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.3e-15
                                        HHHHHHHHHTTCEEEEEETTCCEEETTTCEEEEE-TTSTTTTT...TSSSEEEEEEEEESSSEEEEEEEEE-HHHH CS
                        OB_NTP_bind   1 lraillaGlypqiarkdpskkdyktartktrvfihpsSvlaknekekepewvvytelvettklylrdltaidpawL 76 
                                        ++++++++ y +iark+++k  y ++++ + + ihpsS+l++     ++++v+++  ++t+  y+  +++i+p+ +
  gene1325|gene1325|rna1324|rna1324 636 IQRCIVSSIYYNIARKKDKK--YICLSNFRVCKIHPSSMLRD----CTSQYVLFYRHLSTKTEYIYCCSDINPQVI 705
                                        789***********998877..9****9*************8....****************************** PP

                                        HHHSTTT CS
                        OB_NTP_bind  77 llfagqi 83 
                                        l+ ag++
  gene1325|gene1325|rna1324|rna1324 706 LEEAGNY 712
                                        *999986 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.5e-13   3.4e-10       3     110 ..     300     435 ..     296     436 .. 0.78
   2 ?   -2.7   0.0       5.3   7.3e+03       6       6 ..     644     644 ..     598     680 .. 0.57

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.5e-13
                                        HHHHHHHHHHTTTTSEEEEEESSHHHHHH....HHHH........HHHT......TSTEEEESTTSTHHHHHHHHH CS
                         Helicase_C   3 leallellkleeeggkilifvntidrlek....vkll........lekk......gikvavlhgelpqnereeile 60 
                                        ++++     ++ e+g+il+f++ ++++e     v++            k      ++k+ +++++l+ + + ++++
  gene1325|gene1325|rna1324|rna1324 300 ILHIH----ESCEEGDILVFMTGRNDVEGvvgiVNYWarnkclseG--KgededaDLKAFPFYSQLSEEMQSKVFK 369
                                        34444....445899**********997675553333555544550..14555669*******************9 PP

                                        HHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS....SSH.............HHHHHHHTTSSST CS
                         Helicase_C  61 qfnkgesdvLiatdvaerGidipkvnlVinfdlp....rnv.............tsyiqriGRtgRa 110
                                          ++  ++++++t++ae++++ip++ +Vi+ +l+    +n+             +++ qr+GR+gR 
  gene1325|gene1325|rna1324|rna1324 370 VERN-IRKCIVSTNIAETSLTIPNIGYVIDTGLQkisvYNYdtgeslvtvpvsrANADQRAGRAGRT 435
                                        9954.778**************************76553337788889999999************6 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                                        H CS
                         Helicase_C   6 l 6  
                                        +
  gene1325|gene1325|rna1324|rna1324 644 I 644
                                        1 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   2.4e-08   3.2e-05       4     128 ..     121     253 ..     117     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.4e-08
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......... 70 
                                        +++++v++Ge+G+GK+t + r+l+           +++++ +t p     ++l++ l r++g+   +         
  gene1325|gene1325|rna1324|rna1324 121 KHQVTVLVGEAGSGKSTQVPRYLYLEGYG------DKGIIGCTQPRRAAVTSLASTLERDMGSVVGYsirfdnttt 190
                                        6789********************98544......9999999999999**************988889***99988 PP

                             AAA_22  71 .....erlsseell.ealeqalraravielliiDEaqhlrs...eealeeLrsllnlsrkgvqliLv 128
                                             +  ++  +l e+l + l +++   ++i+DEa+   s   +  +  L+s l+ +r++++li++
  gene1325|gene1325|rna1324|rna1324 191 qktkiRYMTEGIFLqELLGDSLLRKYS--VVILDEAHER-SanlDITMGLLKSALK-KRDDLKLIVM 253
                                        888876666666666777777777777..********97.4344333444444444.5777777765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   1.5e-06    0.0021      92     171 ..     188     260 ..     115     264 .. 0.74
   2 ?   -3.7   0.0       6.2   8.5e+03     117     136 ..     533     552 ..     531     558 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                                        HHHHTTCSEEEEEHHHHHH.HHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  92 skldngvdivvgtpgrldd.llstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlS 166
                                        ++  ++++i ++t g +++ ll +    l++ ++++lDEa++ + +    ++  + ++l ++ +d k    +iv+S
  gene1325|gene1325|rna1324|rna1324 188 TTT-QKTKIRYMTEGIFLQeLLGDSL--LRKYSVVILDEAHERSAN-LDITMGLLKSAL-KKRDDLK----LIVMS 254
                                        333.6799999****99994555555..**************9998.444444444444.4545544....***** PP

                                        SSBS.H CS
                                        xxxx.x RF
                               DEAD 167 ATlp.k 171
                                        AT++ +
  gene1325|gene1325|rna1324|rna1324 255 ATIEaQ 260
                                        **9844 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.2
                                        SHCTTEEEEEEETHHHHHHT CS
                                        xxxxxxxxxxxxxxxxxxxx RF
                               DEAD 117 lnlsqvrflVlDEadrlldq 136
                                        + l++ r+ V+DE+ ++ ++
  gene1325|gene1325|rna1324|rna1324 533 MVLNSPRYGVVDEIATIVSM 552
                                        568888999****9887776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.2e-06     0.003      17      98 ..     121     225 ..     114     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.2e-06
                             AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.La............eelgieastiakllkr 79 
                                        +++v+vl+G AG+GK+t +  +  +     + +ig++   +aA + La             ++ ++  t++k   r
  gene1325|gene1325|rna1324|rna1324 121 KHQVTVLVGEAGSGKSTQVPRYLYLEGYGDKGIIGCTQPRRAAVTsLAstlerdmgsvvgYSIRFDNTTTQKTKIR 196
                                        457**************99988655554456699999888888766773333322222221222344444444433 PP

                             AAA_30  80 lk..........grarlepgtllivDEag 98 
                                        +           g   l++ +++i DEa 
  gene1325|gene1325|rna1324|rna1324 197 YMtegiflqellGDSLLRKYSVVILDEAH 225
                                        33778888888864566677*******96 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.7e-06    0.0051       2     135 ..     120     256 ..     119     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                                        XX--EEEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTT...TS-EEE-------------S CS
                         Flavi_DEAD   2 rkkkltvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealk...glevryktsavkeektgrel 74 
                                        rk+++tvl    G+Gk  +v   l  e +  +       P r  ++ ++  l+   g+ v y+   + +++t++  
  gene1325|gene1325|rna1324|rna1324 120 RKHQVTVLVGEAGSGKSTQVPRYLYLEGYGDKGIIGCTQPRRAAVTSLASTLErdmGSVVGYS-IRFDNTTTQKTK 194
                                        678888888888888888887777778887777777788999999999888862222334444.445688889999 PP

                                        EEEEEHHHHHHHHHHT------SEEEEETTT--SHHHHHHHHHHHHH.HHTTS-EEEEEESS CS
                         Flavi_DEAD  75 vdvmchatftkrllspvrkknyeliimDeahflDPasiaarGyletk.aeegeaalilltat 135
                                        +  m    f + ll +    +y ++i+Deah    +   + G l++  +++++ +li ++at
  gene1325|gene1325|rna1324|rna1324 195 IRYMTEGIFLQELLGDSLLRKYSVVILDEAHERSANLDITMGLLKSAlKKRDDLKLIVMSAT 256
                                        *******************************999888888899987615566899******9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00021      0.28       8      42 ..     119     154 ..     116     207 .. 0.67
   2 ?    0.4   0.0      0.65   8.9e+02     107     135 ..     196     224 ..     180     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                        EETTSEEEEEESTTSSHHHHH.HHHTTSS--SEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                           ABC_tran   8 lkegekvaivGenGaGKStLl.kllagllkpteGei 42 
                                        +++ +++++vGe G+GKSt + + l+ +   ++G i
  gene1325|gene1325|rna1324|rna1324 119 IRKHQVTVLVGEAGSGKSTQVpRYLYLEGYGDKGII 154
                                        568899*************65355665555566666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.65
                                        GGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 107 ssLSgGqkqrvalarallkkpkllllDEp 135
                                        + + +G      l  +ll+k ++++lDE+
  gene1325|gene1325|rna1324|rna1324 196 RYMTEGIFLQELLGDSLLRKYSVVILDEA 224
                                        55555555555677899***********8 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.3e-05     0.074      14      37 ..     113     137 ..     109     142 .. 0.79
   2 ?   -2.7   0.0       3.8   5.3e+03       1      21 [.     401     422 ..     401     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                             AAA_29  14 ghtieidlkg.atlltGpsGsGKST 37 
                                        +  +e+ +k  +t+l+G+ GsGKST
  gene1325|gene1325|rna1324|rna1324 113 HGLMEFIRKHqVTVLVGEAGSGKST 137
                                        555666666669************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.8
                             AAA_29   1 LkrlqlvNWgtfdg.htieidl 21 
                                        L++++++N  t +   t+++++
  gene1325|gene1325|rna1324|rna1324 401 LQKISVYNYDTGESlVTVPVSR 422
                                        7999****99988877777765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.7e-05     0.052       5      78 ..     108     179 ..     105     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                             ATPase   5 IeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                        Ieg+ + l + i + +v+ ++Ge+G+GK++ + ++l+     yg++g++  +  +  ++   a++l  d+  + 
  gene1325|gene1325|rna1324|rna1324 108 IEGFKHGLMEFIRKHQVTVLVGEAGSGKSTQVPRYLYLE--GYGDKGIIGCTQPRRAAVTSLASTLERDMGSVV 179
                                        78888888888999**********************965..789999988877777777777777777776665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.7e-05      0.13     112     170 ..     191     258 ..     177     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                                        HHHHHTH............HHHTTT-SEEEEETGGGTTS.T.....TTHHHHHT---SEEEEEESS-S CS
                             ResIII 112 qsldadseee....eeeseellrdrfdviiiDEaHrlgakk.....swreilekfkeavllglTATpe 170
                                        q+ + + ++e    +e   + l  ++ v+i DEaH  +a+        +++l+k ++ +l+ ++AT+e
  gene1325|gene1325|rna1324|rna1324 191 QKTKIRYMTEgiflQELLGDSLLRKYSVVILDEAHERSANLditmgLLKSALKKRDDLKLIVMSATIE 258
                                        444444444455555555566667778************734545577778999999*********86 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0017       2.3       3      75 ..     123     225 ..     121     249 .. 0.65
   2 ?    1.9   0.0      0.11   1.5e+02      80     134 ..     331     387 ..     325     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                             AAA_24   3 lkiliyGpsgiGKTtlakel..........gpkplfi.................dtekGlksldadkfpdieswed 51 
                                        +  +++G++g+GK+t++ ++                i                   ++G+   + ++f++ ++ ++
  gene1325|gene1325|rna1324|rna1324 123 QVTVLVGEAGSGKSTQVPRYlylegygdkgI-----IgctqprraavtslastlERDMGSVVGYSIRFDNTTTQKT 193
                                        5679************988855555433220.....1344555555556666667777777777777776664444 PP

                             AAA_24  52 fldevvel........aaeladyktlviDtid 75 
                                         + +++e         +  l++y+++++D + 
  gene1325|gene1325|rna1324|rna1324 194 KIRYMTEGiflqellgDSLLRKYSVVILDEAH 225
                                        44444444667777888888888888888765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                             AAA_24  80 lclaevirqnekaeskedkgdgkG.ygelaeefrrllkkl.qelrknvifiahektr 134
                                        ++ ++ +   +k+e+++ + +++  y++l ee+++ + k+ ++ rk+++ +  ++t 
  gene1325|gene1325|rna1324|rna1324 331 YWARNKCLSEGKGEDEDADLKAFPfYSQLSEEMQSKVFKVeRNIRKCIVSTNIAETS 387
                                        56667788899999999999*************999988615677799988887775 PP

>> Nuc_sug_transp  Nucleotide-sugar transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.012        16      23     117 ..     182     283 ..     175     290 .. 0.65
   2 ?    4.6   0.0     0.011        15      59     115 ..     361     417 ..     351     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.012
                     Nuc_sug_transp  23 tlrYartk.edkerylsttavllaeil..klvvclllllkeekskv...kkllrelkkeilakpkdtlklavPsli 92 
                                        ++r+  t+ +++++ + t  ++l+e+l   l+   ++++ +e ++      ++  l k+ l+ ++d lkl v s+ 
  gene1325|gene1325|rna1324|rna1324 182 SIRFDNTTtQKTKIRYMTEGIFLQELLgdSLLRKYSVVILDEAHERsanLDITMGLLKSALK-KRDDLKLIVMSAT 256
                                        56666655445555556777888887743244444444443333320013455556666665.6899********* PP

                     Nuc_sug_transp  93 Ytvqnnllyvals..nLdaatyqvtyq 117
                                           q + +y++ s  n++  ty v  q
  gene1325|gene1325|rna1324|rna1324 257 IEAQKFCDYFGCStfNIEGRTYPVDIQ 283
                                        **********98844677888888776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                     Nuc_sug_transp  59 keekskvkkllrelkkeilakpkdtlklavPsliYtvqnnllyvalsnLdaatyqvt 115
                                        +e++skv k+ r+++k i+++      l++P + Y++   l+ +++ n d +   vt
  gene1325|gene1325|rna1324|rna1324 361 EEMQSKVFKVERNIRKCIVSTNIAETSLTIPNIGYVIDTGLQKISVYNYDTGESLVT 417
                                        56778888999*********999999**********************999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (798 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 5021.17
//
Query:       gene1326|gene1326|rna1325|rna1325  [L=851]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1057  (0.0589548); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 5293.41
//
Query:       gene1327|gene1327|rna1326|rna1326  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-42  142.8   0.0    7.8e-42  142.6   0.0    1.0  1  Ras          Ras family
      7e-30  103.7   0.1    1.1e-29  103.1   0.1    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      3e-18   65.9   0.1    3.8e-18   65.5   0.1    1.1  1  Arf          ADP-ribosylation factor family
    1.7e-07   31.0   0.0    2.5e-05   23.9   0.0    2.1  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.9e-07   31.2   0.0    2.9e-07   30.6   0.0    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
    9.5e-06   25.1   0.0    1.2e-05   24.8   0.0    1.2  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    8.6e-05   22.5   0.0       0.22   11.4   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
    0.00028   20.4   0.0    0.00041   19.8   0.0    1.2  1  SRPRB        Signal recognition particle receptor beta subuni
     0.0069   15.9   0.1       0.09   12.3   0.1    2.2  1  FeoB_N       Ferrous iron transport protein B
     0.0073   16.1   0.1      0.023   14.4   0.0    1.8  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0085   15.9   0.0      0.085   12.6   0.0    1.9  2  ATP_bind_1   Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.015   15.6   0.1      0.077   13.3   0.1    2.2  1  AAA_22       AAA domain
      0.049   13.3   0.2      0.075   12.7   0.2    1.7  1  AAA_24       AAA domain
       0.12   12.2   0.0       0.26   11.2   0.0    1.5  1  MobB         Molybdopterin guanine dinucleotide synthesis pro


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.6   0.0   6.1e-45   7.8e-42       1     160 [.       6     170 ..       6     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 6.1e-45
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegil 76 
                                        K+v++G+s+vGKt+l+ ++ +++ +++y +Tig df +++i v+g++v+l++wDTAGqe+f+s+ ++y r++  ++
  gene1327|gene1327|rna1326|rna1326   6 KIVFLGSSNVGKTTLMSQYLHQEVQRSYGPTIGLDFVSTTIVVSGHRVRLQLWDTAGQERFNSIIPNYTRNSFLAI 81 
                                        99************************************************************************** PP

                                        EEEETTBHHHHHTHHHHHHHHHHHST...TTSEEEEEEETTTGGG..G-SS-HHHHHHHHHHHTSEEEEEBTTTTC CS
                                Ras  77 lvyditsresfenvkkwveeikrvae...envpivLvGnKvDlee..kravsteegeelakelglkfletSAktne 147
                                        +v+d+++++sfe++++w++ ++++ e   ++  i++vGnK Dl++  +r   +e g + ak++g +++et A ++e
  gene1327|gene1327|rna1326|rna1326  82 IVFDMKDKSSFERIDHWINTLSKTSEslgSKARILVVGNKRDLADeeTRGWYKEVGTRKAKKHGGEYVETCAMKHE 157
                                        ***********************99999988************986677889999********************* PP

                                        THHHHHHHHHHHH CS
                                Ras 148 nveeafeellrei 160
                                        ++e+++ ++ r i
  gene1327|gene1327|rna1326|rna1326 158 GIEDLVRAVDRLI 170
                                        ***9988876655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.1   8.4e-33   1.1e-29       1     119 [.       6     123 ..       6     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 8.4e-33
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        K+v++G s+vGKt+l+++++++++++++ +tig+df++++++ ++g       ++v+l++WDtaGqerf+s+ p y
  gene1327|gene1327|rna1326|rna1326   6 KIVFLGSSNVGKTTLMSQYLHQEVQRSYGPTIGLDFVSTTIV-VSG-------HRVRLQLWDTAGQERFNSIIPNY 73 
                                        9************************************99874.444.......4799******************* PP

                                        HCTSCEEEEEEE...GHHHHCHHHHHHHHHHHCS....SS-EEEEEE-TT CS
                                Roc  77 lreaalailvyd...srssenlkeWlkelkkvag....kspvilvgnkiD 119
                                         r++ lai+v+d   ++s+e++++W++ l+k ++    k+ +++vgnk D
  gene1327|gene1327|rna1326|rna1326  74 TRNSFLAIIVFDmkdKSSFERIDHWINTLSKTSEslgsKARILVVGNKRD 123
                                        ***********9764556799********9875423227799******99 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.1     3e-21   3.8e-18      14     170 ..       4     165 ..       1     171 [. 0.85

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 3e-21
                                        EEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE....TTEEEEEEEE-SSGGGGGGGGGGCTTESE CS
                                Arf  14 elrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei....knlkftvwDvGGqeklRplWknYfektda 84 
                                         ++i++lG  n GKtT++ ++ ++e+++   PTig +  + +i    + +++++wD  Gqe+  ++  nY+++   
  gene1327|gene1327|rna1326|rna1326   4 TYKIVFLGSSNVGKTTLMSQYLHQEVQRsYGPTIGLDFVSTTIvvsgHRVRLQLWDTAGQERFNSIIPNYTRNSFL 79 
                                        689*****************99999987478***976555444445589*************************** PP

                                        EEEEEETT-CTTHHHHHHHHHHHCTSGCCT..TSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBT CS
                                Arf  85 vifvvDsadreRleeakeeLkalleeeelk..evallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsa 158
                                         i v D  d++ +e   + +++l +++e    ++ +lv++NK Dl++  ++    +++g ++ k k+  e ++++a
  gene1327|gene1327|rna1326|rna1326  80 AIIVFDMKDKSSFERIDHWINTLSKTSESLgsKARILVVGNKRDLADEETR-GWYKEVGTRKAK-KHGGEYVETCA 153
                                        *****************9999999887764349************987655.566677888888.8999999**** PP

                                        TTTBTHHHHHHH CS
                                Arf 159 vkgeglkeglew 170
                                        +k eg+++ ++ 
  gene1327|gene1327|rna1326|rna1326 154 MKHEGIEDLVRA 165
                                        *****9987654 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0068       8.7       4      26 ..       5      27 ..       2      35 .. 0.83
   2 !   23.9   0.0   1.9e-08   2.5e-05      53     193 ..      34     171 ..      26     172 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0068
                                       EEEEEEESTTSSHHHHHHHHHHH CS
                           GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyk 26
                                        +i+++g  + GKtTL+ + l++
  gene1327|gene1327|rna1326|rna1326  5 YKIVFLGSSNVGKTTLMSQYLHQ 27
                                       57999************987766 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.9e-08
                                        TSCSSCEEEEEE..TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.....STHHHHHHHHHHHHT CS
                           GTP_EFTU  53 giTiksaaisle..ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.....vepqteevlrlalke 121
                                        g Ti    +s+    ++++ +++l Dt G + F++ + + +r   +a++v+d ++      + +  +++ +   ++
  gene1327|gene1327|rna1326|rna1326  34 GPTIGLDFVSTTivVSGHRVRLQLWDTAGQERFNSIIPNYTRNSFLAIIVFDMKDKssferIDHWINTLSKTSESL 109
                                        6666666666664347999***********************************7766666777777777888888 PP

                                        TTE..EEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                           GTP_EFTU 122 gvp..iivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                        g +  i v+ NK D +++e +   +ev ++          ++       + v ++a+k eg+++l++a+++l++
  gene1327|gene1327|rna1326|rna1326 110 GSKarILVVGNKRDLADEETRGWYKEVGTRK------A--KKHG----GEYVETCAMKHEGIEDLVRAVDRLIE 171
                                        7778577888*****************9666......2..2223....4699*****************99876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   2.3e-10   2.9e-07       1     113 [.       6     120 ..       6     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.3e-10
                                        EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT..EEEEEEECGGCSSHHHHHHHHHHHHHHHH CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg..keielvDtpGliegaseekglgkaflale 74 
                                        +++++G +NvGK+tL+++ + ++++ s  p   +d +  ++ ++g   +++l+Dt+G  e   + +++  ++ +  
  gene1327|gene1327|rna1326|rna1326   6 KIVFLGSSNVGKTTLMSQYLHQEVQRSYGPTIGLDFVSTTIVVSGhrVRLQLWDTAG-QE---RFNSIIPNYTR-- 75 
                                        589******************99888888888888877777755534779*******.54...33367777775.. PP

                                        CTSEEEEEEETT.TTCSHHHHHHHHHHHHH.....TTSEEEEEEE CS
                           MMR_HSR1  75 eadlillvvdas.eeklkpldeeleellee.....akkplilvln 113
                                        ++ l+++v+d++ +++++++d+ ++ l +      +k ++++v n
  gene1327|gene1327|rna1326|rna1326  76 NSFLAIIVFDMKdKSSFERIDHWINTLSKTseslgSKARILVVGN 120
                                        456777777766433566665555544433445655566666666 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   9.6e-09   1.2e-05       1     133 [.       6     134 ..       6     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9.6e-09
                          Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardt.lrlgatidve..kse.vrflgnltlnlwDcgGqeafveeylssqkee 72 
                                        k++++G s+ GKt++ s    +yl +++ ++ g ti ++   ++ v   + + l+lwD  Gqe+f     ++ +++
  gene1327|gene1327|rna1326|rna1326   6 KIVFLGSSNVGKTTLMS----QYLHQEVqRSYGPTIGLDfvSTTiVVSGHRVRLQLWDTAGQERFNSIIPNYTRNS 77 
                                        799**********9776....4444444133566664331133304455679************998876666655 PP

                          Gtr1_RagA  73 ifrnvgvliyVfDvesreleedletlkeilealrq.yspeakvfvlihKmDliqedereeif 133
                                         +      i VfD+++++  e ++++ ++l++ ++    +a++ v  +K Dl +e++r    
  gene1327|gene1327|rna1326|rna1326  78 FL-----AIIVFDMKDKSSFERIDHWINTLSKTSEsLGSKARILVVGNKRDLADEETRGWYK 134
                                        54.....3669****99888888888888877765267899************999986554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00017      0.22     102     125 ..       7      30 ..       2      36 .. 0.84
   2 !    9.1   0.0   0.00085       1.1       4      97 ..      65     166 ..      62     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                                        EEEECSTTSSHHHHHHHHCTT--- CS
                        RsgA_GTPase 102 svlvGqSGvGKStLinallpelel 125
                                        +v++G+S vGK+tL+ + l ++ +
  gene1327|gene1327|rna1326|rna1326   7 IVFLGSSNVGKTTLMSQYLHQEVQ 30 
                                        69*************998877655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00085
                                        -S-EETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHT......T-EEEEEEE-GGG--HHH...HHHHHHH CS
                        RsgA_GTPase   4 RknelvrpkvaNvdqllivvslkepelslnlldrfLvlaeek......giepvivlnKiDlleeee...eleelke 70 
                                        R n+++ +   N   ++iv+ +k ++ s +++d  + ++ ++      ++++++v nK Dl++ee+     e    
  gene1327|gene1327|rna1326|rna1326  65 RFNSIIPNYTRNSFLAIIVFDMK-DKSSFERIDHWINTLSKTseslgsKARILVVGNKRDLADEETrgwYKEVGTR 139
                                        66666666666666788888888.88888888888776655322222267889999*********99853444455 PP

                                        HHHHTTSEEEE--TTTHTTHHHHHHHC CS
                        RsgA_GTPase  71 elealgyevllvsaktkegleelkell 97 
                                        + ++ g e + + a ++eg+e+l +++
  gene1327|gene1327|rna1326|rna1326 140 KAKKHGGEYVETCAMKHEGIEDLVRAV 166
                                        667778888888888899999998776 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.2e-07   0.00041       4     125 ..       5     125 ..       2     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.2e-07
                                        -EEEEE-STTSSHHHHHHHHHHSS---B---S...S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG. CS
                              SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq...essaalkvksekgskltliDfPGheklrqklleklkakss. 75 
                                         +++++G s+ GKT+l+ + + ++v++++      +  +++ v s +  +l+l D  G+e++ + + ++  +++s 
  gene1327|gene1327|rna1326|rna1326   5 YKIVFLGSSNVGKTTLMSQYLHQEVQRSYGPTiglDFVSTTIVVSGHRVRLQLWDTAGQERFNSIIPNY--TRNSf 78 
                                        5799*******************9999886543313344444478888999***********9988888..66662 PP

                                        EEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTST CS
                              SRPRB  76 lkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelf 125
                                        l  +vf  D   d+   + +  ++ ++   +e+l  +  il+  nK +l+
  gene1327|gene1327|rna1326|rna1326  79 LAIIVF--DM-KDKSSFERIDHWINTLSKTSESLGSKARILVVGNKRDLA 125
                                        555555..32.234444455666666666777779999999999999975 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1     7e-05      0.09       2      60 ..       6      66 ..       5     166 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT..EEEEEEE----SSS CS
                             FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg..keveivDlPGiYsl 60
                                       +++++G  nvGkttl+ +   ++ + +  p +  +  ++++ ++g   ++++ D  G   +
  gene1327|gene1327|rna1326|rna1326  6 KIVFLGSSNVGKTTLMSQYLHQEVQRSYGPTIGLDFVSTTIVVSGhrVRLQLWDTAGQERF 66
                                       7999************998766655554454444544444444441144556666666444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.8e-05     0.023       3      46 ..       6      51 ..       4      63 .. 0.77
   2 ?   -0.8   0.0      0.89   1.1e+03     124     139 ..     149     164 ..      79     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                          PduV-EutP  3 killiGkvgsGKttLt.qalkge.elkYkktqaiefsdeviDtPGe 46
                                       ki+++G++++GKttL+ q l++e + +Y  t  ++f +++i   G 
  gene1327|gene1327|rna1326|rna1326  6 KIVFLGSSNVGKTTLMsQYLHQEvQRSYGPTIGLDFVSTTIVVSGH 51
                                       89************97255655424579999999999988876665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.89
                          PduV-EutP 124 fevsavekegieellk 139
                                         e+ a+++egie+l++
  gene1327|gene1327|rna1326|rna1326 149 VETCAMKHEGIEDLVR 164
                                        4566777777777765 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.16     2e+02       2      17 ..      10      25 ..       9      40 .. 0.77
   2 !   12.6   0.0   6.6e-05     0.085      69     210 ..      36     172 ..      26     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.16
                         ATP_bind_1  2 vGpaGsGKttfvgals 17
                                       +G   +GKtt++++  
  gene1327|gene1327|rna1326|rna1326 10 LGSSNVGKTTLMSQYL 25
                                       688899*****98754 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.6e-05
                         ATP_bind_1  69 vvaleflresldwl.deelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltd..ptkf 141
                                        ++ l+f+++++  +   +       + l Dt GQ ++  + +           + ++ ++ ++D +  ++   ++ 
  gene1327|gene1327|rna1326|rna1326  36 TIGLDFVSTTI-VVsGHR-----VRLQLWDTAGQERFNSIIPNYT--------RNSFLAIIVFDMKDKSSfeRIDH 97 
                                        55666666666.221223.....3899******************........78888888888888777778888 PP

                         ATP_bind_1 142 isgllsalsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee.........ekykklaeaiaell 208
                                          ++ls  s  l  +   +vv nk Dl++   e+   ++++v + ++ ++  e         e  ++l +a+ +l+
  gene1327|gene1327|rna1326|rna1326  98 WINTLSKTSESLGSKARILVVGNKRDLAD---EETRGWYKEVGTRKAKKHGGEyvetcamkhEGIEDLVRAVDRLI 170
                                        8888***********************87...88889999998888877766677677666655666666666666 PP

                         ATP_bind_1 209 ee 210
                                        ee
  gene1327|gene1327|rna1326|rna1326 171 EE 172
                                        66 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     6e-05     0.077       8      37 ..       7      36 ..       1     196 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6e-05
                             AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaee 37
                                       +v  G s +GKTtl+ ++l+q +++++  +
  gene1327|gene1327|rna1326|rna1326  7 IVFLGSSNVGKTTLMSQYLHQEVQRSYGPT 36
                                       778899***************999877655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.9e-05     0.075       2      22 ..       4      24 ..       3     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                             AAA_24  2 klkiliyGpsgiGKTtlakel 22
                                        +ki+  G+s +GKTtl++++
  gene1327|gene1327|rna1326|rna1326  4 TYKIVFLGSSNVGKTTLMSQY 24
                                       589****************98 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0002      0.26       2      27 ..       7      32 ..       6      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                               MobB  2 lgivgksgsGKTtLleklipelkarg 27
                                       + + g s+ GKTtL+++ +++  +r 
  gene1327|gene1327|rna1326|rna1326  7 IVFLGSSNVGKTTLMSQYLHQEVQRS 32
                                       5789************9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.54
# Mc/sec: 1100.86
//
Query:       gene1328|gene1328|rna1327|rna1327  [L=489]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00054   19.4   0.6     0.0011   18.5   0.6    1.5  1  Pkinase      Protein kinase domain
  ------ inclusion threshold ------
      0.013   14.9   0.0      0.024   14.0   0.0    1.4  1  Kinase-like  Kinase-like
      0.026   13.8   0.8       0.09   12.0   0.2    2.1  2  Pkinase_Tyr  Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.6   1.8e-07    0.0011      37     150 ..      35     142 ..      17     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-07
                                        HCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHH CS
                            Pkinase  37 akkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegle 112
                                        a+k   +++l+  ++lkk+kh+ i+ +y+   ek++l+       +  l+ +++  ++ ++e  k i  +i++++ 
  gene1328|gene1328|rna1327|rna1327  35 ATKLVFTQTLEAYSFLKKIKHDTIIGIYKLNVEKKYLV-------TRRLFPFYSVFKKEAKEFNKYISLKIAQAIM 103
                                        444444778888899***************99988776.......456788887433344455577889******* PP

                                        HHH.HTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSS CS
                            Pkinase 113 ylH.skgiiHrDlKpeNiLidekgelKitDFGlakeles 150
                                        +lH + +i+Hr +  + ++++e+g + ++ F  +++ ++
  gene1328|gene1328|rna1327|rna1327 104 FLHdQCNIVHRNVVADSLFFNEEGGIVLGGFEKSRKSNT 142
                                        ***6667**************999999999988887765 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     4e-06     0.024     142     193 ..      87     139 ..      71     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-06
                        Kinase-like 142 etiarlllTlqlirlaanLqak.glvhgkftvdnllldekgglmlggftaLvr 193
                                        ++   +++ l++ + +  L+++  +vh ++ +d+l+++e+gg++lggf++ ++
  gene1328|gene1328|rna1327|rna1327  87 AKEFNKYISLKIAQAIMFLHDQcNIVHRNVVADSLFFNEEGGIVLGGFEKSRK 139
                                        555556677777777777776537************************98665 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.5e-05      0.09      46     150 ..      41     137 ..      28     147 .. 0.69
   2 ?   -1.9   0.0      0.27   1.6e+03      33      82 ..     294     344 ..     284     348 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                                        HHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHH CS
                        Pkinase_Tyr  46 eelleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLes 121
                                        ++ le ++++kk+kh+ i+ ++ + ++  + ++vt  +    + +  +k+  +++  +    ++l++A+++ +L++
  gene1328|gene1328|rna1327|rna1327  41 TQTLEAYSFLKKIKHDTIIGIYKLNVE--KKYLVTRRL--FPFYSVFKKE-AKEF--N--KYISLKIAQAIMFLHD 107
                                        556677778888888888888877773..335555432..3455555555.3333..3..356789********98 PP

                                        T.TEEEST-SGGGEEEEETTEEEE-STTTH CS
                        Pkinase_Tyr 122 k.klvHrdlaarNvLlsenkvvkisDfGLa 150
                                        + ++vHr++ a   + +e+  + ++ f  +
  gene1328|gene1328|rna1327|rna1327 108 QcNIVHRNVVADSLFFNEEGGIVLGGFEKS 137
                                        648*********999999988877777555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.27
                                        EEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--.EEEEEESSSSEEEEEE- CS
                        Pkinase_Tyr  33 vKtlkeeateeekeelleeakimkklkhpnivk.llgvctkeepllivtey 82 
                                        +K+ +++ +ee+   + e++ ++++ ++ +i++ ++g +++e+ +  v+ +
  gene1328|gene1328|rna1327|rna1327 294 IKCKDKQLREETIVFIKENIPMISQRQQSEILEtMYGYVSDEQGIQSVLRF 344
                                        666655666654444444566666667777775267777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2976.85
//
Query:       gene1329|gene1329|rna1328|rna1328  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-23   80.4  24.9    8.5e-11   41.5   6.5    3.0  3  LRR_8            Leucine rich repeat
    1.8e-11   44.0  28.9    1.9e-07   31.2   4.7    3.6  4  LRR_4            Leucine Rich repeats (2 copies)
     0.0018   18.6  12.0        4.7    8.1   0.7    5.2  3  LRR_1            Leucine Rich Repeat
  ------ inclusion threshold ------
      0.012   15.1   1.5      0.012   15.1   1.5    2.2  2  LRR_9            Leucine-rich repeat
      0.024   15.1   0.2       0.05   14.0   0.2    1.5  1  Tryp_alpha_amyl  Protease inhibitor/seed storage/LTP family
        1.5    9.1  12.8        4.3    7.6   0.1    4.1  4  LRR_6            Leucine Rich repeat


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   3.2   2.4e-13   7.2e-10       3      61 .]     137     193 ..     135     193 .. 0.96
   2 !   41.5   6.5   2.9e-14   8.5e-11       1      60 [.     158     215 ..     158     216 .. 0.97
   3 !   26.6   0.7   1.2e-09   3.6e-06       3      60 ..     206     261 ..     204     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.4e-13
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        L++L+ ++N+lt l+++    l+nLkvL Ls N+++ l p+ + +L++Lr+L+Ls+N L
  gene1329|gene1329|rna1328|rna1328 137 LKVLQACCNYLTRLPQQIGC-LTNLKVLVLSKNRIQKL-PDEIGQLKNLRELNLSQNLL 193
                                        899999**********9999.*****************.9*****************87 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 2.9e-14
                                        TT-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS- CS
                              LRR_8   1 pnLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNr 60 
                                        +nL++L+Ls+Nr+++l+de  + l+nL++L+Ls+Nll tl p+ +s L++L  L++++N 
  gene1329|gene1329|rna1328|rna1328 158 TNLKVLVLSKNRIQKLPDEIGQ-LKNLRELNLSQNLLVTL-PRGISALKALNALHIDDNL 215
                                        59********************.*****************.9****************97 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 1.2e-09
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS- CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNr 60 
                                        L+ L++++N +t+l++   + l +Lk+L++snN+++ + p  +  Lp L +L+ s+++
  gene1329|gene1329|rna1328|rna1328 206 LNALHIDDNLFTVLPPVIGR-LYGLKYLNISNNKIQNI-PLEILKLPFLIELTASSCD 261
                                        899*************9999.*****************.7888888888888877775 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   1.5e-06    0.0045       3      40 ..     137     174 ..     135     175 .. 0.84
   2 !   31.2   4.7   6.5e-11   1.9e-07       1      37 [.     158     194 ..     158     205 .. 0.85
   3 !   17.3   2.1   1.5e-06    0.0046       3      42 ..     206     244 ..     204     250 .. 0.83
   4 !   16.2   1.3   3.6e-06     0.011       3      38 ..     229     261 ..     228     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                        --EEE--SS---E-S-.HHH-TT--EEE-.-S-----GG CS
                              LRR_4   3 LevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdld 40 
                                        L+vL    N lt +p  ++ l+nLk+L Ls N +i++l+
  gene1329|gene1329|rna1328|rna1328 137 LKVLQACCNYLTRLPQqIGCLTNLKVLVLSKN-RIQKLP 174
                                        8999999999******5555*********999.887774 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 6.5e-11
                                        SS--EEE--SS---E-S-.HHH-TT--EEE-.-S---- CS
                              LRR_4   1 pnLevLdLsnNqltdipl.leklpnLkeLdLsgNnlit 37 
                                        +nL+vL Ls N+++++p  +++l+nL+eL+Ls+N l+ 
  gene1329|gene1329|rna1328|rna1328 158 TNLKVLVLSKNRIQKLPDeIGQLKNLRELNLSQN-LLV 194
                                        7*****************7667*********999.554 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 1.5e-06
                                        --EEE--SS---E-S-HHH.-TT--EEE-.-S-----GGGG CS
                              LRR_4   3 LevLdLsnNqltdipllek.lpnLkeLdLsgNnlitdldeL 42 
                                        L  L++ +N  t +p+  + l  Lk+L++ +Nn+i+++ +L
  gene1329|gene1329|rna1328|rna1328 206 LNALHIDDNLFTVLPPVIGrLYGLKYLNI-SNNKIQNI-PL 244
                                        6779999*********5555*********.66699999.44 PP

  == domain 4  score: 16.2 bits;  conditional E-value: 3.6e-06
                                        --EEE--SS---E-S-..HHH-TT--EEE-.-S----- CS
                              LRR_4   3 LevLdLsnNqltdipl..leklpnLkeLdLsgNnlitd 38 
                                        L++L++snN+++ ipl  l klp L eL+ s++    d
  gene1329|gene1329|rna1328|rna1328 229 LKYLNISNNKIQNIPLeiL-KLPFLIELTASSC----D 261
                                        9***************844.6****99987776....4 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.014        43       1      20 [.     159     177 ..     159     180 .. 0.85
   2 !    8.1   1.6    0.0016       4.9       1      21 [.     182     201 ..     182     222 .. 0.83
   3 !    8.1   0.7    0.0016       4.7       2      17 ..     229     244 ..     228     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                              LRR_1   1 nLrhLdLsnnpllglppnsf 20 
                                        nL++L Ls n++ +++p+ +
  gene1329|gene1329|rna1328|rna1328 159 NLKVLVLSKNRI-QKLPDEI 177
                                        8***********.8888776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                              LRR_1   1 nLrhLdLsnnpllglppnsfq 21 
                                        nLr+L+Ls+n l   +p+ ++
  gene1329|gene1329|rna1328|rna1328 182 NLRELNLSQNLL-VTLPRGIS 201
                                        8**********9.55555544 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0016
                              LRR_1   2 LrhLdLsnnpllglpp 17 
                                        L++L++snn + ++p 
  gene1329|gene1329|rna1328|rna1328 229 LKYLNISNNKIQNIPL 244
                                        9*********944433 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   1.5     4e-06     0.012      58     125 ..     129     193 ..      82     198 .. 0.80
   2 ?    2.4   0.9     0.032        96      63     132 ..     226     296 ..     201     311 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4e-06
                              LRR_9  58 dgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsllknpv 125
                                        +g+  ++ lk+l    n ++r+ ++++ +l nl+ lvl++n++q+l d   + +lk+l+ l l +n +
  gene1329|gene1329|rna1328|rna1328 129 EGIGEIQDLKVLQACCNYLTRLPQQIG-CLTNLKVLVLSKNRIQKLPD--EIGQLKNLRELNLSQNLL 193
                                        667778889999999999999998887.68899999999999999988..788888888888887755 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.032
                              LRR_9  63 lkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPl..aslkklellsllknpvtnkkeyr 132
                                        l  lk l ++nn+i +i  ++   lP l el  ++  +++   ++ +  ++lk+  +  l++n +  +++  
  gene1329|gene1329|rna1328|rna1328 226 LYGLKYLNISNNKIQNIPLEIL-KLPFLIELTASSCDFTSKDSIECIgdITLKETCSRHLVRNNLRVRRNIH 296
                                        55689999*******9998876.4899988888887777777777762234455555557777776666654 PP

>> Tryp_alpha_amyl  Protease inhibitor/seed storage/LTP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.7e-05      0.05       1      52 [.     120     165 ..     118     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                        HHHHHHHBCSHHHCCCHSSTTSCSHHHHHHHHHHHHSHHHHHHHHHHHHHHC CS
                    Tryp_alpha_amyl   1 CrqvllqcspalapcqglqqsscqqpsqqCCqqLkqlpeqcrCeairavves 52 
                                        Crq++ +     ++  g  q    ++ q+CC+ L++lp+q  C +  +v+  
  gene1329|gene1329|rna1328|rna1328 120 CRQFVVE----ITEGIGEIQD--LKVLQACCNYLTRLPQQIGCLTNLKVLVL 165
                                        8888888....7777777776..479*****************987666544 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2      0.02        60       3      16 ..     158     171 ..     156     172 .. 0.90
   2 ?    4.2   0.7     0.018        55       3      14 ..     181     192 ..     179     195 .. 0.85
   3 ?   -3.3   0.2       4.7   1.4e+04       5      15 ..     206     216 ..     206     217 .. 0.77
   4 ?    7.6   0.1    0.0014       4.3       5      17 ..     229     241 ..     227     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.02
                              LRR_6   3 thLteLdLsgNdIg 16 
                                        t+L+ L Ls N I+
  gene1329|gene1329|rna1328|rna1328 158 TNLKVLVLSKNRIQ 171
                                        89*********996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.018
                              LRR_6   3 thLteLdLsgNd 14 
                                         +L+eL+Ls N 
  gene1329|gene1329|rna1328|rna1328 181 KNLRELNLSQNL 192
                                        58*******995 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4.7
                              LRR_6   5 LteLdLsgNdI 15 
                                        L +L++ +N +
  gene1329|gene1329|rna1328|rna1328 206 LNALHIDDNLF 216
                                        67899999965 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0014
                              LRR_6   5 LteLdLsgNdIgD 17 
                                        L++L++s N+I++
  gene1329|gene1329|rna1328|rna1328 229 LKYLNISNNKIQN 241
                                        9**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2801.89
//
Query:       gene1330|gene1330|rna1329|rna1329  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-35  119.3  29.0    1.5e-09   37.4   8.8    5.8  6  LRR_8     Leucine rich repeat
    2.9e-23   81.6  34.6    2.8e-05   24.4   0.6    7.6  9  LRR_4     Leucine Rich repeats (2 copies)
    2.3e-17   63.0  13.9    1.3e-06   28.1   4.9    3.1  3  LRR_9     Leucine-rich repeat
  ------ inclusion threshold ------
      0.021   15.3  31.6        4.9    8.1   0.1    8.9  9  LRR_1     Leucine Rich Repeat
       0.59   10.3   0.1       0.59   10.3   0.1    8.0 11  LRR_6     Leucine Rich repeat
          8    6.4   8.7          2    8.4   2.7    2.6  3  DUF3557   Domain of unknown function (DUF3557)


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.5e-06    0.0044       5      43 ..      28      65 ..      24      69 .. 0.70
   2 !   27.5   0.1   6.6e-10     2e-06       2      61 .]      71     128 ..      70     128 .. 0.95
   3 !   34.3   5.0     5e-12   1.5e-08      10      61 .]     125     174 ..     124     174 .. 0.94
   4 !   37.4   8.8   5.1e-13   1.5e-09       2      61 .]     140     197 ..     139     197 .. 0.97
   5 !   23.6   2.9   1.1e-08   3.3e-05       2      61 .]     186     242 ..     185     242 .. 0.95
   6 !   31.7   0.1   3.1e-11   9.3e-08       2      60 ..     254     313 ..     253     314 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                                       EEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGG CS
                              LRR_8  5 sLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspg 43
                                        L+Ls+N++ +++ +  + l+ L  L L++N+++ ++pg
  gene1330|gene1330|rna1329|rna1329 28 WLILSDNKIREVPESIKE-LKTLSRLALNDNRIEEIHPG 65
                                       577777777777655444.77777777777777777775 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 6.6e-10
                                        T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        +Lt +dL++Nrl +l+de+ + l+++  L Ls+N+ + + p+++  +++Lr+    +N++
  gene1330|gene1330|rna1329|rna1329  71 GLTWIDLTRNRLRALPDEMEN-LKRVSGLGLSENNFSEI-PKCIFKMTNLRKFGFFSNKI 128
                                        599****************99.*****************.9**********998888876 PP

  == domain 3  score: 34.3 bits;  conditional E-value: 5e-12
                                        TS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  10 nNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        +N++ +++++  + l nL  +dLsnN++++l p+ f  L++L +L+Ls+N+L
  gene1330|gene1330|rna1329|rna1329 125 SNKIRAIPKDIKF-LINLIKIDLSNNEISSL-PDEFCELRNLNWLNLSNNKL 174
                                        6889999999877.*****************.9*****************98 PP

  == domain 4  score: 37.4 bits;  conditional E-value: 5.1e-13
                                        T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        nL ++dLsnN ++sl+de+ + l+nL++L+LsnN+l+ l p+ + +L +L++L L  N+L
  gene1330|gene1330|rna1329|rna1329 140 NLIKIDLSNNEISSLPDEFCE-LRNLNWLNLSNNKLQKL-PDGINNLVRLEELGLGANNL 197
                                        7889*****************.*****************.9*****************98 PP

  == domain 5  score: 23.6 bits;  conditional E-value: 1.1e-08
                                        T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        +L++L L  N+lt+l+d   ++l++L++L    N+lt ++ +++++L+s+++Ld s+N++
  gene1330|gene1330|rna1329|rna1329 186 RLEELGLGANNLTELPDM--SNLKKLRILPVFKNQLTQVN-QSIACLNSIEKLDFSDNNI 242
                                        69**************95..689****************6.*****************97 PP

  == domain 6  score: 31.7 bits;  conditional E-value: 3.1e-11
                                        T-SEEE-TTS--SEE-TTSSTT.-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS- CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkg.lsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNr 60 
                                        +L++L+L +N+++++d+++Fk+ +s++ ++d s+Nll+ +  + f  +++++ + +  N+
  gene1330|gene1330|rna1329|rna1329 254 TLRYLNLKSNKISKIDPSTFKNrVSSVSIIDVSDNLLSCIPLKFFKTFSNVTVIRVGENP 313
                                        79**************************************99999999999888777775 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.5e-05     0.044       6      39 ..      29      62 ..      27      68 .. 0.73
   2 !   11.3   0.2   0.00012      0.35       3      39 ..      49      85 ..      47      94 .. 0.84
   3 !    9.2   0.1   0.00056       1.7       2      40 ..      71     106 ..      70     110 .. 0.79
   4 !    8.0   0.0    0.0013       3.9       6      39 ..      98     131 ..      93     138 .. 0.81
   5 !   18.8   0.4   5.2e-07    0.0016       1      40 [.     116     155 ..     116     159 .. 0.87
   6 !   21.7  10.2   6.3e-08   0.00019       2      40 ..     140     178 ..     139     184 .. 0.85
   7 !   14.3   0.8   1.4e-05     0.041       2      39 ..     186     222 ..     185     229 .. 0.81
   8 !   24.4   0.6   9.3e-09   2.8e-05       3      41 ..     232     270 ..     230     275 .. 0.84
   9 !    6.2   0.0    0.0048        14       5      33 ..     282     312 ..     278     317 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                       EE--SS---E-S-HHH-TT--EEE...-.-S-----G CS
                              LRR_4  6 LdLsnNqltdiplleklpnLkeLd...LsgNnlitdl 39
                                       L Ls+N+++++p   +++ Lk+L+   L++N +i+ +
  gene1330|gene1330|rna1329|rna1329 29 LILSDNKIREVPE--SIKELKTLSrlaLNDN-RIEEI 62
                                       89********666..5555555555449777.88776 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
                                       --EEE--SS---E-S-.HHH-TT--EEE-.-S-----G CS
                              LRR_4  3 LevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdl 39
                                       L  L L++N++ +i + +++l  L+ +dL++N +++ l
  gene1330|gene1330|rna1329|rna1329 49 LSRLALNDNRIEEIHPgIGSLVGLTWIDLTRN-RLRAL 85
                                       66788*******99997778*********999.77766 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00056
                                        S--EEE--SS---E-S-HHH-TT--EEE...-.-S-----GG CS
                              LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLd...LsgNnlitdld 40 
                                         L+ +dL  N+l+ +p    + nLk ++   Ls+Nn+    +
  gene1330|gene1330|rna1329|rna1329  71 GLTWIDLTRNRLRALPD--EMENLKRVSglgLSENNF----S 106
                                        59999*********666..799999988877999954....4 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0013
                                        EE--SS---E-S-..HHH-TT--EEE-.-S-----G CS
                              LRR_4   6 LdLsnNqltdipl..leklpnLkeLdLsgNnlitdl 39 
                                        L Ls N+ ++ip   + k++nL+++   + n+i+ +
  gene1330|gene1330|rna1329|rna1329  98 LGLSENNFSEIPKciF-KMTNLRKFGF-FSNKIRAI 131
                                        669999*******644.6******998.66688777 PP

  == domain 5  score: 18.8 bits;  conditional E-value: 5.2e-07
                                        SS--EEE--SS---E-S-HHH.-TT--EEE-.-S-----GG CS
                              LRR_4   1 pnLevLdLsnNqltdipllek.lpnLkeLdLsgNnlitdld 40 
                                        +nL++  +++N+++ ip   k l nL ++dLs+N  i++l+
  gene1330|gene1330|rna1329|rna1329 116 TNLRKFGFFSNKIRAIPKDIKfLINLIKIDLSNN-EISSLP 155
                                        79****************8888*********555.777763 PP

  == domain 6  score: 21.7 bits;  conditional E-value: 6.3e-08
                                        S--EEE--SS---E-S-.HHH-TT--EEE-.-S-----GG CS
                              LRR_4   2 nLevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdld 40 
                                        nL+++dLsnN ++++p  +  l nL  L+L +Nn++++l+
  gene1330|gene1330|rna1329|rna1329 140 NLIKIDLSNNEISSLPDeFCELRNLNWLNL-SNNKLQKLP 178
                                        9****************9555*********.666999984 PP

  == domain 7  score: 14.3 bits;  conditional E-value: 1.4e-05
                                        S--EEE--SS---E-S-HHH-TT--EEE-...-S-----G CS
                              LRR_4   2 nLevLdLsnNqltdiplleklpnLkeLdL..sgNnlitdl 39 
                                        +Le+L L+ N+lt++p    + nLk+L +   + n++t++
  gene1330|gene1330|rna1329|rna1329 186 RLEELGLGANNLTELPD---MSNLKKLRIlpVFKNQLTQV 222
                                        79******88****999...88888888656576688876 PP

  == domain 8  score: 24.4 bits;  conditional E-value: 9.3e-09
                                        --EEE--SS---E-S-..HHH-TT--EEE-.-S-----GGG CS
                              LRR_4   3 LevLdLsnNqltdipl..leklpnLkeLdLsgNnlitdlde 41 
                                         e+Ld+s+N++t++p+  + ++  L++L+L +N +i+++d+
  gene1330|gene1330|rna1329|rna1329 232 IEKLDFSDNNITEFPGhvI-GIQTLRYLNLKSN-KISKIDP 270
                                        699**********999633.6*********555.***9986 PP

  == domain 9  score: 6.2 bits;  conditional E-value: 0.0048
                                        EEE--SS---E-S-..HHH-TT--EEE-.-S CS
                              LRR_4   5 vLdLsnNqltdipl..leklpnLkeLdLsgN 33 
                                        ++d s+N l+ ipl  ++ + n +++ + +N
  gene1330|gene1330|rna1329|rna1329 282 IIDVSDNLLSCIPLkfFKTFSNVTVIRVGEN 312
                                        5799***********6666*******99777 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   1.9e-09   5.7e-06      49     147 ..      31     123 ..      25     134 .. 0.87
   2 !   28.1   4.9   4.2e-10   1.3e-06      46     128 ..     143     222 ..     125     225 .. 0.91
   3 !   15.1   0.5   4.2e-06     0.013      33     125 ..     221     314 ..     216     320 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.9e-09
                              LRR_9  49 lsdndirkl.dgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsllkn 123
                                        lsdn+ir++ +++  lk l  l ln+nri  i +g++  +  l+ + lt n+l+ l d   + +lk+++ l l +n
  gene1330|gene1330|rna1329|rna1329  31 LSDNKIREVpESIKELKTLSRLALNDNRIEEIHPGIGSLV-GLTWIDLTRNRLRALPD--EMENLKRVSGLGLSEN 103
                                        8*******9678999*********************9765.79*************99..7899999999999999 PP

                              LRR_9 124 pvtnkkeyrlyviyklkqlrlldf 147
                                          ++ ++     i+k+ +lr ++f
  gene1330|gene1330|rna1329|rna1329 104 NFSEIPK----CIFKMTNLRKFGF 123
                                        9998875....6888888887776 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 4.2e-10
                              LRR_9  46 tidlsdndirkl.dgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsl 120
                                         idls+n+i  l d+f  l+ l+ l l+nn++ ++ +g+++   +leel l  n+l+el d   + +lkkl++l +
  gene1330|gene1330|rna1329|rna1329 143 KIDLSNNEISSLpDEFCELRNLNWLNLSNNKLQKLPDGINNL-VRLEELGLGANNLTELPD---MSNLKKLRILPV 214
                                        59*********9899************************975.58***************9...678999999999 PP

                              LRR_9 121 lknpvtnk 128
                                        +kn +t+ 
  gene1330|gene1330|rna1329|rna1329 215 FKNQLTQV 222
                                        99998875 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 4.2e-06
                              LRR_9  33 vienlGatldqfdtidlsdndirkldgfPl.lkrlktlllnnnrivriaegl.eevlPnleelvltnnelqeladl 106
                                        +++   a l+  + +d+sdn+i ++ g    ++ l+ l l++n+i +i +   ++ + ++ +++  +++l +   l
  gene1330|gene1330|rna1329|rna1329 221 QVNQSIACLNSIEKLDFSDNNITEFPGHVIgIQTLRYLNLKSNKISKIDPSTfKNRVSSV-SIIDVSDNLLSCIPL 295
                                        566667899999*************9976549****************987514555555.445444445555666 PP

                              LRR_9 107 dPlaslkklellsllknpv 125
                                        + + ++++++++ + +np 
  gene1330|gene1330|rna1329|rna1329 296 KFFKTFSNVTVIRVGENPF 314
                                        7777777777777767765 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   4.2e+03       5      23 .]      29      46 ..      28      52 .. 0.83
   2 ?   -1.1   0.0       1.7   5.1e+03       4      17 ..      48      64 ..      45      69 .. 0.66
   3 ?    2.5   0.1      0.12   3.5e+02       2      18 ..      72      87 ..      71     115 .. 0.67
   4 ?    7.8   0.7    0.0021       6.3       1      21 [.     140     159 ..     140     161 .. 0.76
   5 ?    5.2   3.2     0.015        45       1      23 []     163     184 ..     163     184 .. 0.85
   6 ?   -0.2   0.2      0.88   2.6e+03       2      16 ..     187     201 ..     186     222 .. 0.73
   7 ?    2.1   0.0      0.15   4.6e+02       2      15 ..     232     245 ..     231     251 .. 0.80
   8 ?    8.1   0.1    0.0016       4.9       2      22 ..     255     275 ..     254     275 .. 0.91
   9 ?    2.5   0.1      0.11   3.3e+02       5      21 ..     283     299 ..     280     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                              LRR_1  5 LdLsnnpllglppnsfqnL 23
                                       L Ls+n + +  p+s++ L
  gene1330|gene1330|rna1329|rna1329 29 LILSDNKI-REVPESIKEL 46
                                       66899999.8888888765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                              LRR_1  4 hLd...Lsnnpllglpp 17
                                       +L    L++n+++ ++p
  gene1330|gene1330|rna1329|rna1329 48 TLSrlaLNDNRIEEIHP 64
                                       55444499999965554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.12
                              LRR_1  2 LrhLdLsnnpllglppn 18
                                       L+ +dL++n+l + +p+
  gene1330|gene1330|rna1329|rna1329 72 LTWIDLTRNRL-RALPD 87
                                       77889999998.33333 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0021
                              LRR_1   1 nLrhLdLsnnpllglppnsfq 21 
                                        nL ++dLsnn ++  +p+ f+
  gene1330|gene1330|rna1329|rna1329 140 NLIKIDLSNNEIS-SLPDEFC 159
                                        899*********5.5555555 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.015
                              LRR_1   1 nLrhLdLsnnpllglppnsfqnL 23 
                                        nL  L+Lsnn l +++p+ + nL
  gene1330|gene1330|rna1329|rna1329 163 NLNWLNLSNNKL-QKLPDGINNL 184
                                        7889********.9999887765 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 0.88
                              LRR_1   2 LrhLdLsnnpllglp 16 
                                        L++L L+ n+l+ lp
  gene1330|gene1330|rna1329|rna1329 187 LEELGLGANNLTELP 201
                                        777777777776555 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.15
                              LRR_1   2 LrhLdLsnnpllgl 15 
                                         ++Ld s+n+++ +
  gene1330|gene1330|rna1329|rna1329 232 IEKLDFSDNNITEF 245
                                        689*******9655 PP

  == domain 8  score: 8.1 bits;  conditional E-value: 0.0016
                              LRR_1   2 LrhLdLsnnpllglppnsfqn 22 
                                        Lr+L+L +n ++ + p++f+n
  gene1330|gene1330|rna1329|rna1329 255 LRYLNLKSNKISKIDPSTFKN 275
                                        9**********9999999986 PP

  == domain 9  score: 2.5 bits;  conditional E-value: 0.11
                              LRR_1   5 LdLsnnpllglppnsfq 21 
                                        +d+s+n l+++p   f+
  gene1330|gene1330|rna1329|rna1329 283 IDVSDNLLSCIPLKFFK 299
                                        89**********99887 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.73   2.2e+03       8      15 ..      29      36 ..      29      37 .. 0.85
   2 ?   -0.3   0.1      0.49   1.5e+03       4      15 ..      48      59 ..      46      60 .. 0.86
   3 ?   -3.2   0.0       4.3   1.3e+04       8      15 ..      75      82 ..      72      83 .. 0.78
   4 ?   -1.5   0.0       1.2   3.7e+03       3      16 ..     116     129 ..     114     130 .. 0.85
   5 ?    1.8   0.5       0.1   3.1e+02       4      16 ..     140     152 ..     138     153 .. 0.84
   6 ?    1.0   0.9      0.19   5.7e+02       4      16 ..     163     175 ..     160     176 .. 0.80
   7 ?   -1.8   0.0       1.6   4.7e+03       5      16 ..     187     198 ..     185     198 .. 0.86
   8 ?   -3.1   0.0         4   1.2e+04       4      16 ..     208     220 ..     205     220 .. 0.69
   9 ?    6.6   0.3    0.0031       9.1       3      16 ..     230     243 ..     228     243 .. 0.89
  10 ?   10.3   0.1    0.0002      0.59       3      16 ..     253     266 ..     251     267 .. 0.92
  11 ?   -1.9   0.1       1.6   4.9e+03       7      15 ..     282     290 ..     278     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.73
                              LRR_6  8 LdLsgNdI 15
                                       L Ls+N+I
  gene1330|gene1330|rna1329|rna1329 29 LILSDNKI 36
                                       679****9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.49
                              LRR_6  4 hLteLdLsgNdI 15
                                       +L  L L++N I
  gene1330|gene1330|rna1329|rna1329 48 TLSRLALNDNRI 59
                                       89999*****98 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.3
                              LRR_6  8 LdLsgNdI 15
                                        dL+ N +
  gene1330|gene1330|rna1329|rna1329 75 IDLTRNRL 82
                                       69999986 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.2
                              LRR_6   3 thLteLdLsgNdIg 16 
                                        t+L++    +N+I 
  gene1330|gene1330|rna1329|rna1329 116 TNLRKFGFFSNKIR 129
                                        899999999**995 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.1
                              LRR_6   4 hLteLdLsgNdIg 16 
                                        +L + dLs N+I+
  gene1330|gene1330|rna1329|rna1329 140 NLIKIDLSNNEIS 152
                                        57789******97 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.19
                              LRR_6   4 hLteLdLsgNdIg 16 
                                        +L  L+Ls N+++
  gene1330|gene1330|rna1329|rna1329 163 NLNWLNLSNNKLQ 175
                                        66669*****985 PP

  == domain 7  score: -1.8 bits;  conditional E-value: 1.6
                              LRR_6   5 LteLdLsgNdIg 16 
                                        L+eL L  N+++
  gene1330|gene1330|rna1329|rna1329 187 LEELGLGANNLT 198
                                        899*99999986 PP

  == domain 8  score: -3.1 bits;  conditional E-value: 4
                              LRR_6   4 hLteLdLsgNdIg 16 
                                        +L+ L +  N+++
  gene1330|gene1330|rna1329|rna1329 208 KLRILPVFKNQLT 220
                                        6788877778775 PP

  == domain 9  score: 6.6 bits;  conditional E-value: 0.0031
                              LRR_6   3 thLteLdLsgNdIg 16 
                                        +++++Ld s+N+I+
  gene1330|gene1330|rna1329|rna1329 230 NSIEKLDFSDNNIT 243
                                        6889*********7 PP

  == domain 10  score: 10.3 bits;  conditional E-value: 0.0002
                              LRR_6   3 thLteLdLsgNdIg 16 
                                        ++L++L+L++N+I+
  gene1330|gene1330|rna1329|rna1329 253 QTLRYLNLKSNKIS 266
                                        79**********97 PP

  == domain 11  score: -1.9 bits;  conditional E-value: 1.6
                              LRR_6   7 eLdLsgNdI 15 
                                          d+s+N +
  gene1330|gene1330|rna1329|rna1329 282 IIDVSDNLL 290
                                        679****76 PP

>> DUF3557  Domain of unknown function (DUF3557)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   5.3e+03      26      41 ..      29      44 ..      23      78 .. 0.57
   2 ?    8.4   2.7   0.00066         2      22     116 ..     117     209 ..     113     228 .. 0.81
   3 ?    0.3   0.2       0.2   6.1e+02      26      34 ..     258     266 ..     217     307 .. 0.50

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                            DUF3557 26 lsisskgilriPsnlk 41
                                       l +s ++i  +P+++k
  gene1330|gene1330|rna1329|rna1329 29 LILSDNKIREVPESIK 44
                                       5555555666665554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00066
                            DUF3557  22 kvnklsisskgilriPsnlklkvknLeisgserdkilealrplldesslplkslevedtkvsnldhpivqnaklLi 97 
                                        +++k+ + s++i  iP+++k+ ++ ++i +  +++i +   ++++ ++  l++l+++++k+++l   i +  +l  
  gene1330|gene1330|rna1329|rna1329 117 NLRKFGFFSNKIRAIPKDIKFLINLIKI-DLSNNEISSLPDEFCELRN--LNWLNLSNNKLQKLPDGINNLVRLEE 189
                                        689999999*******************.8888899999999999887..*********99999998888777777 PP

                            DUF3557  98 lngeytnprn.slllalknk 116
                                        l     n ++  ++++lk+ 
  gene1330|gene1330|rna1329|rna1329 190 LGLGANNLTElPDMSNLKKL 209
                                        77666555555555555554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.2
                            DUF3557  26 lsisskgil 34 
                                        l ++s++i 
  gene1330|gene1330|rna1329|rna1329 258 LNLKSNKIS 266
                                        222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2863.99
//
Query:       gene133|gene133|rna133|rna133  [L=336]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.5e-07   29.1   0.4    7.5e-07   29.1   0.4    1.9  2  CLTH        CTLH/CRA C-terminal to LisH motif domain
  ------ inclusion threshold ------
      0.059   13.7   0.1       0.14   12.4   0.1    1.6  1  FCH         Fes/CIP4, and EFC/F-BAR homology domain
      0.094   13.3   0.7      0.094   13.3   0.7    1.9  2  Kri1        KRI1-like family
       0.47   10.6   4.6        1.5    9.0   0.1    3.1  3  Flt3_lig    flt3 ligand


Domain annotation for each model (and alignments):
>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.2   5.2e+03      78      82 ..      46      50 ..      25      90 .. 0.59
   2 !   29.1   0.4   1.7e-10   7.5e-07       4      71 ..     116     185 ..     114     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                           CLTH 78 kelek 82
                                   ++lek
  gene133|gene133|rna133|rna133 46 EKLEK 50
                                   22222 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1.7e-10
                           CLTH   4 erqkIiklilegdlseaiewinenkpellesn....snLeFkLkllqfielirgktkdieealeyarenlef 71 
                                      + I+++i++g  +ea++ + e++ el++++     +Le +Lk+ +fie+     ++ ++ale++ +++++
  gene133|gene133|rna133|rna133 116 RVYGIKNQIENGLFEEALSFCREYRVELKSMKceeaASLENDLKVEKFIEMCH-G-QEFDKALEFINKEFKR 185
                                    56789**************************77777*****************.7.789*********9842 PP

>> FCH  Fes/CIP4, and EFC/F-BAR homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.2e-05      0.14       8      48 ..      19      59 ..      13      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.2e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT----TT CS
                            FCH  8 rleqgialledlqeflkeRaeiEkeYakkLqkLakkylkrr 48
                                    l + ++l+e l ++++ R    +eY  kL+kL + + ++ 
  gene133|gene133|rna133|rna133 19 TLRTTCKLMERLFQMYRCRKISKEEYMEKLEKLKEVVGSNI 59
                                   57789****************************99888764 PP

>> Kri1  KRI1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   2.1e-05     0.094      10      46 ..      29      65 ..      21      76 .. 0.79
   2 ?   -1.4   0.1      0.78   3.5e+03      17      33 ..     143     159 ..     134     186 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                           Kri1 10 kkeelkrlkklkreeieeklekikkaageeeaalkel 46
                                   +  ++ r +k+ +ee +eklek+k+++g++ +++k+ 
  gene133|gene133|rna133|rna133 29 RLFQMYRCRKISKEEYMEKLEKLKEVVGSNIDEMKRN 65
                                   5567889*********************666665554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.78
                           Kri1  17 lkklkreeieeklekik 33 
                                    lk++k ee+++  + +k
  gene133|gene133|rna133|rna133 143 LKSMKCEEAASLENDLK 159
                                    45555555433222222 PP

>> Flt3_lig  flt3 ligand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1     0.068     3e+02      53      70 ..      46      63 ..      24      72 .. 0.76
   2 ?    9.0   0.1   0.00034       1.5      59     114 ..     144     198 ..      93     217 .. 0.82
   3 ?    0.0   0.1       0.2   8.9e+02      46     104 ..     226     283 ..     203     295 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.068
                       Flt3_lig 53 rtlerlktvaGsklqell 70
                                   ++le+lk+v Gs++ e+ 
  gene133|gene133|rna133|rna133 46 EKLEKLKEVVGSNIDEMK 63
                                   6799********998865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00034
                       Flt3_lig  59 ktvaGsklqellekvnteidfvekCafqplpsClrfvqtniselledvssqlealk 114
                                    k++  ++  +l +++++e +f+e+C+ q++++ l f++ +  ++ e++ s+l  l 
  gene133|gene133|rna133|rna133 144 KSMKCEEAASLENDLKVE-KFIEMCHGQEFDKALEFINKEFKRVPEQIKSYLPVLV 198
                                    555555555555556665.8*******************99999999999987664 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.2
                       Flt3_lig  46 WhlvlakrtlerlktvaGsklqellekvnteidfv.ekCafqplpsClrfvqtniselle 104
                                    ++  l  r ++r++   G    ++ + +nte +   + C+  +l + + f + +is ll 
  gene133|gene133|rna133|rna133 226 FRRGLKSRLMQRIEY--GMMAYKTYRCINTENNKCpTCCKAFRLREDVPFNKHEISILLC 283
                                    555555566666553..5555566666777765441567778899999999999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2211.61
//
Query:       gene1331|gene1331|rna1330|rna1330  [L=720]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 4807.21
//
Query:       gene1332|gene1332|rna1331|rna1331  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1059.97
//
Query:       gene1333|gene1333|rna1332|rna1332  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-30  105.9  14.0    1.6e-30  105.9  14.0    2.2  2  DHHC           DHHC palmitoyltransferase
     0.0013   17.2   0.2     0.0018   16.8   0.2    1.2  1  TRI12          Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
       0.57   10.0   7.1        1.1    9.1   7.1    1.5  1  zinc_ribbon_2  zinc-ribbon domain
       0.58   10.2   9.0        1.1    9.4   9.0    1.4  1  DZR            Double zinc ribbon


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.8      0.12   5.4e+02      49      71 ..      29      51 ..       1      61 [. 0.63
   2 !  105.9  14.0   3.7e-34   1.6e-30       3     133 ..      69     195 ..      67     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.12
                               DHHC 49 kyFllfllylllllilalvllli 71
                                       +++l +ll  ++++i++l l+++
  gene1333|gene1333|rna1332|rna1332 29 RAYLSLLLLSSIFSIIYLALSIV 51
                                       34555555555555555555443 PP

  == domain 2  score: 105.9 bits;  conditional E-value: 3.7e-34
                               DHHC   3 kelkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvk.lv 77 
                                        + +kfC+ cn ykp+r++Hc++C++cv ++DHhC w+nnc+ + N+ +F+ fl++++l+ +l+++  +  +v  l+
  gene1333|gene1333|rna1332|rna1332  69 HARKFCKRCNNYKPERAHHCSSCGHCVKKMDHHCFWINNCVNYDNQGHFIRFLFFTSLANLLIFTYVCGEFVAiLL 144
                                        6789*****************************************************9977666555555555055 PP

                               DHHC  78 eeekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTtieamkk 133
                                         +++  +   + +    + +l+ + sl+fl+++ ++l+ +l l+l n+T ie++k+
  gene1333|gene1333|rna1332|rna1332 145 FDRHLRHKRDY-Y----ILVLSGMSSLVFLIMTPFFLYLQLRLALMNMTFIEELKQ 195
                                        55555444433.3....45999999****************************998 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2     4e-07    0.0018     284     337 ..       3      56 ..       1      78 [. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4e-07
                              TRI12 284 lvvfalyevygkpvrpivppalfkdtrgfvcillissimgamnlslviiypqqv 337
                                        l++ +l   y  pv  i+ p+ f   r ++ +ll+ssi+  + l+l i+y   v
  gene1333|gene1333|rna1332|rna1332   3 LLISSLMLTYTVPVSEIILPTRFAFKRAYLSLLLLSSIFSIIYLALSIVYRGHV 56 
                                        678889999*****************************************8877 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   7.1   0.00024       1.1       1      21 [.      73      93 ..      73      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00024
                      zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                       fC++C +  +++a  C+ CG+
  gene1333|gene1333|rna1332|rna1332 73 FCKRCNNYKPERAHHCSSCGH 93
                                       9*******************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   9.0   0.00024       1.1       1      31 [.      74     108 ..      66     116 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00024
                                DZR   1 CpqCgeelppdarfCseCgtklkavaa....edrC 31 
                                        C++C++  p++a+ Cs Cg+ +k++ +     ++C
  gene1333|gene1333|rna1332|rna1332  74 CKRCNNYKPERAHHCSSCGHCVKKMDHhcfwINNC 108
                                        77888888888888888888777666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1815.09
//
Query:       gene1334|gene1334|rna1333|rna1333  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-67  228.0  11.6    1.6e-67  227.7  11.6    1.1  1  DUF5095   Domain of unknown function (DUF5095)


Domain annotation for each model (and alignments):
>> DUF5095  Domain of unknown function (DUF5095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.7  11.6     9e-72   1.6e-67       1     241 []      43     271 ..      43     271 .. 0.97

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 9e-72
                            DUF5095   1 kdnPfd..stslikkqketkeekkiaevvaeekelektkekskineddflkvLikkkkkekkekkilsngIynklk 74 
                                        +dnPfd  s+sl+kk++++ +e   ++                +++ +f + L k+k++ k+e+k+l +gI++++ 
  gene1334|gene1334|rna1333|rna1333  43 SDNPFDvlSQSLYKKNEISCKEVPSKQ--------------DLMEDSIFEELLLKAKTEPKNEEKKLCYGIFTSMA 104
                                        69****988888888888777766666..............889999***************************** PP

                            DUF5095  75 ilskeeltkksvkyYkfPfthelkkeksdiyksiyveflsalkslFkeykkaneeFyvkykdellifstelkvskk 150
                                        ++++ e++ ++ ++YkfPf+ e+k++ s++++++y+e+l+a ks+F+eyk++  +F++k+k+++l f++ lk+s +
  gene1334|gene1334|rna1333|rna1333 105 LVTDSEIQIQEKRMYKFPFEVETKNDGSQLFEKMYSEYLIAAKSVFREYKRSSIRFFMKLKNDFLLFDSYLKTSYG 180
                                        **************************************************************************** PP

                            DUF5095 151 lkklLesneiefveenselilsgkevalvlDlilNtklsstqalPfilSkykFensivyevrlkkkkavrskgkik 226
                                        +kk L +nei+f ee+s+li++g+evalv+D+i+N+++ss+ ++PfilS+++Fen+i+++v+l++k+a+r+ +ki+
  gene1334|gene1334|rna1333|rna1333 181 MKKELVRNEIRFEEEGSFLIVKGIEVALVFDYIINIPISSSFCIPFILSESQFENGILFSVKLERKRAIREGKKIL 256
                                        **************************************************************************** PP

                            DUF5095 227 yryiikGplitedfs 241
                                        y+y++ Gp++++d++
  gene1334|gene1334|rna1333|rna1333 257 YSYELLGPFWADDYK 271
                                        *************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1989.57
//
Query:       gene1335|gene1335|rna1334|rna1334  [L=418]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-12   46.9   2.8    1.5e-10   41.0   0.1    3.9  4  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he
  ------ inclusion threshold ------
      0.069   12.9   2.7       0.16   11.7   2.7    1.8  1  RNA_pol_Rpc82  RNA polymerase III subunit RPC82


Domain annotation for each model (and alignments):
>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.1   1.7e-14   1.5e-10       2      61 ..       4      62 ..       3      63 .. 0.97
   2 ?    1.1   0.0     0.047   4.2e+02       3      16 ..      85      98 ..      83     108 .. 0.83
   3 ?   -1.1   0.0      0.24   2.1e+03      13      38 ..     203     228 ..     193     244 .. 0.75
   4 ?    1.7   0.0     0.032   2.9e+02      15      52 ..     288     325 ..     286     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.7e-14
                                       HHHHHHHHCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEEEE CS
                              HTH_9  2 lcteiieehFGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVqyle 61
                                       l+ ei+ + +G++ +k+  +L +++ +t+  +++ t+L  +qV ++L+++iq+rlV+y++
  gene1335|gene1335|rna1334|rna1334  4 LVGEILGD-YGTILQKIGLFLRKRNGSTMEYITQGTSLAYSQVIHGLSLMIQRRLVKYFQ 62
                                       78899999.**************************************************8 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.047
                                       HHHHHHHCSTTHHH CS
                              HTH_9  3 cteiieehFGevva 16
                                       + +++e++FGe va
  gene1335|gene1335|rna1334|rna1334 85 YCSLVEDLFGEEVA 98
                                       5689******9765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.24
                                        THHHHHHHHHHHHSSBEHHHHHHHHS CS
                              HTH_9  13 evvakVvetLlrkgrltlrelvkktk 38 
                                        + ++++++ +l ++  t++ ++++++
  gene1335|gene1335|rna1334|rna1334 203 SKAERIYKSILGRNLVTVDAIIESLE 228
                                        55788999999999999999888765 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.032
                                        HHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHH CS
                              HTH_9  15 vakVvetLlrkgrltlrelvkktkLsldqVkksLvvLi 52 
                                        ++++  ++l++  l  +++v k+ ++   Vkk++  L 
  gene1335|gene1335|rna1334|rna1334 288 ARRIFNMMLEYKSLEDKDIVIKSLVPSHIVKKAVLMLH 325
                                        577888999999999999999999********999885 PP

>> RNA_pol_Rpc82  RNA polymerase III subunit RPC82
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.7   1.8e-05      0.16      67     155 ..     143     228 ..     133     357 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                                        HHHSGT....T..TTCETSSSSSEE......E-TSSEEEE-SHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHH CS
                      RNA_pol_Rpc82  67 sseslkkkegrstadstsngtarKrrketealdpglvlriNlerflvhlRdeaLvqlaksrigettaevyeaaLkl 142
                                        +s++l +  +r  +d++ ++  rK rk    ++      i+++ +++ + +++L  l+k+r+ ++++ +y+ +L  
  gene1335|gene1335|rna1334|rna1334 143 ESKNLGEHMTRDRQDKVNEEVHRKSRK---TVERARFHVIDFDALHAMMINNRLLALVKKRYLSKAERIYKSILGR 215
                                        444444444455566667777777754...488888889***********************************88 PP

                                        TSTSS-GSS-TTS CS
                      RNA_pol_Rpc82 143 leersprlsadll 155
                                        +  + + + + l 
  gene1335|gene1335|rna1334|rna1334 216 NLVTVDAIIESLE 228
                                        7777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2502.76
//
Query:       gene1336|gene1336|rna1335|rna1335  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.3e-105  351.1   9.3   6.6e-105  350.8   9.3    1.1  1  DUF5087   Domain of unknown function (DUF5087)


Domain annotation for each model (and alignments):
>> DUF5087  Domain of unknown function (DUF5087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.8   9.3  3.7e-109  6.6e-105       1     290 [.     102     387 ..     102     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 350.8 bits;  conditional E-value: 3.7e-109
                            DUF5087   1 FKtnfklkefvdyieneivlfsleekkkvklkkslkkyvktnlkkilkyllkniNtlelekicttlllisneleye 76 
                                        FK++f+++++++y+++++  fsl+++ +v++kks++++vk++++ki+++++ n+Nt++l+++c+tl+lis ++ey+
  gene1336|gene1336|rna1335|rna1335 102 FKDAFTIDSLLSYSKEAHS-FSLNVRTEVRMKKSFHTNVKQQIDKIIRHMIVNLNTYDLNTVCSTLNLISGDIEYQ 176
                                        9******************.******************************************************** PP

                            DUF5087  77 eklvilhDiilfledlskllfiisalfnnkeienDilsktikkilsyqlaIdkklyknk.klveflnkikenldLt 151
                                        +klvi hDi+lf++d+s++ fi+salfnn++i +D+l+ tik+il +q+ +d ++++ + ++v ++nki +n++L+
  gene1336|gene1336|rna1335|rna1335 177 HKLVITHDIVLFIDDFSRIPFIVSALFNNQGIYDDVLGSTIKEILFHQCMVDSDINRSHpHIVGYYNKIIDNFELH 252
                                        **************************************************************************** PP

                            DUF5087 152 assislkeellsliekfkvfdvelieerindeifenvasirllchflDwdytYNefivevlypklketknpfyvly 227
                                         +++slk+ + +li +f+vf+    ++ +n++if  ++s+r+lch++DwdytYNefi++vlypkl et+np+y++y
  gene1336|gene1336|rna1335|rna1335 253 PKEKSLKDLCANLIGNFNVFE----DGGFNPAIFPSMYSVRVLCHYMDWDYTYNEFICSVLYPKLRETRNPLYAIY 324
                                        *********************....69************************************************* PP

                            DUF5087 228 lgvlalnalksfgeeeSvekvidelkkvlsekselsiasylfvkqikkkasekwleknkeeis 290
                                        +++ ++nal++fg+ eSve v+  lk+ + ++s+lsi+sylf+kq++++ + +w+e+++ +i 
  gene1336|gene1336|rna1335|rna1335 325 MFTAVFNALRVFGYIESVELVFSRLKELMDDSSDLSIVSYLFIKQVDPERADRWYESQRGNIR 387
                                        *********************************************************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2301.21
//
Query:       gene1337|gene1337|rna1336|rna1336  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-18   65.3   5.0    3.2e-16   59.9   5.0    2.4  1  TAF4      Transcription initiation factor TFIID component TAF
  ------ inclusion threshold ------
       0.96    9.3   4.4        1.1    9.1   1.5    2.6  2  ComC      COMC family


Domain annotation for each model (and alignments):
>> TAF4  Transcription initiation factor TFIID component TAF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   5.0   3.6e-20   3.2e-16       1     272 [.      69     297 ..      69     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 3.6e-20
                               TAF4   1 LnDvlasaGVdLkeEeerLlqssakeasrvseavravvrsekee.pfLqknpLqkklaeiakkeglksidpDvlel 75 
                                        L+D++  +GVdLkeE e +++++   +++++  + ++ +++ +  ++L+  +  +++a+i ++ ++ +++++   l
  gene1337|gene1337|rna1336|rna1336  69 LQDIIQYSGVDLKEEAEHIVRET---ETNINFGEYDEEDANDQIgSLLNVPQFREFIARIGNSRRV-GVSEESFFL 140
                                        89******************444...6666655666666665558*********************.9******** PP

                               TAF4  76 lSlAveerLrgLltklivlskhRrrgekskkrtesltsdvrkqLrelaqkekeeeekrqakRieereglekaakdr 151
                                        l   v+  + + ++k+   sk R++ + s+  +  + +d ++qL  l+q ek e ek   +R              
  gene1337|gene1337|rna1336|rna1336 141 LFQVVRRKILDTVEKMEESSKWRVEYNLSEFIIR-INNDLSRQLWCLEQIEKAELEKFTIRR-------------- 201
                                        *************************777776666.*******************99988833.............. PP

                               TAF4 152 skgedeeekklkaketakevqkeedekarhraANatAlaavgeprkKkyswmsagsgsgggksgaskssssggkgl 227
                                          ge+e +kk+k+      +q++ed  +++r +N+ Alaa+g  ++K  swmsa     +++s a +s  s+    
  gene1337|gene1337|rna1336|rna1336 202 --GEEEGKKKVKK-----TIQEREDLVIKKRLSNTVALAALG-VQQK--SWMSAEDVRVNEESTAFNSIYSPFD-- 265
                                        ..33444444444.....46889999999*************.6665..8***999855555554433333222.. PP

                               TAF4 228 kgksgviserGknglrlrerergkritlrDllaaLEqerrtsksa 272
                                                     + +l+     ++it++Dll++LE++rr  ks 
  gene1337|gene1337|rna1336|rna1336 266 -------------EKALERKVANRTITMKDLLYVLERDRRYNKSI 297
                                        .............112334456689***************99875 PP

>> ComC  COMC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.27   2.4e+03       6      13 ..      43      50 ..      40      50 .. 0.84
   2 ?    9.1   1.5   0.00012       1.1       2      22 ..      53      73 ..      53      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.27
                                       XXXXXXXX CS
                               ComC  6 klnqFeeL 13
                                       +++qFe L
  gene1337|gene1337|rna1336|rna1336 43 TKEQFESL 50
                                       799**976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00012
                                       XXXXXXXXXXXXXXXXXXXXX CS
                               ComC  2 kkkqklnqFeeLktkeLeqIk 22
                                       +++ +++q ee+kt+ L+ I+
  gene1337|gene1337|rna1336|rna1336 53 NNTPNKEQQEEMKTEHLQDII 73
                                       6789**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1317  (0.0734564); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1890.07
//
Query:       gene1338|gene1338|rna1337|rna1337  [L=345]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-54  183.4   0.2      6e-54  182.8   0.2    1.3  1  DUF5096   Domain of unknown function (DUF5096)


Domain annotation for each model (and alignments):
>> DUF5096  Domain of unknown function (DUF5096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.2   3.3e-58     6e-54       2     192 .]     152     343 ..     151     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 3.3e-58
                            DUF5096   2 seeqyksllseafnlyGPtkeefisiaalnllkllknif.ssskkikiiiggddiyneIglilgRlllakktevli 76 
                                        see+y+ ++++af  +GP++eef+siaa++++++++++f +s+ k+++ ++gd+++ +IglilgRlll++++++++
  gene1338|gene1338|rna1337|rna1337 152 SEENYYGMMKRAFCYFGPLEEEFCSIAARQAYRIFSTYFgNSTLKVEVLVSGDGVFPSIGLILGRLLLNSGKKLSV 227
                                        89*************************************999********************************** PP

                            DUF5096  77 lcssknvkivrykfiyennggiikkknresndvsIaladkknievqekktaksvlflgvpe.nakeiknkigiffG 151
                                        +c++  ++ v+yk++y n+ggii +k   +  ++I+ + k+ i + +  +ak +++l++p   ++e ++kig++fG
  gene1338|gene1338|rna1337|rna1337 228 ICNEIPLRSVKYKQSYMNSGGIIANKPSLESTIQIYSCGKALISTWPRSSAKGFMYLDTPGfIVEERETKIGLCFG 303
                                        *************************************************************999************ PP

                            DUF5096 152 vvpeefkkfkgelyliDvgfskklykkygldkefkksliki 192
                                        ++p  f+kf+g +y++D+++++ ly+++gl++ + ks+i++
  gene1338|gene1338|rna1337|rna1337 304 SIPTYFRKFNGIVYFVDMEYPSLLYEEFGLQR-PTKSKIHK 343
                                        ********************************.99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2034.34
//
Query:       gene1339|gene1339|rna1338|rna1338  [L=565]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      7e-50  167.8   3.5    3.5e-27   94.7   0.1    3.0  3  CH         Calponin homology (CH) domain
    2.6e-10   40.0   0.0    1.2e-05   25.1   0.0    2.9  2  CAMSAP_CH  CAMSAP CH domain
  ------ inclusion threshold ------
      0.015   14.2   0.2       0.12   11.1   0.0    2.3  2  DUF5382    Family of unknown function (DUF5382)
       0.15   12.3   4.1          5    7.4   0.1    3.6  4  DUF1722    Protein of unknown function (DUF1722)


Domain annotation for each model (and alignments):
>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.1   7.7e-31   3.5e-27       2     107 ..      12     115 ..      11     117 .. 0.96
   2 !   73.0   0.1   4.5e-24     2e-20       4     108 ..     129     233 ..     126     234 .. 0.94
   3 ?   -1.9   0.1      0.84   3.8e+03      58      73 ..     424     439 ..     364     475 .. 0.58

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 7.7e-31
                                        HHHHHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHHHHHHHHHHHHHHHHTT CS
                                 CH   2 eqkkellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkkleNinlaldvaekklg 77 
                                        +qkk++++W+n++l++ g +++++d++edlrDGv L++Ll +l+ ++v+++ +++++ +k+eN++ +l++++ + +
  gene1339|gene1339|rna1338|rna1338  12 VQKKTFTKWVNEKLAR-GGHEEIKDMFEDLRDGVKLANLLMALQKDTVEYNPVPYTRIQKMENVERVLSFIK-EKK 85 
                                        79************98.58999***********************************************999.*** PP

                                        CHTTSS-HHHHHTTSHHHHHHHHHHHHHHH CS
                                 CH  78 vpkvlieaedlvegknksvltllaqLfraf 107
                                        v++++i+a+d+v+g++k++l+l+++L+++ 
  gene1339|gene1339|rna1338|rna1338  86 VKLINIGASDIVDGNPKLILGLIWSLISRL 115
                                        **************************9875 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 4.5e-24
                                        HHHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHHHHHHHHHHHHHHHHTTCH CS
                                 CH   4 kkellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkkleNinlaldvaekklgvp 79 
                                        ++ellrW++++++++ ++v++ df+++++DG+++ ++++k++p+l++  +   +  +k+ N+++a++vae+ l+++
  gene1339|gene1339|rna1338|rna1338 129 RNELLRWCKEVTNGY-KNVNIVDFSKSWQDGLAFNAIIHKFRPDLIPNFQS-LKSSEKVYNLTQAFKVAERFLNIK 202
                                        789***********9.9999*************************988777.469********************* PP

                                        TTSS-HHHHHT...TSHHHHHHHHHHHHHHHH CS
                                 CH  80 kvlieaedlve...gknksvltllaqLfrafq 108
                                        k+l ++ed++    +++ks++t+++  +r+f+
  gene1339|gene1339|rna1338|rna1338 203 KLL-DVEDIAGvsiPDEKSIMTYVSGYYRKFK 233
                                        ***.******999***************9986 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.84
                                        HHHHHHHHHHHHHHHH CS
                                 CH  58 efkkleNinlaldvae 73 
                                        + kkle ++++ d   
  gene1339|gene1339|rna1338|rna1338 424 ASKKLETLKNVQDKKS 439
                                        4444444444444333 PP

>> CAMSAP_CH  CAMSAP CH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   3.7e-05      0.17      12      82 ..      32      97 ..      28     100 .. 0.82
   2 !   25.1   0.0   2.6e-09   1.2e-05       8      82 ..     143     211 ..     136     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                          CAMSAP_CH 12 pvedllrdlsdGvaLaalihfYcPqliklediclkesmsladslyNiqllqefcerkLgnsvfhltleDll 82
                                       +++d+ +dl+dGv La+l++ +  ++++ + +      +  ++++N++ + +f+++k  ++ +++ + D++
  gene1339|gene1339|rna1338|rna1338 32 EIKDMFEDLRDGVKLANLLMALQKDTVEYNPVP----YTRIQKMENVERVLSFIKEK-KVKLINIGASDIV 97
                                       689*******************99999875555....56668899999999999998.5777777777765 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 2.6e-09
                          CAMSAP_CH   8 plippvedllrdlsdGvaLaalihfYcPqliklediclkesmsladslyNiqllqefcerkLgnsvfhltleDll 82 
                                        ++  ++ d+ ++++dG+a  a+ih ++P+li+     + +s+  ++++yN+ ++++++er L n +  l++eD+ 
  gene1339|gene1339|rna1338|rna1338 143 YKNVNIVDFSKSWQDGLAFNAIIHKFRPDLIPN----F-QSLKSSEKVYNLTQAFKVAERFL-NIKKLLDVEDIA 211
                                        5566788************************75....3.46678899**************9.555556999985 PP

>> DUF5382  Family of unknown function (DUF5382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.8e-05      0.12      54      97 ..     205     248 ..     122     266 .. 0.83
   2 ?    0.4   0.1     0.052   2.3e+02      46     103 ..     351     408 ..     348     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
                            DUF5382  54 tCfedgkrlsvdelrklltllskyyrklkeeelsvrekdeqkri 97 
                                        + +ed  ++s+++ + ++t++s+yyrk+ke e++   ++  k +
  gene1339|gene1339|rna1338|rna1338 205 LDVEDIAGVSIPDEKSIMTYVSGYYRKFKEYEKERSARERVKGV 248
                                        456899999********************998888777776665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.052
                            DUF5382  46 inpdiaietCfedgkrlsvdelrklltllskyyrklkeeelsvrekdeqkrievklry 103
                                        i  +i+i   f++ +++ ++ l++++ + ++  +k + ++ + ++  e  +  + +++
  gene1339|gene1339|rna1338|rna1338 351 IADSIEIRKLFDPSFQSEINALNRVFEFFKHTLSKGESVKEQIQDASELSNKLMEMTF 408
                                        566899*********************9999999887666666666655555555544 PP

>> DUF1722  Protein of unknown function (DUF1722)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.32   1.4e+03      62     108 ..      21      67 ..      15      71 .. 0.74
   2 ?    3.4   0.1      0.02        88      24      98 ..     218     293 ..     212     310 .. 0.88
   3 ?    7.4   0.1    0.0011         5      46      71 ..     363     388 ..     360     407 .. 0.85
   4 ?   -1.9   0.0      0.86   3.9e+03      24      56 ..     417     449 ..     403     460 .. 0.52

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                            DUF1722  62 fkkklsaeekqelleliekYregkvplsvpltlLkhyarky.dneyll 108
                                        +++kl +   +e+ ++ e+ r+g  +l  +l  L++ + +y +++y +
  gene1339|gene1339|rna1338|rna1338  21 VNEKLARGGHEEIKDMFEDLRDGV-KLANLLMALQKDTVEYnPVPYTR 67 
                                        567788888899999999999886.88888888877666663566665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.02
                            DUF1722  24 kepleelaeeYeellmealskpatrkkhinvlqhi.lgyfkkklsaeekqelleliekYregkvplsvpltlLkhy 98 
                                        ++++ ++++ Y+++++e  ++++ r+++  vl+ i +    ++l + + ++ll+li+  +++k ++ ++++ L++ 
  gene1339|gene1339|rna1338|rna1338 218 EKSIMTYVSGYYRKFKEYEKERSARERVKGVLETIdWSIQARNLYEIKARNLLSLIKGLNNQKKEVCKIIRSLNKS 293
                                        5677889999************************9889999999999999**********9999999999888864 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0011
                            DUF1722  46 atrkkhinvlqhilgyfkkklsaeek 71 
                                        ++ ++ in+l++++++fk++ls+ e 
  gene1339|gene1339|rna1338|rna1338 363 PSFQSEINALNRVFEFFKHTLSKGES 388
                                        567899****************9884 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.86
                            DUF1722  24 kepleelaeeYeellmealskpatrkkhinvlq 56 
                                        ke ++++a++  e+l+++  k+++ +k+++ + 
  gene1339|gene1339|rna1338|rna1338 417 KEGFKSIASKKLETLKNVQDKKSKEEKVLESAT 449
                                        445555555555555555555544444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3775.15
//
Query:       gene1340|gene1340|rna1339|rna1339  [L=349]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-21   74.9   0.1    1.2e-20   73.9   0.1    1.4  1  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.1   6.8e-25   1.2e-20       4     146 ..     170     310 ..     168     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 6.8e-25
                                        HHHHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCTTTTTSCHHHHHHHHHHHHHHSSSTTTTGGHHHH CS
                             RhoGAP   4 vekcvefiekrgldtegiyRvsgskarvkelreafdkgkavdsdleeedvhavaslLKrfLrelpepLltkelyee 79 
                                        v +++e +++r++ t+ i+R + +k++  ++ + ++++k v  d+e ++v ++a++LK+++re  + L++ e +e+
  gene1340|gene1340|rna1339|rna1339 170 VFDVIESLKRRAVCTKFIFRYEPDKSEASRIANMVHEDKCV--DIEGTNVLVLANALKNYIREHLDGLIPIEVFEK 243
                                        6789*************************************..8******************************** PP

                                        HHHHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHTHHHH---HHHHHHHHHHHHHT- CS
                             RhoGAP  80 lieaaksedeeerlealkellekLPkenrdtLryLlehLkrvaenskenkMtaknLaivfaPtLlrp 146
                                        + ++  s+d++ +   ++ +   + +++r++L +L+e+L+ + ens++++Mt+++L   f+  L ++
  gene1340|gene1340|rna1339|rna1339 244 IKSCIISNDRHRKEALFSYMPFIFTDAERRLLVSLFELLRIIDENSDVTEMTIDSLLGLFSLVLHPQ 310
                                        **99999999999999999999**********************************99999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2342.83
//
Query:       gene134|gene134|rna134|rna134  [L=584]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.48   10.4   3.2        2.9    7.8   0.1    2.7  3  DUF1533   Protein of unknown function (DUF1533)


Domain annotation for each model (and alignments):
>> DUF1533  Protein of unknown function (DUF1533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2    0.0089   1.6e+02      30      46 ..      19      35 ..      13      36 .. 0.84
   2 ?    7.8   0.1   0.00016       2.9      21      58 ..      62      98 ..      58      99 .. 0.88
   3 ?   -4.0   0.0       0.8   1.4e+04       7      18 ..     501     512 ..     500     521 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0089
                        DUF1533 30 kLklkasvfnkaGentI 46
                                   k+ + ++vf k Gen+I
  gene134|gene134|rna134|rna134 19 KIFIGSEVFYKIGENVI 35
                                   4899***********99 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00016
                        DUF1533 21 nkyslssigkLklkasvfnkaGentIvIkakGYeDvti 58
                                   +ky+l  ++k  + +++f++   ++I++ + G +D+ i
  gene134|gene134|rna134|rna134 62 GKYYLLTKKKMLIYEDLFEEP-IHEIEVLNEGVFDFHI 98
                                   79***88888********777.**********999866 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 0.8
                        DUF1533   7 aIsevtvNGkkl 18 
                                    aI+e ++N+++ 
  gene134|gene134|rna134|rna134 501 AIEEKLINDTNV 512
                                    677778898876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 3304.26
//
Query:       gene1341|gene1341|rna1340|rna1340  [L=812]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-19   70.3  10.8    4.9e-19   68.8  10.8    1.8  1  Telomerase_RBD  Telomerase ribonucleoprotein complex - RNA bi
    9.8e-14   51.4   0.3    3.2e-08   33.4   0.1    3.0  3  RVT_1           Reverse transcriptase (RNA-dependent DNA poly


Domain annotation for each model (and alignments):
>> Telomerase_RBD  Telomerase ribonucleoprotein complex - RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8  10.8   5.4e-23   4.9e-19       2     131 ..     241     363 ..     240     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 5.4e-23
                                        HHHHHHHHHHHHS-HHHH-SCHHHHHHHHHHHHHCCH---SSS--TTTS-S--GGG-GGG-SS.S------HHHHH CS
                     Telomerase_RBD   2 VvaFvravlkkvvpkellGsehnkkvllknvkkfvklrrfeslslhevmqglkvsdvewlspekeksqklslsdae 77 
                                         v+F++ + +k++++ +  ++h +k+l ++++ +++ +r+e+++ +e+m+ +++s +++++     + +++++++ 
  gene1341|gene1341|rna1340|rna1340 241 LVNFLFLISRKLFKDVF--DSHGFKILKSRLSLLIHRNRYETVNKNELMKYFRISGFKFFR-----TARCTRNEFV 309
                                        589**************..9****************************************9.....4689****** PP

                                        HHHHHHHHHHHHHHHTCHHHHHHHH-EEEE--SSS-SEEEE-HHHHHHHHHHHH CS
                     Telomerase_RBD  78 krkellseflywlfdslliplirsfFYvTessktrnrlfyFrkdvWrkltkpal 131
                                         r ++ s+fl++++++l+ip+i+++FY Te+s+++ +++yF++ +W+++++ ++
  gene1341|gene1341|rna1340|rna1340 310 FRFKISSRFLVYIMEKLIIPIISKYFYSTETSFSKFKVYYFPRPIWQHFSDIYI 363
                                        *************************************************99876 PP

>> RVT_1  Reverse transcriptase (RNA-dependent DNA polymerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.69   6.2e+03      18      34 ..     187     203 ..     185     256 .. 0.59
   2 !   14.9   0.0   1.6e-06     0.014      56     135 ..     440     512 ..     417     535 .. 0.77
   3 !   33.4   0.1   3.6e-12   3.2e-08     117     205 ..     558     643 ..     539     681 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.69
                                        -THHHHCTB--...... CS
                              RVT_1  18 dykalnkliakrLkdvl 34 
                                        +yk ++k +++ L+ + 
  gene1341|gene1341|rna1340|rna1340 187 KYKTIQKDTKNILEGIE 203
                                        68888998888877664 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.6e-06
                                        ......HCCHTS--EEEEEEBCCGCCCSBB-GGGGGGG-EEET..........................TEEEEES CS
                              RVT_1  56 edllkalkkkkkaklllklDlkkaFdsvpleellrkltafkvptklinliksflstrsfsvrvnge.eskgryekk 130
                                        e l  +l++  k  ++lk+Dl+++Fd++p + + + ++++  +        s + trsfs+  + + e k ry+ +
  gene1341|gene1341|rna1340|rna1340 440 ERLIPYLSRSVKPLYILKVDLSGCFDNIPQDNVVNLVKKLLSK--------SRYCTRSFSILEESNgELKNRYVCR 507
                                        55666778888999*********************99996666........4477888888875554667777776 PP

                                        B--ST CS
                              RVT_1 131 glpqG 135
                                        + + G
  gene1341|gene1341|rna1340|rna1340 508 TGKVG 512
                                        66665 PP

  == domain 3  score: 33.4 bits;  conditional E-value: 3.6e-12
                                        .......TEEEEESB--ST-TTHHHHHHHHHHHHHTT-T.......TEEECTTEEEEEESSHHHHHHHHHHHHHHH CS
                              RVT_1 117 rvngeeskgryekkglpqGsvlSPllfnlfmnellrelrkra.kgvtllrYaDDililskskeelqelleaveewl 191
                                        + ng   k++ +k+g+ qGsv+S ll++l+  +++  +  ++ k+  l+rY+DD+l++s s +e+ + le +++++
  gene1341|gene1341|rna1340|rna1340 558 KHNG---KFFIQKTGIAQGSVTSTLLCSLYYKSIDDLYFDKIfKEGILTRYIDDFLVISPSIDEILKFLE-ISQTI 629
                                        3333...899***************************998888*********************999997.68899 PP

                                        HHTT--BEGGG-EE CS
                              RVT_1 192 kesglkinpeKtkl 205
                                        +  g+++++eK + 
  gene1341|gene1341|rna1340|rna1340 630 SHLGINFSKEKMES 643
                                        9**********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 5005.95
//
Query:       gene1342|gene1342|rna1341|rna1341  [L=414]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2633.94
//
Query:       gene1343|gene1343|rna1342|rna1342  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.3e-32  110.6   0.0    7.5e-32  110.4   0.0    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.0   4.2e-36   7.5e-32       3     190 .]      28     211 ..      26     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 4.2e-36
                                        HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                         Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                         G t++G+k+++gvvl a+k   +  ++++++  eKi+k  + ++va++Gl++Da ++   ++ ++ +++ +++++
  gene1343|gene1343|rna1342|rna1342  28 SGDTCIGMKSRHGVVLLAEKPKISPLYVAESD--EKIRKAGNSVAVACTGLISDAFYVGYAIKDHVFHHKENFNED 101
                                        799****************9666456664444..9***************************************** PP

                                        TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                         Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                        +++e++  ++ +  +  t + + r +gv+ l   +  eg+ +L+++d+sG+ + +k a++iG g+  +kt lek+ 
  gene1343|gene1343|rna1342|rna1342 102 PTPEIMKVYLNDIFHYFTRSISLRVLGVNSLTSVYK-EGRFSLLHTDCSGKTLFYK-AACIGRGTRRIKTELEKLD 175
                                        ****99999999999999999**********77666.999***************8.******************* PP

                                        STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                         Proteasome 155 kedltleeavelavkalkealerdklsgknievavi 190
                                         +++t ee+v+  vk+l+ a++  k ++  ie++v+
  gene1343|gene1343|rna1342|rna1342 176 IDNMTIEEMVDAGVKVLYMAHDPSKDKEFDIEIGVV 211
                                        ********************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1579.88
//
Query:       gene1344|gene1344|rna1343|rna1343  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-24   85.0   0.1    5.9e-24   84.2   0.1    1.5  1  DWNN           DWNN domain
    1.3e-10   40.9   4.8    1.3e-10   40.9   4.8    2.0  1  zf-CCHC_2      Zinc knuckle
     0.0014   18.6  11.5     0.0034   17.4  11.5    1.7  1  zf-RING_UBOX   RING-type zinc-finger
     0.0061   16.7   9.7     0.0061   16.7   9.7    2.4  2  zf-C3HC4_4     zinc finger of C3HC4-type, RING
     0.0085   16.0  14.9     0.0085   16.0  14.9    2.1  2  zf-RING_5      zinc-RING finger domain
  ------ inclusion threshold ------
      0.011   15.6  12.9      0.011   15.6  12.9    2.0  2  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
      0.018   15.2  10.3      0.018   15.2  10.3    2.3  3  zf-RING_10     zinc RING finger of MSL2
      0.018   15.1   5.2      0.018   15.1   5.2    2.6  2  zf-CCHC        Zinc knuckle
      0.089   12.5   0.4      0.089   12.5   0.4    2.1  3  zf-CCHC_5      GAG-polyprotein viral zinc-finger
       0.66   10.0   5.4        8.3    6.5   0.9    3.0  3  Rubredoxin     Rubredoxin
        2.1    8.3  15.8        0.3   11.0  11.0    2.1  2  zf-C3HC4       Zinc finger, C3HC4 type (RING finger)


Domain annotation for each model (and alignments):
>> DWNN  DWNN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.1   3.6e-27   5.9e-24       1      74 []       5      77 ..       5      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 3.6e-27
                               DWNN  1 vyYkFksqkdyskitfdgtsisvfeLKreIiekkklgkgtdfdLqiynaqtkeeydddselIprntsvivrRvP 74
                                       + Y+F+s+k++s+i+f+gt++ ++eLK eIi+++k+  ++dfdL +++ +t+ee++d+++lI  n++viv+R+P
  gene1344|gene1344|rna1343|rna1343  5 INYRFRSNKNFSRIQFQGTGLPLWELKYEIINQRKM-ISKDFDLLFFDGETNEEINDEYQLISMNSHVIVNRIP 77
                                       78**********************************.99**********************************9 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   4.8   7.9e-14   1.3e-10       1      21 []     109     129 ..     109     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 7.9e-14
                          zf-CCHC_2   1 PpgYvChiCgkkGHyIqdCPt 21 
                                        P++YvC +Cg+kGHyIq+C+t
  gene1344|gene1344|rna1343|rna1343 109 PESYVCFRCGQKGHYIQNCHT 129
                                        9******************97 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  11.5   2.1e-06    0.0034       1      26 [.     202     227 ..     202     244 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                       zf-RING_UBOX   1 CpIClelftdPlvlpCGHtFCreClw 26 
                                        Cp C  l+ +P++++CGHt+C +C++
  gene1344|gene1344|rna1343|rna1343 202 CPSCHCLLVNPIKTSCGHTLCDQCVR 227
                                        ***********5589*********92 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.6   2.6e+03      20      24 ..     113     117 ..     104     120 .. 0.72
   2 !   16.7   9.7   3.7e-06    0.0061       1      26 [.     202     227 ..     202     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                         zf-C3HC4_4  20 fClsC 24 
                                        +C++C
  gene1344|gene1344|rna1343|rna1343 113 VCFRC 117
                                        56666 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.7e-06
                         zf-C3HC4_4   1 CPiCldYLekPvsleCGhsfClsCis 26 
                                        CP C  +L +P+  +CGh+ C +C+ 
  gene1344|gene1344|rna1343|rna1343 202 CPSCHCLLVNPIKTSCGHTLCDQCVR 227
                                        ************************96 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3         1   1.6e+03      25      30 ..     114     119 ..     102     131 .. 0.63
   2 !   16.0  14.9   5.2e-06    0.0085       1      44 []     201     237 ..     201     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1
                          zf-RING_5  25 CekClk 30 
                                        C +C +
  gene1344|gene1344|rna1343|rna1343 114 CFRCGQ 119
                                        444444 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5.2e-06
                          zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44 
                                        +C++C++ l    +++ tsCgH++C++C++       +C +C+k
  gene1344|gene1344|rna1343|rna1343 201 KCPSCHCLL---VNPIKTSCGHTLCDQCVRMDR----KCYVCSK 237
                                        6********...99*****************99....9999975 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.4      0.75   1.2e+03      25      32 ..     113     120 ..     107     130 .. 0.65
   2 ?   15.6  12.9   6.6e-06     0.011       2      49 ..     199     241 ..     198     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.75
                                        E-HHHHHH CS
                         zf-C3HC4_3  25 lCeeCaek 32 
                                        +C +C +k
  gene1344|gene1344|rna1343|rna1343 113 VCFRCGQK 120
                                        56666655 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.6e-06
                                        GSB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B--E CS
                         zf-C3HC4_3   2 deeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpiek 49 
                                        + +C+ C+    n +   CgH+ lC +C++      +kC +C + ie 
  gene1344|gene1344|rna1343|rna1343 199 RLKCPSCHCLLVNPIKTSCGHT-LCDQCVRMD----RKCYVCSKVIEN 241
                                        579*******************.******988....********9985 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.85   1.4e+03      23      40 ..     111     127 ..     101     135 .. 0.66
   2 ?   -3.6   0.0         8   1.3e+04      44      57 ..     181     194 ..     177     196 .. 0.72
   3 ?   15.2  10.3   1.1e-05     0.018       1      59 [.     200     252 ..     200     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.85
                         zf-RING_10  23 HyvCrlCvgkkkklkpsC 40 
                                         yvC +C +k +    +C
  gene1344|gene1344|rna1343|rna1343 111 SYVCFRCGQKGH-YIQNC 127
                                        588888855443.33445 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8
                         zf-RING_10  44 kdyekyeenkqlrl 57 
                                        ++++ky++  ++++
  gene1344|gene1344|rna1343|rna1343 181 QEWKKYKQRSKMTV 194
                                        56788888888876 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.1e-05
                         zf-RING_10   1 lsCvvCckLLvdPlepkekeCqHyvCrlCvgkkkklkpsCsqCk.dyekyeenkqlrlll 59 
                                        l C  C  LLv+P++    +C+H +C +Cv+ ++    +C  C    e+++++ ++++ +
  gene1344|gene1344|rna1343|rna1343 200 LKCPSCHCLLVNPIKT---SCGHTLCDQCVRMDR----KCYVCSkVIENFTQDINMKIEV 252
                                        6899*******99876...9*********98655....6999985789999999999876 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   5.2   1.1e-05     0.018       2      16 ..     113     127 ..     113     128 .. 0.95
   2 ?    1.8   0.5      0.17   2.8e+02       1       7 [.     230     236 ..     230     238 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                        CTSSSSSSSSTTTTS CS
                            zf-CCHC   2 kCynCGepGHiardC 16 
                                        +C++CG+ GH+  +C
  gene1344|gene1344|rna1343|rna1343 113 VCFRCGQKGHYIQNC 127
                                        6***********999 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.17
                                        SCTSSSS CS
                            zf-CCHC   1 rkCynCG 7  
                                        rkCy C 
  gene1344|gene1344|rna1343|rna1343 230 RKCYVCS 236
                                        69****6 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       6.7   1.1e+04      19      30 ..      15      26 ..      15      27 .. 0.80
   2 ?   12.5   0.4   5.5e-05     0.089       5      24 ..     114     133 ..     110     134 .. 0.92
   3 ?   -4.2   0.9       9.1   1.5e+04       5       8 ..     202     205 ..     201     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.7
                                       --SEEGGGEE-- CS
                          zf-CCHC_5 19 hskfdknGnpLs 30
                                       +s+   +G  L+
  gene1344|gene1344|rna1343|rna1343 15 FSRIQFQGTGLP 26
                                       688888998887 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.5e-05
                                        -TTT-SSBS-TTT---SEEG CS
                          zf-CCHC_5   5 CpRCkkgkHwardChskfdk 24 
                                        C RC++  H+ ++Ch   dk
  gene1344|gene1344|rna1343|rna1343 114 CFRCGQKGHYIQNCHTNQDK 133
                                        ***************99887 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 9.1
                                        -TTT CS
                          zf-CCHC_5   5 CpRC 8  
                                        Cp C
  gene1344|gene1344|rna1343|rna1343 202 CPSC 205
                                        9999 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.025        41      29      42 ..     106     119 ..      93     123 .. 0.84
   2 ?   -3.1   0.0       5.3   8.6e+03      31      39 ..     146     154 ..     144     156 .. 0.81
   3 ?    6.5   0.9    0.0051       8.3      30      41 ..     195     206 ..     193     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.025
                                        GGS-TT-BBTTTB- CS
                         Rubredoxin  29 edlPddWvCPdCgv 42 
                                        +++P+ +vC  Cg 
  gene1344|gene1344|rna1343|rna1343 106 KAVPESYVCFRCGQ 119
                                        579*********86 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.3
                                        S-TT-BBTT CS
                         Rubredoxin  31 lPddWvCPd 39 
                                        +P+d+  P+
  gene1344|gene1344|rna1343|rna1343 146 IPKDFLVPV 154
                                        89**99886 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0051
                                        GS-TT-BBTTTB CS
                         Rubredoxin  30 dlPddWvCPdCg 41 
                                        ++Pd  +CP+C 
  gene1344|gene1344|rna1343|rna1343 195 EIPDRLKCPSCH 206
                                        79*********6 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       7.9   1.3e+04      21      25 ..     113     117 ..     112     121 .. 0.70
   2 ?   11.0  11.0   0.00019       0.3       1      31 [.     202     231 ..     202     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 7.9
                                        B-CHH CS
                           zf-C3HC4  21 fCskC 25 
                                        +C+ C
  gene1344|gene1344|rna1343|rna1343 113 VCFRC 117
                                        57777 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00019
                                        -TTT-S--SS-E.E-TTS--B-CHHHHHHHH CS
                           zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilk 31 
                                        Cp C + +++p   + C+H++C +C+r  +k
  gene1344|gene1344|rna1343|rna1343 202 CPSCHCLLVNPI-KTSCGHTLCDQCVRMDRK 231
                                        ************.************986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1080  (0.0602376); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1493.53
//
Query:       gene1345|gene1345|rna1344|rna1344  [L=450]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.7e-18   64.7   0.1    7.7e-18   64.7   0.1    1.9  2  NOC3p      Nucleolar complex-associated protein
  ------ inclusion threshold ------
       0.06   13.6   5.4       0.14   12.4   5.4    1.5  1  RGS        Regulator of G protein signaling domain
       0.11   13.2   2.3       0.19   12.5   2.3    1.4  1  TbpB_A     N-Lobe handle Tf-binding protein B
       0.47   10.8   3.1        0.8   10.1   2.0    1.9  2  CpxA_peri  Two-component sensor protein CpxA, periplasmic dom


Domain annotation for each model (and alignments):
>> NOC3p  Nucleolar complex-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.1   1.7e-21   7.7e-18       2      94 .]       7      96 ..       6      96 .. 0.95
   2 ?   -3.4   0.5       3.2   1.4e+04      64      84 ..     229     250 ..     223     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.7e-21
                              NOC3p  2 akeeiaslassiledPeenlsllkrllklaeskdsavtvrklallsllaVfkDiiPgYrIrsltekekeekvskevkk 79
                                       +k++ias++++i+e+P+enl+++++l+++ ++  s+   + + +lsll+Vfk iiP Y++rsl++     k +++  +
  gene1345|gene1345|rna1344|rna1344  7 QKSRIASICTKIIEEPQENLKMMEELFRMLSDGRSEGGAKGIIYLSLLKVFKAIIPLYKVRSLKDIV---KDKRDNLH 81
                                       799**************************9999999***************************9755...5789999* PP

                              NOC3p 80 lrefEqkLlkvYkky 94
                                       +++++++Llk Y +y
  gene1345|gene1345|rna1344|rna1344 82 IKDYDRSLLKWYASY 96
                                       ************998 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.2
                              NOC3p  64 ltekekee.kvskevkklrefE 84 
                                        l++ eke  k++ +v+  ++ E
  gene1345|gene1345|rna1344|rna1344 229 LKKMEKERlKIQSQVRDEEDIE 250
                                        4444555556666666665555 PP

>> RGS  Regulator of G protein signaling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   5.4   3.1e-05      0.14      23     109 ..     196     282 ..     187     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                                        TCTHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTSTTSTTSSTS-HHHHHH..HHHHHCSSSTTTTTTHHHHHH CS
                                RGS  23 fseenlsFwlaveefkkakeqeelkkkakeIyneylapsspkelnidkklree..lekrlekeqpsrklfeeaqee 96 
                                         +e++ ++w+a     ++  +++ + + k+I+++ l++  ++ l+i++++r+e  +e+r+e+ ++++k+++ +q+ 
  gene1345|gene1345|rna1344|rna1344 196 DEEKAREYWEANRSVSRR--EKNSIFHRKQIFSKKLKKMEKERLKIQSQVRDEedIEERVEEIKTCKKIYDVIQRL 269
                                        566777899999998888..555666789*********************975459******************** PP

                                        HHHHHHHHHHHHH CS
                                RGS  97 vfellekdsypkF 109
                                         f++l+++ y+ +
  gene1345|gene1345|rna1344|rna1344 270 YFTILKRNRYEYY 282
                                        ********99866 PP

>> TbpB_A  N-Lobe handle Tf-binding protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.3   4.2e-05      0.19      30     106 ..     220     295 ..     191     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                             TbpB_A  30 prrniapkdeegeeevplseediekvedellkipkekevkkksdekesfvhshdg..skksrkrdyqYVrsGyvlk 103
                                         r+ i++k+ ++ e+++l++++  +v de++  +  +e  k+ ++ +++++  +    k++r++ y+YV+ G+v +
  gene1345|gene1345|rna1344|rna1344 220 HRKQIFSKKLKKMEKERLKIQS--QVRDEEDIEERVEE-IKTCKKIYDVIQRLYFtiLKRNRYEYYKYVFIGLVKY 292
                                        5777788887888888887443..35665555555555.33344444444444443489999999*********96 PP

                             TbpB_A 104 keg 106
                                         + 
  gene1345|gene1345|rna1344|rna1344 293 RKI 295
                                        554 PP

>> CpxA_peri  Two-component sensor protein CpxA, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.93   4.2e+03      42      65 ..      67      90 ..      55      94 .. 0.71
   2 ?   10.1   2.0   0.00018       0.8       4      60 ..     221     274 ..     219     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.93
                                       ..T---TT--S-EEEEE-TTS-EE CS
                          CpxA_peri 42 rknrkkkkderlrlfltdldgeil 65
                                       r+ +   kd+r +l++ d+d ++l
  gene1345|gene1345|rna1344|rna1344 67 RSLKDIVKDKRDNLHIKDYDRSLL 90
                                       444445679999999999998877 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                                        -EE--HHHHHHHHHHHHHHHHHTSS---HHHHHHHHHH..T---TT--S-EEEEE-T CS
                          CpxA_peri   4 ardipaeelerlleirdkiekrfseeedlkkilkrleerknrkkkkderlrlfltdl 60 
                                        +++i +++l+++++ r ki+++ ++eed+++ + ++++ k+     d  +rl++t l
  gene1345|gene1345|rna1344|rna1344 221 RKQIFSKKLKKMEKERLKIQSQVRDEEDIEERVEEIKTCKKI---YDVIQRLYFTIL 274
                                        5789999************************99999997666...699999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1222  (0.0681577); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2927.16
//
Query:       gene1346|gene1346|rna1345|rna1345  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.38s 00:00:00.87 Elapsed: 00:00:00.55
# Mc/sec: 641.97
//
Query:       gene1347|gene1347|rna1346|rna1346  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-15   55.7   0.8    8.8e-15   55.0   0.1    1.8  2  PIN_6         PIN domain of ribonuclease
    6.9e-10   38.9   2.0    1.3e-09   38.1   2.0    1.4  1  NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.031   14.3   0.8      0.046   13.7   0.8    1.3  1  DZR           Double zinc ribbon


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.1   1.5e-18   8.8e-15       2      89 .]       4      87 ..       3      87 .. 0.91
   2 ?   -2.9   0.0       1.7     1e+04      32      45 ..     196     209 ..     194     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.5e-18
                              PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktD 79
                                       V+D+g li++ l + +    + y+t +V++E++ +++r+ le+l + +evr+Ps+e+v kv++  +k  +++ LS+tD
  gene1347|gene1347|rna1346|rna1346  4 VIDTGYLIER-LLPTEG-LIRGYVTDSVINELKTAESRAYLEFLSFMIEVRNPSEEYVTKVKNDLRK--EVNNLSDTD 77
                                       89******99.555544.4567899**************************************9998..6899***** PP

                              PIN_6 80 ievlALtyeL 89
                                       i+v+ALt+eL
  gene1347|gene1347|rna1346|rna1346 78 IDVVALTLEL 87
                                       ********98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                              PIN_6  32 Eirdkkarerlell 45 
                                        E+r +++re ++  
  gene1347|gene1347|rna1346|rna1346 196 ELRSADQREYIQHQ 209
                                        88888888877764 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   2.0   2.1e-13   1.3e-09       4      58 ..     132     184 ..     130     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.1e-13
                       NOB1_Zn_bind   4 vkswvlrChaCfkvtkdmtkkFCpkCGnktLkrvavsvdengelklhlkknfqln 58 
                                        ++++ +rC++Cf+++++ +  FC+kCG +tL+r++v  ++nge+ +++kk +q++
  gene1347|gene1347|rna1346|rna1346 132 ARKYKTRCYGCFSLFSE-NLDFCKKCGLRTLTRITVADTKNGEM-MFFKKGYQYR 184
                                        89***********9987.689****************9999995.6677777754 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.8   7.7e-06     0.046      27      49 .]     127     157 ..     100     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-06
                                DZR  27 a........edrCpsCgekvdpearfCpeCG 49 
                                        +        ++rC  C +  +++  fC++CG
  gene1347|gene1347|rna1346|rna1346 127 DpefsarkyKTRCYGCFSLFSENLDFCKKCG 157
                                        05555566689*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 1349.08
//
Query:       gene1348|gene1348|rna1347|rna1347  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 610.57
//
Query:       gene1349|gene1349|rna1348|rna1348  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-10   40.4   1.6    4.2e-10   39.3   1.6    1.6  1  NUC153    NUC153 domain


Domain annotation for each model (and alignments):
>> NUC153  NUC153 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   1.6   2.3e-14   4.2e-10       1      24 [.     265     288 ..     265     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.3e-14
                             NUC153   1 DpRFkalFedhdFaIDptspeFkk 24 
                                        D RF a+Fed dF IDpt+pe+k+
  gene1349|gene1349|rna1348|rna1348 265 DKRFEAIFEDDDFTIDPTHPEYKR 288
                                        99*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2032.25
//
Query:       gene1350|gene1350|rna1349|rna1349  [L=52]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-14   51.2  10.1    8.2e-14   51.0  10.1    1.1  1  Ribosomal_L39  Ribosomal L39 protein
  ------ inclusion threshold ------
       0.11   12.3   0.2       0.12   12.2   0.2    1.2  1  DUF2015        Fungal protein of unknown function (DUF2015)


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0  10.1   9.2e-18   8.2e-14       1      42 []       9      50 ..       9      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 9.2e-18
                      Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                       +K+rL+Kalk+N+++PaW+r+++++k + n  rR WR +kLk
  gene1350|gene1350|rna1349|rna1349  9 VKTRLMKALKKNKEIPAWKRMMKEHKGEFNRARRYWRAKKLK 50
                                       59***************************************8 PP

>> DUF2015  Fungal protein of unknown function (DUF2015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   1.4e-05      0.12      75      98 ..      27      50 ..       8      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                            DUF2015 75 kkimkkrrvkFdeARliyteerlk 98
                                       k++mk+++ +F+ AR+ +  ++lk
  gene1350|gene1350|rna1349|rna1349 27 KRMMKEHKGEFNRARRYWRAKKLK 50
                                       799***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.31s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 348.82
//
Query:       gene135|gene135|rna135|rna135  [L=293]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.09   12.0   0.2       0.14   11.4   0.2    1.4  1  IF-2B           Initiation factor 2 subunit family
       0.11   12.6   0.0       0.26   11.3   0.0    1.6  1  Stb3            Putative Sin3 binding protein
       0.68   10.4  10.0       0.16   12.4   2.4    3.1  3  Streptin-Immun  Lantibiotic streptin immunity protein


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   2.3e-05      0.14      34     126 ..     109     198 ..      80     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.3e-05
                                    HHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEE CS
                          IF-2B  34 elrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikeieeadekigdiaaelikdgdtilT 113
                                    + +++i++L +  ++ v++g  +  + k   + + s++vk+++++++  i++l  +i++  ek+++ + + +++++ i+ 
  gene135|gene135|rna135|rna135 109 YCKDQISTLLSHLYNNVNMGVRLLNFQK---ACEYSNRVKNIRSDVMYLINKLGLNILKGIEKVIRDYNNSMNEKEDIIL 185
                                    67899*****************999999...7899*********************999999999999999988888888 PP

                                    ES--SHHHHHHHH CS
                          IF-2B 114 icnsktvlevlra 126
                                     c+   + ++l +
  gene135|gene135|rna135|rna135 186 ECEDLKIKSLLGQ 198
                                    8855444433333 PP

>> Stb3  Putative Sin3 binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.4e-05      0.26      12      68 ..     181     236 ..     174     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                           Stb3  12 peillekGPlaiRhitaalttsvpgFsklspskaRRlvvaalegradkendvvfekv 68 
                                     +i+le   l i+ ++++l ++v +++++    a   v+a+l ++ + end+ f k+
  gene135|gene135|rna135|rna135 181 EDIILECEDLKIKSLLGQLRQKVNEYEEIIREEAISRVLAVLSQG-SVENDIRFAKL 236
                                    689999999**************************99*******9.99******995 PP

>> Streptin-Immun  Lantibiotic streptin immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4     0.082   4.9e+02      52      64 ..      18      30 ..       2      68 .. 0.54
   2 ?    2.2   0.5     0.041   2.5e+02      24      79 ..     130     184 ..     105     191 .. 0.74
   3 ?   12.4   2.4   2.6e-05      0.16      43      81 ..     174     212 ..     160     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.082
                 Streptin-Immun 52 vtleqiekeiekl 64
                                   +++ ++ekeie+ 
  gene135|gene135|rna135|rna135 18 LKVARLEKEIENR 30
                                   5555555555542 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.041
                 Streptin-Immun  24 vlvnlksedeetrrlakydfsklnltesvtleqiekeieklqnelskkideyeelv 79 
                                     l+n++   e + r+     + + l + + l+ i k iek+  + +++++e e+++
  gene135|gene135|rna135|rna135 130 RLLNFQKACEYSNRVKNIRSDVMYLINKLGLN-ILKGIEKVIRDYNNSMNEKEDII 184
                                    56777777777777777777778888877775.55789999999999999998886 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 2.6e-05
                 Streptin-Immun  43 fsklnltesvtleqiekeieklqnelskkideyeelvrk 81 
                                     + +n  e + le  + +i++l  +l +k++eyee++r 
  gene135|gene135|rna135|rna135 174 NNSMNEKEDIILECEDLKIKSLLGQLRQKVNEYEEIIRE 212
                                    3579*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2105.83
//
Query:       gene1351|gene1351|rna1350|rna1350  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-18   66.2   0.4    5.7e-09   36.1   0.0    2.3  2  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
    2.4e-14   53.9   0.2      2e-13   50.9   0.1    2.4  2  mRNA_cap_C       mRNA capping enzyme, C-terminal domain
     0.0089   15.7   0.2       0.35   10.5   0.1    2.7  3  DNA_ligase_A_M   ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.1   2.6e-10   1.6e-06      41     138 ..       5      87 ..       2      96 .. 0.90
   2 !   36.1   0.0   9.5e-13   5.7e-09     145     195 .]     114     162 ..     100     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.6e-10
                                        EEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEEEEEEECTTCEEEEEEEEEEEEEETTEEGTTSBHHHHHH CS
                    mRNA_cap_enzyme  41 ylidRenevyrvenlrfprekdkeklekvldetllDgElvidkveekkkelryliyDivaingvtvaeeplskRle 116
                                        y+ dR+n++y++  ++fp+++          + l+DgE+ ++       ++ y i+D++  +g + ++++l+kRl 
  gene1351|gene1351|rna1350|rna1350   5 YFYDRKNDFYELG-INFPFSS----------QVLVDGEVFLEDGT----TPTYAIFDCLIYEGTSQVSKNLYKRLG 65 
                                        899*********9.*****99..........48******998654....599************************ PP

                                        HHHHHTHHHHHHHHHTTCCCCT CS
                    mRNA_cap_enzyme 117 ilkkelikprneekktglletd 138
                                        + +  + k+ ++ +k ++l+++
  gene1351|gene1351|rna1350|rna1350  66 YAQMFVEKMNENMEKIKVLRKE 87 
                                        **99999999999988887765 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 9.5e-13
                                        EE--EEETTHHHHHHHHCCCCCTTSTEEEEEEEESSSB--SEEEEEEEEE- CS
                    mRNA_cap_enzyme 145 rlKefilleavaklleekfikklshesDGLIfqpvkepyvagrdsdllKwK 195
                                         +Ke+++++        k+i++l+h +DGLIf+p +epy  gr   +lKwK
  gene1351|gene1351|rna1350|rna1350 114 YTKEMMKSYGFWE--IYKKIPELKHGNDGLIFTPANEPYSVGRRGTVLKWK 162
                                        5788888888887..6789*******************************9 PP

>> mRNA_cap_C  mRNA capping enzyme, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.51   3.1e+03      34      56 ..      65      86 ..      39     134 .. 0.67
   2 !   50.9   0.1   3.3e-17     2e-13       7     107 ..     172     269 ..     164     270 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.51
                                       EEEEB---HH...HHHHHHHT-S CS
                         mRNA_cap_C 34 kfaelylseeekeeweelkslne 56
                                        +a++++++  +e++e++k l++
  gene1351|gene1351|rna1350|rna1350 65 GYAQMFVEKM-NENMEKIKVLRK 86
                                       3555666633.555666555443 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 3.3e-17
                                        EEEESSS--TTS--EEEEEEEESTEEEEEEEB---HH...HH..HHHHHT-S--TTEEEEEEE-TTS......... CS
                         mRNA_cap_C   7 klelekyedydakpkfellvlegekyekfaelylseeekeew..eelkslneeldgkIvEcsldeek......... 71 
                                        k                    ++e+ + + +l +s ++ +++  +++   +ee+dgkI E+++d+++         
  gene1351|gene1351|rna1350|rna1350 172 KAV------------------KNERLNYVYDLVCSGKKGKDVvfDHFFCEDEEIDGKIGEFTYDSDGyywdfdelv 229
                                        333..................3344444555555544444433455555668999999999999665566666666 PP

                                        ....-EEEEEE-TT-SS--BHHHHHHHHHHHHTS--HHHH CS
                         mRNA_cap_C  72 ....rWkllriRdDKsepNhisvvekvleSIednvteeeL 107
                                             Wkl+riR+DK++pN+i++v ++leS++dn t+e+L
  gene1351|gene1351|rna1350|rna1350 230 lkrgGWKLYRIRTDKDTPNNIKIVCNILESLKDNLTIEKL 269
                                        65445*********************************98 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.35   2.1e+03      72      84 ..      24      36 ..      16      40 .. 0.76
   2 !   10.5   0.1   5.9e-05      0.35     114     202 ..      39     160 ..      33     162 .. 0.66
   3 ?   -3.1   0.0      0.86   5.1e+03      73     108 ..     213     248 ..     204     281 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.35
                                       SEEEEEEEEEEEE CS
                     DNA_ligase_A_M 72 ksvilDGElvavd 84
                                       ++v++DGE+ + d
  gene1351|gene1351|rna1350|rna1350 24 SQVLVDGEVFLED 36
                                       689*****98755 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.9e-05
                                        EEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB...............................--BTTTEEE-.- CS
                     DNA_ligase_A_M 114 elclfvFDiLyldgesltdeplkeRrklLeeil...............................kesedrvela.e 157
                                         + + +FD+L+++g+s + ++l +R  + +  +                               ++  dr +++ +
  gene1351|gene1351|rna1350|rna1350  39 TPTYAIFDCLIYEGTSQVSKNLYKRLGYAQMFVekmnenmekikvlrkegedgfgekrvpieagTQGLDRTHIHfY 114
                                        577899***********99999999988877776666666777777777777777777777776333333332213 PP

                                        EEEESSHHHHHHHHHHH..HHTTECEEEEEETT-CC-TTCEEEEEEE CS
                     DNA_ligase_A_M 158 slevkdveeleelleea..iseglEGlvvKnpdskYepgkrsknwlK 202
                                        ++e+ ++  + e++++   +++g +Gl+   ++ +Y  g+r  + lK
  gene1351|gene1351|rna1350|rna1350 115 TKEMMKSYGFWEIYKKIpeLKHGNDGLIFTPANEPYSVGRR-GTVLK 160
                                        44444445666666664336667777777777777777777.55555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.86
                                        EEEEEEEEEEEETTTTCBEHHHHHCHHHHCHCCTHH CS
                     DNA_ligase_A_M  73 svilDGElvavdketgeilpfqklasrkkkkkkvee 108
                                        +++ D+  +++d ++      ++  +r++ +k++ +
  gene1351|gene1351|rna1350|rna1350 213 EFTYDSDGYYWDFDELVLKRGGWKLYRIRTDKDTPN 248
                                        566666666777776666666666666666554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.38s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1553.72
//
Query:       gene1353|gene1353|rna1352|rna1352  [L=298]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-21   76.2   0.0    4.4e-21   75.3   0.0    1.5  1  Helicase_C     Helicase conserved C-terminal domain
    0.00087   18.6   0.0     0.0012   18.1   0.0    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.0   4.9e-25   4.4e-21       2     111 .]      69     179 ..      68     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.9e-25
                                        HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH..TTSSSEEEESG CS
                         Helicase_C   2 kleallell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfn..kgesdvLiatd 74 
                                        k+++l++ll k ++eg+k+lif++ti++l+ ++     +++++++++g++p++ r   +++fn  ++ + +L++t+
  gene1353|gene1353|rna1352|rna1352  69 KVKILMDLLkKWKKEGSKVLIFSQTIRMLDIIERC--INKYTYLRMDGRTPTSIRSSLVDRFNrsEDVFIFLLTTK 142
                                        78999****999*****************764444..458***********************7444455****** PP

                                        GGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  75 vaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        v++ G+++++++ ++++d+++n+++  q++ R++R+g
  gene1353|gene1353|rna1352|rna1352 143 VGGLGLNLTGASRIVIYDPDWNPSTDTQAKERAWRYG 179
                                        ***********************************86 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.4e-07    0.0012      42     128 ..      66     156 ..      52     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-07
                      ERCC3_RAD25_C  42 npnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkp.y..iyGetseaerlkilqkfkknpkvntifl.s 113
                                         + k++++  L+k  +k g k+++fs  +  L  + + ++k  y  + G+t+++ r++++++f+++++v   +l  
  gene1353|gene1353|rna1352|rna1352  66 SSCKVKILMDLLKKWKKEGSKVLIFSQTIRMLDIIERCINKYtYlrMDGRTPTSIRSSLVDRFNRSEDVFIFLLtT 141
                                        566888888899999****************99988877764242368***************9998886655437 PP

                      ERCC3_RAD25_C 114 kvgDtsiDlPeanvl 128
                                        kvg   ++l  a+ +
  gene1353|gene1353|rna1352|rna1352 142 KVGGLGLNLTGASRI 156
                                        9**999999888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1829.95
//
Query:       gene1354|gene1354|rna1353|rna1353  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-49  166.7   2.2    1.4e-48  165.4   0.3    2.5  2  SNF2_N         SNF2 family N-terminal domain
    3.8e-09   36.8   0.1    1.4e-07   31.7   0.0    2.7  2  ResIII         Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.011   15.4   0.6        3.5    7.2   0.0    2.9  3  SWI2_SNF2      SWI2/SNF2 ATPase
       0.12   13.1   0.7       0.26   12.0   0.7    1.5  1  ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrola


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1      0.42   1.9e+03     245     285 ..      12      52 ..       4      56 .. 0.65
   2 !  165.4   0.3   3.2e-52   1.4e-48      49     305 ..     155     387 ..     145     390 .] 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.42
                                        THHHHHHHHHHHHHHHHTT-STTEE---GGGT--..S---EEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                             SNF2_N 245 lqrpieaqaekgrsrLlqllqrlmlrrakkdvek..nlPpkte 285
                                        + +++   ++  ++++ +ll+++ + ++k dvek  +l + +e
  gene1354|gene1354|rna1353|rna1353  12 FVEKYL--ERTAAEKIDELLRKIEMHKRKGDVEKvkELEKEIE 52 
                                        555554..56667788889999999999999944224555555 PP

  == domain 2  score: 165.4 bits;  conditional E-value: 3.2e-52
                                        HHHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-E CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  49 aeakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssal 124
                                        + ++++ +GG+LaD+mGLGKT+q++a+++ + +   k             +Li++Pa+++ qW+ e +r+ +  ++
  gene1354|gene1354|rna1353|rna1353 155 LRLYKDGKGGVLADDMGLGKTIQMIAFLAILFQ--SKSIS---------KVLILCPATIVSQWTLEWKRFYPFVRV 219
                                        5678999**********************3333..33333.........39*********************9976 PP

                                        EE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 125 rvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeav 200
                                          + + +++              +  +v + +Y++ + +a         k++ w+ +vlDEgh++kn +++++  v
  gene1354|gene1354|rna1353|rna1353 220 --FFGFSGR--------------NCEGVYLMSYERFKVRA---------KDLLWDVLVLDEGHKIKNRNAQITLSV 270
                                        ..4444432..............489***********777.........7889*********************** PP

                                        HH---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH............HHHHHHHHHHHTT- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxx RF
                             SNF2_N 201 skLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie............aqaekgrsrLlqll 264
                                        +k +++ + +l+GTPiqn+l +l+++++f++++ +g++++f++ +++ i+            ++a+k +  L++l+
  gene1354|gene1354|rna1353|rna1353 271 KKVRAKSKFVLSGTPIQNNLGELWSMFDFVNPGLLGSHTSFHEEFEEVIRrggyksatnlqvEKAYKHSLMLRSLI 346
                                        **************************************************************************** PP

                                        STTEE---GGGT--S---EEEEEEEEE--HHHHHHHH.... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 265 qrlmlrrakkdveknlPpkteeiiflklskverksYnrlle 305
                                        ++++lrr+k++++++lP k+ +i+f+ l++v+ ++Ynr+l+
  gene1354|gene1354|rna1353|rna1353 347 EPYILRRTKSQISHKLPSKEDKIVFCTLTPVQIELYNRVLS 387
                                        *************************************9876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.64   2.9e+03      60      75 ..      58      73 ..       7     105 .. 0.61
   2 !   31.7   0.0   3.1e-11   1.4e-07       4     169 ..     143     285 ..     140     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.64
                                       EESSHHHHHHHHHHGG CS
                             ResIII 60 lvprkslleqtleefk 75
                                       lv+ ks++ + +++ +
  gene1354|gene1354|rna1353|rna1353 58 LVDDKSIVLRVEDRKE 73
                                       3444444444444444 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 3.1e-11
                                        E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                             ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                        l eyQ+  +e +l  +  k+ k g+++   G GKT+ ++++ + l+++++++k+l+l+p  ++++q+  e+k+f++
  gene1354|gene1354|rna1353|rna1353 143 LFEYQQVGVEWMLRLY--KDGKGGVLADDMGLGKTIQMIAFLAILFQSKSISKVLILCPA-TIVSQWTLEWKRFYP 215
                                        6788988888888666..69999************************************7.5889*********** PP

                                        G....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.TTHHH. CS
                             ResIII  80 eaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.swrei. 153
                                          +  +   +sg++ +          ++++++++++ +           ++   dv++ DE H+++  + +++ + 
  gene1354|gene1354|rna1353|rna1353 216 FVR--VFFGFSGRNCEG---------VYLMSYERFKVRA----------KDLLWDVLVLDEGHKIKNRNaQIT-Ls 269
                                        997..556677777777.........9999999999999..........778899999999999999532333.24 PP

                                        HHT---SEEEEEESS- CS
                             ResIII 154 lekfkeavllglTATp 169
                                        ++k++++ ++ l++Tp
  gene1354|gene1354|rna1353|rna1353 270 VKKVRAKSKFVLSGTP 285
                                        7788888888899998 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.4      0.46   2.1e+03     184     218 ..      26      58 ..       7      64 .. 0.53
   2 ?    7.2   0.0   0.00078       3.5       4      55 ..     149     197 ..     145     199 .. 0.79
   3 ?    5.1   0.0    0.0034        15     123     169 ..     250     297 ..     235     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.46
                          SWI2_SNF2 184 DgavvpilYesrlaklelkeeekldeefeeiteel 218
                                        D+   +i+ ++r  ++e  + ++l++e+ee+ ++l
  gene1354|gene1354|rna1353|rna1353  26 DELLRKIEMHKRKGDVE--KVKELEKEIEEVKKGL 58 
                                        44444455544444333..3334666666666655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00078
                          SWI2_SNF2   4 ravekavervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvv 55 
                                        ++ve +++  k  d kgGv+    G GK+++m+ + + l + +++  kv+++
  gene1354|gene1354|rna1353|rna1353 149 VGVEWMLRLYK--DGKGGVLADDMGLGKTIQMIAFLAILFQ-SKSISKVLIL 197
                                        55555554444..579***********************99.7888888876 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0034
                          SWI2_SNF2 123 ivlvDEaHRsqygelakklr.kalpnaafigFTGTPilkkdkktkevF 169
                                        +++ DE+H+ +  + + +l  k ++  + + + GTPi+++  + +++F
  gene1354|gene1354|rna1353|rna1353 250 VLVLDEGHKIKNRNAQITLSvKKVRAKSKFVLSGTPIQNNLGELWSMF 297
                                        4678******999998888636677888999******98765555555 PP

>> ATC_hydrolase  L-2-amino-thiazoline-4-carboxylic acid hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7   5.8e-05      0.26      26     104 ..      10     114 ..       4     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-05
                      ATC_hydrolase  26 keiirkalerlgkergkklaekakakkdkadvekflalyseifek........................enalkfe 77 
                                        k +++k+ler ++e+  +l +k  ++k k dvek+ +l +ei  +                        ++a++fe
  gene1354|gene1354|rna1353|rna1353  10 KSFVEKYLERTAAEKIDELLRKIEMHKRKGDVEKVKELEKEIE-EvkkglvddksivlrvedrkedagsNEAIDFE 84 
                                        57899******************************99974443.3366899999999999********999***** PP

                      ATC_hydrolase  78 vlee.dkdeleidvtrCp..yceawkkeGl 104
                                        +  + d++ +e+   rC+  + ++++ +G+
  gene1354|gene1354|rna1353|rna1353  85 WSGSdDDENIEVFNSRCEkaIGKYCRHMGI 114
                                        ****99999999999995336677777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2271.94
//
Query:       gene1355|gene1355|rna1354|rna1354  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   13.6   1.4       0.24   11.9   0.4    2.4  2  DUF2533   Protein of unknown function (DUF2533)


Domain annotation for each model (and alignments):
>> DUF2533  Protein of unknown function (DUF2533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   1.3e-05      0.24      11      44 ..       8      42 ..       2      45 .. 0.75
   2 ?   -1.1   0.0      0.14   2.6e+03      52      61 ..     116     125 ..      75     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                            DUF2533 11 vkkqnaalk.qfleLeqkREaaIeeavelckkgkp 44
                                        +k ++  k +  +L+qkRE+ +e+++e+ k+ ++
  gene1355|gene1355|rna1354|rna1354  8 LNKWHELKKrHSYMLDQKREKEVEAVIEKVKRTRD 42
                                       55656655514579***************999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.14
                            DUF2533  52 evTkeiNela 61 
                                         vT++i  la
  gene1355|gene1355|rna1354|rna1354 116 SVTERIESLA 125
                                        4556665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1604.07
//
Query:       gene1356|gene1356|rna1355|rna1355  [L=959]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.9e-134  447.8   0.3   3.9e-134  447.8   0.3    1.6  2  DNA_pol_B       DNA polymerase family B
    3.2e-70  236.9   0.6    7.4e-70  235.7   0.6    1.6  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
      1e-13   51.5  10.2    2.2e-13   50.5  10.2    1.6  1  zf-C4pol        C4-type zinc-finger of DNA polymerase delta
    2.4e-06   26.7   0.9    8.7e-06   24.9   0.1    2.1  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral
  ------ inclusion threshold ------
      0.056   13.1   0.0       0.13   11.9   0.0    1.6  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.56     2e+03     252     296 ..      51      97 ..      48     111 .. 0.67
   2 !  447.8   0.3  1.1e-137  3.9e-134       2     459 .]     409     835 ..     408     835 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.56
                                        HHHHHHT.TSTTT--EEEEEEEEEEEE...EETTEEEEEEEEESSTTS CS
                          DNA_pol_B 252 laeevseklfkkplklefekvykkllL...isKKkYaglkvektskan 296
                                        ++e +++ l  k   le+e v k+ +L     KK+++ +++++++++ 
  gene1356|gene1356|rna1355|rna1355  51 IKESIQR-LDIKATVLEVEPVMKQTILgytEGKKRFYKVTLNTSHSSA 97 
                                        5566666.4444567999999999999554579999988888665544 PP

  == domain 2  score: 447.8 bits;  conditional E-value: 1.1e-137
                                        -HHHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHT CS
                          DNA_pol_B   2 plsrvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqah 77 
                                        p+++ +++g +i+++ l++r a +e+fi+p+ +  ++++   ++G++V+ePk+g+y+kpv v+DF+SLYPsi++ +
  gene1356|gene1356|rna1355|rna1355 409 PIEYFFTRGTAIKIFALIYRTAAKEDFIVPEIDPFESNK--SFEGGFVIEPKRGFYNKPVSVMDFSSLYPSIMISN 482
                                        788999************************766664444..5********************************** PP

                                        T-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHH CS
                          DNA_pol_B  78 NlcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalld 153
                                        Nlcyttl+++e+    l           +p  ++f+++++++gllp++L dll++Rk+ik+elk+ekd++ ka l+
  gene1356|gene1356|rna1355|rna1355 483 NLCYTTLLTKEQYRV-LG-G------IKTPTDNYFCSAETKKGLLPRILIDLLDSRKRIKEELKKEKDPALKACLN 550
                                        ********9988744.33.2......24688899****************************************** PP

                                        HHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEB CS
                          DNA_pol_B 154 kqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGD 229
                                         +Qla+K+ aNs+YGftG++++rlpc ++++svT  GRem++ tk+l+e++   +sk++++++     +  viYGD
  gene1356|gene1356|rna1355|rna1355 551 GRQLAVKLCANSLYGFTGASKGRLPCFEISQSVTGFGREMINFTKNLIEEN---FSKKNGYTH-----DSVVIYGD 618
                                        *************************************************88...888899999.....99****** PP

                                        SSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTSEEEEESSGG CS
                          DNA_pol_B 230 TDSvfielkvkdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskanklliKGvdl 305
                                        TDSv+i+++ +d+ +++++ ke+ + +++ +f kp+ lefekvy ++lLi+KK+Yagl ++++++ +k++++G+++
  gene1356|gene1356|rna1355|rna1355 619 TDSVMIDFNEEDIGKVFEMSKEISRFITT-KFVKPVSLEFEKVYYPYLLINKKRYAGLLYSNPDSPSKIDTRGIET 693
                                        *****************************.********************************************** PP

                                        GSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCS CS
                          DNA_pol_B 306 vRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknl 381
                                        vRrdnc lvkev+++vle++l++    r++e++ +++ks++     +l  ++++l+ +v+sk+l+k+ ++y sk+ 
  gene1356|gene1356|rna1355|rna1355 694 VRRDNCGLVKEVVETVLEMILYQ----RNVEKAKRFVKSVV----GDLYLGRIDLSLLVISKSLTKTGDKYGSKQ- 760
                                        ***********************....*************9....999*************************99. PP

                                        HHHHHHHHHHHHC.SS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHH CS
                          DNA_pol_B 382 phlevakrlkkrn.eeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarl 455
                                        +h+e+a++l+kr+  +ap +gdr++Yviv+k k     +  a+e+ edp yvle+nlpid+eyY++ ql k++ r+
  gene1356|gene1356|rna1355|rna1355 761 AHVELAEKLRKRDeSTAPVLGDRVPYVIVKKGK-----GMAAYEKSEDPVYVLENNLPIDTEYYIEqQLSKPLKRI 831
                                        *************7888**************98.....9************************************* PP

                                        HTTS CS
                          DNA_pol_B 456 leai 459
                                        +++i
  gene1356|gene1356|rna1355|rna1355 832 FDPI 835
                                        *986 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.6   2.1e-73   7.4e-70       5     337 .]      22     344 ..      19     344 .. 0.94

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 2.1e-73
                                        TSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTC CS
                     DNA_pol_B_exo1   5 gksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpn 80 
                                        gk + v v +f pyfY+e+ ++ke    ke +ke+ ++l+ k t + +ve+v+k+ ++gy + +++++kv++++++
  gene1356|gene1356|rna1355|rna1355  22 GKPIQVLVRNFFPYFYIEPANDKE--YRKEDIKESIQRLDIKAT-VLEVEPVMKQTILGYTEGKKRFYKVTLNTSH 94 
                                        5556677899**********5555..79****************.*******************99********** PP

                                        HHHHHHHHHHH......CCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCE CS
                     DNA_pol_B_exo1  81 elkkirkelsp......leeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddlia 150
                                            +r  l++      ++  ++vye+ +++  rf+ d +ivg+++++vk       + +s+ ++ ++++++ l++
  gene1356|gene1356|rna1355|rna1355  95 SSAALRAFLESgisirsEKVRFRVYESGFPFVLRFMCDLGIVGMSYLKVK-----SYEVLSTEHLTLSTSYEFLET 165
                                        *********99*****98888*****************************.....556688888999999999999 PP

                                        ETTTCC....S-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE-- CS
                     DNA_pol_B_exo1 151 kpkese....pplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfelt 222
                                         p  +e    ppl++ls+DIec s +  fp ++   dpiiqI  +l+ lg++++  +++f+l+e+           
  gene1356|gene1356|rna1355|rna1355 166 LPPAGEyailPPLKILSIDIECISAGNSFPSSKS--DPIIQIGNTLMLLGSDKHVSQDIFCLKETT---------- 229
                                        999999999*************************..**************99**************.......... PP

                                        SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCS...CTCEEC CS
                     DNA_pol_B_exo1 223 pkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrln...kggrsk 295
                                          ++ pg +v+++dsEkelL+ + +++ ++dPd+i+gYNi+ FD+pYil+R + l ++++s lgr +   k+    
  gene1356|gene1356|rna1355|rna1355 230 --GI-PGANVYWYDSEKELLESWKKYFMEIDPDIIVGYNIKGFDIPYILDRGEVLGINNFSILGRSRkkaKTRDTT 302
                                        ..99.*************************************************************9976666667 PP

                                        CCCESEEEEEECEEEETTSEEEEHHHHHHHHSSSSG-SHHHH CS
                     DNA_pol_B_exo1 296 vseigfskqarekvkisgrihlDlyrvvkrklklpsYkLnav 337
                                        +s+++f++ ++++v+i+gr+++D++ v++r++kl+sY+Ln+v
  gene1356|gene1356|rna1355|rna1355 303 MSSNMFGSISTTEVEIDGRLIVDMMIVIRRDYKLRSYSLNSV 344
                                        7777777*********************************98 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5  10.2   6.1e-17   2.2e-13       1      70 []     870     937 ..     870     937 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 6.1e-17
                           zf-C4pol   1 ClvCkeklkkalCkkCrsdkqesllkllsrlkelekklneletvCqsCaqgsleeevkCdsrdCpvfYeR 70 
                                        C++Ck+   k +C +C +d +  ++k+++++++ ++kln ++ +Cq+C qgs++++v C +rdCp+fY+R
  gene1356|gene1356|rna1355|rna1355 870 CIGCKA-EGKIICGNCVKDFHVYFQKMQQEVEDKKEKLNGCWVECQRC-QGSIHSQVLCVNRDCPIFYMR 937
                                        *****6.4579*****988888899***********************.9*******************9 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   2.4e-09   8.7e-06     106     253 ..     345     489 ..     328     525 .. 0.74
   2 ?   -0.7   0.0      0.14     5e+02     359     386 ..     534     568 ..     525     602 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.4e-09
                        DNA_pol_B_2 106 gfpvekywkekeeivenkelwkekeekkydivketleYckqDvlvlaklllklkesideff....easinifkrpT 177
                                        ++   k +ke+    + +el+ +     +d +     Yc  D  +  +l+ +l+  i+        + + i   +T
  gene1356|gene1356|rna1355|rna1355 345 SIHFLKEQKEDVPPSSIGELQSK----DKDTRRRIASYCLRDTVLPLRLFSTLNVLINY-TelsrVTGVPIEYFFT 415
                                        55555555555555555555444....77777778889999999999999999998883.3467666677744555 PP

                        DNA_pol_B_2 178 isslalaifkqilyrkkkkellapskeldkyiRkayrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthypmPygk 252
                                          ++a +if  i+  + k+ + +p+ + ++   k+  GG++ +p+  g y++++ v D+ SlYPs+m ++ + y++
  gene1356|gene1356|rna1355|rna1355 416 -RGTAIKIFALIYRTAAKEDFIVPEIDPFES-NKSFEGGFViEPK-RGFYNKPVSVMDFSSLYPSIMISNNLCYTT 488
                                        .578*********766667888888877766.6899*****5555.***********************9998887 PP

                        DNA_pol_B_2 253 p 253
                                         
  gene1356|gene1356|rna1355|rna1355 489 L 489
                                        5 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.14
                        DNA_pol_B_2 359 Kekakkeknevkr.......siaKlllNsLYGrFa 386
                                        Ke+ kkek+++ +          Kl  NsLYG  +
  gene1356|gene1356|rna1355|rna1355 534 KEELKKEKDPALKaclngrqLAVKLCANSLYGFTG 568
                                        66666666665541111111457*********776 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.7e-05      0.13      35      88 ..     240     294 ..     235     396 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                     DNA_pol_B_exo2  35 ssekelikkffegvekkkpq.lVsfngrgfDlpvleyralkhgvsapkyfdegde 88 
                                        +sekel+++  +++ +  p  +V++n +gfD+p +  r+ + g++  + + ++++
  gene1356|gene1356|rna1355|rna1355 240 DSEKELLESWKKYFMEIDPDiIVGYNIKGFDIPYILDRGEVLGINNFSILGRSRK 294
                                        689***************98358*************9998888877666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (959 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.51
# Mc/sec: 5665.84
//
Query:       gene1357|gene1357|rna1356|rna1356  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-06   26.2   0.0    1.2e-05   25.5   0.0    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    1.5e-05   25.1   0.0    1.9e-05   24.7   0.0    1.3  1  CENP-T_C       Centromere kinetochore component CENP-T histon
    6.2e-05   23.4   0.6    9.7e-05   22.7   0.6    1.4  1  Histone        Core histone H2A/H2B/H3/H4
    0.00026   21.1   0.0    0.00036   20.6   0.0    1.2  1  TAF            TATA box binding protein associated factor (TA
     0.0054   17.1   0.0     0.0088   16.4   0.0    1.4  1  CENP-S         CENP-S protein
     0.0091   16.1   0.0      0.011   15.8   0.0    1.2  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.013   15.5   0.0    1.3  1  Bromo_TP       Bromodomain associated
       0.21   12.1   0.4       0.37   11.3   0.1    1.5  2  TFIID_20kDa    Transcription initiation factor TFIID subunit 


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   5.2e-09   1.2e-05       7      64 ..      36      92 ..      31      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.2e-09
                                       HHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                      CBFD_NFYB_HMF  7 rvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                       ++++I + + ++r++     + i++++ e+i++ +s A+ +++++krKti+  +i++ 
  gene1357|gene1357|rna1356|rna1356 36 AIRRIARRA-GVRRVGGGCFKEINNAAREYIRDTLSIACIYATHAKRKTITCSDILHS 92
                                       699999999.9999*****************************************986 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   8.6e-09   1.9e-05      12      77 ..      31      96 ..      12      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 8.6e-09
                           CENP-T_C 12 vvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkrq 77
                                       +++k a r   +++  +++    +k + +a  ++++   +    ya Ha+RKti  sD++  +kr 
  gene1357|gene1357|rna1356|rna1356 31 SISKPAIRRIARRAGVRRVGGGCFKEINNAAREYIRDTLSIACIYATHAKRKTITCSDILHSLKRM 96
                                       444444444444457789*******************************************99996 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.6   4.3e-08   9.7e-05      48     125 ..      15      90 ..       6      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.3e-08
                                        HHHHHHHHHXXSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHH CS
                            Histone  48 lkeirkyqkstdlliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkD 123
                                         k i k++++   l+ ++     +r i   +    r+ + +   ++ a+  ++ + ++ A+++a haKR+Tit  D
  gene1357|gene1357|rna1356|rna1356  15 AKGIAKRHRKQSGLTDSISKP-AIRRIAR-RAGVRRVGGGCFKEINNAAREYIRDTLSIACIYATHAKRKTITCSD 88 
                                        555555555444444433322.2555665.77789999999999******************************** PP

                                        HH CS
                            Histone 124 iq 125
                                        i 
  gene1357|gene1357|rna1356|rna1356  89 IL 90 
                                        95 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.6e-07   0.00036       3      66 .]      31      94 ..      29      94 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.6e-07
                                       ---HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH- CS
                                TAF  3 ilpkesvkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsALr 66
                                       +++k +++ iA   G+  +     +++ +  ++ ++     a  +  h+kR+++t +D+ ++L+
  gene1357|gene1357|rna1356|rna1356 31 SISKPAIRRIARRAGVRRVGGGCFKEINNAAREYIRDTLSIACIYATHAKRKTITCSDILHSLK 94
                                       578899******************************************************9997 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.9e-06    0.0088      51      72 ..      74      95 ..      53      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-06
                             CENP-S 51 aFakHAkRstittdDvlLlaRr 72
                                       ++a HAkR+tit +D+l  ++r
  gene1357|gene1357|rna1356|rna1356 74 IYATHAKRKTITCSDILHSLKR 95
                                       69*************9977666 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.1e-06     0.011      11      66 ..      37      92 ..      29      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.1e-06
                        TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlA 66
                                       i+ i +  gv+ +     + + + a  y+ + L+ A ++a+hak+k+++++d+  +
  gene1357|gene1357|rna1356|rna1356 37 IRRIARRAGVRRVGGGCFKEINNAAREYIRDTLSIACIYATHAKRKTITCSDILHS 92
                                       66677777888888888888889999**************************9665 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   5.9e-06     0.013      35      74 ..      60      99 ..      30     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHTT-- CS
                           Bromo_TP 35 iaqkYirelgeqaksfaehagRseptlkDvvltLqelgin 74
                                        a +Yir     a  +a ha R + t +D+  +L+++gi+
  gene1357|gene1357|rna1356|rna1356 60 AAREYIRDTLSIACIYATHAKRKTITCSDILHSLKRMGIK 99
                                       567888888888889***********************96 PP

>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.1   1.4e+04      46      51 ..      21      26 ..      15      29 .. 0.74
   2 ?   11.3   0.1   0.00016      0.37      29      64 ..      60      95 ..      56      96 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.1
                                       HHTT-S CS
                        TFIID_20kDa 46 khRksd 51
                                       +hRk +
  gene1357|gene1357|rna1356|rna1356 21 RHRKQS 26
                                       699876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH CS
                        TFIID_20kDa 29 iaddFvesvtkfacklakhRksdklevrDiqlhler 64
                                        a +++ ++ + ac  a h k +++   Di   l+r
  gene1357|gene1357|rna1356|rna1356 60 AAREYIRDTLSIACIYATHAKRKTITCSDILHSLKR 95
                                       57899*************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.51
# Mc/sec: 606.47
//
Query:       gene1358|gene1358|rna1357|rna1357  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-44  151.7   0.2    1.5e-44  151.6   0.2    1.0  1  Histone        Core histone H2A/H2B/H3/H4
    4.2e-05   23.7   0.0    7.9e-05   22.9   0.0    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
     0.0039   17.5   0.0      0.006   16.9   0.0    1.3  1  CENP-S         CENP-S protein
     0.0063   17.1   0.4     0.0063   17.1   0.4    1.2  1  PAF            PCNA-associated factor histone like domain
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.028   14.5   0.0    1.4  1  CENP-T_C       Centromere kinetochore component CENP-T histon
      0.025   14.7   0.0      0.054   13.7   0.0    1.5  1  TAF            TATA box binding protein associated factor (TA


Domain annotation for each model (and alignments):
>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.2   4.9e-48   1.5e-44       1     131 []       1     130 [.       1     130 [. 0.99

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 4.9e-48
                                        XXEESXEEEXXXXEEXXXXXXXXXXHTTS-SSSSB--TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH. CS
                            Histone   1 marekekarkesektapekkvsakkerkasskskkkkkrryrpgtvalkeirkyqkstdlliqklpfaRvvreivk 76 
                                        m+r+k++a+k+ +++ap+k vs k+ +++ s+s ++k++r++ g  alkeirkyqkstdlli+k pf+R+vre++k
  gene1358|gene1358|rna1357|rna1357   1 MSRTKQTASKALGGKAPRKGVSIKSIPSSGSSSVMAKRTRFKAGALALKEIRKYQKSTDLLIRKRPFQRMVRELCK 76 
                                        99*************************************************************************9 PP

                                        TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHHHT CS
                            Histone  77 sekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArrlr 131
                                          +e++r++a+a++a+qea+E++l+ l+e+A++++ haKRvT++pkDi+l+++++
  gene1358|gene1358|rna1357|rna1357  77 -GGEGMRFQASAIVAFQEAVENFLTNLMEDAYRCVLHAKRVTLMPKDICLVYKIK 130
                                        .**************************************************9985 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.6e-08   7.9e-05      20      63 ..      82     125 ..      64     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.6e-08
                                        -B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHH CS
                      CBFD_NFYB_HMF  20 kiakdAkeliaecveefieelaseAaeickkekrKtikaehikl 63 
                                        ++  +A + ++e+ve f++ l + A++ + ++kr t+++++i l
  gene1358|gene1358|rna1357|rna1357  82 RFQASAIVAFQEAVENFLTNLMEDAYRCVLHAKRVTLMPKDICL 125
                                        38889999**********************************86 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     2e-06     0.006      13      70 ..      69     127 ..      64     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                             CENP-S  13 kiveeeaa.ekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLla 70 
                                        ++v+e ++  +++++  ++i a  e v + l nl +D      HAkR t  ++D+ L+ 
  gene1358|gene1358|rna1357|rna1357  69 RMVRELCKgGEGMRFQASAIVAFQEAVENFLTNLMEDAYRCVLHAKRVTLMPKDICLVY 127
                                        56666544367899999***************************************986 PP

>> PAF  PCNA-associated factor histone like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   2.1e-06    0.0063       1      43 [.       1      40 [.       1      98 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                                PAF  1 mVRTkAdvssarkavaakAprkslgassssssssssspkkkkk 43
                                       m RTk ++    ka ++kAprk ++ +s  ss sss  +k  +
  gene1358|gene1358|rna1357|rna1357  1 MSRTKQTA---SKALGGKAPRKGVSIKSIPSSGSSSVMAKRTR 40
                                       88*****9...79************999999988776444333 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   9.3e-06     0.028      15      75 ..      69     128 ..      55     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.3e-06
                           CENP-T_C  15 klakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk 75 
                                        ++++++ k  g+ ++ +++a+ a ++a ++f+  + eD  +   Ha+R t+  +D+ l  k
  gene1358|gene1358|rna1357|rna1357  69 RMVRELCKG-GEGMRFQASAIVAFQEAVENFLTNLMEDAYRCVLHAKRVTLMPKDICLVYK 128
                                        555555444.78999****************************************998765 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.054      26      61 ..      88     123 ..      80     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHH CS
                                TAF  26 aalLaedveyrlkeivqeaakfmrhskRqkLtvaDv 61 
                                          +  e ve  l + +++a ++  h+kR +L ++D+
  gene1358|gene1358|rna1357|rna1357  88 IVAFQEAVENFLTNLMEDAYRCVLHAKRVTLMPKDI 123
                                        5566778999999**********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 844.63
//
Query:       gene1359|gene1359|rna1358|rna1358  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-19   69.0  22.0    1.1e-07   32.1   1.7    5.0  5  LRR_4     Leucine Rich repeats (2 copies)
    3.6e-16   58.7  14.0    3.4e-05   23.5   2.2    5.1  4  LRR_8     Leucine rich repeat
    5.2e-10   38.6  12.1        0.4   10.8   0.0    6.9  7  LRR_6     Leucine Rich repeat
    9.3e-09   35.0  11.4    0.00042   19.9   0.8    3.1  3  LRR_9     Leucine-rich repeat
    4.7e-05   23.4  15.4        6.6    7.7   0.1    6.9  6  LRR_1     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.36   1.3e+03       4      14 ..      23      33 ..      23      38 .. 0.77
   2 !   32.1   1.7     3e-11   1.1e-07       4      39 ..      44      78 ..      42      81 .. 0.93
   3 !   14.8   0.7   7.9e-06     0.028       4      42 ..      86     122 ..      85     124 .. 0.82
   4 !   29.6   0.3   1.8e-10   6.3e-07       3      36 ..     128     160 ..     126     166 .. 0.90
   5 ?    4.4   0.1     0.016        56       2      31 ..     171     201 ..     170     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.36
                                       -EEE--SS--- CS
                              LRR_4  4 evLdLsnNqlt 14
                                       +++dL+ N+++
  gene1359|gene1359|rna1358|rna1358 23 RTVDLRRNNIS 33
                                       57788888886 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 3e-11
                                       -EEE--SS---E-S-HHH-TT--EEE-.-S-----G CS
                              LRR_4  4 evLdLsnNqltdiplleklpnLkeLdLsgNnlitdl 39
                                       e+LdLs+N++++i+ le+ p Lk LdLs N li+d+
  gene1359|gene1359|rna1358|rna1358 44 EYLDLSDNRIREISDLENVPRLKILDLSYN-LISDI 78
                                       89*************************999.99998 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 7.9e-06
                                        -EEE--SS---E-S-HHH-TT--EEE-.-S-----GGGG CS
                              LRR_4   4 evLdLsnNqltdiplleklpnLkeLdLsgNnlitdldeL 42 
                                        e+L+L +N +++i +l  lp  k+LdL   n i ++++L
  gene1359|gene1359|rna1358|rna1358  86 EELYLISNDISTIRGLD-LPRIKKLDL-AVNDICRIENL 122
                                        79***************.*********.44456566666 PP

  == domain 4  score: 29.6 bits;  conditional E-value: 1.8e-10
                                        --EEE--SS---E-S-HHH-TT--EEE-.-S--- CS
                              LRR_4   3 LevLdLsnNqltdiplleklpnLkeLdLsgNnli 36 
                                        Le+L+L++N+++ +++le l++Lk LdL +Nn +
  gene1359|gene1359|rna1358|rna1358 128 LEELYLGSNRIRAVEGLEDLTSLKILDL-QNNEL 160
                                        9***************************.77776 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.016
                                        S--EEE--SS-.--E-S-HHH-TT--EEE-. CS
                              LRR_4   2 nLevLdLsnNq.ltdiplleklpnLkeLdLs 31 
                                        + evL L+ N+ l+ ++  e lp L+ L L 
  gene1359|gene1359|rna1358|rna1358 171 SVEVLLLGENRdLRVVEKTEHLPRLRILGLE 201
                                        5799****8855999999888******9885 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   2.2   9.5e-09   3.4e-05       5      61 .]      24      75 ..      20      75 .. 0.82
   2 !    8.6   0.0   0.00044       1.6      28      61 .]      86     116 ..      84     116 .. 0.91
   3 !   23.4   0.7     1e-08   3.7e-05      23      61 .]     124     160 ..     118     160 .. 0.91
   4 !   21.0   0.6   5.8e-08   0.00021       2      58 ..     149     202 ..     148     205 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 9.5e-09
                                       EEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  5 sLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       ++dL++N+++ +   + ++ + +++LdLs+N+++ +s   +++ p+L+ LdLs+N +
  gene1359|gene1359|rna1358|rna1358 24 TVDLRRNNISRM---VLNKAELVEYLDLSDNRIREIS--DLENVPRLKILDLSYNLI 75
                                       666666665544...56666789*************9..****************87 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00044
                                        -EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  28 kvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        ++L+L +N ++t++     +Lp++++LdL  N++
  gene1359|gene1359|rna1358|rna1358  86 EELYLISNDISTIR---GLDLPRIKKLDLAVNDI 116
                                        79***********6...899*********99987 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1e-08
                                        T-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  23 glsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        ++  L++L+L++N+++ ++   +++L+sL+ LdL++N L
  gene1359|gene1359|rna1358|rna1358 124 NCITLEELYLGSNRIRAVE--GLEDLTSLKILDLQNNEL 160
                                        66789*************6..****************87 PP

  == domain 4  score: 21.0 bits;  conditional E-value: 5.8e-08
                                        T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS.---GGGGGGGTT--S-.EEE--S CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnN.llttlspgafsgLpsLrsLdLsg 58 
                                        +L++LdL+nN l+++d ++    s+++vL L++N  l++++    ++Lp+Lr L L+ 
  gene1359|gene1359|rna1358|rna1358 149 SLKILDLQNNELEVVDCSMIP--SSVEVLLLGENrDLRVVE--KTEHLPRLRILGLEK 202
                                        79*******************..9**********9999996..99**********986 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.025        91       6      16 ..      23      33 ..      23      33 .. 0.90
   2 !    6.6   0.0    0.0026       9.2       6      15 ..      44      53 ..      42      54 .. 0.88
   3 !   10.8   0.0   0.00011       0.4       4      17 ..      64      77 ..      63      78 .. 0.92
   4 ?   -2.3   0.0       1.8   6.4e+03       6      16 ..      86      96 ..      85      97 .. 0.75
   5 !    5.5   0.0    0.0058        21       4      15 ..     105     116 ..     102     117 .. 0.87
   6 !    6.7   0.0    0.0023       8.4       1      16 [.     124     139 ..     124     141 .. 0.89
   7 !    7.4   0.2    0.0014       5.2       3      16 ..     148     161 ..     146     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.025
                              LRR_6  6 teLdLsgNdIg 16
                                       +++dL+ N+I+
  gene1359|gene1359|rna1358|rna1358 23 RTVDLRRNNIS 33
                                       689******96 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0026
                              LRR_6  6 teLdLsgNdI 15
                                       ++LdLs+N I
  gene1359|gene1359|rna1358|rna1358 44 EYLDLSDNRI 53
                                       79******99 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00011
                              LRR_6  4 hLteLdLsgNdIgD 17
                                        L+ LdLs+N I+D
  gene1359|gene1359|rna1358|rna1358 64 RLKILDLSYNLISD 77
                                       69**********99 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.8
                              LRR_6  6 teLdLsgNdIg 16
                                       +eL L +NdI+
  gene1359|gene1359|rna1358|rna1358 86 EELYLISNDIS 96
                                       56777799997 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.0058
                              LRR_6   4 hLteLdLsgNdI 15 
                                         +++LdL+ NdI
  gene1359|gene1359|rna1358|rna1358 105 RIKKLDLAVNDI 116
                                        689********9 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.0023
                              LRR_6   1 snthLteLdLsgNdIg 16 
                                        ++ +L+eL L +N I 
  gene1359|gene1359|rna1358|rna1358 124 NCITLEELYLGSNRIR 139
                                        689***********96 PP

  == domain 7  score: 7.4 bits;  conditional E-value: 0.0014
                              LRR_6   3 thLteLdLsgNdIg 16 
                                        t+L+ LdL+ N++ 
  gene1359|gene1359|rna1358|rna1358 148 TSLKILDLQNNELE 161
                                        89*********986 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.4   3.7e-06     0.013      20      79 ..      21      78 ..       4      88 .. 0.78
   2 !   19.9   0.8   1.2e-07   0.00042      49     116 ..      90     154 ..      81     157 .. 0.89
   3 !    7.9   0.3   0.00054       1.9      47      99 ..     153     204 ..     150     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.7e-06
                              LRR_9 20 rereldlrgykipvienlGatldqfdtidlsdndirkldgfPllkrlktlllnnnrivri 79
                                       + r +dlr + i+ +    a l   + +dlsdn ir++ ++  + rlk+l l+ n i  i
  gene1359|gene1359|rna1358|rna1358 21 HARTVDLRRNNISRMVLNKAEL--VEYLDLSDNRIREISDLENVPRLKILDLSYNLISDI 78
                                       4577888888888665545555..56699************************9999765 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.2e-07
                              LRR_9  49 lsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkkle 116
                                        l  ndi  + g+  l r+k l l+ n i+ri e+l++++ +leel l +n+++ +  l+ l+slk l+
  gene1359|gene1359|rna1358|rna1358  90 LISNDISTIRGLD-LPRIKKLDLAVNDICRI-ENLGNCI-TLEELYLGSNRIRAVEGLEDLTSLKILD 154
                                        5579999999996.79**************9.6899998.79*********************99886 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00054
                              LRR_9  47 idlsdndirkldgfPllkrlktlllnnnrivriaegleevlPnleelvltnne 99 
                                        +dl++n++  +d       +++lll +nr +r+ e+  e lP+l+ l l + +
  gene1359|gene1359|rna1358|rna1358 153 LDLQNNELEVVDCSMIPSSVEVLLLGENRDLRVVEKT-EHLPRLRILGLEKTS 204
                                        7999********999999***************9985.689***999888766 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.32   1.1e+03       3      13 ..      23      33 ..      22      39 .. 0.82
   2 ?    5.1   0.0     0.013        48       3      15 ..      44      55 ..      43      62 .. 0.74
   3 !    7.5   0.9    0.0022       7.8       1      17 [.      64      80 ..      64     103 .. 0.86
   4 ?    1.3   0.1      0.24   8.4e+02       2      15 ..     106     119 ..     105     126 .. 0.73
   5 ?    5.0   0.0     0.014        50       2      12 ..     128     138 ..     127     148 .. 0.78
   6 !    7.7   0.1    0.0018       6.6       1      13 [.     149     165 ..     149     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.32
                              LRR_1  3 rhLdLsnnpll 13
                                       r+ dL++n+++
  gene1359|gene1359|rna1358|rna1358 23 RTVDLRRNNIS 33
                                       789****9985 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                              LRR_1  3 rhLdLsnnpllgl 15
                                       ++LdLs+n++ + 
  gene1359|gene1359|rna1358|rna1358 44 EYLDLSDNRI-RE 55
                                       79******98.33 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0022
                              LRR_1  1 nLrhLdLsnnpllglpp 17
                                       +L+ LdLs+n ++++++
  gene1359|gene1359|rna1358|rna1358 64 RLKILDLSYNLISDILI 80
                                       69********9976654 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.24
                              LRR_1   2 LrhLdLsnnpllgl 15 
                                         ++LdL  n + ++
  gene1359|gene1359|rna1358|rna1358 106 IKKLDLAVNDICRI 119
                                        68999999988544 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.014
                              LRR_1   2 LrhLdLsnnpl 12 
                                        L++L+L++n++
  gene1359|gene1359|rna1358|rna1358 128 LEELYLGSNRI 138
                                        9********98 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.0018
                              LRR_1   1 nLrhLdLsnnpl....l 13 
                                        +L+ LdL nn l     
  gene1359|gene1359|rna1358|rna1358 149 SLKILDLQNNELevvdC 165
                                        69*********955553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1481.69
//
Query:       gene1360|gene1360|rna1359|rna1359  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-07   30.7   0.0    2.9e-07   30.2   0.0    1.1  1  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.6e-11   2.9e-07      47     106 ..      47     105 ..      37     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.6e-11
                                        HHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-E CS
                         MS_channel  47 snlvaGiillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvtsni 106
                                         nl  G + l++ pf +GD+++i + +G V++i++  + +++ +g +v+iP+s + ++ i
  gene1360|gene1360|rna1359|rna1359  47 DNLYKGAMALATCPFGVGDRIKIDKYDGVVKNISFWYVMLERGKG-YVFIPTSHIYNTVI 105
                                        69999*************************************999.*********98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 694.94
//
Query:       gene136|gene136|rna136|rna136  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-17   61.9   0.2    1.1e-16   61.2   0.2    1.3  1  Ran_BP1   RanBP1 domain


Domain annotation for each model (and alignments):
>> Ran_BP1  RanBP1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.2     6e-21   1.1e-16       7     117 ..      88     202 ..      81     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 6e-21
                                    TTEEEEEEEEEEEEEEETTTTEEEEEEEEEEEEEEETTTTEEEEEEEETTTTEEEEEEEE-TTS-EEESTTESSEEEEEE CS
                        Ran_BP1   7 EdEevlfkqraKLfrfdaekkewkeRGvGdiKilkkkddekvRllmRrdqvlkvcaNhvitkemklkplagsdrslvwta 86 
                                     ++evlfk r KL+ f++e+k  +eR  G + i  + +++ v++ + rdq+ ++  Nh i +++k +p     + ++w++
  gene136|gene136|rna136|rna136  88 QSDEVLFKARCKLYYFSEETKALEERAEGTMIIGMHSKSNLVKITVFRDQIGRLGCNHFINPRFKAQPHGKVSNGWMWMS 167
                                    3579**************************************************************************98 PP

                                    .EE-T..TSS.SEEEEEEEEESSHHHHHHHHHHHH CS
                        Ran_BP1  87 .adaa..dee.akleqlaikfkkkeeadefkkkfe 117
                                      d++  d++ +k++ +++kf ++e  ++f ++++
  gene136|gene136|rna136|rna136 168 tEDTVevDAQrKKIQLFVVKFYSEEDYRRFGEEYD 202
                                    666651244415677789********999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.32s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1366.68
//
Query:       gene1361|gene1361|rna1360|rna1360  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.8e-126  422.7   8.5     2e-126  422.5   8.5    1.0  1  Cpn60_TCP1   TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.018   14.9   0.2      0.044   13.7   0.2    1.7  1  ADH_N_assoc  Alcohol dehydrogenase GroES-associated


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.5   8.5  2.3e-130    2e-126      14     490 ..       1     459 [.       1     460 [. 0.97

  Alignments for each domain:
  == domain 1  score: 422.5 bits;  conditional E-value: 2.3e-130
                                        XEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHH CS
                         Cpn60_TCP1  14 mdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekliaagvhptt 89 
                                        m+Kml  kg++v vTnDGa ilk+l+i+ P a++l+++++ qd e GDGTt+v+iLa+ L++ea+kl   ++hpt+
  gene1361|gene1361|rna1360|rna1360   1 MLKML--KGQNVNVTNDGAFILKNLMIDSPSARILIDSSTGQDWEEGDGTTSVAILASLLVKEASKL---EIHPTR 71 
                                        78999..6999********************************************************...****** PP

                                        HHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCSEECSCCCE CS
                         Cpn60_TCP1  90 iiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieenekeldlgri 165
                                        i +gy++a +k+ e Lk+i  +++ +   +e+L+k+art+l+sk+ +++ e+++++++ A++ +    ++ dl+ +
  gene1361|gene1361|rna1360|rna1360  72 ILKGYRMAQAKCEETLKSI--SFKPS---KEDLIKLARTTLCSKVLKYDLEKFCDICISAIENLG---GRNDLNLV 139
                                        *****************99..88766...79******************************4333...678***** PP

                                        ECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCC.HHHCCCCSCCHHHHHHHHHHHH CS
                         Cpn60_TCP1 166 kvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektet.kttvvlsdaeeleklekaeekq 240
                                        +++k+  g+leds l +G++l+k+++ +    ++ ++k+l+ ++s++ +k ++  +++++s+++ele++e+ e+++
  gene1361|gene1361|rna1360|rna1360 140 QIIKCS-GKLEDSYLDDGFLLKKDIRIE----EMNDPKILIANTSMDQDKIKIfGAKINVSSVNELEEMERMEKAK 210
                                        *****9.56*****************88....679**************9988799******************** PP

                                        HHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEE CS
                         Cpn60_TCP1 241 leellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkve 316
                                        ++e++e+i + gvn +++ + i d  l++l+ +gi a+++++ + +erl++++G++++s++++++++++Gt+k+v+
  gene1361|gene1361|rna1360|rna1360 211 IREKVERISQNGVNMFINRQLIYDHPLQLLKIKGIQAIEHADFDGVERLSNVLGGKILSTFDNIDESSYGTCKNVK 286
                                        **************************************************************************** PP

                                        ECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCC CS
                         Cpn60_TCP1 317 eekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyak 392
                                        +  +g+e+++ +++v++g ++t++l+g+++++lde+er+i+dAl+v++++ ed++vv+GGG++e+++a +l++ya+
  gene1361|gene1361|rna1360|rna1360 287 NVYVGNERVIKFSGVRNG-ASTVVLCGSSKEILDEAERSIHDALCVLSRIKEDPRVVYGGGSSEMAMAVALNDYAM 361
                                        **************6665.9******************************************************** PP

                                        TSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHH CS
                         Cpn60_TCP1 393 svsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrq 468
                                        +vsg e  ai af++AL++ipk+La N+G++++e+ a+lra+hn++++++g++v+sg i++++eagv+D++++k++
  gene1361|gene1361|rna1360|rna1360 362 EVSGVESEAILAFSNALQQIPKILADNGGYNGEEIKASLRAKHNSEKVSHGVNVKSGGISCMKEAGVIDSFRIKHR 437
                                        **************************************************************************** PP

                                        HHHHHHHHHHHHHCEEEEEXXX CS
                         Cpn60_TCP1 469 alksAteaastiLrideiikak 490
                                        ++++A+eaa++i+++d+i+k +
  gene1361|gene1361|rna1360|rna1360 438 VITAASEAAQMIIKCDAIVKCR 459
                                        *******************975 PP

>> ADH_N_assoc  Alcohol dehydrogenase GroES-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   4.9e-06     0.044       9      23 .]     160     174 ..     160     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.9e-06
                        ADH_N_assoc   9 pkdVrVeeVPDPkIe 23 
                                        +kd+r ee+ DPkI+
  gene1361|gene1361|rna1360|rna1360 160 KKDIRIEEMNDPKIL 174
                                        79************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2896.95
//
Query:       gene1362|gene1362|rna1361|rna1361  [L=603]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-13   49.1   1.9    3.9e-11   42.1   0.2    3.7  3  Nic96            Nup93/Nic96
     0.0021   18.6   0.4        5.5    7.5   0.0    3.5  3  NLRC4_HD2        NLRC4 helical domain HD2
  ------ inclusion threshold ------
      0.025   14.7   0.4       0.11   12.5   0.1    2.3  2  ORF6C            ORF6C domain
       0.14   12.4   1.9       0.77   10.1   1.9    2.3  1  Vps39_1          Vacuolar sorting protein 39 domain 1
       0.61   10.6   4.1         68    4.0   0.0    3.7  4  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> Nic96  Nup93/Nic96
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.2   1.1e-14   3.9e-11      48     227 ..     169     325 ..     116     339 .. 0.85
   2 !    2.7   0.2    0.0096        34     430     461 ..     461     492 ..     444     525 .. 0.81
   3 ?   -0.2   0.0     0.074   2.6e+02     391     442 ..     532     583 ..     527     597 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.1e-14
                                        HHHHHHHHHHHHHHHHCC....CTTSSSS-HHHHHHHHHHCTTBESSSCBSSTT--EETTEEHHHHHHHHHTTT-H CS
                              Nic96  48 rryLEkqfleyveeliaknpreaqlggvpsvvnkvraFvrvrlakknlaedaglldevngeplWaliyylLRaGdl 123
                                         r+L +++l+yve+ +++n ++  ++ + ++ +k++aF ++r++     ++   l++ +g+++ a +y l R+G+l
  gene1362|gene1362|rna1361|rna1361 169 IRFLGNEYLRYVERFLKENADK-IKEPLRGNEDKISAFTKLRYS-----KEEYGLEVYEGRYMFAELYTLFRCGLL 238
                                        589***************7766.778889*************94.....4456688999***************** PP

                                        HHHHHHHHHTGGGS-TTTTHHHHHHHHCTTTTSS---TCCCHHHHHHHHHHTTT.-TTS-HHHHHHHHHHHT--CC CS
                              Nic96 124 deAlevvnenkeafrkldrsfaaylkayassedrrlpseleerlkleYnqrirnasedsDpykkavYkiigrcdls 199
                                        d   +++++++  f+++++ f++ + +++ +++r                 i+    + D +k  +    g  d +
  gene1362|gene1362|rna1361|rna1361 239 DSVKNLLERFHVFFEHISHRFKTSFGNWIATKSRPA-------------VPIKI-GGTDDLFKAFLL---GLMDER 297
                                        *****************************9887766.............23444.33349***9875...555999 PP

                                        C-S-T.TC--SHHHHHHHHHHH---TTS CS
                              Nic96 200 rknlhqevaktieDwlWlqLslireddr 227
                                        ++++++ ++ +ieD++W+ L  i+ + +
  gene1362|gene1362|rna1361|rna1361 298 NRRMDEWIIGSIEDFVWMCLISINGEGS 325
                                        999999**************99998766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0096
                                        -HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHC CS
                              Nic96 430 rledAilLydlageydkvlellnrlLsqvlst 461
                                        + ++ i+Ly l  +   v++l+n+++ +++ +
  gene1362|gene1362|rna1361|rna1361 461 EKKKLIKLYYLIDDEALVVNLINEAITEAILS 492
                                        556679***********************984 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.074
                                        S-EEE-HHHHTGGGGT-SSSSHHHHHHHHHHHHHHHHCT-HHHHHHHHHHTT CS
                              Nic96 391 GtripGlieerlkliklddeeeflkkiieqaAreaeekgrledAilLydlag 442
                                        Gt + G+     + ++l+d++ +++ki + a + +e+ g  e+A  L++l+g
  gene1362|gene1362|rna1361|rna1361 532 GTSTLGATPLLDPGFDLTDFKYVVEKIFKLACDVVEKVGDNEMARTLFKLCG 583
                                        56666666666778999999*9****************************98 PP

>> NLRC4_HD2  NLRC4 helical domain HD2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.67   2.4e+03      31      61 ..      73     104 ..      57     128 .. 0.61
   2 !    7.5   0.0    0.0015       5.5      13     103 ..     179     272 ..     177     276 .. 0.72
   3 !    6.6   0.0    0.0029        11      59      82 ..     284     307 ..     280     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.67
                          NLRC4_HD2  31 lekketkellsls.kkaldkalksknghldlf 61 
                                        +++ke+++++++   + ++k +k+++ + dlf
  gene1362|gene1362|rna1361|rna1361  73 SRQKEHEKCVEKMfAQDVKKYIKEMKRENDLF 104
                                        33333323333333455555555555555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0015
                          NLRC4_HD2  13 vvlseeeeksevlkeflelekketkellsls...kkaldkalksknghldlflrFLfGLlsesnqrlleellgqt. 84 
                                        +v ++ +e+ +++ke l  ++ + +++ +l    ++   ++++ +  + +l ++F +GLl +s ++lle+++    
  gene1362|gene1362|rna1361|rna1361 179 YVERFLKENADKIKEPLRGNEDKISAFTKLRyskEEYGLEVYEGRYMFAELYTLFRCGLL-DSVKNLLERFHVFFe 253
                                        666777777777777776666555333333334578899999*****************7.566777777554223 PP

                          NLRC4_HD2  85 klssekkqellkwlkekiq 103
                                        ++s++ k++  +w+ +k++
  gene1362|gene1362|rna1361|rna1361 254 HISHRFKTSFGNWIATKSR 272
                                        9999*********999887 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0029
                          NLRC4_HD2  59 dlflrFLfGLlsesnqrlleellg 82 
                                        dlf  FL+GL+ e+n+r+ e+++g
  gene1362|gene1362|rna1361|rna1361 284 DLFKAFLLGLMDERNRRMDEWIIG 307
                                        89**************99888887 PP

>> ORF6C  ORF6C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         2     7e+03      92     101 ..     350     359 ..     347     361 .. 0.86
   2 ?   12.5   0.1   3.2e-05      0.11      29      58 ..     433     462 ..     422     468 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2
                              ORF6C  92 kdfdkAlefi 101
                                        kd+dkA+++i
  gene1362|gene1362|rna1361|rna1361 350 KDYDKAMSLI 359
                                        89*****998 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.2e-05
                              ORF6C  29 nmpldesekeeiqkkvkkkvvellggkksp 58 
                                         + +d+  + +++kkv++kv+e+l+gk+ +
  gene1362|gene1362|rna1361|rna1361 433 VLGIDSGTCLYLDKKVNQKVIEILKGKNEK 462
                                        567999*********************965 PP

>> Vps39_1  Vacuolar sorting protein 39 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.9   0.00022      0.77      30     101 ..     450     518 ..     444     526 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                            Vps39_1  30 kdveeiLkkekkykeLidlYygkklheeALeLlkeladedeedeedsslkgeketiiqylqklseedldlil 101
                                        ++v eiLk +++ k+Li+lYy    ++  ++L++e +    e    +++ +e+  ii+y +k++ +++  ++
  gene1362|gene1362|rna1361|rna1361 450 QKVIEILKGKNEKKKLIKLYYLIDDEALVVNLINEAIT---EAILSDTDIDEYLEIIEYYEKVECTKQTRVM 518
                                        57899*****************9999999999999999...777888888899999******9988877665 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.019        68      31      76 ..      76     123 ..      65     130 .. 0.79
   2 ?    1.4   0.0      0.12   4.4e+02      21      44 ..     175     200 ..     174     211 .. 0.69
   3 ?   -3.0   0.1       2.9     1e+04      63      78 ..     240     255 ..     239     258 .. 0.81
   4 ?    3.7   0.0     0.025        89      41      75 ..     491     525 ..     477     529 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.019
                    Phage_int_SAM_4  31 rflkkkapeeltkedieaYlnyLanerk...lsastqknalnalsffyk 76 
                                        + ++ k +e++  +d++ Y+  + +e+    +  s ++ ++++l  ++ 
  gene1362|gene1362|rna1361|rna1361  76 KEHE-KCVEKMFAQDVKKYIKEMKRENDlfvVGSSKVSGKIKILEEVFD 123
                                        4567.9******************7776777777777777777776665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                    Phage_int_SAM_4  21 sYlsaikrflrflkkk..apeeltke 44 
                                         Yl++++rfl+ +  k  +p   +++
  gene1362|gene1362|rna1361|rna1361 175 EYLRYVERFLKENADKikEPLRGNED 200
                                        6**********996333355444555 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.9
                    Phage_int_SAM_4  63 tqknalnalsffykkv 78 
                                        ++kn l  + +f++++
  gene1362|gene1362|rna1361|rna1361 240 SVKNLLERFHVFFEHI 255
                                        6889999999999987 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.025
                    Phage_int_SAM_4  41 ltkedieaYlnyLanerklsastqknalnalsffy 75 
                                        l+++di +Yl+     +k+  + q + + al++fy
  gene1362|gene1362|rna1361|rna1361 491 LSDTDIDEYLEIIEYYEKVECTKQTRVMTALKSFY 525
                                        7899**********9*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.59
# Mc/sec: 3059.69
//
Query:       gene1363|gene1363|rna1362|rna1362  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.4   1.8        1.2    9.2   0.1    2.5  2  HTH_54    ParA helix turn helix domain


Domain annotation for each model (and alignments):
>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1   6.7e-05       1.2       3      35 ..      37      70 ..      36      87 .. 0.86
   2 ?    2.9   0.2    0.0063   1.1e+02      36      54 ..     213     231 ..     194     236 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 6.7e-05
                             HTH_54  3 kmLqelteqi.qkqkkElkedeyyqtyskaalak 35
                                       ++L+  +e+i +++++E++e+e y++ ska ++ 
  gene1363|gene1363|rna1362|rna1362 37 RLLEYYSEKIlEEHREEVEEEELYRMLSKARIEV 70
                                       577888888747899***************9875 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0063
                             HTH_54  36 lpklsrrkvdkavsemeae 54 
                                        + ++sr+ v+  +seme++
  gene1363|gene1363|rna1362|rna1362 213 VQEFSRNDVEIKISEMEKA 231
                                        3467899999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2019.53
//
Query:       gene1364|gene1364|rna1363|rna1363  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-10   41.0   0.5      3e-10   40.3   0.5    1.3  1  DUF2439   Protein of unknown function (DUF2439)


Domain annotation for each model (and alignments):
>> DUF2439  Protein of unknown function (DUF2439)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.5   1.7e-14     3e-10       5      76 ..       3      66 ..       2      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.7e-14
                            DUF2439  5 evlYTsqvtkKsKkWhDGflklhsfnkrvvLydeesklvessflknekeeleegeelelekylvqveelise 76
                                       ++ YT+q+ kK K+W+DGf++  +  kr++Ly+++   ++ss  +        ++e+e  kylv ++ +++ 
  gene1364|gene1364|rna1363|rna1363  3 RCVYTAQKSKKLKTWIDGFVE--HKGKRLYLYNSDMMKIDSSLAS------ALDNEMETYKYLVYIDSFENF 66
                                       7********************..999***************9999......578888999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 736.01
//
Query:       gene1365|gene1365|rna1364|rna1364  [L=249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-16   58.6   0.1    7.8e-16   58.2   0.1    1.1  1  Noc2      Noc2p family


Domain annotation for each model (and alignments):
>> Noc2  Noc2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.1   4.3e-20   7.8e-16     120     286 ..      87     245 ..      81     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 4.3e-20
                               Noc2 120 kLiptaryfPlrlhlirsLlrLsestgtfIPvaplllevLeskelkkkpkkkstlkpldfevtlkvpksylktrvy 195
                                        +L+   + +P  + ++r++ ++s  ++ + P++ ++l +L+++   k+ +  ++ +++d + +l  + +  k+++ 
  gene1365|gene1365|rna1364|rna1364  87 ELMERYNDYPHSIFCLRIIKSISG-SKFYTPLSFYILRILRNAISVKNLT--ASGRSIDYD-MLNPDMERCKSEEH 158
                                        67777788999*********9986.79***************55544444..489****98.589999******** PP

                               Noc2 196 qdglieevvellleylallsksiaFPElvlpvvvqLkrflkstkneklrkqlkqLvekleenskfieekRekvefs 271
                                        q  +iee+ +lll++++++sk+i+FPEl+ +v+ +Lk++        +++ + +++  ++e+ +++ ekR+k++++
  gene1365|gene1365|rna1364|rna1364 159 QMFVIEEAGSLLLKHMSMFSKNIGFPELASVVINELKKLRTG----IYKEVIGKMIFDINEQREYVLEKRNKLKLN 230
                                        *************************************99876....67888999999******************* PP

                               Noc2 272 pkdreeveafekelk 286
                                          d +++  fe++++
  gene1365|gene1365|rna1364|rna1364 231 GIDGKAISLFESSIE 245
                                        **********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1728.89
//
Query:       gene1366|gene1366|rna1365|rna1365  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-41  143.2  13.2    1.4e-41  143.0  13.2    1.0  1  Per1        Per1-like family
  ------ inclusion threshold ------
       0.49    9.8  20.2         49    3.2  20.2    2.1  1  Ceramidase  Ceramidase


Domain annotation for each model (and alignments):
>> Per1  Per1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0  13.2   1.6e-45   1.4e-41      38     254 ..      53     270 ..      23     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 1.6e-45
                               Per1  38 hGKWpflrllgiqEpasvlfSllNllvhlkglkklrkeipkssplkkvylvyalvslnawvwSaiFHtrDveltEk 113
                                         G+W f  +lg+ E++s+lfS++Nl++++  ++k+ k+  + ++l k+y +  +++ +a+++S++FH+ + ++t +
  gene1366|gene1366|rna1365|rna1365  53 NGRWGFQPVLGMTEFFSALFSFINLITNILCFHKMLKKHLRVTRLGKLYYIQYYICNLAFIASTLFHIHENSFTRN 128
                                        49******************************88888878888888888888899999****************** PP

                               Per1 114 lDYfsAgavvlsglylavvrlfrlarekkrvk..llltalllalyllHvlyLllvrfdYtYnmaanvvvgllqnll 187
                                         DYf A++++l+g+y+a+vr++ + + + + +  + l+++++++y++H+ +++ ++fdY Yn   + ++  l++l 
  gene1366|gene1366|rna1365|rna1365 129 CDYFLAFLTILFGFYMAFVRVILIGSPSLERAirRPLQCIFILFYAYHIHRMSNIEFDYVYNKVSCAIIITLTLLS 204
                                        *********************875444333323499***************************9999999999999 PP

                               Per1 188 wlllslktlakklvslklillvlllllamllEllDFppllrllDAhalwhlaTipltvlwydflvkD 254
                                         l+  lk ++k  +s  ++l++++++la ++E+ D pp+ +l+D+ha+whl+  + t ++  f   D
  gene1366|gene1366|rna1365|rna1365 205 HLVTFLK-YRKMGHSKNILLFTFFFFLAGAIEIQDVPPYAYLIDSHAIWHLISCISTPFYLLFWSGD 270
                                        9998886.67778888999999******************************999998887776655 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  20.2    0.0055        49      26     233 ..      74     266 ..      64     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0055
                         Ceramidase  26 fvNTlsnllfillallgiynaakkklekrfllaylglalvGlgSalFHaTLkyetQllDelsmiyatalvlyavfs 101
                                        f+N ++n+l++   l+   +++  +l k++++ y    l  + S+lFH   ++ t  +D +  +++++  +y+ f 
  gene1366|gene1366|rna1365|rna1365  74 FINLITNILCFHKMLKKHLRVT--RLGKLYYIQYYICNLAFIASTLFHIHENSFTRNCDYFLAFLTILFGFYMAFV 147
                                        7788888887777666655555..666888888888888899******************9999999999999998 PP

                         Ceramidase 102 e........kksrstrvllgvlltalavvvtllylvlkepvlhqvafalltvlvllrsiyliekkvdksdeaakke 169
                                                  +++ +r l  ++++++a  +  ++ +  + v+++v+ a++++l+ll+ +++    +   + ++  +
  gene1366|gene1366|rna1365|rna1365 148 RviligspsLERAIRRPLQCIFILFYAYHIHRMSNIEFDYVYNKVSCAIIITLTLLSHLVTF---L---KYRKMGH 217
                                        88998766433444556666667777777777777777788888888888888888777777...2...2244445 PP

                         Ceramidase 170 vkklallgliifllgfliWnlDnlfCstltrlrraiglplgvllelHgwWHiltgigayilivl 233
                                         k+++l+ +++fl+g  i +      +++         p++ l++ H++WH++ +i++ +++++
  gene1366|gene1366|rna1365|rna1365 218 SKNILLFTFFFFLAGA-IEI------QDV--------PPYAYLIDSHAIWHLISCISTPFYLLF 266
                                        5555555555555554.333......334........699999**************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1744.70
//
Query:       gene1367|gene1367|rna1366|rna1366  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-13   48.8   6.7    2.8e-05   23.7   0.0    4.5  4  TPR_1          Tetratricopeptide repeat
    3.2e-12   45.6   0.1     0.0099   15.9   0.0    3.6  3  TPR_2          Tetratricopeptide repeat
    5.6e-09   35.5   0.5    2.5e-06   27.0   0.2    2.8  3  TPR_11         TPR repeat
    1.4e-07   31.4   0.1      0.001   19.3   0.0    3.6  3  TPR_17         Tetratricopeptide repeat
    1.2e-06   28.3   9.7       0.14   12.5   0.1    4.8  5  TPR_8          Tetratricopeptide repeat
    2.1e-06   27.3   0.0       0.42   10.8   0.0    3.7  3  TPR_7          Tetratricopeptide repeat
     0.0015   19.0   0.0       0.52   10.9   0.0    2.7  2  TPR_19         Tetratricopeptide repeat
     0.0039   17.9   0.0         16    6.6   0.0    3.7  3  TPR_14         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.016   15.5   0.9        1.8    8.9   0.1    3.1  2  TPR_12         Tetratricopeptide repeat
      0.022   14.5   0.4       0.26   11.0   0.0    2.7  2  TOM20_plant    Plant specific mitochondrial import receptor s
      0.038   14.0   0.2       0.82    9.7   0.0    2.3  2  DUF1160        Protein of unknown function (DUF1160)
      0.043   14.1   0.5       0.07   13.4   0.5    1.4  1  A_deaminase_N  Adenosine/AMP deaminase N-terminal
      0.053   14.2   0.0       0.12   13.0   0.0    1.5  1  TPR_16         Tetratricopeptide repeat
       0.12   13.1   0.3        9.7    7.1   0.0    3.2  3  TPR_6          Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       4.8   6.1e+03      14      23 ..      29      38 ..      28      38 .. 0.80
   2 !   16.4   0.0   4.4e-06    0.0057       6      34 .]      49      77 ..      44      77 .. 0.93
   3 !   23.7   0.0   2.2e-08   2.8e-05       4      33 ..      81     110 ..      78     111 .. 0.91
   4 !    9.3   0.2   0.00082       1.1       3      34 .]     114     144 ..     112     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.8
                                       TT-HHHHHHH CS
                              TPR_1 14 lgkydeAley 23
                                       l+k+d A+++
  gene1367|gene1367|rna1366|rna1366 29 LKKLDLAEKA 38
                                       7999999875 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.4e-06
                                       HHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1  6 nlGnayfklgkydeAleyyekALelnPnn 34
                                        +Gn  ++ g++  A++ y +A+  +P+n
  gene1367|gene1367|rna1366|rna1366 49 SKGNEEYNDGDFRSAIDSYTQAIIYDPTN 77
                                       689************************97 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 2.2e-08
                                        HHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   4 lynlGnayfklgkydeAleyyekALelnPn 33 
                                        l n+++ay klg+ + A+e++e  L ++ +
  gene1367|gene1367|rna1366|rna1366  81 LSNRAAAYSKLGMVENAIEDCENGLNIDDK 110
                                        89**********************999865 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00082
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                         + +lG++y++ ++ + A + +e+ Le++P+n
  gene1367|gene1367|rna1366|rna1366 114 LYIRLGMLYLS-KDKNRAYQIFERGLEVDPKN 144
                                        56666666665.67799*************97 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.8e-06    0.0099       7      34 .]      50      77 ..      44      77 .. 0.91
   2 !   14.6   0.0     2e-05     0.026       3      32 ..      80     109 ..      78     111 .. 0.92
   3 !   11.2   0.0   0.00025      0.32       2      34 .]     113     144 ..     112     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.8e-06
                              TPR_2  7 lGlayyklgdyeeAleafekAleldPnn 34
                                        G+  y+ gd+  A++ + +A+ +dP+n
  gene1367|gene1367|rna1366|rna1366 50 KGNEEYNDGDFRSAIDSYTQAIIYDPTN 77
                                       68899*********************98 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2e-05
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                        +l n++ ay klg  e A+e++e  l +d 
  gene1367|gene1367|rna1366|rna1366  80 YLSNRAAAYSKLGMVENAIEDCENGLNIDD 109
                                        689*********************999986 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00025
                              TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +++ +lG++y+ ++d ++A + fe+ le dP+n
  gene1367|gene1367|rna1366|rna1366 113 KLYIRLGMLYL-SKDKNRAYQIFERGLEVDPKN 144
                                        67899999999.*******************97 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2     2e-09   2.5e-06       1      42 []      51      92 ..      51      92 .. 0.98
   2 !    7.5   0.0    0.0026       3.3       7      40 ..      91     124 ..      90     126 .. 0.91
   3 ?   -2.2   0.0       2.8   3.6e+03      18      27 ..     135     144 ..     130     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2e-09
                             TPR_11  1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42
                                       G++ y  G++  Ai +Y +A+ +dP+n+  ++n+++ay k+G
  gene1367|gene1367|rna1366|rna1366 51 GNEEYNDGDFRSAIDSYTQAIIYDPTNVVYLSNRAAAYSKLG 92
                                       99**************************************98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0026
                             TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                        +G  e+Aie+ ++ l++d +++ +y  LG +y+ 
  gene1367|gene1367|rna1366|rna1366  91 LGMVENAIEDCENGLNIDDKFVKLYIRLGMLYLS 124
                                        67789************************99975 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.8
                             TPR_11  18 kkAlkldPdn 27 
                                        ++ l+ dP+n
  gene1367|gene1367|rna1366|rna1366 135 ERGLEVDPKN 144
                                        678999*998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     8e-07     0.001       2      33 ..      67      98 ..      66      99 .. 0.94
   2 ?    5.1   0.0     0.027        34       2      28 ..     101     127 ..     100     130 .. 0.86
   3 ?    2.7   0.0      0.15     2e+02       2      12 ..     134     144 ..     133     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8e-07
                             TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtAr 33
                                       y++a+ +dP+n++ + n+A +++k+G  + A+
  gene1367|gene1367|rna1366|rna1366 67 YTQAIIYDPTNVVYLSNRAAAYSKLGMVENAI 98
                                       99************************998887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.027
                             TPR_17   2 ylkaleldPnnadaynnLAelllknGd 28 
                                        +++ l +d + +++y  L+ l+l++ +
  gene1367|gene1367|rna1366|rna1366 101 CENGLNIDDKFVKLYIRLGMLYLSKDK 127
                                        688899999*************97655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.15
                             TPR_17   2 ylkaleldPnn 12 
                                        +++ le dP+n
  gene1367|gene1367|rna1366|rna1366 134 FERGLEVDPKN 144
                                        89********9 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3       2.3   2.9e+03      11      26 ..       9      24 ..       9      31 .. 0.86
   2 ?   -1.0   0.1       2.2   2.9e+03      14      26 ..      29      41 ..      24      45 .. 0.81
   3 !    6.4   0.0    0.0097        12      13      33 ..      56      76 ..      49      77 .. 0.83
   4 !   12.5   0.1   0.00011      0.14       6      32 ..      83     109 ..      80     111 .. 0.89
   5 !   12.3   0.1   0.00013      0.16       2      34 .]     113     144 ..     112     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.3
                                       HHHTT-HHHHHHHHHH CS
                              TPR_8 11 ylklgdyeeAkeyyek 26
                                       y+++++   +ke y+ 
  gene1367|gene1367|rna1366|rna1366  9 YFNKKRQYLSKEEYKT 24
                                       8999999999999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                                       TT-HHHHHHHHHH CS
                              TPR_8 14 lgdyeeAkeyyek 26
                                       l++++ A+++ +k
  gene1367|gene1367|rna1366|rna1366 29 LKKLDLAEKASNK 41
                                       8899999998777 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0097
                                       HTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8 13 klgdyeeAkeyyekaleldpd 33
                                       + gd+ +A+ +y +a+ +dp+
  gene1367|gene1367|rna1366|rna1366 56 NDGDFRSAIDSYTQAIIYDPT 76
                                       679*************88886 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00011
                                        HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                        n + +y+klg  e+A+e +e  l +d 
  gene1367|gene1367|rna1366|rna1366  83 NRAAAYSKLGMVENAIEDCENGLNIDD 109
                                        78899***************9999986 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00013
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                        ++y +lg++yl+ +d++ A + +e+ le dp+n
  gene1367|gene1367|rna1366|rna1366 113 KLYIRLGMLYLS-KDKNRAYQIFERGLEVDPKN 144
                                        7899******98.5899**************97 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00033      0.42      11      34 ..      56      77 ..      55      79 .. 0.91
   2 !    9.8   0.0   0.00064      0.82       2      28 ..      81     105 ..      81     113 .. 0.87
   3 ?    2.2   0.0      0.18   2.3e+02       5      34 ..     118     144 ..     114     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                              TPR_7 11 rlGdyeeAielyeqsLaltkdped 34
                                       ++Gd++ Ai+ y+q  a+ +dp++
  gene1367|gene1367|rna1366|rna1366 56 NDGDFRSAIDSYTQ--AIIYDPTN 77
                                       57************..**999986 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00064
                              TPR_7   2 LlnLarlysrlGdyeeAielyeqsLal 28 
                                        L+n a +ys+lG  e+Aie +e   +l
  gene1367|gene1367|rna1366|rna1366  81 LSNRAAAYSKLGMVENAIEDCEN--GL 105
                                        7899***************9997..55 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.18
                              TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdped 34 
                                        L+ ly +  d  +A +++e+  +l+ dp +
  gene1367|gene1367|rna1366|rna1366 118 LGMLYLS-KDKNRAYQIFER--GLEVDPKN 144
                                        5555555.56779999****..**999976 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00041      0.52       4      46 ..      57      99 ..      55     108 .. 0.95
   2 ?    5.1   0.0     0.025        32       8      28 ..     128     148 ..     121     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                             TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46
                                       +gd+ +A++ ++qa+ +dp n   + + A a+ +lg ++ A++
  gene1367|gene1367|rna1366|rna1366 57 DGDFRSAIDSYTQAIIYDPTNVVYLSNRAAAYSKLGMVENAIE 99
                                       69************************************99986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.025
                             TPR_19   8 aeAlalleqalqedpknaear 28 
                                         +A +++e+ l+ dpkn  ++
  gene1367|gene1367|rna1366|rna1366 128 NRAYQIFERGLEVDPKNKVLK 148
                                        689*************98766 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.11   1.4e+02      12      37 ..      55      80 ..      50      86 .. 0.83
   2 ?    4.2   0.0     0.073        94       7      42 ..      84     119 ..      80     121 .. 0.90
   3 ?    6.6   0.0     0.012        16      14      40 ..     124     150 ..     112     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                             TPR_14 12 lalGdpdeAiallrralalaPddaea 37
                                       ++ Gd++ Ai+ + +a+  +P++ ++
  gene1367|gene1367|rna1366|rna1366 55 YNDGDFRSAIDSYTQAIIYDPTNVVY 80
                                       578*************9888887665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.073
                             TPR_14   7 laeallalGdpdeAiallrralalaPddaeawllla 42 
                                        +a+a+  lG  + Ai+ ++  l  + ++  ++++l+
  gene1367|gene1367|rna1366|rna1366  84 RAAAYSKLGMVENAIEDCENGLNIDDKFVKLYIRLG 119
                                        799****************99999999999999886 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                             TPR_14  14 lGdpdeAiallrralalaPddaeawll 40 
                                        + d  +A ++++r l+ +P++ ++  +
  gene1367|gene1367|rna1366|rna1366 124 SKDKNRAYQIFERGLEVDPKNKVLKKQ 150
                                        455567**************9887665 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.13   1.7e+02      32      72 ..      34      71 ..      28      71 .. 0.72
   2 ?    8.9   0.1    0.0014       1.8       6      75 ..      81     141 ..      77     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                             TPR_12 32 iarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72
                                       +a+++   ++ ++a+ +   g   +  g+++ A++ +++a+
  gene1367|gene1367|rna1366|rna1366 34 LAEKA--SNK-QLAEDMKSKGNEEYNDGDFRSAIDSYTQAI 71
                                       55555..333.566667777777777899********9995 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                             TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                        l+n+aa++ +lg  + A+e +e  l+i  +         +  ++ Lg+ly ++++   A +++e+ l+++
  gene1367|gene1367|rna1366|rna1366  81 LSNRAAAYSKLGMVENAIEDCENGLNIDDKF--------VKLYIRLGMLY-LSKDKNRAYQIFERGLEVD 141
                                        4589999999999999999999999888444........45788888888.6668888888888888876 PP

>> TOM20_plant  Plant specific mitochondrial import receptor subunit TOM20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.58   7.4e+02      93     117 ..      57      81 ..      38      88 .. 0.78
   2 ?   11.0   0.0    0.0002      0.26      96     126 ..     127     157 ..      78     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.58
                                        HHHHHHHHHHHHHHHHH-TT-HHHH CS
                        TOM20_plant  93 kenfekatqffqqavdedPdndlyr 117
                                           f  a + + qa+  dP n +y 
  gene1367|gene1367|rna1366|rna1366  57 DGDFRSAIDSYTQAIIYDPTNVVYL 81 
                                        4578899999999999999999996 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                                        HHHHHHHHHHHHHH-TT-HHHHHHHHHHHTH CS
                        TOM20_plant  96 fekatqffqqavdedPdndlyrkslelaaka 126
                                         ++a+q+f++  + dP+n++ +k l+l +k 
  gene1367|gene1367|rna1366|rna1366 127 KNRAYQIFERGLEVDPKNKVLKKQLDLLSKG 157
                                        4689**********************98884 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00064      0.82       9      77 ..      85     155 ..      78     165 .. 0.79
   2 ?    2.0   0.0      0.15   1.9e+02      59      98 ..     174     211 ..     162     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00064
                            DUF1160   9 tpvvaKVavvntelkkylkelerdetfrkklvkvlkmFiereievediyeive...avdgi.kLtkkQidylv 77 
                                            +K  +v+  ++++ + l+ d++f k ++++  ++++++  +++ y+i e    vd+  k+ kkQ+d l 
  gene1367|gene1367|rna1366|rna1366  85 AAAYSKLGMVENAIEDCENGLNIDDKFVKLYIRLGMLYLSKD--KNRAYQIFErglEVDPKnKVLKKQLDLLS 155
                                        56779***************************9999999875..44555555522268888888888988876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                            DUF1160  59 iveavdgi.kLtkkQidylvkqvyenekiisilqkfvdeqr 98 
                                        +++ + g+  L +++id+  + +++n++i ++l++ v++++
  gene1367|gene1367|rna1366|rna1366 174 MIKNM-GMgGLKDSKIDF--NSLFNNKNIRDVLDTVVKDKS 211
                                        55555.344788888887..899999999999999998765 PP

>> A_deaminase_N  Adenosine/AMP deaminase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   5.5e-05      0.07      16      62 ..       4      53 ..       1      77 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                      A_deaminase_N 16 rpteedYetqReallekEeqlslGgnleLnekEeqaNeil...maikqee 62
                                       ++ e +++++R+ l ++E +  +G+  +L+  E+  N+ l   m+ k +e
  gene1367|gene1367|rna1366|rna1366  4 KEIERYFNKKRQYLSKEEYKTIVGALKKLDLAEKASNKQLaedMKSKGNE 53
                                       5667899*******************************995555555554 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.7e-05      0.12       3      54 ..      50      98 ..      49     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.7e-05
                             TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54
                                       ++++ ++ gd++ A+  +++a+ +d   P ++  l +++ a+ ++g ++ A+
  gene1367|gene1367|rna1366|rna1366 50 KGNEEYNDGDFRSAIDSYTQAIIYD---PTNVVYLSNRAAAYSKLGMVENAI 98
                                       68999********************...776668888888888887777776 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.61   7.8e+02      14      29 ..      58      73 ..      42      77 .. 0.75
   2 ?    0.5   0.0      0.94   1.2e+03       6      21 ..      84      99 ..      81     103 .. 0.84
   3 ?    7.1   0.0    0.0076       9.7       5      25 ..     117     136 ..     114     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHHHHHHH CS
                              TPR_6 14 gdtdkAlealerlike 29
                                       gd + A++ + + i  
  gene1367|gene1367|rna1366|rna1366 58 GDFRSAIDSYTQAIIY 73
                                       79999***99998855 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.94
                                       HHHHHHHHHHHHHHHH CS
                              TPR_6  6 lalsyrklgdtdkAle 21
                                       +a +y klg  ++A+e
  gene1367|gene1367|rna1366|rna1366 84 RAAAYSKLGMVENAIE 99
                                       688999999***9998 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0076
                                        HHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6   5 klalsyrklgdtdkAlealer 25 
                                        +l+++y++  d+ +A +++er
  gene1367|gene1367|rna1366|rna1366 117 RLGMLYLSK-DKNRAYQIFER 136
                                        89*****99.*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1537.32
//
Query:       gene1368|gene1368|rna1367|rna1367  [L=388]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-63  214.3  36.8    2.8e-63  214.1  36.8    1.0  1  Aa_trans  Transmembrane amino acid transporter protein


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.1  36.8   1.6e-67   2.8e-63       3     408 ..       3     384 ..       1     385 [. 0.93

  Alignments for each domain:
  == domain 1  score: 214.1 bits;  conditional E-value: 1.6e-67
                           Aa_trans   3 ssalsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrll 78 
                                        ++  s+ ++l+k+ +G+G+L+ Py fk+ G+++G++l++l +++s+++l l + cs++l    r ++ + l++  +
  gene1368|gene1368|rna1367|rna1367   3 TTLASGYITLLKTSIGSGILSFPYLFKTYGILIGIALTMLSGFFSVLGLILYAICSQELG---RTATLSRLATESM 75 
                                        6788999***************************************************97...9*******98888 PP

                           Aa_trans  79 GpkgkliidlailvqlfGvgvsyliligdllpaifesffdt.lllsnvyfilisaliiipLslipnlskLsylSll 153
                                         p+ ++i+d++ ++++fGv++syli++ +llp ++e++f+   l + ++  l++  +i p++ + +l+ L+y+Sl 
  gene1368|gene1368|rna1367|rna1367  76 -PYTRIIVDFSVFLKCFGVALSYLIITRQLLPVLIETIFGVsILSDPNISLLAFISCIGPFAYFNKLDRLKYTSLC 150
                                        .558***********************************99666678888889999999***************** PP

                           Aa_trans 154 alvsslyyivilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkkmtk 229
                                        ++v++++ +vi++l+ +e+++ +  + +e+ v ++s    ++  +g +vF+ft+h +++ i  e++d+s  + m++
  gene1368|gene1368|rna1367|rna1367 151 GVVAIVV-VVIAALYRYEYTPASTPSRAEYFV-PFSY--AWMGGFGKFVFSFTCHQNIFAIHSEMEDNSF-PRMKR 221
                                        *****97.8***************99999988.8888..9***************************888.99*** PP

                           Aa_trans 230 vlllsiilatvlyilvGlvGYltFGnevkgnillnlpkssilivivnlllvlhlilsfplqlhplrqvvenllikk 305
                                        +++++ + a+v+yi++G + Yl +G+ vk+n+l n+p+  +l  +v+ l+v+ +  s+plq+ p+r  + n++   
  gene1368|gene1368|rna1367|rna1367 222 LIYMVATSAAVIYISFGILNYLLYGDRVKDNVLENYPND-VLASVVRGLYVVVMGVSYPLQVNPCRNHLINIISFT 296
                                        ************************************977.5********************************775 PP

                           Aa_trans 306 eavagasekeapkskllrlvirlllvvityliAlsvpslakvlslvGatsstplsfilPalfhlkliktekkslek 381
                                                 ++  +k lr++++++++++t l+A+s   l+ + s++G+t+st++++i+Palf++ +  t+ k+l  
  gene1368|gene1368|rna1367|rna1367 297 ---------QESRKKPLRFIVTTGIIILTCLLAISGMGLGIIYSVIGSTASTFMCLIFPALFYFNMNITKPKGLVI 363
                                        .........555666679***********************************************99999877766 PP

                           Aa_trans 382 lvkkkildlicivlglllvfyglavli 408
                                        +      ++i + +g+++++ +l  +i
  gene1368|gene1368|rna1367|rna1367 364 M------SYIAFLFGVFVFTTSLFNII 384
                                        6......68999999999999888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2536.19
//
Query:       gene1369|gene1369|rna1368|rna1368  [L=425]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-39  135.2   0.1    2.8e-39  134.7   0.1    1.2  1  DEAD             DEAD/DEAH box helicase
    8.4e-22   77.6   0.1    5.1e-21   75.1   0.0    2.3  3  Helicase_C       Helicase conserved C-terminal domain
    2.1e-06   27.8   0.0    3.5e-06   27.1   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
    0.00049   19.9   0.1    0.00092   19.0   0.1    1.4  1  AAA_30           AAA domain
  ------ inclusion threshold ------
       0.04   13.8   0.1      0.076   12.9   0.1    1.4  1  Helicase_RecD    Helicase
      0.078   12.9   0.8       0.51   10.3   0.0    2.3  2  AbbA_antirepres  Antirepressor AbbA
      0.087   13.1   0.1       0.44   10.8   0.1    2.2  2  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7   0.1   1.1e-42   2.8e-39       3     171 ..      64     226 ..      62     230 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 1.1e-42
                                        HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                        iQ++ai+ i++g+d+ ++a+ G+GKT+af++++lq   + ++++++++l+++ tre+a q + +++ ++ +++  v
  gene1369|gene1369|rna1368|rna1368  64 IQKAAIQPIIDGRDIRAQAQSGTGKTGAFAVAALQMC-D-TNQDTTQILVLASTREIAAQNAARFEDLGCFMGAGV 137
                                        9*********************************999.4.578888****************************** PP

                                        EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                         l+ gg++ + ++++l+++++ivvgtpgr+ ++++ ++ln+++++++V+DEad++l+ gf++++++i++++   t+
  gene1369|gene1369|rna1368|rna1368 138 ALLSGGSPISADKAALEKNPHIVVGTPGRVEHMININELNMDNIKLFVIDEADEMLKAGFQEQVKSIFRRI---TN 210
                                        ***********************************************************************...44 PP

                                        TSTTTSEEEEEESSBS.H CS
                                        xxxxxxxxxxxxxxxx.x RF
                               DEAD 155 dgklqrqvivlSATlp.k 171
                                        +   + q+ ++SAT   +
  gene1369|gene1369|rna1368|rna1368 211 K--DEVQIAMFSATYDeE 226
                                        4..4567*******9833 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.1   2.9e+03      11      50 ..     101     144 ..      93     158 .. 0.59
   2 ?   -2.7   0.0       2.8   7.2e+03      12      28 ..     209     227 ..     198     263 .. 0.64
   3 !   75.1   0.0     2e-24   5.1e-21       2     111 .]     277     387 ..     276     387 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                        HHTTTTSEEEEEESSHH.HHHH.HHHHHHHT...TSTEEEESTTS CS
                         Helicase_C  11 kleeeggkilifvntid.rlek.vklllekk...gikvavlhgel 50 
                                        ++++++ +il+ + t++  + + +  ++      g  va l g  
  gene1369|gene1369|rna1368|rna1368 101 DTNQDTTQILVLASTREiAA-QnAARFEDLGcfmGAGVALLSGGS 144
                                        66788889999999998533.234444222234556666666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.8
                                        HTTTTSEEEEEESSHH..H CS
                         Helicase_C  12 leeeggkilifvntid..r 28 
                                        +++++ +i +f+ t d  +
  gene1369|gene1369|rna1368|rna1368 209 TNKDEVQIAMFSATYDeeE 227
                                        4666677777777777432 PP

  == domain 3  score: 75.1 bits;  conditional E-value: 2e-24
                                        HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                         Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                        kl +l++++ ++++ g++++f+n+++++    ++l  k++ ++  + +el+q ere++l++f+ g+ ++Li++  +
  gene1369|gene1369|rna1368|rna1368 277 KLVTLYDIF-RKQRLGQSIVFINSKEDARIvYDWL-IKHEWECELISAELTQAERERTLNRFRGGTARCLISSGLL 350
                                        677899998.89999***********885555666.5778************************************ PP

                                        TSSSTSTTESEEEESSSS..SSHHHHHHHHTTSSSTT CS
                         Helicase_C  77 erGidipkvnlVinfdlp..rnvtsyiqriGRtgRag 111
                                        +rGidi+++++V+ +d+p  +  ++yi+riGR gR+g
  gene1369|gene1369|rna1368|rna1368 351 SRGIDIQNLSVVFCLDVPsfERKSTYIHRIGRSGRYG 387
                                        ******************86669************86 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.4e-09   3.5e-06      29     169 ..      80     223 ..      60     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.4e-09
                                        EEESTTSTHHHHHHHHHHHH.-S.....-EEEEESSHHHHHHHHHHGGGGTGG.........GEEEESSS-B--.. CS
                             ResIII  29 ikmaTGtGKTlvaaklierl.lkkgkeekflflvprkslleqtleefkkflseayke.....igkkvsgdkkkake 98 
                                         ++  GtGKT   a ++ ++  ++++  ++l+l+ ++++  q   +f+++     +       g  +s dk     
  gene1369|gene1369|rna1368|rna1368  80 AQAQSGTGKTGAFAVAALQMcDTNQDTTQILVLASTREIAAQNAARFEDLGCFMGAGvallsGGSPISADKAAL-- 153
                                        67789*****999666666505556666*******************998877765444554444466666666.. PP

                                        .....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS........TTTHHHHHT---SEEEEEES CS
                             ResIII  99 kdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak.......kswreilekfkeavllglTA 167
                                          ++n +i+v t  ++   +     + +el  d++++++iDEa  + ++       + +r+i +k +e  +  ++A
  gene1369|gene1369|rna1368|rna1368 154 --EKNPHIVVGTPGRVEHMI-----NINELNMDNIKLFVIDEADEMLKAgfqeqvkSIFRRITNK-DEVQIAMFSA 221
                                        ..99****************.....8999***************999964543332245555554.4455666899 PP

                                        S- CS
                             ResIII 168 Tp 169
                                        T 
  gene1369|gene1369|rna1368|rna1368 222 TY 223
                                        96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   3.6e-07   0.00092       6     114 ..      65     210 ..      61     219 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.6e-07
                             AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkal..reaweaa.ggrviglAptgkaAkvLa...e........... 64 
                                        Q+aa++ ++ ++d    +++  GtGKt a +++  +   +++   ++++lA+t + A++ a   e           
  gene1369|gene1369|rna1368|rna1368  65 QKAAIQPIIDGRD--IRAQAQSGTGKTGAFAVAalQMCDTNQdTTQILVLASTREIAAQNAarfEdlgcfmgagva 138
                                        9999999999998..7899********776665315555555559********99887755355333333322222 PP

                             AAA_30  65 ..elgieastiakllkrlk................grarlepgtllivDEagmv....dtkqlaallkaaek 114
                                          + g + s  +  l+++                 ++ ++++ +l+++DEa  +     ++q++++++++++
  gene1369|gene1369|rna1368|rna1368 139 llSGGSPISADKAALEKNPhivvgtpgrvehminiNELNMDNIKLFVIDEADEMlkagFQEQVKSIFRRITN 210
                                        2222224444444444444789999999999998966788888*******9755455445566666666666 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     3e-05     0.076       3      99 ..      81     189 ..      80     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                      Helicase_RecD   3 tAdRGRGKSaalGlalaaliaegk..snilvtapskenvktlfeflakglealglke...............eekk 61 
                                        +A+ G+GK+ a ++a+ ++  +++  ++ilv a ++e +++  ++++                          + +
  gene1369|gene1369|rna1368|rna1368  81 QAQSGTGKTGAFAVAALQMCDTNQdtTQILVLASTREIAAQNAARFEDLGCF----MgagvallsggspisaDKAA 152
                                        5899***************999999999999998887666555554332222....22233567777676643333 PP

                      Helicase_RecD  62 kkaekaelrvrkqrieyiapdellklkeqadllvvDEA 99 
                                         +++ + +     r+e++   + l+ + + +l v+DEA
  gene1369|gene1369|rna1368|rna1368 153 LEKNPHIVVGTPGRVEHMININELNMD-NIKLFVIDEA 189
                                        333334444447888887766666655.6899999999 PP

>> AbbA_antirepres  Antirepressor AbbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2      0.31   8.1e+02      52      62 ..     277     287 ..     270     288 .. 0.85
   2 ?   10.3   0.0    0.0002      0.51      10      39 ..     299     328 ..     291     331 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.31
                                        HHHHHHHHHTT CS
                    AbbA_antirepres  52 kllrLydRlrf 62 
                                        kl++Lyd +r+
  gene1369|gene1369|rna1368|rna1368 277 KLVTLYDIFRK 287
                                        8******9886 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                        TTTTHHHHHHHHSSS--HHHHHHHHHHHHH CS
                    AbbA_antirepres  10 teEEqkLLLdiLlnqeYAlellssElaDIE 39 
                                        ++E++ +  d L+++e+  el+s+El+  E
  gene1369|gene1369|rna1368|rna1368 299 SKEDARIVYDWLIKHEWECELISAELTQAE 328
                                        6899999*******************9877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         1   2.6e+03      13      19 ..      83      89 ..      81     116 .. 0.83
   2 ?   10.8   0.1   0.00017      0.44      91     128 ..     178     219 ..     156     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                             AAA_22 13 esGtGKT 19
                                       +sGtGKT
  gene1369|gene1369|rna1368|rna1368 83 QSGTGKT 89
                                       79****9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                             AAA_22  91 v..ielliiDEaqh.lrs...eealeeL.rsllnlsrkgvqliLv 128
                                        +  i+l++iDEa+  l +   +e+++ + r++ n  ++ vq+ ++
  gene1369|gene1369|rna1368|rna1368 178 MdnIKLFVIDEADEmL-KagfQEQVKSIfRRITN--KDEVQIAMF 219
                                        35679*********55.44577777777799999..999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2745.80
//
Query:       gene1370|gene1370|rna1369|rna1369  [L=409]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-26   93.8   0.0    2.2e-26   92.9   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
    1.4e-25   89.7   0.6    3.7e-25   88.3   0.1    2.0  2  PIGA             PIGA (GPI anchor biosynthesis)
    3.3e-25   88.6   0.0    6.1e-25   87.7   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    5.9e-22   78.5   0.1    1.2e-21   77.5   0.1    1.6  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.8e-11   44.1   0.0      4e-11   43.6   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.5e-08   34.8   0.0    3.1e-08   33.7   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
     0.0019   18.6   0.0     0.0052   17.1   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.02   14.6   0.0       0.18   11.5   0.0    2.3  2  Glyco_transf_5   Starch synthase catalytic domain
      0.042   13.6   0.0      0.098   12.4   0.0    1.6  1  CdiI             CDI immunity protein
      0.093   12.7   0.0       0.19   11.7   0.0    1.5  1  Baculo_RING      Baculovirus U-box/Ring-like domain


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0   1.2e-29   2.2e-26       2     166 ..      18     180 ..      17     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 1.2e-29
                     Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeev...elvvrvprvplpllkrllrslaflrrlrrllkrekpD 74 
                                        GG+e+h+++L+++L  +Gh+V v+t+++++  + +    + v+ +  + l+ +  ++  +++l+ ++++++ ek+ 
  gene1370|gene1370|rna1369|rna1369  18 GGIETHIRYLSEELISMGHKVIVITHKTGDLVGCRMvgtIKVYFLDIPVLCRNTTFPSLYSNLPLFKEIFDSEKIE 93 
                                        9*******************************9998787777777777888888999999999************* PP

                     Glyco_transf_4  75 vvHahspaalga..allalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadel 148
                                        +vH h+ ++ ++  +l+ +r  l++++V+t H+ +          +++++++al r +l++ dr+i+vS + +++ 
  gene1370|gene1370|rna1369|rna1369  94 IVHGHQTMSNMCieGLFHART-LNLKTVITDHSIF------EVGPFENIVVNALCRLALKNIDRCICVSYTSKENT 162
                                        ******999976557888887.*************......478889999************************** PP

                     Glyco_transf_4 149 rerygvppekitVipnGv 166
                                        + r  +p eki+Vipn++
  gene1370|gene1370|rna1369|rna1369 163 HIRTMIPLEKIHVIPNAI 180
                                        ****************98 PP

>> PIGA  PIGA (GPI anchor biosynthesis)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3   0.1     2e-28   3.7e-25       1      87 [.      43     128 ..      43     131 .. 0.96
   2 ?   -3.4   0.0       8.7   1.6e+04      67      81 ..     287     301 ..     278     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 2e-28
                               PIGA   1 hayedrkGvryltnglkvYyvPllvlyrevtlptvlstlpllrnillrekidivhghqalstlaheailhaktlGl 76 
                                        h+++d +G r+++ ++kvY++ + vl r++t+p+++s+lpl+++i+  eki+ivhghq++s+++ e ++ha+tl l
  gene1370|gene1370|rna1369|rna1369  43 HKTGDLVGCRMVG-TIKVYFLDIPVLCRNTTFPSLYSNLPLFKEIFDSEKIEIVHGHQTMSNMCIEGLFHARTLNL 117
                                        8899999**9876.79************************************************************ PP

                               PIGA  77 ktvftDhsLfg 87 
                                        ktv tDhs+f 
  gene1370|gene1370|rna1369|rna1369 118 KTVITDHSIFE 128
                                        *********96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.7
                               PIGA  67 ailhaktlGlktvft 81 
                                        ai+ a + Gl++v t
  gene1370|gene1370|rna1369|rna1369 287 AIVEAASCGLHVVST 301
                                        688899999999877 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   3.4e-28   6.1e-25      11     159 ..     192     336 ..     185     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 3.4e-28
                                        TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSH CS
                    Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredl 86 
                                        k +++k++++ +rl  +Kg+dlli a++l++k  +p v+++i+G+g++++ +++  +e el d+v++  ev++e++
  gene1370|gene1370|rna1369|rna1369 192 K-SDEKTVVVASRLMFRKGIDLLIGAIPLICKG-DPTVRIIIVGDGPMKEGIEQVLDENELYDRVEIMHEVDHEKV 265
                                        3.7999*************************98.****************************************** PP

                                        HHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                    Glycos_transf_1  87 eellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                         e++++ d+f+ +s +E f+i+++EA ++gl v+++n+gg+ ev+ +    + +     e+lae++  +l+++
  gene1370|gene1370|rna1369|rna1369 266 GEIMRRGDVFLNTSLTETFCIAIVEAASCGLHVVSTNVGGIHEVLPPDMITFSKI--TCEDLAEKVLMALRKS 336
                                        ********************************************98888333333..4477777777776665 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5   0.1   6.9e-25   1.2e-21       2     132 ..     196     333 ..     195     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 6.9e-25
                                        EEEEEES---GG.GTHHHHHHHHHHHH.HH..EEEEEES---..HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                    Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkd..vrlvivGdgprpeeleelaa..gleerveftGfv..edlaella 71 
                                        ++++  +rl  + kg+dll+ a+pl+ k d  vr++ivGdgp++e +e+ ++  +l +rve++ +v  e++ e+++
  gene1370|gene1370|rna1369|rna1369 196 KTVVVASRLMFR-KGIDLLIGAIPLICKGDptVRIIIVGDGPMKEGIEQVLDenELYDRVEIMHEVdhEKVGEIMR 270
                                        688999999545.**************77568**********556999777568899*********8777****** PP

                                        H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHH CS
                    Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLl 132
                                        + dvf+++s  e+f ++++Ea+++gl vV+t+vggi ev+  + + +++   e+lae++l  l
  gene1370|gene1370|rna1369|rna1369 271 RGDVFLNTSltETFCIAIVEAASCGLHVVSTNVGGIHEVLPPDMITFSKITCEDLAEKVLMAL 333
                                        **********99**************************9966778888778999999998776 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.2e-14     4e-11       1     159 [.      18     178 ..      18     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.2e-14
                    Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvh..rlpvp.rrpspladlaalralrrllrqrrer 73 
                                        gGi+++++ l+++L   Gh V v+t +       ++ + + v+   +pv  r+   +  ++ l+ +++++  ++e+
  gene1370|gene1370|rna1369|rna1369  18 GGIETHIRYLSEELISMGHKVIVITHKTGDLVGCRMVGTIKVYflDIPVLcRNTTFPSLYSNLPLFKEIF--DSEK 91 
                                        8************************7655554435666677763366755255567777899********..**** PP

                    Glyco_trans_4_4  74 pdvvhahsptaglaa...rlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelr. 145
                                        + +vh h+ ++++ +    +ar + +++ v+t h+  ++ g +++  ++ al r++l++ d++++vs    e  + 
  gene1370|gene1370|rna1369|rna1369  92 IEIVHGHQTMSNMCIeglFHAR-TLNLKTVITDHSI-FEVG-PFENIVVNALCRLALKNIDRCICVSYTSKENTHi 164
                                        **********999984434777.88*********96.4333.7898999999***************988865551 PP

                    Glyco_trans_4_4 146 algvpadrvvvvpn 159
                                        +  +p ++++v+pn
  gene1370|gene1370|rna1369|rna1369 165 RTMIPLEKIHVIPN 178
                                        566**********9 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   1.7e-11   3.1e-08      10     138 ..      21     154 ..       6     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.7e-11
                    Glyco_trans_4_2  10 svhtlrlakeLakrgyeVhvitpkkga.kdeleaegihvhrlkvd.....rkgpleylkafklkklikkikPDvvh 79 
                                        ++h + l +eL + g++V vit k+g   +      i+v+ l+++     + +p  y ++  +k++++ +k+ +vh
  gene1370|gene1370|rna1369|rna1369  21 ETHIRYLSEELISMGHKVIVITHKTGDlVGCRMVGTIKVYFLDIPvlcrnTTFPSLYSNLPLFKEIFDSEKIEIVH 96 
                                        57888899***************9998899999*********999887333335555556677************* PP

                    Glyco_trans_4_2  80 ahyakpy.gllgslaarlsgvipvvlsvwGldvlkfpkksk.lkklllklalkkatkvist 138
                                         h++ +   + g + ar ++  ++v++ +  ++++ +++ + +  +l +lalk++++ i+ 
  gene1370|gene1370|rna1369|rna1369  97 GHQTMSNmCIEGLFHARTLN-LKTVITDH--SIFEVGPFENiVVNALCRLALKNIDRCICV 154
                                        ****8883566666688888.78888888..699998888879999**********99986 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       6.5   1.2e+04      72      90 ..     239     257 ..     237     259 .. 0.65
   2 !   17.1   0.0   2.9e-06    0.0052       1      76 [.     274     353 ..     274     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.5
                    Glyco_trans_1_2  72 aarervlaehtydhraeql 90 
                                        +++e+vl e  +  r+e +
  gene1370|gene1370|rna1369|rna1369 239 EGIEQVLDENELYDRVEIM 257
                                        5677777777777777655 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.9e-06
                    Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekirylla....npeerraia 70 
                                        ++Ln+s  e++   ++Eaa cG  ++++   g+ e + p+  +i+f+  + e+laek+  +l+    np++++++ 
  gene1370|gene1370|rna1369|rna1369 274 VFLNTSLTETFCIAIVEAASCGLHVVSTNVGGIHEVLPPD--MITFSkiTCEDLAEKVLMALRksnhNPQDYNKRL 347
                                        5899999******************************998..999998*99*****99888875545667777766 PP

                    Glyco_trans_1_2  71 eaarer 76 
                                        ++ +++
  gene1370|gene1370|rna1369|rna1369 348 KNIYNW 353
                                        666665 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.8e-05      0.18       1      45 [.       5      47 ..       5      79 .. 0.86
   2 ?   -0.1   0.0      0.35   6.3e+02     171     225 ..     103     158 ..      73     163 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.8e-05
                     Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPryga 45
                                       +i +v+  ++p   tGG+  +++ L+++L  +gh+v vi+ + g+
  gene1370|gene1370|rna1369|rna1369  5 NIAMVSDFFYP--STGGIETHIRYLSEELISMGHKVIVITHKTGD 47
                                       57888888888..9*************************988754 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.35
                     Glyco_transf_5 171 Nlayqgrfpkdel.aalglpaedfekldglefygkvnflkagivyadavttVSpty 225
                                        N+ ++g f++ +l  ++ + +++  ++  +e+     + + +++  d+++ VS t 
  gene1370|gene1370|rna1369|rna1369 103 NMCIEGLFHARTLnLKTVITDHSIFEVGPFENIVVNALCRLALKNIDRCICVSYTS 158
                                        56666666665554444444433334555544444444457777777777777665 PP

>> CdiI  CDI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.5e-05     0.098      36      99 ..     318     385 ..     294     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.5e-05
                                        TT--HHHHHHHHHHHHHT--B-SHHHH.....HHH-HHHHHHHHHHHHHHHHHHH.T-S-HHHHHTT-E CS
                               CdiI  36 pdvsdselGkairkaLsksreiepedsd....difdkekvkerykeeekkimeey.gYkskkalfkkmd 99 
                                         +++ ++l ++++ aL ks++  p+d++    +i++ + v++  ++    i +++ gY+++++l+k ++
  gene1370|gene1370|rna1369|rna1369 318 SKITCEDLAEKVLMALRKSNHN-PQDYNkrlkNIYNWKRVARMTEKVYMDIEQTFlGYRNRRELYKGAT 385
                                        568999**************98.665441111677888888888888899988755**********765 PP

>> Baculo_RING  Baculovirus U-box/Ring-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.19      19     114 ..     281     383 ..     269     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                        Baculo_RING  19 keyfhtcatecaic.lediddn.rGvvaitdtGlldlekvlhkecikrf.....rreekrdpykrvikyrfeypfk 87 
                                         e f  + +e a c l+ +  n +G+  +    ++ + k+ +++  ++      + +++ + y++ +k  +++  +
  gene1370|gene1370|rna1369|rna1369 281 TETFCIAIVEAASCgLHVVSTNvGGIHEVLPPDMITFSKITCEDLAEKVlmalrKSNHNPQDYNKRLKNIYNWKRV 356
                                        56677777777777455555542678888888888889999988776642222123566667************** PP

                        Baculo_RING  88 tleeakvlleesktfvGdeeiievykk 114
                                        +    kv+++  +tf+G +++ e+yk 
  gene1370|gene1370|rna1369|rna1369 357 ARMTEKVYMDIEQTFLGYRNRRELYKG 383
                                        ************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2752.24
//
Query:       gene137|gene137|rna137|rna137  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-64  217.0   0.0    1.9e-64  216.8   0.0    1.0  1  MICSWaP   Spore wall protein


Domain annotation for each model (and alignments):
>> MICSWaP  Spore wall protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.8   0.0     1e-68   1.9e-64       2     193 .]      26     220 .]      25     220 .] 0.98

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 1e-68
                        MICSWaP   2 invkvyiseevrekYsdkgedleskvqkvaeelekalNks..lkksnkeir.iefdievsleipneieldkCgksvsela 78 
                                    ++v+vyise++r+k+ dkg+++e++v +vaeele ++N++  ++++++++r ++fd+ vs ++++ei+ldkCgk++s+++
  gene137|gene137|rna137|rna137  26 VPVEVYISEAGRKKFLDKGRSIEDIVGSVAEELELKMNEHvyADRASTDKRkFHFDWSVSGMTSPEIDLDKCGKDTSRFQ 105
                                    89***************************************99999999988**************************** PP

                        MICSWaP  79 slLnnvnnadsatsiIllltCeselyeevfisrglevpyvtqklsiecstrtaiFvEpeedkllsalanAlLkaagvpvn 158
                                    + L ++++++   s+Ill+tCese y+e+fi +g+++p+v+q++++ecs+++a+F+E+e +k++s++anAl+ +ag+p+n
  gene137|gene137|rna137|rna137 106 YDLVQAARDKPGASVILLYTCESEGYSEDFILAGQKTPLVIQRKYPECSNDVATFTETEPMKIESIIANALFITAGSPLN 185
                                    ******************************************************************************** PP

                        MICSWaP 159 npvkleevdggddGvkinirinketieellesecf 193
                                    ++v++eevd+g+dG+k++ir++++++++++   c+
  gene137|gene137|rna137|rna137 186 DMVEFEEVDNGRDGFKRDIRLKTTDFSLFSGGICH 220
                                    ***************************99988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1351.11
//
Query:       gene1371|gene1371|rna1370|rna1370  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-09   36.0   0.2    1.5e-08   34.9   0.1    1.6  1  EF-hand_7       EF-hand domain pair
    8.2e-06   25.3   0.1      0.044   13.7   0.0    4.0  5  EF-hand_6       EF-hand domain
    2.3e-05   24.1   0.2    0.00077   19.3   0.2    2.3  1  EF-hand_8       EF-hand domain pair
    0.00064   19.1   2.0       0.15   11.7   0.0    3.4  4  EF-hand_1       EF hand
     0.0066   16.8   0.0       0.19   12.1   0.0    2.1  2  EF-hand_9       EF-hand domain
  ------ inclusion threshold ------
      0.062   13.3   0.3       0.25   11.4   0.0    1.9  2  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
       0.12   12.3   0.3       0.87    9.6   0.1    2.2  2  RST             RCD1-SRO-TAF4 (RST) plant domain
        4.8    6.9   7.1         28    4.4   0.2    3.6  4  EF-hand_5       EF hand


Domain annotation for each model (and alignments):
>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   6.8e-12   1.5e-08       2      63 ..      75     130 ..      74     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 6.8e-12
                          EF-hand_7   2 eklkeaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisf 63 
                                        e+l+  F+ lD+d++ ++d   l ++l       + ++k+++ee+e+l++ +  d+dG+i +
  gene1371|gene1371|rna1370|rna1370  75 EELQKSFRRLDVDNTSHIDAGKLVQILS------CGENKFTEEEIEELLNILSPDGDGKICY 130
                                        899*******************998999......9999*********************966 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.15   3.3e+02       1      27 [.       6      32 ..       6      35 .. 0.88
   2 ?   -2.2   0.0       2.6   5.7e+03       9      12 ..      55      58 ..      53      65 .. 0.59
   3 ?    2.0   0.0      0.11   2.5e+02      16      27 ..      71      82 ..      70      83 .. 0.85
   4 !   13.7   0.0     2e-05     0.044       1      27 [.      76     102 ..      76     105 .. 0.92
   5 ?    4.7   0.0     0.015        33       1      19 [.     112     130 ..     112     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                          EF-hand_6  1 elreaFklfDkdgdGkidaeElrkalr 27
                                       +l+++++lf  + +  + +e l ++lr
  gene1371|gene1371|rna1370|rna1370  6 RLQKVYQLFAESPTERVPTERLGDILR 32
                                       588999999999999999999***999 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                          EF-hand_6  9 fDkd 12
                                       fD++
  gene1371|gene1371|rna1370|rna1370 55 FDFN 58
                                       5554 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.11
                          EF-hand_6 16 kidaeElrkalr 27
                                       +i++eEl+k +r
  gene1371|gene1371|rna1370|rna1370 71 EITREELQKSFR 82
                                       59******9776 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 2e-05
                          EF-hand_6   1 elreaFklfDkdgdGkidaeElrkalr 27 
                                        el++ F+ +D+d++ +ida  l+++l+
  gene1371|gene1371|rna1370|rna1370  76 ELQKSFRRLDVDNTSHIDAGKLVQILS 102
                                        68899********************98 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.015
                          EF-hand_6   1 elreaFklfDkdgdGkida 19 
                                        e++e+ +++  dgdGki +
  gene1371|gene1371|rna1370|rna1370 112 EIEELLNILSPDGDGKICY 130
                                        57788899999*****976 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   3.4e-07   0.00077       5      43 ..      92     128 ..      69     131 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.4e-07
                          EF-hand_8   5 ItreelrrilrilglkkglseeevdilfrefDtdgdGki 43 
                                        I+  +l+ il+  g + +++eee+++l++ +  dgdGki
  gene1371|gene1371|rna1370|rna1370  92 IDAGKLVQILSC-GEN-KFTEEEIEELLNILSPDGDGKI 128
                                        555555555554.433.6********************9 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.2   2.7e+03      18      26 ..      56      64 ..      53      67 .. 0.61
   2 !   11.7   0.0   6.6e-05      0.15       1      26 [.      76     101 ..      72     103 .. 0.91
   3 ?   -2.1   0.0       1.7   3.9e+03      19      26 ..     113     120 ..     109     121 .. 0.63
   4 !    5.2   0.3    0.0078        18      11      20 ..     122     131 ..     112     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                                       EHHHHHHHH CS
                          EF-hand_1 18 dfeEfkell 26
                                       df+++++++
  gene1371|gene1371|rna1370|rna1370 56 DFNQLVDIC 64
                                       566666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.6e-05
                                        HHHHHHHHHTTTSSSEEEHHHHHHHH CS
                          EF-hand_1   1 elkeiFrefDkDgdGkIdfeEfkell 26 
                                        el++ Fr +D+D++ +Id   ++++l
  gene1371|gene1371|rna1370|rna1370  76 ELQKSFRRLDVDNTSHIDAGKLVQIL 101
                                        799***************98888877 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                                        HHHHHHHH CS
                          EF-hand_1  19 feEfkell 26 
                                        +eE++++l
  gene1371|gene1371|rna1370|rna1370 113 IEELLNIL 120
                                        46666665 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.0078
                                        TTSSSEEEHH CS
                          EF-hand_1  11 kDgdGkIdfe 20 
                                         DgdGkI ++
  gene1371|gene1371|rna1370|rna1370 122 PDGDGKICYD 131
                                        6******986 PP

>> EF-hand_9  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.076   1.7e+02       3      27 ..      10      34 ..       8      41 .. 0.88
   2 !   12.1   0.0   8.5e-05      0.19       3      52 ..      80     127 ..      78     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.076
                          EF-hand_9  3 vFevcDtqktGrVpvsrlidyLrav 27
                                       v++++    t rVp  rl d+Lr  
  gene1371|gene1371|rna1370|rna1370 10 VYQLFAESPTERVPTERLGDILRFA 34
                                       79999999999***********976 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.5e-05
                          EF-hand_9   3 vFevcDtqktGrVpvsrlidyLravtaqdpeeseLeelakelDPdgedas 52 
                                         F+  D++ t  +   +l+++L  +++++ +e e+eel + l Pdg  ++
  gene1371|gene1371|rna1370|rna1370  80 SFRRLDVDNTSHIDAGKLVQIL-SCGENKFTEEEIEELLNILSPDGD-GK 127
                                        48999*****************.58999******************8.44 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.25      32      84 ..      49     100 ..      47     101 .. 0.87
   2 ?   -0.7   0.0      0.66   1.5e+03      55      65 ..     108     118 ..     104     121 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                        EEEESBSSSSHCHHHHHHHTTSBSSHHHHHHHHHTSCHHHHCCTHHHHHHHHH CS
                     Lip_prot_lig_C  32 kiyGDffgpkdieeleekLigvkyekeaieealekidlseyfggieleellel 84 
                                        +i G +f+ +++ ++ e+++  ++++e++++ ++++d+++  ++i++ +l+++
  gene1371|gene1371|rna1370|rna1370  49 SIPGEMFDFNQLVDICERIREREITREELQKSFRRLDVDN-TSHIDAGKLVQI 100
                                        789**********************************554.578888777776 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.66
                                        SSHHHHHHHHH CS
                     Lip_prot_lig_C  55 yekeaieeale 65 
                                        +++e+iee+l+
  gene1371|gene1371|rna1370|rna1370 108 FTEEEIEELLN 118
                                        44444444443 PP

>> RST  RCD1-SRO-TAF4 (RST) plant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.3   6.7e+02      24      38 ..       3      17 ..       1      22 [. 0.81
   2 ?    9.6   0.1   0.00039      0.87      25      51 ..      57      83 ..      46      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.3
                                RST 24 kmdllqkhYedlkkk 38
                                       +m+ lqk Y+ + + 
  gene1371|gene1371|rna1370|rna1370  3 EMKRLQKVYQLFAES 17
                                       7999*****999775 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00039
                                RST 25 mdllqkhYedlkkkkIsreefvrklRs 51
                                       +++l    e+ ++++I+ree+ + +R 
  gene1371|gene1371|rna1370|rna1370 57 FNQLVDICERIREREITREELQKSFRR 83
                                       57778888999************9996 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.028        62      16      23 ..      72      79 ..      71      81 .. 0.85
   2 ?    3.5   0.1     0.024        54       1      12 [.      77      88 ..      77      88 .. 0.87
   3 ?   -4.0   0.1       5.6   1.3e+04      18      22 ..     113     117 ..     112     119 .. 0.69
   4 ?    4.4   0.2     0.013        28      11      17 ..     123     129 ..     123     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.028
                                       E-HHHHHH CS
                          EF-hand_5 16 IskeELkt 23
                                       I++eEL++
  gene1371|gene1371|rna1370|rna1370 72 ITREELQK 79
                                       9*****97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.024
                                       HHHHHHHH-SS- CS
                          EF-hand_5  1 lkdtFqaiDlNg 12
                                       l++ F+++D+++
  gene1371|gene1371|rna1370|rna1370 77 LQKSFRRLDVDN 88
                                       6788******96 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 5.6
                                        HHHHH CS
                          EF-hand_5  18 keELk 22 
                                        +eEL 
  gene1371|gene1371|rna1370|rna1370 113 IEELL 117
                                        68885 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.013
                                        S-SSCE- CS
                          EF-hand_5  11 NgDGkIs 17 
                                        +gDGkI 
  gene1371|gene1371|rna1370|rna1370 123 DGDGKIC 129
                                        9*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1037.32
//
Query:       gene1372|gene1372|rna1371|rna1371  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 952.07
//
Query:       gene1373|gene1373|rna1372|rna1372  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-09   37.8   0.0    3.6e-09   36.8   0.0    1.5  1  KH_6      KH domain


Domain annotation for each model (and alignments):
>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0     2e-13   3.6e-09       1      43 [.     129     172 ..     129     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2e-13
                               KH_6   1 GmlfeVslslvrRll.nhvLeeLgkagpfeiavGlNGriWvkse 43 
                                        G+++   +++vr l  +  L+++gk+++f ia+GlNG++W+ +e
  gene1373|gene1373|rna1372|rna1372 129 GVVLPLDPWKVRLLYlSTALSTIGKKYKFRIALGLNGFVWIEAE 172
                                        8999999*****999*9999*********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1298.46
//
Query:       gene1374|gene1374|rna1373|rna1373  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-21   77.0   3.9      2e-21   76.3   3.9    1.4  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    8.2e-05   22.4   1.5    0.00014   21.7   1.5    1.4  1  KH_2            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   3.9   2.3e-25     2e-21       1      83 []     104     187 ..     104     187 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.3e-25
                                        HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETT CS
                     Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktky 74 
                                        i+e++  +v++Rra+++a++++ ++ga+G++i+vsG+L+ +++a+s k+++G +++  + ++++i++++a+++tk+
  gene1374|gene1374|rna1373|rna1373 104 IREKILGGVQYRRAVNMALKATRHSGAQGCQIIVSGKLK-GQRAKSVKFQDGVLIHsgNAVKDYINTGYATVETKQ 178
                                        7899***********************************.9***************9******************* PP

                                        EEEEEEEEE CS
                     Ribosomal_S3_C  75 GiiGvkVwI 83 
                                        G+iG++V+I
  gene1374|gene1374|rna1373|rna1373 179 GVIGIQVRI 187
                                        *******98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   1.5   1.5e-08   0.00014       1      76 [.      19      93 ..      19      95 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTT CS
                               KH_2  1 eipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkp 76
                                       e++e++++++ ++g s +e++ ++  ++i++++++p  +IG +  ++k+ ++ + +++e + + +V++ ++kV ++
  gene1374|gene1374|rna1373|rna1373 19 ELKEFFEKVLVNEGFSTMELRMQETPIKIILKVAKPHEAIGEKKLRLKQFQHLVAQRLE-VPDENVEIIVEKVHEK 93
                                       6789999999**********88999*********************************7.********999**875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1504.41
//
Query:       gene1375|gene1375|rna1374|rna1374  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-32  112.1   0.4    3.7e-32  111.4   0.4    1.2  1  RIO1             RIO1 family
    1.6e-18   66.7   0.1    3.6e-18   65.6   0.1    1.6  1  Rio2_N           Rio2, N-terminal
    0.00055   19.9   0.1     0.0013   18.7   0.1    1.5  2  APH              Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.017   14.5   0.5       0.03   13.7   0.5    1.4  1  Pkinase          Protein kinase domain
      0.029   13.7   0.3      0.071   12.5   0.1    1.7  2  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
      0.058   13.3   2.2        0.2   11.6   0.1    2.7  3  DUF3447          Domain of unknown function (DUF3447)
      0.095   12.7   0.1       0.47   10.5   0.0    2.1  2  Phage_sheath_1C  Phage tail sheath C-terminal domain
      0.096   12.7   0.0       0.17   11.9   0.0    1.3  1  HU-DNA_bdg       DNA-binding domain


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.4   1.7e-35   3.7e-32      10     181 ..     123     278 ..     115     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.7e-35
                                        TEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEE CS
                               RIO1  10 gkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvm 85 
                                        gk++++K++++++++F++++k +++ ++      ++++  l++++ ++E+ +L++ +++  +vP ++++ rhv+v 
  gene1375|gene1375|rna1374|rna1374 123 GKDCVLKFHRLGRSSFRNVRKNREYASE------RIDWFGLSRASCKREVMYLEKFKDM--NVPAVLDYDRHVIVQ 190
                                        789**********************999......79********************988..8************** PP

                                        E--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHH CS
                               RIO1  86 efigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnal 161
                                        e+++   ++++k +  +     +++++ ++e ++ l  + g+vH+D++e+Nvlv++d + +ID++Q +  ++++a 
  gene1375|gene1375|rna1374|rna1374 191 ELLD--YLPLYKTRVSD----VKTIFHLMIEFIKDLW-RRGYVHGDFNEFNVLVKDD-IKVIDFPQCIRSNDERAI 258
                                        ****..77777776666....7799999999777777.9***************988.999*************** PP

                                        HHHHHHHHHHHHHHHTTC-- CS
                               RIO1 162 efLerDveniikfFrrkgve 181
                                        + L+rD e++ ++F++k+ +
  gene1375|gene1375|rna1374|rna1374 259 HHLRRDFECVLTYFKKKYKY 278
                                        ****************9875 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.1   1.6e-21   3.6e-18       2      81 ..      23      98 ..      22      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.6e-21
                             Rio2_N  2 ryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktl 79
                                       ++Lske++++L++ E +m++h ++p+e+++ +s+++ ++++++  +l+k k++s+ +   +GYkLty+G+D+LA++tl
  gene1375|gene1375|rna1374|rna1374 23 WSLSKEHLKILKTAEKCMKSHTIIPFEVLKYRSQIR-GNFMEHAIDLCKLKFLSYVE---NGYKLTYSGHDCLAINTL 96
                                       78**********************************.788888889*********55...7****************9 PP

                             Rio2_N 80 vk 81
                                       + 
  gene1375|gene1375|rna1374|rna1374 97 RL 98
                                       75 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.62   1.4e+03      35      66 ..     160     185 ..     108     220 .. 0.62
   2 !   18.7   0.1   5.6e-07    0.0013     153     193 ..     214     246 ..     168     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.62
                                        HHHHHHHHHHHHHHHTT-B--B-CTTBS-EEE CS
                                APH  35 eeirrevallrlLakagvpvPevlagdtddee 66 
                                        +++ rev +l  + +    vP+vl++d     
  gene1375|gene1375|rna1374|rna1374 160 ASCKREVMYLEKFKDM--NVPAVLDYD----R 185
                                        4444444444444444..678888873....3 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 5.6e-07
                                        HHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                                APH 153 laalaallpgelptvllHgDlhpgNllvdpddgrvtGviDf 193
                                        ++ +++l++    ++ +HgD++  N+lv+ dd +   viDf
  gene1375|gene1375|rna1374|rna1374 214 IEFIKDLWR----RGYVHGDFNEFNVLVK-DDIK---VIDF 246
                                        566677777....9***************.6666...9**9 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   1.3e-05      0.03      46     149 ..     163     253 ..     103     272 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                        HHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE- CS
                            Pkinase  46 lrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiH 121
                                         rE+ +l+k+k +n+  +++     d+ ++v+e+++   +  l++       +++k i++ ++e ++ l+++g +H
  gene1375|gene1375|rna1374|rna1374 163 KREVMYLEKFKDMNVPAVLD----YDRHVIVQELLD---YLPLYK----TRVSDVKTIFHLMIEFIKDLWRRGYVH 227
                                        33333333333333332222....344555555555...333333....56679********************** PP

                                        SS-SGGGEEEETTTEEEE-SGTTSEESS CS
                            Pkinase 122 rDlKpeNiLidekgelKitDFGlakele 149
                                         D    N+L++  +++K++DF  + + +
  gene1375|gene1375|rna1374|rna1374 228 GDFNEFNVLVK--DDIKVIDFPQCIRSN 253
                                        **********9..99******7766655 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.89     2e+03      50      75 ..     154     179 ..     129     182 .. 0.76
   2 ?   12.5   0.1   3.2e-05     0.071     126     177 ..     212     256 ..     188     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.89
                                Kdo  50 rfklgrtravrEfrllkrLeeagvav 75 
                                        +f l+r+   rE+  l+++++  v++
  gene1375|gene1375|rna1374|rna1374 154 WFGLSRASCKREVMYLEKFKDMNVPA 179
                                        34488888899999999999888875 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.2e-05
                                Kdo 126 avgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradr 177
                                             i++l r+g  H+d++  n+l++ +      i +iD+ ++ +    +r
  gene1375|gene1375|rna1374|rna1374 212 LMIEFIKDLWRRGYVHGDFNEFNVLVKDD------IKVIDFPQCIRSN-DER 256
                                        555789********************988......699***9997765.444 PP

>> DUF3447  Domain of unknown function (DUF3447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.58   1.3e+03      24      38 ..      28      42 ..      24      46 .. 0.77
   2 ?   11.6   0.1   8.9e-05       0.2      24      70 ..      49      96 ..      40      99 .. 0.87
   3 ?   -1.3   0.0      0.94   2.1e+03      46      68 ..     215     253 ..     204     259 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.58
                            DUF3447 24 eClkyqkpdkkcmey 38
                                       e lk  k  +kcm+ 
  gene1375|gene1375|rna1374|rna1374 28 EHLKILKTAEKCMKS 42
                                       678888999999986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.9e-05
                            DUF3447 24 eClkyq.kpdkkcmeyaiisHnidfvtyLmneynleidleycgkynnl 70
                                       e+lky+ ++  + me+ai   + +f++y+ n y+l ++ ++c   n l
  gene1375|gene1375|rna1374|rna1374 49 EVLKYRsQIRGNFMEHAIDLCKLKFLSYVENGYKLTYSGHDCLAINTL 96
                                       89999879999************************9888889887776 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.94
                            DUF3447  46 dfvtyL.........mneynl......e.idleycgkyn 68 
                                        +f++ L         +ne+n+      + id+ +c+++n
  gene1375|gene1375|rna1374|rna1374 215 EFIKDLwrrgyvhgdFNEFNVlvkddiKvIDFPQCIRSN 253
                                        555555555555555677766333211223455587776 PP

>> Phage_sheath_1C  Phage tail sheath C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00021      0.47       4      74 ..     170     239 ..     169     259 .. 0.83
   2 ?   -0.9   0.0      0.74   1.6e+03      18      48 ..     261     291 ..     251     292 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                                        GGGGBHHHHHHHHHHHHHHHHHHHHHHHHHTTTSH.HHHHHHHHHHHHHHHHHHHTTSB-.S--STTSEEEEC CS
                    Phage_sheath_1C   4 edfkkievirtldllrddirstfkkkylgkklnnd.dgralvksalnaylkelqregaie.nfdnksdlevea 74 
                                        e+fk+ +v ++ld+ r  i +++    +   ++++ + ++ ++  ++++ k+l+r+g++  +f+ + ++ v++
  gene1375|gene1375|rna1374|rna1374 170 EKFKDMNVPAVLDYDRHVIVQELLD--YLPLYKTRvSDVKTIFHLMIEFIKDLWRRGYVHgDFN-EFNVLVKD 239
                                        68999***************99999..66666666578999*******************9998.56666655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.74
                                        HHHHHHHHHHHHHHHHTTTSH..HHHHHHHHHH CS
                    Phage_sheath_1C  18 lrddirstfkkkylgkklnnd..dgralvksal 48 
                                        lr+d    +++    kk++ +  dg+++++++l
  gene1375|gene1375|rna1374|rna1374 261 LRRDFECVLTY--FKKKYKYEpeDGWVAFTNEL 291
                                        55665555555..55566544459999999986 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.6e-05      0.17      19      71 ..      31      83 ..      17      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                       EEEEE----EE-HHHHHHHHHHH-TTS-HHHHHHHHHHHHHHHHHHHTTT-EE CS
                         HU-DNA_bdg 19 yiaqvessgsltledIidemvkegtevrketienilnlykrevseaileGysV 71
                                       +i++++ +   + + I  e+ k ++++r   +e++++l k +   ++++Gy++
  gene1375|gene1375|rna1374|rna1374 31 KILKTAEKCMKSHTIIPFEVLKYRSQIRGNFMEHAIDLCKLKFLSYVENGYKL 83
                                       66667777777777788899*******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1952.66
//
Query:       gene1376|gene1376|rna1375|rna1375  [L=333]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-05   22.9   1.1       0.13   11.5   0.1    3.1  3  GLE1      GLE1-like protein
  ------ inclusion threshold ------
       0.26   11.2   9.2       0.18   11.7   2.9    2.3  2  DUF507    Protein of unknown function (DUF507)


Domain annotation for each model (and alignments):
>> GLE1  GLE1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.07   6.3e+02      36      56 ..      86     106 ..      39     129 .. 0.57
   2 !   11.5   0.1   1.4e-05      0.13      21     107 ..     142     214 ..     129     231 .. 0.79
   3 !    8.6   0.0   0.00011      0.96     172     250 ..     240     304 ..     234     305 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.07
                               GLE1  36 gQltnsseqlkkitkelkell 56 
                                        ++ + sse+l+k t+e+++  
  gene1376|gene1376|rna1375|rna1375  86 STFSRSSEELQKTTNEIQSSC 106
                                        334445555555555555554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.4e-05
                               GLE1  21 kkllgdlkrkInpkvgQltnsseqlkkitkelkellesgkpvkvadkpelaykyllnflAkalvsqaetevsakpe 96 
                                        k+  +++k +In+++ Q+++++ q+ ki++ lke  +           +     +++++  ++++q+  +vs++p 
  gene1376|gene1376|rna1375|rna1375 142 KTAQMQAKIQINKRMTQVSGKAGQVDKIFNVLKEYSH-----------S---YVFVETFTLKIIEQGRLQVSSCPG 203
                                        5677899***********************9999882...........2...356777778888888888888887 PP

                               GLE1  97 aAfplArvavg 107
                                        +   +A + + 
  gene1376|gene1376|rna1375|rna1375 204 SYREFAELFCM 214
                                        76666666655 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00011
                               GLE1 172 GiirlYaaiiqtelsksskenphppgleiaWrwlarilnlpleplsnitatllaafLevagnrllkaYgkqfqKll 247
                                        Gi ++Y+ ++  +           ++ ++aW ++a++ln+++   ++ +++++  f++++g  l++  +  f Kl+
  gene1376|gene1376|rna1375|rna1375 240 GIYSIYFGVLEIQ-----------NNADEAWFFIASVLNSRQ---NKLSCYVVECFFSILGGLLFRECRGPFFKLI 301
                                        5555555555551...........233567**********66...5666666666666777777776667787777 PP

                               GLE1 248 eli 250
                                        e++
  gene1376|gene1376|rna1375|rna1375 302 EYV 304
                                        765 PP

>> DUF507  Protein of unknown function (DUF507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.9     2e-05      0.18      21      98 ..      19      94 ..      15     111 .. 0.80
   2 ?    3.1   0.4    0.0089        80     106     155 ..     129     177 ..     121     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                             DUF507 21 nsglielekeleeikkeieeileeelkkEkeldekvkeileeneeeiefervderelFlrikkklaeeegvilnseer 98
                                       n g ie +  +e++ + + ++l e  k ++ ++e+ + +l+++ ++ e+e+++  e+     k       + + s e 
  gene1376|gene1376|rna1375|rna1375 19 NYGEIERKR-REKVDELAYRLLVEREKANQSIEEELQRLLDQENDSAETENISMEEAIEERHKDAPVTSTFSR-SSEE 94
                                       566788777.9******************************************99998776666655566665.4444 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0089
                             DUF507 106 ileellkedlievsvsenkirnkIfkilkeylkeeeeidkevrekiknyk 155
                                        i e++++e+li+ ++++ + + +I k +++   +  ++dk   + +k+y+
  gene1376|gene1376|rna1375|rna1375 129 IEEKIWREKLIMPKTAQMQAKIQINKRMTQVSGKAGQVDKI-FNVLKEYS 177
                                        778999999**999999999999999999999999999874.45566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1776  (0.0990574); expected 358.6 (0.02)
Passed bias filter:                      750  (0.0418317); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2104.01
//
Query:       gene1377|gene1377|rna1376|rna1376  [L=65]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-21   75.5   0.6    2.6e-21   75.4   0.6    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.6   1.4e-25   2.6e-21       5      63 ..       8      63 ..       4      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 1.4e-25
                                       EEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT- CS
                     Ribosomal_S28e  5 lAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArr 63
                                         +V+ vlgrtG +G +tqV++el+++   +r+i R VkGPv +GDi++ lE+erE r+
  gene1377|gene1377|rna1376|rna1376  8 FGKVTHVLGRTGGSGLLTQVKMELMHN---KRTIQRAVKGPVAVGDIIEVLECEREHRK 63
                                       579************************...6*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.47
# Mc/sec: 418.18
//
Query:       gene1378|gene1378|rna1377|rna1377  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-05   22.3   0.1    9.3e-05   21.9   0.1    1.2  1  Bystin    Bystin
  ------ inclusion threshold ------
      0.038   14.0   0.3       0.11   12.5   0.3    1.7  2  CARD      Caspase recruitment domain
       0.09   12.9   0.0       0.11   12.6   0.0    1.3  1  zf-CRD    Cysteine rich domain with multizinc binding regions


Domain annotation for each model (and alignments):
>> Bystin  Bystin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.6e-08   9.3e-05     160     272 ..      57     157 ..      49     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-08
                             Bystin 160 tctlreaaivgsvlakvsipvlhsaaallklaeleysgatslfirvlldKkyaLpykvvdalvfhFlrfreekrel 235
                                        + + +ea ++g  l+kvs+  +     ++ ++  +   +t +++r ll+Kk  ++   +da+  +F +    kr +
  gene1378|gene1378|rna1377|rna1377  57 DLSRKEAEVLGGALKKVSLNHVD---DMVDILVKKNDKNTPILLRYLLEKKKKIS---IDAVQRYFCEEI--KRPI 124
                                        6789*************987554...466677778889999***********996...899999**8644..5558 PP

                             Bystin 236 pvlwhqsllvfaqrYknditedqkeaLldllkkkkhk 272
                                        +  + + llv++++Y ++i+     a+ld +++++h+
  gene1378|gene1378|rna1377|rna1377 125 TSKHLKLLLVMCRNYPSSISP----AILDFCRSNGHP 157
                                        888999**********99986....567777777665 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   1.8e-05      0.11       8      77 ..      38     106 ..      36     114 .. 0.90
   2 ?   -1.9   0.0      0.58   3.4e+03      51      69 ..     146     164 ..     123     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                        HHHHHHHSSHHHHHHHHHHHTTSS-HHHHHHHHT..SSSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHSHH CS
                               CARD   8 rkrLverlkslsglldyLlekkVLteeeeekika..kttrlskareLldlvqkkgekacqaflealkegqpd 77 
                                        ++ L++ +k +s++ + L+ +  L+++e e      k+ +l+++   +d++ kk++k   ++l++l e++++
  gene1378|gene1378|rna1377|rna1377  38 WHDLCKLVK-TSKVYNILRMD--LSRKEAEVLGGalKKVSLNHVDDMVDILVKKNDKNTPILLRYLLEKKKK 106
                                        678999999.99999999999..********99998888****************************97664 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.58
                                        HHHHHHHTSCHHHHHHHHH CS
                               CARD  51 eLldlvqkkgekacqafle 69 
                                        ++ld++++ g   c   le
  gene1378|gene1378|rna1377|rna1377 146 AILDFCRSNGHPICREVLE 164
                                        4566666655555555554 PP

>> zf-CRD  Cysteine rich domain with multizinc binding regions
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05      0.11      61     115 ..      65     121 ..      28     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                             zf-CRD  61 ecsglLkpieekliekipeevlegneveqkilkdylaekgl..tlqdvlkevlekld 115
                                           g Lk++++++++++ + ++++n+  + il +yl ek++  ++++v +  +e+++
  gene1378|gene1378|rna1377|rna1377  65 VLGGALKKVSLNHVDDMVDILVKKNDKNTPILLRYLLEKKKkiSIDAVQRYFCEEIK 121
                                        233669*****************************9766550045555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1265.89
//
Query:       gene1379|gene1379|rna1378|rna1378  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-09   36.5  16.0      2e-08   34.5  16.0    1.9  1  Utp11           Utp11 protein
  ------ inclusion threshold ------
      0.053   13.7   6.7       0.14   12.3   1.7    2.2  2  Nmad5           Nucleotide modification associated domain 5
       0.14   12.5  11.8       0.52   10.6   3.6    2.3  2  DUF349          Domain of Unknown Function (DUF349)
       0.75    9.9   7.9        4.6    7.3   1.6    2.9  3  DUF1664         Protein of unknown function (DUF1664)
        2.3    8.9  10.5         15    6.3   1.1    2.9  3  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac


Domain annotation for each model (and alignments):
>> Utp11  Utp11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5  16.0   5.6e-12     2e-08       3     151 ..       5     138 ..       3     162 .] 0.66

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.6e-12
                              Utp11   3 nHkERsQpaeRaklGlLEKkKDYklRAkdyhkKqaklkaLreKAaerNpDEFyfgMiksktkkgvhv.ekekdrgn 77 
                                          kER Qp++R+k+G LEKkK  ++R  + +k ++++k+ re  +++   E+ fg ++ +  +g+ v + +     
  gene1379|gene1379|rna1378|rna1378   5 IYKERIQPKSRRKYGKLEKKKELVKRLSKINKQRDEIKKAREEIRNKSGQEYFFGYHSVRK-DGRSVyRVD----- 74 
                                        68*****************************************************998776.555651222..... PP

                              Utp11  78 ealsedqvkllktqDlnYvrtkraierkkiekleeelhlleaeakseakeskkkkknkhivFvdseeeakefda 151
                                        +  + +  +l k +   Y+  + ++ + k+ek     + ++ + +++      ++k + ivF  +ee +kef+ 
  gene1379|gene1379|rna1378|rna1378  75 KP-TLE--ELGKIK--AYIDNEIQRSKMKLEKYIPIPSGTHIRFEED-----GSEKDTEIVFGKNEEVRKEFER 138
                                        21.222..222332..5666666666655555543333322222211.....2234566777777777776664 PP

>> Nmad5  Nucleotide modification associated domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.7     4e-05      0.14     111     155 ..       9      51 ..       2      52 .. 0.80
   2 ?    4.4   0.2     0.011        39      99     141 ..     115     160 ..      61     162 .] 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                              Nmad5 111 deiaketkslpkvvleadnplvkrfdelekaqeelrekrkaikat 155
                                        +   k+  ++   +le++++lvkr+ +++k+++e++++r++i+++
  gene1379|gene1379|rna1378|rna1378   9 RIQPKSRRKYG--KLEKKKELVKRLSKINKQRDEIKKAREEIRNK 51 
                                        44444455555..89***************************985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                              Nmad5  99 g...kkletvvlasvdeiaketkslpkvvleadnplvkrfdeleka 141
                                            +k ++ v+++++e+ ke +++++ ++ + +++++++d+l+++
  gene1379|gene1379|rna1378|rna1378 115 EdgsEKDTEIVFGKNEEVRKEFERYMEELFMKRKEVLEKIDKLKDQ 160
                                        2446667778899999999999999999999999999999998875 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.6   0.00014      0.52      27      61 ..      16      50 ..       3      54 .. 0.83
   2 ?    6.8   1.1    0.0023       8.4      13      49 ..     125     161 ..     122     162 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                             DUF349 27 ereenlekKealieeaealaksttdwksatkrlke 61
                                        +   lekK++l++++++++k+ +++k+a++++++
  gene1379|gene1379|rna1378|rna1378 16 RKYGKLEKKKELVKRLSKINKQRDEIKKAREEIRN 50
                                       556689*************9998899999999986 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0023
                             DUF349  13 fferrkahfeeqdaereenlekKealieeaealakst 49 
                                        +f + ++ ++e ++ +ee + k+++ +e++ +l++++
  gene1379|gene1379|rna1378|rna1378 125 VFGKNEEVRKEFERYMEELFMKRKEVLEKIDKLKDQM 161
                                        6777888888888889999999999999999998876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.6    0.0013       4.6      59      88 ..      22      51 ..      18      71 .. 0.92
   2 ?    0.5   0.0      0.16   5.7e+02      74      97 ..      77     100 ..      60     105 .. 0.66
   3 ?    4.4   0.1    0.0098        35      44      75 ..     130     161 ..     127     162 .] 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0013
                            DUF1664 59 atkrhLssridrvdkkldeqkeiskeikee 88
                                       + k++L +r+ +++k+ de k++ +ei+++
  gene1379|gene1379|rna1378|rna1378 22 EKKKELVKRLSKINKQRDEIKKAREEIRNK 51
                                       579***********************9986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.16
                            DUF1664  74 kldeqkeiskeikeevtevredls 97 
                                        +l+e  +i++ i++e+++ + +l+
  gene1379|gene1379|rna1378|rna1378  77 TLEELGKIKAYIDNEIQRSKMKLE 100
                                        566666666666666666665554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0098
                            DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkl 75 
                                        e+v k+ e+ +e+l   +++  ++id++ +++
  gene1379|gene1379|rna1378|rna1378 130 EEVRKEFERYMEELFMKRKEVLEKIDKLKDQM 161
                                        679999*********************99886 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.1    0.0041        15       5      35 ..      21      51 ..       6      56 .. 0.76
   2 ?    1.0   0.0      0.19   6.8e+02      23      56 ..      68     101 ..      60     103 .. 0.67
   3 ?    5.8   1.6    0.0058        21      28      61 ..     128     161 ..     118     162 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0041
                     HIP1_clath_bdg  5 LrKnAevtkqlsvarqaqeeverekkeleee 35
                                       L K  e++k ls   ++++e++++++e+ ++
  gene1379|gene1379|rna1378|rna1378 21 LEKKKELVKRLSKINKQRDEIKKAREEIRNK 51
                                       5577777888888888888888888777654 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                     HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeelek 56 
                                         +v r+ k + eel ++k+  +++++  k++lek
  gene1379|gene1379|rna1378|rna1378  68 RSVYRVDKPTLEELGKIKAYIDNEIQRSKMKLEK 101
                                        5566666666777777777777777777777665 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0058
                     HIP1_clath_bdg  28 ekkeleeelerlkeeaerkleeqkeelekLkrel 61 
                                        + +e+ +e+er  ee  +k +e  e+++kLk ++
  gene1379|gene1379|rna1378|rna1378 128 KNEEVRKEFERYMEELFMKRKEVLEKIDKLKDQM 161
                                        4689999***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2267  (0.126443); expected 358.6 (0.02)
Passed bias filter:                      778  (0.0433934); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1232.57
//
Query:       gene1380|gene1380|rna1379|rna1379  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-08   34.5   0.8    2.6e-08   33.5   0.6    1.6  1  zf-Nse     Zinc-finger of the MIZ type in Nse subunit
     0.0072   15.7   0.5       0.01   15.2   0.5    1.2  1  Rtf2       Rtf2 RING-finger
  ------ inclusion threshold ------
      0.099   13.0   0.1        0.2   12.0   0.0    1.6  1  zf-RING_2  Ring finger domain


Domain annotation for each model (and alignments):
>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.6   4.4e-12   2.6e-08      11      57 .]      83     128 ..      73     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.4e-12
                                        XSB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC-S CS
                             zf-Nse  11 slkCPltlqpfeePvtskkCpHvFEreaIlelikrkktvkCPvagCs 57 
                                        +l CP++++++++ ++   C Hv E++  +++i+++ ++ CP++gC+
  gene1380|gene1380|rna1379|rna1379  83 KLICPISQKEVVDAYIG-DCGHVLEKKEAMKYIRNNSRAICPQIGCN 128
                                        678**********9986.7***************************7 PP

>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5   1.7e-06      0.01     100     157 ..      69     128 ..      51     134 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-06
                               Rtf2 100 eeskkdatkdtkeapfiCpltglemngktkfvalrkCGcVfsek.alkevk...sevClv..Cg 157
                                        +++k++ ++   e + iCp++++e+ +     ++ +CG+V+++k a+k +       C++  C+
  gene1380|gene1380|rna1379|rna1379  69 TNKKEQVECVRMERKLICPISQKEVVDA----YIGDCGHVLEKKeAMKYIRnnsRAICPQigCN 128
                                        344457788889999*********9885....79*******86549999984434447764455 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.4e-05       0.2       3      42 ..      86     124 ..      84     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                          zf-RING_2   3 CpICleelssadsvlllpCgHvfhreClerwlrssst..CPl 42 
                                        CpI ++e+   d + + +CgHv  ++ +++++r++s+  CP 
  gene1380|gene1380|rna1379|rna1379  86 CPISQKEVV--DAY-IGDCGHVLEKKEAMKYIRNNSRaiCPQ 124
                                        555554443..334.446*****999999*******9***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1066.21
//
Query:       gene138|gene138|rna138|rna138  [L=436]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.072   11.9  18.6      0.096   11.5  18.6    1.1  1  Mitofilin      Mitochondrial inner membrane protein
       0.25   10.0   0.2       0.38    9.4   0.2    1.2  1  Prismane       Prismane/CO dehydrogenase family
        4.3    7.9  12.9        6.5    7.3  12.9    1.3  1  SOBP           Sine oculis-binding protein


Domain annotation for each model (and alignments):
>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5  18.6   1.6e-05     0.096      61     206 ..     227     373 ..     173     393 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                      Mitofilin  61 lkeisklqvsavsevtkeskepkeekkkeks.ekqssassevaeeeaeatkkaaeakaqqpkseqekekaleevlkeals 139
                                      eis+    ++s+++k+ ++++++ +  k+ +++++ ++  ++ee +++kk++ ++ ++p  ++e e + ++ +k+ l+
  gene138|gene138|rna138|rna138 227 GVEISSPLKWVLSKSEKKAEDTNSQSQPPKEiKQEKDNPESSSNEESSSEKKEKNTN-KKPSRSHEPEISSKKIKKTSLK 305
                                    455555555566666666655555555555522223444444444444444444443.6666666666666666666666 PP

                      Mitofilin 140 kaekataaakeakdeakkavkeavdklkeasdteeksrek.ardtaleaaeaaaek.eleklkeviela 206
                                    k+++  ++  e   e+k+ ++e+++ ++++s + +++  +  +d+    +ea+ e+  +e+l+++i  +
  gene138|gene138|rna138|rna138 306 KTNSDNLVDLEES-EKKEEIEEHEKRKTNNSLEYLDKINSlRNDQKPREEEALMEEkIREELQKIISHE 373
                                    6666655443333.3444444444444444444333333302233333333333333555555555544 PP

>> Prismane  Prismane/CO dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   6.3e-05      0.38      67     160 ..     313     415 ..     283     432 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.3e-05
                                    TB-SHHHHHHHHHHHHCHHHCC.........SSHHHHHHHHCCHHHCGGGS-SSHHHHHHHCCCHHHHHHHHHHHCHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane  67 vnfddekklkrlaealgieeel.........kdieelaakvaevaledlskeenedirslkellpkglkglyaehaivlg 137
                                    v+ ++++k ++++e  + +++          + +++ + + +e+ +e+  +ee ++i s ++  +k++ + y  + ++++
  gene138|gene138|rna138|rna138 313 VDLEESEKKEEIEEHEKRKTNNsleyldkinSLRNDQKPREEEALMEEKIREELQKIISHESHNLKRRFDGYPALTRIPS 392
                                    34444444444444444444445555544442244444455566777777788899************************ PP

                                    -HHHHHHHHHHHCCCCTTSTHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                       Prismane 138 yadeevveflaktlaglesdpld 160
                                    y+deev ++  ++l+   + p+ 
  gene138|gene138|rna138|rna138 393 YNDEEVRDAQPRILFPSRATPVR 415
                                    ********999998877777766 PP

>> SOBP  Sine oculis-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  12.9    0.0011       6.5      67     189 ..     230     361 ..     205     430 .. 0.35

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                           SOBP  67 LitPdlw........lsncrsrsaspaskrsesvspeps.ksaspsssptssnsskplisvass..skllaeksqepasl 135
                                    + +P  w         +++ s+s+ p++ ++e+ +pe s +++s+s++ ++++++kp  s +++  sk+++++s ++ ++
  gene138|gene138|rna138|rna138 230 ISSPLKWvlsksekkAEDTNSQSQPPKEIKQEKDNPESSsNEESSSEKKEKNTNKKPSRSHEPEisSKKIKKTSLKKTNS 309
                                    44555553222222233344444444444444444433321111111111222222222222210011111111111111 PP

                           SOBP 136 veaplepkkqrkkkpglrkpkqvkagsskssetkagllqkqqkalplsaelees 189
                                     + ++   ++++kk++ ++++++k+++s     k + l ++qk+   +a +ee+
  gene138|gene138|rna138|rna138 310 DNLVDL--EESEKKEEIEEHEKRKTNNSLEYLDKINSLRNDQKPREEEALMEEK 361
                                    111111..1111122222222222222222222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2308  (0.12873); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.35s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 2600.35
//
Query:       gene1381|gene1381|rna1380|rna1380  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-48  165.0   0.0    1.9e-48  164.5   0.0    1.2  1  MOZ_SAS          MOZ/SAS family
    0.00038   20.8   0.0     0.0008   19.8   0.0    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0033   17.0   1.2     0.0078   15.8   0.2    2.0  2  zf-MYST          MYST family zinc finger domain
     0.0084   16.0   0.0      0.016   15.1   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> MOZ_SAS  MOZ/SAS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.5   0.0   4.2e-52   1.9e-48       2     171 ..      99     260 ..      98     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 4.2e-52
                            MOZ_SAS   2 pGkeiYrk..eklsvfevdGekeklycqnLcllaklFldhktlyydvepFlfYvlteadeegahivGyFskekesa 75 
                                        pGk +Y +  e +s+ e+dG++e++ c+ +c + k F+ +ktly dv+ +lfYvl      g ++ G+Fskekes+
  gene1381|gene1381|rna1380|rna1380  99 PGKYVYIDekEGISILEIDGKNESVLCRRICTIGKGFIRRKTLYLDVDGYLFYVLF----CGGKLGGFFSKEKEST 170
                                        899999662267*******************************************9....567899*******766 PP

                            MOZ_SAS  76 eeynlaCilvlPpyqrkgyGklliefsYeLskrekkigtPekPlsdlgllsyrsywkeeilellkekekkkisiee 151
                                         e+nl+C+lvlPpy+ kgyG+l+i++sY L      +gtPekPls+ g++ y++yw++++l++lk+ +++++si++
  gene1381|gene1381|rna1380|rna1380 171 -EHNLSCLLVLPPYRSKGYGSLMIDLSYILG-----TGTPEKPLSKEGRTVYKKYWRNKVLNTLKKATEQEMSIKD 240
                                        .89**************************97.....6*************************************** PP

                            MOZ_SAS 152 isektgikeeDiistleelk 171
                                        is ++g++ +D i+ le l 
  gene1381|gene1381|rna1380|rna1380 241 ISAESGLSIDDTIHGLELLG 260
                                        **************999775 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.8e-07    0.0008       4      49 ..     149     198 ..     145     229 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.8e-07
                                        EEEEEEETTEEEEEEEEEEES...TCTEE..EEE-GGGTTSSHHHHHHHH..T CS
                     Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitr..laVdpeyrgkGiGraLlea..a 49 
                                         ++V+  +gk  Gf + +  +   ++     l V+p yr kG+G+ ++++  +
  gene1381|gene1381|rna1380|rna1380 149 LFYVLFCGGKLGGFFSKEK-EsteHN--LscLLVLPPYRSKGYGSLMIDLsyI 198
                                        5777766566645544333.244444..356*****************96321 PP

>> zf-MYST  MYST family zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.7e-06    0.0078      27      55 .]      66      94 ..      58      94 .. 0.90
   2 ?   -1.2   0.0      0.35   1.5e+03      41      55 .]     162     176 ..     161     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-06
                            zf-MYST 27 ankekLyvCefClkYmksakelerHkkkC 55
                                       ++k+ +y+C+ Cl  + ++ ++ +H+k+C
  gene1381|gene1381|rna1380|rna1380 66 SDKNVVYICDQCLLQYWDSVSFDNHRKDC 94
                                       67899********9999999********* PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.35
                            zf-MYST  41 YmksakelerHkkkC 55 
                                        +++++ke ++H  +C
  gene1381|gene1381|rna1380|rna1380 162 FFSKEKESTEHNLSC 176
                                        78999*******999 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.6e-06     0.016      19      73 ..     138     193 ..     117     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-06
                    Acetyltransf_10  19 pealrerieegealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLl 73 
                                        +++l+  +    +l++v+++ggk+ G+ +  ++ s    +s l V p yr++G+g+ ++
  gene1381|gene1381|rna1380|rna1380 138 RKTLYLDV--DGYLFYVLFCGGKLGGFFSKeKE-StehNLSCLLVLPPYRSKGYGSLMI 193
                                        55555554..7899**************77433.34779****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1811.44
//
Query:       gene1382|gene1382|rna1381|rna1381  [L=586]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-17   61.8   1.8    2.8e-14   53.6   0.6    2.3  2  Glyco_hydro_19  Chitinase class I
  ------ inclusion threshold ------
       0.29   11.4   2.4       0.69   10.2   1.5    2.0  2  GILT            Gamma interferon inducible lysosomal thiol re
        4.3    7.5   5.4        7.6    6.7   5.4    1.3  1  DUF5041         Domain of unknown function (DUF5041)


Domain annotation for each model (and alignments):
>> Glyco_hydro_19  Chitinase class I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.6   4.7e-18   2.8e-14      70     166 ..     437     535 ..     426     539 .. 0.85
   2 !    7.8   0.0   0.00045       2.7     186     225 ..     537     576 ..     532     584 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 4.7e-18
                     Glyco_hydro_19  70 taedgpyawGycfvkekgassdycessakwplaagkkyyGrGpiqlsynynygeaGqai..Gqdllnnpdlvatda 143
                                        +a+ +  ++Gy + +e + ++    + +  + a+gk+y+GrG iqls+  ny++aG+a+  G +l nnp++va+d+
  gene1382|gene1382|rna1381|rna1381 437 IAQCAHESGGYQYIEEIACAGGTGCAGQYGSGAPGKSYHGRGFIQLSWPDNYKAAGEALglGDELYNNPEKVAEDP 512
                                        5666777899***99998766665566677889************************752278************* PP

                     Glyco_hydro_19 144 vvsfktalwfwmtaqspkpschd 166
                                         +  + ++++w ++  ++p +++
  gene1382|gene1382|rna1381|rna1381 513 NLGADVSIYYWESKVANAPGVKE 535
                                        *************9999998765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00045
                     Glyco_hydro_19 186 GyGvitniingglecgkgedtrvedrigfyrrycdilgvd 225
                                         +G  t  ing lec+  + ++ ++r + y    + +g++
  gene1382|gene1382|rna1381|rna1381 537 HFGATTKAINGALECTGSNVDKSKKRYEIYTALVEAFGIS 576
                                        69**************9999*********99888777765 PP

>> GILT  Gamma interferon inducible lysosomal thiol reductase (GILT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.5   0.00012      0.69      54      76 ..      13      35 ..       8      72 .. 0.70
   2 ?   -2.4   0.0      0.95   5.7e+03      52      68 ..     540     556 ..     517     559 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                               GILT 54 ftCqhGeeECegNklqaCalell 76
                                         C  G++EC +N+l  C ++  
  gene1382|gene1382|rna1381|rna1381 13 NACVSGSAECVANTLRVCGIKNQ 35
                                       68****************99876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.95
                               GILT  52 leftCqhGeeECegNkl 68 
                                        ++ +  +G+ EC+g  +
  gene1382|gene1382|rna1381|rna1381 540 ATTKAINGALECTGSNV 556
                                        66777899999998665 PP

>> DUF5041  Domain of unknown function (DUF5041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.4    0.0013       7.6      33     116 ..     114     200 ..     112     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0013
                            DUF5041  33 deYkngkkidrvhefklGkniksleevpeerreairkeeliae.kkkeyelikelsiylrke.tDstavitisvPe 106
                                        de +  k+ +++++ ++G+ +   +e+   +r+ + +++  +e k+++ +  k ++ ++ ++ +Dst+++t++   
  gene1382|gene1382|rna1381|rna1381 114 DEGERKKNHGKMENGEIGEKRSPKNEIGKSKRQSLGEKNESKErKENKKKEPKTVTKTISTSrKDSTTTVTVTKIV 189
                                        677888999**************************88877665156778889*******9999*******998665 PP

                            DUF5041 107 va.kakqrlkl 116
                                        ++ ++ +++kl
  gene1382|gene1382|rna1381|rna1381 190 IQkQQPTEIKL 200
                                        55234445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1922  (0.107201); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.17u 0.36s 00:00:01.52 Elapsed: 00:00:00.56
# Mc/sec: 3138.51
//
Query:       gene1383|gene1383|rna1382|rna1382  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-16   61.2   0.3    3.2e-16   60.0   0.1    1.7  2  AAA              ATPase family associated with various cellul
    3.3e-15   56.2   0.2    8.9e-12   45.1   0.4    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    2.5e-10   40.6   0.0    7.9e-10   39.0   0.0    1.9  1  Rep_fac_C        Replication factor C C-terminal domain
    8.7e-09   35.6   0.1    2.6e-08   34.1   0.0    1.8  1  AAA_assoc_2      AAA C-terminal domain
    4.3e-08   33.5   0.4    0.00081   19.7   0.1    2.7  2  AAA_22           AAA domain
    3.5e-07   30.1   0.0    6.5e-07   29.3   0.0    1.4  1  AAA_24           AAA domain
    1.4e-06   28.2   0.0    3.4e-06   26.9   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.1e-06   27.3   0.0    6.3e-06   26.3   0.0    1.5  1  AAA_14           AAA domain
    4.1e-06   26.8   0.1    2.9e-05   24.1   0.0    2.2  2  Rad17            Rad17 P-loop domain
    4.8e-06   26.5   0.0    7.1e-06   25.9   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    9.8e-06   26.1   0.1     0.0025   18.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    1.9e-05   24.2   0.1       0.22   10.9   0.0    2.6  2  TniB             Bacterial TniB protein
    2.8e-05   24.0   0.6      0.073   12.9   0.1    2.4  2  AAA_11           AAA domain
    4.7e-05   22.9   0.0    0.00038   19.9   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0001   22.9   0.1    0.00028   21.4   0.0    1.9  2  AAA_18           AAA domain
    0.00017   21.6   0.0     0.0038   17.1   0.0    2.4  2  DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau do
     0.0002   21.5   0.0    0.00052   20.1   0.0    1.6  1  Sigma54_activ_2  Sigma-54 interaction domain
    0.00029   20.8   0.3     0.0012   18.9   0.3    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00038   20.0   0.0     0.0008   19.0   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
    0.00068   19.6   0.9       0.13   12.1   0.1    2.5  2  NTPase_1         NTPase
    0.00079   19.2   0.2       0.72    9.6   0.1    2.5  2  DEAD             DEAD/DEAH box helicase
     0.0012   18.6   0.2     0.0072   16.1   0.1    2.2  2  AAA_30           AAA domain
     0.0014   19.2   0.2     0.0049   17.4   0.2    2.1  1  ABC_tran         ABC transporter
     0.0029   17.3   0.0       0.14   11.8   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
     0.0037   17.6   0.6       0.02   15.2   0.6    2.3  1  AAA_19           AAA domain
     0.0039   17.6   0.0     0.0071   16.7   0.0    1.6  1  RNA_helicase     RNA helicase
      0.004   16.9   0.1     0.0099   15.7   0.0    1.6  2  DNA_pol3_delta   DNA polymerase III, delta subunit
     0.0043   16.9   0.0       0.01   15.7   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
     0.0091   16.2   0.7      0.043   14.0   0.7    2.1  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.013   15.0   0.1        2.4    7.6   0.0    2.3  2  PhoH             PhoH-like protein
      0.019   15.1   0.0      0.064   13.4   0.0    1.8  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.022   15.0   0.2      0.043   14.1   0.2    1.6  1  AAA_28           AAA domain
      0.022   13.8   0.2       0.04   13.0   0.0    1.6  2  T2SSE            Type II/IV secretion system protein
      0.024   14.1   0.2      0.056   12.9   0.2    1.7  1  KTI12            Chromatin associated protein KTI12
      0.026   13.7   0.0        0.1   11.7   0.0    1.8  2  DUF815           Protein of unknown function (DUF815)
      0.026   13.9   0.0       0.14   11.4   0.0    2.1  3  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.058   12.7   0.0       0.18   11.1   0.0    1.8  2  Zeta_toxin       Zeta toxin
      0.069   12.3   0.1        2.8    7.0   0.0    2.3  2  NB-ARC           NB-ARC domain
      0.089   12.4   0.4          1    8.9   0.1    2.2  2  AAA_25           AAA domain
      0.095   12.7   0.0          3    7.8   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit
        0.1   13.0   1.2       0.48   10.9   0.1    2.4  2  AAA_17           AAA domain
        0.1   12.3   0.0       0.24   11.1   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
       0.11   12.4   0.0        1.1    9.1   0.0    2.3  1  NACHT            NACHT domain
       0.13   12.2   0.0       0.26   11.3   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.19   11.7   1.9        2.3    8.3   1.9    2.1  1  SBDS_C           SBDS protein C-terminal domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   0.1     8e-19   3.2e-16       1     127 [.      38     150 ..      38     154 .. 0.86
   2 ?   -1.8   0.0       9.5   3.8e+03      42      57 ..     221     236 ..     189     283 .. 0.69

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 8e-19
                                        EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHH CS
                                AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidalak 72 
                                        +ll+GppGtGKT++ak +a++l   +  +le+++s+ +   +      i+ + ++ + k  + +i+++DE+d+++ 
  gene1383|gene1383|rna1382|rna1382  38 LLLSGPPGTGKTTCAKILARKLlpnKEGLLELNASDER--GIDTVRTTIKSFAQR-RIKDcGFKIIILDEADSMTA 110
                                        69*******************9776788**********..666666666666665.4444457***********99 PP

                                        HHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                                AAA  73 srsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                        +            ++++ ++++  ++   ++ +i+++n+  k+ +++  +R+ + 
  gene1383|gene1383|rna1382|rna1382 111 TA-----------QQAMRRVMEIHSS---ECRFILICNTLTKIFEPIQ-SRCAIL 150
                                        99...........***********99...69*****************.9*9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 9.5
                                        HHHHHHHHHHHHHHTS CS
                                AAA  42 sekkirelfkeakeka 57 
                                        s+k+i+++++++ e++
  gene1383|gene1383|rna1382|rna1382 221 SPKRIEKVLEKLMENN 236
                                        5556666665555444 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0036       1.4       2      47 ..      19      63 ..      18      68 .. 0.87
   2 !   45.1   0.4   2.2e-14   8.9e-12      84     162 ..      76     155 ..      67     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0036
                    DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallcee 47
                                       ++++++++  +++s  + h +L++G+ g+gk ++a+ la++ll ++
  gene1383|gene1383|rna1382|rna1382 19 NHTTIELIALIIESRDMPH-LLLSGPPGTGKTTCAKILARKLLPNK 63
                                       6788899999999999998.799*****************998665 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 2.2e-14
                    DNA_pol3_delta2  84 kldqirelieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                         +d++r  i+++ ++ ++    kiii+++a+ mt+ A+ a+ +++E  s++  fiLi +  +k+ ++i+SRc +l 
  gene1383|gene1383|rna1382|rna1382  76 GIDTVRTTIKSFAQRRIKdCGFKIIILDEADSMTATAQQAMRRVMEIHSSECRFILICNTLTKIFEPIQSRCAILM 151
                                        79****77776666555549******************************************************** PP

                    DNA_pol3_delta2 159 fspl 162
                                        f+++
  gene1383|gene1383|rna1382|rna1382 152 FERI 155
                                        9975 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0     2e-12   7.9e-10       1      85 [.     220     297 ..     220     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2e-12
                                        --HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH CS
                          Rep_fac_C   1 phpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGa 76 
                                        p p+ ie++le+++++++eea + ++ +++++ + + d++  +++  k++e        ++l+++g +  r++eG+
  gene1383|gene1383|rna1382|rna1382 220 PSPKRIEKVLEKLMENNVEEALEMFD-KIWDEKFDPLDLIGSFFKAAKNME------NYDLLKVIGLANLRISEGV 288
                                        78***********99**********7.**********************96......899**************** PP

                                        -HHHHHHHH CS
                          Rep_fac_C  77 sehlqlsal 85 
                                        +++lq  ++
  gene1383|gene1383|rna1382|rna1382 289 NSRLQFYGM 297
                                        *****9887 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   6.6e-11   2.6e-08       3      71 ..     171     253 ..     169     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 6.6e-11
                                        X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...............XXXXXXXXXXXXXXXXXXXXXXXX CS
                        AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak..............egkieitledleealqrkalryDk 64 
                                        + +k++++al++++el+dGD+R+ Ln+L+++++++e+               ++ +++ ++ +e+ ++++  ++Dk
  gene1383|gene1383|rna1382|rna1382 171 EGIKINREALDLIVELSDGDMRQSLNILQACINSSETIdqnrivkiiglpspKRIEKVLEKLMENNVEEALEMFDK 246
                                        5699****************************99987789999999999998888888899999999999999999 PP

                                        XXXXHHH CS
                        AAA_assoc_2  65 agdehYd 71 
                                          de +d
  gene1383|gene1383|rna1382|rna1382 247 IWDEKFD 253
                                        9998886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1     2e-06   0.00081       7      63 ..      37      87 ..      32      93 .. 0.76
   2 !   12.1   0.1   0.00044      0.18      81     128 ..      87     132 ..      73     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2e-06
                             AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellra 63
                                       +l++ G++GtGKTt+++ l+++l         + ++++ +++ + + +++++ + ++
  gene1383|gene1383|rna1382|rna1382 37 HLLLSGPPGTGKTTCAKILARKLLPN------KEGLLELNASDERGIDTVRTTIKSF 87
                                       799*******************9643......6666677777777666666666655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00044
                             AAA_22  81 aleqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLv 128
                                          ++ +++++  +++i+DEa+ + +++a +  r+ ++++++ +++iL+
  gene1383|gene1383|rna1382|rna1382  87 FAQRRIKDCGF-KIIILDEADSM-TATAQQAMRRVMEIHSSECRFILI 132
                                        56788889999.***********.888888888888888899999987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.6e-09   6.5e-07       5      93 ..      38     124 ..      35     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.6e-09
                             AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtideleel 80 
                                        +l+ Gp+g+GKTt+ak l  + l+ + e+ l +l+a +   i ++ + ++ +++ + ++ ++k++++D +d +   
  gene1383|gene1383|rna1382|rna1382  38 LLLSGPPGTGKTTCAKIL-ARKLLPNKEG-LLELNASDERGIDTVRTTIKSFAQRRIKDCGFKIIILDEADSMTAT 111
                                        6899**************.****999998.99999999999999******************************99 PP

                             AAA_24  81 claevirqnekae 93 
                                        + + ++r  e+++
  gene1383|gene1383|rna1382|rna1382 112 AQQAMRRVMEIHS 124
                                        9999998877755 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   8.5e-09   3.4e-06       2      57 ..       9      59 ..       8      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.5e-09
                             RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                       rP+ +++ +g ++  e ++++ie+     + + h+ll+GpPG Gktt aki+a++l
  gene1383|gene1383|rna1382|rna1382  9 RPNGVQDIVGNHTTIELIALIIES-----RDMPHLLLSGPPGTGKTTCAKILARKL 59
                                       899999999999999999999875.....4578********************987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.6e-08   6.3e-06       5      97 ..      38     131 ..      34     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.6e-08
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev.pe 78 
                                        l+++G+  +GKTt +k l+++ll +ke  l++n  der  +   +   ++ + ++ +k+ + ++++lDE+  +  +
  gene1383|gene1383|rna1382|rna1382  38 LLLSGPPGTGKTTCAKILARKLLPNKEGLLELNASDERGIDTVRT--TIKSFAQRrIKDCGFKIIILDEADSMtAT 111
                                        7899*******************999**********999765544..3455555448887899*******876257 PP

                             AAA_14  79 wekalkslvdeg.knldviv 97 
                                        +++a++++++ + +++++i+
  gene1383|gene1383|rna1382|rna1382 112 AQQAMRRVMEIHsSECRFIL 131
                                        89999999984446788776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   7.4e-08   2.9e-05       9      72 ..       4      62 ..       1      89 [. 0.83
   2 ?   -0.2   0.1       2.1   8.3e+02     134     173 ..      98     135 ..      89     146 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.4e-08
                              Rad17  9 WfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgik 72
                                        ++ky+P+  +++      ie +     a ++esr    LL+sGP+G gk+t  k+L+++l ++
  gene1383|gene1383|rna1382|rna1382  4 LVNKYRPNGVQDIVGNHTTIELI-----ALIIESRDMPHLLLSGPPGTGKTTCAKILARKLLPN 62
                                       57899999999998887877755.....667777777789******************998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.1
                              Rad17 134 klilvedlPnkfyrdsdalrevirkylrssealplilvit 173
                                        k+i++++  +   +  +a+r v+   ++sse+  ++++ t
  gene1383|gene1383|rna1382|rna1382  98 KIIILDEADSMTATAQQAMRRVME--IHSSECRFILICNT 135
                                        889999998888888888888875..77888855555554 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.8e-08   7.1e-06       3      73 ..      40     107 ..      38     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.8e-08
                    Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEyll 73 
                                         +G pG GK+t+ + l+r+   l +n++    l+++ ++  +    t++sf + ++k++++ki+ilDE+ +
  gene1383|gene1383|rna1382|rna1382  40 LSGPPGTGKTTCAKILARK---LLPNKEGLLELNASDERGIDTVRTTIKSFAQRRIKDCGFKIIILDEADS 107
                                        6899*******99999999...899***999999999999999999**********************855 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.3e-06    0.0025      22      51 ..      33      62 ..      17      74 .. 0.80
   2 ?    5.2   0.0     0.062        25     118     169 ..      79     131 ..      66     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.3e-06
                             AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                        + + +llsG++G+GK++ ++ l+r l  +
  gene1383|gene1383|rna1382|rna1382 33 RDMPHLLLSGPPGTGKTTCAKILARKLLPN 62
                                       34489****************999988876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.062
                             AAA_16 118 rllellkrll.allsrderplvlvlDdlqwadeaslqllaaLlrllesk.pllv 169
                                         ++ ++k+++ ++++      +++lD+++   ++ +q+++  ++  +s  ++++
  gene1383|gene1383|rna1382|rna1382  79 TVRTTIKSFAqRRIKD-CGFKIIILDEADSMTATAQQAMRRVMEIHSSEcRFIL 131
                                        4566677777444444.6678********************9999998766665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00056      0.22      31      59 ..      31      59 ..      18      69 .. 0.80
   2 !   10.4   0.1   0.00077      0.31     108     144 ..      85     121 ..      66     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                               TniB 31 krkrmpnlllvGdsnnGKtmivekFarlh 59
                                       ++ +mp+lll G++ +GKt+ ++  ar+ 
  gene1383|gene1383|rna1382|rna1382 31 ESRDMPHLLLSGPPGTGKTTCAKILARKL 59
                                       6789****************998777665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00077
                               TniB 108 eqqvlrllrelkvrvLiiDEihnllagsarkqrefln 144
                                        ++ + r +++++ +++i+DE +++ a  +++ r++++
  gene1383|gene1383|rna1382|rna1382  85 KSFAQRRIKDCGFKIIILDEADSMTATAQQAMRRVME 121
                                        455667899****************999999998875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00018     0.073      18      42 ..      34      60 ..      19      75 .. 0.72
   2 !    9.2   0.1    0.0023      0.92     197     226 ..      78     105 ..      68     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                             AAA_11 18 e..itliqGPPGtgKTktivellsqll 42
                                       +    l++GPPGtgKT+    l ++ll
  gene1383|gene1383|rna1382|rna1382 34 DmpHLLLSGPPGTGKTTCAKILARKLL 60
                                       444479**********98877777775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0023
                             AAA_11 197 eivltTlsgagsklleklakkfdvviIDEA 226
                                        + v tT  + ++++++++  +f+++i DEA
  gene1383|gene1383|rna1382|rna1382  78 DTVRTTIKSFAQRRIKDC--GFKIIILDEA 105
                                        6799**************..9********9 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.6e-07   0.00038       3      58 ..      14      72 ..      12      95 .. 0.69
   2 ?    0.1   0.0       1.1   4.2e+02     109     132 ..      99     122 ..      96     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.6e-07
                       Mg_chelatase  3 kdvkGqeeakr..aleiaaaGgHnlllvGppGsGKtmlakrlp.sllpplseeealeva 58
                                       +d++G++++ +  al i      +lll GppG+GKt  ak l+ +llp+ +    l+++
  gene1383|gene1383|rna1382|rna1382 14 QDIVGNHTTIEliALIIESRDMPHLLLSGPPGTGKTTCAKILArKLLPNKEGLLELNAS 72
                                       677777777652255566666789****************9963688876655445444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                       Mg_chelatase 109 vLfLDElpefkrkvlevLRePled 132
                                        +++LDE+  +++++ +++R+ +e 
  gene1383|gene1383|rna1382|rna1382  99 IIILDEADSMTATAQQAMRRVMEI 122
                                        689****************99985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     7e-07   0.00028       2      25 ..      39      80 ..      38     178 .. 0.70
   2 ?   -1.1   0.0       6.7   2.7e+03      35      35 ..     217     217 ..     157     259 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7e-07
                             AAA_18  2 lltGtpGvGKttlakeLskrl.gf.................g 25
                                       ll+G+pG+GKtt ak L+++l  +                 +
  gene1383|gene1383|rna1382|rna1382 39 LLSGPPGTGKTTCAKILARKLlPNkegllelnasdergidtV 80
                                       699***************998665765554454444444442 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6.7
                             AAA_18  35 n 35 
                                         
  gene1383|gene1383|rna1382|rna1382 217 I 217
                                        0 PP

>> DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.53   2.1e+02      16      42 ..     177     203 ..     172     205 .. 0.87
   2 !   17.1   0.0   9.6e-06    0.0038       2      65 ..     209     272 ..     208     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.53
                    DNA_pol3_gamma3  16 arlldlleallegdaaaalaelreqya 42 
                                        ++ ldl+ +l +gd+++ l+ l+++++
  gene1383|gene1383|rna1382|rna1382 177 REALDLIVELSDGDMRQSLNILQACIN 203
                                        5679*****************999876 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 9.6e-06
                    DNA_pol3_gamma3   2 saaqVrdmLGladrarlldlleallegdaaaalaelreqyaaGadpvvvlrdLlellhqltllk 65 
                                        +++++ +++Gl + +r+ ++le+l+e ++++al+ +++++++ +dp  ++ ++   ++++ +++
  gene1383|gene1383|rna1382|rna1382 209 DQNRIVKIIGLPSPKRIEKVLEKLMENNVEEALEMFDKIWDEKFDPLDLIGSFFKAAKNMENYD 272
                                        678999****************************************988888877777766555 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.3e-06   0.00052      19     108 ..      33     134 ..      20     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.3e-06
                                        T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H.............HHHHHHTTTSEEEEEE-TT- CS
                    Sigma54_activ_2  19 qsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp.............ldlleqakggtLylkdiadl 81 
                                        + +  ++l G++G+gk+++A++L+ +  p+ e   + + +++              ++ ++     +++l + +++
  gene1383|gene1383|rna1382|rna1382  33 RDMPHLLLSGPPGTGKTTCAKILARKLLPNKEGLLELNASDERgidtvrttiksfaQRRIKDCGFKIIILDEADSM 108
                                        567789****************99877776654333333332233334555433333333335778999******* PP

                                        -HHHHHHHHHHHHHHTTTT-EEEEEEE CS
                    Sigma54_activ_2  82 skaeqkeLlellakaeksslrlVstss 108
                                         + +q+ +  +++    s++r++ ++ 
  gene1383|gene1383|rna1382|rna1382 109 TATAQQAMRRVMEIH-SSECRFILICN 134
                                        *******99988877.89999987764 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.3   2.9e-06    0.0012       1      28 [.      37      66 ..      37     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.9e-06
                                       EEEEE--SSSSHHHHHHHGGGGB..S--EE CS
                              AAA_5  1 dvlLvGppGtgKselaerlaaal..nreve 28
                                       ++lL GppGtgK++ a+ la+ l  n+e +
  gene1383|gene1383|rna1382|rna1382 37 HLLLSGPPGTGKTTCAKILARKLlpNKEGL 66
                                       79*******************998766554 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     2e-06    0.0008      34      92 ..      36      94 ..      15      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2e-06
                              AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkg 92
                                        ++ll Gp GtGKt+++k l +kl ++k   l +n s      +++++i+s  ++r k+
  gene1383|gene1383|rna1382|rna1382 36 PHLLLSGPPGTGKTTCAKILARKLLPNKEGLLELNASDERGIDTVRTTIKSFAQRRIKD 94
                                       4899***********************************************99999875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00033      0.13       1      23 [.      37      59 ..      37      65 .. 0.89
   2 ?    5.6   0.1     0.035        14      91     146 ..      90     145 ..      69     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00033
                                       EEEEE--TTSSHHHHHHHHHHHH CS
                           NTPase_1  1 kvfiTGppGvGKtTlvkkvlell 23
                                       +++++GppG+GKtT+ k ++++l
  gene1383|gene1383|rna1382|rna1382 37 HLLLSGPPGTGKTTCAKILARKL 59
                                       689************99988887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.035
                                        HHHHHH-..EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT CS
                           NTPase_1  91 kalsead..viviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeire 146
                                        + +++++  +i++DE  +m  ++++  + v e+ +se  ++ +       ++ e i++
  gene1383|gene1383|rna1382|rna1382  90 RRIKDCGfkIIILDEADSMTATAQQAMRRVMEIHSSECRFILICNTL--TKIFEPIQS 145
                                        334556577************************99999988877665..345555555 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0092       3.7       6      39 ..      24      60 ..      20      76 .. 0.76
   2 !    9.6   0.1    0.0018      0.72     114     152 ..      89     125 ..      67     141 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0092
                                       HHHHHHHTTCEE...EEEESTTSSHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  6 eaiplilgggdv...lvaaeTGsGKTlaflipvlqiv 39
                                       e i li++ +d+   l++++ G+GKT+++ i + + +
  gene1383|gene1383|rna1382|rna1382 24 ELIALIIESRDMphlLLSGPPGTGKTTCAKILARKLL 60
                                       5677777776542227************999877655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                                        CTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 114 tgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                        +++++   +++++lDEad +     ++ ++r+++ +++ 
  gene1383|gene1383|rna1382|rna1382  89 QRRIKDCGFKIIILDEADSMTAT-AQQAMRRVME-IHSS 125
                                        34533344578**********98.7778888554.4333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.8e-05    0.0072      21     110 ..      38     121 ..      23     134 .. 0.66
   2 ?   -2.5   0.0         9   3.6e+03     145     181 ..     207     244 ..     189     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-05
                             AAA_30  21 avltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepg.tlliv 94 
                                         +l Gp+GtGKtt  k l r+++ +++g + + A+ ++  ++++        ti+++ +r  +    + g +++i 
  gene1383|gene1383|rna1382|rna1382  38 LLLSGPPGTGKTTCAKILaRKLLPNKEGLLELNASDERGIDTVR-------TTIKSFAQRRIK----DCGfKIIIL 102
                                        5789*************978888888888889999888888888.......455555533222....234589999 PP

                             AAA_30  95 DEa.gmv..dtkqlaallk 110
                                        DEa +m+  +++ ++++++
  gene1383|gene1383|rna1382|rna1382 103 DEAdSMTatAQQAMRRVME 121
                                        9984444323333444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9
                             AAA_30 145 gigtaeLtevvRqke.seeraaalalregdaeealeal 181
                                        +i++ ++ +++   + ++++++ ++l e+++eeale++
  gene1383|gene1383|rna1382|rna1382 207 TIDQNRIVKIIGLPSpKRIEKVLEKLMENNVEEALEMF 244
                                        44555555555554446778888888888888888776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   1.2e-05    0.0049      14      92 ..      38     119 ..      33     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-05
                                        EEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGGB-HHHCCHCEEEE-SS...--S-TTSBHHHH.HHHTC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxx RF
                           ABC_tran  14 vaivGenGaGKStLlkllagllkp.teGeilldgkdlkeqeleslrkeigvlpqe...pqlfpeltvren.esdee 84 
                                        + + G+ G+GK+t +k+la++l p +eG ++l+   ++e+ +  +r  i+ + q    ++ f+ + + e   +++ 
  gene1383|gene1383|rna1382|rna1382  38 LLLSGPPGTGKTTCAKILARKLLPnKEGLLELN--ASDERGIDTVRTTIKSFAQRrikDCGFKIIILDEAdSMTAT 111
                                        5689****************9999456666555..55555577777777777777543333443423333533334 PP

                                        HHHHHHHS CS
                                        xxxxxxxx RF
                           ABC_tran  85 iekalskl 92 
                                        +++a++++
  gene1383|gene1383|rna1382|rna1382 112 AQQAMRRV 119
                                        44444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00035      0.14      12      59 ..      23      72 ..      17      77 .. 0.79
   2 ?    3.1   0.0      0.17        70      96     119 ..      99     122 ..      88     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                                       HHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT CS
                    Sigma54_activat 12 leqikkvaktd..lsvlitGesGtGKellaraiheaskrkekpfvavnca 59
                                       +e i+ +++++   ++l+ G  GtGK+++a+ + ++   +++ ++++n +
  gene1383|gene1383|rna1382|rna1382 23 IELIALIIESRdmPHLLLSGPPGTGKTTCAKILARKLLPNKEGLLELNAS 72
                                       55555566555446899****************99999898888888876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.17
                                        EEEEETGGGS-HHHHHHHHHHHHH CS
                    Sigma54_activat  96 tlfLDeigelplelQekLlrvlqe 119
                                        ++ LDe  ++++++Q+ + rv++ 
  gene1383|gene1383|rna1382|rna1382  99 IIILDEADSMTATAQQAMRRVMEI 122
                                        799***************999985 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.6     5e-05      0.02       9     126 ..      34     202 ..      27     214 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-05
                             AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae................ 68 
                                          ++ll+ ++pGtGKT++ k   + l+ +++     + l a  +r  + +r+ ++++ ++                
  gene1383|gene1383|rna1382|rna1382  34 DMPHLLLSGPPGTGKTTCAKILARKLLPNKEG---LLELNASDERGIDTVRTTIKSFAQRrikdcgfkiiildead 106
                                        567899************99999998888754...33344555555555555555544445555555555555544 PP

                             AAA_19  69 ........atTiHrlal......................................ldfddlltealelle..eaee 96 
                                                a       +                                      +d  +     l+ l+  +++e
  gene1383|gene1383|rna1382|rna1382 107 smtataqqA-------MrrvmeihssecrfilicntltkifepiqsrcailmferIDHST----ILGRLReiSNDE 171
                                        332222220.......24444444444555555555555555555555554332211111....222333344444 PP

                             AAA_19  97 ekklqeeellivDEfqdvd.elqyrLlkall 126
                                          k+++e+l ++ E +d d  +  ++l+a+ 
  gene1383|gene1383|rna1382|rna1382 172 GIKINREALDLIVELSDGDmRQSLNILQACI 202
                                        4555445544555666666555566666655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.8e-05    0.0071       2      25 ..      39      62 ..      38     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.8e-05
                       RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                       +l+Gp+g+GK+t+ak La++ll +
  gene1383|gene1383|rna1382|rna1382 39 LLSGPPGTGKTTCAKILARKLLPN 62
                                       799*****************9933 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.5e-05    0.0099      59     170 ..      98     199 ..      96     202 .. 0.91
   2 ?   -2.5   0.0       9.8   3.9e+03      66      87 ..     222     244 ..     211     250 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.5e-05
                                        EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHH CS
                     DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkw 134
                                        +i++l+ +      ++ ++  ++++ ++++  + ++ +ili++  l+   k++  ++++  ++ +++ + + +   
  gene1383|gene1383|rna1382|rna1382  98 KIIILDEA------DSMTATAQQAMRRVMEIHSSECRFILICN-TLT---KIFEPIQSRCAILMFERIDHSTILGR 163
                                        67777777......5689999999*******************.666...9************************* PP

                                        HHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                     DNA_pol3_delta 135 iqkraqelglkiekealelLlelvennlsaikqele 170
                                        + ++++++g+ki +eal+l++el+ +++++  + l+
  gene1383|gene1383|rna1382|rna1382 164 LREISNDEGIKINREALDLIVELSDGDMRQSLNILQ 199
                                        ****************************99877776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.8
                                        -......TT-S-TTHHHHHHHHT CS
                     DNA_pol3_delta  66 pkllt.kesklnekllkeLeeyl 87 
                                        pk ++   +kl+e++++e  e++
  gene1383|gene1383|rna1382|rna1382 222 PKRIEkVLEKLMENNVEEALEMF 244
                                        44444333444444444444444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-05      0.01       1      87 [.      37     121 ..      37     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-05
                              AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkk.Gpvfanllladeinrap 75 
                                        h+ll g PG++kt+ +k la++l  + + +    +l  sd  G++ ++++ k+f  ++      ++++ de +  +
  gene1383|gene1383|rna1382|rna1382  37 HLLLSGPPGTGKTTCAKILARKLLPNKEGL---LELNASDERGIDTVRTTIKSFAQRRiKDCGFKIIILDEADSMT 109
                                        99*******************998877765...4778889999998888888887665245566888999999999 PP

                              AAA_3  76 pktqsalleame 87 
                                        + +q a+  +me
  gene1383|gene1383|rna1382|rna1382 110 ATAQQAMRRVME 121
                                        999999999997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.7   0.00011     0.043       3      24 ..      39      60 ..      38     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00011
                             AAA_33  3 llvGlpGsGKstlaerllkklg 24
                                       ll G+pG+GK+t a+ l++kl 
  gene1383|gene1383|rna1382|rna1382 39 LLSGPPGTGKTTCAKILARKLL 60
                                       688**************99875 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0059       2.4      22      47 ..      38      63 ..      19      65 .. 0.79
   2 ?    5.1   0.1     0.033        13     121     151 ..      98     131 ..      74     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0059
                                       EEEE--TTSSTTHHHHHHHHHHHHTT CS
                               PhoH 22 vfaiGpaGtGKtylavalavealkkk 47
                                       +   Gp GtGKt  a  la ++l +k
  gene1383|gene1383|rna1382|rna1382 38 LLLSGPPGTGKTTCAKILARKLLPNK 63
                                       5678************9999988776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.033
                                        EEEEE-SGGG--HH...HHHHHHTTB-TT-EEEE CS
                               PhoH 121 afvilDEAQnttke...qmkmfltRlGenskvvv 151
                                        +++ilDEA ++t +    m+ ++    +++++++
  gene1383|gene1383|rna1382|rna1382  98 KIIILDEADSMTATaqqAMRRVMEIHSSECRFIL 131
                                        68*******9986511145555555566677665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00016     0.064       5      84 ..      37     113 ..      33     122 .. 0.78
   2 ?   -1.5   0.0       6.1   2.4e+03     117     157 ..     190     238 ..     184     246 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                                        -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGG CS
                              AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEid 78 
                                         +ll gp g+Gkt  ak la+ l   +++ l  ++as+    + v+++++++ + +  +      G  i+ lDE d
  gene1383|gene1383|rna1382|rna1382  37 HLLLSGPPGTGKTTCAKILARKLL-PNKEGLLELNASDERGIDTVRTTIKSFAQRRIKDC-----GfkIIILDEAD 106
                                        6799*******************9.8***********99996777777766666555544.....4459999*999 PP

                                        G----.- CS
                              AAA_2  79 Kihpk.e 84 
                                          +++ +
  gene1383|gene1383|rna1382|rna1382 107 SMTATaQ 113
                                        8888543 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.1
                                        E-TT-EEEEEE--TTHHHHTTTS-S........TTTTSGGG--HHHHHH CS
                              AAA_2 117 dtknilfImtgafgsskisdesrsk........eeeeekkkeeveeelk 157
                                        d ++ l I+   ++ss+++d++r+         ++ e+  ++ +e++++
  gene1383|gene1383|rna1382|rna1382 190 DMRQSLNILQACINSSETIDQNRIVkiiglpspKRIEKVLEKLMENNVE 238
                                        5677777888888888888877776677777663333333333333333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   0.00011     0.043       3      22 ..      39      58 ..      37     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00011
                             AAA_28  3 vitGgestGKTtlleaLaar 22
                                        ++G+++tGKTt ++ La++
  gene1383|gene1383|rna1382|rna1382 39 LLSGPPGTGKTTCAKILARK 58
                                       589**************965 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001      0.04     108     160 ..      16      66 ..       5     121 .. 0.79
   2 ?   -2.8   0.0       6.3   2.5e+03      18      53 ..     151     186 ..     139     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                              T2SSE 108 lgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                        ++ ++++ e ia ++++       +l+sG+ g+GKtt + +l  ++  ++e +
  gene1383|gene1383|rna1382|rna1382  16 IVGNHTTIELIALIIESR--DMPHLLLSGPPGTGKTTCAKILARKLLPNKEGL 66 
                                        555555555555555555..66789**************99988776665655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.3
                              T2SSE  18 hvekpervkvrervdgielreveelekaalerlisr 53 
                                        ++e+ ++  +  r+ +i+ +e  +++++al  +++ 
  gene1383|gene1383|rna1382|rna1382 151 MFERIDHSTILGRLREISNDEGIKINREALDLIVEL 186
                                        555555555545555566666666666665555544 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00014     0.056       1      28 [.      35      62 ..      35     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                                       E.EEEEE--TTSSHHHHHHHHHHHHHHT CS
                              KTI12  1 MpLvvltGlPssGKstrakeLakaleee 28
                                       Mp ++l+G P +GK+t ak La++l  +
  gene1383|gene1383|rna1382|rna1382 35 MPHLLLSGPPGTGKTTCAKILARKLLPN 62
                                       999*******************998654 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00026       0.1      51     110 ..      33      92 ..      21     103 .. 0.90
   2 ?   -1.5   0.0       2.7   1.1e+03      99     117 ..     119     137 ..      88     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00026
                             DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfi 110
                                        +   ++LL G  GtGK ++ k l +++  ++  l+e++ +d + ++++ +++++ ++r i
  gene1383|gene1383|rna1382|rna1382  33 RDMPHLLLSGPPGTGKTTCAKILARKLLPNKEGLLELNASDERGIDTVRTTIKSFAQRRI 92 
                                        556799***********************************9999999999999888765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                             DUF815  99 vellrerperfilfvDDLs 117
                                        v +++++++rfil +  L+
  gene1383|gene1383|rna1382|rna1382 119 VMEIHSSECRFILICNTLT 137
                                        3457788999999998775 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00036      0.14      30      59 ..      27      55 ..      14      63 .. 0.85
   2 ?   -1.9   0.0       4.3   1.7e+03     137     171 ..      87     124 ..      73     163 .. 0.66
   3 ?   -1.9   0.0       4.3   1.7e+03     102     124 ..     222     245 ..     211     288 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                                       EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                       FtsK_SpoIIIE 30 plvldlkkmashllvaGatgsGKStalntL 59
                                       +l+++ + m+ hll+ G +g+GK+t+ + L
  gene1383|gene1383|rna1382|rna1382 27 ALIIESRDMP-HLLLSGPPGTGKTTCAKIL 55
                                       5678899999.**************97765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
                                        HHHHHHHTT---B-TT-...................... CS
                       FtsK_SpoIIIE 137 eiaedpldifgdvflvlDnyddlaaene....ritsLsn 171
                                         +++ ++d  g+  ++lD+ d++ a  +    r++++ +
  gene1383|gene1383|rna1382|rna1382  87 FAQRRIKD-CGFKIIILDEADSMTATAQqamrRVMEIHS 124
                                        44444455.466677777777766665555666665554 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.3
                                        HHHHHHHHHHHH.HHHHHHHHHHH CS
                       FtsK_SpoIIIE 102 peralraleeLv.kemeeryalfr 124
                                        p+r+ ++le+L+ + +ee+ ++f+
  gene1383|gene1383|rna1382|rna1382 222 PKRIEKVLEKLMeNNVEEALEMFD 245
                                        555555555554133444444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00044      0.18      19      52 ..      38      72 ..      27     121 .. 0.84
   2 ?   -0.9   0.0       2.2   8.6e+02     113     155 ..      88     131 ..      74     163 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                         Zeta_toxin 19 illgGqpGAGKselaellkdele.rqgnvvrldpD 52
                                       +ll+G pG GK++ a+ l+++l  ++++ ++l++ 
  gene1383|gene1383|rna1382|rna1382 38 LLLSGPPGTGKTTCAKILARKLLpNKEGLLELNAS 72
                                       589*****************998677888888764 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.2
                         Zeta_toxin 113 laealkkaGYevevvvvavkkelSrlgvldRyeeevae.gRlvp 155
                                        +++++k+ G+++ ++  a +   ++++++ R++e + +  R++ 
  gene1383|gene1383|rna1382|rna1382  88 AQRRIKDCGFKIIILDEADSMTATAQQAMRRVMEIHSSeCRFIL 131
                                        45666777888888777777777888888888777433247665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0071       2.8      14      43 ..      31      58 ..      20     131 .. 0.83
   2 ?    3.2   0.1       0.1        42      92     130 ..     225     267 ..     181     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0071
                                       CTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                             NB-ARC 14 ekdelqslvvalvGmgGvGKttlakqilnk 43
                                       e+ ++    + l+G +G GKtt ak   +k
  gene1383|gene1383|rna1382|rna1382 31 ESRDMP--HLLLSGPPGTGKTTCAKILARK 58
                                       455555..7899**********99866655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                                        HHHHHHHHCCCT..TEEEEEEEE-SHHH..H.....HHHHCHT CS
                             NB-ARC  92 lkrklvrlLltk..rfllvlDDVweeed..wdkigvvlparen 130
                                        +++ l +l+++     l ++D +w+e+   +d ig  ++a +n
  gene1383|gene1383|rna1382|rna1382 225 IEKVLEKLMENNveEALEMFDKIWDEKFdpLDLIGSFFKAAKN 267
                                        4555666777767788999******998899999999998776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0025         1      37      58 ..      39      60 ..      34      76 .. 0.83
   2 ?    1.1   0.0      0.65   2.6e+02     134     157 ..      89     111 ..      70     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                             AAA_25 37 llaGapgtGKttlaldlalava 58
                                       ll G+pgtGKtt a  la +++
  gene1383|gene1383|rna1382|rna1382 39 LLSGPPGTGKTTCAKILARKLL 60
                                       89**********9988887766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.65
                             AAA_25 134 eaaieevegvrlvviDplsralgg 157
                                        +++i++ +g + +++D  +++++ 
  gene1383|gene1383|rna1382|rna1382  89 QRRIKD-CGFKIIILDEADSMTAT 111
                                        689999.89*******99998875 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0074         3      19      51 ..      30      62 ..      14      71 .. 0.77
   2 ?    2.5   0.0      0.33   1.3e+02     127     159 ..      91     125 ..      68     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0074
                                       ....TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                             ResIII 19 lkskrdkrglikmaTGtGKTlvaaklierllkk 51
                                       ++s++  ++l+  + GtGKT +a  l+++ll +
  gene1383|gene1383|rna1382|rna1382 30 IESRDMPHLLLSGPPGTGKTTCAKILARKLLPN 62
                                       4445667999************98888777655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.33
                                        HHHTTT-SEEEEETGGGTTS...TTTHHHHHT--- CS
                             ResIII 127 ellrdrfdviiiDEaHrlgak..kswreilekfke 159
                                        + ++  f++ii DEa  ++a   +++r+++e  ++
  gene1383|gene1383|rna1382|rna1382  91 RIKDCGFKIIILDEADSMTATaqQAMRRVMEIHSS 125
                                        45556788999999999888643488888776554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0012      0.48       2      22 ..      42      67 ..      41     131 .. 0.85
   2 ?    0.1   0.1       2.5   9.9e+02      30      97 ..     164     237 ..     154     254 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                                       E-TTSSHHHHHHHHHHHH.....TEE CS
                             AAA_17  2 GgPGsGKgtqceklveky.....gft 22
                                       G+PG GK+t ++ l++k+     g+ 
  gene1383|gene1383|rna1382|rna1382 42 GPPGTGKTTCAKILARKLlpnkeGLL 67
                                       9**********999999755555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.5
                                        HHHHHHTTTSHSSHHHHC......TSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHH CS
                             AAA_17  30 lreeakrgglakardemr......klpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevl 97 
                                        lre  +++g + +r++++      ++++++   +++  +++ +  ++++ v + g p+ k+ ++ l++l ++ +
  gene1383|gene1383|rna1382|rna1382 164 LREISNDEGIKINREALDlivelsDGDMRQSLNILQACINSSETIDQNRIVKIIGLPSPKRIEKVLEKLMENNV 237
                                        55555566655555555544433344444444444444444444446666777777777776777766665544 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0006      0.24      49     122 ..      37     110 ..      21     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0006
                          IstB_IS21  49 nivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpl 122
                                         ++l Gp+G+GK+  a  l+++   +    l + ++d      +  +  ++a++  +   ++++ilD+    + 
  gene1383|gene1383|rna1382|rna1382  37 HLLLSGPPGTGKTTCAKILARKLLPNKEGLLELNASDERGIDTVRTTIKSFAQRRIKDCGFKIIILDEADSMTA 110
                                        57999***************999876666655555554433334444556665555566677888887765544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0028       1.1       3      24 ..      38      59 ..      37     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                                       EEEEC-TTTCHHHHHHHHHHHH CS
                              NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                       ++l G++G GKTt ++ la+++
  gene1383|gene1383|rna1382|rna1382 38 LLLSGPPGTGKTTCAKILARKL 59
                                       6899************999887 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00065      0.26      19      43 ..      35      59 ..      17      64 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00065
                                       TEEEEEEESTTSSHHHHHHHHHHHT CS
                               TsaE 19 gdvilLeGdLGaGKTtlvrglakal 43
                                          +lL+G+ G+GKTt ++ la++l
  gene1383|gene1383|rna1382|rna1382 35 MPHLLLSGPPGTGKTTCAKILARKL 59
                                       3359*****************9987 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.9    0.0058       2.3      27      77 ..      88     191 ..      44     239 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0058
                                        HHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-............................. CS
                             SBDS_C  27 IekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsi.......................... 76 
                                         ++ +k++g+++ + + a+s  + + +a+++ ++i+  + r  ++c+t                            
  gene1383|gene1383|rna1382|rna1382  88 AQRRIKDCGFKIIILDEADSMTATAQQAMRRVMEIHSSECRFILICNTLTkifepiqsrcailmferidhstilgr 163
                                        556689****************************************976667777777777777777776666666 PP

                                        ...........................C CS
                             SBDS_C  77 ...........................k 77 
                                                                    
  gene1383|gene1383|rna1382|rna1382 164 lreisndegikinrealdlivelsdgdM 191
                                        6666666666665555555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.50
# Mc/sec: 1855.13
//
Query:       gene1384|gene1384|rna1383|rna1383  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.028   14.8   0.0      0.031   14.7   0.0    1.2  1  AAA_16         AAA ATPase domain
      0.055   12.4   0.0      0.087   11.7   0.0    1.3  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
        0.1   12.1   0.4       0.22   11.0   0.3    1.6  1  AAA_7          P-loop containing dynein motor region
       0.11   12.8   0.2       0.17   12.2   0.2    1.3  1  AAA_22         AAA domain
       0.21   12.1   0.0       0.32   11.5   0.0    1.3  1  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.6e-06     0.031      23      51 ..      25      52 ..      11     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.6e-06
                             AAA_16 23 rpelvllsGesGvGKsslvrellralekd 51
                                       ++ ++ ++G++G+GK++ +++l+  ++++
  gene1384|gene1384|rna1383|rna1383 25 STKAIKFVGPRGTGKTRTLNALM-GINGK 52
                                       34788899*************98.34444 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05     0.087      12      60 ..      23      84 ..      16      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                      TrwB_AAD_bind 12 eretqhilivGttGsGKtqalekllrairarg...........draivlDl...tGafvsrfy 60
                                       +r t+ i +vG  G+GKt +l++l+  i+ +            + ++v+D     G+f +r+ 
  gene1384|gene1384|rna1383|rna1383 23 RRSTKAIKFVGPRGTGKTRTLNALMG-INGKTvptletykvtyKNMVVYDVvqrDGDFFERYG 84
                                       67889999***************995.555555777788888888888885333688888875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3     6e-05      0.22      32      54 ..      25      47 ..      12      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6e-05
                              AAA_7 32 nkkpvllvGptGtGKtviikdll 54
                                       + k + +vGp GtGKt +++ l+
  gene1384|gene1384|rna1383|rna1383 25 STKAIKFVGPRGTGKTRTLNALM 47
                                       567889***********999876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   4.7e-05      0.17       4      26 ..      25      47 ..      22      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                             AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                       + + +  +G+ GtGKT++l+ l+
  gene1384|gene1384|rna1383|rna1383 25 STKAIKFVGPRGTGKTRTLNALM 47
                                       6788999************9986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     9e-05      0.32      11      37 ..      26      52 ..      19      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9e-05
                                       TSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 11 gekvaivGenGaGKStLlkllagllkp 37
                                        + + +vG+ G+GK+  l++l+g   +
  gene1384|gene1384|rna1383|rna1383 26 TKAIKFVGPRGTGKTRTLNALMGINGK 52
                                       577899***************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 875.82
//
Query:       gene1385|gene1385|rna1384|rna1384  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-14   54.1   0.0    1.7e-14   53.9   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   9.2e-19   1.7e-14       3     127 .]       5     128 .]       3     128 .] 0.85

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 9.2e-19
                                        HHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEECCC...CCCEEEEE-BSSS-SBSSSEEEE CS
                       Ribosomal_S8   3 iadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeveeek...kkkikielkynkkkksvikklkr 74 
                                        +a+m+ +i+Na++a+k+++ +  +++  ++ l  + + Gyi++f+  ++k   k++i ++++ n+  +++i+    
  gene1385|gene1385|rna1384|rna1384   5 LANMCKAINNASRAGKRQLLLrFSTEEMRKFLFQMLKYGYISGFSHIHDKrngKSIIDLNGRLNR--CGAISPNYI 78 
                                        89*******************5555667888888999*********9444344445888888888..********* PP

                                        -SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                       Ribosomal_S8  75 vskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                        v++ g + + +++ lp   + +G ++  TskG++ +ke+ +++vGG++l y +
  gene1385|gene1385|rna1384|rna1384  79 VKRNGIENF-RARLLP--ARQFGHVLFNTSKGILDHKECLEENVGGKILGYFY 128
                                        ******944.455566..578****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 726.06
//
Query:       gene1386|gene1386|rna1385|rna1385  [L=694]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-92  307.8   0.1    4.6e-92  307.2   0.1    1.2  1  MCM              MCM P-loop domain
    1.5e-30  105.7   1.7    1.6e-28   99.1   1.1    2.3  2  MCM_OB           MCM OB domain
    6.9e-17   61.7   0.1    1.9e-16   60.3   0.1    1.7  1  MCM_lid          MCM AAA-lid domain
    7.2e-07   28.8   0.0    5.8e-05   22.6   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.6e-07   29.2   0.0    5.9e-06   26.3   0.0    2.5  3  AAA_5            AAA domain (dynein-related subfamily)
     0.0046   17.0   0.4       0.01   15.9   0.4    1.5  1  zf-UDP           Zinc-binding RING-finger
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.053   13.4   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
      0.044   14.2   0.1       0.14   12.5   0.0    1.8  2  AAA_16           AAA ATPase domain
      0.086   12.5   0.0       0.55    9.9   0.0    2.0  1  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.2   0.1   2.3e-95   4.6e-92      13     224 .]     318     529 ..     308     529 .. 0.98

  Alignments for each domain:
  == domain 1  score: 307.2 bits;  conditional E-value: 2.3e-95
                                        THHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEE CS
                                MCM  13 diieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravyts 88 
                                          +e++v+siap+i+g+ed+kk +ll+l+g+  + +ed++k+rgdinvllvgdpg+aKsqlLk++ k++ r+vyt+
  gene1386|gene1386|rna1385|rna1385 318 YPVEQMVRSIAPEIFGMEDIKKILLLMLVGAPGRVREDGMKIRGDINVLLVGDPGIAKSQLLKTCVKISRRGVYTT 393
                                        46899*********************************************************************** PP

                                        SSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE-- CS
                                MCM  89 gkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnar 164
                                        gkgss++gLta+v++d+ tge++le+Galvlad+G+cciDe+dkm+e dr ++hE+mEqq++si+KaGi+++Lnar
  gene1386|gene1386|rna1385|rna1385 394 GKGSSGVGLTASVTKDQITGEMILEGGALVLADGGICCIDELDKMNEVDRISIHEVMEQQSVSISKAGINTSLNAR 469
                                        **************************************************************************** PP

                                        EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                                MCM 165 tsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                        + vl Aanp+ gryd k+sv++ni l+ alLsrFD++ +l+D+++ e+De+la+hi+slh
  gene1386|gene1386|rna1385|rna1385 470 CCVLGAANPVRGRYDIKQSVEHNIGLPCALLSRFDVVAILRDEPNLERDESLANHITSLH 529
                                        ********************************************************9987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   1.1   7.8e-32   1.6e-28       2     123 ..     147     276 ..     146     279 .. 0.90
   2 ?    4.6   0.0     0.014        27      66      93 ..     514     541 ..     508     547 .. 0.85

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 7.8e-32
                                        XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES---.....-SB-..TTT-...HHH-EEE-G CS
                             MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvevelee.....PrkCeekeCe...skdpfklet 69 
                                        +R+lrs hig+lv+v+Givt++s+vkp++k a++ c++cg+++  ++        ++C +++C+    ++++ l+t
  gene1386|gene1386|rna1385|rna1385 147 VRELRSMHIGSLVRVSGIVTKVSQVKPSIKVATYICENCGAETYQQVDGdvfdlLEECGSEKCRirnVRGTLILVT 222
                                        8***************************************97665444455555669******9654455999*** PP

                                        GGSEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEE CS
                             MCM_OB  70 ekskfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyr 123
                                        + skf+++q++ +QE ++++p G +Pr+l + ++ +l +k++PGd +   G++ 
  gene1386|gene1386|rna1385|rna1385 223 RGSKFIKHQTVYIQELTGDIPRGCIPRTLVMECYSSLAEKCRPGDVIVAGGVFM 276
                                        ***********************************************9999986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.014
                                        EE-GGGSEEEEEEEEEEE---------- CS
                             MCM_OB  66 kletekskfvdfqklklQEspeevpaGe 93 
                                        +le ++s      +l+lQE+pe++p  e
  gene1386|gene1386|rna1385|rna1385 514 NLERDESLANHITSLHLQEEPESIPYDE 541
                                        6788899999999************866 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.1   9.4e-20   1.9e-16       3      84 ..     542     615 ..     540     617 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 9.4e-20
                                        HHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHH CS
                            MCM_lid   3 lrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedvee 78 
                                        +r  i  a+ ki P+l  + +  l++aYv+ Rke+        ++t+R L sliRLs A+++lrls++v+eed++e
  gene1386|gene1386|rna1385|rna1385 542 IRGIIDEAK-KIDPILPSHLSSRLTDAYVKARKEN-------PYVTPRYLLSLIRLSLAHCRLRLSTEVSEEDINE 609
                                        56668899*.***********************77.......38******************************** PP

                                        HHHHHH CS
                            MCM_lid  79 airllk 84 
                                        a+rl++
  gene1386|gene1386|rna1385|rna1385 610 ALRLMD 615
                                        ****96 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.018        36      20      43 ..     360     383 ..     351     388 .. 0.85
   2 !   22.6   0.0   2.9e-08   5.8e-05      91     162 ..     411     482 ..     403     495 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.018
                       Mg_chelatase  20 aGgHnlllvGppGsGKtmlakrlp 43 
                                         G  n+llvG pG  K+ l k   
  gene1386|gene1386|rna1385|rna1385 360 RGDINVLLVGDPGIAKSQLLKTCV 383
                                        6889*************9988765 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.9e-08
                       Mg_chelatase  91 vGggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcg 162
                                        + g  + + G++ la  G+  +DEl ++++    ++ e +e+++v+is+a  +++  ar+ ++ a+Np +  
  gene1386|gene1386|rna1385|rna1385 411 ITGEMILEGGALVLADGGICCIDELDKMNEVDRISIHEVMEQQSVSISKAGINTSLNARCCVLGAANPVRGR 482
                                        567788999*********************9999**********************************9854 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   3.1e+03      57      78 ..     257     278 ..     250     280 .. 0.88
   2 !   26.3   0.0   2.9e-09   5.9e-06       1     124 [.     364     480 ..     364     493 .. 0.85
   3 ?   -3.2   0.0       3.8   7.5e+03      82     107 ..     607     632 ..     601     662 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                                        --------G-SEEEEESGGG-- CS
                              AAA_5  57 splvraaregeilvlDEverae 78 
                                        s+l +++r g+++v ++v++ +
  gene1386|gene1386|rna1385|rna1385 257 SSLAEKCRPGDVIVAGGVFMPK 278
                                        789999************9865 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 2.9e-09
                                        EEEEE--SSSSHHHHHHHGGGGB.......S--EEEEE--TT--HHHHH--B--.........--------G-SEE CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaal.......nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeil 69 
                                        +vlLvG+pG++Ks+l +   +         ++    v lt++ t+++++g++ +       + ++lv     g i+
  gene1386|gene1386|rna1385|rna1385 364 NVLLVGDPGIAKSQLLKTCVKISrrgvyttGKGSSGVGLTASVTKDQITGEMIL-------EGGALV--LADGGIC 430
                                        69***************999988766777777778899***************6.......889999..889**** PP

                                        EEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                              AAA_5  70 vlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                        ++DE+++++     s + ++e++ +++ + g  ++ ++        v+++anp++
  gene1386|gene1386|rna1385|rna1385 431 CIDELDKMNEVDRISIHEVMEQQSVSISKAGINTSLNAR-----CCVLGAANPVR 480
                                        *********888888999999999998888888877775.....88888888887 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.8
                                        HHHHHHHHHSSEEE..-SSSEEE--- CS
                              AAA_5  82 lnsLlslleerrllleeggelvkakn 107
                                        +n+ l+l++  r++l++ ++++  ++
  gene1386|gene1386|rna1385|rna1385 607 INEALRLMDVTRIPLPKKKKEEVSSK 632
                                        55666888888888888777665554 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4   5.1e-06      0.01       1      39 [.     172     210 ..     172     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.1e-06
                             zf-UDP   1 kplkdlngqiCqiCgddvgltedgelFvacnecafpvcr 39 
                                        kp  ++++ iC+ Cg +   ++dg++F + +ec++  cr
  gene1386|gene1386|rna1385|rna1385 172 KPSIKVATYICENCGAETYQQVDGDVFDLLEECGSEKCR 210
                                        566678899**************************9999 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.053       2     117 ..     365     481 ..     364     493 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                              AAA_3   2 vllegvPGlaktllvkalaka.......ldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanlllade 70 
                                        vll g PG+ak +l k+  k+        +   + + +t+ +    i+G +++e     + +  G     +   de
  gene1386|gene1386|rna1385|rna1385 365 VLLVGDPGIAKSQLLKTCVKIsrrgvytTGKGSSGVGLTASVTKDQITGEMILEG--GALVLADGG----ICCIDE 434
                                        799999*****99988866541111111233345566666666666666666643..455566665....5678** PP

                              AAA_3  71 inrappktqsalleameerqvtvege..thklpepflvlatqnPieqeG 117
                                        +++ +   + ++ e+me++ v+++++  +++l+   +vl + nP+   G
  gene1386|gene1386|rna1385|rna1385 435 LDKMNEVDRISIHEVMEQQSVSISKAgiNTSLNARCCVLGAANPVR--G 481
                                        ********************999765227889************95..4 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05      0.14      26      62 ..     364     398 ..     354     470 .. 0.81
   2 ?   -2.0   0.0         2     4e+03     106     136 ..     530     576 ..     479     579 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                             AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                        +vll+G++G+ Ks l++++   ++++ g++++gk  +
  gene1386|gene1386|rna1385|rna1385 364 NVLLVGDPGIAKSQLLKTCV-KISRR-GVYTTGKGSS 398
                                        79******************.69998.5666666555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                             AAA_16 106 a.................avpelagaeasrllellkrllallsrderp 136
                                                          +++++++ ++s+l   l+++ +++++ e p
  gene1386|gene1386|rna1385|rna1385 530 LqeepesipydeirgiidEAKKIDPILPSHLSSRLTDAYVKARK-ENP 576
                                        13333444444444444466666666667777777777777776.555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00027      0.55      75     142 ..     408     477 ..     352     493 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                                        SSSSTTTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEES CS
                    Sigma54_activat  75 kGaFtGAekekkGlfekadgGtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatn 142
                                        k   tG    + G++  adgG+  +De+ +++      + +v+++++  +++ G +++ ++ + ++ a+n
  gene1386|gene1386|rna1385|rna1385 408 KDQITGEMILEGGALVLADGGICCIDELDKMNEVDRISIHEVMEQQSvsISKAGINTSLNARCCVLGAAN 477
                                        5556777777889******************************998622578999999998888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 4602.05
//
Query:       gene1387|gene1387|rna1386|rna1386  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.049   14.1   0.1      0.075   13.5   0.1    1.3  1  Colicin_D  Colicin D
      0.067   13.2   0.1       0.11   12.6   0.1    1.5  1  EFP_N      Elongation factor P (EF-P) KOW-like domain


Domain annotation for each model (and alignments):
>> Colicin_D  Colicin D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   8.4e-06     0.075      27      71 ..      49      93 ..      32     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.4e-06
                          Colicin_D 27 yekaikkhidnaktvhqgTYrgkdakvvinsntgaavvrdsaGnf 71
                                        +++i   i  +   h+g Y g+d+++v  +++ +   +d +G+ 
  gene1387|gene1387|rna1386|rna1386 49 AKTTISSKILCTGSNHKGIYTGNDSIIVCRPEKVQLKLIDISGTS 93
                                       479999***************************999999999975 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.2e-05      0.11       3      33 ..      14      48 ..      12      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                                       GG--TT-EEEE..TTEE..EEEEEEEEEEETTS-- CS
                              EFP_N  3 selkkGlviei..dgkl..yvVlefehvkpGkGqa 33
                                       +++++G+ i++  +g+l   +V+++  vk Gk +a
  gene1387|gene1387|rna1386|rna1386 14 KDIRPGNYIKVdvNGQLrsAQVIDTSSVKNGKHGA 48
                                       69*****99987789985579********998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 948.41
//
Query:       gene1388|gene1388|rna1387|rna1387  [L=98]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-14   54.0   0.1    2.4e-14   53.3   0.1    1.4  2  Glutaredoxin  Glutaredoxin
  ------ inclusion threshold ------
      0.057   13.8   0.0      0.073   13.5   0.0    1.2  1  DUF836        Glutaredoxin-like domain (DUF836)
       0.16   12.2   0.6       0.23   11.7   0.6    1.3  1  DUF4695       Domain of unknown function (DUF4695)


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   4.1e-18   2.4e-14       3      60 .]      17      74 ..      15      74 .. 0.97
   2 ?   -3.4   0.0         2   1.2e+04      15      23 ..      86      94 ..      84      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 4.1e-18
                                       EEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                       Glutaredoxin  3 lftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                                       + +k++Cp+C  a+++L+e +++f+ei  +++ee+ +e++e  +++t+P +f + k++
  gene1388|gene1388|rna1387|rna1387 17 VVSKRGCPFCLDAVKTLNEWKIEFDEIKNTENEELSKEIEEEYKFPTFPKIFLNKKFI 74
                                       789*****************************************************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                                       HHHHHHHTT CS
                       Glutaredoxin 15 akrlLkelg 23
                                       +k++L+ +g
  gene1388|gene1388|rna1387|rna1387 86 TKEFLDAFG 94
                                       789999876 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.2e-05     0.073       5      57 ..      18      71 ..      16      89 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                       EE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CC....CHCCCC.TTTTEEEECT CS
                             DUF836  5 yskpgChlCeqakekLkelkleegleleviDIakdee....leakYg.leipvlaleg 57
                                        sk+gC+ C +a + L e+k+e + e++    +++ee     e++Y+ ++ p+++l++
  gene1388|gene1388|rna1387|rna1387 18 VSKRGCPFCLDAVKTLNEWKIEFD-EIKN---TENEElskeIEEEYKfPTFPKIFLNK 71
                                       59***************9987777.3333...34444222356677645667777766 PP

>> DUF4695  Domain of unknown function (DUF4695)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   3.8e-05      0.23      48      68 ..      38      58 ..      30      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.8e-05
                            DUF4695 48 vtfdeikevedeGvskeeeek 68
                                       + fdeik++e+e  ske ee 
  gene1388|gene1388|rna1387|rna1387 38 IEFDEIKNTENEELSKEIEEE 58
                                       89***********99987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 635.75
//
Query:       gene1389|gene1389|rna1388|rna1388  [L=421]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-60  203.2   6.9    6.5e-60  202.6   6.9    1.3  1  NMD3      NMD3 family


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.6   6.9   3.6e-64   6.5e-60       1     243 []       4     227 ..       4     227 .. 0.98

  Alignments for each domain:
  == domain 1  score: 202.6 bits;  conditional E-value: 3.6e-64
                               NMD3   1 CcrCGkeieelinglCedCllkevditegiek.ievevCkeCgryl.pkgkWvkaeleseellaeclkklvekgLk 74 
                                        Cc+CG+ ie++  ++C++Cl++ev i+++ ++ ++ve C+ C+ryl p ++W++ ++ s+e l  ++kk   k L+
  gene1389|gene1389|rna1388|rna1388   4 CCKCGILIEPRLMNMCDRCLVTEVTISTKVKRsLSVERCRGCERYLqPPKSWMEFSWGSKEFLLFLIKKN--KTLN 77 
                                        *********99999*********************************666****99**************..**** PP

                               NMD3  75 vseeveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriagg.yyeaiv 149
                                                 + +vd++fi+tep+skri + +t+++         ++q +e+++++++ qCp+C++++++  ++++v
  gene1389|gene1389|rna1388|rna1388  78 --------GLCIVDSNFIYTEPNSKRIMIGLTIRECG-------IEQPLEMKYVIRNMQCPDCAKVEAKqFWNSLV 138
                                        ........99***********************9988.......569***************************** PP

                               NMD3 150 QvRqkrelteeehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvs 225
                                        QvR+k       hkr++ +le+l+lk++a +++s+ik++keGlDfy+ +++aA ++v+fl++++++++k se+l+s
  gene1389|gene1389|rna1388|rna1388 139 QVRHK-----GRHKRMMIYLEHLVLKNSAYEDTSNIKQRKEGLDFYYVDRNAAIRMVNFLQNVLPVRTKMSERLIS 209
                                        *****.....****************************************************************** PP

                               NMD3 226 edkksgkevyrltysvrl 243
                                        +d +++k +y+++ysv++
  gene1389|gene1389|rna1388|rna1388 210 KDVHTSKCNYKFSYSVEI 227
                                        ****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2408.76
//
Query:       gene1390|gene1390|rna1389|rna1389  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.1e-153  510.1   1.9   3.9e-153  509.8   1.9    1.1  1  TIP49            TIP49 P-loop domain
    1.2e-16   60.6   0.0    3.2e-16   59.2   0.0    1.8  1  TIP49_C          TIP49 AAA-lid domain
    4.3e-10   40.1   0.7    4.8e-06   27.0   0.3    2.9  2  AAA              ATPase family associated with various cellul
    1.5e-07   31.3   0.1    1.4e-05   24.8   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.3e-06   28.9   0.1    2.6e-05   24.7   0.1    2.2  1  AAA_16           AAA ATPase domain
    1.4e-06   28.6   0.8     0.0096   16.2   0.0    2.7  2  AAA_22           AAA domain
    0.00034   20.7   0.1       0.27   11.3   0.0    2.7  2  AAA_14           AAA domain
     0.0016   18.4   0.1      0.099   12.6   0.0    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0018   18.2   0.0     0.0037   17.2   0.0    1.6  1  NACHT            NACHT domain
     0.0028   17.4   0.1       0.48   10.1   0.0    2.7  2  Sigma54_activat  Sigma-54 interaction domain
     0.0081   15.6   0.8       0.06   12.7   0.1    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.025   14.5   0.0    1.6  1  Rad17            Rad17 P-loop domain
      0.012   15.6   1.5       0.59   10.0   1.5    2.5  1  ATPase_2         ATPase domain predominantly from Archaea
      0.014   15.7   0.8        2.5    8.4   0.2    2.5  2  AAA_19           AAA domain
      0.024   15.2   0.4      0.059   13.9   0.1    1.9  1  AAA_18           AAA domain
       0.03   14.6   0.2      0.064   13.5   0.0    1.6  1  AAA_28           AAA domain
      0.048   13.7   0.0       0.11   12.5   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.093   12.5   0.1         10    5.7   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   11.9   0.0        0.2   11.2   0.0    1.4  1  AAA_25           AAA domain
       0.14   12.7   0.1        0.3   11.6   0.1    1.7  1  ABC_tran         ABC transporter
       0.14   12.6   0.0        0.4   11.1   0.0    1.8  1  RNA_helicase     RNA helicase
       0.14   11.6   1.6       0.22   11.0   0.1    2.0  2  PhoH             PhoH-like protein
       0.15   11.0   0.4       0.32   10.0   0.0    1.6  2  DUF4776          Domain of unknown function (DUF4776)
       0.22   11.8   0.1       0.52   10.6   0.0    1.6  1  Peptidase_M91    Effector protein
       0.22   11.9   3.2       0.46   10.9   0.0    2.6  3  AAA_17           AAA domain
       0.24   11.1   0.4        1.3    8.7   0.2    2.0  2  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  509.8   1.9  5.7e-156  3.9e-153       2     350 ..       7     359 ..       6     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 509.8 bits;  conditional E-value: 5.7e-156
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49   2 islhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelged 77 
                                        i++hsh+k+LGld  g++ ++ ++++Gq++areaag+ive++k+k+++GravL++Gp+g Gktala++is+elg  
  gene1390|gene1390|rna1389|rna1389   7 IAIHSHVKSLGLDIFGRPIEKPNAVIGQEDAREAAGLIVEMVKTKRMSGRAVLISGPAGCGKTALAVGISEELGPG 82 
                                        99************************************************************************** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-...TTS--EEEEEE-SS- CS
                              TIP49  78 vpfvalsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenpls.kekkikevkitlktake 152
                                        +pf+++sgsevys+evkktevl +alr+si vr++e k+++eGe+vel++ ++enpls ++kk+ke+ itlkt+ke
  gene1390|gene1390|rna1389|rna1389  83 TPFTSMSGSEVYSNEVKKTEVLEEALRRSILVRMRELKDIYEGEIVELRILDEENPLSsYSKKVKEIFITLKTSKE 158
                                        **********************************************************99**************** PP

                                        EEEEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------S--------S---S----XXXXXXXXX CS
                              TIP49 153 ekklklgskiaeellkekvkegDviviekesGkvkklGrsearakefDiekdefvelPkGevekkkevvqevtLhd 228
                                        +kklkl+s+++e+++k+++ +gDv++ie +sG +kklGrsea++++fD+e+d++v++PkGev k+kev+q+vtLhd
  gene1390|gene1390|rna1389|rna1389 159 SKKLKLASSLYEQIDKQRIVNGDVVYIEVNSGVIKKLGRSEAHMNDFDLEADTYVPIPKGEVLKRKEVIQSVTLHD 234
                                        **************************************************************************** PP

                                        XXXXXXXX..XXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49 229 lDvanarp..qdllslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnral 302
                                        lD+ana+p  qd+lsl++++l++kkteite+lr+++n++v++y+e+g+aeivpG+lfiDevh+lD+ecf++l++ +
  gene1390|gene1390|rna1389|rna1389 235 LDMANAKPtgQDMLSLVFRILSPKKTEITERLRNDVNRMVNEYLEKGNAEIVPGILFIDEVHLLDVECFTFLHKII 310
                                        ********99****************************************************************** PP

                                        XXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49 303 eselaPivilatnrgiakirGt.diisphGipvDlldrlliiktekytk 350
                                        es+l+P vi+a+nrg+a i+G+  +  p+Gi++Dlldr++ii+++k+t+
  gene1390|gene1390|rna1389|rna1389 311 ESPLSPTVIFASNRGMAPIKGSnGLLGPFGITKDLLDRIMIITVKKNTD 359
                                        **********************6689******************99876 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.0   4.6e-19   3.2e-16       1      66 []     365     425 ..     365     425 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 4.6e-19
                            TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                        I+++R keE++++d +Al+++++++++++LRY+i+L+ + +++     +++v++++veev+eLF+D
  gene1390|gene1390|rna1389|rna1389 365 IIEMRLKEEELQMDGDALTFFVNLSISKGLRYCISLIPLLKTY-----GGCVTIQNVEEVNELFHD 425
                                        9******************************************.....99***************9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.3   6.9e-09   4.8e-06       1      44 [.      58     103 ..      58     189 .. 0.64
   2 !   10.2   0.0    0.0011      0.74      25      70 ..     253     298 ..     235     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.9e-09
                                        EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHH CS
                                AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgesek 44 
                                        vl++Gp G+GKT+la  + +elg  ++f ++sgse+ s+ v+++e 
  gene1390|gene1390|rna1389|rna1389  58 VLISGPAGCGKTALAVGISEELGpgTPFTSMSGSEVYSNEVKKTEV 103
                                        799*******************655************775555442 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                        EEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                                AAA  25 efleisgsellskyvgesekkirelfkeakekakpsilfiDEidal 70 
                                        ++l+ + +e+++ +  + ++ ++e++++  ++  p ilfiDE++ l
  gene1390|gene1390|rna1389|rna1389 253 RILSPKKTEITERLRNDVNRMVNEYLEKGNAEIVPGILFIDEVHLL 298
                                        55666677778778888888899999886555589********977 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.1e-08   1.4e-05       8      65 ..      30      87 ..      23     120 .. 0.88
   2 ?    3.9   0.0     0.057        39      87     109 ..     289     311 ..     280     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.1e-08
                             RuvB_N  8 eyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkits 65
                                         igqe+ +e   +++e  k+++ +   vl++Gp G Gkt+la  i++elg     ts
  gene1390|gene1390|rna1389|rna1389 30 AVIGQEDAREAAGLIVEMVKTKRMSGRAVLISGPAGCGKTALAVGISEELGPGTPFTS 87
                                       679***********************************************97766655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.057
                             RuvB_N  87 vlfideihrlsraveevlysame 109
                                        +lfide+h l+ +   +l++ +e
  gene1390|gene1390|rna1389|rna1389 289 ILFIDEVHLLDVECFTFLHKIIE 311
                                        8*******999877777766655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.1   3.7e-08   2.6e-05      17     149 ..      46     300 ..      31     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.7e-08
                             AAA_16  17 ervrsgrp..elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqlldea 89 
                                        e+v++ r   ++vl+sG++G+GK++l+  + ++l     ++ ++g  + + +     +l +al r+++l  + + +
  gene1390|gene1390|rna1389|rna1389  46 EMVKTKRMsgRAVLISGPAGCGKTALAVGISEELGPGTPFTsMSGSEVYSNEVKKTEVLEEAL-RRSILVRMRELK 120
                                        44444444449********************99998843333444444442222223355555.445555554444 PP

                             AAA_16  90 esaeleawrekleeala........................................................... 106
                                        +  e e    +++++ +                                                           
  gene1390|gene1390|rna1389|rna1389 121 DIYEGEIVELRILDEENplssyskkvkeifitlktskeskklklasslyeqidkqrivngdvvyievnsgvikklg 196
                                        444444444444444445566666666666699999999999999999999999********************** PP

                             AAA_16 107 .........................................................avpelagaeasrllellkr 125
                                                                                                 + ++ + ++ +rl++ ++r
  gene1390|gene1390|rna1389|rna1389 197 rseahmndfdleadtyvpipkgevlkrkeviqsvtlhdldmanakptgqdmlslvfrILSPKKTEITERLRNDVNR 272
                                        ******************************9999999999999888888888888887777777777999999999 PP

                             AAA_16 126 ll.allsrder...plvlvlDdlqwade 149
                                        ++ ++l+++     p +l++D+++ +d 
  gene1390|gene1390|rna1389|rna1389 273 MVnEYLEKGNAeivPGILFIDEVHLLDV 300
                                        99999999665888899*******9985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.3     0.001      0.71       4      29 ..      54      79 ..      51     183 .. 0.82
   2 !   16.2   0.0   1.4e-05    0.0096      47     117 ..     237     311 ..     197     327 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                             AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                       + + +++ G++G+GKT l+  + e+l
  gene1390|gene1390|rna1389|rna1389 54 SGRAVLISGPAGCGKTALAVGISEEL 79
                                       677899***********997777766 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-05
                             AAA_22  47 lpsst.sskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqhlrseealeeLrslln 117
                                        +++ + + +d+l+ ++r+l  ++ + + +++  + ++++++l++  +   +++l iDE++ l   e++++L+++ +
  gene1390|gene1390|rna1389|rna1389 237 MANAKpTGQDMLSLVFRILSPKKTEITERLRNDVnRMVNEYLEKGNAeivPGILFIDEVHLL-DVECFTFLHKIIE 311
                                        33444689999999999999777775555555554666666666666999************.9******987755 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00039      0.27       2      88 ..      55     151 ..      54     189 .. 0.62
   2 ?    6.7   0.0      0.01       7.1      49     104 ..     270     326 ..     250     354 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                             AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe........kllelileklke....... 62 
                                        +++++i+G+  +GKT l+  + +el  +   +  ++  +    + +++e        ++l  ++    e       
  gene1390|gene1390|rna1389|rna1389  55 GRAVLISGPAGCGKTALAVGISEELG-PGTPFTSMSGSEVYSNEVKKTEvleealrrSILVRMR----Elkdiyeg 125
                                        5899*************999987777.4445555554444443333332111111112333333....13334434 PP

                             AAA_14  63 ekktylflDEiqevpewekalkslvd 88 
                                        e  ++ +lDE   +++ +k +k+++ 
  gene1390|gene1390|rna1389|rna1389 126 EIVELRILDEENPLSSYSKKVKEIFI 151
                                        55567899998888888888887765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                             AAA_14  49 pekllelilek.lkeekktylflDEiqevp.ewekalkslvdegknldvivtGSnskl 104
                                         +++ +++lek   e    +lf+DE++ ++ e +++l +++++      ++  Sn ++
  gene1390|gene1390|rna1389|rna1389 270 VNRMVNEYLEKgNAEIVPGILFIDEVHLLDvECFTFLHKIIESP-LSPTVIFASNRGM 326
                                        22445555555332335578*******99547999999999987.3355555566555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00014     0.099       2      65 ..      58     124 ..      57     141 .. 0.70
   2 ?    2.9   0.0      0.14        99      65      90 ..     286     311 ..     257     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                        EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.........--------......G CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreikngttslvdsplvraar......e 65 
                                        vl+ Gp G+gK+ la  +++ l  +++++ + +++   ++++k    +   +++l+ s+lv  +r      e
  gene1390|gene1390|rna1389|rna1389  58 VLISGPAGCGKTALAVGISEELgpGTPFTSMSGSE-VYSNEVKKTEVL---EEALRRSILV-RMRelkdiyE 124
                                        8999******************9666666665555.555565554443...6777777777.4443444444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                                        G-SEEEEESGGG--HHHHHHHHHHHH CS
                              AAA_5  65 egeilvlDEveraesevlnsLlslle 90 
                                         + il++DEv+ ++ e +  L++++e
  gene1390|gene1390|rna1389|rna1389 286 VPGILFIDEVHLLDVECFTFLHKIIE 311
                                        5789*****************99998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.4e-06    0.0037       1      31 [.      56      86 ..      56     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.4e-06
                                       SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                              NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklpq 31
                                       r v++ G+aG+GKT+L+ ++ +++  g+++ 
  gene1390|gene1390|rna1389|rna1389 56 RAVLISGPAGCGKTALAVGISEELGPGTPFT 86
                                       5799*******************99998876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00069      0.48      11      45 ..      44      78 ..      31     108 .. 0.76
   2 ?    4.5   0.0     0.038        26      94     118 ..     287     311 ..     278     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00069
                                       HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                    Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraihea 45
                                       ++e++k+   +   vli G  G+GK+ la  i e+
  gene1390|gene1390|rna1389|rna1389 44 IVEMVKTKRMSGRAVLISGPAGCGKTALAVGISEE 78
                                       45666666667799***************888664 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.038
                                        TSEEEEETGGGS-HHHHHHHHHHHH CS
                    Sigma54_activat  94 gGtlfLDeigelplelQekLlrvlq 118
                                         G+lf+De++ l++e+ + L ++++
  gene1390|gene1390|rna1389|rna1389 287 PGILFIDEVHLLDVECFTFLHKIIE 311
                                        59***********999888877776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   8.7e-05      0.06       5      65 ..      31      98 ..      29     113 .. 0.70
   2 ?    0.1   0.1      0.66   4.5e+02     107     131 ..     287     311 ..     275     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-05
                       Mg_chelatase  5 vkGqeeakraleiaa.......aGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65
                                       v+Gqe+a++a  + +         g  +l+ Gp+G+GKt la  +++ l p +   ++  ++++s   
  gene1390|gene1390|rna1389|rna1389 31 VIGQEDAREAAGLIVemvktkrMSGRAVLISGPAGCGKTALAVGISEELGPGTPFTSMSGSEVYSNEV 98
                                       6777777776433221111111456789*****************99999999888888888887655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.66
                       Mg_chelatase 107 nGvLfLDElpefkrkvlevLRePle 131
                                         G+Lf+DE+  ++ + +  L + +e
  gene1390|gene1390|rna1389|rna1389 287 PGILFIDEVHLLDVECFTFLHKIIE 311
                                        59******99888887777766655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.6e-05     0.025      45      91 ..      55     102 ..      41     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-05
                              Rad17  45 kriLLisGPsGCgkstvvkvLskelgiklr.ewlnpvslkepdnqksd 91 
                                         r +LisGP+GCgk+     +s elg+      + + ++ + + +k++
  gene1390|gene1390|rna1389|rna1389  55 GRAVLISGPAGCGKTALAVGISEELGPGTPfTSMSGSEVYSNEVKKTE 102
                                        3589***********999999999998653134445555555555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.5   0.00086      0.59      21      55 ..      56      87 ..      44     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00086
                           ATPase_2 21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyi 55
                                       + ++i Gp g+GKtaL   i e+l   +    + +
  gene1390|gene1390|rna1389|rna1389 56 RAVLISGPAGCGKTALAVGISEEL---GPGTPFTS 87
                                       66899***********98888877...33444443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0036       2.5       8      33 ..      53      78 ..      46      88 .. 0.83
   2 ?    5.4   0.0     0.032        22      69     126 ..     229     310 ..     143     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                             AAA_19  8 lkekvllvtaGpGtGKTrvlkhival 33
                                       ++ + +l+ +++G+GKT + ++i ++
  gene1390|gene1390|rna1389|rna1389 53 MSGRAVLISGPAGCGKTALAVGISEE 78
                                       677899***********999888766 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.032
                             AAA_19  69 atTiHrlal............................ldfddlltealelleeaeeekklqeeellivDEfqdvde 116
                                          T+H l +                            l + d + +  e+le+  +  ++    +l++DE+  +d 
  gene1390|gene1390|rna1389|rna1389 229 SVTLHDLDManakptgqdmlslvfrilspkkteiterLRN-DVNRMVNEYLEK-GN-AEI-VPGILFIDEVHLLDV 300
                                        6788888777777777777777777777777665554322.233344555553.33.344.4669**********9 PP

                             AAA_19 117 lqyrLlkall 126
                                          +++l+++ 
  gene1390|gene1390|rna1389|rna1389 301 ECFTFLHKII 310
                                        9999998887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.5e-05     0.059       1      34 [.      58      91 ..      58     179 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.5e-05
                             AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvake 34
                                       +l++G++G+GKt la  +s++lg g+  +++   
  gene1390|gene1390|rna1389|rna1389 58 VLISGPAGCGKTALAVGISEELGPGTPFTSMSGS 91
                                       79******************98654444443333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.3e-05     0.064       2      57 ..      58     116 ..      57     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.3e-05
                             AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwv.edllafae 57 
                                        + i+G+ ++GKT l+  ++++   g+p    ++ e+++++ +k+e  l+++ ++ + ++ 
  gene1390|gene1390|rna1389|rna1389  58 VLISGPAGCGKTALAVGISEElgpGTPFTSMSGSEVYSNEVKKTEV-LEEAlRRSILVRM 116
                                        89*****************99999***************9999885.8777666665554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.11      18      46 ..      48      82 ..      33      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                                       H......TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE 18 l......gdvilLeGdLGaGKTtlvrglakalgve 46
                                       +      g+++l++G+ G+GKT+l+ g+ ++lg  
  gene1390|gene1390|rna1389|rna1389 48 VktkrmsGRAVLISGPAGCGKTALAVGISEELGPG 82
                                       3333445677********************99864 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.015        10       2      17 ..      59      74 ..      58     113 .. 0.82
   2 ?    4.4   0.0     0.038        26      27      85 ..     254     309 ..     243     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                    Viral_helicase1  2 vvhGvpGcGKStlirk 17
                                       +++G +GcGK+ l + 
  gene1390|gene1390|rna1389|rna1389 59 LISGPAGCGKTALAVG 74
                                       799********98665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.038
                    Viral_helicase1  27 vnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylllhaGyilllaal 85 
                                        + +p    +te+   l n+ +r+v+++l++  ++    il++DE  ll+  ++ +l+++
  gene1390|gene1390|rna1389|rna1389 254 ILSPKKTEITER---LRNDVNRMVNEYLEKGNAEIVPGILFIDEVHLLDVECFTFLHKI 309
                                        445555555554...67888888999999888887789**********98888887766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029       0.2      32      65 ..      54      87 ..      46     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                             AAA_25 32 agelallaGapgtGKttlaldlalavatGkpwlg 65
                                        g  +l+ G+ g+GKt+la+ ++ ++  G p++ 
  gene1390|gene1390|rna1389|rna1389 54 SGRAVLISGPAGCGKTALAVGISEELGPGTPFTS 87
                                       57889***************99999888888876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00043       0.3       9      38 ..      53      88 ..      45     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--......S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                           ABC_tran  9 kegekvaivGenGaGKStLlkllagllkp......t 38
                                         g+ v i G+ G+GK+ L+  ++++l p       
  gene1390|gene1390|rna1389|rna1389 53 MSGRAVLISGPAGCGKTALAVGISEELGPgtpftsM 88
                                       67999***************9999998874444332 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00057       0.4       1      39 [.      58      99 ..      58     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00057
                       RNA_helicase  1 iwlyGpsgeGKStlakeLakall..kklklkkkdsvys.rnp 39
                                       ++++Gp+g+GK+ la  ++++l   + + + + ++vys   +
  gene1390|gene1390|rna1389|rna1389 58 VLISGPAGCGKTALAVGISEELGpgTPFTSMSGSEVYSnEVK 99
                                       679**************9999985544466666777774444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00032      0.22      20      38 ..      56      74 ..      40      79 .. 0.78
   2 ?   -2.5   0.1       4.2   2.9e+03     121     145 ..     348     372 ..     343     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                                       SEEEEE--TTSSTTHHHHH CS
                               PhoH 20 divfaiGpaGtGKtylava 38
                                         v + GpaG+GKt lav 
  gene1390|gene1390|rna1389|rna1389 56 RAVLISGPAGCGKTALAVG 74
                                       478999***********95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                                        EEEEE-SGGG--HHHHHHHHTTB-T CS
                               PhoH 121 afvilDEAQnttkeqmkmfltRlGe 145
                                         ++i+    nt +++mk++ +Rl e
  gene1390|gene1390|rna1389|rna1389 348 RIMIITVKKNTDESNMKIIEMRLKE 372
                                        5566666789999999999999865 PP

>> DUF4776  Domain of unknown function (DUF4776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00046      0.32     331     365 ..     137     171 ..     109     180 .. 0.89
   2 ?   -2.4   0.0       2.6   1.8e+03     338     374 ..     223     255 ..     209     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00046
                            DUF4776 331 kpvLhiekkndeyiiTLrplKdaksLakaanpyve 365
                                        +p  + +kk  e++iTL+  K++k L+ a+++y +
  gene1390|gene1390|rna1389|rna1389 137 NPLSSYSKKVKEIFITLKTSKESKKLKLASSLYEQ 171
                                        5666779**********************999865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                            DUF4776 338 kkndeyiiTLrplKdaksLakaanpyvemkPvvFriv 374
                                        +k+    +TL+ l     +a+a+ +  +m   vFri 
  gene1390|gene1390|rna1389|rna1389 223 RKEVIQSVTLHDL----DMANAKPTGQDMLSLVFRIL 255
                                        3444446999999....89999999999*******96 PP

>> Peptidase_M91  Effector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00075      0.52      13      52 ..     227     264 ..     219     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00075
                      Peptidase_M91  13 FkdrveadLdmlsssptGqqlLeelkssksegerkltike 52 
                                         +  +  dLdm +++ptGq++L+ + +  s   +k  i+e
  gene1390|gene1390|rna1389|rna1389 227 IQSVTLHDLDMANAKPTGQDMLSLVFRILSP--KKTEITE 264
                                        5566779***************988777777..5555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00066      0.46       2      65 ..      62     127 ..      61     138 .. 0.76
   2 ?    0.1   0.0       1.5     1e+03      14      55 ..     167     211 ..     159     273 .. 0.72
   3 ?   -1.9   0.0       5.9   4.1e+03      50      71 ..     259     280 ..     217     301 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00066
                                        E-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHH CS
                             AAA_17   2 GgPGsGKgtqceklveky....gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaeki 65 
                                        G+ G+GK+ ++  + e++     ft +s +++  +e+k+ +    ++++r+  l++ +el ++ + +i
  gene1390|gene1390|rna1389|rna1389  62 GPAGCGKTALAVGISEELgpgtPFTSMSGSEVYSNEVKKTEV--LEEALRRSILVRMRELKDIYEGEI 127
                                        999***************7755688899888888****9997..356666666666666666555555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                                        HHHHHHTEEEEEHHHHHHHHHHTT...TSHSSHHHHCTSHHHHHH CS
                             AAA_17  14 klvekygfthlsaGdllreeakrg...glakardemrklpleekk 55 
                                         l e+++ + +  Gd+++ e+++g   +l++++ +m++ +le + 
  gene1390|gene1390|rna1389|rna1389 167 SLYEQIDKQRIVNGDVVYIEVNSGvikKLGRSEAHMNDFDLEADT 211
                                        555666666666688888888877665567777777777666655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 5.9
                                        HHHHHHHHHHHHHHHHHHHHHS CS
                             AAA_17  50 pleekkelqkeaaekiaeeakk 71 
                                        + e++++l+  + + ++e  +k
  gene1390|gene1390|rna1389|rna1389 259 KTEITERLRNDVNRMVNEYLEK 280
                                        3445555555555555554444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0019       1.3       9      38 ..      47      75 ..      45      91 .. 0.82
   2 ?   -0.5   0.0       1.2   8.4e+02     140     185 ..     237     281 ..     229     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                             AAA_30  9 avealltsgdrvavltGpAGtGKttalkal 38
                                       +v++  +sg+  +++ GpAG GKt +  ++
  gene1390|gene1390|rna1389|rna1389 47 MVKTKRMSGR-AVLISGPAGCGKTALAVGI 75
                                       5666667775.99***********987666 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                             AAA_30 140 lveaagigtaeLtevvRqkeseeraaalalregdaeealealadrg 185
                                        +++a+ +g+  L+ v+R+ +++  +++++lr++  +  ++ + ++g
  gene1390|gene1390|rna1389|rna1389 237 MANAKPTGQDMLSLVFRILSPKKTEITERLRNDVNR-MVNEYLEKG 281
                                        55667788889999****99**********987666.666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2729.87
//
Query:       gene139|gene139|rna139|rna139  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.05   14.0   2.7       0.12   12.8   0.7    2.0  2  Vps54           Vps54-like protein
      0.068   13.3   3.4      0.053   13.6   1.7    1.7  2  NRN1            Neuritin protein family
      0.079   13.4   0.6      0.079   13.4   0.6    3.5  3  Pep1_7          Elicitor peptide 1-7
      0.088   10.7   9.5        0.1   10.5   9.5    1.1  1  V_ATPase_I      V-type ATPase 116kDa subunit family
       0.21   11.6   6.8       0.27   11.2   2.4    2.1  2  Talin_middle    Talin, middle domain
       0.42   10.9   8.0          1    9.6   1.7    2.3  2  DUF948          Bacterial protein of unknown function (DUF948
       0.64    9.0   8.5       0.92    8.5   8.5    1.2  1  DUF3987         Protein of unknown function (DUF3987)
       0.65    8.1  12.9       0.88    7.6  12.9    1.1  1  Hid1            High-temperature-induced dauer-formation prot
       0.66    9.5   9.0       0.84    9.2   8.3    1.4  2  Choline_kinase  Choline/ethanolamine kinase
       0.86    9.6   8.6       0.36   10.8   4.5    2.1  2  Rsd_AlgQ        Regulator of RNA polymerase sigma(70) subunit
        1.5    8.6  16.7       0.91    9.3  13.2    1.9  2  PIN_8           PIN like domain
        1.7    7.5  15.5        2.3    7.0  15.5    1.1  1  XRN_M           Xrn1 helical domain
          2    9.0  15.1         15    6.2  12.3    3.1  2  DUF3899         Domain of unknown function (DUF3899)
        3.7    6.3  14.2        4.8    5.9  14.2    1.3  1  ALMT            Aluminium activated malate transporter
        3.8    4.5  12.2          4    4.4  12.2    1.0  1  GREB1           Gene regulated by oestrogen in breast cancer
        8.8    5.1   6.6         10    4.9   6.6    1.1  1  LMBR1           LMBR1-like membrane protein


Domain annotation for each model (and alignments):
>> Vps54  Vps54-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.47   5.3e+02      76     129 ..       3      56 ..       1      61 [. 0.72
   2 ?   12.8   0.7   0.00011      0.12      75     131 ..      83     140 ..      76     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.47
                          Vps54  76 sqslslvialipyvkealerhleeksqesllaefdkvkrdyqehqneihaKLvs 129
                                    s+ l++v+ +i++   ++   + +++++++ ++ ++ +++++  q+++ +K++s
  gene139|gene139|rna139|rna139   3 SRPLAFVCFVITINAGFFDLFSGSSNSQKSSSNEEEENKNVELSQEQLVNKIMS 56 
                                    677888888888888888888755555555566777788888888888888877 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                          Vps54  75 asqslslvialipyvkealerhl.eeksqesllaefdkvkrdyqehqneihaKLvsIm 131
                                     sq l+  ++  ++++ea ++   e+k+q++ ++ ++ +k+++  h n i +K+ +++
  gene139|gene139|rna139|rna139  83 ESQKLQTALSSWKQLQEAAKNAEnEKKKQKKKTNSMNALKKEIPRHTNAIKKKVGKVV 140
                                    5899***************9998667777788888******************98887 PP

>> NRN1  Neuritin protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.6   5.2e+03      31      32 ..      41      42 ..      25      64 .. 0.53
   2 ?   13.6   1.7   4.7e-05     0.053       8      58 ..      61     112 ..      52     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.6
                           NRN1 31 qe 32
                                   ++
  gene139|gene139|rna139|rna139 41 KN 42
                                   22 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.7e-05
                           NRN1   8 fsdCllklGdslaeykee.edeeeqeletickyWdefhaCaltaladCqeea 58 
                                    + + +l+l d+++++k+e  d+e+q+l+t  ++W + ++ a++a  + +++ 
  gene139|gene139|rna139|rna139  61 IDKSVLQLNDEVEKEKKEkLDSESQKLQTALSSWKQLQEAAKNAENEKKKQK 112
                                    56789*******98766516788******************99987765443 PP

>> Pep1_7  Elicitor peptide 1-7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   7.1e-05     0.079      30      67 ..      19      53 ..       6      64 .. 0.71
   2 ?   -0.7   2.6       1.8     2e+03      45      74 ..      99     127 ..      67     131 .. 0.61
   3 ?   -1.4   3.3       3.1   3.4e+03      69      81 ..     182     194 ..     144     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.1e-05
                         Pep1_7 30 lkclGLesssskspsssseeeeeetetvevtsrglvak 67
                                   +  + L s ss+s+ sss e eee+++ve +++ lv k
  gene139|gene139|rna139|rna139 19 F--FDLFSGSSNSQKSSSNE-EEENKNVELSQEQLVNK 53
                                   4..88989999999777776.67778888877777766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.8
                         Pep1_7  45 ssseeeeeetetvevtsrglvakvlkrrpk 74 
                                    +  +++e+e+++ + +++++ a  +k  p+
  gene139|gene139|rna139|rna139  99 EAAKNAENEKKKQKKKTNSMNAL-KKEIPR 127
                                    33333444444444444444333.566665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.1
                         Pep1_7  69 lkrrpkqkeSSGk 81 
                                    ++++ k+++SS+k
  gene139|gene139|rna139|rna139 182 SSKKRKRNPSSSK 194
                                    3344455556655 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   9.5   9.3e-05       0.1      13     119 ..      38     143 ..      22     179 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.3e-05
                     V_ATPase_I  13 Dlnedvnafqrkfvkevr.rcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnen 91 
                                    + n++v+  q + v+++   ++++++++  l++e+ek++k++  +e+   ++ ++  ++ ++l+e  +++e+e k+++++
  gene139|gene139|rna139|rna139  38 EENKNVELSQEQLVNKIMsEVEDIDKSVLQLNDEVEKEKKEKLDSES---QKLQTALSSWKQLQEAAKNAENEKKKQKKK 114
                                    34666666666666666424666666666666666664444444443...333344444555555555555555555555 PP

                     V_ATPase_I  92 leklkkelnelvelkavl.ekakefleee 119
                                    ++++++ ++e+  +++ + +k+ ++++ +
  gene139|gene139|rna139|rna139 115 TNSMNALKKEIPRHTNAIkKKVGKVVNGT 143
                                    55555555555444433314444444433 PP

>> Talin_middle  Talin, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.1      0.06        67      86     131 ..      48      93 ..      27     108 .. 0.70
   2 ?   11.2   2.4   0.00024      0.27      15      79 ..      86     151 ..      81     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.06
                   Talin_middle  86 gaalttIssnlkelsknvrllaaLdddesgdkLleAareLadAfsd 131
                                    +  +  I s ++++ k+v  l+   ++e+++kL + +++L +A+s+
  gene139|gene139|rna139|rna139  48 EQLVNKIMSEVEDIDKSVLQLNDEVEKEKKEKLDSESQKLQTALSS 93 
                                    3447788888888888888887777788999*********999985 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00024
                   Talin_middle  15 aiqeaeeeldkpael.palgdDaaskrwreetldqarqnvssqlaAmtaataqlvsltqasseeee 79 
                                    ++q+a ++ ++ +e+ ++  ++++ ++ + ++++  ++++  +  A++   +++v+ t++++e +e
  gene139|gene139|rna139|rna139  86 KLQTALSSWKQLQEAaKNAENEKKKQKKKTNSMNALKKEIPRHTNAIKKKVGKVVNGTNNEQEGDE 151
                                    456666666666655456688889999999****************************77777665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.7   0.00094         1       9      87 ..       7      97 ..       6     103 .. 0.68
   2 ?    4.8   0.9      0.03        34      24      58 ..     111     145 ..      95     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00094
                         DUF948  9 AFvvLviflivvllkl..........kktldeaaatieele.kqvdpilkevedllakvnelledvne.klekvdplteava 78
                                   AFv  vi +   ++ l          ++  +e ++ +e  + + v++i+ eved+ + v +l ++v++ k ek+d+  ++++
  gene139|gene139|rna139|rna139  7 AFVCFVITINAGFFDLfsgssnsqksSSNEEEENKNVELSQeQLVNKIMSEVEDIDKSVLQLNDEVEKeKKEKLDSESQKLQ 88
                                   66666666666666666666666333222333333444333355789999***********999999878999999888888 PP

                         DUF948 79 dlgesvsel 87
                                   ++  s ++l
  gene139|gene139|rna139|rna139 89 TALSSWKQL 97
                                   876666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.03
                         DUF948  24 lkktldeaaatieelekqvdpilkevedllakvne 58 
                                     kk  ++++a  +e+ +++++i k+v ++++ +n+
  gene139|gene139|rna139|rna139 111 QKKKTNSMNALKKEIPRHTNAIKKKVGKVVNGTNN 145
                                    46667788888889999999999999999999997 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   8.5   0.00082      0.92      53     121 ..      62     128 ..      60     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00082
                        DUF3987  53 dklvlrpleeieaelreeyeeelkeyeaekkaweaelealekkaakakeakaeealaeleaeepeePkl 121
                                    dk vl++  e+e+e +e+ + e ++ +++ + w++ +ea++++ ++  ++k+++++  + a+++e+P++
  gene139|gene139|rna139|rna139  62 DKSVLQLNDEVEKEKKEKLDSESQKLQTALSSWKQLQEAAKNAENE--KKKQKKKTNSMNALKKEIPRH 128
                                    677899999**************************77765444333..788888888888999999976 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  12.9   0.00079      0.88     596     691 ..      30     127 ..      14     137 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00079
                           Hid1 596 deeeeenssessrieesrsesrspslsevpelksslaitddeskaereksatessssqavs..qlremsekarakesaes 673
                                    +++++++++e++++e s+++ ++  +sev+++++s+++ +de ++e++++  ++s++  +     ++++e a++ e++++
  gene139|gene139|rna139|rna139  30 QKSSSNEEEENKNVELSQEQLVNKIMSEVEDIDKSVLQLNDEVEKEKKEKLDSESQKLQTAlsSWKQLQEAAKNAENEKK 109
                                    2222333333333333345556666999*******999999988888776655555543333356677777777777777 PP

                           Hid1 674 teesrqesatskkspsgm 691
                                    +++++++s++  k++ + 
  gene139|gene139|rna139|rna139 110 KQKKKTNSMNALKKEIPR 127
                                    777777777777766544 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.9      0.42   4.7e+02     110     138 ..      36      65 ..      21      89 .. 0.52
   2 ?    9.2   8.3   0.00075      0.84      61     148 ..      44     142 ..      36     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.42
                                    .ECHHGGCC.HCCCTHHHHHHHHHTHHHHH CS
                 Choline_kinase 110 akkekkkkq.lklinledlekeleklekll 138
                                    +++e+k+ +  ++  ++++++e+e++ k +
  gene139|gene139|rna139|rna139  36 EEEENKNVElSQEQLVNKIMSEVEDIDKSV 65 
                                    222222222022233444555555554444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00075
                                    GGGCHHHHHHHHHHHHHHTTCHH............TTSSSS-HHHHHHHHHHHCCS.TT..ECHHGGCCHCCCTHHHHHH CS
                 Choline_kinase  61 dlrepeiskkiAkklaelHslel...........eseskespslwktmqkwllnkeaqtkakkekkkkqlklinledlek 129
                                    +l+++++ +ki ++++ + +++l           e+  +es+ l + + +w + +ea+++a++ekkk++ k+ +++ l+k
  gene139|gene139|rna139|rna139  44 ELSQEQLVNKIMSEVEDIDKSVLqlndevekekkEKLDSESQKLQTALSSWKQLQEAAKNAENEKKKQKKKTNSMNALKK 123
                                    67777777777777777777777888888888877788899999999********************************* PP

                                    HHHTHHHHHHCHGG-EEEE CS
                 Choline_kinase 130 elekleklleelespvvfc 148
                                    e+ +  + ++++  +vv  
  gene139|gene139|rna139|rna139 124 EIPRHTNAIKKKVGKVVNG 142
                                    ****999998877777655 PP

>> Rsd_AlgQ  Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.5   0.00032      0.36      79     133 ..      39      96 ..      15     107 .. 0.78
   2 ?    0.6   0.3      0.43   4.9e+02      80     105 ..     107     132 ..      96     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00032
                       Rsd_AlgQ  79 eaeefgdkelelakelypkieatTeaaldfndkyeeaad...edeleeldedLsklge 133
                                    e+++ + ++ +l++++++++e++ +++l++nd++e++++   ++e ++l+++Ls+  +
  gene139|gene139|rna139|rna139  39 ENKNVELSQEQLVNKIMSEVEDIDKSVLQLNDEVEKEKKeklDSESQKLQTALSSWKQ 96 
                                    455556667899**********************994331113567778888877655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                       Rsd_AlgQ  80 aeefgdkelelakelypkieatTeaa 105
                                     +++++k+++ ++ l ++i + T+a+
  gene139|gene139|rna139|rna139 107 EKKKQKKKTNSMNALKKEIPRHTNAI 132
                                    23334444777777777777777765 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   4.6     0.057        64      76     128 ..      31      81 ..      21      89 .. 0.68
   2 ?    9.3  13.2   0.00081      0.91      26     122 ..      54     148 ..      44     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.057
                          PIN_8  76 kleealkkwakkkaldteelrkelkkqleelkeelkaeleelkksskadkeed 128
                                    k ++  ++++k+ +l++e+l +++ +++e++++++ +  +e++k+ k++   d
  gene139|gene139|rna139|rna139  31 KSSSNEEEENKNVELSQEQLVNKIMSEVEDIDKSVLQLNDEVEKEKKEKL--D 81 
                                    445566778888899999**************999444455555554444..3 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00081
                          PIN_8  26 vlekladrlwvPhqvalEfqrnresviskekkayedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqlee 105
                                    ++ +++d      q   E  +++++ +++e+++++++ ++ ++l++aa++ ++   kk++kkk+ + + l+ke+ +++++
  gene139|gene139|rna139|rna139  54 IMSEVEDIDKSVLQLNDEVEKEKKEKLDSESQKLQTALSSWKQLQEAAKNAEN--EKKKQKKKTNSMNALKKEIPRHTNA 131
                                    5555555445556888999******************************7554..4445555555567************ PP

                          PIN_8 106 lkeelkaeleelkkssk 122
                                    +k+++ +  +  +++++
  gene139|gene139|rna139|rna139 132 IKKKVGKVVNGTNNEQE 148
                                    *****444443333333 PP

>> XRN_M  Xrn1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  15.5    0.0021       2.3      56     162 ..      39     148 ..      23     159 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0021
                          XRN_M  56 dngevkldr...veklvslvgkveekifrkrkeredrkekklakeeeaskedaaneeaavaeeklseskvaksaeaeaea 132
                                    +n++v+l++   v+k++s+v+ +++++ +   e e++k++kl++e+++ +++  + ++ ++ +k +e++++k++++++++
  gene139|gene139|rna139|rna139  39 ENKNVELSQeqlVNKIMSEVEDIDKSVLQLNDEVEKEKKEKLDSESQKLQTALSSWKQLQEAAKNAENEKKKQKKKTNSM 118
                                    57777776544478889999999999998888888888888888888777777766666666666666666666666666 PP

                          XRN_M 133 eaeaeaeakaekekrekaekeleeseeeee 162
                                    +a  ++  ++++  ++k+ k ++ +++e+e
  gene139|gene139|rna139|rna139 119 NALKKEIPRHTNAIKKKVGKVVNGTNNEQE 148
                                    666666666666666665554443333322 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  12.3     0.013        15      12      56 ..       6      48 ..       4     136 .. 0.83
   2 ?   -0.8   0.1         2   2.2e+03      61      72 ..     169     180 ..     117     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                        DUF3899 12 liigillivlnsGfFdgfsygfrklkklflkkskkddsyyeykek 56
                                   l++  ++i++n+GfFd+fs + +  k++ + +  ++ +  e  ++
  gene139|gene139|rna139|rna139  6 LAFVCFVITINAGFFDLFSGSSNSQKSSSNEE--EENKNVELSQE 48
                                   88999*********************997643..33333333333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2
                        DUF3899  61 skkstrplliiG 72 
                                    + k++++ll+iG
  gene139|gene139|rna139|rna139 169 KGKVLKKLLGIG 180
                                    444444444444 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9  14.2    0.0043       4.8     265     387 ..      49     180 ..      21     207 .] 0.62

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0043
                           ALMT 265 gvlrqcaytvealhgci.lseiqapeelrkkfkeelqrv..slesakvlrelaesvkkmkklsk.veellkevkvaaeeL 340
                                    ++++++  +ve ++  + + + ++ +e ++k+ +e q++  +l s k l+e a++ ++ kk++k  +++++ +k+ + + 
  gene139|gene139|rna139|rna139  49 QLVNKIMSEVEDIDKSVlQLNDEVEKEKKEKLDSESQKLqtALSSWKQLQEAAKNAENEKKKQKkKTNSMNALKKEIPRH 128
                                    56777777888886655477888888999998888887622456788999999998888777765788899999999999 PP

                           ALMT 341 qskldskskLlvnsekweaakkkekaeeveekkeeekeseskkeea.....e 387
                                    ++++++k   +vn  ++e++ ++++ + +++   ++ +  + k  +      
  gene139|gene139|rna139|rna139 129 TNAIKKKVGKVVNGTNNEQEGDESDGGDESDGDGKSGRGGKGKVLKkllgiG 180
                                    9999888877777665444444433333333333333333333333344441 PP

>> GREB1  Gene regulated by oestrogen in breast cancer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  12.2    0.0036         4    1095    1224 ..      25     147 ..      13     200 .. 0.53

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0036
                          GREB1 1095 sdaeklsstdnedeelqedgerpksnssavqstsdsvaadaaeessktspvkvekseskdavesglsskasakselse 1172
                                       ++++ s+ ne+ee + + e   s+ + v+++ ++   +  ++s  + +++vek+++++  +++++ +++ +s  + 
  gene139|gene139|rna139|rna139   25 GSSNSQKSSSNEEEENK-NVEL--SQEQLVNKIMSE--VEDIDKSVLQLNDEVEKEKKEKLDSESQKLQTALSSWKQL 97  
                                     44455555566666553.3333..333333222222..2223333344455666666665555555555555554332 PP

                          GREB1 1173 asaaaasaseeakspkasvtseeeeseeskekekeslsketesqlsleaseq 1224
                                      ++aa+ + e++k+ +++ t+++++ ++++ ++++ ++k+  + ++ ++ eq
  gene139|gene139|rna139|rna139   98 -QEAAK-NAENEKKKQKKKTNSMNALKKEIPRHTNAIKKKVGKVVNGTNNEQ 147 
                                     .22222.222233333344555666666666666666655555444333333 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   6.6    0.0092        10     227     323 ..      45     116 ..       8     159 .. 0.42

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0092
                          LMBR1 227 lkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteeslaklekqlika........lqkrertekqwkrll 298
                                    l++ + +                  +k+ +        + ++  +s+ +l+ ++ k+        +qk +     wk+l 
  gene139|gene139|rna139|rna139  45 LSQEQLV------------------NKIMS--------EVEDIDKSVLQLNDEVEKEkkekldseSQKLQTALSSWKQLQ 98 
                                    1111111..................11111........222223333333333222210000000333333333333333 PP

                          LMBR1 299 ekalelediiknksskekefksses 323
                                    e a       kn+++++k+ k++++
  gene139|gene139|rna139|rna139  99 EAA-------KNAENEKKKQKKKTN 116
                                    333.......333333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4690  (0.261587); expected 358.6 (0.02)
Passed bias filter:                     1009  (0.0562775); expected 358.6 (0.02)
Passed Vit filter:                       201  (0.0112109); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.89u 0.40s 00:00:01.29 Elapsed: 00:00:00.57
# Mc/sec: 1097.78
//
Query:       gene1392|gene1392|rna1391|rna1391  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-13   48.6   0.0    1.2e-12   47.9   0.0    1.2  1  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   6.6e-17   1.2e-12       7     149 ..      74     214 ..      70     218 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 6.6e-17
                                        HHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCTTTTTSCHHHHHHHHHHHHHHSSSTTTTGGHHHHHHH CS
                             RhoGAP   7 cvefiekrgldtegiyRvsgskarvkelreafdkgkavdsdleeedvhavaslLKrfLrelpepLltkelyeelie 82 
                                         + +iek+g +++gi+  s s+++v+++ + ++ +++   d  +  + +v   +K + +e  +++++ +  +++ie
  gene1392|gene1392|rna1391|rna1391  74 AMGYIEKNGWKVKGIFISSESEENVNNCVKLLELNEKI--DYPSVHPKDVGMGFKIYVEENLKNIIPLNVRKRVIE 147
                                        6789*********************************9..8*********************************** PP

                                        HHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHTHHHH---HHHHHHHHHHHHHT-TSS CS
                             RhoGAP  83 aaksedeeerlealkellekLPkenrdtLryLlehLkrvaenskenkMtaknLaivfaPtLlrpkse 149
                                        a+k++d+e +   + ++   L+++nr  L++L   +  +  n  en+ +++ +   f+P ++r +se
  gene1392|gene1392|rna1391|rna1391 148 AYKNKDDERKEIIIPRIPFVLSDPNRMFLKSLKNIFLAIETNTGENEVDIDEIYRQFGPLIIRRPSE 214
                                        ***************************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.60
# Mc/sec: 1226.88
//
Query:       gene1393|gene1393|rna1392|rna1392  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 499.06
//
Query:       gene1394|gene1394|rna1393|rna1393  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.9e-08   31.9   8.5    0.00054   19.8   2.0    2.6  2  zf-CCCH    Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    4.2e-07   30.6   2.1      0.017   15.8   0.1    2.5  2  Torus      Torus domain
  ------ inclusion threshold ------
      0.016   15.3   1.7      0.016   15.3   1.7    3.1  3  zf_CCCH_4  Zinc finger domain
       0.18   11.6   8.0        1.2    9.0   0.8    2.7  2  zf-CCCH_4  CCCH-type zinc finger
        1.3    9.6   8.4        7.8    7.1   1.5    2.7  2  zf-CCCH_2  RNA-binding, Nab2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.0   1.5e-07   0.00054       3      25 ..       5      27 ..       4      28 .. 0.91
   2 !   15.3   0.5     4e-06     0.014       5      26 ..     138     158 ..     137     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-07
                                       CHCBCHHHHHS--TTGGG-SSBS CS
                            zf-CCCH  3 telCrffmrtGyCkyGdrCkFaH 25
                                       +  C f+++t  C+yG  C  aH
  gene1394|gene1394|rna1393|rna1393  5 RDVCIFYSKTNGCRYGLECTKAH 27
                                       789****************9777 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4e-06
                                        CBCHHHHHS--TTGGG-SSBSC CS
                            zf-CCCH   5 lCrffmrtGyCkyGdrCkFaHg 26 
                                         C ++ + G C  G+rC F+H+
  gene1394|gene1394|rna1393|rna1393 138 VCTDYEK-GLCGKGERCGFIHV 158
                                        5******.*************6 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   4.8e-06     0.017      71      98 ..       6      34 ..       2      44 .. 0.83
   2 !   14.1   0.2   1.6e-05     0.058      71      92 ..     137     158 ..     103     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
                                       -B-HHHHHT.--SSGGG-SSB-S---SS- CS
                              Torus 71 yfClfFarG.lCakGkkCeylHrlPteed 98
                                        +C+f+++   C +G +C+  Hr+P +++
  gene1394|gene1394|rna1393|rna1393  6 DVCIFYSKTnGCRYGLECTKAHRIPARSK 34
                                       58*****9735**************9987 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.6e-05
                                        -B-HHHHHT--SSGGG-SSB-S CS
                              Torus  71 yfClfFarGlCakGkkCeylHr 92 
                                         +C  + +GlC kG++C ++H 
  gene1394|gene1394|rna1393|rna1393 137 GVCTDYEKGLCGKGERCGFIHV 158
                                        58*******************6 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.4    0.0036        13       1      12 [.       8      20 ..       8      24 .. 0.89
   2 ?   15.3   1.7   4.3e-06     0.016       1      19 []     139     157 ..     139     157 .. 0.98
   3 ?   -3.3   0.2         3   1.1e+04       7      10 ..     184     187 ..     183     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0036
                          zf_CCCH_4  1 Ckfflq.GtCkkG 12
                                       C f+ + + C++G
  gene1394|gene1394|rna1393|rna1393  8 CIFYSKtNGCRYG 20
                                       9************ PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.3e-06
                          zf_CCCH_4   1 CkfflqGtCkkGdkCrFaH 19 
                                        C  + +G C kG++C F+H
  gene1394|gene1394|rna1393|rna1393 139 CTDYEKGLCGKGERCGFIH 157
                                        99****************9 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3
                          zf_CCCH_4   7 GtCk 10 
                                        G+Ck
  gene1394|gene1394|rna1393|rna1393 184 GKCK 187
                                        8886 PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.3    0.0034        12       7      18 ..      12      24 ..       7      27 .. 0.74
   2 ?    9.0   0.8   0.00034       1.2       2      21 ..     138     157 ..     138     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0034
                          zf-CCCH_4  7 a.kGsCrfGdnCr 18
                                         +++Cr+G  C+
  gene1394|gene1394|rna1393|rna1393 12 SkTNGCRYGLECT 24
                                       3489*****8776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00034
                          zf-CCCH_4   2 lCpyfakGsCrfGdnCrFsH 21 
                                        +C+ + kG C  G++C F H
  gene1394|gene1394|rna1393|rna1393 138 VCTDYEKGLCGKGERCGFIH 157
                                        799999************** PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.5    0.0022       7.8       2      17 ..       8      27 ..       8      27 .. 0.74
   2 ?    5.9   0.8    0.0054        19       2      17 ..     139     157 ..     139     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0022
                          zf-CCCH_2  2 Crffpn...C.tnpkCpFaH 17
                                       C f+ +   C ++ +C+ aH
  gene1394|gene1394|rna1393|rna1393  8 CIFYSKtngCrYGLECTKAH 27
                                       77777777788888888777 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0054
                          zf-CCCH_2   2 Crffpn..C.tnpkCpFaH 17 
                                        C ++ +  C ++++C F+H
  gene1394|gene1394|rna1393|rna1393 139 CTDYEKglCgKGERCGFIH 157
                                        77777778**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1778.40
//
Query:       gene1395|gene1395|rna1394|rna1394  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-14   52.3   6.6    2.5e-06   27.7   1.5    2.6  2  LRR_4     Leucine Rich repeats (2 copies)
    3.4e-12   45.9   8.5    2.4e-08   33.6   3.0    3.1  3  LRR_8     Leucine rich repeat
      2e-09   36.7   5.4       0.33   11.7   0.1    4.7  5  LRR_1     Leucine Rich Repeat
    1.9e-07   30.6  10.5       0.37   11.0   0.1    4.5  4  LRR_6     Leucine Rich repeat
      0.002   17.7   0.5     0.0025   17.3   0.5    1.2  1  LRR_9     Leucine-rich repeat


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   1.5   6.9e-10   2.5e-06       4      40 ..      45      81 ..      42      85 .. 0.86
   2 !   26.9   0.3   1.3e-09   4.5e-06       1      38 [.      88     128 ..      88     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 6.9e-10
                                       -EEE--SS---E-S-HHH.-TT--EEE-.-S-----GG CS
                              LRR_4  4 evLdLsnNqltdipllek.lpnLkeLdLsgNnlitdld 40
                                       ++LdLs+N+l+++p+  + l  L eLdL +Nn i++++
  gene1395|gene1395|rna1394|rna1394 45 KKLDLSSNKLKELPSDIGaLNWLVELDL-SNNEIGKIP 81
                                       89*************5554*********.666999985 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.3e-09
                                        SS--EEE--SS---E-S-..HHH-TT...--EEE-.-S----- CS
                              LRR_4   1 pnLevLdLsnNqltdipl..leklpn...LkeLdLsgNnlitd 38 
                                        ++LevL+LsnN+lt++p+  l+ l     Lk+LdL gN ++ +
  gene1395|gene1395|rna1394|rna1394  88 KSLEVLNLSNNKLTSFPWkvLR-LGRtgtLKSLDLRGN-PLYR 128
                                        68****************8866.444556******888.6655 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   2.5   2.7e-08   9.7e-05      19      61 .]      36      77 ..      21      77 .. 0.91
   2 !   33.6   3.0   6.7e-12   2.4e-08       3      61 .]      67     126 ..      66     126 .. 0.90
   3 !    5.9   0.0    0.0029        10       3      22 ..     116     135 ..     114     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.7e-08
                                       TSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8 19 eaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       ea k+++  k LdLs+N+l+ l p  +  L+ L +LdLs+N +
  gene1395|gene1395|rna1394|rna1394 36 EALKTNKLIKKLDLSSNKLKEL-PSDIGALNWLVELDLSNNEI 77
                                       567888999*************.9*****************87 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 6.7e-12
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGT..T--S-.EEE--SS-- CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafs..gLpsLrsLdLsgNrL 61 
                                        L +LdLsnN + +++ e+   +++L+vL+LsnN+lt++ +++++      L+sLdL+gN+L
  gene1395|gene1395|rna1394|rna1394  67 LVELDLSNNEIGKIPEEMND-MKSLEVLNLSNNKLTSFPWKVLRlgRTGTLKSLDLRGNPL 126
                                        779**************977.*******************9986336778*********87 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0029
                                        -SEEE-TTS--SEE-TTSST CS
                              LRR_8   3 LtsLdLsnNrltslddeaFk 22 
                                        L+sLdL+ N l  +  +aF 
  gene1395|gene1395|rna1394|rna1394 116 LKSLDLRGNPLYRIYHTAFG 135
                                        77888888888777777775 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         4   1.5e+04      11      12 ..      21      22 ..      12      33 .. 0.53
   2 !    6.9   0.0    0.0033        12       3      17 ..      45      59 ..      44      64 .. 0.75
   3 !    7.0   0.0    0.0032        12       2      17 ..      67      81 ..      67      84 .. 0.80
   4 !   11.7   0.1   9.2e-05      0.33       1      16 [.      89     104 ..      89     109 .. 0.87
   5 !   10.3   0.0   0.00025      0.91       2      14 ..     116     128 ..     115     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4
                              LRR_1 11 pl 12
                                        l
  gene1395|gene1395|rna1394|rna1394 21 DL 22
                                       33 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0033
                              LRR_1  3 rhLdLsnnpllglpp 17
                                       ++LdLs+n l  lp+
  gene1395|gene1395|rna1394|rna1394 45 KKLDLSSNKLKELPS 59
                                       89********55554 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0032
                              LRR_1  2 LrhLdLsnnpllglpp 17
                                       L +LdLsnn + g++p
  gene1395|gene1395|rna1394|rna1394 67 LVELDLSNNEI-GKIP 81
                                       679*******9.5665 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 9.2e-05
                              LRR_1   1 nLrhLdLsnnpllglp 16 
                                        +L++L+Lsnn l+++p
  gene1395|gene1395|rna1394|rna1394  89 SLEVLNLSNNKLTSFP 104
                                        69**********9887 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00025
                              LRR_1   2 LrhLdLsnnpllg 14 
                                        L++LdL++npl +
  gene1395|gene1395|rna1394|rna1394 116 LKSLDLRGNPLYR 128
                                        9*********933 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.3    0.0011         4       2      15 ..      41      54 ..      40      55 .. 0.85
   2 !   11.0   0.1    0.0001      0.37       3      16 ..      65      78 ..      63      79 .. 0.90
   3 !    8.2   0.4   0.00078       2.8       4      16 ..      89     101 ..      86     102 .. 0.89
   4 !    8.0   0.0   0.00095       3.4       4      14 ..     115     125 ..     115     126 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                              LRR_6  2 nthLteLdLsgNdI 15
                                       n  +++LdLs+N++
  gene1395|gene1395|rna1394|rna1394 41 NKLIKKLDLSSNKL 54
                                       66789*******97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0001
                              LRR_6  3 thLteLdLsgNdIg 16
                                       ++L eLdLs N+Ig
  gene1395|gene1395|rna1394|rna1394 65 NWLVELDLSNNEIG 78
                                       689**********8 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00078
                              LRR_6   4 hLteLdLsgNdIg 16 
                                        +L+ L+Ls N+++
  gene1395|gene1395|rna1394|rna1394  89 SLEVLNLSNNKLT 101
                                        89*********97 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.00095
                              LRR_6   4 hLteLdLsgNd 14 
                                        +L++LdL+gN 
  gene1395|gene1395|rna1394|rna1394 115 TLKSLDLRGNP 125
                                        8*********7 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.5     7e-07    0.0025      45     126 ..      45     127 ..      23     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7e-07
                              LRR_9  45 dtidlsdndirkl.dgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqela.dldPlaslkklell 118
                                          +dls n++++l  ++  l+ l  l l+nn i +i e+++++  +le l l+nn+l+++  ++  l     l++l
  gene1395|gene1395|rna1394|rna1394  45 KKLDLSSNKLKELpSDIGALNWLVELDLSNNEIGKIPEEMNDM-KSLEVLNLSNNKLTSFPwKVLRLGRTGTLKSL 119
                                        56899******99457999********************9885.799*********99874367777777788888 PP

                              LRR_9 119 sllknpvt 126
                                         l  np+ 
  gene1395|gene1395|rna1394|rna1394 120 DLRGNPLY 127
                                        77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1167.51
//
Query:       gene1396|gene1396|rna1395|rna1395  [L=1097]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-36  125.1  28.9    3.8e-36  125.1  28.9    2.5  3  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
    7.4e-13   49.3   0.0    2.3e-10   41.1   0.0    2.6  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.8e-09   37.2   4.0    1.8e-09   37.2   4.0    2.1  2  PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
    1.6e-08   34.3  11.1    3.2e-06   26.8   0.0    3.8  4  E1-E2_ATPase     E1-E2 ATPase
    1.5e-07   31.4   0.0    8.5e-06   25.8   0.0    2.6  2  Cation_ATPase    Cation transport ATPase (P-type)
  ------ inclusion threshold ------
      0.036   13.8   1.6      0.064   13.0   0.1    2.1  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
      0.039   13.8   0.2      0.077   12.8   0.2    1.5  1  AFOR_N           Aldehyde ferredoxin oxidoreductase, N-termin


Domain annotation for each model (and alignments):
>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.22   5.5e+02     176     224 ..      29      77 ..      10      93 .. 0.51
   2 ?   -2.5   0.2       1.4   3.5e+03      44      82 ..     382     420 ..     373     423 .. 0.78
   3 !  125.1  28.9   1.5e-39   3.8e-36       2     245 ..     862    1084 ..     861    1088 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.22
                    PhoLip_ATPase_C 176 wtliliililgsillyflflllyssllps.ssefygvleelfsspsfwlv 224
                                        ++++++i+ ++ + +  +f++++  ++++  ++ y  +++l+ s+  w++
  gene1396|gene1396|rna1395|rna1395  29 YKWYTFIFAVLRLQFSHFFNTFLFFVCMTqLKKEY-LVSSLVASVGPWAM 77 
                                        34555555555442222222222222222112222.34555555444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                    PhoLip_ATPase_C  44 tlvqfwfqfyngfsgqslyeswlltlynllftslpvivl 82 
                                        + ++++ ++++++ g +   +++++ + +lf+s+ +i l
  gene1396|gene1396|rna1395|rna1395 382 VGCMLLAGIFTYMRGATSRPDIVFIRFLVLFSSVIPISL 420
                                        566777788889999999999999999999999988876 PP

  == domain 3  score: 125.1 bits;  conditional E-value: 1.5e-39
                    PhoLip_ATPase_C    2 raSDyaiaqFrfLkrLLlvhGrwsyrRisklilyffyKnvvftlvqfwfqfyngfsgqslyeswlltlynllft 75  
                                          a+D++i++F++ ++LL++hGr+sy+R++k+   ++++ +++t++q++f    +f    l+ + ll+++ +++t
  gene1396|gene1396|rna1395|rna1395  862 LAADFSINKFSHVSDLLFWHGRNSYQRTAKIAHLIIHRGLTLTVIQAIFCSLIYFVPVGLFRGELLMMFITVYT 935 
                                         69************************************************************************ PP

                    PhoLip_ATPase_C   76 slpvivlgifdqdvsaelllkyPelYklgqknklfnlktfllwileglyqsliifflsylvlddssfsdgktnd 149 
                                         +lp++ + i   d+s +++ k+PelYk++++nkl++++ f +wil ++yq++i+++ +yl+           ++
  gene1396|gene1396|rna1395|rna1395  936 FLPIFSI-ICSSDISRSVVVKFPELYKELTENKLLSYRHFSVWILISFYQGTIMMITFYLLK----------QE 998 
                                         *****99.99*******************************************999966664..........46 PP

                    PhoLip_ATPase_C  150 lqlfgtlvftalvlvvnlkvaletktwtliliililgsillyflflllyssllpsssefygvleelfsspsfwl 223 
                                         ++ ++tl+ft+l++  +l+v+l t+++t +++++  +s+++y+++++l + ll ++++fy           f l
  gene1396|gene1396|rna1395|rna1395  999 FFIISTLTFTSLIINELLMVILTTTRMTSMVFVSSGMSLAIYVIYFILRKGLLRYQKPFY----------LFLL 1062
                                         89**************************999999999********988888777666666..........3444 PP

                    PhoLip_ATPase_C  224 vlllvvvvallpdllikvlkrt 245 
                                          +++v ++a+l+ ++ k++ ++
  gene1396|gene1396|rna1395|rna1395 1063 KIAVVNTLAILVSVIQKLWIKY 1084
                                         4555555555555555544444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0     9e-14   2.3e-10       4     210 .]     461     847 ..     458     847 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 9e-14
                                        EEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH.HHCHHHHHHHHHHHHHHHHH...HHHHHETTTEHHHHTHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                          Hydrolase   4 vvfDkdGTLttgepsvedvivsaalalaaaletg.sehpigkalvaaakarsgal...tgfatfigrgayaigkpe 75 
                                        ++ Dk+GTLt+ e++ +++          +  t   ++ i k+l++  + rs      +++ +      +     +
  gene1396|gene1396|rna1395|rna1395 461 LLTDKTGTLTKNEMEMKKIHLGT------ICYTKeLNREISKNLAKVLNSRSDGKrvfSRVKK-----DINARVYD 525
                                        678**********9999977777......2222234555666666666666333212344444.....44445555 PP

                                        HHHHH....HCHHHHHHHHHHHHHHCHHHHHH............................................ CS
                                        xxxxx....xxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                          Hydrolase  76 wltal....dippdlgaaigsaqsqgrtvall............................................ 103
                                        +++al    +++p   ++  s+q+   +++                                              
  gene1396|gene1396|rna1395|rna1395 526 LVQALsvchNVTPVISENEISYQASSPDEVAIvqwtecvgmklyrrdrsriiirdplndeqeyqvlytfpftsetk 601
                                        5555555553444444444444433333333336777777777777777777788888888888889999999999 PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                          Hydrolase 104 ............................................................................ 103
                                                                                                                    
  gene1396|gene1396|rna1395|rna1395 602 rmgiivryneevifflkgadavmkgiikgndwveeeadnmardglrtlviakkilskkefesfedmynkawislid 677
                                        999999999999999999999999999999999999999999999999999************************* PP

                                        ..............TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.....GGGE CS
                                        ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxx RF
                          Hydrolase 104 ..............qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.....ddyf 160
                                                      + ++l++  ++d+  + ++++ +++ L+ a  +v++ltgd  eta ++a+          y+
  gene1396|gene1396|rna1395|rna1395 678 raeamskamgiienNMNVLGITGVEDK--LQDDVKITLENLRNAEMKVWMLTGDKIETAISIARSSRifhrgTTYL 751
                                        *************999***********..************************************88554432222 PP

                                        SEEEEHHCES...STTT................................................SHHHHHHHHHH CS
                                        xxxxxxxxxx...xxxx................................................xxxxxxxxxxx RF
                          Hydrolase 161 daviasdiet...vakp................................................spegkvaaire 185
                                               i+     +++                                                 p +k a++re
  gene1396|gene1396|rna1395|rna1395 752 ------VISNassAGEVkakldllrgsgynslvidgqslsfvvescmdefieiasgleavvgcryTPTQKAAIARE 821
                                        ......2222333333344559999999************************************************ PP

                                        HTST.GGGEEEEESSHHHHHHHHHTT CS
                                        xxxx.xxxxxxxxxxxxxxxxxxxxx RF
                          Hydrolase 186 Lqgk.peevamVGDgvnDaaalaaAg 210
                                        L+ k ++ v+ +GDg nD++++ +A+
  gene1396|gene1396|rna1395|rna1395 822 LKNKtKKCVCCIGDGGNDVSMITEAN 847
                                        *966588899***********99986 PP

>> PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   4.0   6.9e-13   1.8e-09       8      54 ..      13      59 ..       7      71 .. 0.88
   2 ?   -4.1   0.2       5.2   1.3e+04      25      32 ..     932     939 ..     932     940 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 6.9e-13
                    PhoLip_ATPase_N  8 enekkkyasNkIsTsKYtlltFlpknLfeqFrrvaNlYFLviailql 54
                                       ++++++y++N I+++KY+++tF++ +L  qF+++ N + +++++ ql
  gene1396|gene1396|rna1395|rna1395 13 KEQRRRYPRNIIRNQKYKWYTFIFAVLRLQFSHFFNTFLFFVCMTQL 59
                                       445569********************************999999987 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 5.2
                    PhoLip_ATPase_N  25 tlltFlpk 32 
                                        t++tFlp 
  gene1396|gene1396|rna1395|rna1395 932 TVYTFLPI 939
                                        799***97 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.2e-09   3.2e-06      12      64 ..     110     167 ..     100     202 .. 0.81
   2 !   12.3   0.0   3.5e-05      0.09      67     167 ..     328     424 ..     285     428 .. 0.74
   3 ?   -4.2   0.4         4     1e+04     125     172 ..     906     922 ..     887     941 .. 0.50
   4 ?   -1.3   1.9      0.53   1.4e+03     121     158 ..    1027    1076 ..    1017    1079 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.2e-09
                                        TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEE.....E-SEEE-TTTS---S-EE- CS
                       E1-E2_ATPase  12 dgteeeidakelvpGDivllkagdrvpaDgrive.....gsaevdesaLTGEslpvek 64 
                                        ++  ++++++++++GD++ll++++rvpaD+++++     g+  v + +L GE  +  k
  gene1396|gene1396|rna1395|rna1395 110 SQGFVRVPSSKIEVGDLILLEKNERVPADMVLLKtsdvsGQVFVRTDQLDGETDWKLK 167
                                        566789***************************9555544448999999999887655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.5e-05
                                        TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTS CS
                       E1-E2_ATPase  67 gdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgk 142
                                        ++m+ + tv+   ++ + V+ tg+d      a+++ ++++ + ++ k+ ++l +++ ++++ ++ll+ ++++++g 
  gene1396|gene1396|rna1395|rna1395 328 ENMLWMNTVIATCSVLGCVVYTGKD------AKAMLNTSQPRNKIGKIENELNGYMKVLGVGCMLLAGIFTYMRGA 397
                                        6777777777777777777777776......555666666666666666666666667777777777777777777 PP

                                        STT..HHHHHHHHHHHHHS-TTHHHHH CS
                       E1-E2_ATPase 143 sla..eallralallvaaiPcaLplav 167
                                        + +    ++r+l+l+ ++iP+ L ++v
  gene1396|gene1396|rna1395|rna1395 398 TSRpdIVFIRFLVLFSSVIPISLRITV 424
                                        6666588889*************9876 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 4
                                        HHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHHHHHH CS
                       E1-E2_ATPase 125 vvlliallvflialllgkslaeallralallvaaiPcaLplavplala 172
                                        +                                ai c L+ +vp+ l+
  gene1396|gene1396|rna1395|rna1395 906 IQ-------------------------------AIFCSLIYFVPVGLF 922
                                        22...............................233333333333333 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.53
                                         HHHHHHHHHHHHHHHS-STTTSSTT............HHHHHHHHHHHHH CS
                       E1-E2_ATPase  121 vlvpvvlliallvflialllgksla............eallralallvaa 158 
                                          +v+v+  ++l++++i ++l+k+l              a++++la+lv++
  gene1396|gene1396|rna1395|rna1395 1027 SMVFVSSGMSLAIYVIYFILRKGLLryqkpfylfllkIAVVNTLAILVSV 1076
                                         57888999999999999999999888888878888877777888888876 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   3.3e-09   8.5e-06       3      81 ..     533     621 ..     531     625 .. 0.78
   2 ?    2.5   0.0     0.061   1.6e+02      10      29 ..     717     736 ..     705     748 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.3e-09
                      Cation_ATPase   3 cNsaafsensekdevkllGnktEsALlvlaekl.............gldteelreetkkvqeipFnssrKrmsvvl 65 
                                        c++ +    se++      +++E+A+++ +e +               d+ + ++e++ + ++pF+s+ Krm++++
  gene1396|gene1396|rna1395|rna1395 533 CHNVTP-VISENEISYQASSPDEVAIVQWTECVgmklyrrdrsriiIRDPLNDEQEYQVLYTFPFTSETKRMGIIV 607
                                        555555.556677777788999******9999966666666666666666666666******************** PP

                      Cation_ATPase  66 klepekkvrlyvKGAp 81 
                                        +   +++v+ + KGA 
  gene1396|gene1396|rna1395|rna1395 608 RY--NEEVIFFLKGAD 621
                                        *6..5**********6 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.061
                      Cation_ATPase  10 ensekdevkllGnktEsALl 29 
                                        +n+e +++ l+G+k E+A+ 
  gene1396|gene1396|rna1395|rna1395 717 RNAEMKVWMLTGDKIETAIS 736
                                        68999*************85 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       3.6   9.2e+03     147     167 ..     484     504 ..     463     532 .. 0.51
   2 ?   -2.0   0.0      0.97   2.5e+03      15      51 ..     704     740 ..     702     755 .. 0.84
   3 ?   13.0   0.1   2.5e-05     0.064     199     227 ..     823     851 ..     814     870 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.6
                                        EES-HHHHHHHHHHHHHHCTT CS
                        Hydrolase_3 147 ilkdkekldelekelksklnk 167
                                        i+++ke   e+ k+l++ ln+
  gene1396|gene1396|rna1395|rna1395 484 ICYTKELNREISKNLAKVLNS 504
                                        333333333333333333332 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.97
                                        ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHH CS
                        Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvlee 51 
                                        k+++  k ++++l+++++kv   TG +++++++++++
  gene1396|gene1396|rna1395|rna1395 704 KLQDDVKITLENLRNAEMKVWMLTGDKIETAISIARS 740
                                        678889999****************999999988775 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 2.5e-05
                                        CT--GGGEEEEESSGGGHHHHHHSSEEEE CS
                        Hydrolase_3 199 lnisleeviafGDgeNDieMLeaaglgvA 227
                                         n +++ v  +GDg ND++M++ a++g+ 
  gene1396|gene1396|rna1395|rna1395 823 KNKTKKCVCCIGDGGNDVSMITEANVGIG 851
                                        3455666779**************88874 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     3e-05     0.077      49     162 ..     718     840 ..     679     864 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                                        STTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTTSSEEEEEEETCHHHH...HHHCT-SEEEEES--SS-EEEEEET CS
                             AFOR_N  49 spenplvfatGpltgtpapgsgrlvvvaksPltgtlgesnaGgrfgae...lkraGydaivieGkaekpvylvied 121
                                        + e ++ + tG    t+++ ++   ++ +      + ++++ g++ a+   l+ +Gy+ +vi G++ + v+ +  d
  gene1396|gene1396|rna1395|rna1395 718 NAEMKVWMLTGDKIETAISIARSSRIFHRGTTYLVISNASSAGEVKAKldlLRGSGYNSLVIDGQSLSFVVESCMD 793
                                        5566677777766666444433333333443333455556666666652236899********************* PP

                                        TEEEEEE-.TTTTTS-HHHHHHH.HHHHHTS....EEEEE-HHHHTT CS
                             AFOR_N 122 dkveieda.edlwgldtyettea.lkeelgd....kvaviGpaGenl 162
                                        + +ei +  e + g +   t++a + +el++     v++iG  G   
  gene1396|gene1396|rna1395|rna1395 794 EFIEIASGlEAVVGCRYTPTQKAaIARELKNktkkCVCCIGDGGNDV 840
                                        *9***998899999766667666555555555552555***999764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1097 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.83u 0.31s 00:00:01.13 Elapsed: 00:00:00.53
# Mc/sec: 6278.46
//
Query:       gene1397|gene1397|rna1396|rna1396  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-49  165.9   0.4    6.2e-49  165.7   0.4    1.0  1  Ras          Ras family
    7.6e-33  113.3   0.1    1.4e-32  112.4   0.1    1.4  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    3.3e-18   65.8   0.1    4.1e-18   65.4   0.1    1.1  1  Arf          ADP-ribosylation factor family
    8.6e-09   35.2   0.1    6.1e-07   29.2   0.0    2.1  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.4e-08   32.0   0.2    9.1e-08   31.7   0.2    1.1  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    2.9e-05   24.1   0.1    5.8e-05   23.1   0.0    1.5  2  MMR_HSR1     50S ribosome-binding GTPase
    5.4e-05   23.1   0.0      0.014   15.4   0.0    2.1  2  RsgA_GTPase  RsgA GTPase
    0.00012   21.6   0.0    0.00013   21.5   0.0    1.2  1  SRPRB        Signal recognition particle receptor beta subuni
  ------ inclusion threshold ------
      0.018   14.5   0.2      0.027   13.9   0.2    1.2  1  T3SS_TC      Type III secretion systems tip complex component


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.4   3.1e-52   6.2e-49       1     159 [.      11     170 ..      11     173 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 3.1e-52
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegil 76 
                                        K++++G+s vGKt+ll+++ +d+Fk++  +Tigvd  +k+i ++gk++ l+iwDTAGqe+f s++++yyr+a+gil
  gene1397|gene1397|rna1396|rna1396  11 KIIVLGESDVGKTCLLHKYKEDDFKQSLMTTIGVDTVSKSIVLNGKNIMLNIWDTAGQERFFSITKSYYRNADGIL 86 
                                        99************************************************************************** PP

                                        EEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHH..HHHHHHHTSEEEEEBTTTTCTHH CS
                                Ras  77 lvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteeg..eelakelglkfletSAktnenve 150
                                        l++di+++++f+ v++w+  i++ +  nvp+ LvGnK D  ++ + ++ eg  ++ a+e++++++ tSAkt env+
  gene1397|gene1397|rna1396|rna1396  87 LIFDISDERTFSCVDRWFGRIREETG-NVPLFLVGNKRDKVDSATYHAMEGnfKSKAEEMKARYYTTSAKTGENVN 161
                                        **************************.7**************9999888883357889999*************** PP

                                        HHHHHHHHH CS
                                Ras 151 eafeellre 159
                                        ++fe+++  
  gene1397|gene1397|rna1396|rna1396 162 NIFEDMAMV 170
                                        ****99866 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.1   7.2e-36   1.4e-32       1     120 []      11     125 ..      11     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 7.2e-36
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        K++++G+s vGKt+ll+++ ed+f+++  +tigvd+++k+++ ++g       k++ lniWDtaGqerf s++++y
  gene1397|gene1397|rna1396|rna1396  11 KIIVLGESDVGKTCLLHKYKEDDFKQSLMTTIGVDTVSKSIV-LNG-------KNIMLNIWDTAGQERFFSITKSY 78 
                                        9**************************************984.444.......689******************** PP

                                        HCTSCEEEEEEE...GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                                Roc  77 lreaalailvyd...srssenlkeWlkelkkvagkspvilvgnkiDl 120
                                        +r+a+ ++l++d   +r+++ +++W+  +++++g+ p++lvgnk D+
  gene1397|gene1397|rna1396|rna1396  79 YRNADGILLIFDisdERTFSCVDRWFGRIREETGNVPLFLVGNKRDK 125
                                        ***********9776888999***********************995 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.1   2.1e-21   4.1e-18      14     171 ..       9     167 ..       3     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.1e-21
                                        EEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE....TTEEEEEEEE-SSGGGGGGGGGGCTTESE CS
                                Arf  14 elrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei....knlkftvwDvGGqeklRplWknYfektda 84 
                                         ++i++lG    GKt +l+k+k++++++  + Tig ++ + +i    kn+ +++wD  Gqe+  ++ k+Y+++ d+
  gene1397|gene1397|rna1396|rna1396   9 RYKIIVLGESDVGKTCLLHKYKEDDFKQsLMTTIGVDTVSKSIvlngKNIMLNIWDTAGQERFFSITKSYYRNADG 84 
                                        689***********************985789999876543334466***************************** PP

                                        EEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTT CS
                                Arf  85 vifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavk 160
                                        ++ + D +d++ ++   + + ++  +ee  +v+l +++NK D  ++++ + ++ + + +    + k    ++sa +
  gene1397|gene1397|rna1396|rna1396  85 ILLIFDISDERTFSCVDRWFGRI--REETGNVPLFLVGNKRDKVDSATYHAMEGNFKSKAE--EMKARYYTTSAKT 156
                                        *******************9998..677899****************99999988876653..4667778899999 PP

                                        TBTHHHHHHHH CS
                                Arf 161 geglkeglewl 171
                                        ge++++ +e +
  gene1397|gene1397|rna1396|rna1396 157 GENVNNIFEDM 167
                                        99998887765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.016        32       5      21 ..      11      27 ..       8      32 .. 0.89
   2 !   29.2   0.0   3.1e-10   6.1e-07      60     188 ..      46     167 ..      31     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                                       EEEEEESTTSSHHHHHH CS
                           GTP_EFTU  5 nigiighvDhGKtTLtd 21
                                       +i+++g  D GKt+L+ 
  gene1397|gene1397|rna1396|rna1396 11 KIIVLGESDVGKTCLLH 27
                                       689***********985 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 3.1e-10
                                        EEEEE..TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHT...TTEEEEEEE CS
                           GTP_EFTU  60 aisle..ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalke...gvpiivfiN 130
                                        ++s +   ++k+  +n+ Dt G + F + +   +r +Dg +l++d+++  +      +   ++e   +vp++++ N
  gene1397|gene1397|rna1396|rna1396  46 TVSKSivLNGKNIMLNIWDTAGQERFFSITKSYYRNADGILLIFDISDERTFSCVDRWFGRIREetgNVPLFLVGN 121
                                        333333247****************************************8888776665444331236779999** PP

                                        SCGSTHHHHHH.HHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHH CS
                           GTP_EFTU 131 KmDrlkaelke.iveevkqklsrkeeklekygekgekevpvvfgSalkgegvktlleal 188
                                        K D++++   + +  + k+k            e+   +   + +Sa++ge+v++++e +
  gene1397|gene1397|rna1396|rna1396 122 KRDKVDSATYHaMEGNFKSKA-----------EE--MKARYYTTSAKTGENVNNIFEDM 167
                                        *****6554430333333333...........22..24568888999999988877755 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.2   4.6e-11   9.1e-08       1     142 [.      11     147 ..      11     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.6e-11
                          Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtl.rlgati...dveksevrflgnltlnlwDcgGqeafveeylssqkee 72 
                                        k++ +G+s  GKt++     ++y   d   +l +ti    v+ks v + +n++ln+wD  Gqe+f+  +     ++
  gene1397|gene1397|rna1396|rna1396  11 KIIVLGESDVGKTCL----LHKYKEDDFKqSLMTTIgvdTVSKSIVLNGKNIMLNIWDTAGQERFFSIT-----KS 77 
                                        7999**********7....5788888875157888744456678888899****************986.....78 PP

                          Gtr1_RagA  73 ifrnvgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqedereei...feerkeeire 142
                                         +rn + ++ +fD++    e++++   + + ++r+   ++ +f   +K D++++ + + +   f++++ee++ 
  gene1397|gene1397|rna1396|rna1396  78 YYRNADGILLIFDIS---DERTFSCVDRWFGRIREETGNVPLFLVGNKRDKVDSATYHAMegnFKSKAEEMKA 147
                                        89*************...5788999999999************999999999755433330114444444433 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   2.9e-08   5.8e-05       1     114 []      11     122 ..      11     122 .. 0.73
   2 ?   -2.6   0.0       2.9   5.7e+03      76      86 ..     145     155 ..     126     178 .. 0.48

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.9e-08
                                        EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT..EEEEEEECGGCSSHHHHHH.HHHHHHHHH CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg..keielvDtpGliegaseek.glgkaflal 73 
                                        +++++G + vGK+ L+ +  ++  + s +     d++ + + l+g    ++++Dt+G  e    +  +++k++ + 
  gene1397|gene1397|rna1396|rna1396  11 KIIVLGESDVGKTCLLHKYKEDDFKQSLMTTIGVDTVSKSIVLNGknIMLNIWDTAG-QE----RFfSITKSYYR- 80 
                                        589****************99877666666666666666666555225579******.44....44588888885. PP

                                        HCTSEEEEEEETT.TTCSHHHHHHHHHHHHH.TTSEEEEEEES CS
                           MMR_HSR1  74 eeadlillvvdas.eeklkpldeeleellee.akkplilvlnk 114
                                         +ad ill++d+s e++++ +d+ + +++ee  + pl+lv nk
  gene1397|gene1397|rna1396|rna1396  81 -NADGILLIFDISdERTFSCVDRWFGRIREEtGNVPLFLVGNK 122
                                        .89********99533666677777777655566677777776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                                        TSEEEEEEETT CS
                           MMR_HSR1  76 adlillvvdas 86 
                                        +++  +  +a+
  gene1397|gene1397|rna1396|rna1396 145 MKARYYTTSAK 155
                                        44444444433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0054        11     102     122 ..      12      32 ..       3      57 .. 0.80
   2 !   15.4   0.0   6.8e-06     0.014       4      97 ..      70     167 ..      67     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0054
                                        EEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                        ++++G+S vGK+ L+ + +++
  gene1397|gene1397|rna1396|rna1396  12 IIVLGESDVGKTCLLHKYKED 32 
                                        5789***********998875 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 6.8e-06
                                        -S-EETTTTEES--EEEEEEESTTTT--HHHHHHHHHHH..HHTT-EEEEEEE-GGG--HHH...HHHHHHHHHHH CS
                        RsgA_GTPase   4 RknelvrpkvaNvdqllivvslkepelslnlldrfLvla..eekgiepvivlnKiDlleeee...eleelkeelea 74 
                                        R  +++++   N d +l+++ ++ +e + + +dr    +  e+ ++++ +v nK D +++++      ++k++ e+
  gene1397|gene1397|rna1396|rna1396  70 RFFSITKSYYRNADGILLIFDIS-DERTFSCVDRWFGRIreETGNVPLFLVGNKRDKVDSATyhaMEGNFKSKAEE 144
                                        56667778889************.899999*****97762145578899999******9999775556899999** PP

                                        TTSEEEE--TTTHTTHHHHHHHC CS
                        RsgA_GTPase  75 lgyevllvsaktkegleelkell 97 
                                        +  + +++sakt+e+++++ e +
  gene1397|gene1397|rna1396|rna1396 145 MKARYYTTSAKTGENVNNIFEDM 167
                                        ***************99998765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.3e-08   0.00013       4      84 ..      10      90 ..       7     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.3e-08
                                       -EEEEE-STTSSHHHHHHHHHHSS---B---S..S-EEETTG....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE CS
                              SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSq..essaalkv.ksekgskltliDfPGheklrqklleklkaksslkg 78
                                        +++++G sd GKT l+++  +d +k++ +      ++++++  + k+ +l++ D  G+e++ +  +    + +++ g
  gene1397|gene1397|rna1396|rna1396 10 YKIIVLGESDVGKTCLLHKYKEDDFKQSLMTTigVDTVSKSIvLNGKNIMLNIWDTAGQERFFSITKS---YYRNADG 84
                                       689********************99999887655455555556899**************99653333...4666666 PP

                                       EEEEEE CS
                              SRPRB 79 lvfvvD 84
                                       ++ + D
  gene1397|gene1397|rna1396|rna1396 85 ILLIFD 90
                                       666666 PP

>> T3SS_TC  Type III secretion systems tip complex components
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.3e-05     0.027     291     340 ..     121     171 ..     116     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                        TSSEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                            T3SS_TC 291 dseleldnakyqaWqsGfkaqeenlkntlqtltqky.snanslfdnlvkvl 340
                                        + + ++d a y a +  fk++ e++k+   t   k   n n +f+++  vl
  gene1397|gene1397|rna1396|rna1396 121 NKRDKVDSATYHAMEGNFKSKAEEMKARYYTTSAKTgENVNNIFEDMAMVL 171
                                        556689**********************99998886369******999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1153.64
//
Query:       gene1398|gene1398|rna1397|rna1397  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-05   26.1   1.1       0.62   11.0   0.1    4.2  4  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.075   1.3e+03      18      33 ..      92     107 ..      60     110 .. 0.82
   2 !    5.5   0.0     0.002        35       9      37 ..     141     160 ..     132     161 .. 0.78
   3 !    4.1   0.0    0.0055        99      13      34 ..     175     196 ..     168     198 .. 0.86
   4 !   11.0   0.1   3.5e-05      0.62      10      38 .]     212     241 ..     206     241 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.075
                                        EETTSSEEEEEETTSE CS
                               WD40  18 fspdgawlasGsdDgt 33 
                                        +++d +++++G  Dg 
  gene1398|gene1398|rna1397|rna1397  92 YNRDEDYVVTGKFDGR 107
                                        7889999999944886 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.002
                                        SSSSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   9 GHssvtslafspdgawlasGsdDgtvriW 37 
                                        +H sv+++        l+++  D+tv ++
  gene1398|gene1398|rna1397|rna1397 141 AHYSVRDV--------LVTSF-DNTVSLY 160
                                        6756****........**999.****986 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0055
                                        EEEEEEETTSSEEEEEETTSEE CS
                               WD40  13 vtslafspdgawlasGsdDgtv 34 
                                        ++ ++++p  + + +Gs Dgt+
  gene1398|gene1398|rna1397|rna1397 175 ICRVCTDPLLTNIYCGSSDGTI 196
                                        78888888889999**88***9 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 3.5e-05
                                        S.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  10 H.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        H s + +l+ s  g+ l s+++ g v iWd
  gene1398|gene1398|rna1397|rna1397 212 HkSKIVGLDISFCGRHLYSADMEGVVCIWD 241
                                        844599**************99*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1799.11
//
Query:       gene1399|gene1399|rna1398|rna1398  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-15   54.3   0.3    7.8e-07   28.8   0.0    3.0  2  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   4.3e-11   7.8e-07       3      56 ..      12      68 ..      10      74 .. 0.92
   2 !   20.5   0.1   1.8e-08   0.00032       1      69 [.     103     163 ..     103     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.3e-11
                                       EESETTTSSHHHHHHHHHTTSCE.EEEEEEEE..TTTSEEEEEEEEESSHHHHHHHH CS
                              RRM_1  3 VgnLppdvteeeLkelFskfGpi.ksiklvrd..etgkskgfafVeFeskedAekAl 56
                                       + +Lp+ vt +++ e F k+G+  + ikl+++   ++   ++++VeFe+ ed ekA 
  gene1399|gene1399|rna1398|rna1398 12 IPDLPKGVTVKDILEAFPKYGKEiTGIKLSKQrrPKNEDLKVGYVEFETIEDTEKAY 68
                                       568******************977*********9999999***************97 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 1.8e-08
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        ++++++++d++++eL+ l++++      k++    +k k++ f e++++e+ ekAl++ n +k++g++l
  gene1399|gene1399|rna1398|rna1398 103 VYISGVSEDTNKDELSSLLGNC------KISG--GDKGKNYLFAEYDNSEEQEKALNRINTMKINGSKL 163
                                        7999999999999999999875......5555..58999***************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1167.91
//
Query:       gene1400|gene1400|rna1399|rna1399  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-09   35.8   4.1       0.27   12.2   0.0    5.1  5  WD40         WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.044   14.1   0.0       0.71   10.2   0.0    2.9  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
       0.11   12.0   0.0       0.18   11.4   0.0    1.3  1  AbiJ_NTD3    AbiJ N-terminal domain 3


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0035        21       9      35 ..      44      68 ..      30      70 .. 0.82
   2 !    9.1   0.0   0.00041       2.4       6      28 ..      78     101 ..      73     118 .. 0.71
   3 !    5.3   0.0    0.0066        40      12      38 .]     128     152 ..     120     152 .. 0.67
   4 ?   -1.4   0.0      0.86   5.1e+03      12      19 ..     171     178 ..     160     190 .. 0.67
   5 !   12.2   0.0   4.6e-05      0.27       9      36 ..     248     276 ..     239     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0035
                                       SSSSEEEEEEETTSSEEEEEETTSEEE CS
                               WD40  9 GHssvtslafspdgawlasGsdDgtvr 35
                                       +++s++s+   ++g+++++Gs+D+t  
  gene1400|gene1400|rna1399|rna1399 44 TQKSIRSI--ASHGKYMCCGSYDCTAV 68
                                       45678888..889***********975 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00041
                                        EEESS.SSEEEEEEETTSSEEEEE CS
                               WD40   6 tltGH.ssvtslafspdgawlasG 28 
                                        +++G  + v ++afs dg++la +
  gene1400|gene1400|rna1399|rna1399  78 VIEGPdTEVKCVAFSEDGKYLAMA 101
                                        56677556************9733 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0066
                                        SEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  12 svtslafspdgawlasGsdDgtvriWd 38 
                                        +v ++    +g +l++ ++D+tv+++d
  gene1400|gene1400|rna1399|rna1399 128 DVKGC--IFHGGFLFTYGYDNTVKVYD 152
                                        45444..245566777566******98 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.86
                                        SEEEEEEE CS
                               WD40  12 svtslafs 19 
                                         v+++ f+
  gene1400|gene1400|rna1399|rna1399 171 TVWCVIFH 178
                                        59999443 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 4.6e-05
                                        SS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40   9 GH.ssvtslafspdgawlasGsdDgtvri 36 
                                         H ++++++a++  ++ ++sG+dDg + i
  gene1400|gene1400|rna1399|rna1399 248 VHeDFINGIAYDAGKDRIISGGDDGILNI 276
                                        59777********************9876 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.76   4.6e+03      50      62 ..      12      23 ..       7      60 .. 0.60
   2 ?   10.2   0.0   0.00012      0.71      35      64 ..      80     109 ..      67     124 .. 0.82
   3 ?   -1.9   0.0      0.69   4.1e+03      28      44 ..     158     175 ..     134     199 .. 0.55
   4 ?   -1.5   0.0      0.53   3.2e+03      28      65 ..     241     277 ..     222     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.76
                        ANAPC4_WD40 50 gklLavaysdgev 62
                                       +k+Lav +s+g+v
  gene1400|gene1400|rna1399|rna1399 12 EKILAV-HSNGAV 23
                                       555554.333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00012
                        ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrl 64 
                                        +++d ev+++a+++dgk La+a+   +v +
  gene1400|gene1400|rna1399|rna1399  80 EGPDTEVKCVAFSEDGKYLAMATRGKSVWV 109
                                        56899****************998776655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.69
                        ANAPC4_WD40  28 rvwtl.eedkedsevrsL 44 
                                          w+l ++ +e+s+v ++
  gene1400|gene1400|rna1399|rna1399 158 DSWELvQSIDEGSTVWCV 175
                                        333332233344444444 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.53
                        ANAPC4_WD40  28 rvwtleedkedsevrsLaWkpdgklLavaysdgevrll 65 
                                         v ++ e+ ++  ++++a+      +  + +dg ++++
  gene1400|gene1400|rna1399|rna1399 241 IVTSI-ENVHEDFINGIAYDAGKDRIISGGDDGILNII 277
                                        45555.56667778888888888888888888888876 PP

>> AbiJ_NTD3  AbiJ N-terminal domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.9e-05      0.18     110     145 ..     191     226 ..     188     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                          AbiJ_NTD3 110 iNelLrkdGyeLvetgeisgrpvysvrrigagvagr 145
                                        +N+++ + G+eL+ +++ s  p+ysv ++g++ a +
  gene1400|gene1400|rna1399|rna1399 191 VNSYILRNGWELEISKRLSMFPIYSVCSVGRHMAYT 226
                                        89************************9999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1768.67
//
Query:       gene14|gene14|rna14|rna14  [L=295]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0094   16.0   2.4      0.036   14.1   1.2    2.5  2  Myb_DNA-bind_5   Myb/SANT-like DNA-binding domain
  ------ inclusion threshold ------
      0.016   15.3   0.0       0.04   14.0   0.0    1.7  1  DnaJ             DnaJ domain
      0.031   14.5   0.5      0.097   12.9   0.3    2.0  2  Myb_DNA-binding  Myb-like DNA-binding domain


Domain annotation for each model (and alignments):
>> Myb_DNA-bind_5  Myb/SANT-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.37   2.2e+03       1      17 [.     238     254 ..     238     260 .. 0.87
   2 !   14.1   1.2   6.1e-06     0.036      35      63 ..     259     287 ..     251     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.37
             Myb_DNA-bind_5   1 RkknfseeEkevLvelv 17 
                                R+  +++ E+ +L +l+
  gene14|gene14|rna14|rna14 238 RMNSWTPLEVSTLRRLI 254
                                78899******999987 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.1e-06
             Myb_DNA-bind_5  35 kaKsraWeeiaervnalgsveRtaeelkk 63 
                                k K+++We i+e++ +++ ++R+++e+ +
  gene14|gene14|rna14|rna14 259 KTKKNKWEMITEKLAEITKTKRSIKEVME 287
                                789**********************9966 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.7e-06      0.04      25      63 .]      73     108 ..      47     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.7e-06
                                HHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                       DnaJ  25 alkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63 
                                + +yHPD     +  +e+F  ++ A +vL d + R  YD
  gene14|gene14|rna14|rna14  73 MHEYHPDLI---KGCREAFLLVKIARDVLRDRKLRLFYD 108
                                679****99...6778*******************9999 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.5   9.2e+03      31      41 ..     185     197 ..     180     197 .. 0.78
   2 ?   12.9   0.3   1.6e-05     0.097       2      39 ..     240     283 ..     239     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.5
                                T..SS-HHHHHHH CS
            Myb_DNA-binding  31 g..gRtekqcrsr 41 
                                g   R+  ++++r
  gene14|gene14|rna14|rna14 185 GeyDRSQYSIKNR 197
                                5556999999998 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.6e-05
                                SSSBHHHHHHHHHHHHHHT....TCHHHHHHHHT..SS-HHHHH CS
            Myb_DNA-binding   2 gkWteeEdelLleavkkhG....nrWkkIaerlg..gRtekqcr 39 
                                ++Wt+ E   L +++ + G    n+W+ I e+l   ++t+ +++
  gene14|gene14|rna14|rna14 240 NSWTPLEVSTLRRLISLVGktkkNKWEMITEKLAeiTKTKRSIK 283
                                68*********99999999864555******9999988877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1852.59
//
Query:       gene140|gene140|rna140|rna140  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.012   14.6   0.4      0.013   14.4   0.4    1.0  1  Paramyxo_ncap  Paramyxovirus nucleocapsid protein


Domain annotation for each model (and alignments):
>> Paramyxo_ncap  Paramyxovirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   7.4e-07     0.013     387     453 ..      27      93 ..      18     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.4e-07
                  Paramyxo_ncap 387 teeeaklvseiaakttddrtsravgpkqaqvsflrsdrseeeqkraskkeekrekqsrkearesske 453
                                     +e+ k ++     t d++ s   g ++  +sfl+++++++ +++++k+ee+ +++   e +es  +
  gene140|gene140|rna140|rna140  27 RKEDVKNMASRLNSTIDNKRSNLFGDRKKFLSFLKEEKESNDSQESGKNEESGKNEESGEGEESGDN 93 
                                    5788888888888999***********************9999999988887766665554443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 743.77
//
Query:       gene1401|gene1401|rna1400|rna1400  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-12   45.3   0.0    0.00063   20.1   0.0    4.9  5  HEAT_2          HEAT repeats
    1.4e-09   37.3   1.5       0.62   10.5   0.0    7.7  8  HEAT            HEAT repeat
      0.002   17.9   0.1      0.092   12.4   0.0    3.0  3  DNA_alkylation  DNA alkylation repair enzyme
  ------ inclusion threshold ------
      0.022   15.0   0.3        7.2    7.0   0.0    2.9  3  Cohesin_HEAT    HEAT repeat associated with sister chromatid 


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.35   1.6e+03      56      81 ..     105     130 ..      83     137 .. 0.66
   2 !   20.1   0.0   1.4e-07   0.00063       4      87 ..     240     321 ..     238     322 .. 0.87
   3 !    9.8   0.0   0.00023         1       3      57 ..     300     361 ..     298     372 .. 0.81
   4 !    7.0   0.0    0.0017       7.7       3      73 ..     339     413 ..     337     414 .. 0.82
   5 !   11.5   0.0   6.5e-05      0.29       5      51 ..     407     454 ..     403     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.35
                             HEAT_2  56 gaigdpealpaLkellddddddvvRe 81 
                                        + +  +e  +aL+++l+d  + v R 
  gene1401|gene1401|rna1400|rna1400 105 VNMEYKEEKEALRRCLRDSVVGVARC 130
                                        45666677788888888877777665 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.4e-07
                             HEAT_2   4 LlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaigd.pealpaLkellddddddv 78 
                                        L+ +  +d++p vr+  i+  g+   +e +++L e+++d++++vR+a      ++++ ++ +  L  +l+++++++
  gene1401|gene1401|rna1400|rna1400 240 LVPLFLKDSSPTVRALMIQMVGD--KEEFQEMLKEAVSDASWEVRKA-LLCVHRVDTyKSIVIPLINSLNSTPNWR 312
                                        5666669***************6..6779****************85.6788999976888999999999999999 PP

                             HEAT_2  79 vReaAaeaL 87 
                                        +R +++e++
  gene1401|gene1401|rna1400|rna1400 313 IRKEILESI 321
                                        999998886 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00023
                             HEAT_2   3 aLlqalendpdpevrraairaLgrignpea.......lpaLvellededpavRraaaeaLga 57 
                                        +L++ l + p++ +r+++++++     ++         + L+ +l+d+  +vR++a +  g+
  gene1401|gene1401|rna1400|rna1400 300 PLINSLNSTPNWRIRKEILESIEYASKQDGkllkmflGKHLLGYLSDKVYEVRAEASRVVGE 361
                                        6899999999999******9999655554444555556778888899999999999998887 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0017
                             HEAT_2   3 aLlqalendpdpevrraairaLgrignp.....ealpaLvellededpavRraaaeaLgaigdpealpaLkelldd 73 
                                        +Ll +l +d+ +evr++a r+ g++        e lp +  ++++ +   R + ++a+  ++     ++ k+ll d
  gene1401|gene1401|rna1400|rna1400 339 HLLGYL-SDKVYEVRAEASRVVGELVMMypwtiEWLPDIEAIVSSRSYLHRITSVNAALSFDKAHRTEFVKKLLSD 413
                                        688899.9999************765544467788999999999999****9999999888887777777777765 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 6.5e-05
                             HEAT_2   5 lqalendpdpevrraairaLgrignpealpaLvell.ededpavRraa 51 
                                        ++ l +dp ++v+  +++   r g +e ++ +v+ l  ++d+++Rraa
  gene1401|gene1401|rna1400|rna1400 407 VKKLLSDPIENVKLYTLEMVDRHGMDEGIKEIVSGLcVSSDEEIRRAA 454
                                        455559****************************7769*********9 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.4   6.2e+03      12      22 ..     188     198 ..     185     203 .. 0.82
   2 ?    1.1   0.0      0.15   6.5e+02       8      22 ..     214     229 ..     210     231 .. 0.75
   3 ?    2.8   0.0     0.041   1.8e+02       8      19 ..     243     255 ..     238     262 .. 0.76
   4 !    7.8   0.0     0.001       4.5       4      19 ..     269     284 ..     266     286 .. 0.84
   5 ?    3.7   0.0     0.021        96       3      23 ..     300     320 ..     298     322 .. 0.74
   6 !   10.5   0.0   0.00014      0.62       4      28 ..     339     363 ..     336     364 .. 0.92
   7 ?   -0.4   0.0      0.42   1.9e+03       5      18 ..     407     420 ..     405     424 .. 0.78
   8 ?   -0.1   0.0      0.35   1.6e+03       8      20 ..     442     454 ..     437     458 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                                        SSHHHHHHHHH CS
                               HEAT  12 pspeVReaAak 22 
                                        +s++ R+a ak
  gene1401|gene1401|rna1400|rna1400 188 KSWRRRYAIAK 198
                                        68999*99987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.15
                                        HH.T-SSHHHHHHHHH CS
                               HEAT   8 ll.sDpspeVReaAak 22 
                                         l +Dp+ e+R   a 
  gene1401|gene1401|rna1400|rna1400 214 HLsQDPEEEIRICLAS 229
                                        444********87665 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.041
                                        H.HT-SSHHHHHH CS
                               HEAT   8 l.lsDpspeVRea 19 
                                        l l+D+sp VR+ 
  gene1401|gene1401|rna1400|rna1400 243 LfLKDSSPTVRAL 255
                                        5379*******85 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.001
                                        HHHHHHT-SSHHHHHH CS
                               HEAT   4 lllkllsDpspeVRea 19 
                                        +l ++ sD s+eVR+a
  gene1401|gene1401|rna1400|rna1400 269 MLKEAVSDASWEVRKA 284
                                        677899********99 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.021
                                        HHHHHHHT-.SSHHHHHHHHHH CS
                               HEAT   3 PlllkllsD.pspeVReaAaka 23 
                                        Pl ++ l++ p++++R+  +++
  gene1401|gene1401|rna1400|rna1400 300 PL-INSLNStPNWRIRKEILES 320
                                        55.6667777******987766 PP

  == domain 6  score: 10.5 bits;  conditional E-value: 0.00014
                                        HHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                        +ll  lsD+  eVR+ A + +g+l+
  gene1401|gene1401|rna1400|rna1400 339 HLLGYLSDKVYEVRAEASRVVGELV 363
                                        69999*****************986 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 0.42
                                        HHHHHT-SSHHHHH CS
                               HEAT   5 llkllsDpspeVRe 18 
                                        + kllsDp  +V  
  gene1401|gene1401|rna1400|rna1400 407 VKKLLSDPIENVKL 420
                                        67999***999976 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 0.35
                                        HHT-SSHHHHHHH CS
                               HEAT   8 llsDpspeVReaA 20 
                                        l+ +++ e+R+aA
  gene1401|gene1401|rna1400|rna1400 442 LCVSSDEEIRRAA 454
                                        56789999**998 PP

>> DNA_alkylation  DNA alkylation repair enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.081   3.6e+02      38      88 ..      69     117 ..      64     127 .. 0.70
   2 !   12.4   0.0   2.1e-05     0.092     113     197 ..     258     339 ..     246     345 .. 0.85
   3 ?   -0.5   0.0      0.18   8.1e+02     107     155 ..     355     406 ..     351     454 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.081
                     DNA_alkylation  38 lakeffkelkleeelqelaeeLwkspe.rEerllAldlltqakkklaeadle 88 
                                        +++++f++ + e  +++++ +L++sp+    +++ l++++  +k+++ea l+
  gene1401|gene1401|rna1400|rna1400  69 VIRRIFASFPSE--VSKFIGKLLESPFyIQRQVIPLLIVNMEYKEEKEA-LR 117
                                        566666776666..8889********95666777777776666666655.44 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                     DNA_alkylation 113 alladkperrdllkeWaksenlWerRaAivatlklikktdlellleiaeelladkedfiqkAiGwaLrelsktdpd 188
                                        +++ dk e+ +++ + a s+  We R A++++ +   +t  + ++ ++++l + ++++i+k i   +  +sk+d +
  gene1401|gene1401|rna1400|rna1400 258 QMVGDK-EEFQEMLKEAVSDASWEVRKALLCVHRV--DTYKSIVIPLINSLNSTPNWRIRKEILESIEYASKQDGK 330
                                        444454.55555666699************99887..7888999******************************** PP

                     DNA_alkylation 189 lveeFlekh 197
                                        l++ Fl kh
  gene1401|gene1401|rna1400|rna1400 331 LLKMFLGKH 339
                                        *******99 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.18
                     DNA_alkylation 107 askivgalladk...perrdllkeWaksenlWerRaAivatlklikktdlel 155
                                        as++vg+l++++    e++  +++ + s +   r +++ a l++ k+  +e 
  gene1401|gene1401|rna1400|rna1400 355 ASRVVGELVMMYpwtIEWLPDIEAIVSSRSYLHRITSVNAALSFDKAHRTEF 406
                                        5677777777777777777777777777777777777777777766644433 PP

>> Cohesin_HEAT  HEAT repeat associated with sister chromatid cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.4   1.1e+04      20      30 ..     113     123 ..     113     124 .. 0.84
   2 ?    5.4   0.0    0.0053        24      24      40 ..     242     258 ..     239     260 .. 0.82
   3 ?    7.0   0.0    0.0016       7.2      16      37 ..     263     284 ..     258     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.4
                                        HHHHHHHHHSS CS
                       Cohesin_HEAT  20 ldtiarrltDs 30 
                                        ++++ r+l+Ds
  gene1401|gene1401|rna1400|rna1400 113 KEALRRCLRDS 123
                                        578889***98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0053
                                        HHHHHSS-HHHHHHHHH CS
                       Cohesin_HEAT  24 arrltDsspsVRdAaLe 40 
                                           l Dssp VR+ +++
  gene1401|gene1401|rna1400|rna1400 242 PLFLKDSSPTVRALMIQ 258
                                        56799*******98876 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0016
                                        SHHHHHHHHHHHHSS-HHHHHH CS
                       Cohesin_HEAT  16 apevldtiarrltDsspsVRdA 37 
                                         +e+++++++  +D s  VR+A
  gene1401|gene1401|rna1400|rna1400 263 KEEFQEMLKEAVSDASWEVRKA 284
                                        459*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2814.45
//
Query:       gene1402|gene1402|rna1401|rna1401  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-18   65.1   0.1    1.1e-17   64.4   0.1    1.3  1  Methyltransf_11  Methyltransferase domain
    7.1e-15   55.5   0.1    1.5e-14   54.5   0.1    1.5  1  Methyltransf_25  Methyltransferase domain
    7.7e-11   42.0   0.0    9.5e-11   41.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      1e-10   41.7   0.0    1.3e-10   41.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    8.2e-07   29.7   0.4    3.5e-06   27.7   0.4    2.0  1  Methyltransf_12  Methyltransferase domain
    2.9e-06   26.8   0.1    8.6e-06   25.2   0.1    1.8  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      8e-05   22.6   0.0    8.6e-05   22.5   0.0    1.1  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.014   14.3   0.1       0.03   13.2   0.1    1.5  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.025   14.0   0.1       0.19   11.1   0.1    2.1  1  TehB             Tellurite resistance protein TehB
      0.032   13.5   0.1       0.14   11.4   0.1    1.8  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.1   6.2e-21   1.1e-17       1      93 [.      49     134 ..      49     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 6.2e-21
                                        EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-.. CS
                    Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv.. 74 
                                        Ld+GcG+Gr +   +     vvg+D++  +l+ a +++++ gl    v++d+ klpf+d+sfDlv+s  v+hh+  
  gene1402|gene1402|rna1401|rna1401  49 LDAGCGNGRSFLVPE-----VVGLDYCFDLLRDA-KAIRNHGL----VRGDVLKLPFADSSFDLVLSVGVIHHLst 114
                                        8********998887.....***********888.56777764....***************************99 PP

                                        .CCHHHHHHHHHHHEEEEEE CS
                    Methyltransf_11  75 .edpekalkeiaRvLkpgGl 93 
                                         e++ ka++e++RvLk gG+
  gene1402|gene1402|rna1401|rna1401 115 yERRLKAMEEMKRVLKDGGK 134
                                        99*****************7 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.1   8.2e-18   1.5e-14       1      97 []      48     133 ..      48     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 8.2e-18
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                        vLd+GcG+Gr    l   +   +v+g+D+  ++l+ a++       n  +v+gd+ +lpf+d+sfDlv+s+g++hh
  gene1402|gene1402|rna1401|rna1401  48 VLDAGCGNGRSF--L---V--PEVVGLDYCFDLLRDAKAIR-----NHGLVRGDVLKLPFADSSFDLVLSVGVIHH 111
                                        9********754..3...3..579*************9987.....788*********************999999 PP

                                        SSH.HHHHHHHHHHHHHEEEEE CS
                    Methyltransf_25  77 lsd.edlekalkeiarvLkpgG 97 
                                        ls  e++ ka++e++rvLk+gG
  gene1402|gene1402|rna1401|rna1401 112 LSTyERRLKAMEEMKRVLKDGG 133
                                        655166789************9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   5.3e-14   9.5e-11       3     108 ..      44     136 ..      42     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.3e-14
                    Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                        +g  vlD+GCG+G+  ++          vvG+D+  + ++ A+++ +++gl      +gd+ +l+  ++d++fDl+
  gene1402|gene1402|rna1401|rna1401  44 SGSIVLDAGCGNGRSFLVPE--------VVGLDYCFDLLRDAKAI-RNHGL-----VRGDVLKLP--FADSSFDLV 103
                                        67789*******99765544........****************6.66777.....69*******..********* PP

                    Methyltransf_31  79 lsnevlnala...dpdkileeiervlkpggill 108
                                        ls +v+++l+      k++ee++rvlk+gg  l
  gene1402|gene1402|rna1401|rna1401 104 LSVGVIHHLStyeRRLKAMEEMKRVLKDGGKGL 136
                                        ******77661115567888*********9765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0   7.4e-14   1.3e-10      20     163 ..      42     195 ..       8     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 7.4e-14
                    Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehv 95 
                                          +g+ vLd GcG G+        + +v+g D ++ +   a+ +++   +  d  + ++ + +fdl+ +  v++h+
  gene1402|gene1402|rna1401|rna1401  42 YTSGSIVLDAGCGNGRSFL-----VPEVVGLDYCFDLLRDAKAIRNHGLVRGDVLKLPFADSSFDLVLSVGVIHHL 112
                                        456669*********6555.....46889999988877777644444444444457777888************** PP

                    Methyltransf_23  96 pdpp...ellrqiatllkpgGylllseplaslkedrllld............wlylvpagrhisffsarslkelle 156
                                          ++   +++  +++ lk+gG  l+ ++++s k ++++ +            w + ++  r  ++++ + l el++
  gene1402|gene1402|rna1401|rna1401 113 STYErrlKAMEEMKRVLKDGGKGLVYVWGNSVKDKKKFSKiigrpgeeyfatWNLRDDTKRYYYLYDIEGLLELCR 188
                                        *8887779999*********************6666666666666666655598888887888************* PP

                    Methyltransf_23 157 eaGlevv 163
                                        ++G++v+
  gene1402|gene1402|rna1401|rna1401 189 DSGFKVL 195
                                        ****996 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.4   1.9e-09   3.5e-06       1      98 [.      49     134 ..      49     134 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.9e-09
                    Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                        L+ GcG+G+    l ++     ++g+D+  + +    +  ++++n+    v+ ++l l   d  ssfDlv++ +v+
  gene1402|gene1402|rna1401|rna1401  49 LDAGCGNGRS--FLVPE-----VVGLDYCFDLL----RDAKAIRNHG--LVRGDVLKLPFAD--SSFDLVLSVGVI 109
                                        6778888753..34444.....78888888888....2233333333..3444444443333..4*********** PP

                    Methyltransf_12  77 hhl...kdirevldnirklLkpgGr 98 
                                        hhl   + + +++++++++Lk+gG+
  gene1402|gene1402|rna1401|rna1401 110 HHLstyERRLKAMEEMKRVLKDGGK 134
                                        ****988888*************96 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   4.8e-09   8.6e-06      32     151 ..      13     137 ..      10     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.8e-09
                                        HHHHHHHHHHH--S--TT.....EEEEES-TT-HHHHHHHHHHHHHH...EEEEEES-HHHHHHHHHHHHHHTSST CS
                    Ubie_methyltran  32 hrlWkkfveklvavkrga.....kvlDvagGtgDlafklsdsvgekg...kvvvlDinenmLkvgekklkeegkin 99 
                                        h+ + + + + +a++r +     k+lD    +g + ++     g+++   +vv+lD+  ++L+ +++ ++++g   
  gene1402|gene1402|rna1401|rna1401  13 HKFYNENTREFSATRRKHwkmteKFLDSYYTSGSIVLDAGCGNGRSFlvpEVVGLDYCFDLLRDAKA-IRNHG--- 84 
                                        6666666666666666555555599999999999999988888888889999999999999998754.66666... PP

                                        EEEEE--TTT-TTS-T-EEEE...EEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                    Ubie_methyltran 100 ieflqanaeeLpfeddsfDvv...tvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                          ++ ++  +Lpf d sfD+v    v + l     +lka++e+ rvlk GG+ +v
  gene1402|gene1402|rna1401|rna1401  85 --LVRGDVLKLPFADSSFDLVlsvGVIHHLSTYERRLKAMEEMKRVLKDGGKGLV 137
                                        ..6789999**********8621144556677778889999*********97433 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   4.8e-08   8.6e-05      73     175 ..      45     156 ..       1     184 [. 0.68

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.8e-08
                                        TS-EEEES-TT-HHHHH--S-..E.EEEESS....-S.STTEEES-TTS-S--TT-EEEE.....EEES---SS-H CS
                     Methyltransf_8  73 nlvvadlGcGeakiaeavrekekv.rsfdlv....av.nervvacdlakvPledesvdva.....vfclslmgtnl 137
                                          +v d GcG+ +    v e   +  +fdl     a+ n+ +v  d+ k+P +d+s d++     ++ ls     l
  gene1402|gene1402|rna1401|rna1401  45 GSIVLDAGCGNGRSF-LVPEVVGLdYCFDLLrdakAIrNHGLVRGDVLKLPFADSSFDLVlsvgvIHHLSTYERRL 119
                                        45789*******976.44444443279**9622223325557889*************972222234455555444 PP

                                        HHHHHHHHHHEEEEEEEEEEEEGGG-S-HHHHHHHHHC CS
                     Methyltransf_8 138 adflkeanrvlkvGGllkvaevksrfesvklfaraltk 175
                                         + ++e++rvlk GG   v      +++ k+f + + +
  gene1402|gene1402|rna1401|rna1401 120 -KAMEEMKRVLKDGGKGLVYVWGNSVKDKKKFSKIIGR 156
                                        .5689*********987777666677777777776655 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.7e-05      0.03     115     214 ..      44     134 ..      22     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                        TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EEEEEEES CS
                     Methyltransf_9 115 kgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafdtvfsmG 190
                                         g  +ld GcgnG             vvG+d     l   +a+r+       + +lp++       ++fd v+s+G
  gene1402|gene1402|rna1401|rna1401  44 SGSIVLDAGCGNGRSFL------VPEVVGLDYCFDLLRDAKAIRNHGLVRGDVLKLPFA------DSSFDLVLSVG 107
                                        578899******97653......34699*998888888888888766555555566554......579******** PP

                                        -GGG-S-...HHHHHHHHHCTEEEEEE CS
                     Methyltransf_9 191 vlyhrrs...PldhllqlkdqlvkgGe 214
                                        v++h ++    l  + ++k  l+ gG+
  gene1402|gene1402|rna1401|rna1401 108 VIHHLSTyerRLKAMEEMKRVLKDGGK 134
                                        ****87622257777778888888886 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1    0.0001      0.19      32     132 ..      46     137 ..      15     148 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                        -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEESSGGG CS
                               TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstvvlmf 107
                                        + vld gcg+gr  l  +++g d             l++ k + n   ++  ++++  a  d  +d++ls  v+  
  gene1402|gene1402|rna1401|rna1401  46 SIVLDAGCGNGRSFLVPEVVGLDY--------CFDLLRDAKAIRNHGLVRGDVLKLPFA--DSSFDLVLSVGVIHH 111
                                        669**********99999999875........344566666666666556666655544..567888888877777 PP

                                        S-G.GGHHHHHHHHHHTEEEEEEEEE CS
                               TehB 108 lea.eripsiienmqectkvggynli 132
                                        l + er  + +e+m++  k gg  l+
  gene1402|gene1402|rna1401|rna1401 112 LSTyERRLKAMEEMKRVLKDGGKGLV 137
                                        75426666777888888888887765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     8e-05      0.14      60     172 ..      42     145 ..      12     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8e-05
                                        --TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES CS
                               CMAS  60 lkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvg 135
                                           G+ +Ld GcG G  +   v +    vvgl    +  + a k++ + +l r  +v+ l + d    +d v svg
  gene1402|gene1402|rna1401|rna1401  42 YTSGSIVLDAGCGNGRSFL--VPE----VVGLDYCFDLLRDA-KAIRNHGLVR-GDVLKLPFAD--SSFDLVLSVG 107
                                        4678999999999997654..444....89999888877665.5688888665.5677777765..68******** PP

                                        -GGGT.SGGGHHHHHHHHHHHS-TT-EEEEEEEEE--H CS
                               CMAS 136 afehv.gkenydtffkklkkllkedGllllhtitslhk 172
                                        ++ h+  +e+  + ++++k++lk++G  l+       k
  gene1402|gene1402|rna1401|rna1401 108 VIHHLsTYERRLKAMEEMKRVLKDGGKGLVYVWGNSVK 145
                                        ****945688889999*********9877765555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1461.45
//
Query:       gene1403|gene1403|rna1402|rna1402  [L=364]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.8       0.65   10.0   0.0    2.2  2  CYTL1     Cytokine-like protein 1


Domain annotation for each model (and alignments):
>> CYTL1  Cytokine-like protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   3.6e-05      0.65      39      94 ..      68     125 ..      51     142 .. 0.81
   2 ?    0.1   0.1     0.039     7e+02      86     102 ..     248     264 ..     240     274 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.6e-05
                              CYTL1  39 lqksertescvevlPklyldihnscvlaklrdflaspkc..rkvarvealkekvrkly 94 
                                        +++++++  c++   k+++d  ns +++++     ++k   r++ +v+  ke +r+l 
  gene1403|gene1403|rna1402|rna1402  68 FESAKEHFRCMKNYEKMFIDTENSYIISRIEADRRRDKTvkREFNKVMDTKEELRSLL 125
                                        566777889********************98766444431267789999999999886 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.039
                              CYTL1  86 lkekvrklytiinkvcr 102
                                        lk++v +ly  + k+ r
  gene1403|gene1403|rna1402|rna1402 248 LKNRVTRLYDSVVKLYR 264
                                        56666666654444322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.62
# Mc/sec: 1765.13
//
Query:       gene1404|gene1404|rna1403|rna1403  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-52  174.0   0.0    1.2e-51  173.7   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    2.4e-10   40.1   2.3    5.1e-10   39.0   2.3    1.6  1  RLI            Possible Fer4-like domain in RNase L inhibitor


Domain annotation for each model (and alignments):
>> Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7   0.0   1.3e-55   1.2e-51       1     127 []      39     165 ..      39     165 .. 0.99

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 1.3e-55
                                        EEE-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHH CS
                      Ribo_biogen_C   1 ivlspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaa 76 
                                        +vlsp+a++ +spaDr+i+e+ gi  +dcsWa+l++v+fk+l  k++rlLP++vAaNpvnYgkp+kL+c+EAl+a+
  gene1404|gene1404|rna1403|rna1403  39 VVLSPDADQSISPADRDIIERFGIGLIDCSWAQLDSVDFKRLPRKHNRLLPFMVAANPVNYGKPFKLNCAEALSAS 114
                                        89************************************************************************** PP

                                        HHHTT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHHH CS
                      Ribo_biogen_C  77 lyilglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkeyl 127
                                        lyi+g+ke+a e+l+ f++g+eF++ln ++l+eYakc++s evve+q+++l
  gene1404|gene1404|rna1403|rna1403 115 LYICGFKEDAYEILEGFNYGNEFYKLNGDILDEYAKCTSSIEVVEAQNRFL 165
                                        ***********************************************9986 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   2.3   5.6e-14   5.1e-10       1      33 [.       1      33 [.       1      35 [. 0.90

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 5.6e-14
                                       --EEEES---------TTHHHHHTTSEEEESS- CS
                                RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtg 33
                                       mr  i++++qCdPKKC+gk++++ + v+ ++ +
  gene1404|gene1404|rna1403|rna1403  1 MRKIIYEFEQCDPKKCSGKRLIKQNKVQPIKKN 33
                                       8999***********************877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1070.16
//
Query:       gene1405|gene1405|rna1404|rna1404  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-10   38.7   0.0    1.2e-09   37.9   0.0    1.4  1  Lectin_leg-like  Legume-like lectin family


Domain annotation for each model (and alignments):
>> Lectin_leg-like  Legume-like lectin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   6.7e-14   1.2e-09       3     110 ..      38     149 ..      36     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 6.7e-14
                                        CEGGGECCCTSCTCTTSSBTTEEEEET-EEE....SSEEEEE-SSTTEEEEEEESS-BEESSEEEEEEEEEESS-- CS
                    Lectin_leg-like   3 fkrehslkkPylgqgskalpnWeyggsaild....snqirltsdeqskkGslwtkspvaleswevevsFrvtgses 74 
                                        f +e sl  Py+ +  + l nW++ g+ +++    +  + l  +  +++G++   +p+ +e + + +   ++  e+
  gene1405|gene1405|rna1404|rna1404  38 FVQEVSLLSPYVDEIGRFL-NWKTSGEQVIKahgrDSFVQLGYSSPNSSGAILASHPIGSERFGIDIIIEIEEGEK 112
                                        67899********997777.9999998777643324469********************************99999 PP

                                        SS-S-EEEEEEESSSSS.CCSBTTB-SS-EEEEEEEE CS
                    Lectin_leg-like  75 elegdglaiwytsergk.egpvFgskdkfdGlailld 110
                                        + +++g+aiw   e    eg  Fg + +f+Gl +++ 
  gene1405|gene1405|rna1404|rna1404 113 GEGDEGMAIWISDEDVFsEGNCFGRSCNFKGLLVIIK 149
                                        9**********9887766***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1994.25
//
Query:       gene1406|gene1406|rna1405|rna1405  [L=370]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-31  109.6  32.7    6.3e-19   68.6   9.0    2.5  2  Mannosyl_trans2  Mannosyltransferase (PIG-V)
    6.7e-06   26.4  13.4    6.7e-06   26.4  13.4    3.5  3  PMT_2            Dolichyl-phosphate-mannose-protein mannosylt


Domain annotation for each model (and alignments):
>> Mannosyl_trans2  Mannosyltransferase (PIG-V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   9.0   7.1e-23   6.3e-19      51     211 ..      44     193 ..      28     198 .. 0.88
   2 !   46.6  15.5   3.5e-16   3.1e-12     237     398 ..     199     337 ..     195     370 .] 0.83

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 7.1e-23
                    Mannosyl_trans2  51 vekllenlvsWDsvyflkiaenGyeyeheyaflpllplfvsllskevlaplvgllslravlvlsvfslsillflla 126
                                        ++  l+ l+sWD+++fl+i e+Gy   h  af+pllp++ ++++         llsl      +++ +s  + +l+
  gene1406|gene1406|rna1405|rna1405  44 TNSCLKFLLSWDAIHFLEIMEKGYGKAHVVAFFPLLPYMSRVVA--------RLLSLEPY--TTGVLVSCTASVLS 109
                                        46778889******************************999988........56666654..44556777788899 PP

                    Mannosyl_trans2 127 avilsdvsvlvlkareasfkasllfclspaavflasiYseaLfallafsgvyslesgisissvllfalstivrsng 202
                                         v+l+++s +  + ++++  + +lf+++paa+ ++++Yse+Lf+ll + g+y le    + + l+ +l +  rsn+
  gene1406|gene1406|rna1405|rna1405 110 SVLLYRIS-QRRYGNKIAIMSCILFIFNPAAIVYTAMYSESLFMLLFLLGIYFLENNSIVHGTLFLSLCGLCRSNA 184
                                        99999976.5678999************************************************************ PP

                    Mannosyl_trans2 203 lvsvgflmf 211
                                        ++ + f+++
  gene1406|gene1406|rna1405|rna1405 185 ILFAPFIIY 193
                                        *99988875 PP

  == domain 2  score: 46.6 bits;  conditional E-value: 3.5e-16
                    Mannosyl_trans2 237 llLsvillflplvlfqyYaYkqfClqrsaGdevpWCksdvpllYsyiqshYWgvGlLkYyelkqvPnfLlaaPvli 312
                                        +lL++i+l lpl +fqyY+   + +             ++++ Y yiq+  W+ G+L++++lk++Pn L+  P + 
  gene1406|gene1406|rna1405|rna1405 199 ALLRMIVLLLPLGIFQYYSLLMINKATN--------TYRIFIPYFYIQKTLWDQGFLRFFTLKNIPNVLVGLPFIL 266
                                        69****************9988877663........58************************************** PP

                    Mannosyl_trans2 313 lvvysilsyvksrpelflslGlqaseknkklekakdltylsadvfvlvvhaavlvviaflimhvqvltrflsasPl 388
                                        + +y    y +           ++s  n k+    d   + +d+ + v+ ++ l++  ++++h  +  rf+s+ Pl
  gene1406|gene1406|rna1405|rna1405 267 ISLYILREYWN-----------KRSTVNPKMYM--DTQRFNTDMCAIVLLVQTLIT--IFLIHWNMYFRFISFNPL 327
                                        ******99999...........56666666333..666677888888888887765..5999************** PP

                    Mannosyl_trans2 389 lyWfaadllq 398
                                        +yW +a++  
  gene1406|gene1406|rna1405|rna1405 328 IYWMLAEKYY 337
                                        *****99866 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.1   9.3e+02      23      56 ..      12      44 ..       2      54 .. 0.76
   2 !   26.4  13.4   7.5e-10   6.7e-06       4     139 ..      77     203 ..      71     221 .. 0.86
   3 ?    0.9   3.8     0.052   4.6e+02      26     103 ..     255     332 ..     245     363 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.1
                              PMT_2 23 airlvsalagvltilllyllarrlfgkraallaa 56
                                        + ++s +++v  +++ yll+ r f+k++ l+++
  gene1406|gene1406|rna1405|rna1405 12 CLAVASKVFYVGISYFAYLLLPR-FDKSTELIST 44
                                       45567778888888889988888.8888888876 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 7.5e-10
                              PMT_2   4 Pliawllalftklfgf.selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdapl 78 
                                        Pl +++ +++++l+     +   lvs+ a+vl+++lly++ +r++g+++a+++++l  + p  ++++a++  ++++
  gene1406|gene1406|rna1405|rna1405  77 PLLPYMSRVVARLLSLePYTTGVLVSCTASVLSSVLLYRISQRRYGNKIAIMSCILFIFNPAAIVYTAMYS-ESLF 151
                                        999***********97799*************************************************888.8888 PP

                              PMT_2  79 vllwalalylllraleknklkywllagvlfGlgflsKytaallliaallyllisarrilke 139
                                        +ll +l +y+l    e+n++   +   +++ l+ l++ +a+l+++ +++y l + + +l+ 
  gene1406|gene1406|rna1405|rna1405 152 MLLFLLGIYFL----ENNSI---VHGTLFLSLCGLCRSNAILFAP-FIIYPLGK-NALLRM 203
                                        88888888875....67775...67778999999***********.99998888.444444 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.052
                              PMT_2  26 lvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkyw 101
                                        ++ +l+g+  il+   ++r++ +kr  +   + + +  +++ ++a++ +  +l+   ++   +++r++  n l yw
  gene1406|gene1406|rna1405|rna1405 255 IPNVLVGLPFILISLYILREYWNKRSTVNPKMYMDTQRFNTDMCAIVLLVQTLITIFLIHWNMYFRFISFNPLIYW 330
                                        6777888888888888888888888887777777777777777776666555555555555566677777776677 PP

                              PMT_2 102 ll 103
                                        +l
  gene1406|gene1406|rna1405|rna1405 331 ML 332
                                        66 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.36s 00:00:01.03 Elapsed: 00:00:00.57
# Mc/sec: 1946.43
//
Query:       gene1407|gene1407|rna1406|rna1406  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.13   12.6   0.0    3.6  3  DUF3040   Protein of unknown function (DUF3040)
       0.22   11.1   0.1       0.32   10.5   0.1    1.3  1  AOX       Alternative oxidase
       0.29   11.5   6.3       0.73   10.2   6.3    1.8  1  YwiC      YwiC-like protein
       0.52   10.0  28.8        4.8    6.8  28.8    2.1  1  DUF4203   Domain of unknown function (DUF4203)


Domain annotation for each model (and alignments):
>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.8e-05      0.13      45      78 ..      35      68 ..      18      73 .. 0.85
   2 ?   -0.3   0.9      0.29   1.3e+03      46      62 ..     113     129 ..     104     148 .. 0.53
   3 ?    1.2   2.7       0.1   4.6e+02      43      81 ..     160     202 ..     143     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                            DUF3040 45 avlavllfvaGllllvlGvaaaavvlgvvGfvvm 78
                                       + +a++lfv+Gll+ +lG+ a+ + l+v+ f v+
  gene1407|gene1407|rna1406|rna1406 35 REIAIALFVSGLLVNFLGICAKRCSLSVIAFPVL 68
                                       458999************999999*****99776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.29
                            DUF3040  46 vlavllfvaGllllvlG 62 
                                        ++a l +++G++++++ 
  gene1407|gene1407|rna1406|rna1406 113 FMAFLSVALGIVMFFFV 129
                                        44455555566665543 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.1
                            DUF3040  43 rlavlavllfvaGllllvlG.vaaaa...vvlgvvGfvvmlag 81 
                                         +++  ++++ +G+l+lvl   ++     +v++v+G + +++g
  gene1407|gene1407|rna1406|rna1406 160 SYYIYQTIMLCIGILVLVLVkPITFLiyiLVFSVFGSLFIIVG 202
                                        4567777888889999998754444456677777777776665 PP

>> AOX  Alternative oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   7.2e-05      0.32      93     151 ..      91     151 ..      41     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.2e-05
                                AOX  93 eeaenermHllvllklaeptlleRllvllaqg..vffniflllYllsPrvahrlvgyleEe 151
                                        e+a     H+  +lk  + + ++ +++ +a g  +ff++ +++Y+l+  +a++l g+le  
  gene1407|gene1407|rna1406|rna1406  91 ENAPKAIGHVVLFLKKVDANRFFMAFLSVALGivMFFFVKTIIYILMGYLAFHLWGILESS 151
                                        55666667888888777655555555444433226788889*****************975 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   6.3   0.00016      0.73       9      92 ..     113     194 ..     111     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
                               YwiC   9 amllvPlllGlllagpvwahllllvawlvgYlaffplllllkarrrarylkplliYgavallllllalllqpa..l 82 
                                         m++++++lG+++      ++   +  l+gYlaf+  ++l ++  +    ++ +iY  + l++++l+l+l +   +
  gene1407|gene1407|rna1406|rna1406 113 FMAFLSVALGIVMF----FFVKTIIYILMGYLAFHLWGILESSTGETMEGSSYYIYQTIMLCIGILVLVLVKPitF 184
                                        57777777777755....4444566899**************999999999***********99999887655245 PP

                               YwiC  83 lwwallflpl 92 
                                        l+++l+f ++
  gene1407|gene1407|rna1406|rna1406 185 LIYILVFSVF 194
                                        5555555444 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  28.8    0.0011       4.8       3     160 ..      38     213 ..      37     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                            DUF4203   3 gailillGlvlcffGyrlfkltlflsgfllgsllvlvlilkvvvlp...................sslvqgaslva 59 
                                        +++l+++Gl++ f+G++  +++l +++f ++ l++  +++ v +                          +a+   
  gene1407|gene1407|rna1406|rna1406  38 AIALFVSGLLVNFLGICAKRCSLSVIAFPVLRLGIGSIMEVVDKIIadkygtaenapkaighvvlFLKKVDANRFF 113
                                        78899*****************************999998775544778999999999998888866666677777 PP

                            DUF4203  60 alvvGllgGllallfwelglfllgalgGlllallilsllegglitslpskaif...lvivvlgllgavlslklqkl 132
                                        ++++ +++G+++++f +  +++l+  + + l  ++ s+  g  ++ ++    +   ++++++g+l+ vl   ++ l
  gene1407|gene1407|rna1406|rna1406 114 MAFLSVALGIVMFFFVKTIIYILMGYLAFHLWGILESST-GETMEGSSY---YiyqTIMLCIGILVLVLVKPITFL 185
                                        778888999999777777777777755555555555555.444444433...344799****************** PP

                            DUF4203 133 llivatsvvGaaavvlgiDyfvgaglke 160
                                        + i+ +sv+G+ ++++g ++ +g  l+ 
  gene1407|gene1407|rna1406|rna1406 186 IYILVFSVFGSLFIIVGANFGFGLNLEF 213
                                        *******************998887543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1143  (0.0637515); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 1586.53
//
Query:       gene1408|gene1408|rna1407|rna1407  [L=507]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-36  124.8   0.0      6e-36  123.4   0.0    1.8  1  DUF5097        Domain of unknown function (DUF5097)
  ------ inclusion threshold ------
       0.02   14.8   0.2       0.06   13.3   0.0    1.8  2  UNC45-central  Myosin-binding striated muscle assembly centra
      0.085   13.0   0.2       0.16   12.1   0.2    1.4  1  Maf1           Maf1 regulator


Domain annotation for each model (and alignments):
>> DUF5097  Domain of unknown function (DUF5097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.4   0.0     1e-39     6e-36       1     119 []       1     119 [.       1     119 [. 0.99

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 1e-39
                            DUF5097   1 miesiavkrfivkyflknstkdlkelsasivkilsskFlinEkvfikkkekyGrivnlvkkeytvvihndngskke 76 
                                        mies a+k+fi++yf+++s++d+++++ +i++ l + Fl+nE v   k+ +yGri+ +   +y vvi++++g +++
  gene1408|gene1408|rna1407|rna1407   1 MIESFAIKKFIINYFIEHSQEDIDKMVLNIHRHLLRGFLMNEVVYNMKSGEYGRISRVGGARYGVVIQSKDGGHEK 76 
                                        9*************************************************************************** PP

                            DUF5097  77 evklqeltRkeelskndvleflktiTidtplgrllkknvledl 119
                                        ++++++l+R++e+s   v+ +l  iT++tp+gr+lk+n++ ++
  gene1408|gene1408|rna1407|rna1407  77 DCHFSDLARRDEVSASGVKGYLLGITMETPFGRVLKENAFGSI 119
                                        ***************************************9775 PP

>> UNC45-central  Myosin-binding striated muscle assembly central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.94   5.6e+03      36      59 ..     258     281 ..     238     298 .. 0.67
   2 ?   13.3   0.0     1e-05      0.06      76     137 ..     370     440 ..     365     448 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.94
                                        HHHHHHHHHHHHHHSCCTHHHHHH CS
                      UNC45-central  36 efeeaiseflesllekgdeddlln 59 
                                        +++e + e+l++ ++ +++d +++
  gene1408|gene1408|rna1407|rna1407 258 KTHERLIEMLKAEIDNIGMDVFIE 281
                                        566677777777777777776664 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1e-05
                                        HHHHTSTTHHHHHHHHHHS..........S-HHHHHHHHHHHHTT--SSSSSHHHHHHHHHHHHHHHH-SS CS
                      UNC45-central  76 salflsegflesllelves.........kkskkvqlaalellsaAcidkkcrkaiaknyvewLeelvkssd 137
                                        +  f++e f e + e++e+         + + ++ +++l l s A+ d+++r+ ++k+ ++ +e++++   
  gene1408|gene1408|rna1407|rna1407 370 NMFFTTEPFREVVSEKMETskelerrkrELQARLRKPILALDSEASLDTDKRSEVKKELIDTMEKIFQLPT 440
                                        66799999*********988999988888889999*******************************99765 PP

>> Maf1  Maf1 regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.7e-05      0.16       8     110 ..     291     416 ..     288     440 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                               Maf1   8 YsckaagsdkklykkiekeleselessskeslslsaaseslssssPfg.................plsdkssrktl 66 
                                        ++c   ++dkk+    + e  +++ ++++ ++ l++  +++ss    +                 pls+++ r++l
  gene1408|gene1408|rna1407|rna1407 291 FECVCSSKDKKQDDLESIEEPRQVLEKKQWKADLEKFIKETSS----QagidishivpcifakdrPLSKEEIRSRL 362
                                        7788888888776433333333333333333333222222222....223446677777799999*********** PP

                               Maf1  67 ayLiatLnasfpdYDFsslrsseFkkekslksvinnidstLss..........l 110
                                        + L   Ln  f    F ++ s++ +  k+l++ ++++++ L +          l
  gene1408|gene1408|rna1407|rna1407 363 VLLELLLNMFFTTEPFREVVSEKMETSKELERRKRELQARLRKpilaldseasL 416
                                        ***********999***********************99998866555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3216.12
//
Query:       gene1409|gene1409|rna1408|rna1408  [L=443]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-13   49.1  12.0    5.7e-11   42.1   7.5    2.5  2  APG9      Autophagy protein Apg9


Domain annotation for each model (and alignments):
>> APG9  Autophagy protein Apg9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1   4.6e-05      0.82      83     160 ..      69     139 ..      16     161 .. 0.78
   2 !   42.1   7.5   3.2e-15   5.7e-11     232     473 ..     185     434 ..     176     437 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 4.6e-05
                               APG9  83 ltllllvlfllywvlkllkflldlrrlleirsfytelLkisdedlqtisWqevverlvelqkenaltakkkeldal 158
                                        +++ +lv+  +++v ++++++l+l+++ ++   y++ L   +e +++i++++vve +++l+ke +      +l+  
  gene1409|gene1409|rna1408|rna1408  69 FSSATLVVGGVFVVKEAISYVLNLKKMASVFYIYRYIL---QEGIDNIRFKDVVEGVIKLEKEVHNR----DLTGK 137
                                        455678999999999***********999988888877...577*****************985444....45444 PP

                               APG9 159 di 160
                                        d 
  gene1409|gene1409|rna1408|rna1408 138 DF 139
                                        43 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 3.2e-15
                               APG9 232 aeeLrkrfllagvlnlllaPfiviylllyfffryaeelkknpsslgsRrwsplAewklRefNELpHlfeaRlnrsy 307
                                        +ee++ +++++  + +ll+P+i i+++ly+++r +e+ ++n   ++++   p  ++ + + NE pH+ ++ ++++ 
  gene1409|gene1409|rna1408|rna1408 185 IEEINDEMRVISAAIFLLSPIISIFFILYYIVRIIEKSQNNVFYVFKKAHRPSFKYFMAKRNEYPHETRRKIQKGA 260
                                        578889999999***************************************************************9 PP

                               APG9 308 klAskYldqfpseklaiiakfvafvagsia..avlvvl.sll......deelllefei...egrtvlfyltvlgvi 371
                                        ++ +++     ++ +a i++ v+f+++ ++  av ++l ++l      +   +l  +i    + t + yl+ ++  
  gene1409|gene1409|rna1408|rna1408 261 DYLNAFFLAKKRDCIARICSAVSFFLSCLVflAVYLILkTVLvsnpnlN--GILYQDIvlfGKTTNILYLSYFIGG 334
                                        999999999999***************8751144444414446644322..233333324667788999****999 PP

                               APG9 372 lavarslipeenevfdpeallrevlehtHYlpdeW..kgklhteevkkefselfqlkivilleellsvlltPfiLl 445
                                        ++ +  +++ +++  + ++  r  +++   ++++   k   ++++  + ++++f  +i+++l e+ s++++Pf L 
  gene1409|gene1409|rna1408|rna1408 335 MSCCLRCLSLDYASTS-RR--RMFIKWCVLMEQREllKYSENRRRLATLMAKFFVPRIYLFLMEISSPFIVPFQL- 406
                                        9999999997774322.22..33344444444333236677777888888999********************99. PP

                               APG9 446 fslpksaeeivdffreftvevdgvGdvc 473
                                         +l+++ e+i   f+++ +  + vG++ 
  gene1409|gene1409|rna1408|rna1408 407 EKLRRRLERIHTTFNSTDIWEEYVGEIQ 434
                                        89****************9999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2957.96
//
Query:       gene1410|gene1410|rna1409|rna1409  [L=358]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-08   32.7   2.5    6.2e-08   32.7   2.5    1.9  2  CAF1A     Chromatin assembly factor 1 subunit A


Domain annotation for each model (and alignments):
>> CAF1A  Chromatin assembly factor 1 subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.28     5e+03      35      35 ..      31      31 ..      14      46 .. 0.47
   2 !   32.7   2.5   3.4e-12   6.2e-08       2      70 ..     193     254 ..     192     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.28
                              CAF1A 35 k 35
                                       +
  gene1410|gene1410|rna1409|rna1409 31 L 31
                                       2 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 3.4e-12
                              CAF1A   2 llqFyedvRPpYyGTwtkkskvvgarnPfskdekeldYdyDSdaEWeeeeeeegedleseedeeeeeed 70 
                                        +++F+++ +Pp+yG   +k   ++ rn + k ++ ldY+ DSd  We+   e++e +   e+e+eeee 
  gene1410|gene1410|rna1409|rna1409 193 FIKFSDQLKPPFYGFREEK---LHVRNSLLKLPQVLDYEHDSD--WED--AEDAETIGTTEEESEEEEG 254
                                        69************88864...5679****************8..644..3479999988777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2210.71
//
Query:       gene141|gene141|rna141|rna141  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.081   13.3  16.2      0.092   13.2  16.2    1.1  1  DUF4604     Domain of unknown function (DUF4604)
        0.1   12.8   4.9       0.14   12.3   4.9    1.3  1  Tau95_N     Tau95 Triple barrel domain
       0.14   11.1   1.2       0.14   11.1   1.2    1.1  1  CSG2        Ceramide synthase regulator
       0.44   10.7   6.4       0.48   10.5   6.4    1.0  1  DDHD        DDHD domain
        2.3    7.0   7.1        2.5    6.8   7.1    1.0  1  Nucleo_P87  Nucleopolyhedrovirus capsid protein P87
        2.3    7.9   6.9        2.3    7.9   6.9    1.2  1  Connexin    Connexin
        2.8    8.9   7.8        4.2    8.3   7.8    1.3  1  GEN1_C      Holliday junction resolvase Gen1 C-terminal domai
        5.3    5.7  12.2        5.2    5.7  12.2    1.1  1  NPR3        Nitrogen Permease regulator of amino acid transpo
        5.8    5.6   9.6        6.1    5.5   9.6    1.0  1  Presenilin  Presenilin


Domain annotation for each model (and alignments):
>> DUF4604  Domain of unknown function (DUF4604)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  16.2   4.6e-05     0.092     110     163 ..      48     104 ..      13     106 .] 0.47

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                        DUF4604 110 a.......sslaaksskkkkkgkvvgeedeeeedkskakkkekekkkakkkkkkkkkkkkk 163
                                    +       s  +++++kk++ +k +g++++e+  +s+++++ +e++k+++kkkkk kk+k+
  gene141|gene141|rna141|rna141  48 KgsfllpvS--NVRGKKKRREKKRKGSSESES--ESENESESSEENKKTRKKKKKGKKSKN 104
                                    144677443..444446666555556555322..233333444444444455554444444 PP

>> Tau95_N  Tau95 Triple barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.9   7.1e-05      0.14      47     103 ..      36      92 ..       9     105 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.1e-05
                                    TT---EE-EEE----EEEEE.......ETTTT.................................. CS
                        Tau95_N  47 pfshpilgeraptnnlllkvtvpkrtgkkrkrgsse.........sekekdssakelrslednkkk 103
                                    + ++ ++++  ++ ++ll v+  ++++k+r+++++          +         e++s+e+nkk+
  gene141|gene141|rna141|rna141  36 LGASNLVSKSMSKGSFLLPVSNVRGKKKRREKKRKGsseseseseN---------ESESSEENKKT 92 
                                    4477899999999******987655555554444445455543221.........22222222222 PP

>> CSG2  Ceramide synthase regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.2   6.8e-05      0.14      65     117 ..      50     102 ..      12     106 .] 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.8e-05
                           CSG2  65 llllPiarllkeatkssvsekesskenklesnsessleleekvesdeeleekt 117
                                     +llP++++  ++++++ ++k+ss+++++++n+++s+e ++k+ ++++  +k+
  gene141|gene141|rna141|rna141  50 SFLLPVSNVRGKKKRREKKRKGSSESESESENESESSEENKKTRKKKKKGKKS 102
                                    4789*****99998888777777665555555555555555444444444433 PP

>> DDHD  DDHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   6.4   0.00024      0.48      74     161 ..      10     100 ..       2     106 .] 0.39

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                           DDHD  74 Pvsiprykrrkllhlelkesltsigaalkqkvsglvsslsa......llnrslelaeeesaslaessksherasesskas 147
                                    +++i+ +k   ++    +++ +++ +a++   s+lvs+  +       ++++ + +++++++ + ss+s+++++++s++s
  gene141|gene141|rna141|rna141  10 AFAISDAKSLHFR---HEKQRNELHKASGLGASNLVSKSMSkgsfllPVSNVRGKKKRREKKRKGSSESESESENESESS 86 
                                    5666666665544...4444444455555555555554442233333233333333333333333333333333333333 PP

                           DDHD 148 qeskaaesstasss 161
                                    +e+k++++++++ +
  gene141|gene141|rna141|rna141  87 EENKKTRKKKKKGK 100
                                    33222222222222 PP

>> Nucleo_P87  Nucleopolyhedrovirus capsid protein P87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   7.1    0.0013       2.5     375     438 ..      29      96 ..      12     103 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0013
                     Nucleo_P87 375 klp..sdlsaqssvpdkkseasavlptek...rkRrrarklqelssdededssdekevDkekerkRRre 438
                                    +l   s l a   v ++ s+ s+ lp ++   +k+rr +k +  s++e e s++e+e  +e+++ R+++
  gene141|gene141|rna141|rna141  29 ELHkaSGLGASNLVSKSMSKGSFLLPVSNvrgKKKRREKKRKGSSESESE-SENESESSEENKKTRKKK 96 
                                    44333444444555555666666666543111444444444344444444.444444444444444333 PP

>> Connexin  Connexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.9    0.0012       2.3     101     139 ..      61     101 ..      15     106 .] 0.49

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0012
                       Connexin 101 eekekekeeeekeeeekeeekkk..kkekkkkkkkeeekek 139
                                    ++k++ek+++ ++e+e+e+e+++  ++e+kk++kk+++ +k
  gene141|gene141|rna141|rna141  61 KKKRREKKRKGSSESESESENESesSEENKKTRKKKKKGKK 101
                                    22222222222222222222222112222222222222222 PP

>> GEN1_C  Holliday junction resolvase Gen1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.8    0.0021       4.2      35      78 ..      56      99 ..      52     106 .] 0.47

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                         GEN1_C 35 sgeegkreepagreglaededdedeeeeeeasakkkrkkkpydP 78
                                   s+++gk+++ +++++ ++++++e+e+e+e+++++kk++kk++  
  gene141|gene141|rna141|rna141 56 SNVRGKKKRREKKRKGSSESESESENESESSEENKKTRKKKKKG 99
                                   66777777555555555555555544433333333333333332 PP

>> NPR3  Nitrogen Permease regulator of amino acid transport activity 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.2    0.0026       5.2      53     101 ..      56     104 ..      18     106 .] 0.58

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0026
                           NPR3  53 kskrkrssrskekkskesskksesssksesseekksskeseeseekesn 101
                                    ++ r++++r+++k++ +s+++ses+++sessee+k++++++++ +k++n
  gene141|gene141|rna141|rna141  56 SNVRGKKKRREKKRKGSSESESESENESESSEENKKTRKKKKKGKKSKN 104
                                    4455555555555555555555555555555555555555555544444 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.6     0.003       6.1     262     310 ..      42     100 ..      10     106 .] 0.35

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.003
                     Presenilin 262 seksaqsse............seeeseeesseaessaeesseekeseessesseeeeeeee 310
                                     +ks +  +            +++++e++++ +++s++es++e+es+e+++++++++++ +
  gene141|gene141|rna141|rna141  42 VSKSMS--KgsfllpvsnvrgKKKRREKKRKGSSESESESENESESSEENKKTRKKKKKGK 100
                                    222222..13355555555433333333333333333333333222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2164  (0.120698); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 732.70
//
Query:       gene1411|gene1411|rna1410|rna1410  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00085   19.0   4.5      0.002   17.7   4.5    1.6  1  TPD52     Tumour protein D52 family
  ------ inclusion threshold ------
       0.67    9.8   6.0       0.56   10.0   1.7    2.5  2  DivIC     Septum formation initiator


Domain annotation for each model (and alignments):
>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.5   2.3e-07     0.002      21     103 ..      12      96 ..       4     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-07
                              TPD52  21 eptlteeeree...LkseLakleeeivtLrqvLaakekhlaelkrklGltalneLrqnlskswhdvqtsnaYkkts 93 
                                        e ++ e e++e   Lk+e ++l  eiv Lrq + a ek+   +k +    al++Lr+   k  ++v++  +  + +
  gene1411|gene1411|rna1410|rna1410  12 EDAIHEPENKElqrLKQENMRLTGEIVILRQNMIALEKQNFAMKEQKSREALDGLRKT-EKLKKEVDVLRIESRIR 86 
                                        44566666665222689**************************************985.56668888888888888 PP

                              TPD52  94 etlsqagqkt 103
                                        e  s++++k 
  gene1411|gene1411|rna1410|rna1410  87 ENQSRVFKKQ 96 
                                        8888888775 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.7   6.3e-05      0.56      30      60 ..      20      50 ..      15      70 .. 0.88
   2 ?    0.3   0.6     0.068   6.1e+02      39      58 ..      68      86 ..      55      92 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                              DivIC 30 qaelaklkaeneeLeaevkdLksdedyieer 60
                                       ++el++lk+en++L+ e+  L+++  ++e++
  gene1411|gene1411|rna1410|rna1410 20 NKELQRLKQENMRLTGEIVILRQNMIALEKQ 50
                                       689******************9876666665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.068
                                       HHHHHHHHHCC-XXXXXXXX CS
                              DivIC 39 eneeLeaevkdLksdedyie 58
                                       + e+L++ev+ L+  e++i+
  gene1411|gene1411|rna1410|rna1410 68 KTEKLKKEVDVLR-IESRIR 86
                                       4678888888885.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1940.79
//
Query:       gene1412|gene1412|rna1411|rna1411  [L=331]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.3   0.4       0.14   12.2   0.4    1.5  1  PH_BEACH  PH domain associated with Beige/BEACH


Domain annotation for each model (and alignments):
>> PH_BEACH  PH domain associated with Beige/BEACH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4     8e-06      0.14      33      77 ..     196     241 ..     178     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-06
                           PH_BEACH  33 seseeeseltadkkkkdkewkl.seikevhlrrYlLrktAlEiFla 77 
                                           ++e+ + ++++++   w+  +ei +++ r+Yl+ +  +Ei+ +
  gene1412|gene1412|rna1411|rna1411 196 FYVSMEDPKIEEDRHRVTAWNGdEEIAKIEYRKYLIENDTVEIWYK 241
                                        56677888999999******97358******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2053.53
//
Query:       gene1413|gene1413|rna1412|rna1412  [L=651]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1234  (0.068827); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 3722.39
//
Query:       gene1414|gene1414|rna1413|rna1413  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-07   29.9  13.5    5.2e-07   29.4  13.5    1.2  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
    8.9e-07   28.7  13.5    1.3e-06   28.1  13.5    1.3  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
    3.3e-06   27.3  13.5    4.5e-06   26.9  13.5    1.2  1  zf-RING_2       Ring finger domain
      4e-06   26.6  11.5    5.2e-06   26.2  11.5    1.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    0.00013   21.8  12.9    0.00022   21.1  12.9    1.3  1  zf-RING_5       zinc-RING finger domain
     0.0033   17.4  10.3     0.0033   17.4  10.3    1.6  1  zf-RING_UBOX    RING-type zinc-finger
  ------ inclusion threshold ------
      0.012   15.5  11.9       0.02   14.7  11.9    1.4  1  Prok-RING_4     Prokaryotic RING finger family 4
      0.014   15.7  11.5      0.025   14.8  11.5    1.4  1  zf-rbx1         RING-H2 zinc finger domain
       0.57   10.4  12.7        2.3    8.5  12.7    2.1  1  zf-C3HC4_4      zinc finger of C3HC4-type, RING
          1    9.2  10.3        4.8    7.1  10.4    1.9  1  zf-RING_4       RING/Ubox like zinc-binding domain
        1.3    9.0   4.3        1.8    8.5   4.3    1.3  1  Baculo_IE-1     Baculovirus immediate-early protein (IE-0)


Domain annotation for each model (and alignments):
>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4  13.5   3.2e-10   5.2e-07       1      41 []       4      41 ..       4      41 .. 0.99

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.2e-10
                                       -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4  1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41
                                       C +C +e+++ +  ++C+HsfC+ Ci+++l+  ++ +CP+C
  gene1414|gene1414|rna1413|rna1413  4 CRVCDCEISIRH-GTPCGHSFCYLCIKRHLS--GHDTCPVC 41
                                       ************.******************..999***** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1  13.5     8e-10   1.3e-06       2      40 .]       4      41 ..       3      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 8e-10
                         zf-C3HC4_2  2 CpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40
                                       C +C  +++     tpCgH+fC+ Ci+r L+ ++ CP+C
  gene1414|gene1414|rna1413|rna1413  4 CRVCDCEISIR-HGTPCGHSFCYLCIKRHLSGHDTCPVC 41
                                       99999999974.889************************ PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9  13.5   2.8e-09   4.5e-06       2      43 ..       3      41 ..       2      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.8e-09
                          zf-RING_2  2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlC 43
                                        C +C +e+s ++ +   pCgH+f++ C++r+l  + tCP+C
  gene1414|gene1414|rna1413|rna1413  3 LCRVCDCEISIRHGT---PCGHSFCYLCIKRHLSGHDTCPVC 41
                                       5*****999865555...5*********************** PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  11.5   3.2e-09   5.2e-06       3      45 ..       2      43 ..       1      48 [. 0.93

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 3.2e-09
                                       SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT-- CS
                         zf-C3HC4_3  3 eeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCrr 45
                                       ++C +C  + +     pCgH  +C+ C ++ l+ +++Cp+C r
  gene1414|gene1414|rna1413|rna1413  2 NLCRVCDCEISIRHGTPCGHS-FCYLCIKRHLSGHDTCPVCGR 43
                                       58*******9999999*****.*******************87 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1  12.9   1.3e-07   0.00022       2      43 ..       4      42 ..       3      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                          zf-RING_5  2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43
                                       C +C +++   +  + t+CgH+fC  C+k+ l   ++Cp+C+
  gene1414|gene1414|rna1413|rna1413  4 CRVCDCEI---SIRHGTPCGHSFCYLCIKRHLSGHDTCPVCG 42
                                       77787777...78899*************************7 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4  10.3     2e-06    0.0033       1      39 []       4      39 ..       4      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                       zf-RING_UBOX  1 CpIClelft....dPlvlpCGHtFCreClwelskslegafkCP 39
                                       C +C  + +    +    pCGH+FC  C+   +++l+g+ +CP
  gene1414|gene1414|rna1413|rna1413  4 CRVCDCEISirhgT----PCGHSFCYLCI---KRHLSGHDTCP 39
                                       88999888855444....5**********...99999999999 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7  11.9   1.2e-05      0.02       1      39 [.       4      44 ..       4      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                        Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeCfdsk..dlssCPlCqrr 39
                                       C +C  + + +   pCgH +C  C +     + +CP+C rr
  gene1414|gene1414|rna1413|rna1413  4 CRVCDCEISIRHGTPCGHSFCYLCIKRHlsGHDTCPVCGRR 44
                                       77777777777779***********99854666*****997 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  11.5   1.6e-05     0.025      28      54 ..      14      41 ..       2      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                            zf-rbx1 28 vlG.eCgHaFHlhCiskWlktrkvCPlc 54
                                         G  CgH+F   Ci++ l+ +++CP+c
  gene1414|gene1414|rna1413|rna1413 14 RHGtPCGHSFCYLCIKRHLSGHDTCPVC 41
                                       44548*********************** PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  12.7    0.0014       2.3      15      42 .]      18      41 ..       4      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0014
                         zf-C3HC4_4 15 eCGhsfClsCisslqkepdgeqllCplC 42
                                       +CGhsfC  Ci++     d     Cp+C
  gene1414|gene1414|rna1413|rna1413 18 PCGHSFCYLCIKRHLSGHDT----CPVC 41
                                       7***********98877644....9999 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  10.4     0.003       4.8      19      44 ..      18      42 ..       4      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.003
                          zf-RING_4 19 eCgyqiClfCyhrileeeegrCPaCr 44
                                       +Cg+ +C  C +r l+  +  CP C 
  gene1414|gene1414|rna1413|rna1413 18 PCGHSFCYLCIKRHLS-GHDTCPVCG 42
                                       7***********9996.79******4 PP

>> Baculo_IE-1  Baculovirus immediate-early protein (IE-0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.3    0.0011       1.8      95     128 ..      12      42 ..       1      51 [. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                        Baculo_IE-1  95 flkPneccGykicnlcyanlwkfstvyPvcPvck 128
                                         ++  + cG++ c+lc     ++ + + +cPvc 
  gene1414|gene1414|rna1413|rna1413  12 SIRHGTPCGHSFCYLCI---KRHLSGHDTCPVCG 42 
                                        4677788*********6...578899999***95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 578.43
//
Query:       gene1415|gene1415|rna1414|rna1414  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-12   48.1   0.0    1.3e-12   47.9   0.0    1.0  1  RNase_P_Rpp14  Rpp14/Pop5 family
  ------ inclusion threshold ------
       0.13   12.2   0.0        5.1    7.1   0.0    2.3  2  DUF1936        Domain of unknown function (DUF1936)


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   1.4e-16   1.3e-12       1     102 [.       7     107 ..       7     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.4e-16
                                        EEEEEEEEESS......-.HHHHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT CS
                      RNase_P_Rpp14   1 RYllveilypdeeeelte.ksllkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtl 75 
                                        RY++v++  + ++ ++ + + l ++i+++v+  +G + l+++g+ l v+++ p++++a+i+c+   ++ v+ ++++
  gene1415|gene1415|rna1414|rna1414   7 RYVVVKLRPEGNR-SVPSmDVLGSIIKSKVEIDYGRHVLSMVGN-LGVVEYLPHSQIAVIKCDAPACKHVLFTIAT 80 
                                        9********9964.3445699***********************.79***************************** PP

                                        --EETTEEEEEEEEEEESSHHHHHHHT CS
                      RNase_P_Rpp14  76 itkiegrpvvfrvvrvsGTikkaeeea 102
                                        i +i g ++ ++v+ vsG +k+a +++
  gene1415|gene1415|rna1414|rna1414  81 IGEISGFKCSMSVLWVSGILKRAMRKI 107
                                        **********************98876 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00057       5.1      17      31 ..      58      72 ..      47      74 .. 0.78
   2 ?    2.7   0.0     0.013   1.2e+02      18      26 ..      82      90 ..      80      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00057
                                       TS-EEEEEES-TT-- CS
                            DUF1936 17 kGEIKvFRCdredCd 31
                                          I v +Cd ++C 
  gene1415|gene1415|rna1414|rna1414 58 HSQIAVIKCDAPACK 72
                                       567999********7 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.013
                                       S-EEEEEES CS
                            DUF1936 18 GEIKvFRCd 26
                                       GEI  F+C+
  gene1415|gene1415|rna1414|rna1414 82 GEISGFKCS 90
                                       9*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 696.85
//
Query:       gene1416|gene1416|rna1415|rna1415  [L=504]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   4.7e-109  364.5   6.0   6.7e-109  364.0   6.0    1.1  1  PK         Pyruvate kinase, barrel domain
      7e-05   22.1   0.1    0.00016   20.9   0.1    1.5  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
      0.064   13.5   0.0       0.17   12.1   0.0    1.7  1  PK_C       Pyruvate kinase, alpha/beta domain
       0.16   10.9   2.1       0.36    9.8   0.0    2.3  3  IMPDH      IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.0   6.0  1.5e-112  6.7e-109       4     342 ..      88     411 ..      85     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 364.0 bits;  conditional E-value: 1.5e-112
                                        SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTT CS
                                 PK   4 tkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkd 79 
                                        tkivct+GP+++s +k+++li+aG+ ++rlnfshG+ e h e+i n+  +  ++ + vai+lDtkGpe+r+ + +d
  gene1416|gene1416|rna1415|rna1415  88 TKIVCTIGPSTSSKQKIRDLINAGMSIARLNFSHGTREAHLETIRNIMDSRCNVDRYVAIALDTKGPEVRIRTPED 163
                                        9*************************************************************************99 PP

                                        CSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EE CS
                                 PK  80 gkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgv 155
                                          kdi++k+gd l++s + +        +  +d+k++ kd    ++i++dDG++ l+v +v+e+  +++ev  +g+
  gene1416|gene1416|rna1415|rna1415 164 --KDIKVKSGDILHFSSSGRGI-----SIPRIDFKSLSKD----DKIFIDDGRIDLRVASVEEDG-FRCEVMSNGT 227
                                        ..79**********98766544.....3567899988877....89****************999.********** PP

                                        E-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHH CS
                                 PK 156 lgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegve 231
                                        +++ k++n p+ +v ++ ls+ Dk+d+ fg+++g+d+i+asfv + +Dv ++r++++   +++ i++kie+  g++
  gene1416|gene1416|rna1415|rna1415 228 IKNDKSMNFPNIDVGIEFLSDEDKDDIIFGLENGIDIIFASFVSSRKDVGKIRKIVG---SQVPIVSKIESCLGMK 300
                                        *******************************************************96...6799************ PP

                                        THHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHH CS
                                 PK 232 nldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlD 307
                                        n+ ei   sDg+m+arGDlG+ei+++kv+ +qkk++  +++ gkpvi+atqm+esmi +  p r+e+sDv+nav D
  gene1416|gene1416|rna1415|rna1415 301 NIREIASSSDGVMIARGDLGVEIGVDKVFSAQKKILLETKKEGKPVICATQMMESMILKNTPNRSETSDVGNAVAD 376
                                        **************************************************************************** PP

                                        T-SEEEESHHHHTSS-HHHHHHHHHHHHHHHHHTS CS
                                 PK 308 GtDavmLsgetakGkyPveavkamaevaleaekal 342
                                        G D+vmLsge+a G +P+e+vk m+++++ ae+ +
  gene1416|gene1416|rna1415|rna1415 377 GCDCVMLSGESAIGMFPIETVKFMKSICIDAEEYV 411
                                        *******************************9865 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   3.6e-08   0.00016      88     184 ..     265     343 ..     247     360 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.6e-08
                                        EEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHHHTT-TTS CS
                          HpcH_HpaI  88 vlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDlsadlgtkrs 163
                                        +   +v +++++ ++ ++             +++++  iEs +g+kn++eIa++   dgv+++  Dl +++g  + 
  gene1416|gene1416|rna1415|rna1415 265 IFASFVSSRKDVGKIRKI----------VGSQVPIVSKIESCLGMKNIREIASSS--DGVMIARGDLGVEIGVDK- 327
                                        555555555554444444..........45789*******************665..78889999****999876. PP

                                        TTSHHHHHHHHHHHHTTHCEE CS
                          HpcH_HpaI 164 pegtevldareriltaaraag 184
                                             v+ a+++il+  +++g
  gene1416|gene1416|rna1415|rna1415 328 -----VFSAQKKILLETKKEG 343
                                        .....7777888777777766 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.8e-05      0.17      35      65 ..     442     472 ..     433     499 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                                        T-TSSEEEEEESHHHHHHHHHHCTTEEHHH. CS
                               PK_C  35 yrpkvpiiavtpneltarqlalyrGvypvlv 65 
                                          p +pi++v+ ++   r++++yrG++pv  
  gene1416|gene1416|rna1415|rna1415 442 SSPMIPIVVVSGDKWILRRFSIYRGIVPVDG 472
                                        4688************************963 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   8.1e-05      0.36      97     144 ..      92     139 ..      84     151 .. 0.89
   2 ?   -2.5   0.2      0.43   1.9e+03     183     222 ..     280     319 ..     273     325 .. 0.75
   3 ?   -0.7   0.0      0.12   5.5e+02     219     235 ..     367     383 ..     364     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.1e-05
                                        EEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              IMPDH  97 aavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkve 144
                                         ++g +++++++++ l++ag+ +  ++ +hg  e  le++++i ++  
  gene1416|gene1416|rna1415|rna1415  92 CTIGPSTSSKQKIRDLINAGMSIARLNFSHGTREAHLETIRNIMDSRC 139
                                        67999999**********************************987654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.43
                                        HHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              IMPDH 183 rvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdi 222
                                        r + g  vp ++ + ++  + + +++   +DG +   gd+
  gene1416|gene1416|rna1415|rna1415 280 RKIVGSQVPIVSKIESCLGMKNIREIASSSDGVMIARGDL 319
                                        6677778888888888888888888888888877766665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.12
                                        HHHHHHHHHTT-SEEEE CS
                                        xxxxxxxxxxxxxxxxx RF
                              IMPDH 219 sgdivkAlaaGadavml 235
                                        + d+  A+a G d+vml
  gene1416|gene1416|rna1415|rna1415 367 TSDVGNAVADGCDCVML 383
                                        57999***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3188.44
//
Query:       gene1417|gene1417|rna1416|rna1416  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.099   12.6   0.0       0.11   12.4   0.0    1.1  1  Glyco_hydro_44  Glycoside hydrolase family 44


Domain annotation for each model (and alignments):
>> Glyco_hydro_44  Glycoside hydrolase family 44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.3e-06      0.11     148     214 ..      63     137 ..      28     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-06
                                        S---HHHHHHHHHHHHHHHHHH-TT-EEEEEEE-SHHHH.TTT-.......TT..CT..T-SSHHHHHHHHHHHH CS
                     Glyco_hydro_44 148 ekvtydellertidlAkavkaadpdaevlGpaswgwtay.fqsaa.....epd..kaahgnvwfldyyLdqmkea 214
                                        +k+  + +++   ++Akavk++  +aev   +  g  +y +++       ++    + h++++f +y+ ++++++
  gene1417|gene1417|rna1416|rna1416  63 QKLHRKAIVTHLENTAKAVKKINFKAEVSKLVISGDEKYkIKKCLqclevQAAmfVGRHKRKKFYEYFVQSLEDY 137
                                        3778889999999**********************999973333344444222568889***********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 997.97
//
Query:       gene1418|gene1418|rna1417|rna1417  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-19   69.9  15.5    7.1e-19   68.8  15.5    1.5  1  Arv1      Arv1-like family


Domain annotation for each model (and alignments):
>> Arv1  Arv1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8  15.5     4e-23   7.1e-19       1     206 [.       3     182 ..       3     186 .. 0.73

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4e-23
                               Arv1   1 iCieCgepvksLytkYskgnirltkCknCkkvaDkYvEfdnvilfiDllLlkpqaYrHllfNtlereeekfekiks 76 
                                        +CieCg+++k+L+ k s++  +++kC  C k  D+Y E + ++ +iDllLlk +++rH lfN+           k 
  gene1418|gene1418|rna1417|rna1417   3 VCIECGSRAKQLFLKNSSA-KQISKCLVCCKKMDRYFELNGMMKLIDLLLLKRRIFRHYLFNNK----------KD 67 
                                        7************998887.69*****************************************2..........56 PP

                               Arv1  77 lirlvillllfevyltwariekksesessslsaqaivlesakelkqylff........lvlalletlvfhlsilll 144
                                        ++r v+l+l++++  t   ++        ++++ + ++ s + l+++++         ++ +l+etl+f ++++++
  gene1418|gene1418|rna1417|rna1417  68 FTRSVLLMLTVKIL-TAPILQ--------HHKTLRLFF-SGEGLDNVSIAaipiicrdVIESLMETLLFLVLVYAV 133
                                        88999888888877.333232........222222222.4444444444411111112444555555555444444 PP

                               Arv1 145 lslesslsalllkykkarlnalltalllssyaklfpilmlIWeydltalalslikllvllsn 206
                                        ++                +  l++alllss+  lf+ +m++W+y++    l +i++l+++sn
  gene1418|gene1418|rna1417|rna1417 134 FHR------------CIGFIKLSSALLLSSFYYLFIFIMIVWKYQWEEYLL-VIEFLCVASN 182
                                        444............345669************************999997.9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1327.71
//
Query:       gene1419|gene1419|rna1418|rna1418  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-64  218.9   0.2    5.2e-63  213.3   0.2    2.1  1  Hist_deacetyl  Histone deacetylase domain
  ------ inclusion threshold ------
      0.043   14.1   0.3       0.76   10.1   0.0    2.4  2  DUF5491        Family of unknown function (DUF5491)


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.3   0.2   5.9e-67   5.2e-63      40     307 .]      53     287 ..      20     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 213.3 bits;  conditional E-value: 5.9e-67
                                        TTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hist_deacetyl  40 lkvHskeYlelleslsnelkkkeeakekeleeiasklldddtpvspktlkaallavgavleavdavlsgsvkaafv 115
                                        l++H+keYle+l ++                      ++ d+p   ++ + ++l   a+++ +  + +g  k + v
  gene1419|gene1419|rna1418|rna1418  53 LTYHTKEYLENLGKI----------------------ETPDCPDIIGLSRFCELYGSASINSAMILSEG--KYNTV 104
                                        455666666555544......................34568888899999999999999999999988..78888 PP

                                        TT.SS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTST CS
                                        xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hist_deacetyl 116 lv.rPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvHhGnGteeafysdpdvltlSiHryegify 190
                                        ++  ++ HHa+++ +sGFC vN++++ai +l +   ++rv+++D+DvHhG+G+eeaf ++++vltlS+H+y+++f+
  gene1419|gene1419|rna1418|rna1418 105 INwSGGLHHAHKNVPSGFCHVNDIVMAILELLKT--YRRVMYIDIDVHHGDGVEEAFLESDRVLTLSLHKYGDGFF 178
                                        888****************************994..66************************************** PP

                                        TSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hist_deacetyl 191 PgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkPdlilvsaGfDalkgdplgelnlsvegy 266
                                        P+tg+l  +g     ++++nvpl  g++d +y ++fe i+++++++f+Pd+i++++G+D+l +d+lg +nls+eg+
  gene1419|gene1419|rna1418|rna1418 179 PETGTLITTG-----HKAVNVPLLSGIDDPSYKYIFEPIVESCVKKFSPDAIVLQCGADSLGEDRLGCFNLSIEGH 249
                                        ******9997.....689********************************************************** PP

                                        HHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hist_deacetyl 267 keltkklaeladkvkkvvllleGGYnlealaravtavlsal 307
                                        +++++ + +l     ++++l++GGY+l+++ar++++ +++l
  gene1419|gene1419|rna1418|rna1418 250 ASCVRFVNSLGI---PLLCLGGGGYTLTNVARCWAYETAVL 287
                                        ***********8...99******************999875 PP

>> DUF5491  Family of unknown function (DUF5491)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   8.5e-05      0.76       6      63 ..     120     176 ..     117     179 .. 0.79
   2 ?    1.4   0.1     0.044     4e+02      34      47 ..     294     307 ..     284     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.5e-05
                            DUF5491   6 sGfleeipeveaipyllkmylrevlaldididpenpydtafksnGvelnyryhltddd 63 
                                        sGf      v ai  llk y r v+ +did+   +  + af      l    h   d 
  gene1419|gene1419|rna1418|rna1418 120 SGFCHVNDIVMAILELLKTY-RRVMYIDIDVHHGDGVEEAFLESDRVLTLSLHKYGDG 176
                                        77877777899********9.6699******999999999976666666666665555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.044
                            DUF5491  34 ididpenpydtafk 47 
                                        idi  enp+ t f 
  gene1419|gene1419|rna1418|rna1418 294 IDIPRENPFYTYFS 307
                                        89*******99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2449.66
//
Query:       gene1420|gene1420|rna1419|rna1419  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.2e-20   71.9   0.2      9e-20   70.5   0.2    1.9  1  La         La domain
    1.9e-06   27.6   0.0    8.1e-06   25.6   0.0    2.1  1  RRM_1      RNA recognition motif. (a.k.a. RRM, RBD, or RNP do
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.048   13.7   0.0    1.7  1  PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
      0.046   13.5   0.9      0.075   12.8   0.1    1.7  2  MalM       Maltose operon periplasmic protein precursor (MalM


Domain annotation for each model (and alignments):
>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.2     2e-23     9e-20       1      58 [.       9      65 ..       9      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2e-23
                                       HHHHHHHHHHTT-TTT-HHHHHHHTTSTTS---HHHHHTSSHHHHHHSSHHHHHHHHH CS
                                 La  1 ilkQvEfYFSdeNLpkDkFLrkkmdkdpegwVplsliasfkrmkkltkdveliaealr 58
                                       i+ QvEfYFSd+N + DkFLr++   + +g++p+++i sf+r+++l+++ve++ eal+
  gene1420|gene1420|rna1419|rna1419  9 IRSQVEFYFSDANFRVDKFLREQSLVN-DGYIPIKTIVSFNRLRSLEATVEDVKEALK 65
                                       899********************9974.8****************************8 PP

>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.8e-09   8.1e-06       1      58 [.      99     156 ..      99     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.8e-09
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHH CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlea 58 
                                        +++ ++p+d+  e++k+ +s+f   + i++ rd+ ++  g  f e++s+e+A+kAl++
  gene1420|gene1420|rna1419|rna1419  99 IYIDGFPKDMMLEDVKDTLSPFITPVLIRMRRDKGKNFSGSIFAEMKSEEEAQKALSE 156
                                        89*******************99999*****************************985 PP

>> PTS_2-RNA  RNA 2'-phosphotransferase, Tpt1 / KptA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.048      26      59 ..      34      67 ..      29      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                          PTS_2-RNA 26 redGyvkvedlLelpklkslkvtleeikevVesn 59
                                        +dGy+ ++ +++ ++l+sl++t+e++ke+ +++
  gene1420|gene1420|rna1419|rna1419 34 VNDGYIPIKTIVSFNRLRSLEATVEDVKEALKDS 67
                                       68***************************99875 PP

>> MalM  Maltose operon periplasmic protein precursor (MalM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.7e-05     0.075      76     110 ..     172     205 ..     155     227 .. 0.80
   2 ?   -2.7   0.1       1.1   4.8e+03      38      56 ..     239     257 ..     232     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.7e-05
                               MalM  76 aegqkeiYllvytteedlakstklehpakayakal 110
                                        +++++e+Yl++ t+ee+l+++ k+   +k   +a+
  gene1420|gene1420|rna1419|rna1419 172 KQKSEEKYLVIMTKEEYLKEKEKMSAEKKEK-EAR 205
                                        5678899****************99655544.433 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                               MalM  38 vLDeqfkvvatyssskFky 56 
                                        ++D + kvv++ ++++Fk 
  gene1420|gene1420|rna1419|rna1419 239 FVDTKEKVVRMKHAEDFKE 257
                                        6788888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2783  (0.155223); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1951.35
//
Query:       gene142|gene142|rna142|rna142  [L=595]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-94  313.6   0.2    1.2e-93  312.8   0.0    1.5  2  LNS2             LNS2 (Lipin/Ned1/Smp2)
    2.3e-31  107.8   0.6    6.6e-31  106.3   0.1    2.1  2  Lipin_N          lipin, N-terminal conserved region
    3.8e-05   23.4   0.3    0.00013   21.7   0.3    1.9  1  DUF4479          Domain of unknown function (DUF4479)
      0.003   17.2   0.0       0.04   13.5   0.0    2.3  2  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
  ------ inclusion threshold ------
      0.016   14.8   4.0        2.3    7.9   0.2    3.1  3  AbrB_C           AbrB C-terminal domain


Domain annotation for each model (and alignments):
>> LNS2  LNS2 (Lipin/Ned1/Smp2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       2.3   8.2e+03       7      33 ..     119     147 ..     118     150 .. 0.77
   2 !  312.8   0.0   3.4e-97   1.2e-93       2     226 .]     347     567 ..     346     567 .. 0.99

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.3
                           LNS2   7 seqlkslnLkeGkn..eieFsvttklqgt 33 
                                    s++l++l L +G++  +++F v  k++++
  gene142|gene142|rna142|rna142 119 SKRLEQLSLGNGSDlsTLNFDVVMKYKEK 147
                                    67899999999985337889888888765 PP

  == domain 2  score: 312.8 bits;  conditional E-value: 3.4e-97
                           LNS2   2 slrltseqlkslnLkeGkneieFsvttklqgtaeveakiylwksddkivisdidgtitksdvlGhilpllgkdwthkgva 81 
                                    sl+l+se+lk lnLkeGkn+  F+++     ++++e++iylwk d+ki++sdidgtitksdv+Gh++ ++g+dwth+gva
  gene142|gene142|rna142|rna142 347 SLKLNSEELKMLNLKEGKNQAIFKISG---LNKHLEGNIYLWKDDAKIIVSDIDGTITKSDVWGHLYGMIGRDWTHHGVA 423
                                    699**********************97...8899********************************************** PP

                           LNS2  82 klyskikengYkilylsaraigqaeltreylksveqdgvkLPkgPvllspdrllsalkreviekkpeefkiacLkdikkl 161
                                    +ly+ki +ngYki+yl+ara+gq+++t++ylksv qdg+kLP+gPv+lspd +++al+re+i ++pe+fkiacLk+i+ l
  gene142|gene142|rna142|rna142 424 SLYTKIVRNGYKIVYLTARALGQSSSTKSYLKSVYQDGYKLPDGPVILSPDGVFAALYRELIIRRPEDFKIACLKTIQGL 503
                                    ******************************************************************************** PP

                           LNS2 162 fpeeknpfyagfGnritdvisYkavgvpksriftinpkgelkeellkklkssyeslselvdkiFP 226
                                    f  ++npf+agfGn+itdvi+Yka+++p sriftin+kgel  el k+l+ +y++++++vd +FP
  gene142|gene142|rna142|rna142 504 FG-DTNPFVAGFGNKITDVITYKALEIPLSRIFTINHKGELYVELVKTLSGTYRTMNDFVDCMFP 567
                                    **.9************************************************************9 PP

>> Lipin_N  lipin, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.1   1.8e-34   6.6e-31       1      91 [.       1      91 [.       1     100 [. 0.95
   2 ?   -2.8   0.1       1.7   6.1e+03      32      58 ..     177     204 ..     176     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 1.8e-34
                        Lipin_N  1 mnyvgkvlssvkelykeinpatlsGaiDvivveqedgelkcspfhvrFgklkvlrskekvvdievNgeevdlkmklgeaGea 82
                                   m +v+k+++sv+ ly++inp+tlsG+ Dvivve +dg+l+c++f++rFg+l ++  ++++v++++Ng+++d++m+++++Ge 
  gene142|gene142|rna142|rna142  1 MGIVHKLITSVSGLYNNINPITLSGVNDVIVVEGKDGKLRCTEFQLRFGRLYFYGVNNQTVHLFINGKMCDITMSITSQGEL 82
                                   889******************************************************************************* PP

                        Lipin_N 83 fFveeteee 91
                                   fF ++te++
  gene142|gene142|rna142|rna142 83 FFEKDTEDD 91
                                   *****9654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                        Lipin_N  32 veqedgelkcspfhvrFgkl.kvlrske 58 
                                    ++q+d + +   f  rF k+ ++++s+e
  gene142|gene142|rna142|rna142 177 LHQRDHKDSYHDFEKRFVKFgNLINSTE 204
                                    5667777777789999999944555544 PP

>> DUF4479  Domain of unknown function (DUF4479)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   3.6e-08   0.00013       8      57 ..     311     360 ..     307     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.6e-08
                        DUF4479   8 verkgdVvrIfdeetgevvGyNifnaskllelegnGqveLteeqvakLne 57 
                                    +++ +++ +I+++e ++++G+Nif  +k+++ +    ++L+ e ++ Ln 
  gene142|gene142|rna142|rna142 311 INKAKKIMKILENEHNRLLGWNIFGTKKIIKRDVSFSLKLNSEELKMLNL 360
                                    67899*************************666667999**999999995 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.094   3.4e+02      70      84 ..     381     400 ..     341     407 .. 0.75
   2 !   13.5   0.0   1.1e-05      0.04     120     155 ..     421     456 ..     412     474 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.094
                                    T.....TSEEEEEE--BTTT CS
                Acid_phosphat_B  70 a.....dkkdavvfDiDeTv 84 
                                    +     d  +++v DiD T+
  gene142|gene142|rna142|rna142 381 NiylwkDDAKIIVSDIDGTI 400
                                    14555589999********8 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.1e-05
                                    CHHHHHHHHHHTTEEEEEEEEEECCCHHHHHHHHHH CS
                Acid_phosphat_B 120 galelikkvverGvkiffvsgRseeqkaaTvenLkk 155
                                    g  +l+ k+v++G+ki++++ R   q + T + Lk+
  gene142|gene142|rna142|rna142 421 GVASLYTKIVRNGYKIVYLTARALGQSSSTKSYLKS 456
                                    56789*************************997775 PP

>> AbrB_C  AbrB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.6       4.2   1.5e+04       2      10 ..      70      78 ..      70      79 .. 0.80
   2 ?    7.9   0.2   0.00065       2.3       8      34 ..     371     396 ..     370     397 .. 0.89
   3 ?    7.1   0.0    0.0011       4.1      13      27 ..     462     476 ..     457     480 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 4.2
                         AbrB_C  2 CmiTGeise 10
                                   C+iT  i++
  gene142|gene142|rna142|rna142 70 CDITMSITS 78
                                   999988876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00065
                         AbrB_C   8 iseeNisLanGkivLSkeGAeiLikEl 34 
                                    is  N++L +G+i+L k+ A+i+++ +
  gene142|gene142|rna142|rna142 371 ISGLNKHL-EGNIYLWKDDAKIIVSDI 396
                                    7778****.*************99876 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0011
                         AbrB_C  13 isLanGkivLSkeGA 27 
                                    ++L +G ++LS++G+
  gene142|gene142|rna142|rna142 462 YKLPDGPVILSPDGV 476
                                    7999**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 3503.76
//
Query:       gene1421|gene1421|rna1420|rna1420  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-34  119.6   0.0    1.2e-34  119.3   0.0    1.0  1  Peptidase_C97  PPPDE putative peptidase domain


Domain annotation for each model (and alignments):
>> Peptidase_C97  PPPDE putative peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.3   0.0   6.8e-39   1.2e-34       1     146 [.       4     139 ..       4     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 6.8e-39
                                        EEEEEEEEETT...TTHHHHHHHHHHSS-----EEEEEEETTEEEE--T.....T-SEEESTT-STT-.S-SEEEE CS
                      Peptidase_C97   1 akvelivyDlsldkkglarrvyptllGkkieGiyhtgvevygleyafggkekeegGifelkpgttsegakpresie 76 
                                        ++v+l vy l    ++  rr++++ lG k + i+ht++evyg+ey+f +     +Gi+++ pg t +g +p ++++
  gene1421|gene1421|rna1420|rna1420   4 HNVILRVYPLG---DETMRRFVASSLGRKEVQIWHTSIEVYGMEYFF-Q-----NGITKALPGFTIHG-TPVKTHD 69 
                                        7899******9...778999999************************.6.....8*********9999.******* PP

                                        EEEE---HHHHHHHHHHHHTT--GGG-BTTTB-HHHHHHHHHHHHHS----HHHHTHHHHHHTSHHHHHH CS
                      Peptidase_C97  77 igeTevteeevraileelsseytgdkYnLiskNCnhFtdelvdfLtgkkiPewinrlarivlstptvkll 146
                                        +g+T+++e  ++++l +++ ++ ++kY+L+ +NCn+Ft++++ +L++k+iPe+i++l++++l ++ v+++
  gene1421|gene1421|rna1420|rna1420  70 LGTTDIPEIVFEDFLLSIADDFAPHKYHLLRNNCNNFTNTVALYLVEKPIPEYILELQNTALESEAVSSI 139
                                        **************************************************************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1016.06
//
Query:       gene1422|gene1422|rna1421|rna1421  [L=377]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-15   55.1   6.8    1.2e-08   34.9   0.5    3.2  3  WW        WW domain


Domain annotation for each model (and alignments):
>> WW  WW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.4   7.3e-09   0.00013       9      31 .]      14      35 ..      10      35 .. 0.92
   2 !   34.9   0.5   6.4e-13   1.2e-08       3      31 .]      48      75 ..      47      75 .. 0.97
   3 ?   -0.9   0.0       0.1   1.8e+03      15      21 ..     160     166 ..     155     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.3e-09
                                       E-TTTT-EEEEETTT--EESS-- CS
                                 WW  9 wdpdsGrvYYyNheTgetqWekP 31
                                       + pd +r+YYyN +T++++ +kP
  gene1422|gene1422|rna1421|rna1421 14 VAPD-NRTYYYNRRTRKSSFTKP 35
                                       6799.*****************9 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 6.4e-13
                                       TTEEEEE-TTTT-EEEEETTT--EESS-- CS
                                 WW  3 pGWeeqwdpdsGrvYYyNheTgetqWekP 31
                                       ++W+e+++++ G+++Y+N+ Tge+ W +P
  gene1422|gene1422|rna1421|rna1421 48 DPWIECRSKQ-GKTFYHNTITGESRWKRP 75
                                       68********.****************99 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.1
                                        -EEEEET CS
                                 WW  15 rvYYyNh 21 
                                        ++YY+++
  gene1422|gene1422|rna1421|rna1421 160 QKYYVDE 166
                                        68***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2225.06
//
Query:       gene1423|gene1423|rna1422|rna1422  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-18   66.3   1.7    2.4e-18   65.6   1.7    1.4  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
  ------ inclusion threshold ------
      0.021   14.0   0.0      0.027   13.6   0.0    1.1  1  MASE1           MASE1
      0.045   12.2   0.1      0.068   11.6   0.1    1.2  1  DUF4503         Domain of unknown function (DUF4503)
       0.16   11.5   2.2       0.29   10.7   2.2    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.17   12.1   3.4         18    5.6   0.0    2.4  2  DUF2992         Protein of unknown function (DUF2992)


Domain annotation for each model (and alignments):
>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   1.7   6.6e-22   2.4e-18       2      54 .]     149     198 ..     148     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 6.6e-22
                     zinc_ribbon_10   2 fDrvldvLvGddetsaknryalICskChshnGlapkeeleevkyrCpkCgaln 54 
                                        +D ++dv++Gdd+   +++yalIC+kC++hnGl++++e++  +++C++C++ln
  gene1423|gene1423|rna1422|rna1422 149 MDSITDVVLGDDP---STMYALICKKCNHHNGLVHPNEYDLNEFYCYNCNELN 198
                                        899**********...***********************************98 PP

>> MASE1  MASE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.6e-06     0.027     126     178 ..      44      96 ..      38     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.6e-06
                              MASE1 126 iiglalllllgliplaslssswltwwlgsatGvlvvaplllllrrylrqrhrl 178
                                        ++g++++++l+ +++   ++s++++ lgsa+G +vv  ll++l++++ +r  +
  gene1423|gene1423|rna1422|rna1422  44 LVGSFVAIVLSMMYSYLDGQSIILFGLGSAFGCYVVRCLLVYLYEMRIRRLES 96 
                                        678889999999********************************999888765 PP

>> DUF4503  Domain of unknown function (DUF4503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   1.9e-05     0.068     264     316 ..     151     204 ..     144     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.9e-05
                            DUF4503 264 svqGvvvgvdestafsWPvCdrCgsekleqspe..drgafsCgsCssvvtsPvlr 316
                                        s++ vv+g d st ++  +C++C   +   +p+  d ++f+C +C+++ t+P+ r
  gene1423|gene1423|rna1422|rna1422 151 SITDVVLGDDPSTMYAL-ICKKCNHHNGLVHPNeyDLNEFYCYNCNELNTRPKNR 204
                                        788999999******96.9****976644444424889**************987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.2   8.2e-05      0.29       2      25 ..     168     194 ..     167     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.2e-05
                                        EETTTTCEE.CHEE..TSTTCEEESSS CS
                       TF_Zn_Ribbon   2 kCPnCgstn.lveD..pergelvCtdC 25 
                                        +C++C++ n lv +  ++ +e++C +C
  gene1423|gene1423|rna1422|rna1422 168 ICKKCNHHNgLVHPneYDLNEFYCYNC 194
                                        7**********99888*********** PP

>> DUF2992  Protein of unknown function (DUF2992)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.1     0.011        39      74     126 ..      94     146 ..      88     148 .. 0.82
   2 ?    5.6   0.0     0.005        18      30      57 ..     177     205 ..     156     208 .] 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                            DUF2992  74 ikkelkkkgvgtkAqqalklqleqrkkerkkkskekreaekerkfelkqeKrk 126
                                        ++  l++ + ++k q al ++ e+  ++rk   k + e+ +++ f   +++r+
  gene1423|gene1423|rna1422|rna1422  94 LESGLETLKERQKEQIALLKKEESFEATRKVIDKYESESMRRHYFGSIKQRRR 146
                                        55555666678899****************************99987666664 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.005
                            DUF2992  30 Ga.ePkdeevlefilkkyeelkfspavea 57 
                                        G   P+++++ ef + +++el+++p+ + 
  gene1423|gene1423|rna1422|rna1422 177 GLvHPNEYDLNEFYCYNCNELNTRPKNRN 205
                                        5558******************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1372  (0.0765241); expected 358.6 (0.02)
Passed bias filter:                      818  (0.0456244); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1454.46
//
Query:       gene1424|gene1424|rna1423|rna1423  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-46  158.8   0.2    1.3e-46  158.5   0.2    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5   0.2   7.1e-51   1.3e-46       1     190 []       3     183 ..       3     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 7.1e-51
                                        HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHS CS
                         Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlryg 76 
                                        vk+Gtt+vG+k+k gv+laad+r+t+   + s++++ Ki++i+d+i+++ aG+aaDa+ ++r+a++e++l++ +y 
  gene1424|gene1424|rna1423|rna1423   3 VKTGTTIVGMKYKTGVILAADTRSTQRPVV-SDRNCVKIHRITDKIMCCGAGTAADAERVTRMASKELRLFENKYF 77 
                                        79***********************55555.8888***************************************** PP

                                        SGTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHH CS
                         Proteasome  77 rpipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalek 152
                                        r + v+     + +k+  + ++++ + +g++l+++g+d+eg  +Ly i p+Gs+     +++ Gsgs aa+++le 
  gene1424|gene1424|rna1423|rna1423  78 RSPLVS-----HFKKVCTHHLHRYGGGIGAALIVGGIDDEG-CHLYDIHPHGSSSPV-LFTSLGSGSLAAIAMLEG 146
                                        ******.....99*************************888.9**************.6***************** PP

                                        HHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                         Proteasome 153 eykedltleeavelavkalkealerdklsgknievavi 190
                                        +y   +++ ea+ela  a+k+++ +d +sg+ni+v+vi
  gene1424|gene1424|rna1423|rna1423 147 KY-RLMDKGEAIELACDAVKAGVLNDLYSGSNIDVCVI 183
                                        **.99*******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1430.82
//
Query:       gene1425|gene1425|rna1424|rna1424  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-07   30.1   0.0     0.0055   16.0   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    1.3e-05   24.9   0.0       0.12   12.0   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    0.00038   21.1   0.0       0.62   10.6   0.0    2.1  2  Abhydrolase_6  Alpha/beta hydrolase family
    0.00067   19.4   0.0     0.0017   18.1   0.0    1.6  1  FSH1           Serine hydrolase (FSH1)
     0.0014   18.2   0.0     0.0022   17.6   0.0    1.3  1  DLH            Dienelactone hydrolase family
  ------ inclusion threshold ------
      0.013   15.5   0.0       0.03   14.3   0.0    1.5  1  UPF0227        Uncharacterised protein family (UPF0227)
       0.19   11.1   0.0       0.29   10.6   0.0    1.2  1  Peptidase_S9   Prolyl oligopeptidase family


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-06    0.0055      55     117 ..     117     175 ..     106     196 .. 0.78
   2 !   12.1   0.0   3.4e-05     0.086     185     232 ..     196     241 ..     192     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-06
                        Hydrolase_4  55 fddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikakl 117
                                           +++Dl+ + + + +++ ++  ++lG S G+++ ++++++++   ++l+l++P++++++ +
  gene1425|gene1425|rna1424|rna1424 117 ERGIIEDLSPISQWISRRSTRK--VVLGFSIGSAVGVRLAEKCHV--DALVLVNPFISLREVV 175
                                        5567888888877777666555..9***************99877..**********999654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.4e-05
                        Hydrolase_4 185 eraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyH 232
                                        +r ++i++P+ ++ +++D++v+p+ + el+++ +    ++ ++pg+ H
  gene1425|gene1425|rna1424|rna1424 196 SRMKEINAPVYFVVSSNDEIVPPSHTDELIKKTR--LPRMIVIPGADH 241
                                        5788999************************998..578888888888 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   9.9e-05      0.25      75     121 ..     138     179 ..     134     183 .. 0.87
   2 !   12.0   0.0   4.6e-05      0.12     197     251 ..     197     242 ..     181     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.9e-05
                                        EEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHH CS
                      Abhydrolase_1  75 ltlvGhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqa 121
                                         +++G+S G++++  +a+  + +V+alvl+++   ++sl+e   +++
  gene1425|gene1425|rna1424|rna1424 138 KVVLGFSIGSAVGVRLAE--KCHVDALVLVNP---FISLREVVSNIL 179
                                        569***************..59**********...888888777665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.6e-05
                                        HHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                      Abhydrolase_1 197 saklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                        +          k+++ap++++ +++D +vpp++ ++l ++++  r +vi++a H+
  gene1425|gene1425|rna1424|rna1424 197 R---------MKEINAPVYFVVSSNDEIVPPSHTDELIKKTRLPRMIVIPGADHN 242
                                        2.........467777***************99999999966666*******996 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00024      0.62      63     100 ..     134     169 ..      98     183 .. 0.73
   2 !    8.3   0.0    0.0012       3.1     159     208 ..     191     243 ..     178     252 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                        .TTSEEEEEETCHHHHHHHHHHCC..EE.EEES-..--- CS
                      Abhydrolase_6  63 gggpvvlvGHSlGGalalaaaplalvvg.vlldppptal 100
                                        +  + v++G S G a++ ++a  + v + vl++p   + 
  gene1425|gene1425|rna1424|rna1424 134 RSTRKVVLGFSIGSAVGVRLAEKCHVDAlVLVNP---FI 169
                                        345569*************6666644446*****...44 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0012
                                        CHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCHSTTEEET..CE...SSS.- CS
                      Abhydrolase_6 159 gllpaaawadlpvpllvl.ggeDplvprllerllaqagarlp..vvlpgaGH.l 208
                                        +++++++ + + +p++ +  ++D++vp+   + l   + rlp  +v+pga+H  
  gene1425|gene1425|rna1424|rna1424 191 EWNNVSRMKEINAPVYFVvSSNDEIVPPSHTDELI-KKTRLPrmIVIPGADHnE 243
                                        45566666777777754449****99999889998.66666666********52 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.5e-07    0.0017      81     199 ..     115     239 ..      65     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.5e-07
                               FSH1  81 neyegleesldavkdyikengpfdGiiGFSqGaalaallaslleellkea..shpslkfai..lvsGfkleepkye 152
                                         + +g+ e l+ + + i+++   + ++GFS G+a++ +la++ +           sl+ ++  ++ G  l++  ++
  gene1425|gene1425|rna1424|rna1424 115 PSERGIIEDLSPISQWISRRSTRKVVLGFSIGSAVGVRLAEKCHVDALVLvnPFISLREVVsnILFGRVLKHFIVD 190
                                        56677778888899999999999*******************9965433333233334444112334444444444 PP

                               FSH1 153 eyy...eedkiqtptLhvlGelDtvvdeerseaLaeafknsskvlkHpgg 199
                                        e       ++i+ p+ +v+ ++D++v+++ + +L+++++  ++++  pg+
  gene1425|gene1425|rna1424|rna1424 191 EWNnvsRMKEINAPVYFVVSSNDEIVPPSHTDELIKKTRL-PRMIVIPGA 239
                                        42233477889**************************999.777666664 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.6e-07    0.0022      98     171 ..     136     229 ..     112     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.6e-07
                                DLH  98 kkvgvvGfCmGGalalllaaevpevdaavafYG.....................lspekeleeaakikapilalfg 152
                                         + +v Gf +G a+ + la +   vda v   +                     +   +++++ ++i+ap+++++ 
  gene1425|gene1425|rna1424|rna1424 136 TRKVVLGFSIGSAVGVRLAEKC-HVDALVLVNPfislrevvsnilfgrvlkhfiVDEWNNVSRMKEINAPVYFVVS 210
                                        445689****************.7******999999***************999999999**************** PP

                                DLH 153 eeDefipadevekleealk 171
                                         +De++p +++++l ++++
  gene1425|gene1425|rna1424|rna1424 211 SNDEIVPPSHTDELIKKTR 229
                                        **********999988874 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05      0.03      51     183 ..     129     256 ..     113     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                            UPF0227  51 klvaelgddnillvGssLGGyyatrlgerfglrq.vllnPalkplenlagklgeeavqstqetyvleeyhiielka 125
                                        + ++  + +  ++ G s+G  +  rl+e++ + + vl+nP +   e +++ l            vl++  ++e + 
  gene1425|gene1425|rna1424|rna1424 129 QWISRRSTR-KVVLGFSIGSAVGVRLAEKCHVDAlVLVNPFISLREVVSNILFGR---------VLKHFIVDEWNN 194
                                        444444433.7899********************9********999999987552.........445567777777 PP

                            UPF0227 126 lelsrlkrperilvllskqDevldyrravaefraa...aeiveddgdHa..fkdvsehlqqii 183
                                        +   ++ +  +++ + s +De+++ +++ +  ++    + iv+ + dH+  +++++ hl  +i
  gene1425|gene1425|rna1424|rna1424 195 VSRMKEINA-PVYFVVSSNDEIVPPSHTDELIKKTrlpRMIVIPGADHNepMRNFATHLYPVI 256
                                        766555443.45556678999999977766666551115799999999655889999987765 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.29     129     187 ..     190     242 ..     181     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                        HHHHHH-CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SS CS
                       Peptidase_S9 129 kelspyspldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHg 187
                                        +e++++s +++  +++p+ ++++ +D+ vpp+++    ++L kk    ++ + p+++H 
  gene1425|gene1425|rna1424|rna1424 190 DEWNNVSRMKE--INAPVYFVVSSNDEIVPPSHT----DELIKKTRLPRMIVIPGADHN 242
                                        56777788888..********************8....566666667889999999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 1594.55
//
Query:       gene1426|gene1426|rna1425|rna1425  [L=315]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-36  123.7  12.4    1.2e-35  123.3  12.4    1.0  1  Zip       ZIP Zinc transporter


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3  12.4   6.9e-40   1.2e-35       5     328 ..       6     304 ..       3     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 6.9e-40
                                Zip   5 ilaiiaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehth..... 75 
                                        il  ++i+ +sll++l+p ++   +    ++++ +l+ + +G llg  +l L P+ +  ++e++ + + +h     
  gene1426|gene1426|rna1425|rna1425   6 ILFAVIIFSSSLLVCLSPKIITSLK--VVRKVFPFLTLLTAGFLLGVQLLELSPHMVSDCHEHKGHNH-GHhthes 78 
                                        5566788889999999999999776..67*******************************99987765.33346** PP

                                Zip  76 .plagllvllGflllllveklltmivekksshkektpkkasssssesaakksvsndkveeseekedhvaeadtdad 150
                                         +l ++++ l+f++ll ++ ++   ++   +++ek +++++++   +++++++s    +   +    ++  dt a+
  gene1426|gene1426|rna1425|rna1425  79 pMLGFFTAGLSFIFLLAIDTIVLKHKHC--EEEEKKKHTHDTECHGNDPHRRISTRGNNHVPKP--GEKALDTPAS 150
                                        999999999*************976666..4444444444444444444444433333333333..2233445556 PP

                                Zip 151 skeelrngkqeksesekeqaseeedkeklaslkvraiilllglilHsfidGLAlGvssssstgislfiAvllHelp 226
                                         ke +r g  ++s+ +k+++           +++ ++i++lg+++Hsf++GLA+    s +++ sl + ++lH+++
  gene1426|gene1426|rna1425|rna1425 151 GKEAERLGCCDPSGAIKNTS-----------SRTQVFIYILGISIHSFFEGLAFN---SIDKIGSLEMGLILHKVL 212
                                        66666666667777777765...........59********************96...****************** PP

                                Zip 227 eelglgaiLlkaglsrkkavllnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellphE 302
                                        e ++lg++L+ +g++ ++ ++l+l++++++p+Gi+iG +      +     + +i+ +l+ G  + +   e++p  
  gene1426|gene1426|rna1425|rna1425 213 ESFALGVPLFTSGFNFSTGLILALFYSSLTPIGIMIGSA-----PGFFGHTIKNIFKGLALGSIMFMVSIEMIPPM 283
                                        ***************************************.....999***************************56 PP

                                Zip 303 llnekgssslkqsllqllglllGfal 328
                                        + ++k     +  ++ +l ll+G++ 
  gene1426|gene1426|rna1425|rna1425 284 FNHPK-----VSRIHGILTLLIGYLS 304
                                        66666.....8899999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2253.46
//
Query:       gene1427|gene1427|rna1426|rna1426  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 568.08
//
Query:       gene1428|gene1428|rna1427|rna1427  [L=656]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.7e-71  239.0   0.0    6.9e-71  238.5   0.0    1.3  1  XRN_N      XRN 5'-3' exonuclease N-terminus
      1e-62  212.6   4.6    1.7e-43  149.2   1.8    2.3  2  XRN_M      Xrn1 helical domain
  ------ inclusion threshold ------
       0.14   11.9   0.4       0.49   10.2   0.4    2.0  1  zf-CCHC_4  Zinc knuckle


Domain annotation for each model (and alignments):
>> XRN_N  XRN 5'-3' exonuclease N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.5   0.0   1.2e-74   6.9e-71       1     241 [.       1     260 [.       1     261 [. 0.90

  Alignments for each domain:
  == domain 1  score: 238.5 bits;  conditional E-value: 1.2e-74
                                        XXX-HHHHHHHHHSGGGEEE------SSSS-EEEEEEETHHHHHHHHS-SSS-......--SSHHHHHHHHHHHHH CS
                              XRN_N   1 mGvpklfrwlserypkivkevieeeeeeekefdnLYlDmNgiihkcshkedkeekelskkpkteeeifkkifkyid 76 
                                        mGvp+lfrwl+  ++ +++++ e    ++ ++d+LYlD+N+iih+c+++       l+++++ e+++ k++ + id
  gene1428|gene1428|rna1427|rna1427   1 MGVPSLFRWLQLSHKVAIHSILE----NP-SVDCLYLDFNAIIHTCIKP------GLESEEEIERDLHKTVGDFID 65 
                                        9**************99999972....34.8****************77......56779999************* PP

                                        HHHHHH-EEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-BB-............... CS
                              XRN_N  77 rlvkivrprkllylavDGvaPraKmnqqRsRRfrsakeakeekeekeelkeelekeekeee............... 137
                                         ++ ++rprklly+a+DGvaPraK+++qR+RR++sa  +ke ++ k+ +k+e+  ++++e+               
  gene1428|gene1428|rna1427|rna1427  66 YILLKARPRKLLYIAIDGVAPRAKLSHQRARRYKSALGKKEGSSVKSISKTEFAPQSEKERkeegrdeeftgessl 141
                                        ************************************999999553333333333222222233456667889999* PP

                                        ..................-------GGGSSTTSHHHHHHHHHHHHHHHHHHHH-GGGGG-EEEEE-TTS-S-HHHH CS
                              XRN_N 138 ..................eeeekfdsnvitpGtefmeklsealkafikkklkedpawknlkvilsdaevpGEGEhK 195
                                                          +e+e+fd n+itpGt+fme+l++ l  +i++kl++dp  ++lk+i+s+  vpGEGE+K
  gene1428|gene1428|rna1427|rna1427 142 ydkfivedisessslavdVETENFDLNCITPGTPFMERLHNVLISYIQYKLSNDPGVSHLKIIYSSYLVPGEGEQK 217
                                        ******************9********************************************************* PP

                                        HHHHHHHHHTSTTS-TT-EEEEE---THHHHHHHHHT-SSEEEEEE CS
                              XRN_N 196 imefirkqrskpeydpntrhviyglDaDLillsLathepniliLre 241
                                        im+fir+q+   ++ +n  h+iy+ D+DL++l+L++h  ++li+r+
  gene1428|gene1428|rna1427|rna1427 218 IMSFIRSQE---SVARNDVHMIYSPDGDLMFLGLSLHRSKVLIMRD 260
                                        ********9...9999*****************************7 PP

>> XRN_M  Xrn1 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0     2e-21   1.2e-17       2      94 ..     318     410 ..     317     431 .. 0.94
   2 !  149.2   1.8   2.9e-47   1.7e-43     175     358 ..     429     604 ..     414     614 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 2e-21
                              XRN_M   2 fdleriiDDfvFlcFFvGNDFLPhlPsLeiregaidlllkvYkkelkklggyltdngevkldrveklvslvgkvee 77 
                                        f+ eri+ D++FlcF  GNDF+P +P+L+ir  +i+ + ++ +k ++ ++ y+t + +++++  +++ + +++ e+
  gene1428|gene1428|rna1427|rna1427 318 FNEERILNDWIFLCFLLGNDFVPPTPCLDIRFHSIETITEIMAKNFSVTKSYITCSSTINFQALKNFCTILAAKED 393
                                        789************************************************************************* PP

                              XRN_M  78 kifrkrkeredrkekkl 94 
                                         +++++++  d+ ++ l
  gene1428|gene1428|rna1427|rna1427 394 GLYHRKSQSLDKFREGL 410
                                        *******9999988765 PP

  == domain 2  score: 149.2 bits;  conditional E-value: 2.9e-47
                              XRN_M 175 keRYYkekfevsseeieqrrevvqkYveGLcWvlrYYyqGvaSWkWfyPyhyaPFaSDlknladlkikFekgspfk 250
                                        k  YY++k+++++e  + +++v  +Y++GL Wv+ YY  G + W W+yPyh+aP a Dl++++  +i+ + g p++
  gene1428|gene1428|rna1427|rna1427 429 KIQYYASKLNANTE--SDIKNVCYEYIKGLYWVYSYYILGSTGWDWYYPYHFAPLAVDLSKISISEIRINPGLPLR 502
                                        678******99765..57899******************************************************* PP

                              XRN_M 251 pleqLmavlPaaskkalPkayqkLmtdpdSpiidlypedfeidlnGkrvaWqgvaklPfidekrLlealakleeeL 326
                                        pleqL+avlP+ sk  +Pk  q + +d      d yped++ d+  k + Wq v++lPf+d + +l++ a+  ++L
  gene1428|gene1428|rna1427|rna1427 503 PLEQLLAVLPPMSKGMVPKVLQPIFND----YKDCYPEDVKTDMFDKVYLWQEVVLLPFVDFRSILSENASRFNSL 574
                                        ***************************....78******************************************* PP

                              XRN_M 327 teeEkkRNtrksdvlfvsktskkaeallakls 358
                                          e+  RN r  d+lf + +++    ++ +++
  gene1428|gene1428|rna1427|rna1427 575 GYEDLSRNLRSLDLLFTVDKKSSE--VILNMY 604
                                        ***************987765544..344444 PP

>> zf-CCHC_4  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   8.2e-05      0.49      29      47 ..     268     286 ..     268     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.2e-05
                          zf-CCHC_4  29 rLrsfCyiCgvlGHsdkrC 47 
                                        r+++ C  C + GHsd++C
  gene1428|gene1428|rna1427|rna1427 268 RMKKTCAKCKRSGHSDEEC 286
                                        67789************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 4078.60
//
Query:       gene1429|gene1429|rna1428|rna1428  [L=425]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-26   93.2   0.0      3e-26   92.1   0.0    1.6  2  DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
    2.9e-15   56.2   0.0    2.8e-14   53.0   0.0    2.1  1  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B


Domain annotation for each model (and alignments):
>> DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.0   3.3e-30     3e-26       1     130 []      12     147 ..      12     147 .. 0.93
   2 ?   -3.5   0.0       1.2   1.1e+04      38      56 ..     197     215 ..     178     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 3.3e-30
                        DNA_pol_D_N   1 QYaniYfaRleqlkprlleaakekwskeelkvnrildlkeg...eecivvGtiykemklkpsvlkeiakedesapq 73 
                                        Q++ +Y aRl++l+p ++++ak+      +++++il ++e+    +c+++Gt+++  +lkp+++++i+++++++++
  gene1429|gene1429|rna1428|rna1428  12 QFNRTYDARLAELRPYIIKSAKALN--AGPILDSILGIEEEpgnRRCVIIGTLFIASDLKPTIFDKINRKSKKIKE 85 
                                        9**********************99..469**********9999******************************** PP

                        DNA_pol_D_N  74 aerkkyvsekdellLEDesgrvrLs...gsgiesek..lvtGvvvavlGvetengdfeVedi 130
                                         e+k+y+s++ +++LED sgrv+++    s i +++  + tG++++v G++te  +f  edi
  gene1429|gene1429|rna1428|rna1428  86 MEAKTYYSQEIKYFLEDGSGRVEVEfldISWIYQRNfvISTGMCIGVAGAMTERTKFLAEDI 147
                                        ***********************99766667888884455*****************99886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                        DNA_pol_D_N  38 lkegeecivvGtiykemkl 56 
                                        +   +e i++G ++ e k+
  gene1429|gene1429|rna1428|rna1428 197 MTGVKEYIMIGNFFAESKE 215
                                        4444778888888887764 PP

>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   3.1e-18   2.8e-14       1     207 [.     170     378 ..     170     382 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 3.1e-18
                                        EEEEES--S-TT----HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTT CS
                        DNA_pol_E_B   1 vvivsglnldndnrsleaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsiles 76 
                                        v ++sg+ ++n+n+  e +  i+++     + ++  i++Gnf++                 e+ + ++++ls l+s
  gene1429|gene1429|rna1428|rna1428 170 VCFISGPSISNENKNRERMMVIIDYLR--MTGVKEYIMIGNFFA-----------------ESKEVSKQMLSLLDS 226
                                        578999999999999999999999999..999999999999998.................233344556666666 PP

                                        S-..TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEE CS
                        DNA_pol_E_B  77 ll..ekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkresl 150
                                        +l  +  ++ l+P+++D  ++ vlP  P++++l+  +          tNP+ +e+++ +v++t+  +v+dl ++  
  gene1429|gene1429|rna1428|rna1428 227 VLkyAGGRINLIPNIRDFGSR-VLPLSPVHPKLFTLPVGA------NTNPCHLEVDGRKVLITTRFVVEDLLKYLP 295
                                        6655678999***********.************998775......69**************************** PP

                                        SHHHH..........................HS-HHHHHHHHHHHHTBS---SS.--B-GGGGGGGB-GGG---SE CS
                        DNA_pol_E_B 151 kesnt..........................dverlrklvktildqrhlaPlap.tlrpvswdkddalvleplPdv 199
                                        ++ ++                          +  +  ++++ +++ +h++P+ap t+++v++  +d++v+    d+
  gene1429|gene1429|rna1428|rna1428 296 QDLENvqgnnfeykmhldmekineaaprsmsNEGNIIRALEVLMKAGHVCPTAPdTIQSVPFSGKDPFVVTGQVDY 371
                                        **999*************************98889999*******************************9766677 PP

                                        EE---SS- CS
                        DNA_pol_E_B 200 lvlpdelp 207
                                        l ++d  +
  gene1429|gene1429|rna1428|rna1428 372 LCVGD-TD 378
                                        77777.55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2999.45
//
Query:       gene1430|gene1430|rna1429|rna1429  [L=287]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-05   22.9  11.4    0.00049   18.8   5.3    3.1  2  RRN3      RNA polymerase I specific transcription initiation 


Domain annotation for each model (and alignments):
>> RRN3  RNA polymerase I specific transcription initiation factor RRN3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   5.3   2.8e-08   0.00049     304     469 ..      98     239 ..      33     246 .. 0.67
   2 !    2.4   0.3    0.0026        46     530     554 ..     262     286 ..     254     287 .] 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.8e-08
                               RRN3 304 eeeeeeeglelfntLlslFkstiLptyksrhvqFllFhfssldpeladkflglLidialsknepaetRvaAaaYla 379
                                        e+ +++ ++   +  l+ F+  +L   k+r +qFllF ++  +p+ +    g+L++ + ++ +        + Yl+
  gene1430|gene1430|rna1429|rna1429  98 ENLSDAIHDFKIDEVLKAFEVSLL--SKTRNIQFLLFRLCCRNPQAV---FGFLFKLTYKNPT------VYLPYLS 162
                                        55666666677789999*******..59***************9876...5556666655555......3479*** PP

                               RRN3 380 SfvaRAkf...vskeqvrkvvslLvewlekyvdereeevqgpdlkrhkvFYavaQAllYifCFRwrdLlkeeeeke 452
                                        S + R +    v++  vr+++s+    +++  +++             ++ +++Q llYi CFR + ++++++   
  gene1430|gene1430|rna1429|rna1429 163 SLIVRCRIdegVKSGYVRDYLSY----IRSLSRSS-----------SILYVSACQCLLYISCFRREIFMAAKDV-- 221
                                        *****974222444444444444....44333222...........35899******************98764.. PP

                               RRN3 453 kdrkwlqel.kvlqrvii 469
                                         d+ + +++ + ++r+++
  gene1430|gene1430|rna1429|rna1429 222 IDQIFDSGIaRYMNRNVV 239
                                        555566666666666665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.0026
                               RRN3 530 syFPFDPykLprskrfieelYveWs 554
                                         +FPFD   L++    i+e Y++++
  gene1430|gene1430|rna1429|rna1429 262 YFFPFDLPILEKVGDGIHEFYIHFR 286
                                        59********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1823.45
//
Query:       gene143|gene143|rna143|rna143  [L=192]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.021   15.2   5.9      0.024   15.0   2.2    2.3  2  Nnf1        Nnf1
      0.027   13.0   1.5       0.06   11.9   0.6    1.7  2  Herpes_UL6  Herpesvirus UL6 like
      0.027   15.0   0.6       0.17   12.4   0.1    2.2  2  FlgN        FlgN protein
      0.061   13.6   3.5        1.7    9.0   0.2    2.8  3  BLOC1_2     Biogenesis of lysosome-related organelles complex
      0.096   13.2   0.4         19    5.8   0.0    2.9  3  NPV_P10     Nucleopolyhedrovirus P10 protein
       0.16   12.6   4.8        0.5   11.0   0.4    2.7  3  YabA        Initiation control protein YabA
       0.17   12.1   0.2       0.17   12.1   0.2    2.1  3  Med21       Subunit 21 of Mediator complex
       0.28   11.6   3.7        4.7    7.7   1.0    2.9  2  CENP-H      Centromere protein H (CENP-H)
       0.29   11.4   4.7       0.96    9.7   4.6    2.0  1  PHM7_cyt    Cytosolic domain of 10TM putative phosphate trans


Domain annotation for each model (and alignments):
>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.21   4.2e+02      12      30 ..       9      27 ..       7      35 .. 0.83
   2 ?   15.0   2.2   1.2e-05     0.024       5     101 ..      64     161 ..      60     168 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHHHHHHHHTT CS
                           Nnf1 12 efleesiraefeeIleerd 30
                                   ++++++ ++ ++eIl+e++
  gene143|gene143|rna143|rna143  9 AKMRQAYKRAIQEILKEKE 27
                                   5788899999999999975 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHCCHH-.T...........TTSSTTTHHHHHHHHHHHHH CS
                           Nnf1   5 svhkqmvefleesiraefeeIleerdvvekLneLDdlieeAkerree.geeeasrpe.vpphtLpPeeliaahlapakke 82 
                                    s+ +++ + l+++  + f + le +d+ +kLn LD+ + e ++  +  +++e  r e  +  + + + ++  ++ ++k+e
  gene143|gene143|rna143|rna143  64 SAIENIFQGLRSKLSDVFRKKLEMNDISNKLNRLDRDVLEGRTSLRDvTSKEYVR-EiFESYLVNTKVDYIDYIEETKRE 142
                                    56677888999999999******************98888886555413333222.244444555777777777777777 PP

                                    HHHHHHHHHHHHHHHHHHH CS
                           Nnf1  83 eqeeLearlqeleaenael 101
                                    ++e+++   +ele+ ++el
  gene143|gene143|rna143|rna143 143 ALERIRVLKNELEKATEEL 161
                                    7777777777777777765 PP

>> Herpes_UL6  Herpesvirus UL6 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.12   2.5e+02     326     378 ..      38      94 ..      17     107 .. 0.69
   2 ?   11.9   0.6     3e-05      0.06     358     432 ..     108     182 ..      91     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.12
                     Herpes_UL6 326 slvdknklldasqpGfgkggasaqss...ekteqglkksvsnsvikcle.eqineqf 378
                                     l + ++ +d+s++G  ++    ++s   e++ qgl++++s+   k le + i +++
  gene143|gene143|rna143|rna143  38 TLCEDSFFMDSSKAGETHQRDPEETSsaiENIFQGLRSKLSDVFRKKLEmNDISNKL 94 
                                    566667788888887444433322223468899999999998888888733455544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3e-05
                     Herpes_UL6 358 lkksvsn.svikcleeq.ineqfdtiekLkkenelllkklkelekeLerlreeakkeakarevdlltsstdaslenl 432
                                    l+++ s+  v ++ e++ +n+++d i+ +++++   l++++ l++eLe+++ee      +re++l  +++d+ +++ 
  gene143|gene143|rna143|rna143 108 LRDVTSKeYVREIFESYlVNTKVDYIDYIEETKREALERIRVLKNELEKATEELGL--LKRENTLCRNTYDNLISSF 182
                                    5555544146777777658*******************************877764..5556566666666555444 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.45   8.9e+02      85     109 ..       4      28 ..       1      37 [. 0.62
   2 ?   12.4   0.1   8.6e-05      0.17      31      77 ..     124     170 ..     122     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.45
                                    CCHHHHHHHHHHHHHHHHHHHHHHH CS
                           FlgN  85 edeelkelwqelkelleelkelnel 109
                                    + ++l++++q+ k +++e+ +  e+
  gene143|gene143|rna143|rna143   4 DGPRLAKMRQAYKRAIQEILKEKEK 28 
                                    5667777777777777765444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.6e-05
                                    HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHH CS
                           FlgN  31 aLkagdieaLeelleekqellekleqleqkrakllaelglsaeeatl 77 
                                     L++ +++ ++ + e k e le+++ l+++++k+++elgl + e tl
  gene143|gene143|rna143|rna143 124 YLVNTKVDYIDYIEETKREALERIRVLKNELEKATEELGLLKRENTL 170
                                    578889999999****************************9666665 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         2     4e+03      62      73 ..      14      25 ..       7      39 .. 0.49
   2 ?    4.6   0.0      0.02        39      38      74 ..      65     101 ..      58     108 .. 0.91
   3 ?    9.0   0.2   0.00088       1.7       9      47 ..     148     186 ..     141     192 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                        BLOC1_2 62 pylqqidqiekq 73
                                    y++ i++i k+
  gene143|gene143|rna143|rna143 14 AYKRAIQEILKE 25
                                   333333333322 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                        BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqv 74 
                                    +++++ ++l++kl+++ +k+ e++   +++++++++v
  gene143|gene143|rna143|rna143  65 AIENIFQGLRSKLSDVFRKKLEMNDISNKLNRLDRDV 101
                                    6889999**************************9988 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00088
                        BLOC1_2   9 kyleaeleatvedyklLeklNeaasekykklkdvaasle 47 
                                    ++l++ele ++e++ lL++ N+   + y++l ++ ++++
  gene143|gene143|rna143|rna143 148 RVLKNELEKATEELGLLKRENTLCRNTYDNLISSFSKAA 186
                                    789*************************99977776665 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   2.2e+03      50      66 ..      18      34 ..       8      40 .. 0.63
   2 ?    4.1   0.0     0.032        65      25      58 ..      68     101 ..      60     120 .. 0.66
   3 ?    5.8   0.0    0.0096        19      16      55 ..     126     165 ..     124     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                        NPV_P10 50 qLaeletkvenIqdiLn 66
                                   +++e+ ++ e+I+ iL+
  gene143|gene143|rna143|rna143 18 AIQEILKEKEKIKGILT 34
                                   44444455566666666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.032
                        NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                    +  + ++++l dv   + +++++s++L+ l+  v
  gene143|gene143|rna143|rna143  68 NIFQGLRSKLSDVFRKKLEMNDISNKLNRLDRDV 101
                                    5556667777776666666667777777777655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0096
                        NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                    v++kVd ++   +  +e l+ +  l+++L++ +++L  l+
  gene143|gene143|rna143|rna143 126 VNTKVDYIDYIEETKREALERIRVLKNELEKATEELGLLK 165
                                    899*****999999999*****************998776 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1       0.1     2e+02      11      72 ..       9      65 ..       1      81 [. 0.46
   2 ?    0.1   0.0      0.63   1.3e+03      30      40 ..      86      96 ..      56     123 .. 0.48
   3 ?   11.0   0.4   0.00025       0.5       8      52 ..     131     175 ..     126     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..XXXXXXXXXXXXXXXXXXXX CS
                           YabA 11 eeleeqleelleeleelkeelaelleenaeLeleneklrerl..eeeekkekekkkelsegken 72
                                   +++ +  ++  +e+ + ke+++ +l + ++L  +           +++k+ ++++++ +e+ + 
  gene143|gene143|rna143|rna143  9 AKMRQAYKRAIQEILKEKEKIKGILTDPNTLCED-------SffMDSSKAGETHQRDPEETSSA 65
                                   3444444444444444444444444443333211.......13333333333444444444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.63
                                   HHHHHHHHHHH CS
                           YabA 30 elaelleenae 40
                                   e++++ ++ ++
  gene143|gene143|rna143|rna143 86 EMNDISNKLNR 96
                                   22222222222 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00025
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                    d ++ +ee+ +e le+++ lk+el++ +ee   L+ en+  r++ 
  gene143|gene143|rna143|rna143 131 DYIDYIEETKREALERIRVLKNELEKATEELGLLKRENTLCRNTY 175
                                    667889999*****************************9999987 PP

>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.2   2.5e+03     116     137 ..      10      31 ..       6      40 .. 0.55
   2 ?   -2.3   0.0       2.4   4.9e+03     113     113 ..      72      72 ..      43     103 .. 0.52
   3 ?   12.1   0.2   8.5e-05      0.17      96     142 ..     136     182 ..     130     184 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                          Med21 116 eveeereekvkekeellkkvee 137
                                    ++++ ++ +++e  +  +k+++
  gene143|gene143|rna143|rna143  10 KMRQAYKRAIQEILKEKEKIKG 31 
                                    4445555555555444444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                          Med21 113 e 113
                                     
  gene143|gene143|rna143|rna143  72 G 72 
                                    1 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 8.5e-05
                          Med21  96 igsseeeqeerikeLeeelreveeereekvkekeellkkveellrav 142
                                    i+++++e +eri+ L++el+++ ee+    +e+   ++  ++l+++ 
  gene143|gene143|rna143|rna143 136 IEETKREALERIRVLKNELEKATEELGLLKRENTLCRNTYDNLISSF 182
                                    6889999**************************99999999999875 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.18   3.7e+02      16      70 ..       9      68 ..       6      80 .. 0.53
   2 ?    7.7   1.0    0.0024       4.7      50      93 ..     136     179 ..      60     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.18
                         CENP-H 16 lklsqelrelqeeltevekenlrlkrknrelaael.lelakekesek....eklkeelek 70
                                   +k+ q+++ + +e+ + +++++ + +  ++l ++   + ++++ ++     e++++++e+
  gene143|gene143|rna143|rna143  9 AKMRQAYKRAIQEILKEKEKIKGILTDPNTLCEDSfFMDSSKAGETHqrdpEETSSAIEN 68
                                   556666666666666666666666666666666654344443333333444444454544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0024
                         CENP-H  50 llelakekesekeklkeelekleaelkksrqrwrvvknvasaii 93 
                                    ++e+++e+ ++   lk+elek+ +el   +++ ++ +n++ ++i
  gene143|gene143|rna143|rna143 136 IEETKREALERIRVLKNELEKATEELGLLKRENTLCRNTYDNLI 179
                                    33344444444466999*********************999998 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.6   0.00048      0.96      83     119 ..     120     156 ..       6     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00048
                       PHM7_cyt  83 flglkligkkvdaidyyrekleeldeeieeerekvkk 119
                                     ++  l+  kvd idy++e  +e  e+i+ ++++ +k
  gene143|gene143|rna143|rna143 120 IFESYLVNTKVDYIDYIEETKREALERIRVLKNELEK 156
                                    45678999*********************99998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1413  (0.0788109); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1239.06
//
Query:       gene1431|gene1431|rna1430|rna1430  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-19   69.5   0.0    5.3e-19   68.9   0.0    1.3  1  PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.032   14.5   0.0    1.7  1  HD        HD domain


Domain annotation for each model (and alignments):
>> PDEase_I  3'5'-cyclic nucleotide phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.0   5.9e-23   5.3e-19       1     191 [.      93     287 ..      93     320 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 5.9e-23
                                        SSSHHHHHHHHHHHHHHHHCCHCCCCS-HHHHHHHHHHHHHTTTT--S--HHHHHHCT-HHHHHCCC.SS.HHHHH CS
                           PDEase_I   1 YHNfrHAadVlqalfyllkkeklkeeltpleilalliaalcHDvdHpGtnNsFlvnskselailYnd.es.vLEnh 74 
                                        YHN  H ++ l +  ++l++ +  + l  l++++l+ia   HDv+HpG  N    +  + l+++Y + e+   E  
  gene1431|gene1431|rna1430|rna1430  93 YHNLDHLINTLCFGDFILRRLENVSCLPILDKMCLVIALSLHDVGHPGERNR---KKIARLSKMYGNpEAmSFEMI 165
                                        9*****************99998889*************************5...666789999*99533478*** PP

                                        HHHHHHHHHTSGGG-TTTTS-HHHHHHHHHHHHHHHHTTSGGGHHHHHHHHHHHCCTTS-TTTCT......-HHHH CS
                           PDEase_I  75 HlalafqllkkeecnifknlskeeykelrkliielIlaTdmakhfelleklkelvkkkeknslnke.....eeedk 145
                                        H+a++ + + + + ++f+nl+++e ++ +++i+++I aTd+    e+++ ++++  +k++ +l ++     + e  
  gene1431|gene1431|rna1430|rna1430 166 HAAICRKGIVRYRDELFANLDDAELERRMDFIKRMIFATDLRLNKEIIDVFEDKYFEKRRGDLCRKvrngiKGEIS 241
                                        ******99999999*************************************6665554444444337777755555 PP

                                        HHHHHHHHHHHHTGCCCS-HHHHHHHHHHHHHHHHHHHHHHHHCT- CS
                           PDEase_I 146 klllsllikaaDisnptkpweiskkwaelvleEffeqgdeekelgl 191
                                        ++ l++++k aD+s   k ++i +k +    +E+++  d  ++l  
  gene1431|gene1431|rna1430|rna1430 242 EIELKMIVKLADLSSCYKDYRIFNKNSIAFWSEVYDDDDYNRTLRD 287
                                        5668********************************9999887654 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.5e-06     0.032       2      74 ..      96     158 ..      95     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                                        HHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHH CS
                                 HD   2 leHsleVaklarrlaedlge.....eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevek 72 
                                        l+H +++++++  + ++l+        d+ +l++a  lHD+G++ ++                 k  a++ + +++
  gene1431|gene1431|rna1430|rna1430  96 LDHLINTLCFGDFILRRLENvsclpILDKMCLVIALSLHDVGHPGERN---------------RKKIARLSKMYGN 156
                                        589999999999999999999999999******************774...............3333333333333 PP

                                        HH CS
                                 HD  73 rl 74 
                                        ++
  gene1431|gene1431|rna1430|rna1430 157 PE 158
                                        33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2222.87
//
Query:       gene1432|gene1432|rna1431|rna1431  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-06   26.4   0.4    1.1e-05   25.5   0.4    1.4  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.4   6.2e-10   1.1e-05       6     143 ..      48     177 ..      43     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.2e-10
                                        HHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST.......TECEEEEEEEEEESSHHHHHHHHHHH CS
                              THUMP   6 llkegkvnverveagkgrivvelkgekpeedeellkealekar.......giqrvipvcevceadledileaakei 74 
                                         ++e+k   +  +    r++++l ++     +e+  ++++k+r       ++ rv+p  +  + d e+ile+++ +
  gene1432|gene1432|rna1431|rna1431  48 EIEEYKSSTKFAKHDSYRCILFLENR----SAETSLSLFYKLRasktrfeYVYRVVPLDNFFQFDEEKILESVRGL 119
                                        55555666666666677889998888....5666667777777788889*************************** PP

                                        HHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                              THUMP  75 vkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                        ++ k      ++++  + r  h      +++  v  +i ++++l+Vdle+P +++  + +k+ ++is++
  gene1432|gene1432|rna1431|rna1431 120 DESK------SYKIVYEGRLCH-----ADMKERVFNLITKNISLRVDLESPHYIIVTQAFKNSLGISVV 177
                                        **88......9********999.....9**************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1159.76
//
Query:       gene1433|gene1433|rna1432|rna1432  [L=505]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-13   49.9   0.0    3.4e-13   49.6   0.0    1.3  1  GTP_EFTU  Elongation factor Tu GTP binding domain
    1.6e-07   31.2   0.0    3.5e-07   30.1   0.0    1.5  1  EFG_C     Elongation factor G C-terminus
  ------ inclusion threshold ------
      0.049   13.7   0.1       0.11   12.6   0.1    1.6  1  MMR_HSR1  50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   5.8e-17   3.4e-13      73     154 ..       2     106 ..       1     248 [. 0.83

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 5.8e-17
                                        EEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHH CS
                           GTP_EFTU  73 nliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkq 148
                                        +l+DtPGH d + e++++++ +D+av+v+d+  +   q e v++ + + + p+i+++NK D ++ ++   +++  +
  gene1433|gene1433|rna1432|rna1432   2 TLLDTPGHSDLIHETTKAIECIDIAVVVLDICCDLSLQYEVVFNAIAASKKPLIIVLNKTDLIGRDFASFIKKKIE 77 
                                        79*************************************************************9999887777777 PP

                                        HHHHH.......................H CS
                           GTP_EFTU 149 klsrk.......................e 154
                                        +l++                        +
  gene1433|gene1433|rna1432|rna1432  78 HLRSIveekmcprgwfavsskygslsriK 106
                                        77433455555555555555555544441 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   5.9e-11   3.5e-07       2      83 ..     401     483 ..     400     487 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.9e-11
                                        EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE..TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEE CS
                              EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqd.asgrviieaeiPlaeligfateLrslTkGegsfsmefs 76 
                                        +lEP++ vei   +e    v + ++s  Ge++  ++   s  + i + iP+ e++gf+t+Lr ++  ++ +     
  gene1433|gene1433|rna1432|rna1432 401 ILEPLYLVEIVYTSEAEDLVNEMIKSSFGEVIRQKSFpFSMLKSILCYIPVPESFGFETDLRVYSCSKADCIKIPL 476
                                        8***********************************977**************************99999988888 PP

                                        EEEE--H CS
                              EFG_C  77 gYeevpg 83 
                                         +++v  
  gene1433|gene1433|rna1432|rna1432 477 YWRPVSD 483
                                        8888765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.9e-05      0.11      49     114 .]       2      60 ..       1      60 [. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                                        EEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                           MMR_HSR1  49 elvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                        +l+DtpG  +      +l ++  + +e  d++++v+d+  + l+ + e + + +  +kkpli+vlnk
  gene1433|gene1433|rna1432|rna1432   2 TLLDTPG-HS------DLIHETTKAIEcIDIAVVVLDICCD-LSLQYEVVFNAIAASKKPLIIVLNK 60 
                                        79*****.33......4555555556626********8833.5445556666666688********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2934.79
//
Query:       gene1434|gene1434|rna1433|rna1433  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-67  225.8   0.0    9.2e-67  225.3   0.0    1.2  1  Septin         Septin
    3.4e-07   30.4   0.0    5.5e-07   29.7   0.0    1.5  1  MMR_HSR1       50S ribosome-binding GTPase
      2e-05   24.0   0.0    3.5e-05   23.2   0.0    1.3  1  AIG1           AIG1 family
    2.9e-05   24.2   1.5      0.031   14.3   0.3    2.3  2  Dynamin_N      Dynamin family
     0.0048   16.8   0.9       0.14   12.0   0.5    2.8  2  RsgA_GTPase    RsgA GTPase
     0.0059   15.7   0.0      0.027   13.5   0.0    2.1  2  IIGP           Interferon-inducible GTPase (IIGP)
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.025   14.0   0.0    1.4  1  SRPRB          Signal recognition particle receptor beta subu
      0.014   14.9   0.0      0.051   13.1   0.0    1.9  2  FeoB_N         Ferrous iron transport protein B
      0.018   14.4   0.0      0.027   13.8   0.0    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
      0.049   14.2   0.2      0.077   13.5   0.2    1.4  1  ABC_tran       ABC transporter
      0.062   13.3   0.0       0.13   12.3   0.0    1.5  1  GPAT_N         Glycerol-3-phosphate acyltransferase N-termina
      0.085   12.8   0.1       0.52   10.2   0.0    1.9  2  ATPase_2       ATPase domain predominantly from Archaea
       0.11   11.6   0.0       0.19   10.7   0.0    1.3  1  T2SSE          Type II/IV secretion system protein
       0.13   12.1   0.0       0.19   11.6   0.0    1.2  1  Abhydrolase_3  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.3   0.0   7.2e-70   9.2e-67       4     275 ..      15     270 ..      12     273 .] 0.93

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 7.2e-70
                                        EEEEEEEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSSSHH CS
                             Septin   4 eftlmvvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdavdns 79 
                                         ft+m +G +g Gk++++ntl+ +++++++ +e           i+ +   ++ +g+  ++t+iDtpgfG+++d +
  gene1434|gene1434|rna1433|rna1433  15 RFTIMAAGPKGSGKSSFFNTLIGKEIVTSKGQE----------GIDLYMLNLDCEGIMQRITLIDTPGFGETLDDT 80 
                                        79************************9997433..........5778889999999******************** PP

                                        CCCHHHHHHHHHHHHHHHHHCTSS--.SS-----EEEEEEEE-TTSSSS-HHHHHHHHHHTTTS-EEEEESSGGGS CS
                             Septin  80 kswepiveyideqfeeylreesklkR.kkivDkRvHaclyfisPtghglkpldvelmkklsekvnliPviaKaDtl 154
                                        +  e+i ++i+ q++ ++ eesk++R  k  D+RvH++lyfi  t+ glk+ d+ ++kk+s  vn+iPvi+K+D l
  gene1434|gene1434|rna1433|rna1433  81 EIQETICNFIKAQLDMFIAEESKIRRnPKYEDTRVHCLLYFIPSTSFGLKNRDIVFLKKVSGLVNIIPVISKSDGL 156
                                        **************************9999********************************************** PP

                                        -HHHHHHHHHHHHHHHHHTT--------SSSS-SCCHHHHHHHHHHC-SEEB-SSSSEEEESSSEEEEEEETTEEE CS
                             Septin 155 tkeElkefKkkireeleeeeikiyklpdeeededeeakelseklkeslPfaivgsneliekkgkkvrgRkypWGvv 230
                                           E  e+K+++ e++++++i+i++  d  e       ++ ++l++ +Pf iv+++ +      + r R+y+WG v
  gene1434|gene1434|rna1433|rna1433 157 SITERIEVKRQVVEQMRHYNISIFD-LDDPEIY--SSPTAGNDLNSLVPFMIVSADGE----NLESRVRNYQWGSV 225
                                        *************************.5555555..3457899***********99764....456799******** PP

                                        ETT-TTT-SCCHHHHHHHHHCHHHHHHHHHHTHHHHHHHHHH-XX CS
                             Septin 231 evenekhsdFlkLrklllkthledLkevteellYetyRseklskl 275
                                         ++n++h+d  +Lr+lll+th+  L+++t++ +Ye+yR+  l+++
  gene1434|gene1434|rna1433|rna1433 226 SIDNPEHCDLPALRELLLSTHIYGLIDYTASEIYENYRAAVLESE 270
                                        ****************************************99876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   4.3e-10   5.5e-07       2      84 ..      18     100 ..      17     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 4.3e-10
                                        EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT..EEEEEEECGGCSSHHHHHHHHHHHHHHHHC CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg..keielvDtpGliegaseekglgkaflalee 75 
                                        ++ +G   +GKS+++n+l+g+  iv++k +  +d    +++ +g  ++i+l+DtpG + +  ++ ++++++++ ++
  gene1434|gene1434|rna1433|rna1433  18 IMAAGPKGSGKSSFFNTLIGK-EIVTSKGQEGIDLYMLNLDCEGimQRITLIDTPG-FGETLDDTEIQETICNFIK 91 
                                        6778999*************5.67888888888888888886676789********.6433344466666666666 PP

                                        TSEEEEEEE CS
                           MMR_HSR1  76 adlillvvd 84 
                                        a+l +++ +
  gene1434|gene1434|rna1433|rna1433  92 AQLDMFIAE 100
                                        655555544 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.7e-08   3.5e-05       2      75 ..      17      88 ..      16     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.7e-08
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHH CS
                               AIG1  2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivr 75
                                       ti+  G  g+GkS+  N+++gk++ +sk  ++++   + +   +   ++i  iDTPg  ++ ++++ i++ i++
  gene1434|gene1434|rna1433|rna1433 17 TIMAAGPKGSGKSSFFNTLIGKEIVTSKG-QEGIDLYMLNLDCEGIMQRITLIDTPGFGETLDDTE-IQETICN 88
                                       6788899*********************5.89999999888889999**********977665544.4444443 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   2.4e-05     0.031       1      26 [.      18      43 ..      18      49 .. 0.86
   2 !    8.8   0.1    0.0012       1.5      95     124 ..      57      88 ..      44     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S-- CS
                          Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilpr 26
                                       i+  G   sGKSS+ n L+g++i  +
  gene1434|gene1434|rna1433|rna1433 18 IMAAGPKGSGKSSFFNTLIGKEIVTS 43
                                       56779999**************8765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                                        EEETTS-SEEEEE---B-SSSGTTS..HHHHH CS
                          Dynamin_N  95 ilsllvkgltlvDlPGldsvnkrdq..elvke 124
                                        +++   +++tl+D+PG+ ++ +  +  e + +
  gene1434|gene1434|rna1433|rna1433  57 DCEGIMQRITLIDTPGFGETLDDTEiqETICN 88 
                                        56666789*********986655534444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.5   0.00011      0.14     100     161 ..      16      73 ..       2      77 .. 0.58
   2 ?   -0.1   0.0      0.59   7.5e+02      47      79 ..     144     179 ..     121     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                        SEEEEECSTTSSHHHHHHHHCTT-----S------------.--SEEEEEETTTEEEESS-SS CS
                        RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhT.TtavellelaegglliDtPGf 161
                                         t++ +G+ G GKS++ n+l+++ e+    v +k ++G      +     + +  +liDtPGf
  gene1434|gene1434|rna1433|rna1433  16 FTIMAAGPKGSGKSSFFNTLIGK-EI----VTSKGQEGIDLyMLNLDCEGIMQRITLIDTPGF 73 
                                        455668****************9.22....333333333220122233333334456666666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.59
                                        -EEEEEEE-GGG--HHH...HHHHHHHHHHHTTSEE CS
                        RsgA_GTPase  47 iepvivlnKiDlleeee...eleelkeelealgyev 79 
                                        ++++ v++K D l+ +e     +++ e+++++++++
  gene1434|gene1434|rna1433|rna1433 144 VNIIPVISKSDGLSITErieVKRQVVEQMRHYNISI 179
                                        56677999*999998883323334444445444444 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   2.1e-05     0.027      25      74 ..       5      52 ..       1     103 [. 0.70
   2 ?   -0.8   0.0      0.49   6.3e+02     196     215 ..     225     244 ..     200     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                       HHHHHHHHT--EEEEEEESTTSSHHHHHHHHTT--TTSTTS--SSCHSHH CS
                               IIGP 25 keaikeiesaklkiavtGdsGnGkssFinaLRliGheeedsAptGvvett 74
                                       k++i   ++ +  i+  G  G+GkssF n+L  iG+e   s     +   
  gene1434|gene1434|rna1433|rna1433  5 KQMIVRRQNRRFTIMAAGPKGSGKSSFFNTL--IGKEIVTSKGQEGIDLY 52
                                       66788889999*******************8..78876666555555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                                        BBTTBTTSTTHHHHHHHHHH CS
                               IIGP 196 vsnldvsayDFPkLretLlk 215
                                        vs  ++++ D P Lre Ll+
  gene1434|gene1434|rna1433|rna1433 225 VSIDNPEHCDLPALRELLLS 244
                                        88889999999999998875 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     2e-05     0.025       3      59 ..      15      73 ..      13     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                                       --EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG....GGTT-SEEEETT- CS
                              SRPRB  3 kpavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkv.ksekgskltliDfPGh 59
                                       + +++ +G++ sGK s+f+ L  +++ ++          l++  +   +++tliD PG 
  gene1434|gene1434|rna1433|rna1433 15 RFTIMAAGPKGSGKSSFFNTLIGKEIVTSKGQEgIDLYMLNLdCEGIMQRITLIDTPGF 73
                                       557899****************99766554443444444444224456789******96 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.9e-05     0.051       2      74 ..      17      90 ..      16     107 .. 0.67
   2 ?   -1.6   0.0       1.3   1.7e+03      39      59 ..     167     189 ..     156     199 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT..EEEEEEE----SSS.SSSSHHHHHHHHHH CS
                             FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg..keveivDlPGiYsl.sayseeekvardfl 74
                                       t++ +G   +Gk+++fn+l g++   +      ++    +l+++g  ++++++D PG  +  +++ ++e++ ++f+
  gene1434|gene1434|rna1433|rna1433 17 TIMAAGPKGSGKSSFFNTLIGKEIVTSK-GQEGIDLYMLNLDCEGimQRITLIDTPGFGETlDDTEIQETI-CNFI 90
                                       78899****************9866554.33445555555555554599********86541444444444.4444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                        EEEEEETTEEEEEEE-..---SS CS
                             FeoB_N  39 egklklkgkeveivDl..PGiYs 59 
                                        ++  ++++++++i Dl  P iYs
  gene1434|gene1434|rna1433|rna1433 167 QVVEQMRHYNISIFDLddPEIYS 189
                                        23334567999999886677887 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.027      42      77 ..      18      54 ..       2      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                                       EEEE--TTSSHHHHHHHHHHHHHTT--TTT.EEEEEE CS
                       FtsK_SpoIIIE 42 llvaGatgsGKStalntLilSlatthtPee.Vqlili 77
                                       ++ aG +gsGKS + ntLi   ++t++ +e + l+++
  gene1434|gene1434|rna1433|rna1433 18 IMAAGPKGSGKSSFFNTLIGKEIVTSKGQEgIDLYML 54
                                       7889***************865555555443777775 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2     6e-05     0.077      17      60 ..      21      93 ..      12     181 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                                       EESTTSSHHHHHHHHTTSS--.SEEEE............................EETTCEGGGB-HHHCCHC CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxx............................xxxxxxxxxxxxxxxxxx RF
                           ABC_tran 17 vGenGaGKStLlkllagllkp.teGei............................lldgkdlkeqeleslrke 60
                                        G+ G+GKS+++++l+g++    +G+                             +ld+++++e+  ++ +++
  gene1434|gene1434|rna1433|rna1433 21 AGPKGSGKSSFFNTLIGKEIVtSKGQEgidlymlnldcegimqritlidtpgfgeTLDDTEIQETICNFIKAQ 93
                                       6****************99884233323345555555555555555555555555555555555555555555 PP

>> GPAT_N  Glycerol-3-phosphate acyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.8e-05      0.13      34      51 ..     255     272 ..     242     273 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.8e-05
                             GPAT_N  34 meelYqNYknAVlqsGip 51 
                                          e+Y+NY+ AVl+s i+
  gene1434|gene1434|rna1433|rna1433 255 ASEIYENYRAAVLESEIK 272
                                        679***********9875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0004      0.52      19      90 ..      14      93 ..       3     115 .. 0.73
   2 ?    0.2   0.0      0.46   5.9e+02     162     194 ..     149     182 ..     134     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0004
                           ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienl..edkdk..yviyyialreesiskldefie.....eeeekkklekalgiavp 87
                                       ++  ++  Gp+gsGK+++++ +i +    +k++    +y+ +l  e i +  + i+     e+ +++++++++ + ++
  gene1434|gene1434|rna1433|rna1433 14 RRFTIMAAGPKGSGKSSFFNTLIGKEivTSKGQegIDLYMLNLDCEGIMQRITLIDtpgfgETLDDTEIQETICNFIK 91
                                       44556667*********9999987773333333557889999999999888888888999999999999998844433 PP

                           ATPase_2 88 kae 90
                                        a+
  gene1434|gene1434|rna1433|rna1433 92 -AQ 93
                                       .34 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.46
                           ATPase_2 162 iclsSeglfie.rvyneselegrhkyilvddldk 194
                                        +++ S+gl+i  r++ + + +++ +++++  +d 
  gene1434|gene1434|rna1433|rna1433 149 VISKSDGLSITeRIEVKRQVVEQMRHYNISIFDL 182
                                        6677999999777777777777777777777764 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.19     121     151 ..       8      37 ..       2      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                              T2SSE 121 vlrkavrerglilvsGgTgsGKttllyallk 151
                                        ++r+  ++r +i+ +G+ gsGK+ + ++l+ 
  gene1434|gene1434|rna1433|rna1433   8 IVRRQ-NRRFTIMAAGPKGSGKSSFFNTLIG 37 
                                        45555.799******************9985 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.19     100     186 ..     140     220 ..     126     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                        EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSSGGGGGST..TTSGGGCS-SST---EEEEE CS
                      Abhydrolase_3 100 vagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylpeadrddp..laspllaedlsglpptlvvv 173
                                        v+g+v i Pv   +++++ si      +++  ++r+ ++++  + ++ +d+ddp  + sp +++dl+ l p ++v 
  gene1434|gene1434|rna1433|rna1433 140 VSGLVNIIPVI--SKSDGLSI------TERIEVKRQVVEQMRHYNISIFDLDDPeiYSSPTAGNDLNSLVPFMIVS 207
                                        56666666665..34444555......3344478888888777777999***999899999999************ PP

                                        ETT-TTHHHHHHH CS
                      Abhydrolase_3 174 aefDplrdegeay 186
                                        a+ + l ++ + y
  gene1434|gene1434|rna1433|rna1433 208 ADGENLESRVRNY 220
                                        ***9999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1773.83
//
Query:       gene1435|gene1435|rna1434|rna1434  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00077   20.0   0.0     0.0013   19.3   0.0    1.4  1  RNase_PH  3' exoribonuclease family, domain 1


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     7e-08    0.0013      16     132 .]      31     128 ..      17     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7e-08
                                        SEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC- CS
                           RNase_PH  16 nGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrlleralrpsil 91 
                                        +G + +++G+t+v +   g +e+          g+ld+eve+  ++    r+e +++++  e +++l ++++  +l
  gene1435|gene1435|rna1434|rna1434  31 KGVVDVRQGNTQVSVMCGGAKEA----------GKLDIEVEFYAVS----RQEPVNEKRILEYEDVLLDIFSDILL 92 
                                        57888999999998888877755..........4599999977777....45668999999************999 PP

                                        CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                           RNase_PH  92 lekkpkstididitvlssdggslldalinaaslALadagip 132
                                         e    + + i + v ++ g sll+ ++n+++l L  +gip
  gene1435|gene1435|rna1434|rna1434  93 PE----TSVGIKVVVREDGG-SLLSTMVNCITLCLSYFGIP 128
                                        88....55888888889999.****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1497.69
//
Query:       gene1436|gene1436|rna1435|rna1435  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0057   16.4   0.3      0.011   15.4   0.0    1.7  2  Cyclin_N         Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.035   14.1   0.0         14    5.7   0.0    2.7  2  DUF4250          Domain of unknown function (DUF4250)
      0.041   13.8   0.1      0.068   13.1   0.1    1.4  1  Pathogen_betaC1  Beta-satellite pathogenicity beta C1 protein


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.9e-06     0.011      38     102 ..      20      81 ..       6     116 .. 0.79
   2 ?   -3.0   0.1      0.98   5.8e+03      73      83 ..     159     169 ..     154     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-06
                                        HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHT CS
                           Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyit 102
                                        +v +++ + + ++t + ++ ++ R++    ++ +k   +ga+c+ll++Kv+     +le++  ++
  gene1436|gene1436|rna1435|rna1435  20 IVSISRLLGMPQKTTYFTLAIYYRYIL--MMKSRKTIPIGAACILLSGKVNGS-LRSLEHILKAS 81 
                                        67788888999****************..89999999*************555.45555444444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.98
                                        HHHHHHHHHHH CS
                           Cyclin_N  73 lqlvgatcLll 83 
                                        ++ ++++c+++
  gene1436|gene1436|rna1435|rna1435 159 IRSIVVSCIFI 169
                                        56789999998 PP

>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0033        20       7      37 ..      62      92 ..      59      96 .. 0.85
   2 ?    5.7   0.0    0.0023        14      13      35 ..     114     136 ..     113     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0033
                            DUF4250  7 mLlSivNtkLRDeyssldelcedldidkeel 37
                                       +L + vN  LR  ++ l++  +++d+d e+ 
  gene1436|gene1436|rna1435|rna1435 62 LLSGKVNGSLRSLEHILKASYKHYDVDPEKF 92
                                       45568**********************9875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0023
                            DUF4250  13 NtkLRDeyssldelcedldidke 35 
                                        N+++ D y  l++lc d did++
  gene1436|gene1436|rna1435|rna1435 114 NFEMEDPYGFLEKLCMDNDIDRS 136
                                        77788999*************97 PP

>> Pathogen_betaC1  Beta-satellite pathogenicity beta C1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.1e-05     0.068      36      96 ..      45     107 ..      32     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                    Pathogen_betaC1  36 pvlakkkfiipYthegiipPfdfngleegiknilkimyk..dskieefkqedmveaiDilmme 96 
                                          ++k++ +ip + + i+    +ng   ++++ilk+ yk  d++ e+f qed  +aiDi +  
  gene1436|gene1436|rna1435|rna1435  45 ILMMKSRKTIPIGAACILLSGKVNGSLRSLEHILKASYKhyDVDPEKFFQEDYKDAIDIELHA 107
                                        568999999*****************************933456689***********96654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1589.14
//
Query:       gene1437|gene1437|rna1436|rna1436  [L=89]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-22   78.2   9.6    4.3e-22   77.9   9.6    1.0  1  Elf1       Transcription elongation factor Elf1 like
  ------ inclusion threshold ------
       0.73   10.4   7.5        1.8    9.2   0.7    2.7  2  zf-H2C2_2  Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   9.6   4.8e-26   4.3e-22       3      77 ..      12      87 ..      11      88 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 4.8e-26
                               Elf1  3 Rkk.kakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetkvnalsepvDvYskwiDace 77
                                       Rkk k+k++  ++++kl+++F+Cp Cnhe++v++ ++++  ++ ++C+vC ++f++++n+l++ +DvYs w+D+c 
  gene1437|gene1437|rna1436|rna1436 12 RKKvKRKSNVPRRQTKLEKRFNCPLCNHENVVQCIVKRTLMKGFANCSVCDANFSCDANKLTTGIDVYSAWVDECC 87
                                       555599999*****************************************************************95 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.7    0.0002       1.8      12      21 ..      29      38 ..      23      40 .. 0.89
   2 ?    4.7   0.6     0.005        44      16      25 ..      57      66 ..      48      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0002
                          zf-H2C2_2 12 ekpyeCplCd 21
                                       ek+++CplC+
  gene1437|gene1437|rna1436|rna1436 29 EKRFNCPLCN 38
                                       799******8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.005
                          zf-H2C2_2 16 eCplCdkaFk 25
                                       +C++Cd  F+
  gene1437|gene1437|rna1436|rna1436 57 NCSVCDANFS 66
                                       7*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 604.17
//
Query:       gene1438|gene1438|rna1437|rna1437  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.3e-29  100.8   0.1    9.7e-29  100.4   0.1    1.2  1  ThiF       ThiF family
     0.0088   16.3   0.0      0.016   15.4   0.0    1.4  1  TrkA_N     TrkA-N domain
  ------ inclusion threshold ------
      0.048   12.8   0.0       0.27   10.4   0.0    2.0  2  Tubulin_2  Tubulin like
      0.069   11.5   0.0      0.074   11.4   0.0    1.1  1  Smg8_Smg9  Smg8_Smg9
      0.073   13.6   0.1       0.22   12.1   0.1    1.8  2  Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.1   2.7e-32   9.7e-29      20     240 ..       2     268 ..       1     273 [. 0.85

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 2.7e-32
                                        EEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF  20 kvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavte 95 
                                        k+ lvG+Gg G ellk L  +  +++ ++D+D+i l+Nl+R f+f+++d G++K++ aae++++++  ++ + +t+
  gene1438|gene1438|rna1437|rna1437   2 KMILVGCGGTGVELLKVLKDMA-SEVLVIDHDRINLTNLHRLFMFTRQDKGEYKSQKAAEFVSNLYG-IKASFLTQ 75 
                                        789****************995.7899**************************************96.9******* PP

                                        -CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHH.HHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.E CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF  96 ritdetvleellesvDlVvdalDniearrlvnracv.kkgiplieagtlgfegqvvviipgktgcyeCldpssted 170
                                        ri++   + +++ ++D+++ alDnie r+ +n + + ++ + li+ g +g++ ++ ++ +++++c+ C +    e 
  gene1438|gene1438|rna1437|rna1437  76 RIEEV--SVDVFDRYDVIFGALDNIEGRMNLNLMFRrSRCKLLIDCGISGYKAHAKAV-YKESSCLYCIR----EL 144
                                        **884..359************************995555669***************.58********8....56 PP

                                        ECCCCEEHHH.......................................................HHHCT....E- CS
                                        xxxxxxxxxx.......................................................xxxxx....xx RF
                               ThiF 171 ptekkvplct.......................................................siagn....ip 187
                                         +e+ v +c                                                        ++ g     ip
  gene1438|gene1438|rna1437|rna1437 145 YREDGVGMCSlgslpkeitlenrekvlrslvelkrdglgskrekieqivnefnalakeklrtdvfEVTGMydgiIP 220
                                        6666677777777777777777777778888888999999999999999999999999999988866666777899 PP

                                        B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ThiF 188 aiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerakks 240
                                         + ++++v+a+la+    +ll+g++ + ++++ +   ++++fe+++l +++k+
  gene1438|gene1438|rna1437|rna1437 221 NVCFINSVCASLAC----RLLDGPNLSYDFIF-YSGEENMVFEKLHLAKDEKC 268
                                        99999999999987....57788887777777.77777788888888666544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.5e-06     0.016       2      39 ..       4      41 ..       3      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.5e-06
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHH CS
                             TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelre 39
                                       i++G+G +G +l++ L++ ++ +v+vid+d+ ++ +l +
  gene1438|gene1438|rna1437|rna1437  4 ILVGCGGTGVELLKVLKDmAS-EVLVIDHDRINLTNLHR 41
                                       89****************666.6*******977777655 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   7.4e-05      0.27       1      24 [.       4      27 ..       4      92 .. 0.80
   2 ?    0.1   0.0     0.098   3.5e+02     177     244 ..     138     197 ..     136     227 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.4e-05
                          Tubulin_2  1 lviGLGGtGgkvlaelrrrlreel 24
                                       +++G+GGtG + l+ l+++  e l
  gene1438|gene1438|rna1437|rna1437  4 ILVGCGGTGVELLKVLKDMASEVL 27
                                       79****************998877 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.098
                          Tubulin_2 177 ayllrkilkeekqkvkiiglvllPdvfplnkeggervkaNayaaLkELnalkdsdeetelevkypngd 244
                                        +y++r++++e++    +  l  lP+ ++l+       ++  +++L+EL++ +  +++++ e+  ++++
  gene1438|gene1438|rna1437|rna1437 138 LYCIRELYREDGV--GMCSLGSLPKEITLE------NREKVLRSLVELKRDGLGSKREKIEQIVNEFN 197
                                        7888888888887..566666666664333......23335788888888444444444444444444 PP

>> Smg8_Smg9  Smg8_Smg9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.1e-05     0.074     329     411 ..      50     134 ..      26     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.1e-05
                                        ...........................TS---SB..HHHHHHHHHTHHHHTTTS-SS---H..HHHHHHHHHHHHH CS
                          Smg8_Smg9 329 pshfelpslkkwvevakklyellienkkekaeie..ennekvkalLkvlegsLdidkkfsesrcekvlklaisayk 402
                                        + +++  ++ ++v+ +  +   +++++ e+ ++    + + + ++L+++eg ++ +  f +src+  ++ +is yk
  gene1438|gene1438|rna1437|rna1437  50 KGEYKSQKAAEFVSNLYGIKASFLTQRIEEVSVDvfDRYDVIFGALDNIEGRMNLNLMFRRSRCKLLIDCGISGYK 125
                                        566666777777777777777788887444555434555667899******************************* PP

                                        HHHHHHHC- CS
                          Smg8_Smg9 403 enlpalYts 411
                                         +++a Y +
  gene1438|gene1438|rna1437|rna1437 126 AHAKAVYKE 134
                                        *******84 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     6e-05      0.22       2      30 ..       3      31 ..       2      39 .. 0.90
   2 ?   -2.8   0.0       2.6   9.5e+03      23      39 ..      80      96 ..      70     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
                          Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                                       ++ vG G +g+El ++l++++++V v++ 
  gene1438|gene1438|rna1437|rna1437  3 MILVGCGGTGVELLKVLKDMASEVLVIDH 31
                                       788*********************99975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.6
                                       SEEEEEESSSSSSTTSS CS
                          Pyr_redox 23 kkVtvversdkllrllD 39
                                        +V v++r d +  +lD
  gene1438|gene1438|rna1437|rna1437 80 VSVDVFDRYDVIFGALD 96
                                       56777777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1646.98
//
Query:       gene1439|gene1439|rna1438|rna1438  [L=477]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-08   33.0  14.8      0.061   13.5   0.4    7.3  7  TPR_2       Tetratricopeptide repeat
    8.8e-06   25.9  10.1    0.00052   20.2   2.0    4.7  6  TPR_12      Tetratricopeptide repeat
      6e-05   23.6   4.3          2    9.1   0.1    5.1  6  TPR_16      Tetratricopeptide repeat
    0.00014   21.5  16.8      0.015   15.1   0.8    6.1  6  TPR_1       Tetratricopeptide repeat
    0.00047   20.3   0.1      0.013   15.7   0.1    2.7  3  HemY_N      HemY protein N-terminus
  ------ inclusion threshold ------
       0.01   16.2   0.5      0.018   15.4   0.5    1.2  1  DUF1180     Protein of unknown function (DUF1180)
      0.032   14.6   2.4         15    6.2   0.1    4.4  5  TPR_17      Tetratricopeptide repeat
      0.057   14.3   1.1      1e+02    4.2   0.0    4.7  5  TPR_14      Tetratricopeptide repeat
       0.27   11.4   6.9        2.5    8.3   0.7    4.8  5  TPR_7       Tetratricopeptide repeat
        1.1    9.4   8.1        2.5    8.2   1.4    3.6  3  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
        5.1    7.6  22.9         16    6.0   0.0    7.0  8  TPR_8       Tetratricopeptide repeat
        5.3    7.0  19.0       0.21   11.5   0.4    5.3  7  TPR_10      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.4    0.0066       9.9       3      32 ..      39      68 ..      37      70 .. 0.91
   2 !   13.5   0.4   4.1e-05     0.061       3      31 ..      77     105 ..      75     107 .. 0.95
   3 ?    2.4   0.1      0.15   2.2e+02      13      26 ..     203     216 ..     200     216 .. 0.83
   4 ?   -1.0   0.0       1.7   2.5e+03       3      18 ..     282     297 ..     280     298 .. 0.88
   5 ?    4.9   0.0     0.022        33      15      32 ..     327     344 ..     324     346 .. 0.89
   6 !    7.0   0.0     0.005       7.4       4      31 ..     384     411 ..     381     414 .. 0.86
   7 ?    1.8   0.0      0.23   3.4e+02      18      30 ..     431     443 ..     424     446 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0066
                              TPR_2  3 alynlGlayyklgdyeeAleafekAleldP 32
                                        ++++Gl+++k + y eA+  + k+l+l +
  gene1439|gene1439|rna1438|rna1438 39 EYMERGLLLLKEKVYGEAALSYLKCLSLME 68
                                       6899**********************9975 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.1e-05
                              TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                        +++nl+ +++k   y+eA+ + e++l+++
  gene1439|gene1439|rna1438|rna1438  77 VYNNLAICLAKVRAYKEAALYAERSLKIN 105
                                        79*************************98 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.15
                              TPR_2  13 klgdyeeAleafek 26 
                                        ++g+y+eA e  ek
  gene1439|gene1439|rna1438|rna1438 203 RSGKYDEAFEKAEK 216
                                        78******998776 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.7
                              TPR_2   3 alynlGlayyklgdye 18 
                                        +l++  +++++l+++e
  gene1439|gene1439|rna1438|rna1438 282 VLFYASKIHLNLKNHE 297
                                        79999********986 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.022
                              TPR_2  15 gdyeeAleafekAleldP 32 
                                        g+ e+A e+++kAle  P
  gene1439|gene1439|rna1438|rna1438 327 GRNERAQEFLNKALESHP 344
                                        899***********9776 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.005
                              TPR_2   4 lynlGlayyklgdyeeAleafekAleld 31 
                                        l   G ++ ++++  +A+++f+ A+e d
  gene1439|gene1439|rna1438|rna1438 384 LLFKGIVAQARNEVSDAERYFRLAIEAD 411
                                        66789999*****************987 PP

  == domain 7  score: 1.8 bits;  conditional E-value: 0.23
                              TPR_2  18 eeAleafekAlel 30 
                                        + ++e +e+Al+ 
  gene1439|gene1439|rna1438|rna1438 431 KSCREVYEEALKC 443
                                        5678899999985 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   2.0   3.5e-07   0.00052       8      74 ..      42     104 ..      38     106 .. 0.91
   2 ?   -0.1   0.0      0.78   1.2e+03      15      25 ..     203     213 ..     200     216 .. 0.59
   3 ?    3.6   0.0     0.055        82      58      73 ..     326     341 ..     320     344 .. 0.79
   4 ?    1.8   0.1      0.19   2.9e+02      51      74 ..     387     410 ..     369     413 .. 0.73
   5 ?    2.5   0.0      0.12   1.9e+02      10      35 ..     388     413 ..     380     428 .. 0.68
   6 ?   -1.5   0.0       2.2   3.3e+03      23      33 ..     434     444 ..     415     449 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.5e-07
                             TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +++++l++ + y eA   + k+l ++++   + +  ++++++nL++++ +   y+eA  + e++l+i
  gene1439|gene1439|rna1438|rna1438  42 ERGLLLLKEKVYGEAALSYLKCLSLMEEE--DGR--LVSVYNNLAICLAKVRAYKEAALYAERSLKI 104
                                        57899999999***************888..446..*****************************98 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.78
                             TPR_12  15 rlgrydeAlel 25 
                                        r g+ydeA+e 
  gene1439|gene1439|rna1438|rna1438 203 RSGKYDEAFEK 213
                                        45666666654 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.055
                             TPR_12  58 lgryeeAlelleeala 73 
                                         gr e A+e+l++al+
  gene1439|gene1439|rna1438|rna1438 326 HGRNERAQEFLNKALE 341
                                        6888999999999987 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.19
                             TPR_12  51 LgrlyralgryeeAlelleealai 74 
                                         g++ +a+++  +A+++++ a+++
  gene1439|gene1439|rna1438|rna1438 387 KGIVAQARNEVSDAERYFRLAIEA 410
                                        577777777778888888877775 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.12
                             TPR_12  10 aavlrrlgrydeAlellekaleiarr 35 
                                        + v +++ +  +A+++++ a+e+ ++
  gene1439|gene1439|rna1438|rna1438 388 GIVAQARNEVSDAERYFRLAIEADSK 413
                                        55666666666666666666666655 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 2.2
                             TPR_12  23 lellekaleia 33 
                                        +e +e+al  a
  gene1439|gene1439|rna1438|rna1438 434 REVYEEALKCA 444
                                        55566666555 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.34   5.1e+02      37      56 ..      40      60 ..      40      64 .. 0.86
   2 !    9.1   0.1    0.0014         2      30      62 ..      71     103 ..      66     108 .. 0.85
   3 ?   -1.1   0.0       2.1   3.2e+03       7      16 ..     201     210 ..     199     217 .. 0.82
   4 ?    2.1   0.0      0.22   3.2e+02       6      32 ..     322     345 ..     318     354 .. 0.86
   5 !    7.1   0.0    0.0059       8.8      32      65 ..     379     412 ..     371     413 .. 0.86
   6 ?   -3.2   0.0       9.8   1.5e+04      55      64 ..     435     444 ..     426     447 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.34
                             TPR_16 37 llllgdaalrqgrlaeAa.al 56
                                       ++++g+++l+ + + eAa  +
  gene1439|gene1439|rna1438|rna1438 40 YMERGLLLLKEKVYGEAAlSY 60
                                       799**************9444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                             TPR_16  30 sPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                        + + +  +++l+ ++++   ++eAa + ++ l+
  gene1439|gene1439|rna1438|rna1438  71 DGRLVSVYNNLAICLAKVRAYKEAALYAERSLK 103
                                        56678899*****************88888765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.1
                             TPR_16   7 alragdyddA 16 
                                        ++r+g+yd+A
  gene1439|gene1439|rna1438|rna1438 201 LVRSGKYDEA 210
                                        7899999998 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.22
                             TPR_16   6 aalragdyddAaaaleaalkrdpssPd 32 
                                        + + +g+ ++A++ l+ al+++   P+
  gene1439|gene1439|rna1438|rna1438 322 YEVGHGRNERAQEFLNKALESH---PL 345
                                        56789****************9...64 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0059
                             TPR_16  32 daaeAllllgdaalrqgrlaeAaalyraalraap 65 
                                        +++++ll++g +a +++++ +A+ ++r a++a++
  gene1439|gene1439|rna1438|rna1438 379 EDPRFLLFKGIVAQARNEVSDAERYFRLAIEADS 412
                                        4567*************************99875 PP

  == domain 6  score: -3.2 bits;  conditional E-value: 9.8
                             TPR_16  55 alyraalraa 64 
                                        ++y++al++a
  gene1439|gene1439|rna1438|rna1438 435 EVYEEALKCA 444
                                        5556666555 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.4     0.032        48       3      30 ..      39      66 ..      37      69 .. 0.92
   2 !   15.1   0.8   9.7e-06     0.015       3      31 ..      77     105 ..      75     105 .. 0.96
   3 ?   -0.7   0.1      0.97   1.4e+03      15      21 ..     205     211 ..     203     216 .. 0.80
   4 ?    2.3   0.0      0.11   1.7e+02      15      30 ..     327     342 ..     326     344 .. 0.85
   5 !    6.2   0.0    0.0067        10       7      33 ..     387     413 ..     381     414 .. 0.86
   6 ?   -0.9   0.2       1.2   1.7e+03      17      23 ..     437     443 ..     435     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              TPR_1  3 alynlGnayfklgkydeAleyyekALel 30
                                        +  +G++++k + y eA   y k+L+l
  gene1439|gene1439|rna1438|rna1438 39 EYMERGLLLLKEKVYGEAALSYLKCLSL 66
                                       6999**********************87 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.7e-06
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                              TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                        +++nl+ ++ k   y+eA  y e+ L++n
  gene1439|gene1439|rna1438|rna1438  77 VYNNLAICLAKVRAYKEAALYAERSLKIN 105
                                        8**************************98 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.97
                                        T-HHHHH CS
                              TPR_1  15 gkydeAl 21 
                                        gkydeA 
  gene1439|gene1439|rna1438|rna1438 205 GKYDEAF 211
                                        8999995 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.11
                                        T-HHHHHHHHHHHHHH CS
                              TPR_1  15 gkydeAleyyekALel 30 
                                        g+ + A e+ +kALe 
  gene1439|gene1439|rna1438|rna1438 327 GRNERAQEFLNKALES 342
                                        77899*********95 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.0067
                                        HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                        +G + +  ++  +A+ y++ A+e + +
  gene1439|gene1439|rna1438|rna1438 387 KGIVAQARNEVSDAERYFRLAIEADSK 413
                                        8999999****************8876 PP

  == domain 6  score: -0.9 bits;  conditional E-value: 1.2
                                        HHHHHHH CS
                              TPR_1  17 ydeAley 23 
                                        y+eAl++
  gene1439|gene1439|rna1438|rna1438 437 YEEALKC 443
                                        7888887 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   8.8e-06     0.013      31      79 ..       9      57 ..       6      79 .. 0.87
   2 ?    0.9   0.0      0.35   5.2e+02      69      91 ..     323     345 ..     321     355 .. 0.80
   3 ?   -2.2   0.0       3.1   4.6e+03      65      83 ..     387     405 ..     373     418 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.8e-06
                             HemY_N 31 ylllrllrlllrlparvrrwrrrrrerkarealseGlialaeGdfarAe 79
                                       +l+++++++ + + + vr wrr+rrer  re +++Gl+ l e  + +A 
  gene1439|gene1439|rna1438|rna1438  9 FLAIAIVSGAVLVCQGVRTWRRNRRERNIREYMERGLLLLKEKVYGEAA 57
                                       68889999999999*************************9999888886 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                             HemY_N  69 alaeGdfarAekaaakaaklsea 91 
                                        ++++G+ +rA++ ++ka++ ++ 
  gene1439|gene1439|rna1438|rna1438 323 EVGHGRNERAQEFLNKALESHPL 345
                                        6789*************987755 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.1
                             HemY_N  65 eGlialaeGdfarAekaaa 83 
                                        +G++a a  + ++Ae+ ++
  gene1439|gene1439|rna1438|rna1438 387 KGIVAQARNEVSDAERYFR 405
                                        5667777777777776554 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.5   1.2e-05     0.018     101     134 ..       7      40 ..       4      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                            DUF1180 101 rallvlvvvsaavivylvvRtvrlrrrnrktRrY 134
                                         a+l + +vs+av+v+  vRt r  rr+r  R Y
  gene1439|gene1439|rna1438|rna1438   7 SAFLAIAIVSGAVLVCQGVRTWRRNRRERNIREY 40 
                                        57888899************************99 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1      0.01        15       2      26 ..      60      88 ..      59      95 .. 0.72
   2 ?   -1.3   0.0       2.6   3.9e+03       6      29 ..     273     296 ..     269     304 .. 0.73
   3 ?   -1.9   0.0       4.1   6.1e+03       2      12 ..     336     346 ..     335     350 .. 0.80
   4 ?    4.5   0.0     0.036        54       3      28 ..     405     430 ..     403     432 .. 0.84
   5 ?   -2.2   0.1       5.1   7.6e+03       2       9 ..     437     444 ..     436     450 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                             TPR_17  2 ylkalel....dPnnadaynnLAelllkn 26
                                       ylk+l l    d   + +ynnLA +l+k 
  gene1439|gene1439|rna1438|rna1438 60 YLKCLSLmeeeDGRLVSVYNNLAICLAKV 88
                                       66666666444556699*********976 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                             TPR_17   6 leldPnnadaynnLAelllknGdl 29 
                                        + ++ +++ ++++  +++l+++++
  gene1439|gene1439|rna1438|rna1438 273 VLKNSKSVSVLFYASKIHLNLKNH 296
                                        556778888888888888877665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.1
                             TPR_17   2 ylkaleldPnn 12 
                                        + kale +P +
  gene1439|gene1439|rna1438|rna1438 336 LNKALESHPLS 346
                                        579*****976 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.036
                             TPR_17   3 lkaleldPnnadaynnLAelllknGd 28 
                                        + a+e d + +++y +L+ +ll ++d
  gene1439|gene1439|rna1438|rna1438 405 RLAIEADSKFFKPYVYLGGILLGRND 430
                                        569***************99986665 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 5.1
                             TPR_17   2 ylkaleld 9  
                                        y++al++ 
  gene1439|gene1439|rna1438|rna1438 437 YEEALKCA 444
                                        999*9995 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       2.9   4.3e+03      10      35 ..      84     110 ..      78     117 .. 0.66
   2 ?   -0.3   0.0       1.8   2.7e+03      11      25 ..     201     215 ..     199     220 .. 0.78
   3 ?    3.0   0.0      0.16   2.3e+02       6      33 ..     318     345 ..     314     352 .. 0.82
   4 ?    4.2   0.0     0.067     1e+02       6      33 ..     386     413 ..     381     423 .. 0.79
   5 ?   -0.4   0.0       1.9   2.8e+03      17      34 ..     430     447 ..     424     455 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.9
                             TPR_14  10 allalGdpdeAiallrralala.Pdda 35 
                                         l+  + ++eA+ +++r l+ +  d++
  gene1439|gene1439|rna1438|rna1438  84 CLAKVRAYKEAALYAERSLKINiLDNE 110
                                        556667788999999999987644444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.8
                             TPR_14  11 llalGdpdeAiallr 25 
                                        l ++G++deA + ++
  gene1439|gene1439|rna1438|rna1438 201 LVRSGKYDEAFEKAE 215
                                        6799****9987555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.16
                             TPR_14   6 alaeallalGdpdeAiallrralalaPd 33 
                                        ++  ++   G+ ++A + l++al+ +P 
  gene1439|gene1439|rna1438|rna1438 318 DRIIYEVGHGRNERAQEFLNKALESHPL 345
                                        56666667799*************9995 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.067
                             TPR_14   6 alaeallalGdpdeAiallrralalaPd 33 
                                          + +  a+ +  +A++++r a++++ +
  gene1439|gene1439|rna1438|rna1438 386 FKGIVAQARNEVSDAERYFRLAIEADSK 413
                                        55778889999************98765 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.9
                             TPR_14  17 pdeAiallrralalaPdd 34 
                                         +  ++++++al+ a + 
  gene1439|gene1439|rna1438|rna1438 430 DKSCREVYEEALKCAASY 447
                                        346889999999865554 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.8   5.7e+03      17      33 ..      55      71 ..      49      73 .. 0.75
   2 ?    8.3   0.7    0.0017       2.5       2      28 ..      78     104 ..      77     122 .. 0.89
   3 ?   -1.3   0.0       1.9   2.9e+03      10      18 ..     202     210 ..     201     221 .. 0.82
   4 ?   -2.0   0.0       3.2   4.8e+03      13      30 ..     327     342 ..     327     346 .. 0.75
   5 ?    2.1   0.0      0.16   2.4e+02       6      29 ..     388     411 ..     384     418 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.8
                              TPR_7 17 eAielyeqsLaltkdpe 33
                                       eA+  y ++L l ++++
  gene1439|gene1439|rna1438|rna1438 55 EAALSYLKCLSLMEEED 71
                                       78888999997776665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0017
                              TPR_7   2 LlnLarlysrlGdyeeAielyeqsLal 28 
                                        ++nLa +  +++ y+eA+ + e+sL +
  gene1439|gene1439|rna1438|rna1438  78 YNNLAICLAKVRAYKEAALYAERSLKI 104
                                        9**********************8865 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.9
                              TPR_7  10 srlGdyeeA 18 
                                        +r G+y+eA
  gene1439|gene1439|rna1438|rna1438 202 VRSGKYDEA 210
                                        588999999 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.2
                              TPR_7  13 GdyeeAielyeqsLaltk 30 
                                        G+ e+A e++ +  al++
  gene1439|gene1439|rna1438|rna1438 327 GRNERAQEFLNK--ALES 342
                                        78899*9*9999..5554 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.16
                              TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                        + + +++++ ++A+++++ +++ +
  gene1439|gene1439|rna1438|rna1438 388 GIVAQARNEVSDAERYFRLAIEAD 411
                                        5566788999********955544 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.4    0.0017       2.5       7      48 ..      81     123 ..      77     130 .. 0.86
   2 ?    3.2   0.1     0.065        96       4      32 ..     283     311 ..     281     313 .. 0.91
   3 ?   -1.9   0.0       2.5   3.7e+03      18      32 ..     330     344 ..     327     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0017
                                        HHHHHHHHT-HHHHHHHHHHHHHHTT.S-HHHHHHHHHHHHHH CS
                         Fis1_TPR_C   7 lAlGhyklgeYseArryvdalLeiEP.enrQaqsLkeliedki 48 
                                        lA+  +k++ Y+eA  y+++ L+i   +n+ a+ L+  +++++
  gene1439|gene1439|rna1438|rna1438  81 LAICLAKVRAYKEAALYAERSLKINIlDNEKALRLRYECHKAL 123
                                        99*********************98548899999998888764 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.065
                                        HHHHHHHHHHHT-HHHHHHHHHHHHHHTT CS
                         Fis1_TPR_C   4 lYylAlGhyklgeYseArryvdalLeiEP 32 
                                        l+y +  h+ l++++   +++d+ +e+E 
  gene1439|gene1439|rna1438|rna1438 283 LFYASKIHLNLKNHELYEKFIDMAMECEE 311
                                        8999999********************95 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.5
                                        HHHHHHHHHHHHHTT CS
                         Fis1_TPR_C  18 seArryvdalLeiEP 32 
                                        ++A ++++  Le +P
  gene1439|gene1439|rna1438|rna1438 330 ERAQEFLNKALESHP 344
                                        68999******9999 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.0     0.024        36       4      30 ..      40      66 ..      40      69 .. 0.93
   2 ?    4.5   0.6     0.032        48       2      31 ..      76     105 ..      75     105 .. 0.94
   3 ?   -1.5   0.1       2.7   4.1e+03      15      25 ..     205     212 ..     202     218 .. 0.62
   4 ?   -1.4   0.0       2.6   3.8e+03       8      19 ..     287     298 ..     282     306 .. 0.79
   5 ?    6.0   0.0     0.011        16      15      29 ..     327     341 ..     322     344 .. 0.92
   6 ?   -2.4   0.1       5.3   7.8e+03      20      30 ..     353     363 ..     353     365 .. 0.79
   7 ?    2.2   0.0      0.18   2.7e+02      19      33 ..     399     413 ..     382     414 .. 0.79
   8 ?   -0.9   0.1       1.8   2.7e+03      19      29 ..     432     442 ..     428     446 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              TPR_8  4 yynlgsiylklgdyeeAkeyyekalel 30
                                       y+  g+++lk + y eA  +y k+l+l
  gene1439|gene1439|rna1438|rna1438 40 YMERGLLLLKEKVYGEAALSYLKCLSL 66
                                       77899********************97 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.032
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                        ++y+nl+ ++ k   y+eA  y e+ l+++
  gene1439|gene1439|rna1438|rna1438  76 SVYNNLAICLAKVRAYKEAALYAERSLKIN 105
                                        68**************************97 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.7
                                        T-HHHHHHHHH CS
                              TPR_8  15 gdyeeAkeyye 25 
                                        g+y+eA    e
  gene1439|gene1439|rna1438|rna1438 205 GKYDEAF---E 212
                                        6666664...4 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2.6
                                        HHHHHHTT-HHH CS
                              TPR_8   8 gsiylklgdyee 19 
                                        ++i+l+l+++e 
  gene1439|gene1439|rna1438|rna1438 287 SKIHLNLKNHEL 298
                                        578999999985 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.011
                                        T-HHHHHHHHHHHHH CS
                              TPR_8  15 gdyeeAkeyyekale 29 
                                        g+ e A+e+++kale
  gene1439|gene1439|rna1438|rna1438 327 GRNERAQEFLNKALE 341
                                        899***********8 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 5.3
                                        HHHHHHHHHHH CS
                              TPR_8  20 Akeyyekalel 30 
                                        A eyy ++ ++
  gene1439|gene1439|rna1438|rna1438 353 ACEYYLRCKDM 363
                                        7899*999765 PP

  == domain 7  score: 2.2 bits;  conditional E-value: 0.18
                                        HHHHHHHHHHHHHHH CS
                              TPR_8  19 eAkeyyekaleldpd 33 
                                         A+ y++ a+e+d +
  gene1439|gene1439|rna1438|rna1438 399 DAERYFRLAIEADSK 413
                                        6999*******9976 PP

  == domain 8  score: -0.9 bits;  conditional E-value: 1.8
                                        HHHHHHHHHHH CS
                              TPR_8  19 eAkeyyekale 29 
                                        +  e+ye+al+
  gene1439|gene1439|rna1438|rna1438 432 SCREVYEEALK 442
                                        56799999997 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.8   4.2e+03      24      37 ..      40      54 ..      26      69 .. 0.56
   2 ?   11.5   0.4   0.00014      0.21       3      31 ..      76     104 ..      74     105 .. 0.93
   3 ?   -0.4   0.1      0.77   1.1e+03      25      36 ..     119     130 ..     115     130 .. 0.86
   4 ?   -1.0   0.0       1.2   1.8e+03      11      22 ..     200     211 ..     199     213 .. 0.81
   5 ?   -1.9   0.0       2.4   3.6e+03      16      31 ..     327     342 ..     326     343 .. 0.87
   6 ?    5.2   0.2     0.014        21       9      30 ..     388     409 ..     388     411 .. 0.92
   7 ?   -1.9   0.0       2.3   3.5e+03      22      31 ..     434     443 ..     426     444 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                             TPR_10 24 lleealai.rrrllG 37
                                       ++e+ l +  ++++G
  gene1439|gene1439|rna1438|rna1438 40 YMERGLLLlKEKVYG 54
                                       444444443444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                             TPR_10   3 sslnNLanalrqrgrydeAealleealai 31 
                                        s +nNLa+ l +++ y+eA  ++e++l i
  gene1439|gene1439|rna1438|rna1438  76 SVYNNLAICLAKVRAYKEAALYAERSLKI 104
                                        78************************987 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.77
                             TPR_10  25 leealairrrll 36 
                                        +++al++rr++l
  gene1439|gene1439|rna1438|rna1438 119 CHKALDMRRETL 130
                                        689******987 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.2
                             TPR_10  11 alrqrgrydeAe 22 
                                        +l + g+ydeA 
  gene1439|gene1439|rna1438|rna1438 200 RLVRSGKYDEAF 211
                                        56789******6 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.4
                             TPR_10  16 grydeAealleealai 31 
                                        gr ++A ++l +al+ 
  gene1439|gene1439|rna1438|rna1438 327 GRNERAQEFLNKALES 342
                                        89999****9999986 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.014
                             TPR_10   9 analrqrgrydeAealleeala 30 
                                        +++ ++r++  +Ae++++ a++
  gene1439|gene1439|rna1438|rna1438 388 GIVAQARNEVSDAERYFRLAIE 409
                                        78899*************9997 PP

  == domain 7  score: -1.9 bits;  conditional E-value: 2.3
                             TPR_10  22 ealleealai 31 
                                        ++ +eeal +
  gene1439|gene1439|rna1438|rna1438 434 REVYEEALKC 443
                                        3447777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2976.73
//
Query:       gene1440|gene1440|rna1439|rna1439  [L=597]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.5   2.5        6.2    6.9   0.1    2.5  2  DUF3969   Protein of unknown function (DUF3969)


Domain annotation for each model (and alignments):
>> DUF3969  Protein of unknown function (DUF3969)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1   0.00034       6.2      20      64 ..       6      50 ..       4      54 .. 0.92
   2 ?    3.8   0.3    0.0031        56      18      57 ..     190     228 ..     178     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00034
                            DUF3969 20 alklkvisleeaesllFslemlelieelelsdelveiihkgmeLE 64
                                       a+ ++ ++ e + ++ F+ +m+eli++  +  e+ + i  ++eLE
  gene1440|gene1440|rna1439|rna1439  6 AFFTEFVEAEKVVEVDFNQKMIELIRKTIVPVEMEDFISSASELE 50
                                       6667888999999999****************************9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0031
                            DUF3969  18 vealklkvisleeaesllFslemlelieelelsdelveii 57 
                                        + a  + +is++++++++F+le+l    ++ l +e+  ii
  gene1440|gene1440|rna1439|rna1439 190 CFAVDVSRISSGILKEIIFHLETLSNG-KMALYEEIFAII 228
                                        55777899****************987.888999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3950.25
//
Query:       gene144|gene144|rna144|rna144  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.018   14.6   5.1      0.022   14.3   5.1    1.0  1  Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
      0.094   10.7   0.5       0.11   10.5   0.5    1.1  1  Prominin         Prominin


Domain annotation for each model (and alignments):
>> Exosortase_EpsH  Transmembrane exosortase (Exosortase_EpsH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   5.1   2.5e-06     0.022      35     122 ..      20     114 ..       8     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-06
                Exosortase_EpsH  35 alyllwdrwrralaasasll..g.llllllglfl..lallgels.rvlllsalslvlillglvllllGlralrlllf... 105
                                    ++y+l  +++      as++  g + ++l++l+   ++l+++++ rv++ s+++  +++ g++++ +Glr+l ++ +   
  gene144|gene144|rna144|rna144  20 TIYILVVHKDH--LNVASSWdsGsVYAYLALLLGiaRLLASRKAtRVGFYSSIAGSFLAEGVFFIYSGLRGLYSVQRviv 97 
                                    45777777777..3344444463333333333223589999***************************999988877666 PP

                Exosortase_EpsH 106 pllllllalPlpavlva 122
                                    +++l+l+ + +  +l++
  gene144|gene144|rna144|rna144  98 ETFLVLFTVGWMIFLYP 114
                                    88888888887777665 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.5   1.2e-05      0.11     432     472 ..      43      83 ..      41     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.2e-05
                       Prominin 432 ililgLlcGilGlsrtatptdrgcskntGasfLlvgvglsF 472
                                      +l+Ll+Gi  l ++ + t+ g+ +++++sfL  gv +++
  gene144|gene144|rna144|rna144  43 YAYLALLLGIARLLASRKATRVGFYSSIAGSFLAEGVFFIY 83 
                                    568************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 893.86
//
Query:       gene1441|gene1441|rna1440|rna1440  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1903  (0.106141); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1175.66
//
Query:       gene1442|gene1442|rna1441|rna1441  [L=616]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-08   34.1   0.1       0.86   10.0   0.0    6.8  7  HEAT         HEAT repeat
    3.5e-08   33.7   0.0      0.027   14.9   0.0    3.4  3  HEAT_2       HEAT repeats
    2.1e-07   31.1   0.5      1e-05   25.7   0.1    2.6  2  Cnd1         non-SMC mitotic condensation complex subunit 1
     0.0055   16.6   0.1      0.016   15.2   0.1    1.7  1  TILa         TILa domain
     0.0072   14.9   0.4       0.04   12.5   0.1    2.1  2  Adaptin_N    Adaptin N terminal region
  ------ inclusion threshold ------
      0.028   14.3   0.0         12    5.8   0.0    3.0  2  RACo_linker  RACo linker region
       0.22   11.2   1.5       0.51   10.1   1.5    1.6  1  LRRNT        Leucine rich repeat N-terminal domain


Domain annotation for each model (and alignments):
>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.79     2e+03      10      21 ..      75      86 ..      70      87 .. 0.78
   2 ?    4.7   0.0     0.017        43       5      29 ..     125     149 ..     122     150 .. 0.84
   3 ?    3.7   0.0     0.037        96       1      27 [.     157     183 ..     157     184 .. 0.94
   4 ?    2.5   0.0     0.086   2.2e+02       9      27 ..     215     233 ..     210     235 .. 0.84
   5 !   10.0   0.0   0.00034      0.86       4      27 ..     245     268 ..     242     271 .. 0.88
   6 ?    2.9   0.0     0.067   1.7e+02       1      27 [.     280     306 ..     280     307 .. 0.91
   7 ?   -2.3   0.0       3.2   8.1e+03      21      29 ..     331     339 ..     330     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.79
                                       T-SSHHHHHHHH CS
                               HEAT 10 sDpspeVReaAa 21
                                        +++++VR+ ++
  gene1442|gene1442|rna1441|rna1441 75 FHENAKVRKVSL 86
                                       689*****9875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                                        HHHHHT-SSHHHHHHHHHHHHHHHH CS
                               HEAT   5 llkllsDpspeVReaAakaLgalae 29 
                                        l++  +D + +VRe A+  L +++e
  gene1442|gene1442|rna1441|rna1441 125 LVRQARDGNKDVREVALHQLMRFSE 149
                                        667789***********99988876 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.037
                                        HHHHHHHHHT-SSHHHHHHHHHHHHHH CS
                               HEAT   1 llPlllkllsDpspeVReaAakaLgal 27 
                                        +l ++++ ++D + ++R  + ka+g++
  gene1442|gene1442|rna1441|rna1441 157 ILRAVCHGIHDRELSIRVFVSKAIGEF 183
                                        78899********************86 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.086
                                        HT-SSHHHHHHHHHHHHHH CS
                               HEAT   9 lsDpspeVReaAakaLgal 27 
                                        ++D+ ++VR++++ ++  l
  gene1442|gene1442|rna1441|rna1441 215 IEDEYADVRRNTISSVYSL 233
                                        68**********9998776 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.00034
                                        HHHHHHT-SSHHHHHHHHHHHHHH CS
                               HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                        +++  l+D++ +VRe + + L ++
  gene1442|gene1442|rna1441|rna1441 245 FVVDSLNDEDNDVRELCTLYLKKI 268
                                        67889************9999887 PP

  == domain 6  score: 2.9 bits;  conditional E-value: 0.067
                                        HHHHHHHHHT-SSHHHHHHHHHHHHHH CS
                               HEAT   1 llPlllkllsDpspeVReaAakaLgal 27 
                                        ++  +++ l+ +s +V ++ +  Lg+l
  gene1442|gene1442|rna1441|rna1441 280 IVRQICESLKEKSYKVKANILGLLGNL 306
                                        67789****************999987 PP

  == domain 7  score: -2.3 bits;  conditional E-value: 3.2
                                        HHHHHHHHH CS
                               HEAT  21 akaLgalae 29 
                                        ++++g++++
  gene1442|gene1442|rna1441|rna1441 331 FECIGRIVS 339
                                        79*****97 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0     3e-05     0.077       3      77 ..     124     205 ..     122     207 .. 0.79
   2 !   14.9   0.0     1e-05     0.027       5      80 ..     212     296 ..     210     300 .. 0.78
   3 ?    2.7   0.0     0.066   1.7e+02       4      36 ..     284     317 ..     281     325 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                             HEAT_2   3 aLlqalendpdpevrraairaLgrignp.....ealpaLvellededpavRraaaeaLgaig.dpeal..paLkel 70 
                                         L+ ++ +d +++vr  a+++L r+ ++     ++l+a+   + d +  +R  + +a+g+++ +pe++  ++L + 
  gene1442|gene1442|rna1441|rna1441 124 SLVRQA-RDGNKDVREVALHQLMRFSEEekykmKILRAVCHGIHDRELSIRVFVSKAIGEFKgLPEVVaeKLLSKQ 198
                                        688899.9****************9888666667788888888899999***********9636886543677777 PP

                             HEAT_2  71 ldddddd 77 
                                         +++dd+
  gene1442|gene1442|rna1441|rna1441 199 ITSPDDQ 205
                                        7777665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1e-05
                             HEAT_2   5 lqalendpdpevrraairaLgrignp....ealpaLvellededpavRraaaeaLgaig.......dpealpaLke 69 
                                        +  + +d+  +vrr++i +  ++  p    +a++ +v+ l+ded +vR+    +L +i        d+e ++  +e
  gene1442|gene1442|rna1441|rna1441 212 IYGI-EDEYADVRRNTISSVYSLIAPgtasRAFDFVVDSLNDEDNDVRELCTLYLKKISmkyvlaiDKEIVRQICE 286
                                        5566.89*************976555566689************************99655666567777788887 PP

                             HEAT_2  70 llddddddvvR 80 
                                        +l++ +++ v+
  gene1442|gene1442|rna1441|rna1441 287 SLKE-KSYKVK 296
                                        7764.445555 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.066
                             HEAT_2   4 LlqalendpdpevrraairaLgrignp..ealpaL 36 
                                         ++ l + ++++v+++++  Lg+++ +  e++ +L
  gene1442|gene1442|rna1441|rna1441 284 ICESL-KEKSYKVKANILGLLGNLKYEdvEVFSIL 317
                                        56778.89999***********8877622445555 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.044   1.1e+02      60      99 ..     122     160 ..     109     198 .. 0.65
   2 !   25.7   0.1   3.9e-09     1e-05      26     136 ..     211     315 ..     205     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.044
                               Cnd1  60 lselaklleDenprVvanalaalteiseksenaiynllpd 99 
                                        +s l +  +D n+ V++ al+ l+  se++ +  +++l+ 
  gene1442|gene1442|rna1441|rna1441 122 VSSLVRQARDGNKDVREVALHQLMRFSEEE-KYKMKILRA 160
                                        445555555666666666666666666665.333333333 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 3.9e-09
                               Cnd1  26 LrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteiseksenaiynllpdii 101
                                        L  +++De + VR++++  v  Li +++      ++ + + l+De++ V++++ + l++is k    ++ + ++i+
  gene1442|gene1442|rna1441|rna1441 211 LIYGIEDEYADVRRNTISSVYSLIAPGTAS--RAFDFVVDSLNDEDNDVRELCTLYLKKISMKY---VLAIDKEIV 281
                                        566799********************9876..5689999**********************998...899999999 PP

                               Cnd1 102 sklsdalnecsewgqitilefLlsyipkdkqeaes 136
                                         ++ ++l+e s +   +il +L + + +d +  +s
  gene1442|gene1442|rna1441|rna1441 282 RQICESLKEKSYKVKANILGLLGNLKYEDVE-VFS 315
                                        9999999999999999999988777776665.554 PP

>> TILa  TILa domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   6.2e-06     0.016       3      39 ..      24      60 ..      23      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.2e-06
                               TILa  3 kdaqgslipagetWissgCtqsCtCsggaiqCqpfqC 39
                                       +d+++  i++   ++s+gCt +C+C +  +  ++  C
  gene1442|gene1442|rna1441|rna1441 24 TDFEDGSIKSLSDYYSPGCTAECNCHHLVVYLENALC 60
                                       6899999******************998777666666 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.1   2.6e+02      79     127 ..     120     169 ..     111     178 .. 0.62
   2 !   12.5   0.1   1.5e-05      0.04      95     194 ..     222     321 ..     214     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.1
                                        CCCHHHHHHCCSSSHHHHHHHHHHHCCC--CCCH.HHHHHHHHHHHT-SS CS
                          Adaptin_N  79 LvtnslqkDlkdpnqlirglALrvLssirvpela.edlapaikkllkdrs 127
                                        L ++sl + + d n+ +r +AL+ L +++++e    ++++a+   ++dr+
  gene1442|gene1442|rna1441|rna1441 120 LRVSSLVRQARDGNKDVREVALHQLMRFSEEEKYkMKILRAVCHGIHDRE 169
                                        45666777777777777777777777777444332555555555555554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.5e-05
                                        HHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHH CS
                          Adaptin_N  95 irglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvl 170
                                        +r ++++++ s++ p +a   ++ + + l+d+++ vr    l + k+  k+  ++ k+ v +i e+l++k+++v++
  gene1442|gene1442|rna1441|rna1441 222 VRRNTISSVYSLIAPGTASRAFDFVVDSLNDEDNDVRELCTLYLKKISMKYVLAIDKEIVRQICESLKEKSYKVKA 297
                                        578999*************************************************999****************** PP

                                        HHHHHHHHHHCCCCCCCHHHHHHH CS
                          Adaptin_N 171 aAvalleeikkndrlllkllpklv 194
                                        + + ll  +k++d +  ++l +++
  gene1442|gene1442|rna1441|rna1441 298 NILGLLGNLKYEDVEVFSILTSHM 321
                                        *********777777445554444 PP

>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.009        23      23      69 ..     249     299 ..     243     317 .. 0.82
   2 ?    5.8   0.0    0.0049        12      19      61 ..     426     470 ..     423     500 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.009
                        RACo_linker  23 tledpsgDleRLkeaLekqwd....leidlsvLrkLpevLrkgnwkVtval 69 
                                        +l+d   D++ L++   k++     l id +++r++ e L+++ +kV++ +
  gene1442|gene1442|rna1441|rna1441 249 SLNDEDNDVRELCTLYLKKISmkyvLAIDKEIVRQICESLKEKSYKVKANI 299
                                        57788889999988766666334679*********************9976 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0049
                        RACo_linker  19 leePtledpsgDleRLkeaLekqwd..leidlsvLrkLpevLrkg 61 
                                        leeP+ +++  D++RL  +++k+ d    + +++ + + e+L+k+
  gene1442|gene1442|rna1441|rna1441 426 LEEPSGDKKEQDYRRLFGQMKKDSDhrYWFIYHIYKGMNELLHKK 470
                                        79********************99656667777777777777765 PP

>> LRRNT  Leucine rich repeat N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.5    0.0002      0.51       1      14 [.      41      54 ..      41      54 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0002
                                       SSETTSEEECCEEE CS
                              LRRNT  1 aCPrpChCsalvVn 14
                                       +C ++C+C++lvV+
  gene1442|gene1442|rna1441|rna1441 41 GCTAECNCHHLVVY 54
                                       599**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4028.97
//
Query:       gene1443|gene1443|rna1442|rna1442  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   7.3e-110  366.8   0.0   8.3e-110  366.6   0.0    1.0  1  DS               Deoxyhypusine synthase
  ------ inclusion threshold ------
      0.094   12.7   0.0        0.2   11.6   0.0    1.5  1  Glycos_transf_4  Glycosyl transferase family 4
       0.16   12.3   0.0       0.26   11.6   0.0    1.2  1  PHP              PHP domain


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.6   0.0  1.4e-113  8.3e-110       1     287 [.      37     321 ..      37     322 .. 0.96

  Alignments for each domain:
  == domain 1  score: 366.6 bits;  conditional E-value: 1.4e-113
                                 DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlik 76 
                                        e+++s+e++gfq+++l++ai+++++m   ++ +if+g+tsn+issGlr+iia+lvk+k++ v+v T+ggieeD+ik
  gene1443|gene1443|rna1442|rna1442  37 EMIKSFETTGFQGSNLYKAIQEVERM---KDSKIFFGCTSNIISSGLRDIIATLVKRKHIHVLVITGGGIEEDIIK 109
                                        689***********************...6778******************************************* PP

                                 DS  77 algkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqk.....vwspselikelGkein 147
                                        ++++ t++gdf+l +++Lre+g+nRignl++p+eny+++e+w+++++++++e  +     +++ps++i+ lG++in
  gene1443|gene1443|rna1442|rna1442 110 TFKP-TFCGDFNLCGKDLRENGLNRIGNLVIPSENYEDLEKWLNQVINDITEGYTeerprILTPSSFIRILGERIN 184
                                        ****.**********************************************96655566566************** PP

                                 DS 148 deeSilywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhh 223
                                        de+SilywA+kndip+++pa++Dgs+Gd +l fh   ++k +kld+++D+ ++n  ++ +  tgaiilG G++Khh
  gene1443|gene1443|rna1442|rna1442 185 DESSILYWAAKNDIPIYSPAVVDGSMGD-ILSFH--PRRKMVKLDVIEDVYNINCETIFCGDTGAIILGCGIVKHH 257
                                        ****************************.99999..35667*********************************** PP

                                 DS 224 ilnanlmrngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                        ilnanl++ng++y+v i+ aqefdGs++ga+ldEavSwgk+k++a+ vk+++DaTi++PL+v a
  gene1443|gene1443|rna1442|rna1442 258 ILNANLFKNGLEYCVLINNAQEFDGSDAGANLDEAVSWGKVKPGANGVKIFGDATILFPLIVGA 321
                                        *************************************************************976 PP

>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.4e-05       0.2     130     152 ..     231     253 ..     230     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.4e-05
                    Glycos_transf_4 130 lfNrypAkvFmGDsgslflGlvl 152
                                        ++N++  ++F GD+g+++lG  +
  gene1443|gene1443|rna1442|rna1442 231 VYNINCETIFCGDTGAIILGCGI 253
                                        69******************765 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.26      39     111 ..      51     169 ..      35     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                                        BTTHHHHHHHHHHHHTTTTSEEEEEEE................................................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                                PHP  39 nlfgyvefykaakkkykagikpiiGleayvaddse......................................... 73 
                                        nl++++++++++k     + k+ +G+  ++++ +                                          
  gene1443|gene1443|rna1442|rna1442  51 NLYKAIQEVERMK-----DSKIFFGCTSNIISSGLrdiiatlvkrkhihvlvitgggieediiktfkptfcgdfnl 121
                                        6777888888883.....478******99999999***************************************** PP

                                        ...................E....EHHHHHHHHHHHHH.......... CS
                                        .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                                PHP  74 .........kerpshltllaknqeGyknllkllskaylegf.yrkpri 111
                                                  +r  +l++  +n+e++++ l++++++ +eg+ +++pri
  gene1443|gene1443|rna1442|rna1442 122 cgkdlrengLNRIGNLVIPSENYEDLEKWLNQVINDITEGYtEERPRI 169
                                        *******9999**************99999999999999998999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 1904.67
//
Query:       gene1444|gene1444|rna1443|rna1443  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-58  198.4   0.0    1.2e-58  198.1   0.0    1.0  1  FtsJ             FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.082   12.5   0.0       0.12   11.9   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.1   0.0   1.3e-62   1.2e-58       1     176 [.      19     197 ..      19     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 198.1 bits;  conditional E-value: 1.3e-62
                                        CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T....-SEEEEEESSSSHHHTTEEEECS-CCCS CS
                               FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlga...kgkvvavDlqpmaplpgvttiqgditdp 73 
                                        yr+Rs+yKL++ide+++lf++ ++vvDl+aaPG+wsq+++++l +   ++kvv+vD+q + p++g t+i+ dit+ 
  gene1444|gene1444|rna1443|rna1443  19 YRARSVYKLMNIDEEYNLFQNIENVVDLCAAPGSWSQYACEKLMKkggNPKVVSVDVQDIIPIEGATCIKDDITST 94 
                                        9******************************************664445*************************** PP

                                        SHHHHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHH CS
                               FtsJ  74 etiekikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlk 149
                                        +  e i+e l++ ++dlv++Dgapd++g+h++deylq++Ll++al ++l++ k g +fv k ++ge ++ +++++ 
  gene1444|gene1444|rna1443|rna1443  95 SCLESILEVLDGPRADLVMCDGAPDITGIHEIDEYLQMELLMSALATSLRISKAGSSFVGKCLQGEYISCMANHFG 170
                                        **************************************************************************** PP

                                        CCEEEEEEEE-SS--CCG-EEEEEEEE CS
                               FtsJ 150 kfFekvsvvkPkssrsesseeflvcrg 176
                                        +f++k  + kPk+sr es e+fl c+g
  gene1444|gene1444|rna1443|rna1443 171 RFYNKTALLKPKASRTESMECFLYCTG 197
                                        *************************87 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.4e-05      0.12       7      42 ..      38      76 ..      35     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                                       -TT-EEEESS-TTSHHHHHHHH.HTTTTS..EEEEEESS CS
                    Methyltr_RsmB-F  7 qeeetilDlcaaPGgKTthiae.lmknkg..tvvAvdan 42
                                       q+ e ++DlcaaPG+   +  e lmk+ g  +vv vd++
  gene1444|gene1444|rna1443|rna1443 38 QNIENVVDLCAAPGSWSQYACEkLMKKGGnpKVVSVDVQ 76
                                       67799************9987636877653357777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1637.07
//
Query:       gene1445|gene1445|rna1444|rna1444  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-56  191.0   0.4    1.4e-56  190.7   0.4    1.1  1  Rad52_Rad22  Rad52/22 family double-strand break repair prote
  ------ inclusion threshold ------
      0.091   13.3   0.1       0.17   12.5   0.1    1.5  1  FlgT_N       Flagellar assembly protein T, N-terminal domain


Domain annotation for each model (and alignments):
>> Rad52_Rad22  Rad52/22 family double-strand break repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.7   0.4   1.6e-60   1.4e-56       2     150 ..      19     165 ..      18     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 190.7 bits;  conditional E-value: 1.6e-60
                        Rad52_Rad22   2 ietlqskLekklgpeyvsqregksgkkvaylegskviqlaNevFgfnGWsseiesievdeieeeqegqrysvkaea 77 
                                        ++++++ L++klgpe +s r+g +++k+ay+eg+kvi+laN++FgfnGWssei++++vd+ e++++  ++s+++++
  gene1445|gene1445|rna1444|rna1444  19 VRKISKLLNQKLGPEFISYRPGFNMSKIAYVEGWKVISLANRIFGFNGWSSEIRTMSVDYEEADEK--KISLGVSC 92 
                                        67899******************************************************9976666..8******* PP

                        Rad52_Rad22  78 lvrvtlkdGtyrediGfgtatnvpskgeafekakKeAvtdAlKrAllqfgnvlGnclydleqekkvkklkked 150
                                        lvrv+lkdGtyrediGfg+a+n +s+++a+ekakKeA+tdAlKrAl+qfgn+lGnc+yd+++ k+v++++k +
  gene1445|gene1445|rna1444|rna1444  93 LVRVMLKDGTYREDIGFGSAENQRSRAAAYEKAKKEAATDALKRALRQFGNSLGNCCYDKNYIKEVQRIHKIN 165
                                        ****************************************************************999988765 PP

>> FlgT_N  Flagellar assembly protein T, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.9e-05      0.17      16      54 ..     123     161 ..     117     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                             FlgT_N  16 diAreqAredAlkqAllyagaqvgsisslqqllegslte 54 
                                        + A+++A  dAlk Al++ g ++g+    ++++++ +  
  gene1445|gene1445|rna1444|rna1444 123 EKAKKEAATDALKRALRQFGNSLGNCCYDKNYIKEVQRI 161
                                        789*******************99988888877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1337.07
//
Query:       gene1446|gene1446|rna1445|rna1445  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-20   74.1  17.7    1.6e-20   73.6  17.7    1.3  1  Got1      Got1/Sft2-like family
  ------ inclusion threshold ------
        0.2   11.9   6.5       0.04   14.2   2.7    1.9  2  DUF4181   Domain of unknown function (DUF4181)
        6.7    7.1   9.1         41    4.6   9.1    2.1  1  DUF2628   Protein of unknown function (DUF2628)


Domain annotation for each model (and alignments):
>> Got1  Got1/Sft2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6  17.7   2.6e-24   1.6e-20       1     112 [.      56     165 ..      40     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 2.6e-24
                               Got1   1 GvllfllsllglpllflkprkFallytlGnilflastafLiGpkkqlkkmfskerliativyllsllltLyaalvl 76 
                                        G+l fl+s+++++ l  +p+ F l yt++n+lf+++++fL+G++++l+ +fsk+++  ++ ++++++ltLy+ l +
  gene1446|gene1446|rna1445|rna1445  56 GILSFLYSMVKIVRL--SPSGFILPYTVSNFLFFIMFGFLLGFRSYLEGLFSKKKRFHSSWFIGCTFLTLYVVLRY 129
                                        455556666655555..69********************************************************* PP

                               Got1  77 kstlltllfvivqllallwyllsyiPggrsalkkvl 112
                                         ++ll l+f+++q+ ++++++l+++Pgg+s++++++
  gene1446|gene1446|rna1445|rna1445 130 DRYLLNLVFCFIQVTSFVMFSLTFVPGGTSGVSSMV 165
                                        ********************************9886 PP

>> DUF4181  Domain of unknown function (DUF4181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   2.7   6.8e-06      0.04      37     104 ..      57     125 ..      24     129 .. 0.63
   2 ?   -1.6   0.1      0.52   3.1e+03      91     103 ..     133     145 ..     128     154 .. 0.46

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.8e-06
                            DUF4181  37 ilrv.lfiifiilsliiilsreyvdiiilifvflvvlelfRavmewkyereskrYilslaaailflill 104
                                        il+    ++ i+      ++ +y+   +l+f+++  l +fR+++e  ++++++ +   ++ ++++++ +
  gene1446|gene1446|rna1445|rna1445  57 ILSFlYSMVKIVRLSPSGFILPYTVSNFLFFIMFGFLLGFRSYLEGLFSKKKRFHSSWFIGCTFLTLYV 125
                                        4333222233333333444445544449********************766665555555555555443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.52
                            DUF4181  91 ilslaaailflil 103
                                        +l+l+ +++ +  
  gene1446|gene1446|rna1445|rna1445 133 LLNLVFCFIQVTS 145
                                        4444444333222 PP

>> DUF2628  Protein of unknown function (DUF2628)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   9.1    0.0068        41      16      80 ..     106     169 ..      40     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0068
                            DUF2628  16 edgkirlsfnvwAfffgfiwLlyrklwlkalvllviavavsvvlavlgfsdavrlllalliaill 80 
                                        +++++  s+ + + f++ +  l   ++l +lv++ i+v + v+ +++ f ++ + +++ ++++++
  gene1446|gene1446|rna1445|rna1445 106 KKKRFHSSWFIGCTFLTLYVVLRYDRYLLNLVFCFIQVTSFVMFSLT-FVPGGTSGVSSMVNMFF 169
                                        455888999999**********99**************987775555.55555566777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1136.18
//
Query:       gene1447|gene1447|rna1446|rna1446  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-05   25.4   2.3      1e-05   25.4   2.3    2.1  2  Sec61_beta  Sec61beta family
  ------ inclusion threshold ------
       0.19   10.4   0.9       0.21   10.3   0.9    1.0  1  DUF2207     Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   2.3   1.2e-09     1e-05      18      41 .]      32      55 ..      28      55 .. 0.94
   2 ?    1.8   1.8     0.027   2.5e+02      22      32 ..      71      81 ..      66      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.2e-09
                                       B-THHHHHHHHHHHHHHHHHTSS- CS
                         Sec61_beta 18 idPkvVlvlsvafiasVilLhila 41
                                       i+P  Vlv+s++fi+ V+lLhila
  gene1447|gene1447|rna1446|rna1446 32 ISPMQVLVISLIFIGNVFLLHILA 55
                                       9*********************96 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHH CS
                         Sec61_beta 22 vVlvlsvafia 32
                                       +V+ ls+af +
  gene1447|gene1447|rna1446|rna1446 71 MVVLLSIAFSF 81
                                       68888888877 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   2.3e-05      0.21     353     430 ..       5      81 ..       2      85 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.3e-05
                            DUF2207 353 fkkalkkwksavkkkergyfdkkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivll 428
                                        ++ +++++k+   k ++ ++++ ++  +  +++l + li++g +++l +l+ lv+ ++ l   +++l+++++ +++
  gene1447|gene1447|rna1446|rna1446   5 ISGKIQQYKKRQSKLNELLYNQPSRLLISPMQVLVISLIFIGNVFLLHILAKLVP-SSSLPQAAIALMVVLLSIAF 79 
                                        555556666655555666777888999999****************999999999.66666655555555555544 PP

                            DUF2207 429 lf 430
                                         f
  gene1447|gene1447|rna1446|rna1446  80 SF 81 
                                        43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 568.68
//
Query:       gene1448|gene1448|rna1447|rna1447  [L=349]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-12   45.5   0.1    5.5e-09   36.0   0.1    2.1  2  Bac_surface_Ag  Surface antigen


Domain annotation for each model (and alignments):
>> Bac_surface_Ag  Surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00012       2.1       1      41 [.      80     119 ..      80     146 .. 0.72
   2 !   36.0   0.1   3.1e-13   5.5e-09     153     318 ..     187     345 ..     164     349 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00012
                                        STSSSS-EEEEEEEESSSEEEEEEEEEES..TSSTTS-EEEEE CS
                     Bac_surface_Ag   1 NllGtGqslslsaslgsyeqslnlsfteP..yflgdrvslgls 41 
                                        Nl+G++++l++s+s +   + ++++ft+P  +   + +s ++s
  gene1448|gene1448|rna1447|rna1447  80 NLFGKAENLEVSMSTS---KDMSFRFTKPilWKSLSFLSISGS 119
                                        9*************97...999*******55444444444444 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 3.1e-13
                                        EEEEEEEEEEEEESSTTSSSEEEEEEEEEEEEESSSS-.--GGG-B-BSSTTSSTEE-TT-BS-EEEEEEE--BSE CS
                     Bac_surface_Ag 153 ylkldakasyyvpltkekdlvlaarvalgyisgygtkdelpfyerFyaGGsnsvRGfesgglgprdesgdalGGds 228
                                        + k++a++    +lt++  l    ++++g+      ++  ++ er+y+G +  +RG++  ++ p+ + g ++GG+s
  gene1448|gene1448|rna1447|rna1447 187 FSKTQAEMILGKSLTRS--LFTDIHFSTGL----ILGE-PHIAERYYLGEN--IRGYRGMSISPSNC-GLKIGGNS 252
                                        55555555444455532..22233333333....3345.6899******88..***********999.******** PP

                                        EEEEEEEEEEE-SSS-GGTTEEEEEEEEEEEEE-TT--TTTTTTS--TT.....TS-EEEEEEEEEE...EETTEE CS
                     Bac_surface_Ag 229 yavaslElrfplpflkkqnsvrlalFfDaGnvwdkegqspsssrsasst.....aeirasvGvgLrw...qsPlGP 296
                                        +++as  + +  +      + ++ lF+  G v ++++  +s +   +s+     + ++asvG+g  +   +s  GP
  gene1448|gene1448|rna1447|rna1447 253 FFEASHRMGVCKW------QAKGFLFWSLGYVSENRNIVSSLKPVMRSRsykddECFGASVGLGASVpvmKSKDGP 322
                                        ****986666653......4799********988888888877666665999999999999988543222555899 PP

                                        E.EEEEEEEEE-STT--EESEEE CS
                     Bac_surface_Ag 297 l.rfdyAiplkkedgdktqrFqF 318
                                          ++++Aipl++ ++ ++ +F F
  gene1448|gene1448|rna1447|rna1447 323 VvSVSFAIPLTNNRQVQKLQFGF 345
                                        6369*******999955555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2297.05
//
Query:       gene1449|gene1449|rna1448|rna1448  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-13   49.0   0.0    5.8e-13   48.7   0.0    1.1  1  SPC22     Signal peptidase subunit
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.16   11.7   0.0    1.1  1  DEAD      DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> SPC22  Signal peptidase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   6.4e-17   5.8e-13       3     154 ..       6     138 ..       4     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 6.4e-17
                              SPC22   3 qRlnavlalaltvlavlvalialsslflklskakskisnvkvsvaksvrdygsnrkkkdraklkfdldaDlsslfn 78 
                                         Rlna++++++   ++l+++++l s+f++   +  ++s++++   ++++ yg+        ++ f+ ++Dlss f+
  gene1449|gene1449|rna1448|rna1448   6 RRLNALVSFTFNPTVILLLAVFLFSFFVA---KAPPVSDLRI---REYKAYGR------TQVVFFEPSIDLSSQFH 69 
                                        6*************************999...799*****99...88888875......456779999******** PP

                              SPC22  79 WNtKqlFvyltaeYetkknevNqvvlWDkIirskedaklklknvkskYslkdqeksLrgrkvtltLhwnvmPvvGl 154
                                        +N+Kq+Fvy+ + Y +k + +++ ++W +Ii  ++++kl     +s Y +     +L+++   ++L+  + P vG 
  gene1449|gene1449|rna1448|rna1448  70 FNLKQIFVYVRVIYGGKAD-KSE-IIWSRIIGWNDSKKLIGV-FRSTYDI---AGDLSDNP-CFELRGCYFPRVGW 138
                                        ****************999.555.69*****99988876555.5777755...55666654.35555555666665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.8e-05      0.16      43      90 ..      48      91 ..      23     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.8e-05
                                       TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardq 90
                                       k   ++++++ eP+  L  q + nlk+++ y+  r  +i+gg+a +++
  gene1449|gene1449|rna1448|rna1448 48 KAYGRTQVVFFEPSIDLSSQFHFNLKQIFVYV--R--VIYGGKADKSE 91
                                       6677899***********************93..3..57999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 921.31
//
Query:       gene1450|gene1450|rna1449|rna1449  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-14   51.0   0.1    1.9e-13   50.0   0.1    1.4  1  Homeodomain  Homeodomain
  ------ inclusion threshold ------
       0.04   13.8   0.1      0.073   13.0   0.1    1.4  1  Homeobox_KN  Homeobox KN domain
      0.079   12.8   0.0       0.18   11.7   0.0    1.6  1  HTH_23       Homeodomain-like domain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   3.2e-17   1.9e-13       8      53 ..      37      82 ..      33      85 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 3.2e-17
                                       -HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHH CS
                        Homeodomain  8 tkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRa 53
                                       t++q+++L+k Fe ++yps+++r  LA  l+++ r +++WFqN R 
  gene1450|gene1450|rna1449|rna1449 37 TRTQVDVLKKIFEITHYPSHDTRLNLAILLNISPRTIQIWFQNSRS 82
                                       899*****************************************96 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.2e-05     0.073      10      38 ..      53      81 ..      51      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                        Homeobox_KN 10 YPseedKeeLlkeTglsvkqitnWFINaR 38
                                       YPs + +  L+   ++s + i+ WF N R
  gene1450|gene1450|rna1449|rna1449 53 YPSHDTRLNLAILLNISPRTIQIWFQNSR 81
                                       ***************************99 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     3e-05      0.18      24      40 ..      63      79 ..      56      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                             HTH_23 24 AreLgvsrrTvyrwlkr 40
                                       A +L++s+rT++ w + 
  gene1450|gene1450|rna1449|rna1449 63 AILLNISPRTIQIWFQN 79
                                       789***********876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 834.35
//
Query:       gene145|gene145|rna145|rna145  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-08   34.3   0.0      1e-07   32.0   0.0    2.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   5.8e-12     1e-07       1     118 [.      33     194 ..      33     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.8e-12
                                    EEEEEEEEEEEETTSEEEEEEES..SSSTTT.E....E.SS....EEECBTTSHHHHHHHHHHHHHHSE..EE.EEEEEE CS
                          NUDIX   1 klrravgvvllnekgevLlvrrs..kkpfpg.W....e.lP....gGkvepgEtpeeAArREleEEtGl..ea.ellell 65 
                                    +l+ra++v+l+n+++e+L+++r+  k  fp+ W    + +P      ++ p  +++  A+ ++ +E+G+  +  ++l+++
  gene145|gene145|rna145|rna145  33 MLHRAFSVFLFNSRNELLIQKRAsgKLLFPNkWtnsvCsHPfvndLSFINPLLDVKIHAVKRIDHELGIgsILiDDLRFV 112
                                    68*********************99777777897777457799999999999999999**********655455999*** PP

                                    EEEEEEEEEEEEEEE..............................EEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHH CS
                          NUDIX  66 grlhylapydgpygd..............................eheilyvfleevegelepndenevsevrwvpleel 115
                                    +r+ y+a+++++y +                              e e++y+ l+  +  + pn +nevse+r+v  eel
  gene145|gene145|rna145|rna145 113 SRIIYKASPTERYSRilpgipttqkistfpdpnnlsgsyssddfhEWEVDYIILAVSDASPCPN-PNEVSEIRYVCKEEL 191
                                    ***************************************9999776677788888888888888.*************** PP

                                    HHH CS
                          NUDIX 116 lke 118
                                    ++ 
  gene145|gene145|rna145|rna145 192 QEL 194
                                    332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1513.44
//
Query:       gene1451|gene1451|rna1450|rna1450  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.4e-34  117.9   0.1    1.2e-33  117.4   0.1    1.2  1  Metallophos  Calcineurin-like phosphoesterase
     0.0014   19.0   0.2     0.0031   17.9   0.2    1.6  1  STPPase_N    Serine-threonine protein phosphatase N-terminal 


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4   0.1   1.3e-37   1.2e-33       2     201 ..      42     233 ..      41     235 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 1.3e-37
                                        EEEEEESBTBTTCCTHHHHHHHHH..HHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TT CS
                        Metallophos   2 rilvigDlHlalgggqlddllkll..ddllreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNH 74 
                                        +++v+gD+H     gq+ dl+ l+  d +++  k++++l  GD+vdrg  + e++ + +  ++ yp +v l++GNH
  gene1451|gene1451|rna1450|rna1450  42 PVIVCGDIH-----GQFFDLVSLFriDGIPSG-KRYVFL--GDYVDRGKNSLECILFlFLLKILYPENVTLIRGNH 109
                                        799******.....**********77777777.******..*******88888888878999999*********** PP

                                        S........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSC CS
                        Metallophos  75 e........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnlel 141
                                        e        gf+ee+ +kyg+    +++wr+ +evfn + + +l++g  ++l++hGg sp +  sl+++++l++ l
  gene1451|gene1451|rna1450|rna1450 110 EqstinrvyGFYEEIIEKYGN----PRIWRMINEVFNLMCVGCLVDG--RILCVHGGiSPKI-MSLNQMRRLDRLL 178
                                        ********************9....8899******************..********77777.************* PP

                                        HHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 142 eapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                        ++ e+    d+++ d        +    g  p +rgsgyl+g++++ ++l+ +g+  ++++H+
  gene1451|gene1451|rna1450|rna1450 179 PIGEGSefaDILWGD--------PYEGKGFQPSPRGSGYLYGEDVVIRFLELNGLTSIVRSHQ 233
                                        ****99*********........77788888888****************************7 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   3.5e-07    0.0031      22      43 ..      14      35 ..       6      36 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.5e-07
                          STPPase_N 22 LseaEIrqlCakareiFLsQPt 43
                                       Lse EI+ +C+k+ ei++s+P+
  gene1451|gene1451|rna1450|rna1450 14 LSEVEIQDICNKVSEILISEPN 35
                                       99*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1934.35
//
Query:       gene1452|gene1452|rna1451|rna1451  [L=262]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00029   20.7   0.7    0.00044   20.1   0.7    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
     0.0054   16.5   0.2      0.011   15.5   0.2    1.4  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.26   11.6   0.0    1.4  1  PPP5             PPP5 TPR repeat region


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.7   7.3e-08   0.00044      14      99 ..     142     224 ..     126     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.3e-08
                                        HHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHT.SSCETTEEEEEEE--BHHHHHH CS
                    dCMP_cyt_deam_1  14 aakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaakng.gsklegatlyvtlePCsmCaka 88 
                                        + k+  k   +  G +i+ +g++    ++ + +      H+ +  i ++ k + ++  +g   ++  ePC +C++a
  gene1452|gene1452|rna1451|rna1451 142 EVKTR-KNAPICCGTCIIADGKRALSIHEDTDNIL---GHSILKGIEEISKAQiSYLCTGLDAFIFREPCLSCSMA 213
                                        33333.44555566677775555444444444344...5999********99889999****************** PP

                                        HHHHT-SEEEE CS
                    dCMP_cyt_deam_1  89 iiqsgikkvvv 99 
                                        +++ +ik+v++
  gene1452|gene1452|rna1451|rna1451 214 LVHGRIKRVFC 224
                                        *********97 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.9e-06     0.011      57     114 ..     182     240 ..     142     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-06
                        MafB19-deam  57 alqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks.lnkLkvke 114
                                         ++  +k+ +s    ++  ++ +epC  C  a+v +++k++       k+  ++Lk++ 
  gene1452|gene1452|rna1451|rna1451 182 GIEEISKAQISYLCTGLDAFIFREPCLSCSMALVHGRIKRVFCINRVSKGaFSSLKINY 240
                                        5555556666666777778999*******************988887777777777753 PP

>> PPP5  PPP5 TPR repeat region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.26      21      86 ..      91     165 ..      75     169 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                               PPP5  21 ekesasetldlesie..veksYdG.....prLe..eeeekitqeFvkamierfkkgkklhkkyvyaillkvkell 86 
                                        + +s++et+++ + +   +++Y       p ++  +++e+++ e++k+mie++k+ k+ +  +   i+ + k++l
  gene1452|gene1452|rna1451|rna1451  91 DPVSLIETVSVPKYQplTDAQYIEstalwPCIRssRTTEELNIEYIKTMIEEVKTRKNAPICCGTCIIADGKRAL 165
                                        555555555544433223333433222224455556677999***************998888777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1692.72
//
Query:       gene1453|gene1453|rna1452|rna1452  [L=383]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   5.5e-126  420.5   3.8   6.4e-126  420.3   3.8    1.0  1  Ribosomal_L3  Ribosomal protein L3
  ------ inclusion threshold ------
       0.65   10.0   0.1       0.65   10.0   0.1    2.9  3  DUF1639       Protein of unknown function (DUF1639)


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.3   3.8  7.1e-130  6.4e-126       1     369 []       1     357 [.       1     357 [. 0.94

  Alignments for each domain:
  == domain 1  score: 420.3 bits;  conditional E-value: 7.1e-130
                                        XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEE.CHHTTSCCCCCEEEEE CS
                       Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVre.vdkpgskldkkevvea 75 
                                        ms rkf+aprhgsl f prkR++  r+ + +fP+dd+s+pv+lt+f+GyKaGmth++r+ ++ +  k+  +ev++a
  gene1453|gene1453|rna1452|rna1452   1 MSCRKFSAPRHGSLQFCPRKRSKTIRPSAGAFPADDSSQPVHLTGFMGYKAGMTHVIRTkIQAAKNKQLSREVMDA 76 
                                        999******************************************************9626667788889****** PP

                                        EEEEEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHH CS
                       Ribosomal_L3  76 vtvvetppmvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadle 151
                                        vtv+e ppmv+ gvvgy+ t  Glr l  v a  +s+ v rr++ n +  +       sk++     ++  e  ++
  gene1453|gene1453|rna1452|rna1452  77 VTVLEAPPMVVYGVVGYERTVTGLRRLPIVLAPYVSDGVLRRMFGNKHVERE-----NSKRF---CASEETESRIS 144
                                        *******************************************998765543.....34444...23344566799 PP

                                        HHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE--- CS
                       Ribosomal_L3 152 eikkeasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGk 227
                                        eikk+a  vrv++ t+ + +k l  Kkah+ EiqvngG+i+ek+++  ++lek +++ +vF+++e iDvigvtkGk
  gene1453|gene1453|rna1452|rna1452 145 EIKKKAECVRVLVQTQPGLIKKLGLKKAHIAEIQVNGGSISEKVEWCLDMLEKEIHIGEVFKENENIDVIGVTKGK 220
                                        **************************************************************************** PP

                                        EEE-HHHHCT----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT. CS
                       Ribosomal_L3 228 GfeGvvkRWgvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdl 303
                                        Gf+G+vkR+gv+k+prk  +g Rkva+igaw+p+rV+++varaGq+G+h+Rte nk++y +g+   + + +tefdl
  gene1453|gene1453|rna1452|rna1452 221 GFQGTVKRFGVRKQPRKSRKGIRKVACIGAWHPSRVMYSVARAGQMGFHRRTEKNKRVYMVGN--GNSSIRTEFDL 294
                                        ***************************************************************..556789***** PP

                                        SS..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                       Ribosomal_L3 304 tekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                        tek i+PmGGf+hyGevkndfi+vkG+v+Gp+kr+v+lrksl  q   +  ee+  kf+dt+sk g
  gene1453|gene1453|rna1452|rna1452 295 TEKFISPMGGFPHYGEVKNDFIMVKGAVVGPRKRVVTLRKSLDQQ---RPSEELVIKFVDTSSKIG 357
                                        *****************************************9754...6678888********976 PP

>> DUF1639  Protein of unknown function (DUF1639)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.12   1.1e+03      22      30 ..      18      26 ..      16      28 .. 0.89
   2 ?   -1.6   0.8       0.3   2.7e+03      17      29 ..     233     245 ..     229     247 .. 0.70
   3 ?   10.0   0.1   7.3e-05      0.65       5      42 ..     310     345 ..     308     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.12
                            DUF1639 22 PKKRpknVq 30
                                       P+KR+k+++
  gene1453|gene1453|rna1452|rna1452 18 PRKRSKTIR 26
                                       9*****985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.3
                            DUF1639  17 kpprRPKKRpknV 29 
                                        k pr+++K  + V
  gene1453|gene1453|rna1452|rna1452 233 KQPRKSRKGIRKV 245
                                        6778888866655 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 7.3e-05
                            DUF1639   5 EieeDflamtGkkpprRPKKRpknVqkqldslfPGlwL 42 
                                        E+++Df++++G      P+KR  +++k+ld+  P   L
  gene1453|gene1453|rna1452|rna1452 310 EVKNDFIMVKGAVVG--PRKRVVTLRKSLDQQRPSEEL 345
                                        9**********9998..*************98887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2500.38
//
Query:       gene1454|gene1454|rna1453|rna1453  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-20   71.5   2.8    4.7e-20   71.1   2.8    1.2  1  zf-CSL         CSL zinc finger
  ------ inclusion threshold ------
      0.015   15.2   0.6      0.032   14.2   0.2    1.7  2  zinc_ribbon_4  zinc-ribbon domain
      0.015   15.5   0.1      0.025   14.7   0.1    1.4  1  zf-RING_7      C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   2.8   7.8e-24   4.7e-20       1      58 [.      31      84 ..      31      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 7.8e-24
                                       EEEEGGGSEEETTTTEEEEEETTSSEEEEEHHHHHTT....--EEEETTSSEEEEEE- CS
                             zf-CSL  1 develedfefdeeeesyyypCRCgdeFelteedleegaegaevvvqCssCSLwikVkf 58
                                       dev++++f++++e+ ++yypC+Cgd Fe+++edl++g    evv++C+sCSL+i  ++
  gene1454|gene1454|rna1453|rna1453 31 DEVDIKEFKYSKEDRTFYYPCPCGDSFEISLEDLKNG----EVVARCPSCSLIICTVY 84
                                       89***********************************....*************8776 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   5.3e-06     0.032       8      32 ..      53      77 ..      51      80 .. 0.93
   2 ?   -2.2   0.0      0.68     4e+03      10      16 ..      82      88 ..      82      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-06
                      zinc_ribbon_4  8 CkakyeiddeklpakgvkvrCskCg 32
                                       C+  +ei+ e l+ + v +rC+ C+
  gene1454|gene1454|rna1453|rna1453 53 CGDSFEISLEDLKNGEVVARCPSCS 77
                                       99**********************7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.68
                      zinc_ribbon_4 10 akyeidd 16
                                       ++ye++d
  gene1454|gene1454|rna1453|rna1453 82 TVYEVED 88
                                       79***98 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   4.2e-06     0.025      14      30 ..      61      77 ..      60      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-06
                                       HHHHCCSTB-EE-TTT- CS
                          zf-RING_7 14 lselragdevvtCpeCG 30
                                       l +l++g++v++Cp+C+
  gene1454|gene1454|rna1453|rna1453 61 LEDLKNGEVVARCPSCS 77
                                       6799************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 675.44
//
Query:       gene1455|gene1455|rna1454|rna1454  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-16   60.1   7.3    2.1e-16   60.1   7.3    2.8  2  DFRP_C      DRG Family Regulatory Proteins, Tma46
      3e-05   23.9   0.6      3e-05   23.9   0.6    2.0  2  zf_CCCH_4   Zinc finger domain
    0.00019   21.2   0.1    0.00019   21.2   0.1    2.1  3  zf-CCCH     Zinc finger C-x8-C-x5-C-x3-H type (and similar)
     0.0032   17.9   1.2     0.0032   17.9   1.2    2.4  2  zf-CCCH_2   RNA-binding, Nab2-type zinc finger
     0.0069   16.8   1.3     0.0069   16.8   1.3    2.2  2  Fcf2        Fcf2 pre-rRNA processing
  ------ inclusion threshold ------
      0.064   14.0   5.9       0.16   12.7   2.9    2.6  2  Torus       Torus domain
       0.17   11.6  18.0      0.046   13.5   5.7    2.2  2  Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein


Domain annotation for each model (and alignments):
>> DFRP_C  DRG Family Regulatory Proteins, Tma46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -9.3  12.3         7   1.8e+04      36      66 ..      16      49 ..       1      67 [. 0.39
   2 !   60.1   7.3   8.4e-20   2.1e-16       1      80 [.     159     236 ..     159     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: -9.3 bits;  conditional E-value: 7
                             DFRP_C 36 ekkeaeeekeekkkkke...glsGrelfefnpel 66
                                        kke ee++   k+kk+    l   e ++ +++l
  gene1455|gene1455|rna1454|rna1454 16 MKKELEEKAFGLKNKKQkaaILKQIESLNLKEQL 49
                                       3333333332222111122323333333333333 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 8.4e-20
                             DFRP_C   1 kitLEefiEteRakLdkklTpvtletFakWKkkrlekkeaeeekeekkkkkeglsGrelfefnpelaedddeeeee 76 
                                        +++LEe+iE  R+ L +klTp+t+etF++WK++++++++++++k  k+ ++ g  G elfe++ el++dd+e+ee 
  gene1455|gene1455|rna1454|rna1454 159 ELSLEEYIELSRQSLPEKLTPLTEETFKQWKARKQKEEKEHARKV-KALAT-GPKGVELFETRRELFKDDEEAEEL 232
                                        69******************************9988887777773.33333.68*******************998 PP

                             DFRP_C  77 eeee 80 
                                        +++e
  gene1455|gene1455|rna1454|rna1454 233 DYTE 236
                                        7655 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.6   1.2e-08     3e-05       1      19 []      80      98 ..      80      98 .. 0.99
   2 ?   -1.8   0.1       1.4   3.6e+03      13      17 ..     136     140 ..     134     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.2e-08
                          zf_CCCH_4  1 CkfflqGtCkkGdkCrFaH 19
                                       C +fl+ +C+ Gd+C+FaH
  gene1455|gene1455|rna1454|rna1454 80 CINFLNKMCTDGDACKFAH 98
                                       9****************** PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                          zf_CCCH_4  13 dkCrF 17 
                                         kC+F
  gene1455|gene1455|rna1454|rna1454 136 WKCPF 140
                                        58998 PP

>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   7.6e-08   0.00019       1      27 []      75     100 ..      75     100 .. 0.92
   2 ?   -3.6   0.1       4.7   1.2e+04       4       8 ..     118     122 ..     117     122 .. 0.47
   3 ?   -3.2   0.8       3.5   8.9e+03      15      21 ..     138     143 ..     137     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.6e-08
                                        -HCHCBCHHHHHS--TTGGG-SSBSCS CS
                            zf-CCCH   1 yktelCrffmrtGyCkyGdrCkFaHgq 27 
                                        +kt  C +f+    C  Gd+CkFaHg+
  gene1455|gene1455|rna1454|rna1454  75 PKTIQCINFLN-KMCTDGDACKFAHGE 100
                                        58899******.*************96 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.7
                                        HCBCH CS
                            zf-CCCH   4 elCrf 8  
                                        ++C+f
  gene1455|gene1455|rna1454|rna1454 118 RICQF 122
                                        45553 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.5
                                        -TTGGG- CS
                            zf-CCCH  15 CkyGdrC 21 
                                        C++ ++C
  gene1455|gene1455|rna1454|rna1454 138 CPF-PKC 143
                                        777.666 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.2   1.2e-06    0.0032       1      18 []      79      99 ..      79      99 .. 0.97
   2 ?   -0.6   1.1      0.83   2.1e+03      11      15 ..     135     140 ..     133     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.2e-06
                          zf-CCCH_2  1 pCrffpn..C.tnpkCpFaHP 18
                                       +C +f n  C  ++ C+FaH+
  gene1455|gene1455|rna1454|rna1454 79 QCINFLNkmCtDGDACKFAHG 99
                                       8*******************6 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.83
                          zf-CCCH_2  11 p.kCpF 15 
                                        + kCpF
  gene1455|gene1455|rna1454|rna1454 135 DwKCPF 140
                                        557777 PP

>> Fcf2  Fcf2 pre-rRNA processing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   1.3   2.7e-06    0.0069       2      52 ..      17      66 ..      16     112 .. 0.75
   2 ?   -0.0   0.1      0.47   1.2e+03      17      43 ..     177     203 ..     161     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-06
                               Fcf2  2 kktagkkWfnlpkteltpelkrdlqlLklrnvldpkrfyKkedkkkklPky 52
                                       kk+ ++k f+l++++   ++ ++++ L+l++ l++k+ +K+e+ kk++P +
  gene1455|gene1455|rna1454|rna1454 17 KKELEEKAFGLKNKKQKAAILKQIESLNLKEQLEKKERMKREE-KKNVPVK 66
                                       67778888**********************************5.9999644 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.47
                               Fcf2  17 ltpelkrdlqlLklrnvldpkrfyKke 43 
                                        ltp  ++ ++  k r+  ++k++ +k 
  gene1455|gene1455|rna1454|rna1454 177 LTPLTEETFKQWKARKQKEEKEHARKV 203
                                        445555555555566666777777766 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.9   6.3e-05      0.16      44      92 ..      46      99 ..       1     113 [. 0.51
   2 ?    1.5   0.1      0.19   4.9e+02      19      45 ..     177     203 ..     166     242 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                                       S-----S----HHHH----HHH.....HSTT--B-HHHHHT--SSGGG-SSB-S CS
                              Torus 44 kskekaktrcnikkdsGytkad.....kekesyfClfFarGlCakGkkCeylHr 92
                                       k++ + k r++ ++++ +   +        +++ C+ F   +C+ G  C++ H 
  gene1455|gene1455|rna1454|rna1454 46 KEQLEKKERMKREEKKNVPVKQvipvgVDPKTIQCINFLNKMCTDGDACKFAHG 99
                                       2333333333333333322222112212456699*******************4 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.19
                                        --SSS-----TTSS----S-THHHHS- CS
                              Torus  19 keeqegeeyNiWynkwsgeekekkkks 45 
                                         ++ ++e++  W ++ ++eeke+++k 
  gene1455|gene1455|rna1454|rna1454 177 LTPLTEETFKQWKARKQKEEKEHARKV 203
                                        555556666666666664444444333 PP

>> Cwf_Cwc_15  Cwf15/Cwc15 cell cycle control protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   5.7   1.8e-05     0.046      42     100 ..       4      62 ..       2      87 .. 0.79
   2 ?    4.1   4.5     0.013        34      56     135 ..     158     246 ..     143     250 .] 0.48

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                                        TT--HHHHHHS-HHHHHHHHHHHHHHHHH------------------------------ CS
                         Cwf_Cwc_15  42 gqgteeelekrdlraeLeeaeaeakakkrkkaeleaeeeeekekkeeeeeeeeeeakrr 100
                                         q++++++++rd+++eLee+    k+kk+k+a l++ e+ + +++ e++e+ ++e+k++
  gene1455|gene1455|rna1454|rna1454   4 KQQETKQKSTRDMKKELEEKAFGLKNKKQKAAILKQIESLNLKEQLEKKERMKREEKKN 62 
                                        578889999*******************9988888888766666666666655555543 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
                                        HHHHHHHHHHHHHHH-------------------------------------............------------ CS
                         Cwf_Cwc_15  56 aeLeeaeaeakakkrkkaeleaeeeeekekkeeeeeeeeeeakrrkeellee..........areidaddedseee 121
                                         eL  +e  + ++++  ++l++ +ee+ ++ + +++++ee+++ rk ++l++          +re+ +dde+ ee 
  gene1455|gene1455|rna1454|rna1454 158 VELSLEEYIELSRQSLPEKLTPLTEETFKQWK-ARKQKEEKEHARKVKALATgpkgvelfetRRELFKDDEEAEEL 232
                                        45666666555555555555555544322222.2222233333333334444445555554356888887777665 PP

                                        -----..--------- CS
                         Cwf_Cwc_15 122 eeeee..eesdddsds 135
                                        + +e+  +  ++++++
  gene1455|gene1455|rna1454|rna1454 233 DYTERcyS--ESEDEE 246
                                        55544322..222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2414  (0.134642); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 1401.90
//
Query:       gene1456|gene1456|rna1455|rna1455  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-22   80.3   0.0    1.3e-22   80.1   0.0    1.1  1  Mei5_like  Putative double-strand recombination repair-like
  ------ inclusion threshold ------
      0.029   14.5   0.1      0.046   13.8   0.1    1.5  1  LZ3wCH     Leucine zipper with capping helix domain


Domain annotation for each model (and alignments):
>> Mei5_like  Putative double-strand recombination repair-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   1.4e-26   1.3e-22      60     117 ..       1      58 [.       1      59 [. 0.99

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.4e-26
                          Mei5_like  60 liekfkkknkdleeliekwkevieeciiiLkkefelkakevfkafdLkkygfdledyg 117
                                        ++++f++ +++le++ie+wke+i+eci+iL +++++++ e+fkaf L k+gfd+e+yg
  gene1456|gene1456|rna1455|rna1455   1 MMRQFRETHGNLESVIERWKECISECISILCNQYNIPPLEIFKAFPLRKWGFDIEEYG 58 
                                        99*******************************************************8 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.1e-06     0.046      12      47 ..      11      46 ..       2      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-06
                             LZ3wCH 12 kakeaanrWtdnifdikswikekfpkskkelneefg 47
                                       ++++ + rW+  i +++s  ++ +++ + e+++ f 
  gene1456|gene1456|rna1455|rna1455 11 NLESVIERWKECISECISILCNQYNIPPLEIFKAFP 46
                                       6677889**************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 415.92
//
Query:       gene1457|gene1457|rna1456|rna1456  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-25   87.7   0.2    1.2e-24   86.5   0.1    1.6  2  Cyclin_N  Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.085   12.8   0.0       0.23   11.4   0.0    1.7  1  IRS       PTB domain (IRS-1 type)


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.1   1.3e-28   1.2e-24      26     126 ..      21     122 ..       4     123 .. 0.93
   2 ?   -2.0   0.0       0.3   2.7e+03      46      59 ..     146     159 ..     134     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.3e-28
                                        S-H.HHHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHH CS
                           Cyclin_N  26 lnp.emRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvy 100
                                        +++ ++R+ l++wl ev   f  ++ t+ +av +ld++ +++ +   k qlvg+++L+l+aK+ee ++  +ed+v+
  gene1457|gene1457|rna1456|rna1456  21 IHKsSHRRKLVKWLYEVMDDFGYSQVTFSTAVFILDKYTETRGLDLGKYQLVGISALFLSAKIEEKRCKGIEDYVH 96 
                                        445599********************************************************************** PP

                                        HTTTSS-HHHHHHHHHHHHHHTTT-- CS
                           Cyclin_N 101 itdeafteeeilemErliLetLnfdl 126
                                        +td+++++eeil+ E ++Le + f+l
  gene1457|gene1457|rna1456|rna1456  97 VTDNTYSKEEILDKEVEMLEIFGFNL 122
                                        ************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.3
                                        T--TTHHHHHHHHH CS
                           Cyclin_N  46 kltpetlflavnyl 59 
                                        k ++e++f+a +y+
  gene1457|gene1457|rna1456|rna1456 146 KQSQEIFFCAFSYV 159
                                        44689999999885 PP

>> IRS  PTB domain (IRS-1 type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.6e-05      0.23      28      63 ..      12      49 ..       6      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                                       E-SSBEE-..-SSSS---SS--BGGG---EEEETTEEE CS
                                IRS 28 ltseeltL..kkeekrkelvswplttlRryGrdkslFs 63
                                       ++++++ L  +k+++r++lv+w ++ +  +G+++ +Fs
  gene1457|gene1457|rna1456|rna1456 12 VSRKNIKLtiHKSSHRRKLVKWLYEVMDDFGYSQVTFS 49
                                       5666666665999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1528.61
//
Query:       gene1458|gene1458|rna1457|rna1457  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-70  236.0   0.0    5.4e-70  235.7   0.0    1.1  1  E1_dh           Dehydrogenase E1 component
    9.1e-05   22.3   0.1    0.00018   21.3   0.1    1.6  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.21   10.8   0.0    1.4  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
       0.17   11.7   0.3       0.38   10.5   0.1    1.6  2  DUF2857         Protein of unknown function (DUF2857)


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.0   1.2e-73   5.4e-70       2     296 ..      45     339 ..      43     343 .. 0.95

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 1.2e-73
                                        HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T CS
                              E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv 77 
                                        +++ +r + + +d++yk+k ++gf+hls+gqe +  + ++ l+ +D++i++YR++g  ++ g +  eil e+ gk+
  gene1458|gene1458|rna1457|rna1457  45 QMMKIRLTDEIMDREYKEKSIRGFCHLSIGQEGIYAALEHELD-GDMVISSYRCHGLAYVTGCKTLEILGEVLGKQ 119
                                        56677777777889***********************999995.8******************************* PP

                                        ....TTSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHH........HHTS---EEEEEEGGGTT-HHHH CS
                              E1_dh  78 ....kgkggsrhelmyaekesrilggngivgaqvplvaGialaak........iegkkevailliGDgAanqGdvy 141
                                            kgkggs+h l+  +++  ++gg+givgaqvpl+ Gi +a k         ++ ++v+ +++GDgAanqG+v+
  gene1458|gene1458|rna1457|rna1457 120 agvcKGKGGSMH-LY--NRN--FFGGHGIVGAQVPLGLGISYALKykgrllqdRDQGNRVCYAFYGDGAANQGQVW 190
                                        ************.88..666..***********************999999998999******************* PP

                                        HHHHHHHHTT--EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT-- CS
                              E1_dh 142 ealnlaalwklpvifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgp 217
                                        e++n+a +w+lp++fv+eNN+yg+ T+ae  s  ++++   rg  +pg+r+  n ++   ++ + A+++ +e kgp
  gene1458|gene1458|rna1457|rna1457 191 ESFNMAMIWRLPIVFVCENNRYGMWTSAESISTDTNFYL--RGGTMPGIRIAHNNIFGLISVLRYARRYSSE-KGP 263
                                        ***************************************..****************************988.*** PP

                                        EEEEEEE--SS-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHH CS
                              E1_dh 218 llielvtYRyggHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaes 293
                                        +++ + tYR+  Hs+ D+  +yr++ e+++ rk+ d+++  +++L +  + s+ee ++i+++v +eve  v+ a++
  gene1458|gene1458|rna1457|rna1457 264 IIVQIDTYRLCTHSTADERESYRAKGEIDNERKN-DCMEDTRNRLLA--FCSREEIDAIKDRVLEEVERDVDTAKK 336
                                        *********************************9.**********96..89***********************99 PP

                                        S-- CS
                              E1_dh 294 kke 296
                                        +k 
  gene1458|gene1458|rna1457|rna1457 337 SKP 339
                                        875 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   3.9e-08   0.00018      20      90 ..     136     218 ..     124     268 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.9e-08
                                        EEECETTTS-TTTHHHHHHHHHHH............STTSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE CS
                       TPP_enzyme_C  20 syltsgglgtmGyglpaAiGakla............kpdrevvaivGDGgflmi..lqelatavrrnlpitvvvln 81 
                                        +++  gg+g  G ++p ++G++ a            + +r  +a+ GDG+       + +  a+  +lpi++v+ n
  gene1458|gene1458|rna1457|rna1457 136 NFF--GGHGIVGAQVPLGLGISYAlkykgrllqdrdQGNRVCYAFYGDGAANQGqvWESFNMAMIWRLPIVFVCEN 209
                                        444..5****************94455566677653347999********76666456677777778999999998 PP

                                        -SBCCCHHH CS
                       TPP_enzyme_C  82 Negygmtgg 90 
                                        N++ + t  
  gene1458|gene1458|rna1457|rna1457 210 NRYGMWTSA 218
                                        886555544 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.7e-05      0.21     117     182 ..     148     221 ..     136     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.7e-05
                     DXP_synthase_N 117 isaalGlavardlkge........kkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknvGal 182
                                        +  +lG++ a ++kg+        ++ + a  GDga   G  +e++n +   +  ++ +  +N+  + ++  ++
  gene1458|gene1458|rna1457|rna1457 148 VPLGLGISYALKYKGRllqdrdqgNRVCYAFYGDGAANQGQVWESFNMAMIWRLPIVFVCENNRYGMWTSAESI 221
                                        5567777777666665555555446788899**************************99999998766655555 PP

>> DUF2857  Protein of unknown function (DUF2857)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   8.5e-05      0.38      10      57 ..       8      52 ..       5      64 .. 0.79
   2 ?   -2.9   0.0       1.1   4.9e+03      25      42 ..     311     328 ..     305     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.5e-05
                            DUF2857 10 ellkeGdlrrceelGfseeeldaLkqlsledlhalsnsrvsvlkvsvd 57
                                       ++ ++G l+ ++++G+++ee+d  ++l+++++ ++ ++   ++k+++ 
  gene1458|gene1458|rna1457|rna1457  8 HCDAQGILNSIQTHGITKEEIDIVQKLEVDEMVYIYKQ---MMKIRLT 52
                                       5557899999**********************999954...4445555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.1
                            DUF2857  25 fseeeldaLkqlsledlh 42 
                                        +s+ee+da+k   le+++
  gene1458|gene1458|rna1457|rna1457 311 CSREEIDAIKDRVLEEVE 328
                                        688999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2390.15
//
Query:       gene1459|gene1459|rna1458|rna1458  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1364.48
//
Query:       gene1460|gene1460|rna1459|rna1459  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.037   13.7   0.3       0.17   11.5   0.0    1.9  2  FAM176       FAM176 family


Domain annotation for each model (and alignments):
>> FAM176  FAM176 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.4e-06      0.17      23      54 ..      83     114 ..      74     125 .. 0.89
   2 ?   -0.2   0.1     0.041   7.3e+02      29      53 ..     162     183 ..     134     202 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.4e-06
                             FAM176  23 aLlFvlgvcvGLlltLcllviriscrkdlerl 54 
                                         L+F++g+ + L+l  +ll iris+++d++r+
  gene1460|gene1460|rna1459|rna1459  83 RLYFITGIFLFLMLITMLLYIRISYQSDVSRQ 114
                                        69*************************99854 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.041
                             FAM176  29 gvcvGLlltLcllviriscrkdler 53 
                                        ++c+ L l L+l  iri+ + ++e+
  gene1460|gene1460|rna1459|rna1459 162 SLCLNL-LNLIL--IRIAVSINIET 183
                                        444443.33444..44444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1449.67
//
Query:       gene146|gene146|rna146|rna146  [L=405]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-20   71.6   1.1      2e-06   28.4   0.0    4.3  4  WD40          WD domain, G-beta repeat
    4.3e-16   59.0   6.9    4.3e-16   59.0   6.9    1.8  2  Sof1          Sof1-like domain
    1.5e-08   34.8   0.0        1.2    9.5   0.0    4.4  4  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
     0.0094   14.5   0.1      0.072   11.6   0.1    2.1  2  Cytochrom_D1  Cytochrome D1 heme domain
  ------ inclusion threshold ------
      0.038   13.9   0.0       0.22   11.4   0.0    2.0  1  eIF2A         Eukaryotic translation initiation factor eIF2A
       0.11   11.4   0.0       0.96    8.3   0.0    2.0  2  Ge1_WD40      WD40 region of Ge1, enhancer of mRNA-decapping 


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0002      0.61      13      38 .]      59      94 ..      53      94 .. 0.69
   2 ?   -1.1   0.1       1.4   4.1e+03      14      28 ..     222     237 ..     209     245 .. 0.55
   3 !   28.4   0.0   6.5e-10     2e-06       3      38 .]     254     290 ..     252     290 .. 0.94
   4 !   27.4   0.2   1.4e-09   4.2e-06      10      38 .]     306     333 ..     299     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                   EEEEEEETTSSE..........EEEEETTSEEEEEE CS
                           WD40 13 vtslafspdgaw..........lasGsdDgtvriWd 38
                                   +t+l+++++g            +asGs D+ v +Wd
  gene146|gene146|rna146|rna146 59 ITALSYHKEGIHllarhfqqplFASGSFDNQVVLWD 94
                                   5666655555554444444443889**********9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                    EEEEEETTSSEE.EEE CS
                           WD40  14 tslafspdgawl.asG 28 
                                    ++++fsp    + +sG
  gene146|gene146|rna146|rna146 222 NDISFSPMDGHIfVSG 237
                                    3444555444431455 PP

  == domain 3  score: 28.4 bits;  conditional E-value: 6.5e-10
                                    EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    + ++++GH + v s+ f+p g+ +a+Gs D+t+ri+d
  gene146|gene146|rna146|rna146 254 PSGIYRGHgNAVVSVEFNPPGTEIATGSFDKTIRIFD 290
                                    6789****98899**********************98 PP

  == domain 4  score: 27.4 bits;  conditional E-value: 1.4e-09
                                    SSSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  10 HssvtslafspdgawlasGsdDgtvriWd 38 
                                    H +v ++++s+d+++++sGsdDg++r+W+
  gene146|gene146|rna146|rna146 306 H-NVFGVKYSHDSQFIVSGSDDGSIRVWK 333
                                    6.699***********************6 PP

>> Sof1  Sof1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.8   8.4e+03      56      74 ..      11      29 ..       4      41 .. 0.52
   2 !   59.0   6.9   1.4e-19   4.3e-16       2      70 ..     335     403 ..     334     405 .] 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.8
                           Sof1 56 emkeaekrKeenrrkhskk 74
                                   e++ +e++K+   +  +k+
  gene146|gene146|rna146|rna146 11 EEICKERKKDVEYMSFAKD 29
                                   4444555555555555544 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 1.4e-19
                           Sof1   2 kAseklgvlsaReraaleyreaLkekykhmpeikrIarhRhvPkaikkakkekremkeaekrKeenrrk 70 
                                     As+klg+ls +e+ al+y+e Lkekyk++ ei rI++hR +Pk++k++ k+  e ++a++rK++ r+ 
  gene146|gene146|rna146|rna146 335 YASKKLGPLSRKEKDALRYSEILKEKYKEVGEISRISKHRFLPKPLKNTLKTIYESHKARERKRKARES 403
                                    59*************************************************************998865 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0083        25      35      81 ..      63     109 ..      41     117 .. 0.79
   2 ?    4.8   0.0     0.011        34      58      82 ..     197     221 ..     190     240 .. 0.85
   3 !    9.4   0.0   0.00043       1.3      36      75 ..     260     299 ..     255     305 .. 0.88
   4 !    9.5   0.0   0.00039       1.2      38      79 ..     305     346 ..     300     356 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0083
                    ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                    + +++ ++ La + +  l+a +  d++v l d  +  v++ ++++s+
  gene146|gene146|rna146|rna146  63 SYHKEGIHLLARHFQQPLFASGSFDNQVVLWDLGQRSVLRRFECNSS 109
                                    56677888899999999***************************987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                    ANAPC4_WD40  58 sdgevrlldaesgkvvhslsvksek 82 
                                    ++g ++l+d+  gkvvhs+sv+s++
  gene146|gene146|rna146|rna146 197 EQGGLSLFDIRVGKVVHSVSVGSKT 221
                                    578899**************99874 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00043
                    ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhs 75 
                                    ++++ v s++++p g+ +a +  d ++r++d+++ k   +
  gene146|gene146|rna146|rna146 260 GHGNAVVSVEFNPPGTEIATGSFDKTIRIFDVNERKSRDT 299
                                    57899***************************99887655 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.00039
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvk 79 
                                     ++v ++++++d ++++ + +dg++r+ +++  k +  ls k
  gene146|gene146|rna146|rna146 305 MHNVFGVKYSHDSQFIVSGSDDGSIRVWKSYASKKLGPLSRK 346
                                    567899************************999877666555 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   2.4e-05     0.072      13      95 ..     157     238 ..     145     245 .. 0.86
   2 ?   -0.0   0.0     0.083   2.5e+02     299     347 ..     247     293 ..     240     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                                    GGTEEEEEETTT-SEEEEEE-STTEEEEEE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEEEEE-.-TTSEE CS
                   Cytochrom_D1  13 dagkvalldgdskeilavletgyalHisrvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnarsvavS.qddryv 91 
                                       ++++ d ++  + +++ t+y l is         +  +g  g+++l+D+   ++v+ v +G+ +  +  S  d++  
  gene146|gene146|rna146|rna146 157 TSRSIEIFDIERDFSKQQMSTRYPLCISTSAVL--TSIIGVGEQGGLSLFDIRVGKVVHSVSVGSKTNDISFSpMDGHIF 234
                                    56789999999999***********88865444..558999********************************9999998 PP

                                    EEEE CS
                   Cytochrom_D1  92 ivgn 95 
                                    + gn
  gene146|gene146|rna146|rna146 235 VSGN 238
                                    8887 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.083
                                    ETTBT-EEE-HHHHHT--EEEEEE-TTSSEEEEEEE--SSEEEEEETTT CS
                   Cytochrom_D1 299 DkktlekvltlaesaglkvvhvEfnkdGdevwlSvwdgkdalvvyDdkt 347
                                    D + l+    +  + g +vv vEfn  G+e+     d+   + ++D + 
  gene146|gene146|rna146|rna146 247 DIRYLHEPSGIYRGHGNAVVSVEFNPPGTEIATGSFDKT--IRIFDVNE 293
                                    55555555566677788899*******999977766655..66666555 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.3e-05      0.22      52     162 ..     213     324 ..     197     336 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.3e-05
                                    EECCEESSS.EEEEEE-TTSS-EEEEESSSSCEEEEEECS.CEEEEEEEEES--E...EEE-TTSSEEEEE-TTSSS-EE CS
                          eIF2A  52 evvelkkegpihdvaWspkskefaviyGkmpakvslfdlk.vkviskleeqkrNt...iffspkgklvllaGfgnlaGel 127
                                    ++v++  +    d++ sp   ++  + G+ + +++l+d + ++  s + + + N+   + f+p g+ ++++ f  +   +
  gene146|gene146|rna146|rna146 213 HSVSVGSK--TNDISFSPMDGHIF-VSGNEDFCTYLHDIRyLHEPSGIYRGHGNAvvsVEFNPPGTEIATGSFDKT---I 286
                                    44555444..57888888766654.689999999999998766666777777776111579************999...6 PP

                                    EEEETT...TTEEEEEEE-TT--EEEE-TTSSEEEEEE CS
                          eIF2A 128 eiwdvk...kkkkiakaeaanatlvewspdgryvlTat 162
                                     i+dv+   +++++ + +  n   v++s d+++++  +
  gene146|gene146|rna146|rna146 287 RIFDVNerkSRDTYYNKRMHNVFGVKYSHDSQFIVSGS 324
                                    6666663226677888888999999*******999765 PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00032      0.96     188     221 ..     263     296 ..     251     308 .. 0.83
   2 ?    0.8   0.0     0.062   1.8e+02     190     220 ..     308     338 ..     295     347 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00032
                       Ge1_WD40 188 sliveaafspdGtalatasedGevkffqvylede 221
                                      +v+  f p Gt +at s d +++ f v+  ++
  gene146|gene146|rna146|rna146 263 NAVVSVEFNPPGTEIATGSFDKTIRIFDVNERKS 296
                                    4789999**********************97765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.062
                       Ge1_WD40 190 iveaafspdGtalatasedGevkffqvyled 220
                                    +    +s d   +   s dG ++ ++ y ++
  gene146|gene146|rna146|rna146 308 VFGVKYSHDSQFIVSGSDDGSIRVWKSYASK 338
                                    66778999999**************999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2709.83
//
Query:       gene1461|gene1461|rna1460|rna1460  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-17   61.5   0.0      1e-16   61.2   0.0    1.1  1  Peptidase_C13  Peptidase C13 family


Domain annotation for each model (and alignments):
>> Peptidase_C13  Peptidase C13 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   5.8e-21     1e-16       1     177 [.      15     183 ..      15     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 5.8e-21
                                        EEEEEEE---SGGGHHHHHHHHHHHHHHHCTT--GGGEEEEE---.STT-TT-SSTT--BSSTT--B-STT--ESB CS
                      Peptidase_C13   1 lyavlvAGsngydnyrhqadvchayqllkkkglkdenivvvmydD.iaereenPlagkiinkpkgedvykgvkidY 75 
                                        +ya+l+  s+g++nyrh a+v+  y++lk++g++d++i ++ y+  i + ++  ++g ++ + +++  y+     +
  gene1461|gene1461|rna1460|rna1460  15 NYAILLNSSRGFHNYRHMANVYIFYNVLKENGFEDDQILIISYENqIQDVRNVDREG-VYIDEDRRIPYSE----F 85 
                                        69******************************************9888888888888.6666666666655....8 PP

                                        EGGG-SHHHHHHHHHT-TCGTT-------TTSEEEEEEES-EETTEEE-SSSSEEEHHHHHHHHHHHHHCT--SEE CS
                      Peptidase_C13  76 tgkkvtkenflavllGdksvgsgkvlksgkeDnvfiyltdhGapgvlevpeeddleakdLaeaLkkmhakkkykkl 151
                                        + ++ + e+ l+ ++G+      k+ +  ++ nvf+yl+ hG + +l++ +   ++ +dL++ + k+  +    k+
  gene1461|gene1461|rna1460|rna1460  86 RPSASALEDLLNAISGNCP----KLKDADESSNVFVYLNGHGNETFLKFGNIRFMTKDDLMSRIPKLAGRVG--KV 155
                                        9899999999*******96....666889999********************************99987766..9* PP

                                        EEEEESTTGGGGTTT..S-TTSSEEEEE CS
                      Peptidase_C13 152 viyleaceSgsmfee..llkdinvyalt 177
                                        +++l++c++  +++   l+++  ++a++
  gene1461|gene1461|rna1460|rna1460 156 LLVLDTCQADALVDRdaLPDNVFIVATS 183
                                        *************987677766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1541.52
//
Query:       gene1462|gene1462|rna1461|rna1461  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.011   15.5  11.3      0.011   15.5  11.3    1.7  2  TACC_C         Transforming acidic coiled-coil-containing pro
      0.019   14.8   4.4       0.05   13.4   4.4    1.7  1  Band_3_cyto    Band 3 cytoplasmic domain
        0.2   12.2   7.0      0.088   13.4   2.6    2.4  2  ING            Inhibitor of growth proteins N-terminal histon
        1.5    8.7   7.8       0.12   12.2   1.9    2.0  2  Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
        2.2    8.5  16.8      0.027   14.7   7.9    2.3  3  Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
        3.1    8.5   7.4        9.2    7.0   0.2    2.6  2  SlyX           SlyX


Domain annotation for each model (and alignments):
>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.2   3.6e+03     113     135 ..     115     138 ..     104     145 .. 0.58
   2 ?   15.5  11.3   3.8e-06     0.011       2     111 ..     171     285 ..     170     288 .] 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                             TACC_C 113 eslkkcaeeylarvkk.eeqRYqa 135
                                        e+ ++ ++ey + v +   qRY++
  gene1462|gene1462|rna1461|rna1461 115 EASRRNVSEYQEVVPNiSRQRYEE 138
                                        444555555555553314566654 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.8e-06
                             TACC_C   2 sqkdldaalekvkeeveekeeeiqelkkkveelkkenq.....emkkivaefektiaqlieekqkqkelakkeiqk 72 
                                        +++++ +a++ ++e+++ k++ei  lk+k++ l+ + +       +  v + e++i  + ee +k++  + k+i +
  gene1462|gene1462|rna1461|rna1461 171 KEENMRKAIKIQEEDIQAKNQEILLLKEKISRLESKLEiegkeYVRGCVLRGEEAIRIVEEELKKERGDFLKKIGE 246
                                        5789**************************999887544343368999**************************** PP

                             TACC_C  73 vleekeqlladlnsveksfsdlfkryekqkevlegykkn 111
                                          e    ll  +  ++k +++l+++++ +k+ +eg ++ 
  gene1462|gene1462|rna1461|rna1461 247 EAEKTRMLLRRIDGLKKIINELVRKIREMKQKTEGSRRE 285
                                        *9999****************************997765 PP

>> Band_3_cyto  Band 3 cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.4   1.7e-05      0.05     138     185 ..     157     271 ..      68     281 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                        .........................................................................--S CS
                        Band_3_cyto 138 s...................................................................lsssleee 146
                                        s                                                                     +  eee
  gene1462|gene1462|rna1461|rna1461 157 SggggertqeiqiqkeenmrkaikiqeediqaknqeilllkekisrleskleiegkeyvrgcvlrgeeAIRIVEEE 232
                                        0222222222222222223333333333333333345777777788888999999999999999998756666777 PP

                                        STTGGGCCGGGS-TT-EEEEEEEEEETTSSS-EEEEEEE CS
                        Band_3_cyto 147 kkkkkekilkkipegaEatlvLvgevdfLerpviafvRL 185
                                         kk++  +lkki e+aE t +L+ ++d L++ +  +vR 
  gene1462|gene1462|rna1461|rna1461 233 LKKERGDFLKKIGEEAEKTRMLLRRIDGLKKIINELVRK 271
                                        8888899**************************999995 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.6     3e-05     0.088      31      99 ..     125     208 ..     118     209 .. 0.72
   2 ?    0.0   0.1      0.43   1.3e+03       9      29 ..     258     278 ..     230     286 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                                        HHHHHHH.HHHHHHHH.............TS..S-HHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                ING  31 qellkei.dskiekfl.............kngslqknekeeels.riqeelkeaqelldeKiqlaqqaldlvdkhl 91 
                                        qe++++i ++++e+ +              + s    e+ +e++ + +e++++a+++++e iq  +q   l+++++
  gene1462|gene1462|rna1461|rna1461 125 QEVVPNIsRQRYEEHMrkadcvskeykpgDEVSGGGGERTQEIQiQKEENMRKAIKIQEEDIQAKNQEILLLKEKI 200
                                        55555555555555555555555555465555555566666666667789************************** PP

                                        HHHHHCTX CS
                                ING  92 rrLdqdle 99 
                                        +rL+++le
  gene1462|gene1462|rna1461|rna1461 201 SRLESKLE 208
                                        ****9986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.43
                                        GGGHHHHHHHHHHHHHHHHHH CS
                                ING   9 venLPlelqrnltelreiDak 29 
                                        ++ L + +++++ ++re+ +k
  gene1462|gene1462|rna1461|rna1461 258 IDGLKKIINELVRKIREMKQK 278
                                        344444444444444444444 PP

>> Mt_ATP-synt_D  ATP synthase D chain, mitochondrial (ATP5H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.9   3.9e-05      0.12      33     126 ..     114     209 ..     104     214 .. 0.76
   2 ?   -1.3   0.4       0.6   1.8e+03      92     125 ..     230     263 ..     221     280 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                                        HHHHHHHHHHS-SS-----HHHHHHHSSSTTHHHHHHHHHHH--------TTTTHHHHHHH..HHHHHCHHHHHHH CS
                      Mt_ATP-synt_D  33 sdeylrrvaklPeelpkIdWayYkknvakeglVdeFekkYealkipypedkyteevdaeek..evkkeikefkees 106
                                        +++  r+v+++ e +p+I  + Y++ ++k+  V++  k  ++++    e +++ ++++ee+  ++ k  +e +++ 
  gene1462|gene1462|rna1461|rna1461 114 KEASRRNVSEYQEVVPNISRQRYEEHMRKADCVSKEYKPGDEVSGGGGERTQEIQIQKEENmrKAIKIQEEDIQAK 189
                                        5677899***********************9998777777777777777777777766554113344445566677 PP

                                        HHHHHHHHHHHHHHT-XXXX CS
                      Mt_ATP-synt_D 107 kkrieelekeleklksllpf 126
                                        +++i  l++++ +l+s l++
  gene1462|gene1462|rna1461|rna1461 190 NQEILLLKEKISRLESKLEI 209
                                        77777788888888876655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.6
                                        HHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                      Mt_ATP-synt_D  92 ekevkkeikefkeeskkrieelekeleklksllp 125
                                        e+e kke   f ++  ++ e+ ++ l +++ l++
  gene1462|gene1462|rna1461|rna1461 230 EEELKKERGDFLKKIGEEAEKTRMLLRRIDGLKK 263
                                        5666666666666666666666666655555544 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.89   2.7e+03     137     137 ..     114     114 ..      69     152 .. 0.50
   2 ?    4.9   1.9    0.0097        29      75     133 ..     163     214 ..     155     218 .. 0.67
   3 ?   14.7   7.9     9e-06     0.027      46     134 ..     187     280 ..     180     288 .] 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.89
                      Jnk-SapK_ap_N 137 h 137
                                        +
  gene1462|gene1462|rna1461|rna1461 114 K 114
                                        1 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0097
                      Jnk-SapK_ap_N  75 raeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkey 133
                                        r++e  +++e+++++  k  +e ++  ++e+  l+       +++srle+k + + key
  gene1462|gene1462|rna1461|rna1461 163 RTQEIQIQKEENMRKAIKIQEEDIQAKNQEILLLK-------EKISRLESKLEIEGKEY 214
                                        56666677777776666666666655555555555.......88888888876666665 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 9e-06
                      Jnk-SapK_ap_N  46 eeeeaeleelreeleqLeteyerekelrkrae.....eeleeiedqweeerkelqekveqleeenrelelkaknaa 116
                                        +++++e+ +l+e++++Le+++e e ++  r       e +  +e+++++er ++ +k+ +  e++r+l  +++ ++
  gene1462|gene1462|rna1461|rna1461 187 QAKNQEILLLKEKISRLESKLEIEGKEYVRGCvlrgeEAIRIVEEELKKERGDFLKKIGEEAEKTRMLLRRIDGLK 262
                                        7999***************99877766544323444499999********************************** PP

                      Jnk-SapK_ap_N 117 dqlsrleekeaelkkeys 134
                                        + +++l +k  e+k++ +
  gene1462|gene1462|rna1461|rna1461 263 KIINELVRKIREMKQKTE 280
                                        *********999965543 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.4     0.035     1e+02      14      40 ..     181     207 ..     165     214 .. 0.63
   2 ?    7.0   0.2    0.0031       9.2      31      61 ..     256     286 ..     254     288 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.035
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               SlyX  14 fqedtieeLndvvaeqqqqidrlqrql 40 
                                         qe+ i++ n+++    ++i+rl+ +l
  gene1462|gene1462|rna1461|rna1461 181 IQEEDIQAKNQEILLLKEKISRLESKL 207
                                        455555555555555555555555554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0031
                                        HHHHHHHHHHHHHHHT-XXXXXXXXXXXXXX CS
                               SlyX  31 qqidrlqrqlrllaerlkeleessgaseaee 61 
                                        ++id l++ +++l+++++e+++++++s++e+
  gene1462|gene1462|rna1461|rna1461 256 RRIDGLKKIINELVRKIREMKQKTEGSRRED 286
                                        6899*******************99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1463  (0.0815996); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1706.16
//
Query:       gene1463|gene1463|rna1462|rna1462  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0026   17.5   0.4     0.0032   17.2   0.4    1.1  1  Use1             Membrane fusion protein Use1
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.021   14.3   0.0    1.2  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
      0.063   13.6   0.2       0.15   12.4   0.1    1.6  2  DDE_Tnp_IS1      IS1 transposase
       0.16   11.3   0.1        0.2   11.0   0.1    1.1  1  DUF604           Protein of unknown function, DUF604


Domain annotation for each model (and alignments):
>> Use1  Membrane fusion protein Use1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4   7.1e-07    0.0032      93     246 ..      26     173 ..       4     174 .] 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.1e-07
                               Use1  93 keekeeskereeaskelrqkekakyqkelrkellgkndsssspekekeskkkksdedldavlkkhenlqEklaeem 168
                                        ++ +e +   e+ +++l+  +++  ++elr++ l+  d   ++    e  + ++ ++    ++k ++  + +  ++
  gene1463|gene1463|rna1462|rna1462  26 SNGEEMEARIESNITTLKYLTRKITDEELRSKTLKRIDMLCAE---PEVFEMNEVRNRAPGIRKSSEFSDRIERDI 98 
                                        3333344444566799******************999955433...344444889999999*************** PP

                               Use1 169 lsLarnLKenslaasqiikkDtetlsksekaadqnlaslkkeserleehskskvkcllwlllfvvlvvFismvlfi 244
                                        l+ ++ L  + +   +++  D ++l + + ++ +nl  +   se l   + +  +   + +l  v+++Fi m ++i
  gene1463|gene1463|rna1462|rna1462  99 LKYTKRLHGKVKEFMESVDVDSKVLGEVTDKMSRNLMGT---SETLRSLKLKGRNIPALGILTSVMATFIVMYFVI 171
                                        **************************9999988887766...5566666677788888899999********9999 PP

                               Use1 245 ri 246
                                        r+
  gene1463|gene1463|rna1462|rna1462 172 RF 173
                                        97 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.8e-06     0.021     147     197 ..      52     103 ..      18     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.8e-06
                                        HHTT--SEEEEEEEEETTTEEEEEEE.ESS---STTSHHHHHHHCTT--HHH CS
                    Dala_Dala_lig_C 147 kaldlrGlaRvDfflteegeivlnEv.NtlPGfTeiSlfpklakasGlefkk 197
                                        + l  + l R+D+++ e + + +nEv N  PG+ + S f   ++++ l+++k
  gene1463|gene1463|rna1462|rna1462  52 EELRSKTLKRIDMLCAEPEVFEMNEVrNRAPGIRKSSEFSDRIERDILKYTK 103
                                        4689999******************9899**********9999988888765 PP

>> DDE_Tnp_IS1  IS1 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.9e+03      83      89 ..      43      49 ..      20      66 .. 0.54
   2 ?   12.4   0.1   3.4e-05      0.15      82     127 ..      87     129 ..      62     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                        DDE_Tnp_IS1 83 kiytqri 89
                                       k  t++i
  gene1463|gene1463|rna1462|rna1462 43 KYLTRKI 49
                                       2223333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.4e-05
                        DDE_Tnp_IS1  82 skiytqriernnltlrtrlkrlarkslsfsksvelhekvigtylek 127
                                        s  +++rier+ l+     krl  k   f  sv++  kv+g+  +k
  gene1463|gene1463|rna1462|rna1462  87 SSEFSDRIERDILKY---TKRLHGKVKEFMESVDVDSKVLGEVTDK 129
                                        56799*****98875...578899999**************97765 PP

>> DUF604  Protein of unknown function, DUF604
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   4.5e-05       0.2     153     252 ..      32     132 ..      26     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.5e-05
                             DUF604 153 arelekplrtfkewkrkaeeeefafntrevskdpCkrpvvfflksvekekekeeivseYkrkekkkkkeCkskse. 227
                                        + ++e+ + t k  +rk ++ee   +t +  +  C++p vf +++v+++    +  se++ + ++   + +++ + 
  gene1463|gene1463|rna1462|rna1462  32 EARIESNITTLKYLTRKITDEELRSKTLKRIDMLCAEPEVFEMNEVRNRAPGIRKSSEFSDRIERDILKYTKRLHg 107
                                        56788999999999***********************************888888889876665555554444442 PP

                             DUF604 228 ssakkvekikvlskkeeeewkkapr 252
                                        + ++ +e+++v sk   e ++k++r
  gene1463|gene1463|rna1462|rna1462 108 KVKEFMESVDVDSKVLGEVTDKMSR 132
                                        6667788999988887776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1032.50
//
Query:       gene1464|gene1464|rna1463|rna1463  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0053   17.0   0.1      0.092   13.0   0.1    2.5  1  RWD       RWD domain


Domain annotation for each model (and alignments):
>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   5.1e-06     0.092       5     109 ..       2      79 ..       1      82 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-06
                                        HHHHHHHHHSTTTCCCCHT--EE--S-EEEEEEECECCCC....TT-CEEEEEEEEE-SSTTSS--EEEEEECCSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RWD   5 qEleaLesIypdefevienenysikleikikldededeedsefeekkkpslkleiklpeeYPeeaPiislsstenl 80 
                                        +E +aL++I++ ++   +++  +      +k++   +              ++e+++ e+YP+++P++  ++++  
  gene1464|gene1464|rna1463|rna1463   2 DEHDALKYIFGSNLRHYAESTGQ-----IYKISVGDK--------------YFEFRCREDYPNSIPEVLSNVEN-- 56 
                                        67777777777777666644444.....333333322..............79**************9888877.. PP

                                        -HHHHHHHHHHHHHHHHHTTTS--CHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                RWD  81 pkeqvksleekleelaeenlgepvifali 109
                                              ++ e + ++ae   + p+if++i
  gene1464|gene1464|rna1463|rna1463  57 ------EVLEGVIQKAERYVSTPMIFDII 79 
                                        ......56666666666667788888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1049.31
//
Query:       gene1465|gene1465|rna1464|rna1464  [L=392]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-37  129.5  14.3    2.9e-37  128.3  14.3    1.6  1  DUF1686        Protein of unknown function (DUF1686)
  ------ inclusion threshold ------
       0.13   11.2   0.1        0.2   10.6   0.1    1.2  1  Dsl1_N         Retrograde transport protein Dsl1 N terminal
       0.19   10.8   9.7       0.64    9.0   8.8    2.3  1  Acyl_transf_3  Acyltransferase family
       0.21   11.2   3.2       0.17   11.4   0.6    2.0  2  PIRT           Phosphoinositide-interacting protein family
       0.39   10.0  10.6      0.023   14.1   3.7    2.0  2  TssN           Type VI secretion system, TssN


Domain annotation for each model (and alignments):
>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3  14.3   8.1e-41   2.9e-37       3     176 ..     186     357 ..     184     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 8.1e-41
                            DUF1686   3 kvswntalyvlavaGtiiyqiwvLakeyrdkg.veevlreeWsvvgcmvPmlvgllnagvirssvysvtvagigiv 77 
                                         ++ nt ly+l+v G i+y +wv  k+yr +g ++e+lr+  s v +m+Pm+vg+ ++++i+ ++y++t++gi+++
  gene1465|gene1465|rna1464|rna1464 186 WKVCNTTLYSLTVGGSILYLVWVVIKSYRSEGrMKEILRQRLSGVISMIPMVVGIHHTEMIECGTYTLTMMGISAI 261
                                        5789*************************988689***************************************** PP

                            DUF1686  78 mlyvQslvkkkmsrrqvcvvvlgnillasaclagd.klllpgvedrsslvcvglvvfaallllvsyveeggkkaka 152
                                        m+y+Q+lv++km +rq+cvv++ n++la a+  +  ++++   +  + +vc g+v+f++l+ ++ y  +  + +k 
  gene1465|gene1465|rna1464|rna1464 262 MVYAQDLVENKMTWRQICVVGVRNAILAIAYCCEIlRMFMRNEYRLRCCVCGGVVIFVLLVGILCYSSSMKEGSKT 337
                                        *********************************999***********************99999999955555555 PP

                            DUF1686 153 eevgevvksvvlvlsvlvltvvsy 176
                                        +  g+    v++vl+v+++t+vs+
  gene1465|gene1465|rna1464|rna1464 338 RLPGN----VMFVLTVVIGTFVSW 357
                                        55566....**************9 PP

>> Dsl1_N  Retrograde transport protein Dsl1 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   5.6e-05       0.2     283     340 ..       8      65 ..       3      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.6e-05
                                        XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXX--HHHHH CS
                             Dsl1_N 283 ksnaseiledensslkeqvlkindkLkkLsekkksswnydgneieeLLndkqiyknLl 340
                                        +  a++  ed++++++e + +i + L++L ++ ++++   g+ +++++++++i+ +L+
  gene1465|gene1465|rna1464|rna1464   8 QMKANQASEDKKEEVEELLCNIREGLVTLVQNLSNFKDIYGKGLDDIISNERIFETLI 65 
                                        5667788899**********************************************97 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.8   0.00018      0.64      80     276 ..     113     324 ..      98     332 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxx RF
                      Acyl_transf_3  80 lrlliplliwllliillialvaghiqanasanvtlfdet...........................kglmfllfef 128
                                        +r+ +p++ ++ l+ ll+a+   +    + ++   +                              +++  + ++ 
  gene1465|gene1465|rna1464|rna1464 113 IRIGVPIFPTYTLYNLLMAISTLEKMNEVLGDIVKPE-KdrgvkrpiadlylvfvfvlciqtllyyITQKHPKVWK 187
                                        5555555555555555555555555555555555552.23555555555555555555555555555555555555 PP

                                        xxxxxxxxxxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Acyl_transf_3 129 patghlWfLwal.fvlylllpll..lrllrkvrkshlllllilllllslvfirhelfgpatsvgllplpsvlallf 201
                                         ++  l++L +   +lyl+  ++  +r   + +   +  l +++ +++ v+++h+      + +         l +
  gene1465|gene1465|rna1464|rna1464 188 VCNTTLYSLTVGgSILYLVWVVIksYRSEGRMKEILRQRLSGVISMIPMVVGIHHTEMIECGTYT--------LTM 255
                                        55555667777766666666666885555555555555555555555555555555443333333........99* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Acyl_transf_3 202 flfGalladaddrdrnlsrglkislllsllllalillalfgqtdggglvasvliqsaslllvslgimllllllfa 276
                                        +++ a++ +a+d   n+ + +  ++++++  ++l+++++          +++ + ++ +++v+ g+ +++ll+ +
  gene1465|gene1465|rna1464|rna1464 256 MGISAIMVYAQDLVENK-MTWRQICVVGVRNAILAIAYCCEIL-----RMFMRNEYRLRCCVCGGVVIFVLLVGI 324
                                        **************988.7799999999999999999999999.....8*********************99765 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   4.8e-05      0.17      59     124 ..     164     227 ..     158     232 .. 0.84
   2 ?   -1.1   0.1      0.37   1.3e+03      58      94 ..     314     348 ..     308     364 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                               PIRT  59 vfllGvvittlsrnstlknkdkevfklsGpaflslGlmllvcGlvwvpiikkkrkqrqkslflqsl 124
                                        vf++ + i tl     +++k+ +v+k++  +++sl +   ++ lvwv i   +   r k+++ q+l
  gene1465|gene1465|rna1464|rna1464 164 VFVFVLCIQTLL--YYITQKHPKVWKVCNTTLYSLTVGGSILYLVWVVIKSYRSEGRMKEILRQRL 227
                                        678888888874..456778889************************9988888889998888876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                               PIRT  58 avfllGvvittlsrnstlknkdkevfklsGpaflslG 94 
                                         v ++ +++  l+++s +k+ +k   +l G +++ l 
  gene1465|gene1465|rna1464|rna1464 314 GVVIFVLLVGILCYSSSMKEGSK--TRLPGNVMFVLT 348
                                        45555555555555554444333..345555555444 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.7   6.4e-06     0.023      23     138 ..     147     263 ..     123     274 .. 0.78
   2 ?   -0.3   2.5      0.16   5.7e+02      27      85 ..     268     332 ..     252     363 .. 0.35

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-06
                               TssN  23 kknkllkkkklii.yiLlaglvlalpgllgf.lknefvpygyillqilylllGilhlylllkkffkelkekkilfe 96 
                                        k +k    k+ i    L++++vl +  ll +  +++   ++   +++++l +G   ly l+ +++k + ++  ++e
  gene1465|gene1465|rna1464|rna1464 147 KPEKDRGVKRPIAdLYLVFVFVLCIQTLLYYiTQKHPKVWKVCNTTLYSLTVGGSILY-LVWVVIKSYRSEGRMKE 221
                                        444444445544415689999**********5555556778888999***********.99999999999999*** PP

                               TssN  97 illtlivillglvlfvlvfnllselqygvwaatsllvfiipl 138
                                        il   +++++++++ v+  ++++ ++ g + +t + +  i +
  gene1465|gene1465|rna1464|rna1464 222 ILRQRLSGVISMIPMVVGIHHTEMIECGTYTLTMMGISAIMV 263
                                        ***********************9999999988887666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.16
                               TssN  27 llkkkkliiyiLlaglvlalpgllgf..lknefvpygyil.......lqilylllGilhlylllkkff 85 
                                        l+++k     i ++g+  a++++     +   f+ ++y l       ++i++ll+Gil       +++
  gene1465|gene1465|rna1464|rna1464 268 LVENKMTWRQICVVGVRNAILAIAYCceILRMFMRNEYRLrccvcggVVIFVLLVGILCYS---SSMK 332
                                        3333333333333333333332222222222333333322111111134444444444433...3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      661  (0.0368676); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 2469.00
//
Query:       gene1466|gene1466|rna1465|rna1465  [L=541]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-40  136.4  10.8    1.5e-39  135.8  10.8    1.3  1  DUF1686          Protein of unknown function (DUF1686)
  ------ inclusion threshold ------
       0.01   16.1   8.3      0.042   14.1   3.5    2.3  2  TctB             Tripartite tricarboxylate transporter TctB f
      0.024   14.1   1.9        1.4    8.2   0.0    2.7  3  Peptidase_C11    Clostripain family
      0.034   13.9   3.2        9.6    5.9   0.1    3.1  3  DUF713           Protein of unknown function (DUF713)
      0.068   13.8   1.2        2.5    8.8   0.0    2.5  2  Cytochrom_B562   Cytochrome b562
      0.072   12.8   8.8       0.12   12.2   1.4    2.3  2  Mntp             Putative manganese efflux pump
       0.11   12.5   0.0       0.35   10.9   0.0    1.8  1  Peptidase_C27    Rubella virus endopeptidase
       0.45   10.6  14.8        6.5    6.8   9.0    2.5  2  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
       0.47    9.0   3.9      0.087   11.4   0.4    1.4  2  FapA             Flagellar Assembly Protein A
       0.54    9.9  12.4        1.1    9.0  12.4    1.5  1  7tm_3            7 transmembrane sweet-taste receptor of 3 GC
        4.4    7.4   9.5         10    6.2   0.1    2.6  2  DHHC             DHHC palmitoyltransferase
        6.6    6.7  15.6        4.9    7.1  11.0    2.5  2  HisKA_7TM        N-terminal 7TM region of histidine kinase


Domain annotation for each model (and alignments):
>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8  10.8   9.9e-43   1.5e-39       3     179 ..     339     520 ..     337     522 .. 0.90

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 9.9e-43
                            DUF1686   3 kvswntalyvlavaGtiiyqiwvLakeyr.dkgveevlreeWsvvgcmvPmlvgllnagvirssvysvtvagigiv 77 
                                        +++wnt ly+la++G++iy +w+  +ey  d++  +   e W ++++m+Pm+vgl++ g+i+ss+y +t+++ +iv
  gene1466|gene1466|rna1465|rna1465 339 GNAWNTTLYSLALVGAMIYLLWIVKREYNkDDKPVKGNVELWAAIASMMPMIVGLPSMGLIKSSMYCLTMVATSIV 414
                                        679*********************98875155555556689*********************************** PP

                            DUF1686  78 mlyvQslvkkkmsrrqvcvvvlgnillasaclagd.klllpgvedrsslvcvglvvfaallllvsyvee...ggkk 149
                                        +ly+Q+l + +m r++++++++gnil+  a++++  k+l   v++ +  vc+++++f++lll+ sy+ +   g   
  gene1466|gene1466|rna1465|rna1465 415 TLYAQHLSSTGMNRKEMAILMVGNILVVLAYFVDLqKYLEGKVYGSNYQVCIAMIIFVLLLLIGSYMAKnntGAGT 490
                                        *********************************889*9999**************************986643344 PP

                            DUF1686 150 akaeevgevvksvvlvlsvlvltvvsyvkg 179
                                        ++++e+ + +  +v+ +++lv  +vs+v+g
  gene1466|gene1466|rna1465|rna1465 491 ESKQELFSTISYLVFTVTLLVSIFVSWVMG 520
                                        455566666888****************98 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.5   2.8e-05     0.042       5     127 ..     316     447 ..     310     453 .. 0.59
   2 ?    4.2   0.2     0.033        50      37      81 ..     466     513 ..     458     526 .. 0.45

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                               TctB   5 llllllagv.afavgaldtgarvgpgffPlllgvllallgllllvaadgekeekearedwrkllklvlallaalll 79 
                                        l++++++++ +++++  +  +++g +   +l +++l+ + + ll+  ++e +++++    ++ +  ++a++a+++ 
  gene1466|gene1466|rna1465|rna1465 316 LGFIAVGCIqIILWAIGQNDTSLGNAWNTTLYSLALVGAMIYLLWIVKREYNKDDK--PVKGNV-ELWAAIASMMP 388
                                        56667755422335444433455555444444555555544444422333333333..345555.55666779999 PP

                               TctB  80 yallleplGfilatalflllll...g...........reerkwlkalilavvlallvyllFt 127
                                         ++ l+  G+i +++ +l++++   +           +  ++ ++++il v+  l+v   F+
  gene1466|gene1466|rna1465|rna1465 389 MIVGLPSMGLIKSSMYCLTMVAtsiVtlyaqhlsstgM--NR-KEMAILMVGNILVVLAYFV 447
                                        99*************77777776651567788998433..33.6677776666666666664 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.033
                               TctB  37 vllallgllllv....aadgekeekearedwrkllklvlallaalllya 81 
                                        ++++++ llll+    a+  +++++e++++  + +   l++ + ll+ +
  gene1466|gene1466|rna1465|rna1465 466 IAMIIFVLLLLIgsymAKNNTGAGTESKQELFSTI-SYLVFTVTLLVSI 513
                                        55555544444466652222222222222222222.3333333333333 PP

>> Peptidase_C11  Clostripain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00096       1.4     199     246 ..     197     246 ..     180     313 .. 0.79
   2 ?   -2.6   0.1       1.9   2.9e+03     195     234 ..     409     448 ..     399     464 .. 0.79
   3 ?    4.6   0.1     0.012        18     163     190 ..     508     536 ..     494     541 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00096
                      Peptidase_C11 199 ivdsyresyssvrveelsLsvydlskveevlksvdalaedlvkkakk....e 246
                                         +++ r + ++ +  + + s++d +k+ee+ + +d+l+e+ v+ ++k    +
  gene1466|gene1466|rna1465|rna1465 197 NINEMRAKLDNFQ--KNNPSLIDGNKIEEFRRFLDSLIENFVQYTSKlcatD 246
                                        4455555555533..78889*********************99888755441 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                      Peptidase_C11 195 vgrkivdsyresyssvrveelsLsvydlskveevlksvda 234
                                        v+  iv  y++  ss+ ++ ++++++   ++  vl+   +
  gene1466|gene1466|rna1465|rna1465 409 VATSIVTLYAQHLSSTGMNRKEMAILMVGNILVVLAYFVD 448
                                        7889999999999999999999998888777777665555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.012
                      Peptidase_C11 163 ylvaSsseepgeGwdY.svlgevsetkes 190
                                        +l++S ++ +  G++Y ++ g +s+++++
  gene1466|gene1466|rna1465|rna1465 508 TLLVSIFVSWVMGYEYrQFYGSISSSDQD 536
                                        799********************777665 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0064       9.6      29      94 ..       5      69 ..       2      74 .. 0.77
   2 ?    1.9   0.1      0.11   1.7e+02      37      94 ..     144     205 ..     137     216 .. 0.65
   3 ?    4.9   0.0     0.013        19      37      87 ..     221     271 ..     217     276 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0064
                             DUF713 29 kEqewsdwlkklrepivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkL 94
                                        Eqew +++k l + i+++ n+ s+ e  +++++ + + l ++  ++++ e  +  +  l+a n+L
  gene1466|gene1466|rna1465|rna1465  5 NEQEWDNFVKALDDVITSISNQISKRE-AFEENSTKLQGLLDQYFQNVDLEGLKQLRGALNALNAL 69
                                       7*********************99977.66777767777777777777777666666666666665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                             DUF713  37 lkklrepivklknrfsdfeeeikksd..keekklek..edleelqselsnLakkvlsaynkL 94 
                                        +k+  + i ++  ++s+f+++ + +   +e +++ k   +l+ l+ el+ L++ + +   kL
  gene1466|gene1466|rna1465|rna1465 144 IKNSETLIGNISAAYSRFRDNREFNGlfEECQTFLKaeYNLSSLTPELNTLSNNINEMRAKL 205
                                        88889999999999999998766665113333333344455666666666666665554444 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.013
                             DUF713  37 lkklrepivklknrfsdfeeeikksdkeekklekedleelqselsnLakkv 87 
                                        ++++r+ + +l+++f +  +++  +dke ++l++e l+e++ e+  L++ +
  gene1466|gene1466|rna1465|rna1465 221 IEEFRRFLDSLIENFVQYTSKLCATDKEGQSLSRETLTEIKDEAVALRGTL 271
                                        8999***************************************99998765 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.086   1.3e+02      43      93 ..      19      69 ..       5      85 .. 0.72
   2 ?    8.8   0.0    0.0017       2.5      12      84 ..     181     251 ..     176     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.086
                     Cytochrom_B562 43 tpsklekdseeqkdYqeGldklidqldkaealakagkleeakaalkelkdl 93
                                        ++++ ++ ++ ++++e   kl++ ld+  + ++ + l++ + al+ l++l
  gene1466|gene1466|rna1465|rna1465 19 VITSISNQISKREAFEENSTKLQGLLDQYFQNVDLEGLKQLRGALNALNAL 69
                                       455566677777777777777888888877777777777777777777665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                     Cytochrom_B562  12 alkqvakaddaeelkkalkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaealakagkleeak 84 
                                        +++  + + + ++l+++++e+ra  ++ ++++p +l  d ++ ++++  ld li++  +  +++ a + e  +
  gene1466|gene1466|rna1465|rna1465 181 EYNLSSLTPELNTLSNNINEMRAKLDNFQKNNP-SLI-DGNKIEEFRRFLDSLIENFVQYTSKLCATDKEGQS 251
                                        55555566678899*******************.555.68999999999999999887777776666655555 PP

>> Mntp  Putative manganese efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.4      0.04        60      48     125 ..     349     422 ..     313     447 .. 0.63
   2 ?   12.2   1.4   7.9e-05      0.12       7      87 ..     433     513 ..     426     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.04
                               Mntp  48 LlllGlkmivealkeeeeekkekeelslksllllaiatSiDAlavGl.sLallkvnil.lavlliGlvtlvlsllG 121
                                        L+l+G  mi+  +  ++e +k+++ +++ + l  aia S+  + vGl s++l+k +++ l++++  +vt    l +
  gene1466|gene1466|rna1465|rna1465 349 LALVG-AMIYLLWIVKREYNKDDKPVKGNVELWAAIA-SMMPMIVGLpSMGLIKSSMYcLTMVATSIVT----LYA 418
                                        44555.5888888888888887788898888888887.8999****95599998865413333334443....333 PP

                               Mntp 122 lllG 125
                                         +l+
  gene1466|gene1466|rna1465|rna1465 419 QHLS 422
                                        3333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.9e-05
                               Mntp   7 alkialifGlfqalmpliGwllGkllselieavdhwiafllLlllGlkmivealkeeeeekkekeelslkslllla 82 
                                        +l ++ i+ ++  ++ l  +l Gk+  +  + +  +i f+lLll+G +m ++ +   +e+k+e  ++    ++++ 
  gene1466|gene1466|rna1465|rna1465 433 ILMVGNILVVLAYFVDLQKYLEGKVYGSNYQVCIAMIIFVLLLLIGSYMAKNNTGAGTESKQELFSTISYLVFTVT 508
                                        5677778888888899999999*******************************99999988887444444444444 PP

                               Mntp  83 iatSi 87 
                                        + +Si
  gene1466|gene1466|rna1465|rna1465 509 LLVSI 513
                                        44554 PP

>> Peptidase_C27  Rubella virus endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.35       5      43 ..      54      92 ..      51     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                      Peptidase_C27  5 eGlqqlrgavdnaraal.adsdvdfraaartfeldaeaif 43
                                       eGl+qlrga  na  al a s  d++aa  + el+a+ if
  gene1466|gene1466|rna1465|rna1465 54 EGLKQLRGAL-NALNALnALSSEDMQAAISSAELEANYIF 92
                                       8*******98.677777699999**************999 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3    0.0044       6.6      88     140 ..     311     363 ..     297     393 .. 0.74
   2 ?    6.8   9.0    0.0044       6.5       4     114 ..     403     520 ..     401     531 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0044
                    Polysacc_synt_C  88 lrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYllllll 140
                                        + +l   ++a+ ++ i+++++ +   +l + ++ +l   +lvga +Yll +++
  gene1466|gene1466|rna1465|rna1465 311 VGNLCLGFIAVGCIQIILWAIGQNDTSLGNAWNTTLYSLALVGAMIYLLWIVK 363
                                        45555666677777777666666666555555667777778999999987765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0044
                    Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplf...givGaaiatvlallvvavln... 73 
                                        +++l+++ +s+ t++++ L ++g +++ + +l++g ++ ++  ++ + ++    ++G  +  ++a+++  +l+   
  gene1466|gene1466|rna1465|rna1465 403 MYCLTMVATSIVTLYAQHLSSTGMNRKEMAILMVGNILVVLAYFVDLQKYlegKVYGSNYQVCIAMIIFVLLLlig 478
                                        899**********************************888888888877767568999999999988888888444 PP

                    Polysacc_synt_C  74 lyalrrllgikl...ellrrll...kpllaalvmgivvylllllllg 114
                                         y++++ +g      +    l+    +l++++ + +   +++++++g
  gene1466|gene1466|rna1465|rna1465 479 SYMAKNNTGAGTeskQ---ELFstiSYLVFTVTLLVS--IFVSWVMG 520
                                        5778888888885442...444111444444444444..45666655 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       1.7   2.5e+03     371     381 ..      50      60 ..       4      89 .. 0.39
   2 ?   11.4   0.4   5.8e-05     0.087     298     427 ..     152     275 ..     142     300 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                               FapA 371 qlesekkeqlk 381
                                        +++ e ++ql 
  gene1466|gene1466|rna1465|rna1465  50 NVDLEGLKQLR 60 
                                        22222333332 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.8e-05
                               FapA 298 gkivggnikalkevkakklGselgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqle 373
                                        g+i+  + ++ ++ +++  G   + +t ++++ +  +l  +l+ l ++++e++++l++ +k+  +l +    ++  
  gene1466|gene1466|rna1465|rna1465 152 GNISAAYSRFRDNREFN--GLFEECQTFLKAEYNLSSLTPELNTLSNNINEMRAKLDNFQKNNPSLID----GNKI 221
                                        55666666666666666..6666778888888888899999999999999999999999999444444....5556 PP

                               FapA 374 sekkeqlkklletkeklkeeleeleeelkelkeeleskkeeakikvnkeiypgv 427
                                        +e++  l++l+e+  +++++l + ++e ++l+ e  +  +++ ++ + ++  + 
  gene1466|gene1466|rna1465|rna1465 222 EEFRRFLDSLIENFVQYTSKLCATDKEGQSLSRETLTEIKDEAVALRGTLQVEL 275
                                        78999999999999***************9999988886666666665555555 PP

>> 7tm_3  7 transmembrane sweet-taste receptor of 3 GCPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  12.4   0.00071       1.1       7     206 ..     326     521 ..     297     533 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00071
                              7tm_3   7 vllvfikhrntpivkasspelslllLlglllcylslifi.............gkpssvtCilrrwllgvg.ftlvf 68 
                                        ++l+ i  ++t++  a + +l  l L+g+++ yl  i+              ++   ++  ++++++g+  + l+ 
  gene1466|gene1466|rna1465|rna1465 326 IILWAIGQNDTSLGNAWNTTLYSLALVGAMI-YLLWIVKreynkddkpvkgnVELWAAIASMMPMIVGLPsMGLIK 400
                                        3333333344555666666666666666666.44433335555555554444333444444444444444222222 PP

                              7tm_3  69 sallvKtwrvlrifqs.rkgrkskslrd.kqllllvlllvlvqviillvwtlidplstrekseeereevileC... 139
                                        s++ + t+   +i +   ++ +s ++++ k +++    l++  ++++l++ ++d ++                   
  gene1466|gene1466|rna1465|rna1465 401 SSMYCLTMVATSIVTLyAQHLSS-TGMNrKEMAI----LMVGNILVVLAY-FVDLQK---------------Yleg 455
                                        33332222111111111111111.1111233333....333333333344.333211...............0121 PP

                              7tm_3 140 ssssysdiffllllgykglllllgtflafktrkvpsnfneakfitlsilnvlliwlvfiplylllns 206
                                        +    s++ +++++++ +llll+g ++a +   + ++ ++  f t+s l+++++ lv i +++++ +
  gene1466|gene1466|rna1465|rna1465 456 KV-YGSNYQVCIAMIIFVLLLLIGSYMAKNNTGAGTESKQELFSTISYLVFTVTLLVSIFVSWVMGY 521
                                        22.244456667778899**********999998777777777777777777777777777777664 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0068        10      57     127 ..     342     412 ..     331     435 .. 0.79
   2 ?    3.1   5.0     0.065        98      56     119 ..     464     527 ..     431     535 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0068
                               DHHC  57 ylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnlTt 127
                                        + ++l  lalv ++i+l+++v+ e++++   v+ + +l++ +  ++ ++++l  + l++ ++y++    T+
  gene1466|gene1466|rna1465|rna1465 342 WNTTLYSLALVGAMIYLLWIVKREYNKDDKPVKGNVELWAAIASMMPMIVGLPSMGLIKSSMYCLTMVATS 412
                                        56677777888888888888888888888889888888888888888888888888888888866655554 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.065
                               DHHC  56 lylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhly 119
                                        +++++++++ l+l+  ++ k+ +   +++ + ++ + ++l++++++l  +f+ +++   ++++y
  gene1466|gene1466|rna1465|rna1465 464 VCIAMIIFVLLLLIGSYMAKNNTGAGTESKQELFSTISYLVFTVTLLVSIFVSWVMGYEYRQFY 527
                                        4555666666666666666666666666666665555455555555555555555544444554 PP

>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  11.0    0.0033       4.9     122     209 ..     388     474 ..     314     484 .. 0.67
   2 ?    1.6   2.2      0.16   2.3e+02     139     184 ..     465     514 ..     451     533 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0033
                          HisKA_7TM 122 vvlefehGplfwvhlaysyllliagvvlliralirssglyrrqalllligllvPwlanllyl...lglsplpgidl 194
                                        ++++  + + ++  ++y+ +++++++v l  + ++s+g  r+ +++l++g ++ +la+++ l   l      ++  
  gene1466|gene1466|rna1465|rna1465 388 PMIVGLPSMGLIKSSMYCLTMVATSIVTLYAQHLSSTGMNRKEMAILMVGNILVVLAYFVDLqkyL---EG-KVYG 459
                                        3333334444433789999**************************************999995432...33.5555 PP

                          HisKA_7TM 195 tplafaltglllaia 209
                                          + ++++++++ + 
  gene1466|gene1466|rna1465|rna1465 460 SNYQVCIAMIIFVLL 474
                                        555555555555443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                          HisKA_7TM 139 syllliagvvllirali....rssglyrrqalllligllvPwlanllyll 184
                                        +++++i++++lli +++       g+  +q l   i++lv +++ l+ ++
  gene1466|gene1466|rna1465|rna1465 465 CIAMIIFVLLLLIGSYMaknnTGAGTESKQELFSTISYLVFTVTLLVSIF 514
                                        34455555555555555332244448888888888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1218  (0.0679346); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.83u 0.32s 00:00:01.14 Elapsed: 00:00:00.52
# Mc/sec: 3158.35
//
Query:       gene1467|gene1467|rna1466|rna1466  [L=456]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-10   39.4   0.0    8.9e-10   38.5   0.0    1.5  1  Thioredoxin    Thioredoxin
    8.9e-09   35.5   0.0    0.00014   21.8   0.0    2.7  3  Thioredoxin_6  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.021   15.3   0.0      0.074   13.5   0.0    2.0  1  Thioredoxin_2  Thioredoxin-like domain
      0.028   14.1   0.1       0.27   10.9   0.1    2.5  2  DUF953         Eukaryotic protein of unknown function (DUF953
      0.041   14.1   0.0       0.18   12.1   0.0    2.1  2  Glutaredoxin   Glutaredoxin
       0.12   12.2   0.0       0.29   10.9   0.0    1.6  1  TraF           F plasmid transfer operon protein
       0.14   12.3   0.0       0.46   10.7   0.0    1.9  2  Thioredoxin_7  Thioredoxin-like


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   3.5e-13   8.9e-10       2     102 ..     312     416 ..     311     417 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 3.5e-13
                                        EEESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT....TSEEEEEETTTSHHHHHHTT-SSS CS
                        Thioredoxin   2 vlvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkd....kvklakvdvdenedlakkyevegi 73 
                                        v+v+t +n ++ +++++k+ ++ F  + C+hC +++P +e+l e +k+    kv +  +dv  n    ++++++ +
  gene1467|gene1467|rna1466|rna1466 312 VKVVTRNNIKTYLEDTSKDRFIVFGTERCPHCIRIKPIIERLGEIVKEnandKVLVGYCDVGMN--DMNDFDIQFV 385
                                        789999*************************************999998988999999999988..5789****** PP

                                        SEEEEEETTE.EEEEEESS.-HHHHHHHHHH CS
                        Thioredoxin  74 Ptlklfkngk.evkkyega.rekeklaaflk 102
                                        Ptl+l+k+g  e+ +y+g+ r+  +l++f++
  gene1467|gene1467|rna1466|rna1466 386 PTLLLYKSGGrESVRYSGGeRNLLNLVRFIR 416
                                        ********99866666665488888888886 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   5.6e-08   0.00014      12     184 .]     125     288 ..     119     288 .. 0.90
   2 ?   -2.3   0.1       1.4   3.5e+03      55      79 ..     306     332 ..     292     342 .. 0.51
   3 !   10.7   0.0   0.00015      0.38      23      73 ..     370     417 ..     351     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5.6e-08
                                        HHHHTTT-T.TSEEEEE--HHHHHHTT--SSEEEEEETTTTEEEEEETHT--HHHHHHHHHHH---SEEE-SHHHH CS
                      Thioredoxin_6  12 Fekvakelkgdvrfgvtkskevadklgvkepavllfrkfdeekvkydgekitvddlkkfieknslplvreltpena 87 
                                        +++  +++k+ ++  v+++  +a+ lg++ p ++ ++  d+   +y++e ++ ++ k++++   lp ++  ++ n 
  gene1467|gene1467|rna1466|rna1466 125 YKENLQSNKEGFEGFVSTDLSLASSLGIPVPGIYGYNSSDK--LSYKLE-LSDENNKRILSLSNLPIFGFTSSANI 197
                                        677777788778888888999999**************555..799998.99************************ PP

                                        HHHHTSS--EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEESSSS CS
                      Thioredoxin_6  88 eelfeeglppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivdsash 163
                                          +      +++++f +k      +++++++   ++f+  i ++l+   +    l ++gl++++lP +  ++ + +
  gene1467|gene1467|rna1466|rna1466 198 SLYRALSGTIFYIFFDMK---NGPEVLAEYSGTLNDFRYDIRVILIPSIKGSIDLGEYGLTEESLPGCMSISEDGG 270
                                        *******9*******987...56899999999999**999*********9**********************8888 PP

                                        -EEEETTSS--HHHHHHHHHH CS
                      Thioredoxin_6 164 kykyppkdefspeklkeFlkd 184
                                        ky +   +++s e++  F+kd
  gene1467|gene1467|rna1466|rna1466 271 KYIL---KNVSRENISGFIKD 288
                                        8888...89999999999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                                        EEEETH..T--HHHHHHHHHHH---SE CS
                      Thioredoxin_6  55 vkydge..kitvddlkkfieknslplv 79 
                                           + +    t +++k+ +e+ s   +
  gene1467|gene1467|rna1466|rna1466 306 DNASRNvkVVTRNNIKTYLEDTSKDRF 332
                                        333333434455555555555544444 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00015
                                        SEEEEE--HHHHHHTT--S.SEEEEEETTTTEEEEEETHT--HHHHHHHHHH CS
                      Thioredoxin_6  23 vrfgvtkskevadklgvke.pavllfrkfdeekvkydgekitvddlkkfiek 73 
                                        +++g+      ++++++++ p++ll++    e v y+g + +  +l++fi++
  gene1467|gene1467|rna1466|rna1466 370 CDVGMN----DMNDFDIQFvPTLLLYKSGGRESVRYSGGERNLLNLVRFIRE 417
                                        555533....478999***********************99********975 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.074       4      98 ..     327     403 ..     324     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                      Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvr 79 
                                        + k  ++vf ++ Cp C ++k  ++ l ++        +k++++ k+   +c+   +            ++ ++++
  gene1467|gene1467|rna1466|rna1466 327 TSKDRFIVFGTERCPHCIRIKPIIERLGEI--------VKENANDKVLVGYCDVGMN-----------DMNDFDIQ 383
                                        6688899********************777........888999********99986...........3777**** PP

                      Thioredoxin_2  80 gtPtivfldgk.eivarlpG 98 
                                        ++Pt++++    ++  r+ G
  gene1467|gene1467|rna1466|rna1466 384 FVPTLLLYKSGgRESVRYSG 403
                                        ****8866555455556665 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.97   2.5e+03      11      35 ..      37      61 ..      34      63 .. 0.82
   2 ?   10.9   0.1   0.00011      0.27      33      97 ..     335     392 ..     305     414 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.97
                                       HHHH..TSSSEEEEEEB--B-TTS- CS
                             DUF953 11 slkelekeskivfilFlgekdteGe 35
                                       s+ e+ k+ k vf + +g+++ +Ge
  gene1467|gene1467|rna1466|rna1466 37 SMVEILKDMKSVFSYVTGDEKFDGE 61
                                       56777888999*******9998886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                                        TS-BSSHHHHHHHHHHH...HHHHH-SS-EEEE.EEE---HHHHT-TTSHHHH..TS---SSSEEEEET CS
                             DUF953  33 eGesWCPdCvkaepvie...ealkeapedvklv.rvdvGdrevWkdpanpfRkdpklkltgvPtLlrwk 97 
                                         G   CP C++  p+ie   e +ke ++d +lv ++dvG  ++     n       + +++vPtLl +k
  gene1467|gene1467|rna1466|rna1466 335 FGTERCPHCIRIKPIIErlgEIVKENANDKVLVgYCDVGMNDM-----N------DFDIQFVPTLLLYK 392
                                        47788**********9833345666555555553566664432.....2......34556666666665 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.4   6.1e+03      12      26 ..      35      49 ..      25      53 .. 0.59
   2 ?   12.1   0.0   6.8e-05      0.18       2      25 ..     333     356 ..     332     376 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHTTGGE CS
                       Glutaredoxin 12 CkkakrlLkelgvkf 26
                                       ++ ++++Lk+++  f
  gene1467|gene1467|rna1466|rna1466 35 SPSMVEILKDMKSVF 49
                                       445556666665544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.8e-05
                                        EEEESTSSHHHHHHHHHHHHTTGG CS
                       Glutaredoxin   2 vlftkptCpyCkkakrlLkelgvk 25 
                                        ++f++ +Cp+C ++k + ++lg  
  gene1467|gene1467|rna1466|rna1466 333 IVFGTERCPHCIRIKPIIERLGEI 356
                                        69*****************99944 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.29      86     158 ..     286     357 ..     278     400 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                               TraF  86 wqrvllanPeLdytlr.rPvsnlarkvlndarkeekeaalkklakeygLlfFyrgkcpyceaqapilqafadky 158
                                         + vl ++ e+ y+ +  P +n+ r+  + + +++++++l++ +k+ + ++F  ++cp c    pi++++ +  
  gene1467|gene1467|rna1466|rna1466 286 IKDVLDKKAEIFYKSQdEPEDNASRN-VKVVTRNNIKTYLEDTSKDRF-IVFGTERCPHCIRIKPIIERLGEIV 357
                                        67788899999999998999998555.56677789999****999975.789999*************998654 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.5   6.4e+03      46      67 ..     108     129 ..     100     139 .. 0.64
   2 ?   10.7   0.0   0.00018      0.46      13      81 ..     324     391 ..     317     393 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.5
                                        HH.HHHT-EEEEESS--S-GGG CS
                      Thioredoxin_7  46 kaalaekfvllrvdvterdani 67 
                                         +  +++f++ ++d    ++n+
  gene1467|gene1467|rna1466|rna1466 108 SKSRQGNFIVYFLDSSGYKENL 129
                                        4445688888888876555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                                        HHHHT--EEEEE--TT-HHHHHHHHHHHH-.HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                      Thioredoxin_7  13 aaergkpvlvffgaswcftCqalerdflsd.eevkaalaekfvllrvdvterdanileldeqgvPvvafl 81 
                                        ++ + k+ +++fg + c++C +++   +   e vk+ +++k+ +   dv+ +d  + ++d q vP+++++
  gene1467|gene1467|rna1466|rna1466 324 LEDTSKDRFIVFGTERCPHCIRIKPIIERLgEIVKENANDKVLVGYCDVGMNDM-N-DFDIQFVPTLLLY 391
                                        56789******************9998887677777444555555555555554.4.5888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 2472.01
//
Query:       gene1468|gene1468|rna1467|rna1467  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 997.93
//
Query:       gene1469|gene1469|rna1468|rna1468  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-38  132.6   3.2    1.2e-38  132.4   3.2    1.0  1  DUF5093   Domain of unknown function (DUF5093)
    0.00022   21.3   0.2    0.00042   20.4   0.2    1.5  1  RRP7      Ribosomal RNA-processing protein 7 (RRP7) C-termina


Domain annotation for each model (and alignments):
>> DUF5093  Domain of unknown function (DUF5093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   3.2   1.3e-42   1.2e-38       1     131 []       4     129 ..       4     129 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 1.3e-42
                            DUF5093   1 lkleFpFkvkkvenksklkvkierkenivsFsLpfklkltvkseksssvelisveksedefvYvleFesindaieF 76 
                                        l++eFpF++++++ + k++v+++rke++vsF ++++++l++++++     l+s+e+ +++fvY ++F +++ aieF
  gene1469|gene1469|rna1468|rna1468   4 LEIEFPFRIGETHPRLKMEVEMKRKEDLVSFCMEYDMDLVIDNAE-----LKSKEEIRGQFVYAYKFGDLDSAIEF 74 
                                        789******************************************.....9************************* PP

                            DUF5093  77 ienkevkvvseseltdvkelekeldeameeyektekskkkkkKklvededGfiry 131
                                        +en ++k++ +  l+dv+++eke+d +me+ye  ek+ kkkk+++v++edGf++y
  gene1469|gene1469|rna1468|rna1468  75 MENSQAKALATRGLLDVEKVEKEMDLFMEKYETGEKRSKKKKRAIVVGEDGFMKY 129
                                        *****************************************************99 PP

>> RRP7  Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.2   4.7e-08   0.00042       6      45 ..      90     127 ..      85     130 .] 0.86

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.7e-08
                               RRP7   6 seeelqeevdeymeefdkeeeeekkeekkkeeevDeDGfv 45 
                                        + e++++e+d +me++++ e+++kk++ +   +v eDGf+
  gene1469|gene1469|rna1468|rna1468  90 DVEKVEKEMDLFMEKYETGEKRSKKKKRAI--VVGEDGFM 127
                                        67899**************99988777776..9******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 879.21
//
Query:       gene1470|gene1470|rna1469|rna1469  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-42  144.0   8.6      1e-41  143.0   8.6    1.5  1  YIF1      YIF1


Domain annotation for each model (and alignments):
>> YIF1  YIF1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.0   8.6   5.8e-46     1e-41       7     238 ..       1     205 [.       1     206 [] 0.91

  Alignments for each domain:
  == domain 1  score: 143.0 bits;  conditional E-value: 5.8e-46
                               YIF1   7 malqlGqsalsqgqeyveknlnryvsvsalkyyFnVsnsYVlkKlllllfPflhksWsrkseqseesseylppred 82 
                                        m +++G++a+++++ey +k l+  vs++++++yF ++n++VlkKl l+lfPf +k+W  +              e 
  gene1470|gene1470|rna1469|rna1469   1 MEIEIGKEAIRRSTEYANKGLG-AVSLKSFRTYFDIDNTFVLKKLVLILFPFHNKEWVSED-------------EG 62 
                                        67899****************9.689*******************************9544.............45 PP

                               YIF1  83 vnapDLYiPlmalvtYillaglllGlqgkFspelLgikassalavvllevlilklglYllnissasslldlvaysg 158
                                        +  p LY+P+m++++Y+l+ +l lG++g Fspe+Lgi +++ +++ ++ vl+++++ Y++ ++   s+ld++aysg
  gene1470|gene1470|rna1469|rna1469  63 MARPELYVPIMSFISYVLIRALRLGFEGMFSPEKLGIVFTRLFFLEAMCVLFTRVSGYFFDVTL--STLDVAAYSG 136
                                        6789**********************************************************94..89******** PP

                               YIF1 159 YkfvgvivtlllklllgeglvyylvllylvlalafFllrsLklvllpeasetvkksqrkkrkqflflvaavlQlll 234
                                        Yk+v  +++ +    ++++ v ++  +yl++++ +Fl rsLk  ++++ +e      r +r ++lf ++ ++Q ++
  gene1470|gene1470|rna1469|rna1469 137 YKYVIAVLLQI---NRMQY-VRIIGGMYLYVSFFIFLSRSLKRRVMDRGAE------RMRRAYYLFGIV-IVQEFI 201
                                        ***96655444...43455.889***********************99886......899999999988.99*999 PP

                               YIF1 235 mllL 238
                                        ++lL
  gene1470|gene1470|rna1469|rna1469 202 VFLL 205
                                        9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1441.36
//
Query:       gene147|gene147|rna147|rna147  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.9e-44  147.3   0.2    3.5e-16   58.8   0.0    3.1  3  RRM_1         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
    1.1e-10   41.2   0.0    3.4e-05   23.4   0.0    2.8  3  RRM_5         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
    3.4e-08   33.3   0.0    0.00018   21.4   0.0    3.3  3  Nup35_RRM_2   Nup53/35/40-type RNA recognition motif
    5.9e-08   32.5   0.0     0.0038   17.0   0.0    3.0  3  RRM_occluded  Occluded RNA-recognition motif
    1.6e-05   24.9   0.0       0.25   11.5   0.0    3.3  3  RRM_7         RNA recognition motif
      2e-05   24.5   0.0        2.2    8.4   0.0    3.1  3  RRM_3         RNA binding motif
    2.2e-05   24.4   0.0       0.19   11.8   0.0    2.9  3  RNA_bind      RNA binding domain
    0.00033   20.8   0.1          3    8.1   0.0    3.5  3  BRAP2         BRCA1-associated protein 2
    0.00059   19.7   0.0        3.1    7.8   0.0    3.3  3  RL            RL domain
     0.0013   18.7   0.0      0.056   13.5   0.0    2.5  2  Limkain-b1    Limkain b1
     0.0062   16.3   0.1      0.021   14.6   0.1    1.9  2  RRM_Rrp7      Rrp7 RRM-like N-terminal domain
  ------ inclusion threshold ------
      0.023   14.5   0.0        1.4    8.7   0.0    2.5  3  DUF4523       Protein of unknown function (DUF4523)
      0.071   13.3   0.2        2.7    8.2   0.0    2.8  3  PHM7_cyt      Cytosolic domain of 10TM putative phosphate tra


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   2.6e-19   3.5e-16       1      67 [.       5      67 ..       5      70 .. 0.96
   2 !   29.7   0.0     3e-10   4.1e-07       1      67 [.      83     143 ..      83     145 .. 0.93
   3 !   55.7   0.0   2.3e-18   3.1e-15       1      70 []     169     232 ..     169     232 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.6e-19
                                   EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTE CS
                          RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggr 67
                                   lfV+n+p++++ee++  +Fs+fG+i+sik+ r+    ++ f +VeF ++ dA++A+++lng+ l+g 
  gene147|gene147|rna147|rna147  5 LFVSNFPESYSEENINLIFSPFGEIRSIKILRE----PRMFSIVEFRDPLDAKAAIDSLNGRRLHGE 67
                                   8*******************************6....*************************99885 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3e-10
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTE CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggr 67 
                                    ++V+++p+d + eeL ++F+ +Gpi++i+ +      +  + f++F s+ dAe  le ln k   g+
  gene147|gene147|rna147|rna147  83 VIVSGIPSDSSSEELMRFFQYYGPIENITSSD-----HPQTIFIDFLSHKDAEMFLE-LNQKISFGK 143
                                    689**************************999.....6*******************.999877766 PP

  == domain 3  score: 55.7 bits;  conditional E-value: 2.3e-18
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                    +f+ nLp+ +t+ +L +lF kfG+i+s+ + +       g afV++e + +A kA+++++gk +gg++++
  gene147|gene147|rna147|rna147 169 IFIYNLPSKTTKTDLNDLFTKFGEIQSLGILSG------GKAFVNYERELSALKAIRHMDGKIVGGNKVR 232
                                    8*******************************6......***************************9985 PP

>> RRM_5  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   2.5e-08   3.4e-05      29      97 ..       5      72 ..       2      94 .. 0.82
   2 ?    0.2   0.0      0.39   5.3e+02      30      58 ..      84     111 ..      77     157 .. 0.68
   3 !   14.1   0.0     2e-05     0.027      29      98 ..     169     235 ..     156     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.5e-08
                          RRM_5 29 llVyglepdkvnldklFnlfclYgnvervkflktkketalvqmgdasaveravqHLnnaklfgkrleva 97
                                   l+V+++  +    +++  +f+ +g+++ +k+l+  +  ++v+  d  +++ a++ Ln+ +l+g+ l + 
  gene147|gene147|rna147|rna147  5 LFVSNFP-ESYSEENINLIFSPFGEIRSIKILREPRMFSIVEFRDPLDAKAAIDSLNGRRLHGEGLSLH 72
                                   5666664.44556778889********************************************955443 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                          RRM_5  30 lVyglepdkvnldklFnlfclYgnvervk 58 
                                    +V+g+  d +  ++l  +f  Yg +e + 
  gene147|gene147|rna147|rna147  84 IVSGIPSD-SSSEELMRFFQYYGPIENIT 111
                                    67777554.45688999999999999885 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2e-05
                          RRM_5  29 llVyglepdkvnldklFnlfclYgnvervkflktkketalvqmgdasaveravqHLnnaklfgkrleval 98 
                                    +++y+l  +k +   l  lf+ +g+++ + +l    ++a+v+   + ++ +a+ H+ ++ + g++++++l
  gene147|gene147|rna147|rna147 169 IFIYNLP-SKTTKTDLNDLFTKFGEIQSLGILS--GGKAFVNYERELSALKAIRHMDGKIVGGNKVRIVL 235
                                    4578985.56677779****************7..589***********************999999876 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.027        37      22      52 ..      24      55 ..      18      56 .. 0.83
   2 !   21.4   0.0   1.3e-07   0.00018       3      51 ..      82     131 ..      80     133 .. 0.93
   3 ?    3.7   0.0     0.045        62      21      52 ..     187     217 ..     181     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.027
                    Nup35_RRM_2 22 asfGeIvkhyvp.kevsvmyvkfesekdaekA 52
                                     fGeI  + +    + + +v+f+++ da+ A
  gene147|gene147|rna147|rna147 24 SPFGEIRSIKILrEPRMFSIVEFRDPLDAKAA 55
                                   55999999777645588889*********988 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.3e-07
                    Nup35_RRM_2   3 wvaVsGydteli.elVlehFasfGeIvkhyvpkevsvmyvkfesekdaek 51 
                                     v+VsG++ ++  e+  ++F+ +G+I ++  ++   ++++ f s kdae+
  gene147|gene147|rna147|rna147  82 RVIVSGIPSDSSsEELMRFFQYYGPIENITSSDHPQTIFIDFLSHKDAEM 131
                                    59******9998688899******************************97 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.045
                    Nup35_RRM_2  21 FasfGeIvkhyvpkevsvmyvkfesekdaekA 52 
                                    F  fGeI    +  +   ++v +e e +a kA
  gene147|gene147|rna147|rna147 187 FTKFGEIQSLGIL-SGGKAFVNYERELSALKA 217
                                    6778888887776.567799**********99 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00031      0.43       6      68 ..       7      69 ..       3      73 .. 0.86
   2 ?    1.2   0.0      0.25   3.4e+02       8      60 ..      87     137 ..      80     146 .. 0.76
   3 !   17.0   0.0   2.8e-06    0.0038       1      71 [.     166     234 ..     166     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                   RRM_occluded  6 llplsDtvnkariralveekegeikki.vLvpdheGAivefkdekiagkasLaLdgsefegkkl 68
                                   + ++++  ++++i+ ++++  gei+ i +L+     +ivef+d  +a  a+ +L+g +++g+ l
  gene147|gene147|rna147|rna147  7 VSNFPESYSEENINLIFSPF-GEIRSIkILREPRMFSIVEFRDPLDAKAAIDSLNGRRLHGEGL 69
                                   568899999***********.*****9446777889**********9999999*****998766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.25
                   RRM_occluded   8 plsDtvnkariralveekegeikkivLvpdheGAivefkdekiagkasLaLdg 60 
                                    +++   +++++ ++++ + g+i++i      +  ++ f ++k+a  + L+L+ 
  gene147|gene147|rna147|rna147  87 GIPSDSSSEELMRFFQYY-GPIENITSSDHPQTIFIDFLSHKDA-EMFLELNQ 137
                                    566666788888999999.9999999888778888999888885.66677765 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 2.8e-06
                   RRM_occluded   1 ertisllplsDtvnkariralveekegeikkivLvpdheGAivefkdekiagkasLaLdgsefegkklrcG 71 
                                    er+i +++l+ + +k+ +++l+++  gei+ + + +  + A+v ++ e +a ka+  +dg+   g+k+r+ 
  gene147|gene147|rna147|rna147 166 ERSIFIYNLPSKTTKTDLNDLFTKF-GEIQSLGILSGGK-AFVNYERELSALKAIRHMDGKIVGGNKVRIV 234
                                    589**********************.*******998765.9************************999985 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.018        25       2      28 ..       3      29 ..       2      41 .. 0.92
   2 !   11.5   0.0   0.00018      0.25       2      28 ..      81     107 ..      80     139 .. 0.91
   3 ?    4.6   0.0     0.025        35       2      28 ..     167     193 ..     166     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.018
                          RRM_7  2 rkvFvGGlPiDiteeelkatfkefgkv 28
                                    k+Fv   P   +ee+++  f+ fg++
  gene147|gene147|rna147|rna147  3 SKLFVSNFPESYSEENINLIFSPFGEI 29
                                   69***********************97 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00018
                          RRM_7   2 rkvFvGGlPiDiteeelkatfkefgkv 28 
                                    r+v v G+P D + eel++ f+ +g++
  gene147|gene147|rna147|rna147  81 RRVIVSGIPSDSSSEELMRFFQYYGPI 107
                                    79***********************97 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.025
                          RRM_7   2 rkvFvGGlPiDiteeelkatfkefgkv 28 
                                    r +F+  lP   t+++l++ f +fg++
  gene147|gene147|rna147|rna147 167 RSIFIYNLPSKTTKTDLNDLFTKFGEI 193
                                    679**********************87 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0072       9.9       9      60 ..      10      62 ..       4      76 .. 0.81
   2 !    8.4   0.0    0.0016       2.2       4      60 ..      83     139 ..      82     157 .. 0.88
   3 !    6.4   0.0    0.0066       9.2      11      57 ..     176     221 ..     169     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0072
                                   -SSS--HHHHHHHCHCCS-ECEEEE-TTSSE.EEEEESSHHHHHHHHHHHHHC CS
                          RRM_3  9 lnkelsredikellsklgevayvdyekgdke.gevrFkedeeakkalekatea 60
                                   + +  s e+i  ++s +ge++ +   ++    + v F ++ +ak+a++++   
  gene147|gene147|rna147|rna147 10 FPESYSEENINLIFSPFGEIRSIKILREPRMfSIVEFRDPLDAKAAIDSLNGR 62
                                   56778899****************988765428899***********998765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
                                    EEEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC CS
                          RRM_3   4 lklsGlnkelsredikellsklgevayvdyekgdkegevrFkedeeakkalekatea 60 
                                    + +sG+ +++s e++  +++ +g+++ +  ++  ++  + F ++++a+ +le   ++
  gene147|gene147|rna147|rna147  83 VIVSGIPSDSSSEELMRFFQYYGPIENITSSDHPQTIFIDFLSHKDAEMFLELNQKI 139
                                    6789*******************************************9999866655 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0066
                                    SS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHH CS
                          RRM_3  11 kelsredikellsklgevayvdyekgdkegevrFkedeeakkaleka 57 
                                    +++++ d+ +l+ k+ge++  +  +g k + v ++ + +a ka+ ++
  gene147|gene147|rna147|rna147 176 SKTTKTDLNDLFTKFGEIQSLGILSGGK-AFVNYERELSALKAIRHM 221
                                    67899*******************9986.789999998888888765 PP

>> RNA_bind  RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00082       1.1      12      36 ..       6      30 ..       3      60 .. 0.85
   2 ?   -1.5   0.0       1.9   2.6e+03      18      35 ..      90     107 ..      79     138 .. 0.72
   3 !   11.8   0.0   0.00014      0.19      10      62 ..     168     221 ..     156     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00082
                                   EEEE--TT--HHHHHHHTTTSEEEE CS
                       RNA_bind 12 fyvtFPkeWktsDivqlFspfGsvy 36
                                   f   FP+++ +++i   FspfG+++
  gene147|gene147|rna147|rna147  6 FVSNFPESYSEENINLIFSPFGEIR 30
                                   6668******************985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                    TT--HHHHHHHTTTSEEE CS
                       RNA_bind  18 keWktsDivqlFspfGsv 35 
                                    ++   +++++ F+ +G +
  gene147|gene147|rna147|rna147  90 SDSSSEELMRFFQYYGPI 107
                                    555566778888888876 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00014
                                    EEEEEE--TT--HHHHHHHTTTSEEEE.EEEEETTEEEEEEEEE-HHHHHHHHH CS
                       RNA_bind  10 HvfyvtFPkeWktsDivqlFspfGsvy.vsWlddtsAfvaLhrrdqasvvlktl 62 
                                     +f    P++  ++D+ +lF +fG+++ +  l+   Afv  +r  +a  +++ +
  gene147|gene147|rna147|rna147 168 SIFIYNLPSKTTKTDLNDLFTKFGEIQsLGILSGGKAFVNYERELSALKAIRHM 221
                                    4788899******************97467889999999998887777666655 PP

>> BRAP2  BRCA1-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0065         9      33      72 ..      27      63 ..       3      67 .. 0.74
   2 !    8.1   0.0    0.0022         3       6      66 ..      79     134 ..      75     147 .. 0.76
   3 ?    1.6   0.0      0.24   3.2e+02       5      31 ..     164     190 ..     160     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0065
                          BRAP2 33 ekvseiriirdgkenrymvLikfkdqesadeFykefngkk 72
                                    ++++i+i+r   e r+  +++f+d  +a++  +++ng++
  gene147|gene147|rna147|rna147 27 GEIRSIKILR---EPRMFSIVEFRDPLDAKAAIDSLNGRR 63
                                   4455555555...6688999******************97 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0022
                          BRAP2   6 rstllcilavPsylsladllkFvgsvlekvseiriirdgkenrymvLikfkdqesadeFyk 66 
                                    r++ +++  +Ps  s ++l++F++ +   +++i    +++++  ++ i f ++++a+ F +
  gene147|gene147|rna147|rna147  79 RKRRVIVSGIPSDSSSEELMRFFQYY-GPIENI----TSSDHPQTIFIDFLSHKDAEMFLE 134
                                    7899******************9754.456665....456666677788888888877776 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.24
                          BRAP2   5 srstllcilavPsylsladllkFvgsv 31 
                                    s ++ ++i+ +Ps+ +  dl  ++ ++
  gene147|gene147|rna147|rna147 164 SPERSIFIYNLPSKTTKTDLNDLFTKF 190
                                    667899*************99887765 PP

>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.016        22      20      59 ..       9      48 ..       2      61 .. 0.85
   2 ?    3.0   0.0     0.073     1e+02      16      42 ..      82     109 ..      76     127 .. 0.86
   3 !    7.8   0.0    0.0022       3.1      14      42 ..     166     195 ..     155     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                             RL 20 scpskisekkllkylsqhGkinkhFfYeskgvyavvEFse 59
                                   + p+  se+++   +s +G+i++     +  ++ +vEF +
  gene147|gene147|rna147|rna147  9 NFPESYSEENINLIFSPFGEIRSIKILREPRMFSIVEFRD 48
                                   678889999999999***********************74 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.073
                             RL  16 svLis.cpskisekkllkylsqhGkink 42 
                                     v++s +ps+ s ++l++++  +G i++
  gene147|gene147|rna147|rna147  82 RVIVSgIPSDSSSEELMRFFQYYGPIEN 109
                                    455543899****************987 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0022
                             RL  14 ersvLi.scpskisekkllkylsqhGkink 42 
                                    ers+ i ++psk+++++l + + ++G+i++
  gene147|gene147|rna147|rna147 166 ERSIFIyNLPSKTTKTDLNDLFTKFGEIQS 195
                                    899999789*******************97 PP

>> Limkain-b1  Limkain b1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.11   1.5e+02       4      74 ..       4      72 ..       1      81 [. 0.74
   2 !   13.5   0.0   4.1e-05     0.056       6      76 ..     170     236 ..     166     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                     Limkain-b1  4 llvvsnLPtnrdklkkaiknrLrrLsdncGGkvlsisgksavlrfanqeaaeralkrleneDvfGnritvs 74
                                    l+vsn+P +    ++ i+  ++ + +    k+l      +++ f+++  a+ a+  l++   +G+ +++ 
  gene147|gene147|rna147|rna147  4 KLFVSNFPESYS--EENINLIFSPFGEIRSIKILREPRMFSIVEFRDPLDAKAAIDSLNGRRLHGEGLSLH 72
                                   577777777766..666666666666666666676677778999999999999999999998888877765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.1e-05
                     Limkain-b1   6 vvsnLPtnrdklkkaiknrLrrLsdncGG.kvlsi.sgksavlrfanqeaaeralkrleneDvfGnritvsek 76 
                                    +++nLP +        k  L+ L+   G  + l+i sg+ a ++++ + +a +a++ +++  v Gn++ +  k
  gene147|gene147|rna147|rna147 170 FIYNLPSKTT------KTDLNDLFTKFGEiQSLGIlSGGKAFVNYERELSALKAIRHMDGKIVGGNKVRIVLK 236
                                    6677776555......77788888877642334433899****************************998766 PP

>> RRM_Rrp7  Rrp7 RRM-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.4   3.3e+03      48      75 ..      87     111 ..      78     138 .. 0.67
   2 !   14.6   0.1   1.5e-05     0.021      30      65 ..     155     190 ..     133     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                       RRM_Rrp7  48 NlPiettletlkkffqkvalgatiesvv 75 
                                     +P  ++ e+l +ffq     + ie+++
  gene147|gene147|rna147|rna147  87 GIPSDSSSEELMRFFQYY---GPIENIT 111
                                    577777888888888754...4455553 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.5e-05
                       RRM_Rrp7  30 kHqtknndeessrslFlvNlPiettletlkkffqkv 65 
                                    k + +++ ++ +rs+F++NlP +tt   l   f k 
  gene147|gene147|rna147|rna147 155 KRERRDHISSPERSIFIYNLPSKTTKTDLNDLFTKF 190
                                    455555556679***************999999876 PP

>> DUF4523  Protein of unknown function (DUF4523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.053        73     107     147 ..      19      61 ..       6      68 .. 0.78
   2 ?   -3.0   0.0         4   5.5e+03     111     125 ..     101     115 ..      92     126 .. 0.71
   3 ?    8.7   0.0     0.001       1.4     110     148 ..     186     224 ..     153     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.053
                        DUF4523 107 viqrLsvfGpiesvtlc..Grqsavvvfkdiisackavsafqs 147
                                    +    s fG+i+s+ ++   r  ++v f+d   a  a+ +++ 
  gene147|gene147|rna147|rna147  19 INLIFSPFGEIRSIKILrePRMFSIVEFRDPLDAKAAIDSLNG 61 
                                    5555789******98872257889*******999999988765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                        DUF4523 111 LsvfGpiesvtlcGr 125
                                       +Gpie +t+  +
  gene147|gene147|rna147|rna147 101 FQYYGPIENITSSDH 115
                                    456899999987654 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.001
                        DUF4523 110 rLsvfGpiesvtlcGrqsavvvfkdiisackavsafqsr 148
                                      + fG+i+s+ ++    a v ++   sa ka++ +  +
  gene147|gene147|rna147|rna147 186 LFTKFGEIQSLGILSGGKAFVNYERELSALKAIRHMDGK 224
                                    4578********999999**************9987665 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   2.8e+03       4      25 ..       5      25 ..       4      55 .. 0.74
   2 ?    8.2   0.0     0.002       2.7       2      32 ..      81     110 ..      80     153 .. 0.88
   3 ?    2.0   0.0      0.15   2.1e+02       2      27 ..     167     191 ..     166     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                       PHM7_cyt  4 vlvtgiPkelrseeklkeffee 25
                                   ++v++ P++++ ee+++ +f+ 
  gene147|gene147|rna147|rna147  5 LFVSNFPESYS-EENINLIFSP 25
                                   57888888888.6667766654 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.002
                       PHM7_cyt   2 rTvlvtgiPkelrseeklkeffeelypgkvv 32 
                                    r v+v+giP++ +se +l +ff+ + p + +
  gene147|gene147|rna147|rna147  81 RRVIVSGIPSDSSSE-ELMRFFQYYGPIENI 110
                                    7799*********55.59****998887665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.15
                       PHM7_cyt   2 rTvlvtgiPkelrseeklkeffeely 27 
                                    r++++ ++P++++ + +l+++f+++ 
  gene147|gene147|rna147|rna147 167 RSIFIYNLPSKTT-KTDLNDLFTKFG 191
                                    89**********9.778999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1559.72
//
Query:       gene1471|gene1471|rna1470|rna1470  [L=488]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-70  235.8   0.2    7.5e-70  235.0   0.2    1.4  1  Nop       snoRNA binding domain, fibrillarin
    8.8e-08   32.4   0.2    3.2e-07   30.6   0.2    2.1  1  NOP5NT    NOP5NT (NUC127) domain
     0.0012   18.9   0.4       0.94    9.6   0.0    2.8  2  RsbU_N    Phosphoserine phosphatase RsbU, N-terminal domain


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.0   0.2   1.3e-73   7.5e-70       1     229 [.     155     384 ..     155     385 .. 0.94

  Alignments for each domain:
  == domain 1  score: 235.0 bits;  conditional E-value: 1.3e-73
                                        HHHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT.HHHHHHHHHHHHCHHHH-S CS
                                Nop   1 lldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkeedeelakevimaakvtastsm 76 
                                        ll+++dk+in++++r+re+Y+w FpEL  l+k+n eY+++vk + ne+ d + ++ d  +++e ++ +k   ++sm
  gene1471|gene1471|rna1470|rna1470 155 LLEQVDKDINSYSMRIREIYGWVFPELGALLKENHEYISAVKYFVNEEVDSDYTKCDPGINEERLDEIKKLRKNSM 230
                                        689******************************************87666644433555888888888888889** PP

                                        SS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTT CS
                                Nop  77 gaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqi 152
                                        g++ls+ d+ n+k+l++ v +  + r +l +Yl+++ms iAPNl+a++G+ ++ar+is+aGgL nLak+Past q+
  gene1471|gene1471|rna1470|rna1470 231 GMKLSPVDMINLKKLIEIVDNKIKVRGSLGRYLKEKMSSIAPNLAAILGDVLGARIISQAGGLLNLAKAPASTFQL 306
                                        **************************************************************************** PP

                                        TT-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT---.-SHHHHHHHHHHH CS
                                Nop 153 lGaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekd.gslGkklreeiek 226
                                        lGaek+lfr+lk kk+tpkyGl+y s++v+  + +k k +i+R++a+K+++aa+iD f+e++ +++G +l++ i+k
  gene1471|gene1471|rna1470|rna1470 307 LGAEKSLFRSLKmKKRTPKYGLLYTSSYVS-RVRDKDKARICRYIATKCSIAAKIDYFGESRgDEYGVELKSLIDK 381
                                        ************999***************.56*************************99999************* PP

                                        HHH CS
                                Nop 227 klk 229
                                        k++
  gene1471|gene1471|rna1470|rna1470 382 KIQ 384
                                        *97 PP

>> NOP5NT  NOP5NT (NUC127) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.2   5.3e-11   3.2e-07       1      65 []       3      62 ..       3      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5.3e-11
                             NOP5NT  1 fiLfEtaaGYaLfkvkdkkllkkddlvkdsvsdlekfsklvkLkaFqkFesaaeALenanaiseG 65
                                       ++LfE a GY+Lf++k+ + ++k    +   +d+ k+ ++++Lk+  kF+s  eA +  + +s G
  gene1471|gene1471|rna1470|rna1470  3 HLLFEYAGGYGLFELKEYEDMSK----ST-YDDYTKLTQVLNLKSRMKFNSFNEASDHLKCLSQG 62
                                       79***************999988....33.6899*********************9999999877 PP

>> RsbU_N  Phosphoserine phosphatase RsbU, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00016      0.94      16      54 ..     124     163 ..     117     171 .. 0.81
   2 !    6.4   0.1    0.0015       9.2      15      42 ..     215     242 ..     213     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                                        HHHHHHHHHHHHHHHHTT--HHHHHHHHHH.HHHHH-TTS CS
                             RsbU_N  16 eqsLyeaeelsrellekgispeeivelHke.vleelskdl 54 
                                        ++ L  a+e sre +e +++ e+++ +H   +le+++kd+
  gene1471|gene1471|rna1470|rna1470 124 QTVLGLAYEYSREKVEYNVKREDFIVIHTVmLLEQVDKDI 163
                                        45688899********************861567777775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0015
                                        -HHHHHHHHHHHHHHHHTT--HHHHHHH CS
                             RsbU_N  15 deqsLyeaeelsrellekgispeeivel 42 
                                        +e+ L e+++l ++++  ++sp ++++l
  gene1471|gene1471|rna1470|rna1470 215 NEERLDEIKKLRKNSMGMKLSPVDMINL 242
                                        6999**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 3012.52
//
Query:       gene1472|gene1472|rna1471|rna1471  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-55  185.1   0.0    4.5e-54  182.7   0.0    2.0  2  Sua5_yciO_yrdC  Telomere recombination
    1.4e-24   87.2   0.0    2.3e-24   86.5   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin
  ------ inclusion threshold ------
      0.013   15.1   0.0       0.03   14.0   0.0    1.5  1  Phage_tail_X    Phage Tail Protein X


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   0.0   7.5e-58   4.5e-54       7     179 .]      20     191 ..      18     191 .. 0.98
   2 ?   -0.4   0.0      0.11   6.8e+02     134     179 .]     218     262 ..     210     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 7.5e-58
                                        SEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEEE CS
                     Sua5_yciO_yrdC   7 givaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitlll 82 
                                         +v+iptetvYgLa+++ n++aver++e+K+rp+d+pl+v+v+s ++l++++e +++ e  kl++rfwPGp+ ll 
  gene1472|gene1472|rna1471|rna1471  20 DVVVIPTETVYGLAASIHNPRAVERIFELKRRPADNPLIVHVSSEQMLEEIVEGPIPVEYRKLMDRFWPGPLSLLF 95 
                                        69************************************************************************** PP

                                        E..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---S CS
                     Sua5_yciO_yrdC  83 krskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeia 158
                                        k  k+++++++ +gl+t++vr+P+++  ++++e+lg p++a+San+sg+ps+t+ ++v e++g++v++i+dgg+++
  gene1472|gene1472|rna1471|rna1471  96 KS-KDSVSPVIRGGLSTIAVRMPKNKQLLEIIERLGVPVAAPSANVSGRPSPTTVDHVIEDFGDKVEMIIDGGPCS 170
                                        *6.666********************************************************************** PP

                                        SS---EEEETTSSTSSECEXX CS
                     Sua5_yciO_yrdC 159 vgvdstVvdltegkpkilRrG 179
                                        vgv+stVv + +g ++ilR+G
  gene1472|gene1472|rna1471|rna1471 171 VGVESTVVWYADGVLQILRPG 191
                                        *******************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                                        -SSHHHHHHHC-TTSECB-SS---SSS---EEEETTSSTSSECEXX CS
                     Sua5_yciO_yrdC 134 itdaeeveeelgeivdlildggeiavgvdstVvdltegkpkilRrG 179
                                        ++++ + +++ + +  l+l +g   ++ +s +++++e +p i R G
  gene1472|gene1472|rna1471|rna1471 218 VLSPGQKYKHYSPRSPLVLFKG-RPKEMESGILKYIEANPGIARIG 262
                                        5566666778888888999999.55679********9999999966 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   3.9e-28   2.3e-24       3     133 ..     195     331 ..     193     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 3.9e-28
                                        HHHHHHHS-..-..-.......-------------S-SSEEEEE--GGGHHHH.....HHHHHTTS-EEEEEEGGG CS
                               SUA5   3 leeleevld..a..vek...keekpraPGmkyrHYaPkapvvlveaeeeeeaakeekleekkksgkkvgvlatses 71 
                                        +e++++v+d     + +     e++ +PG+ky+HY+P+ p+vl+++  +e ++ + k  e++   +++gv   s  
  gene1472|gene1472|rna1471|rna1471 195 IEDIKDVVDceVvmK-NkieGGEEVLSPGQKYKHYSPRSPLVLFKGRPKEMESGILKYIEANPGIARIGVGLHSGI 269
                                        799999996542222.135578999***********************99999999999999999**999996666 PP

                                        TGG....TSEEEEE..E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHT CS
                               SUA5  72 kea....assvlslslgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAA 133
                                        + +    ++  + + +g  + ++e++rnLF++Lr+lD+   d+ilv g++ +++g A+m+RL++AA
  gene1472|gene1472|rna1471|rna1471 270 NIEtplgRKVDIFN-MG--NVKKEVCRNLFEGLRKLDK-TSDVILVAGIDCNEEGYAIMDRLERAA 331
                                        66677643333333.46..999***************5.67************************9 PP

>> Phage_tail_X  Phage Tail Protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     5e-06      0.03      30      52 ..     252     274 ..     245     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
                                        HHHSTTTTTT-S---TTEEEE-T CS
                       Phage_tail_X  30 leaNPgLAelgpvLphGtavelP 52 
                                        +eaNPg+A +g  L +G+++e P
  gene1472|gene1472|rna1471|rna1471 252 IEANPGIARIGVGLHSGINIETP 274
                                        89******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1941.01
//
Query:       gene1473|gene1473|rna1472|rna1472  [L=559]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.9e-21   74.1   0.0    2.2e-20   72.8   0.0    1.7  1  XPG_I     XPG I-region
    2.5e-14   53.6   0.1    2.9e-13   50.1   0.0    2.6  2  XPG_N     XPG N-terminal domain
     0.0053   16.3   0.0      0.011   15.2   0.0    1.6  1  XPG_I_2   XPG domain containing


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   3.6e-24   2.2e-20       2      94 .]     395     477 ..     394     477 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 3.6e-24
                                        HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHH CS
                              XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkel 77 
                                         ++i+yv+Ap+EA++qc +++ +++vd+vi+eD D+ll+G++ v+rn++  +++        ++e+++lek++k l
  gene1473|gene1473|rna1472|rna1472 395 VFNISYVDAPTEADSQCGFMCYRNIVDGVITEDNDVLLYGGT-VYRNFF--RRDR-------EIEKYSLEKIEKDL 460
                                        589*************************************97.799998..4333.......69************ PP

                                        T--HHHHHHHHHHHCET CS
                              XPG_I  78 gltreqlidlaillgcD 94 
                                        +l+r++li l+ +lg+D
  gene1473|gene1473|rna1472|rna1472 461 RLDRKNLIRLSHMLGSD 477
                                        ***************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   4.9e-17   2.9e-13       1      98 [.       1      84 [.       1      87 [. 0.87
   2 ?   -2.5   0.0       1.2   7.2e+03      11      34 ..     492     520 ..     481     533 .. 0.58

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 4.9e-17
                                       X--TTHHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS-HHHHHHHHHHHHHHHTTEEEEEE CS
                              XPG_N  1 MGikgLlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalentshlmglfsrllrlldfgikPifV 78
                                       MG+++L+k+lk++a  ++v +   +g +la+D s+w+ +           +l+++  + ++ +r+ +ll+ gikPifV
  gene1473|gene1473|rna1472|rna1472  1 MGVRSLWKILKPSA--ERVTP---SGIRLAVDTSIWICQY---------GHLRSDDIVYFFSKRIAKLLYHGIKPIFV 64
                                       **************..66666...6889*********875.........3455567888999**************** PP

                                       E--S--GGGHHHHHHHHHHH CS
                              XPG_N 79 Fdgkapdlkkeelekrserr 98
                                       Fdgkap++k++++  r+ r 
  gene1473|gene1473|rna1472|rna1472 65 FDGKAPEIKRQAILERRRRI 84
                                       ************98888775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                        HHH-..GEEEEEGGGGTT...EEEEEEHH CS
                              XPG_N  11 keva..airsvsiealeg...kklaiDas 34 
                                        + v   +i++ +++ l +   + +aiD+ 
  gene1473|gene1473|rna1472|rna1472 492 EAVRkgSIEEEDVKVLMElylNPVAIDVT 520
                                        33334456666666666655556677765 PP

>> XPG_I_2  XPG domain containing
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-06     0.011      10      58 ..     390     434 ..     382     521 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                            XPG_I_2  10 ieaLknrwkakditevvpgEADkfcAvlA.rklgcaVLTsDSDLlvhdlg 58 
                                         ++L+   +++ +++  p EAD +c ++  r+  + V T+D D+l++  g
  gene1473|gene1473|rna1472|rna1472 390 KDVLD---VFNISYVDAPTEADSQCGFMCyRNIVDGVITEDNDVLLY--G 434
                                        56666...777788889******************************..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3454.29
//
Query:       gene1474|gene1474|rna1473|rna1473  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.082   12.9   9.0       0.16   11.9   9.0    1.5  1  zf-RING_5  zinc-RING finger domain
       0.29   11.5   8.6       0.53   10.7   8.6    1.5  1  zf-RING_2  Ring finger domain
        1.7    8.9   8.6         30    4.9   8.7    2.2  2  FYVE_2     FYVE-type zinc finger


Domain annotation for each model (and alignments):
>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   9.0   2.7e-05      0.16       2      44 .]     259     305 ..     258     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                          zf-RING_5   2 CnkCfekl..skeekfyltsCgHifCekClkkll..ekeavCpiCrk 44 
                                        C +C++ +  +++ +   + C  i+C +Clk+++   ++  C  C++
  gene1474|gene1474|rna1473|rna1473 259 CDVCCKVFtgEDRANLQRLMCNDIICRRCLKQSFlyLSDEFCVKCKQ 305
                                        ********55555559999***************9988899999986 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   8.6   8.9e-05      0.53       2      44 .]     258     304 ..     257     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.9e-05
                          zf-RING_2   2 eCpICleelssads..vlllpCgHvfhreClerwlrssst..CPlCr 44 
                                         C +C++ ++ +d+  +++l C+ +++r Cl++ +   s   C  C+
  gene1474|gene1474|rna1473|rna1473 258 VCDVCCKVFTGEDRanLQRLMCNDIICRRCLKQSFLYLSDefCVKCK 304
                                        6****9999776664466777**********9964444444899996 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   8.7     0.005        30      29     102 ..     236     305 ..     224     309 .. 0.76
   2 ?    3.4   0.1     0.014        85      52      68 ..     295     311 ..     289     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.005
                             FYVE_2  29 lgelkeklekekskrellgnqaklgethCilCleefkllvnskrqCldCklnvCkkCsvenk.kekvwlCkiCse 102
                                        +++l + +    +k ++ ++ +  +++ C  C++ f+     + q l C+  +C++C +++    +   C  C++
  gene1474|gene1474|rna1473|rna1473 236 INHLGRMI----MKTRVFSD-TIPKRDVCDVCCKVFTGEDRANLQRLMCNDIICRRCLKQSFlYLSDEFCVKCKQ 305
                                        45554444....89999999.677899******************************988431233445666665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.014
                             FYVE_2  52 lgethCilCleefkllv 68 
                                        l+++ C++C +++ +l 
  gene1474|gene1474|rna1473|rna1473 295 LSDEFCVKCKQKYDILS 311
                                        78899********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 1785.36
//
Query:       gene1475|gene1475|rna1474|rna1474  [L=491]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-36  125.3   0.0    3.8e-36  124.5   0.0    1.4  1  DEAD        DEAD/DEAH box helicase
      3e-29  101.6   0.0    6.6e-29  100.5   0.0    1.6  1  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
       0.11   12.8   0.0         19    5.6   0.0    2.5  2  AAA_19      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0   6.3e-40   3.8e-36       2     171 ..     135     296 ..     134     299 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 6.3e-40
                                        HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                        ++Qa++ip +l+g+++lv+ + G+GKT+ ++ip+l+++    ++   + +i++P reLa q+ +n+k++ + +++ 
  gene1475|gene1475|rna1474|rna1474 135 PVQAASIPRALKGRNLLVRSKNGTGKTASYVIPMLNAIN--PDELSIQGIILVPIRELALQISRNVKRLSEGMGVA 208
                                        89*********************************9995..699999***************************99 PP

                                        EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                         + ++gg++ +d++ +++ngv+++vgtpgr++dl++++   +s+  +lV+DEad+lld  f++++ r+l+ l    
  gene1475|gene1475|rna1474|rna1474 209 SVPVVGGTNMQDDIIRVSNGVHVMVGTPGRIVDLVEKKIGVISKKVILVFDEADKLLDVTFGETVTRLLELL---- 280
                                        9999*************9*****************87777799999**************************.... PP

                                        TTSTTTSEEEEEESSBS.H CS
                                        xxxxxxxxxxxxxxxxx.x RF
                               DEAD 154 cdgklqrqvivlSATlp.k 171
                                           + +rq+++ SAT+p +
  gene1475|gene1475|rna1474|rna1474 281 ---PRERQILLYSATFPyF 296
                                        ...56789*******9944 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.0   1.1e-32   6.6e-29       2     111 .]     334     442 ..     333     442 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1.1e-32
                                        HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                         Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                        kl +l  ll l+ + ++++if+n+i+++   +ll  +    g+ +  +h++++q++r+ ++++f kg++++L+atd
  gene1475|gene1475|rna1474|rna1474 334 KLICLRSLL-LKLKINQCVIFCNNIRTV---ELLAMRItgmGMPSYFIHSKMTQEDRNIVFHNFLKGKCKILVATD 405
                                        566777777.9999**************...56644445679********************************** PP

                                        GGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  75 vaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                         + rG+d+p+ n+Vinfd+p++++sy +riGR+gR+g
  gene1475|gene1475|rna1474|rna1474 406 LITRGVDVPNTNYVINFDIPKSPESYLHRIGRAGRFG 442
                                        ***********************************86 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0032        19       5      52 ..     141     189 ..     137     289 .. 0.55
   2 ?    4.9   0.0     0.005        30      38      92 ..     343     395 ..     333     471 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0032
                             AAA_19   5 ve.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftg 52 
                                        +  alk ++llv    GtGKT   +  +  +++  +++ + i+lv   +
  gene1475|gene1475|rna1474|rna1474 141 IPrALKGRNLLVRSKNGTGKTASYVIPMLNAINPDELSIQGIILVPIRE 189
                                        5348999**************9887777777777777766666654433 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.005
                             AAA_19  38 ggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddlltealelle 92 
                                         ++k +++++ + + r ++ l+ r++++g++ + iH+   ++ +d++    ++l+
  gene1475|gene1475|rna1474|rna1474 343 LKLKINQCVIFCNNIRTVELLAMRITGMGMPSYFIHSK--MTQEDRNIVFHNFLK 395
                                        456789******************************87..666666666677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 2869.12
//
Query:       gene1476|gene1476|rna1475|rna1475  [L=410]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-35  119.6   0.4    1.5e-34  118.9   0.4    1.3  1  NGP1NT          NGP1NT (NUC091) domain
    8.2e-18   64.5   0.3    3.1e-14   53.0   0.0    2.5  2  MMR_HSR1        50S ribosome-binding GTPase
    4.7e-05   23.3   0.0    0.00012   22.0   0.0    1.7  1  RsgA_GTPase     RsgA GTPase
     0.0001   21.9   0.2    0.00045   19.8   0.0    2.0  2  FeoB_N          Ferrous iron transport protein B
    0.00034   20.7   3.4       0.64   10.0   0.0    3.7  4  Dynamin_N       Dynamin family
    0.00072   19.0   0.2        0.1   12.0   0.0    2.4  2  Arf             ADP-ribosylation factor family
  ------ inclusion threshold ------
      0.021   15.4   0.5       0.04   14.5   0.5    1.4  1  Com_YlbF        Control of competence regulator ComK, YlbF/Ym
      0.043   14.0   0.1         16    5.8   0.0    2.6  2  Roc             Ras of Complex, Roc, domain of DAPkinase
      0.079   12.5   0.3         12    5.3   0.0    3.2  3  GTP_EFTU        Elongation factor Tu GTP binding domain
      0.096   12.7   0.6       0.27   11.2   0.1    2.0  2  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
       0.15   12.1   1.6        2.6    8.0   0.8    2.2  2  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 


Domain annotation for each model (and alignments):
>> NGP1NT  NGP1NT (NUC091) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.4   9.2e-38   1.5e-34       1     127 [.      16     134 ..      16     137 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 9.2e-38
                             NGP1NT   1 mykegkakrdkkGkiikaaalqskeasksariepdrrWFgntrvisqeaLekfreeleekvkdpysvllkrnklPm 76 
                                        m+++g++k++++G+iik+a++qs++a  ++riep+r+WF  +++is ++L++fr+e   k++ py+vll + k+P+
  gene1476|gene1476|rna1475|rna1475  16 MLRSGRPKKNSRGDIIKDAPFQSSKA-DVGRIEPSRKWFSGSKTISPTELDAFRSET--KIESPYNVLLSTGKVPY 88 
                                        99************************.****************************98..99*************** PP

                             NGP1NT  77 sLledkakkkkvklletesfeetFgpkaqrkrpklevsdleelakkaeeka 127
                                        sLled +kk+     ++++f  +Fg+k+ rk+p+l++++leel ++++e +
  gene1476|gene1476|rna1475|rna1475  89 SLLEDGTKKR-----KAKDFGAVFGKKSVRKKPNLQYNSLEELSQQVKEVK 134
                                        *******997.....789****************************99876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2    0.0007       1.1      71     114 .]     158     202 ..     121     202 .. 0.77
   2 !   53.0   0.0   1.9e-17   3.1e-14       2      57 ..     259     328 ..     258     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0007
                                        HHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                           MMR_HSR1  71 laleeadlillvvdaseeklkpldeeleellee..akkplilvlnk 114
                                        + l+++d+i++v+da+ + l  +  +++++++e   +k l++vlnk
  gene1476|gene1476|rna1475|rna1475 158 KVLDSSDVIIHVLDAR-DPLGTMCDKIANYIKEeaPHKHLMYVLNK 202
                                        224458********88.77888888888888776677889999998 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 1.9e-17
                                        EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC................S CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGl................i 57 
                                        v++vG+pN+GKS++in+l ++ +++v+  pg T+  ++++++  g  i+l+D+pG+                i
  gene1476|gene1476|rna1475|rna1475 259 VGFVGYPNTGKSSIINTLRNKeVCKVAPVPGETKVWQYITLT--G-GIYLIDCPGIvpipnydqavlrgavrI 328
                                        89******************9678*****************9..4.7********844444444433333331 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   7.6e-08   0.00012      46     161 ..     193     311 ..     165     315 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.6e-08
                                        T-EEEEEEE-GGG--HHH...HHHHHHHHHHHTTSEEEE--TTTHTT.....HHHHHHHCTT.SEEE.EECSTTSS CS
                        RsgA_GTPase  46 giepvivlnKiDlleeee...eleelkeelealgyevllvsaktkeg.....leelkellkd.ktsv.lvGqSGvG 111
                                        + +++ vlnK+Dl+ +      l+ +++   ++ y+   + ++ +++     l++l++l k+ ++sv +vG    G
  gene1476|gene1476|rna1475|rna1475 193 HKHLMYVLNKVDLIPTGVtakWLRYFSKSHPTIAYHSNSITKNYGKAnliglLKQLSKLYKKrHLSVgFVGYPNTG 268
                                        4578889*******99884444455555555666666555555443222222567777777765655699****** PP

                                        HHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                        RsgA_GTPase 112 KStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                        KS++in+l++++  k++ v  +       T+  + + l  g +liD PG+
  gene1476|gene1476|rna1475|rna1475 269 KSSIINTLRNKEVCKVAPVPGE-------TKVWQYITLTGGIYLIDCPGI 311
                                        *******************997.......88899999999999*****98 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.6   9.8e+02      77      90 ..     161     174 ..     156     206 .. 0.81
   2 !   19.8   0.0   2.8e-07   0.00045       3      62 ..     259     316 ..     257     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.6
                                        TSSSEEEEEEEGGG CS
                             FeoB_N  77 eepdvvvnvvdatn 90 
                                        ++ dv+++v+da  
  gene1476|gene1476|rna1475|rna1475 161 DSSDVIIHVLDARD 174
                                        578999***99975 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.8e-07
                                        EEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSS CS
                             FeoB_N   3 valvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkgkeveivDlPGiYslsa 62 
                                        v +vG pn+Gk++++n+l +++  kv+  pG t   +  +l+     + ++D PGi  + +
  gene1476|gene1476|rna1475|rna1475 259 VGFVGYPNTGKSSIINTLRNKEvCKVAPVPGETKVWQYITLT---GGIYLIDCPGIVPIPN 316
                                        789***************988745888888887655555555...8999******976655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.2      0.33   5.4e+02      56      96 ..     113     157 ..      58     167 .. 0.62
   2 ?    1.9   0.0      0.13   2.1e+02     123     167 ..     157     202 ..     140     203 .. 0.73
   3 !   10.0   0.0   0.00039      0.64       1      30 [.     259     288 ..     259     295 .. 0.87
   4 !    6.4   0.0    0.0053       8.6      98     132 ..     298     338 ..     290     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.33
                                        EEE....T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEE CS
                          Dynamin_N  56 kek....ekkledfsevreeieketekiagankgiskkvillkil 96 
                                        ++k       le++s+  +e+++++++i+++  + +++ i l+ +
  gene1476|gene1476|rna1475|rna1475 113 RKKpnlqYNSLEELSQQVKEVKERKKEIKKEHVKGQSHRIWLELY 157
                                        333422234444444444444555555554444444444544444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                                        HHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTT..EEEEEE- CS
                          Dynamin_N 123 keyikkadiilavtsanhdlsnsealflarevdpkgkr..tivvltk 167
                                         + ++++d+i++v++a   l  +  +++a+ ++++      + vl+k
  gene1476|gene1476|rna1475|rna1475 157 YKVLDSSDVIIHVLDARDPLG-TMCDKIANYIKEEAPHkhLMYVLNK 202
                                        678899***********9887.6666777766666555446666666 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00039
                                        EEEEEBTTTTHHHHHHHHHTS--S---SSS CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnp 30 
                                        + +vG  + GKSS++n L  +++  + p p
  gene1476|gene1476|rna1475|rna1475 259 VGFVGYPNTGKSSIINTLRNKEVCKVAPVP 288
                                        678999*************99998887766 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0053
                                        TTS-SEEEEE---B-SSSGTTS.....HHHHHHH.STTEEE CS
                          Dynamin_N  98 llvkgltlvDlPGldsvnkrdq.....elvkeyi.kkadii 132
                                         l  g+ l+D PG+  +++ dq     ++  e i +++d i
  gene1476|gene1476|rna1475|rna1475 298 TLTGGIYLIDCPGIVPIPNYDQavlrgAVRIENIeDPEDYI 338
                                        5678999***************6666544444444555555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1      0.01        17      49     128 ..     129     206 ..     114     232 .. 0.77
   2 !   12.0   0.0   6.4e-05       0.1       3      47 ..     246     289 ..     244     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.01
                                        EEEEEEETTEEEEEEEE-SSGGGGGGGGGGCT...TESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEE CS
                                Arf  49 nveeleiknlkftvwDvGGqeklRplWknYfe...ktdavifvvDsadreRleeakeeLkalleeeelkevallvl 121
                                        +v+e++ ++ +++   v Gq++  ++W + ++   + d++i+v+D+ d   l ++ +++++ ++ee  ++ +l+ +
  gene1476|gene1476|rna1475|rna1475 129 QVKEVKERKKEIKKEHVKGQSH--RIWLELYKvldSSDVIIHVLDARD--PLGTMCDKIANYIKEEAPHK-HLMYV 199
                                        6777777777777777777764..6777766522267899*****976..58999999999999877665.66677 PP

                                        EE-TTST CS
                                Arf 122 aNKqDlp 128
                                         NK Dl 
  gene1476|gene1476|rna1475|rna1475 200 LNKVDLI 206
                                        8999984 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.4e-05
                                        HHHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSS CS
                                Arf   3 silaklklkkkelrilllGLDnaGKtTilkklkleelvttvPTig 47 
                                        + l+kl + k++l + ++G  n+GK+ i++ l+++e+ ++ P  g
  gene1476|gene1476|rna1475|rna1475 246 KQLSKLYK-KRHLSVGFVGYPNTGKSSIINTLRNKEVCKVAPVPG 289
                                        56778877.999***************************999766 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   2.5e-05      0.04      29     102 ..     121     189 ..     114     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                        HCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Com_YlbF  29 eedeelqklikefkklqkelqekqmkgeelkeeekkelqelkeeldknplvkeyleaeqelnellqevnkiiae 102
                                        ++ eel +++ke+k+++ke+ ++  kg     ++ +   el++ ld+ +++   l+a++ l ++ +++ + i e
  gene1476|gene1476|rna1475|rna1475 121 NSLEELSQQVKEVKERKKEIKKEHVKG-----QSHRIWLELYKVLDSSDVIIHVLDARDPLGTMCDKIANYIKE 189
                                        566899999999999999998866555.....4444788*******************************9987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0      0.01        17      78     120 .]     161     205 ..     110     205 .. 0.85
   2 ?    5.8   0.0    0.0095        16       3      24 ..     260     281 ..     258     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.01
                                        CTSCEEEEEEEGHHH..HCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                                Roc  78 reaalailvydsrss..enlkeWlkelkkvagkspvilvgnkiDl 120
                                         +++++i v+d+r+   +  ++  + +k++a+++ ++ v nk+Dl
  gene1476|gene1476|rna1475|rna1475 161 DSSDVIIHVLDARDPlgTMCDKIANYIKEEAPHKHLMYVLNKVDL 205
                                        678899999998875447889999*******************95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0095
                                        EEESSTTSSHHHHHHCHCT-CC CS
                                Roc   3 vlvGdsgvGKtsllkrfvedkf 24 
                                         +vG  ++GK+s+++ + ++++
  gene1476|gene1476|rna1475|rna1475 260 GFVGYPNTGKSSIINTLRNKEV 281
                                        589*************999876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0075        12      89     135 ..     158     206 ..     153     233 .. 0.83
   2 ?    2.6   0.0     0.054        88       1      24 [.     254     277 ..     254     284 .. 0.90
   3 ?   -0.1   0.0      0.35   5.8e+02      70      81 ..     301     312 ..     290     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0075
                                        HHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE..EEEEEESCGST CS
                           GTP_EFTU  89 rglrvlDgavlvvdaveGvepqteevlrlalkegvp..iivfiNKmDrl 135
                                        + l   D+ + v+da++   +   ++++ +++e  +  ++ ++NK+D +
  gene1476|gene1476|rna1475|rna1475 158 KVLDSSDVIIHVLDARDPLGTMCDKIANYIKEEAPHkhLMYVLNKVDLI 206
                                        567789**********9999999999999988876677*********98 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.054
                                        TCEEEEEEEESTTSSHHHHHHHHH CS
                           GTP_EFTU   1 krirnigiighvDhGKtTLtdrLl 24 
                                        kr++ +g++g  ++GK++++ +L 
  gene1476|gene1476|rna1475|rna1475 254 KRHLSVGFVGYPNTGKSSIINTLR 277
                                        6899***************99987 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.35
                                        EEEEEEEESSSG CS
                           GTP_EFTU  70 ylinliDtPGHv 81 
                                          i liD+PG v
  gene1476|gene1476|rna1475|rna1475 301 GGIYLIDCPGIV 312
                                        5689******76 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00017      0.27      42      74 ..     180     212 ..     132     237 .. 0.74
   2 ?   -1.5   0.1       1.6   2.6e+03      36      65 ..     328     358 ..     320     369 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                       MMR_HSR1_Xtn  42 vDdlidviegnrvYipclyvlNKiDlisleeld 74 
                                         D++ + i+++   ++ +yvlNK+Dli    + 
  gene1476|gene1476|rna1475|rna1475 180 CDKIANYIKEEAPHKHLMYVLNKVDLIPTGVTA 212
                                        799***********************8765554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                       MMR_HSR1_Xtn  36 iredvtvDdlidvi.egnrvYipclyvlNKi 65 
                                        i++  + +d id+i e+ r+ i   y +  +
  gene1476|gene1476|rna1475|rna1475 328 IENIEDPEDYIDMIiEKARNSIAKAYRIQFV 358
                                        5555555666776644455555555555544 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.8    0.0016       2.6      50     109 ..     110     169 ..      95     173 .. 0.86
   2 ?    2.5   0.0      0.08   1.3e+02      52     101 ..     204     253 ..     186     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                     Halogen_Hydrol  50 kkhlkksglsrkelkyiretlkeakekikrlekalkrvrslevikqvreilriarrifka 109
                                        k+  kk +l+ ++l+ + +++ke ke  k+++k+  + +s++++ +++++l+ ++ i+  
  gene1476|gene1476|rna1475|rna1475 110 KSVRKKPNLQYNSLEELSQQVKEVKERKKEIKKEHVKGQSHRIWLELYKVLDSSDVIIHV 169
                                        455566677777888899***********************************9999875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.08
                     Halogen_Hydrol  52 hlkksglsrkelkyiretlkeakekikrlekalkrvrslevikqvreilr 101
                                         l + g++ k l+y+ + +   + + +++ k++ +++ + ++kq++++++
  gene1476|gene1476|rna1475|rna1475 204 DLIPTGVTAKWLRYFSKSHPTIAYHSNSITKNYGKANLIGLLKQLSKLYK 253
                                        45679*****************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1396  (0.0778627); expected 358.6 (0.02)
Passed bias filter:                      895  (0.0499191); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 2506.95
//
Query:       gene1477|gene1477|rna1476|rna1476  [L=319]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-10   39.1   0.4     0.0076   16.5   0.0    3.7  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    5.1e-09   35.9   0.6    4.1e-07   29.8   0.3    2.7  2  DUF2415      Uncharacterised protein domain (DUF2415)
    4.3e-05   24.2   5.3       0.58   11.1   0.2    5.0  5  WD40         WD domain, G-beta repeat
     0.0011   17.5   0.0       0.75    8.0   0.0    2.2  2  Frtz         WD repeat-containing and planar cell polarity ef
  ------ inclusion threshold ------
       0.26   11.6   0.9        1.8    9.0   0.0    2.7  3  Kelch_6      Kelch motif


Domain annotation for each model (and alignments):
>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0012       4.3      49      87 ..      76     114 ..      72     119 .. 0.85
   2 !   11.1   0.0   0.00011      0.38      36      78 ..     142     186 ..     112     194 .. 0.72
   3 !   16.5   0.0   2.1e-06    0.0076      43      82 ..     193     232 ..     183     246 .. 0.87
   4 ?   -2.8   0.0       2.2   7.9e+03      37      63 ..     279     305 ..     269     312 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                        ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvhslsvksekavtcl 87 
                                        ++ +Lav+ s g++++ +  + +v++++  +s ++  c+
  gene1477|gene1477|rna1476|rna1476  76 KDDFLAVGGSRGHLKIKNLATNEVLSQVVSSSINNNICM 114
                                        5789**********************9988777666666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                        ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesg..kvvhslsv 78 
                                        ++  +v+s   +pdgk+L+v+ + + v l+++ +   k+v++l+ 
  gene1477|gene1477|rna1476|rna1476 142 NHVAQVNSCGISPDGKFLVVVGDSNDVFLYSIDNDsyKLVKKLKS 186
                                        66678999999******************9987752256666555 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 2.1e-06
                        ANAPC4_WD40  43 sLaWkpdgklLavaysdgevrlldaesgkvvhslsvksek 82 
                                        s++W+   + +av+++dg v + d+ s  ++h ++ k+++
  gene1477|gene1477|rna1476|rna1476 193 SVSWNSMSSTFAVGTQDGYVCIWDIRSDGMLHRFESKQKD 232
                                        689********************************99987 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.2
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevr 63 
                                        +d+++++  +++ +  + v+++d  + 
  gene1477|gene1477|rna1476|rna1476 279 PDKQITGAIFSEMNDRIFVSTEDQIID 305
                                        566777777777777777777776654 PP

>> DUF2415  Uncharacterised protein domain (DUF2415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.023        84      24      38 ..     209     223 ..     207     229 .. 0.83
   2 !   29.8   0.3   1.2e-10   4.1e-07       1      38 [.     236     271 ..     236     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.023
                            DUF2415  24 vgrvHlvDlRtglde 38 
                                         g+v++ D+R++ + 
  gene1477|gene1477|rna1476|rna1476 209 DGYVCIWDIRSDGML 223
                                        59********96554 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.2e-10
                            DUF2415   1 GAfRvckFSpesglnDLLvisEhvgrvHlvDlRtglde 38 
                                        GA+R +kFS  +++ DLL+++Eh++   + D+R ++ +
  gene1477|gene1477|rna1476|rna1476 236 GAVRNVKFS-LKNSLDLLFFTEHFSFLTVCDMR-DFRR 271
                                        9********.55557******************.8865 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.77   2.8e+03      15      36 ..      74      91 ..      56      93 .. 0.66
   2 ?    2.1   0.0      0.11     4e+02      15      37 ..     113     131 ..      86     132 .. 0.66
   3 !    8.6   0.1     0.001       3.7       9      34 ..     142     168 ..     134     172 .. 0.71
   4 !   11.1   0.2   0.00016      0.58      15      38 .]     193     216 ..     179     216 .. 0.88
   5 ?   -1.1   0.0       1.1   4.1e+03      17      22 ..     272     281 ..     250     304 .. 0.47

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.77
                                       EEEEETTSSEEEEEETTSEEEE CS
                               WD40 15 slafspdgawlasGsdDgtvri 36
                                       +l      ++la G+  g+++i
  gene1477|gene1477|rna1476|rna1476 74 CL----KDDFLAVGGSRGHLKI 91
                                       44....4456888865777776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                                        EEEEETTSSEEEEEETTSEEEEE CS
                               WD40  15 slafspdgawlasGsdDgtvriW 37 
                                        ++    +++ ++ +  D+t++i+
  gene1477|gene1477|rna1476|rna1476 113 CM----NNNRIFICNNDRTLKIF 131
                                        33....33444448779999996 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.001
                                        SS.SSEEEEEEETTSSEEEEEETTSEE CS
                               WD40   9 GH.ssvtslafspdgawlasGsdDgtv 34 
                                         H   v+s+  spdg++l+  +d + v
  gene1477|gene1477|rna1476|rna1476 142 NHvAQVNSCGISPDGKFLVVVGDSNDV 168
                                        4655588888*******9866645555 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00016
                                        EEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  15 slafspdgawlasGsdDgtvriWd 38 
                                        s+++++ ++ +a G+ Dg v iWd
  gene1477|gene1477|rna1476|rna1476 193 SVSWNSMSSTFAVGTQDGYVCIWD 216
                                        6788888888999**********9 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 1.1
                                        E....EETTS CS
                               WD40  17 a....fspdg 22 
                                        +    + pd+
  gene1477|gene1477|rna1476|rna1476 272 CqrvkVFPDK 281
                                        0333333333 PP

>> Frtz  WD repeat-containing and planar cell polarity effector protein Fritz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00037       1.3     282     355 ..      48     121 ..      39     138 .. 0.81
   2 !    8.0   0.0   0.00021      0.75     259     329 ..     144     218 ..     132     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00037
                               Frtz 282 sviLydeerkitklv..kaevvPsliswhpdsaillvasergelqifDlaLspiriqllsedvePksvldlskyfa 355
                                        +v+ y    ++tk +   +++ P+ i    ++  l v+ +rg+l+i +la   +  q++s  ++ +  ++ ++ f 
  gene1477|gene1477|rna1476|rna1476  48 NVVSYSPRENTTKTIyeGVDFFPTSICL--KDDFLAVGGSRGHLKIKNLATNEVLSQVVSSSINNNICMNNNRIFI 121
                                        6777777777777664478899998876..56799**************************999998888877775 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00021
                               Frtz 259 raqvislafnpdedkLllGceDssviLydeerkitklv.kaevvPs...liswhpdsaillvasergelqifDla 329
                                         aqv s+ ++pd   L++    + v Ly  + +  klv k + + +    +sw + s+ + v+ + g + i+D+ 
  gene1477|gene1477|rna1476|rna1476 144 VAQVNSCGISPDGKFLVVVGDSNDVFLYSIDNDSYKLVkKLKSTEDggfSVSWNSMSSTFAVGTQDGYVCIWDIR 218
                                        589*********999999999999****9999888888434444333338***********************95 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.74   2.7e+03       6      22 ..      72      88 ..      68     103 .. 0.72
   2 ?    9.0   0.0    0.0005       1.8       6      43 ..     149     181 ..     145     186 .. 0.85
   3 ?   -2.0   0.1       1.4   5.1e+03      13      37 ..     201     219 ..     190     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.74
                            Kelch_6  6 slvsvggkiYifGGytd 22
                                       s+++ ++++ + G +++
  gene1477|gene1477|rna1476|rna1476 72 SICLKDDFLAVGGSRGH 88
                                       66778888888887776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0005
                            Kelch_6   6 sl.vsvggkiYifGGytdsspylnkvwvydpetksWeql 43 
                                        s+ +s++gk+ ++ G +      n+v++y+++++s + +
  gene1477|gene1477|rna1476|rna1476 149 SCgISPDGKFLVVVGDS------NDVFLYSIDNDSYKLV 181
                                        55699***********7......8*********998765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.4
                            Kelch_6  13 kiYifGGytdsspylnkvwvydpet 37 
                                        + +++G +++       v+++d+++
  gene1477|gene1477|rna1476|rna1476 201 STFAVGTQDG------YVCIWDIRS 219
                                        4555555553......567777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2088.57
//
Query:       gene1478|gene1478|rna1477|rna1477  [L=861]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   44.4   0.2    2.2e-11   43.5   0.2    1.4  1  DUF2428   Putative death-receptor fusion protein (DUF2428)


Domain annotation for each model (and alignments):
>> DUF2428  Putative death-receptor fusion protein (DUF2428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.2   1.2e-15   2.2e-11     118     275 .]     515     648 ..     490     648 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.2e-15
                            DUF2428 118 fleqLlelrHrGAfekayvgFtklcerllrskdeelqklpeqwleelleeikssssklcitRRSAGlPfliqalls 193
                                        ++e+Ll++ H G++ ++++ + +  +  +  ++ +    + ++++  ++++k  + k +  RRS G+P+l+ a+l+
  gene1478|gene1478|rna1477|rna1477 515 LVEVLLHINHLGVILQVSQYLNAALKSGVLGRH-D----LLEIIDMSFNRVK--DCKVS-FRRSGGIPLLFAAILK 582
                                        788999999999999998888776665554444.2....4557788888888..55555.8*************** PP

                            DUF2428 194 sepkkskkklLkrtmkeLlelakkeaseeesesddesdlpqvhalNiLralfrdsrLgeevspyvadglilaiegf 269
                                        s p       +++++++L+el +           +  + +q h+lNiL  ++ d  L++++   + ++++la+++ 
  gene1478|gene1478|rna1477|rna1477 583 SCPFV-----IDNILEKLFELIN-----------RGDNATQLHCLNILSRIIDDGCLSSKIPFKMTELFKLAFRCS 642
                                        *8877.....9***********9...........445799************************************ PP

                            DUF2428 270 sspvWa 275
                                        +s+ Wa
  gene1478|gene1478|rna1477|rna1477 643 RSHPWA 648
                                        *****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 5536.42
//
Query:       gene1479|gene1479|rna1478|rna1478  [L=451]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-84  283.8   0.1    2.3e-84  283.2   0.1    1.3  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.2   0.1   1.3e-88   2.3e-84       4     313 ..     127     445 ..     124     446 .. 0.96

  Alignments for each domain:
  == domain 1  score: 283.2 bits;  conditional E-value: 1.3e-88
                                        HHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                        tRNA-synt_2   4 lrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                          l+n +l lrt+k +  l++rs+++k++r++++e++++ei++P+++++++e+g++lFk+       +++    +L
  gene1479|gene1479|rna1478|rna1478 127 AILTNGHLALRTKKRQLFLKARSHLLKIIRDFYFEREYTEITPPTMVQTQVEGGSTLFKL-------DYYgadaYL 195
                                        568899******************************************************.......78888889* PP

                                        -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessak 151
                                        tqs+qlyle++++   +r ++i +++RaE+srt+rhl+E+t++eae++ ++ + +++ +e li++ +k++ e++++
  gene1479|gene1479|rna1478|rna1478 196 TQSSQLYLETVVPV-SHRAYCIMPSYRAEKSRTRRHLSEYTHVEAELADVDLNGLISSIEALISYSMKRFYEDMKE 270
                                        **************.************************************************************* PP

                                        CCCHTTTTTS..EE-SSS-EEEEHHHHHHHHHTS............-SS--HHHHHHHHHHS--.SEEEEEEEBGG CS
                                        xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                        tRNA-synt_2 152 diefvirrns..kdlkkpfkrltykeaieklnei............gkdldkaderalvkkekn.epvfvtdfPae 212
                                        di +v  + +  k ++ pfk+++y eaie l+++            g+d+  a er+l++  +   pvf+t+f  e
  gene1479|gene1479|rna1478|rna1478 271 DILNVFPNFEfhKVPEVPFKKIKYPEAIELLRSKgykkedgadfelGDDIPDAAERYLIEVIGDgLPVFLTHFLVE 346
                                        **9998776564555556***************9**************************8765269********* PP

                                        GSTTCBBBSTTSTTBBSEEEEEETTE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 213 lkpFyarkeeddkkltesyDllingv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGl 287
                                        +kpFy+rk+e+dk+ltes Dll++g+ E++gGs+R +++e l e +k+++++    ++++wyl++ ++G + hgG+
  gene1479|gene1479|rna1478|rna1478 347 HKPFYMRKDENDKNLTESTDLLFPGIgEILGGSMRQDTYEDLIEGFKRENIS---IDPYYWYLDMARFGPCRHGGY 419
                                        ****************************************************...********************* PP

                                        EEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        tRNA-synt_2 288 glGldRlvmlllgsesIrdviaFPkl 313
                                        glG++R++m l++ e++ +++++P+ 
  gene1479|gene1479|rna1478|rna1478 420 GLGFERFLMGLMKYENVDEATLYPRK 445
                                        ************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3189.15
//
Query:       gene1480|gene1480|rna1479|rna1479  [L=436]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-29  101.0   0.1    1.8e-28   99.4   0.1    1.9  1  Nuf2            Nuf2 family
    0.00036   20.6   9.8    0.00036   20.6   9.8    3.0  3  DHR10           Designed helical repeat protein 10 domain
     0.0049   17.4  27.8     0.0086   16.6  13.5    2.9  3  APG6_N          Apg6 coiled-coil region
  ------ inclusion threshold ------
      0.012   15.2  18.7      0.022   14.3   3.5    2.3  2  HAUS-augmin3    HAUS augmin-like complex subunit 3
      0.026   15.3   1.8      0.026   15.3   1.8    3.1  3  DUF4472         Domain of unknown function (DUF4472)
      0.064   12.8  11.6       0.46   10.0   1.5    2.3  2  MscS_porin      Mechanosensitive ion channel porin domain
      0.075   12.5  33.1       0.94    8.9   5.3    3.0  3  Golgin_A5       Golgin subfamily A member 5
      0.088   12.9  15.1        1.4    9.1   1.8    4.6  4  MetOD2          Metanogen output domain 2
       0.11   11.7  20.1      0.077   12.3   1.0    3.3  3  DUF3450         Protein of unknown function (DUF3450)
       0.43   10.9  13.1        6.2    7.2   3.2    4.6  3  DUF948          Bacterial protein of unknown function (DUF948
       0.56    9.4  18.6       0.63    9.2   2.5    2.7  3  TMPIT           TMPIT-like protein
       0.71    9.9  36.8        3.2    7.8  20.4    3.8  3  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        1.9    9.0  13.0       0.63   10.6   1.6    3.1  3  Spectrin        Spectrin repeat
        2.6    8.1  26.8        1.9    8.5   4.1    4.6  4  DUF1664         Protein of unknown function (DUF1664)
        3.6    7.2  10.6        1.3    8.6   2.7    2.6  2  DUF2968         Protein of unknown function (DUF2968)
        4.5    7.3  13.7        1.7    8.7   3.3    3.3  3  FlxA            FlxA-like protein
        4.6    7.7  17.6        1.2    9.6   1.1    3.6  3  GPS2_interact   G-protein pathway suppressor 2-interacting do
        5.7    6.2  33.1          1    8.7  11.7    3.1  3  GAS             Growth-arrest specific micro-tubule binding
        5.9    6.9  20.7        1.4    9.0   2.4    4.1  4  Noelin-1        Neurogenesis glycoprotein
        7.3    6.0  36.5       0.88    9.0  15.8    2.3  2  HMMR_N          Hyaluronan mediated motility receptor N-termi
        7.8    6.5  23.3        3.5    7.6   6.0    3.2  4  Laminin_II      Laminin Domain II


Domain annotation for each model (and alignments):
>> Nuf2  Nuf2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.1   2.2e-31   1.8e-28       2     136 ..       7     133 ..       6     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 2.2e-31
                               Nuf2   2 dsfplldvreIvaclqelgfevteedlakPtpefvqklyeqfleilmgiseedieqaaraaleeleepelyedslp 77 
                                        +++p l+ +eI+++++e++++++++d+ kPtp+ +q++ye +le+++gi+  d+ +        + + e +e+sl+
  gene1480|gene1480|rna1479|rna1479   7 YAVPDLPIKEIIQYFSEMEINIKASDILKPTPQSTQRIYEILLEVYCGIRTSDMVS-------RIGNIEAFEESLS 75 
                                        679**************************************************944.......2456788****** PP

                               Nuf2  78 llillrslkrflkacgvedFslsDllkPdpkRtrriLSaliNFirFreerseifeelle 136
                                         l l ++++ fl+ +g+e+F l+Dl+ Pd+kR+  iLS ++NF  Fr+++++++e +++
  gene1480|gene1480|rna1479|rna1479  76 YLLLQKRMSGFLRRIGIENFGLRDLA-PDSKRLIGILSVVVNFSMFRDNKRHVYERVCR 133
                                        ************************98.****************************9986 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   8.6     0.073        63      28      95 ..     156     227 ..     135     237 .. 0.74
   2 !   20.6   9.8   4.2e-07   0.00036       5     117 .]     252     364 ..     251     364 .. 0.97
   3 ?    3.6   2.1     0.078        67      53     116 ..     353     416 ..     349     417 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.073
                              DHR10  28 lqvvekdlrsciklleeieaelakleeakkklkelrdaleek....eielrelerkeerlqrqlenaeekle 95 
                                        l+ +e+d ++ i+  +e+e+e+  le++ k+  +++ al +     ++e++e++ k + l+  l n  ++++
  gene1480|gene1480|rna1479|rna1479 156 LEMCERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQEtervKAERNEYSDKLSSLRLMLLNLSQEIT 227
                                        677999999999999999999999999999999999887655111155666666666666666666666655 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 4.2e-07
                              DHR10   5 aeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerke 80 
                                        ++e e +  lE k  +l+++id ++ +++d  ++i+l    ++  +  + ++++++el+ +++++    + l+ + 
  gene1480|gene1480|rna1479|rna1479 252 SKENEIVRGLEVKRMNLKERIDLMELMKEDTMKAITLSLSNKEADKTIDRTNREISELEVQIKNLDSGINALKIRL 327
                                        578899999******************************************************************* PP

                              DHR10  81 erlqrqlenaeeklerlreqaeekreaakarleelre 117
                                         +++rq+++ e k+  l+ + ++  e+  a+le+l++
  gene1480|gene1480|rna1479|rna1479 328 NHVNRQISHIESKIFNLQDNDKRCSEEISAKLEKLKN 364
                                        **********************************985 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.078
                              DHR10  53 eeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleelr 116
                                        ee ++kl++l++++   + e++ + rk+e   r  +n e +l + r+++ +   a +++l +l+
  gene1480|gene1480|rna1479|rna1479 353 EEISAKLEKLKNNYGVVSDERNSIRRKIEENVRLTKNIEYELVKKRNEHVNDITAIQSALCRLK 416
                                        6779999**********************99999999999999999999999999888887776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  13.5     1e-05    0.0086      42     118 ..     142     218 ..     121     240 .. 0.72
   2 !    7.6   3.9    0.0062       5.3      44     124 ..     292     378 ..     266     386 .. 0.64
   3 ?    1.9   0.9      0.35     3e+02      48     107 ..     340     400 ..     326     418 .. 0.43

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                             APG6_N  42 eekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellelee 117
                                         ++ de++ ++++ele  e++ ++ +ee ke+eke   le+el++  +  +al +e er   e+ne++ +l++l  
  gene1480|gene1480|rna1479|rna1479 142 RNEIDEKVHNARKELEMCERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRL 217
                                        3336788899999999999999999999999999999999999988888888888888888888888877776654 PP

                             APG6_N 118 e 118
                                         
  gene1480|gene1480|rna1479|rna1479 218 M 218
                                        4 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0062
                             APG6_N  44 k..qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne....lqlell 113
                                        +   d+ ++++++e+++le + ++l + +++l+     ++++++ +e++  +l+++ +r  +e ++    l+ +  
  gene1480|gene1480|rna1479|rna1479 292 NkeADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNDKRCSEEISAklekLKNNYG 367
                                        0224677888888888888888888888888888888888888888888888888877665555441101333344 PP

                             APG6_N 114 eleeeldslea 124
                                           +e++s+  
  gene1480|gene1480|rna1479|rna1479 368 VVSDERNSIRR 378
                                        45566666555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.35
                             APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee.eerfwreyne 107
                                        ++ +l++  ++ ++e +++le+Lk+     ++ ++ ++   ee  +l ++ e + ++++ne
  gene1480|gene1480|rna1479|rna1479 340 KIFNLQDNDKRCSEEISAKLEKLKNNYGVVSDERNSIRRKIEENVRLTKNiEYELVKKRNE 400
                                        4444444444444445555555544333333333333333333333332213333344444 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.5    0.0071         6      54     147 ..     165     258 ..     135     270 .. 0.84
   2 ?   14.3   3.5   2.6e-05     0.022      57     149 ..     287     382 ..     273     403 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0071
                       HAUS-augmin3  54 ktiepsdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkkl 129
                                        k+ie+s++ +++   le++l++  + ++aL qe +  + e++    +l+ L ++  +l+qe   l+++  +   kl
  gene1480|gene1480|rna1479|rna1479 165 KSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLSQEITCLKTQVVSDPTKL 240
                                        555555555566677888999999999************************************************* PP

                       HAUS-augmin3 130 keaqeelraenaetnavL 147
                                         e+ +e+r+ +++ n+  
  gene1480|gene1480|rna1479|rna1479 241 MELVDEMRCLISKENEIV 258
                                        ********9999988765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.6e-05
                       HAUS-augmin3  57 e...psdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkkl 129
                                            ++++  ++ + ++ +++e+e ++++L + +++L+   ++ +++ + ++  + +lq+++++ +ee +++ +kl
  gene1480|gene1480|rna1479|rna1479 287 TlslSNKEADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNDKRCSEEISAKLEKL 362
                                        332345555588999999********************************************************** PP

                       HAUS-augmin3 130 keaqeelraenaetnavLqq 149
                                        k+    ++ e + +++  ++
  gene1480|gene1480|rna1479|rna1479 363 KNNYGVVSDERNSIRRKIEE 382
                                        *9988888777777666655 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   5.1     0.078        67      40     106 ..     136     204 ..     115     205 .. 0.77
   2 ?    5.1   5.3     0.044        37      35      96 ..     171     229 ..     154     247 .. 0.74
   3 ?   15.3   1.8     3e-05     0.026      19      99 ..     295     379 ..     292     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.078
                            DUF4472  40 lenrvlelelerek..aaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqelsle 106
                                         e+ +l  e++++   a++e +  ++  ++  ee+ke+e+e  vl++++++  k   + +++++++++e
  gene1480|gene1480|rna1479|rna1479 136 DEKLLLRNEIDEKVhnARKELEMCERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAE 204
                                        555555555554433366677777778889999999999999999999999999999999999888776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.044
                            DUF4472  35 nkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefeke 96 
                                         +v   e+++l le+e +   + +++l ++++ +++e++e ++++++l+  +++l++e +  
  gene1480|gene1480|rna1479|rna1479 171 KEV---EKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLSQEITCL 229
                                        333...77777777777888888888888888888888888888888888888888876654 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 3e-05
                            DUF4472  19 tnklreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvv....lkknyqale 90 
                                         +k   + ++e+ el+ ++ +l++ +  l+++ ++ +++i+ ++++   l+++ k+ +ee ++    lk+ny +++
  gene1480|gene1480|rna1479|rna1479 295 ADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNDKRCSEEISAklekLKNNYGVVS 370
                                        5677788999*******************************************99999887753333777887777 PP

                            DUF4472  91 kefekekkk 99 
                                        +e ++ ++k
  gene1480|gene1480|rna1479|rna1479 371 DERNSIRRK 379
                                        777776666 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.5   0.00054      0.46      23      81 ..     161     218 ..     147     248 .. 0.82
   2 ?    7.7   2.9    0.0027       2.3      62     170 ..     292     394 ..     266     416 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00054
                         MscS_porin  23 eqalnlLdkidkskkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilaklsle 81 
                                        ++a + +++ ++ +k++  l+  ++d+ k  r+l qe+e+  k++ +++ ++l++l l 
  gene1480|gene1480|rna1479|rna1479 161 RDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERV-KAERNEYSDKLSSLRLM 218
                                        689999***********************************.77777777777766554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0027
                         MscS_porin  62 alqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLn 137
                                        +     e++   + ++  ++eLe ++++  s   +l+ +l+  n q+  +++ +    + + + ++  +ei+++L+
  gene1480|gene1480|rna1479|rna1479 292 NK----EADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKI---FNLQDNDKRCSEEISAKLE 360
                                        33....444555566777777777777777777777777777777777777644...4444566666666666666 PP

                         MscS_porin 138 staaage.alsqaqrtalqaelaaleaqieeleq 170
                                        +++ +      +      ++e+  + +++ e+e+
  gene1480|gene1480|rna1479|rna1479 361 KLKNNYGvVSDERNSIRRKIEENVRLTKNIEYEL 394
                                        6644444344444445555555555555555555 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   3.9       1.2     1e+03      61      94 ..     143     173 ..     121     186 .. 0.43
   2 ?    8.3  18.0    0.0016       1.4      33     157 ..     182     308 ..     152     324 .. 0.83
   3 ?    8.9   5.3    0.0011      0.94      49     155 ..     313     419 ..     307     426 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                          Golgin_A5  61 eelqklnqqieqlrtelqdleaqqqaeaeslreq 94 
                                        +e+    +++++ r+el+  e+ +++ +e+++e 
  gene1480|gene1480|rna1479|rna1479 143 NEI---DEKVHNARKELEMCERDAKKSIEESKEV 173
                                        222...2233334444433333333333333222 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                          Golgin_A5  33 gsgeeglesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerka 108
                                        ++ ++  + ++al +e + +k+er+ + ++l +l+  + +l +e+  l++q+ ++  +l+e + e++  +++e++ 
  gene1480|gene1480|rna1479|rna1479 182 SELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLSQEITCLKTQVVSDPTKLMELVDEMRCLISKENEI 257
                                        4456666778999*************************************************************** PP

                          Golgin_A5 109 keeveaelerlkeelryle...eelvrskatlqsrikdrekeieklrnqltt 157
                                         + +e +  +lke ++ +e   e+ + +  tl    k+ +k i++ +++++ 
  gene1480|gene1480|rna1479|rna1479 258 VRGLEVKRMNLKERIDLMElmkEDTM-KAITLSLSNKEADKTIDRTNREISE 308
                                        99999998888888765532215555.678889999999******9999975 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0011
                          Golgin_A5  49 ldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelr 124
                                        + +l +  ++l+  l+++n qi+++ +++ +l+++ +  +e++  +l++l+++    + ++++++ ++e+  +  +
  gene1480|gene1480|rna1479|rna1479 313 IKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNDKRCSEEISAKLEKLKNNYGVVSDERNSIRRKIEENVRLTK 388
                                        555566667788889999999999999999999999999999999******************************* PP

                          Golgin_A5 125 yleeelvrskatlqsrikdrekeieklrnql 155
                                         +e elv+++++ ++ i+  ++ + +l+ ++
  gene1480|gene1480|rna1479|rna1479 389 NIEYELVKKRNEHVNDITAIQSALCRLKDDV 419
                                        ****************999999998888776 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       6.1   5.2e+03      33      46 ..      39      52 ..      34      63 .. 0.79
   2 ?    7.6   1.1    0.0046         4      38      78 ..     124     164 ..     119     174 .. 0.88
   3 ?    6.0   0.3     0.014        12      49      85 ..     300     335 ..     294     338 .. 0.82
   4 ?    9.1   1.8    0.0017       1.4      33      85 ..     329     381 ..     324     384 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 6.1
                             MetOD2 33 evnkrllslLsqty 46
                                       ++++r++++L ++y
  gene1480|gene1480|rna1479|rna1479 39 QSTQRIYEILLEVY 52
                                       78899999998877 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0046
                             MetOD2  38 llslLsqtydidddkaevseeieaalknlekkleaqeerlk 78 
                                        + +++++++ ++d+k+   +ei + ++n  k+le  e++ k
  gene1480|gene1480|rna1479|rna1479 124 KRHVYERVCRMNDEKLLLRNEIDEKVHNARKELEMCERDAK 164
                                        4579******************************9998875 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.014
                             MetOD2  49 dddkaevseeieaalknlekkleaqeerlkqikkele 85 
                                        d+ ++e+s e+e  +knl  +++a + rl++++++++
  gene1480|gene1480|rna1479|rna1479 300 DRTNREIS-ELEVQIKNLDSGINALKIRLNHVNRQIS 335
                                        55545554.68899******************99886 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0017
                             MetOD2  33 evnkrllslLsqtydidddkaevseeieaalknlekkleaqeerlkqikkele 85 
                                         vn+++ ++ s++++++d+  + seei+a l+ l+++      + + i++++e
  gene1480|gene1480|rna1479|rna1479 329 HVNRQISHIESKIFNLQDNDKRCSEEISAKLEKLKNNYGVVSDERNSIRRKIE 381
                                        699*********************************98877777777777776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.8     0.013        11      15     113 ..     153     251 ..     147     293 .. 0.76
   2 ?   12.3   1.0   9.1e-05     0.077      32      89 ..     292     349 ..     284     360 .. 0.86
   3 ?    2.0   1.3      0.12     1e+02      41      98 ..     354     412 ..     345     422 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                            DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                         ++l+  +  a+k+++++++++k+i  l+ e ++  +  ral +e+e+ +++++++++ ++s++  + +l ++i+ 
  gene1480|gene1480|rna1479|rna1479 153 RKELEMCERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLSQEITC 228
                                        5677778889999999999999999999999999999999999999999999999999999999999999999887 PP

                            DUF3450  91 ieeierelvpllekmidrLeqfv 113
                                        ++    +    l++++d+++ ++
  gene1480|gene1480|rna1479|rna1479 229 LKTQVVSDPTKLMELVDEMRCLI 251
                                        77655554445555555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.1e-05
                            DUF3450  32 aaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89 
                                         +++ k id+ ++e +el+ ++++l + +++l++  ++++r++++ e++i +l+ + +
  gene1480|gene1480|rna1479|rna1479 292 NKEADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNDK 349
                                        5788899999999999999999999999999999999999999999999999997755 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                            DUF3450  41 klddekqellaeyralkeeleslevyneqlerlvasqeqeias.leeqieeieeierel 98 
                                        +++ + ++l+++y  +++e +s++ + e+  rl ++ e e+ +  +e  ++i++i+++l
  gene1480|gene1480|rna1479|rna1479 354 EISAKLEKLKNNYGVVSDERNSIRRKIEENVRLTKNIEYELVKkRNEHVNDITAIQSAL 412
                                        5666778999***************************9997651567788899888876 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.5      0.11        98      29      83 ..     171     225 ..     141     231 .. 0.79
   2 ?    3.9   0.1     0.076        65      19      69 ..     217     267 ..     212     276 .. 0.83
   3 ?    7.2   3.2    0.0073       6.2      19      72 ..     290     339 ..     282     415 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                             DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                        +e+++ i +le++++   k  ++l+++++++ ++ ne ++k+ +l   + +l++ 
  gene1480|gene1480|rna1479|rna1479 171 KEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLSQE 225
                                        6788888888888888888888888888888888888888887776666666655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.076
                             DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklek 69 
                                         +ll+l++ ++ +++++ +   ++ ++++e++ l++k ne++ +++ k  +
  gene1480|gene1480|rna1479|rna1479 217 LMLLNLSQEITCLKTQVVSDPTKLMELVDEMRCLISKENEIVRGLEVKRMN 267
                                        5778888888888888888889999******************99988655 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0073
                             DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdp 72 
                                           +++ kt+d++++ i ele q++++   +++l    n     vn+++ ++++
  gene1480|gene1480|rna1479|rna1479 290 LSNKEADKTIDRTNREISELEVQIKNLDSGINALKIRLNH----VNRQISHIES 339
                                        5556778888888888888887777776666666444444....3333333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.14   1.2e+02      13      56 ..     144     187 ..     129     192 .. 0.58
   2 ?    9.2   2.5   0.00074      0.63       2      83 ..     175     259 ..     171     281 .. 0.80
   3 ?    8.3   4.9    0.0014       1.2       2      98 ..     304     403 ..     296     425 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.14
                              TMPIT  13 eleetakeykqkleelsklqskcskeikkqkkrlkelksslkkl 56 
                                        e+ e+ ++ +++le +++  +k  +e k+ +k++  l+s+lk++
  gene1480|gene1480|rna1479|rna1479 144 EIDEKVHNARKELEMCERDAKKSIEESKEVEKEILVLESELKDF 187
                                        44444455555555555555555555555555555555555544 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00074
                              TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkee 74 
                                        +e+  le+e+k++ ++++ + q++e++++  ++ s ++++ + +l +l+++++ lk++v    ++  e v+e++  
  gene1480|gene1480|rna1479|rna1479 175 KEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLSQEITCLKTQVVsdpTKLMELVDEMRCL 250
                                        67778999*************************************************9773444444455555555 PP

                              TMPIT  75 lkerkkvlk 83 
                                        +++++++++
  gene1480|gene1480|rna1479|rna1479 251 ISKENEIVR 259
                                        555555554 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0014
                              TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskei....kkqkkrlkelksslkklkksvkeeeeeeveelke 73 
                                        +e++ele ++k+l +  + +k +l+++++++s++ ++i    ++ k+  +e++++l+klk++     ++e +++++
  gene1480|gene1480|rna1479|rna1479 304 REISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIfnlqDNDKRCSEEISAKLEKLKNNY-GVVSDERNSIRR 378
                                        678888888888888888888888888888888877762221233344556667777777764.577788888999 PP

                              TMPIT  74 elkerkkvlkevesllpkknglylk 98 
                                        +++e  +  k++e  l kk+   ++
  gene1480|gene1480|rna1479|rna1479 379 KIEENVRLTKNIEYELVKKRNEHVN 403
                                        9999999999999999998655555 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  20.4    0.0038       3.2       9     114 ..     160     276 ..     146     286 .. 0.79
   2 ?    2.2  11.3       0.2   1.7e+02      15     101 ..     261     346 ..     252     364 .. 0.57
   3 ?    5.4   6.4      0.02        17      14      92 ..     301     383 ..     293     415 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                     CENP-F_leu_zip   9 lekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr..... 79 
                                        +   K+s +++  ++  ++ Le+el++  ++q +++ e E  kae ++  +++  l+  l +l+++++ l+     
  gene1480|gene1480|rna1479|rna1479 160 ERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLSQEITCLKtqvvs 235
                                        44579999999*******************************************************9999877776 PP

                     CENP-F_leu_zip  80 ......sekeeLekelqkkqervseLeslnsslenlleekE 114
                                              +  +e+   + k++e v  Le  ++ l++ +   E
  gene1480|gene1480|rna1479|rna1479 236 dptklmELVDEMRCLISKENEIVRGLEVKRMNLKERIDLME 276
                                        66666544455555566777777777777777777666555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                     CENP-F_leu_zip  15 serkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                         e k  +Lk++++ +e  +e+  +  +    ++E  k ++   + ei el+ + ++l + ++al+   +++++++ 
  gene1480|gene1480|rna1479|rna1479 261 LEVKRMNLKERIDLMELMKEDTMKAITLSLSNKEADK-TIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQIS 335
                                        5667778888888888777777776555555555444.45555555555555555555555555555555555555 PP

                     CENP-F_leu_zip  91 kkqervseLes 101
                                        +  +++ +L+ 
  gene1480|gene1480|rna1479|rna1479 336 HIESKIFNLQD 346
                                        55555554443 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.02
                     CENP-F_leu_zip  14 eserkadsLkdkvenLerelemseenqekvileaEtskaevetlkee....ieelaeelreleldLvalrsekeeL 85 
                                        +++r+ + L+ +++nL++ ++ ++  +++v ++      ++ +l+++     ee++++l++l+ +   ++ e++++
  gene1480|gene1480|rna1479|rna1479 301 RTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNdkrcSEEISAKLEKLKNNYGVVSDERNSI 376
                                        5667777788888888888888888888888888887777777765422225677788888888888888888888 PP

                     CENP-F_leu_zip  86 ekelqkk 92 
                                         ++++++
  gene1480|gene1480|rna1479|rna1479 377 RRKIEEN 383
                                        7777765 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.5       0.1        90      26      79 ..     160     214 ..     142     249 .. 0.59
   2 ?   10.6   1.6   0.00074      0.63      11      94 ..     284     371 ..     278     382 .. 0.78
   3 ?   -1.2   0.0       3.4   2.9e+03      49      67 ..     393     412 ..     374     418 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.1
                                        CSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHTTHTTHHHHH CS
                           Spectrin  26 sedlgkdleevqallkkhkaleaelaaqqervkalnelaekl.ldeghsaseeie 79 
                                        ++d  k++ee ++ +k+   le el++  ++ +al +  e++ +++++++ +  +
  gene1480|gene1480|rna1479|rna1479 160 ERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVkAERNEYSDKLSS 214
                                        4555666666666666666666666664444444444444442444444433333 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00074
                                        HHHHHHHHHHHHHHCCSSCSSSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHH CS
                           Spectrin  11 deleeWieekeellssedlgkdleevqallk....khkaleaelaaqqervkalnelaeklldeghsaseeieerl 82 
                                        ++++  +++ke++ + ++  ++++e++ ++k       al+  l+   +++ +++    +l+d+ +  seei+++l
  gene1480|gene1480|rna1479|rna1479 284 KAITLSLSNKEADKTIDRTNREISELEVQIKnldsGINALKIRLNHVNRQISHIESKIFNLQDNDKRCSEEISAKL 359
                                        56666677788888777778888888877776666777888888888888888888888999999*********** PP

                                        HHHHHHHHHHHH CS
                           Spectrin  83 eelnerWeeLke 94 
                                        e+l +++  +++
  gene1480|gene1480|rna1479|rna1479 360 EKLKNNYGVVSD 371
                                        *****9977665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.4
                                        HHHH.HHHHHHHHHHHHHHH CS
                           Spectrin  49 elaa.qqervkalnelaekl 67 
                                        el   + e+v+++++++++l
  gene1480|gene1480|rna1479|rna1479 393 ELVKkRNEHVNDITAIQSAL 412
                                        44443555556665555554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.7      0.01       8.8      57     120 ..     120     187 ..     114     191 .. 0.62
   2 ?    2.5   1.0      0.17   1.4e+02      43      99 ..     219     275 ..     205     293 .. 0.62
   3 ?    8.5   4.1    0.0022       1.9      69     122 ..     293     346 ..     255     348 .. 0.73
   4 ?    3.7   0.9     0.068        58      45      93 ..     350     398 ..     343     427 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                            DUF1664  57 laatkrhLssridrvd.kkldeqkeiskei...keevtevredlseigedvesvkeavegleskleri 120
                                         ++ krh  +r+ r++ +kl   +ei +++   ++e++  ++d ++  e++++v++ +  les+l++ 
  gene1480|gene1480|rna1479|rna1479 120 FRDNKRHVYERVCRMNdEKLLLRNEIDEKVhnaRKELEMCERDAKKSIEESKEVEKEILVLESELKDF 187
                                        57889999999999951455444444333311155666666677777777777777777777777665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.17
                            DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlsei 99 
                                        + ++s++++ +++++ +   +L++ +d++ + + + +ei + ++ + ++++e ++ +
  gene1480|gene1480|rna1479|rna1479 219 LLNLSQEITCLKTQVVSDPTKLMELVDEMRCLISKENEIVRGLEVKRMNLKERIDLM 275
                                        445666666666666666666666666666666666666666665555555555444 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0022
                            DUF1664  69 drvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                        ++ dk++d +++ ++e++ +++++ +++++++  +++v++ ++++esk+ ++++
  gene1480|gene1480|rna1479|rna1479 293 KEADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQD 346
                                        456777888888888888888888888888888888888888888888877765 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.068
                            DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevr 93 
                                        + s+++    e+l++     s++ +++ +k++e+ +++k+i+ e+ + r
  gene1480|gene1480|rna1479|rna1479 350 RCSEEISAKLEKLKNNYGVVSDERNSIRRKIEENVRLTKNIEYELVKKR 398
                                        4444444444444444455556666666666666666666666654433 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.7    0.0015       1.3     104     175 ..     150     223 ..     126     227 .. 0.84
   2 ?    2.7   0.6       0.1        86     124     175 ..     287     338 ..     255     349 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                            DUF2968 104 leaqk..aqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLq 175
                                         +a k  ++ er  ++s ++ +++++++ v ++  +   ++Q+++ +e++  +a+r+++ ++l++l+  + +L 
  gene1480|gene1480|rna1479|rna1479 150 HNARKelEMCERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSSLRLMLLNLS 223
                                        4454412689******************************************************9987776665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.1
                            DUF2968 124 rLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLq 175
                                        +L+   + a +   + +++ +++  + + L++  +a++ +l+++ rqi++++
  gene1480|gene1480|rna1479|rna1479 287 TLSLSNKEADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIE 338
                                        3333333333333344444455556666777777777777777777776665 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.4     0.088        75      22      81 ..     145     200 ..     141     216 .. 0.65
   2 ?    8.7   3.3     0.002       1.7      10      74 ..     290     350 ..     281     379 .. 0.75
   3 ?    4.7   0.4     0.034        29      20      55 ..     328     363 ..     320     403 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.088
                               FlxA  22 LqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIaqlqqqqaekaqekqq 81 
                                        + + + n+ k+L+    + +++ e      ++++++I +l+++++   + q+   qe++ 
  gene1480|gene1480|rna1479|rna1479 145 IDEKVHNARKELEMCERDAKKSIE----ESKEVEKEILVLESELKDFYKHQRALVQETER 200
                                        667788889999998888888888....55667777777777777554444444333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                               FlxA  10 ssssgsasqiasLqkQiknlqkqLkelses.deltkeekkkqqqliqaQIqqlqaQIaqlqqqqae 74 
                                         s+++ ++ i + +++i++l+ q+k+l +  ++l       + + +  QI+ +++ I  lq  +++
  gene1480|gene1480|rna1479|rna1479 290 LSNKEADKTIDRTNREISELEVQIKNLDSGiNALK-----IRLNHVNRQISHIESKIFNLQDNDKR 350
                                        5788899999999999*********9999944444.....45778888888888888888776554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.034
                               FlxA  20 asLqkQiknlqkqLkelsesdeltkeekkkqqqliq 55 
                                        +  ++Qi+ ++ ++ +l+++d+   ee +++ + ++
  gene1480|gene1480|rna1479|rna1479 328 NHVNRQISHIESKIFNLQDNDKRCSEEISAKLEKLK 363
                                        567899999999999999998888888877766665 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   4.1      0.82     7e+02      33      77 ..     167     211 ..     145     217 .. 0.76
   2 ?    9.6   1.1    0.0014       1.2      21      53 ..     284     316 ..     274     326 .. 0.81
   3 ?    5.4   0.3     0.029        24      36      73 ..     327     364 ..     321     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.82
                      GPS2_interact  33 lqnidkvDREiakveqqiskLkkkqkeleeeaakpkeeekpveps 77 
                                        +++   v +Ei   e++++   k q+ l +e  + k e+++ +++
  gene1480|gene1480|rna1479|rna1479 167 IEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDK 211
                                        55667799999999*****99999999999888877666666554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0014
                      GPS2_interact  21 elvpsrlsKdeLlqnidkvDREiakveqqiskL 53 
                                        ++++  ls  e  + id+  REi+  e qi++L
  gene1480|gene1480|rna1479|rna1479 284 KAITLSLSNKEADKTIDRTNREISELEVQIKNL 316
                                        456667777778899***************998 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.029
                      GPS2_interact  36 idkvDREiakveqqiskLkkkqkeleeeaakpkeeekp 73 
                                        ++ v R i+++e++i +L+   k   ee +   e+ k+
  gene1480|gene1480|rna1479|rna1479 327 LNHVNRQISHIESKIFNLQDNDKRCSEEISAKLEKLKN 364
                                        678***************99999887776666555444 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  11.7    0.0012         1      60     131 ..     146     214 ..     135     235 .. 0.74
   2 ?    3.7  10.3     0.041        35      36     131 ..     293     382 ..     265     393 .. 0.45
   3 ?    3.6   4.8     0.044        37      28     103 ..     320     389 ..     310     421 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                GAS  60 kepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfea 131
                                         e++++a++e+e  +++    +k  ++ k++++++ +le+elkd   +++ l q+ e+v++er+e ++k  +
  gene1480|gene1480|rna1479|rna1479 146 DEKVHNARKELEMCERD---AKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNEYSDKLSS 214
                                        34444444444444433...3344556778888999999999999999999999999999999999999765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.041
                                GAS  36 eelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk.dlkwehev 110
                                        +e +k  +r+++e+se++ + k+l   +++++  +++ ++q+ + e+          +l++ +k  + +++ + e 
  gene1480|gene1480|rna1479|rna1479 293 KEADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIES-------KIFNLQDNDKRCSeEISAKLEK 361
                                        23333333334444444444444444444444444444444444333.......3333333333322123334445 PP

                                GAS 111 leqrfekvekerdelykkfea 131
                                        l+  +  v++er+ +++k e+
  gene1480|gene1480|rna1479|rna1479 362 LKNNYGVVSDERNSIRRKIEE 382
                                        555555555555555555555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.044
                                GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                        I+ lK  +++ +++  + e ++ +++ + kr +e++ +      +L+k  +ny     + ++++++++e  +  k+
  gene1480|gene1480|rna1479|rna1479 320 INALKIRLNHVNRQISHIESKIFNLQDNDKRCSEEISA------KLEKLKNNYGVVSDERNSIRRKIEENVRLTKN 389
                                        55555555555555555555555555555555555443......44444444444444444444444444444444 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.4    0.0016       1.4      31      95 ..     131     196 ..     127     200 .. 0.84
   2 ?    2.9   0.9      0.13   1.1e+02      35      82 ..     206     253 ..     199     276 .. 0.71
   3 ?    6.3   0.9     0.011       9.6      35      88 ..     300     353 ..     291     364 .. 0.81
   4 ?   -1.3   0.1       2.6   2.2e+03      35      54 ..     371     389 ..     347     427 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                           Noelin-1  31 vCsrDarsrqlr.qllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveedrkelsa 95 
                                        vC  +  +  lr ++ ekv+n  +++e+ ++  ++ +++ +++e+ +  les+lk+  ++++ l++
  gene1480|gene1480|rna1479|rna1479 131 VCRMNDEKLLLRnEIDEKVHNARKELEMCERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQ 196
                                        6654444444442799****************************************9999988765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.13
                           Noelin-1  35 DarsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesk 82 
                                        +  s +l +l     nlsq+i  l+    +d   +++    ++ l sk
  gene1480|gene1480|rna1479|rna1479 206 NEYSDKLSSLRLMLLNLSQEITCLKTQVVSDPTKLMELVDEMRCLISK 253
                                        55677899999999***********99999966555555555544444 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.011
                           Noelin-1  35 DarsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvvee 88 
                                        D  +r++ +l+ +++nl   i+ l+ R +     +++ e+ + +l+++ k  +e
  gene1480|gene1480|rna1479|rna1479 300 DRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNDKRCSE 353
                                        778899*********************988888888888888888776665555 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.6
                           Noelin-1  35 Darsrqlrqllekvqnlsqs 54 
                                        D r+   r+++e+v+ l+++
  gene1480|gene1480|rna1479|rna1479 371 DERNSIRRKIEENVR-LTKN 389
                                        333333344444443.3333 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  15.8     0.001      0.88     228     323 ..     140     235 ..     115     247 .. 0.84
   2 ?    2.2  13.1      0.12        99     228     333 ..     270     378 ..     238     397 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                             HMMR_N 228 klleyi.eelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvre 302
                                         l ++i e+++n++++le+++ d +++ e  ke ++ei  L s+L++  ++ ++   + +e++k   +e  ++++ 
  gene1480|gene1480|rna1479|rna1479 140 LLRNEIdEKVHNARKELEMCERDAKKSIEESKEVEKEILVLESELKDFYKH-QRALVQETERVKAERNEYSDKLSS 214
                                        344566268**************************************9995.5566667899**9999******** PP

                             HMMR_N 303 eeekeqtlsaEleelkeklkl 323
                                         +    +ls+E+ +lk ++ +
  gene1480|gene1480|rna1479|rna1479 215 LRLMLLNLSQEITCLKTQVVS 235
                                        ****************99865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                             HMMR_N 228 klleyieelsnvseqlekykldiaqleellkekndeiesLkssLe...ekeqelskqvkdlnekckllekekeelv 300
                                        + ++ +e +++ + ++   +l  +++  +++  n+ei++L  +++      ++l+ + +  n +++ +e++  +l 
  gene1480|gene1480|rna1479|rna1479 270 ERIDLMELMKEDTMKAITLSLSNKEADKTIDRTNREISELEVQIKnldSGINALKIRLNHVNRQISHIESKIFNLQ 345
                                        3333333333333333333445555556666666666666544330003445566666666666666666666666 PP

                             HMMR_N 301 reeeekeqtlsaEleelkeklklkeqeaqklqq 333
                                         +++  ++++sa le+lk++  + ++e + +++
  gene1480|gene1480|rna1479|rna1479 346 DNDKRCSEEISAKLEKLKNNYGVVSDERNSIRR 378
                                        666666666666677666666666666555544 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.7     0.013        11      20      98 ..     143     218 ..     134     235 .. 0.84
   2 ?    5.5   6.0     0.019        16       7      96 ..     294     363 ..     241     364 .. 0.59
   3 ?    7.6   6.0    0.0041       3.5       6      99 ..     293     380 ..     289     386 .. 0.70
   4 ?    3.6   0.6     0.071        60      20      71 ..     353     405 ..     346     418 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHH CS
                         Laminin_II  20 aplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnisei 95 
                                        ++++++++n +++l+  +r++++  e+ k+  k i   +++ k+  k    L++  +++k  +++    sd++s +
  gene1480|gene1480|rna1479|rna1479 143 NEIDEKVHNARKELEMCERDAKKSIEESKEVEKEILVLESELKDFYKHQRALVQETERVKAERNE---YSDKLSSL 215
                                        78999999999999999999999999999999999999999999999999999999999988888...78888888 PP

                                        HHH CS
                         Laminin_II  96 kel 98 
                                        + +
  gene1480|gene1480|rna1479|rna1479 216 RLM 218
                                        876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                         Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                        ea++t+  +                      r++ e + ++k++  +i+  +    ++++++  +++k+ +l+   
  gene1480|gene1480|rna1479|rna1479 294 EADKTIDRTN---------------------REISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDND 348
                                        3333333333.....................333444444444444444444444444444444444444443333 PP

                                        HH....HHHHHHHHH CS
                         Laminin_II  83 easss.lsdniseik 96 
                                        +  s  +s++++++k
  gene1480|gene1480|rna1479|rna1479 349 KRCSEeISAKLEKLK 363
                                        332224555555544 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0041
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                         Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                        +ea++t+  + + + +l+++++n+ + ++ ++  ++++n +++     i   +++ k   +   ++ +kl++lk+ 
  gene1480|gene1480|rna1479|rna1479 293 KEADKTIDRTNREISELEVQIKNLDSGINALKIRLNHVNRQISHIESKIFNLQDNDKRCSE---EISAKLEKLKNN 365
                                        6899999999999999999999999999999999777777777777777777777665554...556666666655 PP

                                        HHH...HHHHHHHHHHHH CS
                         Laminin_II  82 eeassslsdniseikelI 99 
                                              +sd+ + i+  I
  gene1480|gene1480|rna1479|rna1479 366 YGV---VSDERNSIRRKI 380
                                        433...555555554444 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.071
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXX--TTTTT CS
                         Laminin_II  20 aplsqnlentkeklseinrsveetnekvkdankairdArrs.vkkLeklapqL 71 
                                        +++s++le++k+++  + ++ + +  k+++  + ++  + + vkk ++ ++++
  gene1480|gene1480|rna1479|rna1479 353 EEISAKLEKLKNNYGVVSDERNSIRRKIEENVRLTKNIEYElVKKRNEHVNDI 405
                                        68888899999999888888888888888777777776643266777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1707  (0.0952089); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 1.08u 0.33s 00:00:01.41 Elapsed: 00:00:00.56
# Mc/sec: 2324.40
//
Query:       gene148|gene148|rna148|rna148  [L=341]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-16   58.0  14.8    1.8e-15   56.2   6.8    3.0  3  GATA           GATA zinc finger
  ------ inclusion threshold ------
       0.02   15.0   3.2       0.19   11.8   0.2    2.4  2  ArfGap         Putative GTPase activating protein for Arf
      0.044   13.7   6.5        1.3    9.0   0.8    3.3  3  Nudix_N_2      Nudix N-terminal
       0.37   11.0   3.3        1.2    9.3   3.3    1.9  1  DUF4451        Domain of unknown function (DUF4451)
       0.61   10.3   7.5        1.9    8.7   0.6    2.5  2  FYVE           FYVE zinc finger
        0.9    9.8   3.4        6.8    6.9   0.6    2.6  2  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
        2.2    8.4   8.2    1.1e+02    2.9   8.2    2.9  1  DZR            Double zinc ribbon


Domain annotation for each model (and alignments):
>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   6.8     7e-19   1.8e-15       1      35 [.     126     160 ..     126     161 .. 0.98
   2 ?   -0.3   0.1      0.32   8.2e+02      22      30 ..     183     191 ..     176     195 .. 0.70
   3 !    4.8   1.4    0.0085        22      16      34 ..     197     215 ..     184     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 7e-19
                           GATA   1 CsnCgttkTplWRrgpdgnksLCnaCGlyykkkgl 35 
                                    CsnC tt+Tp WRrg +g++ LCnaCGly+k++g+
  gene148|gene148|rna148|rna148 126 CSNCSTTSTPSWRRGDQGKTLLCNACGLYQKLHGR 160
                                    *********************************96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.32
                           GATA  22 LCnaCGlyy 30 
                                    +C +C + +
  gene148|gene148|rna148|rna148 183 VCVSCNISF 191
                                    788887765 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0085
                           GATA  16 pdgnksLCnaCGlyykkkg 34 
                                    ++ + +LC++C  y ++++
  gene148|gene148|rna148|rna148 197 KNAPSHLCESCLDYARSRR 215
                                    567899*****98888765 PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   7.3e-05      0.19       3      41 ..     113     153 ..     111     162 .. 0.81
   2 ?    3.4   0.3     0.031        79       7      45 ..     175     213 ..     170     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                                    HHHHHCCSCCCCB-TTT.-SBS--EEETTTT.EEE-HHHHH CS
                         ArfGap   3 alkellkepenkvCaDC.gakeptWaslnlg.vflCieCsg 41 
                                    + +el ++ ++++C +C +++ p+W     g ++lC  C  
  gene148|gene148|rna148|rna148 113 ITRELKRKAKQRICSNCsTTSTPSWRRGDQGkTLLCNACGL 153
                                    578999999********88899*****97765899*99954 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.031
                                    HCCSCCCCB-TTT-SBS--EEETTTTEEE-HHHHHHHCC CS
                         ArfGap   7 llkepenkvCaDCgakeptWaslnlgvflCieCsgvHrs 45 
                                    l  ++e  vC+ C+ +  t  s n    lC +C    rs
  gene148|gene148|rna148|rna148 175 LKGSHERIVCVSCNISFFTSDSKNAPSHLCESCLDYARS 213
                                    455566679************************877665 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.8    0.0005       1.3       3      29 ..     126     152 ..     124     154 .. 0.96
   2 ?    6.1   0.0     0.004        10      18      29 ..     177     188 ..     173     190 .. 0.88
   3 ?   -1.7   0.1       1.1   2.9e+03      23      28 ..     202     207 ..     195     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0005
                                    -TTT--B-EEE--TT-SS-EEEETTTT CS
                      Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCg 29 
                                    Cs+C t+ +     gD+   l C+aCg
  gene148|gene148|rna148|rna148 126 CSNCSTTSTPSWRRGDQGKTLLCNACG 152
                                    **************************9 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.004
                                    -SS-EEEETTTT CS
                      Nudix_N_2  18 DnreRlvCpaCg 29 
                                    +++eR vC +C+
  gene148|gene148|rna148|rna148 177 GSHERIVCVSCN 188
                                    579********7 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.1
                                    EEETTT CS
                      Nudix_N_2  23 lvCpaC 28 
                                    + C++C
  gene148|gene148|rna148|rna148 202 HLCESC 207
                                    889999 PP

>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.3   0.00048       1.2      12     106 ..     114     200 ..     103     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00048
                        DUF4451  12 vrgekdknekkeglCpiCeeevekkekflklknssyekhlsfeHGvlsngslvpePillrskkrrkakekekegivCpkC 91 
                                    +r    k++ k+ +C+ C +  +++  + +    + +  l  + G++++    + P+++ s  r+ka + ++e ivC +C
  gene148|gene148|rna148|rna148 114 TRE--LKRKAKQRICSNCST--TSTPSWRRG--DQGKTLLCNACGLYQKLHGRTRPYMITSGGRTKALKGSHERIVCVSC 187
                                    444..267788899999994..446667666..55667788899************************************ PP

                        DUF4451  92 neiievslsknkkek 106
                                    n   ++  s++k+ +
  gene148|gene148|rna148|rna148 188 NI--SFFTSDSKNAP 200
                                    *5..44444444333 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.6   0.00074       1.9      33      62 ..     123     151 ..     113     157 .. 0.87
   2 ?    4.5   1.2     0.015        38      33      64 ..     181     209 ..     179     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00074
                                    -EE-STTS-EEE.EEGGGTEEEEEEE-HHH CS
                           FYVE  33 kvvCekCssklvallekeaeeksvrvCkeC 62 
                                    + +C++Cs+++++++ ++ ++ ++ +C++C
  gene148|gene148|rna148|rna148 123 QRICSNCSTTSTPSW-RRGDQGKTLLCNAC 151
                                    568*********999.8888999999**99 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                                    -EE-STTS-EEE.EEGGGTEEEEEEE-HHHHH CS
                           FYVE  33 kvvCekCssklvallekeaeeksvrvCkeCla 64 
                                    ++vC +C  +++   ++ +++++ ++C++Cl+
  gene148|gene148|rna148|rna148 181 RIVCVSCNISFF---TSDSKNAPSHLCESCLD 209
                                    689999988888...45688999999999986 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.6    0.0026       6.8      17      40 .]     125     152 ..     122     152 .. 0.88
   2 ?    2.8   0.1     0.052   1.3e+02      31      39 ..     179     187 ..     171     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0026
                  Auto_anti-p27  17 tCpvC...gvPLmrdr.kggkvyCvaCd 40 
                                     C++C   ++P  r   +g++++C aC+
  gene148|gene148|rna148|rna148 125 ICSNCsttSTPSWRRGdQGKTLLCNACG 152
                                    6****9999*****5598999******6 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.052
                  Auto_anti-p27  31 ggkvyCvaC 39 
                                     ++++Cv+C
  gene148|gene148|rna148|rna148 179 HERIVCVSC 187
                                    4689***** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   8.2     0.044   1.1e+02       1      37 [.     126     190 ..      91     210 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.044
                            DZR   1 CpqCgeelppdar........fCseCgtklkavaa....................edrCpsCgek 37 
                                    C++C +  +p+ r         C++Cg   k   +                     ++C+sC+ +
  gene148|gene148|rna148|rna148 126 CSNCSTTSTPSWRrgdqgktlLCNACGLYQKLHGRtrpymitsggrtkalkgsheRIVCVSCNIS 190
                                    55555553322222222333455555544332222556666666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.55
# Mc/sec: 1867.60
//
Query:       gene1481|gene1481|rna1480|rna1480  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.038   14.0   0.2    1.3  1  Complex1_LYR  Complex 1 protein (LYR family)
      0.044   13.9   0.1       0.05   13.8   0.1    1.1  1  LAM_C         Lysine-2,3-aminomutase


Domain annotation for each model (and alignments):
>> Complex1_LYR  Complex 1 protein (LYR family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   4.3e-06     0.038       5      58 ..       8      65 ..       5      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.3e-06
                       Complex1_LYR  5 sLYRalLRearkfpdyntreyfrrriRdeFrk..nkh..vtDpekieellkkgreeLe 58
                                        LY++l     +f ++ +  yf  +++de      ++   +D+++ie+ lk+ +e+L+
  gene1481|gene1481|rna1480|rna1480  8 NLYKNLESVILQFKSPAFGSYFLKKAKDEYNDiyTRScgKKDERAIERYLKDQEELLD 65
                                       69****9***********************998755577*************999997 PP

>> LAM_C  Lysine-2,3-aminomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.5e-06      0.05      43      96 ..       9      64 ..       3      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-06
                              LAM_C 43 vlrnfeGvitsypePe..nyvkgkaddyfkevypdtekkkeevGisalledeelsl 96
                                       + +n e vi  ++ P    y  +ka+d ++++y+    kk+e  i++ l+d+e  l
  gene1481|gene1481|rna1480|rna1480  9 LYKNLESVILQFKSPAfgSYFLKKAKDEYNDIYTRSCGKKDERAIERYLKDQEELL 64
                                       568************6448999*****************************98655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 564.47
//
Query:       gene1482|gene1482|rna1481|rna1481  [L=576]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-82  276.7   0.7      5e-82  275.8   0.7    1.4  1  VID27       VID27 C-terminal WD40-like domain
    0.00013   22.2   0.9    0.00031   21.0   0.9    1.7  1  VID27_PH    VID27 PH-like domain
  ------ inclusion threshold ------
       0.33   11.1   2.6        5.4    7.3   0.3    3.2  3  UvrB_inter  UvrB interaction domain


Domain annotation for each model (and alignments):
>> VID27  VID27 C-terminal WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.8   0.7   8.3e-86     5e-82       2     348 ..     259     573 ..     258     575 .. 0.93

  Alignments for each domain:
  == domain 1  score: 275.8 bits;  conditional E-value: 8.3e-86
                              VID27   2 knsqlavgykndrsfvvrgdkiGvfkhtddnelefstaiskvetlkgkllsPkkvmlheedrklilqdekdknkly 77 
                                        kn++l vg  ++++f++rg+ +Gvfk+t+d  lef+++i++v + +      +k++ h++ ++li+ d+++++kl+
  gene1482|gene1482|rna1481|rna1481 259 KNKHLVVG--DEMAFITRGKSVGVFKNTNDG-LEFKANIKDVLDDDV-----EKIITHDNCSSLIFLDKSERDKLH 326
                                        79999999..679**************9987.**********98875.....6899******************** PP

                              VID27  78 kmDlerGkvvdewkvhddipvvefapekkfaqlteeqtllGlsknalfriDPrlsgnklvdselkqyaskndfsav 153
                                        k+D+erG+v++ w+v+ +  v+++  ++k  +     +l+Gls+ ++friDPr + +k+v+  +k+y++kn f   
  gene1482|gene1482|rna1481|rna1481 327 KLDVERGEVIETWDVQRN--VNDYFDSQKLVD---TGSLIGLSDYSVFRIDPRAK-SKVVE--SKDYKTKNGFNCG 394
                                        ***************876..599999999755...568***************76.68986..589********** PP

                              VID27 154 attekGyiavasekGdirlfdrlginaktalPalgdpiigldvsadGrwvlatcktyllLiDalikegkneGklgf 229
                                         +t +G++  a + Gd+rl+d++ ++ak+ lP +gd i+++dv+++Gr+++ tck+yl+L       g       +
  gene1482|gene1482|rna1481|rna1481 395 MATSSGHVVAAGKGGDLRLYDKIDKRAKSLLPGFGDEIKYIDVTSNGRHIVCTCKNYLMLTTV---PGD------Y 461
                                        ***********************************************************9643...333......5 PP

                              VID27 230 eksfakdskpkprrLklkpehvaqlqeetkkpvsftkakfntgldseettivtstGpfvitwslkkvlkgkkdpYk 305
                                        ++ ++ ++kp p+rL+lkpeh a+++ee    ++ft+akf t  d++e++i+tstG +v++w+l++vl+gk  +Y+
  gene1482|gene1482|rna1481|rna1481 462 KQPIG-KNKPVPKRLQLKPEHLAYINEE----IDFTPAKFST--DASESSIITSTGSYVVKWNLDDVLNGKLYSYQ 530
                                        66666.468****************887....********86..799***************************** PP

                              VID27 306 ikryeeevvadnfkfgsdknvivalkndvsmvkkkslkkptre 348
                                        + + ++ v+adnf+fg+d nviv++++d++ v+ ++lkkp r+
  gene1482|gene1482|rna1481|rna1481 531 LAKCNDLVIADNFEFGEDSNVIVTMPDDIRKVNVRNLKKPGRK 573
                                        ****************************************998 PP

>> VID27_PH  VID27 PH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.9   5.2e-08   0.00031       6     108 ..     105     203 ..     100     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.2e-08
                           VID27_PH   6 eeaeLhlfDaesgeFilqeeevkaavielgkweYwLqiegeeekewlgqevsadmnpvfnfeylsfifnyvsedge 81 
                                        ++a    ++++ g+F+ +e +v++ ++e + +   ++ie+ +   +  +e+ ++ +   + +  +f++  + e+g 
  gene1482|gene1482|rna1481|rna1481 105 KRAVYSRYNTTIGRFEESEGQVDVFIVEDEVFL--IRIETRN-DVVHFEEIRTETQYYMDQKNATFVWSVM-ENGV 176
                                        555666799999****************99876..5666445.4567899*******************99.9*** PP

                           VID27_PH  82 alSwlLrFkdeeeleefqealmralwe 108
                                         +++ LrF d+ ++ ef ++++ +l+ 
  gene1482|gene1482|rna1481|rna1481 177 FHTFSLRFLDNLDFLEFLSKYIGCLYR 203
                                        *********************999985 PP

>> UvrB_inter  UvrB interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3   0.00091       5.4      27      76 ..     111     159 ..     101     170 .. 0.77
   2 ?   -0.7   0.1      0.28   1.7e+03      35      73 ..     271     312 ..     264     340 .. 0.68
   3 ?    1.4   0.0      0.06   3.6e+02      20      58 ..     481     518 ..     471     530 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00091
                         UvrB_inter  27 dvelkrGtFrvrGdtveifpasaeevairieffgdeiesireidpltgks 76 
                                         ++++ G F+     v++f ++ e   irie  +d + + +ei+ +t+  
  gene1482|gene1482|rna1481|rna1481 111 RYNTTIGRFEESEGQVDVFIVEDEVFLIRIETRNDVV-HFEEIRTETQYY 159
                                        45678899**************7666*****998865.566666666655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.28
                         UvrB_inter  35 FrvrGdtveifpasaeevairieffg...deiesireidplt 73 
                                        F  rG+ v +f  +++   ++ ++++   d +e+i + d  +
  gene1482|gene1482|rna1481|rna1481 271 FITRGKSVGVFKNTNDGLEFKANIKDvldDDVEKIITHDNCS 312
                                        667777777777776666666666655557777777666555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.06
                         UvrB_inter  20 elqYerndvelkrGtFrvrGdtveifpasaeevairief 58 
                                        +l Y ++++++++ +F+   +   i+ ++ ++++++ ++
  gene1482|gene1482|rna1481|rna1481 481 HLAYINEEIDFTPAKFSTDASESSIITST-GSYVVKWNL 518
                                        6899*************999999998888.577776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 3061.56
//
Query:       gene1483|gene1483|rna1482|rna1482  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-14   53.2   0.0    4.2e-14   52.7   0.0    1.2  1  FAD_binding_1  FAD binding domain
    1.7e-07   31.9   0.1    2.8e-06   27.9   0.0    2.5  2  NAD_binding_1  Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_1  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   4.7e-18   4.2e-14      15     187 ..      56     212 ..      47     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.7e-18
                                        EEEE---.-SS--EEEEEEE-TTBT----TT-EEEE-----HHHHHHHHHHHT--T..T-EEEEEESSTT..S--S CS
                      FAD_binding_1  15 knreLtkpesernvihveldisdsglkYetGdhlgvypsNneelVeellellgldpkadevvelkaldeesaekep 90 
                                        + ++L++  s r v  +++d   ++ ++++Gd++g   +Nn++lV+e++e+++ ++      +++  +     k+ 
  gene1483|gene1483|rna1482|rna1482  56 EIEKLEA--SWRDVYRIKFD---EKFHFKPGDSIGMLCPNNDTLVDEIMEVFEVKN---SYCQIRRPG-----KNS 118
                                        5555555..55666666664...7899***************************99...888888888.....799 PP

                                        SSSSEEHHHHHHHTB--SS---HHHHHHHGGG-SSHHHHHHHHHHHH-HHHHHTTTTT--HHHHHHHHHTT---TT CS
                      FAD_binding_1  91 rleptTlrqalkyylditgppskqlleaLaefaseeeekqkLekLssdegakeykelklneartllevleefpsvk 166
                                        +  + ++r  +kyy d+t+ p+k ll +La+  + e++++ +e L+s+eg  +y  +   + + ++++++ f   +
  gene1483|gene1483|rna1482|rna1482 119 FSYTGSIRDFFKYYFDFTSLPRKSLLANLAKGCT-ETNRKYIEYLCSKEGIVDYLGMG-RRWNNIIDIIKTFE-CR 191
                                        ******************************9776.68899***************999.88999********7.68 PP

                                        S-HHHHHHHS-B---EEEEB- CS
                      FAD_binding_1 167 lplefLlevlpqLkpRyYSiS 187
                                        + le+++   +  kpRy+S+ 
  gene1483|gene1483|rna1482|rna1482 192 PVLEEVIGECEIVKPRYFSLI 212
                                        99*****************85 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.3   1.2e+04      38      51 ..     240     253 ..     234     259 .. 0.79
   2 !   27.9   0.0   3.1e-10   2.8e-06       2     101 ..     273     358 ..     272     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                                        CGSTTHHHHHHHHH CS
                      NAD_binding_1  38 edllyreeleelak 51 
                                         d+l+r e+ee++ 
  gene1483|gene1483|rna1482|rna1482 240 SDFLVRSEVEEVEL 253
                                        59999999999865 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 3.1e-10
                                        EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSH CS
                      NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrv 77 
                                        i++GtGiaP++s+  +++      + ++++yG r++ed      l +l    ++ ++v +v    +++      +v
  gene1483|gene1483|rna1482|rna1482 273 ICTGTGIAPFLSFASNLQPH----QSIWIIYGFRNDEDD-----LSKLIGPDKN-VRVSRV----KSST---GIYV 331
                                        9************9998774....78*********9975.....4666444454.444444....3333...5788 PP

                                        HHHHHHHHHH...HSSTTEEEEEECSH CS
                      NAD_binding_1  78 qdalleells...lkkeethvyvCGpp 101
                                        +d l+e +++     +ee+ +y CG  
  gene1483|gene1483|rna1482|rna1482 332 TDYLVERIDEikgYVDEECIAYACGKM 358
                                        888888888877766888889999873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2582.34
//
Query:       gene1484|gene1484|rna1483|rna1483  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   13.1   0.0       0.18   11.9   0.0    1.5  1  DUF2177   Predicted membrane protein (DUF2177)


Domain annotation for each model (and alignments):
>> DUF2177  Predicted membrane protein (DUF2177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     1e-05      0.18      20      74 ..     286     340 ..     279     342 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1e-05
                            DUF2177  20 lglvakklYqeelgellaeevnllaavvfYllyvlgivvfavlpalekesllkal 74 
                                        +g++ +++Y ++l+ ++ +e  +    +f ++ ++gi++fa++ ++ ++++++++
  gene1484|gene1484|rna1483|rna1483 286 VGFMNDQVYFSSLDGFVGTEKTTRGFSMFLIMVSIGIFIFAIVMGIISKTVRHSF 340
                                        6899**************************************9999888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 2009.98
//
Query:       gene1485|gene1485|rna1484|rna1484  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-22   80.1   0.1    2.7e-22   79.1   0.1    1.5  1  CDC73_C   RNA pol II accessory factor, Cdc73 family, C-termin


Domain annotation for each model (and alignments):
>> CDC73_C  RNA pol II accessory factor, Cdc73 family, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.1   1.5e-26   2.7e-22       6     153 ..     116     248 ..     111     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.5e-26
                            CDC73_C   6 iIlvpssasslltlsnvksfledgkyvppdekkkeaskaenevsisrklkkiadskkvrflvvdspekltkedWer 81 
                                        +I+vp+s ss ++lsn+k+f+e+gk+ +  + ++ +   + e++i+           ++f  vd+++++t+edW+r
  gene1485|gene1485|rna1484|rna1484 116 YIVVPQSVSSPVNLSNIKEFFEEGKCSEGIQISEVE---KVELNIDG----------YKFAAVDDVSRFTSEDWKR 178
                                        7**************************998888777...56788877..........89***************** PP

                            CDC73_C  82 VvAVfvtgqewqfksykwsepaelFkkvkgvyvkyeeeevpeevkgwnVkslqlsrskRhrDravveefwea 153
                                        Vv++f++g +wq  ++++++  e+F+ +  +y+  ++ + + ++k+ nV  + ++ +  + D+ +++++ ++
  gene1485|gene1485|rna1484|rna1484 179 VVCIFLDGTKWQVSRWNIRDVGEIFNTIPTFYFIKRGAPGNFYIKNCNV--IGVETHGGKVDKPTLSSIRKR 248
                                        *****************************************99998887..556666666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1754.38
//
Query:       gene1486|gene1486|rna1485|rna1485  [L=555]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-14   51.7   0.7    2.5e-13   50.3   0.7    1.8  1  PFU       PFU (PLAA family ubiquitin binding)
    2.1e-08   34.7  10.6    9.2e-05   23.1   1.2    5.7  6  WD40      WD domain, G-beta repeat
      5e-08   32.9   0.1     0.0027   17.7   0.0    3.1  3  BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
    5.4e-06   26.7   0.9       0.67   10.5   0.0    4.5  4  PQQ_3     PQQ-like domain
  ------ inclusion threshold ------
      0.025   13.8   0.1      0.042   13.1   0.1    1.2  1  PUL       PUL domain


Domain annotation for each model (and alignments):
>> PFU  PFU (PLAA family ubiquitin binding)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.7   6.9e-17   2.5e-13      52     110 ..     349     408 ..     309     411 .. 0.82

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 6.9e-17
                                PFU  52 G...keYDyvfdvdiedgkpplkLpynksdnpyeaAekFleknelsqsyleqivnFiikntk 110
                                        G   k+YD  f+v++e+    ++L +n+++n+ye+AekFl+kn+l+ +++++iv+Fi+kn  
  gene1486|gene1486|rna1485|rna1485 349 GeeaKSYDNTFQVELENK--YYTLSFNNDENVYEVAEKFLRKNKLRDEFRDDIVDFINKNFV 408
                                        344479*********944..579************************************975 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.6   5.8e+03      23      37 ..      23      37 ..      13      37 .. 0.77
   2 ?    2.1   0.0      0.12   4.3e+02      12      37 ..      42      76 ..      31      77 .. 0.61
   3 !   23.1   1.2   2.6e-08   9.2e-05       4      37 ..      97     129 ..      95     130 .. 0.89
   4 !    8.4   0.0    0.0012       4.3      10      37 ..     147     174 ..     141     175 .. 0.76
   5 ?    2.1   0.0      0.11   4.1e+02       6      38 .]     221     255 ..     178     255 .. 0.76
   6 ?   -1.5   0.1       1.6   5.8e+03      27      37 ..     284     293 ..     261     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                                       SEEEEEETTSEEEEE CS
                               WD40 23 awlasGsdDgtvriW 37
                                       ++++ G++ g++r++
  gene1486|gene1486|rna1485|rna1485 23 RMVIGGGREGKIRVY 37
                                       55776799*****97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                       S...........EEEEEEETTSSE....EEEEETTSEEEEE CS
                               WD40 12 s...........vtslafspdgaw....lasGsdDgtvriW 37
                                       s           ++++a           l+ G+ +g++ ++
  gene1486|gene1486|rna1485|rna1485 42 SrnmgiepgqgyINCIA------IgnglLFVGCQNGSIVVY 76
                                       34555555555688883......333335569999999887 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 2.6e-08
                                        EEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   4 lrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                        ++ l+GH s+v++l  +  g++++s+s+D+tv iW
  gene1486|gene1486|rna1485|rna1485  97 VGFLKGHsSNVCCL--DTIGDLVVSSSWDCTVIIW 129
                                        6789***666****..999999************* PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0012
                                        SSS..EEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40  10 Hss..vtslafspdgawlasGsdDgtvriW 37 
                                        H +  v+s++f + ++ + +G+ D+ +ri+
  gene1486|gene1486|rna1485|rna1485 147 H-PtvVWSVKFIDKNTIV-TGCSDKLIRIF 174
                                        6.3447999888888886.6755******8 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.11
                                        EEESSSSEEEEE.EETTSSEEEEE.ETTSEEEEEE CS
                               WD40   6 tltGHssvtsla.fspdgawlasG.sdDgtvriWd 38 
                                        ++++ ++ +s++ + +dg+ l+ + +++g v+++d
  gene1486|gene1486|rna1485|rna1485 221 HYSTKNFMYSISsYTRDGKSLVICtGENGMVMVFD 255
                                        44444444555566777888764547899999987 PP

  == domain 6  score: -1.5 bits;  conditional E-value: 1.6
                                        EEETTSEEEEE CS
                               WD40  27 sGsdDgtvriW 37 
                                         Gs Dg ++++
  gene1486|gene1486|rna1485|rna1485 284 GGS-DGRLYVY 293
                                        356.*999987 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.5e-07    0.0027      14      89 ..      24     100 ..      15     118 .. 0.83
   2 !   11.4   0.1   6.8e-05      0.24      11     105 ..     158     251 ..     150     254 .. 0.69
   3 ?    1.6   0.0     0.076   2.7e+02      56      70 ..     245     259 ..     201     290 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.5e-07
                           BBS2_Mid  14 eLvvgsddfeirvfkee.elvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvksknevvalaaydi 88 
                                         ++ g  + +irv+ ++ +  + i+  +  ++ +++ +  + ++ +NG++ vy+ +e + ++ sk+e+ + + + +
  gene1486|gene1486|rna1485|rna1485  24 MVIGGGREGKIRVYGHDfSRNMGIEPGQGYINCIAIGNGLLFVGCQNGSIVVYSVDECQFQIESKEEMSKTMPVGF 99 
                                        45557899********9555667888999*************************************9988766655 PP

                           BBS2_Mid  89 n 89 
                                         
  gene1486|gene1486|rna1485|rna1485 100 L 100
                                        5 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.8e-05
                           BBS2_Mid  11 geneLvvgsddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvye.kker.lWrvksknevvala 84 
                                        ++n +v g  d  ir+fk++ l+++++ +   v  +++ +++ +++++N  + +    + r + ++++kn + ++ 
  gene1486|gene1486|rna1485|rna1485 158 DKNTIVTGCSDKLIRIFKDGVLTSTFNYHLSYVRSVTVLDKS-IFSVDNEGIVLKTsLDGRvMKHYSTKNFMYSIS 232
                                        579************************997766666655544.456777544443303444145666677777777 PP

                           BBS2_Mid  85 aydingdgtkelivgwsnGkl 105
                                        +y  +  g++ +i++ +nG +
  gene1486|gene1486|rna1485|rna1485 233 SYTRD--GKSLVICTGENGMV 251
                                        77666..57777888888876 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.076
                           BBS2_Mid  56 aleNGtvgvyekker 70 
                                        + eNG+v v++++ r
  gene1486|gene1486|rna1485|rna1485 245 TGENGMVMVFDENLR 259
                                        447888888888776 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.42   1.5e+03      15      35 ..      16      36 ..       8      38 .. 0.78
   2 !   10.5   0.0   0.00019      0.67      12      36 ..      53      76 ..      47      79 .. 0.82
   3 ?    0.4   0.0      0.28   9.9e+02      18      37 ..     235     255 ..     222     257 .. 0.70
   4 !    9.3   0.0   0.00046       1.6      21      36 ..     278     293 ..     267     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.42
                              PQQ_3 15 sspavdgglvyvgtgdGtlyA 35
                                        +++v ++ v  g+  G+++ 
  gene1486|gene1486|rna1485|rna1485 16 KTLLVNDRMVIGGGREGKIRV 36
                                       467899999999999999876 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
                              PQQ_3 12 pvnsspavdgglvyvgtgdGtlyAl 36
                                       ++n+  a+++gl++vg+ +G+++ +
  gene1486|gene1486|rna1485|rna1485 53 YINC-IAIGNGLLFVGCQNGSIVVY 76
                                       5544.79***************987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.28
                              PQQ_3  18 avdgg.lvyvgtgdGtlyAlD 37 
                                        + dg  lv +++++G +  +D
  gene1486|gene1486|rna1485|rna1485 235 TRDGKsLVICTGENGMVMVFD 255
                                        456652455555599999998 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00046
                              PQQ_3  21 gglvyvgtgdGtlyAl 36 
                                        ++++y+g++dG+ly +
  gene1486|gene1486|rna1485|rna1485 278 EDKIYFGGSDGRLYVY 293
                                        799***********87 PP

>> PUL  PUL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.2e-05     0.042      77     152 ..     470     525 ..     460     543 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                PUL  77 rfPalDLlRlllldprvsayfaeeeggktissllslllssalsssapkalennrmlalRllaNlFssplgrellls 152
                                        +f alDL+R +++++ +++ ++          +l ++++ +++      +   +++ +Rll+NlF+ p++  ++l+
  gene1486|gene1486|rna1485|rna1485 470 IFMALDLIRYFMAHKYTFD-LS----------FLFTFTPRDKK------E---AITFVRLLSNLFADPPFNLEILH 525
                                        6899************999.55..........33333333332......3...9****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3768.88
//
Query:       gene1487|gene1487|rna1486|rna1486  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-20   73.7   0.2    8.3e-20   71.8   0.2    2.0  1  SET       SET domain


Domain annotation for each model (and alignments):
>> SET  SET domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.2   4.7e-24   8.3e-20       1     169 []     379     489 ..     379     489 .. 0.91

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 4.7e-24
                                        SCEEEESSXBXTTXEEEEEE.ECCEECHHHHHHHHHH......HTEEEEEXGGXXGGSXHHHHHHHTTSSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                SET   1 GrGvfAtedIpkgeficeyp.eeiiltkdeadksele......aylfslpeapknlaftkelakasastllqklak 69 
                                        G+G+fA+e+I +g f++ey+ e  i++++ea++++         ylf+l                           
  gene1487|gene1487|rna1486|rna1486 379 GYGLFAKEKISRGKFVIEYVgE--IISNEEAERRGAFydlrgcSYLFDLY-------------------------- 426
                                        9*******************77..***********998888886666644.......................... PP

                                        HHHHHHHHHHHHTHHHHHHHXTTTSXXXHCCCCCHCCCHEEEETEEEEEECCCGTTGGGCEEXS.SSSEEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                                SET  70 dqkqaekedtdaalkasskaesdlnaskpeagafsaiagysidaralksgngagplarflNHsC.dpNcnltvqnv 144
                                                                        ++ +i  y++d  ++  gn +    rf+NHs  +pN+n+++  v
  gene1487|gene1487|rna1486|rna1486 427 --------------------------------NRGGIPLYVVD--SRFIGNRS----RFINHSKkNPNLNVSILLV 464
                                        ................................4578889****..55******....******779********** PP

                                        TTSSEEEEEESSXBXTTEEEEEXTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                                SET 145 lrgprvavfAtrdIkkGeEltidYg 169
                                        ++ +r++++A+rdI k+eEl++dYg
  gene1487|gene1487|rna1486|rna1486 465 NGIRRIGFYASRDIDKNEELFFDYG 489
                                        ************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3492.05
//
Query:       gene1488|gene1488|rna1487|rna1487  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.7   1.5     0.0036   17.4   1.5    1.6  1  Med7      MED7 protein


Domain annotation for each model (and alignments):
>> Med7  MED7 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.5     2e-07    0.0036      50     185 ..       9     127 ..       3     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-07
                               Med7  50 pkeLrvlipPeppkegeYrvFGenwsllkdklpsLeeqgieqlyeedesedrkkeLkkLlrslllnfleLlgillk 125
                                        p+  +  +pP++p  ++Y +FG+ +++ ++++p  +++    +   + ++dr keL +L+     +f+eLl   l+
  gene1488|gene1488|rna1487|rna1487   9 PPRFKKKVPPKIP--SSYVSFGTSYKV-ENSVPINTSFPS--M---KFDKDRFKELVNLS---FSAFIELLAFPLD 73 
                                        555666789****..99*********6.999996555443..3...34567777777774...4567777766444 PP

                               Med7 126 nPeqsefeekvedlrllliNmhhllNeyRphQAretlillleeqleekreeiekirkkce 185
                                        +      ee +e ++ +++ ++++lN  + + A  +++ + + ++++k++ +e+ r+k+ 
  gene1488|gene1488|rna1487|rna1487  74 H------EELIEIISSTHLEINQILNGGKGMEAISEIRRIRNDHIRNKNRIAEETRRKIS 127
                                        4......677*******************************************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 923.68
//
Query:       gene1489|gene1489|rna1488|rna1488  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-12   46.9   5.4    8.6e-06   26.4   0.5    3.3  3  WD40         WD domain, G-beta repeat
     0.0028   17.9   0.0      0.027   14.8   0.0    2.5  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   4.9e-08   0.00044       3      38 .]      89     124 ..      87     124 .. 0.82
   2 !   26.4   0.5   9.6e-10   8.6e-06       7      37 ..     137     168 ..     129     169 .. 0.88
   3 ?   -1.2   0.0       0.5   4.5e+03       9      18 ..     187     199 ..     179     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.9e-08
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                         ++++++H +s++s++  +d+ +l s+s+D t+++Wd
  gene1489|gene1489|rna1488|rna1488  89 FIGHIKAHgGSISSIKRYKDKYLL-SCSEDTTIKMWD 124
                                        46778888777****888887776.79*********9 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 9.6e-10
                                        EESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                        ++GH + v s+++s d ++las++ D++++iW
  gene1489|gene1489|rna1488|rna1488 137 YSGHrDYVLSIDVSNDMRYLASCGTDCSIKIW 168
                                        78**888**************9999******* PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.5
                                        SS...SSEEEEEE CS
                               WD40   9 GH...ssvtslaf 18 
                                        +H   +++ +++f
  gene1489|gene1489|rna1488|rna1488 187 THecrFPIECIRF 199
                                        6764344999954 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     3e-06     0.027       1      87 [.      15     103 ..      15     109 .. 0.90
   2 ?   -0.9   0.0      0.24   2.1e+03      48      71 ..     106     129 ..      97     146 .. 0.79
   3 ?   -1.4   0.0      0.32   2.9e+03      38      67 ..     141     170 ..     125     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-06
                        ANAPC4_WD40   1 lswcptmDLiAlatedgellvfRlngqrvwtl...eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvv 73 
                                        +s c++  +++la ++++++v+  +g +v++    e+++e+ + +++    ++  La + + g +++++ ++g+ +
  gene1489|gene1489|rna1488|rna1488  15 MSICNKHRIVSLAGKRSSVIVSYRDGLKVVQRildEHPDENFQCSEFFMAGNDISLALGGKLGIIKMVNLSKGTFI 90 
                                        678***********************9999888777888888999999999999********************** PP

                        ANAPC4_WD40  74 hslsvksekavtcl 87 
                                         +++++  + ++++
  gene1489|gene1489|rna1488|rna1488  91 GHIKAHGGS-ISSI 103
                                        ****99885.7776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.24
                        ANAPC4_WD40  48 pdgklLavaysdgevrlldaesgk 71 
                                         ++k L    +d+++++ d+++  
  gene1489|gene1489|rna1488|rna1488 106 YKDKYLLSCSEDTTIKMWDISELA 129
                                        567888889999999999987655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.32
                        ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrllda 67 
                                           v s+  ++d + La    d ++++  +
  gene1489|gene1489|rna1488|rna1488 141 RDYVLSIDVSNDMRYLASCGTDCSIKIWRI 170
                                        556777777888888998888888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2106.89
//
Query:       gene1490|gene1490|rna1489|rna1489  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-10   40.9   0.0    9.9e-10   38.7   0.0    2.0  2  GHMP_kinases_C  GHMP kinases C terminal
    2.2e-08   34.2   0.2    4.6e-08   33.2   0.2    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.027   14.6   0.3      0.047   13.8   0.3    1.3  1  Tropomyosin_1   Tropomyosin like
       0.21   11.2   0.0       0.37   10.4   0.0    1.3  1  AIRC            AIR carboxylase


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.51   2.3e+03      37      55 ..      64      83 ..      60      83 .. 0.75
   2 !   38.7   0.0   2.2e-13   9.9e-10       8      71 ..     158     218 ..     140     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.51
                     GHMP_kinases_C 37 eellealselG.algaklsG 55
                                       +++l++++e   ++++k sG
  gene1490|gene1490|rna1489|rna1489 64 TDILKEALEIEnVFHGKASG 83
                                       56777777777799999998 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 2.2e-13
                     GHMP_kinases_C   8 gdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkde 71 
                                          l++l +l++++q+  l++++g++p+e+++++++++e G   ak++GaG+G+ +++++k+++e
  gene1490|gene1490|rna1489|rna1489 158 FTLQELYKLIRRNQD--LLDELGVCPEEMKDVVDKMREIG-VEAKITGAGCGGHLVTVVKKEQE 218
                                        57899**********..9**********************.******************77765 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.2     1e-11   4.6e-08       7      66 .]      39      93 ..      35      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1e-11
                                       SSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                     GHMP_kinases_N  7 eiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyGg 66
                                       e P+g+GLG SAA+++ l +   +  +     +k ale+e+ ++ g+ sg+Dv a++ Gg
  gene1490|gene1490|rna1489|rna1489 39 EAPLGCGLGTSAAISLLLSYGKTRNTD----ILKEALEIENVFH-GKASGVDVMACYTGG 93
                                       67*************999999777552....2899*********.*************98 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3     1e-05     0.047      43     111 ..     124     199 ..     121     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1e-05
                      Tropomyosin_1  43 knqqleeevekleeklkeakekaeesekkktnne.......altrkiqlLEeeleesdkkLkettekLretdvkae 111
                                        kn ++   + k +++l +   k++e++ k  + e       +l r++q L +el    +++k+ ++k+re+ v+a 
  gene1490|gene1490|rna1489|rna1489 124 KNTEIAIRLGKRKKELYDEIGKVSEEAYKLLQREftlqelyKLIRRNQDLLDELGVCPEEMKDVVDKMREIGVEAK 199
                                        677777788888888888888888888888888888888999*****************************99885 PP

>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   8.2e-05      0.37      40      79 ..     181     220 ..     179     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.2e-05
                                        HHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS- CS
                               AIRC  40 peelleyaeeaeerglkviIagAGgaahLpgvvaslttlP 79 
                                        pee+++++++++e g+++ I+gAG   hL  vv    ++P
  gene1490|gene1490|rna1489|rna1489 181 PEEMKDVVDKMREIGVEAKITGAGCGGHLVTVVKKEQEIP 220
                                        89****************************9998776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1594.36
//
Query:       gene149|gene149|rna149|rna149  [L=363]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-05   22.5   0.3    0.00022   20.8   0.0    2.0  2  GIT_SHD         Spa2 homology domain (SHD) of GIT


Domain annotation for each model (and alignments):
>> GIT_SHD  Spa2 homology domain (SHD) of GIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.2e-08   0.00022       3      27 ..      36      60 ..      35      61 .. 0.97
   2 ?   -2.2   0.1      0.19   3.5e+03       4      20 ..      75      91 ..      75      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-08
                        GIT_SHD  3 qKLarLsnkqFeeLvtDVydEldRR 27
                                   qK+ +L+ k Fe+Lv+D+  E++RR
  gene149|gene149|rna149|rna149 36 QKMVSLPEKNFEDLVSDIVNEMRRR 60
                                   89999******************** PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.19
                        GIT_SHD  4 KLarLsnkqFeeLvtDV 20
                                   KL+r     F+ Lv D 
  gene149|gene149|rna149|rna149 75 KLSRIHEDGFKSLVLDL 91
                                   67776677799999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2404.70
//
Query:       gene1492|gene1492|rna1491|rna1491  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.1e-45  153.7  10.2    5.4e-43  147.0   4.3    2.0  2  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
      0.068   13.9   1.7       0.76   10.6   0.1    2.2  2  DUF4282     Domain of unknown function (DUF4282)


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.5   3.2e-06     0.028     619     642 ..       2      25 ..       1      29 [. 0.84
   2 !  147.0   4.3     6e-47   5.4e-43     694     813 .]      23     134 ..      19     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.2e-06
                         V_ATPase_I 619 lvcvpvlllvkPlilklkhkkkkk 642
                                        l+c+p++ll kP+++ +k+  k++
  gene1492|gene1492|rna1491|rna1491   2 LLCIPWMLLGKPIYMIFKNMVKRE 25 
                                        89*************999876655 PP

  == domain 2  score: 147.0 bits;  conditional E-value: 6e-47
                         V_ATPase_I 694 eefdfgevfihqvIhtIEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfa 769
                                        ++++++ ++i+q+Ih +Ef Lg iSnT+SYLRLWA+SLAHaqL +Vl+e ++ k         g i+ v+l  v++
  gene1492|gene1492|rna1491|rna1491  23 KREEISSLWINQFIHVVEFGLGLISNTSSYLRLWAVSLAHAQLTRVLHEFTIGKE--------GFITPVVLSSVYI 90 
                                        578999**********************************************993........57888999***** PP

                         V_ATPase_I 770 vltvavLllmeglsafLHaLRLhWVEfqsKFykgdGykFepfsf 813
                                        + t++ L+ megl + LHa+RL+WVEf sKF++g+Gy Fep+ f
  gene1492|gene1492|rna1491|rna1491  91 LGTLVLLIGMEGLGSCLHAMRLNWVEFHSKFFRGKGYLFEPLGF 134
                                        *****************************************976 PP

>> DUF4282  Domain of unknown function (DUF4282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.021   1.9e+02      40      74 ..      40      74 ..       2      75 .. 0.69
   2 ?   10.6   0.1   8.4e-05      0.76       7      28 ..      79     100 ..      77     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.021
                            DUF4282 40 seslsagggllllllaviafllmilllRivlEfli 74
                                       + +l++ + + + l  + + l+ + l R++ Ef i
  gene1492|gene1492|rna1491|rna1491 40 EFGLGLISNTSSYLRLWAVSLAHAQLTRVLHEFTI 74
                                       55677777777888889999999999999999987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 8.4e-05
                            DUF4282   7 fitpkllkvlYilgivlialvl 28 
                                        fitp +l+ +Yilg ++ ++++
  gene1492|gene1492|rna1491|rna1491  79 FITPVVLSSVYILGTLVLLIGM 100
                                        9*************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 903.66
//
Query:       gene1493|gene1493|rna1492|rna1492  [L=577]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.8e-125  418.8  19.3   2.3e-124  416.1  19.3    1.9  1  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
      0.028   14.9   2.5       0.52   10.8   0.1    2.4  2  FlgN        FlgN protein
        1.1    9.3   3.8        2.7    8.0   0.7    2.7  2  LOH1CR12    Tumour suppressor protein


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.1  19.3  3.9e-128  2.3e-124       2     613 ..      25     555 ..      24     564 .. 0.93

  Alignments for each domain:
  == domain 1  score: 416.1 bits;  conditional E-value: 3.9e-128
                         V_ATPase_I   2 eLGelglvqfrDlnedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleee 77 
                                        e+G+ gl++f+Dln+d+++ +  +++e+ +++++  +l++l+  +++ +             e  +++++d++ee+
  gene1493|gene1493|rna1492|rna1492  25 EIGKNGLLHFKDLNKDIKSENLLYTREITHMEKLISRLQYLTGDVKEVD-------------EGIKHSDIDQVEEQ 87 
                                        89*******************************************9922.............3346788******* PP

                         V_ATPase_I  78 lekleeelkelnenleklkkelnelvelkavlekakefleeeeeeeeeeeseeeeeekeeeeeeeseeeeeeelle 153
                                        ++k+ ++l +l++ +++  +++++l+e  ++le++++fl +      +                     ee++ l 
  gene1493|gene1493|rna1492|rna1492  88 VNKFFSRLIQLKSIKKETDTNQTRLKEDLYMLEETENFLGTV-----T---------------------EEAH-L- 135
                                        ***************************************732.....1.....................1111.2. PP

                         V_ATPase_I 154 eeeelsfvaGvikrekveaferilwralrgnlflrqaeieepledpetgekveksvfiiffqgeqlkekikkices 229
                                           +++f++G++++ k   ++++l +alr+nl++r++++e+           +k vfi+f++g++  ek+k i +s
  gene1493|gene1493|rna1492|rna1492 136 --VQFDFMTGIVEKGKKLLIRKVLHQALRRNLVIRTKDVED----------GTKAVFIVFAHGSEALEKVKDIFSS 199
                                        ..3479*********************************99..........479********************** PP

                         V_ATPase_I 230 fgaklyelpeseeereeklkeveeriedlekvleqteealkevleeiakeleewklkvkkekaiyhtLnlfnldvt 305
                                        +g ++ + ++  +e ++ l e++++i++++++ ++++ea++++ e+i +  ++w+ +++ke +iy++Ln++++d +
  gene1493|gene1493|rna1492|rna1492 200 LGGRILDHKK-FRECKRGLLELSATISQMQQIEDHNDEAIRKEQEKIRHLANTWRYYLNKEMKIYQALNKLSFDFD 274
                                        *******998.667999999******************************************************** PP

                         V_ATPase_I 306 kkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNp 381
                                        + +l++e+W+  ee+ +++++ + +    + ++   ++++e++e+pPTyf+tn+fte fQ + ++Y++++Y E+Np
  gene1493|gene1493|rna1492|rna1492 275 RDCLVGEAWILGEEIGKLKRINEIKG---DGTSLFAFEITESEEMPPTYFKTNEFTEPFQILTNTYAVPSYGEINP 347
                                        *****************988765533...34555667778889********************************* PP

                         V_ATPase_I 382 alftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkkkkdeilemlfsgRYiillmGlfsiYtGliYNdif 457
                                        a+ft  tFP lF+ MFGD+ HGllll+++++l+ ++k++k+   +e+l+m++sg+Yiil  ++ +++ Gl+Y d+ 
  gene1493|gene1493|rna1492|rna1492 348 AIFTLFTFPMLFGCMFGDVFHGLLLLCLSVYLIRNSKRFKNC--SETLQMIVSGKYIILTFSIGAMFFGLLYSDFG 421
                                        ****************************************97..6******************************* PP

                         V_ATPase_I 458 skslnlfgSswevkekaveeeelkkekkeekvYpfGlDpaWklaenellflnSlKmKlsvilGviqMlfgvllslv 533
                                        s+++ lf+Ss +                 +++YpfG+D +W++++ne++flnS+KmK+s+i+G+++M++gv++s++
  gene1493|gene1493|rna1492|rna1492 422 SLAIPLFTSSRDS----------------NRTYPFGVDHMWHHSKNEMVFLNSMKMKMSIIIGFLHMSLGVVISFL 481
                                        *********9777................468******************************************** PP

                         V_ATPase_I 534 NalyfkkkldiilefiPqllfllsifgYlvlliiyKWlvdweaekekapsllntlinmflskgkvkeeelyegqet 609
                                        Na+yf++ ++i+  +iPq + ++s++gY+v+liiyKWlv+++      ps++ +l+nmf ++  v  ee+y+ q+ 
  gene1493|gene1493|rna1492|rna1492 482 NAMYFNEPVEIYGVLIPQTIVFCSFVGYMVFLIIYKWLVTSN-----YPSIIGVLVNMFTNPFVV-AEEIYPYQHR 551
                                        ***************************************993.....7*****************.88*******9 PP

                         V_ATPase_I 610 vqvv 613
                                        +q +
  gene1493|gene1493|rna1492|rna1492 552 MQPL 555
                                        9975 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.012        74      62     128 ..      56     126 ..      43     133 .. 0.71
   2 ?   10.8   0.1   8.7e-05      0.52      90     139 ..     214     264 ..     141     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                                        HHHHHHTT--.SCHHHHHHHHCTTCCHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHCCHHHHHHHHHC CS
                               FlgN  62 akllaelgls.aeeatlsellakeedeelkelwqelkelle...elkelnelNgrlieqslefnqrllnll 128
                                        +kl+++l++   + ++++e +++++ ++++e+++++ ++l     +k+  ++N++ ++  l +++++ n+l
  gene1493|gene1493|rna1492|rna1492  56 EKLISRLQYLtGDVKEVDEGIKHSDIDQVEEQVNKFFSRLIqlkSIKKETDTNQTRLKEDLYMLEETENFL 126
                                        444444444444446777788877777777777774444332448999999**********9999998887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.7e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCHXXXX..XXXX CS
                               FlgN  90 kelwqelkelleelkelnelNgrlieqslefnqrllnllqgaank.sntYg 139
                                        k    el++++ + +++ ++N ++i++ +e +++l n  +   nk  ++Y+
  gene1493|gene1493|rna1492|rna1492 214 KRGLLELSATISQMQQIEDHNDEAIRKEQEKIRHLANTWRYYLNKeMKIYQ 264
                                        445558999****************************99888888777776 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.7   0.00045       2.7      52     118 ..      63     127 ..      32     140 .. 0.88
   2 ?    0.6   0.1     0.092   5.5e+02      64     106 ..     192     234 ..     181     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00045
                           LOH1CR12  52 aklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlnelLd 118
                                        + l+  +kevd+ i+   +++ + ++q +++   l ++++++++    q+ l++ + +lE+  ++L 
  gene1493|gene1493|rna1492|rna1492  63 QYLTGDVKEVDEGIKH--SDIDQVEEQVNKFFSRLIQLKSIKKETDTNQTRLKEDLYMLEETENFLG 127
                                        6688899999999987..5778888999**********************************99984 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.092
                           LOH1CR12  64 kiitllaelrekqkqyasyaealskvnelsdqlsriqiiledi 106
                                        k++ ++++l  +   ++++ e   ++ els+ +s++q+i +++
  gene1493|gene1493|rna1492|rna1492 192 KVKDIFSSLGGRILDHKKFRECKRGLLELSATISQMQQIEDHN 234
                                        6667777777777889999999999999999999999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1189  (0.0663171); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3333.69
//
Query:       gene1494|gene1494|rna1493|rna1493  [L=878]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-20   73.8   4.4    3.4e-12   46.4   0.1    2.8  3  AAA_12           AAA domain
    7.7e-19   68.5   1.4      2e-09   37.6   0.0    3.1  3  AAA_11           AAA domain
    8.7e-17   61.6   1.8    2.4e-16   60.1   1.8    1.7  1  Dna2             DNA replication factor Dna2
    4.8e-15   55.9   5.5    8.7e-14   51.8   2.4    3.1  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    9.2e-10   38.6   0.0      2e-09   37.4   0.0    1.5  1  AAA_30           AAA domain
    3.6e-09   37.1   0.0    3.3e-08   34.0   0.0    2.3  2  AAA_19           AAA domain
    2.1e-08   33.9   0.0    4.7e-08   32.7   0.0    1.6  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    1.1e-06   28.9   0.2    7.4e-06   26.2   0.0    2.3  2  Cas_Cas4         Domain of unknown function DUF83
  ------ inclusion threshold ------
      0.011   16.1   0.1       0.53   10.6   0.0    2.5  2  AAA_16           AAA ATPase domain
      0.049   13.7   0.5        5.5    7.0   0.0    3.3  3  AAA_14           AAA domain
      0.052   12.7   0.3        1.2    8.2   0.0    3.1  4  PIF1             PIF1-like helicase
      0.055   13.3   0.0       0.11   12.4   0.0    1.5  1  Helicase_RecD    Helicase
       0.14   11.1   0.0       0.43    9.5   0.0    1.7  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.16   11.3   0.0       0.32   10.3   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.16   12.0   0.0        0.4   10.7   0.0    1.7  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       6.8   8.1e+03      74     127 ..     516     567 ..     491     578 .. 0.68
   2 !   28.4   0.4   9.6e-10   1.1e-06       2      47 ..     724     766 ..     723     783 .. 0.87
   3 !   46.4   0.1   2.8e-15   3.4e-12     112     198 ..     789     862 ..     771     863 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6.8
                             AAA_12  74 kseeekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvell 127
                                        ++ee+k k++ ++  ++E e+  +++ ++ +   +e  +ki +   Yr++   l
  gene1494|gene1494|rna1493|rna1493 516 NDEEKKPKERPRMDENSEHEASSNILGSYNNYALDE--HKIPIPEIYRKEFLQL 567
                                        344455555566666677777777777777666666..6777777777665555 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 9.6e-10
                             AAA_12   2 erSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdae 47 
                                        + Slfe ll++     + L+tqYRm +eI+r++++lfY+++L  ++
  gene1494|gene1494|rna1493|rna1493 724 SLSLFEYLLRED---HSKLRTQYRMGNEIMRLSNTLFYNDQLIGEK 766
                                        579*****9999...899***********************98665 PP

  == domain 3  score: 46.4 bits;  conditional E-value: 2.8e-15
                             AAA_12 112 kkigvitpYraqvellkkklkekeeeksekeievntvdgfQGrekdviilslVRsnekkeigflkderrlNValTR 187
                                        ++  +++ ++aqv+l+++k +            v+tvd+fQG+e d +++ +    + ++   +++  rlNValTR
  gene1494|gene1494|rna1493|rna1493 789 EECTILCYFNAQVDLIREKTR----------CIVETVDRFQGSEDDRVVVVFD---PVSRCEVMESCERLNVALTR 851
                                        6779**************999..........78*************9987764...55667789************ PP

                             AAA_12 188 AkskliivGnk 198
                                        A+++li+vGnk
  gene1494|gene1494|rna1493|rna1493 852 ARKHLILVGNK 862
                                        **********8 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       4.8   5.8e+03     113     175 ..      87     105 ..      58     138 .. 0.45
   2 !   28.8   0.0   8.3e-10   9.9e-07       1      75 [.     566     631 ..     566     643 .. 0.89
   3 !   37.6   0.0   1.7e-12     2e-09     191     257 ..     653     716 ..     634     720 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.8
                             AAA_11 113 vekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqerrklkkerk 175
                                        +e+++e+++ +                                        e   ++ ++ r+
  gene1494|gene1494|rna1493|rna1493  87 FESECEEHS-M----------------------------------------E---CEKENLRQ 105
                                        333333321.1........................................1...11111111 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 8.3e-10
                             AAA_11   1 klndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerll 75 
                                        +lnd+qr a+   l+ ++ ++i+G PGtgK++ i+ l++ l          + k+++L+   +N A  +++++l 
  gene1494|gene1494|rna1493|rna1493 566 QLNDDQRSALFLSLNCRNYRIIHGMPGTGKSTLICLLIKIL---------VHLKKKVLLICYTNLALANITKKLD 631
                                        69***************************************.........5677777777789*******99975 PP

  == domain 3  score: 37.6 bits;  conditional E-value: 1.7e-12
                             AAA_11 191 evldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpat 257
                                         + +++e+v+ T+ + + ++  +   +fd +++DE +q   + +liP +    k+v+vGD+ QL + 
  gene1494|gene1494|rna1493|rna1493 653 AFFENVELVVGTCFSFADPVYVNR--RFDFCVVDEGSQMHLLLALIPVSIS-TKFVIVGDHLQLKPL 716
                                        68899*******************..9*********************999.*************97 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   1.8     2e-19   2.4e-16       7     158 ..      43     233 ..      40     260 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2e-19
                               Dna2   7 kktvvLrddWaetsvekgdiihi............vgkfeeek................................i 38 
                                        + ++ L+++W++++++++d + +                   +                                i
  gene1494|gene1494|rna1493|rna1493  43 NVECRLSGEWCDVEYRVNDRVTVirciccseqdedS------DidcldeifeseceehsmecekenlrqgtqrskI 112
                                        6789*******************7777665555550......1555555555555566667777778888889999 PP

                               Dna2  39 iidnesnllIlhPdlLvsaTsvanslsClRravLqerlkvsge..sskamliGtilHelfqkalleeeldkeklee 112
                                        +i+n++n+l ++ d  v+ T++++sl+C+ + ++++++ +++   +   +liG i+H+++++al +++++ ++l +
  gene1494|gene1494|rna1493|rna1493 113 FITNTKNYLLVEDDP-VAITTLSESLTCRNKRYISSKIASIKLsyTDVRVLIGVIVHSIMERALVQKNFAFDFLIN 187
                                        *********999887.89********************776664578889************************** PP

                               Dna2 113 lldklleknleelyalglteeeakeeikekleeiekwakkyvkksn 158
                                        ++++ +++n+  +y++g++e++a +e  + +++i+ + ++ +++ +
  gene1494|gene1494|rna1493|rna1493 188 QAKRGISENVMLMYKCGIDEKTALNETLKLIRNIHMFKNHKFEAIE 233
                                        ************************************9988766544 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2   1.5e+03      32      75 ..      46      90 ..      28     132 .. 0.73
   2 !   51.8   2.4   7.3e-17   8.7e-14       2     233 ..     586     859 ..     585     860 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                    Viral_helicase1 32 aelltegk..pklpnlsvrtvdsflmalvkstkgkililDEylllh 75
                                       + l  e+   ++  n++v  ++ + ++  ++ +++i  lDE++  +
  gene1494|gene1494|rna1493|rna1493 46 CRLSGEWCdvEYRVNDRVTVIRCICCSEQDE-DSDIDCLDEIFESE 90
                                       4444444477778888888888777777775.78999999987654 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 7.3e-17
                    Viral_helicase1   2 vvhGvpGcGKStlirkllrts.................liltvnrptaelltegk..................... 39 
                                        ++hG+pG GKStli  l++                    ++t            k                     
  gene1494|gene1494|rna1493|rna1493 586 IIHGMPGTGKSTLICLLIKILvhlkkkvllicytnlalANIT------------Kkldgikiytagkegfffktta 649
                                        79**********998777665566675555545554444444............2445555555555********* PP

                    Viral_helicase1  40 .....pklpnlsvrtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfl 110
                                              ++  l v t+ sf  +     +++++++DE  ++h  ++l+l+  s +  ++++GD+lQ +  sr+++ l
  gene1494|gene1494|rna1493|rna1493 650 eaiafFENVELVVGTCFSFADPVYVNRRFDFCVVDEGSQMH--LLLALIPVSISTKFVIVGDHLQLKPLSRSSKEL 723
                                        *9999778888899999****9999999*************..57778988889999*************999888 PP

                    Viral_helicase1 111 lahlpssl..shrvgrrttyllpsdvaeilsak........vgteveversgel...kvetepkgqe.kvlvyltf 172
                                          +l+  l  +++++ rt y+ ++    + +          ++  ++ve+ +++   +++  p+ +e ++l+y  +
  gene1494|gene1494|rna1493|rna1493 724 SLSLFEYLlrEDHSKLRTQYRMGNEIMRLSNTLfyndqligEKRPSSVEFIDTDtidFIALVPSFEEcTILCYFNA 799
                                        888888888999**************99999998888665544444444444444433233333333566666666 PP

                    Viral_helicase1 173 tqalkealgvrevttvhevqGltfdkVtlvllketdlelisesrenllvAlTRhrkslvil 233
                                          +l ++  ++ v tv   qG++ d+V++v + + +++++ es e l vAlTR+rk l+++
  gene1494|gene1494|rna1493|rna1493 800 QVDLIREKTRCIVETVDRFQGSEDDRVVVVFD-PVSRCEVMESCERLNVALTRARKHLILV 859
                                        66666666666889******************.55667777889************99875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.7e-12     2e-09       1     135 [.     566     720 ..     566     760 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.7e-12
                             AAA_30   1 elnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg.ieastiak 75 
                                        +ln++Q++a+   l+ ++ + +++G +GtGK+t++  l +++ + +++v+++  t+ a ++++++l+ i+ +t  k
  gene1494|gene1494|rna1493|rna1493 566 QLNDDQRSALFLSLNCRN-YRIIHGMPGTGKSTLICLLIKILVHLKKKVLLICYTNLALANITKKLDgIKIYTAGK 640
                                        699*******99999997.******************************************998665333333333 PP

                             AAA_30  76 llkrlk.......................grarlepg.tllivDEagmvdtkqlaallkaaeka.gakvilvGDer 126
                                             k                       + + ++++ +  +vDE + +     + ll+ +  + ++k ++vGD+ 
  gene1494|gene1494|rna1493|rna1493 641 EGFFFKttaeaiaffenvelvvgtcfsfaDPVYVNRRfDFCVVDEGSQM-----HLLLALIPVSiSTKFVIVGDHL 711
                                        22222223455555557789*********668999999*******9865.....44555554432589******** PP

                             AAA_30 127 QlasVeaGg 135
                                        Ql++ ++ +
  gene1494|gene1494|rna1493|rna1493 712 QLKPLSRSS 720
                                        ***998854 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   2.7e-11   3.3e-08      11     142 ..     583     714 ..     571     718 .. 0.70
   2 ?    0.0   0.0      0.82   9.8e+02     102     138 ..     824     862 ..     750     866 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.7e-11
                             AAA_19  11 kvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.........atTiHrlal 77 
                                        +  ++ + pGtGK++++   +++lv+l+    +++ll+++t+ A  +++++l++++            tT  ++a+
  gene1494|gene1494|rna1493|rna1493 583 NYRIIHGMPGTGKSTLICLLIKILVHLK----KKVLLICYTNLALANITKKLDGIKIYtagkegfffKTTAEAIAF 654
                                        44578899********************....89******************766655666666664444445544 PP

                             AAA_19  78 ldfddlltealelle....eaeeekklqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQli 142
                                         ++ +l+            + ++   +++++   +vDE +++  l  +L+      ++k+++vGD+ Ql 
  gene1494|gene1494|rna1493|rna1493 655 FENVELV-------VgtcfSFADPVYVNRRFdFCVVDEGSQMHLL-LALIPVSI--STKFVIVGDHLQLK 714
                                        4333333.......033334455666778888******9987643.34444444..266*******9986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.82
                             AAA_19 102 eeellivDEfqdvd..elqyrLlkallgekkklllvGDp 138
                                        ++ +++ D ++  +  e   rL  al+  +k+l+lvG +
  gene1494|gene1494|rna1493|rna1493 824 DRVVVVFDPVSRCEvmESCERLNVALTRARKHLILVGNK 862
                                        333777788887666577788888888777889999976 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   3.9e-11   4.7e-08       4      52 .]     812     859 ..     810     859 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.9e-11
                           UvrD_C_2   4 altihkaQGsefpaVivfdpdlaaarmgelrrrlLYtavTRAreklilv 52 
                                        + t+ ++QGse + V+v+ +  +  +  +++ + L +a+TRAr++lilv
  gene1494|gene1494|rna1493|rna1493 812 VETVDRFQGSEDDRVVVVFDPVSRCE-VMESCERLNVALTRARKHLILV 859
                                        67**********98888777777776.4579****************98 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.98   1.2e+03       3      44 ..     131     174 ..     129     203 .. 0.75
   2 !   26.2   0.0   6.2e-09   7.4e-06      54     133 ..     246     321 ..     195     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.98
                           Cas_Cas4   3 tkiqyyliCkrklwlish..eitleensetvelGkllheesyer 44 
                                        t+++  l C+ k ++ s+   i+l+  + +v +G ++h   ++ 
  gene1494|gene1494|rna1493|rna1493 131 TTLSESLTCRNKRYISSKiaSIKLSYTDVRVLIGVIVHSIMERA 174
                                        56677789*999999998778999999999999****9865555 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6.2e-09
                           Cas_Cas4  54 sikiDvvekekeklvvvEvKkskkkeeaaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelek 128
                                        ++  D +       +v E+K+ k++++++++Q+  Y+l+L+ k+g + +  +l+y+   + +ev+l +++ ++l +
  gene1494|gene1494|rna1493|rna1493 246 KGDADAIG----IDTVLEIKSTKSQRPEHRAQVILYALMLKeKTGDDFS-PFLYYIPAGELVEVKLRHQEIRSLLN 316
                                        56666666....6788*************************88899988.******************99999998 PP

                           Cas_Cas4 129 aikei 133
                                          ++i
  gene1494|gene1494|rna1493|rna1493 317 LRNKI 321
                                        88877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00044      0.53      28      46 ..     586     604 ..     572     656 .. 0.85
   2 ?    2.7   0.0      0.12   1.5e+02     122     163 ..     691     736 ..     671     743 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                             AAA_16  28 llsGesGvGKsslvrellr 46 
                                        +++G++G+GKs+l+  l +
  gene1494|gene1494|rna1493|rna1493 586 IIHGMPGTGKSTLICLLIK 604
                                        79***********966655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                             AAA_16 122 llkrll.allsrderplvlvlDdlq......wadeaslqllaaLlrlle 163
                                        ll +l+ + +s+   ++v+v D+lq        +e sl+l+++Llr+  
  gene1494|gene1494|rna1493|rna1493 691 LLLALIpVSIST---KFVIVGDHLQlkplsrSSKELSLSLFEYLLREDH 736
                                        455566566666...4*********9999999999*********99865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.8   5.7e+03      67     105 ..      80     122 ..      60     127 .. 0.57
   2 ?    7.0   0.0    0.0046       5.5       5      49 ..     585     629 ..     582     719 .. 0.60
   3 ?    2.9   0.0     0.087     1e+02      62     110 ..     817     871 ..     760     875 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.8
                             AAA_14  67 ylflDEiqevpewekal...kslvdeg.knldvivtGSnskll 105
                                        + +lDEi e+++ e+ +   k+ +++g ++ ++++t  +++ll
  gene1494|gene1494|rna1493|rna1493  80 IDCLDEIFESECEEHSMeceKENLRQGtQRSKIFITNTKNYLL 122
                                        4567777776544443311123333334556777776666665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0046
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                         +i G+  +GK+tl+  lik l   k+++l i   +  +++++++
  gene1494|gene1494|rna1493|rna1493 585 RIIHGMPGTGKSTLICLLIKILVHLKKKVLLICYTNLALANITKK 629
                                        589****************88886666666665555555443322 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.087
                             AAA_14  62 e.....ekktylflDEiqevpewekalkslvd..egknldvivtGSnskllskeia 110
                                        +     +++ ++++D +++++ +e++ +  v   +  + ++i+ G +sk+l  +i 
  gene1494|gene1494|rna1493|rna1493 817 RfqgseDDRVVVVFDPVSRCEVMESCERLNVAltRA-RKHLILVGNKSKMLEIDIL 871
                                        12223367899*********9999875555553155.6699*******99987765 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.3   3.6e+02     180     232 ..     344     393 ..     336     446 .. 0.59
   2 ?    8.2   0.0     0.001       1.2      26      66 ..     586     626 ..     566     637 .. 0.79
   3 ?   -3.0   0.0       2.5     3e+03     144     161 ..     704     721 ..     702     776 .. 0.83
   4 ?   -2.0   0.0       1.3   1.5e+03     241     285 ..     765     809 ..     721     847 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.3
                                        -EEEE-S-STTTT...........HHHHHHHHHHHCT---CCCCHH....... CS
                               PIF1 180 kvlkLtknmRllsesldetekkelkeFskwllkigdGkineedeeealieiPe 232
                                        k l+ t+ +R + + +de+e+  +++F+  +l+   G++   d +    e+P+
  gene1494|gene1494|rna1493|rna1493 344 KSLEKTHFLRRQLDAIDEEEARTVESFIPAVLRYQRGTLVGLDLQG---EMPS 393
                                        5566666667666677777777777777777777777765555443...3333 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                                        EEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC CS
                               PIF1  26 FvtGsgGtgKtflwkallkklrsegkivlavAssGvAalll 66 
                                         ++G+ GtgK+ l   l+k+l   +k+vl +  + +A  ++
  gene1494|gene1494|rna1493|rna1493 586 IIHGMPGTGKSTLICLLIKILVHLKKKVLLICYTNLALANI 626
                                        468*******************************9997776 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.5
                                        EEEE--TTS-----SSSS CS
                               PIF1 144 vvlgGDfrQilPviekgs 161
                                         v+ GD  Q+ P+++ ++
  gene1494|gene1494|rna1493|rna1493 704 FVIVGDHLQLKPLSRSSK 721
                                        58899999*999986554 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.3
                                        ..HHCHCCS---SS--...........EEEESSCCHHHHHHHHHH CS
                               PIF1 241 dkieeivsevygdllqeltdkeyleerailcptnedvdeiNnyvl 285
                                        +k  + v+++  d+++ +     +ee +ilc  n +vd i ++  
  gene1494|gene1494|rna1493|rna1493 765 EKRPSSVEFIDTDTIDFIALVPSFEECTILCYFNAQVDLIREKTR 809
                                        55556666666777777777778999999**99999999988764 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.1e-05      0.11       2     104 ..     587     691 ..     586     705 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-05
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke....eekkkkaekaelrvr. 72 
                                        + + +G+GKS+++ l+++ l++ +k ++l+   ++ +++++++ l  g++  +  +     +++++a+      + 
  gene1494|gene1494|rna1493|rna1493 587 IHGMPGTGKSTLICLLIKILVHLKK-KVLLICYTNLALANITKKL-DGIKIYTAGKegffFKTTAEAIAFFE--Nv 658
                                        78899****************9987.6777777777788888887.55554443334555222222222222..23 PP

                      Helicase_RecD  73 ....kqrieyiapdellklkeqadllvvDEAAaipl 104
                                            ++ + +  p  + ++    d+ vvDE ++++l
  gene1494|gene1494|rna1493|rna1493 659 elvvGTCFSFADPVYVNRR---FDFCVVDEGSQMHL 691
                                        4556777777777777665...49999999998876 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00036      0.43      34      63 ..     587     616 ..     577     619 .. 0.88
   2 ?   -3.0   0.0       2.3   2.7e+03      54      87 ..     683     717 ..     677     721 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                                        EEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                               MeaB  34 ltGvPGaGkstlvealglelrrrGkrvavl 63 
                                        + G+PG+Gkstl+  l+  l++  k+v ++
  gene1494|gene1494|rna1493|rna1493 587 IHGMPGTGKSTLICLLIKILVHLKKKVLLI 616
                                        67******************9999998765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.3
                                        HCTT--EE.EEEE------------------HCCC CS
                               MeaB  54 rrrGkrva.vlavDPsspftGGsilGDklRleela 87 
                                        +++G ++  +la+ P s  t   i+GD+l+l+ l+
  gene1494|gene1494|rna1493|rna1493 683 VDEGSQMHlLLALIPVSISTKFVIVGDHLQLKPLS 717
                                        566666652579999999999*******9998776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.32      11      65 ..     571     625 ..     564     635 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                       Mg_chelatase  11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                                        ++ al ++   +   ++ G pG+GK+ l+  l ++l +l+++  l + +  ++a+
  gene1494|gene1494|rna1493|rna1493 571 QRSALFLSLNCRNYRIIHGMPGTGKSTLICLLIKILVHLKKKVLLICYTNLALAN 625
                                        667777777777778999*********************9998877766666655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00034       0.4       8      33 ..     591     616 ..     585     707 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00034
                                        TTSSHHHHHHHHHHHHHHTT--EEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA   8 GGvGKTtlaanLaralarrglrVllv 33 
                                         G+GK+tl + L+++l   +++Vll+
  gene1494|gene1494|rna1493|rna1493 591 PGTGKSTLICLLIKILVHLKKKVLLI 616
                                        59**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.53
# Mc/sec: 4943.65
//
Query:       gene1495|gene1495|rna1494|rna1494  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.0   0.0    1.9e-12   46.7   0.0    1.2  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.031   14.4   0.0    1.3  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   2.1e-16   1.9e-12       2      65 ..       6      68 ..       5      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 2.1e-16
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEE CS
                                LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivli 65
                                       f+++ i+k++ v lk g  ++G+L ++D+++Nl L +v+  ++++    +++l+ iRG++i +i
  gene1495|gene1495|rna1494|rna1494  6 FFRSNIGKRIFVMLKAGVYVSGVLNSIDPYLNLNLLKVKILSNHP-GLDSISLCSIRGSSIKYI 68
                                       78899****************************************.*****************9 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.4e-06     0.031       8      51 ..       7      48 ..       3      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-06
                                       HHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                             SM-ATX  8 ltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                       + s +Gk++ v +k G   +G+++++++   +++ L  ++ +++
  gene1495|gene1495|rna1494|rna1494  7 FRSNIGKRIFVMLKAGVYVSGVLNSIDP--YLNLNLLKVKILSN 48
                                       6788***********************9..77776666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 612.18
//
Query:       gene1496|gene1496|rna1495|rna1495  [L=713]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-07   30.0   4.9    2.2e-06   26.6   4.9    2.5  1  Cullin        Cullin family
  ------ inclusion threshold ------
      0.026   14.6   0.5       0.11   12.6   0.0    2.3  3  DUF1803       Domain of unknown function (DUF1803)
       0.26   11.3   2.7        1.4    9.0   0.4    3.2  2  Cullin_Nedd8  Cullin protein neddylation domain


Domain annotation for each model (and alignments):
>> Cullin  Cullin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   4.9   3.6e-10   2.2e-06       6     452 ..      17     500 ..      14     589 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.6e-10
                             Cullin   6 eaiqeilkknvsklsfeelYravynlvlskekkqgekLydklkelieehlkellkellkeesdeelLkalkkeWed 81 
                                        + ++e l++ + +++ ee+Y+    + +    +  ++L + +++  +++++e  ++   e++  ++ k+l +   +
  gene1496|gene1496|rna1495|rna1495  17 NFVEEYLSRGIATSTCEEIYQISCYMSR---INACRELLKVVRKMSRAFVDESIEKA-CEVDTINIGKYLYEFNFH 88 
                                        5566777777888888999987766666...56789999999999999999988875.445555544444444445 PP

                             Cullin  82 hktsmkmirdifmyldrvyvkklpsvydlglelfrdhvfr..iklkdrlieallkliekeRegevidrsllksvie 155
                                        +  sm++ r++f+ +  v    +  + +l+ +lf + v     k+ + ++ ++ ++i+ eR+ e  ++s   + +e
  gene1496|gene1496|rna1495|rna1495  89 WDRSMNLFRKVFSPITPVE---RGFIDKLSSRLFTRFVKGieDKILEFITYNIREEIDCERKMEKANESGHGN-CE 160
                                        6678999999998887665...667999999999998873236777778889999999999887666544444.44 PP

                             Cullin 156 mlvelgedse........dkk...vYeeeFekafleateefYrae.aeellaensvaseYlkkaeerleeEeerve 219
                                          v+ +++ +        + +    +e+   k+ ++a+    +++ + ++ +e   +   ++  ++r+++E+  ++
  gene1496|gene1496|rna1495|rna1495 161 FSVNKKQKLSqsgsdevgK-EvpdRFESLCRKKQISAIICILQSKgCFNMFSER-IVGCLISALSSRINDESLDIS 234
                                        4433322222355455541.2555788777777777777777666344444443.666779999999*99986665 PP

                             Cullin 220 .......kyldsstkkkllevleeelikkhleelleeelkklledekledLkrlykllsrvdgleeLrkaleeyik 288
                                               ky + + +k    ++e+ li++ +++  +ee+ +++ d + +++++ + +++  +  e+L +a+  y k
  gene1496|gene1496|rna1495|rna1495 235 gikdlidKYRNAEYMKDYFYTVESGLIQRIVTNYTDEEIFSIM-D-REDEMRLSVGFFCASNSEERLVEAIGMYCK 308
                                        55555548999999***********************988888.5.89*************999***********9 PP

                             Cullin 289 eegkaivkdakekektedakkyveklLelkdkfdklvkeafnndkefekaldeafeefvnknkvnsksaellakYi 364
                                        +  k ++            ++++     ++ kf ++ +   ++ +++++ +  + +++vn+n     + e ++ ++
  gene1496|gene1496|rna1495|rna1495 309 KIIKGLSI-----------DDFIGGYYWIYLKFREIENCKDDGYQKIKEGIGRSKRDVVNANI--DCAVESVCTWT 371
                                        77776665...........58***************99999999****************886..5599******* PP

                             Cullin 365 DelLkkg..lkgl.........................................seeeleekldkvlvlfryiedK 397
                                        D+lL+     k+                                           e  l + ++ +  +f + ++K
  gene1496|gene1496|rna1495|rna1495 372 DSLLRGRiaIKEDviegmehtvlipgtkkevrmdtkkalkkigmeeiplesgvwREFLLSNIFEMIGEIFHFCNNK 447
                                        *****8644444489999********************************9999999999999************* PP

                             Cullin 398 DvFekyYkkhLakRLllgksasddaEksmiskLkeecGseftskLegMfkDikls 452
                                        +vFe   +++L  RL+   s s + E+ +i++     ++   +k+  M+kD +  
  gene1496|gene1496|rna1495|rna1495 448 EVFEMSLQNKLGNRLVSRSSISTEWENLLIDRVD--PSKCRLNKMRCMIKDFSER 500
                                        *******************************988..6667789999999997654 PP

>> DUF1803  Domain of unknown function (DUF1803)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.3   1.4e+04      30      56 ..      56      77 ..      54      89 .. 0.53
   2 ?   -3.1   0.1       1.4   8.2e+03      50      64 ..     256     270 ..     236     295 .. 0.63
   3 ?   12.6   0.0   1.8e-05      0.11      39      71 ..     591     623 ..     564     648 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.3
                            DUF1803 30 RelkkeFadqkkldrlldelidaglik 56
                                       R++ ++F     +d+++++  + + i+
  gene1496|gene1496|rna1495|rna1495 56 RKMSRAF-----VDESIEKACEVDTIN 77
                                       6667777.....444455555555554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                            DUF1803  50 idaglikRenkrYkl 64 
                                        +++gli+R    Y+ 
  gene1496|gene1496|rna1495|rna1495 256 VESGLIQRIVTNYTD 270
                                        566666666555543 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 1.8e-05
                            DUF1803  39 qkkldrlldelidaglikRenkrYklnlpifei 71 
                                         k  dr l+ l+ +gl+k +++ Y+lnl+++e 
  gene1496|gene1496|rna1495|rna1495 591 CKTWDRNLEVLVRKGLVKVKERIYSLNLNFWEE 623
                                        56789*************************872 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.18   1.1e+03      25      58 ..     214     250 ..     190     251 .. 0.62
   2 ?    9.0   0.4   0.00024       1.4       5      27 ..     656     678 ..     653     705 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.18
                       Cullin_Nedd8  25 LvsevieqlskrftpsiadikkrIesLiek....eYle 58 
                                        +v   i++ls+r + +  di + I++Li+k    eY++
  gene1496|gene1496|rna1495|rna1495 214 IVGCLISALSSRINDESLDI-SGIKDLIDKyrnaEYMK 250
                                        55566777777665544444.34555555544448886 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00024
                       Cullin_Nedd8   5 aiqaaIVRiMKsrktlshneLvs 27 
                                        ++++ IV+ MKs++ l+ +eL +
  gene1496|gene1496|rna1495|rna1495 656 LLDCKIVKEMKSNRVLNKSELRE 678
                                        689****************9955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.54
# Mc/sec: 3990.63
//
Query:       gene1497|gene1497|rna1496|rna1496  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   21.8   0.0    0.00037   21.0   0.0    1.5  1  SEP       SEP domain


Domain annotation for each model (and alignments):
>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.1e-08   0.00037       1      75 [.      65     141 ..      65     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-08
                                SEP   1 ltlwknGFsvdDGelrsyddpenaeflesikkGevPeelekve.kgeevevnledrrneeykppkkp....kfkaF 71 
                                        +t +knG+ v+ +++++++  +n ++ ++++kG +  +l     +g+  ev  +++ +eeyk+++k+     ++aF
  gene1497|gene1497|rna1496|rna1496  65 ITQYKNGILVE-DKFYDFSVNDNIRLKNMLEKGTFDASLL--GlHGDTAEVAYTEKLEEEYKEESKAhetdPKAAF 137
                                        688*******8.59**************************..5599****************97665212123458 PP

                                SEP  72 sGsG 75 
                                         G+G
  gene1497|gene1497|rna1496|rna1496 138 IGEG 141
                                        8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1248.63
//
Query:       gene1498|gene1498|rna1497|rna1497  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.2   0.0      0.052   13.3   0.0    1.4  1  Cyclin_N  Cyclin, N-terminal domain
      0.081   12.5   0.1       0.12   12.0   0.1    1.2  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.8e-06     0.052      71     125 ..       6      58 ..       2      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.8e-06
                                        CCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTTT- CS
                           Cyclin_N  71 dklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemErliLetLnfd 125
                                        ++++ v+ + ++lA+K eei   +++ l+       ++e il+ E +++e+L+++
  gene1498|gene1498|rna1497|rna1497   6 KEMKDVVYAIVILASKCEEI-HGNIDTLIKKLP-ESNKESILNYESDMFEALDYN 58 
                                        6788999999**********.588888888866.6679***************98 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.3e-05      0.12      46     122 ..      22      95 ..       6      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                            DUF2067  46 ikdiirrikellreklkkekrglfkyslsdllreagapvppdvLvdaLkllGykaelreenvlktnapleevvela 121
                                         ++i   i++l+++  +++k+++  y+ sd++  +++++ ++ L  +L++ G+ a l+e+++++  a+ e +v++a
  gene1498|gene1498|rna1497|rna1497  22 CEEIHGNIDTLIKKLPESNKESILNYE-SDMFEALDYNFHFPSL--YLRMYGILAILQEKGIIRVAAETEGAVKVA 94 
                                        57888999******88899999*****.****9999******99..7*************************9999 PP

                            DUF2067 122 e 122
                                        e
  gene1498|gene1498|rna1497|rna1497  95 E 95 
                                        7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1152.15
//
Query:       gene1499|gene1499|rna1498|rna1498  [L=392]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-46  155.6   0.1    3.5e-45  153.7   0.0    1.9  2  AAA              ATPase family associated with various cellul
    4.8e-13   48.7   0.1    9.9e-13   47.7   0.1    1.6  1  AAA_lid_3        AAA+ lid domain
    2.4e-08   34.3   0.0    4.3e-08   33.5   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
    3.7e-08   33.2   0.4    9.2e-08   31.9   0.4    1.7  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    9.6e-07   28.9   0.0      4e-06   26.9   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
    2.1e-06   28.2   0.1    7.5e-05   23.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    4.2e-05   23.8   1.0     0.0088   16.3   1.0    2.4  1  AAA_22           AAA domain
    4.6e-05   23.2   0.0    0.00011   22.0   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00012   22.6   0.0     0.0054   17.3   0.0    2.6  2  AAA_18           AAA domain
     0.0009   18.5   0.0      0.002   17.4   0.0    1.6  1  TIP49            TIP49 P-loop domain
     0.0011   19.1   0.0      0.002   18.3   0.0    1.5  1  AAA_33           AAA domain
     0.0017   18.1   0.0     0.0038   17.0   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0032   16.9   0.1       0.11   11.9   0.0    2.2  2  PhoH             PhoH-like protein
     0.0034   16.8   0.0       0.01   15.2   0.0    1.8  2  ATPase           KaiC
     0.0054   16.6   0.0      0.016   15.1   0.0    1.8  2  AAA_3            ATPase family associated with various cellul
     0.0076   15.7   0.1      0.017   14.5   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0087   16.1   0.0      0.016   15.2   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0094   15.5   0.0       0.11   12.0   0.0    2.5  3  AAA_25           AAA domain
  ------ inclusion threshold ------
       0.01   15.0   0.0       0.02   14.0   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
      0.011   16.0   0.0       0.02   15.1   0.0    1.4  1  AAA_28           AAA domain
      0.011   15.4   0.3      0.075   12.7   0.0    2.5  4  Sigma54_activat  Sigma-54 interaction domain
      0.015   15.0   0.0        0.1   12.3   0.0    2.1  2  AAA_24           AAA domain
      0.017   15.1   0.0      0.032   14.2   0.0    1.5  1  AAA_14           AAA domain
       0.03   14.7   0.0      0.055   13.9   0.0    1.5  1  RNA_helicase     RNA helicase
      0.035   13.6   0.0      0.059   12.9   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.041   13.2   0.0      0.085   12.1   0.0    1.5  1  Zeta_toxin       Zeta toxin
      0.068   12.3   0.0       0.12   11.5   0.0    1.2  1  Parvo_NS1        Parvovirus non-structural protein NS1
      0.093   11.9   0.0       0.28   10.3   0.0    1.9  2  NB-ARC           NB-ARC domain
       0.11   12.3   0.1       0.24   11.1   0.0    1.6  1  AAA_11           AAA domain
       0.13   12.2   0.0       0.49   10.3   0.0    1.9  2  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.7   0.0   5.9e-48   3.5e-45       1     131 [.     172     304 ..     172     305 .. 0.97
   2 ?   -1.3   0.0       4.6   2.7e+03      15      54 ..     345     381 ..     342     391 .. 0.65

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 5.9e-48
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.. CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.. 74 
                                        vllyGppGtGKTlla+ava++++ +f+++sgsel++ky+ge+++ +relf  a+e+a psi+f+DEid+++++r  
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQCKFIRVSGSELVQKYIGEGSRLVRELFVMAREHA-PSIIFMDEIDSIGSTRgd 246
                                        79******************************************************9.*****************9 PP

                                        .TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                                AAA  75 .sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                         ++++++e +r++ +Ll++ldg++++ +++ vi+atnr+d ldpallr gR+drkie++
  gene1499|gene1499|rna1498|rna1498 247 sNKGSDSEVQRTMLELLNQLDGFESH-NNIKVIMATNRIDILDPALLRtGRIDRKIEFP 304
                                        777799999****************7.66****************************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.6
                                        HHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                                AAA  15 akavakelgvefleisgsellskyvgesekkirelfkeak 54 
                                        +kav++e+g++ l+     ++   +++ e+ +++++k+a 
  gene1499|gene1499|rna1498|rna1498 345 VKAVCTEAGMYALRERRIHVT---QEDFEMAVHKVLKKAG 381
                                        689999988776666655555...5566666666666654 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   1.7e-15   9.9e-13       2      44 ..     328     370 ..     327     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.7e-15
                          AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                        +dl+ +A+++ G+SGA+ +a+c eA++ Alr+ + ++t+edfe
  gene1499|gene1499|rna1498|rna1498 328 IDLEIIASKMVGCSGAEVKAVCTEAGMYALRERRIHVTQEDFE 370
                                        89****************************************8 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   7.1e-11   4.3e-08       6     105 ..     172     265 ..     168     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 7.1e-11
                                        EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                              AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                        +ll gp g+Gkt+la+a+a + ++    k+ir+  sel +    + + +     ++  v a e+   i+++DEid 
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQC----KFIRVSGSELVQ----KYIGEGSRLVRELFVMAREHApsIIFMDEIDS 239
                                        5789******************98....************....88878888888888888888888********* PP

                                        -------------HHHHHHHHHHHH- CS
                              AAA_2  80 ihpkessgadvSregVqrdLLqileg 105
                                        i +++  ++  S  +Vqr +L +l +
  gene1499|gene1499|rna1498|rna1498 240 IGSTRGDSNKGSDSEVQRTMLELLNQ 265
                                        ***99999999************975 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.4   1.5e-10   9.2e-08       1      57 []      59     114 ..      59     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.5e-10
                                        EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                     Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                        V+ V+E +++   ++Vkt  d +++v++   v+ ++Lrpg +Va+ +d++ ++ +LP
  gene1499|gene1499|rna1498|rna1498  59 VGIVVEKMGK-MQVLVKTNPDGKYLVKVEHGVNYDDLRPGVRVALRSDSYDVHRILP 114
                                        77799****9.******************************************9999 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   6.8e-09     4e-06       1      79 [.     171     242 ..     171     294 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.8e-09
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEve 75 
                                        +vlL GppGtgK+ la+ +a+ +++++  v +++      l++++   +++ +lv   +v a +  ++i+++DE++
  gene1499|gene1499|rna1498|rna1498 171 GVLLYGPPGTGKTLLARAVAHHTQCKFIRVSGSE------LVQKYI--GEGSRLVRELFVMAREhAPSIIFMDEID 238
                                        59*************************9998876......999998..4555555555553433689999999999 PP

                                        G--H CS
                              AAA_5  76 raes 79 
                                         + s
  gene1499|gene1499|rna1498|rna1498 239 SIGS 242
                                        8765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.3e-07   7.5e-05      15      48 ..     160     193 ..     139     210 .. 0.79
   2 ?    2.3   0.0      0.32   1.9e+02     122     159 ..     216     264 ..     204     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-07
                             AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellral 48 
                                        ++e++   +p  vll+G++G+GK+ l+r+++++ 
  gene1499|gene1499|rna1498|rna1498 160 LFENLGIAQPKGVLLYGPPGTGKTLLARAVAHHT 193
                                        4555666678********************9754 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.32
                             AAA_16 122 llkrllallsrderplvlvlDdlq...........wadeaslql.laaLl 159
                                        l+++l++ +++ + p ++++D+++             d++ +   l++L 
  gene1499|gene1499|rna1498|rna1498 216 LVRELFVMARE-HAPSIIFMDEIDsigstrgdsnkGSDSEVQRTmLELLN 264
                                        55667777777.778*********66666555555333344444355554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.0   1.5e-05    0.0088       8      30 ..     172     194 ..     167     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                             AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                        ++++G++GtGKT+l+r +++  +
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQ 194
                                        689***************99862 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.8e-07   0.00011      35      95 ..     171     239 ..     145     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.8e-07
                             RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka.....gdlaalltnl...eekdvlfideihr 95 
                                         vllyGpPG Gkt la+ +a+  + k+   sg  l ++     + l+  l  +   ++  ++f+dei  
  gene1499|gene1499|rna1498|rna1498 171 GVLLYGPPGTGKTLLARAVAHHTQCKFIRVSGSELVQKyigegSRLVRELFVMareHAPSIIFMDEIDS 239
                                        69***********************98888887654432311123443333331113446888888865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     9e-06    0.0054       1      25 [.     172     221 ..     172     288 .. 0.61
   2 ?    2.4   0.0      0.35   2.1e+02      18      67 ..     333     380 ..     321     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9e-06
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf.........................g 25 
                                        +ll G+pG+GKt la++++ ++++                          
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQCkfirvsgselvqkyigegsrlvrelF 221
                                        799***************99998888988876666666666666644441 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.35
                             AAA_18  18 Lskrl.gf.gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                        +++++ g+ g +++ v++e g++  ++       ++ +ed+ +++++ l+++
  gene1499|gene1499|rna1498|rna1498 333 IASKMvGCsGAEVKAVCTEAGMYALRERR----IHVTQEDFEMAVHKVLKKA 380
                                        455555889***************99988....8888888888888888775 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.4e-06     0.002      51      92 ..     170     209 ..     143     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.4e-06
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysle 92 
                                        ++vLl Gp+gtGkt la a++++   + +f+ +sgse+ +  
  gene1499|gene1499|rna1498|rna1498 170 KGVLLYGPPGTGKTLLARAVAHHT--QCKFIRVSGSELVQKY 209
                                        89*******************985..699********97665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.3e-06     0.002       2      40 ..     172     212 ..     172     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-06
                             AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgt 40 
                                        vll G+pG+GK+ la+ ++ +++  ++++s  +l +++ g+
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQckFIRVSGSELVQKYIGE 212
                                        7899*************986666779999999987776664 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.3e-06    0.0038      44      71 ..     166     193 ..     147     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.3e-06
                          IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                        i++ ++++l Gp+G+GK+ la a+++++
  gene1499|gene1499|rna1498|rna1498 166 IAQPKGVLLYGPPGTGKTLLARAVAHHT 193
                                        6677899*****************9876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00019      0.11      20      42 ..     170     192 ..     160     200 .. 0.83
   2 ?    2.7   0.0      0.12        74      62     114 ..     241     293 ..     220     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                        SEEEEE--TTSSTTHHHHHHHHH CS
                               PhoH  20 divfaiGpaGtGKtylavalave 42 
                                        + v   Gp GtGKt+la a+a +
  gene1499|gene1499|rna1498|rna1498 170 KGVLLYGPPGTGKTLLARAVAHH 192
                                        557899***********999865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                                        T----SS---------TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGT CS
                               PhoH  62 geelGflpgdleekvdpylrplydaLkdllgaekvekllekgkievaplaymR 114
                                        g   G  +   +  v+  +  l ++L+ + ++++++ ++ +++i +++ a +R
  gene1499|gene1499|rna1498|rna1498 241 GSTRGDSNKGSDSEVQRTMLELLNQLDGFESHNNIKVIMATNRIDILDPALLR 293
                                        444444444456678888889999999999********************999 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-05      0.01       5      37 ..     137     187 ..     134     197 .. 0.85
   2 ?   -2.5   0.0       4.4   2.6e+03     125     150 ..     237     265 ..     207     271 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                             ATPase   5 IeglDeilk..................gGipegrvvlitGepGtGKtifal 37 
                                        I glDe +k                   Gi + + vl++G pGtGKt++a 
  gene1499|gene1499|rna1498|rna1498 137 IGGLDEQIKeirevielpikhpelfenLGIAQPKGVLLYGPPGTGKTLLAR 187
                                        7788888866888888888888888889********************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.4
                             ATPase 125 iDsitgl...ayeekeavaReilrqlvrv 150
                                        iDsi++    +++ +++++ +++ +l+++
  gene1499|gene1499|rna1498|rna1498 237 IDSIGSTrgdSNKGSDSEVQRTMLELLNQ 265
                                        44444442212223334455555555555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.7e-05     0.016       2      31 ..     172     201 ..     171     217 .. 0.93
   2 ?   -2.9   0.0       9.6   5.7e+03      81      98 ..     352     369 ..     312     374 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-05
                              AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                        vll g PG++ktll++a+a++ +++f r+ 
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQCKFIRVS 201
                                        7999***********************995 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.6
                              AAA_3  81 alleameerqvtvegeth 98 
                                        a + a++er++ v++e +
  gene1499|gene1499|rna1498|rna1498 352 AGMYALRERRIHVTQEDF 369
                                        233456666666666555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.9e-05     0.017      24      43 ..     171     190 ..     162     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                       Mg_chelatase  24 nlllvGppGsGKtmlakrlp 43 
                                         +ll+GppG+GKt+la++++
  gene1499|gene1499|rna1498|rna1498 171 GVLLYGPPGTGKTLLARAVA 190
                                        68**************9875 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.7e-05     0.016      19      60 ..     169     210 ..     142     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.7e-05
                                        TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEE CS
                               TsaE  19 gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYe 60 
                                         + +lL+G+ G+GKT l+r++a++ +++ ++     lv++Y 
  gene1499|gene1499|rna1498|rna1498 169 PKGVLLYGPPGTGKTLLARAVAHHTQCKFIRVSGSELVQKYI 210
                                        4559*********************99966655667777774 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   6.7e+02      78      98 ..      30      54 ..      21      89 .. 0.71
   2 !   12.0   0.0   0.00019      0.11      36      56 ..     172     192 ..     146     204 .. 0.90
   3 ?   -1.7   0.0       3.1   1.9e+03     137     173 ..     224     267 ..     214     280 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                             AAA_25 78 saEdsedelrrRlravgeal....r 98
                                       ++E++++el+rR+r ++e++    +
  gene1499|gene1499|rna1498|rna1498 30 VLEQKRAELNRRVRFLREEIsivqE 54
                                       57999*******9988888766653 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00019
                             AAA_25  36 allaGapgtGKttlaldlala 56 
                                        +ll+G+pgtGKt la  +a++
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHH 192
                                        69*************999887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.1
                             AAA_25 137 ieevegvrlvviDplsr..alggdensnsd......vgalveale 173
                                        ++e + +  +  D +++   ++gd+n+ sd      + +l+++l+
  gene1499|gene1499|rna1498|rna1498 224 ARE-HAPSIIFMDEIDSigSTRGDSNKGSDsevqrtMLELLNQLD 267
                                        455.45777777777773334457776666543333344444444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.4e-05      0.02      52     115 ..     168     236 ..     119     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                             DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklvellr...erperfilfvDD 115
                                        + + vLL+G  GtGK  l +a+ ++++ + +r+   e+ ++ + e ++lv++l    +++   i+f+D 
  gene1499|gene1499|rna1498|rna1498 168 QPKGVLLYGPPGTGKTLLARAVAHHTQCKFIRVSgsELVQKYIGEGSRLVRELFvmaREHAPSIIFMDE 236
                                        45679***********************99998434888888888888888764222555667888886 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.3e-05      0.02       2      38 ..     172     213 ..     171     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                             AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileek 38 
                                        + + G+++tGKT l++a a +     ++v   E + +++ e+
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHtqckFIRVSgSELVQKYIGEG 213
                                        6799***************98855445555666666666554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         8   4.8e+03     108     121 ..      22      35 ..      15      40 .. 0.79
   2 ?   12.7   0.0   0.00013     0.075      21      47 ..     168     194 ..     156     213 .. 0.79
   3 ?   -2.2   0.0       4.8   2.9e+03      95     105 ..     230     240 ..     224     247 .. 0.82
   4 ?   -2.7   0.0       6.8   4.1e+03     131     143 ..     271     283 ..     251     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8
                                        HHHHHHHHHHHHSE CS
                    Sigma54_activat 108 elQekLlrvlqege 121
                                        +  +k+lrvl++++
  gene1499|gene1499|rna1498|rna1498  22 AKKAKVLRVLEQKR 35 
                                        56789999999986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                                        SSS-EEEECSTTSSHHHHHHHHHHHST CS
                    Sigma54_activat  21 tdlsvlitGesGtGKellaraiheask 47 
                                        ++  vl+ G  GtGK+llara+ ++++
  gene1499|gene1499|rna1498|rna1498 168 QPKGVLLYGPPGTGKTLLARAVAHHTQ 194
                                        56789***************9965543 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.8
                                        SEEEEETGGGS CS
                    Sigma54_activat  95 GtlfLDeigel 105
                                        +++f+Dei ++
  gene1499|gene1499|rna1498|rna1498 230 SIIFMDEIDSI 240
                                        689*****986 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 6.8
                                        EE--EEEEEEESS CS
                    Sigma54_activat 131 ikvdvriiaatne 143
                                         + ++++i+atn+
  gene1499|gene1499|rna1498|rna1498 271 SHNNIKVIMATNR 283
                                        4567888999886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018       0.1       4      22 ..     171     189 ..     168     198 .. 0.85
   2 ?   -0.4   0.0       1.3   7.9e+02      99     131 ..     246     281 ..     228     290 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                             AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                         +l+yGp+g+GKT la+  
  gene1499|gene1499|rna1498|rna1498 171 GVLLYGPPGTGKTLLARAV 189
                                        589***********99876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.3
                             AAA_24  99 gdgkG.ygelaeefrrllkklqelrk..nvifiahe 131
                                         + kG  +e+++ + +ll++l+ +    n+ +i+ +
  gene1499|gene1499|rna1498|rna1498 246 DSNKGsDSEVQRTMLELLNQLDGFEShnNIKVIMAT 281
                                        344566689999999999999999998877777655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.4e-05     0.032       3      76 ..     170     240 ..     168     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                             AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                        k +++ G+  +GKT l++ ++++      +++ ++  +  +k + + ++l ++++ +++e+  +++f+DEi  +
  gene1499|gene1499|rna1498|rna1498 170 KGVLLYGPPGTGKTLLARAVAHHTQ---CKFIRVSGSELVQKYIGEGSRLVRELFVMAREHAPSIIFMDEIDSI 240
                                        568999**************98777...8999999998777766665555554444444568899******988 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.2e-05     0.055       1      46 [.     172     208 ..     172     246 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.2e-05
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdg 46 
                                        ++lyGp+g+GK++la+ +a++ + k+         +r + ++ +++
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQCKF---------IRVSGSELVQK 208
                                        689**************665554333.........34444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.8e-05     0.059      30      58 ..     166     194 ..     158     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-05
                              AAA_7  30 lknkkpvllvGptGtGKtviikdllkkld 58 
                                        +++ k vll+Gp GtGKt++++ + ++ +
  gene1499|gene1499|rna1498|rna1498 166 IAQPKGVLLYGPPGTGKTLLARAVAHHTQ 194
                                        678899**************999877665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014     0.085      14      53 ..     167     204 ..     159     227 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDd 53 
                                         +Pk +ll G pG GK+ la++++  +  q +++r+++ +
  gene1499|gene1499|rna1498|rna1498 167 AQPKGVLLYGPPGTGKTLLARAVAHHT--QCKFIRVSGSE 204
                                        68*********************9998..88888887655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.12     117     138 ..     172     193 ..     168     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                          Parvo_NS1 117 vwfyGpantGktnlaeaIakav 138
                                        v++yGp+ tGkt la+a a+ +
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHT 193
                                        899****************976 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00048      0.28      23      45 ..     172     194 ..     159     267 .. 0.81
   2 ?   -2.3   0.0       3.5   2.1e+03     131     194 ..     274     341 ..     268     358 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                                        EEEEESTTSSHHHHHHHHCCSHC CS
                             NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                        v l+G +G GKt la+ + ++ +
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHHTQ 194
                                        789***************99943 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                                        TSEEEEEESBCCCCCCS-S-..EEEEEESS--HHHH..HHHHHHCCTS-GGCHH..CHHHHHHHHHHC CS
                             NB-ARC 131 rlrvllTTRdeevanavsat..sekievelLekdea..wellenkvfekkleekesleevakeivekc 194
                                         ++v++ T   ++ + +  +      ++e+ +++e+  +e+l+    +++l +  +le +a ++v ++
  gene1499|gene1499|rna1498|rna1498 274 NIKVIMATNRIDILDPALLRtgRIDRKIEFPQPKESarLEILKIHSRKMNLTKGIDLEIIASKMVGCS 341
                                        55666666555555543322123333444444444422566777777777777777888888887654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0004      0.24      16      41 ..     168     193 ..     151     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                             AAA_11  16 eseitliqGPPGtgKTktivellsql 41 
                                        +++ +l+ GPPGtgKT    ++ ++ 
  gene1499|gene1499|rna1498|rna1498 168 QPKGVLLYGPPGTGKTLLARAVAHHT 193
                                        455589**********7666666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00081      0.49       3      23 ..     172     192 ..     170     200 .. 0.89
   2 ?   -1.7   0.0       3.9   2.3e+03      68     114 ..     216     264 ..     203     268 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00081
                                        EEEEC-TTTCHHHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                        v+l G++G GKT L++ +a+ 
  gene1499|gene1499|rna1498|rna1498 172 VLLYGPPGTGKTLLARAVAHH 192
                                        799*************99986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.9
                                        SS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH............HHHHHC CS
                              NACHT  68 pvsevwavllelperlLlilDglDelvtdlgq...kekqpvrtlLselir 114
                                         v+e +++  e++ ++ + +D +D + +  g        +v++ + el++
  gene1499|gene1499|rna1498|rna1498 216 LVRELFVMAREHAPSIIF-MDEIDSIGSTRGDsnkGSDSEVQRTMLELLN 264
                                        455555555555555544.7888888887777655344455555556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 2480.23
//
Query:       gene15|gene15|rna15|rna15  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-66  222.5   0.3    6.7e-66  222.2   0.3    1.0  1  Rcd1      Cell differentiation family, Rcd1-like
  ------ inclusion threshold ------
      0.014   15.4   0.0       0.04   14.0   0.0    1.8  1  E2F_TDP   E2F/DP family winged-helix DNA-binding domain


Domain annotation for each model (and alignments):
>> Rcd1  Cell differentiation family, Rcd1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.3   7.5e-70   6.7e-66       9     257 ..      29     277 ..      21     279 .. 0.97

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 7.5e-70
                       Rcd1   9 ekreeaLleLskkresvedlallLwesfgtvaaLLqeivsiYpllspptltaaesnrvcnaLallqcvashpetrklflkakip 92 
                                +k  ++L eL ++ ++ + l+l +w    + ++LLqe++  Y++ls++++++ +++r++++L++lq+++s++ ++++f++a++p
  gene15|gene15|rna15|rna15  29 SKDINKLDELFEELKKSPGLSLDIWTHDSMPIFLLQEVITPYMILSTSKFDEVQYHRLYTVLNILQILVSDSRIKRVFVDARFP 112
                                556689****************************************************************************** PP

                       Rcd1  93 lyLypfLnttsksrefEylRltsLgvigaLvktddkevikflldteivplclrimesGselsktvAtfIlqkiLlddeGLeYic 176
                                +y+y++L ++++ +++E+lR+++Lgv+++L+++ d+ v+k+l++te+vpl+l+i++ Gse+s+ ++++++  i+ +d+GL+Y+c
  gene15|gene15|rna15|rna15 113 YYIYRYLVISDSGSKYETLRISALGVVASLLQNGDQYVHKQLKTTEVVPLLLKIVDLGSEASQLLSANVFGLIIGSDDGLNYAC 196
                                ************************************************************************************ PP

                       Rcd1 177 qtaerfsavaevLnkmvvslteepssrllkhvircYlrLsdnprareaLkkclpelLkdktfkellkedpetkkwlkqLle 257
                                qt++rfsa++ ++n++ ++ ++  s++l+k  +r+Y rL+++p++r+ L++  p+ L +++   l+++d e++ ++k+++ 
  gene15|gene15|rna15|rna15 197 QTFDRFSAINLMFNSLASQGVSIGSVKLVKAALRIYIRLCAKPHIRALLSSKKPDGLFTDEAGTLISSDAECRMLFKSFMD 277
                                *****************999999*****************************************************99986 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.4e-06      0.04      11      54 ..      20      94 ..      13      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-06
                    E2F_TDP 11 kfvellkesakgtlslneaakeLv...............................dkkdekvkkRRiYDilNVLe 54
                                +++l+ +++k++ +l+e+ +eL+                               ++k ++v+  R+Y +lN+L+
  gene15|gene15|rna15|rna15 20 DLCKLVISNSKDINKLDELFEELKkspglsldiwthdsmpifllqevitpymilsTSKFDEVQYHRLYTVLNILQ 94
                               46777766778999****************************************9899999*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1770.68
//
Query:       gene150|gene150|rna150|rna150  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.8   0.2      0.038   14.1   0.2    1.3  1  DUF3244   Domain of unknown function (DUF3244)


Domain annotation for each model (and alignments):
>> DUF3244  Domain of unknown function (DUF3244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   2.1e-06     0.038      24      85 ..      55     117 ..      33     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-06
                                    SEEEEE.ETTEEEEEESS--SEEEEEEEETTT--EEEEEEE-GGGTTEEEEE-TTS-SEEEEE CS
                        DUF3244  24 Pitasi.egnilsiefesplsdvtitikdeetgevvyestivnasgstisidlsgeesgeYkl 85 
                                    P  ++  e n   ief ++++d+ ++ ++ ++ +vvy+s + + ++++  i++++    ++k+
  gene150|gene150|rna150|rna150  55 PGYVVRgEKNKFQIEFFTSMTDLRVSRMGPNKIKVVYNSKDRSTNDTYLEISIKNRTIKNFKI 117
                                    444444689999********************************9**********99888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 896.63
//
Query:       gene1501|gene1501|rna1500|rna1500  [L=404]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-20   73.8   7.1    1.2e-20   73.8   7.1    2.3  2  zf-HC5HC2H_2  PHD-zinc-finger like domain
    1.2e-11   44.0   8.0    1.2e-11   44.0   8.0    2.2  2  PHD_2         PHD-finger
    3.9e-07   29.9  10.7    3.9e-07   29.9  10.7    3.5  3  PHD           PHD-finger
    3.4e-05   24.0   8.5    3.4e-05   24.0   8.5    3.2  3  zf-HC5HC2H    PHD-like zinc-binding domain
     0.0006   20.2   0.1    0.00087   19.7   0.1    1.3  1  EPL1          Enhancer of polycomb-like
     0.0033   17.3   5.3     0.0033   17.3   5.3    3.1  3  C1_1          Phorbol esters/diacylglycerol binding domain (C
     0.0062   16.2   9.3     0.0062   16.2   9.3    2.5  2  zf-PHD-like   PHD/FYVE-zinc-finger like domain


Domain annotation for each model (and alignments):
>> zf-HC5HC2H_2  PHD-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.9      0.22   5.5e+02      54      85 ..     134     167 ..     121     173 .. 0.76
   2 !   73.8   7.1   4.5e-24   1.2e-20       2      96 ..     189     279 ..     188     291 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                       zf-HC5HC2H_2  54 lkekCllCkkr....kGaciqCskkeCktafHvtCa 85 
                                         ++ C +C+k       a + C+   C+ + H +C 
  gene1501|gene1501|rna1500|rna1500 134 PSSFCDICTKYtsenDKALVVCQG--CEICVHENCY 167
                                        566788998877766678888888..9999999995 PP

  == domain 2  score: 73.8 bits;  conditional E-value: 4.5e-24
                       zf-HC5HC2H_2   2 eCvlCkkkgGalkktsderwvHvlCallvpevsfsnvaerepvdvekikkerlkekCllCkkrkGaciqCskkeCk 77 
                                        eC +C +++G++k+tsd++w HvlC+++++++sf +  ++ep+dv +++ke   + Cl+C++ +G+ i Cs+  C+
  gene1501|gene1501|rna1500|rna1500 189 ECSFCISTNGVFKQTSDNKWGHVLCVMFNRSLSFGHPLSKEPIDVGSYTKE---SGCLFCDEVRGTVICCSYFACS 261
                                        8************************************************99...7********************* PP

                       zf-HC5HC2H_2  78 tafHvtCalaaglvmeled 96 
                                        +++Hv Cal+ +++++l++
  gene1501|gene1501|rna1500|rna1500 262 KKYHVPCALD-KCYFDLSN 279
                                        ********98.67777655 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   8.0   4.6e-15   1.2e-11       4      35 ..     152     181 ..     150     182 .. 0.95
   2 ?   -6.6   3.6         7   1.8e+04       5      18 ..     253     268 ..     251     269 .. 0.63

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 4.6e-15
                              PHD_2   4 llsCdkCsvaVHasCYGvskesdgeeWlCrrC 35 
                                        l++C++C+++VH++CYG+++ sd   WlCrrC
  gene1501|gene1501|rna1500|rna1500 152 LVVCQGCEICVHENCYGIQDLSDF--WLCRRC 181
                                        8**********************8..****** PP

  == domain 2  score: -6.6 bits;  conditional E-value: 7
                              PHD_2   5 lsCd..kCsvaVHasC 18 
                                        + C+   Cs   H  C
  gene1501|gene1501|rna1500|rna1500 253 ICCSyfACSKKYHVPC 268
                                        6676666776666666 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9  10.7   1.5e-10   3.9e-07       1      50 [.     137     182 ..     137     184 .. 0.91
   2 ?    0.7   0.3       0.2   5.1e+02      22      33 ..     206     217 ..     189     221 .. 0.80
   3 ?    2.8   8.9     0.042   1.1e+02       2      30 ..     242     269 ..     241     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.5e-10
                                        SBTTTTS.TTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                                PHD   1 rCavCkk.ksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50 
                                        +C++C k +s++++ lv+C+gC+ ++H +C+++++      ++ wlC++C 
  gene1501|gene1501|rna1500|rna1500 137 FCDICTKyTSENDKALVVCQGCEICVHENCYGIQDL-----SDFWLCRRCI 182
                                        7******9999**********************965.....447******6 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                                        SCEEETTTSSST CS
                                PHD  22 krwfHqkClkpp 33 
                                        ++w H+ C+ ++
  gene1501|gene1501|rna1500|rna1500 206 NKWGHVLCVMFN 217
                                        689999999776 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.042
                                        BTTTTSTTSTTSCEEEET..TTSCEEETTTS CS
                                PHD   2 CavCkkksdeeeelvqCd..gCkrwfHqkCl 30 
                                        C +C++     +++++C    C++ +H+ C 
  gene1501|gene1501|rna1500|rna1500 242 CLFCDE---VRGTVICCSyfACSKKYHVPCA 269
                                        999999...79******8668*********5 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.2  12.6         7   1.8e+04      36      67 ..     135     168 ..     121     193 .. 0.75
   2 ?    2.6   0.8     0.063   1.6e+02      33      69 ..     184     217 ..     174     222 .. 0.80
   3 !   24.0   8.5   1.3e-08   3.4e-05       1      89 [.     210     287 ..     210     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: -8.2 bits;  conditional E-value: 7
                         zf-HC5HC2H  36 klkCylCk....kkvGaciqCskkkCkkafHvtCak 67 
                                        +  C +C+    ++  a + C+   C+ + H  C  
  gene1501|gene1501|rna1500|rna1500 135 SSFCDICTkytsENDKALVVCQG--CEICVHENCYG 168
                                        56799999555433679999987..99999999975 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.063
                         zf-HC5HC2H  33 erkklkCylCkkkvGaciqCskkkCkkafHvtCakea 69 
                                        ++ +++C++C +++G+  q s    +k  Hv C + +
  gene1501|gene1501|rna1500|rna1500 184 REDSKECSFCISTNGVFKQTSD---NKWGHVLCVMFN 217
                                        567789******9999998888...778888887755 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 1.3e-08
                         zf-HC5HC2H   1 HvvCalwipevvfeeekeiemeeiedvekikkerkklkCylCkkkvGaciqCskkkCkkafHvtCakeagllleee 76 
                                        Hv+C+++  ++ f +  +  +e+i dv    + +k+  C +C++  G +i Cs   C+k++Hv Ca ++ ++++ +
  gene1501|gene1501|rna1500|rna1500 210 HVLCVMFNRSLSFGHPLS--KEPI-DV---GSYTKESGCLFCDEVRGTVICCSYFACSKKYHVPCALDK-CYFDLS 278
                                        778888888887776655..3443.33...34456789****************************975.555554 PP

                         zf-HC5HC2H  77 eekeklksyCkkH 89 
                                            +  syC  H
  gene1501|gene1501|rna1500|rna1500 279 ----NRLSYCIVH 287
                                        ....455666555 PP

>> EPL1  Enhancer of polycomb-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.4e-07   0.00087     105     157 .]      68     116 ..      19     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-07
                               EPL1 105 eks.eeeldd...eveYdMDEeDekWLeelnekrkkegvekisediFEivmdrlEke 157
                                        ++  ee+ +d   ++ Y  D+ D+ +L     +        +se++FE++mdrlEke
  gene1501|gene1501|rna1500|rna1500  68 QTIqEEQGKDffeSILYKVDSYDRHYLHGSHPN--------VSENVFELIMDRLEKE 116
                                        333233333366688999999999999988887........***************8 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   5.3   1.3e-06    0.0033       9      43 ..     133     167 ..     128     174 .. 0.91
   2 ?   -1.8   0.7       1.2     3e+03      29      42 ..     176     190 ..     169     196 .. 0.62
   3 ?    0.4   3.1      0.24   6.1e+02       8      43 ..     236     269 ..     231     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                        SS--B-TTT-SB--SSSS-EEEETTT--EE-CCCC CS
                               C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllvHkkCh 43 
                                        + ++fC+ C +  ++  k  + C+ C+++vH++C+
  gene1501|gene1501|rna1500|rna1500 133 RPSSFCDICTKYTSENDKALVVCQGCEICVHENCY 167
                                        6689*********99*******************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                        EEETTT--EE-CC.C CS
                               C1_1  29 lkCswCkllvHkk.C 42 
                                        + C+ C ++ + k C
  gene1501|gene1501|rna1500|rna1500 176 WLCRRCIYREDSKeC 190
                                        556666555444443 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.24
                                        -SS--B-TTT-SB--SSSS-EEEET..TT--EE-CCCC CS
                               C1_1   8 fkqptfCkhCgeflwgkekqglkCs..wCkllvHkkCh 43 
                                        + +++ C  C+e       + ++Cs  +C+ ++H  C+
  gene1501|gene1501|rna1500|rna1500 236 YTKESGCLFCDEVR----GTVICCSyfACSKKYHVPCA 269
                                        55666677777766....7788888667*******996 PP

>> zf-PHD-like  PHD/FYVE-zinc-finger like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   9.3   2.4e-06    0.0062       1      58 [.     138     196 ..     138     229 .. 0.76
   2 ?   -3.1   5.3         2   5.2e+03      10      29 ..     247     268 ..     240     273 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.4e-06
                        zf-PHD-like   1 CdtCaeskdeekgqlvyCqGCslsyhkaClGkRsaRehlv.tkvgedsFvlqCrrCigl 58 
                                        Cd+C++ ++e+  +lv+CqGC    h +C G     +     +    +    C +Ci++
  gene1501|gene1501|rna1500|rna1500 138 CDICTKYTSENDKALVVCQGCEICVHENCYGIQDLSDFWLcRRCIYREDSKECSFCIST 196
                                        9*******999********************9887775440344445555667777765 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2
                        zf-PHD-like  10 eekgqlvyCq..GCslsyhkaC 29 
                                        e +g++++C    Cs+ yh  C
  gene1501|gene1501|rna1500|rna1500 247 EVRGTVICCSyfACSKKYHVPC 268
                                        5689*****7558******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2543.50
//
Query:       gene1502|gene1502|rna1501|rna1501  [L=1102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-28   99.9   1.4    2.2e-13   49.2   0.0    3.6  3  IKI3      IKI3 family
  ------ inclusion threshold ------
       0.16   12.4   0.7        8.9    6.8   0.4    2.5  2  Diedel    Diedel
       0.24   11.3   4.4        1.2    8.9   0.7    3.0  3  Clathrin  Region in Clathrin and VPS


Domain annotation for each model (and alignments):
>> IKI3  IKI3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.1   0.00085       5.1     107     146 ..      70     109 ..      58     114 .. 0.87
   2 !   49.2   0.0   3.6e-17   2.2e-13     280     455 ..     180     334 ..     149     367 .. 0.78
   3 !   42.2   0.4   4.8e-15   2.9e-11     685     930 ..     532     810 ..     523     811 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.00085
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               IKI3 107 daeekeveivGsiesGieaaawspdeellalvtgeekvvl 146
                                        + +++e++ +G+++ G+ +++ s de  +++++++e +++
  gene1502|gene1502|rna1501|rna1501  70 NKNTAEISEIGRVKDGVVSVSISRDESWCVIISTTEILLF 109
                                        78999***************************99987765 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 3.6e-17
                                        XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXX... CS
                               IKI3 280 sldvvfFErNGLrhgefslrlekeeeevqsLaWsadSevLavrledr....vqlwtisNyhWYLKqelrysasegv 351
                                        s  + f E NGL+hg+      + + ++  L   ++ +vL    ++     ++++ ++N+hWYLK + +++ +  +
  gene1502|gene1502|rna1501|rna1501 180 STGILFVEPNGLEHGN------PLDVQCSTLSFLENEDVLITTEKNDggslLKVFYTKNFHWYLKTSKQVPGKFLC 249
                                        57899**********6......457899************99554444999***************9998877655 PP

                                        XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               IKI3 352 eevkWdpekpltLlvltesgkievvdfafetavsetssendvgtvaViDgkklllTplslanvPPPmsarelelea 427
                                               ++++t+++ +  g+  v+ f fe  +  + +        ViDg+++l T++s   +PPP  + ++el+ 
  gene1502|gene1502|rna1501|rna1501 250 -------TEKNTVVF-ND-GERLVRVFLFEERTRYGPE------YYVIDGNCILYTDFSEKIIPPPFFSTRIELDG 310
                                        .......45554444.44.5666677777776665554......79****************************** PP

                                        XXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                               IKI3 428 avndvafsksnsktlavllsdgelaiae 455
                                        +++dv   k++    ++l++d+  +i++
  gene1502|gene1502|rna1501|rna1501 311 NIIDVFPRKKKG---VILQKDK-AVIFR 334
                                        ****97776664...3444444.44555 PP

  == domain 3  score: 42.2 bits;  conditional E-value: 4.8e-15
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXX CS
                               IKI3 685 pRGNLEtiypriLvLaavrkalkakrYkeAfklcrthRidlnllvDydpe..lFlenveaFvrqvkkvdylnlFls 758
                                          G LEt  pri +La v+k+l +++Yk+A++ c++h i + +  Dyd e  +F++      ++ + +++ n+ l+
  gene1502|gene1502|rna1501|rna1501 532 RHGTLETYTPRIYTLAFVKKLLFDGKYKDAIDRCQRHIIPFGVFLDYDIEfqRFIA----VCKDMHLISFFNEALE 603
                                        459*******************************************9986214554....3455555555555555 PP

                                        X.......XXXXXXXX..XXXXXXXX...................................XXXXXXXXXXXXXXX CS
                               IKI3 759 s.......LkeeDvtk..tlYketls...................................ktkaskeakakakek 790
                                        +       L+ e+v +  +++++t+                                    + + +++ +++++++
  gene1502|gene1502|rna1501|rna1501 604 RlggfdfiLESEEVKRfrKIFNSTIAlesenardyfietvkndesigtsslahlvgwkskrDLHYQETCNNRNRKT 679
                                        51111111567777766678888888*******************************9985444555556666777 PP

                                        XXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXX- CS
                               IKI3 791 dtkesKvnkvcdairkalek...eeesekyllailtayvkkeppeleaaLkliaslkeedeeqaeealkyllfLvd 863
                                        +tk+ K++ + ++ ++ +++   + + e++ + i+  +vk +   ++ aL +        +++  + ++y+l  + 
  gene1502|gene1502|rna1501|rna1501 680 PTKSCKITICGRRPKDFFNElllSLSPERNFKFIIFLLVKVN--RIDLALLMA-------KHDLKAGVEYMLSITS 746
                                        7777788766655555555577699****************9..666666543.......3455699********* PP

                                        --HHHHHHHHTT-HHHHHHHHHCTT--GGGTHHHHHHHHCS-HHHHHHHHHHHHT-HHHHHHHHHCS CS
                               IKI3 864 vnklYdvALGlYdlelallvAqksqkDPkEYLpfLqeLkkleelrrkfeIDdyLkryekAlehlvea 930
                                         n++ +  L  +d  l++ v +  qkD   +L+ +   ++ +e+ rkf+I+d L++  +Al hl+++
  gene1502|gene1502|rna1501|rna1501 747 TNNIINSVLESCDEGLVYEVMKVCQKDSSDFLSLI---HSCPEDLRKFKINDFLENRINALWHLSRT 810
                                        *****************************988875...789***********************986 PP

>> Diedel  Diedel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.025   1.5e+02      47      62 ..     169     184 ..     155     189 .. 0.69
   2 ?    6.8   0.4    0.0015       8.9       9      37 ..     668     692 ..     660     696 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.025
                             Diedel  47 kgkCnifGCnCdkgcl 62 
                                        +gk nifGC+ ++g l
  gene1502|gene1502|rna1501|rna1501 169 RGKYNIFGCTTSTGIL 184
                                        6899*****9988865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0015
                             Diedel   9 fkvengeCekvggkqskketCkatiCadg 37 
                                        +   +++C++ ++k+ +k+ Ck+tiC+ +
  gene1502|gene1502|rna1501|rna1501 668 Y---QETCNNRNRKTPTKS-CKITICGRR 692
                                        4...579999998887776.******976 PP

>> Clathrin  Region in Clathrin and VPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.026   1.5e+02      85     124 ..     709     746 ..     702     776 .. 0.81
   2 ?    8.9   0.7   0.00021       1.2      78     140 ..     847     909 ..     845     912 .. 0.90
   3 ?   -2.5   0.0      0.71   4.3e+03      20      70 ..    1037    1083 ..    1033    1088 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.026
                                        SHHHHHHHHHTTXTHSSHSSXSSSSHCSCHHHHTTTTTXX CS
                           Clathrin  85 lyeeavilykkinefkkaisllkklkdfddaieyaakvsn 124
                                         +++ ++l+ k+n+++ a+ ++k+  d++  +ey   + +
  gene1502|gene1502|rna1501|rna1501 709 NFKFIIFLLVKVNRIDLALLMAKH--DLKAGVEYMLSITS 746
                                        578999*************99877..78888887766655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00021
                                        HHHHT-SSHHHHHHHHHTTXTHSSHSSXSSSSHCSCHHHHTTTTTXXSHHHHHHHHHHHSSXS CS
                           Clathrin  78 klcekadlyeeavilykkinefkkaisllkklkdfddaieyaakvsnpelwekllealldkkp 140
                                        +lc +  + + a+ l+kk +++++a++++ ++  +++a++ + k +     e l++ l+++++
  gene1502|gene1502|rna1501|rna1501 847 NLCAELLPSDKALALFKKAGNVERALEVAVENLYWREALNLYDKENRRGFCELLAHKLVESEK 909
                                        68899999999*****************9999*************999999999998888776 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.71
                                         TT-HHHHCHHHCCHHHCHTS--HHHHHHHHHHHHHTT-HHHHHHTTSS--- CS
                           Clathrin   20 aglleelleyLekvlkedskenpalqtallelyakyddpqeleeflkknnn 70  
                                         ++++e ll++ ek     +++++a +t+ +  + + +   e+++++k+  +
  gene1502|gene1502|rna1501|rna1501 1037 RDSTEDLLKVFEKFKM--KECTTAHNTSFNVVASTIKA--EVDNIFKTEKS 1083
                                         5677888888888885..66999999999999999886..88888886555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.81u 0.32s 00:00:01.13 Elapsed: 00:00:00.51
# Mc/sec: 6537.94
//
Query:       gene1503|gene1503|rna1502|rna1502  [L=271]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-38  131.5   0.1    1.1e-24   87.2   0.0    2.1  2  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.0   6.1e-29   1.1e-24       1     136 [.      79     209 ..      79     213 .. 0.91
   2 !   42.8   0.0   2.3e-15   4.1e-11     167     221 ..     212     267 ..     208     269 .. 0.91

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 6.1e-29
                                        EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHHH CS
                       Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkeel 76 
                                        i+DGNrR+ kk gle+r     +G++++ e++++ +  g + ++++ f+ +N+kR+++ev+ +me++k+  +ke  
  gene1503|gene1503|rna1502|rna1502  79 ICDGNRRYMKKLGLEDRF-TKDEGLQKVYEFINFGYFYGFEEISFFCFALNNLKRTPDEVNGMMEVVKK-KVKEP- 151
                                        89***********88887.************************************************76.55444. PP

                                        HHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHH CS
                       Prenyltransf  77 kellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavr 136
                                         + +  + r+r+ G+l+ll+edv+++l ++e++++ nn+++++ni ++Y+s+dei + ++
  gene1503|gene1503|rna1502|rna1502 152 -KEVGIRPRFRIYGRLDLLEEDVRNRLMDIERESR-NNTDIIVNIFFAYSSEDEISRGIQ 209
                                        .34455778999***********************.6666***************98765 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 2.3e-15
                                        SS-SEEEEESS--S-TTSSTTTTTT-E.EEEESSSGGG--HHHHHHHHHHHHHCHH CS
                       Prenyltransf 167 pdpDlliRtsGeeRlSnFllwqlayse.lyfldvlWPdfskedllealleyqkrer 221
                                          +D+liRt+  +RlSnF++ q+a+ + ++f + lWP+++ ++l  +ll+ + ++r
  gene1503|gene1503|rna1502|rna1502 212 SRVDILIRTGDTKRLSNFMIRQVAKGTsVFFAKPLWPELTTAHLFLILLKHRLEDR 267
                                        579*******************99988899*****************999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1769.43
//
Query:       gene1504|gene1504|rna1503|rna1503  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.067   13.0  22.7       0.22   11.3   6.4    2.3  2  TACC_C        Transforming acidic coiled-coil-containing prot
        6.4    5.9  11.5          1    8.5   6.8    1.9  2  TMPIT         TMPIT-like protein
        9.5    6.1   8.3        2.8    7.8   5.0    1.7  2  Folliculin    Vesicle coat protein involved in Golgi to plasm


Domain annotation for each model (and alignments):
>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.4   3.7e-05      0.22      54     116 ..     233     294 ..     227     310 .. 0.83
   2 ?    7.0   8.6   0.00075       4.5      69     163 ..     313     403 ..     304     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.7e-05
                             TACC_C  54 qlieekqkqkelakkeiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkneeslk 116
                                        + ++++++++++ + +i+k+l++ +q+++++++++k  + + +r++  k+ l ++++n     
  gene1504|gene1504|rna1503|rna1503 233 K-MAQSKQKESMLQSKIDKLLQDIDQIAEKIQDTQKMKDGMTSRLHTKKNHLRNLQANIKEVE 294
                                        4.555667777999*****************************************99977655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00075
                             TACC_C  69 eiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeekL 144
                                        +++k++ ++   la l++ ek fsd +k+y+   +  +   + +e+     +e++ ++++ e+ Y+ Lk   +e L
  gene1504|gene1504|rna1503|rna1503 313 KLSKMMDDQRSKLALLEDEEKIFSDRIKKYDEEYDIGNRELQLDET---RSQEIKRNIEELERLYNVLKIRNNELL 385
                                        67899999999999***********999999666654443334443...45667799******************* PP

                             TACC_C 145 ekAneeiaqvrskakaeta 163
                                        ++ n+e a +r++ + et 
  gene1504|gene1504|rna1503|rna1503 386 NERNKESA-IRNRLELETE 403
                                        ******87.4666666665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   6.8   0.00017         1       5      82 ..     242     325 ..     238     342 .. 0.79
   2 ?   -0.6   0.8       0.1   6.1e+02      14      62 ..     328     376 ..     318     406 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00017
                              TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkee 74 
                                        + l++++++l +  +++ +k+++++k+++ ++++++++k++l++l++++k+++ + +      + +++e+ +l+++
  gene1504|gene1504|rna1503|rna1503 242 SMLQSKIDKLLQDIDQIAEKIQDTQKMKDGMTSRLHTKKNHLRNLQANIKEVEVQRGrtlaliRLSRNELLKLSKM 317
                                        568899999999999**************************************99655666665556666666666 PP

                              TMPIT  75 lkerkkvl 82 
                                        ++++++ l
  gene1504|gene1504|rna1503|rna1503 318 MDDQRSKL 325
                                        66555544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.1
                              TMPIT  14 leetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvke 62 
                                        le+++k +  +++++ +  +   +e++  + r +e+k+++++l++  + 
  gene1504|gene1504|rna1503|rna1503 328 LEDEEKIFSDRIKKYDEEYDIGNRELQLDETRSQEIKRNIEELERLYNV 376
                                        5555566666666666666666666666666666666666666655442 PP

>> Folliculin  Vesicle coat protein involved in Golgi to plasma membrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.63   3.8e+03      25      29 ..      83      87 ..      40     124 .. 0.58
   2 ?    7.8   5.0   0.00046       2.8      71     172 ..     234     336 ..     224     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.63
                         Folliculin 25 sLScE 29
                                       s+S E
  gene1504|gene1504|rna1503|rna1503 83 SFSKE 87
                                       11111 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00046
                         Folliculin  71 ialstdkerlllkawsfiveafeklaaeiqalaeaelereskeeeassaassssalkadgsglsrregssfslske 146
                                        +a s++ke++l ++++ + + + ++a++iq+ ++++  ++s+ ++++++ ++ +a  ++ +  + r+    +ls++
  gene1504|gene1504|rna1503|rna1503 234 MAQSKQKESMLQSKIDKLLQDIDQIAEKIQDTQKMKDGMTSRLHTKKNHLRNLQANIKEVEVQRGRTLALIRLSRN 309
                                        456677799*************************999999998888877777776555555555555666677777 PP

                         Folliculin 147 kylrrsksklkars.LaelvgdediFv 172
                                        ++l+ sk   ++rs La l ++e+iF 
  gene1504|gene1504|rna1503|rna1503 310 ELLKLSKMMDDQRSkLALLEDEEKIFS 336
                                        777777766667754777777777885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2189  (0.122093); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 2824.58
//
Query:       gene1505|gene1505|rna1504|rna1504  [L=883]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-65  220.3   1.4    7.3e-65  219.0   1.4    1.6  1  SNF2_N      SNF2 family N-terminal domain
    1.4e-33  116.1  15.7    3.4e-33  114.8  15.7    1.7  1  DBINO       DNA-binding domain
    5.5e-22   78.2   0.0    1.7e-19   70.2   0.0    3.0  2  Helicase_C  Helicase conserved C-terminal domain
    1.2e-09   38.4   0.6    3.4e-09   36.9   0.0    2.0  2  ResIII      Type III restriction enzyme, res subunit
    6.1e-07   29.4   0.0    1.8e-06   27.8   0.0    1.9  1  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.05   12.8   8.0       0.16   11.1   0.0    4.1  4  HDA2-3      Class II histone deacetylase complex subunits 2 a
        2.9    7.6   5.7        7.2    6.3   5.7    1.7  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   1.4   2.8e-68   7.3e-65      50     349 ..     287     550 ..     266     551 .. 0.90

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 2.8e-68
                                        HHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  50 eakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalr 125
                                        +++ +  +GiLaD+mGLGKTvq+++l++   + +e ++ +       gp+L+v  +s+ld+W +e+ r+++s ++ 
  gene1505|gene1505|rna1504|rna1504 287 SLYDKGINGILADDMGLGKTVQSISLLA---YLYETEEIP-------GPFLVVTISSTLDNWAQEFSRFLPSFKV- 351
                                        6678899*********************...888888877.......**************************76. PP

                                        E--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 126 vlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavs 201
                                         +  +g+    ++++k ++k ++d dvvittY++  ++       + lk+++w++++lDE++ +k+s s+  ++++
  gene1505|gene1505|rna1504|rna1504 352 -CRFSGS----PSERKELKKRFKDSDVVITTYQTAVSDE------KMLKKIKWQYMILDEAQAIKSSMSRRWKTLL 416
                                        .777775....56677799****************9888......9****************************** PP

                                        H---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH.......HHHHHHHHHHHTT-STTEE- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 202 kLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie.......aqaekgrsrLlqllqrlmlr 270
                                        +++++nr++ltGTPiqns+++l++Ll+f+++  f++   f+++++++ie         +ek+ +rL+++l+++mlr
  gene1505|gene1505|rna1504|rna1504 417 SFKARNRLLLTGTPIQNSMQELWALLHFIMPTLFDSLSEFSDWFSKEIEtsatmkkTVDEKSLQRLHTILKPFMLR 492
                                        ******************************************************99999***************** PP

                                        --GGGT--S---EEEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 271 rakkdveknlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnh 346
                                        r k+dv ++l +kt+  ++++ls  ++ +Y+++  ++    +                      +ll++l+++cnh
  gene1505|gene1505|rna1504|rna1504 493 RHKSDVIHELGQKTQIDLYCSLSYRQKVLYKEITRSCSSMEME---------------------NLLMQLKKVCNH 547
                                        *******************************444444333332.....................345666666666 PP

                                        --X CS
                                        xxx RF
                             SNF2_N 347 pql 349
                                        p+l
  gene1505|gene1505|rna1504|rna1504 548 PDL 550
                                        665 PP

>> DBINO  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.8  15.7   1.3e-36   3.4e-33       8     132 ..      83     204 ..      76     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.8 bits;  conditional E-value: 1.3e-36
                              DBINO   8 vwknivkkdipkvyrakaqaekkrlanakkvaklcarevrrkasksskatkdlqlrakrlvremllfwkknekeer 83 
                                         w++   k+i kv+ a++++e++r a ++k++ +care+rr  sk+s++  ++ l++kr+ re+  ++kk e++ +
  gene1505|gene1505|rna1504|rna1504  83 EWMSA-MKNIRKVHSAITSYESARIAFCRKISIICARELRRGLSKTSRT--NPILKSKRIYRELFGHIKKAERSIK 155
                                        56665.59*****************************************..************************* PP

                              DBINO  84 eerkkaekealekakkeeeereakRqqrkLnFLitQTELYshFiskklk 132
                                        ++ kkaeke++e++kke ee+e+ Rq+rk+++L++QTEL+shFi kk k
  gene1505|gene1505|rna1504|rna1504 156 DRSKKAEKEEMERKKKEMEEKEELRQKRKFEYLLSQTELFSHFILKKNK 204
                                        **********************************************987 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.015        39      11      73 ..     318     377 ..     308     383 .. 0.65
   2 !   70.2   0.0   6.7e-23   1.7e-19       3     111 .]     728     838 ..     726     838 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
                                        HHTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEES CS
                         Helicase_C  11 kleeeggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiat 73 
                                        ++ee+ g  l+++ + + l++ ++ + +++  ++kv+++ g  + +er+e  ++f+  +sdv+i+t
  gene1505|gene1505|rna1504|rna1504 318 ETEEIPGPFLVVTISST-LDNwAQEF-SRFlpSFKVCRFSG--SPSERKELKKRFK--DSDVVITT 377
                                        45555555555544443.44332333.2345589*******..9***********5..57899988 PP

  == domain 2  score: 70.2 bits;  conditional E-value: 6.7e-23
                                        HHHHHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGG CS
                         Helicase_C   3 leallell.kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesd.vLiatdv 75 
                                        +  l ell  l++eg++ li+ + +++++   ++l  +kg+++++l+g+l+++ r e++++++ g+   +L++t++
  gene1505|gene1505|rna1504|rna1504 728 MVVLDELLpRLRVEGHRLLIYFQMTRMIDLiEDYL-VRKGYTYLRLDGSLKASVRAEVIKDWQTGDKFiFLLSTRA 802
                                        56678888999*****************8855555.7889***********************988777******* PP

                                        GTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  76 aerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        ++ Gi+++ +++Vi++d ++n+t  +q+++R++R g
  gene1505|gene1505|rna1504|rna1504 803 GGLGINLTAADTVIFYDSDWNPTADQQAMDRAHRLG 838
                                        **********************************86 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.7       2.1   5.4e+03      71      93 ..     151     175 ..     137     207 .. 0.52
   2 !   36.9   0.0   1.3e-12   3.4e-09       2     170 ..     272     431 ..     271     432 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.1
                                        HHHGGGGTGG......GEEEESSS- CS
                             ResIII  71 leefkkflseayke..igkkvsgdk 93 
                                        ++ +k+ +++a ke  + kk++ ++
  gene1505|gene1505|rna1504|rna1504 151 ERSIKDRSKKAEKEemERKKKEMEE 175
                                        4444444444444432111111111 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 1.3e-12
                                        -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                             ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkf 77 
                                        ++l+eyQ++ ++ l++ +  ++  +g+++   G GKT+ +++l ++l++ +++   +++v   s l+ + +ef++f
  gene1505|gene1505|rna1504|rna1504 272 CTLKEYQIKGLNWLVSLY--DKGINGILADDMGLGKTVQSISLLAYLYETEEIPGPFLVVTISSTLDNWAQEFSRF 345
                                        678999999998888666..58889************************9999977777888888899******** PP

                                        TGG....GEEE.ESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...TTT CS
                             ResIII  78 lseaykeigkk.vsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..ksw 150
                                        l++ +  ++ +  s  ++k+ +k+ +++++++tt+q++ +d+       + l++ + +++i DEa  ++++    w
  gene1505|gene1505|rna1504|rna1504 346 LPSFK--VCRFsGSPSERKELKKRFKDSDVVITTYQTAVSDE-------KMLKKIKWQYMILDEAQAIKSSmsRRW 412
                                        *9854..444412222222244666999**************.......778888999*******99999543488 PP

                                        HHHHHT---SEEEEEESS-S CS
                             ResIII 151 reilekfkeavllglTATpe 170
                                        +  l +fk+  +l lT+Tp 
  gene1505|gene1505|rna1504|rna1504 413 KT-LLSFKARNRLLLTGTPI 431
                                        88.6677999********96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   7.2e-10   1.8e-06      16     169 ..     294     430 ..     276     476 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 7.2e-10
                                        EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  16 dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardql 91 
                                        + ++a + G GKT   +i +l+ +yet++ +g   ++v+   +   + ++++++f+     +v+ + g+ ++r++l
  gene1505|gene1505|rna1504|rna1504 294 NGILADDMGLGKTVQ-SISLLAYLYETEEIPG--PFLVVTISSTLDNWAQEFSRFLPS--FKVCRFSGSPSERKEL 364
                                        56777889*****87.999**9***9655555..566666777789999999999996..7899999*99999999 PP

                                        HHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEES CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  92 skldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSA 167
                                        +k  ++ d+v++t +  ++  +++ l+  + ++++lDEa+ + ++ +s+ ++++l+  +         r+ ++l+ 
  gene1505|gene1505|rna1504|rna1504 365 KKRFKDSDVVITTYQTAVS--DEKMLKKIKWQYMILDEAQAIKSS-MSRRWKTLLSFKA---------RNRLLLTG 428
                                        999899********99888..555655666799**********98.8888888766552.........23455555 PP

                                        SB CS
                                        xx RF
                               DEAD 168 Tl 169
                                        T+
  gene1505|gene1505|rna1504|rna1504 429 TP 430
                                        54 PP

>> HDA2-3  Class II histone deacetylase complex subunits 2 and 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.8      0.22   5.5e+02     143     189 ..     151     197 ..     139     210 .. 0.66
   2 ?   -1.7   0.1      0.51   1.3e+03     136     195 ..     349     411 ..     347     417 .. 0.72
   3 ?    2.2   0.1     0.033        86      47      67 ..     524     550 ..     488     552 .. 0.63
   4 ?   11.1   0.0   6.2e-05      0.16      88     251 ..     723     866 ..     716     876 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                                        S--S--S---S-..................-SEEEEEEESS---TTT CS
                             HDA2-3 143 geklydekkkkskdtkknsrktkeklkkkihsltihllsttrqltkd 189
                                        + +++d +kk +k++ + ++k+ e++++  ++ ++++l ++++l ++
  gene1505|gene1505|rna1504|rna1504 151 ERSIKDRSKKAEKEEMERKKKEMEEKEELRQKRKFEYLLSQTELFSH 197
                                        56677777777766666665555555666667777777777766655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.51
                                        SEEEESSS--S--S---S-.....................-SEEEEEEESS---TTTS--TT- CS
                             HDA2-3 136 lkikrysgeklydekkkkskdtkkns.rktkekl..kkkihsltihllsttrqltkdksllen 195
                                        +k+ r+sg +  +++ kk+  +++   +  ++    +k  ++ ++++++ ++ ++ ++s++++
  gene1505|gene1505|rna1504|rna1504 349 FKVCRFSGSPSERKELKKRFKDSDVViTTYQTAVsdEKMLKKIKWQYMILDEAQAIKSSMSRR 411
                                        678899999999999998856666555333333366788889999999999988888877766 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.033
                                        .......HHHHHHHH.HHHHHHH-GGG CS
                             HDA2-3  47 s......ikslticlenlslvanHPsL 67 
                                                  ++ +l +l+ v nHP+L
  gene1505|gene1505|rna1504|rna1504 524 EitrscsSMEMENLLMQLKKVCNHPDL 550
                                        1333334566778888*********99 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 6.2e-05
                                        HT-HHHHHHHHHHHHHTTSS....EEEEEEE-STHHHHHHHHHHTTSSSEEEESSS--S--S---S-......... CS
                             HDA2-3  88 etSgKFkvlndlvnliierkrksslnvlvvakskkeldLiEalllGkklkikrysgeklydekkkkskdtkknsrk 163
                                          SgK+ vl +l+  +  +       +l+  +  + +dLiE +l+ k+ ++ r++g    +  +++          
  gene1505|gene1505|rna1504|rna1504 723 GDSGKMVVLDELLPRLRVEG----HRLLIYFQMTRMIDLIEDYLVRKGYTYLRLDGSLKASVRAEVI--------- 785
                                        56999999999999998888....8999999*************************98877777777......... PP

                                        .........-SEEEEEEESS---TTTS--TT-S-EEEEEE-SST--TTSHHHHHHH---.-------EEEEEETTS CS
                             HDA2-3 164 tkeklkkkihsltihllsttrqltkdksllenikfdliiafDssvdtsspsveslrtqn.rkknklpiirlvpinS 238
                                             k     +++++l +tr         + + +d +i  Ds+ +++ ++  + r ++  + +++ ++rl++  +
  gene1505|gene1505|rna1504|rna1504 786 -----KDWQTGDKFIFLLSTRAGGLG---INLTAADTVIFYDSDWNPTADQQAMDRAHRlGQTRDVTVYRLITRGT 853
                                        .....344456778888888877443...56677899999999999999998888887623445599999999999 PP

                                        HHHHHHHHTS-TT CS
                             HDA2-3 239 ieHvkLcfkkded 251
                                        +e   L+  + +d
  gene1505|gene1505|rna1504|rna1504 854 VEEKVLESANRKD 866
                                        9998888873333 PP

>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.7    0.0028       7.2      33      87 ..     133     187 ..     127     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0028
                         EMC3_TMCO1  33 llqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqeelmedqsem 87 
                                        +l+++ i+++   +++k e+ +++r+++++k+  + k+k++e+++e  ++ + e 
  gene1505|gene1505|rna1504|rna1504 133 ILKSKRIYRELFGHIKKAERSIKDRSKKAEKEEMERKKKEMEEKEELRQKRKFEY 187
                                        678899****************************999999999998877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (883 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1536  (0.0856713); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.28s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 5909.96
//
Query:       gene1506|gene1506|rna1505|rna1505  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.35    9.4   5.4       0.46    9.0   5.4    1.1  1  FapA             Flagellar Assembly Protein A
       0.37    8.7   4.8       0.53    8.2   4.8    1.1  1  Prominin         Prominin
        1.2    9.3  10.6        1.6    8.9   4.0    2.2  2  CREPT            Cell-cycle alteration and expression-elevate
        1.4    9.0   5.4        2.6    8.1   5.4    1.4  1  DUF4337          Domain of unknown function (DUF4337)
        2.1    8.2  13.5        5.9    6.8  13.5    1.6  1  Ax_dynein_light  Axonemal dynein light chain
        2.6    8.2   9.4          1    9.5   0.6    2.2  2  Nup54            Nucleoporin complex subunit 54
        8.2    5.6   8.1         12    5.0   8.1    1.2  1  TMPIT            TMPIT-like protein


Domain annotation for each model (and alignments):
>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   5.4   0.00018      0.46     321     410 ..     245     322 ..     209     326 .] 0.50

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                               FapA 321 gtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeelee 396
                                        ++ ++        e+ e+l+ l+ee +el ++  +l k+ ++l++     +l++ ++e +kk++e +   +++ e 
  gene1506|gene1506|rna1505|rna1505 245 QEMMK-------IEASERLNSLQEERNELYAQKINLMKACSSLES-----DLKEYQEEYVKKVEEMLHDVEDKCER 308
                                        22222.......344444444444444443333333333333333.....33333444555555555555555555 PP

                               FapA 397 leeelkelkeeles 410
                                         e+e kelk++le+
  gene1506|gene1506|rna1505|rna1505 309 YEKENKELKAKLEE 322
                                        55555555555544 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.8   0.00021      0.53     620     695 ..     246     321 ..     236     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00021
                           Prominin 620 kltkvnletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesik 695
                                        +++k++ ++  ++l+e  nel  +k nl ++  +  +dl+++q+e+v+++e+ +++++ + ++ ++en++l+++++
  gene1506|gene1506|rna1505|rna1505 246 EMMKIEASERLNSLQEERNELYAQKINLMKACSSLESDLKEYQEEYVKKVEEMLHDVEDKCERYEKENKELKAKLE 321
                                        56677777778899999999999999*********************************************99876 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.9     0.018        45      81     120 ..     231     270 ..     218     280 .. 0.85
   2 ?    8.9   4.0   0.00063       1.6      79     121 ..     279     321 ..     268     322 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.018
                              CREPT  81 ledfleaqkellakaeekleelkeklekvksvrkelkshi 120
                                          dfl +q+e+++ +e +  e  e+l+ ++++r+el  + 
  gene1506|gene1506|rna1505|rna1505 231 YFDFLVVQNEAIKAQEMMKIEASERLNSLQEERNELYAQK 270
                                        5689999999999999999999999999999999997654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00063
                              CREPT  79 kmledfleaqkellakaeekleelkeklekvksvrkelkshiq 121
                                        ++ +d++e q e ++k ee+l+++++k e+ ++++kelk +++
  gene1506|gene1506|rna1505|rna1505 279 SLESDLKEYQEEYVKKVEEMLHDVEDKCERYEKENKELKAKLE 321
                                        555789999******************************9886 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.4     0.001       2.6      51     100 ..     272     320 ..     234     325 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                            DUF4337  51 hlaeleleqlelllkakaeelaaavdkkiakykkkiarykkekkeikkkA 100
                                        +l++   ++le +lk+ +ee  ++v++   ++++k +ry+ke ke+k+k 
  gene1506|gene1506|rna1505|rna1505 272 NLMKA-CSSLESDLKEYQEEYVKKVEEMLHDVEDKCERYEKENKELKAKL 320
                                        33333.44555555555999999999********************9985 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  13.5    0.0023       5.9     117     186 ..     245     321 ..     237     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                    Ax_dynein_light 117 aeqgkselekkikeLeeekeelekqvaelkaklealekrekerrqeeekkheeei.......eflkksnqqlkeql 185
                                        +e  k e ++++++L+ee++el  q  +l + +++le++ ke ++e  kk ee +       e ++k+n++lk++l
  gene1506|gene1506|rna1505|rna1505 245 QEMMKIEASERLNSLQEERNELYAQKINLMKACSSLESDLKEYQEEYVKKVEEMLhdvedkcERYEKENKELKAKL 320
                                        556777889999**************************99999999988888777777777799**********99 PP

                    Ax_dynein_light 186 e 186
                                        e
  gene1506|gene1506|rna1505|rna1505 321 E 321
                                        8 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.6     0.049   1.3e+02      40      78 ..     237     275 ..     235     279 .. 0.83
   2 ?    9.5   0.6    0.0004         1      39      78 ..     286     324 ..     282     326 .] 0.92

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.049
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nup54  40 aQqkevaqhrerlkeisdrleeleqkhqletsvrlekak 78 
                                        +Q++++++++ +  e s+rl++l+++++   +++++ +k
  gene1506|gene1506|rna1505|rna1505 237 VQNEAIKAQEMMKIEASERLNSLQEERNELYAQKINLMK 275
                                        688899998888889999***999999988888887665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0004
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nup54  39 kaQqkevaqhrerlkeisdrleeleqkhqletsvrlekak 78 
                                        + Q++ v++ +e+l++++d+ e  e k++ e+ ++le+ k
  gene1506|gene1506|rna1505|rna1505 286 EYQEEYVKKVEEMLHDVEDKCERYE-KENKELKAKLEEGK 324
                                        67***********************.**********9866 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   8.1    0.0048        12      18      90 ..     249     321 ..     234     325 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0048
                              TMPIT  18 akeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllp 90 
                                        + e  ++l++l++  +++  +  +  k +++l+s+lk+++++  ++ ee +++++++ ++ +k  ke+++ l 
  gene1506|gene1506|rna1505|rna1505 249 KIEASERLNSLQEERNELYAQKINLMKACSSLESDLKEYQEEYVKKVEEMLHDVEDKCERYEKENKELKAKLE 321
                                        3455677777777778888888888888888888888888887788888888888888888877777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2152  (0.120029); expected 358.6 (0.02)
Passed bias filter:                      834  (0.0465168); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2417.51
//
Query:       gene1507|gene1507|rna1506|rna1506  [L=1017]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-52  178.6   2.8    1.6e-52  178.1   2.8    1.2  1  SMC_N            RecF/RecN/SMC N terminal domain
    3.8e-25   88.5   0.1    1.8e-24   86.3   0.1    2.1  2  SMC_hinge        SMC proteins Flexible Hinge Domain
      4e-19   69.9   9.6      4e-19   69.9   9.6    4.8  3  AAA_23           AAA domain
    1.6e-18   67.6  39.7    4.4e-15   56.3  16.1    3.0  3  AAA_15           AAA ATPase domain
    3.3e-11   43.5   8.1      3e-05   24.0   0.4    3.7  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.4e-08   34.3   0.0    2.6e-08   33.5   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    0.00011   22.7   6.0       0.12   12.9   1.2    4.3  3  ABC_tran         ABC transporter
    0.00026   20.6   0.0    0.00026   20.6   0.0    2.7  3  AAA_27           AAA domain
  ------ inclusion threshold ------
       0.01   15.8   1.1       0.84    9.6   0.0    3.5  3  MtlR             Mannitol repressor
      0.073   12.5   1.0       0.91    8.9   0.1    2.8  2  HBM              Helical bimodular sensor domain


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.1   2.8   9.2e-56   1.6e-52       1     217 [.       2     995 ..       2     998 .. 0.99

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 9.2e-56
                                        EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkk 76 
                                        ++k+++++nFks++ +++ +p+s+s ++ivG+NGSGKs+++ Ai+FvL  +   k   e+  +lih+   +as ++
  gene1507|gene1507|rna1506|rna1506   2 FVKKIRLRNFKSFK-DETLIPLSRSANIIVGRNGSGKSSIVSAIRFVLYGE---KYNCESRVELIHE-GVRASEEE 72 
                                        589**********8.89999****************************744...45899999****9.99****** PP

                                        EEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                              SMC_N  77 aeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske................. 135
                                        a+vei+f + ++    e++e+s++r v  k + ey++++k ++++ev  ll+s +i+ +                 
  gene1507|gene1507|rna1506|rna1506  73 ASVEIVFYDGSEG--CEEKELSVKRVVGIKRD-EYMVDEKIMSREEVLGLLQSREITTSnpyfvvlqeevselavl 145
                                        *******888887..899**********9999.******************************************* PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 146 sdrkryelmkdvagvsgyekdrensismleetkqsenkiellldrieeklrgfeddkkemelrlelekekkrleyg 221
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 222 yierevkeinedisnieslvsndpeesseengdygceirevesklaslisrrkelcidekykeretgieeeirkie 297
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 298 kkrsrfweiekaekknlmnlkrdekenfirsgcikylvgfletlgsrevkpeeieaareslkekikkfkaidsceg 373
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 374 shieegkekkdleeliekrkhlwreerklklsdesireivrsqenrlvamgnigldvyrqikceegvlgyvydlis 449
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 450 vpnelsnafeaavgnalfnivveneevasnvlkkmrdlksrvafmplnrikhkeeeeikdqnvillasqvkcsqqy 525
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 526 rdllrcitknfylcsdlkqalysskryginvvtlfgevvtkegpitggyerrntafqeykkickearkvrgemvri 601
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 602 qhdlkkinreieearmhkedsgggsryyeslksailflqekikilervnrdgldrskvnsrllrlkeeerdlllkn 677
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 678 iwisgeikkidarikeagieikkmsdtigrleeeleksrmykeaieidkeilelkdrrriikemmfneenmdlftr 753
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 754 pkkvnvemeklvrrkhmlinkrnelcerigasdfkslerlfpekkkeeimeeivrinerirglsvvnrtvisqwes 829
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1507|gene1507|rna1506|rna1506 830 yieqknsmrkkledlkydkecilnfmrdldsrkedtmrkaievvregfsefysrltnggtaelysyefsvgiklge 905
                                        **************************************************************************** PP

                                        ......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCC CS
                                        ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                              SMC_N 136 ......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemle 203
                                              lLSgG+k+Lval L+f++q+v+p+ply++Deida+LD + +++v+ l+ke s +   Qfi++++r+e+l+
  gene1507|gene1507|rna1506|rna1506 906 ditntnLLSGGQKALVALCLIFSMQRVNPSPLYVFDEIDANLDTQSRERVSALIKEMSMTcaNQFIITTFRKELLN 981
                                        *******************************************************98877558************* PP

                                        C-SCEEEEEEEETT CS
                                        xxxxxxxxxxxxxx RF
                              SMC_N 204 kadklvgvtkveng 217
                                          dk + v ++e++
  gene1507|gene1507|rna1506|rna1506 982 CGDKYINVDFQEKR 995
                                        ********997765 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.4     6e+03      56      93 ..      17      53 ..       6      57 .. 0.65
   2 !   86.3   0.1   9.9e-28   1.8e-24       2     114 ..     438     546 ..     437     548 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.4
                          SMC_hinge 56 atflpldrikqknkadgandkns.gavplidlvevddel 93
                                        t++pl+r  + n   g n +++  +v++i +v + +++
  gene1507|gene1507|rna1506|rna1506 17 ETLIPLSR--SANIIVGRNGSGKsSIVSAIRFVLYGEKY 53
                                       58888855..44444444444445899999999999987 PP

  == domain 2  score: 86.3 bits;  conditional E-value: 9.9e-28
                          SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkn 77 
                                        +gvlG + dli+v+++   A+eaa+gn+l+++vve+ee+a   ++ +++  + r++f+pl+rik+k++++ +++  
  gene1507|gene1507|rna1506|rna1506 438 EGVLGYVYDLISVPNELSNAFEAAVGNALFNIVVENEEVASNVLKKMRDL-KSRVAFMPLNRIKHKEEEEIKDQ-- 510
                                        79************************************************.9*******************998.. PP

                          SMC_hinge  78 sgavplidlvevddelrkalryllgdtlvvdsldeAe 114
                                         ++  l++ v++ +++r +lr + ++++++++l++A+
  gene1507|gene1507|rna1506|rna1506 511 -NVILLASQVKCSQQYRDLLRCITKNFYLCSDLKQAL 546
                                        .8*********************************96 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   9.6   2.3e-22     4e-19       1     199 [.       5     234 ..       5     242 .. 0.59
   2 ?   -6.3  22.5        10   1.8e+04      74     193 ..     222     393 ..     221     410 .. 0.62
   3 ?  -16.7  28.2        10   1.8e+04     127     188 ..     656     731 ..     473     884 .. 0.58

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.3e-22
                             AAA_23   1 kLkienfrsfrdqe.idFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayv 75 
                                        k++++nf+sf+d++ i +s+  ++I+G NG+GK++i+ Ai+++Lyge+ ++++  +  + ++ v+ +s  + +a+v
  gene1507|gene1507|rna1506|rna1506   5 KIRLRNFKSFKDETlIPLSRSANIIVGRNGSGKSSIVSAIRFVLYGEKYNCES--RVELIHEGVR-AS--EEEASV 75 
                                        79************99******************************9888877..3344455555.34..668999 PP

                             AAA_23  76 eltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskki..ilnlilflgqer....... 142
                                        e+ f + +++      +e+els k  + +k ++    e+  +++++  ll+s++i  ++++++ l++e        
  gene1507|gene1507|rna1506|rna1506  76 EIVFYDGSEGC-----EEKELSVKRVVGIKRDEYMVDEKIMSREEVLGLLQSREIttSNPYFVVLQEEVselavls 146
                                        99997766643.....333333333333322222222222223333334444444444455555555553333333 PP

                             AAA_23 143 ........................feefelkdkke..............rleelekeleeledekkllekleqeke 180
                                                                          +               l+ +e++l+  ed+kk++e ++++++
  gene1507|gene1507|rna1506|rna1506 147 drkryelmkdvagvsgyekdrensI---------SmleetkqsenkielLLDRIEEKLRGFEDDKKEMELRLELEK 213
                                        3323444444444444444444331.........033333334455556777788888888888888888877777 PP

                             AAA_23 181 kekele..eleeeleeilkel 199
                                        ++k+le   +e+e +ei++++
  gene1507|gene1507|rna1506|rna1506 214 EKKRLEygYIEREVKEINEDI 234
                                        777444445555555555554 PP

  == domain 2  score: -6.3 bits;  conditional E-value: 10
                             AAA_23  74 yveltfenkdgrytrsier.erelskkkgkttkkaklelleideleqfisellgskki.............ilnli 135
                                        y+e++++ ++++    i++ e  +s + +++  ++   ++ei+e e ++ +l++++k+             i + i
  gene1507|gene1507|rna1506|rna1506 222 YIEREVKEINED----ISNiESLVSNDPEESSEENGDYGCEIREVESKLASLISRRKElcidekykeretgIEEEI 293
                                        566666666664....333133333333444444556677777777777777777766666666666666644444 PP

                             AAA_23 136 lflgqer..feefelkdkke....................................rleelekeleeledekklle 173
                                          + ++r  f+e+e+++kk+                                    ++e+++++l+e+ ++ k ++
  gene1507|gene1507|rna1506|rna1506 294 RKIEKKRsrFWEIEKAEKKNlmnlkrdekenfirsgcikylvgfletlgsrevkpeEIEAARESLKEKIKKFKAID 369
                                        4444444557777777777777777777788888888888888888888888877777777777777776666666 PP

                             AAA_23 174 kl....eqekekekeleeleeele 193
                                              ++e +++k leel e+ +
  gene1507|gene1507|rna1506|rna1506 370 SCegshIEEGKEKKDLEELIEKRK 393
                                        667776555555555555555444 PP

  == domain 3  score: -16.7 bits;  conditional E-value: 10
                             AAA_23 127 skkiilnlilflgqerfeefel.......kdkkerleelekeleeledekkllekl.......eqekekekeleel 188
                                        ++k +++l+ ++ +er   +++       k+   r++e+  e+++ +d++  le++       +++ e  ke+ el
  gene1507|gene1507|rna1506|rna1506 656 RSKVNSRLLRLKEEERDLLLKNiwisgeiKKIDARIKEAGIEIKKMSDTIGRLEEEleksrmyKEAIEIDKEILEL 731
                                        3333444444444444322222222222211111222222222222222222222211111111111111111111 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3  16.1   2.5e-18   4.4e-15       1     262 [.       1     383 [.       1     411 [. 0.66
   2 ?    0.7   2.5      0.19   3.4e+02     108     178 ..     351     418 ..     337     511 .. 0.65
   3 !   15.9  15.0   4.7e-06    0.0084      45     363 ..     637     974 ..     630     974 .. 0.67

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2.5e-18
                             AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn....................k 55 
                                        M++kki+++NF+s+kd + i+ls + ++++G+N+sGKSsi+ a+ + l  + k+n                    +
  gene1507|gene1507|rna1506|rna1506   1 MFVKKIRLRNFKSFKDeTLIPLSRSANIIVGRNGSGKSSIVSAIRFVLYGE-KYNcesrvelihegvraseeeasV 75 
                                        99**************999***************************99966.777889999999999999999997 PP

                             AAA_15  56 kvikiekedleifeniseskdikIdvef................................................ 83 
                                        + ++ + ++  ++++ s ++ + I+  +                                                
  gene1507|gene1507|rna1506|rna1506  76 EIVFYDGSEGCEEKELSVKRVVGIKRDEymvdekimsreevlgllqsreittsnpyfvvlqeevselavlsdrkry 151
                                        7778888888888888888888887666799999999999999999999999999999999998888777777777 PP

                             AAA_15  84 ........................aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdek 135
                                                                + k+++++ e +l++ e+k + ++ +kke +l   ++++k  l+  ++  e 
  gene1507|gene1507|rna1506|rna1506 152 elmkdvagvsgyekdrensismleETKQSENKIELLLDRIEEKLRGFEDDKKEMELRLELEKEKKRLEYGYIEREV 227
                                        7777777777777777776666532224555555566666666666677777777777777777777777777777 PP

                             AAA_15 136 isvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd... 208
                                        ++++++ s+ e  ++ ++++e+++e+   +  +++++ +kl + ++  +el    k + +++ + ++ R++++   
  gene1507|gene1507|rna1506|rna1506 228 KEINEDISNIESLVS-NDPEESSEENG-DYGCEIREVESKLASLISRRKELCIDEKYKERETGIEEEIRKIEKkrs 301
                                        777766666555433.33333333333.345555666666666666666454555555555556666666665555 PP

                             AAA_15 209 ...edsekkssllgklkekileealqekl.............eeelteklkeiqeklkeidkklaeelk....... 261
                                           e ++ ++++l++lk++ +e+ +++               +e + e+++   e+lke++kk+++  +       
  gene1507|gene1507|rna1506|rna1506 302 rfwEIEKAEKKNLMNLKRDEKENFIRSGCikylvgfletlgsREVKPEEIEAARESLKEKIKKFKAIDScegshie 377
                                        5556666666666666666666655544477778878888886666777777777777777777444443333332 PP

                             AAA_15 262 .....k 262
                                             k
  gene1507|gene1507|rna1506|rna1506 378 egkekK 383
                                        322222 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.19
                             AAA_15 108 lkkkesdlkktikdkklklkknelsdekisvekkks..kkelpkekeeklekekeelkidkedlkklikklee 178
                                        ++  +++lk+ ik++k  +     s+e  ++e+ k+    e  +ek+++l  e+ +lk+ +e+++++ +  e+
  gene1507|gene1507|rna1506|rna1506 351 IEAARESLKEKIKKFKAID-----SCEGSHIEEGKEkkDLEELIEKRKHLWREERKLKLSDESIREIVRSQEN 418
                                        4444555555555555554.....3555555555551144555677777778888888889999999983333 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 4.7e-06
                             AAA_15  45 lFlnnkekkn.........kkvikiekedleifeniseskdikIdvefaekekakeyektlkskekkkadlllkkk 111
                                        lFl++k k            ++++     l+++e +   k+i+I  e    +k + ++k++  + kk     + ++
  gene1507|gene1507|rna1506|rna1506 637 LFLQEKIKILervnrdgldRSKVNSRLLRLKEEERDLLLKNIWISGEI---KKIDARIKEAGIEIKK-----MSDT 704
                                        67787744446666888887778888888999999999**********...2233333333333333.....3445 PP

                             AAA_15 112 esdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid.kedlkklikkleeslkkee.. 184
                                        + +l + +++  ++ +++e+++e+ +++++  +  ++++  ++++ +  +  ++ + +++kl ++ +  ++k    
  gene1507|gene1507|rna1506|rna1506 705 IGRLEEELEKSRMYKEAIEIDKEILELKDRRRI--IKEMMFNEENMDLFTRPKKvNVEMEKLVRRKHMLINKRNel 778
                                        556666677777777777777777777777554..33333444444444444444666666666666666555566 PP

                             AAA_15 185 ...............elknvlksai.iklllisakRnvsdedsekkssllgklkekileealqekleeelteklke 244
                                                         +++ ++ + + +++++  R  s  + +++s + + + +k ++ ++ e l+ +++++l+ 
  gene1507|gene1507|rna1506|rna1506 779 cerigasdfkslerlFPEKKKEEIMeEIVRINERIRGLSVVNRTVISQWESYIEQKNSMRKKLEDLKYDKECILNF 854
                                        6777777777777743333333333134788889999999999999999999999999987777777778888888 PP

                             AAA_15 245 iqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik.......ddeelplnknGsGvqrllllillile 313
                                        + +  + +++++ + + +++ + ++++ +   +g + e+  ++        ++ ++ n  + G++ l + + li++
  gene1507|gene1507|rna1506|rna1506 855 MRDLDSRKEDTMRKAI-EVVREGFSEFYSRLTNGGTAELYSYEfsvgiklGEDITNTNLLSGGQKAL-VALCLIFS 928
                                        8888888888884444.55555555555555555555555555666688666666666666555555.55566777 PP

                             AAA_15 314 aekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitT 363
                                        +++     +++ +++++E++a+L +q  + +  l+ke++ +  +Q iitT
  gene1507|gene1507|rna1506|rna1506 929 MQRV----NPSPLYVFDEIDANLDTQSRERVSALIKEMSMTCANQFIITT 974
                                        7777....7****************************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.4   1.6e-08     3e-05       2     131 ..      27     154 ..      26     287 .. 0.80
   2 !   21.7   1.3   8.5e-08   0.00015     219     296 ..     866     974 ..     571     974 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.6e-08
                             AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                        n+++G+NgsGKS++  a++++     ++e  ++e++      +++ +  + + ei f  + e  ++++   +  + 
  gene1507|gene1507|rna1506|rna1506  27 NIIVGRNGSGKSSIVSAIRFV----LYGEKYNCESRVELIHEGVRASEEEASVEIVFYDGSEGCEEKELSVKRVVG 98 
                                        89******************8....68*****************99999999999999999999999999999999 PP

                             AAA_21  78 lersqv..eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkels 131
                                        ++r+ +   ek+ s+e++l+    +     + + v+ +e+  + +++s+++++el 
  gene1507|gene1507|rna1506|rna1506  99 IKRDEYmvDEKIMSREEVLGLLQSREITTSNPYFVVLQEEVSELAVLSDRKRYELM 154
                                        99999999999999998888777777777777777777777777777777777665 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 8.5e-08
                             AAA_21 219 r............................gvvflengdgqelparel.SdGtkrllalltallralkkg.sllliD 264
                                                                     + + +  + g +++ ++l S G+k l al +++  ++  + +l+++D
  gene1507|gene1507|rna1506|rna1506 866 MrkaievvregfsefysrltnggtaelysYEFSVGIKLGEDITNTNLlSGGQKALVALCLIFSMQRVNPsPLYVFD 941
                                        244555555555555555555666666554455555555556666666*******866666666665556****** PP

                             AAA_21 265 EpEngLHP...kllrrllellkelsrngaQviltT 296
                                        E++++L+    ++++ l++ ++ + +   Q+i+tT
  gene1507|gene1507|rna1506|rna1506 942 EIDANLDTqsrERVSALIKEMSMTCA--NQFIITT 974
                                        ********666666666666644444..6*****9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.5e-11   2.6e-08       2      55 ..       4      54 ..       3      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.5e-11
                             AAA_29  2 krlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLvpakkvrfN 55
                                       k+++l N  +f++ + i+++++ a +++G++GsGKS+++ Ai ++L+++k   +N
  gene1507|gene1507|rna1506|rna1506  4 KKIRLRNFKSFKDeTLIPLSRS-ANIIVGRNGSGKSSIVSAIRFVLYGEK---YN 54
                                       7899*********888999966.5************************99...66 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.2   6.7e-05      0.12      15      32 ..      28      45 ..      23     312 .. 0.90
   2 ?   -2.6   0.0       4.1   7.3e+03      31      58 ..     587     614 ..     558     664 .. 0.55
   3 !    9.3   0.0   0.00088       1.6      46     134 ..     855     942 ..     673     945 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.7e-05
                                       EEEESTTSSHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxx RF
                           ABC_tran 15 aivGenGaGKStLlklla 32
                                        ivG+nG+GKS++++++ 
  gene1507|gene1507|rna1506|rna1506 28 IIVGRNGSGKSSIVSAIR 45
                                       69************9985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                                        HTTSS--SEEEEEETTCEGGGB-HHHCC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  31 lagllkpteGeilldgkdlkeqeleslr 58 
                                        ++++ ++  Ge+   ++dlk++++e+ +
  gene1507|gene1507|rna1506|rna1506 587 ICKEARKVRGEMVRIQHDLKKINREIEE 614
                                        3333333333332223333333333322 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00088
                                        TCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHHHHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  46 gkdlkeqeleslrkeigvlpqe.pqlfpeltvrenesdeeiekalsklglkelkdtvvksspssLSgGqkqrvala 120
                                        ++dl+++++  +rk i+v+ +  +++ ++l   +n  ++e++ +  ++g+k   +++   +++ LSgGqk  val+
  gene1507|gene1507|rna1506|rna1506 855 MRDLDSRKEDTMRKAIEVVREGfSEFYSRL---TNGGTAELYSYEFSVGIKL-GEDIT--NTNLLSGGQKALVALC 924
                                        666666777777777777777744444444...3455667777777777665.44444..6789***********9 PP

                                        HHHHHT....SSEEEEES CS
                                        xxxxxx....xxxxxxxx RF
                           ABC_tran 121 rallkk....pkllllDE 134
                                         ++  +    ++l+++DE
  gene1507|gene1507|rna1506|rna1506 925 LIFSMQrvnpSPLYVFDE 942
                                        887544111146666666 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.5e-07   0.00026       1      54 [.       1      52 [.       1     117 [. 0.90
   2 ?   -3.3   0.3       3.1   5.6e+03     157     190 ..     288     321 ..     286     324 .. 0.78
   3 ?   -2.4   0.4       1.7     3e+03     167     205 ..     582     620 ..     573     621 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                             AAA_27  1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGip 54
                                       M +++++L+ + +f+d++l     +++  +i+G N +GKs++++Ai+ +l+G +
  gene1507|gene1507|rna1506|rna1506  1 MFVKKIRLRNFKSFKDETLIPL--SRSANIIVGRNGSGKSSIVSAIRFVLYGEK 52
                                       6789999*********998543..57889**********************955 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.1
                             AAA_27 157 slrevleaLeaeadelfkprkskkrainealeel 190
                                        +++e + ++e++++++++ +k++k+++++ +++ 
  gene1507|gene1507|rna1506|rna1506 288 GIEEEIRKIEKKRSRFWEIEKAEKKNLMNLKRDE 321
                                        5677888999999999999999998887777655 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.7
                             AAA_27 167 aeadelfkprkskkrainealeeleeakkelreaqvrae 205
                                        +e +++ k+ ++ + ++ + +++l++ ++e++ea +++e
  gene1507|gene1507|rna1506|rna1506 582 QEYKKICKEARKVRGEMVRIQHDLKKINREIEEARMHKE 620
                                        677888888888888999999999999999999988765 PP

>> MtlR  Mannitol repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.44     8e+02      80     132 ..     198     252 ..     188     278 .. 0.73
   2 ?    1.9   0.0      0.11     2e+02      81     114 ..     383     416 ..     376     431 .. 0.88
   3 ?    9.6   0.0   0.00047      0.84      71     127 ..     815     871 ..     807     886 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.44
                               MtlR  80 yeDielfiqlkeelnedek..eyeFsddeildfikelhlvsekslleleeekeee 132
                                        +eD ++ ++l+ el++++k  ey + + e+ +  ++++ +++   ++ ee++ee+
  gene1507|gene1507|rna1506|rna1506 198 FEDDKKEMELRLELEKEKKrlEYGYIEREVKEINEDISNIESLVSNDPEESSEEN 252
                                        8899999999999999998334556788888888888888775544444444443 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.11
                               MtlR  81 eDielfiqlkeelnedekeyeFsddeildfikel 114
                                        +D+e++i+ +++l ++e++++ sd+ i + ++++
  gene1507|gene1507|rna1506|rna1506 383 KDLEELIEKRKHLWREERKLKLSDESIREIVRSQ 416
                                        8**************************9988765 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00047
                               MtlR  71 aLGviskevyeDielfiqlkeelnedekeyeFsddeildfikelhlvseksllelee 127
                                        +L v++++v +  e +i+ k+ +++  +++++  ++il+f+++l + +e ++ ++ e
  gene1507|gene1507|rna1506|rna1506 815 GLSVVNRTVISQWESYIEQKNSMRKKLEDLKYDKECILNFMRDLDSRKEDTMRKAIE 871
                                        8999******************************************99988877654 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.15   2.7e+02      66     106 ..     508     548 ..     473     554 .. 0.87
   2 ?    8.9   0.1   0.00051      0.91     206     250 ..     579     623 ..     574     626 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                                        SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                                HBM  66 spenvrlLqeqlalvqeyrksfnelraayesrnaaRqelds 106
                                        +++nv lL++q++  q+yr+ +  +++++    +++q+l s
  gene1507|gene1507|rna1506|rna1506 508 KDQNVILLASQVKCSQQYRDLLRCITKNFYLCSDLKQALYS 548
                                        58999*****************9999999888888877765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00051
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTXXXXX CS
                                HBM 206 aaleqfkaavaaieqarkemteqgdeivkisdeLyqiqtekrdse 250
                                        +a++++k++ +++ + r em  ++ ++ ki+ e+ ++++ k ds+
  gene1507|gene1507|rna1506|rna1506 579 TAFQEYKKICKEARKVRGEMVRIQHDLKKINREIEEARMHKEDSG 623
                                        689*************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1017 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1780  (0.0992805); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.02u 0.33s 00:00:01.35 Elapsed: 00:00:00.51
# Mc/sec: 5978.78
//
Query:       gene1508|gene1508|rna1507|rna1507  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 684.77
//
Query:       gene1509|gene1509|rna1508|rna1508  [L=451]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00058   19.2   1.7      0.015   14.6   1.7    2.5  1  Ints3     Integrator complex subunit 3
  ------ inclusion threshold ------
      0.069   11.5   0.1       0.11   10.9   0.1    1.2  1  MAD       Mitotic checkpoint protein
        0.3   11.2   1.8       0.41   10.8   0.5    1.8  2  DUF3408   Protein of unknown function (DUF3408)


Domain annotation for each model (and alignments):
>> Ints3  Integrator complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.7   2.5e-06     0.015      20      92 ..     212     279 ..     200     318 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-06
                              Ints3  20 sqlleirtsrkflqlrlspelerklrFllskvklgsqkryqewfakkfLstpesealradlvRyivavihpsn 92 
                                         + l ++t+ ++l ++ls +le ++ F+l++ +  + + + + + k ++++++     + ++R++v++ +p+n
  gene1509|gene1509|rna1508|rna1508 212 LSTLFTPTPLNILSSQLSADLEMNIMFILEHDQ--NFEFHLSLLFKNYIRSEDD---ACRVLRFMVNIPYPQN 279
                                        4556689999*********************94..7788999999999987665...6899**********99 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   1.8e-05      0.11     503     555 ..     327     379 ..     321     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.8e-05
                                MAD 503 keqlekLqaEierlkellkkleedkekkvaslpessltlafkevleLrkeles 555
                                        +++l+ Lq+E  +lk  +k+ ++++e++v+ +      l+f++   L ke+e 
  gene1509|gene1509|rna1508|rna1508 327 AAKLDSLQEEWGALKLAIKSTKKKQEHTVEDVTRMIHSLNFQKYFGLVKEMEK 379
                                        67899************************999999889*************95 PP

>> DUF3408  Protein of unknown function (DUF3408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   6.9e-05      0.41      89     122 ..      82     115 ..      80     125 .. 0.90
   2 ?   -2.6   0.0      0.96   5.7e+03     117     128 ..     173     184 ..     170     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.9e-05
                            DUF3408  89 srelheklarIvrvlgerkmsvsayvdnilrhHL 122
                                         +e +e +  +v+++ + + ++ +++ n+lrhHL
  gene1509|gene1509|rna1508|rna1508  82 TKEAYENILLVVQMMLGYEENIDTLIINLLRHHL 115
                                        5789999******9999****************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.96
                            DUF3408 117 ilrhHLeeYkee 128
                                        + + H++eYk++
  gene1509|gene1509|rna1508|rna1508 173 VTNPHFDEYKKK 184
                                        566799999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3159.72
//
Query:       gene1510|gene1510|rna1509|rna1509  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.1   0.2      0.052   13.4   0.2    1.2  1  C1_1      Phorbol esters/diacylglycerol binding domain (C1 do
      0.059   13.7   0.6       0.11   12.9   0.6    1.4  1  C1_2      C1 domain


Domain annotation for each model (and alignments):
>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.8e-06     0.052       7      39 ..      34      62 ..      29      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-06
                                       --SS--B-TTT-SB--SSSS-EEEETTT--EE- CS
                               C1_1  7 nfkqptfCkhCgeflwgkekqglkCswCkllvH 39
                                       +  +++ C+ C +++   ++ gl C+ C ++ H
  gene1510|gene1510|rna1509|rna1509 34 Q-LSTMNCSLCYKPI---SIKGLLCEGCFYKLH 62
                                       4.67899********...************999 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   1.2e-05      0.11       7      43 ..      26      62 ..      23      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
                               C1_2  7 LtlskgedssesfnCsaCgrkidgffYsCseCdfslh 43
                                       Lt+++   + +++nCs+C ++i+ +   C+ C ++lh
  gene1510|gene1510|rna1509|rna1509 26 LTFEYLARQLSTMNCSLCYKPISIKGLLCEGCFYKLH 62
                                       777777788899*********97888***88*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1372.68
//
Query:       gene151|gene151|rna151|rna151  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-18   67.4   0.1    8.3e-18   65.1   0.0    2.0  2  AAA              ATPase family associated with various cellul
    6.9e-18   65.0   0.1    5.5e-14   52.3   0.1    2.2  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    6.3e-09   36.2   0.3    0.00051   20.3   0.0    2.5  2  AAA_22           AAA domain
    2.4e-08   34.1   0.0    4.2e-08   33.3   0.0    1.4  1  Rad17            Rad17 P-loop domain
    6.9e-08   33.1   0.0      4e-07   30.6   0.0    2.0  1  AAA_16           AAA ATPase domain
    3.1e-07   30.3   0.0    1.3e-06   28.2   0.0    1.9  2  AAA_30           AAA domain
    1.1e-06   28.9   0.2    5.5e-06   26.7   0.0    2.3  2  Rep_fac_C        Replication factor C C-terminal domain
    2.9e-06   27.1   0.0    5.2e-06   26.3   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      6e-06   26.3   0.0    1.1e-05   25.5   0.0    1.3  1  AAA_14           AAA domain
      7e-06   26.1   0.1    0.00026   21.0   0.1    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
    2.7e-05   24.0   0.0    4.6e-05   23.3   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    3.5e-05   24.1   0.0      6e-05   23.4   0.0    1.4  1  RNA_helicase     RNA helicase
    0.00012   21.9   0.0     0.0002   21.1   0.0    1.4  1  AAA_24           AAA domain
    0.00012   21.6   0.1     0.0024   17.3   0.0    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00018   21.9   0.5      0.033   14.5   0.0    2.4  2  AAA_19           AAA domain
    0.00025   21.6   0.0     0.0053   17.3   0.0    2.4  2  AAA_18           AAA domain
    0.00052   20.2   0.1     0.0024   18.0   0.1    2.0  1  AAA_33           AAA domain
    0.00069   18.8   0.0     0.0016   17.6   0.0    1.6  1  MCM              MCM P-loop domain
    0.00094   19.0   0.0     0.0033   17.3   0.0    1.7  2  AAA_11           AAA domain
     0.0011   18.2   0.5       0.15   11.2   0.3    2.4  3  PIF1             PIF1-like helicase
      0.002   17.7   0.0     0.0047   16.5   0.0    1.6  2  AAA_7            P-loop containing dynein motor region
     0.0031   17.8   0.0     0.0064   16.8   0.0    1.6  1  AAA_28           AAA domain
     0.0046   16.0   0.0       0.01   14.8   0.0    1.6  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
     0.0057   16.6   0.0     0.0081   16.1   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0068   16.2   0.5       0.09   12.5   0.1    2.2  2  DEAD             DEAD/DEAH box helicase
     0.0077   16.0   0.1      0.041   13.6   0.1    2.0  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   15.0   0.0      0.016   14.4   0.0    1.2  1  DUF815           Protein of unknown function (DUF815)
      0.014   14.8   0.1        0.1   12.0   0.0    2.1  2  TniB             Bacterial TniB protein
      0.047   14.2   0.0       0.21   12.1   0.0    2.2  1  ABC_tran         ABC transporter
       0.05   13.3   0.0      0.085   12.5   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
      0.053   13.9   0.0       0.17   12.3   0.0    1.9  1  AAA_17           AAA domain
      0.064   13.3   0.0       0.15   12.2   0.0    1.6  1  DUF1192          Protein of unknown function (DUF1192)
      0.071   12.9   0.2         13    5.4   0.0    2.5  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.084   11.9   0.0       0.13   11.3   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.094   12.6   0.0        2.2    8.2   0.0    2.2  2  NACHT            NACHT domain
       0.12   12.4   0.0       0.25   11.3   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   11.0   0.0        0.2   10.3   0.0    1.2  1  SNF2_N           SNF2 family N-terminal domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   1.7e-20   8.3e-18       1     127 [.      39     147 ..      39     151 .. 0.86
   2 ?   -0.5   0.0       3.2   1.6e+03      63      99 ..     253     282 ..     225     304 .. 0.77

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.7e-20
                                    EEEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelg.vefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgses 79 
                                    +l+yGppGtGKT+ ++a+a++l  + +le+++s+ +   +    + i+++ ++ +++   + +++DE+d + ++      
  gene151|gene151|rna151|rna151  39 MLFYGPPGTGKTTSIRAIARSLPrSCVLELNASDER--GIATVRETIKDFASTYSKMM--KLVILDEADMMSRDA----- 109
                                    89********************62667*********..66666666666666655554..9**********8888..... PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                          +n+L + +++++    ++ +++++n+ +k+ p++l +R+++ 
  gene151|gene151|rna151|rna151 110 ------QNALRRIIEDFSA---NTRFCLIANHSRKIIPPIL-SRCTKF 147
                                    ......************9...689****************.9*9875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3.2
                                    EEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                            AAA  63 fiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                    +iD++  +a+++       ++r   ++l+el++ +++
  gene151|gene151|rna151|rna151 253 LIDNLGGIARKS-------KMRNKTKILKELSDIERR 282
                                    688888888888.......677777777777777765 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00075      0.36       2      43 ..      20      60 ..      19      64 .. 0.91
   2 !   52.3   0.1   1.1e-16   5.5e-14      84     162 ..      75     152 ..      63     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00075
                DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakal 43
                                   ++e++  l+++l+ g++ + +Lf+G+ g+gk ++  ++a++l
  gene151|gene151|rna151|rna151 20 NKEVIASLQSILEAGKIPN-MLFYGPPGTGKTTSIRAIARSL 60
                                   78999************86.8**************9999876 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 1.1e-16
                DNA_pol3_delta2  84 kldqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfspl 162
                                     + ++re i+++  +++    k++i+++a++m++ A+Nal +++E+ s+n+ f Li++++ k++++i SRc +++f p+
  gene151|gene151|rna151|rna151  75 GIATVRETIKDFA-STYSKMMKLVILDEADMMSRDAQNALRRIIEDFSANTRFCLIANHSRKIIPPILSRCTKFRFGPI 152
                                    6789999999997.5688899******************************************************9886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.1e-06   0.00051       8      60 ..      39      83 ..      37      89 .. 0.86
   2 !   15.5   0.1   3.3e-05     0.016      76     130 ..      77     131 ..      66     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-06
                         AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrel 60
                                   ++ +G++GtGKTt++r ++++l+        r+ v++ +++ + + +++++ +
  gene151|gene151|rna151|rna151 39 MLFYGPPGTGKTTSIRAIARSLP--------RSCVLELNASDERGIATVRETI 83
                                   5789******************7........8888899999999888877776 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.3e-05
                         AAA_22  76 eellealeqalrarav.ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGt 130
                                      ++e++ + ++++++  +l+i+DEa+ + s +a + Lr++ ++ + ++++ L+  
  gene151|gene151|rna151|rna151  77 ATVRETIKDFASTYSKmMKLVILDEADMM-SRDAQNALRRIIEDFSANTRFCLIAN 131
                                    5566777777777777889**********.********999888888888888765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   8.8e-11   4.2e-08       6     139 ..       2     130 ..       1     136 [. 0.82

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 8.8e-11
                          Rad17   6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkep 85 
                                     ++W eky+P ++ e+   k+ i  ++  l+a  +++      L  GP+G gk+t ++ +++ l  +    ln+   +  
  gene151|gene151|rna151|rna151   2 HQPWTEKYRPGTLLEMVGNKEVIASLQSILEAGKIPNM-----LFYGPPGTGKTTSIRAIARSLPRSCVLELNASDERGI 76 
                                    589**********************************9.....99****************************9997777 PP

                          Rad17  86 dnqksdfkgltekesrflsqiesfke..leLkdakylklqklGddlrtdkklilve 139
                                       ++ +k    + s+++ ++    e  ++ +da++  l++  +d  ++ ++ l+ 
  gene151|gene151|rna151|rna151  77 ATVRETIKDFASTYSKMMKLV-ILDEadMMSRDAQN-ALRRIIEDFSANTRFCLIA 130
                                    777777777777777666554.44440144455665.7888888888888888875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   8.3e-10     4e-07       3      63 ..      18      86 ..      16     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 8.3e-10
                         AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd...........ggiflrgkcdql 63
                                   vG +e ++ L+s+le   +g  +++l++G++G+GK++ +r+++r+l ++           g+ ++r++ +++
  gene151|gene151|rna151|rna151 18 VGNKEVIASLQSILE---AGKIPNMLFYGPPGTGKTTSIRAIARSLPRScvlelnasderGIATVRETIKDF 86
                                   667788899999998...677799************************966666666653344455555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.7e-09   1.3e-06      22     120 ..      40     125 ..      25     132 .. 0.89
   2 ?   -1.5   0.0       3.5   1.7e+03     150     179 ..     158     191 ..     152     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.7e-09
                         AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEagmvd 101
                                    +  Gp+GtGKtt+++a+++ + ++   + + A+ ++  ++++e +   ast  k++            +l+i DEa m++
  gene151|gene151|rna151|rna151  40 LFYGPPGTGKTTSIRAIARSLPRSC-VLELNASDERGIATVRETIKDFASTYSKMM------------KLVILDEADMMS 106
                                    567****************999884.68899************************9............8*********** PP

                         AAA_30 102 tkqlaallkaaekagakvi 120
                                     +  +al +++e+ +a  +
  gene151|gene151|rna151|rna151 107 RDAQNALRRIIEDFSANTR 125
                                    *******999999666554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
                         AAA_30 150 eLtevvRq...ke.seeraaalalregdaeeale 179
                                    +++e+ R    k  ++  aa+ +++egd+++a++
  gene151|gene151|rna151|rna151 158 RIKEICRKegiKYtEDGIAAVSKVSEGDMRKAVN 191
                                    6677777744323356678899999999998876 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       9.4   4.5e+03       9      34 ..     140     168 ..     134     199 .. 0.60
   2 !   26.7   0.0   1.1e-08   5.5e-06       7      87 ..     221     298 ..     208     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 9.4
                                    HHHHHHH...T-HHHHHHHHHHHHHHC-- CS
                      Rep_fac_C   9 ileacln...gdfeeaykklrellvekGy 34 
                                    il+ c +   g +e  ++ ++e   ++G+
  gene151|gene151|rna151|rna151 140 ILSRCTKfrfGPIESTESRIKEICRKEGI 168
                                    66666445564444444444433333333 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 1.1e-08
                                    HHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHHHHHHH CS
                      Rep_fac_C   7 eeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlqlsall 86 
                                    ee++  + n +  e ++ +++l +e+G+ ++ ++ +l  +  ++   + + k +il++l++ie r + G++e+lql a++
  gene151|gene151|rna151|rna151 221 EEVFMDLGNMSMVELRARIEDLRYEYGIDCDALIDNLGGIARKS---KMRNKTKILKELSDIERRRSIGCNEKLQLDAVI 297
                                    566666666778899999**9*****************999985...4789*****99********************98 PP

                                    H CS
                      Rep_fac_C  87 a 87 
                                    +
  gene151|gene151|rna151|rna151 298 S 298
                                    6 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.1e-08   5.2e-06       2     113 ..      10     122 ..       9     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.1e-08
                         RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl........kitsgPvlekag 73 
                                    rP +l e +g ++v ++l+ ++ea k        +l+yGpPG Gktt  + ia+ l  ++        +   + v e  +
  gene151|gene151|rna151|rna151  10 RPGTLLEMVGNKEVIASLQSILEAGKI-----PNMLFYGPPGTGKTTSIRAIARSLPRSCvlelnasdERGIATVRETIK 84 
                                    99*********************9975.....569************999999876443311110000334455667778 PP

                         RuvB_N  74 dlaalltnleekdvlfideihrlsraveevlysamedfrl 113
                                    d+a+  +++   +++ +de   +sr +++ l   +edf+ 
  gene151|gene151|rna151|rna151  85 DFASTYSKMM--KLVILDEADMMSRDAQNALRRIIEDFSA 122
                                    8888877765..57888********************975 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.3e-08   1.1e-05       7      98 ..      41     129 ..      37     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.3e-08
                         AAA_14   7 itGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev.pewekalks 85 
                                      G+  +GKTt ++ ++++l   ++ +l++n  der  +   +   ++ + + +++  +++++lDE+ ++ +++++al++
  gene151|gene151|rna151|rna151  41 FYGPPGTGKTTSIRAIARSLP--RSCVLELNASDERGIATVRE--TIKDFASTYSK-MMKLVILDEADMMsRDAQNALRR 115
                                    679999**********98876..88999999999888654433..56777776666.899*******987468******* PP

                         AAA_14  86 lvdeg.knldvivt 98 
                                    ++++   n ++++ 
  gene151|gene151|rna151|rna151 116 IIEDFsANTRFCLI 129
                                    ***88777777765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0         1   4.9e+02      78      94 ..      20      36 ..      15      39 .. 0.84
   2 !   21.0   0.1   5.3e-07   0.00026       1      91 [.      38     119 ..      38     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                                   -HHHHHHHHHHHHSSEE CS
                          AAA_5 78 esevlnsLlslleerrl 94
                                   ++ev++sL+s+le  ++
  gene151|gene151|rna151|rna151 20 NKEVIASLQSILEAGKI 36
                                   69***********9876 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.3e-07
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HH CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraese 80 
                                    ++l  GppGtgK++ ++ +a+ l r+ +  ++ +   e+ +   re+  ++ + + s+++      ++++lDE ++++++
  gene151|gene151|rna151|rna151  38 NMLFYGPPGTGKTTSIRAIARSLPRSCVLELNAS--DERGIATVRET-IKDFASTYSKMM------KLVILDEADMMSRD 108
                                    57999******************88888777766..45566666664.456777777777......9************* PP

                                    HHHHHHHHHHS CS
                          AAA_5  81 vlnsLlsllee 91 
                                    ++n+L +++e+
  gene151|gene151|rna151|rna151 109 AQNALRRIIED 119
                                    ********997 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   9.6e-08   4.6e-05       5      74 ..      43     105 ..      40     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.6e-08
                Viral_helicase1   5 GvpGcGKStlirkllrtsliltvnrptaelltegk.pklpnlsvrtvdsflmalvkstkgkililDEylll 74 
                                    G pG GK+t+ir ++r+       +++++l   ++ ++  +   +t+++f ++ +k    k++ilDE+ ++
  gene151|gene151|rna151|rna151  43 GPPGTGKTTSIRAIARS------LPRSCVLELNASdERGIATVRETIKDFASTYSKM--MKLVILDEADMM 105
                                    77***************......7777777777776888899999*********996..9*******9776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.2e-07     6e-05       2      80 ..      40     123 ..      39     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.2e-07
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl....klkkkdsvys.rnpeddfwdgYt.gqevvvidDfgqvkdeenpsdlaelir 75 
                                    ++yGp+g+GK+t ++ +a++l ++     +   +  + + r++ +df + Y+   + v+ d+   ++ +  ++ l  +i+
  gene151|gene151|rna151|rna151  40 LFYGPPGTGKTTSIRAIARSLPRSCvlelNASDERGIATvRETIKDFASTYSkMMKLVILDEADMMSRD-AQNALRRIIE 118
                                    79*******************9888888866666777778************77888888888888766.4556666665 PP

                   RNA_helicase  76 lvsst 80 
                                     +s +
  gene151|gene151|rna151|rna151 119 DFSAN 123
                                    55555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.2e-07    0.0002       4      87 ..      38     115 ..      35     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.2e-07
                         AAA_24   4 kiliyGpsgiGKTtlakel...gpkplfidtekGlksldadkfpdieswedfldevvel.aaeladyktlviDtidelee 79 
                                    ++l yGp+g+GKTt+++ +    p+  ++ ++++  +          ++++++++++ + ++  +  k +++D +d + +
  gene151|gene151|rna151|rna151  38 NMLFYGPPGTGKTTSIRAIarsLPRSCVLELNASDER----------GIATVRETIKDFaSTYSKMMKLVILDEADMMSR 107
                                    6899*************99999999999999996633..........234456666666466667788889999999888 PP

                         AAA_24  80 lclaevir 87 
                                     + + ++r
  gene151|gene151|rna151|rna151 108 DAQNALRR 115
                                    88777665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.9e-06    0.0024       5      52 ..      17      66 ..      13      93 .. 0.75
   2 ?    2.3   0.0       0.2        96     109     133 ..      96     120 ..      88     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-06
                   Mg_chelatase  5 vkGqeeakrale.iaaaGg.HnlllvGppGsGKtmlakrlpsllpplsee 52
                                   ++G++e    l+ i  aG+  n+l++GppG+GKt  +++++  lp+    
  gene151|gene151|rna151|rna151 17 MVGNKEVIASLQsILEAGKiPNMLFYGPPGTGKTTSIRAIARSLPRSCVL 66
                                   5566655555533677786359******************9999987654 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.2
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                                    +++LDE+  ++r++ ++LR+ +ed 
  gene151|gene151|rna151|rna151  96 LVILDEADMMSRDAQNALRRIIEDF 120
                                    568*****************99986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.7e-05     0.033       9      35 ..      35      61 ..      28      70 .. 0.82
   2 ?    5.1   0.1     0.057        27     102     126 ..      93     117 ..      66     132 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.7e-05
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivallv 35
                                   k +++l  ++pGtGKT+ +++i + l 
  gene151|gene151|rna151|rna151 35 KIPNMLFYGPPGTGKTTSIRAIARSLP 61
                                   5578999**************998875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.057
                         AAA_19 102 eeellivDEfqdvdelqyrLlkall 126
                                      +l+i DE+ +++  +++ l+++ 
  gene151|gene151|rna151|rna151  93 MMKLVILDEADMMSRDAQNALRRII 117
                                    2459**********55555555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-05    0.0053       3      69 ..      41     122 ..      40     151 .. 0.71
   2 ?    1.8   0.0      0.69   3.4e+02      25      85 ..     156     209 ..     140     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-05
                         AAA_18   3 ltGtpGvGKttlakeLskrl.gf................gvnlrdvakenglllevdpe..aldeskrldedkldkllda 63 
                                      G+pG+GKtt  ++++++l  +                 + ++d a+          +   lde + + +d +++l ++
  gene151|gene151|rna151|rna151  41 FYGPPGTGKTTSIRAIARSLpRScvlelnasdergiatvRETIKDFASTYSKMM----KlvILDEADMMSRDAQNALRRI 116
                                    57*****************85447888887777775554444444444422222....2444689999999999999998 PP

                         AAA_18  64 leenss 69 
                                    +e  s+
  gene151|gene151|rna151|rna151 117 IEDFSA 122
                                    888766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.69
                         AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlae 85 
                                      +++++++++g+ +++d        ++ e+ + k+++ ++++s      +  +id + ++
  gene151|gene151|rna151|rna151 156 ESRIKEICRKEGIKYTEDGI--AAVSKVSEGDMRKAVNDVQGISL-----SLGLIDERNVH 209
                                    56789999**********99..99999999999999999999876.....33355555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1     5e-06    0.0024       3      43 ..      40      81 ..      39     136 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5e-06
                         AAA_33  3 llvGlpGsGKstlaerllkklg.avllssdt........lrrrlfgtdqq 43
                                   l+ G+pG+GK+t ++ +++ l+  ++l+ ++        +        ++
  gene151|gene151|rna151|rna151 40 LFYGPPGTGKTTSIRAIARSLPrSCVLELNAsdergiatV--------RE 81
                                   799*******************967666665333333331........22 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.3e-06    0.0016      33     147 ..      10     119 ..       5     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                                    HHHHHHHHH---EBBBSS.SSBBCSS-.EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEEESSSSSE CS
                            MCM  33 kkaillqlfggvkkkled.ktklrgdi.nvllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaavvrdeetgef 110
                                    + + ll ++g  +  ++  ++   g+i n+l+ g pgt+K++ ++++++ +pr+     ++s + g+ +     e+ ++f
  gene151|gene151|rna151|rna151  10 RPGTLLEMVGNKEVIASLqSILEAGKIpNMLFYGPPGTGKTTSIRAIARSLPRSCVLELNASDERGIATVR---ETIKDF 86 
                                    66777777777775443302334677769*************************************96553...334455 PP

                                    EEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHH CS
                            MCM 111 vleaGalvladkGvcciDefdkmkeedrsalhEamEq 147
                                    +     ++     ++++De d m+++ ++al  ++E+
  gene151|gene151|rna151|rna151  87 ASTYSKMMK----LVILDEADMMSRDAQNALRRIIED 119
                                    555555554....688999999999999999888875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.7e-06    0.0033      10      41 ..      27      60 ..      20      85 .. 0.74
   2 ?   -2.3   0.0       6.5   3.1e+03     214     226 ..      90     102 ..      75     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.7e-06
                         AAA_11 10 iksalsese..itliqGPPGtgKTktivellsql 41
                                   ++s+l+  +    l+ GPPGtgKT+ i ++ ++l
  gene151|gene151|rna151|rna151 27 LQSILEAGKipNMLFYGPPGTGKTTSIRAIARSL 60
                                   45555555544589****************9998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.5
                         AAA_11 214 lakkfdvviIDEA 226
                                    + k +++vi DEA
  gene151|gene151|rna151|rna151  90 YSKMMKLVILDEA 102
                                    4446789999999 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.027        13      19      49 ..      33      63 ..      19      80 .. 0.68
   2 !   11.2   0.3   0.00031      0.15     101     133 ..      92     124 ..      66     132 .. 0.82
   3 ?   -2.8   0.0       5.7   2.8e+03     207     269 ..     175     238 ..     160     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.027
                                   .HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                           PIF1 19 nekgklfFvtGsgGtgKtflwkallkklrse 49
                                   + k  ++ ++G  GtgKt   +a+  +l  +
  gene151|gene151|rna151|rna151 33 AGKIPNMLFYGPPGTGKTTSIRAIARSLPRS 63
                                   3444567789************999998765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00031
                                    HC-SEEEEECGGGSBHHHHHHHHHHHHHHCT-. CS
                           PIF1 101 kktsliiwDEapmverecfealdrtlrdilkek 133
                                    k ++l+i+DEa m++r++ +al r++ d   ++
  gene151|gene151|rna151|rna151  92 KMMKLVILDEADMMSRDAQNALRRIIEDFSANT 124
                                    45789*********************9987765 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.7
                                    HHHHHHHHCT---CCCCHH.................HHCHC.CS---SS--...........EE CS
                           PIF1 207 skwllkigdGkineedeeealieiPedlllkksedkieeiv.sevygdllqeltdkeyleerai 269
                                    +  + k+ +G++ ++ ++ + i++   l+ +++ +k + i+  ++y++++ +l + + +e ra+
  gene151|gene151|rna151|rna151 175 IAAVSKVSEGDMRKAVNDVQGISLSLGLIDERNVHKFNGIApAQIYEEVFMDLGNMSMVELRAR 238
                                    5667788888888888888888888888877777777777634567777776777666666665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   9.8e-06    0.0047      35      82 ..      38      83 ..      17      95 .. 0.78
   2 ?   -2.7   0.0       7.1   3.5e+03      72      98 ..     127     153 ..     102     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.8e-06
                          AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82
                                   ++l++Gp GtGKt+ i+ + ++l+  +  +l +n s     ++++++i
  gene151|gene151|rna151|rna151 38 NMLFYGPPGTGKTTSIRAIARSLP--RSCVLELNASDERGIATVRETI 83
                                   79**********************..5556666666666666666655 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.1
                          AAA_7  72 qtsanqlqdiiesklekrrkgvygPpg 98 
                                    +  an+ ++ii   l + +k  +gP  
  gene151|gene151|rna151|rna151 127 CLIANHSRKIIPPILSRCTKFRFGPIE 153
                                    334777888888888888888888865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-05    0.0064       3      35 ..      40      87 ..      38     125 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                         AAA_28  3 vitGgestGKTtlleaLa...............argypvvpEaareil 35
                                    + G+++tGKTt ++a+a               +rg+ +v+E+  ++ 
  gene151|gene151|rna151|rna151 40 LFYGPPGTGKTTSIRAIArslprscvlelnasdERGIATVRETIKDFA 87
                                   689***************766666666665554447777777666655 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.1e-05      0.01      38      82 ..      42      87 ..      32     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                          AAA_6 38 aGpagtGKtEtvkdLakalakqvvv.fncsdqldykslgkifkGla 82
                                   +Gp gtGKt +++ +a++l + +v+ +n sd+  + ++ +++k +a
  gene151|gene151|rna151|rna151 42 YGPPGTGKTTSIRAIARSLPRSCVLeLNASDERGIATVRETIKDFA 87
                                   7********************9986479999988888887777665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-05    0.0081       8      70 ..      24      84 ..      20     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                       ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie 70
                                   + +l++ile ++ + ++ YGp g GKt+ ++ i+  l  +   v+ ++a  e+ i++++e+i+
  gene151|gene151|rna151|rna151 24 IASLQSILEAGKIPNMLFYGPPGTGKTTSIRAIARSLPRS--CVLELNASDERGIATVRETIK 84
                                   8899*****************************9999543..466667777777777777755 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.47   2.3e+02       9      30 ..      28      52 ..      24      60 .. 0.71
   2 !   12.5   0.1   0.00019      0.09     119     152 ..      91     123 ..      66     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.47
                                   HHHH.TTC..EEEEEESTTSSHHHH CS
                                   xxxx.xxx..xxxxxxxxxxxxxxx RF
                           DEAD  9 plil.ggg..dvlvaaeTGsGKTla 30
                                   + il  g+  ++l  ++ G+GKT+ 
  gene151|gene151|rna151|rna151 28 QSILeAGKipNMLFYGPPGTGKTTS 52
                                   555532223389999********86 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00019
                                    CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnqlpqi 152
                                     + +++++lDEad+++ +  ++ ++ri++ ++  
  gene151|gene151|rna151|rna151  91 SKMMKLVILDEADMMSRD-AQNALRRIIEDFSAN 123
                                    46789**********998.999999999988554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   8.5e-05     0.041      46     138 ..      35     121 ..      19     135 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.5e-05
                      IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqa 125
                                    k  n+++ Gp+G+GK+    a++++  r+ +  l  + e+ +++++       +a++ ++  +++l+ilD+  +  ++++
  gene151|gene151|rna151|rna151  35 KIPNMLFYGPPGTGKTTSIRAIARSLPRSCVLELNASDERGIATVRET--IKDFASTYSK--MMKLVILDEADM--MSRD 108
                                    55699******************9999987766666666666655543..3334444443..4689****9876..6777 PP

                      IstB_IS21 126 eaellfeviekry 138
                                    +++ l ++ie+  
  gene151|gene151|rna151|rna151 109 AQNALRRIIEDFS 121
                                    8888888888755 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.2e-05     0.016      39     128 ..      22     109 ..      12     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                         DUF815  39 alventeqfleglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfilfvDDLsF 118
                                    ++++  +  le  +  n+L++G  GtGK + ++a+ +++ ++   ++e++ +d + + ++ e++++ +  +  ++  +  
  gene151|gene151|rna151|rna151  22 EVIASLQSILEAGKIPNMLFYGPPGTGKTTSIRAIARSLPRSC--VLELNASDERGIATVRETIKDFASTYSKMMKLVIL 99 
                                    5667777888888899********************9998775..45666666666666666666555555444444444 PP

                         DUF815 119 eeeeeeyksL 128
                                    +e +   +  
  gene151|gene151|rna151|rna151 100 DEADMMSRDA 109
                                    5555555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00021       0.1      24      60 ..      25      61 ..      16      82 .. 0.82
   2 ?    0.1   0.1      0.91   4.4e+02     119     138 ..      93     112 ..      70     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                           TniB 24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhp 60
                                   ++L +  ++ ++pn+l++G++ +GKt+ ++  ar+ p
  gene151|gene151|rna151|rna151 25 ASLQSILEAGKIPNMLFYGPPGTGKTTSIRAIARSLP 61
                                   455566678899***************9998887765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.91
                           TniB 119 kvrvLiiDEihnllagsark 138
                                    +++++i+DE + + +  +++
  gene151|gene151|rna151|rna151  93 MMKLVILDEADMMSRDAQNA 112
                                    57899999999887433333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00043      0.21      14     113 ..      39     185 ..      28     202 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00043
                                    EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                       ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............. 79 
                                    + + G+ G+GK+t ++++a+ l   +  +  + + ++e+ +  +r+ i+ +  + +   +l + ++              
  gene151|gene151|rna151|rna151  39 MLFYGPPGTGKTTSIRAIARSLPR-SCVL--ELNASDERGIATVRETIKDFASTYSKMMKLVILDEadmmsrdaqnalrr 115
                                    5678***************99864.2222..2222222223333333333333322222221222223222233334445 PP

                                    ......................................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHH CS
                                    ......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ......................................esdeeiekalsklglkelkdtvvksspssLSgGq 113
                                                                            +++i+++ +k g+k+++d ++    s++S+G 
  gene151|gene151|rna151|rna151 116 iiedfsantrfclianhsrkiippilsrctkfrfgpieSTESRIKEICRKEGIKYTEDGIA--AVSKVSEGD 185
                                    5555555555555555566666666666666666666545555555555555555555544..445555555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00018     0.085       3      74 ..      43     118 ..      41     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                                    ESTTSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS---HHH...HHHHHHHHHHHTTHHHHH CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeeleeqt...eallfaadriehleekik 74 
                                    G  G+GKtt ++++++ l++++      + e g  +++e+i++  +   ++ ++    ea + + d   +l++ i+
  gene151|gene151|rna151|rna151  43 GPPGTGKTTSIRAIARSLPRSCVLeLNASDERGIATVRETIKDFASTYSKMMKLVildEADMMSRDAQNALRRIIE 118
                                    6779******************9888999999999********999555555544455777777777555555554 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00036      0.17       1      79 [.      42     132 ..      42     142 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00036
                                    EE-TTSSHHHHHHHHHHHH...TEEEEEHHHHHH.HHHHTT..TSHSSHHHHCTSHHHHHHHHH....HHHHHHHHHH.H CS
                         AAA_17   1 lGgPGsGKgtqceklveky...gfthlsaGdllr.eeakrg..glakardemrklpleekkelq....keaaekiaee.a 69 
                                    +G+PG GK+t ++ +++ +    +  l+a+d    +++++     a++ ++m+kl + ++ +++    ++a ++i e+ +
  gene151|gene151|rna151|rna151  42 YGPPGTGKTTSIRAIARSLprsCVLELNASDERGiATVRETikDFASTYSKMMKLVILDEADMMsrdaQNALRRIIEDfS 121
                                    7****************994322334788887442333333322356778888765555544443333566666666523 PP

                                    HSSEE.EEEE- CS
                         AAA_17  70 kkkgv.lvdgh 79 
                                    +++ + l+  h
  gene151|gene151|rna151|rna151 122 ANTRFcLIANH 132
                                    44443355555 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0003      0.15      13      35 ..     223     245 ..     215     246 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0003
                        DUF1192  13 igqDLslLSveELeerIalLeaE 35 
                                    +  DL ++S+ EL++rI++L+ E
  gene151|gene151|rna151|rna151 223 VFMDLGNMSMVELRARIEDLRYE 245
                                    568*****************987 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.028        13       2      22 ..      42      62 ..      41      72 .. 0.85
   2 ?    4.9   0.0     0.039        19     191     227 ..      98     136 ..      70     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.028
                     ATP_bind_1  2 vGpaGsGKttfvgalseilel 22
                                    Gp+G GKtt ++a++  l+ 
  gene151|gene151|rna151|rna151 42 YGPPGTGKTTSIRAIARSLPR 62
                                   6************99887765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.039
                     ATP_bind_1 191 ekee..ekykklaeaiaelleefalvlrflplssekees 227
                                     ++e     ++ ++a+++++e+f++++rf+ +++++++ 
  gene151|gene151|rna151|rna151  98 ILDEadMMSRDAQNALRRIIEDFSANTRFCLIANHSRKI 136
                                    22224467789999******************9988775 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026      0.13     107     156 ..      16      63 ..       7      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                          T2SSE 107 dlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                    +++ ++++ + ++++l++   +  ++l+ G+ g+GKtt++ a+   ++ s
  gene151|gene151|rna151|rna151  16 EMVGNKEVIASLQSILEAG--KIPNMLFYGPPGTGKTTSIRAIARSLPRS 63 
                                    5566666677788888888..7789***************9999888776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0046       2.2       3      28 ..      39      64 ..      38      71 .. 0.86
   2 ?    2.2   0.0       0.3   1.5e+02      84     139 ..      96     141 ..      75     168 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0046
                                   EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                   ++  G++G GKTt ++ +a+ + +++
  gene151|gene151|rna151|rna151 39 MLFYGPPGTGKTTSIRAIARSLPRSC 64
                                   5789***************9987765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.3
                                    EEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTS CS
                          NACHT  84 LlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeql 139
                                    L ilD +D +++d ++         L+++i+  +  +  +l++ ++r+   ++  l
  gene151|gene151|rna151|rna151  96 LVILDEADMMSRDAQN--------ALRRIIEDFSANTRFCLIANHSRKI--IPPIL 141
                                    799********98888........7888888777777777777777665..55555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00052      0.25      15      43 ..      28      60 ..      17      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00052
                                   HHCH..TEE..EEEEESTTSSHHHHHHHHHHHT CS
                           TsaE 15 akal..gdv..ilLeGdLGaGKTtlvrglakal 43
                                   ++ l  g++  +l++G+ G+GKTt +r++a++l
  gene151|gene151|rna151|rna151 28 QSILeaGKIpnMLFYGPPGTGKTTSIRAIARSL 60
                                   3333333435599*****************987 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00042       0.2     178     211 ..      94     128 ..      74     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
                                    -SEEEES-GGGT--T.TSHHHHHHHH---S-EEEE CS
                                    xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 178 wkrvvlDEghtlkns.tskaaeavskLstsnrwil 211
                                    +k v+lDE+ ++    ++ ++ +++++s++ r +l
  gene151|gene151|rna151|rna151  94 MKLVILDEADMMSRDaQNALRRIIEDFSANTRFCL 128
                                    688*********99989*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 1924.75
//
Query:       gene1511|gene1511|rna1510|rna1510  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-16   60.5   1.2    1.8e-16   59.8   1.2    1.3  1  TB2_DP1_HVA22  TB2/DP1, HVA22 family
  ------ inclusion threshold ------
      0.051   12.8   0.3      0.057   12.6   0.3    1.0  1  CitMHS         Citrate transporter
      0.095   13.3   0.6       0.22   12.1   0.6    1.6  1  DUF5592        Family of unknown function (DUF5592)


Domain annotation for each model (and alignments):
>> TB2_DP1_HVA22  TB2/DP1, HVA22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   1.2     3e-20   1.8e-16       1      75 [.      58     134 ..      58     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 3e-20
                      TB2_DP1_HVA22   1 Payaslkalesk.eksdetk.wltYWvvfafltvvesladvllswiPfYylfKllfllwlvlpqtqgatyvYekfl 74 
                                        P+ +++  l++  +k++etk +l +W++f++lt ++ + ++++ +iP++y++K++fllw    +++g  ++Y+++l
  gene1511|gene1511|rna1510|rna1510  58 PLQETFVILRQVnPKKEETKhMLVFWMIFGVLTSLDAYYNTIIGFIPLWYTIKFFFLLWAGPLKFRGGIIIYDNIL 133
                                        677788889877677777866*****************************************************98 PP

                      TB2_DP1_HVA22  75 r 75 
                                         
  gene1511|gene1511|rna1510|rna1510 134 T 134
                                        5 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   9.5e-06     0.057     100     182 ..      12     150 ..      11     172 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.5e-06
                                        xxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxx RF
                             CitMHS 100 pivlslakrlkklppl.......lliplalaaniggaltpiGtpttraa.................arpglslpnl 151
                                        pi+ ++ kr++ ++ +       l++++++a ++g ++t   ++    +                 +  + +l+++
  gene1511|gene1511|rna1510|rna1510  12 PILDAIEKRMNIRKEYallgisfLCLVIIMATSLGPLVTSTIGI----IvplqetfvilrqvnpkkEETKHMLVFW 83 
                                        55555556655555554444445666666666666666644444....145779************99******** PP

                                        xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxx..............................x RF
                             CitMHS 152 lllal.........llvgllplvllfmfgvalalpvnap..............................k 182
                                        ++ ++         +++g++pl++++  +++  l+ + p                               
  gene1511|gene1511|rna1510|rna1510  84 MIFGVltsldayynTIIGFIPLWYTI--KFF-FLLWAGPlkfrggiiiydniltripeswyreeggienA 150
                                        **777445555544555556666555..222.22222223344555555555555555555555555554 PP

>> DUF5592  Family of unknown function (DUF5592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.6   3.7e-05      0.22       5      75 ..      15      80 ..      11      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                            DUF5592  5 keisselkinkaiyLtDlllllvlllltmklsslvhaslvvlfyifviilviflviksktNpklrnykaly 75
                                         i+ ++ i k   L  + +l ++++++++l +lv +++     i+v +   f++++ ++Npk+ + k ++
  gene1511|gene1511|rna1510|rna1510 15 DAIEKRMNIRKEYALLGISFLCLVIIMATSLGPLVTSTIG----IIVPLQETFVILR-QVNPKKEETKHML 80
                                       5689999****************************99864....4444455555554.7888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1388.71
//
Query:       gene1512|gene1512|rna1511|rna1511  [L=154]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-18   65.4   1.2    5.6e-18   64.7   1.2    1.3  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    3.7e-13   49.4   0.7    5.8e-13   48.8   0.7    1.4  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
        3.5    7.7   4.9         15    5.7   1.1    2.1  2  Bd3614-deam      Bd3614-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   1.2   9.4e-22   5.6e-18       4     100 ..      12     102 ..      10     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 9.4e-22
                                        HHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEEEE CS
                    dCMP_cyt_deam_1   4 dekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyvtl 79 
                                        ++ ++++a ++a +a +  +++VG+v+vkng i+s  +n+++a++s+  HAE++ ++++    + +  + ++yvt+
  gene1512|gene1512|rna1511|rna1511  12 HSFFMDIAFAEAAKAFDRLEVPVGCVVVKNGTIVSMSHNMTNANKSPLEHAEIISVRNVD---C-S--NSIFYVTC 81 
                                        788*****************************************************9996...3.3..489***** PP

                                        --BHHHHHHHHHHT-SEEEEE CS
                    dCMP_cyt_deam_1  80 ePCsmCakaiiqsgikkvvvg 100
                                        ePC mC  ++  ++  +v++g
  gene1512|gene1512|rna1511|rna1511  82 EPCIMCMGILGRLENVEVYYG 102
                                        **********99999999987 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.7   9.7e-17   5.8e-13       6     104 ..      15     106 ..      10     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 9.7e-17
                        MafB19-deam   6 afrkalaevekatkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlep 81 
                                        ++  a ae+ ka++  e+++g+v+vk++ ++   +n ++ n+++++HaEi +++           ++ + yvt ep
  gene1512|gene1512|rna1511|rna1511  15 FMDIAFAEAAKAFDRLEVPVGCVVVKNGTIVSMSHNMTNANKSPLEHAEIISVRNV-------DCSNSIFYVTCEP 83 
                                        67778899********************************************9877.......346779******* PP

                        MafB19-deam  82 CdmCagaivqaglkklvygagnp 104
                                        C mC g++ + +  ++ yg++n+
  gene1512|gene1512|rna1511|rna1511  84 CIMCMGILGRLENVEVYYGCKNE 106
                                        ****8866444444556666654 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2    0.0076        46      11      40 ..      34      65 ..      23      77 .. 0.73
   2 ?    5.7   1.1    0.0025        15      78      96 ..      75      93 ..      68     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0076
                        Bd3614-deam 11 vAalvsdqGelldaavntnaenk.vL.HAEvn 40
                                       v  +v ++G++++++ n    nk  L HAE+ 
  gene1512|gene1512|rna1511|rna1511 34 VGCVVVKNGTIVSMSHNMTNANKsPLeHAEII 65
                                       55788899*********655555244599975 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0025
                        Bd3614-deam 78 arllvtlqcCkmCAalvva 96
                                       +  +vt ++C mC +++  
  gene1512|gene1512|rna1511|rna1511 75 SIFYVTCEPCIMCMGILGR 93
                                       5689*********998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1032.34
//
Query:       gene1513|gene1513|rna1512|rna1512  [L=1084]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   7.3e-144  480.5  19.6   1.8e-123  413.2  13.3    2.1  2  Myosin_head  Myosin head (motor domain)
    5.4e-13   49.1   0.6    5.4e-13   49.1   0.6    2.2  2  DIL          DIL domain
  ------ inclusion threshold ------
      0.074   13.3   0.0       0.27   11.5   0.0    2.0  1  AAA_22       AAA domain
      0.087   13.2   0.1       0.74   10.1   0.0    2.5  3  AAA_19       AAA domain


Domain annotation for each model (and alignments):
>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.2  13.3  3.9e-127  1.8e-123       2     507 ..       4     474 ..       3     496 .. 0.91
   2 !   71.8   0.6     8e-24   3.6e-20     553     642 ..     489     578 ..     474     600 .. 0.87

  Alignments for each domain:
  == domain 1  score: 413.2 bits;  conditional E-value: 3.9e-127
                                        SBGCGSSS-SHHHHHHHHHHHHHTT--EEEETTEEEEE--SS--STSSHHHHHHHTTS-GGGSSSSHHHHHHHHHH CS
                        Myosin_head   2 edlveLsllneasvlenlkkRykkdliYtysglvlvavnPykklkiysedvikaykgkkreelpPHifaiadeayr 77 
                                        +dl+eL+ lne+++l+ l+kRy++  iYt sglv +a+nPy++++ y+++ ++ +++ + +    H++ +a+  y+
  gene1513|gene1513|rna1512|rna1512   4 DDLCELNDLNEDAILNILEKRYASGRIYTKSGLVFLALNPYESINPYDRKSLQPFSDSTGS---THVHDVAEASYQ 76 
                                        8*******************************************************98875...6*********** PP

                                        HHHHHTSEEEEEEESSTTSSHHHHHHHHHHHHHHHSSSSSCTCTTHHHHHHHHHHHHHHHHHEEEESSETTEESSE CS
                        Myosin_head  78 slledkenqsilisGEsGAGKteatKkvlqylasvaeskekveeeeleekilqsnPilEafGnAktvrndnssRFG 153
                                        +ll +  nq+i+isGEsG GKte+tK v++yl   ++s++     ++e+ki ++n ilEafGnA+t+ ndnssRFG
  gene1513|gene1513|rna1512|rna1512  77 DLLVH-GNQTIVISGESGSGKTENTKLVIKYLVERTASNT-----SIERKITAANAILEAFGNARTILNDNSSRFG 146
                                        **986.69************************98888887.....8****************************** PP

                                        EEEEEEEETTSSEEEEEEEEECE-GGGGT---TT--SBHHHHHHHHCSTHHHHHHTT--TCCGSTTTTTTSSSSBT CS
                        Myosin_head 154 KfieiefdakgkiagakietYLLEksRvvkqakeERnyHiFYqllagaseeekkelkledvkdyaylsqsgeltvd 229
                                        K i++ fd  gki+ga+ etYLLEksRv + +++ERn+HiFYq++a+++ + k+++  +     ++l +    + +
  gene1513|gene1513|rna1512|rna1512 147 KRIKLIFD--GKITGARFETYLLEKSRVTHHETGERNFHIFYQFCASKDFRIKNDFIDT----SSHLGN----KES 212
                                        *******8..789**********************************999999988533....334544....234 PP

                                        TS-HHHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHCTSSEEEECTTSSEEESSHHHHHHHHHHHTS-HHHHHH CS
                        Myosin_head 230 giddseefketkkaldilglseeeqkeifrivaailhlGniefkkeakdeqavledeeklekaaellgvdaeelek 305
                                        +++ se++ +t++a++ +g++   +kei   + +il+lG+i+f+++      ++ ++e  +++++l  +++e +e+
  gene1513|gene1513|rna1512|rna1512 213 IVQLSENYVATCSAMKSVGITR--IKEIEDCLLGILYLGSIQFSDDGI---LKVIRNECFTEFCKLHHIQEEVFEE 283
                                        5677899*************85..788999*************87664...45777888***************** PP

                                        HHHSEEEEETTEEEEEE-BHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-S-SEEEEEEEEE-B---SSB- CS
                        Myosin_head 306 alvkrriktgkevvskalnveqaevardalakaiyerlFdwlverinkslekkkeekksfiGvLDiaGFEifekns 381
                                        +lvk +i+++ e++ +  +++qa ++r+++a+ +y+++F+++   in+ l+ +    +  i vLDi+GFEife n+
  gene1513|gene1513|rna1512|rna1512 284 SLVKFSIQVKGETIEVFNTLKQAVTIRNSMARLLYSNIFNYITASINNCLSGSG---ELSISVLDIFGFEIFESNG 356
                                        **************************************************9887...899**************** PP

                                        HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHTTSSGCGS-GGGCCHHHHHHHHSSSTSHHHHHHHHHTSTTS-HHH CS
                        Myosin_head 382 FEqlcinyvnEkLqqlFnelvlklEqeeYvrEgiewkfidfgldnqaiidLiekkplGilslLdeecllpkatdet 457
                                         +qlcin++nEk+q+ F+++v+ + qe Y+ Egiewk ++f +dn+++i   ek p G+++l+ ee+  + ++ ++
  gene1513|gene1513|rna1512|rna1512 357 LDQLCINWTNEKIQNDFIRKVFREKQEMYKEEGIEWKDVEF-FDNNQCIIDFEK-PCGLMDLISEESFNAWGNTKN 430
                                        *****************************************.888888766777.9******************** PP

                                        HHHHHHHHHTTSTTEEETTSTTTTTEEEEEETTCEEEEE-TTHHHHHH-- CS
                        Myosin_head 458 fleklvkafskhakfeksrlkkgeakFiikHyAgkveYevegfleKnkDt 507
                                        +  k+++  + + k    +    ++k i++HyAg+veY+ + fl+Kn+++
  gene1513|gene1513|rna1512|rna1512 431 LNMKIKSYLNGNIKT---K---FDDKIIVSHYAGDVEYDLRLFLDKNREK 474
                                        *****9998877654...3...36789********************985 PP

  == domain 2  score: 71.8 bits;  conditional E-value: 8e-24
                                        CCCSBHHHHHHHHHHHHHHHHCTSEEEEEEEE-SSSS--TT---HHHHHHHHHHTTHHHHHHHHHHSSSEEEEHHH CS
                        Myosin_head 553 kkfktvgskfkeslaeLmktlestnphfvRCikpnekkkakkldeslvleqlrclGvlegirirraGfpnRitfee 628
                                        ++++ + + fk+s+++L++++++t++++++Ci+pn  kk+k +d+slv +ql  +G+le+ir++++ fp+ i  ++
  gene1513|gene1513|rna1512|rna1512 489 QSKEDLVKYFKDSMNKLLHSINETQAKYIKCIRPNAYKKPKAFDRSLVSKQLAECGILETIRVSKQCFPQEIRKDK 564
                                        456677789******************************************************************* PP

                                        HHHHHGGGSTTSS- CS
                        Myosin_head 629 fvqrYkllakkelk 642
                                        f +rY++l ++  +
  gene1513|gene1513|rna1512|rna1512 565 FENRYRILGSTLFE 578
                                        *******9887653 PP

>> DIL  DIL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.4   1.1e+04       3      18 ..     318     333 ..     317     337 .. 0.82
   2 !   49.1   0.6   1.2e-16   5.4e-13       4      99 ..     936    1028 ..     934    1032 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                                        HHHHHHHHHHHHHHHH CS
                                DIL   3 fsqlfyfinaelfNrl 18 
                                         s++f++i a++ N l
  gene1513|gene1513|rna1512|rna1512 318 YSNIFNYITASINNCL 333
                                        6899999999998876 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 1.2e-16
                                         HHHHHHHHHHHHHHHHHHS-SB-HHHHHHHHHHHHHHHHCCTS-......-GGGGHHHHHHHHHHHC-S--HHH CS
                                DIL    4 sqlfyfinaelfNrlllrkklcsrskGlqlrrnlslledWaeeqgl.eeaaekhlapliqaaqllqlpkssled 76  
                                         ++l++ in+++fN++l +k+++s+++G+q+++n++++ +++++ +  e     +l++  ++++l+ l +s   +
  gene1513|gene1513|rna1512|rna1512  936 NYLLKTINVSVFNEILVKKNFLSFNRGVQINYNVNEIDKFCRSINYlE--GMFNLSHTTSIIRLINLVES-RAT 1006
                                         79****************************************977642..45555555555555555555.344 PP

                                         HHHHC.TT-TSS-HHHHHHHHTT CS
                                DIL   77 lesilrstcpaLnsaQlkrllen 99  
                                         ++ il ++c+ Ln  Q++ ++++
  gene1513|gene1513|rna1512|rna1512 1007 ADLIL-DECSILNCVQINEIVSK 1028
                                         66677.**************987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.9e-05      0.27       5      58 ..      83     139 ..      80     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.9e-05
                             AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllr 58 
                                         + +v+ GesG+GKT   + + + l+e+ + ++   ++ + +   l + ++ +++l+
  gene1513|gene1513|rna1512|rna1512  83 NQTIVISGESGSGKTENTKLVIKYLVERTASNTsieRKITAANAILEAFGNARTILN 139
                                        6789***************99999988776666775444444666666666666655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00016      0.74       8      42 ..      81     115 ..      76     211 .. 0.88
   2 ?   -1.9   0.0      0.88   3.9e+03      90     117 ..     467     495 ..     426     515 .. 0.67
   3 ?   -1.4   0.0       0.6   2.7e+03     104     130 ..    1007    1034 ..     984    1042 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                             AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp 42 
                                        + ++++++ +  G+GKT+ +k ++++lve++  + 
  gene1513|gene1513|rna1512|rna1512  81 HGNQTIVISGESGSGKTENTKLVIKYLVERTASNT 115
                                        5678999********************99886554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.88
                             AAA_19  90 lleeaeeekklqeee.llivDEfqdvdel 117
                                        +l++++e+  l+  +  livDE +  d +
  gene1513|gene1513|rna1512|rna1512 467 FLDKNREKGSLKIFKnDLIVDEQSKEDLV 495
                                        45544455555444457999999876643 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.6
                             AAA_19  104 ellivDEfqdvd.elqyrLlkallgekk 130 
                                         + li DE + ++  ++++++++l  e+ 
  gene1513|gene1513|rna1512|rna1512 1007 ADLILDECSILNcVQINEIVSKLDAEAS 1034
                                         36899*******9999999999986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1084 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.43
# Mc/sec: 7493.73
//
Query:       gene1514|gene1514|rna1513|rna1513  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0079   15.9   0.4       0.31   10.8   0.0    2.4  2  YcxB      YcxB-like protein


Domain annotation for each model (and alignments):
>> YcxB  YcxB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   1.7e-05      0.31       1      43 [.      30      72 ..      30      77 .. 0.80
   2 !    2.9   0.1    0.0051        92      18      38 ..     152     172 ..     150     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.7e-05
                               YcxB  1 itedgiev.dsgggesiipWdsiekvkEtkdyfyLflsggsafi 43
                                       +++d + + + +++ ++ip+++i +v+++++++ + l++g+ ++
  gene1514|gene1514|rna1513|rna1513 30 FYPDRFMIlYKDRKAGEIPYENILRVEKNREGLKFGLKNGT-WV 72
                                       5666664447788889*******************999998.54 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0051
                               YcxB  18 pWdsiekvkEtkdyfyLflsg 38 
                                        ++++++ ++++kd++++f ++
  gene1514|gene1514|rna1513|rna1513 152 HYNEFSLYIKDKDSLVIFEND 172
                                        5999999**********9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1317.17
//
Query:       gene1515|gene1515|rna1514|rna1514  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1783.50
//
Query:       gene1516|gene1516|rna1515|rna1515  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.59
# Mc/sec: 1131.97
//
Query:       gene1517|gene1517|rna1516|rna1516  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-23   82.5  18.3    4.5e-23   82.2  18.3    1.0  1  DUF2463    Protein of unknown function (DUF2463)
  ------ inclusion threshold ------
        2.6    7.8   5.4        9.3    6.0   1.4    2.7  2  Lysis_col  Lysis protein
        6.1    5.0  12.9        6.3    5.0  12.9    1.0  1  DUF2070    Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2  18.3   7.5e-27   4.5e-23      96     210 .]       1     110 [.       1     110 [. 0.94

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 7.5e-27
                            DUF2463  96 iilPslvvpltyLlstscnlvpgqisftdtginilidlliLlllivslvllleeseyllyfaiissiliLvrllke 171
                                        +i+Psl+v++ y+ls+scnl pg+is++d++inili +liLl +++sl+l ++ s ++ y ++is+ liL+r+ +e
  gene1517|gene1517|rna1516|rna1516   1 MIFPSLFVSFSYMLSVSCNLSPGSISLVDSNINILIYILILLRTTTSLILRINRSMFYSYPIVISAFLILLRSIRE 76 
                                        79************************************************************************** PP

                            DUF2463 172 kylpskksslptakwrvaifvliLilavliYvflalesi 210
                                        ky+ skk +l++++      v+iLil +liY+++a +++
  gene1517|gene1517|rna1516|rna1516  77 KYFSSKKRTLSSIS-----VVFILILRFLIYLITARTCL 110
                                        *********99994.....46778888899999998885 PP

>> Lysis_col  Lysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.015        92      12      23 ..       8      19 ..       2      28 .. 0.88
   2 ?    6.0   1.4    0.0016       9.3       4      21 ..      89     106 ..      86     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.015
                          Lysis_col 12 lifsifLLvACQ 23
                                       ++fs +L v C 
  gene1517|gene1517|rna1516|rna1516  8 VSFSYMLSVSCN 19
                                       79*********6 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                          Lysis_col   4 vkvvflFilifsifLLvA 21 
                                        + vvf+ il f i+L+ A
  gene1517|gene1517|rna1516|rna1516  89 ISVVFILILRFLIYLITA 106
                                        68*************987 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  12.9    0.0011       6.3      44     126 ..      30     109 ..       1     122 [. 0.61

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0011
                            DUF2070  44 fglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall.qalvllalvlslalvfalrllv 118
                                          + +l+++l++l++  +l  +l ++rs+f ++ + + +++i+l +i   ++  +        +s++++++lr+l+
  gene1517|gene1517|rna1516|rna1516  30 SNINILIYILILLRTTTSL--ILRINRSMFYSYPIVISAFLILLRSIREKYFSsK--KRTLSSISVVFILILRFLI 101
                                        2233444444444444333..4889999999999999999988888777765542..3344467788999999999 PP

                            DUF2070 119 lvavsdes 126
                                        +++++++ 
  gene1517|gene1517|rna1516|rna1516 102 YLITARTC 109
                                        99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 725.65
//
Query:       gene1518|gene1518|rna1517|rna1517  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-18   66.5   8.8    3.8e-18   66.1   8.8    1.1  1  DUF2463   Protein of unknown function (DUF2463)


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   8.8   2.1e-22   3.8e-18       1      70 [.      41     110 ..      41     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 2.1e-22
                            DUF2463   1 fpvlmyfifekdsfeeslllrfitlllpfsysavqyllllhtnwkssnkpesilhkilyyllnllllaFa 70 
                                        fp+++y++ ++d f+ s+ lr+ t++lpfsysa  +++l+h+nw s ++ e  l kily++lnl +laF+
  gene1518|gene1518|rna1517|rna1517  41 FPIFIYYMASEDLFNRSIPLRLTTVILPFSYSAERHFFLFHKNWMSAYRFELKLDKILYSILNLFFLAFF 110
                                        9********************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 746.15
//
Query:       gene1520|gene1520|rna1519|rna1519  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-15   57.4   2.2    2.7e-15   56.5   2.2    1.4  1  Ribosomal_L23  Ribosomal protein L23


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   2.2   1.5e-19   2.7e-15       1      64 [.      25      89 ..      25      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.5e-19
                                       SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSS CS
                      Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrk 64
                                       d+il  + tEk+ + +++ n++vF V+k+++K+eikka+ +l+g kV+kVntl+ k  kk + r+
  gene1520|gene1520|rna1519|rna1519 25 DIILYALTTEKAARCMDQfNTLVFYVEKTSTKPEIKKAITELYGFKVKKVNTLINKHGKKAYVRF 89
                                       79999*************99*********************************999888854443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 680.10
//
Query:       gene152|gene152|rna152|rna152  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-11   42.9   2.0    7.1e-11   42.1   2.0    1.4  1  DnaJ         DnaJ domain
     0.0018   17.9   0.8     0.0053   16.3   0.8    1.8  1  PIRT         Phosphoinositide-interacting protein family
  ------ inclusion threshold ------
       0.29   11.3   1.4        3.3    7.9   1.4    2.5  1  DUF1196      Protein of unknown function (DUF1196)


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   2.0   1.2e-14   7.1e-11       2      63 .]       3      61 ..       2      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.2e-14
                                   HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                           DnaJ  2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                   +Y++L+++kda+++++ ++Yr l++ y   kn   + + ++F ein+Ay +L+d+ kR  YD
  gene152|gene152|rna152|rna152  3 LYDVLKIPKDATKENVERSYRFLVRLYCQSKN---EMSPDRFAEINKAYTILKDKYKRDFYD 61
                                   8**************************76666...66779*********************9 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.8   8.9e-07    0.0053      43     109 ..     172     238 ..     155     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.9e-07
                           PIRT  43 wdvykkpiivlsvGgavfllGvvittlsrnstlknkdkevfklsGpaflslGlml..lvcGlvwvpiik 109
                                    + +y    i +   ga+fl+  +++t+  n++  ++dk+ f l     + +G m+   ++Glv vpii 
  gene152|gene152|rna152|rna152 172 YALYADGFIDILFSGAIFLVVEILSTI--NTIYYHNDKQKFFLQAKKNIIIGKMIraALFGLVLVPIIP 238
                                    56777777878889*************..9999999******************944589*******95 PP

>> DUF1196  Protein of unknown function (DUF1196)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.4   0.00055       3.3      12      36 ..     239     263 ..     233     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00055
                        DUF1196  12 vflmPtlPfkGvakGiyakqhsiks 36 
                                     fl P l f  +  Giy+k++s+k 
  gene152|gene152|rna152|rna152 239 SFLKPLLFFVQILWGIYSKRYSLKV 263
                                    69********************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1989.98
//
Query:       gene1521|gene1521|rna1520|rna1520  [L=424]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.3e-51  172.8   0.0    9.7e-51  172.2   0.0    1.3  1  SRP54        SRP54-type protein, GTPase domain
    2.1e-05   23.6   0.1    0.00012   21.2   0.0    2.3  4  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00021   21.3   0.5      0.055   13.5   0.0    2.8  3  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00028   21.3   0.7      0.006   17.0   0.0    2.5  2  AAA_17       AAA domain
    0.00046   19.5   0.2     0.0068   15.7   0.0    2.3  2  VirC1        VirC1 protein
    0.00076   19.4   0.9        2.3    8.1   0.0    3.3  3  NTPase_1     NTPase
     0.0012   18.9   1.0     0.0073   16.4   0.2    2.5  2  MMR_HSR1     50S ribosome-binding GTPase
     0.0013   19.0   0.0     0.0039   17.5   0.0    1.8  2  AAA_22       AAA domain
     0.0033   17.9   0.1      0.042   14.3   0.0    2.7  2  AAA          ATPase family associated with various cellular a
      0.009   15.8   0.0      0.019   14.7   0.0    1.5  1  AAA_30       AAA domain
      0.009   15.8   0.1       0.87    9.3   0.0    3.1  3  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
  ------ inclusion threshold ------
      0.011   16.0   1.9      0.041   14.1   1.9    2.2  1  SRP54_N      SRP54-type protein, helical bundle domain
      0.012   15.3   0.0      0.029   14.1   0.0    1.6  1  AAA_24       AAA domain
      0.024   14.6   0.9      0.087   12.7   0.2    2.2  3  RsgA_GTPase  RsgA GTPase
      0.029   14.3   0.7         15    5.5   0.0    3.2  3  AAA_31       AAA domain
      0.078   13.4   0.0       0.42   11.0   0.0    2.1  2  AAA_16       AAA ATPase domain
       0.11   12.5   0.2        6.2    6.8   0.0    2.5  2  AAA_5        AAA domain (dynein-related subfamily)
       0.16   12.2   0.0       0.67   10.1   0.0    2.0  1  AAA_33       AAA domain
       0.87   10.1   7.3       0.29   11.6   0.1    2.4  2  AAA_23       AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.2   0.0     1e-53   9.7e-51       3     195 ..     217     422 ..     215     423 .. 0.93

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 1e-53
                                        EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTT.....EEEEESSTTSCHHHHHH CS
                              SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklg.....vpvikkkeeadpaavak 73 
                                         i +vG++G+GK t+laK+  +l +++ +v ++a+DtfRa+A+eQL+t+ e+ +     v +++k  ++d a+va+
  gene1521|gene1521|rna1520|rna1520 217 SICFVGVNGVGKSTSLAKICYWLLQNKFRVYIAACDTFRAGAIEQLRTHVERFKlgghlVGFYEKGYGKDDASVAR 292
                                        588************************************************9763344467888999********* PP

                                        HHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHS.......SC CS
                              SRP54  74 eavekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeav.......gi 142
                                         a+++a++e++dv+l+DTaGr++n+k+lm+ l+k+ k+ +pd++++v +a++g++ + ++++F++a+       +i
  gene1521|gene1521|rna1520|rna1520 293 CAIQEAQHEGYDVILIDTAGRMHNKKNLMASLTKLIKINNPDHIIYVGEALVGSDSLDHIREFNKAIgdagqsrKI 368
                                        ****************************************************************99844444446* PP

                                        SEEEEESTTS.SSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                              SRP54 143 tgviltklDg.dakgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                        +++ ltk+D+ d k G++l++a +++ Pi f+gvG++  dl+++ +e++v++l+
  gene1521|gene1521|rna1520|rna1520 369 DSILLTKVDTvDNKIGQILNMAFSSHAPILFLGVGQSNSDLSNIGSEDIVNSLM 422
                                        *********8689*************************************9997 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         3   2.8e+03     216     256 ..     113     154 ..     108     168 .. 0.53
   2 ?   -3.3   0.0       3.6   3.4e+03      44      57 ..     163     176 ..     156     178 .. 0.88
   3 !   21.2   0.0   1.3e-07   0.00012      16     132 ..     203     313 ..     189     335 .. 0.84
   4 ?   -2.4   0.0         2   1.9e+03     130     144 ..     400     414 ..     397     422 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3
                                        BSHHHHHHHHHHHHHHHHHTTHHHHHHH..HHHHHHHHHHHHH CS
                               MeaB 216 eGidelvdaieehrevlkktGllekrrr..erakeelrelved 256
                                         Gi +lv+ i++ ++v k+ Gl++   +  e + +++++l+++
  gene1521|gene1521|rna1520|rna1520 113 SGISNLVEVIRK-ATVQKAFGLFKDEIQvsELKDKMTTHLISK 154
                                        677777776654.456666666655443102222333333333 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.6
                                        HHHHHHHHHHHCTT CS
                               MeaB  44 tlvealglelrrrG 57 
                                        tlv+++++el+++G
  gene1521|gene1521|rna1520|rna1520 163 TLVDNITMELAEEG 176
                                        999*******9999 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 1.3e-07
                                        HHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE------------------HCCCTSTT CS
                               MeaB  16 kellerllakaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklRleelavdeg 91 
                                        +++l+++  + G    + + Gv G+Gkst + ++   l ++  rv + a D   +f  G+i   ++ +e++  + g
  gene1521|gene1521|rna1520|rna1520 203 ERMLDKIKRHKGV-FSICFVGVNGVGKSTSLAKICYWLLQNKFRVYIAACD---TFRAGAIEQLRTHVERF--KLG 272
                                        5677888888775.56899******************************99...7999***7666666665..567 PP

                                        EEEEEE-----HHHHHHHHHHHHHHHHHTT-SEEEEEEESS CS
                               MeaB  92 vfiRslpsrGalGGlaaktrevvllleaaGfDvvlietvGv 132
                                         ++     +G     a  +r +++  +  G+Dv+li+t G 
  gene1521|gene1521|rna1520|rna1520 273 GHLVGFYEKGYGKDDASVARCAIQEAQHEGYDVILIDTAGR 313
                                        777888889998888999999999999***********995 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 2
                                        ESSTTHHHHHHTT-S CS
                               MeaB 130 vGvGqsevdvaevvd 144
                                         GvGqs+ d+ ++  
  gene1521|gene1521|rna1520|rna1520 400 LGVGQSNSDLSNIGS 414
                                        69*****99988765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         2   1.9e+03      76      76 ..     147     147 ..      65     217 .. 0.53
   2 !   13.5   0.0   5.8e-05     0.055       9      37 ..     225     253 ..     220     271 .. 0.93
   3 ?    4.8   0.1      0.03        28      23      89 ..     297     381 ..     282     413 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2
                                        E CS
                                        x RF
                               CbiA  76 i 76 
                                        +
  gene1521|gene1521|rna1520|rna1520 147 M 147
                                        2 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.8e-05
                                        TSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA   9 GvGKTtlaanLaralarrglrVllvDaDp 37 
                                        GvGK+t +a+++  l ++++rV    +D+
  gene1521|gene1521|rna1520|rna1520 225 GVGKSTSLAKICYWLLQNKFRVYIAACDT 253
                                        9*********************9988885 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.03
                                        HHH.TT--EEEEE.EEESSCCCCH..HTTEB-HHHH...............CCHCCCHHHHHHCHCHHHH...EEE CS
                                        xxx.xxxxxxxxx.xxxxxxxxxx..xxxxxxxxxx...............xxxxxxxxxxxxxxxxxxx.xxxxx RF
                               CbiA  23 lar.rglrVllvD.aDpqannlai..leglendiep...............dlkrllellealgkkkall.lkiag 78 
                                         a+ +g++V+l+D a+ + n  ++    ++ ++i++               +l+ + e+ +a+g     +  ki +
  gene1521|gene1521|rna1520|rna1520 297 EAQhEGYDVILIDtAGRMHNKKNLmaSLTKLIKINNpdhiiyvgealvgsdSLDHIREFNKAIGDAG--QsRKIDS 370
                                        45547********555554444446655555555558999999999998886666666666666542..1378888 PP

                                        EEEEEESS... CS
                                        xxxxxxxxxxx RF
                               CbiA  79 vvlnrvdgene 89 
                                        ++l++vd  ++
  gene1521|gene1521|rna1520|rna1520 371 ILLTKVDTVDN 381
                                        88888887644 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3      0.28   2.7e+02      33     102 ..     121     191 ..     103     214 .. 0.51
   2 !   17.0   0.0   6.4e-06     0.006       1     108 [.     221     339 ..     221     342 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.28
                                        HHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEEEEEE-SEEEETTEEEESSHHHHHHHH.. CS
                             AAA_17  33 eakrgglakardemrklpleekkelqkeaaekiaeea..kkkgvlvdghprikeqagfldglpkevleelkp 102
                                        ++++   +ka++ ++++ +++ +  +k+    i ++   + ++ lvd   +  +++g+ +  +k ++++++ 
  gene1521|gene1521|rna1520|rna1520 121 VIRKATVQKAFGLFKDE-IQVSELKDKMTTHLISKNVssQITKTLVDNITMELAEEGLESISEKAFKQKMSN 191
                                        44444444444444322.222222222222222222211345678888888888888777777777776643 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.4e-06
                                        EE-TTSSHHHHHHHHHHHH...TEE.EEEHHHHHHHHHHTTTSHSSHHHHC..........TSHHHHHHHHHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklveky...gft.hlsaGdllreeakrgglakardemr..........klpleekkelqkeaa 62 
                                        +G+ G+GK+t ++k+   +   +f  ++ a d +r+ a ++ l ++ ++++          k++ +++  + + a+
  gene1521|gene1521|rna1520|rna1520 221 VGVNGVGKSTSLAKICYWLlqnKFRvYIAACDTFRAGAIEQ-LRTHVERFKlgghlvgfyeKGYGKDDASVARCAI 295
                                        79*************85444445551568899999887655.3344455554556667777999999999999999 PP

                                        HHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                             AAA_17  63 ekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                        ++ ++e + + +l+d+  r+ +++ +++ l+ + ++  +pd+ii++
  gene1521|gene1521|rna1520|rna1520 296 QEAQHE-GYDVILIDTAGRMHNKKNLMASLT-KLIKINNPDHIIYV 339
                                        998887.78899*******988888777776.589999******97 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.22     2e+02     182     222 ..     140     181 ..     109     188 .. 0.75
   2 !   15.7   0.0   7.2e-06    0.0068      11     109 ..     224     328 ..     215     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                              VirC1 182 faalkerGmlhltlenlsaapsmrlilr.nlraaledlavla 222
                                         ++lk++   hl  +n+s++ ++ l+ +  ++ a e l++++
  gene1521|gene1521|rna1520|rna1520 140 VSELKDKMTTHLISKNVSSQITKTLVDNiTMELAEEGLESIS 181
                                        58899**99*********999999886413444555566665 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 7.2e-06
                              VirC1  11 GGaGkttalmglcsalasdgkrvalfeadenr..Pltkwkenalrkgawddacevfv....adelplleaayeeae 80 
                                         G Gk+t+l  +c +l +++ rv +  +d  r   +++ + +  r     +    +      d+ ++   a +ea+
  gene1521|gene1521|rna1520|rna1520 224 NGVGKSTSLAKICYWLLQNKFRVYIAACDTFRagAIEQLRTHVERFKLGGHLVGFYEkgygKDDASVARCAIQEAQ 299
                                        489********************9999998773357888888888888888776654222279999********** PP

                              VirC1  81 geGfdyaladtrgGsselnntiiassdll 109
                                         eG+d+ l+dt g   +  n + + ++l+
  gene1521|gene1521|rna1520|rna1520 300 HEGYDVILIDTAGRMHNKKNLMASLTKLI 328
                                        ***********998877776665555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.34   3.2e+02      98     150 ..     162     215 ..     115     221 .. 0.67
   2 !    7.0   0.0    0.0055       5.1       4      31 ..     220     247 ..     217     260 .. 0.81
   3 !    8.1   0.0    0.0025       2.3      84     146 ..     290     354 ..     276     360 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.34
                                        EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEE.E--SS--SHHHHHHHT-TT- CS
                           NTPase_1  98 viviDEiGkmElkskkfkeaveevLk.sekpvla.vihrrkdlalveeirerkdv 150
                                          ++D i  mEl  + +++  e+++k +  +vl   i+  ++++++++i+++k+v
  gene1521|gene1521|rna1520|rna1520 162 KTLVDNI-TMELAEEGLESISEKAFKqKMSNVLSrLIPSVDHERMLDKIKRHKGV 215
                                        4567777.68888888888888888844444443235555577889999988653 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0055
                                        EE--TTSSHHHHHHHHHHHH...GGGEE CS
                           NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvg 31 
                                          G  GvGK+T + k++  l ++ ++v 
  gene1521|gene1521|rna1520|rna1520 220 FVGVNGVGKSTSLAKICYWLLQNKFRVY 247
                                        56999************99988888875 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0025
                                        HHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT CS
                           NTPase_1  84 lalealrkal.seadviviDEiGkmElkskkfkeaveevLk.sekpvlavihrrk.dlalveeire 146
                                        +a  a+++a+ ++ dvi+iD  G+m  k  ++  ++++++k +++  ++ + ++   ++ +++ire
  gene1521|gene1521|rna1520|rna1520 290 VARCAIQEAQhEGYDVILIDTAGRMHNKK-NLMASLTKLIKiNNPDHIIYVGEALvGSDSLDHIRE 354
                                        455577777768999**********9875.556677888887777677666666666666666665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.7   4.4e+03      33      57 ..     148     170 ..     121     210 .. 0.55
   2 !   16.4   0.2   7.7e-06    0.0073       2      93 ..     218     352 ..     217     382 .. 0.56

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.7
                                        SSSEEEEEEEETTEEEEEEECGGCS CS
                           MMR_HSR1  33 TrdinegrvklkgkeielvDtpGli 57 
                                        T++ + ++v+ ++   +lvD    +
  gene1521|gene1521|rna1520|rna1520 148 TTHLISKNVS-SQITKTLVDNIT-M 170
                                        3334444443.223334444444.3 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 7.7e-06
                                        EEEEESTTSSHHHHHHHHH.....T..STEEESSSTTSSSSEEEEEEEETTEE....................... CS
                           MMR_HSR1   2 vaivGrpNvGKStLinalt.....g..ekaivsdkpgtTrdinegrvklkgke....................... 47 
                                        +++vG   vGKSt + +++     +  ++ i++   +    i++ r +++  +                       
  gene1521|gene1521|rna1520|rna1520 218 ICFVGVNGVGKSTSLAKICywllqNkfRVYIAACDTFRAGAIEQLRTHVE--Rfklgghlvgfyekgygkddasva 291
                                        89****************95555322212233333344444444333322..122333344444445555555566 PP

                                        .............EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT.....TTCSHHH CS
                           MMR_HSR1  48 .............ielvDtpGliegaseekglgkaflalee...adlillvvdas.....eeklkpl 93 
                                                     ++l+Dt+G ++   ++k+l  ++ +l++    d+i++v +a          +++
  gene1521|gene1521|rna1520|rna1520 292 rcaiqeaqhegydVILIDTAGRMH---NKKNLMASLTKLIKinnPDHIIYVGEALvgsdsL---DHI 352
                                        6666666666666********555...4555555555544432269999999865653332...333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       8.9   8.4e+03      74      92 ..     139     160 ..     110     190 .. 0.55
   2 !   17.5   0.0   4.2e-06    0.0039       7     133 ..     217     349 ..     211     352 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.9
                             AAA_22  74 sseellealeqalrarav...i 92 
                                        + +el ++++ +l ++ v   i
  gene1521|gene1521|rna1520|rna1520 139 QVSELKDKMTTHLISKNVssqI 160
                                        4444444444444444433333 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.2e-06
                             AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellra.lglelka......erl 73 
                                        +++ +G  G+GK+t+l+++ ++l +       + +v+   ++    +  ++l++++ r+ lg  l        +++
  gene1521|gene1521|rna1520|rna1520 217 SICFVGVNGVGKSTSLAKICYWLLQN------KFRVYiaACDTFRAGAIEQLRTHVERFkLGGHL-VgfyekgYGK 285
                                        57889******************876......666663355555555777777777765144444.3599988555 PP

                             AAA_22  74 sseell.ealeqalraravielliiDEaqhlr.s...eealeeLrsllnl.srkgvqliLvGtpel 133
                                        +   +   a+++a ++ ++  +++iD a ++  +   ++ l++L ++ n+ +   v   LvG  +l
  gene1521|gene1521|rna1520|rna1520 286 DDASVArCAIQEAQHEGYD--VILIDTAGRMHnKknlMASLTKLIKINNPdHIIYVGEALVGSDSL 349
                                        5555551666666666666..*********965257888888888888866555566666666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       5.3     5e+03      25      25 ..     150     150 ..     108     195 .. 0.54
   2 !   14.3   0.0   4.5e-05     0.042       1      85 [.     218     320 ..     218     412 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.3
                                        E CS
                                AAA  25 e 25 
                                        +
  gene1521|gene1521|rna1520|rna1520 150 H 150
                                        1 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.5e-05
                                        EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS..........................STTHHHHHHH CS
                                AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellsk..........................yvgesekkir 47 
                                        ++++G  G+GK++    ++  l   +++++   + +++                            y ++ ++  r
  gene1521|gene1521|rna1520|rna1520 218 ICFVGVNGVGKSTSLAKICYWLlqnKFRVYIAACDTFR-AgaieqlrthverfklgghlvgfyekgYGKDDASVAR 292
                                        689********776666665544433555555555555.4489999999****************88888888888 PP

                                        HHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHH CS
                                AAA  48 elfkeakekakpsilfiDEidalaksrsgseseeeerv 85 
                                          ++ea+++    +++iD + ++++++         ++
  gene1521|gene1521|rna1520|rna1520 293 CAIQEAQHEG-YDVILIDTAGRMHNKK---------NL 320
                                        8999999987.9***********9988.........33 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.019      22     124 ..     219     341 ..     203     343 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                             AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa....................eelgieastiakll 77 
                                        + +G+ G GK+t+l+++   + ++++rv ++A     A +++                    ++ g + +++a+  
  gene1521|gene1521|rna1520|rna1520 219 CFVGVNGVGKSTSLAKICYWLLQNKFRVYIAACDTFRAGAIEqlrthverfklgghlvgfyeKGYGKDDASVARCA 294
                                        569*****************************99988888883334444433333333333224444444444444 PP

                             AAA_30  78 krlkgrarlepgtllivDEagmv..dtkqlaallkaaekag.akvilvGD 124
                                            ++a+ e  +++++D ag +    + +a+l+k ++ ++  ++i vG 
  gene1521|gene1521|rna1520|rna1520 295 I---QEAQHEGYDVILIDTAGRMhnKKNLMASLTKLIKINNpDHIIYVGE 341
                                        3...33344455*********99555567999999998876688888885 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.2e+03     105     148 ..       4      51 ..       2      71 .. 0.68
   2 ?    2.2   0.0      0.15   1.4e+02       2      31 ..     223     252 ..     222     256 .. 0.89
   3 !    9.3   0.0   0.00092      0.87      93     139 ..     293     341 ..     285     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                             CLP1_P 105 gliIntpGwv.kglga..ellleliealepdvvvvldq.eellnelkr 148
                                        +++ n  G+v +++g+  ++l+++i+ l  + ++ l++ +++  e++ 
  gene1521|gene1521|rna1520|rna1520   4 FCVFNKRGLViHEEGKapDHLNQIIASLDTSKLIGLRKiRDQVMEYEI 51 
                                        688888888744455445999*****9999999999986555555544 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                             CLP1_P   2 pkdsGKSTlarlLlNyalrkgrkpvyvDlD 31 
                                         + +GKST  + ++ ++l+++ ++ +  +D
  gene1521|gene1521|rna1520|rna1520 223 VNGVGKSTSLAKICYWLLQNKFRVYIAACD 252
                                        5789******************99988777 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00092
                             CLP1_P  93 ekleenkkakasgliIntpGwvkglg..aellleliealepdvvvvldq 139
                                          ++e +  + ++++I+t G ++     +  l++li++ +pd+++++++
  gene1521|gene1521|rna1520|rna1520 293 CAIQEAQHEGYDVILIDTAGRMHNKKnlMASLTKLIKINNPDHIIYVGE 341
                                        4456667778999*******9976532389***************9986 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.9   4.3e-05     0.041      19      61 ..     136     177 ..     112     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                                        HHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS CS
                            SRP54_N  19 deedleealkeleeaLleaDVgvkvvkklienvkkkavgekkl 61 
                                        de  + e+ +++ ++L++++V+ +++k l++n+   ++ e+ l
  gene1521|gene1521|rna1520|rna1520 136 DEIQVSELKDKMTTHLISKNVSSQITKTLVDNITM-ELAEEGL 177
                                        66668888889**********************88.5554653 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     3e-05     0.029       4      78 ..     217     315 ..     216     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                             AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie..swedfldevvel.................. 59 
                                        +i+ +G +g+GK+t+++++    l+ + ++    ++ +  ++ +  ++e+++  v+ +                  
  gene1521|gene1521|rna1520|rna1520 217 SICFVGVNGVGKSTSLAKI-CYWLLQNKFR----VYIAACDTFRagAIEQLRTHVERFklgghlvgfyekgygkdd 287
                                        5899***************.4444444444....222222222222444444444444555666666677778888 PP

                             AAA_24  60 .........aaeladyktlviDtidele 78 
                                                 +a+ ++y+++ iDt++ + 
  gene1521|gene1521|rna1520|rna1520 288 asvarcaiqEAQHEGYDVILIDTAGRMH 315
                                        888888888**************99875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   9.2e-05     0.087      63     119 ..     172     235 ..     130     246 .. 0.67
   2 ?   -3.1   0.0       6.5   6.2e+03      71      97 ..     297     324 ..     290     349 .. 0.61
   3 ?   -1.3   0.0       1.9   1.8e+03      50      63 ..     370     383 ..     351     412 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.2e-05
                                        H........HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHH CS
                        RsgA_GTPase  63 e........eleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinal 119
                                                 + +++k++++++ ++ l+ s+++++ l+++k++     +++vG  GvGKSt + ++
  gene1521|gene1521|rna1520|rna1520 172 LaeeglesiSEKAFKQKMSNV-LSRLIPSVDHERMLDKIKRHKGVFSICFVGVNGVGKSTSLAKI 235
                                        222223443456666777766.6677788999999****99999999************977665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.5
                                        HHHHTTSEEEE--TTTH.TTHHHHHHHC CS
                        RsgA_GTPase  71 elealgyevllvsaktk.egleelkell 97 
                                        e ++ gy+v+l+++  + ++ ++l + l
  gene1521|gene1521|rna1520|rna1520 297 EAQHEGYDVILIDTAGRmHNKKNLMASL 324
                                        5566667776665442213444444444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.9
                                        EEEEE-GGG--HHH CS
                        RsgA_GTPase  50 vivlnKiDlleeee 63 
                                         i+l+K+D ++++ 
  gene1521|gene1521|rna1520|rna1520 370 SILLTKVDTVDNKI 383
                                        68999999998865 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3      0.43   4.1e+02      66     104 ..     145     186 ..     106     211 .. 0.55
   2 ?    5.5   0.0     0.016        15      12      40 ..     225     253 ..     217     262 .. 0.89
   3 ?    3.8   0.0     0.051        48     110     145 ..     294     328 ..     274     336 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.43
                             AAA_31  66 eknikeaiiktkvenl.dlipssidLaeaeielvelekk..e 104
                                        +k + ++i k+ ++++ + ++ +i +  ae  l ++++k  +
  gene1521|gene1521|rna1520|rna1520 145 DKMTTHLISKNVSSQItKTLVDNITMELAEEGLESISEKafK 186
                                        334444444444333345555555555555555555554332 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                             AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                        GvGK+T+  +++++l +++ +v +  +D+
  gene1521|gene1521|rna1520|rna1520 225 GVGKSTSLAKICYWLLQNKFRVYIAACDT 253
                                        9********************99887775 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.051
                             AAA_31 110 llekvkde.YDyiiiDcpPsLglltenaLvasdsvii 145
                                        ++++ ++e YD+i+iD+   +   +++ L+as + +i
  gene1521|gene1521|rna1520|rna1520 294 AIQEAQHEgYDVILIDTAGRM--HNKKNLMASLTKLI 328
                                        566666555*******98764..34555666655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.3   1.2e+03     117     154 ..     112     151 ..      64     203 .. 0.65
   2 ?   11.0   0.0   0.00044      0.42      15      85 ..     205     262 ..     200     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                             AAA_16 117 srllellkrllallsrderplvlvlDdlq...wadeaslql 154
                                        s+    l + +++++  ++ + l+ D++q     d ++ +l
  gene1521|gene1521|rna1520|rna1520 112 SSGISNLVEVIRKATV-QKAFGLFKDEIQvseLKDKMTTHL 151
                                        4444555555555555.555666666666333223333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00044
                             AAA_16  15 alervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrql 85 
                                        +l++++++ +  ++ ++G  GvGKs+ + ++   l ++++ +  + cd +              r + ++ql
  gene1521|gene1521|rna1520|rna1520 205 MLDKIKRHKGvFSICFVGVNGVGKSTSLAKICYWLLQNKFRVYIAACDTF--------------RAGAIEQL 262
                                        66667777777677799***********9999666666566655555555..............22333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3       0.1        98      15      95 ..     126     206 ..     116     213 .. 0.86
   2 ?    6.8   0.0    0.0066       6.2       2      30 ..     218     247 ..     217     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.1
                                        HHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--.HHHHHHHHHHH CS
                              AAA_5  15 laerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae.sevlnsLlsll 89 
                                         +++   ++++e+++  l++++t+  +   ++ ++ t+ lvd++ ++ a+eg   + +  ++ + s+vl++L++  
  gene1521|gene1521|rna1520|rna1520 126 TVQKAFGLFKDEIQVSELKDKMTTHLISKNVS-SQITKTLVDNITMELAEEGLESISEKAFKQKmSNVLSRLIPSV 200
                                        55555666689999999999999999999888.599999***********************999*********** PP

                                        HSSEEE CS
                              AAA_5  90 eerrll 95 
                                        +++r+l
  gene1521|gene1521|rna1520|rna1520 201 DHERML 206
                                        *99997 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0066
                                        EEEE--SSSSHHHHHHHGGGGB.S--EEEE CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyv 30 
                                        ++ vG  G+gKs+   +++  l ++++ ++
  gene1521|gene1521|rna1520|rna1520 218 ICFVGVNGVGKSTSLAKICYWLlQNKFRVY 247
                                        799***********9999999974444433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00071      0.67       3     103 ..     219     338 ..     218     340 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00071
                             AAA_33   3 llvGlpGsGKstlaerl....lkklg.avllssdtlrrrlfgtdqqskt..............dytrvldrlyqil 59 
                                         +vG++G+GKst + ++    l++   +++ + dt+r    ++ +++ +               y +   ++ ++ 
  gene1521|gene1521|rna1520|rna1520 219 CFVGVNGVGKSTSLAKIcywlLQNKFrVYIAACDTFRAGAIEQLRTHVErfklgghlvgfyekGYGKDDASVARCA 294
                                        79**********9999855543333344444445555533222222222333555555543333333334445454 PP

                             AAA_33  60 nelarkalsagrnvil.datnlsrrer...arflklarrlgvpvrivv 103
                                           +++a+ +g++vil d   +++++    a + kl + ++ p++i++
  gene1521|gene1521|rna1520|rna1520 295 ---IQEAQHEGYDVILiDTAGRMHNKKnlmASLTKLIK-INNPDHIIY 338
                                        ...88888888887774555555444412255555555.444777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   3.2      0.91   8.6e+02     104     173 ..      84     161 ..      55     210 .. 0.41
   2 ?   11.6   0.1   0.00031      0.29      22      45 ..     218     241 ..     208     409 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.91
                             AAA_23 104 tkkaklelleideleqfise.llgskki...ilnlilflgqer....feefelkdkkerleelekeleeledekkl 171
                                         kk+++++++ ++ e+  +e +l+ + +   i+nl+  + +      f  f+++ + ++l++  +     +++ ++
  gene1521|gene1521|rna1520|rna1520  84 GKKKTRNSIKGRKWEDAGNEeELNYSTSssgISNLVEVIRKATvqkaFGLFKDEIQVSELKDKMTTHLISKNVSSQ 159
                                        2333333333322222222222222222111112221111111222333333333333333322222222222222 PP

                             AAA_23 172 le 173
                                        + 
  gene1521|gene1521|rna1520|rna1520 160 IT 161
                                        22 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00031
                             AAA_23  22 tlItGpNGaGKTTildAiklaLyg 45 
                                         +++G NG GK+T l  i++ L  
  gene1521|gene1521|rna1520|rna1520 218 ICFVGVNGVGKSTSLAKICYWLLQ 241
                                        4899****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      675  (0.0376485); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 2387.88
//
Query:       gene1522|gene1522|rna1521|rna1521  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-44  150.4   0.0    4.3e-44  150.2   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.2   0.0   2.4e-48   4.3e-44       2     170 ..      52     213 ..      51     216 .] 0.96

  Alignments for each domain:
  == domain 1  score: 150.2 bits;  conditional E-value: 2.4e-48
                                        EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBES CS
                     Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlve 77 
                                        +vp+S qt+ +++e g+ +++  ++e +dl+iDGaD +d++ n+iKGgGgal++EK++ ++ak++i+i+++ K+ e
  gene1522|gene1522|rna1521|rna1521  52 YVPSSIQTALKLSEKGFMVSNPLAHEALDLYIDGADYFDKNGNMIKGGGGALTTEKLLHSMAKETIIIVQSCKYKE 127
                                        79************************************************************************** PP

                                        STTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTE CS
                     Rib_5-P_isom_A  78 klgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGV 153
                                        +++   vP+e++p++l++  + l++  g++  +R+a+gk gp++Td gn+i+Dv+ +      + + +e+k+i GV
  gene1522|gene1522|rna1521|rna1521 128 RFDGCFVPIEIIPMSLMKFVSVLKE-YGLNHLVRKATGKVGPLITDLGNCIVDVEYN------AGFISECKHICGV 196
                                        **99*******************97.5***************************993......47899******** PP

                                        EEESEE-S--SEEEEEE CS
                     Rib_5-P_isom_A 154 vetGlFlgladkvlvgk 170
                                        ve+GlF++  ++++v +
  gene1522|gene1522|rna1521|rna1521 197 VEHGLFMSNGRTIIVEE 213
                                        *******9999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1308.15
//
Query:       gene1523|gene1523|rna1522|rna1522  [L=368]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-35  121.9   1.1    2.3e-35  121.9   1.1    1.4  2  RPN7      26S proteasome subunit RPN7
    9.3e-09   35.8   0.0    3.1e-08   34.1   0.0    2.0  2  PCI       PCI domain
  ------ inclusion threshold ------
      0.045   14.4   0.6        0.3   11.8   0.1    2.7  2  Bcl-2     Apoptosis regulator proteins, Bcl-2 family


Domain annotation for each model (and alignments):
>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1       1.8   1.1e+04      26      47 ..      26      47 ..      25      50 .. 0.73
   2 !  121.9   1.1   3.9e-39   2.3e-35       1     173 [.      55     225 ..      55     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.8
                                       HHHTT-HHHHHHHHHHHHHHHH CS
                               RPN7 26 akenlgkeeirrakldlaehYl 47
                                       ak++l k  + ++++dl ++ +
  gene1523|gene1523|rna1522|rna1522 26 AKKKLEKLIVDKCMYDLYKFLV 47
                                       6777888888888888888765 PP

  == domain 2  score: 121.9 bits;  conditional E-value: 3.9e-39
                                        -HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCCCC--SHHHHHHHH CS
                               RPN7   1 DekwveelrkknekeleeLdaelkdakenlgkeeirrakldlaehYlkigdleeAlkaysrireyctslkhkidml 76 
                                        D + +e+l +  +k++eeL++  k+      ++   +   ++ae Y +++d+++ ++++++++ + +sl+ k+d++
  gene1523|gene1523|rna1522|rna1522  55 DHDRMESLLNCKNKKIEELEELRKEET--DNETYRSEVDRRIAELYSQVMDTKNGFEWMRKLIRDDMSLSLKMDIF 128
                                        667899999999999999999999855..334444455569*********************************** PP

                                        HHHHHHHHHTT-HHHHHHHHHHHHCSSS---.HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-GGGT.TTT--HH CS
                               RPN7  77 lnlirvaiffndwdlvskylekakellekggdwerknrlkvyeGlallairkfkeAaellldilstftskellsye 152
                                        l+  r+++ +++++ v++ ++ a +++e+g+dw+r+nr+kvy+Gl +++ r+fk+A  l+ ++l++f+s+e++ y+
  gene1523|gene1523|rna1522|rna1522 129 LCKARMGLILGNKKIVEESIKVADDTYERGCDWDRRNRYKVYKGLFKMMAREFKDAGVLFSEVLPSFESSEVMNYS 204
                                        **************************************************************************** PP

                                        HHHHHHHHHHHHH--HHHHHH CS
                               RPN7 153 dlavyavlcalatldRkdLka 173
                                        + + y+v+c+l+ ++Rk++++
  gene1523|gene1523|rna1522|rna1522 205 RAVRYMVFCGLLGFERKEIET 225
                                        ******************975 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.3   1.3e+04      23      32 ..      28      36 ..       6      53 .. 0.58
   2 !   34.1   0.0   5.2e-12   3.1e-08      25     104 ..     243     342 ..     187     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                                       HHHHHHHHHH CS
                                PCI 23 kdleeellad 32
                                       k+l e+l+ d
  gene1523|gene1523|rna1522|rna1522 28 KKL-EKLIVD 36
                                       222.333333 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 5.2e-12
                                        H....................HHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHH CS
                                PCI  25 l....................eeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEki 80 
                                                             ++ l +d+++   ++ + +++r+r++ qv ++y+   le +a+++++sv+ +E+ 
  gene1523|gene1523|rna1522|rna1522 243 QlatslfecnygnfmndlylfCKSLQDDVFVGRFVNLFCREMRLRVYGQVLESYRLMLLENMAQTFGVSVEYIEQD 318
                                        0444444444444444445559999999999999****************************************** PP

                                        HHHHHHTTSSSEEEETTTTEEEEC CS
                                PCI  81 lvklIrdgeirakidqesgivvfk 104
                                        l ++I +g++ +kid+ sg+++++
  gene1523|gene1523|rna1522|rna1522 319 LGEFIVEGRLWGKIDRISGVIEVT 342
                                        *********************986 PP

>> Bcl-2  Apoptosis regulator proteins, Bcl-2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   7.5e+03      24      38 ..      89     103 ..      70     114 .. 0.48
   2 ?   11.8   0.1     5e-05       0.3      13      67 ..     171     222 ..     156     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                        HH..SSHCHHHHHHH CS
                              Bcl-2  24 elseealelfakvae 38 
                                        e++++ +el+++v++
  gene1523|gene1523|rna1522|rna1522  89 EVDRRIAELYSQVMD 103
                                        332233344444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5e-05
                                        HHHHHHHCHHHHH..SSHCHHHHHHHHCCTTS--SCHHHHHHHHHHHHHHHHHHH CS
                              Bcl-2  13 qeefsrllnrlelseealelfakvaeelfsdgelnWgrvvalfafagalaerlvr 67 
                                        +  f+ +++++   ++a  lf++v+ ++ s++ +n++r v  ++f+g l  + ++
  gene1523|gene1523|rna1522|rna1522 171 KGLFKMMAREF---KDAGVLFSEVLPSFESSEVMNYSRAVRYMVFCGLLGFERKE 222
                                        44455555554...558899*******99999***************99877444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2352.88
//
Query:       gene1525|gene1525|rna1524|rna1524  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-08   33.1   0.1    1.9e-07   30.8   0.1    2.1  1  Nop       snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
       0.72   10.2   3.3       0.29   11.5   0.4    1.8  2  AvrM-A    Flax-rust effector AvrM-A


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   2.1e-11   1.9e-07     150     222 ..     141     202 ..       1     209 [. 0.76

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.1e-11
                                        HTTTT-HHHHCCCHHT---SSSC..HHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHH.HTT----SHHHHHHH CS
                                Nop 150 iqilGaekalfralkkkntpkyG..liyhselvqkatppklkkkiaRllaaKvalaaRiD.afsekdgslGkklre 222
                                        ++  G             t+ yG  l+ +++lv ka +pk+++k++R l++Kv++aa++D + s+ ++++ k++ e
  gene1525|gene1525|rna1524|rna1524 141 VMKYG-------------TKTYGspLLSQHPLVAKA-SPKNQEKLLRKLCCKVTIAAKLDfCGSNFETDFSKQMEE 202
                                        33333.............44455669********77.***********************8766666777777665 PP

>> AvrM-A  Flax-rust effector AvrM-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.54   4.8e+03     108     128 ..       3      23 ..       1      25 [. 0.69
   2 ?   11.5   0.4   3.2e-05      0.29      35     112 ..     166     247 ..     161     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.54
                             AvrM-A 108 eelkkavvalKelEKsvrnak 128
                                          ++ ++++lKel K   + k
  gene1525|gene1525|rna1524|rna1524   3 DTIQVYEENLKELYKMKDEIK 23 
                                        567778888888888766655 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.2e-05
                             AvrM-A  35 eaaEkrlddllkelykkqllefkkkkgekklkkkidviaeklkekakakgk....pidekavqrqfiKeqaklylk 106
                                        +++Ek l +l  ++     l f  +++e+ + k+++ + ++l+ + k++g     p   k  +r  iK   k+   
  gene1525|gene1525|rna1524|rna1524 166 KNQEKLLRKLCCKVTIAAKLDFCGSNFETDFSKQMEEVFNNLESNSKQEGSvlrvPLARKETRRGGIKARRKRSKS 241
                                        589999999999999999999*99**************************83333445556678899999998666 PP

                             AvrM-A 107 deelkk 112
                                         ++ ++
  gene1525|gene1525|rna1524|rna1524 242 SPQKRR 247
                                        655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1776.91
//
Query:       gene1526|gene1526|rna1525|rna1525  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-43  149.6   0.4    5.4e-34  118.1   0.1    2.0  2  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
    9.8e-05   23.0   0.0     0.0063   17.1   0.0    2.3  2  RPA_C          Replication protein A C terminal
  ------ inclusion threshold ------
      0.028   14.3   0.0      0.062   13.2   0.0    1.6  1  DUF3944        Domain of unknown function (DUF3944)
       0.16   12.3   0.0       0.34   11.3   0.0    1.5  1  Rrf2           Transcriptional regulator


Domain annotation for each model (and alignments):
>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.1   1.2e-37   5.4e-34      20     187 ..       9     165 ..       1     172 [. 0.93
   2 !   30.6   0.0     5e-11   2.2e-07     217     272 ..     172     227 ..     163     234 .. 0.85

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1.2e-37
                                        HCSSSSSHCCHHHHHHHSTTSHHHHHHHHHHHHHHCTSEECCC.STTSCECEE--CCCHHHHHTSXHHHHHHHHHH CS
                      RNA_pol_Rpc34  20 rkaseqklfsqqdLqddipslslklllsavqeLldkkllvllknsndeLvyravsreeAkkktslsedeslVysiI 95 
                                        r++  ++++ ++dL  ++p++s+ ++++ ++e l+++ ++l +  ++ L y+           +++  e  +y+ +
  gene1526|gene1526|rna1525|rna1525   9 RSR--PEGVVEEDLSLEFPKMSKVDIARELNECLKRQEISLFR-DKGVLYYKPS-------PVNIDDYELTIYNLV 74 
                                        444..89999*********************************.8888999999.......88999999******* PP

                                        HHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEEESSSTXXXXXXXXXXXXXSTTSSSS CS
                      RNA_pol_Rpc34  96 eesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiYllanLePseevTGGpwftdgelDve 171
                                         +sGneG+w + ik k+n++++++ k+L+s+esk+ iksvk++k+ ++k+Y+l++  Psee+TGG wf+d++ D+e
  gene1526|gene1526|rna1525|rna1525  75 SQSGNEGVWLKVIKDKTNMPHNLIGKVLRSMESKRIIKSVKCLKN-NRKVYVLYDEVPSEEITGGIWFQDNDVDAE 149
                                        *******************************************98.89**************************** PP

                                        THHHHHHHHHHHHHCH CS
                      RNA_pol_Rpc34 172 Fieeleeiifklvkqk 187
                                         +  + eii  +++++
  gene1526|gene1526|rna1525|rna1525 150 CVTRVLEIIQLFLEKR 165
                                        **********999987 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 5e-11
                                        SSSSTXXBXSCHHHHHHHCSTTTSSSXSHCCHHHHHHHHCHSSSCEEETTT.XXXE CS
                      RNA_pol_Rpc34 217 aagyksyptveeiakfineagitkvrLseediqqlvevLvyDgklekvkvsagyrv 272
                                         ++y+  p  eei+ ++++++i +v L  ed ++lv++Lv+Dgk+ek++++  +r+
  gene1526|gene1526|rna1525|rna1525 172 LPEYEDNPALEEIMSYVKNLNILSVPLRAEDLETLVDILVFDGKVEKLHSGSVTRY 227
                                        5689999*****************************************99944443 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.024   1.1e+02      53      88 ..       3      36 ..       1      43 [. 0.88
   2 !   17.1   0.0   1.4e-06    0.0063      47      94 ..      63     108 ..      48     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.024
                                       HHHHHHHH.SXSTTTEEHHHHHHHS.TSXHHHHHHHH CS
                              RPA_C 53 qvlnlikqspeseeGvhvdeiaqkl.rlsvndvkqav 88
                                        vl++i++   ++eGv  + ++ ++ ++s+ d+ + +
  gene1526|gene1526|rna1525|rna1525  3 SVLDFIRS---RPEGVVEEDLSLEFpKMSKVDIAREL 36
                                       69999999...9******************9998755 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.4e-06
                                        SXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHT CS
                              RPA_C  47 ltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsne 94 
                                        + + + +++nl+ q   ++eGv +++i+ k++++ n + +++++++++
  gene1526|gene1526|rna1525|rna1525  63 IDDYELTIYNLVSQ--SGNEGVWLKVIKDKTNMPHNLIGKVLRSMESK 108
                                        566777999***99..9************************9988765 PP

>> DUF3944  Domain of unknown function (DUF3944)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.062      15      30 ..     200     215 ..     197     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                            DUF3944  15 sedLedLfdiLthdkd 30 
                                         edLe+L+diL++d +
  gene1526|gene1526|rna1525|rna1525 200 AEDLETLVDILVFDGK 215
                                        69***********965 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.6e-05      0.34      16      59 ..      72     115 ..      65     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                                        HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                               Rrf2  16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59 
                                         L +++++e v ++ i +++n++++ + k+l+ ++ + ++ksv+
  gene1526|gene1526|rna1525|rna1525  72 NLVSQSGNEGVWLKVIKDKTNMPHNLIGKVLRSMESKRIIKSVK 115
                                        566777777799******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1471.19
//
Query:       gene1527|gene1527|rna1526|rna1526  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-18   65.8   8.0    8.5e-05   23.3   0.1    5.8  6  WD40         WD domain, G-beta repeat
      1e-06   28.9   0.0       0.14   12.5   0.0    4.8  6  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
      0.027   14.4   0.2       0.19   11.7   0.0    2.2  2  Imm12        Immunity protein 12
      0.038   12.9   0.0      0.059   12.3   0.0    1.2  1  PALB2_WD40   Partner and localizer of BRCA2 WD40 domain
      0.062   11.6   0.0      0.086   11.1   0.0    1.2  1  Frtz         WD repeat-containing and planar cell polarity ef
       0.57   10.2   3.0        1.6    8.8   0.2    2.9  3  Kelch_4      Galactose oxidase, central domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0    0.0001      0.31       8      32 ..      17      42 ..      12      48 .. 0.87
   2 !   23.3   0.1   2.9e-08   8.5e-05       2      38 .]      52      89 ..      49      89 .. 0.94
   3 ?    3.7   0.0     0.042   1.2e+02      13      31 ..     105     122 ..      91     125 .. 0.82
   4 !    8.7   0.1    0.0011       3.4       2      36 ..     181     216 ..     180     218 .. 0.86
   5 ?   -1.2   0.0       1.6   4.7e+03      11      29 ..     232     251 ..     223     256 .. 0.65
   6 !   17.7   0.2   1.6e-06    0.0048       2      36 ..     277     312 ..     276     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                       ESS.SSEEEEEEETTSSEEEEEETTS CS
                               WD40  8 tGH.ssvtslafspdgawlasGsdDg 32
                                       + H  ++t ++f++dg++++++++D 
  gene1527|gene1527|rna1526|rna1526 17 KCHeRPITEVKFNHDGDLIFTAGKDS 42
                                       689777****************9885 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2.9e-08
                                       EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38
                                       + +++++GH +s+ sla +  ++ l++Gs D++v +Wd
  gene1527|gene1527|rna1526|rna1526 52 SVIGEYKGHrGSIFSLAIDNKSDALMTGSADQSVILWD 89
                                       56789****999*************************9 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.042
                                        EEEEEEETTSSEEEEEETT CS
                               WD40  13 vtslafspdgawlasGsdD 31 
                                        v +l+f +dg++ +++s D
  gene1527|gene1527|rna1526|rna1526 105 VKGLDFYRDGTLCLACS-D 122
                                        6899********99999.7 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0011
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                        q +++  +H s ++ ++ s+  +++++Gs D   +i
  gene1527|gene1527|rna1526|rna1526 181 QVIKSVNAHtSKINNIRPSRCRTFFITGSTDSQSKI 216
                                        5678899**777*****************9998877 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 1.6
                                        SSEEEEE.EETTSSEEEEEE CS
                               WD40  11 ssvtsla.fspdgawlasGs 29 
                                         +v++ + f+ + + ++ G+
  gene1527|gene1527|rna1526|rna1526 232 EPVNCASiFNTNDKVICVGG 251
                                        46888886666666666665 PP

  == domain 6  score: 17.7 bits;  conditional E-value: 1.6e-06
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                        ++++++++H + ++s++++p+g++ +sG++ gtv i
  gene1527|gene1527|rna1526|rna1526 277 EKIGSYSTHfGTINSVDVHPSGRLYCSGGEEGTVSI 312
                                        56899****777************999******976 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.014        42      37      65 ..      19      47 ..      14      62 .. 0.81
   2 !   12.5   0.0   4.7e-05      0.14       2      80 ..      27     103 ..      26     112 .. 0.90
   3 ?   -0.7   0.0       0.6   1.8e+03      40      61 ..     104     124 ..     100     156 .. 0.74
   4 !    5.6   0.1    0.0066        20      49      86 ..     159     195 ..     137     250 .. 0.81
   5 ?   -1.5   0.0         1   3.1e+03      46      56 ..     240     250 ..     205     282 .. 0.71
   6 ?    4.1   0.0     0.019        58      37      66 ..     285     314 ..     241     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                        ANAPC4_WD40 37 edsevrsLaWkpdgklLavaysdgevrll 65
                                       +++ ++++++++dg l+  a +d+   ll
  gene1527|gene1527|rna1526|rna1526 19 HERPITEVKFNHDGDLIFTAGKDSIATLL 47
                                       5688****************999887776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.7e-05
                        ANAPC4_WD40   2 swcptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsls 77 
                                        +++   DLi  a +d+   + R +g  + +   +++ +++ sLa  ++   L+ + +d +v l d+ +gk+  +++
  gene1527|gene1527|rna1526|rna1526  27 KFNHDGDLIFTAGKDSIATLLRDDGSVIGEY--KGHRGSIFSLAIDNKSDALMTGSADQSVILWDVPTGKMRAQID 100
                                        6788889999999999999999999999888..899************************************9998 PP

                        ANAPC4_WD40  78 vks 80 
                                        +++
  gene1527|gene1527|rna1526|rna1526 101 IGA 103
                                        876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.6
                        ANAPC4_WD40  40 evrsLaWkpdgklLavaysdge 61 
                                         v++L +  dg+ L+ a+sd +
  gene1527|gene1527|rna1526|rna1526 104 VVKGLDFYRDGT-LCLACSDET 124
                                        588899999986.688888865 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.0066
                        ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvhslsvksekavtc 86 
                                        ++++L+   s+g +  +d  + +v++s++++++k ++ 
  gene1527|gene1527|rna1526|rna1526 159 SENFLVYCDSKGGIISVDLRNSQVIKSVNAHTSK-INN 195
                                        6778888888888888888888888888888774.544 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 1
                        ANAPC4_WD40  46 WkpdgklLava 56 
                                        ++ ++k+++v+
  gene1527|gene1527|rna1526|rna1526 240 FNTNDKVICVG 250
                                        45556666665 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.019
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlld 66 
                                        + ++++s+  +p+g+l + + ++g+v++l 
  gene1527|gene1527|rna1526|rna1526 285 HFGTINSVDVHPSGRLYCSGGEEGTVSILA 314
                                        557899999*****************9985 PP

>> Imm12  Immunity protein 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.4e-05      0.19      27      69 ..     130     173 ..     113     191 .. 0.77
   2 ?   -0.2   0.0      0.29   8.8e+02      68     134 ..     206     271 ..     192     275 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                              Imm12  27 iikmrkslkegfkkiffegldrikinlyisgdvsaycdktg.it 69 
                                        +i + ++   +fkk+f+     +ki l is +   ycd  g i 
  gene1527|gene1527|rna1526|rna1526 130 LIGILDTRSGNFKKVFMPTSSPVKILLDISENFLVYCDSKGgII 173
                                        55555666779***************************655154 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
                              Imm12  68 itvtrysrakkeyaaefcidkkywslepvlpvdkkfilfiekslislgeiiekklkaa.g.ydfdgklf 134
                                        it +  s++k     ++ ++k + + epv   +   i+  ++ +i +g+i  + + ++ g   fd+++f
  gene1527|gene1527|rna1526|rna1526 206 ITGSTDSQSKIIDFLDLSVQKTFVCEEPV---NCASIFNTNDKVICVGGINARDVTTTkGkSSFDANFF 271
                                        55555556666556666777777777765...5566888888999999998887765423256888777 PP

>> PALB2_WD40  Partner and localizer of BRCA2 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05     0.059     186     222 ..      69     105 ..      59     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                         PALB2_WD40 186 veGekdallgttvlnniviWnlktGqllkkieigesy 222
                                        ++ + dal++ ++++++++W++ tG++  +i+ig  +
  gene1527|gene1527|rna1526|rna1526  69 IDNKSDALMTGSADQSVILWDVPTGKMRAQIDIGAVV 105
                                        78899****************************9865 PP

>> Frtz  WD repeat-containing and planar cell polarity effector protein Fritz
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.9e-05     0.086     261     319 ..      63     122 ..      60     163 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.9e-05
                               Frtz 261 qvislafnpdedkLllGceDssviLydeerk.itklvkaevvPsliswhpdsaillvase 319
                                         + sla++++ d L+ G+ D+sviL+d  ++ +   + +  v + + ++ d+++ l +s+
  gene1527|gene1527|rna1526|rna1526  63 SIFSLAIDNKSDALMTGSADQSVILWDVPTGkMRAQIDIGAVVKGLDFYRDGTLCLACSD 122
                                        68899**********************876414444566666777777777777777776 PP

>> Kelch_4  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.3   1.3e+04      12      28 ..      31      47 ..      30      49 .. 0.73
   2 ?    8.8   0.2   0.00054       1.6       4      39 ..     236     276 ..     234     277 .. 0.77
   3 ?    0.2   0.1      0.27   7.9e+02      10      21 ..     292     306 ..     286     311 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.3
                            Kelch_4 12 dgtiylfGGrgedgtll 28
                                       dg+++ + G  + +tll
  gene1527|gene1527|rna1526|rna1526 31 DGDLIFTAGKDSIATLL 47
                                       57788899988887766 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00054
                            Kelch_4   4 ghsatsipdgtiylfGGrgedg......tllndlylldlstn 39 
                                        ++s++ + +++++++GG+++ +      +++ d+ ++d+ t 
  gene1527|gene1527|rna1526|rna1526 236 CASIFNT-NDKVICVGGINARDvtttkgKSSFDANFFDVVTC 276
                                        4555666.8**********98888888888888888888775 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.27
                            Kelch_4  10 i...pdgtiylfGGr 21 
                                        +   p+g++y+ GG+
  gene1527|gene1527|rna1526|rna1526 292 VdvhPSGRLYCSGGE 306
                                        434588********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2178.12
//
Query:       gene1528|gene1528|rna1527|rna1527  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-05   24.6   1.3    6.9e-05   22.9   1.3    1.8  1  Tcp10_C   T-complex protein 10 C-terminus
  ------ inclusion threshold ------
      0.036   13.9   0.3      0.044   13.6   0.3    1.1  1  dCache_1  Cache domain


Domain annotation for each model (and alignments):
>> Tcp10_C  T-complex protein 10 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.3   7.6e-09   6.9e-05      22      96 ..      59     126 ..      21     134 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.6e-09
                                        -TTSS-EEEE-TTS-EEEE-TTS-EEEEETTTTEEEEE-TTS-E..EEE-TTS-EEEE-TTS-EEEE-TTS-EEEE CS
                            Tcp10_C  22 sadgktvtvsffNgDvketledgrviYyyaeaqtthttypdgle..vlefpngqiekhykdgskeivfpdgtvksl 95 
                                          d+++ +++++ +D  +           ++++ ++  y  +++  ++ef+ngqiek++++g +ei +pdg++ + 
  gene1528|gene1528|rna1527|rna1527  59 HKDQHQNKTRYYLKDGSTYV---------VKSNQYRYLYDAKTKviTYEFSNGQIEKTFPSGLREIRYPDGSIAIK 125
                                        34444444444444443333.........222222333333333003589********************998766 PP

                                        - CS
                            Tcp10_C  96 k 96 
                                        +
  gene1528|gene1528|rna1527|rna1527 126 N 126
                                        4 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   4.9e-06     0.044      19      93 ..       5      83 ..       3     122 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.9e-06
                           dCache_1 19 anniedvldslenlaetl..asnpslqdlleepnra....neasreslqallksilksnpdisgvylvdadGqviass 90
                                        +ni++++ds+++l+++l  ++n+s++d l+e        ne++r++l+a  k+++ ++++ +   ++ +dG  +++ 
  gene1528|gene1528|rna1527|rna1527  5 QENIKEKIDSIDALMKQLeeNRNISVVDILKEEVLKlrklNEEYRKALEA--KKVMHKDQHQNKTRYYLKDGSTYVVK 80
                                       689***************66666889999998655477765555555555..55665666666666666666655532 PP

                           dCache_1 91 dps 93
                                       +  
  gene1528|gene1528|rna1527|rna1527 81 SNQ 83
                                       211 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1850  (0.103185); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1033.21
//
Query:       gene1529|gene1529|rna1528|rna1528  [L=519]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   6.6e-145  483.5   5.9   7.4e-145  483.3   5.9    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.3   5.9  4.1e-149  7.4e-145       1     490 [.      31     518 ..      31     519 .] 0.98

  Alignments for each domain:
  == domain 1  score: 483.3 bits;  conditional E-value: 4.1e-149
                                        HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLlee 76 
                                        ++++++t+lGP+ m+Km+  k++++ +TnDG++il+el++ hP a++l+e+a++qd+evGDGTt+v++La+e+l+e
  gene1529|gene1529|rna1528|rna1528  31 ISSVIRTCLGPRAMQKMVLTKINSIELTNDGNAILRELDVAHPSARSLIELAKTQDDEVGDGTTSVILLAAEILNE 106
                                        6899************************************************************************ PP

                                        HHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.H CS
                         Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.k 151
                                        + +++++++hp++i++++ kale++++a++  +v+++++   +e+ +++++ s+ sk++s  +  +++l+++Av k
  gene1529|gene1529|rna1528|rna1528 107 MTYILDKDIHPIRICNALSKALETCIKAIDGTSVSLDCS---EEARIEIINGSVVSKVCSILKVPIGRLALEAVkK 179
                                        *****************************9998999988...58889***************************88 PP

                                        CHCCCSEECSCCC.EECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCS CS
                         Cpn60_TCP1 152 lieenekeldlgr.ikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsd 226
                                        ++ ++e+++dl++ +kv+ki gg+ ++se+++G++++k++++p+m + +en+++++++ +Le++k e++t+ ++s+
  gene1529|gene1529|rna1528|rna1528 180 IYVKEENRCDLKSnMKVEKILGGNFMESEVMDGILINKDIIHPQMRRVIENPRIIIIESPLEYKKGESQTSYEFSK 255
                                        888888*****988************************************************************** PP

                                        CCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGG CS
                         Cpn60_TCP1 227 aeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssle 302
                                         +++++ ++ ee+q++e++eki++ + ++v+c+kgi+dlal++l +n+i +lrr+kk+d+ rl+ka+Ga+ vs++e
  gene1529|gene1529|rna1528|rna1528 256 NNDFTRALEIEEEQVREMCEKIVAVKPDIVICEKGISDLALSILFENNITGLRRLKKTDISRLSKACGARSVSRPE 331
                                        **************************************************************************** PP

                                        GGGCGC-EEEEEE.EECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTT CS
                         Cpn60_TCP1 303 dltpeelGtakkv.eeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGG 377
                                        dl+++++Gt + + e  k+g+e+++ ++++ ++k++++++rg+t+++l+e+er+  dA++v+k+++ ++k++pGGG
  gene1529|gene1529|rna1528|rna1528 332 DLEEKHVGTSCGLfEYVKYGEEYYCKFSKCINPKACSVVIRGPTKDILNELERNFMDAVKVAKSIFISPKLCPGGG 407
                                        **********9999************************************************************** PP

                                        CHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTS.XHHHHHHHHHHHHHTTXTTEEEETTTTCEE CS
                         Cpn60_TCP1 378 atelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGl.dpievlaklraahnkgekelgidvesgeii 452
                                        a+e+++a++l ++a  +++ e+ ++  +a+AL +ip +L eN+G+ +p e ++ l+++h+++   +g++  +gei+
  gene1529|gene1529|rna1528|rna1528 408 AVEMAMARELIRNA-GDDEIEAEVFSRVASALAIIPSILLENSGVfNPLEAITLLEKKHEEDS-FYGVNGITGEIV 481
                                        **********5555.58999************************99****************9.************ PP

                                        ECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                         Cpn60_TCP1 453 dlveagvvDplkvkrqalksAteaastiLrideiikak 490
                                        d  +  v++p++vk+q++ksA ea+s++Lrid ii+ k
  gene1529|gene1529|rna1528|rna1528 482 DTRN-LVLEPYAVKSQCIKSAIEAVSQLLRIDGIIESK 518
                                        *966.5*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2887.85
//
Query:       gene1530|gene1530|rna1529|rna1529  [L=1141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.7e-130  434.1   0.0   6.8e-130  433.6   0.0    1.2  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    4.2e-61  206.0   0.0    6.9e-61  205.3   0.0    1.3  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
      4e-44  150.5   0.0      7e-44  149.7   0.0    1.4  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    1.2e-31  109.0   1.4    2.3e-31  108.0   0.3    2.2  2  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.1e-27   96.0   0.0    2.5e-27   94.8   0.0    1.7  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    6.8e-24   83.9   1.7      4e-23   81.5   0.4    2.8  3  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    3.1e-16   59.7   1.0    3.1e-16   59.7   1.0    1.9  2  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.027   14.7   0.7       0.77   10.1   0.2    2.7  2  MlaD            MlaD protein


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.6   0.0    3e-133  6.8e-130       1     390 []     678    1048 ..     678    1048 .. 0.93

  Alignments for each domain:
  == domain 1  score: 433.6 bits;  conditional E-value: 3e-133
                                         HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGG CS
                     RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekge 74  
                                         +a+ +p+++h+qspr+++q+am+kqa+giy++n   r+++ +++l ++qkPlv+t+ ++e+++        ++e
  gene1530|gene1530|rna1529|rna1529  678 CASTIPFPDHNQSPRNTYQSAMGKQAMGIYATNFLLRMDTLSNILFYPQKPLVTTK-SMEYLR--------FKE 742 
                                         6999****************************************************.******........*** PP

                                         S-SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS-.--.-S--..-.....-SS- CS
                     RNA_pol_Rpb2_6   75 lalGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklge.eeitrdipnv.....seea 142 
                                         l++Gqna+VA+++y+GYn+ED+ii+n++++dr++f+s+++++y+ + +  + g  ee++ ++++      ++ +
  gene1530|gene1530|rna1529|rna1529  743 LPSGQNALVAIACYSGYNQEDSIIMNQSAIDRGLFRSFFYRTYTDQESMSRPGVnEEFC-KPNRGsvlrmKNLN 815 
                                         ******************************************88887666666636655.5544458999999* PP

                                         GGGS-TTSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE... CS
                     RNA_pol_Rpb2_6  143 lkkLdedGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsr 216 
                                         ++kLdedG++++g +v+ +d+l+gk+t     l pe    r+ +++    +kd+s+ ++++e+g+Vd+v+v   
  gene1530|gene1530|rna1529|rna1529  816 YNKLDEDGLISPGVRVTGDDVLIGKIT---PILDPE----RSTKEAPVYVYKDSSTAMRRTETGIVDTVIV--- 879 
                                         *************************94...233332....223334444589*******************... PP

                                         ....EE-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTT CS
                     RNA_pol_Rpb2_6  217 ekgdelkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtig 290 
                                              ++++++k+ kv++++ R +q+GDKfasrh+qKG+++++l+qeDmPf++dGiv+Di++NP+++PSRmtig
  gene1530|gene1530|rna1529|rna1529  880 -----TNKDGYKFSKVKIRSGRIPQMGDKFASRHAQKGTIGITLRQEDMPFTSDGIVPDIIINPHAIPSRMTIG 948 
                                         .....78899**************************************************************** PP

                                         HHHHHHHHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS-- CS
                     RNA_pol_Rpb2_6  291 qllEtllgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhl 364 
                                         +l+E+llgk++a++g++ dat+F+g + +ei+  L++ g++++G ev+y+G+tG+kl+a+if+G++Yy++Lkh+
  gene1530|gene1530|rna1529|rna1529  949 HLIECLLGKVSAMSGEEGDATPFSGMSVNEISTRLKSYGFQQRGLEVMYNGMTGRKLRAQIFFGPTYYQRLKHM 1022
                                         ************************************************************************** PP

                                         CCCS----SS--B-TTT--B-SCGGG CS
                     RNA_pol_Rpb2_6  365 vedKihaRstGpyslltqQPlgGkaq 390 
                                         v+dKihaR++Gp + lt+QP++G+++
  gene1530|gene1530|rna1529|rna1529 1023 VDDKIHARARGPLQILTRQPVEGRSR 1048
                                         ************************86 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.3   0.0   3.1e-64   6.9e-61       1     203 []      22     414 ..      22     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: 205.3 bits;  conditional E-value: 3.1e-64
                                        CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSC...EEEEEEEEEEESCSS.ECTTSCEEES.HHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgee...lelkfvsirlgkPvv.desdasereiyPkearl 72 
                                        gLv+qqldSF++fv+++++++i+e+ ai +++ ++  +e    + + f++i+++kP + +esd+++ +++P+ear+
  gene1530|gene1530|rna1529|rna1529  22 GLVRQQLDSFDQFVRTKMQEVINENPAIIVQSAPTAGTEIqkrITVRFGQIYVSKPPIyTESDGRTITVFPNEARI 97 
                                        69**************************999988754433567************865167*************** PP

                                        CTSBXEEEEEEEEEEEECCCC.TCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCE CS
                                        xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1  73 rnltYsaplyvklklvvyekd.nkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGte 147
                                        r+ltY +pl++++ + ++++   +++ k+++v  G lP+Mlrs++cvl+++ +++l++l+Ecp+dqGGyFi+nG+e
  gene1530|gene1530|rna1529|rna1529  98 RDLTYASPLFIDVIKETVSELgVVDKHKYSRVPFGSLPVMLRSSYCVLHGLGDKDLIDLGECPYDQGGYFIVNGSE 173
                                        ************988886554699999************************************************* PP

                                        EEEXEEEE.................................................................... CS
                                        xxxxxxxx.................................................................... RF
                     RNA_pol_Rpb2_1 148 kvivaqek.................................................................... 155
                                        kvivaqe+                                                                    
  gene1530|gene1530|rna1529|rna1529 174 KVIVAQERmasntvyvfkkaqpatythyaeirsvpekssrnpstlsmklcrspgairvslplvkqdiplfvlyral 249
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                     RNA_pol_Rpb2_1 156 ............................................................................ 155
                                                                                                                    
  gene1530|gene1530|rna1529|rna1529 250 gflsdkeiidhilyedddemfellkesieegtvvqdqnvaldyigkrsapvgtpqekritiardllakevlphigt 325
                                        **************************************************************************** PP

                                        .........................................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSS CS
                                        .........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1 156 .........................................laGeLlaslfrvllkklerdvkerlqksleklddl 190
                                                                                 l G+Llaslfr+l+kkl  d  +++qk++e+++++
  gene1530|gene1530|rna1529|rna1529 326 qefcetkkayfigyivqrlllvalgrrnpddrdhygkkrmdLSGPLLASLFRTLFKKLCADTTRHMQKCIENGREF 401
                                        **************************************************************************** PP

                                        SHHHHSCSHHHHH CS
                                        xxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1 191 mlqllvnakpita 203
                                        + +l ++a+ it+
  gene1530|gene1530|rna1529|rna1529 402 NIALGLKASIITQ 414
                                        **********996 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0   3.1e-47     7e-44       1     190 []     183     366 ..     183     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 3.1e-47
                                        -TSCEEEEE-SSSSSE......SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHH CS
                     RNA_pol_Rpb2_2   1 rsngiyvekekdknki......satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIl 70 
                                        +sn++yv+k++++  +      +++  +s+   + + +kl ++ + ++++++ +k++ip++++ +Alg++sd+eI 
  gene1530|gene1530|rna1529|rna1529 183 ASNTVYVFKKAQPATYthyaeiRSVPEKSSRNPSTLSMKLCRSPGAIRVSLPLVKQDIPLFVLYRALGFLSDKEII 258
                                        69************999999955555666666788899************************************** PP

                                        HHHTSSSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHH.CSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTT CS
                     RNA_pol_Rpb2_2  71 ericydsedsqlleelleeleekeeiqtqeealdyigk.vvalrrgeearlqsareilqkrydlgeigreklnkhl 145
                                        ++i y ++d+++ e+l+e+ ee +++q+q++aldyigk +  ++ ++e+r++ ar++l          +e+l+ h+
  gene1530|gene1530|rna1529|rna1529 259 DHILY-EDDDEMFELLKESIEEGTVVQDQNVALDYIGKrSAPVGTPQEKRITIARDLLA---------KEVLP-HI 323
                                        *****.99******************************99999**************95.........99999.** PP

                                        TTSSSTCHH..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                     RNA_pol_Rpb2_2 146 glseslenkrlkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                        g++e +e+k  ka++i+y+++rLl+++lgrr++DD+Dh+g+kR +
  gene1530|gene1530|rna1529|rna1529 324 GTQEFCETK--KAYFIGYIVQRLLLVALGRRNPDDRDHYGKKRMD 366
                                        *********..********************************75 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.5   5.5e+03       5      23 ..     616     634 ..     614     670 .. 0.48
   2 !  108.0   0.3     1e-34   2.3e-31       1      84 [.    1050    1137 ..    1050    1140 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                                        EEHHHHHHHHHHTBHHHHH CS
                     RNA_pol_Rpb2_7   5 fGEMErdaliayGaaalLk 23 
                                         GE   d li+ G  ++L 
  gene1530|gene1530|rna1529|rna1529 616 RGEIKWDNLIGEGFIEFLD 634
                                        5666666666666555553 PP

  == domain 2  score: 108.0 bits;  conditional E-value: 1e-34
                                         BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE....EBTTTTCSSSEEEEEEEHHHHH CS
                     RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan....eCkivkseekiekveipeafkl 70  
                                         GGlrfGEMErd++i++Ga+a+Lkerl++ SDa++++vc+ c+lla+      eCk +++++++++veip+afkl
  gene1530|gene1530|rna1529|rna1529 1050 GGLRFGEMERDCIISHGASAFLKERLMDVSDAYSCYVCNLCGLLAMGGtkvnECKGCNNTTNVSMVEIPYAFKL 1123
                                         9*******************************************99657888********************** PP

                                         HHHHHHHTTBEEEE CS
                     RNA_pol_Rpb2_7   71 LlqeLqslgialkl 84  
                                         L+qeL++++ia+++
  gene1530|gene1530|rna1529|rna1529 1124 LIQELMGMNIAPRI 1137
                                         ***********997 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   1.1e-30   2.5e-27       1      68 []     440     504 ..     440     504 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 1.1e-30
                     RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                        qvl+r+n++s+lshlrrv+++   ++ke k +++R+lh++hwG++Cp+eTPEG+ cGlvk+L+l+a++
  gene1530|gene1530|rna1529|rna1529 440 QVLNRYNFVSTLSHLRRVNTP---IEKEGKLAAPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMAYI 504
                                        89*******************...******************************************87 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   7.2e+03      14      29 ..     444     459 ..     439     468 .. 0.76
   2 !   81.5   0.4   1.8e-26     4e-23       1      61 [.     539     599 ..     539     600 .. 0.99
   3 ?   -0.7   0.0       0.8   1.8e+03      18      31 ..     608     620 ..     604     653 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                                        HCCHHHHHHHHCCTTS CS
                     RNA_pol_Rpb2_4  14 pkklvetlRelRRkgk 29 
                                          ++v+tl +lRR + 
  gene1530|gene1530|rna1529|rna1529 444 RYNFVSTLSHLRRVNT 459
                                        568999*******654 PP

  == domain 2  score: 81.5 bits;  conditional E-value: 1.8e-26
                                        EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE- CS
                     RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiV 61 
                                        VfvNG+++G+++dp +l+++l+ lRR+ +i++evsiv+++++ke++i +D+GR cRPl++V
  gene1530|gene1530|rna1529|rna1529 539 VFVNGVWVGIHSDPVYLIKSLKLLRRSLEIDKEVSIVRDIREKEIRIQSDAGRPCRPLMVV 599
                                        9***********************************************************9 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.8
                                        HHHHHHHCCTTSS- CS
                     RNA_pol_Rpb2_4  18 vetlRelRRkgkis 31 
                                        +e++R+lRR g+i+
  gene1530|gene1530|rna1529|rna1529 608 IEDIRKLRR-GEIK 620
                                        789*****9.5554 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         8   1.8e+04      45      53 ..     192     200 ..     177     201 .. 0.59
   2 !   59.7   1.0   1.4e-19   3.1e-16       1      58 []     621     671 ..     621     671 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8
                                        TSSSST-SE CS
                     RNA_pol_Rpb2_5  45 nskshtyTH 53 
                                        +++  tyTH
  gene1530|gene1530|rna1529|rna1529 192 KAQPATYTH 200
                                        334449999 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.4e-19
                                        HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST.-SSTTTSS--TTSSSST-SEEES-G CS
                     RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleks.reekealeekenskshtyTHcEIhP 58 
                                        wd+L+ eg +E+lD+eEEe +mIam+ + l+++ ++ +       + k   yTHcEIhP
  gene1530|gene1530|rna1529|rna1529 621 WDNLIGEGFIEFLDVEEEEMSMIAMSTKVLNDEcKNSS-------DVKI-SYTHCEIHP 671
                                        ******************************99944333.......5566.********9 PP

>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.12   2.6e+02      14      60 ..     532     577 ..     529     634 .. 0.61
   2 ?   10.1   0.2   0.00034      0.77      14      61 ..     823     875 ..     818     905 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.12
                               MlaD  14 gLkvgapVryrGvtvGrVts.itldpdtrrvtvtvdldkksetsiped 60 
                                         L+  ++V ++Gv vG  ++ ++l +  ++ +  +++d  +e+si +d
  gene1530|gene1530|rna1529|rna1529 532 QLSTATKVFVNGVWVGIHSDpVYLIKSLKLLRRSLEID--KEVSIVRD 577
                                        588899999****9997554247777777777777777..55555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00034
                               MlaD  14 g.LkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsiped.....s 61 
                                        g +++g +V+   v +G++t i ldp++ + ++ v ++k+s+t +++       
  gene1530|gene1530|rna1529|rna1529 823 GlISPGVRVTGDDVLIGKITPI-LDPERSTKEAPVYVYKDSSTAMRRTetgivD 875
                                        559*******************.***9988899999999999999876555540 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.84u 0.37s 00:00:01.21 Elapsed: 00:00:00.54
# Mc/sec: 6319.51
//
Query:       gene153|gene153|rna153|rna153  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-09   36.8   0.7    5.1e-09   36.2   0.7    1.3  1  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
    0.00052   19.9   0.7    0.00084   19.3   0.7    1.3  1  zf-C2H2_6    C2H2-type zinc finger
  ------ inclusion threshold ------
      0.016   15.5   0.5      0.026   14.9   0.5    1.3  1  zf-met       Zinc-finger of C2H2 type


Domain annotation for each model (and alignments):
>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.7   8.6e-13   5.1e-09       1      27 []      55      81 ..      55      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 8.6e-13
                                   ECBBTTTTBBBSSHHHHHCCTTSHHHH CS
                    zf-C2H2_jaz  1 qfYCvlCdKyFksenaldnHlkSKkHK 27
                                   qfYC +Cd++F+se +l  H kS  H+
  gene153|gene153|rna153|rna153 55 QFYCYECDRHFISEDVLIGHRKSSLHR 81
                                   8*************************7 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.7   1.4e-07   0.00084       4      26 ..      58      82 ..      56      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-07
                      zf-C2H2_6  4 CsvCsksFpslqaLggHkks..Hrk 26
                                   C +C++ F s + L+gH+ks  Hrk
  gene153|gene153|rna153|rna153 58 CYECDRHFISEDVLIGHRKSslHRK 82
                                   99****************7659987 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   4.3e-06     0.026       1      25 []      56      80 ..      56      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-06
                         zf-met  1 fyCelCnvtfnsesqlksHlqGKkH 25
                                   fyC  C++ f se +l+ H ++  H
  gene153|gene153|rna153|rna153 56 FYCYECDRHFISEDVLIGHRKSSLH 80
                                   8******************988666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 585.95
//
Query:       gene1531|gene1531|rna1530|rna1530  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-20   73.0   4.0    2.2e-20   72.7   4.0    1.1  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
     0.0055   17.1   0.1     0.0085   16.4   0.1    1.2  1  Histone        Core histone H2A/H2B/H3/H4
     0.0064   16.5   0.1      0.012   15.6   0.0    1.5  1  Bromo_TP       Bromodomain associated
  ------ inclusion threshold ------
      0.079   13.1   0.1      0.099   12.8   0.1    1.3  1  CENP-T_C       Centromere kinetochore component CENP-T histon


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   4.0     5e-24   2.2e-20       2      65 .]      14      78 ..      13      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 5e-24
                                       XXXHHHHHHHHHCC.TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                      CBFD_NFYB_HMF  2 eLPiarvkkImksd.pdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                       +LPia++ kImk+  p+++k+akdAke++++++ efi  ++ +A eic+ e rKt+++e++  A+
  gene1531|gene1531|rna1530|rna1530 14 SLPIANISKIMKKPiPKEAKVAKDAKEIMQKSAGEFIAIITCRAKEICESEARKTVTGEDLIRAM 78
                                       8************************************************************9987 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.9e-06    0.0085      58     128 ..      11      78 ..       5      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                                        XSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHH CS
                            Histone  58 tdlliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlAr 128
                                        td+  + + +++++++      ++ ++ ++a +++q+ +  +++ ++ +A  +++   R+T+t +D+  A+
  gene1531|gene1531|rna1530|rna1530  11 TDRSLPIANISKIMKK---PIPKEAKVAKDAKEIMQKSAGEFIAIITCRAKEICESEARKTVTGEDLIRAM 78 
                                        4555555555555554...45579******************************************98776 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.8e-06     0.012      30      71 ..      40      81 ..      33      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHT CS
                           Bromo_TP 30 EtLteiaqkYirelgeqaksfaehagRseptlkDvvltLqel 71
                                       E +++ a ++i+ ++  ak+ +e ++R ++t +D++++++el
  gene1531|gene1531|rna1530|rna1530 40 EIMQKSAGEFIAIITCRAKEICESEARKTVTGEDLIRAMDEL 81
                                       677888999*******************************98 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.2e-05     0.099       6      74 ..      13      78 ..       9     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.2e-05
                           CENP-T_C  6 pslPaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLm 74
                                        slP a ++k+ k+      ++ak+ k+a + ++k+  +f+  ++   +   +   RKt+  +D+i  m
  gene1531|gene1531|rna1530|rna1530 13 RSLPIANISKIMKKPIP---KEAKVAKDAKEIMQKSAGEFIAIITCRAKEICESEARKTVTGEDLIRAM 78
                                       47899999998877644...589******************************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 705.35
//
Query:       gene1532|gene1532|rna1531|rna1531  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-15   56.3   0.0    1.1e-14   55.1   0.0    1.5  1  RNase_PH  3' exoribonuclease family, domain 1
  ------ inclusion threshold ------
       0.14   12.4   0.0        5.7    7.2   0.0    2.7  3  DUF4242   Protein of unknown function (DUF4242)


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   1.2e-18   1.1e-14       6     132 .]       5     121 ..       2     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.2e-18
                                        EEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHH CS
                           RNase_PH   6 sietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrl 81 
                                        +  +gv++++ GS+++++++t+v + v+gp+ + ++ e d+ +  ldv+ +   ++              +  sr+
  gene1532|gene1532|rna1531|rna1531   5 KSMIGVIPHCTGSSRFSYNNTTVFCIVHGPSDAISRHE-DPEKAFLDVRWK--DMVLI------NGRIYDKYFSRV 71 
                                        5568***************************9944455.544433777776..44422......234577899*** PP

                                        HHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                           RNase_PH  82 leralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                        +er +++ i+le  +  ti+i   v+ +   + l +++naa lALad gip
  gene1532|gene1532|rna1531|rna1531  72 VERVISKNIILELDAWKTIQIIFNVVGEAR-NALFCAVNAALLALADGGIP 121
                                        ***************99*************.*******************9 PP

>> DUF4242  Protein of unknown function (DUF4242)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00064       5.7      38      62 ..      18      41 ..      15      48 .. 0.80
   2 ?    1.5   0.0     0.038   3.4e+02      31      53 ..      88     110 ..      74     111 .. 0.83
   3 ?   -1.1   0.0      0.24   2.2e+03       9      28 ..     145     165 ..     138     181 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00064
                                       EEEETTTTEEEEEEE-S-HHHHHHH CS
                            DUF4242 38 syvtedkgkvfClyeApdeeavreh 62
                                       s ++ ++++vfC++ +p+  a+ +h
  gene1532|gene1532|rna1531|rna1531 18 SRFSYNNTTVFCIVHGPSD-AISRH 41
                                       56788999*********95.55555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.038
                                        GT-EEEEEEEETTTTEEEEEEE- CS
                            DUF4242  31 egvqwlrsyvtedkgkvfClyeA 53 
                                        + +q +   v e ++  fC ++A
  gene1532|gene1532|rna1531|rna1531  88 KTIQIIFNVVGEARNALFCAVNA 110
                                        67899999999********9998 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.24
                                        TT.--HHHHHHHHHHHHHHHG CS
                            DUF4242   9 gg.itaeelaaaaakslavla 28 
                                        ++ i+   ++a+++k+++  +
  gene1532|gene1532|rna1531|rna1531 145 ENvIDSHSFEAISRKNIESAK 165
                                        445777778888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1403.28
//
Query:       gene1533|gene1533|rna1532|rna1532  [L=825]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-59  200.2   0.0    4.4e-42  144.0   0.0    2.4  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    1.2e-51  175.1   0.0    7.2e-51  172.5   0.0    2.1  2  Helicase_RecD    Helicase
    2.9e-24   84.8   0.1    1.3e-23   82.7   0.0    2.2  2  DUF1726          Domain of unknown function (DUF1726)
    1.4e-19   70.7   1.4    9.8e-19   68.0   0.7    2.6  2  tRNA_bind_2      Possible tRNA binding domain
    0.00092   19.4   0.0     0.0069   16.6   0.0    2.2  2  Acetyltransf_1   Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.073   13.5   0.0       0.21   12.0   0.0    1.8  1  Acetyltransf_7   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0   0.0   1.5e-45   4.4e-42       2     138 ..     485     614 ..     484     619 .. 0.94
   2 !   54.9   0.0   2.5e-18   7.6e-15     161     227 .]     613     679 ..     608     679 .. 0.92

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 1.5e-45
                    GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkek.kklpevlcvvqvalEGkiskesvknslsrgkrasGdl 76 
                                        +++l++ssHY+nsPnDLq+l+D+P+h++++L++p++++ k++p+v+c +q+++EGk+ ++        ++ ++G+l
  gene1533|gene1533|rna1532|rna1532 485 MFSLFISSHYRNSPNDLQILADSPRHEILALVTPVEDNgKDIPKVICSLQISFEGKCART--------EHLREGNL 552
                                        899*********************************999*****************9987........67789*** PP

                    GNAT_acetyltr_2  77 ipwtlsqqfqdeefaslsGaRivRiAvhpelqkmGYGsralellekyyegklssleeeeeke 138
                                        ipw++s+++ d +f +  G+RivRiAvhpe+ +mGYG+  l+ll+++++ + +++   ++k+
  gene1533|gene1533|rna1532|rna1532 553 IPWVVSEEHLDPSFLDTYGIRIVRIAVHPEYVGMGYGTMSLNLLINHLSSHSKDIYLMKKKN 614
                                        ************************************************99999887666665 PP

  == domain 2  score: 54.9 bits;  conditional E-value: 2.5e-18
                    GNAT_acetyltr_2 161 prkelpplllklseekpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsle 227
                                        +++ ++ ll + ++  ++++ ++g+sfG+t++L++FW++++f pv ++qt ++ tGEhs i++rsl+
  gene1533|gene1533|rna1532|rna1532 613 KNEGENVLLHRIDDILIPQVGWIGASFGITESLCRFWEKSKFIPVGIKQTVTQETGEHSGIFIRSLN 679
                                        4556778899999999************************************************985 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.28   8.3e+02      53      96 ..      74     118 ..      33     136 .. 0.72
   2 !  172.5   0.0   2.4e-54   7.2e-51       2     177 .]     259     446 ..     258     446 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.28
                      Helicase_RecD  53 lglkeeekkkkaekaelrvrkqrieyiapdellklkeqa.dllvv 96 
                                         + +e ek++++++ +l +r+++ie+i+ +e  +   ++ d+l+ 
  gene1533|gene1533|rna1532|rna1532  74 RQKNEVEKEESEDDLALFIRGNEIEFIEYKESERILGRTvDMLIL 118
                                        333446667777778888889999999999887754432366665 PP

  == domain 2  score: 172.5 bits;  conditional E-value: 2.4e-54
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke...........eekkkkaek 66 
                                        +tA+RGRGKSaalG+ +a++++ g  ++++++p  envkt+f fl++gle+lg+k+            +k+  ++ 
  gene1533|gene1533|rna1532|rna1532 259 ITASRGRGKSAALGISIAQAVNLGLLSVYIASPAIENVKTVFLFLIAGLERLGYKRyvdfkiiyqfrGNKRFMQKI 334
                                        9*******************************************************88888887766333333333 PP

                      Helicase_RecD  67 aelrvrkqrieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlk 142
                                          +  rkq iey++p + lk+    dl+v+DEAAaipl+++  l+  ++ v++atT++GYEGtGr+fs+k+ ++l+
  gene1533|gene1533|rna1532|rna1532 335 EFIGGRKQIIEYFNPMNELKYY--PDLIVIDEAAAIPLTYITGLI-FPNFVIMATTINGYEGTGRAFSVKLSETLR 407
                                        556666**********999987..5********************.999*************************** PP

                      Helicase_RecD 143 ke....kkrelreleleepiRyaegdplEkwlndlLlLd 177
                                        k+    ++  ++e+ ++e+iRy ++dp+E+wl+++LlLd
  gene1533|gene1533|rna1532|rna1532 408 KSsaetNSFVYKEMAMKESIRYGQNDPVENWLYKVLLLD 446
                                        997777666799*************************97 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.0   4.3e-27   1.3e-23       1      93 []     102     191 ..     102     191 .. 0.91
   2 ?   -2.2   0.0       1.4   4.1e+03      72      85 ..     690     703 ..     673     706 .. 0.76

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 4.3e-27
                            DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlyt...dfhkklvveplteevkk 73 
                                        ykese++LG+t+d+l+l++feal+Pn+++  +etVrGGG+iilll+++++ ++l +   d+h+k+       e+++
  gene1533|gene1533|rna1532|rna1532 102 YKESERILGRTVDMLILQDFEALSPNLIATSMETVRGGGAIILLLDSTHSIETLVSrksDIHEKIG------EFEP 171
                                        9***************************************************99985556666655......7899 PP

                            DUF1726  74 rfnkrfirklkehegilivd 93 
                                        r+nkr++++l +++ +l++d
  gene1533|gene1533|rna1532|rna1532 172 RYNKRLFKSLLNSNFALFLD 191
                                        ************99888876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                            DUF1726  72 kkrfnkrfirklke 85 
                                        +++f +rf+ +l++
  gene1533|gene1533|rna1532|rna1532 690 NQNFMARFVGQLSN 703
                                        57899999988876 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.42   1.2e+03       3      46 ..     167     210 ..     166     222 .. 0.72
   2 !   68.0   0.7   3.3e-22   9.8e-19       4     143 ..     688     811 ..     686     820 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.42
                                        HHHHHHHHHH.HHHHHHHHSS------S----------------- CS
                        tRNA_bind_2   3 gafakdFrkR.flsLLsyqFrkfeavlaLsilesknkgeklekse 46 
                                        g+f   ++kR f sLL ++F  f     L+il++ +k++ + ++ 
  gene1533|gene1533|rna1532|rna1532 167 GEFEPRYNKRlFKSLLNSNFALFLDD-QLNILDNISKLDIQGPKV 210
                                        57777888995678******999765.589999888776555555 PP

  == domain 2  score: 68.0 bits;  conditional E-value: 3.3e-22
                                        HHHHHHHHHHHHHHHHHSS------S--------------------------------HHHHHHHHHHHHS---HH CS
                        tRNA_bind_2   4 afakdFrkRflsLLsyqFrkfeavlaLsilesknkgeklekseekkeltkeeldellspfDlkRLesYannllDYh 79 
                                         + ++F  Rf+  Ls +F+k+ ++l+Ls+l+++  g+                ++++s+ D+ R+ + a   +D +
  gene1533|gene1533|rna1532|rna1532 688 GYNQNFMARFVGQLSNSFQKLGPSLSLSLLNNSIVGR--------------GRATYFSSDDISRIRMAAAGKIDLN 749
                                        599****************************998654..............3468********************* PP

                                        HHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHHHHT--SSHHHHHHHHHH CS
                        tRNA_bind_2  80 vilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddlekeLnlpsnQvlalFvkii 143
                                        +++D++p+++++yF g+l+   +Ls +++++Ll +G Q+ks+d++++ L l+  Q+  +++k++
  gene1533|gene1533|rna1532|rna1532 750 LVTDIIPDISRMYFYGKLN--QDLSVLRKSVLLMVGCQNKSIDAVAELLTLKPFQINNILTKVL 811
                                        *******************..99********************************999998876 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.48   1.4e+03      15      46 ..      78     110 ..      65     130 .. 0.73
   2 !   16.6   0.0   2.3e-06    0.0069      58      99 ..     569     609 ..     517     620 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.48
                                        HHHHHHHHHHHHHHHSTTC.EEEEEEETTEEEE CS
                     Acetyltransf_1  15 pnedaseeefeesfsleae.gllvaeedgeliG 46 
                                        + e+++ e+    f++ +e +++ ++e ++++G
  gene1533|gene1533|rna1532|rna1532  78 EVEKEESEDDLALFIRGNEiEFIEYKESERILG 110
                                        333333333455577799978888999999999 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.3e-06
                                        TTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE CS
                     Acetyltransf_1  58 ggvayieslaVspeyrgkGlGsaLlealeerareegikkivl 99 
                                        +  + i ++aV+pey g+G+G++ l+ l+ ++ ++  k i+l
  gene1533|gene1533|rna1532|rna1532 569 TYGIRIVRIAVHPEYVGMGYGTMSLNLLINHLSSH-SKDIYL 609
                                        4556788**********************999887.333455 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     7e-05      0.21      25      48 ..     572     595 ..     528     622 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                                        TCTEEEEE-GGGTTSSHHHHHHHH CS
                     Acetyltransf_7  25 aeitrlaVdpeyrgkGiGraLlea 48 
                                          i r+aV+pey g G+G+  l++
  gene1533|gene1533|rna1532|rna1532 572 IRIVRIAVHPEYVGMGYGTMSLNL 595
                                        35667*************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (825 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 5024.14
//
Query:       gene1534|gene1534|rna1533|rna1533  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-14   53.3   2.3    2.4e-14   52.8   2.3    1.3  1  zf-U1        U1 zinc finger
  ------ inclusion threshold ------
       0.49   10.8   4.5        4.8    7.7   0.6    2.3  2  zf-met       Zinc-finger of C2H2 type
        2.4    8.6   5.7         21    5.6   5.7    2.1  1  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding


Domain annotation for each model (and alignments):
>> zf-U1  U1 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   2.3   4.1e-18   2.4e-14       1      38 []       1      38 [.       1      38 [. 0.99

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 4.1e-18
                                       XXSEEETTTTEEESS-SHHHHHHHHTSHHHHHHHHHHH CS
                              zf-U1  1 mpkYyCdYCdiyLthDspsvRksHngGrkHkenvkdyy 38
                                       m kY+C++C++ L++D++++R+ H +G+kHk ++k+yy
  gene1534|gene1534|rna1533|rna1533  1 MAKYFCEFCNKTLLNDKLRSRRIHFQGAKHKLMRKAYY 38
                                       89***********************************9 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.6    0.0008       4.8       1      10 [.       4      13 ..       4      16 .. 0.91
   2 ?    4.6   0.2    0.0076        45      17      25 .]      22      30 ..      20      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0008
                             zf-met  1 fyCelCnvtf 10
                                       ++Ce Cn+t+
  gene1534|gene1534|rna1533|rna1533  4 YFCEFCNKTL 13
                                       89******95 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0076
                             zf-met 17 ksHlqGKkH 25
                                       + H+qG kH
  gene1534|gene1534|rna1533|rna1533 22 RIHFQGAKH 30
                                       67******* PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   5.7    0.0035        21       1      15 [.       3      17 ..       3      31 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0035
                                       ECBBTTTTBBBSSHH CS
                        zf-C2H2_jaz  1 qfYCvlCdKyFksen 15
                                       +++C+ C+K+  +++
  gene1534|gene1534|rna1533|rna1533  3 KYFCEFCNKTLLNDK 17
                                       69*******988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 764.74
//
Query:       gene1536|gene1536|rna1535|rna1535  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-17   62.3  21.8    6.7e-17   61.9  21.8    1.3  1  MBOAT     MBOAT, membrane-bound O-acyltransferase family
    1.4e-06   28.5   5.7    1.8e-06   28.1   2.7    2.7  2  MBOAT_2   Membrane bound O-acyl transferase family


Domain annotation for each model (and alignments):
>> MBOAT  MBOAT, membrane-bound O-acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9  21.8   7.5e-21   6.7e-17      96     345 ..     168     389 ..      62     392 .. 0.72

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 7.5e-21
                              MBOAT  96 gYvffyplllvGPilsyseymsfvesplsrllytakrnfavalyalflgltylilieyvlskicakdftifkmlss 171
                                        ++++f    lv P+l+++  ++f+     ++      ++  ++++l +    ++++++     + + +++++  + 
  gene1536|gene1536|rna1535|rna1535 168 HFLYF----LVVPTLCFQ--LDFPMRTKRNIKGILLKSIQLLIGFLLF----VLVMDQYAIPSIYRIIDFEDITT- 232
                                        44555....555999998..5666555555544335566666666655....77777777777777777777775. PP

                              MBOAT 172 aqllmrsvimrilllllllfllifdflglwlvalgedilsGlgvngarldrvadrniygdwenavsfsefwraWNi 247
                                               vi  i+++ ++  +l+++f    ++a+ ++ l+ +    a l+ + d  +y +w+na s++efw  WN+
  gene1536|gene1536|rna1535|rna1535 233 -------VIENIINFSISTIILFLIF----FYAVFYCFLDAV----ANLTLFYDSCFYQEWWNASSAREFWALWNR 293
                                        .......3333333333333333322....233444444443....4677889*********************** PP

                              MBOAT 248 pvhkWLlryvYkplgskkfklnkslatlatFlfsAvwHglalgyliwfvlrvllllveklimrlvalsnlkfdrrr 323
                                        pv+ W +r++Y+pl+  +   +k  a l +F++s + H++   + i ++ ++ ++++ +l+ +l+  ++  f +r 
  gene1536|gene1536|rna1535|rna1535 294 PVYLWFKRHIYAPLV--SRGMSKEKAGLVVFTVSGLIHEYVASISI-KKITGWFFITMLLQVPLIHVTE-SFRKRF 365
                                        **************5..67788********************8888.6666666666999999999554.558999 PP

                              MBOAT 324 ailsnvifwlgaflg..pslalll 345
                                        + l+n++fw  ++++  ps++ll+
  gene1536|gene1536|rna1535|rna1535 366 PSLGNFFFWGAFCVIgqPSVLLLY 389
                                        *********888877334555555 PP

>> MBOAT_2  Membrane bound O-acyl transferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.29   2.6e+03      46      62 ..     230     246 ..     213     255 .. 0.73
   2 !   28.1   2.7     2e-10   1.8e-06       4      82 ..     274     346 ..     271     347 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.29
                            MBOAT_2  46 larylqllvaFllSGll 62 
                                        ++++++ ++ F++S ++
  gene1536|gene1536|rna1535|rna1535 230 ITTVIENIINFSISTII 246
                                        67888999999999887 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2e-10
                            MBOAT_2   4 lfgslleayslrrfWgrfWHqlfrrglkstakkilrlllgsklarylqllvaFllSGllHaagdytqlapestall 79 
                                        +++++++a+s r+fW+  W++ +  ++k++++ +l +   s   +  + lv+F++SGl+H+++  +  +  +++ +
  gene1536|gene1536|rna1535|rna1535 274 FYQEWWNASSAREFWAL-WNRPVYLWFKRHIYAPLVSRGMS---KEKAGLVVFTVSGLIHEYVASISIK--KITGW 343
                                        5789***********86.8*************999998888...556889**************99999..99999 PP

                            MBOAT_2  80 fFl 82 
                                        fF+
  gene1536|gene1536|rna1535|rna1535 344 FFI 346
                                        997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2711.93
//
Query:       gene1537|gene1537|rna1536|rna1536  [L=451]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-15   55.1   0.1    1.1e-14   54.2   0.1    1.5  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.1   6.2e-19   1.1e-14       4     134 ..     113     232 ..     110     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 6.2e-19
                    Acyltransferase   4 vtglenlpekgpailvaNHqsylDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnara 78 
                                          g e+ +++gp ++v+NH+s +D++ll+      + +p+ +v   +  l+   l++ ++ + g i ++R+++ ++
  gene1537|gene1537|rna1536|rna1536 113 HIG-EKKRHDGPHVYVSNHTSFVDFFLLSS-----HeFPHACVSERHGGLFG-LLFKSILIRNGSIAFKRSEKVDR 181
                                        455.888899*******************9.....32545555555555554.555555556677888999***** PP

                    Acyltransferase  79 agsleniselleegkl.vviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                                        + ++e+++e +++g   +viFPEGt+ ++   + f+kG+++l      gv+i+Pvai
  gene1537|gene1537|rna1536|rna1536 182 QLVVEKVKEHVRSGGApMVIFPEGTCVNNKFSVLFQKGAFEL------GVTIYPVAI 232
                                        **************999************666**********......9*****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.37s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 2396.31
//
Query:       gene1538|gene1538|rna1537|rna1537  [L=497]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-96  322.4   0.6    4.5e-96  321.7   0.1    1.4  1  Kinesin          Kinesin motor domain
    5.3e-41  140.0   0.4    1.8e-40  138.3   0.0    2.0  2  Microtub_bd      Microtubule binding
      0.001   18.7   5.6     0.0017   18.0   5.6    1.3  1  TMCO5            TMCO5 family
     0.0015   19.1  15.6       0.01   16.4   5.5    2.5  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
  ------ inclusion threshold ------
       0.01   15.4   2.2      0.018   14.6   2.2    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
      0.013   15.5   1.2       0.13   12.3   0.0    2.9  2  FlpD             Methyl-viologen-reducing hydrogenase, delta 
      0.013   15.6   0.6      0.026   14.6   0.6    1.5  1  7TMR-HDED        7TM-HD extracellular
      0.015   15.5   7.1      0.028   14.6   7.1    1.3  1  ATG16            Autophagy protein 16 (ATG16)
      0.046   14.4  15.4        1.4    9.6   7.3    4.6  4  YabA             Initiation control protein YabA
      0.058   13.7   0.4       0.25   11.6   0.1    2.2  1  Glu-tRNAGln      Glu-tRNAGln amidotransferase C subunit
      0.059   13.6  11.8      0.029   14.6   8.1    2.4  2  DUF4164          Domain of unknown function (DUF4164)
       0.06   10.9   6.4       0.09   10.3   6.4    1.2  1  DUF3584          Protein of unknown function (DUF3584)
      0.063   13.8   0.6      0.063   13.8   0.6    2.0  2  Acyl-CoA_ox_N    Acyl-coenzyme A oxidase N-terminal
      0.095   12.1  12.2        1.3    8.4   5.9    2.4  2  DUF4618          Domain of unknown function (DUF4618)
      0.095   13.1   0.1        1.5    9.2   0.0    2.4  2  AAA_16           AAA ATPase domain
        0.1   12.4   4.2       0.66    9.8   0.8    2.4  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        0.1   11.9   0.2       0.18   11.2   0.2    1.4  1  DUF4407          Domain of unknown function (DUF4407)
       0.17   12.3  10.6       0.89   10.0   3.5    2.7  2  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
       0.19   11.8   9.7       0.44   10.6   2.3    3.4  3  DUF1192          Protein of unknown function (DUF1192)
       0.19   12.1   9.2        1.6    9.1   9.4    2.2  1  YlqD             YlqD protein
       0.26   10.2   9.7       0.57    9.1   9.7    1.5  1  IFT57            Intra-flagellar transport protein 57
       0.33   10.2   7.7       0.64    9.3   7.7    1.5  1  DUF3450          Protein of unknown function (DUF3450)
       0.38   10.7   4.0        4.9    7.1   0.7    3.0  2  MerR_2           MerR HTH family regulatory protein
       0.67   10.2  12.4        1.7    8.8  12.4    1.7  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.94    9.4   3.8          2    8.3   3.8    1.5  1  GvpL_GvpF        Gas vesicle synthesis protein GvpL/GvpF
          1    9.7  12.1      0.091   13.1   4.5    2.7  2  DUF641           Plant protein of unknown function (DUF641)
        1.1    9.3  12.1        1.1    9.4   5.2    3.1  3  DUF1664          Protein of unknown function (DUF1664)
        1.2    9.8   8.1         23    5.6   6.9    2.8  1  Syntaxin-6_N     Syntaxin 6, N-terminal
        1.2    9.6  10.8        5.4    7.5   7.3    2.8  2  AAA_23           AAA domain
        1.2    9.3  15.5        5.9    7.2  15.5    2.3  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        1.4    9.3  11.7        1.4    9.2   5.6    2.8  2  BLOC1_2          Biogenesis of lysosome-related organelles co
        1.4    9.2  12.9        6.7    7.0   7.0    2.5  2  THOC7            Tho complex subunit 7
        1.6    8.9  11.9        4.8    7.4  11.2    2.3  1  Fib_alpha        Fibrinogen alpha/beta chain family
        1.8    8.4  11.7      0.096   12.5   3.2    2.7  2  SKA2             Spindle and kinetochore-associated protein 2
        1.9    8.9  12.7        7.3    7.0  12.8    1.8  1  Fez1             Fez1
        2.1    8.2   8.5        4.9    7.0   3.5    3.6  3  DASH_Duo1        DASH complex subunit Duo1
        2.7    8.3  15.2         33    4.8  12.4    3.0  2  DUF5082          Domain of unknown function (DUF5082)
        2.8    7.7  13.9        3.7    7.3   3.4    3.1  3  Spc29            Spindle Pole Component 29
        2.9    6.7  18.8       0.76    8.6  15.0    1.9  2  Spc7             Spc7 kinetochore protein
        3.8    7.6  13.4        3.2    7.8  11.5    1.8  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
        4.8    7.7  10.3         15    6.1   0.9    3.6  3  DUF4208          Domain of unknown function (DUF4208)
          5    6.9  17.5       0.36   10.6   6.8    2.6  2  DUF724           Protein of unknown function (DUF724)
        5.3    7.2  10.8         17    5.5   9.6    2.4  2  RasGAP_C         RasGAP C-terminus
        5.9    6.0  10.1         10    5.3   2.4    2.3  2  TMPIT            TMPIT-like protein
          6    6.2  16.6         12    5.3  16.6    1.4  1  DUF3552          Domain of unknown function (DUF3552)
        6.3    5.3  13.4        3.8    6.0   5.7    2.2  2  FapA             Flagellar Assembly Protein A
        7.4    6.6   8.9        2.2    8.3   4.3    2.4  2  DUF725           Protein of unknown function (DUF725)


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.7   0.1   1.2e-98   4.5e-96      36     332 ..     201     481 ..     188     482 .. 0.93

  Alignments for each domain:
  == domain 1  score: 321.7 bits;  conditional E-value: 1.2e-98
                                        CTTSCEEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBCTTTSBSHHHHHHHHHH CS
                            Kinesin  36 keeeekkfkFdkvfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyTmegkeeeeeGiipraleelF 111
                                        ++++e+ f+Fdkvf+++atq+ vy+e+ ++  +svleGy++++faYGqtgsGKTyTmeg  + ++G+i ral++++
  gene1538|gene1538|rna1537|rna1537 201 TDSKEHGFSFDKVFGPHATQKCVYREM-ESTFQSVLEGYSVCVFAYGQTGSGKTYTMEGV-DGDPGLIVRALKDVY 274
                                        678999********************6.99*****************************8.9************** PP

                                        HHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EEESSHHHHHHHHHH CS
                            Kinesin 112 esikkekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkgltevevksaeevlellek 187
                                         +i++ ke+  + +++++sy+EiYne ++DL++++    +kk++i++++ +  ++  ++ +v +++++++++l++ 
  gene1538|gene1538|rna1537|rna1537 275 CIIEELKED-GWGLDITCSYVEIYNEDVVDLFSED----MKKVTIVHKDVN--IN-MNCISVPIHNISDAIRLFQD 342
                                        *****9998.9**********************99....444555554442..33.578899************** PP

                                        HHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSSTCHHHHHHHHHHHHH CS
                            Kinesin 188 geknrkvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktgaaegerlkEaaniNkS 263
                                        g+++r+v++tk+n++SSRSHav+ ++++ +n++ +++   k + + +vDLAGsEr+s ++ aeg rlkE+++iNkS
  gene1538|gene1538|rna1537|rna1537 343 GARRRSVGSTKCNSKSSRSHAVYILRIKMNNEALKQQ---KEGAMVFVDLAGSERLSVSR-AEGIRLKETQSINKS 414
                                        *****************************99886666...88******************.68************* PP

                                        HHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHHCT CS
                            Kinesin 264 LlaLgrvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaerake 332
                                        L+aLg+v +++ +k  ++hip+R+SkLT+lLq+ L+Gns+t+m+v++sp++++++et+++l+fa+++ +
  gene1538|gene1538|rna1537|rna1537 415 LSALGDVFNSILRK--DSHIPFRNSKLTHLLQSFLSGNSRTIMLVNISPDADHFSETICSLRFADKVGQ 481
                                        **************..*************************************************9865 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.4       7.1   2.7e+03      43      74 ..      99     133 ..      56     142 .. 0.52
   2 !  138.3   0.0   4.7e-43   1.8e-40       7     148 ..     157     304 ..     151     305 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.1
                                        T......TTTEEEE-SEEEECTTHCCCCCCCCHHH CS
                        Microtub_bd  43 e...eekkkkkefsFdrvfeseseqeevfeeisql 74 
                                            + + ++++ ++ r+++ + + + v +e+++ 
  gene1538|gene1538|rna1537|rna1537  99 LqgkDSEIQRMKEELSRILSMNDHLQRVNSEMQCR 133
                                        03333334444445556666666666666666554 PP

  == domain 2  score: 138.3 bits;  conditional E-value: 4.7e-43
                                        HHHHCHHHHHHHCTB-EEEEEEECCCS-T..EEEETTT........TTTEEEE-SEEEECTTHCCCCCCCCHHHHH CS
                        Microtub_bd   7 lRrkleNtiqelkGniRvfarvrpelesek.akikfpe.....eekkkkkefsFdrvfeseseqeevfeeisqlvq 76 
                                        +  kl N+i+ lkG+i + +r+rp++ +++  +i++++     ++++k++ fsFd+vf ++++q+ v+ e++   q
  gene1538|gene1538|rna1537|rna1537 157 TISKLRNEIMVLKGSIQIICRIRPNTPNHHgSRIEISDgylriSTDSKEHGFSFDKVFGPHATQKCVYREMESTFQ 232
                                        5568************************6669999997888898899***************************** PP

                                        HHHTT--EEEEEEES................ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEET CS
                        Microtub_bd  77 saldgynvcifaygqTGsGKtyTmegeeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDl 148
                                        s+l+gy vc+faygqTGsGKtyTmeg + ++g i ra++ ++ +i+elke gw  +i++++veiyne+v Dl
  gene1538|gene1538|rna1537|rna1537 233 SVLEGYSVCVFAYGQTGSGKTYTMEGVDGDPGLIVRALKDVYCIIEELKEDGWGLDITCSYVEIYNEDVVDL 304
                                        ***********************************************************************9 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   5.6   4.5e-06    0.0017      81     183 ..      61     163 ..      29     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.5e-06
                              TMCO5  81 eiLlkevveLqkkisrkeskqddleketlkqkleelkvklqkseescaeqekelakveedyqsvaqlCkdqallik 156
                                          Ll+ + eL++ i+r+++  +d++ ++ ++++e++++ lq  ++  ++ ++el ++ +    +++   +++   +
  gene1538|gene1538|rna1537|rna1537  61 SELLERIEELESAIERLKQ-ASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLN 135
                                        569999***********95.66666667999****************************999************** PP

                              TMCO5 157 kYqealrkmeeeketllleke.vsklqs 183
                                        +Y+e+++k+ee k   l  ke +skl++
  gene1538|gene1538|rna1537|rna1537 136 MYKEKASKLEEIKKECLEHKEtISKLRN 163
                                        ***********66666665551455544 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   5.5   2.7e-05      0.01      17      76 ..      55     114 ..      52     120 .. 0.95
   2 ?    7.5   2.7     0.016       6.1      32      74 ..     119     164 ..     115     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.7e-05
                     HIP1_clath_bdg  17 varqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLe 76 
                                        ++r+  +e+    +ele  +erlk+ ++++++ +++++e +++ l+ k  e++r+k+ L+
  gene1538|gene1538|rna1537|rna1537  55 STRNRESELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELS 114
                                        689999**************************************************9997 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.016
                     HIP1_clath_bdg  32 leeelerlkeeaerkle...eqkeelekLkreleakraelarlkss 74 
                                        ++++l+r+++e + +l+   e++++le++k+e  ++++ +++l++ 
  gene1538|gene1538|rna1537|rna1537 119 MNDHLQRVNSEMQCRLNmykEKASKLEEIKKECLEHKETISKLRNE 164
                                        7788888888887666555588888888888888888888888765 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.2   4.6e-05     0.018     147     235 ..      68     161 ..       7     194 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
                       Exonuc_VII_L 147 eqleelerrlekaikrlleekkqrleklasrlkspee...llerkrqrldeleerleralkkq.......lkkkre 212
                                        e+le++ +rl++a +++++++++++e ++  l+ +++   +++++ +r+ +++++l+r ++++       +k+k++
  gene1538|gene1538|rna1537|rna1537  68 EELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSeiqRMKEELSRILSMNDHLQR-VNSEmqcrlnmYKEKAS 142
                                        2223333355555555555555555555555533223011333333333333333333.11111222222222222 PP

                       Exonuc_VII_L 213 rleelkerlkekleekkerlkkl 235
                                        +lee+k    +++ e+ke+++kl
  gene1538|gene1538|rna1537|rna1537 143 KLEEIK----KECLEHKETISKL 161
                                        233222....2222222233222 PP

>> FlpD  Methyl-viologen-reducing hydrogenase, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00034      0.13      53      99 ..      35      81 ..      33     101 .. 0.81
   2 ?    0.2   0.2       1.9   7.2e+02      77     122 ..     115     161 ..     102     162 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00034
                               FlpD 53 dgVlvlgChpgdChyvkGnekaerrveklkelleelgiepeRvrlee 99
                                       d +l+  C pg C y+ ++  +++r ++l e +eel+   eR++ ++
  gene1538|gene1538|rna1537|rna1537 35 DSILLEICTPGTCGYNGCSRSTRNRESELLERIEELESAIERLKQAS 81
                                       7899999***********************************98654 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.9
                               FlpD  77 rveklkelleelgiepe.RvrleevsaaegekfaevikefvekikeL 122
                                        r+  +++ l++++ e + R+++++ +a++ e++++ + e +e+i +L
  gene1538|gene1538|rna1537|rna1537 115 RILSMNDHLQRVNSEMQcRLNMYKEKASKLEEIKKECLEHKETISKL 161
                                        66677888888887744499999999999999999999999999887 PP

>> 7TMR-HDED  7TM-HD extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   6.9e-05     0.026      50     120 ..      10     118 ..       5     181 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.9e-05
                          7TMR-HDED  50 rqelenlleelee.........lra.......................tseenlselieqlkqarekyaqa..... 88 
                                        ++e++++++e++e         +r+                       + e++l e+ie+l+ a+e+ +qa     
  gene1538|gene1538|rna1537|rna1537  10 IDEIKEVFSEIKEnidgnpssrIRKdsilleictpgtcgyngcsrstrNRESELLERIEELESAIERLKQAsdsni 85 
                                        6778888888666655555555444888888888888888888888888899999999999999999999999998 PP

                          7TMR-HDED  89 ..gaelsdeelrallelsdeeleelqqgieqile 120
                                           ++ + e+++a+l+ +d+e++++++++++il 
  gene1538|gene1538|rna1537|rna1537  86 nsRQS-NVEDINAMLQGKDSEIQRMKEELSRILS 118
                                        84444.788888***************8888764 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   7.1   7.3e-05     0.028      25     137 ..      61     170 ..      51     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.3e-05
                              ATG16  25 nrLldrtsaleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrge 99 
                                        ++Ll+r+++le+  ++l++a+ s+ + +       +++ +  ++  + ++++iq ++++l+++ +    l++ ++e
  gene1538|gene1538|rna1537|rna1537  61 SELLERIEELESAIERLKQASDSNINsR-------QSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSE 129
                                        5688899999998888855544433311.......11111111122345566777777777777777778888888 PP

                              ATG16 100 laqrllelneelqklee...klkedeerlaeleaeraalet 137
                                        ++ rl+  +e+ +klee   +  e +e++ +l++e+ +l+ 
  gene1538|gene1538|rna1537|rna1537 130 MQCRLNMYKEKASKLEEikkECLEHKETISKLRNEIMVLKG 170
                                        88888766665555543222666778888888888777764 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2       1.8     7e+02       5      23 ..      62      80 ..      56      99 .. 0.53
   2 ?    9.6   7.3    0.0038       1.4       8      76 ..      90     161 ..      84     166 .. 0.81
   3 ?    3.0   0.1      0.41   1.6e+02      79      91 ..     236     248 ..     210     254 .. 0.78
   4 ?    2.3   0.0      0.67   2.5e+02      16      54 ..     407     445 ..     401     465 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHH CS
                               YabA  5 elfdkleeleeqleellee 23
                                       el++++eele+ +e+l++ 
  gene1538|gene1538|rna1537|rna1537 62 ELLERIEELESAIERLKQA 80
                                       4555555555555554433 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0038
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXXXXXXXXXXXX CS
                               YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekekkkelsegkenLarl 76 
                                        +++e+++  l+   +e++++keel+++l  n++L+  n++++ rl   +e+ +k +e kke  e ke +++l
  gene1538|gene1538|rna1537|rna1537  90 SNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLnmyKEKASKLEEIKKECLEHKETISKL 161
                                        56888999999999*******************************766555555566666666777777766 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.41
                                        XXXXXXXXXXXXX CS
                               YabA  79 eGFHiCnvlyGsr 91 
                                        eG+ +C   yG++
  gene1538|gene1538|rna1537|rna1537 236 EGYSVCVFAYGQT 248
                                        9**********97 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.67
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXX CS
                               YabA  16 qleelleeleelkeelaelleenaeLeleneklrerlee 54 
                                        ++++++++l++l + ++++l +++++ + n+kl ++l++
  gene1538|gene1538|rna1537|rna1537 407 ETQSINKSLSALGDVFNSILRKDSHIPFRNSKLTHLLQS 445
                                        57889999*************************999854 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00066      0.25       3      27 ..     103     127 ..     102     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00066
                                        HHHHHHHHHHHHHHHHHHTTCGCS- CS
                        Glu-tRNAGln   3 eeEleklakelnsildyveqLqevd 27 
                                        ++E++++++el++il + + Lq+v+
  gene1538|gene1538|rna1537|rna1537 103 DSEIQRMKEELSRILSMNDHLQRVN 127
                                        89*********************98 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   8.1   7.7e-05     0.029       4      82 ..      61     140 ..      58     146 .. 0.92
   2 ?   -1.2   0.1       6.9   2.6e+03      18      44 ..     142     168 ..     138     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.7e-05
                            DUF4164   4 keleaaltrLeaaldsLEkavdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLka 78 
                                        +el +  ++Le a+++L +a+d  +++ +++ ++++a ++  +++ +R+ eeL   +  +  l++vn+E + rL+ 
  gene1538|gene1538|rna1537|rna1537  61 SELLERIEELESAIERLKQASDSNINSRQSNvEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNM 136
                                        567777899*****************998887******************************************98 PP

                            DUF4164  79 aiet 82 
                                          e+
  gene1538|gene1538|rna1537|rna1537 137 YKEK 140
                                        7765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.9
                            DUF4164  18 dsLEkavdrrleaerkrdeleaeieal 44 
                                         +LE+  ++ le +++ ++l++ei  l
  gene1538|gene1538|rna1537|rna1537 142 SKLEEIKKECLEHKETISKLRNEIMVL 168
                                        567777788888888888888888665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   6.4   0.00024      0.09     812     921 ..      55     165 ..      52     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                            DUF3584 812 slaeerpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelklda 887
                                        s++++  +l e+ eelesa+e+l+q     i++ + + + ++  ++  +  +++++e+l+++ ++  +l +++ + 
  gene1538|gene1538|rna1537|rna1537  55 STRNRESELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEM 130
                                        7899999999***********************************************9998888877775555444 PP

                            DUF3584 888 daeqae.gelaerlaaleelkrkrerlsedvkkal 921
                                        +      +e a +l+ ++  + +++    ++++++
  gene1538|gene1538|rna1537|rna1537 131 QCRLNMyKEKASKLEEIKKECLEHKETISKLRNEI 165
                                        33322212334444444444444444444444444 PP

>> Acyl-CoA_ox_N  Acyl-coenzyme A oxidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       9.4   3.6e+03      14      34 ..      62      82 ..      58      89 .. 0.76
   2 ?   13.8   0.6   0.00017     0.063       1      74 [.      91     164 ..      91     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 9.4
                                       HHHHHHHHHHHHHCT-GGGS- CS
                      Acyl-CoA_ox_N 14 eklerrrelesllesdpefdd 34
                                       e ler +eles++e+ ++ +d
  gene1538|gene1538|rna1537|rna1537 62 ELLERIEELESAIERLKQASD 82
                                       568999999999998888777 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00017
                                        -HHHHHHHHHTSHHHHHHHH.HHHHHHCT-GGGS-SSTGGGS-HHHHHHHHHHHHHHHHHHHHHTTSBTTCHHHH CS
                      Acyl-CoA_ox_N   1 dveeltvllaggeeklerrr.elesllesdpefddaedyyflsreeryeealrkatrllkklrelqierkeseee 74 
                                        +ve+++++l+g++ +++r + el ++l+ +  +++ ++ +   r   y+e++ k+ ++ k + e++++ ++  +e
  gene1538|gene1538|rna1537|rna1537  91 NVEDINAMLQGKDSEIQRMKeELSRILSMNDHLQR-VNSEMQCRLNMYKEKASKLEEIKKECLEHKETISKLRNE 164
                                        79****************9989*************.*****************************9876655555 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.9    0.0034       1.3      33     113 ..      53     140 ..      50     141 .. 0.80
   2 ?    6.0   7.2     0.018         7     136     220 ..      88     176 ..      86     184 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0034
                            DUF4618  33 edstakkvrklLqqyeklktvisileksskkqleqakaeLqeweeke...ekklekLeqqleq...lnakvqklqe 102
                                         +st ++ ++lL++ e l+++i+ l+++s +++++ +++ ++++ ++   ++++++++++l +   +n+++q ++ 
  gene1538|gene1538|rna1537|rna1537  53 SRSTRNRESELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLqgkDSEIQRMKEELSRilsMNDHLQRVNS 128
                                        578999999************************9999988877766511167899999998763336888999999 PP

                            DUF4618 103 elnv.LstYkDk 113
                                        e++  L+ Yk+k
  gene1538|gene1538|rna1537|rna1537 129 EMQCrLNMYKEK 140
                                        998658888876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                            DUF4618 136 qqdeldeleelikevleklskkiqkkkekl.....lkslaektlkatqeaLlqktlenqvlkkeiekfrefieele 206
                                        +q ++++++ +++    ++++  ++ ++ l     l+ +    ++   ++ ++k+ + +++kke  +++e i++l+
  gene1538|gene1538|rna1537|rna1537  88 RQSNVEDINAMLQGKDSEIQRMKEELSRILsmndhLQRVN-SEMQCRLNMYKEKASKLEEIKKECLEHKETISKLR 162
                                        5677777777776654444433333222221000022222.22222334556788888899999999999999999 PP

                            DUF4618 207 eeipeLkaeveqLq 220
                                        +ei  Lk +++ ++
  gene1538|gene1538|rna1537|rna1537 163 NEIMVLKGSIQIIC 176
                                        99999999998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       1.2   4.8e+02      78     129 ..      70     119 ..      18     127 .. 0.57
   2 ?    9.2   0.0     0.004       1.5      11      41 ..     226     256 ..     221     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
                             AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaea..srllellkrllal 129
                                         e+ ++ l+++++s + +  +   e+   + + l g+++  +r+ e+l+r+l+ 
  gene1538|gene1538|rna1537|rna1537  70 LESAIERLKQASDS-NINSRQSNVED---INAMLQGKDSeiQRMKEELSRILSM 119
                                        22333333333333.33333332222...3334444444668888888888854 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.004
                             AAA_16  11 qLlsalervrsgrpelvllsGesGvGKsslv 41 
                                        +++s++++v +g + +v+ +G+ G+GK+  +
  gene1538|gene1538|rna1537|rna1537 226 EMESTFQSVLEGYSVCVFAYGQTGSGKTYTM 256
                                        5678999999******************876 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.8    0.0017      0.66     124     172 ..      70     118 ..      61     122 .. 0.89
   2 ?    3.5   0.1      0.15        55     129     175 ..     124     173 ..     118     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0017
                       Bacillus_HBL 124 likeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqg 172
                                        l  ++++lk++ +++ ++ +++v+ ++++l+g++ +i+ +++e++++ +
  gene1538|gene1538|rna1537|rna1537  70 LESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILS 118
                                        55678999************************************99865 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.15
                       Bacillus_HBL 129 kklklklakdsknFktdv...deltsilagdsgvisqlqneiedlqgkik 175
                                        ++ +++++   + +k+++   +e+++     + +is+l+nei  l+g+i+
  gene1538|gene1538|rna1537|rna1537 124 QRVNSEMQCRLNMYKEKAsklEEIKKECLEHKETISKLRNEIMVLKGSIQ 173
                                        555555555566666665222566666667899*************9997 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00046      0.18     114     254 ..      65     127 ..       4     192 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
                            DUF4407 114 eeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekk 189
                                        e+ +e  +++ e+l++a+++ ++  ++++++++a ++ +++++++ ++e+ + l+ +                   
  gene1538|gene1538|rna1537|rna1537  65 ERIEEL-ESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMN------------------- 120
                                        222222.22223333334444444444444444444444444444444444433332................... PP

                            DUF4407 190 aqldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarlealdrlt 254
                                                                                                  + l+r+ 
  gene1538|gene1538|rna1537|rna1537 121 ----------------------------------------------------------DHLQRVN 127
                                        ..........................................................2222222 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9     0.044        17       5      45 ..      74     114 ..      69     118 .. 0.85
   2 ?   10.0   3.5    0.0023      0.89      13      63 ..     120     174 ..     111     177 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.044
                             CC2-LZ   5 akeaekvkkeeieeLkaqlqaaeealaakqeeidelkeeik 45 
                                         ++ ++ + ++i++ + ++++ +  l+ k++ei+++kee++
  gene1538|gene1538|rna1537|rna1537  74 IERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELS 114
                                        455666778999999**********************9976 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0023
                             CC2-LZ  13 keeieeLkaqlqaaeealaakqeeidelkeeikkkee...ele.tisvlkaQaev 63 
                                        ++++++++ ++q+  + +++k ++++e+k+e  +++e   +l+ +i vlk  +++
  gene1538|gene1538|rna1537|rna1537 120 NDHLQRVNSEMQCRLNMYKEKASKLEEIKKECLEHKEtisKLRnEIMVLKGSIQI 174
                                        78899******************************9977777799***9987776 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.3    0.0011      0.44      23      51 ..      61      89 ..      60      91 .. 0.89
   2 ?    4.0   0.2      0.14        53      21      45 ..      91     115 ..      88     121 .. 0.90
   3 ?   -0.5   0.0       3.5   1.3e+03      26      40 ..     155     169 ..     152     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                            DUF1192 23 eELeerIalLeaEIaRleaaiakkkasra 51
                                       +EL erI++Le+ I+Rl++a ++  +sr+
  gene1538|gene1538|rna1537|rna1537 61 SELLERIEELESAIERLKQASDSNINSRQ 89
                                       69******************998888776 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.14
                            DUF1192  21 SveELeerIalLeaEIaRleaaiak 45 
                                        +ve+++++ +   +EI+R+++++++
  gene1538|gene1538|rna1537|rna1537  91 NVEDINAMLQGKDSEIQRMKEELSR 115
                                        69999****************9976 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.5
                            DUF1192  26 eerIalLeaEIaRle 40 
                                        +e I++L+ EI  l+
  gene1538|gene1538|rna1537|rna1537 155 KETISKLRNEIMVLK 169
                                        689********8666 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   9.4    0.0041       1.6      17     107 ..      87     179 ..      52     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0041
                               YlqD  17 lKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaq.qieeiq.eqvekekserlekkkqllqqleqvqkLe 90 
                                        +++   ++++a ++  d+e+q+++ ++ r+++ + + +   +  + + + ++++ s+++e kk+ l+  e ++kL 
  gene1538|gene1538|rna1537|rna1537  87 SRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVnSEMQCRlNMYKEKASKLEEIKKECLEHKETISKLR 162
                                        5666678888999999999999999999999888764332344444414556677889999*************** PP

                               YlqD  91 lgsevkqgqveslvevk 107
                                         +  v +g ++ +++++
  gene1538|gene1538|rna1537|rna1537 163 NEIMVLKGSIQIICRIR 179
                                        *************9986 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   9.7    0.0015      0.57     223     310 ..      82     168 ..      55     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0015
                              IFT57 223 rahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlse 298
                                         +++++ +++ + i++ l+   s++++++e++s+ l+ ++   +++ns+++  l+ y+e+  +l+e+k+++ + +e
  gene1538|gene1538|rna1537|rna1537  82 DSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILS-MNDHLQRVNSEMQCRLNMYKEKASKLEEIKKECLEHKE 156
                                        4667777777778888888888888888888887775.67777778888888888888888888888888888888 PP

                              IFT57 299 gvseltrelaei 310
                                        ++s+l++e   +
  gene1538|gene1538|rna1537|rna1537 157 TISKLRNEIMVL 168
                                        888887776555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   7.7    0.0017      0.64      18      97 ..      70     150 ..      60     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                            DUF3450  18 ldqalkeaekavaaa.aqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                        l++a++  ++a ++   + q+++++++   q   +e++++keel+++   n++l+r+ ++++ +++  +e+ +++e
  gene1538|gene1538|rna1537|rna1537  70 LESAIERLKQASDSNiNSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNMYKEKASKLE 145
                                        5555555555555541555889999999999999****************************************** PP

                            DUF3450  93 eiere 97 
                                        ei++e
  gene1538|gene1538|rna1537|rna1537 146 EIKKE 150
                                        **987 PP

>> MerR_2  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.7     0.013       4.9      67      84 .]      62      79 ..      61      79 .. 0.94
   2 ?    3.1   0.0      0.22        84      17      64 ..     277     328 ..     274     341 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                             MerR_2 67 dLLdrieqLqrelesLrn 84
                                       +LL+rie+L++ +e+L++
  gene1538|gene1538|rna1537|rna1537 62 ELLERIEELESAIERLKQ 79
                                       7***************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.22
                             MerR_2  17 lieLvelgl.iepeiee.e..ewyfdesqlarlekavRLqrDLeinleGiav 64 
                                        ++eL e g+ ++++++  e  ++ + +   ++++k++  ++D +in++ i+v
  gene1538|gene1538|rna1537|rna1537 277 IEELKEDGWgLDITCSYvEiyNEDVVDLFSEDMKKVTIVHKDVNINMNCISV 328
                                        667777777644444442222333333444789999999********99988 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  12.4    0.0046       1.7      44     140 ..      59     162 ..      54     179 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0046
                      Jnk-SapK_ap_N  44 rneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrele.......lka 112
                                        r+ e  +++eel+ ++e+L++  +   + r+   e++  + +  ++e + ++e++++  + n++l+        ++
  gene1538|gene1538|rna1537|rna1537  59 RESELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQrvnsemqCRL 134
                                        4556667899999999999999999999999999888888777777777777777766666666661111111555 PP

                      Jnk-SapK_ap_N 113 knaadqlsrleekeaelkkeysklhere 140
                                        + +++++s+lee ++e  + +++ ++  
  gene1538|gene1538|rna1537|rna1537 135 NMYKEKASKLEEIKKECLEHKETISKLR 162
                                        5555555555555555544444444422 PP

>> GvpL_GvpF  Gas vesicle synthesis protein GvpL/GvpF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.8    0.0051         2      91     193 ..      60     162 ..      49     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0051
                          GvpL_GvpF  91 relLeeeadelreaLerlagkvEygvkvlwde.ealleelleedpelrelreeieaasesgtayllrkrlgqrlee 165
                                        ++ L e+ +el++a+erl+     ++  +  + e++ + l  +d e+++++ee+++  +   ++l+r++ + + + 
  gene1538|gene1538|rna1537|rna1537  60 ESELLERIEELESAIERLKQASDSNINSRQSNvEDINAMLQGKDSEIQRMKEELSRILS-MNDHLQRVNSEMQCRL 134
                                        566778999********************99978888889999***********99888.67************** PP

                          GvpL_GvpF 166 aleerreelaeeleeaLaplaeevrere 193
                                        ++ +++++  ee++++  ++ e+++  +
  gene1538|gene1538|rna1537|rna1537 135 NMYKEKASKLEEIKKECLEHKETISKLR 162
                                        **************99988877765544 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.5   0.00024     0.091      71     126 ..      65     124 ..      48     126 .. 0.74
   2 ?    0.5   1.3       1.9   7.1e+02      75     116 ..     125     166 ..     119     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00024
                             DUF641  71 aeeseleaeiqe....qrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkkle 126
                                        ++ +ele+ i++      s +++ +  v++++a l+ kdsei+++ke+L+++ + n +l+
  gene1538|gene1538|rna1537|rna1537  65 ERIEELESAIERlkqaSDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQ 124
                                        33333444443344347788999******************************9999886 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.9
                             DUF641  75 eleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLe 116
                                        ++++e+q + ++ k     ++++++e+ + ++ i++L++++ 
  gene1538|gene1538|rna1537|rna1537 125 RVNSEMQCRLNMYKEKASKLEEIKKECLEHKETISKLRNEIM 166
                                        455666666666777777777788888888888888888765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       9.1   3.5e+03      73      89 ..       8      24 ..       5      30 .. 0.59
   2 ?    9.4   5.2    0.0028       1.1      39     119 ..      56     136 ..      52     141 .. 0.89
   3 ?    5.9   1.3     0.033        13      65     120 ..     120     175 ..     118     178 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.1
                            DUF1664 73 kkldeqkeiskeikeev 89
                                       +++de ke+ +eike++
  gene1538|gene1538|rna1537|rna1537  8 HRIDEIKEVFSEIKENI 24
                                       45555666666665555 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0028
                            DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                         ++  +++ +++e++ +++++ k+   s+i++ ++++++ +++ +  ++e+++++e+ls+i +  ++++++ ++++
  gene1538|gene1538|rna1537|rna1537  56 TRNRESELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQ 131
                                        556667778899***************************************************9999999999999 PP

                            DUF1664 115 skler 119
                                         +l+ 
  gene1538|gene1538|rna1537|rna1537 132 CRLNM 136
                                        88876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.033
                            DUF1664  65 ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        +++++rv+++++   ++ ke +++++e++++  e +e ++++++ ++ l+++++ i
  gene1538|gene1538|rna1537|rna1537 120 NDHLQRVNSEMQCRLNMYKEKASKLEEIKKECLEHKETISKLRNEIMVLKGSIQII 175
                                        56788899999999999999999999999999999999999999999999888766 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.9     0.059        23       8      95 ..      61     165 ..       1     196 [. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.059
                       Syntaxin-6_N   8 eeVqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetv.................ri 66 
                                        +e  + ++++es ++r ++  +++++s+++++++ +  L+ + ++i+   e+L +                   ++
  gene1538|gene1538|rna1537|rna1537  61 SELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILsmndhlqrvnsemqcrlNM 136
                                        4555666667777777766666666666666666666666666666666666666664444444444444444445 PP

                       Syntaxin-6_N  67 veknpskfkidekelsrrrafveevreev 95 
                                         +++ sk +  +ke  ++++ ++++r+e+
  gene1538|gene1538|rna1537|rna1537 137 YKEKASKLEEIKKECLEHKETISKLRNEI 165
                                        55566666666677777777777777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.3     0.014       5.4     104     198 ..      64     164 ..       7     175 .. 0.58
   2 ?    2.5   0.1      0.48   1.8e+02      25      37 ..     245     257 ..     243     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.014
                             AAA_23 104 tkkaklelleideleqfisellgskkiilnli.lflgqerfeefelkdkke..................rleelek 160
                                            ++ +  i+ l+q  +++++s++++ + i ++l+ ++ e ++ k++++                  rl+ +++
  gene1538|gene1538|rna1537|rna1537  64 LERIEELESAIERLKQASDSNINSRQSNVEDInAMLQGKDSEIQRMKEELSrilsmndhlqrvnsemqcRLNMYKE 139
                                        2222333334477888888899988888866614455555444444555553333333333333333333333333 PP

                             AAA_23 161 eleeledekkllekleqekekekeleeleeeleeilke 198
                                        +               +++e +ke+ e +e++ ++ +e
  gene1538|gene1538|rna1537|rna1537 140 KA-------------SKLEEIKKECLEHKETISKLRNE 164
                                        33.............44444444444445555444444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.48
                             AAA_23  25 tGpNGaGKTTild 37 
                                        +G++G+GKT  ++
  gene1538|gene1538|rna1537|rna1537 245 YGQTGSGKTYTME 257
                                        7********7666 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  15.5     0.015       5.9      17     109 ..      63     159 ..      54     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.015
                        TMF_TATA_bd  17 lsseirrlEgElaslkeelerleaerdeareeivklm....keneelkelkkeleelekeleelqeryetlLellG 88 
                                        l  +i +lE+ ++ lk+   +  ++r++  e+i +++    +e +++ke+ +++ +++ +l+ ++++ +  L +++
  gene1538|gene1538|rna1537|rna1537  63 LLERIEELESAIERLKQASDSNINSRQSNVEDINAMLqgkdSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNMYK 138
                                        4556778888888888888888888888888887777443356667777777777888899999999999999999 PP

                        TMF_TATA_bd  89 eksEeveELraDvaDlKemyk 109
                                        ek+ + eE +++  + Ke + 
  gene1538|gene1538|rna1537|rna1537 139 EKASKLEEIKKECLEHKETIS 159
                                        999999999999888888765 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.68   2.6e+02      62      80 ..      62      80 ..      53      94 .. 0.67
   2 ?    9.2   5.6    0.0037       1.4      12      80 ..     103     171 ..      92     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.68
                            BLOC1_2 62 pylqqidqiekqvteLeea 80
                                       ++l++i+++e  +++L++a
  gene1538|gene1538|rna1537|rna1537 62 ELLERIEELESAIERLKQA 80
                                       4555555555555555543 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0037
                            BLOC1_2  12 eaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                        ++e++  +e+++ +  +N + ++   +++ +++  ++k++kl+e ++e  ++++ i ++ +++  L+  
  gene1538|gene1538|rna1537|rna1537 103 DSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNMYKEKASKLEEIKKECLEHKETISKLRNEIMVLKGS 171
                                        678888899999999999999999999999999999999999999999999999999999998877655 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.0     0.018       6.7      42     113 ..      60     128 ..      49     139 .. 0.73
   2 ?    4.4   0.8      0.11        42      68      99 ..     142     173 ..     128     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.018
                              THOC7  42 kedllldfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLeearatranrkeyde 113
                                        + +ll +++++e++ierl+  +++n   r++     e+i++ ++   +ei+++k++L++   + ++ + ++ 
  gene1538|gene1538|rna1537|rna1537  60 ESELLERIEELESAIERLKQASDSNINSRQSNV---EDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNS 128
                                        456777888888888888888888888777644...667777777777777777777777777766666554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                              THOC7  68 rereryeaekeeieseieavreeieelkaqLe 99 
                                         + e++++e  e +++i+++r+ei  lk +++
  gene1538|gene1538|rna1537|rna1537 142 SKLEEIKKECLEHKETISKLRNEIMVLKGSIQ 173
                                        46788888888888999999999999998876 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  11.2     0.013       4.8      17     127 ..      44     153 ..      31     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.013
                                        E-CCHHHHCCC...CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          Fib_alpha  17 PtgCglqdlll...kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleee 89 
                                        P +Cg ++      + e+++ +++e+le+ +e++++ +   ++ +++ ++ +++ ++  +++d+ i+++++el  +
  gene1538|gene1538|rna1537|rna1537  44 PGTCGYNGCSRstrNRESELLERIEELESAIERLKQAS---DSNINSRQSNVEDINAMLQGKDSEIQRMKEELS-R 115
                                        77777766554000456667777777777777776654...344444444444445555556789********9.* PP

                                        CCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Fib_alpha  90 ilrlketidaqesnirvLqnvlesneqkiqkLeqdidq 127
                                        il +++ +++  s+++   n+++++ +k+++++++  +
  gene1538|gene1538|rna1537|rna1537 116 ILSMNDHLQRVNSEMQCRLNMYKEKASKLEEIKKECLE 153
                                        ********9999****999*********9999998765 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.2   0.00025     0.096      42      98 ..      62     119 ..      53     131 .. 0.88
   2 ?    0.1   0.7       1.7   6.6e+02      51      80 ..     138     166 ..     123     182 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                               SKA2  42 kLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa.elppl 98 
                                        +Ller++++ + ++ Lk+  +   ++++  ++ i++ l +  + +q++++++  + ++
  gene1538|gene1538|rna1537|rna1537  62 ELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELsRILSM 119
                                        7************************************************998655444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.7
                               SKA2  51 keelqaLkeqceellaekkelidkirttlv 80 
                                        ke+ ++L+e  +e l+  ke+i+k+r+ ++
  gene1538|gene1538|rna1537|rna1537 138 KEKASKLEEIKKECLEH-KETISKLRNEIM 166
                                        33333333333333322.244555554444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  12.8     0.019       7.3      23     120 ..      60     158 ..      53     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.019
                               Fez1  23 qaevtqklseivalkaqlrelr.akleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelk 97 
                                         +e+ ++++e+ +   +l++++ +++++++++++++++ l+ k+ e++++++el+r  s ++ l+   ++++  l+
  gene1538|gene1538|rna1537|rna1537  60 ESELLERIEELESAIERLKQASdSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLN 135
                                        5667777777777777777764267888888999999999999999999999999998888888888888888888 PP

                               Fez1  98 elreelselsleeeeaalesdea 120
                                          +e++s+l++ ++e+ +++++ 
  gene1538|gene1538|rna1537|rna1537 136 MYKEKASKLEEIKKECLEHKETI 158
                                        88888777665544443333332 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   3.5     0.013       4.9       6      61 ..      61     117 ..      58     126 .. 0.72
   2 ?    1.5   0.3      0.66   2.5e+02       3      24 ..     110     131 ..     104     161 .. 0.73
   3 ?   -0.3   0.0       2.5   9.6e+02      31      57 ..     406     432 ..     397     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                          DASH_Duo1   6 leqLrkinevienviesLkkak.sniervketvestntLLd.kWirIlsqtehtqrll 61 
                                         e L++i   +e+ ie Lk+a+ sni++ +++ve+ n++L+ k ++I+   e+ +r+l
  gene1538|gene1538|rna1537|rna1537  61 SELLERIE-ELESAIERLKQASdSNINSRQSNVEDINAMLQgKDSEIQRMKEELSRIL 117
                                        55555554.4799999999999999999999999999999744555555555555555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.66
                          DASH_Duo1   3 ekEleqLrkinevienviesLk 24 
                                        ++El  + ++n+ ++ v+++++
  gene1538|gene1538|rna1537|rna1537 110 KEELSRILSMNDHLQRVNSEMQ 131
                                        5677777777777777777665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 2.5
                          DASH_Duo1  31 ervketvestntLLdkWirIlsqteht 57 
                                        ++ ++  +s ++L d + +Il + +h+
  gene1538|gene1538|rna1537|rna1537 406 KETQSINKSLSALGDVFNSILRKDSHI 432
                                        555666678888999999999988875 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  12.4     0.087        33      10     111 ..      58     172 ..      53     175 .. 0.58
   2 ?    4.0   1.5      0.16        59       8      51 ..     123     166 ..     118     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.087
                            DUF5082  10 aqiaelrseiaaleekIerLkeakt.klsdekeslkqkkkklekplnsse....sWkGk.eennydgirs.nless 78 
                                        ++ +el ++i+ le+ IerLk+a++  + + ++++++ +  l++++ + +    ++      n++ + +  +++  
  gene1538|gene1538|rna1537|rna1537  58 NRESELLERIEELESAIERLKQASDsNINSRQSNVEDINAMLQGKDSEIQrmkeELSRIlSMNDHLQRVNsEMQCR 133
                                        56688999*************99862699***************99988744443333333344433333433333 PP

                            DUF5082  79 yqtyv...dkldelidai...eeEIerLenqiseaqgvl 111
                                         + y+   +kl+e++++    +e I++L+n+i+ ++g++
  gene1538|gene1538|rna1537|rna1537 134 LNMYKekaSKLEEIKKEClehKETISKLRNEIMVLKGSI 172
                                        333330003344444332111233555555555555444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.16
                            DUF5082   8 lqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkkle 51 
                                        lq+  +e++ +++ + ek ++L+e k++  + ke++++ ++++ 
  gene1538|gene1538|rna1537|rna1537 123 LQRVNSEMQCRLNMYKEKASKLEEIKKECLEHKETISKLRNEIM 166
                                        67778999999999999999***999999999999999888775 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.8     0.012       4.6     145     175 ..      58      88 ..      54      97 .. 0.85
   2 ?    7.3   3.4    0.0096       3.7     111     164 ..      84     137 ..      80     141 .. 0.90
   3 ?    4.2   1.3      0.09        34     107     140 ..     132     165 ..     125     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.012
                              Spc29 145 tvnseLqekvaeleeevkrlaalehSnrkfr 175
                                           seL e+++ele+ ++rl+  ++Sn + r
  gene1538|gene1538|rna1537|rna1537  58 NRESELLERIEELESAIERLKQASDSNINSR 88 
                                        55789*********************98766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0096
                              Spc29 111 siyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrl 164
                                        +i s+ +++++++ +l+++  eI+ +k el     +n++Lq+   e++ +++++
  gene1538|gene1538|rna1537|rna1537  84 NINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNMY 137
                                        58889999999*************************************998776 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.09
                              Spc29 107 srldsiyssvkkivelekklddqkleIkeLkrel 140
                                         rl++ +++ +k +e++k   ++k++I +L++e+
  gene1538|gene1538|rna1537|rna1537 132 CRLNMYKEKASKLEEIKKECLEHKETISKLRNEI 165
                                        5889999999999999999999999999999987 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       5.2     2e+03      71      89 ..       7      25 ..       6      28 .. 0.75
   2 ?    8.6  15.0     0.002      0.76     170     275 ..      61     165 ..      53     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.2
                               Spc7 71 kkyisegrkiireieeetl 89
                                       +++i+e +++++ei+e++ 
  gene1538|gene1538|rna1537|rna1537  7 QHRIDEIKEVFSEIKENID 25
                                       5678888888888888774 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                               Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkse 245
                                         el e+ +ele+ +e+l++a+++  ++ + ++e +   l+  ++ei++ k+el++  +  ++l+   +e++ + + 
  gene1538|gene1538|rna1537|rna1537  61 SELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNM 136
                                        5788999999999999999999999999999999999999999999999999999999999999999999999999 PP

                               Spc7 246 leeeiaeaervleeckgwsesevsrlkeev 275
                                        ++e+ ++ e++++ec +++e+ +s+l++e 
  gene1538|gene1538|rna1537|rna1537 137 YKEKASKLEEIKKECLEHKET-ISKLRNEI 165
                                        999999999999999988764.77777665 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  11.5    0.0085       3.2      69     165 ..      69     165 ..      50     174 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0085
                            UPF0242  69 kleekeakl.teldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeq 143
                                        +le+ ++ l ++ d +++  + ++e+ ++  +    e++ ++eel r    n +Lq   ++++   +++k e  ++
  gene1538|gene1538|rna1537|rna1537  69 ELESAIERLkQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNMYK-EKASK 143
                                        2222222220222344444444555555555555555666666666666666666654444444444444.33455 PP

                            UPF0242 144 Laekqellqeyqetieeqrsvl 165
                                        L+e ++   e +eti+++r+++
  gene1538|gene1538|rna1537|rna1537 144 LEEIKKECLEHKETISKLRNEI 165
                                        6666666666666666666654 PP

>> DUF4208  Domain of unknown function (DUF4208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9     0.038        15       6      57 ..      58     109 ..      53     125 .. 0.79
   2 ?    2.0   2.3      0.75   2.9e+02      11      53 ..     130     171 ..     118     187 .. 0.72
   3 ?    2.3   0.0      0.62   2.4e+02      38      77 ..     406     447 ..     393     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.038
                            DUF4208   6 mdeeeckellrpvkksLkrLkkltkekllskkerakilkkeLlkiGdfIdel 57 
                                        + e+e+ e ++ ++++ +rLk+++++++ s++++++ ++  L+   ++I+ +
  gene1538|gene1538|rna1537|rna1537  58 NRESELLERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRM 109
                                        44556888999999***********************999998665555555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.75
                            DUF4208  11 ckellrpvkksLkrLkkltkekllskkerakilkkeLlkiGdf 53 
                                        ++  l+  k++  +L++ +ke  l+ ke +++l++e++ +   
  gene1538|gene1538|rna1537|rna1537 130 MQCRLNMYKEKASKLEEIKKE-CLEHKETISKLRNEIMVLKGS 171
                                        444555556666788888555.89**********999876555 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.62
                            DUF4208  38 erakilkkeLlkiGdfIdellkekke..ekkeklkkhlWefv 77 
                                        ++ + ++k L ++Gd  +++l++ ++   +++kl++ l +f+
  gene1538|gene1538|rna1537|rna1537 406 KETQSINKSLSALGDVFNSILRKDSHipFRNSKLTHLLQSFL 447
                                        56788999*************998877766677777666665 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   3.1      0.28   1.1e+02     133     184 ..      61     109 ..      50     112 .. 0.63
   2 ?   10.6   6.8   0.00094      0.36      87     150 ..     106     169 ..     104     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.28
                             DUF724 133 delekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeav 184
                                        +el ++i ele   ++    k+a+d++i + +s++e+++  l+   +e +++
  gene1538|gene1538|rna1537|rna1537  61 SELLERIEELESAIER---LKQASDSNINSRQSNVEDINAMLQGKDSEIQRM 109
                                        3444555555555543...447778888888888888888877777776655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00094
                             DUF724  87 VkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk 150
                                        ++ +++ l+++ls++d+ +++ +e+++  +  +e++s+ +++++e  e +++i++l+++ ++lk
  gene1538|gene1538|rna1537|rna1537 106 IQRMKEELSRILSMNDHLQRVNSEMQCRLNMYKEKASKLEEIKKECLEHKETISKLRNEIMVLK 169
                                        78999*****************************************************999998 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.6     0.045        17       8      79 ..      63     140 ..      57     163 .. 0.80
   2 ?   -1.1   0.1         5   1.9e+03      31      63 ..     144     176 ..     143     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.045
                           RasGAP_C   8 alenlkeLeelg....vi..srennyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYk 77 
                                        +le+++eLe++         s+ n+ q+ +++I++ ++ k++ ++++keEl+++ +  ++L+  n+ ++ +l+ Yk
  gene1538|gene1538|rna1537|rna1537  63 LLERIEELESAIerlkQAsdSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNMYK 138
                                        56666666654322223322445788999**********************************************9 PP

                           RasGAP_C  78 ay 79 
                                        + 
  gene1538|gene1538|rna1537|rna1537 139 EK 140
                                        86 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5
                           RasGAP_C  31 lneIakdirnkgrlrekrkeElesleetlktLs 63 
                                        l+eI+k+  ++++ + k ++E+ +l+  ++ ++
  gene1538|gene1538|rna1537|rna1537 144 LEEIKKECLEHKETISKLRNEIMVLKGSIQIIC 176
                                        678888888888888888888888887777665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.4     0.027        10      34      90 ..      55     114 ..      49     119 .. 0.84
   2 ?    2.8   9.1      0.15        56      22      88 ..      89     164 ..      65     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.027
                              TMPIT  34 kcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvlkevesllp 90 
                                        ++++++++  +r++el+s++++lk++++   ++++++ve+++++l+ +++ ++++++ l 
  gene1538|gene1538|rna1537|rna1537  55 STRNRESELLERIEELESAIERLKQASDsniNSRQSNVEDINAMLQGKDSEIQRMKEELS 114
                                        5667778888999999999999999866777899999****************9999886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                              TMPIT  22 kqkleelsklqskcskeikkqkkrlkel...ksslkklkksvk......eeeeeeveelkeelkerkkvlkevesl 88 
                                        ++++e+++++ +   +ei++ k++l+++   +++l++++++++      +e+++++ee+k+e  e k++++++ + 
  gene1538|gene1538|rna1537|rna1537  89 QSNVEDINAMLQGKDSEIQRMKEELSRIlsmNDHLQRVNSEMQcrlnmyKEKASKLEEIKKECLEHKETISKLRNE 164
                                        3344555555555555555555554443000444555555544677777777777777777777777777665543 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  16.6     0.031        12      53     149 ..      65     164 ..      53     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.031
                            DUF3552  53 ealleakeeihklreelekelkerrnelqrlekRllqkeetLdrkeeslek...keesleekekelkqkeqsleek 125
                                        e + e    i +l++  ++++++r+++++ ++  l+ k+ +++r +e+l++    +++l++ ++e++ + +  +ek
  gene1538|gene1538|rna1537|rna1537  65 ERIEELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRilsMNDHLQRVNSEMQCRLNMYKEK 140
                                        55666777899*********************************99999853337999****************** PP

                            DUF3552 126 eeeleelveeqrqeLerisgLtke 149
                                         ++lee+++e  ++ e is+L +e
  gene1538|gene1538|rna1537|rna1537 141 ASKLEEIKKECLEHKETISKLRNE 164
                                        *********************876 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.9     0.013       4.9     334     408 ..      55     134 ..      46     141 .. 0.58
   2 ?    6.0   5.7      0.01       3.8     337     441 ..      97     202 ..      93     212 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                               FapA 334 elkeklkeleeeleeleeeleklkkk....ikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkel 404
                                        +++++ +el e++eele+ +e+lk++    i++ ++  +  +++ + k +++++++e++ ++ +   +l++   e+
  gene1538|gene1538|rna1537|rna1537  55 STRNRESELLERIEELESAIERLKQAsdsnINSRQSNVEdINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEM 130
                                        5677779999999999999999999955554444442222444444455555555555544444444444444444 PP

                               FapA 405 keel 408
                                        + +l
  gene1538|gene1538|rna1537|rna1537 131 QCRL 134
                                        4444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.01
                               FapA 337 eklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk. 411
                                        ++l+  + e+++++eel ++ ++ ++l+  +      + +++++k+   ++e++k+e  e++e + +l +e+    
  gene1538|gene1538|rna1537|rna1537  97 AMLQGKDSEIQRMKEELSRILSMNDHLQRVNS---EMQCRLNMYKEKASKLEEIKKECLEHKETISKLRNEIMVLk 169
                                        55666677888888888888888444444222...22345555555555555555555555555555555555552 PP

                               FapA 412 ..keea.kikvnkeiypgvkikigkkkliikre 441
                                           + + +i+ n   + g +i+i +  l+i+ +
  gene1538|gene1538|rna1537|rna1537 170 gsIQIIcRIRPNTPNHHGSRIEISDGYLRISTD 202
                                        222222366666677777777777666666666 PP

>> DUF725  Protein of unknown function (DUF725)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4      0.28   1.1e+02      24      68 ..      49      93 ..      47      97 .. 0.87
   2 ?    8.3   4.3    0.0059       2.2      11     103 ..      68     160 ..      65     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.28
                             DUF725 24 ytkCistaeeekaeidekyeeerqqlessakeicsalqkCdsled 68
                                       y+ C +++ ++ +e+ e++ee  + +e+ ++ + s++++ +s+++
  gene1538|gene1538|rna1537|rna1537 49 YNGCSRSTRNRESELLERIEELESAIERLKQASDSNINSRQSNVE 93
                                       999***********************9999999999987666655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0059
                             DUF725  11 pelnevaeqyeaeytkCistaeeekaeidekyeeerqqlessakeicsalqkCdsledaldafeCyakagsenski 86 
                                        +el+++ e  +++ ++ i++ ++++++i++ ++ + +++++ ++e+ + l+  d+l+ + + ++C  ++ +e+++ 
  gene1538|gene1538|rna1537|rna1537  68 EELESAIERLKQASDSNINSRQSNVEDINAMLQGKDSEIQRMKEELSRILSMNDHLQRVNSEMQCRLNMYKEKASK 143
                                        567778888888888889999******************************************************* PP

                             DUF725  87 lysisanAtelaaklse 103
                                        l++i+++  e ++++s+
  gene1538|gene1538|rna1537|rna1537 144 LEEIKKECLEHKETISK 160
                                        *****998888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1826  (0.101846); expected 358.6 (0.02)
Passed bias filter:                      848  (0.0472977); expected 358.6 (0.02)
Passed Vit filter:                       172  (0.0095934); expected 17.9 (0.001)
Passed Fwd filter:                        55  (0.00306766); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 1.05u 0.33s 00:00:01.38 Elapsed: 00:00:00.55
# Mc/sec: 2737.04
//
Query:       gene1539|gene1539|rna1538|rna1538  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0059   16.9   3.1      0.018   15.3   0.1    2.7  2  zf-C2H2_2  C2H2 type zinc-finger (2 copies)
  ------ inclusion threshold ------
      0.037   14.5   2.1      0.039   14.4   0.1    2.2  2  zf-C2H2    Zinc finger, C2H2 type
      0.064   14.1   0.1      0.064   14.1   0.1    2.6  3  zf-C2H2_4  C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.099   5.9e+02      52      76 ..       2      24 ..       1      34 [. 0.71
   2 !   15.3   0.1   3.1e-06     0.018      47      80 ..     111     143 ..      87     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.099
                          zf-C2H2_2 52 eClyCekefkslealreHmkkkgHc 76
                                       +C  C+ e     ++++H +++ H+
  gene1539|gene1539|rna1538|rna1538  2 KCSACQVEI--GGNIKAHYASEVHK 24
                                       788888874..46788888888886 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.1e-06
                          zf-C2H2_2  47 ieekleClyCekefkslealreHmkkkgHckine 80 
                                        i+ +  C++C + f++ + lr H+++ +H+  ++
  gene1539|gene1539|rna1538|rna1538 111 IN-NRVCYVCYEAFSDYDGLRRHISSGNHRSAMT 143
                                        44.499***********************98765 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3       2.8   1.7e+04      18      23 .]      96     101 ..      95     101 .. 0.68
   2 ?   14.4   0.1   6.5e-06     0.039       2      23 .]     115     138 ..     115     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                        HHHHCC CS
                            zf-C2H2  18 rHirtH 23 
                                         H+++H
  gene1539|gene1539|rna1538|rna1538  96 IHYKSH 101
                                        577777 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.5e-06
                                        EETTTTEEESSHHHHHHHHHC..C CS
                            zf-C2H2   2 kCpdCgksFkrksnLkrHirt..H 23 
                                        +C +C + F++ + L+rHi++  H
  gene1539|gene1539|rna1538|rna1538 115 VCYVCYEAFSDYDGLRRHISSgnH 138
                                        6******************97555 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       2.2   1.3e+04       2       7 ..       2       7 ..       2      10 .. 0.80
   2 ?   -1.5   0.2       1.2   6.9e+03       3       7 ..      86      90 ..      84     101 .. 0.49
   3 ?   14.1   0.1   1.1e-05     0.064       2      21 ..     115     134 ..     114     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                          zf-C2H2_4 2 kCpiCg 7
                                      kC+ C+
  gene1539|gene1539|rna1538|rna1538 2 KCSACQ 7
                                      799994 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                          zf-C2H2_4  3 CpiCg 7 
                                       C +C+
  gene1539|gene1539|rna1538|rna1538 86 CLFCD 90
                                       55552 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.1e-05
                          zf-C2H2_4   2 kCpiCgksFsskkaLlrHlk 21 
                                         C +C + Fs++++L+rH+ 
  gene1539|gene1539|rna1538|rna1538 115 VCYVCYEAFSDYDGLRRHIS 134
                                        6*****************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1262.62
//
Query:       gene1540|gene1540|rna1539|rna1539  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-49  166.3   1.1    5.7e-49  166.0   1.1    1.1  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0   1.1   3.2e-53   5.7e-49       1     159 [.      47     228 ..      47     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 3.2e-53
                                        EEEEE-TTCSEEEEEETTT...........TEEEEEEE-SSSB-BSSEEEEETT--BT.......CCBEETSSSEE CS
                    Pyrophosphatase   1 vvvEiprgsnaKyeidkee...........gklrldrvlftskgypanYGfipqTled.......telkGDgDPlD 58 
                                        vv Eipr +n K+ei+kee           g +r+++++f+ kgy +nYG++pqT+e+        ++kGD+DPlD
  gene1540|gene1540|rna1539|rna1539  47 VVNEIPRFENGKFEINKEErfnpikqdsknGWPRFVKNVFPMKGYLWNYGALPQTWENpheidkhVGAKGDNDPLD 122
                                        799*************************************************************99********** PP

                                        EEEESSS---TTEEEEEEEEEEEEEEETTEEEEEEEEEETTSGGGTT-SSGGG...STHHHHHHHHHHHHHTTTTS CS
                    Pyrophosphatase  59 vlvlgeeplspgevvevkvlGvlamiDegetDdKiiavpvkdprlkkindied...lpgllleeiehfFetykdle 131
                                        v+++g ++ + gev+++kvlG +a++De+e D+K+++++v+d++ k+indied    ++ lle++  +Fe+yk ++
  gene1540|gene1540|rna1539|rna1539 123 VIEIGARRKEIGEVYQAKVLGSIALVDEDECDWKVVVIDVNDEKAKEINDIEDvrkAYRGLLEQTIFWFENYKVPD 198
                                        *****7777**********************************99********888555666************** PP

                                        CCT-SE.EEE.EEEEHHHHHHHHHHHHHHH CS
                    Pyrophosphatase 132 gkkknv.kve.ewkdkeeAekvieeahery 159
                                        gk+kn  +++ ++ +ke++++++++ahe++
  gene1540|gene1540|rna1539|rna1539 199 GKSKNSfALDgKYMNKEFTVNIVKSAHENW 228
                                        **99877*********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1756.09
//
Query:       gene154|gene154|rna154|rna154  [L=500]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3326.48
//
Query:       gene1541|gene1541|rna1540|rna1540  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.1e-49  165.5   0.0    8.2e-49  165.3   0.0    1.0  1  Ras        Ras family
    3.3e-25   88.6   0.0    1.3e-24   86.7   0.0    1.7  2  Roc        Ras of Complex, Roc, domain of DAPkinase
    4.8e-08   32.7   0.0    5.7e-08   32.4   0.0    1.1  1  Arf        ADP-ribosylation factor family
     0.0034   16.8   0.0      0.005   16.2   0.0    1.3  1  Gtr1_RagA  Gtr1/RagA G protein conserved region
  ------ inclusion threshold ------
      0.022   14.2   0.0      0.031   13.7   0.0    1.2  1  SRPRB      Signal recognition particle receptor beta subunit
        0.1   12.0   0.0       0.15   11.4   0.0    1.2  1  TniB       Bacterial TniB protein
        0.1   12.4   0.0       0.15   11.8   0.0    1.3  1  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
       0.19   12.2   0.0       0.49   10.9   0.0    1.6  1  ABC_tran   ABC transporter


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.0   3.7e-52   8.2e-49       1     160 [.      10     178 ..      10     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 3.7e-52
                                        EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET.TEEEEEEEEEETTSGGGHHHHHHHHTTESEE CS
                                Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd.gkevkleiwDTAGqeefkslrelyyrdaegi 75 
                                        K+v++Gd+a+GKt+ll  f +++F+e+y++T+ vd+++ke+++d +k v+l +wDTAGqe+++++r+l+y++++ +
  gene1541|gene1541|rna1540|rna1540  10 KVVIIGDGACGKTCLLEVFRRNQFPETYIPTV-VDNFVKEVKIDdDKYVSLALWDTAGQEDYDTIRPLSYKETDLV 84 
                                        9*******************************.**********967899*************************** PP

                                        EEEEETTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGG........G-SS-HHHHHHHHHHHT.SEEEEE CS
                                Ras  76 llvyditsresfenvk.kwveeikrvaeenvpivLvGnKvDlee........kravsteegeelakelg.lkflet 141
                                        ll+y i++++   n++ kw+ eik++++ + ++ L+G K D+++        + +vs++eg+++a++++ +kf+e+
  gene1541|gene1541|rna1540|rna1540  85 LLCYTIENKKKIPNISrKWLMEIKNYCP-SSQFFLIGLKKDVRDmedptvdkSSMVSESEGRKIADNINaAKFFEC 159
                                        ***************99***********.59********************999***************99***** PP

                                        BTTTTCTHHHHHHHHHHHH CS
                                Ras 142 SAktnenveeafeellrei 160
                                        S +t+env+ +f e++++i
  gene1541|gene1541|rna1540|rna1540 160 SSRTRENVNLVFLEAAKHI 178
                                        ***************9987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.0   5.8e-28   1.3e-24       1     119 [.      10     124 ..      10     125 .. 0.87
   2 ?   -0.5   0.0      0.61   1.4e+03      12      66 ..     135     184 ..     130     196 .. 0.55

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 5.8e-28
                                        EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHH CS
                                Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhply 76 
                                        Kvv++Gd++ GKt+ll+ f +++f e++ +t+  +f++ ev ki+     +  k v+l++WDtaGqe++++++pl 
  gene1541|gene1541|rna1540|rna1540  10 KVVIIGDGACGKTCLLEVFRRNQFPETYIPTVVDNFVK-EV-KID-----D-DKYVSLALWDTAGQEDYDTIRPLS 77 
                                        9*******************************999864.55.333.....2.3679******************** PP

                                        HCTSCEEEEEEEGHHHH...CH.HHHHHHHHHHCSSS-EEEEEE-TT CS
                                Roc  77 lreaalailvydsrsse...nl.keWlkelkkvagkspvilvgnkiD 119
                                        ++e +l++l+y+ ++++   n+ ++Wl e+k+++++s+++l+g k D
  gene1541|gene1541|rna1540|rna1540  78 YKETDLVLLCYTIENKKkipNIsRKWLMEIKNYCPSSQFFLIGLKKD 124
                                        ***********96655412243379******************9998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.61
                                        HHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SG CS
                                Roc  12 KtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGq 66 
                                        K+s++++   +k+ ++ ++    + ++++ ++++ v       +   +iW t G 
  gene1541|gene1541|rna1540|rna1540 135 KSSMVSESEGRKIADNINAAKFFECSSRTRENVNLVFL-----EAAKHIWNTKGA 184
                                        66666666666655555544444444444334433322.....233478888775 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.5e-11   5.7e-08      11     164 ..       5     167 ..       1     177 [. 0.72

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.5e-11
                                        .TTEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEE.EEEEEE...TTEEEEEEEE-SSGGGGGGGGGGCTT CS
                                Arf  11 kkkelrilllGLDnaGKtTilkklkleelvt.tvPTigfn.veelei...knlkftvwDvGGqeklRplWknYfek 81 
                                        ++k+ +++++G  + GKt +l+ ++ +++ +  +PT+  n v+e++i   k +++ +wD  Gqe    +    +++
  gene1541|gene1541|rna1540|rna1540   5 THKSGKVVIIGDGACGKTCLLEVFRRNQFPEtYIPTVVDNfVKEVKIdddKYVSLALWDTAGQEDYDTIRPLSYKE 80 
                                        4799************************976379**9877589***9777789**********98888888899** PP

                                        ESEEEEEEETT-CTTHHHHHHHHHHHCTSGC.CTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGG....SS.SSSSE CS
                                Arf  82 tdavifvvDsadreRleeakeeLkalleeee.lkevallvlaNKqDlpealseeelrellglee....lk.gkrkl 151
                                        td v+ +    +++++ + +++   l+e ++   + ++ +++ K+D+++  + +  ++++  e+    +  + +  
  gene1541|gene1541|rna1540|rna1540  81 TDLVLLCYTIENKKKIPNISRKW--LMEIKNyCPSSQFFLIGLKKDVRDMEDPTVDKSSMVSESegrkIAdNINAA 154
                                        *****999999999998876653..333333033556666677777766443332222222222333344344556 PP

                                        EEEEEBTTTTBTH CS
                                Arf 152 eiqkcsavkgegl 164
                                        + ++cs  ++e++
  gene1541|gene1541|rna1540|rna1540 155 KFFECSSRTRENV 167
                                        6777777777765 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-06     0.005       1      64 [.      10      73 ..      10     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-06
                          Gtr1_RagA  1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafvee 64
                                       kv+++G +  GKt++ ++   n  ++  +   +   v++ ++   + + l lwD  Gqe++ + 
  gene1541|gene1541|rna1540|rna1540 10 KVVIIGDGACGKTCLLEVFRRNQFPETYIPTVVDNFVKEVKIDDDKYVSLALWDTAGQEDYDTI 73
                                       899***************99999999988888888889999999999************98654 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.4e-05     0.031       4      60 ..       9      68 ..       6      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                       -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG.....GGTT-SEEEETT-G CS
                              SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkv..ksekgskltliDfPGhe 60
                                        +v+++G   +GKT l++    +++ +t++     +++++v  +++k  +l+l D  G+e
  gene1541|gene1541|rna1540|rna1540  9 GKVVIIGDGACGKTCLLEVFRRNQFPETYIPTvVDNFVKEVkiDDDKYVSLALWDTAGQE 68
                                       679**************************9988888888883355556677778888876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.8e-05      0.15      33      62 ..       6      35 ..       2      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.8e-05
                               TniB 33 krmpnlllvGdsnnGKtmivekFarlhppe 62
                                       ++  +++++Gd ++GKt ++e F+r++ pe
  gene1541|gene1541|rna1540|rna1540  6 HKSGKVVIIGDGACGKTCLLEVFRRNQFPE 35
                                       5667899*****************998655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.7e-05      0.15       3      42 ..      12      45 ..      10      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
                             AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggi 42
                                       v+iG+ ++GK+ LL+ +      +r+++++t++++   ++
  gene1541|gene1541|rna1540|rna1540 12 VIIGDGACGKTCLLEVF------RRNQFPETYIPTVVDNF 45
                                       9****************......88889998888776665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.49       7      37 ..       4      34 ..       1      44 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkp 37
                                       k +++ kv+i+G+  +GK+ Ll+++ ++  p
  gene1541|gene1541|rna1540|rna1540  4 KTHKSGKVVIIGDGACGKTCLLEVFRRNQFP 34
                                       6678899*****************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1284.51
//
Query:       gene1542|gene1542|rna1541|rna1541  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-16   58.5   0.2    7.2e-16   58.1   0.2    1.3  1  Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein


Domain annotation for each model (and alignments):
>> Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.2     4e-20   7.2e-16      25     121 .]      53     148 ..      11     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4e-20
                                        TTEEEEEESS-HHHHHHHHHHTTT-EEEEEEEEEECCSECCEEEEEEEEE--TTS-HHHHHHHHHHHHHHHHHCTT CS
                        Cofilin_ADF  25 keeivveeegetyeelreelpeseprYavydveyehddeskrsklvfIswvPdsapikqkmlyasskdalkkelkg 100
                                        k + ++ee +et+ee++e ++e++p+++vyd+ + +dd+ ++++l++Is++P+ + + +k+ y+++  +lk+ l  
  gene1542|gene1542|rna1541|rna1541  53 KRKYTIEELHETFEEFLEGINEKDPCFVVYDFIHFDDDGIQKNTLCLISYIPEHLMPLEKVAYSTNVLNLKDLL-D 127
                                        33444555555999999999******************************************************.9 PP

                                        SEEEEEE-CGGCCSHHHHHHH CS
                        Cofilin_ADF 101 isveieatdldelteeelkek 121
                                        isv+i + +++++  +++ ek
  gene1542|gene1542|rna1541|rna1541 128 ISVHIPIKKKSDFIFDDIAEK 148
                                        ************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 921.81
//
Query:       gene1543|gene1543|rna1542|rna1542  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 818.99
//
Query:       gene1544|gene1544|rna1543|rna1543  [L=282]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-55  186.3   5.7    1.4e-54  185.4   5.7    1.4  1  Pox_MCEL         mRNA capping enzyme
    7.7e-15   55.4   0.0    2.1e-14   54.0   0.0    1.7  2  Methyltransf_25  Methyltransferase domain
      5e-14   52.4   0.0    6.6e-14   52.0   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    3.3e-13   50.1   0.0    6.4e-13   49.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      1e-10   42.2   0.0    2.5e-10   41.0   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    1.2e-10   41.5   0.0    1.7e-10   41.0   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    2.3e-06   27.0   0.0      5e-05   22.6   0.0    2.2  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
    6.7e-05   22.4   0.0    0.00011   21.7   0.0    1.3  1  TehB             Tellurite resistance protein TehB
    0.00055   20.0   0.0      0.001   19.1   0.0    1.5  1  Methyltransf_32  Methyltransferase domain
    0.00087   18.9   0.0     0.0013   18.3   0.0    1.2  1  MTS              Methyltransferase small domain
      0.001   18.5   0.0     0.0026   17.2   0.0    1.7  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0047   16.2   0.1     0.0097   15.2   0.1    1.5  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0062   16.3   0.2      0.064   13.0   0.0    2.1  2  N6_N4_Mtase      DNA methylase
     0.0089   15.7   0.0      0.014   15.0   0.0    1.2  1  NodS             Nodulation protein S (NodS)
  ------ inclusion threshold ------
      0.016   15.9   2.3       0.16   12.6   0.0    3.1  4  Bin3             Bicoid-interacting protein 3 (Bin3)
      0.028   14.0   0.0      0.044   13.4   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
      0.091   12.8   0.1       0.37   10.8   0.0    2.1  2  DUF4346          Domain of unknown function (DUF4346)


Domain annotation for each model (and alignments):
>> Pox_MCEL  mRNA capping enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4   5.7   1.4e-57   1.4e-54       9     291 ..       3     254 ..       1     277 [. 0.89

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 1.4e-57
                           Pox_MCEL   9 evtdlvathynerpetgellkkRiastiiylrnlnNyiKslLiseyasktkldesnklkvLdldcgkGgDLeKyek 84 
                                        + ++ +++hyn+ +e g  ++ R++s+ i +rn nN+iK  Li +y++k ++       vLdl+cgkGgDL Kyek
  gene1544|gene1544|rna1543|rna1543   3 NKKEEIRKHYNSIKERG--REVRQRSRAINIRNTNNFIKACLIRLYTKKGDT-------VLDLGCGKGGDLLKYEK 69 
                                        567789***********..899*****************************9.......***************** PP

                           Pox_MCEL  85 geIsklvatDiaeesieeckeRYnklrsekkskyykFdaelirsdsfvssvrevfedyelkfdivslQFaiHYsFe 160
                                        ++I+++ ++Diae si+++  R    +++k+    +F++ + + d ++++++        +fdivs QF++HY+F 
  gene1544|gene1544|rna1543|rna1543  70 AGIDEYYGIDIAEISIRDAYVRA---ENMKR----RFKVSFKAQDVYNQHISL-----GRQFDIVSSQFSFHYAFS 133
                                        *****************997766...33333....59999********99974.....569*************** PP

                           Pox_MCEL 161 seekartvlrNvaellasGGkvlgTtpdgdelskltvkklkviekdlpsfgNsiyvvkfeeekievplfGakYeyn 236
                                        s e  ++ l Nv + l++GG++++T+p+ +++       l++ +    ++ N+ y+++++++++      ++Y++ 
  gene1544|gene1544|rna1543|rna1543 134 SDESLDISLGNVVRHLKPGGYFIITVPSKEVI-------LERYR--RGKISNEFYKIEIDKKEDAPIESVKEYRFT 200
                                        ********************************.......34443..34688*********888777677899**** PP

                           Pox_MCEL 237 ledvvkdvpEyivkfealvklaeeYgleLvdkkdfaeiieesikkelkklikrvs 291
                                        l d v++++Ey v+f ++   +++ g++L+++k f +++ee+  +++++l k+++
  gene1544|gene1544|rna1543|rna1543 201 LVDSVNNCVEYFVEFTKMLDGFKKLGVVLIERKGFIDFLEEE-SRRNQELFKHMR 254
                                        ******************************************.555788888876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0     2e-17   2.1e-14       1      97 []      53     153 ..      53     153 .. 0.87
   2 ?   -2.3   0.0       7.2   7.6e+03      21      36 ..     196     211 ..     172     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 2e-17
                                        EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH..TTTTEEEEESBCCGBSS.STTTEEEEEEEST CS
                    Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee..eglnvefvqgdaedlpf.edgsfDlvvssga 73 
                                        vLdlGcG+G ++l+  k+ g  +++g+Di+e  ++ a  rae+  ++++v+f  +d+ + +    ++fD+v s+++
  gene1544|gene1544|rna1543|rna1543  53 VLDLGCGKGGDLLKYEKA-GIDEYYGIDIAEISIRDAYVRAENmkRRFKVSFKAQDVYNQHIsLGRQFDIVSSQFS 127
                                        9*****************.69*************99988887754666*********776641556********** PP

                                        GGG..SSHHHHHHHHHHHHHHEEEEE CS
                    Methyltransf_25  74 lhh..lsdedlekalkeiarvLkpgG 97 
                                        +h+   sde l+  l ++ r+LkpgG
  gene1544|gene1544|rna1543|rna1543 128 FHYafSSDESLDISLGNVVRHLKPGG 153
                                        **983456778889***********9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.2
                                        SSEEEEEESSHHHHHH CS
                    Methyltransf_25  21 kakvtgvDiseemlea 36 
                                        ++++t vD   +++e+
  gene1544|gene1544|rna1543|rna1543 196 EYRFTLVDSVNNCVEY 211
                                        4666777766666655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   6.2e-17   6.6e-14       2     119 ..      48     165 ..      47     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 6.2e-17
                    Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieelekl.ledekf 75 
                                        +kg +vlDlGCG+G ++++   ++g   e++GiDi e +i+ A  +a++ +    v+F+++d+ +     l  ++f
  gene1544|gene1544|rna1543|rna1543  48 KKGDTVLDLGCGKGGDLLKYE-KAG-IDEYYGIDIAEISIRDAYVRAENMKRRfKVSFKAQDVYNQH-IsLG-RQF 119
                                        6899**************999.444.257*******************9999999********9944.2266.9** PP

                    Methyltransf_31  76 Dlilsnevlnaladpdkile....eiervlkpggilliedprllaelp 119
                                        D++ s+  +++  ++d+ l     ++ r lkpgg+++i+ p+  +e++
  gene1544|gene1544|rna1543|rna1543 120 DIVSSQFSFHYAFSSDESLDislgNVVRHLKPGGYFIITVPS--KEVI 165
                                        **9999666555555544444444***************999..3333 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0     6e-16   6.4e-13       1      96 []      54     157 ..      54     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 6e-16
                                        EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHH..HHHCCHHT-EEEETTEECCC..TSS-TT-EEEEEEES-C CS
                    Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlkla..kekaseeglkvefvvadaek..lpfednsfDlvvssevl 71 
                                        Ld+GcG+G  + +++k+g  +++g+D+++  ++ a  ++++ ++++kv+f  +d+ +  + +   +fD+v s++++
  gene1544|gene1544|rna1543|rna1543  54 LDLGCGKGGDLLKYEKAGiDEYYGIDIAEISIRDAyvRAENMKRRFKVSFKAQDVYNqhISLGR-QFDIVSSQFSF 128
                                        8*******************************666336666666669*********73355555.*********** PP

                                        CC-....CCHHHHHHHHHHHEEEEEEEEE CS
                    Methyltransf_11  72 hhv....edpekalkeiaRvLkpgGllvi 96 
                                        h+     e ++  l +++R LkpgG+++i
  gene1544|gene1544|rna1543|rna1543 129 HYAfssdESLDISLGNVVRHLKPGGYFII 157
                                        ****99999******************97 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   2.4e-13   2.5e-10       1      99 []      54     155 ..      54     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.4e-13
                    Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg..ssfDlvvasn 74 
                                        L++GcG G  l   +++    ey+g+Di + +i da  +    +  +  +v ++a+d+ +++ +   +fD+v + +
  gene1544|gene1544|rna1543|rna1543  54 LDLGCGKGGDLLKYEKA-GIDEYYGIDIAEISIRDAYVRAENMK--RRFKVSFKAQDVYNQHISlgRQFDIVSSQF 126
                                        8*************999.7889***********55544444444..444677777777666666668********* PP

                    Methyltransf_12  75 vlhhl....kdirevldnirklLkpgGrl 99 
                                         +h+     + ++ +l n+ ++LkpgG++
  gene1544|gene1544|rna1543|rna1543 127 SFHYAfssdESLDISLGNVVRHLKPGGYF 155
                                        *****999999999999**********85 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.6e-13   1.7e-10      19     124 ..      46     164 ..      22     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.6e-13
                    Methyltransf_23  19 klraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae....kakkaqkdqfdeqeaae....pqgkfdl 85 
                                        + ++g  vLd+GcG+G  l  +++ g  +++g+D+ ++ +  a     + k  +k++f +q+  +      ++fd+
  gene1544|gene1544|rna1543|rna1543  46 YTKKGDTVLDLGCGKGGDLLKYEKAGIdEYYGIDIAEISIRDAYvraeNMKRRFKVSFKAQDVYNqhisLGRQFDI 121
                                        368889**********99999*****999******9887776668888555555555544444444444666**** PP

                    Methyltransf_23  86 Ivlrevlehvp....dppellrqiatllkpgGylllseplasl 124
                                        +++ ++++       ++   l ++ ++lkpgGy+++++p ++ 
  gene1544|gene1544|rna1543|rna1543 122 VSSQFSFHYAFssdeSLDISLGNVVRHLKPGGYFIITVPSKEV 164
                                        ***9999876623225779999****************98765 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.076        80      47      66 ..      43      59 ..      14      61 .. 0.77
   2 !   22.6   0.0   4.8e-08     5e-05     134     199 ..      94     159 ..      80     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.076
                                       HHHHHTSSS-ECEEEEET-T CS
                     NNMT_PNMT_TEMT 47 lqtlatgekkgdtllDiGaG 66
                                       ++      kkgdt+lD+G G
  gene1544|gene1544|rna1543|rna1543 43 IR---LYTKKGDTVLDLGCG 59
                                       33...33589********99 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 4.8e-08
                                        HEEEEEE--TTSSSTTTTSS-SS..EEEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEE CS
                     NNMT_PNMT_TEMT 134 lvkrvlkvdvhqspvvlagvqlpkkadvvvtifcleaacedleeylralrnlasllkpGGhlvlgg 199
                                        ++kr +kv  + ++v    ++l +++d+v++ f++ +a ++ e+   +l n++++lkpGG++++++
  gene1544|gene1544|rna1543|rna1543  94 NMKRRFKVSFKAQDVYNQHISLGRQFDIVSSQFSFHYAFSSDESLDISLGNVVRHLKPGGYFIITV 159
                                        57777888888888888889999****************************************986 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     1e-07   0.00011      33     133 ..      52     158 ..      32     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1e-07
                                        EEEEES-TTSHHHHHHHHTT-E.EEEEES-HHHH..HHHHHHHHHTT-TTEEEEE--GGG..----S-EEEEEEES CS
                               TehB  33 kvldlgcgqgrnslylsllgyd.vtawdknensi..afleeikekenlknistalydine..aklderydfilstv 103
                                         vldlgcg+g + l  +  g d    +d  e si  a+++  + k  +k +s +  d+ +  ++l +++d++ s  
  gene1544|gene1544|rna1543|rna1543  52 TVLDLGCGKGGDLLKYEKAGIDeYYGIDIAEISIrdAYVRAENMKRRFK-VSFKAQDVYNqhISLGRQFDIVSSQF 126
                                        69******************98356899999999333555555555565.77777777551167789***999988 PP

                                        SG..GGS-GGGHHHHHHHHHHTEEEEEEEEEE CS
                               TehB 104 vl..mfleaeripsiienmqectkvggynliv 133
                                         +   f   e++   + n+ ++ k+ggy +i 
  gene1544|gene1544|rna1543|rna1543 127 SFhyAFSSDESLDISLGNVVRHLKPGGYFIIT 158
                                        762257889999999*************9875 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.8e-07     0.001       6      91 ..      31     110 ..       4     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.8e-07
                    Methyltransf_32   6 verlaelvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkr 81 
                                        ++++ +++++ l +l  +++  tv+D+G+Gkg  +  l++ ek    + +gid+ e  +++a  rae+++++f  +
  gene1544|gene1544|rna1543|rna1543  31 IRNTNNFIKACLIRL-YTKKGDTVLDLGCGKG--GDLLKY-EKAGIDEYYGIDIAEISIRDAYVRAENMKRRF--K 100
                                        667778888866664.566689**********..9*****.44446789*********************999..5 PP

                    Methyltransf_32  82 lsfaelsiee 91 
                                        +sf+ +++ +
  gene1544|gene1544|rna1543|rna1543 101 VSFKAQDVYN 110
                                        5555555443 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0013      27     139 ..      45     159 ..      38     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                                        CHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHH..TTGCEEEEE-STTTTST..TS-E CS
                                MTS  27 lpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenlea..nklevevvasdvleeve..ekkf 98 
                                        l +++ ++vlDlGcG G   ++  k+  + e   +d+   +++ a   +e+   +++v++ a+dv+++     ++f
  gene1544|gene1544|rna1543|rna1543  45 LYTKKGDTVLDLGCGKGGDLLKYEKAGID-EYYGIDIAEISIRDAYVRAENmkRRFKVSFKAQDVYNQHIslGRQF 119
                                        55567889*********655555554444.355555555555554444443004456*********99764569** PP

                                        EEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEE CS
                                MTS  99 dlivsNPPfhagkatelavaeeliaeAkeaLkegGeLliVa 139
                                        d++ s   fh     ++++ +  + +  ++Lk+gG ++i +
  gene1544|gene1544|rna1543|rna1543 120 DIVSSQFSFHYAFSSDESL-DISLGNVVRHLKPGGYFIITV 159
                                        **********999955555.5556778999****9988755 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.4e-06    0.0026     158     230 ..      46     122 ..      38     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                               PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva.lseellk.....eeka 227
                                        + k+g++vlD+G+G G   +   k g ++ +++Di e++++ a    +  +++++++v   ++++ +      +++
  gene1544|gene1544|rna1543|rna1543  46 YTKKGDTVLDLGCGKGGDLLKYEKAGIDEYYGIDIAEISIRDAYV--RAENMKRRFKVSfKAQDVYNqhislGRQF 119
                                        7899************999*********************98854..33345555555312233332222235667 PP

                               PrmA 228 dvi 230
                                        d++
  gene1544|gene1544|rna1543|rna1543 120 DIV 122
                                        766 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.2e-06    0.0097      52     164 ..      39     157 ..      32     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.2e-06
                                        HHHHTTTT--TT-EEEEES-TTSHHHHHHH.....HHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GG CS
                               CMAS  52 dlileklelkpGmtlLdiGcGWGslvrrav.....erydvkvvglTlSkeqaklakkrvdeldlerkvevklldye 122
                                        +  l +l  k+G+t+Ld+GcG G+ + +       e y++++  + + +  + +a+++  +  ++ k++  + ++ 
  gene1544|gene1544|rna1543|rna1543  39 KACLIRLYTKKGDTVLDLGCGKGGDLLKYEkagidEYYGIDIAEISIRD-AYVRAENMKRRFKVSFKAQDVYNQHI 113
                                        666778999************9986655430111134556666555533.33333333334444444444444555 PP

                                        G-----SEEEEES-GGGT..SGGGHHHHHHHHHHHS-TT-EEEE CS
                               CMAS 123 dldekvdrvvsvgafehv..gkenydtffkklkkllkedGllll 164
                                         l  ++d v+s   f       e++d    ++ + lk++G +++
  gene1544|gene1544|rna1543|rna1543 114 SLGRQFDIVSSQFSFHYAfsSDESLDISLGNVVRHLKPGGYFII 157
                                        67779998888666653334556778888888888888888775 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   6.1e-05     0.064     184     223 ..      42      82 ..       5      90 .. 0.85
   2 ?    1.3   0.0      0.22   2.3e+02      41     110 ..     144     217 ..     136     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
                                        HHHHHS-TT-EEEETT-TT.THHHHHHHHTT-EEEEEESSH CS
                        N6_N4_Mtase 184 lIklstkkgdivlDpFaGS.GtTavaakelgrkfiGieiee 223
                                        lI+l+tkkgd+vlD  +G  G  +++ k+   +++Gi+i e
  gene1544|gene1544|rna1543|rna1543  42 LIRLYTKKGDTVLDLGCGKgGDLLKYEKAGIDEYYGIDIAE 82 
                                        79****************94456666666667799999877 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.22
                                        HHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCC.......S-B--EEEEEEEE CS
                        N6_N4_Mtase  41 evrrvLkddgsifiniddseikkelkaladeifggffllnvivwkkpnsmpesnkd.......rltsthEyilvfs 109
                                        +v r Lk++g ++i +  +e    l    + ++  + +++  + kk+ +  es+k+       ++++  Ey++ f+
  gene1544|gene1544|rna1543|rna1543 144 NVVRHLKPGGYFIITVPSKEVI--LERYRRGKIS-NEFYKIEIDKKEDAPIESVKEyrftlvdSVNNCVEYFVEFT 216
                                        6789999999999999888864..4444444444.66666666666666666666666666667777777777777 PP

                                        S CS
                        N6_N4_Mtase 110 k 110
                                        k
  gene1544|gene1544|rna1543|rna1543 217 K 217
                                        6 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05     0.014      45     150 ..      51     163 ..      32     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                               NodS  45 adalevGcaaGa.lterlapyckrltvvdvveeaiararer...vkesshiswivsdv..qqfstdekfdlivvae 114
                                          +l++Gc  G  l +      +    +d+ e +i  a  r   +k+  ++s+  +dv  q++s+ ++fd++    
  gene1544|gene1544|rna1543|rna1543  51 DTVLDLGCGKGGdLLKYEKAGIDEYYGIDIAEISIRDAYVRaenMKRRFKVSFKAQDVynQHISLGRQFDIVSSQF 126
                                        35889999876524444445567778899999999888776222555678********666799******988876 PP

                               NodS 115 vlyy.iedvaelraavrnlvsllapdgqlvfGsarda 150
                                         ++y  +  + l  ++ n+v+ l+p+g+++   + ++
  gene1544|gene1544|rna1543|rna1543 127 SFHYaFSSDESLDISLGNVVRHLKPGGYFIITVPSKE 163
                                        66552678899*******************9877655 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.2   1.2e+03      54      75 ..       3      24 ..       1      49 [. 0.68
   2 ?   -2.2   0.0         6   6.3e+03      46      66 ..      86     106 ..      77     129 .. 0.67
   3 ?   12.6   0.0   0.00016      0.16      18     107 ..     134     223 ..     128     224 .. 0.76
   4 ?    1.8   0.1      0.36   3.8e+02      26      67 ..     215     257 ..     213     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                               Bin3 54 klseelkenykelklrpedfee 75
                                       +++ee++++y+++k r  ++++
  gene1544|gene1544|rna1543|rna1543  3 NKKEEIRKHYNSIKERGREVRQ 24
                                       5567777778777777665443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6
                               Bin3  46 wksYkkkkklseelkenykel 66 
                                         + Y +++++++++k ++k+ 
  gene1544|gene1544|rna1543|rna1543  86 RDAYVRAENMKRRFKVSFKAQ 106
                                        566777777777777666553 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00016
                               Bin3  18 gDeglkrlfkkiyellkpgGvlilEpqewksYkkkkklseelkenykelklrpe..dfeevLleevgfesveelee 91 
                                         De l   + +++++lkpgG++i+   +++   ++ ++  ++++++ ++++ ++  +  e ++e + f++v+++++
  gene1544|gene1544|rna1543|rna1543 134 SDESLDISLGNVVRHLKPGGYFIITVPSKEVILERYRR-GKISNEFYKIEIDKKedAPIESVKE-YRFTLVDSVNN 207
                                        699999999****************9999888877777.7889999999987763233344444.99999999987 PP

                               Bin3  92 keeeskgfkRpilvyr 107
                                          e    f + +  ++
  gene1544|gene1544|rna1543|rna1543 208 CVEYFVEFTKMLDGFK 223
                                        7666566666666555 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.36
                               Bin3  26 fkkiyellkpgGvlilEpqewksYk.kkkklseelkenykelk 67 
                                        f+k+ +  k+ Gv+++E + +  +  +++++++el ++++  +
  gene1544|gene1544|rna1543|rna1543 215 FTKMLDGFKKLGVVLIERKGFIDFLeEESRRNQELFKHMRVRR 257
                                        88999999999*********99998344555666655544434 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.1e-05     0.044       9      54 ..      45      90 ..      39     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                               MetW  9 elikpgsrvldlGcGdG.ellellkeekqvdg.rGleldeegvaecva 54
                                        + k+g +vldlGcG+G +ll++   + ++d  +G+++ e ++ ++  
  gene1544|gene1544|rna1543|rna1543 45 LYTKKGDTVLDLGCGKGgDLLKYE--KAGIDEyYGIDIAEISIRDAYV 90
                                       5568899********962666654..4578753699998888877655 PP

>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0         2   2.1e+03      31      56 ..       8      31 ..       2      49 .. 0.65
   2 ?   10.8   0.0   0.00036      0.37       2      47 ..     138     182 ..     137     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                            DUF4346 31 vakhysnainekGlavdpetgevisc 56
                                       + khy n i e+G+ v  + ++ i++
  gene1544|gene1544|rna1543|rna1543  8 IRKHY-NSIKERGREVRQR-SRAINI 31
                                       45666.6788888877665.344444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00036
                            DUF4346   2 ldeklskRaielDpaGYflikvdreaklivakhysnainekGlavd 47 
                                        ld +l + + +l p+GYf+i+v ++ + i+ ++ + +i ++ + ++
  gene1544|gene1544|rna1543|rna1543 138 LDISLGNVVRHLKPGGYFIITVPSK-EVILERYRRGKISNEFYKIE 182
                                        566777777899*********9543.33333333334443333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 1920.17
//
Query:       gene1545|gene1545|rna1544|rna1544  [L=514]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-07   30.4   4.9    3.2e-07   30.4   4.9    1.9  2  Sec5      Exocyst complex component Sec5
  ------ inclusion threshold ------
      0.082   12.9   0.1       0.53   10.3   0.1    2.2  1  DUF489    Protein of unknown function (DUF489)


Domain annotation for each model (and alignments):
>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   4.9   3.5e-11   3.2e-07       4     165 ..      53     200 ..      50     225 .. 0.87
   2 ?   -2.4   0.0      0.38   3.4e+03      45      56 ..     418     429 ..     387     469 .. 0.56

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3.5e-11
                               Sec5   4 lkslvksnftkfvkvkdtldqiykefseskteaqedslveeLeeslneairkttllfkpvlenkekadklraalev 79 
                                         k+lvk++f kfv++   l++i  +++++     ++  +++Le++++ +++k  ++   +   ++ + +      +
  gene1545|gene1545|rna1544|rna1544  53 NKQLVKQHFGKFVQCRTVLEEIWIDIKQKGY---DKEFTSDLENNIKVIEEKFRKMTSGISGDNRGEVSEGRREYY 125
                                        69************************75555...446789*********************999999999999999 PP

                               Sec5  80 iernkflFnLPksLkesiakgdydklindYkkakslfestrqslveedkkqvkvfkkvwsevekiieeyrkklwek 155
                                         +r+  lFn+ + Lk+++++   +++++ Yk+a +++e+          k +  ++kvw+ + +   e+ + ++++
  gene1545|gene1545|rna1544|rna1544 126 RKRYALLFNIKSDLKRNLHN--LERFVDIYKEAMKMYEEL---------KSSVYVQKVWNSIHDERCEFLEIIYKN 190
                                        9*****************86..689***************.........577789*******99999999999999 PP

                               Sec5 156 Lleldesqee 165
                                        ++ ++ s +e
  gene1545|gene1545|rna1544|rna1544 191 IQRPRCSFHE 200
                                        9888744444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.38
                               Sec5  45 Leeslneairkt 56 
                                        +++ +++ ++k 
  gene1545|gene1545|rna1544|rna1544 418 INNYMDNHATKV 429
                                        222222222222 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   5.9e-05      0.53      97     154 ..     220     278 ..     213     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.9e-05
                                        HHHHHHHHHHTTHHHHTTS.-TTSHHHHHHHHHHHHHHTGGGSS-----S-CCHHC-HH CS
                             DUF489  97 alaklgerieqierqlehf.dllhenvlanlasiYsdtiSklgpriqvkGepevLqqee 154
                                        ++++l  + ++ + +  +   l + + l+++ + Y +++++++ +iq++G+ +++q  e
  gene1545|gene1545|rna1544|rna1544 220 IMNTLLVNFKENSVKNLELsYLDEGECLNEITRHYLKIMGRVNGKIQIQGTDHYFQCIE 278
                                        555555555555544444414555688999************************99655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1230  (0.0686039); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3262.02
//
Query:       gene1546|gene1546|rna1545|rna1545  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-38  130.1   0.7    3.4e-38  129.8   0.7    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.8   0.7   1.9e-42   3.4e-38       1     113 [.      26     138 ..      26     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.8 bits;  conditional E-value: 1.9e-42
                                        --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE CS
                    Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrG 76 
                                        +++l++k k + l  apq++ +vlek++veak+PnsA+Rk+vr +Li  gk++taf+p +g++ +++ +dev+v+G
  gene1546|gene1546|rna1545|rna1545  26 KRALGTKYKHSVLGRAPQAKAIVLEKIGVEAKQPNSAIRKAVRCQLIATGKRITAFVPYDGSVTYIESNDEVTVEG 101
                                        578899********************************************************************** PP

                                        --.....BTTSTTEEEEBETS---TSSSTTTTT---- CS
                    Ribosom_S12_S23  77 irrkgkavkDlpGvrykvvkvagvslkalskykkekp 113
                                        +++kg++ +D+pG+r+kv kv++vsl+a + +kkekp
  gene1546|gene1546|rna1545|rna1545 102 FGKKGRSFGDIPGIRFKVCKVQNVSLHAIFTGKKEKP 138
                                        ***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 859.40
//
Query:       gene1547|gene1547|rna1546|rna1546  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-06   27.7   0.0    1.6e-05   25.5   0.0    1.9  2  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
       0.01   15.7   1.9       0.03   14.2   1.9    1.9  1  UIM       Ubiquitin interaction motif
      0.041   13.7   0.2      0.058   13.2   0.2    1.2  1  Ssl1      Ssl1-like


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.6e-09   1.6e-05       1     103 [.       5     109 ..       5     114 .. 0.86
   2 ?   -0.1   0.0      0.25   1.5e+03      59      93 ..     172     207 ..     143     208 .] 0.74

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.6e-09
                              VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallk....slpgdrvglvtfsd.gpevlipltkdkakilnalrnlea 71 
                                        +v++ D+    +n+dy p+rl  +k+ ve+l++    +++++++g++     +++ +i++tk +  i+++l++++ 
  gene1547|gene1547|rna1546|rna1546   5 IVVLFDNGMASQNQDYLPSRLIVQKETVESLISrkfeDNQENTIGIIPLVQtQSNDIITPTKQRPYIKTFLNEIKL 80 
                                        689999999************************644444799*****9988689*********************6 PP

                              VWA_2  72 kgggtnlaaaLqlarkalkkrrkgekrvivli 103
                                         + + ++   L++   +++++    + ++++i
  gene1547|gene1547|rna1546|rna1546  81 -SRNVDIMGCLSQSLHIFNQKD--SPGCMLVI 109
                                        .6*********99999999775..44444444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.25
                              VWA_2  59 kakilnalrnleak.gggtnlaaaLqlarkalkkrr 93 
                                         +++l+++++ e   +++  la+a++l  ++ kk++
  gene1547|gene1547|rna1546|rna1546 172 ADRVLSFINGDEHLeEDDPELAEAIRLSLEEQKKQQ 207
                                        667777777766667789999999999988888765 PP

>> UIM  Ubiquitin interaction motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.9     5e-06      0.03       1      17 []     187     203 ..     187     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-06
                                UIM   1 dEdedLqrAlalSlqEa 17 
                                        ++d +L+ A++lSl+E+
  gene1547|gene1547|rna1546|rna1546 187 EDDPELAEAIRLSLEEQ 203
                                        69**************7 PP

>> Ssl1  Ssl1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   9.7e-06     0.058       3      74 ..      10      84 ..       7     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.7e-06
                                       E-SGGGGSSSSSS-HHHHHHHHHHHHHHHHHHHSTT-EEEEEEEETTEEEEE.EEEE..S-HHHHHHHHHHHTTS CS
                               Ssl1  3 DlsrameekdlkpsrlavviklleefveeffdqnPisqlgliavkdkkaekl.tels..GnprkhikaLkslrev 74
                                       D   a +++d  psrl v+ +++e+ +++ f+ n    +g+i + + +++ + t  +    ++++++++k  r+v
  gene1547|gene1547|rna1546|rna1546 10 DNGMASQNQDYLPSRLIVQKETVESLISRKFEDNQENTIGIIPLVQTQSNDIiTPTKqrPYIKTFLNEIKLSRNV 84
                                       556677899*********************************877666555414333003334555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1419.98
//
Query:       gene1548|gene1548|rna1547|rna1547  [L=536]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-41  140.5  28.6    8.5e-41  140.2  28.6    1.0  1  TLC       TLC ATP/ADP transporter


Domain annotation for each model (and alignments):
>> TLC  TLC ATP/ADP transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2  28.6   4.7e-45   8.5e-41      24     491 .]      42     519 ..      31     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 4.7e-45
                                TLC  24 kkllplllllflilfnysilrdlKDslvvtasesgAEvipFlKvwgvlPsAilftliyaklsnklskekvFyiivs 99 
                                        k  l++ ll  l++++ + l  l D ++++++      i F+K  +vlP+ + f++i  k  + ls+ ++  +i+ 
  gene1548|gene1548|rna1547|rna1547  42 KSTLLFGLLYALLSYIDAFLYILGDMVMMSSQ--IPSSILFIKSVLVLPVTFFFIVIVQKGLKFLSQPRMLEVILI 115
                                        56677778888888999999999999999998..666799*********************************999 PP

                                TLC 100 fflvffllFafvlyPlr....ellhleaeadklesilppglkgli...alvrnWsyalfYvlaELWgsvvlsllfW 168
                                        +  +ffl+F+fv++P r    + ++ ++++ ++ ++++ +l  +     ++++Ws +++Y++aELWgs+++s +f+
  gene1548|gene1548|rna1547|rna1547 116 ISSMFFLFFGFVVWPYRgrlqQDFFWSRDIFSDGKMKVRHLDFFFpifLVFNEWSSTILYLVAELWGSLIISFMFF 191
                                        999************8722223455677777888888888887761115679***********************9 PP

                                TLC 169 gfaneitkveeakrFYsllglvanlalivaGevlillsnirkklasavdsweeslkvlvlivvilgliilllyrll 244
                                          a +  +  + k+F + ++l++ + ++ +G ++++l + r  l+   +++e++++++ ++  +l++i  +   ++
  gene1548|gene1548|rna1547|rna1547 192 SRAIHQCTEAQVKKFLPTVSLISGIVMLSSGLLTKNLNSYRDGLP--YHKKERLFSYVFVATSMLTVITAMASFFV 265
                                        888888888888*************************99666555..56778889999999999999999999999 PP

                                TLC 245 nkkvltderlylaekkkkkkkkkklslkesfklllrskyllliavlviayglsinlvEvvWKaqikelyptp.ney 319
                                        ++++ +++  y   ++kk +k++k+++ +s++++ rs++l+ ++  v+a  ++ n++E++++  i    +++    
  gene1548|gene1548|rna1547|rna1547 266 DRTIPKEDSEY---ESKKVQKARKMGFVKSLRIMRRSRFLMAMTEAVVAASVCSNIFEATYRGGIILGAAQAsSPR 338
                                        99998777775...4444567789***************************************9977655541456 PP

                                TLC 320 nafmgkltsltGvvtilimll.....ssnilrkfgWtvaAlitPlillvtgvlFFslilfek..elaeliasllgt 388
                                        +++m+kl+ +t ++t ++ l+     + +++ + gW+  A+++P + ++t +lFF +++f++  e  +++ +   +
  gene1548|gene1548|rna1547|rna1547 339 SSYMNKLNAMTQIITSVFLLVmffkpATHLIERRGWLLVAIVAPAVAIITLLLFFPMVFFNNitEDDQILPTEGHM 414
                                        899999999999888665544122335789*****************************99832345677777789 PP

                                TLC 389 splllavvvGaiqnilsksaKyslfDatkemayipldeeskvkgkaaidvvgarlGKSggsliqqllliif..atl 462
                                           +l  + G+    + + +Ky +fD +ke a i + + ++ + +   d++g  +GK  gs+  +l+ ++f    +
  gene1548|gene1548|rna1547|rna1547 415 GRFVLENYAGMFLTTIIRISKYCFFDVAKEAASIRVSPIHRHSFRGIHDGLGINIGKTIGSVYCTLITVVFdvRDV 490
                                        99***********************************************************999888888876667 PP

                                TLC 463 asispllavvlllvilvwiiavkklekqf 491
                                         +++ + +v + + +++wi +v  ++k++
  gene1548|gene1548|rna1547|rna1547 491 RNMVSISTVFVGVFCVIWIRSVFYISKKY 519
                                        777777777777889**********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 3562.24
//
Query:       gene1549|gene1549|rna1548|rna1548  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 967.93
//
Query:       gene1550|gene1550|rna1549|rna1549  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-48  162.3   0.1    1.5e-47  161.6   0.1    1.3  1  DEAD           DEAD/DEAH box helicase
    2.7e-30  104.9   0.1    6.3e-28   97.3   0.0    3.2  3  Helicase_C     Helicase conserved C-terminal domain
    3.6e-09   36.9   0.0    6.4e-09   36.0   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
     0.0037   16.5   0.0      0.006   15.8   0.0    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.6   0.1   3.4e-51   1.5e-47       1     176 []      25     191 ..      25     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 3.4e-51
                                        -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidl 76 
                                        t+iQ+++ip ilgg+d+++  +TGsGKTlaf++p++++++   +++   +li++PtreL  q+++ ++ f + ++l
  gene1550|gene1550|rna1549|rna1549  25 TEIQEQVIPVILGGNDIIAVSQTGSGKTLAFVLPIVSCLLL--KDRSFYCLIIAPTRELSSQIAECFNMFEE-TGL 97 
                                        79*************************************86..999********************988877.89* PP

                                        EEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  77 rvlliiggvaardqlskldngvdivvgtpgrlddll.stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                        rv+l++gg++ + q ++l++++++vvgtpgr+++++ +t+++++++vr lVlDEadr+ +q+f d++++i+++l  
  gene1550|gene1550|rna1549|rna1549  98 RVCLLVGGTSFNVQANQLSKHPHVVVGTPGRIAEHVlKTKSFRIERVRKLVLDEADRFFEQDFVDDLETIIRSL-- 171
                                        ******************999*************88799***********************************.. PP

                                        HCTTSTTTSEEEEEESSBSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 152 itcdgklqrqvivlSATlpkdvkkl 176
                                             k++rq+++++AT++++++kl
  gene1550|gene1550|rna1549|rna1549 172 -----KEKRQTLLFTATMSDEISKL 191
                                        .....56788*********998875 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.036   1.6e+02      10      61 ..      64     117 ..      54     125 .. 0.73
   2 ?    0.7   0.0      0.14   6.4e+02       4      33 ..     165     194 ..     159     212 .. 0.64
   3 !   97.3   0.0   1.4e-31   6.3e-28       2     111 .]     226     334 ..     225     334 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.036
                                        HHHTTTTSEEEEEESSHH...HHHH...HHHHHHHTTSTEEEESTTSTHHHHHHHHHH CS
                         Helicase_C  10 lkleeeggkilifvntid...rlek...vklllekkgikvavlhgelpqnereeileq 61 
                                        l l+ +   +li+++t++   +      ++++ e+ g++v+ l g ++ n +   l++
  gene1550|gene1550|rna1549|rna1549  64 L-LKDRSFYCLIIAPTRElssQ--IaecFNMF-EETGLRVCLLVGGTSFNVQANQLSK 117
                                        3.66777778999999996442..13356666.5669********9999988877765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                                        HHHHHHHHHTTTTSEEEEEESSHH.HHHH..HH CS
                         Helicase_C   4 eallellkleeeggkilifvntid.rlek..vk 33 
                                        e++++     +e++++l+f+ t + +++k   +
  gene1550|gene1550|rna1549|rna1549 165 ETIIRS---LKEKRQTLLFTATMSdEISKlsNS 194
                                        344444...489999999999888666554333 PP

  == domain 3  score: 97.3 bits;  conditional E-value: 1.4e-31
                                        HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGT CS
                         Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvae 77 
                                        k + l+ell + + g  +++fv  + ++  ++l l+k g+++ +lhgel q++ree+++ f++ +++vL++tdv++
  gene1550|gene1550|rna1549|rna1549 226 KNASLVELL-EMNPGISVIVFVSMCITARVMSLALSKLGFHSEALHGELIQEKREETMRMFKESKFNVLVCTDVGS 300
                                        567789999.89999***********886578888899************************************** PP

                                        SSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  78 rGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        rG+di  v+lVinfd+p+n ++yi+r+GRt+Rag
  gene1550|gene1550|rna1549|rna1549 301 RGLDISHVDLVINFDVPKNGKDYIHRVGRTARAG 334
                                        ********************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.4e-12   6.4e-09      25     170 ..      39     185 ..      22     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.4e-12
                                        SEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--... CS
                             ResIII  25 krglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkka.ke 98 
                                        + ++ +  TG+GKTl   + ++  ll k +   +l+++p+++l +q  e f+ f ++    ++  v g + +   +
  gene1550|gene1550|rna1549|rna1549  39 NDIIAVSQTGSGKTLAFvLPIVSCLLLKDRSFYCLIIAPTRELSSQIAECFNMFEETGLR-VCLLVGGTSFNVqAN 113
                                        56788999********9788888899998989**********************999965.666666666665556 PP

                                        .....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---.SEEEEEESS-S CS
                             ResIII  99 kdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfke.avllglTATpe 170
                                        + s++ +++v t  ++ ++      ++++++ +r   ++ DEa r+ ++   +  + i++++ke    l +TAT+ 
  gene1550|gene1550|rna1549|rna1549 114 QLSKHPHVVVGTPGRIAEHV----LKTKSFRIERVRKLVLDEADRFFEQdfvDDLETIIRSLKEkRQTLLFTATMS 185
                                        6699****************....889999999999************9555488888999987456699****85 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-06     0.006      62     154 ..     241     336 ..     208     358 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                      ERCC3_RAD25_C  62 kiivfsDn.....vfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqis 132
                                         +ivf        v++L      ++ + ++Ge  +++r + ++ fk++ k+n+++   vg   +D+ +   +i  +
  gene1550|gene1550|rna1549|rna1549 241 SVIVFVSMcitarVMSLALSKLGFHSEALHGELIQEKREETMRMFKES-KFNVLVCTDVGSRGLDISHVDLVINFD 315
                                        56666554000004444444455667889****************987.8***********************998 PP

                      ERCC3_RAD25_C 133 shfgsrrqeaqrlGriLrakkk 154
                                              +    r+Gr  ra ++
  gene1550|gene1550|rna1549|rna1549 316 VPKNG-KDYIHRVGRTARAGRS 336
                                        87665.4678899998888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.37s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 2079.11
//
Query:       gene155|gene155|rna155|rna155  [L=973]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-21   74.8   1.5    8.2e-20   71.1   0.1    2.5  2  E1-E2_ATPase   E1-E2 ATPase
    9.7e-21   75.0   0.0    1.4e-20   74.5   0.0    1.3  1  Hydrolase      haloacid dehalogenase-like hydrolase
    5.1e-05   23.3   0.0    0.00012   22.1   0.0    1.7  1  Cation_ATPase  Cation transport ATPase (P-type)
    0.00015   21.6   0.0       0.09   12.5   0.0    2.4  2  Hydrolase_3    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.033   14.6   0.0    1.5  1  HAD            haloacid dehalogenase-like hydrolase
       0.11   12.5   0.1        0.3   11.2   0.1    1.7  1  HAD_2          Haloacid dehalogenase-like hydrolase
       0.14   12.0   0.6       0.44   10.4   0.1    2.1  2  DUF2618        Protein of unknown function (DUF2618)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.1   3.2e-23   8.2e-20      16     180 ..     227     409 ..     209     410 .. 0.89
   2 ?    2.2   0.1     0.044   1.1e+02     106     144 ..     824     862 ..     813     885 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 3.2e-23
                                    EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-................G-TTEE-TT-EEEE. CS
                   E1-E2_ATPase  16 eeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvek................ekgdmvfsGtvvvs. 78 
                                    + + +++l pGD++++ +  +vp+D  +++gs+ v+e++L GEs p  k                +k++ +++Gt +v  
  gene155|gene155|rna155|rna155 227 KIVSSENLFPGDVIKITSTTSVPCDLLLIKGSCAVNEAMLSGESIPLAKedisernpgnifdrckDKRHILYAGTEIVVi 306
                                    5599************************************************************99*********76655 PP

                                    ..-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                   E1-E2_ATPase  79 ..geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallv 156
                                       ++++ V++tg +te g ++r +  + ++ t   +++  ++  l +++++++++++     +gks  + ll+++ +l+
  gene155|gene155|rna155|rna155 307 kdSPLVCFVLHTGFETEKGGLVRKMMCT-EEVTVNDREAFIFIFALLVFAVIASFYAYKEGKRMGKSNYKLLLEVILILT 385
                                    55*************************9.78888888888888888888888888888888778888779********** PP

                                    HHS-TTHHHHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 157 aaiPcaLplavplalalgarrlak 180
                                     ++P  Lp+ +++a+   +r+l +
  gene155|gene155|rna155|rna155 386 NVVPTELPMELSMAVNSCVRALVR 409
                                    *************99888877766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.044
                                    ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSST CS
                   E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialllgksl 144
                                    skk pl+++++ ++ + v++ +++ ++ f++++ + +++
  gene155|gene155|rna155|rna155 824 SKKRPLTNIINPYIVTSVVFQVAVHIASFFVMIRRVREI 862
                                    8999***************************99876665 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   5.6e-24   1.4e-20       1     209 [.     426     693 ..     426     694 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 5.6e-24
                                    SSEEEEESBTTTBCHHHHHHHHHHHH.......CHHHHHHHHHH..HHCHHHHHHHHHHHHHHHHH.HHHHHETTTE... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.......alalaaaletg..sehpigkalvaaakarsgal.tgfatfigrg... 67 
                                    +++++fDk+GTLt++ ++v  +  +          + + +l  g  +  p+   + ++ k  + +  + f++ i +    
  gene155|gene155|rna155|rna155 426 VDVCCFDKTGTLTESVMEVAALRHETensisvlSSCHSLVLLDGkvTGDPLETSIYEYLKSTGSPGnKCFEHKIHKTysf 505
                                    5899*********9999999988888665555533344444444888888888888888888444446666655555677 PP

                                    ..................HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..................TTHHHHH CS
                                    ..................xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..................xxxxxxx RF
                      Hydrolase  68 ..................ayaigkpewltal.dippdlgaaigsaqsqgrtvall..................qaralav 110
                                                      + ++g pe ++++ d  p++ ++  ++ ++g  v  l                  +    + 
  gene155|gene155|rna155|rna155 506 cselrrmtvvaeseemkfVGMKGAPEAVKQHlDSVPEFYNDYKEYATEGYRVLALgfkpikkqakydredvesNLSFAGF 585
                                    777777777778888889**************999999999999999999999999**********99999865555555 PP

                                    HHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..........GGGESEEEEHHCES........ST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxx........xx RF
                      Hydrolase 111 ftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..........ddyfdaviasdiet........va 172
                                    + +    k+k+++  ++++L+  g +vv++tgdn  ta+ + +++G                  ++  e         +a
  gene155|gene155|rna155|rna155 586 VLFD-C-KLKKDVGNTIETLHTSGHKVVMITGDNALTARNVSKKIGipdkavegseI-------DKMLESdeffsisiFA 656
                                    5555.4.6**************************************98544443332.......33333356666667** PP

                                    TTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 173 kpspegkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                     ++p +k+++i++++  ++ ++m GDg nD+ al+ A
  gene155|gene155|rna155|rna155 657 RADPTHKERIIEKYNKAGRYTLMCGDGTNDVGALKSA 693
                                    ***************88888***************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   4.8e-08   0.00012      18      87 ..     470     536 ..     433     540 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4.8e-08
                  Cation_ATPase  18 kllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkr 87 
                                    k++G++ E+++ ++ +    ++ +   e+k+ +++ F s+ +rm+vv +   e+   + +KGApe + ++
  gene155|gene155|rna155|rna155 470 KVTGDPLETSIYEYLKST-GSPGNKCFEHKIHKTYSFCSELRRMTVVAES--EEMKFVGMKGAPEAVKQH 536
                                    689*************99.899999999*********************6..599999*******99766 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0023         6      18      66 ..     594     640 ..     589     654 .. 0.81
   2 !   12.5   0.0   3.5e-05      0.09     194     237 ..     665     708 ..     661     717 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0023
                                    HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE CS
                    Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali 66 
                                    +   ++i+ l+  g+kvv  TG +  ++++v +++g+   ++   G+ i
  gene155|gene155|rna155|rna155 594 KDVGNTIETLHTSGHKVVMITGDNALTARNVSKKIGIPDKAV--EGSEI 640
                                    556689*****************************9875444..46666 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.5e-05
                                    HHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHH CS
                    Hydrolase_3 194 klakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkk 237
                                    ++++++n     ++  GDg ND+  L+ a +g+A+  a   v+k
  gene155|gene155|rna155|rna155 665 RIIEKYNKAGRYTLMCGDGTNDVGALKSAHVGIALMEAPVVVQK 708
                                    68899999999************************999877766 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.3e-05     0.033      94     188 .]     600     691 ..     585     691 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            HAD  94 laahraaGdrvvvvSgglrplvepllaelg..adevlatelevddrltgelglegkpvrgegkvaalrewlaaegegidl 171
                                    ++  +  G++vv+++g +   ++ + ++ g   ++v ++e++   ++    + +  +++ ++++++ ++    e+++ + 
  gene155|gene155|rna155|rna155 600 IETLHTSGHKVVMITGDNALTARNVSKKIGipDKAVEGSEID---KMLESDEFFSISIFARADPTHKER--IIEKYNKAG 674
                                    5556799***********************955555555433...333333466666666777777788..777888888 PP

                            HAD 172 eevvayGDspsDlpllr 188
                                      +  +GD+ +D+ +l+
  gene155|gene155|rna155|rna155 675 RYTLMCGDGTNDVGALK 691
                                    88***********9986 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012       0.3      78     173 ..     590     695 ..     565     700 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                          HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesy......Fdvivtsedvekk....KPdpeviekalek 147
                                    +k+ ++v +++e+L+  g+k+  +T  ++ ++++  +++gi +       +d+++ s++++        dp+  e+++ek
  gene155|gene155|rna155|rna155 590 CKLKKDVGNTIETLHTSGHKVVMITGDNALTARNVSKKIGIPDKavegseIDKMLESDEFFSIsifaRADPTHKERIIEK 669
                                    78899***********************************9753333333999999999987667778899999****** PP

                          HAD_2 148 lklkkeeviyvGDsptDieaakkagi 173
                                    ++     ++++GD ++D+ a k a +
  gene155|gene155|rna155|rna155 670 YNKAGRYTLMCGDGTNDVGALKSAHV 695
                                    *****************999988876 PP

>> DUF2618  Protein of unknown function (DUF2618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.3   5.9e+03      24      30 ..     650     656 ..     649     662 .. 0.86
   2 ?   10.4   0.1   0.00017      0.44       6      31 ..     853     878 ..     850     881 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                        DUF2618  24 FSYSlFa 30 
                                    FS S+Fa
  gene155|gene155|rna155|rna155 650 FSISIFA 656
                                    9*****8 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00017
                        DUF2618   6 mAHiRRTRHimmPSYRSCFSYSlFaS 31 
                                       iRR R i  P Y   FS Sl +S
  gene155|gene155|rna155|rna155 853 FVMIRRVREIEAPVYNEKFSPSLMNS 878
                                    567**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (973 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.26s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 6606.14
//
Query:       gene1551|gene1551|rna1550|rna1550  [L=515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-16   60.3   1.9    3.2e-16   59.5   1.9    1.4  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.067   13.4   0.7       0.12   12.5   0.7    1.4  1  Aha1_N      Activator of Hsp90 ATPase, N-terminal


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   1.9   3.6e-20   3.2e-16       4     204 ..     304     505 ..     301     507 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 3.6e-20
                                        HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHH.HHTT-SS-TT-EEESSSEEEEEEE CS
                         MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGii.llfekpfkiGDlveigdieGtVed 78 
                                        l  +++ +g+++v+ llg+n s lla      +  +  + d+i+++   +i ll+++p+++GD+v i + e +V +
  gene1551|gene1551|rna1550|rna1550 304 LMAVAMYFGVILVMILLGINYSGLLATILPSMVTFSWIFSDTIKEIYNCFIfLLVNHPYDCGDRVVIDGEELYVSS 379
                                        55678889999999***********99999999***************987256777******************* PP

                                        E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS CS
                         MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdk 154
                                        + l++ +++  +gr+v+iP+s+l+ ++i+N +r sg++  +v i v  +++++ + k+ + + +a++e+ +  +  
  gene1551|gene1551|rna1550|rna1550 380 VDLLSSTFTGVNGRLVFIPTSTLFRAKIHNIRR-SGKQFSEVGILVSKTTSFDTALKLKDGITKAVSESTKSFS-- 452
                                        *********************************.************************************9997.. PP

                                        -EEEEEEEE-SSSEEEEEEEEEET.......TTHHHHHHHHHHHHHHHHHHHT- CS
                         MS_channel 155 ellvvldefgdsslnfevrvfvkt....vvpeeylsvqseinlrikkileeegi 204
                                          + ++ ef +++ n+++ + ++     ++++++ + ++ei+   ++++++++i
  gene1551|gene1551|rna1550|rna1550 453 -GEIYIREFRAEGDNVKISFAIQHqsnfQDIKKKHDRRAEIVNILEREMKAQKI 505
                                        .66677777777777777777776333355666666666666656666666655 PP

>> Aha1_N  Activator of Hsp90 ATPase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   1.4e-05      0.12      52     121 ..     428     503 ..     425     512 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                             Aha1_N  52 fiydlklklewegtvk.kedgkkvkGeieipelssenddddyeievsvkk.....deekkekqklkelikskgvpk 121
                                        + +d +lkl+  +t + +e+ k+++Gei i e+  e d+ ++++ ++ ++     +++ +++++++++++++++++
  gene1551|gene1551|rna1550|rna1550 428 TSFDTALKLKDGITKAvSESTKSFSGEIYIREFRAEGDNVKISFAIQHQSnfqdiKKKHDRRAEIVNILEREMKAQ 503
                                        679999999988887789***************9998888888888888788777667777777777777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1209  (0.0674327); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3669.46
//
Query:       gene1553|gene1553|rna1552|rna1552  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-17   63.9   0.1    4.7e-17   62.5   0.0    1.6  2  HIT            HIT domain
    7.2e-05   23.2   0.0    0.00011   22.7   0.0    1.2  1  DcpS_C         Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
      0.034   13.9   0.0       0.05   13.3   0.0    1.2  1  GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-te


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   7.9e-21   4.7e-17       5      95 ..      10      98 ..       8     101 .. 0.96
   2 ?   -1.5   0.0      0.73   4.3e+03      45      71 ..     122     148 ..     112     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 7.9e-21
                                       -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT CS
                                HIT  5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahag 82
                                       +++v+++++++++f + +p  p h+L+ p  + +++ +lt+ee ++l+ +v+  +k l++    +g+++ +++g+ ag
  gene1553|gene1553|rna1552|rna1552 10 YDHVIVRTKHSFVFTNLRPFLPLHILISPISKKQRIYELTNEETSDLFNTVRVAMKGLKD--LCDGFTLGVQDGPCAG 85
                                       689********************************************************9..568************* PP

                                       -SSSS-EEEEEEC CS
                                HIT 83 qsvahlHiHvipr 95
                                       q+v+h+H+H++pr
  gene1553|gene1553|rna1552|rna1552 86 QTVFHVHVHIVPR 98
                                       ************8 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.73
                                        HHHHHHHHHHHHHHHHHHHTCTTCCCE CS
                                HIT  45 eeelakllsavkkvakalqkkfknkgl 71 
                                        + e +++ ++++k+ + ++k f  +gl
  gene1553|gene1553|rna1552|rna1552 122 AREYGEMKKEADKLKEIIGKAFDSEGL 148
                                        567778888889998888888877765 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.8e-08   0.00011      14     101 ..      11      97 ..       4     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.8e-08
                                        B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT CS
                             DcpS_C  14 ervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhyq 89 
                                        + v++++++  v+  ++p  +lh+l+ p ++ + +++Lt+e+ + l + +++a k +++   +     ++ g  + 
  gene1553|gene1553|rna1552|rna1552  11 DHVIVRTKHSFVFTNLRPFLPLHILISPISKKQRIYELTNEETSDLFNTVRVAMKGLKDLCDG-FTLGVQDGPCAG 85 
                                        4567899999************************************************99944.555555555566 PP

                                        --S-S--EEEEE CS
                             DcpS_C  90 PsvyhlHlHvis 101
                                        ++v+h+H+H++ 
  gene1553|gene1553|rna1552|rna1552  86 QTVFHVHVHIVP 97 
                                        6********985 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.3e-06      0.05      42     119 ..      23      94 ..       6     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.3e-06
                                        E--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCTS---EEEEEE---SCCCTTTT--EEE CS
                      GalP_UDP_tr_C  42 vvpylakWPfevlllrkaevkslaeladeekedlaailkklarkydnlfetsfeysmGlhqaplnaeednswlHaH 117
                                         +      P+++l+ + ++++++ el++ee++dl  +++  ++   +l      + +G+ + p ++   ++ +H+H
  gene1553|gene1553|rna1552|rna1552  23 FTNLRPFLPLHILISPISKKQRIYELTNEETSDLFNTVRVAMKGLKDLC---DGFTLGVQDGPCAG---QTVFHVH 92 
                                        3444445699****************************97776666664...57999997766655...4445555 PP

                                        EE CS
                      GalP_UDP_tr_C 118 fe 119
                                        ++
  gene1553|gene1553|rna1552|rna1552  93 VH 94 
                                        43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 915.15
//
Query:       gene1554|gene1554|rna1553|rna1553  [L=259]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-05   21.7   2.5    8.2e-05   21.6   1.1    1.6  2  HECT_2    HECT-like Ubiquitin-conjugating enzyme (E2)-binding


Domain annotation for each model (and alignments):
>> HECT_2  HECT-like Ubiquitin-conjugating enzyme (E2)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.1   4.6e-09   8.2e-05     129     202 ..      78     139 ..      72     159 .. 0.80
   2 ?   -1.9   0.0     0.063   1.1e+03     301     329 ..     191     223 ..     158     234 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.6e-09
                             HECT_2 129 kikrwkdLPSenwaemmdfWhCHkpdehedsedenaatkgygasn..klspqegdglvdltsfllaesdcqglkls 202
                                        ++k ++ LP e w+e++d W CH+ +              + +    + +p+eg +l+ +++fl++ sd+ +  ++
  gene1554|gene1554|rna1553|rna1553  78 TYKSLNRLPQEGWEELIDCWSCHNCE--------------FRTMLslSPHPREGGLLLSNFFFLINDSDLPKCCRN 139
                                        678899*******************9..............333222377899999*************98875444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.063
                             HECT_2 301 s....ssssssssleaqramKvlYkdeieeeda 329
                                        +      + ++++l  + amKv  k+  +  ++
  gene1554|gene1554|rna1553|rna1553 191 FyktmVITIENKTLCKKEAMKVGVKETDKPIEK 223
                                        333333334556777777777766644444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1497.36
//
Query:       gene1555|gene1555|rna1554|rna1554  [L=1059]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.5   0.7        4.4    7.4   0.0    4.1  5  CARD      Caspase recruitment domain


Domain annotation for each model (and alignments):
>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.57     1e+04      15      26 ..      84      97 ..      71     100 .. 0.71
   2 ?   -1.7   0.0      0.17     3e+03      53      80 ..     491     519 ..     482     522 .. 0.81
   3 ?   -1.8   0.0      0.18   3.3e+03      28      43 ..     543     559 ..     540     564 .. 0.77
   4 ?    0.4   0.0     0.038   6.8e+02       7      33 ..     643     668 ..     638     678 .. 0.87
   5 ?    7.4   0.0   0.00025       4.4      43      68 ..    1032    1057 ..    1026    1059 .] 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.57
                                       SS..HHHHHHHHHH CS
                               CARD 15 lk..slsglldyLl 26
                                        +  ++++l+dyL+
  gene1555|gene1555|rna1554|rna1554 84 GNtnDIEYLFDYLV 97
                                       44567899999997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.17
                                        HHHHHTSCHHHHHHHHHHHHH.HSHHHHH CS
                               CARD  53 ldlvqkkgekacqaflealke.gqpdlas 80 
                                         d+++  g++  +af+++l + +++ l+ 
  gene1555|gene1555|rna1554|rna1554 491 EDTMKHPGKAHVDAFCRYLHQiEDQGLVN 519
                                        588889999999********999998876 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.18
                                        TTSS-HHHHHHHHT.SS CS
                               CARD  28 kkVLteeeeekika.kt 43 
                                         +VL+ee +e+i+  ++
  gene1555|gene1555|rna1554|rna1554 543 MEVLSEESCERILDiRG 559
                                        68*********987555 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.038
                                        THHHHHHHSSHHHHHHHHHHHTTSS-H CS
                               CARD   7 nrkrLverlkslsglldyLlekkVLte 33 
                                        +rk++v++l   +++ ++L++++ L+e
  gene1555|gene1555|rna1554|rna1554 643 ERKKIVKTLF-QNRYVPHLIKCGMLKE 668
                                        79999***99.9***********9987 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.00025
                                         SSHHHHHHHHHHHHHTSCHHHHHHHH CS
                               CARD   43 ttrlskareLldlvqkkgekacqafl 68  
                                         ++  s ar+Ll+++++k++k++  +l
  gene1555|gene1555|rna1554|rna1554 1032 KDISSAARKLLSIIERKHNKGGYQLL 1057
                                         667899**************986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1059 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.84u 0.28s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 6749.18
//
Query:       gene1556|gene1556|rna1555|rna1555  [L=382]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-51  173.3   0.1    8.9e-51  172.2   0.0    1.5  2  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
    3.2e-25   89.3   2.3    2.7e-14   53.5   0.1    2.3  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    0.00019   21.5   0.0    0.00035   20.7   0.0    1.4  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
  ------ inclusion threshold ------
       0.17   12.2   0.0       0.51   10.7   0.0    1.8  2  FtsH_ext        FtsH Extracellular


Domain annotation for each model (and alignments):
>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.2   0.0     2e-54   8.9e-51       5     172 ..       7     172 ..       3     174 .. 0.98
   2 ?   -3.2   0.0       1.4   6.5e+03      38      74 ..     304     340 ..     300     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 2e-54
                     HMG_CoA_synt_N   5 vgilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlev 80 
                                         gi++le  lp+ y++q e+ +  + e  k  iglg  +mg  s red  sl+l  v++l+ r+ ++   +grlev
  gene1556|gene1556|rna1555|rna1555   7 FGIIGLEYQLPSLYINQEEVANNIDFEVDKIKIGLGLEQMGVPSRREDAISLALNAVSRLITRYGVSPLDVGRLEV 82 
                                        69********************99**************************************************** PP

                     HMG_CoA_synt_N  81 gtetiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgna 156
                                        gte+  d sks+ks l +lf   gnt + g d + acy gt+al+na+ w+ess wdgr a+vva d+a+y++ n+
  gene1556|gene1556|rna1555|rna1555  83 GTESNPDGSKSIKSYLTDLFP--GNTSMCGCDNVHACYSGTNALLNAIAWMESSLWDGRFAIVVATDVAMYKDKNC 156
                                        ********************7..5**************************************************** PP

                     HMG_CoA_synt_N 157 rptggagavalligpd 172
                                         ptggagava+l+gp+
  gene1556|gene1556|rna1555|rna1555 157 LPTGGAGAVAILLGPN 172
                                        ***************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                     HMG_CoA_synt_N  38 glgqtrmgfvsdredinslsltvvqkllertkldyda 74 
                                        g g +   f+ +r     +     ++l er++++y+ 
  gene1556|gene1556|rna1555|rna1555 304 GSGTSSSMFCLERVSKGCMITGFRERLSERKEISYQE 340
                                        6677777888888888888888889999999999875 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.3   1.6e-12   7.3e-09      10      85 ..     184     249 ..     178     252 .. 0.91
   2 !   53.5   0.1   5.9e-18   2.7e-14     135     277 ..     252     377 ..     248     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.6e-12
                                        EEE----SEE---TT-S--EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH------GGG-SEEEE--SSHHHHHH CS
                     HMG_CoA_synt_C  10 shmehayDFykPdlaseYPvvDGklslscYlkaldrcYksyskkvkkitkdadkeftlddfdyvifhsPfcklvqk 85 
                                         +  + +DF kP+    +Pvv Gk s++ Y +a + cY +++kk+          + l +fdy+++hsP+++l +k
  gene1556|gene1556|rna1555|rna1555 184 HYFSNQFDFMKPKELHPFPVVKGKESIENYRTAFEICYGELKKKM----------DDLGSFDYIALHSPYTRLPEK 249
                                        58899*******999**************************9995..........5688************99766 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 5.9e-18
                                        HHHHHHHHHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSH CS
                     HMG_CoA_synt_C 135 iakelfkkkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsi 210
                                        +a+++  kk  +sl +++++Gn Y asly +l+sll   ++d   g++++lfsYGsG ++s+f l+   +      
  gene1556|gene1556|rna1555|rna1555 252 VANHIDRKKFIKSLEASRKNGNAYSASLYLSLISLL--DGHDGEIGEKVLLFSYGSGTSSSMFCLERVSKGC---- 321
                                        566777889999************************..8999999******************986443333.... PP

                                        HHHHTTTTHHHHHHTSEEE-HHHHHHHHHHHHHHTT--SB---S-GGGS-TT-EEEEEE-TTS-EEE CS
                     HMG_CoA_synt_C 211 ldiakvldlkkkLdsRkevtPeefeealelrekahlkknfkpqgsidsLaegtyyLeevDdkfRRsY 277
                                             ++ ++++L +Rke++   ++e ++l e+   + n+++q +   +    yyL+++   f R+Y
  gene1556|gene1556|rna1555|rna1555 322 ----MITGFRERLSERKEIS---YQEFIKLIEDPIPQDNYETQEK---VYLPGYYLKRIS-SFARHY 377
                                        ....35778*********97...777799999********99865...455669****96.577777 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   7.7e-08   0.00035       9      82 ..     232     308 ..     224     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.7e-08
                                        GG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH...HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTT CS
                      ACP_syn_III_C   9 edidalvphqanlriidavakklglpeekvvvnl...deyGntsaasiplaLdeaveegklkpgdlvllvgfGaGl 81 
                                         ++d++ +h    r+ ++++   +++++k++++l   ++ Gn  +as+ l L  +++ ++ + g++vll++ G G 
  gene1556|gene1556|rna1555|rna1555 232 GSFDYIALHSPYTRLPEKICVANHIDRKKFIKSLeasRKNGNAYSASLYLSLISLLDGHDGEIGEKVLLFSYGSGT 307
                                        5689************************999998655789***********************************9 PP

                                        E CS
                      ACP_syn_III_C  82 t 82 
                                        +
  gene1556|gene1556|rna1555|rna1555 308 S 308
                                        8 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.1   9.3e+03      65      84 ..     265     284 ..     258     293 .. 0.76
   2 ?   10.7   0.0   0.00011      0.51      25      40 ..     308     346 ..     294     358 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                           FtsH_ext  65 gvsttkkgnstttystptlg 84 
                                        +++++k+gn++++  + +l 
  gene1556|gene1556|rna1555|rna1555 265 LEASRKNGNAYSASLYLSLI 284
                                        56778899999888888744 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                           FtsH_ext  25 g.......................stkeisyseFledle 40 
                                        +                        +keisy+eF++ +e
  gene1556|gene1556|rna1555|rna1555 308 SssmfclervskgcmitgfrerlsERKEISYQEFIKLIE 346
                                        3335666666666666666666669***********999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2746.91
//
Query:       gene1557|gene1557|rna1556|rna1556  [L=543]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-39  136.5  28.9    1.4e-39  136.2  28.9    1.0  1  TLC       TLC ATP/ADP transporter


Domain annotation for each model (and alignments):
>> TLC  TLC ATP/ADP transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2  28.9   7.6e-44   1.4e-39      18     491 .]      38     528 ..      21     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 7.6e-44
                                TLC  18 verlelkkllplllllflilfnysilrdlKDslvvtasesgAEvipFlKvwgvlPsAilftliyaklsnklskekv 93 
                                        + r e +++l+l+ll+  i+++++++ +l++ +++  +      + F+K   + P  + f+ +     n ++  k+
  gene1557|gene1557|rna1556|rna1556  38 IARNEWSRVLYLSLLFGAITVVHTTMGNLREMILMGRQ--DPMSMFFIKSIFLPPCSLFFVWTIQLGLNFFTPSKM 111
                                        778999*****************************999..677899******99*9999999999999******** PP

                                TLC  94 FyiivsfflvffllFafvlyPlrellhleaea......dklesilppglkg.lialvrnWsyalfYvlaELWgsvv 162
                                        F i++ +f  ++++F++v++P++ ++  +         d +   l +++   +  ++++W+ + +++ +E+Wg +v
  gene1557|gene1557|rna1556|rna1556 112 FDITLILFSGCYIFFGLVMWPFKAYIQKDFYWardifgDGKMESLRVHFLYpVFLVFNEWTSSFLFLCSEMWGALV 187
                                        **********************9987655433011111333444555554415678899***************** PP

                                TLC 163 lsllfWgfaneitkveeakrFYsllglvanlalivaGevlillsnirkklasavdsweeslkvlvlivvilgliil 238
                                        +s +f  f+ne+ + ++++r+ s+ ++   +++ ++  ++ ++ + r ++  ++  +e  ++vl+l+++++ l +l
  gene1557|gene1557|rna1556|rna1556 188 VSYFFNLFTNEVSTRKQSQRYISVYNISNAISIFLSAIFTLMFNKWRDSVVFET--KELGFRVLILALAFIVLGVL 261
                                        ****************************99**9999999999998766665555..55555555555555555667 PP

                                TLC 239 llyrllnkkvltderlylaekkkkkkkkkklslkesfklllrskyllliavlviayglsinlvEvvWKaqik..el 312
                                         l ++++k +l  +++ ++e+k+ + kkk++++ke  k l rsk ll i++ v+ yg+s  lvE+++K+ i   + 
  gene1557|gene1557|rna1556|rna1556 262 GLKKYIEKRILPIPVFLIKEAKTPNVKKKEVEIKEVGKALSRSKLLLAISLNVLLYGVSSTLVEATFKSGIAvgAK 337
                                        88999***************************************************************98742256 PP

                                TLC 313 yp..tpneynafmgkltsltGvvtilim..llssnilrkfgWtvaAlitPlillvtg......vlFFslilfekel 378
                                        y   +++++++f + +  ++ ++++l++     s +++k gW   A + P++++v +      v+F+ +  +    
  gene1557|gene1557|rna1556|rna1556 338 YTnnSKETFSNFYNGMEQIIIAMSLLVVvnTPYSALIKKGGWKYVASL-PIMVVVFSffsvflVAFYNVGAYGGGN 412
                                        651156789999999988877776665524667899********9987.666665542211113344444444444 PP

                                TLC 379 aeliasllgtspl.llavvvGaiqnilsksaKyslfDatkemayipldeeskvkgkaaidvvgarlGKSggsliqq 453
                                            + + g +p+ +l  ++G + n   k  Ky   Da+ke   + +d+  + k ka+ d+++ +lGKS gs+i +
  gene1557|gene1557|rna1556|rna1556 413 VLFGSLFKGRKPMfFLENTLGLVTNASLKIGKYLGADASKEAISMQIDPLYRAKYKAVYDGLCGKLGKSLGSVICT 488
                                        444445567888725789********************************************************** PP

                                TLC 454 llliif..atlasispllavvlllvilvwiiavkklekqf 491
                                        ++  i   + +   s + ++ + ++i+ w+++ + l+k+f
  gene1557|gene1557|rna1556|rna1556 489 IMTGIWdiTDIRMASSVSGILVAIIIMLWLCVLRYLNKKF 528
                                        *99988756677777777888888999***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3514.99
//
Query:       gene1558|gene1558|rna1557|rna1557  [L=303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-23   82.5   0.0    5.5e-23   81.7   0.0    1.4  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   3.1e-27   5.5e-23       5     151 ..     135     290 ..     131     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 3.1e-27
                                        CTT-SEEEEESSTCHH.HHHHSSSS.-STT--HHHHHHHCCCCCCCHHG...............CTEEEEESSS.. CS
                                UDG   5 ppdakvvivGeaPgae.edatglpFsgragnllrkllneaglkrdlese...............qgvyitnvvkcr 64 
                                         + +kvvi G++P+++ ++a gl Fs++ g  +++ l+++ l+  ++ e               +gv+++n v+  
  gene1558|gene1558|rna1557|rna1557 135 LEATKVVIMGQDPYHNdNQAMGLSFSVPMGVPIPPSLKNIYLEISSDIEgfeipshgdlsmwakRGVLLLNDVLTV 210
                                        5789************999***********777766666555554455567***********************44 PP

                                        ..SECGCTTCCCCTCCHH.HHHHHHHHHH....SSEEEEESHHHHHH..HHHHSCESCCCSCT..SEEEEES-SST CS
                                UDG  65 ppgnrdtptsaeikacap.lleeeiellk....prlivllGktaakallgeklgklrgklleak.irvlplphPsp 134
                                          +nr  p+s+   ++++ ++ + ++ ++    + +++l+G++a+ +          gk++ +  + vl++ hPsp
  gene1558|gene1558|rna1557|rna1557 211 T-KNR--PNSHA-GIGWReFTSRILQTINerctNVVFMLWGRHAQAK----------GKFISRSkHLVLACGHPSP 272
                                        2.466..*****.9**999*************5556***********..........9****988*********** PP

                                        TTTT.TTTSHHHHHHHHH CS
                                UDG 135 lnrn.ffksnpelkaeaw 151
                                        l+ n ff++++++ka+ +
  gene1558|gene1558|rna1557|rna1557 273 LSSNhFFGCKHFSKANKY 290
                                        ***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2266.83
//
Query:       gene1559|gene1559|rna1558|rna1558  [L=552]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-52  178.2  28.5    3.1e-52  177.9  28.5    1.0  1  TLC       TLC ATP/ADP transporter


Domain annotation for each model (and alignments):
>> TLC  TLC ATP/ADP transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.9  28.5   1.7e-56   3.1e-52      13     491 .]      29     530 ..      18     530 .. 0.83

  Alignments for each domain:
  == domain 1  score: 177.9 bits;  conditional E-value: 1.7e-56
                                TLC  13 aalwp.....verlelkkllplllllflilfnysilrdlKDslvvtasesgAEvipFlKvwgvlPsAilftliyak 83 
                                        ++ wp     + r e k    l++++    ++ys  r +KDs v++ +     +i+FlK+  vlP+ i++t +  k
  gene1559|gene1559|rna1558|rna1558  29 STTWPlsrirIARCEWKLWSALAFIFGASAYIYSFSRVMKDSFVLSRQ--LPVAISFLKTCFVLPMSIIATGVVQK 102
                                        555662221155667788889999999999*****************9..6678********************** PP

                                TLC  84 lsnklskekvFyiivsfflvffllFafvlyPlrel....lhleaeadklesilppglkglia...lvrnWsyalfY 152
                                        l  + +  kvF +++  f   ++l + vl+P+ +     ++ ++++ ++e++ ++g++ l a   ++++W+ +  Y
  gene1559|gene1559|rna1558|rna1558 103 LLMTRTISKVFDYTLLAFSFLYTLTGAVLFPFARSiqpgFYFSRDIFADEKMAYKGFEFLFAiflIFNEWTTSFVY 178
                                        *******************************98762222567888888999999999987662225799******* PP

                                TLC 153 vlaELWgsvvlsllfWgfaneitkveeakrFYsllglvanlalivaGevlillsnirkklasavdsweeslkvlvl 228
                                        v aEL+gs+v++ +f  fane ++v+++ r  +l+ +v+n+ l+++ e + + s+ +k+ + ++ sw +   +++ 
  gene1559|gene1559|rna1558|rna1558 179 VCAELFGSLVVQFMFLSFANEALTVRQSTRMVPLFYVVSNILLLLSSESTSFYSRKVKEWDYDTTSWVTNSFFVIF 254
                                        *******************************************************999999999988654333333 PP

                                TLC 229 ivvilgliilllyrllnkkvltderlylaekkkkkkkkkklslkesfklllrskyllliavlviayglsinlvEvv 304
                                           ++ +i  l+ ++ ++++l+++ +  +e  kkk kk+++++ es+kl+++sk+l+ + +  + y   +nl+E  
  gene1559|gene1559|rna1558|rna1558 255 G--VIIAITYLVKKYAENTILKKQLFIRTEGVKKKGKKSSAGFSESLKLMAQSKFLVAMVLNALFYYAGTNLIESS 328
                                        2..3334556667889999****99998888888999999************************************ PP

                                TLC 305 WKaqik...elyp.tpneynafm.gkltsltGvvtilim.llssnilrkfgWtvaAlitPlillvtgvlFFslilf 374
                                        WK+ i      y+ ++++y+a + +  + ++G+ +++i     s++++ +gW + A+++Pl+ lv +++ F+  +f
  gene1559|gene1559|rna1558|rna1558 329 WKNGISvaaDAYNmEKRAYSASIvSGEQRVVGALVAIILlTPISTLVQTHGWITMAIVPPLVTLVSSIVVFGSAFF 404
                                        ***99722245542456787644155567888766655526789999*******************9999888777 PP

                                TLC 375 e......kelaelias.llgtsp.lllavvvGaiqnilsksaKyslfDatkemayipldeeskvkgkaaidvvgar 442
                                        +       ++  +++s + g++p  +l   +G  +    k aKy+++D +ke   + +d+  + + ka+ d+++ +
  gene1559|gene1559|rna1558|rna1558 405 NysnyppGKTGVVLSSlVKGYTPnFYLECNIGIYCVSGMKIAKYAFYDISKEAISLQIDPLYRPRLKAVYDGLCGK 480
                                        6222222233334444156889845799************************************************ PP

                                TLC 443 lGKSggsliqqll.liifatlasispllavvlllvilvwiiavkklekqf 491
                                        lGKS gsl  ++  l+ +  + + +p+   + l++  +wi++v  l++++
  gene1559|gene1559|rna1558|rna1558 481 LGKSIGSLYAMFWsLMGYNDVRAAAPITLGMWLIISPIWIFSVIYLNRKY 530
                                        *******9887752666799***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3623.61
//
Query:       gene1560|gene1560|rna1559|rna1559  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-36  124.1   0.0    5.2e-36  123.9   0.0    1.1  1  Proteasome      Proteasome subunit
    4.9e-05   22.9   0.0    0.00014   21.5   0.0    1.8  1  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   0.0   5.8e-40   5.2e-36       1     189 [.      27     209 ..      27     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 5.8e-40
                                        HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHS CS
                         Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlryg 76 
                                        v+++  +v +k++d+vv+a+ k+++ + kl ++s+ +  ++++++++v+++Gl +D++++++r+++ a+++ ++ g
  gene1560|gene1560|rna1559|rna1559  27 VNNALPIVTVKSRDMVVCAS-KKVP-QGKL-EESSPTSFYRVSEKCYVGITGLPGDIDYVIKRIKMVANRKTFSLG 99 
                                        5778889*************.7899.5677.55557**************************************** PP

                                        SGTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHH CS
                         Proteasome  77 rpipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalek 152
                                        +++++++l++++a+k+q+ +q+s  r    ++ i g+d+e+ p +yq+d+sG ++ + +a+a G++   ++ ++ek
  gene1560|gene1560|rna1559|rna1559 100 TEVTPDILCRSFADKIQQLIQSSEERSAAFNASIFGFDREK-PMIYQTDMSGISYPC-YATASGEKHGKMTKFIEK 173
                                        **************************************777.***************.8*****99999******* PP

                                        HHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                         Proteasome 153 eykedltleeavelavkalkealerdklsgknievav 189
                                        +y++d++ +e++e+a+ al e++  d ++ ++iev++
  gene1560|gene1560|rna1559|rna1559 174 SYRKDMEGKELFEVAIGALLESIGTD-SGCSEIEVCY 209
                                        ************************77.9999999986 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.5e-08   0.00014       6      23 .]       9      26 ..       8      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.5e-08
                     Proteasome_A_N  6 ttFSPdGRLfQVEYAmkA 23
                                       ++F+ dG+L+Q+EY ++A
  gene1560|gene1560|rna1559|rna1559  9 NIFNSDGKLLQIEYGLEA 26
                                       69************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1746.66
//
Query:       gene156|gene156|rna156|rna156  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-40  137.7   0.0    3.4e-40  137.6   0.0    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.6   0.0   1.9e-44   3.4e-40       3     190 .]       9     191 ..       7     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 1.9e-44
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                     G++++++++++ v++++dkr+ +g +++sk+ + +i+++ ++++v+++  ++D+++l rr+r++ +l++l+++r++ +e
  gene156|gene156|rna156|rna156   9 YGGSILAMASENAVAIMSDKRLGMGPITVSKD-FVRIHRMGPRLYVGLSTFVPDTQVLLRRIRKNYNLFKLEEQREMEPE 87 
                                    599*************************9999.9********************************************** PP

                                    HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                     Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                        +++++++  +++++  p++ + ++ag+  +g+p++  +d++Gs++++kd+va+G++++  ++++e++y++++++e 
  gene156|gene156|rna156|rna156  88 ----ELSNMISFLLYSKRTSPYITAPIVAGLSSDGRPYISGMDCIGSITSPKDFVATGTAAKNLMGICEALYRPNMDEEN 163
                                    ....**************************************************************************** PP

                                    HHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                     Proteasome 163 avelavkalkealerdklsgknievavi 190
                                    ++ +  +a  +a++rd+lsg++++++vi
  gene156|gene156|rna156|rna156 164 LFVTCAQAFLNAVDRDALSGWGADCYVI 191
                                    *************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1366.32
//
Query:       gene1561|gene1561|rna1560|rna1560  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-19   68.1   0.0    7.5e-17   61.4   0.0    2.2  1  adh_short       short chain dehydrogenase
    4.8e-06   26.6   0.0       0.11   12.4   0.0    2.1  2  KR              KR domain
    1.2e-05   25.0   0.0    0.00098   18.7   0.0    2.2  2  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.016   15.1   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding
      0.031   13.8   0.0      0.092   12.2   0.0    1.8  1  Epimerase       NAD dependent epimerase/dehydratase family
       0.11   12.4   0.1        1.3    9.0   0.0    2.3  2  CedA            Cell division activator CedA


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   2.5e-20   7.5e-17       1     191 [.       9     171 ..       9     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2.5e-20
                                        SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                          adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                        k+v+ tG+s+G+G++iakelak+G  v v+++s++         +   +++ ++q+D+          ++  + + 
  gene1561|gene1561|rna1560|rna1560   9 KTVCLTGGSRGLGLEIAKELAKKGSYVHVIGKSPQSF-------GH--ENIKYYQIDLL---------KEKPDITT 66 
                                        79*****************************998866.......32..24889999987.........44567789 PP

                                        SESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHH CS
                          adh_short  77 kldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsA 151
                                        + d+++ N G   g++ f +++ +e+ +++++N+   ++l + v  +       + v+v S+ ++++++++++Y+A
  gene1561|gene1561|rna1560|rna1560  67 PFDIVISNLGTsVGNKRFDDMEYNEVMDMLKLNVELHLWLLKNVRYK-------KFVFVNSILSQQGLPEYSMYCA 135
                                        99*********888999*************************98777.......79******************** PP

                                        HHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHC CS
                          adh_short 152 sKaavagltrslakelaptgirvnavaPGlvdTdmakelr 191
                                        sK +++ l +sl++e ++t    ++++P  ++T++ +e+r
  gene1561|gene1561|rna1560|rna1560 136 SKSFIHTLNQSLRREGKDT----MIIYPYKINTPLFREVR 171
                                        ******************9....899*******9998876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   3.6e-05      0.11       3      32 ..      11      41 ..       9      67 .. 0.76
   2 !   12.3   0.0   3.9e-05      0.12     118     173 ..     105     157 ..      71     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                                       EEEETTTSHHHHHHHHHHHHHH.S-EEEEE- CS
                                 KR  3 ylitGGlGgLGlelarwlaekg.arhlvlls 32
                                       + +tGG  gLGle+a+ la+kg   h++  s
  gene1561|gene1561|rna1560|rna1560 11 VCLTGGSRGLGLEIAKELAKKGsYVHVIGKS 41
                                       679*******************445555444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.9e-05
                                        HHHHHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHHHHHHHHHTEEEE CS
                                 KR 118 nLhelledesldffvlfSSiagllgsagqanYaaaNaflDalaeyrrsqglpavsi 173
                                         L   l++ + + fv++ Si +  g ++ + Y a  +f+++l ++ r++g  ++ i
  gene1561|gene1561|rna1560|rna1560 105 WL---LKNVRYKKFVFVNSILSQQGLPEYSMYCASKSFIHTLNQSLRREGKDTMII 157
                                        33...33456789*************************************998765 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0098        29       3      24 ..      17      38 ..      15      52 .. 0.84
   2 !   18.7   0.0   3.3e-07   0.00098      69     184 ..      67     172 ..      56     190 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0098
                                       TTSHHHHHHHHHHHTT-EEEEE CS
                       adh_short_C2  3 asgIGraiAkalaeeGaevvlt 24
                                        +g+G +iAk+la++G  v + 
  gene1561|gene1561|rna1560|rna1560 17 SRGLGLEIAKELAKKGSYVHVI 38
                                       59**************988775 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.3e-07
                                        SEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHH CS
                       adh_short_C2  69 klDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaa 144
                                         +Di++ n g +   +++f +++ +e+ ++l+ n+   + l+k +     +  + v + s+ +++++p+y++y+a+
  gene1561|gene1561|rna1560|rna1560  67 PFDIVISNLGTSVG-NKRFDDMEYNEVMDMLKLNVELHLWLLKNV-----RYKKFVFVNSILSQQGLPEYSMYCAS 136
                                        58***********9.9********************999999998.....45899********************* PP

                                        HHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT CS
                       adh_short_C2 145 KaalealtrylAvelgpkgiRvNavspgpikTlaasgikg 184
                                        K  ++ l ++l +e  +       + p  i+T++ +++++
  gene1561|gene1561|rna1560|rna1560 137 KSFIHTLNQSLRREGKD----TMIIYPYKINTPLFREVRD 172
                                        *9887777776555444....5557777777777666665 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   5.3e-06     0.016       1     107 [.      15     129 ..      15     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.3e-06
                                        TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHH CS
                     NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdee 76 
                                        G++ + G +++kel+++g   v+++  +p+++     +e+++  ++d+++  +  +  +  d+V+s+lg++ ++++
  gene1561|gene1561|rna1560|rna1560  15 GGSRGLGLEIAKELAKKG-SYVHVIGKSPQSFG----HENIKYYQIDLLK--EKPDITTPFDIVISNLGTSVGNKR 83 
                                        89999************6.88999999999997....89*********95..456788899*******88777444 PP

                                        H...............HHHHHHHHHHCT--EEEEEEETTTTSGCGC CS
                     NAD_binding_10  77 g...............aknivdaakeagvkRfvlvsaigvgdevpg 107
                                                        ++  +  +k+   k+fv+v +i +++  p+
  gene1561|gene1561|rna1560|rna1560  84 FddmeynevmdmlklnVELHLWLLKNVRYKKFVFVNSILSQQGLPE 129
                                        44456677778776666666889999**********9998864443 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.1e-05     0.092       1      75 [.      11      80 ..      11     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HH.HHHHHHHHHT-SEEEE--S.-- CS
                          Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrs.alerlfkeeqpdavihlAa.vg 75
                                       +++tG++  +G  ++k+l++kg  v+++ + ++++ +++++    +++dl++++ +++  f+     ++ +l+  vg
  gene1561|gene1561|rna1560|rna1560 11 VCLTGGSRGLGLEIAKELAKKGSYVHVIGKSPQSFGHENIK---YYQIDLLKEKpDITTPFDI----VISNLGTsVG 80
                                       689*******************9999999999999988775...7999999877455555542....3334433333 PP

>> CedA  Cell division activator CedA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.21   6.2e+02      34      54 ..     103     124 ..      92     146 .. 0.73
   2 ?    9.0   0.0   0.00042       1.3      31      49 ..     169     187 ..     163     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.21
                               CedA  34 dvwvlkn.kyvafllvgerfrr 54 
                                         +w+lkn +y  f++v   + +
  gene1561|gene1561|rna1560|rna1560 103 HLWLLKNvRYKKFVFVNSILSQ 124
                                        6899998679999998776554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00042
                               CedA  31 eyrdvwvlknkyvafllvg 49 
                                        e rdvw l + yva  l+ 
  gene1561|gene1561|rna1560|rna1560 169 EVRDVWTLDANYVAVRLLK 187
                                        78************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1504.71
//
Query:       gene1562|gene1562|rna1561|rna1561  [L=336]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-28   99.8   0.0    2.4e-28   99.3   0.0    1.2  1  Pkinase      Protein kinase domain
    2.6e-09   36.8   0.0    4.8e-09   35.9   0.0    1.3  1  Pkinase_Tyr  Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   2.6e-32   2.4e-28      16     264 .]      25     262 ..       9     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 2.6e-32
                                        EEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHH CS
                            Pkinase  16 ykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladlle 90 
                                        +  v+k+ g  + + ++kk+k+ +  e + +++E  i  +++hp++++ +  f++ ++l+lv e  ++  la+l++
  gene1562|gene1562|rna1561|rna1561  25 FIEVRKRVGGLYHLRVMKKKKIIDYGEcDMIQNEYYIRSRIRHPFLINTICGFQDYEHLFLVSEQSQNY-LANLIS 99 
                                        555667777888889999999998888899************************************976.****** PP

                                        HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-.SGTTSEESSSSCSBCTTTSCGGGS- CS
                            Pkinase  91 rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKit.DFGlakelessskltsfvgtseYlA 165
                                         +g +s +  ++++++il +++ylHskg+ +  l p+N++i ++g++K+  DF           + +f    eY +
  gene1562|gene1562|rna1561|rna1561 100 SEGRFSAKVSRFYMAEILLAIQYLHSKGFTYGFLSPKNMMIGDDGHIKLKyDFLNGIDCV----VGDFEENIEYAS 171
                                        *************************************************53774444444....45688999**** PP

                                        HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHH CS
                            Pkinase 166 PEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdll 241
                                            ++ e+++ +D+Ws+G+ily +l g +pf++   ++     +++          +++ ++ ++ ++e+a++l+
  gene1562|gene1562|rna1561|rna1561 172 IDYANSGEFGPVSDYWSMGIILYHMLGGITPFAAPGMDS----VITR---------IKTNRIRFPEFFDEHARNLI 234
                                        *********************************333333....3333.........345688999999******** PP

                                        HHHT-SSGCCSTT.....HHHHHTSGGG CS
                            Pkinase 242 kkllkkdpkkRlt.....aeellqhpyl 264
                                        +kll   p++Rl+     ae++ +hp++
  gene1562|gene1562|rna1561|rna1561 235 SKLLVTSPRDRLGymeedAEMIRKHPFF 262
                                        *************999999999999998 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   5.4e-13   4.8e-09      45     250 ..      52     246 ..      37     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 5.4e-13
                                        HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHH CS
                        Pkinase_Tyr  45 keelleeakimkklkhpnivkllgvctkeepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLe 120
                                         +++ +e+ i ++++hp +++ +    + e+l++v e  + + L + + ++   +++ k    +++++  +++yL+
  gene1562|gene1562|rna1561|rna1561  52 CDMIQNEYYIRSRIRHPFLINTICGFQDYEHLFLVSEQSQ-NYLANLISSE--GRFSAKVSRFYMAEILLAIQYLH 124
                                        55677899999****************9*******99765.5888888887..8888888889999********** PP

                                        HTTEEEST-SGGGEEEEETTEEEE-.STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHH CS
                        Pkinase_Tyr 121 skklvHrdlaarNvLlsenkvvkis.DfGLardiekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvll 195
                                        sk +    l+ +N+++ ++ ++k+  Df   + i       + ++ + ++++ ++   ++++f   sD Ws G++l
  gene1562|gene1562|rna1561|rna1561 125 SKGFTYGFLSPKNMMIGDDGHIKLKyDF--LNGI-----DCVVGDFEENIEYASIDYANSGEFGPVSDYWSMGIIL 193
                                        ***********************96344..3344.....3567888999*************************** PP

                                        HHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBHHHHHHHHHHT-SSGGGS- CS
                        Pkinase_Tyr 196 wEiftlgespypglkneevleklkegkrlekpekcpeelyelmkkcweedpeeRp 250
                                        + ++  g +p++     +v++++k+ +r++ pe   e+  +l++k + ++p++R 
  gene1562|gene1562|rna1561|rna1561 194 YHMLG-GITPFAAPGMDSVITRIKT-NRIRFPEFFDEHARNLISKLLVTSPRDRL 246
                                        ***99.********9999**99976.69999999999999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1968.34
//
Query:       gene1563|gene1563|rna1562|rna1562  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-11   43.4   0.1    5.1e-11   42.6   0.1    1.4  1  NIF       NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   2.8e-15   5.1e-11       2     156 .]      81     222 ..      80     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 2.8e-15
                                NIF   2 tLVLDLDetLvhsklekskklkvegekvevsvlkRpgldefLkelsklyevvifTasseeyaeavidildpekkll 77 
                                        t+V+D+++ Lv  k+        +  ++++ v kR + d fL + +++ye+v  + ss ++ +  ++ +dp+++ +
  gene1563|gene1563|rna1562|rna1562  81 TIVFDCEDFLVKKKF--------SFFSFDFLVTKRSFTDLFLFHSAHIYELVHVSESSVSFSRYLLHRIDPYGC-I 147
                                        99*********9886........345689********************************************8.9 PP

                                NIF  78 shrlyrescvkkkgeyvKdLsllgrdlsrvvivDdspdsfelqpe.ngipiksffsdkkDneLlkllpllkela.. 150
                                        s+++y ++    k    K L   +r+l+++v++  ++ ++++  + n+++ +++ + + +  Ll ll++l++l+  
  gene1563|gene1563|rna1562|rna1562 148 SYKVYCKDK---KMFSSKHL---NRPLEKFVVISTREGEYHRDFNeNILRLEKWQG-EPEWGLLGLLNFLHNLHfi 216
                                        988887777...33455655...66***************997766********85.67889*********99977 PP

                                NIF 151 kvddvr 156
                                         v+d+r
  gene1563|gene1563|rna1562|rna1562 217 GVKDFR 222
                                        778876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 1746.76
//
Query:       gene1564|gene1564|rna1563|rna1563  [L=445]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-16   60.8   0.1    2.4e-13   50.5   0.0    2.4  2  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
  ------ inclusion threshold ------
       0.23   11.2   0.3        2.9    7.7   0.0    2.3  2  CUE             CUE domain


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0   0.00023       2.1       2      63 ..     201     253 ..     200     261 .. 0.81
   2 !   50.5   0.0   2.7e-17   2.4e-13     127     189 ..     272     336 ..     260     391 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00023
                                        EEEEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTE CS
                     PI3_PI4_kinase   2 sagiykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvass 63 
                                        s ++yk gddl +d  +++ +k m+ +      +      l  y+vipl+r++gi+e+v+ +
  gene1564|gene1564|rna1563|rna1563 201 SRVMYKKGDDLTKDLFVLETIKYMSRLIG---VD------LVAYRVIPLSREEGIVEVVDGV 253
                                        6799**********888888888866553...33......57899************99865 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 2.7e-17
                                        SHHHHHHH...HHHHHHHHHHHHHHHHHHT-TT--TTTEEEETTTSEEEESSTTTCCTCSHCSSSS CS
                     PI3_PI4_kinase 127 saeewlea...rkqFvrslaklsvldyilgngDRhldNilvdktsgklihIDfGlilpdewkllpf 189
                                        ++ +++++    k Fv  l ++sv+ y++g+gDR+++N++v  ++g ++hIDf + +++e+k +  
  gene1564|gene1564|rna1563|rna1563 272 KCSDYGRSlekKKMFVDTLCGYSVACYVMGVGDRNPGNMMV-AKDGRFFHIDFSYVFGNEPKPISH 336
                                        55667766666999***************************.***************999998775 PP

>> CUE  CUE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00032       2.9      20      42 .]      25      47 ..      23      47 .. 0.89
   2 ?    1.0   0.1      0.04   3.5e+02      12      22 ..      56      66 ..      56      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00032
                                       HHHHHHHCTTTHHHHHHHHHHCC CS
                                CUE 20 IravLrasngnvEatinaLLegs 42
                                       +++ L++s+ ++E ++ ++L+++
  gene1564|gene1564|rna1563|rna1563 25 VSKLLEDSDKDIEKAVAKYLCLQ 47
                                       6789****************985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.04
                                       STTS-HHHHHH CS
                                CUE 12 FPdldeevIra 22
                                       FP+++e +I++
  gene1564|gene1564|rna1563|rna1563 56 FPSFSEVDIED 66
                                       9********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2666.38
//
Query:       gene1565|gene1565|rna1564|rna1564  [L=573]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-51  172.7   1.9    2.1e-50  170.3   0.9    2.3  2  Rep_fac-A_C      Replication factor-A C terminal domain
    7.5e-19   67.5   0.2    1.8e-18   66.3   0.2    1.6  1  REPA_OB_2        Replication protein A OB domain
    3.3e-15   55.8   3.3    9.7e-11   41.5   0.8    4.1  4  tRNA_anti-codon  OB-fold nucleic acid binding domain
    6.5e-11   42.1   0.0      1e-09   38.3   0.0    2.4  2  Rep-A_N          Replication factor-A protein 1, N-terminal d
    1.7e-06   27.9   0.1    0.00084   19.1   0.0    2.6  2  CDC24_OB3        Cell division control protein 24, OB domain 
  ------ inclusion threshold ------
      0.022   14.8   0.2        2.1    8.5   0.2    3.1  3  Izumo-Ig         Izumo-like Immunoglobulin domain
       0.03   14.5   0.3        1.6    9.0   0.0    3.7  4  tRNA_anti_2      OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.17   4.4e+02      56      80 ..     202     226 ..     199     251 .. 0.87
   2 !  170.3   0.9   8.3e-54   2.1e-50       1     146 []     421     566 ..     421     566 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                                        EEEEEE-SS-EEEEEEEHHHHHHHH CS
                        Rep_fac-A_C  56 lsikvsDstgqlwvtlFneaaekll 80 
                                         ++++sD t q+ + +F+++   ++
  gene1565|gene1565|rna1564|rna1564 202 FNFEISDGTAQVKIICFSDCVDIFF 226
                                        6899***************988776 PP

  == domain 2  score: 170.3 bits;  conditional E-value: 8.3e-54
                                        EEEEEEEEEEEETTTTEEEB--STT---B-EEETTTEEEETTTTEEESS--EEEEEEEEEE-SS-EEEEEEEHHHH CS
                        Rep_fac-A_C   1 yfsvkatvsfikkdnlvYkACpsedCnkKvveeedgewrCekCdkeveepkyryilsikvsDstgqlwvtlFneaa 76 
                                        y ++++tv+f+k+d+l+Y++C+ e+CnkKv +ee+g++rCe+C++++e+++yry++s+++ D+tgq+wv+lF+eaa
  gene1565|gene1565|rna1564|rna1564 421 YSTIQGTVMFLKEDALWYTSCKGEGCNKKVAMEESGNYRCERCNMTYEDCNYRYMVSMHLGDFTGQIWVSLFDEAA 496
                                        789************************************************************************* PP

                                        HHHHSS-HHHHHHHCCC-HHHHHHHHHHTTT-EEEEEEEEE----------EEEEEEEEE--HHHHHHHH CS
                        Rep_fac-A_C  77 ekllglsaeelkklkeedeeefekiiekvklkeflfrlrvkeesyndesrvrytvvkvepvdykkeskrl 146
                                          ++g+sa+e+k+++ee+++e++++i+++ ++e+lfr+++k++synde r+ry+ ++v  +d+ keskrl
  gene1565|gene1565|rna1564|rna1564 497 SGFFGISAREMKEMSEESPTELQTLIRRMYFRECLFRIKSKQDSYNDELRMRYSGLNVITLDILKESKRL 566
                                        *******************************************************************987 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.2   6.8e-22   1.8e-18      11      98 .]     292     377 ..     283     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 6.8e-22
                          REPA_OB_2  11 sivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFggrs 86 
                                        + +Dvigvvk+v   s+++ +st++el kr+  lvDesg sv++tlWg +ae  + +   v+ lk++kvs+F+g +
  gene1565|gene1565|rna1564|rna1564 292 TYCDVIGVVKEVYSPSTVMIRSTQNELLKRDAILVDESG-SVRLTLWGPKAEI-DIEGGMVLGLKSIKVSEFNGIT 365
                                        579***********************************9.7********9875.9********************* PP

                          REPA_OB_2  87 lsllssstlkvn 98 
                                        +s++  s+++vn
  gene1565|gene1565|rna1564|rna1564 366 ISTTGGSQVVVN 377
                                        ********9986 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.8   3.8e-14   9.7e-11       1      69 [.     177     259 ..     177     266 .. 0.91
   2 !    6.3   0.0    0.0038       9.7      21      54 ..     323     353 ..     296     380 .. 0.80
   3 ?   -2.8   0.0       2.5   6.5e+03      30      50 ..     397     418 ..     394     429 .. 0.77
   4 !    5.4   0.0    0.0072        18      18      39 ..     475     496 ..     471     517 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 3.8e-14
                                        EEEEEEEEEEE.......EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTS.... CS
                    tRNA_anti-codon   1 VtvaGrvtsis.......drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpgg.... 64 
                                        +t++Grv+ +s        +++gkv+++++ Dgt+++++++f++ ++ ++  +++G+v+ ++ G+vk+ +++    
  gene1565|gene1565|rna1564|rna1564 177 WTIKGRVVVKSdirrftnHKGEGKVFNFEISDGTAQVKIICFSDCVDIFFPIVEVGKVYIISkGTVKTANKQystn 252
                                        79****************9**************************************************8885555 PP

                                        ..SEEEE CS
                    tRNA_anti-codon  65 ..elelk 69 
                                          ++e++
  gene1565|gene1565|rna1564|rna1564 253 pfDYEII 259
                                        5556665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0038
                                        EEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEE CS
                    tRNA_anti-codon  21 idlrDgtgriqvvlfreeatklaenlkeGdvvrv 54 
                                        ++l D++g+++++l+     k   +++ G+v++ 
  gene1565|gene1565|rna1564|rna1564 323 AILVDESGSVRLTLWG---PKAEIDIEGGMVLGL 353
                                        6799***********9...666666666666555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.5
                                        EEEEEET.HHHHHHHTTS-TTS CS
                    tRNA_anti-codon  30 iqvvlfr.eeatklaenlkeGd 50 
                                        +qv+l r ee+++l +++ke+ 
  gene1565|gene1565|rna1564|rna1564 397 MQVSLPRkEEKRRLIQEVKENE 418
                                        7999999888888888888765 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0072
                                        EEEEEEEETTEEEEEEEETHHH CS
                    tRNA_anti-codon  18 vifidlrDgtgriqvvlfreea 39 
                                        ++++ l D tg+i v+lf+e+a
  gene1565|gene1565|rna1564|rna1564 475 MVSMHLGDFTGQIWVSLFDEAA 496
                                        67899**************544 PP

>> Rep-A_N  Replication factor-A protein 1, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   3.9e-13     1e-09       3      82 ..       5      86 ..       3     100 .. 0.85
   2 ?    0.8   0.0       0.2     5e+02      25      52 ..     188     214 ..     179     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 3.9e-13
                                       TTHHHHHHHTTSTS-....-TEEEEEEEEEE--..SSSS-EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EEEE CS
                            Rep-A_N  3 egaiaailetgdasl....kpvlQvvelkkinskaeesseRyrlllsDgknkakamlatqLnslvksgklqklsivrl 76
                                       +g+++a+ + ++++     +p+lQ++ l k+++ a  +++Ryr+ lsDg++++k++++++L+++ ++g ++k s+++ 
  gene1565|gene1565|rna1564|rna1564  5 PGTVEALYN-SQTNNplykNPILQITSLGKLSV-AIGDKQRYRVNLSDGVSYMKGIFSSELTPHFEKGLVSKYSLIKP 80
                                       677888888.6666667889**********998.66899*************************************98 PP

                                       EEEEEE CS
                            Rep-A_N 77 teyvvn 82
                                        ++ v 
  gene1565|gene1565|rna1564|rna1564 81 GRFSVR 86
                                       888765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                                        EEEEE--..SSSS-EEEEEEESSSEEEE CS
                            Rep-A_N  25 elkkinskaeesseRyrlllsDgknkak 52 
                                        ++++ + +++ +++ + + +sDg++++k
  gene1565|gene1565|rna1564|rna1564 188 DIRRFT-NHKGEGKVFNFEISDGTAQVK 214
                                        566654.46788999********99876 PP

>> CDC24_OB3  Cell division control protein 24, OB domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0     0.003       7.8      19      76 ..     192     246 ..     175     265 .. 0.75
   2 !   19.1   0.0   3.3e-07   0.00084      38     219 ..     327     516 ..     286     521 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.003
                          CDC24_OB3  19 freknsekkkmdryslrieDttGaidatlweeagklhfkrlrvGhlvllsgLatsetk 76 
                                        f + ++e  k++  +++i D t++++++ ++  +   f  ++vG++ ++s+ + ++ +
  gene1565|gene1565|rna1564|rna1564 192 FTNHKGE-GKVF--NFEISDGTAQVKIICFSDCVDIFFPIVEVGKVYIISKGTVKTAN 246
                                        3233333.4677..9*******************999999*****9999976555444 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.3e-07
                          CDC24_OB3  38 DttGaidatlweeagklhfkrlrvGhlvllsgLatsetkqskklevswveg...ecgaslvnlStlpallnSscLr 110
                                        D++G++++tlw     +++ +++ G ++ l+++  se +    + +s++ g    ++  +    +l ++ +S    
  gene1565|gene1565|rna1564|rna1564 327 DESGSVRLTLWGP---KAEIDIEGGMVLGLKSIKVSEFN---GITISTTGGsqvVVNPDIPEAHELAGWYQSIGKD 396
                                        6666666667655...33334556666666666666555...3444444444444555555666666666666666 PP

                          CDC24_OB3 111 klsplsdlssetssta..kevkldhfvvealiv........itslaHssCgrpv...sggeleCefCqcsvaevvr 173
                                        ++++l + +++++  +  ke++l    ++++++        +ts     C+++v   ++g+  Ce C++++++  +
  gene1565|gene1565|rna1564|rna1564 397 MQVSLPRKEEKRRLIQevKENELAYSTIQGTVMflkedalwYTSCKGEGCNKKVameESGNYRCERCNMTYEDCNY 472
                                        6666654444444444667888888888899989999999999999999********7799**********7777* PP

                          CDC24_OB3 174 efeleitLdddtssaklfalctgqtaielLqispeeFselsedeqi 219
                                         + + + L d t++  + + + +++a  +  is+ e +e+se++ +
  gene1565|gene1565|rna1564|rna1564 473 RYMVSMHLGDFTGQ--IWVSLFDEAASGFFGISAREMKEMSEESPT 516
                                        ***********666..88899*********************9866 PP

>> Izumo-Ig  Izumo-like Immunoglobulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.61   1.6e+03      50      71 ..      30      51 ..      27      63 .. 0.83
   2 ?    1.9   0.0     0.093   2.4e+02      36      68 ..     304     336 ..     270     343 .. 0.83
   3 ?    8.5   0.2   0.00081       2.1      53      71 ..     447     465 ..     429     479 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.61
                                       EEEE-S--GGG-EEEEEEEEES CS
                           Izumo-Ig 50 tLtkkmvrledaGtYRCeldtv 71
                                       +L k  v++ d+ +YR +l++ 
  gene1565|gene1565|rna1564|rna1564 30 SLGKLSVAIGDKQRYRVNLSDG 51
                                       68899999*********99875 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.093
                                        TTS-EEEEEEES-SEEEE-S--GGG-EEEEEEE CS
                           Izumo-Ig  36 enssetllskgkdstLtkkmvrledaGtYRCel 68 
                                         + s +++ +++++ L ++++ ++++G+ R +l
  gene1565|gene1565|rna1564|rna1564 304 YSPSTVMIRSTQNELLKRDAILVDESGSVRLTL 336
                                        455778899999999999*********999776 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00081
                                        E-S--GGG-EEEEEEEEES CS
                           Izumo-Ig  53 kkmvrledaGtYRCeldtv 71 
                                         k+v++e++G+YRCe  ++
  gene1565|gene1565|rna1564|rna1564 447 NKKVAMEESGNYRCERCNM 465
                                        679***********96554 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   2.9e+03      75      95 .]      80     100 ..      47     100 .. 0.81
   2 ?    9.0   0.0   0.00064       1.6      18      58 ..     179     221 ..     169     271 .. 0.80
   3 ?   -0.4   0.0      0.53   1.4e+03      43      88 ..     325     391 ..     323     398 .. 0.45
   4 ?   -0.4   0.0      0.52   1.3e+03       8      57 ..     409     455 ..     405     508 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                        tRNA_anti_2  75 kgrlsvYeprGsyqlivedie 95 
                                         gr+sv +++Gs+ +++++i+
  gene1565|gene1565|rna1564|rna1564  80 PGRFSVRSKDGSVYIYIQEIQ 100
                                        588899999999999999886 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00064
                        tRNA_anti_2  18 lkkavwvrGeisnlkrka.sghvY.ftLkDekakisavifrsr 58 
                                        +k++v+v+ +i  +++++ +g v+ f+++D +a++++++f+  
  gene1565|gene1565|rna1564|rna1564 179 IKGRVVVKSDIRRFTNHKgEGKVFnFEISDGTAQVKIICFSDC 221
                                        57889*********97555886665***************854 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.53
                        tRNA_anti_2  43 LkDekakisavifrsraaklkft..l...................edGmkVlvkgrl.svYeprGsyq 88 
                                        L+De+ +++ +++  +a +++++  +                   + G +V+v+  + + +e  G yq
  gene1565|gene1565|rna1564|rna1564 325 LVDESGSVRLTLWGPKA-EIDIEggMvlglksikvsefngitistTGGSQVVVNPDIpEAHELAGWYQ 391
                                        66777777777776444.33322110112222222222222223266666666655434555555555 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.52
                        tRNA_anti_2   8 raikelleaelkkavwvrGeisnlkrkasghvYftLkDekakisavifrs 57 
                                        r i+e+ e+el    +++G +  lk+     +Y + k e ++ ++++ +s
  gene1565|gene1565|rna1564|rna1564 409 RLIQEVKENEL-AYSTIQGTVMFLKE--DALWYTSCKGEGCNKKVAMEES 455
                                        56667777788.55889999988854..7788888887777777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3821.99
//
Query:       gene1566|gene1566|rna1565|rna1565  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-20   72.1   0.0    5.7e-20   71.9   0.0    1.0  1  PRP38     PRP38 family


Domain annotation for each model (and alignments):
>> PRP38  PRP38 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   0.0   3.2e-24   5.7e-20      12     163 ..       6     162 ..       2     164 .] 0.96

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 3.2e-24
                              PRP38  12 iekivrerIleseYykenlfglkalaelvdeiveklkhieglvlggtekpstflClllKLlqlkptkkqieelln. 86 
                                        i++++re+Il+se +k n+ + ++  ++v  i++ l+ i+gl++g   +p +flCl+ K+  + ++++ + + l+ 
  gene1566|gene1566|rna1565|rna1565   6 INRMTREKILSSEEFK-NMRSFTE-PDVVGSICS-LNSIGGLIKG---IPHKFLCLIQKMGAISMKEEVVATSLEd 75 
                                        89**************.*******.*********.******8888...577************************* PP

                              PRP38  87 ...............nedskYiralgllYlRlvlepkelykllepllnDyrklkrrekdgevdpkgvklitidelv 147
                                                          + Y  a  l+YlRl+ + +e   l++++l D rk+ +++ ++     + + i++d ++
  gene1566|gene1566|rna1565|rna1565  76 lrpsepgpldssmkvFRGNVYFIAASLMYLRLSKRFHEYKPLVRSFLMDFRKIPIIDGQN-----NKEFIYLDVFA 146
                                        *************9977788999*********************************9999.....999******** PP

                              PRP38 148 ddLltkdricgtiLpr 163
                                        ddLl+k+ri+++ L r
  gene1566|gene1566|rna1565|rna1565 147 DDLLNKNRIFNVHLNR 162
                                        *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1153.10
//
Query:       gene1567|gene1567|rna1566|rna1566  [L=940]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-06   28.0   0.1    6.7e-06   25.9   0.0    2.1  2  IBN_N         Importin-beta N-terminal domain
  ------ inclusion threshold ------
       0.27   11.4   2.7          8    6.7   0.0    3.6  3  Helicase_PWI  N-terminal helicase PWI domain


Domain annotation for each model (and alignments):
>> IBN_N  Importin-beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   7.5e-10   6.7e-06       1      71 [.      23      87 ..      23      89 .. 0.93
   2 ?   -2.3   0.0       0.5   4.5e+03       9      33 ..     376     404 ..     372     417 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.5e-10
                                       HHHHHHHHHCSTCHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHGGSCCCHCGSXHHHHHHHHHHHHHH CS
                              IBN_N  1 AekqLkqlekqpgflsallqilanseselevRqlAalyLknlitkhWsdeeekqslpseekeqIrnnllnl 71
                                       Ae  L +lek  +f+ +l +  ++++++  +R ++a+y+kn+i k W+       + se+++++ +n+l+l
  gene1567|gene1567|rna1566|rna1566 23 AESILMNLEKDLTFVMSLPHTCMKDSDV-TLRRISAIYFKNTIIKQWK-----DDMYSEVRKYLIENILDL 87
                                       8999************************.*******************.....589999999999999876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.5
                                        HCSTCHHHHHHHHHHC.TTSH.H.HHH.H CS
                              IBN_N   9 ekqpgflsallqilan.sese.l.evR.q 33 
                                        e+++g  s+l+++l + +e++ l ++R  
  gene1567|gene1567|rna1566|rna1566 376 ETFQGIISYLVSVLGKyKENPtLdNTRpA 404
                                        55899999999999887666642366654 PP

>> Helicase_PWI  N-terminal helicase PWI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.031   2.8e+02       2      64 ..      47     113 ..      46     124 .. 0.70
   2 ?    6.7   0.0    0.0009         8       9      51 ..     249     291 ..     244     300 .. 0.88
   3 ?   -0.1   0.0      0.11     1e+03      70      91 ..     356     377 ..     344     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.031
                       Helicase_PWI   2 kdelsvkeidafWLqrelkkiykDaeeaqelaeevleiLkse..ade.lrelEnk.Lvelldydkfd 64 
                                        ++++++++i a + + ++ k  kD++ ++  +  + +iL      d+ +r   n+ Lv++++ +k++
  gene1567|gene1567|rna1566|rna1566  47 DSDVTLRRISAIYFKNTIIKQWKDDMYSEVRKYLIENILDLFlyGDDiTRTAYNAiLVHIFNTEKLN 113
                                        5678999****************99876666555555555443223335555444288899988864 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0009
                       Helicase_PWI   9 eidafWLqrelkkiykDaeeaqelaeevleiLkseadelrelE 51 
                                         i +f+ + el+++++D ++ q +  + l+i+++ ++++ ++E
  gene1567|gene1567|rna1566|rna1566 249 GIKKFYKNNELSEYITDMHRFQMIYATFLKIIQERSEHTADVE 291
                                        6999*******************************87777777 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.11
                       Helicase_PWI  70 lknrekivyctklaqaqseeek 91 
                                        l+nr +i++c   ++ ++e+e+
  gene1567|gene1567|rna1566|rna1566 356 LRNRLSILFCDIISKVKQEQET 377
                                        79********999998887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (940 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 6021.28
//
Query:       gene1568|gene1568|rna1567|rna1567  [L=511]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   3.1e-142  474.7   1.6   3.5e-142  474.5   1.6    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.073   13.2   0.2       0.16   12.1   0.2    1.5  1  Ku_PK_bind  Ku C terminal domain like


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.5   1.6    4e-146  3.5e-142       1     490 [.      31     508 ..      31     509 .. 0.97

  Alignments for each domain:
  == domain 1  score: 474.5 bits;  conditional E-value: 4e-146
                                        HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHH CS
                         Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLlee 76 
                                        +a+++++tlGP GmdK+   +g+++vvTnDGatilk+++++hP+ kllv ++esqd+evGDGTt+vv+L++e+l+ 
  gene1568|gene1568|rna1567|rna1567  31 IAEFLESTLGPYGMDKLF--AGKEIVVTNDGATILKHMKVKHPVGKLLVGISESQDSEVGDGTTSVVVLTAEILNC 104
                                        7999**************..6899**************************************************** PP

                                        HHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHC CS
                         Cpn60_TCP1  77 aekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvkl 152
                                         ++li++  +   i+e++ +++++++e+ +++  +++++   +e+L+k+a+t+++sk +++e++++s++vvdAv  
  gene1568|gene1568|rna1567|rna1567 105 LKSLIKDSFDLESIRECLSELRAACIEHVEKM--SVEVD---DEMLYKLAETCVTSKNIRHEKKHFSRMVVDAV-- 173
                                        ********************************..66665...58******************************.. PP

                                        HCCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SST...TSSCEEECEEEEEESS-BS--HHCCHHHCCCC CS
                         Cpn60_TCP1 153 ieenekeldlgrikvvkieggsledselveGlvldkgvlsp...dmpkklenakvllldvsLeiektetkttvvls 225
                                           +++  d+++i+++k++ggs+ ds  v+G++++k ++++   + pk+++n+k+l+l+v+Le++++  ++++++ 
  gene1568|gene1568|rna1567|rna1567 174 --RQSRVDDMESIGIKKVQGGSIGDSIAVNGVAFEKCFTYAgyeQQPKRISNPKILCLNVELEWKSERDNAEMRVG 247
                                        ..3335799*******************************999999****************************** PP

                                        SCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCG CS
                         Cpn60_TCP1 226 daeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssl 301
                                         +ee++k+++ae++++ ++l++ii+sg+nvv++  +i d+a++++ak+gi+++ rv+k+dl r++  +G++++ s 
  gene1568|gene1568|rna1567|rna1567 248 GVEEYQKVVNAEWTIISRKLDEIIDSGANVVLSSLSIGDYATQYFAKHGIFCAGRVSKEDLGRVVGSCGGRILGST 323
                                        ***************************************************************************9 PP

                                        GGGGCGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTT CS
                         Cpn60_TCP1 302 edltpeelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGG 377
                                        + l++ +lG+++ +ee+++g+ ++ ++e+    +++ti+lrg+ ++vl+ei ra++dA++vv+ a++ +++v GGG
  gene1568|gene1568|rna1567|rna1567 324 DYLED-SLGSCELFEERQLGKLRYNYFEG-GGMNACTIILRGPGQEVLEEIGRAVHDAICVVRTALKTRRAVSGGG 397
                                        77766.7*********************9.8889****************************************** PP

                                        CHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEE CS
                         Cpn60_TCP1 378 atelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiid 453
                                        ++e+el+k+++e+++++  ++ ++++a+++A+e+ip +La+N G+d+i+++++lr++h++g +  g+++  + ++d
  gene1568|gene1568|rna1567|rna1567 398 SVEMELSKMIREKSMEYGNKKVFVAKAVGQAFEKIPLLLAKNFGFDTISIIQDLRKKHANGSVYQGVSI--EGVRD 471
                                        **************************************************************9999998..5578* PP

                                        CCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                         Cpn60_TCP1 454 lveagvvDplkvkrqalksAteaastiLrideiikak 490
                                        + + g+++pl+vk++++k+++  a++i++id +i+a+
  gene1568|gene1568|rna1567|rna1567 472 MRDLGIYEPLEVKKNMIKASFNGAASIIMIDSTIMAE 508
                                        **********************************986 PP

>> Ku_PK_bind  Ku C terminal domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.8e-05      0.16      27     102 ..      98     180 ..      79     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                         Ku_PK_bind  27 ksvIeqlvedslgd.ssydkaveclkalReeai...eeeepelyNdFlrdlkkklqs.e..ggdrrefWkelvkke 95 
                                        ++ I + +++ ++d  + + + ecl+ lR ++i   e+  +e+ ++ l +l +++ + +  ++++++f  ++v++ 
  gene1568|gene1568|rna1567|rna1567  98 TAEILNCLKSLIKDsFDLESIRECLSELRAACIehvEKMSVEVDDEMLYKLAETCVTsKniRHEKKHFS-RMVVDA 172
                                        4444444555555423458888999999999994444456777999*********99768888888888.465554 PP

                         Ku_PK_bind  96 .klglIsk 102
                                         + + +++
  gene1568|gene1568|rna1567|rna1567 173 vRQSRVDD 180
                                        24555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3124.99
//
Query:       gene1569|gene1569|rna1568|rna1568  [L=3135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-33  113.7   1.1    3.8e-19   68.8   0.4    3.2  3  AAA_6            Hydrolytic ATP binding site of dynein motor 
    2.6e-20   72.9  10.8    2.6e-20   72.9  10.8    4.4  4  DHC_N2           Dynein heavy chain, N-terminal region 2
    5.9e-15   55.5   0.0    3.6e-06   27.0   0.0    4.5  4  AAA_5            AAA domain (dynein-related subfamily)
    1.3e-11   45.2   1.0    0.00051   20.5   0.0    4.4  4  AAA_16           AAA ATPase domain
    5.8e-09   36.3   0.1       0.04   14.2   0.0    4.8  4  AAA_22           AAA domain
    8.2e-08   31.7  10.4    8.2e-08   31.7  10.4    1.7  2  MT               Microtubule-binding stalk of dynein motor
    4.7e-06   27.1   0.1          5    7.6   0.0    5.6  5  AAA              ATPase family associated with various cellul
    1.4e-05   25.1   0.1       0.18   11.7   0.0    3.6  3  RsgA_GTPase      RsgA GTPase
    1.7e-05   24.4   0.0       0.26   10.8   0.0    3.8  4  AAA_7            P-loop containing dynein motor region
    2.3e-05   24.0   0.0     0.0093   15.7   0.0    3.9  4  AAA_29           P-loop containing region of AAA domain
    0.00024   20.9   0.0        3.6    7.3   0.0    3.9  3  AAA_24           AAA domain
     0.0016   18.2   0.0        5.4    6.7   0.0    3.5  3  AAA_30           AAA domain
     0.0078   16.8   0.4       0.49   10.9   0.0    4.4  5  AAA_18           AAA domain
     0.0092   16.5   0.0     0.0092   16.5   0.0    4.3  3  ABC_tran         ABC transporter
     0.0098   16.3   0.1         16    5.9   0.0    4.5  4  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.068   13.0   0.0    2.6  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.018   15.0   0.0        1.8    8.5   0.0    3.2  3  NACHT            NACHT domain
      0.022   14.5   0.0         14    5.4   0.0    3.5  3  Sigma54_activat  Sigma-54 interaction domain
      0.041   14.0   0.0       0.48   10.5   0.0    2.9  2  MMR_HSR1         50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.4     4e-22   3.8e-19       1     108 [.    1560    1666 ..    1560    1670 .. 0.95
   2 !   41.9   0.0   6.4e-14   6.1e-11     132     222 ..    1670    1752 ..    1666    1786 .. 0.90
   3 ?   -3.3   0.0       3.6   3.4e+03     310     327 .]    1804    1821 ..    1788    1821 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4e-22
                              AAA_6    1 YgyeYlgnserLviTpltdrcyltltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldyksl 74  
                                         Yg+eY    + +v T l  r+  +++ +l+  +g+ ++G +gtGKtE+vk   + ++k v+vf c+++++  +l
  gene1569|gene1569|rna1568|rna1568 1560 YGFEYYP-PTDIVFTSLVCRVVSSIVISLRSLCGAILYGRSGTGKTESVKYYCRLVGKPVFVFCCNEGCELATL 1632
                                         8999975.5689************************************************************** PP

                              AAA_6   75 gkifkGlaqsGaWgCfdeFnrielevLSvvaqqi 108 
                                          ++++  + +G++ CfdeFnr++ e++S  ++ i
  gene1569|gene1569|rna1568|rna1568 1633 RNVIEAGVLTGSYLCFDEFNRLSEEIMSGATELI 1666
                                         *****999********************887765 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 6.4e-14
                              AAA_6  132 nksvgifitmnpgyagrteLPdnLkalfRpvammvPdlelIaeimLfseGfkeakelakklvtlykllseqlsk 205 
                                         ++++++f+tmn gy+gr +LP +L+ +f ++ + +Pd++ I++            e+++k+++l+  ++ ++sk
  gene1569|gene1569|rna1568|rna1568 1670 KERTKFFLTMNIGYKGRYQLPRSLRGVFGEIRIDTPDMKDIIDHY--------CGEVSEKVYSLMCEVEANVSK 1735
                                         678899***********************************9975........4589***************** PP

                              AAA_6  206 qdhydfglralksvlka 222 
                                         q+hydfglra+  + ++
  gene1569|gene1569|rna1568|rna1568 1736 QEHYDFGLRAVRMIARQ 1752
                                         ***********988665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.6
                              AAA_6  310 lkvrhgvmlvGetgsgKt 327 
                                         l+ r+gv+++G+ g gK+
  gene1569|gene1569|rna1568|rna1568 1804 LESRRGVLIIGRNGVGKS 1821
                                         57899***********97 PP

>> DHC_N2  Dynein heavy chain, N-terminal region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       5.9   5.6e+03      17      53 ..     689     729 ..     676     758 .. 0.53
   2 ?    0.1   0.0      0.35   3.3e+02      30      79 ..    1050    1104 ..    1025    1115 .. 0.68
   3 !   72.9  10.8   2.8e-23   2.6e-20       4     392 ..    1123    1484 ..    1120    1489 .. 0.83
   4 ?    1.6   0.6      0.13   1.2e+02     138     192 ..    2659    2716 ..    2563    2727 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 5.9
                                        XXXXXXXXXXXX.....XXX....XXXXXXXXXXXXXXXXX CS
                             DHC_N2  17 lvsewqekleewkktpfkel....dveeleeevkellkklk 53 
                                         ++ + +++e++ ++++k++    ++e+l ++v +l+ +++
  gene1569|gene1569|rna1568|rna1568 689 EIDMVFSSMEKILEMKWKDVketkEIEDLMNKVGALEDRVY 729
                                        34444444555555566666633444444444444444443 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.35
                                         ....XXX..XXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXX CS
                             DHC_N2   30 ktpfkel..dveeleeevkellkklkklpkalke...wevakelkekieefkevl 79  
                                         ++pf+++  + e+l ee+++l++k++ ++k+  e   w+v+k+lk++ +e+ e +
  gene1569|gene1569|rna1568|rna1568 1050 DIPFDTIrlRRESLIEETRDLEEKINDVTKEKDElifWPVFKSLKARYKELGERI 1104
                                         5667666446679999999999999999988444899777777776654443332 PP

  == domain 3  score: 72.9 bits;  conditional E-value: 2.8e-23
                                         XXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             DHC_N2    4 ikkelellkklwdlvsewqekleewkktpfkeldveeleeevkellkklkklpkalkewevakelkekieefke 77  
                                         + ++l  l+  wd++s+ +++l++++++++ ++d++++ +++k +   + ++  +      +ke+ +ki+ +  
  gene1569|gene1569|rna1568|rna1568 1123 LNEKLAVLDGEWDSFSKLSSSLKKYESQKVCNVDINQITSFLKLID--VGRFHAR-----YYKEFLNKIRHYTA 1189
                                         66788888999***************************99998555..3344445.....9************* PP

                                         XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX.XXXXXXXXXXXX.XXXXXXXXXXXXX-HHHHHHHHHHH CS
                             DHC_N2   78 vlplieelrnpalrerHwkelsellgvikdpdseesltlgdllelgll.eeeieeisekAtkEaslekalkkie 150 
                                          +  +++l++  +++++ +                 + +++++ +  + +e+ie+ ++  + E+++e+ ++k++
  gene1569|gene1569|rna1568|rna1568 1190 ACGYLQHLKSLYMKKKYFDVE---------------MEVKQFFFM--FnKEDIEQKITDSRIEYEVERYIEKVR 1246
                                         *************95443322...............456667777..449************************ PP

                                         HHHTS---EEEE-SSS.TEEE..THHHHHHHHHHHHHHHHTCSSSTT..THHHHHHHHHHHHHHHHHHHHHHHH CS
                             DHC_N2  151 eewkelefelteykdsgvfilkgvdeiielledhivklqsmksspyvkpfeeeveewekklsrlqeildewlkv 224 
                                          e + +++e+   +d    +++++d i  +++  +v+  s++  +  ++f ee+++    +sr+ ++l+ + +v
  gene1569|gene1569|rna1568|rna1568 1247 GEISLMKLETRFTRDG-QLVVSNIDAIGDKINKLLVEHDSISRFNKKHFFFEELNDARLLMSRCLDLLSCLEEV 1319
                                         ************9998.557888*****************9988888789************************ PP

                                         HHHHHHHHHHT.THHHHHHTHHHHHHHHHHHHHHHHHHHHHHTTSGGGG...ST.T....HHHHHHHHHHHHHH CS
                             DHC_N2  225 QrkWlyLepifssedirkqlpeeakrFksvdkewkkimkevskdpnvleatskp.g....llekleelneqlek 293 
                                         Qr  l   ++fss      l+ eak+++ + + + + +   +++ +v++  + + +     ++kl e++  l++
  gene1569|gene1569|rna1568|rna1568 1320 QRGVLEFTNVFSS----DLLQFEAKKYSMIRQRFSDRLFGSNSS-EVVRSKDAElEallpFKDKLLEMKRDLDD 1388
                                         ***********87....59****************977766555.67775333331455699************ PP

                                         HHHHHHHHHHHHHHHSTTHHHH-HHHHHHHHHTTTTSGGGHHHHHHHHSSEEEESE.....EEEEEETTS-EEE CS
                             DHC_N2  294 iqksLneyLekkRlafpRFyFlsddeLleilsqskdpsavqphlkkcFegiaslefeekkeitgmiskegEkve 367 
                                         i ++L+ +L + R+  pR+yF+sd++L++ l +        + +  +  +i+s+  e++ +++g+ s  gE+v 
  gene1569|gene1569|rna1568|rna1568 1389 ISRGLKTFLKRYRKETPRLYFISDEDLIKALNNRF----YYEEIARMMFNIDSII-EKNGSVIGFES-CGERVM 1456
                                         *******************************5433....3444556667888886.56788888887.689999 PP

                                         EE.....E.EEEHHHHHHHHHHHHHHHH CS
                             DHC_N2  368 lse...argnveeWLneleeemkktlke 392 
                                         l++   ++++  ++++ + +e+ +tlk+
  gene1569|gene1569|rna1568|rna1568 1457 LEKevrIDQDLASFIRIFSKEISDTLKS 1484
                                         8867666666667777777777777765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.13
                                         X-HHHHHHHHHHHHHHTS---EEEE-SSS.TEEE......THHHHHHHHHHHHHHHHTC CS
                             DHC_N2  138 kEaslekalkkieeewkelefelteykdsgvfilkg....vdeiielledhivklqsmk 192 
                                         k a++e++++++++e +++++ l++ k++ +++ ++    +++iie+l+d++ k + mk
  gene1569|gene1569|rna1568|rna1568 2659 KLADIENMIEAMKDEYSASTLRLETTKTE-ISTADEkaslINKIIEELSDEVDKWKRMK 2716
                                         44678888888888888888888777655.33333333345666777777776666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.2e-07   0.00039       3      83 ..    1594    1660 ..    1592    1674 .. 0.88
   2 !   27.0   0.0   3.8e-09   3.6e-06       1     133 [.    1809    1931 ..    1809    1944 .. 0.86
   3 ?    1.8   0.0      0.23   2.2e+02       2      41 ..    2001    2045 ..    2000    2080 .. 0.74
   4 ?   -2.2   0.0       3.9   3.7e+03       2      30 ..    2254    2282 ..    2253    2286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.2e-07
                                         EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                              AAA_5    3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76  
                                         +L G +GtgK+e +++++++++++v++  ++++ + ++l+  +e          ++l+     g+ l++DE++r
  gene1569|gene1569|rna1568|rna1568 1594 ILYGRSGTGKTESVKYYCRLVGKPVFVFCCNEGCELATLRNVIEA---------GVLT-----GSYLCFDEFNR 1653
                                         8************************************99999996.........8888.....*********** PP

                                         --HHHHH CS
                              AAA_5   77 aesevln 83  
                                         ++ e+++
  gene1569|gene1569|rna1568|rna1568 1654 LSEEIMS 1660
                                         9999875 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 3.8e-09
                                         EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------......G-SE CS
                              AAA_5    1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar......egei 68  
                                         +vl++G  G+gKs+l++ +  a ++e + ++ +r++   +++g r+  + t +++ds++ r  r      + + 
  gene1569|gene1569|rna1568|rna1568 1809 GVLIIGRNGVGKSTLIKTVQDARKAECFHYN-PRNMG--KVFGWRD--DVTGEWRDSKFIRDLRrnmhreKECW 1877
                                         59*********************99999875.56565..5788887..99*******************99999 PP

                                         EEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHH CS
                              AAA_5   69 lvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspa 133 
                                         +v+D++   +s +++ ++s+l+e+rll  ++ge+++ +         +++++ + +    +l+pa
  gene1569|gene1569|rna1568|rna1568 1878 FVFDGIV--DSFWIEDFNSILDENRLLCLSSGERIRIPDH-----YKFVFESTSME----KLTPA 1931
                                         99****9..9*************************99986.....66776666655....44444 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.23
                                         EEEE--SSSSHHHHHHHGG..GGB...S--EEEEE--TT--HHHH CS
                              AAA_5    2 vlLvGppGtgKselaerla..aal...nreveyvqltrdtteedl 41  
                                         +l+ G+ G+gK++l+e++    ++   ++ +e  ++ r++ e+ +
  gene1569|gene1569|rna1568|rna1568 2001 LLIRGEAGVGKRSLIEEVFpdNVIvieGKGLEASMIERKLGEDRI 2045
                                         7899**********9987411222455555555555555555555 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.9
                                         EEEE--SSSSHHHHHHHGGGGBS--EEEE CS
                              AAA_5    2 vlLvGppGtgKselaerlaaalnreveyv 30  
                                         +++ Gp+ +gK +l+++  ++++ +v +v
  gene1569|gene1569|rna1568|rna1568 2254 IVIEGPKMSGKHWLIRECMRRMKINVKMV 2282
                                         67889999***********9998877766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.1   3.9e+03      67     142 ..    1340    1412 ..    1324    1418 .. 0.63
   2 ?    6.0   0.1     0.015        14      25      60 ..    1591    1624 ..    1573    1655 .. 0.76
   3 !   13.5   0.0   7.5e-05     0.071      25      51 ..    1808    1834 ..    1795    1872 .. 0.78
   4 !   20.5   0.0   5.4e-07   0.00051      17      88 ..    1991    2051 ..    1981    2135 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.1
                             AAA_16   67 ipysalaqalareellrqllde...aesaeleawrekleealaavpelagaea...srllellkrllallsrde 134 
                                           ys++ q +  ++l+    +e   +++aelea   + ++ l+         +    ++ + lk +l+++++ e
  gene1569|gene1569|rna1568|rna1568 1340 KKYSMIRQRF-SDRLFGSNSSEvvrSKDAELEALLPFKDKLLE-------M-KrdlDDISRGLKTFLKRYRK-E 1403
                                         4567777777.44777766666665444455555555555555.......1.13457889999999988888.6 PP

                             AAA_16  135 rp.lvlvlD 142 
                                          p l+++ D
  gene1569|gene1569|rna1568|rna1568 1404 TPrLYFISD 1412
                                         662555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                             AAA_16   25 elvllsGesGvGKsslvrellralekdggiflrgkc 60  
                                         +  +l+G sG+GK+  v+   r + k   +f+ + +
  gene1569|gene1569|rna1568|rna1568 1591 CGAILYGRSGTGKTESVKYYCRLVGKP--VFVFCCN 1624
                                         6789*************9999655555..4444444 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 7.5e-05
                             AAA_16   25 elvllsGesGvGKsslvrellralekd 51  
                                         + vl++G  GvGKs+l++++++a +++
  gene1569|gene1569|rna1568|rna1568 1808 RGVLIIGRNGVGKSTLIKTVQDARKAE 1834
                                         89*******************655544 PP

  == domain 4  score: 20.5 bits;  conditional E-value: 5.4e-07
                             AAA_16   17 ervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88  
                                         er+++++ +++l++Ge+GvGK sl++e++     d++i+++gk  +       s++ + l  e+ ++ +  e
  gene1569|gene1569|rna1568|rna1568 1991 ERLAKDGRRALLIRGEAGVGKRSLIEEVF----PDNVIVIEGKGLEA------SMIERKL-GEDRIKRIRGE 2051
                                         56666666*********************....577*********99......7888888.55777777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00012      0.11       9      62 ..    1594    1638 ..    1592    1676 .. 0.88
   2 !   14.2   0.0   4.2e-05      0.04       5      52 ..    1807    1845 ..    1804    1875 .. 0.80
   3 ?    2.6   0.0      0.16   1.5e+02       4      34 ..    1997    2027 ..    1994    2071 .. 0.81
   4 ?   -2.2   0.0       4.9   4.6e+03       5      28 ..    2251    2274 ..    2249    2281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                             AAA_22    9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellr 62  
                                         +++G sGtGKT +++ + +           +++v+ +++++++++++l++ +  
  gene1569|gene1569|rna1568|rna1568 1594 ILYGRSGTGKTESVKYYCRLV---------GKPVFVFCCNEGCELATLRNVIEA 1638
                                         79******************9.........9************99999988765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.2e-05
                             AAA_22    5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpssts 52  
                                         ++ ++++G  G+GK+tl++++++           ++e++++++ + ++
  gene1569|gene1569|rna1568|rna1568 1807 RRGVLIIGRNGVGKSTLIKTVQDAR---------KAECFHYNPRNMGK 1845
                                         66689*******************9.........88888888888774 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.16
                             AAA_22    4 tagilvvtGesGtGKTtllrrlleqldeeak 34  
                                         +++ l++ Ge+G+GK  l+++++  ++++++
  gene1569|gene1569|rna1568|rna1568 1997 GRRALLIRGEAGVGKRSLIEEVFPDNVIVIE 2027
                                         7899***********9999998876666555 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 4.9
                             AAA_22    5 agilvvtGesGtGKTtllrrlleq 28  
                                          +++v+ G++ +GK +l+r+ +++
  gene1569|gene1569|rna1568|rna1568 2251 GYSIVIEGPKMSGKHWLIRECMRR 2274
                                         6799**************998765 PP

>> MT  Microtubule-binding stalk of dynein motor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.4   4.1e+03     299     335 ..    1143    1180 ..    1095    1184 .. 0.55
   2 !   31.7  10.4   8.7e-11   8.2e-08       3     296 ..    2423    2712 ..    2421    2716 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
                                 MT  299 avenfksqektlcgdvllitafvsy..vgfftkkyrqel 335 
                                         +++++ sq++    d+  it+f+    vg f  +y +e+
  gene1569|gene1569|rna1568|rna1568 1143 SLKKYESQKV-CNVDINQITSFLKLidVGRFHARYYKEF 1180
                                         3333333322.2345666666655411355655555555 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 8.7e-11
                                 MT    3 lengllklqstaaqvddlkaklaaqevelkqknedadkliqvvgvetekvskekaiadeeekkvavinkevkkk 76  
                                         l +gl k++   ++   l++  + ++ +l++ n + d  ++ +    +++ +ek++    +  ++   k  +kk
  gene1569|gene1569|rna1568|rna1568 2423 LVEGLQKIEEFRKEAWALRSESSQKKKDLQELNSKLDWQLEKIIASQKQLENEKSVIGSRKSEMEGALKINQKK 2496
                                         66789999999999999999999999999999999998888888888999*******99999999999989999 PP

                                 MT   77 qkdceedlakaepallaaqealntlnktnltelksfgsppdavvnvaaavmvllaprgkvpkdr.swkaakivm 149 
                                         q   ++ la a+  l  ++ +++ l k+ l+e+k +  pp+ + n   av+ l+    k   ++  wk   i +
  gene1569|gene1569|rna1568|rna1568 2497 QEVMDKRLAMAKTLLEESKRSIEELPKSSLSEIKVMINPPEIIRNTIEAVFWLVEGASKGDTEKiEWKR-LIQF 2569
                                         999***********************************************9999877777766625875.6889 PP

                                 MT  150 akvdafldslinfdkenihenclkaikeylndpefepefikskslaaaglcswvinivrfyevycdvepkrqal 223 
                                          k + f+  + n +   i++     + e +++p f  e  ++ s a++ l  wv+   ++  ++ ++ p    +
  gene1569|gene1569|rna1568|rna1568 2570 VKREDFVSKVLNCKGTTIPD----ILEELMSNPLFTYEKAQNASKACGSLFMWVMARYKYARIMAEILPMEEEI 2639
                                         99999*********999997....578999***************************************98776 PP

                                 MT  224 ekanaelaaaqeklaaikakiaelnanlaeltaafekatadklkcqqeaeatartislanrlvgglasenvrw 296 
                                            ++ +++++  + +  +k+a++++ +  +  ++  +t      + e  +++   sl n+++  l+ e  +w
  gene1569|gene1569|rna1568|rna1568 2640 AVLDSSIKKSRGEIEKEEKKLADIENMIEAMKDEYSASTLRLETTKTEISTADEKASLINKIIEELSDEVDKW 2712
                                         6666666666666666666666666666666666655555555555566666666666676666666666555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0053         5       2      70 ..    1594    1654 ..    1593    1669 .. 0.75
   2 !    6.7   0.0    0.0099       9.4       1      30 [.    1810    1839 ..    1810    1883 .. 0.86
   3 ?   -0.3   0.0       1.4   1.3e+03       2      39 ..    2002    2036 ..    2001    2085 .. 0.63
   4 ?   -3.0   0.0       9.5   8.9e+03      81     126 ..    2786    2827 ..    2784    2832 .. 0.69
   5 ?    4.4   0.1     0.051        49      29      84 ..    2998    3043 ..    2985    3064 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                                         EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                                AAA    2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidal 70  
                                         +lyG  GtGKT  +k  ++ +g +++ + + e +        + +r+++++       s l +DE+ +l
  gene1569|gene1569|rna1568|rna1568 1594 ILYGRSGTGKTESVKYYCRLVGKPVFVFCCNEGC------ELATLRNVIEAG-VLT-GSYLCFDEFNRL 1654
                                         79******************99999988888877......566666666543.332.366666666665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0099
                                         EEEESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                                AAA    1 vllyGppGtGKTllakavakelgvefleis 30  
                                         vl++G  G+GK++l+k v    ++e++  +
  gene1569|gene1569|rna1568|rna1568 1810 VLIIGRNGVGKSTLIKTVQDARKAECFHYN 1839
                                         799**************9988777776655 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                                         EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSST CS
                                AAA    2 llyGppGtGKTllakavakelgvefleisgsellskyv 39  
                                         l+ G  G+GK +l++ v  +   +++ i+g+ l  +++
  gene1569|gene1569|rna1568|rna1568 2002 LIRGEAGVGKRSLIEEVFPD---NVIVIEGKGLEASMI 2036
                                         7889*************998...555555555553322 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 9.5
                                         HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSE CS
                                AAA   81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdr 126 
                                         +++++ ++L +++d+ ++      +i+++n+  ++ +      Rf +
  gene1569|gene1569|rna1568|rna1568 2786 FDRDIYKALKRQMDNATH-----SIILVSNSRANFYKGYTYnCRFAE 2827
                                         577889999999999999.....377777776666655555455555 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.051
                                         EETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHH CS
                                AAA   29 isgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeer 84  
                                         ++ ++++s   +e+++kire+++e ++++  +i +i +i+ l++++        ++
  gene1569|gene1569|rna1568|rna1568 2998 MKITSVISAGPKENNEKIREMLEEKSQES--KIYLIKNIHYLGNAK--------KT 3043
                                         677788888999**********9966666..***********9988........22 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.9   3.7e+03     102     113 ..    1593    1604 ..    1575    1608 .. 0.80
   2 !   11.7   0.0   0.00019      0.18      96     124 ..    1803    1832 ..    1774    1842 .. 0.82
   3 !    8.7   0.0    0.0016       1.5      23     123 ..    1921    2022 ..    1914    2054 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.9
                                         EEEECSTTSSHH CS
                        RsgA_GTPase  102 svlvGqSGvGKS 113 
                                         ++l G SG GK+
  gene1569|gene1569|rna1568|rna1568 1593 AILYGRSGTGKT 1604
                                         789********7 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
                                         HCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                        RsgA_GTPase   96 llkd.ktsvlvGqSGvGKStLinallpele 124 
                                          l++ + ++++G  GvGKStLi++++   +
  gene1569|gene1569|rna1568|rna1568 1803 GLESrRGVLIIGRNGVGKSTLIKTVQDARK 1832
                                         56664667899************9988655 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0016
                                         EESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                        RsgA_GTPase   23 vslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkel 96  
                                          s++ ++l++ +l+r+ +++ e++ + + +l   D ++ e +++   +++ ++ ++ l+  ++++  ++++++l
  gene1569|gene1569|rna1568|rna1568 1921 ESTSMEKLTPATLTRVFLVYMEEDES-LHMLDGQDATSIEGDVRYDGSRIPEFPFRKLIPTEEQSFYAKSIERL 1993
                                         56777778888888866666555544.34577778777777788888888888887777777777778888888 PP

                                         CTT..SEEEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase   97 lkd..ktsvlvGqSGvGKStLinallpel 123 
                                          kd  +  ++ G+ GvGK +Li+++ p++
  gene1569|gene1569|rna1568|rna1568 1994 AKDgrRALLIRGEAGVGKRSLIEEVFPDN 2022
                                         88776677888************999975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.11     1e+02      34      56 ..    1591    1613 ..    1569    1627 .. 0.76
   2 !   10.8   0.0   0.00028      0.26      22      62 ..    1796    1836 ..    1788    1845 .. 0.82
   3 !    5.9   0.0    0.0084         8      13      53 ..    1977    2018 ..    1970    2023 .. 0.82
   4 ?   -3.8   0.0       8.1   7.6e+03      29      58 ..    2247    2276 ..    2244    2281 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                              AAA_7   34 kpvllvGptGtGKtviikdllkk 56  
                                            +l+G +GtGKt  +k +++ 
  gene1569|gene1569|rna1568|rna1568 1591 CGAILYGRSGTGKTESVKYYCRL 1613
                                         56789*********999988765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00028
                              AAA_7   22 ysyllelllknkkpvllvGptGtGKtviikdllkkldkeky 62  
                                         y+ +l+  l++++ vl++G  G+GK+++ik++ ++ + e +
  gene1569|gene1569|rna1568|rna1568 1796 YKEVLTYGLESRRGVLIIGRNGVGKSTLIKTVQDARKAECF 1836
                                         66778888999*******************98877766555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0084
                              AAA_7   13 lVptvdtvrysyllelllknkkp.vllvGptGtGKtviikdl 53  
                                         l+pt ++  y   +e l k ++  +l+ G++G+GK ++i+++
  gene1569|gene1569|rna1568|rna1568 1977 LIPTEEQSFYAKSIERLAKDGRRaLLIRGEAGVGKRSLIEEV 2018
                                         79*************9999877615667*******9999874 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 8.1
                              AAA_7   29 llknkkpvllvGptGtGKtviikdllkkld 58  
                                         +l++++++++ Gp+ +GK  +i++++++++
  gene1569|gene1569|rna1568|rna1568 2247 ILHRGYSIVIEGPKMSGKHWLIRECMRRMK 2276
                                         6778899999**************999987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.5   1.4e+03      38      50 ..      67      79 ..      62      86 .. 0.88
   2 ?   -0.6   0.1       1.2   1.1e+03      25      36 ..    1593    1604 ..    1582    1605 .. 0.80
   3 !   15.7   0.0   9.9e-06    0.0093      21      41 ..    1807    1826 ..    1795    1839 .. 0.79
   4 ?    1.8   0.0      0.21     2e+02      22      39 ..    1996    2015 ..    1982    2018 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.5
                             AAA_29 38 llDAiqalLvpak 50
                                       ++DAi+ l++pa+
  gene1569|gene1569|rna1568|rna1568 67 MIDAISNLIIPAT 79
                                       79*********98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.2
                             AAA_29   25 tlltGpsGsGKS 36  
                                          +l G+sG+GK+
  gene1569|gene1569|rna1568|rna1568 1593 AILYGRSGTGKT 1604
                                         789********6 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 9.9e-06
                             AAA_29   21 lkgatlltGpsGsGKSTllDA 41  
                                         ++  +l++G++G+GKSTl+  
  gene1569|gene1569|rna1568|rna1568 1807 RR-GVLIIGRNGVGKSTLIKT 1826
                                         34.59*************954 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.21
                             AAA_29   22 kg..atlltGpsGsGKSTll 39  
                                         +g  a l+ G+ G+GK +l+
  gene1569|gene1569|rna1568|rna1568 1996 DGrrALLIRGEAGVGKRSLI 2015
                                         4455899*********9998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0038       3.6       6      34 ..    1594    1626 ..    1592    1656 .. 0.82
   2 !    6.9   0.0    0.0048       4.6       5      22 ..    1810    1827 ..    1806    1844 .. 0.87
   3 ?    1.4   0.0      0.24   2.3e+02       5      30 ..    2001    2030 ..    1998    2077 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0038
                             AAA_24    6 liyGpsgiGKTtlakel....gpkplfidtekG 34  
                                         ++yG sg+GKT ++k +    g+ ++++ +++G
  gene1569|gene1569|rna1568|rna1568 1594 ILYGRSGTGKTESVKYYcrlvGKPVFVFCCNEG 1626
                                         69***************9996444444445544 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0048
                             AAA_24    5 iliyGpsgiGKTtlakel 22  
                                         +li+G +g+GK+tl+k+ 
  gene1569|gene1569|rna1568|rna1568 1810 VLIIGRNGVGKSTLIKTV 1827
                                         89**************98 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.24
                             AAA_24    5 iliyGpsgiGKTtlakel.gpkplfi...d 30  
                                         +li G++g+GK +l+ e  ++++++i    
  gene1569|gene1569|rna1568|rna1568 2001 LLIRGEAGVGKRSLIEEVfPDNVIVIegkG 2030
                                         6899**************999999996663 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.21     2e+02      21      38 ..    1593    1610 ..    1585    1617 .. 0.85
   2 !    6.7   0.0    0.0057       5.4      16      45 ..    1806    1834 ..    1797    1847 .. 0.83
   3 ?    5.0   0.0     0.019        18       8      38 ..    1988    2018 ..    1981    2028 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.21
                             AAA_30   21 avltGpAGtGKttalkal 38  
                                         a+l G+ GtGKt ++k +
  gene1569|gene1569|rna1568|rna1568 1593 AILYGRSGTGKTESVKYY 1610
                                         5899********999876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0057
                             AAA_30   16 sgdrvavltGpAGtGKttalkalreaweaa 45  
                                         s+ r +++ G+ G GK+t++k++++a +a+
  gene1569|gene1569|rna1568|rna1568 1806 SR-RGVLIIGRNGVGKSTLIKTVQDARKAE 1834
                                         44.578999**************9987765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.019
                             AAA_30    8 aavealltsgdrvavltGpAGtGKttalkal 38  
                                         + +e+l+++g+r  ++ G AG GK  +++++
  gene1569|gene1569|rna1568|rna1568 1988 KSIERLAKDGRRALLIRGEAGVGKRSLIEEV 2018
                                         56899*******************9988765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       8.1   7.7e+03      17      86 ..    1427    1508 ..    1415    1515 .. 0.70
   2 ?   -1.8   0.0       4.5   4.2e+03       2      17 ..    1594    1609 ..    1594    1660 .. 0.84
   3 !   10.9   0.0   0.00052      0.49       1      61 [.    1810    1863 ..    1810    1905 .. 0.68
   4 ?   -2.6   0.0       7.9   7.4e+03       3      18 ..    2003    2018 ..    2002    2128 .. 0.69
   5 ?   -2.7   0.0       8.6   8.1e+03      47      87 ..    2781    2816 ..    2751    2859 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.1
                             AAA_18   17 eLskrlgfgvnlrdvakenglllevdpe....aldeskrldedkldklldaleenss...........aleegk 75  
                                         e++++    +n+ +++ +ng++++++      +l+++ r+d+d    +    +e+s+            +eeg 
  gene1569|gene1569|rna1568|rna1568 1427 EIARM---MFNIDSIIEKNGSVIGFESCgervMLEKEVRIDQDLASFIRIFSKEISDtlkswfykgleGMEEGC 1497
                                         44444...799999999999999999888888888888888888666555555555577777777777666666 PP

                             AAA_18   76 nlvidghlael 86  
                                         + +i+++++e+
  gene1569|gene1569|rna1568|rna1568 1498 PSIISDLIVEF 1508
                                         66777766665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                             AAA_18    2 lltGtpGvGKttlake 17  
                                         +l G +G+GKt+  k+
  gene1569|gene1569|rna1568|rna1568 1594 ILYGRSGTGKTESVKY 1609
                                         68999******97665 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00052
                             AAA_18    1 IlltGtpGvGKttlakeL..skrlgf.gvnlrdvakenglllevdpealdeskrldedkldkll 61  
                                         +l+ G  GvGK+tl k +  +++ ++ ++n r + k  g++++v+ e   +          k +
  gene1569|gene1569|rna1568|rna1568 1810 VLIIGRNGVGKSTLIKTVqdARKAECfHYNPRNMGKVFGWRDDVTGE--WRDS--------KFI 1863
                                         7899**************44333345788888888888888888888..2222........222 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 7.9
                             AAA_18    3 ltGtpGvGKttlakeL 18  
                                         + G +GvGK +l +e+
  gene1569|gene1569|rna1568|rna1568 2003 IRGEAGVGKRSLIEEV 2018
                                         5677899998888876 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 8.6
                             AAA_18   47 deskrldedkldklldaleenssaleegknlvidghlaele 87  
                                           ++r+d+d  ++l ++++++      ++ ++++  +a+++
  gene1569|gene1569|rna1568|rna1568 2781 YGCDRFDRDIYKALKRQMDNAT-----HSIILVSNSRANFY 2816
                                         5666666666555555555542.....45555555444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.6   1.5e+03      16      33 ..    1595    1612 ..    1586    1616 .. 0.83
   2 !   16.5   0.0   9.8e-06    0.0092       6      34 ..    1802    1830 ..    1798    1911 .. 0.87
   3 ?   -2.4   0.0       6.8   6.4e+03      14      29 ..    2001    2016 ..    1996    2049 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                                         EEESTTSSHHHHHHHHTT CS
                                         xxxxxxxxxxxxxxxxxx RF
                           ABC_tran   16 ivGenGaGKStLlkllag 33  
                                         + G++G+GK+  +k  ++
  gene1569|gene1569|rna1568|rna1568 1595 LYGRSGTGKTESVKYYCR 1612
                                         88********88887666 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 9.8e-06
                                         EEEETTSEEEEEESTTSSHHHHHHHHTTS CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran    6 lklkegekvaivGenGaGKStLlkllagl 34  
                                           l+  + v i+G+nG GKStL+k++   
  gene1569|gene1569|rna1568|rna1568 1802 YGLESRRGVLIIGRNGVGKSTLIKTVQDA 1830
                                         5677778899**************98765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.8
                                         EEEEESTTSSHHHHHH CS
                                         xxxxxxxxxxxxxxxx RF
                           ABC_tran   14 vaivGenGaGKStLlk 29  
                                         + i Ge G GK +L++
  gene1569|gene1569|rna1568|rna1568 2001 LLIRGEAGVGKRSLIE 2016
                                         6789*******99985 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.07        66       2      22 ..    1594    1614 ..    1593    1679 .. 0.88
   2 ?    5.9   0.0     0.017        16       1      20 [.    1810    1829 ..    1810    1888 .. 0.84
   3 ?   -2.7   0.0       8.3   7.8e+03       2      17 ..    2002    2017 ..    2001    2023 .. 0.83
   4 ?   -0.5   0.0       1.7   1.6e+03      18      53 ..    2790    2824 ..    2785    2859 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.07
                       RNA_helicase    2 wlyGpsgeGKStlakeLakal 22  
                                         +lyG+sg+GK+  +k+ ++ +
  gene1569|gene1569|rna1568|rna1568 1594 ILYGRSGTGKTESVKYYCRLV 1614
                                         69***********99977765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.017
                       RNA_helicase    1 iwlyGpsgeGKStlakeLak 20  
                                         +++ G++g+GKStl+k++ +
  gene1569|gene1569|rna1568|rna1568 1810 VLIIGRNGVGKSTLIKTVQD 1829
                                         5799************9544 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 8.3
                       RNA_helicase    2 wlyGpsgeGKStlake 17  
                                         ++ G++g+GK +l++e
  gene1569|gene1569|rna1568|rna1568 2002 LIRGEAGVGKRSLIEE 2017
                                         789*******888876 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 1.7
                       RNA_helicase   18 LakallkklklkkkdsvysrnpeddfwdgYtgqevv 53  
                                         + kal +++++ +++ + + n++ +f++gYt  ++ 
  gene1569|gene1569|rna1568|rna1568 2790 IYKALKRQMDNATHSIILVSNSRANFYKGYT-YNCR 2824
                                         6778888997777666666***********9.4444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.2e-05     0.068       3      24 ..    1811    1832 ..    1810    1886 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-05
                             AAA_21    3 vliGpNgsGKSnLLdaldllar 24  
                                         ++iG+Ng+GKS+L+++ + ++ 
  gene1569|gene1569|rna1568|rna1568 1811 LIIGRNGVGKSTLIKTVQDARK 1832
                                         79*************9977655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.7   4.5e+03       4      14 ..    1594    1604 ..    1593    1611 .. 0.88
   2 ?    8.5   0.0    0.0019       1.8       3      27 ..    1810    1834 ..    1808    1841 .. 0.83
   3 ?    2.3   0.0      0.15   1.4e+02       2      19 ..    2000    2017 ..    1999    2020 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.7
                                         EEEC-TTTCHH CS
                              NACHT    4 ilqGeaGsGKT 14  
                                         il G++G GKT
  gene1569|gene1569|rna1568|rna1568 1594 ILYGRSGTGKT 1604
                                         799*******9 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0019
                                         EEEEC-TTTCHHHHHHHHHHHHCTS CS
                              NACHT    3 vilqGeaGsGKTtLlqklalawaeg 27  
                                         v++ G++G+GK+tL++ + +a +++
  gene1569|gene1569|rna1568|rna1568 1810 VLIIGRNGVGKSTLIKTVQDARKAE 1834
                                         89**************998776554 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.15
                                         CEEEEC-TTTCHHHHHHH CS
                              NACHT    2 lvilqGeaGsGKTtLlqk 19  
                                          ++++GeaG+GK  L+++
  gene1569|gene1569|rna1568|rna1568 2000 ALLIRGEAGVGKRSLIEE 2017
                                         689*********988765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   1.9e+03      23      38 ..    1591    1606 ..    1576    1621 .. 0.78
   2 ?    5.4   0.0     0.015        14      20      49 ..    1805    1834 ..    1794    1846 .. 0.78
   3 ?    4.2   0.0     0.032        31      14      43 ..    1989    2019 ..    1980    2026 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                         S-EEEECSTTSSHHHH CS
                    Sigma54_activat   23 lsvlitGesGtGKell 38  
                                         +  ++ G sGtGK+  
  gene1569|gene1569|rna1568|rna1568 1591 CGAILYGRSGTGKTES 1606
                                         556899*******865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                                         TSSS-EEEECSTTSSHHHHHHHHHHHSTTT CS
                    Sigma54_activat   20 ktdlsvlitGesGtGKellaraiheaskrk 49  
                                         +++  vli G +G+GK++l +++ +a+k +
  gene1569|gene1569|rna1568|rna1568 1805 ESRRGVLIIGRNGVGKSTLIKTVQDARKAE 1834
                                         56678**************99998877655 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.032
                                         HHHHHCTSS.S-EEEECSTTSSHHHHHHHHH CS
                    Sigma54_activat   14 qikkvaktd.lsvlitGesGtGKellaraih 43  
                                         +i+++ak     +li+Ge G+GK  l + ++
  gene1569|gene1569|rna1568|rna1568 1989 SIERLAKDGrRALLIRGEAGVGKRSLIEEVF 2019
                                         5566665443789**********99877665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00051      0.48       2      22 ..    1810    1830 ..    1809    1840 .. 0.83
   2 ?   -2.1   0.0       4.1   3.9e+03       4      30 ..    2003    2029 ..    2001    2108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00051
                                         EEEEESTTSSHHHHHHHHHTS CS
                           MMR_HSR1    2 vaivGrpNvGKStLinaltge 22  
                                         v+i+Gr  vGKStLi++  ++
  gene1569|gene1569|rna1568|rna1568 1810 VLIIGRNGVGKSTLIKTVQDA 1830
                                         78*************998665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                                         EEESTTSSHHHHHHHHHTSTEEESSST CS
                           MMR_HSR1    4 ivGrpNvGKStLinaltgekaivsdkp 30  
                                         i G   vGK +Li   + +++iv + +
  gene1569|gene1569|rna1568|rna1568 2003 IRGEAGVGKRSLIEEVFPDNVIVIEGK 2029
                                         779999******999988777775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (3135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1365  (0.0761336); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 1.80u 0.36s 00:00:02.16 Elapsed: 00:00:00.63
# Mc/sec: 15059.51
//
Query:       gene1570|gene1570|rna1569|rna1569  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.57
# Mc/sec: 1540.33
//
Query:       gene157|gene157|rna157|rna157  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-71  240.4  25.1    2.8e-71  240.2  25.1    1.0  1  8TM_micro  8TM Microsporidial transmembrane domain


Domain annotation for each model (and alignments):
>> 8TM_micro  8TM Microsporidial transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.2  25.1   1.6e-75   2.8e-71       1     254 [.      17     262 ..      17     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 240.2 bits;  conditional E-value: 1.6e-75
                      8TM_micro   1 RifdilkllskysykdeveeeellrenkiaevqsiilykitktlflllilllDllsslllkskdYfllssllPndliSle 80 
                                    R +d+++++++y++ ++++++e+l++ +i++v++ii+ k++  ++    +++D+++s+l++s++Yf++ss+lP+d iS+e
  gene157|gene157|rna157|rna157  17 RFYDVPSFCYNYHSPETHYQQEFLKPSTIPTVYQIIPRKYFIYVS----AICDFTVSRLMNSEKYFIYSSFLPADSISIE 92 
                                    89*****************************99999888877777....8****************************** PP

                      8TM_micro  81 nllivlikkkyeellkllllalsvfyaP.....drslLnylilvllkllnyekeytkcHaPslnifwflnlqmfeqYsel 155
                                    nll+ l  k  ++  ++ll +lsvfyaP     ++++L+y+++      +y k+y++  +Psl+i wf++l++f+qYs++
  gene157|gene157|rna157|rna157  93 NLLVILG-KAHKDATSFLLTHLSVFYAPlltrsSSYVLSYIYP------AYRKDYENSYRPSLSIAWFFHLNIFPQYSRY 165
                                    ***9998.699*********************9999*******......9****************************** PP

                      8TM_micro 156 fydiflivflfLlslvkkstklelilvFkdstyksylllilkkkdkllnllvllaiiesyvsyllrltgvvNlNFlnWsn 235
                                    fyd f++++++++slv +++++e+il+Fk s+yk+yll+i +  + l ++++l++++e+y++yl+++ g++N+NFlnWs+
  gene157|gene157|rna157|rna157 166 FYDTFYALMIYIFSLVPEDQRMEIILLFKPSNYKNYLLYIVD--SPLFHFYLLIFVVENYIQYLFKIHGIGNPNFLNWSY 243
                                    ******************************************..************************************ PP

                      8TM_micro 236 lvfvilfllalklkilsvk 254
                                    l f++lf+++++   l+ +
  gene157|gene157|rna157|rna157 244 LAFTCLFIFERRGGALISQ 262
                                    ********99987766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1848.06
//
Query:       gene1571|gene1571|rna1570|rna1570  [L=372]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-77  258.0   0.7    5.2e-77  257.6   0.7    1.2  1  MOZ_SAS         MOZ/SAS family
      1e-19   69.9   1.5    2.1e-19   68.9   1.5    1.6  1  zf-MYST         MYST family zinc finger domain
    7.8e-19   67.3   0.1    1.6e-18   66.4   0.1    1.5  1  Tudor-knot      RNA binding activity-knot of a chromodomain
     0.0058   16.5   0.0      0.014   15.3   0.0    1.7  1  Chromo          Chromo (CHRromatin Organisation MOdifier) dom
  ------ inclusion threshold ------
      0.048   14.1   0.0       0.11   13.0   0.0    1.6  1  Acetyltransf_7  Acetyltransferase (GNAT) domain
      0.082   11.1   0.0        0.1   10.7   0.0    1.1  1  PsaA_PsaB       Photosystem I psaA/psaB protein
       0.13   12.4   0.0       0.31   11.2   0.0    1.5  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h


Domain annotation for each model (and alignments):
>> MOZ_SAS  MOZ/SAS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.6   0.7     2e-80   5.2e-77       1     175 [.     167     339 ..     167     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 257.6 bits;  conditional E-value: 2e-80
                            MOZ_SAS   1 ppGkeiYrkeklsvfevdGekeklycqnLcllaklFldhktlyydvepFlfYvlteadeegahivGyFskekesae 76 
                                        ppG+eiYr+ +ls+fe dG+ +k yc+nL+ll+klFldhk+lyyd++ F+fYvl++ +++g++ivGyFskek+s++
  gene1571|gene1571|rna1570|rna1570 167 PPGREIYRDGNLSFFECDGHIQKNYCRNLSLLSKLFLDHKSLYYDIDVFMFYVLCRLEDNGYQIVGYFSKEKMSEQ 242
                                        8*************************************************************************** PP

                            MOZ_SAS  77 eynlaCilvlPpyqrkgyGklliefsYeLskrekkigtPekPlsdlgllsyrsywkeeilellkekekkkisieei 152
                                        +ynlaCil+lP  qrkgyGk+li+fsY Lskre++i++PekPlsdlgllsyr+yw+e+i+e+l++  ++k+si++i
  gene1571|gene1571|rna1570|rna1570 243 GYNLACILTLPFEQRKGYGKILIDFSYLLSKRENMISGPEKPLSDLGLLSYRTYWMEVIVEYLSK--HSKTSIADI 316
                                        ***************************************************************97..4589***** PP

                            MOZ_SAS 153 sektgikeeDiistleelkllky 175
                                        s++t+i+e+Dii tl+++k+l+ 
  gene1571|gene1571|rna1570|rna1570 317 SKETHISEDDIIGTLSAYKMLRI 339
                                        *******************9975 PP

>> zf-MYST  MYST family zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   1.5   8.2e-23   2.1e-19       1      55 []     108     162 ..     108     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 8.2e-23
                            zf-MYST   1 vkniekieiGeyeiktWYfSpYPeelankekLyvCefClkYmksakelerHkkkC 55 
                                        +kn++ki + ++ +++WYfSpYP+ +a+++ +y+CefCl Y+++ ++l  H k+C
  gene1571|gene1571|rna1570|rna1570 108 MKNVKKIMLRNHLVDAWYFSPYPKAIAESDVVYICEFCLYYFSTMDNLVLHAKQC 162
                                        69***************************************************** PP

>> Tudor-knot  RNA binding activity-knot of a chromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   6.1e-22   1.6e-18       3      54 ..       8      62 ..       6      63 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 6.1e-22
                                       TTTEEEEEE...TTSCEEEEEEEEEEETSSCEEEEEEETTS-CCC-EEEETTTEE CS
                         Tudor-knot  3 vgckvlvrk...kdgelrkAeilsirekkgkyeYYVHYeefNkRlDeWVsaerid 54
                                       vg kv+v+k   +++e+ kAeil +r+ k+  e+YVHY+e+N+RlDeWV+++ +d
  gene1571|gene1571|rna1570|rna1570  8 VGFKVPVKKivnGTEEVFKAEILGRRTNKSGLEFYVHYVELNRRLDEWVDGSMVD 62
                                       899************************************************9987 PP

>> Chromo  Chromo (CHRromatin Organisation MOdifier) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   5.5e-06     0.014       5      48 ..      28      69 ..      27      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-06
                                       EEEEEEEETTEECEEEEEEETTSTGGGTEEEEGGGCSSHSHHHH CS
                             Chromo  5 rIidhrtdkdgleleYlVKWkglpysentWEpeenlekcfqeli 48
                                       +I+++rt+k+gl  e++V++ +l+   + W + + ++ + + +i
  gene1571|gene1571|rna1570|rna1570 28 EILGRRTNKSGL--EFYVHYVELNRRLDEWVDGSMVDLDDPSQI 69
                                       69**********..******************998887766655 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.1e-05      0.11      12      49 ..     228     272 ..     213     305 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                                        TEEEEEEEEEEES.....TCTEEEEE-GGGTTSSHHHHHHHH....T CS
                     Acetyltransf_7  12 gkivGfialslld.....aeitrlaVdpeyrgkGiGraLlea....a 49 
                                         +ivG+ + +  +     +++ ++ ++p  ++kG+G+ L+++     
  gene1571|gene1571|rna1570|rna1570 228 YQIVGYFSKE--KmseqgYNLACILTLPFEQRKGYGKILIDFsyllS 272
                                        4667755433..2446545555599****************844441 PP

>> PsaA_PsaB  Photosystem I psaA/psaB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.1e-05       0.1     552     691 ..     181     322 ..     155     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.1e-05
                          PsaA_PsaB 552 fpcdGPGrGGtc.dvsawdavflalfwmyntisvvifyfswkmlsdvwgtveltgaqfaessitinGwlrdflwaq 626
                                        f cdG  +   c ++s   ++fl    +y  i v +fy   +   +   + + + + f++  +  +G+    + + 
  gene1571|gene1571|rna1570|rna1570 181 FECDGHIQKNYCrNLSLLSKLFLDHKSLYYDIDVFMFYVLCRLEDN---GYQ-IVGYFSKEKMSEQGYNLACILTL 252
                                        7888887776663567788888888888888888888888877773...333.44788888888888888888888 PP

                          PsaA_PsaB 627 ssqvinsygsslsvyallflaghlvwa.....fslmflisgrGywqelieslvwaheklklaplikPral 691
                                          +  ++yg+ l  +++l+     + +     +s + l+s+r yw e+i   +  h+k+ +a++ k   +
  gene1571|gene1571|rna1570|rna1570 253 PFEQRKGYGKILIDFSYLLSKRENMISgpekpLSDLGLLSYRTYWMEVIVEYLSKHSKTSIADISKETHI 322
                                        8888888988888888888765544332333367899*************************99876655 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.31      17      49 ..     300     332 ..     298     334 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                        HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHH CS
                              HTH_9  17 kVvetLlrkgrltlrelvkktkLsldqVkksLv 49 
                                         +ve+L ++++ ++ +++k+t +s d +  +L+
  gene1571|gene1571|rna1570|rna1570 300 VIVEYLSKHSKTSIADISKETHISEDDIIGTLS 332
                                        69************************9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1226  (0.0683808); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2411.39
//
Query:       gene1572|gene1572|rna1571|rna1571  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.4e-22   77.5   0.7    1.3e-21   77.0   0.7    1.3  1  UPF0113_N  UPF0113 Pre-PUA domain
      9e-18   64.3   0.0    2.1e-17   63.2   0.0    1.6  2  UPF0113    UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> UPF0113_N  UPF0113 Pre-PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.7   1.4e-25   1.3e-21       1      82 []       2      80 ..       2      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.4e-25
                          UPF0113_N  1 RklseeetrivfekLtkyigdnvkelldrkdgtycfrlkkkrVyyvseellklaetikpenlisaGtclGkftktkkF 78
                                       R+l++ee++ v +kL+ +igdnv+ +l+   g+  + l+++rV+++se++  + ++i+++nli+aGt++G+ftk + F
  gene1572|gene1572|rna1571|rna1571  2 RDLKQEEEKEVLKKLKFFIGDNVHRILS---GEDKLFLHNQRVMLLSEKMRAATSMISRKNLIMAGTVIGRFTKGGSF 76
                                       89**************************...6679******************************************* PP

                          UPF0113_N 79 rlsi 82
                                       rl i
  gene1572|gene1572|rna1571|rna1571 77 RLGI 80
                                       **87 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.7   6.2e+03      33      41 ..      38      46 ..      20      61 .. 0.64
   2 !   63.2   0.0   2.3e-21   2.1e-17       1      76 []      93     172 ..      93     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.7
                            UPF0113 33 nqvvvVlne 41
                                       nq+v++l+e
  gene1572|gene1572|rna1571|rna1571 38 NQRVMLLSE 46
                                       444444444 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 2.3e-21
                            UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt...k.aspgkivvknlaDiGe 72 
                                        k+++k +ae++ +YG++ lk++i + +e+++ n +v+V+n+ + plG+G+++      + a+   +v+ ++ D Ge
  gene1572|gene1572|rna1571|rna1571  93 KIWIKNSAEMNYVYGNNSLKSHIFRSSEGIPINAGVFVFNQHDVPLGFGITALTPqgySnAKGHALVLLRQSDTGE 168
                                        89*************************************************9855899779*************** PP

                            UPF0113  73 YlRr 76 
                                        YlR+
  gene1572|gene1572|rna1571|rna1571 169 YLRN 172
                                        ***6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1066.44
//
Query:       gene1573|gene1573|rna1572|rna1572  [L=797]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-14   51.8   0.3    2.6e-13   50.3   0.3    1.9  1  Helicase_C     Helicase conserved C-terminal domain
    4.4e-13   49.5   0.0    2.4e-12   47.1   0.0    2.2  2  HA2            Helicase associated domain (HA2)
    3.9e-06   26.7   0.5    1.3e-05   25.1   0.5    1.9  1  DEAD           DEAD/DEAH box helicase
    0.00082   19.7   0.0     0.0021   18.4   0.0    1.6  1  AAA_19         AAA domain
     0.0019   18.5   0.1     0.0065   16.8   0.1    2.0  1  AAA_22         AAA domain
     0.0023   17.9   1.1      0.025   14.6   1.1    2.7  1  AAA_14         AAA domain
     0.0046   17.0   0.4       0.47   10.4   0.0    3.0  3  ResIII         Type III restriction enzyme, res subunit
     0.0047   15.1   0.0     0.0074   14.4   0.0    1.2  1  Herpes_ori_bp  Origin of replication binding protein
     0.0076   16.8   0.0       0.16   12.5   0.0    2.5  2  AAA_18         AAA domain
  ------ inclusion threshold ------
      0.012   15.6   1.0      0.034   14.1   0.1    2.3  2  ATPase_2       ATPase domain predominantly from Archaea
      0.033   14.1   0.6      0.077   12.9   0.6    1.6  1  NTPase_1       NTPase
      0.035   14.5   0.0       0.12   12.8   0.0    2.0  1  OB_NTP_bind    Oligonucleotide/oligosaccharide-binding (OB)-f
      0.042   13.0   0.0      0.086   12.0   0.0    1.4  1  NB-ARC         NB-ARC domain
      0.096   12.7   0.0       0.26   11.2   0.0    1.7  1  Flavi_DEAD     Flavivirus DEAD domain
       0.18   12.2   0.0       0.51   10.7   0.0    1.7  1  AAA_16         AAA ATPase domain
       0.65    9.3   9.5       0.62    9.4   3.2    2.9  2  ATPase         KaiC


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.3   2.3e-16   2.6e-13      16     111 .]     415     527 ..     402     527 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 2.3e-16
                                        TSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEE CS
                         Helicase_C  16 ggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlV 88 
                                           il+f+++++++++  + l e +  +i+v++lh++l++ ++e+++ +    +++v++at++ae++i+i ++ +V
  gene1573|gene1573|rna1572|rna1572 415 SASILVFLTSKQEIYQlKNRL-EDSgmDITVLPLHSSLSKVDQEAVFIKTV--NRKVVLATNIAETSITIADIVFV 487
                                        5689********999844444.555688*******************9994..578******************** PP

                                        EESSSSSSH.................HHHHHHHTTSSSTT CS
                         Helicase_C  89 infdlprnv.................tsyiqriGRtgRag 111
                                        i+ +  +n                  +++iqr+GR+gR g
  gene1573|gene1573|rna1572|rna1572 488 IDSGKVKNKtvdsegvtrysvdfitkSNAIQRMGRAGRTG 527
                                        ******9855799999**********************86 PP

>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         4   4.5e+03      15      36 ..     433     454 ..     426     481 .. 0.86
   2 !   47.1   0.0   2.2e-15   2.4e-12       1      67 [.     588     652 ..     588     690 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4
                                HA2  15 gnlTelGrkmaelPlsprlakm 36 
                                        ++l + G  +  lPl+ +l+k+
  gene1573|gene1573|rna1572|rna1572 433 NRLEDSGMDITVLPLHSSLSKV 454
                                        678889999999****999996 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 2.2e-15
                                HA2   1 AlelLvalgALdeegnlTelGrkmaelPlsprlakmLlaaaeleegcldevitivAalsveeiflee 67 
                                        A+++L+ lgA+de+ nlT++G+km+++P++prla++L +     e+++ e++++++++s +  + ++
  gene1573|gene1573|rna1572|rna1572 588 AITRLQGLGAVDENLNLTDIGKKMSRYPIEPRLARLLCTQG--LEDIFTEILALISLISSGTEIKKN 652
                                        7889*********************************9994..46*************965444333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.5   1.1e-08   1.3e-05      17     171 ..     201     341 ..     180     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                                        EEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  17 vlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqls 92 
                                        v+v ++TG GKT+   ip +  +ye     + ++ +  P r  a  +  ++++  ++   +    + g + r + +
  gene1573|gene1573|rna1572|rna1572 201 VFVTGATGCGKTTQ--IPQF--LYEGGLGMEGMIGVTQPRRISATSISARINEEANE---N----LCGYKIRYEST 265
                                        789999******86..6666..8886444455777999******9999999999884...2....33788889988 PP

                                        HHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  93 kldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSAT 168
                                        +  ++++i ++t g l++ ++ + + ls+ +++++DE+++ + +   d + +i+ ++ +  ++   + +++++SAT
  gene1573|gene1573|rna1572|rna1572 266 VT-SETKIKIMTDGVLLKEIQ-EDFLLSKYSVIIIDEIHERSTN--IDLLISIIPRIMKVRKERGCELRLVLMSAT 337
                                        88.99*************995.7788**************9999..45555555555444333333455******* PP

                                        BS.H CS
                                        xx.x RF
                               DEAD 169 lp.k 171
                                           +
  gene1573|gene1573|rna1572|rna1572 338 GDvE 341
                                        7644 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0021       8     126 ..     196     316 ..     189     333 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                             AAA_19   8 lkekvllvtaGpGtGKTrvlkhival.....lvelggvkpeeillvaftgrAakelrerlaalgae.atTiHrlal 77 
                                         ++++++vt+  G+GKT+ + + + +        +g  +p++i + +   r  +e +e+l +++ +  +T+ +   
  gene1573|gene1573|rna1572|rna1572 196 RASPIVFVTGATGCGKTTQIPQFLYEgglgmEGMIGVTQPRRISATSISARINEEANENLCGYKIRyESTVTSE-- 269
                                        5678999***********998876541111034556667899999999999999***99977666654555533.. PP

                             AAA_19  78 ldfddlltealelleeaeeekklqeee.llivDEfqdvdelqyrLlkall 126
                                          ++ ++++   ll+e +e+  l +++ ++i+DE+ + +  +  L++ ++
  gene1573|gene1573|rna1572|rna1572 270 --TKIKIMTDGVLLKEIQEDFLL-SKYsVIIIDEIHERSTNIDLLISIIP 316
                                        ..222232333456665665555.7777******9987776666666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   5.8e-06    0.0065       7     128 ..     200     334 ..     195     343 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.8e-06
                             AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............ 70 
                                        i++vtG +G+GKTt + ++l++            + + vt p   s +++  ++ ++ +++l +            
  gene1573|gene1573|rna1572|rna1572 200 IVFVTGATGCGKTTQIPQFLYEGGLG------MEGMIGVTQPRRISATSISARINEEANENLCGykiryestvtse 269
                                        789******************98655......7778899999999**************999999****9888855 PP

                             AAA_22  71 ...erlsseellealeqalrarav...ielliiDEaqhlrs...eealeeLrsllnl...srkgvqliLv 128
                                           +  +   ll+ +++ +         +++iiDE++   s   + +++ + +++++   + + ++l+L+
  gene1573|gene1573|rna1572|rna1572 270 tkiKIMTDGVLLKEIQEDF----LlskYSVIIIDEIHER-StniDLLISIIPRIMKVrkeRGCELRLVLM 334
                                        5554444444444444444....344448********97.422233333333334447666666666666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.1   2.3e-05     0.025       3      81 ..     199     309 ..     197     410 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.3e-05
                             AAA_14   3 kilvitGaRrvGKTtllkqlikell.........vkkesilyinldderd.................kkladpe.. 50 
                                        +i+++tGa  +GKTt + q+++e           +++++i   ++    +                       +  
  gene1573|gene1573|rna1572|rna1572 199 PIVFVTGATGCGKTTQIPQFLYEGGlgmegmigvTQPRRISATSISARINeeanenlcgykiryestV-----Tse 269
                                        799*****************999888999998875555554444444333333344555444433220.....022 PP

                             AAA_14  51 .....kllelileklke..............ekktylflDEiqevpewek 81 
                                                        +              +k +++++DEi+e ++  +
  gene1573|gene1573|rna1572|rna1572 270 tkikiM----------TdgvllkeiqedfllSKYSVIIIDEIHERSTNID 309
                                        233221..........02333333334677678899******99755444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.07        78       4      39 ..     160     213 ..     157     221 .. 0.65
   2 !   10.4   0.0   0.00042      0.47     109     147 ..     267     307 ..     234     339 .. 0.62
   3 ?   -2.0   0.0       2.8   3.2e+03      96     118 ..     396     432 ..     352     458 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.07
                                        E-HHHHHHHHHHT........................TTSEEEEEESTTSTHHH CS
                             ResIII   4 lreyQeeaienlleklks..................krdkrglikmaTGtGKTl 39 
                                        lrey ++ + n +e +++                  +    +++  aTG+GKT 
  gene1573|gene1573|rna1572|rna1572 160 LREYDTKTLGNRREDIEEfrktlpiyyekgeiicavRASPIVFVTGATGCGKTT 213
                                        5666666666666666556666666766666666633333555889*******7 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00042
                                        EEHHHHHHTH................HHHTTT-SEEEEETGGGTTS. CS
                             ResIII 109 ttiqsldadseee........eeeseellrdrfdviiiDEaHrlgak 147
                                        t++ ++      +        +e +e++l +++ viiiDE H  + +
  gene1573|gene1573|rna1572|rna1572 267 TSETKI------KimtdgvllKEIQEDFLLSKYSVIIIDEIHERSTN 307
                                        233333......133335577778******************98875 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.8
                                        -.....................-SEEEEEHHHHHHTH CS
                             ResIII  96 a..............kekdstnkkilvttiqsldads 118
                                        +              ++  s ++ +++t+ q++++ +
  gene1573|gene1573|rna1572|rna1572 396 RkmnegktdvigsgvSNDTSASILVFLTSKQEIYQLK 432
                                        1233344445677666666777777777888777766 PP

>> Herpes_ori_bp  Origin of replication binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.6e-06    0.0074      46     151 ..     195     301 ..     182     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                      Herpes_ori_bp  46 srtrpvlvvRApmGsGkttALiewLkevldsedlsvlvvsCRrsFtntlserfnraGlsgFvtYldseeyilnere 121
                                         r+ p+  v  + G Gktt + ++L e     +  + v   Rr  + ++s r+n++  ++ + Y    e  ++  +
  gene1573|gene1573|rna1572|rna1572 195 VRASPIVFVTGATGCGKTTQIPQFLYEGGLGMEGMIGVTQPRRISATSISARINEEANENLCGYKIRYESTVTSET 270
                                        47889********************99877888899999*************************999999999889 PP

                      Herpes_ori_bp 122 frrlivqlEsLhRvsen.lldnYDvlilDEv 151
                                          +++     L+ ++e+ ll +Y v+i+DE+
  gene1573|gene1573|rna1572|rna1572 271 KIKIMTDGVLLKEIQEDfLLSKYSVIIIDEI 301
                                        9999999999****9874789*********9 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00014      0.16       1      84 [.     201     303 ..     201     310 .. 0.90
   2 ?    1.1   0.0      0.48   5.4e+02      24     114 ..     346     439 ..     334     442 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                             AAA_18   1 IlltGtpGvGKtt.lakeLskrl.gf.................gvnlrdvakenglllevdpe.aldeskrldedk 56 
                                        +++tG+ G+GKtt + + L + + g+                 + ++++ a en + +    e  + ++ +++++ 
  gene1573|gene1573|rna1572|rna1572 201 VFVTGATGCGKTTqIPQFLYEGGlGMegmigvtqprrisatsiSARINEEANENLCGYKIRYEsTVTSETKIKIMT 276
                                        79*********994568888876666888999****************************9999999999999999 PP

                             AAA_18  57 ldklldaleenssaleegknlvidghla 84 
                                        + +ll++++e    l + ++++id +++
  gene1573|gene1573|rna1572|rna1572 277 DGVLLKEIQEDFL-LSKYSVIIIDEIHE 303
                                        99********997.9*********9876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.48
                             AAA_18  24 f.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.........aleegknlvidghlaelese 89 
                                        f g++  +v++e++   + + e     ++ +ed+l ++ + ++++           ++ egk+ vi + +++  s+
  gene1573|gene1573|rna1572|rna1572 346 FlGDIKVFVCPEKRFQVSTFYE-----EKTEEDYLSAAYERIRKIVLsgsgtrkkrKMNEGKTDVIGSGVSNDTSA 416
                                        4566666666666666666666.....6666677666666666666678888888899999999999999999999 PP

                             AAA_18  90 aakdikkvvLtasp..eelleRlekRg 114
                                        +      v+Lt +    +l+ Rle+ g
  gene1573|gene1573|rna1572|rna1572 417 SIL----VFLTSKQeiYQLKNRLEDSG 439
                                        888....99999994446888888766 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     3e-05     0.034      18     127 ..     196     301 ..     190     328 .. 0.64
   2 ?   -1.8   0.1       2.2   2.4e+03      30      64 ..     399     432 ..     351     507 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3e-05
                           ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..........g 83 
                                          ++i+f++G  g+GKt+ + +++ +     +  i +++ r++s ++++  i+ee +++    ++          +
  gene1573|gene1573|rna1572|rna1572 196 RASPIVFVTGATGCGKTTQIPQFLYEGGLGMEGMIGVTQPRRISATSISARINEEANENLCGYKIryestvtsetK 271
                                        5679********************9997778899999999999999999999977777654444433322222221 PP

                           ATPase_2  84 iavpkaeleeilk..eksklvfkaielllekikkkgkkiiiiiDel 127
                                        i++ ++ +  +lk  ++  l+ k+               +iiiDe+
  gene1573|gene1573|rna1572|rna1572 272 IKIMTDGV--LLKeiQEDFLLSKY--------------SVIIIDEI 301
                                        11111111..22212222222222..............34444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                           ATPase_2  30 gsGKtaLlkeiienledkdkyviyyialreesisk 64 
                                        + GKt ++   ++n  + +   +++++ +e+++ k
  gene1573|gene1573|rna1572|rna1572 399 NEGKTDVIGSGVSNDTSAS-ILVFLTSKQEIYQLK 432
                                        4466666666666664433.344554444444333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   6.8e-05     0.077       2     122 ..     201     319 ..     200     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                                        EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEE.TTEEE CS
                           NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprv.gkyvv 76 
                                        vf+TG  G GKtT + +    l + g+ ++G++     ++ + +  +   ++++ +++L+  + + e  v ++ ++
  gene1573|gene1573|rna1572|rna1572 201 VFVTGATGCGKTTQIPQ---FLYEGGLGMEGMIGVTQPRRISATSIS-ARINEEANENLCGYKIRYESTVtSETKI 272
                                        89***********7665...56677*******965544433333333.3467888899999994444444033344 PP

                                        -HHHHHHHHHHHHHHHH..HHH-EEEE---STTGGG-HHHHHHHHHHH CS
                           NTPase_1  77 dvesfeelalealrkal..seadviviDEiGkmElkskkfkeaveevL 122
                                        ++   + + l+ +++ +  s+  vi+iDEi +   ++  +++ + +++
  gene1573|gene1573|rna1572|rna1572 273 KI-MTDGVLLKEIQEDFllSKYSVIIIDEIHERSTNIDLLISIIPRIM 319
                                        43.46889999999988889999******9766666666666665555 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011      0.12      48      75 ..     768     796 ..     722     797 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                        SSSEEEEEEEEESSS.EEEEEEEEE-HHH CS
                        OB_NTP_bind  48 epewvvytelvettk.lylrdltaidpaw 75 
                                         +++vv+++lv+++  ly++++t +++aw
  gene1573|gene1573|rna1572|rna1572 768 SDDFVVFETLVSSKGkLYMKNVTIVEKAW 796
                                        456**********766***********99 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.6e-05     0.086      21     119 ..     199     309 ..     194     329 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                                        EEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE....EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS CS
                             NB-ARC  21 lvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv....vvsktdkseeiletilkeLslseddleekeeves 91 
                                         +v++ G  G+GKtt + q l +     g   ++++ v     +s t+ s +i e+ +++L+  +   e+  ++e 
  gene1573|gene1573|rna1572|rna1572 199 PIVFVTGATGCGKTTQIPQFLYE----GGlGMEGMIGVtqprRISATSISARINEEANENLCGYKIRYESTVTSET 270
                                        589************99998888....3336777777756668999999999999999999988777766666666 PP

                                        .........HHHHHHH.HCCCTTEEEEEEEE-SHHH.H. CS
                             NB-ARC  92 .........lkrklvr.lLltkrfllvlDDVweeed.wd 119
                                                 l +++++ +Ll+k +++++D + e  +  d
  gene1573|gene1573|rna1572|rna1572 271 kikimtdgvLLKEIQEdFLLSKYSVIIIDEIHERSTnID 309
                                        788999999777776439*************99877544 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.26      46     135 ..     248     337 ..     196     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                        HHHHHHHTTTS-EEE-------------SEEEEEHHHHHHHHHHT------SEEEEETTT....--SH.HHHHHHH CS
                         Flavi_DEAD  46 laemeealkglevryktsavkeektgrelvdvmchatftkrllspvrkknyeliimDeah....flDP.asiaarG 116
                                         +e +e l g ++ry+++++     ++  + +m    + k + ++    +y +ii+De h     +D   si  r 
  gene1573|gene1573|rna1572|rna1572 248 NEEANENLCGYKIRYESTVT-----SETKIKIMTDGVLLKEIQEDFLLSKYSVIIIDEIHerstNIDLlISIIPRI 318
                                        46888999999999998877.....4445899****************************3333344325888887 PP

                                        HHHHHHHTTS-EEEEEESS CS
                         Flavi_DEAD 117 yletkaeegeaalilltat 135
                                        +  +k++  e  l+l++at
  gene1573|gene1573|rna1572|rna1572 319 MKVRKERGCELRLVLMSAT 337
                                        7777777778889999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00045      0.51      18      43 ..     194     217 ..     190     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                             AAA_16  18 rvrsgrpelvllsGesGvGKsslvre 43 
                                        +vr++  ++v+++G+ G+GK++ + +
  gene1573|gene1573|rna1572|rna1572 194 AVRAS--PIVFVTGATGCGKTTQIPQ 217
                                        55555..9*************97655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.2   0.00055      0.62      21      49 ..     200     226 ..     194     327 .. 0.86
   2 ?    2.3   0.4     0.079        88      52     127 ..     420     500 ..     408     517 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00055
                             ATPase  21 vvlitGepGtGKtifalqFlikgaekyge 49 
                                        +v +tG +G+GKt+   qFl++g    g 
  gene1573|gene1573|rna1572|rna1572 200 IVFVTGATGCGKTTQIPQFLYEGGL--GM 226
                                        789*******************933..44 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.079
                             ATPase  52 vfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaee..kdkedleelieelaea...ikeikakr 122
                                        vf t  ++  +l+++ +  G+d++ l  + +l  +d  +  +++ ++     +++ e + ++a++   i++ k+k+
  gene1573|gene1573|rna1572|rna1572 420 VFLTSKQEIYQLKNRLEDSGMDITVLPLHSSLSKVDQEAVFIKTVNRkvVLATNIAETSITIADIvfvIDSGKVKN 495
                                        67777777799***************99999999999999988555444334444444444443311133334444 PP

                             ATPase 123 vviDs 127
                                          +Ds
  gene1573|gene1573|rna1572|rna1572 496 KTVDS 500
                                        44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.88u 0.36s 00:00:01.24 Elapsed: 00:00:00.57
# Mc/sec: 4215.90
//
Query:       gene1574|gene1574|rna1573|rna1573  [L=460]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-40  137.9   0.0    4.6e-40  137.2   0.0    1.3  1  DEAD          DEAD/DEAH box helicase
    1.2e-23   83.6   0.3    6.2e-23   81.3   0.1    2.3  3  Helicase_C    Helicase conserved C-terminal domain
      7e-12   45.4   0.2    1.5e-11   44.3   0.2    1.5  1  DUF4217       Domain of unknown function (DUF4217)
    0.00089   19.3   0.0     0.0017   18.4   0.0    1.4  1  ResIII        Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.036   14.4   0.0      0.096   13.0   0.0    1.7  2  AAA_19        AAA domain
      0.062   13.5   0.0        0.1   12.7   0.0    1.3  1  Helicase_C_2  Helicase C-terminal domain
      0.072   12.4   0.0       0.14   11.5   0.0    1.5  1  CMS1          U3-containing 90S pre-ribosomal complex subunit
       0.21   11.3   0.0        0.3   10.8   0.0    1.2  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.0   2.1e-43   4.6e-40       1     176 []      28     194 ..      28     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 2.1e-43
                                        -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyi 74 
                                        td+Q+ ++p++l+g+dv+v+ +TG+GKT+aflip+l+++y+    g+    a+i++PtreLa q+ + + ++++  
  gene1574|gene1574|rna1573|rna1573  28 TDVQRMCVPEMLKGKDVVVQSPTGTGKTMAFLIPILSCIYDGkgSGNLDVVAMIITPTRELAMQIKEVA-ELFD-- 100
                                        79**************************************996668888999************97655.5556.. PP

                                        TSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  75 dlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                         +r++++igg + ++++++++ +  ivvgtpgrl++++s+   ++s++r +VlDEad+ll  gf++++ +++++l 
  gene1574|gene1574|rna1573|rna1573 101 -VRCECFIGGMNIEKDYERMKGEFSIVVGTPGRLLEIVSKDIKKFSRIRHVVLDEADKLLGFGFEEKLMQLIKKL- 174
                                        .7999***************777***************877778*******************************. PP

                                        HHCTTSTTTSEEEEEESSBSHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 151 qitcdgklqrqvivlSATlpkdvkkl 176
                                              +++r + ++SAT++++v+kl
  gene1574|gene1574|rna1573|rna1573 175 ------PKNRVTGLFSATINDSVDKL 194
                                        ......567779********999986 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.7   1.3e+04      20      53 ..      80     113 ..      78     127 .. 0.66
   2 ?   -1.4   0.0       1.3   2.8e+03       5      51 ..     166     213 ..     164     221 .. 0.67
   3 !   81.3   0.1   2.8e-26   6.2e-23       5     111 .]     226     331 ..     222     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.7
                                        EEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHH CS
                         Helicase_C  20 lifvntidrlekvklllekkgikvavlhgelpqn 53 
                                        +i+++t++ + ++k + e +++++ ++ g ++ +
  gene1574|gene1574|rna1573|rna1573  80 MIITPTRELAMQIKEVAELFDVRCECFIGGMNIE 113
                                        6777777744335555566778887777777654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                                        HHHHHHHHTTTTSEEEEEESSHH.HHHHHHHHHHHTTSTEEEESTTST CS
                         Helicase_C   5 allellkleeeggkilifvntid.rlekvklllekkgikvavlhgelp 51 
                                        +l++l+k+  +++ + +f+ ti+ +++k++    ++ +++ v ++ +p
  gene1574|gene1574|rna1573|rna1573 166 KLMQLIKKLPKNRVTGLFSATINdSVDKLSRASLRNPVSINVGNSAMP 213
                                        566666656677777889999987777633333356677777777776 PP

  == domain 3  score: 81.3 bits;  conditional E-value: 2.8e-26
                                        HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                         Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                        +l +l+   ++g++++if  t+++++  + ll +    ++ ++hg+++q+er+++ ++f +g+  +L +tdva+rG
  gene1574|gene1574|rna1573|rna1573 226 KLFALI-DIVNGRRCIIFFATCNQVDFfFGLLSRIGLENIYKIHGKISQDERNKVYKEFCQGN-SLLFCTDVAARG 299
                                        555565.6689**************876666633336899*******************7766.8*********** PP

                                        STSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        id+ +v+lV++fd+p++++++++r+GRt+R g
  gene1574|gene1574|rna1573|rna1573 300 IDFRDVDLVVHFDVPKEYSNIVHRSGRTARNG 331
                                        ******************************76 PP

>> DUF4217  Domain of unknown function (DUF4217)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.2   6.8e-15   1.5e-11      12      61 .]     379     428 ..     377     428 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 6.8e-15
                            DUF4217  12 drdlkelAqkAfvsyvraYsvhlakeiFrvkkLdlealAksfGLleaPki 61 
                                        d +l  l++kAfvsy+r+Y++h a++i++ k Ld+++lA+ f L ++P +
  gene1574|gene1574|rna1573|rna1573 379 DSNLLSLSVKAFVSYIRSYKEHFASYILDYKGLDFDSLAELFFLEKIPGM 428
                                        678999*****************************************976 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.5e-07    0.0017      24     169 ..      41     187 ..      23     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.5e-07
                                        TSEEEEEESTTSTHHHHHHHHHHHH-S..........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B CS
                             ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkee.....kflflvprkslleqtleefkkflseaykeigkkvsgdkk 94 
                                         k ++++ +TGtGKT+  +  i ++   gk +      ++++ p+++l  q +e  + f   +  +ig+   ++ +
  gene1574|gene1574|rna1573|rna1573  41 GKDVVVQSPTGTGKTMAFLIPILSCIYDGKGSgnldvVAMIITPTRELAMQIKEVAELFDVRCECFIGGMNIEKDY 116
                                        578899***********999999988887777889888999************99999988887665444333333 PP

                                        --.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT---SEEEE.EE CS
                             ResIII  95 kakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekfkeavllg.lT 166
                                        ++    + + +i+v t  +l ++       ++ ++ +r+  ++ DEa +l +    ++  ++++k++++ + g ++
  gene1574|gene1574|rna1573|rna1573 117 ER---MKGEFSIVVGTPGRLLEIV-----SKDIKKFSRIRHVVLDEADKLLGFgfeEKLMQLIKKLPKNRVTGlFS 184
                                        33...58999************99.....55555566677899999988877544435445455554444444367 PP

                                        SS- CS
                             ResIII 167 ATp 169
                                        AT+
  gene1574|gene1574|rna1573|rna1573 185 ATI 187
                                        776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.3e-05     0.096       2     126 ..      32     175 ..      31     184 .. 0.63
   2 ?   -2.7   0.0       3.1   6.9e+03      38      57 ..     330     349 ..     320     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                             AAA_19   2 reave.alkekvllvtaGpGtGKTrvlkh.ivallvelggvkp..eeillvaftgrAakelrerlaalgaeatTiH 73 
                                        r  v   lk k ++v  + GtGKT      i++++ + +g        +++++t+  a++++e  + ++++ + + 
  gene1574|gene1574|rna1573|rna1573  32 RMCVPeMLKGKDVVVQSPTGTGKTMAFLIpILSCIYDGKGSGNldVVAMIITPTRELAMQIKEVAELFDVRCECFI 107
                                        556644789999************875541555555555443333445789************9999999988887 PP

                             AAA_19  74 rlalldfddlltealelle.............eaeeekklqeeellivDEfqdv.....delqyrLlkall 126
                                        +   ++++++ + + + +              + ++ kk+ +  +++ DE+  +     +e  ++L+k+l+
  gene1574|gene1574|rna1573|rna1573 108 GG--MNIEKDYERMKGEFSivvgtpgrlleivS-KDIKKFSRIRHVVLDEADKLlgfgfEEKLMQLIKKLP 175
                                        65..44444333333333455667777776753.3445553666999999987633322344555666665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                             AAA_19  38 ggvkpeeillvaftgrAake 57 
                                        +g k e+il v ++++A  e
  gene1574|gene1574|rna1573|rna1573 330 NGCKGESILFVMPNEKAYTE 349
                                        3466799*********9876 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.6e-05       0.1       4      85 ..     230     307 ..     227     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                       Helicase_C_2   4 llevvp.ggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGi 78 
                                        l+++v+  ++++ff   ++++ ++  l++ + ++ ++i  + ++ +r+kv +e+ +    +++l+++       Gi
  gene1574|gene1574|rna1573|rna1573 230 LIDIVNgRRCIIFFATCNQVDFFFGLLSRIGLENIYKIHGKISQDERNKVYKEFCQ---GNSLLFCTD--VAARGI 300
                                        56666646899*********************9999**9999*************9...999****99..999*** PP

                       Helicase_C_2  79 dfsddll 85 
                                        df+d  l
  gene1574|gene1574|rna1573|rna1573 301 DFRDVDL 307
                                        ***8654 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.1e-05      0.14     178     209 ..     123     154 ..      81     180 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.1e-05
                               CMS1 178 igiavGtpgRildLleeeslsvdeLkrivlDa 209
                                         +i vGtpgR+l+++ ++  + + ++++vlD 
  gene1574|gene1574|rna1573|rna1573 123 FSIVVGTPGRLLEIVSKDIKKFSRIRHVVLDE 154
                                        6899**************************96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013       0.3       3     100 ..      28     158 ..      26     180 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                             AAA_30   3 naeQaaavealltsgdrvavltGpAGtGKtta..lkalreaweaag...grvi..glAptgkaAkvLae....... 64 
                                        ++ Q+  v ++l+++d  +v++ p GtGKt+a  +  l  +++ +g    +v+  +++pt + A +++e       
  gene1574|gene1574|rna1573|rna1573  28 TDVQRMCVPEMLKGKD--VVVQSPTGTGKTMAflIPILSCIYDGKGsgnLDVVamIITPTRELAMQIKEvaelfdv 101
                                        6779999999**9999..99**********7622556677777777778444433788999999888874444444 PP

                             AAA_30  65 ..elgieastiakllkrlk...................grarlepgtllivDEagmv 100
                                          e+ i +++i+k  +r+k                   + +++++ + ++ DEa  +
  gene1574|gene1574|rna1573|rna1573 102 rcECFIGGMNIEKDYERMKgefsivvgtpgrlleivskDIKKFSRIRHVVLDEADKL 158
                                        444446888888888777788888888888888888776667777788888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2976.05
//
Query:       gene1575|gene1575|rna1574|rna1574  [L=554]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0044   16.6   0.0     0.0093   15.6   0.0    1.5  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.085   13.2   0.0       0.13   12.6   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-06    0.0093      23     146 ..      41     157 ..      34     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-06
                                        GGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHHHHT CS
                    NTP_transferase  23 klvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaaelle 98 
                                         l+pv++  ++i+++ls l ++++ +  vvl  ++ ++v e++k+++  + +++i+       + + ++  ++  +
  gene1575|gene1575|rna1574|rna1574  41 SLFPVANI-PMIEYVLSSLCDQKFFN--VVLAGNDCEEVVEHVKRTELDE-RMNIISLGCDGKSLGDLMRHIDDNG 112
                                        57999999.****************9..88888999*********98544.7776655555544444555555555 PP

                                        TSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CT CS
                    NTP_transferase  99 deksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeat 146
                                         e+  + +lv+ ++h++++ ++ +v+k++e+++   +t+++ p+e ++
  gene1575|gene1575|rna1574|rna1574 113 FEF--DELLVIYANHYTNYPLRSIVNKHREDKS-FVMTLFLHPNESNS 157
                                        555..479************************9.66777777766655 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.4e-05      0.13      18      66 ..      42      91 ..      33     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                       HHCCCCCCHHHHHHHHHCTT.-CEEEEECSH.CHHHHHHTTCTS-EEE-T CS
                       NTP_transf_3 18 llplggkpllervldalraagvdevvvvggd.eevlaalarlgvrvvede 66
                                       l p+++ p++e+vl +l ++++ +vv++g+d eev ++++r++++   + 
  gene1575|gene1575|rna1574|rna1574 42 LFPVANIPMIEYVLSSLCDQKFFNVVLAGNDcEEVVEHVKRTELDERMNI 91
                                       7899***************************8899999998877655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3751.47
//
Query:       gene1576|gene1576|rna1575|rna1575  [L=914]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-65  218.3   0.1    1.4e-64  217.6   0.1    1.3  1  MutS_V        MutS domain V
    1.3e-34  118.9   0.1    3.4e-34  117.5   0.0    1.8  2  MutS_I        MutS domain I
    1.7e-23   83.9   0.0    4.2e-23   82.6   0.0    1.7  1  MutS_III      MutS domain III
    2.5e-15   56.6   2.6    7.8e-15   55.0   2.6    1.9  1  MutS_IV       MutS family domain IV
     0.0066   16.4   0.4      0.015   15.2   0.4    1.6  1  Phage_Mu_Gam  Bacteriophage Mu Gam like protein
  ------ inclusion threshold ------
       0.04   14.4   0.1        2.2    8.8   0.0    2.7  2  ABC_tran      ABC transporter
       0.96    9.9   0.0       0.96    9.9   0.0    3.5  3  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.6   0.1   5.7e-68   1.4e-64       2     187 ..     730     911 ..     729     912 .. 0.97

  Alignments for each domain:
  == domain 1  score: 217.6 bits;  conditional E-value: 5.7e-68
                                        EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                             MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                        ++tG+nm+Gkst+lr ++  v+l+q+G  v +ek+e +++d+iftR+ga D+lakg+stFmvE++Eta+ilk++t+
  gene1576|gene1576|rna1575|rna1575 730 VLTGANMGGKSTLLRTICFNVILSQMGMDVCCEKMETPLFDRIFTRIGARDNLAKGESTFMVELKETATILKHSTR 805
                                        89************************************************************************** PP

                                        TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEE CS
                             MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykv 153
                                        +slvi+DElGRGtst dG +ia av+eyl + +++++lf+tHyh + +   ++e v+n  +  + + +divfly++
  gene1576|gene1576|rna1575|rna1575 806 NSLVIMDELGRGTSTKDGECIARAVIEYLKR-KECHVLFSTHYHGIIE---NVEGVSNGYMGSVVKGKDIVFLYRL 877
                                        *****************************98.79**********9875...5679********************* PP

                                        EES--SS--HHHHHHHTT--HHHHHHHHHHHHHT CS
                             MutS_V 154 kegaaeksyGikvaklaglPesvverArevlkel 187
                                         +g+++ s+G+ va++ag+Pe++verA+++ ++l
  gene1576|gene1576|rna1575|rna1575 878 MSGVSRDSHGLYVARMAGVPEDIVERAEKIRERL 911
                                        *****************************99887 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   0.0   1.3e-37   3.4e-34       1     111 [.     132     255 ..     132     257 .. 0.96
   2 ?   -3.7   0.0       5.3   1.4e+04      56      67 ..     891     902 ..     877     904 .. 0.66

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 1.3e-37
                                        HHHHHHHHCCCHH-TTCEEEEEETTEEEEECHHHHHHHHHCSSSSTT.ESSSSC.EEEEEEEHHHHHHHHHHHHHT CS
                             MutS_I   1 tplmkqylelkkkykdavlffrvGdfYelfgeDAviaareleitltkrkkssekeipmagvPehalekylrkLvek 76 
                                        tp++kq++++kk+++d+++ff++G+fYel+++DA+i+a+++++ +t    ++ + ++m+g+Pe++l+++ r+++e+
  gene1576|gene1576|rna1575|rna1575 132 TPFEKQFWDIKKEHFDTIVFFKKGKFYELYENDALIGAKLFDLRIT----DRVN-MRMSGFPESSLDYWTRRFLEH 202
                                        8*********************************************....6677.********************* PP

                                        T-EEEEEEE-S-HHHH..................S.S--EEEEEEEBTTC-TT CS
                             MutS_I  77 gykVavveqtetpaek..................kgvvkrevvrviTpGtltd 111
                                        gyk+a+v+q+e++  k                  +++++re+ ++iT+Gt+++
  gene1576|gene1576|rna1575|rna1575 203 GYKIARVDQSENMIGKqirerdemskskergiakNKIIRRELKEIITQGTIYN 255
                                        *************999************99999756**************986 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.3
                                        EEEEEEEHHHHH CS
                             MutS_I  56 ipmagvPehale 67 
                                         +magvPe  +e
  gene1576|gene1576|rna1575|rna1575 891 ARMAGVPEDIVE 902
                                        689999987665 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   1.7e-26   4.2e-23       2     191 .]     398     687 ..     397     687 .. 0.75

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.7e-26
                                        HHHHTTSSS-TTS.SSSS-HHHHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHHT..TT.HHHHHHHHTT- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           MutS_III   2 TlrnLeilenlrggskegsLlgvldrTvTamGaRlLrewllqPltdleeInaRldaVeeleneelreelrellrrl 77 
                                        Tl n+e+++n  +g++e++L++++d T+Ta G+RlLr+w+++Pl+++++I +R+++   +++ e  ++lr+ l r+
  gene1576|gene1576|rna1575|rna1575 398 TLWNMEVFKNNYNGTDEKTLFKTVDFTSTAGGQRLLRRWMMAPLIKKDDIVRRQEMGRMFKEIE-TSRLRDVLVRI 472
                                        899****88855568899***************************************9997666.999******** PP

                                        --HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHH............................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                           MutS_III  78 pDleRllsrislgkakardlkallealkaleelvallekeklaesee............................. 124
                                        +D eRlls++++g+  ++dl++++  ++++ e  ++l++ +++++                               
  gene1576|gene1576|rna1575|rna1575 473 GDGERLLSKLYNGNPAVKDLSKFIGCIDTCREAFNILGHMMRERDCGntraiaekaeecfrkideiltwhrrvydv 548
                                        ************998999*999877777777777888777665444477777766666666665555555555555 PP

                                        ...............HHHHHHHHHHB-SS--SSGGGS--B-T.................................. CS
                                        ...............xxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                           MutS_III 125 ...............eslaelleeaideeplalekegedlra.................................. 151
                                                                                 +                                  
  gene1576|gene1576|rna1575|rna1575 549 tdteispgeqnedelC-------------------------Hlisekekieddlneylqrqrdrlrspsvkfkdig 599
                                        5544444444332220.........................13444444444444455556666666779999999 PP

                                        .............................................HHHHHHHHHH....HHHHHHHH...THHHHH CS
                                        .............................................xxxxxxxxxx....xxxxxxxx...xxxxxx RF
                           MutS_III 152 .............................................iealeqelfq....elleevee...alerlr 175
                                                                                     +    +++fq     l++ +     ++  +r
  gene1576|gene1576|rna1575|rna1575 600 keifqievpketkvppdyyimsstkntnryysrdlkklveryiecE----ERIFQskgsLLRRAIGVllpHVIFFR 671
                                        99*************************************9865542....344442221444444222448999** PP

                                        HHHHHHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxx RF
                           MutS_III 176 rlaealaeLDvllSlA 191
                                        ++   +a +D+ lS+A
  gene1576|gene1576|rna1575|rna1575 672 QMFWEIANIDCYLSFA 687
                                        ***************9 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   2.6   3.1e-18   7.8e-15       5      92 .]     562     647 ..     559     647 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 3.1e-18
                                        HHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--SEEEEEECTCEEEEECCCHH CS
                            MutS_IV   5 eLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpkefirlqtlknseryttaelk 80 
                                        eL  l + +e++e++l+e+++++r +l+ +s+k++++++  +++ev+++  +kvp+++ +++++kn +ry++ +lk
  gene1576|gene1576|rna1575|rna1575 562 ELCHLISEKEKIEDDLNEYLQRQRDRLRSPSVKFKDIGKEIFQIEVPKE--TKVPPDYYIMSSTKNTNRYYSRDLK 635
                                        6777788999*************************************54..6************************ PP

                                        HHHHHHHHHHHH CS
                            MutS_IV  81 kleaelleaeee 92 
                                        kl +++ e+ee+
  gene1576|gene1576|rna1575|rna1575 636 KLVERYIECEER 647
                                        *********986 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4     6e-06     0.015       2      75 ..     526     597 ..     525     606 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTHHHH-..-----EE CS
                       Phage_Mu_Gam   2 eeanwalrkiaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYaeankdeLfkdgktKslk 75 
                                        e+a++++rki e+ + + ++ + +++ei    e+ e+el  l +e+e++e+ l +Y + ++d L + + +K ++
  gene1576|gene1576|rna1575|rna1575 526 EKAEECFRKIDEILTWHRRVYDVTDTEISP-GEQNEDELCHLISEKEKIEDDLNEYLQRQRDRL-RSPSVKFKD 597
                                        79**************************87.5778999*************************9.588887665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.071   1.8e+02      73     129 ..     511     573 ..     438     574 .. 0.73
   2 ?    8.8   0.0   0.00087       2.2      11      35 ..     726     750 ..     724     766 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.071
                                        TSBHHHH......HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSE CS
                                        xxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  73 eltvren......esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkl 129
                                        ++ +re+      +  e++e+  +k++ + + +++v++ + +++S G++   +l+ ++ +k k+
  gene1576|gene1576|rna1575|rna1575 511 HM-MRERdcgntrAIAEKAEECFRKIDEILTWHRRVYDVTdTEISPGEQNEDELCHLISEKEKI 573
                                        33.44556666665666677777777777766666655445**************999999886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00087
                                        TSEEEEEESTTSSHHHHHHHHTTSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  11 gekvaivGenGaGKStLlkllagll 35 
                                         ++++++G n  GKStLl++++ ++
  gene1576|gene1576|rna1575|rna1575 726 KRILVLTGANMGGKSTLLRTICFNV 750
                                        57899****************8665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   4.9      0.37   9.5e+02      84     196 ..      95     248 ..      11     253 .. 0.67
   2 ?   -2.5   3.2       2.3     6e+03     177     197 ..     562     582 ..     366     642 .. 0.71
   3 ?    9.9   0.0   0.00037      0.96      18      41 ..     725     748 ..     713     753 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.37
                             AAA_23  84 grytrsier.erelskkkgkttkkaklellei...deleqfisellgskkiilnlilflgqer.........feef 146
                                        +r +r++e+ + ++ +kkg++ ++  + l+ +   + l+ f ++  ++kk+ ++ i+f+++++             
  gene1576|gene1576|rna1575|rna1575  95 RR-YRFMEDiRDKNGRKKGDEGYDPSTLLIPEneyNRLTPFEKQFWDIKKEHFDTIVFFKKGKfyelyendaL--- 166
                                        22.344444222222233344444444444442445555555556668899************5544443330... PP

                             AAA_23 147 elkdkke........................................rleelekeleeledekkllekleqekeke 182
                                                                                       r+++ e+ + ++  e++++ k +++    
  gene1576|gene1576|rna1575|rna1575 167 ------IgaklfdlritdrvnmrmsgfpessldywtrrflehgykiaRVDQSENMIGKQIRERDEMSKSKER--GI 234
                                        ......133444466666777888888888899999999999999999999999999999999999987544..55 PP

                             AAA_23 183 keleeleeeleeil 196
                                        ++ + +++el+ei+
  gene1576|gene1576|rna1575|rna1575 235 AKNKIIRRELKEII 248
                                        56666666666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                             AAA_23 177 qekekekeleeleeeleeilk 197
                                        ++     e e++e++l+e+l+
  gene1576|gene1576|rna1575|rna1575 562 ELCHLISEKEKIEDDLNEYLQ 582
                                        222233355566666665554 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00037
                             AAA_23  18 skgltlItGpNGaGKTTildAikl 41 
                                         k + ++tG N  GK+T+l+ i++
  gene1576|gene1576|rna1575|rna1575 725 QKRILVLTGANMGGKSTLLRTICF 748
                                        677899****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (914 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 5466.19
//
Query:       gene1577|gene1577|rna1576|rna1576  [L=366]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-17   63.4   0.2    3.3e-09   37.2   0.0    2.4  3  Ank_2     Ankyrin repeats (3 copies)
    5.4e-16   58.9   6.5    5.4e-16   58.9   6.5    2.1  2  DHHC      DHHC palmitoyltransferase
    4.7e-11   43.0   0.5    6.4e-06   26.6   0.0    3.9  4  Ank_4     Ankyrin repeats (many copies)
    2.3e-10   39.8   0.4     0.0018   18.6   0.0    4.0  4  Ank_3     Ankyrin repeat
    2.7e-08   33.9   1.5      0.019   15.2   0.0    3.9  4  Ank_5     Ankyrin repeats (many copies)
    1.5e-05   25.2   0.0       0.43   11.1   0.0    3.8  3  Ank       Ankyrin repeat


Domain annotation for each model (and alignments):
>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   4.7e-11   1.4e-07      18      80 ..      23      91 ..       6      94 .. 0.77
   2 !   37.2   0.0   1.1e-12   3.3e-09       1      83 []      34     127 ..      34     127 .. 0.85
   3 !    5.7   0.0    0.0074        22       1      46 [.     101     149 ..     101     162 .. 0.62

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 4.7e-11
                              Ank_2 18 egadpnk..ngktaLhyAakngnleivklLleh...ad....ndgrtpLhyAarsghleivklLlekgadin 80
                                       +++   k  +g   +h+A +++nl++++ ++e    a+        +pL+yA  +++++++k+L+e+gadi 
  gene1577|gene1577|rna1576|rna1576 23 NNY---KfsDGTGLIHWASMYNNLDMCRRMMECrgaANsvggVLDSSPLYYALYNSNYKVMKFLIENGADIR 91
                                       223...234899999****************966764454566688*********99*************96 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 1.1e-12
                              Ank_2   1 LhlAakngnlelvklLl.egadpn..k..ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsgh 65 
                                        +h+A++++nl++++ ++ +   +n      + ++L+yA  n n +++k+L+e+      ++++g   Lh ++r++ 
  gene1577|gene1577|rna1576|rna1576  34 IHWASMYNNLDMCRRMMeCRGAANsvGgvLDSSPLYYALYNSNYKVMKFLIENgadiryVNKSGLGLLHTCVRFDD 109
                                        69****999********955455644157789**********99********88676667799**********987 PP

                              Ank_2  66 leivklLlekgadinlkd 83 
                                           + lLl +gad+n+kd
  gene1577|gene1577|rna1576|rna1576 110 VLGMILLLSYGADVNTKD 127
                                        7777788889******98 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0074
                              Ank_2   1 LhlAakngnlelvklLl.egadpn.k..ngktaLhyAakngnleivklLl 46 
                                        Lh ++++++   + lLl +gad+n k  +++t   yA  +g ++ v+ +l
  gene1577|gene1577|rna1576|rna1576 101 LHTCVRFDDVLGMILLLsYGADVNtKdtKNRTLWTYAKVKGARN-VQRFL 149
                                        56677765442334444688888873467778777888888766.44444 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.5         1   3.1e+03      62      62 ..     207     207 ..     164     241 .. 0.49
   2 !   58.9   6.5   1.8e-19   5.4e-16       5      66 ..     270     331 ..     266     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                               DHHC  62 l 62 
                                        l
  gene1577|gene1577|rna1576|rna1576 207 L 207
                                        1 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 1.8e-19
                               DHHC   5 lkfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilal 66 
                                        ++fC+tc  +k +  kHc++Cnrcvl+fDHhCp++n+ci +  +  F   ll+++++++ +l
  gene1577|gene1577|rna1576|rna1576 270 ENFCYTCLGRKGDGVKHCSICNRCVLEFDHHCPCINSCISKDIMGLFRRHLLSTFTVTVNVL 331
                                        79*********************************************888888888776554 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   4.4e-08   0.00013       2      55 .]      31      84 ..      30      84 .. 0.80
   2 !   26.6   0.0   2.1e-09   6.4e-06       3      48 ..      66     110 ..      64     117 .. 0.91
   3 ?    2.7   0.0     0.068     2e+02      19      33 ..     115     128 ..     113     137 .. 0.77
   4 ?   -2.6   0.0       3.1   9.3e+03      19      32 ..     352     365 ..     350     366 .] 0.79

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.4e-08
                              Ank_4  2 ltaLhyaaisgrlelvrlLle.kgadinaqdnrsGe...talhiAakrgnveilklLl 55
                                       ++++h+a ++++l+++r+  e +ga  n +    G    ++l++A++++n+++ k+L+
  gene1577|gene1577|rna1576|rna1576 31 TGLIHWASMYNNLDMCRRMMEcRGA-ANSV---GGVldsSPLYYALYNSNYKVMKFLI 84
                                       689*****************53675.3444...2222337*****************8 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 2.1e-09
                              Ank_4   3 taLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnv 48 
                                        ++L ya + +++++ ++L+e+gadi ++ n+sG+ +lh ++++ +v
  gene1577|gene1577|rna1576|rna1576  66 SPLYYALYNSNYKVMKFLIENGADIRYV-NKSGLGLLHTCVRFDDV 110
                                        7899************************.************99774 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.068
                              Ank_4  19 lLlekgadinaqdnr 33 
                                        lLl++gad+n   + 
  gene1577|gene1577|rna1576|rna1576 115 LLLSYGADVNTK-DT 128
                                        699*******98.43 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.1
                              Ank_4  19 lLlekgadinaqdn 32 
                                        l+l+ g+di + ++
  gene1577|gene1577|rna1576|rna1576 352 LILAAGMDIRRPKP 365
                                        78899***998765 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0046        14       5      23 ..      33      51 ..      30      58 .. 0.85
   2 !   18.6   0.0     6e-07    0.0018       4      29 ..      66      90 ..      64      91 .. 0.94
   3 !   10.0   0.0   0.00039       1.2       2      30 ..      97     124 ..      96     125 .. 0.91
   4 ?   -3.4   0.0         6   1.8e+04      19      29 ..     350     360 ..     345     361 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0046
                              Ank_3  5 pLhlAarsgnleivkfLle 23
                                       ++h+A +++nl++++ + e
  gene1577|gene1577|rna1576|rna1576 33 LIHWASMYNNLDMCRRMME 51
                                       68************99887 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 6e-07
                              Ank_3  4 tpLhlAarsgnleivkfLlenkgadv 29
                                       +pL++A+ + n++++kfL+e +gad+
  gene1577|gene1577|rna1576|rna1576 66 SPLYYALYNSNYKVMKFLIE-NGADI 90
                                       8*******************.8***9 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00039
                              Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvn 30 
                                        G  +Lh+++r++++  +++Ll  +gadvn
  gene1577|gene1577|rna1576|rna1576  97 GLGLLHTCVRFDDVLGMILLLS-YGADVN 124
                                        5669**********99******.*****9 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 6
                              Ank_3  19 kfLlenkgadv 29 
                                        + L+   g+d+
  gene1577|gene1577|rna1576|rna1576 350 IVLILAAGMDI 360
                                        45555578887 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0022       6.5      19      37 ..      33      52 ..      22      62 .. 0.79
   2 !   15.2   0.0   6.5e-06     0.019      18      54 ..      66     102 ..      60     104 .. 0.92
   3 !    8.1   0.0    0.0012       3.5      33      56 .]     114     137 ..     109     163 .. 0.86
   4 ?   -3.1   0.0       3.6   1.1e+04      28      42 ..     345     360 ..     344     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0022
                              Ank_5 19 pLhvAakygaadvvrlLl.a 37
                                        +h+A+ y+++d++r+++  
  gene1577|gene1577|rna1576|rna1576 33 LIHWASMYNNLDMCRRMMeC 52
                                       6899999*********9933 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 6.5e-06
                              Ank_5  18 tpLhvAakygaadvvrlLlargadlnltdsrGltald 54 
                                        +pL +A ++ +  v+++L+++gad++  +++Gl +l+
  gene1577|gene1577|rna1576|rna1576  66 SPLYYALYNSNYKVMKFLIENGADIRYVNKSGLGLLH 102
                                        8*******************************98876 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0012
                              Ank_5  33 rlLlargadlnltdsrGltaldlA 56 
                                        +lLl +gad n++d  ++t++ +A
  gene1577|gene1577|rna1576|rna1576 114 ILLLSYGADVNTKDTKNRTLWTYA 137
                                        556689999999999999999887 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 3.6
                              Ank_5  28 aadvvrlLl.argadl 42 
                                        + +v+++L+ a g+d+
  gene1577|gene1577|rna1576|rna1576 345 SVTVFIVLIlAAGMDI 360
                                        5678888888888886 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.054   1.6e+02       6      24 ..      34      54 ..      29      59 .. 0.77
   2 !   11.1   0.0   0.00014      0.43       4      31 ..      66      94 ..      65      95 .. 0.85
   3 !    6.5   0.0    0.0042        12       6      31 ..     101     127 ..      97     128 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.054
                                       HHHHHHHTTHHHHHHHH.T.T CS
                                Ank  6 LHlAatngkkriiklLL.h.G 24
                                        H+A++++++++++    + G
  gene1577|gene1577|rna1576|rna1576 34 IHWASMYNNLDMCRRMMeCrG 54
                                       6**********9997776435 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00014
                                       BHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                                Ank  4 TPLHlAatngkkriiklLL.hGAnlnald 31
                                       +PL +A +n +  + k+L+ +GA++  ++
  gene1577|gene1577|rna1576|rna1576 66 SPLYYALYNSNYKVMKFLIeNGADIRYVN 94
                                       7****99888899******99***86555 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0042
                                        HHHHHHHTTHHHHHH..HH.TTTSTTCBT CS
                                Ank   6 LHlAatngkkriikl..LL.hGAnlnald 31 
                                        LH +++++  +++ +  LL +GA++n +d
  gene1577|gene1577|rna1576|rna1576 101 LHTCVRFD--DVLGMilLLsYGADVNTKD 127
                                        77767777..57765325566*****988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2371.74
//
Query:       gene1578|gene1578|rna1577|rna1577  [L=266]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1539.35
//
Query:       gene1579|gene1579|rna1578|rna1578  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1006.59
//
Query:       gene1580|gene1580|rna1579|rna1579  [L=358]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-27   96.0   0.0    2.8e-27   95.8   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   1.6e-31   2.8e-27       3     207 ..      48     344 ..      46     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 1.6e-31
                                        HHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHH...HHTT..TCEESSSSEEEEGGGGGSTTT..BCSSSB. CS
                      Peptidase_M24   3 irkaariasaaleavleaikpgvterelaaeieattl...krhg..arglafppivasgenaavlhy..tpndrv. 70 
                                         r+aa+++++a+ +v + i+pg+t  e+ + ie+ t+   +  g   +g++fp  ++ + n++++hy  +p d++ 
  gene1580|gene1580|rna1579|rna1579  48 ARRAAEAHRRARYKVQSIIRPGITLLEIVKSIEDSTRvllS--GerNNGIGFP--AGMSMNSCAAHYsvNPEDQDi 119
                                        69**************99***************77553323..3459999999..************644444448 PP

                                        .--TTEEEEEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTB CS
                      Peptidase_M24  71 .lkegdlvlidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesagl 145
                                         l e+d++++d+g + +g + D+++T+++    +e + l+ a++e++e++ik +  +v++ +i++ + ev+ s+++
  gene1580|gene1580|rna1579|rna1579 120 iLTEDDVLKVDFGTHSNGRIMDSAFTIAFK---QEFEPLLMAAKEGTETGIKSLGIDVRVCDIGRDINEVISSYEM 192
                                        89*************************995...45556***********************************854 PP

                                        ........CCGBSSCSEEEESS.SSSEE..EEEESSSTTCSSB--TTBEEEEEE......EEEEETTT........ CS
                      Peptidase_M24 146 ........akffphglGHgvGl.evhde..gpsvsresndgrkleeGmvftiEp......giyfapge........ 196
                                                 +++  + GH++ + ++h++   p v+  ++d ++++    +++E+      g               
  gene1580|gene1580|rna1579|rna1579 193 vvdgntwaIRPVSDLHGHSISQfKIHGGisIPPVN--NKDITRITGDTFYAVETfattgkG------Findrppcs 260
                                        55666666588899*******99***984444455..567888888888999996666442......122224444 PP

                                        .........................................................................EEE CS
                      Peptidase_M24 197 .........................................................................ggv 199
                                                                                                                   +
  gene1580|gene1580|rna1579|rna1579 261 hfmlntyksrklynkdlmkvyefvrdsfgtlpfsprhldyynlvegsslksvnlltmmglfipypplndidgcRIA 336
                                        4455555555566666667777777777777777788888888888888888888888888888888888876688 PP

                                        EEBEEEEE CS
                      Peptidase_M24 200 riedtvlv 207
                                        ++e+t+++
  gene1580|gene1580|rna1579|rna1579 337 QFEHTIYL 344
                                        88888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2290.11
//
Query:       gene158|gene158|rna158|rna158  [L=149]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 918.63
//
Query:       gene1581|gene1581|rna1580|rna1580  [L=879]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     8e-119  397.2   0.0   1.9e-118  395.9   0.0    1.6  1  DUF3591       Protein of unknown function (DUF3591)
    1.7e-22   79.3   0.3    5.2e-22   77.7   0.3    1.9  1  Bromodomain   Bromodomain
    8.9e-05   22.2   1.8    0.00019   21.2   1.8    1.5  1  zf-CCHC_6     Zinc knuckle
  ------ inclusion threshold ------
       0.06   13.4   1.3       0.12   12.5   1.3    1.6  1  zf-CCHC       Zinc knuckle
       0.13   12.3   0.0       0.26   11.3   0.0    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 


Domain annotation for each model (and alignments):
>> DUF3591  Protein of unknown function (DUF3591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.9   0.0  5.3e-122  1.9e-118       1     397 [.     226     612 ..     226     640 .. 0.92

  Alignments for each domain:
  == domain 1  score: 395.9 bits;  conditional E-value: 5.3e-122
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......x.xxxx RF
                            DUF3591   1 fnlsnDkaYealkenkqskvrstlgnlkveHSlpAlkLqlpfyktklskkelrsfHrprlkvk.......k.kakg 68 
                                        +n+s Dk+Y +       k +++lg+  v+HSlpAl+L   fyk + +k+elr+fHrp+++v+         +++ 
  gene1581|gene1581|rna1580|rna1580 226 YNISLDKYYGQES-----KAKNSLGTFGVQHSLPALRLDPIFYKNNHTKEELRNFHRPKFTVSgngirfkAlESTR 296
                                        8********9884.....55789**********************************************7346788 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591  69 keekellkktkDLslkdtskvvllEYseeyPpllsnvGMgsklinYYrkkkekDtsrpklelGetvvlepedksPF 144
                                        ++ ++++kk+ +L++kd s + l+EYsee P +l n GM s l  YYrk++++D+  p  + ++ +vl+ped sPF
  gene1581|gene1581|rna1580|rna1580 297 NKVQSIIKKAGELTVKDGSPFSLFEYSEEDPFFLVNSGMVSLLNIYYRKSNARDEYAP--DQSQYTVLDPEDPSPF 370
                                        8899*****************************************************9..999************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 145 lnlGevepgetvqtlennliraPifkhkvkstDFLlirsttkekkkyylreidnlfvvGqtlPlveVpgphsrkvt 220
                                        + +G+v+pg+++q+l+nnl+ aP+fkh  +s D+L+i ++  +++ +  r+idnl++vGq++Pl eV +phsrk +
  gene1581|gene1581|rna1580|rna1580 371 FGFGDVAPGTSIQALTNNLFIAPVFKH--SSGDYLCIAESAPDGEFLVYRSIDNLYCVGQQFPLEEVYAPHSRKLN 444
                                        ***************************..789*******9999********************************* PP

                                        xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 221 nfsknrLkviiyrllrkske..krikvedikkafpdqselqiRkrLkefaeyqrkgedsgvWklkeeerlpseeei 294
                                         f+knrLkv ++rl+++++   k+++++++ ++fp  se + Rk Lke+a++ +kg+ ++vW+l+++  l  ee++
  gene1581|gene1581|rna1580|rna1580 445 IFCKNRLKVAAFRLFNNKEGgnKELRISQLDEMFPYFSEGSKRKWLKEYADCVKKGR-DNVWVLRPSSALLGEEDL 519
                                        ******************998788*******************************99.78**************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 295 rklvtPEdvcllesmqvgeqrlkdagyakeeeeeeedekkeeskleleeqlapWnttknFlaAtqgkamlqlhGeg 370
                                        rklvtPE++c++esm++ge++l+d+gy++  e+++e+        e e    pW +++nF++A++g+ +l+l+G g
  gene1581|gene1581|rna1580|rna1580 520 RKLVTPENICQYESMLAGERKLQDSGYKMVVESDDEE-------NEEEMVPPPWCLSRNFVNACNGRGLLELNGPG 588
                                        ***************************9998888774.......466788899*********************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DUF3591 371 DPtGrgegfsfvrtsmKegfkkagesk 397
                                        DPtG+gegfsf +++ K+g +    ++
  gene1581|gene1581|rna1580|rna1580 589 DPTGIGEGFSFRKIRLKRGNE---IEN 612
                                        *****************9552...222 PP

>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7   0.3   1.4e-25   5.2e-22       3      82 ..     769     848 ..     764     850 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 1.4e-25
                                        HHHHHBHTTTCGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHH CS
                        Bromodomain   3 kilsellehklaepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngegsvi 78 
                                         +l+++++ + + +F++pv++++fpdy+ ++++P+dL+tIk k+++nkYk++ +f +dl+l+ +N+rkynge++ +
  gene1581|gene1581|rna1580|rna1580 769 DLLTQFFQIPYSVAFHRPVSTKKFPDYPLIVSNPIDLTTIKTKVRHNKYKKFNEFLEDLELMQNNCRKYNGEDHSL 844
                                        5678999999999************************************************************999 PP

                                        HHHH CS
                        Bromodomain  79 yela 82 
                                        + +a
  gene1581|gene1581|rna1580|rna1580 845 TRIA 848
                                        8877 PP

>> zf-CCHC_6  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.8   5.2e-08   0.00019       4      21 ..     723     740 ..     721     758 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.2e-08
                          zf-CCHC_6   4 CknCGAFGHtarSkrCPm 21 
                                        C+nCG  GH+ ++k CP 
  gene1581|gene1581|rna1580|rna1580 723 CGNCGQVGHMKTNKSCPK 740
                                        *****************6 PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.3   3.4e-05      0.12       2      14 ..     722     734 ..     721     740 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                                        CTSSSSSSSSTTT CS
                            zf-CCHC   2 kCynCGepGHiar 14 
                                        +C nCG++GH++ 
  gene1581|gene1581|rna1580|rna1580 722 TCGNCGQVGHMKT 734
                                        699********85 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.2e-05      0.26      13      22 ..     697     706 ..     696     706 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.2e-05
                       BCA_ABC_TP_C  13 ndPrVieAYL 22 
                                        +dPrVi+AYL
  gene1581|gene1581|rna1580|rna1580 697 SDPRVIKAYL 706
                                        7********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (879 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 5828.42
//
Query:       gene1582|gene1582|rna1581|rna1581  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   15.0   0.1        2.5    8.5   0.0    2.5  2  DUF4258   Domain of unknown function (DUF4258)


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1    0.0033        59       7      27 ..      64      90 ..      61     137 .. 0.73
   2 ?    8.5   0.0   0.00014       2.5      13      33 ..     151     171 ..     149     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0033
                            DUF4258  7 ermaeRgIseedieevlenG......e 27
                                       +  +   I e++ie++l+ G      +
  gene1582|gene1582|rna1581|rna1581 64 RAVKTKAIVESQIEKLLDEGmklidsT 90
                                       55567789************7666543 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00014
                            DUF4258  13 gIseedieevlenGeiieeys 33 
                                         I+e+ +++++e+Ge++e+ys
  gene1582|gene1582|rna1581|rna1581 151 SIDEDHLSDAMEYGELVEKYS 171
                                        59******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1178.95
//
Query:       gene1583|gene1583|rna1582|rna1582  [L=354]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-07   29.7   0.2    1.2e-06   28.5   0.2    1.7  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.025   14.9   0.0    1.6  1  AAA_assoc_2      AAA C-terminal domain
      0.022   15.2   0.2       0.06   13.8   0.2    1.7  1  AAA              ATPase family associated with various cellul
      0.032   13.7   0.5      0.079   12.5   0.1    1.8  2  DUF4506          Domain of unknown function (DUF4506)
      0.063   13.0   0.0       0.13   12.0   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.095   13.0   0.9       0.14   12.5   0.2    1.6  2  AAA_19           AAA domain
        0.1   13.2   0.0        0.2   12.3   0.0    1.5  1  DUF3067          Domain of unknown function (DUF3067)


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   4.5e-10   1.2e-06      23     160 ..      37     185 ..      18     188 .. 0.61

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 4.5e-10
                    DNA_pol3_delta2  23 LfeGdegigkkelalnlakallceeknetk.pcgecksckkieqgkhpDvivi........eteeker......si 83 
                                        +++G  g gkk++ l+l+++l   +++ +    +  +  kkie   +    ++        +     +      si
  gene1583|gene1583|rna1582|rna1582  37 ILHGGPGHGKKTTLLCLVTHLYGGSPEMKIrTVEVLSGAKKIEVSYMESNEYVeispsqygH-----HdkaviqSI 107
                                        44555677777777777777777666655422222233334332222222222222222221.....011111112 PP

                    DNA_pol3_delta2  84 kldqir.elieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                         ++  + + i ++ +++ ++  +++ i+ ae++t +A+ al +t+E  s+   ++L+ ++ ++l++++rSRc  l+
  gene1583|gene1583|rna1582|rna1582 108 IKEMGQtKPILSMLKSAKKAPIRLVAITSAEELTLEAQAALRRTIEMYSSVLRVVLVCNELSRLIEPVRSRCFFLR 183
                                        11111112233445667778889999***********************************************999 PP

                    DNA_pol3_delta2 159 fs 160
                                        + 
  gene1583|gene1583|rna1582|rna1582 184 IP 185
                                        86 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   9.9e-06     0.025       2      52 ..     202     253 ..     201     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.9e-06
                                        XX.XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX.XXXXXXXXXXXX CS
                        AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLE.laaeaaeakegkieitledle 52 
                                        ++++++ ++ le +++ ++G +R+aL +LE ++ ++ ++++++ +i+ +dl+
  gene1583|gene1583|rna1582|rna1582 202 KENYAIPKEKLEEICKESEGNMRRALCILElFCFNMIDKETKRPKINVKDLK 253
                                        56789999**********************6566666666888888888776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.3e-05      0.06       1     124 [.      36     179 ..      36     184 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                                        EEEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS...............................STTHHH CS
                                AAA   1 vllyGppGtGKTllakavakel..gvefleisgsellsk...............................yvgese 43 
                                        ++l+G pG GK ++   ++++l  g++ ++i   e+ls                                 + + +
  gene1583|gene1583|rna1582|rna1582  36 LILHGGPGHGKKTTLLCLVTHLygGSPEMKIRTVEVLSGakkievsymesneyveispsqyghhdkaviqSIIKEM 111
                                        589*******988888888887453444444444444333445556666667777788874444455555222333 PP

                                        HHHHHHHHHHHHTS.TS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTH CS
                                AAA  44 kkirelfkeakeka.kp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldp 117
                                         +++ +++ +k+ + +p   + i  +++l+ +           ++++L + ++ +++    + v++++n+ ++l +
  gene1583|gene1583|rna1582|rna1582 112 GQTKPILSMLKSAKkAPiRLVAITSAEELTLE-----------AQAALRRTIEMYSS---VLRVVLVCNELSRLIE 173
                                        33333333322222334455555555555555...........5*************...599************* PP

                                        HHHSTTS CS
                                AAA 118 allrgRf 124
                                        +++ +R+
  gene1583|gene1583|rna1582|rna1582 174 PVR-SRC 179
                                        ***.898 PP

>> DUF4506  Domain of unknown function (DUF4506)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   3.1e-05     0.079      23      54 ..      62      92 ..      51     113 .. 0.84
   2 ?   -2.8   0.0       1.6   4.1e+03      83     111 ..     243     271 ..     226     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                            DUF4506 23 prggeeiasltivseartmEv.YlqleeYlgTv 54
                                       p+   +i+ ++++s a+++Ev Y++++eY++ +
  gene1583|gene1583|rna1582|rna1582 62 PE--MKIRTVEVLSGAKKIEVsYMESNEYVEIS 92
                                       44..89***************666*****9855 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                            DUF4506  83 staackiKllslgekqcvliskvvvalrp 111
                                        +  ++++K l+l  + +v+++  +v+ ++
  gene1583|gene1583|rna1582|rna1582 243 KRPKINVKDLKLDWELMVMGISSIVKSNQ 271
                                        44567777777777777777766666555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     5e-05      0.13       2      55 ..       8      56 ..       7      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                             RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGk.ttlakiiak 55
                                       rPks++  +g+ek+ + lk +        e++ h++l+G PG Gk ttl  ++++
  gene1583|gene1583|rna1582|rna1582  8 RPKSFDSIVGREKISSVLKSY------TLETIPHLILHGGPGHGKkTTLLCLVTH 56
                                       999999999999999988765......46899************73677666654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   5.5e-05      0.14      12      35 ..      35      58 ..      29      82 .. 0.85
   2 ?   -2.9   0.0         3   7.6e+03      43      51 ..     127     135 ..     102     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                             AAA_19 12 vllvtaGpGtGKTrvlkhivallv 35
                                       +l++ +GpG GK ++l + v++l 
  gene1583|gene1583|rna1582|rna1582 35 HLILHGGPGHGKKTTLLCLVTHLY 58
                                       6899****************9986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3
                             AAA_19  43 eeillvaft 51 
                                        ++i lva t
  gene1583|gene1583|rna1582|rna1582 127 APIRLVAIT 135
                                        344444444 PP

>> DUF3067  Domain of unknown function (DUF3067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.9e-05       0.2      32      82 ..      80     132 ..      50     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.9e-05
                                        EEETTSTT-.SS-HHHHHHHHHHHHH.HHHHHS-HHHHHHHHHH-----BTTB CS
                            DUF3067  32 wkyleqasf.plteqeYlehldavae.llnelgavdqvrefleetkkkPrlgk 82 
                                          y+e++++ +++ ++Y +h +av++ +++e+g+++ + ++l+++kk P    
  gene1583|gene1583|rna1582|rna1582  80 VSYMESNEYvEISPSQYGHHDKAVIQsIIKEMGQTKPILSMLKSAKKAPIRLV 132
                                        579999999899********9998753789******************97544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2383.25
//
Query:       gene1584|gene1584|rna1583|rna1583  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-08   32.8   0.3    1.4e-07   31.7   0.3    1.6  1  Ada3      Histone acetyltransferases subunit 3


Domain annotation for each model (and alignments):
>> Ada3  Histone acetyltransferases subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.3   7.8e-12   1.4e-07      49     106 ..     151     208 ..      98     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 7.8e-12
                               Ada3  49 revsliNgarkarLlelvkermayqeyqtiledlDkqvqqaYlKrtrtlkkkkkkkrs 106
                                        r++++iN++rk+ L++ ++er+ayq y  +++ +D++ +   +K++ + kkk+ ++++
  gene1584|gene1584|rna1583|rna1583 151 RKQVTINNKRKEVLARKLRERLAYQGYWMVMRAIDSDMEGLLTKKKGKKKKKEGGEEK 208
                                        89***************************************99988777776666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1242  (0.0692732); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1811.22
//
Query:       gene1585|gene1585|rna1584|rna1584  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-83  278.0   1.1    6.7e-83  277.9   1.1    1.0  1  Methyltransf_8   Hypothetical methyltransferase
    6.5e-07   29.9   0.0    1.1e-05   25.9   0.0    2.6  2  Methyltransf_11  Methyltransferase domain
    0.00018   22.2   0.0      0.058   14.1   0.0    2.8  2  Methyltransf_25  Methyltransferase domain
    0.00025   20.9   0.3      0.057   13.2   0.3    2.2  1  Methyltransf_31  Methyltransferase domain
     0.0078   14.8   0.1       0.07   11.7   0.1    1.9  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.026   14.4   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
      0.054   13.2   0.0      0.086   12.5   0.0    1.3  1  Herpes_UL7       Herpesvirus UL7 like


Domain annotation for each model (and alignments):
>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.9   1.1   2.6e-86   6.7e-83       2     219 .]       3     210 .]       2     210 .] 0.99

  Alignments for each domain:
  == domain 1  score: 277.9 bits;  conditional E-value: 2.6e-86
                                        XXXXX-HHHHHHHHHHHHHHHHHS-HHHHHHHHHH-HHHHHHHHHHHHHHHCTSSS-HHHHHHHHHCTS-TTS-EE CS
                     Methyltransf_8   2 leakikkrldgarfrflneklytgesskavdlfkedpeafdlyhkgfrsqvkkWPenPldviirklkkkkdnlvva 77 
                                        le+k+ krl+g++fr+ln+++y+g++ k++dl        +lyh++++ qvk+WP+nPld+ii+k+k+k +++v+a
  gene1585|gene1585|rna1584|rna1584   3 LEKKLMKRLEGGKFRMLNDRMYHGKGLKKKDL--------RLYHELYDLQVKRWPVNPLDIIIEKIKEKGGDMVIA 70 
                                        899*****************************........************************************ PP

                                        EES-TT-HHHHH--S-..EEEEESS-SSTTEEES-T.TS-S--TT-EEEEEEES---SS-HHHHHHHHHHHEEEEE CS
                     Methyltransf_8  78 dlGcGeakiaeavrekekvrsfdlvavnervvacdl.akvPledesvdvavfclslmgtnladflkeanrvlkvGG 152
                                        d+GcG+a+ia   +e+e+v+s+dl++ ++ +v cd+ +++Pled+svd+av+cls+m +n+a+++ke+nr+lk  G
  gene1585|gene1585|rna1584|rna1584  71 DVGCGDARIA---KEFENVISLDLHPSKKGIVRCDMsKRIPLEDKSVDIAVCCLSMMIENIAVPTKEINRILKENG 143
                                        **********...99*********************889************************************* PP

                                        EEEEEEEGGG-S-HHHHHHHHHCTTEEEEEEE--STTEEEEEEEE-SSS-TT---GG--------XX CS
                     Methyltransf_8 153 llkvaevksrfesvklfaraltklGfevkskdlsnkqfvlfefkkvekkgkkrelglklkpclykkr 219
                                        +++vaev+sr++ v+l++r+++ +Gfe+k++d+sn+qfv+f++kkv  k+ k+ +++kl p lykkr
  gene1585|gene1585|rna1584|rna1584 144 YWYVAEVRSRIPGVRLLERKFEAFGFEIKQVDVSNEQFVIFVLKKVLSKNWKKLPQIKLMPWLYKKR 210
                                        ******************************************************************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.4e-09   1.1e-05       2      95 ..      71     146 ..      70     147 .. 0.85
   2 ?   -0.0   0.0      0.56   1.4e+03      45      74 ..     157     186 ..     146     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.4e-09
                                        EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.TSS-TT-EEEEEEES-CCC-CC CS
                    Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek.lpfednsfDlvvssevlhhved 76 
                                        dvGcG  r+a++++    +v+ +Dl +             g    +v++d++k +p+ed+s+D+ v+  +++  e+
  gene1585|gene1585|rna1584|rna1584  71 DVGCGDARIAKEFE----NVISLDLHPSKK----------G----IVRCDMSKrIPLEDKSVDIAVCCLSMMI-EN 127
                                        89999999999999....999999988876..........3....4778888658************986655.57 PP

                                        HHHHHHHHHHHEEEEEEEE CS
                    Methyltransf_11  77 pekalkeiaRvLkpgGllv 95 
                                         +   kei R+Lk +G+ +
  gene1585|gene1585|rna1584|rna1584 128 IAVPTKEINRILKENGYWY 146
                                        9999************976 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.56
                                        EEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                    Methyltransf_11  45 vefvvadaeklpfednsfDlvvssevlhhv 74 
                                        v++++  +e + fe +++D+   ++v++ +
  gene1585|gene1585|rna1584|rna1584 157 VRLLERKFEAFGFEIKQVDVSNEQFVIFVL 186
                                        667788888888888888887777766665 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.3e-05     0.058      50      97 .]      98     143 ..      69     143 .. 0.72
   2 ?   -1.1   0.0       1.2   3.1e+03      40      67 ..     153     176 ..     146     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                        EEESBC.CGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                    Methyltransf_25  50 fvqgda.edlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                        +v++d+ +++p+ed+s+D+ v++ +++ +  e+++   kei r+Lk++G
  gene1585|gene1585|rna1584|rna1584  98 IVRCDMsKRIPLEDKSVDIAVCCLSMM-I--ENIAVPTKEINRILKENG 143
                                        5677884569************64433.3..4677779********998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                                        HHHHTTTTEEEEESBCCGBSSSTTTEEE CS
                    Methyltransf_25  40 raeeeglnvefvqgdaedlpfedgsfDl 67 
                                        r+    + v++++ ++e++ fe +++D+
  gene1585|gene1585|rna1584|rna1584 153 RI----PGVRLLERKFEAFGFEIKQVDV 176
                                        44....5677777888888887777776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3   2.2e-05     0.057      60     113 ..     100     151 ..      63     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                    Methyltransf_31  60 qgdiee.leklledekfDlilsnevlnaladpdkileeiervlkpggilliedpr 113
                                        ++d+ + ++  led+++D+ ++ ++ + + + +   +ei r lk++g+  ++++r
  gene1585|gene1585|rna1584|rna1584 100 RCDMSKrIP--LEDKSVDIAVC-CLSMMIENIAVPTKEINRILKENGYWYVAEVR 151
                                        689999999..99******999.88899**********************99998 PP

>> Methyltransf_29  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   2.8e-05      0.07     165     218 ..      97     148 ..      48     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                    Methyltransf_29 165 ailavlgtkrlpyPsrsfdlihCsrCridwteedgilllevdRvlRpgGyfvls 218
                                         i+    +kr+p   +s d++ C  C+    e+ ++   e++R+l+ +Gy+ ++
  gene1585|gene1585|rna1584|rna1584  97 GIVRCDMSKRIPLEDKSVDIAVC--CLSMMIENIAVPTKEINRILKENGYWYVA 148
                                        55555568999**********99..888899999*****************765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     1e-05     0.026      25     124 ..      68     154 ..      41     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                    Methyltransf_23  25 rvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppe 100
                                         + d+GcG+ + ++    ++ +v+  Dl p + +i+      + d+  ++  ++++  + + +l++++e++  p++
  gene1585|gene1585|rna1584|rna1584  68 VIADVGCGDARIAK----EFENVISLDLHPSKKGIV------RCDMSKRIPLEDKSVDIAVCCLSMMIENIAVPTK 133
                                        6669******9888....55799********99998......4444444445556668888899***********9 PP

                    Methyltransf_23 101 llrqiatllkpgGylllseplasl 124
                                            i+++lk++Gy ++ e+ ++ 
  gene1585|gene1585|rna1584|rna1584 134 ---EINRILKENGYWYVAEVRSRI 154
                                        ...8899999*****999986655 PP

>> Herpes_UL7  Herpesvirus UL7 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.4e-05     0.086      79     105 ..     111     137 ..     103     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.4e-05
                         Herpes_UL7  79 dnlldfeLCvllsyLENcsslspsllv 105
                                        d+++d++ C+l +++EN+  +++++ +
  gene1585|gene1585|rna1584|rna1584 111 DKSVDIAVCCLSMMIENIAVPTKEINR 137
                                        57899*************888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1449.02
//
Query:       gene1586|gene1586|rna1585|rna1585  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1288  (0.0718389); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 840.20
//
Query:       gene1587|gene1587|rna1586|rna1586  [L=544]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-40  136.7   0.0    9.2e-40  135.8   0.0    1.4  1  Ndc80_HEC     HEC/Ndc80p family
      0.003   17.6   3.8      0.003   17.6   3.8    4.3  3  DUF5595       Domain of unknown function (DUF5595)
     0.0059   17.1   7.0     0.0059   17.1   7.0    3.7  3  APG6_N        Apg6 coiled-coil region
     0.0076   16.3   8.7     0.0076   16.3   8.7    3.9  4  BRE1          BRE1 E3 ubiquitin ligase
  ------ inclusion threshold ------
        2.4    8.0   7.0       0.17   11.7   1.0    2.2  3  Viral_P18     ssRNA positive strand viral 18kD cysteine rich 
        4.5    8.0   6.9       0.84   10.3   1.0    2.5  2  Bin3          Bicoid-interacting protein 3 (Bin3)


Domain annotation for each model (and alignments):
>> Ndc80_HEC  HEC/Ndc80p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   3.1e-43   9.2e-40      25     148 ..      38     159 ..      11     164 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 3.1e-43
                          Ndc80_HEC  25 verDprplrdksfqseliqellefLkennfehsisaktlksPsqkdfssifkfLykrldpsyefqkkieeevvkil 100
                                        ++rD r +r+k ++++++ ++l+fL en+++ ++s+k+l++Ps+kdf+sifkfLy ++d ++ f++++e+evv+++
  gene1587|gene1587|rna1586|rna1586  38 KRRDMRMVREKGYRQQCVDTILKFLVENGYDGQVSQKILHNPSSKDFQSIFKFLYGFID-DFMFSSRFEDEVVMVM 112
                                        579********************************************************.9*************** PP

                          Ndc80_HEC 101 kelrYPfaesisKsqlaAvgtphtwptllaaLhWlvelaklleelses 148
                                        k+lrYP+  +i+Ksql+A+ tphtwp +l++  W+vel+    +l ++
  gene1587|gene1587|rna1586|rna1586 113 KNLRYPYCGEITKSQLSAI-TPHTWPVILSMCSWVVELIGHGASLLQQ 159
                                        *******************.*****************98766555555 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   3.8     1e-06     0.003       3      70 ..     159     226 ..     158     229 .. 0.83
   2 ?    0.6   0.4      0.21   6.3e+02      40      63 ..     269     292 ..     254     300 .. 0.63
   3 ?    0.3   3.4      0.26   7.8e+02      51      71 ..     304     324 ..     297     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1e-06
                            DUF5595   3 eedgievnkLFldYtvkcYekFmqgeDtFeeedaeleskLkelynvdeaqlesleeeekrLeeEierl 70 
                                        +e++  v++ F++Y+ + Y +Fm+g+ +    ++e+e k  e+y    +++ + + e  r ee i+++
  gene1587|gene1587|rna1586|rna1586 159 QEEEKSVESCFFEYVCDGYMRFMEGDEDDAGLEEEFERKVTEIYTGMFREIDRKKDELARIEEMISES 226
                                        57788899*****************9999999999999999999988888888777777777766665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                            DUF5595  40 skLkelynvdeaqlesleeeekrL 63 
                                        +kL e    +e+++e l+++e+ L
  gene1587|gene1587|rna1586|rna1586 269 NKLSEDIMRIEEEIEGLKAQEEGL 292
                                        344444555566666666666555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.26
                            DUF5595  51 aqlesleeeekrLeeEierle 71 
                                        ++++++++e+  L +E+er++
  gene1587|gene1587|rna1586|rna1586 304 EDVKEMNAEKIELFKELERMK 324
                                        556666666666666666653 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   7.0     2e-06    0.0059      25     127 ..     174     290 ..     156     296 .. 0.82
   2 !    7.6   9.9    0.0017       5.2      52     102 ..     302     352 ..     288     363 .. 0.85
   3 ?   -2.1  13.1       1.8   5.3e+03      33      95 ..     451     514 ..     414     517 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2e-06
                             APG6_N  25 rdaYeeflkklkkekkeeek..............qdeeleeleeeleklekeeeelleeLkelekereeleaelaa 86 
                                        +d Y++f++  ++++  ee+              + +  ++   ++e++ +e ++  e   el+++++el ++l+ 
  gene1587|gene1587|rna1586|rna1586 174 CDGYMRFMEGDEDDAGLEEEferkvteiytgmfrEIDRKKDELARIEEMISESRKIAESRGELDRKKKELTDDLNM 249
                                        788888888888887777767778888888855422222333444888889999999999**************** PP

                             APG6_N  87 leeelealeeeeerfwreynelqlelleleeeldsleaqye 127
                                        l + +++le ++++++   n+l+ + ++ eee + l+aq e
  gene1587|gene1587|rna1586|rna1586 250 LIASEKQLEGKKRKYLGTINKLSEDIMRIEEEIEGLKAQEE 290
                                        *************************************9966 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0017
                             APG6_N  52 leeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfw 102
                                          e+++++++e+ el++eL++++ e+e l +e+ ++e+e++++ ee e+ +
  gene1587|gene1587|rna1586|rna1586 302 NPEDVKEMNAEKIELFKELERMKPEKEGLMKEVGEQEREAQERVEEVEKLF 352
                                        446699*************************************99998765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.8
                             APG6_N  33 kklkkekkeeekqdeeleeleeeleklekeeee.lleeLkelekereeleaelaaleeeleale 95 
                                        +k + +++e++k+++e+e le+el kl+ e ++ ll   ++l+k++  l++ l+++  e e+++
  gene1587|gene1587|rna1586|rna1586 451 EKKEISENEQRKSKTEMELLENELLKLNLESNTsLLMSEQKLQKAKIVLDRTLNSINYEREEIN 514
                                        4333333333347899*******999998877526778889*************9999999876 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.3     4e+03      18      34 ..     208     224 ..     191     231 .. 0.66
   2 !   16.3   8.7   2.5e-06    0.0076       9      94 ..     237     322 ..     234     323 .. 0.97
   3 ?    1.3   0.3      0.12   3.6e+02       1      33 [.     330     362 ..     330     371 .. 0.83
   4 ?    0.4   6.3      0.23     7e+02      38      79 ..     451     492 ..     415     516 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                               BRE1  18 qlskkvkeltileekkl 34 
                                        +++ k+ el++ ee ++
  gene1587|gene1587|rna1586|rna1586 208 EIDRKKDELARIEEMIS 224
                                        45556666666666554 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.5e-06
                               BRE1   9 ekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkeleke 84 
                                         + ++el + l++++++ + le kk ++   ++k  + ++ ++ +++ l+++   L+++++K++   e+ ke+ +e
  gene1587|gene1587|rna1586|rna1586 237 DRKKKELTDDLNMLIASEKQLEGKKRKYLGTINKLSEDIMRIEEEIEGLKAQEEGLRAQITKQKINPEDVKEMNAE 312
                                        67789*********************************************************************** PP

                               BRE1  85 fvrklkelek 94 
                                         +++ kele+
  gene1587|gene1587|rna1586|rna1586 313 KIELFKELER 322
                                        *********8 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.12
                               BRE1   1 lqkELvklekafeelseqlskkvkeltileekk 33 
                                        l kE+ + e++ +e  e+++k+ ++l+ l +++
  gene1587|gene1587|rna1586|rna1586 330 LMKEVGEQEREAQERVEEVEKLFFDLKGLRDEI 362
                                        568888999999999999999999998887776 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.23
                               BRE1  38 aekakadqkyfaamrskdalenelkkLnkllsKsselieqLk 79 
                                         +k+  ++++   + +++ lenel kLn   + s  ++eq  
  gene1587|gene1587|rna1586|rna1586 451 EKKEISENEQRKSKTEMELLENELLKLNLESNTSLLMSEQKL 492
                                        4677789999999999************99999888877654 PP

>> Viral_P18  ssRNA positive strand viral 18kD cysteine rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.1   6.2e+03      49      65 ..     105     122 ..      99     129 .. 0.73
   2 ?   11.7   1.0   5.6e-05      0.17      49     119 ..     244     320 ..     237     324 .. 0.66
   3 ?   -2.8   0.2       1.8   5.2e+03      62      82 ..     437     460 ..     415     494 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                          Viral_P18  49 eedvymlifvleq.ycGe 65 
                                        e++v m++  l   ycGe
  gene1587|gene1587|rna1586|rna1586 105 EDEVVMVMKNLRYpYCGE 122
                                        667777777666569998 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 5.6e-05
                          Viral_P18  49 eedvymlifvleqycGekh.yklsealkdvsddel....kldrlearresllasiqk.klkayd..ekiallaekf 116
                                         +d+ mli   +q  G+k  y   +++ + s+d +    +++ l+a++e l+a+i k k++  d  e  a   e f
  gene1587|gene1587|rna1586|rna1586 244 TDDLNMLIASEKQLEGKKRkY--LGTINKLSEDIMrieeEIEGLKAQEEGLRAQITKqKINPEDvkEMNAEKIELF 317
                                        68999*****9**99999843..3455555555444455999*************651555555112334444455 PP

                          Viral_P18 117 kkl 119
                                        k+l
  gene1587|gene1587|rna1586|rna1586 318 KEL 320
                                        655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.8
                          Viral_P18  62 ycGekh...yklsealkdvsddel 82 
                                        yc +k     kl+   k++s++e 
  gene1587|gene1587|rna1586|rna1586 437 YCSDKLvmaGKLYLEKKEISENEQ 460
                                        555554333344544455444443 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.5      0.65     2e+03      56      94 ..     289     328 ..     279     350 .. 0.66
   2 ?   10.3   1.0   0.00028      0.84      22     101 ..     431     510 ..     427     520 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.65
                               Bin3  56 seelkenykelklrpedfeevLleevg.fesveeleekee 94 
                                        +e l++++++ k++ped++e+  e++  f++ e+++ ++e
  gene1587|gene1587|rna1586|rna1586 289 EEGLRAQITKQKINPEDVKEMNAEKIElFKELERMKPEKE 328
                                        4566777788888888888887775431444444443332 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00028
                               Bin3  22 lkrlfkkiyellkpgGvlilEpqewksYkkkkklseelkenykelklrpedfeevLleevgfesveeleekeeesk 97 
                                        l + +k + ++l   G+l lE +e ++ +++k+++e    + + lkl+ e+ +++L++e ++++ + + +++ +s 
  gene1587|gene1587|rna1586|rna1586 431 LNSRLKYCSDKLVMAGKLYLEKKEISENEQRKSKTEMELLENELLKLNLESNTSLLMSEQKLQKAKIVLDRTLNSI 506
                                        7788999********************9988888777666668899999999*****9999998887765555544 PP

                               Bin3  98 gfkR 101
                                         ++R
  gene1587|gene1587|rna1586|rna1586 507 NYER 510
                                        5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1435  (0.0800379); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.86u 0.31s 00:00:01.17 Elapsed: 00:00:00.55
# Mc/sec: 2985.74
//
Query:       gene1588|gene1588|rna1587|rna1587  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.9e-101  338.0   0.0   2.2e-101  337.7   0.0    1.0  1  Fibrillarin  Fibrillarin
     0.0049   16.6   0.0     0.0079   15.9   0.0    1.3  1  GCD14        tRNA methyltransferase complex GCD14 subunit
  ------ inclusion threshold ------
      0.053   13.3   0.1      0.082   12.6   0.1    1.2  1  PCMT         Protein-L-isoaspartate(D-aspartate) O-methyltran


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.7   0.0  3.7e-105  2.2e-101       1     224 [.      49     275 ..      49     277 .. 0.99

  Alignments for each domain:
  == domain 1  score: 337.7 bits;  conditional E-value: 3.7e-105
                                        EEEECSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTE....EEEEE-TTTSHHHHHHHTT-S--S--TTS CS
                        Fibrillarin   1 veeheklegvyivkekgdarlatknlvpgekvYgEklikveee....EyRvWnpfrsKlaaailkglkelpikkgs 72 
                                        +e+h+++ gvy+ ++k+d  l+t++lvpg++vYgE++i+ve e    EyRvWn +rsKlaa+i+ g+++++i +gs
  gene1588|gene1588|rna1587|rna1587  49 IEPHKRFPGVYVGRGKEDL-LLTRSLVPGTSVYGERRISVEVEgekvEYRVWNVYRSKLAAGIVCGVENIHIGPGS 123
                                        689*************999.*******************99988899***************************** PP

                                        EEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEES CS
                        Fibrillarin  73 kvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDv 148
                                        kvLYlGa+sGttvsHvsDivg++g+vyavefs+r++r+li+++ kR nivPi+eDAr+P++Yr+lv+ vD+if+Dv
  gene1588|gene1588|rna1587|rna1587 124 KVLYLGASSGTTVSHVSDIVGKDGMVYAVEFSERSGRDLINMSMKRANIVPIIEDARHPSRYRMLVPIVDCIFSDV 199
                                        **************************************************************************** PP

                                        SSTTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEE CS
                        Fibrillarin 149 aqpdqarilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgky 224
                                        +qpdq+ri+a+na++flkegg + +sika+++++   +e+vf++ev+ l+++++k+ eqv+lep+ekdha++vgk+
  gene1588|gene1588|rna1587|rna1587 200 SQPDQTRIVALNAQYFLKEGGGVDVSIKANCVNSSIPAETVFADEVNILRKSNIKPREQVTLEPFEKDHAMIVGKF 275
                                        *************************************************************************986 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-06    0.0079      33     127 ..     114     205 ..      92     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                              GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsq.lvtvthrDvckeGfd 107
                                        + ++++ pGs+v+  G+ sg+  + ++  v+  G ++++ef e+  +     + +  ++  ++     D+ +    
  gene1588|gene1588|rna1587|rna1587 114 VENIHIGPGSKVLYLGASSGTTVSHVSDIVGKDGMVYAVEFSERSGRD----LINMSMKRaNIVPIIEDARHPSRY 185
                                        578999****************99*****************8765433....333334332333344566655554 PP

                              GCD14 108 eevsgkvDavfLDlPaPwea 127
                                        + +   vD++f D+ +P++ 
  gene1588|gene1588|rna1587|rna1587 186 RMLVPIVDCIFSDVSQPDQT 205
                                        667799*********99976 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.4e-05     0.082      66     108 ..     114     156 ..     100     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                        HHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBH CS
                               PCMT  66 lellelkkgarvLevGsGsGyltavlarlvgekgrvvsierik 108
                                        +e +++ +g++vL +G+ sG     ++ +vg++g v ++e ++
  gene1588|gene1588|rna1587|rna1587 114 VENIHIGPGSKVLYLGASSGTTVSHVSDIVGKDGMVYAVEFSE 156
                                        5678899********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1822.76
//
Query:       gene1589|gene1589|rna1588|rna1588  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-30  105.6   6.4    4.2e-30  104.9   0.0    2.5  3  Ribosomal_L28e  Ribosomal L28e protein family
    3.2e-05   24.5   8.2    3.2e-05   24.5   8.2    2.1  2  Mak16           Mak16 protein C-terminal region
  ------ inclusion threshold ------
      0.035   14.1   0.5      0.056   13.5   0.5    1.3  1  MtlR            Mannitol repressor
      0.052   13.6   1.4      0.052   13.6   1.4    2.3  3  ORF6C           ORF6C domain


Domain annotation for each model (and alignments):
>> Ribosomal_L28e  Ribosomal L28e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   9.3e-34   4.2e-30       2     115 .]       6     118 ..       6     118 .. 0.94
   2 ?   -2.1   0.1       1.4   6.2e+03      61      89 ..     136     151 ..     126     163 .. 0.42
   3 ?    3.5   0.8     0.025   1.1e+02      76     111 ..     194     230 ..     173     231 .. 0.69

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 9.3e-34
                     Ribosomal_L28e   2 iWelvrnnn..sFlvktrtsnkqtFsrepyNltglhsrkysglanskavtVreekkgvvlvtkkkerahkpakawe 75 
                                        iW  +      sF++kt+   + t++r+++N+tg+++r +++lansk++tVr+ ++++ l++k++er h p+ a+e
  gene1589|gene1589|rna1588|rna1588   6 IWRNIGGDGycSFKMKTE---EDTLCRNQNNVTGICNRFSCPLANSKYATVRAVGEELSLFVKEPERVHIPRDAYE 78 
                                        67888666688*****54...599**************************************************** PP

                     Ribosomal_L28e  76 kvklsknsrkalkqiakllkkyrpdlrkaalaRlskitqs 115
                                        ++kls+n+++alkqi+++l+  +++++++++++lsk+tq+
  gene1589|gene1589|rna1588|rna1588  79 EIKLSSNYEEALKQIEENLEFWDEKIIHKCKQKLSKLTQY 118
                                        *******************977****************96 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                     Ribosomal_L28e  61 tkkkerahkpakawekvkls.knsrkalkq 89 
                                         kk               ++ +++ +alk+
  gene1589|gene1589|rna1588|rna1588 136 RKKR--------------MNrREKLRALKT 151
                                        2222..............222222222222 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.025
                     Ribosomal_L28e  76 kvkls.knsrkalkqiakllkkyrpdlrkaalaRlsk 111
                                        k++ + k + + +++ ++ +++ ++d++k+a++++++
  gene1589|gene1589|rna1588|rna1588 194 KKQNRkKRYVADIEESDTMFEAEPRDIKKKAKKKATM 230
                                        33333344444566666667878***********985 PP

>> Mak16  Mak16 protein C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       0.7   3.2e+03      47      58 ..      84      95 ..      71     132 .. 0.58
   2 !   24.5   8.2   7.2e-09   3.2e-05       1      71 [.     137     207 ..     137     230 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.7
                              Mak16 47 kafkkvlekeee 58
                                       + ++++l+++ee
  gene1589|gene1589|rna1588|rna1588 84 SNYEEALKQIEE 95
                                       445555655542 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 7.2e-09
                              Mak16   1 kkKverRekrReeKAlaAAklekaIekeLleRLksgaYgdiynveekafkkvlekeeeeeeeeeeeeeeee 71 
                                        kk+++rRek R  K l   + ek+I  eL+ RL+sg+Yg  ++ + +  +++  ++e+++++++    + e
  gene1589|gene1589|rna1588|rna1588 137 KKRMNRREKLRALKTLNKINFEKNIGDELMLRLESGIYGTELKDRFHLANEAAVEREKKQNRKKRYVADIE 207
                                        699************************************97776666666555444322222222222211 PP

>> MtlR  Mannitol repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   1.3e-05     0.056      75     147 ..      72     145 ..      71     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                               MtlR  75 iskevyeDielfiqlkeelnedekeyeFsddeildfik.elhlvsekslleleeekeeed.dsllyqlqqqryeq 147
                                        i +++ye i+l ++ +e l++ e+++eF d++i++  k +l+ +++  l +le  ke+   + ++ + + +r+e+
  gene1589|gene1589|rna1588|rna1588  72 IPRDAYEEIKLSSNYEEALKQIEENLEFWDEKIIHKCKqKLSKLTQ-YLRRLEYFKEHGRtEYMVRKKRMNRREK 145
                                        7899***************************999877615666665.4455555444443355555555566665 PP

>> ORF6C  ORF6C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.63   2.8e+03      92     102 ..      84      94 ..      74     102 .. 0.56
   2 ?   -0.6   0.3       0.3   1.4e+03      22      22 ..     103     103 ..      80     159 .. 0.67
   3 ?   13.6   1.4   1.1e-05     0.052       3      49 ..     183     229 ..     181     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.63
                              ORF6C  92 kdfdkAlefie 102
                                        +++++Al+ ie
  gene1589|gene1589|rna1588|rna1588  84 SNYEEALKQIE 94 
                                        35555555554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.3
                              ORF6C  22 r 22 
                                        +
  gene1589|gene1589|rna1588|rna1588 103 K 103
                                        2 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 1.1e-05
                              ORF6C   3 elllealkehdekieeidervkkLeenmpldesekeeiqkkvkkkvv 49 
                                         l+ ea+ e ++k+++ +  v+++ee+ +++e+e ++i+kk+kkk +
  gene1589|gene1589|rna1588|rna1588 183 HLANEAAVEREKKQNRKKRYVADIEESDTMFEAEPRDIKKKAKKKAT 229
                                        68899***************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1584  (0.0883485); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1340.50
//
Query:       gene1590|gene1590|rna1589|rna1589  [L=237]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-38  132.0   2.3    5.6e-38  131.0   2.3    1.4  1  LUC7      LUC7 N_terminus


Domain annotation for each model (and alignments):
>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.0   2.3   3.1e-42   5.6e-38       1     236 [.       3     216 ..       3     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 131.0 bits;  conditional E-value: 3.1e-42
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXX-EEE--S--SSS-S--SSSS-S-EEEGGGHH.HHHHHHHHHHHHHH-XX CS
                               LUC7   1 daaralLdeLmGrnrnlapsekkkkvnfedpevCksylvkfCphdlfinTkadlGpCk.kiHdeelkeeYeearks 75 
                                        d ar++Ld L+G +r+  +  k+ +     ++vC + lv+fCp +lf+nT++ +G+Ck + H+e  k+eY++  k+
  gene1590|gene1590|rna1589|rna1589   3 DRAREVLDMLLGPDRDIYDPGKSFS---AKKDVCIYMLVSFCPFELFRNTRKSIGKCKyNNHEEYYKAEYNRGGKE 75 
                                        789*************999866654...6899*************************9889************666 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               LUC7  76 kkklgyeeeflrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelgeeGkV 151
                                         +  +ye eflr l ++   v+  i++++   e++ +      +       +++e ee  +k+ +++e+lg+eG+V
  gene1590|gene1590|rna1589|rna1589  76 -RYEEYEWEFLRLLVEIALRVQDEIREQN--SENMVDV-----SL----LGKIQEKEEVFNKMYQDIERLGMEGNV 139
                                        .559**********999999888887533..3333333.....33....6789999******************** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               LUC7 152 deaqklmkeveelkeekeeleqqyeaaaaneeseasqekkmkvCeiCGaflivgDaqqRiedHlmGKqHlGyaklr 227
                                        +ea + ++e+e+++ee e++++ y          +s+   m+ C +CG  l+ +D++ +i +Hl+G++H G+ ++r
  gene1590|gene1590|rna1589|rna1589 140 EEAWHSFNECEKVREELERIKEAYY--------VKSNGVGMEKCTVCGVNLVLSDTDAKISRHLNGRLHRGHLRVR 207
                                        ********************97774........5688889************************************ PP

                                        XXXXXXX.. CS
                               LUC7 228 ealeelkek 236
                                        ++l el ek
  gene1590|gene1590|rna1589|rna1589 208 NKLGELLEK 216
                                        ***999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1525.09
//
Query:       gene159|gene159|rna159|rna159  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-14   53.5   0.0    6.1e-14   52.5   0.0    1.5  1  Plus-3    Plus-3 domain
  ------ inclusion threshold ------
        1.7    9.1   7.5       0.16   12.5   2.1    1.9  2  DUF3752   Protein of unknown function (DUF3752)


Domain annotation for each model (and alignments):
>> Plus-3  Plus-3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   6.8e-18   6.1e-14       2     104 ..      84     178 ..      83     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 6.8e-18
                         Plus-3   2 lnkirlsRskleklleepffedavkgcfvRvkigeeretgqpvyrlaqivgvkeeekgkpykl..kkgkkttnkylklrh 79 
                                    ++++ ++R+++++ +++pff+d+v g f R +i+         y +++ivgv    kg  y+l  ++++ +tn yl+++ 
  gene159|gene159|rna159|rna159  84 FSQCIVTRDMIARNVFKPFFDDFV-GHFTRARIN-------GLYLVVKIVGV-G--KGDVYSLwiDRNEIKTNRYLDIST 152
                                    679*******************97.9*******9.......38*********.5..899****95447999********* PP

                         Plus-3  80 gkse.ksfrlekvSnspfteeEferw 104
                                    g+++ k+fr+e++Snsp  +eE+e+ 
  gene159|gene159|rna159|rna159 153 GTRTyKNFRIENISNSPLLREEYEDV 178
                                    *666699****************985 PP

>> DUF3752  Protein of unknown function (DUF3752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.1   1.8e-05      0.16      68     132 ..      14      88 ..       2      96 .. 0.79
   2 ?   -1.2   0.3       0.3   2.7e+03      68      86 ..     243     261 ..     194     267 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                        DUF3752  68 akekkreeeetaekvkeynekkRgksLveehqekkkkkkkk..........eeeeddpskraFDrekDmalgrri 132
                                     +e+  e+ee+++++ e+ e+kR + L+++h+e +k k+kk          ++     +++++D ++ m+ ++ i
  gene159|gene159|rna159|rna159  14 DREELYESEEDKRALLEMPETKREEILYKRHAELQKFKEKKeleekmmglkKKAPSVTKEKIYDTDNFMEFSQCI 88 
                                    4556667799************************99988888989998876666667778888888888876655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.3
                        DUF3752  68 akekkreeeetaekvkeyn 86 
                                    + ++k+++ e ++k++e  
  gene159|gene159|rna159|rna159 243 ELKDKKAAMEYQKKIEEIE 261
                                    2222333344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1479  (0.0824921); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1827.15
//
Query:       gene1591|gene1591|rna1590|rna1590  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2370.82
//
Query:       gene1592|gene1592|rna1591|rna1591  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0013   19.1  14.0      0.002   18.5  14.0    1.3  1  Got1      Got1/Sft2-like family


Domain annotation for each model (and alignments):
>> Got1  Got1/Sft2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  14.0   1.1e-07     0.002       8     111 ..      14     106 ..       7     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-07
                               Got1   8 s....llglpllflkprkFallytlGnilflastafLiGpkkqlkkmfskerliativyllsllltLyaalvlkst 79 
                                        +    l+g +ll++     ++l+  Gn+l+++++++L    k+  +++++e++ + +++++++l+ +y ++     
  gene1592|gene1592|rna1591|rna1591  14 GmfvfLVGGILLMD-----RALMISGNLLIIIGISLLARS-KM-FTLLRPEKIQGMVIFVVAVLFLIY-GFL---- 77 
                                        33344556677888.....899*************99754.45.55*******************999.776.... PP

                               Got1  80 lltllfvivqllallwyllsyiPggrsalkkv 111
                                            +++++++l+l+ +l + iP+ r++l+++
  gene1592|gene1592|rna1591|rna1591  78 ---AFGFLLEILGLFLLLRDNIPTFRAVLRTL 106
                                        ...8************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 779.21
//
Query:       gene1593|gene1593|rna1592|rna1592  [L=600]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-40  137.6   0.0      1e-39  137.2   0.0    1.2  1  DAO            FAD dependent oxidoreductase
    2.2e-26   92.2   0.0    3.9e-26   91.4   0.0    1.4  1  DAO_C          C-terminal domain of alpha-glycerophosphate ox
    7.3e-08   31.9   3.5     0.0016   17.6   1.2    2.1  2  FAD_binding_2  FAD binding domain
     0.0023   17.2   0.1     0.0043   16.3   0.1    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0026   17.1   0.9     0.0035   16.6   0.1    1.5  2  Thi4           Thi4 family
     0.0038   16.6   2.9     0.0038   16.6   2.9    2.0  3  FAD_oxidored   FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.018   15.2   0.2       0.15   12.3   0.5    2.2  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.025   13.7   3.2      0.071   12.2   0.4    2.2  2  GIDA           Glucose inhibited division protein A
      0.091   11.5   0.6       0.15   10.7   0.6    1.3  1  HI0933_like    HI0933-like protein


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.0     5e-43     1e-39       1     351 [.      44     407 ..      44     408 .. 0.76

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 5e-43
                                        EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH.....HHHHHHHHHHHHHH CS
                                DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeas.....elarlslealeelr 69 
                                        d+vi+GGG +G+++A++ a+rg  V+l+e+  ++gsg+S+++++l+h+g+ryl++a       ++rl+ +al+e+ 
  gene1593|gene1593|rna1592|rna1592  44 DLVIVGGGSTGAGCALDGATRGlkVALVEAL-DFGSGTSSKSTKLVHGGVRYLASAVsnldwSQYRLVWQALDERS 118
                                        89****************************9.9999***************9**8778999966699999999998 PP

                                        HHHHHHSSTTSEEEEEEEEEESSH....HHHHHHHHHHHHH....HHTTTTEEEEEHHHHHHHSTT..STTTSEEE CS
                                DAO  70 eleeelgididyrrtGllslaade....eelealdkllall....leagldaelldaeevrelepa..lpgllgal 135
                                         + +   + +    + l++++ ++        +l kl++ +    +++g +++++ ++e+ +++p+   ++l+ga+
  gene1593|gene1593|rna1592|rna1592 119 TMFKI-SPYLTNSIKILVPIY-SRilipYYYLGL-KLYD-WisglKSLG-KSYFIGRKEAIDVFPHvnKKNLCGAM 189
                                        88877.332323333333332.221111011122.2222.234425444.5679***99******97443999*** PP

                                        EETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEE..EEE--GGGHHHH CS
                                DAO 136 fypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttp.gendaada..vVnaaGawsdll 207
                                        +y d gq d+ +    l  +a  +G+  +++  v +l  e+gk++gv+ r++  g + +++   v+n++G ++d l
  gene1593|gene1593|rna1592|rna1592 190 VYFD-GQQDDVRNNVMLVMTAVYHGAVAVNYLSVNSLVTEEGKITGVRcRDSItGFEIEIKSagVINSTGNFADGL 264
                                        ****.777****************************98889******99444445553345579**********77 PP

                                        .HTT.CTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCS CS
                                DAO 208 .gll.keldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevd 281
                                         ++  ++ +  + +  g+++v+ p++ ++ +   ++ +p  + d+r  +++p+  g++lvG+t+++ +++ +p+++
  gene1593|gene1593|rna1592|rna1592 265 rKMNdGNAKEIMIQSSGTHIVI-PKEYAPKE--MGFLDP-LTGDNRIAFFMPWM-GKTLVGSTDVKSKNEASPSPT 335
                                        566665555566999*******.76664433..566666.8888999******8.99*******88888888**** PP

                                        HHHHHHHHHHHHHHS...GGG..CGEEEEEEEEEEETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                                DAO 282 eedidellealrklf...Pql..gdvlrkwaGlrplpdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                         ed++ l +++r++    P+l  ++v+  w+G+rpl+ +  +   +++v+ +++   ++ +Gl + ++ Gk++ +
  gene1593|gene1593|rna1592|rna1592 336 KEDLEFLVHEVRAYTsqnPNLkkDEVSAIWTGIRPLVKDVEVSETSSIVRKHFVQ--AEKNGLLTVTG-GKWTIY 407
                                        ***************555554447799********75444443333345544544..35688888888.888765 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.0   1.9e-29   3.9e-26       1     126 []     430     551 ..     430     551 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 1.9e-29
                                        --TTS---TT--.......TT-STTHT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HHHHHHHHH CS
                              DAO_C   1 crTkklpLvGaenwsknlaaelaqeygldeevaehLaerYGsraeevlelakedekpelaerlspelpyieaevvY 76 
                                        c+Tk ++++Ga+++ ++++++++++++++++va++L++ YG++a ++ ++ k+d+    ++ ls ++ y   ev+Y
  gene1593|gene1593|rna1592|rna1592 430 CVTKYVQILGANGYGEDTWISVQKKLNVPKDVAKRLVRFYGTNALKLSKYIKKDR----KKLLSVKYSYFSEEVEY 501
                                        9***********************************************9999887....79*************** PP

                                        HHHHS---SHHHHHHTTS-HHHH-HHHHHHHHHHHHHHHHHHTT--HHHH CS
                              DAO_C  77 avrhEmartlvDvlaRRtrlafldadaalealpevaelmaeelgWdearr 126
                                        ++++Ema+++ Dvl  R+ + ++d+++a  ++++v+e++++++gWd++r+
  gene1593|gene1593|rna1592|rna1592 502 CIDNEMAVRICDVLCNRLMIGLMDVKEAYGCIEKVLETFKRKHGWDADRC 551
                                        **********************************************9985 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.2   8.3e-07    0.0016       1      41 [.      44      84 ..      44     107 .. 0.88
   2 !   14.6   0.0   6.8e-06     0.013     160     208 ..     218     265 ..     201     287 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.3e-07
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG- CS
                      FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggataws 41
                                       D++++G+G  G  +Al  a +Glkva+ve  +  +g++  s
  gene1593|gene1593|rna1592|rna1592 44 DLVIVGGGSTGAGCALDGATRGLKVALVEALDFGSGTSSKS 84
                                       89****************************99877776655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.8e-06
                                        ESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.... CS
                      FAD_binding_2 160 erteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallk 208
                                        + +++++L++e+g++tG+ ++++ +g e +i++ +v+  tg+f    l+
  gene1593|gene1593|rna1592|rna1592 218 NYLSVNSLVTEEGKITGVRCRDSITGFEIEIKSAGVINSTGNFAD-GLR 265
                                        55789**************************************95.333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   2.1e-06    0.0043       1      31 [.      43      76 ..      43     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                        Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlve...l 31
                                       +d+v++GgG  G  +al+ a+ g+kv+lve    
  gene1593|gene1593|rna1592|rna1592 43 FDLVIVGGGSTGAGCALDGATRGLKVALVEaldF 76
                                       589**************************75440 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.8e-06    0.0035       8      57 ..      33      80 ..      28      89 .. 0.84
   2 ?   -4.0   0.1       3.5     7e+03     112     135 ..     213     235 ..     202     241 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                               Thi4  8 yfedllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                       ++ + l+    D+vivG+Gs+G  +a   a++ +lkva++e+ + +G G+
  gene1593|gene1593|rna1592|rna1592 33 AMMERLESETFDLVIVGGGSTGAGCALDGATR-GLKVALVEA-LDFGSGT 80
                                       55566667788********************9.*******96.7888776 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.5
                                        TEEEEESEEEEEEEEETBTEEEEE CS
                               Thi4 112 nvkllnavaveDlivregegvaGv 135
                                        ++  +n ++v+ l++ e  +++Gv
  gene1593|gene1593|rna1592|rna1592 213 GAVAVNYLSVNSLVTEE-GKITGV 235
                                        55567888888888888.678877 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.9   1.9e-06    0.0038       1      38 [.      44      81 ..      44     100 .. 0.89
   2 ?   -0.6   0.0      0.32   6.4e+02     110     144 ..     222     258 ..     193     263 .. 0.75
   3 ?   -3.9   0.0       3.2   6.3e+03     213     271 ..     336     390 ..     277     395 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.9e-06
                       FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                       D+v+vGGg+ G  +A+  a +G kv+Lve  ++  G++
  gene1593|gene1593|rna1592|rna1592 44 DLVIVGGGSTGAGCALDGATRGLKVALVEALDFGSGTS 81
                                       99***************************988765555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.32
                       FAD_oxidored 110 lvevekegkriesvtveske.g.rktirAkvfiDATg 144
                                        + + ++e+++i++v+++++  g +++i++  +i +Tg
  gene1593|gene1593|rna1592|rna1592 222 VNSLVTEEGKITGVRCRDSItGfEIEIKSAGVINSTG 258
                                        3455556679******9999999******99999998 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.2
                       FAD_oxidored 213 pegydparyelarvfeaklskgklpgektdvnwprvstdli.enldlpeaeyegreqire 271
                                        +e+++    e  r ++   ++++l+++ +   w+  ++ ++ + ++++e++   r+++++
  gene1593|gene1593|rna1592|rna1592 336 KEDLEFLVHEV-RAYTS--QNPNLKKDEVSAIWT--GIRPLvKDVEVSETSSIVRKHFVQ 390
                                        22222222222.33333..444455444444442..677777777777777777777764 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   7.7e-05      0.15       1      65 [.      47     114 ..      47     116 .. 0.72
   2 ?   -0.7   0.0      0.84   1.7e+03      31      66 ..     400     436 ..     398     438 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                                        EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE...TTCEECTS---EEETTHHHHCHHHH CS
                      NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev...pgvrvdygahifhgsgyypnvrrll 65 
                                        IvG+G +G+ +A   a +g++v l+e+ d  +G ++  +    +gvr+   a    ++++y+ v++ l
  gene1593|gene1593|rna1592|rna1592  47 IVGGGSTGAGCALDGATRGLKVALVEALDFGSGTSSKSTKlvhGGVRYLASAVSNLDWSQYRLVWQAL 114
                                        9**************************98866766655444645666444444444556677776665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.84
                                        SSGGG-EECE.TTCEECTS---EEETTHHHHCHHHHC CS
                      NAD_binding_8  31 lGGraasyev.pgvrvdygahifhgsgyypnvrrllr 66 
                                        +GG+++ y+   + ++d+ +++f    + p v+++++
  gene1593|gene1593|rna1592|rna1592 400 TGGKWTIYRKiAEDAIDLAVSTFSLKPKGPCVTKYVQ 436
                                        799999998878899*******966556788887776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   3.6e-05     0.071       1      28 [.      44      71 ..      44     107 .. 0.84
   2 ?    1.8   0.2     0.052     1e+02     111     159 ..     215     268 ..     198     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                               GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                       d++++GgG  G  +Al  a +G+kv+L+
  gene1593|gene1593|rna1592|rna1592 44 DLVIVGGGSTGAGCALDGATRGLKVALV 71
                                       689************************9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.052
                                        EEEEES-EEEEEECTTEEEEEEETT.....S-EEEECEEEE--TT-BT-EEEET CS
                               GIDA 111 leiieeeveeliveekkvkgvvted.....getikakavviatGtflkgkihig 159
                                        + +   +v++l++ee+k++gv+ +d     + +ik+  v+ +tG f +g   + 
  gene1593|gene1593|rna1592|rna1592 215 VAVNYLSVNSLVTEEGKITGVRCRDsitgfEIEIKSAGVINSTGNFADGLRKMN 268
                                        566667899999999*****987762221145677889*******999876554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6   7.5e-05      0.15       2      31 ..      44      73 ..      43      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.5e-05
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                        HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                       d++++GgG  G  +A+  a+rg +V+l+e+
  gene1593|gene1593|rna1592|rna1592 44 DLVIVGGGSTGAGCALDGATRGLKVALVEA 73
                                       89**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.95
# Mc/sec: 1911.30
//
Query:       gene1594|gene1594|rna1593|rna1593  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-05   25.1   2.2    0.00015   21.5   0.1    2.2  2  RabGAP-TBC  Rab-GTPase-TBC domain


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   8.3e-09   0.00015      31     107 ..      16      91 ..       7      94 .. 0.82
   2 !    3.2   0.3    0.0033        60     127     195 ..     151     221 ..     143     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.3e-09
                         RabGAP-TBC  31 sekeksklekseeskelsqIkkDvprtfpesesfknkqgqnqLeriLkaysiynpevgYcqGmndivaplllvsld 106
                                        + +++++ + +++ +e + I++Dv rt      +k+ ++ + L+++L++     p + Y+qGm+ +++++ l++ +
  gene1594|gene1594|rna1593|rna1593  16 KTEDDEYVSVERDYNERRVIENDVRRTELLGVDKKDYKMVKFLKKLLFVELDKIP-IRYTQGMSEVASVFVLYYFQ 90 
                                        3445555666777788999********99447778889*********99888888.***************99987 PP

                         RabGAP-TBC 107 e 107
                                        e
  gene1594|gene1594|rna1593|rna1593  91 E 91 
                                        6 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0033
                         RabGAP-TBC 127 ytsslpg.lkrklkvleellkkkdpklykh.lkeegldlelfaikwfltlflrefp.letvlrlwDlllege 195
                                        ++ +l+  +  ++k+ +e +k++ +   k  +k  +l+++ f +  +lt flr+++ +e v ++++++l  +
  gene1594|gene1594|rna1593|rna1593 151 FKRKLEPlVTDDFKIYKENMKIFVEMMKKRgIKIPELESYKF-MGSILTFFLRNLSkIEDVHKVFEIILSCP 221
                                        555543337778888888888888888888666677766655.56788888877652699999999888433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1949.27
//
Query:       gene1595|gene1595|rna1594|rna1594  [L=623]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-85  287.6   0.0    1.6e-85  287.3   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.3   0.0     9e-90   1.6e-85      18     422 ..      55     504 ..      37     505 .. 0.82

  Alignments for each domain:
  == domain 1  score: 287.3 bits;  conditional E-value: 9e-90
                                        CSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHH CS
                        AMP-binding  18 gegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayileds 93 
                                        ge    + +e+++ ++++A+ + +   +++d+V+i++ n++ew+v+ +a  + G++ vpl++t+++e ++ ile++
  gene1595|gene1595|rna1594|rna1594  55 GEVVYRSANEVWKDAESIARLIGQ-MTEPKDTVGIYSVNRYEWIVTEMASYMCGCTNVPLYSTFSPENVQLILEET 129
                                        566667889***********9987.89************************************************* PP

                                        TESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS......-TSCCCS-BTTSEE CS
                        AMP-binding  94 eakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae......kpeeeeelkpddla 162
                                        ++kv++   ++++  + l+++ +k  + ++v+++d+de  +e+ +++   ++  ++      +  +e+ ++ ddla
  gene1595|gene1595|rna1594|rna1594 130 GMKVCV--ASADKaRQLLDSVLEKGGKLSCVVLMDRDEEVRERLENAGIRTYYFEDaaslsgEVGKERYPSGDDLA 203
                                        ******..66666678888888888999********99998866665555544432678888444556789***** PP

                                        EEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE- CS
                        AMP-binding 163 yiiYTSGTTGkPKGVmlshrnlvanvaslk..letr..fklkeddvvlsilplahifglilelllallsGatvvll 234
                                        +i+YTSGT GkPKGVml+h+n+++ va +    ++r   +l++ddv+ls+lplah+++  ++++++++ G+++v++
  gene1595|gene1595|rna1594|rna1594 204 TICYTSGTSGKPKGVMLTHKNFISGVAGVFrgSNERemVRLSRDDVYLSYLPLAHVMER-ICVNISVAYGCKIVFF 278
                                        ****************************988533334444666***************6.**************** PP

                                        TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHC.............................. CS
                        AMP-binding 235 pkdaaldpklllelieklkvtviagvPrvleallesgalkaakkak.............................. 280
                                        +++++     ++e+    k+t+i +vPrvl+ + e+ +++  +++k                              
  gene1595|gene1595|rna1594|rna1594 279 RGNSK----EIKEDYLIVKPTFIISVPRVLNLFKEKIEEN--VRQKnilvrgifraslwykkwrvsrgelrnrlld 348
                                        *9987....356888889***************5543333..2222344555566666666666666666666666 PP

                                        .........CGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTE CS
                        AMP-binding 281 .........dlss.lrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgv 346
                                                 ++++ + +vl+g +pl +e+l  ++a++ +++++gYG+TE+ g  + ++ + d+     vG p+p +
  gene1595|gene1595|rna1594|rna1594 349 wlvfdkvskEFGGrIGQVLCGSAPLKKEVLVYMQAVLSCRIFQGYGQTENVGTGI-VQ-PLDCYLYDNVGIPFPSN 422
                                        666655555666666669************************************9.77.566678999******** PP

                                        EEEEE-TTTSCBEE......TTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETT.SEEEEEE CS
                        AMP-binding 347 evkivDeetgepvp......dgee.GellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrlded.Gyleivg 414
                                        evk+ + + ge+        +  + Ge+l+rg +v++gY+k+p++t e f+ +++wlrTGD+g +d+d G + ++g
  gene1595|gene1595|rna1594|rna1594 423 EVKLGEIS-GELKSeygrryPSCKiGEILLRGDNVTQGYFKRPSETLELFT-SDGWLRTGDIGMFDTDtGMFSVIG 496
                                        ****9887.6666455555533336*************************9.757**********9888******* PP

                                        ECCCEEEE CS
                        AMP-binding 415 Rkkdlikl 422
                                        R kd +k+
  gene1595|gene1595|rna1594|rna1594 497 RVKDGFKT 504
                                        ****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3778.80
//
Query:       gene1596|gene1596|rna1595|rna1595  [L=643]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-32  109.8   0.0    1.6e-31  108.8   0.0    1.5  1  Beta-Casp        Beta-Casp domain
    7.7e-23   80.9   0.0    1.8e-22   79.7   0.0    1.7  1  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
    2.3e-19   70.2   0.1    3.7e-19   69.5   0.1    1.3  1  Lactamase_B      Metallo-beta-lactamase superfamily
      1e-15   57.4   0.1    2.3e-15   56.2   0.1    1.6  1  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
      8e-11   41.8   0.1    2.9e-10   40.0   0.1    1.8  2  Lactamase_B_2    Beta-lactamase superfamily domain
    3.7e-07   29.9   0.2    7.3e-07   28.9   0.2    1.4  1  CPSF73-100_C     Pre-mRNA 3'-end-processing endonuclease poly
    4.6e-07   29.3   0.0    1.1e-06   28.1   0.0    1.5  1  Beta_lactamase3  Putative beta-lactamase-like family
    7.2e-05   22.7   0.0    0.00021   21.3   0.0    1.7  1  Lactamase_B_3    Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   7.3e-35   1.6e-31       1     110 []     241     362 ..     241     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 7.3e-35
                                        HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGGE-SHH....HHH.H..HH............... CS
                          Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyaeveakslewmesk.keeln............... 60 
                                        aqell++Lee+w+++ +  +k+piy++s la++++ vY++y       + +m+++ ++ l+               
  gene1596|gene1596|rna1595|rna1595 241 AQELLLILEEHWNSNTS-LQKIPIYYASALAKRCMGVYQTY-------IGMMNERiQK-LSlvrnpfafkyvknlk 307
                                        7***********99773.3459*******************.......9999999754.3345889999******* PP

                                        .....HS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                          Beta-Casp  61 .....sskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                             +++gp+vi+as+gml++G sr+l++++++d++n+vi++gy++ gTl++++
  gene1596|gene1596|rna1595|rna1595 308 gidsfDDEGPCVIMASPGMLQSGLSRDLFERWCSDSKNAVIIPGYCVDGTLAKEI 362
                                        *****889********************************************986 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.0   8.2e-26   1.8e-22       1     189 [.      24     199 ..      24     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 8.2e-26
                      Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekv.iptvdliLLshatlehlGayallyakfksklllnipvyatlpv 75 
                                        ++e  + +i+lD+G++        +l +l+ v ++++d+i ++h  l+h +a+++l  k       + +vy t+p+
  gene1596|gene1596|rna1595|rna1595  24 IVECGGRTIMLDCGVHPAYT-GVASLPFLDLVdLSKIDAIFITHFHLDHAAALPFLTEKT----SFKGKVYMTHPT 94 
                                        5778889*********9755.4567888887668********************999764....3589******** PP

                      Lactamase_B_6  76 vkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkisk 151
                                        +++ + +l d+++  ++    d +  + +d  +++d+i+++ Y+Q++++k    g+ + a+naGh+lG++++ i+ 
  gene1596|gene1596|rna1595|rna1595  95 KAILKWLLNDYIRLINA--ASDADFYTESDLIKCYDRIIPIDYHQEVNVK----GIKVKALNAGHVLGAAMFLIEI 164
                                        *********99886655..466667799******************9988....7********************* PP

                      Lactamase_B_6 152 esekivYavdwnhakeshLngaalldssgkvleqllrp 189
                                        e  k++Y  d++ + ++hL++a+   s+g  ++ l+++
  gene1596|gene1596|rna1595|rna1595 165 EKSKVLYTGDFSREEDRHLKAAE---SPGCKIDGLITE 199
                                        *******************9984...677777777665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.1   1.7e-22   3.7e-19       3     159 ..      17     183 ..      15     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.7e-22
                                        CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                        Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78 
                                        +++ +++++e +g++i+ D+G++++++  a+++++  +++ ++da+++TH+HlDH+++l+ l+e+t ++  ++  +
  gene1596|gene1596|rna1595|rna1595  17 EVGRSCVIVECGGRTIMLDCGVHPAYTGVASLPFLDLVDLSKIDAIFITHFHLDHAAALPFLTEKTSFKGKVYMTH 92 
                                        56789*********************************************************************** PP

                                        HHCCHCHHHHHHHHHCCHH..........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCC CS
                        Lactamase_B  79 apalfmeeaddaasrkgll..........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggk 144
                                          + +  ++  ++ r  +           + +   d  ++ +  +++n+ g++      g++ g+  + +e++  k
  gene1596|gene1596|rna1595|rna1595  93 PTKAILKWLLNDYIRLINAasdadfytesDLIKCYDRIIPIDYHQEVNVKGIKVKALNAGHVLGAAMFLIEIEKSK 168
                                        *********9999998888**********8888888999************************************* PP

                                        EEEECTTTSSHHCCC CS
                        Lactamase_B 145 vlftGDallagetgr 159
                                        vl+tGD++ ++++ +
  gene1596|gene1596|rna1595|rna1595 169 VLYTGDFSREEDRHL 183
                                        ********9988765 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.1     1e-18   2.3e-15       2      58 ..     377     436 ..     376     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1e-18
                              RMMBL   2 ipvkarieeidfSgHadknellelirklkprnvilvHGeeeatsalarllk...eeegid 58 
                                        +++++++e+i+fS+H d+ +  ++i+  +p+++++vHGe +++++l++ ++   e++gi+
  gene1596|gene1596|rna1595|rna1595 377 LRLNMSVEYISFSAHVDFTQNSQFIEECQPKHLFFVHGEMNEMQRLRNVIQqrnEKKGIE 436
                                        5789**********************************************6333555555 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.1   1.3e-13   2.9e-10       1     148 [.      30     180 ..      30     207 .. 0.79
   2 ?   -1.4   0.0      0.62   1.4e+03      39     200 ..     390     413 ..     385     454 .. 0.60

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.3e-13
                                        SEEEES--TT....HHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCC CS
                      Lactamase_B_2   1 rriLiDagpd....lrqq.alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavle 71 
                                        r i +D+g            l+ l     + +l++ida+++th H DH a l++l e +  k ++y +  + a+l+
  gene1596|gene1596|rna1595|rna1595  30 RTIMLDCGVHpaytG--VaSLPFL----DLVDLSKIDAIFITHFHLDHAAALPFLTEKTSFKGKVYMTHPTKAILK 99 
                                        678888888854321..1234444....67789************************4444468999999999777 PP

                                        TTCGHHHCHTT...............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEEC CS
                      Lactamase_B_2  72 anfvylaleee...............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieg 132
                                          +    +  +               +  ++ ++d ++++ ++  g++++a  a h  g          + ++ie 
  gene1596|gene1596|rna1595|rna1595 100 WLLNDYIRLINaasdadfytesdlikCYDRIIPIDYHQEVNVK--GIKVKALNAGHVLGA---------AMFLIEI 164
                                        66554444444477788888889999****************9..899***999999998.........99***** PP

                                        TTEEEEEESS-S---H CS
                      Lactamase_B_2 133 ggkrvyyigDtgyipe 148
                                        ++ +v+y+gD  + ++
  gene1596|gene1596|rna1595|rna1595 165 EKSKVLYTGDFSREED 180
                                        **********986554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.62
                                        --HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE- CS
                      Lactamase_B_2  39 aHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatparhks 114
                                        aH+D +++  ++ e++pk                                                          
  gene1596|gene1596|rna1595|rna1595 390 AHVDFTQNSQFIEECQPK---------------------------------------------------------- 407
                                        455555555555555554.......................................................... PP

                                        -CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTT CS
                      Lactamase_B_2 115 grrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltpeeaveaaad 190
                                                                                                                    
  gene1596|gene1596|rna1595|rna1595   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                                        SSSSEEEEES CS
                      Lactamase_B_2 191 lgakrlvliH 200
                                             l+++H
  gene1596|gene1596|rna1595|rna1595 408 ----HLFFVH 413
                                        ....444444 PP

>> CPSF73-100_C  Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2   3.3e-10   7.3e-07       4     123 ..     469     580 ..     467     610 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.3e-10
                       CPSF73-100_C   4 sGvLVqkdfklsllapeDLre..ytgLstttitqkqrlplsasiellkwaleqlfgdveeleekekkktllvmgcv 77 
                                        +G++V  + ++ + + ++L e  y   +   i ++qr+p++++  llk  l   f +  e+e+         +g+v
  gene1596|gene1596|rna1595|rna1595 469 EGIIVGTEDDIRIYKRDELIEskY---KEMNIYERQRIPYNSTAVLLKQVLMDGFSELVEVESG------FMIGNV 535
                                        689999999999999999988334...445699***************9999999988877654......345*** PP

                       CPSF73-100_C  78 tvrveskgeveleWesnllnDmiADsviavllsvesspasvkrssk 123
                                        +v+++  +ev+leW+s+   D++A s+  ++  +  + +svk s+ 
  gene1596|gene1596|rna1595|rna1595 536 HVKLD-GQEVVLEWKSSYADDVLAISISKMISGIGLKTKSVKLSKM 580
                                        *****.************************************7765 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   4.7e-10   1.1e-06      60     185 ..      58     183 ..      51     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.7e-10
                    Beta_lactamase3  60 nidkifvts...snslgifFlkkdv....piYiTkpvYeqlllrlkellslqvvyeeeeekqdlkiveeidierlk 128
                                         id if+t+     + ++ Fl ++     ++Y+T+p    l+  l+++  l     + ++        e+d+ +  
  gene1596|gene1596|rna1595|rna1595  58 KIDAIFITHfhlDHAAALPFLTEKTsfkgKVYMTHPTKAILKWLLNDYIRLINAASDADF------YTESDLIKCY 127
                                        577777775333345555565554422336999999999999999999999888777777......5688999999 PP

                    Beta_lactamase3 129 rnvkfiryneliyfddltieakaagtflGWvnyllevekkkilayisslslkkklsl 185
                                         +++ i y++ ++++ ++++a  ag  lG  ++l+e+ek k + y+  +s ++   l
  gene1596|gene1596|rna1595|rna1595 128 DRIIPIDYHQEVNVKGIKVKALNAGHVLGAAMFLIEIEKSK-VLYTGDFSREEDRHL 183
                                        9****************************************.999999998876555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   9.2e-08   0.00021       6     125 ..      19     185 ..      17     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 9.2e-08
                      Lactamase_B_3   6 ghnsflletagarilvDPfka..nlgyeppa.......eeaDlvlisqaledHahletlkql.............. 58 
                                        g +++ +e +g +i++D +    ++g++  +        ++D++ i++ + dHa++ +                  
  gene1596|gene1596|rna1595|rna1595  19 GRSCVIVECGGRTIMLDCGVHpaYTGVASLPfldlvdlSKIDAIFITHFHLDHAAALPFLTEktsfkgkvymthpt 94 
                                        89***************985433444444448899999***************99876555467887778887777 PP

                      Lactamase_B_3  59 ................................aenvkvleegeslevggleiravatshdavggsergenngflle 102
                                                                        ++++  ++  ++++v+g++++a ++ h      + g   +fl+e
  gene1596|gene1596|rna1595|rna1595  95 kailkwllndyirlinaasdadfytesdlikcYDRIIPIDYHQEVNVKGIKVKALNAGH------VLG-AAMFLIE 163
                                        77777777555555555444444333333333333333333555666666665555555......666.69***** PP

                      Lactamase_B_3 103 qdgltiyhlGhlahelsseelke 125
                                         ++ ++++ G+ + e ++ +lk+
  gene1596|gene1596|rna1595|rna1595 164 IEKSKVLYTGDFSRE-EDRHLKA 185
                                        ************985.5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4105.73
//
Query:       gene1597|gene1597|rna1596|rna1596  [L=673]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-85  287.3   0.0    2.1e-85  286.9   0.0    1.1  1  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.9   0.0   1.1e-89   2.1e-85      18     422 ..     105     554 ..      87     555 .. 0.82

  Alignments for each domain:
  == domain 1  score: 286.9 bits;  conditional E-value: 1.1e-89
                                        CSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHH CS
                        AMP-binding  18 gegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayileds 93 
                                        ge    + +e+++ ++++A+ + +   +++d+V+i++ n++ew+v+ +a  + G++ vpl++t+++e ++ ile++
  gene1597|gene1597|rna1596|rna1596 105 GEVVYRSANEVWKDAESIARLIGQ-MTEPKDTVGIYSVNRYEWIVTEMASYMCGCTNVPLYSTFSPENVQLILEET 179
                                        566667889***********9987.89************************************************* PP

                                        TESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS......-TSCCCS-BTTSEE CS
                        AMP-binding  94 eakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae......kpeeeeelkpddla 162
                                        ++kv++   ++++  + l+++ +k  + ++v+++d+de  +e+ +++   ++  ++      +  +e+ ++ ddla
  gene1597|gene1597|rna1596|rna1596 180 GMKVCV--ASADKaRQLLDSVLEKGGKLSCVVLMDRDEEVRERLENAGIRTYYFEDaaslsgEVGKERYPSGDDLA 253
                                        ******..66666678888888888999********99998866665555544432678888444556789***** PP

                                        EEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE- CS
                        AMP-binding 163 yiiYTSGTTGkPKGVmlshrnlvanvaslk..letr..fklkeddvvlsilplahifglilelllallsGatvvll 234
                                        +i+YTSGT GkPKGVml+h+n+++ va +    ++r   +l++ddv+ls+lplah+++  ++++++++ G+++v++
  gene1597|gene1597|rna1596|rna1596 254 TICYTSGTSGKPKGVMLTHKNFISGVAGVFrgSNERemVRLSRDDVYLSYLPLAHVMER-ICVNISVAYGCKIVFF 328
                                        ****************************988533334444666***************6.**************** PP

                                        TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHC.............................. CS
                        AMP-binding 235 pkdaaldpklllelieklkvtviagvPrvleallesgalkaakkak.............................. 280
                                        +++++     ++e+    k+t+i +vPrvl+ + e+ +++  +++k                              
  gene1597|gene1597|rna1596|rna1596 329 RGNSK----EIKEDYLIVKPTFIISVPRVLNLFKEKIEEN--VRQKnilvrgifraslwykkwrvsrgelrnrlld 398
                                        *9987....356888889***************5543333..2222344555566666666666666666666666 PP

                                        .........CGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTE CS
                        AMP-binding 281 .........dlss.lrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgv 346
                                                 ++++ + +vl+g +pl +e+l  ++a++ +++++gYG+TE+ g  + ++ + d+     vG p+p +
  gene1597|gene1597|rna1596|rna1596 399 wlvfdkvskEFGGrIGQVLCGSAPLKKEVLVYMQAVLSCRIFQGYGQTENVGTGI-VQ-PLDCYLYDNVGIPFPSN 472
                                        666655555666666669************************************9.77.566678999******** PP

                                        EEEEE-TTTSCBEE......TTSE.EEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETT.SEEEEEE CS
                        AMP-binding 347 evkivDeetgepvp......dgee.GellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrlded.Gyleivg 414
                                        evk+ + + ge+        +  + Ge+l+rg +v++gY+k+p++t e f+ +++wlrTGD+g +d+d G + ++g
  gene1597|gene1597|rna1596|rna1596 473 EVKLGEIS-GELKSeygrryPSCKiGEILLRGDNVTQGYFKRPSETLELFT-SDGWLRTGDIGMFDTDtGMFSVIG 546
                                        ****9887.6666455555533336*************************9.757**********9888******* PP

                                        ECCCEEEE CS
                        AMP-binding 415 Rkkdlikl 422
                                        R kd +k+
  gene1597|gene1597|rna1596|rna1596 547 RVKDGFKT 554
                                        ****9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4257.31
//
Query:       gene1598|gene1598|rna1597|rna1597  [L=769]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.4e-184  611.8   0.0   1.4e-183  611.2   0.0    1.3  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    4.4e-19   68.3   0.3    1.2e-18   66.9   0.3    1.8  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
  ------ inclusion threshold ------
       0.11   13.1   0.1       0.27   11.8   0.1    1.7  1  ATP-cone         ATP cone domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.2   0.0  2.3e-187  1.4e-183       1     524 []     211     731 ..     211     731 .. 0.98

  Alignments for each domain:
  == domain 1  score: 611.2 bits;  conditional E-value: 2.3e-187
                                        EEE......BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                                        xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                    Ribonuc_red_lgC   1 ssCfvlsv.edslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgG. 74 
                                        +sCf++++ eds+e++++t++++a ++k++gG+Glnl+ +Rakgs +k+t+g+++G+++++++++a+ ++++qg  
  gene1598|gene1598|rna1597|rna1597 211 ASCFLITPkEDSIEGVYHTINQTAIITKFSGGIGLNLHSIRAKGSALKNTGGKSNGIIPLIQVFNATKRYINQGAe 286
                                        69****999******************************************************************9 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Ribonuc_red_lgC  75 kRrGAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygee 150
                                        +R+G++++yle+wH++i++f+d++ k tg ee r+++++i+++v+dlFme+vk+d++w+Lf+P+++v le+++gee
  gene1598|gene1598|rna1597|rna1597 287 RRPGSIAIYLEPWHMEIFDFLDIR-KSTGPEEFRARDIFIALWVNDLFMERVKNDEEWSLFCPSQAVGLEDMWGEE 361
                                        999*********************.99************************************************* PP

                                        .................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Ribonuc_red_lgC 151 feeeyeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyes 226
                                        f+e y ++e++  i+++ v+a++L+++i+e+++etg+P++++kD++Nr +++  ++ g I+++NlC+Ei+ +++ +
  gene1598|gene1598|rna1597|rna1597 362 FNELYCKYEKT--ISRTVVPAQKLWKAIIEAQIETGTPYMCYKDACNRLSNQ--QHLGIIKSSNLCTEIVEYSSGD 433
                                        **********9..77779**********************************..********************99 PP

                                        ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                        .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Ribonuc_red_lgC 227 .vavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmglada 301
                                         v+vCnLasi L+ fv     ++  fd++++++v+++++ +L++vid ++yp++e++++++k+R+iG+Gv+glad+
  gene1598|gene1598|rna1597|rna1597 434 eVSVCNLASISLPMFV-----KNGMFDFESFRNVVRIITINLNKVIDSSYYPVEEAKTSNMKHRPIGIGVQGLADL 504
                                        89**************.....478**************************************************** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..X......XXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                    Ribonuc_red_lgC 302 laklgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdef..eekekedweeLree 375
                                        +a l++p++s+ea++++++i+e+++y a++aS+elA+ +gpfp++++s++skgi++++ +  + ++k+dwe Lre+
  gene1598|gene1598|rna1597|rna1597 505 FAILKLPFESDEARSLNKEIFEAMYYFALEASCELAESEGPFPSYKGSPISKGIFHFELAgkKASNKWDWEGLRER 580
                                        ************************************************************6544459********* PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...X CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                    Ribonuc_red_lgC 376 ikkyGlrnamvtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki...l 448
                                        ikk+G rn+ ++al+PT+ +S+i g+++++eP+ +++y++++ +gef +vn++++++L klglws e+++ i   +
  gene1598|gene1598|rna1597|rna1597 581 IKKHGTRNSLLIALMPTAGTSQIFGNNEAFEPYASNIYTRRTHAGEFQIVNQYLIDDLVKLGLWSYEMKNLIienE 656
                                        ************************************************************************7666 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Ribonuc_red_lgC 449 esvqgleeipeeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                        +s+q++ +ip +i++++kta++i+++++i+++a++q +idqs+S++i++  + t+++++++++++++ GlK+ +yY
  gene1598|gene1598|rna1597|rna1597 657 GSIQNIISIPPKIREIYKTAWEIKMRSVIDLAADRQAFIDQSQSLNIFI-AKPTYSQLTSMHFYGYHCGLKTGMYY 731
                                        66***********************************************.*************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.3     2e-22   1.2e-18       1      81 [.     136     206 ..     136     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 2e-22
                    Ribonuc_red_lgN   1 kkltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlm 76 
                                        ++++y+++ +l+++Y+++  ++ ivE+pq++fmR Al ++          ++ ++++e+yd++s+++f++a+Ptl 
  gene1598|gene1598|rna1597|rna1597 136 YLFNYFGMLTLMKSYMIRVGDE-IVERPQDVFMRTALQIHK---------TNFKRVKETYDMLSRHYFTHATPTLY 201
                                        5799****************77.*****************9.........************************** PP

                    Ribonuc_red_lgN  77 naGte 81 
                                        n+  +
  gene1598|gene1598|rna1597|rna1597 202 NSCLK 206
                                        *9766 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   4.5e-05      0.27      36      85 ..      38      91 ..       4      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHHHHHHIIT-BHHHHHHHHHHHHH....HSS-HHHHHHHHHHHHHHH CS
                           ATP-cone 36 iaeeveaevrkrlrdgisteeIqdlvektli....ehpdyavaaayilyrnlrk 85
                                        ++e+ +++ ++  +g++ +e+ d   +t++    +hp+y+ + ++i+++++++
  gene1598|gene1598|rna1597|rna1597 38 NVSELMDKIISGWCEGMTKKEVVDYCSETAAsmitKHPEYGRISSRIIVSYIHE 91
                                       4567777778888899***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.53
# Mc/sec: 4361.19
//
Query:       gene1599|gene1599|rna1598|rna1598  [L=524]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-11   42.7   1.2    5.9e-11   42.7   1.2    2.0  2  TFIID_20kDa    Transcription initiation factor TFIID subunit 
     0.0089   16.1   0.0      0.016   15.3   0.0    1.4  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
  ------ inclusion threshold ------
      0.013   15.7   0.2      0.013   15.7   0.2    1.8  2  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7     1e+04      30      40 ..      72      82 ..      71      86 .. 0.75
   2 !   42.7   1.2   9.8e-15   5.9e-11      15      65 ..     451     501 ..     442     504 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHH CS
                        TFIID_20kDa 30 addFvesvtkf 40
                                       +ddFv+  t+ 
  gene1599|gene1599|rna1598|rna1598 72 IDDFVKARTEE 82
                                       79999877665 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 9.8e-15
                                        S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH CS
                        TFIID_20kDa  15 etkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhlern 65 
                                         + +de+v++ + e+ d Fv+ +++ +c+la hRk d++e  D++l l+ +
  gene1599|gene1599|rna1598|rna1598 451 RKDIDEEVKEFIYELCDGFVDHIIHMSCALAYHRKKDVVELCDVKLALKTE 501
                                        5689********************************************976 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.7e-06     0.016       7      72 ..     441     503 ..     435     515 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                        TFIID-31kDa   7 darlihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqsrle 72 
                                        d+++i+ +++   +   +e+V + + +++  ++ ++++ + +la h+kk+ v+l dv+lA+++++ 
  gene1599|gene1599|rna1598|rna1598 441 DVETIEDLIERKDI---DEEVKEFIYELCDGFVDHIIHMSCALAYHRKKDVVELCDVKLALKTEVG 503
                                        66677777766554...6789999999999*******************************99986 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.5       2.8   1.7e+04      49      61 ..      22      34 ..      19      36 .. 0.74
   2 ?   15.7   0.2   2.2e-06     0.013      18      65 .]     451     498 ..     445     498 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                                       CCTTSSCE-HHHH CS
                      CBFD_NFYB_HMF 49 kkekrKtikaehi 61
                                       kk+krK +  + +
  gene1599|gene1599|rna1598|rna1598 22 KKSKRKVVDNKNV 34
                                       7899999987665 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.2e-06
                                        XS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                      CBFD_NFYB_HMF  18 arkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65 
                                         + i +++ke+i+e +  f+ ++  +++ ++ ++k+  +   ++klA+
  gene1599|gene1599|rna1598|rna1598 451 RKDIDEEVKEFIYELCDGFVDHIIHMSCALAYHRKKDVVELCDVKLAL 498
                                        45599****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3379.34
//
Query:       gene1600|gene1600|rna1599|rna1599  [L=158]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-46  156.9   0.0    2.7e-46  156.7   0.0    1.0  1  UQ_con     Ubiquitin-conjugating enzyme
    8.5e-07   28.7   0.0    1.1e-06   28.4   0.0    1.2  1  Prok-E2_B  Prokaryotic E2 family B
     0.0045   17.3   0.0     0.0061   16.8   0.0    1.3  1  RWD        RWD domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7   0.0   4.5e-50   2.7e-46       1     139 [.      10     146 ..      10     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 4.5e-50
                                        HHHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE CS
                             UQ_con   1 rlqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd 76 
                                        rl+ e++++++++p+g+sa++++ ++l++w ++i+gp++++Ye+g+F+l + fp+ YP++pPkv+f+t+ifH+n+ 
  gene1600|gene1600|rna1599|rna1599  10 RLAIEMESMSRDPPPGCSASPISPNELDKWIAVITGPPGSVYEDGIFELLIVFPPFYPFSPPKVTFKTRIFHCNIF 85 
                                        67889999***************99**************************************************9 PP

                                        TTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHHH CS
                             UQ_con  77 ksGevcldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvkey 139
                                        ++ ++cldiLk++ Wspalt++++llsi+sLl++pn ++plnkeaa+l++++r+ey++k+ke+
  gene1600|gene1600|rna1599|rna1599  86 EK-NICLDILKDQ-WSPALTIDKILLSIISLLQDPNSDDPLNKEAADLYRNNRAEYNRKAKEW 146
                                        77.8*******77.**********************************************987 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.8e-10   1.1e-06      34     127 ..      52     134 ..      27     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.8e-10
                          Prok-E2_B  34 sggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLClleeeldldewdpngsvadvleqlqqvLnegi 109
                                        + g+++l +v+p+++p++pp+v  + +       H+n f++ +Cl       d+w p+ ++ ++l ++  +L++  
  gene1600|gene1600|rna1599|rna1599  52 EDGIFELLIVFPPFYPFSPPKVTFKTRI-----FHCNIFEKNICL---DILKDQWSPALTIDKILLSIISLLQDPN 119
                                        6799******************999877.....6***********...999**********************777 PP

                          Prok-E2_B 110 sgdedaefagEfqsYwes 127
                                        s+d    + +E++ ++ +
  gene1600|gene1600|rna1599|rna1599 120 SDDP---LNKEAADLYRN 134
                                        7766...56666665554 PP

>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     1e-06    0.0061      52     114 ..      53     117 ..       9     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-06
                                        CEEEEEEEEE-SSTTSS--EEEEEECC.SS-HHHHHH.HHHHHHHHHHHT.TTS--CHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                                RWD  52 kpslkleiklpeeYPeeaPiislsste.nlpkeqvks.leekleelaeen.lgepvifalidwlke 114
                                        +  ++l i +p+ YP ++P++++++      +   k+ + + l+++++     + ++ ++i++l++
  gene1600|gene1600|rna1599|rna1599  53 DGIFELLIVFPPFYPFSPPKVTFKTRIfH-CNIFEKNiCLDILKDQWSPAlTIDKILLSIISLLQD 117
                                        5568999******************9942.333333348899999999988899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 970.45
//
Query:       gene16|gene16|rna16|rna16  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-45  152.0   2.3    6.9e-45  151.8   2.3    1.0  1  DMAP1_like  Putative DMAP1-like


Domain annotation for each model (and alignments):
>> DMAP1_like  Putative DMAP1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.8   2.3   3.9e-49   6.9e-45       3     113 .]      21     131 ..      19     131 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.8 bits;  conditional E-value: 3.9e-49
                 DMAP1_like   3 flkllknieelkkkRksilerhfgEllkyaideledkelkikeiinkkqsypnvfLaSslgfskstwnkkvekiLkkfgldkkl 86 
                                +l++l++ie+++++R+++l++hf+El +y+i+eled+++ i+++ink+ +yp++fLaSslgf+k+twn+++e++L+++g+ k++
  gene16|gene16|rna16|rna16  21 YLEILNSIESIRRDRDDVLSTHFNELSTYNINELEDRNAVIRRLINKEFTYPSAFLASSLGFNKTTWNRDYERTLREIGMYKRP 104
                                999********************************************************************************* PP

                 DMAP1_like  87 kyptlrnmlrfEkLKyLiikymekkkk 113
                                ky+tlrnml+fEkLK+L+i+y+e+k+k
  gene16|gene16|rna16|rna16 105 KYSTLRNMLLFEKLKWLVIRYHEAKQK 131
                                ************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 900.64
//
Query:       gene160|gene160|rna160|rna160  [L=339]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.094   12.7   0.0    1.7  1  Topo_C_assoc  C-terminal topoisomerase domain


Domain annotation for each model (and alignments):
>> Topo_C_assoc  C-terminal topoisomerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.2e-06     0.094      25      58 ..     101     134 ..      91     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-06
                   Topo_C_assoc  25 SkinYlDPRitvawckkhdvpiekiFsktlleKf 58 
                                     k+ YlDPR  + +++  d+p+ ++F k  l+ f
  gene160|gene160|rna160|rna160 101 EKVPYLDPRAKYFFIDIKDIPLYRMFLKNNLRSF 134
                                    5899**********************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2294.38
//
Query:       gene1601|gene1601|rna1600|rna1600  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.066   13.4   0.0       0.13   12.5   0.0    1.5  1  SLD5_C    DNA replication complex GINS protein SLD5 C-terminu


Domain annotation for each model (and alignments):
>> SLD5_C  DNA replication complex GINS protein SLD5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.3e-06      0.13      11      55 ..     188     228 ..     178     229 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.3e-06
                             SLD5_C  11 vgkdvgtvtieelgedgdvelekGdiyvvRYsvvkdlvesGkveL 55 
                                         ++d+g v+  ++g+   +el+k+ iy+++ s+v +l+ +G v  
  gene1601|gene1601|rna1600|rna1600 188 TLEDCGVVM--DEGDL--IELKKDRIYFIKRSAVSHLIGNGLVRI 228
                                        377775444..55566..89*******************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1620.13
//
Query:       gene1602|gene1602|rna1601|rna1601  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-25   89.8   0.0    2.6e-25   89.5   0.0    1.2  1  AAA_18           AAA domain
    2.1e-10   41.1   0.0    4.1e-10   40.2   0.0    1.5  1  AAA_17           AAA domain
    3.2e-05   23.9   0.6      0.081   12.8   0.2    2.1  2  dNK              Deoxynucleoside kinase
    5.9e-05   22.8   0.3      0.055   13.2   0.1    2.3  2  Thymidylate_kin  Thymidylate kinase
    0.00011   22.4   0.1    0.00022   21.4   0.1    1.6  1  SKI              Shikimate kinase
    0.00042   20.7   0.0    0.00072   20.0   0.0    1.4  1  AAA              ATPase family associated with various cellul
    0.00054   20.1   0.2      0.019   15.0   0.2    2.4  1  ADK              Adenylate kinase
     0.0012   18.8   0.6      0.004   17.1   0.1    2.0  2  NTPase_1         NTPase
     0.0019   18.4   0.0      0.015   15.5   0.0    2.0  1  AAA_33           AAA domain
      0.002   18.4   0.0     0.0068   16.7   0.0    1.8  2  AAA_28           AAA domain
     0.0059   16.1   0.1     0.0078   15.7   0.1    1.2  1  KTI12            Chromatin associated protein KTI12
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.047   13.4   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.023   14.4   0.1       0.28   10.9   0.0    2.2  3  PRK              Phosphoribulokinase / Uridine kinase family
      0.032   14.0   1.3      0.078   12.7   1.3    1.9  1  AAA_24           AAA domain
      0.044   12.8   0.2       0.87    8.5   0.2    2.1  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.091   13.2   0.0       0.13   12.6   0.0    1.4  1  RNA_helicase     RNA helicase
       0.12   11.7   1.6       0.28   10.5   1.6    1.9  2  ATPase           KaiC
       0.14   12.4   0.0       0.21   11.8   0.0    1.4  1  AAA_22           AAA domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.0   2.6e-28   2.6e-25       1     129 [.       3     123 ..       3     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 2.6e-28
                             AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegk 75 
                                        Il+tGtpGvGKtt++  +sk+ ++ +++++ ++ en+l++e+ +    +s+ +d++    + + l+++     + +
  gene1602|gene1602|rna1601|rna1601   3 ILVTGTPGVGKTTFSSFISKKFKIpHIEISRYIEENNLYEEYSEV--YKSLLFDDKT---VKESLKKHVL---DKE 70 
                                        99*******************999*********************..7777777777...9999999865...667 PP

                             AAA_18  76 nlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeil 129
                                        +++id h + +++  a+d++ + Lta+ e+l++Rl++Rgy e+kiken e+ei+
  gene1602|gene1602|rna1601|rna1601  71 SYIIDTHSCGMVERTAFDLV-FLLTAPIEVLYKRLKERGYDEDKIKENVECEIF 123
                                        77******************.*******************************97 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   4.2e-13   4.1e-10       1     132 [.       6     114 ..       6     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.2e-13
                                        EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEE CS
                             AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlv 76 
                                        +G PG+GK+t ++ + +k++++h++ + ++     +++l ++ +e+ k  l ++k + + +++++ +   k+ +++
  gene1602|gene1602|rna1601|rna1601   6 TGTPGVGKTTFSSFISKKFKIPHIEISRYIE----ENNLYEEYSEVYKSLLFDDKTVKESLKKHVLD---KESYII 74 
                                        69***********************988884....45777788999999999*************98...588*** PP

                                        EE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SH CS
                             AAA_17  77 dghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddne 132
                                        d+h +              ++e    d+++ll a+ e++++r+++   rg d+d +
  gene1602|gene1602|rna1601|rna1601  75 DTHSCG-------------MVERTAFDLVFLLTAPIEVLYKRLKE---RGYDEDKI 114
                                        ***983.............334556799*********99988876...56666655 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.2   8.1e-05     0.081       1      68 [.       3      65 ..       3      85 .. 0.72
   2 !   10.9   0.1   0.00029      0.29     115     150 ..      80     117 ..      45     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                                       EEEEESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                                dNK  1 ivveGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqq 68
                                       i v G+ g+GK+t+ +++skk++++++e  ++++  +++n L   Y ++ + s+ ++++ + + lk++
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKKFKIPHIE--ISRY--IEENNLYEEYSEVYK-SLLFDDKTVKESLKKH 65
                                       6799******************887775..7778..666666666666554.6666666666666655 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00029
                                        HHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT...T CS
                                dNK 115 nlleelakpdlliYLkasletclerikkRgreeek...k 150
                                         ++e  a +dl+  L a++e++++r+k+Rg  e+k   +
  gene1602|gene1602|rna1601|rna1601  80 GMVERTA-FDLVFLLTAPIEVLYKRLKERGYDEDKikeN 117
                                        2334444.9*********************988765444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0018       1.8       3      34 ..       7      38 ..       5      74 .. 0.82
   2 !   13.2   0.1   5.5e-05     0.055     119     170 ..      88     139 ..      69     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSST CS
                    Thymidylate_kin  3 GlDGaGKttqaellkerlkeegikvvltrepg 34
                                       G  G+GKtt++ ++ +++k  +i++ +  e+ 
  gene1602|gene1602|rna1601|rna1601  7 GTPGVGKTTFSSFISKKFKIPHIEISRYIEEN 38
                                       7779***************9999877776665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.5e-05
                                        SEEEEEESSHHHHHTSCCTTSSTTTSHHHHH..HHHHHHHHHHHHHHHTTSTEE CS
                    Thymidylate_kin 119 dltflldvdpevalkRlakrdeldeeeeeql..dflrkvrerylelakederil 170
                                        dl+fll  + ev +kRl++r+  +++++e+   +++  vre   +l++  e ++
  gene1602|gene1602|rna1601|rna1601  88 DLVFLLTAPIEVLYKRLKERGYDEDKIKENVecEIFGVVREEVEDLFE--EGYY 139
                                        9*********************65666655422689999999999994..4444 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   2.2e-07   0.00022       1     106 [.       9     108 ..       9     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.2e-07
                                        TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHT.S-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGS CS
                                SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtg.ksiaeifeeegeegFrelEsevlkelleeeglViatGGGavls 75 
                                        +G+GK+t+   ++kk +++ i++ ++ie+++   + +e+++      ++   + + k++l++e+++i t  + ++ 
  gene1602|gene1602|rna1601|rna1601   9 PGVGKTTFSSFISKKFKIPHIEISRYIEENNLyEEYSEVYKSL-LFDDKTVKESLKKHVLDKESYIIDTHSCGMV- 82 
                                        69*************************9888769999999844.4555566666777889999****99333333. PP

                                        HHHHHHHHHHSEEEEEE--HHHHHHHHHHTT CS
                                SKI  76 eenrellkekgiviyLdvsleellerlkadk 106
                                           r++     +v++L +++e+l++rlk++ 
  gene1602|gene1602|rna1601|rna1601  83 --ERTAFD---LVFLLTAPIEVLYKRLKERG 108
                                        ..333334...788*************9876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.2e-07   0.00072       1      33 [.       3      35 ..       3      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.2e-07
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTT CS
                                AAA  1 vllyGppGtGKTllakavakelgvefleisgse 33
                                       +l++G+pG+GKT++ + + k+++++ +eis   
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKKFKIPHIEISRYI 35
                                       699**********************99999755 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.9e-05     0.019       1      28 [.       5      32 ..       5     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                                       EEESTTSSHHHHHHHHHHHHTSEEEEHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                ADK  1 llGaPgaGKGtqaeklvkkyglahlstG 28
                                       + G+Pg GK t ++ + kk++++h+   
  gene1602|gene1602|rna1601|rna1601  5 VTGTPGVGKTTFSSFISKKFKIPHIEIS 32
                                       57**********************9754 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     4e-06     0.004       1      24 [.       2      25 ..       2      38 .. 0.88
   2 ?   -1.4   0.1         2     2e+03     142     165 ..     112     135 ..      97     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-06
                                       EEEEE--TTSSHHHHHHHHHHHH. CS
                           NTPase_1  1 kvfiTGppGvGKtTlvkkvlellk 24
                                       k+++TG pGvGKtT+ + ++++ k
  gene1602|gene1602|rna1601|rna1601  2 KILVTGTPGVGKTTFSSFISKKFK 25
                                       699************999998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                        HHHHT-TT-EEEE--TTTTTTHHH CS
                           NTPase_1 142 eeirerkdvkvfevteenrdalle 165
                                        ++i+e+ + ++f v +e+ + l+e
  gene1602|gene1602|rna1601|rna1601 112 DKIKENVECEIFGVVREEVEDLFE 135
                                        567777788888888888777776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05     0.015       2     103 ..       3     101 ..       3     131 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                             AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrr..rlfgtdqqsktdytrvldrlyqilnelarkalsagrnvil 75 
                                        +l+ G pG+GK+t++  + kk +  +++   +++  +l+++   s+  y+ +l++ + +++e ++k    + ++i+
  gene1602|gene1602|rna1601|rna1601   3 ILVTGTPGVGKTTFSSFISKKFKIPHIEISRYIEenNLYEE--YSE-VYKSLLFDDK-TVKESLKKHVLDKESYII 74 
                                        6789****************999666555554441155532..222.2333333322.345666666667777777 PP

                             AAA_33  76 datnlsrrerarflklarrlgvpvrivv 103
                                        d   +   er +f+ ++  l +p+++++
  gene1602|gene1602|rna1601|rna1601  75 DTHSCGMVERTAFDLVFL-LTAPIEVLY 101
                                        777777777777776665.444555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.8e-06    0.0068       1      66 [.       2      64 ..       2      83 .. 0.70
   2 ?    0.1   0.0      0.83   8.3e+02     103     128 ..      81     108 ..      24     120 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.8e-06
                             AAA_28  1 kivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwvedllafaervleeqlee 66
                                       ki +tG+++ GKTt ++ ++++ ++p++ E+ r i e++l ++    +  ++ l f ++ ++e l++
  gene1602|gene1602|rna1601|rna1601  2 KILVTGTPGVGKTTFSSFISKKfKIPHI-EISRYIEENNLYEEYS--EV-YKSLLFDDKTVKESLKK 64
                                       799*****************99677766.6777777666666654..22.45666666666666554 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.83
                             AAA_28 103 aarekrydlvfllppapei..dddgeRr 128
                                         +++   dlvfll    e+  ++ +eR 
  gene1602|gene1602|rna1601|rna1601  81 MVERTAFDLVFLLTAPIEVlyKRLKERG 108
                                        3455567776666644433345555554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   7.9e-06    0.0078       4      64 ..       3      66 ..       1      78 [. 0.72

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.9e-06
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--E.EEE-THHHH.TTSS.S--.GGGHHHHHHHHHHHH CS
                              KTI12  4 vvltGlPssGKstrakeLakaleeekrsv.vviddeslgiekds.ykd.sakekalRsslrsav 64
                                       +++tG P +GK+t+++ ++k+++  ++++  +i+++ l  e ++ yk+   + k++++sl+++v
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKKFKIPHIEIsRYIEENNLYEEYSEvYKSlLFDDKTVKESLKKHV 66
                                       89*********************97776524555555543434447741457788888887776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.7e-05     0.047      36      59 ..       3      26 ..       1      39 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                             RuvB_N 36 vllyGpPGlGkttlakiiakelgv 59
                                       +l++G PG+Gktt+++ i+k++++
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKKFKI 26
                                       899***************998765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.28       2      54 ..       3      57 ..       3      76 .. 0.70
   2 ?    0.7   0.0      0.37   3.7e+02     152     167 ..     104     119 ..      97     122 .. 0.84
   3 ?    0.2   0.0      0.53   5.3e+02     154     167 ..     106     119 ..     105     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                PRK  2 IgvagsSGaGkttvarklekifgrekvk.aaei.egdsflrldraekdleleerk 54
                                       I v+g  G Gktt++  + k f+  +++ + +i e     ++ +++k+l  +++ 
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKKFKIPHIEiSRYIeENNLYEEYSEVYKSLLFDDKT 57
                                       669********************77766123334444445566666666666655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.37
                                PRK 152 iaeRGrsleavldsil 167
                                         +eRG++ + ++++++
  gene1602|gene1602|rna1601|rna1601 104 LKERGYDEDKIKENVE 119
                                        689********99876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.53
                                PRK 154 eRGrsleavldsil 167
                                        eRG++ + ++++++
  gene1602|gene1602|rna1601|rna1601 106 ERGYDEDKIKENVE 119
                                        67777777777654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   7.8e-05     0.078       4      22 ..       2      20 ..       1      78 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.8e-05
                             AAA_24  4 kiliyGpsgiGKTtlakel 22
                                       kil++G +g+GKTt+ + +
  gene1602|gene1602|rna1601|rna1601  2 KILVTGTPGVGKTTFSSFI 20
                                       9**************8766 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2   0.00087      0.87      32      52 ..       3      23 ..       1      27 [. 0.80
   2 ?    2.3   0.0     0.067        67     222     263 ..      94     135 ..      72     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00087
                                       EEEEE-TTSSHHHHHHHHHHH CS
                               MeaB 32 vGltGvPGaGkstlvealgle 52
                                       + +tG+PG+Gk t+ + +  +
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKK 23
                                       669**********98766655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.067
                                        HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               MeaB 222 vdaieehrevlkktGllekrrrerakeelrelvedellkrvk 263
                                        ++ ie   + lk+ G  e + +e+++ e++ +v++e+ + + 
  gene1602|gene1602|rna1601|rna1601  94 TAPIEVLYKRLKERGYDEDKIKENVECEIFGVVREEVEDLFE 135
                                        55677788899*************************998765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00013      0.13       1      29 [.       3      27 ..       3      84 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                       RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklk 29
                                       i+++G +g+GK+t++  ++k++      +
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKKFK----IP 27
                                       6899*************777776....22 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.6   0.00028      0.28      22      40 ..       3      20 ..       1     135 [. 0.85
   2 ?   -0.3   0.0      0.56   5.6e+02      61      98 ..      98     135 ..      89     158 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00028
                             ATPase 22 vlitGepGtGKtifalqFl 40
                                       +l+tG+pG GKt+f+  F+
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSS-FI 20
                                       89************84.55 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.56
                             ATPase  61 edlrenakslGwdlekleeegklaiidasesaeesaee 98 
                                        e l+++ k+ G d +k++e+ +  i  +++++ e+  e
  gene1602|gene1602|rna1601|rna1601  98 EVLYKRLKERGYDEDKIKENVECEIFGVVREEVEDLFE 135
                                        56788888888888888888888887777776665544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.21       8      30 ..       3      25 ..       2      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                             AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                       ++vtG +G+GKTt    + ++++
  gene1602|gene1602|rna1601|rna1601  3 ILVTGTPGVGKTTFSSFISKKFK 25
                                       79***********9988888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1111.90
//
Query:       gene1603|gene1603|rna1602|rna1602  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.6  17.4      0.067   13.0  17.4    1.2  1  FAM184    Family with sequence similarity 184, A and B


Domain annotation for each model (and alignments):
>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  17.4   3.7e-06     0.067      47     185 ..      12     158 ..       2     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-06
                             FAM184  47 eeldlkqkiaeleesleqhekekrqalaefeqykrrveerelkleaehsqkvvelsreveevkrkFeeklrqfaq. 121
                                        +e + k k++e   ++++ +++k++ l +   + + +e +e + ++++ +k+ ++ ++v++v+++F  +l  f + 
  gene1603|gene1603|rna1602|rna1602  12 REENYKAKVKEKTYEESEKQSKKEKRLYDL--QCKVMELEEEENQKAFDKKLKKMLTDVKKVENHFGRALPPFLKk 85 
                                        334444444444444455556677778888..78999999999*************************98666541 PP

                             FAM184 122 ...lqeqleqekekaLeelrkkhr.eeveeLlkeqeaqsekllkeqekl.....eekhkaeveklkeeveele 185
                                             +   +  +ka++el + ++ +e  + +ke ++++e+++k+ +k+      e+ k+e+++ k+++++ +
  gene1603|gene1603|rna1602|rna1602  86 flmSPKVYTRSHKKAIDELLSRYEpKESIDTQKEDKNDEERISKDLSKIlvikdGEQRKKELKEFKDSTKDGT 158
                                        100455556**********999975899999*****************9888887788888888888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2456  (0.136985); expected 358.6 (0.02)
Passed bias filter:                      782  (0.0436165); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 2690.30
//
Query:       gene1604|gene1604|rna1603|rna1603  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2044.10
//
Query:       gene1605|gene1605|rna1604|rna1604  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-15   56.0   0.0    8.2e-15   55.6   0.0    1.1  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   4.6e-19   8.2e-15       3     127 ..      18     134 ..      16     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.6e-19
                                        GGTSSTTTTTTTTT-..S--.......S--.........---..GGG..---.EEEEHHHHHHTTTTGTTS.--.. CS
                     Ribosomal_L27A   3 ktgGrGhkGqkkrsg..vkk.kpgfeGGqmplyrrlpkrGfk..nskfkkey.kvvnlkdLdelideerle.la.. 69 
                                        ++gGrG +G  ++ +  + + +p++  G+          G++  ++k++ +y ++++  +L+ +i++e++      
  gene1605|gene1605|rna1604|rna1604  18 HSGGRGLAGGFSHMKtfFTRfHPDY-HGKR---------GMRvyHRKENSNYaRPISSARLWGVIPKEQRYeFLdn 83 
                                        78***********999877789998.4555.........999765554444479***********99988633378 PP

                                        .----EEEGGGTTTTSSS....SEEEE--S..---.--EEEESEE-HHHHHHHHHTT-EEE CS
                     Ribosomal_L27A  70 .deaeeidleelaeaglikkkdgvKvlgkg..eltkklkvkaskfSkkAkekIeaaGGkve 127
                                         d++++id++e+          g++v+  g   l++++ vka++f+++Ake+Ie++GGk +
  gene1605|gene1605|rna1604|rna1604  84 sDKVPVIDVREF----------GYHVVIGGklPLERPIVVKARYFTPSAKEEIERVGGKWI 134
                                        999*********..........996666661456889*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       211  (0.0117686); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 867.86
//
Query:       gene1606|gene1606|rna1605|rna1605  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-72  242.3   1.4    1.2e-71  241.4   0.5    1.7  2  Kinesin      Kinesin motor domain
    4.3e-14   52.7   0.2    3.9e-13   49.6   0.1    2.5  2  Microtub_bd  Microtubule binding


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.4   0.5   1.3e-75   1.2e-71      48     330 ..      49     294 ..      15     297 .. 0.90
   2 ?   -1.6   0.0      0.11   9.6e+02      35      58 ..     366     389 ..     334     402 .. 0.62

  Alignments for each domain:
  == domain 1  score: 241.4 bits;  conditional E-value: 1.3e-75
                                        EEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBCTTTSBSHHHHHHHHHHHHHHHCTTTHEE CS
                            Kinesin  48 vfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyTmegkeeeeeGiipraleelFesikkekeekek 123
                                         +  + t++evy+e++++ ++++l+  n+t+faYGqtgsGKTyTm g   +eeGii  a++++ ++          
  gene1606|gene1606|rna1605|rna1605  49 SILTNMTNAEVYKECVREEIQKFLNEENCTVFAYGQTGSGKTYTMLGG--DEEGIIKLAIRDILDRR--------- 113
                                        4445789****************************************7..679**********9875......... PP

                                        EEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EEESSHHHHHHHHHHHHHHHTSTTSSC CS
                            Kinesin 124 efsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkgltevevksaeevlellekgeknrkvaetkl 199
                                           v +sylEiYne+++DL +++      ++++ + ++++  ++++l  ++v++ e+v +++e++eknrk+++t++
  gene1606|gene1606|rna1605|rna1605 114 --PVGISYLEIYNEKLFDLSNNS------EVQMFNVENRN--VISNLWVEHVDKWEDVASFIERCEKNRKFGTTEF 179
                                        ..489*************97766......46777777765..9********************************* PP

                                        TSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSSTCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            Kinesin 200 neeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktgaaegerlkEaaniNkSLlaLgrvisaLa 275
                                        n++SSRSH+v+++t +++n+         + +ln++DLAGsEras++     +r+kE++ iN+SLlaL +++++  
  gene1606|gene1606|rna1605|rna1605 180 NTKSSRSHTVVQVTYNSNNR---------VRTLNMIDLAGSERASRSM----DRRKEGSFINRSLLALCTIVNNVG 242
                                        *************9999884.........458***********99999....479********************* PP

                                        HTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHH CS
                            Kinesin 276 ekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaera 330
                                        +    k+  +R+SkLTr+Lq+sL+G+++ + i+t+sp ++++ee++stlkfa+r 
  gene1606|gene1606|rna1605|rna1605 243 NG---KYLGFRNSKLTRVLQSSLDGRTNLVAICTLSPYEDCIEESVSTLKFAARL 294
                                        99...***********************************************985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.11
                                        ECTTSCEEEEESEEEETTS-HHHH CS
                            Kinesin  35 nkeeeekkfkFdkvfdeeatqeev 58 
                                        + +++ekk  +dkv++e+++ ++ 
  gene1606|gene1606|rna1605|rna1605 366 KIRSKEKKVDYDKVCSEKDSISRA 389
                                        556667777777777776664443 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   4.4e-17   3.9e-13      21     148 ..       9     130 ..       3     130 .. 0.79
   2 ?   -1.5   0.0      0.25   2.2e+03      43      62 ..     361     384 ..     332     395 .. 0.69

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 4.4e-17
                                        B-EEEEEEECCCS-T.EEEETTT........TTTEEEE-SEEEECTTHCCCCCCCC.HHHHHHHHTT--EEEEEEE CS
                        Microtub_bd  21 niRvfarvrpelesekakikfpe.....eekkkkkefsFdrvfeseseqeevfeei.sqlvqsaldgynvcifayg 90 
                                        +i v  r+rp+  ++    k++e      + +k+ +++  r + ++ +++ev++e+ +  +q  l++ n+++fayg
  gene1606|gene1606|rna1605|rna1605   9 KIKVSIRLRPSMGDK-EVWKTSEdglwhVHGQKRVKYNGFRSILTNMTNAEVYKECvREEIQKFLNEENCTVFAYG 83 
                                        677777888877775.344444346776556777888877888899999999999637899*************** PP

                                        S................ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEET CS
                        Microtub_bd  91 qTGsGKtyTmegeeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDl 148
                                        qTGsGKtyTm g  +e+g i+ a++ i++             + ++++eiynek+ Dl
  gene1606|gene1606|rna1605|rna1605  84 QTGSGKTYTMLG-GDEEGIIKLAIRDILDRRP----------VGISYLEIYNEKLFDL 130
                                        ************.8889999999999987544..........4588899999998886 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.25
                                        T.......TTTEEEE-SEEEECTT CS
                        Microtub_bd  43 e....eekkkkkefsFdrvfeses 62 
                                        +    ++++k+k+  +d+v +++ 
  gene1606|gene1606|rna1605|rna1605 361 SyeypKIRSKEKKVDYDKVCSEKD 384
                                        033447789999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3063.36
//
Query:       gene1607|gene1607|rna1606|rna1606  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 790.46
//
Query:       gene1608|gene1608|rna1607|rna1607  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-12   47.5   0.5    2.3e-12   46.5   0.5    1.5  1  FYRN      F/Y-rich N-terminus
  ------ inclusion threshold ------
       0.13   12.3   0.3       0.32   11.1   0.3    1.6  1  CARD      Caspase recruitment domain


Domain annotation for each model (and alignments):
>> FYRN  F/Y-rich N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.5   2.6e-16   2.3e-12       3      51 .]      90     143 ..      88     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.6e-16
                               FYRN   3 ltvlslGelvpds.pkfhteryIyPvGYkstRlYw....stkdprkrclYtceI 51 
                                        l +++lG+++ +s + f++++++yPv+Y+++R Y+     +   ++ +lYtc+I
  gene1608|gene1608|rna1607|rna1607  90 LVIYNLGKIPSPSmKPFYSQKNVYPVDYMCKRAYYgkrdELLAGKREVLYTCTI 143
                                        89************99*******************7777777789********9 PP

>> CARD  Caspase recruitment domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   3.5e-05      0.32      19      57 ..      15      53 ..      10      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHTTSS-HHHHHHHHT.SSSHHHHHHHHHHHHH CS
                               CARD 19 sglldyLlekkVLteeeeekika.kttrlskareLldlvq 57
                                       ++l+ +L+ ++ L+e e+eki + + + + + r+L+d+++
  gene1608|gene1608|rna1607|rna1607 15 KRLMGALRRRDFLKE-EMEKIGQdLQKLEAHRRVLVDILR 53
                                       678999999999976.566777769999999******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1283.77
//
Query:       gene1609|gene1609|rna1608|rna1608  [L=639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-06   26.2   0.1    1.9e-05   24.3   0.1    1.8  1  CLASP_N   CLASP N terminal


Domain annotation for each model (and alignments):
>> CLASP_N  CLASP N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   1.1e-09   1.9e-05      14     198 ..      47     213 ..      34     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.1e-09
                            CLASP_N  14 gketelnwdaReknilklrslikgnvpedaveelleclkqlleailkalssLrttlsstgchllkelaiqlkeqld 89 
                                         ke e  w++  + +lkl   +k     +  +++le+     e+i+++++s r+ l   ++ llk ++++l+++++
  gene1609|gene1609|rna1608|rna1608  47 KKEDENTWSKINDVLLKLAANVKCA---EEARKVLESAE---ELIIRSMQSDRSRLAGSALGLLKSCICILGSEFE 116
                                        4777777777777777777666655...33444555555...*********************************7 PP

                            CLASP_N  90 pmveillptLlkllgdtKkiisqnanqalaallsnasfspri.lqvlsvalqdKnvqpReysaiwLkilltrfesh 164
                                         m+ ++l  L k++g+   ++ + ++ +l  l++n++++    +    + + +Knv+  ++    +    + ++  
  gene1609|gene1609|rna1608|rna1608 117 -MAGQYLGPLAKVCGKSSRVFYSRGEEVLIELCKNVNIKVYArFFNEYSSCANKNVRVAIFKG--I----EAWA-- 183
                                        .77888889****************************54444444444556667766543332..2....2333.. PP

                            CLASP_N 165 kskleasllldliekslkkgleDanptVRetaRs 198
                                            e s++++l+e ++ kg  Da + VR++ + 
  gene1609|gene1609|rna1608|rna1608 184 ----EGSEGIELFEGLVAKGRRDAFSDVRDVCKR 213
                                        ....444466777777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 3847.22
//
Query:       gene1610|gene1610|rna1609|rna1609  [L=477]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-67  225.7   0.0    7.2e-67  225.1   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    6.2e-12   45.9   1.0    1.1e-11   45.0   1.0    1.5  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
       0.06   13.6   0.0       0.17   12.1   0.0    1.7  1  DUF3762        Protein of unknown function (DUF3762)
       0.13   12.7   0.0       0.29   11.6   0.0    1.5  1  DUF2630        Protein of unknown function (DUF2630)


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   0.0   1.6e-70   7.2e-67       1     213 []     139     364 ..     139     364 .. 0.98

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 1.6e-70
                                        SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS...........S.EEEEEEESEEHHHHHHHHHHCH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x.xxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd...........d.aiiyvgiGergnevaevleefp 64 
                                        Gi+ +D + +i++Gq++ i++a+g+++++i++++++q+              + ai+++++G + ++++ + ++f+
  gene1610|gene1610|rna1609|rna1609 139 GISSIDIMNSIARGQKIPIFSASGLPHNEIAAQICRQAGLVkrkdsidssddNfAIVFAAMGVNVETANFFRNSFE 214
                                        899**********************************8655788999***9769********************** PP

                                        HSSGGGGEEEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  65 egtimkrtvlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypa 139
                                         ++ + rt l++n +n+p+++r++++++++t+AEy+++ ++k+vl+i++++s +a+Alre+s++ +e+p+++gyp+
  gene1610|gene1610|rna1609|rna1609 215 ASGSIGRTALFLNLANDPTIERIITPRLALTAAEYLAYeKEKHVLVIMTDMSSYADALREVSAAREEVPGRRGYPG 290
                                        *************************************999************************************ PP

                                        THHHHHHHHHTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab 140 ylgaklaslyERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                        y++++l+++yERag+++ r+Gs+t++++++++++D+++p+++ t +it+g+i++d+++++r+++P+invl S+S
  gene1610|gene1610|rna1609|rna1609 291 YMYTDLSTIYERAGRLEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIYVDRQIHNRQIYPPINVLPSLS 364
                                        ************************************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   1.0   2.6e-15   1.1e-11       1      69 []      16      82 ..      16      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.6e-15
                                       EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                      ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                       iv v+Gp+v+ ++ +    ++ ++++  l++ g+ ++g++l++ + k++++v+++t+G+++  t V++TG
  gene1610|gene1610|rna1609|rna1609 16 IVGVNGPLVIMDNIRF--LKYAEIVSLTLPD-GSIRQGQVLEVCGKKAVIQVFEGTSGIDVkETQVTFTG 82
                                       799********66666..888888888888*.*****************************9*******9 PP

>> DUF3762  Protein of unknown function (DUF3762)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.9e-05      0.17      30      70 ..     238     278 ..     230     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.9e-05
                            DUF3762  30 lrcrldyhaaetdfrdeekhvryvyndvssaanrprtvssr 70 
                                        +  rl   aae    ++ekhv  +  d+ss a+  r vs+ 
  gene1610|gene1610|rna1609|rna1609 238 ITPRLALTAAEYLAYEKEKHVLVIMTDMSSYADALREVSAA 278
                                        5679999*******************************975 PP

>> DUF2630  Protein of unknown function (DUF2630)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.6e-05      0.29      30      52 ..     429     450 ..     415     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                            DUF2630  30 eeeErarLkeleeeLDqcWDLLr 52 
                                        +++ +++L+++ ++LD +WDLL+
  gene1610|gene1610|rna1609|rna1609 429 SQR-HDELRTVSQSLDIAWDLLK 450
                                        333.799**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3139.35
//
Query:       gene161|gene161|rna161|rna161  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-07   29.9  10.5    1.8e-05   24.0  10.5    2.8  1  TAP42     TAP42-like family


Domain annotation for each model (and alignments):
>> TAP42  TAP42-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  10.5     1e-09   1.8e-05     173     312 ..     107     227 ..      31     236 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-09
                                    S-..HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC...--XXXXXXXXXXXX..XXXXXXXXXXXX..XXXXXXXXX CS
                          TAP42 173 eD..eeevRelylaqlklavlkafqelesieqEleiLeaapkeeeqeeskakkgpllskqgkplrPftilstReelqkkV 250
                                     D  + e Re ++++++++++++++++e++++E+ +L++ + ++++               + ++ +  +++R ++++  
  gene161|gene161|rna161|rna161 107 YDfiDWEDREWVMKLIEYFYIMSMKNIEHLNREIMLLQNKSDKNPR-------------GNEGMECIR-VDSRGRVENVL 172
                                    34557789******************************76654422.............223344444.48999998866 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXX....XXXXXXXXXXXX CS
                          TAP42 251 fgpghslPtMtvdEyleeevrrGniiegggeasakeeeeeedeeedeekadeeetqkarawD 312
                                    +g   + PtMt+dE++e+ +++     + +    ++e+++  +++d  +++ + ++++ + D
  gene161|gene161|rna161|rna161 173 VG--RNDPTMTLDEFAEKIMAEMD---KDSSLPPQDETSSTSSDDD-PSRE-KLLKRDDERD 227
                                    65..899*************9644...4433333333333334434.1111.2333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1831.74
//
Query:       gene1611|gene1611|rna1610|rna1610  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.15   11.9   0.0       0.18   11.7   0.0    1.2  1  Qn_am_d_aIV  Quinohemoprotein amine dehydrogenase, alpha subu


Domain annotation for each model (and alignments):
>> Qn_am_d_aIV  Quinohemoprotein amine dehydrogenase, alpha subunit domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.8e-06      0.18      60     112 ..       5      58 ..       1      76 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-06
                        Qn_am_d_aIV  60 deeaekdeDveyvgklaakglftPasa.GPnpaRklstnnvGnlkVvAtvedeg 112
                                         ++ ++d+   y +  +++  + Pa++  P p+Rk  +  vG+l+ +A+ e+ +
  gene1611|gene1611|rna1610|rna1610   5 RKRKARDQLSPYSNPGEESDHHSPAVEsSPLPNRKRAKARVGDLSTIANSETLK 58 
                                        5566677777888888999999***9879*******************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 813.70
//
Query:       gene1612|gene1612|rna1611|rna1611  [L=504]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-58  198.6   0.0    1.2e-58  198.4   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
    3.3e-54  183.6   0.8    6.3e-54  182.7   0.0    1.7  2  iPGM_N         BPG-independent PGAM N-terminus (iPGM_N)
    5.6e-05   22.7   0.0    0.00021   20.8   0.0    1.9  2  Sulfatase      Sulfatase
    0.00093   19.3   0.0      0.065   13.3   0.0    2.7  2  PglZ           PglZ domain
     0.0013   18.4   0.0     0.0046   16.6   0.0    1.8  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.4   0.0   3.3e-62   1.2e-58       2     247 ..       3     479 ..       2     480 .. 0.96

  Alignments for each domain:
  == domain 1  score: 198.4 bits;  conditional E-value: 3.3e-62
                                        EEEEEEETTBB----.GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH......... CS
                                        xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......... RF
                      Metalloenzyme   2 kvvlvvlDGlGeapa.delnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel......... 67 
                                        +v lvv+DG+G+ +a ++ na++ ++   +++L ++  ++ l++ahg  vglp++ mgnsevgHl++         
  gene1612|gene1612|rna1611|rna1611   3 NVCLVVIDGWGYDEAsTRGNAVNESRCQWMKTLSQS-RHSLLLHAHGRYVGLPDGLMGNSEVGHLTIgsgrvieqd 77 
                                        689********9876488999*************99.33349********************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                      Metalloenzyme  68 ............................................................................ 67 
                                                                                                                    
  gene1612|gene1612|rna1611|rna1611  78 ilridkaieegrlrsmlrkevqevegkihlvgmvsdggvhshirhlkgileslrdlgeevfihcvsdgrdteprvf 153
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                      Metalloenzyme  68 ............................................................................ 67 
                                                                                                                    
  gene1612|gene1612|rna1611|rna1611 154 lkylsevegfcqkigigkvasiagrfytmdrasnnkrtelsfqemtsgeevqgevrdyilgmyeeglsdetlrpfl 229
                                        **************************************************************************** PP

                                        .........................................................................HHH CS
                                        .........................................................................xxx RF
                      Metalloenzyme  68 .........................................................................lri 70 
                                                                                                                  +i
  gene1612|gene1612|rna1611|rna1611 230 vdkrgkiepedtiiffnfradrmrqitsrfaengnniitmteykkelkskvlfekvcvkntlaeimsshgmihSHI 305
                                        *************************************************************************99* PP

                                        HTT-----EEEEEEEE-S---SSHHHHHT--EEEE--SHHSTT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Metalloenzyme  71 setvkfahvtffwnggrsgyfnpleereeipsdtvitfdlqpemkavevaekaldailsgkfdlvvvniknaDmvG 146
                                        +e +k ahvt+f+ngg+++ f + ++ +  ps+ v  fd +p m ++ev+ +++ +i sg   lv+ n++ +DmvG
  gene1612|gene1612|rna1611|rna1611 306 AEKEKEAHVTYFFNGGKEQAFLN-QKTIIHPSPNVESFDAAPSMASKEVTSSVIAEIGSG-VPLVIANLAPPDMVG 379
                                        *********************99.7777779**************************998.*************** PP

                                        HTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S-- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Metalloenzyme 147 HtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvk 222
                                        Htg+leat  aie  De+++ i +a+++++ +l+vtADHgnae+m++++ + +  Ht+ +VP++i + +  +++++
  gene1612|gene1612|rna1611|rna1611 380 HTGNLEATKMAIEFTDECIGSIYKACKSNGYTLIVTADHGNAEKMIDEEGNCCKTHTTSKVPLIICEGKPGRPSSS 455
                                        *****************************************************************99886654544 PP

                                        SSHHHHTT-TTEEEEGGGHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Metalloenzyme 223 egakfrekggLanvaatllnllgle 247
                                         g    ++ +L +va+t+l+++g+ 
  gene1612|gene1612|rna1611|rna1611 456 WG-YIDSNYSLRDVAPTVLEIMGIP 479
                                        44.67779************99975 PP

>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   0.0   1.8e-57   6.3e-54       3     214 ..      83     273 ..      81     274 .. 0.89
   2 ?   -2.0   0.1      0.57   2.1e+03      36      46 ..     296     306 ..     279     315 .. 0.84

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 1.8e-57
                                        HHHHCTGGGG-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT- CS
                             iPGM_N   3 kaiedgslfenealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapks 78 
                                        kaie+g+l +      + +++++ ++++Hl+G++SdGgVHShi+hl+ +le  ++ g  +v++h++ DGRDt+p+ 
  gene1612|gene1612|rna1611|rna1611  83 KAIEEGRLRS-----MLRKEVQEVEGKIHLVGMVSDGGVHSHIRHLKGILESLRDLGE-EVFIHCVSDGRDTEPRV 152
                                        5555555543.....344567777889******************************8.***************** PP

                                        HHHHHHHHHHHHHHCT--EEEEEEEHHHHT--SS-HHHHHHHHHHHCCSSSEEECTTHHHHHHHHHHTT--GGG-- CS
                             iPGM_N  79 aleyleeleeklkelgvgkiasvsGRyyaMDRdkrwervekaydalvkgegeskaesaveaieesyakgetDefve 154
                                         l+yl+e+e +++++g+gk+as+ GR+y+MDR ++ +r+e  ++ +++ge    + ++ ++i  +y++g +De + 
  gene1612|gene1612|rna1611|rna1611 153 FLKYLSEVEGFCQKIGIGKVASIAGRFYTMDRASNNKRTELSFQEMTSGEEV--QGEVRDYILGMYEEGLSDETLR 226
                                        ***********************************************99643..3589****************** PP

                                        -EEE...TCCGGS--TT-EEEE----CCCCHHHHHHHHSTTHHCC.--TT-EEEESS-S- CS
                             iPGM_N 155 ptviaeegkkegtikdgDaviffNFRaDRareltraltdkefkefekakklklvtmteYd 214
                                        p+++    +k g+i+ +D++iffNFRaDR+r++t+ +++   ++       +++tmteY+
  gene1612|gene1612|rna1611|rna1611 227 PFLV----DKRGKIEPEDTIIFFNFRADRMRQITSRFAE---NGN------NIITMTEYK 273
                                        ****....7889**************************5...233......488999997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.57
                                        -SS--SS--CH CS
                             iPGM_N  36 lSdGgVHShid 46 
                                         S+G +HShi 
  gene1612|gene1612|rna1611|rna1611 296 SSHGMIHSHIA 306
                                        68999***986 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.23   8.1e+02       2      25 ..       3      26 ..       2      46 .. 0.77
   2 !   20.8   0.0   5.9e-08   0.00021     211     309 .]     384     478 ..     287     478 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.23
                                       EEEEEEESSE-TTGSGGGTTTSCS CS
                          Sulfatase  2 nvvliladdlgagdlglyggktat 25
                                       nv l+++d +g++  ++ g+ +++
  gene1612|gene1612|rna1611|rna1611  3 NVCLVVIDGWGYDEASTRGNAVNE 26
                                       999**********99999998876 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 5.9e-08
                                        HHHHHHHHHHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSSCCCGHHTTSSSCTTCSSSHHHHBEEEEEEETTTSH CS
                          Sulfatase 211 leaylnsveyvDdligrvlaaLeenglldntlvvftSDhgasleesngplrggkganayeggtrvPllvwwpgeka 286
                                        lea   ++e +D++ig++++a     +++  ++++t+Dhg +    +     g+  ++++   +vPl++   +  +
  gene1612|gene1612|rna1611|rna1611 384 LEATKMAIEFTDECIGSIYKAC----KSNGYTLIVTADHGNAE---KMIDEEGNC-CKTHTTSKVPLIICEGKPGR 451
                                        55556689**************....788889*********54...566666666.8889999******9988888 PP

                                        C....EEECSEEEGGGHHHHHHHHTTE CS
                          Sulfatase 287 p....rvseelvshiDlfptildlagi 309
                                        p    +  +  +s+ D++pt+l+ +gi
  gene1612|gene1612|rna1611|rna1611 452 PssswGYIDSNYSLRDVAPTVLEIMGI 478
                                        8778888888899************97 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.029   1.1e+02       2      27 ..       3      28 ..       2      41 .. 0.85
   2 !   13.3   0.0   1.8e-05     0.065     134     169 ..     382     420 ..     368     423 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.029
                               PglZ  2 kvfvIisDalryeaweelkqlLnked 27
                                        v+++++D+ +y+++ +  + +n+ +
  gene1612|gene1612|rna1611|rna1611  3 NVCLVVIDGWGYDEASTRGNAVNESR 28
                                       69*************99888877765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.8e-05
                               PglZ 134 ksfeaveeslkelkelvksllee...ngykvlltaDHGf 169
                                           ea + +++++ e + s+  +   ngy++++taDHG+
  gene1612|gene1612|rna1611|rna1611 382 GNLEATKMAIEFTDECIGSIYKAcksNGYTLIVTADHGN 420
                                        456889999999999999998755569***********7 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.6   5.9e+03     195     218 ..      72      97 ..      59     125 .. 0.60
   2 !   16.6   0.0   1.3e-06    0.0046     175     235 ..     367     421 ..     344     430 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                                        HHHHHHHHHHHHHH..HHHHHHHHHT CS
                       Phosphodiest 195 pevedalrrvDkai..gdLlealder 218
                                          +e+ + r+Dkai  g+L++ l+++
  gene1612|gene1612|rna1611|rna1611  72 RVIEQDILRIDKAIeeGRLRSMLRKE 97 
                                        44777888888888333566666666 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.3e-06
                                        EEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---E CS
                       Phosphodiest 175 lllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGma 235
                                        l++ +l  +D vgH  G + ++++ a++  D++ig +++a + +     +++i+++DHG a
  gene1612|gene1612|rna1611|rna1611 367 LVIANLAPPDMVGH-TG-NLEATKMAIEFTDECIGSIYKACKSN----GYTLIVTADHGNA 421
                                        78889999******.44.888999*******************9....9**********65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2993.48
//
Query:       gene1613|gene1613|rna1612|rna1612  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0028   18.2   4.7     0.0055   17.3   4.7    1.5  1  Ribosomal_60s  60s Acidic ribosomal protein


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   4.7     3e-07    0.0055      18      88 .]      25     101 .]      15     101 .] 0.49

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-07
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--SS--ST CS
                      Ribosomal_60s  18 veaarvkllvkalegkdieellangaakla.......aaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedddmGfg 86 
                                        v +++++ ++k++   +  ++++  +  ++       +++  aaa  + ++ ++   e+kkee + Eee+ +  fg
  gene1613|gene1613|rna1612|rna1612  25 VTKEKIDSVFKFFGLASHPKICEFFEMDALeiknllmSSTQEAAAPMEGKGPSDTPGEAKKEEVP-EEEEVEIDFG 99 
                                        44444444444444444444443333333344455553334444444455555555555555555.5788888888 PP

                                        TT CS
                      Ribosomal_60s  87 LF 88 
                                        +F
  gene1613|gene1613|rna1612|rna1612 100 MF 101
                                        88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 674.94
//
Query:       gene1614|gene1614|rna1613|rna1613  [L=411]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-22   80.5   0.1    1.6e-22   79.9   0.1    1.2  1  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
  ------ inclusion threshold ------
      0.045   13.9   0.0       0.69   10.1   0.0    2.5  2  CDC48_N      Cell division protein 48 (CDC48), N-terminal dom


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.1   1.8e-26   1.6e-22      24     211 .]     183     368 ..     179     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.8e-26
                                        HHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS-TTSEEEEE--TTBTT-S-SBS CS
                        DNA_pol_E_B  24 qgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesllekttvvlvPgpnDpanstvlP 99 
                                        + +    + +dvlil+G+f+d  ++   +s +    +  + ++  +l+++l++  +  +v+lvP++nD a+ +v+P
  gene1614|gene1614|rna1613|rna1613 183 DRVL--IEDVDVLILVGPFIDPLQNDTSESPG----SMMERVFIPKLKEWLSRR-SDSKVILVPSTNDMACLNVFP 251
                                        5555..6789***********76666644443....456666666666666665.589****************** PP

                                        B----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHH.............HS-HHHH CS
                        DNA_pol_E_B 100 qqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesnt.............dverlrk 162
                                        q P+      +i+    ++++v+NP+++ ln+  ++++s d+  +++ e+   +++              ++rl++
  gene1614|gene1614|rna1613|rna1613 252 QGPI------DISDE--RIVCVSNPCEFFLNEFLIAISSLDTALEISSEECFYDSKsenekdacgkllfGNDRLER 319
                                        ****......33333..489***************************999988888899***************** PP

                                        HHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEEE---SS--EEE CS
                        DNA_pol_E_B 163 lvktildqrhlaPlaptlrpvswdkddalvleplPdvlvlpdelpeFak 211
                                        ++ +++ qr + P++p++  vs+   +  ++++ Pd+++++++l++F++
  gene1614|gene1614|rna1613|rna1613 320 ISYHLIFQRTFLPVFPSMNVVSYSVPESISMDTAPDIYIIVSKLKYFCR 368
                                        ***********************************************95 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   7.7e-05      0.69      16      43 ..     106     133 ..      96     139 .. 0.89
   2 ?    0.2   0.0     0.098   8.8e+02      12      53 ..     231     269 ..     223     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7.7e-05
                                        EEEE-HHHHHHHTS-TTSEEEEECCCCE CS
                            CDC48_N  16 ivridpedmeelglepgdvveiegkrkT 43 
                                        iv ++ e +++++++pg++v i+gk+ T
  gene1614|gene1614|rna1613|rna1613 106 IVKLNLEHLQRYSVFPGQIVAIKGKNGT 133
                                        89999*******************9755 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.098
                                        SSTTEEEE.-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTT CS
                            CDC48_N  12 vgrgivri.dpedmeelglepgdvveiegkrkTvaivwpaepe 53 
                                        ++ +++ + +++dm+ l+++p   ++i+ +r    iv+ ++p+
  gene1614|gene1614|rna1613|rna1613 231 SDSKVILVpSTNDMACLNVFPQGPIDISDER----IVCVSNPC 269
                                        5556666635689999999999999999988....66666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2455.45
//
Query:       gene1615|gene1615|rna1614|rna1614  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-06   27.2   6.4    5.7e-06   26.1   6.4    1.6  1  PHD          PHD-finger
  ------ inclusion threshold ------
      0.039   13.7   0.1      0.052   13.2   0.1    1.2  1  SHE3         SWI5-dependent HO expression protein 3
      0.082   12.8   1.7       0.35   10.7   0.3    2.0  2  Sigma70_ner  Sigma-70, non-essential region
      0.099   11.9   0.3       0.16   11.2   0.3    1.3  1  ISG65-75     Invariant surface glycoprotein
        0.1   12.6   0.3       0.51   10.4   0.0    2.1  3  DUF1732      Domain of unknown function (DUF1732)
       0.16   12.3   0.4        3.6    7.9   0.1    2.0  2  Gp-FAR-1     Nematode fatty acid retinoid binding protein (Gp
       0.21   11.1   1.4       0.89    9.1   0.3    1.9  2  DUF4795      Domain of unknown function (DUF4795)
          2    8.2   4.8         16    5.4   0.0    3.2  4  CCDC92       Coiled-coil domain of unknown function


Domain annotation for each model (and alignments):
>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   6.4   2.5e-09   5.7e-06       2      51 ..     132     177 ..     131     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.5e-09
                                        BTTTTSTTSTTSCEEEET..TTS.CEEETTTSSSTHSHHSHHSSTBSSTTTHT CS
                                PHD   2 CavCkkksdeeeelvqCd..gCk.rwfHqkClkppleseekpegewlCekCke 51 
                                        C  C++     + ++ Cd  +Ck +wfH +C++++      p+  w+C++C++
  gene1615|gene1615|rna1614|rna1614 132 C-RCGR--PPFKSMIACDstDCKrKWFHFECVGISSP----PKAPWVCPECRK 177
                                        7.7888..67899****9556*846**********66....5567******86 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.3e-05     0.052     132     206 ..      33     108 ..       9     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                                        HHHHHHHHHHHHHHHHH.HHSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               SHE3 132 qqeieeLkesleklkle.nekqleelqerissndkdidtkldsynnkkknlesieeeknkkllkkleslaseldle 206
                                        +  ie+L+++ +++k+   +k le + +++ + +k+i ++l s  ++ k+++s+ ee +kk +++++++    dle
  gene1615|gene1615|rna1614|rna1614  33 DGRIERLRRKCKRYKEKfVRKPLERYARKVGKYHKAIRKLLRSNGDSGKTFKSVIEELKKKCEELCSKADVSFDLE 108
                                        5679**********988346789**********************************9999999999887777765 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00015      0.35     103     139 ..       6      42 ..       2      54 .. 0.90
   2 ?    1.6   0.1     0.095   2.1e+02      79     110 ..      61      92 ..      44      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                        Sigma70_ner 103 kareelseefkefrLtpkqidrLveqlrslvervraq 139
                                        ++ +++ ee++++rL +  + +L+ ++ + +er+r++
  gene1615|gene1615|rna1614|rna1614   6 EVFDKMLEEIQQLRLDAIYFTKLTSRMDGRIERLRRK 42 
                                        67799*****************************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.095
                        Sigma70_ner  79 elreqyeklrkalkkkgrkskkyekareelse 110
                                        ++ + ++ +rk+l  +g + k  + ++eel +
  gene1615|gene1615|rna1614|rna1614  61 KVGKYHKAIRKLLRSNGDSGKTFKSVIEELKK 92 
                                        56677777777777777777777777777754 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   7.2e-05      0.16      66     108 ..      55      97 ..      36     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-05
                           ISG65-75  66 ienakekvdyyvekleslleeakekgtltesdaeklkkaceeA 108
                                        +e +  kv +y++ +++ll+++   g++ +s +e+lkk cee 
  gene1615|gene1615|rna1614|rna1614  55 LERYARKVGKYHKAIRKLLRSNGDSGKTFKSVIEELKKKCEEL 97 
                                        677889**********************************995 PP

>> DUF1732  Domain of unknown function (DUF1732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.79   1.8e+03      20      34 ..       2      16 ..       1      34 [. 0.72
   2 ?   -1.4   0.0       1.1   2.4e+03      15      28 ..      35      48 ..      21      65 .. 0.64
   3 ?   10.4   0.0   0.00023      0.51      19      59 ..      62     102 ..      52     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.79
                            DUF1732 20 kshlkelrelleeee 34
                                       +sh++ ++++lee +
  gene1615|gene1615|rna1614|rna1614  2 QSHFEVFDKMLEEIQ 16
                                       677777777776543 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                            DUF1732 15 ElvRlkshlkelre 28
                                        ++Rl+  +k+++e
  gene1615|gene1615|rna1614|rna1614 35 RIERLRRKCKRYKE 48
                                       45666666666655 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00023
                            DUF1732  19 lkshlkelrelleeeesvGrkLdFllQElnReanTigskan 59 
                                        + ++ k++r+ll+++++ G+++  ++ El++ +  ++ska 
  gene1615|gene1615|rna1614|rna1614  62 VGKYHKAIRKLLRSNGDSGKTFKSVIEELKKKCEELCSKAD 102
                                        5678899********************************85 PP

>> Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FAR-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.05   1.1e+02      57      96 ..      25      64 ..       8      73 .. 0.83
   2 ?    7.9   0.1    0.0016       3.6      25      57 ..      68     101 ..      61     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.05
                           Gp-FAR-1 57 aeklqaklkekvdkLspeakeFvkkliakgrkleaqvlag 96
                                       + kl + ++ +++ L+ + k + +k + k ++ +a+ + +
  gene1615|gene1615|rna1614|rna1614 25 FTKLTSRMDGRIERLRRKCKRYKEKFVRKPLERYARKVGK 64
                                       5789999999***************998888888876655 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                           Gp-FAR-1  25 qlkevvkn.ykgyknedellaalKkkspaLyeka 57 
                                        +++++ ++  ++ k+ + ++++lKkk ++L +ka
  gene1615|gene1615|rna1614|rna1614  68 AIRKLLRSnGDSGKTFKSVIEELKKKCEELCSKA 101
                                        455555554999******************9987 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.003       6.8     111     155 ..       8      49 ..       1      55 [. 0.84
   2 ?    9.1   0.3    0.0004      0.89       7      82 ..      27     102 ..      25     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.003
                            DUF4795 111 lkkaldtLqeelkekldrlelepLkeqleerlkelqkelqeamek 155
                                         +k+l+++q   + +ld++ +++L +++++r++ l+ + + + ek
  gene1615|gene1615|rna1614|rna1614   8 FDKMLEEIQ---QLRLDAIYFTKLTSRMDGRIERLRRKCKRYKEK 49 
                                        678888888...899********************9999877654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0004
                            DUF4795   7 ellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkad..keeveeelaekadkeaLatk 80 
                                        +l + +   ie l +++++   k k + k le++ +k+   +k+i++l  +++d  k+  +  +++k  +e L++k
  gene1615|gene1615|rna1614|rna1614  27 KLTSRMDGRIERLRRKCKR--YKEKFVRKPLERYARKVGKYHKAIRKLLRSNGDsgKTFKSVIEELKKKCEELCSK 100
                                        5677888999999999988..777778999**********************883356667778999999999999 PP

                            DUF4795  81 vs 82 
                                        ++
  gene1615|gene1615|rna1614|rna1614 101 AD 102
                                        84 PP

>> CCDC92  Coiled-coil domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.39   8.8e+02      17      33 ..       3      19 ..       1      21 [. 0.81
   2 ?    2.8   0.1     0.046     1e+02      29      38 ..      36      45 ..      35      59 .. 0.87
   3 ?   -2.8   0.0       2.6   5.7e+03      26      37 ..      66      77 ..      64      78 .. 0.79
   4 ?    5.4   0.0    0.0071        16      29      39 ..      87      97 ..      86     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.39
                             CCDC92 17 qhaatLkgLHkEIekLq 33
                                        h ++ ++  +EI++L+
  gene1615|gene1615|rna1614|rna1614  3 SHFEVFDKMLEEIQQLR 19
                                       57788888889****98 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.046
                             CCDC92 29 IekLqkenkd 38
                                       Ie+L++++k 
  gene1615|gene1615|rna1614|rna1614 36 IERLRRKCKR 45
                                       9*******95 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.6
                             CCDC92 26 HkEIekLqkenk 37
                                       Hk I+kL + n 
  gene1615|gene1615|rna1614|rna1614 66 HKAIRKLLRSNG 77
                                       999999988875 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0071
                             CCDC92 29 IekLqkenkdL 39
                                       Ie+L+k++ +L
  gene1615|gene1615|rna1614|rna1614 87 IEELKKKCEEL 97
                                       99********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1210  (0.0674884); expected 358.6 (0.02)
Passed bias filter:                      803  (0.0447878); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1178.93
//
Query:       gene1616|gene1616|rna1615|rna1615  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-18   64.1   0.1    2.2e-17   62.9   0.0    1.7  2  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1      0.49   8.7e+03      38      46 ..      41      49 ..      33      58 .. 0.52
   2 !   62.9   0.0   1.2e-21   2.2e-17       1      63 []      62     123 ..      62     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.49
                                       HHHHHHHHH CS
                               DnaJ 38 eaeekFkei 46
                                       +a+++F   
  gene1616|gene1616|rna1615|rna1615 41 KARKAFSLH 49
                                       455555544 PP

  == domain 2  score: 62.9 bits;  conditional E-value: 1.2e-21
                                        HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                               DnaJ   1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63 
                                        dyY+iLgv+kda++ +Ik+a+  l++k+HPD+  +  e++     i++Ay +L +pekR++YD
  gene1616|gene1616|rna1615|rna1615  62 DYYDILGVPKDATQPQIKRAFNMLIMKFHPDRT-GMHESSAVSGMIQNAYTTLGNPEKRRRYD 123
                                        8********************************.8888888899******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1156.33
//
Query:       gene1617|gene1617|rna1616|rna1616  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.9e-49  163.2   3.8    2.7e-18   65.5   0.3    3.6  3  RRM_1        RNA recognition motif. (a.k.a. RRM, RBD, or RNP 
    4.4e-07   29.8   0.8     0.0049   16.8   0.1    3.4  3  Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
    5.2e-06   26.5   1.5       0.17   12.0   0.1    4.1  3  RRM_7        RNA recognition motif
     0.0045   17.0   1.3       0.11   12.6   0.0    3.0  4  RRM_3        RNA binding motif
     0.0073   16.3   0.0        1.1    9.4   0.0    3.2  3  RNA_bind     RNA binding domain
  ------ inclusion threshold ------
       0.01   16.2   2.2        1.6    9.2   0.2    2.8  2  NOP5NT       NOP5NT (NUC127) domain
      0.016   15.4   0.7         13    5.9   0.1    4.0  5  PHM7_cyt     Cytosolic domain of 10TM putative phosphate tran
       0.02   14.8   0.0       0.23   11.5   0.0    2.6  2  RL           RL domain
      0.025   14.8   0.0      0.051   13.7   0.0    1.5  1  ExbD         Biopolymer transport protein ExbD/TolR


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.3   1.4e-21   2.7e-18       1      67 [.      13      82 ..      13      85 .. 0.88
   2 !   56.5   0.1   9.3e-19   1.9e-15       2      62 ..     109     170 ..     108     176 .. 0.94
   3 !   40.5   0.0     9e-14   1.8e-10       1      69 [.     215     283 ..     215     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.4e-21
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHH...HTTEEETTE CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlea...lngkklggr 67
                                       +fV+nLp++ t ++L + Fs fG+i+s+k+ ++ +gkskg++fV+F+ k +A+k +++   lng +lgg+
  gene1617|gene1617|rna1616|rna1616 13 IFVKNLPESFTSKDLDDAFSMFGEIVSCKVATTPQGKSKGYGFVQFKEKKAAKKVIKNfnnLNGLMLGGN 82
                                       8*******************************************************97222455566665 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 9.3e-19
                                        EEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTT.E CS
                              RRM_1   2 fVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealng.k 62 
                                        f++n+p d+te+eL el+  +G+++s+  + + +gk+kgfaf +Fes+e+A +A+++l+g  
  gene1617|gene1617|rna1616|rna1616 109 FIKNFPVDTTEKELLELLVRYGKVTSLYFPIKDDGKPKGFAFANFESHESALNAINNLHGaF 170
                                        9**********************************************************944 PP

  == domain 3  score: 40.5 bits;  conditional E-value: 9e-14
                                        EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                              RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                        l+++n+p+    eeL  +F++fG+i+s ++  d  ++ k +a++ + ++e+A  A+e+ n+  l+g++l
  gene1617|gene1617|rna1616|rna1616 215 LYITNIPEGFGAEELNNIFKEFGSITSMSVGIDGANSQKQYAYICYSTPEEASIAVERGNEIYLDGNRL 283
                                        8*****************************************************************987 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0018       3.6      21      51 ..      31      66 ..      31      67 .. 0.92
   2 ?    1.6   0.0      0.14   2.8e+02      21      52 ..     126     162 ..     117     163 .. 0.82
   3 !   16.8   0.1   2.5e-06    0.0049      21      53 .]     233     270 ..     222     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0018
                        Nup35_RRM_2 21 FasfGeIvkhyvp.....kevsvmyvkfesekdaek 51
                                       F  fGeIv   v      k++ + +v+f+ +k+a+k
  gene1617|gene1617|rna1616|rna1616 31 FSMFGEIVSCKVAttpqgKSKGYGFVQFKEKKAAKK 66
                                       566******999999999999*************97 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                        Nup35_RRM_2  21 FasfGeIvkhyvp.....kevsvmyvkfesekdaekA 52 
                                        +  +G+++  y+p     k + +++  fes  +a  A
  gene1617|gene1617|rna1616|rna1616 126 LVRYGKVTSLYFPikddgKPKGFAFANFESHESALNA 162
                                        5569*********999996688999999999999877 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 2.5e-06
                        Nup35_RRM_2  21 FasfGeIvkhyvp.....kevsvmyvkfesekdaekAL 53 
                                        F++fG I+ ++v+     +++ ++y+++ ++ +a +A+
  gene1617|gene1617|rna1616|rna1616 233 FKEFGSITSMSVGidganSQKQYAYICYSTPEEASIAV 270
                                        99***************9889**************997 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   8.6e-05      0.17       3      73 ..      12      74 ..      10     102 .. 0.75
   2 !    7.7   0.0    0.0019       3.8       4      37 ..     108     142 ..     106     172 .. 0.74
   3 ?    2.9   0.1     0.058   1.2e+02       5      29 ..     216     240 ..     212     300 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.6e-05
                              RRM_7  3 kvFvGGlPiDiteeelkatfkefgkvlvdwPkkaeskkkaaenskaakgyvflvfedeksvkaLleactee 73
                                        +Fv  lP   t ++l ++f+ fg+++    k a +++         kgy f+ f+++k+ k+++++ ++ 
  gene1617|gene1617|rna1616|rna1616 12 NIFVKNLPESFTSKDLDDAFSMFGEIVS--CKVATTPQ------GKSKGYGFVQFKEKKAAKKVIKNFNNL 74
                                       59**********************9863..22222222......2357***************99987655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0019
                              RRM_7   4 vFvGGlPiDiteeelkatfkefgkvl.vdwPkkae 37 
                                         F+   P+D te+el + + ++gkv+ + +P k  
  gene1617|gene1617|rna1616|rna1616 108 CFIKNFPVDTTEKELLELLVRYGKVTsLYFPIKDD 142
                                        589999******************96256676643 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.058
                              RRM_7   5 FvGGlPiDiteeelkatfkefgkvl 29 
                                        ++  +P     eel++ fkefg+++
  gene1617|gene1617|rna1616|rna1616 216 YITNIPEGFGAEELNNIFKEFGSIT 240
                                        6677788888889999999999875 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   5.3e-05      0.11      11      85 ..      20     100 ..      12     104 .. 0.73
   2 ?   -2.6   0.0       2.9   5.9e+03      15      55 ..     119     164 ..     113     169 .. 0.48
   3 ?   -2.6   0.1       2.8   5.6e+03       7      26 ..     186     205 ..     184     207 .. 0.80
   4 ?    1.7   0.0      0.13   2.7e+02      15      60 ..     226     276 ..     215     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                                        SS--HHHHHHHCHCCS-ECEEEE-...TTSSE..EEEEESSHHHHHHHHHHHHHC.-B-CCTSSEEEEE--HHHHH CS
                              RRM_3  11 kelsredikellsklgevayvdye...kgdke..gevrFkedeeakkalekatea.klkikdaevtlelLeGeeEk 80 
                                        +  + +d+ +++s +ge+    ++   +g+++  g v+Fke+++akk++++  +   l++  +++ +el + +  k
  gene1617|gene1617|rna1616|rna1616  20 ESFTSKDLDDAFSMFGEIVSCKVAttpQGKSKgyGFVQFKEKKAAKKVIKNFNNLnGLMLGGNKIAVELYNPDMKK 95 
                                        566788899999999966544433111455552256***************9999889999999999988877766 PP

                                        HHHHH CS
                              RRM_3  81 eywkk 85 
                                         + kk
  gene1617|gene1617|rna1616|rna1616  96 GESKK 100
                                        66555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                                        HHHHHHHCHCCS-EC..EEEE-TTSSE...EEEEESSHHHHHHHHH CS
                              RRM_3  15 redikellsklgeva..yvdyekgdke...gevrFkedeeakkale 55 
                                         +++ ell ++g+v   y   +++ k    +   F+++e+a +a++
  gene1617|gene1617|rna1616|rna1616 119 EKELLELLVRYGKVTslYFPIKDDGKPkgfAFANFESHESALNAIN 164
                                        5566666666666641133223222221112344555555655555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.8
                                        EE-SSS--HHHHHHHCHCCS CS
                              RRM_3   7 sGlnkelsredikellsklg 26 
                                        +G  ke   e++++++++l+
  gene1617|gene1617|rna1616|rna1616 186 KGQRKEERAEELRKMFEQLS 205
                                        57788888899999999876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.13
                                        HHHHHHHCHCCS.....-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC CS
                              RRM_3  15 redikellsklg.....evayvdyekgdkegevrFkedeeakkalekatea 60 
                                         e++ ++++++g     +v+  + ++ ++ +++ + ++eea  a+e   e+
  gene1617|gene1617|rna1616|rna1616 226 AEELNNIFKEFGsitsmSVGIDGANSQKQYAYICYSTPEEASIAVERGNEI 276
                                        577888999999333333333334555667899999999999999988777 PP

>> RNA_bind  RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00053       1.1       9      62 ..      11      71 ..       3      79 .. 0.70
   2 ?   -2.0   0.0         2   3.9e+03      12      35 ..     109     132 ..     104     135 .. 0.85
   3 ?    2.9   0.0     0.056   1.1e+02       8      36 ..     212     240 ..     207     276 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00053
                                       EEEEEEE--TT--HHHHHHHTTTSEEEEEEEEETT....E...EEEEEEEE-HHHHHHHHH CS
                           RNA_bind  9 eHvfyvtFPkeWktsDivqlFspfGsvyvsWlddt....s...AfvaLhrrdqasvvlktl 62
                                         +f    P+++  +D+ + Fs fG++    +  t    s    fv  +++++a+ v+k+ 
  gene1617|gene1617|rna1616|rna1616 11 GNIFVKNLPESFTSKDLDDAFSMFGEIVSCKVATTpqgkSkgyGFVQFKEKKAAKKVIKNF 71
                                       56888899*****************986444443311111222688888888888888876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2
                                        EEEE--TT--HHHHHHHTTTSEEE CS
                           RNA_bind  12 fyvtFPkeWktsDivqlFspfGsv 35 
                                        f   FP +  ++++++l   +G+v
  gene1617|gene1617|rna1616|rna1616 109 FIKNFPVDTTEKELLELLVRYGKV 132
                                        55579999999999****9**998 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.056
                                        XEEEEEEE--TT--HHHHHHHTTTSEEEE CS
                           RNA_bind   8 ReHvfyvtFPkeWktsDivqlFspfGsvy 36 
                                        R+ ++    P+ +  +++ + F+ fGs+ 
  gene1617|gene1617|rna1616|rna1616 212 RKNLYITNIPEGFGAEELNNIFKEFGSIT 240
                                        556666678999999***********875 PP

>> NOP5NT  NOP5NT (NUC127) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0088        18       7      36 ..      50      76 ..      44      79 .. 0.84
   2 ?    9.2   0.2   0.00081       1.6      45      62 ..     149     166 ..     146     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0088
                             NOP5NT  7 aaGYaLfkvkdkkllkkddlvkdsvsdlek 36
                                       + GY+  + k+kk  kk  ++k+ +++l+ 
  gene1617|gene1617|rna1616|rna1616 50 SKGYGFVQFKEKKAAKK--VIKN-FNNLNG 76
                                       78*************99..5555.999876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00081
                             NOP5NT  45 aFqkFesaaeALenanai 62 
                                        aF+ Fes ++AL+++n++
  gene1617|gene1617|rna1616|rna1616 149 AFANFESHESALNAINNL 166
                                        8***************87 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         1     2e+03       4      25 ..      13      33 ..      12      47 .. 0.69
   2 ?    5.9   0.1    0.0067        13     118     140 ..      47      69 ..      36      81 .. 0.81
   3 ?    3.0   0.0     0.054   1.1e+02      91     139 ..     110     163 ..      82     177 .. 0.67
   4 ?   -0.6   0.0       0.7   1.4e+03       4      14 ..     215     225 ..     184     235 .. 0.58
   5 ?    0.8   0.0      0.25   4.9e+02       4      28 ..     215     238 ..     212     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1
                           PHM7_cyt  4 vlvtgiPkelrseeklkeffee 25
                                       ++v+++P++ +s+ +l++ f+ 
  gene1617|gene1617|rna1616|rna1616 13 IFVKNLPESFTSK-DLDDAFSM 33
                                       799*******977.35555543 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0067
                           PHM7_cyt 118 kkkplgaaFvtfesersaaavak 140
                                        + k +g++Fv+f+++++a++v+k
  gene1617|gene1617|rna1616|rna1616  47 QGKSKGYGFVQFKEKKAAKKVIK 69 
                                        56889***********9999976 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.054
                           PHM7_cyt  91 kkvdaidyyrekleeldeeieeerekv.....kkkplgaaFvtfesersaaava 139
                                         k   +d  +++l el  ++ +  + +     + kp+g aF  fes +sa +++
  gene1617|gene1617|rna1616|rna1616 110 IKNFPVDTTEKELLELLVRYGKVTSLYfpikdDGKPKGFAFANFESHESALNAI 163
                                        355666667777777777777777655666656799**********99997775 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.7
                           PHM7_cyt   4 vlvtgiPkelr 14 
                                        + +t+iP+   
  gene1617|gene1617|rna1616|rna1616 215 LYITNIPEGFG 225
                                        34555555555 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.25
                           PHM7_cyt   4 vlvtgiPkelrseeklkeffeelyp 28 
                                        + +t+iP+     e+l+++f+e+  
  gene1617|gene1617|rna1616|rna1616 215 LYITNIPEGFG-AEELNNIFKEFGS 238
                                        679********.6669****99764 PP

>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.58   1.2e+03      21      42 ..      18      39 ..      14      72 .. 0.70
   2 ?   11.5   0.0   0.00011      0.23      20      62 ..     112     158 ..     108     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.58
                                 RL 21 cpskisekkllkylsqhGkink 42
                                       +p+ ++ k+l + +s++G+i +
  gene1617|gene1617|rna1616|rna1616 18 LPESFTSKDLDDAFSMFGEIVS 39
                                       6778888888888999998865 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                                 RL  20 scpskisekkllkylsqhGkinkhFf.Yeskgv...yavvEFsekes 62 
                                        + p +++ek+ll+ l ++Gk+++++f  +  g    +a   F+++es
  gene1617|gene1617|rna1616|rna1616 112 NFPVDTTEKELLELLVRYGKVTSLYFpIKDDGKpkgFAFANFESHES 158
                                        56889*****************9887255666677788888887777 PP

>> ExbD  Biopolymer transport protein ExbD/TolR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.051      34      88 ..     240     298 ..     232     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                               ExbD  34 eplevdlPsssstqk....eveekelirisisadgsiyldkkavsveelaqklkerkak 88 
                                        +++ v +  ++s+++    +++ +e+  i+++  ++iyld+++++v+++++kl+ +k+k
  gene1617|gene1617|rna1616|rna1616 240 TSMSVGIDGANSQKQyayiCYSTPEEASIAVERGNEIYLDGNRLQVSYFKNKLERMKEK 298
                                        556666666666666789999**********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 2401.05
//
Query:       gene1619|gene1619|rna1618|rna1618  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-21   74.7   0.0    1.3e-20   73.3   0.0    1.8  1  TAF            TATA box binding protein associated factor (TA
      5e-19   68.4   0.0    1.1e-18   67.4   0.0    1.6  1  TAF6_C         TAF6 C-terminal HEAT repeat domain
  ------ inclusion threshold ------
      0.039   14.2   1.7       0.47   10.8   0.0    3.2  3  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a


Domain annotation for each model (and alignments):
>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   2.2e-24   1.3e-20       3      65 ..       2      64 ..       1      65 [. 0.98

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 2.2e-24
                                       ---HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH CS
                                TAF  3 ilpkesvkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsAL 65
                                       +++ke++k  A+s Gi+n+ d+a+++L +d+eyr+ke+ qe +kfm  skR+kL+ +D+++AL
  gene1619|gene1619|rna1618|rna1618  2 LFSKETLKSFAQSKGISNIDDDALRVLSQDLEYRIKEVCQEGSKFMVGSKRTKLSIDDINYAL 64
                                       689***********************************************************8 PP

>> TAF6_C  TAF6 C-terminal HEAT repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   1.8e-22   1.1e-18       2      88 ..     252     330 ..     251     332 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.8e-22
                             TAF6_C   2 ltcllakklgakseledhwaLRdfAAslLakilkkysssyktLkprvtrtllkvlldpkkslgtlyGallglaalG 77 
                                        +tc+++k++        + ++R+ AA++++++++++s syktL pr+++tl+k++ld++k+ +t+yGall+l++l 
  gene1619|gene1619|rna1618|rna1618 252 ITCVIGKSV--------DDEVRRVAADVVKYVFSNFSGSYKTLAPRIINTLSKAWLDKEKTESTQYGALLCLSSLS 319
                                        789999999........5689******************************************************* PP

                             TAF6_C  78 eeavrklvlpn 88 
                                        +++v++++ p+
  gene1619|gene1619|rna1618|rna1618 320 KHVVETVIKPK 330
                                        ********997 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.9e-05      0.47      16      65 .]      15      64 ..      10      64 .. 0.94
   2 ?   -0.6   0.5      0.28   1.7e+03      10      41 ..     175     209 ..     173     221 .. 0.58
   3 ?   -0.4   0.0      0.25   1.5e+03      14      29 ..     259     275 ..     256     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.9e-05
                                       TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                      CBFD_NFYB_HMF 16 pdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                       +++ +i +dA  ++++ +e  i+e+++e+++ +  +kr  ++ ++i  A+
  gene1619|gene1619|rna1618|rna1618 15 KGISNIDDDALRVLSQDLEYRIKEVCQEGSKFMVGSKRTKLSIDDINYAL 64
                                       68999*****************************************9886 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.28
                                        HHHHCCTTXS-B-HHHHHH...HHHHHHHHHHHHH CS
                      CBFD_NFYB_HMF  10 kImksdpdarkiakdAkel...iaecveefieela 41 
                                        k+++ ++ +++ia +  +    i++ v  f++++ 
  gene1619|gene1619|rna1618|rna1618 175 KVIQAMETDEQIAMECLHNesgIQQLVPYFVHHFN 209
                                        66666666666766654422226666666666664 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.25
                                        CC.TTXS-B-HHHHHHH CS
                      CBFD_NFYB_HMF  14 sd.pdarkiakdAkeli 29 
                                        s  +++r++a d+ +++
  gene1619|gene1619|rna1618|rna1618 259 SVdDEVRRVAADVVKYV 275
                                        55589999****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2327.18
//
Query:       gene1620|gene1620|rna1619|rna1619  [L=254]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-19   68.5   2.1      2e-17   63.1   2.1    3.0  1  ORC2      Origin recognition complex subunit 2


Domain annotation for each model (and alignments):
>> ORC2  Origin recognition complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   2.1   1.1e-21     2e-17      44     323 ..      14     235 ..       2     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 1.1e-21
                                        HHHHHHHTT-EEEE--SS--HHHHHHHHSSS----SSS-EEEE----TT--SHHHHHHHHHTT--S.---SSS--H CS
                               ORC2  44 qwlfeLeqGFslllyGvGSKrklleeFaeellskrkdgpvvvvnGylpsltlkdilseiasallekkeakklsssv 119
                                        + ++ L+  F++l+yG+GSK+ ll++   +++              ++++   +il+ei +++   ++ + +  s 
  gene1620|gene1620|rna1619|rna1619  14 KEYNVLTRSFNILFYGYGSKKPLLKKMFPTAIY---------L--NCRTMGRHEILAEIVDTVRRRSRLETQRVSK 78 
                                        55677999****************997666332.........3..36889999********999996666666666 PP

                                        HHHHHHHHHHHHS--S-..S--EEEES-SSSTTTTSHHHHHHHHTTTT-SSSEEEEE--STTHHHH--HHHHTTS- CS
                               ORC2 120 aaqlekilslleekeseeksklylvihniDgpsLrkekaqalLarLaaipqIhliasiDhinapllwdssklsqfn 195
                                        + +++ i + + +++    +k  l+  n+D  +L            + +++ +++ +i+ ++  + ++ +  ++fn
  gene1620|gene1620|rna1619|rna1619  79 TSTIKDIDEAIGTRK----EKYKLIMANFDFSMLEF----------SGLKNFAILGTIEGVD--IRFSLEDIERFN 138
                                        677777777776553....5689**********987..........5578889999999887..567889999*** PP

                                        EEE---------GGGGGG--.-TT---.--.----HHHHHHHHHHS-HHHHHHHHHHHHHHHT------------- CS
                               ORC2 196 fvfhdvtTfapysaElsfedevlellgrskrrvggkegakfVLkSLtenarklfklLveeqLekkeseekkekskk 271
                                        f+f d+tTf+py++E+     +  +lg     +++ e+ + V++S++ n+r ++k     +L              
  gene1620|gene1620|rna1619|rna1619 139 FIFRDLTTFDPYEEEI-----IGIHLG-----ATKVEASSRVVSSVPRNSRVVLKE----ILL------------- 187
                                        ***************9.....334455.....467889999*********976654....444............. PP

                                        -------BHHHHHHHHHHS--SSSGGGHHHHHHHHTTTTSS-B--------B CS
                               ORC2 272 gseeagveykelynkareefivssemalrtlLkEFkDHklikskkdasgtev 323
                                          +e  v+++el+++ +++ + +s+++  ++++EF+DH+l+k+k+   gtev
  gene1620|gene1620|rna1619|rna1619 188 -CNEDTVSLSELFERTKRKLFLTSKASVLSMISEFIDHGLLKIKN---GTEV 235
                                        .47889************************************854...4454 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1548.12
//
Query:       gene162|gene162|rna162|rna162  [L=526]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-09   36.4   0.0    1.7e-08   34.7   0.0    2.0  2  XPG_I      XPG I-region
  ------ inclusion threshold ------
      0.098   12.9   0.2       0.94    9.7   0.0    2.5  2  AAA_lid_1  AAA+ lid domain


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.1     1e+04      29      43 ..      92     106 ..      88     131 .. 0.70
   2 !   34.7   0.0   1.9e-12   1.7e-08       3      94 .]     141     225 ..     139     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
                                    EEE-SSSHHHHTT-S CS
                          XPG_I  29 aviseDsDlllFGap 43 
                                    ++   DsD+ll  + 
  gene162|gene162|rna162|rna162  92 GISHADSDTLLSEGL 106
                                    556679999985554 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 1.9e-12
                                    HT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-S.EEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT--H CS
                          XPG_I   3 mgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGap.kvlrnlskkkskkkkekekkkvevidlekvlkelgltr 81 
                                     g+ +++Ap+ A AqcayL++++ ++++  + sD+llF +  k++ ++s+++ k         ++v++ ++ l+ ++l++
  gene162|gene162|rna162|rna162 141 KGVVVITAPYSATAQCAYLMSAEACSYAFGK-SDVLLFDGVdKIILDMSDGSGKP-------CLDVFHKSRFLEFFNLNS 212
                                    6999************************998.******6654******9444444.......59**************** PP

                                    HHHHHHHHHHCET CS
                          XPG_I  82 eqlidlaillgcD 94 
                                      +  l +llgcD
  gene162|gene162|rna162|rna162 213 RTFSALGLLLGCD 225
                                    ************9 PP

>> AAA_lid_1  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0001      0.94      29      53 ..      42      66 ..      21      78 .. 0.85
   2 ?   -0.8   0.1       0.2   1.8e+03      46      66 ..     433     455 ..     423     469 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0001
                      AAA_lid_1 29 lrdlsnifqgllfssaevlkapldl 53
                                     d+s i++gllf   ev+kapl  
  gene162|gene162|rna162|rna162 42 YVDVSSIWKGLLFGIEEVVKAPLSK 66
                                   5699******************975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                      AAA_lid_1  46 vlkapldlirl..ylheservyg 66 
                                     lk  + l+rl  y++e + vy 
  gene162|gene162|rna162|rna162 433 TLKYYVRLVRLfnYIKEVKEVYE 455
                                    67778889998555788888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3625.53
//
Query:       gene1621|gene1621|rna1620|rna1620  [L=1063]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-31  108.4   3.6    3.3e-31  108.4   3.6    2.7  3  Sec7      Sec7 domain


Domain annotation for each model (and alignments):
>> Sec7  Sec7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.26   4.6e+03       9      40 ..     148     182 ..     135     191 .. 0.72
   2 !  108.4   3.6   1.8e-35   3.3e-31      36     182 ..     326     479 ..     299     480 .. 0.84
   3 ?    0.2   0.0     0.029   5.3e+02      14      69 ..     580     646 ..     555     676 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.26
                                        HHHHHH-HHHHHHHHHHCCCC...TSSHHHHHHHH CS
                               Sec7   9 aekFnkkpkkgikyliekgll...eedpksiakfl 40 
                                         + F +k k+++  +++++++    ++++ ia+f+
  gene1621|gene1621|rna1620|rna1620 148 FKVFLEKKKEFLRLFADRKMYkdiGCTEDLIANFC 182
                                        56677788888888888888854445577777776 PP

  == domain 2  score: 108.4 bits;  conditional E-value: 1.8e-35
                                        HHHHHHHTCCS-HHHHHHHHCSGGHHHHHHHHHHHCTS--TT--HHHHHHHHCCCS-B-SSHHHHHHHHHHHHHHH CS
                               Sec7  36 iakflketpgldkkklGeylgkekefnkevlkefvdlfdfsglrldeAlRlflssfrlpgEaqkierilekFaeky 111
                                          ++l++ ++ d kklG +l+k k  n+  l+ f+d+fdf ++ + + lR+fl sf l  E q i r++e++a+ky
  gene1621|gene1621|rna1620|rna1620 326 SLELLRYFEETDLKKLGAFLCKLK--NEAYLRIFADTFDFFDMAVLDGLRMFLLSFYLSAEGQVIHRVIEVYADKY 399
                                        34667777999*************..************************************************** PP

                                        HHTTC.........TCG-SHHHHHHHHHHHHHHHHHHC-TTSCCS--HHHHHHCTTTTBTTB---HHHHHHHHHHH CS
                               Sec7 112 feqnp.........evfenadavfvLaysiimLntdlhnpqvkkkmtledFiknnrgindgkdlpeefLeeiYdsI 178
                                        + +n          +  ++++ vf L++s ++Lnt+ hnp+vk k t++d++k +   +   ++  e+Le++Y+sI
  gene1621|gene1621|rna1620|rna1620 400 YLDNAgrctfmdidKDNKTKEFVFNLSFSFLVLNTKFHNPNVKAKPTFKDYMKDFTAEEIPLSFRMEYLESMYQSI 475
                                        *7664333333333445899***********************************87666569************* PP

                                        HHS- CS
                               Sec7 179 keee 182
                                        k+++
  gene1621|gene1621|rna1620|rna1620 476 KKKP 479
                                        *997 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.029
                                        H-HHHHHHHHHHCCCCTSSHHHHHHHHHHTCCS-HHHHHHHHCSGG...........HHHHHHHHHH CS
                               Sec7  14 kkpkkgikyliekglleedpksiakflketpgldkkklGeylgkek...........efnkevlkef 69 
                                        ++  k+i+ +i    ++ +++  a++l   +++dk++ G+ l++             +++++ ++++
  gene1621|gene1621|rna1620|rna1620 580 EDTLKFIESFIYYFRMKGNASLYATLLDVLSKIDKQRSGSVLSDFGisflknspgkdRIQQQYRDAY 646
                                        3333333333333333444555555555556666666666666333333333344444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1063 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.50
# Mc/sec: 6337.63
//
Query:       gene1622|gene1622|rna1621|rna1621  [L=886]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   25.4   0.1    3.2e-05   24.3   0.1    1.6  1  RhoGEF    RhoGEF domain


Domain annotation for each model (and alignments):
>> RhoGEF  RhoGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   1.8e-09   3.2e-05      25     161 ..     257     402 ..     227     421 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.8e-09
                                        CCCHHCTCCHHHHHHHHCTTHHHHHHHHHHHHHHHHHHHH.............................HHHTTSS CS
                             RhoGEF  25 kplselevlseeeikiiFsnieeilelhrsflleeLeerl...........................k.eseeqke 72 
                                        k      + ++   +++F  + +++++  + +++++++                             + e ++++ 
  gene1622|gene1622|rna1621|rna1621 257 KV-----LKEKTGFENVFKGFCKVHSFE-KRFISSMKDIAeeagfevdrvlsdpqyfasemkargfrEiEMDDKEI 326
                                        33.....346788899************.66655454444555999999999999988887666555166667777 PP

                                        -S-SHHHHHHHHSTHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSGGGTT--HHHHTTHHHHHHHHHHH CS
                             RhoGEF  73 aqsigdvflkfadkfkkYseYcsnypnalkllkelskknkkfkafleeaeerpecskldLeslLikPvqRlprYpL 148
                                         +++ d f++++d f+ Y++ +  ++++++ lk+ +           ++   p  s +  +++     qR++rYp+
  gene1622|gene1622|rna1621|rna1621 327 VERVLDSFESNLDGFRCYEDMMLSHEESIESLKKAK-----------DCAGVP--SHRVVDDCFCNCLQRIVRYPI 389
                                        8999999*****99********************43...........444445..46889**************** PP

                                        HHHHHHHTS-TTS CS
                             RhoGEF 149 LLkellkntpesh 161
                                        L++++l+n+ ++ 
  gene1622|gene1622|rna1621|rna1621 390 LIDDILRNLTDEI 402
                                        ********97763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (886 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 5932.17
//
Query:       gene1623|gene1623|rna1622|rna1622  [L=1040]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.46   11.0   1.6        1.4    9.5   0.2    2.7  3  PC_rep    Proteasome/cyclosome repeat


Domain annotation for each model (and alignments):
>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2     8e-05       1.4       1      16 [.     641     656 ..     641     664 .. 0.81
   2 ?   -3.4   0.0      0.95   1.7e+04      13      31 ..     852     870 ..     852     872 .. 0.82
   3 ?   -2.6   0.2      0.54   9.6e+03       6      15 ..     907     916 ..     907     920 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 8e-05
                                        HHHHHHHHHCTTSTCH CS
                             PC_rep   1 GAllALGlihaGsgne 16 
                                        G++ +LG+++aGsgn 
  gene1623|gene1623|rna1622|rna1622 641 GCVVGLGMLYAGSGNI 656
                                        8999**********96 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.95
                                        STCHHHHHHHHHHHHHHSS CS
                             PC_rep  13 sgneeaislLkpylsdtsa 31 
                                        s+n ++i +L+ +++ t++
  gene1623|gene1623|rna1622|rna1622 852 SCNLDVIRILRRQIKATET 870
                                        578889****999988875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.54
                                        HHHHCTTSTC CS
                             PC_rep   6 LGlihaGsgn 15 
                                        LG++ +G gn
  gene1623|gene1623|rna1622|rna1622 907 LGIVACGMGN 916
                                        8*****9666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1040 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.81u 0.35s 00:00:01.16 Elapsed: 00:00:00.55
# Mc/sec: 5664.58
//
Query:       gene1624|gene1624|rna1623|rna1623  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-19   67.6   0.2    1.2e-18   66.8   0.2    1.4  1  XPA_C        XPA protein C-terminus
     0.0045   16.7   0.1     0.0055   16.5   0.1    1.1  1  DUF4391      Domain of unknown function (DUF4391)
     0.0067   16.4   3.7      0.015   15.4   3.7    1.6  1  XPA_N        XPA protein N-terminal
  ------ inclusion threshold ------
        4.9    6.6   4.5        7.3    6.0   4.5    1.2  1  Herpes_UL56  Herpesvirus UL56 protein
        8.2    5.0   8.2         10    4.6   8.2    1.1  1  TT_ORF1      TT viral orf 1


Domain annotation for each model (and alignments):
>> XPA_C  XPA protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.2   3.3e-22   1.2e-18       2      51 .]      72     118 ..      71     118 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 3.3e-22
                              XPA_C   2 ysLiTkTeakedYLLtdedLkdrelLkflkkkNPhnstwgdMkLYlklqV 51 
                                        ++++TkT++++dYLLt+++Lk+   L+fl+++NP+++tw++M LYl+++V
  gene1624|gene1624|rna1623|rna1623  72 LKFVTKTSCISDYLLTNDELKE---LRFLERPNPRKGTWSNMYLYLQSEV 118
                                        689*******************...**********************998 PP

>> DUF4391  Domain of unknown function (DUF4391)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.5e-06    0.0055     108     220 ..      62     163 ..      37     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-06
                            DUF4391 108 ahkRlnqadkgkivleeefitewlpedeeslelekasdieaafldalalknlpktdlkalYqelidklialeaasl 183
                                         + R  + ++ k+v++ + i++ l +++e  el         fl+  + ++ + ++++ + q+ ++ +++ +    
  gene1624|gene1624|rna1623|rna1623  62 SVCRTCRCNALKFVTKTSCISDYLLTNDELKEL--------RFLERPNPRKGTWSNMYLYLQSEVEEIAIRKW--- 126
                                        555666666778888899999988555555555........67777777777777777777777777777666... PP

                            DUF4391 184 tgefsl.eskediaerrerlaeieelekeiaklkkklk 220
                                         g + + e++++  +rr+  ++i++l+k+i++l+++ +
  gene1624|gene1624|rna1623|rna1623 127 -GSLDKvEETKRGRKRRADDRKIRRLKKRIKELRRRTR 163
                                        .9999999**************************9865 PP

>> XPA_N  XPA protein N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.7   4.1e-06     0.015       3      29 ..      42      68 ..      40      70 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.1e-06
                              XPA_N  3 kCdeCgkefldSyLldnFdysVCDkCR 29
                                       +C+ C ++ ldS   ++F+ sVC +CR
  gene1624|gene1624|rna1623|rna1623 42 RCKYCLQIPLDSEMKKTFGISVCRTCR 68
                                       7*************************9 PP

>> Herpes_UL56  Herpesvirus UL56 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.5     0.002       7.3      69      99 ..     131     161 ..     118     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.002
                        Herpes_UL56  69 egevsergrsrraaqraarrarrraerrarr 99 
                                        + e ++rgr rra  r  rr ++r +   rr
  gene1624|gene1624|rna1623|rna1623 131 KVEETKRGRKRRADDRKIRRLKKRIKELRRR 161
                                        568899***************9997543333 PP

>> TT_ORF1  TT viral orf 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   8.2    0.0029        10      25      86 ..     127     189 ..      99     195 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0029
                            TT_ORF1  25 rrrrrrrrvRR.Rrrgrrrrr.rrrrrrrrrrrkrkklilkqwqPetirkckIkGllplvicge 86 
                                         +  + + ++R R+r+   r+ rr  +r +  r+r ++ ++    ++i+  k++G ++ + cg 
  gene1624|gene1624|rna1623|rna1623 127 GSLDKVEETKRgRKRRADDRKiRRLKKRIKELRRRTRIDVRND-EKHIHTFKVEGDICRCECGM 189
                                        4444444444544443444444777777777777777777764.47888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1237  (0.0689944); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1329.54
//
Query:       gene1625|gene1625|rna1624|rna1624  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-49  167.4   0.0    2.3e-49  167.2   0.0    1.1  1  UFD1      Ubiquitin fusion degradation protein UFD1


Domain annotation for each model (and alignments):
>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.2   0.0   1.3e-53   2.3e-49       8     173 .]      18     184 ..      12     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: 167.2 bits;  conditional E-value: 1.3e-53
                               UFD1   8 ysvsmkaereelekggkiiLPpsaLdeLtrlnieyPmlFelsnkkkkksthagVleFtaeegtvylPewmmenlgl 83 
                                         ++++    ++++ ggk+i P+s+L +L++ +i+ P++Fe+s+++  ++th+gVleFt eeg+v++P+wm+++l +
  gene1625|gene1625|rna1624|rna1624  18 SPIKF-DGGNQNNFGGKVIVPQSVLVDLVSFQIQPPFTFEISHSDGIYKTHCGVLEFTGEEGQVVVPSWMYQQLAM 92 
                                        57788.688999******************************999999**************************** PP

                               UFD1  84 eegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikynd.kvyelkvlevkp.es 157
                                        e++d v +++++ p gkfvkl p+s+dfl+i++pk  Le+ Lrn+++L++gd i +++ +  + +++v +++p ++
  gene1625|gene1625|rna1624|rna1624  93 EDADEVVLRYMTFPIGKFVKLIPHSVDFLEIENPKLELESCLRNYQVLSEGDEILCQFDEiGSIRFTVAHIEPpSN 168
                                        **********************************************************762579********7256 PP

                               UFD1 158 avsiietdlevdfaeP 173
                                        av+i++tdl vdf eP
  gene1625|gene1625|rna1624|rna1624 169 AVYIVDTDLAVDFLEP 184
                                        *************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1410.42
//
Query:       gene1626|gene1626|rna1625|rna1625  [L=515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3487.01
//
Query:       gene1627|gene1627|rna1626|rna1626  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-49  166.9   0.0    5.3e-49  166.5   0.0    1.1  1  CK_II_beta      Casein kinase II regulatory subunit
  ------ inclusion threshold ------
      0.064   12.3   0.1       0.09   11.9   0.1    1.1  1  Tmemb_55A       Transmembrane protein 55A
      0.077   12.6   0.1      0.077   12.6   0.1    1.8  2  STAT1_TAZ2bind  STAT1 TAZ2 binding domain


Domain annotation for each model (and alignments):
>> CK_II_beta  Casein kinase II regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   0.0   8.8e-53   5.3e-49       2     182 .]      21     192 ..      20     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 8.8e-53
                         CK_II_beta   2 WiswflslkgneyfvevdedfiedkfnltgLseevpnykealelildveeeeeleeseksevessaelLYgliHar 77 
                                        W+  f+++k+n+ +v+v+++f+ed+fn++gL++ ++n +e+++ ild+           +   ++++ LY liH+r
  gene1627|gene1627|rna1626|rna1626  21 WVGDFMHRKENHAIVRVPDEFLEDRFNIIGLDRYIKNLEETYNSILDK---------GPRRNLKEESSLYYLIHQR 87 
                                        ***********************************************3.........33444566789******** PP

                         CK_II_beta  78 yiltkkglakmlekykkkefgrCprvlCekq.kvLPvGlsdkpgektvklyCpkCedvYspkssrsrsidGafFGt 152
                                        yi+tk+gl+++l+k+ ++e+g+Cprv C+++  ++PvGlsd p++++ k+yC +C +vY+pk + +  +dG+ +G+
  gene1627|gene1627|rna1626|rna1626  88 YIFTKSGLEAILDKVMSREYGVCPRVGCKSSvGMVPVGLSDGPSKSSTKIYCHNCVNVYEPKGNLQ-LLDGCAWGR 162
                                        ****************************765279*****************************776.********* PP

                         CK_II_beta 153 tfphlllltypelepkkskekyepriyGfk 182
                                        +fph+l+l ++   p++  e+y+priyGf+
  gene1627|gene1627|rna1626|rna1626 163 SFPHFLILAHSYHFPSRMYEEYVPRIYGFR 192
                                        *****************************7 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.5e-05      0.09     111     158 ..     101     146 ..      94     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                          Tmemb_55A 111 kvssqri.aCprpnckriinLgPveagpvspelqpvgvrviCghCkntf 158
                                        kv+s+   +Cpr  ck  + + Pv    +s+ ++  ++++ C  C n +
  gene1627|gene1627|rna1626|rna1626 101 KVMSREYgVCPRVGCKSSVGMVPV---GLSDGPSKSSTKIYCHNCVNVY 146
                                        566655427***************...99****************9976 PP

>> STAT1_TAZ2bind  STAT1 TAZ2 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.3e-05     0.077       7      17 ..      10      20 ..       9      21 .. 0.95
   2 ?   -2.9   0.2      0.92   5.5e+03      14      18 ..      38      42 ..      38      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                     STAT1_TAZ2bind  7 ENLLPMSPedY 17
                                       ENLL MSP++Y
  gene1627|gene1627|rna1626|rna1626 10 ENLLRMSPDEY 20
                                       9*********9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.92
                     STAT1_TAZ2bind 14 PedYg 18
                                       P+++ 
  gene1627|gene1627|rna1626|rna1626 38 PDEFL 42
                                       9**95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1293.13
//
Query:       gene1628|gene1628|rna1627|rna1627  [L=1779]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-45  155.8   1.8    1.5e-45  155.8   1.8    2.3  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    6.3e-12   45.0   3.6    3.1e-10   39.4   2.7    3.3  2  DNA_pol_B       DNA polymerase family B
    1.1e-11   44.0   0.0    1.1e-08   34.1   0.0    2.6  2  DUF1744         Domain of unknown function (DUF1744)
    1.7e-08   34.4   0.2    1.2e-07   31.7   0.2    2.3  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
    1.3e-07   31.8   0.0    3.9e-07   30.2   0.0    1.8  1  RNase_H_2       RNase_H superfamily
  ------ inclusion threshold ------
      0.026   14.3   1.4      0.074   12.8   1.4    1.7  1  PRKCSH-like     Glucosidase II beta subunit-like
        0.3   10.4   3.0        0.5    9.7   3.0    1.2  1  DUF4407         Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.8   1.8   5.9e-49   1.5e-45       2     337 .]      50     365 ..      49     365 .. 0.92
   2 ?   -3.9   1.4       2.2   5.6e+03      31      84 ..     611     664 ..     599     717 .. 0.60

  Alignments for each domain:
  == domain 1  score: 155.8 bits;  conditional E-value: 5.9e-49
                                        ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEES CS
                     DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvs 77 
                                        +eeg++ +v+  ++ p+f+++a+d + +   +e+l+++y +++ ++++  +++ ++ ++l         +lkv ++
  gene1628|gene1628|rna1627|rna1627  50 DEEGGEFLVK-IPYFPSFLVRASDYDIT---EEYLRKKYAGEIHDMERTHRIDFKEENHLNKEPGM---FLKVRFK 118
                                        5666666776.5***********66665...9***************8888888888887666666...******* PP

                                        STCHHHHHHHHHHH........................CCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEE CS
                     DNA_pol_B_exo1  78 npnelkkirkelsp........................leeivdvyeydvdylerflidnkivgfgwysvkkylvr 129
                                        + +   ++ kel++                        ++ i+++ e+d++  +  + d ki+ ++wy        
  gene1628|gene1628|rna1627|rna1627 119 TESGFGEALKELKRivarnrvqksheydcfgeerttnaENLIESIHEHDIPTEVATVNDLKIRCGKWYGFY----- 189
                                        ************99************************999***************************988..... PP

                                        GCC--C-.SEEEEEETTTSCEETTTCCS-EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEE CS
                     DNA_pol_B_exo1 130 aegkisncdveidcdvddliakpkesepplrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearkl 205
                                            ++  ++ +  ++++++       p+lr+l+FDIe+ +k++kfp++e   d++++Is+  +  g        l
  gene1628|gene1628|rna1627|rna1627 190 ----YT-GEMYVVEKSERIVF------PDLRILAFDIETSKKPLKFPNPES--DEVMMISIKTECGG-------EL 245
                                        ....33.33333334667777......9***********************..**************.......9* PP

                                        EEECCCTSS----EE--SSTCSTTE.EEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTC CS
                     DNA_pol_B_exo1 206 ftlrecaseeeedfeltpkpeypgv.kvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykv 280
                                        +++r  +s+ +  fe+ pk++++ v +v+++ +E  +L +f+e+i++++P  +t++N+ +FD+p++++R++     
  gene1628|gene1628|rna1627|rna1627 246 IVNRRLVSKSIRRFEYNPKEDMQCVfDVVNESDEEGVLIRFVEMIQRHRPHLVTTFNGASFDFPFLEKRMS----- 316
                                        ***********************************************************************..... PP

                                        CHCG.SCCSCTCEECCCCESEEEEEECEEEETTSEEEEHHHHHHHHSSSS..G-SHHHH CS
                     DNA_pol_B_exo1 281 klsklgrlnkggrskvseigfskqarekvkisgrihlDlyrvvkrklklp..sYkLnav 337
                                                 + g+s  +  gf+ q+ e + ++ ++hlD+y++vkr+++lp  s+ L+av
  gene1628|gene1628|rna1627|rna1627 317 ---------RYGISLRETAGFA-QKDEYYISPFIVHLDCYKWVKRDSYLPagSQGLKAV 365
                                        .........99***99999999.999999999*************************98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.2
                                        HHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHH CS
                     DNA_pol_B_exo1  31 evkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkk 84 
                                         +k+++k+ ++      +++++   + +k++yg  k++++ ++ s+  ++e++ 
  gene1628|gene1628|rna1627|rna1627 611 RIKKQIKKEKGFVGDRDEELKQRAKKYSKEIYGKAKRKENCVRSSTVCQREVPF 664
                                        555555554444444333555555566666666666665555555544444444 PP

>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.082   2.1e+02       5      47 ..     429     479 ..     425     493 .. 0.71
   2 !   39.4   2.7   1.2e-13   3.1e-10     101     414 ..     643     984 ..     545    1039 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.082
                                        HHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS..........-S--- CS
                          DNA_pol_B   5 rvledgqqirveslLlrlakeegfilpdrtekkgkeee.........gYqGa 47 
                                         +l +g+ +  e lL+ +a e+++++p+++++ +k +e         +Y G+
  gene1628|gene1628|rna1627|rna1627 429 LALCQGSGTLCEALLISEAIEYKVVIPEKRKE-KKIQEynghiaesiTYVGG 479
                                        577889999999***************66655.4444334555555445555 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 1.2e-13
                                        .TEEE-TCC-EEE-.TTS---HHHHHHHHHHHHHHHHHHHHHCS--H..............HHHHHHHHHHHHHHH CS
                          DNA_pol_B 101 leveveprlvefvk.ksvregllpklLkdllakRkaikkelkeekde..............fekalldkqQlalKv 161
                                         + + ++++v+  +  +++   + + ++++ ++R  +k+   e++++              +  +++ + Q a K+
  gene1628|gene1628|rna1627|rna1627 643 GKAKRKENCVRSSTvCQREVPFYVETVRKFRDQRYVYKRLYSEAQKAfeaarteeerkhamKSVVVYSSLQIAHKC 718
                                        3333444444433322333456667777777777777777777777788888888888876677899********* PP

                                        HHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS...........T-EEEEEBSS CS
                          DNA_pol_B 162 taNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeea....eee..klkviYGDTD 231
                                        + Ns+YG++  ++sr +++++Aa v + G ++++k++e+vek + +l+   ++   +    +    ++    G   
  gene1628|gene1628|rna1627|rna1627 719 VLNSFYGYVMRKSSRWYSMEMAAIVCNVGGNIIKKAREIVEKIGISLEL--DTDGIWclvpSSLisSYTLPSGKKF 792
                                        *****************************************88322222..2222111222111233333334444 PP

                                        EEEEE-....S-SSHHHHHHHHHHHH.HHHHT.TSTTT--EEEEEEEEEEEE........EETTEEEEEEEEESST CS
                          DNA_pol_B 232 Svfiel....kvkdveellkigkela.eevseklfkkplklefekvykkllL........isKKkYaglkvektsk 294
                                        S+  +l     +k+  +  +  +++  +++++  +++ +  e++  yk +lL        + KK+Y+ +  +    
  gene1628|gene1628|rna1627|rna1627 793 SLLSSLlnhfVCKKFTNH-QYQEKVDgRYITR--MENSIFFEIDGPYKAMLLpasteenrLLKKRYVIIDRN---- 861
                                        444333222144444443.4455555155555..7888**************5555444445****988877.... PP

                                        TSE.EEEESSGGGSTTS-HHHHHHHHHHHHHHSSS.......S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EE CS
                          DNA_pol_B 295 ank.lliKGvdlvRrdncklvkevikkvlelllkdet...eersleeglealksilkdvleeleenkvplekfvls 366
                                         n+  + KG ++ Rr+  +++k+  +++    l   +   + +sl e+ ++  +il +++ e  +  + le +  s
  gene1628|gene1628|rna1627|rna1627 862 -NRiAELKGFEVKRRGELEIIKKFQEELFLHFLDGSNlreCYESLAEVCRYWLDIL-RSRGEYIDDDTILELLSES 935
                                        .66579**********************9999998444445555556666666666.3334444555578889999 PP

                                        EEESS.CCCSSGCCSHHHHHHHHHHHHC.SS---TTCEEEEEEBETSS. CS
                          DNA_pol_B 367 kelskepenyksknlphlevakrlkkrn.eeapevgdrisYvivekkke 414
                                        +++sk  + y  ++ +    a r+ +   e   e + + +Y+i +  ++
  gene1628|gene1628|rna1627|rna1627 936 RSMSKGFDGYGGRKSSLTVTALRMSEVLgEGILEEKLKCEYIIAAYPEN 984
                                        9999999999888855555566776666455577888888888887663 PP

>> DUF1744  Domain of unknown function (DUF1744)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00069       1.8     123     162 ..    1362    1397 ..    1344    1404 .. 0.86
   2 !   34.1   0.0   4.2e-12   1.1e-08     264     396 ..    1450    1585 ..    1413    1588 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00069
                            DUF1744  123 aelielaryadvPlgnlesddllfliDiffaRrLkksnvv 162 
                                         + + + ++y+ +P+ n+++     l+D++f R+L+k++vv
  gene1628|gene1628|rna1627|rna1627 1362 ELMCKTSKYTGIPIFNVDE----QLMDVLFYRELRKNKVV 1397
                                         567899**********965....589***********998 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 4.2e-12
                            DUF1744  264 l....ssaafrvLrslvkswlddalkgnkladllvqhlvrWvespsslLyDpaLrrlvqnlmkKvflqLlaefk 333 
                                         l    s++ f+vLr+ +k+ + d ++g +  +ll+ ++ +W+++ +s +    Lr++  +l+k+ ++ L ++++
  gene1628|gene1628|rna1627|rna1627 1450 LfggvSRNDFNVLRNFLKRVVLDSIRGVEGTKLLLRNIGSWIRR-DSGIICTELRNICCMLQKRYMMNLAKKLR 1522
                                         44444999**********************************86.66777899********************* PP

                            DUF1744  334 rlgskvvyAdfnkillkTsKksvenayaYveyilkairskelFkflelkikkyWdlLlwmDea 396 
                                              v+      il++T+K s ++a+ +++++ k       ++++++k ++ ++ L ++ + 
  gene1628|gene1628|rna1627|rna1627 1523 DERYDVICVAGDMILINTEKISEKSALEFFQHVRKKGLGLCGYEMMKMKLNRKFQRLAFVSPS 1585
                                         ************************************999999999999999999999998765 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.2   4.5e-11   1.2e-07      27     174 ..     270     412 ..     248     415 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.5e-11
                     DNA_pol_B_exo2  27 vkslgeeessekelikkffegvekkkpqlV.sfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsry 101
                                        v+++ + es+e+ ++ +f e++++++p+lV +fng +fD+p le r  ++g+s ++ +   +     k + y+s +
  gene1628|gene1628|rna1627|rna1627 270 VFDVVN-ESDEEGVLIRFVEMIQRHRPHLVtTFNGASFDFPFLEKRMSRYGISLRETAGFAQ-----KDEYYISPF 339
                                        455544.4567888889*************55*********************998776666.....445678887 PP

                     DNA_pol_B_exo2 102 strhlDLmdlls..eygaranakLdel..akllglPGKlgvdGskVaelyqegklkeireYcetDvlnTYlvylrl 173
                                           hlD +  +   +y +  ++ L+ +  akl  +P  ++ + + V    + ++ +++++Y  +D + TY++y+++
  gene1628|gene1628|rna1627|rna1627 340 I-VHLDCYKWVKrdSYLPAGSQGLKAVtkAKLGYFPDEVDPE-DMVGL--AISDPDRMASYSVSDSVATYFLYIKY 411
                                        4.69**999996336888889999887335667789776654.34443..345678899**************998 PP

                     DNA_pol_B_exo2 174 e 174
                                        +
  gene1628|gene1628|rna1627|rna1627 412 V 412
                                        6 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.5e-10   3.9e-07      39     119 ..     275     375 ..     260     385 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.5e-10
                          RNase_H_2  39 eepeeekailelflellekkka.lvtfngksFDvpflkrlfkkyklde...............eefrhiDLlkelr 98 
                                        +e +ee  + +++ ++ + +++ + tfng+sFD+pfl++++++y ++                + + h+D +k+++
  gene1628|gene1628|rna1627|rna1627 275 NESDEEGVLIRFVEMIQRHRPHlVTTFNGASFDFPFLEKRMSRYGISLretagfaqkdeyyisPFIVHLDCYKWVK 350
                                        44566666666665555555552678***************8888877778888888777775556********** PP

                          RNase_H_2  99 kkkl...esysLksveke.lgierr 119
                                        +  +    s +Lk+v k+ lg+  +
  gene1628|gene1628|rna1627|rna1627 351 RDSYlpaGSQGLKAVTKAkLGYFPD 375
                                        99999**555*****9998998776 PP

>> PRKCSH-like  Glucosidase II beta subunit-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.4   2.9e-05     0.074      86     175 ..     558     647 ..     544     648 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                        PRKCSH-like  86 sgyiesfkvdd.gvcdydic..cdGsdeelgkcenkca.eiarkfeelleeankkvkkglkikeelllaakkklde 157
                                        ++ i ++k++  ++ d d c  cd sde l +c+++ +  ++ ++ + ++e+ +++kk +k  + ++     + +e
  gene1628|gene1628|rna1627|rna1627 558 PNIILTNKLQPiSIVDEDTCirCDFSDE-LNECQKRMEwTMKVEYIAASREETERIKKQIKKEKGFVG---DRDEE 629
                                        6667777776436888888777******.999*99987245668999999**********99998875...56789 PP

                        PRKCSH-like 158 lkkklkeledslkakkkr 175
                                        lk++ k+ ++++  k kr
  gene1628|gene1628|rna1627|rna1627 630 LKQRAKKYSKEIYGKAKR 647
                                        999999999998877665 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.0    0.0002       0.5     111     222 ..     585     700 ..     581     711 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0002
                            DUF4407 111 elaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.......gtgttgva 179
                                        el+e q++++ + k ++ aa+++e++++++qi++ ++ +   +++l++  +++ ke+ g+            t  +
  gene1628|gene1628|rna1627|rna1627 585 ELNECQKRMEWTMKVEYIAASREETERIKKQIKKEKGFVGDRDEELKQRAKKYSKEIYGKAkrkencvR-SSTVCQ 659
                                        67788888888888899999***************************************9955555532.222335 PP

                            DUF4407 180 Gkgpaakekkaqldaaqaelaelkakldatarlaalraelael 222
                                        ++ p + e  ++  +++   + l ++  a+++++a+r+e ++ 
  gene1628|gene1628|rna1627|rna1627 660 REVPFYVETVRKFRDQRYVYKRLYSE--AQKAFEAARTEEERK 700
                                        55555555777777777777777777..777777777776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 1.02u 0.32s 00:00:01.34 Elapsed: 00:00:00.51
# Mc/sec: 10502.03
//
Query:       gene1629|gene1629|rna1628|rna1628  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.35s 00:00:00.86 Elapsed: 00:00:00.54
# Mc/sec: 784.53
//
Query:       gene1630|gene1630|rna1629|rna1629  [L=561]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-30  105.3   0.0    6.6e-30  104.4   0.0    1.5  1  ABC_tran      ABC transporter
    5.8e-12   45.8  13.8    8.2e-12   45.3  13.8    1.1  1  ABC_membrane  ABC transporter transmembrane region
    1.8e-09   37.4   3.3    7.7e-08   32.0   3.3    2.5  1  SMC_N         RecF/RecN/SMC N terminal domain
    9.6e-07   28.9   2.3    0.00067   19.5   0.1    2.7  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00011   22.1   1.7    0.00011   22.1   1.7    2.5  3  AAA_15        AAA ATPase domain
     0.0017   18.4   0.4      0.012   15.7   0.0    2.4  2  MMR_HSR1      50S ribosome-binding GTPase
      0.003   17.5   0.3        2.3    8.1   0.0    2.4  2  NTPase_1      NTPase
     0.0049   16.9   0.4        0.1   12.7   0.1    2.4  2  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
      0.016   14.3   0.1      0.047   12.7   0.1    1.7  1  IIGP          Interferon-inducible GTPase (IIGP)
      0.026   14.2   0.0      0.069   12.9   0.0    1.7  1  AAA_24        AAA domain
      0.032   14.0   1.5      0.064   13.0   0.0    2.3  2  AAA_29        P-loop containing region of AAA domain
      0.044   14.2   0.4       0.57   10.6   0.4    2.3  1  AAA           ATPase family associated with various cellular 
      0.084   13.4   3.1      0.083   13.4   1.7    1.8  1  AAA_23        AAA domain
        0.1   11.8   0.0        0.2   10.8   0.0    1.4  1  DUF815        Protein of unknown function (DUF815)
        0.1   12.5   0.1       0.29   11.0   0.0    1.7  2  RsgA_GTPase   RsgA GTPase
       0.11   12.2   0.0       0.23   11.1   0.0    1.5  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.11   12.3   0.0       0.21   11.4   0.0    1.4  1  DEAD          DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   6.3e-33   6.6e-30       4     137 .]     353     498 ..     350     498 .. 0.92

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 6.3e-33
                                        EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                         + ++++gek++i+G+nG+GKS+++++l++ l+  +Gei +dg +l++++++s+r+ i+++pq+++lf+++ v en
  gene1630|gene1630|rna1629|rna1629 353 FNGEIRKGEKIGIIGKNGCGKSSFINALLRFLE-YKGEIYIDGVELRRIRKSSVRNLISFVPQNHHLFNGT-VLEN 426
                                        67899**************************98.7************************************.99** PP

                                        ...........HHHTC........HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                        ...........xxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  80 ...........esdee........iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                   +            ++++lskl+  +  +t v+++++ LSgGqkqrv+ +ra++k++++++lDEpt
  gene1630|gene1630|rna1629|rna1629 427 iayscnsieyeD---VlkkcvhfnAHEMLSKLEKGY--QTLVGENGKFLSGGQKQRVSFMRAMVKDSDIVVLDEPT 497
                                        999999886540...24566678899******9888..9************************************9 PP

                                        T CS
                                        x RF
                           ABC_tran 137 a 137
                                        +
  gene1630|gene1630|rna1629|rna1629 498 S 498
                                        6 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3  13.8   7.8e-15   8.2e-12       5     259 ..      23     276 ..      19     287 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 7.8e-15
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ABC_membrane   5 illailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrkl 80 
                                        +++++l+  l + f  ++ +i + +++k ++ t + +++++ +++l +   i++l++  +  ++ + l+ +     
  gene1630|gene1630|rna1629|rna1629  23 VFFIMLSSKLHFEFQKLITKIEQYIVGKTTDGT-DPSRLLISFMVLPINHYIASLIYKLISAYIIQLLMGKSFHHC 97 
                                        677888888888888888888888888777777.8999************************************** PP

                                        HHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHH CS
                       ABC_membrane  81 fkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliil 156
                                        ++  l ++   f +  +G++ s++ +  + + +++  ++ ++f +++ ++ g+++ +  +  +  ++++ ++++++
  gene1630|gene1630|rna1629|rna1629  98 LREYLLMNYHGFHHLGSGQIHSLVERRSNAIVSFMRIFFADIFFNVTYVMWGFLYFCRCSMGIVTLTIVQILVYAV 173
                                        *****************************************************99999999999999999999999 PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ABC_membrane 157 vsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitq 232
                                        vs+  + i + +++k++ a++ as+ ++ +l+++  +k++++ee++l+k+   + ++ + ++++  +ng++  ++ 
  gene1630|gene1630|rna1629|rna1629 174 VSWRGTIIRNHFRRKYNAAYNTASNRLYGVLQNYDIIKSYNKEEKELSKYLGTVWDVGRHSRRYDQVNGFVEFFQK 249
                                        999999999******************************************************************* PP

                                        HHHHHHHHHHHHHHHHHHHTTSSTHHH CS
                       ABC_membrane 233 llgllsyalalwfGttlvisgelsvgd 259
                                        +l+++ +a+  ++ +   + + + +g+
  gene1630|gene1630|rna1629|rna1629 250 SLFFIPNAFLVFMIVNGYMFKSMRIGN 276
                                        *****9999988766666666666666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   3.3   7.3e-11   7.7e-08      28     212 ..     364     541 ..     354     547 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 7.3e-11
                                        EEEESTTSSHHHHHHHHHHHCTT.........TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  28 aivGpNGSGKsnlldAilFvLGer........sakklrseklsdlihkskekasvkkaeveitfdnedkklkieke 95 
                                         i+G+NG+GKs++++A+l  L  +        + + +r++++++li+   +++++ +++v   +  + ++      
  gene1630|gene1630|rna1629|rna1629 364 GIIGKNGCGKSSFINALLRFLEYKgeiyidgvELRRIRKSSVRNLISFVPQNHHLFNGTVLENIAYSCNS------ 433
                                        69**************987775442222222267899999999999997888888888888776666665...... PP

                                        CEEEEEEEETTSEEEEEETTEEE-H.HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  96 evsisrrvkrkgeseykingkevtk.kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                           i+ + + k+  ++   +   +  k ++ l+   g + + LSgG+k+ v+    f   +vk + +++lDe  ++
  gene1630|gene1630|rna1629|rna1629 434 ---IEYEDVLKKCVHFNAHEMLSKLeKGYQTLV---GENGKFLSGGQKQRVS----FMRAMVKDSDIVVLDEPTSN 499
                                        ...555555555533333333334323344444...446789******9654....44668999************ PP

                                        S-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 171 LDeknvkkvaellkeksknaQfivislreemlekadklvgvt 212
                                        LD+   k+++e++ +k k+  ++ + +++++l+  dk++g+ 
  gene1630|gene1630|rna1629|rna1629 500 LDADSEKELVEMILKKMKDKTVFLVVHDHDLLRGFDKILGLH 541
                                        ************************************999986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.7   2.8e+03     131     190 ..     212     273 ..     186     336 .. 0.59
   2 !   19.5   0.1   6.4e-07   0.00067       3      92 ..     364     457 ..     363     470 .. 0.73
   3 !    8.5   0.0    0.0015       1.6     257     297 ..     486     526 ..     470     532 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.7
                             AAA_21 131 svsepndlqfgkaltditsrawsllllldglrke..rigllnifadyfgfakekrllqrlvr 190
                                        s+++++++ ++ + t  +   +s + ++ +++ e  +++l++i+++++ f+ +++++++ +r
  gene1630|gene1630|rna1629|rna1629 212 SYNKEEKELSKYLGTVWDVGRHSRRYDQVNGFVEffQKSLFFIPNAFLVFMIVNGYMFKSMR 273
                                        44444444444444444444444444444444444555555555555544444444444444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.4e-07
                             AAA_21   3 vliGpNgsGKSnLLdaldllarl..drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryrygl 76 
                                        ++iG+Ng+GKS+++ al  +  +    +++g    + ++++ r  +s+ + ++    ++   +    +++ ++y+ 
  gene1630|gene1630|rna1629|rna1629 364 GIIGKNGCGKSSFINALLRFLEYkgEIYIDGVELRRIRKSSVRNLISFVPQNHHLFNGTVLEN-IAYSCNSIEYED 438
                                        69***************6665557777777777777777777777777777777777777777.777777777777 PP

                             AAA_21  77 rlersqv...eeklssvet 92 
                                         l++  +    e+ls +e+
  gene1630|gene1630|rna1629|rna1629 439 VLKKCVHfnaHEMLSKLEK 457
                                        7777666666666666655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0015
                             AAA_21 257 kg.sllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                        k+ +++++DEp ++L+    ++l+e++ ++ + +  v+l+ H
  gene1630|gene1630|rna1629|rna1629 486 KDsDIVVLDEPTSNLDADSEKELVEMILKKMK-DKTVFLVVH 526
                                        3339***********************55555.566666655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.5       1.6   1.7e+03     237     267 ..     287     313 ..     186     329 .. 0.63
   2 !   22.1   1.7     1e-07   0.00011      15      50 ..     338     387 ..     336     517 .. 0.76
   3 ?   -0.8   0.0      0.94   9.9e+02     309     354 ..     480     518 ..     471     529 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                             AAA_15 237 elteklkeiqeklkeidkklaeelkkilkkk 267
                                        el+  +     klk+ +++++e+l++i+++ 
  gene1630|gene1630|rna1629|rna1629 287 ELRNGIM----KLKDSIFTMNENLTDIFDSR 313
                                        2222222....33333344444444444443 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1e-07
                             AAA_15  15 kdveidlsee..............ltvliGkNnsGKSsilealdlFlnnk 50 
                                        +dv+i++ ++                 +iGkN++GKSs+++al  Fl+ k
  gene1630|gene1630|rna1629|rna1629 338 SDVSIHIGNKlviegfngeirkgeKIGIIGKNGCGKSSFINALLRFLEYK 387
                                        566666666666666666666666788********************966 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.94
                             AAA_15 309 llileaekkdekeeknvilliEEPEahLHpqaqkvlikllkeland 354
                                        +++++ ++        +i++++EP  +L  +  k+l++ +++  +d
  gene1630|gene1630|rna1629|rna1629 480 FMRAMVKDS-------DIVVLDEPTSNLDADSEKELVEMILKKMKD 518
                                        555555555.......9*******9999999999999988776665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.012       1      21 [.     362     382 ..     362     404 .. 0.89
   2 ?   -0.5   0.1       1.2   1.3e+03      43      82 ..     485     525 ..     471     546 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                        EEEEEESTTSSHHHHHHHHHT CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltg 21 
                                        +++i+G+   GKS++inal++
  gene1630|gene1630|rna1629|rna1629 362 KIGIIGKNGCGKSSFINALLR 382
                                        699****************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                        ETTEEEEEEECGGCSS.HHHHHHHHHHHHHHHHC.TSEEEEE CS
                           MMR_HSR1  43 lkgkeielvDtpGlie.gaseekglgkaflalee.adlillv 82 
                                        +k+++i+++D p   + +a++ek+l + +l++ +   ++l+v
  gene1630|gene1630|rna1629|rna1629 485 VKDSDIVVLDEPT-SNlDADSEKELVEMILKKMKdKTVFLVV 525
                                        3456667777776.3334445555555555544412333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0022       2.3       2      44 ..     363     406 ..     362     412 .. 0.87
   2 !    7.2   0.1    0.0043       4.5      56     136 ..     448     529 ..     442     549 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                                        EEEE--TTSSHHHHHHHHHHHH....GGGEEEEEEEEE------ CS
                           NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss.gvkvgGfyteevreggrr 44 
                                        + i G+ G GK+ +++ +l+ l+ + ++ ++G+  +++r+   r
  gene1630|gene1630|rna1629|rna1629 363 IGIIGKNGCGKSSFINALLRFLEYKgEIYIDGVELRRIRKSSVR 406
                                        7899******************99845889***99999988776 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0043
                                        -EEEEEETT---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT..TTSEEE CS
                           NTPase_1  56 eegiLarveakreprvgkyvvdvesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk..sekpvl 129
                                         +++L++ e+  +  vg+   ++   ++  ++ +r +++++d++v+DE     l + + ke ve +Lk  ++k v 
  gene1630|gene1630|rna1629|rna1629 448 AHEMLSKLEKGYQTLVGENGKFLSGGQKQRVSFMRAMVKDSDIVVLDEPT-SNLDADSEKELVEMILKkmKDKTVF 522
                                        56778888888888888888889888899999999999**********64.4677777788999999877778888 PP

                                        EE--SS- CS
                           NTPase_1 130 avihrrk 136
                                         v+h ++
  gene1630|gene1630|rna1629|rna1629 523 LVVHDHD 529
                                        8999875 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   9.7e-05       0.1       1      20 [.     363     382 ..     363     390 .. 0.93
   2 ?    1.8   0.0      0.21   2.3e+02      89     136 ..     476     526 ..     419     533 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-05
                                        EEEEEBTTTTHHHHHHHHHT CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlg 20 
                                        i ++G+   GKSS++naLl+
  gene1630|gene1630|rna1629|rna1629 363 IGIIGKNGCGKSSFINALLR 382
                                        789***************96 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.21
                                        S-EEEEEEETTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEE CS
                          Dynamin_N  89 kvillkilsllvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavt 136
                                        + +++     ++++++++D P  +  ++ ++   e++ + +k+++++l+v 
  gene1630|gene1630|rna1629|rna1629 476 QRVSFMRAMVKDSDIVVLDEPTSNLDADSEKelvEMILKKMKDKTVFLVVH 526
                                        366666667778888888888888877777744455555555555555554 PP

>> IIGP  Interferon-inducible GTPase (IIGP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.5e-05     0.047      37      56 ..     362     382 ..     348     389 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                                        EEEEEESTTSSHHHHHHHH.T CS
                               IIGP  37 kiavtGdsGnGkssFinaL.R 56 
                                        ki ++G+ G GkssFinaL R
  gene1630|gene1630|rna1629|rna1629 362 KIGIIGKNGCGKSSFINALlR 382
                                        7899**************725 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.5e-05     0.069       2      70 ..     360     463 ..     359     467 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                             AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.............................. 47 
                                        + ki i+G++g GK+++++ l  ++l    e     +d+ ++ +i+                              
  gene1630|gene1630|rna1629|rna1629 360 GEKIGIIGKNGCGKSSFINAL-LRFLEYKGEI---YIDGVELRRIRkssvrnlisfvpqnhhlfngtvleniaysc 431
                                        5699*****************.9999887777...55555555555553443334444444444444444444444 PP

                             AAA_24  48 ...swedfldevvel......aaeladyktlv 70 
                                            +ed+l+++v +      ++ +++y+tlv
  gene1630|gene1630|rna1629|rna1629 432 nsiEYEDVLKKCVHFnahemlSKLEKGYQTLV 463
                                        44444444444444488888888888888887 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       7.2   7.6e+03      51      59 ..     190     198 ..     187     199 .. 0.77
   2 ?   13.0   0.0     6e-05     0.064      20      44 ..     358     382 ..     341     387 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.2
                             AAA_29  51 kvrfNkaan 59 
                                        ++++N a+n
  gene1630|gene1630|rna1629|rna1629 190 NAAYNTASN 198
                                        578999998 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6e-05
                             AAA_29  20 dlkg.atlltGpsGsGKSTllDAiqa 44 
                                        + kg  + ++G++G GKS+++ A+  
  gene1630|gene1630|rna1629|rna1629 358 R-KGeKIGIIGKNGCGKSSFINALLR 382
                                        4.333778*************99875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00054      0.57       3      98 ..     365     521 ..     363     526 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00054
                                        EESSTTSSHHHHHHHHHHHHTHE..................................................... CS
                                AAA   3 lyGppGtGKTllakavakelgve..................................................... 25 
                                        ++G  G+GK+++++a+ + l+ +                                                     
  gene1630|gene1630|rna1629|rna1629 365 IIGKNGCGKSSFINALLRFLEYKgeiyidgvelrrirkssvrnlisfvpqnhhlfngtvleniayscnsieyedvl 440
                                        689****************964433444444444555555555555555555555555555555555555555555 PP

                                        ..EEEEETTTCSSS.............STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHH CS
                                AAA  26 ..fleisgsellsk.............yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervv 86 
                                          ++ ++++e+lsk              +  + +k r  f +a  k    i+++DE  +   ++      +e+++v
  gene1630|gene1630|rna1629|rna1629 441 kkCVHFNAHEMLSKlekgyqtlvgengKFLSGGQKQRVSFMRAMVKD-SDIVVLDEPTSNLDAD------SEKELV 509
                                        55555555555555888998877777744444445555555555554.5899999988887777......778888 PP

                                        HHHHHHHHHTTT CS
                                AAA  87 nqLlteldgvkk 98 
                                        + +l+++++ + 
  gene1630|gene1630|rna1629|rna1629 510 EMILKKMKDKTV 521
                                        888888887765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.7   7.8e-05     0.083      23      40 ..     364     381 ..     337     519 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.8e-05
                             AAA_23  23 lItGpNGaGKTTildAik 40 
                                         I+G+NG+GK+++++A+ 
  gene1630|gene1630|rna1629|rna1629 364 GIIGKNGCGKSSFINALL 381
                                        69**************96 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019       0.2      56      98 ..     363     408 ..     355     421 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                             DUF815  56 vLLwGarGtGKSslvkallneyaeeg...Lrlievekedlkelpkl 98 
                                        + ++G+ G+GKSs + all+ ++ +g   +  +e+++ + +++ +l
  gene1630|gene1630|rna1629|rna1629 363 IGIIGKNGCGKSSFINALLRFLEYKGeiyIDGVELRRIRKSSVRNL 408
                                        5679***************988877776744444444443344333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.29     100     121 ..     361     382 ..     322     392 .. 0.82
   2 ?   -3.8   0.0       9.9     1e+04      80     109 ..     439     467 ..     423     468 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                        SEEEEECSTTSSHHHHHHHHCT CS
                        RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                        + + ++G+ G GKS++inall 
  gene1630|gene1630|rna1629|rna1629 361 EKIGIIGKNGCGKSSFINALLR 382
                                        667799*************975 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.9
                                        EE--TTTHTTHHHHHHHCTTSEEEEECSTT CS
                        RsgA_GTPase  80 llvsaktkegleelkellkdktsvlvGqSG 109
                                        +l +   + +++e+ ++l++   +lvG+ G
  gene1630|gene1630|rna1629|rna1629 439 VLKKCV-HFNAHEMLSKLEKGYQTLVGENG 467
                                        433333.34555666677777777777765 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00022      0.23      11      46 ..     357     391 ..     349     455 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                        EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  11 ivqGqrtlipgafgvGktvisqslskqsnsddaiiy 46 
                                        i +G++++i+g++g+Gk+  +++l++  + +   iy
  gene1630|gene1630|rna1629|rna1629 357 IRKGEKIGIIGKNGCGKSSFINALLRFLEYK-GEIY 391
                                        679******************9999987666.3343 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.21      63     152 ..     423     519 ..     355     524 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                        HHHHHHHHTTTST....SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH.....CTTEEEEEEET CS
                                        xxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx RF
                               DEAD  63 tlnnlkkfkkyid....lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln.....lsqvrflVlDE 129
                                        +l+n+  +++ i+    l         +a++ lskl++g++ +vg  g++++  ++++++     +++  ++VlDE
  gene1630|gene1630|rna1629|rna1629 423 VLENIAYSCNSIEyedvL---KKCVHFNAHEMLSKLEKGYQTLVGENGKFLSGGQKQRVSfmramVKDSDIVVLDE 495
                                        456666666665532222...22334567899********************88777766667779999******* PP

                                        HHHHHHT.TTHHHHHHHHHHSHHH CS
                                        xxxxxxx.xxxxxxxxxxxxxxxx RF
                               DEAD 130 adrlldq.gfsdfinrilnqlpqi 152
                                            ld  + ++ ++ il++++++
  gene1630|gene1630|rna1629|rna1629 496 PTSNLDAdSEKELVEMILKKMKDK 519
                                        999999845566666677777544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3940.87
//
Query:       gene163|gene163|rna163|rna163  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-41  140.0   0.0      6e-41  139.7   0.0    1.0  1  Ras        Ras family
    1.2e-16   61.0   0.0    2.2e-16   60.2   0.0    1.4  1  Roc        Ras of Complex, Roc, domain of DAPkinase
      2e-08   33.9   0.0    2.7e-08   33.5   0.0    1.2  1  Arf        ADP-ribosylation factor family
     0.0035   17.4   0.0     0.0058   16.7   0.0    1.3  1  MMR_HSR1   50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.017   14.5   0.0    1.2  1  SRPRB      Signal recognition particle receptor beta subunit
      0.072   12.8   0.9        7.9    6.2   0.4    2.6  2  PduV-EutP  Ethanolamine utilisation - propanediol utilisation


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7   0.0     2e-44     6e-41       2     160 ..      13     183 ..      12     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 2e-44
                                    EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                    l ++G+  +GKts+l+r+vk +F +e  +T+ +++ +++ + ++  v+l++wDTAGq+e+ ++r+l + +a+ i++vy+i
  gene163|gene163|rna163|rna163  13 LTIIGSATCGKTSILTRHVKRTFGTEISPTV-FNSVSNTYKHKDYVVELRLWDTAGQDEYARFRHLALPSADYIMIVYAI 91 
                                    679****************************.************************************************ PP

                                    TBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGG............G-SS-HHHHHHHHHHHT.SEEEEEBTTTTC CS
                            Ras  82 tsresfenvk.kwveeikrvaeenvpivLvGnKvDlee............kravsteegeelakelg.lkfletSAktne 147
                                    ++r+s+ +vk ++v ++k++a+ + +  LvG K+Dl+e            +  ++t+eg el++++g + ++e+SAk+n 
  gene163|gene163|rna163|rna163  92 DDRSSYAEVKnSLVGQVKEKAP-QAKYFLVGAKIDLREdckrleelarsgDSPITTSEGLELSQSIGaIGYFECSAKNNI 170
                                    **********899*********.5*******************************************9************ PP

                                    THHHHHHHHHHHH CS
                            Ras 148 nveeafeellrei 160
                                    +++++fe++ + +
  gene163|gene163|rna163|rna163 171 GIDDIFEKISKYA 183
                                    ********98865 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   7.3e-20   2.2e-16       2     120 .]      13     126 ..      12     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 7.3e-20
                                    EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSC CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaa 81 
                                    + ++G ++ GKts+l+r+v+++f ++ ++t+  +++++ +   k+   ++    v+l++WDtaGq+++   ++l l +a+
  gene163|gene163|rna163|rna163  13 LTIIGSATCGKTSILTRHVKRTFGTEISPTVFNSVSNT-Y---KH---KD--YVVELRLWDTAGQDEYARFRHLALPSAD 83 
                                    689***************************98877543.3...22...22..3599************************ PP

                                    EEEEEEE..GH.HHHCH.HHHHHHHHHHCSSS-EEEEEE-TTT CS
                            Roc  82 lailvyd..sr.ssenl.keWlkelkkvagkspvilvgnkiDl 120
                                     +++vy   +r s++++ ++ + ++k++a++++ +lvg kiDl
  gene163|gene163|rna163|rna163  84 YIMIVYAidDRsSYAEVkNSLVGQVKEKAPQAKYFLVGAKIDL 126
                                    ****995434414566626799*******************95 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0     9e-12   2.7e-08      15     174 ..      11     182 ..       2     183 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 9e-12
                                    EEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEE.EEEEETT..EEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEE CS
                            Arf  15 lrilllGLDnaGKtTilkklkleelvt.tvPTigfnv.eeleikn..lkftvwDvGGqeklRplWknYfektdavifvvD 90 
                                     ++ ++G  + GKt il++  +  + t ++PT+   v ++ ++k+  +++++wD  Gq++  ++ +  +++ d ++ v  
  gene163|gene163|rna163|rna163  11 KQLTIIGSATCGKTSILTRHVKRTFGTeISPTVFNSVsNTYKHKDyvVELRLWDTAGQDEYARFRHLALPSADYIMIVYA 90 
                                    567799999**********99999877589998655514556665447999***************9******9888888 PP

                                    TT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSS.........SSSSEEEEEEBTTTT CS
                            Arf  91 sadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelk.........gkrkleiqkcsavkg 161
                                      dr+  +e k+ L   ++e+  + ++  +++ K+Dl+e+ ++ e  +  g + ++         +   +  ++csa ++
  gene163|gene163|rna163|rna163  91 IDDRSSYAEVKNSLVGQVKEKAPQ-AKYFLVGAKIDLREDCKRLEELARSGDSPITtseglelsqSIGAIGYFECSAKNN 169
                                    8899**********9999877665.55666688*****999887765555555544333333433455667788999999 PP

                                    BTHHHHHHHHHHH CS
                            Arf 162 eglkeglewlses 174
                                     g+++ +e++s++
  gene163|gene163|rna163|rna163 170 IGIDDIFEKISKY 182
                                    9999999988875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.9e-06    0.0058       3     103 ..      14     110 ..      12     124 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.9e-06
                                    EEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSE. CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseekglgkaflaleeadl. 78 
                                     i+G    GK++++ + +++    ++s + +     ++++ +     e++l+Dt+G  +     +  + + lal +ad  
  gene163|gene163|rna163|rna163  14 TIIGSATCGKTSILTRHVKRtfGTEISPTVFNSVSNTYKHKD--YvVELRLWDTAG-QD-----EYARFRHLALPSADYi 85 
                                    79*****************95446888888888888888665..3479********.33.....3233333344456651 PP

                                    .EEEEEETTTTCSHHHHHHHHHHHHH CS
                       MMR_HSR1  79 .illvvdaseeklkpldeeleellee 103
                                     i++ +d + +++++++++l    +e
  gene163|gene163|rna163|rna163  86 mIVYAIDDR-SSYAEVKNSLVGQVKE 110
                                    155566644.5688887777665544 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.8e-06     0.017       4      84 ..      11      92 ..       8     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.8e-06
                                   -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GG..TT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEE CS
                          SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekg..skltliDfPGheklrqklleklkaksslkglvfv 82
                                   +++ ++G   +GKTs++tr  + ++ +       +s+++ + ++k+   +l+l D  G+++ + ++ +  + ++    +v+ 
  gene163|gene163|rna163|rna163 11 KQLTIIGSATCGKTSILTRHVKRTFGTEISPTvFNSVSNTY-KHKDyvVELRLWDTAGQDEYA-RFRHLALPSADYIMIVYA 90
                                   56789**************9988776555444578888888.344412678889999999875.455555666667777777 PP

                                   EE CS
                          SRPRB 83 vD 84
                                   +D
  gene163|gene163|rna163|rna163 91 ID 92
                                   77 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.4    0.0027       7.9       2      19 ..      11      29 ..      10     104 .. 0.86
   2 ?    4.7   0.0    0.0078        23     116     142 ..     154     180 ..     140     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0027
                      PduV-EutP  2 kkilliGkvgsGKtt.Ltq 19
                                   k++ +iG+  +GKt+ Lt+
  gene163|gene163|rna163|rna163 11 KQLTIIGSATCGKTSiLTR 29
                                   78899*********93444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0078
                      PduV-EutP 116 ksaGaekifevsavekegieellkyle 142
                                    +s Ga   fe sa +++gi+++++ ++
  gene163|gene163|rna163|rna163 154 QSIGAIGYFECSAKNNIGIDDIFEKIS 180
                                    56899999**************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1348.48
//
Query:       gene1631|gene1631|rna1630|rna1630  [L=828]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-05   24.8   0.0      4e-05   23.5   0.0    1.7  1  IBN_N     Importin-beta N-terminal domain
  ------ inclusion threshold ------
       0.11   13.1   0.2       0.29   11.7   0.2    1.6  1  DUF4046   Protein of unknown function (DUF4046)


Domain annotation for each model (and alignments):
>> IBN_N  Importin-beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.4e-09     4e-05       4      68 ..      27      98 ..      24     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.4e-09
                                       HHHHHHC..STCHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHGGSCCCHC.......GSXHHHHHHHHHHH CS
                              IBN_N  4 qLkqlek..qpgflsallqilanseselevRqlAalyLknlitkhWsdeeekq.......slpseekeqIrnnl 68
                                       ++ +l++  ++ f s l++++ + +s  ++R+ ++++Lkn+++++  d e ++        +  e +e+++n l
  gene1631|gene1631|rna1630|rna1630 27 KILELQSndFERFISILVEVFGDLKSNDQLRMVSGIILKNSLHAN--DPELQKgclsrwlGMRCESREYVKNML 98
                                       5555555559*************66666*****************..666666699999999999999999987 PP

>> DUF4046  Protein of unknown function (DUF4046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.2e-05      0.29      19      63 ..     225     269 ..     216     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
                            DUF4046  19 gfWgneeeevqhrlklclryvvlqklkikpqeillevkksfliky 63 
                                        g W  ++ee+ h+l +c+  +v+   k+  + il ++  ++l ++
  gene1631|gene1631|rna1630|rna1630 225 GIWNGNDEELIHKLMICFNRLVMLNYKFIQKSILENMLAQYLGRF 269
                                        78*999*********************999999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (828 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 5340.85
//
Query:       gene1632|gene1632|rna1631|rna1631  [L=876]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-24   85.6  10.7    7.3e-24   84.6  10.7    1.5  1  FH2       Formin Homology 2 Domain
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.027   14.1   0.1    1.5  1  DUF4038   Protein of unknown function (DUF4038)
       0.18   12.3   1.7        2.6    8.6   0.5    3.1  2  DUF104    Protein of unknown function DUF104
        1.4    9.4   5.7          1    9.8   3.4    2.0  2  DUF4200   Domain of unknown function (DUF4200)


Domain annotation for each model (and alignments):
>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6  10.7   1.6e-27   7.3e-24      12     368 ..     521     858 ..     519     862 .. 0.89

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1.6e-27
                                        ------EESSGGCTTSCCCCTCCHHHHCTSHHHHHHHHTBSC--HCCH......HCSCCTTCCESSS-HHHHHHHH CS
                                FH2  12 kplhWdkvkpsqdrstvWdklkeesfekeldlseleelFsakekkkkkkksekskkskkkkkkvklLdpkrsqnia 87 
                                        kplhW  + +++++  ++d+++    + ++d++++ee+F +  ++          +sk+k+ + ++ ++ r   ++
  gene1632|gene1632|rna1631|rna1631 521 KPLHWIPLARAEKT--IFDDVDGI--NADIDYKRFEEIFCEPFSE---------HESKSKQIQKSIVEDGRLFLVS 583
                                        89******999997..******76..679***********99886.........667889999999********** PP

                                        HHHHHH...TS-HHHHHHHHHTTTTCCCTHHHHHHHHHHCGGHHHHHHHHCTCTSGTTB-HHHHHHHHHTTSTTHH CS
                                FH2  88 IlLkkl...kltaeeiveaileldeealdlellenLlkmaPtkeelkklkeykgevseLseaeqFllelvkiprle 160
                                          Lk+l   ++t+e + + + + d+ al+l+ l n+ km P+ ee++ l   + ++ +Ls+ e+ +l+ ++   ++
  gene1632|gene1632|rna1631|rna1631 584 LSLKHLemrNITPENVYSILKSPDN-ALELQDLLNIEKMYPDHEEVMNLI--SAAPGSLSKVEKAMLAYSQLLDVR 656
                                        ****996666678888877777777.***********************8..8899******************** PP

                                        HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHSTCS.TT.CS-SEE-GGGGGGCC CS
                                FH2 161 kRleallfkstfeeeveelkrslealeaaseeLknskkfkklLeliLalGNymNdgt.rr.gqAkGFkLssLlkLs 234
                                        k +e+l+f  ++ +e+  ++  l+ l ++++++ +sk+++ +L++iL++GN mN    ++ ++A+GF+LssL+  s
  gene1632|gene1632|rna1631|rna1631 657 KLIEILIFERKLFDEIFLIEGTLSRLLEVCSKILDSKSLRVVLKMILEIGNTMNFRYsMNkKKASGFRLSSLYVFS 732
                                        ******************************************************64413359************** PP

                                        CSB-STTTSBHHHHHHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT- CS
                                FH2 235 dvKstdnkttLLHylvkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsd 310
                                        + +++ n+t+L  +l ++++ +    + + +eL+ + +   ++ e+l+   +k++  ++   ++le  +     ++
  gene1632|gene1632|rna1631|rna1631 733 NYRGK-NNTSLFPFLFQMLEANGVRPEYLLEELSPIHD---LKNEELTRMREKINYFIEMYTEKLELLDL---LEE 801
                                        ***97.569*****************************...56666666666666777777888888887...777 PP

                                        THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--TTCCHHHHHHHHHHHHH CS
                                FH2 311 kflevlkeflkeaeeklkkleeelkeakelvkelveYfgedkkevspeeffkilreFl 368
                                         ++e + +f++ a +kl++++ + k+ +     +   fge++   +++e+ ++l++Fl
  gene1632|gene1632|rna1631|rna1631 802 SVKEEYAKFFRFACSKLESVSCNFKKFHLYSSMIKCKFGEEE-ARNLKEILVTLSDFL 858
                                        9*************************9987777777899866.699999999999998 PP

>> DUF4038  Protein of unknown function (DUF4038)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.1e-06     0.027     107     151 ..      74     116 ..      60     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                                        -HHHHHTT.......SS-HHHHHHHHHHHHHHHTT-SEEEEEECCC- CS
                            DUF4038 107 wgdkvkegw..gpenifnaekakeygkylvaRYkalpiiWllggDrd 151
                                        +     + w  ++eni+  ++ ke++k++ + Yk++ +iW++g + +
  gene1632|gene1632|rna1631|rna1631  74 F----GQCWenSTENITRRNNTKELIKFFNDNYKDRFMIWCTGENLK 116
                                        3....4556545899****************************6654 PP

>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.5   0.00057       2.6      10      40 ..     475     505 ..     473     514 .. 0.81
   2 ?    0.9   0.0      0.15   6.5e+02      34      57 ..     530     554 ..     517     555 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00057
                             DUF104  10 EnGvLKPLekvdLkEGeevkikIeeakeilk 40 
                                        E+G LKPLe + L+ G e  + ++  k ilk
  gene1632|gene1632|rna1631|rna1631 475 ESGQLKPLELIVLSPGIEKTVNLKTKKIILK 505
                                        89****************9998888333333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                             DUF104  34 e.akeilkklkgilkeadeeeleel 57 
                                        +  k+i ++++gi  ++d++++ee+
  gene1632|gene1632|rna1631|rna1631 530 RaEKTIFDDVDGINADIDYKRFEEI 554
                                        45689******************97 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   1.3e+04      47      65 ..     394     412 ..     390     430 .. 0.78
   2 ?    9.8   3.4   0.00023         1       9     108 ..     769     870 ..     767     873 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                            DUF4200  47 llkfdkflkendakraral 65 
                                        ++kf+ f+k + +k ++ +
  gene1632|gene1632|rna1631|rna1631 394 IAKFCAFMKYCPEKAREFI 412
                                        6799999999988887755 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00023
                            DUF4200   9 fevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkek..eaei 82 
                                        ++ +e+l +++e+i+   e  +++ e l+  e+  +e+++kf +f  +  +  +   kk +  + ++k k  e+e 
  gene1632|gene1632|rna1631|rna1631 769 DLKNEELTRMREKINYFIEMYTEKLELLDLLEESVKEEYAKFFRFACSKLESVSCNFKKFHLYSSMIKCKfgEEEA 844
                                        57899****************************************************************988999* PP

                            DUF4200  83 kklkaeietlkseiekleekleeykk 108
                                        ++lk+ ++tl  ++  +++ le+y++
  gene1632|gene1632|rna1631|rna1631 845 RNLKEILVTLSDFLCSMKQHLEQYRR 870
                                        ************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (876 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.53
# Mc/sec: 4997.91
//
Query:       gene1633|gene1633|rna1632|rna1632  [L=357]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-20   73.4   0.0    2.4e-20   72.5   0.0    1.5  1  Acyltransferase  Acyltransferase
  ------ inclusion threshold ------
      0.034   14.2   0.1      0.086   12.9   0.1    1.6  1  Acyltransf_C     Acyltransferase C-terminus


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   2.6e-24   2.4e-20      13     107 ..      83     202 ..      59     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 2.6e-24
                    Acyltransferase  13 kgpailvaNHqsylDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnaraagslenise 87 
                                         ++ ++++NH +++D+l+  ++l+  + + +++ ii+k +l +ipllg +m+ ++fif++Rk  ++++  ++ +s+
  gene1633|gene1633|rna1632|rna1632  83 RNRNVVISNHLTEYDWLFVCCVLHYLKrF-EDLCIILKMSLRNIPLLGYGMKFFQFIFLNRKVSKDREIIMSGASR 157
                                        46789******************888867.********************************************** PP

                    Acyltransferase  88 lleegkl.vviFPEGtrsre........................g 107
                                        l +egk+ +++FPEGt   +                        +
  gene1633|gene1633|rna1632|rna1632 158 LKKEGKYdLLLFPEGTYIDKcshpkshkwsveanvevegkgfdpE 202
                                        ***************999995455555555555555555555553 PP

>> Acyltransf_C  Acyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.6e-06     0.086      19      51 ..     263     296 ..     259     308 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-06
                       Acyltransf_C  19 leevPed.eeelaeWlhelfeeKDklleeFyktg 51 
                                        l+ +P++  ++   +l +lfeeK+k++  F k++
  gene1633|gene1633|rna1632|rna1632 263 LDYIPNNdGMDGDDFLLKLFEEKEKMISRFRKEN 296
                                        5678999559999*****************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2275.92
//
Query:       gene1634|gene1634|rna1633|rna1633  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-49  167.3   0.0    2.7e-49  166.9   0.0    1.1  1  NIF       NLI interacting factor-like phosphatase


Domain annotation for each model (and alignments):
>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.9   0.0   1.5e-53   2.7e-49       2     150 ..      52     204 ..      51     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 166.9 bits;  conditional E-value: 1.5e-53
                                NIF   2 tLVLDLDetLvhskleksk....klkve.gekvevsvlkRpgldefLkelsklyevvifTasseeyaeavidildp 72 
                                        tLVLDLD+tLvhs++e+++     ++v+  ++++++v++Rp++ ef++ +  +yev+ifTa+++eya++vid++d 
  gene1634|gene1634|rna1633|rna1633  52 TLVLDLDNTLVHSTFEMPEfydfCVEVPrSRDMPIYVKVRPHATEFINGVGDIYEVIIFTAAKKEYARKVIDMIDM 127
                                        9**************998668765566688899******************************************* PP

                                NIF  73 ekkllshrlyrescvkkkgeyvKdLsllgrdlsrvvivDdspdsfelqpengipiksffsdkkDneLlkllpllke 148
                                        +k+ +++ lyresc+ ++g yvKdL  lgr+l++v++vDdsp+s+e+qp ngi+i+++++  +D++Llk++++lk 
  gene1634|gene1634|rna1633|rna1633 128 NKN-IKYSLYRESCTLTNGRYVKDLCRLGRPLHKVILVDDSPHSYEFQPGNGIHIPPYTGALDDDSLLKVMKYLKG 202
                                        **9.**********877**********************************************************9 PP

                                NIF 149 la 150
                                        l 
  gene1634|gene1634|rna1633|rna1633 203 LP 204
                                        86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1466.81
//
Query:       gene1635|gene1635|rna1634|rna1634  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-30  106.0   1.2    4.9e-30  105.6   1.2    1.2  1  Metallophos  Calcineurin-like phosphoesterase


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.6   1.2   2.7e-34   4.9e-30       3     201 ..      52     237 ..      50     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 2.7e-34
                                        EEEEESBTBTTCCTHHHHHHHHHHHHHHH.TTESEEEEESTSSSSS..HHHHHHHHH.HHHHHHHTSEEEEEC-TT CS
                        Metallophos   3 ilvigDlHlalgggqlddllkllddllre.ekpdlvllaGDlvdrg..dlekellel.laalvkypipvylllGNH 74 
                                        + v+gD+H     g+++d+l++l+   ++ ek +l+l  GD+vdrg  +++  ll + +++l+k   ++yll+GNH
  gene1635|gene1635|rna1634|rna1634  52 VNVVGDVH-----GHFYDVLNMLSLMEDPsEKTYLFL--GDYVDRGynSVDLILLLFlYKRLYK--GNLYLLRGNH 118
                                        569*****.....**********99944447999999..*******776666455554555555..89******** PP

                                        S........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSC CS
                        Metallophos  75 e........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnlel 141
                                        e        gf+ee+ +ky+        wr + e f++lp+a+++    k++++hGg  p+   sld + + ++  
  gene1635|gene1635|rna1634|rna1634 119 EtrmlssvyGFKEECVRKYDL----VVYWRIC-EAFQYLPVAAIVLR--KYFCVHGGlVPGM--SLDFIMKHDRVG 185
                                        ******************997....5566776.9*************..********55555..666666666666 PP

                                        HHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 142 eapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                        e++e +d++++d        ++ ++g +   rg+gylfg+++l+++l+++g+ + +++H+
  gene1635|gene1635|rna1634|rna1634 186 EITEINDILWSD--------PDETPGFRKSQRGAGYLFGEDVLKNFLNEHGLSHFVRSHQ 237
                                        6666669*****........***************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2174.30
//
Query:       gene1636|gene1636|rna1635|rna1635  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-08   33.1   0.0    5.4e-07   29.7   0.0    2.3  1  FeS_assembly_P  Iron-sulfur cluster assembly protein


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0     3e-11   5.4e-07       3      62 ..      31     106 ..      29     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3e-11
                                        HHHHHHTT-B-TTTSSBCCCCT---E.......EEE-T.........-EEEEEE--SSTT-TTHHHHHHHHHHHHC CS
                     FeS_assembly_P   3 avlaaLrtVtDPelgvdlvslglvre.......idieg.........gkVsvditltypacslaeairadaeaalr 62 
                                        +v++ +r+++DPe++ +l +lg+v++       i+ ++           V+v + +t+p+cs+a+ i   ++a+l 
  gene1636|gene1636|rna1635|rna1635  31 TVFELIRDIRDPEHPYTLEQLGVVSKerisiglINSDDatlsiglpiKYVRVMFKPTIPHCSMAAVIGLCIKAQLS 106
                                        699***************************9996666666666668899******************999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 965.99
//
Query:       gene1637|gene1637|rna1636|rna1636  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-30  104.6   9.5    4.5e-30  103.9   9.5    1.3  1  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
       0.02   15.1   4.2      0.032   14.5   4.2    1.3  1  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
        1.2    9.4   8.6       0.11   12.7   2.4    2.0  2  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
        1.3    8.9   4.4       0.78    9.6   0.2    2.0  2  DUF866         Eukaryotic protein of unknown function (DUF866


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   9.5     1e-33   4.5e-30       2      75 ..      18      91 ..      17      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1e-33
                                       EEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EE CS
                      Ribosomal_L44  2 HtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfel 75
                                       + +hkv+q+kk+kd++ aqg+Rry+rkq+gygGqtkp++++kaK+tKK+vl+leCt+Ck +++k+lkRak++ +
  gene1637|gene1637|rna1636|rna1636 18 YSTHKVSQAKKSKDNPRAQGNRRYARKQRGYGGQTKPILRRKAKVTKKLVLKLECTKCKFAHQKPLKRAKHVIF 91
                                       789********************************************************************976 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.2   7.2e-06     0.032      41      90 .]       5      76 ..       2      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.2e-06
                                       STCCCTB-TTT--B--CTTTEEEEEE-SSS-E................................EEEEETTTT CS
                               Rpr2 41 psvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka.......................dvlvvtClaCg 90
                                       p+ + t+CkkC+++ +  v+   + + + +  +++++ a                        vl+ +C++C+
  gene1637|gene1637|rna1636|rna1636  5 PKTRNTFCKKCSNYSTHKVSQAKKSKDNPRA-QGNRRYArkqrgyggqtkpilrrkakvtkkLVLKLECTKCK 76
                                       67799***************99999764444.3444444578899999999999999999988889******6 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.4   2.4e-05      0.11      19      61 ..       5      47 ..       2      54 .. 0.89
   2 ?   -0.2   0.4      0.26   1.2e+03       9      17 ..      70      78 ..      61      89 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                       NOB1_Zn_bind 19 kdmtkkFCpkCGnktLkrvavsvdengelklhlkknfqlnlrG 61
                                       ++++  FC+kC n + ++v+   +++ + +   ++++  ++rG
  gene1637|gene1637|rna1636|rna1636  5 PKTRNTFCKKCSNYSTHKVSQAKKSKDNPRAQGNRRYARKQRG 47
                                       578899***************9999999999999998888888 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.26
                       NOB1_Zn_bind  9 lrChaCfkv 17
                                       l+C+ C   
  gene1637|gene1637|rna1636|rna1636 70 LECTKCKFA 78
                                       456666544 PP

>> DUF866  Eukaryotic protein of unknown function (DUF866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.6     0.063   2.8e+02      65      81 ..      12      28 ..       5      57 .. 0.64
   2 ?    9.6   0.2   0.00017      0.78      22      42 ..      63      83 ..      54     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.063
                                       -SSSS--EEEEEE-.-T CS
                             DUF866 65 cklckressisikkete 81
                                       ck+c++ s+ ++ ++++
  gene1637|gene1637|rna1636|rna1636 12 CKKCSNYSTHKVSQAKK 28
                                       66666666666555322 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
                                       T--EEEEEEETTSS.-EEEEE CS
                             DUF866 22 dfeytfkvkctsCreehpkev 42
                                       + + ++k++ct+C+  h+k+ 
  gene1637|gene1637|rna1636|rna1636 63 TKKLVLKLECTKCKFAHQKPL 83
                                       66789************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1126  (0.0628033); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 827.14
//
Query:       gene1638|gene1638|rna1637|rna1637  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-46  156.7   0.0    3.2e-46  156.5   0.0    1.0  1  UQ_con     Ubiquitin-conjugating enzyme
    0.00017   21.3   0.0    0.00019   21.2   0.0    1.1  1  Prok-E2_B  Prokaryotic E2 family B
  ------ inclusion threshold ------
       0.11   12.8   0.1       0.22   11.8   0.1    1.4  1  RWD        RWD domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.5   0.0   5.3e-50   3.2e-46       1     138 [.       8     143 ..       8     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 5.3e-50
                                        HHHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE CS
                             UQ_con   1 rlqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd 76 
                                        rl+k+lk+++k++ + i a++ +d +l++w ++i+gpe tp+egg+F l l fpe+YP +pP+v+fv+++fHPn++
  gene1638|gene1638|rna1637|rna1637   8 RLMKDLKRVRKNSFKTIFAEPLED-DLMTWVAVIFGPESTPFEGGTFSLVLAFPETYPQDPPNVRFVSEMFHPNIY 82 
                                        89*********************7.*************************************************** PP

                                        TTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHH CS
                             UQ_con  77 ksGevcldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvke 138
                                        ++Ge+cldiL+ ++Wsp++++  vl+siqsLl++pn+ sp+n++aa+l+ +++  y +kvk+
  gene1638|gene1638|rna1637|rna1637  83 PNGELCLDILN-NRWSPSYDVMGVLISIQSLLNDPNTASPANTDAATLFLSNPILYAEKVKN 143
                                        ***********.55*********************************************987 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.1e-08   0.00019      33     113 ..      46     122 ..       6     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.1e-08
                          Prok-E2_B  33 t..sggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLClleeeldldewdpngsvadvleqlqqvLn 106
                                        t  +ggt+ l l +p+++p+ pp v+ + +      p i++ +g+LCl       + w p   v  vl ++q +Ln
  gene1638|gene1638|rna1637|rna1637  46 TpfEGGTFSLVLAFPETYPQDPPNVRFVSEM---FHPNIYP-NGELCL---DILNNRWSPSYDVMGVLISIQSLLN 114
                                        1458************************999...89*****.******...8999********************9 PP

                          Prok-E2_B 107 .egisgde 113
                                          + ++  
  gene1638|gene1638|rna1637|rna1637 115 dPNTASPA 122
                                        86766655 PP

>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.7e-05      0.22      55      78 ..      53      76 ..      49     116 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                                       EEEEEEE-SSTTSS--EEEEEECC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                                RWD 55 lkleiklpeeYPeeaPiislsste 78
                                       ++l   +pe+YP+ +P +++ s+ 
  gene1638|gene1638|rna1637|rna1637 53 FSLVLAFPETYPQDPPNVRFVSEM 76
                                       789999************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1012.11
//
Query:       gene1639|gene1639|rna1638|rna1638  [L=828]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-63  214.3   0.7      4e-63  213.2   0.7    1.5  1  SNF2_N         SNF2 family N-terminal domain
    9.3e-21   74.3   0.0    7.8e-20   71.3   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    3.1e-14   53.3   0.1    1.1e-13   51.6   0.1    2.0  1  ResIII         Type III restriction enzyme, res subunit
    1.1e-10   41.6   0.0    2.9e-10   40.2   0.0    1.8  2  DEAD           DEAD/DEAH box helicase
    1.4e-10   41.2   3.7    9.1e-10   38.6   3.7    2.6  1  SLIDE          SLIDE
    4.4e-06   26.1   0.1    2.2e-05   23.8   0.0    2.1  2  HDA2-3         Class II histone deacetylase complex subunits 
      9e-05   22.2   0.0    0.00022   21.0   0.0    1.7  1  SWI2_SNF2      SWI2/SNF2 ATPase
    0.00019   20.7   0.0    0.00039   19.7   0.0    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    0.00079   20.2   0.2     0.0026   18.5   0.2    1.9  1  HAND           HAND
  ------ inclusion threshold ------
      0.021   14.9   0.5      0.048   13.7   0.5    1.5  1  DUF1640        Protein of unknown function (DUF1640)
      0.052   13.6   0.5       0.95    9.5   0.1    3.2  3  AAA_14         AAA domain
      0.065   13.2   0.1        3.5    7.6   0.0    2.7  2  Baculo_RING    Baculovirus U-box/Ring-like domain
        5.4    7.2   8.7        2.1    8.4   0.5    2.9  3  DUF4110        Domain of unknown function (DUF4110)
        7.6    6.4   7.2         14    5.5   0.7    3.4  3  Scm3           Centromere protein Scm3


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.2   0.7   3.1e-66     4e-63      50     349 ..      70     336 ..      58     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: 213.2 bits;  conditional E-value: 3.1e-66
                                        HHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N  50 eakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalr 125
                                          ++++ ++iLaDemGLGKT+q++a++   r+ ++++k+          +Liv P+s+l +W++e+++++++ ++r
  gene1639|gene1639|rna1638|rna1638  70 NMHENSINCILADEMGLGKTLQTIAFLGYIRYVRKEKKK----------HLIVLPKSTLANWKREFKKFMPNYKVR 135
                                        5678999*********************66665544444..........7************************** PP

                                        E--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 126 vlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavs 201
                                        v++ + ++    ++++  + +    d ++ttY++  + +      + l+ v+w ++++DE+h++kn++s ++++v+
  gene1639|gene1639|rna1638|rna1638 136 VFYSSRKE----MRKEAEEIMSSRWDACLTTYEMCINAK------NILNTVNWSYIIIDEAHRIKNEHSLLSKIVR 201
                                        *9999975....334567889999************777......8****************************** PP

                                        H---S-EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHHHHHHHHHHHHHTT-STTEE---GGGT- CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 202 kLstsnrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpieaqaekgrsrLlqllqrlmlrrakkdve 277
                                         +s ++r+++tGTP+qn++++l++Ll+f+ +e+f++ + f++ + + i + + + ++r++++lq + lrr k dve
  gene1639|gene1639|rna1638|rna1638 202 IFSCDHRLLITGTPLQNNVHELWALLNFIVPEIFNDAEKFERYVMN-IDEGDGEAIKRIRSVLQLFFLRREKIDVE 276
                                        ****************************************998665.6669************************* PP

                                        -S---EEEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH---X CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SNF2_N 278 knlPpkteeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnhpql 349
                                        k lPpk+   ++ kls+++r++Y              llkr+   l ++++ k  +++ +++lr++cnhp+l
  gene1639|gene1639|rna1638|rna1638 277 KGLPPKKIINLYSKLSAMQREWYR------------MLLKRDLSPLGNTRDPKGMLMNVVMQLRKCCNHPYL 336
                                        ************************............77777766666666555779**************98 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.3   1.6e+03      13      55 ..     103     145 ..      89     171 .. 0.60
   2 !   71.3   0.0   6.1e-23   7.8e-20       2     111 .]     357     470 ..     356     470 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                        TTTTSEEEEEESSHHHHHHHHHHHHHT..TSTEEEESTTSTHHHH CS
                         Helicase_C  13 eeeggkilifvntidrlekvklllekk..gikvavlhgelpqner 55 
                                        ++e++k li++++ + ++  + + +k+  ++kv v++++ + + r
  gene1639|gene1639|rna1638|rna1638 103 RKEKKKHLIVLPKSTLANWKREF-KKFmpNYKVRVFYSSRK-EMR 145
                                        56666777777766655444444.23345666666666432.222 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 6.1e-23
                                        HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHH...TTSSSEE CS
                         Helicase_C   2 kleallell.kleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfn...kgesdvL 70 
                                        k+ +l +ll +++++g+++lif++   +l+    l+      g+k+++++g+++ +er e++++fn   ++++ +L
  gene1639|gene1639|rna1638|rna1638 357 KMMMLDKLLaNFKAKGSRVLIFSQMSMMLDI---LEDYAvfkGYKYCRIDGSTSYRERTEAIDAFNaegSDKFIFL 429
                                        5667788888899****************65...422224469***********************86667888** PP

                                        EESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                         Helicase_C  71 iatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        ++t++++ Gi++  +++V+ fd ++n++   q+ +R++R+g
  gene1639|gene1639|rna1638|rna1638 430 LTTRAGGLGINLSTADTVVLFDSDWNPQMDLQAQDRAHRIG 470
                                        ***************************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.1   8.6e-17   1.1e-13       2     169 ..      55     215 ..      54     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 8.6e-17
                                        -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S......-EEEEESSHHHHHHHHHHGGG CS
                             ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee.kflflvprkslleqtleefkk 76 
                                        +el++yQ+e ++ l++    ++  + +++ + G GKTl  +++  +++  +ke+ k l++ p+ + l  +++efkk
  gene1639|gene1639|rna1638|rna1638  55 HELKDYQIEGLNWLINMH--ENSINCILADEMGLGKTLQTIAFLGYIRYVRKEKkKHLIVLPKST-LANWKREFKK 127
                                        5899*******9999776..6888999**********9988877777666666626666666655.567******* PP

                                        GTGG....GEEEESSS-B--..........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T. CS
                             ResIII  77 flseaykeigkkvsgdkkka...kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk. 148
                                        f+++++  +  ++s++k+++   +e+ s+ ++ ++tt+++  +++       + l   +  +iiiDEaHr++ ++ 
  gene1639|gene1639|rna1638|rna1638 128 FMPNYK--VRVFYSSRKEMRkeaEEIMSSRWDACLTTYEMCINAK-------NILNTVNWSYIIIDEAHRIKNEHs 194
                                        ****98..6666666666665667889**************9999.......778888899************853 PP

                                        TTHHHHHT---SEEEEEESS- CS
                             ResIII 149 swreilekfkeavllglTATp 169
                                           +i++ f+   +l +T+Tp
  gene1639|gene1639|rna1638|rna1638 195 LLSKIVRIFSCDHRLLITGTP 215
                                        667799**************9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.2e-13   2.9e-10      13     149 ..      74     203 ..      58     223 .. 0.74
   2 ?   -3.3   0.0       5.2   6.6e+03      47      94 ..     372     415 ..     359     423 .. 0.67

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.2e-13
                                        TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaar 88 
                                        +  ++++a e G GKTl  +  +  i y   +k+++k liv P   La+   +++kkf+ ++++rv    + ++ r
  gene1639|gene1639|rna1638|rna1638  74 NSINCILADEMGLGKTLQTIAFLGYIRYV--RKEKKKHLIVLPKSTLAN-WKREFKKFMPNYKVRVF-YSSRKEMR 145
                                        3348999*********9866555555554..89999***********97.6899******9877775.33466778 PP

                                        HHHHHHH.TTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                        xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  89 dqlskld.ngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                        ++ +++  ++ d  ++t +++++   ++ ln+ + +++++DEa+r+ ++     +++i++ +
  gene1639|gene1639|rna1638|rna1638 146 KEAEEIMsSRWDACLTTYEMCIN--AKNILNTVNWSYIIIDEAHRIKNE--HSLLSKIVRIF 203
                                        8888885266************9..667899***************998..44444444444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.2
                                        S-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  47 gpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskl 94 
                                        g ++li     +++ ++l+++  fk y   +++ i g++++r+  +++
  gene1639|gene1639|rna1638|rna1638 372 GSRVLIF-SQMSMMLDILEDYAVFKGY---KYCRIDGSTSYRERTEAI 415
                                        4444444.4556778888888888885...778888888888877776 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   3.7   7.1e-13   9.1e-10       1     113 [.     712     815 ..     712     816 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 7.1e-13
                              SLIDE   1 ekiikqIekgekkieklkelkellkkkveqyknplqelkikyppsnkgkkeyteeeDrfllvllaky.Gygny.ek 74 
                                        ekii++I+++++k+ek+ +++e++++ +e++++ l         ++++k     +  + ll+l+ ky  y n+ e 
  gene1639|gene1639|rna1638|rna1638 712 EKIISSINRSQRKMEKRSRIREIIERDFEDISRKLG--------KTRSKL---GDYNNLLLNLYRKYiDYPNWvEC 776
                                        7*****************************998554........444444...566789*****99989***87** PP

                              SLIDE  75 ikkeiresplFrfDwflksrtpqelqkRcetLlklveke 113
                                        i+k+i    +++fD++l srt +++qk+++ L+ ++ k+
  gene1639|gene1639|rna1638|rna1638 777 IRKDILGLTEYKFDYYLLSRTNSDIQKHVNHLVDTLVKS 815
                                        *********************************999986 PP

>> HDA2-3  Class II histone deacetylase complex subunits 2 and 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.67   8.5e+02     162     202 ..     141     182 ..      56     222 .. 0.61
   2 !   23.8   0.0   1.7e-08   2.2e-05      51     247 ..     321     494 ..     284     507 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.67
                                        ...........-SEEEEEEESS---TTT.S--TT-S-EEEEE CS
                             HDA2-3 162 rktkeklkkkihsltihllsttrqltkd.ksllenikfdlii 202
                                        rk+ +k  ++i+s+ +    tt ++  + k++l++++ + ii
  gene1639|gene1639|rna1638|rna1638 141 RKEMRKEAEEIMSSRWDACLTTYEMCINaKNILNTVNWSYII 182
                                        333333455555555554333333333326666666665555 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.7e-08
                                        HHHHH.HHHHHHH-GGGT--TT--S-S-STTHHHHHHHT-HHHHHHHHHHHHHTTSS....EEEEEEE-STHHHHH CS
                             HDA2-3  51 lticlenlslvanHPsLLvdHympkklllkelpeklaetSgKFkvlndlvnliierkrksslnvlvvakskkeldL 126
                                        +++++ +l+   nHP+L  d   p   +     ++++e+SgK+ +l +l+     +       vl+ ++    ld+
  gene1639|gene1639|rna1638|rna1638 321 MNVVM-QLRKCCNHPYLFPDA-EPEPYT---NDKHIIENSGKMMMLDKLLANFKAKG----SRVLIFSQMSMMLDI 387
                                        44444.788888999998774.555554...5679****************999999....99************* PP

                                        HHHHHTTSSSEEEESSS--S--S---S-..................-SEEEEEEESS---TTTS--TT-S-EEEEE CS
                             HDA2-3 127 iEalllGkklkikrysgeklydekkkkskdtkknsrktkeklkkkihsltihllsttrqltkdksllenikfdlii 202
                                        +E + + k+ k+ r +g + y+e  +              +  +   s+++++l ttr         + + +d ++
  gene1639|gene1639|rna1638|rna1638 388 LEDYAVFKGYKYCRIDGSTSYRERTEAI------------DAFNAEGSDKFIFLLTTRAGGLG---INLSTADTVV 448
                                        *************************999............33344456788899998887444...5556679*** PP

                                        E-SST--TTSHHHHHHH---.-------EEEEEETTSHHHHHHHHT CS
                             HDA2-3 203 afDssvdtsspsveslrtqn.rkknklpiirlvpinSieHvkLcfk 247
                                         fDs+ +++ +   + r ++  +k++++++rl++ n++e    +++
  gene1639|gene1639|rna1638|rna1638 449 LFDSDWNPQMDLQAQDRAHRiGQKKQVVVFRLISENTVEERIVYRS 494
                                        *********99888888876244556************98766665 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.7e-07   0.00022      27     162 ..      84     220 ..      60     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.7e-07
                          SWI2_SNF2  27 qGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka..geekpkqaesrkeLkelle...keseki 97 
                                         G GK+l+ + +   ++  +++++k ++v  ++ L +  +++f+k+  + +  +  +srke++++ e   +++ + 
  gene1639|gene1639|rna1638|rna1638  84 MGLGKTLQTIAFLGYIRYVRKEKKKHLIVLPKSTLAN-WKREFKKFmpNYKVRVFYSSRKEMRKEAEeimSSRWDA 158
                                        6889999999999999997788888888889999976.67778877333334445566666666553111233344 PP

                          SWI2_SNF2  98 ifttiqKfeeeekeklevlsereniivlvDEaHRsqyg.elakklrkalpnaafigFTGTPilkkd 162
                                        ++tt +   +    + + l++ +  ++++DEaHR + + +l +k+ +++   +++  TGTP++++ 
  gene1639|gene1639|rna1638|rna1638 159 CLTTYEMCIN----AKNILNTVNWSYIIIDEAHRIKNEhSLLSKIVRIFSCDHRLLITGTPLQNNV 220
                                        4444444433....346888888899********98764899********************9865 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     3e-07   0.00039      38     137 ..     350     456 ..     339     498 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3e-07
                      ERCC3_RAD25_C  38 lyvmnpnkfracefLikyhekrgDkiivfsDnvfa...Lkeyakklkkpy..iyGetseaerlkilqkfkknpkvn 108
                                         ++ n+ k+++++ L+   +++g ++++fs   +    L++ya    ++y  i G+ts +er++ +++f+++ + +
  gene1639|gene1639|rna1638|rna1638 350 HIIENSGKMMMLDKLLANFKAKGSRVLIFSQMSMMldiLEDYAVFKGYKYcrIDGSTSYRERTEAIDAFNAEGSDK 425
                                        567899************************976651226899987766665599****************998888 PP

                      ERCC3_RAD25_C 109 tifl..skvgDtsiDlPeanvliqisshfgs 137
                                         ifl   + g   i+l +a  ++  +s+   
  gene1639|gene1639|rna1638|rna1638 426 FIFLltTRAGGLGINLSTADTVVLFDSDWNP 456
                                        8887446889999999999988887776654 PP

>> HAND  HAND
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2     2e-06    0.0026      26      54 ..     610     638 ..     589     675 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                                        ------GGC--S--CCHHHHHHHHHHHHH CS
                               HAND  26 aPKqiniqdfqffpkeLkeLqekEqlayk 54 
                                        +P+ i+  ++qf+p+eL+++qekE   y+
  gene1639|gene1639|rna1638|rna1638 610 KPRIIEYPEYQFYPRELQDIQEKEIKLYE 638
                                        59**********************98775 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   3.8e-05     0.048      10     115 ..     654     766 ..     648     770 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                            DUF1640  10 LeekG..ftkeqAeaimsaltevlneslekvakslvskselekseylqkaalselrkevqise.....rsefaalr 78 
                                        L ++G  +tk+  ++ ++a+++v ++++ k+a  l  + ++e  +  +   + elr+  +i       + ++++  
  gene1639|gene1639|rna1638|rna1638 654 LLSQGfdWTKKDFQSFVKAMEKVGKDNVPKIAMLLSHRDDVEAYHKVFWERINELRDAEKIISsinrsQRKMEKRS 729
                                        555664478999999*****************************************98777666666677889999 PP

                            DUF1640  79 seteklqreleklkqkLreeidklkadirldlnleKg 115
                                        + +e ++r++e +  kL +  +kl +  +l lnl ++
  gene1639|gene1639|rna1638|rna1638 730 RIREIIERDFEDISRKLGKTRSKLGDYNNLLLNLYRK 766
                                        99*******************************9887 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.49   6.3e+02      74     118 ..     116     157 ..      66     168 .. 0.71
   2 ?    9.5   0.1   0.00074      0.95      62     101 ..     171     215 ..     115     227 .. 0.68
   3 ?   -1.6   0.0         2   2.6e+03      17      47 ..     475     504 ..     472     527 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.49
                             AAA_14  74 qevpewekalkslvdegknldvivtGSnskllskeiatslagrva 118
                                        + + +w++  k+++ ++   +v v  S+ k + ke+++ ++ r +
  gene1639|gene1639|rna1638|rna1638 116 STLANWKREFKKFMPNY---KVRVFYSSRKEMRKEAEEIMSSRWD 157
                                        45567888888888766...6666678899999999999988876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00074
                             AAA_14  62 e....ekktylflDEiqevpewekalkslvdeg.knldvivtGSn 101
                                        +     + +y+++DE++++++  + l ++v+    + ++++tG  
  gene1639|gene1639|rna1638|rna1638 171 NilntVNWSYIIIDEAHRIKNEHSLLSKIVRIFsCDHRLLITGTP 215
                                        1233346789*******************9966456788998865 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                             AAA_14  17 tllkqlikellvkkesilyinldderdkkla 47 
                                        +++++li+e+   +e+i+y +l++ r++++ 
  gene1639|gene1639|rna1638|rna1638 475 VVVFRLISENT-VEERIVYRSLQKLRLDDIL 504
                                        67889999998.7899999999998886544 PP

>> Baculo_RING  Baculovirus U-box/Ring-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0027       3.5      95     128 ..       9      42 ..       3      46 .. 0.89
   2 ?    2.5   0.1       0.1   1.3e+02       7      37 ..     141     171 ..     136     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0027
                        Baculo_RING  95 lleesktfvGdeeiievykkvlkrvtsedaldve 128
                                        ll++ k f+Gd+e  + +   +++v  +d   +e
  gene1639|gene1639|rna1638|rna1638   9 LLKKYKNFIGDNEFFRAFIPNYEEVIGGDDEPIE 42 
                                        799*********************9999887776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                        Baculo_RING   7 lkdrkaaaeklikeyfhtcatecaicledid 37 
                                         k+ +  ae ++  ++++c t  ++c++  +
  gene1639|gene1639|rna1638|rna1638 141 RKEMRKEAEEIMSSRWDACLTTYEMCINAKN 171
                                        57788899******************99755 PP

>> DUF4110  Domain of unknown function (DUF4110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0017       2.1      25      64 ..     119     160 ..     115     169 .. 0.81
   2 ?    3.2   0.1     0.075        96      18      70 ..     620     676 ..     609     684 .. 0.73
   3 ?   -2.6   0.3       4.6   5.9e+03      62      87 ..     710     736 ..     699     740 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                            DUF4110  25 eeWqelaieslkekgaek..kseKelkkeafelAeerywelr 64 
                                        ++W+++  + + + + ++  +s Ke++kea e+ ++r+  + 
  gene1639|gene1639|rna1638|rna1638 119 ANWKREFKKFMPNYKVRVfySSRKEMRKEAEEIMSSRWDACL 160
                                        667777777777766666889*****************9997 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.075
                            DUF4110  18 dFfaRTseeWqelaieslkekgaek....kseKelkkeafelAeerywelrpvLeel 70 
                                        +F+ R  ++ qe+ i+  +e +  +     ++Kel  ++f+  ++ ++   +++e++
  gene1639|gene1639|rna1638|rna1638 620 QFYPRELQDIQEKEIKLYEEGKVLSqsdmVRKKELLSQGFDWTKKDFQSFVKAMEKV 676
                                        577777777777666655543322244678899999999999999998888888876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.6
                            DUF4110  62 elrpvLeelralede.qeeagigevve 87 
                                        ++++++  +++ + + ++ ++i+e++e
  gene1639|gene1639|rna1638|rna1638 710 DAEKIISSINRSQRKmEKRSRIREIIE 736
                                        455666666666666666666666665 PP

>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.067        85       4      24 ..     144     164 ..     142     167 .. 0.88
   2 ?    5.5   0.7     0.011        14      22      54 .]     508     542 ..     505     542 .. 0.81
   3 ?   -3.4   0.1       6.5   8.3e+03      12      22 ..     725     737 ..     720     749 .. 0.48

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.067
                                        HHHHHHHHHHHHHHHHHHHHH CS
                               Scm3   4 lreesderlkkrwesifeKYe 24 
                                         r+e++e +++rw+  +  Ye
  gene1639|gene1639|rna1638|rna1638 144 MRKEAEEIMSSRWDACLTTYE 164
                                        599***********9999888 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                                        HHHSG..GGSS--B-T.TT-S.B-XXXXXXXXXXX CS
                               Scm3  22 KYeridfedqgDEIDl.atge.ivvDnGhlrelrd 54 
                                        +Y+r     q++ ID+ a+g  i +D+G++++++d
  gene1639|gene1639|rna1638|rna1638 508 RYHRNSTVSQSELIDIlANGMeIGEDEGKDESIDD 542
                                        5666566788******966656********99875 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.5
                                        H..HHHHHHHHHH CS
                               Scm3  12 l..kkrwesifeK 22 
                                        +  ++r  +i+e+
  gene1639|gene1639|rna1638|rna1638 725 MekRSRIREIIER 737
                                        4443444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (828 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.85u 0.35s 00:00:01.20 Elapsed: 00:00:00.54
# Mc/sec: 4606.07
//
Query:       gene1640|gene1640|rna1639|rna1639  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-34  116.5   0.1    9.5e-34  115.8   0.1    1.3  1  Rad10          Binding domain of DNA repair protein Ercc1 (ra
    0.00015   22.3   0.0    0.00028   21.4   0.0    1.4  1  HHH_5          Helix-hairpin-helix domain
     0.0051   16.9   0.0      0.012   15.7   0.0    1.6  1  HHH_2          Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.024   14.9   0.0      0.058   13.7   0.0    1.6  1  HHH_3          Helix-hairpin-helix motif
       0.12   12.1   0.7       0.24   11.2   0.1    1.8  2  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin


Domain annotation for each model (and alignments):
>> Rad10  Binding domain of DNA repair protein Ercc1 (rad10/Swi10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.1   2.6e-37   9.5e-34       2     113 ..       2     110 ..       1     111 [. 0.96

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 2.6e-37
                              Rad10   2 ilvserqkgnplLkslknvpwey.kdivpDyvigsttcvlflslkyhklhpeYieerlkklkkkyklrvlLvlvDv 76 
                                        i vs+ qkgn++L++l+n +w+y ++i+pDy ++ ++  lflsl++h+++peYi++r++klk  yk+rvlLv+vDv
  gene1640|gene1640|rna1639|rna1639   2 IKVSPLQKGNSVLDYLSNATWHYdNSITPDYEVNGSVALLFLSLRFHSCKPEYIYKRINKLK-PYKVRVLLVHVDV 76 
                                        88*********************999************************************.899********** PP

                              Rad10  77 edseevlkeLnkicilndltlllawsaeeaaryletl 113
                                         +++++++eL ++     lt++l++s ee++ry++ +
  gene1640|gene1640|rna1639|rna1639  77 PNYSKMIRELFRTVS---LTMVLGFSVEECSRYIQGF 110
                                        ************976...5***************975 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   7.7e-08   0.00028       4      53 ..     132     180 ..     129     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.7e-08
                                        HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                              HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                        L s ++++++++  +l+   ++++++  ++ ee  +i+G+Gk +Ae ii 
  gene1640|gene1640|rna1639|rna1639 132 LCSFPKVNKSDVQQILKD-CGTLQKFFGKSSEEMERIQGLGKSKAEEIIK 180
                                        77899*************.99***************************96 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.4e-06     0.012      17      56 ..     144     183 ..     132     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.4e-06
                              HHH_2  17 klLakrFksldaLkkasleeLlevddiGeeiAqsivefFe 56 
                                        +++ k +++l+++   s ee+  +++ G+  A++i+++++
  gene1640|gene1640|rna1639|rna1639 144 QQILKDCGTLQKFFGKSSEEMERIQGLGKSKAEEIIKYLN 183
                                        6788999*******************************97 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.058      12      33 ..     160     181 ..     159     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                              HHH_3  12 saeeLqklpGlgpklAknIvay 33 
                                        s ee++++ Glg+++A++I++y
  gene1640|gene1640|rna1639|rna1639 160 SSEEMERIQGLGKSKAEEIIKY 181
                                        689******************9 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.6   5.8e+03      14      27 ..      37      50 ..      33      50 .. 0.79
   2 ?   11.2   0.1   6.7e-05      0.24      35      66 ..     152     183 ..     148     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                                       BHHHHT--HHHHHH CS
                      RNA_pol_A_CTD 14 sIeeLeLSvRslNc 27
                                       s++ L LS R + c
  gene1640|gene1640|rna1639|rna1639 37 SVALLFLSLRFHSC 50
                                       67789999998877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.7e-05
                                        BHHHHHHS-HHHHTTSSS-SSHHHHHHHHHHH CS
                      RNA_pol_A_CTD  35 tvgeLvklseeeLlkikNlGkKSleEIkekLe 66 
                                        t++    +s ee++ i+ lGk   eEI++ L+
  gene1640|gene1640|rna1639|rna1639 152 TLQKFFGKSSEEMERIQGLGKSKAEEIIKYLN 183
                                        667777799*******************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1312.55
//
Query:       gene164|gene164|rna164|rna164  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-27   93.1   1.2    5.5e-17   61.8   0.2    2.3  2  Myb_DNA-bind_6   Myb-like DNA-binding domain
    2.4e-24   85.3   1.3    5.6e-16   58.5   0.1    2.4  2  Myb_DNA-binding  Myb-like DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.8   0.2      0.053   13.7   0.0    2.0  2  SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
      0.014   15.4   0.1        1.7    8.7   0.0    2.6  3  SLIDE            SLIDE
      0.041   14.0   0.0        2.2    8.5   0.0    2.6  2  Rap1_C           TRF2-interacting telomeric protein/Rap1 - C 


Domain annotation for each model (and alignments):
>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.2   1.5e-20   5.5e-17       1      60 []      10      70 ..      10      70 .. 0.98
   2 !   36.9   0.1   8.9e-13   3.2e-09       1      43 [.      62     102 ..      62     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.5e-20
                 Myb_DNA-bind_6  1 WteeEdeiLlklvekyg.ndWknIaealnrRtpkqcfdrwknkLrpkisrkkwskeedirL 60
                                   Wt+ EdeiL+ +v+kyg n+W+++++ l+ +tp+qc+ rw++  +p  ++++ws+eed++L
  gene164|gene164|rna164|rna164 10 WTKTEDEILRAGVMKYGiNKWSKVSSLLPSKTPSQCRLRWQEYANPLANNSEWSAEEDEKL 70
                                   *****************99*********88****************************998 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 8.9e-13
                 Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkL 43 
                                    W++eEde+L+   ++++ +W++I +al+ R+ +qc +r+++ L
  gene164|gene164|rna164|rna164  62 WSAEEDEKLILTAKTFHPQWSLIGQALG-RNGQQCYERYNE-L 102
                                    ****************************.***********9.5 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.1   1.6e-19   5.6e-16       3      45 ..       9      52 ..       7      53 .. 0.97
   2 !   25.8   0.1   2.5e-09   8.8e-06       2      45 ..      60     102 ..      59     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1.6e-19
                                   SSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHHHHH CS
                Myb_DNA-binding  3 kWteeEdelLleavkkhG.nrWkkIaerlggRtekqcrsrwrny 45
                                   +Wt+ Ede+L  +v k+G n+W+k+++ l+++t+ qcr+rw+ y
  gene164|gene164|rna164|rna164  9 SWTKTEDEILRAGVMKYGiNKWSKVSSLLPSKTPSQCRLRWQEY 52
                                   8*****************************************98 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.5e-09
                                    SSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHHH CS
                Myb_DNA-binding   2 gkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrny 45 
                                    ++W++eEde+L+   k +  +W++I + l gR + qc +r++ +
  gene164|gene164|rna164|rna164  60 SEWSAEEDEKLILTAKTFHPQWSLIGQAL-GRNGQQCYERYNEL 102
                                    58***************************.6**********976 PP

>> SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.4   1.5e+03      27      44 ..       8      25 ..       2      34 .. 0.70
   2 ?   13.7   0.0   1.5e-05     0.053      14      51 ..      46      84 ..      39     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.4
                SANT_DAMP1_like 27 edWtkeetdyLfdlckey 44
                                    +Wtk+e + L   + +y
  gene164|gene164|rna164|rna164  8 VSWTKTEDEILRAGVMKY 25
                                   469999988887666666 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.5e-05
                SANT_DAMP1_like 14 eytdeeYeellke.edWtkeetdyLfdlckeydlrfvvi 51
                                   +   +eY++ l++ ++W+ ee ++L+  +k++  ++ +i
  gene164|gene164|rna164|rna164 46 RLRWQEYANPLANnSEWSAEEDEKLILTAKTFHPQWSLI 84
                                   666789***9998456********************998 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00048       1.7      50      77 ..       8      35 ..       2      49 .. 0.88
   2 ?    4.3   0.0     0.011        39      42      67 ..      52      77 ..      39      96 .. 0.71
   3 ?   -2.1   0.0         1   3.7e+03      59      80 ..     125     148 ..     110     155 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00048
                          SLIDE 50 keyteeeDrfllvllakyGygnyekikk 77
                                   +++t+ eD++l   + kyG++++ k+ +
  gene164|gene164|rna164|rna164  8 VSWTKTEDEILRAGVMKYGINKWSKVSS 35
                                   569*********************9975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                          SLIDE 42 yppsnkgkkeyteeeDrfllvllaky 67
                                   y++  ++++e++ eeD+ l+ + + +
  gene164|gene164|rna164|rna164 52 YANPLANNSEWSAEEDEKLILTAKTF 77
                                   4555566778*********9976655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1
                          SLIDE  59 fllvllaky..Gygnyekikkeir 80 
                                     +l + +    G +n +++kk+i 
  gene164|gene164|rna164|rna164 125 EILKMANARmsGCKNRKDLKKKIL 148
                                    444444432235555555555554 PP

>> Rap1_C  TRF2-interacting telomeric protein/Rap1 - C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0006       2.2      48      81 ..      10      50 ..       6      52 .. 0.84
   2 ?    2.9   0.0     0.032   1.2e+02      48      57 ..      62      93 ..      55     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0006
                         Rap1_C 48 WteedDeaL.......kagderdlerlekkhgeerierRrk 81
                                   Wt+ +De+L       + +++++++ l   ++ +++++R++
  gene164|gene164|rna164|rna164 10 WTKTEDEILragvmkyGINKWSKVSSLLPSKTPSQCRLRWQ 50
                                   *********66555444499999999999999999999996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.032
                         Rap1_C 48 WteedDeaL......................k 57
                                   W++e+De+L                      +
  gene164|gene164|rna164|rna164 62 WSAEEDEKLiltaktfhpqwsligqalgrngQ 93
                                   88899998877766666655555555544430 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 981.25
//
Query:       gene1641|gene1641|rna1640|rna1640  [L=225]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-08   33.0   0.0    6.6e-08   32.2   0.0    1.4  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    0.00039   20.7   0.0     0.0011   19.3   0.0    1.8  2  KH_6      KH domain
  ------ inclusion threshold ------
        0.1   12.9   0.0       0.18   12.2   0.0    1.3  1  DUF5085   Domain of unknown function (DUF5085)


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.1e-11   6.6e-08       2      37 ..       5      40 ..       4      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.1e-11
                                       E-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                             ECR1_N  2 VtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                        +PGe +  ++ ++rGhGT  ++++i++++ G v++
  gene1641|gene1641|rna1640|rna1640  5 FLPGEEVLESDGYIRGHGTQLKDSHIVSTYFGKVRI 40
                                       58********************************97 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.5   9.2e+03       8      25 ..      95     111 ..      95     116 .. 0.68
   2 !   19.3   0.0   1.8e-07    0.0011      26      43 ..     169     186 ..     144     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                               KH_6   8 lslvrRllnhvLeeLgka 25 
                                        ++ v+R+++   +e++++
  gene1641|gene1641|rna1640|rna1640  95 PGAVQRRKQES-DEMSMR 111
                                        67899999877.777665 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.8e-07
                               KH_6  26 gpfeiavGlNGriWvkse 43 
                                         ++ ++ G+NG+iW+ + 
  gene1641|gene1641|rna1640|rna1640 169 DSIKVIAGCNGYIWIGRR 186
                                        4589***********976 PP

>> DUF5085  Domain of unknown function (DUF5085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05      0.18      59      88 ..      96     125 ..      82     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                            DUF5085  59 iavneelkpseelkfrsyyyidnllvgrlt 88 
                                         av++ +++s+e+++rs++ i++l+v  ++
  gene1641|gene1641|rna1640|rna1640  96 GAVQRRKQESDEMSMRSFFDINDLVVSEIQ 125
                                        5899********************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1657.77
//
Query:       gene1642|gene1642|rna1641|rna1641  [L=496]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-26   92.6   0.0    3.1e-26   91.8   0.0    1.4  1  Beta-Casp      Beta-Casp domain
    1.3e-20   73.6   0.0    2.3e-20   72.8   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    2.8e-17   62.4   0.0      6e-17   61.3   0.0    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
      1e-16   61.6   0.0    3.4e-12   46.8   0.0    2.1  2  Lactamase_B    Metallo-beta-lactamase superfamily
    2.1e-09   37.2   0.0    1.4e-08   34.5   0.0    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
    7.7e-06   25.9   0.0    2.3e-05   24.4   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.089   12.8   0.1       0.18   11.8   0.1    1.5  1  V-set_CD47     CD47 immunoglobulin-like domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   1.2e-29   3.1e-26       1     109 [.     240     357 ..     240     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.2e-29
                                        HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGGE-SHH....HHH..H....HH............ CS
                          Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyaeveakslewmesk..ke..eln............ 60 
                                        aqel++lL+ +w++     lk+p+y++s l++ka e+Yk++ +       ++++   ++  e n            
  gene1642|gene1642|rna1641|rna1641 240 AQELCLLLDGYWERT---GLKIPVYFSSGLTEKANEIYKKFIS-------YTNETvkRKifERNvfeykhikpfqk 305
                                        7***********883...4679*******************55.......33333321123333566667778888 PP

                                        ...HS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
                          Beta-Casp  61 ...sskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrk 109
                                           ++kgp+v++as+gml++G+s +++k+++ed++n+vi++gy+++gT+g+k
  gene1642|gene1642|rna1641|rna1641 306 yymENKGPMVLFASPGMLHSGMSLRMFKEWCEDEKNLVIIPGYCVRGTIGEK 357
                                        888889********************************************86 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0     9e-24   2.3e-20       2     175 ..      19     187 ..      18     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 9e-24
                      Lactamase_B_6   2 LeldnvkiLlDvGwd.....eskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyat 72 
                                        +++ + +i+ D+G++     e ++ + s +++ ++  + +d +++sh  l+h Ga+++    f++ ++ n pvy t
  gene1642|gene1642|rna1641|rna1641  19 VTIGGRTIMFDCGMHmgfndERRFPDFSYISKTKSFDKAIDCVVISHFHLDHCGALPY----FTEVCGYNGPVYMT 90 
                                        6778889*****99722111233333345555555679*****************864....446799******** PP

                      Lactamase_B_6  73 lpvvkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWk 148
                                        lp+++   v+l d    +++++ + ++ ++ +di ++++k++t+  + + +   + ++ +it+y aGh+lG+++++
  gene1642|gene1642|rna1641|rna1641  91 LPTKEVCPVLLDDF---RKIVEGKGDSIFTYQDILNCMKKVTTINMNETYK---HDEDFYITPYYAGHVLGAAMFH 160
                                        ********998887...45666677789****************9999864...55799***************** PP

                      Lactamase_B_6 149 iskesekivYavdwnhakeshLngaal 175
                                        +  + +++vY  d++ + ++hL  a++
  gene1642|gene1642|rna1641|rna1641 161 VVVGDQSVVYTGDYSTTPDKHLGPASI 187
                                        **********************88876 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   2.4e-20     6e-17       3      62 .]     373     432 ..     371     432 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.4e-20
                              RMMBL   3 pvkarieeidfSgHadknellelirklkprnvilvHGeeeatsalarllkeeegidvfiP 62 
                                        ++++++ ++ fS+Had +++l++i++ +prnv+lvHGe+  +++l+r ++e +gi +f+P
  gene1642|gene1642|rna1641|rna1641 373 DIRLEVRNLAFSAHADAQGILNVIEQCSPRNVMLVHGERSRMKQLKRNIEERFGIPTFLP 432
                                        799**********************************************9999****998 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.3e-15   3.4e-12       4      69 ..      12      82 ..       9      96 .. 0.94
   2 !   12.8   0.0   3.4e-05     0.088     125     162 ..     148     185 ..     125     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.3e-15
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH.....HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHC CS
                        Lactamase_B  4 dpvnsyliegdggviLiDtGtsteaaraal.....elaalglkpkdvdavilTHlHlDHiGglgglveatd 69
                                       ++ +++l++ +g++i++D+G++  ++++++      + + +  +k +d v+++H+HlDH+G+l++++e  +
  gene1642|gene1642|rna1641|rna1641 12 VGRSCVLVTIGGRTIMFDCGMHMGFNDERRfpdfsYISKTKSFDKAIDCVVISHFHLDHCGALPYFTEVCG 82
                                       5789**************************************************************99766 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.4e-05
                                        HECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                        Lactamase_B 125 vtggpghghghgvveygggkvlftGDallagetgridl 162
                                         + g++ g+  ++v  g+++v++tGD + +++  +++ 
  gene1642|gene1642|rna1641|rna1641 148 YYAGHVLGAAMFHVVVGDQSVVYTGDYSTTPDKHLGPA 185
                                        5899***************************9999988 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   5.4e-12   1.4e-08       2     151 ..      25     183 ..      24     210 .. 0.70
   2 ?   -0.0   0.0      0.21   5.3e+02      39      74 ..     385     421 ..     381     441 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.4e-12
                                        EEEES--TT......HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCC CS
                      Lactamase_B_2   2 riLiDagpd......lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavle 71 
                                         i +D+g         r +  ++ ++ +  d+  +id V+++h H DH+  l+ + e ++ + p+y ++ + +v  
  gene1642|gene1642|rna1641|rna1641  25 TIMFDCGMHmgfndeRRFPDFSYISKTKSFDK--AIDCVVISHFHLDHCGALPYFTEVCGYNGPVYMTLPTKEVCP 98 
                                        67777777766555433333444434444555..9**********************999899*****99999555 PP

                                        TTCGHHHCHTT..............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECT CS
                      Lactamase_B_2  72 anfvylaleee..............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegg 133
                                          ++ + + +e              +  +v++++ +e+ + + +++ it+  a h  g         ++ +++  g
  gene1642|gene1642|rna1641|rna1641  99 VLLDDFRKIVEgkgdsiftyqdilnCMKKVTTINMNETYKHD-EDFYITPYYAGHVLGA-------AMFHVVV--G 164
                                        5544444444455555555555*******************7.6877777777777776.......3444444..6 PP

                                        TEEEEEESS-S---HH.HH CS
                      Lactamase_B_2 134 gkrvyyigDtgyipee.ig 151
                                        +++v+y+gD  ++p++ +g
  gene1642|gene1642|rna1641|rna1641 165 DQSVVYTGDYSTTPDKhLG 183
                                        9***********9954133 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                                        --HHHHGGGGCCCC.C--EEEEEE.EEHHHHHHCCTTC CS
                      Lactamase_B_2  39 aHyDHlaglltlre.lrpkklply.apkgvlavleanf 74 
                                        aH+D+  g+l + e ++p+++ l+ + ++ +++l++n+
  gene1642|gene1642|rna1641|rna1641 385 AHADAQ-GILNVIEqCSPRNVMLVhGERSRMKQLKRNI 421
                                        677777.6666666566666554447777777777765 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   8.9e-09   2.3e-05       6     120 ..      13     180 ..      11     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 8.9e-09
                      Lactamase_B_3   6 ghnsflletagarilvDPfkanlgyeppa...............eeaDlvlisqaledHahl.etlkql....... 58 
                                        g +++l++++g +i+ D +  ++g++ ++               + +D+v+is+ + dH+ + +   ++       
  gene1642|gene1642|rna1641|rna1641  13 GRSCVLVTIGGRTIMFDCGM-HMGFNDERrfpdfsyisktksfdKAIDCVVISHFHLDHCGAlPYFTEVcgyngpv 87 
                                        89***************984.44444444445577777778888***************9651556667999**** PP

                      Lactamase_B_3  59 .....................................aenvkvleegeslevg.gleiravatshdavggsergen 96 
                                                                              ++v++++  e+++ + +++i+   +      g++ g  
  gene1642|gene1642|rna1641|rna1641  88 ymtlptkevcpvllddfrkivegkgdsiftyqdilncMKKVTTINMNETYKHDeDFYITPYYA------GHVLG-A 156
                                        ******999999998888888888877777755555555555555555555433444443333......44566.6 PP

                      Lactamase_B_3  97 ngflleqdgltiyhlGhlahelss 120
                                         +f++ +++ ++++ G+ ++++++
  gene1642|gene1642|rna1641|rna1641 157 AMFHVVVGDQSVVYTGDYSTTPDK 180
                                        99***9***********9985433 PP

>> V-set_CD47  CD47 immunoglobulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1     7e-05      0.18      60     104 ..     442     490 ..     436     496 .] 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-05
                                        EEETTTTEEEEGGGTT-BE.GGGGGTB--EEEEHHHHH-EEE....EEEE CS
                         V-set_CD47  60 ifnktekkstsesfpsakl.sellkgdasLkldfsdalsGnY....tCev 104
                                        ++n+++ ++  ++  s  +  +l+k+++sL+++ s + +GnY    +Ce 
  gene1642|gene1642|rna1641|rna1641 442 SKNTINLRI-RKESISKYFkPSLSKSKVSLRMKLSSEKKGNYidvmSCEE 490
                                        556665555.444555556789********************55555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.34s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 2872.71
//
Query:       gene1643|gene1643|rna1642|rna1642  [L=549]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-16   60.9   0.2    1.2e-16   60.9   0.2    1.5  2  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.7   1.9         1   1.8e+04       5      21 ..      73      89 ..      70     102 .. 0.52
   2 !   60.9   0.2   6.5e-21   1.2e-16       3     171 ..     343     528 ..     341     541 .. 0.86

  Alignments for each domain:
  == domain 1  score: -5.7 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHHTTT CS
                         MS_channel  5 kiliivvgilivlsllg 21
                                       ++ +iv+ +l +l ++ 
  gene1643|gene1643|rna1642|rna1642 73 LLSTIVISLLFILLSIA 89
                                       44455555555555554 PP

  == domain 2  score: 60.9 bits;  conditional E-value: 6.5e-21
                                        HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEE CS
                         MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVed 78 
                                        +++ ++ v+   i+l  +g++++ ll++   ++la ++ + ++i +l  G+++l+++pf++GD v+i +++++V +
  gene1643|gene1643|rna1642|rna1642 343 AINTVVAVFLCFIYLIIFGIPPKELLTLTLSGSLAFSFIASKIIPDLYRGFMMLTTHPFDVGDDVTIDGVDYRVYE 418
                                        5677888999999999************************************************************ PP

                                        E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-T.. CS
                         MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlk.. 152
                                         gl++t++   +g  +   ns l++++ +N++r  +++ i ++++++ + +v++  +  + + e++++ p + +  
  gene1643|gene1643|rna1642|rna1642 419 FGLTSTSLIGENGGKIKFLNSDLWKKKLVNMTR-APEKIIMFNFNLNPDIKVEEFGRFKSLIHEFIRKRPFDYDds 493
                                        *********************************.********************************9999888766 PP

                                        ................TS-EEEEEEEE-SSSEEEE CS
                         MS_channel 153 ................dkellvvldefgdsslnfe 171
                                                        + ++  + ++++++s +f 
  gene1643|gene1643|rna1642|rna1642 494 fsiqaktegfssidvlSCTMILRCKNYKTKSKKFV 528
                                        66666666666666654444445555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 3525.71
//
Query:       gene1644|gene1644|rna1643|rna1643  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-06   27.2   0.0    7.3e-06   25.7   0.0    1.8  2  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
      0.033   14.0   0.2       0.13   12.1   0.2    1.9  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   8.1e-10   7.3e-06       1     233 []       6     240 ..       6     240 .. 0.72
   2 ?   -3.9   0.0      0.89     8e+03     190     202 ..     245     257 ..     244     279 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.1e-10
                                        EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTS..EEEEEEEBSCTCHHHHHHHHHTTCEEEEECCH.......... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                      Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaD..vlgLQEvdddelsriplllalggflgasstsp.......... 64 
                                        l+wNvn++         + d++ ++l +++ D  ++ LQE  d   s+i+  l  ++++ +   s           
  gene1644|gene1644|rna1643|rna1643   6 LSWNVNNK-------EGVGDAIPKILGHTNSDmiLISLQEHFDVYSSVIKPVL--KMYPSYRVISVdrvfglwsiv 72 
                                        79*****4.......45899*********99833555***5555555544444..444444444446777777777 PP

                                        .............ECSSSTTSSEEEEEECSTE..EEEEEEEEEETSSSSGCEEEEEEEEEEEEEEECCCHHGHHHH CS
                                        .............xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos  65 .............tgggggggnggavlsrfpl..tslfrrtfiefndlvaalrreplaakleqlniashrdhdlvr 125
                                                     ++g+ g  n+g+ + + ++    + ++                          a+  +++ + 
  gene1644|gene1644|rna1643|rna1643  73 lskerytastirmGFGPLGLINKGVCVTKISNgvIFISCHLS------------------------AHQENNKKRL 124
                                        888878777777766666777777766666665533333333........................3333333333 PP

                                        HHHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTHHSSCESCETTTTTTTTTTTEB-B.. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      Exo_endo_phos 126 dlqllalllqvealnadrgapvivaGDfNarpsdddsrvlrtrglalapapvglyllgggptptyvtraggsrl.. 199
                                        ++++ +     ++ ++ +++ vi+aGD+N+                                          r+  
  gene1644|gene1644|rna1643|rna1643 125 KEIRKIFECICDEESLKSTDTVILAGDMNF------------------------------------------RIsg 158
                                        444444444445688999999*********..........................................**** PP

                                        .......................................................EEEEEEC.HHHCCEEEEEEEC CS
                                        .......................................................xxxxxxx.xxxxxxxxxxxxx RF
                      Exo_endo_phos 200 .......................................................Drilasp.alalfrsgvlppp 219
                                                                                               Dr+++s+    +f +++    
  gene1644|gene1644|rna1643|rna1643 159 glknldyskakendqcnefkraypsfsegiidfkptykyivatnelcserqpswcDRVFVSTsYTSTFNAYR---- 230
                                        *************************************************************84444443333.... PP

                                        CHHEEC.TSSCSSSB CS
                                        xxxxxx.xxxxxxxx RF
                      Exo_endo_phos 220 lalvrr.ealtlSDH 233
                                             + +++++SDH
  gene1644|gene1644|rna1643|rna1643 231 -----SaYNVKISDH 240
                                        .....146889**** PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.89
                                        TTTTTTEB-BEEE CS
                                        xxxxxxxxxxxxx RF
                      Exo_endo_phos 190 yvtraggsrlDri 202
                                        +v + gg r+Dr+
  gene1644|gene1644|rna1643|rna1643 245 CVFEVGGKRIDRT 257
                                        6777788999986 PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.5e-05      0.13       3     118 ..     108     243 ..     106     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                    Exo_endo_phos_2   3 iisvYippsd.....elenlestlekllselksp...kiiilGDfN......akhplWgsedtdssargeeLiefl 64 
                                        +is+  + ++     +l+++ + +e +++e + +   ++i++GD+N      +k+ ++++ +++  ++++e+ ++ 
  gene1644|gene1644|rna1643|rna1643 108 FISCHLSAHQennkkRLKEIRKIFECICDEESLKstdTVILAGDMNfrisggLKNLDYSKAKEN--DQCNEFKRAY 181
                                        67777777777666666777777777777666556789********444433466777776655..7777777777 PP

                    Exo_endo_phos_2  65 eehslsllnllksgptfkssng......sstiDltltsdnlals..kleleeedlgSDHrpi 118
                                         ++s  ++  +++ +  + +n+       s+ D +++s++ +    + +   +   SDH+pi
  gene1644|gene1644|rna1643|rna1643 182 PSFSEGIIDFKPTYKYIVATNElcserqPSWCDRVFVSTSYTSTfnAYRSAYNVKISDHKPI 243
                                        77777766444433333333334555558*********999999986666777889***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1729.20
//
Query:       gene1645|gene1645|rna1644|rna1644  [L=2403]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-91  307.0   0.7    3.2e-91  306.0   0.7    1.6  1  HECT      HECT-domain (ubiquitin-transferase)
    5.3e-06   25.7   0.1    3.5e-05   22.9   0.1    2.2  3  DUF913    Domain of Unknown Function (DUF913)
  ------ inclusion threshold ------
      0.026   14.5   0.1      0.095   12.7   0.1    1.9  1  DUF3883   Domain of unknown function (DUF3883)
      0.091   13.1   0.0       0.37   11.2   0.0    2.1  1  Carm_PH   Carmil pleckstrin homology domain
       0.12   12.3   0.7       0.36   10.8   0.0    2.2  2  DUF3361   Domain of unknown function (DUF3361)


Domain annotation for each model (and alignments):
>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.0   0.7     9e-95   3.2e-91       2     306 ..    2098    2402 ..    2097    2403 .] 0.96

  Alignments for each domain:
  == domain 1  score: 306.0 bits;  conditional E-value: 9e-95
                                         HHHHHHT-GGGSSEEESSTTSSSEEE-TTHHHHS.....HHHHHHHHHHHHHTT--BSS-B-HHHHHHHTT-.- CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT    2 llskelldpklglfeeesedsgtlypkpssseee.llklfeflGkvlGkaiyeeilldlpfsraflkfllgeek 74  
                                         ll+k+lldp++ lfe ++ d+ t +p+++s+ +  +l++f+f+G++++kai+++  ++l++s++++k++lg ++
  gene1645|gene1645|rna1644|rna1644 2098 LLAKDLLDPNFALFEFSTGDKTTTVPCKNSYVNPeHLSYFKFVGRIVAKAIMDGNFINLHLSKFIYKHILG-KN 2170
                                         799************************998877797899********************************.6* PP

                                         --TCHHHHH-HHHHHHHHHHH..HS-GGG...GT-BSEEEEE.TTEEEEEESSTTGGGSB--TTTHHHHHHHHH CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT   75 itledleeidpelakslkellslesnteevedlaLtFtipen.agasatieLipnGanipVtnenkkeYiklyv 147 
                                         ++l+dle++dpe++ksl++++  +++    e+l+LtF+++   +g ++t eLi++Gan+ V+++nk eYi+l +
  gene1645|gene1645|rna1644|rna1644 2171 CDLQDLESTDPEFYKSLAWIR--DNHV--DESLGLTFSFDDVnFGIHRTAELIEGGANVFVNDTNKTEYINLAT 2240
                                         *********************..4444..489******99889******************************* PP

                                         HHHHTGGGHHHHHHHHHHHHTTS-HHHHTTS-HHHHHHHHBCSSS.--HHHHHHTEEEETT--TTSHHHHHHHH CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT  148 nyllkksvekqleaflkGfsevipskalklfdaeelellisGedelidvedlrrnteykggynaesetiewlwe 221 
                                         +y+l +++e ql+a+++G+ e++ ++al++fd++elelli+G  + id++d+++nt y g y+++s+t+ w+w+
  gene1645|gene1645|rna1644|rna1644 2241 QYRLFNGIELQLSALKSGLFEILGNEALEMFDENELELLICGIPD-IDIDDWKSNTLYYG-YTESSKTVIWFWK 2312
                                         ********************************************7.************75.************* PP

                                         HHHHS-HHHHHHHHHHHHSSSS--TTCGGG-.....B--EEEEE-S..-TTS--EEEGGGTEEEE---SSHHHH CS
                                         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               HECT  222 ilkefspeekrlfLqFvTgssrlPlgGfael.....hpkftierkskedetrLPtahTCfnlLklpdYsskeil 290 
                                         ++k+f+  +++++LqFvTg+s lP++Gf++l      +kf i+r+s +  ++LPtahTCfn+L lp+Yss+e l
  gene1645|gene1645|rna1644|rna1644 2313 AVKSFNSVNRAKLLQFVTGTSTLPFEGFSHLqgnneVQKFSIHRVS-DRMDSLPTAHTCFNQLVLPEYSSYESL 2385
                                         *********************************9999*******99.999************************ PP

                                         HHHHHHHHHHH.H--XX CS
                                         xxxxxxxxxxx.xxxxx RF
                               HECT  291 kekLltAieet.egFel 306 
                                          + L++Ai+e+  gF++
  gene1645|gene1645|rna1644|rna1644 2386 LKYLTLAINECsTGFGF 2402
                                         ***********999*86 PP

>> DUF913  Domain of Unknown Function (DUF913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.54   1.9e+03     339     361 ..     371     393 ..     362     396 .. 0.85
   2 !   22.9   0.1   9.9e-09   3.5e-05      70     257 ..     404     581 ..     382     617 .. 0.87
   3 ?   -3.5   0.0         1   3.7e+03     123     155 ..    1205    1237 ..    1203    1247 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.54
                             DUF913 339 snnslcreFvekgGiellldllt 361
                                        sn++  +eF++k+G+++l + l+
  gene1645|gene1645|rna1644|rna1644 371 SNSKGISEFISKNGVKILTEYLE 393
                                        5677889**********998775 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 9.9e-09
                             DUF913  70 qlLKslLkfikhlmqssgsgtdrllrnlidssqLlksLrkIienakvfGssvwslAvnilsdfihnePtslavlqe 145
                                          L+  ++ ++ +    ++ +   + n+ ds   l++    i++  +  + ++s+ v ils+f+++eP +++v  +
  gene1645|gene1645|rna1644|rna1644 404 INLRYAFRILSDIYM--DERNRAEVGNFEDSA-FLDITVATIKKLCLLDARLVSVCVGILSSFMFDEPLNFPVFMK 476
                                        568888888888888..888888899999999.999988889999999999************************* PP

                             DUF913 146 aglteslLeallakgilpsrEvlasiPnvlsalcLNnaGlelfksskaleslfeifespehvkamesdgdlasnlG 221
                                        +g    +L +  +  + ps E +++  + ++a +LN + ++ +++ + l +l+ +    e++  m    +  +++ 
  gene1645|gene1645|rna1644|rna1644 477 KGAG-IVLRT--QLSVEPSMEYVSAFISYIDAFSLNLKFQNKIVEGEYLFKLLVVCREGEFLGSM----NGTNKIM 545
                                        **75.66777..7899*************************************************....4455666 PP

                             DUF913 222 ssfdELvRhhpsLktaiikavikmlarvvelgkeka 257
                                        s +  L+ hhp +k++i+k     ++ +++l+ +ka
  gene1645|gene1645|rna1644|rna1644 546 SLLNVLIMHHPVFKQDILKFYAHGINYLKALCGTKA 581
                                        77899*****************************99 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1
                             DUF913  123 slAvnilsdfihnePtslavlqeaglteslLea 155 
                                          lA+++l ++++n P +l  +   ++ ++++e 
  gene1645|gene1645|rna1644|rna1644 1205 GLAIQLLCEIMFNNPFLLYDICRYQVLNTIYEK 1237
                                         689***************999999999999887 PP

>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.7e-05     0.095      26      52 ..    1664    1691 ..    1644    1716 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                            DUF3883   26 e.dglgYDiesvdkedgeerfIEVKtta 52  
                                           ++  YDi+s ++++++e+ IEVK+ +
  gene1645|gene1645|rna1644|rna1644 1664 YrESFFYDIRSESTKESDEETIEVKGNL 1691
                                         237899******988888********87 PP

>> Carm_PH  Carmil pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.37       5      45 ..     767     810 ..     765     818 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                            Carm_PH   5 kavkletksdklesrilvlsk...fRlfilsakvptkiertfhi 45 
                                        ++vkle +  k +sr+ vl +   + lf+l+++ p  ie++f+i
  gene1645|gene1645|rna1644|rna1644 767 IRVKLEESTAKEDSRLYVLQSiylCNLFLLQKMYPGMIEASFDI 810
                                        58*****************8655599****************86 PP

>> DUF3361  Domain of unknown function (DUF3361)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.36       4      85 ..     377     466 ..     376     492 .. 0.85
   2 ?   -4.1   0.2       3.8   1.4e+04      63      96 ..    1725    1762 ..    1719    1776 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                            DUF3361   4 qeFisrdGlkllvkiveegke....sgeilayaLtafleL.mdh.givsWdtlsd.eFikkiasivnks.aadasi 71 
                                        +eFis++G+k+l++++e+ +e    ++ +l ya + + ++ md  +  +  +++d +F+   +  ++k    da++
  gene1645|gene1645|rna1644|rna1644 377 SEFISKNGVKILTEYLEHAEEydidENINLRYAFRILSDIyMDErNRAEVGNFEDsAFLDITVATIKKLcLLDARL 452
                                        69****************988898888899***9999986576536677778876268888888999889999*** PP

                            DUF3361  72 lqrslaiLesivln 85 
                                        +  ++ iL s++  
  gene1645|gene1645|rna1644|rna1644 453 VSVCVGILSSFMFD 466
                                        *******9998765 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.8
                            DUF3361   63 nks.aadasilqrslaiLesivlnssel...yelveke 96  
                                         +k  ++++ + + s a++ s+v ++++    ++ v+  
  gene1645|gene1645|rna1644|rna1644 1725 SKDvKMKKVVFEVSEAMISSLVASKEDSlssHDAVKFR 1762
                                         45556677788888888888888887552224444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.06u 0.28s 00:00:01.34 Elapsed: 00:00:00.49
# Mc/sec: 14742.98
//
Query:       gene1646|gene1646|rna1645|rna1645  [L=496]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2920.77
//
Query:       gene1647|gene1647|rna1646|rna1646  [L=561]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   14.4   4.9       0.65   10.6   0.1    3.4  3  VCBS      Repeat domain in Vibrio, Colwellia, Bradyrhizobium 


Domain annotation for each model (and alignments):
>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.14   2.6e+03      41      55 ..      63      77 ..      22     101 .. 0.56
   2 ?   10.6   0.1   3.7e-05      0.65      12      59 ..     179     227 ..     175     228 .. 0.67
   3 ?    4.0   0.1    0.0042        75       2      56 ..     309     372 ..     308     377 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.14
                               VCBS 41 gggtgvavgDlDgDG 55
                                         ++ v +gD+ g G
  gene1647|gene1647|rna1646|rna1646 63 EKIHLVIPGDFTGTG 77
                                       333345555555544 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 3.7e-05
                               VCBS  12 vand.gg...lrvyrnngdGtftdvtktslggsgggtgvavgDlDgDGdlDl 59 
                                        v++d +g   lrv+ n+ +G  ++v   ++  ++ +  +++gD++g+G  D+
  gene1647|gene1647|rna1646|rna1646 179 VVDDgDGgklLRVLSNR-NG--EFVNYFEMRLPNEIGPIVFGDFNGNGMNDM 227
                                        55531332344445554.55..5556678888888999**********9885 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0042
                               VCBS   2 ldgDGrlDlvva.....ndgglrvyrnng...dGtftdvtkt.slggsgggtgvavgDlDgDGd 56 
                                        l   Gr+D++++     n+ ++ v++nn    d +f+++  + +l    +  ++   D+++ G+
  gene1647|gene1647|rna1646|rna1646 309 LKAKGRQDFFIImkdidNSTKVGVLENNSvpdDIRFEKAVYNeDLFNLKNVISISCCDYNNKGR 372
                                        55669*******9966445668889998766555677664332444466788999999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3616.86
//
Query:       gene1648|gene1648|rna1647|rna1647  [L=515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   87.0  23.2      8e-23   80.9  16.4    2.3  2  MFS_1            Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.034   14.1   0.2       0.24   11.4   0.0    2.6  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9  16.4     9e-27     8e-23      11     327 ..      16     439 ..       7     441 .. 0.80
   2 !   12.5   0.5   5.8e-06     0.052     112     185 ..     435     509 ..     433     514 .. 0.82

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 9e-27
                              MFS_1  11 arsilgpalplalaedlgispse.....igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll 80 
                                         ++ +   +p+al+++ g++  +     i ll+++y+l  ++  +++G+++    r+++l   l +f++   l+++
  gene1648|gene1648|rna1647|rna1647  16 FSFYFVYDIPSALSHHVGFDTESgieykITLLYSVYSLPNIIVPVFFGWITHI--RKSTLAKLLCTFVFLgHLIFT 89 
                                        3334444556677777776666677788999*******************665..777666666666666334444 PP

                              MFS_1  81 ...fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..W 150
                                           + s  + ++l++r+l G+g+ +++ + + li+  f+++e g+a+g++s  + lG++   l+ ++la+ +g  +
  gene1648|gene1648|rna1647|rna1647  90 agvW-SRNFkVMLIGRFLFGIGGESFAVIQNRLISYEFKGKELGFAMGIFSCIARLGTVANFLFTPFLADTIGrmF 164
                                        3345.77777***************************************************************777 PP

                              MFS_1 151 ravfyilaivsllafvlfllllpeepperkrkspkeee...................................... 188
                                        + v  i+  ++ l+     l +  + +er+ k  k+++                                      
  gene1648|gene1648|rna1647|rna1647 165 PCVIGIFLTLLGLW-----LCFKINSSERSHKILKQKLielqkegfgdeiqdgkmhleegflndpgltafsetids 235
                                        77766666666666.....44444555555544444445999********************************** PP

                              MFS_1 189 .........................................................kgtgpaplvpawkallkdp 207
                                                                                                 ++ +p+ l++  ++l+  p
  gene1648|gene1648|rna1647|rna1647 236 tsesmpnvlsipespffhdyseskprelpqadpilfdnpfspwkcddregitiksrlEKAKPKVLFEESGMLFYEP 311
                                        ************************************************9999999997777777777688888888 PP

                              MFS_1 208 vl.........w.illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgr 273
                                         l         + il+ +++lf++++s ++t  p+++q+++gls ++++g +la +   +++l  ++++++d +g 
  gene1648|gene1648|rna1647|rna1647 312 RLegknthhsaFyILVGMSFLFALIWSPFYTVAPILFQKRYGLS-AISSGNILATIEGTSLVLITFTSAIADAYGF 386
                                        7776654444324777777777777777****************.8***************************999 PP

                              MFS_1 274 rrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasd 327
                                        +  +++++ +l+l+  + +++++  s+ +++ +l + G   ++++p++ +l+s+
  gene1648|gene1648|rna1647|rna1647 387 KLWMIMSGCILFLLGHSGIFFNFL-SPYASATLLGFSGPLIACYWPCIPSLVSE 439
                                        666666666666665566666666.5555555555566699999******9987 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 5.8e-06
                              MFS_1 112 dwfpkeergraigllsagfslGailgpllgglla.sslg..Wravfyilaivsllafvlfllllpeepperkrksp 184
                                         ++++e  g +++ ++   +l++ + p++ ++la       +  v   + ++++la++l+++l++ +++++   + 
  gene1648|gene1648|rna1647|rna1647 435 SLVSEESLGTGFATIYCILNLAFTFSPIVVAFLAtG--DdtYDNVEAYILVIGMLALILVGFLFYLNKKQSLGLNR 508
                                        56788999**************************44..25699998888888888888888999888888777666 PP

                              MFS_1 185 k 185
                                        k
  gene1648|gene1648|rna1647|rna1647 509 K 509
                                        5 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.31   2.8e+03      24      34 ..     169     179 ..     167     182 .. 0.62
   2 ?   11.4   0.0   2.6e-05      0.24      12      41 ..     469     502 ..     468     503 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.31
                                        XXXXXXXXXXX CS
                    Gram_pos_anchor  24 GllallggllL 34 
                                        G++++l+gl L
  gene1648|gene1648|rna1647|rna1647 169 GIFLTLLGLWL 179
                                        66666666666 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.6e-05
                                        XX....XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Gram_pos_anchor  12 TG....engnifltaaGllallggllLlvkrRKk 41 
                                        TG    +n +++ ++ G lal++ ++L++  +K+
  gene1648|gene1648|rna1647|rna1647 469 TGddtyDNVEAYILVIGMLALILVGFLFYLNKKQ 502
                                        7755556999999**************9999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3159.82
//
Query:       gene1649|gene1649|rna1648|rna1648  [L=401]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-42  144.1   0.2    8.3e-42  142.7   0.0    1.8  2  AAA              ATPase family associated with various cellul
    1.9e-21   75.7   0.1    4.3e-21   74.6   0.1    1.6  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    1.2e-13   50.6   0.2    2.9e-13   49.4   0.2    1.7  1  AAA_lid_3        AAA+ lid domain
    1.2e-06   28.6   0.0    6.7e-06   26.1   0.0    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    2.9e-06   27.5   0.0    1.1e-05   25.6   0.0    1.9  1  AAA_2            AAA domain (Cdc48 subfamily)
    6.1e-06   26.1   0.0    2.3e-05   24.2   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.1e-05   25.9   0.8      0.029   14.8   0.0    3.0  3  AAA_16           AAA ATPase domain
     0.0044   17.3   3.8       0.28   11.5   0.0    3.1  3  AAA_22           AAA domain
     0.0049   16.4   0.0      0.017   14.7   0.0    1.9  1  AAA_7            P-loop containing dynein motor region
     0.0058   16.1   0.1       0.12   11.8   0.0    2.3  2  PhoH             PhoH-like protein
     0.0078   15.4   0.0      0.014   14.6   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.024   14.0   0.1    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.017   15.3   0.0      0.034   14.3   0.0    1.6  1  AAA_33           AAA domain
      0.017   14.4   1.3       0.91    8.8   0.0    3.0  3  ATPase           KaiC
      0.023   14.7   0.1      0.072   13.1   0.0    1.9  2  AAA_14           AAA domain
      0.024   15.0   0.0      0.085   13.3   0.0    2.0  1  RNA_helicase     RNA helicase
      0.028   14.2   0.1      0.078   12.7   0.1    1.8  1  AAA_24           AAA domain
      0.031   14.0   0.1       0.27   10.9   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
      0.054   13.2   0.0        0.1   12.3   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.055   13.1   0.0       0.14   11.9   0.0    1.7  1  Prot_ATP_OB_N    Proteasomal ATPase OB N-terminal domain
       0.11   12.3   0.2       0.37   10.5   0.0    2.0  2  AAA_11           AAA domain
       0.11   13.0   0.0       0.52   10.9   0.0    2.2  1  AAA_18           AAA domain
       0.18   10.9   1.1        0.3   10.1   1.1    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.35   11.0   1.9       0.37   10.8   0.5    1.7  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.7   0.0   1.1e-44   8.3e-42       1     132 []     185     318 ..     185     318 .. 0.96
   2 ?   -2.4   0.1         8   5.9e+03      15      52 ..     358     392 ..     356     397 .. 0.64

  Alignments for each domain:
  == domain 1  score: 142.7 bits;  conditional E-value: 1.1e-44
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.. CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.. 74 
                                        vl+yGppGtGKTl+a+a a++++++fl++ g++l+++y+g++++ +r+ f+ akek+ p+i+fiDEida++ +r  
  gene1649|gene1649|rna1648|rna1648 185 VLMYGPPGTGKTLMARACASKTNATFLKLAGPQLVQMYIGDGARLVRDAFALAKEKK-PTIIFIDEIDAIGAKRsd 259
                                        79******************************************************8.****************88 PP

                                        .TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                                AAA  75 .sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                         +++ ++e +r++ +Ll++ldg++++e+ v +i+atnr+d ldpallr gR+drkie++l
  gene1649|gene1649|rna1648|rna1648 260 sDQTGDREVQRTMLELLNQLDGFSSSEE-VKIIAATNRVDILDPALLRsGRLDRKIEFPL 318
                                        76778889999999***********866.****************************985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8
                                        HHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                                AAA  15 akavakelgvefleisgsellskyvgesekkirelfke 52 
                                        +kav+ e+g+  l+ + +e+    + + ++ i+e++++
  gene1649|gene1649|rna1648|rna1648 358 CKAVCVEAGMAALRKEKTEIS---QNDFMDGIQEVLSR 392
                                        788888888777777777777...44555555555555 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.1   5.8e-24   4.3e-21       1      57 []      70     125 ..      70     125 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 5.8e-24
                                        EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                     Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                        V++V+Evldd ++a+V  s++  ++++++g++p+++LrpgDlVa++kdt+++fEkLP
  gene1649|gene1649|rna1648|rna1648  70 VGNVVEVLDD-QSAVVNASTRMSSYLPITGLIPNSELRPGDLVALHKDTNIVFEKLP 125
                                        9*********.*********************************************9 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.2   3.9e-16   2.9e-13       1      45 []     340     384 ..     340     384 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 3.9e-16
                          AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfee 45 
                                        dv+++eLA+ TeG+ GA  +a+c eA+++Alr   +ei++ df++
  gene1649|gene1649|rna1648|rna1648 340 DVNFDELARSTEGFNGAQCKAVCVEAGMAALRKEKTEISQNDFMD 384
                                        9******************************************75 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     9e-09   6.7e-06       1     134 [.     184     304 ..     184     307 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 9e-09
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                        +vl+ GppGtgK+ +a+  a+ +n++++  ++++      l++ +   +g +  +d  +  + +++ i+++DE++ 
  gene1649|gene1649|rna1648|rna1648 184 GVLMYGPPGTGKTLMARACASKTNATFLKLAGPQ------LVQMYI-GDGARLVRDAFALAKEKKPTIIFIDEIDA 252
                                        59**************************999998......777776.68888888998888888***********9 PP

                                        --HHHHHHHHH.HHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                              AAA_5  77 aesevlnsLls.lleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                        +  +  +s ++   e +r +le +++l ++++    e++ +ia++n++d     l+pal
  gene1649|gene1649|rna1648|rna1648 253 IGAKRSDSDQTgDREVQRTMLELLNQLDGFSS---SEEVKIIAATNRVD----ILDPAL 304
                                        98655555433033444444444455555544...24588888888888....555665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.5e-08   1.1e-05       6     104 ..     185     277 ..     180     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.5e-08
                                        EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHH..HHHHHHTTT-HHHHTTSEEEEETGGG CS
                              AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlv..srligappgyvgaeegGivllDEidK 79 
                                        +l+ gp g+Gkt++a+a a+  ++    ++  +   +l +      +   +rl+  + +  + ++  i+++DEid 
  gene1649|gene1649|rna1648|rna1648 185 VLMYGPPGTGKTLMARACASKTNA----TFLKLAGPQLVQ----MYIGdgARLVRDAFALAKEKKPTIIFIDEIDA 252
                                        6899***************99995....777777777777....33331156666666666677777********* PP

                                        -------------HHHHHHHHHHHH CS
                              AAA_2  80 ihpkessgadvSregVqrdLLqile 104
                                        i +k+s + +    +Vqr +L +l 
  gene1649|gene1649|rna1648|rna1648 253 IGAKRSDSDQTGDREVQRTMLELLN 277
                                        ***9999999999*********996 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.1e-08   2.3e-05      31      96 ..     180     253 ..     159     259 .. 0.77
   2 ?   -2.0   0.0       3.5   2.6e+03      23      38 ..     290     305 ..     280     338 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.1e-08
                             RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaal......ltnleekdvlfideihrl 96 
                                        ++   vl+yGpPG Gkt +a+  a++ ++++   +gP l +   gd a l      l++ ++  ++fidei  +
  gene1649|gene1649|rna1648|rna1648 180 KPPKGVLMYGPPGTGKTLMARACASKTNATFLKLAGPQLVQMyiGDGARLvrdafaLAKEKKPTIIFIDEIDAI 253
                                        556679*******************************997643366655511111144556678******9866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                             RuvB_N  23 ieaakkreealdhvll 38 
                                        i aa +r + ld  ll
  gene1649|gene1649|rna1648|rna1648 290 IIAATNRVDILDPALL 305
                                        4445555555544444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.9e-05     0.029      24      47 ..     182     205 ..     152     223 .. 0.77
   2 !    8.6   0.1    0.0031       2.3     120     146 ..     227     257 ..     212     288 .. 0.72
   3 ?   -2.2   0.0       6.5   4.8e+03      74     127 ..     320     390 ..     306     399 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.9e-05
                             AAA_16  24 pelvllsGesGvGKsslvrellra 47 
                                        p  vl +G++G+GK+ ++r+++  
  gene1649|gene1649|rna1648|rna1648 182 PKGVLMYGPPGTGKTLMARACASK 205
                                        589****************99963 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                             AAA_16 120 lellkrllallsrderplvlvlDdlq.....w 146
                                        ++l+++++al+++ ++p+++++D+++     +
  gene1649|gene1649|rna1648|rna1648 227 ARLVRDAFALAKE-KKPTIIFIDEIDaigakR 257
                                        5677888899999.999*********666552 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 6.5
                             AAA_16  74 qalareellrqlldeaesaeleawrekleeala.................avpelagaea....srllellkrll 127
                                        +al r + + q+++++ s   +   ++l ++++                 a ++ +        +++ + +++ l
  gene1649|gene1649|rna1648|rna1648 320 NALGR-KRILQIHARKMSVRDDVNFDELARSTEgfngaqckavcveagmaALRKEK---TeisqNDFMDGIQEVL 390
                                        55633.56666666655555555555555555566666666555554333222222...1333677777777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.6   1.2e+03      48     107 ..       9      64 ..       3      86 .. 0.62
   2 !   11.5   0.0   0.00037      0.28       9      29 ..     186     206 ..     180     226 .. 0.78
   3 ?    4.9   0.1      0.04        30      87     126 ..     238     291 ..     224     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.6
                             AAA_22  48 psstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlrs.ee 107
                                          +++++++l+++ +++   +++ +  ++  ++++ + ++++    + i ++++++ + ++
  gene1649|gene1649|rna1648|rna1648   9 MDQSNPEEFLEKIREKIRMLNSE-TRILQSRVSTIKHDISTK---NASIAENMERI-RlNK 64 
                                        55668888888888888875555.333333334444444444...44777777777.4344 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00037
                             AAA_22   9 vvtGesGtGKTtllrrlleql 29 
                                        + +G++GtGKT+ +r  +++ 
  gene1649|gene1649|rna1648|rna1648 186 LMYGPPGTGKTLMARACASKT 206
                                        679************999886 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.04
                             AAA_22  87 raravielliiDEaqhlr...s...........eealeeLrsllnl.srkgvqli 126
                                        ++++ + ++ iDE++ +    s            ++le L +l  + s+  v++i
  gene1649|gene1649|rna1648|rna1648 238 KEKK-PTIIFIDEIDAIGakrSdsdqtgdrevqRTMLELLNQLDGFsSSEEVKII 291
                                        3333.589*********88761556778878888888888777776767777766 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.2e-05     0.017      25      68 ..     174     209 ..     168     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                              AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkldkekylsltin 68 
                                        + +l +k  k vl++Gp GtGKt++++ + +k +         +
  gene1649|gene1649|rna1648|rna1648 174 FAKLNIKPPKGVLMYGPPGTGKTLMARACASKTN--------AT 209
                                        66778888999***************99988877........33 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00017      0.12      21      42 ..     184     205 ..     172     210 .. 0.84
   2 ?    1.6   0.0      0.21   1.6e+02      71     117 ..     263     309 ..     233     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                                        EEEEE--TTSSTTHHHHHHHHH CS
                               PhoH  21 ivfaiGpaGtGKtylavalave 42 
                                         v + Gp GtGKt++a a+a +
  gene1649|gene1649|rna1648|rna1648 184 GVLMYGPPGTGKTLMARACASK 205
                                        58899*************9965 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.21
                                        -------TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT-- CS
                               PhoH  71 dleekvdpylrplydaLkdllgaekvekllekgkievaplaymRGrT 117
                                        + +  v+  +  l ++L+ + ++e+v+ +  ++++ +++ a +R   
  gene1649|gene1649|rna1648|rna1648 263 TGDREVQRTMLELLNQLDGFSSSEEVKIIAATNRVDILDPALLRSGR 309
                                        455678888899999**************************999555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.9e-05     0.014      48     116 ..     177     250 ..     137     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.9e-05
                             DUF815  48 leglpannvLLwGarGtGKSslvkallneyaeegLrli..evekedlkelpklve...llrerperfilfvDDL 116
                                        l+ +p + vL++G  GtGK  + +a+ ++++++ L+l   ++ +  + +  +lv+   +l+++++  i+f+D +
  gene1649|gene1649|rna1648|rna1648 177 LNIKPPKGVLMYGPPGTGKTLMARACASKTNATFLKLAgpQLVQMYIGDGARLVRdafALAKEKKPTIIFIDEI 250
                                        34578899*************************98875334444555555555442226889999999999975 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.2e-05     0.024      25      42 ..     185     202 ..     173     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                       Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                        +l++GppG+GKt++a++ 
  gene1649|gene1649|rna1648|rna1648 185 VLMYGPPGTGKTLMARAC 202
                                        89*************975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.6e-05     0.034       2      28 ..     185     211 ..     185     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-05
                             AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                        vl+ G+pG+GK+  a+  + k+ a++l
  gene1649|gene1649|rna1648|rna1648 185 VLMYGPPGTGKTLMARACASKTNATFL 211
                                        79****************999996654 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.26   1.9e+02      57      95 ..      15      53 ..       3      85 .. 0.56
   2 ?    8.8   0.0    0.0012      0.91      21      37 ..     184     200 ..     172     208 .. 0.87
   3 ?    1.1   0.0      0.28   2.1e+02     114     153 ..     236     278 ..     225     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.26
                             ATPase 57 eepaedlrenakslGwdlekleeegklaiidasesaees 95
                                       ee  e++re++++l  +++ l+++ + +  d+s++++ +
  gene1649|gene1649|rna1648|rna1648 15 EEFLEKIREKIRMLNSETRILQSRVSTIKHDISTKNASI 53
                                       233344555555555555555555555555555554444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                             ATPase  21 vvlitGepGtGKtifal 37 
                                         vl++G pGtGKt++a 
  gene1649|gene1649|rna1648|rna1648 184 GVLMYGPPGTGKTLMAR 200
                                        5899***********96 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.28
                             ATPase 114 aikeikakrvviDsitgl.ayeekeav..aReilrqlvrvlkk 153
                                          ke+k + + iD i+++ a+++++++   Re  r++++ l++
  gene1649|gene1649|rna1648|rna1648 236 LAKEKKPTIIFIDEIDAIgAKRSDSDQtgDREVQRTMLELLNQ 278
                                        4678888889999999887655554442235555555555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       8.7   6.5e+03      37      60 ..       2      25 ..       1      35 [. 0.63
   2 ?   13.1   0.0   9.6e-05     0.072       5      76 ..     185     253 ..     182     293 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.7
                             AAA_14 37 nldderdkkladpekllelilekl 60
                                       +l++ +  ++++pe++le i+ek+
  gene1649|gene1649|rna1648|rna1648  2 SLEELEMMDQSNPEEFLEKIREKI 25
                                       566666667777777777777774 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.6e-05
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla..dpekllelileklkeekktylflDEiqev 76 
                                        +++ G+  +GKT +++ ++++         +++l  +++ ++   d ++l +  ++++ke+k t++f+DEi  +
  gene1649|gene1649|rna1648|rna1648 185 VLMYGPPGTGKTLMARACASKTN-----ATFLKLAGPQLVQMYigDGARLVRDAFALAKEKKPTIIFIDEIDAI 253
                                        67899*************97766.....66666666666443311444666666666566799********877 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.085       1      65 [.     185     240 ..     185     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee 65 
                                        +++yGp+g+GK+++a+             k++ ++ + +  + +++Y g  + ++ D  +  +e+
  gene1649|gene1649|rna1648|rna1648 185 VLMYGPPGTGKTLMARA---------CASKTNATFLKLAGPQLVQMYIGDGARLVRDAFALAKEK 240
                                        679**************.........455667777777777777777777777777776666554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1    0.0001     0.078       5      76 ..     185     252 ..     182     300 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                             AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtek.GlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                        +l+yGp+g+GKT +a+    + ++ f+ + +  l +++  ++        ++d+++  +++++   +++iD id 
  gene1649|gene1649|rna1648|rna1648 185 VLMYGPPGTGKTLMARACasKTNATFLKLAGpQLVQMYIGDGA-----RLVRDAFALAKEKKP--TIIFIDEIDA 252
                                        799************9997777777776655334444444433.....335555555444444..4566666655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.27      20      46 ..     180     206 ..     167     220 .. 0.81
   2 ?   -0.6   0.1       1.3   9.4e+02     131     142 ..     284     295 ..     233     301 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                                        TSSS-EEEECSTTSSHHHHHHHHHHHS CS
                    Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheas 46 
                                        k +  vl+ G  GtGK+l+ara+ +++
  gene1649|gene1649|rna1648|rna1648 180 KPPKGVLMYGPPGTGKTLMARACASKT 206
                                        55578****************987654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                                        EE--EEEEEEES CS
                    Sigma54_activat 131 ikvdvriiaatn 142
                                         + +v+iiaatn
  gene1649|gene1649|rna1648|rna1648 284 SSEEVKIIAATN 295
                                        334567777776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014       0.1      47      71 ..     182     206 ..     171     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                          IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                         +++++ Gp+G+GK+ +a a + ++
  gene1649|gene1649|rna1648|rna1648 182 PKGVLMYGPPGTGKTLMARACASKT 206
                                        56899*************9988765 PP

>> Prot_ATP_OB_N  Proteasomal ATPase OB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.14       3      53 ..      71     121 ..      69     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                      Prot_ATP_OB_N   3 GtflavnsqdgtadVlvggr.rmrVavsPlvdaeeLrpGqeVlLnEalvvVe 53 
                                        G +++v  +d++a V  + r    +++  l++ +eLrpG+ V L    ++V 
  gene1649|gene1649|rna1648|rna1648  71 GNVVEVL-DDQSAVVNASTRmSSYLPITGLIPNSELRPGDLVALHKDTNIVF 121
                                        7788888.688877766666234799*******************9999995 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1         2   1.5e+03     161     189 ..      19      47 ..       5      81 .. 0.55
   2 ?   10.5   0.0    0.0005      0.37      19      42 ..     184     207 ..     172     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2
                             AAA_11 161 skleqerrklkkerkelskeleeaeesle 189
                                        +k +++ r l++e + l++++ +++  ++
  gene1649|gene1649|rna1648|rna1648  19 EKIREKIRMLNSETRILQSRVSTIKHDIS 47 
                                        33333333333333333333333333332 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0005
                             AAA_11  19 itliqGPPGtgKTktivellsqll 42 
                                         +l+ GPPGtgKT +  +  s+ +
  gene1649|gene1649|rna1648|rna1648 184 GVLMYGPPGTGKTLMARACASKTN 207
                                        4799*********87777666664 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0007      0.52       2      51 ..     186     241 ..     185     301 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0007
                             AAA_18   2 lltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpealdeskr 51 
                                        l  G+pG+GKt +a++ +++++                      +               +d++al ++k+
  gene1649|gene1649|rna1648|rna1648 186 LMYGPPGTGKTLMARACASKTNAtflklagpqlvqmyigdgarlV---------------RDAFALAKEKK 241
                                        678**************9998556788884444444444444443...............44443333333 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1    0.0004       0.3      62     108 ..      18      64 ..       3      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                              Atg14  62 iknkkakleelksliadlrerlqelkdklsqlkkeieekkkklakls 108
                                        +++ ++k++ l s++++l++r++++k+++s+ +++i+e  ++++ ++
  gene1649|gene1649|rna1648|rna1648  18 LEKIREKIRMLNSETRILQSRVSTIKHDISTKNASIAENMERIRLNK 64 
                                        5667899******************************9999987655 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5    0.0005      0.37      47     101 ..       6      60 ..       5      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0005
                         TPR_MLP1_2  47 relvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqkeel 101
                                         e++ +++  + l+++re++  l++e + l++++ + k++++++ +s++e  e++
  gene1649|gene1649|rna1648|rna1648   6 LEMMDQSNPEEFLEKIREKIRMLNSETRILQSRVSTIKHDISTKNASIAENMERI 60 
                                        589999999999************************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      808  (0.0450667); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 2425.59
//
Query:       gene1650|gene1650|rna1649|rna1649  [L=401]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   86.2   1.2    1.2e-24   86.2   1.2    2.1  2  Bromodomain      Bromodomain
    2.8e-05   24.3   0.3     0.0005   20.3   0.0    2.5  3  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0009   19.6   0.5     0.0039   17.6   0.5    2.0  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0017   18.3   0.1      0.035   14.0   0.0    2.3  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.025   14.3   0.4       0.08   12.7   0.4    1.8  1  PI3K_p85B        PI3-kinase family, p85-binding domain
       0.11   12.5   0.0       0.27   11.1   0.0    1.7  1  RNA_pol_Rpb1_3   RNA polymerase Rpb1, domain 3


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.1   6.1e+03      49      67 ..     153     171 ..     151     171 .. 0.87
   2 !   86.2   1.2   3.9e-28   1.2e-24       4      83 ..     295     374 ..     292     375 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.1
                                        T--SSHHHHHHHHHHHHHH CS
                        Bromodomain  49 nkYksladfeadlkllfsN 67 
                                        ++Y+ ++d+   l+ +f+N
  gene1650|gene1650|rna1649|rna1649 153 HEYRIIEDLSPLLNKMFEN 171
                                        7999999999999999998 PP

  == domain 2  score: 86.2 bits;  conditional E-value: 3.9e-28
                                        HHHHBHTTTCGGGGCSTT-GCCSTTHHHH.SS---HHHHHHHHHTT--SSHHHHHHHHHHHHHHHHHHSHTTSHHH CS
                        Bromodomain   4 ilsellehklaepFlepvdpeefpdyyavikkPldLstIkkklesnkYksladfeadlkllfsNarkyngegsviy 79 
                                        ++s+l   + a pFl+pvdp e+pdyy+ i++P+dLst+ +kl++n+Yk+++ f  d++l+++N+  yng++++++
  gene1650|gene1650|rna1649|rna1649 295 LISDLQVSPYAWPFLKPVDPVEVPDYYKQISNPMDLSTMMSKLKNNEYKYVESFVRDMNLMVNNCFAYNGKDTQYH 370
                                        577888888899**************************************************************** PP

                                        HHHH CS
                        Bromodomain  80 elae 83 
                                        ++a+
  gene1650|gene1650|rna1649|rna1649 371 KCAQ 374
                                        **97 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.7e-07    0.0005      27      94 ..      73     136 ..      49     153 .. 0.75
   2 ?    1.2   0.0      0.14   4.1e+02      86     117 .]     165     195 ..     161     195 .. 0.75
   3 ?   -3.2   0.0       3.2   9.6e+03      42      54 ..     214     226 ..     201     249 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.7e-07
                                        HHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                     Acetyltransf_1  27 sfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                        +  ++a+  +++   +e++G i++++  +  +g ++i +laV+ +++ kG+G  +++   e  +ee i
  gene1650|gene1650|rna1649|rna1649  73 FDTKHAN-MVLVNSAEEVVGGICYRPFFE--RGFVEIVFLAVDYDFQVKGVGGFMMDLFKEVIKEE-I 136
                                        3223333.44478889*************..9*********************9998888866666.3 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                                        HHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                     Acetyltransf_1  86 eerareegikkivlaveedndaairlYeklGF 117
                                        + +++e+     +l + +dn  ai++++k GF
  gene1650|gene1650|rna1649|rna1649 165 LNKMFENDSGPFYLVTYADN-FAIGYFRKQGF 195
                                        56677776655699777776.9*****88**9 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.2
                                        TEEEEEEEEEEEE CS
                     Acetyltransf_1  42 geliGfisllkip 54 
                                        g+++ +  ++ i+
  gene1650|gene1650|rna1649|rna1649 214 GTIVECHVFWEIN 226
                                        3333333333333 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.5   1.3e-06    0.0039       6      75 ..      81     196 ..      75     197 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                        EEEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH...........TTSEEE............ CS
                     Acetyltransf_7   6 fVaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea...........aekgii............ 54 
                                         ++   +++vG i++ +       ei +laVd +++ kG+G  ++++                +            
  gene1650|gene1650|rna1649|rna1649  81 VLVNSAEEVVGGICYRPFFergfVEIVFLAVDYDFQVKGVGGFMMDLfkevikeeiksC----Kwkfadnvlgtyk 152
                                        4455668999999999988888778888******************5467665544440....2333344444444 PP

                                        .........................EEEEEETHHHHHHHHHHTTEE CS
                     Acetyltransf_7  55 .........................leqlelnaekaikfYeklGFe 75 
                                                                 l +++ ++  ai++++k GF+
  gene1650|gene1650|rna1649|rna1649 153 heyriiedlspllnkmfendsgpfyL-VTYADN-FAIGYFRKQGFT 196
                                        44555555555555555554444221.223322.678888888886 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.2e-05     0.035      22      86 ..      69     137 ..      51     154 .. 0.78
   2 ?    1.6   0.0     0.082   2.4e+02      87     108 ..     175     197 ..     161     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                    Acetyltransf_10  22 lrerieegealllvaeeggkivGvielrdgs.....hisllfVdpeyrgqGigkaLleaveeeaekdgik 86 
                                        lr+ +++++a +++++  +++vG i +r        +i  l+Vd +++ +G+g  +++  +e + k++ik
  gene1650|gene1650|rna1649|rna1649  69 LRQVFDTKHANMVLVNSAEEVVGGICYRPFFergfvEIVFLAVDYDFQVKGVGGFMMDLFKEVI-KEEIK 137
                                        577789999999**********99977655556689*****************99999998888.55555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.082
                    Acetyltransf_10  87 l.eltvnaspyavpfYeklGFka 108
                                           l   a++ a+++++k+GF++
  gene1650|gene1650|rna1649|rna1649 175 PfYLVTYADNFAIGYFRKQGFTT 197
                                        4467788999***********86 PP

>> PI3K_p85B  PI3-kinase family, p85-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   2.7e-05      0.08       8      37 ..     231     260 ..     227     265 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                          PI3K_p85B   8 eatLseiKeeLweeakkyplfgllkdpsdY 37 
                                        +  + +iK++L+ee+kk   ++++++ +dY
  gene1650|gene1650|rna1649|rna1649 231 QEIIGNIKKKLFEEMKKINTYHIVHKIDDY 260
                                        567999************************ PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.1e-05      0.27      64     116 ..     210     284 ..     144     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.1e-05
                                        BEEHHHHHHCCCHCCCCEEEE.....SSSS..................STSEEECSSEEEES--SHHHHSSSSTTS CS
                     RNA_pol_Rpb1_3  64 lwtgkqtfsrilpneinyerk.....neek..................dgkvlikngelikGvidkkvvgkksqgs 116
                                         + g +++ + +++einy +k     n++k                  d++  ik  e+i Gv+d k v   ++++
  gene1650|gene1650|rna1649|rna1649 210 DYEGGTIVECHVFWEINYLKKqeiigNIKKklfeemkkintyhivhkiDDYSRIKSIEDIPGVLDAKYVS-RENSD 284
                                        567899**************86666544449999**********************************98.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2716.22
//
Query:       gene165|gene165|rna165|rna165  [L=493]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-49  169.2   0.7    3.7e-49  168.5   0.7    1.4  1  Sec1      Sec1 family
  ------ inclusion threshold ------
      0.075   12.7   0.0       0.12   12.0   0.0    1.5  1  GH101_N   Endo-alpha-N-acetylgalactosaminidase N-terminal
       0.15   11.9   0.3       0.42   10.3   0.3    1.8  2  FAM184    Family with sequence similarity 184, A and B


Domain annotation for each model (and alignments):
>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.5   0.7   6.1e-53   3.7e-49       2     575 .]      26     484 ..      25     484 .. 0.76

  Alignments for each domain:
  == domain 1  score: 168.5 bits;  conditional E-value: 6.1e-53
                                    EEEE-HHHHHHHHTT--HHHHHTTTEE...ETT..T--S-.....BTTSEEEEEE-S-HHHHHHHHHHHHSS-SBS-EEE CS
                           Sec1   2 vLvlDkelskilssvlkvsdlleegVt...kieklkkrepskrealphlkaiyflrptkenidrlakdfisarrykeyhi 78 
                                    vLv+D + ++il  ++  s+  ++++    +ie  ++re        ++++iyf+r ++  ++++ kdf  +r y +y  
  gene165|gene165|rna165|rna165  26 VLVYDSYGASILKNFFVKSEFISHNIVisqRIE--EHRER------VDFPVIYFVRGDENVVEMINKDF-GSRLYPSYAA 96 
                                    8*********************9*999666666..45766......69******************998.5599****** PP

                                    EESS---HHHHHHHHH..SG.GGGEEEEE----SEEEETTEEE-STTHHHHSTTG.....GG.......--HHHHHHHHH CS
                           Sec1  79 fftprlseslleglakadeevvkkvklkelnldfvplesdlfslnpelplsfrdlyldndnsaleeeieslldriakgLl 158
                                    ++++ +    l+ l k     vk      + +dfvp+e+++f    ++                            k+L 
  gene165|gene165|rna165|rna165  97 CVLSECQG--LQPLVK-----VK-----RVDVDFVPFEQKVFKA--DP----------------------------KQLY 134
                                    **998854..888876.....55.....677***********88..32............................4677 PP

                                    HHHHHH-..--EEEE-TT-HHHHHHHH..........HHHHTTT--SS--EEEEE-GGG-SSTTTS---BHHHHHHHHS- CS
                           Sec1 159 svllslekkiPiirykgsaasmvakkladelkekidskknfesessrqrpvLiIlDRsvDlvtpllhqwTYqaliddllg 238
                                    sv  +l +++ ++ y g    +v++ l +++++ + +        ++ +  LiIlDRs+Dl tpllh +T+  ++ dl  
  gene165|gene165|rna165|rna165 135 SVARTL-NTVFNVSYSG----SVCRGLGEMVEKMMGD--------EERKGELIILDRSIDLFTPLLHFFTFRTMLEDLE- 200
                                    777777.6777888999....4688999999998887........556778***************************5. PP

                                    -BTEEEEEE--SSSEEEEEE--TT...-TTHHHHTTSBHHHHHHHHHHHHHHHHHHH.HTTT...-TTHHHHHHHHHH-G CS
                           Sec1 239 glnnnnvvleeepkeekeaelvess.sDeffaelrhlnfgevgeklkkeakeyqeen.ekkrngakesiadlkkfvaklp 316
                                    ++   n ++           +  +   D++++++++ + gev++ l++ a+ +++ + +  +   k + + l+k+v + p
  gene165|gene165|rna165|rna165 201 IE---NMEV-----------FEKKYmGDKIWESVKNAHLGEVNSILRNHAHMLSKVAqKLDT---KVDNKGLMKMVLEAP 263
                                    44...2222...........2235668***************************99933333...447799********* PP

                                    GGHHHHHHHHHHHHHHHHHHHHS-HHH.HHHHHHHHHHHH....SS--.B--..-HHHHHHHH..-TTS-H.HHHHHHHH CS
                           Sec1 317 elqeekkklskHtnlaeellkevkkrkldellelEqdlat....gesdkkikekkvieeliad..deptseledklRLll 390
                                       + k++lsk + la+++ ++++   l+++ e+Eq lat    +      k    ++e+ +   +++++   dk+R+ll
  gene165|gene165|rna165|rna165 264 AAAKTKESLSKILALAQKCYDRFD--YLSRFNEIEQLLATgydkS----GGKWSMKVDEVFEYlkSSGIER-PDKIRILL 336
                                    ***********************9..8*************66432....4444444555555453355555.6******* PP

                                    HHHH...-B.-HT--GG..........GGHHHHGGGGG........---.BGGG-------.......---------S.. CS
                           Sec1 391 lyslvegglkekelkellr......elvqsalygleylktlrsleklgllkkrkgkksskkksslklikeeedeesnydl 464
                                    l+  +  +l+e+e+  l++      e++            + + e+                     i  +   +++y  
  gene165|gene165|rna165|rna165 337 LLKANGYQLQENEVGLLKSigfkdeEIDV----------SFDNHEN--------------------FIPLRGPGSNKY-- 384
                                    **997334444433333222222212222..........2333333....................122222334455.. PP

                                    .TT-----HHHHHHHHHTTT-S-TTTS-BSS-GGGS--------------------------S-EEEEEEEEEE-HHHHH CS
                           Sec1 465 sgvsryaPllvrlvealikgkklssespslskkdpsqeesssslrsakktnsaskesaekkkkqrviVffvGGvTysEir 544
                                     +vsry P l +++ + i  k+  + + +  +++         + ++ ++++  + +++ + ++   V++ GG+T++Eir
  gene165|gene165|rna165|rna165 385 -EVSRYEPVLANVLRSFIG-KQKGHLQINRLTSSRI-------HLKSLRKSHLLSVKKDISYQKLYCVYITGGITFEEIR 455
                                    .79***************8.5555555555554432.......3344444444444444448899*************** PP

                                    HHHHHT...TSSSEEEEEEEEE--HHHHHH. CS
                           Sec1 545 alrllskqekknkeiiigttsilnpksflee 575
                                     + +++++   ++eii+g+++i++p+s++e+
  gene165|gene165|rna165|rna165 456 VAYEIGESL--GVEIIVGSDNIITPRSYVEQ 484
                                    ******855..****************9986 PP

>> GH101_N  Endo-alpha-N-acetylgalactosaminidase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.12      67     114 ..     284     331 ..     227     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                        GH101_N  67 srfGvflkykdednnifvGYDkeGWfWeyksekvsayyqkkrveaPkk 114
                                     rf    ++++ ++ +  GYDk+G  W++k ++v +y++++ +e P k
  gene165|gene165|rna165|rna165 284 DRFDYLSRFNEIEQLLATGYDKSGGKWSMKVDEVFEYLKSSGIERPDK 331
                                    566666677778888899*************************99975 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   7.1e-05      0.42      17      57 ..     218     258 ..     214     285 .. 0.85
   2 ?   -1.9   0.0       0.4   2.4e+03      32      62 ..     269     299 ..     264     304 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.1e-05
                         FAM184  17 qalkeaHeeeiqqilaetrekilqykskveeeldlkqkiae 57 
                                    +++k+aH  e++ il++ ++ + +  +k++ + d k  ++ 
  gene165|gene165|rna165|rna165 218 ESVKNAHLGEVNSILRNHAHMLSKVAQKLDTKVDNKGLMKM 258
                                    789*******************************9977665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.4
                         FAM184  32 aetrekilqykskveeeldlkqkiaeleesl 62 
                                    +e   kil++ +k  +  d   + +e+e+ l
  gene165|gene165|rna165|rna165 269 KESLSKILALAQKCYDRFDYLSRFNEIEQLL 299
                                    6778899999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3102.12
//
Query:       gene1651|gene1651|rna1650|rna1650  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-24   85.2   0.6    3.2e-24   85.2   0.6    1.7  2  PAP2      PAP2 superfamily
  ------ inclusion threshold ------
      0.012   15.3  15.1        2.7    7.6  15.1    3.5  1  PAP2_3    PAP2 superfamily
       0.12   12.1   7.6      0.057   13.1   1.0    2.7  3  FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
       0.46    9.7  12.8       0.21   10.9   6.8    2.2  2  EpsG      EpsG family
       0.79    9.7   4.2        0.7    9.9   1.0    2.4  2  DUF3377   Domain of unknown function (DUF3377)
        1.6    8.7   9.6       0.84    9.6   1.0    3.2  3  LrgA      LrgA family


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.72   2.2e+03      83      93 ..      49      80 ..      24      91 .. 0.47
   2 !   85.2   0.6   1.1e-27   3.2e-24       3     126 ..     101     232 ..      98     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.72
                               PAP2 83 g.....................lvllalilll 93
                                       +                     + + ++i+l+
  gene1651|gene1651|rna1650|rna1650 49 SisdrsiskpylrhetitfaeiTAVSVVIPLV 80
                                       33344444444444444444443344444444 PP

  == domain 2  score: 85.2 bits;  conditional E-value: 1.1e-27
                               PAP2   3 lalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletses..keakesfPSgHsafafalalllalllr 76 
                                        l++lla +++  +++ +K+++gr+RP+fl ++ +  ++++    +++   e+++sfPSgH+++a++++++l+l+  
  gene1651|gene1651|rna1650|rna1650 101 LSFLLACLITSSIVENMKNIIGRLRPDFLSRCSPAGGKCTG---NPRviLEGRRSFPSGHTSIAACGFIFLMLFAS 173
                                        55666666666666777********************9664...556789***********************998 PP

                               PAP2  77 rkrkkig.........lvllalillllavlvalsRlylgvHflsDvlaGlliGialaal 126
                                        + +   +           ll+l +l++ + v++sR+ +  Hf sDv++G +iG++++++
  gene1651|gene1651|rna1650|rna1650 174 KEFGLPRlrakmnqvfVFLLYLAFLMVPIAVGASRVMDSKHFISDVVGGGVIGVLVGVA 232
                                        8888766889999***99*************************************9986 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  15.1   0.00091       2.7      42     187 ..      76     229 ..      15     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00091
                             PAP2_3  42 qvtllvlvllf.lrrrerlre..flttlllatllgllvyalfPaagPrlleeagfvdtvaaaslagalrdgasrav 114
                                        +++l+++++++ +++ er++e  f++++lla+l+++ ++  +     rl      +d+ +  s ag       +  
  gene1651|gene1651|rna1650|rna1650  76 VIPLVLMFVILrINTIERVYEvyFYLSFLLACLITSSIVENMKNIIGRLR-----PDFLSRCSPAG------GKCT 140
                                        44444455555566667776622456677777777777776666666666.....46666666666......2223 PP

                             PAP2_3 115 llrgtienglaafPSlHvawallvalalwrlrrkr................llrvlalllnvlmivatvatgnHYl 174
                                          +++i +g  +fPS H+ +a +  ++l+ +++k                 ll +++l++++++ ++ v    H++
  gene1651|gene1651|rna1650|rna1650 141 GNPRVILEGRRSFPSGHTSIAACGFIFLMLFASKEfglprlrakmnqvfvfLLYLAFLMVPIAVGASRVMDSKHFI 216
                                        34566778899*********9876655555544444444444445656565666778888899999********** PP

                             PAP2_3 175 vDviaGvalalva 187
                                         Dv++G ++++++
  gene1651|gene1651|rna1650|rna1650 217 SDVVGGGVIGVLV 229
                                        *******999875 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.27   8.1e+02       3      22 ..      20      39 ..      18      56 .. 0.80
   2 ?    1.2   0.4     0.085   2.6e+02      66     108 ..      74     116 ..      70     124 .. 0.73
   3 ?   13.1   1.0   1.9e-05     0.057      69     131 ..     165     230 ..     156     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.27
                           FtsK_4TM  3 llkEllgllllllalfllla 22
                                       ++kE++ ++++ ++l++l +
  gene1651|gene1651|rna1650|rna1650 20 MAKEMVIVMIVSMGLLFLSS 39
                                       78899999998888877765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.085
                           FtsK_4TM  66 awllvvlllawglrllrrkslerrllrllgalllllasaalfa 108
                                        +++++++l++++lr+ + +++ +  + l ++l  l++s++++ 
  gene1651|gene1651|rna1650|rna1650  74 SVVIPLVLMFVILRINTIERVYEVYFYLSFLLACLITSSIVEN 116
                                        6788888888888888888777666666666666667777665 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 1.9e-05
                           FtsK_4TM  69 lvvlllawglrllrr.........kslerrllrllgalllllasaalfalrlasledelpggaGGvlGrlla 131
                                        +++l+l      +++         +++++  ++ll++++l++ +a+ ++  ++s ++  ++  GGv+G l++
  gene1651|gene1651|rna1650|rna1650 165 FIFLML------FASkefglprlrAKMNQVFVFLLYLAFLMVPIAVGASRVMDSKHFISDVVGGGVIGVLVG 230
                                        333333......333222222333457788**************************************9997 PP

>> EpsG  EpsG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.8     7e-05      0.21     168     269 ..      25     125 ..       1     130 [. 0.71
   2 ?    2.3   0.3     0.029        87     222     268 ..     165     209 ..     149     220 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7e-05
                               EpsG 168 llllafillllllldlilsllslllliseryesYlesdeysggtiggvqlaillfilfllllkkileekkkekl.. 241
                                        ++++    ++++ l +++s++++     +  ++ ++  + + +ti +  ++++ +++ l+l+++il+ +  e+   
  gene1651|gene1651|rna1650|rna1650  25 VIVM----IVSMGLLFLSSAIEPYERPFSISDRSISKPYLRHETITFAEITAVSVVIPLVLMFVILRINTIERVye 96 
                                        3333....33333334666666666666789999999999999999999999999999999999999999987787 PP

                               EpsG 242 .klflnllliglallllllslsvilsRls 269
                                         +++l +ll +l+   ++ ++++i++Rl 
  gene1651|gene1651|rna1650|rna1650  97 vYFYLSFLLACLITSSIVENMKNIIGRLR 125
                                        67777777777777777777779999985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.029
                               EpsG 222 filfllllkkileekkkeklklflnllliglallllllslsvilsRl 268
                                        fi+++l+  k +     +  k+ + ++++ ++ +l+++ + v +sR+
  gene1651|gene1651|rna1650|rna1650 165 FIFLMLFASKEFGLPRLRA-KMNQVFVFLLYLAFLMVPIA-VGASRV 209
                                        3333222222222222222.55555555555555554444.555555 PP

>> DUF3377  Domain of unknown function (DUF3377)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.66     2e+03      21      33 ..      18      30 ..      14      38 .. 0.59
   2 ?    9.9   1.0   0.00023       0.7      27      44 ..      70      87 ..      62      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.66
                            DUF3377 21 deesgtvnaiaVv 33
                                       d+ ++ + ++++v
  gene1651|gene1651|rna1650|rna1650 18 DNMAKEMVIVMIV 30
                                       4446666677766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00023
                            DUF3377 27 vnaiaVvvPlvLllciLv 44
                                        +a+ Vv+PlvL+ +iL 
  gene1651|gene1651|rna1650|rna1650 70 ITAVSVVIPLVLMFVILR 87
                                       589**********99996 PP

>> LrgA  LrgA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.12   3.6e+02      34      58 ..      16      40 ..       1      46 [. 0.66
   2 ?    2.1   0.2     0.061   1.8e+02      18      35 ..      75      92 ..      61     121 .. 0.65
   3 ?    9.6   1.0   0.00028      0.84      23      66 ..     168     211 ..     158     233 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                               LrgA 34 vklekveeaadfllkhlallFvPag 58
                                       v+ ++ +e+  +++  + llF+ ++
  gene1651|gene1651|rna1650|rna1650 16 VSDNMAKEMVIVMIVSMGLLFLSSA 40
                                       4555667777778888888887665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.061
                               LrgA 18 sviGlllLlllLltkivk 35
                                        vi l+l++++L  + ++
  gene1651|gene1651|rna1650|rna1650 75 VVIPLVLMFVILRINTIE 92
                                       578888888888754332 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00028
                               LrgA  23 llLlllLltkivklekveeaadfllkhlallFvPagvgvmeyld 66 
                                        l+L++   +++ +l+   +   ++l +la+l vP++vg    +d
  gene1651|gene1651|rna1650|rna1650 168 LMLFASKEFGLPRLRAKMNQVFVFLLYLAFLMVPIAVGASRVMD 211
                                        33344444888888887777788889***********9544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1578.90
//
Query:       gene1652|gene1652|rna1651|rna1651  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-42  143.8   0.1    4.8e-42  143.6   0.1    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.1   2.7e-46   4.8e-42       2     188 ..       7     183 ..       6     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 2.7e-46
                                        HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                         Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                        k+Gtt+++ik+++gv+++ad+r+++g ++ s+ t +K+ +i+++i+v+ +G+ aD++++ +++++ +++y+  +  
  gene1652|gene1652|rna1651|rna1651   7 KTGTTIIAIKYDGGVLIGADSRTSMGTYIPSRVT-DKLTQITNKIFVCRSGSSADTQMISEYLKMYLNMYSRLESS 81 
                                        79***************************99996.************************************88888 PP

                                        GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEES.TTHHHHHHHHHH CS
                         Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiG.sgseaaktalek 152
                                         ++v+    r+a+++++ ++++    ++++l++ag+d  ++p++++i+  Gs++e++   aiG sgs +++++++ 
  gene1652|gene1652|rna1651|rna1651  82 VPSVH----RAATLASKIIYEN--PTLLAGLIVAGYD--DKPRVFNISLGGSLMECD--WAIGgSGSAFIYGYCDM 147
                                        88888....8888888888777..6799*********..66***************8..77777************ PP

                                        HHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                         Proteasome 153 eykedltleeavelavkalkealerdklsgknieva 188
                                        ++++ ++lee++++++ a+++a++rd++sg+ i++ 
  gene1652|gene1652|rna1651|rna1651 148 NWRSGMSLEEGIKFIKDAVSSAIRRDNASGGCIRMS 183
                                        *******************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1203.08
//
Query:       gene1653|gene1653|rna1652|rna1652  [L=697]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-94  315.7   0.5    4.9e-94  314.7   0.1    1.7  2  tRNA-synt_1c     tRNA synthetases class I (E and Q), catalyti
    2.5e-32  112.2   0.0    4.6e-32  111.3   0.0    1.5  1  tRNA-synt_1c_C   tRNA synthetases class I (E and Q), anti-cod
  ------ inclusion threshold ------
      0.031   14.2   0.0       0.13   12.2   0.0    2.1  2  ApoC-I           Apolipoprotein C-I (ApoC-1)
      0.081   12.9   0.4       0.16   12.0   0.4    1.5  1  tRNA_synt_1c_R1  Glutaminyl-tRNA synthetase, non-specific RNA
       0.13   12.5   0.7        1.4    9.3   0.2    2.4  2  DUF4358          Domain of unknown function (DUF4358)


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.32   1.1e+03     269     298 ..      80     108 ..      63     141 .. 0.66
   2 !  314.7   0.1   1.4e-97   4.9e-94       1     313 [.     197     508 ..     197     509 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.32
                                        HHHHHHCTB-HHHHHHHHHHHCCCSSS.EE CS
                       tRNA-synt_1c 269 lnflrrlGwtpekerelftreeliksfdln 298
                                        l+++ ++  ++e+   +++++e+++++ + 
  gene1653|gene1653|rna1652|rna1652  80 LRYMEKRSASVEEMAAFVKANEVSEED-IR 108
                                        456666666667777777776666655.33 PP

  == domain 2  score: 314.7 bits;  conditional E-value: 1.4e-97
                                        S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGG CS
                       tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsd 76 
                                        kV+tRf+PeP+G LHiGh ka+ ln+ +Ak+++G  +lR++DT+p+ e++e+++si+ed+ wlg+++ +k+t +sd
  gene1653|gene1653|rna1652|rna1652 197 KVVTRFPPEPNGILHIGHVKAINLNFEYAKKFGGYTYLRYDDTNPKNEEAEYFDSIYEDVRWLGFEP-YKVTASSD 271
                                        79*****************************************************************.******** PP

                                        GHHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSS.......HSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-E CS
                       tRNA-synt_1c  77 rfdelkkyaeeLikkGkAYvcectkeeleeereeqe.......klgskerdrydeenlklfeeemkkgkaegekav 145
                                        +f ++ ++  +LikkGkAY c+ ++ee+ e r+e +       ++ s++r+r++eenl++f +em +gk e++ka+
  gene1653|gene1653|rna1652|rna1652 272 YFGKMTEFGFQLIKKGKAYICHLSQEEICERRREFTsndmkvrTYLSQYRNRSVEENLRIF-QEMIDGKWEEGKAC 346
                                        ****************************99999877788888878899*************.7899********** PP

                                        EEESSBTTSS.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHH CS
                       tRNA-synt_1c 146 vRlkideess.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwll 220
                                        +R+k+d+ ++   + Dlv  r+  +    h+   vk+ +yPtY+fa +++D+le++th+++t ef +++++y wll
  gene1653|gene1653|rna1652|rna1652 347 LRFKMDTYTKnPLMLDLVGIRVLDAV---HPTKNVKYTVYPTYEFALCVSDSLEDVTHSFCTREFFTRQESYTWLL 419
                                        *******99989******99997666...*********************************************** PP

                                        HHTT-S.-EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS. CS
                       tRNA-synt_1c 221 ealglevppfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfd 296
                                        ++l+++ +p+++e++rln+++++lSKRkl  l  +k+  + dd+r+++++++rr+G++p++++ ++++ +l+ +  
  gene1653|gene1653|rna1652|rna1652 420 DQLEIY-KPIQWEFSRLNISNTVLSKRKLIPL--VKYGIDLDDPRLFTIKGMRRRGFPPNAINAFCRSLGLTFAE- 491
                                        ******.*************************..78888*********************************999. PP

                                        EEEEHHHHHHHHHHHHH CS
                       tRNA-synt_1c 297 lnresksleafdrkkLe 313
                                        +++ +k+le f+r +L+
  gene1653|gene1653|rna1652|rna1652 492 TTVDVKKLENFVRAELN 508
                                        9************9997 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   1.3e-35   4.6e-32       2     174 .]     512     677 ..     511     677 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.3e-35
                     tRNA-synt_1c_C   2 pRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereD........akrlkpgeevrLkel 69 
                                        +R+m+V+dp+kvti n +   ++++++p +p   +  tr+v f++ iyie++D        + rl+p++ v L +l
  gene1653|gene1653|rna1652|rna1652 512 RRIMCVKDPLKVTIMNSE---PCNISIPDFPG--SSITRDVSFTPVIYIEKSDfmekgdkdFLRLTPEQPVGLYKL 582
                                        7**************866...89*********..899*************************************** PP

                     tRNA-synt_1c_C  70 ynikveevekdesgevtelkleydgesleearkkkgiihWvsaeeaveaevrlYdrLfk..eeededfl..lnpds 141
                                        y ikv +v+  ++g  +e   + +g        +k++ihWv  +++v++e+r+Y+ L++  +++d+++l  +n+ds
  gene1653|gene1653|rna1652|rna1652 583 YPIKVVKVT--DDGILAE---RWNG-------VPKKFIHWVG-SDSVKIEMRMYSPLWTsfTPKDSTYLeeMNKDS 645
                                        ******995..4566655...4444.......4889******.59************77444445556678***** PP

                     tRNA-synt_1c_C 142 lkvleeglaepalanlkkgdivQfeRiGyfrvd 174
                                        l+vl  gl+++ +  ++++d++Qf+RiGyf+vd
  gene1653|gene1653|rna1652|rna1652 646 LEVL-YGLCDKRIVGARPEDKFQFQRIGYFCVD 677
                                        **97.***************************8 PP

>> ApoC-I  Apolipoprotein C-I (ApoC-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05      0.13      13      52 ..     274     312 ..     269     319 .. 0.84
   2 ?   -2.6   0.0       1.5   5.4e+03      33      41 ..     555     563 ..     552     565 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                                        HHHCHHHHHHHHHHCCHCCCHCTTSSSSCCHHHHHHHHHH CS
                             ApoC-I  13 dklkEfgktledKaraaieeIkqSelpaktrnWfsetfek 52 
                                         k+ Efg +l  K +a i + +q e+ +  r+  s+   k
  gene1653|gene1653|rna1652|rna1652 274 GKMTEFGFQLIKKGKAYICHLSQEEICERRREFTSND-MK 312
                                        59*************************9999855544.34 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                        HCTTSSSSC CS
                             ApoC-I  33 IkqSelpak 41 
                                        I++S++++k
  gene1653|gene1653|rna1652|rna1652 555 IEKSDFMEK 563
                                        99*****98 PP

>> tRNA_synt_1c_R1  Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   4.4e-05      0.16       7     127 ..       8     114 ..       3     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                    tRNA_synt_1c_R1   7 fksiGLsekkaketlknkklsaslkevieeagveekgldkkkgalLyslatklkkqalekrelivkyIvegklkts 82 
                                        f+++ +s++k   ++k++++++++++++   + ++         lLy+la + +k+     +l+++ I  + +k +
  gene1653|gene1653|rna1652|rna1652   8 FERLEISSEKRCQVMKKEQVVKNMERIFLGRDFSN--------RLLYTLACTAPKN--ADVDLLANLIDGKIIKHE 73 
                                        67777777777777777777777777776655555........7******888876..8899************** PP

                    tRNA_synt_1c_R1  83 lqvdaAlkYlskkkeeeideaefekacGVGvevtpeqieeaVeky 127
                                          ++++l+Y++k + +  + a+f ka     ev++e+i+++++ +
  gene1653|gene1653|rna1652|rna1652  74 SMLKECLRYMEKRSASVEEMAAFVKA----NEVSEEDIRKHIDRM 114
                                        **********6666655566789988....488999999888765 PP

>> DUF4358  Domain of unknown function (DUF4358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00039       1.4      25      65 ..      73     113 ..      70     122 .. 0.88
   2 ?    0.6   0.0      0.19   6.7e+02       8      59 ..     637     685 ..     633     691 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00039
                            DUF4358  25 kddvedyvayvsassasadevlivkakdeedaeevkkalee 65 
                                        +++++++  y+++ sas++e++ +  ++e  +e+++k ++ 
  gene1653|gene1653|rna1652|rna1652  73 ESMLKECLRYMEKRSASVEEMAAFVKANEVSEEDIRKHIDR 113
                                        57899******************999999999999999876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                            DUF4358   8 dlkeldeddlkklygldkddvedyvayvsassasadevlivkakdeedaeev 59 
                                         l+e+++d l+ lygl ++    +v+  ++++++ + +  + +++++++e++
  gene1653|gene1653|rna1652|rna1652 637 YLEEMNKDSLEVLYGLCDKR---IVGARPEDKFQFQRIGYFCVDKSTTEENI 685
                                        58999***********9985...45556777777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4567.13
//
Query:       gene1654|gene1654|rna1653|rna1653  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-13   50.5   1.5    2.1e-13   49.9   1.5    1.3  1  Homeodomain     Homeodomain
    2.3e-11   43.4   0.7    4.6e-11   42.4   0.7    1.5  1  Homeobox_KN     Homeobox KN domain
  ------ inclusion threshold ------
      0.037   13.5   0.1      0.053   13.0   0.1    1.2  1  Homez           Homeodomain leucine-zipper encoding, Homez
      0.055   12.8   0.0       0.16   11.3   0.0    1.6  2  DUF3450         Protein of unknown function (DUF3450)
       0.12   12.2   0.0       0.24   11.3   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   1.5   5.9e-17   2.1e-13       6      56 ..      93     143 ..      89     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5.9e-17
                                        SS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        Homeodomain   6 tftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56 
                                        +f k  +e+Le+ Fe ++yps+ e+ +LAk ++L+++q+ +WF N+R + k
  gene1654|gene1654|rna1653|rna1653  93 RFPKFITEALERSFEIDQYPSETEKSRLAKICKLSTKQINNWFTNKRNRSK 143
                                        57777899*****************************************98 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.7   1.3e-14   4.6e-11      10      40 .]     111     141 ..     109     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.3e-14
                        Homeobox_KN  10 YPseedKeeLlkeTglsvkqitnWFINaRrR 40 
                                        YPse +K +L+k ++ls+kqi+nWF N R+R
  gene1654|gene1654|rna1653|rna1653 111 YPSETEKSRLAKICKLSTKQINNWFTNKRNR 141
                                        *****************************99 PP

>> Homez  Homeodomain leucine-zipper encoding, Homez
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.053      31      52 ..     119     140 ..     102     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                              Homez  31 kLckksklsaqqVrdWFaskes 52 
                                         L+k  kls++q+ +WF  k +
  gene1654|gene1654|rna1653|rna1653 119 RLAKICKLSTKQINNWFTNKRN 140
                                        688999***********99976 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.4e-05      0.16      64     125 ..      17      78 ..       8      82 .. 0.92
   2 ?   -1.6   0.1      0.38   1.4e+03      25      48 ..     117     140 ..     108     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                            DUF3450  64 evyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfveldlPflleeRq 125
                                        ++y e  +r+v+++++ +++  ++i ++  i+++++ +le+ i  +++fv   + f  +e +
  gene1654|gene1654|rna1653|rna1653  17 RIYVEANNRIVDEMDSMVDKFVKSIGSVPDISTGVSAYLEERIRYIREFVVDSIGFSISEFR 78 
                                        7899999********************************************99999988866 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.38
                            DUF3450  25 aekavaaaaqsqkkidklddekqe 48 
                                        +++  ++ + s k+i+++  +k++
  gene1654|gene1654|rna1653|rna1653 117 KSRLAKICKLSTKQINNWFTNKRN 140
                                        455666667788899999888765 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.6e-05      0.24      10      34 ..     116     140 ..     110     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.6e-05
                     YdaS_antitoxin  10 gqkaLAealgvsqqaVsqWlkgkkq 34 
                                        + ++LA+ +  s +++++W   k++
  gene1654|gene1654|rna1653|rna1653 116 EKSRLAKICKLSTKQINNWFTNKRN 140
                                        5789***************987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1080.92
//
Query:       gene1655|gene1655|rna1654|rna1654  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-19   68.4   0.1    6.5e-19   67.6   0.1    1.5  1  Homeobox_KN  Homeobox KN domain
    8.6e-07   28.7   0.0    1.9e-06   27.6   0.0    1.6  1  Homeodomain  Homeodomain
  ------ inclusion threshold ------
       0.16   11.5   0.0        0.4   10.2   0.0    1.6  2  Homez        Homeodomain leucine-zipper encoding, Homez


Domain annotation for each model (and alignments):
>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.1   1.1e-22   6.5e-19       1      40 []     137     176 ..     137     176 .. 1.00

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.1e-22
                        Homeobox_KN   1 WflahlhnPYPseedKeeLlkeTglsvkqitnWFINaRrR 40 
                                        W+ ++++nPYPs+++K+ L+++Tgl  +qi+nWFINaRrR
  gene1655|gene1655|rna1654|rna1654 137 WLKENMDNPYPSDAEKAYLCQKTGLGPAQINNWFINARRR 176
                                        ***************************************9 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.2e-10   1.9e-06      20      54 ..     142     176 ..     120     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.2e-10
                                        HHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Homeodomain  20 eenrypsaeereeLAkklgLeerqVkvWFqNrRak 54 
                                          n+yps +e++ L +k+gL  +q+ +WF N R +
  gene1655|gene1655|rna1654|rna1654 142 MDNPYPSDAEKAYLCQKTGLGPAQINNWFINARRR 176
                                        359*****************************976 PP

>> Homez  Homeodomain leucine-zipper encoding, Homez
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.1   6.6e+03      40      51 ..     131     142 ..     130     145 .. 0.69
   2 ?   10.2   0.0   6.8e-05       0.4      32      47 ..     155     170 ..     148     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.1
                              Homez  40 aqqVrdWFaske 51 
                                         q  r+W    +
  gene1655|gene1655|rna1654|rna1654 131 SQLLRSWLKENM 142
                                        566799987766 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.8e-05
                              Homez  32 LckksklsaqqVrdWF 47 
                                        Lc+k++l   q+ +WF
  gene1655|gene1655|rna1654|rna1654 155 LCQKTGLGPAQINNWF 170
                                        9*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1526.28
//
Query:       gene1656|gene1656|rna1655|rna1655  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-11   42.0   0.0      2e-10   41.0   0.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.1e-14     2e-10       2     130 .]      17     129 ..      16     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.1e-14
                                        EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE- CS
                    Sacchrp_dh_NADP   2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnl 76 
                                        +i Ga G+ ++ ++e  ++++ v  ++++a r+ +k +        + f  +++ ++ +++ +a++   +++++n+
  gene1656|gene1656|rna1655|rna1655  17 IIYGAsGYAARYIIEAFKAEN-V--RLALAARNISKIKD-------KAFPVYECEIDGIDK-IASM---TKILINC 78 
                                        677888888888888877764.6..88888888888333.......347788888888888.6666...89***** PP

                                        SSGG..GHHHHHHHHHHHT-EEEESS-BCGCCSCHCCSHHHHHTHHHHHHCTSEEE CS
                    Sacchrp_dh_NADP  77 sppi..ssldvlkaCietgvhyvdtsiskeertnyalreavlklkekakeagvtav 130
                                        ++p+  ++++++k Ci++g+hy+d+s      + y+ +  + k++++a+++gv+++
  gene1656|gene1656|rna1655|rna1655  79 VGPYsrYGESIVKSCIRNGTHYMDISG-----EVYFFELIINKYHDEAARKGVYII 129
                                        ****9999****************999.....99*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2374.95
//
Query:       gene1657|gene1657|rna1656|rna1656  [L=471]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2686.78
//
Query:       gene1658|gene1658|rna1657|rna1657  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-08   34.1   1.5    1.7e-08   34.1   1.5    2.3  3  zf-CCCH_4        CCCH-type zinc finger
    2.4e-08   33.6  11.8    1.4e-06   28.0   1.1    2.2  2  zf-CCCH          Zinc finger C-x8-C-x5-C-x3-H type (and simil
    6.8e-08   32.3  12.8    4.2e-07   29.8   4.8    3.0  2  zf_CCCH_4        Zinc finger domain
    2.7e-05   24.3   2.5    4.1e-05   23.8   2.5    1.3  1  zf-CCCH_3        Zinc-finger containing family
  ------ inclusion threshold ------
      0.014   16.1   4.3       0.03   15.0   4.1    1.7  2  Torus            Torus domain
      0.068   13.7  17.4       0.59   10.7   3.7    2.6  2  zf-CCCH_2        RNA-binding, Nab2-type zinc finger
       0.41   11.0   6.7        2.7    8.4   3.0    2.2  2  Lustrin_cystein  Lustrin, cysteine-rich repeated domain


Domain annotation for each model (and alignments):
>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   1.5   6.5e-12   1.7e-08       2      22 .]      47      67 ..      46      67 .. 0.97
   2 ?   -2.8   0.3       2.4   6.3e+03       2       6 ..      72      76 ..      72      82 .. 0.71
   3 ?   -0.3   0.2       0.4     1e+03      17      21 ..      87      91 ..      87      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 6.5e-12
                          zf-CCCH_4  2 lCpyfakGsCrfGdnCrFsHd 22
                                       lC++f+ +sC+ GdnC++sHd
  gene1658|gene1658|rna1657|rna1657 47 LCKFFLMNSCKHGDNCTYSHD 67
                                       9*******************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                          zf-CCCH_4  2 lCpyf 6 
                                       +C+ f
  gene1658|gene1658|rna1657|rna1657 72 PCKAF 76
                                       68866 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.4
                          zf-CCCH_4 17 CrFsH 21
                                       C FsH
  gene1658|gene1658|rna1657|rna1657 87 CPFSH 91
                                       88999 PP

>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   1.1   5.6e-10   1.4e-06       1      26 [.      43      67 ..      43      68 .. 0.93
   2 !   10.8   3.8   0.00014      0.37       5      26 ..      72      92 ..      69      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 5.6e-10
                                       -HCHCBCHHHHHS--TTGGG-SSBSC CS
                            zf-CCCH  1 yktelCrffmrtGyCkyGdrCkFaHg 26
                                       y+t lC+ff+   +Ck+Gd+C ++H+
  gene1658|gene1658|rna1657|rna1657 43 YRTILCKFFLM-NSCKHGDNCTYSHD 67
                                       7899***9999.*************7 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                                       CBCHHHHHS--TTGGG-SSBSC CS
                            zf-CCCH  5 lCrffmrtGyCkyGdrCkFaHg 26
                                       +C+ f+ + +C++   C+F+H 
  gene1658|gene1658|rna1657|rna1657 72 PCKAFHLRKSCSR-KDCPFSHA 92
                                       8************.*******5 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   4.8   1.6e-10   4.2e-07       1      19 []      48      66 ..      48      66 .. 1.00
   2 !    5.2   1.1    0.0091        23       1      19 []      73      91 ..      73      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.6e-10
                          zf_CCCH_4  1 CkfflqGtCkkGdkCrFaH 19
                                       Ckffl ++Ck+Gd+C+++H
  gene1658|gene1658|rna1657|rna1657 48 CKFFLMNSCKHGDNCTYSH 66
                                       ******************* PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0091
                          zf_CCCH_4  1 Ckfflq.GtCkkGdkCrFaH 19
                                       Ck f+   +C++ d C+F+H
  gene1658|gene1658|rna1657|rna1657 73 CKAFHLrKSCSRKD-CPFSH 91
                                       77777778887765.88888 PP

>> zf-CCCH_3  Zinc-finger containing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   2.5   1.6e-08   4.1e-05       8      61 ..      48      98 ..      42     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.6e-08
                          zf-CCCH_3  8 cyffyystctkGdscpfrheeaalGsetvctlWqegrclrevckfrhmeidkkr 61
                                       c ff    c+ Gd+c++ h  + + +     +  +  c r+ c f h  ++ + 
  gene1658|gene1658|rna1657|rna1657 48 CKFFLMNSCKHGDNCTYSHDTSKFPCKA---FHLRKSCSRKDCPFSHAPLSDQA 98
                                       99*******************9996553...456788**********9876554 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   4.1   1.2e-05      0.03      65      93 ..      40      68 ..      11      87 .. 0.76
   2 ?   -0.3   0.2      0.69   1.8e+03      71      92 ..      71      92 ..      67     106 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                       HHSTT--B-HHHHHT--SSGGG-SSB-S- CS
                              Torus 65 dkekesyfClfFarGlCakGkkCeylHrl 93
                                        ++ ++++C fF    C++G +C+y H+ 
  gene1658|gene1658|rna1657|rna1657 40 PNNYRTILCKFFLMNSCKHGDNCTYSHDT 68
                                       3677889********************74 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.69
                                       -B-HHHHHT--SSGGG-SSB-S CS
                              Torus 71 yfClfFarGlCakGkkCeylHr 92
                                       + C  F     ++ k+C + H 
  gene1658|gene1658|rna1657|rna1657 71 FPCKAFHLRKSCSRKDCPFSHA 92
                                       5666665444445689999996 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.8    0.0012       3.1       2      17 ..      48      66 ..      47      66 .. 0.93
   2 ?   10.7   3.7   0.00023      0.59       2      18 .]      73      92 ..      72      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                          zf-CCCH_2  2 Crffpn..C.tnpkCpFaH 17
                                       C+ff    C  +++C+++H
  gene1658|gene1658|rna1657|rna1657 48 CKFFLMnsCkHGDNCTYSH 66
                                       ****9889*********** PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                          zf-CCCH_2  2 Crffpn...CtnpkCpFaHP 18
                                       C+ f     C +++CpF+H+
  gene1658|gene1658|rna1657|rna1657 73 CKAFHLrksCSRKDCPFSHA 92
                                       555555567**********5 PP

>> Lustrin_cystein  Lustrin, cysteine-rich repeated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.0    0.0011       2.7       9      43 ..      39      73 ..      31      73 .. 0.81
   2 ?    4.1   0.1     0.023        60      17      30 ..      80      91 ..      74      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                    Lustrin_cystein  9 lldesgqpvtCsps.sssCPsgysChfssttessvC 43
                                       + ++  +++ C  +  +sC  g  C++s++t+++ C
  gene1658|gene1658|rna1657|rna1657 39 TPNN-YRTILCKFFlMNSCKHGDNCTYSHDTSKFPC 73
                                       4443.45599********************999877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.023
                    Lustrin_cystein 17 vtCspssssCPsgy 30
                                       ++Cs   ++CP+ +
  gene1658|gene1658|rna1657|rna1657 80 KSCSR--KDCPFSH 91
                                       68997..8***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 666.30
//
Query:       gene1659|gene1659|rna1658|rna1658  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-06   27.2   0.0    1.9e-05   24.8   0.0    2.1  1  GHMP_kinases_N  GHMP kinases N terminal domain
     0.0013   19.0   0.0     0.0031   17.8   0.0    1.5  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.069   13.5   0.0       0.16   12.4   0.0    1.6  1  DUF3991         Protein of unknown function (DUF3991)


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   3.2e-09   1.9e-05       7      65 ..     113     207 ..     107     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.2e-09
                                        SSHTTSSSCHHHHHHHHHHHHHHHHTT...............................EHHHH......HHHHHHH CS
                     GHMP_kinases_N   7 eiPvgaGLGSSAAlavalvaAllallg...............................lslee......aklalea 45 
                                            ++G+GSSA++ v++v+All++ +                               lsl+e      +  ++  
  gene1659|gene1659|rna1658|rna1658 113 PTREKTGIGSSACILVSIVYALLKFHQedlekiilqdsfngwgksprfqgdlrswlghLSLSEeivehvLPVTYLV 188
                                        55679*********************87777777777777777777777776666555444225744333344444 PP

                                        HHHHHHHHHHSHHHHHHHHS CS
                     GHMP_kinases_N  46 erlaqggngsggDvaasvyG 65 
                                        ++++   +gsg D+ ++++G
  gene1659|gene1659|rna1658|rna1658 189 HQKVN-QEGSGSDAICCLLG 207
                                        44443.45999999999988 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.2e-07    0.0031      20      81 ..     279     333 ..     270     336 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.2e-07
                     GHMP_kinases_C  20 sqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralre 81 
                                        + +      ++i+p  + e+l + se++++g ++sGaGg +++ a+ +d  +   v+r + +
  gene1659|gene1659|rna1658|rna1658 279 MRD----ISIDIVPKKQYEILMKTSEYDIWGCGISGAGGDDCIWAISDDYKD---VYRYWEK 333
                                        444....37899**********************************966665...6666655 PP

>> DUF3991  Protein of unknown function (DUF3991)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.6e-05      0.16       1      60 [.     274     349 ..     274     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                            DUF3991   1 aYLtkqRkisreiiaefaekkllyedey.............gNavFvykDengkvvgaekrgt...tyekpfkgla 60 
                                        +YL   R is +i+ +  ++ l +++ey               +++ + D++++ + +ek  t    +e +++g++
  gene1659|gene1659|rna1658|rna1658 274 EYLNAMRDISIDIVPKKQYEILMKTSEYdiwgcgisgaggdDCIWAISDDYKDVYRYWEKVFTftfVTEVSYRGIC 349
                                        5***************************77777776665545*******************999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2168.07
//
Query:       gene1660|gene1660|rna1659|rna1659  [L=677]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-22   80.9   0.0    2.1e-22   80.1   0.0    1.4  1  ABC_tran     ABC transporter
    0.00025   20.9   0.3     0.0021   17.9   0.0    2.6  4  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0079   15.7   0.2      0.019   14.4   0.2    1.5  1  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.052   13.3   0.0      0.099   12.3   0.0    1.4  1  AAA_30       AAA domain
      0.057   13.3   0.1       0.12   12.3   0.1    1.5  1  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   5.8e-26   2.1e-22       1     137 []      42     189 ..      42     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 5.8e-26
                                        EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpe 73 
                                        l+ vs +++ g++ +++G++G  K+tL++l+ g +++     G+il++g++ ++   + + ++i++l q++++ p 
  gene1660|gene1660|rna1659|rna1659  42 LNGVSATFESGKLSVVMGPSGGSKTTLMNLIVGIVQKhsmSYGKILFQGEERDQ---NTWLSRIAYLNQDDCIVPY 114
                                        789********************************9988889******999888...9999*************** PP

                                        SBHHHH.........HHHTC......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                        xxxxxx.........xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  74 ltvren.........esdee......iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                        +tv+e          +++++      ++ +++kl +++lkdt +    + +SgG+++rv++a  ++  p++l+lDE
  gene1660|gene1660|rna1659|rna1659 115 TTVYEYiyfcvncrtAKKRRgsvgeiVSSVMKKLHIQDLKDTMM----TAISGGERKRVMIAVEFAASPDVLILDE 186
                                        ************99744444778888*****************9....**************************** PP

                                        TTT CS
                                        xxx RF
                           ABC_tran 135 pta 137
                                        pt+
  gene1660|gene1660|rna1659|rna1659 187 PTS 189
                                        *96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.8   6.5e+03     223     244 ..      18      39 ..       8      42 .. 0.74
   2 ?   -1.0   0.0      0.35   1.3e+03       2      22 ..      55      75 ..      54     115 .. 0.84
   3 !   17.9   0.0   5.8e-07    0.0021     255     296 ..     176     217 ..     128     221 .. 0.84
   4 ?   -2.7   0.1       1.1     4e+03     116     191 ..     299     374 ..     261     413 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.8
                             AAA_21 223 flengdgqelparelSdGtkrl 244
                                        +++++   e+p  +lS+G k +
  gene1660|gene1660|rna1659|rna1659  18 LEVENVVLEVPNEDLSSGSKYV 39 
                                        5566667899********9876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.35
                             AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                        v+ Gp g  K++L+ ++ ++
  gene1660|gene1660|rna1659|rna1659 55 SVVMGPSGGSKTTLMNLIVGI 75
                                       6899***********999776 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 5.8e-07
                             AAA_21 255 lkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                        + ++++l++DEp +gL+ +l  +l++++k+ + ++  +++tT
  gene1660|gene1660|rna1659|rna1659 176 AASPDVLILDEPTSGLDSHLAFELIQMVKQYAIENNSIVITT 217
                                        3344****************************999*****99 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 1.1
                             AAA_21 116 rgirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrs 191
                                        ++  +  ++++ k+   s+ n +++ + ++ i +r + +++ ++ ++k+ri+   + + y++f+  +++++++++ 
  gene1660|gene1660|rna1659|rna1659 299 QEGNSKTKDRVMKHDGNSPINLPFSLSKALMIAKRQFIIEWRSWRMLKNRILEMVFLGFYIYFMYPINFVGKFINY 374
                                        4455556666677777777777777777777777777777777777777666666666666666666666666555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   5.4e-06     0.019     109     197 ..     136     217 ..      43     223 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
                                        EEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 109 seykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                        s  +i  + ++k  +++l ++++  ++++SgGe++ v++a+ fA    +p  + +lDe  + LD +   ++ +++k
  gene1660|gene1660|rna1659|rna1659 136 SVGEIVSSVMKKLHIQDL-KDTM--MTAISGGERKRVMIAVEFAA---SPD-VLILDEPTSGLDSHLAFELIQMVK 204
                                        444555555544444443.3333..3479*************996...454.569********************* PP

                                        HHCTTSEEEEE-S CS
                                        xxxxxxxxxxxxx RF
                              SMC_N 185 eksknaQfivisl 197
                                        +   +   ivi+ 
  gene1660|gene1660|rna1659|rna1659 205 QYAIENNSIVITT 217
                                        9998888888775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.8e-05     0.099      12     114 ..      47     205 ..      43     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                             AAA_30  12 alltsgdrvavltGpAGtGKttalkalreaweaag.....................................grvi 50 
                                        a+ +sg+ ++v+ Gp G  Ktt+++ ++ +++++                                      ++ i
  gene1660|gene1660|rna1659|rna1659  47 ATFESGK-LSVVMGPSGGSKTTLMNLIVGIVQKHSmsygkilfqgeerdqntwlsriaylnqddcivpyttvYEYI 121
                                        5566775.*********************99998667777777777777777777777777777777777777777 PP

                             AAA_30  51 glAptgkaAkvLaeelgieastiakllkrlk...................grarlepg.tllivDE.agmvdtkql 105
                                         +  + + Ak+ + ++g   s++ k l+ ++                   + ++++++ ++li DE ++ +d++ +
  gene1660|gene1660|rna1659|rna1659 122 YFCVNCRTAKKRRGSVGEIVSSVMKKLHIQDlkdtmmtaisggerkrvmiA-VEFAASpDVLILDEpTSGLDSHLA 196
                                        777777777777777776555555555555567777777777777777753.445555577777774455677766 PP

                             AAA_30 106 aallkaaek 114
                                         +l++ +++
  gene1660|gene1660|rna1659|rna1659 197 FELIQMVKQ 205
                                        666666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.3e-05      0.12      96     123 ..      48      76 ..      21     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                                        HCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpel 123
                                         +++ k+sv++G+SG  K+tL+n +++  
  gene1660|gene1660|rna1659|rna1659  48 TFESgKLSVVMGPSGGSKTTLMNLIVGIV 76 
                                        555559******************99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 4211.29
//
Query:       gene166|gene166|rna166|rna166  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-31  106.4   0.3    6.7e-31  106.1   0.3    1.1  1  GSHPx     Glutathione peroxidase
     0.0011   18.9   0.2     0.0027   17.6   0.2    1.7  1  AhpC-TSA  AhpC/TSA family


Domain annotation for each model (and alignments):
>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.3   7.5e-35   6.7e-31       1     107 [.      10     117 ..      10     118 .. 0.99

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 7.5e-35
                                    GGGBEEEBTTSSEEEGGGGTTSEEEEEEEESSSTTHH.HHHHHHHHHHHHGGGTEEEEEEEE-TTTT---S-GGGHHHTS CS
                          GSHPx   1 iyelsakdidgekvkleklrgkvvlivnvaskCglte.qykeleelqkrykdkglvilgfPCnqfgkqepgsdeeikkfr 79 
                                    +y+lsa++ dg+kv++e+++g v++ivnvas C l+e +yk + +l +++ +kgl+il fPCnq+ kqe +  eei++  
  gene166|gene166|rna166|rna166  10 FYSLSARKWDGSKVDFETFKGCVLIIVNVASSCKLAEsNYKSFVNLLSKFYKKGLRILLFPCNQYLKQESKPIEEIHEGI 89 
                                    79**********************************99****************************************** PP

                                    SHTTT-SSEEB--BBSSSTTB-HHHHHH CS
                          GSHPx  80 qgkyevtfellekievnGekedplykfl 107
                                     +ky+ +fe+++ki+v Ge+ +p++k+l
  gene166|gene166|rna166|rna166  90 VKKYSDKFEIFDKIDVFGEEIHPVFKHL 117
                                    **************************98 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2     3e-07    0.0027       7      71 ..      12      75 ..       7     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-07
                                   --EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH CS
                       AhpC-TSA  7 dfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe 71
                                   + ++ ++dg +v+++++kg +++++ +++ +c+ ++   +++ +l+ +f ++g+ ++   +++  
  gene166|gene166|rna166|rna166 12 SLSARKWDGSKVDFETFKGCVLIIVNVAS-SCKLAESNYKSFVNLLSKFYKKGLRILLFPCNQYL 75
                                   5677899************9999999999.**************************998876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1289.15
//
Query:       gene1661|gene1661|rna1660|rna1660  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-31  106.8   1.2    1.8e-29  102.3   1.2    2.0  1  DUF5099   Domain of unknown function (DUF5099)


Domain annotation for each model (and alignments):
>> DUF5099  Domain of unknown function (DUF5099)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   1.2   9.9e-34   1.8e-29       1     109 []      17     109 ..      17     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 9.9e-34
                            DUF5099   1 KkpklvliinkysevskeeikklkkkygikivkligekkdkvlikeeidfenksvlpdlvilcndklvFklkspll 76 
                                        K pk++lii++y+++s++e+k +k+               +v ++  idfe+k+++++lvilcn+ l+F+l +pl+
  gene1661|gene1661|rna1660|rna1660  17 KVPKTMLIIDRYGTISEKEKKGIKD---------------SV-MEVDIDFEEKTTHYSLVILCNTALRFNLINPLT 76 
                                        89***************99988888...............22.22369**************************** PP

                            DUF5099  77 lykaEilfkrkdfsedvlvkaLehYseCeirnG 109
                                        l+++Ei+f+r+ fs++v+ +aL+hYseCeirnG
  gene1661|gene1661|rna1660|rna1660  77 LAECEIWFTRRVFSSRVFADALTHYSECEIRNG 109
                                        ********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 657.44
//
Query:       gene1662|gene1662|rna1661|rna1661  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-26   91.8   0.0    3.3e-26   91.6   0.0    1.0  1  UQ_con    Ubiquitin-conjugating enzyme
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.039   13.8   0.0    1.4  1  UEV       UEV domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.6   0.0   3.7e-30   3.3e-26       1     137 [.      19     154 ..      19     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.6 bits;  conditional E-value: 3.7e-30
                                        HHHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB..TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTB CS
                             UQ_con   1 rlqkelkelakkkpsgisaklvddenlfewkvlikgp.edtpYeggvFklelefpedYPlkpPkvkfvtkifHPnv 75 
                                        rl++e+k+++  + +++s++ +++ + + ++v  + p ++++Yeg v ++++++p+ YP+kpPk+ +  k+fHPn+
  gene1662|gene1662|rna1661|rna1661  19 RLKTEIKSIELLPGTSLSVDKSSE-ERYVMEVGYTMPiTEGIYEGRVLRFKIKIPHAYPFKPPKLLCLDKVFHPNI 93 
                                        688899988888888888888775.44555554444439************************************* PP

                                        ETTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHH CS
                             UQ_con  76 dksGevcldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvk 137
                                        d +G+vc++iL+   W+p++ lesv++++ +++ e   e++ln+ a++ll+ d e++ + +k
  gene1662|gene1662|rna1661|rna1661  94 DDDGNVCMEILRLG-WRPTHGLESVFVNLYVIFVEITGEDALNTLAGDLLRMDYERFVRIAK 154
                                        ************55.**************************************999988775 PP

>> UEV  UEV domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.4e-06     0.039      15     109 ..      29     119 ..      15     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                                        EEEEEEEEE-TTS-EEEEEEEEEEEE-S...SSTTS-EEEEEEE--TTTTTS--EEEE-GCC--TSGGGGGB-TTS CS
                                UEV  15 lkprtevytfedgesklllnlkGtipvk...ykgatyniPiliwvlesyPveaPivyvkptksmvikknenvdaqG 87 
                                        l p t++ +++++e++  +++  t+p++   y+g+++     i ++++yP+++P +    +       + n+d +G
  gene1662|gene1662|rna1661|rna1661  29 LLPGTSLSVDKSSEERYVMEVGYTMPITegiYEGRVLR--FKIKIPHAYPFKPPKLLCLDKVF-----HPNIDDDG 97 
                                        55666677788888888999999999982223444444..46789*********986654444.....569***** PP

                                        BB--HHHHS--TTT--HHHHHH CS
                                UEV  88 lvylpyLeeWkreksnlvslvq 109
                                        +v +++L+  +r++  l s+  
  gene1662|gene1662|rna1661|rna1661  98 NVCMEILRLGWRPTHGLESVFV 119
                                        *******964444666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1004.48
//
Query:       gene1663|gene1663|rna1662|rna1662  [L=80]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 503.26
//
Query:       gene1664|gene1664|rna1663|rna1663  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-21   74.9   0.4    3.5e-21   74.9   0.4    1.7  2  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.4     2e-25   3.5e-21       2      75 ..      14      87 ..      13      89 .. 0.96
   2 ?   -1.6   0.2      0.15   2.7e+03      57      64 ..     112     119 ..      94     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 2e-25
                                       EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS- CS
                     Ribosomal_S24e  2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglae 75
                                       v v+Hpg + ps++eir k+ ++y+++++++vv  f++++G ++tt +akiY s+ea+  +E+kh++a+ + +e
  gene1664|gene1664|rna1663|rna1663 14 VVVYHPGMPIPSQEEIRGKISELYQTNKKNIVVGDFKNRYGTHRTTLKAKIYSSAEALSNTEKKHIVAKLTGKE 87
                                       689****************************************************************9987765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.15
                                        HHHHHHS- CS
                     Ribosomal_S24e  57 eaakkfEp 64 
                                        +a+kk E+
  gene1664|gene1664|rna1663|rna1663 112 KAMKKAEK 119
                                        44555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1203  (0.067098); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 723.03
//
Query:       gene1665|gene1665|rna1664|rna1664  [L=59]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-18   66.3   2.2    2.1e-18   66.2   2.2    1.0  1  Ribosomal_S30   Ribosomal protein S30
  ------ inclusion threshold ------
      0.035   13.8   0.1      0.039   13.7   0.1    1.0  1  TAF1D           TATA box-binding protein-associated factor 1D
      0.095   12.5   0.4       0.13   12.1   0.4    1.2  1  zinc_ribbon_12  Probable zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   2.2   3.6e-22   2.1e-18       3      58 .]       3      58 ..       1      58 [. 0.92

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 3.6e-22
                                       BX-STTTTHHHHHS--...-----------THHHHHHHHHHHTTSSS--SSSSS-S--- CS
                      Ribosomal_S30  3 hGsLarAGKVrnqTPK...veKqekkKkptGRakkRlqYnrRfvnvvvggkkkkgpnsq 58
                                       + ++++AGKVrnqTPK   veK+ +kK  +GR+++Rl++++R  + ++++++k+++n+q
  gene1665|gene1665|rna1664|rna1664  3 TITINKAGKVRNQTPKdpvVEKE-RKK--CGRCRQRLKFEKRNDMGYFEVAGKMKLNPQ 58
                                       5699************9877777.777..****************************97 PP

>> TAF1D  TATA box-binding protein-associated factor 1D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.6e-06     0.039      93     142 ..       7      55 ..       2      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-06
                              TAF1D  93 ekkkrlkdkgvqfpfvesengrkplpwkkiLtyEqavarGffnyieklKy 142
                                        +k  ++++++++ p+ve+e  +k    ++ L++E+    G+f+   k+K 
  gene1665|gene1665|rna1664|rna1664   7 NKAGKVRNQTPKDPVVEKER-KKCGRCRQRLKFEKRNDMGYFEVAGKMKL 55 
                                        466789***********985.67779*****************9999886 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   2.2e-05      0.13      17      44 ..      15      39 ..      14      40 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                     zinc_ribbon_12 17 qlPkkflllkkkqqklrCGaCsevlsfs 44
                                       q Pk+ ++ k+   + +CG+C + l+f+
  gene1665|gene1665|rna1664|rna1664 15 QTPKDPVVEKE---RKKCGRCRQRLKFE 39
                                       78999999444...579*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 383.68
//
Query:       gene1666|gene1666|rna1665|rna1665  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-13   48.4   0.4      1e-12   47.5   0.4    1.4  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.4   5.7e-17     1e-12      10      65 ..      34     101 ..      29     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 5.7e-17
                                        EEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET............EEEEEEEEEEEGGGEEEE CS
                                LSM  10 kvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk............ekrklglvliRGnnivli 65 
                                         v+v l+n+r++ G+++++D++ Nl + d++e+ +                +r+lg+v+iRG++++l+
  gene1666|gene1666|rna1665|rna1665  34 PVLVSLRNNRKVMGKVIAYDRHYNLLMGDAKEIGNMRGrnkgkkkrqgcdFSRRLGNVFIRGDTVILV 101
                                        69******************************98665589999***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 788.98
//
Query:       gene1667|gene1667|rna1666|rna1666  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-27   93.9   0.1    4.2e-26   91.9   0.0    1.9  2  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.071   12.4   1.6        3.1    7.1   0.0    2.2  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   4.6e-30   4.2e-26       1     142 [.      46     173 ..      46     174 .. 0.97
   2 ?   -0.3   0.0      0.13   1.1e+03      91     115 ..     213     237 ..     186     266 .. 0.64

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 4.6e-30
                                        EEEE--TT--HHHHHHHHHHHHHSSES.EEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH CS
                    CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleed.livgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltr 74 
                                        +++G++D++H+GH+r l+qak+l+    l+vgv+ d+ + + k   +++++eR e l ++++vdevi+ +pwelt 
  gene1667|gene1667|rna1666|rna1666  46 YCDGVYDLFHYGHARSLKQAKNLFPDVyLLVGVTDDNITTRLKgNLVMNEKERAEGLIHCRYVDEVITSAPWELTS 121
                                        689**********************99***************77******************************** PP

                                        HHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                    CTP_transf_like  75 evlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                        e+++k+k+d  ++++++++++     +  e+i++ vk +++          +++  rt+giS++ i++
  gene1667|gene1667|rna1666|rna1666 122 EFIQKHKID--FVAHDDIPYKG----EGKEDIYKFVKDMGM----------FIPIRRTKGISTSGIIT 173
                                        *********..**********9....59*************..........*************9986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.13
                                        HHHHHHHHCHHHHHHHHHHHHHEEE CS
                    CTP_transf_like  91 advledfsewkeleeilgnvklvvv 115
                                         +++++++  +e++ei ++ +++ +
  gene1667|gene1667|rna1666|rna1666 213 NEMIKNVDIQREIDEIRKEIRIAMR 237
                                        4455566556677777777666665 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00035       3.1       6      31 ..      39      62 ..      34      68 .. 0.86
   2 ?    4.4   0.3    0.0022        20     244     273 ..     198     227 ..     189     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00035
                                       BTTEEEEEEEEEBTTS--BHHHHHHH CS
                       tRNA-synt_1e  6 eekkvtlYvCGptvydashlGhaRsl 31
                                       +++ v +Y+ G  vyd  h GhaRsl
  gene1667|gene1667|rna1666|rna1666 39 TNRPVRIYCDG--VYDLFHYGHARSL 62
                                       57789999988..8**********86 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0022
                                        E--EEETTBE--TTTT---BHHHHHTTS-H CS
                       tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdp 273
                                          +l++++ kmsk ++ +i+  d+ ++ d 
  gene1667|gene1667|rna1666|rna1666 198 ISFLHMKRIKMSKKMNEMIKNVDIQREIDE 227
                                        6799**************999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1885.58
//
Query:       gene1668|gene1668|rna1667|rna1667  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-24   84.2   0.1    5.7e-24   84.2   0.1    2.5  3  Mnd1             Mnd1 HTH domain
    2.1e-12   46.9   2.1    2.1e-12   46.9   2.1    3.0  4  LZ3wCH           Leucine zipper with capping helix domain
    0.00036   20.9   1.2     0.0008   19.7   0.6    1.9  2  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.014   15.3   0.3       0.05   13.5   0.0    2.0  3  TrmB             Sugar-specific transcriptional regulator Trm
      0.045   13.4   0.0      0.096   12.4   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family
      0.061   13.7  11.1      0.057   13.7  10.2    1.4  1  OmpH             Outer membrane protein (OmpH-like)
        0.1   11.5   2.6       0.11   11.4   2.6    1.1  1  LMBR1            LMBR1-like membrane protein
        1.6    7.5   5.5        1.8    7.3   5.5    1.1  1  O-antigen_lig    O-antigen ligase like membrane protein


Domain annotation for each model (and alignments):
>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.1   2.5e-27   5.7e-24       1      60 []      15      73 ..      15      73 .. 0.98
   2 ?   -3.1   0.3       4.6     1e+04      15      27 ..      85      94 ..      82     102 .. 0.53
   3 ?   -1.1   0.5       1.1   2.5e+03      15      31 ..     119     135 ..     114     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 2.5e-27
                               Mnd1  1 ileifqeskefytlKeleklapkekgivsqsVkdvlqsLvdDglveveKiGssnvyWsFp 60
                                       +lei++ s++f++l+ele l++k kgiv++++k++lq+LvdDglv veK+G+sn+yWsF+
  gene1668|gene1668|rna1667|rna1667 15 LLEIIRGSRSFFKLQELENLGSK-KGIVANTIKEILQQLVDDGLVTVEKVGTSNLYWSFA 73
                                       689********************.***********************************5 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.6
                               Mnd1 15 Keleklapkekgi 27
                                       Kel  ++++   +
  gene1668|gene1668|rna1667|rna1667 85 KELVEECKS---M 94
                                       555554444...3 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.1
                               Mnd1  15 Keleklapkekgivsqs 31 
                                        Kele+++   ++i + +
  gene1668|gene1668|rna1667|rna1667 119 KELESKLNALAKIEEEQ 135
                                        99**9999988888776 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       2.8   6.2e+03      29      44 ..      71      86 ..      70      96 .. 0.56
   2 ?   -2.8   0.3       3.3   7.4e+03      37      37 ..      94      94 ..      78     107 .. 0.58
   3 ?    2.6   0.2     0.064   1.4e+02      31      46 ..     110     125 ..     108     135 .. 0.79
   4 !   46.9   2.1   9.3e-16   2.1e-12      11      55 .]     158     202 ..     150     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                             LZ3wCH 29 swikekfpkskkelne 44
                                       s+ +e+  k++  ++e
  gene1668|gene1668|rna1667|rna1667 71 SFASEGVQKKNLKFKE 86
                                       5555555555544444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.3
                             LZ3wCH 37 k 37
                                       +
  gene1668|gene1668|rna1667|rna1667 94 M 94
                                       1 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.064
                             LZ3wCH  31 ikekfpkskkelneef 46 
                                        i++++  ++kel++ +
  gene1668|gene1668|rna1667|rna1667 110 ISKNYTEERKELESKL 125
                                        89**********9987 PP

  == domain 4  score: 46.9 bits;  conditional E-value: 9.3e-16
                             LZ3wCH  11 kkakeaanrWtdnifdikswikekfpkskkelneefgIetDeDyg 55 
                                        k+  +  n   dnif i++++++kf ++k e+n++fgI+ D+Dy+
  gene1668|gene1668|rna1667|rna1667 158 KEIVDEYNKIIDNIFIIQDYVCNKFSMEKPEFNSNFGIPQDLDYI 202
                                        444444556666********************************7 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.6   3.6e-07    0.0008      24     102 ..      31     111 ..      10     127 .. 0.69
   2 ?   -1.5   0.0       1.4   3.1e+03      47      83 ..     135     171 ..     128     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.6e-07
                                        HHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXX.XXXXXXXXXXXXXXXXXXXXX..XXX CS
                    Penicillinase_R  24 veeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeav.asavkqlldklfegsvkelva..afv 96 
                                         e l ++k    +T+k +l++Lv+ gl++ ek g + +Y + +se   + + + k+l+++   +  +e++   +++
  gene1668|gene1668|rna1667|rna1667  31 LENLGSKKGIVANTIKEILQQLVDDGLVTVEKVGTSNLYWSFASEGVQKkNLKFKELVEECK-SMSEEILKkkKHL 105
                                        57788999999*****************************9999965540555666665554.3444444312355 PP

                                        XXXXXX CS
                    Penicillinase_R  97 eeekls 102
                                        e+e +s
  gene1668|gene1668|rna1667|rna1667 106 ENERIS 111
                                        555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                        HTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXX CS
                    Penicillinase_R  47 kKgllsrekegrafiYsplvseeeavasavkqlldkl 83 
                                        +K+ ls+ +e   +iY   v+ ++ +  + ++++d++
  gene1668|gene1668|rna1667|rna1667 135 QKEELSKFEETDPTIYDKFVDDRKEIVDEYNKIIDNI 171
                                        4555555666666666665555555555555555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.2e-05      0.05      30      62 ..      36      69 ..      29      72 .. 0.80
   2 ?   -2.2   0.0       1.8   3.9e+03      14      30 ..      84     100 ..      81     111 .. 0.76
   3 ?   -2.2   0.1       1.8     4e+03      47      47 ..     129     129 ..      96     151 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.2e-05
                                       CCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEE CS
                               TrmB 30 eelgvprskvYevLrsLedkGlVerek.grpklY 62
                                       ++ g+  +++ e+L++L+d GlV++ek g+ +lY
  gene1668|gene1668|rna1667|rna1667 36 SKKGIVANTIKEILQQLVDDGLVTVEKvGTSNLY 69
                                       66688889******************94444455 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                        CHHHHHHCCCHHCHHCC CS
                               TrmB  14 YlaLlklgpatadeiae 30 
                                        ++ L++++++  +ei +
  gene1668|gene1668|rna1667|rna1667  84 FKELVEECKSMSEEILK 100
                                        55678888877777766 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.8
                                        H CS
                               TrmB  47 e 47 
                                         
  gene1668|gene1668|rna1667|rna1667 129 A 129
                                        3 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.3e-05     0.096      28      58 ..      32      62 ..      27      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                               GntR 28 reLaaefgVsrttvReALrrLeaeglverrq 58
                                       + L ++ g+ ++t+ e L++L+ +glv++++
  gene1668|gene1668|rna1667|rna1667 32 ENLGSKKGIVANTIKEILQQLVDDGLVTVEK 62
                                       6789999*********************975 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7  10.2   2.6e-05     0.057      25     107 ..      81     166 ..      56     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHH CS
                               OmpH  25 ekkfkklqaeleakekelqklqeelqkkakkle.keekeqelqkkeqelqqkqqqkaqelqkkqqe...llkpild 96 
                                        + kfk+l +e +++ +e+ k+++ l+++  + +  +e+++el+ k ++l +  +++++el k ++    ++++++d
  gene1668|gene1668|rna1667|rna1667  81 NLKFKELVEECKSMSEEILKKKKHLENERIS-KnYTEERKELESKLNALAKIEEEQKEELSKFEETdptIYDKFVD 155
                                        3366*********************955544.248899999**********5555559999988666666667777 PP

                                        HHHHHHHHHHH CS
                               OmpH  97 kinkaikevak 107
                                          +++++e++k
  gene1668|gene1668|rna1667|rna1667 156 DRKEIVDEYNK 166
                                        77777777665 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.6   4.9e-05      0.11     236     321 ..      83     192 ..      27     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                              LMBR1 236 sisesdp.lrkyleeilkkvPeeiaeklks.......nenkteeslaklekqlika...............lqkre 288
                                        +++e  +  ++++eeilkk  +  +e++++       + ++++++lak e++++++               + +r+
  gene1668|gene1668|rna1667|rna1667  83 KFKELVEeCKSMSEEILKKKKHLENERISKnyteerkELESKLNALAKIEEEQKEElskfeetdptiydkfVDDRK 158
                                        23333332345666666643333333333344444445666777888888888888888899999999999***** PP

                              LMBR1 289 rtekqwkrllekalelediiknksskek.efkss 321
                                        ++ +++++++++++ ++d + nk s ek ef+s+
  gene1668|gene1668|rna1667|rna1667 159 EIVDEYNKIIDNIFIIQDYVCNKFSMEKpEFNSN 192
                                        ******************9999988765366665 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.5   0.00081       1.8     265     351 ..      71     170 ..      41     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00081
                      O-antigen_lig 265 py.spiyrrkelkekeieiksekk......eeeeikne.ikenykseglk.....eavleqyeyandkqfsqellk 327
                                        ++ s+ +++k+lk ke  ++ +        ++++++ne i +ny  e  +     +a  +++e+++++  + e ++
  gene1668|gene1668|rna1667|rna1667  71 SFaSEGVQKKNLKFKELVEECKSMseeilkKKKHLENErISKNYTEERKElesklNALAKIEEEQKEELSKFEETD 146
                                        544444555555555443332222245555777777778888888887777788999******************* PP

                      O-antigen_lig 328 eeveslllsnRdlqlkvlkqvykn 351
                                          +  + +++R+  +++++++++n
  gene1668|gene1668|rna1667|rna1667 147 PTIYDKFVDDRKEIVDEYNKIIDN 170
                                        ***************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2815  (0.157008); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 1246.14
//
Query:       gene1669|gene1669|rna1668|rna1668  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2666.61
//
Query:       gene1670|gene1670|rna1669|rna1669  [L=303]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.36   10.7   0.0    1.9  1  zf-C2H2_3  zinc-finger of acetyl-transferase ESCO


Domain annotation for each model (and alignments):
>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     2e-05      0.36       4      32 ..     173     202 ..     171     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2e-05
                          zf-C2H2_3   4 Ldlgqksfga.sqCkeCgMvYnpgspeDek 32 
                                        +d++ +      qCk Cg+ Y  + + De+
  gene1670|gene1670|rna1669|rna1669 173 IDVDPSVLYPpNQCKLCGLRYEDTPEGDEQ 202
                                        6777777777678********999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1853.21
//
Query:       gene167|gene167|rna167|rna167  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-14   51.4   0.9    1.3e-13   50.8   0.9    1.3  1  TFIIA_gamma_C  Transcription initiation factor IIA, gamma sub
    1.1e-09   38.2   0.0    1.5e-09   37.7   0.0    1.3  1  TFIIA_gamma_N  Transcription initiation factor IIA, gamma sub


Domain annotation for each model (and alignments):
>> TFIIA_gamma_C  Transcription initiation factor IIA, gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.9   1.5e-17   1.3e-13       1      45 []      56      99 ..      56      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.5e-17
                  TFIIA_gamma_C  1 tfKgkLdtYrfcDdVWtFiiknvefklendetvkvdkvKIVACns 45
                                   +fKgk+d Y+++D+VW F  k++ ++l+n e++++  v IVAC++
  gene167|gene167|rna167|rna167 56 SFKGKVDFYNHVDGVWRFQTKDFVMSLNN-EYFRAGDVNIVACDA 99
                                   6***************************9.999**********96 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   1.7e-13   1.5e-09       2      44 ..       2      44 ..       1      53 [. 0.96

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.7e-13
                  TFIIA_gamma_N  2 YelYRrstlGtaLtdaLDeliqegkIspqlamkVLeqFDksin 44
                                   Ye+YR+  +G+aL+  +De ++++ ++p+    +Le FD s+ 
  gene167|gene167|rna167|rna167  2 YEFYRQLMVGKALEKIIDEKVNSNVLTPNQGKYILEAFDLSVP 44
                                   ***************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.33s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 655.99
//
Query:       gene1671|gene1671|rna1670|rna1670  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0047   16.2   1.1     0.0089   15.3   0.3    1.9  2  NUP214    Nucleoporin or Nuclear pore complex subunit NUP214=
  ------ inclusion threshold ------
      0.046   13.3   0.3       0.11   12.1   0.3    1.7  1  DUF4222   Domain of unknown function (DUF4222)


Domain annotation for each model (and alignments):
>> NUP214  Nucleoporin or Nuclear pore complex subunit NUP214=Nup159
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   9.9e-07    0.0089      67     154 ..     165     254 ..     155     279 .. 0.78
   2 ?   -2.0   0.0      0.19   1.7e+03     154     191 ..     301     336 ..     292     343 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.9e-07
                                        EEEEEEETTE.EEEEESSEEEEEESSSTT.EEEEEE-SS-EE..EEETTEEEEEE...TTSEEEEEETT....EEE CS
                             NUP214  67 viavkflndevvlvstksellsldleelseleeihklekdlvelkllkstlllld...snnqLsaldlskkelksl 139
                                         ++++f+  + +lv+t++++++ldl++l   ++i+  + ++    ++++ l++ +   ++ +L++l++++k  +s+
  gene1671|gene1671|rna1670|rna1670 165 PMFICFYLFRELLVVTRNQVFHLDLNNLRL-STIYLTNLKIQ-SVVFQDRLYIQEgtkKHVRLTSLNIEDKAAESI 238
                                        589999998889***************986.88888888887.457899999976211445699999998888666 PP

                                        .ECSEEEEEE-SSEEE CS
                             NUP214 140 .aenvasfDvledkLv 154
                                          en++ + + e+ +v
  gene1671|gene1671|rna1670|rna1670 239 yIENLMNISIGETIVV 254
                                        2588888777665444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.19
                                        EEEETTS-EEEEEEEEEEE...EEE---HHHHTS-TTT CS
                             NUP214 154 vvllkdksvqvfeleneeeekskelslPselkeelkde 191
                                         vl ++ sv+v +++ +++e    +  P++l+  l++ 
  gene1671|gene1671|rna1670|rna1670 301 FVLWDNGSVKVIDIDLKKKE-DYLMKFPENLE-MLEEM 336
                                        46777888888888866663.45566666664.33334 PP

>> DUF4222  Domain of unknown function (DUF4222)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   1.2e-05      0.11      21      39 ..      64      82 ..      51      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                            DUF4222 21 svdenrVtFrRdGYehpcv 39
                                       ++d+ +V++ RdGY+++ v
  gene1671|gene1671|rna1670|rna1670 64 KIDNYNVIYSRDGYQFDIV 82
                                       56777***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2360.12
//
Query:       gene1672|gene1672|rna1671|rna1671  [L=779]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-50  169.8   0.0    1.5e-49  168.3   0.0    1.8  1  AAA_12           AAA domain
      8e-47  160.2   0.8    1.3e-27   97.3   0.0    2.7  3  AAA_11           AAA domain
    3.3e-13   49.8   0.1    2.1e-12   47.2   0.0    2.2  2  AAA_30           AAA domain
    4.2e-12   46.3  12.4    2.6e-11   43.7  12.4    2.3  1  UPF1_Zn_bind     RNA helicase (UPF2 interacting domain)
    1.8e-10   41.3   0.0    3.9e-10   40.2   0.0    1.6  1  AAA_19           AAA domain
    8.8e-08   32.3   0.4    5.6e-07   29.7   0.0    2.4  3  ResIII           Type III restriction enzyme, res subunit
    1.1e-06   28.5   0.3      0.047   13.2   0.0    2.7  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
    9.7e-06   25.1   0.0    1.6e-05   24.4   0.0    1.3  1  ATPase           KaiC
    1.5e-05   24.9   0.0    3.6e-05   23.6   0.0    1.7  1  DEAD             DEAD/DEAH box helicase
    1.5e-05   24.4   1.8    0.00056   19.3   0.3    2.7  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    3.4e-05   24.0   0.0    7.6e-05   22.9   0.0    1.6  1  DUF5599          Domain of unknown function (DUF5599)
     0.0019   17.7   0.0     0.0073   15.8   0.1    2.0  2  PhoH             PhoH-like protein
  ------ inclusion threshold ------
      0.014   14.6   0.2        1.1    8.3   0.1    2.5  2  PIF1             PIF1-like helicase
      0.015   15.1   0.0      0.031   14.1   0.0    1.6  1  Helicase_RecD    Helicase
       0.02   14.3   0.0       0.14   11.6   0.0    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.021   15.1   0.0       0.25   11.6   0.1    2.4  2  AAA_22           AAA domain
      0.041   14.3   0.1       0.13   12.6   0.1    1.9  1  AAA              ATPase family associated with various cellul
      0.079   12.7   0.0       0.23   11.1   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
       0.15   12.1   0.0       0.39   10.7   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
        2.1    8.7   8.3        7.2    7.0   8.3    1.9  1  zf-UBP           Zn-finger in ubiquitin-hydrolases and other 
        3.1    8.0  15.7       0.13   12.5   6.5    3.1  2  zf-AN1           AN1-like Zinc finger


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   0.0   1.8e-52   1.5e-49       2     198 ..     544     725 ..     543     726 .. 0.90

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 1.8e-52
                             AAA_12   2 erSlferllkkekekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkreleaqealeeplep.lvfidvekse 76 
                                        ++Slferl++ +   + +L++qYRm+ +++++ps++fY+g+L ++ +   r             p  +f+ + + e
  gene1672|gene1672|rna1671|rna1671 544 KQSLFERLISIG-VVPYVLSIQYRMDTDLCEWPSEMFYNGELLTGGKRFCRFDL--------GIPtNFFYVCYGRE 610
                                        79**********.*****************************999876665544........45515566665555 PP

                             AAA_12  77 eekekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQ 152
                                        e +  + +s+iN++Ea  + +++++l+k+g++e  ++igvitpY+ q +++ +++  +e+ +    +e++ vdgfQ
  gene1672|gene1672|rna1671|rna1671 611 EVSA-SGTSFINQAEALYCESIIRHLFKCGVTE--NQIGVITPYEGQRSYILNRIFGAEPGN----LEISNVDGFQ 679
                                        5555.56**************************..9*******************9888887....9********* PP

                             AAA_12 153 GrekdviilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                        Grekd+ii+slVRsn  + igf+ d+rr+NV lTRAk+ l+i+Gn+
  gene1672|gene1672|rna1671|rna1671 680 GREKDFIIVSLVRSNLYQGIGFVGDKRRMNVTLTRAKHGLVIIGNP 725
                                        ********************************************96 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         6   5.1e+03     137     167 ..     250     269 ..     210     287 .. 0.58
   2 !   62.1   0.1   8.2e-20     7e-17       1     120 [.     338     440 ..     338     454 .. 0.88
   3 !   97.3   0.0   1.5e-30   1.3e-27     160     259 ..     437     534 ..     428     536 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6
                             AAA_11 137 akelrafeeeeekeklkkskekskskleqer 167
                                        +k           e+ k++k+ks+++++   
  gene1672|gene1672|rna1671|rna1671 250 KK-----------EIGKNKKNKSNNDEKGLH 269
                                        22...........222222222222222222 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 8.2e-20
                             AAA_11   1 klndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr 76 
                                        kln sq++a++ al ++  tliqGPPGtgKT +  +++ +          k+++ ++Lv apSN+AvD+l++++ +
  gene1672|gene1672|rna1671|rna1671 338 KLNTSQETAVRAALGRKV-TLIQGPPGTGKTLVSSSIVYNF--------VKHYGGKVLVVAPSNTAVDQLTLKIHK 404
                                        69**************95.***************9999999........5899********************999 PP

                             AAA_11  77 glldsegekykpkivRvgnee.eriseavksvsleekvekrleke 120
                                                 +++k++Rv++   e  +++v+ +sl e +++ +e +
  gene1672|gene1672|rna1671|rna1671 405 ---------TGLKVLRVMSRRrECGQSDVSFLSLHENLRELQEGR 440
                                        .........9*********99755678888888888888777654 PP

  == domain 3  score: 97.3 bits;  conditional E-value: 1.5e-30
                             AAA_11 160 kskleqerrklkkerkelskeleeaeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstl 235
                                        ++ ++++ + +++  + +s   +e+ esl++++l++ae++ +T++++g+k ++k+  +f +v+IDEA q++Ep +l
  gene1672|gene1672|rna1671|rna1671 437 QEGRKKKDEGCRDNGRYNSIYNDEVSESLKKQLLNQAEVITCTCVTSGQKMFNKF--RFHYVLIDEAVQSTEPLSL 510
                                        4445555566666666666677899999***************************..9****************** PP

                             AAA_11 236 iPlrlgakkvvLvGDpkQLpatvi 259
                                        iPl +g+kk+vLvGD+kQL +t++
  gene1672|gene1672|rna1671|rna1671 511 IPLVYGCKKLVLVGDHKQLGPTIL 534
                                        **********************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       9.7   8.3e+03     136     159 ..     133     156 ..     132     162 .. 0.86
   2 !   47.2   0.0   2.5e-15   2.1e-12       2     130 ..     339     531 ..     338     533 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 9.7
                             AAA_30 136 vlrdlveaagigtaeLtevvRqke 159
                                        v+++l+ea+  +  e++e +Rq++
  gene1672|gene1672|rna1671|rna1671 133 VFSSLIEAECRKEREIKESMRQEN 156
                                        78999999999999*******975 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 2.5e-15
                             AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkal.reaweaaggrviglAptgkaAkvLaeelgieastiakl 76 
                                        ln++Q++av+a+l+ +  v++++Gp+GtGKt + +++  + +++ gg+v+++Ap+++a ++L+ ++  ++  + ++
  gene1672|gene1672|rna1671|rna1671 339 LNTSQETAVRAALGRK--VTLIQGPPGTGKTLVSSSIvYNFVKHYGGKVLVVAPSNTAVDQLTLKIHKTGLKVLRV 412
                                        89**********9887..9****************9945666666******************6555555555555 PP

                             AAA_30  77 lkrlk....................................................................gra 84 
                                        ++r +                                                                    +  
  gene1672|gene1672|rna1671|rna1671 413 MSRRRecgqsdvsflslhenlrelqegrkkkdegcrdngrynsiyndevseslkkqllnqaevitctcvtsgqK-- 486
                                        544445556666666666777777799999999999999999999999999999999*************9653.. PP

                             AAA_30  85 rlepg..tllivDEagmvdtkqlaallkaaekagakvilvGDerQlas 130
                                         +++   + +++DEa    +++  +l+  +     k++lvGD++Ql++
  gene1672|gene1672|rna1671|rna1671 487 MFNKFrfHYVLIDEAV--QSTEPLSLIPLVYG-CKKLVLVGDHKQLGP 531
                                        333322599*****94..55566677777766.689*********986 PP

>> UPF1_Zn_bind  RNA helicase (UPF2 interacting domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7  12.4   3.1e-14   2.6e-11       2      74 ..       2      65 ..       1     115 [. 0.90

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 3.1e-14
                       UPF1_Zn_bind  2 aCaYCgisdpesvvkCaackkwFCngkgktsashivthlvrskhkevslhkesplgdtvleCyncgsknvflL 74
                                       +C+YC+   +e +++C +c+k+FCn+++++s shiv hlv+++hk++ +          ++C +cg+ n+f+L
  gene1672|gene1672|rna1671|rna1671  2 KCQYCEA--AEFLIECITCGKHFCNSHSASSISHIVFHLVKARHKSIRI-------GGDIKCRKCGEDNLFKL 65
                                       6****76..578**********************************998.......45689**********98 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   4.6e-13   3.9e-10       1     141 [.     343     529 ..     343     533 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.6e-13
                             AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....... 68 
                                        q+ av+ al +kv l+ ++pGtGKT v   iv  +v+  g    ++l+va+ + A+++l+ ++++ g++       
  gene1672|gene1672|rna1671|rna1671 343 QETAVRaALGRKVTLIQGPPGTGKTLVSSSIVYNFVKHYGG---KVLVVAPSNTAVDQLTLKIHKTGLKvlrvmsr 415
                                        899**98*****************************99976...8***************9997777776666666 PP

                             AAA_19  69 ..........atTiHrlal...................................ldfddlltealelle......e 93 
                                                          l                                     ++++l +++e++        
  gene1672|gene1672|rna1671|rna1671 416 rrecgqsdvsF-------LslhenlrelqegrkkkdegcrdngrynsiyndevsESLKKQLLNQAEVITctcvtsG 484
                                        66555544442.......0555666788999999999999999999987777663333444344445448886542 PP

                             AAA_19  94 aeeekklqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQl 141
                                        ++  +k+  ++ ++++DE+ + +    +L+  ++g kk l+lvGD++Ql
  gene1672|gene1672|rna1671|rna1671 485 QKMFNKF--RFhYVLIDEAVQST-EPLSLIPLVYGCKK-LVLVGDHKQL 529
                                        2333444..4469*****86554.45679999996666.*********8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.1   4.3e+03      28      40 ..      72      84 ..      61      91 .. 0.82
   2 ?   -1.6   0.2       2.7   2.3e+03      67      96 ..     235     264 ..     234     279 .. 0.65
   3 !   29.7   0.0   6.5e-10   5.6e-07       4     141 ..     339     501 ..     336     519 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.1
                                       EEEESTTSTHHHH CS
                             ResIII 28 likmaTGtGKTlv 40
                                       ++  a+G+G Tlv
  gene1672|gene1672|rna1671|rna1671 72 IFCNACGSGRTLV 84
                                       57789******98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                                        HHHHHHHGGGGTGG....GEEEESSS-B-- CS
                             ResIII  67 leqtleefkkflseaykeigkkvsgdkkka 96 
                                        +e+++ +++k++++++keigk++++++++ 
  gene1672|gene1672|rna1671|rna1671 235 YERMEWALRKLYNTYKKEIGKNKKNKSNND 264
                                        577777778888888888777776666665 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 6.5e-10
                                        E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG..... CS
                             ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef..... 74 
                                        l+  Qe+a+++ l      ++k  li+ + GtGKTlv+ ++++++ k+++  k+l+++p+++ ++q+  ++     
  gene1672|gene1672|rna1671|rna1671 339 LNTSQETAVRAAL------GRKVTLIQGPPGTGKTLVSSSIVYNFVKHYG-GKVLVVAPSNTAVDQLTLKIhktgl 407
                                        5666777777776......78899**********************9866.5****************88855555 PP

                                        .........GGGTGG..........GEEEESSS-B--.......-SEEEEEHHHHHHTH................. CS
                             ResIII  75 .........kkflseayke......igkkvsgdkkkakekdstnkkilvttiqsldadseee.............e 122
                                                 +++ ++++++        +  +g+kkk  e+ ++n ++  +  ++++++++++             +
  gene1672|gene1672|rna1671|rna1671 408 kvlrvmsrrRECGQSDVSFlslhenLRELQEGRKKKD-EGCRDNGRYNSIYNDEVSESLKKQllnqaevitctcvT 482
                                        6655555543333333333554444444455555555.55555555555555555555544466667777777766 PP

                                        ....HHHTTT-SEEEEETG CS
                             ResIII 123 eeseellrdrfdviiiDEa 141
                                        + ++ + + rf +++iDEa
  gene1672|gene1672|rna1671|rna1671 483 SGQKMFNKFRFHYVLIDEA 501
                                        6667777777778888887 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.8   1.5e+03     168     203 ..     165     263 ..      78     282 .. 0.58
   2 !   12.9   0.1   6.8e-05     0.058       1      68 [.     339     428 ..     339     479 .. 0.74
   3 !   13.2   0.0   5.5e-05     0.047     238     294 ..     476     528 ..     429     529 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.8
                                        H...............................................................HHHCCCHHHHHC CS
                      UvrD-helicase 168 k...............................................................keelslskskae 180
                                        k                                                                +  + ++++  
  gene1672|gene1672|rna1671|rna1671 165 KycyfyfqngdnelkinigdeirlthksgfvlngfvsgetfseelkveveipgdyprsgytveyLWRGVCYERMEW 240
                                        2555666666666666666666666666666666666666666666666666666666666666666666666666 PP

                                        HHHHHHHHHHHTTCCTTHHCHSS CS
                      UvrD-helicase 181 elrelvskakekqlspkelkkaf 203
                                         lr+l +++k++  ++k++k+++
  gene1672|gene1672|rna1671|rna1671 241 ALRKLYNTYKKEIGKNKKNKSNN 263
                                        77777777777666666666544 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.8e-05
                                        SSHHHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH....... CS
                      UvrD-helicase   1 lnpeqreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee....... 67 
                                        ln++q+ a++    ++ +l+   +G+GKT v  + + + +k+      ++lvv   n A + l  +i++       
  gene1672|gene1672|rna1671|rna1671 339 LNTSQETAVRAalGRKVTLIQGPPGTGKTLVSSSIVYNFVKHY---GGKVLVVAPSNTAVDQLTLKIHKtglkvlr 411
                                        68999999999866778899999********999888888888...7889*****************997666665 PP

                                        ................H CS
                      UvrD-helicase  68 ................a 68 
                                                         
  gene1672|gene1672|rna1671|rna1671 412 vmsrrrecgqsdvsflS 428
                                        54444444444444330 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 5.5e-05
                                        HHHHHHHHCHHHHHHHHHHSSEEEESSG.GG-BHHHHHHHHHHHTTTTTEEEEE-GGG CS
                      UvrD-helicase 238 allelleeneelaealrerykeiliDEy.QDTnkiQyrilkllasgheelfmvGDpkQ 294
                                         +++  +++++++++   r++++liDE+ Q T++   +++ l++  + +l++vGD kQ
  gene1672|gene1672|rna1671|rna1671 476 ITCTCVTSGQKMFNK--FRFHYVLIDEAvQSTEP--LSLIPLVYGCK-KLVLVGDHKQ 528
                                        445555666666665..57999*****8799988..58999999998.8********* PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.9e-08   1.6e-05       4      71 ..     323     406 ..     320     417 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.9e-08
                             ATPase   4 gIeglDeilk...............gGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa.edl 63 
                                        gI  +D+i++               +    ++v+li G pGtGKt+++   +++ +++yg +++ v+   +a  +l
  gene1672|gene1672|rna1671|rna1671 323 GISNIDHIFSppnlpklntsqetavRAALGRKVTLIQGPPGTGKTLVSSSIVYNFVKHYGGKVLVVAPSNTAvDQL 398
                                        77777777766777777777777777777899***********************************988885566 PP

                             ATPase  64 renakslG 71 
                                          ++++ G
  gene1672|gene1672|rna1671|rna1671 399 TLKIHKTG 406
                                        66666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.2e-08   3.6e-05       3      72 ..     342     407 ..     340     438 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.2e-08
                                        HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk 72 
                                         Q+ a+ ++lg +  l++++ G+GKTl+ +  v++ v    +  g k+l+v+P+   + q   ++ k + 
  gene1672|gene1672|rna1671|rna1671 342 SQETAVRAALGRKVTLIQGPPGTGKTLVSSSIVYNFV----KHYGGKVLVVAPSNTAVDQLTLKIHKTGL 407
                                        699*************************999999888....67888*********999999888877654 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   6.5e-07   0.00056       1      55 [.     353     406 ..     353     504 .. 0.75
   2 ?    3.6   0.1     0.038        32     345     360 ..     707     722 ..     704     724 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.5e-07
                            DUF2075   1 kavvlVtGvaGtGKtvvllnllaeleddeeer.tavylsvNhplvlvlrealakke 55 
                                        ++v l++G +GtGKt+v ++++++    +++  ++ ++  ++  v+ l  ++ k+ 
  gene1672|gene1672|rna1671|rna1671 353 RKVTLIQGPPGTGKTLVSSSIVYNF--VKHYGgKVLVVAPSNTAVDQLTLKIHKTG 406
                                        6899********************9..44433033344455556666666665555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.038
                            DUF2075 345 ayrVLLtRGrkGlyiy 360
                                        +++V LtR+ +Gl+i 
  gene1672|gene1672|rna1671|rna1671 707 RMNVTLTRAKHGLVII 722
                                        78************95 PP

>> DUF5599  Domain of unknown function (DUF5599)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   8.9e-08   7.6e-05       2      73 ..     153     213 ..     152     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 8.9e-08
                            DUF5599   2 tqddisvrWdvglnkkrlasFvlpkldsgelrlvvGDelrlkykgseaeeWegeghvvkltdssseevtleL 73 
                                        +q+++ vrW+    k ++++F++++ d+ el++ +GDe+rl +k    + +  +g v+  t   see+ +e+
  gene1672|gene1672|rna1671|rna1671 153 RQENVFVRWE----KMKYCYFYFQNGDN-ELKINIGDEIRLTHK----SGFVLNGFVSGET--FSEELKVEV 213
                                        699******7....789********887.*************87....5566666665544..334444443 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   8.6e-06    0.0073       5      49 ..     339     383 ..     335     409 .. 0.79
   2 ?   -2.6   0.0       3.7   3.2e+03     122     157 ..     495     528 ..     489     537 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.6e-06
                                        -SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS- CS
                               PhoH   5 ktkeQkeylealkkndivfaiGpaGtGKtylavalavealkkkkv 49 
                                         +++Q+++++a    +++ + Gp GtGKt+++ ++  + +k+   
  gene1672|gene1672|rna1671|rna1671 339 LNTSQETAVRAALGRKVTLIQGPPGTGKTLVSSSIVYNFVKHYGG 383
                                        6889***************************99988877776444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                                        EEEE-SG.GG--HHHHHHHHTTB-TT-EEEEEE---- CS
                               PhoH 122 fvilDEA.QnttkeqmkmfltRlGenskvvvtGdvtq 157
                                        +v++DEA Q+t++ ++  ++   G   k+v++Gd +q
  gene1672|gene1672|rna1671|rna1671 495 YVLIDEAvQSTEPLSLIPLVY--G-CKKLVLVGDHKQ 528
                                        788888845555544333332..2.236777788777 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0013       1.1       6      64 ..     343     396 ..     338     413 .. 0.76
   2 ?    3.6   0.0     0.035        30     135     157 ..     511     533 ..     458     549 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                                        HHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHH.HHCHCTCCCEEEEESSHHHHH CS
                               PIF1   6 QkkvfdaiieavlnekgklfFvtGsgGtgKtflwkall.kklrsegkivlavAssGvAal 64 
                                        Q+++++a+         k+  ++G  GtgKt +   ++ ++++  g +vl+vA s  A  
  gene1672|gene1672|rna1671|rna1671 343 QETAVRAA------LGRKVTLIQGPPGTGKTLVSSSIVyNFVKHYGGKVLVVAPSNTAVD 396
                                        55555444......233567899**********998752788999********9987754 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.035
                                        .-SCCCC-EEEEE--TTS----- CS
                               PIF1 135 idkpFGGktvvlgGDfrQilPvi 157
                                        i   +G k +vl GD +Q+ P i
  gene1672|gene1672|rna1671|rna1671 511 IPLVYGCKKLVLVGDHKQLGPTI 533
                                        56689**************9987 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.7e-05     0.031       2      57 ..     358     414 ..     357     503 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflak.glealglke 57 
                                        +++ +G+GK+ +   ++ +++++   ++lv+aps+++v++l+  ++k gl+ l++ +
  gene1672|gene1672|rna1671|rna1671 358 IQGPPGTGKTLVSSSIVYNFVKHYGGKVLVVAPSNTAVDQLTLKIHKtGLKVLRVMS 414
                                        7899*******************99***************98666541666666554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.73   6.3e+02      27      52 ..      73      98 ..      70     131 .. 0.70
   2 ?   11.6   0.0   0.00016      0.14      17      42 ..     348     373 ..     339     398 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.73
                       Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplsee 52
                                       ++ + GsG+t++ +r  +++ + + +
  gene1672|gene1672|rna1671|rna1671 73 FCNACGSGRTLVEERCLTIIKSPEVQ 98
                                       66789********9999998655443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00016
                       Mg_chelatase  17 iaaaGgHnlllvGppGsGKtmlakrl 42 
                                         aa G+   l+ GppG+GKt++ + +
  gene1672|gene1672|rna1671|rna1671 348 RAALGRKVTLIQGPPGTGKTLVSSSI 373
                                        4889999**************99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00029      0.25       4      32 ..     352     380 ..     349     405 .. 0.77
   2 ?   -0.3   0.0       1.4   1.2e+03      81     123 ..     707     746 ..     704     752 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldee 32 
                                        +++++++ G++GtGKT++   ++++++++
  gene1672|gene1672|rna1671|rna1671 352 GRKVTLIQGPPGTGKTLVSSSIVYNFVKH 380
                                        57899*************99999998766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                             AAA_22  81 aleqalraravielliiDEaqhlrseealeeLrsllnlsrkgv 123
                                        +++  l +++  +l+ii +   l++++++++L s+++  +kg+
  gene1672|gene1672|rna1671|rna1671 707 RMNVTLTRAKH-GLVIIGNPTTLMKHDMWSNLLSFYD--KKGL 746
                                        56667777777.9999999999879***********9..7776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00016      0.13       2      21 ..     357     376 ..     356     417 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                        EEESSTTSSHHHHHHHHHHH CS
                                AAA   2 llyGppGtGKTllakavake 21 
                                        l+ GppGtGKTl+ ++++ +
  gene1672|gene1672|rna1671|rna1671 357 LIQGPPGTGKTLVSSSIVYN 376
                                        789**********9999866 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00027      0.23       7      44 ..     338     375 ..     335     400 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                        HHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                    Sigma54_activat   7 alkelleqikkvaktdlsvlitGesGtGKellaraihe 44 
                                        +l++  e++ ++a  +  +li+G  GtGK+l++++i  
  gene1672|gene1672|rna1671|rna1671 338 KLNTSQETAVRAALGRKVTLIQGPPGTGKTLVSSSIVY 375
                                        567778888999999999**************998744 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00045      0.39       3      46 ..     357     403 ..     355     426 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00045
                                        EEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B- CS
                              AAA_5   3 lLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrre 46 
                                        l++GppGtgK+ ++ ++   +       + v  +++t  ++l+ +++
  gene1672|gene1672|rna1671|rna1671 357 LIQGPPGTGKTLVSSSIVYNFvkhYGGKVLVVAPSNTAVDQLTLKIH 403
                                        899***********999988888744555566677788888876665 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   8.3    0.0084       7.2       1      40 [.       3      44 ..       2      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0084
                                       -TTTH--.SSEEEETTT--EEE-TTT..T.-HHHHHHHHH--- CS
                             zf-UBP  1 CseCnsenknlWlCLkCghvgCgrks..n.ghalkHyeetrHp 40
                                       C+ C+++ + l  C++Cg+++C   s  + +h+  H+ + rH 
  gene1672|gene1672|rna1671|rna1671  3 CQYCEAA-EFLIECITCGKHFCNSHSasSiSHIVFHLVKARHK 44
                                       8999976.67777**********6654446*******999985 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   6.5   0.00015      0.13       1      29 [.       3      28 ..       3      33 .. 0.88
   2 ?    0.3   0.1      0.92   7.8e+02      14      21 ..      52      59 ..      42      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                             zf-AN1  1 CsfksCkkkdflpfkCryCgkvFClkHrl 29
                                       C++  C   +f  ++C +Cgk+FC +H  
  gene1672|gene1672|rna1671|rna1671  3 CQY--CEAAEF-LIECITCGKHFCNSHSA 28
                                       885..*99999.89*************75 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.92
                             zf-AN1 14 fkCryCgk 21
                                       +kCr+Cg+
  gene1672|gene1672|rna1671|rna1671 52 IKCRKCGE 59
                                       79****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.96u 0.29s 00:00:01.25 Elapsed: 00:00:00.54
# Mc/sec: 4329.51
//
Query:       gene1673|gene1673|rna1672|rna1672  [L=644]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1212  (0.0676); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3730.19
//
Query:       gene1674|gene1674|rna1673|rna1673  [L=430]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 3145.91
//
Query:       gene1675|gene1675|rna1674|rna1674  [L=450]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-45  152.9   0.1    1.4e-44  151.9   0.1    1.5  1  DEAD           DEAD/DEAH box helicase
    9.1e-25   87.2   0.3    5.7e-24   84.6   0.1    2.3  3  Helicase_C     Helicase conserved C-terminal domain
    7.6e-10   39.1   0.0    1.8e-09   37.8   0.0    1.6  1  ResIII         Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.026   13.7   0.0    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
      0.054   13.8   0.5       0.19   12.0   0.5    1.9  1  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.9   0.1   3.9e-48   1.4e-44       2     172 ..      26     191 ..      25     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 3.9e-48
                                        HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                        +iQ+++ip +l+g+d++++ +TG+GKTlaflip+lq++++   ++++g  +liv+PtreLa q+++ l++++k+++
  gene1675|gene1675|rna1674|rna1674  26 EIQQRVIPVALEGNDIIGSSQTGTGKTLAFLIPILQRLTDLqwRREDGLGCLIVTPTRELALQIFDVLTRVGKHTT 101
                                        79************************************888999******************************** PP

                                        SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH.HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  76 lrvlliiggvaardqlskldngvdivvgtpgrlddll.stgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                        l++ li+ggv+a+++  k+ +++ i++ tpgr++++l ++  l+++++++lVlDEad++ ++gf++ ++ il+ + 
  gene1675|gene1675|rna1674|rna1674 102 LNAGLIMGGVEAENESLKI-STMSILICTPGRFLQHLqENPCLKTENIQILVLDEADKMIEMGFKEILEDILEYI- 175
                                        *******************.9****************4455599*******************************. PP

                                        HHCTTSTTTSEEEEEESSBSHH CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD 151 qitcdgklqrqvivlSATlpkd 172
                                              ++++q++++SAT++ +
  gene1675|gene1675|rna1674|rna1674 176 ------PSKKQTLLFSATPKAS 191
                                        ......45567*******9843 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.7   9.7e+03      13      35 ..      70      93 ..      60     129 .. 0.53
   2 ?   -0.9   0.0      0.58   2.1e+03       6      35 ..     168     196 ..     163     217 .. 0.63
   3 !   84.6   0.1   1.6e-27   5.7e-24       1     110 [.     227     337 ..     227     338 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                                       TTTTSEEEEEESSHH.HHHHHHHH CS
                         Helicase_C 13 eeeggkilifvntid.rlekvkll 35
                                       +e+g  +li+++t++  l+ +++l
  gene1675|gene1675|rna1674|rna1674 70 REDGLGCLIVTPTRElALQIFDVL 93
                                       555666778888887533323333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                                        HHHHHHHTTTTSEEEEEESSHHHHHHHHHH CS
                         Helicase_C   6 llellkleeeggkilifvntidrlekvkll 35 
                                        l ++l+   +++++l+f+ t +    +++l
  gene1675|gene1675|rna1674|rna1674 168 LEDILEYIPSKKQTLLFSATPKAST-ARIL 196
                                        4445555578999999999988442.3444 PP

  == domain 3  score: 84.6 bits;  conditional E-value: 1.6e-27
                                        HHHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                         Helicase_C   1 dkleallellkleeeggkilifvntidrlekvklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                        dk+++l  ++ +++ + k ++f  t+++++  +ll e+     +v +l g ++q++r++++++f k++  +L +td
  gene1675|gene1675|rna1674|rna1674 227 DKISYLHTFI-RSNPEVKGIVFFSTCKEVKFHHLLFERLklRNRVFCLSGGISQRQRIDTFKRFVKEKNGILFCTD 301
                                        6889999998.899999**********99765555444445789********************998888****** PP

                                        GGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                         Helicase_C  75 vaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                         ++rG+d+pkv++Vi++d+p nv++y++r+GRt+R 
  gene1675|gene1675|rna1674|rna1674 302 LGSRGLDFPKVDVVIQYDCPCNVETYVHRVGRTARN 337
                                        ***********************************7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   5.1e-13   1.8e-09      31     170 ..      45     189 ..      23     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.1e-13
                                        ESTTSTHHHHH.HHHHHHH-S.........-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--..... CS
                             ResIII  31 maTGtGKTlva.aklierllkkgkee....kflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekds 101
                                          TGtGKTl   + + +rl+  ++++     +l++ p+++l  q  + ++++ + ++ ++g ++ g + ++++ ++
  gene1675|gene1675|rna1674|rna1674  45 SQTGTGKTLAFlIPILQRLTDLQWRRedglGCLIVTPTRELALQIFDVLTRVGKHTTLNAGLIMGGVEAENESLKI 120
                                        68*******9988999999988888789****************************9997777777777777779* PP

                                        ..-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS....TTTHHHHHT-.--SEEEEEESS-S CS
                             ResIII 102 tnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak...kswreilekf.keavllglTATpe 170
                                        ++++il+ t  ++ +++    +e+  l+ +++++++ DEa ++ ++   +  + ile++ +++  l ++ATp+
  gene1675|gene1675|rna1674|rna1674 121 STMSILICTPGRFLQHL----QENPCLKTENIQILVLDEADKMIEMgfkEILEDILEYIpSKKQTLLFSATPK 189
                                        *****************....777788888888************766446666799996568889******7 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-06     0.026      84     151 ..     272     337 ..     227     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                      ERCC3_RAD25_C  84 yiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLra 151
                                         + G +s+++r++ +++f k++    +f   +g   +D+P+  v+iq +           r+Gr  r 
  gene1675|gene1675|rna1674|rna1674 272 CLSGGISQRQRIDTFKRFVKEK-NGILFCTDLGSRGLDFPKVDVVIQYDCPCNV-ETYVHRVGRTARN 337
                                        478***************8875.5689********************8876544.3445666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   5.2e-05      0.19      75     132 ..     125     189 ..      44     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.2e-05
                             AAA_22  75 seell.ealeqalrarav.....ielliiDEaqhlrs...eealeeLrsllnlsrkgvqliLvGtpe 132
                                           +   ++ q+l++        i++l++DEa+++++   +e+le++ +     +k+ +l++  tp+
  gene1675|gene1675|rna1674|rna1674 125 ILICTpGRFLQHLQENPClktenIQILVLDEADKMIEmgfKEILEDILEYI--PSKKQTLLFSATPK 189
                                        555666677777877777888889**********87434677777764443..47777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 2411.02
//
Query:       gene1676|gene1676|rna1675|rna1675  [L=422]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-88  296.3   0.0    3.1e-88  295.9   0.0    1.2  1  Enolase_C  Enolase, C-terminal TIM barrel domain
      2e-37  128.3   0.0      3e-37  127.7   0.0    1.3  1  Enolase_N  Enolase, N-terminal domain
    3.4e-06   26.8   0.0    5.4e-06   26.1   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
     0.0097   15.1   0.1      0.018   14.2   0.1    1.4  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.9   0.0   6.8e-92   3.1e-88       3     279 ..     155     421 ..     153     422 .] 0.97

  Alignments for each domain:
  == domain 1  score: 295.9 bits;  conditional E-value: 6.8e-92
                                        EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SS CS
                          Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqs 78 
                                         +P+P +nv+nGG h+gn++ +qe m++    + ++  + +G+ +y++lk+ +++kyg   t+vGdeGGfaP +++
  gene1676|gene1676|rna1675|rna1675 155 KMPIPHFNVLNGGVHSGNAMTVQEIMVVYQ-HNDLERNIECGCVLYESLKKTISEKYGVLHTSVGDEGGFAPPIEK 229
                                        59************************9965.678999*************************************** PP

                                        HHHHHHHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-.EEE CS
                          Enolase_C  79 nkealdliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyP.ivs 153
                                         +++ldli ea  +   ++++kia+d a+ ef  ++d+ky+ld++          t+ +l + y e+++kyP i+s
  gene1676|gene1676|rna1675|rna1675 230 LEDGLDLILEASRRC-NRTDMKIAIDFAANEFT-RDDGKYELDGEV--------YTTRDLGEKYMEVIRKYPqIYS 295
                                        ***********8776.5789************9.778******998........8999**************899* PP

                                        EES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT- CS
                          Enolase_C 154 iedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagy 229
                                        +edp+ e+d+++w+ + +++gdk+ ivGddlt tnp+ +++a  +k++n+ll+k nqiG+++e+++a+k+a++ g 
  gene1676|gene1676|rna1675|rna1675 296 LEDPFSEKDYDGWRWINAKVGDKINIVGDDLTATNPQLVENAGLRKMCNTLLVKPNQIGTISETIKAIKIARKYGM 371
                                        **************************************************************************** PP

                                        EEEEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHH CS
                          Enolase_C 230 gvvvshrsGetedttiadlavglsaGqiktGaparserlakynqllriee 279
                                         ++vshrsGeted +i+dl+vg+ a  +k+Gap+r er++kynqllr++e
  gene1676|gene1676|rna1675|rna1675 372 KIMVSHRSGETEDHFISDLSVGVGAEYMKSGAPCRGERVSKYNQLLRLNE 421
                                        ***********************************************987 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.0   6.7e-41     3e-37       3     127 ..      19     142 ..      17     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 6.7e-41
                                        EEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHH.T CS
                          Enolase_N   3 kvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapal.i 77 
                                        ++k r il SrG pTvev+++t +g+  r+++psGaS g+kea+ + Dg  + y+g+gv+ +++n+n++ ++ l +
  gene1676|gene1676|rna1675|rna1675  19 SIKSRMILTSRGYPTVEVDLITGKGV-YRSSCPSGASRGSKEAVVISDG-GNLYNGRGVRAVINNINDISRSLLeL 92 
                                        799*******************9885.6********************9.89****************99999944 PP

                                        TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-H CS
                          Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelpl 127
                                        +++++dq++iD++l++lDgt+nksk+G+N i+a+S A++k++A +++  +
  gene1676|gene1676|rna1675|rna1675  93 EYNAADQQNIDNFLLDLDGTNNKSKIGGNGIIALSTAFCKMGAGYSNKRV 142
                                        9******************************************9988765 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.2e-09   5.4e-06      63     155 ..     284     376 ..     207     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-09
                                        HHHHHHHGGGTESEEESSSSTTTHHHHHHHHHH.HH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSH CS
                           MR_MLE_C  63 irvareleeldllwlEEPvppeddleglaelra.ra.sipiaagEslys.radfrelleagavdivqpdvsrvgGi 135
                                        ++v+r+  + +++ lE+P++   d++g +++ a    +i i+++   ++ ++ ++++  ++ +  + ++++++g i
  gene1676|gene1676|rna1675|rna1675 284 MEVIRKY-P-QIYSLEDPFSE-KDYDGWRWINAkVGdKINIVGDDLTATnPQLVENAGLRKMCNTLLVKPNQIGTI 356
                                        4455555.3.6999******9.67********964479******98887588888888999*************** PP

                                        HHHHHHHHHHHHTT-EEEEB CS
                           MR_MLE_C 136 tearkvaalaeafgvpvapH 155
                                        +e++k +++a+++g+++++ 
  gene1676|gene1676|rna1675|rna1675 357 SETIKAIKIARKYGMKIMVS 376
                                        ***************98765 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   4.1e-06     0.018     135     203 ..     314     383 ..     307     400 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-06
                             MAAL_C 135 ekgikvelvaDeWcntledirefvd.aeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetd 203
                                        + g k+++v D+ + t  ++ e +  ++ ++ + +k   +G+i++ti+a+ ++++ g+++++   + et+
  gene1676|gene1676|rna1675|rna1675 314 KVGDKINIVGDDLTATNPQLVENAGlRKMCNTLLVKPNQIGTISETIKAIKIARKYGMKIMVSHRSGETE 383
                                        567899********999998877753789*******************************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.53
# Mc/sec: 2383.25
//
Query:       gene1677|gene1677|rna1676|rna1676  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-14   54.4   2.6    1.4e-14   54.1   2.6    1.1  1  Rpr2      RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   2.6   7.9e-19   1.4e-14       3      72 ..      10      77 ..       8      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 7.9e-19
                                       HHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E CS
                               Rpr2  3 nfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkk 72
                                        +Ly  a       +p+++r+ +k+++ +s+k+q+rl++++krtvC  C ++lipg++c  rv +++++ 
  gene1677|gene1677|rna1676|rna1676 10 MYLYCTAFR--TVGIPSVHRRKMKKIKMISNKYQIRLSREIKRTVCPGCYTILIPGFNCVSRVTREENGL 77
                                       577766664..7899************************************************9866654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 640.26
//
Query:       gene1678|gene1678|rna1677|rna1677  [L=631]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-80  269.4   0.1    3.1e-80  269.4   0.1    2.0  3  Dynamin_M    Dynamin central region
    2.2e-53  180.8   0.8    5.1e-53  179.6   0.8    1.7  1  Dynamin_N    Dynamin family
    2.1e-24   85.5   6.7    6.4e-24   83.9   6.7    1.9  1  GED          Dynamin GTPase effector domain
    1.6e-05   24.9   0.1    4.4e-05   23.5   0.1    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.034   13.1   0.0      0.084   11.8   0.0    1.8  2  PAP_central  Poly(A) polymerase central domain
      0.067   13.1   1.1        2.4    8.0   0.2    2.5  2  RsgA_GTPase  RsgA GTPase
        0.2   11.0   2.4        5.6    6.2   0.3    2.6  2  AIG1         AIG1 family


Domain annotation for each model (and alignments):
>> Dynamin_M  Dynamin central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.1       2.2   5.6e+03     227     250 ..      88     111 ..      72     115 .. 0.72
   2 !  269.4   0.1   1.2e-83   3.1e-80       1     282 [.     215     495 ..     215     498 .. 0.97
   3 ?   -2.4   0.2      0.84   2.1e+03     111     111 ..     570     570 ..     510     611 .. 0.59

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.2
                          Dynamin_M 227 kelkrFpnLreeikevvedllreq 250
                                        k ++ F ++++ei + ++++l+++
  gene1678|gene1678|rna1677|rna1677  88 KRYTDFDEVKKEIIKETNRILKSK 111
                                        366778888888888888888766 PP

  == domain 2  score: 269.4 bits;  conditional E-value: 1.2e-83
                          Dynamin_M   1 vvdilenkvipLklGYvgVvnRsqkdInkkksieealkkEkaFFeshpayrkladkaGtpyLakkLnqiLvehIrk 76 
                                        vvdil++++i L+lG+v VvnRsq+dI+k+k i++alk+E+ FF++h++y++ + ++Gt yL+ kL++iL ehIr+
  gene1678|gene1678|rna1677|rna1677 215 VVDILAGRIICLRLGFVPVVNRSQQDIEKNKGIQQALKDEEVFFSTHESYKRNKAYCGTSYLIAKLHNILHEHIRQ 290
                                        79************************************************************************** PP

                          Dynamin_M  77 slPelkkkineklqklekeleelgeskpsdeektklllqlitkfkedfkklieGesevstkelsggarireiFnet 152
                                        +lP+l+++in+ + +++++l+ lg+      + ++ ++++i+ +++ f+++++G+ e + +el ggar+++ Fn++
  gene1678|gene1678|rna1677|rna1677 291 CLPDLQERINSGMIDAQNNLRDLGNVCL---SPKENVMRIINGVSKRFSDILSGNVESKGNELMGGARLNYAFNHH 363
                                        ************************9765...68999*******************8877***************** PP

                          Dynamin_M 153 lekslekidpleelsdeeirtairnsrGrelplfvpekaFealvkkqikkleepalkcvelVyeelekiveklek. 227
                                        ++k ++++ +l+++ de+ir +++ns+G+++ l++ ++aFe+l++  ++ +++++lk+v +V++el ++++++ + 
  gene1678|gene1678|rna1677|rna1677 364 FSKFINRLGALDNIHDEQIRALLYNSSGSSSVLLFGQAAFEKLARVSVESFKPHSLKLVSIVFSELVRMIKHIVDg 439
                                        ************************************************************************7777 PP

                          Dynamin_M 228 .elkrFpnLreeikevvedllreqeeptkemienliemelayintnhpdfigalka 282
                                         +++r+p+L e+i +   ++++e+ + t++++e++i+++++yi t+hpdfi+ ++ 
  gene1678|gene1678|rna1677|rna1677 440 sTMSRYPALGERIISSAIRMFKERCDATHKLVESFIDWNTGYISTKHPDFIKWSEM 495
                                        9**************************************************98876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.84
                          Dynamin_M 111 k 111
                                        +
  gene1678|gene1678|rna1677|rna1677 570 A 570
                                        1 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.6   0.8     2e-56   5.1e-53       1     168 []      32     206 ..      32     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 2e-56
                                        EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEECCT---CCS...SSEEEE..T-EB--CHHHHHHHHH CS
                          Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplelqlgeeeeaseravkeelkek..ekkledfsevreeiek 74 
                                        i+v+GsqSsGKSSvl++++g+dilprg++++Trrpl+lql +++++        + ++  ek+++df+ev++ei k
  gene1678|gene1678|rna1677|rna1677  32 IVVIGSQSSGKSSVLENIIGRDILPRGTGIVTRRPLILQLIHSKTED-----HAVFNHfpEKRYTDFDEVKKEIIK 102
                                        89****************************************99933.....3333333688************** PP

                                        HHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTS.........HHHHHHH.STTEEEEEEEETTS CS
                          Dynamin_N  75 etekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdq.........elvkeyi.kkadiilavtsanh 140
                                        et++i ++++++s ++i+lk +s +v +ltlvDlPGl +v+++dq         e++++y+ +k+++ilav+san+
  gene1678|gene1678|rna1677|rna1677 103 ETNRILKSKNDVSPQPIILKYYSSKVLTLTLVDLPGLVRVPTNDQpkdictkitEMCRKYVsNKNALILAVSSANT 178
                                        **************************************************************************** PP

                                        -CCC-CHHHHHHHHSTTBTTEEEEEE-C CS
                          Dynamin_N 141 dlsnsealflarevdpkgkrtivvltkl 168
                                        d+sns+al+larevd + +rti+vltk+
  gene1678|gene1678|rna1677|rna1677 179 DISNSDALQLAREVDHNYERTIGVLTKV 206
                                        **************************96 PP

>> GED  Dynamin GTPase effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   6.7   2.5e-27   6.4e-24       2      91 ..     541     630 ..     540     631 .] 0.98

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 2.5e-27
                                        XXXXTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHCCCCCHHHCCTTSGGGHHHHT---SCHCCCCHHHHH CS
                                GED   2 eeseveeirslvksYfnivrktiadqiPkaimhllvneakeslqkellakLykkedldeLLkEdeeiaekRkelkk 77 
                                        e++e+ +i+s+v+sYf+i++k + dq+Pkaim+ lv++a++slq+ l+ ++y++ed+d++ +E+ee++ +R ++++
  gene1678|gene1678|rna1677|rna1677 541 ETIEISMIKSMVESYFEITKKIVVDQVPKAIMCELVKKAENSLQETLFMEIYNREDIDTIASESEEVKMERSRIES 616
                                        7899************************************************************************ PP

                                        HHHHHHHHCCCCCH CS
                                GED  78 rlealkkAreilse 91 
                                        +l+alk+A++i+ +
  gene1678|gene1678|rna1677|rna1677 617 MLKALKQAYDIICS 630
                                        ***********986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   1.7e-08   4.4e-05       1     102 [.      31     190 ..      31     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.7e-08
                                        EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE............................. CS
                           MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke............................. 47 
                                        +++++G   +GKS+++  ++g+      +  +Tr +   ++ ++++e                             
  gene1678|gene1678|rna1677|rna1677  31 QIVVIGSQSSGKSSVLENIIGRDILPRGTGIVTRRPLILQLIHSKTEdhavfnhfpekrytdfdevkkeiiketnr 106
                                        589*******************9999**********888877454335788999999999999999999******* PP

                                        ........................EEEEECGGCSS..HHHHHH.......HHHHHHHHHHCTSEEEEEEETTTTCS CS
                           MMR_HSR1  48 ........................ielvDtpGlie..gaseek.......glgkaflaleeadlillvvdaseekl 90 
                                                                ++lvD+pGl+   ++++ k       ++ +++ ++++  lil v +a+ +++
  gene1678|gene1678|rna1677|rna1677 107 ilkskndvspqpiilkyysskvltLTLVDLPGLVRvpTNDQPKdictkitEMCRKYVSNKN-ALILAVSSAN-TDI 180
                                        ********************************96334223333123322345555555544.5666666544.323 PP

                                        HHHHHHHHHHHH CS
                           MMR_HSR1  91 kpldeeleelle 102
                                           +++  +l +
  gene1678|gene1678|rna1677|rna1677 181 --SNSDALQLAR 190
                                        ..3334444433 PP

>> PAP_central  Poly(A) polymerase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   2.7e+03      40      74 ..     147     186 ..     117     200 .. 0.68
   2 ?   11.8   0.0   3.3e-05     0.084      12      59 ..     237     331 ..     231     569 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                                        xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
                        PAP_central  40 kreevlekleklvkefvkk.....lkevpedldlkddslL 74 
                                        + +++ +k++++++++v++     l+  + ++d+++++ L
  gene1678|gene1678|rna1677|rna1677 147 QPKDICTKITEMCRKYVSNknaliLAVSSANTDISNSDAL 186
                                        5567788888888888888777764445555555555544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.3e-05
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxx...................... RF
                        PAP_central  12 tekdlklteeLieeLkeqnlfeseeetkkree.......vlekleklvkefvkk...................... 58 
                                        +++d+++++ ++++Lk++++f s++e+ kr++        ++kl+++++e +++                      
  gene1678|gene1678|rna1677|rna1677 237 SQQDIEKNKGIQQALKDEEVFFSTHESYKRNKaycgtsyLIAKLHNILHEHIRQclpdlqerinsgmidaqnnlrd 312
                                        689****************************999999999************999888766666554444444444 PP

                                        ..................x RF
                        PAP_central  59 ..................l 59 
                                                          +
  gene1678|gene1678|rna1677|rna1677 313 lgnvclspkenvmriingV 331
                                        4444444444444444440 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.03        78      92     123 ..      22      53 ..       8      64 .. 0.83
   2 ?    8.0   0.2   0.00093       2.4       6     104 ..     156     258 ..     151     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.03
                                        HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                        RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallpel 123
                                        +++++++   +v++G+   GKS++++++++++
  gene1678|gene1678|rna1677|rna1677  22 SISNKIELPQIVVIGSQSSGKSSVLENIIGRD 53 
                                        5677777778899************9998864 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00093
                                        -EETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH...HHHHHHHHHHHTT.S CS
                        RsgA_GTPase   6 nelvrpkvaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee...eleelkeelealg.y 77 
                                        +e+ r+ v+N + l++ vs ++ ++s++   ++  ++ ++  + + vl+K+Dl+++ +   ++ + +    +lg +
  gene1678|gene1678|rna1677|rna1677 156 TEMCRKYVSNKNALILAVSSANTDISNSDALQLAREVDHNYERTIGVLTKVDLMDSGTdvvDILAGRIICLRLGfV 231
                                        78999***********999999999999888888888888888888********9998655444445556666745 PP

                                        EEEE--TTTHTTHHHHHHHCTTSEEEE CS
                        RsgA_GTPase  78 evllvsaktkegleelkellkdktsvl 104
                                        +v+  s+++ e+ + ++++lkd+ +++
  gene1678|gene1678|rna1677|rna1677 232 PVVNRSQQDIEKNKGIQQALKDEEVFF 258
                                        666777777788888999988876655 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3    0.0022       5.6       2      25 ..      31      54 ..      30      65 .. 0.91
   2 ?    3.6   0.1     0.014        35      49     101 ..     129     185 ..     100     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0022
                                       EEEEESSTTSSHHHHHHHHHTS-- CS
                               AIG1  2 tivlvGktgnGkSaTgNsilgkka 25
                                       +iv++G   +GkS+   +i+g+++
  gene1678|gene1678|rna1677|rna1677 31 QIVVIGSQSSGKSSVLENIIGRDI 54
                                       69*******************975 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                                        EEEEEEE--SCCCT..TCCHHCHHHHHHH.HHHHCTT-ESEEEEEEETT.B-SHHHH CS
                               AIG1  49 kkinViDTPglfdl..svsadkiskeivr.clllseegihalllvlslg.rfteede 101
                                         ++  +D Pgl+ +  +++ ++i+ +i++ c ++ ++    +l v s++ ++++ d 
  gene1678|gene1678|rna1677|rna1677 129 LTLTLVDLPGLVRVptNDQPKDICTKITEmCRKYVSNKNALILAVSSANtDISNSDA 185
                                        67899******6651156889999999873555555544445555666667776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1040  (0.0580066); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4393.33
//
Query:       gene1679|gene1679|rna1678|rna1678  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.9e-20   71.3   0.4    1.9e-19   70.2   0.4    1.5  1  DcpS_C      Scavenger mRNA decapping enzyme C-term binding
    6.5e-09   36.6   0.1    1.8e-08   35.2   0.1    1.7  1  DcpS        Scavenger mRNA decapping enzyme (DcpS) N-terminal
  ------ inclusion threshold ------
      0.014   16.1   0.1      0.034   14.9   0.1    1.6  1  HIT         HIT domain
       0.02   14.6   0.0      0.052   13.2   0.0    1.7  1  Spore_YhaL  Sporulation protein YhaL
      0.059   13.5   0.0       0.19   11.9   0.0    1.8  2  FAM150      FAM150 family


Domain annotation for each model (and alignments):
>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.2   0.4   5.2e-23   1.9e-19       2     108 ..     134     244 ..     133     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 5.2e-23
                                        -HHHHHHTTSS..-B-EEEE-SSEEEEE-SS....-SSSEEEEEEESS.---SGGG--TTTTTHHHHHHHHHHHHH CS
                             DcpS_C   2 wvfnilakgke..pervvyedekfvvlkDik....pkaklhllvipkr.dikslrdLtkehlpllkemrekakkvi 70 
                                        w+ ni  k+k   +e+++yed ++++++D+k    + ++lhll+i k+  +k++rd++  + ++l + +eka +v+
  gene1679|gene1679|rna1678|rna1678 134 WMDNITLKNKRnvNENILYEDGEIMIIPDYKwncqNIDALHLLIIFKDlGLKTVRDID--NWEILVRAQEKASNVL 207
                                        77777666666579*****************965444********************8..89************** PP

                                        HHTT-T-EEEEE--SCCCT--S-S--EEEEE....... CS
                             DcpS_C  71 eekynevdaeelrvgvhyqPsvyhlHlHvisldfespg 108
                                        e ++ ++d +++ +++hy+P++ +lH+Hvi+++   +g
  gene1679|gene1679|rna1678|rna1678 208 ETMF-SLDFNHVFMFFHYRPTYLRLHIHVINIKIAYEG 244
                                        9999.78************************9877665 PP

>> DcpS  Scavenger mRNA decapping enzyme (DcpS) N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   4.9e-12   1.8e-08      23     102 ..      39     107 ..      18     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.9e-12
                               DcpS  23 llGtidsepAililektafeteeaaklaslkesleelknlgandiYtwllavlkqkeeelpdlkinliyPatekhi 98 
                                         +G+i++++Aili+ +++ ++++     ++ +    ++n+++n+iY+++ ++          +   +iyPate hi
  gene1679|gene1679|rna1678|rna1678  39 YIGRIRDKKAILIFPRQSVSKDTF---IQFLSL--PMENIQSNNIYYSYRVLG------PIYINFRVIYPATEDHI 103
                                        359*****************9994...333322..34679**********933......5889999********** PP

                               DcpS  99 kKYs 102
                                        kKYs
  gene1679|gene1679|rna1678|rna1678 104 KKYS 107
                                        ***8 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   9.6e-06     0.034       3      93 ..     145     236 ..     143     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.6e-06
                                        CC-CCEEEE-SSEEEEE-SS-SSS....SEEEEEESS.TGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEE CS
                                HIT   3 eipstvvyeddlvlafldidpkap....ghlLvipkk.hlselhdlteeelakllsavkkvakalqkkfknkglrv 73 
                                        + +++++yed +++++ d +   +     hlL+i k+  l+++ d++      l++a +k  ++l++ f+ ++ +v
  gene1679|gene1679|rna1678|rna1678 145 NVNENILYEDGEIMIIPDYKWNCQnidaLHLLIIFKDlGLKTVRDID--NWEILVRAQEKASNVLETMFSLDFNHV 218
                                        56788999999999998876544322228******************..566688888888888999999999999 PP

                                        EEEESGGGT-SSSS-EEEEE CS
                                HIT  74 vinngahagqsvahlHiHvi 93 
                                        ++   +h  ++   lHiHvi
  gene1679|gene1679|rna1678|rna1678 219 FM--FFHYRPTYLRLHIHVI 236
                                        99..9**************9 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.052      21      50 ..      19      48 ..      17      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                         Spore_YhaL 21 ktakeEreldqefIEkEGevylerleeere 50
                                       k   +E  ldq+ +++EG+ y+ r++ +++
  gene1679|gene1679|rna1678|rna1678 19 KDIIKEFILDQSLVNSEGNLYIGRIRDKKA 48
                                       667789999*****************9986 PP

>> FAM150  FAM150 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.3e-05      0.19      37      79 ..      28      70 ..       9      84 .. 0.85
   2 ?   -2.4   0.0       1.4   5.1e+03     100     107 ..     263     270 ..     254     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                             FAM150 37 dysleekekkdykksqdeqrvieivpRDlrmkekFlkhltGpl 79
                                       d sl ++e + y  +  +++ i i+pR    k+ F+++l+ p+
  gene1679|gene1679|rna1678|rna1678 28 DQSLVNSEGNLYIGRIRDKKAILIFPRQSVSKDTFIQFLSLPM 70
                                       6778888999999999999999****************98665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                             FAM150 100 tiPayykR 107
                                        t P+yyk+
  gene1679|gene1679|rna1678|rna1678 263 TDPSYYKK 270
                                        7899**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1666.47
//
Query:       gene1680|gene1680|rna1679|rna1679  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-94  316.9   0.0      2e-94  316.7   0.0    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  316.7   0.0   1.1e-98     2e-94       4     367 .]      28     406 ..      21     406 .. 0.92

  Alignments for each domain:
  == domain 1  score: 316.7 bits;  conditional E-value: 1.1e-98
                                        HHHHHHHHS-HHHHHHHTT----HHHHHHHSSS---------EEE.EEEEETTEEEEEEE---STTHHHHHHHHHH CS
                        HMG-CoA_red   4 eRrklleelteeeleelkeesldeevadkmiEnviGyvqlPlGva.gpllingkeylvPmAteEgslvAsasrgak 78 
                                        + r+ +ee t+ ++  +++e+  +ev+++++En+iGy ++PlGv  + +lin++e+++P+At+Eg+lvAs++rg+k
  gene1680|gene1680|rna1679|rna1679  28 KLRERIEEATGIRIGGVEYEEDYSEVINRCCENLIGYKKVPLGVSsRGVLINNREFFIPIATTEGALVASMNRGIK 103
                                        34455566777777777666666*********************8689**************************** PP

                                        HHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHHHTHHHHHHHHHHCSHHCCT-EEEEEEE.EE-SSEEEEE CS
                        HMG-CoA_red  79 ainesgGvkttvlkdgmtraqvvllesvedaaelkkwiekkeeleelanaaestsrggglkdiev.vlagrlvvlr 153
                                        ++n++gGv+ +  + g+tr+ +++++++ +a ++ +wi+ +e + +l++  ++ sr+ ++++ie  +++g+ v+++
  gene1680|gene1680|rna1679|rna1679 104 LMNACGGVEGYAENIGITRGFIMRFKTFGEAMRFYQWIKVEESVANLKRIGNKGSRYLRINKIESkHVVGEDVYIK 179
                                        **************************************************************************** PP

                                        EEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHH CS
                        HMG-CoA_red 154 lkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekilk 229
                                        ++ ++gDAmG+Nm++ka+ ++++ i++ f++++l+si+sN+ctdkk+s +n+++grg+++ +++ i ++ +++i+ 
  gene1680|gene1680|rna1679|rna1679 180 VYGYSGDAMGMNMITKACVQISSEITRMFPNSSLVSISSNTCTDKKWSGENYCNGRGRRIFMNIKIDDKNCREIIG 255
                                        **************************************************************************** PP

                                        HHHHHHH-HHHH...HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTTSEEETTTEEEEEEEEE.--- CS
                        HMG-CoA_red 230 asaealvdlnra.nigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaaleevedgdlygsvtlPsleV 304
                                        +  ++++d++++  ++      ggfn++aaN++a +flA GqDl +v ess+++ ++++++ + l +s+ +Ps+ V
  gene1680|gene1680|rna1679|rna1679 256 VGIDKILDVYHSkVVVGGSLVLGGFNCQAANYVAGMFLALGQDLGQVIESSNCVLSMKKFTADVLSVSLFMPSVTV 331
                                        ************544444444488************************************8888************ PP

                                        -SBSHHHHH-HHHHHHHHTT---HH...............HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                        HMG-CoA_red 305 GtvGGgtklppqaellkllgvkgak............nakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                        G++GGgt+l+p +++lk  +  + +                L   + +++L +els+l +La++ l+++H++l+r
  gene1680|gene1680|rna1679|rna1679 332 GVIGGGTHLEPSKSFLKQFNKGNDDyiitnkdedkssGPGYLGLAVGTAVLGGELSLLGSLANNTLMESHLRLNR 406
                                        ****************5555544445999999886544457********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      645  (0.0359752); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2543.15
//
Query:       gene168|gene168|rna168|rna168  [L=615]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-13   49.9   0.2    5.6e-13   49.3   0.2    1.3  1  Nucleoporin2  Nucleoporin autopeptidase


Domain annotation for each model (and alignments):
>> Nucleoporin2  Nucleoporin autopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.2   3.1e-17   5.6e-13       5     144 ..     484     615 .]     480     615 .] 0.85

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 3.1e-17
                                    EEES-HHHHHTS-HHHHTSBSS-EEEETTTEEEEESS-B--GGG-HHHHBTTTEEEETTEEEESSSCCC.---TTSTT-S CS
                   Nucleoporin2   5 ytePsleeLkkmseeelsavkdFtvgrkgvGsveFlepvdlssldldeiagkivklekkevtVYpdeekekppvGegLNk 84 
                                    yt P++e++k+m     ++v+++++g ++ G++e+l++v+ s++++ +i ++ + ++k++v+V  +      pvG gLN+
  gene168|gene168|rna168|rna168 484 YTIPPIEDIKHM-----REVHNLIIGFEDKGRIEYLDTVNASEITMANI-QSKIYFSKESVVV--N-----DPVGVGLNR 550
                                    788888888766.....67******************************.8889999999998..2.....489****** PP

                                    -EEEEESS---B-TTT--B---TT-H.....HHHHHHHHHHH-SSSEEEEEETTTTEEEEEES-- CS
                   Nucleoporin2  85 paeitLenvwpkdkatkeeikdkska.....rvkkhieklkkvegteFvsydpetgtwtfkVeHF 144
                                    +a++++e+v+p +++  + ik ++k+       ++++  lk+ +  +Fv y+ e+gt++++V+HF
  gene168|gene168|rna168|rna168 551 RARVYVEGVFPYSRSLGDYIKGEQKQfplkgIQERFVYGLKNDTVKKFVGYEYERGTYVYDVNHF 615
                                    ************9997777776666532222466788889999*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 3647.24
//
Query:       gene1681|gene1681|rna1680|rna1680  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-13   49.0   1.3    3.7e-13   49.0   0.2    1.7  2  ubiquitin    Ubiquitin family
    0.00078   19.8   0.8     0.0039   17.6   0.1    2.5  2  Ubiquitin_2  Ubiquitin-like domain
     0.0016   18.6   0.2     0.0032   17.6   0.2    1.5  1  RPN13_C      UCH-binding domain
     0.0047   16.9   0.2      0.013   15.5   0.2    1.8  1  Ubiquitin_4  Ubiquitin-like domain
     0.0048   16.8  10.0       0.59   10.1   0.5    2.6  2  STI1         STI1 domain
     0.0068   16.3   0.0      0.017   15.1   0.0    1.7  1  UBA          UBA/TS-N domain
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.028   14.2   0.1    1.6  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
       0.12   12.4   0.1       0.24   11.4   0.1    1.4  1  HOIP-UBA     HOIP UBA domain pair
       0.36   10.8   2.8       0.68    9.9   0.0    2.6  3  Prefoldin_2  Prefoldin subunit


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.2   1.9e-16   3.7e-13      17      69 ..      20      73 ..       5      76 .. 0.91
   2 ?   -3.6   0.1       4.8   9.5e+03      15      26 ..     223     234 ..     222     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.9e-16
                                       TTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE.-TTSBHGGHTTSTTEEEEEEE CS
                          ubiquitin 17 esdtveelKekiaekegipaeqqrLiysGkvL.edertleeygiqdgstlhlvl 69
                                        +dt+e+lK +i+e +g+p+++q L+++ ++L ++++ l+e+gi++++tlhl  
  gene1681|gene1681|rna1680|rna1680 20 MTDTLESLKLRIQEITGVPVDSQVLLFNDRILsDNNKELKELGIENDCTLHLKK 73
                                       59******************************888999*************965 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                                        EETTSBHHHHHH CS
                          ubiquitin  15 veesdtveelKe 26 
                                        v+ +d+++elK+
  gene1681|gene1681|rna1680|rna1680 223 VKYKDKLAELKQ 234
                                        566788888886 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1     2e-06    0.0039      22      80 ..      20      71 ..       3      76 .. 0.86
   2 ?   -1.1   0.0       1.3   2.6e+03      28      49 ..     134     154 ..     124     167 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                       TTSBHHHHHHHHHHHH---TTCEEEEEE.-SSSSEEECSSGCCSBCCCCT--TTEEEEE CS
                        Ubiquitin_2 22 ksltieelKekLelitGtspasmrLqlyddkkdnevsklddddalLgsYgvkdgmrihV 80
                                        ++t+e+lK +++ itG++++s+ L +           l+d+++ L++ g+++ +++h 
  gene1681|gene1681|rna1680|rna1680 20 MTDTLESLKLRIQEITGVPVDSQVLLFN-------DRILSDNNKELKELGIENDCTLHL 71
                                       578**********************887.......236799999999999999999996 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                        HHHHHHHHHH---TTCEEEEEE CS
                        Ubiquitin_2  28 elKekLelitGtspasmrLqly 49 
                                        +l++ Le+ + ++p++m+ ql+
  gene1681|gene1681|rna1680|rna1680 134 NLQDELEM-FSMNPEYMNTQLK 154
                                        56666665.4578888888887 PP

>> RPN13_C  UCH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   1.6e-06    0.0032      18      91 ..      83     157 ..      68     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                            RPN13_C  18 evsLs.diltpealspllsdpevveeLashLPe..egeateeelretlrSPqfrqalsslsqALqsgqlgpvlsql 90 
                                        + +++ +++++  ++++l++p+++++++++ P   e+ +++ elr +++S++++  l+++s   + + +++ l++l
  gene1681|gene1681|rna1680|rna1680  83 KPDFTaSMMKNPLVKNFLKNPDAMRSIVEMFPGlkEEMNSNPELRMVMNSSNLQDELEMFSM--NPEYMNTQLKNL 156
                                        444441456888999******************98888999*******************85..444455555555 PP

                            RPN13_C  91 g 91 
                                        +
  gene1681|gene1681|rna1680|rna1680 157 D 157
                                        5 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   6.6e-06     0.013      57      88 ..      43      74 ..      39      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.6e-06
                        Ubiquitin_4 57 cLsfegekLkddkaklkeygirnkselsFvkr 88
                                       +L f+++ L+d++++lke+gi+n+++l+  k+
  gene1681|gene1681|rna1680|rna1680 43 VLLFNDRILSDNNKELKELGIENDCTLHLKKK 74
                                       699*************************9887 PP

>> STI1  STI1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.5   0.00029      0.59       2      29 ..      84     111 ..      83     112 .. 0.87
   2 !    9.9   3.4   0.00035      0.69       2      45 ..     114     157 ..     114     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                               STI1   2 pelfaklaanPetrellsDPefvaklee 29 
                                        p+  a +++nP ++++l++P+ +  + e
  gene1681|gene1681|rna1680|rna1680  84 PDFTASMMKNPLVKNFLKNPDAMRSIVE 111
                                        8999****************98877665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00035
                               STI1   2 pelfaklaanPetrellsDPefvakleeiqsNPqalqqymsDpr 45 
                                        p l + + +nPe+r  ++ + ++  le ++ NP  +++++++ +
  gene1681|gene1681|rna1680|rna1680 114 PGLKEEMNSNPELRMVMNSSNLQDELEMFSMNPEYMNTQLKNLD 157
                                        56778899*******************************99855 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.3e-06     0.017       4      36 ..     227     260 ..     224     261 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.3e-06
                                        HHHHHHHHTTS-HH.HHHHHHHHTTTSHHHHHHH CS
                                UBA   4 eaiqrLveMGFdre.evveALratgnNeErAvey 36 
                                        +++++L++ GF++  ++ +AL a+++++E  + y
  gene1681|gene1681|rna1680|rna1680 227 DKLAELKQIGFSDTrRNFMALMACNGDLEGSIMY 260
                                        7899*************************87765 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-05     0.028      20      70 ..      21      71 ..      18      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                                       TSBHHHHHHHHHHHHT----TT-EEEETTEE--TT.SBGGGSS--TTEEEEE CS
                          Rad60-SLD 20 tttvskLieayrkkkgipeeqkvrLiFDGeeLdpn.stvedldiedgdtidv 70
                                       t t++ L+ + ++  g+p+ ++++L+F+++ L++n + +++l+ie++ t+++
  gene1681|gene1681|rna1680|rna1680 21 TDTLESLKLRIQEITGVPV-DSQVLLFNDRILSDNnKELKELGIENDCTLHL 71
                                       679999*************.99**********765167*********99985 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.24     101     138 ..     226     263 ..     218     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                           HOIP-UBA 101 rkKvkelaslgffdreevveaLrqsgGdvegAlveLqr 138
                                        + K+ el++ gf+d  +   aL + +Gd+eg+++ Lq 
  gene1681|gene1681|rna1680|rna1680 226 KDKLAELKQIGFSDTRRNFMALMACNGDLEGSIMYLQE 263
                                        789******************************99995 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.43   8.6e+02      20      40 ..      16      36 ..       9      46 .. 0.53
   2 ?    9.9   0.0   0.00034      0.68       3      44 ..     128     169 ..     127     180 .. 0.88
   3 ?   -2.9   0.5       3.3   6.5e+03      84      96 ..     221     233 ..     217     235 .. 0.39

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.43
                                       HHHHHHHHHHHHHHHHHHHHH CS
                        Prefoldin_2 20 qikqletqlkelelvleelel 40
                                        i+++   l+ l+l ++e+  
  gene1681|gene1681|rna1680|rna1680 16 AIAMMTDTLESLKLRIQEITG 36
                                       344444444445555555544 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00034
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT CS
                        Prefoldin_2   3 linkfqqlqqqlqqlaqqikqletqlkelelvleelellded 44 
                                        ++++ ++lq++l+++ ++ + ++tqlk+l+ +   le+++  
  gene1681|gene1681|rna1680|rna1680 128 MVMNSSNLQDELEMFSMNPEYMNTQLKNLDITMSKLENIPGG 169
                                        677899*******************************99865 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 3.3
                                        HHHHHHHHHHHHH CS
                        Prefoldin_2  84 qleklekeleelk 96 
                                        ql k + +l+elk
  gene1681|gene1681|rna1680|rna1680 221 QLVKYKDKLAELK 233
                                        3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1801.66
//
Query:       gene1682|gene1682|rna1681|rna1681  [L=1024]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-21   77.1   2.4    1.9e-21   76.6   1.1    2.0  2  RasGAP_C  RasGAP C-terminus
    9.8e-12   45.0   0.0    3.1e-11   43.4   0.0    2.0  1  CH        Calponin homology (CH) domain
    6.8e-07   29.2   5.6    2.9e-05   23.9   0.1    2.9  3  RasGAP    GTPase-activator protein for Ras-like GTPase


Domain annotation for each model (and alignments):
>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.4   8.3e+03      26      61 ..     652     687 ..     650     693 .. 0.72
   2 !   76.6   1.1   3.2e-25   1.9e-21       3     135 ..     819     945 ..     817     947 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.4
                           RasGAP_C  26 nyqellneIakdirnkgrlrekrkeElesleetlkt 61 
                                        +yq++l+++++     ++ + + ++El +l+ +  +
  gene1682|gene1682|rna1681|rna1681 652 RYQSILSKLTNVSSLDNYFQFESMNELGKLKRATVH 687
                                        788888888887777777777777777777766555 PP

  == domain 2  score: 76.6 bits;  conditional E-value: 3.2e-25
                           RasGAP_C   3 elkkkalenlkeLeelgvisrennyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYka 78 
                                        +lk+++++ l+ Le++++ sr+n y ell ++a+di  ++ + e+r +El++ e  +++L+ + +yl+ ++e Y++
  gene1682|gene1682|rna1681|rna1681 819 QLKESIIDDLNFLEDKNITSRHNLYSELLFMLAQDIVILRFMSEERSKELRINEISYDNLCYRDDYLSGKIELYQN 894
                                        89************************************************************************** PP

                           RasGAP_C  79 yienvleqlkkkkgklpfskqyfkkrelkksgklpkfgsykysakqLeekgVLleie 135
                                        y+++ +++l+ kk      ++ f     ++ ++ +k g++kysa++L+  gVL++i 
  gene1682|gene1682|rna1681|rna1681 895 YLNSFVAKLAIKK------RSLFGFSGTDDITRDSKYGTHKYSAEKLMSMGVLVQIY 945
                                        ***********97......7788889999*************************996 PP

>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   5.2e-15   3.1e-11       5     106 ..      47     147 ..      43     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 5.2e-15
                                        HHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTT.HHHHHHHHHHHHHHHHHHTTCH CS
                                 CH   5 kellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnks.efkkleNinlaldvaekklgvp 79 
                                        +e+  W+ + +  + p ++ e+fee +r Gv+L ++   +ap++v+ + +    ++++ +Nin++ld ++ ++g+p
  gene1682|gene1682|rna1681|rna1681  47 EEAKSWLGDFT--DVP-ESFEEFEEEMRKGVILTDICRIFAPSSVKNVFVDSIlQYRHTDNINYFLDGLM-QIGLP 118
                                        66677888877..323.4469***********************888888555**************999.***** PP

                                        TTSS.-HHHHHTTSHH.HHHHHHHHHHHH CS
                                 CH  80 kvli.eaedlvegknk.svltllaqLfra 106
                                        ++   e+ dl+e+kn+ +v+ ++++L++ 
  gene1682|gene1682|rna1681|rna1681 119 EYFHfEVIDLYEKKNFvKVIYCIHALAHL 147
                                        **************************986 PP

>> RasGAP  GTPase-activator protein for Ras-like GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2         1     6e+03     103     140 ..     284     325 ..     276     338 .. 0.69
   2 !   23.9   0.1   4.9e-09   2.9e-05      13     140 ..     441     553 ..     430     556 .. 0.88
   3 !    7.4   0.1   0.00052       3.1     164     206 ..     558     599 ..     555     601 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1
                             RasGAP 103 sqmle.knldkLkelvneildsIfks...leqlPvgiRiick 140
                                        s+m++ + +++L++ +++ +dsI+++   ++++   iR+i++
  gene1682|gene1682|rna1681|rna1681 284 SEMVKeNLIENLHHKISKKFDSIYAKeaqIKDIETRIRLIVQ 325
                                        555553446888888888888888753336666666666655 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.9e-09
                             RasGAP  13 senpndll.rsnsvvsklleeytkrpegqeyLkkilkpllqkilekedlnlelDPrkiyeelkkkkesktgkkses 87 
                                         e+p + +  s s+  kl+ +y++  +g   L++ +  +++++   e+ +++ +P  iy  l +++++        
  gene1682|gene1682|rna1681|rna1681 441 VEFPIHHTlSSGSICHKLMVNYFRISQGSFSLRDKILHIVKNL---ENIEVDANPVLIYTMLFNQSTTV------- 506
                                        5555555558999************999999999887888875...899999**********9998875....... PP

                             RasGAP  88 sgkksekeaselekvsqmleknldkLkelvneildsIfksleqlPvgiRiick 140
                                              ++a+e+e+v++ ++++l+ ++ ++++ ld + + +e++P+ +R+ +k
  gene1682|gene1682|rna1681|rna1681 507 ------DKALENERVREAVQTRLMVMRGVISSALDLLESCIESIPYILRYFLK 553
                                        ......789*****************************************998 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00052
                             RasGAP 164 sflflrfliPaivnPklfglvdkqiseeqrrnLtliaKllqnl 206
                                        ++++  f++P i++P+ f     ++s++ r++++ i+K+l  +
  gene1682|gene1682|rna1681|rna1681 558 GMFYTEFVMPFILAPDAFIES-FEVSKSLRNKCFIISKVLEYI 599
                                        568889************555.899**************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1024 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 6358.02
//
Query:       gene1683|gene1683|rna1682|rna1682  [L=611]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-14   54.2   0.1    3.5e-14   53.0   0.1    1.6  1  GCP_C_terminal  Gamma tubulin complex component C-terminal
    1.6e-11   44.4   0.1    3.6e-11   43.2   0.1    1.5  1  GCP_N_terminal  Gamma tubulin complex component N-terminal


Domain annotation for each model (and alignments):
>> GCP_C_terminal  Gamma tubulin complex component C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1   3.9e-18   3.5e-14       6     217 ..     377     557 ..     373     597 .. 0.71

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 3.9e-18
                     GCP_C_terminal   6 kllkrylLlgqgdFisrLldalfdelwkpasselrlaLtslLeeairssnaqqsdelkddlsfaldlpevleelda 81 
                                        + +++ +L+g+ dFi+ L   l+d+++ + +s      + +L++air++                + +e++++l +
  gene1683|gene1683|rna1682|rna1682 377 EGIRNTFLFGRCDFIETLFLYLKDSKDLSRKS-----FSYILDLAIRNTYG--------------NADEFTSKLGV 433
                                        679*******************9998876555.....668*******8643..............45566688874 PP

                     GCP_C_terminal  82 kldpdslegldfltLeYkvpwplslvitpealekYqriFrfLlrvkrvefalsslwkrrkatgarsvllkrarllr 157
                                           +d+ + ++ + L  +v+ p s+++t+e++ k  +iF+fL+++krve+ l ++  ++ +++++          +
  gene1683|gene1683|rna1682|rna1682 434 Y-IVDNENKYENFALFCQVDYPASIIVTKESILKLVKIFQFLWKLKRVEHLLLRVSGMKIQKTSK--------IKV 500
                                        4.4667789999*****************************************765233333333........446 PP

                     GCP_C_terminal 158 qemlhfvsqlqyYvldeviessWreleeklkkeatdldelieaHeafLdsilkkclLrsk 217
                                            +++ ++ y+v+ evie +W+ + +  +     l+el+   e+ Ld +++ c ++  
  gene1683|gene1683|rna1682|rna1682 501 ISYKTLLYKINYFVFEEVIERKWKFFSSVGE--MP-LNELRLGIERALDGVINTCQIGGG 557
                                        6788999****************98876554..33.555555555555555555544433 PP

>> GCP_N_terminal  Gamma tubulin complex component N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1     4e-15   3.6e-11     160     298 ..     220     361 ..     216     367 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 4e-15
                     GCP_N_terminal 160 llsellervsrpflemlekWileGelsDpynEfFveenesvakeklkeddseklweekYtlrkemlPsflseelae 235
                                        +++++le+ +  + + l+ +++ G + D+ nEfF+  ++s+           + w e+++++   +P f+s+ la+
  gene1683|gene1683|rna1682|rna1682 220 FYRKVLESSCLHINNCLREFLFTGCFRDDTNEFFICRKTSI-----------EPW-EEFSIDFGLVPYFISNRLAQ 283
                                        899********************************999999...........579.69****************** PP

                     GCP_N_terminal 236 kIletGkslnflres...................cgdsewiekteseekel...........eyiddleelsssls 281
                                        kIl +Gk   +lr +                   c                           e i+d+ +  ++l 
  gene1683|gene1683|rna1682|rna1682 284 KILYIGKCSFLLRGCsaskmlslddlheaqisgeC---------------RskgiqsynfldEEIEDSPKHINILN 344
                                        *********99999854444444443333332222...............03333333333333555668889999 PP

                     GCP_N_terminal 282 lsleelidsayklaskr 298
                                         +lee+id + + ++++
  gene1683|gene1683|rna1682|rna1682 345 PGLEESIDMMLHRINRE 361
                                        99999999888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.47
# Mc/sec: 3918.38
//
Query:       gene1684|gene1684|rna1683|rna1683  [L=215]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-41  139.8   0.1    1.2e-40  139.4   0.1    1.1  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.1   6.5e-45   1.2e-40       9     156 ..      54     204 ..      46     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 6.5e-45
                      Pro_isomerase   9 kGrivieLfadkaPktvenFlklvkeg........fYdgttFhRvikgfmvqgGdptgktsageqekkggesirai 76 
                                         Gr+++eL+ ++aPkt++nF +lvk g         Y+g+ FhR+i+gfm+qgGd+  ++ +g+ +  +g   +++
  gene1684|gene1684|rna1683|rna1683  54 SGRVTFELYWNEAPKTARNFYELVK-GteigdgfyKYEGSLFHRIIPGFMMQGGDILMGNGTGSISIYDG---KPF 125
                                        7***********************5.558888888899*****************999855455443344...59* PP

                      Pro_isomerase  77 pdEitsklkh.krGalamartgkepnsagsqFfItlkeaphldgkytvFGkVv.eGmdvvekiekvetdeerpkkn 150
                                        +dE     +h + G l+ma++g  pn++gsqFfIt++++phld+k++vFG+V  e++ +++ i++v+t ++rp+ +
  gene1684|gene1684|rna1683|rna1683 126 ADEDF-IKTHdSIGKLSMANSG--PNTNGSQFFITFAPQPHLDRKHVVFGNVSeESIPLINDIQRVNTRHARPVIP 198
                                        ***95.5557588********8..8****************************99************999****** PP

                      Pro_isomerase 151 vkivsa 156
                                        vkiv+ 
  gene1684|gene1684|rna1683|rna1683 199 VKIVKS 204
                                        ***986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1276.13
//
Query:       gene1685|gene1685|rna1684|rna1684  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.6e-112  373.3   0.0   1.2e-111  373.0   0.0    1.1  1  Peptidase_M17    Cytosol aminopeptidase family, catalytic dom
    5.2e-06   26.3   0.4    9.9e-06   25.4   0.1    1.6  2  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.0   0.0  1.3e-115  1.2e-111       1     311 []     182     491 ..     182     491 .. 0.95

  Alignments for each domain:
  == domain 1  score: 373.0 bits;  conditional E-value: 1.3e-115
                                        HHHHHHHHS-TTTS-HHHHHHHHHHHHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SSTT CS
                      Peptidase_M17   1 nlardlvntpaneltpeklaeeaeelakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgakek 76 
                                        n+ar l +tpan ++p+ + e+a++  + + +v+vev+ ++ +++k m++ll+V++gS +++p+l++ +y+g++ +
  gene1685|gene1685|rna1684|rna1684 182 NFARFLGDTPANLMNPTLFTEYATKYLQGKRNVTVEVFGKDFMKSKSMNLLLSVSQGS-SQEPKLLVAKYRGKSGE 256
                                        69********************9995455556**************************.56*************** PP

                                        SEEEEEEEEEEEEEE-TTSS--HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTTEE CS
                      Peptidase_M17  77 ekklalVGKGitfDtGGlslKpsasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpgdv 152
                                          +lalVGKG++fD+GG+slKpsa m  mk+Dm G+A+vl+a+ ++a++++++nv +v+pl+eN++sg+a+kpgdv
  gene1685|gene1685|rna1684|rna1684 257 GVDLALVGKGVCFDSGGISLKPSARMCRMKGDMLGGASVLSAFGVIADMGVKINVDLVIPLVENLPSGTATKPGDV 332
                                        **************************************************************************** PP

                                        EE-TTS-EEEES-TTGCHHHHHHHHHHHHHGCT--SEEEEEE---THHHHHHTTTSEEEEES-HHHHHHHHHHHHH CS
                      Peptidase_M17 153 itamnGktvevlnTDaEGRLvLADalayaeekekpdlivdvATLTgavvvalGkkaaglfsnddelaeelekagee 228
                                        +  mnGk+ve++nTDaEGRL+LADal+ya+ + +p++++dvATLTga+ +alG+ + g+f++dd+l+e + ++g +
  gene1685|gene1685|rna1684|rna1684 333 YIGMNGKSVEIDNTDAEGRLILADALVYAQ-ERNPTYVFDVATLTGAMSIALGDVFIGYFTEDDNLSEMIYRSGID 407
                                        *****************************6.67******************************************* PP

                                        HS-EEEE----HHHGGGG--SSSSEESS-SSSSTHHHHHHHHHHTTSSE.CGEEEEE-TTTTES.BTTB.S..EE- CS
                      Peptidase_M17 229 agervwrlpleeeykkqlkskvaDlknvgkkrragaitAalFLkefvke.tpWaHlDiagtalkekealkkekgat 303
                                        a++  wr+pl++ y  ++ks+vaDlkn+g++r +g++ Aa+FL+efvk+  +W+H+Diag++ +++++  + +g+t
  gene1685|gene1685|rna1684|rna1684 408 ANDPTWRMPLSQLYLPAMKSDVADLKNTGEGRYGGSSSAAIFLNEFVKKeCKWVHFDIAGVMGSNNNKGVYGDGMT 483
                                        ***********88*****************9999*************77799*********975444444449*** PP

                                        -TTHHHHH CS
                      Peptidase_M17 304 GvgvrtLv 311
                                        G+ v +Lv
  gene1685|gene1685|rna1684|rna1684 484 GCSVPVLV 491
                                        ***99885 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1   1.1e-09   9.9e-06      27     122 ..      64     152 ..      47     156 .. 0.89
   2 ?   -3.9   0.0       1.3   1.2e+04      35      49 ..     251     265 ..     248     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.1e-09
                    Peptidase_M17_N  27 ellkegdftGkagevlvlralsgekakrvllVGLGkeee...ltaealrkaagaaaralkgakvttiavalplegk 99 
                                        e l++++++G+ ge + l++ +g      ++VG+Gk +e   l + + rka++++ +a+++    +i ++l     
  gene1685|gene1685|rna1684|rna1684  64 EFLNSLGAKGNLGENYILPERNGR---ITVFVGIGKVDEnilLVKSNARKAGASGYKAVSQ--FRNIEISLG---- 130
                                        6789999***********999976...6799*****************************9..888888888.... PP

                    Peptidase_M17_N 100 nsdekaeaaaegallglYrfdry 122
                                         s+  a+++++g+ l++Y+++ +
  gene1685|gene1685|rna1684|rna1684 131 -SEFMAREVVSGIILASYKYQFL 152
                                        .6689***************855 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.3
                    Peptidase_M17_N  35 tGkagevlvlralsg 49 
                                         Gk+ge + l  +++
  gene1685|gene1685|rna1684|rna1684 251 RGKSGEGVDLALVGK 265
                                        699999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3289.99
//
Query:       gene1686|gene1686|rna1685|rna1685  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.062   13.8   0.8        1.5    9.4   0.1    3.2  3  EF-hand_12  EF-hand fold domain
        2.7    7.9   5.3       0.84    9.6   0.2    2.8  3  DUF3781     Protein of unknown function (DUF3781)


Domain annotation for each model (and alignments):
>> EF-hand_12  EF-hand fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.13   1.1e+03      19      61 ..     136     176 ..     119     190 .. 0.76
   2 ?   -0.6   0.0      0.21   1.9e+03      18      24 ..     259     265 ..     241     333 .. 0.61
   3 ?    9.4   0.1   0.00016       1.5      49      83 ..     379     413 ..     369     421 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                         EF-hand_12  19 edkeeipWelfanilhkhllkatkqdpikpkrklssfefeyiq 61 
                                         +k    We    + +  ll  + q+  k  r l+++ ++  q
  gene1686|gene1686|rna1685|rna1685 136 REK--SGWECILVLANDILLIGAVQKGFKKYRLLNAYSYSIAQ 176
                                        433..3688888888888999999**********999987655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.21
                         EF-hand_12  18 fedkeei 24 
                                        f+dk+e+
  gene1686|gene1686|rna1685|rna1685 259 FHDKAEM 265
                                        5555554 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00016
                         EF-hand_12  49 krklssfefeyiqkkffgnkssvskkevdefWskf 83 
                                        + k+s+++f+y+ ++f++n+s+  kk +d+  +  
  gene1686|gene1686|rna1685|rna1685 379 NLKFSKYDFSYLMEHFLKNRSEYRKKYLDSAMKDI 413
                                        5689*****************99999888766555 PP

>> DUF3781  Protein of unknown function (DUF3781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       1.6   1.4e+04      62      68 ..     168     174 ..     167     175 .. 0.85
   2 ?   -1.2   0.1      0.21   1.9e+03      16      45 ..     297     328 ..     293     342 .. 0.71
   3 ?    9.6   0.2   9.3e-05      0.84       6      40 ..     365     399 ..     361     421 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.6
                            DUF3781  62 Nassyti 68 
                                        Na+sy i
  gene1686|gene1686|rna1685|rna1685 168 NAYSYSI 174
                                        9****88 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.21
                            DUF3781  16 RIkknLslse..ddvveyckeiildknakiek 45 
                                        +I+k   l++  +dv +y +e + ++++ i++
  gene1686|gene1686|rna1685|rna1685 297 KINKIQPLNNfiEDVFKYFNEFLYEQDDLIKE 328
                                        55554443332279999999999988887765 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 9.3e-05
                            DUF3781   6 kihttelgieRIkknLslseddvveyckeiildkn 40 
                                         +++t+ ++e I++nL++s+ d   ++++ +++  
  gene1686|gene1686|rna1685|rna1685 365 DVKYTDSVLELINQNLKFSKYDFSYLMEHFLKNRS 399
                                        589*******************9999988888763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2773.07
//
Query:       gene1687|gene1687|rna1686|rna1686  [L=579]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-16   59.3   0.0    1.1e-15   57.6   0.0    1.9  1  HGTP_anticodon  Anticodon binding domain
    4.4e-10   39.8   0.1    1.5e-09   38.1   0.1    2.1  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.48   10.4   2.3       0.37   10.7   0.3    1.8  2  IceA2           Helicobacter pylori IceA2 protein


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   1.8e-19   1.1e-15      12      93 ..     489     570 ..     474     571 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.8e-19
                                        HHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHH CS
                     HGTP_anticodon  12 eeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldel 87 
                                        +e+ e   k+++ L ++g+ v++++++ sig+k++ +d+lgipf ++ +++ l+++ vt+r+rd+++q+rv++++ 
  gene1687|gene1687|rna1686|rna1686 489 NEFDEHILKIKRFLTDNGLVVHVNERSCSIGRKYSSCDELGIPFFITFDPDFLKDNMVTIRERDSMQQIRVEVEKC 564
                                        35889999******************************************************************99 PP

                                        HHHHHH CS
                     HGTP_anticodon  88 veklke 93 
                                         +++ e
  gene1687|gene1687|rna1686|rna1686 565 SSIVLE 570
                                        888765 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   2.4e-13   1.5e-09       8      99 ..     167     260 ..     161     458 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.4e-13
                                        SEEEEE-SSSHHHHHHHHHHHEE.EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2b   8 dreyiLkPtneetfvelirdevl.rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrd 82 
                                        d+ + L+P+  ++    +++    ++ +LP+  + i+  yR+E s  +GL+RvreF+q + + f+++++ d     
  gene1687|gene1687|rna1686|rna1686 167 DQTMFLRPETAQGQFLNFKKLYEyNNGKLPFASASIGKAYRNEISPRSGLIRVREFDQAEIEHFVLAEEKDHPKFG 242
                                        677899***9999999998764467766****************9555******************8778888888 PP

                                        HHHHHHHHH.HHTT.SCE CS
                                        xxxxxxxxx.xxxxxxxx RF
                       tRNA-synt_2b  83 likaisrif.erlglefr 99 
                                         +k+++  f +++g e+ 
  gene1687|gene1687|rna1686|rna1686 243 TVKEVKLKFiKEVGTEEI 260
                                        888887665244566654 PP

>> IceA2  Helicobacter pylori IceA2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       1.5   9.1e+03      11      19 ..     186     194 ..     185     195 .. 0.79
   2 ?   10.7   0.3   6.2e-05      0.37       5      47 ..     386     429 ..     383     437 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                              IceA2  11 kiqeyenGi 19 
                                        k+ ey+nG 
  gene1687|gene1687|rna1686|rna1686 186 KLYEYNNGK 194
                                        778999995 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 6.2e-05
                              IceA2   5 vkvvnGkiqey.enGiykRtYdsnivavdvdGhvvavvtakGkv 47 
                                        + +vnG  qey e  i       n ++v+ dGhv++   +k k 
  gene1687|gene1687|rna1686|rna1686 386 MEMVNGFTQEYiEQNISSSEEKKNYLNVKFDGHVISFECSKVKN 429
                                        568********666667777889*************99998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 4158.45
//
Query:       gene1688|gene1688|rna1687|rna1687  [L=341]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2061.58
//
Query:       gene1689|gene1689|rna1688|rna1688  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-57  193.7   0.1    1.9e-57  193.5   0.1    1.0  1  Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)


Domain annotation for each model (and alignments):
>> Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.5   0.1     1e-61   1.9e-57       6     174 ..       4     183 ..       1     184 [. 0.96

  Alignments for each domain:
  == domain 1  score: 193.5 bits;  conditional E-value: 1e-61
                      Pur_DNA_glyco   6 dalevAkeLLGkvlvreleegkvagrivEtEAYlgeeDpAshayrgr.ternavmFgppgtlYvYliygihhclnv 80 
                                        ++ e+A+eLLGk+l+r++e ++++g+ivEtEAY+g+eD+A+h y gr tern++m++++gt+YvY iyg++ c+n+
  gene1689|gene1689|rna1688|rna1688   4 PCIELARELLGKILCRRMEGKTMKGMIVETEAYVGREDKACHGYGGRrTERNSAMYMRAGTCYVYKIYGMYECFNI 79 
                                        7899***************99*************************99**************************** PP

                      Pur_DNA_glyco  81 vteeegeasaVLiRalevveglelmrarrg.......lanGPgkLcqaLgidke.lngadlleseelvle.keeae 147
                                        ++ e+  +++VLiRa+e++ g++lmr++rg       +anGP+kLc a+gi+++  +++ +++s+++++e + e++
  gene1689|gene1689|rna1688|rna1688  80 SSVED--GAGVLIRAVEPLCGISLMRRHRGgrvkdrdIANGPSKLCIAMGITRKeIDKEWIMSSSKIWIEeGMEVA 153
                                        **666..89********************************************9999****99*******877999 PP

                      Pur_DNA_glyco 148 eeeivagpRiGiskaae...lpwRfyikgn 174
                                        +++++ g+RiGi++ +e   + +Rfyik+n
  gene1689|gene1689|rna1688|rna1688 154 DTSVIVGKRIGIRNCGEweeKELRFYIKDN 183
                                        **************777777********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1285.93
//
Query:       gene1690|gene1690|rna1689|rna1689  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.061   12.9   0.3      0.092   12.3   0.3    1.3  1  PspA_IM30    PspA/IM30 family
      0.066   13.4   0.2       0.11   12.7   0.2    1.5  1  T3SchapCesA  Type III secretion system filament chaperone Ces


Domain annotation for each model (and alignments):
>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     1e-05     0.092      76     119 ..      60     107 ..      37     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                          PspA_IM30  76 aALtkg....eeeLArealaeikslekqaealetqlaqqrsaveqlrk 119
                                        + L+k+    ++eL re++ e +sl++++++l + + +++s+ e+l+ 
  gene1690|gene1690|rna1689|rna1689  60 ECLEKQvserAQELCRELIFEHESLKEKVARLGEAAGNSESSFEELKS 107
                                        455666666699**********************************97 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.2e-05      0.11      10      60 ..      59     110 ..      46     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                        T3SchapCesA  10 kelldkkirsei.eaikkiiaefdvvkesvnilsekaktdpqaaeklnklie 60 
                                        ke l+k++     e  + +i e + +ke+v  l e a  +  + e+l+ li 
  gene1690|gene1690|rna1689|rna1689  59 KECLEKQVSERAqELCRELIFEHESLKEKVARLGEAAGNSESSFEELKSLII 110
                                        899999997654277899*****************************99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1078.28
//
Query:       gene169|gene169|rna169|rna169  [L=455]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2754.37
//
Query:       gene1691|gene1691|rna1690|rna1690  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-17   61.4  14.4    6.1e-07   29.1   1.7    3.9  3  LRR_8     Leucine rich repeat
    1.3e-14   54.0  17.7      6e-05   23.3   1.2    5.1  6  LRR_4     Leucine Rich repeats (2 copies)
    8.7e-08   31.7  14.6        1.7    9.5   0.1    7.8  8  LRR_1     Leucine Rich Repeat
     0.0055   16.2  10.3       0.15   11.5   4.8    2.8  3  LRR_9     Leucine-rich repeat
  ------ inclusion threshold ------
      0.012   15.7  17.1        1.6    8.9   0.1    6.1  6  LRR_6     Leucine Rich repeat


Domain annotation for each model (and alignments):
>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.9   1.6e-09   5.6e-06       5      61 .]      58     112 ..      56     112 .. 0.94
   2 !   29.1   1.7   1.7e-10   6.1e-07       2      61 .]     101     158 ..     100     158 .. 0.97
   3 !   23.4   1.8     1e-08   3.7e-05       3      61 .]     171     231 ..     170     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.6e-09
                                        EEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   5 sLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        ++++++N++ s++ +  + l++L  L++++N++++l p  + + ++Lr+Ld+s+N++
  gene1691|gene1691|rna1690|rna1690  58 EVNIQKNKICSIPSKIES-LKKLLRLYMNDNQIQSL-PPEIGSVERLRELDVSNNNI 112
                                        6899********999998.*****************.8999**************98 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1.7e-10
                                        T-SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   2 nLtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        +L++Ld+snN+++ l+ e  + l+ L+ L+ snN+l++l p  ++ Lp L++L  +gN+L
  gene1691|gene1691|rna1690|rna1690 101 RLRELDVSNNNISWLPVEITH-LQWLTKLNVSNNSLRRL-PVEMRVLPFLKELRADGNKL 158
                                        7*****************998.*****************.9*****************98 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 1e-08
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGG...GTT--S-.EEE--SS-- CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspga...fsgLpsLrsLdLsgNrL 61 
                                        L++++L nN +++++    k ++nLk +d +nN++++++++    + + ++L+ +dL+gN+L
  gene1691|gene1691|rna1690|rna1690 171 LERISLGNNLFEEIPEVIGK-MENLKKIDFRNNRIRRVNRKLvdiLFDNRNLELIDLRGNDL 231
                                        8899**********998888.*****************98653336788***********98 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4     6e-06     0.022       6      40 ..      59      93 ..      56      98 .. 0.86
   2 !   23.3   1.2   1.7e-08     6e-05       1      39 [.      77     112 ..      77     117 .. 0.85
   3 !   18.9   2.8   4.2e-07    0.0015       2      39 ..     101     138 ..     100     140 .. 0.83
   4 !   15.0   0.2   7.1e-06     0.026       3      36 ..     125     158 ..     123     166 .. 0.84
   5 !   21.2   0.1   7.6e-08   0.00027       3      39 ..     171     207 ..     170     211 .. 0.92
   6 ?    2.3   0.2     0.071   2.5e+02      23      38 ..     219     230 ..     209     237 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6e-06
                                       EE--SS---E-S-.HHH-TT--EEE-.-S-----GG CS
                              LRR_4  6 LdLsnNqltdipl.leklpnLkeLdLsgNnlitdld 40
                                       ++++ N++ +ip+ +e+l++L  L++++N +i++l+
  gene1691|gene1691|rna1690|rna1690 59 VNIQKNKICSIPSkIESLKKLLRLYMNDN-QIQSLP 93
                                       688999999****9889*********666.999885 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 1.7e-08
                                        SS--EEE--SS---E-S-.HHH-TT--EEE-.-S-----G CS
                              LRR_4   1 pnLevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdl 39 
                                        ++L  L+ ++Nq++++p+ +++   L+eLd+s+N    ++
  gene1691|gene1691|rna1690|rna1690  77 KKLLRLYMNDNQIQSLPPeIGSVERLRELDVSNN----NI 112
                                        58899*************6667*********888....44 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 4.2e-07
                                        S--EEE--SS---E-S-.HHH-TT--EEE-.-S-----G CS
                              LRR_4   2 nLevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdl 39 
                                        +L++Ld snN+++ +p  +  l  L++L++s+N  +++l
  gene1691|gene1691|rna1690|rna1690 101 RLRELDVSNNNISWLPVeITHLQWLTKLNVSNN-SLRRL 138
                                        7************88886667*********666.55554 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 7.1e-06
                                        --EEE--SS---E-S-..HHH-TT--EEE-.-S--- CS
                              LRR_4   3 LevLdLsnNqltdipl..leklpnLkeLdLsgNnli 36 
                                        L++L+ snN l+ +p      lp LkeL   gN ++
  gene1691|gene1691|rna1690|rna1690 125 LTKLNVSNNSLRRLPVemRV-LPFLKELRADGN-KL 158
                                        9***************7666.*******99888.44 PP

  == domain 5  score: 21.2 bits;  conditional E-value: 7.6e-08
                                        --EEE--SS---E-S-.HHH-TT--EEE-.-S-----G CS
                              LRR_4   3 LevLdLsnNqltdipl.leklpnLkeLdLsgNnlitdl 39 
                                        Le ++L+nN   +ip  ++k+ nLk++d  +Nn+i+++
  gene1691|gene1691|rna1690|rna1690 171 LERISLGNNLFEEIPEvIGKMENLKKIDF-RNNRIRRV 207
                                        899*************8778*********.999**887 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.071
                                        TT--EEE-.-S----- CS
                              LRR_4  23 pnLkeLdLsgNnlitd 38 
                                         nL+ +dL gN    d
  gene1691|gene1691|rna1690|rna1690 219 RNLELIDLRGN----D 230
                                        56777777666....3 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.3   8.3e+03       5      19 ..      59      72 ..      57      76 .. 0.65
   2 ?    3.6   0.0      0.04   1.4e+02       1      17 [.      78      94 ..      78      98 .. 0.80
   3 !    9.5   0.1   0.00046       1.7       1      16 [.     101     116 ..     101     122 .. 0.84
   4 !    7.6   0.0     0.002       7.1       2      16 ..     125     139 ..     124     142 .. 0.88
   5 ?    2.1   0.0      0.13   4.7e+02       2      22 ..     148     167 ..     147     168 .. 0.87
   6 ?    1.3   0.0      0.24   8.5e+02       2      13 ..     171     182 ..     170     190 .. 0.79
   7 ?    4.4   0.2     0.023        82       1      12 [.     193     204 ..     193     215 .. 0.84
   8 !    5.7   0.0    0.0082        29       1      14 [.     220     233 ..     220     251 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.3
                              LRR_1  5 LdLsnnpllglppns 19
                                        ++  n + + +p+ 
  gene1691|gene1691|rna1690|rna1690 59 VNIQKNKI-CSIPSK 72
                                       68888988.555544 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.04
                              LRR_1  1 nLrhLdLsnnpllglpp 17
                                       +L +L++++n++ +lpp
  gene1691|gene1691|rna1690|rna1690 78 KLLRLYMNDNQIQSLPP 94
                                       6889********76666 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00046
                              LRR_1   1 nLrhLdLsnnpllglp 16 
                                        +Lr+Ld+snn+++ lp
  gene1691|gene1691|rna1690|rna1690 101 RLRELDVSNNNISWLP 116
                                        69*********97665 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.002
                              LRR_1   2 LrhLdLsnnpllglp 16 
                                        L++L++snn+l +lp
  gene1691|gene1691|rna1690|rna1690 125 LTKLNVSNNSLRRLP 139
                                        899********8887 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.13
                              LRR_1   2 LrhLdLsnnpllglppnsfqn 22 
                                        L++L   +n l + +p++f+ 
  gene1691|gene1691|rna1690|rna1690 148 LKELRADGNKL-CALPSTFEE 167
                                        999*99*****.999999986 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.24
                              LRR_1   2 LrhLdLsnnpll 13 
                                        L+++ L+nn ++
  gene1691|gene1691|rna1690|rna1690 171 LERISLGNNLFE 182
                                        89999*999874 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.023
                              LRR_1   1 nLrhLdLsnnpl 12 
                                        nL+++d +nn++
  gene1691|gene1691|rna1690|rna1690 193 NLKKIDFRNNRI 204
                                        8*********98 PP

  == domain 8  score: 5.7 bits;  conditional E-value: 0.0082
                              LRR_1   1 nLrhLdLsnnpllg 14 
                                        nL+ +dL++n l +
  gene1691|gene1691|rna1690|rna1690 220 NLELIDLRGNDLMR 233
                                        8*********9944 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.5     0.001       3.8      25      75 ..      60     111 ..      52     113 .. 0.46
   2 !   11.5   4.8   4.3e-05      0.15      44     159 ..     102     213 ..      95     220 .. 0.85
   3 !    6.9   1.5    0.0011       3.9      60      91 ..     188     219 ..     161     238 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.001
                              LRR_9  25 dlrgykipvienlGatldqfdtidlsdndirkld.gfPllkrlktlllnnnr 75 
                                        +++ +ki  i     +l ++  + ++dn+i+ l  ++  ++rl+ l ++nn 
  gene1691|gene1691|rna1690|rna1690  60 NIQKNKICSIPSKIESLKKLLRLYMNDNQIQSLPpEIGSVERLRELDVSNNN 111
                                        4444444444444444444444444455544443234444444444444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.3e-05
                              LRR_9  44 fdtidlsdndirkld.gfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklell 118
                                        +  +d+s+n+i  l  ++ +l+ l  l ++nn ++r+  ++ +vlP l+el   +n+l  l     + ++  le +
  gene1691|gene1691|rna1690|rna1690 102 LRELDVSNNNISWLPvEITHLQWLTKLNVSNNSLRRLPVEM-RVLPFLKELRADGNKLCALPS--TFEEFYVLERI 174
                                        556899*****99964799*****************99887.69**************99988..8999******* PP

                              LRR_9 119 sllknpvtnkkeyrlyviyklkqlrlldfr..kvklkereeae 159
                                        sl +n   + +e    vi k+++l+ +dfr  ++++ +r+  +
  gene1691|gene1691|rna1690|rna1690 175 SLGNNLFEEIPE----VIGKMENLKKIDFRnnRIRRVNRKLVD 213
                                        *99999888876....99***********84457777776555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0011
                              LRR_9  60 fPllkrlktlllnnnrivriaegleevlPnle 91 
                                        +  ++ lk + + nnri+r++ +l ++l   +
  gene1691|gene1691|rna1690|rna1690 188 IGKMENLKKIDFRNNRIRRVNRKLVDILFDNR 219
                                        4578999***************9999885433 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.48   1.7e+03       4      15 ..      55      66 ..      52      68 .. 0.82
   2 ?    1.8   0.1     0.091   3.3e+02       4      16 ..      78      90 ..      75      91 .. 0.86
   3 ?    8.9   0.1   0.00046       1.6       5      16 ..     102     113 ..     100     113 .. 0.91
   4 ?    6.2   0.9    0.0034        12       1      15 [.     121     135 ..     121     136 .. 0.86
   5 ?    1.2   0.0      0.14   4.9e+02       4      15 ..     193     204 ..     190     205 .. 0.88
   6 ?    4.1   0.2     0.016        58       2      15 ..     218     231 ..     217     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.48
                              LRR_6  4 hLteLdLsgNdI 15
                                       ++ e++++ N+I
  gene1691|gene1691|rna1690|rna1690 55 CVVEVNIQKNKI 66
                                       67799*****99 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.091
                              LRR_6  4 hLteLdLsgNdIg 16
                                       +L  L +++N+I+
  gene1691|gene1691|rna1690|rna1690 78 KLLRLYMNDNQIQ 90
                                       7999*******97 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00046
                              LRR_6   5 LteLdLsgNdIg 16 
                                        L+eLd+s N+I+
  gene1691|gene1691|rna1690|rna1690 102 LRELDVSNNNIS 113
                                        9*********96 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0034
                              LRR_6   1 snthLteLdLsgNdI 15 
                                        + ++Lt+L++s N +
  gene1691|gene1691|rna1690|rna1690 121 HLQWLTKLNVSNNSL 135
                                        5689*********76 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.14
                              LRR_6   4 hLteLdLsgNdI 15 
                                        +L++ d + N I
  gene1691|gene1691|rna1690|rna1690 193 NLKKIDFRNNRI 204
                                        89********99 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.016
                              LRR_6   2 nthLteLdLsgNdI 15 
                                        n++L+  dL+gNd+
  gene1691|gene1691|rna1690|rna1690 218 NRNLELIDLRGNDL 231
                                        99**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1657.35
//
Query:       gene1692|gene1692|rna1691|rna1691  [L=405]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-46  158.6   0.0    2.3e-46  158.3   0.0    1.1  1  Pkinase         Protein kinase domain
    3.9e-22   78.8   0.0    5.7e-22   78.2   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    3.1e-06   26.9   0.1    1.3e-05   24.9   0.1    1.8  2  RIO1            RIO1 family
     0.0014   18.7   0.0     0.0019   18.1   0.0    1.3  1  APH             Phosphotransferase enzyme family
     0.0015   17.9   0.1     0.0022   17.4   0.1    1.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.065   12.8   0.1        0.1   12.2   0.1    1.3  1  Choline_kinase  Choline/ethanolamine kinase
      0.093   12.9   0.0       0.16   12.2   0.0    1.3  1  ABC1            ABC1 family
       0.13   11.9   0.0       0.91    9.1   0.0    2.0  2  FTA2            Kinetochore Sim4 complex subunit FTA2


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   0.0     1e-49   2.3e-46       1     264 []      40     335 ..      40     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 1e-49
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS....CTTB--EEEEEEESSE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk....hpnivrlyevfeekde 72 
                                        y ++  lG+G+fG+V+++v   +g++vA+K++k++ +  + e   ++E++il+kl      ++ v +++vf  k++
  gene1692|gene1692|rna1691|rna1691  40 YMVIGMLGTGTFGQVVRCV-GPDGEEVAIKVVKNQPKYYNYE---MNEVRILHKLLynnlNDRFVAIKDVFMYKQH 111
                                        567789*************.7**************9999888...9********9844556667************ PP

                                        EEEEEE--TTEBHHHHHH..HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTE..EEE-SGT CS
                            Pkinase  73 lylvleyveggeladlle..rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekge..lKitDFG 143
                                        l++v e++  + l ++l+  r + l++++++ i+kq+leg+  l   giiH+DlKpeNiLi   +    +Ki+DFG
  gene1692|gene1692|rna1691|rna1691 112 LCIVEELLGRN-LYTFLKmtRFKGLDHSTVRTILKQVLEGMIQLSVLGIIHCDLKPENILIAdYD-TfkVKIIDFG 185
                                        *******9955.888888755556*************************************9433.347******* PP

                                        TSEESSSSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHH CS
                            Pkinase 144 lakelessskltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilki 219
                                         a    + s  + +v +++Y+APEv+ + +y++++D+WslG+i yel+ g+p+f+   gk+    ++dq+ +i+ +
  gene1692|gene1692|rna1691|rna1691 186 SAVTSPQVS--HFYVQSRYYRAPEVILGIPYGSSCDIWSLGCIGYELYVGNPLFP---GKD----NMDQMGRIYGL 252
                                        *98877755..88999***************************************...444....56666666666 PP

                                        CT...SHH...HHHTTS.....................................-HHHHHHHHHHT-SSGCCSTTH CS
                            Pkinase 220 lg...etkeklpeasei.....................................seeakdllkkllkkdpkkRlta 255
                                        lg      + +++ ++                                      ++ ++++l k l+  +  R+ a
  gene1692|gene1692|rna1691|rna1691 253 LGslpM--FMIEHGKNSnvffekengyrfvgptsgftledmkkvirskgglegdDDMFIEFLLKTLQPSHLIRPDA 326
                                        665431..2333333333356666788999***********************99999****************** PP

                                        HHHHTSGGG CS
                            Pkinase 256 eellqhpyl 264
                                        ++l  h+yl
  gene1692|gene1692|rna1691|rna1691 327 RSLSGHSYL 335
                                        999999996 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   2.6e-25   5.7e-22       6     215 ..      45     246 ..      41     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2.6e-25
                                        EEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB....--EEEEEESSSSEE CS
                        Pkinase_Tyr   6 klGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpni....vkllgvctkeepll 77 
                                         lG G+fG+Vv++        + ++Va+K++k++ +    +  ++e++i++kl  +n+    v++  v + +++l+
  gene1692|gene1692|rna1691|rna1691  45 MLGTGTFGQVVRCVGP-----DGEEVAIKVVKNQPKYY--NYEMNEVRILHKLLYNNLndrfVAIKDVFMYKQHLC 113
                                        79***********999.....899*******8877666..67799*****99966665333388888888999999 PP

                                        EEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE..TTEEEE-STTTHE CS
                        Pkinase_Tyr  78 ivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlse..nkvvkisDfGLar 151
                                        iv e++   +L +fL+ ++ + l+ +++  +  qv +Gm  L+   ++H dl   N+L+++  + +vki DfG a 
  gene1692|gene1692|rna1691|rna1691 114 IVEELLGR-NLYTFLKMTRFKGLDHSTVRTILKQVLEGMIQLSVLGIIHCDLKPENILIADydTFKVKIIDFGSAV 188
                                        99999865.9********9*****************************************854569*******998 PP

                                        ETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHH CS
                        Pkinase_Tyr 152 diekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevl 215
                                        +  + ++ +       +  + apE++    + s+ D+Ws G + +E++  g+  +pg +n++ +
  gene1692|gene1692|rna1691|rna1691 189 TSPQVSHFY-----VQSRYYRAPEVILGIPYGSSCDIWSLGCIGYELYV-GNPLFPGKDNMDQM 246
                                        883333333.....3334678**************************98.88888888777655 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.41   9.1e+02       2      25 ..      54      77 ..      53      88 .. 0.77
   2 !   24.9   0.1   5.6e-09   1.3e-05      69     155 ..      99     190 ..      71     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.41
                                       EEEEEETTTEEEEEEEE-S---SS CS
                               RIO1  2 VyhavsedgkevaiKiyktstteF 25
                                       V  +v  dg+evaiK+ k + + +
  gene1692|gene1692|rna1691|rna1691 54 VVRCVGPDGEEVAIKVVKNQPKYY 77
                                       5567778999******99887666 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 5.6e-09
                                        T--S--EEEEETT.EEEEE--EETTEEGGBHHHCG.-.HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEET CS
                               RIO1  69 gvpvPkpielkrh.vlvmefigedgvaapklkdve.e.eeeaeelyeevleemrklykeaglvHaDLSeyNvlvde 141
                                         v + ++  +k+h ++v e++g++ +   k+   +   ++  ++++++vle m++l    g++H+DL   N+l+ +
  gene1692|gene1692|rna1691|rna1691  99 FVAIKDVFMYKQHlCIVEELLGRNLYTFLKMTRFKgLdHSTVRTILKQVLEGMIQLS-VLGIIHCDLKPENILIAD 173
                                        46666778888885789999**9999999999999756999***********99998.***************976 PP

                                        T...EEEE--GTTEEET CS
                               RIO1 142 d...kvviIDvsQavel 155
                                            kv iID++ av+ 
  gene1692|gene1692|rna1691|rna1691 174 YdtfKVKIIDFGSAVTS 190
                                        435899******99974 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   8.6e-07    0.0019     163     200 ..     154     191 ..      87     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.6e-07
                                        SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEE CS
                                APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfedaglgp 200
                                         +  +++H+Dl+p N+l+ + d+  + +iDf+ a+++p
  gene1692|gene1692|rna1691|rna1691 154 LSVLGIIHCDLKPENILIADYDTFKVKIIDFGSAVTSP 191
                                        455799*************44444448********998 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   9.9e-07    0.0022      91     167 ..     110     185 ..      76     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.9e-07
                                Kdo  91 rAlllterlegaqdLedllakwae..laeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwli 164
                                        + l ++e+l g ++L ++l+  +   l+++  r++lk+v   + +l  +g+ H dl + nil+   +   +++ +i
  gene1692|gene1692|rna1691|rna1691 110 QHLCIVEELLG-RNLYTFLKMTRFkgLDHSTVRTILKQVLEGMIQLSVLGIIHCDLKPENILIADYD--TFKVKII 182
                                        45556666655.456677665444569999*********************************9997..******* PP

                                Kdo 165 Dld 167
                                        D+ 
  gene1692|gene1692|rna1691|rna1691 183 DFG 185
                                        *96 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.6e-05       0.1     144     171 ..     156     184 ..      65     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.6e-05
                                        -EEEE-S--SGGGEEE.-.CTTEEEE--G CS
                     Choline_kinase 144 pvvfcHnDlqegNillnk.eekklvlIDF 171
                                         +   H+Dl ++Nil ++ ++ k+ +IDF
  gene1692|gene1692|rna1691|rna1691 156 VLGIIHCDLKPENILIADyDTFKVKIIDF 184
                                        36778*********99652677******* PP

>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     7e-05      0.16      19      46 ..      46      73 ..      38     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7e-05
                               ABC1 19 iAaASiaqVhrAklksgeeVavKvqrpg 46
                                       ++++ ++qV r + ++geeVa+Kv +++
  gene1692|gene1692|rna1691|rna1691 46 LGTGTFGQVVRCVGPDGEEVAIKVVKNQ 73
                                       578899******************9876 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.28   6.2e+02      20      62 ..      36      78 ..      31      99 .. 0.73
   2 ?    9.1   0.0   0.00041      0.91     159     204 ..     113     170 ..      91     188 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.28
                               FTA2 20 aekdiefleyLgkglhsiVlk.vkirgkeYALKlFrfleaeele 62
                                       +++++  + +Lg g+ ++V++ v  +g+e A+K+ +++ +++ +
  gene1692|gene1692|rna1691|rna1691 36 KNQKYMVIGMLGTGTFGQVVRcVGPDGEEVAIKVVKNQ-PKYYN 78
                                       44788899999999999999856788999999988776.44444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00041
                               FTA2 159 aIVKel............ellkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyi 204
                                        +IV el            +++  ++++   +l+++l+ + +l  lgI++ Dlk+en++
  gene1692|gene1692|rna1691|rna1691 113 CIVEELlgrnlytflkmtRFKGLDHSTVRTILKQVLEGMIQLSVLGIIHCDLKPENIL 170
                                        45555555555555555477788888888999***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2466.00
//
Query:       gene1693|gene1693|rna1692|rna1692  [L=874]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-19   70.1   0.2    3.9e-19   68.5   0.2    1.8  1  Sin3_corepress  Sin3 family co-repressor
    1.8e-17   64.0  12.4      1e-08   35.3   3.5    5.7  5  Sin3a_C         C-terminal domain of Sin3a protein
    1.1e-15   57.4   8.4    4.4e-08   33.1   0.1    4.4  4  PAH             Paired amphipathic helix repeat
  ------ inclusion threshold ------
      0.029   14.5   0.2      0.029   14.5   0.2    2.9  3  zf-C2H2_aberr   Aberrant zinc-finger


Domain annotation for each model (and alignments):
>> Sin3_corepress  Sin3 family co-repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.2   8.7e-23   3.9e-19       5      89 ..     419     499 ..     415     506 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 8.7e-23
                     Sin3_corepress   5 psYrlLpksyqqpkcsgrdelekevLNdewvsvptwasedsgsfkasrknqyeealfrcEderyelDmvieanrst 80 
                                         sYr Lp++ +   ++ +d +++evLN +++ +pt++seds + ++ ++n +eealfr+Eder e D++ie+++  
  gene1693|gene1693|rna1692|rna1692 419 GSYRILPEELR---SERQDPISREVLNFTCIGCPTFESEDS-NYVFLKRNVHEEALFRIEDERSEADLAIERIQYF 490
                                        69*******55...7778***********************.6999****************************** PP

                     Sin3_corepress  81 iklleelak 89 
                                        i++le++ +
  gene1693|gene1693|rna1692|rna1692 491 INSLEQIIS 499
                                        *****9965 PP

>> Sin3a_C  C-terminal domain of Sin3a protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0     0.001       4.5      59     118 ..     107     168 ..      81     176 .. 0.78
   2 ?    2.9   0.0     0.017        74     218     244 ..     452     478 ..     428     513 .. 0.69
   3 ?   -3.3   0.1       1.3   5.7e+03      46      77 ..     584     626 ..     551     636 .. 0.43
   4 !   35.3   3.5   2.3e-12     1e-08      56     131 ..     692     765 ..     669     778 .. 0.87
   5 !   16.2   0.0   1.5e-06    0.0068     195     284 ..     796     862 ..     774     864 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.001
                            Sin3a_C  59 lrl..eseeeeeeyYsqllelveklldGeidqsqfEdslRemfgikaYklfTldKliqalvk 118
                                        l+   e+ +++   Y+++le ++++  G+id +++   +R +f  ka  + T+ + + a +k
  gene1693|gene1693|rna1692|rna1692 107 LNKikEEYINDMVTYDNFLETMRDFKFGKIDAEEVCRAVRVLFRDKAHLIETFNDYLPAHLK 168
                                        33334466888899*********************************999998877666555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.017
                            Sin3a_C 218 ereklkkvfLkRnlkaerkeeekkeee 244
                                        e+e+++ vfLkRn+++e+  + ++e++
  gene1693|gene1693|rna1692|rna1692 452 ESEDSNYVFLKRNVHEEALFRIEDERS 478
                                        56889999******7776555444443 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.3
                            Sin3a_C  46 elgldkkesealalrle...........seeeeeeyYsqllel 77 
                                         +g  +k+se++   ++           +++++ ++ + +++l
  gene1693|gene1693|rna1692|rna1692 584 VVGPSHKSSEKTIFTTKnivetgekglkASIDDRDVVTDVMDL 626
                                        2222233333332222123333333333444555555555555 PP

  == domain 4  score: 35.3 bits;  conditional E-value: 2.3e-12
                            Sin3a_C  56 alalrleseeeeeeyYsqllelveklldGeidqsqfEdslRemfgikaYklfTldKliqalvkqlqtivsDekcqe 131
                                         ++++l  e+++++ Y ++ +l+ ++++ +id ++fEd++Re+   k++kl+ + K+i+++ kq+  +++++++ +
  gene1693|gene1693|rna1692|rna1692 692 PINSKL--EQPNTSKYLEVKNLCIEFMKKNIDGHTFEDKIRELTDCKGFKLYNIKKMISKIEKQIIILIENKQSFD 765
                                        344444..7899999****************************************************999887665 PP

  == domain 5  score: 16.2 bits;  conditional E-value: 1.5e-06
                            Sin3a_C 195 veaeerwkeYvesYvlveptegvereklkkvfLkRnlkaerkeeekkeeeeqekaekeeeaekeleveekleiric 270
                                         e++e w eY+e++ +  p e+++   ++ +fL+R++             +++           l+  ++l+i+ +
  gene1693|gene1693|rna1692|rna1692 796 PEEDEMWDEYIEKFETLAPCEEIP--ISNAPFLPRTC-------------KKP------PITGYLK--QDLKIQLN 848
                                        467899*****************7..7899*******.............122......1234556..******** PP

                            Sin3a_C 271 lnsyklvyvpgted 284
                                          +yk+ y+ +te 
  gene1693|gene1693|rna1692|rna1692 849 PMTYKIKYITETES 862
                                        ************96 PP

>> PAH  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   9.9e-12   4.4e-08       2      45 .]     120     163 ..     120     163 .. 0.98
   2 !   19.1   0.1   2.3e-07     0.001       2      43 ..     287     328 ..     286     331 .. 0.85
   3 !    7.4   0.6    0.0011       4.9       4      44 ..     359     398 ..     356     399 .. 0.91
   4 ?   -3.2   0.0       2.2   9.8e+03      15      30 ..     611     626 ..     607     629 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 9.9e-12
                                PAH   2 vYkeFLdiLhdyqkeqidskeVyeqVskLFhdhpdLlreFnqFL 45 
                                        +Y+ FL++++d++  +id +eV+  V+ LF+d  +L++ Fn +L
  gene1693|gene1693|rna1692|rna1692 120 TYDNFLETMRDFKFGKIDAEEVCRAVRVLFRDKAHLIETFNDYL 163
                                        6****************************************997 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.3e-07
                                PAH   2 vYkeFLdiLhdyqkeqidskeVyeqVskLFhdhpdLlreFnq 43 
                                        vY +F++iL++ q +    +   ++V +L+  +pdL+++F++
  gene1693|gene1693|rna1692|rna1692 287 VYRSFVEILQSHQVKNGLFEKMKAEVNSLLWESPDLCEDFER 328
                                        8************764336778899***************84 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0011
                                PAH   4 keFLdiLhdyqkeqidskeVyeqVskLFhdhpdLlreFnqF 44 
                                        + FL++ + ++++ i+ k++   +s L++d ++L+++ ++F
  gene1693|gene1693|rna1692|rna1692 359 DDFLKCINYFNQKFINEKDLLDLISPLLKD-EELIKGLKSF 398
                                        57***********99*************76.7899999888 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 2.2
                                PAH  15 keqidskeVyeqVskL 30 
                                        k++id  +V++ V +L
  gene1693|gene1693|rna1692|rna1692 611 KASIDDRDVVTDVMDL 626
                                        5689999***999776 PP

>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.076   3.4e+02      99     142 ..     339     383 ..     289     403 .. 0.78
   2 ?   14.5   0.2   6.5e-06     0.029      48     132 ..     448     533 ..     441     540 .. 0.72
   3 ?   -2.9   0.2       1.4   6.4e+03      48      66 ..     684     702 ..     641     755 .. 0.52

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.076
                      zf-C2H2_aberr  99 kkedsvv.nlsdvitendvlkdilltifvngvikiiDidkkdliy 142
                                        + e +++  ++++++++d+l d l+ i       i++ d  dli+
  gene1693|gene1693|rna1692|rna1692 339 HDEKNILqRIKELLKSKDLLDDFLKCINYFNQKFINEKDLLDLIS 383
                                        334444426999************999777777888888877776 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.5e-06
                      zf-C2H2_aberr  48 ivelentelleehlekehaakllellkeleieikkteet..ekvnykgkivelkkedsvvnlsdvitendvlkdil 121
                                         + +e  +  +  l+++  +++l  +++   e +   e+    +n+ ++i  l+k+ ++  + d+  +++++k+il
  gene1693|gene1693|rna1692|rna1692 448 CPTFESEDSNYVFLKRNVHEEALFRIEDERSEADLAIERiqYFINSLEQIISLNKDSEI-SMRDIKMSSGIIKEIL 522
                                        46667777777777777666666666554444443333300369999999999998887.**************** PP

                      zf-C2H2_aberr 122 ltifvngviki 132
                                        ++i+ ++  +i
  gene1693|gene1693|rna1692|rna1692 523 KSIYDKSAPEI 533
                                        ****9997766 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.4
                      zf-C2H2_aberr  48 ivelentelleehlekeha 66 
                                        + e+++++ +++ le+  +
  gene1693|gene1693|rna1692|rna1692 684 LLEIKKMDPINSKLEQPNT 702
                                        3333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.58
# Mc/sec: 4557.62
//
Query:       gene1694|gene1694|rna1693|rna1693  [L=276]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-08   32.2   6.1    9.3e-08   32.0   1.0    2.2  2  zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal


Domain annotation for each model (and alignments):
>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.4    0.0046        83      42      70 ..     132     160 ..     125     192 .. 0.78
   2 !   32.0   1.0   5.2e-12   9.3e-08     136     190 ..     210     265 ..     185     274 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0046
                        zf-SNAP50_C  42 fkssfffiedtfynDlrnpeaidysepil 70 
                                         ++ ff ie t+y ++ ++++i++++ + 
  gene1694|gene1694|rna1693|rna1693 132 SSKVFFAIEKTIYLQTIDDNSIKFATMVF 160
                                        4456888*************999998554 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 5.2e-12
                        zf-SNAP50_C 136 Plrlfkk.klrrkkCkvCekfsakwvvlndkllpedpsyfCdkCfrslhydkngek 190
                                        P+++ k+   r + Ck+C k++a   + nd +lpe++ ++C+kCf++l +dk+g+ 
  gene1694|gene1694|rna1693|rna1693 210 PYVSVKHlYGRAQLCKCCLKNNAVLKIANDPILPEKKKFICKKCFELLFLDKEGDS 265
                                        777777757899****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1724.98
//
Query:       gene1695|gene1695|rna1694|rna1694  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      0.002   17.8   0.0     0.0039   16.9   0.0    1.4  1  ubiquitin  Ubiquitin family


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.2e-07    0.0039      21      46 ..      20      45 ..      15      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHHTSSGGGEEEEETTE CS
                          ubiquitin 21 veelKekiaekegipaeqqrLiysGk 46
                                       + +lK kia k gip+++q ++++Gk
  gene1695|gene1695|rna1694|rna1694 20 IGDLKTKIALKYGIPTDSQCIVFNGK 45
                                       789**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1032.62
//
Query:       gene1696|gene1696|rna1695|rna1695  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-18   66.2   4.7    4.4e-18   65.9   4.7    1.1  1  MAT1            CDK-activating kinase assembly factor MAT1
    3.2e-16   59.0   8.5    8.1e-16   57.6   8.3    1.8  2  zf-C3HC4_5      Zinc finger, C3HC4 type (RING finger)
    3.1e-06   26.9   8.4    6.4e-06   25.9   8.4    1.6  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
    1.5e-05   24.8   7.9    3.5e-05   23.6   7.9    1.6  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    2.7e-05   23.9   8.0    5.5e-05   22.9   8.0    1.6  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
    4.6e-05   23.7   7.2      8e-05   22.9   7.2    1.4  1  zf-RING_2       Ring finger domain
    8.4e-05   22.5   7.2    0.00019   21.3   7.2    1.6  1  zf-RING_5       zinc-RING finger domain
     0.0026   17.7   0.4        2.3    8.3   0.0    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0081   15.7   2.4       0.99    9.0   0.2    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0085   16.1   7.2      0.016   15.2   7.2    1.5  1  zf-RING_UBOX    RING-type zinc-finger
  ------ inclusion threshold ------
      0.013   14.9   1.5        3.9    7.0   0.1    2.6  2  zf-ribbon_3     zinc-ribbon domain
      0.016   15.0  11.9      0.074   12.9  10.9    2.1  2  zf-RING_4       RING/Ubox like zinc-binding domain
       0.02   15.0   2.7      0.033   14.3   2.7    1.4  1  zf-UDP          Zinc-binding RING-finger
      0.076   13.0   2.1       0.15   12.1   2.1    1.5  1  zinc-ribbons_6  zinc-ribbons
      0.081   12.8   9.4        1.9    8.4   9.5    2.2  2  Prok-RING_4     Prokaryotic RING finger family 4
       0.13   12.2   0.0        0.3   11.0   0.0    1.7  1  L51_S25_CI-B8   Mitochondrial ribosomal protein L51 / S25 / C
       0.17   11.9   5.4       0.91    9.6   5.0    2.1  2  DZR             Double zinc ribbon
       0.33   10.9   7.5        5.2    7.1   2.7    2.5  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.61   10.2   6.3        4.5    7.5   2.4    2.9  2  Zn-ribbon_8     Zinc ribbon domain
        2.8    7.9   6.5          6    6.8   1.9    2.5  2  DUF3797         Domain of unknown function (DUF3797)
        7.1    6.9  10.5         16    5.8  10.5    1.6  1  zf-C3HC4_4      zinc finger of C3HC4-type, RING


Domain annotation for each model (and alignments):
>> MAT1  CDK-activating kinase assembly factor MAT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   4.7   5.1e-21   4.4e-18       1     114 [.      53     166 ..      53     174 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 5.1e-21
                               MAT1   1 LRknkFrvQiFeDvevekEvdiRkrvlkifNkkeeDFesLkeYndYLeeveeivfnLtngidveeTekkleqYeke 76 
                                        LRk ++ + +FeD++vekE+++Rk ++k+f ++ee+F++ ++YndYLe+ ee vf   n    +  ++++++ +  
  gene1696|gene1696|rna1695|rna1695  53 LRKINYIKPTFEDITVEKECKVRKVLMKVFGREEEEFADVAKYNDYLEKFEEFVFEVLNIKGESLVKERIKEIQDM 128
                                        9********************************************************999999999********** PP

                               MAT1  77 nkelIlknkeklkqeeeeleeleelekeekeekrkeek 114
                                         + +Il+   k    ++ l+ ++++ +  kee+ k++k
  gene1696|gene1696|rna1695|rna1695 129 GEGSILNPIPKTIPGKSVLQTRKRQSHDLKEERSKIQK 166
                                        ******************************99999886 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   8.3   9.5e-19   8.1e-16       3      49 ..       5      50 ..       3      52 .. 0.94
   2 ?   -2.8   0.0         7     6e+03       2      20 ..      88     106 ..      87     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 9.5e-19
                         zf-C3HC4_5  3 iCPvCkssrYlnpdleflinpeCYhkmCesCvdRlFsdGPnqCPvag 49
                                        CPvCks+ Ylnpd+ + i p C+hkmCesC+ R+F+ G ++CP  g
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKSDIYLNPDIVIYISP-CFHKMCESCMLRIFNRGQAPCPECG 50
                                       6******************88.**********************876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
                         zf-C3HC4_5   2 eiCPvCkssrYlnpdlefl 20 
                                        e   v k + Yl +  ef+
  gene1696|gene1696|rna1695|rna1695  88 EFADVAKYNDYLEKFEEFV 106
                                        5566889999999877776 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   8.4   7.5e-09   6.4e-06       1      41 []       6      49 ..       6      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7.5e-09
                                       -TTT-S--SS-E.....E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4  1 CpiCleeakepn....elleCkHsfCskCirkilksrkkvkCPlC 41
                                       Cp+C++ +  +      +++C H++C++C+++i + r++ +CP+C
  gene1696|gene1696|rna1695|rna1695  6 CPVCKSDIYLNPdiviYISPCFHKMCESCMLRIFN-RGQAPCPEC 49
                                       99999876555558889******************.********* PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   7.9   4.1e-08   3.5e-05       2      49 ..       3      55 ..       2      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.1e-08
                                       GSB-TTTSSS...BS-..EEETTEEEEEE-HHHHHHHHH.TT-B-TTT--B--E CS
                         zf-C3HC4_3  2 deeCviCler...prn..vvllpCgHlvlCeeCaekllk.rkkkCpiCrrpiek 49
                                       ++ C++C++    + +  + + pC H  +Ce+C+ ++ +  ++ Cp C +  +k
  gene1696|gene1696|rna1695|rna1695  3 ERRCPVCKSDiylNPDivIYISPCFHK-MCESCMLRIFNrGQAPCPECGTMLRK 55
                                       789******5555444114555*****.**********989*******987665 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   8.0   6.4e-08   5.5e-05       1      40 []       5      49 ..       5      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.4e-08
                         zf-C3HC4_2  1 kCpiCl.dmlkdpsvvt...pCgHvfCqkCilrsLeekn.eCPlC 40
                                       +Cp+C  d + +p  v+   pC H+ C++C+lr  ++++  CP C
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKsDIYLNPDIVIyisPCFHKMCESCMLRIFNRGQaPCPEC 49
                                       6****835666885444566*******************9****9 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   7.2   9.4e-08     8e-05       2      43 ..       5      49 ..       4      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.4e-08
                          zf-RING_2  2 eCpICleel.ssadsvl.llpCgHvfhreClerwlrssst.CPlC 43
                                        Cp+C +++  ++d v+ + pC H ++++C+ r++++ +  CP C
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKSDIyLNPDIVIyISPCFHKMCESCMLRIFNRGQApCPEC 49
                                       6****888845556655566*************98777779**99 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   7.2   2.3e-07   0.00019       1      43 [.       5      50 ..       5      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.3e-07
                          zf-RING_5  1 hCnkCfekl..skeekfyltsCgHifCekClkkll.ekeavCpiCr 43
                                       +C++C + +  +++  +y+ +C H +Ce+C+ + +   +a Cp C+
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKSDIylNPDIVIYISPCFHKMCESCMLRIFnRGQAPCPECG 50
                                       6********9999**********************9999******7 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0027       2.3       1      10 [.       5      14 ..       5      22 .. 0.73
   2 !    7.0   0.1    0.0068       5.8       2       9 ..      46      53 ..      45      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0027
                     DNA_ligase_ZBD  1 hCPvCGsavv 10
                                       +CPvC s + 
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKSDIY 14
                                       5******886 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0068
                     DNA_ligase_ZBD  2 CPvCGsav 9 
                                       CP+CG+ +
  gene1696|gene1696|rna1695|rna1695 46 CPECGTML 53
                                       *****977 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2      0.01       8.5       2      15 ..       5      17 ..       4      20 .. 0.78
   2 !    9.0   0.2    0.0012      0.99      15      29 ..      39      53 ..      29      67 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.01
                                       EETTTTCEECHEET CS
                       TF_Zn_Ribbon  2 kCPnCgstnlveDp 15
                                       +CP+C+s+ ++++p
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKSD-IYLNP 17
                                       7*****96.66665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                                       TSTTCEEESSSSBEE CS
                       TF_Zn_Ribbon 15 pergelvCtdCGlVl 29
                                       ++rg   C++CG++l
  gene1696|gene1696|rna1695|rna1695 39 FNRGQAPCPECGTML 53
                                       7899999****9987 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   7.2   1.8e-05     0.016       1      39 []       6      47 ..       6      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                       zf-RING_UBOX  1 CpICl.elftdP..lv.l.pCGHtFCreClwelskslegafkCP 39
                                       Cp+C+ + + +P  ++   pC H  C++C   l+  ++g+  CP
  gene1696|gene1696|rna1695|rna1695  6 CPVCKsDIYLNPdiVIyIsPCFHKMCESCM--LRIFNRGQAPCP 47
                                       *****77777***744666***********..899999999998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0046       3.9       1      11 [.       2      13 ..       2      18 .. 0.80
   2 ?    6.4   0.2    0.0071       6.1       5      10 ..      46      51 ..      42      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0046
                        zf-ribbon_3  1 stvrCPnCGa.p 11
                                       +++rCP C++ +
  gene1696|gene1696|rna1695|rna1695  2 EERRCPVCKSdI 13
                                       589*****9866 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0071
                        zf-ribbon_3  5 CPnCGa 10
                                       CP+CG+
  gene1696|gene1696|rna1695|rna1695 46 CPECGT 51
                                       888887 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.8     0.048        41      36      45 ..       2      11 ..       1      14 [. 0.83
   2 ?   12.9  10.9   8.7e-05     0.074       1      43 [.       6      49 ..       6      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.048
                          zf-RING_4 36 eegrCPaCre 45
                                       ee rCP C++
  gene1696|gene1696|rna1695|rna1695  2 EERRCPVCKS 11
                                       578*****98 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.7e-05
                          zf-RING_4  1 cplCdeel.detdkdlkpCeCgyqiClfCyhrileeeegrCPaC 43
                                       cp+C +++  + d  ++  +C +++C  C  ri ++ ++ CP+C
  gene1696|gene1696|rna1695|rna1695  6 CPVCKSDIyLNPDIVIYISPCFHKMCESCMLRIFNRGQAPCPEC 49
                                       999999997788999999************************** PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.7   3.8e-05     0.033       8      63 ..       3      56 ..       1      65 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                             zf-UDP  8 gqiCqiCgddvgltedgelFvacnecafpvcrpcyeyerkdgnqsCPqCktrykrl 63
                                       ++ C +C  d+ l+   ++ + ++ c   +c +c+      g+  CP+C t+ ++ 
  gene1696|gene1696|rna1695|rna1695  3 ERRCPVCKSDIYLNP--DIVIYISPCFHKMCESCMLRIFNRGQAPCPECGTMLRKI 56
                                       677********9976..57778899***********99999*9*********9885 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.1   0.00017      0.15       2      42 ..       5      56 ..       4      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                       --SSS-S--EE-S.........SEEE-TTT--EE..EEEEE-SSS-S---EE CS
                     zinc-ribbons_6  2 kCpeCqqelekrg.........eqyhCeaCqedl..kkealCpeCeqelevl 42
                                        Cp C++ +  +           +  Ce+C  ++  + +a CpeC+  l ++
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKSDIYLNPdiviyispcFHKMCESCMLRIfnRGQAPCPECGTMLRKI 56
                                       6*******99666699***999999*****98542245899*****999876 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3     0.052        44      31      40 ..       4      13 ..       1      19 [. 0.81
   2 ?    8.4   9.5    0.0022       1.9       1      41 [.       6      54 ..       6      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.052
                        Prok-RING_4 31 ssCPlCqrri 40
                                        +CP+C++ i
  gene1696|gene1696|rna1695|rna1695  4 RRCPVCKSDI 13
                                       58****9876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                        Prok-RING_4  1 CvlCgeq.....ekkailepCgHlvCkeCfdskdls...sCPlCqrris 41
                                       C +C++      + ++ ++pC H +C++C     +     CP C + + 
  gene1696|gene1696|rna1695|rna1695  6 CPVCKSDiylnpDIVIYISPCFHKMCESCMLRIFNRgqaPCPECGTMLR 54
                                       77777777777788999************98884333568****98765 PP

>> L51_S25_CI-B8  Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00036       0.3      14      41 ..      14      68 ..      13      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00036
                                       TT-TTSEEEEEE..SS-SS-EEEEE-SS-.........................- CS
                      L51_S25_CI-B8 14 ykNPavpivvrr..rsgdgPallaiYfng.........................r 41
                                       y NP++ i++++  ++  + ++l i+++g                         +
  gene1696|gene1696|rna1695|rna1695 14 YLNPDIVIYISPcfHKMCESCMLRIFNRGqapcpecgtmlrkinyikptfeditV 68
                                       67**********7766667**********88888888888777777777777773 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.0    0.0011      0.91      12      49 .]       3      50 ..       1      55 [. 0.82
   2 ?    7.5   3.9    0.0048       4.1       1      25 [.      31      56 ..      26      74 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                                DZR 12 arfCseCgtklkavaa.........edrCpsCgek.vdpearfCpeCG 49
                                        r C+ C++++   ++         +++C sC     + +++ CpeCG
  gene1696|gene1696|rna1695|rna1695  3 ERRCPVCKSDIYLNPDiviyispcfHKMCESCMLRiFNRGQAPCPECG 50
                                       577999999986556688999999999999999886777888899998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0048
                                DZR  1 CpqCgeel.ppdarfCseCgtklkav 25
                                       C +C+  + + ++  C+eCgt l++ 
  gene1696|gene1696|rna1695|rna1695 31 CESCMLRIfNRGQAPCPECGTMLRKI 56
                                       77787775145555899999988754 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.7    0.0061       5.2       4      22 ..       3      21 ..       1      35 [. 0.82
   2 ?    4.9   2.0      0.03        25       5      29 ..      29      52 ..      25      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0061
                        Prok-RING_1  4 gkkCpvCgkelkeedDiVv 22
                                       + +CpvC+  +  + DiV+
  gene1696|gene1696|rna1695|rna1695  3 ERRCPVCKSDIYLNPDIVI 21
                                       789***************8 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.03
                        Prok-RING_1  5 kkCpvCgkelkeedDiVvCpeCgtp 29
                                       k C+ C  ++ +      CpeCgt 
  gene1696|gene1696|rna1695|rna1695 29 KMCESCMLRIFNRGQ-APCPECGTM 52
                                       678888877666644.57*****95 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.11        94      26      35 ..       3      12 ..       1      13 [. 0.73
   2 ?    7.5   2.4    0.0053       4.5      23      38 ..      40      55 ..      27      56 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.11
                        Zn-ribbon_8 26 ltaCPeCgse 35
                                       +  CP C+s+
  gene1696|gene1696|rna1695|rna1695  3 ERRCPVCKSD 12
                                       445****985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0053
                        Zn-ribbon_8 23 dapltaCPeCgsevrr 38
                                        + + +CPeCg  +r+
  gene1696|gene1696|rna1695|rna1695 40 NRGQAPCPECGTMLRK 55
                                       334566*****99988 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.9     0.007         6      15      43 ..       5      32 ..       4      38 .. 0.84
   2 ?    2.9   0.2      0.12     1e+02      14      21 ..      44      51 ..      39      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.007
                            DUF3797 15 qCPeCgNnkvlNsegkviieddtfyreCk 43
                                        CP+C+ +  lN +  + i+   f + C+
  gene1696|gene1696|rna1695|rna1695  5 RCPVCKSDIYLNPDIVIYIS-PCFHKMCE 32
                                       5***********99999987.58999995 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                            DUF3797 14 vqCPeCgN 21
                                       + CPeCg 
  gene1696|gene1696|rna1695|rna1695 44 APCPECGT 51
                                       56****96 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  10.5     0.018        16       1      42 []       6      49 ..       6      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.018
                         zf-C3HC4_4  1 CPiCld..YLekPvsl...eCGhsfClsCisslqkepdgeqllCplC 42
                                       CP+C +  YL+  + +   +C h +C sC+ ++ +  ++   +Cp+C
  gene1696|gene1696|rna1695|rna1695  6 CPVCKSdiYLNPDIVIyisPCFHKMCESCMLRIFNRGQA---PCPEC 49
                                       9***7555776555554466*************999865...8**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1253.00
//
Query:       gene1697|gene1697|rna1696|rna1696  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-71  239.3   0.0    4.4e-71  239.1   0.0    1.0  1  TIM             Triosephosphate isomerase
  ------ inclusion threshold ------
       0.09   12.9   0.0       0.18   12.0   0.0    1.6  1  HGTP_anticodon  Anticodon binding domain
       0.17   12.3   0.0       0.28   11.6   0.0    1.4  1  AAA             ATPase family associated with various cellula


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.1   0.0   7.3e-75   4.4e-71       1     242 [.       5     234 ..       5     235 .. 0.95

  Alignments for each domain:
  == domain 1  score: 239.1 bits;  conditional E-value: 7.3e-75
                                        -EEEEE-TBTS-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BH CS
                                TIM   1 kliagNwKmnktleeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsa 76 
                                        kl++gNwKmn +l++  +l+k+++++  +   + +ia+pf y++ +k+++  + +k+gaq++s+  +G++TGevsa
  gene1697|gene1697|rna1696|rna1696   5 KLLGGNWKMNSSLQTF-DLVKNFRKNFFD-GNDAFIAVPFPYIHIAKEIFP-EYIKVGAQDCSQFINGPYTGEVSA 77 
                                        5789*******99866.688998888777.89************9999996.9*********************** PP

                                        HHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHHTT.HHHHHHHHHHHHTTTS-C CS
                                TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleereagkteevvkeqlkeilkklde 152
                                        +m+k++g++yvi+GHsErr++f+Et+ ++ kK+++a ++gl++ilC+GE+++ re+g   +++k+ql ++ ++++ 
  gene1697|gene1697|rna1696|rna1696  78 SMIKEMGAEYVIVGHSERRKWFGETSTVISKKIRNARNQGLNVILCIGEDEKCREDGGYLDALKDQLLSLKEDISG 153
                                        **************************************************************************99 PP

                                        CCGGCEEEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTTSEEEEESS--TTTHHHHHTSTT--EEE CS
                                TIM 153 ealknvviAYePvWAiGtgktatpeqaqevhaairkelaekvskevaekirilYGGsvnkenakellkqkdidGlL 228
                                        e   ++ +AYePvWAiGtgk+ t++q+ ev++ i+++     +k+     r++YGGsv+  n++++l+ +++dG+L
  gene1697|gene1697|rna1696|rna1696 154 E---DIDVAYEPVWAIGTGKVPTNRQISEVISSIKNW-----GKDLGFYGRVIYGGSVSILNCQTILDVEEVDGFL 221
                                        9...99*******************************.....6778999*************************** PP

                                        ESGGGCSHHHHHHH CS
                                TIM 229 vGgaslkaesFlki 242
                                        +Gg+slk++ F+ i
  gene1697|gene1697|rna1696|rna1696 222 IGGTSLKMD-FCMI 234
                                        *******88.9887 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     3e-05      0.18      39      64 ..     104     129 ..      95     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3e-05
                                        STHHHHHHHHHHTT-SEEEEE-HHHH CS
                     HGTP_anticodon  39 esigkkireadllgipfavvvGekel 64 
                                          i kkir+a+++g ++++ +Ge+e 
  gene1697|gene1697|rna1696|rna1696 104 TVISKKIRNARNQGLNVILCIGEDEK 129
                                        5689********************95 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.7e-05      0.28      17      99 ..      78     154 ..      74     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                                        HHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHH CS
                                AAA  17 avakelgvefleisgsellskyvgesekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqLlt 91 
                                        +++ke+g+e++ +  se + k++ge++  i++ +++a+++    +il i E ++  ++      +  + + +qLl+
  gene1697|gene1697|rna1696|rna1696  78 SMIKEMGAEYVIVGHSERR-KWFGETSTVISKKIRNARNQG-LnVILCIGEDEKCRED-----GGYLDALKDQLLS 146
                                        5678999999999999998.*****************9998.5599999997766433.....3667777777777 PP

                                        HHHHTTTS CS
                                AAA  92 eldgvkkk 99 
                                          ++ + +
  gene1697|gene1697|rna1696|rna1696 147 LKEDISGE 154
                                        77666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 1374.39
//
Query:       gene1698|gene1698|rna1697|rna1697  [L=1024]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-59  199.3  14.6    8.2e-59  199.3  14.6    3.3  3  CRM1_C         CRM1 C terminal
    3.1e-31  108.5   2.6    3.1e-31  108.5   2.6    4.2  5  Xpo1           Exportin 1-like protein
    7.9e-24   83.5   3.9    6.7e-23   80.6   0.6    3.2  3  CRM1_repeat_3  CRM1 / Exportin repeat 3
    7.2e-23   80.0   2.1    1.7e-22   78.8   0.8    2.5  2  CRM1_repeat_2  CRM1 / Exportin repeat 2
    3.3e-09   36.5   0.3    1.2e-08   34.7   0.3    2.1  1  IBN_N          Importin-beta N-terminal domain
    2.1e-07   30.3   0.0    2.1e-07   30.3   0.0    3.5  4  CRM1_repeat    Chromosome region maintenance or exportin repe
  ------ inclusion threshold ------
        2.1    8.8   5.9       0.98    9.9   0.3    3.0  3  DUF2779        Domain of unknown function(DUF2779)


Domain annotation for each model (and alignments):
>> CRM1_C  CRM1 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.18   4.7e+02     236     295 ..     250     312 ..     230     333 .. 0.73
   2 ?   -0.1   0.4      0.16   4.1e+02     236     299 ..     508     563 ..     504     583 .. 0.66
   3 !  199.3  14.6   3.2e-62   8.2e-59      32     320 ..     725    1003 ..     704    1004 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.18
                             CRM1_C 236 aelLaklirlvesgsikvpllee...eqvtsnkvflseyvvellsnaFpnlsqkqveafvvgl 295
                                        +  L  li++v+ g+ k     +   ++ ++   ++++ ++e+l+  F++ ++++v +   g+
  gene1698|gene1698|rna1697|rna1697 250 VACLSCLIEIVDLGRNKNLARSHeieNAEKEKILVIHRQCIEFLKMYFNKFQEERVYEVYGGM 312
                                        456777788877765443333324546677777888999999999999999999997766555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                             CRM1_C 236 aelLaklirlvesgsikvplleeeqvtsnkvflseyvvellsnaFpnlsqkqveafvvglfela 299
                                        +++L++l++l e +s k+  +    ++sn +f++    ++l +     +++ +++ v++lfe+ 
  gene1698|gene1698|rna1697|rna1697 508 VNILKHLLALCEMKSFKTDKAV---IASNIMFIIGQYHRFLLH-----NKSFLKTVVKKLFEFM 563
                                        5799999999999888888777...889998876555444432.....2333444444444444 PP

  == domain 3  score: 199.3 bits;  conditional E-value: 3.2e-62
                             CRM1_C   32 tktpkvrllrtvkkeiLkLietyiekaedleevlnnlveplleavLvdYkknvpeardaevLsllttlveklen 105 
                                          + ++++++++vk ei++L+ t+i+++     v++++v++++e+v++dYk n+  ++++++L l +++v++ en
  gene1698|gene1698|rna1697|rna1697  725 KEGTAFNNAKAVKAEIIELFTTVIDSKF----VQSDFVNMVCEKVIFDYK-NNSIYKEPAILALGSSIVRNAEN 793 
                                         345789******************8877....*****************9.7889******************9 PP

                             CRM1_C  106 ....lisdevpkileavfectldmikkdfeeyPehrveFfellrainkkcfkallk..lpseqfklvidsivwa 173 
                                             ++ ++ + +++a++e+++ ++++  e++ e++++++ l++++   +f+++++  +++++f++v+++++++
  gene1698|gene1698|rna1697|rna1697  794 dgsvIYLQREAFLISALIEPSVPFVMQADENL-EISKNYLLLMESMLLFSFNSFFSslFSQPSFRQVYNTLLYS 866 
                                         9998999*************************.**********************9989*************** PP

                             CRM1_C  174 fkHterdvaetgLnillellknveekkkeaanqFyknyylsllkevlkvltDtdhksgfklqaelLaklirlve 247 
                                         +  ++rdv++ +Ln+l+ ++k++ e   +++ qFy+++y+s+l+++l++++D d++++f++q++l+a +ir+  
  gene1698|gene1698|rna1697|rna1697  867 LI-CIRDVSDLSLNCLTIIFKKCYE---QKIFQFYAQNYMSTLENILGIIFDRDMRYNFDQQCLLFAFMIRI-- 934 
                                         **.**********************...9999****************************************.. PP

                             CRM1_C  248 sgsikvplleeeqvtsnkvflseyvvellsnaFpnlsqkqveafvvglfelandlkkfkehlrDflislkefs 320 
                                           s ++p+l+   ++ n ++lsey+v l+ ++Fpn++q++v++f+ glfel++d++ fkeh+ Df+++++ef+
  gene1698|gene1698|rna1697|rna1697  935 --SKDIPSLD--GINPNVNILSEYIVGLFMKSFPNITQESVKIFSIGLFELCGDDEVFKEHVDDFRVKVYEFG 1003
                                         ..7799****..************************************************************7 PP

>> Xpo1  Exportin 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.49   1.3e+03     116     130 ..      47      62 ..      11      77 .. 0.70
   2 !  108.5   2.6   1.2e-34   3.1e-31       2     149 .]     109     256 ..     108     256 .. 0.98
   3 ?   -0.3   0.0       0.4     1e+03      22      53 ..     370     407 ..     356     438 .. 0.68
   4 ?   -3.1   0.0       2.9   7.4e+03      83     136 ..     510     563 ..     504     576 .. 0.62
   5 ?   -2.5   0.2       1.8   4.7e+03     139     139 ..     871     871 ..     835     913 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.49
                                        TTS-HHHHHTSC.HHH CS
                               Xpo1 116 swidiglivnnp.lln 130
                                        sw+++++i+nn+ l +
  gene1698|gene1698|rna1697|rna1697  47 SWMKVDYILNNSkLQE 62 
                                        59******99542554 PP

  == domain 2  score: 108.5 bits;  conditional E-value: 1.2e-34
                                        HHHHHHHHHHHHHHHHHHTTTTSTTHHHHHHHHHCT..HHHHHHHHHHHHHHHHHHHTSHTTTSCHHHHHHHHHHH CS
                               Xpo1   2 kflrnklaealaelflqeypnnWpsffddllsllss.spsglelllriLkvlpeEiadfsrskleqerrndlkdll 76 
                                        +++++ l+ +l+e++++++p +Wp+f++dl++ ++  s++++ + l+iLk+l+eE++ fs+++ ++ r++ l+++l
  gene1698|gene1698|rna1697|rna1697 109 NYVLQELNTILIEIAKKDWPRRWPTFITDLINVSQGiSMEVCRNSLNILKRLNEEVFIFSEDSITTVRKRLLRNQL 184
                                        6899********************************99************************************** PP

                                        HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTTS-HHHHHTSCHHHHHHHHCCSCCCHHHHHHHH CS
                               Xpo1  77 rsnvqkilelllqileqsqskkqsselveavLkclsswvswidiglivnnpllnllfqlLsdpelreaavecL 149
                                        + ++++i+ ++ +ile+s++++  + l+ea+L+ ++ ++  ++++ i+ +++++l++++L +++ + a++ cL
  gene1698|gene1698|rna1697|rna1697 185 KIEFPQIFGFIKTILEYSRNTEMDEGLLEATLESFQCFCGSMPLDFIFLTEIIDLVLEHL-NSMHSVACLSCL 256
                                        ************************************************************.788899999998 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.4
                                        TTSTTHHHHHHHHHCT.......HHHHHHHHHHHHHHH CS
                               Xpo1  22 nnWpsffddllsllsss......psglelllriLkvlp 53 
                                        ++W++f+ dl s +           +  +++ iL+ l+
  gene1698|gene1698|rna1697|rna1697 370 ETWNKFVFDLYSEFPFTnqdstkRLRRLNYIGILNQLM 407
                                        79********9877543234444444556666666665 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.9
                                        HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTTS-HHHHHTSCHHHHHHHHC CS
                               Xpo1  83 ilelllqileqsqskkqsselveavLkclsswvswidiglivnnpllnllfqlL 136
                                        il+ ll + e+ + k +++ ++++++ +++++ +    ++ + +++++ lf+++
  gene1698|gene1698|rna1697|rna1697 510 ILKHLLALCEMKSFKTDKAVIASNIMFIIGQYHRFLLHNKSFLKTVVKKLFEFM 563
                                        555555555555554467778888888888887766666666666666666666 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 1.8
                                        C CS
                               Xpo1 139 p 139
                                         
  gene1698|gene1698|rna1697|rna1697 871 R 871
                                        2 PP

>> CRM1_repeat_3  CRM1 / Exportin repeat 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.6   2.6e-26   6.7e-23       1      50 [.     475     524 ..     475     525 .. 0.96
   2 ?    2.4   0.0     0.065   1.7e+02      29      47 ..     548     566 ..     546     569 .. 0.86
   3 ?   -3.5   0.0       4.6   1.2e+04      27      40 ..     594     607 ..     592     610 .. 0.83

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 2.6e-26
                      CRM1_repeat_3   1 dgseWswnnlnkLCWAiGSISgamseedEkrfLvtvikdLLnLceekrgk 50 
                                        d++eW++n ln+LCWAiGSISga+se +E++f+v+++k+LL Lce+k+ k
  gene1698|gene1698|rna1697|rna1697 475 DDKEWDCNYLNRLCWAIGSISGAFSEVNEREFFVNILKHLLALCEMKSFK 524
                                        679********************************************987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.065
                      CRM1_repeat_3  29 EkrfLvtvikdLLnLceek 47 
                                         k+fL tv+k+L+++++e 
  gene1698|gene1698|rna1697|rna1697 548 NKSFLKTVVKKLFEFMDED 566
                                        699**********998865 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.6
                      CRM1_repeat_3  27 edEkrfLvtvikdL 40 
                                        e+++ f++ ++k+L
  gene1698|gene1698|rna1697|rna1697 594 ENDEIFIIYILKNL 607
                                        677889*****998 PP

>> CRM1_repeat_2  CRM1 / Exportin repeat 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   4.3e+03      24      39 ..     162     177 ..     160     180 .. 0.86
   2 !   78.8   0.8   6.7e-26   1.7e-22       2      68 .]     396     462 ..     395     462 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                      CRM1_repeat_2  24 eEVliveneeGeivre 39 
                                        eEV+i  +++   vr 
  gene1698|gene1698|rna1697|rna1697 162 EEVFIFSEDSITTVRK 177
                                        8*****9999888886 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 6.7e-26
                      CRM1_repeat_2   2 kqlYkeiLsqlrlvlierMakPeEVliveneeGeivretvkdtdtialYktmretLvyLthLdvedt 68 
                                        + +Y  iL+ql+ +l+++M++PeEV+iv++e++e++r +++dtd+i++Y++mr +L++L++L  ed+
  gene1698|gene1698|rna1697|rna1697 396 RLNYIGILNQLMGTLVDKMPRPEEVFIVVDEYNEVIRKKMTDTDQIEFYRKMRGCLYHLAFLIEEDM 462
                                        678***********************************************************99987 PP

>> IBN_N  Importin-beta N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.3   4.7e-12   1.2e-08       1      73 [.      34      99 ..      34     100 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.7e-12
                                       HHHHHHHHHCSTCHHHHHHHHHHCTTSHHHHHHHHHHHHHHHHHHHGGSCCCHCGSXHHHHHHHHHHHHHHHH CS
                              IBN_N  1 AekqLkqlekqpgflsallqilanseselevRqlAalyLknlitkhWsdeeekqslpseekeqIrnnllnllg 73
                                       Ae+ L +++++p+++ ++ +il ns+++ e+ + A+++L+ +i+ +Ws       +++e k+ +r ++ +l++
  gene1698|gene1698|rna1697|rna1697 34 AERVLLKFKELPNSWMKVDYILNNSKLQ-ESHYVALQLLESMIKVKWS------LFDEEMKQGLRMYVFQLVI 99
                                       8999************************.*******************......************9999876 PP

>> CRM1_repeat  Chromosome region maintenance or exportin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   8.3e-11   2.1e-07       5      37 .]     348     380 ..     345     380 .. 0.96
   2 ?   -0.9   0.3      0.47   1.2e+03      14      22 ..     499     507 ..     497     508 .. 0.91
   3 ?   -3.3   0.0       2.7   6.9e+03      12      18 ..     671     677 ..     671     678 .. 0.88
   4 ?   -2.5   0.1       1.5   3.9e+03      18      23 ..     984     989 ..     983     989 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 8.3e-11
                                        HHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHH CS
                        CRM1_repeat   5 aalqYLvkISeVedrEiFKICLEYWnkLvseLY 37 
                                        a+l YL++IS+++  +iF +  E Wnk+v +LY
  gene1698|gene1698|rna1697|rna1697 348 AGLGYLIQISKINNSNIFSVAFETWNKFVFDLY 380
                                        6999****************************9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.47
                                        HHHHSHHHH CS
                        CRM1_repeat  14 SeVedrEiF 22 
                                        SeV++rE F
  gene1698|gene1698|rna1697|rna1697 499 SEVNEREFF 507
                                        9******88 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.7
                                        HHHHHHS CS
                        CRM1_repeat  12 kISeVed 18 
                                        +IS+Ve+
  gene1698|gene1698|rna1697|rna1697 671 MISNVEE 677
                                        7*****9 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.5
                                        SHHHHH CS
                        CRM1_repeat  18 drEiFK 23 
                                        d+E+FK
  gene1698|gene1698|rna1697|rna1697 984 DDEVFK 989
                                        99***9 PP

>> DUF2779  Domain of unknown function(DUF2779)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       3.7   9.5e+03      69      87 ..     291     309 ..     245     334 .. 0.54
   2 ?    9.9   0.3   0.00038      0.98      56     101 ..     529     574 ..     498     584 .. 0.83
   3 ?   -0.1   0.1      0.46   1.2e+03      69     106 ..     880     914 ..     850     925 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.7
                            DUF2779  69 gsvvvynksfEksrlkela 87 
                                          + +y+++f ++r+ e +
  gene1698|gene1698|rna1697|rna1697 291 EFLKMYFNKFQEERVYEVY 309
                                        3333444444444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00038
                            DUF2779  56 elieeLikiiekegsvvvynksfEksrlkelaqlfpeykeelkqii 101
                                          +++++ ii++   ++ +nksf k+++k+l + ++e+ e +k+++
  gene1698|gene1698|rna1697|rna1697 529 VIASNIMFIIGQYHRFLLHNKSFLKTVVKKLFEFMDEDHEGIKDMA 574
                                        4567888999999**************************9999875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.46
                            DUF2779  69 gsvvvynksfEksrlkelaqlfpeykeelkqiienlvD 106
                                          +++++k +E+++ +  aq   +y   l++i   ++D
  gene1698|gene1698|rna1697|rna1697 880 CLTIIFKKCYEQKIFQFYAQ---NYMSTLENILGIIFD 914
                                        56788999999999999998...777778888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1024 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 6507.58
//
Query:       gene1699|gene1699|rna1698|rna1698  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-19   69.0   1.4    1.4e-12   47.6   0.0    2.1  2  CoaE      Dephospho-CoA kinase
    0.00037   20.8   0.0    0.00052   20.3   0.0    1.3  1  AAA_28    AAA domain
  ------ inclusion threshold ------
      0.036   13.9   0.0      0.055   13.3   0.0    1.4  1  dNK       Deoxynucleoside kinase
      0.047   14.2   0.7      0.093   13.3   0.6    1.8  1  AAA_18    AAA domain
       0.07   13.4   0.1        0.1   12.8   0.1    1.6  1  AAA_22    AAA domain
      0.095   11.9   0.0       0.13   11.5   0.0    1.2  1  DUF2075   Uncharacterized conserved protein (DUF2075)
       0.12   11.9   0.1       0.19   11.3   0.1    1.3  1  cobW      CobW/HypB/UreG, nucleotide-binding domain
       0.13   12.8   0.5       0.14   12.6   0.5    1.4  1  ABC_tran  ABC transporter
       0.22   10.5   0.3       0.33   10.0   0.3    1.3  1  T2SSE     Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.6   1.4e-07   0.00028       2      39 ..       3      40 ..       2      47 .. 0.91
   2 !   47.6   0.0   7.1e-16   1.4e-12      67     178 ..      46     154 ..      41     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.4e-07
                                       EEEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHHTTC CS
                               CoaE  2 ivgltGgiasGKstvanlfadlgvpivDaDlvArqvve 39
                                       i+++tGgi++GK+++ n++++ g   +  D + +++ +
  gene1699|gene1699|rna1698|rna1698  3 IIAITGGIGTGKTALLNILKARGQATINVDGLVHEILN 40
                                       89****************************99998865 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 7.1e-16
                                        HHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHH--S...SEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHH CS
                               CoaE  67 aLrkkvFadpeekkaLnallhPlirreikkelakles...kyvlldvPLLvEkqlekliervlvvdvelelqveRl 139
                                         +r++ F+dp+ +ka ++ + P i  e++k++ +l      +v++++PLL+E +l++ +  ++vv+++++lq+ R 
  gene1699|gene1699|rna1698|rna1698  46 SIRQRFFTDPKFRKAHEKKIRPKIYIETAKRVIYLLLagySVVFIEIPLLFELDLHHYFY-TIVVACDENLQMMRG 120
                                        689***************************99888776889999*************996.6789*******9986 PP

                                        HHCCTSTHHHHHHHHHHS--HHHHHHH-SEEEE-.SSHH CS
                               CoaE 140 vardgvseeevkaiiaaQlseeerlaladvvldNdssla 178
                                              +   +k++++ Q++ e++++la+ v+ N+++++
  gene1699|gene1699|rna1698|rna1698 121 R-----KISYLKERLSFQIPMEKKIKLAQEVIYNNGNID 154
                                        4.....4556789***********************987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.6e-07   0.00052       2      32 ..       4      36 ..       3      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.6e-07
                             AAA_28  2 ivitGgestGKTtlleaLaargypvv..pEaar 32
                                       i+itGg +tGKT ll+ L+arg  ++     + 
  gene1699|gene1699|rna1698|rna1698  4 IAITGGIGTGKTALLNILKARGQATInvDGLVH 36
                                       89*******************877664455555 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.7e-05     0.055       1      25 [.       4      29 ..       4      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                                       EEEEESTTSSHHHHHHHHHCCST.CE CS
                                dNK  1 ivveGnIgaGKstlvklLskklg.vk 25
                                       i++ G Ig GK+ l+++L+ + + + 
  gene1699|gene1699|rna1698|rna1698  4 IAITGGIGTGKTALLNILKARGQaTI 29
                                       89*****************9887433 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   4.7e-05     0.093       1      25 [.       4      32 ..       4     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                             AAA_18  1 IlltGtpGvGKttlakeLskrlgf....g 25
                                       I++tG +G+GKt l + L+ r++      
  gene1699|gene1699|rna1698|rna1698  4 IAITGGIGTGKTALLNILKARGQAtinvD 32
                                       89****************99962224431 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.3e-05       0.1       6      36 ..       2      32 ..       1     131 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                             AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakae 36
                                       +i+++tG  GtGKT ll+ l+ + ++ ++ +
  gene1699|gene1699|rna1698|rna1698  2 RIIAITGGIGTGKTALLNILKARGQATINVD 32
                                       689***************9999876555444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.4e-05      0.13       2      75 ..       2      75 ..       1      82 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.4e-05
                            DUF2075  2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnls 75
                                       +++ +tG+ GtGKt +l+ l a+ + + +    v+ + N++ ++ +r+++  + + +k  e+  +++ +i++++
  gene1699|gene1699|rna1698|rna1698  2 RIIAITGGIGTGKTALLNILKARGQATINVDGLVHEILNGEDIKSIRQRFFTDPKFRKAHEKKIRPKIYIETAK 75
                                       5889************9999998877888888888888999999999999888867777777778888887765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   9.5e-05      0.19       2      25 ..       3      27 ..       2      56 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.5e-05
                                       EEEEEESTTCCHHHHHHHHH.CT-- CS
                               cobW  2 vtvltGflGsGKTtLlnhll.enra 25
                                       ++ +tG +G+GKT+Lln l  + +a
  gene1699|gene1699|rna1698|rna1698  3 IIAITGGIGTGKTALLNILKaRGQA 27
                                       5789************866533333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.5   7.1e-05      0.14      13      51 ..       3      46 ..       1     167 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--...SEEEE..EETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx..xxxxxxxxx RF
                           ABC_tran 13 kvaivGenGaGKStLlkllagllkp...teGei..lldgkdlke 51
                                       ++ai+G  G+GK+ Ll++l    +      G +   l+g+d+k+
  gene1699|gene1699|rna1698|rna1698  3 IIAITGGIGTGKTALLNILKARGQAtinVDGLVheILNGEDIKS 46
                                       79*****************9876652222333332244555554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00017      0.33     131     149 ..       3      21 ..       1      35 [. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                              T2SSE 131 lilvsGgTgsGKttllyal 149
                                        +i ++Gg g+GKt ll++l
  gene1699|gene1699|rna1698|rna1698   3 IIAITGGIGTGKTALLNIL 21 
                                        688**************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1375.73
//
Query:       gene1700|gene1700|rna1699|rna1699  [L=699]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.26   11.8   3.6        3.2    8.3   0.1    3.4  4  DUF16     Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.039   6.9e+02      15      44 ..     126     163 ..     113     175 .. 0.60
   2 ?    8.3   0.1   0.00018       3.2      76     103 ..     425     452 ..     417     453 .. 0.87
   3 ?   -2.9   0.0      0.55   9.9e+03      83      99 ..     484     500 ..     471     505 .. 0.80
   4 ?    0.6   0.1     0.043   7.8e+02      32      61 ..     546     575 ..     525     610 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.039
                                        .XTTB-BHHHHHH........B-..BHHHHHHHHHHHH CS
                              DUF16  15 vkteYVTrkqlne........fkdsnkqrLkkieakvd 44 
                                         ++++V  ++ ++        f  s+k++L  i+  v+
  gene1700|gene1700|rna1699|rna1699 126 SEERHVISRNVQQvtkqsnkiFYVSTKNELSYINMVVE 163
                                        44444444444444222222355557777777766665 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00018
                                        H.......HHHHHHHHHHHHHHHHHHHC CS
                              DUF16  76 eelnkvdetleliletLqkinkRlDsie 103
                                         e+  +de ++++l+tL +i++R+ +ie
  gene1700|gene1700|rna1699|rna1699 425 GEIRLLDEKINMVLKTLREIGERVNKIE 452
                                        458899********************99 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.55
                                        .HHHHHHHHHHHHHHHH CS
                              DUF16  83 etleliletLqkinkRl 99 
                                        + l+ ++etL +++ Rl
  gene1700|gene1700|rna1699|rna1699 484 DELQRMIETLGNLEARL 500
                                        56788888888888887 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.043
                                        BHHHHHHHHHHHH...HHHHHHHHHHHHHH CS
                              DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqg 61 
                                        n+ +Lk+++  vd l  ++nk++++     
  gene1700|gene1700|rna1699|rna1699 546 NEDHLKNVKRAVDGLHTSFNKQNEIKGLIS 575
                                        445555555555555555555555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3812.52
//
Query:       gene17|gene17|rna17|rna17  [L=408]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-21   76.7  24.8    1.7e-21   76.7  24.8    2.2  2  Choline_transpo  Plasma-membrane choline transporter
  ------ inclusion threshold ------
        3.7    7.7   5.1       0.85    9.8   0.5    2.4  2  S1FA             DNA binding protein S1FA


Domain annotation for each model (and alignments):
>> Choline_transpo  Plasma-membrane choline transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   2.8      0.23     2e+03     259     273 ..      52      66 ..      11     106 .. 0.47
   2 !   76.7  24.8   1.9e-25   1.7e-21       5     326 .]     106     391 ..     101     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.23
            Choline_transpo 259 gkllialltgliayl 273
                                +++ i+l+  l+ayl
  gene17|gene17|rna17|rna17  52 VNVGIMLIFLLAAYL 66 
                                222232222333332 PP

  == domain 2  score: 76.7 bits;  conditional E-value: 1.9e-25
            Choline_transpo   5 ivavllllllivlrkrirlaiallkvaskaiksnpslllvplltllllllvsafwivvavalylassgestdkvnsgsesglaa 88 
                                 +++ l+++++ +   ++l+  ++++++k+++ n+   + + ++ll+++ + ++ +++++ +     g+++         g   
  gene17|gene17|rna17|rna17 106 TFGISLVFYFWSIKPILPLMGPMIEATAKILSLNL---IGCTILLLASVSLQVIQSFIFLKV----LGNDD--------AGK-- 172
                                455566666777777779*********99999994...333333333433333333333333....33332........222.. PP

            Choline_transpo  89 vefessskvkalllyllfgllWtleflralqqvtvagavasWYfskkkdlpskfpvlkslkraltyhlGSialgSlilaivqll 172
                                         +++ +++++  +Wt    +++ qv+v+g+v ++  +     + k ++++s++ a+   lGSi ++ li+a v+++
  gene17|gene17|rna17|rna17 173 ---------TIMSVLFILNSYWTFFNTIYFAQVVVSGIVTTHVKN-----EKKGSFWESFYIAF-MALGSISFAGLIMAAVSTA 241
                                .........4799999***************************99.....334679*****999.58***************** PP

            Choline_transpo 173 rlileylekklkkk.enavakcllcclkcclwclekflkflnrnayimvaiyGksFcesakdafellkrnglrvavldsvvdfv 255
                                ++++e+ +++ +++ +++++++++    c+l+++  +++ +n   + + a++G+++ es +++++l+ ++g  +++++  ++ v
  gene17|gene17|rna17|rna17 242 KFLVERERNRNRERgSSNIINIII---LCILSIVGDLVNLMNELVFPYLAVHGTKYTESVSKSYNLIEEKGGIILLSNIAIEKV 322
                                *****8444444445555555544...458999**************************************9888888888877 PP

            Choline_transpo 256 lflgklliallt.gliaylllkatltnpeelnsplvpllvvfiiayliasiflsvyesavdtifvcfaeDpe 326
                                +f+  l++ +++ + ++ lll++ +++++ l++    + +v+   ++ +  fls+++s++ +++  ++e pe
  gene17|gene17|rna17|rna17 323 IFFCLLFFIYFIaSGTTALLLRNPSYQND-LTYF--TVGIVCAPLITFVYSFLSMFSSGTLALIYSYLESPE 391
                                77776666666626668889998777775.6666..44444444444445899***************9886 PP

>> S1FA  DNA binding protein S1FA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   9.5e-05      0.85      13      37 ..      49      73 ..      43      76 .. 0.87
   2 ?   -3.3   0.4       1.2   1.1e+04      10      34 ..     310     334 ..     308     338 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.5e-05
                       S1FA 13 vllvvggllllflvgnyvlyvyaqk 37
                               +l v +g++l+fl++ y+ + ya k
  gene17|gene17|rna17|rna17 49 LLTVNVGIMLIFLLAAYLGFRYAAK 73
                               466789*****************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                       S1FA  10 Glivllvvggllllflvgnyvlyvy 34 
                                G+i+l  ++   ++f+   + +y  
  gene17|gene17|rna17|rna17 310 GIILLSNIAIEKVIFFCLLFFIYFI 334
                                5666666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2270.61
//
Query:       gene170|gene170|rna170|rna170  [L=785]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-28   98.0   8.3    0.00012   22.3   0.0    8.9  8  PC_rep         Proteasome/cyclosome repeat
    6.5e-13   48.9   0.0    1.4e-07   31.8   0.0    4.0  3  HEAT_2         HEAT repeats
    9.1e-06   25.5   0.0          2    8.9   0.0    5.3  6  HEAT           HEAT repeat
     0.0013   19.2   0.1        1.2    9.7   0.0    3.6  3  HEAT_EZ        HEAT-like repeat
     0.0078   16.3   0.9       0.13   12.4   0.0    3.0  2  TPR_2          Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.022   14.8   0.0        0.4   10.7   0.0    2.8  4  Cnd1           non-SMC mitotic condensation complex subunit 1
      0.097   13.3   0.0       0.45   11.1   0.0    2.2  1  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
       0.81    9.4   2.2        0.9    9.3   0.3    2.1  2  SPOB_a         Sensor_kinase_SpoOB-type, alpha-helical domain


Domain annotation for each model (and alignments):
>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.25   5.6e+02       5      31 ..     315     339 ..     315     342 .. 0.76
   2 !   18.5   0.0     9e-07     0.002       1      29 [.     344     371 ..     344     376 .. 0.87
   3 !   21.4   0.0   1.1e-07   0.00024       1      26 [.     382     407 ..     382     412 .. 0.90
   4 !   13.0   0.0   4.8e-05      0.11       2      29 ..     418     445 ..     417     448 .. 0.87
   5 ?    0.3   0.1       0.5   1.1e+03      15      34 ..     477     496 ..     476     497 .. 0.88
   6 !   22.3   0.0   5.3e-08   0.00012       1      34 [.     498     531 ..     498     532 .. 0.95
   7 !   10.4   0.0   0.00033      0.73       1      31 [.     533     562 ..     533     566 .. 0.80
   8 ?    5.5   0.0     0.011        25       7      35 .]     573     601 ..     572     601 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.25
                                    HHHHHCTTSTCHHHHHHHHHHHHHHSS CS
                         PC_rep   5 ALGlihaGsgneeaislLkpylsdtsa 31 
                                    ++G+ih+ + n   +++Lk+yl++ ++
  gene170|gene170|rna170|rna170 315 SIGMIHLFNSNP--YEILKNYLPSEVS 339
                                    578888884444..99******99875 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 9e-07
                                    HHHHHHHHHCTTSTCHHHHHHHHHHHHHH CS
                         PC_rep   1 GAllALGlihaGsgneeaislLkpylsdt 29 
                                    GAl+ALGli aG+ +ee +++L+  l+ t
  gene170|gene170|rna170|rna170 344 GALMALGLIKAGTFSEEDTEYLLYFLD-T 371
                                    9*********************98874.4 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 1.1e-07
                                    HHHHHHHHHCTTSTCHHHHHHHHHHH CS
                         PC_rep   1 GAllALGlihaGsgneeaislLkpyl 26 
                                    G +l+LGli++Gs n+e++s Lk++ 
  gene170|gene170|rna170|rna170 382 GVCLGLGLINMGSANSEILSKLKELS 407
                                    669********************984 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 4.8e-05
                                    HHHHHHHHCTTSTCHHHHHHHHHHHHHH CS
                         PC_rep   2 AllALGlihaGsgneeaislLkpylsdt 29 
                                    +++++G+++++s+n e+++ Lk +  dt
  gene170|gene170|rna170|rna170 418 SVYGMGMLGLNSWNVEILEDLKAISGDT 445
                                    78********************885555 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.5
                                    CHHHHHHHHHHHHHHSSHHH CS
                         PC_rep  15 neeaislLkpylsdtsaevr 34 
                                    ne+ ++++ ++lsd++  v+
  gene170|gene170|rna170|rna170 477 NEDSRNYINELLSDKDPIVK 496
                                    78899***********9886 PP

  == domain 6  score: 22.3 bits;  conditional E-value: 5.3e-08
                                    HHHHHHHHHCTTSTCHHHHHHHHHHHHHHSSHHH CS
                         PC_rep   1 GAllALGlihaGsgneeaislLkpylsdtsaevr 34 
                                    G +l+LG ++ G+g+ ++is L+py+ d s++v+
  gene170|gene170|rna170|rna170 498 GGVLSLGSAFVGTGRLSVISFLLPYINDGSDDVK 531
                                    789***************************9986 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.00033
                                    HHHHHHHHHCTTSTCHHHHHHHHHHHHHHSS CS
                         PC_rep   1 GAllALGlihaGsgneeaislLkpylsdtsa 31 
                                    +A++A+Gl+++ +++  +   L+p+  + + 
  gene170|gene170|rna170|rna170 533 AAVIAIGLVCCDNRDL-LVGTLEPLSENHNF 562
                                    69**********7777.99999999666555 PP

  == domain 8  score: 5.5 bits;  conditional E-value: 0.011
                                    HHHCTTSTCHHHHHHHHHHHHHHSSHHHH CS
                         PC_rep   7 GlihaGsgneeaislLkpylsdtsaevra 35 
                                    Gl   G+g+   +++L+ +++d+++ vr+
  gene170|gene170|rna170|rna170 573 GLFLSGTGDKVCTNILEALMYDSNNLVRQ 601
                                    6666799******************9985 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0097        22      14      82 ..     377     453 ..     344     459 .. 0.73
   2 !    6.8   0.0    0.0038       8.6      25      56 ..     473     504 ..     472     519 .. 0.87
   3 !   31.8   0.0   6.2e-11   1.4e-07       2      85 ..     517     605 ..     516     608 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0097
                         HEAT_2  14 pevrraairaLg....rignpealpaLvellededpavRraaaeaLgaigd....pealpaLkellddddddvvRea 82 
                                    pe+++ ++  Lg      +n e+l  L el + + +   +a +  +g +g+     e l+ Lk++  d++ ++v+ a
  gene170|gene170|rna170|rna170 377 PELAYGVCLGLGlinmGSANSEILSKLKELSKVDRTLLVEASVYGMGMLGLnswnVEILEDLKAISGDTEFERVKIA 453
                                    56788888899977554567799999999999999999999999999999522225577777777766666777765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0038
                         HEAT_2  25 grignpealpaLvellededpavRraaaeaLg 56 
                                    g+++n+++++++ ell+d+dp v +  + +Lg
  gene170|gene170|rna170|rna170 473 GTMANEDSRNYINELLSDKDPIVKAGGVLSLG 504
                                    6799**********************999998 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 6.2e-11
                         HEAT_2   2 daLlqalendpdpevrraairaLg..rignpea.lpaLvellededpavRraaaeaLgai....gdpealpaLkellddd 74 
                                    + Ll ++ nd +++v+raa++a+g   ++n+++ + +L +l e+++  vR+a+a  Lg +    gd+   ++L++l+  d
  gene170|gene170|rna170|rna170 517 SFLLPYI-NDGSDDVKRAAVIAIGlvCCDNRDLlVGTLEPLSENHNFFVRAAVAIILGLFlsgtGDKVCTNILEALM-YD 594
                                    579999*.****************5445777777************************8767434555556666666.67 PP

                         HEAT_2  75 dddvvReaAae 85 
                                    ++ +vR++A +
  gene170|gene170|rna170|rna170 595 SNNLVRQSACI 605
                                    88999999865 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.9   1.3e+04       1      11 [.       6      16 ..       6      21 .. 0.84
   2 ?   -2.3   0.0       3.5   7.8e+03      12      25 ..     102     115 ..      93     116 .. 0.82
   3 ?    1.2   0.0      0.27   6.1e+02       6      25 ..     485     504 ..     482     505 .. 0.80
   4 !    8.9   0.0   0.00091         2       2      28 ..     516     542 ..     515     542 .. 0.90
   5 ?    2.9   0.0     0.077   1.7e+02       5      29 ..     553     577 ..     549     579 .. 0.78
   6 ?    4.8   0.0     0.018        40       4      21 ..     587     604 ..     585     608 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.9
                                   HHHHHHHHHT- CS
                           HEAT  1 llPlllkllsD 11
                                   +lP + +ll+D
  gene170|gene170|rna170|rna170  6 ILPNIKSLLRD 16
                                   79***9*9999 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.5
                                    SSHHHHHHHHHHHH CS
                           HEAT  12 pspeVReaAakaLg 25 
                                    ++ +VR+ +++ +g
  gene170|gene170|rna170|rna170 102 TDGKVRDFVLRVIG 115
                                    6779***9999988 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.27
                                    HHHHT-SSHHHHHHHHHHHH CS
                           HEAT   6 lkllsDpspeVReaAakaLg 25 
                                     +llsD++p V +  +++Lg
  gene170|gene170|rna170|rna170 485 NELLSDKDPIVKAGGVLSLG 504
                                    589*******9987777776 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.00091
                                    HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                           HEAT   2 lPlllkllsDpspeVReaAakaLgala 28 
                                    + +ll  ++D s +V +aA+ a+g ++
  gene170|gene170|rna170|rna170 516 ISFLLPYINDGSDDVKRAAVIAIGLVC 542
                                    7899*******************9765 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.077
                                    HHHHHT-SSHHHHHHHHHHHHHHHH CS
                           HEAT   5 llkllsDpspeVReaAakaLgalae 29 
                                    l  l +  + +VR+a+a  Lg +++
  gene170|gene170|rna170|rna170 553 LEPLSENHNFFVRAAVAIILGLFLS 577
                                    56666778889*********98877 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.018
                                    HHHHHHT-SSHHHHHHHH CS
                           HEAT   4 lllkllsDpspeVReaAa 21 
                                    +l  l+ D++  VR++A+
  gene170|gene170|rna170|rna170 587 ILEALMYDSNNLVRQSAC 604
                                    455566***********9 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00053       1.2      29      53 ..     515     539 ..     493     541 .. 0.82
   2 ?   -2.0   0.0       2.5   5.6e+03      43      53 ..     563     573 ..     548     575 .. 0.68
   3 ?    5.3   0.0     0.013        29      33      50 ..     588     605 ..     562     606 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                        HEAT_EZ  29 ilpaLlalLnddsdeVRaaAagaLg 53 
                                    ++ +Ll+  nd sd+V+ aA++a+g
  gene170|gene170|rna170|rna170 515 VISFLLPYINDGSDDVKRAAVIAIG 539
                                    89999999****************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.5
                        HEAT_EZ  43 eVRaaAagaLg 53 
                                     VRaa+a+ Lg
  gene170|gene170|rna170|rna170 563 FVRAAVAIILG 573
                                    68999999998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.013
                        HEAT_EZ  33 LlalLnddsdeVRaaAag 50 
                                    L al+ d++ +VR+ A++
  gene170|gene170|rna170|rna170 588 LEALMYDSNNLVRQSACI 605
                                    4555599999******96 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0     6e-05      0.13       6      27 ..      54      75 ..      49      79 .. 0.89
   2 ?    0.8   0.2       0.3   6.7e+02      10      30 ..     191     211 ..     190     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6e-05
                          TPR_2  6 nlGlayyklgdyeeAleafekA 27
                                   +l ++y+ l dye+A+e+  +A
  gene170|gene170|rna170|rna170 54 CLSKIYFVLEDYEKAIEYALRA 75
                                   7899**************9998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.3
                          TPR_2  10 ayyklgdyeeAleafekAlel 30 
                                    ay++l d e+ +e+ e+  + 
  gene170|gene170|rna170|rna170 191 AYFYLEDIEKVKELIERLMKE 211
                                    8************99998775 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.33   7.4e+02      24      39 ..     482     497 ..     421     507 .. 0.74
   2 ?    0.1   0.0      0.33   7.4e+02      26      39 ..     484     497 ..     467     538 .. 0.69
   3 ?   -2.4   0.0         2   4.4e+03      30      45 ..     523     538 ..     508     548 .. 0.71
   4 ?   10.7   0.0   0.00018       0.4      23      72 ..     585     638 ..     563     665 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.33
                           Cnd1  24 epLrkrLkDedpyVRk 39 
                                    + +++ L+D+dp V+ 
  gene170|gene170|rna170|rna170 482 NYINELLSDKDPIVKA 497
                                    3344455555555544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.33
                           Cnd1  26 LrkrLkDedpyVRk 39 
                                    +++ L+D+dp V+ 
  gene170|gene170|rna170|rna170 484 INELLSDKDPIVKA 497
                                    45555555555554 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2
                           Cnd1  30 LkDedpyVRktaaivv 45 
                                    ++D +  V++ a+i++
  gene170|gene170|rna170|rna170 523 INDGSDDVKRAAVIAI 538
                                    5677777777777765 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00018
                           Cnd1  23 vepLrkrLkDedpyVRktaaivvakL...ilndmvkekg.flselaklleDenp 72 
                                    ++ L++ + D++  VR+ a i+   +    ++++v + + ++++l+kl+ D+++
  gene170|gene170|rna170|rna170 585 TNILEALMYDSNNLVRQSACIGAGFItmqCNPELVPNYKrIIERLNKLIVDKKE 638
                                    556788999************999998899****999888***********875 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.45      11      83 ..     566     639 ..     561     648 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                  Vac14_Fab1_bd  11 aavaialekkikeyleeivkpvlkc.fsDkdsrvRyyacEslyniakvakgevlkllneifdalvklvaDsdes 83 
                                    aavai l+  ++   +++ + +l++ + D+++ vR  ac     i+ +++ e++ + ++i + l kl+ D++e+
  gene170|gene170|rna170|rna170 566 AAVAIILGLFLSGTGDKVCTNILEAlMYDSNNLVRQSACIGAGFITMQCNPELVPNYKRIIERLNKLIVDKKEN 639
                                    799999999999999*******986368******************************************9876 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.2     5e+03      33      45 ..      59      71 ..      57      72 .. 0.86
   2 ?    9.3   0.3    0.0004       0.9      29      52 ..     188     211 ..     186     213 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.2
                         SPOB_a 33 ylqLgkydkaeey 45
                                   y  L+ y+ka ey
  gene170|gene170|rna170|rna170 59 YFVLEDYEKAIEY 71
                                   77799*****998 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0004
                         SPOB_a  29 vIsGylqLgkydkaeeyieevvke 52 
                                    vI+ y  L+ ++k++e+ie+++ke
  gene170|gene170|rna170|rna170 188 VIDAYFYLEDIEKVKELIERLMKE 211
                                    9********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (785 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 5028.03
//
Query:       gene1701|gene1701|rna1700|rna1700  [L=599]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-09   35.7  10.3    6.8e-08   31.5   6.0    3.1  2  Adaptin_N  Adaptin N terminal region


Domain annotation for each model (and alignments):
>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   6.0   3.8e-12   6.8e-08       3     292 ..      26     300 ..      24     310 .. 0.79
   2 !    1.0   0.1    0.0066   1.2e+02     365     393 ..     310     338 ..     301     383 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.8e-12
                                        HHCCHHHHHHCCSSS-SCHHHHHHHHHHHHHHHCT---GHHHHHHHCCCCSS-CHHHHHHHHHHHHHCTTSCCHHC CS
                          Adaptin_N   3 kriqqelaeilnsnkdddekkkeavkkliylialGedvsflffevvklvaskdfelKrlvYlylellaeesedlal 78 
                                        + i +e +++ +s+k ++  ++ ++ k iy+ +l+++v +   + ++   s+ + +K  +Yl l+ +  e+ + ++
  gene1701|gene1701|rna1700|rna1700  26 SAIIKEKRRMISSSKTEPYVRHSNILKSIYMKMLSYKVNEI--DFLNACESDVLRIKTAGYLGLMTM--ENNEYVI 97 
                                        5566777899999999**********************986..779******************987..566678* PP

                                        CCCHHHHHHCCSSSHHHHHHHHHHHCCC-.-CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCH CS
                          Adaptin_N  79 LvtnslqkDlkdpnqlirglALrvLssir.vpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkql 153
                                        +++n+++kDl+ ++   r+ AL+++++++ + + +  l+  i  + + +     kkA++a+++l    +  +    
  gene1701|gene1701|rna1700|rna1700  98 MAINTIMKDLEKRE--TRNDALTSICNLSnDGSALSNLMGHI--CPNGKGDPFHKKALVAFFRLNPDAKISVVG-- 167
                                        ***********987..69***********6556668888888..5566666779*****998764444433333.. PP

                                        HHHHHHCTT-SSHHHHHHHHHHHHHH.HCCCCCCCHHHHH.HHCCHHHHHHCS-HHHHHHHHHHHCC-.--SSHHH CS
                          Adaptin_N 154 veeikellsdkdpgvvlaAvalleei.kkndrlllkllpk.lvrrLcnllteldpwlqvkiiklltrl.arqepee 226
                                                  +dp+ v+   +++  i kk++r+  +l +      L+ +++++dp+l++k+++++  l ++ +  +
  gene1701|gene1701|rna1700|rna1700 168 ----------QDPSEVYVKSQIIMDIfKKTERI--DLTENdVLFLLSLFMKSSDPFLKIKLLQIFGVLhSKAQLVL 231
                                        ..........34444444445666666899999..8776514455666679**************87614556666 PP

                                        H..HHHHHHHCGGCG........CSSCHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHH CS
                          Adaptin_N 227 rskkellesllnllq........ssnnaVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtll 292
                                        +  k ll+s+++ +         +   a+ +e+++++ +++++++    + +   rl++s+++n ry   +   
  gene1701|gene1701|rna1700|rna1700 232 D--KALLDSIEATIIppkdkarpQIEIALAIEAAEFLLKVEKSTPR---VETFILRLIESQNPNSRYFGFKIVR 300
                                        6..68********999***9999999999**********9999995...5566689999********8876665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.0066
                                        HHHHHHSCCHHHHHHHHHHHHHTTXXHHH CS
                          Adaptin_N 365 grlaekfatdaewvldvllellslsgesv 393
                                        +++++k    ++++l++++ l++  + + 
  gene1701|gene1701|rna1700|rna1700 310 IDCCIKLGLHHNQCLNTFVSLITRNNHKS 338
                                        47********************9877444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3786.05
//
Query:       gene1702|gene1702|rna1701|rna1701  [L=263]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-09   37.8   0.3    3.6e-09   37.0   0.3    1.4  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.3     2e-13   3.6e-09       1     127 [.       6     130 ..       6     134 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2e-13
                              PIN_4   1 fVlDTnvlLhdpealksf.....keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvq 71 
                                        +V DTnv++++++++k++       +    i  +Vl+ELd  K ++       +ar+a+r+l+++ +    +l ++
  gene1702|gene1702|rna1701|rna1701   6 IVPDTNVFISHLDIVKKLyedefPVDVIMSISRVVLRELDYNKGKMM------EAREAIRFLEKVYNAPITELEGR 75 
                                        699***************98877777888999**********99997......88999999999988776666666 PP

                              PIN_4  72 tsaeelpeee......seseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                         ++++++  +      +  ++nD++Il++a +        + v+++ D+   +k k  ++e+
  gene1702|gene1702|rna1701|rna1701  76 LKDSSMDVVDcaklipN-IKNNDDEILNFASKQI------HPVILTGDKAFYLKSKCYNVES 130
                                        66444442212233322.569*******997432......3467788888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1664.05
//
Query:       gene1703|gene1703|rna1702|rna1702  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-19   69.0  22.5    3.6e-19   69.0  22.5    3.5  3  zf-CHY       CHY zinc finger
    6.4e-10   39.2   3.7    6.4e-10   39.2   3.7    5.7  5  zf-RING_2    Ring finger domain
      6e-07   29.3   4.6      6e-07   29.3   4.6    6.6  4  zf-RING_5    zinc-RING finger domain
    7.5e-06   25.7   3.9    7.5e-06   25.7   3.9    6.0  5  zf-C3HC4_3   Zinc finger, C3HC4 type (RING finger)
    1.2e-05   25.0   4.1    1.2e-05   25.0   4.1    6.2  5  zf-C3HC4_2   Zinc finger, C3HC4 type (RING finger)
    0.00022   21.0   5.6    0.00022   21.0   5.6    6.4  4  zf-C3HC4     Zinc finger, C3HC4 type (RING finger)
    0.00026   20.4   2.9    0.00026   20.4   2.9    1.9  2  Rtf2         Rtf2 RING-finger
    0.00043   20.5   5.3    0.00043   20.5   5.3    5.3  4  zf-rbx1      RING-H2 zinc finger domain
     0.0068   16.3   0.0     0.0068   16.3   0.0    7.0  8  Prok-RING_1  Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0  22.5   1.8e-22   3.6e-19       1      75 []       3      76 ..       3      76 .. 0.99
   2 ?    1.4   7.3      0.23   4.5e+02      43      73 ..      88     133 ..      79     136 .. 0.59
   3 !    9.0   7.2   0.00097       1.9      14      73 ..     159     225 ..     146     227 .] 0.62

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 1.8e-22
                             zf-CHY  1 CkHykravvairapcCkklyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefaeyfCpiCkll 75
                                       C+Hy+++ + +r++cC+kly+Cr CH+++e+h+++r+ev++++c+ C+  q+ka+ C++C + +++yfC++C+l+
  gene1703|gene1703|rna1702|rna1702  3 CNHYSNN-CLVRFECCSKLYPCRLCHDKVESHKANRYEVSQMVCIGCNLLQRKAQSCSQCLRAVSKYFCSKCNLW 76
                                       *******.****************************************************************985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                             zf-CHY  43 lcllCeteq.ekavlCkkCkk...........efaey......fCpiCk 73 
                                        +c +C++ + ++a  C +C++           +           CpiC 
  gene1703|gene1703|rna1702|rna1702  88 KCNVCRRGDpKIAFHCDACQTclvatgsknhiH---VenstsgNCPICA 133
                                        477777766445666777777666655444441...0334444677775 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00097
                             zf-CHY  14 pcCkklyaCreCHeeledhelerlevkevlcl...lCeteqekavlCkkCkk....efaey..fCpiCk 73 
                                        +  +++y+C  C +   d ++ +++v+++l +      +e ++ v+C++C++    +      +Cp C 
  gene1703|gene1703|rna1702|rna1702 159 EFIRETYTCPICSKPIGDTSTINKKVEHLLEMepsYPGQEAKNIVKCNNCNNlskcKS--TwdKCPFCG 225
                                        446789*******665555555555554444400045566677888****99764322..244799996 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.9  13.1         9   1.8e+04      21      43 ..       3      26 ..       1      49 [. 0.55
   2 ?  -14.4  21.5         9   1.8e+04      19      44 .]      58      93 ..      23      93 .. 0.55
   3 ?   -1.1   5.1       1.3   2.5e+03       2      31 ..      88     111 ..      87     125 .. 0.61
   4 !   39.2   3.7   3.2e-13   6.4e-10       2      43 ..     128     170 ..     127     171 .. 0.88
   5 ?    2.6   2.9     0.086   1.7e+02      26      43 ..     205     224 ..     193     225 .. 0.63

  Alignments for each domain:
  == domain 1  score: -7.9 bits;  conditional E-value: 9
                          zf-RING_2 21 CgHvfhreClerwlrssst...CPlC 43
                                       C+H +  +Cl r ++ +s+   C lC
  gene1703|gene1703|rna1702|rna1702  3 CNH-YSNNCLVR-FECCSKlypCRLC 26
                                       544.44555555.3333333445555 PP

  == domain 2  score: -14.4 bits;  conditional E-value: 9
                          zf-RING_2 19 l.pCgH...v.fhreClerwlrssst......CPlCr 44
                                       + +C       f+ +C + w  s  +      C +Cr
  gene1703|gene1703|rna1702|rna1702 58 CsQCLRavsKyFCSKC-NLWDSSDGQifhcnkCNVCR 93
                                       2235433333388888.55533333344444488887 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                          zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreCle 31 
                                        +C +C     ++d  ++ +C    +++Cl 
  gene1703|gene1703|rna1702|rna1702  88 KCNVCR----RGDPKIAFHCD--ACQTCLV 111
                                        688884....44444444354..5778874 PP

  == domain 4  score: 39.2 bits;  conditional E-value: 3.2e-13
                          zf-RING_2   2 eCpICleel.ssadsvlllpCgHvfhreClerwlrssstCPlC 43 
                                        +CpIC e++  s + ++ll CgH+ h+ C+++++r++ tCP+C
  gene1703|gene1703|rna1702|rna1702 128 NCPICAEDMlGSLEILVLLRCGHSLHERCFNEFIRETYTCPIC 170
                                        6****888746667777779*********************** PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.086
                          zf-RING_2  26 hreClerwlrssst...CPlC 43 
                                        + +C +++ + +st   CP+C
  gene1703|gene1703|rna1702|rna1702 205 CNNC-NNLSKCKSTwdkCPFC 224
                                        5566.342333333567**** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -31.0  38.1         9   1.8e+04      39      42 ..      70      73 ..       1     108 [. 0.70
   2 ?   -4.9  14.6         9   1.8e+04       1      43 [.      85     133 ..      85     134 .. 0.76
   3 !   29.3   4.6     3e-10     6e-07       1      44 []     128     172 ..     128     172 .. 0.93
   4 ?    1.1   4.6       0.2   3.9e+02      25      43 ..     205     225 ..     203     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: -31.0 bits;  conditional E-value: 9
                          zf-RING_5 39 CpiC 42
                                       C+ C
  gene1703|gene1703|rna1702|rna1702 70 CSKC 73
                                       3333 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 9
                          zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkll.........ekeavCpiCr 43 
                                        hCnkC  +    ++ +   C   +C++Cl               + +CpiC 
  gene1703|gene1703|rna1702|rna1702  85 HCNKCNVCR-RGDPKIAFHCD--ACQTCLVATGsknhihvenSTSGNCPICA 133
                                        788888888.33444445565..899999888889999999999999***95 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 3e-10
                          zf-RING_5   1 hCnkCfekl.skeekfyltsCgHifCekClkkllekeavCpiCrk 44 
                                        +C++C e +  + e  +l++CgH+++e+C+++   + ++CpiC+k
  gene1703|gene1703|rna1702|rna1702 128 NCPICAEDMlGSLEILVLLRCGHSLHERCFNEFIRETYTCPICSK 172
                                        6********777777****************************86 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.2
                          zf-RING_5  25 CekClkkll..ekeavCpiCr 43 
                                        C++C + ++     ++Cp+C+
  gene1703|gene1703|rna1702|rna1702 205 CNNCNNLSKckSTWDKCPFCG 225
                                        999988877778899*****6 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   7.2       2.7   5.4e+03      28      48 ..      15      31 ..       1      35 [. 0.58
   2 ?  -10.5  21.5         9   1.8e+04      23      49 ..      43      67 ..      19      95 .. 0.47
   3 ?    2.9  12.3     0.051     1e+02       3      46 ..      87     135 ..      85     139 .. 0.86
   4 !   25.7   3.9   3.8e-09   7.5e-06       3      48 ..     127     175 ..     125     177 .. 0.87
   5 ?    3.4   3.5     0.035        70      25      44 ..     204     225 ..     197     227 .] 0.65

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                                       HHHHHHHHTT-B-TTT--B-- CS
                         zf-C3HC4_3 28 eCaekllkrkkkCpiCrrpie 48
                                       eC++kl      C +C+ ++e
  gene1703|gene1703|rna1702|rna1702 15 ECCSKL----YPCRLCHDKVE 31
                                       455555....66666666665 PP

  == domain 2  score: -10.5 bits;  conditional E-value: 9
                                       EEE-HHHHHHHHHTT-B-TTT--B--E CS
                         zf-C3HC4_3 23 lvlCeeCaekllkrkkkCpiCrrpiek 49
                                       + +C  C     ++ ++C  C r ++k
  gene1703|gene1703|rna1702|rna1702 43 M-VCIGCNLLQ-RKAQSCSQCLRAVSK 67
                                       2.444444333.344444444444332 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.051
                                        SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH.........TT-B-TTT--B CS
                         zf-C3HC4_3   3 eeCviClerprnvvllpCgHlvlCeeCaekllk.........rkkkCpiCrrp 46 
                                        ++C +C + + ++++    H+ +C++C+    +          + +CpiC ++
  gene1703|gene1703|rna1702|rna1702  87 NKCNVCRRGDPKIAF----HCDACQTCLVATGSknhihvensTSGNCPICAED 135
                                        68*************....8889999998877677888899999******876 PP

  == domain 4  score: 25.7 bits;  conditional E-value: 3.8e-09
                                        SB-TTTSSS....BS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B-- CS
                         zf-C3HC4_3   3 eeCviCler....prnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpie 48 
                                          C+iC e      +  vll+CgH  l e+C++++ +++ +CpiC +pi 
  gene1703|gene1703|rna1702|rna1702 127 GNCPICAEDmlgsLEILVLLRCGHS-LHERCFNEFIRETYTCPICSKPIG 175
                                        68******544437778999*****.**********************96 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.035
                                        E-HHHHHHHHH..TT-B-TTT- CS
                         zf-C3HC4_3  25 lCeeCaekllk..rkkkCpiCr 44 
                                         C++C +  +     +kCp+C 
  gene1703|gene1703|rna1702|rna1702 204 KCNNCNNLSKCksTWDKCPFCG 225
                                        466775433222366******5 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   4.1       7.4   1.5e+04       2       6 ..      23      27 ..       2      35 .. 0.64
   2 ?  -11.6  14.1         9   1.8e+04      22      28 ..      69      75 ..      45      92 .. 0.69
   3 ?   -3.6   5.1       5.3   1.1e+04       2      28 ..      89     111 ..      88     118 .. 0.59
   4 !   25.0   4.1   6.1e-09   1.2e-05       1      40 []     128     170 ..     128     170 .. 0.78
   5 ?   -1.9   5.3       1.6   3.2e+03      25      40 .]     213     224 ..     200     224 .. 0.62

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 7.4
                         zf-C3HC4_2  2 CpiCl 6 
                                       C +C 
  gene1703|gene1703|rna1702|rna1702 23 CRLCH 27
                                       44444 PP

  == domain 2  score: -11.6 bits;  conditional E-value: 9
                         zf-C3HC4_2 22 fCqkCil 28
                                       fC+kC l
  gene1703|gene1703|rna1702|rna1702 69 FCSKCNL 75
                                       6777754 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.3
                         zf-C3HC4_2   2 CpiCldmlkdpsvvtpCgHvfCqkCil 28 
                                        C +C     dp   + C    Cq C+ 
  gene1703|gene1703|rna1702|rna1702  89 CNVCRR--GDPKIAFHCD--ACQTCLV 111
                                        777743..3555555663..6777765 PP

  == domain 4  score: 25.0 bits;  conditional E-value: 6.1e-09
                         zf-C3HC4_2   1 kCpiCl.dmlkd..psvvtpCgHvfCqkCilrsLeekneCPlC 40 
                                        +CpiC  dml     +v+  CgH+ ++ C+ + ++e   CP+C
  gene1703|gene1703|rna1702|rna1702 128 NCPICAeDMLGSleILVLLRCGHSLHERCFNEFIRETYTCPIC 170
                                        5****83454430024556************************ PP

  == domain 5  score: -1.9 bits;  conditional E-value: 1.6
                         zf-C3HC4_2  25 kCilrsLeekneCPlC 40 
                                        kC  ++    ++CP C
  gene1703|gene1703|rna1702|rna1702 213 KCKSTW----DKCPFC 224
                                        444444....69**99 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -24.1  31.3         9   1.8e+04       3      41 .]      25      73 ..       1      92 [. 0.71
   2 ?   -4.5  12.5         9   1.8e+04      16      41 .]     102     132 ..      86     132 .. 0.74
   3 !   21.0   5.6   1.1e-07   0.00022       1      41 []     129     170 ..     129     170 .. 0.91
   4 ?   -4.3   7.2         9   1.8e+04      22      41 .]     205     224 ..     197     224 .. 0.55

  Alignments for each domain:
  == domain 1  score: -24.1 bits;  conditional E-value: 9
                                       TT-S--SS-E...............E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4  3 iCleeakepn..............elleCkHsfCskCirkilksrkkvkCPlC 41
                                       +C ++++ ++               ll+ k + Cs+C+r + k    + C +C
  gene1703|gene1703|rna1702|rna1702 25 LCHDKVESHKanryevsqmvcigcNLLQRKAQSCSQCLRAVSK----YFCSKC 73
                                       5555555555555555555555554555555678888888877....446666 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 9
                                        TTS--B-CHHHHHHHHC.......TSSB--TTT CS
                           zf-C3HC4  16 eCkHsfCskCirkilks.......rkkvkCPlC 41 
                                         C    C++C++   ++       +++ +CP+C
  gene1703|gene1703|rna1702|rna1702 102 HC--DACQTCLVATGSKnhihvenSTSGNCPIC 132
                                        45..3799999999988899997777777**** PP

  == domain 3  score: 21.0 bits;  conditional E-value: 1.1e-07
                                        -TTT-S--SS-E....E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4   1 CpiCleeakepn...elleCkHsfCskCirkilksrkkvkCPlC 41 
                                        CpiC e +        ll C+Hs+++ C  + ++  ++++CP+C
  gene1703|gene1703|rna1702|rna1702 129 CPICAEDMLGSLeilVLLRCGHSLHERCFNEFIR--ETYTCPIC 170
                                        ****9998777766679*****************..9999**** PP

  == domain 4  score: -4.3 bits;  conditional E-value: 9
                                        -CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4  22 CskCirkilksrkkvkCPlC 41 
                                        C++C      +++  kCP C
  gene1703|gene1703|rna1702|rna1702 205 CNNCNNLSKCKSTWDKCPFC 224
                                        44443222222455556666 PP

>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   2.6       3.5     7e+03     143     149 ..      60      66 ..      21      77 .. 0.62
   2 !   20.4   2.9   1.3e-07   0.00026     114     173 ..     126     185 ..     107     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.5
                               Rtf2 143 kalkevk 149
                                        + l++v 
  gene1703|gene1703|rna1702|rna1702  60 QCLRAVS 66 
                                        2344444 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.3e-07
                               Rtf2 114 pfiCpltglemngktkfvalrkCGcVfsekalkevk..sevClvCgkeykeedviplnptke 173
                                           Cp+ + +m g  + ++l  CG+ + e+ + e+   + +C+ C+k+  +++   +n + e
  gene1703|gene1703|rna1702|rna1702 126 SGNCPICAEDMLGSLEILVLLRCGHSLHERCFNEFIreTYTCPICSKPIGDTST--INKKVE 185
                                        457********************************745777*******987765..455555 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   2.6       6.6   1.3e+04      32      43 ..       3      13 ..       1      27 [. 0.57
   2 ?  -19.6  27.0         9   1.8e+04       2      54 ..      88     132 ..      16     133 .. 0.86
   3 !   20.5   5.3   2.2e-07   0.00043       8      54 ..     123     170 ..     120     171 .. 0.84
   4 ?    0.2   1.4      0.49   9.7e+02      25      32 ..     214     221 ..     190     225 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.6
                            zf-rbx1 32 CgHaFHlhCisk 43
                                       C+H +  +C+ +
  gene1703|gene1703|rna1702|rna1702  3 CNH-YSNNCLVR 13
                                       555.35555544 PP

  == domain 2  score: -19.6 bits;  conditional E-value: 9
                            zf-rbx1   2 tCaiCrneleeacieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlc 54 
                                        +C +Cr    + + +c+a +  +c v++G+ +H  H++      +t+ +CP+c
  gene1703|gene1703|rna1702|rna1702  88 KCNVCRRGDPKIAFHCDACQ--TCLVATGSKNHI-HVE-----NSTSGNCPIC 132
                                        68889877777777776663..399999999997.443.....3557777777 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 2.2e-07
                            zf-rbx1   8 neleeacieckapgdee.cpvvlGeCgHaFHlhCiskWlktrkvCPlc 54 
                                        n+ +++c+ c ++   +   +vl +CgH+ H  C ++ +++  +CP+c
  gene1703|gene1703|rna1702|rna1702 123 NSTSGNCPICAEDMLGSlEILVLLRCGHSLHERCFNEFIRETYTCPIC 170
                                        677789999998877775444556************************ PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.49
                            zf-rbx1  25 cpvvlGeC 32 
                                        c+ ++ +C
  gene1703|gene1703|rna1702|rna1702 214 CKSTWDKC 221
                                        55555555 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   2.6       5.1     1e+04      34      49 ..       3      19 ..       2      24 .. 0.67
   2 ?   -0.5   0.6      0.63   1.3e+03       6      16 ..      22      32 ..      18      49 .. 0.79
   3 ?   -5.2   7.9         9   1.8e+04       6      27 ..      69      90 ..      52      94 .. 0.72
   4 ?   -4.8   6.8         9   1.8e+04       5      28 ..      87     108 ..      83     110 .. 0.56
   5 !   16.3   0.0   3.4e-06    0.0068       3      37 ..     125     159 ..     123     163 .. 0.92
   6 ?    4.0   0.1     0.024        48       5      16 ..     165     176 ..     161     180 .. 0.80
   7 ?   -1.7   4.5       1.5     3e+03      17      28 ..     199     210 ..     195     224 .. 0.65
   8 ?    0.3   0.3      0.35   6.9e+02       5      11 ..     219     225 ..     215     227 .] 0.70

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.1
                        Prok-RING_1 34 CyekagkC.vneelhsk 49
                                       C ++ ++C v +e++sk
  gene1703|gene1703|rna1702|rna1702  3 CNHYSNNClVRFECCSK 19
                                       77788888555666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.63
                        Prok-RING_1  6 kCpvCgkelke 16
                                        C +C++++++
  gene1703|gene1703|rna1702|rna1702 22 PCRLCHDKVES 32
                                       69999988765 PP

  == domain 3  score: -5.2 bits;  conditional E-value: 9
                        Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                                        C+ C+   +++  i  C +C 
  gene1703|gene1703|rna1702|rna1702 69 FCSKCNLWDSSDGQIFHCNKCN 90
                                       5667766666667777777774 PP

  == domain 4  score: -4.8 bits;  conditional E-value: 9
                        Prok-RING_1   5 kkCpvCgkelkeedDiVvCpeCgt 28 
                                        +kC+vC++   +   +  C++C t
  gene1703|gene1703|rna1702|rna1702  87 NKCNVCRRGDPKI--AFHCDACQT 108
                                        5777777532222..445666655 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 3.4e-06
                        Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCgtpyHraCyek 37 
                                        t  +Cp+C + +     i v   Cg + H  C+++
  gene1703|gene1703|rna1702|rna1702 125 TSGNCPICAEDMLGSLEILVLLRCGHSLHERCFNE 159
                                        5668****************************987 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.024
                        Prok-RING_1   5 kkCpvCgkelke 16 
                                          Cp+C+k++ +
  gene1703|gene1703|rna1702|rna1702 165 YTCPICSKPIGD 176
                                        68*****99876 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 1.5
                        Prok-RING_1  17 edDiVvCpeCgt 28 
                                        ++ iV C +C  
  gene1703|gene1703|rna1702|rna1702 199 AKNIVKCNNCNN 210
                                        567899999964 PP

  == domain 8  score: 0.3 bits;  conditional E-value: 0.35
                        Prok-RING_1   5 kkCpvCg 11 
                                        +kCp Cg
  gene1703|gene1703|rna1702|rna1702 219 DKCPFCG 225
                                        5777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.59
# Mc/sec: 1150.40
//
Query:       gene1704|gene1704|rna1703|rna1703  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-09   34.9   0.5    1.1e-05   24.1   0.1    2.2  2  GDI       GDP dissociation inhibitor


Domain annotation for each model (and alignments):
>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   2.4e-05      0.42     107     139 ..     106     138 ..      88     169 .. 0.79
   2 !   24.1   0.1   6.3e-10   1.1e-05     211     255 ..     174     222 ..     164     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 2.4e-05
                                        EEEEETCEEEE--SSHHHHHC-TTS-HHHHHHH CS
                                GDI 107 syvykegkiakvpanelealaspllglfekrra 139
                                         y+  +gki+k+p +++e   s++l+l ek  +
  gene1704|gene1704|rna1703|rna1703 106 FYIDSSGKIYKIPYTKTEIADSDILSLREKYLV 138
                                        477789***********************9765 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 6.3e-10
                                        HHHHHCCC....SS-SEEEETT-TTHHHHHHHHHHHHTT-EEETS--EC CS
                                GDI 211 yaeslary....gkspylyplyGlGelpqgfarlsaiyGGtymlnkpvd 255
                                        y+e ++ry    g+ p+lyp yGl e+ + f+r  ++ G  y+l+   +
  gene1704|gene1704|rna1703|rna1703 174 YSERMFRYarnfGNVPFLYPEYGLKEISEMFSRSNSMCGAGYVLDSALV 222
                                        555555541111689*****************************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2146.11
//
Query:       gene1705|gene1705|rna1704|rna1704  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-33  114.4   2.7    2.2e-33  114.1   2.7    1.0  1  Med31            SOH1
  ------ inclusion threshold ------
      0.041   13.2   0.1      0.049   13.0   0.1    1.1  1  Mannosyl_trans3  Mannosyltransferase putative


Domain annotation for each model (and alignments):
>> Med31  SOH1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   2.7   2.5e-37   2.2e-33       2      93 ..       4      95 ..       3      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 2.5e-37
                                       HHHHHHHHHHHHHCSHHHHHHTTSSSSSSSTHHHHHHHGGGGGSTTCCCTT--CHHHHHHHHHHSSTTCCCCTCTCHH CS
                              Med31  2 krFeleleFvqsLanpaYlshLaqekyledeafiaYLkYLeywkepeYakfltyPqcLkaLellqeeefrkelkkpev 79
                                       +rFe eleFvq L+np+Yl++La+e+y+e+e+f +YL+YLeyw++peY++fl+yPqcL +Le l++ ++++ ++++++
  gene1705|gene1705|rna1704|rna1704  4 SRFERELEFVQLLCNPEYLRWLAHEGYFESEEFRSYLRYLEYWRRPEYSRFLSYPQCLAILERLNNGNVNDIMNNESL 81
                                       69**************************************************************************** PP

                                       HHHHHHHHHHH-XX CS
                              Med31 80 vealekqqllewqk 93
                                       ++al +qq+  w +
  gene1705|gene1705|rna1704|rna1704 82 FSALGEQQYFIWLN 95
                                       *********99976 PP

>> Mannosyl_trans3  Mannosyltransferase putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.4e-06     0.049     110     163 ..      28      82 ..      24     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-06
                    Mannosyl_trans3 110 dklFeseeYkktglll..wkdrdlwkrstspkfyeiaenklepskeeskyfgkker 163
                                        + +Fesee++++  +l  w+++++ +    p++  i+e +l + + +  +++++  
  gene1705|gene1705|rna1704|rna1704  28 EGYFESEEFRSYLRYLeyWRRPEYSRFLSYPQCLAILE-RLNNGNVNDIMNNESLF 82 
                                        779********9877666********************.88888888888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 691.23
//
Query:       gene1706|gene1706|rna1705|rna1705  [L=1110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-113  379.8   0.3   6.2e-113  377.8   0.3    1.9  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    4.1e-48  163.6   1.0    6.7e-48  162.9   1.0    1.3  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    6.1e-31  106.7   0.3    1.9e-30  105.1   0.3    2.0  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
      2e-20   72.7   0.0    3.9e-20   71.8   0.0    1.5  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    3.6e-20   72.0   1.9    9.3e-20   70.7   1.9    1.8  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    4.7e-19   68.8   1.0      1e-18   67.6   1.0    1.6  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    2.2e-11   44.2   0.0    7.1e-11   42.5   0.0    2.0  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  377.8   0.3  2.4e-116  6.2e-113       1     390 []     675    1023 ..     675    1023 .. 0.94

  Alignments for each domain:
  == domain 1  score: 377.8 bits;  conditional E-value: 2.4e-116
                                         HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGG CS
                     RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekge 74  
                                         va l+p+++h+qspr+++q+am+kqa+g +sln  kr+++ + +l+++++P+v+t+  +++++        ++e
  gene1706|gene1706|rna1705|rna1705  675 VAGLVPFPHHNQSPRNTYQCAMGKQAIGHISLNVKKRFDSVILQLTYTHRPMVSTK-ILDLIN--------YNE 739 
                                         68999***************************************************.999999........*** PP

                                         S-SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..--SS-GGGS-T CS
                     RNA_pol_Rpb2_6   75 lalGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnvseealkkLde 148 
                                         +++Gqna+VAvmsy+GY+iEDa++ln+++++r++f+  ++k++++  ++ + g +++    p++     + Ld+
  gene1706|gene1706|rna1705|rna1705  740 IPAGQNAMVAVMSYSGYDIEDALVLNKASIERGLFRVEVYKTTTTLLKKHSSGMSDVLWPNPKE-----SVLDD 808 
                                         ******************************************7777788888887766555444.....79*** PP

                                         TSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE CS
                     RNA_pol_Rpb2_6  149 dGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdel 222 
                                         dG+ ++g+ vk+g i+v+k+  ++            i     + v + + ++++g ++++dkv +        +
  gene1706|gene1706|rna1705|rna1705  809 DGLGKPGKMVKDGTIYVNKM--SP------------I-----DGVYKFTGKIHRGDPAYIDKVLI--------T 855 
                                         *******************7..22............2.....235567788999***********........5 PP

                                         -TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHH CS
                     RNA_pol_Rpb2_6  223 kagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtl 296 
                                         +++ + l+k +++q+R +++GDK++srhGqKGvv+li++qeDmPf ++G+v+Di++NP+g+PSRmt+g+++E++
  gene1706|gene1706|rna1705|rna1705  856 RSQDQVLIKTMLRQTRPPEIGDKLSSRHGQKGVVGLIVRQEDMPFNDQGVVPDIIMNPHGFPSRMTVGKIIELI 929 
                                         5667889******************************************************************* PP

                                         HHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS-- CS
                     RNA_pol_Rpb2_6  297 lgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKih 370 
                                          gka+ +egk +d+t+F++++ ee ++ L+++g+++sGk+ +++G+tG +l a+if+G+++y++Lkh+v+dKih
  gene1706|gene1706|rna1705|rna1705  930 SGKAGVVEGKIFDSTAFKENSVEETCNILASHGFSYSGKDCFTSGTTGAPLTAYIFFGPVFYQRLKHMVADKIH 1003
                                         ******************9999**************************************************** PP

                                         --SS--B-TTT--B-SCGGG CS
                     RNA_pol_Rpb2_6  371 aRstGpyslltqQPlgGkaq 390 
                                         +R++Gp   lt+QP++G+++
  gene1706|gene1706|rna1705|rna1705 1004 MRARGPRAILTRQPTEGRSK 1023
                                         ******************86 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.9   1.0   2.6e-51   6.7e-48       1     198 [.      18     392 ..      18     397 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.9 bits;  conditional E-value: 2.6e-51
                                        CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSB CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnlt 76 
                                        gLv+q+++S+++fv+++++  +++++ + s+ + +     ++lk+ +ir+g P+++e ++++++++P e+rlr++t
  gene1706|gene1706|rna1705|rna1705  18 GLVRQHIESYDYFVDHEIKALMRANQIVDSDIDHT-----FYLKYLDIRVGMPSIEE-NMVNYNVFPIECRLRDVT 87 
                                        69*****************************9976.....*****************.****************** PP

                                        XEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTT..........S.HHHHHHTTS.TTS..SSEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxx RF
                     RNA_pol_Rpb2_1  77 YsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlse..........aseeelvelkEcpldqGGyFi 142
                                        Ysa++yv++++v+    n++ i +++v iG++P+Mlrs++c+l +          + ++++ e +Ecpld+GGyFi
  gene1706|gene1706|rna1705|rna1705  88 YSANIYVDIEYVR----NRQIIVKRDVCIGKMPVMLRSSRCHLRKeakgsiegsrTRDRKIKESQECPLDVGGYFI 159
                                        *************....8*************************862222222222457899*************** PP

                                        ETTCEEEEXEEEE............................................................... CS
                                        xxxxxxxxxxxxx............................................................... RF
                     RNA_pol_Rpb2_1 143 inGtekvivaqek............................................................... 155
                                        i+G+e+vi+ qe+                                                               
  gene1706|gene1706|rna1705|rna1705 160 IRGIERVILIQEQlsknriiiesgpkglfasvtsstdehksktsvtikddcyylknsmfneeipvvivmkalgltq 235
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                     RNA_pol_Rpb2_1 156 ............................................................................ 155
                                                                                                                    
  gene1706|gene1706|rna1705|rna1705 236 dkeiaecvgkeyfeiivpsfgecilkevftkeqallyisnyirlrpednrieevltilsekvlpnvqiegcnlrkk 311
                                        **************************************************************************** PP

                                        .................................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSS.....SSSHH CS
                                        .................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx RF
                     RNA_pol_Rpb2_1 156 .................................laGeLlaslfrvllkklerdvkerlqkslekld.....dlmlq 193
                                                                         laG+Ll+ lf++ +k+++ ++k++++k l k       d+ + 
  gene1706|gene1706|rna1705|rna1705 312 giyialmirrltqtrlnilkeddkdfvgnkrfeLAGQLLSILFEDTFKRFNFELKKSIDKILSKRSraqefDALTF 387
                                        *************************************************************999874554444444 PP

                                        HHSCS CS
                                        xxxxx RF
                     RNA_pol_Rpb2_1 194 llvna 198
                                        l ++a
  gene1706|gene1706|rna1705|rna1705 388 LNLQA 392
                                        44555 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   0.3   7.5e-34   1.9e-30       1      85 [.    1025    1108 ..    1025    1110 .] 0.94

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 7.5e-34
                                         BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHH CS
                     RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqe 74  
                                         GGl++GEMErd+li+yGa++l+ erl+i+SD +e++vc++c++la ++ C ++k++ k++k+++p+a+klL+qe
  gene1706|gene1706|rna1705|rna1705 1025 GGLKLGEMERDCLIGYGASSLITERLMISSDVFEAYVCKSCGVLAFKDCCVVCKDT-KPSKIKMPYACKLLFQE 1097
                                         9*********************************************8888888876.589999*********** PP

                                         HHHTTBEEEEE CS
                     RNA_pol_Rpb2_7   75 Lqslgialkll 85  
                                         L+s++i ++l+
  gene1706|gene1706|rna1705|rna1705 1098 LMSMNILPRLH 1108
                                         ******99986 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.0   1.5e-23   3.9e-20       2      68 .]     423     486 ..     422     486 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1.5e-23
                     RNA_pol_Rpb2_3   2 vldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                        vl r +++s +  +++++s+   ++k+rk + +R lh s+wG++Cpv+TPEGe+cGlvk+Lalla++
  gene1706|gene1706|rna1705|rna1705 423 VLSRHSYISAVGMMTKINSH---FEKTRKVSGPRSLHTSSWGMLCPVDTPEGESCGLVKNLALLAEI 486
                                        78999*************99...*****************************************997 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   1.9   3.6e-23   9.3e-20       1      61 [.     523     583 ..     523     584 .. 0.99

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 3.6e-23
                                        EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE- CS
                     RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiV 61 
                                        Vf+NG+++G++++ + +ve+++  RRkg + ++vsi+  ++++ ++ia+D+GRvcRPli++
  gene1706|gene1706|rna1705|rna1705 523 VFLNGDIVGIIDNVDFFVEQFKLHRRKGLVGKFVSIYKVRTERVIHIASDNGRVCRPLIVI 583
                                        9***********************************************************8 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   1.0   4.1e-22     1e-18       2     188 ..     175     342 ..     165     344 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 4.1e-22
                                        TSCEEEEE-SSSSSESSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSS CS
                     RNA_pol_Rpb2_2   2 sngiyvekekdknkisatvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericyds 77 
                                        +n+i+ e+ ++     a+vtss+ + +++++++ kd+ ++ + +   +++ip+viv+kAlgl++d+eI e +   +
  gene1706|gene1706|rna1705|rna1705 175 KNRIIIESGPKGL--FASVTSSTDEHKSKTSVTIKDDCYY-LKNSMFNEEIPVVIVMKALGLTQDKEIAECVG--K 245
                                        3444444444443..5799999999999888777776666.55568888*********************887..5 PP

                                        TTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCH CS
                     RNA_pol_Rpb2_2  78 edsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslen 153
                                        e+++++   + e   ke + t+e+al yi + ++lr++++ r+++   il           ek+++ ++++    n
  gene1706|gene1706|rna1705|rna1705 246 EYFEIIVPSFGECILKE-VFTKEQALLYISNYIRLRPEDN-RIEEVLTIL----------SEKVLPNVQIEGC--N 307
                                        9********99998876.5799*********777766655.555544466..........4566657777777..5 PP

                                        H..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEE CS
                     RNA_pol_Rpb2_2 154 krlkaqdilymidrLlslklgrrevDDiDhlgnkR 188
                                         r+k  +i+ mi+rL + +l+  ++DD+D +gnkR
  gene1706|gene1706|rna1705|rna1705 308 LRKKGIYIALMIRRLTQTRLNILKEDDKDFVGNKR 342
                                        557*******************************9 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   2.8e-14   7.1e-11       1      52 [.     628     662 ..     628     723 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 2.8e-14
                                        HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-S CS
                     RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyT 52 
                                        ++dLl+eg +EylD++EE++++Ia+ ped+ ++                  T
  gene1706|gene1706|rna1705|rna1705 628 FSDLLEEGFIEYLDVNEENDCLIALRPEDIVEET-----------------T 662
                                        89****************************8872.................2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.85u 0.37s 00:00:01.22 Elapsed: 00:00:00.55
# Mc/sec: 6034.19
//
Query:       gene1707|gene1707|rna1706|rna1706  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-19   68.1   0.2    4.4e-19   68.0   0.2    1.0  1  ubiquitin    Ubiquitin family
    2.8e-07   30.3   0.5    3.1e-07   30.1   0.5    1.0  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
    0.00082   19.5   0.5     0.0057   16.7   0.5    1.9  1  Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
  ------ inclusion threshold ------
      0.021   14.8   0.2        1.4    9.1   0.1    2.0  2  Ubiquitin_4  Ubiquitin-like domain
      0.044   14.2   0.1       0.11   13.0   0.1    1.7  1  Ubiquitin_2  Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.2   1.2e-22   4.4e-19       1      72 []       3      75 ..       3      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.2e-22
                                       EEEEETTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE.-TTSBHGGHTTSTTEEEEEEESSC CS
                          ubiquitin  1 itvktldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvL.edertleeygiqdgstlhlvlrlr 72
                                       i+vkt  g++++l v++++tv++lK ki++ e ipaeqqrL+ +G++L +++ tl++++i +g+++h+vl lr
  gene1707|gene1707|rna1706|rna1706  3 IKVKTIAGRDLELNVDPEETVLDLKLKIESIELIPAEQQRLVSNGRILmKEKDTLASLNIVSGNVVHMVLALR 75
                                       89*******************************************************************9876 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.5   8.7e-11   3.1e-07       1      72 []       1      72 [.       1      72 [. 0.95

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 8.7e-11
                                       EEEEEEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE-.-TTSBGGGSS--TTEEEEEEX CS
                          Rad60-SLD  1 ikiilkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeL.dpnstvedldiedgdtidvvi 72
                                       ++i++k+  g +++++V+p++tv +L+ + ++ + ip+ +++rL+ +G+ L ++++t+++l i  g ++++v+
  gene1707|gene1707|rna1706|rna1706  1 MQIKVKTIAGRDLELNVDPEETVLDLKLKIESIELIPA-EQQRLVSNGRILmKEKDTLASLNIVSGNVVHMVL 72
                                       89************************************.*********97527899**************986 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5   1.6e-06    0.0057       4      80 ..       2      71 ..       1      75 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                                       EEEEEETTS-EEEEEEEETT-BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-.TTSBCCCCS-TTTTTTTS- CS
                        Rad60-SLD_2  4 elkfrlvdGsDigpvkfsdaatvaelkekviaqWPkdkeekpksvndlklilaGkiLe.nnktlkelrlplgevkggv 80
                                       ++k++   G D+ +++ ++++tv +lk k+ +      e  p  +++ +l+++G+iL  +  tl++l++++g+v ++v
  gene1707|gene1707|rna1706|rna1706  2 QIKVKTIAGRDL-ELNVDPEETVLDLKLKIES-----IELIP--AEQQRLVSNGRILMkEKDTLASLNIVSGNVVHMV 71
                                       688888899975.7888999999999999843.....33344..45569*******986888***********94443 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00038       1.4       1      32 [.       1      32 [.       1      42 [. 0.90
   2 ?    4.7   0.0    0.0089        32      58      85 ..      43      70 ..      38      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
                        Ubiquitin_4  1 lkvtvkkldgeslevvvkqnatvkdLkkaier 32
                                       ++++vk   g+ le+ v+   tv dLk  ie 
  gene1707|gene1707|rna1706|rna1706  1 MQIKVKTIAGRDLELNVDPEETVLDLKLKIES 32
                                       7899***********************99985 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0089
                        Ubiquitin_4 58 LsfegekLkddkaklkeygirnkselsF 85
                                       L+ +g+ L ++k++l+++ i ++  ++ 
  gene1707|gene1707|rna1706|rna1706 43 LVSNGRILMKEKDTLASLNIVSGNVVHM 70
                                       88999***************99998875 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.1e-05      0.11      16      48 ..      13      45 ..       2      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                                       EEEEEETTSBHHHHHHHHHHHH---TTCEEEEE CS
                        Ubiquitin_2 16 serrfsksltieelKekLelitGtspasmrLql 48
                                        e +++++ t+ +lK k+e i  ++++++rL  
  gene1707|gene1707|rna1706|rna1706 13 LELNVDPEETVLDLKLKIESIELIPAEQQRLVS 45
                                       58899*************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 529.88
//
Query:       gene1709|gene1709|rna1708|rna1708  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 995.07
//
Query:       gene1710|gene1710|rna1709|rna1709  [L=690]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.1e-101  341.1  17.3   1.6e-101  340.5  17.3    1.2  1  Sec6       Exocyst complex component Sec6
  ------ inclusion threshold ------
      0.036   14.8   3.6        2.9    8.6   0.0    3.8  3  PMC2NT     PMC2NT (NUC016) domain
      0.042   14.2   1.1       0.68   10.3   0.3    2.8  2  MbeB_N     MbeB-like, N-term conserved region


Domain annotation for each model (and alignments):
>> Sec6  Exocyst complex component Sec6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.5  17.3  2.6e-105  1.6e-101       3     574 .]     162     687 ..     160     687 .. 0.95

  Alignments for each domain:
  == domain 1  score: 340.5 bits;  conditional E-value: 2.6e-105
                                        HHHHHHHHHHHHHHHHHHSTTSSSCHHHH....HHHHHHHHHHHHHCCCCS.----TT--...............- CS
                               Sec6   3 kvdkliekFdkllweiirslielvregntslvvrlvkiverEekeDeklealreltkkekd.....eedaanfrar 73 
                                         ++k + +F +++ ei++++ie     n++++ ++v+ive+Ee +D  +++ +e + +e++     +++++++ ar
  gene1710|gene1710|rna1709|rna1709 162 TIEKNSLDFTAKILEICEEFIE-----NHEVMGKVVQIVEKEESRDDLTRKVQEGENSEDPvlrelHKMYRMYTAR 232
                                        6889999***************.....99**********************99999996667977778888888** PP

                                        ----HHHHHHHHHHHHHHHHCTS--S---TT--HHHHH...HHHHHHHHHHHHCCCCCS-TTT-HHHHHHHHHHHH CS
                               Sec6  74 rprnykkkflealeesveerfeeckekfseddkklellenldwlledLevVkdelaplfPpswkifktyvkiYhnk 149
                                        +p+  k+k+++++e sv+ +f++++ +       + +++++d++l+dL+++k++++  f+p    f+ ++ +Yhn+
  gene1710|gene1710|rna1709|rna1709 233 KPKMLKDKVIKSIEVSVKSKFDKLRDE-------EIFVNKMDFVLNDLSFIKENIKLSFYP----FDDILILYHNN 297
                                        ************************985.......56679**********************....*********** PP

                                        HHHHHHHHTTS-.--HHHHHHHHHHHHHHHH.HTTTSSHHHC.CCC.---SS-HHHHHHHHHHHHHHHHHHHHHHH CS
                               Sec6 150 lhdllqelvsse.leaedilailewvkkYskklsklnpelefkkke.lkpllldekkeeLledYlklivkkmkeWl 223
                                        l+ +l+e  ++e l+a++ilai+e+v +Y+++ ++   +++ k+++ l+  ll++ ++eLle+Y+++ ++k+keW+
  gene1710|gene1710|rna1709|rna1709 298 LKLFLDE--NTErLDAGEILAIIEYVGNYYNTIES---KFN-KIADaLGRRLLSN-ETELLEKYTRTAQEKLKEWI 366
                                        *****85..7777**************99988888...444.47788*******9.******************** PP

                                        HHHHHHHHHHHHCT---..EESSSEE-CHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               Sec6 224 dnllktEvkkftereeppeededglyvlplpvdvfqmlaeqvdvaaeskqakilvgvleelsellksrqdawqell 299
                                        +n+ + E +kf++r+e+ ++de++++ +p++v+++q++++q++ +    +++i++++++++ ++++ +++++ e +
  gene1710|gene1710|rna1709|rna1709 367 MNINRIEIEKFYARNEELSRDEEDKLISPGFVSLLQIIRMQLEPI--AFNKRIFAHITRTITKYCEVFRENLVEAM 440
                                        *********************************************..8999************************* PP

                                        HC-TTSTT.............HHHHHHHHHHHHHHHHH...HHHHHC.........---HHHHHHHHHHHHHHHHH CS
                               Sec6 300 eeelkkymsvknnereeskpglveyliAlaNdqlkcadyaeslsskylelvsskyeeriteefeelldgfvdlske 375
                                        e+++k  +++++      k+g+ +++i+++N+ lk+++y++sl s +            ++e++el d+f+d+ k 
  gene1710|gene1710|rna1709|rna1709 441 EKDFKPSCEMSS------KAGYEDFCIMFGNSGLKITQYITSLPSYH------------NNEVKELGDIFIDILKA 498
                                        ******987777......899***********************999............89*************** PP

                                        HHHHHCHHHHCCTTCCCCHHHHTTTSSHHHHHHHHHHHHTTTTGGGS.S-HHHHHHHHHHHHHHHHHHHHHHHCSS CS
                               Sec6 376 aisalleiifnDLkpalsklftkkWytgelmeqivetiedYlndykeylspelfevlleelldelvveYlralrkk 451
                                          ++l+e+i+  ++pa++k+ft +W++g++++ ++ t++d+l+dy++++s+  f ++++el+ ++v++Y+++l +k
  gene1710|gene1710|rna1709|rna1709 499 SNTFLSEFIIYACQPAIDKIFTDEWCSGNVTKVVLLTLQDFLSDYQNTMSEYSFITFIHELSTSIVLAYMKQLGRK 574
                                        **************************************************************************** PP

                                        ----SHHHHHHHHHHHHHHHHHHHHHHHHTT-...---CCCCTTHHHH...HHHH--SHHHHHHHHHHHHHS-TT- CS
                               Sec6 452 klkfaakkqkkfaekikrDaeklydffeklgs.eedaaylkqklraielllelleledpdavplevetllesypdi 526
                                        ++ +    + ++++ +k+D++kly++++++g+ e+  ++l++ l++i     l+e++++d++++ev++l+  ypdi
  gene1710|gene1710|rna1709|rna1709 575 RAII----ASECSKVLKSDHTKLYELLSNYGDkEDVGTCLSPILKIIP----LMETRNDDLFIVEVKSLKLIYPDI 642
                                        ****....************************9999************....9999999***************** PP

                                        -HHHHHHHHHCCSS-STCHHHHHHHHTT---SS----....-SSCCCS CS
                               Sec6 527 sedhveavlkaRkDldksevkelveqlkeikkevesavepprtifsrv 574
                                        ++ ++++++k R+Dl+++++k+l ++lke+  + +s++   +tifsr+
  gene1710|gene1710|rna1709|rna1709 643 KKGFIKTIIKKRQDLTEDQKKALTDRLKECFADEASKE---KTIFSRL 687
                                        ********************************988887...7***996 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.027   1.6e+02      19      49 ..      23      53 ..       4      87 .. 0.75
   2 ?    1.0   0.1      0.12     7e+02      23      69 ..     161     208 ..     146     219 .. 0.55
   3 ?    8.6   0.0   0.00048       2.9      16      55 ..     323     362 ..     321     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                             PMC2NT 19 rsldpefaksldeqserllslinsllklaas 49
                                       +s++++++++ +++ ++l ++i+++ +++ +
  gene1710|gene1710|rna1709|rna1709 23 ESVERSTKEAYEHHDQNLTEMISKCYSSILN 53
                                       68899999999************99877644 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                             PMC2NT  23 pefaksldeqserllslinsllklaaskseisas.sklededdveekf 69 
                                        + + k+  + ++++l++ ++++++++  +++ ++ +k+e+ dd+++k+
  gene1710|gene1710|rna1709|rna1709 161 NTIEKNSLDFTAKILEICEEFIENHEVMGKVVQIvEKEESRDDLTRKV 208
                                        333333333444555555555555555555544477777777766554 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00048
                             PMC2NT  16 dfyrsldpefaksldeqserllslinsllklaaskseisa 55 
                                        ++y++++++f+k  d+ ++rlls  ++ll+  +   + + 
  gene1710|gene1710|rna1709|rna1709 323 NYYNTIESKFNKIADALGRRLLSNETELLEKYTRTAQEKL 362
                                        69**************************998877766644 PP

>> MbeB_N  MbeB-like, N-term conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00011      0.68      15      41 ..      18      44 ..       5      52 .. 0.88
   2 ?    1.1   0.0     0.084     5e+02      20      34 ..     243     257 ..     240     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                             MbeB_N 15 skeqaeSteemvksafekheksvkeaL 41
                                       ++++ eS+e+++k a e h ++++e +
  gene1710|gene1710|rna1709|rna1709 18 LQTKLESVERSTKEAYEHHDQNLTEMI 44
                                       7899*******************9866 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.084
                             MbeB_N  20 eSteemvksafekhe 34 
                                        +S+e +vks f k++
  gene1710|gene1710|rna1709|rna1709 243 KSIEVSVKSKFDKLR 257
                                        79***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (690 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1067  (0.0595125); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 4122.51
//
Query:       gene171|gene171|rna171|rna171  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-16   60.9  14.7    1.3e-12   48.0   2.9    2.4  2  CIAPIN1   Cytokine-induced anti-apoptosis inhibitor 1, Fe-S b


Domain annotation for each model (and alignments):
>> CIAPIN1  Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   3.8   5.9e-08    0.0011      11      32 ..      42      63 ..      30      67 .. 0.78
   2 !   48.0   2.9   7.5e-17   1.3e-12      67      99 ..      66      98 ..      62      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.9e-08
                        CIAPIN1 11 kakkrrkackdctCGlkeleee 32
                                   + + + +ackdctCGlke++e 
  gene171|gene171|rna171|rna171 42 RGSVKTRACKDCTCGLKEKQEI 63
                                   455688************9985 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 7.5e-17
                        CIAPIN1 67 tssCgsCaLGDafrCsgCPylGlPafkpGekve 99
                                   +s+Cg+C  GDafrCsgCP lGlP++++Ge v+
  gene171|gene171|rna171|rna171 66 RSACGNCHKGDAFRCSGCPSLGLPPYEAGEVVS 98
                                   699***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 804.08
//
Query:       gene1711|gene1711|rna1710|rna1710  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-17   61.8  10.1    1.8e-15   57.3  10.1    2.0  1  Erv26     Transmembrane adaptor Erv26


Domain annotation for each model (and alignments):
>> Erv26  Transmembrane adaptor Erv26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3  10.1     1e-19   1.8e-15       5     176 ..       8     158 ..       4     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1e-19
                              Erv26   5 ellsylglvlgflfltlaiasgLyYlsElvEEhtvlakrllkrliyaiiaiqvllllvdkfpltltllsivshvvy 80 
                                        +ll ++g + g++ l + i  ++ Y    +E+ +  ak+ ++ +i++  +++++lll  + +++++l+s+  ++ +
  gene1711|gene1711|rna1710|rna1710   8 SLLLIVGSIGGLVGLGIGIVKAIDY----IEDKAYAAKKHIESIIQISAGLHIILLL-RGVSIFQILFSLSVQYAF 78 
                                        5788899999999999999999988....69*********************99976.89**************** PP

                              Erv26  81 lqnlrrfPvvkltdplfllscvlvvlnhylwfrh.FskkqarlkkessyykkkkdvpsfteiasffglcvWlvPfa 155
                                        +  l+ +P+vk+ +p f++  +  +lnh+l++r  Fsk+                    +ei+ +f+l vW  Pf 
  gene1711|gene1711|rna1710|rna1710  79 YCLLDIYPLVKMDNPYFIYGTIASLLNHFLVIRLlFSKP----------------GIYGAEIVLYFAL-VWTTPFC 137
                                        ********************************9636666................122379******8.9****** PP

                              Erv26 156 lfvsLsAgdnvLPtmgsesas 176
                                        +f+sLsA+d+vL   g+ s +
  gene1711|gene1711|rna1710|rna1710 138 FFLSLSANDEVLFVRGKASPN 158
                                        ************888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1158.12
//
Query:       gene1712|gene1712|rna1711|rna1711  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0028   17.1   0.0     0.0032   16.9   0.0    1.1  1  SAC3_GANP  SAC3/GANP family


Domain annotation for each model (and alignments):
>> SAC3_GANP  SAC3/GANP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-07    0.0032     165     227 ..      36     101 ..       9     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-07
                                        ---TTHHHHHHHHHHHTTT-...HHHHHHHCTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHT CS
                          SAC3_GANP 165 eelpneaefrayylLlnlrd...pdilrevqelpseilkspevqlalklvaalqennyvrffklvk 227
                                         + +n a ++ay+lL++l++   +++ ++++++    l++p ++l++++  +++ + + r+ + v+
  gene1712|gene1712|rna1711|rna1711  36 PSTENSAFIKAYMLLYHLSTgtkKRFYTTIETVTPTELENPSIKLVIEVDMCMNIGAVERLKNAVE 101
                                        56799*************6654489999*****99999****************999777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1060.73
//
Query:       gene1714|gene1714|rna1713|rna1713  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.094   12.3   0.0       0.15   11.7   0.0    1.3  1  LepB_N    LepB N-terminal domain


Domain annotation for each model (and alignments):
>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.1e-06      0.15      37      72 ..     124     159 ..     117     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.1e-06
                             LepB_N  37 lkaekeekklkqfariDwGaafrnfakpeNnedils 72 
                                        l++++ e+++ +f+r+  G+afr + + e  edil 
  gene1714|gene1714|rna1713|rna1713 124 LHSSNVENESSSFVRVSEGKAFRSYEESESSEDILP 159
                                        567888999*************************84 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1399.94
//
Query:       gene1715|gene1715|rna1714|rna1714  [L=588]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-83  273.2  26.4      7e-09   36.1   0.4   14.0 14  Sel1             Sel1 repeat
    0.00016   22.1   4.2         15    6.5   0.0    7.4 11  TPR_6            Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.32   10.9   1.6        3.9    7.5   0.0    3.0  4  Surfac_D-trimer  Lung surfactant protein D coiled-coil trimer
       0.73   10.5   5.0         54    4.5   0.0    4.7  5  TEX29            Testis-expressed sequence 29 protein


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.024   1.1e+02      12      35 ..      53      76 ..      51      79 .. 0.86
   2 ?   -0.4   0.0      0.46   2.1e+03       3      32 ..      82     110 ..      81     115 .. 0.74
   3 !   21.3   0.3   6.8e-08    0.0003       3      38 .]     133     166 ..     131     166 .. 0.90
   4 !   19.4   0.0   2.8e-07    0.0013       7      37 ..     173     201 ..     172     202 .. 0.94
   5 !   24.8   0.0   5.5e-09   2.4e-05       2      36 ..     204     236 ..     203     238 .. 0.92
   6 !   33.0   0.7   1.4e-11   6.3e-08       1      38 []     239     274 ..     239     274 .. 0.96
   7 !   25.3   0.1   3.9e-09   1.7e-05       1      37 [.     275     309 ..     275     310 .. 0.92
   8 !   24.2   0.0   8.7e-09   3.9e-05       2      36 ..     312     344 ..     311     346 .. 0.91
   9 !   22.7   0.1   2.4e-08   0.00011       4      37 ..     350     381 ..     348     382 .. 0.92
  10 !   14.3   0.0   1.1e-05     0.049       3      38 .]     385     418 ..     383     418 .. 0.90
  11 !   36.1   0.4   1.6e-12     7e-09       1      38 []     419     454 ..     419     454 .. 0.95
  12 !    7.6   0.0    0.0014       6.3       3      38 .]     457     490 ..     457     490 .. 0.88
  13 !   23.4   0.0   1.5e-08   6.9e-05       2      33 ..     492     521 ..     491     526 .. 0.90
  14 !   21.6   0.1   5.7e-08   0.00025       5      35 ..     531     559 ..     527     562 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.024
                               Sel1 12 lylnGlgvpkDpekAiewyekAAe 35
                                       +y++G g+  D +kA+  y kAA 
  gene1715|gene1715|rna1714|rna1714 53 CYEFGIGTTVDMKKAEMGYTKAAL 76
                                       89*************998888886 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.46
                               Sel1   3 AmyrLGmfylylnGlgvpk...DpekAiewyek 32 
                                        A+ rL+ +    +G+  p+   D+++A++++ k
  gene1715|gene1715|rna1714|rna1714  82 ALIRLAFIR--RFGR--PTaiiDRQEAERHLDK 110
                                        778899444..8888..5556799***998866 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 6.8e-08
                               Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A y LG   +y++G gvp Dp +A+++y  +A  G+
  gene1715|gene1715|rna1714|rna1714 133 ARYCLG--VCYQEGYGVPVDPLLAVKYYSESAYEGN 166
                                        666699..999********************99886 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 2.8e-07
                               Sel1   7 LGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        LG  y++l+G gv+k++e A+e+++ A e+ 
  gene1715|gene1715|rna1714|rna1714 173 LG--YCFLKGFGVEKNEEIAVELFKYASEKK 201
                                        9*..***********************9975 PP

  == domain 5  score: 24.8 bits;  conditional E-value: 5.5e-09
                               Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeq 36 
                                         A+y+ G   +y++G+gv+++  kA+e y+++ ++
  gene1715|gene1715|rna1714|rna1714 204 TALYNIG--FCYEEGRGVERNFFKAFEMYKLSSKM 236
                                        69*****..999******************99876 PP

  == domain 6  score: 33.0 bits;  conditional E-value: 1.4e-11
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        ++A+++LG   +y++G+gv +D +kA+e+y+k+A qG+
  gene1715|gene1715|rna1714|rna1714 239 SYAQNALG--NCYEEGKGVNRDLQKAFEFYKKSALQGY 274
                                        68******..999***********************96 PP

  == domain 7  score: 25.3 bits;  conditional E-value: 3.9e-09
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                        ++ +++L+   +y++G g++k  +kA+ewy++AA qG
  gene1715|gene1715|rna1714|rna1714 275 PSGQCNLA--FCYQKGIGTKKCLQKAFEWYKRAAVQG 309
                                        5789****..999********************9665 PP

  == domain 8  score: 24.2 bits;  conditional E-value: 8.7e-09
                               Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekAAeq 36 
                                         A ++ G  y+y+nGlg+p+  +kAi+wy+ +A+ 
  gene1715|gene1715|rna1714|rna1714 312 RAKHNIG--YCYQNGLGTPQCMSKAIYWYKESASE 344
                                        577899*..***********************986 PP

  == domain 9  score: 22.7 bits;  conditional E-value: 2.4e-08
                               Sel1   4 myrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                         ++LG   +y++G gv +D+++A++++   A++G
  gene1715|gene1715|rna1714|rna1714 350 IHALG--VCYQHGYGVSRDERLAVRYFNEGAKAG 381
                                        678**..999*********************998 PP

  == domain 10  score: 14.3 bits;  conditional E-value: 1.1e-05
                               Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A   L+  ++y  G+gv   pek + ++++AAe+++
  gene1715|gene1715|rna1714|rna1714 385 AIISLA--LCYRSGTGVRISPEKSFSLMKRAAEMNN 418
                                        666799..999**********************986 PP

  == domain 11  score: 36.1 bits;  conditional E-value: 1.6e-12
                               Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        a+A++ LG  y+y++G g+ k++++Ai+wye++A+q++
  gene1715|gene1715|rna1714|rna1714 419 ASAQNTLG--YYYEEGYGTLKNIREAIRWYEMSAKQDN 454
                                        6899****..999***********************96 PP

  == domain 12  score: 7.6 bits;  conditional E-value: 0.0014
                               Sel1   3 AmyrLGmfylylnGlgvpkDpekAiewyekAAeqGd 38 
                                        A+++L    ly+nG  +p+D+++++ ++ ++ ++G+
  gene1715|gene1715|rna1714|rna1714 457 ALFNLS--SLYFNGVHIPPDEKLGVSLLFRSRDLGN 490
                                        899***..778***99*******9999988888875 PP

  == domain 13  score: 23.4 bits;  conditional E-value: 1.5e-08
                               Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyekA 33 
                                         A++ LG  y++++G gv+k+p++A+e+y +A
  gene1715|gene1715|rna1714|rna1714 492 RAANTLG--YCFEKGIGVEKNPKLAFEHYTQA 521
                                        67888**..*********************99 PP

  == domain 14  score: 21.6 bits;  conditional E-value: 5.7e-08
                               Sel1   5 yrLGmfylylnGlgvpkDpekAiewyekAAe 35 
                                        y+LG   +y+nG g+  D +kA++++ k+ +
  gene1715|gene1715|rna1714|rna1714 531 YNLG--RCYENGIGTGIDLDKALYYFYKSSS 559
                                        9***..999******9***********9875 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   6.8e+03       1      13 [.     132     144 ..     132     159 .. 0.77
   2 ?   -1.5   0.0       1.2   5.3e+03       6      23 ..     173     194 ..     172     195 .. 0.85
   3 !    6.5   0.0    0.0033        15       2      14 ..     205     221 ..     204     231 .. 0.69
   4 ?    0.8   0.0      0.22     1e+03       6      25 ..     245     268 ..     244     275 .. 0.85
   5 ?   -3.2   0.0         4   1.8e+04       5      13 ..     280     288 ..     280     296 .. 0.77
   6 ?   -1.0   0.0      0.81   3.6e+03       5      13 ..     316     325 ..     313     333 .. 0.77
   7 ?   -0.6   0.0       0.6   2.7e+03       6      24 ..     353     375 ..     350     376 .. 0.85
   8 ?   -1.6   0.0       1.3   5.8e+03       6      13 ..     389     396 ..     384     401 .. 0.78
   9 ?   -1.7   0.0       1.4   6.3e+03       2      13 ..     457     468 ..     456     495 .. 0.79
  10 ?   -3.5   0.0         4   1.8e+04       6      23 ..     497     518 ..     497     522 .. 0.64
  11 !    6.0   0.1    0.0048        22       2      23 ..     529     554 ..     528     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                                        HHHHHHHHHHHHH CS
                              TPR_6   1 dAlyklalsyrkl 13 
                                        +A y l+ +y+++
  gene1715|gene1715|rna1714|rna1714 132 YARYCLGVCYQEG 144
                                        57777999*9985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                        HHHHHHHH....HHHHHHHHHH CS
                              TPR_6   6 lalsyrkl....gdtdkAleal 23 
                                        l+++++k+    ++ + A+e++
  gene1715|gene1715|rna1714|rna1714 173 LGYCFLKGfgveKNEEIAVELF 194
                                        8999999989988999999988 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0033
                                        HHHHHHHHHHHH....H CS
                              TPR_6   2 Alyklalsyrkl....g 14 
                                        Aly+++ +y+++     
  gene1715|gene1715|rna1714|rna1714 205 ALYNIGFCYEEGrgveR 221
                                        9*********9744443 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.22
                                        HHHHHHHH....HHHHHHHHHHHH CS
                              TPR_6   6 lalsyrkl....gdtdkAlealer 25 
                                        l+ +y+++     d +kA e +++
  gene1715|gene1715|rna1714|rna1714 245 LGNCYEEGkgvnRDLQKAFEFYKK 268
                                        799***987997799999999876 PP

  == domain 5  score: -3.2 bits;  conditional E-value: 4
                                        HHHHHHHHH CS
                              TPR_6   5 klalsyrkl 13 
                                        +la +y+k+
  gene1715|gene1715|rna1714|rna1714 280 NLAFCYQKG 288
                                        5899**984 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 0.81
                                        HHHHHHHH.H CS
                              TPR_6   5 klalsyrk.l 13 
                                        +++++y++ l
  gene1715|gene1715|rna1714|rna1714 316 NIGYCYQNgL 325
                                        89****9955 PP

  == domain 7  score: -0.6 bits;  conditional E-value: 0.6
                                        HHHHHHHH....HHHHHHHHHHH CS
                              TPR_6   6 lalsyrkl....gdtdkAleale 24 
                                        l+ +y+ +     d + A+++++
  gene1715|gene1715|rna1714|rna1714 353 LGVCYQHGygvsRDERLAVRYFN 375
                                        79999998889889999999997 PP

  == domain 8  score: -1.6 bits;  conditional E-value: 1.3
                                        HHHHHHHH CS
                              TPR_6   6 lalsyrkl 13 
                                        lal+yr++
  gene1715|gene1715|rna1714|rna1714 389 LALCYRSG 396
                                        8****985 PP

  == domain 9  score: -1.7 bits;  conditional E-value: 1.4
                                        HHHHHHHHHHHH CS
                              TPR_6   2 Alyklalsyrkl 13 
                                        Al++l  +y+++
  gene1715|gene1715|rna1714|rna1714 457 ALFNLSSLYFNG 468
                                        899999999976 PP

  == domain 10  score: -3.5 bits;  conditional E-value: 4
                                        HHHHHHHH....HHHHHHHHHH CS
                              TPR_6   6 lalsyrkl....gdtdkAleal 23 
                                        l+++++k+    +++  A e +
  gene1715|gene1715|rna1714|rna1714 497 LGYCFEKGigveKNPKLAFEHY 518
                                        6889998766665555555555 PP

  == domain 11  score: 6.0 bits;  conditional E-value: 0.0048
                                        HHHHHHHHHHHH...H.HHHHHHHHH CS
                              TPR_6   2 Alyklalsyrkl...g.dtdkAleal 23 
                                        A y+l+++y+++   g d dkAl ++
  gene1715|gene1715|rna1714|rna1714 529 AGYNLGRCYENGigtGiDLDKALYYF 554
                                        569********989999999999877 PP

>> Surfac_D-trimer  Lung surfactant protein D coiled-coil trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.6   1.2e+04      25      34 ..      71      80 ..      67      82 .. 0.83
   2 ?    7.5   0.0   0.00086       3.9      13      35 ..     254     278 ..     243     280 .. 0.85
   3 ?    0.9   0.1     0.094   4.2e+02      16      29 ..     293     306 ..     290     308 .. 0.84
   4 ?   -2.8   0.0       1.4   6.2e+03      14      23 ..     565     574 ..     563     575 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.6
                                       HHHHHHTTTE CS
                    Surfac_D-trimer 25 YkKavLFPdG 34
                                       Y Ka+L  +G
  gene1715|gene1715|rna1714|rna1714 71 YTKAALSDNG 80
                                       99**998888 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00086
                                        HHHHHHHHHHHHHHHHHH..TTTEE CS
                    Surfac_D-trimer  13 GklqrLqnafsqYkKavL..FPdGq 35 
                                        G  + Lq af  YkK +L  +P Gq
  gene1715|gene1715|rna1714|rna1714 254 GVNRDLQKAFEFYKKSALqgYPSGQ 278
                                        55578************98889998 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.094
                                        HHHHHHHHHHHHHH CS
                    Surfac_D-trimer  16 qrLqnafsqYkKav 29 
                                        + Lq af  Yk+a+
  gene1715|gene1715|rna1714|rna1714 293 KCLQKAFEWYKRAA 306
                                        569********997 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.4
                                        HHHHHHHHHH CS
                    Surfac_D-trimer  14 klqrLqnafs 23 
                                         lqrL+ ++s
  gene1715|gene1715|rna1714|rna1714 565 SLQRLKKILS 574
                                        699**99987 PP

>> TEX29  Testis-expressed sequence 29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.9   8.4e+03      36      53 ..      51      68 ..      43      76 .. 0.78
   2 ?    3.6   0.1     0.023     1e+02      29      51 ..     173     195 ..     166     199 .. 0.91
   3 ?   -0.4   0.3      0.39   1.8e+03      28      44 ..     280     296 ..     276     308 .. 0.72
   4 ?    4.5   0.0     0.012        54      27      50 ..     495     522 ..     488     527 .. 0.73
   5 ?   -3.8   0.0         4   1.8e+04      28      37 ..     532     541 ..     531     543 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                              TEX29 36 gvCyekavpiyvqvfsal 53
                                       + Cye  + ++v++ +a 
  gene1715|gene1715|rna1714|rna1714 51 SFCYEFGIGTTVDMKKAE 68
                                       679999999999987765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.023
                              TEX29  29 LgcCfykgvCyekavpiyvqvfs 51 
                                        Lg Cf kg   ek   i v++f+
  gene1715|gene1715|rna1714|rna1714 173 LGYCFLKGFGVEKNEEIAVELFK 195
                                        89*****************9996 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.39
                              TEX29  28 eLgcCfykgvCyekavp 44 
                                        +L  C+ kg+  +k++ 
  gene1715|gene1715|rna1714|rna1714 280 NLAFCYQKGIGTKKCLQ 296
                                        58899999997777665 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.012
                              TEX29  27 keLgcCfykgvCyek....avpiyvqvf 50 
                                          Lg Cf kg+  ek    a   y+q+f
  gene1715|gene1715|rna1714|rna1714 495 NTLGYCFEKGIGVEKnpklAFEHYTQAF 522
                                        579**********993333344555555 PP

  == domain 5  score: -3.8 bits;  conditional E-value: 4
                              TEX29  28 eLgcCfykgv 37 
                                        +Lg+C+ +g+
  gene1715|gene1715|rna1714|rna1714 532 NLGRCYENGI 541
                                        5888988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3664.36
//
Query:       gene1716|gene1716|rna1715|rna1715  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0043   16.9   0.0     0.0071   16.1   0.0    1.3  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     4e-07    0.0071       9      54 ..      51      89 ..      48      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-07
                                       TSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHH CS
                              RRM_1  9 dvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAek 54
                                        +t++ L+e F ++  i++i++++       ++af  F+s  + ++
  gene1716|gene1716|rna1715|rna1715 51 GTTRQALEEAFHEVDLIEDIRVFK-------RYAFLSFKSNANIDH 89
                                       58**********************.......8*******9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1069.73
//
Query:       gene1717|gene1717|rna1716|rna1716  [L=1424]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-34  120.0   0.8    8.6e-22   78.2   0.0    2.9  3  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
    1.3e-07   31.2   0.2    5.6e-07   29.1   0.1    2.0  2  PI3Ka           Phosphoinositide 3-kinase family, accessory d
     0.0012   18.9   0.2     0.0053   16.8   0.2    2.1  1  IL15            Interleukin 15
  ------ inclusion threshold ------
       0.16   12.4   0.0        0.4   11.0   0.0    1.6  1  DUF4542         Domain of unknown function (DUF4542)


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.4   1.8e+03      31     104 ..     748     811 ..     743     857 .. 0.68
   2 !   39.1   0.0   1.6e-13   7.3e-10       4      76 ..    1171    1239 ..    1169    1248 .. 0.94
   3 !   78.2   0.0   1.9e-25   8.6e-22     125     249 ..    1250    1372 ..    1241    1373 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.4
                                        HTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHHHHHHHHCTTSTCHHHHHHHHHCHCHCCHHHHHCC CS
                     PI3_PI4_kinase  31 kennpkrrklalktysviplgrkcgiielvassetaaslldeklekkgvpptasveslrvaldkkklkkekklk 104
                                        ++++ k     ++ ys+i +g++  i  l  s+e +    +  +  +   ++a++++    ld++  k+ek++ 
  gene1717|gene1717|rna1716|rna1716 748 NPKEAKS----HNMYSIIHTGTNDSIASLESSTENISLHSSSPM--HSTSCNAQMKI----LDENIRKREKSVS 811
                                        5555565....999999999999999988887777665555555..36777777777....5555555555554 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1.6e-13
                                         EEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHHHHHHHH CS
                     PI3_PI4_kinase    4 giykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvassetaaslldeklek 76  
                                         +i+k gdd+rqd+l +q++++++ + ++ n++      l++y+v++++++ giie++++s++ +++ +e+ ++
  gene1717|gene1717|rna1716|rna1716 1171 LIFKSGDDCRQDMLALQIISMFESIFKQANLDIF----LYPYRVMATSSGTGIIEVIPNSKSRDQIGKENINN 1239
                                         79*******************************9....******************************99976 PP

  == domain 3  score: 78.2 bits;  conditional E-value: 1.9e-25
                                         SSSHHHHHHHHHHHHHHHHHHHHHHHHHT-TT--TTTEEEETTTSEEEESSTTTCCTCSHCSSSS-.SSSSSS- CS
                     PI3_PI4_kinase  125 spsaeewlearkqFvrslaklsvldyilgngDRhldNilvdktsgklihIDfGlilpdewkllpfpqekvPfrl 198 
                                         +++ e +l a+ +F++sla++s + y l++ DRh++Ni++ ++ g +ihIDfG++l+ ++ +l+++    P++l
  gene1717|gene1717|rna1716|rna1716 1250 FKESEGYLTAICNFASSLAGYSLVVYFLNIKDRHNGNIMI-DDRGRMIHIDFGYMLEMSPGNLNIE---APLKL 1319
                                         5677889999******************************.***************9999999976...9**** PP

                                         THHHHHHT..STTCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHCCSSC CS
                     PI3_PI4_kinase  199 trelvlai..dpskdeglfresceealealrrdqnlltrllkkavkdglilwe 249 
                                         t+e+ +++     k +++++e++ + + alrr ++ l+++++ +++++l++++
  gene1717|gene1717|rna1716|rna1716 1320 TKEIEELLggISGKGFKIYQELMIKGFLALRRRSKDLVMMMDSFADSKLPCYK 1372
                                         ********7556678999*******************************9986 PP

>> PI3Ka  Phosphoinositide 3-kinase family, accessory domain (PIK domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   1.3e-10   5.6e-07      95     181 ..     986    1076 ..     978    1080 .. 0.77
   2 ?   -1.4   0.0      0.29   1.3e+03     132     159 ..    1078    1107 ..    1071    1119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.3e-10
                                         HHHHHHHHHSHHHHHHHHHHHHHHHHGGSSSSSSHHHHHHHHHHHHSHHHHHHHHHHHHHHH......HCCTHH CS
                              PI3Ka   95 eyavkvLekasdeelllYllQLVqalkyepikdsalaefLlkralknkrlghfffWyLksei......edkevs 162 
                                         + a ++L++++d  +++Y++QLVq l++ ++ +    + L + a+    ++h+++W+Lk+++      ++ e  
  gene1717|gene1717|rna1716|rna1716  986 SRAFERLKDFKD-RMQFYVPQLVQMLRHKKVFEMTF-SALKDLAKDDEYVAHQLIWNLKANLytdgwaDKDECR 1057
                                         557789999976.69**************6655554.457889*******************988885444557 PP

                                         HHHHHHHHHHHHHCHHHHH CS
                              PI3Ka  163 erfksllesylrklskslk 181 
                                         ++f + +e+++ ++s++ +
  gene1717|gene1717|rna1716|rna1716 1058 STFIRCIEEIMGEMSEESR 1076
                                         7777777777777776655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.29
                                         HHHHHHHHHSH..HHHHHHHHHHHHHHHCC CS
                              PI3Ka  132 efLlkralknk..rlghfffWyLkseiedk 159 
                                          fL++   +n   r++++++ yL+s  ++k
  gene1717|gene1717|rna1716|rna1716 1078 MFLIEEEFVNSltRISSELIPYLRSSKDEK 1107
                                         59999999998779**********987433 PP

>> IL15  Interleukin 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   1.2e-06    0.0053      20     108 ..    1022    1109 ..    1012    1121 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                               IL15   20 slsdvikDLeileelinsihldatLYtes.dvkpeCkvqalkCfllElrvileeeiekeeeikeevenliknan 92  
                                          l+d+ kD e + +     +l+a LYt+    k eC+ + ++C  +E+   + ee  +   i+ee++n+++ + 
  gene1717|gene1717|rna1716|rna1716 1022 ALKDLAKDDEYVAHQ-LIWNLKANLYTDGwADKDECRSTFIRCI-EEIMGEMSEESRHMFLIEEEFVNSLTRIS 1093
                                         467777777777743.34688999***6423344*********6.5555556666699999************* PP

                               IL15   93 knlkslkdeskteseC 108 
                                         ++l  +   sk e+  
  gene1717|gene1717|rna1716|rna1716 1094 SELIPYLRSSKDEKRR 1109
                                         ***9998888877765 PP

>> DUF4542  Domain of unknown function (DUF4542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     9e-05       0.4      10      56 ..     906     952 ..     904     959 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9e-05
                            DUF4542  10 avdtlaseyarlrPkltsaippYnaqkdkhakaYfrsktvkkvLkkt 56 
                                        av++ +s+   + P++t+ i++++ ++  h+++ f++k+v+++L+++
  gene1717|gene1717|rna1716|rna1716 906 AVSNFSSNEDLSFPERTQLISRFDTTDLIHIQNTFKQKMVQRLLERS 952
                                        6888898889999*******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.26s 00:00:01.03 Elapsed: 00:00:00.42
# Mc/sec: 10247.91
//
Query:       gene1718|gene1718|rna1717|rna1717  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-20   72.1   1.9    1.1e-19   71.1   1.9    1.5  1  Pescadillo_N  Pescadillo N-terminus
    2.1e-09   37.6   0.0    5.3e-09   36.4   0.0    1.7  1  BRCT_2        BRCT domain, a BRCA1 C-terminus domain
  ------ inclusion threshold ------
       0.28   12.0   1.3       0.53   11.1   1.3    1.4  1  SUZ           SUZ domain


Domain annotation for each model (and alignments):
>> Pescadillo_N  Pescadillo N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   1.9   1.8e-23   1.1e-19       9     201 ..      10     189 ..       5     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.8e-23
                       Pescadillo_N   9 kkyitrkqalkkLqlslkdFRrLCilKGiyPrepkkkkkankgstaaktyYyakdikfLlhepilekfreikafak 84 
                                        kkyi++  ++++L l++k+F +L  l G++P  pk+++k+++g+     yY   d + Llh ++ +k+   + +++
  gene1718|gene1718|rna1717|rna1717  10 KKYISKDLVMRNLDLQEKEFDKLVTLCGVHPYIPKNNRKVDQGD---GFYYRISDANKLLHSDVYRKLIINRDLEN 82 
                                        89***************************************976...89999************************ PP

                       Pescadillo_N  85 klkkalakkekekakrleknkpkykldhiikeRYPtfidAlrdldDaLsliflfatlpktkkikekliekcerlae 160
                                        k k+ ++ + + k+k+++ ++  y    +ik R   f +A+++l+ +Ls ++l  +l+ ++ i+        ++ e
  gene1718|gene1718|rna1717|rna1717  83 KKKRYTGTGFEYKIKNIHYKE--YGYVDLIKSRCKGFGEAVDELNHTLSNLYLGRMLNLNDGIS--------EVIE 148
                                        ****************99875..66789*************************99999888886........4678 PP

                       Pescadillo_N 161 efqayviksrslrkvFlSiKGiYyqaeikgqkvtWlvPykf 201
                                         f+++v+k+  l+ +++S  GiY q ++ + kv W vPy  
  gene1718|gene1718|rna1717|rna1717 149 MFERFVAKKSLLEYSYMSKSGIYNQMTLGKVKVVWFVPYPG 189
                                        9**************************************75 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   8.8e-13   5.3e-09       2      84 ..     274     349 ..     273     350 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.8e-13
                             BRCT_2   2 sklFeglrFYindaepspsreklkklIeknGGevvetitsavyiviaesneeelaekrkrrvvspkyIkdCikkgk 77 
                                        +k+F++ +FYi   e ++    l+ ++ ++GG +ve++++a+++ i+e+ +   +  ++  +++p+y++dC+++gk
  gene1718|gene1718|rna1717|rna1717 274 RKIFSDVKFYI---ESKAVEGALRLIVLSCGGSIVESPHEANIH-ISEKID---EMVENVAYLQPQYLFDCLNQGK 342
                                        68*********...77799*******************988666.555554...568999**************** PP

                             BRCT_2  78 llpleny 84 
                                         l  e+y
  gene1718|gene1718|rna1717|rna1717 343 RLYAESY 349
                                        **99988 PP

>> SUZ  SUZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.3   8.9e-05      0.53      29      46 ..     219     235 ..     215     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                                SUZ  29 sesssssktleEREaeYa 46 
                                        s+++ss   leERE++Y+
  gene1718|gene1718|rna1717|rna1717 219 SSEESS-SELEEREEAYN 235
                                        445555.79********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2448.80
//
Query:       gene1719|gene1719|rna1718|rna1718  [L=581]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-78  262.8   0.2    6.6e-78  262.0   0.2    1.4  1  Kinesin       Kinesin motor domain
    2.7e-09   37.1   0.1    1.3e-08   34.9   0.0    2.3  2  Microtub_bd   Microtubule binding
    5.3e-05   23.2   0.2    0.00012   22.1   0.2    1.7  1  SAM_2         SAM domain (Sterile alpha motif)
  ------ inclusion threshold ------
      0.022   15.1   0.3      0.077   13.4   0.1    1.9  2  AAA_16        AAA ATPase domain
      0.098   12.7   0.4        7.6    6.6   0.0    3.1  3  Hjc           Archaeal holliday junction resolvase (hjc)
       0.41   11.2   3.6        7.9    7.1   0.0    3.2  2  Syntaxin-6_N  Syntaxin 6, N-terminal
       0.47   10.9   3.9         13    6.4   0.0    3.0  3  Cep57_MT_bd   Centrosome microtubule-binding domain of Cep57
        3.7    7.6   7.4        4.4    7.3   0.7    2.6  2  DUF87         Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.0   0.2     3e-81   6.6e-78      26     332 ..     201     484 ..     165     485 .. 0.91

  Alignments for each domain:
  == domain 1  score: 262.0 bits;  conditional E-value: 3e-81
                                        CEEEEEEEEECTTSCEEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHHHTBCTTTSBS CS
                            Kinesin  26 eeekkskkenkeeeekkfkFdkvfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyTmegkeeeeeG 101
                                        +ee+ + + +   e+++f+Fd+ fd ++++ +vy+e++k++v++v++G  +t++ YGqtg+GKTyTm  k   + G
  gene1719|gene1719|rna1718|rna1718 201 HEERLRVDLRPYVEHHRFRFDYSFDWDKKNIDVYRECVKDIVNHVVSGGLGTVLVYGQTGTGKTYTMLEK---DIG 273
                                        555566666778899*****************************************************86...79* PP

                                        HHHHHHHHHHHHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS--EEESS CS
                            Kinesin 102 iipraleelFesikkekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkgltevevks 177
                                        +++ a+++l    ++           +v++ EiY+ ++yDLL++      k++++re +  g v++++ +e+ ++ 
  gene1719|gene1719|rna1718|rna1718 274 MMYLAIKDLMVFKDH----------GTVTFCEIYMGQVYDLLDNG-----KRIQLREVN--GVVHLSNSREEVFRG 332
                                        ********9766543..........3699**************98.....457888855..469************ PP

                                        HHHHHHHHHHHHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSSTCHHH CS
                            Kinesin 178 aeevlellekgeknrkvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktgaaeger 253
                                        +++vl+++++g + rk++ t +n++SSRSHav+ ++ + k++++++  kv+++++ +vDLAGsEr s++++++++ 
  gene1719|gene1719|rna1718|rna1718 333 YSQVLSIIDRGMSLRKTGMTGANSKSSRSHAVILVNFSDKKVEKGDP-KVHSGSIVFVDLAGSERGSDRRETRSDV 407
                                        *****************************************996665.89********************999999 PP

                                        HHHHHHHHHHHHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHH CS
                            Kinesin 254 lkEaaniNkSLlaLgrvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaer 329
                                         +E+a+iNkSLlaL+++i+ + ++  +kh p+R+SkLT++L++s+ G+s+t++i+tvsp+sen+e+tl+tl++a+r
  gene1719|gene1719|rna1718|rna1718 408 KNEGAEINKSLLALKECIRGMEKD--KKHLPFRQSKLTQILKNSFIGTSRTCLIATVSPTSENVEHTLNTLRYASR 481
                                        9***********************..************************************************** PP

                                        HCT CS
                            Kinesin 330 ake 332
                                        +ke
  gene1719|gene1719|rna1718|rna1718 482 IKE 484
                                        996 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   5.9e-12   1.3e-08      44     122 ..     210     287 ..     171     305 .. 0.79
   2 ?   -2.8   0.1       2.5   5.6e+03      43      65 ..     484     515 ..     448     531 .. 0.53

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 5.9e-12
                                        ...TTTEEEE-SEEEECTTHCCCCCCCC.HHHHHHHHTT--EEEEEEES................ST-HCHHHHHH CS
                        Microtub_bd  44 eekkkkkefsFdrvfeseseqeevfeei.sqlvqsaldgynvcifaygqTGsGKtyTmegeeeeagmipraveeif 118
                                        +   ++++f+Fd  f+ ++++ +v+ e+ + +v+ +++g   +++ ygqTG GKtyTm +  ++ gm+  a++ ++
  gene1719|gene1719|rna1718|rna1718 210 RPYVEHHRFRFDYSFDWDKKNIDVYRECvKDIVNHVVSGGLGTVLVYGQTGTGKTYTMLE--KDIGMMYLAIKDLM 283
                                        4567899*******************974789**************************99..88899989988887 PP

                                        HHHH CS
                        Microtub_bd 119 etis 122
                                         +  
  gene1719|gene1719|rna1718|rna1718 284 VFKD 287
                                        6654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                                        T............TTTEEEE-SEEEECTTHCC CS
                        Microtub_bd  43 e.........eekkkkkefsFdrvfeseseqe 65 
                                        e         +e+ ++++f+ +r +++ ++++
  gene1719|gene1719|rna1718|rna1718 484 EsvvpkekrsKESPNANRFTSQRRLPEMTSKQ 515
                                        13344344444455555565555555555433 PP

>> SAM_2  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.2   5.5e-08   0.00012      10      64 ..       5      59 ..       1      61 [. 0.89

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.5e-08
                                       HHHHHHTTTGGGHHHHHHTTCSHHHHHTTSCHHHHHHTTHHHHHHHHHHHHHHHH CS
                              SAM_2 10 aeWLrsiglkqytdnFrdagitgaelllrlteedLkrlGitsvghrkkilkkiqe 64
                                         +L + + ++  + F++ gi+  +ll++l+ +dL+++Gi+++++r+k++  i+e
  gene1719|gene1719|rna1718|rna1718  5 RTYLAESKVEHLYQLFERIGIDESQLLAKLKYSDLEKIGIENLIERRKVFDIINE 59
                                       5688888999999**********8888**********************988887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.4e-05     0.077      13      39 ..     239     265 ..     234     270 .. 0.88
   2 ?   -2.1   0.0         2   4.5e+03      72     101 ..     478     506 ..     441     564 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                             AAA_16  13 lsalervrsgrpelvllsGesGvGKss 39 
                                        +++++ v sg+ + vl++G+ G+GK+ 
  gene1719|gene1719|rna1718|rna1718 239 KDIVNHVVSGGLGTVLVYGQTGTGKTY 265
                                        67889999******************6 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                             AAA_16  72 laqalareellrqlldeaesaeleawrekl 101
                                        +a+ + +e+++ ++++ +es +++++  + 
  gene1719|gene1719|rna1718|rna1718 478 YASRI-KESVVPKEKRSKESPNANRFTSQR 506
                                        56667.557777777776665555555432 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.074   1.7e+02      51      83 ..       3      36 ..       1      46 [. 0.75
   2 ?    6.6   0.0    0.0034       7.6      29      60 ..     186     217 ..     172     225 .. 0.90
   3 ?   -1.0   0.0      0.81   1.8e+03      57      73 ..     556     572 ..     531     576 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.074
                                       SSEEEEEHHHHHHHHHHHHHHTCE.EEEEEEETT CS
                                Hjc 51 keriylkkeqvekllefarkagge.lllavklqg 83
                                       + r yl + +ve+l ++ ++ g++   l +kl+ 
  gene1719|gene1719|rna1718|rna1718  3 DLRTYLAESKVEHLYQLFERIGIDeSQLLAKLKY 36
                                       5699*****************9961345556555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0034
                                        SS-SEEEEETTEEEEEEEEEESSSEEEEEHHH CS
                                Hjc  29 plpDviAirgdvvlviEvKsskkeriylkkeq 60 
                                        p  D+++++g+ v+v E + +++ r+y++++ 
  gene1719|gene1719|rna1718|rna1718 186 PNLDIVGVEGKDVIVHEERLRVDLRPYVEHHR 217
                                        567*************************9875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.81
                                        EHHHHHHHHHHHHHHTC CS
                                Hjc  57 kkeqvekllefarkagg 73 
                                         +e++ek+l+f+++   
  gene1719|gene1719|rna1718|rna1718 556 TSEELEKVLNFCKELEK 572
                                        6799********98655 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0035       7.9      35      83 ..     396     444 ..     371     459 .. 0.82
   2 ?    2.2   1.8      0.12   2.7e+02      34      61 ..     524     555 ..     465     578 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0035
                       Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsr 83 
                                        + ++ +etr++++++  +i++ l  L+e +r +ek++++   ++++l++
  gene1719|gene1719|rna1718|rna1718 396 RGSDRRETRSDVKNEGAEINKSLLALKECIRGMEKDKKHLPFRQSKLTQ 444
                                        5677899****************************99987666666654 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                       Syntaxin-6_N  34 s....tseeldetrteLrkalrsiewdledLe 61 
                                        s     s+  d +++e+r++l++ie  +  L+
  gene1719|gene1719|rna1718|rna1718 524 SsksdLSKTRDTLMHEIRRTLSKIESRIPSLK 555
                                        13333677788888888999999988876665 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0056        13       9      38 ..     417     446 ..     412     451 .. 0.86
   2 ?    4.2   0.6     0.027        61      32      67 ..     515     550 ..     512     556 .. 0.85
   3 ?   -2.1   0.0       2.4   5.3e+03       5      23 ..     552     573 ..     549     575 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0056
                        Cep57_MT_bd   9 pkeaLaevlkeLedEfehlklelqelaaqy 38 
                                        +  aL+e ++++e++ +hl ++ ++l + +
  gene1719|gene1719|rna1718|rna1718 417 SLLALKECIRGMEKDKKHLPFRQSKLTQIL 446
                                        5679********************998765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.027
                        Cep57_MT_bd  32 qelaaqynaldpslgkrkRkdLaeeleelvkrlEaK 67 
                                        qel++ + ++ +s  ++ R++L++e+++ ++++E++
  gene1719|gene1719|rna1718|rna1718 515 QELEKVFIESSKSDLSKTRDTLMHEIRRTLSKIESR 550
                                        677777777777888999****************85 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.4
                        Cep57_MT_bd   5 psqspkeaLaevl...keLedE 23 
                                        ps +  e+L++vl   keLe+E
  gene1719|gene1719|rna1718|rna1718 552 PSLKTSEELEKVLnfcKELEKE 573
                                        6778889999998555566666 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.7     0.002       4.4      26      40 ..     253     267 ..     251     268 .. 0.92
   2 ?    3.1   1.0      0.04        89     131     192 ..     505     563 ..     459     580 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
                              DUF87  26 lAilgsTGsGKSntv 40 
                                        +++ g+TG+GK++t+
  gene1719|gene1719|rna1718|rna1718 253 VLVYGQTGTGKTYTM 267
                                        579***********8 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.04
                              DUF87 131 keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdlial 192
                                        +++  +++s++ +ek++ e    k++l+k ++ +++++ ++l+++ ++  s  ++s++l++ 
  gene1719|gene1719|rna1718|rna1718 505 QRRLPEMTSKQELEKVFIESS--KSDLSKTRDTLMHEIRRTLSKIESRIPSL-KTSEELEKV 563
                                        444455555555555555554..44555555555555555555555555554.444433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3543.80
//
Query:       gene1720|gene1720|rna1719|rna1719  [L=550]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-92  310.1   0.1    1.4e-92  309.8   0.1    1.1  1  CTP_synth_N    CTP synthase N-terminus
    1.9e-46  158.2   0.0    4.2e-46  157.1   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    4.3e-08   33.2   0.3    9.4e-06   25.5   0.1    3.2  3  Peptidase_C26  Peptidase C26
     0.0015   18.2   0.4     0.0059   16.2   0.4    1.9  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.29   10.9   0.0    1.6  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.8   0.1   3.9e-96   1.4e-92       1     265 []      17     290 ..      17     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.8 bits;  conditional E-value: 3.9e-96
                                        EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHH CS
                        CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRf 76 
                                        ky++v+GGv+Sg+GkGi+ +s+gallksrg  vt ikiDPYln++a +l p+ehGEv+vl+dG+e+D+D+GnYeRf
  gene1720|gene1720|rna1719|rna1719  17 KYVIVSGGVISGVGKGIVGSSIGALLKSRGHIVTHIKIDPYLNYNARMLAPCEHGEVYVLEDGHECDMDFGNYERF 92 
                                        8*************************************************************************** PP

                                        HT----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.H.C........T.-SEEEEEE-S CS
                        CTP_synth_N  77 ldikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakk.v........e.advviveigG 142
                                          +kl+  n+i+ G++++++i++e++G+ lGkt+qv phv+d++ +ri+ v ++ v        + +dvv++e+gG
  gene1720|gene1720|rna1719|rna1719  93 NMLKLSIINSISGGRLFHDIIKREQEGHLLGKTLQVNPHVIDDVIRRIKVVGETpVesfedghtSiPDVVVIELGG 168
                                        *************************************************999986588888875269********* PP

                                        -TTSGGGHHHHHHHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HH CS
                        CTP_synth_N 143 tvgdieslpfleairqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleee 218
                                        tvg++es  + +a+ +l++++gk+n++++ v +++ l+ +ge+ktk++q+ ++++r++G++ dii+cr +++ +e+
  gene1720|gene1720|rna1719|rna1719 169 TVGEYESSIYTDALAKLQHDVGKNNCAFVSVDYLTELE-SGEQKTKSIQMGCRNFRAFGLTHDIIICRGTRAPTED 243
                                        *************************************5.9************************************ PP

                                        HHHHHHHHCT--GGGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                        CTP_synth_N 219 vkekialfcnvekeavisvkdvesiyevpllleeqglaelileklkl 265
                                        +++ki++ c v+  +vi  +++es+y+vp  leeqgl +++ ++l l
  gene1720|gene1720|rna1719|rna1719 244 TRRKISKNCWVPLPNVIGLPNLESVYSVPRFLEEQGLVDSLYKTLGL 290
                                        *****************************************999975 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   0.0   1.2e-49   4.2e-46       4     189 ..     327     543 ..     326     544 .. 0.86

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 1.2e-49
                                        ESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                             GATase   4 Dnydsvtenlvhalvelgvkvevvpidasaeeile.llknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                        D+y s+++ l+ +++++gv+ve+ +++a+     e  l+++dgi+++gG+g++gv gkieai++aren+iP+LGIC
  gene1720|gene1720|rna1719|rna1719 327 DSYTSLVHGLKFSGASIGVNVEIEWVNAEEYC--EsDLSKCDGIIIPGGFGARGVSGKIEAIRYARENGIPLLGIC 400
                                        9**************************75443..3369************************************** PP

                                        HHHHHHHHHTTTEEE............................EEECEEEEEEEEEEEETTT..CGGTTTTSEEEE CS
                             GATase  79 LGmQllaiefgrkvv............................kekekehhggtmrlgddet..allyglknevie 124
                                        LG Ql +ie++r+v                               k+    g + +l d     ++lyg k++++e
  gene1720|gene1720|rna1719|rna1719 401 LGYQLCVIEMCRNVLgmkdafseefqpdgkdlvvrfisdengvVDKRLRVGGSQVKLMD--GlvKRLYGGKETIRE 474
                                        ************99988999888888888888888875555443333455555555555..166************ PP

                                        EEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                             GATase 125 rhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                        rhrHr+ev  +   +l  +gl++++ s+d+ +  +i+e++  + fvgvQFHPE++ +p++p++l ++li 
  gene1720|gene1720|rna1719|rna1719 475 RHRHRFEVVWEkvqDLRAHGLKFVGFSNDG-KATKIFELSThRyFVGVQFHPEFIARPNQPHPLITGLIS 543
                                        ********98889999999********776.8999999999888********************999875 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.69   2.5e+03     117     137 ..      99     119 ..      97     146 .. 0.73
   2 ?    3.5   0.0     0.014        50      36      67 ..     342     373 ..     327     378 .. 0.86
   3 !   25.5   0.1   2.6e-09   9.4e-06      96     216 .]     384     526 ..     376     526 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.69
                      Peptidase_C26 117 llnvalGGtlyqdieeqsglt 137
                                        ++n   GG+l+ di +++++ 
  gene1720|gene1720|rna1719|rna1719  99 IINSISGGRLFHDIIKREQEG 119
                                        689999999999998644433 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                      Peptidase_C26  36 agglpvllpieedeedvkaildkldgllltGg 67 
                                        + g+ v +   + ee++++ l+k+dg++++Gg
  gene1720|gene1720|rna1719|rna1719 342 SIGVNVEIEWVNAEEYCESDLSKCDGIIIPGG 373
                                        56778888888899*****************9 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 2.6e-09
                      Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe............q..saashavkve... 154
                                          ir a e+g+P+lgiC+G+ql  + +  ++    ++   +++  +++            +  +   ++++v    
  gene1720|gene1720|rna1719|rna1719 384 EAIRYARENGIPLLGICLGYQLCVIEMCRNVLGMKDA---FSEEFQPDgkdlvvrfisdeNgvV--DKRLRVGgsq 454
                                        5689999****************88877665444333...333333333445665555442332..3333333445 PP

                      Peptidase_C26 155 ...kgsllaellg.seeievnslHhqaike......laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                            ++l+++l+g +e+i+    H++ +         a++l+ +  ++Dg    i   +++  ++gvQ+HPE
  gene1720|gene1720|rna1719|rna1719 455 vklMDGLVKRLYGgKETIRERHRHRFEVVWekvqdlRAHGLKFVGFSNDGKATKIFELSTHRYFVGVQFHPE 526
                                        556788999999868888888888887754677777899***********9888777776779********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   1.7e-06    0.0059      34      87 ..     359     405 ..     340     417 .. 0.80
   2 ?   -2.4   0.0      0.83     3e+03      45      77 ..     449     481 ..     433     485 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                           GATase_3  34 deslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqm 87 
                                        +++l +++d +i+pGg+  +        sg  eai+ a e+g+p+lgiC G+q+
  gene1720|gene1720|rna1719|rna1719 359 ESDL-SKCDGIIIPGGFGARG------VSGKIEAIRYARENGIPLLGICLGYQL 405
                                        3455.66*********98665......5788999*******************7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.83
                           GATase_3  45 ilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                         ++G++  + d  ++r  g +e i+e ++   +
  gene1720|gene1720|rna1719|rna1719 449 RVGGSQVKLMDGLVKRLYGGKETIRERHRHRFE 481
                                        579999999999999999999999999887665 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.2e-05      0.29      46     106 ..     341     405 ..     329     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.2e-05
                                        EEEE-SEEGG........GCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
                          DJ-1_PfpI  46 lkvtvdasld........dvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpql 106
                                        +++ v++ ++        + + ++ D +++pGG   +  ++ +   +e ++ + e+g ++  IC g ql
  gene1720|gene1720|rna1719|rna1719 341 ASIGVNVEIEwvnaeeycESDLSKCDGIIIPGGFG-ARGVSGK---IEAIRYARENGIPLLGICLGYQL 405
                                        5555555555555555556667799*********9.7777765...999****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3416.16
//
Query:       gene172|gene172|rna172|rna172  [L=192]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.024   14.8   2.2      0.054   13.6   2.2    1.5  1  bZIP_1          bZIP transcription factor
      0.032   13.4   0.3      0.043   13.0   0.3    1.1  1  Nuc_sug_transp  Nucleotide-sugar transporter
        0.1   12.2   0.1       0.14   11.7   0.1    1.1  1  CDPS            Cyclodipeptide synthase
       0.14   12.6   4.3       0.25   11.8   4.3    1.4  1  ZapB            Cell division protein ZapB
       0.15   10.2   4.6        2.9    5.9   0.0    2.0  2  HOOK            HOOK protein
       0.15   12.2   1.1       0.21   11.7   1.1    1.3  1  Herpes_BLRF2    Herpesvirus BLRF2 protein
       0.15   12.2   1.5       0.44   10.7   1.7    1.7  2  NYD-SP28_assoc  Sperm tail C-terminal domain
       0.45   10.6   4.2       0.78    9.8   4.2    1.3  1  GvpG            Gas vesicle protein G
       0.61   10.2   5.9       0.65   10.1   0.4    2.9  3  DUF5595         Domain of unknown function (DUF5595)
        4.7    7.4  10.7        1.1    9.4   6.0    2.1  2  bZIP_2          Basic region leucine zipper


Domain annotation for each model (and alignments):
>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.2     3e-05     0.054      24      54 ..     105     135 ..     105     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  24 KqaeieeLerrvkaLekeNksLkseleelkk 54 
                                    +++e+e+L+++ + L  eN++L+ +++e+++
  gene172|gene172|rna172|rna172 105 REMEVEQLKEETERLMRENEELRGRINEMNN 135
                                    689***********************99875 PP

>> Nuc_sug_transp  Nucleotide-sugar transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   2.4e-05     0.043      39      96 ..      13      69 ..       4      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                 Nuc_sug_transp 39 ttavllaeilklvvclllllkeekskvkkllrelkkeilakpkdtlklavPsliYtvq 96
                                    ++  l +i+ l+  + +++k+  +k+  + ++++k+++++ k+t+ +++Ps +Y v 
  gene172|gene172|rna172|rna172 13 KSTLSLEDIVFLLDKVDIMFKTPDCKI-LFYKNVEKALVHHFKETYEICIPSRVYSVN 69
                                   556667888888889999999999999.999************************996 PP

>> CDPS  Cyclodipeptide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.1e-05      0.14     118     183 ..     111     185 ..     105     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.1e-05
                                    HHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCHHHS-.........---HHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                           CDPS 118 elraeveralaedeelreacdemvrqvlerrlkdee.........apseaqleaaleYllaElPffldtpailgv 183
                                    +l++e+er ++e+eelr  ++em ++ ++r  +++e            e++l a +e +  E P++l+++  lg 
  gene172|gene172|rna172|rna172 111 QLKEETERLMRENEELRGRINEMNNAWIDRGFEEGEfksvdeevlSRMEKDLVALREQVDLEHPLILEAWYRLGE 185
                                    799***************************9999889999998888889999999999*********99988775 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   4.3   0.00014      0.25      20      64 ..     109     160 ..     106     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                           ZapB  20 itlLqmeieeLkeeneelkeenrele.......eeneqlkeereawqerlkk 64 
                                    +++L++e e+L++eneel  +++e++        e  ++k   e++ +r++k
  gene172|gene172|rna172|rna172 109 VEQLKEETERLMRENEELRGRINEMNnawidrgFEEGEFKSVDEEVLSRMEK 160
                                    4566666666666666666666666666666664444455555556666555 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.9    0.0034       6.1     192     221 ..     106     135 ..     105     149 .. 0.86
   2 ?    5.9   0.0    0.0016       2.9     632     669 ..     152     189 ..     145     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0034
                           HOOK 192 dkqlsllqeEknaLlaenkklqerlselen 221
                                    ++++ +l eE + L+ en++l+ r++e++n
  gene172|gene172|rna172|rna172 106 EMEVEQLKEETERLMRENEELRGRINEMNN 135
                                    688999999999999999999999999885 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0016
                           HOOK 632 dkkieslerevekakllreqeEkLivsAwYnlglalqr 669
                                    ++ ++++e+++ + + + + e  Li  AwY+lg +  +
  gene172|gene172|rna172|rna172 152 EEVLSRMEKDLVALREQVDLEHPLILEAWYRLGEEYIK 189
                                    466789999988889999***************88766 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.1   0.00012      0.21       2      44 ..     107     163 ..     106     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                   Herpes_BLRF2   2 ltvEdlaaelakLkvENkaLkkklkssvs..............pkdeeLTaaekeav 44 
                                    ++vE+l++e  +L  EN++L+ ++++  +               ++e+L   ek++v
  gene172|gene172|rna172|rna172 107 MEVEQLKEETERLMRENEELRGRINEMNNawidrgfeegefksVDEEVLSRMEKDLV 163
                                    89*********************9766555555555555555566667777777765 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.2   1.3e+04      11      25 ..      35      49 ..      34      52 .. 0.72
   2 ?   10.7   1.7   0.00024      0.44      36      58 ..     110     132 ..     107     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.2
                 NYD-SP28_assoc 11 peeklklWdalekaL 25
                                   p+ k+ +++  ekaL
  gene172|gene172|rna172|rna172 35 PDCKILFYKNVEKAL 49
                                   666777788888887 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00024
                 NYD-SP28_assoc  36 aklieetesLekqNeeLrnlLkq 58 
                                    ++l eete L+++NeeLr ++++
  gene172|gene172|rna172|rna172 110 EQLKEETERLMRENEELRGRINE 132
                                    57899*************98876 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.2   0.00044      0.78      17      67 ..     110     160 ..     108     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00044
                           GvpG  17 eqvqeraeeqlddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLea 67 
                                    eq++e++e+ + ++e+lr ++ +++ +  +   +e eF    ee+L r+e+
  gene172|gene172|rna172|rna172 110 EQLKEETERLMRENEELRGRINEMNNAWIDRGFEEGEFKSVDEEVLSRMEK 160
                                    89***********************99777779****************94 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.81   1.5e+03      31      48 ..      42      59 ..      41      65 .. 0.84
   2 ?   10.1   0.4   0.00036      0.65      32      70 ..      86     126 ..      84     129 .. 0.86
   3 ?    1.2   0.2      0.22     4e+02      30      46 ..     146     162 ..     142     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.81
                        DUF5595 31 FeeedaeleskLkelynv 48
                                   +++++++l  ++ke y++
  gene172|gene172|rna172|rna172 42 YKNVEKALVHHFKETYEI 59
                                   667888999999999987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00036
                        DUF5595  32 eeedaeleskLkely..nvdeaqlesleeeekrLeeEierl 70 
                                    +e+d ele  ++ l+   + e ++e+l+ee +rL+ E e+l
  gene172|gene172|rna172|rna172  86 PEVDLELERFFEGLFfgGIREMEVEQLKEETERLMRENEEL 126
                                    6899999999999984458899***************9987 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.22
                        DUF5595  30 tFeeedaeleskLkely 46 
                                    +F+ +d+e+ s++++ +
  gene172|gene172|rna172|rna172 146 EFKSVDEEVLSRMEKDL 162
                                    78999999999987643 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   6.0   0.00061       1.1      25      52 ..     107     134 ..     105     136 .. 0.90
   2 ?   -0.3   0.1      0.64   1.1e+03      33      49 ..     154     170 ..     151     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00061
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  25 akeeeleervkeLeeeNaqLrqkveqLe 52 
                                    ++ e+l+e+ ++L++eN++Lr ++ +++
  gene172|gene172|rna172|rna172 107 MEVEQLKEETERLMRENEELRGRINEMN 134
                                    6789*******************99886 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                                    HHHHHHHHHHHHHHHHH CS
                         bZIP_2  33 rvkeLeeeNaqLrqkve 49 
                                     + ++e++  +Lr++v+
  gene172|gene172|rna172|rna172 154 VLSRMEKDLVALREQVD 170
                                    56789999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1143  (0.0637515); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1254.66
//
Query:       gene1721|gene1721|rna1720|rna1720  [L=538]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.4   10.9   9.9       0.19   11.9   1.2    3.3  4  DUF3654   Protein of unknown function (DUF3654)


Domain annotation for each model (and alignments):
>> DUF3654  Protein of unknown function (DUF3654)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.6      0.36   6.5e+03      10      41 ..      51      82 ..      36      91 .. 0.60
   2 ?   -2.1   0.1      0.23   4.2e+03      48      67 ..     116     135 ..     100     164 .. 0.67
   3 ?   11.9   1.2   1.1e-05      0.19      64     116 ..     224     277 ..     203     281 .. 0.85
   4 ?    3.4   0.0    0.0045        81      25     108 ..     287     369 ..     283     402 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.36
                            DUF3654 10 eeekkkeeevlqkikeygesLctkekqeeive 41
                                       e+e kk+ + +q + e  e+L+ + k  + +e
  gene1721|gene1721|rna1720|rna1720 51 EREIKKTTNEYQGVLENIERLSLNSKECKTIE 82
                                       33445555566666666666666666555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.23
                            DUF3654  48 daCkeiwerleedrksflle 67 
                                         aC+e+ ++ e+++ + l++
  gene1721|gene1721|rna1720|rna1720 116 PACEEVAKEQESENGDGLIR 135
                                        58999998877666555555 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 1.1e-05
                            DUF3654  64 fllelyaeglmlkalkakldeeeveepllavvdhelLidahkeykidv.vkELv 116
                                         + +++  +l +k+++++l +eeve++ l++ d+e  i+   e+k+d+ +kE++
  gene1721|gene1721|rna1720|rna1720 224 AIFGVLRDNLRKKVVEKNLTDEEVERNNLFFKDTEFYIHNVPEWKLDIvMKEII 277
                                        4789999**************************************996268877 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.0045
                            DUF3654  25 eygesLctkekqeeiveaqkivcdaCkeiwerleedrksfllelyaeglmlkalkakldeeeveepllavvdhelL 100
                                        e +e++ t +++ + v a    ++ C e+++rl++ r++  +++  + + +k  ++k +e  v +  l + d++ +
  gene1721|gene1721|rna1720|rna1720 287 EAVETFETSDRMPKSVSASYKRFQGCFEMFRRLRSKRHEKGVKVINRAI-TKLFDPKRHEPSVYSYFLEFADITHF 361
                                        78999999***********99****************999999988765.68999999999998888899999999 PP

                            DUF3654 101 idahkeyk 108
                                        ++++  + 
  gene1721|gene1721|rna1720|rna1720 362 LRTYPGHP 369
                                        99887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3812.06
//
Query:       gene1722|gene1722|rna1721|rna1721  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.058   13.2   0.0    1.4  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-06     0.058       1      50 [.       8      57 ..       8      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-06
                                       EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHH CS
                              RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeske 50
                                       lf+gn+p +  +e L e++s fG+ik++k  r   g s ++ +V+++ + 
  gene1722|gene1722|rna1721|rna1721  8 LFLGNIPDSFGNELLMEMLSIFGEIKEFKRGRCLEGISSKWVIVNYHEPA 57
                                       89*************************99888777777778888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1423  (0.0793686); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1579.25
//
Query:       gene1723|gene1723|rna1722|rna1722  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-20   73.4   0.1    1.5e-20   73.2   0.1    1.0  1  BolA      BolA-like protein


Domain annotation for each model (and alignments):
>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.1   8.3e-25   1.5e-20       1      73 [.      13      89 ..      13      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 8.3e-25
                               BolA  1 LtealkpehlevedeShkhagha....eaggetHFkvvivseaFegkslvarhRlvyalLkeelakgiHALslktkt 73
                                       L++++ p++lev++ S  h gh+    e+g etHF+v++ s+ F+g++  +rhRlvy++L+  ++ g+HA+++++ +
  gene1723|gene1723|rna1722|rna1722 13 LKNEFCPTRLEVKNTSCDHTGHRiieqEEGLETHFHVRVRSAMFNGMKFTDRHRLVYKTLEFAFSLGLHAIEIDCDS 89
                                       7899*********************99889*******************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.56
# Mc/sec: 503.43
//
Query:       gene1724|gene1724|rna1723|rna1723  [L=249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-07   31.8   0.0    1.8e-07   31.1   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0     1e-11   1.8e-07       5     109 ..      21     130 ..      17     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1e-11
                                        TSTEEEEEEEESS.CSCHHHHHHHHHHCT--EEEEE-HHH..HCH-HHHHHHHHHTTEEEEE--SS--EG..GGSH CS
                    Polysacc_deac_1   5 gkksvalTfDdgp.rdntteilpvLkkykvkatffviggl..vedypdevremaasGveignHtinhsnl..krls 75 
                                        +  ++a+ f dgp r +t+++l++L++ +vkatf ++ ++  v++  ++ r+ +++G+++g     + +   ++ls
  gene1724|gene1724|rna1723|rna1723  21 TSGMIAINFVDGPvRGVTDRVLNTLDELGVKATFSFTVNQkaVGNVGQLYRRAVNEGHTVGLRIDPRMDDgcQNLS 96 
                                        56799********999*****************955444336*******************99887776677**** PP

                                        HHHHHHHHHHHHHHHHHHHS----EEE-GGGEE- CS
                    Polysacc_deac_1  76 eeevrreierakdalrkalgreprlfryPygsas 109
                                        ++ +++ ++r  d +    g e+r+   P     
  gene1724|gene1724|rna1723|rna1723  97 RDALEENVDREIDTIDGLSGTEVRYASVPINNGE 130
                                        *************************999964433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1596.09
//
Query:       gene1725|gene1725|rna1724|rna1724  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2223.70
//
Query:       gene1726|gene1726|rna1725|rna1725  [L=385]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-19   69.4   0.1    3.6e-18   65.9   0.1    2.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
      0.037   14.6   1.0      0.074   13.6   1.0    1.4  1  DUF4473       Domain of unknown function (DUF4473)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.1     4e-22   3.6e-18       3     291 ..      78     360 ..      75     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 4e-22
                                        HS--EEEEEEETSSS.-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT.-SSHHHHHHHHHHHHHHHHHHH CS
                       tRNA-synt_1b   3 erplrvysGidPTgk.lHlGylvplkklvelqkaghevffliaDlhAiigdps.kaeerklrkreevlenaikaql 76 
                                        ++ + +y+G  P+ k +H+G++vp+    + q ++ ++ ++i     +++d +   +  kl+++ +  ++ +k ++
  gene1726|gene1726|rna1725|rna1725  78 NKSFYLYTGRGPSTKaMHIGHVVPFLLCKYVQ-DTFRIPLVI----QMTDDEKfLWKNIKLEDAIKNGKENVKDIV 148
                                        68899***************************.777777766....3677777655566666666666666788** PP

                                        HHTCHTTTEEEEETHHHHTTH.HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCH CS
                       tRNA-synt_1b  77 akgldpekaevvlqsewlehl.elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllka 151
                                        a g+dp+ + ++ + e      +    +++  +l++ +++  f   ++++ +   ++  e+  p+  +  + ++++
  gene1726|gene1726|rna1725|rna1725 149 ALGFDPKLTYIFSNVESSHRFeKNVLKISKTINLNEASKVFGFNM-SSNIGQ-IAFPSKEIA-PCFSSS-FKFIEK 220
                                        ******999899887766665233334555566677777777776.777777.567777877.777665.444555 PP

                                        S...EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSS.BTTCETTCGC-BTTCCHHHHHHHHH CS
                       tRNA-synt_1b 152 d...lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGek.KmSKSagnsaIfLddekesvkkkiq 223
                                        +   lvp   DQ+  ++l+rd a+ +++k    kp++++v ll++l+G + KmS S++ns I+Ldd++e+++ ki 
  gene1726|gene1726|rna1725|rna1725 221 EaicLVPAAVDQDPYFRLARDKAKILGEK----KPVSVYVSLLPDLKGVNrKMSASDPNSSIYLDDSQETIRRKIT 292
                                        55899***********************9....****************99************************8 PP

                                        .HCHCSTTC..SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHH CS
                       tRNA-synt_1b 224 .kavtdsde..evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnel 291
                                          a++  ++  e ++ + ++  ++   +e+l ++++ ++  e+e++   + +++++ +++k++  ++++ +
  gene1726|gene1726|rna1725|rna1725 293 vHAYSGGRKtlEEHREKGGNIDVDV-PFEYLRYFLDDDE--ELEKYRSGYTKGEITSKEMKEKCIAVIQDF 360
                                        3566766669999999999999999.9*********999..*********************998888776 PP

>> DUF4473  Domain of unknown function (DUF4473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.0   8.3e-06     0.074      29      75 ..     333     383 ..     332     384 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-06
                            DUF4473  29 ekfksefaka....kgdkeaakkafeklkaevdafiktqseeDqaaykafv 75 
                                        ek++s++ k     k  ke+  ++++++ +++++ +k+++eeD +a+ ++ 
  gene1726|gene1726|rna1725|rna1725 333 EKYRSGYTKGeitsKEMKEKCIAVIQDFVSKYQEARKKVTEEDVKAFMDIN 383
                                        578888888888889999****************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2620.11
//
Query:       gene1727|gene1727|rna1726|rna1726  [L=593]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.2e-220  732.0   3.4   4.9e-220  731.8   3.4    1.0  1  HSP70           Hsp70 protein
    7.2e-20   71.1   2.4    7.1e-18   64.5   0.8    2.3  2  MreB_Mbl        MreB/Mbl protein
    0.00021   21.6   0.6       0.98    9.9   0.0    3.1  2  FtsA            Cell division protein FtsA
     0.0046   16.7   0.0      0.013   15.2   0.0    1.8  2  FGGY_C          FGGY family of carbohydrate kinases, C-termin
     0.0066   15.8   1.4        1.1    8.4   0.0    3.0  3  Hydantoinase_A  Hydantoinase/oxoprolinase
     0.0072   15.6   0.1       0.17   11.1   0.0    2.4  2  StbA            StbA protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  731.8   3.4  1.7e-223  4.9e-220       1     557 [.      15     568 ..      15     592 .. 0.96

  Alignments for each domain:
  == domain 1  score: 731.8 bits;  conditional E-value: 1.7e-223
                                        EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTTSEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSH CS
                              HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkkerlvGeaAkrqavtnpkntvfsvKrliGrkfsdp 76 
                                        +iGiDLGttns+v+v+++g++ +i+n+eg+rtt svv+  k+e lvG+++k++  t pknt+f+ KrliGrk++dp
  gene1727|gene1727|rna1726|rna1726  15 IIGIDLGTTNSCVSVVKNGEPVIIENQEGERTTSSVVSILKDEILVGSQSKNKILTHPKNTIFASKRLIGRKLDDP 90 
                                        69************************************************************************** PP

                                        HHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHH CS
                              HSP70  77 evqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqat 152
                                        ev k +k lp++ +++ ng+++++++  g+k++p qi+a++L+klk+ ae++l+++v + vitvPaYfnd+qRqat
  gene1727|gene1727|rna1726|rna1726  91 EVRKYVKGLPFDTTSHCNGDVWIKID--GKKYSPAQIGAFILSKLKSSAESFLNHPVVKSVITVPAYFNDSQRQAT 164
                                        *************************9..************************************************ PP

                                        HHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHH CS
                              HSP70 153 kdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDe 228
                                        kdAg+iAGL+v+R++NepTAaalaYGldk+    n++vyDlGggtfd+Silel++Gvf+vkaT+gDt lGGedfD+
  gene1727|gene1727|rna1726|rna1726 165 KDAGRIAGLEVVRVINEPTAAALAYGLDKAA-RGNIAVYDLGGGTFDISILELSDGVFHVKATNGDTFLGGEDFDN 239
                                        ******************************9.9******************************************* PP

                                        HHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHH CS
                              HSP70 229 alvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelve 303
                                        ++v+++ve+fk keg+dls+d++al r+ke aek+Kk+LSss  ++i++++++  + +  +ls++++R++fe +v+
  gene1727|gene1727|rna1726|rna1726 240 EVVKFIVEDFKGKEGVDLSDDTNALARIKECAEKIKKDLSSSLVSRIDIPYICNVRGEaRHLSKEITRNEFEGIVK 315
                                        *****************************************************999668***************** PP

                                        HHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCG CS
                              HSP70 304 dllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgee 379
                                        ++++rt+ep++kal+da+l+  +i++v+lvGG+tR+P v+ +vke+fg eps ++npDeava+GAA+q+gvl+g  
  gene1727|gene1727|rna1726|rna1726 316 KIVDRTIEPCKKALADAGLDCTDIKHVILVGGMTRMPYVRRVVKEIFGIEPSVEINPDEAVAKGAAIQGGVLAG-- 389
                                        **************************************************************************.. PP

                                        CSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEE CS
                              HSP70 380 evkdllllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeld 455
                                        ev+++lllDv pLslgie+lggv++k+i+rnttip k++q+fst +dnqt+v+i+v+qger++++dnk lg+ +l+
  gene1727|gene1727|rna1726|rna1726 390 EVDNVLLLDVAPLSLGIELLGGVFNKIIRRNTTIPFKETQIFSTSEDNQTEVDIKVYQGERAMAADNKYLGQIKLK 465
                                        **************************************************************************** PP

                                        CESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHH CS
                              HSP70 456 gippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieak 531
                                         ipp+prGvp+ieVtf+ danG+ +v+a+d +t+  ++++i  s+gl+e+ei++mv++ ee ++ d+ k++++e  
  gene1727|gene1727|rna1726|rna1726 466 SIPPLPRGVPRIEVTFESDANGMYKVTAQDSATKMPQSLEIIPSSGLTEKEIDRMVREGEELKHLDEIKRRKAEVV 541
                                        ***************************************************************************9 PP

                                        HHHHHHHHHHHHHHHHH.GGGSTHHHH CS
                              HSP70 532 neaeelvyslekkleee.aekvseaek 557
                                         ++ el+ + ++ l +  ++ +s+ +k
  gene1727|gene1727|rna1726|rna1726 542 VSTGELFGKGADDLGKVpKDDLSKLNK 568
                                        999999988888877765555554333 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0019       5.6       2      24 ..      14      38 ..      13      81 .. 0.67
   2 !   64.5   0.8   2.4e-21   7.1e-18      93     316 ..     145     381 ..     123     387 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0019
                                       SEEEEEE-SSEEEEEETTTE..EEE CS
                           MreB_Mbl  2 kdlgiDLGtantlvyvkgkg..ivl 24
                                       + +giDLGt+n  v v  +g  +++
  gene1727|gene1727|rna1726|rna1726 14 NIIGIDLGTTNSCVSVVKNGepVII 38
                                       569********99976554422444 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 2.4e-21
                                        --EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EE.EEEE-SS-EEEEEEETTEE CS
                           MreB_Mbl  93 kprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnm.vvdiGggttevavislggi 167
                                          + vi+vP   ++ +r+A k+a + aG + v +i+ep aAA+  gl+ + ++gn+ v d+Gggt +++++ l++ 
  gene1727|gene1727|rna1726|rna1726 145 VVKSVITVPAYFNDSQRQATKDAGRIAGLEVVRVINEPTAAALAYGLDKA-ARGNIaVYDLGGGTFDISILELSDG 219
                                        33559*******************************************65.55655388*************9987 PP

                                        EEEEEES.....-SHHHHHHHHHHHHHHHHS....EE--HHHHHHHHHH.H-BSS--HHHH....EEEEEEEETTT CS
                           MreB_Mbl 168 vtsksvr.....vaGdeldeaiikyirkkyn....lliGertaekikie.igsavkeeeee....kmeikGrdlvt 229
                                        v           ++G+++d++++k+i ++++    + + + t    +i+  ++ +k++ ++    +++i   + v 
  gene1727|gene1727|rna1726|rna1726 220 VFHVKATngdtfLGGEDFDNEVVKFIVEDFKgkegVDLSDDTNALARIKeCAEKIKKDLSSslvsRIDIPYICNVR 295
                                        65443321333389************99997333344444444333332022222222211244467777777777 PP

                                        TCEEEE..EEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE CS
                           MreB_Mbl 230 glpkev..evsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseetglpvkv 303
                                        g ++++  e++ +e +  +k+ v + +e  k++L ++  + ++di  + ++l+GG + +  ++++++e +g++ +v
  gene1727|gene1727|rna1726|rna1726 296 GEARHLskEITRNEFEGIVKKIVDRTIEPCKKALADAGLD-CTDI--KHVILVGGMTRMPYVRRVVKEIFGIEPSV 368
                                        7777542267777777777777777777777777776665.4566..6799************************* PP

                                        -SSTTTHHHHHHH CS
                           MreB_Mbl 304 aedpltcvakGtg 316
                                          +p ++vakG++
  gene1727|gene1727|rna1726|rna1726 369 EINPDEAVAKGAA 381
                                        ***********97 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0007       2.1       1      24 [.      16      39 ..      16     188 .. 0.87
   2 !    9.9   0.0   0.00033      0.98       2      88 ..     201     366 ..     200     383 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0007
                                       EEEEE-SSSEEEEEEETTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                               FtsA  1 alvDiGagktdvavaedgalvhlr 24
                                       +++D+G++ ++v+v+++g++v ++
  gene1727|gene1727|rna1726|rna1726 16 IGIDLGTTNSCVSVVKNGEPVIIE 39
                                       58***************9876543 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00033
                                        EEEE-SSSEEEEEEETTE.EEE...EEEES-....-HHHHHHH...................HHHHHT--HHHHHH CS
                                        xxxxxxxxxxxxxxxxxx.xxx...xxxxxx....xxxxxxxx...................xxxxxxxxxxxxxx RF
                               FtsA   2 lvDiGagktdvavaedga.lvh...lrvigv....ggngitkd...................iakalrtaveeAer 50 
                                        + D+G+g+ d++++e +  + h   +   +     gg+ ++++                     +al    e Ae+
  gene1727|gene1727|rna1726|rna1726 201 VYDLGGGTFDISILELSDgVFHvkaT---NGdtflGGEDFDNEvvkfivedfkgkegvdlsdDTNALARIKECAEK 273
                                        6699*********9997643334442...22344666666666555555555555555544555677888888999 PP

                                        HHHHH--S--..................EEEEEHHHHH...................................GGG CS
                                        xxxxxxxxxx..................xxxxxxxxxx...................................xxx RF
                               FtsA  51 ikikyGsala..................ekeigrkels...................................ggs 73 
                                        ik++  s l                   +kei+r+e +                                   g +
  gene1727|gene1727|rna1726|rna1726 274 IKKDLSSSLVsridipyicnvrgearhlSKEITRNEFEgivkkivdrtiepckkaladagldctdikhvilvgGMT 349
                                        9976666555777777777777776666555555555588888999999999999999999999999999999999 PP

                                        GSTTHHHHHHHHH..T- CS
                                        xxxxxxxxxxxxx..xx RF
                               FtsA  74 alpnleelaeral..sp 88 
                                         +p +++++++++  +p
  gene1727|gene1727|rna1726|rna1726 350 RMPYVRRVVKEIFgiEP 366
                                        99999999999986644 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.8   5.3e+03      77     100 ..      23      46 ..      19      48 .. 0.84
   2 !   15.2   0.0   4.3e-06     0.013     149     196 ..     338     386 ..     305     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                             FGGY_C  77 laaaeavadaggvvfvpafsglra 100
                                         +++ +v+++g++v++ +  g+r+
  gene1727|gene1727|rna1726|rna1726  23 TNSCVSVVKNGEPVIIENQEGERT 46 
                                        5778899999******99999997 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.3e-06
                             FGGY_C 149 pldrlavdGGgskndllmqllAdilg.vpVerpktaeatalGaAilAav 196
                                        +++ ++++GG+++ + ++++  +i+g  p +   ++ea+a GaAi ++v
  gene1727|gene1727|rna1726|rna1726 338 DIKHVILVGGMTRMPYVRRVVKEIFGiEPSVEINPDEAVAKGAAIQGGV 386
                                        5999**********************766666666***********997 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00037       1.1      78     127 ..      12      61 ..       4      77 .. 0.77
   2 ?    3.3   0.1     0.013        40      65      97 ..     185     215 ..     166     228 .. 0.77
   3 ?    1.2   0.0     0.061   1.8e+02     180     265 ..     249     364 ..     239     381 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00037
                     Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsleteiagvkvrlpaldirtvgag 127
                                        ++++I++D+G T   vs++k+ge+ +  ++e  + + ++ ++  +++ +g
  gene1727|gene1727|rna1726|rna1726  12 SSNIIGIDLGTTNSCVSVVKNGEPVIIENQEGERTTSSVVSILKDEILVG 61 
                                        579*********************77777775555555555555666555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.013
                     Hydantoinase_A  65 GvvgaaatsklagekkvItfDmGGTstDvslik 97 
                                         + ++    ++a   ++ ++D+GG ++D+s ++
  gene1727|gene1727|rna1726|rna1726 185 AALAYGL--DKAARGNIAVYDLGGGTFDISILE 215
                                        3333333..6777789*************9864 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.061
                     Hydantoinase_A 180 flsgpdgdqkldvelarrafeelakelnlk............................veevAegilsvavenman 227
                                        f  g++g   +d   a + ++e+a++++++                              +  egi+++ v+   +
  gene1727|gene1727|rna1726|rna1726 249 FK-GKEGVDLSDDTNALARIKECAEKIKKDlssslvsridipyicnvrgearhlskeiTRNEFEGIVKKIVDRTIE 323
                                        55.6666666777777778888888888888888888888888888888888887666455557788888888888 PP

                     Hydantoinase_A 228 avrklsvergldpkeltlvv.fGGaG..aqhaaalaeelgv 265
                                        + +k + + gld ++   v+ +GG    + +  ++ e +g+
  gene1727|gene1727|rna1726|rna1726 324 PCKKALADAGLDCTDIKHVIlVGGMTrmPYVRRVVKEIFGI 364
                                        88888888888887766554145554334444455555555 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.035     1e+02     142     180 ..     176     214 ..     160     244 .. 0.76
   2 !   11.1   0.0   5.6e-05      0.17     214     295 ..     281     364 ..     232     376 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.035
                               StbA 142 vkvlPeslPagfealkeldeleslLiiDlGGttLDvakv 180
                                        v+v+ e   a+     + +   +  + DlGG t D++ +
  gene1727|gene1727|rna1726|rna1726 176 VRVINEPTAAALAYGLDKAARGNIAVYDLGGGTFDISIL 214
                                        667777666666665555566677899*********965 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.6e-05
                               StbA 214 trtssfladeliknrkdeeyLkrrindedkresvlevinekvkkLkerviravsefsgythvmvvGGGael..iae 287
                                          +s   +  + + r +  +L+++i+ ++    v +++++  +  k+ + +a    ++++hv++vGG + +  +  
  gene1727|gene1727|rna1726|rna1726 281 SLVSRIDIPYICNVRGEARHLSKEITRNEFEGIVKKIVDRTIEPCKKALADAGLDCTDIKHVILVGGMTRMpyVRR 356
                                        44566777788999**************99999**********************************988654777 PP

                               StbA 288 aikkatev 295
                                         +k+ +++
  gene1727|gene1727|rna1726|rna1726 357 VVKEIFGI 364
                                        78887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3636.23
//
Query:       gene1728|gene1728|rna1727|rna1727  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-30  105.2   0.2    4.6e-30  104.1   0.2    1.7  1  ArfGap      Putative GTPase activating protein for Arf
  ------ inclusion threshold ------
      0.029   14.5   0.3        3.2    8.0   0.1    2.3  2  zf-RING_13  RING/Ubox like zinc-binding domain
      0.034   14.4   0.3      0.067   13.4   0.3    1.5  1  Synuclein   Synuclein


Domain annotation for each model (and alignments):
>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.2   7.6e-34   4.6e-30       2      91 ..       7      96 ..       6     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 7.6e-34
                                       HHHHHHCCSCCCCB-TTT-SBS--EEETTTTEEE-HHHHHHHCCS.TTT--EEETTTS---HHHHHHHHHTCHHHHHH CS
                             ArfGap  2 kalkellkepenkvCaDCgakeptWaslnlgvflCieCsgvHrslgvhiskvrsltldkwedeelellkalgNkkane 79
                                       k++k l+  +enk+CaDC+ ++p Was+++g+f+C +C++vHrslgv++s+v+s++ld w+++e  ++k+++N+k+++
  gene1728|gene1728|rna1727|rna1727  7 KEVKILRDIEENKRCADCSGPNPPWASVTYGIFICFDCASVHRSLGVKTSFVKSVNLDIWDEKEYLFMKHGSNEKFRK 84
                                       678889999********************************************************************* PP

                                       HHTTTC-TTTSG CS
                             ArfGap 80 ileaklpkeekr 91
                                       +le++    ++ 
  gene1728|gene1728|rna1727|rna1727 85 FLEQYGLVGREM 96
                                       ***998444443 PP

>> zf-RING_13  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00053       3.2      10      61 ..      29      80 ..      19      84 .. 0.84
   2 ?    4.5   0.0    0.0066        40      19      39 ..     142     165 ..     130     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00053
                                       --SEEETTS-EE-TTTHHHTTTSS-EEESSSSS-SBGGGBSSSBTTTTSS-- CS
                         zf-RING_13 10 apvaksacggwfcgncvpyhaghchttslfancghdimyrstyctmcegspk 61
                                        p a  + g ++c +c   h      ts+      di     y  m  gs  
  gene1728|gene1728|rna1727|rna1727 29 PPWASVTYGIFICFDCASVHRSLGVKTSFVKSVNLDIWDEKEYLFMKHGSNE 80
                                       466777888899**********************************999976 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0066
                                        -EE...-TTTHHHTTTSS-EEESS CS
                         zf-RING_13  19 gwf...cgncvpyhaghchttslf 39 
                                        gw+     ncv    g c tt l 
  gene1728|gene1728|rna1727|rna1727 142 GWMnrsSTNCVNRSRGPCSTTGLE 165
                                        66533357*************985 PP

>> Synuclein  Synuclein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.1e-05     0.067      54     125 ..     171     241 ..     160     249 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                          Synuclein  54 tvaektkeqasvvgeavvtsvnavaektvegaeniaaatGlvkkedlekdlpeeegeeasevedealldeee 125
                                        +  +   +  s+vg a+++s++ ++ ktve  + ++++t  + k++  + l +  +++  +++d  +++e++
  gene1728|gene1728|rna1727|rna1727 171 SLHNSIASTLSIVGSAIFSSAKIITDKTVEYGGIVVSSTKSIIKDNSSS-LASIFKKKELAPKDHIKVPEKQ 241
                                        55566678899*******************9999999888555554432.2222222223344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1571.89
//
Query:       gene1729|gene1729|rna1728|rna1728  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-11   44.9   5.7    1.5e-11   44.7   5.7    1.0  1  Cornichon  Cornichon protein


Domain annotation for each model (and alignments):
>> Cornichon  Cornichon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   5.7   8.2e-16   1.5e-11       5     120 ..       7     120 ..       3     121 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 8.2e-16
                          Cornichon   5 ilaliltaallflsvyfiialsDleadyinpidlcsklNplvlpelilhafltllfllsgewilfllnlpllayni 80 
                                        +++l+l+++l+++ +y i a+ D+e+   ++++ c+++ +l  +e+ l ++l+++  ls++++++ l++++++y++
  gene1729|gene1729|rna1728|rna1728   7 LASLLLSTILCIVELYKIEAVVDVESRRASSYNACDRILRLADVEFKLLVLLMVAQTLSLSYTSL-LTVLVFVYEL 81 
                                        689***********************************************************999.778889**** PP

                          Cornichon  81 yrvmskqglydpteifnqlkkhkkesmiklafylllffiy 120
                                        ++   ++ ++ + + f+q  + k e ++k  fy+ll++ y
  gene1729|gene1729|rna1728|rna1728  82 QKK-GSETTISALNFFKQKRWIKIEIFCKTSFYVLLLYKY 120
                                        **5.8999***************************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 771.20
//
Query:       gene1730|gene1730|rna1729|rna1729  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      6e-31  106.9   0.1    9.1e-31  106.3   0.1    1.3  1  JAB         JAB1/Mov34/MPN/PAD-1 ubiquitin protease
    1.3e-07   31.4   0.0      2e-07   30.8   0.0    1.3  1  Prok-JAB    Prokaryotic homologs of the JAB domain
     0.0001   22.7   0.2    0.00018   21.9   0.2    1.4  1  MitMem_reg  Maintenance of mitochondrial structure and functi
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.035   14.2   0.0    1.5  1  UPF0172     Uncharacterised protein family (UPF0172)


Domain annotation for each model (and alignments):
>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.1     2e-34   9.1e-31       2     116 ..      17     127 ..      16     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2e-34
                                        SSCEEEEEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHH CS
                                JAB   2 svqavhleslvllkildhalrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksel 77 
                                        + ++v+++sl+llk+l+h + +     evmGl++Ge+ d++tv++++vfa+p+++t+ +v+ v++  ++ +++++ 
  gene1730|gene1730|rna1729|rna1729  17 TSETVQISSLALLKMLKHGRAGIPL--EVMGLMLGEFVDEYTVKVVDVFAMPQSGTNVTVESVDP--IFQMEMMSI 88 
                                        5789*********************..********************************777766..555999999 PP

                                        HHHHCTT.SEEEEEEEESSSS-SS--HHHHHHHHHHHHHS CS
                                JAB  78 lkklrgr.ervvGWYhshpditvwlsevdvrtqalyqrmd 116
                                        lk + gr e vvGWYhshp++++wls vd++tq+++++++
  gene1730|gene1730|rna1729|rna1729  89 LKAT-GRhETVVGWYHSHPGFGCWLSTVDISTQQSFEKLC 127
                                        9998.777***************************99876 PP

>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   4.4e-11     2e-07       4      91 ..      27     119 ..      24     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.4e-11
                           Prok-JAB   4 vlsalvaharrahpeEtcGlllgkeseseevivvplvnewsn...rfeipdpedslarlkf...earerglevvgi 73 
                                        +l ++++h r+  p E  Gl+lg+  ++  v vv++  ++ +   ++++++ + ++++ ++   +a+ r ++vvg 
  gene1730|gene1730|rna1729|rna1729  27 ALLKMLKHGRAGIPLEVMGLMLGEFVDEYTVKVVDVF-AMPQsgtNVTVESVDPIFQMEMMsilKATGRHETVVGW 101
                                        5789********************9555555555555.44444774444444444444444679************ PP

                           Prok-JAB  74 wHSHpggsarPSetDrrd 91 
                                        +HSHpg +   S  D+++
  gene1730|gene1730|rna1729|rna1729 102 YHSHPGFGCWLSTVDIST 119
                                        *****9887666666665 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2     4e-08   0.00018       1      81 [.     163     277 ..     163     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4e-08
                         MitMem_reg   1 Eaeei..gvehllkpsiqdasstlstglnrqyyslki................................lqerldl 42 
                                        E++++  ++++l  p+ +    ++++gln++yys +i                                 ++ l+l
  gene1730|gene1730|rna1729|rna1729 163 EPRQVtsNIGYLKTPTLI----SIIHGLNKHYYSFNItcrkndleqkmllnlhrktwadnlklrnikkeRENVLKL 234
                                        99****************....****************************************************** PP

                         MitMem_reg  43 ikdYlkkveege.lpvnheilrnlqkll...nllPhleteele 81 
                                        i++Y k+ +e++ l+ ++  + +++k++    ll ++e++ +e
  gene1730|gene1730|rna1729|rna1729 235 IESYGKACKEERnLTGKNLDMAKIGKVDyrrRLLEKCEENIME 277
                                        *********8876444444666666666221334455554444 PP

>> UPF0172  Uncharacterised protein family (UPF0172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.8e-06     0.035       2     115 ..      21     136 ..      20     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.8e-06
                            UPF0172   2 vevssqAYvKlllHaaKyptqaVnGvLlgkkssskskvevtDa..vPLfH...ssltlspmlevAlaqvesyakek 72 
                                        v++ss A +K+l H       +V+G++lg+  ++ + v+v+D+  +P      +  ++ p++++ ++ + + + + 
  gene1730|gene1730|rna1729|rna1729  21 VQISSLALLKMLKHGRAGIPLEVMGLMLGEFVDEYT-VKVVDVfaMPQSGtnvTVESVDPIFQMEMMSILKATGR- 94 
                                        799***************************988885.*****722566655555667789999999999887666. PP

                            UPF0172  73 glvivGyYqanerlsdtelsslaekiadkiaenfsdavllvvd 115
                                        + ++vG+Y+++  ++   ls++  +  +  ++ +++av++vvd
  gene1730|gene1730|rna1729|rna1729  95 HETVVGWYHSHPGFGC-WLSTVDISTQQSFEKLCKRAVAVVVD 136
                                        899******9877762.33333444444444444455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1710.71
//
Query:       gene173|gene173|rna173|rna173  [L=585]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-53  181.4   0.8      3e-53  180.9   0.8    1.2  1  Pkinase          Protein kinase domain
    1.3e-25   90.2   0.2    2.7e-25   89.1   0.2    1.5  1  Pkinase_Tyr      Protein tyrosine kinase
    0.00064   19.7   0.0      0.011   15.6   0.0    2.1  2  APH              Phosphotransferase enzyme family
    0.00088   18.7   0.0     0.0014   18.0   0.0    1.3  1  Kinase-like      Kinase-like
     0.0034   17.0   2.5       0.13   11.8   0.1    2.9  3  FTA2             Kinetochore Sim4 complex subunit FTA2
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.029   14.0   0.0    1.6  1  RIO1             RIO1 family
      0.053   12.9   0.0       0.11   11.9   0.0    1.4  1  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
      0.059   13.0   0.0        0.1   12.2   0.0    1.2  1  Caps_synth_GfcC  Capsule biosynthesis GfcC


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.8   1.3e-56     3e-53       2     264 .]     289     539 ..     288     539 .. 0.89

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 1.3e-56
                                    EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEEEEE-- CS
                        Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyevfeekdelylvleyv 80 
                                    e l+++G+G+++kVyk++    ++ +A+K+++   ++k+ + ++++Ei++l k+k  p+iv++++   ++d+l+++ley 
  gene173|gene173|rna173|rna173 289 EILKQIGKGGSSKVYKVL--LGSNVYALKRVELIGDEKMLN-SYINEINLLYKFKgTPEIVEIIDHEISEDYLHILLEYG 365
                                    6789**************..7999**********9999875.9************************************* PP

                                    TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS...BCTT CS
                        Pkinase  81 eggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk...ltsf 157
                                    e++ l ++++ +g ls++ +k++++q+l  ++ +H ++iiH+DlKp+N+L+  kg +K++DFG++k ++++++    +++
  gene173|gene173|rna173|rna173 366 ETD-LSKIIR-RGGLSMNFIKDVWEQMLLIVKRVHMERIIHCDLKPANFLFV-KGRVKLIDFGISKVIRNDTTsilSEEQ 442
                                    *66.*****7.699**************************************.******************999*999** PP

                                    TSCGGGS-HHHH..TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-H CS
                        Pkinase 158 vgtseYlAPEvl..keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseise 235
                                    +gt +Y++PE +  +++++ +++D+WslG+ilye+   +pp++   +   + + +++   i+k+ + +++k+   s+ ++
  gene173|gene173|rna173|rna173 443 CGTVNYMSPEAVtqNKSKVARSSDIWSLGCILYEMAHSRPPLY---E---YPNLIQK---IQKLQEYSEFKY---SSKNK 510
                                    ************74445669***********************...2...2233333...445544434443...44466 PP

                                    HHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 236 eakdllkkllkkdpkkRltaeellqhpyl 264
                                     a  ++k++l +dpkkR+t++ ll+h++l
  gene173|gene173|rna173|rna173 511 LAVMVMKECLVRDPKKRPTIDTLLNHRFL 539
                                    78999*********************996 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.2   1.2e-28   2.7e-25       2     257 ..     289     535 ..     288     537 .. 0.89

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.2e-28
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl.khpnivkllgvctkeepllivt 80 
                                    e+ k++G+G  +kV++  l       +   a+K ++   +e+  ++ ++e++++ k+   p+iv+++   ++e+ l i++
  gene173|gene173|rna173|rna173 289 EILKQIGKGGSSKVYKVLLG------SNVYALKRVELIGDEKMLNSYINEINLLYKFkGTPEIVEIIDHEISEDYLHILL 362
                                    67899************999......66789****9999******************99********************* PP

                                    E--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEE CS
                    Pkinase_Tyr  81 eyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyv 160
                                    ey +  dL+k +r+     l+++ + ++  q+   ++ ++ ++++H dl   N L   +  vk+ DfG+++ i +d +  
  gene173|gene173|rna173|rna173 363 EYGE-TDLSKIIRRG---GLSMNFIKDVWEQMLLIVKRVHMERIIHCDLKPANFLFV-KGRVKLIDFGISKVIRNDTTSI 437
                                    **76.59******98...8999999999999999999******************99.789******************* PP

                                    ETTSSTSGGGGS-HHHHHHSE..EEHHHHHHHHHHHHHHHHTTSSGTTTTS.HHHHHHHHHHTTEES-BBTTSBHHHHHH CS
                    Pkinase_Tyr 161 kkeeaklpvkWmapEslkekk..ftsksDvWsfGvllwEiftlgespypgl.kneevleklkegkrlekpekcpeelyel 237
                                     +ee+   v++m+pE+++++k  +  +sD+Ws G +l+E++  ++ p+ ++ +  + ++kl+e  + +  +k ++    +
  gene173|gene173|rna173|rna173 438 LSEEQCGTVNYMSPEAVTQNKskVARSSDIWSLGCILYEMAH-SRPPLYEYpNLIQKIQKLQEYSEFKYSSK-NKLAVMV 515
                                    *****************9988668899*************99.88888877455666666666666655553.3444578 PP

                                    HHHHT-SSGGGS--HHHHHH CS
                    Pkinase_Tyr 238 mkkcweedpeeRptfselve 257
                                    mk+c+ +dp++Rpt+ +l++
  gene173|gene173|rna173|rna173 516 MKECLVRDPKKRPTIDTLLN 535
                                    ***************99875 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.025        56       3     106 ..     292     398 ..     290     399 .. 0.76
   2 !   15.6   0.0   5.1e-06     0.011     152     196 ..     386     427 ..     348     430 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.025
                                    EEE--.SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-..B--B-CTTBS-EEETTEEEEEEE----E CS
                            APH   3 relsggasnrtylvttpagryvlrrnpparaaeeirrevallrlLakagv..pvPevlagdtddeeigllfalieyvpgr 80 
                                    ++++ g s+++y+v  ++  y+l+r++    +  + ++  +  lL k +    + e+++ + +++ + +l +  e    +
  gene173|gene173|rna173|rna173 292 KQIGKGGSSKVYKVLLGSNVYALKRVELIGDEKMLNSYINEINLLYKFKGtpEIVEIIDHEISEDYLHILLEYGETDLSK 371
                                    7899999******************9999677777788888888888888656777777776666666666666666666 PP

                                    E-SS.HHHHHHHHHHHHHHHHHHCCHH CS
                            APH  81 sllr.klsaaqlpellealgeflaalh 106
                                    +++r  ls++ +++++e++    +++h
  gene173|gene173|rna173|rna173 372 IIRRgGLSMNFIKDVWEQMLLIVKRVH 398
                                    666687788888888887777766666 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.1e-06
                                    HHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 152 vlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                    v+++++  + +   ++++H+Dl+p N+l+   +grv  +iDf+ +
  gene173|gene173|rna173|rna173 386 VWEQMLLIVKRVHMERIIHCDLKPANFLFV--KGRV-KLIDFGIS 427
                                    5666555555566799**************..8998.8****965 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.4e-07    0.0014     153     252 ..     390     486 ..     384     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.4e-07
                    Kinase-like 153 lirlaanLqakglvhgkftvdnllldekgglmlggf..taLvragtkvvlseve...kgfaPpEllgsrggytrknktkm 227
                                    ++ ++   + + ++h ++++ n+l+  kg+++l +f  ++ +r  t   lse +   + +  pE + +       nk k+
  gene173|gene173|rna173|rna173 390 MLLIVKRVHMERIIHCDLKPANFLFV-KGRVKLIDFgiSKVIRNDTTSILSEEQcgtVNYMSPEAVTQ-------NKSKV 461
                                    556788999**************996.79****98733689999999999877767788999999988.......8999* PP

                    Kinase-like 228 thkldaWqlGlviyriwclklPltl 252
                                    + + d W lG   y ++    Pl +
  gene173|gene173|rna173|rna173 462 ARSSDIWSLGCILYEMAHSRPPLYE 486
                                    ****************988888765 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.82   1.8e+03      44     104 ..      40     100 ..      36     101 .. 0.77
   2 !   11.8   0.1   5.9e-05      0.13      22      51 ..     286     315 ..     279     338 .. 0.88
   3 ?    3.9   0.0     0.016        36     172     212 ..     381     425 ..     372     428 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.82
                           FTA2  44 rgkeYALKlFrfleaeele..eaeedlkiprealkelasysdpfasECRAfgRLk.eagredlA 104
                                    ++ eY L++  ++ +      + ++d ++ re++  ++  + +f++   A+ R++ eag+e+lA
  gene173|gene173|rna173|rna173  40 GDDEYSLRIWLDYIW---LlmDGTKDMTEARETFRMIKMRFCKFYNYWEAYIRFEiEAGNENLA 100
                                    567888888777733...2447777888889999999999999999999999996577799887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.9e-05
                           FTA2  22 kdiefleyLgkglhsiVlkvkirgkeYALK 51 
                                    +++e+l+ +gkg +s V+kv  + ++YALK
  gene173|gene173|rna173|rna173 286 REVEILKQIGKGGSSKVYKVLLGSNVYALK 315
                                    489**************************9 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.016
                           FTA2 172 elevsqlpkllrdlkklhklgIvvrDlkeenyi....dgkLvDls 212
                                    +++ +  +++l  +k++h + I++ Dlk+ n++      kL+D++
  gene173|gene173|rna173|rna173 381 NFIKDVWEQMLLIVKRVHMERIIHCDLKPANFLfvkgRVKLIDFG 425
                                    56667778999999*****************87553334688886 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.029     108     152 ..     384     427 ..     371     450 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTE CS
                           RIO1 108 eelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQa 152
                                    +++ e++l  ++  ++  +++H+DL   N l+ +++v +ID++ +
  gene173|gene173|rna173|rna173 384 KDVWEQMLLIVK-RVHMERIIHCDLKPANFLFVKGRVKLIDFGIS 427
                                    456667776544.45589***********************9755 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.8e-05      0.11     105     167 ..     369     425 ..     364     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
                            Kdo 105 LedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                    L +++++   l+ +  +  +++   ++++ h   + H dl + n+l+ ++      + liD+ 
  gene173|gene173|rna173|rna173 369 LSKIIRR-GGLSMNFIKDVWEQMLLIVKRVHMERIIHCDLKPANFLFVKGR-----VKLIDFG 425
                                    5555554.33666777889****************************9985.....9999995 PP

>> Caps_synth_GfcC  Capsule biosynthesis GfcC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.5e-05       0.1       4      73 ..     433     502 ..     431     520 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                Caps_synth_GfcC   4 qtvevvlkgkeldlslasavrleqllldaqlaaniywpgaalsdlaaqaeaekqrqevlqqLaeleksad 73 
                                     t+++ ++++  ++++ s++ ++q  ++++++ +i+++g +l ++a+   +  ++ +++q++++l++ ++
  gene173|gene173|rna173|rna173 433 DTTSILSEEQCGTVNYMSPEAVTQNKSKVARSSDIWSLGCILYEMAHSRPPLYEYPNLIQKIQKLQEYSE 502
                                    58899999999****************************************************9998322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3864.35
//
Query:       gene1731|gene1731|rna1730|rna1730  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.096   12.9   0.0       0.14   12.4   0.0    1.2  1  SYCP2_SLD  Synaptonemal complex 2 Spt16M-like domain


Domain annotation for each model (and alignments):
>> SYCP2_SLD  Synaptonemal complex 2 Spt16M-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.7e-06      0.14      44      99 ..      36      89 ..      24      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-06
                          SYCP2_SLD 44 neeealwesvslskeeveeyslkekdkkkvltillkkpitiskkegkkielhFdse 99
                                       ++ ++ w+sv++s    + y+++e++ +k   i l++   +++ke +++++ F+++
  gene1731|gene1731|rna1730|rna1730 36 DSASTAWNSVKISFPGYHRYDIRENEPRKFELIDLTQ--YFGEKEEMQFRIDFETK 89
                                       556799***********************99999986..67999999****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 795.64
//
Query:       gene1732|gene1732|rna1731|rna1731  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-18   66.2   0.0    2.1e-18   65.9   0.0    1.2  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.052   13.0   0.0       0.12   11.9   0.0    1.7  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.0   2.3e-22   2.1e-18       3      66 ..      14      82 ..      12      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.3e-22
                                       EEEEES--HHHHHHHHHHHTTS...TTEEEEEEECSSTTTSEEEEEEEEST..SS-HHHHHHHHHHHHH CS
                        RNA_pol_L_2  3 tfeingEDhTLgnlLrhlllkn...psVefagYkipHPlepkmnlriqtks..snnpleaLkkalkdll 66
                                       t+++n+EDhT++n+Lr+++ kn   ++Ve +gY+ipHP+ +  n++iq +s  s++p + Lkk ++ l+
  gene1732|gene1732|rna1731|rna1731 14 TIQVNKEDHTIMNPLRWCISKNfvgEKVELVGYTIPHPSDDVSNITIQFSSesSQTPPNLLKKMIEGLE 82
                                       89**************************************99999999877767899999999888775 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.12       2      60 ..      15      76 ..      14      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          RNA_pol_L  2 fllrgvdhtlgNaLRrillsevpgvaiea.......pvvkvntdkdklilevetdgslkPeealke 60
                                        +++++dht++N LR ++  +  g  +e        p    ++d ++++++  +  s +P ++lk+
  gene1732|gene1732|rna1731|rna1731 15 IQVNKEDHTIMNPLRWCISKNFVGEKVELvgytiphP----SDDVSNITIQFSSESSQTPPNLLKK 76
                                       57889**********9998776555555555755333....4777778888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 694.06
//
Query:       gene1733|gene1733|rna1732|rna1732  [L=314]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0054   16.8   1.1      0.015   15.4   0.4    2.1  2  STT3_PglB_C  STT3/PglB C-terminal beta-barrel domain


Domain annotation for each model (and alignments):
>> STT3_PglB_C  STT3/PglB C-terminal beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   8.3e-07     0.015      15      75 ..     182     243 ..     174     245 .. 0.87
   2 ?   -2.2   0.0      0.25   4.5e+03      46      73 ..     275     300 ..     250     304 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.3e-07
                                        EEETTTEEEETTT.TEEEETTEEEEEEEEEEEEETTTTEEEE..EE--TT--EEEEEETTTT CS
                        STT3_PglB_C  15 veLgnGivlskdf.kslkiggqkvpvktfveteydkngklkvketeidskaqlyvifmkdYg 75 
                                        ve+  G  +skd+ ++++++++k+++k f  ++   n  l+v+ ++i ++  + v+++k+ g
  gene1733|gene1733|rna1732|rna1732 182 VEIFQGKAISKDLpQEVSFEKNKISLKGFSSIQEAFNSSLEVENKKITKEPLIIVLVVKEQG 243
                                        5666677788887478***********************************99999999865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.25
                                        EETTTTEEEE..EE--TT--EEEEEETT CS
                        STT3_PglB_C  46 eydkngklkvketeidskaqlyvifmkd 73 
                                        +y kng  +   + ++s++  +v+ mkd
  gene1733|gene1733|rna1732|rna1732 275 SYAKNGDKDW--YGYESNGVRNVLGMKD 300
                                        4556665555..7777888888887877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2157.01
//
Query:       gene1734|gene1734|rna1733|rna1733  [L=1156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-58  196.3   0.1    1.5e-57  195.3   0.1    1.5  1  CPSF_A    CPSF A subunit region


Domain annotation for each model (and alignments):
>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3   0.1   8.5e-62   1.5e-57       3     303 ..     811    1106 ..     809    1128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 8.5e-62
                                         EEEEE-T..TT-EEEEE--TTEEEEEEEE--B-SSTTT---B--EEEEEEE---SSS--E.EEEEEEEEEE-.. CS
                             CPSF_A    3 siklvdpiskeeidsleLeenEavlsvksvelessettkekkellvVGtafnlgedpaarsGrilvfeiiev.. 74  
                                          + l+++   e i+++eL+enE++++vk++ l++ +++ +k ++l+V+t+f++ged++ar Gr++v+eii+v  
  gene1734|gene1734|rna1733|rna1733  811 YVDLYSE-RYEHISTYELDENEYIFDVKYLVLDDMQGNYGKSPFLLVCTTFIEGEDRPAR-GRLHVLEIISVvp 882 
                                         6778876.56688***********************************************.************* PP

                                         ....SS--EEEEEEEEEEEES----EEEETTEEEEE-SSEEEEEEE-TTS-EEEEEEEE-SS-EEEEEEETTEE CS
                             CPSF_A   75 ....petnrkLklvhkeevkgavtalaefqGrllvgvgqkvrvydlgedktLlrkafldtqlyvvslkvlgnri 144 
                                             p  + kLk++  e++kg++  ++e++G++++++g k+++y++++ + +++  f+d +++++s++v++n+i
  gene1734|gene1734|rna1733|rna1733  883 slesPFRDCKLKVLGIEKTKGSIVQCSEVRGKIALCLGTKIMIYKIDRSTGIIPIGFYDLHIFTSSISVMKNYI 956 
                                         ****999******************************************************************* PP

                                         EEEESSS-EEEEEE-SSS--EEEEEEESS---EEEEEEE--SSS.EEEEEETTSEEEEEE--TTSGGGTTTT.E CS
                             CPSF_A  145 ivgDlmkSvtfveydeenyklilfardtqkrwvtaaeflvdged.tvlvaDkfgnlfvlrydpeasessdgdpr 217 
                                         +++D++++++f+ +++++ +l+l++ +   ++vt++e+l  g++ +++++D++g ++ ++y p++  s+dg  +
  gene1734|gene1734|rna1733|rna1733  957 LASDIYRGLSFFFFQSKPIRLHLISSSEPLKNVTSTELLTAGNElSMVCCDAKGTIHAYTYSPNNIISMDGA-K 1029
                                         ************************************************************************.* PP

                                         EEEEEEEE-SS----E...EEEE.SSS--S-EEEEEE-TTS-EEEEEE.--HHHHHHHHHHHHHHHHHS--SSS CS
                             CPSF_A  218 leeraefhlgeivtslrkgslvpgeaesssspqllyatldGsigllvPliseeeyrrlqaLqqqLrkelkhlgG 291 
                                         l +r+e+ ++  + s+   s +   ++s     +++ + +  + +lv+ ++++ y  l ++q++++ +lk+++G
  gene1734|gene1734|rna1733|rna1733 1030 LVKRSEMKTNLGRLSS---SGIGFRKNS-----IMFYSKTNLLIYLVG-MDDSYYLKLLKIQTSIMVHLKSVLG 1094
                                         ********99999999...433334445.....999999999999***.************************* PP

                                         --HHHHS---.. CS
                             CPSF_A  292 ldhrafRsyysp 303 
                                         l++r + +   +
  gene1734|gene1734|rna1733|rna1733 1095 LNQRDYLNSDIH 1106
                                         ******998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.47
# Mc/sec: 7328.44
//
Query:       gene1735|gene1735|rna1734|rna1734  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-15   55.4   1.0    7.9e-15   55.4   1.0    3.3  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   1.0   4.4e-19   7.9e-15       1      66 []      52     126 ..      52     126 .. 0.88
   2 ?   -5.2   7.7         1   1.8e+04       7      19 ..     265     277 ..     131     381 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 4.4e-19
                                        S-HHHHHHHHHHHHHHHHHGGGS-H..........HHHHHHHH.HHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                    CDP-OH_P_transf   1 nlPnaiTllrlllsvlailllltyyp........lvlaillll.iasltDalDGklARrlnqvstlGkllDslaD 66 
                                        ++Pna+Tl++++++ ++++l l ++p        l la +ll+ +++++D+lDG +ARr+++ s lG+l+D+++D
  gene1735|gene1735|rna1734|rna1734  52 IAPNALTLCGFAAMGISLCLTLLFDPylcnpprlLSLANFLLMfVYFTCDNLDGAQARRTGTGSPLGQLFDHGVD 126
                                        58**********99999999999999*******95555554444******************999********99 PP

  == domain 2  score: -5.2 bits;  conditional E-value: 1
                                        HHHHHHHHHHHHH CS
                    CDP-OH_P_transf   7 Tllrlllsvlail 19 
                                        T+lr+++  ++++
  gene1735|gene1735|rna1734|rna1734 265 TFLRIISFTTSFV 277
                                        5555555333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2503.64
//
Query:       gene1736|gene1736|rna1735|rna1735  [L=289]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.022   15.2   0.7      0.048   14.2   0.7    1.5  1  zf-CCCH_2  RNA-binding, Nab2-type zinc finger
      0.054   12.7   0.1      0.082   12.1   0.1    1.2  1  DUF815     Protein of unknown function (DUF815)
       0.17   11.7   0.5       0.23   11.2   0.5    1.2  1  DUF2538    Protein of unknown function (DUF2538)
        1.2    9.3   4.5        1.6    8.9   0.9    2.4  2  zf_CCCH_4  Zinc finger domain


Domain annotation for each model (and alignments):
>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   1.1e-05     0.048       2      18 .]      88     104 ..      88     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                          zf-CCCH_2   2 CrffpnCtnpkCpFaHP 18 
                                        Cr++  C+ ++C F H+
  gene1736|gene1736|rna1735|rna1735  88 CRDGDECRTKNCIFLHG 104
                                        ****************6 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.8e-05     0.082     135     206 ..     118     189 ..     115     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.8e-05
                             DUF815 135 sleakpenvliyaTsNrRhLlpeklsdneeleeeeihaseaveekl.sLsdRFGlwlgFykldqeeYleivek 206
                                        +l+ k e v i  T+ +R  ++e+ ++ne  + +++++s    e l + + RFG    F++l+ e+Yl + e 
  gene1736|gene1736|rna1735|rna1735 118 GLKGKEEGVDIVETAPKRRKITESNENNEV-VFNKVNESRHNPEDLkTYAARFGRITNFKRLNPEKYLVVFED 189
                                        6788999999*************9888777.677777766655555389*******************98765 PP

>> DUF2538  Protein of unknown function (DUF2538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   5.2e-05      0.23       3      97 ..     136     233 ..     134     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.2e-05
                            DUF2538   3 rktyekirhidkvfdrleqqiieskdrahlrkelfyvndehrenyealliyykes.eenplvdgacyivalpeife 77 
                                        rk  e  ++ + vf+++++   + +d + +   +  + + +r n e  l+ +++  + n lv+++  ++  p i +
  gene1736|gene1736|rna1735|rna1735 136 RKITESNENNEVVFNKVNESRHNPEDLKTYAARFGRITNFKRLNPEKYLVVFEDPeSANELVKSSELVLEDPGIKK 211
                                        78889999999************************************9999988625799*************999 PP

                            DUF2538  78 aldvfes..elplsfvydengl 97 
                                          +v++   ++ l  +++e+++
  gene1736|gene1736|rna1735|rna1735 212 FYNVIDNlvKVELRKLFEEQEI 233
                                        9999997224445557777665 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9   0.00035       1.6       4      16 ..      83      95 ..      82      95 .. 0.93
   2 ?    1.3   0.1     0.088   3.9e+02      14      19 .]      98     103 ..      97     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00035
                          zf_CCCH_4  4 flqGtCkkGdkCr 16
                                       +++ tC+ Gd Cr
  gene1736|gene1736|rna1735|rna1735 83 YKRKTCRDGDECR 95
                                       899*********8 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.088
                          zf_CCCH_4  14 kCrFaH 19 
                                        +C F+H
  gene1736|gene1736|rna1735|rna1735  98 NCIFLH 103
                                        8***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1813.19
//
Query:       gene1737|gene1737|rna1736|rna1736  [L=78]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-09   36.4   0.0    4.3e-09   35.9   0.0    1.3  1  LSM       LSM domain
     0.0046   17.0   0.1     0.0074   16.4   0.1    1.4  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   4.8e-13   4.3e-09       3      60 ..      15      65 ..      13      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4.8e-13
                                       HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGG CS
                                LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGn 60
                                       l  +++kk+t+ + +g+ + G+L++fD+  N+vL+++ e++ ++ ++  l      G 
  gene1737|gene1737|rna1736|rna1736 15 LGRFKGKKITITFIDGKSVTGKLTSFDDVGNCVLKKCGEWDYGN-TVVCL------GR 65
                                       67899************************************997.44444......33 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.3e-07    0.0074       4      39 ..      12      43 ..       9      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.3e-07
                           DUF150_C  4 aedFarflGelVkvklklpvegrkkftGkivevdee 39
                                       ++d  rf G+++++++     ++k +tGk+ ++d+ 
  gene1737|gene1737|rna1736|rna1736 12 LSDLGRFKGKKITITFI----DGKSVTGKLTSFDDV 43
                                       57889************....*************64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 574.72
//
Query:       gene1738|gene1738|rna1737|rna1737  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-19   69.7   0.3    2.3e-19   69.2   0.3    1.2  1  Motile_Sperm  MSP (Major sperm protein) domain
     0.0066   16.0   0.0     0.0082   15.7   0.0    1.2  1  Filo_VP24     Filovirus membrane-associated protein VP24


Domain annotation for each model (and alignments):
>> Motile_Sperm  MSP (Major sperm protein) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.3   2.6e-23   2.3e-19       2      94 ..       4      90 ..       3      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 2.6e-23
                                       SEEESSSEEEEESSTSSHEEEEEEEEE-SSSSEEEEEEES-TTTEEEESSEEEETTTCEEEEEEEEESSSSSTTSTCC CS
                       Motile_Sperm  2 lkidPsdllvfaaelnkqgtsklklkNtskkrvaFkvkttapkkyrvrPnvGiikpgesveitvtlkpldeepsekkk 79
                                       +k+ P++++  + ++   ++s+  ++N+s + v +k+ktt+p+ y+vrPn+G+i p++++e++vtl  ++  +s    
  gene1738|gene1738|rna1737|rna1737  4 IKVMPQTTIRVKRNK---RSSTFVVQNNSMESVGYKIKTTKPRDYIVRPNMGLIVPMQQAEVEVTLSESTVPDS---S 75
                                       7999**999999998...9********************************************99999666664...8 PP

                                       EEEEEEEEES-TT-S CS
                       Motile_Sperm 80 dkfviqylevpgdek 94
                                       +kf+i+++ ++++ +
  gene1738|gene1738|rna1737|rna1737 76 HKFLIEIYRFDWRRS 90
                                       *******99955554 PP

>> Filo_VP24  Filovirus membrane-associated protein VP24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.1e-07    0.0082     159     219 ..      14      75 ..       2     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.1e-07
                                        HHHHHHCTS--S-SSS---.EEEEEETTEEEEEEEETTCEEEEEEECCCC------EEEEEE CS
                          Filo_VP24 159 kfinkldalhvvndnGkls.sieikltnqtiiitrvnmGflvelreidikpccgetvlsesv 219
                                           nk  +  vv +n + s   +ik+t+ +  i r nmG++v +++ +++ + +e+ + +s 
  gene1738|gene1738|rna1737|rna1737  14 VKRNKRSSTFVVQNNSMESvGYKIKTTKPRDYIVRPNMGLIVPMQQAEVEVTLSESTVPDSS 75 
                                        55688888899988888773589**************************9988876665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 991.14
//
Query:       gene1739|gene1739|rna1738|rna1738  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.077   12.7  30.2       0.89    9.3   1.7    5.2  5  zf-CCHC_4  Zinc knuckle
       0.42   10.5  29.4       0.28   11.0   0.6    5.7  5  zf-CCHC_2  Zinc knuckle
        1.9    8.5  15.1        2.3    8.2   1.2    4.6  4  CLIP1_ZNF  CLIP1 zinc knuckle
          4    7.7  28.4          1    9.6   1.5    5.3  5  zf-CCHC    Zinc knuckle


Domain annotation for each model (and alignments):
>> zf-CCHC_4  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.5    0.0015       6.9      33      48 ..      82      97 ..      80      98 .. 0.90
   2 ?    9.3   1.7    0.0002      0.89      33      48 ..     104     119 ..     102     120 .. 0.92
   3 ?    7.6   2.5   0.00071       3.2      32      48 ..     121     137 ..     120     138 .. 0.91
   4 ?    3.2   0.1     0.016        74      31      48 ..     145     162 ..     144     163 .. 0.90
   5 ?    3.2   0.6     0.016        73      32      48 ..     181     197 ..     178     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0015
                          zf-CCHC_4 33 fCyiCgvlGHsdkrCd 48
                                        C+ Cg + H++++C 
  gene1739|gene1739|rna1738|rna1738 82 TCFRCGEMSHEFRECT 97
                                       6**************7 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0002
                          zf-CCHC_4  33 fCyiCgvlGHsdkrCd 48 
                                        +C  C + GH++++C+
  gene1739|gene1739|rna1738|rna1738 104 ICVLCSRNGHVREQCP 119
                                        8**************8 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00071
                          zf-CCHC_4  32 sfCyiCgvlGHsdkrCd 48 
                                        + C+ C+ +GHs + C+
  gene1739|gene1739|rna1738|rna1738 121 RYCTRCRGFGHSLDVCP 137
                                        57**************8 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.016
                          zf-CCHC_4  31 rsfCyiCgvlGHsdkrCd 48 
                                        + +C  C    Hs+++C+
  gene1739|gene1739|rna1738|rna1738 145 QEMCKACPAGKHSIEDCP 162
                                        578**************8 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.016
                          zf-CCHC_4  32 sfCyiCgvlGHsdkrCd 48 
                                        ++C  C+  +H +++C+
  gene1739|gene1739|rna1738|rna1738 181 KACPKCFSRNHFIDDCS 197
                                        579*************7 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.7     0.078   3.5e+02       6      11 ..      83      88 ..      82      96 .. 0.80
   2 ?    7.1   1.5    0.0011       4.9       5      20 ..     104     119 ..     104     119 .. 0.96
   3 ?    5.2   0.6    0.0042        19       6      20 ..     123     137 ..     122     138 .. 0.91
   4 ?   11.0   0.6   6.3e-05      0.28       5      20 ..     147     162 ..     147     163 .. 0.92
   5 ?    3.7   0.6     0.013        57       9      19 ..     186     196 ..     182     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.078
                          zf-CCHC_2  6 ChiCgk 11
                                       C +Cg 
  gene1739|gene1739|rna1738|rna1738 83 CFRCGE 88
                                       ****96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0011
                          zf-CCHC_2   5 vChiCgkkGHyIqdCP 20 
                                        +C +C   GH   +CP
  gene1739|gene1739|rna1738|rna1738 104 ICVLCSRNGHVREQCP 119
                                        799************9 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0042
                          zf-CCHC_2   6 ChiCgkkGHyIqdCP 20 
                                        C +C   GH    CP
  gene1739|gene1739|rna1738|rna1738 123 CTRCRGFGHSLDVCP 137
                                        *********998888 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 6.3e-05
                          zf-CCHC_2   5 vChiCgkkGHyIqdCP 20 
                                        +C++C +  H I dCP
  gene1739|gene1739|rna1738|rna1738 147 MCKACPAGKHSIEDCP 162
                                        7****9999******* PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.013
                          zf-CCHC_2   9 CgkkGHyIqdC 19 
                                        C++  H+I dC
  gene1739|gene1739|rna1738|rna1738 186 CFSRNHFIDDC 196
                                        99999****** PP

>> CLIP1_ZNF  CLIP1 zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.09     4e+02       1       6 [.      75      80 ..      75      80 .. 0.88
   2 ?    3.6   0.1     0.014        63       4      17 .]     105     118 ..     105     118 .. 0.92
   3 ?    8.2   1.2   0.00051       2.3       3      15 ..     122     134 ..     122     136 .. 0.90
   4 ?    2.8   0.1     0.025   1.1e+02      11      17 .]     154     161 ..     154     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.09
                          CLIP1_ZNF  1 RpYCdn 6 
                                       R++Cd+
  gene1739|gene1739|rna1738|rna1738 75 RYFCDT 80
                                       9***95 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                          CLIP1_ZNF   4 CdnCEvFGHdTedC 17 
                                        C +C + GH  e+C
  gene1739|gene1739|rna1738|rna1738 105 CVLCSRNGHVREQC 118
                                        9********98888 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00051
                          CLIP1_ZNF   3 YCdnCEvFGHdTe 15 
                                        YC  C  FGH ++
  gene1739|gene1739|rna1738|rna1738 122 YCTRCRGFGHSLD 134
                                        **********875 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.025
                          CLIP1_ZNF  11 G.HdTedC 17 
                                        G H +edC
  gene1739|gene1739|rna1738|rna1738 154 GkHSIEDC 161
                                        88****** PP

>> zf-CCHC  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.5   0.00023         1       2      18 .]      82      98 ..      82      98 .. 0.88
   2 ?    6.1   0.5    0.0029        13       6      17 ..     108     119 ..     103     119 .. 0.89
   3 ?    4.8   0.9    0.0075        33       2      17 ..     122     137 ..     121     138 .. 0.81
   4 ?   -1.2   0.2      0.58   2.6e+03      11      17 ..     156     162 ..     156     163 .. 0.78
   5 ?    5.0   0.8    0.0062        28       2      17 ..     182     197 ..     181     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00023
                                       CTSSSSSSSSTTTTSTS CS
                            zf-CCHC  2 kCynCGepGHiardCpk 18
                                       +C++CGe+ H  r+C+k
  gene1739|gene1739|rna1738|rna1738 82 TCFRCGEMSHEFRECTK 98
                                       7*******998888886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0029
                                        SSSSSSTTTTST CS
                            zf-CCHC   6 CGepGHiardCp 17 
                                        C + GH+  +Cp
  gene1739|gene1739|rna1738|rna1738 108 CSRNGHVREQCP 119
                                        999********9 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0075
                                        CTSSSSSSSSTTTTST CS
                            zf-CCHC   2 kCynCGepGHiardCp 17 
                                         C +C + GH    Cp
  gene1739|gene1739|rna1738|rna1738 122 YCTRCRGFGHSLDVCP 137
                                        7*********776666 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.58
                                        STTTTST CS
                            zf-CCHC  11 HiardCp 17 
                                        H   dCp
  gene1739|gene1739|rna1738|rna1738 156 HSIEDCP 162
                                        6677**9 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.0062
                                        CTSSSSSSSSTTTTST CS
                            zf-CCHC   2 kCynCGepGHiardCp 17 
                                        +C +C +  H+  dC+
  gene1739|gene1739|rna1738|rna1738 182 ACPKCFSRNHFIDDCS 197
                                        68899999*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1419.58
//
Query:       gene1740|gene1740|rna1739|rna1739  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.2e-41  140.9   0.1    9.4e-41  140.6   0.1    1.2  1  Metallophos  Calcineurin-like phosphoesterase
    1.4e-16   60.6   0.3    2.8e-16   59.7   0.3    1.5  1  STPPase_N    Serine-threonine protein phosphatase N-terminal 


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6   0.1     1e-44   9.4e-41       2     201 ..      57     248 ..      56     251 .. 0.94

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 1e-44
                                        EEEEEESBTBTTCCTHHHHHHHHHHHH..HHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TT CS
                        Metallophos   2 rilvigDlHlalgggqlddllkllddl..lreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNH 74 
                                        ++ ++gD+H     gq++dllkl+++   ++ + ++l+l  GD+vdrg  + e++ l la+++k+p++++ll+GNH
  gene1740|gene1740|rna1739|rna1739  57 PVKICGDVH-----GQYYDLLKLFEHGgfPP-SSNYLFL--GDYVDRGKQSLETICLlLAYKIKFPNNFFLLRGNH 124
                                        5789*****.....**********9996444.599****..*******77777777779***************** PP

                                        S........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSC CS
                        Metallophos  75 e........gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnlel 141
                                        e        gf++e++++y+       +w+ ++e+fn++p+a+l++g  ++l++hGg sp+l +s d+++ + +++
  gene1740|gene1740|rna1739|rna1739 125 EcasinriyGFYDECKRRYD-----TTIWKLFTECFNWIPIAALVDG--RILCMHGGiSPDL-KSMDQIKAIARPT 192
                                        ******************99.....899*******************..********77777.************* PP

                                        HHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                        Metallophos 142 eapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                        ++p++g   d++++d       +   v g+  + rg + +fg++ +e++l+ +++dl++++H+
  gene1740|gene1740|rna1739|rna1739 193 DVPDEGllcDLLWSD-------PDPSVRGWGENDRGVSVTFGPDTVERFLETHNLDLICRAHQ 248
                                        ***************.......888899999999****************************8 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.3   3.1e-20   2.8e-16       1      47 [.       8      54 ..       8      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 3.1e-20
                          STPPase_N  1 vDdiIerLlevrgkpggkkvqLseaEIrqlCakareiFLsQPtLLeL 47
                                       +D iIe+Ll+vr+++ g+ v+L eaEIr+lC k+ e+F +QPtL e+
  gene1740|gene1740|rna1739|rna1739  8 LDRIIEKLLSVRNSKLGRLVHLAEAEIRYLCEKSTEVFKQQPTLVEV 54
                                       7************8888***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2011.12
//
Query:       gene174|gene174|rna174|rna174  [L=332]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-67  228.8   3.9    1.2e-67  228.6   3.9    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.6   3.9   6.7e-72   1.2e-67     149     490 ..       5     331 ..       1     332 [] 0.91

  Alignments for each domain:
  == domain 1  score: 228.6 bits;  conditional E-value: 6.7e-72
                                    HHHCHCCCSEECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                     Cpn60_TCP1 149 AvklieenekeldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                    A+k +e    + d  +i+vvk+ gg l+d +  + ++l++++     p   +++k+ +++++L+ +kt++++++ ++d +
  gene174|gene174|rna174|rna174   5 AIKGMEH--AKGDKRKIRVVKKIGGGLDDVKAYKSILLECDLKDI--P---KKVKLGVIQFCLSAPKTNMDSKILINDSA 77 
                                    4433333..5688999*************************8866..5...7899************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B.....-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGG CS
                     Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgi.....ddlalhflakngilalrrvkkkdlerlakatGatavssled 303
                                     +ekl ++e+++++e+++ki+ksg++++v+qk+i     +dla hfl++ +i +++ v++kd++ ++ +++ ++vs+++ 
  gene174|gene174|rna174|rna174  78 LMEKLIQEERRYILEMCKKIKKSGCTLLVIQKSIlreslSDLASHFLKQLNISVVNSVDRKDVDYICSTMNVQPVSEIDL 157
                                    *****************************************************************************988 PP

                                    GGCGC-EEEEEEEECCETT.CCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                     Cpn60_TCP1 304 ltpeelGtakkveeekigs.ekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                    l++   G+  +v   + g+ e ++ i++      +til+rg  d+v++e+er+++dAl+vvk++ e + +vpGGG++e+ 
  gene174|gene174|rna174|rna174 158 LNS---GSLVDV---ETGEvEGMLEIKG----YGCTILVRGCDDMVVEEAERSLNDALCVVKCLEELPFLVPGGGSIEMG 227
                                    888...554455...3344155666887....89********************************************** PP

                                    HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCT.XEE CS
                     Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveag.vvD 461
                                    +a +l+e  +     + ++ + +akA+e +p+ La+NaGl p e++++lr++ ++++  +gi+v+sg++ d+v +  vv+
  gene174|gene174|rna174|rna174 228 IALMLSESTE----GNVYVLREIAKAFEGVPYFLARNAGLYPVEIVSELRNELKQND-YVGISVRSGHAGDMVREDsVVQ 302
                                    *****44444....589****************************************.*************887655*** PP

                                    EHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                     Cpn60_TCP1 462 plkvkrqalksAteaastiLrideiikak 490
                                    p+kv  +++++A e++s+iL+id+i+ a+
  gene174|gene174|rna174|rna174 303 PAKVSINVITLAIETVSMILKIDDILPAR 331
                                    *************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2303.96
//
Query:       gene1741|gene1741|rna1740|rna1740  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-28   97.6   0.0    4.6e-27   95.2   0.0    2.2  3  eIF2A          Eukaryotic translation initiation factor eIF2A
     0.0039   16.3   0.1       0.16   10.9   0.0    2.2  2  Coatomer_WDAD  Coatomer WD associated region
  ------ inclusion threshold ------
      0.065   13.5   0.1        3.1    8.1   0.0    2.8  3  DUF5300        Domain of unknown function (DUF5300)
       0.41   10.5   2.9         18    5.1   0.7    2.5  2  PAZ            PAZ domain


Domain annotation for each model (and alignments):
>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.48   2.1e+03     127     158 ..      43      74 ..      37      78 .. 0.84
   2 ?   -2.4   0.0      0.82   3.7e+03     140     162 ..     130     152 ..     115     155 .. 0.75
   3 !   95.2   0.0     1e-30   4.6e-27       6     193 ..     180     359 ..     175     360 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                                        EEEEETTTTEEEEEEE-TT--EEEE-TTSSEE CS
                              eIF2A 127 leiwdvkkkkkiakaeaanatlvewspdgryv 158
                                        +  +d  +kk i ++e ++   +e s dgr v
  gene1741|gene1741|rna1740|rna1740  43 VRYYDLVDKKMILEIEMEKPREIEMSEDGRSV 74 
                                        45699999999999999999999999999865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.82
                                        EEE-TT--EEEE-TTSSEEEEEE CS
                              eIF2A 140 kaeaanatlvewspdgryvlTat 162
                                         ++a++ +++e+  +g++v  at
  gene1741|gene1741|rna1740|rna1740 130 PFHASKVSVLEFFISGEFVFLAT 152
                                        46788899999999999998776 PP

  == domain 3  score: 95.2 bits;  conditional E-value: 1e-30
                                        ECEEEEEE-TTTTEEEEEEE.E--TT-CEEEEEEEEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEESSS CS
                              eIF2A   6 adkvklkWnkkGtsllvlvstevdktnksyygetelyliklkkkksevvelkkegpihdvaWspkskefaviyGkm 81 
                                        ++  +lk  k+G + l+l  t     n+sy  e+++y+ +++  + +++      p+h  a    s+ fa+++G +
  gene1741|gene1741|rna1740|rna1740 180 LQGFSLKTHKSGRYALLLLMTS--YVNNSYFPESDVYFHDINRRSFKSLGY---SPVHSYA--FLSSGFAICHGSQ 248
                                        55667888999***99999987..6789***********999888887743...5899776..56788******** PP

                                        SCEEEEEECSCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEEEETTTTEEEEEEE-TT--EEEE-TTSSE CS
                              eIF2A  82 pakvslfdlkvkviskleeqkrNtiffspkgklvllaGfgnlaGeleiwdvkkkkkiakaeaanatlvewspdgry 157
                                        p++vs++ l++k+ +++ +  rN iff++++++ ++aGf nl+G++e++ v ++k  ak++   a+lv+w+ +g+y
  gene1741|gene1741|rna1740|rna1740 249 PSSVSVHGLDGKLEYNFPKGIRNRIFFNQHENIAVFAGFDNLSGDIEVFHVPSRKLTAKLNVLGASLVDWKENGSY 324
                                        **************************************************************************** PP

                                        EEEEE-TTT-SSS-EEEEEETTTEEEEEEE-TTEEE CS
                              eIF2A 158 vlTattaprlrvdngfkiwsysGklvykkefdelyq 193
                                        +  +tt+   + dn ++++ y G+ + + +f+ l+ 
  gene1741|gene1741|rna1740|rna1740 325 FYVSTTS-YFQEDNKITLYDYYGRKIAERKFESLFS 359
                                        ******9.7999*********************996 PP

>> Coatomer_WDAD  Coatomer WD associated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   3.7e-05      0.16     117     170 ..      33      86 ..      17     138 .. 0.78
   2 !    3.3   0.0    0.0076        34     127     176 ..     293     348 ..     209     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.7e-05
                                        XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXX CS
                      Coatomer_WDAD 117 GalLgvksegsvsfYDweqgklvrridvkkvknVvwsddgelvalvs.kdtvyil 170
                                        G +  +k +  v  YD+  +k++ +i+++k +++ +s+dg  v ++s k ++++l
  gene1741|gene1741|rna1740|rna1740  33 GRVAWIKGNL-VRYYDLVDKKMILEIEMEKPREIEMSEDGRSVGILSgKGEMVVL 86 
                                        6666677777.99****************99**************9634444444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0076
                                        .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXX. CS
                      Coatomer_WDAD 127 svsfYDweqgklvrridvkkvknVvwsddgelvalv......skdtvyilsynlea 176
                                         + ++++ ++kl ++++v   + V w+++g+++ +       +++++++++y  ++
  gene1741|gene1741|rna1740|rna1740 293 DIEVFHVPSRKLTAKLNVLGASLVDWKENGSYFYVSttsyfqEDNKITLYDYYGRK 348
                                        4889***************99***********999844444337777777766653 PP

>> DUF5300  Domain of unknown function (DUF5300)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.88   3.9e+03      32      54 ..      54      76 ..      41      85 .. 0.70
   2 ?    1.9   0.0     0.062   2.8e+02       6      61 ..      92     147 ..      87     157 .. 0.86
   3 ?    8.1   0.0   0.00069       3.1      45      92 ..     332     379 ..     326     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.88
                                       E--B..-TT-EEEEEESSS---- CS
                            DUF5300 32 vgalekgsketielsedaksitk 54
                                       +  +e ++ + ie+sed +s+  
  gene1741|gene1741|rna1740|rna1740 54 ILEIEMEKPREIEMSEDGRSVGI 76
                                       55677788888999999888765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.062
                                        EEEEEE-SSS-BS-EEEESSSS-EEEE--B..-TT-EEEEEESSS----EEEEEEB CS
                            DUF5300   6 titikntsafelknvkvkfngekevtvgalekgsketielsedaksitkvevsGtt 61 
                                        +++ +n s f + n  + +       + ++e+++ e   +     s+ +  +sG+ 
  gene1741|gene1741|rna1740|rna1740  92 KLKAENVSRFRISNSLIGYVSSSSFYIHQIEEDKIEKSPFHASKVSVLEFFISGEF 147
                                        567789************************99999999999999999999999985 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00069
                                        EEESSS----EEEEEEBTTS-EEEEEE----SS-EEEEE-EETTTEE- CS
                            DUF5300  45 lsedaksitkvevsGttesgkkFtghFsGlvsndtevvveldEdmdlg 92 
                                          +++++it  +  G     +kF   Fs  v  +te ++el+    l+
  gene1741|gene1741|rna1740|rna1740 332 YFQEDNKITLYDYYGRKIAERKFESLFSASVYGKTEEFIELERPERLN 379
                                        5678999999*******************************9766555 PP

>> PAZ  PAZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1    0.0054        24      41      74 ..     114     143 ..      97     145 .. 0.89
   2 ?    5.1   0.7     0.004        18      53      76 ..     328     348 ..     320     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0054
                                        CEEEEEEEESS--TTSEECCTTCT..CECCHHHH CS
                                PAZ  41 ktyyvadittdlapsstFpdkdkeneitfaeYfk 74 
                                          +y+ +i +d+ ++s F  +  +  +++ e+f+
  gene1741|gene1741|rna1740|rna1740 114 SSFYIHQIEEDKIEKSPFHAS--K--VSVLEFFI 143
                                        689****************99..5..99***997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.004
                                        -TTSEECCTTCT..CECCHHHHCC CS
                                PAZ  53 apsstFpdkdkeneitfaeYfkkk 76 
                                        + +s F+ +   n+it+++Y+ +k
  gene1741|gene1741|rna1740|rna1740 328 STTSYFQED---NKITLYDYYGRK 348
                                        567899999...78*******887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2618.42
//
Query:       gene1742|gene1742|rna1741|rna1741  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-43  146.8   2.2      6e-43  145.6   2.2    1.7  1  SRP_TPR_like  Putative TPR-like repeat
    8.7e-08   32.3   3.1    3.3e-07   30.4   3.1    2.0  1  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
    3.8e-05   23.3   0.4       0.31   10.9   0.0    2.7  2  TPR_1         Tetratricopeptide repeat
    0.00046   20.1   5.1        0.7   10.1   0.5    3.4  3  TPR_2         Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.045   13.9   0.0      0.093   12.8   0.0    1.5  1  HTH_9         RNA polymerase III subunit RPC82 helix-turn-hel


Domain annotation for each model (and alignments):
>> SRP_TPR_like  Putative TPR-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.6   2.2   1.7e-46     6e-43       1     116 [.       8     115 ..       8     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 1.7e-46
                       SRP_TPR_like   1 eneeyekilrlegkelkkfkvvaliklekyeeaLkllkkgsalsedvrfEkaYvlYklkkykkalkilkkveaeek 76 
                                        +n+++e+i+rle++e+++f++va+i+++k++eaLk++++gs       fE+aYv+Yklkkykkal+il+++++e +
  gene1742|gene1742|rna1741|rna1741   8 KNDCHEEISRLEHPEFSRFRAVAFISMGKFKEALKYTEEGS-------FERAYVFYKLKKYKKALRILRHIDTE-G 75 
                                        5899*************************************.......**************************.* PP

                       SRP_TPR_like  77 vkvlksqvlYrlgsyekAYklLskekkedelvvNllAvds 116
                                        +kvl+sq+lY+lg+y++AY++L+++k++d++vvNl+A+++
  gene1742|gene1742|rna1741|rna1741  76 SKVLTSQCLYYLGYYNTAYQILAEVKRDDDIVVNLQAMKG 115
                                        **************************************97 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   3.1   9.1e-11   3.3e-07      17      81 ..      39      99 ..      16     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 9.1e-11
                                       .HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                             ANAPC3 17 aaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81
                                       +a ++ +e ++  A+++y++++yk+A+++lr       ++g+ +l+ qcl+ L+ y+ A+++L +
  gene1742|gene1742|rna1741|rna1741 39 EALKYTEEGSFERAYVFYKLKKYKKALRILRHI----DTEGSKVLTSQCLYYLGYYNTAYQILAE 99
                                       5778999999***********************....************************9965 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   8.7e-05      0.31       7      25 ..      27      45 ..      26      47 .. 0.91
   2 !    9.7   0.1   0.00022      0.77       6      21 ..      50      65 ..      48      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.7e-05
                                       HHHHHHHTT-HHHHHHHHH CS
                              TPR_1  7 lGnayfklgkydeAleyye 25
                                       +++a+ ++gk++eAl+y e
  gene1742|gene1742|rna1741|rna1741 27 RAVAFISMGKFKEALKYTE 45
                                       799*************976 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00022
                                       HHHHHHHHTT-HHHHH CS
                              TPR_1  6 nlGnayfklgkydeAl 21
                                        ++++++kl+ky++Al
  gene1742|gene1742|rna1741|rna1741 50 ERAYVFYKLKKYKKAL 65
                                       589************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00043       1.5       6      26 ..      26      46 ..      21      47 .. 0.88
   2 !   10.1   0.5    0.0002       0.7       5      22 ..      49      66 ..      46      70 .. 0.87
   3 ?    1.5   0.1      0.12   4.2e+02       9      21 ..      82      94 ..      79     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                              TPR_2  6 nlGlayyklgdyeeAleafek 26
                                        ++ a + +g+++eAl++ e+
  gene1742|gene1742|rna1741|rna1741 26 FRAVAFISMGKFKEALKYTEE 46
                                       6899**************987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                              TPR_2  5 ynlGlayyklgdyeeAle 22
                                       ++++++ ykl++y++Al+
  gene1742|gene1742|rna1741|rna1741 49 FERAYVFYKLKKYKKALR 66
                                       89**************98 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                              TPR_2  9 layyklgdyeeAl 21
                                       +++y+lg y+ A 
  gene1742|gene1742|rna1741|rna1741 82 QCLYYLGYYNTAY 94
                                       7999999998775 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05     0.093      20      50 ..     283     314 ..     282     315 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                                        HHHHHHSSBEHHHHHHHHS.STHHHHHHHHHH CS
                              HTH_9  20 etLlrkgrltlrelvkktk.LsldqVkksLvv 50 
                                         tL ++g+l++++l++ktk  + +++k+ L+v
  gene1742|gene1742|rna1741|rna1741 283 LTLCKNGCLPSQKLLEKTKkWPESSIKNCLSV 314
                                        5899*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1802.91
//
Query:       gene1743|gene1743|rna1742|rna1742  [L=346]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-51  175.2   0.0    2.4e-51  174.7   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
      2e-10   41.2   0.0    2.7e-10   40.8   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    2.8e-09   36.3  11.5    0.00012   21.6   2.1    2.8  2  Hexapep          Bacterial transferase hexapeptide (six repea
    8.6e-05   20.9   3.4    0.00015   20.1   3.4    1.3  1  DUF4954          Domain of unknown function (DUF4954)
      0.003   16.6   1.0      0.005   15.8   1.0    1.5  1  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
      0.077   12.7   0.0       0.12   12.0   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
       0.14   11.9  14.6       0.11   12.2   7.5    3.2  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7   0.0   9.2e-55   2.4e-51       1     242 [.       9     234 ..       9     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 9.2e-55
                                        EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEE CS
                    NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevl 76 
                                        kavIL+GG+GtRL+PLt t++k+lvp+++k +++ +++++l+ +gi+eii+ l+++ + +++e     ++fg++v 
  gene1743|gene1743|rna1742|rna1742   9 KAVILVGGYGTRLRPLTYTVPKPLVPFANK-PILRHQIEALVGAGIKEIILALNYYSELIIREVRDYSNEFGINVI 83 
                                        79****************************.*************************99999999999********* PP

                                        EEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEE CS
                    NTP_transferase  77 ialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvie 152
                                        ++ e+e+ gtA+++ala+++le +     ++vL++D+ ++  ++e++ ++ ++++  + t++ + ve++++yG+i 
  gene1743|gene1743|rna1742|rna1742  84 YSKEQEPLGTAGPLALARKYLEGHT----FFVLNSDITCRFPLREMLSFHLSHGK--EGTILSTGVEDPSRYGLII 153
                                        **********************999....8*************************..8999*************** PP

                                        ECTTS.BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE CS
                    NTP_transferase 153 adeeg.rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdae 227
                                        ++e+   v++f EKPk+a+ s+ +++GiY+ n++vl+       el+ + +   +i+pk+ ee + ++ f+ ++  
  gene1743|gene1743|rna1742|rna1742 154 TEENTsLVQTFLEKPKNAT-SNRINAGIYILNPSVLDRV-----ELR-ECSIEREIFPKMAEERQLQV-FDLEG-- 219
                                        *966659************.******************9.....564.445567999**999998886.69999.. PP

                                        -EEEXSSHHHHHHHH CS
                    NTP_transferase 228 yWsDvGtldsllean 242
                                         W+D+G++ ++++ +
  gene1743|gene1743|rna1742|rna1742 220 FWMDIGQPADYIKGQ 234
                                        6**********9865 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.1e-13   2.7e-10       1      96 [.      10     116 ..      10     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.1e-13
                                        EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH......CHHHHHHTTCTS-EEE- CS
                       NTP_transf_3   1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggd......eevlaalarlgvrvved 65 
                                        aviL GG ++R+   +   +K+l+p+++kp+l+++++al  ag++e++++ ++      +ev+++ +++g+ v++ 
  gene1743|gene1743|rna1742|rna1742  10 AVILVGGYGTRLRplTytvPKPLVPFANKPILRHQIEALVGAGIKEIILALNYyseliiREVRDYSNEFGINVIYS 85 
                                        79**********8541568**********************************8755555999999999*****99 PP

                                        TTSS.-SHHHHHHHHHHHH.SSSCEEEEETT- CS
                       NTP_transf_3  66 edpg.kgplaslaaalraaadadavlvlacDm 96 
                                        ++++  g+++ la a + + +   ++vl  D+
  gene1743|gene1743|rna1742|rna1742  86 KEQEpLGTAGPLALARKYL-EGHTFFVLNSDI 116
                                        8876478888888888877.677777777775 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.8     3e-07   0.00076      10      35 ..     258     277 ..     256     281 .. 0.56
   2 !   21.6   2.1   4.8e-08   0.00012       2      35 ..     279     311 ..     278     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3e-07
                                        E-TTEEEETTEEE-TTEEEETTEEEE CS
                            Hexapep  10 IgpfaviggnVkIGdnvkIgagvvig 35 
                                        I +++vig nVkIG+nv+I      +
  gene1743|gene1743|rna1742|rna1742 258 IESNVVIGKNVKIGKNVTI------T 277
                                        4555555555555555555......4 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 4.8e-08
                                        EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                            Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                        ++I +nv Ig +++i  + ++G n++I+ +++i+
  gene1743|gene1743|rna1742|rna1742 279 STIFDNVEIGDNVII-KDSIVGWNTRIEDNATIN 311
                                        7899******99999.9999************97 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   3.4   5.7e-08   0.00015     189     261 ..     260     328 ..     252     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.7e-08
                            DUF4954 189 kNvkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavisrcfv.Gqavklkkqfsae 261
                                         Nv ig+  +i    +++n ti       veiG++Vi++d+i+   ++i+d a+i+ c v G a+++++ fs+ 
  gene1743|gene1743|rna1742|rna1742 260 SNVVIGKNVKIGKNVTITNSTIFD----NVEIGDNVIIKDSIVGWNTRIEDNATINSCCVlGYATTVER-FSIL 328
                                        588999998888888888888875....589************************98755388877764.5555 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   1.9e-06     0.005     256     333 ..     259     331 ..     192     346 .] 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-06
                         Fucokinase 256 tstafsaiknkkekkkesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilq 331
                                        +s++   +  k+ k+ ++++++nS +  +v++g++ +i++s ++ n++i+ n  + ++++   ++  ++   +il 
  gene1743|gene1743|rna1742|rna1742 259 ESNV---VIGKNVKIGKNVTITNSTIFDNVEIGDNVIIKDSIVGWNTRIEDNATINSCCVLGYAT--TVERFSILS 329
                                        2222...2223334478888888888888888888888888888888888888888888776643..555555555 PP

                         Fucokinase 332 tl 333
                                        ++
  gene1743|gene1743|rna1742|rna1742 330 SV 331
                                        55 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.12       1      55 [.       8      64 ..       8      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                                       EEEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGG CS
                               IspD  1 vvvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvsedd 55
                                       v +vi   G G+R++     +pK ++  +++++l h ++al +   +++i+++++ + 
  gene1743|gene1743|rna1742|rna1742  8 VKAVILVGGYGTRLRpltYTVPKPLVPFANKPILRHQIEALVG-AGIKEIILALNYYS 64
                                       56899999*****85332799*********************9.789*****998765 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       3.6   9.2e+03      26      32 ..     176     182 ..     176     183 .. 0.78
   2 ?   12.2   7.5   4.4e-05      0.11       1      26 [.     261     293 ..     257     298 .. 0.86
   3 ?    7.3   3.1    0.0015       3.8       1      28 [.     284     312 ..     284     318 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                                        E-TT-EE CS
                          Hexapep_2  26 vgaGvvi 32 
                                        + aG++i
  gene1743|gene1743|rna1742|rna1742 176 INAGIYI 182
                                        5699998 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.4e-05
                                        .EEE-TT-EE-TT-EE.......SEEE-TT-EE CS
                          Hexapep_2   1 pviIGdnCliGanagi.......GvslGdncvv 26 
                                        +v IG+n+ iG+n +i        v++Gdn+++
  gene1743|gene1743|rna1742|rna1742 261 NVVIGKNVKIGKNVTItnstifdNVEIGDNVII 293
                                        699**********99877555644******998 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0015
                                        .EEE-TT-EE-TT-EES..EEE-TT-EE-T CS
                          Hexapep_2   1 pviIGdnCliGanagiG..vslGdncvvga 28 
                                        +v IGdn++i +++++G  + ++dn+++ +
  gene1743|gene1743|rna1742|rna1742 284 NVEIGDNVII-KDSIVGwnTRIEDNATINS 312
                                        588*******.99***999*******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2089.39
//
Query:       gene1744|gene1744|rna1743|rna1743  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-07   29.3   0.0    2.1e-06   27.8   0.0    1.8  2  Pam16     Pam16


Domain annotation for each model (and alignments):
>> Pam16  Pam16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.044   7.9e+02      11      33 ..      12      34 ..       3      41 .. 0.71
   2 !   27.8   0.0   1.2e-10   2.1e-06      56     104 ..      36      84 ..      27     113 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.044
                                       XXXXXXXXXXXXXXXXXXX.XXX CS
                              Pam16 11 vagtqvvgkalaralrqeiaaar 33
                                         g++v+ ka+a+++ + +   r
  gene1744|gene1744|rna1743|rna1743 12 NEGGKVLYKAVAKTISDIMVGDR 34
                                       46899999999999988776655 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.2e-10
                                        -HHHHHHHHT--G--SHHHHHHHHHHHHHHT-CCCTS-HHHHHHHHHHH CS
                              Pam16  56 sleeslkilnveedlnreevekryehlfevndkskGGslylqskvfrak 104
                                        s  e+  il+++   ++++v + +  ++  n k+ GGs y+qsk++ a 
  gene1744|gene1744|rna1743|rna1743  36 SKMEAEMILDISPSTSEDKVRESFLRMYYANAKENGGSPYIQSKILGAY 84 
                                        667999**************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 675.24
//
Query:       gene1745|gene1745|rna1744|rna1744  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2125.54
//
Query:       gene1746|gene1746|rna1745|rna1745  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-12   45.5   0.1    8.8e-12   45.1   0.1    1.2  1  Ribosomal_S10  Ribosomal protein S10p/S20e


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   4.9e-16   8.8e-12       2      94 ..      23     113 ..      22     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.9e-16
                                        EEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HH CS
                      Ribosomal_S10   2 irlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatke 76 
                                        i + S + k ++k+++++++  k +  +++  v lP+k +++t+l++p+++ +k ++++++ +h R + + +at +
  gene1746|gene1746|rna1745|rna1745  23 IDMASLEEKRINKVCREFYEYGKTFIDNLQREVVLPKKIESITTLRNPSGQgTKKWSRYKMIIHLRNFYL-EATHQ 97 
                                        6788999***************************************************************.59999 PP

                                        HHHHHS-...S---SS-E CS
                      Ribosomal_S10  77 tidtllkllqlnlpegVs 94 
                                        ++++++++l+    + V+
  gene1746|gene1746|rna1745|rna1745  98 QLEKVVQFLKNF--PHVE 113
                                        ***999988765..5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 844.37
//
Query:       gene1747|gene1747|rna1746|rna1746  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-15   56.0   0.1      5e-15   55.5   0.1    1.2  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    0.00055   20.3   0.2     0.0011   19.4   0.0    1.6  2  Histone        Core histone H2A/H2B/H3/H4
  ------ inclusion threshold ------
      0.016   15.1   0.3        1.1    9.2   0.1    2.2  2  TrmB           Sugar-specific transcriptional regulator TrmB
       0.14   11.9   0.6       0.49   10.2   0.1    2.0  2  B2             RNA binding protein B2


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   1.1e-18     5e-15       2      65 .]       9      73 ..       8      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.1e-18
                                       XXXHHHHHHHHHCC.TTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                      CBFD_NFYB_HMF  2 eLPiarvkkImksd.pdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                        LP+a+v+k++ s+ p++  + k++ke+++ +++ f++ l+ eA++ c++ek+Kti++eh+ +A+
  gene1747|gene1747|rna1746|rna1746  9 TLPKATVDKMVSSMlPKNSVVPKESKEIFQSACVYFLNMLTLEANKACEEEKKKTISYEHVYKAL 73
                                       69***********************************************************9997 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.4e-07    0.0011      86     129 ..      31      74 ..       7      76 .. 0.88
   2 ?   -2.0   0.1      0.96   4.3e+03      49      67 ..     113     131 ..      85     133 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.4e-07
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                            Histone  86 aeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                        +e+ +++q+a+ ++l  l+ eAn+++++ K++Ti  +++  A++
  gene1747|gene1747|rna1746|rna1746  31 KESKEIFQSACVYFLNMLTLEANKACEEEKKKTISYEHVYKALK 74 
                                        667789********************************998876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.96
                                        HHHHHHHHXXSXXSXHHHH CS
                            Histone  49 keirkyqkstdlliqklpf 67 
                                         e+ ++q+ + +++ kl+f
  gene1747|gene1747|rna1746|rna1746 113 MEELHNQQIKLFQNAKLQF 131
                                        3444444444455555555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0075        34      34      58 ..      10      34 ..       5      44 .. 0.84
   2 ?    9.2   0.1   0.00024       1.1      14      53 ..      44      83 ..      38     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0075
                                       SSCHCHHHHHHHHHHCTSEEEESST CS
                               TrmB 34 vprskvYevLrsLedkGlVerekgr 58
                                       +p+++v ++++s++ k  V  ++++
  gene1747|gene1747|rna1746|rna1746 10 LPKATVDKMVSSMLPKNSVVPKESK 34
                                       79************99999877765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00024
                                       CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                               TrmB 14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                       +l +l+l+  +a e  ++  +++  vY++L++L    +++
  gene1747|gene1747|rna1746|rna1746 44 FLNMLTLEANKACEEEKKKTISYEHVYKALKNLGFENYID 83
                                       6788999999999999999**************8776665 PP

>> B2  RNA binding protein B2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00011      0.49      49      66 ..      12      29 ..       6      34 .. 0.91
   2 ?   -1.5   0.0      0.49   2.2e+03      39      53 ..      51      65 ..      48      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                                 B2 49 kltvsrmvtsllekPsvv 66
                                       k tv++mv+s+l k svv
  gene1747|gene1747|rna1746|rna1746 12 KATVDKMVSSMLPKNSVV 29
                                       88**************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.49
                                 B2 39 dnlqaclnkakltvs 53
                                       +  +ac +  k+t+s
  gene1747|gene1747|rna1746|rna1746 51 EANKACEEEKKKTIS 65
                                       566899999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1057.04
//
Query:       gene1748|gene1748|rna1747|rna1747  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.2   0.5      0.027   13.6   0.5    1.4  1  FANCAA    Fanconi anemia-associated
      0.062   13.3   0.1       0.11   12.6   0.0    1.4  1  TUDOR     Tudor domain
       0.11   12.7   0.1       0.17   12.1   0.1    1.4  1  SesA      N-terminal domain on NACHT_NTPase and P-loop NTPase


Domain annotation for each model (and alignments):
>> FANCAA  Fanconi anemia-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   4.5e-06     0.027      18      75 ..      60     118 ..      31     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-06
                             FANCAA  18 sERvsslKkaidqknqaLksLNqvlnisclllssqeke.kkpisCtvtakwsrllqrds 75 
                                        sE  s + k    k  aL+   ++l  +++l+ ++e+  + pisC+++ak+s+l+  ds
  gene1748|gene1748|rna1747|rna1747  60 SECLSNIQKPCLDKKTALMLPKEALENCVALVGRKENRyRIPISCKGRAKRSSLKACDS 118
                                        4666666555666788999999*********9999988899************998775 PP

>> TUDOR  Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05      0.11      11      89 ..      41     117 ..      31     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                        EEEEEETTEEEEEEGGHHHHHHHHHHHHHHHHTSSCCTCSSS--TT-EEEEEETTTTEEEEEEEEEECTTTEEEEE CS
                              TUDOR  11 vsaiespskfyiqpkeqskkleklteelqeyyaskkkaellapavgegcvavfsedgkwyRAkiteslddqkveVl 86 
                                        +s+i+ +++      ++s++ +++++++q+ +  kk a +l+++  e+cva++ ++++ yR  i ++ ++++ ++ 
  gene1748|gene1748|rna1747|rna1747  41 LSHINTTCNPSL--PSSSTSKSECLSNIQKPCLDKKTALMLPKEALENCVALVGRKENRYRIPISCKGRAKRSSLK 114
                                        556665555555..56777889999************************************999777777666665 PP

                                        ETT CS
                              TUDOR  87 fiD 89 
                                         +D
  gene1748|gene1748|rna1747|rna1747 115 ACD 117
                                        555 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.8e-05      0.17      29      76 ..      28      77 ..       7      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                               SesA 29 revgkrLplvqetLedaksqlesskldedtesa..ikpvlesckekatkl 76
                                       +e+++ L +v+++L++++++++ s  +++t ++  + ++ + c +k t+l
  gene1748|gene1748|rna1747|rna1747 28 KEIKEVLKTVRDVLSHINTTCNPSLPSSSTSKSecLSNIQKPCLDKKTAL 77
                                       578889****************9998888777677999999998887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 912.92
//
Query:       gene1749|gene1749|rna1748|rna1748  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-06   25.9   2.0    1.5e-05   24.7   2.0    1.6  1  KH_1      KH domain
     0.0003   20.8   0.0    0.00069   19.7   0.0    1.6  1  KH_8      Krr1 KH1 domain
  ------ inclusion threshold ------
       0.03   14.2   0.1      0.064   13.1   0.1    1.5  1  KH_4      KH domain
      0.047   13.5   1.3       0.11   12.4   1.0    1.8  1  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   2.0   3.4e-09   1.5e-05       9      64 ..     109     156 ..     102     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.4e-09
                                        GHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                               KH_1   9 slvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                        + +griIG+ G++ + I+e +  kI v  +        ++++ G+ e+   A++++
  gene1749|gene1749|rna1748|rna1748 109 RAIGRIIGREGKTKNAIEEFSRSKIIVQ-D-------QMIHLLGTIENTRIARDAV 156
                                        469****************88*****87.4.......47*************9986 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.5e-07   0.00069      19      80 ..      23      85 ..      14      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                               KH_8 19 eekikk.lleekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvle 80
                                       +  i + ++e  k+++++++k r ++++T e+T DP  + ++ + i+ +  g p+e a  +l+
  gene1749|gene1749|rna1748|rna1748 23 WMRIYTpIVEICKIQIRMNIKGRCVEMRTCEHTEDPSYLERSAQYIEAVHIGFPIEDAIAILK 85
                                       5555441457789*********************************************99986 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05     0.064      39      54 ..     110     125 ..      96     130 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                               KH_4  39 dlGrvIGkrGrtldAl 54 
                                         +Gr+IG++G+t +A+
  gene1749|gene1749|rna1748|rna1748 110 AIGRIIGREGKTKNAI 125
                                        69**********9998 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   2.4e-05      0.11      36      68 ..     111     142 ..      92     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                        HHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                               KH_2  36 pgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                         g++IG++G++ ++i++  r +i +++++ ++l
  gene1749|gene1749|rna1748|rna1748 111 IGRIIGREGKTKNAIEEFSRSKI-IVQDQMIHL 142
                                        69********************9.588877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1263.37
//
Query:       gene1750|gene1750|rna1749|rna1749  [L=366]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-19   69.3   0.1    7.2e-19   68.2   0.1    1.6  1  XPG_N       XPG N-terminal domain
    5.5e-16   58.7   0.2      2e-15   56.9   0.0    2.1  2  XPG_I       XPG I-region
     0.0049   17.4   0.0       0.01   16.4   0.0    1.6  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.034   14.2   0.2      0.098   12.7   0.2    1.7  1  DUF1013     Protein of unknown function (DUF1013)
      0.047   14.3   0.1       0.13   12.9   0.0    1.7  2  HHH_5       Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.1     2e-22   7.2e-19       1     100 [.       1      98 [.       1      99 [. 0.96

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2e-22
                                        X--TTHHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS-HHHHHHHHHHHHHHHTTEEEE CS
                              XPG_N   1 MGikgLlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalentshlmglfsrllrlldfgikPi 76 
                                        MGi+gLl++++      + +i ++  ++++iD+ +wly++l  v+e+   ++ + +h+++++++++ l  +gi+Pi
  gene1750|gene1750|rna1749|rna1749   1 MGISGLLPIVATKL--VKRHISSYRHQRIGIDGHAWLYQILSFVAEEMFFKVPTRKHITMFEEKVKVLESYGITPI 74 
                                        **********9988..7889******************************************************** PP

                                        EEE--S--GGGHHHHHHHHHHHHH CS
                              XPG_N  77 fVFdgkapdlkkeelekrserrqe 100
                                        +V dg+ ++ k+e+ +kr  ++++
  gene1750|gene1750|rna1749|rna1749  75 IVLDGDTLSSKEETNRKRYIKKDK 98 
                                        ******************887765 PP

>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       3.6   1.3e+04      63      71 ..      92     100 ..      77     119 .. 0.52
   2 !   56.9   0.0   5.7e-19     2e-15       3      94 .]     140     221 ..     138     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.6
                                        CEEEEEEHH CS
                              XPG_I  63 kkvevidle 71 
                                        +++++ + +
  gene1750|gene1750|rna1749|rna1749  92 RYIKKDKNR 100
                                        222222222 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 5.7e-19
                                        HT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT CS
                              XPG_I   3 mgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkelg 78 
                                         +++y+++p+E +Aq++yL++ g++d++++eDsDl+ +G++++l ++     ++        v++++   + +  g
  gene1750|gene1750|rna1749|rna1749 140 INVEYIISPYESDAQLCYLERIGYIDCILTEDSDLIPYGSNRILYKFD----NT-------FVQEFTRGCLSEARG 204
                                        689*******************************************97....22.......244444432333333 PP

                                        -.-HHHHHHHHHHHCET CS
                              XPG_I  79 l.treqlidlaillgcD 94 
                                           +e+++d++il+gcD
  gene1750|gene1750|rna1749|rna1749 205 RdFEENILDISILSGCD 221
                                        31346678888888887 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.9e-06      0.01       6      52 ..     211     255 ..     208     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.9e-06
                         5_3_exonuc   6 iidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenldelk 52 
                                        i d+  L G   D +  ++g+G  tA kLl++ +++e+++e l++ k
  gene1750|gene1750|rna1749|rna1749 211 ILDISILSG--CDYLASIQGVGVVTAHKLLSKEKTVEKVVEYLQHRK 255
                                        556666666..688999************************887422 PP

>> DUF1013  Protein of unknown function (DUF1013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.7e-05     0.098      54     104 ..      86     134 ..      71     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                            DUF1013  54 kkkkgkrytpvskRqdkpdaiawllknhpelkdaqiakLvgtTketieair 104
                                        ++++ kry  + k +++ +a  wl+kn pe +   + + ++ Tke++++i 
  gene1750|gene1750|rna1749|rna1749  86 EETNRKRY--IKKDKNRKEAEHWLVKNDPEKAKGFMRQCIAVTKEIVSDIA 134
                                        44444555..678899*******************************9984 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.9     1e+04       6      25 ..       2      21 ..       1      23 [. 0.80
   2 ?   12.9   0.0   3.6e-05      0.13       3      31 ..     222     249 ..     221     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.9
                                       TSTT--HHHHHHHHTTT--S CS
                              HHH_5  6 svsGiGpktAlallsaGies 25
                                       ++sG+ p +A +l++  i+s
  gene1750|gene1750|rna1749|rna1749  2 GISGLLPIVATKLVKRHISS 21
                                       68888888999999988877 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 3.6e-05
                                        HHHTSTT--HHHHHHHHTTT--SHHHHHH CS
                              HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaa 31 
                                        +L s++G+G +tA +lls+  ++ve++++
  gene1750|gene1750|rna1749|rna1749 222 YLASIQGVGVVTAHKLLSK-EKTVEKVVE 249
                                        699****************.668998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2423.68
//
Query:       gene175|gene175|rna175|rna175  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-34  119.8   0.3    1.5e-34  119.5   0.3    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.5   0.3   8.4e-39   1.5e-34       3      98 ..      21     114 ..      19     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 8.4e-39
                                    HHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   3 divkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaeklia 82 
                                    ++++t+lGP+G+dKm+v +  k+vvTnDGatilk l+ +hP+  +l++++++qdee+GDGTt+vv+Lag+Lle++++l++
  gene175|gene175|rna175|rna175  21 QTLSTSLGPRGLDKMIVRDK-KTVVTNDGATILKYLN-QHPIHGILSNMSAAQDEECGDGTTSVVVLAGCLLESISNLLE 98 
                                    789**************666.9***************.****************************************** PP

                                    CTXXHHHHHHHHHHHH CS
                     Cpn60_TCP1  83 agvhpttiiegyekal 98 
                                    ++vhp++i++ +e a+
  gene175|gene175|rna175|rna175  99 RNVHPSVICDNLEIAK 114
                                    ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 714.60
//
Query:       gene1751|gene1751|rna1750|rna1750  [L=493]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-18   66.6   0.0      3e-18   66.2   0.0    1.2  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
    3.7e-15   55.4  10.6    4.1e-09   36.1   1.3    2.8  2  LRR_8          Leucine rich repeat
    2.1e-12   47.0  11.9    3.1e-06   27.4   1.2    2.9  2  LRR_4          Leucine Rich repeats (2 copies)
    0.00017   21.7  12.3         13    6.8   0.3    5.5  4  LRR_1          Leucine Rich Repeat
     0.0045   16.5   3.2     0.0093   15.5   3.2    1.4  1  LRR_9          Leucine-rich repeat
     0.0089   16.0  11.7        1.9    8.7   0.6    4.4  4  LRR_6          Leucine Rich repeat


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0     1e-21     3e-18       1     218 [.     175     449 ..     175     468 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1e-21
                                        EEEEESTG................CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEE CS
                                        xxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos   1 ltwNvngq................aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgas 60 
                                        +t+N++++                +        r   +++++  y+ D+l+LQE+  ++ +++   ++++ + + s
  gene1751|gene1751|rna1750|rna1750 175 GTFNILSNlwaakltyapswvinpE-------FRREGILQEIVLYNVDILCLQEIELYSFFDFYKEQLEMRCSYDS 243
                                        5899999999999999955555432.......55667******************************884444444 PP

                                        ECCH.....ECSSSTTSSEEEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE................ CS
                                        xxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                      Exo_endo_phos  61 stsp.....tgggggggnggavlsrfpltslfrrtfiefndlvaalrreplaakleqlni................ 115
                                           p     +++  +  +g+a+++r+  ++l+   +i+f ++v ++ r +++  l++ +                 
  gene1751|gene1751|rna1750|rna1750 244 IIYPrgkvrSVPDKKAVDGCAIFWRRNKFRLIAQFPIDFYQKVSQDTRFNTNQELLDRYGkkdnvaigallerpng 319
                                        44446666778999************************************************************** PP

                                        ...........CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SSSTSGGGBSCGHHHHHHCTTTHH... CS
                                        ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                      Exo_endo_phos 116 ...........ashrdhdlvrdlqllalllqvealnadrgapvivaGDfNarpsdddsrvlrtrglalapapv... 177
                                                   +++  +d    +  l+    +++ +++++a +++ GDfN+  s+ ++ +++t+  +l    +   
  gene1751|gene1751|rna1750|rna1750 320 qqilvvnthifWDPDYPDIKLLQTVLLIEEIRKIISRHPNAYLFLQGDFNSLRSSSVYKSITTQTIDLTDFGNiah 395
                                        *******99999999999999999999999999***************************9999999888773555 PP

                                        .............SSCESCETTTTTTTTTTTEB-BEEEEEECHHHCCEEEEEEE CS
                                        .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Exo_endo_phos 178 .............glyllgggptptyvtraggsrlDrilaspalalfrsgvlpp 218
                                                     +  +l++   +t+ t+ +   +D+i++ +++ l ++++  +
  gene1751|gene1751|rna1750|rna1750 396 hlsiqelgdglklNDSYLNQDLGFTNFTPVFKDVIDYIFYDSRMVLASVLSPVE 449
                                        556677778899******************************999998887654 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   1.3   1.4e-12   4.1e-09       6      61 .]      27      80 ..      25      80 .. 0.97
   2 !   32.4   2.4     2e-11   5.9e-08       3      61 .]      70     126 ..      69     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1.4e-12
                                       EE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8  6 LdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61
                                       LdL++  + +++++ F  ++  +vL+LsnN+++t+ p+ + +L+ L+ L+Ls N++
  gene1751|gene1751|rna1750|rna1750 27 LDLCSQGIRNISKSLFD-MRFIRVLNLSNNEIETI-PKEICNLRCLEVLNLSKNKI 80
                                       9****************.*****************.9*****************97 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 2e-11
                                        -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                              LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                        L++L+Ls+N++ s+++e  k + +Lk+L+Ls+Nl++ + p  +  L +L+sL + +N+L
  gene1751|gene1751|rna1750|rna1750  70 LEVLNLSKNKIRSIPPEIGK-VVSLKELNLSDNLISNI-PMEIGTLYNLESLEIANNPL 126
                                        899*****************.9****************.9*****************97 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   1.2     1e-09   3.1e-06       4      40 ..      48      84 ..      47      88 .. 0.88
   2 !   23.5   3.7   1.8e-08   5.5e-05       2      41 ..      92     132 ..      91     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1e-09
                                       -EEE--SS---E-S-..HHH-TT--EEE-.-S-----GG CS
                              LRR_4  4 evLdLsnNqltdipl..leklpnLkeLdLsgNnlitdld 40
                                       +vL+LsnN + +ip   + +l  L++L+Ls N +i++++
  gene1751|gene1751|rna1750|rna1750 48 RVLNLSNNEIETIPKeiC-NLRCLEVLNLSKN-KIRSIP 84
                                       89*************733.6*********999.999985 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.8e-08
                                        S--EEE--SS---E-S-HHH.-TT--EEE-.-S-----GGG CS
                              LRR_4   2 nLevLdLsnNqltdipllek.lpnLkeLdLsgNnlitdlde 41 
                                        +L++L+Ls+N ++ ip   + l nL++L + +N+li ++++
  gene1751|gene1751|rna1750|rna1750  92 SLKELNLSDNLISNIPMEIGtLYNLESLEIANNPLIVPFNT 132
                                        8****************5555*********88877766655 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.3    0.0042        13       3      21 ..      48      65 ..      46      67 .. 0.74
   2 !    6.2   0.0    0.0068        20       2      17 ..      70      85 ..      69      90 .. 0.79
   3 !    6.2   0.2    0.0068        20       1      15 [.      92     106 ..      92     110 .. 0.84
   4 !    6.8   0.4    0.0043        13       1      13 [.     115     127 ..     115     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0042
                              LRR_1  3 rhLdLsnnpllglppnsfq 21
                                       r+L+Lsnn ++  +p  ++
  gene1751|gene1751|rna1750|rna1750 48 RVLNLSNNEIE-TIPKEIC 65
                                       89********6.5555555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0068
                              LRR_1  2 LrhLdLsnnpllglpp 17
                                       L++L+Ls n + ++pp
  gene1751|gene1751|rna1750|rna1750 70 LEVLNLSKNKIRSIPP 85
                                       9**********55555 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0068
                              LRR_1   1 nLrhLdLsnnpllgl 15 
                                        +L++L+Ls+n ++++
  gene1751|gene1751|rna1750|rna1750  92 SLKELNLSDNLISNI 106
                                        69********98665 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0043
                              LRR_1   1 nLrhLdLsnnpll 13 
                                        nL++L + nnpl+
  gene1751|gene1751|rna1750|rna1750 115 NLESLEIANNPLI 127
                                        8**********94 PP

>> LRR_9  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   3.2   3.1e-06    0.0093      46     125 ..      49     126 ..      28     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                              LRR_9  46 tidlsdndirkl.dgfPllkrlktlllnnnrivriaegleevlPnleelvltnnelqeladldPlaslkklellsl 120
                                         ++ls+n+i  +  ++  l+ l++l l++n+i+ i +++++v+ +l+el l++n + ++     + +l +le+l +
  gene1751|gene1751|rna1750|rna1750  49 VLNLSNNEIETIpKEICNLRCLEVLNLSKNKIRSIPPEIGKVV-SLKELNLSDNLISNIPM--EIGTLYNLESLEI 121
                                        579*******9955799***********************987.7************9964..4566666777777 PP

                              LRR_9 121 lknpv 125
                                         +np+
  gene1751|gene1751|rna1750|rna1750 122 ANNPL 126
                                        77776 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.013        38       4      16 ..      46      58 ..      44      59 .. 0.85
   2 !    6.8   0.4    0.0027       8.2       3      16 ..      68      81 ..      66      82 .. 0.88
   3 !    8.7   0.6   0.00064       1.9       4      17 ..      92     105 ..      91     106 .. 0.91
   4 ?    0.3   0.1      0.33     1e+03       4      14 ..     115     125 ..     112     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
                              LRR_6  4 hLteLdLsgNdIg 16
                                        ++ L+Ls N+I 
  gene1751|gene1751|rna1750|rna1750 46 FIRVLNLSNNEIE 58
                                       5799*******95 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0027
                              LRR_6  3 thLteLdLsgNdIg 16
                                       ++L+ L+Ls N+I 
  gene1751|gene1751|rna1750|rna1750 68 RCLEVLNLSKNKIR 81
                                       79**********96 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00064
                              LRR_6   4 hLteLdLsgNdIgD 17 
                                        +L+eL+Ls+N I++
  gene1751|gene1751|rna1750|rna1750  92 SLKELNLSDNLISN 105
                                        79********9986 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.33
                              LRR_6   4 hLteLdLsgNd 14 
                                        +L++L+++ N 
  gene1751|gene1751|rna1750|rna1750 115 NLESLEIANNP 125
                                        89*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3024.53
//
Query:       gene1752|gene1752|rna1751|rna1751  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.021   14.6   0.1      0.041   13.6   0.1    1.6  1  Ribosomal_S7e  Ribosomal protein S7e


Domain annotation for each model (and alignments):
>> Ribosomal_S7e  Ribosomal protein S7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.3e-06     0.041      37     155 ..      28     137 ..       2     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-06
                                        T--ECEEEEEEETSSCEEEEEEEEHHHHHHTTTCHHHHHHHHHHHC.SSEEEEEEE-----SSCG.TTSTSS--TT CS
                      Ribosomal_S7e  37 elqissakevevkkkkkaivifvpvpllkafqkiqqrlvreLeKkfsgkhvvfvaqRrilkkptrrskkkqkrprs 112
                                         +   +++ v + +++k++ + vp ++l  +q   +++++   ++f++  ++f+ +  i  ++           + 
  gene1752|gene1752|rna1751|rna1751  28 MFSKIAIQIVICDNGEKVMAVKVPRSILPGVQMNYSNIIKAAKQQFHDYYIIFIRNFEIEAREDG---------NA 94 
                                        444445555556799***************************************99999888877.........56 PP

                                        SSHHHHHHHHHHHHCTTS-EEEEEEEE-SSS-EEEEEEEESCT CS
                      Ribosomal_S7e 113 rtltaVhdaiLedlvyPseivGkrirvrldgskllkvfLdkkd 155
                                         t ++V    L + ++P  ++G r+ vr     ++ v+L+++ 
  gene1752|gene1752|rna1751|rna1751  95 VTKSMVEKTWLANACFPFLLTGIRTDVRGINDVVINVLLERRT 137
                                        678899999*****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1073.62
//
Query:       gene1753|gene1753|rna1752|rna1752  [L=707]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-35  121.2   0.0    9.7e-35  120.3   0.0    1.4  1  Sec23_trunk     Sec23/Sec24 trunk domain
    2.8e-16   59.2   0.1    5.2e-16   58.3   0.1    1.5  1  Sec23_helical   Sec23/Sec24 helical domain
    4.2e-16   59.5   0.0    8.9e-16   58.4   0.0    1.6  1  Sec23_BS        Sec23/Sec24 beta-sandwich domain
    6.6e-10   38.9   8.3      2e-09   37.4   8.3    1.9  1  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
    9.1e-05   22.3   0.2    0.00069   19.5   0.2    2.2  1  Gelsolin        Gelsolin repeat


Domain annotation for each model (and alignments):
>> Sec23_trunk  Sec23/Sec24 trunk domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   2.7e-38   9.7e-35       3     229 ..     118     358 ..     117     371 .. 0.88

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 2.7e-38
                                        --EEEEEEE-SHHHHHHTHHHHHHHHHHHHCTTSSTSTT-EEEEEEESSSEEEEETSTTS.......SSSEEEEEC CS
                        Sec23_trunk   3 ppvflFviDvsleaikegelkalkeslkqsLdllPeepralvglitfdsvvhffelksel.......rqpkelvvs 71 
                                        p vf+F++D++     ++   +lk++lk +L+ +P  ++alvg+i +++ +++ el+  +       +++ke+ ++
  gene1753|gene1753|rna1752|rna1752 118 PVVFFFIVDICTF--DDQRHILLKDALKAALEGIP--DDALVGFIKYGTNIELLELSGASprkthlfSGKKEYNAE 189
                                        88*********99..67777889************..********************9999999***899999888 PP

                                        HTTSCC......SSTSSSSSEETTTTHHHHHHHHHHHHH.HSTT-TTC-----HHHHHHHHHHHHCHCT..S-EEE CS
                        Sec23_trunk  72 dlqdvf......lpladrlLvplseseavledlLeelpe.mfavtagkrperalgpalkaavellkave..tggki 138
                                         l+ +       +  + ++L   se+ + l d++e+l++ +f+v +  +p r++g+a+++a++ll++ +  t+ k 
  gene1753|gene1753|rna1752|rna1752 190 VLKSLNttpkfeSQVVGKFLKRKSECYDFLYDVIENLEKdPFPVLTAYKPVRCTGSAVSLAFSLLETNFpdTAVKY 265
                                        777665666664445599************************************************99999***** PP

                                        EEEESS---SSTTTS..S-SBTTSCCTSSTTCHHCHSCSSSCHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHH CS
                        Sec23_trunk 139 ivfvgslptvgaggk..lksredeslldidkekaklvkkadkfYkkLakecvkqgisvDlFlfsldyvdlaelkql 212
                                        ++f  +++t g+g+   +k +e+ +    +++  ++   a kfY++L++++   g+s+D+ +++   v++  ++ l
  gene1753|gene1753|rna1752|rna1752 266 LLFTQGPCTFGPGTTtpIKFKEKGRNEHLEENDPMYAGPARKFYTSLGERMNSVGHSLDILAATIVDVGICHMERL 341
                                        ************976224555555555555666899999************************************* PP

                                        HHTTT-EEEEETTTCCH CS
                        Sec23_trunk 213 aeltgGqvvlydsFsae 229
                                        +++tgG++++++ F +e
  gene1753|gene1753|rna1752|rna1752 342 TSMTGGMLIMAQDFDRE 358
                                        **************955 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   1.5e-19   5.2e-16       1     102 [.     473     570 ..     473     571 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.5e-19
                                        -HHHHHHHHHHHHHHHTTTS-HHHHHHHHHHHHHHHHHHHHHH-------------GGGTTHHHHHHHHHTSTTTS CS
                      Sec23_helical   1 DqeavtvllakqaidkalesgladarealdtslvdllsayrkvgasgsspsqlqlpeslklLPlyilallKspafr 76 
                                        Dqe+v+v+ a+ ++ k  e +++d  + +d+ l+++++a+ ++  +   ps+l+lp+s+  +P y++ +++s  ++
  gene1753|gene1753|rna1752|rna1752 473 DQETVAVFQARFLLLKKYE-EIKDCERMIDKNLIRFTKAFARYDRG--VPSSLVLPDSMAYYPNYMFFFRRSL-LV 544
                                        9***********9999976.9***********************98..9************************.77 PP

                                        -.-TT--HHHHHHHHHHHHH--HHHHH CS
                      Sec23_helical  77 g.gnsvpaDervfalslllslpvdqll 102
                                        + gn++p De++++l ll + +v+++l
  gene1753|gene1753|rna1752|rna1752 545 QtGNNSP-DETAYYLTLLYNQKVSDSL 570
                                        7699999.**************99987 PP

>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   2.5e-19   8.9e-16       1      95 [.     379     461 ..     379     462 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 2.5e-19
                                        EEEEEEEEEE-TTEEEEEEESSSEECSTBESSEESECSESEEEEEEEETT--EEEEEEESSBTCTTSEEEEEEEEE CS
                           Sec23_BS   1 gfnatlevrtSkelkvsgliGncvslsnvsekeiGeggtsewklcsldpdstlavyfdideklksgkqayiQfatl 76 
                                        gfna+++v+tSk+l+ +g+iG+  s s          g   w+++s+ p++++++ fd++ + k+g++ y+Q++t+
  gene1753|gene1753|rna1752|rna1752 379 GFNAKIQVKTSKNLEYKGIIGQGRSSS----------GC--WRIGSIFPSTNISILFDKKPEAKHGEFGYVQLITQ 442
                                        79**********************998..........88..*******************99************** PP

                                        EEETTSEEEEEEEEEEEEE CS
                           Sec23_BS  77 YthssgerrlRVttvalpv 95 
                                        Y+ s+++  +RVtt+a+ +
  gene1753|gene1753|rna1752|rna1752 443 YQRSDKKLLVRVTTFARMF 461
                                        ***************9976 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   8.3   5.5e-13     2e-09       1      38 [.      50      87 ..      50      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 5.5e-13
                     zf-Sec23_Sec24  1 PirCrrCraylNpfckidfggkrwiCnfCnhknevppe 38
                                       Pi C +C  +lNp+c++dfg ++w C +Cn+ + +p++
  gene1753|gene1753|rna1752|rna1752 50 PIYCMSCNGVLNPHCNVDFGRQTWNCVICNNNTALPSH 87
                                       9**********************************987 PP

>> Gelsolin  Gelsolin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.9e-07   0.00069       6      75 ..     587     671 ..     585     672 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-07
                                        EEBSSSGGGEETTSEEEEEESSEEEEEEHTT.SHHHHHHHHHHHHHHHH..............HCTTTTTSEEEEE CS
                           Gelsolin   6 kvvklsssslesgdcyLLdngftiflWiGke.ssqeeknfaadlaaeld..............seerfplpelire 66 
                                          v+++s+sle++ +++Ld++ ++ +W G+  +++  ++   + + e+                 er p+p++  +
  gene1753|gene1753|rna1752|rna1752 587 NAVEVDSKSLEPDVILVLDTFHNVVVWKGEYfAQWVREGYHEQPEYEFLksilknseemaislCAERLPTPQFCIT 662
                                        5799******************999999998866665555544444444455566666777786777888888888 PP

                                        ETTHHHHHH CS
                           Gelsolin  67 dqgkeparF 75 
                                        +q+k+++r+
  gene1753|gene1753|rna1752|rna1752 663 EQNKSQQRI 671
                                        888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 4375.14
//
Query:       gene1754|gene1754|rna1753|rna1753  [L=682]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-78  261.1   0.0    7.8e-78  260.6   0.0    1.2  1  MCM              MCM P-loop domain
    5.4e-22   78.0   0.2    2.7e-21   75.8   0.7    2.0  2  MCM_lid          MCM AAA-lid domain
    1.8e-18   66.6   0.3      3e-18   65.9   0.3    1.4  1  MCM_OB           MCM OB domain
      8e-09   35.2   0.9    4.5e-05   22.9   0.0    3.1  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.3e-08   34.1   0.0    4.9e-08   33.1   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0045   16.8   0.0      0.019   14.8   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
     0.0085   15.8   0.1      0.029   14.1   0.1    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.028   13.9   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.018   14.7   0.0        2.8    7.6   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.036   14.1   0.0       0.29   11.1   0.0    2.5  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
       0.04   14.3   0.0       0.66   10.4   0.0    2.6  2  AAA              ATPase family associated with various cellul
       0.12   12.3   0.1       0.39   10.6   0.1    1.9  1  gag_pre-integrs  GAG-pre-integrase domain
       0.31   11.4   2.5       0.35   11.2   0.3    2.2  2  AAA_16           AAA ATPase domain
       0.37   11.1   2.7        1.4    9.2   2.7    2.0  1  C1_4             TFIIH C1-like domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.6   0.0   6.1e-81   7.8e-78       2     223 ..     274     492 ..     273     493 .. 0.98

  Alignments for each domain:
  == domain 1  score: 260.6 bits;  conditional E-value: 6.1e-81
                                        HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHH CS
                                MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyv 77 
                                         +e+k++ak ++i+ +lv+s++ siyg+e +k +++l+lfgg++k++ + + +r++ +vl+vgdpg++Ks+lL ++
  gene1754|gene1754|rna1753|rna1753 274 FDEFKKMAKAENILASLVHSLYSSIYGNELIKIGLVLSLFGGTRKSAGQ-HGIRSETHVLIVGDPGLGKSKLLLST 348
                                        5799****************************************98876.99************************ PP

                                        HHHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                                MCM  78 eklapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                        + ++p++ y+sg+ +++agLt++ ++d+ +ge++ +aGalv+ad+Gvcc+Defdk+++  + al+EamE+q +sia
  gene1754|gene1754|rna1753|rna1753 349 CGILPKSSYVSGNFTTTAGLTVSLTHDPISGEYMADAGALVVADNGVCCLDEFDKIDD--HAALFEAMEDQRVSIA 422
                                        ********************************************************99..9*************** PP

                                        SSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                                MCM 154 KaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                        K+G+++++++r++v+aA+np++g++d++ks++eni++++ lLsrFDl+f+llD+ +e++ ++++ +++++
  gene1754|gene1754|rna1753|rna1753 423 KGGVICSVPTRSTVIAATNPRNGHFDRSKSMEENIRFDPGLLSRFDLVFLLLDDLSEKECYMISGQVLKK 492
                                        ****************************************************************999875 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.9   6.3e+03      52      74 ..     116     138 ..     100     144 .. 0.84
   2 !   75.8   0.7   2.1e-24   2.7e-21       1      86 [.     530     607 ..     530     608 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.9
                                        HHHHHHHHHHHHHHHTSSSE-HH CS
                            MCM_lid  52 LesliRLseAlAklrlsevvtee 74 
                                        L  l+ ++ A++++ +++vv+++
  gene1754|gene1754|rna1753|rna1753 116 LGKLVFMTGAVCRVGFKRVVSTK 138
                                        666788999********999886 PP

  == domain 2  score: 75.8 bits;  conditional E-value: 2.1e-24
                                        HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHH CS
                            MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedv 76 
                                        e++rkYi+yar++++P+l+ +ake+++e+Y+++Rk+          +++R LesliRL+eA Ak++l++++t+ d+
  gene1754|gene1754|rna1753|rna1753 530 EIIRKYISYARANVFPVLNRSAKEAIKEWYADMRKKG--------GVSTRDLESLIRLTEAKAKIELRSIATKADA 597
                                        689********************************76........489**************************** PP

                                        HHHHHHHHHH CS
                            MCM_lid  77 eeairllkes 86 
                                        e +i+l+k++
  gene1754|gene1754|rna1753|rna1753 598 EFCIELYKRT 607
                                        ******9875 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.3   2.3e-21     3e-18       4     123 ..     110     236 ..     107     239 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.3e-21
                                        G--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES---.....-SB-..TTT-HHH-EEE-GG..GS CS
                             MCM_OB   4 dlrsehigklvkveGivtrasevkpklkkavfeckkcgktvevelee.....PrkCeekeCeskdpfklete..ks 72 
                                        d+++ ++gklv ++G v r+   +   +k++fec+kcg +v v++++     P  C + +C+ +++f+l+ +  + 
  gene1754|gene1754|rna1753|rna1753 110 DIDRVNLGKLVFMTGAVCRVGFKRVVSTKMFFECSKCGDVVCVDVKNniyrvPGAC-KGSCN-SRSFVLMRNhpEM 183
                                        678889********************************98888777777778****.77***.5777776665699 PP

                                        EEEEEEEEEEE------..-------EEEEEEEGGGTT---TT-EEEEEEEEE CS
                             MCM_OB  73 kfvdfqklklQEspeev..paGelPrslevileddlvdkvkPGdrvevtGiyr 123
                                        +++d q++k+QE  +       ++Pr++++il+d+ v ++ PGd v++tG++ 
  gene1754|gene1754|rna1753|rna1753 184 ECKDIQEIKIQEIYGGSgeDGNRIPRTVDCILYDEFVGTLAPGDIVQITGVLG 236
                                        ************99877534558***************************985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.53   6.8e+02      39      69 ..      29      57 ..      27      68 .. 0.75
   2 !    8.8   0.1   0.00073      0.93      22      50 ..     328     356 ..     316     375 .. 0.85
   3 !   22.9   0.0   3.5e-08   4.5e-05      92     165 ..     378     448 ..     373     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.53
                       Mg_chelatase 39 akrlpsllpplseeealevakiasvagkkee 69
                                        krl+s+l++   +++le+++ + +++ ++ 
  gene1754|gene1754|rna1753|rna1753 29 KKRLTSILAETGLDDILETRTYH-ISK-QRL 57
                                       68****************99887.444.333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00073
                       Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsllppls 50 
                                        + ++l+vG pG GK+ l     ++lp+ s
  gene1754|gene1754|rna1753|rna1753 328 ETHVLIVGDPGLGKSKLLLSTCGILPKSS 356
                                        4589**********************976 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 3.5e-08
                       Mg_chelatase  92 GggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklk 165
                                         g   +  G++  a nGv  LDE+ +++ ++  +L e +ed++v+i++    ++ p+r +++aa+Np   g+++
  gene1754|gene1754|rna1753|rna1753 378 SGEYMADAGALVVADNGVCCLDEFDKIDDHA--ALFEAMEDQRVSIAKGGVICSVPTRSTVIAATNPR-NGHFD 448
                                        56678899*******************9986..89********************************5.45555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   3.9e-11   4.9e-08       1     128 [.     330     451 ..     330     467 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.9e-11
                                        EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESG CS
                              AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEv 74 
                                        +vl+vG+pG gKs+l  + +  l ++   v +  +tt++ l+ ++  +  +g++    ++lv  +    +++lDE+
  gene1754|gene1754|rna1753|rna1753 330 HVLIVGDPGLGKSKLLLSTCGILPKSSY-VSG-NFTTTAGLTVSLTHDpiSGEYMADAGALV--VADNGVCCLDEF 401
                                        79*********************76653.333.45777777777776666888888999999..88889******* PP

                                        GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--....-TT CS
                              AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld...rsln 128
                                        +++++++  +L   +e++r+++++gg  ++++        +via++np++    +++
  gene1754|gene1754|rna1753|rna1753 402 DKIDDHA--ALFEAMEDQRVSIAKGGVICSVPTR-----STVIAATNPRNghfDRSK 451
                                        ****986..7*********************997.....7*********96643333 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.5e-05     0.019       1     113 [.     330     443 ..     330     452 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                              AAA_3   1 hvllegvPGlaktllvkalakal.dlefkriqftpdllPsdilGtevfeekekefefkkGpvfan...llladein 72 
                                        hvl+ g PGl+k +l  + + +l + ++    ft+    + ++ +   +  + e+   +G+++     +   de +
  gene1754|gene1754|rna1753|rna1753 330 HVLIVGDPGLGKSKLLLSTCGILpKSSYVSGNFTT---TAGLTVSLTHDPISGEYMADAGALVVAdngVCCLDEFD 402
                                        89999999999988776666555256677777775...46677777777888888888888653223377889998 PP

                              AAA_3  73 rappktqsalleameerqvtve..gethklpepflvlatqnPi 113
                                        +     ++al+eame+++v+++  g   ++p+  +v+a+ nP 
  gene1754|gene1754|rna1753|rna1753 403 KID--DHAALFEAMEDQRVSIAkgGVICSVPTRSTVIAATNPR 443
                                        876..579***********99722567899***********96 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   2.3e-05     0.029      31     117 ..     326     423 ..     316     445 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                             RuvB_N  31 ealdhvllyGpPGlGkttl....akiiake..lgvklkitsgPvlekagd.....la..alltnleekdvlfidei 93 
                                        ++  hvl++G PGlGk+ l    + i+ k   +  ++ +t+g +++ + d      +  a    + ++ v  +de 
  gene1754|gene1754|rna1753|rna1753 326 RSETHVLIVGDPGLGKSKLllstCGILPKSsyVSGNFTTTAGLTVSLTHDpisgeYMadAGALVVADNGVCCLDEF 401
                                        5667************987333345776542266788889998887666532222221112234678889999**9 PP

                             RuvB_N  94 hrlsraveevlysamedfrldivi 117
                                         +++ ++   l+ amed r+ i  
  gene1754|gene1754|rna1753|rna1753 402 DKIDDHA--ALFEAMEDQRVSIAK 423
                                        9999875..79*******998864 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05     0.028      30      83 ..     325     378 ..     319     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                              AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiie 83 
                                        ++++ +vl+vG+ G GK+ ++ +++  l+k++y+s +++ +a  + + + d i 
  gene1754|gene1754|rna1753|rna1753 325 IRSETHVLIVGDPGLGKSKLLLSTCGILPKSSYVSGNFTTTAGLTVSLTHDPIS 378
                                        78899*********************************9999999888877665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.02        25      18      37 ..     324     343 ..     316     364 .. 0.87
   2 ?    7.6   0.0    0.0022       2.8      84     144 ..     383     443 ..     374     460 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.02
                                        HCTSSS-EEEECSTTSSHHH CS
                    Sigma54_activat  18 vaktdlsvlitGesGtGKel 37 
                                         ++++++vli+G+ G GK+ 
  gene1754|gene1754|rna1753|rna1753 324 GIRSETHVLIVGDPGLGKSK 343
                                        567899************86 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0022
                                        -BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEE..SBTSSSEEE--EEEEEEESS- CS
                    Sigma54_activat  84 ekkGlfekadgGtlfLDeigelplelQekLlrvlqegeve..rvGsskeikvdvriiaatned 144
                                        + +G++  ad+G+  LDe  +++ +  + L++++++++v+  + G   ++++   +iaatn  
  gene1754|gene1754|rna1753|rna1753 383 ADAGALVVADNGVCCLDEFDKIDDH--AALFEAMEDQRVSiaKGGVICSVPTRSTVIAATNPR 443
                                        56799***************99765..79*****998764216677789999999****9965 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.29      39      76 .]     216     257 ..     203     257 .. 0.86
   2 ?   -1.6   0.0       2.2   2.8e+03      42      61 ..     473     492 ..     465     517 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                        HHHHHTTS-TTSEEEEEEEEEECTTS....SEEEEEEEEEEE CS
                    tRNA_anti-codon  39 atklaenlkeGdvvrvtGrvkrrpgg....elelkveeiell 76 
                                        ++++  +l +Gd+v++tG ++   ++    +l+++ +++e++
  gene1754|gene1754|rna1753|rna1753 216 YDEFVGTLAPGDIVQITGVLGVEFENdnlyKLTVHTNNMEII 257
                                        5688999***************95555699999999999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                        HHTTS-TTSEEEEEEEEEEC CS
                    tRNA_anti-codon  42 laenlkeGdvvrvtGrvkrr 61 
                                        l+++l e  ++ ++G+v + 
  gene1754|gene1754|rna1753|rna1753 473 LLDDLSEKECYMISGQVLKK 492
                                        56778888888888887554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00052      0.66       1     111 [.     331     442 ..     331     467 .. 0.78
   2 ?    0.7   0.0      0.53   6.8e+02      16      88 ..     589     659 ..     587     667 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00052
                                        EEEESSTTSSHHHHHHHHHHHH.THEEEEEETTTCSSSSTTHHHHHHHH.HHHHHHHTS....TSEEEEEETGGGH CS
                                AAA   1 vllyGppGtGKTllakavakel.gvefleisgsellskyvgesekkire.lfkeakeka....kpsilfiDEidal 70 
                                        vl++G pG GK+ l  + +  l ++++++ + ++    +v+ + + i++ ++++a   a    +  +  +DE+d++
  gene1754|gene1754|rna1753|rna1753 331 VLIVGDPGLGKSKLLLSTCGILpKSSYVSGNFTTTAGLTVSLTHDPISGeYMADAG--AlvvaDNGVCCLDEFDKI 404
                                        799******************97688888888888877777777777751444444..34475569********** PP

                                        HHHHTTCCCHHHHHHHHHHHHHHHHTTTS..........SSTEEEEEEESS CS
                                AAA  71 aksrsgseseeeervvnqLlteldgvkkk..........eskvivigatnr 111
                                          +             ++L++++++++ +            + +vi+atn 
  gene1754|gene1754|rna1753|rna1753 405 DDH-------------AALFEAMEDQRVSiakggvicsvPTRSTVIAATNP 442
                                        544.............59999999999998888888888556788888885 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.53
                                        HHHHHHHTHEE.EEEETTTCSSS...STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHH CS
                                AAA  16 kavakelgvef.leisgsellsk...yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvn 87 
                                        +++a+++++ef +e+   +++sk      +++k+++++++e  + ++ + +  +E+++l++s        +++ vn
  gene1754|gene1754|rna1753|rna1753 589 RSIATKADAEFcIELYKRTFISKenmPRNKRSKDFSQVLREYVKRKGGCLISSEELYSLVSSF------GSSKPVN 658
                                        6788888877767777777776666667788899999999854444369**********9988......3333444 PP

                                        H CS
                                AAA  88 q 88 
                                        +
  gene1754|gene1754|rna1753|rna1753 659 E 659
                                        4 PP

>> gag_pre-integrs  GAG-pre-integrase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0003      0.39      30      65 ..      48      82 ..      46      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                    gag_pre-integrs 30 RLGHpsfsrlkkLfkkgllpglkisksevCeaCqlg 65
                                       R  H+s +rl++L++k +l+ +  ++   C +C+++
  gene1754|gene1754|rna1753|rna1753 48 RTYHISKQRLENLVEKRFLDTNA-GNLLLCVSCAIS 82
                                       667*****************955.9999*****986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00027      0.35      23      51 ..     327     355 ..     308     378 .. 0.76
   2 ?   -1.7   0.1       2.6   3.3e+03     138     151 ..     395     408 ..     387     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                             AAA_16  23 rpelvllsGesGvGKsslvrellralekd 51 
                                        ++  vl++G++G GKs+l+ +    l k+
  gene1754|gene1754|rna1753|rna1753 327 SETHVLIVGDPGLGKSKLLLSTCGILPKS 355
                                        3389**************97766555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.6
                             AAA_16 138 vlvlDdlqwadeas 151
                                        v +lD+++++d++ 
  gene1754|gene1754|rna1753|rna1753 395 VCCLDEFDKIDDHA 408
                                        779********954 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.7    0.0011       1.4      20      41 ..     135     156 ..     125     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                               C1_4  20 eltssryrCekCkndFCiDCDv 41 
                                         +t+++++C kC ++ C+D   
  gene1754|gene1754|rna1753|rna1753 135 VSTKMFFECSKCGDVVCVDVKN 156
                                        4799***************755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 4300.45
//
Query:       gene1755|gene1755|rna1754|rna1754  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-40  139.0   0.9    1.6e-40  138.4   0.9    1.3  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.9   8.9e-45   1.6e-40       7     137 .]      36     257 ..      27     257 .. 0.97

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 8.9e-45
                                        CCCSEESSTEEXXXSSXXX................................................CCSBXXXXX CS
                      Ribosomal_S8e   7 skhkrkltGgkakllrkkr................................................kielgrkek 34 
                                        +k++ kl G+kakl++kk+                                                ki+++r+ek
  gene1755|gene1755|rna1754|rna1754  36 AKKANKLFGIKAKLFAKKQraakiqlkkdmkmreskkrnieisaesnplphflldrelqekakdindKIKQQRQEK 111
                                        68999************999******************************************************** PP

                                        XXEE...........SSHEEEEEEETTCEEEE..............................EEESESEEEEEETT CS
                      Ribosomal_S8e  35 atkl...........gaervkvvrvrgGkrkk..............................ralrlkkanvthpe 69 
                                          k+           ++e++ vv   +Gkrk                               +a+r+k+a+v+hpe
  gene1755|gene1755|rna1754|rna1754 112 GSKYsvplpkihplpEKEVFGVV--VSGKRKSkhwkrmvtkpcfvgsdftrkppkyerfirpMAMRFKTAHVSHPE 185
                                        ****9999999877669999999..999999999****************************************** PP

                                        TTEEEEEEEEEEECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEE....EEEESEHHHHSSEEEEEE CS
                      Ribosomal_S8e  70 ekvtkklkIlgVkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvv....AqvtsrPgqdGcvnavlL 137
                                        ++ t++lkI+g kknp++  y+ lg+l+Kg+iievdvs+Lg+v  sgk++    Aq+t++P++dGcvnavlL
  gene1755|gene1755|rna1754|rna1754 186 LNSTFNLKIIGLKKNPHSDVYTGLGILSKGTIIEVDVSPLGLVNGSGKIIwgkyAQITNNPENDGCVNAVLL 257
                                        ***********************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1525  (0.0850577); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1692.11
//
Query:       gene1756|gene1756|rna1755|rna1755  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.5e-126  419.0   0.0   6.7e-126  418.8   0.0    1.1  1  Rad51     Rad51
    2.6e-10   40.2   0.0    3.8e-10   39.7   0.0    1.1  1  RecA      recA bacterial DNA recombination protein
    9.2e-08   31.7   0.1    1.6e-07   30.9   0.1    1.5  1  ATPase    KaiC
    7.7e-06   26.4   0.8    2.5e-05   24.8   0.8    1.9  1  HHH_5     Helix-hairpin-helix domain
    0.00051   19.7   0.0    0.00078   19.1   0.0    1.2  1  AAA_25    AAA domain
      0.004   17.4   0.0     0.0082   16.4   0.0    1.4  1  AAA_22    AAA domain
     0.0047   16.7   0.0      0.011   15.5   0.0    1.5  1  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.8   0.0  2.6e-129  6.7e-126       1     254 [.      78     331 ..      78     332 .. 1.00

  Alignments for each domain:
  == domain 1  score: 418.8 bits;  conditional E-value: 2.6e-129
                                        -S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEE CS
                              Rad51   1 lgfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavy 76 
                                        +gf++a+ ++++rsel+ lttGs+++D+lL+GG+e+gsiteifGefr+Gktqlcht++vt+qlp e+gGg gka+y
  gene1756|gene1756|rna1755|rna1755  78 MGFTTASAYHQRRSELVYLTTGSSEVDKLLNGGFESGSITEIFGEFRTGKTQLCHTVAVTCQLPPEQGGGGGKAMY 153
                                        79************************************************************************** PP

                                        EESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH----- CS
                              Rad51  77 idtegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgr 152
                                        idtegtfr+erlv iaer++ld++ev++n++yaRay+++hq++ll +a+a+++e+k+++li+Ds+talyRtdfsgr
  gene1756|gene1756|rna1755|rna1755 154 IDTEGTFRSERLVPIAERFGLDPNEVMDNISYARAYNSDHQSQLLIKASAMMSESKYSVLIIDSATALYRTDFSGR 229
                                        **************************************************************************** PP

                                        --THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEE CS
                              Rad51 153 gelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeR 228
                                        gel +Rq +l+k+lr+L +la+ f+vav+itnqvv++vdg+  +f++d kkPigG+++ahasttRl+lrkg+ge+R
  gene1756|gene1756|rna1755|rna1755 230 GELGARQLHLAKYLRSLVNLAETFRVAVIITNQVVSNVDGAVGMFAGDIKKPIGGNIMAHASTTRLYLRKGRGETR 305
                                        **************************************************************************** PP

                                        EEEEES-SSS-S-EEEEEEETTEEE- CS
                              Rad51 229 ivkvvdsPnlpeleavfaigeeGied 254
                                        i+k++dsP+lpe+eavfai+e+Gi+d
  gene1756|gene1756|rna1755|rna1755 306 ICKIYDSPCLPESEAVFAITEQGIND 331
                                        ************************98 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   1.5e-13   3.8e-10      27     221 ..      89     299 ..      67     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.5e-13
                                        .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH......HTT--EEEEESS----HH CS
                               RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq......kkggvaafidaehaldpk 96 
                                        ++ ++  +++Gs  +d  l  GG+  G i+ei+G   +Gkt l+  + + +q        gg a +id+e ++ ++
  gene1756|gene1756|rna1755|rna1755  89 RRSELVYLTTGSSEVDKLLN-GGFESGSITEIFGEFRTGKTQLCHTVAVTCQlppeqgGGGGKAMYIDTEGTFRSE 163
                                        456777899*******9997.*********************9888777777433211246899******999865 PP

                                        ....HHHHTT--GGG-E..EE.....--SSHHHHHHHHHHHHTTT--SEEEEE-TTT---STT-----------HH CS
                               RecA  97 ....yakklGvdidell..vs.....qpdtGeqaleiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglq 161
                                             a+++G+d +e++  +s     + d+  q l  a a++  +   ++++ds +al  +++  G     ++g +
  gene1756|gene1756|rna1755|rna1755 164 rlvpIAERFGLDPNEVMdnISyarayNSDHQSQLLIKASAMMSESKYSVLIIDSATALY-RTDFSGR---GELGAR 235
                                        333369******88876444422222457777878778888888999**********97.5566543...334444 PP

                                        HHHHHHHHHHHHHHHTTT--EEEEEEE----....-------------HHHHHHH-SEEEEEEE CS
                               RecA 162 arlmsqalrkltgaisksntvvifinqirek....iGvmfgnpetttGGralkfyasvrldvrr 221
                                           +++ lr l    +  +++vi  nq+       +G+  g+ +   GG+ +   ++ rl +r+
  gene1756|gene1756|rna1755|rna1755 236 QLHLAKYLRSLVNLAETFRVAVIITNQVVSNvdgaVGMFAGDIKKPIGGNIMAHASTTRLYLRK 299
                                        44568999*******************9775222279999999*****************9998 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   6.4e-11   1.6e-07       2     167 ..      97     266 ..      96     330 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 6.4e-11
                             ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgae.....kygepgvfvtveepa..edlrenaksl 70 
                                         tg  + D++l+gG+ +g+++ i Ge  tGKt ++ + +++          g + +++ +e +   e l   a+++
  gene1756|gene1756|rna1755|rna1755  97 TTGSSEVDKLLNGGFESGSITEIFGEFRTGKTQLCHTVAVTCQLppeqgGGGGKAMYIDTEGTFrsERLVPIAERF 172
                                        589999********************************99854311111237889******987779********* PP

                             ATPase  71 GwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeek.....eavaR 141
                                        G d +++ ++  + +  a++s+++          ++l+ +   +++e k + ++iDs t+l y+++     e  aR
  gene1756|gene1756|rna1755|rna1755 173 GLDPNEVMDN--ISYARAYNSDHQ----------SQLLIKASAMMSESKYSVLIIDSATAL-YRTDfsgrgELGAR 235
                                        **********..777777777654..........8999999********************.44321111111244 PP

                             ATPase 142 .....eilrqlvrvlkklgvTailvseksss 167
                                             ++lr lv+  +  +v  i+++++ s+
  gene1756|gene1756|rna1755|rna1755 236 qlhlaKYLRSLVNLAETFRVAVIITNQVVSN 266
                                        2222257888888888888888888888773 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.8   9.7e-09   2.5e-05      14      56 ..      31      73 ..      25      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 9.7e-09
                                       HHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                              HHH_5 14 tAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                       ++ +l++aG+++ve la a + +L +i+G++  +++++i e+ 
  gene1756|gene1756|rna1755|rna1755 31 DIAKLIEAGFTTVESLAFAPKRQLLSIKGFSDIKVDKLIKEAA 73
                                       6779***********************************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.1e-07   0.00078      20     187 ..     101     261 ..      88     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.1e-07
                             AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravge 95 
                                         ++++l+ g    g+++ ++G   tGKt l+  +a+++ +  p  g      gk +y+++E++     +Rl  + e
  gene1756|gene1756|rna1755|rna1755 101 SEVDKLLNGGFESGSITEIFGEFRTGKTQLCHTVAVTCQL-PPEQG---GGGGKAMYIDTEGTF--RSERLVPIAE 170
                                        5677888888899***************988888877774.33333...479***********8..6899999999 PP

                             AAA_25  96 alrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd....... 164
                                         + +d ++   ++      + + +d++++ll  +     a + e  ++ +++iD+ +++++ d     +       
  gene1756|gene1756|rna1755|rna1755 171 RFGLDPNEVMDNISY---ARAYNSDHQSQLLIKA----SAMMSE-SKYSVLIIDSATALYRTDFSGRGElgarqlh 238
                                        986666666665544...3556666666663332....334444.4599***********9988877776666554 PP

                             AAA_25 165 vgalvealeriarrtgaavllvh 187
                                         ++ +  l ++a+ +++av+++ 
  gene1756|gene1756|rna1755|rna1755 239 LAKYLRSLVNLAETFRVAVIITN 261
                                        48888888888888888888875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.2e-06    0.0082       4     127 ..     113     259 ..     111     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-06
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......... 70 
                                        + +i+ ++Ge  tGKT l+ +++ + +  +++   + + ++++  +   +++ l  +++ +gl+ ++         
  gene1756|gene1756|rna1755|rna1755 113 SGSITEIFGEFRTGKTQLCHTVAVTCQLPPEQGGGGGKAMYIDTEGTF-RSERLVPIAERFGLDPNEvmdnisyar 187
                                        568899******************998777777688888888888888.777779*******************99 PP

                             AAA_22  71 ...erlsseellealeqalraravielliiDEaqhlr....s.........eealeeLrsllnl.srkgvqliL 127
                                           + ++s+ l++a +  +++++   +liiD a  l     s           + ++Lrsl+nl +++ v++i+
  gene1756|gene1756|rna1755|rna1755 188 aynSDHQSQLLIKASAMMSESKYS--VLIIDSATALYrtdfSgrgelgarqLHLAKYLRSLVNLaETFRVAVII 259
                                        986666666666888888888888..*********987766256777777788888889999998888888876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.1e-06     0.011       7      79 ..     119     223 ..     116     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.1e-06
                             AAA_24   7 iyGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvel..... 59 
                                        i+G+  +GKT l+ +              g k+ +idte+ ++s     +           ++++d + +      
  gene1756|gene1756|rna1755|rna1755 119 IFGEFRTGKTQLCHTVavtcqlppeqgggGGKAMYIDTEGTFRSERLVPI---AerfglDPNEVMDNISYArayns 191
                                        89**************************************6655444444...44568877888888888889999 PP

                             AAA_24  60 ............aaeladyktlviDtidelee 79 
                                                       +++y++l+iD+++ l++
  gene1756|gene1756|rna1755|rna1755 192 dhqsqllikasaMMSESKYSVLIIDSATALYR 223
                                        99*******999889999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2125.62
//
Query:       gene1757|gene1757|rna1756|rna1756  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-20   72.1   0.0    4.5e-20   71.3   0.0    1.4  1  TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa s
  ------ inclusion threshold ------
      0.062   12.1   0.3      0.074   11.8   0.3    1.0  1  UPF0061      Uncharacterized ACR, YdiU/UPF0061 family


Domain annotation for each model (and alignments):
>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0     5e-24   4.5e-20       1      49 [.      18      66 ..      18      67 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 5e-24
                        TFIID_30kDa  1 PiIPDavtayyLekaGletsDprlarlvsLaaqKFisdiaadAyqyski 49
                                       P++P++vt+y++ekaG+ tsD+++++lvsL a+KF++dia +++qy++i
  gene1757|gene1757|rna1756|rna1756 18 PLLPESVTDYFMEKAGVATSDQSVKKLVSLLAHKFVTDIAVSSFQYHRI 66
                                       99**********************************************8 PP

>> UPF0061  Uncharacterized ACR, YdiU/UPF0061 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   8.3e-06     0.074     312     391 ..       6      85 ..       4     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-06
                            UPF0061 312 aeeleealeeykevyttkYaqlmlkkLGleklsekekefdselleellelLqetqvdYneffveLaeskskkwrde 387
                                         +el+++l++y+  + ++ ++ +++k G+ + +++ k+  s l ++ ++ ++ ++++Y++  ++ a++++++++++
  gene1757|gene1757|rna1756|rna1756   6 FNELKQNLDNYTPLLPESVTDYFMEKAGVATSDQSVKKLVSLLAHKFVTDIAVSSFQYHRINQKAAQKDKRFAKEK 81 
                                        689**************************9999*****999999*****************999999999888866 PP

                            UPF0061 388 aesi 391
                                        + ++
  gene1757|gene1757|rna1756|rna1756  82 KPTF 85 
                                        5544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 618.32
//
Query:       gene1758|gene1758|rna1757|rna1757  [L=448]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-23   82.9   0.0    1.4e-22   80.6   0.0    2.1  1  AAA              ATPase family associated with various cellul
    8.7e-06   26.1   0.0    5.5e-05   23.5   0.0    2.3  2  AAA_22           AAA domain
    3.6e-05   23.8   0.5     0.0014   18.7   0.3    3.0  2  ResIII           Type III restriction enzyme, res subunit
     0.0018   17.8   0.0     0.0038   16.8   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0028   17.8   0.0     0.0069   16.5   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0093   15.8   0.5       0.02   14.7   0.0    1.8  2  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.021   14.2   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.019   14.9   0.1      0.094   12.7   0.0    2.3  2  AAA_5            AAA domain (dynein-related subfamily)
      0.029   14.5   0.0      0.082   13.1   0.0    1.8  2  AAA_33           AAA domain
      0.035   14.5   0.0        0.1   13.0   0.0    1.7  2  AAA_16           AAA ATPase domain
       0.04   13.1   0.0      0.083   12.1   0.0    1.5  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.059   13.8   0.0       0.15   12.4   0.0    1.8  1  RNA_helicase     RNA helicase
       0.11   12.7   0.0       0.24   11.6   0.0    1.6  1  UPF0114          Uncharacterized protein family, UPF0114
       0.11   12.2   0.0       0.27   10.9   0.0    1.6  1  AAA_30           AAA domain
       0.14   12.9   0.0       0.26   11.9   0.0    1.4  1  Pex14_N          Peroxisomal membrane anchor protein (Pex14p)
       0.14   11.9   0.0        1.3    8.7   0.0    2.4  1  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   1.2e-25   1.4e-22       2     131 ..     173     338 ..     172     339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.2e-25
                                        EEESSTTSSHHHHHHHHHHHHTHE............EEEEETTTCSSS............................ CS
                                AAA   2 llyGppGtGKTllakavakelgve............fleisgsellsk............................ 37 
                                        l++GppGtGKTl++k ++  ++ +                       +                            
  gene1758|gene1758|rna1757|rna1757 173 LFHGPPGTGKTLFMKKLIYLVDLNikflkmrnemgeK----------Efesmdhneklirakqmesltritfvtps 238
                                        8*****************9975442233333444440..........14444445555555555555555555555 PP

                                        .....STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEE CS
                                AAA  38 .....yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.eskvivi 106
                                             yvge+ek+ir+lf++a   +   + +fiDE+d ++++rs+++++ + +++ ++l+ + g  ++ +s+v++ 
  gene1758|gene1758|rna1757|rna1757 239 slnnkYVGETEKNIRGLFQSANDGKyWATFVFIDEVDVFFSKRSDRSQDYTLKAQTEFLNTIGGACDRvNSTVFLF 314
                                        55555****************9999766***********************************9988878899*** PP

                                        EEESSGGGSTHHHHSTTSSEEEETT CS
                                AAA 107 gatnrpdkldpallrgRfdrkieie 131
                                        gatn +d ld+a+  +Rf+ ++e++
  gene1758|gene1758|rna1757|rna1757 315 GATNLYDVLDDAFK-RRFSGVYEFS 338
                                        **************.7**9998876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   4.9e-08   5.5e-05       4     137 .]     168     323 ..     165     323 .. 0.66
   2 ?   -1.2   0.0         2   2.2e+03      42      81 ..     334     370 ..     328     414 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.9e-08
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............erpevv....fvtlpsstsskdllrellra 63 
                                        t++  + +G++GtGKT+ +++l +  d  +k  +            +         ++ +++ +s++ +     + 
  gene1758|gene1758|rna1757|rna1757 168 TQRNFLFHGPPGTGKTLFMKKLIYLVDLNIKFLKmrnemgekefesM----DhnekLIRAKQMESLTRITFVTPSS 239
                                        7788899******************9876555555666655333331....0222244444444444554445555 PP

                             AAA_22  64 lglelkaerlsseellealeqalraravielliiDEaqhlr...s........eealeeLrsllnl.srkgvqliL 127
                                        l+++  +   +++ ++ +++ a + ++   ++ iDE++ ++   s        +++ e+L ++    +r + +++L
  gene1758|gene1758|rna1757|rna1757 240 LNNKYVG--ETEKNIRGLFQSANDGKYWATFVFIDEVDVFFskrSdrsqdytlKAQTEFLNTIGGAcDRVNSTVFL 313
                                        5544444..777777777777777777699*********88776265567777444444444433355999***** PP

                             AAA_22 128 vGtpelrkll 137
                                        +G ++l+++l
  gene1758|gene1758|rna1757|rna1757 314 FGATNLYDVL 323
                                        ****999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                             AAA_22  42 vvfvtlpsstsskdllrellralglelkaerlsseellea 81 
                                        v+++ lp+++++ ++l+e l + ++e  +   ++ +l+++
  gene1758|gene1758|rna1757|rna1757 334 VYEFSLPNEEERLEILEEYLGDCNREVTN---RLNDLVRM 370
                                        55666777777777777777777766666...33333333 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   1.2e-06    0.0014      17     141 ..     163     274 ..     139     297 .. 0.74
   2 ?    0.5   0.0      0.48   5.4e+02      56      85 ..     309     348 ..     291     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                                        ......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS CS
                             ResIII  17 eklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgd 92 
                                        ++++ + ++++l++ + GtGKTl + kli+ +       ++ fl  r+++ e+   ef+++ +++     k ++ +
  gene1758|gene1758|rna1757|rna1757 163 KSIE-TTQRNFLFHGPPGTGKTLFMKKLIYLVDL-----NIKFLKMRNEMGEK---EFESMDHNE-----KLIRAK 224
                                        4444.9999************************9.....68899999999986...677766665.....344444 PP

                                        -B--.......-SEEEEEHHHHHHTH........HHHTTT-S..........EEEEETG CS
                             ResIII  93 kkkakekdstnkkilvttiqsldadseeeeeeseellrdrfd..........viiiDEa 141
                                        + ++       ++i+++t +sl+++      e+e++ r+ f+          +++iDE+
  gene1758|gene1758|rna1757|rna1757 225 QMES------LTRITFVTPSSLNNKY---VGETEKNIRGLFQsandgkywatFVFIDEV 274
                                        4444......5677788888888888...666666666666666667777777777875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.48
                                        -EEEEESSHHHHHHHHHHGGGGTGG..............G CS
                             ResIII  56 kflflvprkslleqtleefkkflseayke..........i 85 
                                         ++fl   ++l++ + ++fk+ +s  y++          i
  gene1758|gene1758|rna1757|rna1757 309 STVFLFGATNLYDVLDDAFKRRFSGVYEFslpneeerleI 348
                                        7899999**************9999988776654444433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.4e-06    0.0038      14      58 ..     150     194 ..     142     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-06
                              AAA_7  14 VptvdtvrysyllelllknkkpvllvGptGtGKtviikdllkkld 58 
                                        V+   tv  + l + + + ++++l+ Gp GtGKt+ +k+l+  +d
  gene1758|gene1758|rna1757|rna1757 150 VNLLRTVPEKDLHKSIETTQRNFLFHGPPGTGKTLFMKKLIYLVD 194
                                        6666677777788888899********************766555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.2e-06    0.0069       4      83 ..     170     280 ..     167     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-06
                                        --EEEE--TTSSHHHHHHHHHHHTT-.......................-EEEE.EGGG---......----THHH CS
                              AAA_2   4 isilllgptgvGktelakalaellfv...................kkekklira.daselle......eeevehlv 53 
                                         ++l+ gp g+Gkt+  k+l  l ++                   ++++klira  + +l+       +   +++v
  gene1758|gene1758|rna1757|rna1757 170 RNFLFHGPPGTGKTLFMKKLIYLVDLnikflkmrnemgekefesmDHNEKLIRAkQMESLTRitfvtpSSLNNKYV 245
                                        58*************6666666666666666668887777777775555555541444444466665555556666 PP

                                        HHHHHHTTT-HHHHTTS.....EEEEETGGG---- CS
                              AAA_2  54 srligappgyvgaeegG.....ivllDEidKihpk 83 
                                         + + +  g  + +++G      v++DE+d   +k
  gene1758|gene1758|rna1757|rna1757 246 GETEKNIRGLFQSANDGkywatFVFIDEVDVFFSK 280
                                        66666666666666666*************77775 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       4.9   5.5e+03     132     139 ..      19      26 ..       5      68 .. 0.54
   2 !   14.7   0.0   1.8e-05      0.02      16      41 ..     169     193 ..     155     241 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.9
                             AAA_11 132 eleklake 139
                                         +e+++++
  gene1758|gene1758|rna1757|rna1757  19 DEEEYEEA 26 
                                        11111111 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.8e-05
                             AAA_11  16 eseitliqGPPGtgKTktivellsql 41 
                                        ++  +l++GPPGtgKT +  +l+  +
  gene1758|gene1758|rna1757|rna1757 169 QR-NFLFHGPPGTGKTLFMKKLIYLV 193
                                        22.47***********8877777655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.9e-05     0.021      22      46 ..     169     193 ..     162     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                       Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsll 46 
                                        + n+l+ GppG+GKt+  k+l  l+
  gene1758|gene1758|rna1757|rna1757 169 QRNFLFHGPPGTGKTLFMKKLIYLV 193
                                        5799****************99885 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.4e-05     0.094       2      42 ..     172     212 ..     171     276 .. 0.87
   2 ?   -1.6   0.0       2.2   2.5e+03     113     138 .]     305     331 ..     279     331 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-05
                                        EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlk 42 
                                        +l  GppGtgK+ ++++l  ++  ++    ++  + e+++ 
  gene1758|gene1758|rna1757|rna1757 172 FLFHGPPGTGKTLFMKKLIYLVDLNIKFLKMRNEMGEKEFE 212
                                        7899******************9999999998888888865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                                        ......-EEEEEESS--.-TT-TTHHHHTT- CS
                              AAA_5 113 r.....frviatanpldrslnelspalrsRf 138
                                        +     + +++++n  d     l+ a+++Rf
  gene1758|gene1758|rna1757|rna1757 305 DrvnstVFLFGATNLYD----VLDDAFKRRF 331
                                        04444466777777777....9999999999 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.3e-05     0.082       3      20 ..     173     190 ..     172     242 .. 0.74
   2 ?   -2.8   0.0       5.7   6.3e+03      50      65 ..     362     377 ..     325     409 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.3e-05
                             AAA_33   3 llvGlpGsGKstlaerll 20 
                                        l++G+pG+GK+ + ++l+
  gene1758|gene1758|rna1757|rna1757 173 LFHGPPGTGKTLFMKKLI 190
                                        89*************996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.7
                             AAA_33  50 rvldrlyqilnelark 65 
                                        + l++l +++n++a++
  gene1758|gene1758|rna1757|rna1757 362 NRLNDLVRMTNGMAQS 377
                                        3333333344444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     9e-05       0.1      20      44 ..     165     189 ..     144     206 .. 0.74
   2 ?   -2.7   0.0         6   6.8e+03     137     149 ..     267     279 ..     251     309 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9e-05
                             AAA_16  20 rsgrpelvllsGesGvGKsslvrel 44 
                                         + + ++ l++G++G+GK+  +++l
  gene1758|gene1758|rna1757|rna1757 165 IETTQRNFLFHGPPGTGKTLFMKKL 189
                                        333349*************988776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6
                             AAA_16 137 lvlvlDdlqwade 149
                                        + +++D+++ + +
  gene1758|gene1758|rna1757|rna1757 267 TFVFIDEVDVFFS 279
                                        6789999995544 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.4e-05     0.083       3     102 ..     171     279 ..     169     321 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-05
                            DUF2075   3 vvlVtGvaGtGKtvvllnllael.......eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfi 71 
                                         +l +G +GtGKt+ + +l++ +       ++ +e  ++ + s  h++ l+  +++++ +     + +f  +ss+ 
  gene1758|gene1758|rna1757|rna1757 171 NFLFHGPPGTGKTLFMKKLIYLVdlnikflKMRNEMGEKEFESMDHNEKLIRAKQMESLT-----RITFVTPSSLN 241
                                        68899**************99988877777666777777777777777666666665444.....44444444444 PP

                            DUF2075  72 nnlsef.......kkaeekkeepkedvvivDEAhrllt 102
                                        n++            + +++ +  +++v +DE     +
  gene1758|gene1758|rna1757|rna1757 242 NKYVGEteknirgLFQSANDGKYWATFVFIDEVDVFFS 279
                                        44442233333221122234444566777777666666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014      0.15       2      22 ..     173     193 ..     172     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                       RNA_helicase   2 wlyGpsgeGKStlakeLakal 22 
                                        +++Gp+g+GK++++k+L+  +
  gene1758|gene1758|rna1757|rna1757 173 LFHGPPGTGKTLFMKKLIYLV 193
                                        69**************98655 PP

>> UPF0114  Uncharacterized protein family, UPF0114
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.24      48      82 ..      72     106 ..      47     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                            UPF0114  48 lavleliDlvLigtvllivglGlYelFvskldlee 82 
                                         + + + D++ +++v+li+g+ +Y+ F+ +   e+
  gene1758|gene1758|rna1757|rna1757  72 ANPVRIKDVFYLAIVILIFGYVIYKVFIPNGGYEQ 106
                                        5557788*********************8876654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.27      16      39 ..     167     190 ..     159     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                             AAA_30  16 sgdrvavltGpAGtGKttalkalr 39 
                                        +++r  + +Gp+GtGKt  +k+l 
  gene1758|gene1758|rna1757|rna1757 167 TTQRNFLFHGPPGTGKTLFMKKLI 190
                                        44457899************9875 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00023      0.26      74     149 ..      19      98 ..       3      99 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                            Pex14_N  74 satpqpqaasqtsqsspspsppaqqqqqqy..............rpPivtypefltkppkppppPlrtwrdllita 135
                                        ++  ++ +++q+ ++ + p++        +              r+ + +y   + k++ p+    ++ +d++++a
  gene1758|gene1758|rna1757|rna1757  19 DE--EEYEEAQERTKGNMPEE--------KgtdvnndilvaliyRKILKYYGIKQKKTKTPKTANPVRIKDVFYLA 84 
                                        22..22222222222222221........01122233467888555556665555556666677788********* PP

                            Pex14_N 136 talaglgaglygls 149
                                         ++  +g+++y+++
  gene1758|gene1758|rna1757|rna1757  85 IVILIFGYVIYKVF 98 
                                        ***********985 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0012       1.3      16      45 ..     163     200 ..     153     330 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                        HHHCTSSS-EEEECSTTSSHHHHHHHHHH........H CS
                    Sigma54_activat  16 kkvaktdlsvlitGesGtGKellaraihe........a 45 
                                        k++ +t+ + l +G  GtGK+l+ +++           
  gene1758|gene1758|rna1757|rna1757 163 KSIETTQRNFLFHGPPGTGKTLFMKKLIYlvdlnikfL 200
                                        556678899*************9987755455555552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 2721.65
//
Query:       gene1759|gene1759|rna1758|rna1758  [L=371]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-15   55.1   0.1      2e-06   27.7   0.0    2.4  2  PLDc_2    PLD-like domain
      0.003   17.7   1.7       0.52   10.6   0.1    2.7  2  PLDc      Phospholipase D Active site motif


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   2.3e-10     2e-06       5     126 ..      35     164 ..      32     167 .. 0.68
   2 !   24.9   0.0   1.6e-09   1.5e-05      71     132 ..     273     339 ..     256     340 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.3e-10
                             PLDc_2   5 iksAkksidiatyyfvsdrei...ldallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfe. 76 
                                        + ++++s+++a+ +f  d e+   ld l ++++rg  + +++ +   ++++ + ++l  +    +e g+e  +   
  gene1759|gene1759|rna1758|rna1758  35 LLQTSESVYMASLFFGQDGEMediLDILEEKKRRGL-ITVIFID---KNRGAAGRRLEFI----QERGLESTFHLi 102
                                        557799*********555554442888888888885.5555555...3344333334444....555555333333 PP

                             PLDc_2  77 ...t.....ll.....gslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakele 126
                                           t     ++     + +H+K++++d +++i+ ++N++++++  + +  ++i++kel++ ++
  gene1759|gene1759|rna1758|rna1758 103 dlsTsclfpAKlnelfRVFHTKALVFD-DITILSGANMDASYMVNRIDRYLEIQSKELTDMIK 164
                                        23224444411456789*********7.699*************************9998765 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.6e-09
                             PLDc_2  71 evrvfetllgslHaKlyli.dgk..tvivGSsNltkrgldlnlEln..vviedkelakeleeeFerl 132
                                         +++ +++  s+H K+++  ++k   +i+GSsN+++r+++++ E+n  +v++d+  +++l+ee e+l
  gene1759|gene1759|rna1758|rna1758 273 SIYELNKKGYSFHLKGFWGfKDKtaATIIGSSNFNRRSTERDDETNylIVTSDPGHIQKLREEVEYL 339
                                        455555434789***99865655335568**********9999988224556779999999998875 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   5.8e-05      0.52       5      25 ..     121     140 ..     117     143 .. 0.88
   2 !    5.8   0.3    0.0019        17      17      28 .]     299     310 ..     280     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                                        E---EEEETTTEEEEE---SS CS
                               PLDc   5 hHqKivivDdrvafvGgaNLc 25 
                                         H+K +++Dd  ++++gaN++
  gene1759|gene1759|rna1758|rna1758 121 FHTKALVFDDI-TILSGANMD 140
                                        5********98.********8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0019
                                        EEEE---SSHHH CS
                               PLDc  17 afvGgaNLcdgr 28 
                                        +++G++N+++++
  gene1759|gene1759|rna1758|rna1758 299 TIIGSSNFNRRS 310
                                        89*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2368.24
//
Query:       gene1760|gene1760|rna1759|rna1759  [L=662]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-16   60.3   0.0    4.8e-16   59.0   0.0    1.7  1  HA2              Helicase associated domain (HA2)
    2.4e-15   56.8   0.2      1e-14   54.8   0.0    2.1  2  Helicase_C       Helicase conserved C-terminal domain
    1.3e-14   54.3   0.1      3e-14   53.1   0.1    1.7  1  OB_NTP_bind      Oligonucleotide/oligosaccharide-binding (OB)
    5.2e-06   26.3   0.1      1e-05   25.4   0.1    1.4  1  DEAD             DEAD/DEAH box helicase
    2.1e-05   24.9   0.0      4e-05   24.0   0.0    1.4  1  AAA_19           AAA domain
    0.00017   21.4   0.0     0.0003   20.6   0.0    1.3  1  AAA_30           AAA domain
    0.00029   21.1   0.1    0.00069   19.9   0.1    1.5  1  AAA_22           AAA domain
    0.00052   20.1   0.2      0.017   15.2   0.2    2.3  1  ResIII           Type III restriction enzyme, res subunit
     0.0056   16.3   0.1      0.015   14.9   0.1    1.7  1  SRP54            SRP54-type protein, GTPase domain
     0.0057   16.6   0.0      0.016   15.1   0.0    1.7  1  Rad17            Rad17 P-loop domain
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.032   13.6   0.0    1.6  1  ATPase           KaiC
      0.014   14.7   0.0      0.024   13.9   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.035   13.9   0.0        3.8    7.2   0.0    2.9  3  AAA_11           AAA domain
      0.042   13.6   0.1       0.12   12.2   0.0    1.8  2  DNA_pol3_delta   DNA polymerase III, delta subunit
      0.049   12.7   0.1       0.14   11.2   0.0    1.7  2  T2SSE            Type II/IV secretion system protein
      0.075   12.9   0.0       0.16   11.8   0.0    1.6  1  Helicase_RecD    Helicase
       0.11   12.5   1.4        1.3    9.1   1.4    2.4  1  AAA_14           AAA domain
       0.12   12.1   0.3       0.29   10.8   0.1    1.8  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> HA2  Helicase associated domain (HA2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   4.8e-19   4.8e-16       1     108 []     436     527 ..     436     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 4.8e-19
                                HA2   1 AlelLvalgALdeegnlTelGrkmaelPlsprlakmLlaaaeleegcldevitivAalsveeifleeneeekeeee 76 
                                        AlelL++l A++ +g++T++G + +++Pl+p +a  L+++a+l  gcld+v  i+A+lsv+++    +++++    
  gene1760|gene1760|rna1759|rna1759 436 ALELLYYLRAIEGNGKITPIGVQASKIPLEPEMAVSLIVSAKL--GCLDDVSIIAAMLSVGNVWQGISRHSQ---- 505
                                        89**************************************888..*****************9977775443.... PP

                                HA2  77 eeeekakkkrkeeekarrklahkdaegDhltl 108
                                                  k++ +  +k+ah d++gDh++l
  gene1760|gene1760|rna1759|rna1759 506 --------LYKAFLH--AKAAHFDKRGDHFSL 527
                                        ........2333333..456777777998875 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         5     5e+03      66      83 ..     166     183 ..     153     217 .. 0.70
   2 !   54.8   0.0     1e-17     1e-14       6     110 ..     252     374 ..     242     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5
                                        SSSEEEESGGGTSSSTST CS
                         Helicase_C  66 esdvLiatdvaerGidip 83 
                                        ++dv+i   + er+i+i+
  gene1760|gene1760|rna1759|rna1759 166 KYDVVIVDEAHERSINID 183
                                        566666666666666663 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 1e-17
                                        HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                         Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                        ++++ +++ee g+il+f++ +++++    ll e    +++v++l+++l+ +e+e ++++ +  +++v++at++ae+
  gene1760|gene1760|rna1759|rna1759 252 VVQI-HRTEESGDILVFLTGKEEINGgRALLMEALgdDVEVCCLYSTLSPEEQEIAFKKVK--KRKVVLATNIAET 324
                                        3444.68999************9987755554544678**********************5..578********** PP

                                        SSTSTTESEEEESSSSSSH..................HHHHHHHTTSSST CS
                         Helicase_C  79 GidipkvnlVinfdlprnv..................tsyiqriGRtgRa 110
                                        +i+i+++++V++++  +++                  ++++qr+GR+gR 
  gene1760|gene1760|rna1759|rna1759 325 SITIEGIKYVVDCGRSKQMrysasfgmdileigwiskSQAKQRAGRAGRT 374
                                        ****************88888999999**********************6 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.1     3e-17     3e-14       4      80 ..     582     652 ..     579     655 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3e-17
                                        HHHHHHTTCEEEEEETTCCEEETTTCEEEEE-TTSTTTTT...TSSSEEEEEEEEESSSEEEEEEEEE-HHHHHHH CS
                        OB_NTP_bind   4 illaGlypqiarkdpskkdyktartktrvfihpsSvlaknekekepewvvytelvettklylrdltaidpawLllf 79 
                                        + +aG+++++a+   s+ +y+   ++t++fih sS+++k    + p++++y++l +t k y+r+++ ++ + Ll+ 
  gene1760|gene1760|rna1759|rna1759 582 SFCAGYFMNVAKL--SEGSYTSIFNDTQCFIHSSSCMSK----QHPKYILYHSLCRTEKEYARYCMEVTQEDLLKG 651
                                        68*********44..4555999889*************9....*****************************9986 PP

                                        S CS
                        OB_NTP_bind  80 a 80 
                                        a
  gene1760|gene1760|rna1759|rna1759 652 A 652
                                        6 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1     1e-08     1e-05       7     171 ..      66     210 ..      61     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1e-08
                                        HHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD   7 aiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                        +++ + + + +l++++TG GKT+     +l        k+  ++++  P r  a  +++++ + ++ ++l ++  +
  gene1760|gene1760|rna1759|rna1759  66 IFDKLEKSQVLLIEGNTGCGKTTKIPKYLL--------KKYERIVCTQPRRIAAISIAKKVARDMN-VKLGEE--V 130
                                        555666777889***********9777777........55579******************99999.344444..5 PP

                                        TTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DEAD  83 ggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgkl 158
                                        g + + d++s    ++++ ++t g l++ ++  k  l++  ++++DEa++ + +   d +   l+ +  +     +
  gene1760|gene1760|rna1759|rna1759 131 GYSIRFDDRSSS--KTRLKYATDGILIREINGDK-YLKKYDVVIVDEAHERSIN--IDILLGYLKLILAKR----S 197
                                        544444444444..78999*********996333.5*************99887..566666666663332....4 PP

                                        TSEEEEEESSBSH CS
                                        xxxxxxxxxxxxx RF
                               DEAD 159 qrqvivlSATlpk 171
                                        + +vi++SATl++
  gene1760|gene1760|rna1759|rna1759 198 DIRVIIMSATLNS 210
                                        566********83 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     4e-08     4e-05       9     118 ..      72     182 ..      64     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4e-08
                             AAA_19   9 kekvllvtaGpGtGKTrvl.khivallvelggvkpeeillvaftgrAakelrerlaalgae............atT 71 
                                        k++vll+ +  G+GKT+ + k  ++ ++++   +p++i++++ +++ a+ ++ +l   g+e             +T
  gene1760|gene1760|rna1759|rna1759  72 KSQVLLIEGNTGCGKTTKIpKYLLKKYERIVCTQPRRIAAISIAKKVARDMNVKL---GEEvgysirfddrssSKT 144
                                        68899999********988466889***************************999...555434433333322222 PP

                             AAA_19  72 iHrlalldfddlltealelle.........eaeeekklqeeellivDEfqdvdelq 118
                                          rl                +         e + +k l++ +++ivDE+ + +  +
  gene1760|gene1760|rna1759|rna1759 145 --RL----------------KyatdgilirEINGDKYLKKYDVVIVDEAHERSINI 182
                                        ..22................22223333338899999*6666******98766555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     3e-07    0.0003      18      97 ..      73     175 ..      64     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3e-07
                             AAA_30  18 drvavltGpAGtGKtt.....alkalreaweaaggrviglAptgkaAkvLa....eelgi......eastiakllk 78 
                                         +v +++G  G GKtt     +lk++++++ ++ +r+++++  +k+A++++    ee+g       ++s+  +l +
  gene1760|gene1760|rna1759|rna1759  73 SQVLLIEGNTGCGKTTkipkyLLKKYERIVCTQPRRIAAISIAKKVARDMNvklgEEVGYsirfddRSSSKTRLKY 148
                                        3599***********9555556788888888899**************9994444444443344445555555555 PP

                             AAA_30  79 rlk........grarlepgtllivDEa 97 
                                        +++        g + l++ +++ivDEa
  gene1760|gene1760|rna1759|rna1759 149 ATDgilireinGDKYLKKYDVVIVDEA 175
                                        5559999999866788888*******9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   6.9e-07   0.00069       4     127 ..      72     203 ..      69     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.9e-07
                             AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......... 70 
                                        + ++l++ G +G+GKTt + ++l ++           e + +t p      +++++++r+++++l +         
  gene1760|gene1760|rna1759|rna1759  72 KSQVLLIEGNTGCGKTTKIPKYLLKK----------YERIVCTQPRRIAAISIAKKVARDMNVKLGEevgysirfd 137
                                        56899*******************95..........4545555555557788888888888888877888888889 PP

                             AAA_22  71 erlsseellealeqalrarav........ielliiDEaqhlrs...eealeeLrsllnlsrkgvqliL 127
                                         r ss+  l++ ++ +  r            ++i+DEa+   s   + +l +L+ +l  +r+++++i+
  gene1760|gene1760|rna1759|rna1759 138 DRSSSKTRLKYATDGILIREIngdkylkkYDVVIVDEAHER-SiniDILLGYLKLILA-KRSDIRVII 203
                                        5555555556666666666666777778888********97.5446778888865555.588888876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   1.7e-05     0.017      22     170 ..      71     209 ..      54     210 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.7e-05
                                        .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH....HHHHHHHHHGGGGTGG....GEEEESSS- CS
                             ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprk....slleqtleefkkflseaykeigkkvsgdk 93 
                                        ++ + +li+  TG+GKT   +k+ ++llkk++  +++   pr+    s+ ++  ++++  l e+   +g +++ d 
  gene1760|gene1760|rna1759|rna1759  71 EKSQVLLIEGNTGCGKT---TKIPKYLLKKYE--RIVCTQPRRiaaiSIAKKVARDMNVKLGEE---VGYSIRFDD 138
                                        45556677778888887...477777777644..777777776333344444444444444433...333343333 PP

                                        B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS..T...TTHH.HHHT---SEEEE CS
                             ResIII  94 kkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak.k...swre.ilekfkeavllg 164
                                        +++     +++++  +t   l +++      + ++  +++dv+i+DEaH  + + +    + + il k ++  ++ 
  gene1760|gene1760|rna1759|rna1759 139 RSS-----SKTRLKYATDGILIREI------NGDKYLKKYDVVIVDEAHERSINiDillGYLKlILAKRSDIRVII 203
                                        333.....55555555555555555......555677899*********9999751566666649999999***** PP

                                        EESS-S CS
                             ResIII 165 lTATpe 170
                                        ++AT++
  gene1760|gene1760|rna1759|rna1759 204 MSATLN 209
                                        ****86 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.5e-05     0.015       2     126 ..      74     209 ..      73     221 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                        EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE..........SSTTSC CS
                              SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik..........kkeead 67 
                                        +v+l+ G +G GKTt + K    l k+ +   +v++   R+aA+   k +a+ ++v++ +          +++ + 
  gene1760|gene1760|rna1759|rna1759  74 QVLLIEGNTGCGKTTKIPKY---LLKKYE--RIVCTQPRRIAAISIAKKVARDMNVKLGEevgysirfddRSSSKT 144
                                        689999*********99884...343333..478999999***999999999999998766666677765444445 PP

                                        HHHHHHHHH.....HHHH.HTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBH CS
                              SRP54  68 paavakeav.....ekak.eekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattg 126
                                          ++a +++     +  k  +k+dvv+vD a    ++ +++    k+  + ++d  +++++at+ 
  gene1760|gene1760|rna1759|rna1759 145 RLKYATDGIlireiNGDKyLKKYDVVIVDEAHERSINIDILLGYLKLILAKRSDIRVIIMSATLN 209
                                        56666665521111222214669999999887666665555544444444455555555666655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.016      30      67 ..      58      96 ..      55     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                              Rad17 30 evkewlkadvLesrkkriLLisGPsGCgkstvv.kvLsk 67
                                        v++ ++  + + +k ++LLi G +GCgk+t + k L k
  gene1760|gene1760|rna1759|rna1759 58 TVEDKMDEIFDKLEKSQVLLIEGNTGCGKTTKIpKYLLK 96
                                       5777888777777888***************98444544 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.2e-05     0.032       7      45 ..      62      99 ..      57     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                             ATPase  7 glDeilkgGipegrvvlitGepGtGKtifalqFlikgae 45
                                        +Dei+ + + + +v li G++G+GKt+   ++l+k  e
  gene1760|gene1760|rna1759|rna1759 62 KMDEIF-DKLEKSQVLLIEGNTGCGKTTKIPKYLLKKYE 99
                                       69***9.99*******************99999988765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.4e-05     0.024       2      98 ..      74     176 ..      73     180 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                            DUF2075   2 avvlVtGvaGtGKtvvllnllael.......eddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssf 70 
                                        +v+l++G++G GKt    + l +        +  +    ++   v ++ + +l e++ ++    +++++ + +++ 
  gene1760|gene1760|rna1759|rna1759  74 QVLLIEGNTGCGKTTKIPKYLLKKyerivctQPRRIAAISIAKKVARDMNVKLGEEVGYSI---RFDDRSS-SKTR 145
                                        799***********98877776665665433222233333333444455556666666666...2222222.2222 PP

                            DUF2075  71 innlsef...kkaeekkeepkedvvivDEAh 98 
                                         + ++ +   ++ + +k  +k dvvivDEAh
  gene1760|gene1760|rna1759|rna1759 146 LKYATDGiliREINGDKYLKKYDVVIVDEAH 176
                                        222222245577779**************** PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0038       3.8       7      41 ..      63      97 ..      57     147 .. 0.81
   2 ?    3.4   0.0     0.056        56     216     247 ..     165     193 ..     157     194 .. 0.69
   3 ?   -3.4   0.0       6.6   6.5e+03      19      40 ..     565     586 ..     559     625 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0038
                             AAA_11  7 reaiksalseseitliqGPPGtgKTktivellsql 41
                                        + i   l++s++ li+G  G+gKT+ i ++l + 
  gene1760|gene1760|rna1759|rna1759 63 MDEIFDKLEKSQVLLIEGNTGCGKTTKIPKYLLKK 97
                                       566777899999**************999887665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.056
                             AAA_11 216 kkfdvviIDEAaqavEpstliPlrlgakkvvL 247
                                        kk+dvvi+DEA    E s+ i ++lg  k++L
  gene1760|gene1760|rna1759|rna1759 165 KKYDVVIVDEA---HERSINIDILLGYLKLIL 193
                                        589*******8...566666666666555555 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 6.6
                             AAA_11  19 itliqGPPGtgKTktivellsq 40 
                                         ++++GPP +   k+++++++ 
  gene1760|gene1760|rna1759|rna1759 565 CSMFEGPPKSDENKVVLSFCAG 586
                                        6889999998888999888765 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.12      78     149 ..      58     129 ..      40     132 .. 0.90
   2 ?   -3.5   0.1       7.8   7.7e+03      93     137 ..     198     247 ..     169     259 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                        THHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HH CS
                     DNA_pol3_delta  78 kllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkraqelglkieke 149
                                           +++ e++++l ++ +L+++++    + +k+ k+L kk+  + +++++    +   +k+a+++++k+++e
  gene1760|gene1760|rna1759|rna1759  58 TVEDKMDEIFDKLEKSQVLLIEGNTGCGKTTKIPKYLLKKYERIVCTQPRRIAAISIAKKVARDMNVKLGEE 129
                                        55567899****************88999999*************************************987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.8
                                        SEEEEEEES.S--HHHH......HHHHHTTTEEEEEE----TTTHHHHHHH CS
                     DNA_pol3_delta  93 dtlLiliapkklderkk......lvklLkkkatvveaktlkeeelkkwiqk 137
                                        d+  i+++   l+++k        +  +k k   +e++ lk +e+ +++++
  gene1760|gene1760|rna1759|rna1759 198 DIRVIIMSA-TLNSEKFvsffkcQTVGIKHKMFPLEIFFLKRSEVMDYLSE 247
                                        444555555.45444444333333333444444555555555555555555 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00014      0.14     111     149 ..      56      93 ..      47     117 .. 0.82
   2 ?   -2.5   0.0       2.1   2.1e+03     250     272 ..     236     258 ..     228     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                              T2SSE 111 eealkekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                         e++++k++e+  k  ++ +++l+ G Tg GKtt +   
  gene1760|gene1760|rna1759|rna1759  56 GETVEDKMDEIFDKL-EKSQVLLIEGNTGCGKTTKIPKY 93 
                                        577889999999999.99999*************87443 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                              T2SSE 250 veaaelkssilavvdivvrlvrk 272
                                        +++ e+ +++ +vv++vv++ r+
  gene1760|gene1760|rna1759|rna1759 236 LKRSEVMDYLSEVVKTVVQIHRT 258
                                        78899999***********9986 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.16       2     100 ..      78     176 ..      77     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                      Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke.......eekkkkaekaelr 70 
                                        + ++ G GK++ + +     + +++ +i++t p++ ++ ++ + +a+ ++    +e        ++++++++ + +
  gene1760|gene1760|rna1759|rna1759  78 IEGNTGCGKTTKIPK----YLLKKYERIVCTQPRRIAAISIAKKVARDMNVKLGEEvgysirfDDRSSSKTRLKYA 149
                                        566777888776544....44456789**************99999988754444478866554444444445555 PP

                      Helicase_RecD  71 vrkqrieyiapdellklkeqadllvvDEAA 100
                                        +++  i+ i+ d+ lk+    d+++vDEA 
  gene1760|gene1760|rna1759|rna1759 150 TDGILIREINGDKYLKKY---DVVIVDEAH 176
                                        558888888888888865...9*******5 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.4    0.0013       1.3       2      97 ..      73     203 ..      72     233 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                             AAA_14   2 rkilvitGaRrvGKTtllkqlikell.....vkkesilyinldderd......................kkladpe 50 
                                        +++l+i+G   +GKTt + +++ +++     +++++i  i++ ++                        +     +
  gene1760|gene1760|rna1759|rna1759  73 SQVLLIEGNTGCGKTTKIPKYLLKKYerivcTQPRRIAAISIAKKVArdmnvklgeevgysirfddrssS-----K 143
                                        5799************998887777769988888888888887765544555555555544444332221.....1 PP

                             AAA_14  51 .....kllelileklke..............ekktylflDEiqev....pewekalkslvdegknldviv 97 
                                                        +              +k  +++ DE++e     + +  +lk ++ ++++++vi+
  gene1760|gene1760|rna1759|rna1759 144 trlkyA----------TdgilireingdkylKKYDVVIVDEAHERsiniDILLGYLKLILAKRSDIRVII 203
                                        112111..........012222223334555566667888887653332444445555555555666665 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00029      0.29       2      40 ..      77     117 ..      76     131 .. 0.75
   2 ?   -3.1   0.0       5.4   5.4e+03      61      72 ..     165     176 ..     160     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                    Viral_helicase1   2 vvhGvpGcGKStlirkllrts..liltvnrptaelltegkp 40 
                                        ++ G  GcGK+t i k l ++  +i+ + ++++++++ +k+
  gene1760|gene1760|rna1759|rna1759  77 LIEGNTGCGKTTKIPKYLLKKyeRIVCTQPRRIAAISIAKK 117
                                        78999************999888666666666666666654 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.4
                    Viral_helicase1  61 tkgkililDEyl 72 
                                        +k++++i+DE+ 
  gene1760|gene1760|rna1759|rna1759 165 KKYDVVIVDEAH 176
                                        358999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 4178.07
//
Query:       gene1761|gene1761|rna1760|rna1760  [L=320]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-39  133.5   0.0      1e-21   77.6   0.0    2.2  2  CTP_transf_like  Cytidylyltransferase-like
      0.003   17.4   0.3        3.8    7.4   0.0    3.2  3  FAD_syn          FAD synthetase
  ------ inclusion threshold ------
      0.015   15.9   0.0      0.053   14.2   0.0    2.0  1  PglD_N           PglD N-terminal domain


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.6   0.0   1.7e-25     1e-21       2     139 ..      11     132 ..      10     136 .. 0.96
   2 !   54.0   0.0   3.2e-18   1.9e-14       2      90 ..     182     266 ..     181     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 1.7e-25
                                        EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHH CS
                    CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltrev 76 
                                        a+G+FD++H+GH++ l+q k l+++ li gv+s+ + +++k  p++  +eR+e ++ +++vde+++++p++++++ 
  gene1761|gene1761|rna1760|rna1760  11 ADGCFDMFHYGHANALRQSKGLGDY-LIAGVHSSLSINQEKgLPVMEDDERYEVVQGCRYVDEIVRDAPFVTQMDM 85 
                                        89***********************.**************77********************************** PP

                                        HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHH CS
                    CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstk 139
                                        ++++++   ++++g d + d     + ++ +  v+  ++          +k+ +rt giS+t+
  gene1761|gene1761|rna1760|rna1760  86 IREYGVS--VVAHGNDIILDS----NGQDSYFQVRKTGM----------FKEVERTIGISTTE 132
                                        *******..**********97....99999999999999..........99**********98 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 3.2e-18
                                        EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHH CS
                    CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltre 75 
                                        ++G+FD++H GH   l+ a++++++ livg++ de++k ++   p+ s +eR+ +l  +++vde ++v+p+ + +e
  gene1761|gene1761|rna1760|rna1760 182 VDGNFDLFHAGHVVSLRIAREMGDY-LIVGIHDDETTKEYTrnYPVLSTKERILTLMSCRYVDE-VVVSPYLIGNE 255
                                        79***********************.**************5589********************.9********** PP

                                        HHHHTTTTEEEEEEE CS
                    CTP_transf_like  76 vlkklkpdklylvig 90 
                                        +++k+++     ++g
  gene1761|gene1761|rna1760|rna1760 256 FIEKHGIS----IVG 266
                                        ******98....333 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0023        14       8      30 ..       8      30 ..       2      38 .. 0.83
   2 ?    0.2   0.0      0.11   6.3e+02      97     134 ..      79     117 ..      72     133 .. 0.73
   3 !    7.4   0.0   0.00064       3.8       7      84 ..     178     249 ..     172     259 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0023
                            FAD_syn  8 avvtlGnFDGvHlGHqallkkav 30
                                       +v + G FD +H GH + l++ +
  gene1761|gene1761|rna1760|rna1760  8 KVWADGCFDMFHYGHANALRQSK 30
                                       567779**********9998876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                            FAD_syn  97 Fiekl.lveklkvkavvvGfdfrfGkkregdvellkelg 134
                                        F++++ ++++++v++v+ G+d  + ++++++  ++++ g
  gene1761|gene1761|rna1760|rna1760  79 FVTQMdMIREYGVSVVAHGNDIILDSNGQDSYFQVRKTG 117
                                        665544556999999999999988888887776666655 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00064
                            FAD_syn   7 gavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlv 82 
                                        + + + GnFD +H GH   l+    +a+e g  ++v + + + ++  +  ++   L+t e+ l+l++   vd+v+v
  gene1761|gene1761|rna1760|rna1760 178 KVAFVDGNFDLFHAGHVVSLR----IAREMGDYLIVGIHDDETTKEYT--RNYPVLSTKERILTLMSCRYVDEVVV 247
                                        445555**********87665....45555566666666665555554..23333566666666666666777777 PP

                            FAD_syn  83 vd 84 
                                         +
  gene1761|gene1761|rna1760|rna1760 248 SP 249
                                        65 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   8.9e-06     0.053      14      56 ..     195     239 ..     190     265 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.9e-06
                             PglD_N  14 v.adiieangeyeiigflDdnkk.tevegypvlgkaiellkslse 56 
                                        v ++i++ +g+y i+g+ Dd+ + + + +ypvl++   +l  +s 
  gene1761|gene1761|rna1760|rna1760 195 VsLRIAREMGDYLIVGIHDDETTkEYTRNYPVLSTKERILTLMSC 239
                                        44799***************986155678****987766665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1920.68
//
Query:       gene1762|gene1762|rna1761|rna1761  [L=535]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-97  325.2   0.0    3.5e-97  324.9   0.0    1.1  1  CTP_synth_N    CTP synthase N-terminus
    2.1e-46  158.1   0.0      4e-46  157.2   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    6.5e-08   32.6   0.1      9e-06   25.6   0.1    2.8  2  Peptidase_C26  Peptidase C26
     0.0014   18.2   0.4     0.0057   16.3   0.4    1.9  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
      0.085   12.9   0.0       0.12   12.4   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
       0.12   12.2   0.0       0.28   11.0   0.0    1.5  1  DJ-1_PfpI      DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.9   0.0  1.2e-100   3.5e-97       1     265 []       2     275 ..       2     275 .. 0.98

  Alignments for each domain:
  == domain 1  score: 324.9 bits;  conditional E-value: 1.2e-100
                                        EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHH CS
                        CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRf 76 
                                        kyi+v+GGv+Sg GkG++++s+gallksrg  vt ikiDPYln++a +l p+ehGEv+vlddG+e+DlDlGnYeRf
  gene1762|gene1762|rna1761|rna1761   2 KYIFVSGGVISGAGKGVVSSSIGALLKSRGHIVTHIKIDPYLNYNARMLAPCEHGEVYVLDDGSECDLDLGNYERF 77 
                                        8*************************************************************************** PP

                                        HT----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.H.C........T.-SEEEEEE-S CS
                        CTP_synth_N  77 ldikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakk.v........e.advviveigG 142
                                        ++i+l+ +n+it+Gk++ +vi++e++G+ lGkt+qv phv+d++ +ri+ v ++ v        + +dvv++e+gG
  gene1762|gene1762|rna1761|rna1761  78 VGINLEGANAITSGKVFFDVIKREQEGHLLGKTLQVNPHVIDDVIRRIKVVGETpVesfedghtSiPDVVVIELGG 153
                                        *************************************************999986588888875269********* PP

                                        -TTSGGGHHHHHHHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HH CS
                        CTP_synth_N 143 tvgdieslpfleairqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleee 218
                                        tvg++es  + +a+ +l++++gk+n++++ v +++ l+ +ge+ktk++q+ ++++r++G++ dii+cr +++ +e+
  gene1762|gene1762|rna1761|rna1761 154 TVGEYESSIYTDALAKLQHDVGKNNCAFVSVDYLTELE-SGEQKTKSIQMGCRNFRAFGLTHDIIICRGTRAPTED 228
                                        *************************************5.9************************************ PP

                                        HHHHHHHHCT--GGGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                        CTP_synth_N 219 vkekialfcnvekeavisvkdvesiyevpllleeqglaelileklkl 265
                                        +++ki++ c v+  +vi  +++es+y+vp  leeqgl +++ ++l l
  gene1762|gene1762|rna1761|rna1761 229 TRRKISKNCWVPLPNVIGLPNLESVYSVPRFLEEQGLVDSLYKTLGL 275
                                        *****************************************999975 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.0   1.3e-49     4e-46       4     189 ..     312     528 ..     311     529 .. 0.86

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 1.3e-49
                                        ESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                             GATase   4 Dnydsvtenlvhalvelgvkvevvpidasaeeile.llknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                        D+y s+++ l+ +++++gv+ve+ +++a+     e  l+++dgi+++gG+g++gv gkieai++aren+iP+LGIC
  gene1762|gene1762|rna1761|rna1761 312 DSYTSLVHGLKFSGASIGVNVEIEWVNAEEYC--EsDLSKCDGIIIPGGFGARGVSGKIEAIRYARENGIPLLGIC 385
                                        9**************************75443..3369************************************** PP

                                        HHHHHHHHHTTTEEE............................EEECEEEEEEEEEEEETTT..CGGTTTTSEEEE CS
                             GATase  79 LGmQllaiefgrkvv............................kekekehhggtmrlgddet..allyglknevie 124
                                        LG Ql +ie++r+v                               k+    g + +l d     ++lyg k++++e
  gene1762|gene1762|rna1761|rna1761 386 LGYQLCVIEMCRNVLgmkdafseefqpdgkdlvvrfisdengvVDKRLRVGGSQVKLMD--GlvKRLYGGKETIRE 459
                                        ************99988999888888888888888875555443333455555555555..166************ PP

                                        EEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                             GATase 125 rhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                        rhrHr+ev  +   +l  +gl++++ s+d+ +  +i+e++  + fvgvQFHPE++ +p++p++l ++li 
  gene1762|gene1762|rna1761|rna1761 460 RHRHRFEVVWEkvqDLRAHGLKFVGFSNDG-KATKIFELSThRyFVGVQFHPEFIARPNQPHPLITGLIS 528
                                        ********98889999999********776.8999999999888********************999875 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.016        48      36      67 ..     327     358 ..     312     363 .. 0.86
   2 !   25.6   0.1     3e-09     9e-06      96     216 .]     369     511 ..     361     511 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.016
                      Peptidase_C26  36 agglpvllpieedeedvkaildkldgllltGg 67 
                                        + g+ v +   + ee++++ l+k+dg++++Gg
  gene1762|gene1762|rna1761|rna1761 327 SIGVNVEIEWVNAEEYCESDLSKCDGIIIPGG 358
                                        56778888888899*****************9 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 3e-09
                      Peptidase_C26  96 aLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe............q..saashavkve... 154
                                          ir a e+g+P+lgiC+G+ql  + +  ++    ++   +++  +++            +  +   ++++v    
  gene1762|gene1762|rna1761|rna1761 369 EAIRYARENGIPLLGICLGYQLCVIEMCRNVLGMKDA---FSEEFQPDgkdlvvrfisdeNgvV--DKRLRVGgsq 439
                                        5689999****************88877665444333...333333333445665555442332..3333333445 PP

                      Peptidase_C26 155 ...kgsllaellg.seeievnslHhqaike......laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                            ++l+++l+g +e+i+    H++ +         a++l+ +  ++Dg    i   +++  ++gvQ+HPE
  gene1762|gene1762|rna1761|rna1761 440 vklMDGLVKRLYGgKETIRERHRHRFEVVWekvqdlRAHGLKFVGFSNDGKATKIFELSTHRYFVGVQFHPE 511
                                        556788999999868888888888887754677777899***********9888777776779********9 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   1.9e-06    0.0057      34      87 ..     344     390 ..     325     402 .. 0.80
   2 ?   -2.3   0.0      0.96   2.9e+03      45      77 ..     434     466 ..     418     470 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                           GATase_3  34 deslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqm 87 
                                        +++l +++d +i+pGg+  +        sg  eai+ a e+g+p+lgiC G+q+
  gene1762|gene1762|rna1761|rna1761 344 ESDL-SKCDGIIIPGGFGARG------VSGKIEAIRYARENGIPLLGICLGYQL 390
                                        3455.66*********98665......5788999*******************7 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.96
                           GATase_3  45 ilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                         ++G++  + d  ++r  g +e i+e ++   +
  gene1762|gene1762|rna1761|rna1761 434 RVGGSQVKLMDGLVKRLYGGKETIRERHRHRFE 466
                                        579999999999999999999999999887665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.1e-05      0.12       8      43 ..      12      47 ..       6     452 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                       TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  8 GGvGKTtlaanLaralarrglrVllvDaDpqannla 43
                                       +G+GK +++ +++++l+ rg+ V  ++ Dp  n  a
  gene1762|gene1762|rna1761|rna1761 12 SGAGKGVVSSSIGALLKSRGHIVTHIKIDPYLNYNA 47
                                       8*****************************976554 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.5e-05      0.28      46     106 ..     326     390 ..     314     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.5e-05
                                        EEEE-SEEGG........GCTCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHH CS
                          DJ-1_PfpI  46 lkvtvdasld........dvkaaeyDalvlpGGragperlrenekvvelvkefaekgklvaaICagpql 106
                                        +++ v++ ++        + + ++ D +++pGG   +  ++ +   +e ++ + e+g ++  IC g ql
  gene1762|gene1762|rna1761|rna1761 326 ASIGVNVEIEwvnaeeycESDLSKCDGIIIPGGFG-ARGVSGK---IEAIRYARENGIPLLGICLGYQL 390
                                        5555555555555555556667799*********9.7777765...999****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3351.67
//
Query:       gene1763|gene1763|rna1762|rna1762  [L=546]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-136  455.5   0.4   1.8e-136  455.0   0.4    1.2  1  tRNA-synt_1g  tRNA synthetases class I (M)
    8.6e-06   24.3   0.2    7.7e-05   21.1   0.0    2.5  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    0.00018   21.5   0.0    0.00034   20.6   0.0    1.5  1  Anticodon_1   Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
        1.3    9.2   5.1       0.64   10.2   0.6    2.8  3  Zn-ribbon_8   Zinc ribbon domain
        4.9    6.6   6.2       0.41   10.0   1.0    1.9  2  zf-RanBP      Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  455.0   0.4  4.9e-140  1.8e-136       2     391 .]       5     396 ..       4     396 .. 0.96

  Alignments for each domain:
  == domain 1  score: 455.0 bits;  conditional E-value: 4.9e-140
                                        EEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                       tRNA-synt_1g   2 lvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeike 76 
                                        ++t+alpY+n+++HlG+++ +v+s+D+++Ry++++ge v+++cgtDe+Gt+ie++A ++g tp++++e++++ +k+
  gene1763|gene1763|rna1762|rna1762   5 FITSALPYVNNQPHLGNVIgSVLSGDVYSRYCKKKGETVVYICGTDEYGTAIEMEAISRGKTPQDVCEENRKLHKQ 80 
                                        79************************************************************************** PP

                                        HHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE CS
                       tRNA-synt_1g  77 lfkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqc 152
                                        +++++ni+fd++g t+  +h+e+vq++f k++++g+++e+e+eqlyc+++  fl+dryv g+C  c++ +argdqc
  gene1763|gene1763|rna1762|rna1762  81 VYDWFNIEFDYFGFTSLPAHTEVVQDLFMKMYNNGYFSEQEVEQLYCNTCVIFLADRYVVGKCKFCGDLRARGDQC 156
                                        **************************************************************************** PP

                                        -TTSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-E CS
                       tRNA-synt_1g 153 eecgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlais 228
                                        ++cg+++++ el+ p+++i+g++p+vk+t+hlff+l++f+ +l++ ++++ + +++n+++i ++w++ +  +++++
  gene1763|gene1763|rna1762|rna1762 157 DACGHTYNSLELVSPECSICGTTPIVKSTTHLFFDLEAFKPRLEKLYKTNGHLWSQNAQNIFNQWISMEFFPRCMT 232
                                        ***********************************************888888*********************** PP

                                        SS-S..SS-EET..TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHH CS
                       tRNA-synt_1g 229 rdld..wGipvP..gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifw 300
                                        rdl+  wG+pvP  + e+kv+YVW+dA+igY++++k l+      ++++e+    ke+elv+f+gkd++ FHti++
  gene1763|gene1763|rna1762|rna1762 233 RDLKfnWGVPVPlkKFEGKVFYVWFDAPIGYLTFLKDLV-----GKDFEEWR---KESELVQFMGKDNVSFHTIIF 300
                                        9975338******99***********************9.....689**988...58******************* PP

                                        HHHHHH..TT----S-EEEE--EEE--------------HHHHHHH..H-HHHHHHHHHHHS-T.TS-EEE-HHHH CS
                       tRNA-synt_1g 301 Paillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealer..ldadllRYylaaeape.kkDldfswedf 371
                                        Pa+l +  +e+ + k+++a+eyl++e++K+SkSr+ +++  ++++    ++ ++RYyl++ +pe +kD++f+++df
  gene1763|gene1763|rna1762|rna1762 301 PAMLYAtgEEYPMIKRLSATEYLMFENQKFSKSRKHGIFGLDLVNGnlGKSCVWRYYLLKIRPEsTKDSNFTFHDF 376
                                        ****998899*********************************9987345668*******7776269********* PP

                                        HHHHHHHCCCHHHHHHHHH. CS
                       tRNA-synt_1g 372 vervNseLadklgnlvnRvl 391
                                        ++ v ++L+++lgnlvnRvl
  gene1763|gene1763|rna1762|rna1762 377 QQSVTADLINNLGNLVNRVL 396
                                        ******************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.2e-08   7.7e-05      28      80 ..       7      60 ..       2     139 .. 0.89
   2 ?    0.2   0.1     0.046   1.7e+02     361     433 ..     169     245 ..     161     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-08
                        tRNA-synt_1 28 vdgPPyvtGslHiGhalaktlk.divirykrmkGkevlyvpGwDhaGlaieakv 80
                                       +   Pyv+ ++H+G+++ ++l  d+  ry + kG++v y  G+D  G aie++ 
  gene1763|gene1763|rna1762|rna1762  7 TSALPYVNNQPHLGNVIGSVLSgDVYSRYCKKKGETVVYICGTDEYGTAIEMEA 60
                                       45569****************768999************************974 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.046
                        tRNA-synt_1 361 svpfcerskkpiiyrateqWfvrvkeladaalkave.kvqfvpkskekryaswle.niqdWciSRqr..wWGhrip 432
                                          p c+  ++  i+++t+  f  +++++  + k  + + ++  + +++ +++w+  +    c+ R++   WG+++p
  gene1763|gene1763|rna1762|rna1762 169 VSPECSICGTTPIVKSTTHLFFDLEAFKPRLEKLYKtNGHLWSQNAQNIFNQWISmEFFPRCMTRDLkfNWGVPVP 244
                                        56778888888888899999999999999988888877788889999******97467889****984469*9999 PP

                        tRNA-synt_1 433 l 433
                                        l
  gene1763|gene1763|rna1762|rna1762 245 L 245
                                        7 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   9.4e-08   0.00034       1      93 [.     416     504 ..     416     542 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.4e-08
                        Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllr 75 
                                        d+  + e+n+l +++ +++ee ++++ ++ +++       + y++     + +e+    ++    + + ++  l  
  gene1763|gene1763|rna1762|rna1762 416 DKKCIEEVNELYRKYLRKMEEIKLREGLQVVMDI--SRRGNEYIQE---GIRNEDR---KShFFCLGFSIIGLLGT 483
                                        6788899**************************6..6778888876...3433332...2335588899999999* PP

                        Anticodon_1  76 llaPfmPfitEelwqr...ee 93 
                                        ll+PfmP ++ e+ +    ee
  gene1763|gene1763|rna1762|rna1762 484 LLHPFMPLTSSEILKMcnlEE 504
                                        *************95555533 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.79   2.8e+03       7      12 ..     142     147 ..     138     152 .. 0.71
   2 ?   10.2   0.6   0.00018      0.64       7      36 ..     155     181 ..     155     184 .. 0.82
   3 ?   -3.4   0.0       3.2   1.2e+04      12      20 ..     272     280 ..     272     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.79
                        Zn-ribbon_8   7 rCeeCg 12 
                                        +C+ Cg
  gene1763|gene1763|rna1762|rna1762 142 KCKFCG 147
                                        477776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00018
                        Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs.ev 36 
                                        +C++Cgh+++ l  +s    ++C  Cg  + 
  gene1763|gene1763|rna1762|rna1762 155 QCDACGHTYNSLELVS----PECSICGTtPI 181
                                        6*********998766....56****98665 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.2
                        Zn-ribbon_8  12 ghefevlqs 20 
                                        g++fe++++
  gene1763|gene1763|rna1762|rna1762 272 GKDFEEWRK 280
                                        789**9997 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.4       2.5     9e+03       7      10 ..     127     130 ..     125     130 .. 0.62
   2 ?   10.0   1.0   0.00011      0.41       6      26 ..     155     178 ..     155     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.5
                                        -SSS CS
                           zf-RanBP   7 CskC 10 
                                        C++C
  gene1763|gene1763|rna1762|rna1762 127 CNTC 130
                                        5665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                                        E-SSS-.-EEESS..SSB-TTT-- CS
                           zf-RanBP   6 dCskCl.vqNfaw..stkCvaCqa 26 
                                        +C++C+ ++N+++  s++C +C++
  gene1763|gene1763|rna1762|rna1762 155 QCDACGhTYNSLElvSPECSICGT 178
                                        8*********9763389*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3347.00
//
Query:       gene1764|gene1764|rna1763|rna1763  [L=902]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-09   36.0   0.1        1.9    9.0   0.1    7.8  8  HEAT      HEAT repeat
    9.8e-05   22.7   0.0       0.11   12.9   0.0    4.1  5  HEAT_2    HEAT repeats
     0.0015   18.3   0.2        0.1   12.3   0.2    3.7  5  RIX1      rRNA processing/ribosome biogenesis
     0.0039   16.9   0.0        1.1    8.9   0.0    3.4  3  NUC173    NUC173 domain


Domain annotation for each model (and alignments):
>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.021        93       4      30 ..     254     280 ..     252     281 .. 0.87
   2 !    9.0   0.1   0.00043       1.9       4      30 ..     289     315 ..     288     316 .. 0.92
   3 !    8.1   0.0    0.0008       3.6       7      30 ..     549     572 ..     548     573 .. 0.92
   4 ?   -0.4   0.0      0.42   1.9e+03      16      29 ..     679     692 ..     676     694 .. 0.83
   5 ?    0.9   0.0      0.17   7.5e+02       1      28 [.     699     726 ..     699     728 .. 0.83
   6 ?    1.9   0.0     0.077   3.5e+02       2      19 ..     776     793 ..     775     803 .. 0.84
   7 ?   -1.4   0.0      0.89     4e+03       1      19 [.     818     836 ..     818     847 .. 0.79
   8 ?   -2.8   0.0       2.6   1.2e+04       5      18 ..     857     870 ..     856     871 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.021
                                        HHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                               HEAT   4 lllkllsDpspeVReaAakaLgalaev 30 
                                        ++ ++ ++++p++Re + + +g+++ +
  gene1764|gene1764|rna1763|rna1763 254 AIEECFTSKEPHIREVVGNVVGTFIYH 280
                                        689999***********9999998765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00043
                                        HHHHHHT-SSHHHHHHHHHHHHHHHHC CS
                               HEAT   4 lllkllsDpspeVReaAakaLgalaev 30 
                                        lll+l  + + e R++++++++ ++e+
  gene1764|gene1764|rna1763|rna1763 289 LLLSLAGSRNDEARKTCIRCITGICEF 315
                                        7899999******************97 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0008
                                        HHHT-SSHHHHHHHHHHHHHHHHC CS
                               HEAT   7 kllsDpspeVReaAakaLgalaev 30 
                                        +ll+D+s+e+R   +ka+g la++
  gene1764|gene1764|rna1763|rna1763 549 RLLRDSSSEIRIRGLKAIGGLAKI 572
                                        689*******************97 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.42
                                        HHHHHHHHHHHHHH CS
                               HEAT  16 VReaAakaLgalae 29 
                                         R++A ++Lg +++
  gene1764|gene1764|rna1763|rna1763 679 ARKNATESLGCISR 692
                                        59********9976 PP

  == domain 5  score: 0.9 bits;  conditional E-value: 0.17
                                        HHHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   1 llPlllkllsDpspeVReaAakaLgala 28 
                                        +l++l+ +l++++ ++R  + + +  l 
  gene1764|gene1764|rna1763|rna1763 699 ILDILIDNLESEDKNQRTGSSLGISVLG 726
                                        7999*************87777776665 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.077
                                        HHHHHHHHT-SSHHHHHH CS
                               HEAT   2 lPlllkllsDpspeVRea 19 
                                        lP++  +++D++p  R+ 
  gene1764|gene1764|rna1763|rna1763 776 LPMIEDAMMDEDPVYRSL 793
                                        8************99875 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 0.89
                                        HHHHHHHHHT-SSHHHHHH CS
                               HEAT   1 llPlllkllsDpspeVRea 19 
                                        ll+l++ ++ Dp p + ++
  gene1764|gene1764|rna1763|rna1763 818 LLNLIWANILDPVPTIQQS 836
                                        7899999999999988665 PP

  == domain 8  score: -2.8 bits;  conditional E-value: 2.6
                                        HHHHHT-SSHHHHH CS
                               HEAT   5 llkllsDpspeVRe 18 
                                        +++ l +ps +VR+
  gene1764|gene1764|rna1763|rna1763 857 VQQGLFHPSGRVRK 870
                                        678899*******7 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.051   2.3e+02      34      80 ..     253     303 ..     229     310 .. 0.59
   2 ?    2.7   0.0     0.037   1.7e+02      23      55 ..     273     309 ..     251     351 .. 0.64
   3 ?    0.2   0.0      0.23     1e+03       7      27 ..     550     569 ..     546     595 .. 0.76
   4 !   12.9   0.0   2.4e-05      0.11       4      49 ..     668     716 ..     665     758 .. 0.79
   5 ?   -1.0   0.0      0.54   2.4e+03      12      48 ..     745     791 ..     735     796 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.051
                             HEAT_2  34 paLvellededpavRraaaeaLgai....gdpealpaLkellddddddvvR 80 
                                        +a+ e+ ++++p++R+ + +  g +    g +++ ++L+ l+ + +d+ ++
  gene1764|gene1764|rna1763|rna1763 253 QAIEECFTSKEPHIREVVGNVVGTFiyhfGMEKVHDLLLSLAGSRNDEARK 303
                                        555556666666666666666653323335566666666655555555433 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.037
                             HEAT_2  23 aLg....rignpealpaLvellededpavRraaaeaL 55 
                                        + g     +g +++ ++L++l+ + + + R++ ++ +
  gene1764|gene1764|rna1763|rna1763 273 VVGtfiyHFGMEKVHDLLLSLAGSRNDEARKTCIRCI 309
                                        4444444456666666777777777777776666655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.23
                             HEAT_2   7 alendpdpevrraairaLgri 27 
                                        +l +d++ e+r++ ++a+g +
  gene1764|gene1764|rna1763|rna1763 550 LL-RDSSSEIRIRGLKAIGGL 569
                                        33.777777777777777743 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 2.4e-05
                             HEAT_2   4 LlqalendpdpevrraairaLg...ri.gnpealpaLvellededpavRr 49 
                                        L+  l ++ + e r++a ++Lg   ri g++e+l++L++ le+ed + R 
  gene1764|gene1764|rna1763|rna1763 668 LVDSL-TSWNREARKNATESLGcisRIvGPQEILDILIDNLESEDKNQRT 716
                                        55666.77888899999999998886558899999999999999888776 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.54
                             HEAT_2  12 pdpevrraairaLg.....rignpea.....lpaLvellededpavR 48 
                                        p+p v++ +++a+      +++ p+a     lp++ +++ dedp  R
  gene1764|gene1764|rna1763|rna1763 745 PSPFVQQGILKAMCyffqrTYQVPSAyvhsmLPMIEDAMMDEDPVYR 791
                                        77888888888888655543344433444459999999999999776 PP

>> RIX1  rRNA processing/ribosome biogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.082   3.7e+02      44      86 ..     284     326 ..     253     342 .. 0.85
   2 ?   -1.6   0.0      0.44     2e+03      63      99 ..     414     453 ..     368     467 .. 0.70
   3 !   12.3   0.2   2.3e-05       0.1      46      98 ..     619     672 ..     510     695 .. 0.80
   4 ?   -2.9   0.0       1.1   4.8e+03      49      74 ..     778     803 ..     761     810 .. 0.67
   5 ?   -3.9   0.1       2.2   9.9e+03     139     165 ..     817     847 ..     813     850 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.082
                               RIX1  44 hklvtrilsLlqskspegrwaGvcLakvtveesgeellssgst 86 
                                        +k +  +lsL  s+++e+r + ++ +  ++e  g  ++s++++
  gene1764|gene1764|rna1763|rna1763 284 EKVHDLLLSLAGSRNDEARKTCIRCITGICEFVGRDIVSYSGP 326
                                        56777899**********************9888777777766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.44
                               RIX1  63 waGvcLakvtveesgeellssgstWlrallsiLekp...d 99 
                                          Gv L+kv  + +  +  + + +++ ++ siL ++   +
  gene1764|gene1764|rna1763|rna1763 414 ERGVSLLKVFERICDRISSEDAWEYFDQISSILFSSkgrE 453
                                        3588888888888888888888888888888887775542 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 2.3e-05
                               RIX1  46 lvtrilsLlqskspegrwaGvcLakvtveesgeells.sgstWlrallsiLekp 98 
                                         v  il  l+sk+++++  Gv L+++++ +s+ee+ +   ++W+r  + ++ + 
  gene1764|gene1764|rna1763|rna1763 619 IVPNILPILKSKEQKAVASGVMLLHTICVNSPEECEKiGMKEWIRISYELVDSL 672
                                        67789999************************6666526689999999888877 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.1
                               RIX1  49 rilsLlqskspegrwaGvcLakvtve 74 
                                         i   + +++p  r +G++L++ +v 
  gene1764|gene1764|rna1763|rna1763 778 MIEDAMMDEDPVYRSLGINLIRHVVL 803
                                        45555666777788888888877765 PP

  == domain 5  score: -3.9 bits;  conditional E-value: 2.2
                               RIX1 139 allqlleee....letvlealstllplhPtt 165
                                        +ll+l+  +    + t+ +++ +++  + t+
  gene1764|gene1764|rna1763|rna1763 817 HLLNLIWANildpVPTIQQSFDECMESFATI 847
                                        5555555456666666666666666666665 PP

>> NUC173  NUC173 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.037   1.7e+02      40      82 ..     248     290 ..     212     304 .. 0.78
   2 ?    2.5   0.0     0.023     1e+02      11      76 ..     295     360 ..     285     362 .. 0.88
   3 !    8.9   0.0   0.00025       1.1      25      91 ..     642     712 ..     618     719 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.037
                             NUC173  40 lkkilktlgelreseefelkkeadevigaairamGpevvLevl 82 
                                        +   ++ + e+ +s+e + ++ + +v+g+ i + G e+v ++l
  gene1764|gene1764|rna1763|rna1763 248 FGYSVQAIEECFTSKEPHIREVVGNVVGTFIYHFGMEKVHDLL 290
                                        667899999999999999*******************998766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.023
                             NUC173  11 slkyqaawkevlevlsalfeklgkrsspllkkilktlgelreseefelkkeadevigaairamGpe 76 
                                          +  +a k ++++++ ++e +g  +  +  ++l  lg    +++   + +a ++++ a + +Gp+
  gene1764|gene1764|rna1763|rna1763 295 GSRNDEARKTCIRCITGICEFVGRDIVSYSGPVLDILGGFVVDRNRFIRVDAANAMSYAFKLIGPQ 360
                                        5566789999****************889***************777******************8 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00025
                             NUC173  25 lsalfeklgkrsspl.lkkilktlgelrese...efelkkeadevigaairamGpevvLevlPLnleeeee 91 
                                        l +++ +  ++++++ +k+ ++   el +s    + e +k+a+e +g++ r +Gp+ +L++l  nle+e++
  gene1764|gene1764|rna1763|rna1763 642 LHTICVNSPEECEKIgMKEWIRISYELVDSLtswNREARKNATESLGCISRIVGPQEILDILIDNLESEDK 712
                                        444444444444333377777766666666532235899***********************999997633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (902 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 5198.25
//
Query:       gene1765|gene1765|rna1764|rna1764  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-38  132.5  31.3    2.6e-32  112.3   2.7    2.9  3  Utp14     Utp14 protein


Domain annotation for each model (and alignments):
>> Utp14  Utp14 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.7   0.9    0.0042        75     140     183 ..      41      83 ..      37      95 .. 0.70
   2 !   25.4  18.1   2.8e-10   5.1e-06     211     262 ..      89     140 ..      78     160 .. 0.80
   3 !  112.3   2.7   1.4e-36   2.6e-32     604     753 ..     173     322 ..     150     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.0042
                              Utp14 140 Fplqqdkkkekktlaalaskfkprtelekkiasileesglaeek 183
                                        F  ++++kk++k++ +   +  p+t lek +++il+ ++  +e+
  gene1765|gene1765|rna1764|rna1764  41 FNAAEQRKKKNKRTRENFYEIVPSTSLEKMMDKILHGEKT-KES 83 
                                        5444444444555555559999*************99886.554 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 2.8e-10
                              Utp14 211 mRellfreeakakRikKIKSKtYrRihrKekekeeekeeealeetdpeaale 262
                                        +R+ ++   +k +Rik+IKSK+YrRi+r+ ++k +e+ ee+ +e++ +++ e
  gene1765|gene1765|rna1764|rna1764  89 ERNFKYEFDKKMRRIKRIKSKAYRRIRRQSRLKSKEAMEENTQEKQGAEQDE 140
                                        6888888899**************************8888877744443333 PP

  == domain 3  score: 112.3 bits;  conditional E-value: 1.4e-36
                              Utp14 604 lpvalkqreliaeAFAgDDVvae..FekEKkevveeedpkevdktLPGWGsWaGegvkkrkkkkrkflkkv.egvk 676
                                        ++++++q++l++ AF +D  ++e  F+kEK+e+++ee+p++++  LPGWG+WaG g++  k k++ +++++ eg+k
  gene1765|gene1765|rna1764|rna1764 173 SREENEQEKLVRLAFKDDMEEQEkvFAKEKEEIMNEEAPRVEEVVLPGWGEWAGPGLEVIKTKNN-TIRNIvEGIK 247
                                        67899**********8864444355************************************9966.788887***9 PP

                              Utp14 677 kkkRkDaklknVIInEkrdkkaakylvsqLPfpFeskeqYErslrlPlGpeWntketfqkltkPrVvvkqGavIkP 752
                                          +RkD + +++IInEk+ +  +++l  +LPf ++   +Y +++++ + +e nt + f++l++ +     G++I+P
  gene1765|gene1765|rna1764|rna1764 248 YSNRKDFNRSHIIINEKAPEVDKRFL-AELPFGYTE-SEYNEKINASVSRERNTLRIFKRLVRAKTCHTNGKIIEP 321
                                        999***************98777766.58*****87.57************************************* PP

                              Utp14 753 l 753
                                         
  gene1765|gene1765|rna1764|rna1764 322 F 322
                                        7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2052  (0.114451); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 1858.83
//
Query:       gene1766|gene1766|rna1765|rna1765  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.17   12.4   0.0    1.3  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.2e-06      0.17       2      58 ..      44      98 ..      43     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.2e-06
                                       EEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTSSSSTTTTTTHHHHHHHHH CS
                               Sld5  2 eLPlWlaelLkrqrrveieppewlspesleailedetkssdlpslpphflelavkll 58
                                       ++P +l + L r++ +e++    l +  l++i+++++++ dl+s  p+f+ l  +ll
  gene1766|gene1766|rna1765|rna1765 44 DVPYFLVDFLLRNGHCELDMG-VLPESLLSDIKAKPSAV-DLRSVCPYFFYLYSTLL 98
                                       79***************9875.788999***********.**********9886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1162.97
//
Query:       gene1767|gene1767|rna1766|rna1766  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-15   57.5   0.0    2.7e-15   56.5   0.0    1.5  1  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    5.5e-12   45.8   0.3      1e-11   45.0   0.3    1.5  1  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.052   14.2   0.6         13    6.4   0.0    2.8  2  EXOSC1       Exosome component EXOSC1/CSL4
      0.071   13.2   1.0       0.41   10.8   0.1    2.5  2  UBA_2        Ubiquitin associated domain (UBA)
       0.17   12.6   1.4        0.4   11.4   1.2    1.9  1  E1_UFD       Ubiquitin fold domain


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   7.6e-19   2.7e-15       1     114 [.     126     227 ..     126     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 7.6e-19
                                        HHHCTHHHHTTTTS-HHHHHHHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHH CS
                        EIF_2_alpha   1 lyeevgwklyekyghaydaFklaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIk 76 
                                        ly+++g+ ++e++g++y  F  + ++ +++d+    +++  ++++ ik++++ +++k+radi++ c +k G++ Ik
  gene1767|gene1767|rna1766|rna1766 126 LYKKMGYDKEEEFGSLYYFFARVKDNGDIMDD----DDIGLTIKNLIKEQFQASTYKVRADIDVICSSKGGINSIK 197
                                        7******************************9....788899999999**************************** PP

                                        HHHHHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES CS
                        EIF_2_alpha  77 eaLkageeasneeeveeeeevkikliapPeYvltvetl 114
                                        +++ ++ +         + +++ +li  P+Y++t  ++
  gene1767|gene1767|rna1766|rna1766 198 KVFAEALG--------LDPRLEFYLIKTPTYSVTRVSS 227
                                        ****4444........4589*************97766 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.3   2.8e-15     1e-11       2      74 ..      14      87 ..      13      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.8e-15
                                       STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEE CS
                                 S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsi 74
                                       p++ge+v+G V+s+  +G+  +l+  ++ eg+v + els + rv+++ +v kvG+     vlkvd+++++i+ls+
  gene1767|gene1767|rna1766|rna1766 14 PKEGEIVMGRVVSIGGDGLTLNLLeyGDLEGLVLLGELSKR-RVKNIQQVTKVGNIEICNVLKVDEEKGYIDLSM 87
                                       89**********************999**************.********************************8 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0037        13       2      27 ..      14      39 ..      13      67 .. 0.72
   2 ?    5.4   0.4    0.0075        27      12      58 ..      62     109 ..      53     184 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0037
                                       S-TT-EEEEEEEEEESSEEEEEEEEE CS
                             EXOSC1  2 PkegdvVLarvtrlrkkqalveilsv 27
                                       Pkeg++V++rv+ +     ++++l  
  gene1767|gene1767|rna1766|rna1766 14 PKEGEIVMGRVVSIGGDGLTLNLLEY 39
                                       9***********99877666666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0075
                                        EEEEESSEEEEEEEEECTBSBCCCEEECCCTTSS--STS...TTSSCCHC CS
                             EXOSC1  12 vtrlrkkqalveilsvegennvlsdsgvgangegavkei...eaggglds 58 
                                        vt++ + + ++++l v++e ++ +d+ ++++ e+   e     a ++l+ 
  gene1767|gene1767|rna1766|rna1766  62 VTKVGN-IEICNVLKVDEE-KGYIDLSMSKVTENEKVECketSAKNKLAY 109
                                        444443.456788888555.666666655555554444420033333333 PP

>> UBA_2  Ubiquitin associated domain (UBA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.36   1.3e+03      19      30 ..      69      80 ..      67     112 .. 0.71
   2 ?   10.8   0.1   0.00011      0.41       6      19 ..     123     136 ..     122     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.36
                              UBA_2 19 eIieaLekaeks 30
                                       eI ++L+ +e++
  gene1767|gene1767|rna1766|rna1766 69 EICNVLKVDEEK 80
                                       899999988877 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                              UBA_2   6 vsaLsktMGYdkde 19 
                                        vs L k+MGYdk+e
  gene1767|gene1767|rna1766|rna1766 123 VSDLYKKMGYDKEE 136
                                        899**********9 PP

>> E1_UFD  Ubiquitin fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2   0.00011       0.4      16      66 ..      87     134 ..      72     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                             E1_UFD  16 ldyfkekkklevsmislgvsllYasflpkkkdkerlklklselveevtkkk 66 
                                        ++++ e+ k+e +  s +++l Y  +++    ++rlk+++s+l++++  +k
  gene1767|gene1767|rna1766|rna1766  87 MSKVTENEKVECKETSAKNKLAYHIMFK---AAKRLKMEVSDLYKKMGYDK 134
                                        6788999*****************9988...999***********887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1967.20
//
Query:       gene1768|gene1768|rna1767|rna1767  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   37.8   0.0    1.5e-09   37.4   0.0    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.14   12.2   0.0    1.2  1  RNase_P_pop3    RNase P subunit Pop3


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.7e-13   1.5e-09       6      68 ..      20      82 ..      15      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.7e-13
                                       HHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHH CS
                     Ribosomal_L7Ae  6 vlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskk 68
                                       ++ + +++g+l  G+k++ k +  g + l +l +d++p +   +l+alc++++++y++v  k 
  gene1768|gene1768|rna1767|rna1767 20 LVTEQAERGTLSSGIKKCQKCVLEGSKGLLVLTADTTPMDLITHLPALCEDRGIKYIFVRKKS 82
                                       5666788999*************************************************9875 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05      0.14      73     116 ..      44      88 ..       7     100 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                       RNase_P_pop3  73 ddvvllvcnkD.tPsvLlsqlpllvavanltvklvqlpksaqakl 116
                                        +   llv++ D tP  L+++lp l++   ++   v    s+ +++
  gene1768|gene1768|rna1767|rna1767  44 GSKGLLVLTADtTPMDLITHLPALCEDRGIKYIFVRKKSSIPNRF 88 
                                        4446899999977************99887766666666665655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 817.78
//
Query:       gene1769|gene1769|rna1768|rna1768  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1913.54
//
Query:       gene1770|gene1770|rna1769|rna1769  [L=329]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.5e-68  228.9   0.0    7.5e-68  228.7   0.0    1.0  1  Pkinase        Protein kinase domain
    4.6e-34  117.9   0.0    7.4e-34  117.2   0.0    1.3  2  Pkinase_Tyr    Protein tyrosine kinase
    2.9e-07   30.1   0.0    4.3e-07   29.5   0.0    1.2  1  Kinase-like    Kinase-like
    2.5e-06   26.7   0.0    3.4e-06   26.3   0.0    1.3  1  Haspin_kinase  Haspin like kinase domain
     0.0014   18.1   0.4     0.0023   17.3   0.1    1.4  2  Kdo            Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.034   14.1   0.1       0.18   11.7   0.1    1.9  2  APH            Phosphotransferase enzyme family
      0.068   12.8   0.3          2    8.0   0.1    2.1  2  FTA2           Kinetochore Sim4 complex subunit FTA2


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.7   0.0   2.9e-71   7.5e-68       1     264 []      22     297 ..      22     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 228.7 bits;  conditional E-value: 2.9e-71
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE.SSEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee.kdelyl 75 
                                        y+k++++GeG+fG+V+ a   + +  +A+Kk++kek+  + +  ++rEi+ l++++hp i++l+e++ e + ++y+
  gene1770|gene1770|rna1769|rna1769  22 YKKIRTIGEGTFGQVILAG--KGRARYALKKVNKEKEGLSVT--TIREIQALREMNHPSIIKLIEMVVEpNGDVYM 93 
                                        7899**************9..68999*********9998775..9********************98775889*** PP

                                        EEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSS CS
                            Pkinase  76 vleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakeless 151
                                        v+ y + + l+++++ +   +++e+k+i++qi++g++y+Hskg++HrDlK++NiL+d++ +  i+DFG+a+++++s
  gene1770|gene1770|rna1769|rna1769  94 VFPYFPYD-LNRFIR-SNRPTSDEIKHIFYQIVKGVHYIHSKGVMHRDLKSANILLDHRLNASIADFGMARHVTKS 167
                                        ******77.*****7.5678899***************************************************** PP

                                        CSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT.SHH. CS
                            Pkinase 152 skltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg.etke 225
                                          +t  ++t +Y++PE+l ++++y+ +vDvWslG+il e++ g+++f+   g++    e+ qle+i++  g  ++ 
  gene1770|gene1770|rna1769|rna1769 168 GMYTPGMVTLWYRPPEILlGSSSYTYSVDVWSLGCILTEMYLGHMIFQ---GST----EILQLEMIIHACGsINES 236
                                        ******************999***************************...444....566666677667755666 PP

                                        ..HHHTTS......................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 226 klpeasei......................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                        ++p  +++                      +e+a  l++++l+ dp+kR+t++++++++y+
  gene1770|gene1770|rna1769|rna1769 237 TYPGVQNLpgfrnfrlpqsprrieaiiakhDESAVGLVSRMLCLDPSKRITMDQIIENKYF 297
                                        77777777888888*********************************************98 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   2.9e-37   7.4e-34       3     209 ..      24     217 ..      22     243 .. 0.88
   2 ?   -3.4   0.0       1.8   4.6e+03     237     257 ..     273     293 ..     255     294 .. 0.78

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 2.9e-37
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEE.SSSSEE CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvct.keepll 77 
                                          +++GeG+fG+V+ +         + + a+K++++e++   +   ++e++ +++++hp i+kl+ +++  ++ ++
  gene1770|gene1770|rna1769|rna1769  24 KIRTIGEGTFGQVILAGKG------RARYALKKVNKEKEGL-SVTTIREIQALREMNHPSIIKLIEMVVePNGDVY 92 
                                        5789*********998766......8999*****7776666.8999********************99978889** PP

                                        EEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEET CS
                        Pkinase_Tyr  78 ivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardi 153
                                        +v+ y ++ dL+ f+r++   + t +++ ++ +q+ kG++y++sk ++Hrdl + N+Ll+++  + i+DfG+ar++
  gene1770|gene1770|rna1769|rna1769  93 MVFPYFPY-DLNRFIRSN---RPTSDEIKHIFYQIVKGVHYIHSKGVMHRDLKSANILLDHRLNASIADFGMARHV 164
                                        *******9.9*******9...88999999*********************************************** PP

                                        TTSSEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSSGTTTTS CS
                        Pkinase_Tyr 154 ekddeyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlgespypgl 209
                                        +k+  y   + + + + + +pE+l  ++ +t + DvWs G +l E++  g++ ++g 
  gene1770|gene1770|rna1769|rna1769 165 TKSGMY---TPGMVTLWYRPPEILLGSSsYTYSVDVWSLGCILTEMYL-GHMIFQGS 217
                                        666666...4677889999***98766559***************986.77766665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                                        HHHHHT-SSGGGS--HHHHHH CS
                        Pkinase_Tyr 237 lmkkcweedpeeRptfselve 257
                                        l+++ +  dp++R t+ +++e
  gene1770|gene1770|rna1769|rna1769 273 LVSRMLCLDPSKRITMDQIIE 293
                                        556666779999999999986 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   1.7e-10   4.3e-07     146     269 ..     117     233 ..      94     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.7e-10
                        Kinase-like 146 rlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggft...aLvragtkvvlsevekgfaPpEllgsrgg 218
                                        +++   q+++ + ++++kg++h ++++ n+lld++    + +f+   +  + g + +  +v   + PpE+l     
  gene1770|gene1770|rna1769|rna1769 117 KHIF-YQIVKGVHYIHSKGVMHRDLKSANILLDHRLNASIADFGmarHVTKSGMYTP-GMVTLWYRPPEILLG--- 187
                                        5555.7999**********************************73335666677777.99999******9866... PP

                        Kinase-like 219 ytrknktkmthkldaWqlGlviyriwclklPltlateeakeewkfklckki 269
                                                +t+++d+W lG     ++  ++ ++  te  + e + + c  i
  gene1770|gene1770|rna1769|rna1769 188 -----SSSYTYSVDVWSLGCILTEMYLGHMIFQGSTEILQLEMIIHACGSI 233
                                        .....3679**********99888887777777777777777666666655 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.3e-09   3.4e-06     179     259 ..      84     166 ..      20     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.3e-09
                      Haspin_kinase 179 yseqqlflvlllkdkGtdLeev...klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidl 251
                                        + e +  +++++ +   dL+++   +  + +++++if+qivk ++   +k    HRdL+  niL+d+ ln  + d+
  gene1770|gene1770|rna1769|rna1769  84 VVEPNGDVYMVFPYFPYDLNRFirsNRPTSDEIKHIFYQIVKGVHYIHSK-GVMHRDLKSANILLDHRLNASIADF 158
                                        55556667777777777888876545556789***************999.677********************** PP

                      Haspin_kinase 252 klsRless 259
                                         ++R  ++
  gene1770|gene1770|rna1769|rna1769 159 GMARHVTK 166
                                        ****8743 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.9   7.5e+03      56      69 ..      60      73 ..      48      77 .. 0.68
   2 !   17.3   0.1   9.1e-07    0.0023     104     170 ..     101     162 ..     100     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.9
                                Kdo 56 travrEfrllkrLe 69
                                        +  rE+++l++++
  gene1770|gene1770|rna1769|rna1769 60 VTTIREIQALREMN 73
                                       45568888888765 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 9.1e-07
                                Kdo 104 dLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkar 170
                                        dL+ ++++ +++     ++++ ++ + ++ +h+ gv+H+dl   nill+ +     ++++ D+  ar
  gene1770|gene1770|rna1769|rna1769 101 DLNRFIRS-NRPTSDEIKHIFYQIVKGVHYIHSKGVMHRDLKSANILLDHRL----NASIADFGMAR 162
                                        66666665.445555556788899999**********************997....77788876666 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.24   6.3e+02       2      49 ..      25      74 ..      24     131 .. 0.65
   2 ?   11.7   0.1   6.9e-05      0.18     166     197 ..     133     162 ..     127     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.24
                                       EEEE--.SSCEEEEEEETT--EEEEEE-TT..S-HHHHHHHHHHHHHHHH CS
                                APH  2 vrelsggasnrtylvttpagryvlrrnppa..raaeeirrevallrlLak 49
                                       +r ++ g+  ++ l + ++ ry+l+ ++++   +  ++ re + lr ++ 
  gene1770|gene1770|rna1769|rna1769 25 IRTIGEGTFGQVILAGKGRARYALKKVNKEkeGLSVTTIREIQALREMNH 74
                                       66677777777777788888*****9999966555555566666665543 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 6.9e-05
                                        EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                                APH 166 tvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                        ++++H+Dl++ N+l+d + +    + Df++a+
  gene1770|gene1770|rna1769|rna1769 133 KGVMHRDLKSANILLDHRLNAS--IADFGMAR 162
                                        789*************554444..99999987 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.033        86      15      51 ..      14      49 ..      11      76 .. 0.80
   2 ?    8.0   0.1   0.00078         2     176     214 ..     118     161 ..     105     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.033
                               FTA2 15 pFdfsaekdiefleyLgkglhsiVlkvkirgkeYALK 51
                                       +F+ ++  +++ +  +g+g+ ++V+ +  ++  YALK
  gene1770|gene1770|rna1769|rna1769 14 RFTITKM-EYKKIRTIGEGTFGQVILAGKGRARYALK 49
                                       6666666.88889999********************9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00078
                               FTA2 176 sqlpkllrdlkklhklgIvvrDlkeenyi.....dgkLvDlsaa 214
                                         ++ ++++ ++ +h+ g+++rDlk+ n++     + ++ D+++a
  gene1770|gene1770|rna1769|rna1769 118 HIFYQIVKGVHYIHSKGVMHRDLKSANILldhrlNASIADFGMA 161
                                        568899*******************9985433336777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1991.56
//
Query:       gene177|gene177|rna177|rna177  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-17   63.7   0.1    1.2e-17   63.5   0.1    1.1  1  RRM_1         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
    5.7e-06   25.9   0.0    7.3e-06   25.6   0.0    1.0  1  RRM_5         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
      6e-05   22.8   0.0    7.2e-05   22.6   0.0    1.1  1  RRM_occluded  Occluded RNA-recognition motif
  ------ inclusion threshold ------
      0.051   13.7   0.0      0.081   13.0   0.0    1.6  1  RRM_7         RNA recognition motif
      0.092   12.8   0.0       0.12   12.5   0.0    1.2  1  RNA_bind      RNA binding domain
        0.1   12.6   0.0       0.13   12.3   0.0    1.1  1  RRM_3         RNA binding motif
       0.21   11.8   0.1        3.5    7.8   0.1    1.9  2  PHM7_cyt      Cytosolic domain of 10TM putative phosphate tra


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.1   4.6e-21   1.2e-17       1      69 [.       9      75 ..       9      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 4.6e-21
                                   EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                          RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69
                                   lfV+nLp+dv+++++ elF+++G i  i++     +++ g afV ++  e+A+kA++++ng+ lg++ l
  gene177|gene177|rna177|rna177  9 LFVRNLPKDVSKDKIIELFEEYGTIIQIRVGV--EKNTAGNAFVGYDRVESARKAVRHMNGYYLGDKYL 75
                                   8************************7777777..5******************************9976 PP

>> RRM_5  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.8e-09   7.3e-06      26      97 ..       6      78 ..       2      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.8e-09
                          RRM_5 26 gsVllVyglepdkvnldklFnlfclYgnvervk..flktkketalvqmgdasaveravqHLnnaklfgkrleva 97
                                     +l+V +l  + v  dk+  lf  Yg + +++  + k+  ++a+v      ++ +av H+n+  l +k l++ 
  gene177|gene177|rna177|rna177  6 TQILFVRNLP-KDVSKDKIIELFEEYGTIIQIRvgVEKNTAGNAFVGYDRVESARKAVRHMNGYYLGDKYLNIG 78
                                   6789999995.56889*************866611678899*************************99999985 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.8e-08   7.2e-05       3      73 ..       8      80 ..       6      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.8e-08
                   RRM_occluded  3 tisllplsDtvnkariralveekegeikkivLvpdheG...AivefkdekiagkasLaLdgsefegkklrcGtv 73
                                   ++ + +l+  v+k++i +l+ee+ g i +i +  +++    A+v ++ +++a ka+  ++g+ + +k l++G  
  gene177|gene177|rna177|rna177  8 ILFVRNLPKDVSKDKIIELFEEY-GTIIQIRVGVEKNTagnAFVGYDRVESARKAVRHMNGYYLGDKYLNIGYW 80
                                   677889*****************.*****99988776522479****************************965 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.2e-05     0.081       4      29 ..       9      34 ..       6      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                          RRM_7  4 vFvGGlPiDiteeelkatfkefgkvl 29
                                   +Fv  lP D++++++++ f+e+g+++
  gene177|gene177|rna177|rna177  9 LFVRNLPKDVSKDKIIELFEEYGTII 34
                                   6999*******************864 PP

>> RNA_bind  RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.5e-05      0.12      11      62 ..       8      65 ..       2      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                                   EEEE.E--TT--HHHHHHHTTTSEEE...EEEEEETT..EEEEEEEEE-HHHHHHHHH CS
                       RNA_bind 11 vfyv.tFPkeWktsDivqlFspfGsv...yvsWlddt..sAfvaLhrrdqasvvlktl 62
                                   +++v   Pk+  +  i++lF+ +G++   +v   ++t   Afv+  r ++a+ +++ +
  gene177|gene177|rna177|rna177  8 ILFVrNLPKDVSKDKIIELFEEYGTIiqiRVGVEKNTagNAFVGYDRVESARKAVRHM 65
                                   6666358*****************8521144444444225999999999999998877 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.2e-05      0.13       3      56 ..       8      64 ..       7      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.2e-05
                                   EEEEEE-SSS--HHHHHHHCHCCS-ECEEEE...-TTSSEEEEEESSHHHHHHHHHH CS
                          RRM_3  3 ilklsGlnkelsredikellsklgevayvdy...ekgdkegevrFkedeeakkalek 56
                                   il++  l k++s+++i el++++g++  + +   ++++ ++ v ++  e+a+ka+ +
  gene177|gene177|rna177|rna177  8 ILFVRNLPKDVSKDKIIELFEEYGTIIQIRVgveKNTAGNAFVGYDRVESARKAVRH 64
                                   77888899****************98877652223456678899999999*999876 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0014       3.5       4      28 ..       9      32 ..       6      44 .. 0.85
   2 ?    3.2   0.0     0.037        95     114     139 ..      37      62 ..      31      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0014
                       PHM7_cyt  4 vlvtgiPkelrseeklkeffeelyp 28
                                   ++v+++Pk+++ ++k+ e+fee+  
  gene177|gene177|rna177|rna177  9 LFVRNLPKDVS-KDKIIELFEEYGT 32
                                   89*********.999******9864 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.037
                       PHM7_cyt 114 rekvkkkplgaaFvtfesersaaava 139
                                    r  v+k++ g aFv ++  +sa +++
  gene177|gene177|rna177|rna177  37 RVGVEKNTAGNAFVGYDRVESARKAV 62 
                                    556788899*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 545.48
//
Query:       gene1771|gene1771|rna1770|rna1770  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-21   76.5   0.0    1.7e-21   76.3   0.0    1.0  1  DCP1      Dcp1-like decapping family


Domain annotation for each model (and alignments):
>> DCP1  Dcp1-like decapping family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   9.6e-26   1.7e-21       4     116 ..       9     119 ..       6     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 9.6e-26
                                        HHHHHHHHH-TTEEEEEEEEEEEEEEEEETTTTEEEEEEEEEEEEEEEETT.S-EEEEEEESSSS--EEEEESSGG CS
                               DCP1   4 lnlrvLqrldpsiesildtashvvlYkfnessqeWektdieGtLfvvkrskepryglivlNrkslenliedltkel 79 
                                        +  r +++ d   +++l +++++++Y+++    eW+k +ieGt+ +++r  +p +g++v+Nrksl++++++ltke+
  gene1771|gene1771|rna1770|rna1770   9 ILAREIRKEDRLFKDLLFVSNFASVYHYS---GEWDKLNIEGTFVMYSRACHPFVGIYVFNRKSLKDFCLHLTKET 81 
                                        56678999********************6...8******************************************* PP

                                        GEEEETTEEEEEETTT.EEEEEEESSHHHHHHHHHHHH CS
                               DCP1  80 elelqgeyliyrteee.evfgiWfyeeedreriasllk 116
                                         + ++++++++++      +g+Wf+++++ +++ + l+
  gene1771|gene1771|rna1770|rna1770  82 SFGVKKNFMTINKGGMdGTHGLWFHNDSHPQEVLKRLE 119
                                        ***********9998889**************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 734.07
//
Query:       gene1772|gene1772|rna1771|rna1771  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-08   34.8   1.6    1.8e-08   34.1   1.6    1.4  1  Synaptobrevin  Synaptobrevin
    0.00012   22.0   0.2    0.00023   21.1   0.2    1.6  1  Longin         Regulated-SNARE-like domain
  ------ inclusion threshold ------
      0.021   14.1   0.3      0.038   13.3   0.3    1.4  1  Vps54_N        Vacuolar-sorting protein 54, of GARP complex


Domain annotation for each model (and alignments):
>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   1.6     3e-12   1.8e-08       4      83 ..     130     209 ..     126     211 .] 0.92

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3e-12
                                        HHHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHTXXXXXXXXXXXXXX CS
                      Synaptobrevin   4 klakikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkqarklkrkmwwknmkliiililvvlil 79 
                                        + a+  a v+e+k+++ e ++ +++r+e++++L+  +++++++aq  +k+ +++  k +++++ ++++++++++++
  gene1772|gene1772|rna1771|rna1771 130 NYAQGMAVVEETKGLLAESLNMIIKRDENINNLKGLASRMTTEAQMMQKNIQRMHLKSMLNDYWIYVVFAVLIVLF 205
                                        566677889******************************************************9999999999999 PP

                                        XXXX CS
                      Synaptobrevin  80 ilii 83 
                                        +++i
  gene1772|gene1772|rna1771|rna1771 206 LYYI 209
                                        9998 PP

>> Longin  Regulated-SNARE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   3.9e-08   0.00023      20      65 ..      60     105 ..      42     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.9e-08
                             Longin  20 hdsytfhylaedgltylviadesyprrlaFafLeeikreFlakygt 65 
                                        + +++f++ +++g+++ vi+d+  +++la  +++++++ F + y  
  gene1772|gene1772|rna1771|rna1771  60 DTRFVFYFKISSGIVFAVISDRYTSSKLASGYIDQVAEAFGKIYVD 105
                                        56899***********************************887753 PP

>> Vps54_N  Vacuolar-sorting protein 54, of GARP complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   6.4e-06     0.038      58     120 ..     127     191 ..     113     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-06
                            Vps54_N  58 kreefvkelseveeiekelkesvvickngrraLdlakkeltr..tsLellakskkrqllkkllkt 120
                                        + ++++++++ vee++  l es++++ +  ++++  k  ++r  t+ +++ k+ +r  lk++l++
  gene1772|gene1772|rna1771|rna1771 127 RDSNYAQGMAVVEETKGLLAESLNMIIKRDENINNLKGLASRmtTEAQMMQKNIQRMHLKSMLND 191
                                        56789**********************99998888776666422478899999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1409  (0.0785878); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1330.47
//
Query:       gene1773|gene1773|rna1772|rna1772  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00029   21.1   6.3        0.1   13.1   1.6    2.6  2  zf-C2H2       Zinc finger, C2H2 type
    0.00073   20.2  11.7      0.081   13.8   0.4    2.9  3  zf-C2H2_4     C2H2-type zinc finger
     0.0049   17.3   9.8     0.0081   16.5   0.2    3.2  3  zf-H2C2_2     Zinc-finger double domain
  ------ inclusion threshold ------
      0.017   15.2   0.4       0.17   12.0   0.1    2.4  2  DUF2256       Uncharacterized protein conserved in bacteria (
      0.026   14.3   0.2      0.056   13.2   0.2    1.6  1  Cys_rich_KTR  Cysteine-rich KTR
      0.049   13.8   3.1       0.28   11.3   3.1    2.3  1  Zn-ribbon_8   Zinc ribbon domain
      0.073   13.4   1.3        1.3    9.4   1.1    2.2  2  zf-C2H2_8     C2H2-type zinc ribbon
      0.078   13.1   1.9        5.2    7.3   0.3    2.6  2  zf-DBF        DBF zinc finger
        0.4   10.7   0.3        0.4   10.7   0.3    3.1  3  zf-C2H2_6     C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2    0.0005      0.99       3      23 .]     105     125 ..     103     125 .. 0.96
   2 !   13.1   1.6     5e-05       0.1       3      23 .]     137     157 ..     135     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0005
                                        ETTTTEEESSHHHHHHHHHCC CS
                            zf-C2H2   3 CpdCgksFkrksnLkrHirtH 23 
                                        C+ C ++F +   L+ H+  H
  gene1773|gene1773|rna1772|rna1772 105 CESCEEVFDTFKKLQIHRALH 125
                                        999***************998 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5e-05
                                        ETTTTEEESSHHHHHHHHHCC CS
                            zf-C2H2   3 CpdCgksFkrksnLkrHirtH 23 
                                        Cp+C+k+F  +  L+ H r H
  gene1773|gene1773|rna1772|rna1772 137 CPVCKKTFDERRKLMLHSRYH 157
                                        ******************999 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       3.8   7.6e+03      19      23 ..      90      94 ..      82      95 .. 0.75
   2 !   13.8   0.4   4.1e-05     0.081       1      23 [.     103     125 ..     103     126 .. 0.91
   3 !   13.0   1.5   7.3e-05      0.15       3      23 ..     137     157 ..     135     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.8
                          zf-C2H2_4 19 Hlkth 23
                                       H k+h
  gene1773|gene1773|rna1772|rna1772 90 HKKKH 94
                                       99999 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.1e-05
                          zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkth 23 
                                        f C+ C ++F + k+L+ H + h
  gene1773|gene1773|rna1772|rna1772 103 FGCESCEEVFDTFKKLQIHRALH 125
                                        56*****************9988 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 7.3e-05
                          zf-C2H2_4   3 CpiCgksFsskkaLlrHlkth 23 
                                        Cp+C+k+F  +++L  H + h
  gene1773|gene1773|rna1772|rna1772 137 CPVCKKTFDERRKLMLHSRYH 157
                                        ************9**9*9998 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.023        45       5      26 .]      90     114 ..      89     114 .. 0.77
   2 !   16.5   0.2   4.1e-06    0.0081       2      24 ..     118     144 ..     117     146 .. 0.89
   3 ?    0.6   0.2      0.46   9.2e+02       2      10 ..     150     158 ..     149     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                          zf-H2C2_2   5 HirkHtgekp...yeCplCdkaFkt 26 
                                        H +kH  e     + C++C  +F t
  gene1773|gene1773|rna1772|rna1772  90 HKKKHSTEASrdtFGCESCEEVFDT 114
                                        999999664225599*****99975 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 4.1e-06
                          zf-H2C2_2   2 LrrHirkHt...ge.kpyeCplCdkaF 24 
                                        L+ H + H+   ge +p+ Cp+C+k+F
  gene1773|gene1773|rna1772|rna1772 118 LQIHRALHKdtsGEaNPLFCPVCKKTF 144
                                        6779999999999988*********** PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.46
                          zf-H2C2_2   2 LrrHirkHt 10 
                                        L+ H r H+
  gene1773|gene1773|rna1772|rna1772 150 LMLHSRYHK 158
                                        788*****7 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.36   7.1e+02      10      23 ..     105     118 ..     101     121 .. 0.87
   2 ?   12.0   0.1   8.7e-05      0.17       9      23 ..     136     150 ..     131     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.36
                            DUF2256  10 CavCgrpftwRkkW 23 
                                        C  C+  f   kk 
  gene1773|gene1773|rna1772|rna1772 105 CESCEEVFDTFKKL 118
                                        99*****9988886 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.7e-05
                            DUF2256   9 iCavCgrpftwRkkW 23 
                                         C+vC++ f  R+k 
  gene1773|gene1773|rna1772|rna1772 136 FCPVCKKTFDERRKL 150
                                        5************96 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   2.8e-05     0.056      17      35 ..     124     142 ..     116     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                       Cys_rich_KTR  17 iredTvLknfpLfCPKCkq 35 
                                        + +dT  +  pLfCP Ck+
  gene1773|gene1773|rna1772|rna1772 124 LHKDTSGEANPLFCPVCKK 142
                                        56899999**********8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.1   0.00014      0.28       6      34 ..     103     142 ..     102     151 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                        Zn-ribbon_8   6 YrCeeCghefe.........vlqsis.daplta.CPeCgs 34 
                                        + Ce+C ++f+         +l++ +  ++++  CP C++
  gene1773|gene1773|rna1772|rna1772 103 FGCESCEEVFDtfkklqihrALHKDTsGEANPLfCPVCKK 142
                                        77*********88877766655555444458889****87 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.1   0.00063       1.3      26      85 ..      91     153 ..      79     154 .. 0.69
   2 ?    3.9   0.0     0.032        64      41      60 ..     138     157 ..     127     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00063
                          zf-C2H2_8  26 sptqslegklfrcstascaetfpsmqelvahtklhykpn...ryfkcencllrfrthrslfkh 85 
                                        + ++s+e  +    + sc e f ++++l  h  lh         + c  c   f   r l+ h
  gene1773|gene1773|rna1772|rna1772  91 KKKHSTEASRDTFGCESCEEVFDTFKKLQIHRALHKDTSgeaNPLFCPVCKKTFDERRKLMLH 153
                                        445667777777777899999999999999999998653111334577777777777777655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.032
                          zf-C2H2_8  41 ascaetfpsmqelvahtklh 60 
                                        + c +tf   ++l+ h++ h
  gene1773|gene1773|rna1772|rna1772 138 PVCKKTFDERRKLMLHSRYH 157
                                        679**************999 PP

>> zf-DBF  DBF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.3    0.0026       5.2       6      18 ..     105     117 ..     100     127 .. 0.80
   2 ?    4.8   0.1     0.015        30       3      25 ..     134     157 ..     132     160 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0026
                             zf-DBF   6 CEnCrvkfedlee 18 
                                        CE C++ f+ +++
  gene1773|gene1773|rna1772|rna1772 105 CESCEEVFDTFKK 117
                                        *********9983 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                             zf-DBF   3 sGYCEnCrvkfedle.eHlksekH 25 
                                        + +C +C+++f++     l+s+ H
  gene1773|gene1773|rna1772|rna1772 134 PLFCPVCKKTFDERRkLMLHSRYH 157
                                        669********9876345555555 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.9       2.1   4.1e+03      20      25 ..      90      95 ..      90      97 .. 0.84
   2 ?   10.7   0.3    0.0002       0.4       2      26 ..     103     127 ..     102     128 .. 0.92
   3 ?    7.6   0.2     0.002       3.9       4      11 ..     137     144 ..     137     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.1
                          zf-C2H2_6 20 HkksHr 25
                                       Hkk H 
  gene1773|gene1773|rna1772|rna1772 90 HKKKHS 95
                                       ****96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                          zf-C2H2_6   2 heCsvCsksFpslqaLggHkksHrk 26 
                                        + C  C ++F +++ L  H++ H++
  gene1773|gene1773|rna1772|rna1772 103 FGCESCEEVFDTFKKLQIHRALHKD 127
                                        88******************99976 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.002
                          zf-C2H2_6   4 CsvCsksF 11 
                                        C+vC+k+F
  gene1773|gene1773|rna1772|rna1772 137 CPVCKKTF 144
                                        ******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 987.78
//
Query:       gene1774|gene1774|rna1773|rna1773  [L=90]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-10   41.3   9.9    2.1e-10   40.7   9.9    1.3  1  zf-RING_2     Ring finger domain
    5.4e-08   32.6  10.7    7.8e-08   32.1  10.7    1.3  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    7.2e-08   32.6  10.4    1.7e-07   31.4  10.4    1.6  1  zf-rbx1       RING-H2 zinc finger domain
    2.4e-07   30.5   9.5    3.2e-07   30.1   9.5    1.2  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    1.1e-06   28.3   7.5    1.1e-06   28.3   7.5    1.8  2  zf-RING_11    RING-like zinc finger
    5.6e-06   26.3   6.2    8.8e-06   25.6   6.2    1.3  1  zf-RING_UBOX  RING-type zinc-finger
      3e-05   23.8   8.4      4e-05   23.4   8.4    1.2  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
      0.001   19.1   6.3     0.0022   18.0   6.3    1.6  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
     0.0014   18.5   2.9      0.002   17.9   2.9    1.2  1  zf-RING_6     zf-RING of BARD1-type protein
     0.0063   16.1   7.1     0.0097   15.5   7.1    1.3  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
      0.007   16.3  10.3      0.019   14.9  10.4    1.6  2  zf-RING_5     zinc-RING finger domain
  ------ inclusion threshold ------
      0.025   14.7  10.2      0.049   13.8  10.2    1.5  1  zf-C3HC4_4    zinc finger of C3HC4-type, RING
       0.14   12.0   3.3       0.19   11.6   3.3    1.2  1  zf-Nse        Zinc-finger of the MIZ type in Nse subunit


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   9.9   1.5e-13   2.1e-10       2      44 .]      46      86 ..      45      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.5e-13
                          zf-RING_2  2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44
                                       +C+ICle +++ +++ll  C+H+fh +C+  w++ ++tCP Cr
  gene1774|gene1774|rna1773|rna1773 46 KCCICLEYIKE-SKALL-GCNHSFHLNCIYLWFNMKRTCPSCR 86
                                       8*****88865.44444.6***********************9 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1  10.7   5.7e-11   7.8e-08       1      41 []      47      85 ..      47      85 .. 0.99

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 5.7e-11
                                       -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                           zf-C3HC4  1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41
                                       C iCle++ke + ll C+Hsf+ +Ci  + +  +k++CP C
  gene1774|gene1774|rna1773|rna1773 47 CCICLEYIKESKALLGCNHSFHLNCIYLWFN--MKRTCPSC 85
                                       *******************************..9******* PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4  10.4   1.2e-10   1.7e-07      12      55 .]      45      86 ..      39      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.2e-10
                            zf-rbx1 12 eacieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55
                                       e+c  c +  +e  + +l  C+H+FHl+Ci  W++ +++CP cr
  gene1774|gene1774|rna1773|rna1773 45 EKCCICLEYIKE-SK-ALLGCNHSFHLNCIYLWFNMKRTCPSCR 86
                                       455555555555.34.4557***********************8 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   9.5   2.3e-10   3.2e-07       1      40 []      46      85 ..      46      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.3e-10
                         zf-C3HC4_2  1 kCpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40
                                       kC iCl+ +k+   +  C+H+f+ +Ci  + + k  CP C
  gene1774|gene1774|rna1773|rna1773 46 KCCICLEYIKESKALLGCNHSFHLNCIYLWFNMKRTCPSC 85
                                       7*************************************** PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.4   7.5e+03       6      14 ..      33      41 ..      33      42 .. 0.76
   2 !   28.3   7.5   7.9e-10   1.1e-06       2      29 .]      47      72 ..      46      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.4
                         zf-RING_11  6 Leefkpgqa 14
                                       L+e+++ ++
  gene1774|gene1774|rna1773|rna1773 33 LDEMAEADE 41
                                       789998776 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 7.9e-10
                         zf-RING_11  2 CsICLeefkpgqalfilpCsHtFHfkCI 29
                                       C+ICLe +k+++al  l C+H FH++CI
  gene1774|gene1774|rna1773|rna1773 47 CCICLEYIKESKAL--LGCNHSFHLNCI 72
                                       *************9..88*********9 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   6.2   6.4e-09   8.8e-06       1      39 []      47      83 ..      47      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.4e-09
                       zf-RING_UBOX  1 CpIClelftdP.lvlpCGHtFCreClwelskslegafkCP 39
                                       C ICle  ++   +l+C H+F+ +C+     + +++++CP
  gene1774|gene1774|rna1773|rna1773 47 CCICLEYIKESkALLGCNHSFHLNCI---YLWFNMKRTCP 83
                                       ********9773245***********...78899999999 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   8.4   2.9e-08     4e-05       2      47 ..      44      89 ..      43      90 .] 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.9e-08
                                       GSB-TTTSSSBS-.EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                         zf-C3HC4_3  2 deeCviClerprn.vvllpCgHlvlCeeCaekllkrkkkCpiCrrpi 47
                                       +e+C+iCle  ++  +ll C+H  +  +C   + ++k++Cp Cr+ +
  gene1774|gene1774|rna1773|rna1773 44 KEKCCICLEYIKEsKALLGCNHS-FHLNCIYLWFNMKRTCPSCRKAV 89
                                       789******966626889*****.9*******************987 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   6.3   1.6e-06    0.0022      44      81 ..      56      89 ..      28      90 .] 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                       TS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB- CS
                         zf-ANAPC11 44 dcplvlGkckhnfhlhcilkwletetskglcpmcrqtf 81
                                       +   +lG c+h+fhl ci+ w++    k  cp cr+++
  gene1774|gene1774|rna1773|rna1773 56 ESKALLG-CNHSFHLNCIYLWFNM---KRTCPSCRKAV 89
                                       4445555.*************985...789*****875 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.9   1.5e-06     0.002       9      47 ..      46      86 ..      40      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                          zf-RING_6  9 rcsrctdilrepvclggcehifcsncisdcfg..sgcpvcy 47
                                       +c  c + ++e   l gc+h f  nci   f     cp c 
  gene1774|gene1774|rna1773|rna1773 46 KCCICLEYIKESKALLGCNHSFHLNCIYLWFNmkRTCPSCR 86
                                       799************************99986225799995 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   7.1     7e-06    0.0097       4      47 ..      44      84 ..      41      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7e-06
                       Zn_ribbon_17  4 lksCayCelavkgrvvlcgvCeHvlHasCarewfenddlaeCps 47
                                       +++C++C   +k +  l   C+H  H +C+  wf+++    Cps
  gene1774|gene1774|rna1773|rna1773 44 KEKCCICLEYIKESKAL-LGCNHSFHLNCIYLWFNMKR--TCPS 84
                                       689****8888777666.67****************99..8987 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.0      0.24   3.3e+02      35      42 ..      43      50 ..      34      52 .. 0.78
   2 !   14.9  10.4   1.4e-05     0.019       1      44 []      46      87 ..      46      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.24
                          zf-RING_5 35 keavCpiC 42
                                       ++ +C+iC
  gene1774|gene1774|rna1773|rna1773 43 EKEKCCIC 50
                                       67899999 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.4e-05
                          zf-RING_5  1 hCnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44
                                       +C +C e +  +e   l+ C H+f+ +C+   ++ +++Cp Crk
  gene1774|gene1774|rna1773|rna1773 46 KCCICLEYI--KESKALLGCNHSFHLNCIYLWFNMKRTCPSCRK 87
                                       699999999..77778999**************9********97 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  10.2   3.5e-05     0.049       1      42 []      47      85 ..      47      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                         zf-C3HC4_4  1 CPiCldYLekP.vsleCGhsfClsCisslqkepdgeqllCplC 42
                                       C iCl+Y+++  + l C hsf l+Ci+ + + +     +Cp C
  gene1774|gene1774|rna1773|rna1773 47 CCICLEYIKESkALLGCNHSFHLNCIYLWFNMK----RTCPSC 85
                                       99******98626789***********988777....469998 PP

>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.3   0.00014      0.19       1      56 [.      34      85 ..      34      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                       SXXXXXSSBXXSB-TTTSSB-SSEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC- CS
                             zf-Nse  1 delaieeerislkCPltlqpfeePvtskkCpHvFEreaIlelikrkktvkCPvagC 56
                                       de+a   e  + kC + l++++e      C+H+F  + I   +  + +  CP   C
  gene1774|gene1774|rna1773|rna1773 34 DEMAEADEVEKEKCCICLEYIKESKALLGCNHSFHLNCIYLWF--NMKRTCPS--C 85
                                       5666666788899*********999999***********9999..88888997..6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 548.29
//
Query:       gene1775|gene1775|rna1774|rna1774  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.6   0.0       0.31   11.1   0.0    1.2  1  DUF2322   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2322  Uncharacterized protein conserved in bacteria (DUF2322)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.7e-05      0.31      62      86 ..       6      30 ..       1      40 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.7e-05
                            DUF2322 62 lelfaehtadakanpgkHPNidrLl 86
                                        ++ ae  +dak+ p kHP + + l
  gene1775|gene1775|rna1774|rna1774  6 YNILAEGCSDAKDSPAKHPDLSLTL 30
                                       57899**************987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 762.77
//
Query:       gene1776|gene1776|rna1775|rna1775  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-15   55.7   2.6    6.1e-15   55.5   0.1    2.3  2  LsmAD     LsmAD domain


Domain annotation for each model (and alignments):
>> LsmAD  LsmAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   3.4e-19   6.1e-15       1      69 [.     137     202 ..     137     203 .. 0.95
   2 ?   -2.3   0.3      0.38   6.9e+03      41      53 ..     269     281 ..     261     287 .. 0.60

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.4e-19
                              LsmAD   1 FgvkstYdEnlYTtkldksspeykereaeAeriArEIessastnahvaeerglkvddsgldEEdkYSaV 69 
                                        F+++ ++dE+ Y+  ldkss+ yk +   A+ri++EI+ss++t++h+ eergl    +  ++Ed YS V
  gene1776|gene1776|rna1775|rna1775 137 FNIDNKFDEEEYMDVLDKSSNWYKSKLLMARRIEKEIMSSTTTDPHRLEERGL---GRTPENEDMYSTV 202
                                        99***************************************************...445799*****99 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.38
                              LsmAD  41 astnahvaeergl 53 
                                        +++++  +eer++
  gene1776|gene1776|rna1775|rna1775 269 NEESSNTQEERKN 281
                                        4445566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2128.70
//
Query:       gene1777|gene1777|rna1776|rna1776  [L=425]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-39  134.1   0.0    6.9e-39  133.3   0.0    1.4  1  AAA           ATPase family associated with various cellular 
    7.5e-13   48.1   0.0    2.1e-12   46.6   0.0    1.8  1  AAA_lid_3     AAA+ lid domain
    8.8e-08   32.0   0.4    1.6e-06   28.0   0.2    2.8  2  Vps4_C        Vps4 C terminal oligomerisation domain
    8.1e-05   22.4   0.0    0.00018   21.3   0.0    1.8  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
    0.00018   21.5   0.0     0.0013   18.7   0.0    2.4  1  AAA_5         AAA domain (dynein-related subfamily)
    0.00033   20.9   1.9      0.015   15.5   0.8    2.9  2  AAA_22        AAA domain
     0.0015   18.7   0.0     0.0036   17.4   0.0    1.7  1  AAA_2         AAA domain (Cdc48 subfamily)
     0.0029   18.0   0.4      0.028   14.8   0.4    2.5  1  AAA_16        AAA ATPase domain
     0.0042   16.5   0.2        2.8    7.3   0.0    2.6  3  TniB          Bacterial TniB protein
     0.0059   15.9   0.0       0.01   15.0   0.0    1.4  1  TIP49         TIP49 P-loop domain
     0.0094   15.4   0.1      0.018   14.4   0.1    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.047   13.3   0.1          2    7.9   0.0    2.3  2  AAA_25        AAA domain
      0.079   12.8   0.2        1.2    8.9   0.0    2.6  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.082   13.2   0.0       0.17   12.2   0.0    1.5  1  AAA_19        AAA domain
      0.082   12.2   0.5         13    5.1   0.2    2.6  2  ATPase        KaiC
      0.094   11.8   0.0       0.16   11.0   0.0    1.4  1  MCM           MCM P-loop domain
       0.13   12.3   0.1       0.44   10.6   0.0    1.9  2  AAA_14        AAA domain
       0.13   12.0   0.0       0.24   11.1   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
       0.13   11.8   0.3       0.37   10.3   0.2    1.8  2  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.0   7.3e-42   6.9e-39       1     132 []     190     320 ..     190     320 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 7.3e-42
                                        EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                                AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                        +ll+GppGtGKT++ k +a++++++f++is+s+l+sk+vge+ek +r+lf  a++++ ps++fiDEid+l ++rs+
  gene1777|gene1777|rna1776|rna1776 190 LLLFGPPGTGKTMIGKCIASQCKATFFSISASSLTSKWVGEGEKMVRALFYLARSMQ-PSVVFIDEIDSLLSQRSD 264
                                        69******************************************************9.****************** PP

                                        CCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESSGGGSTHHHHSTTSSEEEETTS CS
                                AAA  77 seseeeervvnqLlteldgvkkk.eskvivigatnrpdkldpallrgRfdrkieiel 132
                                        +e+e ++r+  ++l ++dg  ++  ++++vigatnrp+++d+a + +R+ ++i+++l
  gene1777|gene1777|rna1776|rna1776 265 NENEGSRRIKTEFLVQFDGAGTSdGDRILVIGATNRPHEIDEAAR-RRLVKRIYVPL 320
                                        *******************97775778******************.7******9985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   2.2e-15   2.1e-12       3      44 ..     345     396 ..     344     412 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2.2e-15
                          AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrr..........gikeitmedfe 44 
                                        dl+e+A++TeGySG D+ +lcreA+l+ lr+          ++  i+ edf+
  gene1777|gene1777|rna1776|rna1776 345 DLNEVAKMTEGYSGSDIFNLCREASLEPLREiddiedfkseDTRPISLEDFR 396
                                        9******************************666665553222247777776 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.62   5.8e+02      35      58 ..     331     354 ..     321     356 .. 0.83
   2 !   28.0   0.2   1.7e-09   1.6e-06      27      61 .]     388     422 ..     375     422 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.62
                             Vps4_C  35 lkalkkarptVskeDLekheeFTk 58 
                                        +  +k+ r t  ++DL++  + T+
  gene1777|gene1777|rna1776|rna1776 331 EHLIKEYRNTLEHADLNEVAKMTE 354
                                        5679999*********99988775 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.7e-09
                             Vps4_C  27 PpvtlkDflkalkkarptVskeDLekheeFTkefG 61 
                                        +p++l+Df ka ++ +++Vs+ DLe + ++  +fG
  gene1777|gene1777|rna1776|rna1776 388 RPISLEDFRKATRQIKKSVSERDLEIYSDWNTKFG 422
                                        59********************************9 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.9e-07   0.00018      36      98 ..     190     260 ..     152     315 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.9e-07
                             RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvleka.....gdlaalltnl...eekdvlfideihrlsr 98 
                                        +ll+GpPG Gkt + k ia++ ++++ + s+  l  +       ++  l  l    +  v+fidei  l +
  gene1777|gene1777|rna1776|rna1776 190 LLLFGPPGTGKTMIGKCIASQCKATFFSISASSLTSKwvgegEKMVRALFYLarsMQPSVVFIDEIDSLLS 260
                                        79**********************99888887775432222234554444441114568*******98754 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.4e-06    0.0013       2     137 ..     190     311 ..     189     312 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-06
                                        EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                              AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                        +lL GppGtgK+++ + +a+  +++++ +  ++      l+ ++   ++++++v   ++  ar  +++++++DE++
  gene1777|gene1777|rna1776|rna1776 190 LLLFGPPGTGKTMIGKCIASQCKATFFSISASS------LTSKWV--GEGEKMVRALFY-LARsmQPSVVFIDEID 256
                                        89*******************999999877666......677777..333344444333.4444578999999999 PP

                                        G--HHHHHHHHHHHHSSEEE..-SSSEEE---.................-EEEEEESS--.-TT-TTHHHHTT CS
                              AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddller...........frviatanpldrslnelspalrsR 137
                                                   sll++r    +eg +++k +   +l +           + vi+++n+++    e+++a r+R
  gene1777|gene1777|rna1776|rna1776 257 -----------SLLSQRSDNENEGSRRIKTE---FLVQfdgagtsdgdrILVIGATNRPH----EIDEAARRR 311
                                        ...........44444444444444444332...22223334555556677777777777....777777776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.8   1.6e-05     0.015       8      67 ..     190     262 ..     184     295 .. 0.61
   2 ?   -0.5   0.0       1.5   1.4e+03      40      71 ..     310     354 ..     295     401 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                             AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.............erpevvfvtlpsstsskdllrellralgle 67 
                                        l+++G++GtGKT+  + +++q ++  +                + ++ +f+ + s   s  +  e+ + l ++
  gene1777|gene1777|rna1776|rna1776 190 LLLFGPPGTGKTMIGKCIASQCKATFFSISassltskwvgegeKMVRALFYLARSMQPSVVFIDEIDSLLSQR 262
                                        79*******************8444444445566666666443333333444444444444455555555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.5
                             AAA_22  40 pevv...fvtlpsstsskdllrellralglelka..........e 71 
                                        +++v   +v lp+  +++++ ++l +++ + l++          e
  gene1777|gene1777|rna1776|rna1776 310 RRLVkriYVPLPENLGRRQMVEHLIKEYRNTLEHadlnevakmtE 354
                                        333442244444444677777777777666666644444444444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.9e-06    0.0036       7     129 ..     191     300 ..     187     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-06
                                        EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                              AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                        ll gp g+Gkt++ k +a+  ++    ++  + as+l+     e e+     + a  +  +  +  +v++DEid  
  gene1777|gene1777|rna1776|rna1776 191 LLFGPPGTGKTMIGKCIASQCKA----TFFSISASSLTSkwVGEGEK----MVRALFYLARSMQPSVVFIDEIDSL 258
                                        678****************9995....************33233333....334444566777889********** PP

                                        ------------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE-- CS
                              AAA_2  81 hpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgaf 129
                                         +++s +++  +  + + +L  ++g+  +d        + il+I +++ 
  gene1777|gene1777|rna1776|rna1776 259 LSQRSDNENEGSRRIKTEFLVQFDGAGTSDG-------DRILVIGATNR 300
                                        9986666666666677777777777644433.......44566655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.4     3e-05     0.028      21      61 ..     184     221 ..     174     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                             AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                        +g p  +ll G++G+GK+ + ++++ + +++   f++  + 
  gene1777|gene1777|rna1776|rna1776 184 RGPPKGLLLFGPPGTGKTMIGKCIASQCKAT---FFSISAS 221
                                        666799*******************777766...3333333 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0053         5      36      57 ..     188     209 ..     178     222 .. 0.83
   2 !    7.3   0.0    0.0029       2.8     106     147 ..     233     274 ..     222     293 .. 0.83
   3 ?   -3.1   0.0       4.6   4.3e+03      66      95 ..     309     338 ..     297     350 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0053
                               TniB  36 pnlllvGdsnnGKtmivekFar 57 
                                        + lll+G++ +GKtmi +  a+
  gene1777|gene1777|rna1776|rna1776 188 KGLLLFGPPGTGKTMIGKCIAS 209
                                        689************9776555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0029
                               TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalk 147
                                        k+ ++   l r++++ v+ iDEi++ll+ ++++ +e    +k
  gene1777|gene1777|rna1776|rna1776 233 KMVRALFYLARSMQPSVVFIDEIDSLLSQRSDNENEGSRRIK 274
                                        55666778889****************999888877666555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.6
                               TniB  66 daekvpvlvvqappkpdekrlyaaiLealg 95 
                                        +++ v+ ++v +p++   +++ ++++++ +
  gene1777|gene1777|rna1776|rna1776 309 RRRLVKRIYVPLPENLGRRQMVEHLIKEYR 338
                                        333445555555555555555555555444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05      0.01      26     103 ..     156     238 ..     121     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                        XXXXXXXXXXXX..XXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  26 lvGqkkareaag..vivelikekklaG.....ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevk 94 
                                        ++G k+ ++a    v+  +++ + ++G     +++Ll Gp+gtGkt +   i+ +      f ++s+s + s  v 
  gene1777|gene1777|rna1776|rna1776 156 IIGLKDVKKAINeiVLWPMLRPDLFTGlrgppKGLLLFGPPGTGKTMIGKCIASQCK--ATFFSISASSLTSKWVG 229
                                        5666666666542234456666666555445589******************99875..7899*******999999 PP

                                        XXXXXXXXX CS
                              TIP49  95 ktevltqal 103
                                          e +++al
  gene1777|gene1777|rna1776|rna1776 230 EGEKMVRAL 238
                                        888887764 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.9e-05     0.018      25      43 ..     190     208 ..     187     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                       Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                        lll+GppG+GKtm+ k+++
  gene1777|gene1777|rna1776|rna1776 190 LLLFGPPGTGKTMIGKCIA 208
                                        89*************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0021         2      34      50 ..     188     204 ..     173     214 .. 0.76
   2 ?    2.9   0.0     0.077        72     131     166 ..     236     271 ..     229     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                             AAA_25  34 elallaGapgtGKttla 50 
                                        +  ll+G+pgtGKt++ 
  gene1777|gene1777|rna1776|rna1776 188 KGLLLFGPPGTGKTMIG 204
                                        5579**********986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.077
                             AAA_25 131 daleaaieevegvrlvviDplsralgg.densnsdvg 166
                                        +al   +++  ++ +v iD ++++l+  + n+n+  +
  gene1777|gene1777|rna1776|rna1776 236 RALFYLARS-MQPSVVFIDEIDSLLSQrSDNENEGSR 271
                                        566667777.57***********99997666665544 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   1.8e+03      94     127 ..     132     165 ..      53     170 .. 0.62
   2 ?    0.5   0.0      0.46   4.3e+02       3      22 ..     191     210 ..     190     227 .. 0.80
   3 ?    8.9   0.0    0.0013       1.2     235     270 ..     226     259 ..     221     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                             AAA_21  94 lesgllldkrsleeedvfnpeargirggvsvfsl 127
                                         es++ ++ r+++ e+ ++ ++++i g+++v+++
  gene1777|gene1777|rna1776|rna1776 132 VESYIVDRIRNEILEKTVDVKWDDIIGLKDVKKA 165
                                        4566666666666777777777777666666665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.46
                             AAA_21   3 vliGpNgsGKSnLLdaldll 22 
                                        +l Gp g+GK+ + +++   
  gene1777|gene1777|rna1776|rna1776 191 LLFGPPGTGKTMIGKCIASQ 210
                                        689***********999654 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0013
                             AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngL 270
                                          +++G k + + l +l+r  ++ s+++iDE+++ L
  gene1777|gene1777|rna1776|rna1776 226 KWVGEGEKMV-RALFYLARSMQP-SVVFIDEIDSLL 259
                                        5689999999.999999999999.*********966 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018      0.17      12      61 ..     189     234 ..     184     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                             AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrer 61 
                                         ll+ ++pGtGKT + k+i + ++++      +i + ++t++ + e ++ 
  gene1777|gene1777|rna1776|rna1776 189 GLLLFGPPGTGKTMIGKCIASQCKATF----FSISASSLTSKWVGEGEKM 234
                                        5899***********999999888877....6677777777766665555 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.013        13      22      37 ..     190     205 ..     184     215 .. 0.87
   2 ?    4.7   0.0     0.017        16     103     137 ..     230     265 ..     207     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                             ATPase  22 vlitGepGtGKtifal 37 
                                         l+ G pGtGKt++++
  gene1777|gene1777|rna1776|rna1776 190 LLLFGPPGTGKTMIGK 205
                                        5899*********986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                             ATPase 103 dleelieelaeaikeikakrvviDsitgl.ayeeke 137
                                        + e++++ l +  ++++ + v iD i++l ++++++
  gene1777|gene1777|rna1776|rna1776 230 EGEKMVRALFYLARSMQPSVVFIDEIDSLlSQRSDN 265
                                        5578999999*******************7554443 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.16      12      93 ..     142     222 ..     135     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                        STHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-E.EEEEESSTSTHHHHHHHHHHHSSSEEE CS
                                MCM  12 kdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdin.vllvgdpgtaKsqlLkyveklapravy 86 
                                        ++i+ek v+     i+g +dvkkai   ++ ++ + +   t lrg  + +ll g pgt+K+ + k +++  + a++
  gene1777|gene1777|rna1776|rna1776 142 NEILEKTVDVKWDDIIGLKDVKKAINEIVLWPMLRPDL-FTGLRGPPKgLLLFGPPGTGKTMIGKCIASQCK-ATF 215
                                        5788999999999*************999999996443.3669*987538899********99999986554.455 PP

                                        EESSSSS CS
                                MCM  87 tsgkgss 93 
                                         s+++ss
  gene1777|gene1777|rna1776|rna1776 216 FSISASS 222
                                        5554444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       5.9   5.6e+03      51      86 ..     131     169 ..     113     171 .. 0.55
   2 ?   10.6   0.0   0.00046      0.44       5      75 ..     190     257 ..     187     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.9
                             AAA_14  51 kllelileklke...ekktylflDEiqevpewekalksl 86 
                                        +++++i +++++   ek+  +  D i  +++++ka++++
  gene1777|gene1777|rna1776|rna1776 131 NVESYIVDRIRNeilEKTVDVKWDDIIGLKDVKKAINEI 169
                                        455555555444453344447778888888888888776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00046
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqe 75 
                                        l++ G+  +GKT++ k ++++    k  ++ i+  + + k   + ek+ ++++ ++++ + +++f+DEi  
  gene1777|gene1777|rna1776|rna1776 190 LLLFGPPGTGKTMIGKCIASQC---KATFFSISASSLTSKWVGEGEKMVRALFYLARSMQPSVVFIDEIDS 257
                                        7899**********87777554...5999999999998888777776776666664445889*******76 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.24      49      77 ..     189     217 ..     185     268 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                          IstB_IS21  49 nivllGpsGvGKshlaialgveavragls 77 
                                        +++l+Gp+G+GK+ +   ++ +  ++ +s
  gene1777|gene1777|rna1776|rna1776 189 GLLLFGPPGTGKTMIGKCIASQCKATFFS 217
                                        689***********999998775444333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00039      0.37      35      68 ..     189     219 ..     184     258 .. 0.76
   2 ?   -3.5   0.0       6.8   6.4e+03      10      36 ..     314     340 ..     309     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                              AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltin 68 
                                         +ll Gp GtGKt+i k + ++++ + +++   +
  gene1777|gene1777|rna1776|rna1776 189 GLLLFGPPGTGKTMIGKCIASQCKATFFSI---S 219
                                        689************999988888333333...3 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.8
                              AAA_7  10 seilVptvdtvrysyllelllknkkpv 36 
                                        ++i+Vp  +++  + ++e+l+k+ +++
  gene1777|gene1777|rna1776|rna1776 314 KRIYVPLPENLGRRQMVEHLIKEYRNT 340
                                        678899999998889999998887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2612.54
//
Query:       gene1778|gene1778|rna1777|rna1777  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 829.59
//
Query:       gene1779|gene1779|rna1778|rna1778  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-80  270.0   9.2    5.9e-80  269.0   9.2    1.4  1  PTR2       POT family


Domain annotation for each model (and alignments):
>> PTR2  POT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.0   9.2   3.3e-84   5.9e-80       1     378 [.      71     426 ..      71     430 .. 0.90

  Alignments for each domain:
  == domain 1  score: 269.0 bits;  conditional E-value: 3.3e-84
                                        CHHHHHHHHHHHHHHHHCCCCTTTTSS--S--TCHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTT-SSSSCHHHHH CS
                               PTR2   1 fktIllgsiiyaiGhvvlalsaipslksaesagvrvallfigLalIalGtGgiKpnvSafgadqfeekdprersrf 76 
                                        ++tI+++s++y++G ++l++ ++ s +++        ll+++L++Ia+GtGgiKp+v+afg+dqf +++ +  ++f
  gene1779|gene1779|rna1778|rna1778  71 YNTIVVLSSLYLTGTSLLTYCSVVSGSPE--------LLVTSLLMIAVGTGGIKPCVAAFGGDQFGPDEAQNLRKF 138
                                        79********************8888787........*************************************** PP

                                        HHHHHHHHHHHHHHHHHHHHHHHCT......T-HHHHHHHHHHHHHHHHHHHHCTTTS-EE------SHHHHCCCH CS
                               PTR2  77 FsiFyfsiNvGSLlsliitpylqen......vgyplgFgipavlmiiallvFllGsrlykkkppkgnvltkvfkvl 146
                                        F +Fyf iN+GS++s+++tp++ +       ++ypl+Fg +  l+  ++l F+ G++ly  kp ++  ++++f+ l
  gene1779|gene1779|rna1778|rna1778 139 FDFFYFTINIGSMVSMVVTPVMSSAtcfgkqSCYPLAFGASSTLLGTSILLFATGTNLYVIKPARKRQFSRSFRSL 214
                                        **********************999999999********************************************9 PP

                                        SHHHHHCCCHHHHHHHHHHHHHSHHHHHH---HHCCHCHHHHHHHHH-HHTHHCHHHHHCCCHHHHHHHHHHHHHH CS
                               PTR2 147 lvaaknkvkkirssagkkklhwldkakeldkalsileivvegivfnimtkkkveevkrllrvvplflpliifwaly 222
                                        +  +k k+    s+ g+ +++ +    + +                 + + + ++ kr lr++ +  p+++fwaly
  gene1779|gene1779|rna1778|rna1778 215 VQNMK-KL--LWSMPGSDEEPDTLRTPSET----------------ACEVYEEDDKKRTLRILRILGPAVFFWALY 271
                                        44333.33..34555454444444443322................3567799*********************** PP

                                        HHHHCHHHHHHHTST-..BE.S.SCB--GGGGHHHHHHHHHHHHHHHHHCTHHHHHHTTSSCCCCHHHHHHHHHHH CS
                               PTR2 223 aQmgttlvlqartmnr..ki.g.sfeippaqlqvlnailillliPifdklvypllrkltlgltslkkiavGlflas 294
                                        +Q+++++v+q+++mn   +i g +  + p+q+q++n+ +illliP+f +l+ypll  +++  ++ +k++vG+ las
  gene1779|gene1779|rna1778|rna1778 272 DQQSSSWVVQGSKMNAhqSIfGyKVDVLPSQMQAFNSAFILLLIPVFSNLIYPLLGWIRVFSSPEEKMGVGIALAS 347
                                        ***********9998522677878899*****************************9997777889********** PP

                                        HHHHHHHHHHHHHCCHHHT----------TCCCHHHHHHHHHHHHHCCCHHHHHHCTSS-TTTCCCCHHHHHHHHH CS
                               PTR2 295 lafaiaaivelkraktlpelpeaeevqisvlwlipqylligiselfasiggleffykeapksmkslitglflltna 370
                                        l+f+  + +e  +  +      ++ +++s+lw+ipqy++++++e++++++g+e++y eap++mks+  +++llt  
  gene1779|gene1779|rna1778|rna1778 348 LSFFCSGYLEHRIGVAE-----FTGQKLSILWQIPQYIILTAGEIMLNVTGMEYMYAEAPETMKSVALSMWLLTVT 418
                                        **********9998774.....66779************************************************* PP

                                        HHHHHHHH CS
                               PTR2 371 lgnflssv 378
                                        +gn+l   
  gene1779|gene1779|rna1778|rna1778 419 AGNLLVMG 426
                                        **998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3181.22
//
Query:       gene1780|gene1780|rna1779|rna1779  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0039   17.8   5.9     0.0066   17.1   5.9    1.3  1  DUF4728   Domain of unknown function (DUF4728)
     0.0089   15.4   5.8      0.013   14.9   5.8    1.2  1  TssN      Type VI secretion system, TssN
  ------ inclusion threshold ------
       0.21   10.3   1.3       0.22   10.3   1.3    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
       0.34   11.0   6.4       0.29   11.3   4.8    1.7  2  DUF4234   Domain of unknown function (DUF4234)


Domain annotation for each model (and alignments):
>> DUF4728  Domain of unknown function (DUF4728)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   5.9   1.5e-06    0.0066      29      87 ..      40      94 ..      35      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                            DUF4728 29 lPWLinslvslvleigilvalvllvsvieakidrlialliifflllvLniyiyygiysl 87
                                       + W+i+s+v++   i   ++l l+ s ++ k+ ++ ++ +i+++++ L+i ++  iys+
  gene1780|gene1780|rna1779|rna1779 40 IQWIIFSIVTFFYGI---FHLPLITSNMD-KLFKMDMMALITVVIFTLQIIMLFIIYSM 94
                                       57*******888666...66666666666.334555666677999************97 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.8   2.8e-06     0.013      57     116 ..      37      97 ..      33     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-06
                               TssN  57 fvpygyillqilylllGilhlylllkkffkelkekk.ilfeilltlivillglvlfvlvfn 116
                                         + +++i++ i++++ Gi+hl l++ ++ k +k++   l++++++ ++i++ ++++++  +
  gene1780|gene1780|rna1779|rna1779  37 KMKIQWIIFSIVTFFYGIFHLPLITSNMDKLFKMDMmALITVVIFTLQIIMLFIIYSMHPD 97 
                                        577899****************9*********99997778888888888888888887655 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   4.9e-05      0.22     388     450 ..      40     113 ..      11     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 4.9e-05
                            DUF2207 388 lgliilglilillallllvll..........lvfllilllillliaiivlllfsrllgrr..teeGaellakwkg 450
                                        + +ii++++ ++++++ l l+           +++li+++i+ l++i++++++ ++ + +  t++ +e++++++ 
  gene1780|gene1780|rna1779|rna1779  40 IQWIIFSIVTFFYGIFHLPLItsnmdklfkmDMMALITVVIFTLQIIMLFIIY-SMHPDLfgTKYNREVRSYIER 113
                                        44556666666666666555577788999965555555555555544444444.444443445555555555544 PP

>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.8   8.2e+03       9      15 ..       9      15 ..       4      22 .. 0.66
   2 ?   11.3   4.8   6.5e-05      0.29       6      61 ..      42      94 ..      39      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.8
                            DUF4234  9 LsivTlG 15
                                       L i+Tl 
  gene1780|gene1780|rna1779|rna1779  9 LAIFTLV 15
                                       5555553 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.5e-05
                            DUF4234  6 vilLsivTlGIYslyWlykltrelnrlsgrkkttslllvflllslitcgiysivwa 61
                                       +i++sivT+  Y+++ l  +t+++++l +   +++ l+ +++++l ++ ++ i+ +
  gene1780|gene1780|rna1779|rna1779 42 WIIFSIVTF-FYGIFHLPLITSNMDKLFKM--DMMALITVVIFTLQIIMLFIIYSM 94
                                       9********.9******************9..666666656776655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 835.37
//
Query:       gene1781|gene1781|rna1780|rna1780  [L=30]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (30 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 215.90
//
Query:       gene1782|gene1782|rna1781|rna1781  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-21   77.0   0.0    7.4e-21   74.5   0.0    1.9  1  adh_short        short chain dehydrogenase
    1.2e-12   47.9   0.0    3.6e-12   46.4   0.0    1.7  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.3e-06   28.5   0.2    3.1e-05   23.9   0.2    2.1  1  KR               KR domain
    3.8e-06   26.5   0.0    7.2e-06   25.6   0.0    1.5  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00059   19.5   0.1     0.0018   18.0   0.0    1.7  2  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 
     0.0011   19.0   0.0     0.0045   17.0   0.0    2.0  1  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0012   18.9   0.0     0.0018   18.4   0.0    1.2  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0057   16.0   0.0     0.0097   15.2   0.0    1.3  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
     0.0072   16.9   0.1      0.065   13.8   0.1    2.1  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.02   14.8   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
       0.02   14.5   0.0       0.03   13.9   0.0    1.2  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.042   13.3   0.1      0.095   12.1   0.0    1.6  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.058   13.2   0.0        0.2   11.5   0.0    1.8  2  Helicase_RecD    Helicase
      0.095   11.9   0.0       0.34   10.1   0.0    1.8  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.097   12.0   0.0       0.16   11.3   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.11   12.7   0.0        1.1    9.5   0.0    2.3  2  PPR_2            PPR repeat family
       0.13   12.9   0.0       0.23   12.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
       0.13   12.7   0.0       0.29   11.6   0.0    1.5  1  NAD_binding_7    Putative NAD(P)-binding
       0.14   11.9   0.0       0.24   11.1   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   7.9e-24   7.4e-21       1     192 [.      32     207 ..      32     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 7.9e-24
                                        SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                          adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                        k +lv+G+ssG+G+a+a+ l ++G +v++++rs + le + ++ +     + +  +Dv+++++ +           
  gene1782|gene1782|rna1781|rna1781  32 KKILVVGGSSGLGLAFAQILKEAGNNVTITSRSVQSLELLRSKWG-----FETKVLDVNTMDSQK---------SA 93 
                                        689**********************************88888877.....788889998777654.........45 PP

                                        SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                          adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152
                                          d +  +AGi++++ f++ s e +++++++N+ g++ + ++ +    +++  r + ++S+ ++  ++g+++Ys s
  gene1782|gene1782|rna1781|rna1781  94 DFDYIFCCAGISHPSYFADQSFELFKETMNTNYLGTVAVLKHYTAI--NKKPMRFIMIGSTLSLLTFPGFSSYSPS 167
                                        89***************************************98777..89999*********************** PP

                                        HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                          adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                        Kaa+ +l+ +l++e+++ g++    +++ ++T+  + +++
  gene1782|gene1782|rna1781|rna1781 168 KAALLSLFYTLRDEMKELGVELYFYNTASIQTPGFEMENK 207
                                        *******************************998776665 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   3.8e-15   3.6e-12       3     164 ..      40     187 ..      37     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.8e-15
                                        TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                       adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnag 78 
                                         sg+G a A+ l+e+G +v +t ++ ++   +e l ++ g e   +DV+  ++ ++           +D+++ +ag
  gene1782|gene1782|rna1781|rna1781  40 SSGLGLAFAQILKEAGNNVTITSRSVQS---LELLRSKWGFETKVLDVNTMDSQKS---------ADFDYIFCCAG 103
                                        58**********************9998...999999***999999*999887655.........478******** PP

                                        --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                       adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtry 154
                                        i+++  + f++ s e f++++++n  ++++++k+   + k+  + + + s+ +  ++p+ + y+ +Kaal +l  +
  gene1782|gene1782|rna1781|rna1781 104 ISHP--SYFADQSFELFKETMNTNYLGTVAVLKHYTAINKKPMRFIMIGSTLSLLTFPGFSSYSPSKAALLSLFYT 177
                                        ****..******************************************************************9888 PP

                                        HHHHHGGGTE CS
                       adh_short_C2 155 lAvelgpkgi 164
                                        l  e+ + g+
  gene1782|gene1782|rna1781|rna1781 178 LRDEMKELGV 187
                                        8777766666 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   3.3e-08   3.1e-05       4     160 ..      35     175 ..      33     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3.3e-08
                                        EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHH CS
                                 KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikae 78 
                                        l++GG  gLGl++a+ l e g +++ ++sRs        + ++ l+++ g e +v  +Dv   d+ +++       
  gene1782|gene1782|rna1781|rna1781  35 LVVGGSSGLGLAFAQILKEAG-NNVTITSRSV-------QSLELLRSKwGFETKV--LDVNTMDSQKSA------- 93 
                                        9*************9998887.5899*****2.......3566666655666665..566555544332....... PP

                                        SS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT..S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                 KR  79 eppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled..esldffvlfSSiagllgsagqanYaaa 152
                                              ++ +Ag+++ + +++++ e +++ ++    G+  + +  +   ++   f+++ S  +ll  +g ++Y+  
  gene1782|gene1782|rna1781|rna1781  94 --DFDYIFCCAGISHPSYFADQSFELFKETMNTNYLGTVAVLKHYTAinKKPMRFIMIGSTLSLLTFPGFSSYSPS 167
                                        ..33569******************************9876444333357777899*****************998 PP

                                        HHHHHHHH CS
                                 KR 153 NaflDala 160
                                         a l +l 
  gene1782|gene1782|rna1781|rna1781 168 KAALLSLF 175
                                        77665554 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   7.6e-09   7.2e-06       1     116 [.      34     152 ..      34     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.6e-09
                                        EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                          Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavgg 76 
                                        ilV+G++  +G a+++ l+e+g +v+  +r  ++   ++l+ +   e +++d + ++   k+ ++d+++ +A++++
  gene1782|gene1782|rna1781|rna1781  34 ILVVGGSSGLGLAFAQILKEAGNNVTITSRSVQS--LELLRSKWGFETKVLDVNTMDSQ-KSADFDYIFCCAGISH 106
                                        89********************999999999444..44555558889999988877775.4469************ PP

                                        H....HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT..EEEEEEEG CS
                          Epimerase  77 v....aassedpadfieknlqgtlnlleaarkagvk..rllflsSs 116
                                        +    ++s+e  ++++++n  gt+ +l+   + + k  r++ ++S+
  gene1782|gene1782|rna1781|rna1781 107 PsyfaDQSFELFKETMNTNYLGTVAVLKHYTAINKKpmRFIMIGST 152
                                        93333478888899**************9999888888******96 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.9e-06    0.0018      34      58 ..      27      49 ..      18      61 .. 0.68
   2 ?   -2.8   0.0       5.8   5.5e+03      29      48 ..     132     151 ..     128     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                                       -----.-SEEEEESTSSHHHHHHHH CS
                    Eno-Rase_NADH_b 34 kkiekgpkkvLviGaStGYGLAsri 58
                                       ++i  + kk+Lv+G+S+G GLA   
  gene1782|gene1782|rna1781|rna1781 27 HEI--SNKKILVVGGSSGLGLAFAQ 49
                                       223..47***************654 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.8
                                        HHHHS-----.-SEEEEEST CS
                    Eno-Rase_NADH_b  29 yvksqkkiekgpkkvLviGa 48 
                                          k+ ++i+k+p + + iG+
  gene1782|gene1782|rna1781|rna1781 132 VLKHYTAINKKPMRFIMIGS 151
                                        45677788888999999997 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-06    0.0045       1      68 [.      42     104 ..      42     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
                                        HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TT.ESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCS CS
                         ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakk.lG.adevinykeadlverikeltggegvdvvfecvGs 68 
                                        g+Gla  q++k +G +v+ +++s + lel+++  G  + v++ +++d     ++     ++d++f c+G+
  gene1782|gene1782|rna1781|rna1781  42 GLGLAFAQILKEAGNNVTITSRSVQSLELLRSkWGfETKVLDVNTMD----SQKSA---DFDYIFCCAGI 104
                                        89*****************************99**999999993312....22333...78999999883 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.9e-06    0.0018       3      88 ..      22     107 ..      20     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                                        HHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHH.HHHT-S CS
                       Shikimate_DH   3 akkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelke.llaead 77 
                                        a+++ +++++kk+l++G      l++ ++l++  ++v+++ R+++  + l+++  g e+++l+++ +++   a++d
  gene1782|gene1782|rna1781|rna1781  22 ARHQRHEISNKKILVVGGSSGLGLAFAQILKEAGNNVTITSRSVQSLELLRSKW-GFETKVLDVNTMDSqKSADFD 96 
                                        56666789*********9998899999999998899******************.666999999999751568899 PP

                                        EEEE-SSSSS- CS
                       Shikimate_DH  78 vvisataseep 88 
                                         ++++ + ++p
  gene1782|gene1782|rna1781|rna1781  97 YIFCCAGISHP 107
                                        99999887776 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     1e-05    0.0097      29      73 ..      24      68 ..      19      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1e-05
                                       HCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCH CS
                      THF_DHG_CYH_C 29 etgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdl 73
                                       +++ e+++kk++vvG s+ +g + a++L+e++  Vt++ ++ ++l
  gene1782|gene1782|rna1781|rna1781 24 HQRHEISNKKILVVGGSSGLGLAFAQILKEAGNNVTITSRSVQSL 68
                                       67889**************************99999998877766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   6.8e-05     0.065       2      35 ..      34      68 ..      33      74 .. 0.82
   2 ?    0.4   0.0       1.1     1e+03      46      60 ..     178     192 ..     176     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-05
                                       EEEECS.SHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                          Pyr_redox  2 vvvvGg.GyiglElAgalaelgkkVtvversdkll 35
                                       ++vvGg + +gl +A++l+e g++Vt+  rs + l
  gene1782|gene1782|rna1781|rna1781 34 ILVVGGsSGLGLAFAQILKEAGNNVTITSRSVQSL 68
                                       666665268******************99987665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                                        HHHHHHHTTEEEECS CS
                          Pyr_redox  46 lqeklekngievlln 60 
                                        l+++++++g+e+++ 
  gene1782|gene1782|rna1781|rna1781 178 LRDEMKELGVELYFY 192
                                        789********9975 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-05      0.02       1     100 [.      38     153 ..      38     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                        TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC... CS
                     NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk... 73 
                                        G++ + G + ++ l ++g  +vt+  R+ ++l+ l+++ g e+ ++dv++ ++  +  ++ d +++++g ++    
  gene1782|gene1782|rna1781|rna1781  38 GGSSGLGLAFAQILKEAG-NNVTITSRSVQSLELLRSKWGFETKVLDVNTMDS--QKSADFDYIFCCAGISHPsyf 110
                                        889999***********6.8*****************************9998..6678*********87776676 PP

                                        ...HHHH.............HHHHHH..HHHHCT--EEEEEEETT CS
                     NAD_binding_10  74 ...deeg.............aknivd..aakeagvkRfvlvsaig 100
                                                            ++++++   a +++  Rf+++++  
  gene1782|gene1782|rna1781|rna1781 111 adqS--FelfketmntnylgTVAVLKhyTAINKKPMRFIMIGSTL 153
                                        5330..245555557777887777762234456677888888765 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.1e-05      0.03       2      51 ..      29      79 ..      28     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                                       HHTS-EEEES-SH.HHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EE CS
                               IlvN  2 lkgkkiaviGyGs.qGhaqalnlrdsgldvvvglregsksvkkAkeegfev 51
                                       +++kki v+G  s  G a a+ l+++g +v+++ r+ ++     ++ gfe+
  gene1782|gene1782|rna1781|rna1781 29 ISNKKILVVGGSSgLGLAFAQILKEAGNNVTITSRSVQSLELLRSKWGFET 79
                                       789******96552589****************999886555566667764 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001     0.095      58     129 ..      83     151 ..      35     153 .. 0.67
   2 ?   -2.3   0.0       2.5   2.3e+03     151     187 ..     162     198 ..     158     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                        E--TT-HHHHHHHHHHHT-SEEEE--S---....HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEE CS
                      GDP_Man_Dehyd  58 kgDltDssslerllaevqpdevynLAAqsh....VdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaSt 129
                                         ++  Ds+      +++++d ++  A+ sh     d+sfe  ++t+++n lGt+ +L+   a++ +k +rf+ +++
  gene1782|gene1782|rna1781|rna1781  83 DVNTMDSQ------KSADFDYIFCCAGISHpsyfADQSFELFKETMNTNYLGTVAVLKHYTAIN-KKPMRFIMIGS 151
                                        44444444......6778889999999998444447899999******************9998.5789**99876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                        SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTT CS
                      GDP_Man_Dehyd 151 sPYaaaKlyadwivvnyreayglfavngilfnhespr 187
                                        s Y+ +K++   +    r++ +   v   ++n+ s  
  gene1782|gene1782|rna1781|rna1781 162 SSYSPSKAALLSLFYTLRDEMKELGVELYFYNTASIQ 198
                                        8899999999999999999999888888888887765 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021       0.2       9      59 ..      38      88 ..      37     123 .. 0.83
   2 ?   -1.3   0.0       1.7   1.7e+03      33      58 ..     165     193 ..     163     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                      Helicase_RecD  9 GKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeee 59
                                       G S+ lGla a++++e+ +n+ +t+ s ++++ l +    + + l++++ +
  gene1782|gene1782|rna1781|rna1781 38 GGSSGLGLAFAQILKEAGNNVTITSRSVQSLELLRSKWGFETKVLDVNTMD 88
                                       67999**************************99998887777777666533 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                      Helicase_RecD  33 apskenvktlfeflakglealglke...e 58 
                                        +psk+++ +lf  l+ ++++lg++    +
  gene1782|gene1782|rna1781|rna1781 165 SPSKAALLSLFYTLRDEMKELGVELyfyN 193
                                        79999999999999999999998765441 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00036      0.34     135     174 ..      24      64 ..      14      80 .. 0.77
   2 ?   -1.0   0.0      0.86   8.2e+02      93     114 ..      88     110 ..      66     152 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00036
                                        HHCCSS-TSEEEEES-SH.HHHHHHHHHHHHT-EEEEEESS CS
                                        xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                        Pyr_redox_2 135 alklkllpkrivvvGgGy.iGvElAaalaklgkevtlvear 174
                                          +++  +k+i+vvGg+   G+ +A+ l+++g +vt+  + 
  gene1782|gene1782|rna1781|rna1781  24 HQRHEISNKKILVVGGSSgLGLAFAQILKEAGNNVTITSRS 64 
                                        3445555699*9999865499***************97765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.86
                                        TCEEEEEESEEEE---.EEE-BC CS
                                        xxxxxxxxxxxxxxxx.xxxxxx RF
                        Pyr_redox_2  93 gdeekiaydklvlAtG.ssprdl 114
                                        +++++ ++d+++ + G s+p  +
  gene1782|gene1782|rna1781|rna1781  88 DSQKSADFDYIFCCAGiSHPSYF 110
                                        33344555555555554444444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.16      26      73 ..      21      69 ..      15     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                       TCCGSBS-GTTSEEEEES.-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                       2-Hacid_dh_C 26 ekallgkelsgktvGiiG.lGrIGqavakrlkafgmkviaydrskkkee 73
                                       +++++ +e+s+k++ ++G    +G a+a++lk+ g +v++++rs ++ e
  gene1782|gene1782|rna1781|rna1781 21 RARHQRHEISNKKILVVGgSSGLGLAFAQILKEAGNNVTITSRSVQSLE 69
                                       5677889******999972567*********************988655 PP

>> PPR_2  PPR repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0         1   9.9e+02      25      35 ..     178     188 ..     168     189 .. 0.84
   2 ?    9.5   0.0    0.0012       1.1       6      41 ..     212     249 ..     210     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1
                              PPR_2  25 lfneMkkrgle 35 
                                        l +eMk+ g+e
  gene1782|gene1782|rna1781|rna1781 178 LRDEMKELGVE 188
                                        779****9997 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                              PPR_2   6 yNtlIsglck.kgkveeAfklfneMkkrgl.ePnsyTy 41 
                                        y+  I g+     + e Af++++ Mk+r++   +++Ty
  gene1782|gene1782|rna1781|rna1781 212 YTKAIEGMISpSSARERAFSFLSGMKRRSVvASDAFTY 249
                                        66667777666777899***********9879999999 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00024      0.23       7      77 ..      42     107 ..      34     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                                        TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEEESTGGGS CS
                    Methyltransf_25   7 GtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlp.fedgsfDlvvssgalhhl 77 
                                        G G   ++++k+ g  +vt +  s + le  r++       +e  + d+++++ ++++ fD+++++ +++h 
  gene1782|gene1782|rna1781|rna1781  42 GLGLAFAQILKEAG-NNVTITSRSVQSLELLRSKW-----GFETKVLDVNTMDsQKSADFDYIFCCAGISHP 107
                                        44555566667766.9*****************99.....699999999999746888*******8778773 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.29       3      46 ..      27      78 ..      26     112 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                      NAD_binding_7  3 ldlkgkkvlvvGgGe.vAarkvrklleagakvtvvapevkeele........e 46
                                       +++++kk+lvvGg + +++  ++ l eag +vt+ +  v++ le        e
  gene1782|gene1782|rna1781|rna1781 27 HEISNKKILVVGGSSgLGLAFAQILKEAGNNVTITSRSVQS-LEllrskwgfE 78
                                       7899*******997549*******************99622.22233333331 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.24      27      85 ..      12      71 ..       5      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                    Methyltransf_16 27 vlvkylekklakelganelsklsvlELGsGtGlvGlavael..lpeakviltDlee.llell 85
                                       + v+y+        +++e s++++l +G  +Gl Gla+a+     + +v++t ++   lell
  gene1782|gene1782|rna1781|rna1781 12 I-VIYFFLRHRARHQRHEISNKKILVVGGSSGL-GLAFAQIlkEAGNNVTITSRSVqSLELL 71
                                       3.33433334456789************99997.*****995338899***98775355655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 1757.50
//
Query:       gene1783|gene1783|rna1782|rna1782  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-36  124.2   0.4    3.4e-36  123.5   0.4    1.3  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    3.5e-24   85.1   0.2    3.5e-24   85.1   0.2    1.9  2  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin
  ------ inclusion threshold ------
      0.067   13.6   0.3       0.15   12.4   0.3    1.6  1  DUF4014   Protein of unknown function (DUF4014)


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.4   5.6e-40   3.4e-36       4     101 ..     103     203 ..     100     204 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 5.6e-40
                                        HHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTC..EEEEEE-SGGGTH CS
                           Sod_Fe_C   4 elaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeak..plLalDvwehAYy 76 
                                        +l e i+++fgs ek+ ++f+  a+++fgsGw+wL+++++ + L i +t nqd+ ++k+++  p+L+lDvwehAYy
  gene1783|gene1783|rna1782|rna1782 103 KLLECIDKSFGSQEKMVEKFNGIAASLFGSGWVWLCYRRNeGVLVIRKTYNQDSICMKTSStiPILGLDVWEHAYY 178
                                        79999********************************988468***********999765567************* PP

                                        HHHTT-HHHHHHHHGGGBBHHHHHH CS
                           Sod_Fe_C  77 ldyqnkradYieafwnvvnWkevee 101
                                        l+y+n+ra+Y++++w+vvnW  v++
  gene1783|gene1783|rna1782|rna1782 179 LKYKNARAEYVANWWKVVNWGMVNK 203
                                        *********************9986 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.2   5.9e-28   3.5e-24       2      81 ..       3      91 ..       2      92 .. 0.97
   2 ?   -1.7   0.2      0.68   4.1e+03      33      43 ..     187     197 ..     174     222 .. 0.53

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 5.9e-28
                                       ------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHH.........HHHHHHHHHHHH CS
                           Sod_Fe_N  2 yeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlk.........klekalrnnagg 70
                                       + Lp+L+Y+ydaLeP +++et+  Hh+kHh++Y+n l +++++  +++++l+ +v+k         + +++l n  gg
  gene1783|gene1783|rna1782|rna1782  3 FALPNLDYPYDALEPFVDEETMRTHHTKHHQGYINSLERTIRNNGLEDQDLNFYVTKsrrirglkdNVRRDLINFSGG 80
                                       99*****************************************************999******99999********* PP

                                       HHHHHHHHHTB CS
                           Sod_Fe_N 71 hvnHslfwknl 81
                                       h nHslfwk++
  gene1783|gene1783|rna1782|rna1782 81 HYNHSLFWKMM 91
                                       *********99 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.68
                                        HHHHHHHHHHH CS
                           Sod_Fe_N  33 tYvnnlNkale 43 
                                         Yv n+ k+++
  gene1783|gene1783|rna1782|rna1782 187 EYVANWWKVVN 197
                                        45555544433 PP

>> DUF4014  Protein of unknown function (DUF4014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.6e-05      0.15      34      65 ..     176     207 ..     145     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                            DUF4014  34 iffiwlagvqaekiaewyssivwgpfnklhnk 65 
                                         +++     +ae +a+w+  + wg  nk+ + 
  gene1783|gene1783|rna1782|rna1782 176 AYYLKYKNARAEYVANWWKVVNWGMVNKIFEE 207
                                        4667777889******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1309.54
//
Query:       gene1784|gene1784|rna1783|rna1783  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-08   34.6   0.0    4.4e-08   33.2   0.0    1.6  1  Erf4      Golgin subfamily A member 7/ERF4 family
  ------ inclusion threshold ------
       0.12   12.5   0.0       0.13   12.3   0.0    1.1  1  ENTH      ENTH domain


Domain annotation for each model (and alignments):
>> Erf4  Golgin subfamily A member 7/ERF4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0     5e-12   4.4e-08       2     115 ..       8     110 ..       7     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 5e-12
                               Erf4   2 vripRdystgdlapqFstllppeLsgyiseeefeeiinkiNeilaeafspysvrnildnvlglltlylwslvlkth 77 
                                        + ipRd  t d  ++F t++p+++ ++i++++++eii+ +N+ l+  +sp s  ++++      t+ ++  +++ +
  gene1784|gene1784|rna1783|rna1783   8 IQIPRDPRT-D-GISFITSMPEIMAEKIERQKWKEIISGLNDVLYGLESP-SLVSFIK------TVSIIPFLVS-T 73 
                                        789999866.3.67************************************.4444443......4445555555.5 PP

                               Erf4  78 ykkklkklekyieelNeelfkerglkiisprrsgylsl 115
                                         ++   ++e+y++e+N+  +++ g++ii+p  + y+ l
  gene1784|gene1784|rna1783|rna1783  74 PQNAYVRVEEYLSEANKL-LERYGIRIIHPGHHQYVEL 110
                                        6778899*********76.5999*******98888766 PP

>> ENTH  ENTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05      0.13      22      79 ..      23      80 ..      18     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHTTSHHHHHHHHHHHHHHHHH--GGGHHHHHHHHHHHHHHHHHS-HHHHH CS
                               ENTH 22 kllteiarltyskkelseiisvitkrLqnnkgkewrsvlKaLtlieYLlknGseqvid 79
                                       + + ei+  + + ++++eiis +   L   ++ +  s +K+  +i +L+ + +++ ++
  gene1784|gene1784|rna1783|rna1783 23 TSMPEIMAEKIERQKWKEIISGLNDVLYGLESPSLVSFIKTVSIIPFLVSTPQNAYVR 80
                                       6899***********************99********************876664443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 748.81
//
Query:       gene1785|gene1785|rna1784|rna1784  [L=1018]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.1e-194  646.7   0.1   1.8e-193  644.1   0.1    1.9  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    7.9e-24   84.4   0.0      2e-23   83.0   0.0    1.7  1  Anticodon_1   Anticodon-binding domain of tRNA
    2.3e-14   53.0   0.5    6.6e-05   21.8   0.0    4.2  3  tRNA-synt_1g  tRNA synthetases class I (M)
     0.0013   18.1   0.0      0.034   13.5   0.0    2.6  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  644.1   0.1  3.9e-197  1.8e-193       2     601 ..      15     647 ..      14     648 .. 0.92

  Alignments for each domain:
  == domain 1  score: 644.1 bits;  conditional E-value: 3.9e-197
                        tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                        ++e W + ++f+k+ e +k +++f+++dgPP++tG +H+Gh+l  t+kd+v+r+ +++G++v++++GwD++Gl++e
  gene1785|gene1785|rna1784|rna1784  15 VLEYWRNGKCFEKACEMSKGREKFTFYDGPPFATGLPHYGHILSGTIKDTVTRFFYQQGYDVDRRFGWDCHGLPVE 90 
                                        7899************************************************************************ PP

                        tRNA-synt_1  78 akvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladk 153
                                        ++++kklg++ ++e+ k+g ++++e++r+++++y++e++k v+rlG+++ f + y T+d e++e+v+++f++l+++
  gene1785|gene1785|rna1784|rna1784  91 YEIDKKLGISSRDEVLKMGIDKYNEECRKIVMKYSSEWEKIVERLGRWISFRNGYRTMDREFMESVWNIFKELFNR 166
                                        **************************************************************************** PP

                        tRNA-synt_1 154 gliyrgkklvnwstklktalselEv..eykdkkdalihvafpl...adkeevklviaTTtPeTllgdtavavnpel 224
                                         liyrg +++++st+++t+ls++E   +ykd++d+++ +afpl    ++ + +lv++TTtP+Tl+++ a++vn  +
  gene1785|gene1785|rna1784|rna1784 167 NLIYRGFRVMPFSTACSTPLSNFESnqNYKDVSDPSVLIAFPLlegLGGYKLSLVAWTTTPWTLPSNCALVVNSGF 242
                                        ************************9999***************544445559************************ PP

                        tRNA-synt_1 225 dyvitkeklilaeallkslvkkesekkiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvVk 293
                                         y++ ++k  +    ++ + +  +++kil+++ gkeLeg+e+e+p+       ++  +++ +  +v+   GtGvV+
  gene1785|gene1785|rna1784|rna1784 243 LYGVFEHKQRFYLMHVDRIEEYFKDTKILKKISGKELEGLEYEQPFsyfeeyrKKGFFRVYTSGFVTDTDGTGVVH 318
                                        ***54444444445566666667899************************9988889******************* PP

                        tRNA-synt_1 294 iaPahdedDyevgkkynl.....evinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpf 364
                                        +aP+++e Dy+v  + +l      v++++de+g++t+e+++++g +v+d++k++++++k+k   l +++i h++pf
  gene1785|gene1785|rna1784|rna1784 319 CAPGFGECDYNVFVEKGLirendLVPCPVDENGRYTDEVKDYAGRYVKDCDKSILSDIKDK--VLMNQRIVHKYPF 392
                                        ******************99998899**********************************9..777899******* PP

                        tRNA-synt_1 365 cerskkpiiyrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsket 439
                                        c+rs++p++y++++ Wfv+vk+ + ++l+++ek++++pk  k kr+++wlen++dW iSR+r+WG++ipl+ +++ 
  gene1785|gene1785|rna1784|rna1784 393 CWRSDTPLLYKLVPNWFVKVKDHVCSLLRNNEKINWIPKDiKYKRFHNWLENARDWSISRNRFWGTPIPLWTTEDY 468
                                        ***************************************9899********************************* PP

                        tRNA-synt_1 440 eevvvreelkelvagreeeeaekkalekeakdkl..kkekgelekdedvlDvWFsSgswpfstlgype........ 505
                                         ++++  +++el++    + +++ ++++e++d++  +k+ +e++++e+vlD+WF+Sgs+p+++ ++p+        
  gene1785|gene1785|rna1784|rna1784 469 SDMICIGSVEELER---LSGRKIVDIHREFIDDIviHKNGKEYRRVEEVLDCWFESGSMPYAQDHWPFckevgagl 541
                                        *****777777666...7888899999999999988888889*************************833333222 PP

                        tRNA-synt_1 506 .....edtee.......lkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslg 569
                                             +   e       +k+ fpa+++ eGlD++rgW+++l ++s  l+++  f +v+v+g+v++e+GrKmSK+l+
  gene1785|gene1785|rna1784|rna1784 542 edlsvT-D-EdgkwkklVKENFPANFIGEGLDQTRGWFYTLHVISSLLFDQPAFLNVIVNGIVLAEDGRKMSKRLK 615
                                        222211.1.122222236789******************************************************* PP

                        tRNA-synt_1 570 NvidpldvikkygadalRltlilsdvgrdinl 601
                                        N++dp+ ++++ygad+lR++l++s+v++++nl
  gene1785|gene1785|rna1784|rna1784 616 NYPDPSLILNTYGADSLRMYLLSSPVVEAENL 647
                                        ***************************99987 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   4.5e-27     2e-23       1     149 [.     688     818 ..     688     821 .. 0.94

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 4.5e-27
                        Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrl 76 
                                        d wi + ln++  + te+++ y+++ +++ +  f ++dl++wy+++ ++++ s +        +vl evl  ++++
  gene1785|gene1785|rna1784|rna1784 688 DDWIKTSLNNFTVSLTEKMKGYELSSILTLALRF-IDDLSNWYIRIYRKEIRSGHH-------TVLGEVLLRFSIV 755
                                        78*******************************6.9**************987665.......9************ PP

                        Anticodon_1  77 laPfmPfitEelwqreeeelgkkesimlaewpekaeelekeleeeevellkeivkairklrselkikpsselk 149
                                        +aPf+Pf++E+ +    ++l+  es++ +e+p ++    +++    +e++k+i++a+r+lr+ + i+ +++lk
  gene1785|gene1785|rna1784|rna1784 756 MAPFTPFFSEYSY----QSLNPGESVHFQEYPTCN---SGTH---PFEMAKSIITAVRRLREMNSISLKTPLK 818
                                        *************....899999*********987...7888...9**********************99976 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.5e-08   6.6e-05       8     130 ..      45     186 ..      43     191 .. 0.77
   2 !    9.8   0.2   6.5e-05      0.29     185     239 ..     409     464 ..     375     472 .. 0.70
   3 !   15.0   0.0   1.8e-06     0.008     308     373 ..     590     656 ..     539     670 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.5e-08
                                        B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-H................HHH CS
                       tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtp................eel 66 
                                        p+a+g +H Gh+l+  + D ++R+  ++g++v    g D hG p+e + +k+ g++                 +++
  gene1785|gene1785|rna1784|rna1784  45 PFATGLPHYGHILSGTIKDTVTRFFYQQGYDVDRRFGWDCHGLPVEYEIDKKlGISSrdevlkmgidkyneecRKI 120
                                        7899******************************************997653366541111111111111111455 PP

                                        HHHHHHHHHHHHHHTT..---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE CS
                       tRNA-synt_1g  67 vekvheeikelfkkln..isfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderfl 130
                                        v k+++e +++ ++l+  isf + +rt ++e  e v +ifk+l +++liy++     +++++++ l
  gene1785|gene1785|rna1784|rna1784 121 VMKYSSEWEKIVERLGrwISFRNGYRTMDREFMESVWNIFKELFNRNLIYRGFRVMPFSTACSTPL 186
                                        6666666666777765669999999*************************9999999988887766 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.5e-05
                                        EE-GGGGHHHHHHHH.HH-TT...SHHHHHHHH.HHHHT----EE-ESS-SSS-EET..T CS
                       tRNA-synt_1g 185 ffklskfekklkewieeeeke...leenvkkivkewlkegLkdlaisrdldwGipvP..g 239
                                        f k++++   l +  e+        ++   k  ++wl++  +d++isr+  wG p+P   
  gene1785|gene1785|rna1784|rna1784 409 FVKVKDHVCSLLRNNEK---InwiPKDIKYKRFHNWLEN-ARDWSISRNRFWGTPIPlwT 464
                                        55544444444333322...23324555667789***99.9****************652 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1.8e-06
                                        T----S-EEEE--.EEE--------------HHHHHHHH-HHHHHHHHHH.HS-TTS-EEE-HHHHHH CS
                       tRNA-synt_1g 308 elklpkkvvahey.ltvegkKlSkSrgvvvkakealerldadllRYylaa.eapekkDldfswedfve 373
                                        +  +  +v++++  l  +g+K+Sk  ++  +++ +l+++ ad lR yl++    e ++l f+++ + e
  gene1785|gene1785|rna1784|rna1784 590 QPAF-LNVIVNGIvLAEDGRKMSKRLKNYPDPSLILNTYGADSLRMYLLSsPVVEAENLRFNENGVKE 656
                                        3333.455566651556799*************************99999678889999999877655 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.037   1.7e+02       9      48 ..      37      76 ..      30      80 .. 0.86
   2 !   13.5   0.0   7.5e-06     0.034     232     299 ..     587     657 ..     581     659 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.037
                                       EEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                       tRNA-synt_1e  9 kvtlYvCGptvydashlGhaRslvafDilrrilqalgYdv 48
                                       k t+Y   p +    h Gh  s  + D + r++ ++gYdv
  gene1785|gene1785|rna1784|rna1784 37 KFTFYDGPPFATGLPHYGHILSGTIKDTVTRFFYQQGYDV 76
                                       667777777888899************************9 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.5e-06
                                        HSSS--EEEEEEE--.EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-T..TS-EEE-HHHHHHH CS
                       tRNA-synt_1e 232 afdkqlvkyflhngh.lkiegekmsksLknfitikdvlkkfdprqlRllllsahy..rsqldfkeelleea 299
                                        +fd++     + ng+ l  +g+kmsk Lkn+     +l+++ +  lR++lls      ++l f+e+ ++e+
  gene1785|gene1785|rna1784|rna1784 587 LFDQPAFLNVIVNGIvLAEDGRKMSKRLKNYPDPSLILNTYGADSLRMYLLSSPVveAENLRFNENGVKEV 657
                                        566443333444554156689*****************************997652246788888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1018 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.91u 0.36s 00:00:01.27 Elapsed: 00:00:00.58
# Mc/sec: 5250.67
//
Query:       gene1786|gene1786|rna1785|rna1785  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0048   17.3   2.4         34    5.0   2.3    4.8  4  NPV_P10         Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
      0.017   15.5   1.6       0.47   10.8   0.0    3.3  3  BTB_2           BTB/POZ domain
      0.082   13.1  14.1      0.078   13.2   6.0    3.5  3  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
      0.083   13.3   1.6       0.63   10.5   0.8    2.6  2  DASH_Dad2       DASH complex subunit Dad2
       0.12   12.4   0.0       0.44   10.6   0.0    1.9  1  HTH_35          Winged helix-turn-helix DNA-binding
       0.13   12.6   1.8        3.5    8.0   1.8    2.6  1  DUF2935         Domain of unknown function (DUF2935)
       0.16   12.4   2.5        3.9    7.9   0.1    3.5  3  ACP_PD          Acyl carrier protein phosphodiesterase
       0.21   12.0  12.7      0.093   13.2   9.4    2.0  2  Fez1            Fez1
       0.22   12.0  11.0        0.1   13.0   3.0    3.5  2  ZapB            Cell division protein ZapB
       0.27   10.9   8.0      0.089   12.5   0.4    3.2  4  RPW8            Arabidopsis broad-spectrum mildew resistance 
       0.28   11.6  10.1        3.1    8.3   8.3    2.9  3  CENP-H          Centromere protein H (CENP-H)
       0.28   11.5  13.2       0.57   10.5   5.2    3.0  2  OmpH            Outer membrane protein (OmpH-like)
       0.31   11.1  12.6      0.054   13.6   7.5    2.3  2  ADIP            Afadin- and alpha -actinin-Binding
       0.32   11.3   2.2        2.4    8.5   0.4    3.3  3  DUF948          Bacterial protein of unknown function (DUF948
       0.34   10.7   9.8        7.5    6.3   6.5    2.6  2  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
       0.34   10.7  16.1       0.14   12.0  13.1    1.8  2  KASH_CCD        Coiled-coil region of CCDC155 or KASH
       0.35   11.5   9.1        1.6    9.4   6.4    3.3  3  YabA            Initiation control protein YabA
       0.45   10.4  10.4      0.077   12.9   1.1    3.1  4  PhaP_Bmeg       Polyhydroxyalkanoic acid inclusion protein (P
       0.52   10.7  12.2      0.069   13.5   4.6    3.2  3  Tup_N           Tup N-terminal
       0.68   10.5  12.4          1   10.0   5.5    3.2  2  Syntaxin-6_N    Syntaxin 6, N-terminal
       0.92    9.4   6.4       0.68    9.8   1.5    3.0  3  Sec34           Sec34-like family
       0.99    9.4  12.8        1.5    8.8   7.4    3.2  3  Rootletin       Ciliary rootlet component, centrosome cohesio
          1    9.5  13.9        2.3    8.4   7.0    3.5  4  Fib_alpha       Fibrinogen alpha/beta chain family
        1.6    8.1   4.5        4.9    6.5   0.2    3.1  3  DUF99           Protein of unknown function DUF99
        1.9    8.9  16.0          2    8.8   2.8    4.0  3  BLOC1_2         Biogenesis of lysosome-related organelles com
        2.3    8.5  11.3        2.8    8.2   9.8    2.0  1  THOC7           Tho complex subunit 7
        2.8    8.0  14.1        1.6    8.8   5.5    3.4  3  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        2.9    8.6   9.4        7.6    7.3   7.2    2.9  2  FliD_N          Flagellar hook-associated protein 2 N-terminu
        3.5    8.0   8.3        1.4    9.2   2.4    3.2  3  DUF5638         Family of unknown function (DUF5638)
        4.4    8.3  15.0        1.3    9.9   1.7    3.6  3  PRKG1_interact  cGMP-dependent protein kinase interacting dom
        4.5    7.1   5.5       0.76    9.6   0.2    2.3  2  PhageMin_Tail   Phage-related minor tail protein
        5.4    7.1   8.6        3.6    7.7   5.0    2.6  3  Cauli_DNA-bind  Caulimovirus DNA-binding protein
          6    6.5  14.7       0.33   10.6   6.3    2.8  3  Laminin_I       Laminin Domain I
        8.6    7.1  15.0        3.1    8.6   5.4    4.1  4  Occludin_ELL    Occludin homology domain


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.34   1.8e+02      23      45 ..     166     188 ..     164     196 .. 0.87
   2 ?    1.2   0.0         1   5.3e+02      38      56 ..     210     228 ..     203     244 .. 0.76
   3 ?    5.0   2.3     0.064        34       4      59 ..     264     319 ..     261     387 .. 0.89
   4 ?    0.4   0.1       1.8   9.4e+02      20      32 ..     375     387 ..     357     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.34
                            NPV_P10  23 lqqqvddvqenlpdvtelnekLd 45 
                                        ++q+++ +  +l+d++e+++kL 
  gene1786|gene1786|rna1785|rna1785 166 VSQSINGLLGDLRDIEEISHKLR 188
                                        67899999999*******99996 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1
                            NPV_P10  38 telnekLdaqsaqLaelet 56 
                                        +e+ ++Ld+ s +L++l+ 
  gene1786|gene1786|rna1785|rna1785 210 SEVVKQLDKCSRELEDLKR 228
                                        6888999999999999976 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.064
                            NPV_P10   4 niLlvIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                         +L  Ir+ +k +++  + ++ + ++ ++ l+d tel+ k+d++ ++ a+++++v 
  gene1786|gene1786|rna1785|rna1785 264 DVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVA 319
                                        5888999999999999999999999999999999*******999877777777665 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.8
                            NPV_P10  20 Vdalqqqvddvqe 32 
                                        V+ lq+++d+++ 
  gene1786|gene1786|rna1785|rna1785 375 VNELQSKIDEIRR 387
                                        4455555555554 PP

>> BTB_2  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00089      0.47      18      77 ..     167     223 ..     162     227 .. 0.84
   2 ?   -1.8   0.0       7.8   4.1e+03      53      79 ..     262     286 ..     243     300 .. 0.57
   3 ?    1.5   0.0      0.72   3.8e+02      22      53 ..     333     360 ..     319     383 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00089
                                        HTSTTSTTTSSGG....GGEETTTTEEEE-S-HHHHHHHHHHHHS.S-B---TTS-HHHH CS
                              BTB_2  18 srkpdtlLgkllkteelddydeetneyffDRspklFetiLnyyrtggkLhrpeevelksl 77 
                                        s+  ++lLg+l +   ++  +++ +++ffD  +k+Fe+ L y r+  ++ ++ +++ ++l
  gene1786|gene1786|rna1785|rna1785 167 SQSINGLLGDLRD---IEEISHKLRRMFFDMRSKSFEAELGYARSSSEVVKQLDKCSREL 223
                                        5667889999999...5688888899*******************988877778888776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.8
                                        HHHHHHHHHS.S-B---TTS-HHHHHH CS
                              BTB_2  53 FetiLnyyrtggkLhrpeevelkslle 79 
                                         + +L+ +r+  +++ +e ++ +  ++
  gene1786|gene1786|rna1785|rna1785 262 LKDVLKGIRK--RVKTMESMSQEVEMK 286
                                        4445555555..444444444444444 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.72
                                        TSTTTSSGG....GGEETTTTEEEE-S-HHHH CS
                              BTB_2  22 dtlLgkllkteelddydeetneyffDRspklF 53 
                                        dt L++ lk       +++++++ +DR++k+ 
  gene1786|gene1786|rna1785|rna1785 333 DT-LKEALK---KTVESNKKKSITIDRQKKII 360
                                        33.444444...245677778999***99875 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       4.3   2.3e+03      53      53 ..     209     209 ..     162     234 .. 0.50
   2 ?   13.2   6.0   0.00015     0.078       9      85 ..     271     344 ..     266     367 .. 0.77
   3 ?    3.1   0.3       0.2   1.1e+02      64      88 ..     396     420 ..     376     422 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.3
                        TMF_TATA_bd  53 m 53 
                                        +
  gene1786|gene1786|rna1785|rna1785 209 S 209
                                        1 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00015
                        TMF_TATA_bd   9 psvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlL 84 
                                        + v+++e++s+e+  +E E++++ +++++l+ + d++ +e ++ ++ +    +l++++++++k ++ l+e ++++ 
  gene1786|gene1786|rna1785|rna1785 271 KRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVA---RLSTKNAKIRKDYDTLKEALKKTV 343
                                        57899*****************999999999999999999998885554...555555555555555555555555 PP

                        TMF_TATA_bd  85 e 85 
                                        e
  gene1786|gene1786|rna1785|rna1785 344 E 344
                                        4 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.2
                        TMF_TATA_bd  64 keleelekeleelqeryetlLellG 88 
                                        +  ++le+e+++ ++r +  L ll 
  gene1786|gene1786|rna1785|rna1785 396 SIKSKLEEEIADYERRMSDFLSLLN 420
                                        5568999999999999999999986 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.9     1e+03       4      20 ..     216     232 ..     206     239 .. 0.68
   2 ?   10.5   0.8    0.0012      0.63      18      75 ..     256     313 ..     253     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.9
                          DASH_Dad2   4 iaeKraELeaLkqlrdl 20 
                                        + +  +ELe+Lk+++ +
  gene1786|gene1786|rna1785|rna1785 216 LDKCSRELEDLKRINGM 232
                                        44445677777777765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                          DASH_Dad2  18 rdlsdslakqleeLeeklstladgteavasVlanWqnvlraismaslkllqkaeeeae 75 
                                         d+s++l++ l+ + ++++t+++ ++ v+   ++++nvl+  +  + k+ +  +e+a+
  gene1786|gene1786|rna1785|rna1785 256 YDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENAS 313
                                        689************************************8877777777665555333 PP

>> HTH_35  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00083      0.44       6      37 ..     264     295 ..     261     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00083
                             HTH_35   6 dIiAaLrkrgttLaalsreaglssstlsnalt 37 
                                        d+   +rkr  t+ ++s+e ++++++ +n+l+
  gene1786|gene1786|rna1785|rna1785 264 DVLKGIRKRVKTMESMSQEVEMKEKEYENVLK 295
                                        778889************************97 PP

>> DUF2935  Domain of unknown function (DUF2935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.8    0.0066       3.5      31     102 ..     278     352 ..     185     356 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0066
                            DUF2935  31 dlikeakefkkeFekllaeavelseglv.......rasseleeavakLneealkltreliqFkkellekvlscklf 99 
                                         + +e +  +ke+e++l++  el              + +  eava+L ++  k  + + ++k+ l++ v+s+k +
  gene1786|gene1786|rna1785|rna1785 278 SMSQEVEMKEKEYENVLKDYTEL----KgkmdriiNENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESNKKK 349
                                        33444444455555555555555....0444576678888999999999999999999999999999999999999 PP

                            DUF2935 100 sii 102
                                        si+
  gene1786|gene1786|rna1785|rna1785 350 SIT 352
                                        887 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.9   1.5e+03      51      76 ..     173     198 ..     170     227 .. 0.64
   2 ?    7.9   0.1    0.0074       3.9      55      99 ..     256     300 ..     254     304 .. 0.89
   3 ?    2.0   0.0      0.51   2.7e+02      68     101 ..     304     337 ..     300     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.9
                             ACP_PD  51 wLesYaelegieralqrmarrlkras 76 
                                        +L   +++e i + l+rm   ++ +s
  gene1786|gene1786|rna1785|rna1785 173 LLGDLRDIEEISHKLRRMFFDMRSKS 198
                                        57788899999999999975555444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0074
                             ACP_PD  55 YaelegieralqrmarrlkrasklaeaieeleenyaeleadFlef 99 
                                        Y   + ++++l+++ +r+k  +++++ +e  e++y+++ +d++e+
  gene1786|gene1786|rna1785|rna1785 256 YDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTEL 300
                                        55667899****************************999999875 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.51
                             ACP_PD  68 marrlkrasklaeaieeleenyaeleadFleffp 101
                                        m+r ++ +++++ea++ l ++ a++++d+ ++ +
  gene1786|gene1786|rna1785|rna1785 304 MDRIINENASFSEAVARLSTKNAKIRKDYDTLKE 337
                                        7777777788*****************9988755 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1         4   2.1e+03      71     100 ..     199     227 ..     166     243 .. 0.53
   2 ?   13.2   9.4   0.00018     0.093      20     142 ..     242     387 ..     236     417 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4
                               Fez1  71 cenelqrkkseaellrekvekleeelkelr 100
                                         e+el  ++s++e++++ ++k+++el++l+
  gene1786|gene1786|rna1785|rna1785 199 FEAELGYARSSSEVVKQ-LDKCSRELEDLK 227
                                        33333333333333333.444444444444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00018
                               Fez1  20 kdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk.......kseaellrek 88 
                                        kd   + + k ++   +   l+++ + ++++ ++++++++++e k++e e++ ++  +         +e+  ++e 
  gene1786|gene1786|rna1785|rna1785 242 KDFGIDTSVKENDFYDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELkgkmdriINENASFSEA 317
                                        7888899999999999999999999999999999999999999999995554443333323334445566666666 PP

                               Fez1  89 vekleeelkelreelselsleeeeaa..lesdeakaqrqe.....................aeeleelkreverlr 141
                                        v +l+++ +++r+++ +l++  ++++  +++++    rq+                     +       ++++++r
  gene1786|gene1786|rna1785|rna1785 318 VARLSTKNAKIRKDYDTLKEALKKTVesNKKKSITIDRQKkiidvlqsrigdecilpvnelQ-------SKIDEIR 386
                                        66666666666665555443333332111111112222224455565555555533333221.......3333333 PP

                               Fez1 142 a 142
                                        +
  gene1786|gene1786|rna1785|rna1785 387 R 387
                                        3 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.0    0.0002       0.1      10      66 ..     287     343 ..     269     345 .. 0.93
   2 ?    2.5   0.2      0.39     2e+02      19      65 ..     374     415 ..     358     421 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0002
                               ZapB  10 EskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLL 66 
                                        E+ +++ +  +t+L+ ++++   en++ +e  ++l+ +n + +++   ++e lkk +
  gene1786|gene1786|rna1785|rna1785 287 EKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTV 343
                                        888999****************************************99999999865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.39
                               ZapB  19 titlLqmeieeLkeeneelkeenrele.....eeneqlkeereawqerlkkL 65 
                                         + +Lq +i+e +++                 +  ++l+ee +  ++r++  
  gene1786|gene1786|rna1785|rna1785 374 PVNELQSKIDEIRRRA----------DseldlSIKSKLEEEIADYERRMSDF 415
                                        5566666666666655..........02223344455555555555555555 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.6     3e+03      49      70 ..     214     228 ..     210     237 .. 0.59
   2 ?   12.5   0.4   0.00017     0.089      18      68 ..     243     293 ..     229     304 .. 0.83
   3 ?    0.7   0.3      0.71   3.7e+02      37      75 ..     304     342 ..     295     355 .. 0.72
   4 ?    0.9   0.4      0.63   3.3e+02      17      70 ..     315     365 ..     310     389 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.6
                               RPW8  49 keieklnkeldrpreeieeLkk 70 
                                        k       +ld++  e+e+Lk+
  gene1786|gene1786|rna1785|rna1785 214 K-------QLDKCSRELEDLKR 228
                                        4.......44555555555543 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00017
                               RPW8  18 kaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeL 68 
                                        +  ++ + k  df   +k L++ l+ i+  vk +e++++e++ +++e e+ 
  gene1786|gene1786|rna1785|rna1785 243 DFGIDTSVKENDFYDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENV 293
                                        444678889999*9***************************9999998865 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.71
                               RPW8  37 LestleritPvvkeieklnkeldrpreeieeLkklLeka 75 
                                        +++ +++ + + + + +l+++  + r++ + Lk+ L+k 
  gene1786|gene1786|rna1785|rna1785 304 MDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKT 342
                                        555555556666777777777777777777777777765 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.63
                               RPW8  17 lkaileakkksldfksilkrLestleritPvvkeieklnkeldrpreeieeLkk 70 
                                         +a+ + + k+++++   + L++ l++ + +    +k +  +dr+++ i+ L++
  gene1786|gene1786|rna1785|rna1785 315 SEAVARLSTKNAKIRKDYDTLKEALKKTVES---NKKKSITIDRQKKIIDVLQS 365
                                        5677777777777777777777776654333...22333335666666665555 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.94     5e+02      28      85 ..     176     233 ..     162     247 .. 0.58
   2 ?    8.3   8.3    0.0058       3.1       5      85 ..     273     353 ..     262     367 .. 0.88
   3 ?    7.6   4.3    0.0095         5       3      71 ..     306     385 ..     304     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.94
                             CENP-H  28 eltevekenlrlkrknrelaaellelakekesekeklkeelekleaelkksrqrwrvv 85 
                                        +l ++e+ + +l+r    + ++  e +   ++ ++++ ++l+k  +el++ ++   ++
  gene1786|gene1786|rna1785|rna1785 176 DLRDIEEISHKLRRMFFDMRSKSFEAELGYARSSSEVVKQLDKCSRELEDLKRINGMI 233
                                        5555555555555555555555544455555555667777777777777666665554 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0058
                             CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleaelkksrq 80 
                                        ++  + +s+e++  ++e+++++++ te++ +  r+ ++n++  + +++l+ ++++ +++++   e+l++ ++  ++
  gene1786|gene1786|rna1785|rna1785 273 VKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESNKK 348
                                        66778899999***********************************999999999997888888888888888888 PP

                             CENP-H  81 rwrvv 85 
                                        ++ ++
  gene1786|gene1786|rna1785|rna1785 349 KSITI 353
                                        88776 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0095
                             CENP-H   3 plieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...........eklkee 67 
                                         +i+++   s+++++ls++ ++++++ +++++  +++ + n+++  ++ +++k  +  +           ++l+++
  gene1786|gene1786|rna1785|rna1785 306 RIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESNKKKSITIDRQKKIIDVLQsrigdecilpvNELQSK 381
                                        57899999****************************************7666654444445675555544444444 PP

                             CENP-H  68 lekl 71 
                                        ++++
  gene1786|gene1786|rna1785|rna1785 382 IDEI 385
                                        4444 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.1      0.11        57      18      51 ..     259     292 ..     250     304 .. 0.69
   2 ?   10.5   5.2    0.0011      0.57       7      77 ..     304     389 ..     302     421 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.11
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               OmpH  18 kaaqeqlekkfkklqaeleakekelqklqeelqk 51 
                                         +a +++ k ++k+ +++e++ +e++ +++e+++
  gene1786|gene1786|rna1785|rna1785 259 SKALKDVLKGIRKRVKTMESMSQEVEMKEKEYEN 292
                                        4555555566688888999999999999999972 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0011
                                        HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH.................. CS
                               OmpH   7 vqkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqe.................. 64 
                                        +++i++e   + +a ++l +k +k+++++++++++l+k +e  +kk+ +    +++++                  
  gene1786|gene1786|rna1785|rna1785 304 MDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESNKKKSITI---DRQKKiidvlqsrigdecilpvn 376
                                        89**************************************9998544443...23333322444444445666666 PP

                                        .HHHHHHHHHHHHH CS
                               OmpH  65 .lqkkeqelqqkqq 77 
                                         lq k +e+++ ++
  gene1786|gene1786|rna1785|rna1785 377 eLQSKIDEIRR-RA 389
                                        66666666666.33 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   7.5    0.0001     0.054      27     129 ..     248     357 ..     203     363 .. 0.74
   2 ?   -1.2   0.2       3.6   1.9e+03      66      91 ..     388     413 ..     377     418 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0001
                               ADIP  27 tekveeniaaiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlere.......lalvqa 95 
                                        t  +e++   + + + ++l+  ++  ++ es++++++ +e e+e+  +++  lk +  +  +e       +a +  
  gene1786|gene1786|rna1785|rna1785 248 TSVKENDFYDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINEnasfseaVARLST 323
                                        4467778888889999999999999999999999999999999987777776666655555550000000555566 PP

                               ADIP  96 kerqlekklktleqklknekeelqrlknalqqik 129
                                        k ++++k++ tl+++lk++ e++++   ++++ k
  gene1786|gene1786|rna1785|rna1785 324 KNAKIRKDYDTLKEALKKTVESNKKKSITIDRQK 357
                                        7777777777888888888888877777777766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.6
                               ADIP  66 eaeierlqskierlktqleqlerela 91 
                                        +a++e + s  ++l+++ +++er+++
  gene1786|gene1786|rna1785|rna1785 388 RADSELDLSIKSKLEEEIADYERRMS 413
                                        56666667778899999999999875 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       3.5   1.8e+03      36      61 ..     210     235 ..     204     245 .. 0.62
   2 ?    8.5   0.4    0.0045       2.4      24      88 ..     258     322 ..     254     330 .. 0.85
   3 ?   -0.2   0.0       2.4   1.2e+03      29      66 ..     319     356 ..     313     370 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.5
                             DUF948  36 eelekqvdpilkevedllakvnelle 61 
                                         e+ kq+d+ ++e+edl +    +++
  gene1786|gene1786|rna1785|rna1785 210 SEVVKQLDKCSRELEDLKRINGMIAK 235
                                        56667777777777776544444444 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0045
                             DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                        ++k l+ + + i++  k ++++++eve   ++ +++l+d +e   k+d+++++ a  +e+v+ l+
  gene1786|gene1786|rna1785|rna1785 258 VSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLS 322
                                        67778888888888889999999999999999999999999999999999999999999998876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.4
                             DUF948  29 deaaatieelekqvdpilkevedllakvnelledvnek 66 
                                         ++++  ++++k+ d + + ++++++  ++    + ++
  gene1786|gene1786|rna1785|rna1785 319 ARLSTKNAKIRKDYDTLKEALKKTVESNKKKSITIDRQ 356
                                        55555556677777777777777776666544444444 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.017       8.8     120     164 ..     233     277 ..     206     283 .. 0.83
   2 ?    6.3   6.5     0.014       7.5      88     174 ..     276     367 ..     274     370 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.017
                       Bacillus_HBL 120 evkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlq 164
                                         +k++++++k++  ++  ++++F    + l+ +l+g  + +++++
  gene1786|gene1786|rna1785|rna1785 233 IAKDVVGAIKDFGIDTSVKENDFYDVSKALKDVLKGIRKRVKTME 277
                                        5899********************************999998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                       Bacillus_HBL  88 yktlveav..dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsg... 158
                                        ++ +++ v  ++k+ +++l+++++L+ ++  + +e  + ++++ +l +k ak  k+++t ++ l+++++++++   
  gene1786|gene1786|rna1785|rna1785 276 MESMSQEVemKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESNKKksi 351
                                        577899996677777899*******999888777777777777777777777777777777777777777663111 PP

                       Bacillus_HBL 159 visqlqneiedlqgki 174
                                        +i+  ++ i  lq+ i
  gene1786|gene1786|rna1785|rna1785 352 TIDRQKKIIDVLQSRI 367
                                        4555566666666555 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.2   2.2e+03      53      75 ..     207     229 ..     180     232 .. 0.78
   2 ?   12.0  13.1   0.00026      0.14      46     190 ..     260     407 ..     251     408 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.2
                           KASH_CCD  53 kstQqalqkaklleeEleelkal 75 
                                        +s+   +++    + Ele+lk++
  gene1786|gene1786|rna1785|rna1785 207 RSSSEVVKQLDKCSRELEDLKRI 229
                                        55555666666777899998875 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00026
                           KASH_CCD  46 eeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdel 121
                                        ++Lk  lk   + ++ ++++++E+e   +  +++     +lk +  ++  en s ++ ++ L  +n k++ + d+l
  gene1786|gene1786|rna1785|rna1785 260 KALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTL 335
                                        5799999999999999999****99888888888889999999999999*************************** PP

                           KASH_CCD 122 kkklkeLlkekaeLkkqlheleellaekeall.eektkqieeLkltieEyssiie.eLrae.ksrLeeqlqq 190
                                        k+ lk+ ++++ +    ++  ++++   ++ +  e    ++eL++ i+E+++  + eL +  ks+Lee++++
  gene1786|gene1786|rna1785|rna1785 336 KEALKKTVESNKKKSITIDRQKKIIDVLQSRIgDECILPVNELQSKIDEIRRRADsELDLSiKSKLEEEIAD 407
                                        ***********9999999999999987665552678899***********987776999883579**99875 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       6.3   3.3e+03      12      28 ..     211     227 ..     168     239 .. 0.72
   2 ?    9.4   6.4     0.003       1.6       4      71 ..     291     358 ..     251     367 .. 0.82
   3 ?    7.5   1.1     0.012       6.3      30      71 ..     317     358 ..     314     411 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 6.3
                                        HHHHHHHHHHHHHHHHH CS
                               YabA  12 eleeqleelleeleelk 28 
                                        e+ +ql+++++ele+lk
  gene1786|gene1786|rna1785|rna1785 211 EVVKQLDKCSRELEDLK 227
                                        44555666666666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.003
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXX CS
                               YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegke 71 
                                        +++++  +el+ +++++ +e ++  e++a+l  +na+++ + ++l+e l+++ +++k+k+ ++++ k+
  gene1786|gene1786|rna1785|rna1785 291 ENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESNKKKSITIDRQKK 358
                                        45666777888888888888888888888888888888888888888888888888888877777665 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.012
                                        HHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXX CS
                               YabA  30 elaelleenaeLeleneklrerleeeekkekekkkelsegke 71 
                                        ++a+l  +na+++ + ++l+e l+++ +++k+k+ ++++ k+
  gene1786|gene1786|rna1785|rna1785 317 AVARLSTKNAKIRKDYDTLKEALKKTVESNKKKSITIDRQKK 358
                                        455666667777777777777776666666666655555544 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       4.6   2.4e+03       7       7 ..      58      58 ..      15     125 .. 0.61
   2 ?    1.8   1.0      0.39     2e+02      90     132 ..     255     296 ..     185     307 .. 0.54
   3 ?    1.0   1.5      0.67   3.5e+02      37      75 ..     260     298 ..     246     331 .. 0.53
   4 ?   12.9   1.1   0.00015     0.077      25     110 ..     312     396 ..     306     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 4.6
                          PhaP_Bmeg  7 e 7 
                                       e
  gene1786|gene1786|rna1785|rna1785 58 E 58
                                       2 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.39
                          PhaP_Bmeg  90 ieEwtdkleevsakleklalspsKssldllkkaeeqleetvks 132
                                        + +    l++v+  + k  +  + s+ + ++  e+++e+++k 
  gene1786|gene1786|rna1785|rna1785 255 FYDVSKALKDVLKGIRK-RVKTMESMSQEVEMKEKEYENVLKD 296
                                        33444444444433332.2333333333334444444444443 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.67
                          PhaP_Bmeg  37 kalkqqqdlvkeltkalselekeskqltaeledqlqktv 75 
                                        kalk++ + +++  k ++++ +e    + e+e+ l+++ 
  gene1786|gene1786|rna1785|rna1785 260 KALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYT 298
                                        344444444444444444444444444444444444332 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 0.00015
                          PhaP_Bmeg  25 aslskqvEqltLkalkqqqdlvkeltkalselekeskqltaeledqlqktvenlrskaGnkvednieEwtdkleev 100
                                        as+s+ v  l+ k  k  +d+   l++al++  + +k+    + d+++k ++ l+s+ G +  + ++E++ k++e+
  gene1786|gene1786|rna1785|rna1785 312 ASFSEAVARLSTKNAKIRKDYD-TLKEALKKTVESNKKKSITI-DRQKKIIDVLQSRIGDECILPVNELQSKIDEI 385
                                        5666777777777777777776.78888888888777776667.9******************************* PP

                          PhaP_Bmeg 101 sakle.klals 110
                                          + + +l+ls
  gene1786|gene1786|rna1785|rna1785 386 RRRADsELDLS 396
                                        *9987346665 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.2   3.8e+03      41      65 ..     177     202 ..     166     227 .. 0.61
   2 ?   13.5   4.6   0.00013     0.069       5      76 ..     275     346 ..     262     347 .. 0.92
   3 ?   -0.2   0.2       2.4   1.3e+03      57      68 ..     396     407 ..     375     414 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.2
                              Tup_N  41 lqqirqtlyeLeeahrkik.qqYEee 65 
                                        l  i +  + L + + +++ +++E e
  gene1786|gene1786|rna1785|rna1785 177 LRDIEEISHKLRRMFFDMRsKSFEAE 202
                                        55555555555555555542234444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00013
                              Tup_N   5 lLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahrkikqqYEeeiarLkaeLesr 76 
                                         ++   qE +  ++e++++ +   e+  k+   i+E +++ +++  L ++  ki++ Y+   ++Lk+++es+
  gene1786|gene1786|rna1785|rna1785 275 TMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESN 346
                                        5788889999999999999999999999***************************************99975 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.4
                              Tup_N  57 kikqqYEeeiar 68 
                                        +ik + Eeeia 
  gene1786|gene1786|rna1785|rna1785 396 SIKSKLEEEIAD 407
                                        466777777765 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.15        77      38      70 ..     204     236 ..     165     277 .. 0.68
   2 ?   10.0   5.5    0.0019         1       6      85 ..     279     357 ..     255     369 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.15
                       Syntaxin-6_N  38 eldetrteLrkalrsiewdledLeetvrivekn 70 
                                         + + ++e+ k+l++ + +ledL++  +++ k+
  gene1786|gene1786|rna1785|rna1785 204 GYARSSSEVVKQLDKCSRELEDLKRINGMIAKD 236
                                        455667899999999999999999998888774 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0019
                       Syntaxin-6_N   6 vkeeVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvr.iveknpsk.fkid 77 
                                        + +eV+ + ++ e++++ +++l+ + +   +++ +++e+   L ++  +i++d + L+e+ + +ve+n++k   id
  gene1786|gene1786|rna1785|rna1785 279 MSQEVEMKEKEYENVLKDYTELKGKMDRiiNENASFSEAVARLSTKNAKIRKDYDTLKEALKkTVESNKKKsITID 354
                                        567888888888888888888777766666699***************************9547888876645544 PP

                       Syntaxin-6_N  78 ekelsrrr 85 
                                             r++
  gene1786|gene1786|rna1785|rna1785 355 -----RQK 357
                                        .....444 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.1   5.9e+02      68      96 ..     174     201 ..     150     228 .. 0.60
   2 ?   -1.1   0.0       2.9   1.5e+03      12      30 ..     209     227 ..     204     236 .. 0.71
   3 ?    9.8   1.5    0.0013      0.68       8      68 ..     279     339 ..     255     360 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.1
                              Sec34  68 LkyFeeldpitrkLnspgsslvksesFle 96 
                                        L   +++++i++kL++  ++ ++s+sF  
  gene1786|gene1786|rna1785|rna1785 174 LGDLRDIEEISHKLRRMFFD-MRSKSFEA 201
                                        55555666666666666666.66666642 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                              Sec34  12 cdelleqtdealeqLeele 30 
                                          e+++q+d++ ++Le+l+
  gene1786|gene1786|rna1785|rna1785 209 SSEVVKQLDKCSRELEDLK 227
                                        5667777777777777776 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0013
                              Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                         ++e++   ++ +++l++ +el+ k++++ ++  s++ea  +l +++ ++++ +++++e L
  gene1786|gene1786|rna1785|rna1785 279 MSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEAL 339
                                        3333333334444445555555555555555555555555555555555555444444444 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.4   7.4e+02     159     175 ..     186     203 ..     181     217 .. 0.76
   2 ?    8.8   7.4    0.0029       1.5      50     137 ..     272     358 ..     203     394 .. 0.75
   3 ?    0.8   0.1      0.81   4.3e+02      18      39 ..     375     397 ..     373     414 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.4
                          Rootletin 159 avrrqfselksat.erdL 175
                                        ++rr+f +++s+  e +L
  gene1786|gene1786|rna1785|rna1785 186 KLRRMFFDMRSKSfEAEL 203
                                        79********97425555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0029
                          Rootletin  50 kltlllssareleeeesadleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreel 125
                                        +++++ s+ +e+e  +++++e++l+   e + + +++ ++n+ + e +   +++n ++++d + l++ ++++ e+ 
  gene1786|gene1786|rna1785|rna1785 272 RVKTMESMSQEVEM-KEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESN 346
                                        22222244555555.56699***************************************************99999 PP

                          Rootletin 126 eqkekewreeee 137
                                        ++k+ +  ++++
  gene1786|gene1786|rna1785|rna1785 347 KKKSITIDRQKK 358
                                        888877665554 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.81
                          Rootletin  18 vskLqaKvlqYkkrc.seleqrl 39 
                                        v++Lq+K+ + ++r  sel+  +
  gene1786|gene1786|rna1785|rna1785 375 VNELQSKIDEIRRRAdSELDLSI 397
                                        67889999998888623444333 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.58   3.1e+02      32      98 ..     165     234 ..     163     245 .. 0.64
   2 ?    2.2   0.3      0.37   1.9e+02      32      93 ..     211     276 ..     205     286 .. 0.47
   3 ?    8.4   7.0    0.0044       2.3      28     126 ..     288     383 ..     283     391 .. 0.80
   4 ?   -1.4   0.1       4.5   2.4e+03      81      97 ..     396     412 ..     374     419 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.58
                                        CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHCCCHHHHHHH CS
                          Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn....dnvikksskeleeeilrlketid 98 
                                        +v+++++ l  +l++i++ +++ +++  +++++  e++  ++ +     + + k s+ele +  r++  i 
  gene1786|gene1786|rna1785|rna1785 165 NVSQSINGLLGDLRDIEEISHKLRRMFFDMRSKSFEAELGYARSssevVKQLDKCSRELE-DLKRINGMIA 234
                                        678888888899999999888888888888776665554444433111333444556666.6666666665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.37
                                        CCCHHHCCCCCCCCCCCCHHH.HHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHCCCHH CS
                          Fib_alpha  32 dvkkdlekleneleeisnstk.eaeelvkeikdslrekqkskkdn...dnvikksskeleeeilrl 93 
                                        +v k+l+k  +ele++++ +   a+++v +ikd   ++  +++d    ++++k++ k +++++ ++
  gene1786|gene1786|rna1785|rna1785 211 EVVKQLDKCSRELEDLKRINGmIAKDVVGAIKDFGIDTSVKENDFydvSKALKDVLKGIRKRVKTM 276
                                        566666666666666666544134556666666655544444442222233333333333333222 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0044
                                        CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHH CS
                          Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesn 103
                                        k  ++v kd ++l+ ++++i n++ + +e v +++++   + k  kd d++ + ++k++e    +   tid+q + 
  gene1786|gene1786|rna1785|rna1785 288 KEYENVLKDYTELKGKMDRIINENASFSEAVARLSTK---NAKIRKDYDTLKEALKKTVE-SNKKKSITIDRQKKI 359
                                        5567899999*****************9999998766...55556666789999999999.8888999******** PP

                                        HHHHHHHHHHH.HHHHHHHHHHHH CS
                          Fib_alpha 104 irvLqnvlesn.eqkiqkLeqdid 126
                                        i vLq+ + +     +++L+++id
  gene1786|gene1786|rna1785|rna1785 360 IDVLQSRIGDEcILPVNELQSKID 383
                                        ******986541446667777666 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4.5
                                        HHHHHHHHCCCHHHHHH CS
                          Fib_alpha  81 ksskeleeeilrlketi 97 
                                        +++++leeei+++++++
  gene1786|gene1786|rna1785|rna1785 396 SIKSKLEEEIADYERRM 412
                                        35566666666666654 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0093       4.9     101     144 ..     251     294 ..     246     317 .. 0.74
   2 ?    0.4   0.1       0.7   3.7e+02     104     133 ..     331     359 ..     326     375 .. 0.79
   3 ?    0.4   0.1      0.71   3.8e+02     102     129 ..     392     418 ..     388     422 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0093
                                        S---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EE CS
                              DUF99 101 eepdlgklekaLrkhfpdeeeRlelieklgerieevektgeely 144
                                        +e d+ ++ kaL++ +++ ++R++++e++ +++e  ek+ e++ 
  gene1786|gene1786|rna1785|rna1785 251 KENDFYDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVL 294
                                        67788889*********************777777766444443 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.7
                                        -HHHHHHCCT.TSTTHHHHHHHHHHC.--- CS
                              DUF99 104 dlgklekaLrkhfpdeeeRlelieklgeri 133
                                        d ++l++aL+k ++ ++++  +i +  ++i
  gene1786|gene1786|rna1785|rna1785 331 DYDTLKEALKKTVESNKKKSITIDRQ-KKI 359
                                        55789***********9999999988.444 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.71
                                        ---HHHHHHCCT.TSTTHHHHHHHHHHC CS
                              DUF99 102 epdlgklekaLrkhfpdeeeRleliekl 129
                                        e dl+ ++++L++++ d e+R++ + +l
  gene1786|gene1786|rna1785|rna1785 392 ELDLS-IKSKLEEEIADYERRMSDFLSL 418
                                        56656.9***************987776 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1       0.2     1e+02      79      93 ..     211     225 ..     208     227 .. 0.91
   2 ?    8.8   2.8    0.0037         2       3      71 ..     254     322 ..     252     330 .. 0.76
   3 ?    3.8   2.6      0.14        72      21      74 ..     317     367 ..     303     369 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.2
                            BLOC1_2  79 eavseLDeyskeLEa 93 
                                        e+v++LD+ s+eLE+
  gene1786|gene1786|rna1785|rna1785 211 EVVKQLDKCSRELED 225
                                        79***********95 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0037
                            BLOC1_2   3 mfekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqie 71 
                                         f +vsk l+  l++ ++ +k++e + ++++ k k++++v+++ ++   k+++  +e +++ + + ++ 
  gene1786|gene1786|rna1785|rna1785 254 DFYDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLS 322
                                        677899999999****************99999999999988877766666666666665555555554 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.14
                            BLOC1_2  21 dyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqv 74 
                                         +  L + N +  + y+ lk+    l+k++e  ++k+ +++ +++ id ++ ++
  gene1786|gene1786|rna1785|rna1785 317 AVARLSTKNAKIRKDYDTLKE---ALKKTVESNKKKSITIDRQKKIIDVLQSRI 367
                                        455555566666666666665...567788888888899999999999999887 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   9.8    0.0054       2.8      17     118 ..     267     367 ..     207     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0054
                              THOC7  17 krltkrllklltsla..esteeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseieavree 90 
                                        k + kr+ + +   +  +++ e  e+ +e++l d+++++  ++r+ + +++ ++ ++r+ +++++i +    ++e 
  gene1786|gene1786|rna1785|rna1785 267 KGIRKRVKT-M---EsmSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEA 338
                                        333344444.3...2335668999*******************************************999999999 PP

                              THOC7  91 ieelkaqLeearat.ranrkeydelaekI 118
                                         ++  ++++++  t  +++k +d+l  +I
  gene1786|gene1786|rna1785|rna1785 339 LKKTVESNKKKSITiDRQKKIIDVLQSRI 367
                                        99999998888765145566667776666 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.83   4.4e+02      98     117 ..     209     228 ..     166     235 .. 0.58
   2 ?    8.8   5.5     0.003       1.6      17      99 ..     276     358 ..     257     367 .. 0.54
   3 ?    1.6   0.5       0.5   2.6e+02      98     114 ..     398     414 ..     374     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.83
                         TPR_MLP1_2  98 keelekelselekriedlne 117
                                         +e  k+l+++ + +edl+ 
  gene1786|gene1786|rna1785|rna1785 209 SSEVVKQLDKCSRELEDLKR 228
                                        33444445555555555544 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.003
                         TPR_MLP1_2  17 keeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleesee 92 
                                         e+  ++++  +++ e+  + ++e + k  r ++++a+ ++++++l ++ +++++++ +lk++++++ ++++++  
  gene1786|gene1786|rna1785|rna1785 276 MESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDYDTLKEALKKTVESNKKKSI 351
                                        2333344444445555555555555555555566666666666666666666666666666666666666666665 PP

                         TPR_MLP1_2  93 sweeqke 99 
                                         +++qk+
  gene1786|gene1786|rna1785|rna1785 352 TIDRQKK 358
                                        5555555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.5
                         TPR_MLP1_2  98 keelekelselekried 114
                                        k++le+e+++ e+r+ d
  gene1786|gene1786|rna1785|rna1785 398 KSKLEEEIADYERRMSD 414
                                        67888899988888887 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.2     0.014       7.6       4      62 ..     257     326 ..     255     365 .. 0.65
   2 ?   -1.7   0.0       9.2   4.9e+03      27      37 ..     398     408 ..     374     422 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX.GGGGG..........X CS
                             FliD_N   4 Dtdslvkqlmkaerakldkleqkktklewkqsayrelnsklsnlksalsalsk.sstfs..........a 62 
                                        D+++ +k+++k  r++++++e+  +++e k ++y+++ ++ ++lk +++ + + +++fs          a
  gene1786|gene1786|rna1785|rna1785 257 DVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINeNASFSeavarlstknA 326
                                        888889999999999*****************************99996443335555422222222220 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 9.2
                                        XXXXXXXHHHH CS
                             FliD_N  27 ktklewkqsay 37 
                                        k+kle+++++y
  gene1786|gene1786|rna1785|rna1785 398 KSKLEEEIADY 408
                                        33444444444 PP

>> DUF5638  Family of unknown function (DUF5638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       7.5     4e+03      16      45 ..      91     119 ..      86     124 .. 0.71
   2 ?   -0.2   0.0       2.3   1.2e+03       3      19 ..     210     226 ..     208     244 .. 0.77
   3 ?    9.2   2.4    0.0027       1.4      43      91 ..     280     328 ..     253     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 7.5
                                        HHHHT.------HHHHHHHHHHHHHHHHHHH CS
                            DUF5638  16 lsalf.edkelsekikkqlqeiktyYnesft 45 
                                        ls+++ ++++++eki k ++  ++y+++ f 
  gene1786|gene1786|rna1785|rna1785  91 LSSIYkTYMKVNEKIDKLIR--REYFDRTFV 119
                                        67777677788888887776..577777775 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.3
                                        HHHHHHHHHHHHHHHHH CS
                            DUF5638   3 tklekrLseCdeklsal 19 
                                        +++ k+L +C+ +l+ l
  gene1786|gene1786|rna1785|rna1785 210 SEVVKQLDKCSRELEDL 226
                                        5678999****999986 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0027
                                        HHHT--SHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHTTT---H CS
                            DUF5638  43 sftkakkektkeeiveeYeelvlllsqvkngeisadeAleaiekktesr 91 
                                        s +   kek+ e+++++Y el  ++ ++ n++ s+ eA++ +++k+++ 
  gene1786|gene1786|rna1785|rna1785 280 SQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKI 328
                                        44456789999*******************************9887653 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       1.4   7.1e+02      44      83 ..     191     230 ..     169     238 .. 0.66
   2 ?    9.9   1.7    0.0025       1.3      53     101 ..     274     322 ..     249     324 .. 0.80
   3 ?    1.8   3.6      0.85   4.5e+02       9      72 ..     328     404 ..     325     419 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.4
                     PRKG1_interact  44 svskrssllelekrerrslerkiseleeelkeleeLraen 83 
                                         ++ rs++ e+e    rs  + +++l++  +ele+L++ n
  gene1786|gene1786|rna1785|rna1785 191 FFDMRSKSFEAELGYARSSSEVVKQLDKCSRELEDLKRIN 230
                                        4556666666666666666666666777777777776555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0025
                     PRKG1_interact  53 elekrerrslerkiseleeelkeleeLraenqrLkdEngALiRViskLs 101
                                        ++ ++ ++++e k +e+e+ lk  +eL+ + +r+ +En +    +++Ls
  gene1786|gene1786|rna1785|rna1785 274 KTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLS 322
                                        334444556666777888999*******************999999998 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.85
                     PRKG1_interact   9 ekeenerLkreLeelekelselkseleklkqq...rqe.........svskrssllelekrerrslerkis.elee 71 
                                         +++ ++Lk+ L+++ ++ ++   ++++ k+     q+          ++ +s++ e+++r  ++l+ +i+ +lee
  gene1786|gene1786|rna1785|rna1785 328 IRKDYDTLKEALKKTVESNKKKSITIDRQKKIidvLQSrigdecilpVNELQSKIDEIRRRADSELDLSIKsKLEE 403
                                        5788899999999999999999999999775444322334445555422223333333444444444333323333 PP

                     PRKG1_interact  72 e 72 
                                        e
  gene1786|gene1786|rna1785|rna1785 404 E 404
                                        3 PP

>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0014      0.76     145     187 ..     229     279 ..     202     288 .. 0.73
   2 ?   -1.1   0.3       2.7   1.4e+03     150     190 ..     315     356 ..     292     363 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                      PhageMin_Tail 145 l....tkeaaealkklGistkdaqgkm....ksldeiledlsealkkltda 187
                                        +     k++  a+k++Gi+t   ++++    k l+++l+ +++++k++++ 
  gene1786|gene1786|rna1785|rna1785 229 IngmiAKDVVGAIKDFGIDTSVKENDFydvsKALKDVLKGIRKRVKTMESM 279
                                        24445679999********74444444444599999999999999999665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.7
                      PhageMin_Tail 150 aealkklGistkdaq.gkm.ksldeiledlsealkkltda.qra 190
                                        +ea+    +stk+a+  k   +l+e+l+++ e+ kk + + +r+
  gene1786|gene1786|rna1785|rna1785 315 SEAVAR--LSTKNAKiRKDyDTLKEALKKTVESNKKKSITiDRQ 356
                                        344433..567777765556888888888888777765555554 PP

>> Cauli_DNA-bind  Caulimovirus DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       5.3   2.8e+03      36      46 ..     223     233 ..     177     275 .. 0.63
   2 ?    7.7   5.0    0.0068       3.6       5      76 ..     287     360 ..     283     388 .. 0.77
   3 ?   -1.7   0.0       5.6     3e+03      16      41 ..     376     403 ..     362     414 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.3
                                        HHHHHHHHHHH CS
                     Cauli_DNA-bind  36 kesleevaaki 46 
                                         e+l  +   i
  gene1786|gene1786|rna1785|rna1785 223 LEDLKRINGMI 233
                                        22222333333 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0068
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHH...HHHHHH.T-TTHHHHHHHHTXXXXXXXX CS
                     Cauli_DNA-bind   5 aseieevlsdqkkieaeikaileklgstkpekesleevaakiikd...ltkkid.ececnkeiveildkkqdkqii 76 
                                         +e e+vl+d ++++ +++ i++ ++s  +    l +  aki kd   l + ++   e nk+    +d+  +k+ii
  gene1786|gene1786|rna1785|rna1785 287 EKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAKIRKDydtLKEALKkTVESNKKKSITIDR--QKKII 360
                                        68999**************************************99332333333135666666655655..34444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.6
                                        HHHHHHHHHHHHHHHTS--..HHHHHHH CS
                     Cauli_DNA-bind  16 kkieaeikaileklgstkp..ekeslee 41 
                                        ++++++i++i  +  s+ +  +k++lee
  gene1786|gene1786|rna1785|rna1785 376 NELQSKIDEIRRRADSELDlsIKSKLEE 403
                                        5677888888888877765224556655 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.2   1.2e+03     120     146 ..     180     206 ..     176     235 .. 0.62
   2 ?   10.6   6.3   0.00063      0.33      15     112 ..     256     349 ..     248     365 .. 0.86
   3 ?   -0.1   0.2       1.1     6e+02     173     198 ..     396     421 ..     375     423 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.2
                          Laminin_I 120 lseelaeaqrlLeelrsRdftkqleea 146
                                        ++e   +  r+   +rs+ f+++l  a
  gene1786|gene1786|rna1785|rna1785 180 IEEISHKLRRMFFDMRSKSFEAELGYA 206
                                        555666666777777777776665444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00063
                          Laminin_I  15 ykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaek 90 
                                        y +   l+d  k ++++++  ++ ++++e++eke e++ ++  eL +k+ +   +     +    ++ + ++  +k
  gene1786|gene1786|rna1785|rna1785 256 YDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKDYTELKGKMDRIINENASFSE----AVARLSTKNAK 327
                                        677788999999999************************************9998665555....55556667889 PP

                          Laminin_I  91 ikkladnikeilekvatlnene 112
                                        i+k  d++ke+l+k+++ n+++
  gene1786|gene1786|rna1785|rna1785 328 IRKDYDTLKEALKKTVESNKKK 349
                                        ***************9999965 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 1.1
                          Laminin_I 173 aLkealrdsLaeyeakLsDlrellee 198
                                        ++k +l++++a+ye  +sD  +ll++
  gene1786|gene1786|rna1785|rna1785 396 SIKSKLEEEIADYERRMSDFLSLLNK 421
                                        57888999999999999999999876 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0         2   1.1e+03      20      36 ..      94     110 ..      86     152 .. 0.82
   2 ?    1.2   0.2       1.2   6.3e+02      54      72 ..     204     222 ..     177     278 .. 0.57
   3 ?    7.5   0.8     0.012       6.5      20      69 ..     255     303 ..     248     310 .. 0.84
   4 ?    8.6   5.4    0.0059       3.1      10      87 ..     283     365 ..     273     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2
                       Occludin_ELL  20 eYkeYkelhaeleevsk 36 
                                         Yk+Y++++++++++ +
  gene1786|gene1786|rna1785|rna1785  94 IYKTYMKVNEKIDKLIR 110
                                        59999999999988654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.2
                       Occludin_ELL  54 eykkieeeilqeykklkkd 72 
                                         y++  +e+++++ k++++
  gene1786|gene1786|rna1785|rna1785 204 GYARSSSEVVKQLDKCSRE 222
                                        4555555555555554432 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.012
                       Occludin_ELL  20 eYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69 
                                         Y+  k+l++ l+ ++k+++ +e++ +e + ++key+++ ++ + e+k +
  gene1786|gene1786|rna1785|rna1785 255 FYDVSKALKDVLKGIRKRVKTMESMSQEVEMKEKEYENVLKD-YTELKGK 303
                                        577778899999999999999999999999999999999998.7777654 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0059
                       Occludin_ELL  10 rerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklkk.dpeyqekkk 80 
                                         e  ++e+++  k Y el+ +++ + ++ + +++ + +l++++      y++++e + ++ ++ kk + +  ++kk
  gene1786|gene1786|rna1785|rna1785 283 VEMKEKEYENVLKDYTELKGKMDRIINENASFSEAVARLSTKNAkirkDYDTLKEALKKTVESNKKkSITIDRQKK 358
                                        4455789*****************9999888887777777666656678888999988888887775788888888 PP

                       Occludin_ELL  81 rceyLke 87 
                                         +++L++
  gene1786|gene1786|rna1785|rna1785 359 IIDVLQS 365
                                        8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2463  (0.137375); expected 358.6 (0.02)
Passed bias filter:                      976  (0.0544369); expected 358.6 (0.02)
Passed Vit filter:                       161  (0.00897987); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.97u 0.36s 00:00:01.33 Elapsed: 00:00:00.54
# Mc/sec: 2357.85
//
Query:       gene1787|gene1787|rna1786|rna1786  [L=678]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-35  122.0   0.0    4.3e-35  121.0   0.0    1.5  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.8e-06   27.9   0.0    8.6e-06   25.7   0.0    2.1  2  EFG_C        Elongation factor G C-terminus
    3.4e-05   23.9   0.0    9.2e-05   22.5   0.0    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.079   13.4   0.0        0.2   12.1   0.0    1.6  1  GTP_EFTU_D2  Elongation factor Tu domain 2


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.0   0.0   9.6e-39   4.3e-35       5     182 ..       8     177 ..       4     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 9.6e-39
                                        EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSS CS
                           GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGH 80 
                                          ++++h+DhGKt+L+d+L+++ g+is+  + a++ r+lDt+++E+ rgiT k +aisle   + y + +iDtPGH
  gene1787|gene1787|rna1786|rna1786   8 IASVVAHIDHGKTSLIDSLVASQGRISR--TLAGSVRFLDTREDEQTRGITLKLSAISLE--HNGYGYVFIDTPGH 79 
                                        5689************************..888999************************..************** PP

                                        GGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...HHHHHHHHHHHHHHHHHH CS
                           GTP_EFTU  81 vdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...kaelkeiveevkqklsrk 153
                                        vdF + +  +    D  +++vd++eG++p+t  +++  +  g + ++++NK+D++   +    e+ +++   +s+ 
  gene1787|gene1787|rna1786|rna1786  80 VDFESLIQSSSIFSDNFLILVDVNEGITPRTYSLVKYTK--GKRCVLALNKIDKIsspQ----ELLQKILLVVSSI 149
                                        *********************************999765..7789*********96542....3333333333333 PP

                                        HHHHHHHHHTTTTTEEEEEEBTTTTBTHH CS
                           GTP_EFTU 154 eeklekygekgekevpvvfgSalkgegvk 182
                                        ++  e+  ++ e   +v+ ++a    g++
  gene1787|gene1787|rna1786|rna1786 150 NGLAEEDLFEWE-ANNVILCCATLCYGIN 177
                                        444444444443.5556666666555555 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.98   4.4e+03      11      35 ..     132     156 ..     131     169 .. 0.76
   2 !   25.7   0.0   1.9e-09   8.6e-06       7      81 ..     569     644 ..     566     646 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.98
                                        EEEECCCCCCHHHHHHHCT-EEEEE CS
                              EFG_C  11 ievpeeyvgkvisdlssrrGeiedm 35 
                                        i+ p+e+++k++  +ss +G  e+ 
  gene1787|gene1787|rna1786|rna1786 132 ISSPQELLQKILLVVSSINGLAEED 156
                                        899********99999988877765 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.9e-09
                                        EEEEEEEECCCCCCHHHHHHH.CT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE- CS
                              EFG_C   7 vkveievpeeyvgkvisdlss.rrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeev 81 
                                        +++ i+++e ++g+++++ls+   + +++  ++++g+ +++  iP     +f +e+r  TkG++++ ++  gY+ v
  gene1787|gene1787|rna1786|rna1786 569 YECSISIQEMFIGEAYKSLSKhSYAVVQESYEEKTGFYVLTVLIPQFLYSNFLEEIRVRTKGTAYLLVKDVGYRFV 644
                                        899******************8899999999999***************************************976 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     2e-08   9.2e-05       9     114 .]      16     128 ..       9     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-08
                                        TSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHH CS
                           MMR_HSR1   9 NvGKStLinaltg................ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgk 68 
                                          GK++Li +l+                 ++ + +++ g T++   + ++++g  ++++DtpG ++     ++l +
  gene1787|gene1787|rna1786|rna1786  16 DHGKTSLIDSLVAsqgrisrtlagsvrflDTREDEQTRGITLKLSAISLEHNGYGYVFIDTPGHVD----FESLIQ 87 
                                        57*********9655566666666554434667788889999999999999999*********665....333443 PP

                                        HHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                           MMR_HSR1  69 aflaleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                        +    + +d +l++vd++ e+++p   +l ++   ++k+++l+lnk
  gene1787|gene1787|rna1786|rna1786  88 SSS--IFSDNFLILVDVN-EGITPRTYSLVKYT--KGKRCVLALNK 128
                                        333..3479*******87.88****99999997..58999999998 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05       0.2       7      61 ..     297     348 ..     292     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                        EEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEES CS
                        GTP_EFTU_D2   7 rvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaik 61 
                                        r++ Gt+++Gd+v+    + +      + + sl+ f  +e ++ +++ + ++v + 
  gene1787|gene1787|rna1786|rna1786 297 RLFCGTVRVGDTVYSADgMNV----SECIVESLYLFGINELIEKNEVSGSNLVCMG 348
                                        999************877765....459********99999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4308.88
//
Query:       gene1788|gene1788|rna1787|rna1787  [L=178]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-09   38.1   6.3    1.9e-09   37.2   6.3    1.4  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
    2.1e-08   33.9   7.2    4.3e-08   32.9   7.2    1.6  1  Prok-RING_4   Prokaryotic RING finger family 4
    1.1e-07   31.7   8.6    1.1e-07   31.7   8.6    1.7  2  zf-RING_5     zinc-RING finger domain
    1.2e-07   31.5   7.8    1.2e-07   31.5   7.8    2.1  2  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    5.5e-07   29.8  10.3    5.5e-07   29.8  10.3    1.7  2  zf-RING_2     Ring finger domain
    8.1e-07   29.0   8.1    8.1e-07   29.0   8.1    2.2  2  zf-RING_UBOX  RING-type zinc-finger
    7.4e-05   22.5   9.8    0.00022   21.0   9.8    1.9  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    0.00019   21.5  14.2    0.00021   21.4  11.2    2.4  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING
  ------ inclusion threshold ------
      0.011   15.7   5.2      0.023   14.8   5.1    1.6  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
      0.056   13.7   9.8       0.14   12.5   9.8    1.7  1  zf-rbx1       RING-H2 zinc finger domain
        0.4   10.7   8.0        2.1    8.4   8.5    1.9  2  DZR           Double zinc ribbon


Domain annotation for each model (and alignments):
>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   6.3   1.2e-12   1.9e-09       2      47 ..      46      93 ..      45      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.2e-12
                                       GSB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHH...TT-B-TTT--B- CS
                         zf-C3HC4_3  2 deeCviClerprnvvllpCgHlvlCeeCaekllk...rkkkCpiCrrpi 47
                                       + +C iC+++p+  vl pCgHl +C  C+  + +     k Cp Cr+ +
  gene1788|gene1788|rna1787|rna1787 46 EYTCNICYSQPEGPVLTPCGHL-FCWGCLYVWSQstgGCKFCPTCRSRM 93
                                       568*******************.*********9899999*******876 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   7.2   2.6e-11   4.3e-08       1      41 [.      49      94 ..      49      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.6e-11
                        Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeCfdskdls.....sCPlCqrris 41
                                       C +C +q++ ++l pCgHl+C  C+  +  s      CP C++r++
  gene1788|gene1788|rna1787|rna1787 49 CNICYSQPEGPVLTPCGHLFCWGCLYVWSQStggckFCPTCRSRME 94
                                       9***************************888798878999999875 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.4   1.2e+04      27      33 ..      30      36 ..      29      40 .. 0.53
   2 !   31.7   8.6   6.5e-11   1.1e-07       2      43 ..      49      90 ..      48      91 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.4
                          zf-RING_5 27 kClkkll 33
                                       +C+ ++ 
  gene1788|gene1788|rna1787|rna1787 30 TCIENAN 36
                                       4555544 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 6.5e-11
                          zf-RING_5  2 CnkCfeklskeekfyltsCgHifCekClkkll...ekeavCpiCr 43
                                       Cn+C+++    e+++lt+CgH fC+ Cl   +   + ++ Cp+Cr
  gene1788|gene1788|rna1787|rna1787 49 CNICYSQP---EGPVLTPCGHLFCWGCLYVWSqstGGCKFCPTCR 90
                                       ********...*****************99888999********9 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.61   9.9e+02      24      32 ..      30      38 ..      28      44 .. 0.67
   2 !   31.5   7.8   7.1e-11   1.2e-07       1      41 []      49      89 ..      49      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.61
                                       HHHHHHHHC CS
                           zf-C3HC4 24 kCirkilks 32
                                       +Ci++ +++
  gene1788|gene1788|rna1787|rna1787 30 TCIENANEK 38
                                       688888773 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 7.1e-11
                                       -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB-.-TTT CS
                           zf-C3HC4  1 CpiCleeakepnelleCkHsfCskCirkilksrkkvk.CPlC 41
                                       C+iC + ++ p+ l++C+H fC  C+  + +s + +k CP+C
  gene1788|gene1788|rna1787|rna1787 49 CNICYSQPEGPV-LTPCGHLFCWGCLYVWSQSTGGCKfCPTC 89
                                       ************.******************9777777**** PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       6.6   1.1e+04      28      37 ..      30      39 ..      29      41 .. 0.66
   2 !   29.8  10.3   3.4e-10   5.5e-07       2      44 .]      48      90 ..      47      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.6
                          zf-RING_2 28 eClerwlrss 37
                                       +C+e+ ++++
  gene1788|gene1788|rna1787|rna1787 30 TCIENANEKK 39
                                       5888776665 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 3.4e-10
                          zf-RING_2  2 eCpICleelssadsvlllpCgHvfhreClerwlrssst...CPlCr 44
                                       +C IC+   s+++ ++l+pCgH f++ Cl  w +s+     CP+Cr
  gene1788|gene1788|rna1787|rna1787 48 TCNICY---SQPEGPVLTPCGHLFCWGCLYVWSQSTGGckfCPTCR 90
                                       6****8...7777888889*************888877889****9 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.1   3.4e+03      23      32 ..      30      41 ..      29      48 .. 0.50
   2 !   29.0   8.1     5e-10   8.1e-07       1      39 []      49      87 ..      49      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                       zf-RING_UBOX 23 eClw..elsksl 32
                                        C++  +++ks+
  gene1788|gene1788|rna1787|rna1787 30 TCIEnaNEKKSS 41
                                       599434333333 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 5e-10
                       zf-RING_UBOX  1 CpIClelftdPlv.lpCGHtFCreCl..welskslegafkCP 39
                                       C IC+++ + P v +pCGH FC+ Cl  w  s+s +g   CP
  gene1788|gene1788|rna1787|rna1787 49 CNICYSQPEGP-VlTPCGHLFCWGCLyvW--SQSTGGCKFCP 87
                                       *****9999**.636***********777..66666666666 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   9.8   1.3e-07   0.00022       2      40 .]      49      89 ..      48      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                         zf-C3HC4_2  2 CpiCldmlkdpsvvtpCgHvfCqkCilrsLeekn...eCPlC 40
                                       C iC+   + p v+tpCgH fC  C+  + ++      CP+C
  gene1788|gene1788|rna1787|rna1787 49 CNICYSQPEGP-VLTPCGHLFCWGCLYVWSQSTGgckFCPTC 89
                                       *********99.*************98865554323368888 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.9     0.039        64      23      42 .]      30      52 ..      27      52 .. 0.78
   2 !   21.4  11.2   1.3e-07   0.00021       1      42 []      49      89 ..      49      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.039
                         zf-C3HC4_4 23 sCisslqkepdgeq...llCplC 42
                                       +Ci++  +++++ q   ++C  C
  gene1788|gene1788|rna1787|rna1787 30 TCIENANEKKSSHQsreYTCNIC 52
                                       68888887777766677***999 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.3e-07
                         zf-C3HC4_4  1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeqllCplC 42
                                       C iC +  e Pv  +CGh fC  C++ ++++  g   +Cp C
  gene1788|gene1788|rna1787|rna1787 49 CNICYSQPEGPVLTPCGHLFCWGCLYVWSQSTGGC-KFCPTC 89
                                       99*****************************9997.88***9 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   5.1   1.4e-05     0.023      46      84 ..      59      96 ..      37      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                       -EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB--BE CS
                         zf-ANAPC11 46 plvlGkckhnfhlhcilkwletetskglcpmcrqtfklk 84
                                       p vl  c h f   c++ w ++    + cp cr  ++++
  gene1788|gene1788|rna1787|rna1787 59 P-VLTPCGHLFCWGCLYVWSQSTGGCKFCPTCRSRMEIE 96
                                       3.6789****************************99876 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   9.8   8.4e-05      0.14       9      55 .]      44      90 ..      27      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                            zf-rbx1  9 eleeacieckapgdeecpvvlGeCgHaFHlhCiskWlkt...rkvCPlcr 55
                                       + e +c  c ++ +    +vl  CgH F   C+  W ++    k CP+cr
  gene1788|gene1788|rna1787|rna1787 44 SREYTCNICYSQPEG---PVLTPCGHLFCWGCLYVWSQStggCKFCPTCR 90
                                       456678888888887...6777*****************888889****8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.5    0.0013       2.1       8      48 ..      42      89 ..      29      90 .. 0.79
   2 ?    6.4   0.7    0.0054       8.8      10      23 ..      81      94 ..      76     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                                DZR  8 lppdarfCseCgtklkavaa....edrCpsCgek...vdpearfCpeC 48
                                       ++++  +C+ C ++++ +      + +C+ C +     + +++fCp C
  gene1788|gene1788|rna1787|rna1787 42 HQSREYTCNICYSQPEGPVLtpcgHLFCWGCLYVwsqSTGGCKFCPTC 89
                                       667888********9865558999*******998422445799***99 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0054
                                DZR 10 pdarfCseCgtklk 23
                                        + +fC++C+++++
  gene1788|gene1788|rna1787|rna1787 81 GGCKFCPTCRSRME 94
                                       56689999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 933.10
//
Query:       gene1789|gene1789|rna1788|rna1788  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-07   30.2   0.2      9e-07   28.8   0.2    1.8  1  HRDC      HRDC domain
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.025   14.4   0.0    1.6  2  Maf       Maf-like protein


Domain annotation for each model (and alignments):
>> HRDC  HRDC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.2     1e-10     9e-07       2      64 ..     276     338 ..     275     341 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1e-10
                                        HHHHHHHHHHHHHHHHHHTS-HHHHS-HHHHHHHHHH---SHHHHHTSTTT-HHHHHHHHHHH CS
                               HRDC   2 lallkaLrewReelAreedvppyvvfpdktLleiAeklPttleeLlqiegvgkrklekygeei 64 
                                        +++l+ L ++R+ lAr++d++ ++v++d++ + + +++Ptt+e + ++ +  +  ++++  ++
  gene1789|gene1789|rna1788|rna1788 276 EEILENLLKLRRFLARSNDESVHYVMTDDQVVRLLKAKPTTQEKMVEVLKRLSPLARQHIMDF 338
                                        689******************************************999766666666665555 PP

>> Maf  Maf-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.78     7e+03      50      58 ..      64      72 ..      26      84 .. 0.56
   2 ?   14.4   0.0   2.8e-06     0.025      23      78 ..     256     329 ..     240     349 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.78
                                       EEEEEEEEE CS
                                Maf 50 igaDtvvvl 58
                                       i  Dt+v++
  gene1789|gene1789|rna1788|rna1788 64 IRPDTIVAI 72
                                       444666665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.8e-06
                                        E------HHHHHHHHHHHHHHHHH..................TCEEEEEEEEEECE---SSHHHHHHHHHHHTT CS
                                Maf  23 vpsdvdeaeelvlrlAeaKaeava..................alvigaDtvvvlilgKPkdeeealemLkklsg 78 
                                        +++++de+++++ r   +  e+++                  ++v++ D+vv l   KP+++e+ +e+Lk+ls 
  gene1789|gene1789|rna1788|rna1788 256 CSKEIDETKDMASRYGISEDEEILenllklrrflarsndesvHYVMTDDQVVRLLKAKPTTQEKMVEVLKRLSP 329
                                        45677774455555555555545455555555555555565566*********9999**************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2325.64
//
Query:       gene1790|gene1790|rna1789|rna1789  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-35  120.7   7.5    4.2e-35  120.5   7.5    1.0  1  ORMDL     ORMDL family
  ------ inclusion threshold ------
        9.6    6.8  11.1        4.3    8.0   2.3    2.1  2  DUF5592   Family of unknown function (DUF5592)


Domain annotation for each model (and alignments):
>> ORMDL  ORMDL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   7.5   4.6e-39   4.2e-35       2     136 .]      13     141 ..      12     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 4.6e-39
                              ORMDL   2 kntewvnskglwviyiviilllkllllalpgvseevawtltnlvhnlvtyillHwikGtPfetadqgeydeltlWE 77 
                                        +n++w+ ++g+w+i++++i+llk++l+++  +s+++ w+l  +++n+ t+i++H+i G+Pf++    +y+ +t+WE
  gene1790|gene1790|rna1789|rna1789  13 QNVAWTLQRGSWIIHVLVIFLLKMTLSVV--FSDSIGWQLSLIIYNISTFIFFHMIPGDPFND----RYSLYTFWE 82 
                                        79***************************..******************************99....********* PP

                              ORMDL  78 QidegeqytptrkfLtvvPivLfllsthytkydlelfvinlivllvvvipKlpfmhrvR 136
                                        Q+ e+ + tp   f++++P + f + ++++k+++ lf++++++l++v+ipK++fmh  R
  gene1790|gene1790|rna1789|rna1789  83 QLSEQLEGTPDLIFIALFPLIAFTIINFIVKWNTFLFWLCIASLFIVTIPKFGFMHLRR 141
                                        ********************************************************887 PP

>> DUF5592  Family of unknown function (DUF5592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.3   0.00048       4.3      25      57 ..      28      62 ..      24      72 .. 0.72
   2 ?    4.0   1.7    0.0085        76      21      59 ..      93     131 ..      88     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00048
                            DUF5592 25 llvlllltmklsslvhaslvvlf..yifviilvif 57
                                       +lv++ll m+ls ++  s+ +    +i +i   if
  gene1790|gene1790|rna1789|rna1789 28 VLVIFLLKMTLSVVFSDSIGWQLslIIYNISTFIF 62
                                       899****************9865214444444444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0085
                            DUF5592  21 Dlllllvlllltmklsslvhaslvvlfyifviilviflv 59 
                                        Dl +++++ l+++++ + + +  + lf  +++ l i+++
  gene1790|gene1790|rna1789|rna1789  93 DLIFIALFPLIAFTIINFIVKWNTFLFWLCIASLFIVTI 131
                                        999**********99888877666666666655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 967.46
//
Query:       gene179|gene179|rna179|rna179  [L=336]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-16   60.4   0.1    7.5e-13   48.4   0.0    2.2  2  Adap_comp_sub  Adaptor complexes medium subunit family


Domain annotation for each model (and alignments):
>> Adap_comp_sub  Adaptor complexes medium subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   2.1e-05      0.38      12      44 ..     115     146 ..     107     159 .. 0.85
   2 !   48.4   0.0   4.2e-17   7.5e-13     138     264 .]     222     336 .]     192     336 .] 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.1e-05
                                    X-EEEEEEEEEEEEEE-TTS-EEEEEEEEEEEE CS
                  Adap_comp_sub  12 kneiyldviErvsvlvdkkGkilksevqGtiac 44 
                                    +n++yldv+E ++++vd +G+++ +  +G++ +
  gene179|gene179|rna179|rna179 115 SNNVYLDVCEDLNAIVD-DGRVVVNRTDGRCYL 146
                                    79**************8.689998888887765 PP

  == domain 2  score: 48.4 bits;  conditional E-value: 4.2e-17
                                    E-S-TT-EEEEEEEEEE--TT-EEEEEEESSTT-EEEEETTEEEEEE--EETT-EE..EEEEEEE--------------. CS
                  Adap_comp_sub 138 enfkkkltlenvkisiplpkevsnlaiktskGkakynpeenaleWtikklpggnesslsgeleleaesekkeenprdgkl 217
                                    +  ++  ++++++i +p+pk +s+++ ++s Gk  y++e+++l+Wt+kk   ++       +++++e ++  +  r   +
  gene179|gene179|rna179|rna179 222 C--QSPTKFDWLEICFPIPKMASKVVKSHSLGKSVYDEENDLLRWTFKKEVVKRAR-----ISYRVEMFEGCSDLR---P 291
                                    3..345689****************************************8888755.....999999999999887...5 PP

                                    EEEEEEEET--SS---EEEEEEE-------EEEEEEEEEEEEEEE-- CS
                  Adap_comp_sub 218 vsveFkipgftaSgikVeslkveeresykpfkwvryvtvsgeyeiri 264
                                    + ++F i++++  ++++e+ ++    + +++ w+ry++ sg+yeir+
  gene179|gene179|rna179|rna179 292 IIINFCIKEWKNPKVRIERAECI--GNPCVCFWIRYSMASGRYEIRM 336
                                    ***********************..7*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2325.20
//
Query:       gene1791|gene1791|rna1790|rna1790  [L=475]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-20   71.5   4.0       0.03   14.4   0.0    8.2  8  TPR_2       Tetratricopeptide repeat
    2.6e-15   55.5  10.4    0.00089   19.0   0.0    7.5  8  TPR_1       Tetratricopeptide repeat
    6.6e-15   54.0  12.5       0.01   16.0   0.0    7.5  7  TPR_8       Tetratricopeptide repeat
    1.3e-11   43.6   0.8    0.00015   21.5   0.0    6.8  8  TPR_7       Tetratricopeptide repeat
    1.8e-08   34.6   0.6       0.14   12.4   0.0    5.9  6  TPR_12      Tetratricopeptide repeat
    2.6e-08   34.3   0.0      0.025   15.1   0.0    4.8  5  TPR_19      Tetratricopeptide repeat
      5e-08   33.1   0.0       0.72   10.8   0.0    6.7  8  TPR_14      Tetratricopeptide repeat
      2e-06   27.8   0.3    0.00079   19.6   0.0    4.2  4  TPR_17      Tetratricopeptide repeat
    2.2e-05   25.0   0.0       0.28   11.9   0.0    3.6  3  TPR_16      Tetratricopeptide repeat
    6.4e-05   23.1  13.0      0.024   14.9   5.3    3.9  3  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    0.00067   20.1   0.2         10    7.0   0.1    5.4  5  TPR_6       Tetratricopeptide repeat
    0.00071   19.7   0.0        2.2    8.5   0.0    3.1  3  TPR_9       Tetratricopeptide repeat
     0.0025   17.6   0.3       0.93    9.4   0.0    4.4  6  TPR_10      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.026   13.5   2.5      0.049   12.6   0.1    2.4  3  NatB_MDM20  N-acetyltransferase B complex (NatB) non catalyti
       0.78    9.9   7.9         26    5.0   0.5    4.8  5  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.019        22       7      26 ..      39      58 ..      33      59 .. 0.86
   2 !   11.2   0.1   0.00026      0.31       5      25 ..      66      86 ..      62      90 .. 0.88
   3 ?    3.7   0.0      0.07        83       6      29 ..     119     142 ..     118     144 .. 0.91
   4 !    6.6   0.0    0.0079       9.5       6      32 ..     213     239 ..     209     241 .. 0.90
   5 !   14.1   0.0   3.2e-05     0.038       2      28 ..     277     303 ..     276     303 .. 0.93
   6 !    8.4   0.0    0.0022       2.6       3      30 ..     311     338 ..     309     342 .. 0.87
   7 !   14.4   0.0   2.5e-05      0.03       2      34 .]     344     376 ..     343     376 .. 0.94
   8 ?   -2.3   0.0       5.8   6.9e+03      13      27 ..     389     403 ..     387     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                              TPR_2  7 lGlayyklgdyeeAleafek 26
                                       +  ++y +g+y +Al ++ k
  gene1791|gene1791|rna1790|rna1790 39 MSIILYLNGEYSRALFHLHK 58
                                       6789************9987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00026
                              TPR_2  5 ynlGlayyklgdyeeAleafe 25
                                       y+  l+y k++dy++A++ +e
  gene1791|gene1791|rna1790|rna1790 66 YYESLCYKKKKDYKKAIKSLE 86
                                       8999**************998 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.07
                              TPR_2   6 nlGlayyklgdyeeAleafekAle 29 
                                         lG++y  +g  ee +e++ k+l+
  gene1791|gene1791|rna1790|rna1790 119 LLGDLYTLSGYREEGIEHYIKSLA 142
                                        69*****************99886 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0079
                              TPR_2   6 nlGlayyklgdyeeAleafekAleldP 32 
                                        n ++ y++lg  ++ + +fe + + dP
  gene1791|gene1791|rna1790|rna1790 213 NAARRYFNLGMNDKSKSCFELVRRKDP 239
                                        78999***************9999888 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 3.2e-05
                              TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                          + +lG+ y ++gdy++ + +f+++l
  gene1791|gene1791|rna1790|rna1790 277 NTWKALGNFYSHQGDYQRSVLCFKRSL 303
                                        5799********************987 PP

  == domain 6  score: 8.4 bits;  conditional E-value: 0.0022
                              TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                         +  lG+  +++++y+ A ++f+ +l+ 
  gene1791|gene1791|rna1790|rna1790 311 TYTLLGYESIQRNEYDVAMKYFNLSLKM 338
                                        57789******************99986 PP

  == domain 7  score: 14.4 bits;  conditional E-value: 2.5e-05
                              TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +a +  Gl+y k  +++ A+ +++kA+e +P+n
  gene1791|gene1791|rna1790|rna1790 344 RAMFGCGLVYTKTERLDNAEFFLKKAIETNPGN 376
                                        578999*************************87 PP

  == domain 8  score: -2.3 bits;  conditional E-value: 5.8
                              TPR_2  13 klgdyeeAleafekA 27 
                                        ++g  ++ +++f++A
  gene1791|gene1791|rna1790|rna1790 389 RKGLTDQSIRLFKEA 403
                                        666778999999998 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       0.2   2.4e+02      10      26 ..      42      58 ..      41      58 .. 0.86
   2 !   10.3   0.6   0.00042       0.5       9      25 ..      70      86 ..      70      90 .. 0.88
   3 ?   -2.1   0.0       3.5   4.2e+03      17      28 ..     130     141 ..     119     142 .. 0.67
   4 ?    1.1   0.0      0.34   4.1e+02      11      32 ..     218     239 ..     218     241 .. 0.83
   5 !   19.0   0.0   7.4e-07   0.00089       2      33 ..     277     308 ..     276     309 .. 0.91
   6 ?    3.5   0.1      0.06        71       2      30 ..     310     338 ..     309     342 .. 0.88
   7 !   18.5   0.0     1e-06    0.0012       2      34 .]     344     376 ..     343     376 .. 0.92
   8 ?   -2.1   0.0       3.4   4.1e+03      11      27 ..     387     403 ..     386     404 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
                                       HHHHTT-HHHHHHHHHH CS
                              TPR_1 10 ayfklgkydeAleyyek 26
                                       +++ +g+y  Al +  k
  gene1791|gene1791|rna1790|rna1790 42 ILYLNGEYSRALFHLHK 58
                                       7899********98765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00042
                                       HHHHHTT-HHHHHHHHH CS
                              TPR_1  9 nayfklgkydeAleyye 25
                                       ++y k+++y++A++  e
  gene1791|gene1791|rna1790|rna1790 70 LCYKKKKDYKKAIKSLE 86
                                       69***********9876 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.5
                                        HHHHHHHHHHHH CS
                              TPR_1  17 ydeAleyyekAL 28 
                                         +e +e+y k L
  gene1791|gene1791|rna1790|rna1790 130 REEGIEHYIKSL 141
                                        578899998887 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.34
                                        HHHTT-HHHHHHHHHHHHHHST CS
                              TPR_1  11 yfklgkydeAleyyekALelnP 32 
                                        yf+lg+ d+   ++e + + +P
  gene1791|gene1791|rna1790|rna1790 218 YFNLGMNDKSKSCFELVRRKDP 239
                                        99***********997666665 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 7.4e-07
                                        HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                              TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPn 33 
                                        ++++ lGn y ++g+y+  + ++++ L ++++
  gene1791|gene1791|rna1790|rna1790 277 NTWKALGNFYSHQGDYQRSVLCFKRSLCIEED 308
                                        68************************988765 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.06
                                        HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                        +++  lG+   + ++yd A +y++  L+ 
  gene1791|gene1791|rna1790|rna1790 310 YTYTLLGYESIQRNEYDVAMKYFNLSLKM 338
                                        579999*****************998875 PP

  == domain 7  score: 18.5 bits;  conditional E-value: 1e-06
                                        HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                              TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +a ++ G++y k +++d A+ + +kA+e nP n
  gene1791|gene1791|rna1790|rna1790 344 RAMFGCGLVYTKTERLDNAEFFLKKAIETNPGN 376
                                        677888*************************87 PP

  == domain 8  score: -2.1 bits;  conditional E-value: 3.4
                                        HHHTT-HHHHHHHHHHH CS
                              TPR_1  11 yfklgkydeAleyyekA 27 
                                        y ++g  d+ +  +++A
  gene1791|gene1791|rna1790|rna1790 387 YTRKGLTDQSIRLFKEA 403
                                        77888899999999998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.7   0.00047      0.56       9      27 ..      70      88 ..      68      90 .. 0.88
   2 ?    4.8   0.1     0.034        40       6      28 ..     119     141 ..     118     142 .. 0.93
   3 ?    5.2   0.0     0.025        30      11      25 ..     218     232 ..     212     234 .. 0.86
   4 !    8.4   0.0    0.0023       2.7       6      28 ..     281     303 ..     277     308 .. 0.89
   5 !    9.8   0.3   0.00084         1       3      30 ..     311     338 ..     309     338 .. 0.93
   6 !   16.0   0.0   8.4e-06      0.01       2      33 ..     344     375 ..     343     376 .. 0.88
   7 ?   -1.1   0.0       2.6   3.1e+03      11      27 ..     387     403 ..     385     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                                       HHHHHTT-HHHHHHHHHHH CS
                              TPR_8  9 siylklgdyeeAkeyyeka 27
                                       ++y+k++dy++A++++e  
  gene1791|gene1791|rna1790|rna1790 70 LCYKKKKDYKKAIKSLELI 88
                                       68**************965 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.034
                                        HHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkeyyekal 28 
                                        +lg++y   g  ee +e y k l
  gene1791|gene1791|rna1790|rna1790 119 LLGDLYTLSGYREEGIEHYIKSL 141
                                        69*****************9976 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.025
                                        HHHTT-HHHHHHHHH CS
                              TPR_8  11 ylklgdyeeAkeyye 25 
                                        y++lg  +++k+++e
  gene1791|gene1791|rna1790|rna1790 218 YFNLGMNDKSKSCFE 232
                                        9*************9 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0023
                                        HHHHHHHHTT-HHHHHHHHHHHH CS
                              TPR_8   6 nlgsiylklgdyeeAkeyyekal 28 
                                         lg+ y+ +gdy+ ++ ++++ l
  gene1791|gene1791|rna1790|rna1790 281 ALGNFYSHQGDYQRSVLCFKRSL 303
                                        69******************987 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00084
                                        HHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                              TPR_8   3 ayynlgsiylklgdyeeAkeyyekalel 30 
                                         y +lg+  ++ ++y+ A++y++  l++
  gene1791|gene1791|rna1790|rna1790 311 TYTLLGYESIQRNEYDVAMKYFNLSLKM 338
                                        699********************99986 PP

  == domain 6  score: 16.0 bits;  conditional E-value: 8.4e-06
                                        CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                              TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                        +a++  g++y k++++++A+ +++ka+e +p 
  gene1791|gene1791|rna1790|rna1790 344 RAMFGCGLVYTKTERLDNAEFFLKKAIETNPG 375
                                        56666799********************9996 PP

  == domain 7  score: -1.1 bits;  conditional E-value: 2.6
                                        HHHTT-HHHHHHHHHHH CS
                              TPR_8  11 ylklgdyeeAkeyyeka 27 
                                        y  +g  ++++  +++a
  gene1791|gene1791|rna1790|rna1790 387 YTRKGLTDQSIRLFKEA 403
                                        88999999999999998 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.7   9.2e+03      13      19 ..      16      22 ..       6      22 .. 0.68
   2 ?    3.1   0.0     0.099   1.2e+02       9      28 ..      72      91 ..      69     100 .. 0.76
   3 ?    5.1   0.0     0.022        26       4      27 ..     119     142 ..     118     149 .. 0.90
   4 ?    0.5   0.0      0.68   8.1e+02       4      28 ..     213     235 ..     211     239 .. 0.79
   5 !   21.5   0.0   1.3e-07   0.00015       1      32 [.     278     309 ..     278     313 .. 0.92
   6 ?   -0.5   0.0       1.4   1.7e+03      11      29 ..     321     339 ..     317     346 .. 0.80
   7 ?   -2.1   0.0       4.6   5.5e+03       6      31 ..     350     373 ..     347     376 .. 0.75
   8 ?    3.1   0.0     0.096   1.1e+02       9      29 ..     387     405 ..     385     411 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.7
                              TPR_7 13 GdyeeAi 19
                                       +dye+Ai
  gene1791|gene1791|rna1790|rna1790 16 RDYETAI 22
                                       6888887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.099
                              TPR_7  9 ysrlGdyeeAielyeqsLal 28
                                       y +  dy++Ai+ +e  L  
  gene1791|gene1791|rna1790|rna1790 72 YKKKKDYKKAIKSLELILDG 91
                                       77788*******99987644 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.022
                              TPR_7   4 nLarlysrlGdyeeAielyeqsLa 27 
                                         L++ly   G++ee ie+y +sLa
  gene1791|gene1791|rna1790|rna1790 119 LLGDLYTLSGYREEGIEHYIKSLA 142
                                        69*******************775 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.68
                              TPR_7   4 nLarlysrlGdyeeAielyeqsLal 28 
                                        n ar y++lG  ++  +++e   + 
  gene1791|gene1791|rna1790|rna1790 213 NAARRYFNLGMNDKSKSCFEL--VR 235
                                        6777799************97..55 PP

  == domain 5  score: 21.5 bits;  conditional E-value: 1.3e-07
                              TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                        ++ +L++ ys +Gdy++ + ++++sL +++d 
  gene1791|gene1791|rna1790|rna1790 278 TWKALGNFYSHQGDYQRSVLCFKRSLCIEEDS 309
                                        5789**********************999885 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 1.4
                              TPR_7  11 rlGdyeeAielyeqsLalt 29 
                                        ++++y+ A +++  sL + 
  gene1791|gene1791|rna1790|rna1790 321 QRNEYDVAMKYFNLSLKML 339
                                        4799*******99888765 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 4.6
                              TPR_7   6 arlysrlGdyeeAielyeqsLaltkd 31 
                                        + +y +  + ++A+ ++++  a++  
  gene1791|gene1791|rna1790|rna1790 350 GLVYTKTERLDNAEFFLKK--AIETN 373
                                        6678888999999888888..66655 PP

  == domain 8  score: 3.1 bits;  conditional E-value: 0.096
                              TPR_7   9 ysrlGdyeeAielyeqsLalt 29 
                                        y r G +++ i+l+++  a++
  gene1791|gene1791|rna1790|rna1790 387 YTRKGLTDQSIRLFKE--AFC 405
                                        999************9..765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.3   6.4e+03      52      67 ..      40      55 ..      37      59 .. 0.73
   2 ?    2.3   0.0      0.17   2.1e+02      12      29 ..      71      88 ..      60      94 .. 0.68
   3 ?    2.0   0.0      0.22   2.6e+02       8      31 ..     119     142 ..     116     144 .. 0.88
   4 !   12.4   0.0   0.00012      0.14       4      74 ..     277     338 ..     274     341 .. 0.76
   5 !    9.7   0.0   0.00083      0.99      19      73 ..     325     371 ..     320     374 .. 0.76
   6 ?   -0.2   0.0       1.1   1.3e+03      13      29 ..     387     403 ..     385     404 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.3
                             TPR_12 52 grlyralgryeeAlel 67
                                       ++++++ g+y  Al +
  gene1791|gene1791|rna1790|rna1790 40 SIILYLNGEYSRALFH 55
                                       6677888888888755 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.17
                             TPR_12 12 vlrrlgrydeAlelleka 29
                                       ++ + ++y +A++ le  
  gene1791|gene1791|rna1790|rna1790 71 CYKKKKDYKKAIKSLELI 88
                                       566666666666666544 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.22
                             TPR_12   8 nlaavlrrlgrydeAlellekale 31 
                                         l+++++  g  +e +e++ k+l+
  gene1791|gene1791|rna1790|rna1790 119 LLGDLYTLSGYREEGIEHYIKSLA 142
                                        599999999999*********996 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00012
                             TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                        +++  l++++ ++g+y+ +  +++++l i      +d+     t+  Lg    ++++y+ A ++++ +l++
  gene1791|gene1791|rna1790|rna1790 277 NTWKALGNFYSHQGDYQRSVLCFKRSLCIE-----EDS----YTYTLLGYESIQRNEYDVAMKYFNLSLKM 338
                                        68888*********************6555.....444....25666666666777777777777777766 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00083
                             TPR_12  19 ydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                        yd A ++++ +l +     G+++    +++++ g +y +++r++ A+ +l++a++
  gene1791|gene1791|rna1790|rna1790 325 YDVAMKYFNLSLKML----GDNY----RAMFGCGLVYTKTERLDNAEFFLKKAIE 371
                                        555555555555555....3333....79************************97 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 1.1
                             TPR_12  13 lrrlgrydeAlelleka 29 
                                        ++r g  d++++l+++a
  gene1791|gene1791|rna1790|rna1790 387 YTRKGLTDQSIRLFKEA 403
                                        78889999999999887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0         1   1.2e+03      33      52 ..      41      60 ..      30      71 .. 0.58
   2 ?    6.3   0.0     0.012        14       4      55 ..      46      92 ..      43     102 .. 0.70
   3 ?    5.5   0.0     0.021        25      14      47 ..     265     298 ..     263     315 .. 0.84
   4 !   15.1   0.0   2.1e-05     0.025       2      57 ..     320     375 ..     319     380 .. 0.94
   5 !   14.0   0.0   4.7e-05     0.056       5      49 ..     357     401 ..     353     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1
                             TPR_19 33 eallalgqldeAealLdalp 52
                                       ++l+ +g++  A   L +l 
  gene1791|gene1791|rna1790|rna1790 41 IILYLNGEYSRALFHLHKLN 60
                                       55555666666655555554 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                             TPR_19  4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55
                                       +g y +Al +l ++     + +  +++   ++ + +++++A++ L+ +++ +
  gene1791|gene1791|rna1790|rna1790 46 NGEYSRALFHLHKL-----NTWTSKYYESLCYKKKKDYKKAIKSLELILDGK 92
                                       67777777777776.....333333333669***************998755 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.021
                             TPR_19  14 leqalqedpknaearllLAeallalgqldeAeal 47 
                                         +++++++p++++ + +L + +  +g+++    +
  gene1791|gene1791|rna1790|rna1790 265 CKNLIKHAPDSPNTWKALGNFYSHQGDYQRSVLC 298
                                        6888999*********************976655 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 2.1e-05
                             TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                        ++++ y+ A++++   l+   +n +a  +   ++ ++ +ld Ae  L+++ e +p 
  gene1791|gene1791|rna1790|rna1790 320 IQRNEYDVAMKYFNLSLKMLGDNYRAMFGCGLVYTKTERLDNAEFFLKKAIETNPG 375
                                        67899***********************************************9997 PP

  == domain 5  score: 14.0 bits;  conditional E-value: 4.7e-05
                             TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLd 49 
                                        +++++A  +l++a++ +p+n+ ++   ++ +   g +d+ ++l +
  gene1791|gene1791|rna1790|rna1790 357 ERLDNAEFFLKKAIETNPGNLQIKVHAMKFYTRKGLTDQSIRLFK 401
                                        689***********************************9988776 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.8   2.1e+03      14      32 ..      75      97 ..      69     106 .. 0.72
   2 ?   -1.4   0.0       5.2   6.2e+03       7      30 ..     120     143 ..     118     150 .. 0.86
   3 ?   -1.6   0.0       5.9   7.1e+03       8      32 ..     215     239 ..     214     239 .. 0.81
   4 ?    4.4   0.0     0.071        85       9      42 ..     250     283 ..     246     284 .. 0.86
   5 !   10.8   0.0   0.00061      0.72       1      34 [.     276     309 ..     276     317 .. 0.85
   6 ?    0.4   0.0       1.4   1.6e+03      12      37 ..     320     345 ..     311     348 .. 0.76
   7 !    8.6   0.0    0.0032       3.8       8      40 ..     350     382 ..     344     386 .. 0.86
   8 ?    2.3   0.0      0.32   3.8e+02       9      27 ..     385     403 ..     382     406 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.8
                             TPR_14 14 lGdpdeAiallrrala....laP 32
                                         d+++Ai+ l+ +l+    ++P
  gene1791|gene1791|rna1790|rna1790 75 KKDYKKAIKSLELILDgkveRDP 97
                                       57999******999875444444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.2
                             TPR_14   7 laeallalGdpdeAiallrralal 30 
                                        l++++  +G  +e i+++ + la+
  gene1791|gene1791|rna1790|rna1790 120 LGDLYTLSGYREEGIEHYIKSLAK 143
                                        78999999999*****99988875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.9
                             TPR_14   8 aeallalGdpdeAiallrralalaP 32 
                                        a+ +++lG  d++  +++ + +++P
  gene1791|gene1791|rna1790|rna1790 215 ARRYFNLGMNDKSKSCFELVRRKDP 239
                                        788999**99999988887777766 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.071
                             TPR_14   9 eallalGdpdeAiallrralalaPddaeawllla 42 
                                         +l++  d  e   l++ ++++aPd++ +w +l+
  gene1791|gene1791|rna1790|rna1790 250 TILWHCKDVYELGMLCKNLIKHAPDSPNTWKALG 283
                                        57888888888889999*************9997 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.00061
                             TPR_14   1 peallalaeallalGdpdeAiallrralalaPdd 34 
                                        p+ ++al+ ++ ++Gd+++++ +++r l    d+
  gene1791|gene1791|rna1790|rna1790 276 PNTWKALGNFYSHQGDYQRSVLCFKRSLCIEEDS 309
                                        689**********************998777665 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.4
                             TPR_14  12 lalGdpdeAiallrralalaPddaea 37 
                                         ++ ++d A+++++  l+   d+ +a
  gene1791|gene1791|rna1790|rna1790 320 IQRNEYDVAMKYFNLSLKMLGDNYRA 345
                                        578899*******9999877777665 PP

  == domain 7  score: 8.6 bits;  conditional E-value: 0.0032
                             TPR_14   8 aeallalGdpdeAiallrralalaPddaeawll 40 
                                        + ++   +++d A+  l++a++++P+++++  +
  gene1791|gene1791|rna1790|rna1790 350 GLVYTKTERLDNAEFFLKKAIETNPGNLQIKVH 382
                                        56888999*******************988765 PP

  == domain 8  score: 2.3 bits;  conditional E-value: 0.32
                             TPR_14   9 eallalGdpdeAiallrra 27 
                                        +++ + G +d++i+l+++a
  gene1791|gene1791|rna1790|rna1790 385 KFYTRKGLTDQSIRLFKEA 403
                                        7899************998 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.5   7.8e+03      22      33 ..      42      53 ..      38      54 .. 0.82
   2 ?   -0.2   0.0       1.4   1.7e+03      22      34 .]      71      83 ..      66      83 .. 0.85
   3 !   19.6   0.0   6.6e-07   0.00079       1      31 [.     264     294 ..     264     296 .. 0.95
   4 ?    2.1   0.0      0.26   3.1e+02       2      12 ..     366     376 ..     365     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.5
                             TPR_17 22 lllknGdlmtAr 33
                                       +l+ nG++ +A+
  gene1791|gene1791|rna1790|rna1790 42 ILYLNGEYSRAL 53
                                       789999999986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                             TPR_17 22 lllknGdlmtArq 34
                                       +++k++d+++A++
  gene1791|gene1791|rna1790|rna1790 71 CYKKKKDYKKAIK 83
                                       7999999999985 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 6.6e-07
                             TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmt 31 
                                        l+++ +++ P++++ +  L+++++++Gd+++
  gene1791|gene1791|rna1790|rna1790 264 LCKNLIKHAPDSPNTWKALGNFYSHQGDYQR 294
                                        6899*************************98 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.26
                             TPR_17   2 ylkaleldPnn 12 
                                        ++ka+e +P n
  gene1791|gene1791|rna1790|rna1790 366 LKKAIETNPGN 376
                                        68*******99 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.19   2.3e+02      34      61 ..      62      89 ..      48      97 .. 0.82
   2 ?    6.2   0.0     0.014        17      23      54 ..     268     296 ..     264     309 .. 0.84
   3 !   11.9   0.0   0.00024      0.28       4      66 ..     316     375 ..     313     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.19
                             TPR_16 34 aeAllllgdaalrqgrlaeAaalyraal 61
                                       + + ++  +++ +++++++A+  ++  l
  gene1791|gene1791|rna1790|rna1790 62 WTSKYYESLCYKKKKDYKKAIKSLELIL 89
                                       677899999************7666555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                             TPR_16  23 alkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                        ++k +   Pd +  + +lg+ + +qg++++ +
  gene1791|gene1791|rna1790|rna1790 268 LIKHA---PDSPNTWKALGNFYSHQGDYQRSV 296
                                        67888...888889**************9976 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00024
                             TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                        +++ +++++yd A ++++  lk+     d+++A+++ g+++ +  rl+ A+ ++++a++  p+
  gene1791|gene1791|rna1790|rna1790 316 GYESIQRNEYDVAMKYFNLSLKML---GDNYRAMFGCGLVYTKTERLDNAEFFLKKAIETNPG 375
                                        66667999****************...99999*******************999999999887 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.3     2e-05     0.024       3      80 ..      16      86 ..      14      88 .. 0.92
   2 ?    1.9   0.1      0.22   2.7e+02      11      49 ..     264     302 ..     248     317 .. 0.81
   3 !    8.8   0.1    0.0016       1.9       2      78 ..     322     399 ..     321     403 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                             ANAPC3  3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80
                                       ++y++Aifl   l    ++ +e   l +  lylng+y rA+  l+k+    ++  + y    c+ k k y++Ai+ Le
  gene1791|gene1791|rna1790|rna1790 16 RDYETAIFLTACLT---QQKSEYKTLMSIILYLNGEYSRALFHLHKL----NTWTSKYYESLCYKKKKDYKKAIKSLE 86
                                       68********9999...7778888888********************....999999*999*************9997 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.22
                                        HHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                             ANAPC3  11 laerllaaetespedayllAlclylngqykrAyellrka 49 
                                        l+  l +  ++sp+   +l+  + ++g+y+r    ++++
  gene1791|gene1791|rna1790|rna1790 264 LCKNLIKHAPDSPNTWKALGNFYSHQGDYQRSVLCFKRS 302
                                        5566667788999999999***********988887776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0016
                                        TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                             ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAi 76 
                                        +n y+ A+ ++++ l++  +++ + +  +l++ ++++ + A  +l+ka ++n+ +l++ + + + +   +  ++ i
  gene1791|gene1791|rna1790|rna1790 322 RNEYDVAMKYFNLSLKMLGDNYRAMFGCGLVYTKTERLDNAEFFLKKAiETNPGNLQIKVHAMKFYTRKGLTDQSI 397
                                        688999*********8888888888889************************999998887777666666666555 PP

                                        HH CS
                             ANAPC3  77 aa 78 
                                        ++
  gene1791|gene1791|rna1790|rna1790 398 RL 399
                                        55 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0087        10       4      27 ..      66      89 ..      64      90 .. 0.85
   2 ?    4.0   0.0     0.079        94       6      31 ..     214     239 ..     213     239 .. 0.90
   3 ?   -1.2   0.0       3.6   4.3e+03       8      24 ..     284     300 ..     281     301 .. 0.75
   4 ?    0.9   0.0      0.76   9.1e+02       2      32 ..     345     375 ..     344     376 .. 0.87
   5 ?   -2.3   0.0       8.1   9.7e+03      12      25 ..     389     402 ..     384     403 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0087
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                              TPR_6  4 yklalsyrklgdtdkAlealerli 27
                                       y+  l+y+k +d+ kA++ le ++
  gene1791|gene1791|rna1790|rna1790 66 YYESLCYKKKKDYKKAIKSLELIL 89
                                       66679****99*******999765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.079
                                        HHHHHHHHHHHHHHHHHHHHHHHH-T CS
                              TPR_6   6 lalsyrklgdtdkAlealerlikeYP 31 
                                        +a+ y++lg  dk++  +e ++++ P
  gene1791|gene1791|rna1790|rna1790 214 AARRYFNLGMNDKSKSCFELVRRKDP 239
                                        67889**99************99987 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.6
                                        HHHHHHHHHHHHHHHHH CS
                              TPR_6   8 lsyrklgdtdkAleale 24 
                                          y  +gd+++++  ++
  gene1791|gene1791|rna1790|rna1790 284 NFYSHQGDYQRSVLCFK 300
                                        5566799***9987776 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.76
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                              TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPd 32 
                                        A++  +l y k+ + d+A   l++ i+  P+
  gene1791|gene1791|rna1790|rna1790 345 AMFGCGLVYTKTERLDNAEFFLKKAIETNPG 375
                                        7788899999966**************9996 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 8.1
                                        HHHHHHHHHHHHHH CS
                              TPR_6  12 klgdtdkAlealer 25 
                                        + g td++++++++
  gene1791|gene1791|rna1790|rna1790 389 RKGLTDQSIRLFKE 402
                                        55689****99975 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   2.3e+03       5      22 ..      72      89 ..      70     102 .. 0.79
   2 !    7.1   0.0    0.0049       5.9      20      55 ..     267     302 ..     259     312 .. 0.86
   3 !    8.5   0.0    0.0018       2.2       6      61 ..     320     375 ..     316     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                              TPR_9  5 aireedweralavverll 22
                                       +  ++d+ +a++ +e++l
  gene1791|gene1791|rna1790|rna1790 72 YKKKKDYKKAIKSLELIL 89
                                       566788888888888887 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0049
                              TPR_9  20 rllllaPddpeerrdRGlllaqlGclsaAladLeay 55 
                                         l+  aPd+p  +   G  + ++G+++  + ++ + 
  gene1791|gene1791|rna1790|rna1790 267 NLIKHAPDSPNTWKALGNFYSHQGDYQRSVLCFKRS 302
                                        577789*********************998887765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0018
                              TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapd 61 
                                        i+++++++a+++ ++ l +  d  +  +  Gl++ + ++l  A + L  +++ +p 
  gene1791|gene1791|rna1790|rna1790 320 IQRNEYDVAMKYFNLSLKMLGDNYRAMFGCGLVYTKTERLDNAEFFLKKAIETNPG 375
                                        899****************************************9999999998885 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.4     4e+03       8      30 ..     120     142 ..     119     143 .. 0.87
   2 ?   -3.1   0.1       6.7     8e+03       6      16 ..     212     222 ..     211     223 .. 0.82
   3 !    9.4   0.0   0.00078      0.93       8      31 ..     282     305 ..     281     310 .. 0.90
   4 ?   -0.3   0.0      0.93   1.1e+03       5      25 ..     312     332 ..     309     338 .. 0.77
   5 ?    1.6   0.0      0.22   2.7e+02       9      31 ..     350     372 ..     350     373 .. 0.91
   6 ?   -3.3   0.0         8   9.6e+03      12      29 ..     387     404 ..     386     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                             TPR_10   8 LanalrqrgrydeAealleeala 30 
                                        L+ +++  g ++e  ++++++la
  gene1791|gene1791|rna1790|rna1790 120 LGDLYTLSGYREEGIEHYIKSLA 142
                                        78889999999999999999997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.7
                             TPR_10   6 nNLanalrqrg 16 
                                        +N a++++++g
  gene1791|gene1791|rna1790|rna1790 212 SNAARRYFNLG 222
                                        68899999887 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00078
                             TPR_10   8 LanalrqrgrydeAealleealai 31 
                                        L+n ++++g+y++++  ++++l i
  gene1791|gene1791|rna1790|rna1790 282 LGNFYSHQGDYQRSVLCFKRSLCI 305
                                        9**************999999987 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.93
                             TPR_10   5 lnNLanalrqrgrydeAeall 25 
                                        ++ L+    qr++yd A++++
  gene1791|gene1791|rna1790|rna1790 312 YTLLGYESIQRNEYDVAMKYF 332
                                        6667777779*******9997 PP

  == domain 5  score: 1.6 bits;  conditional E-value: 0.22
                             TPR_10   9 analrqrgrydeAealleealai 31 
                                        + +++++ r+d Ae +l++a+++
  gene1791|gene1791|rna1790|rna1790 350 GLVYTKTERLDNAEFFLKKAIET 372
                                        689***********999999986 PP

  == domain 6  score: -3.3 bits;  conditional E-value: 8
                             TPR_10  12 lrqrgrydeAealleeal 29 
                                        +++ g  d++ +l++ea 
  gene1791|gene1791|rna1790|rna1790 387 YTRKGLTDQSIRLFKEAF 404
                                        777788899999999986 PP

>> NatB_MDM20  N-acetyltransferase B complex (NatB) non catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.3      0.41   4.9e+02     210     254 ..      18      60 ..      17      63 .. 0.83
   2 ?   12.6   0.1   4.1e-05     0.049     166     251 ..     316     401 ..     285     402 .. 0.86
   3 ?   -3.7   0.0       3.6   4.3e+03     308     318 ..     422     432 ..     421     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.41
                         NatB_MDM20 210 iqaillLeflltksphNfqlkLlLvrlYlllGagslalklyskLd 254
                                        ++ ++ L   lt+ +++++ ++ ++ lYl  G +s+al + +kL+
  gene1791|gene1791|rna1790|rna1790  18 YETAIFLTACLTQQKSEYKTLMSII-LYL-NGEYSRALFHLHKLN 60 
                                        578999999*********9866655.676.599999999999997 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.1e-05
                         NatB_MDM20 166 iYraslrlgaelletesqpsddlallaahalldlseks.......vdstlliqaillLeflltksphNfqlkLlLv 234
                                         Y+++       +  e++ + ++ +l+ ++l d +++         + + l +a   L ++++ +p N q+k+  +
  gene1791|gene1791|rna1790|rna1790 316 GYESI-------QRNEYDVAMKYFNLSLKMLGDNYRAMfgcglvyTKTERLDNAEFFLKKAIETNPGNLQIKVHAM 384
                                        44444.......445999999***************99******999999************************** PP

                         NatB_MDM20 235 rlYlllGagslalklys 251
                                        ++Y++ G++++  +l++
  gene1791|gene1791|rna1790|rna1790 385 KFYTRKGLTDQSIRLFK 401
                                        **********9999987 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.6
                         NatB_MDM20 308 kgsYskieefi 318
                                        kgs++++eef+
  gene1791|gene1791|rna1790|rna1790 422 KGSFTNVEEFL 432
                                        8********96 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.6   4.3e+03      14      21 ..      46      53 ..      39      57 .. 0.82
   2 ?    5.0   0.5     0.021        26       5      28 ..      66      89 ..      64      94 .. 0.92
   3 ?   -1.2   0.0       1.8   2.1e+03      14      32 ..     289     307 ..     281     310 .. 0.83
   4 ?    0.5   0.0      0.55   6.6e+02      15      31 ..     323     339 ..     314     347 .. 0.82
   5 ?    4.3   0.0     0.036        43      11      38 ..     353     380 ..     346     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                                       HT-HHHHH CS
                         Fis1_TPR_C 14 lgeYseAr 21
                                        geYs+A+
  gene1791|gene1791|rna1790|rna1790 46 NGEYSRAL 53
                                       79****97 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHT-HHHHHHHHHHHH CS
                         Fis1_TPR_C  5 YylAlGhyklgeYseArryvdalL 28
                                       Yy +l + k ++Y++A + ++ +L
  gene1791|gene1791|rna1790|rna1790 66 YYESLCYKKKKDYKKAIKSLELIL 89
                                       9****************9999888 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.8
                                        HT-HHHHHHHHHHHHHHTT CS
                         Fis1_TPR_C  14 lgeYseArryvdalLeiEP 32 
                                        +g+Y+++  + ++ L iE 
  gene1791|gene1791|rna1790|rna1790 289 QGDYQRSVLCFKRSLCIEE 307
                                        79*****999999998886 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.55
                                        T-HHHHHHHHHHHHHHT CS
                         Fis1_TPR_C  15 geYseArryvdalLeiE 31 
                                         eY+ A++y +  L++ 
  gene1791|gene1791|rna1790|rna1790 323 NEYDVAMKYFNLSLKML 339
                                        69********9999875 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.036
                                        HHHHT-HHHHHHHHHHHHHHTTS-HHHH CS
                         Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenrQaq 38 
                                        ++k  + ++A  +++  +e  P+n Q +
  gene1791|gene1791|rna1790|rna1790 353 YTKTERLDNAEFFLKKAIETNPGNLQIK 380
                                        7899999*******************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2995.93
//
Query:       gene1792|gene1792|rna1791|rna1791  [L=447]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-13   50.1   3.1    4.4e-13   49.1   0.6    2.1  2  UTP15_C         UTP15 C terminal
    3.1e-06   26.7   4.6       0.01   15.2   0.3    2.3  2  WD40_like       WD40-like domain
     0.0015   17.9   0.7       0.45    9.8   0.0    3.2  3  CPSF_A          CPSF A subunit region
     0.0056   17.5   0.1       0.74   10.8   0.0    3.5  4  WD40            WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.024   14.7   1.0       0.35   10.9   0.1    2.9  3  BBS2_Mid        Ciliary BBSome complex subunit 2, middle regi
      0.046   14.2   0.8         37    5.0   0.2    3.4  3  PQQ_3           PQQ-like domain
       0.14   12.4   0.5        0.7   10.2   0.3    2.1  2  Formyl_trans_C  Formyl transferase, C-terminal domain
       0.15   11.6   0.0       0.24   11.0   0.0    1.3  1  PQQ_2           PQQ-like domain


Domain annotation for each model (and alignments):
>> UTP15_C  UTP15 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.15   3.3e+02       8      28 ..      47      69 ..      43      76 .. 0.79
   2 !   49.1   0.6     2e-16   4.4e-13      14     141 ..     315     439 ..     302     444 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                            UTP15_C  8 divie..ekkkkklkkydklLrk 28
                                        +vi+  e+kkkk+ k+d+++ +
  gene1792|gene1792|rna1791|rna1791 47 AVVIKkgENKKKKIVKFDRDISA 69
                                       567754688**********9875 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 2e-16
                            UTP15_C  14 kkkkklkkydklLrkfryskALdavlekkvekspevvvtlleeLrhRgalraALagrdeeslepiLkfllkhitdp 89 
                                        +   k + +++ L++f+y+k +  ++ek   ++ ++v+++++ + ++++ + AL++ + +++e+iL  +++  t  
  gene1792|gene1792|rna1791|rna1791 315 NPLVKFSFLERRLNAFEYKKSMIHAMEK---RDIQKVFAVMNYIHEKQKFEHALQDLNRREVERILDVIIEFFTVR 387
                                        456788889*******************...89******************************************* PP

                            UTP15_C  90 ryvsllvdvanvlldlyseklgqseeldelvkrLkrkvreevelakellelk 141
                                        + v++  + ++++l ly++++ + + l + ++ L +++ +e+ +++e l+  
  gene1792|gene1792|rna1791|rna1791 388 ELVPVFSECIETILSLYERDIRDDSMLSRKIEVLGAAIDDELYFQEENLRSI 439
                                        *********************************************9977665 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   4.5e-06      0.01      57     144 ..      32     126 ..      24     135 .. 0.83
   2 !   14.3   0.8   8.3e-06     0.019      21     183 ..     122     283 ..     119     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.5e-06
                          WD40_like  57 lvvtlDGtills.....llenee..evenekieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIk 125
                                        l++  DG ++ +     +++++e  + ++ k + dis ++  +d  + G + G+i v  +  +++  +  +++ ++
  gene1792|gene1792|rna1791|rna1791  32 LCCCKDGIVVGCknravVIKKGEnkKKKIVKFDRDISAIDAWEDLTAYGDEGGEIKVVGRMRTIVRHYQEHEARVN 107
                                        788888888654222225677665567788999*************************99999************* PP

                          WD40_like 126 eikiennkiysLsesafiv 144
                                        eiki+++++ s s++  i+
  gene1792|gene1792|rna1791|rna1791 108 EIKINEDMLISCSDDMKIK 126
                                        ***********99987664 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.3e-06
                          WD40_like  21 ddkctvlkleslesvsivesfedSvifvklld..ddlilvvtlDGtillslleneeevenekieedistvkviddk 94 
                                        d k+++++l   esv  +++ +d   +vk +d  d +i  ++ DG i  + l+  + v +++ +  +s+v+++++ 
  gene1792|gene1792|rna1791|rna1791 122 DMKIKIFELSRAESVATIAENTD---YVKSIDvgDGMIFSGSYDGFINGYSLSTFKRVFEHNTKRRVSKVRILGGG 194
                                        55667777777777766666655...8888874355999*********************************9986 PP

                          WD40_like  95 lliGtnkGsiyvfskdlq.leevllgqsseIkeikiennkiysLsesafivfdlfsqnieykisvkdiktfeiien 169
                                         +  ++  ++ v + +    e+    +  e+ ++    +++y+ s +a +    +  ++  ki v+++    +i +
  gene1792|gene1792|rna1791|rna1791 195 RVAFASGNEVCVIDVENGgKEIGKAFHIKEVTSMVFYAGRLYTVSLDANVRVFTTDLRMISKIGVQGGILSISI-F 269
                                        5555555556555444220333344455666667777********88877554666688889999876443333.6 PP

                          WD40_like 170 kdilligtegeili 183
                                         d+l++g e++ ++
  gene1792|gene1792|rna1791|rna1791 270 DDVLCLGLEDREVL 283
                                        9*******998665 PP

>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.011        24      88     120 ..      24      56 ..       8      81 .. 0.83
   2 !    9.8   0.0    0.0002      0.45      80     132 ..     172     225 ..     160     253 .. 0.85
   3 ?   -1.0   0.0      0.39   8.8e+02     148     177 ..     344     373 ..     317     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.011
                                        EEES----EEEETTEEEEE-SSEEEEEEE-TTS CS
                             CPSF_A  88 evkgavtalaefqGrllvgvgqkvrvydlgedk 120
                                        e++g++t+l+ +++ ++vg+ +  +v + ge+k
  gene1792|gene1792|rna1791|rna1791  24 EQEGPITSLCCCKDGIVVGCKNRAVVIKKGENK 56 
                                        678*****************9999999988887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0002
                                        EEEEEEEEEEES----EEEE.TTEEEEE-SSEEEEEEE-TTS-EEEEEEEE-SS CS
                             CPSF_A  80 kLklvhkeevkgavtalaef.qGrllvgvgqkvrvydlgedktLlrkafldtql 132
                                         +k v+++++k  v+ +  +  Gr++ + g+ v+v d+++ ++ ++kaf+ +++
  gene1792|gene1792|rna1791|rna1791 172 TFKRVFEHNTKRRVSKVRILgGGRVAFASGNEVCVIDVENGGKEIGKAFHIKEV 225
                                        6999****************899*****************99999999987776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.39
                                        ESSS-EEEEEE-SSS--EEEEEEESS---E CS
                             CPSF_A 148 DlmkSvtfveydeenyklilfardtqkrwv 177
                                        D++k + +++y  e++k+    +d+++r+v
  gene1792|gene1792|rna1791|rna1791 344 DIQKVFAVMNYIHEKQKFEHALQDLNRREV 373
                                        899999999999999999999999999998 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.28   6.2e+02      11      34 ..      27      48 ..      18      50 .. 0.72
   2 !   10.8   0.0   0.00033      0.74       3      37 ..      95     128 ..      93     129 .. 0.80
   3 ?   -0.6   0.0       1.3     3e+03      24      34 ..     155     165 ..     140     166 .. 0.75
   4 ?   -2.3   0.0       4.6     1e+04      10      36 ..     221     246 ..     219     247 .. 0.53

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.28
                                       SSEEEEEEETTSSEEEEEETTSEE CS
                               WD40 11 ssvtslafspdgawlasGsdDgtv 34
                                       +++tsl+ ++dg  +  G++++ v
  gene1792|gene1792|rna1791|rna1791 27 GPITSLCCCKDGIVV--GCKNRAV 48
                                       569999999999885..8776666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00033
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                         +r++  H   v+ +    + ++l+s+sdD +++i+
  gene1792|gene1792|rna1791|rna1791  95 IVRHYQEHeARVNEI--KINEDMLISCSDDMKIKIF 128
                                        6899999*7668877..33667799*********97 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.3
                                        EEEEEETTSEE CS
                               WD40  24 wlasGsdDgtv 34 
                                        +++sGs+Dg +
  gene1792|gene1792|rna1791|rna1791 155 MIFSGSYDGFI 165
                                        3679*999976 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.6
                                        S.SSEEEEEEETTSSE....EEEEETTSEEEE CS
                               WD40  10 H.ssvtslafspdgaw....lasGsdDgtvri 36 
                                        H + vts+       +    l + s D +vr+
  gene1792|gene1792|rna1791|rna1791 221 HiKEVTSM------VFyagrLYTVSLDANVRV 246
                                        77778888......222222233355777776 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       0.2   4.5e+02      14      78 ..      38     102 ..      34     113 .. 0.80
   2 ?   10.9   0.1   0.00016      0.35      11      82 ..     112     187 ..     104     195 .. 0.78
   3 ?   -2.1   0.0       1.7   3.9e+03      18      35 ..     238     256 ..     233     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.2
                           BBS2_Mid  14 eLvvgsddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvkskn 78 
                                         +vvg ++  + + k+e+ +++i + ++ +s ++  ++  ay+ e G ++v  ++  + r+ +++
  gene1792|gene1792|rna1791|rna1791  38 GIVVGCKNRAVVIKKGENKKKKIVKFDRDISAIDAWEDLTAYGDEGGEIKVVGRMRTIVRHYQEH 102
                                        68999999999999999999999999999888888888899999999998877777666665555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00016
                           BBS2_Mid  11 geneLvvgsddfeirvfk..eeelvaeitetekvvslarlekerfayaleNGtvgvyekk..erlWrvksknevva 82 
                                        +e+ L+ +sdd++i++f+  + e va+i e+   v  +++ +  +  +   G +  y+ +  +r+ ++ +k++v +
  gene1792|gene1792|rna1791|rna1791 112 NEDMLISCSDDMKIKIFElsRAESVATIAENTDYVKSIDVGDGMIFSGSYDGFINGYSLStfKRVFEHNTKRRVSK 187
                                        5789*************72255899999999999999999999999888899998887542257777777776665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                           BBS2_Mid  18 gsddfeirvfkee.elvae 35 
                                         s d ++rvf  + +++++
  gene1792|gene1792|rna1791|rna1791 238 VSLDANVRVFTTDlRMISK 256
                                        5789999999988555555 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.016        37      15      33 ..     147     165 ..     138     172 .. 0.82
   2 ?    1.0   0.0      0.29   6.4e+02      18      39 ..     190     210 ..     178     211 .. 0.81
   3 ?    4.3   0.0     0.026        59      15      36 ..     226     247 ..     221     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.016
                              PQQ_3  15 sspavdgglvyvgtgdGtl 33 
                                         s  v++g ++ g++dG +
  gene1792|gene1792|rna1791|rna1791 147 KSIDVGDGMIFSGSYDGFI 165
                                        677899***********87 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.29
                              PQQ_3  18 avdgglvyvgtgdGtlyAlDae 39 
                                         ++gg+v +++g + ++ +D e
  gene1792|gene1792|rna1791|rna1791 190 ILGGGRVAFASG-NEVCVIDVE 210
                                        57899******9.999999987 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.026
                              PQQ_3  15 sspavdgglvyvgtgdGtlyAl 36 
                                        +s++++ g++y+++ d +++ +
  gene1792|gene1792|rna1791|rna1791 226 TSMVFYAGRLYTVSLDANVRVF 247
                                        7899*************99987 PP

>> Formyl_trans_C  Formyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00031       0.7      63      91 ..      34      62 ..       3      67 .. 0.83
   2 ?   -0.7   0.0      0.74   1.7e+03      57      86 ..     103     134 ..      64     143 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                                       TT..TEEEE-SBSEEEEEEEEETTS--EE CS
                     Formyl_trans_C 63 vdkggllvacgdgallilelqlegkkams 91
                                         k+g++v+c+++a+ i++ + ++kk+++
  gene1792|gene1792|rna1791|rna1791 34 CCKDGIVVGCKNRAVVIKKGENKKKKIVK 62
                                       56899*****************9999986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.74
                                        TTSEEETT...TEEEE-S.BSEEEEEEEEETT CS
                     Formyl_trans_C  57 pGtivavdkg.gllvacg.dgallilelqleg 86 
                                          ++ +++ +  +l+ c+ d  ++i el +++
  gene1792|gene1792|rna1791|rna1791 103 EARVNEIKINeDMLISCSdDMKIKIFELSRAE 134
                                        55566666565789999966668888777665 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.24     161     219 ..     180     239 ..     132     261 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                              PQQ_2 161 rvgdisgrpvvaeg.tVyassgqgrllal.dlatgrrlw.ske.issinglpildgdllyvvs 219
                                         +++  +++++ +g +V ++sg++  +++ d+++g ++  +   i+++++  +  ++ ly+vs
  gene1792|gene1792|rna1791|rna1791 180 NTKRRVSKVRILGGgRVAFASGNE--VCViDVENGGKEIgKAFhIKEVTS-MVFYAGRLYTVS 239
                                        333444455555444666666666..666666666655433334555655.333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2702.08
//
Query:       gene1793|gene1793|rna1792|rna1792  [L=845]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-17   62.1   0.2      4e-07   29.9   0.1    2.6  2  PLDc        Phospholipase D Active site motif
    1.8e-15   57.0   0.0      2e-09   37.5   0.0    2.6  2  PLDc_2      PLD-like domain
  ------ inclusion threshold ------
       0.04   13.2   0.0      0.074   12.4   0.0    1.3  1  RE_NgoFVII  NgoFVII restriction endonuclease


Domain annotation for each model (and alignments):
>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   7.9e-11   4.7e-07       3      28 .]     402     427 ..     401     427 .. 0.97
   2 !   29.9   0.1   6.7e-11     4e-07       2      28 .]     678     704 ..     677     704 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.9e-11
                                        BEE---EEEETTTEEEEE---SSHHH CS
                               PLDc   3 gthHqKivivDdrvafvGgaNLcdgr 28 
                                        +thH+Kiv +D r+a+vGg +L  gr
  gene1793|gene1793|rna1792|rna1792 402 WTHHEKIVAIDQRIAYVGGIDLAPGR 427
                                        9*********************9997 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 6.7e-11
                                        TBEE---EEEETTTEEEEE---SSHHH CS
                               PLDc   2 mgthHqKivivDdrvafvGgaNLcdgr 28 
                                        ++ +H+Ki+ivD++ a+vG+aNL+d++
  gene1793|gene1793|rna1792|rna1792 678 QIYVHSKIIIVDGTSAIVGSANLNDRS 704
                                        5789*********************97 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     8e-07    0.0048      28     103 ..     345     425 ..     329     439 .. 0.69
   2 !   37.5   0.0   3.3e-13     2e-09       3     127 ..     554     730 ..     552     736 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8e-07
                             PLDc_2  28 allkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet.........llgslHaKlylidgktv 94 
                                         l+++a++g ++ril+ +++   ga + +s+++++ l  + + +++v ++            + H+K++ id++++
  gene1793|gene1793|rna1792|rna1792 345 VLKRLAEEGIRIRILVYKEIL--GALNIDSNRTCEFL-SNLHRRIEVLMHpngigrapiY-WTHHEKIVAIDQRIA 416
                                        3566*************9776..44555555555444.5444455555533344555542.467************ PP

                             PLDc_2  95 ivGSsNltk 103
                                        +vG+  l +
  gene1793|gene1793|rna1792|rna1792 417 YVGGIDLAP 425
                                        ***987665 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 3.3e-13
                             PLDc_2   3 qliksAkksidiatyyf.............vsdreildallkaakrg..vkvrilldskkd............... 48 
                                        ++i+++k+ i+i +++f              + ++++++++ka ++g   kv ill+   +               
  gene1793|gene1793|rna1792|rna1792 554 EMIQNSKRFIYIENQFFitkcssapgfpenAVGKALVERIIKADRNGeeFKVYILLPL-FPildtgisvgptpame 628
                                        78999************9*99999999998889999**********966788899997.67899************ PP

                             PLDc_2  49 .........................dagavdeaslkelkellleagvevrvfetllgslHaKlylidgktvivGSs 99 
                                                                 d    ++  l  lk+  +  g++v     ++  +H+K++++dg+ +ivGS+
  gene1793|gene1793|rna1792|rna1792 629 iiriqeqsisrgegslyqvlkengvD--PSKYIVLMSLKKA-CFDGLKVVH---QQIYVHSKIIIVDGTSAIVGSA 698
                                        ***97666666666666666444211..2223344444444.444444332...22578***************** PP

                             PLDc_2 100 Nltkrgl..dlnlElnvviedk..elakelee 127
                                        Nl++r++  ++++E+++ +e +   + k l++
  gene1793|gene1793|rna1792|rna1792 699 NLNDRSMlgTRDTEIALLVEEEggSIHKLLRK 730
                                        *******999999**99999887555555544 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.2e-05     0.074      47     122 ..     651     720 ..     624     738 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                        HXXXHHHHHHHHHHHHHHHHCTSEEEEEXSSS.XBXXXEEEEEET.TEEEEEEESXXSXXTTS.XXXSBXEEEEEE CS
                         RE_NgoFVII  47 eglskrlheallklnkklseegigevkvsysv.kvHsKlYiwkkdgkplsAliGSANlssngl.rtrqrEtlvdld 120
                                        +g + +++  l+ l+k      ++ +kv+     vHsK+ i        sA++GSANl    +  tr  E+++ ++
  gene1793|gene1793|rna1792|rna1792 651 NGVDPSKYIVLMSLKKAC----FDGLKVVHQQiYVHSKIIIVDGT----SAIVGSANLNDRSMlGTRDTEIALLVE 718
                                        677777788888888888....78899888888999999886555....**********999999******99988 PP

                                        .H CS
                         RE_NgoFVII 121 te 122
                                        +e
  gene1793|gene1793|rna1792|rna1792 719 EE 720
                                        44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (845 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.53
# Mc/sec: 4796.74
//
Query:       gene1794|gene1794|rna1793|rna1793  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-68  229.8   0.1    4.2e-68  229.4   0.1    1.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.1e-11   44.9   0.2    4.7e-10   39.6   0.2    2.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.8e-09   36.7   0.1      4e-08   33.4   0.1    2.1  1  AAA_31       AAA domain
    0.00022   20.5   1.5     0.0014   17.9   0.2    2.3  2  ArsA_ATPase  Anion-transporting ATPase
    0.00042   19.7   0.0    0.00056   19.3   0.0    1.2  1  MipZ         ATPase MipZ
     0.0011   18.8   0.2     0.0042   16.9   0.0    1.8  2  AAA_26       AAA domain
     0.0078   16.1   0.0      0.025   14.5   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.025   14.4   0.0    1.3  1  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.019   14.1   0.1      0.039   13.1   0.1    1.5  1  NB-ARC       NB-ARC domain
       0.02   14.4   0.1      0.051   13.0   0.1    1.8  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.024   14.8   1.6      0.024   14.8   1.6    2.3  2  zf-MYND      MYND finger
      0.064   13.2   0.2       0.14   12.1   0.2    1.5  1  NTPase_1     NTPase
      0.068   12.9   0.0       0.11   12.3   0.0    1.4  1  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.094   11.7   0.0       0.11   11.5   0.0    1.2  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.12   12.2   0.0       0.25   11.2   0.0    1.4  1  APS_kinase   Adenylylsulphate kinase
       0.16   11.6   0.0       0.32   10.7   0.0    1.4  1  AAA_30       AAA domain
       0.17   11.4   0.0       0.36   10.4   0.0    1.5  2  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.4   0.1     4e-71   4.2e-68       2     226 ..      48     273 ..      47     287 .. 0.96

  Alignments for each domain:
  == domain 1  score: 229.4 bits;  conditional E-value: 4e-71
                               ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvm 76 
                                        ++ ++a++SgKGGVGKSt++ n+A  ++++g+++++lD+D+ Gpsiprl+ +++ ++ +++ +++Pve+ + +kv+
  gene1794|gene1794|rna1793|rna1793  48 IRIIVAIMSGKGGVGKSTITRNIAECISARGVSTCILDLDLSGPSIPRLTATDGMSMCETNGMMQPVEVnRFLKVV 123
                                        67799*************************************************99999998999***9667**** PP

                               ParA  77 SigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevalad 152
                                        S g++ +s  e  ++ + +k++a+k+ll +++++ +D L++D+PP  +De+l +++ ++ +  +iVttpq+ a++d
  gene1794|gene1794|rna1793|rna1793 124 SAGYVQNSYGEGRMFSSRLKTNALKKLLGHCNYKGVDTLLLDTPPNVTDEHLGMVNFIKPRLGIIVTTPQKFAMQD 199
                                        **********************************************************99999************* PP

                               ParA 153 vkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplv 226
                                        v ++i++++k+k++vlG+veNm+ f+cp+c++ +++f++ g+e+++++ gvp+lg+i l+++i+++sd g+ + 
  gene1794|gene1794|rna1793|rna1793 200 VIRQIDFCRKAKIDVLGIVENMKKFICPSCNHPKSVFRSTGVESYCKSNGVPYLGSINLRQDIAKTSDMGNAVR 273
                                        **********************************************************************9654 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.2   4.5e-13   4.7e-10       1     123 [.      52     267 ..      52     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 4.5e-13
                                        EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH...HTTEB-HHHH................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx................... RF
                               CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai...leglendiep................... 54 
                                        +ai+s+kGGvGK+t++ n+a +++ rg  +  +D+D  +++       +g ++   +                   
  gene1794|gene1794|rna1793|rna1793  52 VAIMSGKGGVGKSTITRNIAECISARGVSTCILDLDLSGPSIPRltaTDGMSM---Cetngmmqpvevnrflkvvs 124
                                        69*************************************99885333333333...25669999999999999999 PP

                                        ..........................................................................CC CS
                                        ..........................................................................xx RF
                               CbiA  55 ..........................................................................dl 56 
                                                                                                                  d+
  gene1794|gene1794|rna1793|rna1793 125 agyvqnsygegrmfssrlktnalkkllghcnykgvdtllldtppnvtdehlgmvnfikprlgiivttpqkfamqDV 200
                                        9999999999999999999999999999999999999999999999999999999999999999999999999988 PP

                                        HCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCH CS
                                        xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  57 krllellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapa 123
                                        +r + ++++ ++   +l    +++ ++    + +  +   + ++e +++  gvp lg+i  ++++a+   
  gene1794|gene1794|rna1793|rna1793 201 IRQIDFCRKAKID--VLgivENMKKFICPSCNHP-KSVFRSTGVESYCKSNGVPYLGSINLRQDIAKTSD 267
                                        8888888888865..3345555555555555555.35556777888887779999999999999988665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   3.8e-11     4e-08       3     165 ..      51     208 ..      49     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.8e-11
                             AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkv 78 
                                        ++ai+  KGGvGK+T + n+a++++ +g  + + DlD  + +  +l  +      +++e+       + +++  +v
  gene1794|gene1794|rna1793|rna1793  51 IVAIMSGKGGVGKSTITRNIAECISARGVSTCILDLDLSGPSIPRLTATD---GMSMCET-------NGMMQPVEV 116
                                        789**********************************9998887665322...2233333.......333333332 PP

                             AAA_31  79 enl.dlips.sidLaeaeielvelekkeeilkellekvkde.YDyiiiDcpPsL..glltenaLvasdsviipvqa 149
                                        ++  +++ + +++ +  e ++++ + k+++lk+ll + + +  D  ++D+pP++  + l +  ++     ii++ +
  gene1794|gene1794|rna1793|rna1793 117 NRFlKVVSAgYVQNSYGEGRMFSSRLKTNALKKLLGHCNYKgVDTLLLDTPPNVtdEHLGMVNFIKPRLGIIVTTP 192
                                        33325665514555666889999999*********99987669*********99545899999999********** PP

                             AAA_31 150 eayaleGleqllktie 165
                                        +++a++ + + +++ +
  gene1794|gene1794|rna1793|rna1793 193 QKFAMQDVIRQIDFCR 208
                                        ****998776666655 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.4e-06    0.0014       4      38 ..      53      87 ..      49      91 .. 0.91
   2 ?    1.2   0.1      0.16   1.7e+02     113     169 ..     147     204 ..     143     230 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                        ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                        +++GKGGVGK+t+   +a  +s  g ++ ++ +D
  gene1794|gene1794|rna1793|rna1793 53 AIMSGKGGVGKSTITRNIAECISARGVSTCILDLD 87
                                       479***********************999999877 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.16
                                        HHHHHHHHHCSSSSEEEEESBS..CCHTCGGGGHHHHHHHHHHHHHHHHH..HHHHHHHHH CS
                        ArsA_ATPase 113 feellkyvkeeeydvvvlDtaP..TGhtlrllslpevleklleklvklke..klsplakql 169
                                        +++ll +++ +  d+++lDt+P  T + l+++   + ++  l  +v + +  +++++++q+
  gene1794|gene1794|rna1793|rna1793 147 LKKLLGHCNYKGVDTLLLDTPPnvTDEHLGMV---NFIKPRLGIIVTTPQkfAMQDVIRQI 204
                                        55566666666678888888873344444444...34444444333333322334444443 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.3e-07   0.00056       3      78 ..      52     128 ..      49     207 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.3e-07
                                        EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHH.HHHHHHHHHT------EEE-SSS-HHHH CS
                               MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryle.nraataerkglsLplpealalseaeeae 77 
                                        + +   kGG Gkst++  +a +++++G++   +dldl   ++ r    + + + e +g+  p+   + l+ +++  
  gene1794|gene1794|rna1793|rna1793  52 VAIMSGKGGVGKSTITRNIAECISARGVSTCILDLDLSGPSIPRLTAtDGMSMCETNGMMQPVEVNRFLKVVSAGY 127
                                        446678*******************************999999876514556667777766665555444444433 PP

                                        T CS
                               MipZ  78 v 78 
                                        v
  gene1794|gene1794|rna1793|rna1793 128 V 128
                                        3 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.2   1.3e+03       9      31 ..      58      80 ..      52      82 .. 0.81
   2 !   16.9   0.0     4e-06    0.0042     132     195 ..     187     263 ..     185     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                             AAA_26  9 dtgvGKTvvslgLvralkrkgvk 31
                                         gvGK++++  +++ ++++gv+
  gene1794|gene1794|rna1793|rna1793 58 KGGVGKSTITRNIAECISARGVS 80
                                       668*******9999999888875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4e-06
                             AAA_26 132 ilVargglgtinqllltiealrqknvrvlGvilNk.......vrnpe......nvetlekksgipvlGvvPylpdl 194
                                        i+V+++++ ++++++ +i+++r+ ++ vlG++ N        +++p+       ve+++k++g+p lG++   +d+
  gene1794|gene1794|rna1793|rna1793 187 IIVTTPQKFAMQDVIRQIDFCRKAKIDVLGIVENMkkficpsCNHPKsvfrstGVESYCKSNGVPYLGSINLRQDI 262
                                        79999*****************************8565543333332555566*****************988776 PP

                             AAA_26 195 e 195
                                         
  gene1794|gene1794|rna1793|rna1793 263 A 263
                                        5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.4e-05     0.025      84     122 ..      32      73 ..      12      83 .. 0.77
   2 ?   -2.9   0.0       5.4   5.7e+03      30      51 ..     142     163 ..     138     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.4e-05
                                        TTTHTTHHHHHHHCTT.S..EEEEECSTTSSHHHHHHHHCTT CS
                        RsgA_GTPase  84 aktkegleelkellkd.k..tsvlvGqSGvGKStLinallpe 122
                                        +++  ++++++e+l + +  ++++ G+ GvGKSt+  ++++ 
  gene1794|gene1794|rna1793|rna1793  32 MQQDPDIKAIQENLGGiRiiVAIMSGKGGVGKSTITRNIAEC 73 
                                        4566789999999999851145689**********9999876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.4
                                        --HHHHHHHHHHHHHTT-EEEE CS
                        RsgA_GTPase  30 lslnlldrfLvlaeekgiepvi 51 
                                        l++n l+++L +++ kg++ ++
  gene1794|gene1794|rna1793|rna1793 142 LKTNALKKLLGHCNYKGVDTLL 163
                                        6778888888888888877655 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.4e-05     0.025       1      36 [.      57      92 ..      57     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                             CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                       G+  +GKST++r++++ +  +g +++++DlD+  ++
  gene1794|gene1794|rna1793|rna1793 57 GKGGVGKSTITRNIAECISARGVSTCILDLDLSGPS 92
                                       66789**************************87655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.7e-05     0.039       7      42 ..      40      72 ..      34      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                             NB-ARC  7 kviekLlekdelqslvvalvGmgGvGKttlakqiln 42
                                       +++e+L    ++  +v  ++G+gGvGK+t+ ++i +
  gene1794|gene1794|rna1793|rna1793 40 AIQENLG---GIRIIVAIMSGKGGVGKSTITRNIAE 72
                                       5555555...6665566678************9975 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.9e-05     0.051       5      31 ..      55      81 ..      50     129 .. 0.84
   2 ?   -2.9   0.0       3.4   3.6e+03     167     185 ..     205     223 ..     189     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.9e-05
                          Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkv 31
                                       + GkGG+Gkst + n++  ++++g   
  gene1794|gene1794|rna1793|rna1793 55 MSGKGGVGKSTITRNIAECISARGVST 81
                                       46****************999988655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.4
                          Fer4_NifH 167 kyaksggvrlgGliinsrk 185
                                         + ++ ++ + G++ n +k
  gene1794|gene1794|rna1793|rna1793 205 DFCRKAKIDVLGIVENMKK 223
                                        3667788899999999775 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.6   2.2e-05     0.024       8      27 ..      14      33 ..       3      36 .. 0.72
   2 ?    1.0   0.4      0.43   4.6e+02       6      22 ..     209     245 ..     205     248 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                                       B-SCE-TTTS-SEESSHHHH CS
                            zf-MYND  8 ealkkCagCksvfYCskeCq 27
                                        +++ C+gC +v YCs+  q
  gene1794|gene1794|rna1793|rna1793 14 GKAEECKGCPNVSYCSQPMQ 33
                                       34459***********9766 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.43
                                        -..........B-SC.E-TTT........S-S...EES CS
                            zf-MYND   6 k.........aealk.kCagC........ksv...fYC 22 
                                        k         ++ +k  C+ C        + +    YC
  gene1794|gene1794|rna1793|rna1793 209 KakidvlgivENMKKfICPSCnhpksvfrS-TgveSYC 245
                                        555555555434444689999555333330.1334666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00013      0.14       3      29 ..      54      80 ..      52      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                       EEE--TTSSHHHHHHHHHHHH...GGG CS
                           NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvk 29
                                       +++G+ GvGK+T+ ++++e ++ +gv+
  gene1794|gene1794|rna1793|rna1793 54 IMSGKGGVGKSTITRNIAECISARGVS 80
                                       679******************999997 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.11       3      57 ..      57     111 ..      55     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                         ATP_bind_1   3 GpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvm 57 
                                        G  G+GK+t++++++e +++rg s  ++ LD    ++p   a+d + + +++ +m
  gene1794|gene1794|rna1793|rna1793  57 GKGGVGKSTITRNIAECISARGVSTCILDLDLSGPSIPRLTATDGMSMCETNGMM 111
                                        889****************************776666665565555555555555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.11      33      70 ..      54      91 ..      31     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                       EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                               MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                        + G  G+Gkst++ ++++ + +rG    +l +D s p
  gene1794|gene1794|rna1793|rna1793 54 IMSGKGGVGKSTITRNIAECISARGVSTCILDLDLSGP 91
                                       46899***************************997765 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.25       4      39 ..      52      87 ..      49      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                         APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                       v  ++G  g GKsti++++++ + ++g+s+ +Ld d
  gene1794|gene1794|rna1793|rna1793 52 VAIMSGKGGVGKSTITRNIAECISARGVSTCILDLD 87
                                       56799****************************965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0003      0.32      20      50 ..      52      82 ..      38      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                             AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                       va++ G  G GK+t+ + ++e + a+g + +
  gene1794|gene1794|rna1793|rna1793 52 VAIMSGKGGVGKSTITRNIAECISARGVSTC 82
                                       78999*******************9997655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00034      0.36      34      61 ..      51      79 ..      34      87 .. 0.86
   2 ?   -3.7   0.0       6.8   7.2e+03     111     150 ..     131     166 ..     115     166 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                             AAA_25 34 elallaGapgtGKttlaldlalava.tGk 61
                                        +a+  G +g+GK+t++ ++a +++ +G 
  gene1794|gene1794|rna1793|rna1793 51 IVAIMSGKGGVGKSTITRNIAECISaRGV 79
                                       5899****************999986665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.8
                             AAA_25 111 v.eslpLfakdrggtlltadvdaleaaieevegvrlvviDp 150
                                        + ++ ++f+    + l t ++++l  ++++ +gv+ + +D+
  gene1794|gene1794|rna1793|rna1793 131 SyGEGRMFS----SRLKTNALKKLLGHCNY-KGVDTLLLDT 166
                                        444555544....22345667777777777.7788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1978.92
//
Query:       gene1795|gene1795|rna1794|rna1794  [L=578]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-30  104.6   0.0    9.4e-30  103.9   0.0    1.3  1  ABC_tran       ABC transporter
    5.8e-17   62.2  15.1    8.9e-17   61.6  15.1    1.2  1  ABC_membrane   ABC transporter transmembrane region
    7.5e-07   29.3   3.7    0.00042   20.2   0.7    2.3  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0004   20.1   0.3      0.001   18.8   0.3    1.6  1  AAA_29         P-loop containing region of AAA domain
    0.00048   20.0   1.9    0.00099   18.9   1.9    1.4  1  AAA_15         AAA ATPase domain
    0.00076   19.0   0.3      0.028   13.9   0.2    2.4  2  SMC_N          RecF/RecN/SMC N terminal domain
     0.0068   16.9   0.4      0.013   16.0   0.4    1.5  1  AAA_23         AAA domain
      0.008   15.6   0.1      0.013   14.9   0.1    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.066   12.1   0.1       0.11   11.4   0.1    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
      0.067   13.1   0.1       0.15   12.0   0.1    1.5  1  Rad17          Rad17 P-loop domain
      0.088   13.2   0.0       0.17   12.3   0.0    1.4  1  AAA_16         AAA ATPase domain
        0.1   12.3   0.4       0.25   11.0   0.2    1.7  2  AAA_24         AAA domain
       0.11   12.1   0.1       0.23   11.1   0.1    1.5  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
       0.13   11.4   0.1       0.19   10.9   0.1    1.2  1  DAP3           Mitochondrial ribosomal death-associated prote
       0.32   11.1   2.1       0.22   11.6   0.2    1.6  1  DUF87          Helicase HerA, central domain
       0.54    9.4   2.7       0.41    9.8   0.2    1.9  2  G-alpha        G-protein alpha subunit
          1    9.2   5.0        1.6    8.6   0.3    3.1  4  NTPase_1       NTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.0   8.9e-33   9.4e-30       1     137 []     357     505 ..     357     505 .. 0.89

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 8.9e-33
                                        EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltv 76 
                                        l+ v+lk+++g k+aivG+nG+GKSt+lk+l++  +  +G+i +dg ++k++   s+rk ig++pq+++lf+e+ v
  gene1795|gene1795|rna1794|rna1794 357 LNGVNLKVEKGDKMAIVGSNGSGKSTILKTLLKFCS-YQGTICIDGMNIKTIGNGSFRKIIGYVPQNSSLFNET-V 430
                                        789*******************************98.7************************************.6 PP

                                        HHH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                        xxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  77 ren................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                          n                +++ +i++ + +l+  +   t+v++s++++SgG++q++ + rall++p++l++DEpt
  gene1795|gene1795|rna1794|rna1794 431 MYNikygnpgvsdygvvelAKRFNIHDSIMRLERGY--FTNVGESGRHISGGERQKIIILRALLRRPEILIMDEPT 504
                                        66669**99988777774444444666666666666..788899*******************************9 PP

                                        T CS
                                        x RF
                           ABC_tran 137 a 137
                                        +
  gene1795|gene1795|rna1794|rna1794 505 S 505
                                        6 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6  15.1   8.4e-20   8.9e-17       7     273 ..      37     299 ..      29     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 8.4e-20
                                        HHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ABC_membrane   7 lailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfk 82 
                                        ++++++  ++ +++++++i d l +   +e       + ++l+  l+ + ++ lq y++  + +++ +   r +f+
  gene1795|gene1795|rna1794|rna1794  37 SIFAGKYFEVKVASCISHISDGLGS---AEV--PRGRIAMFLATSLMGIMFTELQGYVFVGAIQYVYRYTLRTTFE 107
                                        3444444444444555555555544...222..44678888888899999999*********************** PP

                                        HHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHHSHHHHHHHHHHHHHHHHH CS
                       ABC_membrane  83 kilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltf.vgglivmfylgwkltlvllailpliilv 157
                                          ++++++ f++   G++ s +t+    ++d++  ++  +f  ++++ ++gl v++ lg   ++++++ + ++ ++
  gene1795|gene1795|rna1794|rna1794 108 YFIQMDTEPFESYGLGTIQSIITRKSKAISDFVEVSVQNLFPVVASLgFVGLEVYLKLGALASVIIVFAVSVYGFI 183
                                        *******************************999999888887765426777788889****************** PP

                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       ABC_membrane 158 saviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitql 233
                                        ++ ia + ++++   ++a + as++++++ls+++ V +f++ ++++++++ +l e ++ g +  +   +l++++ l
  gene1795|gene1795|rna1794|rna1794 184 TISIALRRNRIRAALNNAENTASNIVYDTLSNHESVVSFNNYDIEVRRYDGKLVEIERFGTSLFRGLYILNMVQKL 259
                                        **************************************************************************** PP

                                        HHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
                       ABC_membrane 234 lgllsyalalwfGttlvisgelsvgdlvvflslfailfga 273
                                        ++ ++++l++ +G++ ++s+ ++ ++l+++ + + il++ 
  gene1795|gene1795|rna1794|rna1794 260 IFAFLNSLMIALGVYGMLSSRMDGKTLIFYATTSRILLMN 299
                                        ********************************99999876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.7     4e-07   0.00042       2      51 ..     370     421 ..     369     427 .. 0.81
   2 !    9.4   0.1    0.0008      0.84     235     283 ..     475     521 ..     472     538 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4e-07
                             AAA_21   2 nvliGpNgsGKSnLLdaldllarl....drdvegltdelsggggirkipslldl 51 
                                        ++++G NgsGKS++L++l  l+++       ++g++++  g+g++rki+++ + 
  gene1795|gene1795|rna1794|rna1794 370 MAIVGSNGSGKSTILKTL--LKFCsyqgTICIDGMNIKTIGNGSFRKIIGYVPQ 421
                                        58****************..5555559966678888899999999998887665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0008
                             AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellk 283
                                        r++S G ++ + +l allr++    +l+ DEp ++L+ ++   ++  +++
  gene1795|gene1795|rna1794|rna1794 475 RHISGGERQKIIILRALLRRP---EILIMDEPTSNLDKEAEIDIIkNIID 521
                                        58899*****99999999999...9************9776666644444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   9.7e-07     0.001      13      39 ..     358     384 ..     353     389 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.7e-07
                             AAA_29  13 dghtieidlkgatlltGpsGsGKSTll 39 
                                        +g  ++++  + + ++G +GsGKST+l
  gene1795|gene1795|rna1794|rna1794 358 NGVNLKVEKGDKMAIVGSNGSGKSTIL 384
                                        556778885569**************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.9   9.4e-07   0.00099      23      70 ..     368     409 ..     355     418 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.4e-07
                             AAA_15  23 eeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifen 70 
                                        +  + ++G N+sGKS+il+ l +F + +      +i i+  ++++  n
  gene1795|gene1795|rna1794|rna1794 368 D-KMAIVGSNGSGKSTILKTLLKFCSYQ-----GTICIDGMNIKTIGN 409
                                        3.899*******************9954.....555555555555555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   2.6e-05     0.028      26      44 ..     369     387 ..     340     396 .. 0.82
   2 ?    2.7   0.0     0.071        74     136     202 ..     476     538 ..     425     551 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                                        EEEEEESTTSSHHHHHHHH CS
                                        xxxxxxxxxxxxxxxxxxx RF
                              SMC_N  26 ftaivGpNGSGKsnlldAi 44 
                                          aivG+NGSGKs +l  +
  gene1795|gene1795|rna1794|rna1794 369 KMAIVGSNGSGKSTILKTL 387
                                        469************9886 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.071
                                        CS-HHHHH.HHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                        xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 136 lLSgGekt.LvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                         +SgGe++ ++ l    A+   ++  + ++De  ++LD++    + + +   + +  +i i ++ ++l
  gene1795|gene1795|rna1794|rna1794 476 HISGGERQkIIILR---AL--LRRPEILIMDEPTSNLDKEAEIDIIKNIIDFEGSLTVIAIVHNLDLL 538
                                        57888765122222...22..24445889*********987766666666665567777777766665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   1.2e-05     0.013      22      42 ..     370     391 ..     341     431 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                             AAA_23  22 tlItGpNGaGKTTil.dAikla 42 
                                         +I+G NG+GK+Til   +k++
  gene1795|gene1795|rna1794|rna1794 370 MAIVGSNGSGKSTILkTLLKFC 391
                                        48*************4445555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.2e-05     0.013      39      60 ..     358     388 ..     321     392 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                                        -..........SEEEE--TTSSHHHHHHHHH CS
                       FtsK_SpoIIIE  39 a.........shllvaGatgsGKStalntLi 60 
                                                    + ++G+ gsGKSt l+tL+
  gene1795|gene1795|rna1794|rna1794 358 NgvnlkvekgDKMAIVGSNGSGKSTILKTLL 388
                                        14445555566899***************97 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001      0.11      16      44 ..     368     396 ..     355     401 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                      TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargd 44 
                                         +++ivG+ GsGK++ l+ ll+    +g 
  gene1795|gene1795|rna1794|rna1794 368 DKMAIVGSNGSGKSTILKTLLKFCSYQGT 396
                                        5799*****************98777765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00014      0.15      40      94 ..     362     417 ..     353     435 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                              Rad17  40 LesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkg 94 
                                        L+ +k   + i G  G gkst++k L k  +++    ++++++k   n     + g
  gene1795|gene1795|rna1794|rna1794 362 LKVEKGDKMAIVGSNGSGKSTILKTLLKFCSYQGTICIDGMNIKTIGNgSFRKIIG 417
                                        555555667899******************************99877744445555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.17      27      59 ..     370     402 ..     355     430 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                             AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgk 59 
                                        + ++G  G+GKs+++++ll+  + +g i++ g 
  gene1795|gene1795|rna1794|rna1794 370 MAIVGSNGSGKSTILKTLLKFCSYQGTICIDGM 402
                                        6799****************9999998887764 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         5   5.3e+03      60      78 ..     199     217 ..     121     221 .. 0.67
   2 ?   11.0   0.2   0.00024      0.25       3      23 ..     368     393 ..     366     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 5
                             AAA_24  60 aaeladyktlviDtidele 78 
                                        + ++++ + +v Dt++  e
  gene1795|gene1795|rna1794|rna1794 199 NNAENTASNIVYDTLSNHE 217
                                        5667777888888887665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                             AAA_24   3 lkiliyGpsgiGKTtlakel.....g 23 
                                         k++i+G++g+GK+t++k+l      
  gene1795|gene1795|rna1794|rna1794 368 DKMAIVGSNGSGKSTILKTLlkfcsY 393
                                        699****************9555554 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00022      0.23      11      45 ..     364     399 ..     356     477 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                        EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                        ATP-synt_ab  11 ivqGqrtlipgafgvGktvisqslskqsnsdd.aii 45 
                                        + +G +++i+g +g Gk++i+++l+k ++ +  ++i
  gene1795|gene1795|rna1794|rna1794 364 VEKGDKMAIVGSNGSGKSTILKTLLKFCSYQGtICI 399
                                        569***********************9866643443 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00018      0.19      20      65 ..     364     409 ..     354     426 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                                        SS---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-GGGGTS CS
                               DAP3  20 kkkvkrlvltGekgsGKSvlLlqalayAlekgwvvlhvpeaedlvn 65 
                                         +k  ++ + G +gsGKS+ L  +l ++  +g + +   + + + n
  gene1795|gene1795|rna1794|rna1794 364 VEKGDKMAIVGSNGSGKSTILKTLLKFCSYQGTICIDGMNIKTIGN 409
                                        578899*************************999887666655555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0002      0.22      25      45 ..     369     389 ..     352     397 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                              DUF87  25 HlAilgsTGsGKSntvavLle 45 
                                         +Ai+gs GsGKS+  + Ll+
  gene1795|gene1795|rna1794|rna1794 369 KMAIVGSNGSGKSTILKTLLK 389
                                        69****************996 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2         1   1.1e+03     228     281 ..     172     227 ..     170     230 .. 0.82
   2 ?    9.8   0.2   0.00038      0.41      24      45 ..     368     389 ..     352     408 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                                        EEEEEEEGGGTT-B-SS-TTSBHHHHHHHHHHCCCC-...GGGTTSEEEEEEE-HHH CS
                            G-alpha 228 aiiFlvslsefdqvlyedekvnrleeslklFkeicnn...kllkntpiiLflnKlDi 281
                                        +i+F vs+ +f  + +   + nr++ +l+  ++  +n     l n + ++ +n +Di
  gene1795|gene1795|rna1794|rna1794 172 IIVFAVSVYGFITISIA-LRRNRIRAALNNAENTASNivyDTLSNHESVVSFNNYDI 227
                                        58999999999776666.669999999999999999966677778888998898887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00038
                                        EEEEEEESTTSSHHHHHHHHHH CS
                            G-alpha  24 vkllllGqseSGKsTilkqlkl 45 
                                         k+ ++G+++SGKsTilk l +
  gene1795|gene1795|rna1794|rna1794 368 DKMAIVGSNGSGKSTILKTLLK 389
                                        48999*************9864 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.3   4.5e+03      28      77 ..     177     228 ..     171     241 .. 0.57
   2 ?   -0.2   0.0      0.79   8.4e+02      17      64 ..     315     361 ..     311     368 .. 0.81
   3 ?    8.6   0.3    0.0015       1.6       2      40 ..     370     409 ..     369     419 .. 0.78
   4 ?   -0.0   0.0      0.69   7.3e+02      69     123 ..     468     521 ..     444     557 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.3
                                        GGEEEEEEEEE-------EEEEEET.T--EEEEEETT..---SSEETTEEE- CS
                           NTPase_1  28 vkvgGfyteevreggrrigFkivdlasgeegiLarve..akreprvgkyvvd 77 
                                        v+v Gf+t  +  + +ri   + + ++   +i   +   +++ +++ +y ++
  gene1795|gene1795|rna1794|rna1794 177 VSVYGFITISIALRRNRIRAALNNAENTASNIVYDTLsnHESVVSFNNYDIE 228
                                        6777888877777777776666666333333333222333444455555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.79
                                        HHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT CS
                           NTPase_1  17 kkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarve 64 
                                         ++ e+l s+++ v+    + + + g+ i F+ v l  g+++iL  v+
  gene1795|gene1795|rna1794|rna1794 315 LNAREVL-SEDYDVKTSESQSIVKFGKNITFSNVHLYYGDKKILNGVN 361
                                        5566677.67788888899999999******************99887 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0015
                                        EEEE--TTSSHHHHHHHHHHHH...GGG.EEEEEEEEE-- CS
                           NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvk.vgGfyteevre 40 
                                        ++i G+ G+GK+T++k +l+ ++ +g   ++G+  + + +
  gene1795|gene1795|rna1794|rna1794 370 MAIVGSNGSGKSTILKTLLKFCSYQGTIcIDGMNIKTIGN 409
                                        6899*****************9988753267777666655 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.69
                                        SEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                           NTPase_1  69 prvgkyvvdvesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk 123
                                         +vg+   ++   e+  + +lr  l++++++++DE  +  l  +  ++ ++++++
  gene1795|gene1795|rna1794|rna1794 468 TNVGESGRHISGGERQKIIILRALLRRPEILIMDEPTS-NLDKEAEIDIIKNIID 521
                                        56777777777778888888998889999999999432.4444444555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 3341.24
//
Query:       gene1796|gene1796|rna1795|rna1795  [L=295]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1982.57
//
Query:       gene1797|gene1797|rna1796|rna1796  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   12.1   0.6       0.46   10.7   0.1    2.0  2  CTU2      Cytoplasmic tRNA 2-thiolation protein 2


Domain annotation for each model (and alignments):
>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.42   7.6e+03      46      53 ..       3      10 ..       2      18 .. 0.82
   2 ?   10.7   0.1   2.6e-05      0.46       6      35 ..     211     240 ..     207     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.42
                               CTU2 46 ekCalCgl 53
                                       ++C +C  
  gene1797|gene1797|rna1796|rna1796  3 HRCVICTY 10
                                       79****86 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 2.6e-05
                               CTU2   6 tekFilklekdfpstvstvvrTgeKLvknk 35 
                                        +++Fi k+e++ + +v +++ T++K+v+ k
  gene1797|gene1797|rna1796|rna1796 211 LSRFISKMESKNSLVVFNILNTVKKIVAGK 240
                                        579***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1429.40
//
Query:       gene1798|gene1798|rna1797|rna1797  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-10   39.6   0.7    1.3e-09   38.1   0.7    1.8  1  Spindle_Spc25  Chromosome segregation protein Spc25
    0.00013   21.8   0.7     0.0002   21.3   0.7    1.2  1  Bacillus_HBL   Bacillus haemolytic enterotoxin (HBL)
     0.0014   18.8   3.9     0.0026   18.0   3.9    1.4  1  DUF1319        Protein of unknown function (DUF1319)
     0.0015   17.5   7.2      0.002   17.0   7.2    1.2  1  Spc7           Spc7 kinetochore protein
     0.0085   15.8   6.5      0.012   15.3   6.5    1.3  1  SHE3           SWI5-dependent HO expression protein 3
  ------ inclusion threshold ------
      0.098   12.5   9.6       0.16   11.8   9.6    1.3  1  DUF724         Protein of unknown function (DUF724)
       0.12   11.8   2.2       0.17   11.3   2.2    1.1  1  Peptidase_C98  Ubiquitin-specific peptidase-like, SUMO isopep
       0.72   10.3  15.5       0.12   12.9   2.3    2.3  2  ZapB           Cell division protein ZapB


Domain annotation for each model (and alignments):
>> Spindle_Spc25  Chromosome segregation protein Spc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.7   5.9e-13   1.3e-09       3      73 .]     163     229 ..     161     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.9e-13
                      Spindle_Spc25   3 eedklkfvFtnidpkdperefsftLdvsedtyevlecsPkLedeeleelleeLnetndlgkFlkevRkaFk 73 
                                        +e+++k+vF++i+p+d   e+ +tLd+s ++  v++  P++ d  le+    + e++ ++ Fl  +Rk+F+
  gene1798|gene1798|rna1797|rna1797 163 RENVIKIVFSRICPEDSV-ECFVTLDLSMED-AVIDLFPRMYD--LEKANGVFRECRSFHDFLAVIRKEFR 229
                                        6899*************6.9**********8.5*******776..*************************6 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.7   8.7e-08    0.0002      73     152 ..      20      98 ..      11     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.7e-08
                       Bacillus_HBL  73 tiqdiigYstkFqsyyktlveavdkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvde 148
                                        +i+d+ gY ++F + +  l+  +   dk+e   ll+   +++++  +  ++l+ e ++lk+++++d+k++k+  de
  gene1798|gene1798|rna1797|rna1797  20 IINDLEGYLEMFRNHARFLRGRI-SRDKQEGEVLLQTVTSTLNEMRERNERLVDERNALKSRIEQDTKDLKASEDE 94 
                                        57899******************.99999999***************************************99887 PP

                       Bacillus_HBL 149 ltsi 152
                                          + 
  gene1798|gene1798|rna1797|rna1797  95 KHEL 98 
                                        6554 PP

>> DUF1319  Protein of unknown function (DUF1319)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   3.9   1.1e-06    0.0026       6      96 ..      53     149 ..      50     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                            DUF1319   6 aeevkitkrela.hniaviadrvalgskv..nlkslkivkekrrslekqlkklkselkklrelylerrPlskqeve 78 
                                         ++v  t++e+   n  ++ +r al s++  + k+lk+  +++++l +q+++l+ +   l+e + e++ + +  v+
  gene1798|gene1798|rna1797|rna1797  53 LQTVTSTLNEMReRNERLVDERNALKSRIeqDTKDLKASEDEKHELMNQIRELEMNNLDLKEVFQEKKGIENAFVK 128
                                        567778888875268999***********555677************************************99998 PP

                            DUF1319  79 ..elvveiskqPk.lieeeal 96 
                                          el+ e  kq   l+e +a+
  gene1798|gene1798|rna1797|rna1797 129 kmELIFERNKQREaLMEAKAE 149
                                        335777777775426666666 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   7.2   9.1e-07     0.002     157     277 ..      16     136 ..       2     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.1e-07
                               Spc7 157 lLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleel 232
                                        +++   + l+ +l+ ++++   l+ ++ + +++ e l +     L+e+re+ ++l  e +++k ++++ +++l+++
  gene1798|gene1798|rna1797|rna1797  16 VMDGIINDLEGYLEMFRNHARFLRGRISRDKQEGEVLLQTVTSTLNEMRERNERLVDERNALKSRIEQDTKDLKAS 91 
                                        5666778899999999999999999999999999999999999********************************* PP

                               Spc7 233 eekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevka 277
                                        e++  el +q++ele +    ++v +e+kg+++  v++++  +++
  gene1798|gene1798|rna1797|rna1797  92 EDEKHELMNQIRELEMNNLDLKEVFQEKKGIENAFVKKMELIFER 136
                                        *********************************999999877766 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   6.5   5.4e-06     0.012      34     131 ..      54     154 ..      18     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.4e-06
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH CS
                               SHE3  34 elaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssaseteleee 109
                                        ++++++ +++ e    l +E + L+s ++  ++ lk  e+e +el +++ el++++  lk+ +++++  e++  ++
  gene1798|gene1798|rna1797|rna1797  54 QTVTSTLNEMRERNERLVDERNALKSRIEQDTKDLKASEDEKHELMNQIRELEMNNLDLKEVFQEKKGIENAFVKK 129
                                        556666667777888888999999999************************************************* PP

                                        HHHH...HHHHHHHHHHHHHHHHHH CS
                               SHE3 110 lerl...kvqYdalvdsqkeYkehY 131
                                        +e +   + q +al++++ e+ ++Y
  gene1798|gene1798|rna1797|rna1797 130 MELIferNKQREALMEAKAEWFKRY 154
                                        **98555678899999998887777 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   9.6     7e-05      0.16      92     163 ..      55     130 ..      50     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7e-05
                             DUF724  92 srlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk....ekkeaadkeiarl 163
                                        +  ++L +++++ ++l +er++l+++ie+++++ +  e+e +el ++i+ele+++  lk    ekk  +++ ++++
  gene1798|gene1798|rna1797|rna1797  55 TVTSTLNEMRERNERLVDERNALKSRIEQDTKDLKASEDEKHELMNQIRELEMNNLDLKevfqEKKGIENAFVKKM 130
                                        445778899**********************************************999977754443333333333 PP

>> Peptidase_C98  Ubiquitin-specific peptidase-like, SUMO isopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.2   7.5e-05      0.17      22     131 ..      34     150 ..      24     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.5e-05
                      Peptidase_C98  22 hletlkkalseleseeeslvkrlltkyeqaqallketqkk..kakeevvkvpsd...vlekaeeeLeevRkkvfkk 92 
                                        h + l+ ++s++++e e l+++++ + +++ +  ++   +  + k+++++ ++d     ++ +e ++++R+  +++
  gene1798|gene1798|rna1797|rna1797  34 HARFLRGRISRDKQEGEVLLQTVTSTLNEMRERNERLVDErnALKSRIEQDTKDlkaSEDEKHELMNQIRELEMNN 109
                                        778999999999*****999999999888877766554442123344444444333266777888999**999987 PP

                      Peptidase_C98  93 l..qpkLkcklGkeespvfalpllLkldslaeklfkssfsw 131
                                        l  +   + k G e++ v  + l+ + +++ e l++++ +w
  gene1798|gene1798|rna1797|rna1797 110 LdlKEVFQEKKGIENAFVKKMELIFERNKQREALMEAKAEW 150
                                        522677899***************************99999 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.3   5.2e-05      0.12      23      64 ..      38      83 ..      33      84 .. 0.80
   2 ?    2.8   5.4     0.074   1.7e+02      21      51 ..      96     140 ..      88     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                               ZapB 23 LqmeieeLkeen....eelkeenreleeeneqlkeereawqerlkk 64
                                       L+ +i++ k+e     ++ ++  +e++e ne+l +er+a+++r+++
  gene1798|gene1798|rna1797|rna1797 38 LRGRISRDKQEGevllQTVTSTLNEMRERNERLVDERNALKSRIEQ 83
                                       888999999998444455566677888****************985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.074
                               ZapB  21 tlLqmeieeLkeeneelkeenrele..............eeneql 51 
                                         +L ++i+eL++ n  lke  +e +              e n+q 
  gene1798|gene1798|rna1797|rna1797  96 HELMNQIRELEMNNLDLKEVFQEKKgienafvkkmelifERNKQR 140
                                        578888888888888888888888877776655555555333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1776  (0.0990574); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1530.64
//
Query:       gene1799|gene1799|rna1798|rna1798  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.93   10.4   4.6       0.82   10.6   1.2    2.5  2  DUF4065   Protein of unknown function (DUF4065)
        1.6    8.7  11.5       0.04   13.9   4.5    1.9  2  PGA2      Protein trafficking PGA2


Domain annotation for each model (and alignments):
>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.24   2.2e+03      59      78 ..      49      62 ..      24      93 .. 0.56
   2 ?   10.6   1.2   9.1e-05      0.82      47     102 ..     191     270 ..     119     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.24
                            DUF4065 59 eklekkekkeveeleddkea 78
                                       +k e+ e+++      +++ 
  gene1799|gene1799|rna1798|rna1798 49 KKSEQVEYED------EEYR 62
                                       2222221111......1111 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9.1e-05
                            DUF4065  47 kpieekeeeisdeklekkekkeveeleddkeae.........................lseeekevidkvikkykd 97 
                                        + +e kee  ++e++e+k++k+v + e+  +++                         l++eeke+++++i ++  
  gene1799|gene1799|rna1798|rna1798 191 NYEE-KEESDISEEMEEKDMKDVGKVEKVLTKDvlrgmfrggrialrdllrgvktrfgLNDEEKELVKEFIGENCT 265
                                        2222.3333333456666666666655555555899999*********************************9999 PP

                            DUF4065  98 lsase 102
                                        ++++e
  gene1799|gene1799|rna1798|rna1798 266 FDTDE 270
                                        98775 PP

>> PGA2  Protein trafficking PGA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.6      0.57   5.1e+03      75      85 ..      50      60 ..      40      69 .. 0.48
   2 ?   13.9   4.5   4.4e-06      0.04      77     135 ..     152     211 ..     104     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.57
                               PGA2 75 ksgesdeddde 85
                                       ks++++ +d+e
  gene1799|gene1799|rna1798|rna1798 50 KSEQVEYEDEE 60
                                       22333333333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.4e-06
                               PGA2  77 gesdedddegeeeed.vakasgvpewgkkarkrqkkvlkkleeeaeerkkeeeddkdiae 135
                                        +e d ddd  +++ + ++     ++  ++a +r +++++++ee++e++ +ee+++kd+++
  gene1799|gene1799|rna1798|rna1798 152 EEIDFDDDFDDDDGEeTNVFVVREKRLNSAGRRMRNIMENYEEKEESDISEEMEEKDMKD 211
                                        4445555544443332455555566678999***************99999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1817.96
//
Query:       gene1800|gene1800|rna1799|rna1799  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-11   42.8   0.0    1.9e-10   41.1   0.0    1.9  2  TAF8_C    Transcription factor TFIID complex subunit 8 C-term
    0.00058   19.8   0.1     0.0021   18.0   0.0    1.8  2  Bromo_TP  Bromodomain associated


Domain annotation for each model (and alignments):
>> TAF8_C  Transcription factor TFIID complex subunit 8 C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.7   6.3e+03      14      23 ..      79      88 ..      72      90 .. 0.64
   2 !   41.1   0.0   2.1e-14   1.9e-10       1      49 []     104     152 ..     104     152 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.7
                             TAF8_C 14 TYkrTpvyne 23
                                       TY + +v++e
  gene1800|gene1800|rna1799|rna1799 79 TYEKEEVEKE 88
                                       7777777665 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 2.1e-14
                             TAF8_C   1 yiPshlPpfPppHTYkrTpvyneretdpkkirekaaeqsrlaekaLrkL 49 
                                        +i++++P+fPp+H +++T v+    ++++ + ++++eqs  +e +L++L
  gene1800|gene1800|rna1799|rna1799 104 HIYDFMPSFPPTHAFRQTIVKGGSRSSKSMNVKNRLEQSLRTEGNLLRL 152
                                        9*********************************************998 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-07    0.0021      15      64 ..      12      61 ..       2      65 .. 0.93
   2 ?   -1.2   0.0      0.24   2.2e+03      48      61 ..     130     143 ..     120     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-07
                                       HHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHH CS
                           Bromo_TP 15 ileeaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDv 64
                                        l+e+G++++e  aLE ++  ++ Y++e  +++ s + h  +s +tl D+
  gene1800|gene1800|rna1799|rna1799 12 YLKEIGYEAVERKALEVFMASLEVYMLEYLKSVASVSRHGLKSHSTLLDI 61
                                       589*******************************************9998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.24
                                        HHHHTTSS-SS--H CS
                           Bromo_TP  48 ksfaehagRseptl 61 
                                        ++ +++ +R+e++l
  gene1800|gene1800|rna1799|rna1799 130 SKSMNVKNRLEQSL 143
                                        45569999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1142.08
//
Query:       gene180|gene180|rna180|rna180  [L=514]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      6e-60  202.8   2.9    7.7e-59  199.2   2.9    2.0  1  Pkinase         Protein kinase domain
    1.2e-32  113.3   0.2    2.3e-32  112.3   0.2    1.4  1  Pkinase_Tyr     Protein tyrosine kinase
    2.4e-05   23.3   0.7    3.4e-05   22.8   0.7    1.2  1  Pkinase_fungal  Fungal protein kinase
    5.4e-05   23.2   0.1      0.013   15.5   0.0    2.3  2  APH             Phosphotransferase enzyme family
    5.8e-05   22.8   0.7    0.00015   21.5   0.2    1.9  3  RIO1            RIO1 family
     0.0061   15.5   0.1      0.015   14.3   0.1    1.6  2  Haspin_kinase   Haspin like kinase domain
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.031   13.9   0.0    1.3  1  FTA2            Kinetochore Sim4 complex subunit FTA2
      0.037   13.4   0.1      0.063   12.6   0.1    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.089   12.4   0.6       0.35   10.4   0.3    2.1  2  WaaY            Lipopolysaccharide core biosynthesis protein 
       0.19   11.3   0.7       0.35   10.4   0.7    1.4  1  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   2.9   4.3e-62   7.7e-59       1     263 [.       4     229 ..       4     230 .. 0.95

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 4.3e-62
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE-- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyv 80 
                                    y+  + +GeG++++Vy ++ +etg++vAvK+  ++ +   +   + rEi++l  ++h+niv++++ fe+++++++v e++
  gene180|gene180|rna180|rna180   4 YKLRRVIGEGASSTVYGGI-SETGEEVAVKVAPRRGKAAGM---AYREIRMLDCVRHENIVKVIDRFESENHVCIVEELC 79 
                                    677899*************.7************99999876...7*********************************** PP

                                    TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBCTTTSC CS
                        Pkinase  81 eggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskltsfvgt 160
                                    + + l ++l+ +  ++e+ a ki++ il gl+++Hs giiHrDlK  NiL++ ++ +Ki+DFGl++ +e++s  ++f+gt
  gene180|gene180|rna180|rna180  80 DLN-LVSFLN-EYEIDENVALKILRMILCGLRHIHSIGIIHRDLKLGNILLK-ENTVKICDFGLSCYVEENS--HEFCGT 154
                                    *66.888886.689**************************************.999**************88..9***** PP

                                    GGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHH CS
                        Pkinase 161 seYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdl 240
                                     +YlAPEv++++ey++++D+Ws+G+i+y llt+k  ++           ld                    ++see++dl
  gene180|gene180|rna180|rna180 155 MDYLAPEVIDGKEYTQNIDIWSAGIIFYVLLTKKKFYE----------SLDS------------------LKCSEELRDL 206
                                    **************************************..........5666..................257******* PP

                                    HHHHT-SSGCCSTTHHHHHTSGG CS
                        Pkinase 241 lkkllkkdpkkRltaeellqhpy 263
                                    l+kll++d++kR++a+e+l h+ 
  gene180|gene180|rna180|rna180 207 LEKLLERDETKRISASEALMHRS 229
                                    *******************9975 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.2   1.3e-35   2.3e-32       2     218 ..       5     203 ..       4     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 1.3e-35
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivte 81 
                                    +l + +GeGa ++V+ g  +     + ++VavK+  ++ ++    + ++e++++  ++h+nivk++    +e++++iv e
  gene180|gene180|rna180|rna180   5 KLRRVIGEGASSTVYGGISE-----TGEEVAVKVAPRRGKAA--GMAYREIRMLDCVRHENIVKVIDRFESENHVCIVEE 77 
                                    57899************999.....999*******6655554..8999******************************** PP

                                    --TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEE CS
                    Pkinase_Tyr  82 yvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvk 161
                                    +++  +L +fL++    +++ +  l++   + +G+++++s  ++Hrdl   N+Ll+ +++vki+DfGL+  +e     ++
  gene180|gene180|rna180|rna180  78 LCDL-NLVSFLNEY---EIDENVALKILRMILCGLRHIHSIGIIHRDLKLGNILLK-ENTVKICDFGLSCYVE-----EN 147
                                    **98.8*****998...999***********************************9.789***********93.....33 PP

                                    TTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH CS
                    Pkinase_Tyr 162 keeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevlekl 218
                                    ++e    + ++apE+++ k++t++ D+Ws G++ + ++t  ++ y++l++ ++ e l
  gene180|gene180|rna180|rna180 148 SHEFCGTMDYLAPEVIDGKEYTQNIDIWSAGIIFYVLLT-KKKFYESLDSLKCSEEL 203
                                    445556799**************************9999.56667777666665555 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.7   1.9e-08   3.4e-05     308     405 ..      97     185 ..      54     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.9e-08
                 Pkinase_fungal 308 llealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlk 387
                                    +l+ lr  + g+r  +  +gi+HrD   +Nil+       e++  + D+ l + +++     +++e  GT+ ++a ev+ 
  gene180|gene180|rna180|rna180  97 ALKILRMILCGLRHIH-SIGIIHRDLKLGNILLK------ENTVKICDFGLSCYVEE-----NSHEFCGTMDYLAPEVID 164
                                    6888999999******.*****************......88999**********96.....456689************ PP

                 Pkinase_fungal 388 geeHsyrhDLES...ffyvll 405
                                    g+e +   D+ S   +fyvll
  gene180|gene180|rna180|rna180 165 GKEYTQNIDIWSagiIFYVLL 185
                                    **9999999988555799997 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.01        19       3      66 ..       8      71 ..       7      81 .. 0.85
   2 !   15.5   0.0   7.1e-06     0.013     159     198 ..     110     143 ..      89     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.01
                                   EEE--.SSCEEEEEEETT-.-EEEEEE-TT.S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEE CS
                            APH  3 relsggasnrtylvttpag.ryvlrrnppa.raaeeirrevallrlLakagvpvPevlagdtddee 66
                                   r+++ gas+ +y   +++g +++++++p + +aa  + re ++l+ ++  ++ v +v++  +++++
  gene180|gene180|rna180|rna180  8 RVIGEGASSTVYGGISETGeEVAVKVAPRRgKAAGMAYREIRMLDCVRHENI-V-KVIDRFESENH 71
                                   78999****99999999955**********9***************999988.4.77774456655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.1e-06
                                    H--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 159 llpgelptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                    + +   + +++H+Dl++gN+l++ +++    + Df+++++
  gene180|gene180|rna180|rna180 110 HIH---SIGIIHRDLKLGNILLK-ENTVK--ICDFGLSCY 143
                                    555...5799*************.77777..99**99886 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         1   1.8e+03       2      17 ..      18      33 ..      17      40 .. 0.90
   2 !   21.5   0.2   8.2e-08   0.00015      51     160 ..      40     149 ..      24     157 .. 0.82
   3 ?   -3.1   0.0       2.8   5.1e+03      99     135 ..     195     233 ..     184     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                                   EEEEEETTTEEEEEEE CS
                           RIO1  2 VyhavsedgkevaiKi 17
                                   Vy ++se+g+eva+K+
  gene180|gene180|rna180|rna180 18 VYGGISETGEEVAVKV 33
                                   999************8 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 8.2e-08
                                    HHHHHHHHHHHHHHHHHTT.--S--EEEEETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEE CS
                           RIO1  51 vklwaekEfrnLkrleeag.vpvPkpielkrhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglv 128
                                    +  +a +E+r+L ++++++ v+v +  e ++hv + e +  d + +  l+++e +e+ a ++++++l  +r +    g++
  gene180|gene180|rna180|rna180  40 AAGMAYREIRMLDCVRHENiVKVIDRFESENHVCIVEELC-DLNLVSFLNEYEiDENVALKILRMILCGLRHIH-SIGII 117
                                    566899*********9998799**********98777776.466777789999557777888888888777766.***** PP

                                    ESS-STTSEEEETTEEEE--GTTEEETTSTTH CS
                           RIO1 129 HaDLSeyNvlvdedkvviIDvsQaveldhpna 160
                                    H DL   N+l++e+ v i D++ +  +++++ 
  gene180|gene180|rna180|rna180 118 HRDLKLGNILLKENTVKICDFGLSCYVEENSH 149
                                    *********************98887766554 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.8
                                    HHCG-HHHHHHHHHHHHH..HHHHHHHTSTEEESS-STT CS
                           RIO1  99 kdveeeeeaeelyeevle..emrklykeaglvHaDLSey 135
                                    + ++ +ee+++l+e++le  e +++ +   l H  +S +
  gene180|gene180|rna180|rna180 195 DSLKCSEELRDLLEKLLErdETKRISASEALMHRSFSRF 233
                                    444546788888888888777888888888888777766 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.1   3.8e+03     109     136 ..      11      63 ..       5      86 .. 0.58
   2 !   14.3   0.1   8.2e-06     0.015     230     257 ..     118     144 ..      96     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.1
                  Haspin_kinase 109 seklssevyqtke.kdkevvlKvipl........................evl 136
                                    +e+ ss vy   + + +ev++Kv p                          v+
  gene180|gene180|rna180|rna180  11 GEGASSTVYGGISeTGEEVAVKVAPRrgkaagmayreirmldcvrhenivKVI 63 
                                    56777888876554778888888876666666666655444444444443333 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.2e-06
                  Haspin_kinase 230 HRdLhldniLvdknlnvtlidlklsRle 257
                                    HRdL+l+niL+++n +v ++d+ ls + 
  gene180|gene180|rna180|rna180 118 HRDLKLGNILLKEN-TVKICDFGLSCYV 144
                                    ***********987.7******999765 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.031     157     212 ..      71     139 ..      28     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                           FTA2 157 iraIVKel.........ellkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyi....dgkLvDls 212
                                     ++IV el         +  + +e++  ++l+ +l  l+ +h+ gI++rDlk  n++      k++D++
  gene180|gene180|rna180|rna180  71 HVCIVEELcdlnlvsflNEYEIDENVALKILRMILCGLRHIHSIGIIHRDLKLGNILlkenTVKICDFG 139
                                    46788887888888777556899*******************************998554345788887 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.5e-05     0.063     107     155 ..      85     132 ..      62     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                            Kdo 107 dllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqee 155
                                     +l++  e++e++  ++l+ +    + +h++g+ H+dl   nill+++ 
  gene180|gene180|rna180|rna180  85 SFLNE-YEIDENVALKILRMILCGLRHIHSIGIIHRDLKLGNILLKENT 132
                                    44443.4478888888999999999********************9986 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.12   2.2e+02     169     213 ..      44      86 ..      22      96 .. 0.76
   2 ?   10.4   0.3    0.0002      0.35     119     179 ..      72     139 ..      58     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.12
                           WaaY 169 kkdevriidlsgkrasaerkakdridlerhygikneirdlgyyll 213
                                       e+r++d    r  +  k  dr++ e h+ i +e+ dl   ++
  gene180|gene180|rna180|rna180  44 AYREIRMLDCV--RHENIVKVIDRFESENHVCIVEELCDLNLVSF 86 
                                    55677877764..555667999***************99987665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0002
                           WaaY 119 imiieyiegielv...dmpeiddevkakikqsi....eklhqlgmvsgdphrgnfivkkdevriidls 179
                                    + i+e +  ++lv   +  eid++v  ki + i    +++h+ g++  d + gn+++k++ v+i d+ 
  gene180|gene180|rna180|rna180  72 VCIVEELCDLNLVsflNEYEIDENVALKILRMIlcglRHIHSIGIIHRDLKLGNILLKENTVKICDFG 139
                                    5566655555554111446899999988866442222899*************************963 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7    0.0002      0.35     136     176 ..     103     143 ..      48     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                                    HHHH..CHGG-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EE CS
                 Choline_kinase 136 klle..elespvvfcHnDlqegNillnkeekklvlIDFEYagy 176
                                     +l   ++ +++   H Dl  gNill  +e+++ + DF  ++y
  gene180|gene180|rna180|rna180 103 MILCglRHIHSIGIIHRDLKLGNILL--KENTVKICDFGLSCY 143
                                    333345666779999***********..999*******99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.52
# Mc/sec: 2979.31
//
Query:       gene1802|gene1802|rna1801|rna1801  [L=633]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-28   99.2   0.0      3e-28   98.5   0.0    1.3  1  MutL_C          MutL C terminal dimerisation domain
    1.9e-05   24.3   0.0    3.9e-05   23.3   0.0    1.5  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    9.2e-05   22.9   0.0    0.00022   21.7   0.0    1.6  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    0.00013   21.8   0.0    0.00023   21.0   0.0    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> MutL_C  MutL C terminal dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   6.6e-32     3e-28       5     147 .]     461     597 ..     459     597 .. 0.93

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 6.6e-32
                                        EEEEETTTEEEEEETTE....EEEEEHHHHHHHHHHHHHHHHCCHSSB-EEEEEEEEEEE--HHHHHHHHHCHHHH CS
                             MutL_C   5 algqvhgtyilaenedg....lvlvDqhaAherilyeklkeqlkeeelksQpLliPlvlelspeeaalleehkeeL 76 
                                        ++gq+++++i+ + +++    lv vDqhaA+e  ++e +k+++     k+Q+ ++P++l+l+p e+ +++++ e++
  gene1802|gene1802|rna1801|rna1801 461 VIGQFNNGFIISKLKKNdkiyLVAVDQHAADEIRNFESIKKTFRL---KKQSVIVPVKLDLTPIEEVIVNDNLELF 533
                                        89*********99855445667889*******************9...9*************************** PP

                                        HHCT-EEEE-STTEEEEEEEECCCTTTSHHHHHHHHHHHHCCCSS-H-HCCHHHHHHHHCTTSSSSSS--- CS
                             MutL_C  77 aklGfeleefgpnslivravPallrqqnleelirelleelaekgkesleekleellatmachssvkagrrl 147
                                        +++Gf++++      +++++P++++q ++ + ++elle++++++ e   +++++++a+ ac++sv++g+ l
  gene1802|gene1802|rna1801|rna1801 534 ERNGFVIKN-----GMLETIPVYKNQVFGVKEFQELLEDMKNDEYE--FKRIRNIIASKACRTSVMIGDAL 597
                                        ********5.....8***************************9963..69*****************9976 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   8.7e-09   3.9e-05      41     116 ..     235     305 ..     224     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.7e-09
                                        EEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEEEEEESSGGEE-TSSTT----EETTHHCHHHHHHHHHHH CS
                     DNA_mis_repair  41 kqflfvNgRlvkskelkkaireaYkellpkgrypvvvLnleidpeevDvNvhPtKreVrfqdeeevieaieealke 116
                                        kq++f  +R++++k + + i++ ++  l ++  p++vL ++      DvNv  +K+eV f de+ +++++++++ +
  gene1802|gene1802|rna1801|rna1801 235 KQLMFSEKRPISNKRILNGIKNEFN--LYAEGSPTFVLVIK---GYGDVNVSTDKSEVIFGDETGILNLLRSEIGR 305
                                        7889999******************..999999*****997...667***********************999865 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   4.8e-08   0.00022       8      52 ..      24      61 ..      19     145 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4.8e-08
                                       HHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTH CS
                          HATPase_c  8 qiisnlvdNavkfatkageieveikaseddlvisveDnGiGipke 52
                                        ++++l++N+++  + ++ i+v+i+  +   +++veDnG+Gi+  
  gene1802|gene1802|rna1801|rna1801 24 IVVKELIENSID--SGCTWIRVRID--D---SVTVEDNGCGISDL 61
                                       589*********..57888888888..4...9**********973 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.1e-08   0.00023       3      47 ..      22      60 ..      19     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.1e-08
                        HATPase_c_3  3 lekAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmse 47
                                       +++++ el++Ns+d+ ++ + + +++      ++++eD+G G+s 
  gene1802|gene1802|rna1801|rna1801 22 TYIVVKELIENSIDSGCTWIRVRIDD------SVTVEDNGCGISD 60
                                       4789*********************9......69*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (633 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 4163.50
//
Query:       gene1803|gene1803|rna1802|rna1802  [L=369]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.7e-109  366.3  10.6   5.9e-109  364.5  10.6    1.7  1  TIP49            TIP49 P-loop domain
    1.6e-20   73.0   0.3    1.6e-20   73.0   0.3    2.2  2  TIP49_C          TIP49 AAA-lid domain
    7.3e-07   29.7   2.5    0.00039   20.8   0.4    2.4  2  AAA              ATPase family associated with various cellul
      9e-05   22.8   0.2       0.55   10.5   0.1    2.4  2  AAA_22           AAA domain
    0.00032   20.7   0.4       0.27   11.3   0.1    3.0  3  AAA_14           AAA domain
     0.0013   19.2   0.1      0.012   16.0   0.1    2.1  2  AAA_16           AAA ATPase domain
     0.0043   17.1   1.0       0.34   10.9   0.2    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0046   16.7   0.6       0.72    9.6   0.1    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0049   16.2   0.1       0.01   15.2   0.1    1.6  1  DnaB_C           DnaB-like helicase C terminal domain
      0.005   16.6   0.2        2.4    7.8   0.1    2.6  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.044   13.2   0.5        3.7    6.9   0.1    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.048   13.4   0.2         12    5.5   0.0    2.4  2  AAA_30           AAA domain
        0.1   12.5   0.1       0.16   11.8   0.1    1.3  1  NACHT            NACHT domain
       0.14   12.2   0.1        0.3   11.1   0.1    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.15   12.2   0.0        4.9    7.3   0.0    2.3  2  Sigma54_activ_2  Sigma-54 interaction domain
        0.2   12.0   1.2        2.3    8.6   1.2    2.4  1  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.5  10.6  5.2e-112  5.9e-109      42     350 ..       1     288 [.       1     289 [. 0.98

  Alignments for each domain:
  == domain 1  score: 364.5 bits;  conditional E-value: 5.2e-112
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-E CS
                              TIP49  42 likekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqalrksigvrikeekev 117
                                        +++++k +G+ vL++G++g+Gktalai++sk+lg   pf+++sg+e+ysle++k+e++tqalrks+g+rike+ +v
  gene1803|gene1803|rna1802|rna1802   1 MVESNK-GGKIVLIKGERGSGKTALAIGLSKSLG-GAPFNSISGTEIYSLEMSKSEAITQALRKSVGLRIKESVKV 74 
                                        566777.9**************************.89*************************************** PP

                                        EEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS- CS
                              TIP49 118 leGevveleveeaenplskekkikevkitlktakeekklklgskiaeellkekvkegDviviekesGkvkklGrse 193
                                        +eGevv+l+                 +i+lkt+++e+++++g+k+ +el+kekv++gD++ i +e+Gkv k+G+s 
  gene1803|gene1803|rna1802|rna1802  75 IEGEVVSLSG---------------RRIVLKTVDMESSFDIGEKMRNELDKEKVSTGDIVRIVRERGKVYKIGTSV 135
                                        *******954...............689************************************************ PP

                                        SS------S--------S---S----XXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49 194 arakefDiekdefvelPkGevekkkevvqevtLhdlDvanarpqdllslllqllkskkteiteklreeinkkvaky 269
                                         +++e   ++++f+++P+Ge+ + +e vqe++Lhd+Dv+n +++++l+l+    +++++ei++++r+e+nkkv+++
  gene1803|gene1803|rna1802|rna1802 136 VKKTEVVGTDTRFIPCPEGELIRIREEVQEISLHDIDVVNNKAEGYLALF----SGETGEIRAEIRDEVNKKVWNW 207
                                        ****9999******************************************....********************** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49 270 veegkaeivpGvlfiDevhmlDiecfsylnraleselaPivilatnrgiakirGtdiisphGipvDlldrlliikt 345
                                        ++egkae+v+GvlfiDevhmlDie+f++ln+a+e++++P+++++tn+  + irGtd isp+G+p+D++dr+lii++
  gene1803|gene1803|rna1802|rna1802 208 INEGKAEVVRGVLFIDEVHMLDIESFAFLNKAIEEDFCPVILISTNKKECIIRGTDEISPYGLPRDFIDRALIISM 283
                                        **************************************************************************** PP

                                        XXXXX CS
                              TIP49 346 ekytk 350
                                        eky+k
  gene1803|gene1803|rna1802|rna1802 284 EKYCK 288
                                        ***87 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       4.1   4.5e+03       2      57 ..     157     171 ..     155     176 .. 0.51
   2 !   73.0   0.3   1.5e-23   1.6e-20       1      66 []     294     358 ..     294     358 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.1
                            TIP49_C   2 lkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedv 57 
                                        ++iR +                                          +e++++d+
  gene1803|gene1803|rna1802|rna1802 157 IRIREE-----------------------------------------VQEISLHDI 171
                                        344444.........................................445555555 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 1.5e-23
                            TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFlD 66 
                                        I+++R+ eE++++d++A+d+L++i++ ++LRY+++Llt++ + a+kr++k v++ed+e+  eLFlD
  gene1803|gene1803|rna1802|rna1802 294 IISHRILEEDIHIDSKAMDKLVSISEVSGLRYSMNLLTISGLRASKRGGK-VTLEDIERTFELFLD 358
                                        9***********************************************99.**************9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.4   3.5e-07   0.00039       1     104 [.      11     119 ..      11     139 .. 0.76
   2 !    8.5   0.1    0.0022       2.5      26      70 ..     184     228 ..     168     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.5e-07
                                        EEEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEE.TGGGHHHH CS
                                AAA   1 vllyGppGtGKTllakavakelg.vefleisgsellskyvgesekkirelfkeakeka.kpsilfiD.Eidalaks 73 
                                        vl+ G  G GKT+la  + k+lg ++f +isg+e+ s  +++s + i + +++    + k s+ +i+ E+ +l ++
  gene1803|gene1803|rna1802|rna1802  11 VLIKGERGSGKTALAIGLSKSLGgAPFNSISGTEIYSLEMSKS-EAITQALRKSVGLRiKESVKVIEgEVVSLSGR 85 
                                        6899******************66************4444444.44444444432233655665554499999999 PP

                                        H...TTCCCHHHHHHHHHHHHHHHHTTTSSSTEE CS
                                AAA  74 r...sgseseeeervvnqLlteldgvkkkeskvi 104
                                        r   ++ + e++ ++ +++ +eld++k ++++++
  gene1803|gene1803|rna1802|rna1802  86 RivlKTVDMESSFDIGEKMRNELDKEKVSTGDIV 119
                                        9999899999999999999999999999855554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0022
                                        EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                                AAA  26 fleisgsellskyvgesekkirelfkeakekakpsilfiDEidal 70 
                                        +++ +  e++ ++  e +kk+ + ++e k++    +lfiDE++ l
  gene1803|gene1803|rna1802|rna1802 184 LFSGETGEIRAEIRDEVNKKVWNWINEGKAEVVRGVLFIDEVHML 228
                                        5556667888889999999999999998888744********987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00049      0.55       3      30 ..       6      33 ..       3     114 .. 0.79
   2 !   10.3   0.0   0.00057      0.64      81     130 ..     203     252 ..     160     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                             AAA_22  3 ktagilvvtGesGtGKTtllrrlleqld 30
                                       k+ +i+++ Ge G+GKT l+  l ++l 
  gene1803|gene1803|rna1802|rna1802  6 KGGKIVLIKGERGSGKTALAIGLSKSLG 33
                                       57899*************9977776665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00057
                             AAA_22  81 aleqalrarav...ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGt 130
                                        ++++ +++ ++   +++l iDE++ l   e + +L +  +  ++ +++iL+ t
  gene1803|gene1803|rna1802|rna1802 203 KVWNWINEGKAevvRGVLFIDEVHML-DIESFAFLNKAIE--EDFCPVILIST 252
                                        444555555556778***********.8888888866667..78888888766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00024      0.27       2      37 ..       8      41 ..       7      90 .. 0.71
   2 !    6.5   0.0    0.0074       8.3      54     103 ..     206     255 ..     162     267 .. 0.71
   3 ?   -1.6   0.0       2.2   2.5e+03      64      78 ..     351     365 ..     328     368 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                             AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyin 37
                                       +ki++i+G R +GKT l+  l k+l      +  i+
  gene1803|gene1803|rna1802|rna1802  8 GKIVLIKGERGSGKTALAIGLSKSLG--GAPFNSIS 41
                                       589**************988887766..33333333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0074
                             AAA_14  54 elileklkeekktylflDEiqev.pewekalkslvdegknldvivtGSnsk 103
                                        + i e   e  + +lf+DE++++  e + +l++ ++e+  + vi+   n+k
  gene1803|gene1803|rna1802|rna1802 206 NWINEGKAEVVRGVLFIDEVHMLdIESFAFLNKAIEED-FCPVILISTNKK 255
                                        33333322234668********9447899999999988.777777776665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.2
                             AAA_14  64 kktylflDEiqevpe 78 
                                        ++  lflDE+  v++
  gene1803|gene1803|rna1802|rna1802 351 RTFELFLDEARGVEN 365
                                        344489999887776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.1e-05     0.012      23      63 ..       7      47 ..       1      97 [. 0.73
   2 ?    0.9   0.0      0.47   5.3e+02     136     155 ..     217     236 ..     129     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                             AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                       ++ +vl+ Ge+G+GK++l+  l ++l ++ +  ++g+   +
  gene1803|gene1803|rna1802|rna1802  7 GGKIVLIKGERGSGKTALAIGLSKSLGGAPFNSISGTEIYS 47
                                       239***************98888888876322244444444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.47
                             AAA_16 136 plvlvlDdlqwadeaslqll 155
                                          vl++D+++ +d +s ++l
  gene1803|gene1803|rna1802|rna1802 217 RGVLFIDEVHMLDIESFAFL 236
                                        3699******9998887776 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.2   0.00031      0.34       2      34 ..      11      44 ..      10     144 .. 0.74
   2 ?    4.4   0.0     0.032        36      67      92 ..     218     243 ..     189     249 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                              AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvqltr 34
                                       vl++G+ G+gK+ la  l++ l +++++ + +t+
  gene1803|gene1803|rna1802|rna1802 11 VLIKGERGSGKTALAIGLSKSLgGAPFNSISGTE 44
                                       89********************988888777776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.032
                                        SEEEEESGGG--HHHHHHHHHHHHSS CS
                              AAA_5  67 eilvlDEveraesevlnsLlslleer 92 
                                         +l++DEv++++ e ++ L++ +ee+
  gene1803|gene1803|rna1802|rna1802 218 GVLFIDEVHMLDIESFAFLNKAIEED 243
                                        589*******************9985 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.017        20      36      67 ..      11      43 ..       4      70 .. 0.81
   2 !    9.6   0.1   0.00064      0.72      86     118 ..     218     251 ..     213     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                             RuvB_N 36 vllyGpPGlGkttlakiiakelg.vklkitsgP 67
                                       vl+ G  G Gkt+la  ++k lg + +++ sg 
  gene1803|gene1803|rna1802|rna1802 11 VLIKGERGSGKTALAIGLSKSLGgAPFNSISGT 43
                                       899*************99999972456666665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00064
                             RuvB_N  86 dvlfideihrlsraveevlysame.dfrldivig 118
                                         vlfide+h l+ +   +l +a+e df+  i+i 
  gene1803|gene1803|rna1802|rna1802 218 GVLFIDEVHMLDIESFAFLNKAIEeDFCPVILIS 251
                                        69********************963666555554 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.1e-06      0.01      17      76 ..       6      68 ..       1     118 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.1e-06
                                       XTTXEEEEEEXTTSSHHHHHHHHHHHHH.H..CSTSEEEEEESSSXHHHHHHHHHHHHHTXXH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             DnaB_C 17 qkgdliiiAarpsmGktalalniaenaa.v..keklpvavfslemsaeqlvqRllsseaeids 76
                                       + g++++i +  + Gktala+ + ++   +  ++  +  ++slems+++ +++ l +  +++ 
  gene1803|gene1803|rna1802|rna1802  6 KGGKIVLIKGERGSGKTALAIGLSKSLGgApfNSISGTEIYSLEMSKSEAITQALRKSVGLRI 68
                                       6789999*****************9965222245557*************9999988776554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0021       2.4      24      42 ..      10      28 ..       2      54 .. 0.82
   2 !    6.1   0.0    0.0072       8.1      94     119 ..     217     242 ..     209     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0021
                                       -EEEECSTTSSHHHHHHHH CS
                    Sigma54_activat 24 svlitGesGtGKellarai 42
                                        vli+Ge G+GK+ la  +
  gene1803|gene1803|rna1802|rna1802 10 IVLIKGERGSGKTALAIGL 28
                                       59***********999655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0072
                                        TSEEEEETGGGS-HHHHHHHHHHHHH CS
                    Sigma54_activat  94 gGtlfLDeigelplelQekLlrvlqe 119
                                         G+lf+De++ l++e  + L ++++e
  gene1803|gene1803|rna1802|rna1802 217 RGVLFIDEVHMLDIESFAFLNKAIEE 242
                                        79***********9998888777776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0033       3.7      21      65 ..       7      50 ..       3      67 .. 0.74
   2 ?    4.0   0.0     0.025        28     106     133 ..     216     243 ..     210     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0033
                       Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65
                                       Gg  +l+ G  GsGKt la  l++ l      +++  ++i+s+  
  gene1803|gene1803|rna1802|rna1802  7 GGKIVLIKGERGSGKTALAIGLSKSLGGAPF-NSISGTEIYSLEM 50
                                       88889**************999988876543.4555666666655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.025
                       Mg_chelatase 106 hnGvLfLDElpefkrkvlevLRePledg 133
                                         +GvLf+DE+  ++ + +  L + +e+ 
  gene1803|gene1803|rna1802|rna1802 216 VRGVLFIDEVHMLDIESFAFLNKAIEED 243
                                        58*********99999999999998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.011        13      17      42 ..       7      32 ..       3      97 .. 0.75
   2 ?    5.5   0.0     0.011        12      89     121 ..     217     249 ..     186     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.011
                             AAA_30 17 gdrvavltGpAGtGKttalkalreaw 42
                                       g ++++++G  G+GKt +  +l + +
  gene1803|gene1803|rna1802|rna1802  7 GGKIVLIKGERGSGKTALAIGLSKSL 32
                                       56799***********9877776655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                             AAA_30  89 gtllivDEagmvdtkqlaallkaaekagakvil 121
                                        + +l +DE+ m+d++++a l ka+e++   vil
  gene1803|gene1803|rna1802|rna1802 217 RGVLFIDEVHMLDIESFAFLNKAIEEDFCPVIL 249
                                        46899****************999997677776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00015      0.16       2      24 ..      10      32 ..       9      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                       CEEEEC-TTTCHHHHHHHHHHHH CS
                              NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                       +v+++Ge GsGKT+L+ +l   +
  gene1803|gene1803|rna1802|rna1802 10 IVLIKGERGSGKTALAIGLSKSL 32
                                       699************99887665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00027       0.3      19      46 ..       8      35 ..       1      48 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                       TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                               TsaE 19 gdvilLeGdLGaGKTtlvrglakalgve 46
                                       g+++l++G+ G+GKT+l+ gl k+lg +
  gene1803|gene1803|rna1802|rna1802  8 GKIVLIKGERGSGKTALAIGLSKSLGGA 35
                                       6789*******************99865 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0044       4.9      24      59 ..      11      44 ..       4      74 .. 0.76
   2 ?    2.5   0.0      0.13   1.4e+02      68     106 ..     215     252 ..     180     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0044
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH CS
                    Sigma54_activ_2 24 vfltGekGsgkelvArlLhknsgpwleifvverlak 59
                                       v+++Ge Gsgk+  A  L+k+ g+  ++f+ +++ +
  gene1803|gene1803|rna1802|rna1802 11 VLIKGERGSGKTALAIGLSKSLGG--APFNSISGTE 44
                                       9**************999999888..7777766664 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                                        TTTSEEEEEE-TT--HHHHHHHHHHHHHHTTTT-EEEEE CS
                    Sigma54_activ_2  68 akggtLylkdiadlskaeqkeLlellakaeksslrlVst 106
                                        +  g+L++ +++ l+ +  + L +++++   + + l+st
  gene1803|gene1803|rna1802|rna1802 215 VVRGVLFIDEVHMLDIESFAFLNKAIEED-FCPVILIST 252
                                        6789*********************9987.444444444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.2     0.002       2.3      96     130 ..     211     245 ..       2     251 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
                             AAA_19  96 eekklqeeellivDEfqdvdelqyrLlkallgek.k 130
                                         + ++  + +l++DE+ ++d   +++l++  +e+  
  gene1803|gene1803|rna1802|rna1802 211 GKAEV-VRGVLFIDEVHMLDIESFAFLNKAIEEDfC 245
                                        33344.4669**********8888888777655545 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.34s 00:00:01.02 Elapsed: 00:00:00.54
# Mc/sec: 2068.58
//
Query:       gene1804|gene1804|rna1803|rna1803  [L=611]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.7e-108  361.2   0.0   2.4e-108  360.7   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.6e-43  147.4   0.1    2.9e-43  146.6   0.1    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.8e-11   44.3   2.6    4.8e-11   43.0   2.6    1.8  1  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
       0.16   11.4   0.1       0.35   10.3   0.1    1.5  1  ProQ_C           ProQ C-terminal domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  360.7   0.0  5.4e-112  2.4e-108       1     213 []     235     458 ..     235     458 .. 0.98

  Alignments for each domain:
  == domain 1  score: 360.7 bits;  conditional E-value: 5.4e-112
                                        SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH.......SSGG CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxx RF
                        ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe.......gtim 69 
                                        G+r+lD+lfp+vqG++t+ipgafg+Gktvisqslsk+snsd ai+yvg+Gergne++evl+efp+       ++im
  gene1804|gene1804|rna1803|rna1803 235 GQRILDSLFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSD-AIVYVGCGERGNEMSEVLMEFPKltvggkdDSIM 309
                                        9****************************************.***********************999865444** PP

                                        GGEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab  70 krtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgakl 145
                                        krtvlvantsn+pvaareasiytgit++Ey+rdqg+nv+++ads+srwaeAlreis+rl empad+gypaylgakl
  gene1804|gene1804|rna1803|rna1803 310 KRTVLVANTSNMPVAAREASIYTGITISEYLRDQGMNVSMMADSTSRWAEALREISGRLAEMPADSGYPAYLGAKL 385
                                        **************************************************************************** PP

                                        HHHHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                        xxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        ATP-synt_ab 146 aslyERagka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                        a +yERag++     p+rtGsvtiv avsp+ggDfsdpvt+ tlgi+++f++LdkklaqrkhfP+in+  S+S
  gene1804|gene1804|rna1803|rna1803 386 AFFYERAGSVvclgsPKRTGSVTIVGAVSPPGGDFSDPVTSSTLGIVQVFWGLDKKLAQRKHFPSINWNLSYS 458
                                        ************************************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.6   0.1   6.4e-47   2.9e-43       1     120 [.     106     225 ..     106     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.6 bits;  conditional E-value: 6.4e-47
                                        EETTS-BHHHHHHHHTS.BE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEE CS
                    ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgs.fierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkv 75 
                                        yDGiqrpL++i+e +g  fi++Gv++pal+re+++ef+pkv+ gd v ggdi+G+v e++lie ki+vppk +gkv
  gene1804|gene1804|rna1803|rna1803 106 YDGIQRPLKEIREGTGGiFIPKGVNIPALNREREYEFVPKVRIGDYVVGGDIFGSVYENSLIETKILVPPKESGKV 181
                                        9**************999********************************************************** PP

                                        EEE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEE CS
                    ATP-synt_ab_Xtn  76 keiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkek 120
                                        + ia++g+yt++d+++e+et++g + e+ ++++wPvr prp++ek
  gene1804|gene1804|rna1803|rna1803 182 VFIARQGNYTLKDVVMELETSKG-KMEMFMYHTWPVRVPRPIEEK 225
                                        *******************9996.9******************99 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   2.6   1.1e-14   4.8e-11       1      69 []      28      90 ..      28      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.1e-14
                                       EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                      ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                       +++v+Gpvv   ++ig  +++y++++v+     ++l g+++ ++ d++ ++v+++t Gl +G+ ++rTG
  gene1804|gene1804|rna1803|rna1803 28 VYSVSGPVVVGCDMIG--CAMYELVKVG--S--EGLAGEIIKIDKDRATIQVYEDTNGLCVGDVIVRTG 90
                                       689*************..**********..7..9**********************************9 PP

>> ProQ_C  ProQ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   7.7e-05      0.35      13      36 ..      50      73 ..      49      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.7e-05
                                       --SSSS---EEEEEE-SSSEEEEE CS
                             ProQ_C 13 VklGkspmpAtileiaKddVrVqL 36
                                       Vk+G+  +++ i+ i+Kd +++q+
  gene1804|gene1804|rna1803|rna1803 50 VKVGSEGLAGEIIKIDKDRATIQV 73
                                       9*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 3526.86
//
Query:       gene1805|gene1805|rna1804|rna1804  [L=320]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-60  202.5   0.0    8.4e-60  202.4   0.0    1.0  1  Pkinase         Protein kinase domain
      7e-27   94.3   0.1    1.1e-26   93.7   0.1    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
     0.0035   16.7   0.0     0.0048   16.3   0.0    1.3  1  Kinase-like     Kinase-like
     0.0037   16.3   0.1      0.006   15.6   0.1    1.5  1  Haspin_kinase   Haspin like kinase domain
  ------ inclusion threshold ------
      0.011   15.4   0.1      0.018   14.7   0.1    1.4  1  RIO1            RIO1 family
      0.027   14.4   0.0       0.13   12.2   0.0    1.8  2  APH             Phosphotransferase enzyme family
       0.03   13.7   0.1      0.042   13.2   0.1    1.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.054   12.3   1.2       0.23   10.2   0.1    2.2  3  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.4   0.0   3.7e-63   8.4e-60       1     264 []      15     296 ..      15     296 .. 0.92

  Alignments for each domain:
  == domain 1  score: 202.4 bits;  conditional E-value: 3.7e-63
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH..HHHHHHHHHHHHHSCTTB--EEEEEEE..SSE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke..kkvlrEikilkklkhpnivrlyevfee..kde 72 
                                        yekl ++ +GsfG+Vyk+++++++k +A+K+++ +   +++     ++rE+ ilk+ + +n++++ ev+e    ++
  gene1805|gene1805|rna1804|rna1804  15 YEKLCRISSGSFGNVYKVRRTADSKVFALKRMNPSMCYDTNGfsILYIREVMILKHARNKNVMKIEEVVEGneIND 90 
                                        67778899***************************988877777899**********************9744579 PP

                                        EEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEES CS
                            Pkinase  73 lylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakel 148
                                        +++v+e+++ + l+++++r + ++ + ++++ +qil+gl++lH  g+iHrDlKp+NiL+ ++g++Ki+DFGla+ +
  gene1805|gene1805|rna1804|rna1804  91 FFIVMECCDID-LKSVIHRVREMDVRLIRFFRWQILQGLKFLHGIGVIHRDLKPSNILLMRNGDVKIADFGLARVM 165
                                        99*******88.******9999****************************************************** PP

                                        SSSCSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT.. CS
                            Pkinase 149 essskltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg.. 221
                                        es+  +t+ v+t +Y+A Evl ++++y +++D+Ws+G+i+ e+l g+p+++   g+     e+dql +i+k+lg  
  gene1805|gene1805|rna1804|rna1804 166 EST--MTNLVVTLWYRAIEVLlGSESYNESIDMWSVGCIVGEMLKGEPILP---GEG----EIDQLGRIFKLLGyp 232
                                        *95..7***************999***************************...555....899*99******987 PP

                                        ....SHH...HHHTTS.................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                            Pkinase 222 ....etkeklpeasei.................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                               ++lp+ ++i                 ++e+  + ++ll+ dp++R++a+++l+++++
  gene1805|gene1805|rna1804|rna1804 233 edsdFDGFDLPHFKNIkkpksfstsfekefgsyDSEVVAFTRNLLSFDPRRRYSASQALSSRFM 296
                                        7665334566666666999999*************************************99886 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.1   4.9e-30   1.1e-26       6     203 ..      20     210 ..      15     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 4.9e-30
                                        EEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH...HHHHHHHHHHHHTS-BTTB--EEEEEE..SSSSE CS
                        Pkinase_Tyr   6 klGeGafGkVvegtlkgekekkevkVavKtlkeeateee...keelleeakimkklkhpnivkllgvct..keepl 76 
                                        ++ +G+fG+V++ + +     ++   a+K ++ ++  ++   +   ++e+ i+k+ +++n++k+  v+   + +  
  gene1805|gene1805|rna1804|rna1804  20 RISSGSFGNVYKVRRT----ADSKVFALKRMNPSMCYDTngfSILYIREVMILKHARNKNVMKIEEVVEgnEINDF 91 
                                        689*********9999....6667789****87665554234566789*********************6445569 PP

                                        EEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEE CS
                        Pkinase_Tyr  77 livteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLard 152
                                        +iv+e ++  dL++ +++   ++++++ +  f +q+ +G+++L+   ++Hrdl   N+Ll +n  vki+DfGLar 
  gene1805|gene1805|rna1804|rna1804  92 FIVMECCDI-DLKSVIHRV--REMDVRLIRFFRWQILQGLKFLHGIGVIHRDLKPSNILLMRNGDVKIADFGLARV 164
                                        999*98886.9*******8..889999899999******************************************9 PP

                                        TTTSSEEEETTSSTSGGGGS-HHHHHHSE.EEHHHHHHHHHHHHHHHHTTSS CS
                        Pkinase_Tyr 153 iekddeyvkkeeaklpvkWmapEslkekk.ftsksDvWsfGvllwEiftlge 203
                                        +      ++ ++  + + + a+E+l  ++ ++++ D+Ws G ++ E+++ ge
  gene1805|gene1805|rna1804|rna1804 165 M-----ESTMTNLVVTLWYRAIEVLLGSEsYNESIDMWSVGCIVGEMLK-GE 210
                                        9.....55567788888889****98776599999***********997.54 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-06    0.0048     111     192 ..      89     162 ..      60     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                        Kinase-like 111 vnallllpaasvdleilnkvlqkrsethkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekgglmlg 186
                                         + ++++    +dl   ++v++ + e + +l    r ++ lq +     L+  g++h ++++ n+ll+++g +++ 
  gene1805|gene1805|rna1804|rna1804  89 NDFFIVMECCDIDL---KSVIHRVREMDVRLIRFFRWQI-LQGL---KFLHGIGVIHRDLKPSNILLMRNGDVKIA 157
                                        35666677777775...4667777777888888888888.6554...569999*********************** PP

                        Kinase-like 187 gftaLv 192
                                        +f+ L 
  gene1805|gene1805|rna1804|rna1804 158 DFG-LA 162
                                        *97.44 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.7e-06     0.006     228     259 ..     136     167 ..       9     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-06
                      Haspin_kinase 228 FEHRdLhldniLvdknlnvtlidlklsRless 259
                                          HRdL+  niL+ +n+ v + d+ l+R+ +s
  gene1805|gene1805|rna1804|rna1804 136 VIHRDLKPSNILLMRNGDVKIADFGLARVMES 167
                                        55**************************9833 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     8e-06     0.018      56     150 ..      62     160 ..      16     172 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8e-06
                                        HHHHHHHHHHHHTT.--S--EE...EEETTEEEEE--E.ETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTST CS
                               RIO1  56 ekEfrnLkrleeag.vpvPkpi...elkrhvlvmefig.edgvaapklkdveeeeeaeelyeevleemrklykeag 126
                                         +E+ +Lk +++++ +++ +++   e+++  +vme ++ + +  + ++++++  + ++   +++l+ + k+++  g
  gene1805|gene1805|rna1804|rna1804  62 IREVMILKHARNKNvMKIEEVVegnEINDFFIVMECCDiDLKSVIHRVREMD-VRLIRFFRWQILQGL-KFLHGIG 135
                                        5677777777776634444444111688899*******66677778888888.667777888999865.5666*** PP

                                        EEESS-STTSEEEETT.EEEE--GT CS
                               RIO1 127 lvHaDLSeyNvlvded.kvviIDvs 150
                                        ++H DL   N+l+ ++ +v i D++
  gene1805|gene1805|rna1804|rna1804 136 VIHRDLKPSNILLMRNgDVKIADFG 160
                                        ************9999899999986 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.44   9.8e+02      13      78 ..      29      99 ..      18     121 .. 0.69
   2 ?   12.2   0.0   5.6e-05      0.13     167     199 ..     135     165 ..     110     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.44
                                       EEEEEETT..--EEEEEE-TT..S-HHHHH....HHHHHHHHHHHTT-.B--B-CTTBS-EEETTEEEEEEE--- CS
                                APH 13 tylvttpa..gryvlrrnppa..raaeeir....revallrlLakagv.pvPevlagdtddeeigllfalieyvp 78
                                       +y+v  +a  + ++l+r +p+  +  + ++    rev +l++ ++ +v ++ ev+     ++ei   f ++e ++
  gene1805|gene1805|rna1804|rna1804 29 VYKVRRTAdsKVFALKRMNPSmcYDTNGFSilyiREVMILKHARNKNVmKIEEVVE----GNEINDFFIVMECCD 99
                                       66666555336899999999987666666667778888888888887777766666....355555666666655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5.6e-05
                                        EEE-SS-SGGGEEEC..TTEEEEE---TT-EEE CS
                                APH 167 vllHgDlhpgNllvdpddgrvtGviDfedaglg 199
                                        +++H+Dl+p N+l+  +++    + Df++a+++
  gene1805|gene1805|rna1804|rna1804 135 GVIHRDLKPSNILLMRNGDVK--IADFGLARVM 165
                                        689************555555..9*****9987 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.9e-05     0.042     103     155 ..     100     152 ..      62     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                                Kdo 103 qdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqee 155
                                        +dL+ ++ + +e++++l r    ++ +  + lh +gv H+dl + nill  ++
  gene1805|gene1805|rna1804|rna1804 100 IDLKSVIHRVREMDVRLIRFFRWQILQGLKFLHGIGVIHRDLKPSNILLMRNG 152
                                        688888888888999999999999999999*******************9887 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.1   2.3e+02     186     212 ..      63      89 ..      61     112 .. 0.87
   2 ?   10.2   0.1    0.0001      0.23     316     389 ..     125     187 ..     110     199 .. 0.82
   3 ?   -3.0   0.0       1.1   2.4e+03      19      70 ..     244     294 ..     242     297 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                     Pkinase_fungal 186 sEaelLkkaeergvegvarlvahedve 212
                                        +E+ +Lk+a++++v  +  +v  ++++
  gene1805|gene1805|rna1804|rna1804  63 REVMILKHARNKNVMKIEEVVEGNEIN 89 
                                        6999**************999988876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0001
                     Pkinase_fungal 316 IkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkge 389
                                        ++g++ L+  +g++HrD    Nil++     ++    ++D+ la  ++         + + Tl + aievl g+
  gene1805|gene1805|rna1804|rna1804 125 LQGLKFLH-GIGVIHRDLKPSNILLM-----RNGDVKIADFGLARVMES-----TMTNLVVTLWYRAIEVLLGS 187
                                        57889999.9****************.....677788999999999984.....33457889999999999864 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.1
                     Pkinase_fungal  19 dwedvlvvgelkkkseeeklkkallqLaryarevfaaqptRrFvigftlcgs 70 
                                        ++++++ +  +  + e+ +  +   +++   r+ ++ +p+Rr+    +l + 
  gene1805|gene1805|rna1804|rna1804 244 HFKNIKKPKSFSTSFEK-EFGSYDSEVVAFTRNLLSFDPRRRYSASQALSSR 294
                                        56666666666666665.5555556778888899999999999877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2145.94
//
Query:       gene1806|gene1806|rna1805|rna1805  [L=428]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2902.94
//
Query:       gene1807|gene1807|rna1806|rna1806  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-10   38.4   0.0    1.5e-08   34.2   0.0    2.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.5e-07   29.5   0.0    1.3e-06   28.6   0.0    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      2e-05   23.5   0.0    3.6e-05   22.6   0.0    1.4  1  HI0933_like     HI0933-like protein
    0.00026   20.7   0.1    0.00071   19.3   0.0    1.7  2  DAO             FAD dependent oxidoreductase
    0.00037   19.8   0.0     0.0042   16.4   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00099   18.4   0.0     0.0014   18.0   0.0    1.2  1  FAD_binding_3   FAD binding domain
     0.0011   17.5   0.0      0.077   11.4   0.0    2.1  2  FMO-like        Flavin-binding monooxygenase-like
     0.0015   18.6   0.0     0.0044   17.0   0.0    1.7  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0017   17.8   0.0     0.0023   17.4   0.0    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0022   18.5   0.0       0.21   12.1   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0028   16.8   0.0      0.005   16.0   0.0    1.4  1  FAD_binding_2   FAD binding domain
      0.008   16.6   0.0       0.75   10.3   0.0    2.3  2  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.094   11.8   0.0       0.21   10.7   0.0    1.5  2  GIDA            Glucose inhibited division protein A
       0.17   10.7   0.0       0.24   10.2   0.0    1.1  1  Trp_halogenase  Tryptophan halogenase
       0.21   11.7   0.0         11    6.0   0.0    2.9  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
       0.22   10.5   0.0        0.3   10.1   0.0    1.2  1  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   1.4e-11   1.5e-08       2     161 ..       2     143 ..       1     191 [. 0.65

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.4e-11
                                        SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvk 77 
                                        +v++iGgGpAGl +a  l   +++vtl e ++  + +g l+ + ll  ++    +s+        + + ++   ++
  gene1807|gene1807|rna1806|rna1806   2 KVCIIGGGPAGLYTAASLVPRNIDVTLHE-KE--PEVGGLYRYSLLPPSRMSP-FSK--------LFKCKN---FS 62 
                                        8***************************4.44..3333444333333333332.222........222333...55 PP

                                        EEESCEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-S CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                        Pyr_redox_2  78 idpgkkkvklekkkegdeekiaydklvlAtGs.sprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgG 151
                                        +  ++ +v +e ++   + + ++d+ v+AtGs  +r+l ipG  e+++ ++++ +s  + +      ++++++G G
  gene1807|gene1807|rna1806|rna1806  63 LKLNS-EVDIERLR---GMEKEFDAFVIATGSpGSRRLSIPGR-EYCINGLDIARSWGGEQPGYSIgNKVLIIGMG 133
                                        54444.55554444...33458*********9899999*****.***999666666666555544389******** PP

                                        HHHHHHHHHH CS
                                        xxxxxxxxxx RF
                        Pyr_redox_2 152 yiGvElAaal 161
                                         +++++  +l
  gene1807|gene1807|rna1806|rna1806 134 DVSMDIVRFL 143
                                        **99987776 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.1e-09   1.3e-06       1      33 [.       5      37 ..       5      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.1e-09
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                      NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                       I+G+G +Gl++A+ L  +++dv+l ek + +GG
  gene1807|gene1807|rna1806|rna1806  5 IIGGGPAGLYTAASLVPRNIDVTLHEKEPEVGG 37
                                       9*******************************9 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.2e-08   3.6e-05       2      36 ..       2      36 ..       1      41 [. 0.95

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.2e-08
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                        HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                       +v +iGgG+AGl++A+s+  r+ +V+l ek++++g
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNIDVTLHEKEPEVG 36
                                       799****************************9987 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.3e-07   0.00071       1      33 [.       2      36 ..       2      39 .. 0.93
   2 ?   -1.9   0.0       1.7   1.9e+03     193     202 ..      81      90 ..      63     141 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.3e-07
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                                DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                       +v+iiGGG +Gl tA  L  r+  Vtl ek++++g
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNidVTLHEKEPEVG 36
                                       59*****************88889*******9988 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                                        EEEEEE--GG CS
                                DAO 193 adavVnaaGa 202
                                        +da V+a+G 
  gene1807|gene1807|rna1806|rna1806  81 FDAFVIATGS 90 
                                        4566666652 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.8e-06    0.0042       2      57 ..       5      63 ..       4      80 .. 0.87
   2 ?    1.1   0.0      0.17   1.9e+02     129     179 ..      85     139 ..      78     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-06
                        Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgnignsiyry....pkemtfispsftseklei 57
                                       IiG+GPaGl +a  l   ++ d++  Ek+  +  +yry    p +m  +s+ f+ +++++
  gene1807|gene1807|rna1806|rna1806  5 IIGGGPAGLYTAASLVPRNI-DVTLHEKEPEVGGLYRYsllpPSRMSPFSKLFKCKNFSL 63
                                       9*******************.89******99999***97777788888888888887766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.17
                        Pyr_redox_3 129 iiAtGefdkPnklnipGeeklvkhyskv......kefhkyagqkvvViGgknSavDa 179
                                        +iAtG     ++l+ipG e +++    +      +++    g+kv++iG ++ ++D+
  gene1807|gene1807|rna1806|rna1806  85 VIATGS-PGSRRLSIPGRE-YCINGLDIarswggEQPGYSIGNKVLIIGMGDVSMDI 139
                                        678887.555667888887.6765444422222233433449999****99999996 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-06    0.0014       3      33 ..       2      32 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-06
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                      FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       +V+I+G+GpaGl +a  L  + ++v+l ek 
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNIDVTLHEKE 32
                                       7*****************9999999998886 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   6.9e-05     0.077       3      43 ..       2      42 ..       1      51 [. 0.96
   2 ?    4.2   0.0     0.011        12     169     199 ..     110     140 ..      50     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.9e-05
                           FMO-like  3 kvaviGaGvsGlasikccleegleptcfersddiGGlwrfk 43
                                       kv +iG+G +Gl +  + +  +++ t  e+  ++GGl+r++
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNIDVTLHEKEPEVGGLYRYS 42
                                       89*************************************96 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.011
                           FMO-like 169 yfhsrdykepevfkgkrvlviGlGnsggdia 199
                                        +  s    +p    g +vl+iG+G+ + di 
  gene1807|gene1807|rna1806|rna1806 110 IARSWGGEQPGYSIGNKVLIIGMGDVSMDIV 140
                                        44555567899999**************996 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.9e-06    0.0044       1      44 [.       4      41 ..       4      50 .. 0.89
   2 ?   -2.0   0.0       2.8   3.1e+03     140     155 ..      75      90 ..      66      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.9e-06
                      NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrt 44
                                       +i+G+Gp+Gl++++ L+ r     ++++tl ++++   g+ +r 
  gene1807|gene1807|rna1806|rna1806  4 CIIGGGPAGLYTAASLVPR-----NIDVTLHEKEPEV-GGLYRY 41
                                       59***************99.....5********9998.899986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.8
                      NAD_binding_9 140 dgaslaadaVvLAlGh 155
                                        +g + ++da v+A+G 
  gene1807|gene1807|rna1806|rna1806  75 RGMEKEFDAFVIATGS 90 
                                        5667899*******96 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.1e-06    0.0023       2      46 ..       3      47 ..       2      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                       FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatd 46
                                       v+++GGgpaG+  A +   +   v L e+++ +GGl    l+++ 
  gene1807|gene1807|rna1806|rna1806  3 VCIIGGGPAGLYTAASLVPRNIDVTLHEKEPEVGGLYRYSLLPPS 47
                                       99*********************************9988887665 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00019      0.21       1      35 [.       2      36 ..       2      80 .. 0.79
   2 ?    3.9   0.1     0.071        80       1      19 [.     126     155 ..     126     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                          Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                       kv ++GgG  gl  A+ l   + +Vt+ e ++++ 
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNIDVTLHEKEPEVG 36
                                       689****************************9997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.071
                                        EEEEECSSHHHHHHHHHH...........H CS
                          Pyr_redox   1 kvvvvGgGyiglElAgal...........a 19 
                                        kv+++G G++ ++   +l           +
  gene1807|gene1807|rna1806|rna1806 126 KVLIIGMGDVSMDIVRFLfgwsgaqfkfpK 155
                                        799********9998888555555555550 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.4e-06     0.005       2      37 ..       3      38 ..       2      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                      FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                       v +iG+G AGL  A+++  ++ +v++ eke+e+gg 
  gene1807|gene1807|rna1806|rna1806  3 VCIIGGGPAGLYTAASLVPRNIDVTLHEKEPEVGGL 38
                                       77******************************9985 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00067      0.75       9      45 ..       2      36 ..       1      96 [. 0.69
   2 ?    4.2   0.0     0.051        57       7      26 ..     124     143 ..     123     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00067
                      NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele 45
                                       kv+++GgG+ ++  + +l++ + +vt+  +e  +e+ 
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNIDVTLHEKE--PEVG 36
                                       79************************98887..3443 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.051
                      NAD_binding_7   7 gkkvlvvGgGevAarkvrkl 26 
                                        g kvl++G G+v +  vr l
  gene1807|gene1807|rna1806|rna1806 124 GNKVLIIGMGDVSMDIVRFL 143
                                        579*********98766655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018      0.21       1      30 [.       2      31 ..       2      45 .. 0.87
   2 ?   -3.2   0.0         3   3.4e+03     140     150 ..      80      90 ..      67     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                               GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                       +v +iGgG AG+  A+ +  ++++v+L+ +
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNIDVTLHEK 31
                                       699************************943 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                                        EECEEEE--TT CS
                               GIDA 140 kakavviatGt 150
                                        + +a+viatG+
  gene1807|gene1807|rna1806|rna1806  80 EFDAFVIATGS 90 
                                        456999***98 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00021      0.24       1      34 [.       2      32 ..       2      37 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                     Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                       k+ i+GGG+aG  +Aa l       ++vtl e+e
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRN---IDVTLHEKE 32
                                       799********77777665544...688887765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.33   3.7e+02      14      37 ..       2      25 ..       1      34 [. 0.79
   2 ?   -0.1   0.0      0.78   8.7e+02      63      86 ..      68      91 ..      56      94 .. 0.76
   3 ?    6.0   0.0      0.01        11      12      51 ..     124     163 ..     118     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.33
                                       EEEEES-SHHHHHHHHHHHCCT-C CS
                       Shikimate_DH 14 kvlliGaGemaelvakhLlakgvk 37
                                       kv++iG G  +  +a  L+ ++++
  gene1807|gene1807|rna1806|rna1806  2 KVCIIGGGPAGLYTAASLVPRNID 25
                                       789999999999999888877765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.78
                                       EEEGCGHHHHHHT-SEEEE-SSSS CS
                       Shikimate_DH 63 alkleelkellaeadvvisatase 86
                                        +++e l+ + +e+d  ++at+s+
  gene1807|gene1807|rna1806|rna1806 68 EVDIERLRGMEKEFDAFVIATGSP 91
                                       467788888889*********997 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.01
                                        T-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHH CS
                       Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerake 51 
                                        ++kvl+iG G ++  +++ L   +  +      tler+k+
  gene1807|gene1807|rna1806|rna1806 124 GNKVLIIGMGDVSMDIVRFLFGWSGAQFKFPKNTLERVKK 163
                                        589***************9987655556555556666555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00027       0.3       2      34 ..       3      33 ..       2      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                      Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                       v +iG+GpAgl  Aa l     ++ v+l e  p
  gene1807|gene1807|rna1806|rna1806  3 VCIIGGGPAGLYTAASL--VPRNIDVTLHEKEP 33
                                       78***************..66667777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1801.28
//
Query:       gene1808|gene1808|rna1807|rna1807  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-20   72.6   0.0    3.3e-20   72.3   0.0    1.1  1  TRAPP     Transport protein particle (TRAPP) component


Domain annotation for each model (and alignments):
>> TRAPP  Transport protein particle (TRAPP) component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   1.8e-24   3.3e-20       1     145 [.       1     143 [.       1     144 [. 0.89

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1.8e-24
                              TRAPP   1 fafllgelvsylqrdskdveevekrLekmGyrvGlrllelllarerpretdilevlkfickdlWkllfgkqidnlk 76 
                                        +++l+  +v+yl+++    +eve+ L+++Gy+vG++lle  ++    re  i ++l  i+ d+ +l  +      k
  gene1808|gene1808|rna1807|rna1807   1 MSYLVCGMVEYLMEQR---KEVEADLKAIGYEVGVKLLEICNFE---REVHIPTLLYRITFDFLSLASDSDKRIEK 70 
                                        6899********9865...5789****************66665...58999999999*99*99988776666665 PP

                              TRAPP  77 tn.hrgeyvltdnefpltrfvelpke...lsylaflcGiirGaLenlgfpakVtahelpsdelrgrttfeikv 145
                                         +  +++y ltd++ ++++f ++p+e    s ++++cG+i++aL + g++++V a   ps+++++r +f+ik+
  gene1808|gene1808|rna1807|rna1807  71 AKdIDKTYLLTDTDGIFSKFMSVPNEwdgFSADSIVCGMIQAALMASGYNSEVVAYPKPSESFPNRIIFQIKI 143
                                        5556777******99*********9998888************************99999***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 972.96
//
Query:       gene1809|gene1809|rna1808|rna1808  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-32  112.2   0.1    1.9e-32  111.4   0.1    1.4  1  Forkhead  Forkhead domain


Domain annotation for each model (and alignments):
>> Forkhead  Forkhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.4   0.1   1.1e-36   1.9e-32       1      82 [.     111     192 ..     111     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 1.1e-36
                                        ------HHHHHHHHHHT-TTT-B-HHHHHHHHHCC-HHHHCC.-CCHHHHHHHHHHHHC--EEETT.-T.TSS--E CS
                           Forkhead   1 skPpysYaaLIaqAiksspekkltLseIyefieenfpyyrtaakkgWqnSirhnLslnkcFekvpreee.egkgsl 75 
                                        skP++sYa++I++Ai++s+ +kltLseIy++ie+ f+yyr+ a+  W+nSirhnLslnkcF+kvpr+   +gkg  
  gene1809|gene1809|rna1808|rna1808 111 SKPSLSYAQIITRAIRTSKVGKLTLSEIYKWIEDSFEYYRY-ANPVWKNSIRHNLSLNKCFKKVPRDPGtRGKGGR 185
                                        69***************************************.59*********************9665369**** PP

                                        EE--TTH CS
                           Forkhead  76 wtidpes 82 
                                        w++d + 
  gene1809|gene1809|rna1808|rna1808 186 WMLDYDF 192
                                        ***9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1718.70
//
Query:       gene1810|gene1810|rna1809|rna1809  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-16   61.6   0.0      2e-16   60.8   0.0    1.4  1  ABC_tran  ABC transporter
     0.0078   16.1   0.1       0.33   10.7   0.0    2.4  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.036   14.3   0.0    1.5  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
       0.02   14.3   0.2       0.16   11.4   0.2    2.1  1  SMC_N     RecF/RecN/SMC N terminal domain
       0.46   10.9   4.8        2.5    8.6   4.8    2.1  1  AAA_23    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   5.5e-20     2e-16       2     137 .]      31     184 ..      30     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 5.5e-20
                                        EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTS CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpel 74 
                                        k+++ +++ g+++a++G +G+ K+t ++++ag       t+Geil+d+++ ++     ++k + +  q+    +el
  gene1810|gene1810|rna1809|rna1809  31 KDLDANFESGKLYAFMGTSGSSKTTTMEAIAGVIPFgslTSGEILMDNNERSD---DTWEKMSTYERQKGYTIDEL 103
                                        789999**************************9876888********888877...67778888888888888888 PP

                                        BHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHH......TSSEEEE CS
                                        xxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx......xxxxxxx RF
                           ABC_tran  75 tvren...........esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallk......kpkllll 132
                                        tv e            es+++ie+a++++  + l   +v+s+  ++LSgG+++rv +a +++k      k k++ll
  gene1810|gene1810|rna1809|rna1809 104 TVDEFvyystvfslpnESKKNIEEAMDEVLGNLLGLGHVRSNRmEKLSGGERKRVGIAISFMKmlllegKLKVVLL 179
                                        88888888889999*98888888888776554444444444434**************99886444444889**** PP

                                        ESTTT CS
                                        xxxxx RF
                           ABC_tran 133 DEpta 137
                                        DEpt+
  gene1810|gene1810|rna1809|rna1809 180 DEPTS 184
                                        ***96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.023        83       4      35 ..      45      80 ..      42     112 .. 0.72
   2 !   10.7   0.0   9.2e-05      0.33     251     299 ..     168     216 ..     140     217 .. 0.76
   3 ?   -4.1   0.0       2.9     1e+04     226     243 ..     259     276 ..     250     280 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.023
                             AAA_21  4 liGpNgsGKSnLLdaldllarl....drdvegltde 35
                                       + G  gs K++ ++a+ ++  +     +++ ++++e
  gene1810|gene1810|rna1809|rna1809 45 FMGTSGSSKTTTMEAIAGVIPFgsltSGEILMDNNE 80
                                       66889***********99976666653333333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 9.2e-05
                             AAA_21 251 llralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                        ll    k +++l+DEp + L+  l  +++++  ++++rng+ vilt H+p
  gene1810|gene1810|rna1809|rna1809 168 LLLEG-KLKVVLLDEPTSELDSGLAVKVVRFArDYARRNGSIVILTVHQP 216
                                        33333.339***********************555555888889999988 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2.9
                             AAA_21 226 ngdgqelparelSdGtkr 243
                                        +g + e+ ++ + +Gtk+
  gene1810|gene1810|rna1809|rna1809 259 PGTDTEFIFSLFTSGTKE 276
                                        466777777788888876 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.036      27      87 ..     144     197 ..     127     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                            SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                        s+++++lSGGe+     + +a ++  ++      e +l++v+LDE  s+lD+  + +++++
  gene1810|gene1810|rna1809|rna1809 144 SNRMEKLSGGER---KRVGIAISFMKMLLL----EGKLKVVLLDEPTSELDSGLAVKVVRF 197
                                        78999*******...677788889999999....469**************9877777766 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   4.4e-05      0.16     131     195 ..     144     210 ..      22     231 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                                        T-STTCS-HHHHHHHHHHHHHH..HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 131 giskelLSgGektLvalaLlfA..iqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195
                                           +e LSgGe++ v +a+ f   +    +  ++llDe  ++LD     kv+++ +    +   ivi
  gene1810|gene1810|rna1809|rna1809 144 SNRMEKLSGGERKRVGIAISFMkmLLLEGKLKVVLLDEPTSELDSGLAVKVVRFARDYARRNGSIVI 210
                                        223559************9998766667788899**********99999988888865544444433 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.8    0.0007       2.5      10      68 ..      29      86 ..      24     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0007
                             AAA_23 10 f.rdqeidF.skgltlItGpNGaGKTTildAiklaL.ygetprlsrksgrgfeksdveiese 68
                                       + +d + +F s +l+++ G  G+ KTT ++Ai  +  +g  +  s+  +  + +++ +  ++
  gene1810|gene1810|rna1809|rna1809 29 LiKDLDANFeSGKLYAFMGTSGSSKTTTMEAIAGVIpFGSLT--SG--EILMDNNERSDDTW 86
                                       4578888996669*******************9887788532..22..34444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1803.46
//
Query:       gene181|gene181|rna181|rna181  [L=600]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3966.75
//
Query:       gene1811|gene1811|rna1810|rna1810  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-24   85.2   0.0      5e-24   84.9   0.0    1.1  1  IF4E      Eukaryotic initiation factor 4E


Domain annotation for each model (and alignments):
>> IF4E  Eukaryotic initiation factor 4E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   2.8e-28     5e-24      16     152 ..      22     155 ..       6     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 2.8e-28
                                        --SS-SGGG-EEEEEEEEHHHHHHHHHHS--GGGB-SSEEEEEEETT--SSTTSHHHHS-EEEEEEE-----HHHH CS
                               IF4E  16 sksenyeeslkkvatfstveeFwslynnlkkpsklkvksdyhlFkkgikPmWEdpankkGGkwvirlkkkekldrl 91 
                                         ++++ye++lk+++t ++ e++  l+++lk+ +k+ ++  +++Fk+gi+P+WEd++n +G  w+++lkk e+++r+
  gene1811|gene1811|rna1810|rna1810  22 VSKDTYEKDLKSICTLESQEHLAYLLHHLKEFDKIDKQFYINVFKEGISPVWEDKNNMNGCDWSLMLKK-EVCQRY 96 
                                        67889***************************************************************9.99**** PP

                                        HHHHHHHHHTT-SS--.-SEEEEEEEE-SSEEEEEEEES-TT-HHHHHHHHHHHHHT---- CS
                               IF4E  92 WeelllaligeqleeeedeicGvvvsvRkkedrisiWtrdasdeekvekigeklkevlelp 152
                                        +e+ll++l + ++++   e +G+v   +++  ++siW r    +    +i  +lk++l+++
  gene1811|gene1811|rna1810|rna1810  97 FERLLISLCSGYFKTF--EPTGIVGIHKDNRFKLSIWSRGLPPTTDCGEIISELKAALQID 155
                                        *************877..889999999*************988899999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1125.02
//
Query:       gene1812|gene1812|rna1811|rna1811  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.015   15.5   0.4      0.026   14.7   0.4    1.4  1  NusB        NusB family
      0.021   15.1   0.2      0.023   15.0   0.2    1.2  1  dsDNA_bind  Double-stranded DNA-binding domain


Domain annotation for each model (and alignments):
>> NusB  NusB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4     3e-06     0.026      64     126 ..       5      71 ..       1      71 [. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-06
                                        HHHHHHTTTT-......-GGGS-HHHHHHHHHHHHHHTTS-SSHHHHHHH.HHHHHHHHS-HHHHHHHH CS
                               NusB  64 Deliekllknw......plerlskvdraiLrlavyellylddvPakvaineavelakkygdeksakFvN 126
                                        Deli+k l+++      +l+ ++k    +L+ a+++ +y   + +  + ne++e+a+k ++++s+  vN
  gene1812|gene1812|rna1811|rna1811   5 DELIRKILDEKslealgTLKHINKEKGEALQNALVQHFYV--TRKLISYNEYIEIARKTEEKNSKPCVN 71 
                                        5666666655511111155667788889************..99*******************999888 PP

>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   2.6e-06     0.023      36     110 ..       2      74 ..       1      75 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-06
                                        -SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS---XXXXX..XX CS
                         dsDNA_bind  36 eakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvaekkketkivisr 110
                                        ++  +++++iL+++  e L++++  ++e+ ea++n L+q       r+ ++ ++ +e+ ++ +ek+++  ++++r
  gene1812|gene1812|rna1811|rna1811   2 DQSDELIRKILDEKSLEALGTLKHINKEKGEALQNALVQHFYVT--RKLISYNEYIEIARKTEEKNSKPCVNFKR 74 
                                        5778999*******************************976543..45566666666666666655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 506.84
//
Query:       gene1813|gene1813|rna1812|rna1812  [L=1460]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-20   71.7   0.1    4.9e-19   68.6   0.1    2.5  2  CNOT1_CAF1_bind  CCR4-NOT transcription complex subunit 1 CAF
    1.6e-13   50.9   0.1      6e-13   49.1   0.1    2.0  1  CNOT1_HEAT       CCR4-NOT transcription complex subunit 1 HEA
      4e-09   35.9   0.1    1.3e-08   34.3   0.1    1.9  1  CNOT1_TTP_bind   CCR4-NOT transcription complex subunit 1 TTP
    3.5e-08   33.5   1.0    9.4e-08   32.1   1.0    1.7  1  DUF3819          Domain of unknown function (DUF3819)


Domain annotation for each model (and alignments):
>> CNOT1_CAF1_bind  CCR4-NOT transcription complex subunit 1 CAF1-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.23     1e+03      55      94 ..     212     251 ..     210     257 .. 0.90
   2 !   68.6   0.1   1.1e-22   4.9e-19      76     206 ..     616     740 ..     599     755 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.23
                                        T-GGGHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHBS CS
                    CNOT1_CAF1_bind  55 iepnfhklYlkllekleskkLaeevlketlknikklLnse 94 
                                        i+p f +++ +ll+ + +   ++++l+  +kn ++++ ++
  gene1813|gene1813|rna1812|rna1812 212 IQPKFSRVFEDLLTGFARGAPNSFILHVLFKNHSEMMLQK 251
                                        6899***************************999887665 PP

  == domain 2  score: 68.6 bits;  conditional E-value: 1.1e-22
                                        HHHHHHHHHHHHHHHHHBS-G..GGS-HHHHHHHHHHHHHHTGGGT----TTTB-HHHHHHHHHHTT-HHHHHHHH CS
                    CNOT1_CAF1_bind  76 aeevlketlknikklLnsektlessserslLknLgsWLGsiTlarnkpikhknlalkeLLleayekgrlevvipfv 151
                                        + + ++++l+ +k++L+ ++     +e ++ knLg  LG + la+n+ ++++++++k+ +++++e  r+ + + f+
  gene1813|gene1813|rna1812|rna1812 616 YLQFVRKSLEFLKIFLDYRN----RNEEQIAKNLGLILGGVMLAKNRIVTSEQFDFKKFVVKSVECRRILFGVKFI 687
                                        44445555666666665555....599999********************************************** PP

                                        HHHHGGGGG-TTTSTT-HHHHHHHHHHHHHHHHT---HHHHHHHHHHHHHTT--T CS
                    CNOT1_CAF1_bind 152 ckvLesakkSkvFkppnpWlmailklLaelyeladlklnlkFeievLckeLkldl 206
                                        +  L++ k   vF p+npW+m+il lL+e+y+++     ++ ei+ L+ +++++l
  gene1813|gene1813|rna1812|rna1812 688 SSFLRQGKYGIVFVPNNPWMMSILGLLSEIYSCTP--KAIRDEIQGLFDHFSVEL 740
                                        ********************************987..678999999999999886 PP

>> CNOT1_HEAT  CCR4-NOT transcription complex subunit 1 HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.1   1.3e-16     6e-13       3     144 ..     219     349 ..     216     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.3e-16
                                        HHHHHHHHHHHHS-GGGHHHHC--HHHHHHHHHS-S-........-SHHHHHHHHTT-HHHHHHHS.-TTCHHHCH CS
                         CNOT1_HEAT   3 lidelfplflsnhpnsalvlhklweidrqlllkalvdayakdplelsrIldvaqelkilsellnkl.pfnfaldLa 77 
                                        ++  l++ f  + p  +++lh l ++ ++++l++ +    ++   +sr+ld+  e+k+l  + + l p ++++d+ 
  gene1813|gene1813|rna1812|rna1812 219 VFEDLLTGFARGAP-NSFILHVLFKNHSEMMLQKALI-LVREGIPVSRVLDMFLEHKMLPLVSELLdPPELCFDII 292
                                        44455555554555.899***9997776666665554.3788889*********************7777****** PP

                                        HHHHHHT---HHHHHHHH--TT...THHHHHHHHHHHHH--T.......TTSSSSTTTS--HHHHHH CS
                         CNOT1_HEAT  78 alasrreyldlekwledklkehgekfvqalldfLeekakqelerqeekpsnepepkskslsvetvat 144
                                        +l s r++l+l  wl+++l++ +++fv+ l+ +L+ k+++ +e     p     +k+ +l+ve++ t
  gene1813|gene1813|rna1812|rna1812 293 VLSSIRDHLNLGIWLSNNLTTRKDEFVRLLVLYLDSKISKCKE-----P-----EKMFPLNVEIMGT 349
                                        **************************************99883.....2.....3466677766655 PP

>> CNOT1_TTP_bind  CCR4-NOT transcription complex subunit 1 TTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.1   2.8e-12   1.3e-08      32     165 ..     389     516 ..     362     527 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.8e-12
                     CNOT1_TTP_bind  32 eveeeansyFqklYseeisveevietLkkfksskskrekevfacmiknLfdEyrffpqYPekeLkitaqLfGsiie 107
                                         +eeea ++  ++ + +  +e+ i+++k+f   +s   ke+ + +   L++ y  + + P++ L  +a L+G++i+
  gene1813|gene1813|rna1812|rna1812 389 RIEEEASNFISQIINSQRGIESSINQIKEFLRGNS-LSKELASRIFSALLENYGSLYKLPNSDL--IALLYGGLIK 461
                                        59****************************98766.569**********************987..799******* PP

                     CNOT1_TTP_bind 108 eqLvsykalgiaLrivLealrkppgskmfefgikaLeqfksrLkeypqycqhlasiph 165
                                        e+++ +   ++a++++  +l+ p++ + + fg   Le f   L  yp    ++++i+ 
  gene1813|gene1813|rna1812|rna1812 462 EKVFPKPYRRMAIEYIKGSLKYPENDREYSFGFRCLEVF---LPSYPSILPEIEEIES 516
                                        *************************************99...5556665555555554 PP

>> DUF3819  Domain of unknown function (DUF3819)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   1.0   2.1e-11   9.4e-08       3     132 ..     768     889 ..     766     896 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.1e-11
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT---HHHHHHH.HHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF3819   3 lkklvqlaierairEiiqpvversvtiAvitteelvkKDFalepdenkmrka.ahlmvrnLagsLalvtckepLre 77 
                                        +++++ la++ ++rEi   +ve+++++A+ t   l    F + p e+ m+    ++mv nL++ L+lv+++ep+++
  gene1813|gene1813|rna1812|rna1812 768 VRHVISLALDLSVREICGAIVEKACSVAIQTGMVL----FRTMPVEKGMEYVlFRNMVVNLTKFLCLVSAQEPIKA 839
                                        6899***************************9999....8899999999976269********************* PP

                                        HHHHHHHH-----..-------.---HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            DUF3819  78 sissnlrqllknaltkqlkeqeleqaiqilvndNlelacaliekaaaekavreid 132
                                         is n+  ++k     +l+ ++  + + +++ +N  ++c+li++a a k+ ++i 
  gene1813|gene1813|rna1812|rna1812 840 CISGNVSYFMKLC---SLDLST--ERVFKVALENQTVCCELIQRAGASKVSESIS 889
                                        ******9888776...444444..557788999**************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.26s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 10405.35
//
Query:       gene1814|gene1814|rna1813|rna1813  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-81  273.2   8.0    1.2e-81  273.0   8.0    1.0  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.0   8.0   6.7e-86   1.2e-81       1     190 [.       2     190 ..       2     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 273.0 bits;  conditional E-value: 6.7e-86
                                        -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..-- CS
                     Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvsk 76 
                                        ga++ylre++++kqsdv+r+llr+r++eyrq+ ++ rve+pt l+rAr+LGY+akqG+v++ +rv++G++k+++++
  gene1814|gene1814|rna1813|rna1813   2 GAINYLREIHRRKQSDVMRYLLRIRVCEYRQRGECFRVEKPTFLERARTLGYRAKQGYVLYIARVKKGNMKRNYHN 77 
                                        6899************************************************************************ PP

                                        -SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGS CS
                     Ribosomal_L15e  77 gktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwick 152
                                        g+t++k++++g+n++kp+ ++qa ae  +g+k+pnl vLnSYwvg+D++ykyyEvi+vD++h+airnd+kinwick
  gene1814|gene1814|rna1813|rna1813  78 GNTRGKCVNAGINQIKPSLRKQASAEMVAGKKCPNLGVLNSYWVGQDAAYKYYEVIMVDRHHPAIRNDSKINWICK 153
                                        **************************************************************************** PP

                                        GGGTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TGG CS
                     Ribosomal_L15e 153 kvhkhRelrGltsagkksRGlrkkglkgaekirgsrra 190
                                        +++khRe+rGltsa++ksRGl +kg++++++++gsrr+
  gene1814|gene1814|rna1813|rna1813 154 NTMKHRECRGLTSASRKSRGL-GKGVRFNKSKGGSRRS 190
                                        *********************.**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1393.96
//
Query:       gene1815|gene1815|rna1814|rna1814  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-23   80.8   4.2    8.6e-23   79.6   4.2    1.6  1  Fip1      Fip1 motif


Domain annotation for each model (and alignments):
>> Fip1  Fip1 motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   4.2   4.8e-27   8.6e-23       1      41 [.      45      85 ..      45      86 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.8e-27
                               Fip1  1 didldqleekpWrkpGaDisDYFNYGfdEetWkeYcekqek 41
                                       d+d++++ +kpW+kpGaDi+DYFNYGf+E tW+eYc++q++
  gene1815|gene1815|rna1814|rna1814 45 DYDIESFTDKPWNKPGADITDYFNYGFNETTWREYCNMQRR 85
                                       89************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1134.36
//
Query:       gene1816|gene1816|rna1815|rna1815  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-09   37.9   1.9    1.2e-09   37.9   1.9    2.5  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
    1.6e-05   24.7   8.1    0.00043   20.1   0.4    3.1  3  TFIIS_C         Transcription factor S-II (TFIIS)
  ------ inclusion threshold ------
       0.83   10.0   7.5       0.68   10.3   3.1    2.7  2  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
        2.1    8.2  11.1        1.9    8.3   3.5    2.5  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   1.9   2.7e-13   1.2e-09       2      35 ..       4      37 ..       4      38 .. 0.94
   2 ?    2.8   0.0     0.024   1.1e+02      21      28 ..      68      76 ..      61      79 .. 0.79
   3 ?   -2.9   0.6       1.5   6.8e+03      22      27 ..      98     103 ..      90     104 .. 0.60

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.7e-13
                                       EBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                     RNA_POL_M_15KD  2 kFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                       +FC +C NlL+pked+++  ++C +C  +++a +
  gene1816|gene1816|rna1815|rna1815  4 RFCKECSNLLYPKEDDSTLFLACKSCEHIQEAKS 37
                                       7*****************77**********9975 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.024
                                       E.EEESSSS CS
                     RNA_POL_M_15KD 21 n.feCrqCg 28
                                       +  +C +Cg
  gene1816|gene1816|rna1815|rna1815 68 IkIDCKNCG 76
                                       557999998 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.5
                                        EEESSS CS
                     RNA_POL_M_15KD  22 feCrqC 27 
                                        + C  C
  gene1816|gene1816|rna1815|rna1815  98 YLCCRC 103
                                        666666 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.22   9.9e+02      31      35 ..       6      10 ..       5      12 .. 0.56
   2 !    8.1   0.1   0.00055       2.4      25      36 ..      20      31 ..      16      33 .. 0.87
   3 !   20.1   0.4   9.7e-08   0.00043       2      39 .]      71     108 .]      70     108 .] 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                            TFIIS_C 31 CtkCg 35
                                       C++C 
  gene1816|gene1816|rna1815|rna1815  6 CKECS 10
                                       55554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00055
                            TFIIS_C 25 mtvfykCtkCgh 36
                                       +t+f  C++C+h
  gene1816|gene1816|rna1815|rna1815 20 STLFLACKSCEH 31
                                       79********99 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 9.7e-08
                            TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                         C++Cg ++  +fq      D    ++y C+ C h W+
  gene1816|gene1816|rna1815|rna1815  71 DCKNCGFNKGLYFQSRGGEDDVALNIYYLCCRCHHLWT 108
                                        7************888888899999***********96 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.1   0.00015      0.68      45      90 .]       3      76 ..       1      76 [. 0.70
   2 ?   -0.1   0.1      0.26   1.2e+03      84      90 .]      98     104 ..      83     108 .] 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                                       CTB-TTT--B--CTTTEEEEE...E-SSS-E....................................EEEEETTTT CS
                               Rpr2 45 rtvCkkCgsvlipgvtcsvrv...enkskkkkkkkkka...........................dvlvvtClaCg 90
                                       +++Ck+C+++l p    s+     +  s ++ ++ k++                            ++++ C++Cg
  gene1816|gene1816|rna1815|rna1815  3 DRFCKECSNLLYPKEDDSTLFlacK--SCEHIQEAKSHrlyaknfrpkhtsielyakdlaqdptlPSIKIDCKNCG 76
                                       689**********987776663331..3333322222256677778888888888999999999866679*****7 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.26
                                        EEETTTT CS
                               Rpr2  84 vtClaCg 90 
                                        + C++C+
  gene1816|gene1816|rna1815|rna1815  98 YLCCRCH 104
                                        5555553 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.9    0.0084        38      25      53 ..       6      32 ..       5      33 .. 0.73
   2 ?    8.3   3.5   0.00043       1.9      22      53 ..      69     106 ..      60     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0084
                     zinc_ribbon_10 25 CskChshnGlapkeeleevkyrCpkCgal 53
                                       C++C   n l+pke+ +++   C +C ++
  gene1816|gene1816|rna1815|rna1815  6 CKECS--NLLYPKEDDSTLFLACKSCEHI 32
                                       66663..5577788888888889999875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00043
                     zinc_ribbon_10  22 alICskChshnGlap.....keele.evkyrCpkCgal 53 
                                        ++ C++C  + Gl+      +++ + ++ y C  C +l
  gene1816|gene1816|rna1815|rna1815  69 KIDCKNCGFNKGLYFqsrggEDDVAlNIYYLCCRCHHL 106
                                        566***********97766533333256999****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 735.28
//
Query:       gene1817|gene1817|rna1816|rna1816  [L=263]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-08   32.9   0.0    7.5e-08   32.3   0.0    1.2  1  TPP1      Shelterin complex subunit, TPP1/ACD


Domain annotation for each model (and alignments):
>> TPP1  Shelterin complex subunit, TPP1/ACD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   4.2e-12   7.5e-08       2      95 ..       9      96 ..       8     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.2e-12
                                       -HHHHHHHT--TTTS--HHHHT-..GGGEEEEEEEEE.EETTEEEEEEE-SS-EEEEEE-HHHHHHHHHHHSS-TTSS CS
                               TPP1  2 WIeklvleaiklssdlspslntnkskaqllkvlkfaqdtsnsaitavlsDsthkIlaiftreavenfereekeritse 79
                                       WIek++ e+            + +++++ ++v++++++++++  ++++sDs+h+I +i+t+e++e f +e  + i  +
  gene1817|gene1817|rna1816|rna1816  9 WIEKTIYEQMYDGHW-----RRRQQASFNAQVIDIGKKVKDGGFEVCVSDSRHFIDSILTKESIEAFGKEIACGI-ED 80
                                       999999888877777.....56778999999999999*********************************99888.9* PP

                                       -TTSEEEEES-EEEEE CS
                               TPP1 80 tkgclllikdaslvfq 95
                                       ++gc++++ ++  v++
  gene1817|gene1817|rna1816|rna1816 81 IRGCYITVDKFHYVYH 96
                                       ********99986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1451.51
//
Query:       gene1818|gene1818|rna1817|rna1817  [L=851]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-42  144.6   2.7    1.3e-39  136.1   0.0    3.0  2  AAA_2            AAA domain (Cdc48 subfamily)
    7.8e-29   99.7   1.6    7.8e-29   99.7   1.6    2.8  2  AAA_lid_9        AAA lid domain
    7.3e-24   84.7   0.4    1.8e-11   44.6   0.0    3.6  3  AAA              ATPase family associated with various cellul
    5.7e-16   58.8   1.3    2.9e-10   40.3   0.0    3.4  2  AAA_5            AAA domain (dynein-related subfamily)
    4.5e-14   53.2   0.3    2.5e-05   24.7   0.0    4.9  4  AAA_16           AAA ATPase domain
    1.5e-12   47.4   1.5    8.7e-12   44.9   0.0    3.2  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    7.6e-09   35.5   0.2    6.5e-05   22.7   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
    1.8e-08   34.0   0.7      0.035   13.5   0.0    3.5  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    7.9e-08   32.2   0.0    0.00059   19.6   0.0    2.8  2  IstB_IS21        IstB-like ATP binding protein
    2.5e-07   30.8   0.4      0.024   14.6   0.0    3.6  2  AAA_14           AAA domain
    2.1e-06   28.0   4.2      0.034   14.4   0.3    4.7  2  AAA_22           AAA domain
    4.4e-06   26.5   2.0       0.16   11.7   0.0    4.2  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    8.6e-06   25.4   0.0      0.055   13.0   0.0    2.8  2  AAA_7            P-loop containing dynein motor region
    1.2e-05   25.2   0.0      0.048   13.6   0.0    2.6  2  NACHT            NACHT domain
    1.4e-05   24.6   0.0       0.26   10.7   0.0    3.5  3  TniB             Bacterial TniB protein
    2.5e-05   23.6   3.2       0.27   10.4   0.0    3.6  3  TIP49            TIP49 P-loop domain
    7.1e-05   22.9   0.0    0.00084   19.4   0.0    2.6  2  Clp_N            Clp amino terminal domain, pathogenicity isl
    0.00011   21.5   0.4      0.023   13.9   0.1    3.1  3  NB-ARC           NB-ARC domain
    0.00013   22.1   0.0        1.5    8.8   0.0    4.1  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00013   21.3   0.4       0.13   11.5   0.0    3.2  3  Zeta_toxin       Zeta toxin
     0.0002   21.3   1.1       0.13   12.2   0.0    3.7  3  RsgA_GTPase      RsgA GTPase
    0.00022   21.2   0.1        0.9    9.6   0.0    3.0  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00024   20.9   0.2      0.026   14.2   0.1    2.6  2  AAA_30           AAA domain
    0.00055   20.5   2.0        1.8    9.1   0.0    3.9  3  ABC_tran         ABC transporter
    0.00055   20.3   0.0        1.4    9.3   0.0    3.2  2  RNA_helicase     RNA helicase
    0.00079   19.6   0.4        6.7    6.9   0.0    3.6  3  AAA_33           AAA domain
    0.00089   19.6   2.1       0.13   12.5   0.3    3.7  3  AAA_19           AAA domain
     0.0013   19.0   0.0       0.88    9.8   0.0    2.8  2  Roc              Ras of Complex, Roc, domain of DAPkinase
     0.0013   18.6   0.2        1.3    8.9   0.1    3.3  3  NTPase_1         NTPase
     0.0018   17.4   0.1       0.74    8.8   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
      0.002   18.1   3.6       0.48   10.4   0.0    3.6  3  ResIII           Type III restriction enzyme, res subunit
     0.0022   17.9   9.7      0.057   13.3   0.1    4.6  5  ATPase_2         ATPase domain predominantly from Archaea
     0.0024   17.6   0.1        4.1    7.2   0.0    3.1  3  AAA_29           P-loop containing region of AAA domain
     0.0032   17.2   0.1       0.16   11.7   0.0    2.6  2  AAA_24           AAA domain
     0.0039   17.0   0.0       0.18   11.6   0.0    3.3  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0059   16.5   0.3        7.1    6.5   0.0    3.1  2  AAA_3            ATPase family associated with various cellul
     0.0065   16.6   0.0      0.038   14.1   0.0    2.3  1  Torsin           Torsin
     0.0071   15.9   0.1        1.3    8.6   0.0    3.2  2  AAA_25           AAA domain
     0.0076   16.8   9.8       0.17   12.5   0.1    4.2  3  AAA_18           AAA domain
     0.0094   15.4   0.6       0.18   11.2   0.0    2.4  2  ParA             NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.021   14.0   3.0        1.8    7.7   0.0    3.2  4  DUF815           Protein of unknown function (DUF815)
      0.025   14.2   0.6        8.6    5.9   0.0    3.0  2  SRP54            SRP54-type protein, GTPase domain
      0.035   13.6   0.0       0.84    9.0   0.0    2.8  2  PhoH             PhoH-like protein
       0.04   13.3   4.0       0.46    9.8   0.0    3.8  4  AAA_8            P-loop containing dynein motor region D4
      0.043   13.0   2.6          2    7.6   0.0    3.4  3  ArsA_ATPase      Anion-transporting ATPase
      0.063   13.4   0.0      0.063   13.4   0.0    4.2  3  DUF87            Helicase HerA, central domain
      0.066   13.3   0.1        3.2    7.9   0.0    3.4  3  MMR_HSR1         50S ribosome-binding GTPase
       0.17   11.6   0.9         19    4.9   0.0    3.2  3  ATP_bind_1       Conserved hypothetical ATP binding protein
        1.4    9.1  10.9        4.5    7.5   0.4    3.7  3  Lge1             Transcriptional regulatory protein LGE1
        2.4    8.6   6.2         21    5.6   0.0    3.9  2  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0094       3.4       2      77 ..     186     266 ..     185     278 .. 0.82
   2 !  136.1   0.0   3.6e-42   1.3e-39       1     170 [.     577     738 ..     577     739 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0094
                                        ----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS....... CS
                              AAA_2   2 piisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG....... 70 
                                         +++ +l+g  gvGkt + + +a+l+   + +  + +da+ +    +v ++v+   +  ++  + +          
  gene1818|gene1818|rna1817|rna1817 186 TKSNAILVGMPGVGKTAIVNGIAQLIA--NGEIPTLKDAKIYNV--DVGSMVAGTSHRGDFEERLKSLVkeaettp 257
                                        5789999*******************8..466668899999999..999999988887777666655556666779 PP

                                        ..EEEEETG CS
                              AAA_2  71 ..ivllDEi 77 
                                          i+++DEi
  gene1818|gene1818|rna1817|rna1817 258 gvILFIDEI 266
                                        999999*99 PP

  == domain 2  score: 136.1 bits;  conditional E-value: 3.6e-42
                                        -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS...... CS
                              AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG...... 70 
                                        +pi+ +lllgptgvGktelaka+a  lf ++ek++ ++d+s++      e ++++liga+ gyvg++egG      
  gene1818|gene1818|rna1817|rna1817 577 KPIGAFLLLGPTGVGKTELAKAVAMELF-DDEKNMLVLDMSDYGN----EMSITKLIGASAGYVGYNEGGaltepi 647
                                        5899************************.****************....*************************** PP

                                        ......EEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS- CS
                              AAA_2  71 ......ivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrs 140
                                              ++llDE+d +h+            V+++L+q+l++g++td +g  vd++n+++Imt+++g++   ++ + 
  gene1818|gene1818|rna1817|rna1817 648 knrpynVILLDEVDLAHQ-----------TVLNVLYQLLDEGRVTDGKGTVVDFRNCVLIMTSNLGQEIMMRSPE- 711
                                        ******************...........******************************************9655. PP

                                        STTTTSGGG--HHHHHHTT--HHHHTT--E CS
                              AAA_2 141 keeeeekkkeeveeelkkglipEllgRlpe 170
                                            +e+ k+e+e+++ +++ p l++R++ 
  gene1818|gene1818|rna1817|rna1817 712 ---LDENDKKEIERLVLNKFGPPLVNRIDN 738
                                        ...58899999*****************96 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.7   1.6   2.2e-31   7.8e-29       1     100 [.     328     427 ..     328     434 .. 0.92
   2 ?   -1.3   2.4       5.8   2.1e+03      63      65 ..     454     456 ..     421     494 .. 0.50

  Alignments for each domain:
  == domain 1  score: 99.7 bits;  conditional E-value: 2.2e-31
                          AAA_lid_9   1 seeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeeleklek 76 
                                        s+e++i++Lrglke++e++Hgvki d+al+ a++ Sk+Yis+r+lPd AIDl+D+a+a++ ++ es+p+++ ++++
  gene1818|gene1818|rna1817|rna1817 328 SIEDSITMLRGLKERLEAYHGVKIADSALVYAANSSKKYISNRRLPDVAIDLVDTACASAVIALESEPQKILNAKS 403
                                        689************************************************************************* PP

                          AAA_lid_9  77 elaklekekealekeeekekaerl 100
                                        +++kle ek++le + ++ek+e+ 
  gene1818|gene1818|rna1817|rna1817 404 KVWKLELEKASLEIDLAREKDEQT 427
                                        ***********9877765555443 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.8
                          AAA_lid_9  63 kke 65 
                                        k++
  gene1818|gene1818|rna1817|rna1817 454 KEK 456
                                        222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       7.1   2.6e+03      61      89 ..      37      62 ..       2      95 .. 0.50
   2 !   44.6   0.0   4.9e-14   1.8e-11       2     111 ..     191     302 ..     190     326 .. 0.80
   3 !   35.8   0.0   2.6e-11   9.3e-09       2     115 ..     583     705 ..     582     717 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 7.1
                                       EEEEETGGGHHHHHTTCCCHHHHHHHHHH CS
                                AAA 61 ilfiDEidalaksrsgseseeeervvnqL 89
                                       +++ D    l++     + +e+e++ n+L
  gene1818|gene1818|rna1817|rna1817 37 VILNDQTSILCSVL---SIDEKEDIKNKL 62
                                       22222222222222...334444444444 PP

  == domain 2  score: 44.6 bits;  conditional E-value: 4.9e-14
                                        EEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTSTS.EEEEEE CS
                                AAA   2 llyGppGtGKTllakavakel.........gvefleisgsell..skyvgesekkirelfkeakekakp.silfiD 65 
                                        +l+G pG+GKT++++ +a+ +         +++++++++ +++   ++ g+ e++++ l+kea++   p +ilfiD
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIAQLIangeiptlkDAKIYNVDVGSMVagTSHRGDFEERLKSLVKEAETT--PgVILFID 264
                                        79******************75555555545999***99999964559**************9886..66****** PP

                                        TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                                AAA  66 EidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                        Ei+ + ++    +++ +++++n L + l   +       +igat++
  gene1818|gene1818|rna1817|rna1817 265 EIHIVLGAG---KTDGAMDAANMLKPGLAAGTI-----KCIGATTH 302
                                        ******999...889999999999888887776.....37777776 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 2.6e-11
                                        EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS............STTHHHHHHHHHHHHHHHTSTS.EE CS
                                AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk............yvgesekkirelfkeakekakp.si 61 
                                        ll Gp G+GKT lakava el   + ++l +++s+  ++            yvg +e    +l + +k+   p  +
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELfddEKNMLVLDMSDYGNEmsitkligasagYVGYNEGG--ALTEPIKNR--PyNV 654
                                        89******************977657788888888886667777666666666655543..344444443..669* PP

                                        EEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESSGGGS CS
                                AAA  62 lfiDEidalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnrpdkl 115
                                        +++DE+d  +++            +n+L++ ld+ +           +++++i+++n  +++
  gene1818|gene1818|rna1817|rna1817 655 ILLDEVDLAHQTV-----------LNVLYQLLDEGRVTdgkgtvvdFRNCVLIMTSNLGQEI 705
                                        ********98777...........**********9999999999996669999999986555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.9e-05     0.011       2      75 ..     190     267 ..     189     319 .. 0.83
   2 !   40.3   0.0     8e-13   2.9e-10       2     124 ..     582     703 ..     581     715 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-05
                                        EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--............--------..G-SEEEE CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreik...ngttslvdsplvraar..egeilvl 71 
                                         +LvG pG+gK+ ++  +a+++ n e+ +    +++   d+   +       g+ + + ++lv++a+   g il++
  gene1818|gene1818|rna1817|rna1817 190 AILVGMPGVGKTAIVNGIAQLIaNGEIPTLK-DAKIYNVDVGSMVA-GtshRGDFEERLKSLVKEAEttPGVILFI 263
                                        59********************766555544.44444444333333.23558999999999999999889999999 PP

                                        ESGG CS
                              AAA_5  72 DEve 75 
                                        DE++
  gene1818|gene1818|rna1817|rna1817 264 DEIH 267
                                        9997 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 8e-13
                                        EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--..........--------..G-SEEEE CS
                              AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik.ngttslvdsplvraar..egeilvl 71 
                                        +lL+Gp+G+gK+ela+ +a  l   ++++++  ++++ +e  ++  +  + +     + ++l++ ++     +++l
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAMELfddEKNMLVLDMSDYGNEMSITKLIGASaGYVGYNEGGALTEPIKnrPYNVILL 657
                                        79*****************99999999999999999999999999999884455555666777777787889**** PP

                                        ESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                              AAA_5  72 DEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                        DEv+ a++ vln+L +ll+e r+  +  g++v+++n        +i+t+n  +
  gene1818|gene1818|rna1817|rna1817 658 DEVDLAHQTVLNVLYQLLDEGRVT-DGKGTVVDFRN------CVLIMTSNLGQ 703
                                        ***********************9.55555566666......99999999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   6.9e-08   2.5e-05       2      47 ..     168     210 ..     167     220 .. 0.82
   2 ?    3.6   0.0      0.22        79     116     145 ..     239     267 ..     215     285 .. 0.81
   3 !   12.9   0.0   0.00031      0.11      15      51 ..     569     606 ..     551     629 .. 0.79
   4 ?    5.4   0.0     0.059        21     137     162 ..     653     678 ..     642     691 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.9e-08
                             AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellra 47 
                                        ++GR+ee++q+ ++l++    + ++ +l+G++GvGK+++v+ +++ 
  gene1818|gene1818|rna1817|rna1817 168 VIGRDEEIRQVIEILSKK---TKSNAILVGMPGVGKTAIVNGIAQL 210
                                        78******8888888744...447899*************998854 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.22
                             AAA_16 116 asrllellkrllallsrderplvlvlDdlq 145
                                        + ++ e lk+l++ +++  + ++l++D+++
  gene1818|gene1818|rna1817|rna1817 239 RGDFEERLKSLVKEAET-TPGVILFIDEIH 267
                                        4789999*****99999.555*******99 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00031
                             AAA_16  15 alervrsgrp.elvllsGesGvGKsslvrellralekd 51 
                                         ++  r++ p ++ ll G+ GvGK+ l+++++ +l +d
  gene1818|gene1818|rna1817|rna1817 569 RVGLSREDKPiGAFLLLGPTGVGKTELAKAVAMELFDD 606
                                        4444556666899***************9998777665 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.059
                             AAA_16 137 lvlvlDdlqwadeaslqllaaLlrll 162
                                         v++lD+++ a ++ l++l++Ll+++
  gene1818|gene1818|rna1817|rna1817 653 NVILLDEVDLAHQTVLNVLYQLLDEG 678
                                        69*********************985 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   2.4e-14   8.7e-12       1      74 [.     745     818 ..     745     825 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.4e-14
                                        SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSS CS
                      ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelk 74 
                                        L++e + kI++ ++++l+krl+ +++++e++  ++d ++ek  ++ yGAR L+r+iq +   +l + +l ++ +
  gene1818|gene1818|rna1817|rna1817 745 LDRESMYKILEYQMAELKKRLNGKNISFEISSGVRDDVIEKVHSSTYGARLLKRFIQSNFVHALTKILLMKTNE 818
                                        899**************************************************************999987755 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1    0.0011      0.41       2     103 ..     169     267 ..     168     275 .. 0.81
   2 !   22.7   0.0   1.8e-07   6.5e-05      24     124 ..     581     682 ..     551     714 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                                        ---SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEB.SSS CS
                    Sigma54_activat   2 igesealkelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGh.ekG 76 
                                        ig++e++++++e ++k   t+++ +++G  G+GK+ + + i +     ++++ ++  a+i +  + s + G+ ++G
  gene1818|gene1818|rna1817|rna1817 169 IGRDEEIRQVIEILSKK--TKSNAILVGMPGVGKTAIVNGIAQLIA--NGEIPTLKDAKIYNVDVGSMVAGTsHRG 240
                                        78889999999988875..56778999**************99887..4555677788888888888888862579 PP

                                        SSTTTSS-BEHHHHHTTTSEEEEETGG CS
                    Sigma54_activat  77 aFtGAekekkGlfekadgGtlfLDeig 103
                                         F    k+     e++ g +lf+Dei+
  gene1818|gene1818|rna1817|rna1817 241 DFEERLKSLVKEAETTPGVILFIDEIH 267
                                        999888888888888889999999998 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.8e-07
                                        -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BE..HHHHHTTTSEE CS
                    Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekk..GlfekadgGtl 97 
                                          l++G +G+GK+ la+a+  +   +ek+++ ++++++ +e+  ++L G ++G + G ++  +    +++    ++
  gene1818|gene1818|rna1817|rna1817 581 AFLLLGPTGVGKTELAKAVAMELFDDEKNMLVLDMSDYGNEMSITKLIGASAG-YVGYNEGGAltEPIKNRPYNVI 655
                                        5799**********************************************998.78877765544567778889** PP

                                        EEETGGGS-HHHHHHHHHHHHHSEEES CS
                    Sigma54_activat  98 fLDeigelplelQekLlrvlqegever 124
                                        +LDe+     ++ + L ++l+eg+v+ 
  gene1818|gene1818|rna1817|rna1817 656 LLDEVDLAHQTVLNVLYQLLDEGRVTD 682
                                        ******9999999*********99875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00093      0.34       9      50 ..     173     215 ..     165     257 .. 0.68
   2 ?    6.6   0.1     0.013       4.5      25      45 ..     582     602 ..     579     628 .. 0.83
   3 !   13.5   0.0   9.9e-05     0.035     109     205 ..     654     748 ..     640     750 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00093
                       Mg_chelatase   9 eeakralei.aaaGgHnlllvGppGsGKtmlakrlpsllppls 50 
                                        ee ++++ei +   + n +lvG pG GKt + + +++l+++ +
  gene1818|gene1818|rna1817|rna1817 173 EEIRQVIEIlSKKTKSNAILVGMPGVGKTAIVNGIAQLIANGE 215
                                        455667777345677899*****************99987643 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                       Mg_chelatase  25 lllvGppGsGKtmlakrlpsl 45 
                                        +ll+Gp G GKt lak+++  
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAME 602
                                        799*************98754 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 9.9e-05
                       Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekectcsekeierYlsk 184
                                        v++LDE+   +++vl+vL + l++g+vt  +  + v+f  ++ l+++ N+ +   ++++e + + +++  +  l+k
  gene1818|gene1818|rna1817|rna1817 654 VILLDEVDLAHQTVLNVLYQLLDEGRVTDGKG-TVVDFR-NCVLIMTSNLGQEIMMRSPELDENDKKEIERLVLNK 727
                                        899***********************986554.567775.899**********999999999888888888899** PP

                       Mg_chelatase 185 lsgplldRidlqvevkkleae 205
                                           pl++Rid  +  ++l++e
  gene1818|gene1818|rna1817|rna1817 728 FGPPLVNRIDNVIYFNNLDRE 748
                                        **********99988877665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0019      0.69      45      73 ..     185     213 ..     158     269 .. 0.66
   2 !   19.6   0.0   1.6e-06   0.00059      50      97 ..     582     629 ..     550     677 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0019
                          IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavr 73 
                                        ++k n +l+G +GvGK+ +   +++  ++
  gene1818|gene1818|rna1817|rna1817 185 KTKSNAILVGMPGVGKTAIVNGIAQLIAN 213
                                        6789*************998888764433 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1.6e-06
                          IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdg 97 
                                        ++llGp+GvGK+ la a+++e   +++++l + ++d  +e+++ +  g
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAMELFDDEKNMLVLDMSDYGNEMSITKLIG 629
                                        79******************************9999999998877655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00043      0.15       5      76 ..     190     269 ..     186     318 .. 0.74
   2 !   14.6   0.0   6.8e-05     0.024       5      90 ..     582     678 ..     580     686 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00043
                             AAA_14   5 lvitGaRrvGKTtllkqlikell.......vkkesilyinldderdkkla..dpe.kllelileklkeekktylfl 70 
                                         +++G+  vGKT +++ +++  +        k+ +i  +++ +    ++   d+e +l +l++e  +     +lf+
  gene1818|gene1818|rna1817|rna1817 190 AILVGMPGVGKTAIVNGIAQL-IangeiptLKDAKIYNVDVGSMVAGTSHrgDFEeRLKSLVKEAET-TPGVILFI 263
                                        6899**********9888744.447778777777777777777655332223555244455555444.47899*** PP

                             AAA_14  71 DEiqev 76 
                                        DEi+ v
  gene1818|gene1818|rna1817|rna1817 264 DEIHIV 269
                                        ***987 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.8e-05
                             AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe..........kllelileklke........ 62 
                                         ++ G+  vGKT l+k ++ el+ +++++l +++ d  ++++  ++                 e   +        
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAMELFDDEKNMLVLDMSDYGNEMSI-TKligasagyvgY-----NE---Ggaltepik 648
                                        6799***************9999999********998885433.2223333333331.....22...022333453 PP

                             AAA_14  63 .ekktylflDEiqevpe.wekalkslvdeg 90 
                                         +  ++++lDE+  + + + ++l +l+deg
  gene1818|gene1818|rna1817|rna1817 649 nRPYNVILLDEVDLAHQtVLNVLYQLLDEG 678
                                        244566******998652666777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0025      0.89       3      51 ..     185     233 ..     182     286 .. 0.77
   2 !   14.4   0.3   9.4e-05     0.034       7     117 ..     581     676 ..     575     688 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0025
                             AAA_22   3 ktagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                        kt++  +++G +G+GKT  ++ +++   + + ++ ++++++ v++ s  
  gene1818|gene1818|rna1817|rna1817 185 KTKSNAILVGMPGVGKTAIVNGIAQLIANGEIPTLKDAKIYNVDVGSMV 233
                                        588999**************99999887777777777777777776655 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.4e-05
                             AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleal 82 
                                          ++ G++G+GKT l++ ++++l  +      ++  +  +++  ++  ++ + +    g  + +          al
  gene1818|gene1818|rna1817|rna1817 581 AFLLLGPTGVGKTELAKAVAMELFDD------EKNMLVLDMSDYGNEMSITKLIGASAGYVGYN-------EGGAL 643
                                        56899****************99533......55556677777776666666666666643333.......34677 PP

                             AAA_22  83 eqalraravielliiDEaqhlrseealeeLrslln 117
                                        ++ +++r    ++++DE++   ++++l+ L +ll+
  gene1818|gene1818|rna1817|rna1817 644 TEPIKNRPY-NVILLDEVDLA-HQTVLNVLYQLLD 676
                                        888888888.89999999999.8999999988888 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.8    0.0044       1.6      33      94 ..     187     267 ..     161     274 .. 0.52
   2 !   11.7   0.0   0.00043      0.16      30      57 ..     576     603 ..     549     611 .. 0.81
   3 ?    0.6   0.0       1.2   4.3e+02      84     112 ..     651     679 ..     639     689 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0044
                             RuvB_N  33 ldhvllyGpPGlGkttl....akiiak.el....gvklk.itsgPvl...ekagdlaalltnl......eekdvlf 89 
                                            +l+G PG+Gkt++    a++ia+ e+    ++k+  +  g ++   ++ gd+   l++l      +++ +lf
  gene1818|gene1818|rna1817|rna1817 187 KSNAILVGMPGVGKTAIvngiAQLIANgEIptlkDAKIYnVDVGSMVagtSHRGDFEERLKSLvkeaetTPGVILF 262
                                        3456899********9722225555552221111222221223333322245666655555541111112345788 PP

                             RuvB_N  90 ideih 94 
                                        ideih
  gene1818|gene1818|rna1817|rna1817 263 IDEIH 267
                                        88887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00043
                             RuvB_N  30 eealdhvllyGpPGlGkttlakiiakel 57 
                                        ++++   ll Gp G+Gkt lak +a el
  gene1818|gene1818|rna1817|rna1817 576 DKPIGAFLLLGPTGVGKTELAKAVAMEL 603
                                        4567889******************998 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.2
                             RuvB_N  84 ekdvlfideihrlsraveevlysamedfr 112
                                        + +v+++de+   +++v +vly+ +++ r
  gene1818|gene1818|rna1817|rna1817 651 PYNVILLDEVDLAHQTVLNVLYQLLDEGR 679
                                        5689******************9987755 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0023      0.82      31      55 ..     185     209 ..     168     220 .. 0.78
   2 !   13.0   0.0   0.00015     0.055      36      82 ..     582     628 ..     572     634 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0023
                              AAA_7  31 knkkpvllvGptGtGKtviikdllk 55 
                                        k k + +lvG  G+GKt+i++ + +
  gene1818|gene1818|rna1817|rna1817 185 KTKSNAILVGMPGVGKTAIVNGIAQ 209
                                        456789**************98765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00015
                              AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                                        +ll GptG+GKt ++k +  +l +++ ++l++ +s + + +++ ++i
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAMELFDDEKNMLVLDMSDYGNEMSITKLI 628
                                        79***************777777799999999999998888888777 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00013     0.048       4      32 ..     191     219 ..     188     230 .. 0.90
   2 !    8.8   0.0    0.0041       1.5       4      27 ..     583     606 ..     581     617 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                                        EEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                              NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqg 32 
                                        il G +G+GKT+ + ++a+++a g+ p  
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIAQLIANGEIPTL 219
                                        899*********************98875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0041
                                        EEEC-TTTCHHHHHHHHHHHHCTS CS
                              NACHT   4 ilqGeaGsGKTtLlqklalawaeg 27 
                                        +l G+ G+GKT L++ +a+++ ++
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFDD 606
                                        789***************998665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0064       2.3      22      59 ..     174     211 ..     168     254 .. 0.75
   2 !   10.7   0.0   0.00072      0.26     113     184 ..     251     324 ..     215     327 .. 0.77
   3 ?    2.1   0.0      0.31   1.1e+02      36      55 ..     580     599 ..     552     610 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0064
                               TniB  22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlh 59 
                                        ++++++e  ++k  +n++lvG + +GKt+iv+  a+l 
  gene1818|gene1818|rna1817|rna1817 174 EIRQVIEILSKKTKSNAILVGMPGVGKTAIVNGIAQLI 211
                                        567778888888889****************9877655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00072
                               TniB 113 rllrelkvrvLiiDEihnll.agsarkqreflnalksLgnelkipivlvGteeal.ralrtDpqlasRFepial 184
                                        +  +++   +L iDEih +l ag+ +    + n+lk       i  +++ t++ + + +++Dp +++RF ++ +
  gene1818|gene1818|rna1817|rna1817 251 KEAETTPGVILFIDEIHIVLgAGKTDGAMDAANMLKPGLAAGTIKCIGATTHDEYrKYVEKDPAFERRFVQVVV 324
                                        44444455699******9885788899999*******99999******9998765168***********98765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.31
                               TniB  36 pnlllvGdsnnGKtmivekF 55 
                                           ll+G++ +GKt +++  
  gene1818|gene1818|rna1817|rna1817 580 GAFLLLGPTGVGKTELAKAV 599
                                        5689***********99865 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2    0.0015      0.55      42      93 ..     181     229 ..     158     237 .. 0.75
   2 ?    2.1   0.1      0.25        91     274     289 ..     252     268 ..     235     270 .. 0.78
   3 !   10.4   0.0   0.00076      0.27      21      97 ..     546     626 ..     527     631 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0015
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                              TIP49  42 likekklaGravLlaGpsgtGktalaiaiskelg.edvpfvalsgsevyslev 93 
                                        ++  kk    a+ l+G +g Gkta+  +i++ ++  ++p  +l+ +++y ++v
  gene1818|gene1818|rna1817|rna1817 181 ILS-KKTKSNAI-LVGMPGVGKTAIVNGIAQLIAnGEIP--TLKDAKIYNVDV 229
                                        333.33344566.57****************99833454..678888888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                                        XXXXXXXX.XXXXXXXX CS
                              TIP49 274 kaeivpGv.lfiDevhm 289
                                        +ae  pGv lfiDe+h+
  gene1818|gene1818|rna1817|rna1817 252 EAETTPGViLFIDEIHI 268
                                        58999**857******8 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00076
                                        XXXXXXXXXXXXXXXX..XXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              TIP49  21 keeeglvGqkkareaa..gvi...velikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                        + ++ + Gq +a +a+  +++   v l +e+k  G a Ll Gp+g Gkt la a++ el +d + + +     y +
  gene1818|gene1818|rna1817|rna1817 546 RIKNRIFGQSHAVDAVvdSILqsrVGLSREDKPIG-AFLLLGPTGVGKTELAKAVAMELFDDEKNMLVLDMSDYGN 620
                                        45556777777777752223322245667777554.78899******************97766555555555888 PP

                                        XXXXXX CS
                              TIP49  92 evkkte 97 
                                        e++ t 
  gene1818|gene1818|rna1817|rna1817 621 EMSITK 626
                                        887765 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.4e-06   0.00084       2      34 ..      18      50 ..      17      51 .. 0.94
   2 ?   -0.1   0.0       2.9   1.1e+03       9      36 ..      95     120 ..      89     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.4e-06
                                       HHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHH CS
                              Clp_N  2 qelAkslghqyistEHLLlALleeddGlaarlL 34
                                        ++A ++ ++ +++EHLL+++l++ +++++++L
  gene1818|gene1818|rna1817|rna1817 18 LDEAIANSNNVVEPEHLLKVILNDQTSILCSVL 50
                                       689***************************998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.9
                                        TCSSB-HHHHHHHHHHSCTSHHHHHHHH CS
                              Clp_N   9 ghqyistEHLLlALleeddGlaarlLkk 36 
                                        g++y+s+  L l Ll  +   +++l+ +
  gene1818|gene1818|rna1817|rna1817  95 GDSYVSVNALVLQLLTVK--SIKELISN 120
                                        899999999999888877..66666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   6.5e-05     0.023       2      41 ..     172     208 ..     171     214 .. 0.87
   2 ?   -2.9   0.0       8.7   3.1e+03      45      70 ..     309     335 ..     304     346 .. 0.74
   3 ?    4.1   0.0     0.064        23      22      43 ..     581     602 ..     560     628 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                                        HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHC CS
                             NB-ARC   2 eksvekviekLlekdelqslvvalvGmgGvGKttlakqil 41 
                                        ++++++vie L++k +++     lvGm+GvGKt +++ i 
  gene1818|gene1818|rna1817|rna1817 172 DEEIRQVIEILSKKTKSN---AILVGMPGVGKTAIVNGIA 208
                                        67899*******998888...6799**********98775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.7
                                        CCCCCCBT.EEEEEEEESXXHHHHHHH CS
                             NB-ARC  45 devegrFd.svawvvvsktdkseeile 70 
                                         e +  F+ ++++vvvs+ + + +i+ 
  gene1818|gene1818|rna1817|rna1817 309 VEKDPAFErRFVQVVVSEPSIEDSITM 335
                                        556668998899*****9998888864 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.064
                                        EEEEEESTTSSHHHHHHHHCCS CS
                             NB-ARC  22 vvalvGmgGvGKttlakqilnk 43 
                                           l G  GvGKt lak +  +
  gene1818|gene1818|rna1817|rna1817 581 AFLLLGPTGVGKTELAKAVAME 602
                                        45688***********998755 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0043       1.5       8     116 ..     196     360 ..     190     566 .. 0.77
   2 ?    7.6   0.0      0.01       3.7       8      87 ..     588     731 ..     584     831 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0043
                                        TTSSHHHHHHHHHHHHHHTT......--EEEEEEEESSCCCCH......HTTEB-HHHH................. CS
                                        xxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxx......xxxxxxxxxx................. RF
                               CbiA   8 GGvGKTtlaanLaralarrg......lrVllvDaDpqannlai......leglendiep................. 54 
                                         GvGKT ++ ++a+++a+++       ++  vD++ +   +++             ++                  
  gene1818|gene1818|rna1817|rna1817 196 PGVGKTAIVNGIAQLIANGEiptlkdAKIYNVDVGSMVAGTSHrgdfeeR------LKSlvkeaettpgvilfide 265
                                        59***************865222222577788888888888874444332......22255556689999999999 PP

                                        ...........................CCHCCCHHHHHHCHCHHHH.......EEEEEEEEESS...-TTCHHHHH CS
                                        ...........................xxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  55 ...........................dlkrllellealgkkkall.....lkiagvvlnrvdgeneetllkeale 98 
                                                                   ++k ++ + ++ ++k+  +      +++ vv+  +  e+++t+l+   e
  gene1818|gene1818|rna1817|rna1817 266 ihivlgagktdgamdaanmlkpglaagTIKCIGATTHDEYRKYVEKdpafeRRFVQVVVSEPSIEDSITMLRGLKE 341
                                        9999999999999999999999999996666666666666666666667666777777777777766666655444 PP

                                        HHHHHC.TS-EEE.EEE--C CS
                                        xxxxxx.xxxxxx.xxxxxx RF
                               CbiA  99 elkqry.gvpvlg.viprde 116
                                        +l++ y gv++ +  + +  
  gene1818|gene1818|rna1817|rna1817 342 RLEA-YhGVKIADsALVYAA 360
                                        4443.336666665444443 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.01
                                        TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                               CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................. 54 
                                         GvGKT la + a  l +++++ l++D+   +n  + + +l +  +                              
  gene1818|gene1818|rna1817|rna1817 588 TGVGKTELAKAVAMELFDDEKNMLVLDMSDYGNEMS-ITKLIGASAGyvgyneggaltepiknrpynvilldevdl 662
                                        69*************************655545555.344444333344456668888888888888888888888 PP

                                        .....................................................CCHCCCHHHHHHCHCHHHH..EE CS
                                        .....................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                               CbiA  55 .....................................................dlkrllellealgkkkalllkia 77 
                                                                                             d                   +i 
  gene1818|gene1818|rna1817|rna1817 663 ahqtvlnvlyqlldegrvtdgkgtvvdfrncvlimtsnlgqeimmrspeldenDK-----------------KEIE 721
                                        8888888888888888888888888887777666655544444444444444433.................4444 PP

                                        EEEEEEESS. CS
                                        xxxxxxxxxx RF
                               CbiA  78 gvvlnrvdge 87 
                                        ++vln+++++
  gene1818|gene1818|rna1817|rna1817 722 RLVLNKFGPP 731
                                        4444444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.4   1.6e+03      67      92 ..     140     165 ..     122     167 .. 0.77
   2 ?    6.0   0.0     0.018       6.4      10      40 ..     181     211 ..     172     220 .. 0.79
   3 !   11.5   0.0   0.00036      0.13      13      54 ..     575     618 ..     563     622 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.4
                         Zeta_toxin  67 adpkkaseltqkdaselvekllqeai 92 
                                         ++++a ++++++a  +ve+++q ++
  gene1818|gene1818|rna1817|rna1817 140 RNSDDATDVMSRFAVNMVEQARQNVF 165
                                        46788888888888888888888776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                         Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdel 40 
                                        + s++++   +l+G pG GK+++ + +++ +
  gene1818|gene1818|rna1817|rna1817 181 ILSKKTKSNAILVGMPGVGKTAIVNGIAQLI 211
                                        55678888899*************9988765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00036
                         Zeta_toxin  13 qerPk.lillgGqpGAGKselaellkdele.rqgnvvrldpDdl 54 
                                        +++P+ + ll G +G GK+ela++++ el   ++n+++ld  d+
  gene1818|gene1818|rna1817|rna1817 575 EDKPIgAFLLLGPTGVGKTELAKAVAMELFdDEKNMLVLDMSDY 618
                                        46665467899******************9899******98776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00036      0.13      71     121 ..     159     209 ..     135     230 .. 0.71
   2 ?    5.1   0.0     0.054        19     103     121 ..     583     601 ..     572     620 .. 0.85
   3 ?   -0.9   0.0       3.6   1.3e+03      44      93 ..     733     786 ..     691     794 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00036
                                        HHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                        RsgA_GTPase  71 elealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallp 121
                                        + ++  +++++ + ++ +++ e+ ++ +++ ++lvG  GvGK++++n +++
  gene1818|gene1818|rna1817|rna1817 159 QARQNVFDPVIGRDEEIRQVIEILSKKTKSNAILVGMPGVGKTAIVNGIAQ 209
                                        333333555555555555555566666667789**************9875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.054
                                        EEECSTTSSHHHHHHHHCT CS
                        RsgA_GTPase 103 vlvGqSGvGKStLinallp 121
                                        +l+G++GvGK+ L +a++ 
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAM 601
                                        799**********988765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.6
                                        HTT-EEEEEEE-GGG--HHH....HHHHHHHHHHHTTSEEEE--TTTHTTHHHH CS
                        RsgA_GTPase  44 ekgiepvivlnKiDlleeee....eleelkeelealgyevllvsaktkegleel 93 
                                         ++i+ vi++n +D  +  +    ++ elk++l+  ++++ + s  + + +e++
  gene1818|gene1818|rna1817|rna1817 733 VNRIDNVIYFNNLDRESMYKileyQMAELKKRLNGKNISFEISSGVRDDVIEKV 786
                                        467888889988888877776666777777777777776666666655555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0025       0.9       5      44 ..     173     212 ..     169     233 .. 0.82
   2 !    8.0   0.0    0.0073       2.6      21      43 ..     581     603 ..     542     609 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0025
                                        HHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT CS
                               TsaE   5 eetealgkklakalgdvilLeGdLGaGKTtlvrglakalg 44 
                                        ee++++ + l k++++  +L G  G+GKT++v g+a+ + 
  gene1818|gene1818|rna1817|rna1817 173 EEIRQVIEILSKKTKSNAILVGMPGVGKTAIVNGIAQLIA 212
                                        778888888988888899*****************99764 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0073
                                        EEEEEESTTSSHHHHHHHHHHHT CS
                               TsaE  21 vilLeGdLGaGKTtlvrglakal 43 
                                        ++lL G+ G+GKT l++++a +l
  gene1818|gene1818|rna1817|rna1817 581 AFLLLGPTGVGKTELAKAVAMEL 603
                                        3899**************99876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   7.3e-05     0.026       9      97 ..     178     266 ..     172     286 .. 0.62
   2 ?    3.9   0.0      0.11        39      22      46 ..     583     608 ..     577     681 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.3e-05
                             AAA_30   9 avealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg.ieastiakllkrlk.. 81 
                                        ++e l ++++  a+l+G +G GKt +++++++++++ +       pt k Ak  + ++g + a t ++   + +  
  gene1818|gene1818|rna1817|rna1817 178 VIEILSKKTKSNAILVGMPGVGKTAIVNGIAQLIANGEI------PTLKDAKIYNVDVGsMVAGTSHRGDFEERlk 247
                                        5555666667779********************997652......4444444444444422333333322222233 PP

                             AAA_30  82 ...grarlepgtllivDEa 97 
                                           ++a+ +pg +l +DE+
  gene1818|gene1818|rna1817|rna1817 248 slvKEAETTPGVILFIDEI 266
                                        4444455556666666665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                             AAA_30  22 vltGpAGtGKttalkal.reaweaag 46 
                                        +l Gp G GKt + ka+  e++++++
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVaMELFDDEK 608
                                        688************99556666553 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3     0.016       5.8      11      42 ..     187     216 ..     181     260 .. 0.77
   2 ?   -0.1   0.0       3.4   1.2e+03      21      80 ..     271     358 ..     270     483 .. 0.65
   3 !    9.1   0.0     0.005       1.8      15      42 ..     583     610 ..     577     638 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                                        TSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGei 42 
                                         +   +vG  G GK+ +++ +a+l    +Gei
  gene1818|gene1818|rna1817|rna1817 187 KSNAILVGMPGVGKTAIVNGIAQLIA--NGEI 216
                                        567789*****************985..7888 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.4
                                        TSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.......B-HHHCCHCEEEE-SS--S-TTSBHHHH........ CS
                                        xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxx........ RF
                           ABC_tran  21 GaGKStLlkllagllkp..teGeilldgkdlke.......qeleslrkeigvlpqepqlfpeltvren........ 79 
                                        GaGK+  ++  a++lkp  ++G+i++ g+ +++       ++  + r+ ++v+  ep++ + +t+ +         
  gene1818|gene1818|rna1817|rna1817 271 GAGKTDGAMDAANMLKPglAAGTIKCIGATTHDeyrkyveKDPAFERRFVQVVVSEPSIEDSITMLRGlkerleay 346
                                        6666666666666666666777777776666666666666666677777777777777777777544444445554 PP

                                        ...........H CS
                                        ...........x RF
                           ABC_tran  80 ...........e 80 
                                                   +
  gene1818|gene1818|rna1817|rna1817 347 hgvkiadsalvY 358
                                        444444333331 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.005
                                        EEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  15 aivGenGaGKStLlkllagllkpteGei 42 
                                         ++G++G GK+ L+k++a +l ++e ++
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFDDEKNM 610
                                        69**************998876655444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.018       6.4       2      36 ..     191     226 ..     190     234 .. 0.80
   2 !    9.3   0.0     0.004       1.4       2      24 ..     583     605 ..     582     622 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                       RNA_helicase   2 wlyGpsgeGKStlakeLakall.kklklkkkdsvys 36 
                                        +l+G +g+GK+ +++ +a+ ++ +++ + k+ ++y 
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIAQLIAnGEIPTLKDAKIYN 226
                                        589*************99998855667777677765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.004
                       RNA_helicase   2 wlyGpsgeGKStlakeLakallk 24 
                                        +l Gp+g+GK+ lak +a +l +
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFD 605
                                        589*************9999874 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.55     2e+02      30      91 ..     121     181 ..     102     186 .. 0.76
   2 ?    6.2   0.0      0.03        11       3      20 ..     191     208 ..     190     216 .. 0.87
   3 ?    6.9   0.0     0.019       6.7       3      28 ..     583     613 ..     582     690 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.55
                             AAA_33  30 sdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrrerarflkl 91 
                                        s ++r+r++ ++ ++k+  +r +d++++ ++++a  + +++r+ ++d    + +e ++++++
  gene1818|gene1818|rna1817|rna1817 121 SEDIRKRVE-EQSKNKKFDSRNSDDATDVMSRFAVNMVEQARQNVFDPVIGRDEEIRQVIEI 181
                                        455677777.566677788999999999*99*999999999999998666666666666655 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.03
                             AAA_33   3 llvGlpGsGKstlaerll 20 
                                        +lvG+pG+GK+  + +++
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIA 208
                                        79*********9988776 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.019
                             AAA_33   3 llvGlpGsGKstlaerllkklg.....avll 28 
                                        ll G+ G+GK+ la+ ++ +l      + +l
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFddeknMLVL 613
                                        678*************998876555555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       2.6   9.3e+02      90     118 ..      34      63 ..       5      71 .. 0.68
   2 !   12.5   0.3   0.00037      0.13       7      78 ..     184     272 ..     178     441 .. 0.71
   3 ?    3.3   0.0      0.26        95      12      35 ..     581     604 ..     574     616 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.6
                             AAA_19  90 lle..eaeeekklqeeellivDEfqdvd.elq 118
                                        ll+   +++++ l  + +l +DE  d++ +l+
  gene1818|gene1818|rna1817|rna1817  34 LLKviLNDQTSIL--CSVLSIDEKEDIKnKLI 63 
                                        4444322445555..889********985544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00037
                             AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkp.........eeillvaftgrAakelrerlaalgaeatTiH 73 
                                        + ++++ ++++ pG GKT ++++i +l+ + g+++          +   +va t++     +erl++l +ea+T  
  gene1818|gene1818|rna1817|rna1817 184 KKTKSNAILVGMPGVGKTAIVNGIAQLIAN-GEIPTlkdakiynvDVGSMVAGTSH-RGDFEERLKSLVKEAETTP 257
                                        55678899***********99998776654.4454456655555433444555544.3567777777777777666 PP

                             AAA_19  74 rlal..........l 78 
                                        ++ l           
  gene1818|gene1818|rna1817|rna1817 258 GVILfideihivlgA 272
                                        553344444444442 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.26
                             AAA_19  12 vllvtaGpGtGKTrvlkhivallv 35 
                                         +l++++ G GKT++ k++  +l 
  gene1818|gene1818|rna1817|rna1817 581 AFLLLGPTGVGKTELAKAVAMELF 604
                                        5799**********9988776655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.039        14       3      21 ..     191     209 ..     189     234 .. 0.83
   2 !    9.8   0.0    0.0025      0.88       3      29 ..     583     609 ..     582     626 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.039
                                        EEESSTTSSHHHHHHCHCT CS
                                Roc   3 vlvGdsgvGKtsllkrfve 21 
                                        +lvG  gvGKt +++ + +
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIAQ 209
                                        89***********997765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0025
                                        EEESSTTSSHHHHHHCHCT-CCC-EEE CS
                                Roc   3 vlvGdsgvGKtsllkrfvedkfsekek 29 
                                        +l+G +gvGKt l+k +  + f+++++
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFDDEKN 609
                                        79****************999998765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0037       1.3       3      25 ..     191     213 ..     189     219 .. 0.86
   2 ?   -1.7   0.0       6.5   2.3e+03      80     104 ..     241     266 ..     223     267 .. 0.78
   3 ?    5.8   0.0     0.032        12       3      24 ..     583     604 ..     581     611 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0037
                                        EEE--TTSSHHHHHHHHHHHH.. CS
                           NTPase_1   3 fiTGppGvGKtTlvkkvlellks 25 
                                        ++ G+pGvGKt +v+ +++l+++
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIAQLIAN 213
                                        789***************99976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.5
                                        HHHHHHHHHHHHHHHHH-.EEEE--- CS
                           NTPase_1  80 sfeelalealrkalsead.viviDEi 104
                                        +fee   + +++a ++++ ++ iDEi
  gene1818|gene1818|rna1817|rna1817 241 DFEERLKSLVKEAETTPGvILFIDEI 266
                                        48899889999999999955679**9 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.032
                                        EEE--TTSSHHHHHHHHHHHH. CS
                           NTPase_1   3 fiTGppGvGKtTlvkkvlellk 24 
                                        ++ Gp GvGKt l k v+ +l 
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELF 604
                                        678*************998885 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.016       5.9     116     177 ..     176     233 ..     105     259 .. 0.74
   2 !    8.8   0.0    0.0021      0.74     130     162 ..     580     612 ..     535     628 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                              T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqv 177
                                         ++ e+l+k   ++ + ++ G  g GKt +++ + + i++   +i t+ D+  ++++   +v
  gene1818|gene1818|rna1817|rna1817 176 RQVIEILSKK--TKSNAILVGMPGVGKTAIVNGIAQLIANG--EIPTLKDAKIYNVDVGSMV 233
                                        5666777777..78899999*****************9988..8999999887777655555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                              T2SSE 130 glilvsGgTgsGKttllyallkeinksderivt 162
                                        g +l+ G+Tg GKt l+ a+  e+ ++++++++
  gene1818|gene1818|rna1817|rna1817 580 GAFLLLGPTGVGKTELAKAVAMELFDDEKNMLV 612
                                        6899***************99999988777654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.024       8.5      10      49 ..     173     212 ..     153     219 .. 0.85
   2 ?   -2.2   0.4       9.8   3.5e+03      85     121 ..     434     472 ..     412     490 .. 0.59
   3 !   10.4   0.0    0.0013      0.48       8      60 ..     554     613 ..     549     616 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                                        HHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH- CS
                             ResIII  10 eaienlleklkskrdkrglikmaTGtGKTlvaaklierll 49 
                                        e i++++e l++k + +++++   G+GKT +   +++ ++
  gene1818|gene1818|rna1817|rna1817 173 EEIRQVIEILSKKTKSNAILVGMPGVGKTAIVNGIAQLIA 212
                                        55888999999899999*************9877776655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.8
                                        GEEEESSS-B--.........-SEEEEEHHHHHHTH... CS
                             ResIII  85 igkkvsgdkkka..kekdstnkkilvttiqsldadseee 121
                                        +++k+++ kk++   e++  + k ++++ ++l++++e +
  gene1818|gene1818|rna1817|rna1817 434 VCEKIEELKKSIepMEEAYLKEKRHIIESKKLKKRLEDT 472
                                        666677766666665555566666666777777777444 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0013
                                        HHHHHHHHT............TTS...EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                             ResIII   8 Qeeaienlleklks......krdk...rglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                        Q +a++++++++ +      ++dk    +l+  +TG+GKT +a +++ +l+    e+++l+l
  gene1818|gene1818|rna1817|rna1817 554 QSHAVDAVVDSILQsrvglsREDKpigAFLLLGPTGVGKTELAKAVAMELFDD--EKNMLVL 613
                                        77888888877666677777444456688999***********8888888886..4477765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00016     0.057       4      44 ..     171     211 ..     168     255 .. 0.86
   2 ?   -2.1   0.0       8.3     3e+03     109     128 ..     246     267 ..     240     276 .. 0.65
   3 ?   -1.5   1.0       5.6     2e+03     108     119 ..     433     444 ..     381     510 .. 0.59
   4 ?    7.1   0.0     0.013       4.7      24      50 ..     583     609 ..     572     678 .. 0.83
   5 ?   -0.8   0.0       3.3   1.2e+03      49      82 ..     737     765 ..     725     818 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00016
                           ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiienl 44 
                                        R++e++++ eil++++++   + G  g+GKta+++ i++  
  gene1818|gene1818|rna1817|rna1817 171 RDEEIRQVIEILSKKTKSNAILVGMPGVGKTAIVNGIAQLI 211
                                        9*********************************9988765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8.3
                           ATPase_2 109 llekikkkgkk..iiiiiDelq 128
                                        l+  +k+  +   +i++iDe+ 
  gene1818|gene1818|rna1817|rna1817 246 LKSLVKEAETTpgVILFIDEIH 267
                                        3444455544477888888875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 5.6
                           ATPase_2 108 lllekikkkgkk 119
                                        ++ eki++ +k 
  gene1818|gene1818|rna1817|rna1817 433 SVCEKIEELKKS 444
                                        333322222221 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.013
                           ATPase_2  24 fiYGpegsGKtaLlkeiienledkdky 50 
                                        ++ Gp g+GKt L k ++ +l d +k+
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFDDEKN 609
                                        678**************9999665543 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 3.3
                           ATPase_2  49 kyviyyialreesiskldefieeeeekkklekal 82 
                                        ++viy+++l +es  k+ e+     +  +l+k l
  gene1818|gene1818|rna1817|rna1817 737 DNVIYFNNLDRESMYKILEY-----QMAELKKRL 765
                                        46899999999988888777.....222222222 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.011       4.1      21      47 ..     186     212 ..     176     218 .. 0.82
   2 ?    6.3   0.0     0.022       7.7      23      43 ..     580     600 ..     572     608 .. 0.82
   3 ?   -1.4   0.0       5.7   2.1e+03      29      47 ..     678     696 ..     673     700 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                             AAA_29  21 lkgatlltGpsGsGKSTllDAiqalLv 47 
                                        +k++ +l+G  G+GK++++  i+ l+ 
  gene1818|gene1818|rna1817|rna1817 186 TKSNAILVGMPGVGKTAIVNGIAQLIA 212
                                        445899*************99998865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.022
                             AAA_29  23 gatlltGpsGsGKSTllDAiq 43 
                                        ga+ll Gp+G+GK+ l  A++
  gene1818|gene1818|rna1817|rna1817 580 GAFLLLGPTGVGKTELAKAVA 600
                                        689**********98877665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 5.7
                             AAA_29  29 GpsGsGKSTllDAiqalLv 47 
                                        G+   GK T++D  + +L+
  gene1818|gene1818|rna1817|rna1817 678 GRVTDGKGTVVDFRNCVLI 696
                                        66667*******8777775 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.25        91       3      22 ..     188     207 ..     186     275 .. 0.79
   2 !   11.7   0.0   0.00045      0.16       5      87 ..     582     673 ..     581     688 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.25
                             AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                         + +++G +g+GKT +++ +
  gene1818|gene1818|rna1817|rna1817 188 SNAILVGMPGVGKTAIVNGI 207
                                        56789*********998766 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00045
                             AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel...........aaeladyktl 69 
                                        +l+ Gp g+GKT lak       ++d ek +  ld  ++ +  s+++++ + +             + ++++y+++
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAV--AMELFDDEKNMLVLDMSDYGNEMSITKLIGASAGYvgyneggaltePIKNRPYNVI 655
                                        5899**************..55555666666666666666555666666655555677788899988888999999 PP

                             AAA_24  70 viDtideleelclaevir 87 
                                         +D +d + + +l+ +++
  gene1818|gene1818|rna1817|rna1817 656 LLDEVDLAHQTVLNVLYQ 673
                                        999999888777766655 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.9   6.9e+02       5      40 ..     174     208 ..     107     221 .. 0.60
   2 !   11.6   0.0    0.0005      0.18      15      50 ..     575     610 ..     564     624 .. 0.87
   3 ?   -0.5   0.0       2.6   9.5e+02     102     129 ..     650     677 ..     642     680 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.9
                    DNA_pol3_delta2   5 alkilskalksgrlahayLfeGdegigkkelalnla 40 
                                         +++  ++l++++ ++a+L  G  g+gk ++ + +a
  gene1818|gene1818|rna1817|rna1817 174 EIRQVIEILSKKTKSNAIL-VGMPGVGKTAIVNGIA 208
                                        3344444444444444444.3555555555555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0005
                    DNA_pol3_delta2  15 sgrlahayLfeGdegigkkelalnlakallceekne 50 
                                        +++   a+L+ G++g+gk ela+++a++l+ +ekn 
  gene1818|gene1818|rna1817|rna1817 575 EDKPIGAFLLLGPTGVGKTELAKAVAMELFDDEKNM 610
                                        5667789***********************999885 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.6
                    DNA_pol3_delta2 102 skkkiiiiedaekmtksAaNalLktlEE 129
                                          + +i+++++++ ++   N l ++l E
  gene1818|gene1818|rna1817|rna1817 650 RPYNVILLDEVDLAHQTVLNVLYQLLDE 677
                                        46889*****************999988 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.02       7.1       3      24 ..     191     212 ..     189     220 .. 0.89
   2 ?    6.2   0.0     0.025         9       3     109 ..     583     698 ..     581     711 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                              AAA_3   3 llegvPGlaktllvkalakald 24 
                                        +l g+PG++kt +v+ +a+ + 
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIAQLIA 212
                                        7899**************9875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.025
                              AAA_3   3 llegvPGlaktllvkalakaldlefkri......qftpdllPsdilGtevfeekekefefkkGpvfa...nlllad 69 
                                        ll g  G++kt l+ka+a  l  + k +       +  ++  + ++G++      +e    + p+ +   n++l d
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFDDEKNMlvldmsDYGNEMSITKLIGASAGYVGYNEGGALTEPIKNrpyNVILLD 658
                                        5566677777777777776664333332111111223334444444444333333333333334432333899*** PP

                              AAA_3  70 einrappktqsalleameerqvtvegethklpepflvlat 109
                                        e++ a   +   l + ++e +vt ++ t    ++ +++ t
  gene1818|gene1818|rna1817|rna1817 659 EVDLAHQTVLNVLYQLLDEGRVTDGKGTVVDFRNCVLIMT 698
                                        **********************987766544444444444 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0    0.0001     0.038      15      80 ..     539     606 ..     531     618 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.0001
                                        -HHHHHHHHHHH--S-HHHHHHHHHHH.HHHHT-SS-SS-E.EEEEEE-TTSSHHHHHHHHHHHHSTT CS
                             Torsin  15 nleeLekdlekklfGqhlvkklvvksv.kaylenekpkkpL.vlsfhGwtGtGknfvaeiiaenlyrd 80 
                                        +l e+++ +++++fGq  + + vv s+ ++ +   + +kp+ ++ + G tG Gk  +a+ +a +l+ d
  gene1818|gene1818|rna1817|rna1817 539 RLMEMSSRIKNRIFGQSHAVDAVVDSIlQSRVGLSREDKPIgAFLLLGPTGVGKTELAKAVAMELFDD 606
                                        67788999********8888888888637899999*****9567789****************99987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0036       1.3      33      97 ..     187     253 ..     157     285 .. 0.66
   2 ?    3.6   0.0      0.12        44      36      56 ..     582     602 ..     578     611 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0036
                             AAA_25  33 gelallaGapgtGKttlaldlalavatGk.pwlg..pvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                        ++ a+l+G pg+GKt+++  +a  +a G+ p l+  ++ +  +  + v++   + ++++Rl+ + +++
  gene1818|gene1818|rna1817|rna1817 187 KSNAILVGMPGVGKTAIVNGIAQLIANGEiPTLKdaKIYNVDVGSM-VAGTSHRGDFEERLKSLVKEA 253
                                        56689*****************999977624444542222222222.233333447777777766655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                             AAA_25  36 allaGapgtGKttlaldlala 56 
                                         ll G++g+GKt la  +a +
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAME 602
                                        5899**********9888776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0094       3.4       2      22 ..     191     211 ..     191     256 .. 0.79
   2 ?   -1.2   0.2       7.8   2.8e+03      35      81 ..     408     462 ..     390     475 .. 0.68
   3 !   12.5   0.1   0.00046      0.17       2      25 ..     583     618 ..     583     714 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0094
                             AAA_18   2 lltGtpGvGKttlakeLskrl 22 
                                        +l G+pGvGKt + + ++++ 
  gene1818|gene1818|rna1817|rna1817 191 ILVGMPGVGKTAIVNGIAQLI 211
                                        689*********999888765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 7.8
                             AAA_18  35 nglllevdpe.aldeskrldedkldklldaleenss.......aleegknlvidg 81 
                                         +l+    +    +e+++  +++l+++ +++ee  +       a+ ++k  +i++
  gene1818|gene1818|rna1817|rna1817 408 LELEKASLEIdLAREKDEQTMKRLESVCEKIEELKKsiepmeeAYLKEKRHIIES 462
                                        5555444444555777888888888888888887777777777556666666665 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00046
                             AAA_18   2 lltGtpGvGKttlakeLskrlgf.............g 25 
                                        ll G+ GvGKt+lak+++ +l f              
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMEL-FddeknmlvldmsdY 618
                                        589**************7775.333333343333331 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.39   1.4e+02       7      56 ..     190     238 ..     185     257 .. 0.79
   2 !   11.2   0.0    0.0005      0.18      13      61 ..     588     638 ..     582     662 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.39
                               ParA   7 avlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveee 56 
                                        a+l g  GVGK+ +   +A  + ++g    l Da iy  ++ +++  +++
  gene1818|gene1818|rna1817|rna1817 190 AILVGMPGVGKTAIVNGIAQLI-ANGEIPTLKDAKIYNVDVGSMVAGTSH 238
                                        6777889*******99999766.566677899999999999999876554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0005
                               ParA  13 GGVGKStvavnlAlaLakkglkvgllDaDiyGp..siprllgveeekpeqs 61 
                                         GVGK+ +a  +A++L + ++++ +lD+  yG   si +l+g++   +  +
  gene1818|gene1818|rna1817|rna1817 588 TGVGKTELAKAVAMELFDDEKNMLVLDMSDYGNemSITKLIGASAGYVGYN 638
                                        6*******************************6448899999887655544 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0049       1.8      26      79 ..     164     213 ..     146     232 .. 0.74
   2 ?   -3.1   0.2       9.6   3.5e+03     115     133 ..     418     436 ..     418     482 .. 0.60
   3 ?    5.0   0.0     0.032        12      52      85 ..     578     611 ..     548     635 .. 0.80
   4 ?   -2.0   0.0       4.6   1.6e+03     141     216 ..     691     766 ..     639     775 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0049
                             DUF815  26 klddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyae 79 
                                         +d ++g d++ ++++    + l++++ +n++L+G  G+GK ++v  + + +a+
  gene1818|gene1818|rna1817|rna1817 164 VFDPVIGRDEEIRQVI----EILSKKTKSNAILVGMPGVGKTAIVNGIAQLIAN 213
                                        5555555555555544....46777888999**************999887665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.6
                             DUF815 115 DLsFeeeeeeyksLksvLe 133
                                        DL+ e++e+++k L sv e
  gene1818|gene1818|rna1817|rna1817 418 DLAREKDEQTMKRLESVCE 436
                                        6677777777777777765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.032
                             DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli 85 
                                        p    LL G  G+GK  l ka+  e+ +++  ++
  gene1818|gene1818|rna1817|rna1817 578 PIGAFLLLGPTGVGKTELAKAVAMELFDDEKNML 611
                                        556789*****************99987764444 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.6
                             DUF815 141 envliyaTsNrRhLlpeklsdneeleeeeihaseaveeklsLsdRFGlwlgFykldqeeYleiveklakklglele 216
                                         n ++  TsN  + +  +  + +e++++ei++    +    L +R   ++ F++ld+e+  +i+e  +++l+ +l+
  gene1818|gene1818|rna1817|rna1817 691 RNCVLIMTSNLGQEIMMRSPELDENDKKEIERLVLNKFGPPLVNRIDNVIYFNNLDRESMYKILEYQMAELKKRLN 766
                                        5666667777543333333333333456666554444445678888888888888888888888877777666655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1      0.04        14       4      26 ..     190     212 ..     187     220 .. 0.85
   2 ?    5.9   0.0     0.024       8.6       4      34 ..     582     612 ..     580     618 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.04
                                        EEEEESTTSSHHHHHHHHHHHHH CS
                              SRP54   4 illvGlqGaGKTttlaKLaallk 26 
                                         +lvG+ G+GKT  +  +a+l+ 
  gene1818|gene1818|rna1817|rna1817 190 AILVGMPGVGKTAIVNGIAQLIA 212
                                        689***********999998876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.024
                                        EEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                              SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvll 34 
                                        +ll+G++G+GKT  +  +a  l +++k++l+
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAMELFDDEKNMLV 612
                                        699*********9999999988888777765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.76   2.7e+02       5      36 ..     171     204 ..     167     217 .. 0.73
   2 ?    9.0   0.0    0.0024      0.84      23      48 ..     583     608 ..     571     626 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.76
                                        -SHHHHHHHHHHH..H-SEEEEE--TTSSTTHHH CS
                               PhoH   5 ktkeQkeylealk..kndivfaiGpaGtGKtyla 36 
                                        +++e ++++e+l+  +++  + +G  G GKt + 
  gene1818|gene1818|rna1817|rna1817 171 RDEEIRQVIEILSkkTKSNAILVGMPGVGKTAIV 204
                                        55666788888885455588999********774 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                                        EEE--TTSSTTHHHHHHHHHHHHTTS CS
                               PhoH  23 faiGpaGtGKtylavalavealkkkk 48 
                                          +Gp+G GKt la a+a+e++ ++k
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFDDEK 608
                                        568*****************998765 PP

>> AAA_8  P-loop containing dynein motor region D4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0013      0.46      15      81 ..     177     257 ..     169     274 .. 0.67
   2 ?   -2.0   0.1       4.9   1.8e+03     208     242 ..     425     459 ..     412     463 .. 0.76
   3 ?    1.5   0.0      0.41   1.5e+02      22      42 ..     577     597 ..     575     620 .. 0.88
   4 ?   -1.2   0.0       2.9     1e+03      84     112 ..     653     681 ..     642     682 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                              AAA_8  15 rilRvlr.qprghaLlvGvgGsGrqsltk.LAafiaelelfqievtkkykeke............fredlkkllkk 76 
                                        ++  +l+ + +++a+lvG+ G G+  +++ +A  ia+ e+ +++  k y+++             f+e lk+l+k+
  gene1818|gene1818|rna1817|rna1817 177 QVIEILSkKTKSNAILVGMPGVGKTAIVNgIAQLIANGEIPTLKDAKIYNVDVgsmvagtshrgdFEERLKSLVKE 252
                                        455566514689************9987559999999998888777777665322333333333377777777777 PP

                              AAA_8  77 agikq 81 
                                        a +  
  gene1818|gene1818|rna1817|rna1817 253 AETTP 257
                                        76554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                              AAA_8 208 eieeelkesivkvlvevhssveelsekfleelkrk 242
                                        e + +  es+++ + e+ +s+e + e +l+e ++ 
  gene1818|gene1818|rna1817|rna1817 425 EQTMKRLESVCEKIEELKKSIEPMEEAYLKEKRHI 459
                                        44445556889999999999999999999997765 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.41
                              AAA_8  22 qprghaLlvGvgGsGrqsltk 42 
                                        +p g +Ll+G  G G+  l+k
  gene1818|gene1818|rna1817|rna1817 577 KPIGAFLLLGPTGVGKTELAK 597
                                        68999************9998 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 2.9
                              AAA_8  84 vvfllsdnqiieesfledinnlLntGevp 112
                                         v ll++ +++++++l+ + +lL +G v+
  gene1818|gene1818|rna1817|rna1817 653 NVILLDEVDLAHQTVLNVLYQLLDEGRVT 681
                                        588999********************996 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.83     3e+02     174     215 ..     155     196 ..     116     217 .. 0.72
   2 ?    1.8   0.9       0.3   1.1e+02     174     233 ..     418     472 ..     361     510 .. 0.63
   3 ?    7.6   0.0    0.0054         2       5      35 ..     583     613 ..     580     617 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.83
                                        HCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEES CS
                        ArsA_ATPase 174 glggvsieealeeleetkeeikkveeiltdpertsfrlVvip 215
                                        +++++  +++++ +  + eei++v eil+ ++++  +lV  p
  gene1818|gene1818|rna1817|rna1817 155 NMVEQARQNVFDPVIGRDEEIRQVIEILSKKTKSNAILVGMP 196
                                        455555556777777777777777777777777777777655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                                        HCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHT CS
                        ArsA_ATPase 174 glggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkky 233
                                        +l+  + e+++++le++ e+i+++++ ++  e          Ek  + E++++ k L+  
  gene1818|gene1818|rna1817|rna1817 418 DLAREKDEQTMKRLESVCEKIEELKKSIEPMEE-----AYLKEKRHIIESKKLKKRLEDT 472
                                        555555555666666666666666555544444.....2334445555555544444444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0054
                                        EEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                        ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvlli 35 
                                        l+ G  GVGKt ++ a+a++l + +k++l++
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVAMELFDDEKNMLVL 613
                                        566888***********************98 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2         4   1.4e+03     112     191 ..      54     150 ..      42     186 .. 0.51
   2 ?    0.1   0.1       1.9     7e+02      23      49 ..     186     213 ..     168     224 .. 0.77
   3 ?   13.4   0.0   0.00018     0.063      26      64 ..     582     618 ..     581     670 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4
                              DUF87 112 paaavqrsvleealdqakakeekeklssdepveklleelk...................kekeelrklknqaiarl 168
                                        ++++++ ++++++   ak + + ++  + e+++++l   +                   k+ +el ++++++++r+
  gene1818|gene1818|rna1817|rna1817  54 EKEDIKNKLIRRIGGFAK-QYNCTEPRIGESLARVLMAAEnggdsyvsvnalvlqlltvKSIKELISNSEDIRKRV 128
                                        555555555555555555.455555555555555555555444444444444444444433334444455555555 PP

                              DUF87 169 ldkledllrkggsfsnsstdlia 191
                                        +++ ++ +++ ++  ++ td+++
  gene1818|gene1818|rna1817|rna1817 129 EEQSKNKKFDSRNS-DDATDVMS 150
                                        54444444444444.44444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.9
                              DUF87  23 trHlAil.gsTGsGKSntvavLleelle 49 
                                        t++ Ail g+ G+GK+  v  + + +++
  gene1818|gene1818|rna1817|rna1817 186 TKSNAILvGMPGVGKTAIVNGIAQLIAN 213
                                        677788669**********999888875 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00018
                              DUF87  26 lAilgsTGsGKSntvavLleellekkgatililDpHGEY 64 
                                        ++ lg TG+GK+ +++    el  ++  ++l+lD+  +Y
  gene1818|gene1818|rna1817|rna1817 582 FLLLGPTGVGKTELAKAVAMELF-DDEKNMLVLDMS-DY 618
                                        6789*******************.**********94.55 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0089       3.2       2      21 ..     190     209 ..     189     268 .. 0.88
   2 ?   -0.7   0.0       4.2   1.5e+03      46      67 ..     375     399 ..     300     464 .. 0.63
   3 ?    0.7   0.0       1.5   5.3e+02       3      20 ..     583     600 ..     581     616 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0089
                                        EEEEESTTSSHHHHHHHHHT CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                        +++vG+p vGK+ ++n + +
  gene1818|gene1818|rna1817|rna1817 190 AILVGMPGVGKTAIVNGIAQ 209
                                        689*************9875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4.2
                                        EEEEEEECGGC.....SSHHHHHHHHH CS
                           MMR_HSR1  46 keielvDtpGl.....iegaseekglg 67 
                                          i lvDt+       +e  se +++ 
  gene1818|gene1818|rna1817|rna1817 375 VAIDLVDTACAsaviaLE--SEPQKIL 399
                                        346666666632222211..2222222 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.5
                                        EEEESTTSSHHHHHHHHH CS
                           MMR_HSR1   3 aivGrpNvGKStLinalt 20 
                                        +++G + vGK+ L +a  
  gene1818|gene1818|rna1817|rna1817 583 LLLGPTGVGKTELAKAVA 600
                                        689*********998875 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.053        19       2      21 ..     193     212 ..     192     230 .. 0.88
   2 ?   -0.6   0.1       2.7   9.6e+02     150     197 ..     403     452 ..     365     485 .. 0.53
   3 ?    3.1   0.0       0.2        71       2      31 ..     585     614 ..     584     632 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.053
                         ATP_bind_1   2 vGpaGsGKttfvgalseile 21 
                                        vG++G+GKt +v+ +++++ 
  gene1818|gene1818|rna1817|rna1817 193 VGMPGVGKTAIVNGIAQLIA 212
                                        8************9998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.7
                         ATP_bind_1 150 samlrlelPhvvvlnkfDllkeklekeleffedv.ealslllekee...eky 197
                                        s + +lel    +  ++Dl++ek+e+ ++++e v e++++l+++ e   e+y
  gene1818|gene1818|rna1817|rna1817 403 SKVWKLELEK--ASLEIDLAREKDEQTMKRLESVcEKIEELKKSIEpmeEAY 452
                                        4444444443..2335666665555555555543122222222222333333 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.2
                         ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvN 31 
                                        +Gp G+GKt + +a++  l + ++++ v+ 
  gene1818|gene1818|rna1817|rna1817 585 LGPTGVGKTELAKAVAMELFDDEKNMLVLD 614
                                        7*************9877766667777765 PP

>> Lge1  Transcriptional regulatory protein LGE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.4     0.012       4.5      30      56 ..     396     422 ..     382     423 .. 0.86
   2 ?    5.5   1.0     0.055        20      19      43 ..     425     449 ..     418     460 .. 0.78
   3 ?    1.0   0.3       1.4   5.1e+02      24      47 ..     461     484 ..     453     487 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.012
                               Lge1  30 kqleelklkvlkleleldlleeqierd 56 
                                        +++ + k kv+klele+++le   +r+
  gene1818|gene1818|rna1817|rna1817 396 QKILNAKSKVWKLELEKASLEIDLARE 422
                                        788999**************9777776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.055
                               Lge1  19 esklkeiesldkqleelklkvlkle 43 
                                        e++ k +es+++++eelk+ ++ +e
  gene1818|gene1818|rna1817|rna1817 425 EQTMKRLESVCEKIEELKKSIEPME 449
                                        5677888999999999998888777 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.4
                               Lge1  24 eiesldkqleelklkvlkleleld 47 
                                        e+++l k+le++kl + + e e d
  gene1818|gene1818|rna1817|rna1817 461 ESKKLKKRLEDTKLRLAQAERERD 484
                                        999************999998865 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.058        21       1      17 [.     193     209 ..     193     256 .. 0.80
   2 ?    3.9   0.0      0.19        69       1      28 [.     585     617 ..     585     623 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.058
                                        EE-TTSSHHHHHHHHHH CS
                             AAA_17   1 lGgPGsGKgtqceklve 17 
                                        +G+PG+GK+ +++ +++
  gene1818|gene1818|rna1817|rna1817 193 VGMPGVGKTAIVNGIAQ 209
                                        7*********9999887 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.19
                                        EE-TTSSHHHHHHHHHHHH.....TEEEEEHHH CS
                             AAA_17   1 lGgPGsGKgtqceklveky.....gfthlsaGd 28 
                                        lG+ G+GK+++++ ++ ++     +  +l ++d
  gene1818|gene1818|rna1817|rna1817 585 LGPTGVGKTELAKAVAMELfddekNMLVLDMSD 617
                                        699*********999977655555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1672  (0.0932567); expected 358.6 (0.02)
Passed bias filter:                      799  (0.0445647); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              50  [number of targets reported over threshold]
# CPU time: 0.89u 0.31s 00:00:01.20 Elapsed: 00:00:00.49
# Mc/sec: 5183.47
//
Query:       gene1819|gene1819|rna1818|rna1818  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-17   62.7   0.0    5.6e-17   62.4   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   3.2e-21   5.6e-17       1     212 [.       1     220 [.       1     221 [. 0.74

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 3.2e-21
                       TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsr......aleilldllaeeleleapmgkekepleeayeeiae 70 
                                        +lylVG G+ + +++T+r+l+a+k++  v+ +  +       l+ +++l+          g+++ p+++++ e+ +
  gene1819|gene1819|rna1818|rna1818   1 MLYLVGFGLHSYKDITLRGLEAVKNSTKVYLES-YtsihgePLDAFEELI----------GRKVYPADREMMEQTD 65 
                                        79***************************8777.2233233566665555..........4556777777777777 PP

                       TP_methylase  71 alaealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.... 142
                                        +++++  + ++V llv G Pl+++t+s ++  +ra+e+g++vevi   s+++ + ++   + + g++v+       
  gene1819|gene1819|rna1818|rna1818  66 RIVDESSE-ENVSLLVVGTPLFATTHSDIM--IRAKEKGVKVEVIHNASIINVLGCCGLYSYSFGRVVSIPYfagr 138
                                        77777777.58*******************..88888****************99998888886666655556555 PP

                       TP_methylase 143 lpglakeeereleallan....gdtlvllkaprk.............laelaelLkealyddttpvavveragted 201
                                        +     ++ + +++++ n     +tl ll+   +             + e+ ++L   l +++t++++++r g + 
  gene1819|gene1819|rna1818|rna1818 139 W-----KPTSFYDNIVRNyqnnLHTLCLLDIKADenrfmsvneaidqILEAGKILNSDLVNENTRIFAICRFGSPT 209
                                        3.....35555555555555559******555523466664444222444444444449999************** PP

                       TP_methylase 202 ervvrgtleel 212
                                        e++v g++++l
  gene1819|gene1819|rna1818|rna1818 210 EEMVYGRIGDL 220
                                        99999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1614.30
//
Query:       gene1820|gene1820|rna1819|rna1819  [L=1254]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.099   13.2   1.7        2.2    8.8   0.0    3.4  3  PIN_6     PIN domain of ribonuclease
        4.1    7.9  10.0         12    6.4   4.4    2.9  2  DUF2115   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> PIN_6  PIN domain of ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00025       2.2      13      81 ..     221     289 ..     214     292 .. 0.80
   2 ?   -3.8   0.1         2   1.8e+04      33      63 ..     401     433 ..     398     443 .. 0.54
   3 ?    1.5   0.1     0.048   4.3e+02      28      77 ..     924     972 ..     908     975 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                              PIN_6  13 lsslqnlaeklyttpeVvaEirdkkarerlellp.lelevrePspesvkkvtefakktGDlsvLSktDie 81 
                                        +ssl +++++  + + V +E+rd++a++ l +   ++++    +p ++  v + ak t+   v S++D  
  gene1820|gene1820|rna1819|rna1819 221 YSSLVSMGHSAPVAKGVADEVRDANAEKALRVKRaYDISQPPLNPGYIPQV-NLAKATNAKDVVSDADKA 289
                                        68899999999*******************997633666555577777776.588999999999988865 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                              PIN_6  33 irdkkare..rlellplelevrePspesvkkvt 63 
                                        i +k+ ++   l+    + ++ eP +++++k +
  gene1820|gene1820|rna1819|rna1819 401 INEKRLNRaqDLSSYLTKKHITEPIRRALQKLN 433
                                        555544431133333346667777666666654 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.048
                              PIN_6  28 eVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSk 77 
                                        +V +Ei++k+    l+++ ++ +v+  +++ ++ + +  +ktG+ + L k
  gene1820|gene1820|rna1819|rna1819 924 AVSEEIKKKTPDVPLDMA-VTDSVKGSEESFISEILSKIRKTGNGKALAK 972
                                        789999999999999994.67789999999*************9999987 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.4    0.0014        12       9      97 ..     456     545 ..     452     560 .. 0.68
   2 ?    3.5   0.3      0.01        91      25      91 ..     977    1044 ..     955    1066 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0014
                            DUF2115   9 lkkeaskisieDlmkisarlekeikklpekyrkelseslteylfeaykelkn.krsgdkseykeevideeel.kef 82 
                                        +  ++++ s eDl k++++le++ ++l+++ rk+   ++ + + ++ + + n +r+++++++k+ +i++e   +++
  gene1820|gene1820|rna1819|rna1819 456 ILTDVATSSAEDLAKAQQNLENSRAQLKPNGRKTNALNFLSKV-STERAIQNmNRKNEEMQNKAIQIQKEANeNNA 530
                                        556788999********************99998777776644.44556666667777777776666655431455 PP

                            DUF2115  83 lemleeqceeekeek 97 
                                        +++ ee   + +e++
  gene1820|gene1820|rna1819|rna1819 531 VKTAEEHLAKAAEQQ 545
                                        666666666655554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.01
                            DUF2115   25 sarlekeikklpekyrkelseslteylfeaykelkn.krsgdkseykeevideeelkeflemleeqce 91  
                                         ++++  e + + ++y kel++++++   +   +++n   ++++s  k+ +i +e++ +++++l+e   
  gene1820|gene1820|rna1819|rna1819  977 NGKVDGEKAGIVDEYNKELINDYMSSSSTVESQIRNnIIRKAESYAKGMNISTETFLNMISQLPESAI 1044
                                         55666677778899**********************87777788888888999988888888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1936  (0.107981); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.04u 0.35s 00:00:01.39 Elapsed: 00:00:00.53
# Mc/sec: 7146.61
//
Query:       gene182|gene182|rna182|rna182  [L=470]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-70  236.3   0.2    3.6e-70  235.5   0.2    1.4  1  Beta_lactamase3  Putative beta-lactamase-like family
    6.3e-05   22.5   0.0    0.00012   21.6   0.0    1.3  1  Lactamase_B_6    Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.5   0.2     4e-74   3.6e-70       1     213 [.       1     209 [.       1     210 [. 0.99

  Alignments for each domain:
  == domain 1  score: 235.5 bits;  conditional E-value: 4e-74
                Beta_lactamase3   1 MalvklsilkeksyylleteeesllfdypseiygknfrlgtfekrkkklkleiikvkaenidkifvtssnslgifFlkkd 80 
                                    M+l+k + + +ks+y+l+  e+++l+dyps iyg  f++++f+k +k+lkl+++k + ++id+i+v++s+slg++Fl+kd
  gene182|gene182|rna182|rna182   1 MVLIKRISSGSKSCYILQASEQTFLLDYPSRIYGMHFSFPSFNKGPKPLKLILPK-FVDDIDHILVSRSDSLGVLFLEKD 79 
                                    9999***************************************************.************************ PP

                Beta_lactamase3  81 vpiYiTkpvYeqlllrlkellslqvvyeeeeekqdlkiveeidierlkrnvkfiryneliyfddltieakaagtflGWvn 160
                                    +piYiT+pv+eq+l+++++ll l+++ye+eee  +  ++ +++ier+k n +fi++ne  +fdd+ i++k+agtf+GW n
  gene182|gene182|rna182|rna182  80 IPIYITEPVFEQILIKYQNLLRLSIHYEDEEE--HGISIRDANIERFKGNARFIKFNEKCQFDDVLITPKPAGTFIGWTN 157
                                    *******************************9..********************************************** PP

                Beta_lactamase3 161 yllevekkkilayisslslkkklslemkpiksdvlllnvnqlktkentiddfs 213
                                    yl+e +++++++y+ssl++k +ls e  +i+sd+l++n+++   ++++i++fs
  gene182|gene182|rna182|rna182 158 YLIELNNRRTIYYLSSLANKLRLSQESGSISSDYLIINTDR-PPSSHNIEEFS 209
                                    *************************************9998.9999******8 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.3e-08   0.00012      30     159 ..      54     170 ..      41     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.3e-08
                  Lactamase_B_6  30 ekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpedseelel..edid 107
                                     k ++++d+iL+s ++   lG    l+        ++ip+y t pv++   +  ++l + + + + e+++ +++   +i+
  gene182|gene182|rna182|rna182  54 PKFVDDIDHILVSRSD--SLGV---LFL------EKDIPIYITEPVFEQILIKYQNLLRLSIHYEDEEEHGISIrdANIE 122
                                    678999******9987..5883...333......468***********98888888887665555555554544227788 PP

                  Lactamase_B_6 108 eafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYa 159
                                    +   + + +k++ k +    +d+++it+  aG  +G t + i+ +  + +Y 
  gene182|gene182|rna182|rna182 123 RFKGNARFIKFNEKCQ----FDDVLITPKPAGTFIGWTNYLIELNNRRTIYY 170
                                    88899999***99964....678*******************9988877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3276.20
//
Query:       gene1821|gene1821|rna1820|rna1820  [L=288]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-14   54.0   2.8      0.029   15.2   0.0    5.6  6  WD40         WD domain, G-beta repeat
    5.5e-07   29.8   0.0        1.9    8.8   0.0    4.4  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
        4.5    7.1   0.0        4.5    7.1   0.0    3.2  5  Toxin_31     Scorpion acidic alpha-KTx toxin family


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   7.8e-05      0.46      10      37 ..      20      48 ..      14      49 .. 0.79
   2 !    5.1   0.0    0.0077        46      18      38 .]      77      97 ..      59      97 .. 0.79
   3 !   10.4   0.0   0.00016      0.96      12      36 ..     115     141 ..     104     141 .. 0.83
   4 !    7.0   0.0    0.0019        11       9      37 ..     157     184 ..     147     185 .. 0.72
   5 !   15.2   0.0   4.9e-06     0.029       4      37 ..     190     228 ..     187     229 .. 0.87
   6 ?   -2.6   0.1       2.2   1.3e+04      14      26 ..     247     259 ..     244     267 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.8e-05
                                       SSS.EEEEEEETTSSEEE.EEETTSEEEEE CS
                               WD40 10 Hss.vtslafspdgawla.sGsdDgtvriW 37
                                       H++ ++s+ ++ +++ ++ s+s Dg vri+
  gene1821|gene1821|rna1820|rna1820 20 HKDaIHSIETDFSQKRILtSCS-DGMVRIF 48
                                       8445999998888888762667.******7 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0077
                                       EETTSSEEEEEETTSEEEEEE CS
                               WD40 18 fspdgawlasGsdDgtvriWd 38
                                       f   g ++as+  +g+v iW+
  gene1821|gene1821|rna1820|rna1820 77 FLNQGEFIASSYFNGKVIIWK 97
                                       778899**99988*******6 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00016
                                        SEEEEE..EETTSSEEEEEETTSEEEE CS
                               WD40  12 svtsla..fspdgawlasGsdDgtvri 36 
                                        sv+++a  ++ d+  l++G+ Dg+vri
  gene1821|gene1821|rna1820|rna1820 115 SVNDIAgrWDGDSFTLFCGCSDGNVRI 141
                                        499999888888888999977*****8 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0019
                                        SS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40   9 GH.ssvtslafspdgawlasGsdDgtvriW 37 
                                         H ++v+s+  s   + ++sG++D +v +W
  gene1821|gene1821|rna1820|rna1820 157 CHrFGVSSV--SAMENGFVSGGMDYSVAVW 184
                                        476666666..333333679********** PP

  == domain 5  score: 15.2 bits;  conditional E-value: 4.9e-06
                                        EEEEESS.SSEEEEEEETTSSE....EEEEETTSEEEEE CS
                               WD40   4 lrtltGH.ssvtslafspdgaw....lasGsdDgtvriW 37 
                                        +  ++ H ++v+ +a++p +++    +a++s+Dg+v i+
  gene1821|gene1821|rna1820|rna1820 190 VARFRDHkGFVRNVAVCPTNSFkllcIATCSEDGSVIIY 228
                                        567899*666************998889********997 PP

  == domain 6  score: -2.6 bits;  conditional E-value: 2.2
                                        EEEEEETTSSEEE CS
                               WD40  14 tslafspdgawla 26 
                                        +sl++s +g  l+
  gene1821|gene1821|rna1820|rna1820 247 YSLSWSFSGFSLS 259
                                        5787777775554 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0026        16      37      76 ..      20      59 ..       9      66 .. 0.82
   2 !    5.4   0.0    0.0038        22      40      77 ..      71     108 ..      60     120 .. 0.83
   3 !    8.8   0.0   0.00032       1.9      45      70 ..     122     147 ..     106     169 .. 0.81
   4 !    4.8   0.0    0.0059        35      10      64 ..     216     269 ..     203     286 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                        ANAPC4_WD40 37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhsl 76
                                       ++  ++s++   + k +  ++sdg vr+++  +++  h l
  gene1821|gene1821|rna1820|rna1820 20 HKDAIHSIETDFSQKRILTSCSDGMVRIFSKGTAESPHDL 59
                                       6677888888899999**************9998887766 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0038
                        ANAPC4_WD40  40 evrsLaWkpdgklLavaysdgevrlldaesgkvvhsls 77 
                                          ++  + ++g+++a +y +g+v + + e g+  ++++
  gene1821|gene1821|rna1820|rna1820  71 PATKAIFLNQGEFIASSYFNGKVIIWKYEGGRFNKKYE 108
                                        5666678899****************999998877665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00032
                        ANAPC4_WD40  45 aWkpdgklLavaysdgevrlldaesg 70 
                                        +W  d   L  ++sdg+vr+l + s 
  gene1821|gene1821|rna1820|rna1820 122 RWDGDSFTLFCGCSDGNVRILTVDSS 147
                                        59999999*************99875 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.0059
                        ANAPC4_WD40  10 iAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrl 64 
                                        iA  +edg+++++  +g +  + ++   ++   sL+W+ +g  L v+y  ++ + 
  gene1821|gene1821|rna1820|rna1820 216 IATCSEDGSVIIYTRKGSEY-KSQKIILEEPCYSLSWSFSGFSLSVGYGSSKFKC 269
                                        56666777888877777663.3346677788999*************99887765 PP

>> Toxin_31  Scorpion acidic alpha-KTx toxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0   0.00075       4.5       7      20 ..      39      52 ..      37      56 .. 0.89
   2 ?   -3.2   0.6       1.3   7.5e+03      33      37 .]     132     136 ..     131     136 .. 0.83
   3 ?   -4.1   0.0       2.5   1.5e+04      19      29 ..     176     186 ..     176     187 .. 0.78
   4 ?    3.1   0.1     0.014        82       7      23 ..     218     236 ..     216     238 .. 0.72
   5 ?   -3.7   0.0       1.8   1.1e+04      24      35 ..     258     269 ..     256     269 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00075
                           Toxin_31  7 sCsDemCviYCkGe 20
                                       sCsD m  i+ kG 
  gene1821|gene1821|rna1820|rna1820 39 SCSDGMVRIFSKGT 52
                                       8***********96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                           Toxin_31  33 CkCsD 37 
                                        C CsD
  gene1821|gene1821|rna1820|rna1820 132 CGCSD 136
                                        88998 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2.5
                           Toxin_31  19 GeeYstGvCDG 29 
                                        G +Ys  v +G
  gene1821|gene1821|rna1820|rna1820 176 GMDYSVAVWEG 186
                                        66899999776 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.014
                           Toxin_31   7 sCsDemCv.iYC.kGeeYs 23 
                                        +Cs++  v iY  kG eY 
  gene1821|gene1821|rna1820|rna1820 218 TCSEDGSViIYTrKGSEYK 236
                                        89977655168659***95 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 1.8
                           Toxin_31  24 tGvCDGPqkCkC 35 
                                          v  G  k kC
  gene1821|gene1821|rna1820|rna1820 258 LSVGYGSSKFKC 269
                                        567778889999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2259.31
//
Query:       gene1822|gene1822|rna1821|rna1821  [L=850]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-58  196.8   0.0    4.1e-58  196.1   0.0    1.4  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.2e-22   79.8   0.0    3.1e-22   78.4   0.0    1.8  1  EFG_C        Elongation factor G C-terminus
    1.1e-17   64.0   0.0    3.3e-17   62.4   0.0    1.8  2  EFG_IV       Elongation factor G, domain IV
    1.8e-10   41.1   0.0    4.6e-10   39.8   0.0    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    3.6e-10   39.8   0.0    8.5e-10   38.6   0.0    1.6  1  EFG_II       Elongation Factor G, domain II
     0.0013   18.8   0.1     0.0038   17.3   0.1    1.8  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.086   12.7   0.1       0.77    9.7   0.0    2.3  2  SWIB         SWIB/MDM2 domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.1   0.0   1.6e-61   4.1e-58       1     183 [.      17     227 ..      17     349 .. 0.84

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 1.6e-61
                                        TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE............ CS
                           GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle............ 64 
                                        k+irni++i+hvDhGK+TLtd+L+ k++++sk   + ++ r++D++++E++rgiTiks+aisl+            
  gene1822|gene1822|rna1821|rna1821  17 KNIRNISVIAHVDHGKSTLTDCLVIKAKIVSK---DSGGGRYMDSREDEQQRGITIKSSAISLHfqvekevleayt 89 
                                        69****************************99...456689*********************************** PP

                                        ....TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTH CS
                           GTP_EFTU  65 ....ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlk 136
                                            ++++++linliD+PGHvdFs+ev+++lrv+Dga++vvd+v+G+++qte+vl +a +e++ + +++NK+Dr++
  gene1822|gene1822|rna1821|rna1821  90 kegdTNGTEFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDCVDGICVQTETVLGQAMNERIIPTLVLNKLDRAI 165
                                        998669********************************************************************** PP

                                        HHHHHHHHHHHHHHHHH.............HHHHHHHHHTTT......TTEEEEEEBTTTTBTHH.....H CS
                           GTP_EFTU 137 aelkeiveevkqklsrk.............eeklekygekge......kevpvvfgSalkgegvk.....t 183
                                         el+  +e++ + l+r+             +          +      ++ ++ f+S+l+g+g++      
  gene1822|gene1822|rna1821|rna1821 166 LELEYPPEKLGEVLRRRvegfnaklstlgyN---------FKveslmpEKNEISFCSGLQGWGFTlrlfaR 227
                                        ***********99977777775544444322.........225556666789**********998544440 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0   1.2e-25   3.1e-22       1      85 [.     731     816 ..     731     819 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.2e-25
                                        EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE..TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEE CS
                              EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqd.asgrviieaeiPlaeligfateLrslTkGegsfsmef 75 
                                        +l+EPi++vei++p++y+g++++ l s+rG+ ed+++  ++++++i++++P++e+++f+++L+s ++G++  sm+f
  gene1822|gene1822|rna1821|rna1821 731 ILYEPIYEVEITTPNDYSGAITTILLSKRGTAEDFKTLpGNDTTMITGTLPVKESFTFNEDLKSGSRGKAGASMRF 806
                                        589***********************************99************************************ PP

                                        EEEEE--HHH CS
                              EFG_C  76 sgYeevpgdk 85 
                                        s+Y+ +pg++
  gene1822|gene1822|rna1821|rna1821 807 SHYSTLPGSL 816
                                        ******9986 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.81   2.1e+03       4      43 ..     573     607 ..     570     626 .. 0.63
   2 !   62.4   0.0   1.3e-20   3.3e-17      14     120 ..     621     728 ..     611     729 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.81
                                        ESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTT CS
                             EFG_IV   4 ayrEtirkpvkereeklkkqsggdgqyakvileiePleeg 43 
                                         y E i+  v+  e k+ k    +++  ++++++ePl+++
  gene1822|gene1822|rna1821|rna1821 573 TYFEGITSAVT--EPKMTK---SANKHNRIYMTVEPLDQN 607
                                        55555555555..334444...367778999*****9833 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 1.3e-20
                                        CHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEE CS
                             EFG_IV  14 kereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvt 89 
                                        k +   + ++ +++ ++ k+i++  P+  +  n +vd+tkg+++ +e++e+v++Gf+ a+++Gpl+ge ++++k++
  gene1822|gene1822|rna1821|rna1821 621 KTMITNFREKLEIRDDWVKKIWCYAPE-INPLNLLVDATKGISIINEIKEHVNTGFRAAVNDGPLIGEVMRGLKFE 695
                                        5566678899999*************5.7*********************************************** PP

                                        EEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                             EFG_IV  90 Lldgslhe..vdsseaafkpaarralkeallkA 120
                                        L d++lh+  ++++  ++ + +++ +k  ll+A
  gene1822|gene1822|rna1821|rna1821 696 LRDAVLHAdaIHRGINQLLQPVKNLCKGLLLAA 728
                                        **************9998888888887777766 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   1.8e-13   4.6e-10       2      74 .]     400     481 ..     399     481 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 1.8e-13
                                        EEEEEEEEESEEETTEEEEEEC.TCTTSEE........EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSS CS
                        GTP_EFTU_D2   2 tvalgrvysGtlkkGdevrilg.ndtskke........ivtrissletfhededeavaganaGvivaikgledaii 68 
                                        ++a+grv+sG++ +G+++r+    +++ +e        +   + ++ +++++   +v+ ++aG+i++i+g++d+++
  gene1822|gene1822|rna1821|rna1821 400 FIAFGRVFSGKIYPGMKIRVQEpGYSPTSEelsntslvHNKSVLRTVVMMGRGYKDVPNCPAGNIIGIVGIDDCLK 475
                                        69******************7777777777********999********************************999 PP

                                        TTCEEE CS
                        GTP_EFTU_D2  69 vGdtlt 74 
                                        ++ t+t
  gene1822|gene1822|rna1821|rna1821 476 KTGTIT 481
                                        999885 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   3.3e-13   8.5e-10       3      67 ..     497     560 ..     496     563 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 3.3e-13
                             EFG_II   3 ePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkrey 67 
                                         Pv+++a+++k  +d  kl++ L++l++ Dp   ver++  ++  +++ G lHlei ++ l+ +y
  gene1822|gene1822|rna1821|rna1821 497 SPVVKVAVSAKRPEDLGKLQEGLNKLAQSDPLCLVERNDK-GQSTIACAGSLHLEICLKDLQDQY 560
                                        59*****************************999999976.88999***************9988 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.5e-06    0.0038       3     114 .]      23     160 ..      21     160 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                                        EEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE............................... CS
                           MMR_HSR1   3 aivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke............................... 47 
                                         ++ +   GKStL   l+ ++ ivs+  g  r +  ++ +  + +                               
  gene1822|gene1822|rna1821|rna1821  23 SVIAHVDHGKSTLTDCLVIKAKIVSKDSGGGRYMDSREDE--Q-Qrgitikssaislhfqvekevleaytkegdtn 95 
                                        56667788**********9999999999999988877654..2.22455667777888888888999999999999 PP

                                        .....EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                           MMR_HSR1  48 .....ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                             i+l+D pG ++       ++ ++ a  + +d +l+vvd+  +++  + e++     ++++  +lvlnk
  gene1822|gene1822|rna1821|rna1821  96 gteflINLIDSPGHVD-------FSSEVTAALRvTDGALVVVDCV-DGICVQTETVLGQAMNERIIPTLVLNK 160
                                        99999********665.......666666666647********99.445445455544433334444677776 PP

>> SWIB  SWIB/MDM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0003      0.77      33      73 ..     553     594 ..     550     595 .. 0.90
   2 ?   -0.1   0.0      0.35     9e+02      19      31 ..     633     645 ..     617     650 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                               SWIB  33 ennLqdpedkreilcDekLkklfggkdr.vkffempkllkkH 73 
                                         ++Lqd+  k  i+ D+ L + f+g  + v+ ++m+k  +kH
  gene1822|gene1822|rna1821|rna1821 553 LKDLQDQYAKIPIIADDPLVTYFEGITSaVTEPKMTKSANKH 594
                                        689********************777556***********99 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.35
                               SWIB  19 srpevvkklweYI 31 
                                         r + vkk+w Y 
  gene1822|gene1822|rna1821|rna1821 633 IRDDWVKKIWCYA 645
                                        58999******95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (850 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 5105.32
//
Query:       gene1823|gene1823|rna1822|rna1822  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-09   36.0   0.3    9.1e-09   35.5   0.3    1.4  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    3.8e-06   27.3   0.2    5.3e-06   26.8   0.2    1.3  1  Histone        Core histone H2A/H2B/H3/H4


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.3     1e-12   9.1e-09       2      52 ..      13      63 ..      12      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1e-12
                                       XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTT CS
                      CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkek 52
                                       ++Pi+r k+Im+  +d++ki  +++++ ++++e+f++e+ + + +++ k++
  gene1823|gene1823|rna1822|rna1822 13 RFPISRLKRIMQLNEDIGKIGASVPVVASKAIEMFLTEIVELTLKEARKKS 63
                                       79*************************************999988877765 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   5.9e-10   5.3e-06      54     112 ..       3      60 ..       2      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.9e-10
                                        HHHXXSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            Histone  54 yqkstdlliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllak 112
                                        +q+s +++  ++p++R ++ i++ +++  +i a+ +++  +a+E +l+e+ e++ + a+
  gene1823|gene1823|rna1822|rna1822   3 RQESQKKKLTRFPISR-LKRIMQLNEDIGKIGASVPVVASKAIEMFLTEIVELTLKEAR 60 
                                        58899999999*****.***********************************9977666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 586.85
//
Query:       gene1824|gene1824|rna1823|rna1823  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.0   0.1        0.1   12.3   0.1    1.3  1  DUF434    Protein of unknown function (DUF434)


Domain annotation for each model (and alignments):
>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   5.7e-06       0.1      10      28 ..      41      59 ..      36      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-06
                             DUF434 10 ryLLnRGYpkksalelVgn 28
                                        yLLn+ Y+k++al+ ++n
  gene1824|gene1824|rna1823|rna1823 41 EYLLNNKYNKEKALDHISN 59
                                       6**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 729.59
//
Query:       gene1825|gene1825|rna1824|rna1824  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-32  111.7   0.0    2.5e-32  111.7   0.0    2.0  3  DUF382    Domain of unknown function (DUF382)
    9.8e-21   73.4   1.3    2.1e-20   72.3   1.3    1.6  1  PSP       PSP


Domain annotation for each model (and alignments):
>> DUF382  Domain of unknown function (DUF382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.42   3.8e+03      75      95 ..      25      45 ..      18      47 .. 0.68
   2 !  111.7   0.0   2.8e-36   2.5e-32       2     123 ..      51     170 ..      50     174 .. 0.93
   3 ?   -3.2   0.1      0.96   8.6e+03      69      91 ..     283     305 ..     270     318 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.42
                             DUF382 75 eeekslkekarekvqpklgkl 95
                                       +++++ ++++re +q + + l
  gene1825|gene1825|rna1824|rna1824 25 RSSSNKRQRKREALQNRYEDL 45
                                       455667888888888887766 PP

  == domain 2  score: 111.7 bits;  conditional E-value: 2.8e-36
                             DUF382   2 kPevvevaDvdakdPvllvklKssknvvpvpshWsskreylsgkrglekkpfelPkfikeTgieelrealeekeee 77 
                                        +Pe++e++D +++dP++++++K+  + vpvp+hW+s    +   r++ k+++++P+ + +Tgi elr++++e+e+ 
  gene1825|gene1825|rna1824|rna1824  51 HPELLEIEDSTCPDPIFHNEMKGRGG-VPVPKHWKSSSGRMF-PRSYYKPSYRIPRNVMKTGIPELRKMMKEREAG 124
                                        8*********************9877.*******87766555.34799**************************** PP

                             DUF382  78 kslkekarekvqpklgkldidykkLhdaFfklqtkPkllkfGdlyy 123
                                        +sl+e++rek+ pklg+  +d+++L++aFf  + kP+l+++G+++ 
  gene1825|gene1825|rna1824|rna1824 125 MSLRERIREKLYPKLGRSLVDQQVLYEAFFLEKGKPYLSNYGEFFE 170
                                        *******************************************996 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.96
                             DUF382  69 ealeekeeekslkekarekvqpk 91 
                                        e++  +++e++  e+ r+ v  k
  gene1825|gene1825|rna1824|rna1824 283 ERVVINNNETTQDESPRAEVATK 305
                                        44444444444445555555444 PP

>> PSP  PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   1.3   2.3e-24   2.1e-20       2      45 ..     182     225 ..     181     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 2.3e-24
                                PSP   2 PGviSaeLReALglqegqlPpWiykMqrlGlPPgYpklkipGln 45 
                                        PGviS+eL eALg+ +g++PpW+++Mq++G+PP+Yp+ kipGln
  gene1825|gene1825|rna1824|rna1824 182 PGVISNELMEALGIDDGAPPPWLFNMQKHGMPPSYPDAKIPGLN 225
                                        9******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 1948.15
//
Query:       gene1826|gene1826|rna1825|rna1825  [L=287]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-52  177.7   0.0    3.4e-52  177.4   0.0    1.1  1  Pkinase         Protein kinase domain
    9.8e-37  126.6   0.0    1.2e-36  126.3   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    3.3e-07   29.4   0.0    6.7e-06   25.1   0.0    2.0  2  Pkinase_fungal  Fungal protein kinase
     0.0019   17.6   0.0     0.0031   16.9   0.0    1.4  1  Kinase-like     Kinase-like
     0.0078   15.6   0.1      0.013   14.9   0.1    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4   0.0   9.4e-56   3.4e-52       2     248 ..       5     245 ..       4     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 9.4e-56
                                        EEEEEEEEESSEEEEEEEETTTT.EEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEE CS
                            Pkinase   2 ekleklGeGsfGkVykaveketg.kivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylv 76 
                                        + ++kl +G  G+Vy     ++g +++A+K i  + +k      + rE+kil  ++h++iv+l+++f +++ ++++
  gene1826|gene1826|rna1825|rna1825   5 RFIRKLSRGVHGTVYLLETIDSGkEKMACKSILWKYKKY-----AEREVKILSLISHKRIVKLLDFFPRDSGIFII 75 
                                        5689999********998887762689***999886665.....458***************************** PP

                                        EE--TTEBHHHHHH....HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTE........EEE- CS
                            Pkinase  77 leyveggeladlle....rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekge........lKit 140
                                        leyv++g+l+++++    ++   +++ + +++ qi+ gl+ylH+k+i HrD+Kp+NiLi++           +K++
  gene1826|gene1826|rna1825|rna1825  76 LEYVNCGSLHEMIShlveNNYRAPNCLVWSVLVQIADGLRYLHNKHIAHRDIKPSNILIERV-FvqsgalieFKLC 150
                                        *************9998666669999999*******************************52.224566889**** PP

                                        SGTTSEESSSSCSBCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHH CS
                            Pkinase 141 DFGlakelessskltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqleki 216
                                        DF +akel +++++ ++ gt+ Y+APEv++++ y  ++D+WslGv +yellt k pf+g++++e    +++q    
  gene1826|gene1826|rna1825|rna1825 151 DFAMAKELYEGNRTCEIAGTPSYMAPEVVSREYYNISIDIWSLGVSVYELLTLKKPFEGRSRDE-LFGMIKQ---- 221
                                        **********************************************************776666.4445555.... PP

                                        HHHCTSHH...HHHTTS-HHHHHHHHHHT-SS CS
                            Pkinase 217 lkilgetkeklpeaseiseeakdllkkllkkd 248
                                                  lp+  + + e+ +l++++l+k+
  gene1826|gene1826|rna1825|rna1825 222 --------ARLPQVISPDIELERLIRRCLSKN 245
                                        ........344445555667777777777665 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.0   3.4e-40   1.2e-36       2     245 ..       5     245 ..       4     253 .. 0.89

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 3.4e-40
                                        EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEE CS
                        Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepll 77 
                                        ++ +kl +G  G+V+  +     ++ ++k a K++  ++++       +e+ki++ ++h++ivkll +  +++ ++
  gene1826|gene1826|rna1825|rna1825   5 RFIRKLSRGVHGTVYLLETI---DSGKEKMACKSILWKYKKY----AEREVKILSLISHKRIVKLLDFFPRDSGIF 73 
                                        57899**********99988...888999*****97777666....679*************************** PP

                                        EEEE--TTEBHHHHHHHTCTTTSBHHHHH..HHHHHHHHHHHHHHHTTEEEST-SGGGEEEEE.......TTEEEE CS
                        Pkinase_Tyr  78 ivteyvkgGdLlkfLrkkekekltlkdll..sfalqvAkGmeyLeskklvHrdlaarNvLlse.......nkvvki 144
                                        i++eyv+ G+L++++ +  +++ +  + l  s+ +q+A+G++yL++k++ Hrd+   N+L+++           k+
  gene1826|gene1826|rna1825|rna1825  74 IILEYVNCGSLHEMISHLVENNYRAPNCLvwSVLVQIADGLRYLHNKHIAHRDIKPSNILIERvfvqsgaLIEFKL 149
                                        ***************99988888888865227889***************************999988655578** PP

                                        -STTTHEETTTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHT CS
                        Pkinase_Tyr 145 sDfGLardiekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklke 220
                                        +Df++a+++++ +++    e      +mapE+++++ ++ + D+Ws Gv ++E++t  ++p++g +  e++ ++k+
  gene1826|gene1826|rna1825|rna1825 150 CDFAMAKELYEGNRTC---EIAGTPSYMAPEVVSREYYNISIDIWSLGVSVYELLT-LKKPFEGRSRDELFGMIKQ 221
                                        *********6555544...4556679******************************.799*********9999875 PP

                                        TEES-BBTTSBHHHHHHHHHHT-SS CS
                        Pkinase_Tyr 221 gkrlekpekcpeelyelmkkcweed 245
                                          rl++  +   el +l+++c++++
  gene1826|gene1826|rna1825|rna1825 222 -ARLPQVISPDIELERLIRRCLSKN 245
                                        .7999999999**********9886 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.018        64     158     201 ..      16      61 ..       5      68 .. 0.82
   2 !   25.1   0.0   1.9e-09   6.7e-06     311     390 ..     106     183 ..      97     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.018
                     Pkinase_fungal 158 TtcwrarkegergkeyvvK.dsWrdaerk.sEaelLkkaeergveg 201
                                         t++  ++ ++ ++++  K + W+ ++   +E+++L  ++++ +  
  gene1826|gene1826|rna1825|rna1825  16 GTVYLLETIDSGKEKMACKsILWKYKKYAeREVKILSLISHKRIVK 61 
                                        5799999999998899999568**999888*********8877655 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 1.9e-09
                     Pkinase_fungal 311 alrDaIkghrsLflkagiLHrDiSenNilitds..kkegerkglLiDLDlakelsddssesgarertGTleFmaie 384
                                        +l +   g+r L+ ++ i HrDi   Nili     ++ +  +  L D+ +akel +    +  +e  GT+ +ma e
  gene1826|gene1826|rna1825|rna1825 106 VLVQIADGLRYLH-NKHIAHRDIKPSNILIERVfvQSGALIEFKLCDFAMAKELYEG---NRTCEIAGTPSYMAPE 177
                                        667777899****.****************966534445666667777777777753...34488*********** PP

                     Pkinase_fungal 385 vlkgee 390
                                        v++ e 
  gene1826|gene1826|rna1825|rna1825 178 VVSREY 183
                                        *98654 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.6e-07    0.0031     151     254 ..     108     211 ..      72     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.6e-07
                        Kinase-like 151 lqlirlaanLqakglvhgkftvdnllldekg.......glmlggft...aLvragtkvvlseve..kgfaPpEllg 214
                                        +q+     +L++k + h ++++ n+l ++ +        ++l +f    +L+       +   +   ++  pE+++
  gene1826|gene1826|rna1825|rna1825 108 VQIADGLRYLHNKHIAHRDIKPSNILIERVFvqsgaliEFKLCDFAmakELYEGNRTCEI---AgtPSYMAPEVVS 180
                                        6666666899***************87765422223334677777511134333333333...2334577778887 PP

                        Kinase-like 215 srggytrknktkmthkldaWqlGlviyriwclklPltlat 254
                                        +           + +++d W lG+++y +  lk P++   
  gene1826|gene1826|rna1825|rna1825 181 R---------EYYNISIDIWSLGVSVYELLTLKKPFEGRS 211
                                        7.........357799*******************98754 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   3.5e-06     0.013     124     166 ..     107     152 ..      80     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-06
                                Kdo 124 lkavgrliaklhragvnHadlyaknillqqee...eeeaeiwliDl 166
                                        l +++   + lh+ ++ H+d+ + nil++      ++ +e+ l D+
  gene1826|gene1826|rna1825|rna1825 107 LVQIADGLRYLHNKHIAHRDIKPSNILIERVFvqsGALIEFKLCDF 152
                                        67999999********************998843344455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1815.10
//
Query:       gene1827|gene1827|rna1826|rna1826  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-44  149.6  14.6    1.2e-43  149.2  14.6    1.1  1  Cation_efflux    Cation efflux family
  ------ inclusion threshold ------
        3.9    7.1   9.6       0.19   11.4   1.4    2.2  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
          4    7.3   6.7       0.36   10.7   0.5    2.5  2  DUF2976          Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2  14.6     2e-47   1.2e-43       5     198 ..      28     221 ..      26     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 2e-47
                      Cation_efflux   5 llanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllg 80 
                                        l++ l++++ el + + tnSl+llad++h l+d+++++++ll+l +++kp+++r++fGy+r+e +g+lvs+ l+++
  gene1827|gene1827|rna1826|rna1826  28 LFIILMFMFLELWGHWKTNSLSLLADSLHLLVDILGFIVSLLSLSWAKKPSSKRMTFGYHRIEIIGSLVSIGLIWA 103
                                        678889********************************************************************** PP

                      Cation_efflux  81 lavfllleaiqklikegereihaglalvvalvslvvnlalllilrragrkl....rsaalkaaalhvlgDaltslg 152
                                        ++ +l +e+++k++  ++ ei+ g+ + +a+v+++vn ++++ l+    ++    ++ +++a ++hv gD+++s+g
  gene1827|gene1827|rna1826|rna1826 104 AVGYLAVESFHKYL--HPSEIDGGMFFSIAVVGFFVNCVCVYVLHYDEYQHklkhKNLNIRATYVHVVGDLIQSVG 177
                                        **************..99************************9999888888888********************* PP

                      Cation_efflux 153 vlvsalvillfnlksgplaDpvaslligliilysalkllkeslseL 198
                                        v+++ +v+++++ k   ++D ++++++++++l+s+  +lk+ +++L
  gene1827|gene1827|rna1826|rna1826 178 VIIAGMVTYFYPSKA--IVDVICTMFFSVLVLVSTGFVLKDGVRIL 221
                                        **********97777..***************************99 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.3    0.0045        27      64     172 ..      29     137 ..      23     145 .. 0.69
   2 ?   11.4   1.4   3.2e-05      0.19      46     103 ..     122     210 ..     115     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0045
                    Cation_ATPase_C  64 vtllvffltlllfgisekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllq 139
                                        +++l+f++  l+ ++++      s  a ++ +++ +l+ i+ +l+l   +++  k + +   ++ +++ l+s++l+
  gene1827|gene1827|rna1826|rna1826  29 FIILMFMFLELWGHWKTNS---LSLLADSLHLLVDILGFIVSLLSLSWAKKPSSKRMTFGYHRIEIIGSLVSIGLI 101
                                        3334444444323333332...246677888888788878888877777777777455557889999999999777 PP

                    Cation_ATPase_C 140 vlivyv...pglnavfgtaplsleewlialllalvv 172
                                         + v +     ++++++ +++++ +++ +++++++v
  gene1827|gene1827|rna1826|rna1826 102 WAAVGYlavESFHKYLHPSEIDGGMFFSIAVVGFFV 137
                                        76665534446*********************9997 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.2e-05
                    Cation_ATPase_C  46 iskkmlrriliqgllqalvtllvffltlllfgisekenkls...............................snya 90 
                                        i+++m++ i+++g+++  v+++v+ +  ++++ ++k+ +++                               +++ 
  gene1827|gene1827|rna1826|rna1826 122 IDGGMFFSIAVVGFFVNCVCVYVLHYDEYQHKLKHKNLNIRatyvhvvgdliqsvgviiagmvtyfypskaiVDVI 197
                                        7899***************99999999999999998888889999******************************* PP

                    Cation_ATPase_C  91 qtmaFitlvlsqi 103
                                         tm+F +lvl+++
  gene1827|gene1827|rna1826|rna1826 198 CTMFFSVLVLVST 210
                                        *********9876 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5     6e-05      0.36      29      83 ..      91     146 ..      82     149 .. 0.85
   2 ?   -2.7   0.9       0.9   5.4e+03      79      79 ..     185     185 ..     163     213 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6e-05
                            DUF2976  29 illgLvlaavaflaVakaalkkfnei.segkaewgkfgltlvvGvvllvvviwLlt 83 
                                        i++ Lv  ++   aV + a+++f+ + + +  + g f +++vvG+ +  v+++ l 
  gene1827|gene1827|rna1826|rna1826  91 IIGSLVSIGLIWAAVGYLAVESFHKYlHPSEIDGGMFFSIAVVGFFVNCVCVYVLH 146
                                        566677777777889999999**999899999*********************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.9
                            DUF2976  79 i 79 
                                         
  gene1827|gene1827|rna1826|rna1826 185 T 185
                                        2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2001.59
//
Query:       gene1828|gene1828|rna1827|rna1827  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-46  157.5   0.0    2.8e-46  157.2   0.0    1.1  1  Methyltransf_4   Putative methyltransferase
    2.1e-06   27.4   0.0    3.4e-06   26.7   0.0    1.3  1  MTS              Methyltransferase small domain
    2.9e-05   24.7   0.0      6e-05   23.7   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
    8.6e-05   22.4   0.0    0.00022   21.1   0.0    1.6  2  Methyltransf_31  Methyltransferase domain
    0.00012   21.2   0.1    0.00023   20.3   0.0    1.4  2  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
    0.00039   21.1   0.0     0.0011   19.6   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
    0.00069   20.2   0.0     0.0039   17.8   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
     0.0064   16.0   0.0      0.011   15.3   0.0    1.4  1  DOT1             Histone methylation protein DOT1
  ------ inclusion threshold ------
       0.02   14.2   0.0      0.037   13.3   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
      0.044   13.6   0.0      0.056   13.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
      0.066   13.1   0.0       0.15   12.0   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
       0.16   11.9   0.0       0.26   11.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.0   1.8e-49   2.8e-46       2     163 ..      45     206 ..      44     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 1.8e-49
                                        -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEE CS
                     Methyltransf_4   2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekif 77 
                                        +p +++iGcG+G+fl++ A+knP  n+lG+Eir kv a+v ++ie+l++ N  ++r++al +l+++++ g+l+kif
  gene1828|gene1828|rna1827|rna1827  45 RPDFVDIGCGYGKFLMKVAEKNPGRNVLGLEIRDKVCAYVRANIENLRIPNAGVMRTNALIFLPNIFSGGQLSKIF 120
                                        789************************************************************************* PP

                                        EES-----SGGGGGGSTTSHHHHHHHHHHEEEEEEEEEEESHHHHHHHHHHHHHCSTTEEESSCCCSCCTCHCHHC CS
                     Methyltransf_4  78 ilFPDPwfKkrhhKrRllqpellkelarvLkkgGvlelaTDveeyaeemlkvleeeplferlskeeeleeeplsvl 153
                                        ilFPDP+fKkr++K R++ +++++ +++ L+++G l++ TDve+++  m++v+ +++ fe ls+ee++++++  ++
  gene1828|gene1828|rna1827|rna1827 121 ILFPDPHFKKRKQKGRIVCQQMMEVYEYLLRNEGRLYISTDVEDLFDYMVDVILAHKGFEPLSEEEMNKDPLFYMI 196
                                        *********************************************************************9988555 PP

                                        CCSSTTCCCC CS
                     Methyltransf_4 154 riatkyeqkv 163
                                           t +  ++
  gene1828|gene1828|rna1827|rna1827 197 SKDTDEALRA 206
                                        5555554444 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.3e-09   3.4e-06      30     137 ..      43     158 ..      35     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.3e-09
                                        CTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC........EEEEE-STTTTSTTS- CS
                                MTS  30 elsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle........vevvasdvleeveekk 97 
                                        +++ + +D+GcG+G   +++a+++p  +v  +++  +  +  ++n+e+ ++         + ++  ++++  +  k
  gene1828|gene1828|rna1827|rna1827  43 NRRPDFVDIGCGYGKFLMKVAEKNPGRNVLGLEIRDKVCAYVRANIENLRIPnagvmrtnALIFLPNIFSGGQLSK 118
                                        456678****************************************999988865555555566677788888788 PP

                                        EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEE CS
                                MTS  98 fdlivsNPPfhagkatelavaeeliaeAkeaLkegGeLli 137
                                        + ++   P f++ k++   v +++++  +  L+++G+L+i
  gene1828|gene1828|rna1827|rna1827 119 IFILFPDPHFKKRKQKGRIVCQQMMEVYEYLLRNEGRLYI 158
                                        8888899*******************************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0     4e-08     6e-05       2      71 ..      49     122 ..      48     154 .. 0.75
   2 ?   -2.0   0.0       4.2   6.3e+03      53      80 ..     160     185 ..     138     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4e-08
                                        EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BS..SSTTTEEEEEEE CS
                    Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaed.lp..fedgsfDlvvss 71 
                                        +d+GcG G++++++a++ +  +v+g++i ++ ++++r+++e+ ++ n+ +++ +a   lp  f  g+   +++ 
  gene1828|gene1828|rna1827|rna1827  49 VDIGCGYGKFLMKVAEKNPGRNVLGLEIRDKVCAYVRANIENLRIpNAGVMRTNALIfLPniFSGGQLSKIFIL 122
                                        7****************856********************8865567777777764424444555566555555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.2
                                        SBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                    Methyltransf_25  53 gdaedlpfedgsfDlvvssgalhhlsde 80 
                                         d+edl   d  +D++++  +++ ls+e
  gene1828|gene1828|rna1827|rna1827 160 TDVEDLF--DYMVDVILAHKGFEPLSEE 185
                                        4555542..3467777775556666655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.4e-07   0.00022       6      58 ..      47      98 ..      42     124 .. 0.88
   2 ?   -1.4   0.0       1.2   1.8e+03      98     111 ..     147     160 ..     127     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
                    Methyltransf_31  6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveF 58
                                        ++D+GCG G+++ + a e +p+ +v G++i  ++  + r+n ++l + n+ +
  gene1828|gene1828|rna1827|rna1827 47 DFVDIGCGYGKFLMKVA-EKNPGRNVLGLEIRDKVCAYVRANIENLRIPNAGV 98
                                       578**************.99***********************9999887755 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                    Methyltransf_31  98 ervlkpggillied 111
                                        e +l+++g+l i++
  gene1828|gene1828|rna1827|rna1827 147 EYLLRNEGRLYIST 160
                                        44455555555443 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.6e-07   0.00023     171     258 ..      10     103 ..       2     110 .. 0.84
   2 ?   -2.9   0.1       1.7   2.5e+03      35      56 ..     148     171 ..     141     177 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.6e-07
                    tRNA_U5-meth_tr 171 vyrq..vensftqPnaav..nekmleWalevtqeskgdllelycGnGnfslalarnf..ekvlateiakssveaaq 240
                                         yrq    n f   n  +  n + ++Wa     +++ d++++ cG+G f + +a++   ++vl  ei     +  +
  gene1828|gene1828|rna1827|rna1827  10 LYRQraHANPFKDSNIVIppNPQSVDWASYFEINRRPDFVDIGCGYGKFLMKVAEKNpgRNVLGLEIRDKVCAYVR 85 
                                        455411567788888887657899****************************998754489*************** PP

                    tRNA_U5-meth_tr 241 yniaankidnvqiirlsa 258
                                        +ni++ +i n  ++r  a
  gene1828|gene1828|rna1827|rna1827  86 ANIENLRIPNAGVMRTNA 103
                                        **********99999876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                    tRNA_U5-meth_tr  35 yrlraefrlwhe..eddlyyimfd 56 
                                        y lr e rl+     +dl+ +m d
  gene1828|gene1828|rna1827|rna1827 148 YLLRNEGRLYIStdVEDLFDYMVD 171
                                        666666666643115567766665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.5e-07    0.0011       1      38 [.      49      86 ..      49     105 .. 0.83
   2 ?   -2.2   0.0       4.9   7.4e+03      61      73 ..     165     176 ..     140     189 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.5e-07
                    Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedake 38
                                       ++iGcG G +l+ ++ek+p+ +++g++i  ++++  ++
  gene1828|gene1828|rna1827|rna1827 49 VDIGCGYGKFLMKVAEKNPGRNVLGLEIRDKVCAYVRA 86
                                       69**************************9999855444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.9
                    Methyltransf_12  61 ldggssfDlvvas 73 
                                        l++   +D+++a+
  gene1828|gene1828|rna1827|rna1827 165 LFD-YMVDVILAH 176
                                        222.256666665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.6e-06    0.0039       1      43 [.      49      93 ..      49     111 .. 0.84
   2 ?   -0.4   0.0       1.2   1.8e+03      47      74 ..     157     182 ..     134     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT- CS
                    Methyltransf_11  1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl 43
                                       +d+GcG G+++ ++a++   ++v+g+++ +++ +++++++++ ++
  gene1828|gene1828|rna1827|rna1827 49 VDIGCGYGKFLMKVAEKNpgRNVLGLEIRDKVCAYVRANIENLRI 93
                                       59*************55556*******************998775 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                        ETTEECCCTSS-TT-EEEEEEES-CCC- CS
                    Methyltransf_11  47 fvvadaeklpfednsfDlvvssevlhhv 74 
                                        ++  d+e+  + d  +D+++++  ++ +
  gene1828|gene1828|rna1827|rna1827 157 YISTDVED--LFDYMVDVILAHKGFEPL 182
                                        57777887..567788888888777655 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.4e-06     0.011      39      88 ..      41      90 ..      31     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.4e-06
                                       T--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
                               DOT1 39 nlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88
                                       ++++   FvD+G G G+  +++a +   ++ +G+Ei d+ +++ +++ e 
  gene1828|gene1828|rna1827|rna1827 41 EINRRPDFVDIGCGYGKFLMKVAEKNPGRNVLGLEIRDKVCAYVRANIEN 90
                                       6677778**********************************999887665 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.5e-05     0.037      66     110 ..      48      93 ..      40     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                        EEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-S CS
                               CMAS  66 lLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldl 110
                                         +diGcG+G+ +++ +e+  + +v+gl + ++  +++++++++l +
  gene1828|gene1828|rna1827|rna1827  48 FVDIGCGYGKFLMKVAEKNpGRNVLGLEIRDKVCAYVRANIENLRI 93 
                                        68********988888764389**********99999999998765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.056      21      55 ..      43      79 ..      34     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                    Methyltransf_23 21 raggrvLdiGcGtGillevlrengf..svtgvDlspe 55
                                       +++   +diGcG+G +l   +e+    +v g +++++
  gene1828|gene1828|rna1827|rna1827 43 NRRPDFVDIGCGYGKFLMKVAEKNPgrNVLGLEIRDK 79
                                       6778899*******9888776664445999*999865 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.8e-05      0.15      15      64 ..      45      94 ..      38     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.8e-05
                    Methyltransf_18 15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagle 64
                                          ++DiG+  g   +++++++  ++v+  +i+++ ++  ++nie+ ++ 
  gene1828|gene1828|rna1827|rna1827 45 RPDFVDIGCGYGKFLMKVAEKNPGRNVLGLEIRDKVCAYVRANIENLRIP 94
                                       55789***************************************998765 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.26      24      75 ..      43      92 ..      34     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                    Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                       +++ + vD+G+G g     +a   k+ + +v+g+++++++++  ++  e+l+
  gene1828|gene1828|rna1827|rna1827 43 NRRPDFVDIGCGYGKFLMKVAE--KNPGRNVLGLEIRDKVCAYVRANIENLR 92
                                       667899******9854444444..46799**********9998888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1338.49
//
Query:       gene1829|gene1829|rna1828|rna1828  [L=310]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2095.55
//
Query:       gene1830|gene1830|rna1829|rna1829  [L=458]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-21   74.7   0.0    1.5e-20   74.0   0.0    1.3  1  Hexokinase_1     Hexokinase
    1.8e-05   24.3   0.4    6.6e-05   22.4   0.4    2.0  2  Hexokinase_2     Hexokinase
  ------ inclusion threshold ------
       0.13   12.3   0.5       0.82    9.7   0.1    2.3  2  Lac_bphage_repr  Lactococcus bacteriophage repressor


Domain annotation for each model (and alignments):
>> Hexokinase_1  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0   0.0   2.4e-24   1.5e-20       5     196 ..      33     236 ..      29     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 2.4e-24
                                        HHHHH---HHHHHHHHHHHHHHHHHHHS.S.STS--EE----S---S--E...EEEEEEEESSSEEEEEEEEEE.. CS
                       Hexokinase_1   5 ilkqfelsdeklkelvdrfleemekgLakekeslkmlptyvtrlPtGkek...GtylAlDlGgtnlRvllveLl.. 75 
                                         + +f ++d +++e++++f e + k  + + ++  +l + ++ + ++ e+     +l +D+Ggt+l++  + +   
  gene1830|gene1830|rna1829|rna1829  33 KVTSFPIQDFEIQEIKKAFSERIAKAQEAS-SDGDFLRSHIDLIKSEVEHprcSSFLVIDVGGTHLKIGEILIDfs 107
                                        567899999**********99999998855.446788888777777666544488****************88888 PP

                                        .....SSS........-EEEEEEEEE--GGGGGSBHHHHHHHHHHHHHHHHHHH....ST..T-S-EEEEEEE-SS CS
                       Hexokinase_1  76 .....ges........kveitqekykipeelktgtaeeLFdfiakciaefleeegeekkeekeeeelplGftFSFP 138
                                               +        + +    ky+  +++ +++  +  +++a++iaef  +e  ++        ++  +t+S+P
  gene1830|gene1830|rna1829|rna1829 108 frkcgV-NplcfdgviECSPSFYKYPDTSKIPNENRITWNEWVAEKIAEFYGQEPPKS---G----IDGCLTLSYP 175
                                        876650.1555554334444444555555566667777889************98764...4....999******* PP

                                        EE-SBTT--EE-S--TT---..TT-T.TSBHHHHHHHHHHHTT-SEEEEEEE-HHHHHHHH CS
                       Hexokinase_1 139 veqtsldegtlirwtKgfai..kdve.gkdvvqllqealerkglpvkvvalvNDTvgtlls 196
                                        + qts++++t+ r+tK+f    ++ + g +vv++l+++l+ ++++v+v+++vND+++t ++
  gene1830|gene1830|rna1829|rna1829 176 LLQTSINHATIERVTKNFCFkvDESTfGVNVVEALNSSLRDRNVNVHVNCVVNDSTATYMA 236
                                        *****************8774344336********************************98 PP

>> Hexokinase_2  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.99   5.9e+03     189     213 ..     165     189 ..     156     201 .. 0.71
   2 !   22.4   0.4   1.1e-08   6.6e-05       2     238 ..     246     448 ..     245     450 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.99
                                        EEESHHHHHSTTHHHHHHHHHHHHH CS
                       Hexokinase_2 189 gvdGslyekypkfrerlqealrell 213
                                        g+dG l   yp  ++ +++a+ e +
  gene1830|gene1830|rna1829|rna1829 165 GIDGCLTLSYPLLQTSINHATIERV 189
                                        7888888888888888877775544 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.1e-08
                                        EEEEESSSEEEEEEEEGGG-GGGTTTS-TTSEEEEE--GGGTTTT-SS-..--HHHHHH..HHHSSSTTS-HHHHC CS
                       Hexokinase_2   2 iGlIlGtGtNacyleklsnieklegkkeksgemviNtEwgafgdegklpllrtkyDkel..deespnpgeqlfEkm 75 
                                        iG++lGtGtN +   k +  e         + +++N Ewg+ +       ++t+ D ++  d e+ n   ++++ +
  gene1830|gene1830|rna1829|rna1829 246 IGIVLGTGTNSSFCVKKKGSE---------EMVLYNSEWGSTNV---PRSILTEADLAVitDLETRNISYNIIDVL 309
                                        9**********9998876666.........5689********75...6667999997653388899999******* PP

                                        CSHHHHHHHHHHHHHHHHC.TSSSC....CCCSTTSS-THHHHHHHC--BTT-HHHHHHHHHCCS---.-HHHHHH CS
                       Hexokinase_2  76 iSGmYLGelvrlvlldlieekllfkgkseklktpysldteflseieedesedleevrevleellglesvteedlei 151
                                         +G  L +++ + l +l+ e +      +   +++ l++++ s+i        e  ++++ e ++l++       i
  gene1830|gene1830|rna1829|rna1829 310 AGGCKLNDIIFNRLKNLHPE-VYE----KYAGEEEVLRSMIHSAIT-------EPSKSIFGEDIQLHR-------I 366
                                        *****************964.443....233445556777777777.......456788888866654.......7 PP

                                        HHHHHHHHHHHHHHHHCHHHHHHHHH-.....SSEEEEEESHHHHHSTTHHHHHHHHHHHHHT--S.-SEEEEE-- CS
                       Hexokinase_2 152 vrevceavsrRaarlvAagiaallkklgkeekekvtvgvdGslyekypkfrerlqealrellgeepekkvklklae 227
                                        +  +++   +R+ ++ +a   a+++   k + ++vt   +G  +    k re l+  +++    +p+ +v+l+   
  gene1830|gene1830|rna1829|rna1829 367 LISMINHFNTRGIKILGALSSAIIDSCMK-DVQEVTLILNGMAFS-NRKLREALEVEMKNA---HPNIDVNLVFFG 437
                                        777888889****************9545.46899999***9998.556666666666555...577999999999 PP

                                        -TTTHHHHHHH CS
                       Hexokinase_2 228 dGsgvGAAlia 238
                                        ++s+ G A + 
  gene1830|gene1830|rna1829|rna1829 438 NASLEGSAFVS 448
                                        99999999875 PP

>> Lac_bphage_repr  Lactococcus bacteriophage repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.17     1e+03      23      35 ..      22      34 ..      19      37 .. 0.85
   2 ?    9.7   0.1   0.00014      0.82      10      24 ..     135     149 ..     129     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.17
                    Lac_bphage_repr 23 WVSFDGkPltDeV 35
                                       W S DGk  t  V
  gene1830|gene1830|rna1829|rna1829 22 WSSVDGKQTTNKV 34
                                       *******998877 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                    Lac_bphage_repr  10 aklvDdskvDWdeWV 24 
                                         k+  ++++ W+eWV
  gene1830|gene1830|rna1829|rna1829 135 SKIPNENRITWNEWV 149
                                        566689********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2772.52
//
Query:       gene183|gene183|rna183|rna183  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-05   23.3   0.0       0.08   12.9   0.0    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00036   21.0   3.2    0.00061   20.2   0.9    2.1  2  HAGH_C         Hydroxyacylglutathione hydrolase C-terminus
  ------ inclusion threshold ------
      0.059   12.9   0.0      0.094   12.2   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.3e-05      0.08      42      72 ..      63      93 ..      61      97 .. 0.87
   2 !    8.4   0.0   0.00033         2     132     158 ..     124     150 ..     112     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                   GGGEEEEE-SBSSHHHHTTGGGCTTHHCCEE CS
                    Lactamase_B 42 pkdvdavilTHlHlDHiGglgglveatdvpv 72
                                    +++ +++ TH H DH  g ++++e  +  +
  gene183|gene183|rna183|rna183 63 KRRLVYLFTTHKHQDHSCGIPYIMENSPDTQ 93
                                   68899*******************9887665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00033
                                    SCCEEEEEETTCCEEEECTTTSSHHCC CS
                    Lactamase_B 132 ghghgvveygggkvlftGDallagetg 158
                                    + ++   +y +g++l tGD+l+    g
  gene183|gene183|rna183|rna183 124 HTMDSFCYYVDGRFLATGDTLFFLGCG 150
                                    555666789************976655 PP

>> HAGH_C  Hydroxyacylglutathione hydrolase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.13   7.9e+02       1      16 [.     182     197 ..     182     205 .. 0.79
   2 !   20.2   0.9     1e-07   0.00061      39      80 .]     206     244 ..     199     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.13
                         HAGH_C   1 EYtlsNlkFalsvepd 16 
                                    +Y ++N++F++++ p 
  gene183|gene183|rna183|rna183 182 DYNEQNIRFTEELYPV 197
                                    699*******998775 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1e-07
                         HAGH_C  39 pstladEkktNpFLRldepevqkavg.eevevfaaLRelKdnF 80 
                                      +l+dE+++NpF+ l++  +   ++ +e e++  LRe+K++F
  gene183|gene183|rna183|rna183 206 FLRLKDEMEYNPFFNLRR--IF--TKgSEEEMMGNLRERKNRF 244
                                    5689************86..32..232559************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05     0.094      29      65 ..      64     100 ..      50     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                    .SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHH CS
                  Lactamase_B_2  29 ppidaVllthaHyDHlaglltlrelrpkklplyapkg 65 
                                    +++  ++ th+H DH +g++ + e +p+  ++ + +g
  gene183|gene183|rna183|rna183  64 RRLVYLFTTHKHQDHSCGIPYIMENSPDTQRISGFEG 100
                                    4788899****************97776655655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1389.05
//
Query:       gene1831|gene1831|rna1830|rna1830  [L=275]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-34  119.7   0.0    1.4e-34  119.4   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.4   0.0   7.6e-39   1.4e-34       3     210 .]      21     233 ..      19     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 7.6e-39
                                        HHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS.HHHHHHHHHHHHH CS
                       AP_endonuc_2   3 aaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear.reesvdalkraie 77 
                                        + +++G d++ +f+++++ + +  + + + ++++++++ l+  ++ +++ +   +    ++   ++s ++l + +e
  gene1831|gene1831|rna1830|rna1830  21 QMESLGLDTCAIFLKSQRRYLA--PPMREGVAEMFKARVLHPEMIVPHGSYLINFG---NPSlVDKSMECLVDDLE 91 
                                        56799***************97..68888888888888888888888887777655...45567788********* PP

                                        HHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHH CS
                       AP_endonuc_2  78 laaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldav 151
                                        +++ LG+++ ++hpG   +   +++  +++ +  ++n+++     +++++++E++ag+g+  g   eel++++++v
  gene1831|gene1831|rna1830|rna1830  92 RCRSLGIKMYNMHPG---SDKTRDKTGCLRSISHNINKALSR--VQDITILIENMAGQGNVVGStfEELRDIIEKV 162
                                        ***************...88999999****************..67****************************** PP

                                        TTTT.EEEEEEHHHHHHH......TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                       AP_endonuc_2 152 dspn.vgvclDtgHllia......eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                        + +  +g+clDt+Hl+ a      ee+++++++++++      +k++Hi+D+k  lg+++drh++ig+G+i
  gene1831|gene1831|rna1830|rna1830 163 EERErIGICLDTCHLFGAgfdittEERFAEVMERFDRIiglkfLKAMHINDSKEALGSRKDRHESIGKGMI 233
                                        *********************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1815.38
//
Query:       gene1832|gene1832|rna1831|rna1831  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-12   47.8  14.3    1.8e-12   47.4  14.3    1.2  1  Syntaxin    Syntaxin
     0.0092   15.1   3.8      0.016   14.3   3.8    1.3  1  DUF2252     Uncharacterized protein conserved in bacteria (DU
  ------ inclusion threshold ------
      0.069   13.5  13.0       0.71   10.3   7.9    2.3  2  Syntaxin_2  Syntaxin-like protein
       0.18   12.3   9.3        2.5    8.7   0.1    3.1  3  Spectrin    Spectrin repeat
       0.21   11.5   3.5       0.38   10.7   0.5    2.5  2  HSBP1       Heat shock factor binding protein 1
       0.22   10.7  10.6        1.8    7.7  10.6    2.0  1  Sec1        Sec1 family
       0.31   10.9   2.5        5.4    6.9   0.0    2.8  3  DUF2721     Protein of unknown function (DUF2721)
       0.97    9.3   5.2       0.31   10.9   1.2    1.9  2  Folliculin  Vesicle coat protein involved in Golgi to plasma 
          1    9.9   4.3        1.2    9.6   1.6    2.1  2  IZUMO       Izumo sperm-egg fusion, Ig domain-associated
        2.9    7.9   5.8        2.9    7.9   0.2    2.6  3  Noelin-1    Neurogenesis glycoprotein
        3.2    8.3  16.9          2    8.9   1.8    3.3  3  DUF16       Protein of unknown function DUF16
        4.2    6.4  14.1        1.4    7.9   6.5    2.1  2  Atg14       Vacuolar sorting 38 and autophagy-related subunit
        6.9    6.7  11.7        2.3    8.2   2.3    2.5  2  Laminin_II  Laminin Domain II


Domain annotation for each model (and alignments):
>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4  14.3   1.3e-15   1.8e-12       1     188 [.       1     190 [.       1     200 [. 0.90

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 1.3e-15
                           Syntaxin   1 leeffkeveeikkeiekleeevkklkkqneesktst.raksvk.lkkrmesdikeikkraesvkarLeaLdksnke 74 
                                        +++f+k+ ++i ++ie+l++  ++++   ++  +s+ ++++ k l ++++ + ++ +  ++++k+r+++++ +  e
  gene1832|gene1832|rna1831|rna1831   1 MQDFLKDSKRILNDIETLNSYTNSIDYLSSQKNSSVlSKEEEKgLNNQIDVLNERFRVLSRNIKERIDSFSSETTE 76 
                                        899***************98877766554444333214444455******************************** PP

                           Syntaxin  75 nekksgegsavdRirksqtaaLrkklkevmteynelrekireeykerieRrlevtGkevseeeieelietgesevf 150
                                         ek s++      +rk + +a +kkl e+++ y+e + ++re+  ++ + ++ ++  +++e+eiee i +++ + +
  gene1832|gene1832|rna1831|rna1831  77 LEKDSKKDRFYHETRKIHLHAQSKKLTEAINRYRESQIRHREDEVDKFRLQYIIAKPDATEKEIEEFIGDDDGTKV 152
                                        ************************************************************************9998 PP

                           Syntaxin 151 lqkllqeqrgarealseieeRhkevlelekslkeLhql 188
                                         +     + +a+  l+e e+R+k+++++e+ ++e+ +l
  gene1832|gene1832|rna1831|rna1831 153 ASAYALGAHSAQGILEEAENRKKNIKKIEEMVQEIVDL 190
                                        888888889999**********************9876 PP

>> DUF2252  Uncharacterized protein conserved in bacteria (DUF2252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   3.8   1.2e-05     0.016     110     226 ..      17     130 ..       6     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                            DUF2252 110 avesYrealrdlaerealdewyeridvelleeatseeakgvvrkalekarkrtreklldkltelee..gkrrikdd 183
                                        +++sY+++++ l++++++++  ++ +  l ++   +  ++++r + ++ ++r  +++ ++ tele+  +k+r+  +
  gene1832|gene1832|rna1831|rna1831  17 TLNSYTNSIDYLSSQKNSSVLSKEEEKGLNNQ--IDVLNERFRVLSRNIKER-IDSFSSETTELEKdsKKDRFY-H 88 
                                        5789************9999974433322222..222333333333333333.345666677776542444444.6 PP

                            DUF2252 184 ppkllrlseaereaieaalesyaetlpadrrelldrfrlkDva 226
                                        + + ++l+ a+++++++a+++y+e++ ++r + +d+frl+ ++
  gene1832|gene1832|rna1831|rna1831  89 ETRKIHLH-AQSKKLTEAINRYRESQIRHREDEVDKFRLQYII 130
                                        66777888.899**************************98766 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.9   0.00052      0.71       3      95 ..      13     118 ..      10     122 .. 0.84
   2 ?    6.0   0.2     0.011        15      27      61 ..     172     206 ..     159     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00052
                         Syntaxin_2   3 snlqkinsnvstleklvkqLgtk....kdteelreklhelieeinelikktnellkklsqldnsssds........ 66 
                                        + + ++ns +++++ l +q +++     + + l+++++ l e+ + l+++++e++ ++s+ +  ++++        
  gene1832|gene1832|rna1831|rna1831  13 NDIETLNSYTNSIDYLSSQKNSSvlskEEEKGLNNQIDVLNERFRVLSRNIKERIDSFSSETTELEKDskkdrfyh 88 
                                        56788888888888888885555554378999**************************997777766679999*** PP

                         Syntaxin_2  67 .qqklqkekLkkdfkealqeFqkiqrqyae 95 
                                         ++k+     +k+++ea++++ ++q + +e
  gene1832|gene1832|rna1831|rna1831  89 eTRKIHLHAQSKKLTEAINRYRESQIRHRE 118
                                        *9999999999999*******999977665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.011
                         Syntaxin_2  27 dteelreklhelieeinelikktnellkklsqldn 61 
                                        + ++  +k++e+++ei +l++ +++ ++k +++ +
  gene1832|gene1832|rna1831|rna1831 172 NRKKNIKKIEEMVQEIVDLLNLISQEVSKRTEVVE 206
                                        44555577777777777777777777776555554 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0018       2.5      37     101 ..       2      68 ..       1      72 [. 0.75
   2 ?    0.0   0.2      0.87   1.2e+03      55      85 ..      90     121 ..      76     126 .. 0.63
   3 ?    7.1   1.0    0.0054       7.4      31      86 ..     150     206 ..     134     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT..HTTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Spectrin  37 qallkkhkaleaelaaqqervkalnelaeklldeg..hsaseeieerleelnerWeeLkelaaerkq 101
                                        q+ lk+ k++ +++++     ++++ l+++  ++   +++++ ++++++ lner++ L++ ++er +
  gene1832|gene1832|rna1831|rna1831   2 QDFLKDSKRILNDIETLNSYTNSIDYLSSQKNSSVlsKEEEKGLNNQIDVLNERFRVLSRNIKERID 68 
                                        66777778888888888777778873333332332337899***********************975 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.87
                                        HHHHHHHHHHHHH.HHTTHTTHHHHHHHHHHH CS
                           Spectrin  55 ervkalnelaekl.ldeghsaseeieerleel 85 
                                        +r  +l ++++kl ++ + + + +i++r +e+
  gene1832|gene1832|rna1831|rna1831  90 TRKIHLHAQSKKLtEAINRYRESQIRHREDEV 121
                                        44445566666664444466666666666665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0054
                                        SSHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHH CS
                           Spectrin  31 kdleevqallk.khkaleaelaaqqervkalnelaeklldeghsaseeieerleeln 86 
                                         +++++ al     +++ +e +++++++k+++e+ ++++d     s+e+++r+e ++
  gene1832|gene1832|rna1831|rna1831 150 TKVASAYALGAhSAQGILEEAENRKKNIKKIEEMVQEIVDLLNLISQEVSKRTEVVE 206
                                        555555555544678889999*****************9999999999999988775 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   0.00027      0.38      14      41 ..      52      79 ..      46      80 .. 0.92
   2 ?    0.3   0.1      0.46   6.4e+02      26      39 ..     177     190 ..     174     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                              HSBP1 14 lqdkFqtmsdqilsriDdMssriDdLEk 41
                                       l+++F  +s +i +riD  ss   +LEk
  gene1832|gene1832|rna1831|rna1831 52 LNERFRVLSRNIKERIDSFSSETTELEK 79
                                       899******************9999998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.46
                              HSBP1  26 lsriDdMssriDdL 39 
                                        +++i++M + i dL
  gene1832|gene1832|rna1831|rna1831 177 IKKIEEMVQEIVDL 190
                                        67999998888777 PP

>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  10.6    0.0013       1.8     242     336 ..      60     209 ..      25     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0013
                                        EEEEEE--SSSEEEEEE--TT...-TTHHHHTTSBHHHHHHHHHHHHHHHHHHH.HTTT...-............. CS
                               Sec1 242 nnnvvleeepkeekeaelvess.sDeffaelrhlnfgevgeklkkeakeyqeen.ekkrngak............. 302
                                        ++n+++  ++ +++++el  +s +D+f+ e+r  +  + ++kl++ +++y+e+  + +  +++             
  gene1832|gene1832|rna1831|rna1831  60 SRNIKERIDSFSSETTELEKDSkKDRFYHETRKIHLHAQSKKLTEAINRYRESQiRHR--EDEvdkfrlqyiiakp 133
                                        44555555558899999999999****************************8773322..2234467777777777 PP

                                        .........................................TTHHHHHHHHHH-GGGHHH.HHHHHHHHHHHHHHH CS
                               Sec1 303 .........................................esiadlkkfvaklpelqee.kkklskHtnlaeell 336
                                                                                 ++i++++++v+++ +l  + ++++sk t ++e+++
  gene1832|gene1832|rna1831|rna1831 134 datekeieefigdddgtkvasayalgahsaqgileeaenrkKNIKKIEEMVQEIVDLLNLiSQEVSKRTEVVEAIN 209
                                        7555555555555555555555555555555555555555566666666666655444444666666666666665 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0039       5.4      23      67 ..      19      63 ..      15      72 .. 0.85
   2 ?   -1.8   0.1         2   2.7e+03      18      39 ..      98     119 ..      89     129 .. 0.66
   3 ?    3.1   0.0      0.06        83      14      83 ..     190     259 ..     183     269 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0039
                            DUF2721 23 ariadrirqLedeleelaeeeeedeelakeiknlrrRarlirrai 67
                                       +++++ i  L+++ +++  ++ee++ l+++i++l++R r+++r i
  gene1832|gene1832|rna1831|rna1831 19 NSYTNSIDYLSSQKNSSVLSKEEEKGLNNQIDVLNERFRVLSRNI 63
                                       6677888889988888888888899**************998865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                            DUF2721  18 ltnRlariadrirqLedeleel 39 
                                         + +l+  ++r+r+ + +++e 
  gene1832|gene1832|rna1831|rna1831  98 QSKKLTEAINRYRESQIRHRED 119
                                        4566777777877777666643 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.06
                            DUF2721  14 lllvltnRlariadrirqLedeleelaeeeee.deelakeiknlrrRarlirrailllvlsallvvlvvll 83 
                                        ll+ ++  +++ ++ ++ ++d l + +e+++  +++l+  ++  + Ra+ i+r ++ ++l + l+ l+ ++
  gene1832|gene1832|rna1831|rna1831 190 LLNLISQEVSKRTEVVEAINDDLITGEENTAAaNADLESALA-YQIRATRIKRVFVYGILIIGLIFLIYFT 259
                                        666677777777777777777777777776664555555555.7789999999999998877776666554 PP

>> Folliculin  Vesicle coat protein involved in Golgi to plasma membrane transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.2   0.00023      0.31      72     167 ..      36     132 ..      34     148 .. 0.68
   2 ?   -0.1   0.2      0.55   7.5e+02      89     114 ..     177     202 ..     154     240 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                         Folliculin  72 alstdkerlllkawsfiveafeklaaeiqalaeaelereskeeeassaassssa.lkadgsglsrregssfslske 146
                                        +ls+++e+ l ++++++ e f+ l ++i+++ ++  +++++ e+ s++++  ++  k + ++ s++ +++ +  +e
  gene1832|gene1832|rna1831|rna1831  36 VLSKEEEKGLNNQIDVLNERFRVLSRNIKERIDSFSSETTELEKDSKKDRFYHEtRKIHLHAQSKKLTEAINRYRE 111
                                        6889999*************************99998877766655544433334333333333333444444445 PP

                         Folliculin 147 kylrrsksklkarsLaelvgd 167
                                        +  r++++++++  L  ++ +
  gene1832|gene1832|rna1831|rna1831 112 SQIRHREDEVDKFRLQYIIAK 132
                                        555666655555555555554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.55
                         Folliculin  89 veafeklaaeiqalaeaelereskee 114
                                        ++++e++++ei +l +   ++ sk++
  gene1832|gene1832|rna1831|rna1831 177 IKKIEEMVQEIVDLLNLISQEVSKRT 202
                                        34455555555554444443333322 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.6   0.00088       1.2      48     113 ..      51     115 ..       6     121 .. 0.74
   2 ?    0.4   0.1      0.61   8.4e+02      80     101 ..     178     199 ..     158     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00088
                                        GGGGGGSEEEHHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS CS
                              IZUMO  48 aenkflgvvdeetlekvasslkkelkrltdsdlkgelllkeLlwllqkqkkklkealkefqkealc 113
                                          n+  +v+ ++++++   s+ +e+++l++++ k++++ +     l+ q kkl+ea++++++  + 
  gene1832|gene1832|rna1831|rna1831  51 VLNERFRVL-SRNIKERIDSFSSETTELEKDSKKDRFYHETRKIHLHAQSKKLTEAINRYRESQIR 115
                                        444455544.578999999*********************99999***************997665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.61
                                        --HHHHHHHHHHHHHHHHHHHH CS
                              IZUMO  80 lkgelllkeLlwllqkqkkklk 101
                                         k e +++e+++ll+   +++ 
  gene1832|gene1832|rna1831|rna1831 178 KKIEEMVQEIVDLLNLISQEVS 199
                                        3333333433333333333332 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.33   4.5e+02      71      92 ..      44      65 ..       5      70 .. 0.58
   2 ?    1.8   0.6      0.18   2.4e+02      42      89 ..      61     108 ..      39     119 .. 0.64
   3 ?    7.9   0.2    0.0021       2.9      35      82 ..     171     218 ..     161     235 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.33
                           Noelin-1 71 ktetllktlesklkvveedrke 92
                                         +++++ l+++++v++ + ke
  gene1832|gene1832|rna1831|rna1831 44 GLNNQIDVLNERFRVLSRNIKE 65
                                       3457777788888877777665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                           Noelin-1  42 rqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveed 89 
                                        r+++e++   s +   l++  ++d  y ++ +  l+  ++kl+++ + 
  gene1832|gene1832|rna1831|rna1831  61 RNIKERIDSFSSETTELEKDSKKDRFYHETRKIHLHAQSKKLTEAINR 108
                                        556666777777777777777777666666666666666666666555 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0021
                           Noelin-1  35 DarsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesk 82 
                                        + r++++++++e vq + + ++++++  s+  + v+  +  l t e++
  gene1832|gene1832|rna1831|rna1831 171 ENRKKNIKKIEEMVQEIVDLLNLISQEVSKRTEVVEAINDDLITGEEN 218
                                        6799********************999999888888776655555554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.3     0.099   1.4e+02      35      73 ..      11      65 ..       1      78 [. 0.35
   2 ?    5.8   1.4     0.014        19      29      77 ..      79     127 ..      73     146 .. 0.73
   3 ?    8.9   1.8    0.0015         2      21      76 ..     136     217 ..     133     235 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.099
                                       HHHHHHHHHH....................HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              DUF16 35 rLkkieakvd.................klgeqinkleqkvekqgekikelkveqka 73
                                        L++ie+ ++                   +e+ + l+++++ ++e+ + l+ ++k 
  gene1832|gene1832|rna1831|rna1831 11 ILNDIET-LNsytnsidylssqknssvLSKEEEKGLNNQIDVLNERFRVLSRNIKE 65
                                       4444443.231222222222222222222222222333333333333333333322 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                                        -..BHHHHHHHHHHHH...HHHHHHHHHHHH.HHHHHHHHHHHHHHHHH. CS
                              DUF16  29 kdsnkqrLkkieakvdklgeqinkleqkvek.qgekikelkveqkaqgee 77 
                                        kds k r+ +   k++ l  q +kl++++++  + +i++ + e+++ + +
  gene1832|gene1832|rna1831|rna1831  79 KDSKKDRFYHETRKIH-LHAQSKKLTEAINRyRESQIRHREDEVDKFRLQ 127
                                        7888999998888888.5567889999987626779**999999987755 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0015
                                        BHHHHHHB-............................BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHH CS
                              DUF16  21 Trkqlnefkds..........................nkqrLkkieakvdklgeqinkleqkvekqgekikelkve 70 
                                        T k+++ef  +                           k+++kkie+ v+     +n + q+v+k +e ++ ++ +
  gene1832|gene1832|rna1831|rna1831 136 TEKEIEEFIGDddgtkvasayalgahsaqgileeaenRKKNIKKIEEMVQEIVDLLNLISQEVSKRTEVVEAINDD 211
                                        77888888766678888888888888888888888878999*********99999***********9999888776 PP

                                        HHHHHH CS
                              DUF16  71 qkaqge 76 
                                          + +e
  gene1832|gene1832|rna1831|rna1831 212 LITGEE 217
                                        655555 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.5     0.001       1.4      61     151 ..      20     132 ..       8     143 .. 0.83
   2 ?    3.3   1.4     0.026        35      55     121 ..     163     229 ..     122     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                              Atg14  61 kiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk......................kR 114
                                           n+ ++l+++k+ + +++e+ + l+ +++ l+++ +  +++++++ d+ +                      + 
  gene1832|gene1832|rna1831|rna1831  20 SYTNSIDYLSSQKNSSVLSKEEEKGLNNQIDVLNERFRVLSRNIKERIDSFSsettelekdskkdrfyhetrkiHL 95 
                                        5678889999******************************************999999999999999999888888 PP

                              Atg14 115 rsdleslqneleerrkkqiaklqdaikrieqklssls 151
                                        +++ ++l++ ++ +r++qi+   d++ + + ++   +
  gene1832|gene1832|rna1831|rna1831  96 HAQSKKLTEAINRYRESQIRHREDEVDKFRLQYIIAK 132
                                        8888899999999999999888887776655555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                              Atg14  55 aeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdlesl 121
                                        a+   ++++n+k++++++   ++++ + l+++++ +s++++ +e+    l +  ++++  ++dles+
  gene1832|gene1832|rna1831|rna1831 163 AQGILEEAENRKKNIKKIEEMVQEIVDLLNLISQEVSKRTEVVEAINDDLITGEENTAAANADLESA 229
                                        4444556666777777777777777777777777777777777776666666666666666666654 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.3     0.033        45      25      81 ..       7      62 ..       1      79 [. 0.73
   2 ?    8.2   2.3    0.0016       2.3       2      55 ..     174     227 ..     163     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.033
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                         Laminin_II 25 nlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81
                                       + +++ ++++++n+  + ++ + +++n   ++ +++ k L++++++L ++++ l   
  gene1832|gene1832|rna1831|rna1831  7 DSKRILNDIETLNSYTNSIDYLSSQKNS-SVLSKEEEKGLNNQIDVLNERFRVLSRN 62
                                       5567788888999886666655555555.556778889************9988654 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0016
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         Laminin_II   2 kelaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair 55 
                                        k+++++++e ++e+ + l+ +sq++++  e ++ in+++   +e+  +an  ++
  gene1832|gene1832|rna1831|rna1831 174 KKNIKKIEEMVQEIVDLLNLISQEVSKRTEVVEAINDDLITGEENTAAANADLE 227
                                        788999999999999999999999999999999999997666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2058  (0.114786); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 1723.31
//
Query:       gene1833|gene1833|rna1832|rna1832  [L=344]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   45.0  11.9    1.2e-11   45.0  11.9    3.2  3  zf-CHY    CHY zinc finger


Domain annotation for each model (and alignments):
>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   4.7      0.09   1.6e+03      42      73 ..     126     159 ..     111     161 .. 0.61
   2 !    6.1   1.0    0.0009        16      20      49 ..     195     224 ..     182     233 .. 0.82
   3 !   45.0  11.9   6.5e-16   1.2e-11       1      65 [.     255     316 ..     255     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.09
                             zf-CHY  42 vlcllCeteqekavlCkkCkk...efaeyfCpiCk 73 
                                        + ++ Ce   + +  C++C++     +   Cp Ck
  gene1833|gene1833|rna1832|rna1832 126 TSIVSCECL-NLQAGCNRCGRileMPGPTECPGCK 159
                                        334455554.4567799998855223334699997 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0009
                             zf-CHY  20 yaCreCHeeledhelerlevkevlcllCet 49 
                                         +C++CH + e+ el   ++ +++c +C +
  gene1833|gene1833|rna1832|rna1832 195 LSCDSCHMNYETSELGIGDTFRIKCYECLS 224
                                        57*****99999999999999999999975 PP

  == domain 3  score: 45.0 bits;  conditional E-value: 6.5e-16
                             zf-CHY   1 CkHykravvairapcCkklyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkkefa 65 
                                        C+Hyk+++ ++r+pcC++ly+C+ CH+e++ h +++++  +++c lC++eq ++++C  C+ +++
  gene1833|gene1833|rna1832|rna1832 255 CRHYKKSYRWFRFPCCNSLYPCDICHDEESGH-VHQMAN-KMVCGLCSKEQGVSKACD-CGMNLK 316
                                        ***************************99988.555554.589**************7.877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2015.53
//
Query:       gene1834|gene1834|rna1833|rna1833  [L=624]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-35  123.0   0.0      3e-17   63.4   0.0    2.6  2  ABC_tran      ABC transporter
    9.2e-12   44.9   3.2    0.00057   19.4   0.1    4.0  4  SMC_N         RecF/RecN/SMC N terminal domain
    1.8e-10   40.4   0.5    1.8e-10   40.4   0.5    2.1  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    4.7e-09   36.5   6.2      0.048   13.5   0.0    4.3  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.1e-05   25.9   0.0      0.053   13.9   0.0    2.4  2  AAA_16        AAA ATPase domain
      2e-05   24.2   7.5    3.7e-05   23.4   1.6    2.7  2  Fer4          4Fe-4S binding domain
    2.4e-05   24.2   8.0      0.022   14.5   0.1    3.3  3  AAA_15        AAA ATPase domain
    2.6e-05   24.2   0.1       0.16   11.8   0.0    3.2  4  RsgA_GTPase   RsgA GTPase
    0.00013   22.4   0.0       0.53   10.7   0.0    2.7  2  AAA           ATPase family associated with various cellular 
    0.00016   21.3   0.2       0.61    9.9   0.1    2.5  2  AAA_29        P-loop containing region of AAA domain
     0.0003   20.8   0.9       0.03   14.2   0.0    3.1  2  Rad17         Rad17 P-loop domain
     0.0021   18.4   0.5        7.4    7.0   0.0    3.7  3  RNA_helicase  RNA helicase
     0.0027   17.6   1.0       0.23   11.4   0.0    2.5  2  NACHT         NACHT domain
     0.0036   17.3   1.8     0.0036   17.3   1.8    2.5  2  Fer4_6        4Fe-4S binding domain
     0.0057   16.7   2.1     0.0057   16.7   2.1    2.2  2  Fer4_10       4Fe-4S dicluster domain
      0.009   15.7   2.4       0.28   10.8   0.0    2.6  2  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
       0.01   15.9  12.0      0.025   14.7  12.0    1.7  1  Fer4_21       4Fe-4S dicluster domain
      0.012   16.1   2.0      0.012   16.1   2.0    2.4  3  Fer4_7        4Fe-4S dicluster domain
       0.03   13.5   0.1          6    6.0   0.0    2.5  2  NB-ARC        NB-ARC domain
      0.031   14.6   0.8        5.6    7.2   0.0    3.1  3  AAA_22        AAA domain
      0.041   14.1  15.0      0.092   12.9  15.0    1.6  1  Fer4_9        4Fe-4S dicluster domain
      0.047   14.2   9.8       0.36   11.3   0.1    3.2  2  AAA_23        AAA domain
       0.13   12.3   1.8        1.2    9.1   0.1    2.9  2  AAA_5         AAA domain (dynein-related subfamily)
       0.27   11.4  11.1       0.15   12.2   2.1    2.5  2  Fer4_2        4Fe-4S binding domain
       0.32   10.7   1.7         20    4.8   0.3    2.6  2  AAA_24        AAA domain
       0.45   11.6  16.5       0.18   12.8   4.2    2.7  2  Fer4_3        4Fe-4S binding domain
        5.2    8.1  15.5       0.48   11.4   3.3    2.8  2  Fer4_16       4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0   4.4e-20     3e-17      10     136 ..     104     272 ..     102     273 .. 0.78
   2 !   56.9   0.0   4.6e-18     3e-15       8     137 .]     396     517 ..     389     517 .. 0.79

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 4.4e-20
                                        TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG......B-HHHCCHCEEEE-SS. CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx......xxxxxxxxxxxxxxxx. RF
                           ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke......qeleslrkeigvlpqe. 67 
                                        +g+++++vG nG GKSt lk+l+g+ kp+ G+             ++g +l+       +   +  ++i+++    
  gene1834|gene1834|rna1833|rna1833 104 PGKVLGLVGTNGIGKSTALKILSGEIKPNLGKYdnppgweailgYFKGSELQGyftkilEGQLKITSKIQYIDRLp 179
                                        89*******************************9999999999977788887755555545555566666666663 PP

                                        --S-TTSBHHHH..................HHHTC..HHHHHHHSTTGG.........TTCBGESTTSGGS-HHHH CS
                                        xxxxxxxxxxxx..................xxxxx..xxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxx RF
                           ABC_tran  68 pqlfpeltvren..................esdee..iekalsklglke.........lkdtvvksspssLSgGqk 114
                                        + l+++ +   +                  +  ++  ++++l+k+++k+         + +++++++ ++LSgG+ 
  gene1834|gene1834|rna1833|rna1833 180 KMLKRRFS---SgvrntleslsldddgtapD--DKllVKDVLEKMDQKKkknyyiekmCLKNILDRDIEELSGGEL 250
                                        33444443...13445698888877776432..33568888888888888888888888888888888******** PP

                                        HHHHHHHHHHHTSSEEEEESTT CS
                                        xxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran 115 qrvalarallkkpkllllDEpt 136
                                        qr +la a +++++++++DEp+
  gene1834|gene1834|rna1833|rna1833 251 QRFSLALACMQQSDVYIFDEPS 272
                                        *********************7 PP

  == domain 2  score: 56.9 bits;  conditional E-value: 4.6e-18
                                        EETTSEEEEEESTTSSHHHHHHHHTTSS--S.EEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.HH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                           ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpt.eGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.es 81 
                                        +  +e+++++GenG GK+tL+ l+agl kp+ e+e ++ + +lk    ++l k  g++ +    f  + +r++   
  gene1834|gene1834|rna1833|rna1833 396 FCDSEIIVFLGENGMGKTTLVGLVAGLIKPDlEEEFTMLSYSLKP--QKILPKYKGTVREL---FMSK-IRSSfMN 465
                                        55689*************************614444444444444..66666666666655...3333.4555345 PP

                                        HTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ABC_tran  82 deeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        ++ ++++++ l+++++ d+ v    ++LSgG+ qr+a+a +l k+++++l+DEp+a
  gene1834|gene1834|rna1833|rna1833 466 QSFVNDVIKPLNIEYTYDQLV----QNLSGGELQRIAIAICLGKDANIYLIDEPSA 517
                                        5569***********99***9....*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0       0.1        69      20      40 ..     101     121 ..      87     126 .. 0.75
   2 !   19.4   0.1   8.6e-07   0.00057     133     206 ..     241     311 ..     184     323 .. 0.76
   3 ?    3.0   0.0      0.09        60      11      41 ..     385     416 ..     379     420 .. 0.71
   4 !   17.3   0.0   3.8e-06    0.0026     135     186 ..     481     534 ..     426     557 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.1
                                        EETTSSEEEEEESTTSSHHHH CS
                                        xxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N  20 lpfsksftaivGpNGSGKsnl 40 
                                        +p   ++  +vG NG GKs  
  gene1834|gene1834|rna1833|rna1833 101 IPRPGKVLGLVGTNGIGKSTA 121
                                        5556677889*********75 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 8.6e-07
                                        STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-S CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                              SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekad 206
                                        ++e+LSgGe +  +laL      ++++ +y++De  + LD k++   a+ ++e  ++ + +iv+ ++  +l  ++
  gene1834|gene1834|rna1833|rna1833 241 DIEELSGGELQRFSLALA----CMQQSDVYIFDEPSSYLDVKQRLSAAKEIRELCEDnSYVIVVEHDLAILDLMS 311
                                        4569*****998777765....6778889***********************98765499999999877777665 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.09
                                        TTEECEEEEEET.TSSEEEEEESTTSSHHHHH CS
                                        xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                              SMC_N  11 ksyagktvilpf.sksftaivGpNGSGKsnll 41 
                                         s++ + +++ f ++++ + +G+NG GK+ l+
  gene1834|gene1834|rna1833|rna1833 385 ESFRLEVKEGTFcDSEIIVFLGENGMGKTTLV 416
                                        566555555555256678889********986 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 3.8e-06
                                        T......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                        x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N 135 e......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                        +      +LSgGe + +a+a+ +     k a +yl+De  a LD  ++ ++++++k+ 
  gene1834|gene1834|rna1833|rna1833 481 TydqlvqNLSGGELQRIAIAICL----GKDANIYLIDEPSAFLDSDQRIAISKVIKKF 534
                                        15555559******999998886....58999***********************974 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.5   2.8e-13   1.8e-10       1      35 []      11      42 ..      11      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.8e-13
                                       --EEEES---------TTHHHHHTTSEEEESS--S CS
                                RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                       +rlAiv+++ C+P+ C   +c + cpv  ++tg++
  gene1834|gene1834|rna1833|rna1833 11 TRLAIVNFELCKPSQCAS-ECRKACPV--NKTGRE 42
                                       59****************.********..****96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   1.5   0.00033      0.22       3      21 ..     109     127 ..     107     165 .. 0.83
   2 !   13.5   0.0   7.2e-05     0.048     228     282 ..     236     287 ..     135     308 .. 0.70
   3 !    7.6   0.1    0.0044       2.9       1      78 [.     401     467 ..     401     485 .. 0.72
   4 ?    3.7   0.0     0.069        46     234     283 ..     486     532 ..     476     545 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                             AAA_21   3 vliGpNgsGKSnLLdaldl 21 
                                        +l+G Ng GKS+ L++l++
  gene1834|gene1834|rna1833|rna1833 109 GLVGTNGIGKSTALKILSG 127
                                        79***************64 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.2e-05
                             AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell 282
                                        +  ++++ elS G ++ + l++a+ ++    +++++DEp + L+ k   + ++ +
  gene1834|gene1834|rna1833|rna1833 236 NILDRDIEELSGGELQRFSLALACMQQS---DVYIFDEPSSYLDVKQRLSAAKEI 287
                                        4456778899***************988...*************96553333444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0044
                             AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryrygl 76 
                                        + v+ G Ng GK++L  +  +l           ++++   ++++ +++l +  + ++ + +++e++++++r ++  
  gene1834|gene1834|rna1833|rna1833 401 IIVFLGENGMGKTTLVGLVAGL-----------IKPDLEEEFTMLSYSLKPQKILPKYKGTVRELFMSKIRSSFMN 465
                                        5799************999998...........4566666677777777777777766666666666666666665 PP

                             AAA_21  77 rl 78 
                                        + 
  gene1834|gene1834|rna1833|rna1833 466 QS 467
                                        55 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.069
                             AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellk 283
                                        + +lS G ++    ++++l  +    ++liDEp ++L+      + +++k
  gene1834|gene1834|rna1833|rna1833 486 VQNLSGGELQR-IAIAICLGKDA--NIYLIDEPSAFLDSDQRIAISKVIK 532
                                        56678888777.56666665554..8***********9877777776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0017       1.1      16     130 ..      96     197 ..      94     258 .. 0.71
   2 !   13.9   0.0   7.9e-05     0.053      24      61 ..     396     432 ..     386     475 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                             AAA_16  16 lervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeae 90 
                                        l+r+  +rp  ++ l+G  G+GKs+ ++ l  +++ +      gk+d         + ++a+   ++++  + +  
  gene1834|gene1834|rna1833|rna1833  96 LHRLPIPRPgKVLGLVGTNGIGKSTALKILSGEIKPN-----LGKYDNP-------PGWEAI-L-GYFKGSELQGY 157
                                        56777788888899**************999999999.....6666665.......444555.3.55666666656 PP

                             AAA_16  91 saeleawrekleealaavpelagaeasrllellkrllall 130
                                         ++  + + k+++ ++ ++ l+  +++r+   +++ l+ l
  gene1834|gene1834|rna1833|rna1833 158 FTKILEGQLKITSKIQYIDRLPKMLKRRFSSGVRNTLESL 197
                                        6666666666666666666666666666655555555444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.9e-05
                             AAA_16  24 p...elvllsGesGvGKsslvrellralekdggiflrgkcd 61 
                                            e++++ Ge G+GK++lv  ++  ++ d    l+++++
  gene1834|gene1834|rna1833|rna1833 396 FcdsEIIVFLGENGMGKTTLVGLVAGLIKPD----LEEEFT 432
                                        455599****************999888877....666555 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4     0.096        64      13      21 ..      29      37 ..      28      37 .. 0.90
   2 !   23.4   1.6   5.5e-08   3.7e-05       2      24 .]      51      73 ..      50      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.096
                                       HHHHHSTTT CS
                               Fer4 13 aCvevCPvg 21
                                       +C ++CPv+
  gene1834|gene1834|rna1833|rna1833 29 ECRKACPVN 37
                                       6******98 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 5.5e-08
                                       EEETTTSSS-THHHHHSTTTEEE CS
                               Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       vi e +CigC aC + CP+ AI+
  gene1834|gene1834|rna1833|rna1833 51 VISEVLCIGCSACQKKCPFKAIS 73
                                       577889***************96 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.5   0.00064      0.43      28      83 ..     110     172 ..      94     257 .. 0.51
   2 ?   -0.1   0.5      0.89   5.9e+02     322     365 ..     261     303 ..     214     307 .. 0.74
   3 !   14.5   0.1   3.4e-05     0.022      13      84 ..     383     509 ..     382     551 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00064
                             AAA_15  28 liGkNnsGKSsilealdlFlnnkekkn...............kkvikiekedleifeniseskdikIdvef 83 
                                        l+G+N++GKS++l++l      + k n               +    ++ ++l+ +  +  + ++kI+ + 
  gene1834|gene1834|rna1833|rna1833 110 LVGTNGIGKSTALKILS----GEIKPNlgkydnppgweailgY----FKGSELQGYFTKILEGQLKITSKI 172
                                        9**************94....3322224444456666633331....333333333333444444444333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.89
                             AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +++++++++EP  +L  ++  + +k ++el +dn+  vi+  H 
  gene1834|gene1834|rna1833|rna1833 261 QQSDVYIFDEPSSYLDVKQRLSAAKEIRELCEDNS-YVIVVEHD 303
                                        33578888888888888888888888888888887.67766665 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.4e-05
                             AAA_15  13 slkdveidlsee......ltvliGkNnsGKSsilealdlFlnnkekkn.......................kkvik 59 
                                         ++++ ++++e       + v+ G+N+ GK++++ +   +++ + + +                        +  k
  gene1834|gene1834|rna1833|rna1833 383 TYESFRLEVKEGtfcdseIIVFLGENGMGKTTLVGLVAGLIKPDLEEEftmlsyslkpqkilpkykgtvreLFMSK 458
                                        5666777777777777779***********************9944445799999**************9966789 PP

                             AAA_15  60 iekedleifeniseskdikIdvef..........................a 84 
                                        i +++++++  ++  k++ I++++                          +
  gene1834|gene1834|rna1833|rna1833 459 IRSSFMNQSFVNDVIKPLNIEYTYdqlvqnlsggelqriaiaiclgkdanI 509
                                        99**********************777777666666665554444433330 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0033       2.2      99     126 ..     105     132 ..      90     139 .. 0.85
   2 ?   -2.9   0.0       8.3   5.5e+03      93     110 ..     306     323 ..     276     323 .. 0.72
   3 !   11.8   0.0   0.00024      0.16      96     120 ..     396     420 ..     358     435 .. 0.74
   4 ?   -1.5   0.0       3.1   2.1e+03      93     110 ..     551     568 ..     478     571 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0033
                                        TSEEEEECSTTSSHHHHHHHHCTT---- CS
                        RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelk 126
                                        +k+  lvG  G+GKSt ++ l +e + +
  gene1834|gene1834|rna1833|rna1833 105 GKVLGLVGTNGIGKSTALKILSGEIKPN 132
                                        578889***************9987655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.3
                                        HHHHCTTSEEEEECSTTS CS
                        RsgA_GTPase  93 lkellkdktsvlvGqSGv 110
                                        + +l++d  +vl GqSG+
  gene1834|gene1834|rna1833|rna1833 306 ILDLMSDFGCVLYGQSGA 323
                                        556666777899999995 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00024
                                        HCTTSEEEEECSTTSSHHHHHHHHC CS
                        RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinall 120
                                         ++++++v++G+ G+GK+tL+  ++
  gene1834|gene1834|rna1833|rna1833 396 FCDSEIIVFLGENGMGKTTLVGLVA 420
                                        56779***************97765 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 3.1
                                        HHHHCTTSEEEEECSTTS CS
                        RsgA_GTPase  93 lkellkdktsvlvGqSGv 110
                                        + ++l+dk++v+ G+ Gv
  gene1834|gene1834|rna1833|rna1833 551 VGTYLADKVIVFEGEPGV 568
                                        457888999999999887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0028       1.9       3      75 ..     110     188 ..     108     234 .. 0.77
   2 !   10.7   0.0    0.0008      0.53       2      50 ..     403     455 ..     402     472 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0028
                                        EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTH.HHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                                AAA   3 lyGppGtGKTllakavakelgvefleisgsellskyvge.sekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                        l+G+ G+GK+++ k +  e++ ++ + + +  ++ ++g  + ++++++f+++ e +   + +i  iD + ++ k+r
  gene1834|gene1834|rna1833|rna1833 110 LVGTNGIGKSTALKILSGEIKPNLGKYDNPPGWEAILGYfKGSELQGYFTKILEGQlkiTSKIQYIDRLPKMLKRR 185
                                        89*******************9999998888887766652456788999888777777777899999999999988 PP

                                        ..T CS
                                AAA  75 ..s 75 
                                          s
  gene1834|gene1834|rna1833|rna1833 186 fsS 188
                                        431 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0008
                                        EEESSTTSSHHHHHHHHHHHHT....HEEEEEETTTCSSSSTTHHHHHHHHHH CS
                                AAA   2 llyGppGtGKTllakavakelg....vefleisgsellskyvgesekkirelf 50 
                                        ++ G  G+GKT+l+  va  ++     ef  +s s   +k++ + +  +relf
  gene1834|gene1834|rna1833|rna1833 403 VFLGENGMGKTTLVGLVAGLIKpdleEEFTMLSYSLKPQKILPKYKGTVRELF 455
                                        789***************99764443445554444444444455555555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00092      0.61      12      39 ..      94     122 ..      90     126 .. 0.87
   2 !    8.7   0.0    0.0022       1.4      23      40 ..     400     417 ..     389     431 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00092
                             AAA_29  12 fdghtieidlkg.atlltGpsGsGKSTll 39 
                                        f+ h+++i + g +  l+G++G GKST l
  gene1834|gene1834|rna1833|rna1833  94 FKLHRLPIPRPGkVLGLVGTNGIGKSTAL 122
                                        6779999999998888***********76 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                             AAA_29  23 gatlltGpsGsGKSTllD 40 
                                        +++++ G++G GK+Tl+ 
  gene1834|gene1834|rna1833|rna1833 400 EIIVFLGENGMGKTTLVG 417
                                        47889***********95 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   4.6e-05      0.03      44      81 ..     104     141 ..      95     180 .. 0.84
   2 ?    3.3   0.3      0.11        70     131     168 ..     505     543 ..     388     550 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                              Rad17  44 kkriLLisGPsGCgkstvvkvLskelgiklrewlnpvs 81 
                                        + ++L + G  G gkst++k+Ls e  ++l ++ np  
  gene1834|gene1834|rna1833|rna1833 104 PGKVLGLVGTNGIGKSTALKILSGEIKPNLGKYDNPPG 141
                                        568999************************99999965 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                              Rad17 131 tdkklilvedlPnkfyrds..dalrevirkylrssealpl 168
                                         d ++ l+ d P+ f  +    a+ +vi+k+++s++ +++
  gene1834|gene1834|rna1833|rna1833 505 KDANIYLI-DEPSAFLDSDqrIAISKVIKKFIYSNNKIAF 543
                                        23344444.4588887655234678999999999887554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.027        18       3      24 ..     110     131 ..     108     146 .. 0.83
   2 ?    1.2   0.1       0.7   4.7e+02      17      42 ..     210     236 ..     208     240 .. 0.80
   3 ?    7.0   0.0     0.011       7.4       1      36 [.     402     437 ..     402     472 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.027
                       RNA_helicase   3 lyGpsgeGKStlakeLakallk 24 
                                        l+G +g+GKSt+ k L+ ++  
  gene1834|gene1834|rna1833|rna1833 110 LVGTNGIGKSTALKILSGEIKP 131
                                        78************99888765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.7
                       RNA_helicase  17 eLakallkklklkkkdsvys.rnpedd 42 
                                         L+k++l+k+++kkk+++y+ + + ++
  gene1834|gene1834|rna1833|rna1833 210 LLVKDVLEKMDQKKKKNYYIeKMCLKN 236
                                        5899***************96666555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.011
                       RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                        i++ G++g GK+tl+  +a  +  +l+++ +   ys
  gene1834|gene1834|rna1833|rna1833 402 IVFLGENGMGKTTLVGLVAGLIKPDLEEEFTMLSYS 437
                                        7899***********998777777776666555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5     0.052        35       3      22 ..     108     127 ..     106     135 .. 0.82
   2 !   11.4   0.0   0.00035      0.23       2      24 ..     401     423 ..     400     469 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.052
                                        EEEEC-TTTCHHHHHHHHHH CS
                              NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                        + l G +G+GK+t l+ l  
  gene1834|gene1834|rna1833|rna1833 108 LGLVGTNGIGKSTALKILSG 127
                                        5689*********9997765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00035
                                        CEEEEC-TTTCHHHHHHHHHHHH CS
                              NACHT   2 lvilqGeaGsGKTtLlqklalaw 24 
                                        +++  Ge+G+GKTtL+  +a ++
  gene1834|gene1834|rna1833|rna1833 401 IIVFLGENGMGKTTLVGLVAGLI 423
                                        58899**********97655444 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.8       0.6     4e+02       7      21 ..      19      36 ..      16      40 .. 0.84
   2 !   17.3   1.8   5.4e-06    0.0036       2      24 .]      50      72 ..      49      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.6
                             Fer4_6  7 dkCi..gC.gdCvrvCPe 21
                                       ++C   +C  +C ++CP 
  gene1834|gene1834|rna1833|rna1833 19 ELCKpsQCaSECRKACPV 36
                                       57887789889******7 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.4e-06
                             Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                       ++i + +CigC +C + CP++ai
  gene1834|gene1834|rna1833|rna1833 50 SVISEVLCIGCSACQKKCPFKAI 72
                                       688899**************998 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2  16.7   0.00045       0.3       4      56 .]      16      68 ..      13      68 .. 0.79
   2 !   16.7   2.1   8.6e-06    0.0057       3      23 ..      51      71 ..      49      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                            Fer4_10  4 idddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       ++ + C   +C+ +C+kaCP+   ++ +++ + +e++  +    C+gc aC+++CP
  gene1834|gene1834|rna1833|rna1833 16 VNFELCkpSQCAsECRKACPV---NKTGRECIRIEKKSVISEVLCIGCSACQKKCP 68
                                       5667785558989********...66667777777777777778***********9 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 8.6e-06
                            Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                       vi +  Ci+C +C+k CP+++
  gene1834|gene1834|rna1833|rna1833 51 VISEVLCIGCSACQKKCPFKA 71
                                       677889************965 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.047        31       3      22 ..     107     126 ..     105     136 .. 0.80
   2 !   10.8   0.0   0.00042      0.28       2      27 ..     400     425 ..     399     436 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.047
                                        EEEEEESTTSSHHHHHHHHH CS
                              SRP54   3 villvGlqGaGKTttlaKLa 22 
                                        v+ lvG++G+GK t+l  L+
  gene1834|gene1834|rna1833|rna1833 107 VLGLVGTNGIGKSTALKILS 126
                                        6679**********987665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                                        EEEEEEESTTSSHHHHHHHHHHHHHH CS
                              SRP54   2 nvillvGlqGaGKTttlaKLaallkk 27 
                                        ++i+++G +G+GKTt ++ +a l+k 
  gene1834|gene1834|rna1833|rna1833 400 EIIVFLGENGMGKTTLVGLVAGLIKP 425
                                        589**************999988775 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7  12.0   3.8e-05     0.025      10      57 ..      25      72 ..      14      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                            Fer4_21 10 gC.gkCliaCe..dtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57
                                       +C  +C +aC+  +t+ ++i+i++k+v  + e  C+GC  C + CP  ++i
  gene1834|gene1834|rna1833|rna1833 25 QCaSECRKACPvnKTGRECIRIEKKSV--ISEVLCIGCSACQKKCPF-KAI 72
                                       452479****7336899*****98877..56789************7.776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   3.3         1   6.8e+02      37      51 ..      20      37 ..       6      38 .. 0.71
   2 ?    7.0  15.5     0.013       8.6       5      52 .]      26      71 ..      20      71 .. 0.78
   3 ?   16.1   2.0   1.9e-05     0.012       2      19 ..      57      74 ..      56      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1
                             Fer4_7 37 kC..lgCga.CvavCPtg 51
                                        C  ++C + C ++CP++
  gene1834|gene1834|rna1833|rna1833 20 LCkpSQCASeCRKACPVN 37
                                       553347777799999986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                             Fer4_7  5 Cg.aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                       C   C +aCpv+    +     +  +k +i++  C+gC aC++ CP++a
  gene1834|gene1834|rna1833|rna1833 26 CAsECRKACPVNKTGRECI---RIEKKSVISEVLCIGCSACQKKCPFKA 71
                                       5337999999887776654...33356799999*************986 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.9e-05
                             Fer4_7  2 CigCgaCvaaCpvkaiel 19
                                       CigC aC++ Cp kai++
  gene1834|gene1834|rna1833|rna1833 57 CIGCSACQKKCPFKAISI 74
                                       9************99986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.021        14      21      41 ..     106     126 ..      98     185 .. 0.82
   2 ?    6.0   0.0     0.009         6      16      37 ..     397     416 ..     389     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.021
                                        EEEEEEESTTSSHHHHHHHHC CS
                             NB-ARC  21 lvvalvGmgGvGKttlakqil 41 
                                         v++lvG  G+GK+t +k   
  gene1834|gene1834|rna1833|rna1833 106 KVLGLVGTNGIGKSTALKILS 126
                                        589************776554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.009
                                        TTSCSEEEEEEESTTSSHHHHH CS
                             NB-ARC  16 delqslvvalvGmgGvGKttla 37 
                                        ++++  ++ + G  G+GKttl+
  gene1834|gene1834|rna1833|rna1833 397 CDSE--IIVFLGENGMGKTTLV 416
                                        4555..9999**********97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2       0.1        70       7      25 ..     107     125 ..     103     136 .. 0.85
   2 ?   -0.5   0.0         2   1.4e+03      55     117 ..     210     292 ..     196     324 .. 0.69
   3 ?    7.2   0.0    0.0084       5.6       7      27 ..     401     421 ..     398     520 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                             AAA_22   7 ilvvtGesGtGKTtllrrl 25 
                                        +l ++G  G+GK+t l+ l
  gene1834|gene1834|rna1833|rna1833 107 VLGLVGTNGIGKSTALKIL 125
                                        66799*********99865 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2
                             AAA_22  55 dllrellralglelka............erlsseell.ealeqalrarav...ielliiDEaqh.lr...seeale 110
                                         l +++l+++++++k+               + eel    l++ + a a      + i DE    l+   +  a +
  gene1834|gene1834|rna1833|rna1833 210 LLVKDVLEKMDQKKKKnyyiekmclkniLDRDIEELSgGELQRFSLALACmqqSDVYIFDEPSSyLDvkqRLSAAK 285
                                        5677788888877777777777777777555555555566666666666666667888888777676654366666 PP

                             AAA_22 111 eLrslln 117
                                        e+r+l +
  gene1834|gene1834|rna1833|rna1833 286 EIRELCE 292
                                        6666655 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0084
                             AAA_22   7 ilvvtGesGtGKTtllrrlle 27 
                                        i+v  Ge G+GKTtl+  ++ 
  gene1834|gene1834|rna1833|rna1833 401 IIVFLGENGMGKTTLVGLVAG 421
                                        89999*********9876665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  15.0   0.00014     0.092       4      51 .]      25      72 ..      21      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                             Fer4_9  4 gCg.aCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                       +C  +C +aCp + + +++ + + +  + +   CigC aC ++Cp +ai
  gene1834|gene1834|rna1833|rna1833 25 QCAsECRKACPVNKTGRECIRIEKKSVISEV-LCIGCSACQKKCPFKAI 72
                                       6862599999999999999999999877655.9************9887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   6.4      0.46     3e+02      23     159 ..     109     285 ..     101     299 .. 0.45
   2 ?   11.3   0.1   0.00054      0.36      17      36 ..     396     416 ..     382     419 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.46
                             AAA_23  23 lItGpNGaGKTTildAiklaLyget.prlsrks....................grgfeksdveiese......... 68 
                                         ++G NG GK+T l  +     ge  p+l++ +                             +   e         
  gene1834|gene1834|rna1833|rna1833 109 GLVGTNGIGKSTALKILS----GEIkPNLGKYDnppgweailgyfkgselqgyF--------TKILEgqlkitski 172
                                        57999******9887654....33214444433455666655665433333221........21111222231113 PP

                             AAA_23  69 ...gkvkayvelt.......fenkdgry...................trsiererelskkkgkttkkaklellei. 114
                                           +       +        f      +                   +     ++ l k+  ++ +++k+++ +i 
  gene1834|gene1834|rna1833|rna1833 173 qyiD-------RLpkmlkrrF------SsgvrntleslsldddgtapD-----DKLLVKDVLEKMDQKKKKNYYIe 230
                                        3331.......2222222112......022223445555555433342.....22222222222222222222222 PP

                             AAA_23 115 .....deleqfisellgskkiilnli.lflgqer....feefelkdkkerleele 159
                                             + l++ i+el g + ++++l  ++++q++     e+ +  d k+rl +++
  gene1834|gene1834|rna1833|rna1833 231 kmclkNILDRDIEELSGGELQRFSLAlACMQQSDvyifDEPSSYLDVKQRLSAAK 285
                                        2344588888888888888887755514555555666522222233334333333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00054
                             AAA_23  17 F.skgltlItGpNGaGKTTil 36 
                                        F ++ + ++ G+NG GKTT++
  gene1834|gene1834|rna1833|rna1833 396 FcDSEIIVFLGENGMGKTTLV 416
                                        4677899************96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.55   3.7e+02       4      21 ..     110     127 ..     108     136 .. 0.85
   2 ?    9.1   0.1    0.0018       1.2       3      42 ..     403     444 ..     401     515 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.55
                                        EE--SSSSHHHHHHHGGG CS
                              AAA_5   4 LvGppGtgKselaerlaa 21 
                                        LvG  G+gKs+  + l+ 
  gene1834|gene1834|rna1833|rna1833 110 LVGTNGIGKSTALKILSG 127
                                        9*********99988875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0018
                                        EEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH CS
                              AAA_5   3 lLvGppGtgKselaerlaaal..nreveyvqltrdtteedlk 42 
                                        + +G+ G gK++l+  +a ++    e e  +l+ ++++++++
  gene1834|gene1834|rna1833|rna1833 403 VFLGENGMGKTTLVGLVAGLIkpDLEEEFTMLSYSLKPQKIL 444
                                        789******************876666667777777776665 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.8      0.11        70       5      21 ..      16      35 ..      12      36 .. 0.68
   2 ?   12.2   2.1   0.00023      0.15       9      21 ..      56      68 ..      51      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
                             Fer4_2  5 vdtdrC.i.gC.gaCvsaCP 21
                                       v+ + C   +C + C++aCP
  gene1834|gene1834|rna1833|rna1833 16 VNFELCkPsQCaSECRKACP 35
                                       56666632368559****** PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00023
                             Fer4_2  9 rCigCgaCvsaCP 21
                                        CigC+aC++ CP
  gene1834|gene1834|rna1833|rna1833 56 LCIGCSACQKKCP 68
                                       5************ PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.031        20       4      22 ..     107     125 ..     105     134 .. 0.82
   2 ?    4.1   0.0     0.051        34       5      19 ..     402     416 ..     399     428 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                             AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                         + ++G +giGK+t +k l
  gene1834|gene1834|rna1833|rna1833 107 VLGLVGTNGIGKSTALKIL 125
                                        6789**********99876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.051
                             AAA_24   5 iliyGpsgiGKTtla 19 
                                        i+  G++g+GKTtl+
  gene1834|gene1834|rna1833|rna1833 402 IVFLGENGMGKTTLV 416
                                        7889*********97 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.4      0.21   1.4e+02       3      14 ..      25      37 ..      21      38 .. 0.79
   2 ?   12.8   4.2   0.00027      0.18       1      15 []      57      71 ..      57      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.21
                             Fer4_3  3 gC.gaCvevCPvg 14
                                       +C + C ++CPv+
  gene1834|gene1834|rna1833|rna1833 25 QCaSECRKACPVN 37
                                       58448******97 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00027
                             Fer4_3  1 CtgCgaCvevCPvgA 15
                                       C+gC+aC + CP +A
  gene1834|gene1834|rna1833|rna1833 57 CIGCSACQKKCPFKA 71
                                       ************998 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   4.4       1.1   7.3e+02       4      19 ..      25      41 ..      20      54 .. 0.72
   2 ?   11.4   3.3   0.00073      0.48       2      18 ..      57      73 ..      56      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.1
                            Fer4_16  4 tCgk.CaevCPtnaike 19
                                       +C   C ++CP+n    
  gene1834|gene1834|rna1833|rna1833 25 QCASeCRKACPVNKTGR 41
                                       67666999999987655 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00073
                            Fer4_16  2 CgtCgkCaevCPtnaik 18
                                       C++C +C + CP +ai+
  gene1834|gene1834|rna1833|rna1833 57 CIGCSACQKKCPFKAIS 73
                                       999*********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.75u 0.36s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 3656.35
//
Query:       gene1835|gene1835|rna1834|rna1834  [L=264]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-28   99.2   0.2    2.7e-28   98.6   0.2    1.3  1  Sad1_UNC  Sad1 / UNC-like C-terminal


Domain annotation for each model (and alignments):
>> Sad1_UNC  Sad1 / UNC-like C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.2   1.5e-32   2.7e-28       3     131 ..     143     263 ..     141     264 .] 0.96

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.5e-32
                                        EE-B-GGGGGSS--STT-SEEEESS-EEEEEEEEEEEEEEEEEEE---GGGSG-TTSB-EEEEEEESSTT----EE CS
                           Sad1_UNC   3 keakapkvilqedyspgeCwsfkgsrgfvvieLseeiiveavtlehveksvapisSapKdfevsgskrypekkwvl 78 
                                        +++k+p++i++e++s+geC sfkg ++ ++i++++ei+++ v   h +++   +sSa+ +fev+ + +     +  
  gene1835|gene1835|rna1834|rna1834 143 RKYKDPATIFDENVSVGECLSFKGCNCKFFIDFDKEITIDRVGFYHPRTKD--TSSAIHEFEVFCYGSNG---RLS 213
                                        67899********************************************66..************99998...66* PP

                                        EEEEE--TTS-SEEEEE--TT----EEEEEEEE--BSS-SSEEEESEEEEEEE CS
                           Sad1_UNC  79 lgefsydedgknaqtFeleeskdilvkyvkleilsnyGneeytclyrlrVyGt 131
                                        lgef+yd d + +qtFele+ k   ++ +++ i+sn+Gn+++tc+y+++++G+
  gene1835|gene1835|rna1834|rna1834 214 LGEFKYDVDACGFQTFELEKVK---TNSIEFAIRSNGGNKKFTCIYKVYLFGN 263
                                        *********************9...9**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1612.46
//
Query:       gene1836|gene1836|rna1835|rna1835  [L=436]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.4    8.4   4.5       0.22   11.0   0.1    2.0  2  DUF3087   Protein of unknown function (DUF3087)


Domain annotation for each model (and alignments):
>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   1.1      0.23   4.2e+03      28      65 ..      52      87 ..      39     102 .. 0.55
   2 ?   11.0   0.1   1.3e-05      0.22      12      96 ..     122     209 ..     112     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.23
                            DUF3087 28 vlsllfstllialfgeeevsnfhlnllGvvlalvltaa 65
                                       ++sl +s l+i+l+g+  +  f+  ++ vv+ l+ +++
  gene1836|gene1836|rna1835|rna1835 52 IVSL-TSFLIIELLGNRMS-LFVDTFIEVVVYLIFMFM 87
                                       3443.46677777775544.666666666665555443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.3e-05
                            DUF3087  12 rkklnrvivalv....allavlsllfstllialfgeeevsnfhlnllGvvlalvltaailrklktkpfmaevvYvW 83 
                                        rk+ ++vi+  +    ++  v+s  +++ +i   g + v n+ + llG +lal++t+++   + +k+  + + Y W
  gene1836|gene1836|rna1835|rna1835 122 RKEDRKVILSTAinikTSVSVVSSWIGQDIIMCGGCHRV-NILISLLGLFLALLTTFLLPATVPNKEEERLIDYMW 196
                                        455555554443000145566666667766666555555.*******************999************** PP

                            DUF3087  84 rLKqllnkiyrkl 96 
                                        +L  + +ki    
  gene1836|gene1836|rna1835|rna1835 197 NLSEAWKKIKSTY 209
                                        ******9998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2484.79
//
Query:       gene1837|gene1837|rna1836|rna1836  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-08   32.4   0.0    2.2e-06   28.1   0.0    2.3  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.013   2.4e+02      48     107 ..      78     150 ..      14     151 .. 0.77
   2 !   28.1   0.0   1.2e-10   2.2e-06      10      73 ..     183     242 ..     174     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.013
                    PseudoU_synth_1  48 vkgsgFldhqVRamvgvlfav..............gqgklspedvkellnakkrkkiavetapavglvlfhvrY 107
                                        +  +g++d++V a+  v+  v              ++ ++++ + + +ln  ++++i v    +v+   f++r+
  gene1837|gene1837|rna1836|rna1836  78 LVYAGRTDSGVSAINMVASGVvisrvlepnrsyviTKDDHKEYKYDIMLNNYLPSDIRVIGWAPVPD-TFNARF 150
                                        5668999999999988887777788888888888888888888888888888888888887777777.677666 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 1.2e-10
                    PseudoU_synth_1  10 dfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgkl 73 
                                        +f  f+k   ++ +++r++ e++i      +++ +++++k+++Fl+++VR +v ++ + g+g++
  gene1837|gene1837|rna1836|rna1836 183 NFYYFSKHSDKNARYERKLDECRII----DDGDIYYLDIKARAFLHNMVRKIVWAVQKSGKGEE 242
                                        567788888888*************....88999*******************99988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1834.18
//
Query:       gene1838|gene1838|rna1837|rna1837  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-36  122.9   0.0    7.8e-36  122.8   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.0   4.4e-40   7.8e-36       2     135 ..       5     136 ..       4     137 .] 0.96

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 4.4e-40
                                        SSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS CS
                     Ribosomal_S19e   2 vkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGg 77 
                                        +++V +e++ +al ++Lk+++k+ + +  d++Ktg++ke+ap ++dW+++R+Asi+R++ ++g v+ e l+k YG+
  gene1838|gene1838|rna1837|rna1837   5 IYEVRPEKFNDALKSYLKSTNKVVPLQDYDIMKTGEGKEQAPIEDDWYFTRMASIVRQISIKGAVTPEFLAKRYGS 80 
                                        79************************************************************************** PP

                                        -------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXX CS
                     Ribosomal_S19e  78 kkrrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeeva 135
                                        +k+rg+rps++v+a  ++  ++l++L+++g+++++ k   +lt+kG++ + +i+e+v 
  gene1838|gene1838|rna1837|rna1837  81 RKNRGCRPSKYVNAYPEIGVSVLENLKNMGWINEHPK--DMLTEKGRTVVKEIIEKVR 136
                                        ********************************65544..8**************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 797.48
//
Query:       gene1839|gene1839|rna1838|rna1838  [L=222]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-06   24.9   0.1    0.00029   20.1   0.1    2.1  2  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.0     0.004        72      99     133 ..      73     105 ..      49     127 .. 0.80
   2 !   20.1   0.1   1.6e-08   0.00029     286     328 ..     164     206 ..     158     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.004
                                        EEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE---- CS
                                TGT  99 sfqsridGskvlltpeesieiqeklgsDiimaldd 133
                                        ++ s+  G+  +l+ +++ ei e l++D +  +d 
  gene1839|gene1839|rna1838|rna1838  73 TLVSKR-GH-YKLKRQKYEEILEVLKPDYYADFDT 105
                                        556664.77.9999**************9999885 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.6e-08
                                        -SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH CS
                                TGT 286 sCytCknytraylhhllktkemlgaiLltiHNlhyylelfkri 328
                                        +C +C + +  yl+ l   kem + + l+iHN  ++ e f++i
  gene1839|gene1839|rna1838|rna1838 164 DCKCCGDLSAGYLKYLWSIKEMNALTYLAIHNYNVLDEVFEAI 206
                                        7****99*********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1449.11
//
Query:       gene1840|gene1840|rna1839|rna1839  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-35  122.0   1.6    1.9e-35  121.8   1.6    1.0  1  Pho88     Phosphate transport (Pho88)
  ------ inclusion threshold ------
        0.1   12.5   1.0       0.13   12.1   1.0    1.1  1  EOS1      N-glycosylation protein
        0.2   12.1   1.1       0.32   11.4   1.1    1.3  1  RIC3      Resistance to inhibitors of cholinesterase homologu


Domain annotation for each model (and alignments):
>> Pho88  Phosphate transport (Pho88)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   1.6   3.1e-39   1.9e-35       4     174 ..      10     176 ..       8     177 .] 0.95

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 3.1e-39
                              Pho88   4 qvtnlviilvlmqvskkidfedpevllyvRilYvvsqliillvylyikskikkknDlttlkyvepasplske.eek 78 
                                        q  n ++++v m vs k  f+ p+ ++++R +Y++s+li+l+  lyi++kik++nD + +k++  a+ ++++ ee+
  gene1840|gene1840|rna1839|rna1839  10 QFVNFALSIVSMKVSGKPMFQTPKAIWILRGAYLCSNLIQLVFSLYIMQKIKSTNDSRKVKIKREATLFKDNnEEE 85 
                                        77899***************************************************************99998888 PP

                              Pho88  79 lvttTvkdYDlaelkkllksilmgvammafmhlymkytnPLllQsimplknllesnlvkihllgkpaegdLkRPFk 154
                                         +++T+  YD +el k+ + ++++  ++ ++hl++k+++PL++Qs +p++nll ++l   ++++kp    + RPF+
  gene1840|gene1840|rna1839|rna1839  86 EEEMTYASYDESELTKVSRTAVIQFLIITVLHLKWKVIQPLFVQSFVPIRNLLLNPLYTAYVWNKP----VLRPFE 157
                                        88****************************************************************....88**** PP

                              Pho88 155 aaagllgaaeaktdkksiek 174
                                         a+ l+++a a ++kk +++
  gene1840|gene1840|rna1839|rna1839 158 -ANMLFQKAPAVSEKKRVKE 176
                                        .6777888877777777765 PP

>> EOS1  N-glycosylation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   2.2e-05      0.13      51     174 ..      15     139 ..       4     140 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                               EOS1  51 plvllllsvlsad.keqplaaWivisttlt...lseivqswvtSnladaeldsrevksrssaaerleskasslrqg 122
                                        +l  + ++v ++   + p a+Wi+ +  l+   +  +++ ++   +++ ++dsr+vk +  a+    +++++ +++
  gene1840|gene1840|rna1839|rna1839  15 ALSIVSMKVSGKPmFQTPKAIWILRGAYLCsnlIQLVFSLYIMQKIKS-TNDSRKVKIKREATLF--KDNNEEEEE 87 
                                        455555555554445678899999998877332456788999999975.4667777773333322..222222222 PP

                               EOS1 123 ksrhkrsvskseakkkrertsskrtldleeivvravvPvgvlsfltmviLlr 174
                                        + +  ++ +++ +k +r+ + +   +   ++ ++ + P+ v sf+ +  Ll+
  gene1840|gene1840|rna1839|rna1839  88 EMTYASYDESELTKVSRTAVIQFLIITVLHLKWKVIQPLFVQSFVPIRNLLL 139
                                        2222222222222455555556666667777899999********9998886 PP

>> RIC3  Resistance to inhibitors of cholinesterase homologue 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   5.3e-05      0.32      84     126 ..      50      99 ..      49     105 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                               RIC3  84 lvfilYtllKikskkkkekskeakakkkakenakkkte.......teeeL 126
                                        lvf lY++ Kiks+++++k k +++ +  k n++ ++e        e+eL
  gene1840|gene1840|rna1839|rna1839  50 LVFSLYIMQKIKSTNDSRKVKIKREATLFKDNNEEEEEemtyasyDESEL 99 
                                        69*************99977633333333333333333344444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1257.05
//
Query:       gene184|gene184|rna184|rna184  [L=781]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-17   61.1  10.5    0.00017   21.9   0.1    7.3  7  LRR_4     Leucine Rich repeats (2 copies)
    1.1e-10   41.1   8.6      0.006   16.3   0.2    6.2  6  LRR_8     Leucine rich repeat
     0.0013   18.6  14.9       0.93    9.7   0.0    7.5  9  LRR_6     Leucine Rich repeat
  ------ inclusion threshold ------
      0.016   15.6  14.8         20    6.2   0.3    7.8  9  LRR_1     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.7e-07   0.00074       3      41 ..     137     170 ..     136     172 .. 0.95
   2 ?   -1.4   0.0      0.78   3.5e+03       6      14 ..     181     189 ..     180     193 .. 0.70
   3 ?    1.9   0.0     0.075   3.4e+02       6      33 ..     199     223 ..     197     228 .. 0.59
   4 ?    2.6   0.1     0.043   1.9e+02       4      33 ..     233     277 ..     233     286 .. 0.56
   5 !   21.9   0.1   3.8e-08   0.00017       1      35 [.     287     317 ..     287     323 .. 0.90
   6 !   13.8   0.0   1.4e-05     0.062       3      41 ..     326     362 ..     324     365 .. 0.82
   7 ?   -1.0   0.1      0.61   2.7e+03       2      14 ..     367     379 ..     366     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.7e-07
                                    --EEE--SS---E-S-HHH-TT--EEE-.-S-----GGG CS
                          LRR_4   3 LevLdLsnNqltdiplleklpnLkeLdLsgNnlitdlde 41 
                                    L++L L n+++++ip ++ +  L +LdLs+N    d+++
  gene184|gene184|rna184|rna184 137 LRKLKLVNCRIKKIPDIS-MMRLAYLDLSHN----DISG 170
                                    9*****************.************....9975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.78
                                    EE--SS--- CS
                          LRR_4   6 LdLsnNqlt 14 
                                    ++Ls+N ++
  gene184|gene184|rna184|rna184 181 VNLSHNEIS 189
                                    678888877 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.075
                                    EE--SS---E-S-HHH-TT--E..EE-.-S CS
                          LRR_4   6 LdLsnNqltdiplleklpnLke..LdLsgN 33 
                                    Ld s+N++t   +   + + ++  LdLs N
  gene184|gene184|rna184|rna184 199 LDVSHNKVTR--F---FQDFTYrrLDLSYN 223
                                    8888888886..5...33333333666555 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.043
                                    -EEE--SS---E-S-..HH............H.-TT--EEE-.-S CS
                          LRR_4   4 evLdLsnNqltdipl..le............k.lpnLkeLdLsgN 33 
                                    +vL+Ls+++++++ +  ++            + + nL  L+++++
  gene184|gene184|rna184|rna184 233 RVLNLSQTMVKSLASktIRklvmdgtkrvklGaFENLVFLSINDC 277
                                    578888888888776552233344445555533666666666554 PP

  == domain 5  score: 21.9 bits;  conditional E-value: 3.8e-08
                                    SS--EEE--SS---E-S-HHH-TT--EEE-.-S-- CS
                          LRR_4   1 pnLevLdLsnNqltdiplleklpnLkeLdLsgNnl 35 
                                    ++L+vL  +nN + ++p    +p+L++Ld+s+N l
  gene184|gene184|rna184|rna184 287 KKLRVLKARNNLIEEVPV---FPSLEYLDISSN-L 317
                                    69*************999...*********999.5 PP

  == domain 6  score: 13.8 bits;  conditional E-value: 1.4e-05
                                    --EEE--SS---E-S-HHH-TT--EEE-.-S-----GGG CS
                          LRR_4   3 LevLdLsnNqltdiplleklpnLkeLdLsgNnlitdlde 41 
                                     ++Ld s Nq+  ++l +  + L +LdLs N ++ ++++
  gene184|gene184|rna184|rna184 326 VRFLDASKNQIMVFDLWG-WDRLAHLDLSYN-PLVNFEN 362
                                    799*********977766.*********999.5546655 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 0.61
                                    S--EEE--SS--- CS
                          LRR_4   2 nLevLdLsnNqlt 14 
                                     L++L+L ++ ++
  gene184|gene184|rna184|rna184 367 ELRFLNLKGTDIK 379
                                    5889999888887 PP

>> LRR_8  Leucine rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.3e-06     0.006       3      59 ..     137     186 ..     136     188 .. 0.83
   2 ?    0.3   0.1      0.13     6e+02      30      40 ..     181     191 ..     178     199 .. 0.80
   3 !    4.4   0.0    0.0073        33       5      42 ..     198     230 ..     194     234 .. 0.76
   4 ?   -1.4   0.0      0.46   2.1e+03      28      48 ..     233     253 ..     227     254 .. 0.78
   5 !    8.3   0.2   0.00043       1.9      24      42 ..     305     323 ..     287     336 .. 0.72
   6 !   11.3   0.1   5.1e-05      0.23      24      61 .]     344     378 ..     342     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                                    -SEEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGGGGGTT--S-.EEE--SS CS
                          LRR_8   3 LtsLdLsnNrltslddeaFkglsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgN 59 
                                    L++L L n r+++++d +     +L +LdLs+N ++ +   +++g    +  +Ls+N
  gene184|gene184|rna184|rna184 137 LRKLKLVNCRIKKIPDISMM---RLAYLDLSHNDISGVV--CLRGY--FDTVNLSHN 186
                                    89****************99...7***********9984..66665..555555555 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                                    EE--SS---GG CS
                          LRR_8  30 LdLsnNllttl 40 
                                     +Ls+N+++++
  gene184|gene184|rna184|rna184 181 VNLSHNEISRV 191
                                    58999999875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0073
                                    EEE-TTS--SEE-TTSSTT-TT--EEE--SS---GGGG CS
                          LRR_8   5 sLdLsnNrltslddeaFkglsnLkvLdLsnNllttlsp 42 
                                    +Ld+s+N+ t   +++ +     + LdLs+N l++ ++
  gene184|gene184|rna184|rna184 198 NLDVSHNKVTRFFQDFTY-----RRLDLSYNPLEFYHA 230
                                    688888888888888887.....688888888887765 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.46
                                    -EEE--SS---GGGGGGGTT- CS
                          LRR_8  28 kvLdLsnNllttlspgafsgL 48 
                                    +vL+Ls+   ++l  ++++ L
  gene184|gene184|rna184|rna184 233 RVLNLSQTMVKSLASKTIRKL 253
                                    589999988888877776655 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.00043
                                    -TT--EEE--SS---GGGG CS
                          LRR_8  24 lsnLkvLdLsnNllttlsp 42 
                                    +++L++Ld+s+Nl +t+ +
  gene184|gene184|rna184|rna184 305 FPSLEYLDISSNLVHTVPN 323
                                    4799999999999999853 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 5.1e-05
                                    -TT--EEE--SS---GGGGGGGTT--S-.EEE--SS-- CS
                          LRR_8  24 lsnLkvLdLsnNllttlspgafsgLpsLrsLdLsgNrL 61 
                                    + +L +LdLs+N l  ++   f+    Lr+L+L g+++
  gene184|gene184|rna184|rna184 344 WDRLAHLDLSYNPLVNFE--NFDRI-ELRFLNLKGTDI 378
                                    6789********999996..*****.********9987 PP

>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   1.3e+04       5      15 ..     137     147 ..     136     148 .. 0.85
   2 !    9.7   0.0   0.00021      0.93       3      17 ..     156     170 ..     154     171 .. 0.85
   3 ?    2.0   0.0     0.063   2.8e+02       7      16 ..     180     189 ..     179     191 .. 0.89
   4 ?    1.2   0.1      0.11   5.1e+02       8      16 ..     199     207 ..     198     207 .. 0.88
   5 ?    1.4   0.0       0.1   4.5e+02       6      15 ..     216     225 ..     216     226 .. 0.85
   6 ?   -2.7   0.1         2   9.1e+03       5      15 ..     269     279 ..     268     280 .. 0.81
   7 !    4.8   0.0     0.008        36       3      14 ..     306     317 ..     306     321 .. 0.86
   8 ?    2.2   0.0     0.054   2.4e+02       5      14 ..     347     356 ..     346     358 .. 0.84
   9 ?   -1.5   0.0      0.82   3.7e+03       5      15 ..     368     378 ..     368     380 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                          LRR_6   5 LteLdLsgNdI 15 
                                    L++L L  + I
  gene184|gene184|rna184|rna184 137 LRKLKLVNCRI 147
                                    89999999988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                          LRR_6   3 thLteLdLsgNdIgD 17 
                                    + L +LdLs+NdI++
  gene184|gene184|rna184|rna184 156 MRLAYLDLSHNDISG 170
                                    56889********97 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.063
                          LRR_6   7 eLdLsgNdIg 16 
                                    +++Ls+N+I+
  gene184|gene184|rna184|rna184 180 TVNLSHNEIS 189
                                    68******96 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.11
                          LRR_6   8 LdLsgNdIg 16 
                                    Ld+s+N+++
  gene184|gene184|rna184|rna184 199 LDVSHNKVT 207
                                    9*****986 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.1
                          LRR_6   6 teLdLsgNdI 15 
                                    + LdLs+N +
  gene184|gene184|rna184|rna184 216 RRLDLSYNPL 225
                                    68******76 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 2
                          LRR_6   5 LteLdLsgNdI 15 
                                    L  L++++++I
  gene184|gene184|rna184|rna184 269 LVFLSINDCGI 279
                                    7779999*998 PP

  == domain 7  score: 4.8 bits;  conditional E-value: 0.008
                          LRR_6   3 thLteLdLsgNd 14 
                                    ++L++Ld+s+N 
  gene184|gene184|rna184|rna184 306 PSLEYLDISSNL 317
                                    58*********6 PP

  == domain 8  score: 2.2 bits;  conditional E-value: 0.054
                          LRR_6   5 LteLdLsgNd 14 
                                    L +LdLs+N 
  gene184|gene184|rna184|rna184 347 LAHLDLSYNP 356
                                    679******7 PP

  == domain 9  score: -1.5 bits;  conditional E-value: 0.82
                          LRR_6   5 LteLdLsgNdI 15 
                                    L+ L+L+g dI
  gene184|gene184|rna184|rna184 368 LRFLNLKGTDI 378
                                    789*****999 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.92   4.1e+03       2      15 ..     137     149 ..     136     154 .. 0.77
   2 ?    3.2   0.0     0.045     2e+02       2      13 ..     158     169 ..     157     177 .. 0.83
   3 ?   -1.7   0.0       1.8     8e+03       5      13 ..     181     189 ..     179     193 .. 0.79
   4 ?   -2.6   0.0       3.5   1.6e+04       5      13 ..     199     207 ..     198     211 .. 0.79
   5 ?    4.2   0.0     0.021        93       3      13 ..     216     226 ..     216     245 .. 0.84
   6 ?   -0.1   0.1      0.52   2.3e+03       1      16 [.     268     283 ..     268     286 .. 0.82
   7 ?   -3.1   0.0         4   1.8e+04       1      12 [.     288     299 ..     288     303 .. 0.78
   8 ?    3.7   0.0     0.031   1.4e+02       1      11 [.     307     317 ..     307     333 .. 0.82
   9 ?    6.2   0.3    0.0044        20       2      14 ..     347     359 ..     346     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.92
                          LRR_1   2 LrhLdLsnnpllgl 15 
                                    Lr+L L n+++  +
  gene184|gene184|rna184|rna184 137 LRKLKLVNCRIK-K 149
                                    999******983.3 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.045
                          LRR_1   2 LrhLdLsnnpll 13 
                                    L +LdLs+n ++
  gene184|gene184|rna184|rna184 158 LAYLDLSHNDIS 169
                                    779******985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.8
                          LRR_1   5 LdLsnnpll 13 
                                     +Ls+n ++
  gene184|gene184|rna184|rna184 181 VNLSHNEIS 189
                                    79****985 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.5
                          LRR_1   5 LdLsnnpll 13 
                                    Ld+s+n  +
  gene184|gene184|rna184|rna184 199 LDVSHNKVT 207
                                    99****865 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.021
                          LRR_1   3 rhLdLsnnpll 13 
                                    r+LdLs+npl+
  gene184|gene184|rna184|rna184 216 RRLDLSYNPLE 226
                                    79*******93 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 0.52
                          LRR_1   1 nLrhLdLsnnpllglp 16 
                                    nL  L ++++ + +l+
  gene184|gene184|rna184|rna184 268 NLVFLSINDCGIRCLS 283
                                    7899******997765 PP

  == domain 7  score: -3.1 bits;  conditional E-value: 4
                          LRR_1   1 nLrhLdLsnnpl 12 
                                    +Lr+L  +nn +
  gene184|gene184|rna184|rna184 288 KLRVLKARNNLI 299
                                    799998888866 PP

  == domain 8  score: 3.7 bits;  conditional E-value: 0.031
                          LRR_1   1 nLrhLdLsnnp 11 
                                    +L++Ld+s+n 
  gene184|gene184|rna184|rna184 307 SLEYLDISSNL 317
                                    69*******96 PP

  == domain 9  score: 6.2 bits;  conditional E-value: 0.0044
                          LRR_1   2 LrhLdLsnnpllg 14 
                                    L hLdLs+npl +
  gene184|gene184|rna184|rna184 347 LAHLDLSYNPLVN 359
                                    77********933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (781 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 4542.53
//
Query:       gene1841|gene1841|rna1840|rna1840  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-10   41.8   0.6    1.7e-10   41.2   0.6    1.3  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
       0.03   14.6   0.3      0.041   14.2   0.3    1.3  1  Img2      Mitochondrial large subunit ribosomal protein (Img2


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.6   1.9e-14   1.7e-10       3      64 ..      35      93 ..      33     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.9e-14
                               SUI1  3 pkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrk 64
                                       + i+++++q++g KkvT+++++   g   ++l++ lkk+++c+g   +d+   iq+QGd  +
  gene1841|gene1841|rna1840|rna1840 35 NIIRVKVQQKKGTKKVTIIENI--PGELRESLLSSLKKEMGCGGILLDDK-SSIQLQGDKTN 93
                                       579*******************..455679***************99988.79******875 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   4.6e-06     0.041      20      61 ..      43      94 ..      29     112 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-06
                               Img2 20 krggtkkltvirkieGDia.alredLrkalee.........lvkvnevtgki 61
                                       +++gtkk+t+i +i G++   l + L+k ++          +++++  + + 
  gene1841|gene1841|rna1840|rna1840 43 QKKGTKKVTIIENIPGELReSLLSSLKKEMGCggillddksSIQLQGDKTNM 94
                                       457*************976368888888887544333332224444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 811.83
//
Query:       gene1842|gene1842|rna1841|rna1841  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-07   30.1   0.1    9.7e-07   28.5   0.0    1.9  2  RRM_1        RNA recognition motif. (a.k.a. RRM, RBD, or RNP 
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.078   13.0   0.0    1.7  1  Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
       0.21   12.1   2.1          1    9.9   2.1    2.2  1  zf-CCCH_2    RNA-binding, Nab2-type zinc finger


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.4   8.3e+03      21      33 ..      13      25 ..       7      26 .. 0.75
   2 !   28.5   0.0   1.6e-10   9.7e-07      17      70 .]      47     101 ..      37     101 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                                       TTSCEEEEEEEEE CS
                              RRM_1 21 kfGpiksiklvrd 33
                                         G++++i+++ +
  gene1842|gene1842|rna1841|rna1841 13 SGGSFSNIRVIQK 25
                                       5688999999875 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.6e-10
                                        HHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                              RRM_1  17 elFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                        e+F++fG ik+i + +  +   s+  a++++ + e+A+ +++++++  l+g++lk
  gene1842|gene1842|rna1841|rna1841  47 EFFGQFGAIKKIVVNKRtSSLESTASAYITYSTDEEAKTCIQEVDESLLDGKVLK 101
                                        89**************99999*******************************986 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.3e-05     0.078      19      51 ..      47      85 ..      38      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.3e-05
                        Nup35_RRM_2 19 ehFasfGeIvkhyvp......kevsvmyvkfesekdaek 51
                                       e+F +fG I k+ v        ++ ++y+++ +  +a++
  gene1842|gene1842|rna1841|rna1841 47 EFFGQFGAIKKIVVNkrtsslESTASAYITYSTDEEAKT 85
                                       5**************999999999*******99988875 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.1   0.00017         1       2      17 ..     110     128 ..     100     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                          zf-CCCH_2   2 Crffpn...CtnpkCpFaH 17 
                                        C f+     C n +C++ H
  gene1842|gene1842|rna1841|rna1841 110 CTFYLRnaiCQNSDCMYLH 128
                                        888888999********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1428.07
//
Query:       gene1843|gene1843|rna1842|rna1842  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-30  105.1   0.0    3.5e-30  104.9   0.0    1.0  1  Proteasome  Proteasome subunit
  ------ inclusion threshold ------
      0.073   12.5   0.0        0.1   12.1   0.0    1.2  1  Lyase_8     Polysaccharide lyase family 8, super-sandwich dom


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.9   0.0   3.9e-34   3.5e-30       2     189 ..      30     213 ..      29     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.9 bits;  conditional E-value: 3.9e-34
                                        HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                         Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                        + G tvvG++ k   +l+a +     s l++ +  +K+f id++ +++f+G ++D++++v+++  +  ++++  gr
  gene1843|gene1843|rna1842|rna1842  30 ELGNTVVGLRNKKVGILIAHNEKR--SRLADAQ--KKVFSIDKRSLFTFSGITNDGEQIVDYLIDKSIREEIIKGR 101
                                        579****************96666..9995555..9**************************************** PP

                                        GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHH CS
                         Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktaleke 153
                                        p +   + + + + + + t  +grr +gvs l++   e +g +L +++p G   e  + ++iG++s++ +t+le+ 
  gene1843|gene1843|rna1842|rna1842 102 PTHFLDVFEDLLRDTFERTIVDGRRLYGVSGLYMT--EYEGIRLVEFNPKGYAREV-NGMSIGCRSQSSRTVLEAY 174
                                        ********************************655..45569**************.7****************** PP

                                        H..STTBSHHHHHHHHHHHHHHHH.HHBTTSCSSEEEEE CS
                         Proteasome 154 y..kedltleeavelavkalkeal.erdklsgknievav 189
                                            e+++ ee+v++ + alk+a+ e+d+l+++n+e+ v
  gene1843|gene1843|rna1842|rna1842 175 CekYENMNTEELVRVGIMALKNAHpEDDALTSENVEIWV 213
                                        9999********************999**********98 PP

>> Lyase_8  Polysaccharide lyase family 8, super-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.1e-05       0.1      92     163 ..      27      96 ..      14     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                                        ----S-S-EEEEESSSCEEEEEEEEETT..SSEEEEEEEEEESS-EEEEEEEEEE-SSSEEEEEEEEEEEET CS
                            Lyase_8  92 atkskesfvGGvsdgeyGaagmdlkkkgakstltakKsWfflddeivalgagitssstaaveTtidqrklng 163
                                        +t++  + v G+ + ++G+   + +k+   + + a+K  f +d++ ++  +git++ ++ v   id+ ++++
  gene1843|gene1843|rna1842|rna1842  27 QTTELGNTVVGLRNKKVGILIAHNEKRS--RLADAQKKVFSIDKRSLFTFSGITNDGEQIVDYLIDKSIREE 96 
                                        455566788899999******9999999..779************************998988888877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 1340.40
//
Query:       gene1844|gene1844|rna1843|rna1843  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.16   12.4   0.0       0.21   12.0   0.0    1.2  1  MitMem_reg  Maintenance of mitochondrial structure and functi


Domain annotation for each model (and alignments):
>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.2e-05      0.21      34      92 ..      38     102 ..      18     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.2e-05
                         MitMem_reg  34 kilqerldlikdYlkkve....egelpvnhe..ilrnlqkllnllPhleteelekefnvetnDvl 92 
                                        + +++  ++ik Y k+v     ++ l  n+   +l+ + k+++ l  l+++++e+++ + + Dv 
  gene1844|gene1844|rna1843|rna1843  38 ETMEDLEERIKGYFKEVLrvspTDSLYFNEGfrMLNFVEKIFKELRELNESAMERSIRSPMDDVI 102
                                        557888888*********4444444666666669***********************99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 837.17
//
Query:       gene1845|gene1845|rna1844|rna1844  [L=205]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-32  109.7   4.1      5e-15   55.4   0.0    2.4  2  Myb_DNA-binding  Myb-like DNA-binding domain
    5.6e-26   90.6   5.6    4.4e-18   65.3   0.8    2.4  2  Myb_DNA-bind_6   Myb-like DNA-binding domain
  ------ inclusion threshold ------
       0.01   15.9   0.1        4.5    7.3   0.1    2.6  2  SLIDE            SLIDE
      0.018   15.0   0.2      0.018   15.0   0.2    2.7  3  Myb_DNA-bind_7   Myb DNA-binding like
      0.018   15.2   0.2        3.7    7.8   0.0    2.4  2  SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
       0.14   12.3   0.3       0.62   10.2   0.1    2.1  2  Spore_III_AB     Stage III sporulation protein AB (spore_III_


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   2.0   4.9e-18   1.5e-14       1      46 []      20      66 ..      20      66 .. 0.98
   2 !   55.4   0.0   1.7e-18     5e-15       1      43 [.      72     114 ..      72     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 4.9e-18
                                       CSSSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHHHHHT CS
                    Myb_DNA-binding  1 rgkWteeEdelLleavkkhG.nrWkkIaerlggRtekqcrsrwrnyl 46
                                       +g+W  eEde+Ll++vk++  ++W+ Ia++lg+R +kqcr+rw+n+l
  gene1845|gene1845|rna1844|rna1844 20 KGPWRHEEDEKLLKLVKEFSpKNWSFIAKKLGSRVGKQCRERWHNHL 66
                                       79******************9************************97 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 1.7e-18
                                        CSSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHH CS
                    Myb_DNA-binding   1 rgkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwr 43 
                                        ++++t eE+ l++e++ k+GnrW++Ia++l+gRt+++++++w+
  gene1845|gene1845|rna1844|rna1844  72 KKPFTMEEEALIIELHSKFGNRWSEIAKYLPGRTDNAIKNYWN 114
                                        689***************************************8 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.8   1.5e-21   4.4e-18       1      57 [.      23      80 ..      23      82 .. 0.96
   2 !   33.8   0.4   9.9e-12     3e-08       1      46 [.      75     120 ..      75     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 1.5e-21
                     Myb_DNA-bind_6  1 WteeEdeiLlklvekyg.ndWknIaealnrRtpkqcfdrwknkLrpkisrkkwskeed 57
                                       W +eEde+Llklv++++ ++W+ Ia+ l+ R  kqc++rw+n+L+p+i +k+++ ee+
  gene1845|gene1845|rna1844|rna1844 23 WRHEEDEKLLKLVKEFSpKNWSFIAKKLGSRVGKQCRERWHNHLNPQITKKPFTMEEE 80
                                       99**************9669********99*************************998 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 9.9e-12
                     Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkLrpk 46 
                                        +t eE+ ++++l++k+gn W++Ia+ l+ Rt ++++++w++++  +
  gene1845|gene1845|rna1844|rna1844  75 FTMEEEALIIELHSKFGNRWSEIAKYLPGRTDNAIKNYWNSSIQRR 120
                                        799************************55************77333 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0042        12      49      79 ..      20      50 ..       3      55 .. 0.82
   2 ?    7.3   0.1    0.0015       4.5      44     102 ..      68     120 ..      53     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0042
                              SLIDE 49 kkeyteeeDrfllvllakyGygnyekikkei 79
                                       k  ++ eeD+ ll l++++  +n+  i k++
  gene1845|gene1845|rna1844|rna1844 20 KGPWRHEEDEKLLKLVKEFSPKNWSFIAKKL 50
                                       44599******************99998765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0015
                              SLIDE  44 psnkgkkeyteeeDrfllvllakyGygnyekikkeiresplFrfDwflksrtpqelqkR 102
                                        p+ ++k  +t ee++ ++ l +k+G + + +i k +      r D  +k +  + +q+R
  gene1845|gene1845|rna1844|rna1844  68 PQITKKP-FTMEEEALIIELHSKFGNR-WSEIAKYLPG----RTDNAIKNYWNSSIQRR 120
                                        5666676.****************976.8888776543....44555555555555555 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.21   6.4e+02       9      49 ..      21      62 ..      15      72 .. 0.74
   2 ?   15.0   0.2   5.9e-06     0.018       7      62 ..      71     126 ..      65     148 .. 0.83
   3 ?   -0.5   0.1      0.39   1.2e+03      56      80 ..     168     192 ..     158     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.21
                     Myb_DNA-bind_7  9 kkWskeetekFYkaLsqfG.tDFsliaklfpkrtrrqlKlKF 49
                                        +W +ee ek  k +++f   ++s+iak + +r  +q ++++
  gene1845|gene1845|rna1844|rna1844 21 GPWRHEEDEKLLKLVKEFSpKNWSFIAKKLGSRVGKQCRERW 62
                                       579999999988888887535777777777777766666655 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 5.9e-06
                     Myb_DNA-bind_7   7 ktkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKFkkEerknpeliek 62 
                                        ++k+ + ee  +  +  s+fG  +s iak++p+rt++ +K+ +++  ++++e++++
  gene1845|gene1845|rna1844|rna1844  71 TKKPFTMEEEALIIELHSKFGNRWSEIAKYLPGRTDNAIKNYWNSSIQRRSEKVRR 126
                                        567788889999999999**************************999999999876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.39
                     Myb_DNA-bind_7  56 npeliekalkkrkeldleefkeeae 80 
                                          + i++ +++ +++d ++f+e+ e
  gene1845|gene1845|rna1844|rna1844 168 SVQDISEHVSNARSFDEDDFDEMDE 192
                                        4578888899999999999988765 PP

>> SANT_DAMP1_like  SANT/Myb-like domain of DAMP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0012       3.7      26      52 ..      20      47 ..       3      57 .. 0.77
   2 ?    5.1   0.0    0.0085        25      18      52 ..      60      98 ..      52     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0012
                    SANT_DAMP1_like 26 eedWtkeetdyLfdlckeydlr.fvvia 52
                                       +  W +ee ++L++l+ke+  + +  ia
  gene1845|gene1845|rna1844|rna1844 20 KGPWRHEEDEKLLKLVKEFSPKnWSFIA 47
                                       456****************854366665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0085
                    SANT_DAMP1_like 18 eeYeellke....edWtkeetdyLfdlckeydlrfvvia 52
                                       e ++++l+     +  t ee   +++l +++  r+  ia
  gene1845|gene1845|rna1844|rna1844 60 ERWHNHLNPqitkKPFTMEEEALIIELHSKFGNRWSEIA 98
                                       5566666664543669*******************9876 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00021      0.62      70     119 ..      43      92 ..      24      98 .. 0.84
   2 ?   -1.2   0.0      0.65     2e+03      15      36 ..     151     172 ..     138     199 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                                        HHHHHHHHH.STSS-HHHHHHHHHHHHGGGS---HHHHHHHHHHHHHHT- CS
                       Spore_III_AB  70 feevaerleekegesfeeaweeavekllkklaLkkedkeilkelgeslgy 119
                                        ++ +a++l ++ g++ +e+w+++++ ++ k +++ e+ +++ el +++g+
  gene1845|gene1845|rna1844|rna1844  43 WSFIAKKLGSRVGKQCRERWHNHLNPQITKKPFTMEEEALIIELHSKFGN 92 
                                        455788888889********************************999996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.65
                                        XXXXXXXXXXHHHHHHHHHHHH CS
                       Spore_III_AB  15 iGfalakrlkrrlkeleelkra 36 
                                        +G+ l+++++++ k+   ++ +
  gene1845|gene1845|rna1844|rna1844 151 LGISLQANMSQKTKRSSSVQDI 172
                                        3333333333333333322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1413.23
//
Query:       gene1846|gene1846|rna1845|rna1845  [L=320]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-49  167.3   1.7    5.1e-49  166.8   1.7    1.2  1  RabGAP-TBC  Rab-GTPase-TBC domain


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   1.7   2.8e-53   5.1e-49      34     215 .]      96     276 ..      75     276 .. 0.89

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 2.8e-53
                         RabGAP-TBC  34 eksklekseeskelsqIkkDvprtfpes..esfknkqgqnqLeriLkaysiynpevgYcqGmndivaplllvslde 107
                                        ++  +  s++s +++qI+ Dv+rtf+ +  ++++++ gq +L++iL ays+ynpevgYcqGm+ ++a+ll ++ +e
  gene1846|gene1846|rna1845|rna1845  96 NY-SNLISKKSGYEHQIHVDVQRTFRRHflFNKEYGRGQCELFNILTAYSNYNPEVGYCQGMSSVAALLL-MYFPE 169
                                        33.44555667889************66477777789*********************************.88899 PP

                         RabGAP-TBC 108 eeaFwcfvsLlekyklrdlytsslpglkrklkvleellkkkdpklykhlkeegldlelfaikwfltlflrefplet 183
                                        eeaF ++vs++++++l+ l+ ++l+++ r +++ +e++k+  p++y hl ++++d+ ++a+ w+ltlf + f++++
  gene1846|gene1846|rna1845|rna1845 170 EEAFEMLVSIIKNNNLEALFDKKLSKVPRVQRIQDEVFKALIPEVYGHLLHQNIDIGVYAVGWYLTLF-TRFDIKL 244
                                        99******************************************************************.77***** PP

                         RabGAP-TBC 184 vlrlwDlllege.kfvllrvalailklleeell 215
                                        vlr+wD++l+ + +  ++++a+ ilk++  ++l
  gene1846|gene1846|rna1845|rna1845 245 VLRMWDFFLFFDfSA-FIFFAAGILKFFARKIL 276
                                        ******666445255.8899999*****99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2172.36
//
Query:       gene1847|gene1847|rna1846|rna1846  [L=193]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-10   40.7   7.5    4.7e-10   39.6   7.5    1.6  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   7.5   2.6e-14   4.7e-10       2     220 ..      12     183 ..      11     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2.6e-14
                                        XXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX.....................XXXXXXXXXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin   2 kyllfffnllfwligivllavG..vwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigalken 75 
                                        k+++ff+  l+++ g+   +vG  v+l           +++e  + p  + ++  ++++l +l ++lG  + + ++
  gene1847|gene1847|rna1846|rna1846  12 KVVFFFIQALVFISGVGGSIVGttVYL-----------TAHELLQIPEKVLVISYLLSILEVLSAILGYTALVSRR 76 
                                        899******************955666...........344556788888899999******************** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXX--HHH........HHHHHHHHHHHHHHHHHH.THHHHHHHHHHT---SSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                        Tetraspanin  76 kcllltfsllllvlfllelaagilgfvfsdkargkvseiinnaievkyrddldlkkc.qnlldslqkklsCCGvns 150
                                        k  +l+++l+ l+l+ ++ ++++ g++ +++             ++ + d+  ++   +n  +++q+k++CCG+++
  gene1847|gene1847|rna1846|rna1846  77 KLRMLVYVLITLILMNTQAMMAVKGWTIYER-------------SRAWGDWRWSS-LtENQRSFVQTKFKCCGFSN 138
                                        ***********************99999999.............45566665553.3389**************99 PP

                                        H..HHGSSTT-SSSCGCC..................S--HHHHHHHHC--XXXXX.XXXX.XXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        Tetraspanin 151 ykDwsdnpsrencsvPesCclptpnqayleasksiytegCidklvnwiksnlkllgggvaalgliqlvgi 220
                                        ++D          s P +C                  +gC d +++  ++   l+  ++++l +++ vgi
  gene1847|gene1847|rna1846|rna1846 139 PTDR---------SGP-NCGG---------------GKGCADVVYKLSRNVSVLMQRILMFLFFFESVGI 183
                                        9998.........333.4554...............4677777777666666666666665555776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1268.40
//
Query:       gene1848|gene1848|rna1847|rna1847  [L=388]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-06   27.3  13.0    2.1e-06   27.3  13.0    2.8  3  DUF4407         Domain of unknown function (DUF4407)
     0.0029   17.7   9.5         11    6.0   0.1    4.9  6  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
  ------ inclusion threshold ------
      0.039   13.4  34.2       0.59    9.5  21.0    3.1  3  Golgin_A5       Golgin subfamily A member 5
      0.059   13.0  36.1       0.61    9.6   8.8    4.4  3  Filament        Intermediate filament protein
      0.081   13.0   0.0      0.081   13.0   0.0    4.0  4  DUF1515         Protein of unknown function (DUF1515)
       0.27    9.6  43.2     0.0084   14.5  30.9    2.9  3  MAD             Mitotic checkpoint protein
       0.41   10.7  27.3        2.2    8.3   0.1    5.4  5  DUF1664         Protein of unknown function (DUF1664)
       0.68   10.4  18.1         15    6.1   0.1    5.9  5  NPV_P10         Nucleopolyhedrovirus P10 protein
       0.84    9.7  41.2      0.019   15.0   9.6    3.3  3  SYCE1           Synaptonemal complex central element protein 
        1.1    9.6  34.8        4.6    7.6  19.5    3.3  3  Fez1            Fez1
        1.5    8.8  43.6        1.6    8.8   1.9    5.3  5  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        1.6    9.4  18.7        6.4    7.5   0.2    5.8  5  SlyX            SlyX
        1.9    8.6  35.1        6.1    7.0  12.7    4.8  3  ATG16           Autophagy protein 16 (ATG16)
        3.3    7.9  33.2       0.26   11.4   5.8    4.9  4  Fib_alpha       Fibrinogen alpha/beta chain family
        4.7    6.8   7.6         15    5.2   0.1    4.2  4  YvrJ            YvrJ protein family
        5.9    7.0  20.4        9.7    6.3   0.6    5.4  6  TolA_bind_tri   TolA binding protein trimerisation
        8.6    6.8  20.1         17    5.9   1.5    5.7  6  LPP             Lipoprotein leucine-zipper
        8.7    5.6  14.1        0.7    9.1   0.0    3.6  4  CorA            CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4     0.016        16     173     233 ..       8      82 ..       1     112 [. 0.76
   2 !   27.3  13.0   2.1e-09   2.1e-06     102     235 ..     132     275 ..     130     298 .. 0.81
   3 ?   -0.3   0.0      0.56   5.6e+02     122     145 ..     345     368 ..     316     375 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.016
                            DUF4407 173 tgttgvaGkgpaakekkaqldaaqaelaelkakld..............atarlaalraelaeleaerakeraas 233
                                        ++++g++ + ++  e +++l + +a +++l++k++                ++l++l +e+++l+++r+k+ +++
  gene1848|gene1848|rna1847|rna1847   8 KRIPGIHSYLAVIGELRQELGKVTASINDLRDKISsiykqerenspkndLYKKLDELGSEIKSLKEDRSKAFNSK 82 
                                        556667778888888899999999999999999888888888777777766777777777777777776665544 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.1e-09
                            DUF4407 102 kiFekeIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttg 177
                                        k+Fe+eI+   +++++  + e+k++la +++a+l+ l+++i++l++ i+++++ +d  +ae++ e++ + + + + 
  gene1848|gene1848|rna1847|rna1847 132 KMFESEIENLRKQKKNIGVLEQKSKLALDMKAKLDVLNSEIKDLSQRIAEKQSIVDGIKAELK-EINDQEKPKNPT 206
                                        79***********************************************************99.555555556677 PP

                            DUF4407 178 vaGkgpaakekkaqldaaqaelaelkakld..............atarlaalraelaeleaerakeraasqa 235
                                        ++G++++ ++ k++  ++++++++ ++k++               ++   al+++++e+++++++ +++++a
  gene1848|gene1848|rna1847|rna1847 207 IEGYEKNIQALKSKRGELSEKIKAQQEKIRekeieydkfleemaIAQ---ALEKQKEEIKQRISALEEQKNA 275
                                        9***********************99999999999999999555444...4444444444444444433333 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.56
                            DUF4407 122 elkeqlaaaltaelaeleaqiaal 145
                                        ++  + ++++++++++le++i++ 
  gene1848|gene1848|rna1847|rna1847 345 SQVVEKRKEFESRISDLERKISEE 368
                                        111111222444444444444433 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.011        11      32      83 ..      19      75 ..      11      88 .. 0.66
   2 ?    4.0   0.2     0.047        46      39      73 ..      53      87 ..      30     124 .. 0.74
   3 ?    3.3   1.6     0.079        79      65     115 ..     134     193 ..     100     201 .. 0.52
   4 ?    3.5   1.6     0.069        69      41      80 ..     159     197 ..     135     236 .. 0.48
   5 ?    4.0   1.2     0.048        48      30      60 ..     249     279 ..     211     292 .. 0.77
   6 ?    3.3   0.0     0.077        76      18      56 ..     329     367 ..     323     377 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                       Baculo_PEP_C 32 ilaqlatlldaietqLnalsedlksllaeldt.....rldtlltnLtdalnalqdtl 83
                                       ++++l + l ++  ++n+l ++++s  ++ ++     +l + l++L + +++l+++ 
  gene1848|gene1848|rna1847|rna1847 19 VIGELRQELGKVTASINDLRDKISSIYKQEREnspknDLYKKLDELGSEIKSLKEDR 75
                                       447777777777777777777777766655446666677777777777777777544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.047
                       Baculo_PEP_C 39 lldaietqLnalsedlksllaeldtrldtlltnLt 73
                                        ++++ ++L++l +++ksl ++ ++++++ +++L 
  gene1848|gene1848|rna1847|rna1847 53 PKNDLYKKLDELGSEIKSLKEDRSKAFNSKSEALG 87
                                       4678889999********99999999999999885 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.079
                       Baculo_PEP_C  65 ldtlltnLtdalnalq.........dtlrneLtnlnsiltnLlssvtNinstLnnllqal 115
                                        +++ ++nL ++ +++           +++ +L+ lns++ +L   ++  +s + ++ + l
  gene1848|gene1848|rna1847|rna1847 134 FESEIENLRKQKKNIGvleqksklaLDMKAKLDVLNSEIKDLSQRIAEKQSIVDGIKAEL 193
                                        444444444443333333333333345566666666666666666665555444444444 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.069
                       Baculo_PEP_C  41 daietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                         +++ +L+ l++++k+l++ ++++ ++ ++ +++ l++++
  gene1848|gene1848|rna1847|rna1847 159 LDMKAKLDVLNSEIKDLSQRIAEK-QSIVDGIKAELKEIN 197
                                        334444444444444444444432.333333444444443 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.048
                       Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllae 60 
                                        + i+ +l++++++i+++++al+e+ ++l++e
  gene1848|gene1848|rna1847|rna1847 249 MAIAQALEKQKEEIKQRISALEEQKNALSKE 279
                                        5677888888888888888888776666554 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.077
                       Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlks 56 
                                        ++++++ +++q+   ++q+ +  ++ e+++++l+ ++++
  gene1848|gene1848|rna1847|rna1847 329 MNPTIEVLKSQKKDFASQVVEKRKEFESRISDLERKISE 367
                                        788899999999999999999999999999999998876 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.0     0.006         6      70     180 ..      20     122 ..       2     133 .. 0.66
   2 ?    9.5  21.0    0.0006      0.59      33     177 ..     122     271 ..     118     279 .. 0.76
   3 ?    3.7   0.1     0.035        35     116     155 ..     333     372 ..     323     379 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.006
                          Golgin_A5  70 ieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdre 145
                                        i +lr+el ++ a     ++ lr++++++ +q + e++ k+++ ++l +l  e+++l+e+ +++ ++  + +   e
  gene1848|gene1848|rna1847|rna1847  20 IGELRQELGKVTA----SINDLRDKISSIYKQER-ENSPKNDLYKKLDELGSEIKSLKEDRSKAFNSKSEALGAYE 90 
                                        5555555554444....45777888888888776.67777788888888888888888888877666666665444 PP

                          Golgin_A5 146 keieklrnqlttk.slsssseselesRlkqLtesLi 180
                                        +    ++ +++ +  ++  s +e+++R++++   Li
  gene1848|gene1848|rna1847|rna1847  91 T----IKGEVQPEkGKKMMSAQEIDNRMREINLKLI 122
                                        4....3444433213344467888888888776666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0006
                          Golgin_A5  33 gsgeeglesstalsaeldelkqerdl.....lree.lqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeql 102
                                         s++ +++ +++ + e+++l+++++      ++++   +++ +++ l +e++dl ++  ae +s+ + ++   +++
  gene1848|gene1848|rna1847|rna1847 122 ISTKCDSKMEKMFESEIENLRKQKKNigvleQKSKlALDMKAKLDVLNSEIKDLSQRI-AEKQSIVDGIKAELKEI 196
                                        455566666777888899886555431221122221346788999*********9998.55555555555555556 PP

                          Golgin_A5 103 eeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrnqlttkslsssseselesRlkqLte 177
                                        + ++k k+ + +  e+  + l++ + el+++ +  q++i+++e e +k  ++++  +  + +++e+ +R+ +L e
  gene1848|gene1848|rna1847|rna1847 197 NDQEKPKNPTIEGYEKNIQALKSKRGELSEKIKAQQEKIREKEIEYDKFLEEMAIAQALEKQKEEIKQRISALEE 271
                                        6666677777778999999*************************************9999************988 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.035
                          Golgin_A5 116 lerlkeelryleeelvrskatlqsrikdrekeieklrnql 155
                                        +e lk + +   +++v+++++++sri d e++i++ r+ l
  gene1848|gene1848|rna1847|rna1847 333 IEVLKSQKKDFASQVVEKRKEFESRISDLERKISEERKVL 372
                                        4444445555555666666666666666666666666555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   8.8   0.00061      0.61      28     153 ..      35     147 ..      29     168 .. 0.76
   2 ?    2.5   2.9      0.09        89      21      48 ..     253     280 ..     243     310 .. 0.77
   3 ?    2.5   0.0     0.087        87     233     267 ..     334     368 ..     324     377 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00061
                                        XXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           Filament  28 keLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEa 103
                                        ++L+ ki+  +++ ++e+s  ++ly k+l+el +++++l+++r+++    +++  ++e+++  ++ e +k++   +
  gene1848|gene1848|rna1847|rna1847  35 NDLRDKISSIYKQ-ERENSPKNDLY-KKLDELGSEIKSLKEDRSKAFNSKSEALGAYETIKGEVQPEKGKKMMSAQ 108
                                        5799999999999.88888777777.67********************************************9999 PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX CS
                           Filament 104 elkalrkdldeatlarvdLekkvesLke.elaflkkvheeEvkelqkqvse 153
                                        e+ +  ++++ + l  +  ++k+e++ e e++ l+k           q ++
  gene1848|gene1848|rna1847|rna1847 109 EIDNRMREIN-LKLISTKCDSKMEKMFEsEIENLRK-----------QKKN 147
                                        9999999985.5566666777777553325555554...........3333 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.09
                                        XXXXXXXXXXXXXXXXXXXXXXXXXX.X CS
                           Filament  21 raLEqenkeLeakieeleekksaevskl 48 
                                        +aLE++++e++++i++lee+k+a +++ 
  gene1848|gene1848|rna1847|rna1847 253 QALEKQKEEIKQRISALEEQKNALSKEE 280
                                        7899999999999999999975443332 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.087
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Filament 233 eslkkqkasleaqlaeleerleaeleklqeklsel 267
                                        e lk+qk+   +q+ e  +++e+ +++l++k+se 
  gene1848|gene1848|rna1847|rna1847 334 EVLKSQKKDFASQVVEKRKEFESRISDLERKISEE 368
                                        44444444444444444444444444444444443 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.2e-05     0.081       2      54 ..      19      73 ..      18     100 .. 0.87
   2 ?    1.2   1.3      0.36   3.6e+02      14      59 ..     135     182 ..     121     204 .. 0.58
   3 ?    0.5   2.5      0.59   5.8e+02       7      63 ..     218     280 ..     207     303 .. 0.67
   4 ?   -0.1   0.2      0.95   9.4e+02      38      70 ..     347     379 ..     332     387 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                            DUF1515  2 idagvlqqlgtllaevkelredlk..rsedrsdasrakmyrkmdelvervtaleg 54
                                       +++ + q+lg++ a +++lr+++     ++r ++ + ++y+k+del   +++l+ 
  gene1848|gene1848|rna1847|rna1847 19 VIGELRQELGKVTASINDLRDKISsiYKQERENSPKNDLYKKLDELGSEIKSLKE 73
                                       67899******************966567899999***********998888765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.36
                            DUF1515  14 laevkelredlk...rsedrsdasrakmyrkmdelvervtalegsvvkl 59 
                                         +e+++lr++ k     e++s+ +  +m+ k+d l   ++ l   +++ 
  gene1848|gene1848|rna1847|rna1847 135 ESEIENLRKQKKnigVLEQKSKLA-LDMKAKLDVLNSEIKDLSQRIAEK 182
                                        568889988777554567777654.567777776666655554444332 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.59
                            DUF1515   7 lqqlgtllaevkelredlkrsedrsd......asrakmyrkmdelvervtalegsvvklkadi 63 
                                        + + g+l  ++k  +e++++ e   d      a+   + ++ +e+ +r++ale    +l ++ 
  gene1848|gene1848|rna1847|rna1847 218 KSKRGELSEKIKAQQEKIREKEIEYDkfleemAIAQALEKQKEEIKQRISALEEQKNALSKEE 280
                                        555667777777777777744433221111114455677888899999999998877776655 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.95
                            DUF1515  38 myrkmdelvervtalegsvvklkaditsvkevt 70 
                                        + +k  e+  r++ le  +++ ++ +t++ +  
  gene1848|gene1848|rna1847|rna1847 347 VVEKRKEFESRISDLERKISEERKVLTAMPPTD 379
                                        334444555666666666666666666666555 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.1      0.12   1.2e+02     423     464 ..      40      75 ..      13     104 .. 0.55
   2 ?   14.5  30.9   8.5e-06    0.0084      48     223 ..     112     290 ..      93     300 .. 0.81
   3 ?    1.1   0.2     0.095        94     186     209 ..     345     368 ..     328     386 .. 0.49

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.12
                                MAD 423 elqalrqqesladassskeevdslkkkleeLelerqrLreqk 464
                                         + +  +qe ++ +       + l+kkl+eL  e ++L+e +
  gene1848|gene1848|rna1847|rna1847  40 KISSIYKQERENSP------KNDLYKKLDELGSEIKSLKEDR 75 
                                        22222222222222......4566666666666666665543 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.5e-06
                                MAD  48 drnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiekq 123
                                        +r++e++ ++    k++++ e+  + +iE+ r++kkn   l+    +k++   +++   + l+ e+++l + i ++
  gene1848|gene1848|rna1847|rna1847 112 NRMREINLKLI-STKCDSKMEKMFESEIENLRKQKKNIGVLE----QKSKLALDMKAKLDVLNSEIKDLSQRIAEK 182
                                        45555555443.346778999999999***998888887764....56778888888899**************** PP

                                MAD 124 elelsekeseleelqerldllkkklseleqliqqlekkqkelae....aeqrikeLefeiqs...qeddslivkns 192
                                        ++ +   + el+e++ + + ++ +++++e+ iq l++k  el+e    ++++i+e e e  +       ++ +++ 
  gene1848|gene1848|rna1847|rna1847 183 QSIVDGIKAELKEINDQEKPKNPTIEGYEKNIQALKSKRGELSEkikaQQEKIREKEIEYDKfleEMAIAQALEKQ 258
                                        *************************************987765411116889999999999943333445568899 PP

                                MAD 193 ksel.aripelekelerlreenkklnelkenk 223
                                        k+e+ +ri+ le+++++l +e +kln +k + 
  gene1848|gene1848|rna1847|rna1847 259 KEEIkQRISALEEQKNALSKEESKLNPSKFDS 290
                                        999999********************888765 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.095
                                MAD 186 slivknskselaripelekelerl 209
                                        s++v++ k+   ri++le+++ + 
  gene1848|gene1848|rna1847|rna1847 345 SQVVEKRKEFESRISDLERKISEE 368
                                        223333332223333333333322 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.23   2.3e+02      97     121 ..      21      45 ..       3      48 .. 0.70
   2 ?    3.5   0.5     0.068        68      44     119 ..      55     132 ..      48     137 .. 0.74
   3 ?    5.5   4.8     0.017        17      56     120 ..     160     224 ..     135     230 .. 0.68
   4 ?    3.9   1.0     0.051        51      53      79 ..     251     277 ..     243     286 .. 0.77
   5 ?    8.3   0.1    0.0022       2.2      39      85 ..     329     375 ..     327     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
                            DUF1664  97 seigedvesvkeaveglesklerie 121
                                         e+++++ +v + +++l  k+++i 
  gene1848|gene1848|rna1847|rna1847  21 GELRQELGKVTASINDLRDKISSIY 45 
                                        4556777778888888888887773 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.068
                            DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav..egleskl 117
                                        +++ k+l+++ +++++ k++ s+  ++  + l + + i+ e++ e  +     +ei++ +++++     ++ +sk+
  gene1848|gene1848|rna1847|rna1847  55 NDLYKKLDELGSEIKSLKEDRSKAFNSKSEALGAYETIKGEVQPEKGKKMMSAQEIDNRMREINLKLisTKCDSKM 130
                                        4567888888888998888888888888888888888888888888888888888888888776432114456666 PP

                            DUF1664 118 er 119
                                        e+
  gene1848|gene1848|rna1847|rna1847 131 EK 132
                                        55 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.017
                            DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                        +++a  + L+s+i+ + +++ e + i   ik+e++e++++ +  +  +e  ++ ++ l+sk  ++
  gene1848|gene1848|rna1847|rna1847 160 DMKAKLDVLNSEIKDLSQRIAEKQSIVDGIKAELKEINDQEKPKNPTIEGYEKNIQALKSKRGEL 224
                                        44444455677777777777777777777777777777777777777777777777777766655 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.051
                            DUF1664  53 vseslaatkrhLssridrvdkkldeqk 79 
                                        + ++l+++k+++++ri  ++++ ++ +
  gene1848|gene1848|rna1847|rna1847 251 IAQALEKQKEEIKQRISALEEQKNALS 277
                                        457899999999999999998877654 PP

  == domain 5  score: 8.3 bits;  conditional E-value: 0.0022
                            DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskei 85 
                                        ++  +e + +q +++ +++ + +++++sri  +++k+ e  ++ +++
  gene1848|gene1848|rna1847|rna1847 329 MNPTIEVLKSQKKDFASQVVEKRKEFESRISDLERKISEERKVLTAM 375
                                        5566777888889999*********************9998887766 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.024        24      33      61 ..      16      44 ..       8      47 .. 0.85
   2 ?    6.1   0.1     0.015        15      10      56 ..      31      73 ..      27      97 .. 0.82
   3 ?    2.3   6.1      0.24   2.4e+02       8      38 ..     167     197 ..     105     239 .. 0.78
   4 ?    2.1   1.1      0.28   2.8e+02      16      61 ..     224     272 ..     211     293 .. 0.48
   5 ?   -0.6   0.0       1.9   1.9e+03      33      66 ..     339     373 ..     329     380 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                            NPV_P10 33 nlpdvtelnekLdaqsaqLaeletkvenI 61
                                        l  + el ++L + +a++++l +k+++I
  gene1848|gene1848|rna1847|rna1847 16 YLAVIGELRQELGKVTASINDLRDKISSI 44
                                       5666889*******************999 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                            NPV_P10 10 radikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56
                                        a i+++ dk++++ +   + +en+p+ ++l +kLd++  ++++l++
  gene1848|gene1848|rna1847|rna1847 31 TASINDLRDKISSIYK---QERENSPK-NDLYKKLDELGSEIKSLKE 73
                                       5678889999977765...56899999.88********999999986 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.24
                            NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvt 38 
                                        v  ++ik++++++   q+ vd ++++l++++
  gene1848|gene1848|rna1847|rna1847 167 VLNSEIKDLSQRIAEKQSIVDGIKAELKEIN 197
                                        3334555555555555555555555555533 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.28
                            NPV_P10  16 vddkVdalqqqvddvqenlpdv...telnekLdaqsaqLaeletkvenI 61 
                                        +++k++a q+++ + + +  ++     + + L++q +++++  +++e+ 
  gene1848|gene1848|rna1847|rna1847 224 LSEKIKAQQEKIREKEIEYDKFleeMAIAQALEKQKEEIKQRISALEEQ 272
                                        4555555555553222222222000223444444444443333333333 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.9
                            NPV_P10  33 nlpdv.telnekLdaqsaqLaeletkvenIqdiLn 66 
                                        + +d+ +++ ek  +    + +le k+++  ++L+
  gene1848|gene1848|rna1847|rna1847 339 QKKDFaSQVVEKRKEFESRISDLERKISEERKVLT 373
                                        44444245666777777788888888888888887 PP

>> SYCE1  Synaptonemal complex central element protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   9.6     2e-05     0.019      33     140 ..      52     162 ..      28     164 .. 0.88
   2 ?    3.4  19.8     0.075        74      32     152 .]     155     279 ..     150     279 .. 0.80
   3 ?    0.7   0.5       0.5   4.9e+02      68     102 ..     338     369 ..     328     374 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                              SYCE1  33 alkealkrElDsLnaEkvhLee....vlnkKqealriLqlhcqekeseaqrkqelseeckqrieeltskiqeeklk 104
                                        + k+ l + lD+L  E  +L+e     +n K eal   ++   e + e+ +k +  +e ++r+ e++ k+  +k+ 
  gene1848|gene1848|rna1847|rna1847  52 SPKNDLYKKLDELGSEIKSLKEdrskAFNSKSEALGAYETIKGEVQPEKGKKMMSAQEIDNRMREINLKLISTKCD 127
                                        456779999*******999997666689*********************************************997 PP

                              SYCE1 105 rrklrlefeeqleelmeqhkdlwefhveqrlakeir 140
                                          k+++ fe + e+l +q k++  ++++ +la +++
  gene1848|gene1848|rna1847|rna1847 128 S-KMEKMFESEIENLRKQKKNIGVLEQKSKLALDMK 162
                                        6.56777***************99999999998775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.075
                              SYCE1  32 qalkealkrElDsLnaEkvhLeevlnkKqealriLqlhcqekeseaqrkqelseeckqrieeltskiqeeklkrrk 107
                                         +l   +k  lD Ln E   L +   +Kq ++  ++ + +e + + + k+ + e  +++i++l+sk  e  +k + 
  gene1848|gene1848|rna1847|rna1847 155 SKLALDMKAKLDVLNSEIKDLSQRIAEKQSIVDGIKAELKEINDQEKPKNPTIEGYEKNIQALKSKRGELSEKIKA 230
                                        5566678999*******************************9999999999999*******999998887776666 PP

                              SYCE1 108 lrlefeeq...leelmeqhkdlwefhv.eqrlakeiralesskeqLlkE 152
                                        ++ +++e+   +++ +e+     ++++ ++ +++ i+ale+ k+ L kE
  gene1848|gene1848|rna1847|rna1847 231 QQEKIREKeieYDKFLEEMAIAQALEKqKEEIKQRISALEEQKNALSKE 279
                                        6665554311145556666666667777888999999999999999887 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.5
                              SYCE1  68 lhcqekeseaqrkqelseeckqrieeltskiqeek 102
                                         + ++  s+     e ++e + ri+ l+ ki ee+
  gene1848|gene1848|rna1847|rna1847 338 SQKKDFASQ---VVEKRKEFESRISDLERKISEER 369
                                        333333322...34456788888999999988886 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   7.6     0.054        54      50     169 ..      30     145 ..       3     154 .. 0.53
   2 ?    7.6  19.5    0.0046       4.6      33     160 ..     150     278 ..     139     290 .. 0.68
   3 ?    2.1   0.1      0.24   2.4e+02      14      33 ..     335     354 ..     326     380 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.054
                               Fez1  50 keeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa..lesdeakaq 123
                                          ++i++l++++++       + ++ +r++s ++ l +k+++l +e+k+l+e+ s++ ++++ea   +e+ + ++q
  gene1848|gene1848|rna1847|rna1847  30 VTASINDLRDKISS-------IYKQ-ERENSPKNDLYKKLDELGSEIKSLKEDRSKAFNSKSEALgaYETIKGEVQ 97 
                                        33333333333222.......2221.23344445566778889999999999888877666666544333333344 PP

                               Fez1 124 rqe...aeeleelkreverlraeLkeerqkkeeqassFeqERrtWqeeK 169
                                         ++   + +++e ++++ +++ +L   +    ++++ Fe+E +  +++K
  gene1848|gene1848|rna1847|rna1847  98 PEKgkkMMSAQEIDNRMREINLKLISTKCD-SKMEKMFESEIENLRKQK 145
                                        333111233333333333344344433333.456677888766655555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0046
                               Fez1  33 ivalkaqlr.elrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsels 107
                                        +++ k++l  +++akl+  ++eik+l++++ ek+  ++ +++el++ +++++ ++ ++e +e++++ l+++  els
  gene1848|gene1848|rna1847|rna1847 150 VLEQKSKLAlDMKAKLDVLNSEIKDLSQRIAEKQSIVDGIKAELKEINDQEKPKNPTIEGYEKNIQALKSKRGELS 225
                                        5555666533899**********************************99999999999999999999999888877 PP

                               Fez1 108 leeeeaalesdeakaqrqe....aeeleelkreverlraeLkeerqkkeeqassFeq 160
                                        ++ + ++++ +e++ + ++    +    +  + +e+ ++e+k+   + eeq+++  +
  gene1848|gene1848|rna1847|rna1847 226 EKIKAQQEKIREKEIEYDKfleeM----AIAQALEKQKEEIKQRISALEEQKNALSK 278
                                        665555444444433433343332....33333444444444444444444444333 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.24
                               Fez1  14 lLKqQLkdsqaevtqklsei 33 
                                        +LK+Q kd  ++v +k +e 
  gene1848|gene1848|rna1847|rna1847 335 VLKSQKKDFASQVVEKRKEF 354
                                        45555555555555554442 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.9    0.0016       1.6      36     105 ..       2      77 ..       1     109 [. 0.78
   2 ?    0.4   7.8      0.61   6.1e+02      18      88 ..      60     144 ..      52     160 .. 0.72
   3 ?    0.3   9.4      0.66   6.6e+02      30      98 ..     135     188 ..     109     199 .. 0.51
   4 ?    2.0  24.5      0.19   1.9e+02       4     138 ..     143     276 ..     142     278 .. 0.88
   5 ?    4.2   0.1      0.04        40      74     107 ..     332     369 ..     315     379 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                     CENP-F_leu_zip  36 seenqekvileaEtskaevetlkeeieelaeelreleldLvalr......sekeeLekelqkkqervseLeslnss 105
                                        ++en+ k i    +  a + +l++e+ + +++ ++l+ +++++       s k++L k+l +  +++++L++ +s+
  gene1848|gene1848|rna1847|rna1847   2 QQENRRKRIPGIHSYLAVIGELRQELGKVTASINDLRDKISSIYkqerenSPKNDLYKKLDELGSEIKSLKEDRSK 77 
                                        5666666666666677777788888888888888888888887678878788999*************99987765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.61
                     CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskaevetlkeei....eelaeelreleldLvalr.......... 79 
                                        k d L   +++L+ +   + ++++++    Et k ev+  k ++    +e+ +++re++l+L +++          
  gene1848|gene1848|rna1847|rna1847  60 KLDELGSEIKSLKEDRSKAFNSKSEALGAYETIKGEVQPEKGKKmmsaQEIDNRMREINLKLISTKcdskmekmfe 135
                                        6688889999999999999999999999999999999876655422225677778888888877776666666655 PP

                     CENP-F_leu_zip  80 sekeeLeke 88 
                                        se e+L k+
  gene1848|gene1848|rna1847|rna1847 136 SEIENLRKQ 144
                                        566665443 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.66
                     CENP-F_leu_zip  30 erelemseenqekvileaEtskaevetlkeeieelaeelr...eleldLvalrsekeeLekelqkkqervse 98 
                                        e+e+e++ ++                  k++i  l+++ +   +++++L+ l se ++L + + +kq+ v+ 
  gene1848|gene1848|rna1847|rna1847 135 ESEIENLRKQ------------------KKNIGVLEQKSKlalDMKAKLDVLNSEIKDLSQRIAEKQSIVDG 188
                                        3333333332..................23333333332222245555555666666666666666655543 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.19
                     CENP-F_leu_zip   4 kklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79 
                                        k+++  + L +  + a  +k k + L++e++++ +   +    ++  kae+++++++ +  + + +  e +++al+
  gene1848|gene1848|rna1847|rna1847 143 KQKKNIGVLEQKSKLALDMKAKLDVLNSEIKDLSQRIAEKQSIVDGIKAELKEINDQEKPKNPTIEGYEKNIQALK 218
                                        777777777777777888999999********999999999999*************9999*************** PP

                     CENP-F_leu_zip  80 sekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtqlkel 138
                                        s + eL ++++ +qe++ e e    ++ + + ++ q   + kee k++++ L+ q++ l
  gene1848|gene1848|rna1847|rna1847 219 SKRGELSEKIKAQQEKIREKEIEYDKFLEEMAIA-QALEKQKEEIKQRISALEEQKNAL 276
                                        *******************998888777777776.556677999***********9987 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.04
                     CENP-F_leu_zip  74 dLvalrsekeeLekelqkkqe....rvseLeslnssle 107
                                         ++ l+s+k++ + ++ +k++    r+s+Le+  s+ +
  gene1848|gene1848|rna1847|rna1847 332 TIEVLKSQKKDFASQVVEKRKefesRISDLERKISEER 369
                                        56667777777777776665312225555555555444 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.14   1.4e+02      19      53 ..      20      54 ..      17      84 .. 0.74
   2 ?    7.5   0.2    0.0064       6.4      13      48 ..     166     201 ..     158     210 .. 0.82
   3 ?    2.1   0.4      0.31   3.1e+02      30      55 ..     211     236 ..     204     248 .. 0.71
   4 ?    3.4   1.8      0.12   1.2e+02      34      61 ..     253     280 ..     245     287 .. 0.78
   5 ?    1.1   0.0      0.65   6.5e+02       2      19 ..     355     372 ..     353     377 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                               SlyX 19 ieeLndvvaeqqqqidrlqrqlrllaerlkelees 53
                                       i eL +++ +    i  l+ ++  ++++ +e +++
  gene1848|gene1848|rna1847|rna1847 20 IGELRQELGKVTASINDLRDKISSIYKQERENSPK 54
                                       55666666666666666666666666666666555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0064
                                        HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                               SlyX  13 afqedtieeLndvvaeqqqqidrlqrqlrllaerlk 48 
                                          +   i++L++ +ae q  +d ++++l++++++ k
  gene1848|gene1848|rna1847|rna1847 166 DVLNSEIKDLSQRIAEKQSIVDGIKAELKEINDQEK 201
                                        556677999999999999999999999999999875 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.31
                                        HHHHHHHHHHHHHHHHT-XXXXXXXX CS
                               SlyX  30 qqqidrlqrqlrllaerlkeleessg 55 
                                        ++ i++l+ +  +l e++k+ +e+ +
  gene1848|gene1848|rna1847|rna1847 211 EKNIQALKSKRGELSEKIKAQQEKIR 236
                                        56777777777888888877777654 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.12
                                        HHHHHHHHHHHHT-XXXXXXXXXXXXXX CS
                               SlyX  34 drlqrqlrllaerlkeleessgaseaee 61 
                                        ++l++q +++++r+++lee+++a  +ee
  gene1848|gene1848|rna1847|rna1847 253 QALEKQKEEIKQRISALEEQKNALSKEE 280
                                        5688888999999999999888766555 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.65
                                        HHHHHHHHHHHHHHHHHH CS
                               SlyX   2 eerleeLEiklafqedti 19 
                                        e+r+ +LE k++   +++
  gene1848|gene1848|rna1847|rna1847 355 ESRISDLERKISEERKVL 372
                                        789999999988766655 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6  11.1     0.067        66      11     164 ..      49     197 ..      41     199 .. 0.66
   2 ?    7.0  12.7    0.0061       6.1     102     176 ..     191     265 ..     188     283 .. 0.85
   3 ?    3.2   0.1     0.093        93     126     153 ..     345     372 ..     323     376 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.067
                              ATG16  11 arqekafaeliqaynrLldrtsaleaenaklekaaasaks..sksskksakekeasasqsnskqsakiqsleqkla 84 
                                        + ++++ ++l++   +L   +++l++ ++k+ ++ ++a    ++ +     e +     ++ k+  + q+ ++++ 
  gene1848|gene1848|rna1847|rna1847  49 R-ENSPKNDLYKKLDELGSEIKSLKEDRSKAFNSKSEALGayETIKG----EVQP----EKGKKMMSAQEIDNRMR 115
                                        4.466777777777777777777777766664444444433322222....2222....22234555666677777 PP

                              ATG16  85 qlreelaelyksrgelaqrllelneelqklee...klkedeerlaeleaeraaletklkdreeelrekeklvqdlq 157
                                        +++  l  + k  ++++++  +  e l+k+++    l+++++   +++a+  +l+ ++kd+ ++++ek+  v+ ++
  gene1848|gene1848|rna1847|rna1847 116 EINLKLIST-KCDSKMEKMFESEIENLRKQKKnigVLEQKSKLALDMKAKLDVLNSEIKDLSQRIAEKQSIVDGIK 190
                                        766666554.666677777777777777777733347889999999****************************** PP

                              ATG16 158 DElsaLq 164
                                         El   +
  gene1848|gene1848|rna1847|rna1847 191 AELKEIN 197
                                        **98765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0061
                              ATG16 102 qrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                                          l+e n++ + ++ +++  e+++++l+++r +l++k+k ++e++reke   +++ +E++  q   +q Ee +++
  gene1848|gene1848|rna1847|rna1847 191 AELKEINDQEKPKNPTIEGYEKNIQALKSKRGELSEKIKAQQEKIREKEIEYDKFLEEMAIAQALEKQKEEIKQR 265
                                        579999999999*****************************************9999998877766666665554 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.093
                              ATG16 126 aeleaeraaletklkdreeelrekeklv 153
                                         ++ ++r++ e +++d+e ++ e +k++
  gene1848|gene1848|rna1847|rna1847 345 SQVVEKRKEFESRISDLERKISEERKVL 372
                                        3445555666666666666666666654 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   7.5       0.4   3.9e+02      32     112 ..      29     112 ..      19     159 .. 0.60
   2 ?   11.4   5.8   0.00027      0.26      31     106 ..     159     237 ..     149     250 .. 0.82
   3 ?    4.5   1.0     0.037        37      22      53 ..     251     282 ..     249     287 .. 0.85
   4 ?    2.3   0.1      0.17   1.7e+02      70     102 ..     338     370 ..     327     376 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.4
                                        CCCHHHCCCCCCCCCCCCHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HH CS
                          Fib_alpha  32 dvkkdlekleneleeisnstke...aeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.sn 103
                                        +v+ ++++l++++++i ++++e    ++l k++++   e ++ k+d ++++++ s+ l   ++++k +++ +  ++
  gene1848|gene1848|rna1847|rna1847  29 KVTASINDLRDKISSIYKQEREnspKNDLYKKLDELGSEIKSLKEDRSKAFNSKSEALG-AYETIKGEVQPEKgKK 103
                                        56667777777777665554441114566666666666666666666777777777776.6777776666555555 PP

                                        HHHHHHHHH CS
                          Fib_alpha 104 irvLqnvle 112
                                        +   q++ +
  gene1848|gene1848|rna1847|rna1847 104 MMSAQEIDN 112
                                        555555433 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00027
                                        CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCCCHHHHHHHCCHHH CS
                          Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksske...leeeilrlketidaqesn 103
                                         d+k +l+ l++e++++s++  e +++v  ik  l+e + ++k+++ +i+ ++k+   l+++  +l e+i+aq ++
  gene1848|gene1848|rna1847|rna1847 159 LDMKAKLDVLNSEIKDLSQRIAEKQSIVDGIKAELKEINDQEKPKNPTIEGYEKNiqaLKSKRGELSEKIKAQQEK 234
                                        58999*******************************99999988877777666651116678889999***99999 PP

                                        HHH CS
                          Fib_alpha 104 irv 106
                                        ir+
  gene1848|gene1848|rna1847|rna1847 235 IRE 237
                                        997 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.037
                                        HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHH CS
                          Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstke 53 
                                        ++++l+k+++++k++++ le++ + +s+++++
  gene1848|gene1848|rna1847|rna1847 251 IAQALEKQKEEIKQRISALEEQKNALSKEESK 282
                                        789999*************9998888877665 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.17
                                        HHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                          Fib_alpha  70 kskkdndnvikksskeleeeilrlketidaqes 102
                                        ++kkd  + + + +ke e++i++l+++i+++ +
  gene1848|gene1848|rna1847|rna1847 338 SQKKDFASQVVEKRKEFESRISDLERKISEERK 370
                                        444445667777788888899999999887665 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.63   6.3e+02      24      35 ..      28      39 ..      26      40 .. 0.81
   2 ?    2.4   0.1      0.11   1.1e+02      21      35 ..      59      73 ..      58      74 .. 0.92
   3 ?    5.2   0.1     0.015        15      21      35 ..     163     177 ..     161     178 .. 0.92
   4 ?   -1.8   0.2       2.3   2.3e+03      19      31 ..     354     366 ..     353     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.63
                               YvrJ 24 deLtksIeeLse 35
                                        + t sI++L++
  gene1848|gene1848|rna1847|rna1847 28 GKVTASINDLRD 39
                                       56799*****87 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                               YvrJ 21 kkLdeLtksIeeLse 35
                                       kkLdeL   I+ L+e
  gene1848|gene1848|rna1847|rna1847 59 KKLDELGSEIKSLKE 73
                                       7***********987 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.015
                               YvrJ  21 kkLdeLtksIeeLse 35 
                                        +kLd L+  I++Ls+
  gene1848|gene1848|rna1847|rna1847 163 AKLDVLNSEIKDLSQ 177
                                        69***********97 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 2.3
                               YvrJ  19 iEkkLdeLtksIe 31 
                                        +E ++ +L   I 
  gene1848|gene1848|rna1847|rna1847 354 FESRISDLERKIS 366
                                        8999999998886 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2      0.02        20      29      71 ..      22      70 ..      17      74 .. 0.63
   2 ?   -2.7   0.0       6.4   6.4e+03      60      69 ..     108     117 ..     106     118 .. 0.83
   3 ?    6.3   0.6    0.0098       9.7      13      43 ..     151     181 ..     134     199 .. 0.79
   4 ?   -1.8   0.1       3.5   3.4e+03      33      70 ..     213     250 ..     207     256 .. 0.66
   5 ?    0.4   1.3      0.72   7.1e+02       9      33 ..     255     279 ..     246     284 .. 0.54
   6 ?    5.2   0.0     0.022        22       2      23 ..     354     375 ..     353     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.02
                      TolA_bind_tri 29 alqqelreLRGqiEelqyqleqleerQr......dlYldlDerlrklea 71
                                       +l+qel +   +i +l+ +++++ ++ r      dlY++lDe+ +++++
  gene1848|gene1848|rna1847|rna1847 22 ELRQELGKVTASINDLRDKISSIYKQERenspknDLYKKLDELGSEIKS 70
                                       4556666666666666666666665554223333799999999888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.4
                      TolA_bind_tri  60 ldlDerlrkl 69 
                                        +++D+r+r++
  gene1848|gene1848|rna1847|rna1847 108 QEIDNRMREI 117
                                        7899999987 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0098
                      TolA_bind_tri  13 learsqlllelqqqlealqqelreLRGqiEe 43 
                                        le++s+l l++  +l+ l++e+++L   i e
  gene1848|gene1848|rna1847|rna1847 151 LEQKSKLALDMKAKLDVLNSEIKDLSQRIAE 181
                                        45566899***************99766655 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.5
                      TolA_bind_tri  33 elreLRGqiEelqyqleqleerQrdlYldlDerlrkle 70 
                                         ++ L+ +  el+ +++  +e+ r+  ++ D+ l+++ 
  gene1848|gene1848|rna1847|rna1847 213 NIQALKSKRGELSEKIKAQQEKIREKEIEYDKFLEEMA 250
                                        56666666667777777777777777777777776665 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.72
                      TolA_bind_tri   9 LErilearsqlllelqqqlealqqe 33 
                                        LE++ e  +q +  l +q +al++e
  gene1848|gene1848|rna1847|rna1847 255 LEKQKEEIKQRISALEEQKNALSKE 279
                                        4444444445555555555555555 PP

  == domain 6  score: 5.2 bits;  conditional E-value: 0.022
                      TolA_bind_tri   2 ledrvarLErilearsqlllel 23 
                                        +e+r++ LEr+++ + ++l+ +
  gene1848|gene1848|rna1847|rna1847 354 FESRISDLERKISEERKVLTAM 375
                                        79************99999988 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.7     7e+02       4      19 ..      29      44 ..      20      57 .. 0.64
   2 ?    4.3   0.1     0.055        54      12      33 ..      57      78 ..      51      95 .. 0.63
   3 ?    5.9   1.5     0.017        17       1      35 [.     164     198 ..     164     201 .. 0.92
   4 ?    4.0   0.1     0.066        65       7      30 ..     212     235 ..     207     241 .. 0.86
   5 ?    1.1   0.7      0.52   5.2e+02       3      25 ..     260     282 ..     253     287 .. 0.72
   6 ?   -2.2   0.0       5.8   5.8e+03       4      16 ..     353     365 ..     329     367 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.7
                                LPP  4 eLssqVsqLkskvdql 19
                                       ++++ +++L +k++++
  gene1848|gene1848|rna1847|rna1847 29 KVTASINDLRDKISSI 44
                                       3445566666666655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.055
                                LPP 12 Lkskvdqlssdvnsakaaaqaa 33
                                       L +k d+l s+++s+k++  +a
  gene1848|gene1848|rna1847|rna1847 57 LYKKLDELGSEIKSLKEDRSKA 78
                                       5555555555555555554444 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.017
                                LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                        kld L+s++++L++ +++ +s v+ +ka+++++ +
  gene1848|gene1848|rna1847|rna1847 164 KLDVLNSEIKDLSQRIAEKQSIVDGIKAELKEIND 198
                                        7999***********************99998876 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.066
                                LPP   7 sqVsqLkskvdqlssdvnsakaaa 30 
                                        +++++Lksk  +ls+++++ ++ +
  gene1848|gene1848|rna1847|rna1847 212 KNIQALKSKRGELSEKIKAQQEKI 235
                                        5799************99988776 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.52
                                LPP   3 deLssqVsqLkskvdqlssdvns 25 
                                        +e+ + +s+L+++ ++ls++ ++
  gene1848|gene1848|rna1847|rna1847 260 EEIKQRISALEEQKNALSKEESK 282
                                        46667788888888888877655 PP

  == domain 6  score: -2.2 bits;  conditional E-value: 5.8
                                LPP   4 eLssqVsqLkskv 16 
                                        e  s +s+L++k+
  gene1848|gene1848|rna1847|rna1847 353 EFESRISDLERKI 365
                                        3445566666666 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00071       0.7     151     207 ..      18      74 ..      12      94 .. 0.85
   2 ?   -0.0   0.2      0.44   4.4e+02     122     145 ..     160     185 ..     132     199 .. 0.69
   3 ?   -0.5   3.5       0.6   5.9e+02     120     187 ..     207     274 ..     204     288 .. 0.77
   4 ?    0.3   0.0      0.35   3.5e+02     124     168 ..     330     373 ..     327     378 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00071
                               CorA 151 relaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerllem 207
                                          + +lr++l+k+  +++++r+ +++++++++++  + +  + l++l +e+++l e+
  gene1848|gene1848|rna1847|rna1847  18 AVIGELRQELGKVTASINDLRDKISSIYKQERENSPKNDLYKKLDELGSEIKSLKED 74 
                                        56899************************9999999999988899999999988876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.44
                               CorA 122 rlfellekleeeldeledel..edst 145
                                        ++ + l+ l++e+++l++++  ++s+
  gene1848|gene1848|rna1847|rna1847 160 DMKAKLDVLNSEIKDLSQRIaeKQSI 185
                                        45667888888888888888544444 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.6
                               CorA 120 vdrlfellekleeeldeledeledstkkeilrelaqlrrrlvkl..rralapnrevlkrllakaddklld 187
                                        ++ +++ +++l++++ el++ + + ++++i+++ +++ + l ++   +al  ++e +k++++ a++++ +
  gene1848|gene1848|rna1847|rna1847 207 IEGYEKNIQALKSKRGELSEKI-KAQQEKIREKEIEYDKFLEEMaiAQALEKQKEEIKQRIS-ALEEQKN 274
                                        6789999999999999999999.889999999999999888887778888888888888887.3333333 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.35
                               CorA 124 fellekleeeldeledeledstkkeilrelaqlrrrlvklrrala 168
                                        ++++e l+++ ++  +++  +++ke+ +++++l+r++ + r++l+
  gene1848|gene1848|rna1847|rna1847 330 NPTIEVLKSQKKDFASQV-VEKRKEFESRISDLERKISEERKVLT 373
                                        455666666666666666.56666666666666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2740  (0.152825); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        61  (0.00340231); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 1.14u 0.35s 00:00:01.48 Elapsed: 00:00:00.56
# Mc/sec: 2093.96
//
Query:       gene1849|gene1849|rna1848|rna1848  [L=529]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-51  166.8  17.5    2.2e-08   33.3   0.1    8.7  8  PUF       Pumilio-family RNA binding repeat
     0.0024   18.4   0.1        2.9    8.5   0.1    2.9  2  LOB       Lateral organ boundaries (LOB) domain
  ------ inclusion threshold ------
      0.094   12.6   0.3        9.8    6.0   0.0    3.5  4  sCache_2  Single Cache domain 2


Domain annotation for each model (and alignments):
>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00041       2.4       2      30 ..     217     245 ..     216     247 .. 0.83
   2 !   15.9   0.0   1.2e-06    0.0073       8      28 ..     259     279 ..     255     286 .. 0.78
   3 !   24.2   0.0   2.8e-09   1.7e-05       2      34 ..     289     319 ..     288     320 .. 0.83
   4 !   33.3   0.1   3.7e-12   2.2e-08       2      27 ..     323     348 ..     322     353 .. 0.91
   5 !   32.9   0.1     5e-12     3e-08       3      35 .]     358     390 ..     356     390 .. 0.90
   6 !   32.4   0.3   7.1e-12   4.2e-08       2      34 ..     393     425 ..     392     426 .. 0.93
   7 !    5.4   0.3    0.0026        16       1      24 [.     428     451 ..     428     462 .. 0.86
   8 !   19.3   0.0     1e-07   0.00062       3      34 ..     472     503 ..     470     504 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00041
                                        HGGGHHHHHTSTTHHHHHHHHHHHSCHHH CS
                                PUF   2 ikgnlvqLstdqyGnyvvQkllehateeq 30 
                                        +k+ ++++s+dq G++ +Q+  +  ++e+
  gene1849|gene1849|rna1848|rna1848 217 MKEICISISKDQEGSRCIQRKMDNISKEE 245
                                        566689**************999966665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-06
                                        HHHTSTTHHHHHHHHHHHSCH CS
                                PUF   8 qLstdqyGnyvvQkllehate 28 
                                        +Ls + +Gnyv+Qk++   te
  gene1849|gene1849|rna1848|rna1848 259 ELSANLFGNYVIQKIIPLVTE 279
                                        6999***********976444 PP

  == domain 3  score: 24.2 bits;  conditional E-value: 2.8e-09
                                        HGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHH CS
                                PUF   2 ikgnlvqLstdqyGnyvvQkllehateeqkkli 34 
                                        + g ++ Ls+++yG++v+Qkl ++  ++++++i
  gene1849|gene1849|rna1848|rna1848 289 LVGQIHLLSVHPYGCRVIQKLVDV--SPDVDFI 319
                                        6688999***************95..6666666 PP

  == domain 4  score: 33.3 bits;  conditional E-value: 3.7e-12
                                        HGGGHHHHHTSTTHHHHHHHHHHHSC CS
                                PUF   2 ikgnlvqLstdqyGnyvvQkllehat 27 
                                         kgnl++L+ dq+Gn+v+Qk++e+++
  gene1849|gene1849|rna1848|rna1848 323 VKGNLLELIEDQNGNHVIQKCIEKCK 348
                                        79**********************97 PP

  == domain 5  score: 32.9 bits;  conditional E-value: 5e-12
                                        GGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHHH CS
                                PUF   3 kgnlvqLstdqyGnyvvQkllehateeqkklil 35 
                                        ++n + L+t++yG++v+Q++le ++ee++k+i+
  gene1849|gene1849|rna1848|rna1848 358 SKNSLFLATHKYGCRVIQRMLEFCKEEEIKDIV 390
                                        6777779***********************995 PP

  == domain 6  score: 32.4 bits;  conditional E-value: 7.1e-12
                                        HGGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHH CS
                                PUF   2 ikgnlvqLstdqyGnyvvQkllehateeqkkli 34 
                                        +++n+ +L+ dqyGnyv+Q++l++ +e++k l+
  gene1849|gene1849|rna1848|rna1848 393 LINNIKTLVDDQYGNYVIQHILTVGKEKEKNLV 425
                                        799************************999886 PP

  == domain 7  score: 5.4 bits;  conditional E-value: 0.0026
                                        HHGGGHHHHHTSTTHHHHHHHHHH CS
                                PUF   1 sikgnlvqLstdqyGnyvvQklle 24 
                                        +i+++  +Ls+ ++ ++vv+++ +
  gene1849|gene1849|rna1848|rna1848 428 KIIEKSYELSKCKFSSNVVEQCVK 451
                                        5889999**************976 PP

  == domain 8  score: 19.3 bits;  conditional E-value: 1e-07
                                        GGGHHHHHTSTTHHHHHHHHHHHSCHHHHHHH CS
                                PUF   3 kgnlvqLstdqyGnyvvQkllehateeqkkli 34 
                                        k+   ++++d yGnyvvQ+l + ++e+ +k i
  gene1849|gene1849|rna1848|rna1848 472 KPGMYSMCIDMYGNYVVQRLYDSSGENIRKEI 503
                                        778899**************998888877766 PP

>> LOB  Lateral organ boundaries (LOB) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0     0.002        12      28      77 ..     256     304 ..     245     315 .. 0.83
   2 !    8.5   0.1   0.00049       2.9      10      74 ..     341     405 ..     337     429 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.002
                                LOB  28 eefaavhkvFGasnvlkllkevpeekredavkslvyeAearlrdPvyGcv 77 
                                        ++ +  +++FG   ++k++  v+ee+r+++++slv + +    +P yGc 
  gene1849|gene1849|rna1848|rna1848 256 AAAELSANLFGNYVIQKIIPLVTEEERTRLTTSLVGQIHLLSVHP-YGCR 304
                                        55566689***************************9999988888.8884 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00049
                                LOB  10 rkCsedCvlapyfpae..kaeefaavhkvFGasnvlkllkevpeekredavkslvyeAearlrdPvy 74 
                                        +kC e+C  ++++ ++  k++ f a hk +G + ++++l+ ++ee+ +d+v+ l+ + ++ ++d  y
  gene1849|gene1849|rna1848|rna1848 341 QKCIEKCKDRRIILQQfsKNSLFLATHK-YGCRVIQRMLEFCKEEEIKDIVEILINNIKTLVDDQ-Y 405
                                        7999***999988664215555666666.9*********************99998877776665.4 PP

>> sCache_2  Single Cache domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.39   2.3e+03      83     100 ..     225     242 ..     191     248 .. 0.59
   2 ?    6.0   0.0    0.0016       9.8      77     109 ..     325     355 ..     320     362 .. 0.74
   3 ?   -1.0   0.0      0.24   1.4e+03      34      49 ..     383     398 ..     381     410 .. 0.77
   4 ?    1.6   0.0     0.038   2.3e+02      83     105 ..     401     423 ..     393     433 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                           sCache_2  83 lkDanGkyiirelvkeak 100
                                         kD++G + i+  +++++
  gene1849|gene1849|rna1848|rna1848 225 SKDQEGSRCIQRKMDNIS 242
                                        356666666666555555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                           sCache_2  77 GknasnlkDanGkyiirelvkeakkkgggfvty 109
                                        G  ++ + D+nG+++i++ +++ k  + +++ +
  gene1849|gene1849|rna1848|rna1848 325 GNLLELIEDQNGNHVIQKCIEKCK--DRRIILQ 355
                                        66667789**************99..4444444 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.24
                           sCache_2  34 eeeaqeevkelvnglk 49 
                                        eee+++ v++l+n++k
  gene1849|gene1849|rna1848|rna1848 383 EEEIKDIVEILINNIK 398
                                        6888888888888887 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.038
                           sCache_2  83 lkDanGkyiirelvkeakkkggg 105
                                        + D+ G+y+i+ ++  +k+k++ 
  gene1849|gene1849|rna1848|rna1848 401 VDDQYGNYVIQHILTVGKEKEKN 423
                                        67999*************65554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2964.06
//
Query:       gene1850|gene1850|rna1849|rna1849  [L=402]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-32  113.0  33.2    1.9e-32  112.5  33.2    1.2  1  Aa_trans  Transmembrane amino acid transporter protein
  ------ inclusion threshold ------
          1    9.4   3.6       0.85    9.7   0.9    2.2  2  UPF0370   Uncharacterised protein family (UPF0370)
          6    6.1  37.2      0.019   14.3   6.4    2.9  3  EpsG      EpsG family


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5  33.2   3.2e-36   1.9e-32       3     402 ..       5     394 ..       3     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 3.2e-36
                           Aa_trans   3 ssalsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrll 78 
                                         s ++av+ ++ ++vG+G+ ++PyAfk++G++  ++l++++a+ +  + + ++ ++k+  sg++n +Y+ ++ + +
  gene1850|gene1850|rna1849|rna1849   5 LSNKDAVVAMVLSMVGTGITFMPYAFKSAGYLNAIFLMIFFAMGTAVSCYCISYAAKY--SGHENPTYSSIA-SSI 77 
                                        578899***************************************************9..79*********5.556 PP

                           Aa_trans  79 GpkgkliidlailvqlfGvgvsyliligdllpa...ifesffdtlllsnvyfilisaliiipLslipnlskLsylS 151
                                        ++ + +i++++i+++   ++v +    +dl++     +++++++++ s+ +++li a+ ++ Ls ++ ls L  + 
  gene1850|gene1850|rna1849|rna1849  78 STTLGYIVNVSIFFNGYLAAVNFYRYLSDLIVGnsyYIQNLTSDYEKSRKVVVLILAVPFLYLSSKKTLSGLALTT 153
                                        6668999********999999999999999975111455555669******************************* PP

                           Aa_trans 152 llalvsslyyivilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkkm 227
                                        +l++ s+ly+  ++ +     ++++   ++e +    ++  +l  +++ ++ + +++a++++i++e+++ s+  ++
  gene1850|gene1850|rna1849|rna1849 154 YLSIASVLYL--AFLMAYLFFTVGSTFAIGEVKP---FN-ESLGESVPFFISSMVCQANMVKIYAEMENKSN-RNI 222
                                        *******993..4444444456677777777765...33.478889999999999**************999.99* PP

                           Aa_trans 228 tkvlllsiilatvlyilvGlvGYltFGnevkgnillnlpkss...............ilivivnlllvlhlilsfp 288
                                        + v+l + +  +++  l+Gl+GY++FG+ v g+i++ l+  +               i+  ++   ++l l++++p
  gene1850|gene1850|rna1849|rna1849 223 MIVSLGAATGGMLVNCLIGLSGYFVFGDGVSGEIITELSDMNnpvnkhlrsgwdkknIMSGMAVYGMMLTLFGGYP 298
                                        ************************************99887778999********999****************** PP

                           Aa_trans 289 lqlhplrqvvenllikkeavagasekeapkskllrlvirlllvvityliAlsvpslak..vlslvGatsstplsfi 362
                                        +q+ p+++++ ++l  +        k+++++   r  i +ll+++++++ l +++l+   +  ++Gat+s + +f+
  gene1850|gene1850|rna1849|rna1849 299 IQVNPVVDMIFKNLPVE--------KRTEVN---RKGIVILLFLVAIFLNL-MQELKTkvIKKFLGATFSNSVAFV 362
                                        **************553........444444...44444444444444442.344432226689************ PP

                           Aa_trans 363 lPalfhlkliktekksleklvkkkildlicivlglllvfy 402
                                        +P +++l ++k ++    ++        +++++g+++++ 
  gene1850|gene1850|rna1849|rna1849 363 YPFVYYLSIKKEKSLLSTSV--------CIFMIGMSVMVS 394
                                        *********99998555444........444444444433 PP

>> UPF0370  Uncharacterised protein family (UPF0370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1         1   6.1e+03      10      35 ..     129     155 ..     127     157 .. 0.65
   2 ?    9.7   0.9   0.00014      0.85      10      35 ..     326     351 ..     324     355 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                            UPF0370  10 villllvGil.lngikeLkrvdhkkfL 35 
                                        v+l+l v  l l + k L+ +  + +L
  gene1850|gene1850|rna1849|rna1849 129 VVLILAVPFLyLSSKKTLSGLALTTYL 155
                                        566666665425667778877777777 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                            UPF0370  10 villllvGillngikeLkrvdhkkfL 35 
                                        vill+lv i+ln ++eLk    kkfL
  gene1850|gene1850|rna1849|rna1849 326 VILLFLVAIFLNLMQELKTKVIKKFL 351
                                        89****************99999998 PP

>> EpsG  EpsG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   2.0      0.19   1.2e+03      69     104 ..      14      50 ..       2      63 .. 0.52
   2 ?   -4.1  22.8       1.2   7.2e+03     163     260 ..      79     177 ..      21     226 .. 0.71
   3 ?   14.3   6.4   3.2e-06     0.019     175     310 ..     247     392 ..     222     401 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.19
                               EpsG  69 filalitllllfvfikkysknlflslllf.llslffl 104
                                        ++l+++ +++ f+ + + s  ++ +++l+ ++ + ++
  gene1850|gene1850|rna1849|rna1849  14 MVLSMVGTGITFMPYAFKSAGYLNAIFLMiFFAMGTA 50 
                                        4445555555555444444444444444444444333 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 1.2
                               EpsG 163 klkllllllafillllllldlilsllslllliseryesYlesdeysggtiggvqlaillfilfllllkkileekkk 238
                                        +++ ++++++++++ +l  ++++ +ls+l++++++y   l+sd++ + ++  v l++ + +l+l  +k +     +
  gene1850|gene1850|rna1849|rna1849  79 TTLGYIVNVSIFFNGYLAAVNFYRYLSDLIVGNSYYIQNLTSDYEKSRKV--VVLILAVPFLYLSSKKTLSGLALT 152
                                        477889999999*******************9999999999999998875..444444444443444444444444 PP

                               EpsG 239 ekl...klflnllliglalllllls 260
                                         +l   ++++  +l++++++ ++++
  gene1850|gene1850|rna1849|rna1849 153 TYLsiaSVLYLAFLMAYLFFTVGST 177
                                        3334444444444444444444444 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 3.2e-06
                               EpsG 175 llllllldlilsllslllliseryesYlesdeysggtig...gvqlaillfilf.........llllkkileekkk 238
                                        ++   +   i++ ls   ++++ +++ l+s++  +++++   ++++++ lf  +         ++++++  e++ +
  gene1850|gene1850|rna1849|rna1849 247 VFGDGVSGEIITELS---DMNNPVNKHLRSGWDKKNIMSgmaVYGMMLTLFGGYpiqvnpvvdMIFKNLPVEKRTE 319
                                        444444444555555...5677999999999999998887777777777777778999998877777777766666 PP

                               EpsG 239 eklklflnllliglallllllsls.vilsRlsl.yflifqiillppllkklfkrkkrrlilliliillflflfv 310
                                         + k +++ll+++ ++l l++ l+  ++  +    f+ +   +++p++++l  +k++ l+ ++++i+++++  +
  gene1850|gene1850|rna1849|rna1849 320 VNRKGIVILLFLVAIFLNLMQELKtKVIKKFLGaTFSNSVA-FVYPFVYYLSIKKEKSLLSTSVCIFMIGMSVM 392
                                        55599999999999999999999995555555515666655.99999999999999999888887777765443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2203.50
//
Query:       gene185|gene185|rna185|rna185  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.022   14.6   0.0    1.2  1  UL97      UL97
      0.063   12.1   2.0      0.077   11.8   0.1    1.8  2  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> UL97  UL97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.5e-06     0.022      45     127 ..      52     132 ..      45     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-06
                           UL97  45 lrlvPisrnklremynPafrPlvlqklllvdvheafPlaglrrycnlelsalanvlllcllrlldkrGldevrlytekll 124
                                    +++v   ++ lr++y+P+ r l+   + l++v    P   +  y ++ +  +a v  l ++ +l+  G + ++l  ++ +
  gene185|gene185|rna185|rna185  52 MKRVEYKKRFLRKVYDPGHRTLIG--FALCEVLSMVPFYYMVGYWKTMVINIALVASLSIIPMLNSSGRRTIQLERNEEF 129
                                    57788888889*********9986..5679********99************************************9999 PP

                           UL97 125 fkl 127
                                    fk 
  gene185|gene185|rna185|rna185 130 FKI 132
                                    986 PP

>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3     0.043   3.8e+02     114     159 ..       5      50 ..       2      67 .. 0.71
   2 ?   11.8   0.1   8.6e-06     0.077      48      78 ..      82     112 ..      69     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.043
                        DUF2079 114 hpevlaiPllllalllalrrrkwllllvlilllllvredlslvvvi 159
                                    h + +  +l + + +  l  +    l ++++lll+++ d+s+++ +
  gene185|gene185|rna185|rna185   5 HSLAIKALLTFICTTAVLVHEGSFRLYLCVALLLATSFDVSVIFYF 50 
                                    5555554555555555555666677778888899999999998866 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.6e-06
                        DUF2079  48 lllaplyalfPsvltLllvqalllslgglpl 78 
                                    l ++p+y++ ++++t+ +  al++sl+++p 
  gene185|gene185|rna185|rna185  82 LSMVPFYYMVGYWKTMVINIALVASLSIIPM 112
                                    6689*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1045.32
//
Query:       gene1851|gene1851|rna1850|rna1850  [L=556]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-39  132.8  17.8      9e-09   35.8   1.3    6.5  6  WD40          WD domain, G-beta repeat
    6.6e-38  129.9   9.4    6.6e-38  129.9   9.4    2.2  3  TFIID_NTD2    WD40 associated region in TFIID subunit, NTD2 d
    1.3e-10   41.5   0.1     0.0028   17.9   0.0    5.1  5  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
     0.0031   16.9   0.2       0.52    9.6   0.0    3.5  4  WD40_like     WD40-like domain
  ------ inclusion threshold ------
      0.026   13.2   0.1      0.065   11.9   0.1    1.7  1  Nup160        Nucleoporin Nup120/160
       0.59   10.7   5.6        1.8    9.1   4.3    2.2  2  Hemocyanin_N  Hemocyanin, all-alpha domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.059   1.8e+02      10      37 ..     250     280 ..     243     281 .. 0.72
   2 !   26.4   0.3     3e-09   8.8e-06       5      38 .]     316     350 ..     313     350 .. 0.90
   3 !   21.6   0.1   9.2e-08   0.00027       3      38 .]     356     392 ..     354     392 .. 0.91
   4 !   22.0   0.0   6.9e-08   0.00021      11      38 .]     407     434 ..     398     434 .. 0.88
   5 !   35.8   1.3     3e-12     9e-09       3      38 .]     440     476 ..     438     476 .. 0.93
   6 !   31.0   0.2     1e-10     3e-07       2      38 .]     481     518 ..     480     518 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.059
                                        SSS...EEEEEEETTSSEEEEEETTSEEEEE CS
                               WD40  10 Hss...vtslafspdgawlasGsdDgtvriW 37 
                                        H+     t+   s d +++a+G +D  + ++
  gene1851|gene1851|rna1850|rna1850 250 HNTyegLTAAEISNDLKLMACGFKDSYIEVY 280
                                        5333446666677788******9****9987 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 3e-09
                                        EEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        ++l GH ++v++l+f +++++l+s+s D+tv +W+
  gene1851|gene1851|rna1850|rna1850 316 YKLVGHsGPVYGLKFFSSNKFLVSSSQDCTVCLWS 350
                                        5678**777*************************5 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 9.2e-08
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        +l+++++H ++v+++++ p+  ++asG  D+   +W+
  gene1851|gene1851|rna1850|rna1850 356 LLGVYKAHaFPVWCVDVAPNDYFFASGAGDRQAIVWS 392
                                        6899****999****************55*******5 PP

  == domain 4  score: 22.0 bits;  conditional E-value: 6.9e-08
                                        SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40  11 ssvtslafspdgawlasGsdDgtvriWd 38 
                                        s+vt+++f+p++++l++Gs D+ vr+ d
  gene1851|gene1851|rna1850|rna1850 407 SDVTAVKFHPNSNYLFTGSSDHRVRMHD 434
                                        57****************99*****865 PP

  == domain 5  score: 35.8 bits;  conditional E-value: 3e-12
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                         +r++ GH + vt++++s+ g++lasGs+D+tv +Wd
  gene1851|gene1851|rna1850|rna1850 440 VVRIFCGHtDTVTCIDVSHCGKFLASGSKDRTVLLWD 476
                                        5899****666*************************9 PP

  == domain 6  score: 31.0 bits;  conditional E-value: 1e-10
                                        EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                        ++l+++ GH + v s++f+ +g+ las++ D++vr+Wd
  gene1851|gene1851|rna1850|rna1850 481 KLLGKYVGHeNTVFSVSFCFYGSVLASCGADNSVRLWD 518
                                        67899****999****************99*******9 PP

>> TFIID_NTD2  WD40 associated region in TFIID subunit, NTD2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   9.4   2.2e-41   6.6e-38       4     130 .]      16     141 ..      13     141 .. 0.97
   2 ?   -2.6   0.0         2     6e+03      67      89 ..     219     241 ..     213     259 .. 0.83
   3 ?   -2.1   0.1       1.4   4.1e+03      60      95 ..     272     306 ..     250     310 .. 0.65

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 2.2e-41
                                        XHHHHHHHHHHHHHHHTS-HHHHHHHGGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGGGGHH.HHHHHTT-- CS
                         TFIID_NTD2   4 pekyekayelLkkwiessldiykpeLsrllyPvFvhlyLelvakgaeeeakkFfekfkedhealhkedlkkLasis 79 
                                        ++++e++y +Lk+wie+sld++k++L  llyP+F+h+y++l+++++++eak+Ffek+++dh ++  e++k+++si 
  gene1851|gene1851|rna1850|rna1850  16 KDQMEASYVSLKTWIEDSLDLFKNDLLPLLYPLFIHIYFDLIQQNKTDEAKEFFEKYRNDHYNKS-EEIKQFESIY 90 
                                        7899*********************************************************9765.56******** PP

                                        SHHHHHHSHHHHHHHHS-EEEEEEHHHHHHHHHHHHHTT-HHHHHHHHHHE CS
                         TFIID_NTD2  80 spehleenelakafrenkyriklskaafelLlrfLeekekavllkilnehl 130
                                        + +h++en++a +f+++ky++++ ++af+lL++fLee++ +++lkiln+hl
  gene1851|gene1851|rna1850|rna1850  91 TIQHIHENNFAYTFKSSKYHLSMGRYAFDLLINFLEERNLTYILKILNQHL 141
                                        *************************************************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2
                                        GHH.HHHHHTT--SHHHHHHSHH CS
                         TFIID_NTD2  67 lhkedlkkLasisspehleenel 89 
                                        + +++++kL+ + +   +++n+l
  gene1851|gene1851|rna1850|rna1850 219 QINAEIEKLKDLCKRVAVNKNNL 241
                                        55678999999999999999875 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.4
                                        HGGGGGGGHH.HHHHHTT--SHHHHHHSHHHHHHHH CS
                         TFIID_NTD2  60 fkedhealhkedlkkLasisspehleenelakafre 95 
                                        fk++  + ++ + ++L++++s+++l+++++ k+++e
  gene1851|gene1851|rna1850|rna1850 272 FKDSYIEVYSLTNEALKKLKSSSELAKSDI-KTLNE 306
                                        566666666666677778888888777765.34445 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.052   1.5e+02      45      76 ..     260     290 ..     232     308 .. 0.73
   2 ?    1.0   0.0      0.18   5.3e+02      37      67 ..     321     351 ..     316     371 .. 0.85
   3 !   17.9   0.0   9.5e-07    0.0028      39      88 ..     407     455 ..     385     458 .. 0.85
   4 !   12.5   0.0   4.6e-05      0.14      37      88 ..     447     497 ..     444     500 .. 0.85
   5 !    6.6   0.0    0.0032       9.7      37      89 ..     489     542 ..     485     545 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.052
                        ANAPC4_WD40  45 aWkpdgklLavaysdgevrlldaesgkvvhsl 76 
                                        + ++d kl+a +++d+ +++++  ++  +++l
  gene1851|gene1851|rna1850|rna1850 260 EISNDLKLMACGFKDSYIEVYSLTNEA-LKKL 290
                                        5567889**************998754.3444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrllda 67 
                                        +++ v +L++  ++k+L+ + +d +v l + 
  gene1851|gene1851|rna1850|rna1850 321 HSGPVYGLKFFSSNKFLVSSSQDCTVCLWSL 351
                                        5678999****************99988775 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 9.5e-07
                        ANAPC4_WD40  39 sevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                        s v++++++p+ + L  + sd +vr++d++++ vv+ +  + +++vtc++
  gene1851|gene1851|rna1850|rna1850 407 SDVTAVKFHPNSNYLFTGSSDHRVRMHDINTASVVRIFCGH-TDTVTCID 455
                                        689********************************999555.558***96 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 4.6e-05
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                        +  +v+++  ++ gk+La + +d +v l d++s k++ ++  +++ +v +++
  gene1851|gene1851|rna1850|rna1850 447 HTDTVTCIDVSHCGKFLASGSKDRTVLLWDIQSSKLLGKYVGHEN-TVFSVS 497
                                        56789*******************************999866655.566665 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0032
                        ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldae..sgkvvhslsvksekavtclgW 89 
                                        ++++v s+++   g++La   +d++vrl d    +g ++ ++ +ks+    c+++
  gene1851|gene1851|rna1850|rna1850 489 HENTVFSVSFCFYGSVLASCGADNSVRLWDRAdhKGGCLGTYYTKSTP-LLCVKF 542
                                        56789999999*****************99751145566666666553.666655 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.66     2e+03       7      36 ..     260     289 ..     254     315 .. 0.68
   2 ?    0.6   0.0     0.094   2.8e+02       2      42 ..     366     407 ..     365     410 .. 0.80
   3 !    9.6   0.0   0.00017      0.52       2      46 ..     408     452 ..     407     456 .. 0.92
   4 ?    3.2   0.0     0.016        46       4      42 ..     452     490 ..     449     511 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.66
                          WD40_like   7 diskkgslilyGgkddkctvlkleslesvs 36 
                                        +is++ +l++ G kd  + v++l ++ ++ 
  gene1851|gene1851|rna1850|rna1850 260 EISNDLKLMACGFKDSYIEVYSLTNEALKK 289
                                        566666777777777777777777665544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.094
                          WD40_like   2 eiYsidiskkgslilyGgkddkctvlklesles.vsivesfe 42 
                                        +++ +d+ ++  +++ G+ d ++ v ++ + +    i+ s++
  gene1851|gene1851|rna1850|rna1850 366 PVWCVDVAPNDYFFASGAGDRQAIVWSVTTSKPeRLIISSLS 407
                                        5899**********************9988764144556665 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00017
                          WD40_like   2 eiYsidiskkgslilyGgkddkctvlkleslesvsivesfedSvi 46 
                                        ++ ++ + ++++++  G+ d+++++ ++++  +v i+ + +d v 
  gene1851|gene1851|rna1850|rna1850 408 DVTAVKFHPNSNYLFTGSSDHRVRMHDINTASVVRIFCGHTDTVT 452
                                        57789999******************************9999986 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.016
                          WD40_like   4 YsidiskkgslilyGgkddkctvlkleslesvsivesfe 42 
                                          id+s+ g++++ G+kd ++ + +++s ++     + e
  gene1851|gene1851|rna1850|rna1850 452 TCIDVSHCGKFLASGSKDRTVLLWDIQSSKLLGKYVGHE 490
                                        579***********************9998766555555 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.2e-05     0.065     167     255 ..     343     443 ..     277     459 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                                        TS-EEEEEE.......ETTEEEEEEEEE-------B--TTTT..TSS--SS---TT-ECEEEEET.........TT CS
                             Nup160 167 dggllklkr.......dedggawkesvfepksfllslsgllg.lladpsrrksgasvalsldvavavvei....gq 230
                                        d++++  ++         + +a+ + +++ + +  ++    g ++a ++   ++  + l ++  ++v+ +    ++
  gene1851|gene1851|rna1850|rna1850 343 DCTVCLWSLdllcllgVYKAHAFPVWCVDVAPNDYFFASGAGdRQAIVWSVTTSKPERLIISSLSDVTAVkfhpNS 418
                                        45444444444555554445666666666666666666666666666676667777788899999999999999** PP

                                        TEEEEEETT-EEEEEETTTTEEEEE CS
                             Nup160 231 tylfalsrdgkLrvWnlltgkclat 255
                                        +ylf+ s+d+++r+ +++t+++++ 
  gene1851|gene1851|rna1850|rna1850 419 NYLFTGSSDHRVRMHDINTASVVRI 443
                                        *********************9986 PP

>> Hemocyanin_N  Hemocyanin, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.3   0.00061       1.8       8      84 ..      45     122 ..      43     132 .. 0.82
   2 ?   -0.4   0.0      0.53   1.6e+03      40      81 ..     188     229 ..     179     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00061
                                        HHHTTTTTTS--TTSHHHHHHHC--TCCGGGGBS-HHHHHHHHHHHHH-.---TTS---TTS.HHHHHHHHHHHHH CS
                       Hemocyanin_N   8 vlellehvhqplykeelielgkefkveenidkYenveevkeflellkqgkllpkgeiFslfn.eehrkearglfrl 82 
                                        ++ l+ h++ +l +++  + +kef  + + d+Y++ ee+k+f + +  +++ +++  ++    + h+ + r  f+l
  gene1851|gene1851|rna1850|rna1850  45 LYPLFIHIYFDLIQQNKTDEAKEFFEKYRNDHYNKSEEIKQFESIYTIQHIHENNFAYTFKSsKYHLSMGRYAFDL 120
                                        577999******999999999999778888*******************999999999865415566666666776 PP

                                        HH CS
                       Hemocyanin_N  83 ly 84 
                                        l+
  gene1851|gene1851|rna1850|rna1850 121 LI 122
                                        66 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.53
                                        BS-HHHHHHHHHHHHH-.---TTS---TTSHHHHHHHHHHHH CS
                       Hemocyanin_N  40 YenveevkeflellkqgkllpkgeiFslfneehrkearglfr 81 
                                        Y+     +++l+l kq+++ pk++ +    ++   e+++l +
  gene1851|gene1851|rna1850|rna1850 188 YRYDHLETYVLQLRKQREMKPKDSPYKPNASQINAEIEKLKD 229
                                        443334444789999999999999999999988888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 3317.62
//
Query:       gene1852|gene1852|rna1851|rna1851  [L=537]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-35  119.9   4.3      3e-10   39.8   0.3    8.3  9  Arm              Armadillo/beta-catenin-like repeat
    9.1e-10   38.9   1.6    2.2e-09   37.6   1.6    1.6  1  IBB              Importin beta binding domain
    3.1e-08   33.9   0.3     0.0005   20.5   0.1    3.7  3  HEAT_EZ          HEAT-like repeat
    3.3e-08   33.8   0.0      0.096   13.1   0.0    3.6  3  HEAT_2           HEAT repeats
    3.4e-07   30.0   0.4      0.015   15.5   0.1    4.7  4  HEAT             HEAT repeat
    1.3e-05   24.7   0.0    2.6e-05   23.7   0.0    1.5  1  Arm_3            Atypical Arm repeat
     0.0056   16.7   0.3        8.1    6.6   0.1    3.4  3  Leuk-A4-hydro_C  Leukotriene A4 hydrolase, C-terminal
  ------ inclusion threshold ------
      0.011   15.9   1.4        6.7    7.0   0.1    3.8  3  RICTOR_V         Rapamycin-insensitive companion of mTOR, dom
      0.097   12.7   0.1       0.72    9.9   0.0    2.5  3  Cnd1             non-SMC mitotic condensation complex subunit


Domain annotation for each model (and alignments):
>> Arm  Armadillo/beta-catenin-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       7.1   1.4e+04      30      38 ..      42      50 ..      39      50 .. 0.80
   2 !   15.9   0.0   4.8e-06    0.0096       1      22 [.      81     102 ..      81     112 .. 0.88
   3 !    6.7   0.1    0.0038       7.6      28      41 .]     138     151 ..     136     151 .. 0.88
   4 !   39.8   0.3   1.5e-13     3e-10       2      40 ..     154     192 ..     153     193 .. 0.96
   5 !    9.5   0.1   0.00051         1       3      39 ..     197     238 ..     194     238 .. 0.92
   6 !   10.2   0.0   0.00031      0.61       2      40 ..     245     281 ..     244     282 .. 0.88
   7 !   14.7   0.0   1.1e-05     0.023       2      41 .]     343     386 ..     342     386 .. 0.82
   8 !   15.8   0.0   5.5e-06     0.011       3      39 ..     390     426 ..     388     428 .. 0.93
   9 ?   -3.4   0.0       5.9   1.2e+04      26      37 ..     467     478 ..     450     479 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.1
                                       HHHHHHHHH CS
                                Arm 30 eeAawALsN 38
                                        ++a+A+sN
  gene1852|gene1852|rna1851|rna1851 42 SVSASAISN 50
                                       678999999 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.8e-06
                                        SHHHHHHHHHTTHHHHHHHHTT CS
                                Arm   1 nsenkdavieaGavppLvrLLs 22 
                                        +s++++ vi++G+vp++++L++
  gene1852|gene1852|rna1851|rna1851  81 DSPPIQPVIDSGCVPRFIELMD 102
                                        689*****************98 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0038
                                        HHHHHHHHHHHHTT CS
                                Arm  28 vqeeAawALsNLaa 41 
                                        ++ eAaw ++N+++
  gene1852|gene1852|rna1851|rna1851 138 IRVEAAWVITNISS 151
                                        788*********96 PP

  == domain 4  score: 39.8 bits;  conditional E-value: 1.5e-13
                                        HHHHHHHHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                                Arm   2 senkdavieaGavppLvrLLssedeevqeeAawALsNLa 40 
                                         +++++vi++Gavp L+++L ++++ v+ +++wAL+N+a
  gene1852|gene1852|rna1851|rna1851 154 TQQTKVVIDCGAVPLLIQMLLDTNDAVLDQSVWALGNIA 192
                                        5899**********************************8 PP

  == domain 5  score: 9.5 bits;  conditional E-value: 0.00051
                                        HHHHHHHHTTHHHHHHHHTT.....TSSHHHHHHHHHHHHHH CS
                                Arm   3 enkdavieaGavppLvrLLs.....sedeevqeeAawALsNL 39 
                                        + +d + e Ga++  + LL        + +++++ +w LsNL
  gene1852|gene1852|rna1851|rna1851 197 GMRDIILETGALDTVLGLLLklhgsAIHIKIVRNLTWLLSNL 238
                                        5899999***************99999**************9 PP

  == domain 6  score: 10.2 bits;  conditional E-value: 0.00031
                                        HHHHHHHHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHHT CS
                                Arm   2 senkdavieaGavppLvrLLssedeevqeeAawALsNLa 40 
                                        ++n + ++++  +++L +L++  d+e++ +A wALs++ 
  gene1852|gene1852|rna1851|rna1851 245 PPNEQNMRKS--LDVLFKLINIRDPEIVSDAYWALSYIV 281
                                        6677888888..999999*******************96 PP

  == domain 7  score: 14.7 bits;  conditional E-value: 1.1e-05
                                        HHHHHHHHHTTHHHHHHHHTT....TSSHHHHHHHHHHHHHHTT CS
                                Arm   2 senkdavieaGavppLvrLLs....sedeevqeeAawALsNLaa 41 
                                        ++++ a+i++G ++ +    +     + +++++e++w+LsN++a
  gene1852|gene1852|rna1851|rna1851 343 DDQTSALIRMGFMKFFRPVFYrlenKKQPRLRKEICWTLSNITA 386
                                        67777777777777777777777788999*************96 PP

  == domain 8  score: 15.8 bits;  conditional E-value: 5.5e-06
                                        HHHHHHHHTTHHHHHHHHTTTSSHHHHHHHHHHHHHH CS
                                Arm   3 enkdavieaGavppLvrLLssedeevqeeAawALsNL 39 
                                        ++ +av+++  vp L++ +ss    +++eA+wA+ NL
  gene1852|gene1852|rna1851|rna1851 390 DHAKAVVDMDLVPLLIDSMSSYELFIRKEACWAVLNL 426
                                        67799*******************************9 PP

  == domain 9  score: -3.4 bits;  conditional E-value: 5.9
                                        HHHHHHHHHHHH CS
                                Arm  26 eevqeeAawALs 37 
                                        +e+q++++ + +
  gene1852|gene1852|rna1851|rna1851 467 PEMQCQILDCFR 478
                                        688888888876 PP

>> IBB  Importin beta binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   1.6   1.1e-12   2.2e-09       9      45 ..       9      45 ..       3      73 .. 0.73

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.1e-12
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                IBB  9 gkdaeelRrrReeeqvelRKqkreeqllKrRnvaaea 45
                                       +k +e+ R+ Ree+qvelR+qk+ee l+K+Rn++++a
  gene1852|gene1852|rna1851|rna1851  9 SKTTENRRKMREEQQVELRQQKKEELLSKKRNLSVSA 45
                                       4456667777***********************6622 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.5e-07    0.0005       4      55 .]     139     191 ..     136     191 .. 0.74
   2 ?   -3.4   0.0       7.8   1.6e+04       7      13 ..     273     279 ..     270     287 .. 0.77
   3 !    9.1   0.0   0.00095       1.9       1      51 [.     371     422 ..     369     423 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-07
                            HEAT_EZ   4 RraAawaLGrlaggepellqplvp.eilpaLlalLnddsdeVRaaAagaLgnl 55 
                                        R  Aaw++ ++ +g  ++ + +++  ++p+L+++L d +d+V  ++++aLgn+
  gene1852|gene1852|rna1851|rna1851 139 RVEAAWVITNISSGTTQQTKVVIDcGAVPLLIQMLLDTNDAVLDQSVWALGNI 191
                                        6667777766665555553322222689***********************98 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.8
                            HEAT_EZ   7 AawaLGr 13 
                                        A+waL+ 
  gene1852|gene1852|rna1851|rna1851 273 AYWALSY 279
                                        7899874 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00095
                            HEAT_EZ   1 wrvRraAawaLGrlaggepellqp.lvpeilpaLlalLnddsdeVRaaAaga 51 
                                        +r+R   +w+L+++ +g +++ +  +  +++p+L+  +++ +  +R+ A++a
  gene1852|gene1852|rna1851|rna1851 371 PRLRKEICWTLSNITAGTADHAKAvVDMDLVPLLIDSMSSYELFIRKEACWA 422
                                        799**********8889999988845569******9999999999******9 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0    0.0001       0.2      16      60 ..     138     193 ..     136     219 .. 0.76
   2 ?    4.5   0.0     0.023        46      28      58 ..     250     280 ..     221     310 .. 0.81
   3 !   13.1   0.0   4.8e-05     0.096       7      55 ..     364     423 ..     359     461 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                             HEAT_2  16 vrraairaLgrignp...........ealpaLvellededpavRraaaeaLgaigd 60 
                                        +r +a++++ +i +             a+p+L+++l d++ av  + ++aLg i+ 
  gene1852|gene1852|rna1851|rna1851 138 IRVEAAWVITNISSGttqqtkvvidcGAVPLLIQMLLDTNDAVLDQSVWALGNIAG 193
                                        6888888888665544455666666677************************9953 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.023
                             HEAT_2  28 gnpealpaLvellededpavRraaaeaLgai 58 
                                        + +++l+ L++l++  dp++   a +aL+ i
  gene1852|gene1852|rna1851|rna1851 250 NMRKSLDVLFKLINIRDPEIVSDAYWALSYI 280
                                        44599***********************866 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 4.8e-05
                             HEAT_2   7 alendpdpevrraairaLg.....rignp.........ealpaLvellededpavRraaaeaL 55 
                                        +len + p +r++++++L      +             +++p+L++ +++ +  +R++a++a 
  gene1852|gene1852|rna1851|rna1851 364 RLENKKQPRLRKEICWTLSnitagT---AdhakavvdmDLVPLLIDSMSSYELFIRKEACWAV 423
                                        689999*************665542...234455666677*********************97 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.84   1.7e+03      15      30 ..     137     152 ..     136     153 .. 0.88
   2 !   15.5   0.1   7.6e-06     0.015       2      28 ..     166     192 ..     165     194 .. 0.96
   3 ?    2.5   0.0      0.11   2.2e+02       3      28 ..     360     385 ..     358     388 .. 0.85
   4 ?    5.5   0.1     0.012        25       1      31 []     400     430 ..     400     430 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.84
                                        HHHHHHHHHHHHHHHC CS
                               HEAT  15 eVReaAakaLgalaev 30 
                                        ++R  Aa+ +++++++
  gene1852|gene1852|rna1851|rna1851 137 KIRVEAAWVITNISSG 152
                                        68999*******9986 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 7.6e-06
                                        HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   2 lPlllkllsDpspeVReaAakaLgala 28 
                                        +Pll+++l D++  V + +++aLg++a
  gene1852|gene1852|rna1851|rna1851 166 VPLLIQMLLDTNDAVLDQSVWALGNIA 192
                                        7************************98 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.11
                                        HHHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   3 PlllkllsDpspeVReaAakaLgala 28 
                                        P++ +l + + p+ R+  +++L ++ 
  gene1852|gene1852|rna1851|rna1851 360 PVFYRLENKKQPRLRKEICWTLSNIT 385
                                        77888778899************997 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.012
                                        HHHHHHHHHT-SSHHHHHHHHHHHHHHHHCS CS
                               HEAT   1 llPlllkllsDpspeVReaAakaLgalaevl 31 
                                        l+Pll+  +s+ + ++R+ A++a+ +l+ ++
  gene1852|gene1852|rna1851|rna1851 400 LVPLLIDSMSSYELFIRKEACWAVLNLMYHC 430
                                        789999998888889***********99887 PP

>> Arm_3  Atypical Arm repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.3e-08   2.6e-05       1      42 [.     494     535 ..     494     537 .] 0.92

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.3e-08
                              Arm_3   1 npyalliEeagGldkIeaLQnheneeIYkkAlkIiekYFsee 42 
                                        np+++ + ea+ +d Ie LQ++ +  + +kA+ Ii  +F+  
  gene1852|gene1852|rna1851|rna1851 494 NPIYEKMVEADIVDAIEGLQDSGDRTVSDKAYSIIVDFFDGV 535
                                        78888889*******************************987 PP

>> Leuk-A4-hydro_C  Leukotriene A4 hydrolase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.15     3e+02       7      47 ..     232     274 ..     228     309 .. 0.79
   2 !    6.6   0.1    0.0041       8.1      64      86 ..     347     369 ..     296     377 .. 0.83
   3 ?    4.3   0.0      0.02        40      28      72 ..     424     469 ..     403     474 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.15
                                        HHHHHHHHTT-..GGG-HHHHHHHHHHTIIIT---HHHHHHHH CS
                    Leuk-A4-hydro_C   7 vlfLekLleke..kplpaekleaLdelYklseskNaeirlrwl 47 
                                        + +L++L + +  +p +++  ++Ld l+kl + ++ ei +  +
  gene1852|gene1852|rna1851|rna1851 232 TWLLSNLNRGRnpPPNEQNMRKSLDVLFKLINIRDPEIVSDAY 274
                                        55677887744335666888899***************98765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0041
                                        HHTTT---HHHHHHHHHHHHTT- CS
                    Leuk-A4-hydro_C  64 eflgsqGrmkfvrplYraLnkvd 86 
                                        + l + G mkf rp++  L + +
  gene1852|gene1852|rna1851|rna1851 347 SALIRMGFMKFFRPVFYRLENKK 369
                                        567779***********998844 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.02
                                        HHHHTIIIT.---HHHHHHHHHHHHHTT-GGGHHHHHHHTTT---H CS
                    Leuk-A4-hydro_C  28 LdelYklse.skNaeirlrwlqlalkakyeeavpevaeflgsqGrm 72 
                                        L+ +Y+ ++  +N++ +++wl++++ ++  +a++   +++ ++  m
  gene1852|gene1852|rna1851|rna1851 424 LNLMYHCNNlPTNSDTKFEWLKILMDNGFIDALQSYLDVVPNVPEM 469
                                        666788666368*****************99999998888776555 PP

>> RICTOR_V  Rapamycin-insensitive companion of mTOR, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.25   5.1e+02       7      37 ..     143     174 ..     140     178 .. 0.79
   2 ?    7.0   0.1    0.0033       6.7       5      34 ..     183     213 ..     179     224 .. 0.80
   3 ?    3.9   0.0     0.031        62       4      55 ..     375     427 ..     372     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                           RICTOR_V   7 LWaiGhigs.selGielldeydivedivelae 37 
                                         W i +i s +++  +++ ++ +v+ ++++  
  gene1852|gene1852|rna1851|rna1851 143 AWVITNISSgTTQQTKVVIDCGAVPLLIQMLL 174
                                        5********444555588888*****999976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0033
                           RICTOR_V   5 aaLWaiGhigsselGie.lldeydivedive 34 
                                        ++ Wa+G+i+   +G++ ++ e+ ++++++ 
  gene1852|gene1852|rna1851|rna1851 183 QSVWALGNIAGDSEGMRdIILETGALDTVLG 213
                                        689************9987777666666655 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.031
                           RICTOR_V   4 KaaLWaiGhigsselGie.lldeydivedivelaeespvlslRGtafyvLgli 55 
                                        K   W++ +i + +   +  + ++d+v+ +++ + + + +  +  +  vL+l+
  gene1852|gene1852|rna1851|rna1851 375 KEICWTLSNITAGTADHAkAVVDMDLVPLLIDSMSSYELFIRKEACWAVLNLM 427
                                        7778******99766666688888**********9999999999999999987 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00036      0.72      36      90 ..     137     196 ..     131     269 .. 0.83
   2 ?   -1.4   0.0       1.1   2.1e+03      58      88 ..     253     283 ..     245     312 .. 0.78
   3 ?   -2.3   0.0         2   4.1e+03      35      53 ..     413     433 ..     398     451 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00036
                               Cnd1  36 yVRktaaivvakL.....ilndmvkekgflselaklleDenprVvanalaalteisekse 90 
                                         +R  aa v++++      + ++v++ g +  l ++l D+n+ V + ++ al +i+  se
  gene1852|gene1852|rna1851|rna1851 137 KIRVEAAWVITNIssgttQQTKVVIDCGAVPLLIQMLLDTNDAVLDQSVWALGNIAGDSE 196
                                        6899999999999998644555899999**************************998854 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                               Cnd1  58 gflselaklleDenprVvanalaalteisek 88 
                                        + l+ l kl++  +p++v+ a  al+ i + 
  gene1852|gene1852|rna1851|rna1851 253 KSLDVLFKLINIRDPEIVSDAYWALSYIVDV 283
                                        5677788888999999999999999888765 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                               Cnd1  35 pyVRktaaivvakL..ilndm 53 
                                          +Rk a  +v++L  + n++
  gene1852|gene1852|rna1851|rna1851 413 LFIRKEACWAVLNLmyHCNNL 433
                                        568999999999995433444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 3180.72
//
Query:       gene1853|gene1853|rna1852|rna1852  [L=431]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-84  282.0   0.0    7.7e-84  281.8   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    3.2e-08   33.2   0.0    4.3e-08   32.8   0.0    1.1  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.016   14.5   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.071   11.8   0.0       0.11   11.2   0.0    1.2  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.0   1.7e-87   7.7e-84       1     370 [.      33     396 ..      33     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 1.7e-87
                                        EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHH CS
                        Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainl 76 
                                        i++d + tt++ ++Vlda+  +yt   +n+h+ +h++g++a + ve+ar++va li+ +  +eiiftsG+te++nl
  gene1853|gene1853|rna1852|rna1852  33 IFFDVQSTTPVDPRVLDAMLPFYTTVFGNPHSRTHRYGWQAEAGVEKARSQVASLIGCDP-NEIIFTSGATESNNL 107
                                        799********************************************************7.*************** PP

                                        HHHHCCCC.-TTTS..EEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBE CS
                        Aminotran_5  77 valslars.lkpgd..eivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvs 149
                                        +++++    lk+g+  +i++ ++eh++ l ++++l+ + g++v+++p+ ++g +d+++++ +++e+t lv++++v+
  gene1853|gene1853|rna1852|rna1852 108 ALKGVSGFkLKEGKpvHIITLQTEHKCVLDTCRNLE-ENGIEVTYLPVGKDGVVDIEDIRRNIKENTVLVSVSAVN 182
                                        *****9999999986699*****************8.77************************************* PP

                                        TTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS CS
                        Aminotran_5 150 nvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkelleklepll 225
                                        +++Gtiqp+ eigkl+k+kg+l+++Daaq++g+++idv+++++D+l++ +hK++gP+GiG+lyvr++  +++ pl 
  gene1853|gene1853|rna1852|rna1852 183 SEIGTIQPLGEIGKLCKEKGVLFHTDAAQGAGKMKIDVNEMNIDLLSMCAHKIYGPKGIGALYVRRRPRVRMIPLI 258
                                        **************************************************************************** PP

                                        .STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCT.STTEEEE CS
                        Aminotran_5 226 lggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlks.lpgvrly 300
                                         gg+       +e++       +++GT   + ++g+g+a+e++ + ++++  ++ k+l+++l++  k+ ++gv ++
  gene1853|gene1853|rna1852|rna1852 259 NGGG-------QERG-------LRSGTVASPLAVGFGKAAEIC-SKEMKRDFEYIKKLSDKLKSIFKKnIEGVIIN 319
                                        ****.......9999.......9********************.8899******************8769999997 PP

                                        S.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-H CS
                        Aminotran_5 301 gpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynte 365
                                        g+  ++ ++++v+++f+ v+ e + ++L++  Ia++sG++c+    +p+++++al        +++R+++++ +  
  gene1853|gene1853|rna1852|rna1852 320 GS--EDGNPGCVNVSFPFVEGESLLMYLKD--IALSSGSACTsaslEPSYVLRALGrddevahSSIRFGIGRFTLP 391
                                        75..8***********************98..**********9999999999999999***************999 PP

                                        HHHHH CS
                        Aminotran_5 366 eevdr 370
                                        +evd 
  gene1853|gene1853|rna1852|rna1852 392 QEVDV 396
                                        99985 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   9.6e-12   4.3e-08      33     207 ..      76     244 ..      68     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 9.6e-12
                                        HHHHHHHHHHHHTT-S..EEEEES-HHHHHHHHH......HHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEE CS
                    Beta_elim_lyase  33 tvnrLedavaelfgke..aalfvpqGtaAnsill......kill.qrgeevivtepahihfdetgaiaelagvklr 99 
                                        +v++   +va l+g +   ++f+   t +n+++l      k+   ++ + + ++ +     d++++++e +g++++
  gene1853|gene1853|rna1852|rna1852  76 GVEKARSQVASLIGCDpnEIIFTSGATESNNLALkgvsgfKLKEgKPVHIITLQTEHKCVLDTCRNLEE-NGIEVT 150
                                        677788888998888765778998899*******877765333334555555666677889999**966.8999** PP

                                        EE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHH CS
                    Beta_elim_lyase 100 dlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaa 175
                                         l+  ++G +d+e++++ ike      ++ l+s+   +n+   ++ +++ l e+ +++k++g+ +h D+A     a
  gene1853|gene1853|rna1852|rna1852 151 YLPVGKDGVVDIEDIRRNIKE------NTVLVSVSA-VNS---EIGTIQPLGEIGKLCKEKGVLFHTDAAQG---A 213
                                        ****999**************......678888865.555...455667788999**************965...5 PP

                                        HHHTS-CHHHHTTSSEEEEESSSTT-.-SS-EE CS
                    Beta_elim_lyase 176 kslgeivkemfsyvDsvtmslkKdll.anvGgv 207
                                         +++ +v em   +D ++m++ K  +   +G++
  gene1853|gene1853|rna1852|rna1852 214 GKMKIDVNEM--NIDLLSMCAHKIYGpKGIGAL 244
                                        6779999999..599*****9995431345555 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.6e-06     0.016      41     150 ..      95     214 ..      71     231 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.6e-06
                                        EEEESSHHHHHHHHHHH...TTTTTT-..EEEEESSS-...THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG- CS
                    DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLra...lgvgpgd..eVIvpsltF...vatanavlelgakpvfvDvdpdtynidpaaieaai 108
                                         i +s +t+++ laL+    +++++g+   +I+ ++     + t     e+g ++ ++ v  ++  +d ++i++ i
  gene1853|gene1853|rna1852|rna1852  95 IIFTSGATESNNLALKGvsgFKLKEGKpvHIITLQTEHkcvLDTCRNLEENGIEVTYLPVG-KDGVVDIEDIRRNI 169
                                        5666777888888888776744444441155665555511134666667778888888887.8899********** PP

                                        -TTE..EEEEEB-G.GGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                    DegT_DnrJ_EryC1 109 tert..kaIlpVhl.yGqvadmdalkaiaakhglkvieDaAhAlG 150
                                         e+t    + +V+   G +  + ++ ++++++g+ +  DaA++ G
  gene1853|gene1853|rna1852|rna1852 170 KENTvlVSVSAVNSeIGTIQPLGEIGKLCKEKGVLFHTDAAQGAG 214
                                        ****664555555437999999********************998 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.5e-05      0.11     166     239 ..     146     213 ..     118     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.5e-05
                                        T-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTGG CS
                      Pyridoxal_deC 166 gvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAyaG 239
                                        g+++ ++p+ ++g +  ++ ++ i+e+     +   v + +  +  g    l e+g++c++ ++  H DAA + 
  gene1853|gene1853|rna1852|rna1852 146 GIEVTYLPVGKDGVVDIEDIRRNIKENT----V--LVSVSAVNSEIGTIQPLGEIGKLCKEKGVLFHTDAAQGA 213
                                        4567777777777666666666665433....2..456666678888899*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2521.00
//
Query:       gene1854|gene1854|rna1853|rna1853  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-25   87.6   0.5    1.2e-24   86.7   0.5    1.4  1  UDPGP            UTP--glucose-1-phosphate uridylyltransferase
      5e-07   30.2   0.0    7.1e-07   29.7   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00029   20.5   0.0    0.00046   19.8   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
     0.0007   19.4   0.0     0.0011   18.8   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> UDPGP  UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7   0.5   2.8e-28   1.2e-24      37     340 ..      20     312 ..       3     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 2.8e-28
                              UDPGP  37 yedl.kekeeekkell..nklavlkLnGglGtsmGckgpKslieVrdgktfLdlivqqieelnkkynvdvPlvlmn 109
                                         +dl ++ ++  +e+l  + l v+ L Gg+Gt++G + pK+l++++ gkt+++  ++ i+e+ +kyn ++ + +m+
  gene1854|gene1854|rna1853|rna1853  20 LNDLgRRYKKVGEEALrkKSLGVVILSGGQGTRLGSDAPKGLFKIK-GKTLFEWHMETIREIIDKYNANITVFIMT 94 
                                        4455433444455555335599***********************7.89*************************** PP

                              UDPGP 110 SfnTdedtekilk.kykkkkvdiltfnqsryPriskesllpvekkakkeekeewyPpGhGdlyesLknsglldkll 184
                                        S  Tde+ +++++ k ++  v+i++f+q +   + ++ + p+e         +  P G+Gd+++++++ +      
  gene1854|gene1854|rna1853|rna1853  95 SSFTDEAVRNYFQgKDFG--VKIHFFKQRNSLCVGTDGK-PLEYYGG----YAESPYGNGDIFKAIQQVN------ 157
                                        *************66666..*********9999998876.6665554....5668**********96655...... PP

                              UDPGP 185 aeGkeyiFvsniDN.lgatvDlkilnllvekkaeflmevtektradvkgGtlieyegklrlleiaqvpkehveefk 259
                                         eG+e + v +iDN l+++ D+ +++ + + + + l + + k ++++ g  l+  +gklr+ e+ +  + + e  +
  gene1854|gene1854|rna1853|rna1853 158 LEGIEALNVISIDNvLAKILDPVFVGAFFSGNYDILSKSVTKGEKESVGAFLM--DGKLRIKEYGEN-DANGEGIQ 230
                                        59*******************************************99999986..7********998.44445555 PP

                              UDPGP 260 svkkfkifntnniwinlkalkrlveekelkleiivnkktldegekviqletavgaaiksF........kkavginV 327
                                                n +n  +  +++k++ + +  +++  ++  ++  + k+i+  +++g + + F        +k  +inV
  gene1854|gene1854|rna1853|rna1853 231 G-------NICNHMFGTSFIKKMRNVDLPEHKAFKKIAYTI-DGKLIKPLKPNGFKKETFifdsfeytHKNGVINV 298
                                        5.......555555566777777655555666655554433.344888888888888888888888889999**** PP

                              UDPGP 328 pR.srflpvkttsd 340
                                        pR ++f+p+k+  d
  gene1854|gene1854|rna1853|rna1853 299 PReKEFSPLKNGMD 312
                                        **999*****9877 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.6e-10   7.1e-07       1      41 [.      42      89 ..      42     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.6e-10
                                       EEEEEESS-TTTTT..THHHHCCCCCCHHHHHHHHHCTT.-C......E CS
                       NTP_transf_3  1 aviLAGGrSsRmgg..dKallplggkpllervldalraagvd......e 41
                                       +viL GG+++R+g+  +K l +++gk+l+e++++++r+  +d       
  gene1854|gene1854|rna1853|rna1853 42 VVILSGGQGTRLGSdaPKGLFKIKGKTLFEWHMETIREI-IDkynaniT 89
                                       69***********999********************998.765555443 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     1e-07   0.00046       3      84 ..      43     124 ..      41     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-07
                                        EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH....TT-SEEEEEEETTTHHHHHHHHTTSGGGTSE CS
                    NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan....sgieeiivvltqehsflveeqlkegskfgve 74 
                                        vIL+GG+GtRL    ++ +k l+ + gk +l++  ++++ +     + + +++++t+    ++ +++ +g++fgv+
  gene1854|gene1854|rna1853|rna1853  43 VILSGGQGTRL---GSDAPKGLFKIKGK-TLFEWHMETIREiidkYNANITVFIMTSSFTDEAVRNYFQGKDFGVK 114
                                        9*********7...68999999999999.****999998876633445557899999999999999999******* PP

                                        EEEEEESS-- CS
                    NTP_transferase  75 vlialepegk 84 
                                        + +  ++++ 
  gene1854|gene1854|rna1853|rna1853 115 IHFFKQRNSL 124
                                        **99998865 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.4e-07    0.0011       3      40 ..      42      79 ..      40     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.4e-07
                                       EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHC CS
                               IspD  3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdalla 40
                                       vvi   G+G+R++++ pK ++++kg+tl e+ ++++ +
  gene1854|gene1854|rna1853|rna1853 42 VVILSGGQGTRLGSDAPKGLFKIKGKTLFEWHMETIRE 79
                                       8999**************************98876643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2456.44
//
Query:       gene1855|gene1855|rna1854|rna1854  [L=520]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-12   47.9   5.6    4.3e-07   29.7   1.9    2.6  3  MSC        Man1-Src1p-C-terminal domain
  ------ inclusion threshold ------
      0.039   14.5   0.3       0.15   12.6   0.3    2.0  1  FeoB_Cyto  FeoB cytosolic helical domain
       0.12   12.2   0.3       0.54   10.1   0.0    2.2  2  DivIC      Septum formation initiator
       0.13   12.0   0.9       0.62    9.8   0.0    2.4  2  HeH        HeH/LEM domain
        0.3   10.9   5.2         35    4.3   0.0    3.9  4  SAP        SAP domain


Domain annotation for each model (and alignments):
>> MSC  Man1-Src1p-C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.3   4.6e+03     136     186 ..      20      72 ..      12      97 .. 0.53
   2 !   19.4   0.0   1.7e-07    0.0006      51     124 ..     287     351 ..     224     375 .. 0.86
   3 !   29.7   1.9   1.2e-10   4.3e-07     206     338 .]     385     508 ..     357     508 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
                                MSC 136 lseeeLkeslsekksksis..keefeelwkealkeLkkeeeivvredsesese 186
                                        l++++L+++++e+  + i   + + +el ++  +++ k+ +++++++++ + e
  gene1855|gene1855|rna1854|rna1854  20 LTKTQLRKIMYENGVEAIPplTAKKSELIDAYKENIYKRIDVLMSRRKNISME 72 
                                        55566666666644333221123334555555566666666655555444333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.7e-07
                                MSC  51 CtpCPehAiCysnlevkCepgyvlkphplslggllPlppsCvpdsekerkvkevakkalelLreknakvecges 124
                                        C+p Peh++   n ++ C++g+++k+ +l         ++C++d+++e+++++ +k++ ++L+++ + + +g  
  gene1855|gene1855|rna1854|rna1854 287 CIPLPEHSKIN-NGRLACDKGFIIKHGILR--------DYCIEDNRHEKEMSKKIKELKKILERRSGDYMYGMI 351
                                        **********9.77***********66655........9****************************9998876 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 1.2e-10
                                MSC 206 lkcrlrrsvretlary.rllllgl...llllllilylrsrlrsrraekerveelvkevlerLkkqkkkhaedpsta 277
                                        ++ ++r+s++++++ y r +++++   ++++++i+++    ++++++ +  +++vk++ + L +q + ++++ +  
  gene1855|gene1855|rna1854|rna1854 385 YSVNARVSMKTFFRYYfRRMIMIStplAIIIIMIKIIGMFRKKKKERLQAAQKIVKDIADVLVRQIYVSTRNANFP 460
                                        333334444444333312222222342444555555666666666667888899**************99999775 PP

                                MSC 278 pepylslvqLRDdvLqdehslkernrlWkkvekvveqnsnVrtsleevhGeimrvWeWiGs 338
                                        +   + ++qL+D +          +++W++ ek + +nsn+r s  e       +WeW+G+
  gene1855|gene1855|rna1854|rna1854 461 S--HVYIEQLKDCFGV-------DRKVWREAEKMIRRNSNIRESCIE----GKSAWEWVGP 508
                                        5..999*****98754.......469********************9....5689****96 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   4.1e-05      0.15       3      47 ..     326     383 ..     324     456 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                          FeoB_Cyto   3 eeiEkaiekleellkes...nlkaklppRwlAlklLegDeelleelk..........e 47 
                                        +e  k+i++l+++l+      +   +p++ + +klL  D+e++e+lk           
  gene1855|gene1855|rna1854|rna1854 326 KEMSKKIKELKKILERRsgdYMYGMIPTKSVPVKLLSSDPEIIERLKkevgivisneM 383
                                        67889999******9997777888999********************55555544440 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.73   2.6e+03      31      45 ..     323     337 ..     314     346 .. 0.65
   2 ?   10.1   0.0   0.00015      0.54      47      77 ..     358     387 ..     356     390 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.73
                                        HHHHHHHHHHHHHHH CS
                              DivIC  31 aelaklkaeneeLea 45 
                                        ++ ++++++++eL++
  gene1855|gene1855|rna1854|rna1854 323 RHEKEMSKKIKELKK 337
                                        555566666666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                                        HCC-XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              DivIC  47 vkdLksdedyieerARselglvkpgEtvyrv 77 
                                        vk+L+sd++ ie+  + e g v ++E++y v
  gene1855|gene1855|rna1854|rna1854 358 VKLLSSDPEIIERLKK-EVGIVISNEMIYSV 387
                                        899*99***9999988.************87 PP

>> HeH  HeH/LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00017      0.62       3      31 ..      19      49 ..      18      50 .. 0.89
   2 ?   -0.8   0.2      0.37   1.3e+03       5      14 ..     331     340 ..     329     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                                HeH  3 sLtVaqLRriLvehgvey..PsnaKKadLve 31
                                       +Lt  qLR+i  e+gve   P +aKK++L++
  gene1855|gene1855|rna1854|rna1854 19 KLTKTQLRKIMYENGVEAipPLTAKKSELID 49
                                       67778************7779********95 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.37
                                HeH   5 tVaqLRriLv 14 
                                        ++ +L++iL 
  gene1855|gene1855|rna1854|rna1854 331 KIKELKKILE 340
                                        7899****97 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0098        35       1      13 [.      17      29 ..      17      36 .. 0.88
   2 ?    1.6   0.0      0.07   2.5e+02      23      34 ..      43      54 ..      39      55 .. 0.87
   3 ?    4.0   0.5     0.012        44       5      16 ..     331     342 ..     328     343 .. 0.87
   4 ?   -0.5   0.0      0.32   1.1e+03      26      33 ..     366     373 ..     365     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0098
                                       HTT--HHHHHHHH CS
                                SAP  1 lskltVaeLKeeL 13
                                       ++klt ++L++++
  gene1855|gene1855|rna1854|rna1854 17 YTKLTKTQLRKIM 29
                                       89********986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.07
                                       -HHHHHHHHHHH CS
                                SAP 23 kKaeLieRLkey 34
                                       kK eLi+ +ke 
  gene1855|gene1855|rna1854|rna1854 43 KKSELIDAYKEN 54
                                       8*******9985 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.012
                                        -HHHHHHHHHHT CS
                                SAP   5 tVaeLKeeLkkr 16 
                                        + +eLK++L++r
  gene1855|gene1855|rna1854|rna1854 331 KIKELKKILERR 342
                                        899*******99 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.32
                                        HHHHHHHH CS
                                SAP  26 eLieRLke 33 
                                        e+ieRLk+
  gene1855|gene1855|rna1854|rna1854 366 EIIERLKK 373
                                        89****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1477  (0.0823805); expected 358.6 (0.02)
Passed bias filter:                      787  (0.0438954); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3779.93
//
Query:       gene1856|gene1856|rna1855|rna1855  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1461.10
//
Query:       gene1857|gene1857|rna1856|rna1856  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-45  155.4   0.0    1.7e-45  155.1   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.099   12.5   0.3        1.5    8.7   0.1    2.7  3  SUB1_ProdP9      SUB1 protease Prodomain ProdP9


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.1   0.0   1.9e-49   1.7e-45       6     230 ..      24     231 ..      19     241 .. 0.91

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 1.9e-49
                                        HHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHH CS
                    polyprenyl_synt   6 ealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnk 81 
                                         +l+y++  gGK+lR  + +++ + l+ +    e+ ++++  vell+aa L++DD+mD+se+RRG+pc++ + G k
  gene1857|gene1857|rna1856|rna1856  24 FLLDYNL-DGGKELRYKAYIHVLKELGGD--LNERNLIMGYSVELLQAALLIIDDLMDNSELRRGKPCYYFKRGAK 96 
                                        5799***.*******************44..34789**************************************** PP

                                        HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTH.HHCH CS
                    polyprenyl_synt  82 lAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTa.ylfa 156
                                         ++ d++flla++ +ll +       + + +s  +++t+ Gq  d+  + ++++s   +++y +i + KT+ y+f+
  gene1857|gene1857|rna1856|rna1856  97 -TLKDAFFLLAIIRNLLDEK------AKNAYSSSIFKTCLGQTHDTIRKTRSEYS---VKTYTAIAESKTGaYTFY 162
                                        .****************987......4479***************9666566666...****************** PP

                                        HHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HH CS
                    polyprenyl_synt 157 lpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspe 230
                                        lp+ l+ + ag   ee ++l ++++   l+FQ+qDDyl++f  pe+ gK   +D++e kct+ +    ++++p+
  gene1857|gene1857|rna1856|rna1856 163 LPAILGYVSAGK--EEPKRLWNFCNLGALIFQMQDDYLNFF--PEKSGKS-MNDLEEMKCTWFTSRISHMKDPA 231
                                        ***********5..5569***********************..*******.***********998888877776 PP

>> SUB1_ProdP9  SUB1 protease Prodomain ProdP9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.49   4.4e+03      58      70 ..      39      51 ..      23      61 .. 0.65
   2 ?    0.1   0.0     0.083   7.5e+02      34      52 ..     179     197 ..     166     201 .. 0.87
   3 ?    8.7   0.1   0.00017       1.5      14      66 ..     234     288 ..     224     291 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.49
                        SUB1_ProdP9 58 ieyikileekGal 70
                                         yi++l+e G  
  gene1857|gene1857|rna1856|rna1856 39 KAYIHVLKELGGD 51
                                       4688888887654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.083
                        SUB1_ProdP9  34 klanlknlksiiielkedt 52 
                                        +l n+ nl ++i ++++d 
  gene1857|gene1857|rna1856|rna1856 179 RLWNFCNLGALIFQMQDDY 197
                                        688999**********995 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00017
                        SUB1_ProdP9  14 sffeeslleedvlsfles..kGklanlknlksiiielkedttdeelieyikilee 66 
                                         +f e l+ +d+ls ++   +   +nl +l s ++   ++     l  +i++le 
  gene1857|gene1857|rna1856|rna1856 234 RYFSEGLVTPDLLSIIRGlfREYSSNLDELLSRLLSTVDEDEKAVLSVFISFLES 288
                                        58**************973356789***999999988888888889999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1652.64
//
Query:       gene1858|gene1858|rna1857|rna1857  [L=460]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.023   14.5   6.0      0.075   12.8   5.3    2.1  1  Nsp1_C         Nsp1-like C-terminal region
      0.084   12.7   2.0        3.8    7.4   0.4    2.3  2  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.3   8.4e-06     0.075      15      85 ..     321     391 ..     312     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.4e-06
                             Nsp1_C  15 lknktldelinkWtteLeeqekeFeeqakkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyies 85 
                                          + tl e+i++ t +Lee+ + F+e+ak+v e D+ ++++ ++ + +++ ++e e+  ++ +++ e++e+
  gene1858|gene1858|rna1857|rna1857 321 FMQMTLGEIIQQQTRKLEENIRVFKEKAKEVFEQDERIIRSLNNYKLIRNRIEEEERVIAETEENVEFFEK 391
                                        556799***************************************99999999999999999999999875 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0034        31      34      58 ..     328     352 ..     327     358 .. 0.89
   2 ?    7.4   0.4   0.00043       3.8       2      37 ..     423     458 ..     422     460 .] 0.94

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0034
                                        HHHCCCCHHHHHHHHHHHHHHHHHH CS
                      Synaptobrevin  34 deLvdktenLqssaqqFkkqarklk 58 
                                        + ++++t +L+++ + Fk++a+++ 
  gene1858|gene1858|rna1857|rna1857 328 EIIQQQTRKLEENIRVFKEKAKEVF 352
                                        5789*****************9985 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00043
                                        XXHHHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHC CS
                      Synaptobrevin   2 ndklakikaevdevkdimkeNidkvlergekldeLv 37 
                                        n++++++k+e dev  +++eN + ++  +ekl+ L+
  gene1858|gene1858|rna1857|rna1857 423 NKTIETLKDEEDEVMCLVNENYNLITTIEEKLEILE 458
                                        67899****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 2649.88
//
Query:       gene1859|gene1859|rna1858|rna1858  [L=657]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-17   63.0   0.7    1.6e-17   63.0   0.7    2.9  3  HSP70     Hsp70 protein
    5.3e-10   38.6   0.1      6e-08   31.9   0.0    2.9  2  MreB_Mbl  MreB/Mbl protein
  ------ inclusion threshold ------
       0.14   12.7   3.5         38    5.0   0.1    3.4  3  DUF883    Bacterial protein of unknown function (DUF883)
        3.7    7.4   7.5        3.4    7.5   0.3    2.8  3  DSPc      Dual specificity phosphatase, catalytic domain


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1     0.012        55       2      33 ..       4      34 ..       3      54 .. 0.82
   2 !   63.0   0.7   3.6e-21   1.6e-17     136     587 ..     100     522 ..      79     533 .. 0.81
   3 ?   -2.3   4.0       0.2   8.9e+02     486     527 ..     590     631 ..     577     654 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.012
                                       EEEEEXSSEEEEEEEETTEEEEEXXTTSXSSE CS
                              HSP70  2 iGiDLGttnsvvavmeggkievianeegnrtt 33
                                       +GiD+G+ ++vva  + ++ +v  +e+g+r+ 
  gene1859|gene1859|rna1858|rna1858  4 VGIDIGNYKTVVASSK-DNGKVYGDEQGKRSI 34
                                       8***********9766.566899999999976 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 3.6e-21
                                        EEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEE CS
                              HSP70 136 avitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfe 211
                                         ++tvP Yf++++R+   d ++   L+   ++ +  A+++   + +++ +++ l++D+G +  ++ + ++ek vf+
  gene1859|gene1859|rna1858|rna1858 100 MCMTVPVYFKEKERRILIDIASAIDLKLEGLITDISAMGMFGCVRRESMPNEFLLFDFGFSKSTAGLFSFEKNVFK 175
                                        689************************************9777777889*************************** PP

                                        EEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTTE CS
                              HSP70 212 vkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedgk 287
                                         +      ++G  +fDe+l++ +ve+        l+++k + +r+k++ +k+K +L s+++ +i+l ++t     +
  gene1859|gene1859|rna1858|rna1858 176 PLYMK-AVKVGSMQFDEKLIDIIVEKHS------LERSKLIRERIKRNLDKIKTTLNSTRNCNIQL-FITE----N 239
                                        88765.5789**************9765......557889999***************66666665.3333....3 PP

                                        EEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTH CS
                              HSP70 288 dlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDea 363
                                         l+++++ +++++ ve +++++ + v ++++++k++      +++vGG +    ++e+++e ++   + t++  + 
  gene1859|gene1859|rna1858|rna1858 240 PLEISVTQDEYKKAVEVYINELNSFVDSVMEETKFSG----VIEVVGGNSISFLIKEMLNEKIEY--QATLDVSDS 309
                                        699*****************************99874....5889****9777777777777654..556777778 PP

                                        HHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEE.EEEEESSTTSS.SEEEEEEE CS
                              HSP70 364 vaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtkliernttiptkks.qvfstaadnqt.aveievlq 437
                                         aiG+A+  +  s        ll D++   ++i+++g+ ++ +   n    t+    + ++++ n++ ++ ie+l 
  gene1859|gene1859|rna1858|rna1858 310 AAIGSALGMACRSL---RARYLLHDIIGREISIQIQGEEVNPTVIFNP---TELVeGIPKIVTYNRKgSFVIEIL- 378
                                        89999998888777...55789**************998887766664...443337889999999999999775. PP

                                        SSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHH CS
                              HSP70 438 gerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkd 513
                                              +d + +++ e+++++   +  + i+V+f+i + G + v++ + e++++ + +    ++ +   ++ +   
  gene1859|gene1859|rna1858|rna1858 379 ------EDGEVISTLEIEKVE--TDEAKPIHVSFSIGKFGTVCVTSVECEDSIDYKYKPFRISEID---MDYIKAL 443
                                        ......68899*********9..677889******************9999888887655555555...5555555 PP

                                        HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.GGGSTHHHHHHHHHHHHHHHCHTTSSC....HHHHHHHHH CS
                              HSP70 514 aeesaeedkkkkeaieakneaeelvyslekkleee.aekvseaekekvesaieeLkeeleeee....keeieakte 584
                                        + ++++e+   ++    +ne+e+++  l ++l ++ ++ ++e+e ++v++ + +L ++ ++e     +e  ++ ++
  gene1859|gene1859|rna1858|rna1858 444 EIKYRNEELGLERIGGMRNELETMAVGLGDALYNKfSKIITEDELSAVKEIAMDLFDTPQSETvgqeEEVKHSVLS 519
                                        66788888888888899***************9997888888999*********9998766664432233333344 PP

                                        HHH CS
                              HSP70 585 elk 587
                                        +l+
  gene1859|gene1859|rna1858|rna1858 520 KLE 522
                                        444 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.2
                                        TTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHH CS
                              HSP70 486 ketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkea 527
                                        ++   e +  i++  +  + e+e+  k+aee ++e +kk e 
  gene1859|gene1859|rna1858|rna1858 590 ENFITEIKCDIQKYLEKAKIEVEEKRKEAEEKSKEKEKKDED 631
                                        444444444444444434444444333333332222222211 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.3e-11     6e-08      76     297 ..      80     298 ..       1     323 [. 0.81
   2 !    3.5   0.0    0.0059        27      63      86 ..     531     554 ..     482     563 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.3e-11
                                        HHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEH.HHHHHHHTT--TTSSS-EEEE CS
                           MreB_Mbl  76 ellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevlliee.plaAAiGaglpveepsgnmvv 150
                                        +++ ++i++v k+++ ++p + ++vP    e err ++++a+ +  +   li + + +   G+    + p+  ++ 
  gene1859|gene1859|rna1858|rna1858  80 AMFMKYIDRVVKRNTPTHPPMCMTVPVYFKEKERRILIDIASAIDLKLEGLITDiSAMGMFGCVRRESMPNEFLLF 155
                                        6888899999**********************************9997777666156677899999999******* PP

                                        EE-SS-EEEEEEETTEEE....EEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHH.EEE CS
                           MreB_Mbl 151 diGggttevavislggiv....tsksvrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeee.kme 221
                                        d G  ++   + s+   v    ++k+v+v+  ++de++i+ i +k++l   +   e+ik ++ +++++ +++ + +
  gene1859|gene1859|rna1858|rna1858 156 DFGFSKSTAGLFSFEKNVfkplYMKAVKVGSMQFDEKLIDIIVEKHSLERSKLIRERIKRNLDKIKTTLNSTrNCN 231
                                        **************99884444689*************************************99887766554666 PP

                                        EEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHH CS
                           MreB_Mbl 222 ikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseet 297
                                        i  +  +t  p e++v+++e ++a++  ++++ + v +v+e+t+           i ++GG ++   ++++l+e++
  gene1859|gene1859|rna1858|rna1858 232 I--QLFITENPLEISVTQDEYKKAVEVYINELNSFVDSVMEETKFS---G----VIEVVGGNSISFLIKEMLNEKI 298
                                        6..6899***********************************9732...2....2335556555555555555555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0059
                                        EETTEESSHHHHHHHHHHHHHHHH CS
                           MreB_Mbl  63 lkdGviadlevaeellkyfikkvk 86 
                                         k+Gvi+dle  ++++++f k+ +
  gene1859|gene1859|rna1858|rna1858 531 YKNGVIEDLEKHKDMINEFRKEHS 554
                                        699***************988765 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.042   1.9e+02      23      51 ..     200     228 ..     191     233 .. 0.86
   2 ?    3.9   0.1     0.019        84       4      62 ..     485     543 ..     483     554 .. 0.86
   3 ?    5.0   0.1    0.0085        38      29      64 ..     593     628 ..     572     637 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.042
                             DUF883  23 deageeaeelRerleerlerarerlrdae 51 
                                        +++ e  + +Rer++ +l++ + +l+ ++
  gene1859|gene1859|rna1858|rna1858 200 KHSLERSKLIRERIKRNLDKIKTTLNSTR 228
                                        677888999**************999876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.019
                             DUF883   4 eaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaa 62 
                                        e+el ++ + + +l+++ ++e+  + ee++  + ++le + ++l+d ++ v e  ++  
  gene1859|gene1859|rna1858|rna1858 485 EDELSAVKEIAMDLFDTPQSETVGQEEEVKHSVLSKLEFVSKKLNDYKNGVIEDLEKHK 543
                                        6889999999999*********************************9999888776655 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0085
                             DUF883  29 aeelRerleerlerarerlrdaeeavaerakeaaea 64 
                                        + e++  ++++le+a+ ++++ +++++e++ke  ++
  gene1859|gene1859|rna1858|rna1858 593 ITEIKCDIQKYLEKAKIEVEEKRKEAEEKSKEKEKK 628
                                        678999999*************99999999997765 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3   0.00076       3.4      18      73 ..     219     272 ..     205     277 .. 0.78
   2 ?    3.5   0.2     0.013        60      41      77 ..     522     557 ..     502     558 .. 0.78
   3 ?   -2.5   0.1      0.94   4.2e+03      50      71 ..     595     616 ..     573     622 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00076
                                        TCSEEEEESSSSSECECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT CS
                               DSPc  18 gitlvinvtkevpnanalkkseieklripvedehetkiskyleeavefidkakqkg 73 
                                        +i+ ++n t++++ + +  +++  ++++  +de+++ ++ y++e+++f+d+++++ 
  gene1859|gene1859|rna1858|rna1858 219 KIKTTLNSTRNCNIQLF-ITENPLEISV-TQDEYKKAVEVYINELNSFVDSVMEET 272
                                        79999****99997533.3444555555.45569*****************98875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.013
                                        EEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEE CS
                               DSPc  41 eklripvedehetkiskyleeavefidkakqkgkkvl 77 
                                        e+++ +++d +++ + ++le+ +++i+++++++ kv+
  gene1859|gene1859|rna1858|rna1858 522 EFVSKKLND-YKNGVIEDLEKHKDMINEFRKEHSKVF 557
                                        444444566.89999******************9995 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.94
                                        STTSCCGGGHHHHHHHHHHHHH CS
                               DSPc  50 ehetkiskyleeavefidkakq 71 
                                        e + +i+kyle+a+  +++ ++
  gene1859|gene1859|rna1858|rna1858 595 EIKCDIQKYLEKAKIEVEEKRK 616
                                        5566788999998888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2299  (0.128228); expected 358.6 (0.02)
Passed bias filter:                      860  (0.047967); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.89u 0.38s 00:00:01.27 Elapsed: 00:00:00.54
# Mc/sec: 3650.34
//
Query:       gene1860|gene1860|rna1859|rna1859  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.025   15.2   0.0      0.035   14.7   0.0    1.2  1  EB1_binding  EB-1 Binding Domain


Domain annotation for each model (and alignments):
>> EB1_binding  EB-1 Binding Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.9e-06     0.035      80     120 ..      63     104 ..      39     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-06
                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                        EB1_binding  80 petnentvsertpfsssssskhsspsGavaa.rvtpfnynps 120
                                         e+  +  ser  +ss +ssk +sp+Ga+ + r+  f  np 
  gene1860|gene1860|rna1859|rna1859  63 AEAIGDGKSERLDLSSLASSKADSPAGAIKSlRIGKFKINPE 104
                                        566666779*******************96449*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1538.89
//
Query:       gene186|gene186|rna186|rna186  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-19   68.8   1.1    7.5e-19   67.8   0.1    1.9  2  Ribosomal_L5    Ribosomal protein L5
    5.6e-19   68.1   0.0    1.5e-18   66.7   0.0    1.7  2  Ribosomal_L5_C  ribosomal L5P family C-terminus


Domain annotation for each model (and alignments):
>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.1   8.3e-23   7.5e-19       1      57 []       7      60 ..       7      60 .. 0.99
   2 ?   -1.0   0.1      0.26   2.3e+03       9      20 ..      63      74 ..      62      88 .. 0.67

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 8.3e-23
                                   SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                   Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                   N+M+++r++K+ i+++  e+g +   l++aak+L+++tGQkPv +ka+ +i+nF+iR
  gene186|gene186|rna186|rna186  7 NPMREIRIKKLSIHICARESGPK---LDRAAKVLEQLTGQKPVTSKARMTIRNFGIR 60
                                   9**********************...******************************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.26
                                   EEEEEEEE-SSS CS
                   Ribosomal_L5  9 eKivinmgvGea 20
                                   eKi +++ v   
  gene186|gene186|rna186|rna186 63 EKIAVHVNVSGK 74
                                   799999988633 PP

>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.29   2.6e+03      64      89 ..      12      39 ..       4      59 .. 0.62
   2 !   66.7   0.0   1.7e-22   1.5e-18       1      83 [.      64     142 ..      64     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.29
                 Ribosomal_L5_C 64 kgifGmditivttak...tdeearallke 89
                                   ++i+ ++i+i+ +++    d+ a+ +l++
  gene186|gene186|rna186|rna186 12 IRIKKLSIHICARESgpkLDRAAK-VLEQ 39
                                   556666677766666553344333.4444 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 1.7e-22
                 Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak.. 78 
                                    +i+v+v++ g+k+ye+l+++l v++++l+      +  f+++G ++fGi+e+i++ +++yd+ +gifGmd+++v++++  
  gene186|gene186|rna186|rna186  64 KIAVHVNVSGKKAYELLNTALRVKEYELK------EGCFSNNGCFGFGIEEHIDL-GLKYDPAIGIFGMDFFVVLSRPgd 136
                                    69***************************......9*******************.**********************54 PP

                 Ribosomal_L5_C  79 .tdeea 83 
                                     +++++
  gene186|gene186|rna186|rna186 137 rVSKRK 142
                                    433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 1002.86
//
Query:       gene1861|gene1861|rna1860|rna1860  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.50
# Mc/sec: 636.17
//
Query:       gene1862|gene1862|rna1861|rna1861  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.6e-07   29.2   0.7    1.4e-06   28.1   0.6    1.6  1  Sec20       Sec20
     0.0041   15.1   1.5      0.005   14.8   1.5    1.2  1  V_ATPase_I  V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
        3.4    7.6   8.1        7.5    6.5   4.3    2.9  2  TRIQK       Triple QxxK/R motif-containing protein family
        6.7    6.8   9.9       0.61   10.2   1.3    2.7  2  TssO        Type VI secretion system, TssO


Domain annotation for each model (and alignments):
>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.6   3.1e-10   1.4e-06       9      89 ..      78     158 ..      70     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.1e-10
                              Sec20   9 slraisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkklerrdktdkllvflalglflacv 84 
                                        +l +  +l+  ++ + + n + l +st +l  l+    ++e+vl  +++ +k  +r+++t+ +lv+ al  f++++
  gene1862|gene1862|rna1861|rna1861  78 ELENTVKLVHRQIGKADTNQQILGKSTLKLMGLNYTSNDIEKVLVDTRRKIKESQRQERTEGFLVLAALLVFMLVC 153
                                        56777789999*************************************************************9999 PP

                              Sec20  85 vyvvk 89 
                                        + +++
  gene1862|gene1862|rna1861|rna1861 154 ILILF 158
                                        99886 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.5   1.1e-06     0.005      32     130 ..      17     135 ..       6     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-06
                         V_ATPase_I  32 cdemerklrfleeeieklekavikeeea....................eesleapeekeldeleeelekleeelke 87 
                                         +++ r+ +f+++ i+++ek+  ++ e+                    e++ +++ +++ldele++++ +++++ +
  gene1862|gene1862|rna1861|rna1861  17 QEDLRRHASFVQTMIRDYEKNLYEKGEYddssksrvkdwrdrlykitqEHKDTSEGAENLDELENTVKLVHRQIGK 92 
                                        57888999999999999888888877778899999999999999998777888889999***************** PP

                         V_ATPase_I  88 lnenleklkkelnelvelkavlekakefleeeeeeeeeeesee 130
                                         ++n++ l k++ +l+ l++  + ++++l +++++ +e++++e
  gene1862|gene1862|rna1861|rna1861  93 ADTNQQILGKSTLKLMGLNYTSNDIEKVLVDTRRKIKESQRQE 135
                                        ***************************9987744333333332 PP

>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.069   3.1e+02       4      37 ..      22      57 ..      19      80 .. 0.76
   2 ?    6.5   4.3    0.0017       7.5      31      73 ..     120     161 ..      64     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.069
                              TRIQK  4 kdasaaklpvdqYRKqiGk.Qdyk.knKdvlkatkl 37
                                       + as +++ +  Y K++ +  +y    K+ +k+ ++
  gene1862|gene1862|rna1861|rna1861 22 RHASFVQTMIRDYEKNLYEkGEYDdSSKSRVKDWRD 57
                                       678888999999999986546665246777777765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0017
                              TRIQK  31 vlkatklkAeakksasg.ikevllvlvailvlllalYalfflnl 73 
                                        vl +t+ k   k s      e +lvl+a+lv++l++ +++f ++
  gene1862|gene1862|rna1861|rna1861 120 VLVDTRRKI--KESQRQeRTEGFLVLAALLVFMLVCILILFDKF 161
                                        555565553..4333320347899************99999777 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.8   0.00082       3.7      81     121 ..     111     151 ..      44     152 .. 0.80
   2 ?   10.2   1.3   0.00014      0.61       3      33 ..     133     162 ..     131     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00082
                               TssO  81 vfleneIkkdlndikntygknssdeRykmyaqiakfykmll 121
                                         +  n+I+k l+d + ++++ + +eR + + ++a ++ ++l
  gene1862|gene1862|rna1861|rna1861 111 NYTSNDIEKVLVDTRRKIKESQRQERTEGFLVLAALLVFML 151
                                        5889******************************9998776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00014
                               TssO   3 kkErrsgflyflllFlvtvlllflivffffk 33 
                                        ++Er++gfl + +l++++++++  i+f +f 
  gene1862|gene1862|rna1861|rna1861 133 RQERTEGFLVLAALLVFMLVCIL-ILFDKFV 162
                                        689******99999999887777.8886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1887  (0.105248); expected 358.6 (0.02)
Passed bias filter:                      986  (0.0549947); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1104.64
//
Query:       gene1863|gene1863|rna1862|rna1862  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.2e-19   67.9  16.8    1.1e-17   64.1  16.8    2.4  1  MFS_1_like  MFS_1 like family
    7.3e-09   35.0  18.7    7.3e-09   35.0  18.7    2.2  2  MFS_1       Major Facilitator Superfamily
     0.0049   15.5  21.3     0.0063   15.1   2.8    4.2  4  MFS_2       MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1  16.8   1.8e-21   1.1e-17      44     376 ..      56     398 ..      12     403 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 1.8e-21
                         MFS_1_like  44 pltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwilfll.v 118
                                          t ++   ++g++ D+fg+    ++ +lll ++l+  l+ + p                      +f  +f++ +
  gene1863|gene1863|rna1862|rna1862  56 LGTIFFTNIFIGTMNDKFGRSHLFIVGALLLTCALLQ-LFYVEP-------------------YVGIFPGMFWInL 111
                                        44668888899*******9887766666666655555.664442...................4566777776624 PP

                         MFS_1_like 119 vlasfflaailvlldaatlkel....gedrkdyGrqrlfGsvGyaifafitGilidhysvnllp...ysallyvla 187
                                        +l+ +f ++i +lld a+l  l    +  ++ yG+q+l+G+ Gy+++  ++   i +      +   y    +v +
  gene1863|gene1863|rna1862|rna1862 112 LLYMAFNNGIPPLLDKAVLDYLngipEAGARAYGKQKLWGTAGYGLSCKVIEKCIKFGDEFKFGnlrY--YSLVTT 185
                                        5788999***************9998888999*******************99997765533334333..222222 PP

                         MFS_1_like 188 allvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienF................ 247
                                        al  i ++++l+ + te  ++   + +  + +++++n ++++f+l++l+ g++  ++  +                
  gene1863|gene1863|rna1862|rna1862 186 ALSSILVFSLLKSPATEGRTAR--RDIMANCKELMRNGSYLFFILMILLNGITRQALSIYhtvyltdvlqikgydl 259
                                        2222222222334444444443..34457889******************************************** PP

                         MFS_1_like 248 ......lflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii.....en 312
                                                 YL    + ++ + ++++ g+v e+++++    + +++G+v+  +ia l+ i+r   y ++     ++
  gene1863|gene1863|rna1862|rna1862 260 psswpyWLQYL-VEFFNESPVATTTFCGMVFEVVMLYNFPAISKRIGLVWPFFIAQLFQIFRVGCYFLLdyndpNV 334
                                        ***99756677.334566677889999***********************************99999999888788 PP

                         MFS_1_like 313 awlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdl 376
                                        +  + +ie+  g+ fgll  +av+ + ++ p++l++t q +++g++  lG+   +l+ G l+ +
  gene1863|gene1863|rna1862|rna1862 335 FLYCCLIELTRGMYFGLLQPSAVQLAMNLCPPHLKSTSQMIYHGTFTALGSLATTLVFGNLFSE 398
                                        88999**********************************************9999999988854 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0  18.7   1.2e-12   7.3e-09      44     350 ..      58     386 ..      17     389 .. 0.82
   2 ?   -4.1   0.1      0.93   5.6e+03      67     231 ..     420     433 ..     414     446 .. 0.44

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.2e-12
                              MFS_1  44 gaavaslplGrlsdrfGrrrvlllglllfalglllllfa....sslw.lllvlrvlqGlgagalfpagaaliadwf 114
                                        + +++++++G + d+fGr  ++++g+ll+  +ll l+++      ++ ++++  +l  ++  ++ p+   ++ d+ 
  gene1863|gene1863|rna1862|rna1862  58 TIFFTNIFIGTMNDKFGRSHLFIVGALLLTCALLQLFYVepyvGIFPgMFWINLLLYMAFNNGIPPLLDKAVLDYL 133
                                        347889999***********999999999999666665544423388899999999999***************** PP

                              MFS_1 115 pk..eergraigllsagfslGailgpllggllasslg....Wravfyilaivsllafvlfllllpeepperkrksp 184
                                        ++  e  +ra+g   +   +G+ l   +   ++  +g    +  + y   + ++l+ +l  ++ + + p+ +  + 
  gene1863|gene1863|rna1862|rna1862 134 NGipEAGARAYGKQKLWGTAGYGLSCKVIEKCI-KFGdefkFGNLRYYSLVTTALSSIL--VFSLLKSPATEGRTA 206
                                        *99788999****************99999888.4555888777777777777777777..666667777777777 PP

                              MFS_1 185 keeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls................... 241
                                        +++      a++++   ++++  +l ++++++ll+++  ++l+++ ++yl +vl ++                   
  gene1863|gene1863|rna1862|rna1862 207 RRD----IMANCKE---LMRNGSYL-FFILMILLNGITRQALSIYHTVYLTDVLQIKgydlpsswpywlqylveff 274
                                        777....6666666...55555555.5**********************99999999999**************** PP

                              MFS_1 242 ...glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl...iG 311
                                            + +++     ++++ +++   + ++s+r+g  ++ ++a l+ ++ + +++ll   + +v+l++ +++    G
  gene1863|gene1863|rna1862|rna1862 275 nesPVATTT---FCGMVFEVVMLYNFPAISKRIGLVWPFFIAQLFQIFRVGCYFLLDYNDPNVFLYC-CLIeltRG 346
                                        765544444...4455555555999**********************************66666666.444566** PP

                              MFS_1 312 fglgfvfpsllalasdlappeeagtasglfn.tagslgga 350
                                        + +g+ +ps+  la++l+pp+   t + ++  t+ +lg++
  gene1863|gene1863|rna1862|rna1862 347 MYFGLLQPSAVQLAMNLCPPHLKSTSQMIYHgTFTALGSL 386
                                        ***************************9999666667665 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.93
                              MFS_1  67 lglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg 142
                                        +                                                                           
  gene1863|gene1863|rna1862|rna1862 420 FVN------------------------------------------------------------------------- 422
                                        222......................................................................... PP

                              MFS_1 143 llasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialll 218
                                                                                                                    
  gene1863|gene1863|rna1862|rna1862   - ----------------------------------------------------------------------------   -
                                        ............................................................................ PP

                              MFS_1 219 fffgfsglltllp 231
                                          ++f++++t l+
  gene1863|gene1863|rna1862|rna1862 423 --ICFASVTTGLF 433
                                        ..22222222222 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   1.9     0.001       6.2     268     332 ..      54     117 ..      17     137 .. 0.74
   2 !    5.2   0.2    0.0011       6.6       3      31 ..     227     255 ..     225     257 .. 0.86
   3 !   15.1   2.8     1e-06    0.0063     248     333 ..     264     350 ..     261     358 .. 0.82
   4 ?   -0.5   0.0      0.06   3.6e+02     136     189 ..     374     436 ..     354     460 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.001
                              MFS_2 268 vtisal.lgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaa 332
                                        ++++++  + +++  ++ ++g+ +++++gall+   l+ ++ +  + ++  +  ++ +++ +++a+
  gene1863|gene1863|rna1862|rna1862  54 PMLGTIfFTNIFIGTMNDKFGRSHLFIVGALLLTCALLQLFYV--EPYVGIFPGMFWINLLLYMAF 117
                                        4666663455788889999999999999999888888877777..556666666666666655544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0011
                              MFS_2   3 glgalaanilsvllatylliFytdvlgls 31 
                                        +l  l  +i+  +l++y ++++tdvl+++
  gene1863|gene1863|rna1862|rna1862 227 ILMILLNGITRQALSIYHTVYLTDVLQIK 255
                                        56667889999***************996 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1e-06
                              MFS_2 248 lYyltyvlg..ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvll 321
                                         Y l+y ++  n+s +++ +++ ++  ++++  ++++ kr+g    +++++l++i+   + +ll+ ++  +fl ++
  gene1863|gene1863|rna1862|rna1862 264 PYWLQYLVEffNESPVATTTFCGMVFEVVMLYNFPAISKRIGLVWPFFIAQLFQIFRVGCYFLLDYNDPNVFLYCC 339
                                        69999999998889999999999*****************************************555555555555 PP

                              MFS_2 322 viagfgvgvaal 333
                                        +i  ++ g+ + 
  gene1863|gene1863|rna1862|rna1862 340 LI-ELTRGMYFG 350
                                        55.555555443 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.06
                              MFS_2 136 tsvrsflsvlggvlaailafllvlilgg.........lkserkgylifaliialLmllgviiv 189
                                        + +  ++++lg+++++++ + l+   ++          + + k ++ + + +a ++++++++ 
  gene1863|gene1863|rna1862|rna1862 374 MIYHGTFTALGSLATTLVFGNLFSEDKMkgkdipiedRAANYKMFFFVNICFASVTTGLFVYK 436
                                        556667777888888888777777777777777755444444444455555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2991.65
//
Query:       gene1864|gene1864|rna1863|rna1863  [L=478]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-28   97.3  20.3    1.4e-26   93.3  20.3    2.2  1  MFS_1_like     MFS_1 like family
    1.2e-13   50.8  22.9    5.4e-09   35.4   6.0    2.6  2  MFS_1          Major Facilitator Superfamily
    9.2e-09   34.8  17.3    1.3e-08   34.3  17.3    1.2  1  Nuc_H_symport  Nucleoside H+ symporter


Domain annotation for each model (and alignments):
>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3  20.3   2.3e-30   1.4e-26      41     366 ..      52     390 ..      50     403 .. 0.81

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 2.3e-30
                         MFS_1_like  41 lilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwilfl 116
                                         +l +++++   ++++l Dr+g+   +++  l ls+++f  l+ +          k+          + ++ ++ +
  gene1864|gene1864|rna1863|rna1863  52 GVLLFITFFTNIFIATLNDRLGRPRILMVYLLSLSCIFFQ-LFYVK---------KY---------VKSIYLMFWI 108
                                        5899***********************************9.55333.........11.........3445555555 PP

                         MFS_1_like 117 lvvlasfflaailvlldaatlkel....gedrkdyGrqrlfGsvGyaifafitGilidh.ysvnllpysallyv.l 186
                                         ++ +     +i++lld ++l  l        + yG+qr++G++Gy ++ fi+  +i   + +n +++  l y  l
  gene1864|gene1864|rna1863|rna1863 109 NLFGYLGTNTPIMALLDKIILDYLaespDVGVRAYGKQRIWGTIGYLLSIFIIERIIRGgMGTNAIDFTNLKYYsL 184
                                        55666667889*************5543334567*******************99886425556666434444404 PP

                         MFS_1_like 187 aallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienF............... 247
                                        a+ +++++lv++ l++   e k+   ++ ++ +++++n+e+++f++++l+ g++ +++  +               
  gene1864|gene1864|rna1863|rna1863 185 AITIICVCLVMAFLKDSGSECKDLSLNTASEWKELMRNREYLFFIFIILLNGFTRSAMTIYlpiytnyvlnvkpya 260
                                        444444444444444445555555556669999******************************************* PP

                         MFS_1_like 248 ........lflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii..... 310
                                                +   L  l+ s    +++++++  +e+ ++f+   + +k+G+   l++a ++ ++rf+ly ++     
  gene1864|gene1864|rna1863|rna1863 261 lptswptwIRNGLRILNDS--PFSTITVFEISLEMGILFYFDAISRKIGLLLPLLLAQVSQVIRFSLYLVLphtnp 334
                                        **99766655555445544..56889999*******************************************9888 PP

                         MFS_1_like 311 enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralG 366
                                        +++ ++ ++evL+gi fgl ++++v+ ++k+ p++l++t q +++g+++ +G+   
  gene1864|gene1864|rna1863|rna1863 335 HVFAFCCLFEVLKGINFGLSHGSGVQLAEKMCPPHLKTTSQMIYNGTFMAVGSVTA 390
                                        88899**********************************************98765 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   7.2   8.1e-09   4.8e-05     212     329 ..      17     128 ..       3     158 .. 0.80
   2 !   35.4   6.0     9e-13   5.4e-09     150     351 ..     176     389 ..     142     391 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.1e-09
                              MFS_1 212 llialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalllllla 287
                                        +l++++++   +++l  +  l+++e +g++   l+g  +++l +++++  ++++ l drlgr r+l++ ll+l+++
  gene1864|gene1864|rna1863|rna1863  17 ILYVAISM--QYYTLHKFRSLFAKEMFGIGEKELSG--VGVLLFITFFTNIFIATLNDRLGRPRILMVYLLSLSCI 88 
                                        66666666..88889999999*********559999..9***********************66666666666666 PP

                              MFS_1 288 alglallavtssavllllvlvliGf.glgfvfpsllalasdla 329
                                        ++ l+++  +   v ++++++ i + g+  ++++++al+++ +
  gene1864|gene1864|rna1863|rna1863  89 FFQLFYVKKY---VKSIYLMFWINLfGYLGTNTPIMALLDKII 128
                                        6666666666...9999999999999************99876 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 9e-13
                              MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                                        ++ + y   +++++++ l++++l ++ +e k  s  +          ++ wk+l +++  +++++++ll++f  s+
  gene1864|gene1864|rna1863|rna1863 176 FTNLKYYSLAITIICVCLVMAFLKDSGSECKDLSLNTA---------SE-WKELMRNREYLFFIFIILLNGFTRSA 241
                                        44554555556666544555666666666666655555.........67.9999999988889999999999**** PP

                              MFS_1 226 lltllplylqevlgls.....................glllaglllallalvgailallagrlsdrlgrrrrllla 280
                                        ++++lp+y++ vl+ +                     + +++ +++ ++  +g+ +   + ++s+++g   +llla
  gene1864|gene1864|rna1863|rna1863 242 MTIYLPIYTNYVLNVKpyalptswptwirnglrilndSPFSTITVFEISLEMGILF--YFDAISRKIGLLLPLLLA 315
                                        ***********************************995588888888888888777..****************** PP

                              MFS_1 281 llllllaalglallavtssavllllvlvl...iGfglgfvfpsllalasdlappeeagtasglfn.tagslggal 351
                                         ++ ++ + ++++l++t +++++++ +++    G+ +g+  +s   la +++pp+   t + ++n t+ ++g++ 
  gene1864|gene1864|rna1863|rna1863 316 QVSQVIRFSLYLVLPHT-NPHVFAFCCLFevlKGINFGLSHGSGVQLAEKMCPPHLKTTSQMIYNgTFMAVGSVT 389
                                        *****************.8888888777778688899999*************************7777777765 PP

>> Nuc_H_symport  Nucleoside H+ symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3  17.3   2.1e-12   1.3e-08      52     364 ..      60     400 ..      25     441 .. 0.73

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.1e-12
                      Nuc_H_symport  52 lspilvgiiaDkflsaervlavlhligavv...l.flaaqvtefealflvlLvysl.aymPtlaltnsiafanlr. 121
                                        ++ i++ ++ D+     r+l+v  l  + +   l ++   v     +f++ L   l +  P +al + i    l+ 
  gene1864|gene1864|rna1863|rna1863  60 FTNIFIATLNDRLG-RPRILMVYLLSLSCIffqLfYVKKYVKSIYLMFWINLFGYLgTNTPIMALLDKIILDYLAe 134
                                        55666777777754.45666666555444401130334445566667777666444366799*******9999988 PP

                      Nuc_H_symport 122 ..Dv.vtdfprirvlGtvGfilasla...flllvvsladlelsrlqlliaagvslllavyaltLPkiPakkkakqs 191
                                          Dv v+++++ r++Gt+G++l+ +    ++   ++   ++ ++l+++  a++ + + +   +L +  ++ k + s
  gene1864|gene1864|rna1863|rna1863 135 spDVgVRAYGKQRIWGTIGYLLSIFIierIIRGGMGTNAIDFTNLKYYSLAITIICVCLVMAFLKDSGSECK-DLS 209
                                        8877689****************66533233334678899********999998888888888988884444.444 PP

                      Nuc_H_symport 192 lkkllgldafvLlknkrllvfflvslllavvlqiyyvfa...nafLtevak................ivvklasil 248
                                        l++    +   L++n++ l f ++ ll + +   + ++      ++ +v+                 i+ + +   
  gene1864|gene1864|rna1863|rna1863 210 LNTA--SEWKELMRNREYLFFIFIILLNGFTRSAMTIYLpiyTNYVLNVKPyalptswptwirnglrILNDSPFST 283
                                        4443..44446899998888878888888776665555400044555555499************99999999999 PP

                      Nuc_H_symport 249 lslsqva.eilfiLtlpfflkrfGikkvlllslvaaalrfalfaygaddepvgvvlllLslivyGvaydffyitay 323
                                        +++  ++ e+ +++ +  + ++ G+   lll+ v++++rf+l+      +p +++   L  ++ G+ +   + ++ 
  gene1864|gene1864|rna1863|rna1863 284 ITVFEISlEMGILFYFDAISRKIGLLLPLLLAQVSQVIRFSLYLVLPHTNPHVFAFCCLFEVLKGINFGLSHGSGV 359
                                        999999978888889999***************************9999999999999999*************** PP

                      Nuc_H_symport 324 vfvdkevpkdirasaqGlflllvnGvGallgsilsgalvem 364
                                           +k  p+++++++q +++     vG++ +s+ +  +   
  gene1864|gene1864|rna1863|rna1863 360 QLAEKMCPPHLKTTSQMIYNGTFMAVGSVTASLYFRYVFRN 400
                                        *******************************9988765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2745.23
//
Query:       gene1865|gene1865|rna1864|rna1864  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1381.32
//
Query:       gene1866|gene1866|rna1865|rna1865  [L=1000]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-06   26.8   0.1       0.39   11.1   0.0    5.1  4  HEAT_2         HEAT repeats
    0.00021   21.3   0.1          4    8.0   0.0    5.8  6  HEAT           HEAT repeat
  ------ inclusion threshold ------
      0.055   13.5   7.0        2.8    8.0   0.0    4.5  4  Cnd1           non-SMC mitotic condensation complex subunit 1
      0.056   13.1   0.1      0.056   13.1   0.1    3.3  4  TFA2_Winged_2  TFA2 Winged helix domain 2


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   8.7e-05      0.39       3      37 ..      10      49 ..       8     159 .. 0.84
   2 ?    1.8   0.0     0.071   3.2e+02       8      28 ..     222     241 ..     216     291 .. 0.75
   3 !    5.6   0.0    0.0047        21       7      58 ..     320     372 ..     316     390 .. 0.83
   4 ?   -2.8   0.0         2     9e+03      31      59 ..     750     778 ..     738     786 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-05
                             HEAT_2  3 aLlqalendpdpevrraairaLg......rignpealpaLv 37
                                        L+++l n+++++ r++a   Lg      r+ +pe+++ L 
  gene1866|gene1866|rna1865|rna1865 10 ELIERL-NSKNWKDRQEAYSILGslwsegRMPDPEVVEKLQ 49
                                       699***.****************999988888888877765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.071
                             HEAT_2   8 lendpdpevrraairaLgrig 28 
                                        + +d ++++r +a r++ r +
  gene1866|gene1866|rna1865|rna1865 222 A-SDDNWKIRLEAMRNIKRVA 241
                                        3.5666777777776666544 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0047
                             HEAT_2   7 alendpdpevrraai.raLgri.gnpealpaLvellededpavRraaaeaLgai 58 
                                        +l  +++p+vr + +  +L ++ +++e ++++ +++ d+  +vR  a++ + +i
  gene1866|gene1866|rna1865|rna1865 320 FL-GHKNPQVRLNLLdYSLRDLqNDKEFIKMIGNCILDPVGDVRNKAIDVATEI 372
                                        56.789999999999889997525679999999999999999999999988877 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2
                             HEAT_2  31 ealpaLvellededpavRraaaeaLgaig 59 
                                        + l+++++ l d++p v + a + L+ i 
  gene1866|gene1866|rna1865|rna1865 750 SGLELILDHLIDSNPGVSEVAFKRLVNII 778
                                        55888999999999999999988887764 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.21   9.4e+02       5      28 ..      11      34 ..       9      36 .. 0.84
   2 ?   -1.2   0.0      0.77   3.5e+03       2      28 ..     107     130 ..     106     134 .. 0.66
   3 !    8.0   0.0   0.00089         4       5      29 ..     218     242 ..     214     244 .. 0.86
   4 ?   -0.5   0.0      0.47   2.1e+03       9      19 ..     321     331 ..     319     334 .. 0.84
   5 ?   -2.9   0.0       2.7   1.2e+04       9      22 ..     354     367 ..     349     374 .. 0.77
   6 ?    3.3   0.0     0.028   1.2e+02       2      28 ..     752     778 ..     752     780 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.21
                                       HHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT  5 llkllsDpspeVReaAakaLgala 28
                                       l++ l++++++ R+ A   Lg l 
  gene1866|gene1866|rna1865|rna1865 11 LIERLNSKNWKDRQEAYSILGSLW 34
                                       78899*****98988888888875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.77
                                        HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   2 lPlllkllsDpspeVReaAakaLgala 28 
                                        l +l +ll ++sp+   ++a aL a++
  gene1866|gene1866|rna1865|rna1865 107 LEVLSELLGSKSPK---NVAGALSAIC 130
                                        66777778888877...5666666665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00089
                                        HHHHHT-SSHHHHHHHHHHHHHHHH CS
                               HEAT   5 llkllsDpspeVReaAakaLgalae 29 
                                        +l+  sD+++++R  A +++ ++a+
  gene1866|gene1866|rna1865|rna1865 218 FLRGASDDNWKIRLEAMRNIKRVAR 242
                                        78889*************9999876 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.47
                                        HT-SSHHHHHH CS
                               HEAT   9 lsDpspeVRea 19 
                                        l +++p+VR +
  gene1866|gene1866|rna1865|rna1865 321 LGHKNPQVRLN 331
                                        789******87 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 2.7
                                        HT-SSHHHHHHHHH CS
                               HEAT   9 lsDpspeVReaAak 22 
                                        + Dp  +VR  A+ 
  gene1866|gene1866|rna1865|rna1865 354 ILDPVGDVRNKAID 367
                                        479999***99975 PP

  == domain 6  score: 3.3 bits;  conditional E-value: 0.028
                                        HHHHHHHHT-SSHHHHHHHHHHHHHHH CS
                               HEAT   2 lPlllkllsDpspeVReaAakaLgala 28 
                                        l l+l  l D++p V e A+k L++++
  gene1866|gene1866|rna1865|rna1865 752 LELILDHLIDSNPGVSEVAFKRLVNII 778
                                        67899****************999997 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2     0.046   2.1e+02       2      65 ..     229     293 ..     228     314 .. 0.79
   2 ?    8.0   0.0   0.00062       2.8      50      94 ..     337     381 ..     323     411 .. 0.80
   3 ?   -2.4   0.0      0.96   4.3e+03      45      63 ..     564     582 ..     560     584 .. 0.83
   4 ?    3.6   0.1     0.013        60      60     106 ..     752     798 ..     739     825 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.046
                               Cnd1   2 iRalairtlg.cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselak 65 
                                        iR  a+r +  + r  +   +l   L++r+ D + +V   ++ v+ +L  + m ++kg++++l++
  gene1866|gene1866|rna1865|rna1865 229 IRLEAMRNIKrVARTLEYNNELNVLLCRRIGDVNNQVFYVTLEVIDELRPKSMEIVKGLIERLKE 293
                                        55566666666666666667777789999999999999999999999999999999999999876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00062
                               Cnd1  50 lndmvkekgflselaklleDenprVvanalaalteiseksenaiy 94 
                                        l+d+  +k+f++++ +++ D+   V++ a+ + tei ++ +n + 
  gene1866|gene1866|rna1865|rna1865 337 LRDLQNDKEFIKMIGNCILDPVGDVRNKAIDVATEIYKRHGNVFD 381
                                        6788999********************************876543 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.96
                               Cnd1  45 vakLilndmvkekgflsel 63 
                                        v  L++ndmv+e g+++++
  gene1866|gene1866|rna1865|rna1865 564 VEYLLSNDMVEELGMMDRV 582
                                        66789*******9998875 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.013
                               Cnd1  60 lselaklleDenprVvanalaalteiseksenaiynllpdiisklsd 106
                                        l+ +++ l D+np V++ a   l +i + + + +++   +i+s++s 
  gene1866|gene1866|rna1865|rna1865 752 LELILDHLIDSNPGVSEVAFKRLVNIIDSEIESLLSFSNSIVSSISI 798
                                        67788999*********************889999999999998875 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2       1.7   7.8e+03      35      45 ..      97     107 ..      94     111 .. 0.85
   2 ?   -1.9   0.1       0.6   2.7e+03      18      37 ..     186     205 ..     172     210 .. 0.82
   3 ?   -2.9   0.0       1.3   5.9e+03      30      49 ..     448     467 ..     447     479 .. 0.75
   4 ?   13.1   0.1   1.3e-05     0.056       1      40 [.     599     652 ..     599     674 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                      TFA2_Winged_2  35 leeLeaegeil 45 
                                        +e Le++ e+l
  gene1866|gene1866|rna1865|rna1865  97 IERLEDTEEVL 107
                                        89999999997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.6
                      TFA2_Winged_2  18 GikvkdLkdswpdveealee 37 
                                         i+ k+L++   ++++ +ee
  gene1866|gene1866|rna1865|rna1865 186 PIQQKELMEEFEKCSPVVEE 205
                                        58889****99999999997 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                      TFA2_Winged_2  30 dveealeeLeaegeilvlrt 49 
                                        d+++++e+ ++e +i   r+
  gene1866|gene1866|rna1865|rna1865 448 DCSKDVEQRAKEDDIGSKRK 467
                                        89999999999988866555 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 1.3e-05
                      TFA2_Winged_2   1 rnkeeLlalLkkrp..............kaeGikvkdLkdswpdveealeeLea 40 
                                        ++++e+l+l+kk++              k + ++v+++  ++pd   +++eLe+
  gene1866|gene1866|rna1865|rna1865 599 KSNDEILKLVKKYKmfrgdkkqfiegikKGGKVEVEEVIKGCPDFLSFVDELEG 652
                                        689*****************999999977889********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1000 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       963  (0.0537119); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.52
# Mc/sec: 5816.12
//
Query:       gene1867|gene1867|rna1866|rna1866  [L=310]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-07   30.3   0.0    8.5e-07   29.3   0.0    1.6  1  Brix      Brix domain


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   4.7e-11   8.5e-07       1     166 [.     117     260 ..     117     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.7e-11
                                        BTT--HHHHHHHHHHHHHCTTSEEEEEEECT...-TTTHHHHHHH...-HHHHHHHH..HCTCSEEEEEE..SSTT CS
                               Brix   1 grktssrlrqllkdlrslmkphtasflkrns...nklkdlvelag...vthlellse..kndcslfvfelskkrPn 68 
                                        +r++ss+l ++ k l  +++ ++     r++    ++ d   +a+   +t +++++e   +++sl ++ +    P 
  gene1867|gene1867|rna1866|rna1866 117 SRSPSSQLLHFSKQLSLVLNGENFI---RGQlceEEISD---VAHkhgYTCVVIVHEnrGRPASLAISYF----PF 182
                                        6889999************886655...55522235556...454557**********999*********....** PP

                                        EEEEEEEEE.CECTGGGSTTTSTS-TT---EEEEES.HHH.....HHHHHHHHHHH..SEEEG..-B-GG-SEEEE CS
                               Brix  69 gptlefkve.nyslmkdlkkakktefgsrPllvfngkenf.....kllksllqdlFrvpkislkspklsglrrvvl 138
                                        gpt+ f +  ++ +++ ++ +       +  ++ +   n+      ++k+ +  lF  pk        sg +r+v+
  gene1867|gene1867|rna1866|rna1866 183 GPTMRFTIIdHFLTRRTFPLS------PKVYFICD---NMegpvgIKVKERIALLF--PKC-------SGAKRIVS 240
                                        *******87589999999876......44568888...66666779**********..866.......8******* PP

                                        EEES.CCTTTECEEEEEEEEEEE..STT CS
                               Brix 139 ftaaenqetdktisfRhYaiklkksgkk 166
                                        +    n + d ti fRhY i+   +g k
  gene1867|gene1867|rna1866|rna1866 241 LV---NRN-D-TIAFRHYLIE---KGDK 260
                                        **...555.7.9********6...3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1816.17
//
Query:       gene1868|gene1868|rna1867|rna1867  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-38  132.5  11.7    2.1e-38  132.2  11.7    1.1  1  DER1      Der1-like family


Domain annotation for each model (and alignments):
>> DER1  Der1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.2  11.7   1.2e-42   2.1e-38       1     190 [.      13     198 ..      13     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 1.2e-42
                               DER1   1 iPavTRllltatvvltllgrlelispaklvlsyelvvkkvQiwRlltsllyfsstgfsflinlyfiyqysskLEeg 76 
                                        +P++TR+++++   ++ll+ ++ +sp  l++s+ l++kk+ iwR++ts+lyf+   ++++++++f+y+ys++LEeg
  gene1868|gene1868|rna1867|rna1867  13 VPPITRYMILLISTVALLVYIDAVSPYSLYYSP-LFLKKLEIWRVFTSFLYFGRPTLDMFMHVVFLYRYSRMLEEG 87 
                                        7*****************************985.9***************************************** PP

                               DER1  77 sfrgrsadyvylllflavlitllglladlvvLgqalilaivYvwskknkdvqvsFfgvlrvkakylPlvllafsfl 152
                                          +  +++y +l+++   ++ +++    +++Lg+++ ++i+Y+w+k+n++  v+ fg +++ a ylP++l +f++l
  gene1868|gene1868|rna1867|rna1867  88 CVS--TSEYFWLIFVISSALFVISNIYGISALGTSFSSTITYIWTKRNPRAIVQIFGFISFPAFYLPFILPGFMLL 161
                                        655..5577777666554444444423589********************************************** PP

                               DER1 153 lge.svvvsligilvghiyyfledkypiklnGkdllktP 190
                                         +   ++ +++gi+vgh++ +++d+yp    G+d+l+tP
  gene1868|gene1868|rna1867|rna1867 162 SKRsISIDDVLGIVVGHLFHYFKDVYPR--WGRDILRTP 198
                                        **9555699*****************96..589999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2052.65
//
Query:       gene1869|gene1869|rna1868|rna1868  [L=573]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-16   59.5   0.6    5.8e-16   58.2   0.1    2.0  2  Spt5-NGN  Early transcription elongation factor of RNA pol II
    4.6e-09   35.9  14.4     0.0051   16.7   0.0    5.1  5  KOW       KOW motif
  ------ inclusion threshold ------
      0.055   14.0   1.5      0.094   13.3   1.5    1.3  1  CTD       Spt5 C-terminal nonapeptide repeat binding Spt4


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.63   3.8e+03      40      55 ..       3      18 ..       1      20 [. 0.76
   2 !   58.2   0.1   9.8e-20   5.8e-16       2      82 ..      84     157 ..      83     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.63
                           Spt5-NGN 40 pdelkGyiyvEAdrka 55
                                       +   + y+ +EA++++
  gene1869|gene1869|rna1868|rna1868  3 RRPTSKYVSIEASEED 18
                                       555678******9875 PP

  == domain 2  score: 58.2 bits;  conditional E-value: 9.8e-20
                           Spt5-NGN   2 iwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpi 77 
                                        +++v+++ g Ere+ +++       +++   +I+S+++ d+lkGy y+EA +k++v +al++++ v ++  + vp 
  gene1869|gene1869|rna1868|rna1868  84 LFIVRVKRGSEREILMKI-------IENDPKNIFSIICKDGLKGYLYIEAFQKQHVIDALDSLRGVSRNRVSVVPQ 152
                                        8*****************.......4444558******************************************** PP

                           Spt5-NGN  78 kEved 82 
                                        kE+ +
  gene1869|gene1869|rna1868|rna1868 153 KEMIE 157
                                        **976 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00037       2.2       2      29 ..     168     195 ..     167     197 .. 0.90
   2 !    7.9   3.2    0.0005         3       1      24 [.     268     291 ..     268     297 .. 0.90
   3 !    7.4   0.1   0.00073       4.4      12      26 ..     322     336 ..     321     353 .. 0.86
   4 !   16.7   0.0   8.5e-07    0.0051       3      29 ..     384     410 ..     382     415 .. 0.87
   5 ?   -2.9   0.0       1.3   7.6e+03       2      14 ..     526     538 ..     525     549 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00037
                                        TSEEEESSSTTTTCEEEEEEEETTTTEE CS
                                KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrV 29 
                                        G++ ++  G++k++  k+ + d++ vr+
  gene1869|gene1869|rna1868|rna1868 168 GEWGRIRKGKYKNDLVKIIEFDEEMVRI 195
                                        6777999*****************9987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0005
                                        TTSEEEESSSTTTTCEEEEEEEET CS
                                KOW   1 pGdhVkVvsGphkGktGkVvkvdq 24 
                                        +Gd V+V++G   G +G+V +++ 
  gene1869|gene1869|rna1868|rna1868 268 VGDKVRVTRGELIGIKGVVRSING 291
                                        7******************99986 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00073
                                        TTTCEEEEEEEETTT CS
                                KOW  12 hkGktGkVvkvdqhk 26 
                                        +kG+ G+Vvk d+  
  gene1869|gene1869|rna1868|rna1868 322 YKGENGVVVKADKRE 336
                                        9**********9875 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 8.5e-07
                                        SEEEESSSTTTTCEEEEEEEETTTTEE CS
                                KOW   3 dhVkVvsGphkGktGkVvkvdqhkvrV 29 
                                        ++V++ sG +kG  G+V++vd++  r+
  gene1869|gene1869|rna1868|rna1868 384 KEVQIQSGEYKGHSGVVKEVDRNMCRI 410
                                        689999***************987665 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 1.3
                                        TSEEEESSSTTTT CS
                                KOW   2 GdhVkVvsGphkG 14 
                                         d V V++G  kG
  gene1869|gene1869|rna1868|rna1868 526 NDLVCVLGGEKKG 538
                                        6889999999888 PP

>> CTD  Spt5 C-terminal nonapeptide repeat binding Spt4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.5   1.6e-05     0.094       3      55 ..     436     464 ..     431     486 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                                CTD   3 rTPawnsaggsrTPawgadgsrTpayggagsrtPawnagskTPahgaagsrTP 55 
                                        r P +++ +gsrTP +++ g +Tp y++                        P
  gene1869|gene1869|rna1868|rna1868 436 RPPRYTGLTGSRTPGYKTPGYKTPGYKT------------------------P 464
                                        4455555555555555554544444443........................3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3485.72
//
Query:       gene1870|gene1870|rna1869|rna1869  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-07   31.1   0.8    5.9e-07   29.8   0.8    1.7  1  Brix      Brix domain


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.8   3.3e-11   5.9e-07      72     192 ..      62     157 ..       9     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 3.3e-11
                                        EEEEEECECTGGGSTTTSTS-TT---EEEEES.HHH.....HHHHHHHHHHH..SEEEG..-B-GG-SEEEEEEES CS
                               Brix  72 lefkvenyslmkdlkkakktefgsrPllvfngkenf.....kllksllqdlFrvpkislkspklsglrrvvlftaa 142
                                        l +k+ +y++++ l+ +k +++ ++P l++n   nf      ++   l ++F  p         ++ r+v+ ft++
  gene1870|gene1870|rna1869|rna1869  62 LVLKIVQYKSRDYLRVSKPISKDHPPQLIVN---NFttdigMKIVDFLANMF--PFN-------QSSRQVANFTVQ 125
                                        56899**************************...99999999**********..733.......499*******55 PP

                                        .CCTTTECEEEEEEEEEEE..STTTTECT..T..EEEEEEESEEEEEEEE CS
                               Brix 143 enqetdktisfRhYaiklkksgkklpnlekekkerveLeEiGPrfdLklr 192
                                             d +i+fR Y+      g+k p           +e +GP+++L+l 
  gene1870|gene1870|rna1869|rna1869 126 G----D-FIYFRLYKYC---FGEKNP----------IMENVGPHLTLRLW 157
                                        4....6.9****99996...344545..........799********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 1074.75
//
Query:       gene187|gene187|rna187|rna187  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00059   19.7   0.0    0.00083   19.2   0.0    1.4  1  Leo1      Leo1-like protein


Domain annotation for each model (and alignments):
>> Leo1  Leo1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.6e-08   0.00083      58      91 ..      30      63 ..      17      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.6e-08
                           Leo1 58 teikeSNArivrWsDGSlsLqlGsevfdvtrkal 91
                                   +++  SN+++v+ +DGS  L+ Gs++f ++  ++
  gene187|gene187|rna187|rna187 30 HREGRSNTKLVKFKDGSWYLKNGSQMFPLKAVPS 63
                                   56678**********************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 550.02
//
Query:       gene1871|gene1871|rna1870|rna1870  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-56  191.7   2.9    1.6e-56  191.7   2.9    1.8  2  Septin    Septin
     0.0033   17.5   0.0     0.0092   16.1   0.0    1.8  1  MMR_HSR1  50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.74   10.3   4.3       0.36   11.3   0.8    2.2  2  DUF2533   Protein of unknown function (DUF2533)


Domain annotation for each model (and alignments):
>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7   2.9   2.6e-60   1.6e-56       1     271 [.      36     283 ..      36     290 .. 0.91
   2 ?   -3.5   0.3      0.84     5e+03     173     266 ..     323     329 ..     300     350 .. 0.50

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 2.6e-60
                                        XEEEEEEEEEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE---BSSSS CS
                             Septin   1 kgieftlmvvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGdav 76 
                                        kg+e++++ vG+ glG +tlin++f+  l++++          ++ +i+ ++++i e+++ l++ ++         
  gene1871|gene1871|rna1870|rna1870  36 KGFELNVLAVGRRGLGTSTLINSIFAAPLVDKK----------RSNTITVTRNEIVENDISLEISIVTY------- 94 
                                        79****************************996..........3345777888999999*******953....... PP

                                        SHHCCCHHHHHHHHHHHHHHHHHCTSS--SS-----EEEEEEEE-TTSSSS-HHHHHHHHHHTTTS-EEEEESSGG CS
                             Septin  77 dnskswepiveyideqfeeylreesklkRkkivDkRvHaclyfisPtghglkpldvelmkklsekvnliPviaKaD 152
                                          ++  +p+++yi+   +ey+++e+ l++  ++D+R+H+cly++   +  l + +++ m +ls+++nl+P+i KaD
  gene1871|gene1871|rna1870|rna1870  95 -HETDISPVIDYINAMNREYFDNEQGLYK-AFKDNRIHVCLYLLP--SDTLAEQEIKNMYELSQRCNLVPIIPKAD 166
                                        .345678*******************996.689*********995..5689************************* PP

                                        GS-HHHHHHHHHHHHHHHHHTT--------SSSS-SCCHHHHHHHHHHC-SEEB-SSSSEEEESSSEEEEEEETTE CS
                             Septin 153 tltkeElkefKkkireeleeeeikiyklpdeeededeeakelseklkeslPfaivgsneliekkgkkvrgRkypWG 228
                                        + + +El   K+++r+ l++++i+ + ++  e+  d + +e+  ++ e++Pfa+++s++++e+ g+ vrgRky WG
  gene1871|gene1871|rna1870|rna1870 167 MYMPDELIYAKETVRQILSKNNISFFIPYFNEN--DGDLTEEVADIVENIPFAVIASETMYEHGGEIVRGRKYTWG 240
                                        **************************9444444..468889*********************************** PP

                                        EEETT-TTT-SCCHHHHHHHHHCHHHHHHHHHHTHHHHHHHHH CS
                             Septin 229 vvevenekhsdFlkLrklllkthledLkevteellYetyRsek 271
                                         ++v+ e+++dF+ L++ll+ t+l +L  +t++l+Y++yR++ 
  gene1871|gene1871|rna1870|rna1870 241 FINVDLEENNDFKRLQRLLIYTNLDELVTKTDHLFYNNYRKKI 283
                                        ****************************************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.84
                                        TT--------SSSS-SCCHHHHHHHHHHC-SEEB-SSSSEEEESSSEEEEEEETTEEEETT-TTT-SCCHHHHHHH CS
                             Septin 173 eeikiyklpdeeededeeakelseklkeslPfaivgsneliekkgkkvrgRkypWGvvevenekhsdFlkLrklll 248
                                        e                                                                           
  gene1871|gene1871|rna1870|rna1870 323 E--------------------------------------------------------------------------- 323
                                        2........................................................................... PP

                                        HHCHHHHHHHHHHTHHHH CS
                             Septin 249 kthledLkevteellYet 266
                                                    e+  e+
  gene1871|gene1871|rna1870|rna1870 324 ------------EMEMEK 329
                                        ............222233 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-06    0.0092       2      99 ..      42     151 ..      41     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-06
                                        EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSE.EEEEEE..ETTEEEEEEECGGCS........SHHHHH CS
                           MMR_HSR1   2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdi.negrvk..lkgkeielvDtpGli........egasee 63 
                                        v+ vGr   G StLin+++ +     + s++  +Tr+  +e  ++  ++   ++ +D+  +i        e  ++e
  gene1871|gene1871|rna1870|rna1870  42 VLAVGRRGLGTSTLINSIFAAplvDKKRSNTITVTRNEiVENDISleISIVTYHETDISPVIdyinamnrEYFDNE 117
                                        788****************975433455555555555422222332233344677777776533333332123344 PP

                                        HHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHH CS
                           MMR_HSR1  64 kglgkaflaleeadlillvvdaseeklkpldeelee 99 
                                        +gl kaf++ ++ ++ l+++ +  +  +++ +++ e
  gene1871|gene1871|rna1870|rna1870 118 QGLYKAFKD-NRIHVCLYLLPSD-TLAEQEIKNMYE 151
                                        589999996.5579999998833.323333344433 PP

>> DUF2533  Protein of unknown function (DUF2533)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.46   2.7e+03      51      73 ..      71      93 ..      66      99 .. 0.84
   2 ?   11.3   0.8     6e-05      0.36      22      65 ..     307     350 ..     294     355 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                            DUF2533 51 NevTkeiNelakkgivptRklVt 73
                                       N++T   Ne+ ++ i  +  +Vt
  gene1871|gene1871|rna1870|rna1870 71 NTITVTRNEIVENDISLEISIVT 93
                                       89999999999999988888877 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6e-05
                            DUF2533  22 leLeqkREaaIeeavelckkgkpfsvekiNevTkeiNelakkgi 65 
                                          L++k E+ I +  e+  + ++f +ek+N + +++Ne+++++ 
  gene1871|gene1871|rna1870|rna1870 307 KILNDKYESRIKALKEEEMEMEKFYTEKLNSLDDKMNEISNQME 350
                                        568999999999999999999*******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2583.57
//
Query:       gene1872|gene1872|rna1871|rna1871  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00074   20.0   0.2      0.004   17.7   0.2    2.2  1  PCI       PCI domain
  ------ inclusion threshold ------
       0.19   12.0   3.0         14    6.0   0.2    2.6  2  DUF5503   Family of unknown function (DUF5503)


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   4.4e-07     0.004      12     104 ..     207     295 ..     147     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.4e-07
                                        HTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHH..CESEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                                PCI  12 sgnlsgfseelkdleeelladdglaqllesLekkvrerllrqvsk..iyssislerlaklldlsvdevEkilvklI 85 
                                        +gn++g +e  ++l +e++         +  ++k++  +l+ +++    +++s++++++ll+++++ v +i+ k  
  gene1872|gene1872|rna1871|rna1871 207 EGNVKGLEEKHNKL-NEIFG-----SSADIIKEKAYMIALINICFseVGKKVSIKKIEELLKIPSKMVIYIVLKSF 276
                                        44444444444444.22222.....1344445555555555555566889************************** PP

                                        HTTSSSEEEETTTTEEEEC CS
                                PCI  86 rdgeirakidqesgivvfk 104
                                          g+i++ id e+gi++f 
  gene1872|gene1872|rna1871|rna1871 277 GLGLINGWIDGEEGILYFD 295
                                        *****************96 PP

>> DUF5503  Family of unknown function (DUF5503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0017        16      66     108 ..     103     145 ..      85     152 .. 0.86
   2 ?    6.0   0.2    0.0016        14      54      82 ..     154     182 ..     149     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0017
                            DUF5503  66 nmlsefkllhseyfewgdyslwfqdfsiynkigfimiekirel 108
                                          + e+k +    few +  +  +   +yn +gf + +ki+++
  gene1872|gene1872|rna1871|rna1871 103 IEINELKGIEKRLFEWKNLKMPRNVRIMYNLLGFKFYQKIQNV 145
                                        4578999999***********999999************9875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0016
                            DUF5503  54 kftpisedsklfnmlsefkllhseyfewg 82 
                                        k+  +se  +l++ l e+ ll  e+f++ 
  gene1872|gene1872|rna1871|rna1871 154 KYVNLSETEELMDTLVEYALLSKEFFNFT 182
                                        78999*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       847  (0.0472419); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2483.55
//
Query:       gene1873|gene1873|rna1872|rna1872  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-16   60.4   3.2    0.00014   22.6   0.1    4.9  5  WD40         WD domain, G-beta repeat
     0.0043   17.3   0.0       0.66   10.3   0.0    3.1  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
       0.12   12.9   0.3         63    4.2   0.1    3.6  5  PQQ_3        PQQ-like domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.1e-06    0.0063       5      33 ..       7      36 ..       3      41 .. 0.88
   2 ?    2.7   0.0     0.046   2.7e+02      14      38 .]      58      82 ..      47      82 .. 0.81
   3 !   22.6   0.1   2.3e-08   0.00014       3      38 .]      88     122 ..      86     122 .. 0.87
   4 !   14.5   0.0   8.6e-06     0.051       3      38 .]     128     162 ..     126     162 .. 0.77
   5 ?   -2.0   0.0       1.3   7.9e+03       9      25 ..     172     189 ..     166     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                                       EEEESS.SSEEEEEEETTSSEEEEEETTSE CS
                               WD40  5 rtltGH.ssvtslafspdgawlasGsdDgt 33
                                        +l+ H s++ sl+ +p+ a+las+s+Dgt
  gene1873|gene1873|rna1872|rna1872  7 AILKIHnSWIKSLDIDPYDAFLASSSMDGT 36
                                       56888*777********************9 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.046
                                       EEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40 14 tslafspdgawlasGsdDgtvriWd 38
                                        + +fs+ +++++++  Dg +r +d
  gene1873|gene1873|rna1872|rna1872 58 EDAKFSKTQPYIFCALLDGLIRSYD 82
                                       4556*********8877****9887 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 2.3e-08
                                        EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                         +r++ GH ssv +l  + + + ++sGs D+tvr Wd
  gene1873|gene1873|rna1872|rna1872  88 FIREYYGHtSSVLCL--DTYDKRIFSGSSDCTVRAWD 122
                                        6899****999****..77777799**99*******9 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 8.6e-06
                                        EEEEEESS.SSEEEEEEETTSSE....EEEEETTSEEEEEE CS
                               WD40   3 clrtltGH.ssvtslafspdgaw....lasGsdDgtvriWd 38 
                                         + + +GH  +vt++       +    + s+s+Dg+v +Wd
  gene1873|gene1873|rna1872|rna1872 128 SVSVMKGHrLPVTHI------MFrnglIYSSSMDGNVFLWD 162
                                        577889**8889999......334443679999*******9 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 1.3
                                        SS.SSEEEEEEETTSSEE CS
                               WD40   9 GH.ssvtslafspdgawl 25 
                                        G  ssvts++ +++  ++
  gene1873|gene1873|rna1872|rna1872 172 GFaSSVTSMCMCDETLFV 189
                                        554679999766665555 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00011      0.66      38      78 ..      13      53 ..       6      59 .. 0.90
   2 ?    1.0   0.0     0.086   5.1e+02      48      87 ..      64     102 ..      54     107 .. 0.81
   3 ?    2.4   0.0     0.033     2e+02      45      88 ..     101     143 ..      95     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                        ANAPC4_WD40 38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsv 78
                                       +s ++sL   p + +La +  dg+  ++d+e+++++ +++ 
  gene1873|gene1873|rna1872|rna1872 13 NSWIKSLDIDPYDAFLASSSMDGTTGIVDIETKQLLITIPL 53
                                       677999****************************9998876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.086
                        ANAPC4_WD40  48 pdgklLavaysdgevrlldaesgkvvhslsvksekavtcl 87 
                                        +    +  a  dg +r +d  + + ++++  +++ +v cl
  gene1873|gene1873|rna1872|rna1872  64 KTQPYIFCALLDGLIRSYDLVDREFIREYYGHTS-SVLCL 102
                                        55566778899****************9977776.59998 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.033
                        ANAPC4_WD40  45 aWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                        +    +k +  + sd +vr  d+ s + v+ ++ ++   vt + 
  gene1873|gene1873|rna1872|rna1872 101 CLDTYDKRIFSGSSDCTVRAWDVRSRNSVSVMKGHRLP-VTHIM 143
                                        5556678899999************9999999888774.77665 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.7   1.6e+04      24      37 ..      69      82 ..      67      83 .. 0.76
   2 ?    4.2   0.1     0.011        63      19      40 .]     104     125 ..      92     125 .. 0.84
   3 ?    4.1   0.0     0.012        69      20      37 ..     145     162 ..     134     165 .. 0.82
   4 ?   -1.3   0.0       0.6   3.6e+03      13      29 ..     177     192 ..     167     196 .. 0.75
   5 ?   -2.8   0.0       1.7     1e+04      10      29 ..     249     268 ..     244     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
                              PQQ_3 24 vyvgtgdGtlyAlD 37
                                       ++++  dG ++++D
  gene1873|gene1873|rna1872|rna1872 69 IFCALLDGLIRSYD 82
                                       67777799999888 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.011
                              PQQ_3  19 vdgglvyvgtgdGtlyAlDaet 40 
                                        +++ +++ g++d t++A D ++
  gene1873|gene1873|rna1872|rna1872 104 TYDKRIFSGSSDCTVRAWDVRS 125
                                        57899**************986 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.012
                              PQQ_3  20 dgglvyvgtgdGtlyAlD 37 
                                         +gl+y +++dG+++  D
  gene1873|gene1873|rna1872|rna1872 145 RNGLIYSSSMDGNVFLWD 162
                                        589**********98666 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.6
                              PQQ_3  13 vnsspavdgglvyvgtg 29 
                                        v +s+ + + +++v+ g
  gene1873|gene1873|rna1872|rna1872 177 V-TSMCMCDETLFVSVG 192
                                        3.678888999999876 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 1.7
                              PQQ_3  10 pgpvnsspavdgglvyvgtg 29 
                                        pg ++  +a  ++++++gt+
  gene1873|gene1873|rna1872|rna1872 249 PGNIVKVTASKERIIVAGTS 268
                                        44555555666777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1961.44
//
Query:       gene1874|gene1874|rna1873|rna1873  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-29  102.4   0.0      3e-29  102.2   0.0    1.1  1  Pkinase         Protein kinase domain
    1.5e-11   44.0   0.0      2e-11   43.7   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
      3e-08   32.9   0.0    4.8e-08   32.2   0.0    1.3  1  Pkinase_fungal  Fungal protein kinase
    3.2e-05   24.0   0.0    0.00012   22.0   0.0    1.8  2  APH             Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   6.8e-33     3e-29       1     198 [.       8     211 ..       8     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 6.8e-33
                                        EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEE CS
                            Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk.hpnivrlyevfeekdelyl 75 
                                        y+  e++G+G+fGkVyk++ ke++k +A+K  +++++  +  + +++Ei+  ++l+ +++i  l++   +    +l
  gene1874|gene1874|rna1873|rna1873   8 YTICEEIGKGGFGKVYKVRTKEDQKAYALKLEDNKEKGRR--NVIINEIQAYNELQgCDEIPLLVDHGFHRALAFL 81 
                                        67789*************************8777766664..47***********************9999999** PP

                                        EEE--TTEBHHHHHHHHSS.--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSS CS
                            Pkinase  76 vleyveggeladllerkgs.lseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakeles 150
                                        vl + +  +l+d+ler+   ++ + a  +ak++l  +e++H+kg ++rDlKpeN+++d ++++ ++DFG++  + +
  gene1874|gene1874|rna1873|rna1873  82 VLPLFR-YSLKDILERHPRfFTRRSATIVAKKLLGTIEFIHKKGRLYRDLKPENVMFDYNNKVYLIDFGMSMPYLR 156
                                        ******.56******8776699*************************************************98877 PP

                                        SCS.......BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STT CS
                            Pkinase 151 ssk.......ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfs 198
                                        +          ++++gt +Y++    ++ e s+  D+ sl  +l+ l+    p+ 
  gene1874|gene1874|rna1873|rna1873 157 KDGshipeirGKNVCGTLWYMSINTHRGVEQSRRDDLESLFYLLILLYKSGLPWI 211
                                        766799***99**********9777777777777777777666666666666665 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   4.4e-15     2e-11       3     155 ..      10     156 ..       8     187 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 4.4e-15
                                        EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEE CS
                        Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkkl.khpnivkllgvctkeepll 77 
                                        + +++G+G fGkV++ + k    +++   a+K  +++ ++ +++ +++e++  ++l   ++i  l+    ++   +
  gene1874|gene1874|rna1873|rna1873  10 ICEEIGKGGFGKVYKVRTK----EDQKAYALKLEDNK-EKGRRNVIINEIQAYNELqGCDEIPLLVDHGFHRALAF 80 
                                        6789*************99....77778899987555.555599************999************9**** PP

                                        EEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEET CS
                        Pkinase_Tyr  78 ivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardi 153
                                        +v+ + ++ +L++ L+++  + +t ++ + +a ++   +e++++k  + rdl   Nv+ + n++v + DfG++   
  gene1874|gene1874|rna1873|rna1873  81 LVLPLFRY-SLKDILERH-PRFFTRRSATIVAKKLLGTIEFIHKKGRLYRDLKPENVMFDYNNKVYLIDFGMSMPY 154
                                        *****999.8********.99999999999******************************************9876 PP

                                        TT CS
                        Pkinase_Tyr 154 ek 155
                                         +
  gene1874|gene1874|rna1873|rna1873 155 LR 156
                                        44 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.1e-11   4.8e-08     324     405 ..     121     201 ..     110     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.1e-11
                     Pkinase_fungal 324 lkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesga....rertGTleFmaievlkgeeHsyrh 395
                                        +k+g L rD   +N+++       ++k  LiD+ + + + +++ ++ +    ++  GTl +m+i+  +g e s r+
  gene1874|gene1874|rna1873|rna1873 121 HKKGRLYRDLKPENVMFD-----YNNKVYLIDFGMSMPYLRKDGSHIPeirgKNVCGTLWYMSINTHRGVEQSRRD 191
                                        48999************9.....7899***********99876666445555899********************* PP

                     Pkinase_fungal 396 DLESffyvll 405
                                        DLES+fy+l+
  gene1874|gene1874|rna1873|rna1873 192 DLESLFYLLI 201
                                        ********97 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.2   8.8e+02      12      59 ..      21      71 ..      11      99 .. 0.70
   2 !   22.0   0.0   2.8e-08   0.00012     163     198 ..     120     153 ..      68     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.2
                                       EEEEEEETT.-.-EEEEEE-TT..S-HHHHHHHHHHHHHHHHTT-B--B-CT CS
                                APH 12 rtylvttpa.g.ryvlrrnppa..raaeeirrevallrlLakagvpvPevla 59
                                       ++y+v t++ +  y+l++   +     + i +e + +  L++ +  +P +++
  gene1874|gene1874|rna1873|rna1873 21 KVYKVRTKEdQkAYALKLEDNKekGRRNVIINEIQAYNELQGCDE-IPLLVD 71
                                       589999998756999999444434688888888888888888866.777776 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 2.8e-08
                                        SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                                APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                          +++ l +Dl+p N+++d  +++v ++iDf+++++
  gene1874|gene1874|rna1873|rna1873 120 IHKKGRLYRDLKPENVMFD-YNNKV-YLIDFGMSMP 153
                                        6788999************.88998.9******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1945.37
//
Query:       gene1875|gene1875|rna1874|rna1874  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.5e-44  149.2   0.0    6.1e-44  149.1   0.0    1.1  1  UQ_con     Ubiquitin-conjugating enzyme
    0.00014   21.5   0.0    0.00019   21.2   0.0    1.2  1  Prok-E2_B  Prokaryotic E2 family B
    0.00067   19.9   0.0    0.00099   19.4   0.0    1.3  1  RWD        RWD domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.1   0.0     1e-47   6.1e-44      10     138 ..      31     158 ..      13     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 149.1 bits;  conditional E-value: 1e-47
                                        HHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBETTSBB-CGG CS
                             UQ_con  10 akkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvdksGevcldi 85 
                                        ++++++ i+  +  + ++f+w++ ++ pe+++Y+ggvFkl ++f+++YP+kpPk++f+t+i+HPn+++sG +c+di
  gene1875|gene1875|rna1874|rna1874  31 KDSTSKYIKIVPFVSGDFFTWEAYLTAPEESVYKGGVFKLLITFSNEYPFKPPKITFKTPIYHPNINSSGMICIDI 106
                                        44555666666666689*********************************************************** PP

                                        GSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHH CS
                             UQ_con  86 LkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvke 138
                                        L +e Wspaltl+svlls++ Ll++pn ++pl+ e+a+ +k+++eey+++ +e
  gene1875|gene1875|rna1874|rna1874 107 LGKE-WSPALTLNSVLLSLLTLLDDPNADDPLRPEVADIYKTNKEEYRQRCRE 158
                                        **66.********************************************9976 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.1e-08   0.00019       4     111 ..      36     135 ..      33     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.1e-08
                          Prok-E2_B   4 nwlaaaealaadelaakdgkkaierssvktsggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLCll 79 
                                        ++ +  + ++ d+++ +++ +a e+s +k  gg+++l + +++++p+ pp++  + p      p in+ +g +C  
  gene1875|gene1875|rna1874|rna1874  36 KYIKIVPFVSGDFFTWEAYLTAPEESVYK--GGVFKLLITFSNEYPFKPPKITFKTPI---YHPNINS-SGMICI- 104
                                        67777788899999999999999998876..**************************9...67999**.******. PP

                          Prok-E2_B  80 eeeldldewdpngsvadvleqlqqvLn.egisg 111
                                               ew p+ ++  vl +l  +L+  ++ +
  gene1875|gene1875|rna1874|rna1874 105 --DILGKEWSPALTLNSVLLSLLTLLDdPNADD 135
                                        ..8888999999999999999999998444443 PP

>> RWD  RWD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.7e-07   0.00099      47      84 ..      60     100 ..      10     132 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.7e-07
                                        ..TT-CEEEEEEEEE-SSTTSS--EEEEEECC...SS-HHH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                                RWD  47 feekkkpslkleiklpeeYPeeaPiislsste...nlpkeq 84 
                                         +  k   +kl i++++eYP ++P+i+++++    n++ + 
  gene1875|gene1875|rna1874|rna1874  60 ESVYKGGVFKLLITFSNEYPFKPPKITFKTPIyhpNINSSG 100
                                        556667789********************998555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1002.56
//
Query:       gene1876|gene1876|rna1875|rna1875  [L=1025]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-19   68.9  29.6    3.5e-18   65.8  29.6    2.6  1  SMC_N           RecF/RecN/SMC N terminal domain
    6.3e-14   52.9   7.9    6.3e-14   52.9   7.9    5.7  2  AAA_23          AAA domain
    2.6e-09   37.3  53.1      3e-07   30.5  11.0    3.3  2  AAA_15          AAA ATPase domain
    9.5e-05   22.3  10.9     0.0055   16.6   0.1    2.9  3  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    0.00016   21.4   0.0    0.00028   20.6   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.012   15.3   0.0    3.3  4  AAA_27          AAA domain
      0.053   13.9   0.1        8.4    6.7   0.0    2.9  2  AAA_16          AAA ATPase domain
        1.5    8.8  13.6      0.054   13.5   2.2    3.6  3  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8  29.6   1.6e-21   3.5e-18       5     198 ..      12     988 ..       8    1009 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.6e-21
                                        EEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              SMC_N   5 leienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeve 80 
                                        +++enF+++  k++ l+f +sf++i GpNGSGKs++ +A+  v+G + +   r + + + +         ++a++e
  gene1876|gene1876|rna1875|rna1875  12 MRLENFQTF--KKIFLKFCPSFNFIAGPNGSGKSSIANAMVLVFGGTPKIIGRGKGVGEYVRF-----GEEEARIE 80 
                                        789******..7*********************************877766688888888887.....55677777 PP

                                        EEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT..................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                              SMC_N  81 itfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske..................... 135
                                        + +  ++k+       v + r ++r+++s+y+ +gk  +k+e++ l+ + + ++                      
  gene1876|gene1876|rna1875|rna1875  81 VGVWIKGKE-------VRLCRCISRNNQSRYFADGKAYKKTEYEGLIGKLKENIGnlcqflpqekaseftrlspen 149
                                        765556665.......*******************************9988777789******************* PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 150 llgevllsvgdeeilrymkeleeleternkvadileacgrkkecvertvevlekdvkranekkkkeeririmdekr 225
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 226 dwihyklytdeygmvrrnisllkkqietkneevvnieskikelksseaykeinelckvleeydmnlvdlvekagni 301
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 302 hqeiemlgvdeeslrnkrekrisnterlekeildlqeeiskleippqpqeldearikvletkmsdlmrtrgkiqhe 377
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 378 saelkrlvddlslkrkkfhemdemrlqmlrkyhadtykavcwlrenkhqfkdevieppfvqlrikdaryalevenf 453
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 454 lgfqslspficksaddfetfvrimkdekkwminaieaiktdkrarkeeegisknmlkelgfegvlsdfiecreetm 529
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 530 nylivagnfdlipvskasvdenlvfrktnvkrmaaggryieikksrygseyaiiynplksrnlfsqnlslreleei 605
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 606 eeelgrknstrreneeklkgilkdcevidkelqglyrerslynsqmmeikrketharvlkgsmdrkklemkmlkdt 681
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 682 kdldeeemkineskrklealwknkcdelskclsdegyfdvfrsasklfreiinvnkniealeesikvgekikeele 757
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 758 ekviekkkessklkkmieekkvrlekierkeeydkalaqlpntideldeeiikekaqikfynidskavgefevrek 833
                                        **************************************************************************** PP

                                        ............................................................................ CS
                                        ............................................................................ RF
                              SMC_N 136 ............................................................................ 135
                                                                                                                    
  gene1876|gene1876|rna1875|rna1875 834 dlkelnediskyskilesvkkkslrirdilvdkigrivsrideqfrnlfrkvggdgrvmfiydeldackwkfnimv 909
                                        **************************************************************************** PP

                                        ..............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE CS
                                        ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                              SMC_N 136 ..............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivi 195
                                                        SgGe++++ + +l+Aiq++kp+p+ l+Dei++ +D +n k v ++l + sk+   Qf++i
  gene1876|gene1876|rna1875|rna1875 910 kfhdddslevlnshRQSGGERSVAIILFLLAIQHYKPSPFRLVDEINQGMDGNNEKLVHDILVALSKEgnEQFFMI 985
                                        **************99**********************************************977775559****9 PP

                                        -SS CS
                                        xxx RF
                              SMC_N 196 slr 198
                                        + +
  gene1876|gene1876|rna1875|rna1875 986 TPK 988
                                        965 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   7.9   2.8e-17   6.3e-14       2     193 ..      12     219 ..      11     257 .. 0.70
   2 ?  -65.3  88.4         8   1.8e+04     153     198 ..     683     807 ..     201     856 .. 0.74

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 2.8e-17
                             AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                        +++enf+ f++  + F + ++ I GpNG+GK++i +A+ l+++g ++  +r++g   + + v+++   + +a +e+
  gene1876|gene1876|rna1875|rna1875  12 MRLENFQTFKKIFLKFCPSFNFIAGPNGSGKSSIANAMVLVFGGTPKIIGRGKG---VGEYVRFG---EEEARIEV 81 
                                        589*****************************************9888888776...55666654...55788888 PP

                             AAA_23  78 tfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke 153
                                         +  k+++    + r +  ++ +++++++a+++  +++e e +i +l   k++i nl++fl+qe++ ef + ++++
  gene1876|gene1876|rna1875|rna1875  82 GVWIKGKE----V-RLCRCISRNNQSRYFADGKAYKKTEYEGLIGKL---KENIGNLCQFLPQEKASEFTRLSPEN 149
                                        85444453....3.445556666666677776666666655555433...44566999999999988888877777 PP

                             AAA_23 154 ............rleelekeleeledekkllekl..................eqekekekeleeleeele 193
                                                    ++  + keleele+e++++ +                   e+  ++ +e +++ee++ 
  gene1876|gene1876|rna1875|rna1875 150 llgevllsvgdeEILRYMKELEELETERNKVADIleacgrkkecvertvevlEKDVKRANEKKKKEERIR 219
                                        7778888888887777777777777777766655455576677777777776333333334444444443 PP

  == domain 2  score: -65.3 bits;  conditional E-value: 8
                             AAA_23 153 e.......................................................................rlee 157
                                        +                                                                       +lee
  gene1876|gene1876|rna1875|rna1875 683 DldeeemkineskrklealwknkcdelskclsdegyfdvfrsasklfreiinvnkniealeesikvgekikeELEE 758
                                        1222222222233333333333333333333333333333333333333333333222222222222221112222 PP

                             AAA_23 158 .lekeleeledekkllekl.......eqekekekeleeleeeleeilke 198
                                         ++++++e ++ kk +e++       e+++e+ k+l +l +++ e+++e
  gene1876|gene1876|rna1875|rna1875 759 kVIEKKKESSKLKKMIEEKkvrlekiERKEEYDKALAQLPNTIDELDEE 807
                                        1233333333333333333333333233334444444444444444433 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5  11.0   1.4e-10     3e-07       6     255 ..      12     346 ..      10     403 .. 0.47
   2 !   13.2  31.3   2.4e-05     0.054      54     363 ..     622     986 ..     587     986 .. 0.66

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.4e-10
                             AAA_15   6 ikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn......kkvikiekedleifenisesk 75 
                                        ++++NF  +k++ +++ ++++++ G+N+sGKSsi++a+ l +  + k                   e+ +  +e+ 
  gene1876|gene1876|rna1875|rna1875  12 MRLENFQTFKKIFLKFCPSFNFIAGPNGSGKSSIANAMVLVFGGTPKIIgrgkgvG----------EYVRFGEEEA 77 
                                        679****************************************9933335555550..........5555555555 PP

                             AAA_15  76 dikIdvef.................................................................... 83 
                                        +i++ v+                                                                     
  gene1876|gene1876|rna1875|rna1875  78 RIEVGVWIkgkevrlcrcisrnnqsryfadgkaykkteyegligklkenignlcqflpqekaseftrlspenllge 153
                                        5555555555555555555666666666666655555555555555555555666666666666666666666666 PP

                             AAA_15  84 ...................................aekekakeyektlkskekkkadlllkkkesdlkktikdkkl 124
                                                                           +    +ke      ++  +  ++++k+ ++++kk  + +++
  gene1876|gene1876|rna1875|rna1875 154 vllsvgdeeilrymkeleeleternkvadileacgR----KKE----CVERTVEVLEKDVKRANEKKKKEERIRIM 221
                                        666666666666666666555544443333322221....222....22222333333444444444444444444 PP

                             AAA_15 125 klkknelsdekisvekkkskkelpkekeeklekekeelkid.......kedlkklikkleeslkkee.......el 186
                                        + k + + ++ +++e  + ++++  +k+  ++k++e + i+       ++++ k i++l + l++++       e 
  gene1876|gene1876|rna1875|rna1875 222 DEKRDWIHYKLYTDEYGMVRRNISLLKKQIETKNEEVVNIEskikelkSSEAYKEINELCKVLEEYDmnlvdlvE- 296
                                        444444444444444444433333333333333333333331000000222222222222222222244443331. PP

                             AAA_15 187 knvlksaiiklllisakRnvsd..edsekkssllgklkekileealqekleeelteklkeiqeklkeidkk 255
                                                       +  n+ +  e   + +++l ++ ek +++      +e+l++++ ++qe++++++  
  gene1876|gene1876|rna1875|rna1875 297 ---------------KAGNIHQeiEMLGVDEESLRNKREKRISN------TERLEKEILDLQEEISKLEIP 346
                                        ...............22222221111112222222222222222......222223333333333322222 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.4e-05
                             AAA_15  54 n.......kkvikiekedleifeniseskdikIdvef..................aek.ekakeyektlkskekkk 103
                                        +       ++vi++e + l  +++ ++s++++I+ ++                  + k +k+ ++e+ + ++ k+k
  gene1876|gene1876|rna1875|rna1875 622 KlkgilkdCEVIDKELQGLYRERSLYNSQMMEIKRKEtharvlkgsmdrkklemkMLKdTKDLDEEEMKINESKRK 697
                                        0446666667788888888888899999999999999999999999998888766233666666677777777788 PP

                             AAA_15 104 adlllkkkesdlkktikdkklklk...knelsdekisvekkks..kkelpkekeeklekekeelkid..kedlkkl 172
                                         + l+k+k+++l+k + d+ + +    +++l  e+i+v+k+ +  + ++++ ++ k+e+e++ ++++  +++lkk 
  gene1876|gene1876|rna1875|rna1875 698 LEALWKNKCDELSKCLSDEGYFDVfrsASKLFREIINVNKNIEalEESIKVGEKIKEELEEKVIEKKkeSSKLKKM 773
                                        8889******999999999887641114455555555555555554445555555555555555555334455555 PP

                             AAA_15 173 ikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl..........eeel 238
                                        i+                 ++   l+ i+ k ++++ + +   +++++l+e+i++e++q k+           e  
  gene1876|gene1876|rna1875|rna1875 774 IE-----------------EKKVRLEKIERKEEYDKALAQL-PNTIDELDEEIIKEKAQIKFynidskavgeFEVR 831
                                        55.................4444444444444444444433.4445555555555555555555544445533334 PP

                             AAA_15 239 teklkeiqeklkeidkklaeelk......kilkkkidkikkfnykgkkneeieik..................... 287
                                        +++lke++e++++ +k+l++ +k      +il +ki  i++    ++ n     +                     
  gene1876|gene1876|rna1875|rna1875 832 EKDLKELNEDISKYSKILESVKKkslrirDILVDKIGRIVSRIDEQFRNL----Frkvggdgrvmfiydeldackw 903
                                        55667777777777777766666667777555555555544444444444....3455589999999999999999 PP

                             AAA_15 288 ...........ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkela 352
                                                   d  e+  + + sG  r + +il++l ++      +++ ++l++E+      ++ k +++ l  l+
  gene1876|gene1876|rna1875|rna1875 904 kfnimvkfhddDSLEVLNSHRQSGGERSVAIILFLLAIQHY----KPSPFRLVDEINQGMDGNNEKLVHDILVALS 975
                                        999*****977444444445555666666666666666666....6****************************** PP

                             AAA_15 353 ndnktQviitT 363
                                        ++++ Q ++ T
  gene1876|gene1876|rna1875|rna1875 976 KEGNEQFFMIT 986
                                        ******99866 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.5e-06    0.0055       1      33 [.      31      56 ..      31      82 .. 0.78
   2 ?   -3.8   0.1       3.9   8.8e+03      47     103 ..     551     608 ..     536     629 .. 0.56
   3 !   11.1   2.2   0.00011      0.25     116     296 ..     780     986 ..     676     987 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                             AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdveglt 33
                                       +n++ GpNgsGKS++  a+ l+++       +t
  gene1876|gene1876|rna1875|rna1875 31 FNFIAGPNGSGKSSIANAMVLVFG-------GT 56
                                       89*****************99964.......33 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.9
                             AAA_21  47 slldlydpeipfefeieeflsqgvryryglrlersqv.eeklssvetllesgllldkr 103
                                        +l +++   ++++ + +  +++++ry  ++ + ++ + ++ l+s++  l+  +   ++
  gene1876|gene1876|rna1875|rna1875 551 NLVFRKTNVKRMAAGGRYIEIKKSRYGSEYAIIYNPLkSRNLFSQNLSLRELEEIEEE 608
                                        5555555555555566666667777777777777776544444444444444444444 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00011
                             AAA_21 116 rgirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke...rigllnifadyfgfakekrllqrl 188
                                        r +++ ++++++k+l   +  +++  + +++ ++++ +++ ++ + ++    +++l ++  d  +++k+++ +++ 
  gene1876|gene1876|rna1875|rna1875 780 RLEKIERKEEYDKALAQLPNTIDELDEEIIKEKAQIKFYNIDSKAVGEFevrEKDLKELNEDISKYSKILESVKKK 855
                                        3333333333333333333333333333333333333333333333322344666666666666666666666665 PP

                             AAA_21 189 vrslklveielsdlgegeeliasvderlrer..............................gvvflengdgqelpa 234
                                        + +++++      +g  +++  ++                                      v f+++++   l++
  gene1876|gene1876|rna1875|rna1875 856 SLRIRDILVDK--IGR-IVSRIDE------QfrnlfrkvggdgrvmfiydeldackwkfniMVKFHDDDSLEVLNS 922
                                        55555554332..222.2333333......14444458999*******************8888888888888888 PP

                             AAA_21 235 relSdGtkrllalltallralkkg.sllliDEpEngLHP...kllrrllell.kelsrngaQviltT 296
                                        +  S G ++++ +l +l+ ++ k+ ++ l+DE+  g++    kl++ +l  l ke    + Q+++ T
  gene1876|gene1876|rna1875|rna1875 923 HRQSGGERSVAIILFLLAIQHYKPsPFRLVDEINQGMDGnneKLVHDILVALsKEG---NEQFFMIT 986
                                        888*******988888888888888********99999977777777776663333...35888877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00028       4      49 ..      12      56 ..       9      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                             AAA_29  4 lqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                       ++l N +tf++  +++ ++ + +++Gp+GsGKS++  A+  ++ ++
  gene1876|gene1876|rna1875|rna1875 12 MRLENFQTFKKIFLKFCPS-FNFIAGPNGSGKSSIANAMVLVFGGT 56
                                       7888999****99999988.6******************9998665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   5.1e-06     0.012       6      52 ..      12      54 ..       8     125 .. 0.86
   2 ?   -2.5   0.1       1.4   3.1e+03     137     183 ..     173     218 ..     167     229 .. 0.74
   3 ?   -2.4   0.1       1.3   2.9e+03     160     188 ..     628     656 ..     590     683 .. 0.65
   4 ?   -3.0   0.4       2.1   4.6e+03     174     205 ..     751     782 ..     732     806 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.1e-06
                             AAA_27  6 LdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfG 52
                                       ++Le +  f+   l+f    +++ +i GpN +GKs++ +A+   +fG
  gene1876|gene1876|rna1875|rna1875 12 MRLENFQTFKKIFLKFC---PSFNFIAGPNGSGKSSIANAMVL-VFG 54
                                       67999999999999998...9*******************974.444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
                             AAA_27 137 lleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrai 183
                                        l  ++++++ +L + +   + +++++e Le++ ++  +++k+++ +i
  gene1876|gene1876|rna1875|rna1875 173 LETERNKVADILEACGRKKECVERTVEVLEKDVKRANEKKKKEE-RI 218
                                        55677888888888888888888899999999988888888777.33 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.3
                             AAA_27 160 evleaLeaeadelfkprkskkraineale 188
                                        +  e +++e + l+++r+  + +++e ++
  gene1876|gene1876|rna1875|rna1875 628 KDCEVIDKELQGLYRERSLYNSQMMEIKR 656
                                        44455666666666666655544444444 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.1
                             AAA_27 174 kprkskkrainealeeleeakkelreaqvrae 205
                                        k +++ ++++ e+++e +++kk ++e++vr e
  gene1876|gene1876|rna1875|rna1875 751 KIKEELEEKVIEKKKESSKLKKMIEEKKVRLE 782
                                        33344444555555666666666665555543 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0038       8.4      28      45 ..      33      50 ..      24     214 .. 0.69
   2 ?    4.0   0.0     0.026        59     106     164 ..     839     926 ..     750     935 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0038
                             AAA_16 28 llsGesGvGKsslvrell 45
                                       ++ G+ G+GKss++++  
  gene1876|gene1876|rna1875|rna1875 33 FIAGPNGSGKSSIANAMV 50
                                       899***********8765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.026
                             AAA_16 106 a...........avpelagaea...........srllellkrllallsrderplvlvlDdlq........wadeas 151
                                        +           +v++ +  ++           sr+ e++++l+++   d+r + ++ D+l+         +++++
  gene1876|gene1876|rna1875|rna1875 839 NediskyskileSVKKKSLRIRdilvdkigrivSRIDEQFRNLFRKVGGDGR-VMFIYDELDackwkfniMVKFHD 913
                                        023333333333333333333344555555677***********99999888.*********88866666444466 PP

                             AAA_16 152 lqllaaLlrlles 164
                                         + l+ L + ++s
  gene1876|gene1876|rna1875|rna1875 914 DDSLEVLNSHRQS 926
                                        6666666666665 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.2   2.4e-05     0.054      49     105 ..     230     286 ..     194     293 .. 0.86
   2 ?    0.1   0.3      0.31     7e+02     147     175 ..     786     814 ..     773     821 .. 0.80
   3 ?    0.2   0.3      0.29   6.4e+02      65      93 ..     830     858 ..     818     885 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                     Halogen_Hydrol  49 kkkhlkksglsrkelkyiretlkeakekikrlekalkrvrslevikqvreilriarr 105
                                         k +  + g+ r+ + +++++++   e++  +e  +k+++s+e+ k+++e++++ ++
  gene1876|gene1876|rna1875|rna1875 230 YKLYTDEYGMVRRNISLLKKQIETKNEEVVNIESKIKELKSSEAYKEINELCKVLEE 286
                                        44455559*********************************************9876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.31
                     Halogen_Hydrol 147 ksketrealeetrqlLdelaealekdlqk 175
                                        +++e  +al++  +++del+e++ k+  +
  gene1876|gene1876|rna1875|rna1875 786 RKEEYDKALAQLPNTIDELDEEIIKEKAQ 814
                                        34677999*************99887655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.29
                     Halogen_Hydrol  65 yiretlkeakekikrlekalkrvrslevi 93 
                                        + ++ lke  e+i++ +k+l +v++ +++
  gene1876|gene1876|rna1875|rna1875 830 VREKDLKELNEDISKYSKILESVKKKSLR 858
                                        44555666666666666666655555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1025 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2563  (0.142953); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.38u 0.34s 00:00:01.72 Elapsed: 00:00:00.57
# Mc/sec: 5406.52
//
Query:       gene1877|gene1877|rna1876|rna1876  [L=132]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.025   13.8   0.2       0.69    9.1   0.0    2.0  2  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
       0.21   12.3   1.7        3.8    8.3   0.2    2.2  2  Ground-like     Ground-like domain


Domain annotation for each model (and alignments):
>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0    0.0041        37     193     243 ..      12      61 ..       2      64 .. 0.76
   2 ?    9.1   0.0   7.7e-05      0.69     207     260 ..      71     124 ..      59     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0041
                     DXP_synthase_N 193 kayeklkkevkkllkkigkklaelakklkeslkellvpgtlfeelgfkYlG 243
                                        +  ++l +  k++l+k+++kl+e+++ ++ ++k+l +  +l e l+ +Y+G
  gene1877|gene1877|rna1876|rna1876  12 NIASELIEIKKAILEKMRHKLKETFSSVSMEAKNLPLL-SLIEGLERNYTG 61 
                                        44556667778888999999999999999999999554.799999999998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 7.7e-05
                     DXP_synthase_N 207 kkigkklaelakklkeslkellvpgtlfeelgfkYlGpidGhdleelikvleev 260
                                        k i+k++a+ +kk  + + ++  ++ +f+  g+k +Gp dG++++ +++ ++ +
  gene1877|gene1877|rna1876|rna1876  71 KIITKRVAKSTKKRPSVVIQVEDQSFVFDGDGLKVVGPWDGQQYKGMLDEINGI 124
                                        33455666666666666666666799******************9999877765 PP

>> Ground-like  Ground-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2   0.00042       3.8      14      46 ..      10      41 ..       3      46 .. 0.87
   2 ?    3.6   0.1     0.012   1.1e+02      21      56 ..      65      99 ..      44     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00042
                        Ground-like 14 eenmkqssasdskkaiqkaleekfgssfevics 46
                                       ++n+  s ++++kkai +++ +k++++f  +  
  gene1877|gene1877|rna1876|rna1876 10 RRNI-ASELIEIKKAILEKMRHKLKETFSSVSM 41
                                       5799.99*********************98865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                        Ground-like 21 sasdskkaiqkaleekfgssfevicsegdfsytifa 56
                                        +++ kk i+k++ +  +++  v++  +d s+ +f 
  gene1877|gene1877|rna1876|rna1876 65 MIRKNKKIITKRVAKSTKKRPSVVIQVEDQSF-VFD 99
                                       45666789999999999999999988888777.665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1277  (0.0712254); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.37s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 758.17
//
Query:       gene1878|gene1878|rna1877|rna1877  [L=475]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.4e-69  232.4   5.0    1.6e-68  231.1   5.0    1.7  1  Kinesin      Kinesin motor domain
    2.5e-09   37.2   0.5    1.1e-08   35.2   0.5    2.2  1  Microtub_bd  Microtubule binding
  ------ inclusion threshold ------
      0.014   15.7   0.0      0.046   14.0   0.0    1.9  1  HHH_3        Helix-hairpin-helix motif
        2.4    8.2   5.3        1.3    9.1   0.0    2.6  2  Dynamin_N    Dynamin family


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   5.0   3.5e-72   1.6e-68      71     333 .]       1     227 [.       1     227 [. 0.95

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 3.5e-72
                                        HTTSEEEEEEEESTTSSHHHHHTBCTTTSBSHHHHHHHHHHHHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTT CS
                            Kinesin  71 leGynatifaYGqtgsGKTyTmegkeeeeeGiipraleelFesikkekeekekefsvkvsylEiYneeiyDLLesk 146
                                        ++G n t+f+YG tg+GKTyTm g+ + + G++ + ++++               s+ vsy+EiYne+iyDLLe+k
  gene1878|gene1878|rna1877|rna1877   1 MKGHNQTLFCYGSTGAGKTYTMVGH-SGSYGLMHNLVKDVLAYG-----------SFLVSYMEIYNEKIYDLLEPK 64 
                                        68**********************8.999**********99876...........4789***************98 PP

                                        TTSTSSEBEEEECTTSCCEEETTS--EEESSHHHHHHHHHHHHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTT CS
                            Kinesin 147 kskkkkklkiredskkgevyvkgltevevksaeevlellekgeknrkvaetklneeSSRSHavftitleqknlkee 222
                                              +l +re +   ++++ +l +++v+++ee+ e++++g knr++aetkln++SSRSH +++i + ++     
  gene1878|gene1878|rna1877|rna1877  65 ------ELVLRECNG--TIVIPNLFNKRVENIEEFEEVFRQGTKNRTTAETKLNKNSSRSHGILRISVGEH----- 127
                                        ......577888654..69***********************************************99875..... PP

                                        TCEEEEEEEEEEEEEEECCCHHHHSSTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGH CS
                            Kinesin 223 teekvkisklnLvDLAGsErasktgaaegerlkEaaniNkSLlaLgrvisaLaekkkskhipYRdSkLTrlLqdsL 298
                                                klnL+DLAGsE+ +ktg+ eg rl+E+++iN+SL++Lg+v++a+ +   +k ipYRdSkLTrlLqdsL
  gene1878|gene1878|rna1877|rna1877 128 --------KLNLIDLAGSENNRKTGN-EGIRLTESNSINRSLFVLGKVVNAILKG--EKRIPYRDSKLTRLLQDSL 192
                                        ........499**************6.8***************************..******************* PP

                                        SSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHHCTT CS
                            Kinesin 299 gGnsktlmivtvspssenleetlstlkfaerakei 333
                                        gG+s   +i+++  +s+ + ++++tl+fa++ ++i
  gene1878|gene1878|rna1877|rna1877 193 GGSSLCYIIANIVGDSSGMGDSINTLSFASKSRNI 227
                                        *******************************9997 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.5   2.4e-12   1.1e-08      80     149 .]       2      61 ..       1      61 [. 0.91

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.4e-12
                                        TT--EEEEEEES................ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEETT CS
                        Microtub_bd  80 dgynvcifaygqTGsGKtyTmegeeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDlL 149
                                        +g n ++f+yg+TG+GKtyTm g++ + g ++++v+ ++   s l          ++++eiynek++DlL
  gene1878|gene1878|rna1877|rna1877   2 KGHNQTLFCYGSTGAGKTYTMVGHSGSYGLMHNLVKDVLAYGSFL----------VSYMEIYNEKIYDLL 61 
                                        789********************9999999999999888877777..........999**********98 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     1e-05     0.046      14      47 ..     424     457 ..     417     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1e-05
                              HHH_3  14 eeLqklpGlgpklAknIvayReknGpfksreeLl 47 
                                         +++klp +g+k A++Iv++ +    f+++++L+
  gene1878|gene1878|rna1877|rna1877 424 FDIKKLPRVGDKRAQAIVDFVNGGNFFETLNDLK 457
                                        5789*****************9999*******98 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00028       1.3      56     119 ..      82     145 ..      63     177 .. 0.80
   2 ?   -0.9   2.4      0.34   1.5e+03       4      16 ..     297     309 ..     294     418 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00028
                                        EEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTS CS
                          Dynamin_N  56 kekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdq 119
                                        +++ +++e+f+ev ++ +k + ++++++++ s++ + +   s  +++l+l+Dl G  ++ k   
  gene1878|gene1878|rna1877|rna1877  82 NKRVENIEEFEEVFRQGTKNRTTAETKLNKNSSRSHGILRISVGEHKLNLIDLAGSENNRKTGN 145
                                        3447888999999888888888899999999999*********************988665544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                                        EEBTTTTHHHHHH CS
                          Dynamin_N   4 vGsqSsGKSSvln 16 
                                        +G  ++GKSS++ 
  gene1878|gene1878|rna1877|rna1877 297 IGGKKKGKSSLIY 309
                                        7888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3027.58
//
Query:       gene1879|gene1879|rna1878|rna1878  [L=374]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-53  179.9   0.3    2.5e-53  179.2   0.3    1.3  1  STE       STE like transcription factor
  ------ inclusion threshold ------
      0.064   13.1   0.0       0.16   11.8   0.0    1.7  1  DUF2015   Fungal protein of unknown function (DUF2015)


Domain annotation for each model (and alignments):
>> STE  STE like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.2   0.3   2.7e-57   2.5e-53       2     110 .]      25     132 ..      24     132 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.2 bits;  conditional E-value: 2.7e-57
                                STE   2 virrykleeeegfiscvlwknlfyitgtdivkilvykleafGrkitdkkkfeeGifsdlrnlkigvdavleepkse 77 
                                         i++++l++ + +i+cvlw+++f+itgtdivkilv+++++ Gr++t+ kkfeeG+fsdlrnlk+g+da+le p+se
  gene1879|gene1879|rna1878|rna1878  25 RIKKFQLKNGD-YIHCVLWNMHFFITGTDIVKILVWRFQNAGRCLTSLKKFEEGVFSDLRNLKPGIDATLEGPRSE 99 
                                        69********8.**************************************************************** PP

                                STE  78 fldllyknkclrtqkkqkvfywfsvphdklfld 110
                                        fl++lykn c+rtqkkqkvfyw+svphd lf+d
  gene1879|gene1879|rna1878|rna1878 100 FLEFLYKNGCIRTQKKQKVFYWYSVPHDALFCD 132
                                        *******************************98 PP

>> DUF2015  Fungal protein of unknown function (DUF2015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.8e-05      0.16      27      65 ..     304     347 ..     281     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                            DUF2015  27 eeylysrlpssFeedieaGlsssnFdl....seNi.esgdsRaG 65 
                                        ++ +y++ pssF e++ +G+s ++Fd     +e i ++++sR+G
  gene1879|gene1879|rna1878|rna1878 304 KSKIYNTTPSSFLEELPDGFSLDDFDFlkdrAEKInADDESRQG 347
                                        5667**********************843332334234557887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 2233.12
//
Query:       gene1880|gene1880|rna1879|rna1879  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1188.01
//
Query:       gene188|gene188|rna188|rna188  [L=718]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-05   23.6   1.4     0.0062   15.4   1.4    3.2  1  Cse1            Cse1
  ------ inclusion threshold ------
      0.043   13.5   0.0        0.3   10.7   0.0    2.0  2  DNA_ligase_A_M  ATP dependent DNA ligase domain


Domain annotation for each model (and alignments):
>> Cse1  Cse1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.4     7e-07    0.0062      58     128 ..     163     217 ..     123     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7e-07
                                    HHHHHHHHHHHSSS--HHHHHTHHHHHHHHHHHHH--SGGG-TT-SSS--HHHHHHHHHHHHHHHHHHH-H CS
                           Cse1  58 lllvklfydlnsqdlPeffEdnlkelmealhkylsldnplletdddeeasvleklkasicelvqlyvekye 128
                                      ++ +f++l +qd+ +ffE+n +++++ + k+l  ++  l+              ++ice+++l+v+ky 
  gene188|gene188|rna188|rna188 163 ENILGMFHSLVFQDIHPFFENNADKFIGSFCKLLRKNV--LQ--------------KDICEVFNLFVTKYP 217
                                    357789**************************997543..22..............355555555555555 PP

>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.069   6.2e+02     112     173 ..      83     153 ..      56     159 .. 0.73
   2 ?   10.7   0.0   3.4e-05       0.3      39     138 ..     282     391 ..     277     394 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.069
                                    HSEEEEEEEEEEEE.......TTEEHTTSCHHHHHHHHHHHB..--BTTTEEE--EEEESSHHHHHHHHHH CS
                 DNA_ligase_A_M 112 eaelclfvFDiLyl.......dgesltdeplkeRrklLeeil..kesedrvelaeslevkdveeleellee 173
                                    +  + +f+F+ Ly+         e+l   p +   k+L+ ++   ++  r ++++   +k++e  ++++++
  gene188|gene188|rna188|rna188  83 NFGILCFFFETLYFhgatwdgLVEDLCANPNERSVKVLNHMFnkYRICSRSDALYGEIIKNIELCQDIFKK 153
                                    55677899999999666664334567899999999999999933334455566666666777776766666 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3.4e-05
                                    TTEEEEEETTS-B-GG....GCHHHHHHHHHHBSTTESEEEEEEEEEEEETTTTCBEHHHHHCHHHHCHCC.....THHH CS
                 DNA_ligase_A_M  39 gdkvklfSRrlkdita....akpelvkalkeafkkdeksvilDGElvavdketgeilpfqklasrkkkkkk.....veek 109
                                    +++v l+SR+l +  +       e++ +l++ f +  +s ++DGE+ +   e++ i+    l+ r k++++     ++++
  gene188|gene188|rna188|rna188 282 NEDVLLYSRNLLKGYDvnrgIIIEMIGHLRRVFGDGWESTVIDGEIATPMDEERLIFLCMALKMRLKEAVDrctdiIRNS 361
                                    678999***9866555544666777788899999**************66666888888888888888885444555666 PP

                                    HHHSEEEEEEEEEEE.ETTEEHTTSCHHHH CS
                 DNA_ligase_A_M 110 lkeaelclfvFDiLy.ldgesltdeplkeR 138
                                     +  +l+++ F  L  +d   ++d ++ +R
  gene188|gene188|rna188|rna188 362 KSVGYLSVVSFRYLLsIDSHAIIDPEYISR 391
                                    567777888886543145555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4815.55
//
Query:       gene1881|gene1881|rna1880|rna1880  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00045   20.0   0.0    0.00064   19.5   0.0    1.2  1  SAGA-Tad1  Transcriptional regulator of RNA polII, SAGA, subu
  ------ inclusion threshold ------
       0.43   10.6   3.2       0.22   11.5   0.6    1.9  2  Gin        Inhibitor of sigma-G Gin


Domain annotation for each model (and alignments):
>> SAGA-Tad1  Transcriptional regulator of RNA polII, SAGA, subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   7.1e-08   0.00064     184     231 ..     117     164 ..     105     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 7.1e-08
                          SAGA-Tad1 184 elpdtdsLrkRmekiaeeeGLvggvsadcaellnlaldvyLKnliesc 231
                                         +   d +++R  + +   GL++ v+++cae l+ +l+ y+++++++c
  gene1881|gene1881|rna1880|rna1880 117 RMIAKDEVKERFRECSIGLGLSNDVEKECAEHLKKGLQIYIQKIVNRC 164
                                        56778999*************************************999 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       1.1   9.7e+03      27      39 ..       5      17 ..       3      21 .. 0.63
   2 ?   11.5   0.6   2.5e-05      0.22       4      30 ..     145     171 ..     143     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
                                       HHHHS---S---X CS
                                Gin 27 ivntevddpkYef 39
                                       i +  +d+ kY+ 
  gene1881|gene1881|rna1880|rna1880  5 IKTFIIDNFKYKI 17
                                       5555677888875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.5e-05
                                        T--EESSEE-SSS--EEHHHHHHHHHH CS
                                Gin   4 CekekeeGiiilgkfICeeCekkivnt 30 
                                        C ++ ++G+ i+ ++I ++C++ki+ t
  gene1881|gene1881|rna1880|rna1880 145 CAEHLKKGLQIYIQKIVNRCNRKITIT 171
                                        999*********************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1099.93
//
Query:       gene1882|gene1882|rna1881|rna1881  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-07   29.4   0.3    1.1e-06   28.6   0.3    1.4  1  RNase_PH_C  3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
        0.1   13.1   0.1        1.8    9.1   0.1    2.1  1  RNase_PH    3' exoribonuclease family, domain 1


Domain annotation for each model (and alignments):
>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   1.2e-10   1.1e-06       2      62 ..     161     222 ..     160     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.2e-10
                                        --EEEEEEEETTE.EEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHH CS
                         RNase_PH_C   2 pviavtvgkvddq.fvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaie 62 
                                        ++++ tv+++++  fv+Dpt+ Ee+ s g + +++++ ++ +  + eg   +d+e +++ i+
  gene1882|gene1882|rna1881|rna1881 161 IPVSKTVALFNNGyFVVDPTMIEEEASCGLMHVFISNEGKLMGCLSEGNCDIDQEVFVNIIK 222
                                        78999*****8655**********************999996766666666*******9998 PP

>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0002       1.8       3     123 ..      31     137 ..      29     146 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0002
                                        EEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHH CS
                           RNase_PH   3 RslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeie 77 
                                        R+ ++    ++q +GS++++ G  ++  s++   +++  +   ++++g+  +  +   + s e+        + i+
  gene1882|gene1882|rna1881|rna1881  31 RKAHVICSSIAQGDGSVRVKRGWSEIEISIQFKETPE--TLGaSNVPGE-ILGSNELYMESIEF--------SKIA 95 
                                        5556666667777777777777777777777777552..2222444443.33333344555555........4455 PP

                                        HHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHH CS
                           RNase_PH  78 lsrlleralrpsillekkpkstididitvlssdggslldalinaas 123
                                        + +++++ +++++  + + k  i++   +ls+dg +++d+ ++++s
  gene1882|gene1882|rna1881|rna1881  96 IPKIITSKILELL--SSY-KVGIRVEFSILSNDG-NIYDLFFIGLS 137
                                        5555555555544..455.389999999999999.99999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1353.70
//
Query:       gene189|gene189|rna189|rna189  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.1   0.0      0.089   12.1   0.0    2.0  2  CPSF_A    CPSF A subunit region
      0.058   13.6   0.1       0.12   12.6   0.1    1.5  1  HALZ      Homeobox associated leucine zipper
      0.076   13.1   0.3       0.14   12.2   0.3    1.4  1  DivIVA    DivIVA protein
        0.1   12.5   0.0        8.3    6.4   0.0    2.6  2  DUF4907   Domain of unknown function (DUF4907)
       0.14   12.2   0.0       0.34   10.9   0.0    1.6  1  Prp19     Prp19/Pso4-like
       0.19   11.3   1.1       0.35   10.5   1.1    1.4  1  PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-te


Domain annotation for each model (and alignments):
>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.42   1.2e+03     223     223 ..     215     215 ..     130     289 .. 0.49
   2 ?   12.1   0.0     3e-05     0.089      87     127 ..     315     354 ..     264     373 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.42
                                    E CS
                         CPSF_A 223 e 223
                                    +
  gene189|gene189|rna189|rna189 215 T 215
                                    2 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3e-05
                                    EEEES----EEEETTEEEEE-SSEEEEEEE-TTS-EEEEEE CS
                         CPSF_A  87 eevkgavtalaefqGrllvgvgqkvrvydlgedktLlrkaf 127
                                     e+kg++ +l  ++ +llvg+ + v+++dl+e+k+ +r   
  gene189|gene189|rna189|rna189 315 IEQKGTILSLGFIRSHLLVGQPEGVMIWDLEEKKS-MRIQI 354
                                    5789******************************4.44444 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.1e-05      0.12       9      31 ..      12      34 ..       7      37 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                           HALZ  9 vLKasYdaLksdydsLkkenekL 31
                                   + K++Yd   +++ sL++en +L
  gene189|gene189|rna189|rna189 12 AIKQQYDTIMAENRSLRQENVRL 34
                                   34555555555555555555555 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   4.7e-05      0.14      23      60 ..       6      43 ..       3      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXX CS
                         DivIVA 23 VdeFLdqvakdyeallkeneelkekvkeleeklkeyke 60
                                   ++++Ld + ++y +++ en++l+++  +l e+ ++y+ 
  gene189|gene189|rna189|rna189  6 IEAYLDAIKQQYDTIMAENRSLRQENVRLVEANSQYAR 43
                                   579*********************99999888888765 PP

>> DUF4907  Domain of unknown function (DUF4907)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0028       8.3       4      38 ..      36      70 ..      33      78 .. 0.83
   2 ?    3.3   0.0     0.026        78       3      21 ..     240     258 ..     238     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                        DUF4907  4 qvegGyGYqIllnekvlIkQpfIPaisgkkpFkte 38
                                   + ++ y  +I++ ++++ +Q++IP+ +  ++F + 
  gene189|gene189|rna189|rna189 36 EANSQYARKIQYYTSLMNRQKHIPSSDPGSSFIRA 70
                                   567778889****************9999999665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                        DUF4907   3 fqvegGyGYqIllnekvlI 21 
                                    +  +gG+ Y ++  +k+lI
  gene189|gene189|rna189|rna189 240 VSPDGGFVYAVVNRNKILI 258
                                    6779*************99 PP

>> Prp19  Prp19/Pso4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.34       5      31 ..       6      32 ..       4      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Prp19  5 iPslLstlqnEWDalmletfelrkqle 31
                                   i ++L ++++++D +m e+ +lr+++ 
  gene189|gene189|rna189|rna189  6 IEAYLDAIKQQYDTIMAENRSLRQENV 32
                                   668899******************875 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   0.00012      0.35      14      30 .]      21      37 ..      21      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                       PikAIV_N 14 LkEnERLRqqNrrLtAA 30
                                   + En  LRq+N rL++A
  gene189|gene189|rna189|rna189 21 MAENRSLRQENVRLVEA 37
                                   67*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2308.83
//
Query:       gene19|gene19|rna19|rna19  [L=668]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-05   22.6   5.0    5.4e-05   22.6   5.0    4.7  6  DUF3450       Protein of unknown function (DUF3450)
     0.0078   16.2   0.7     0.0078   16.2   0.7    3.1  4  ExsD          Antiactivator protein ExsD
  ------ inclusion threshold ------
      0.024   14.7  45.8      0.069   13.2   7.8    4.8  5  ADIP          Afadin- and alpha -actinin-Binding
      0.049   13.4  54.8      0.021   14.6   7.5    5.4  5  DUF4201       Domain of unknown function (DUF4201)
       0.23   10.3  58.5       0.81    8.5   8.8    4.7  5  Spc7          Spc7 kinetochore protein
       0.49   10.8  13.0       0.87   10.0   0.3    5.2  5  LPP           Lipoprotein leucine-zipper
        1.9    9.0  63.4        0.2   12.2   7.8    5.5  5  APG6_N        Apg6 coiled-coil region
          5    7.3  18.7       0.37   11.0   1.2    4.4  5  SesA          N-terminal domain on NACHT_NTPase and P-loop NT
        5.1    7.4  44.8       0.13   12.6   6.4    5.3  6  DUF4164       Domain of unknown function (DUF4164)
        6.4    6.9  54.6       0.14   12.4   6.7    4.3  4  ATG16         Autophagy protein 16 (ATG16)


Domain annotation for each model (and alignments):
>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   5.0     3e-08   5.4e-05      16      88 ..      88     160 ..      78     165 .. 0.93
   2 ?    1.0   0.9      0.12   2.2e+02      44      88 ..     200     244 ..     178     250 .. 0.60
   3 ?    1.6   3.3     0.079   1.4e+02      39     107 ..     209     277 ..     204     282 .. 0.76
   4 ?    3.4   2.0     0.022        39      23      71 ..     256     304 ..     248     312 .. 0.79
   5 ?    2.7   5.2     0.036        64      50     114 ..     340     408 ..     316     442 .. 0.52
   6 ?   -0.8   0.2      0.43   7.7e+02      24      51 ..     611     638 ..     592     657 .. 0.44

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3e-08
                    DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                  l+++ +e+++ v+++++  ++i k+++ek++l+ +++++++ le l+  n++l+r++++q+++i+  +e+ 
  gene19|gene19|rna19|rna19  88 RVLKDVSQEKSELVKNEEKYKERIRKMNEEKESLEIKINKMESDLEFLNRGNQELSRIIRDQKNKIQAFKEKA 160
                                56899**************************************************************999876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                    DUF3450  44 dekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                +  +e   e+ +l++e+++ e ++e+l++ + s+e++ + l++++
  gene19|gene19|rna19|rna19 200 EYMKERGGEIGRLRDEAKQGEEERERLSKKIVSLEKNNELLRKKL 244
                                555555556666666666666666666666666665555555444 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.079
                    DUF3450  39 idklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmid 107
                                i +l de+++ ++e ++l++++ sle+ ne l++ ++  e+ i   + +++++   e++++  +ekm +
  gene19|gene19|rna19|rna19 209 IGRLRDEAKQGEEERERLSKKIVSLEKNNELLRKKLEMKESAIGVCNSELSKLISKEKRIENEIEKMKE 277
                                667888888888888888888888888888888888888888887777777777777777777777655 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.022
                    DUF3450  23 keaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqle 71 
                                +e +k ++++++++++i+k+++ ++ +++ y+a ++++e l+ + +++ 
  gene19|gene19|rna19|rna19 256 SELSKLISKEKRIENEIEKMKERASYYERLYKATNSQNEYLNRQLSKMI 304
                                5667888899999999999999999999999999999998877766654 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.036
                    DUF3450  50 laeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel....vpllekmidrLeqfve 114
                                l+++++ ++++ + +  ne+++  ++++ +e+++l+ + ++++e +++     + ++e+++++ e++ e
  gene19|gene19|rna19|rna19 340 LKRIKRYRKRIHDQKRINEKQRIEIQDLSREVERLRDEVSRLQEERTKAinanSKIMEELMSKVERLLE 408
                                344444444444444444444444444444444444444444333332211113344444444444444 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 0.43
                    DUF3450  24 eaekavaaaaqsqkkidklddekqella 51 
                                  +++ a +++  k  d+l+  k++ + 
  gene19|gene19|rna19|rna19 611 MLKRTDALQEKFDKLEDHLNAIKNSDKV 638
                                3333333333333333333333333333 PP

>> ExsD  Antiactivator protein ExsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   4.3e-06    0.0078      94     187 ..     106     201 ..     101     207 .. 0.85
   2 ?   -1.1   0.3      0.79   1.4e+03     133     169 ..     253     288 ..     212     311 .. 0.49
   3 ?   -1.0   1.9      0.75   1.3e+03     111     172 ..     335     390 ..     318     416 .. 0.56
   4 ?   -3.1   0.0       3.4   6.1e+03     199     217 ..     621     632 ..     597     654 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.3e-06
                       ExsD  94 lldqeiltlsvkveeLeiqinqleikkefWsklaEkessqireqllklveslq..tklkaq.kaelvelesklkeseklvveaW 174
                                + ++ i ++ +++e Lei+in++e   ef ++ + + s +ir+q  k ++  +  + l+++  + +  ++++l+   k++ e+ 
  gene19|gene19|rna19|rna19 106 KYKERIRKMNEEKESLEIKINKMESDLEFLNRGNQELSRIIRDQKNK-IQAFKekADLEKRnCDSFRSINGELEILRKKALEKC 188
                                567789999***********************888899999999888.8876611556544157899***************** PP

                       ExsD 175 Pnfqkslsnlkel 187
                                 +++k++  lke+
  gene19|gene19|rna19|rna19 189 DVYEKEIGVLKEY 201
                                **********998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.79
                       ExsD 133 qireqllklveslqtklkaqkaelvelesklkesekl 169
                                 + ++l k + s + ++++++++++e +s  ++  k+
  gene19|gene19|rna19|rna19 253 VCNSELSK-LISKEKRIENEIEKMKERASYYERLYKA 288
                                34444444.3333444555554444444433333333 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.75
                       ExsD 111 iqinqleikkefWsklaEkessqireqllklveslqtklkaqkaelvelesklkeseklvve 172
                                + +n l+ +k++ +++ +   ++i e++  ++++l  +++   +e+  l++    + +++++
  gene19|gene19|rna19|rna19 335 VEQNDLKRIKRYRKRIHD--QKRINEKQRIEIQDLSREVERLRDEVSRLQE----ERTKAIN 390
                                667888888888777654..4567777777777776554444444333332....2222222 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 3.4
                       ExsD 199 aLeelWdalitlendleaa 217
                                  +       +le++l+a+
  gene19|gene19|rna19|rna19 621 KFD-------KLEDHLNAI 632
                                111.......122222221 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   7.8   3.9e-05     0.069      38     118 ..      87     167 ..      54     204 .. 0.76
   2 ?   11.0   7.0   0.00018      0.33      59     124 ..     213     278 ..     210     283 .. 0.94
   3 ?    6.2   1.2    0.0057        10      60     108 ..     256     304 ..     254     310 .. 0.82
   4 ?    4.7   7.2     0.017        30      50     112 ..     338     401 ..     334     421 .. 0.78
   5 ?    2.6   0.3     0.071   1.3e+02     101     145 ..     605     649 ..     581     655 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                       ADIP  38 inviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeel 118
                                + v+ ++ q +++  + +e+++e+irk++ e+e+l+ ki++++  le l r ++ + +  r+++ k+++ ++k+  ek+  
  gene19|gene19|rna19|rna19  87 MRVLKDVSQEKSELVKNEEKYKERIRKMNEEKESLEIKINKMESDLEFLNRGNQELSRIIRDQKNKIQAFKEKADLEKRNC 167
                                444444444455555677888888888888888888888888888888888888888888888888888888888877655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00018
                       ADIP  59 netirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkna 124
                                 ++ ++ e e erl++ki +l++++e l+++l+  +++    + +l +l++k k+   e++++k  
  gene19|gene19|rna19|rna19 213 RDEAKQGEEERERLSKKIVSLEKNNELLRKKLEMKESAIGVCNSELSKLISKEKRIENEIEKMKER 278
                                57789999*******************************************************975 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0057
                       ADIP  60 etirkleaeierlqskierlktqleqlerelalvqakerqlekklktle 108
                                 +++kl +  +r +++ie++k++ + +er  ++ +++   l+++l + +
  gene19|gene19|rna19|rna19 256 SELSKLISKEKRIENEIEKMKERASYYERLYKATNSQNEYLNRQLSKMI 304
                                5567777888899999999999999999999999999999999988765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.017
                       ADIP  50 rdleqreslnetirkleaeierlqskierlktqleqlerela.lvqakerqlekklktleqklk 112
                                 dl+  + + ++i++ +  +e+++ +i+ l++++e+l+ e++ l++++++ ++++ k  e+ + 
  gene19|gene19|rna19|rna19 338 NDLKRIKRYRKRIHDQKRINEKQRIEIQDLSREVERLRDEVSrLQEERTKAINANSKIMEELMS 401
                                56666677889999999999999999**************998888888888887766555544 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.071
                       ADIP 101 ekklktleqklknekeelqrlknalqqiktqyahelkkkdreiek 145
                                + +l +  + +  ++e++ +l+  l +ik++ +++  k   +i+ 
  gene19|gene19|rna19|rna19 605 TSTLHEMLKRTDALQEKFDKLEDHLNAIKNSDKVDAEKVHDQIKA 649
                                233333333333444444444444444444444444444444443 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4  12.1      0.46   8.3e+02      67     170 ..      78     179 ..      76     186 .. 0.76
   2 ?    8.9   6.0   0.00064       1.1      84     139 ..     186     241 ..     150     242 .. 0.89
   3 ?    4.3   5.7     0.016        30      82     138 ..     240     296 ..     238     312 .. 0.87
   4 ?   14.6   7.5   1.2e-05     0.021      74     135 ..     338     399 ..     334     421 .. 0.91
   5 ?    4.5   0.4     0.015        26      90     133 ..     605     649 ..     594     663 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.46
                    DUF4201  67 rlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdkt 150
                                ++++ + + + +l+++ +  ++l ++ ++ k+++++++e++++l+ +++k + + + l + n++l++   + ++ ++   ++++
  gene19|gene19|rna19|rna19  78 KMSLVCESLMRVLKDVSQEKSELVKNEEKYKERIRKMNEEKESLEIKINKMESDLEFLNRGNQELSRIIRD-QKNKIQA-FKEK 159
                                78888888899999999999999999999999999999999999999999999999999999998876666.6666665.6666 PP

                    DUF4201 151 kekveekrksvkkLrrkvki 170
                                 +  +   +s +++  +++i
  gene19|gene19|rna19|rna19 160 ADLEKRNCDSFRSINGELEI 179
                                66555555555555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00064
                    DUF4201  84 eklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllr 139
                                ek + +e+e   lk+ +ke+  ++ +lr+e  + ++er++l k+   l++ ++llr
  gene19|gene19|rna19|rna19 186 EKCDVYEKEIGVLKEYMKERGGEIGRLRDEAKQGEEERERLSKKIVSLEKNNELLR 241
                                66779999********************************************9997 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.016
                    DUF4201  82 lkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggll 138
                                l++kl m es    +++el+++  ++++++ e++k k++ + +++ ++  ++q++ l
  gene19|gene19|rna19|rna19 240 LRKKLEMKESAIGVCNSELSKLISKEKRIENEIEKMKERASYYERLYKATNSQNEYL 296
                                799999999999999999999999999999999999999999999999988888765 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 1.2e-05
                    DUF4201  74 ktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqg 135
                                +++++++ ++++ h  ++ +++++ e++++ ++ ++lr+e++++++er+k+ + n+k+ +++
  gene19|gene19|rna19|rna19 338 NDLKRIKRYRKRIHDQKRINEKQRIEIQDLSREVERLRDEVSRLQEERTKAINANSKIMEEL 399
                                89999***************************************************997765 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.015
                    DUF4201  90 eselselkkelkekeerlaklrkelykvkl.erdklrkqneklkq 133
                                +s+l+e+ k+++ ++e+ +kl+++l+  k+ ++  ++k ++++k+
  gene19|gene19|rna19|rna19 605 TSTLHEMLKRTDALQEKFDKLEDHLNAIKNsDKVDAEKVHDQIKA 649
                                788999999999999999999999999986245566666766665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  12.6    0.0021       3.9     136     262 ..      45     172 ..      43     176 .. 0.76
   2 ?    8.5   8.8   0.00045      0.81     177     281 ..     171     271 ..     167     275 .. 0.82
   3 ?    0.6   5.2      0.11     2e+02     203     250 ..     239     286 ..     235     299 .. 0.80
   4 ?    4.9  14.2    0.0056        10     148     253 ..     293     392 ..     278     416 .. 0.47
   5 ?    7.2   0.2    0.0011         2     165     213 ..     604     652 ..     588     660 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0021
                       Spc7 136 llegLkegleenleglee.dkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieek 218
                                ll +L+++++e+ ++l + d+e L++   + d  +  + e   ++ + + +++++  + e+  ke+++++ ee ++l+ +i++ 
  gene19|gene19|rna19|rna19  45 LLTSLQNVYNEINTNLVAgDNEGLKNVILNSDVKMSLVCESLMRVLKDVSQEKSELVKNEEKYKERIRKMNEEKESLEIKINKM 128
                                6777777777776666433777777776666555555555555555555555555555566679******************** PP

                       Spc7 219 kkelaelqeqleeleekieelkeqkseleeeiaeaervleeckg 262
                                + +l+ l++  +el+  i + k++++ ++e+   ++r ++  ++
  gene19|gene19|rna19|rna19 129 ESDLEFLNRGNQELSRIIRDQKNKIQAFKEKADLEKRNCDSFRS 172
                                ******************************99988888877665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00045
                       Spc7 177 aeleeeleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                 +++ ele l+++a  le++d  ++e+  l+e ++e   ei ++++e ++ +e++e+l++ki +l+++ + l+++++ +e+ + 
  gene19|gene19|rna19|rna19 171 RSINGELEILRKKA--LEKCDvyEKEIGVLKEYMKERGGEIGRLRDEAKQGEEERERLSKKIVSLEKNNELLRKKLEMKESAI- 251
                                57788999999966..66777769*****************************************999999999999666555. PP

                       Spc7 259 eckgwsesevsrlkeevkaleel 281
                                   g+ +se+s+l ++ k++e++
  gene19|gene19|rna19|rna19 252 ---GVCNSELSKLISKEKRIENE 271
                                ...55566777777666666665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.11
                       Spc7 203 elreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeei 250
                                 lr++l+  ++ i   + el++l ++ +++e++ie++ke+ s +e   
  gene19|gene19|rna19|rna19 239 LLRKKLEMKESAIGVCNSELSKLISKEKRIENEIEKMKERASYYERLY 286
                                589999999999999999999999999999999999988877666544 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.0056
                       Spc7 148 legleedkelLekqeeel..dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                 e l+++ +++ ++ +++   e+ p+ +ee +++++e    ++  + +e+ d ++++ +r+++ ++k   e+++ e+++l +++
  gene19|gene19|rna19|rna19 293 NEYLNRQLSKMIRDTDKIeiPEYDPNAQEEMTAISNE----KN-GNGVEQNDLKRIKRYRKRIHDQKRINEKQRIEIQDLSREV 371
                                4444444444333333331133444444444433333....33.3345556666666666666666666666666666666666 PP

                       Spc7 230 eeleekieelkeqkseleeeiaea 253
                                e+l+++++ l+e+++++   i++ 
  gene19|gene19|rna19|rna19 372 ERLRDEVSRLQEERTKA---INAN 392
                                66666666665555432...2222 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0011
                       Spc7 165 ldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                                 ++ l+e+ ++ ++l+e+++kl++  + ++++dk + e++++++++ k+
  gene19|gene19|rna19|rna19 604 TTSTLHEMLKRTDALQEKFDKLEDHLNAIKNSDKVDAEKVHDQIKAYKN 652
                                577899999*********************************9998776 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.073   1.3e+02       1      37 [.     124     160 ..     110     161 .. 0.83
   2 ?    0.9   0.0      0.35   6.2e+02       6      29 ..     255     278 ..     251     281 .. 0.79
   3 ?   -3.1   0.1       5.9   1.1e+04      10      26 ..     294     310 ..     290     312 .. 0.65
   4 ?   10.0   0.3   0.00048      0.87       2      36 ..     364     398 ..     363     406 .. 0.83
   5 ?    1.1   0.1      0.29   5.2e+02      11      28 ..     617     634 ..     608     650 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.073
                        LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                k++++ s+++ L++  ++ls  + + k+ +qa ke A
  gene19|gene19|rna19|rna19 124 KINKMESDLEFLNRGNQELSRIIRDQKNKIQAFKEKA 160
                                6788888888888888888888999999999988877 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
                        LPP   6 ssqVsqLkskvdqlssdvnsakaa 29 
                                +s++s+L sk + ++++++++k+ 
  gene19|gene19|rna19|rna19 255 NSELSKLISKEKRIENEIEKMKER 278
                                578888888888999998888865 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.9
                        LPP  10 sqLkskvdqlssdvnsa 26 
                                + L+++ +++  d++++
  gene19|gene19|rna19|rna19 294 EYLNRQLSKMIRDTDKI 310
                                55777777777776654 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.00048
                        LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                ++ Ls +V++L ++v+ l+++ ++a +a  ++ eE
  gene19|gene19|rna19|rna19 364 IQDLSREVERLRDEVSRLQEERTKAINANSKIMEE 398
                                6789***************9977777666666665 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.29
                        LPP  11 qLkskvdqlssdvnsaka 28 
                                +L++k+d+l++ +n++k+
  gene19|gene19|rna19|rna19 617 ALQEKFDKLEDHLNAIKN 634
                                688888888888887764 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  12.0     0.015        28      49     120 ..      90     161 ..      53     178 .. 0.77
   2 ?   10.3   5.8   0.00041      0.74      20      89 ..     183     249 ..     175     257 .. 0.89
   3 ?    2.8   3.6     0.086   1.5e+02      69     122 ..     257     310 ..     254     314 .. 0.70
   4 ?   12.2   7.8   0.00011       0.2      24     109 ..     339     424 ..     334     436 .. 0.88
   5 ?    2.6   1.4       0.1   1.9e+02       9      48 ..     606     642 ..     603     657 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.015
                     APG6_N  49 leeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeld 120
                                l++  +e ++l k ee+  e ++++ +e+e+le ++++ e+ le l++ +++  r  ++++ + + ++e+ d
  gene19|gene19|rna19|rna19  90 LKDVSQEKSELVKNEEKYKERIRKMNEEKESLEIKINKMESDLEFLNRGNQELSRIIRDQKNKIQAFKEKAD 161
                                456667777777777777788888888888888888888888887777777777777777777777776655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00041
                     APG6_N  20 qaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaalee 89 
                                +a +++d Ye+    lk++ ke      e+ +l++e ++ e+e+e+l +++  lek++e l+++l+  e+
  gene19|gene19|rna19|rna19 183 KALEKCDVYEKEIGVLKEYMKERG---GEIGRLRDEAKQGEEERERLSKKIVSLEKNNELLRKKLEMKES 249
                                567899999999999999987766...7*************************************98876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.086
                     APG6_N  69 eLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsl 122
                                eL +l ++++++e+e+++ +e ++  e+  ++  ++   l+++l+++  + d++
  gene19|gene19|rna19|rna19 257 ELSKLISKEKRIENEIEKMKERASYYERLYKATNSQNEYLNRQLSKMIRDTDKI 310
                                677777777777777777777777777777777777777777777776666655 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.00011
                     APG6_N  24 erdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne 107
                                + +  +++ k+++++k+ +ekq+ e+++l +e+e+l++e ++l+ee  ++ ++++++ +el +  e l ++++e +  + e + 
  gene19|gene19|rna19|rna19 339 DLKRIKRYRKRIHDQKRINEKQRIEIQDLSREVERLRDEVSRLQEERTKAINANSKIMEELMSKVERLLEKNREYQGIIYELRG 422
                                566778899999999999999*****************************************9999999999999888877766 PP

                     APG6_N 108 lq 109
                                 +
  gene19|gene19|rna19|rna19 423 RD 424
                                55 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.1
                     APG6_N   9 lLleeldkqleqaekerdaYeeflkklkkekkeeekqdee 48 
                                + l e+ k+ ++++++ d++e+ l+ +k+++k +    e+
  gene19|gene19|rna19|rna19 606 STLHEMLKRTDALQEKFDKLEDHLNAIKNSDKVDA---EK 642
                                67889999999999999999999999998865533...22 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.2   0.00021      0.37       1      78 [.      39     123 ..      39     164 .. 0.80
   2 ?   -0.8   0.6      0.94   1.7e+03      33      86 ..     242     292 ..     224     311 .. 0.59
   3 ?   -1.1   0.1       1.2   2.1e+03      86     109 ..     337     363 ..     321     374 .. 0.69
   4 ?    0.2   1.4      0.44   7.9e+02      75     115 ..     363     403 ..     336     413 .. 0.67
   5 ?    5.2   0.0     0.013        24       7      40 ..     601     634 ..     596     637 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                       SesA   1 isstiaiveaaiklydaikd......ikglpeaFrevgkrLplvqetLedaksqlesskldedtesa.ikpvlesckekatkle 77 
                                iss+i+++++++ +y++i++       +gl++ + +   +  lv+e L ++ + ++++k++  ++++  k+ +++ +e+ ++le
  gene19|gene19|rna19|rna19  39 ISSLITLLTSLQNVYNEINTnlvagdNEGLKNVILNSDVKMSLVCESLMRVLKDVSQEKSELVKNEEkYKERIRKMNEEKESLE 122
                                8************************99****************************99999887666667888887777666666 PP

                       SesA  78 e 78 
                                 
  gene19|gene19|rna19|rna19 123 I 123
                                4 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.94
                       SesA  33 krLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapa 86 
                                k+L++ + +   ++s+l++  ++e+    i++ +e+ ke+a   e++ ++++ +
  gene19|gene19|rna19|rna19 242 KKLEMKESAIGVCNSELSKLISKEK---RIENEIEKMKERASYYERLYKATNSQ 292
                                5555555555555555555555543...26677777777777776666666333 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.2
                       SesA  86 apadsrleryrkavrs...lgkgskVE 109
                                +++ +r++ryrk +     +++++++E
  gene19|gene19|rna19|rna19 337 QNDLKRIKRYRKRIHDqkrINEKQRIE 363
                                445588889988865444477777777 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.44
                       SesA  75 kleeifekvapapad.srl.eryrkavrslgkgskVEtLmkgi 115
                                +++++ ++v++ +++ srl e+ +ka+    + + +E+Lm+++
  gene19|gene19|rna19|rna19 363 EIQDLSREVERLRDEvSRLqEERTKAINA--NSKIMEELMSKV 403
                                56777777755555557775555555444..667777777765 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.013
                       SesA   7 iveaaiklydaikdikglpeaFrevgkrLplvqe 40 
                                 v+++++l++ +k +  l+e+F++ +++L  +++
  gene19|gene19|rna19|rna19 601 TVRTTSTLHEMLKRTDALQEKFDKLEDHLNAIKN 634
                                5789999**********************99986 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.6   1.2e+04      63      79 ..      47      63 ..      46      66 .. 0.82
   2 ?   12.6   6.4   7.3e-05      0.13      20      85 ..      90     155 ..      84     158 .. 0.93
   3 ?    8.5   5.6    0.0013       2.3       6      68 ..     219     285 ..     214     300 .. 0.83
   4 ?    0.7   9.0      0.37   6.6e+02      26      74 ..     353     405 ..     337     413 .. 0.71
   5 ?   -0.1   0.2      0.66   1.2e+03      15      52 ..     394     433 ..     386     434 .. 0.79
   6 ?    2.0   0.2      0.15   2.6e+02       9      32 ..     614     637 ..     604     651 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.6
                    DUF4164 63 arleevnrEvsrrLkaa 79
                               ++l++v +E++ +L+a 
  gene19|gene19|rna19|rna19 47 TSLQNVYNEINTNLVAG 63
                               67999999999999875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.3e-05
                    DUF4164  20 LEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietira 85 
                                L + ++++ e  +++++++++i++++e+++ L+ ++ + e  ++ l+++n+E+sr +    ++i+a
  gene19|gene19|rna19|rna19  90 LKDVSQEKSELVKNEEKYKERIRKMNEEKESLEIKINKMESDLEFLNRGNQELSRIIRDQKNKIQA 155
                                778899999999*******************************************99998888876 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0013
                    DUF4164   6 leaaltrLeaaldsLEka...vdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleev 68 
                                 e+  +rL++++ sLEk    + ++le +++  +  ++e+++l + ++R+++e+ + + ra++ e++
  gene19|gene19|rna19|rna19 219 GEEERERLSKKIVSLEKNnelLRKKLEMKESAiGVCNSELSKLISKEKRIENEIEKMKERASYYERL 285
                                567789**********86222677787777667999*************************998876 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.37
                    DUF4164  26 rrleaerkr...deleaeiealgedrsRLaeeLdqaearaar.leevnrEvsr 74 
                                +++ +e++r   ++l +e+e+l+++ sRL ee ++a + +++ +ee+ + v r
  gene19|gene19|rna19|rna19 353 QKRINEKQRieiQDLSREVERLRDEVSRLQEERTKAINANSKiMEELMSKVER 405
                                44444444458899***************999888866554415555555555 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.66
                    DUF4164  15 aaldsLEkavdrrleaerkrdeleaei..ealgedrsRLa 52 
                                + +++L + v+r le++r+ + +  e+  + ++ed+ R +
  gene19|gene19|rna19|rna19 394 KIMEELMSKVERLLEKNREYQGIIYELrgRDMKEDKGRVD 433
                                5678889999999999999988777776688999998865 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.15
                    DUF4164   9 altrLeaaldsLEkavdrrleaer 32 
                                 ++ L++++d+LE+ +++  ++++
  gene19|gene19|rna19|rna19 614 RTDALQEKFDKLEDHLNAIKNSDK 637
                                456799999999998876555544 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   6.7   7.9e-05      0.14      76     148 ..      83     155 ..      47     162 .. 0.89
   2 ?    3.3   9.4     0.045        81      76     151 ..     202     277 ..     178     311 .. 0.79
   3 ?    1.7  13.2      0.14   2.5e+02     119     191 ..     337     409 ..     320     414 .. 0.87
   4 ?    6.4   2.0    0.0053       9.5      59     127 ..     579     645 ..     536     653 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                      ATG16  76 iqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                ++sl   l+ + +e +el k  ++ ++r++++nee + le k++++e+ l+ l++ +++l++ ++d++++++ 
  gene19|gene19|rna19|rna19  83 CESLMRVLKDVSQEKSELVKNEEKYKERIRKMNEEKESLEIKINKMESDLEFLNRGNQELSRIIRDQKNKIQA 155
                                5677778889999******************************************************999875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.045
                      ATG16  76 iqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekek 151
                                +++   ++ +lr+e ++   +r+ l++++++l++  + l++kl+ +e+++   ++e ++l  k k+ e+e++  ++
  gene19|gene19|rna19|rna19 202 MKERGGEIGRLRDEAKQGEEERERLSKKIVSLEKNNELLRKKLEMKESAIGVCNSELSKLISKEKRIENEIEKMKE 277
                                5556667788999999999999999999999999999999999999999999999999998877777777665443 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.14
                      ATG16 119 kedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENkeLveRWmkr 191
                                ++d +r+++ ++++ + ++  ++++ e++++ + v+ l+DE+s Lq + ++a  ++ k+ +E  + veR++++
  gene19|gene19|rna19|rna19 337 QNDLKRIKRYRKRIHDQKRINEKQRIEIQDLSREVERLRDEVSRLQEERTKAINANSKIMEELMSKVERLLEK 409
                                5677899999999999999999999999999999999999999999999999999999999999999999876 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0053
                      ATG16  59 kekeasasq.....snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlae 127
                                +       +      +s+ +++++++++k++++ + l e++k+   l+++  +l++ l + +++ k d+e++++
  gene19|gene19|rna19|rna19 579 N-------KnfgkdAESRGESDVSTTSPKTVRTTSTLHEMLKRTDALQEKFDKLEDHLNAIKNSDKVDAEKVHD 645
                                2.......02233344667899********************************************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2885  (0.160912); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); expected 17.9 (0.001)
Passed Fwd filter:                        87  (0.00485247); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.54u 0.38s 00:00:01.92 Elapsed: 00:00:00.59
# Mc/sec: 3395.72
//
Query:       gene190|gene190|rna190|rna190  [L=479]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.5   1.0      0.045   14.3   0.1    2.1  2  PH        PH domain


Domain annotation for each model (and alignments):
>> PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.28     5e+03      28      58 ..     191     221 ..     188     244 .. 0.65
   2 ?   14.3   0.1   2.5e-06     0.045      15     104 ..     405     476 ..     383     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.28
                                    TEEEEESSTTCTTESSEEEEEESTTEEEEEE CS
                             PH  28 sellyykndksekdkepkgsislsncevvev 58 
                                    s+l++ k+++ e++++p +s+  + ++ +++
  gene190|gene190|rna190|rna190 191 SCLYIKKKEQVEEKSSPSRSVFSNPLSNSRT 221
                                    5666666666677777777777766666655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.5e-06
                                    SCSEEEEEEEEETTEEEEESSTTCTTESSEEEEEESTTEEEEEEECTTSSSSTSEEEEEESTSSSTEEEEEEESSHHHHH CS
                             PH  15 kkswkkrwfvLkdsellyykndksekdkepkgsislsncevvevvatedpkrkfcfelriverngsrtyllqasseeerk 94 
                                      +wk + f + ++ l+ y+++      +  +++ ls+c v        ++  fc+e      +g + + l+a+ e er 
  gene190|gene190|rna190|rna190 405 E-GWKAYLFKFVGKALICYEKS------RVFKILLLSGCNVLP-----VGQVAFCLEK-----SG-EGIELYATCEKERD 466
                                    2.89999999999999999999......999999999999997.....4677777776.....77.9************* PP

                                    HHHHHHHHHH CS
                             PH  95 eWikaiqsai 104
                                    +Wi++i++ i
  gene190|gene190|rna190|rna190 467 AWISDIKEYI 476
                                    ******9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2900.56
//
Query:       gene191|gene191|rna191|rna191  [L=734]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-86  289.2   4.4    1.1e-85  286.5   0.9    2.6  3  Muskelin_N      Muskelin N-terminus
    1.5e-19   69.8   4.0    8.7e-06   25.9   0.1    6.6  6  Kelch_3         Galactose oxidase, central domain
      9e-17   60.7   1.9    0.00089   19.2   0.0    5.7  6  Kelch_5         Kelch motif
    1.1e-16   60.0   2.6    3.1e-05   23.7   0.0    6.1  6  Kelch_2         Kelch motif
    1.1e-13   50.9   6.9      0.026   14.8   0.0    6.2  6  Kelch_6         Kelch motif
    9.9e-09   35.1   5.3        1.1    9.3   0.1    6.4  5  Kelch_4         Galactose oxidase, central domain
    3.4e-07   29.8   3.8    5.6e-05   22.7   0.2    5.0  6  Kelch_1         Kelch motif
    8.9e-07   29.1   0.1    3.6e-06   27.1   0.1    2.1  2  F5_F8_type_C    F5/8 type C domain
    0.00053   20.0   0.1     0.0042   17.1   0.0    2.1  2  Sad1_UNC        Sad1 / UNC-like C-terminal
  ------ inclusion threshold ------
       0.21   11.7   0.9        1.5    9.0   0.2    2.4  2  Ribosomal_L38e  Ribosomal L38e protein family


Domain annotation for each model (and alignments):
>> Muskelin_N  Muskelin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  286.5   0.9   6.2e-89   1.1e-85       4     199 .]      10     197 ..       7     197 .. 0.98
   2 ?   -2.7   0.0       2.5   4.6e+03      78     133 ..     521     576 ..     516     581 .. 0.73
   3 ?    3.1   0.1     0.042        75     121     192 ..     608     684 ..     580     691 .. 0.69

  Alignments for each domain:
  == domain 1  score: 286.5 bits;  conditional E-value: 6.2e-89
                                    E--EEEEEES---TT--GGGGG---TT-TTSSEE-S-SSS---EEEEEEEEEEEEEEEE---SS--TTSEEEEEEEEEEE CS
                     Muskelin_N   4 elsyeihsyssyssaylPenilvdkPndqnsrWsaetnseeqyliLkleksaivkkitfGkyekshvcnlkkfrvyggrd 83 
                                     ++yeihsys+y+s+y+P+ni++++P+d+nsrWs++tn++ qy+iLk++ s++v +itfGky+k+hv+n+kk+r++++ d
  gene191|gene191|rna191|rna191  10 AIPYEIHSYSTYASVYVPNNIKRNDPMDPNSRWSTSTNDHLQYIILKVPPSLVV-TITFGKYNKMHVSNVKKMRISVSED 88 
                                    69*************************************************999.9************************ PP

                                    TTEEEEEEEE---SSS--EEEE---EETT...EE--EEEEEEEEEEESSS-S--EE--EEEEEE--HHHHGGGS--XXXX CS
                     Muskelin_N  84 eeemvelLegGLkndseketfnLkvkkeekieeslaikyikivPLlawgvefnfsiWyveLrGlddasavsatlknrell 163
                                    ++e+ e+L+gGLkndse+etfnL+vk+    e + +++y+ki+PL+awgv+f++s+W+veLrG+ d   v+++++++e++
  gene191|gene191|rna191|rna191  89 GVEYKEVLCGGLKNDSEMETFNLLVKD----EAYYIAQYVKIEPLAAWGVNFSYSLWFVELRGIMD---VEKFIRYNEMI 161
                                    **************************9....789********************************...*********** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Muskelin_N 164 lekkalrlcLkyfrqkgyldifevlekktkvklehe 199
                                    ++++++r cL+++r+ g++d++e+lek++++k+e+e
  gene191|gene191|rna191|rna191 162 VFGRSMRSCLRFLRDSGFRDVYEILEKRSSDKIEDE 197
                                    **********************************86 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                    EEEEEETTEEEEEEEE---SSS--EEEE---EETT...EE--EEEE.EEEEEEESSS CS
                     Muskelin_N  78 vyggrdeeemvelLegGLkndseketfnLkvkkeekieeslaikyi.kivPLlawgv 133
                                    + g r++++++e+L   L  d++ +  ++ +  + ki +     y+  iv L ++g+
  gene191|gene191|rna191|rna191 521 IGGQRNKNSIREILFYSLDTDTVYQSVPFPINGDGKIIQR-GLLYLsEIVVLFCHGK 576
                                    4466888899999999999999999988888887777444.4444426777777776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.042
                                    EEEEEEEEEESSS-S.--EE--EEEEEE--HHH...HGGGS--XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX CS
                     Muskelin_N 121 kyikivPLlawgvef.nfsiWyveLrGlddasa...vsatlknrelllekkalrlcLkyf.rqkgyldifevlekkt 192
                                      + i PL   +++f ++  W+  + G ++  +   v+ +  +r   + +k +r + k++ r++ yl+++++ ekk+
  gene191|gene191|rna191|rna191 608 TGVDIKPLSRSAHQFiQMNGWFYLFGGNVSERTdrrVNDMWVFRLEKKTNKEIRHLSKFLvRKHKYLHLLGIDEKKA 684
                                    4589**********967999**9999998843311144444555566667778888888646777888777766665 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   4.9e-09   8.7e-06       2      45 ..     262     304 ..     261     306 .. 0.85
   2 !   15.1   0.1   1.2e-05     0.021       1      27 [.     363     389 ..     363     396 .. 0.93
   3 ?    4.8   0.1      0.02        35      16      49 .]     457     504 ..     446     504 .. 0.77
   4 ?    3.4   0.0     0.056     1e+02       1      31 [.     515     543 ..     515     550 .. 0.90
   5 ?    3.6   0.0     0.048        87      20      35 ..     586     602 ..     570     621 .. 0.74
   6 !   11.5   0.0   0.00015      0.28       4      30 ..     629     656 ..     627     663 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.9e-09
                        Kelch_3   2 drlyifGGlgddgqdrlndvyvydldtntWaei...aslppaRagha 45 
                                    ++ly++GG++  g + l d+++y  +  +W+ei   +++p+ R++h 
  gene191|gene191|rna191|rna191 262 GSLYVYGGWN--GVEELEDFWRYKDG--EWTEIkvdGRTPGKRSCHR 304
                                    579*******..***********776..56655556**********6 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.2e-05
                        Kelch_3   1 gdrlyifGGlgddgqdrlndvyvydld 27 
                                    gd+l +fGG+ + ++d ++ +y+++ld
  gene191|gene191|rna191|rna191 363 GDKLCVFGGRSTEREDIYSGLYMFSLD 389
                                    79************************7 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.02
                        Kelch_3  16 drlndvyvydldtn.....tWaei.......aslpp..aRaghaatai 49 
                                    d +n+ +++++++       W+++       +++p+   R gh++++i
  gene191|gene191|rna191|rna191 457 DESNSRHELSTSSSglvisRWTMVrsdtvqpPNTPSlkSRLGHSMVFI 504
                                    667777888887777888889955555556688899*********976 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.056
                        Kelch_3   1 gdrlyifGGlgddgqdrlndvyvydldtntW 31 
                                    +++l i+GG +  + ++  + + y+ldt+t+
  gene191|gene191|rna191|rna191 515 NNSLAIIGGQR--NKNSIREILFYSLDTDTV 543
                                    689********..99999****9***99985 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.048
                        Kelch_3  20 dvyvydldtntWaei.a 35 
                                    dvy y+l +  W+++ a
  gene191|gene191|rna191|rna191 586 DVYTYSLTRKRWTKViA 602
                                    9************7751 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 0.00015
                        Kelch_3   4 lyifGGlgddg.qdrlndvyvydldtnt 30 
                                    +y+fGG+   +   r+nd++v+ l++ t
  gene191|gene191|rna191|rna191 629 FYLFGGNVSERtDRRVNDMWVFRLEKKT 656
                                    7*******85547888********9876 PP

>> Kelch_5  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.9e-07   0.00089       1      37 [.     248     282 ..     248     283 .. 0.87
   2 !    8.4   0.0    0.0012       2.2       1      37 [.     296     336 ..     296     337 .. 0.84
   3 !   15.9   0.1   5.3e-06    0.0096       2      40 ..     351     389 ..     350     390 .. 0.92
   4 ?   -1.0   0.0       1.1   1.9e+03       4      16 ..     495     508 ..     495     540 .. 0.70
   5 ?   -3.7   0.1       7.5   1.3e+04      33      39 ..     586     592 ..     586     593 .. 0.88
   6 !   11.2   0.0   0.00016      0.29       2      40 ..     614     653 ..     614     655 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.9e-07
                        Kelch_5   1 iPppRaghcavtvsekiYvyGGkvgrdgsvsddvyvL 37 
                                    +P+ R gh ++  ++++YvyGG++g   +   d++++
  gene191|gene191|rna191|rna191 248 WPCERGGHQMAEMDGSLYVYGGWNG--VEELEDFWRY 282
                                    7***********************6..7666666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                        Kelch_5   1 iPppRaghcavtvsekiYvyGGkvg..rdgsvs..ddvyvL 37 
                                    +P  R++h ++  ++k+Y++G ++   +++ +s  +d++ +
  gene191|gene191|rna191|rna191 296 TPGKRSCHRMISNKSKLYLMGKYIPlsSRKAFSgrSDIWAF 336
                                    6999********************87667777677788865 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 5.3e-06
                        Kelch_5   2 PppRaghcavtvsekiYvyGGkvgrdgsvsddvyvLdlp 40 
                                    P  +++h +v+ ++k+ v+GG++++++++++ +y ++l 
  gene191|gene191|rna191|rna191 351 PGNIYDHQMVATGDKLCVFGGRSTEREDIYSGLYMFSLD 389
                                    6679********************999999999999985 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.1
                        Kelch_5   4 pRaghcavtvs.ek 16 
                                    +R gh++v+ + ++
  gene191|gene191|rna191|rna191 495 SRLGHSMVFIPpDY 508
                                    68899999774333 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 7.5
                        Kelch_5  33 dvyvLdl 39 
                                    dvy+++l
  gene191|gene191|rna191|rna191 586 DVYTYSL 592
                                    8****98 PP

  == domain 6  score: 11.2 bits;  conditional E-value: 0.00016
                        Kelch_5   2 PppRaghcavtvsekiYvyGGkvg.rdgsvsddvyvLdlp 40 
                                    P +R+ h ++  ++  Y++GG v+ r++   +d++v+ l+
  gene191|gene191|rna191|rna191 614 PLSRSAHQFIQMNGWFYLFGGNVSeRTDRRVNDMWVFRLE 653
                                    7888888888889999********************9885 PP

>> Kelch_2  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.8e-08   3.1e-05       2      41 ..     252     288 ..     251     288 .. 0.96
   2 !    6.6   0.0    0.0046       8.2       2      28 ..     300     323 ..     299     342 .. 0.79
   3 !    5.8   0.0    0.0079        14       3      20 ..     355     372 ..     354     397 .. 0.81
   4 ?   -3.1   0.0       5.3   9.5e+03       4      34 ..     498     535 ..     496     541 .. 0.55
   5 ?    4.7   0.0     0.018        32      29      46 ..     584     601 ..     575     604 .. 0.86
   6 !   13.1   0.0   3.9e-05     0.071       2      41 ..     617     656 ..     616     656 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.8e-08
                        Kelch_2   2 rgghsssvpggkiyvvGGahtdnpnlsssdvhvldlekhv 41 
                                    rggh ++ ++g +yv+GG+   n+++  +d++ + +++++
  gene191|gene191|rna191|rna191 252 RGGHQMAEMDGSLYVYGGW---NGVEELEDFWRYKDGEWT 288
                                    89*****************...**************9995 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0046
                        Kelch_2   2 rgghsssvpggkiyvvGGahtdnpnls 28 
                                    r++h + +  +k+y++G +    p++s
  gene191|gene191|rna191|rna191 300 RSCHRMISNKSKLYLMGKY---IPLSS 323
                                    99****************9...55554 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0079
                        Kelch_2   3 gghsssvpggkiyvvGGa 20 
                                    + h ++  g+k++v+GG+
  gene191|gene191|rna191|rna191 355 YDHQMVATGDKLCVFGGR 372
                                    67999999*********9 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5.3
                        Kelch_2   4 ghsssvp..........ggkiyvvGGahtdnpnlsssdvhv 34 
                                    ghs++ +          ++ + ++GG     +  s++ + +
  gene191|gene191|rna191|rna191 498 GHSMVFIppdyiegsiyNNSLAIIGGQ---RNKNSIREILF 535
                                    666666556666555556666677775...55555555555 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.018
                        Kelch_2  29 ssdvhvldlekhvWeevt 46 
                                    s+dv+++ l  ++W++v 
  gene191|gene191|rna191|rna191 584 SIDVYTYSLTRKRWTKVI 601
                                    79*************986 PP

  == domain 6  score: 13.1 bits;  conditional E-value: 3.9e-05
                        Kelch_2   2 rgghsssvpggkiyvvGGahtdnpnlsssdvhvldlekhv 41 
                                    r+ h +  ++g+ y++GG  +  +++  +d++v++lek++
  gene191|gene191|rna191|rna191 617 RSAHQFIQMNGWFYLFGGNVSERTDRRVNDMWVFRLEKKT 656
                                    778888999****************************985 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.1   1.1e+04      37      46 ..     236     245 ..     233     247 .. 0.80
   2 !   14.8   0.0   1.5e-05     0.026       4      43 ..     254     290 ..     248     300 .. 0.88
   3 !   10.9   0.0   0.00024      0.44       4      23 ..     356     375 ..     354     390 .. 0.78
   4 !    8.3   0.0    0.0016       2.9       9      46 ..     513     550 ..     496     554 .. 0.86
   5 ?   -0.7   0.1       1.1   1.9e+03      28      43 ..     585     600 ..     582     602 .. 0.88
   6 !   14.7   0.0   1.5e-05     0.027       2      39 ..     617     656 ..     616     669 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.1
                        Kelch_6  37 tksWeqlppl 46 
                                    t +W+++p+ 
  gene191|gene191|rna191|rna191 236 TLVWTEIPRT 245
                                    779****985 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.5e-05
                        Kelch_6   4 ghslvsvggkiYifGGytdsspylnkvwvydpetksWeql 43 
                                    gh+++ ++g++Y++GG+++  + l ++w+y  +++ W+++
  gene191|gene191|rna191|rna191 254 GHQMAEMDGSLYVYGGWNG-VEELEDFWRY--KDGEWTEI 290
                                    79*****************.78899****9..88888875 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00024
                        Kelch_6   4 ghslvsvggkiYifGGytds 23 
                                     h++v+ g+k+++fGG++  
  gene191|gene191|rna191|rna191 356 DHQMVATGDKLCVFGGRSTE 375
                                    69***************875 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0016
                        Kelch_6   9 svggkiYifGGytdsspylnkvwvydpetks.Weqlppl 46 
                                    ++++++ i+GG+ +  ++ + +++y+++t++  + +p +
  gene191|gene191|rna191|rna191 513 IYNNSLAIIGGQRN-KNSIREILFYSLDTDTvYQSVPFP 550
                                    689***********.9**************835556654 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.1
                        Kelch_6  28 nkvwvydpetksWeql 43 
                                     +v+ y++  k+W+++
  gene191|gene191|rna191|rna191 585 IDVYTYSLTRKRWTKV 600
                                    68999********986 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 1.5e-05
                        Kelch_6   2 raghslvsvggkiYifGGytds..spylnkvwvydpetks 39 
                                    r +h+++ ++g +Y+fGG++    + ++n++wv+++e k+
  gene191|gene191|rna191|rna191 617 RSAHQFIQMNGWFYLFGGNVSErtDRRVNDMWVFRLEKKT 656
                                    789*****************99*************99665 PP

>> Kelch_4  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.076   1.4e+02       2      41 ..     252     287 ..     252     297 .. 0.68
   2 !    9.3   0.1   0.00064       1.1       4      38 ..     356     390 ..     354     392 .. 0.83
   3 !    8.6   0.0   0.00099       1.8       9      40 ..     512     542 ..     495     550 .. 0.77
   4 ?    2.0   0.0      0.12   2.1e+02      30      44 ..     586     600 ..     584     608 .. 0.86
   5 !    7.6   0.0    0.0021       3.7      13      40 ..     627     656 ..     616     661 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.076
                        Kelch_4   2 RaghsatsipdgtiylfGGrgedgtllndlylldlstntW 41 
                                    R+gh++    dg++y++GG ++  + l d ++   ++++W
  gene191|gene191|rna191|rna191 252 RGGHQMAEM-DGSLYVYGGWNGV-EELEDFWR--YKDGEW 287
                                    666666666.79*******7765.45555555..455555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00064
                        Kelch_4   4 ghsatsipdgtiylfGGrgedg.tllndlylldlst 38 
                                    +h++++++ +++ +fGGr+++   +++ ly ++l +
  gene191|gene191|rna191|rna191 356 DHQMVATG-DKLCVFGGRSTEReDIYSGLYMFSLDD 390
                                    79*****7.78888******8568999999888765 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00099
                        Kelch_4   9 sipdgtiylfGGrgedgtllndlylldlstnt 40 
                                    si++++++++GG+ ++  +  ++ +++l t t
  gene191|gene191|rna191|rna191 512 SIYNNSLAIIGGQRNK-NSIREILFYSLDTDT 542
                                    45789**********9.699999999998887 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.12
                        Kelch_4  30 dlylldlstntWrrl 44 
                                    d+y ++l+ ++W+++
  gene191|gene191|rna191|rna191 586 DVYTYSLTRKRWTKV 600
                                    9999*********98 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0021
                        Kelch_4  13 gtiylfGGrgedg..tllndlylldlstnt 40 
                                    g +ylfGG  ++    ++nd++++ l+ +t
  gene191|gene191|rna191|rna191 627 GWFYLFGGNVSERtdRRVNDMWVFRLEKKT 656
                                    668*****9998678*********997765 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.2   3.1e-08   5.6e-05       2      41 ..     252     289 ..     251     291 .. 0.90
   2 ?   -1.0   0.0      0.77   1.4e+03       2      21 ..     300     319 ..     299     337 .. 0.81
   3 ?    0.8   0.0       0.2   3.6e+02       5      22 ..     357     374 ..     355     389 .. 0.77
   4 ?   -1.2   0.0      0.87   1.6e+03      16      37 ..     520     541 ..     514     544 .. 0.75
   5 ?   -2.6   0.2       2.3   4.2e+03      28      42 ..     586     600 ..     584     600 .. 0.88
   6 ?    1.8   0.0       0.1   1.8e+02       5      38 ..     620     656 ..     616     658 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.1e-08
                                    BBSEEEEEETTEEEEEEEBCSSSBEEEEEEEETTTTEEEE CS
                        Kelch_1   2 ragagavvvggkiYviGGsdggnalssvevyDpetntWre 41 
                                    r g+ ++ ++g +Yv GG++g + l ++++y    ++W+e
  gene191|gene191|rna191|rna191 252 RGGHQMAEMDGSLYVYGGWNGVEELEDFWRYK--DGEWTE 289
                                    7789999************************8..778876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.77
                                    BBSEEEEEETTEEEEEEEBC CS
                        Kelch_1   2 ragagavvvggkiYviGGsd 21 
                                    r+++ + +   k+Y +G + 
  gene191|gene191|rna191|rna191 300 RSCHRMISNKSKLYLMGKYI 319
                                    88999999999999999776 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.2
                                    EEEEEETTEEEEEEEBCS CS
                        Kelch_1   5 agavvvggkiYviGGsdg 22 
                                    + +v+ g+k+ v+GG++ 
  gene191|gene191|rna191|rna191 357 HQMVATGDKLCVFGGRST 374
                                    77999**********986 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.87
                                    EEEEBCSSSBEEEEEEEETTTT CS
                        Kelch_1  16 viGGsdggnalssvevyDpetn 37 
                                    +iGG+++ n+ + +  y++ t+
  gene191|gene191|rna191|rna191 520 IIGGQRNKNSIREILFYSLDTD 541
                                    79***99887776666666665 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 2.3
                                    EEEEEETTTTEEEEE CS
                        Kelch_1  28 svevyDpetntWrel 42 
                                    +v+ y+++ + W+++
  gene191|gene191|rna191|rna191 586 DVYTYSLTRKRWTKV 600
                                    7899********986 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.1
                                    EEEEEETTEEEEEEEBCS...SSBEEEEEEEETTTTE CS
                        Kelch_1   5 agavvvggkiYviGGsdg...gnalssvevyDpetnt 38 
                                    + +  ++g  Y +GG  +    +++++ +v+ +e++t
  gene191|gene191|rna191|rna191 620 HQFIQMNGWFYLFGGNVSertDRRVNDMWVFRLEKKT 656
                                    555566666799****99************9888765 PP

>> F5_F8_type_C  F5/8 type C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1     2e-09   3.6e-06       5     124 ..      18     141 ..      14     143 .. 0.67
   2 ?   -2.8   0.0       3.6   6.5e+03      70      84 ..     590     603 ..     576     624 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2e-09
                                    SSCSSTTTGGGGGGSS...STTSSEEESSSSTTEEEEEEEEEEEEEEEEEEEECSSTT.SSEEEEEEEEEESSSSSEEEE CS
                   F5_F8_type_C   5 sseesgewpaaaaldG...nkntaWsssssddkqwlqvdLgkpkkidgvvtqgrqdgg.nayvksykiqvsddgetWttv 80 
                                    +s++++ + ++++  +   ++n++Ws+s++d+ q++ ++   p  +   +t g  +++   +vk+ +i+vs+dg ++++v
  gene191|gene191|rna191|rna191  18 YSTYASVYVPNNIKRNdpmDPNSRWSTSTNDHLQYIILKV--PPSLVVTITFGKYNKMhVSNVKKMRISVSEDGVEYKEV 95 
                                    5555666644444443123679*******99767776555..55555556666666677********************* PP

                                    EEECEEESSSSSSSEEEEEE....EEEEEEEEEEEEEE.EESSSSSEEE CS
                   F5_F8_type_C  81 kdekvpgnsdnstpvtntfd....ppvkaryvrltpts.wnggngialr 124
                                         +++s+    +t ++         a+yv+++p++ w  + +++l+
  gene191|gene191|rna191|rna191  96 LCGGLKNDSE---METFNLLvkdeAYYIAQYVKIEPLAaWGVNFSYSLW 141
                                    **44444444...5555554200233566*********99988888887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                                    EESSSSSEEEEEEEC CS
                   F5_F8_type_C  70 vsddgetWttvkdek 84 
                                    +s+  + Wt+v + k
  gene191|gene191|rna191|rna191 590 YSLTRKRWTKVIA-K 603
                                    7888899999988.2 PP

>> Sad1_UNC  Sad1 / UNC-like C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0042      40     123 ..      61     140 ..      22     147 .. 0.76
   2 ?    0.0   0.0      0.44   7.9e+02      60     114 ..     644     695 ..     634     701 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                                    EEEEEEEE---GGGSG-TTSB-EEEEEEESSTT----EEEEEEE--TTS-SEEEEE--TT---..-EEEEEEEE--BSS- CS
                       Sad1_UNC  40 iveavtlehveksvapisSapKdfevsgskrypekkwvllgefsydedgknaqtFeleeskdi..lvkyvkleilsnyGn 117
                                     v ++t   ++k   +  S++K++++s+s+++ e k+vl g  +   + ++++tF+l  ++++  +++yvk+e l  +G 
  gene191|gene191|rna191|rna191  61 LVVTITFGKYNK---MHVSNVKKMRISVSEDGVEYKEVLCGGLK---NDSEMETFNLLVKDEAyyIAQYVKIEPLAAWGV 134
                                    455677777777...468*************************9...889999***9988766779************99 PP

                                    SSEEEE CS
                       Sad1_UNC 118 eeytcl 123
                                    ++  +l
  gene191|gene191|rna191|rna191 135 NFSYSL 140
                                    877666 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.44
                                    B-EEEEEEESSTT----EEEEEEE--TTS-SEEEEE--TT----EEEEEEEE--B CS
                       Sad1_UNC  60 pKdfevsgskrypekkwvllgefsydedgknaqtFeleeskdilvkyvkleilsn 114
                                    + d+ v+ ++++ +k+  +l +f   +++k++    ++e+k  +v+y++ ++ls+
  gene191|gene191|rna191|rna191 644 VNDMWVFRLEKKTNKEIRHLSKFL-VRKHKYLHLLGIDEKK--AVDYLRTSVLSM 695
                                    567778889999999999*****9.6999999999999999..999999999886 PP

>> Ribosomal_L38e  Ribosomal L38e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.55   9.9e+02       4      22 ..     199     217 ..     197     220 .. 0.90
   2 ?    9.0   0.2   0.00083       1.5      28      60 ..     658     692 ..     642     698 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.55
                 Ribosomal_L38e   4 ikdiKeFLeiarrkDaksv 22 
                                    +k i+++Le  r +D+++v
  gene191|gene191|rna191|rna191 199 VKHIRKLLESHRYEDVEAV 217
                                    789************9987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00083
                 Ribosomal_L38e  28 k..kdntKfKvRcsryLYTLvvkdkekaeklkqsL 60 
                                    k  ++  Kf vR ++yL+ L +++k+ ++ l+ s+
  gene191|gene191|rna191|rna191 658 KeiRHLSKFLVRKHKYLHLLGIDEKKAVDYLRTSV 692
                                    3556778******************9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (734 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 4376.32
//
Query:       gene192|gene192|rna192|rna192  [L=507]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-44  151.3   0.0    5.8e-44  149.9   0.0    1.7  2  DEAD             DEAD/DEAH box helicase
    4.6e-31  107.4   2.6    5.8e-30  103.9   0.1    3.3  4  Helicase_C       Helicase conserved C-terminal domain
      3e-08   33.9   0.0    6.1e-08   32.9   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
    0.00093   18.1   0.1      0.011   14.5   0.0    2.7  3  UTP25            Utp25, U3 small nucleolar RNA-associated SSU
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.096   12.4   0.0    1.8  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.039   14.3   0.0      0.072   13.4   0.0    1.7  1  AAA_19           AAA domain
      0.063   12.6   0.4       0.18   11.1   0.0    1.9  2  CMS1             U3-containing 90S pre-ribosomal complex subu
      0.088   13.1   0.3        3.4    7.9   0.3    2.7  1  AAA_22           AAA domain
       0.18   11.9   0.7       0.51   10.5   0.0    2.0  3  Helicase_C_2     Helicase C-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.9   0.0   2.9e-47   5.8e-44       2     172 ..     122     278 ..     121     282 .. 0.93
   2 ?   -3.0   0.0       2.6   5.3e+03      66     104 ..     354     396 ..     350     401 .. 0.64

  Alignments for each domain:
  == domain 1  score: 149.9 bits;  conditional E-value: 2.9e-47
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                     iQ+ +ip +++g++++++a+TG+GKT++flip++++    k+ ++p+a i++PtreL+eq+ ++++k+    ++rv++i
  gene192|gene192|rna192|rna192 122 IIQKYCIPSMVEGRNLICRAPTGMGKTMCFLIPIIERY---KQMKKPQACIISPTRELCEQIRTETSKLVYGSKIRVVSI 198
                                    59*********************************998...79************************************* PP

                                    ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                    +g+   +++l    +gvdi+v+tpgrl+dll++g+++ls+++++VlDEad+lld+gf+  i++i++ +       +++ q
  gene192|gene192|rna192|rna192 199 YGK---KQDLPSY-AGVDIIVATPGRLIDLLHKGRVDLSEIKMFVLDEADKLLDMGFEVPIKEIHKYI-------PKNTQ 267
                                    **6...4457777.89****************************************************.......56678 PP

                                    EEEEESSBSHH CS
                                    xxxxxxxxxxx RF
                           DEAD 162 vivlSATlpkd 172
                                    ++++SAT + +
  gene192|gene192|rna192|rna192 268 TCLFSATYSPK 278
                                    *******9855 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                    HHHHHTTTSTSEEEEEETTSSHHHHHHHHH...TT.CSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx.xxxxxxx RF
                           DEAD  66 nlkkfkkyidlrvlliiggvaardqlskld...ng.vdivvgt 104
                                    +++k++k+ ++ ++ + g+++++d  ++l+   ng   ++v+t
  gene192|gene192|rna192|rna192 354 EVEKVLKKSGVLCVTLHGDKEQSDRNEALKgfrNGrFPVMVAT 396
                                    5677777777555566677777777777733324456666665 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.9   7.7e+03      48      70 ..      87     109 ..      85     111 .. 0.74
   2 ?    0.6   0.0      0.34   6.8e+02      12      49 ..     160     201 ..     149     207 .. 0.69
   3 ?    0.5   0.1      0.38   7.5e+02      14      75 ..     263     327 ..     251     332 .. 0.66
   4 !  103.9   0.1   2.9e-33   5.8e-30      11     110 ..     334     433 ..     313     434 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.9
                                    TTSTHHHHHHHHHHHHTTSSSEE CS
                     Helicase_C  48 gelpqnereeileqfnkgesdvL 70 
                                    ++ +++e+ ++l++f++  s+ L
  gene192|gene192|rna192|rna192  87 SKVKTSEKVKTLNSFKELCSQAL 109
                                    67788999999999987555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                                    HTTTTSEEEEEESSHHHHHH....HHHHHHHT....TSTEEEESTT CS
                     Helicase_C  12 leeeggkilifvntidrlek....vklllekk....gikvavlhge 49 
                                    ++ ++ ++ i+++t++ +e+    ++          +i+v+ ++g+
  gene192|gene192|rna192|rna192 160 KQMKKPQACIISPTRELCEQirteTSK----LvygsKIRVVSIYGK 201
                                    5678889999******99765544222....134457999988885 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.38
                                    TTTSEEEEEESSHH.HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH..TTSSSEEEESGG CS
                     Helicase_C  14 eeggkilifvntid.rlek.vklllekkgikvavlhgelpqnereeileqfn..kgesdvLiatdv 75 
                                     ++ ++ +f+ t + +l + ++++l + +++v  + +e+  n ++ei+e  n  k    +L  +d+
  gene192|gene192|rna192|rna192 263 PKNTQTCLFSATYSpKLTRmINYFLPEDKVSV-EIPSETLRNIKQEIVEVRNkkKALLSILQNSDI 327
                                    56778888888888855445688876666666.777788888888888887732233346666655 PP

  == domain 4  score: 103.9 bits;  conditional E-value: 2.9e-33
                                    HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
                     Helicase_C  11 kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                                     +e++ +k+l+fv++++++ +v+ +l+k+g+ +++lhg+ +q++r+e+l+ f++g++ v++at+va+rGidi++++lVin
  gene192|gene192|rna192|rna192 334 RMEVQPDKVLVFVERKSECGEVEKVLKKSGVLCVTLHGDKEQSDRNEALKGFRNGRFPVMVATSVAARGIDIKDIKLVIN 413
                                    5688999**********998888888999*************************************************** PP

                                    SSSSSSHHHHHHHHTTSSST CS
                     Helicase_C  91 fdlprnvtsyiqriGRtgRa 110
                                    +d+pr++++yi+riGRtgR 
  gene192|gene192|rna192|rna192 414 YDIPRDIKEYIHRIGRTGRE 433
                                    *******************6 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   3.1e-11   6.1e-08      24     168 ..     134     274 ..      88     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 3.1e-11
                                    TSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                         ResIII  24 dkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                                     ++++  ++TG+GKT++  + +ier+++  k+ ++ ++ p+++l+eq ++e +k+    + ++  ++ ++++ +   +  
  gene192|gene192|rna192|rna192 134 GRNLICRAPTGMGKTMCFlIPIIERYKQM-KKPQACIISPTRELCEQIRTETSKLVYGSKIRVVSIYGKKQDLP---SYA 209
                                    45677899**********88999999986.668******************99999998655555555555555...9** PP

                                    .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT---SEE.EEEESS CS
                         ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilekfkeavl.lglTAT 168
                                      +i+v+t  +l   +     ++ + + +++++++ DEa +l ++     ++ei ++++++++   ++AT
  gene192|gene192|rna192|rna192 210 GVDIIVATPGRLIDLL-----HKGRVDLSEIKMFVLDEADKLLDMGfevPIKEIHKYIPKNTQtCLFSAT 274
                                    ****************.....99999******************94446899999999665541557887 PP

>> UTP25  Utp25, U3 small nucleolar RNA-associated SSU processome protein 25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.6   1.2e+03      72      99 ..     161     188 ..     157     206 .. 0.79
   2 ?    1.6   0.2     0.048        95     240     277 ..     299     336 ..     195     342 .. 0.60
   3 !   14.5   0.0   5.7e-06     0.011     326     414 ..     335     421 ..     227     443 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.6
                          UTP25  72 gftrpkvLillptreaalevvelllkll 99 
                                     +++p+  i+ ptre + ++ ++  kl+
  gene192|gene192|rna192|rna192 161 QMKKPQACIISPTRELCEQIRTETSKLV 188
                                    5689999**********99876666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.048
                          UTP25 240 dqakllRQtlvfssyetpeinslfnskleNlaGkvkvk 277
                                    ++ ++++Q +v  + ++  + s+++++  Nl+G+++++
  gene192|gene192|rna192|rna192 299 ETLRNIKQEIVEVRNKKKALLSILQNSDINLKGSWRME 336
                                    33455666666666666666666666666777666665 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 5.7e-06
                          UTP25 326 ssskssgiliyipsyfdfvrvrnylkeekvsfaaiseysskkevsraRelFfkgkkkvlLyteRlhffrRykikgvkkvi 405
                                     + + +++l+++    +   v++ lk++ v  ++++  +++++ ++a + F +g+  v++ t  +   r  +ik++k vi
  gene192|gene192|rna192|rna192 335 MEVQPDKVLVFVERKSECGEVEKVLKKSGVLCVTLHGDKEQSDRNEALKGFRNGRFPVMVATSVAA--RGIDIKDIKLVI 412
                                    4567899*******************************************************9885..99********** PP

                          UTP25 406 lYklPenpe 414
                                     Y++P   +
  gene192|gene192|rna192|rna192 413 NYDIPRDIK 421
                                    *****8754 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.7   3.5e+03      39      59 ..      86     107 ..      63     120 .. 0.63
   2 ?   12.4   0.0   4.8e-05     0.096      27     117 ..     304     393 ..     280     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                Viral_helicase1  39 k.pklpnlsvrtvdsflmalvk 59 
                                      + +++++v+t++sf + +++
  gene192|gene192|rna192|rna192  86 DsKVKTSEKVKTLNSFKELCSQ 107
                                    2245667777777777776654 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.8e-05
                Viral_helicase1  27 vnrptaelltegk...pklpnlsvrtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipfh 103
                                    + ++ +e++++ k   + l+n++++   s+ m   +    k+l++ E  + + G+++ ++++s++ +v l GD +Q+  +
  gene192|gene192|rna192|rna192 304 IKQEIVEVRNKKKallSILQNSDINLKGSWRMEVQP---DKVLVFVER-KSECGEVEKVLKKSGVLCVTLHGDKEQSDRN 379
                                    45566677777778899999999999999***9876...5999999*9.8899************************999 PP

                Viral_helicase1 104 srnasfllahlpss 117
                                    +  + f + ++p+ 
  gene192|gene192|rna192|rna192 380 EALKGFRNGRFPVM 393
                                    99998888888775 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.6e-05     0.072       7      65 ..     131     187 ..     124     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                         AAA_19   7 alkekvllvtaGpGtGKTrv.lkhivallvelggvkpeeillvaftgrAakelrerlaal 65 
                                     ++ ++l+  a+ G+GKT + l  i++ +++++     +  ++++t+  ++++r+++++l
  gene192|gene192|rna192|rna192 131 MVEGRNLICRAPTGMGKTMCfLIPIIERYKQMK---KPQACIISPTRELCEQIRTETSKL 187
                                    5678899999********972455666666666...4688899***********999655 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.2e-05      0.18     178     209 ..     211     242 ..     207     249 .. 0.92
   2 ?   -3.5   0.1       2.7   5.4e+03     216     238 ..     305     327 ..     300     331 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.2e-05
                           CMS1 178 igiavGtpgRildLleeeslsvdeLkrivlDa 209
                                    + i v tpgR++dLl+++ + ++e+k  vlD 
  gene192|gene192|rna192|rna192 211 VDIIVATPGRLIDLLHKGRVDLSEIKMFVLDE 242
                                    568899************************96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.7
                           CMS1 216 nrgildiretrkeviklLgakev 238
                                    +++i+++r+ +k+++ +L   ++
  gene192|gene192|rna192|rna192 305 KQEIVEVRNKKKALLSILQNSDI 327
                                    46788999999999999987766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0017       3.4       7     103 ..     136     246 ..     131     276 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                         AAA_22   7 ilvvtGesGtGKTtl.....lrrlleqldeeakaee.......erpevvfvtlpsst.sskdllrellralglelka... 70 
                                     l++ +++G+GKT++     ++r+++ ++ +            e  e+++ + +++  +sk     +  +      +   
  gene192|gene192|rna192|rna192 136 NLICRAPTGMGKTMCflipiIERYKQMKKPQ----AciisptrELCEQIRTETSKLVyGSKIRVVSIYGK------Kqdl 205
                                    6788888888888873222234444443222....12222333333333333333332222222222222......0233 PP

                         AAA_22  71 ...........erlsseellealeqalrarav....ielliiDEaqhl 103
                                                +        +l + l++ +v    i+++++DEa++l
  gene192|gene192|rna192|rna192 206 psyagvdiivaTP-------GRLIDLLHKGRVdlseIKMFVLDEADKL 246
                                    4344444433233.......3344444444444444666999999985 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       4.4   8.7e+03      39      63 ..      80     107 ..      62     115 .. 0.56
   2 ?   -2.4   0.0       2.3   4.6e+03       5      69 ..     259     321 ..     255     325 .. 0.55
   3 ?   10.5   0.0   0.00026      0.51       5      84 ..     335     409 ..     333     417 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.4
                   Helicase_C_2  39 eifvee....keesrekvleeykekkkkg 63 
                                    ++++ e    k++++ k+l+++ke  +++
  gene192|gene192|rna192|rna192  80 PVVEDEdskvKTSEKVKTLNSFKE-LCSQ 107
                                    444433455666777777777777.4444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                   Helicase_C_2   5 levvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillav 69 
                                     +++p+++     S ++  ++++ ++  l ++k+++     +e+ +++ +e+ e+++k+++ll++
  gene192|gene192|rna192|rna192 259 HKYIPKNTQTCLFSATYSPKLTRMINYFLPEDKVSVEI--PSETLRNIKQEIVEVRNKKKALLSI 321
                                    55666666666666666666666666655555444433..3555566666666556666666665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00026
                   Helicase_C_2   5 levvpggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddl 84 
                                    +ev p++vlvf+   +   ev ++lk+++    +++   +++++r++ l+ +++  ++  +++a+       Gid++d +
  gene192|gene192|rna192|rna192 335 MEVQPDKVLVFVERKSECGEVEKVLKKSGVL-CVTLHGDKEQSDRNEALKGFRN--GRFPVMVATS--VAARGIDIKDIK 409
                                    6899***********************9952.23333344889***********..9999999988..9999****9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.35s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 2863.83
//
Query:       gene193|gene193|rna193|rna193  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-12   46.7   0.0    7.5e-12   45.8   0.0    1.4  1  AAA              ATPase family associated with various cellul
    7.2e-11   42.1   0.0    4.5e-08   33.0   0.1    2.2  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    9.6e-07   28.7   0.0    1.4e-06   28.2   0.0    1.3  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.5e-06   28.0   0.1     0.0001   22.7   0.0    2.2  2  AAA_16           AAA ATPase domain
      3e-06   27.6   0.1    1.8e-05   25.0   0.1    2.0  1  AAA_22           AAA domain
      3e-06   27.4   0.0    5.6e-06   26.5   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
    2.4e-05   24.2   0.0    5.2e-05   23.1   0.0    1.5  1  AAA_24           AAA domain
    3.2e-05   23.7   0.2     0.0028   17.4   0.2    2.2  1  IstB_IS21        IstB-like ATP binding protein
    5.8e-05   22.6   0.2     0.0047   16.3   0.0    2.6  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.3e-05   23.0   0.0    0.00012   22.1   0.0    1.5  1  AAA_14           AAA domain
    0.00011   22.2   0.8     0.0072   16.3   0.0    2.7  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00012   22.3   0.0    0.00021   21.6   0.0    1.3  1  AAA_28           AAA domain
     0.0004   20.9   0.0    0.00077   20.0   0.0    1.5  1  AAA_18           AAA domain
    0.00046   20.5   0.0      0.001   19.4   0.0    1.6  1  RNA_helicase     RNA helicase
     0.0014   19.0   0.0     0.0028   18.0   0.0    1.5  1  Rep_fac_C        Replication factor C C-terminal domain
     0.0015   18.3   0.0        0.7    9.6   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
      0.002   17.5   0.0     0.0068   15.8   0.0    1.7  2  TniB             Bacterial TniB protein
     0.0022   18.2   0.0     0.0034   17.5   0.0    1.3  1  AAA_33           AAA domain
     0.0047   17.3   0.4       0.27   11.6   0.0    2.2  2  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.022   14.2   0.1        1.8    7.9   0.0    2.2  2  PhoH             PhoH-like protein
       0.03   14.2   0.0      0.065   13.1   0.0    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
      0.037   13.4   0.0        0.1   12.0   0.0    1.6  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.038   13.9   0.3       0.34   10.8   0.3    2.5  1  Rad17            Rad17 P-loop domain
      0.043   13.4   0.0      0.065   12.8   0.0    1.4  1  AAA_25           AAA domain
       0.05   13.4   0.0      0.073   12.8   0.0    1.3  1  AAA_11           AAA domain
      0.058   13.4   0.0       0.11   12.5   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
      0.061   13.2   0.0       0.62   10.0   0.0    2.1  2  NACHT            NACHT domain
      0.067   12.4   0.0      0.091   11.9   0.0    1.2  1  NB-ARC           NB-ARC domain
      0.078   13.2   0.0       0.12   12.6   0.0    1.3  1  Roc              Ras of Complex, Roc, domain of DAPkinase
       0.13   11.6   0.4       0.86    8.9   0.0    1.9  2  ATPase           KaiC
       0.13   12.3   0.0       0.42   10.6   0.0    1.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   11.3   0.0       0.18   10.9   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.14   12.1   0.1       0.61   10.0   0.0    1.9  2  NTPase_1         NTPase
       0.14   11.8   0.1       0.45   10.2   0.1    1.8  1  AAA_30           AAA domain
       0.14   10.7   0.0        0.2   10.3   0.0    1.1  1  AAA_13           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   1.5e-14   7.5e-12       1     125 [.      36     135 ..      36     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.5e-14
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +llyGppGtGKT++a+ +a+      le+++s+ +   ++   ++i+ + +++ +    + +++DE ++l+++       
  gene193|gene193|rna193|rna193  36 LLLYGPPGTGKTTFAHLLANR----KLELNASDER--GISVIRERIKVYASTLDKD---KTIILDECENLTSDA------ 100
                                    69******************9....79********..7777777777777776655...6899*******9999...... PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSS CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfd 125
                                         +  L +++++  +    + +i +tn+p+k+  +l+ +R+ 
  gene193|gene193|rna193|rna193 101 -----QHCLRRVIEDSVN----TRFIFITNYPSKIIGPLR-SRLV 135
                                    .....**********998....69****************.9985 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0085       4.3      14      46 ..      28      60 ..      18      73 .. 0.79
   2 !   33.0   0.1   8.9e-11   4.5e-08      99     161 ..      80     141 ..      65     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0085
                DNA_pol3_delta2 14 ksgrlahayLfeGdegigkkelalnlakallce 46
                                   + gr +  +L++G+ g+gk ++a  la++ l  
  gene193|gene193|rna193|rna193 28 SDGRGHPNLLLYGPPGTGKTTFAHLLANRKLEL 60
                                   35899999******************9876655 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 8.9e-11
                DNA_pol3_delta2  99 preskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfsp 161
                                    ++  k k ii++++e++t+ A+  l +++E+   n+ fi+it+ ++k++ ++rSR   +kfs 
  gene193|gene193|rna193|rna193  80 STLDKDKTIILDECENLTSDAQHCLRRVIEDS-VNTRFIFITNYPSKIIGPLRSRLVSVKFSL 141
                                    455789***********************997.99**************************85 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.7e-09   1.4e-06      27     111 ..      29     111 ..       7     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.7e-09
                         RuvB_N  27 kkreealdhvllyGpPGlGkttlakiiak.elgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevly 105
                                      r++    +llyGpPG Gktt+a+++a+ +l+ +     g  + +++ +    ++l++++ + +de   l++ ++  l 
  gene193|gene193|rna193|rna193  29 DGRGH--PNLLLYGPPGTGKTTFAHLLANrKLELNASDERGISVIRER-IKVYASTLDKDKTIILDECENLTSDAQHCLR 105
                                    34443..469*****************973577777777776665543.66677899*********************** PP

                         RuvB_N 106 samedf 111
                                      +ed 
  gene193|gene193|rna193|rna193 106 RVIEDS 111
                                    *99996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     2e-07    0.0001      11      46 ..      20      55 ..      19      78 .. 0.75
   2 ?    3.9   0.0      0.12        64     116     161 ..      63     110 ..      54     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2e-07
                         AAA_16 11 qLlsalervrsgrp.elvllsGesGvGKsslvrellr 46
                                   +L+++l+  ++gr+ +++ll+G++G+GK++ +  l++
  gene193|gene193|rna193|rna193 20 HLKNILR-KSDGRGhPNLLLYGPPGTGKTTFAHLLAN 55
                                   5777787.5567777*****************99886 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                         AAA_16 116 a.srllellkrll.allsrderplvlvlDdlqwadeaslqllaaLlrl 161
                                    + +r   ++++ + +++s+ ++   ++lD+ + + ++ ++ l+   ++
  gene193|gene193|rna193|rna193  63 SdERGISVIRERIkVYASTLDKDKTIILDECENLTSDAQHCLRRVIED 110
                                    3478888999999999***99999***************999877665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   3.5e-08   1.8e-05       6      85 ..      34     110 ..      29     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.5e-08
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv....fvtlpsstsskdllrellralglelkaerlsseellea 81 
                                      l+++G++GtGKTt +  l++++ e ++ +e++ +v+    +v+++ + + k++  + +++l++       + +++l++
  gene193|gene193|rna193|rna193  34 PNLLLYGPPGTGKTTFAHLLANRKLELNASDERGISVIreriKVYASTLDKDKTIILDECENLTS-------DAQHCLRR 106
                                    5689********************99999999999999995566666666999998888888885.......56666644 PP

                         AAA_22  82 leqa 85 
                                    + + 
  gene193|gene193|rna193|rna193 107 VIED 110
                                    4444 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.1e-08   5.6e-06      19     109 ..      31     122 ..      15     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-08
                                    T-SS-EEEEEETT--HHHHHHCC--TTS-EE-.....-SSTTHHHH-HHHHHHHTTTSEEEEEE-TT--HHHHHHHHHHH CS
                Sigma54_activ_2  19 qsklpvfltGekGsgkelvArlLhknsgpwle.....ifvverlaklpldlleqakggtLylkdiadlskaeqkeLlell 93 
                                    + + +++l G++G+gk+++A lL++ + +  +     i v+ + +k  +++l+  k+ t++l + ++l +++q  L  ++
  gene193|gene193|rna193|rna193  31 RGHPNLLLYGPPGTGKTTFAHLLANRKLELNAsdergISVIRERIKVYASTLD--KDKTIILDECENLTSDAQHCLRRVI 108
                                    67899*******************98766444000114444444444455555..6889********************* PP

                                    HHHTTTT-EEEEEEEE CS
                Sigma54_activ_2  94 akaeksslrlVstssk 109
                                    + +   + r+++++ +
  gene193|gene193|rna193|rna193 109 EDS--VNTRFIFITNY 122
                                    *99..99****99865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     1e-07   5.2e-05       4      86 ..      35     105 ..      33     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-07
                         AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtek..GlksldadkfpdieswedfldevvelaaeladyktlviDtideleelc 81 
                                    ++l+yGp+g+GKTt+a  l ++ l ++  +  G                 +++ ++  a  l++ kt+++D  + l + +
  gene193|gene193|rna193|rna193  35 NLLLYGPPGTGKTTFAHLLANRKLELNASDerGIS--------------VIRERIKVYASTLDKDKTIILDECENLTSDA 100
                                    689****************9999999875511332..............3456666677777777888888777777766 PP

                         AAA_24  82 laevi 86 
                                     + ++
  gene193|gene193|rna193|rna193 101 QHCLR 105
                                    66554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   5.5e-06    0.0028      46     146 ..      32     120 ..      18     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.5e-06
                      IstB_IS21  46 kkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqa 125
                                     + n++l Gp+G+GK+ +a  l+ +  + + s      e+    ++     ++++  +++l k + +ilD++  ++l ++
  gene193|gene193|rna193|rna193  32 GHPNLLLYGPPGTGKTTFAHLLANRKLELNASD-----ER---GIS--VIRERIKVYASTLDKDKTIILDEC--ENLTSD 99 
                                    578*******************99998877652.....22...222..223456667777888888888886..456667 PP

                      IstB_IS21 126 eaellfeviekryerrsiiit 146
                                    +++ l +vie+ +++r i it
  gene193|gene193|rna193|rna193 100 AQHCLRRVIEDSVNTRFIFIT 120
                                    778888888888888888887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.1e-06    0.0047      21      43 ..      32      54 ..      15      76 .. 0.81
   2 ?    3.4   0.0     0.086        44     109     133 ..      87     111 ..      74     135 .. 0.81
   3 ?   -1.2   0.0       2.1   1.1e+03     178     193 ..     119     134 ..     112     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.1e-06
                   Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlp 43
                                   G+ nlll+GppG+GKt  a+ l+
  gene193|gene193|rna193|rna193 32 GHPNLLLYGPPGTGKTTFAHLLA 54
                                   6679*************999876 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.086
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledg 133
                                     ++LDE+ ++++++  +LR+ +ed 
  gene193|gene193|rna193|rna193  87 TIILDECENLTSDAQHCLRRVIEDS 111
                                    57899*************9999985 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.1
                   Mg_chelatase 178 ierYlsklsgplldRi 193
                                    i++Y sk+ gpl  R+
  gene193|gene193|rna193|rna193 119 ITNYPSKIIGPLRSRL 134
                                    679*********9997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.4e-07   0.00012       4      97 ..      35     118 ..      32     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.4e-07
                         AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev.peweka 82 
                                     l++ G+  +GKTt+++ l++++l       ++n  der  +   +   ++++ + l + k++ ++lDE  ++ ++++++
  gene193|gene193|rna193|rna193  35 NLLLYGPPGTGKTTFAHLLANRKL-------ELNASDERGISVIRE--RIKVYASTL-D-KDKTIILDECENLtSDAQHC 103
                                    57899**********999986666.......999999888665434..356666654.3.5678*******98467**** PP

                         AAA_14  83 lkslvdegknldviv 97 
                                    l+++++++ n ++i+
  gene193|gene193|rna193|rna193 104 LRRVIEDSVNTRFIF 118
                                    ******997777765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-05    0.0072       1      21 [.      35      55 ..      35      65 .. 0.89
   2 ?    3.7   0.1      0.11        57      65      91 ..      84     110 ..      59     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                                   EEEEE--SSSSHHHHHHHGGG CS
                          AAA_5  1 dvlLvGppGtgKselaerlaa 21
                                   ++lL GppGtgK+++a  la 
  gene193|gene193|rna193|rna193 35 NLLLYGPPGTGKTTFAHLLAN 55
                                   69**************99986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                    G-SEEEEESGGG--HHHHHHHHHHHHS CS
                          AAA_5  65 egeilvlDEveraesevlnsLlsllee 91 
                                    + ++++lDE e++ s+++  L +++e+
  gene193|gene193|rna193|rna193  84 KDKTIILDECENLTSDAQHCLRRVIED 110
                                    7789******************99998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.1e-07   0.00021       3      66 ..      37     110 ..      35     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.1e-07
                         AAA_28   3 vitGgestGKTtlleaLaar..........gypvvpEaareileeklakgedalpwvedllafaervleeqlee 66 
                                     + G+++tGKTt +  La+r          g++v++E    + + + ++++ +l++ e+l   a+++l+  +e+
  gene193|gene193|rna193|rna193  37 LLYGPPGTGKTTFAHLLANRklelnasderGISVIRERIKVYASTLDKDKTIILDECENLTSDAQHCLRRVIED 110
                                    689***************55555555556699999999999999999999988887777777677777666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.5e-06   0.00077       2      36 ..      37      75 ..      36     116 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.5e-06
                         AAA_18  2 lltGtpGvGKttlakeLskrl.gf...gvnlrdvakeng 36
                                   ll G+pG+GKtt+a+ L++r  ++    ++ ++v++e+ 
  gene193|gene193|rna193|rna193 37 LLYGPPGTGKTTFAHLLANRKlELnasDERGISVIRERI 75
                                   689**************8884344677444444444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     2e-06     0.001       2      64 ..      37      99 ..      36     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2e-06
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfwdgYtgqevvvidDfgqvkde 64
                                   +lyGp+g+GK+t+a+ La++ l+   +++   + + r+  + + +  ++ + ++ d+  + +++
  gene193|gene193|rna193|rna193 37 LLYGPPGTGKTTFAHLLANRKLELNASDE-RGISViRERIKVYASTLDKDKTIILDECENLTSD 99
                                   79****************99985554444.4555548888888899999999998888777655 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.4e-06    0.0028      16      88 .]     210     277 ..     198     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.4e-06
                                    T-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHHHHHHHHH CS
                      Rep_fac_C  16 gdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlqlsallar 88 
                                    ++  e+ +   ++   +Gysa ++++ql    k     +e q++e+  +l++ e + v+G+s++l l +ll r
  gene193|gene193|rna193|rna193 210 ANRPEVMNYA-KEFLREGYSALQLVRQLSGSNKG----SEVQSAEFHLVLSFLEEKSVSGCSDELILYNLLGR 277
                                    5555666667.488899**************887....4999*************************999875 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0014       0.7      23      46 ..      34      57 ..      14      70 .. 0.82
   2 ?    6.2   0.0     0.015       7.5      94     122 ..      85     113 ..      80     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                                   S-EEEECSTTSSHHHHHHHHHHHS CS
                Sigma54_activat 23 lsvlitGesGtGKellaraiheas 46
                                    ++l+ G  GtGK+++a+++ +++
  gene193|gene193|rna193|rna193 34 PNLLLYGPPGTGKTTFAHLLANRK 57
                                   579***************997754 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                                    TSEEEEETGGGS-HHHHHHHHHHHHHSEE CS
                Sigma54_activat  94 gGtlfLDeigelplelQekLlrvlqegev 122
                                    + t+ LDe ++l+ ++Q+ L rv+++   
  gene193|gene193|rna193|rna193  85 DKTIILDECENLTSDAQHCLRRVIEDSVN 113
                                    5699********************98765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-05    0.0068      21      74 ..      19      72 ..      13      82 .. 0.89
   2 ?   -1.3   0.0       2.4   1.2e+03     121     133 ..      86      98 ..      56     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                           TniB 21 erLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlv 74
                                   ++L+++l++ +    pnlll+G++ +GKt+ ++  a+++ + + +d++ + v+ 
  gene193|gene193|rna193|rna193 19 DHLKNILRKSDGRGHPNLLLYGPPGTGKTTFAHLLANRKLELNASDERGISVIR 72
                                   689999999999999*********************999999999998888875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                           TniB 121 rvLiiDEihnlla 133
                                    + +i+DE +nl +
  gene193|gene193|rna193|rna193  86 KTIILDECENLTS 98 
                                    6789999999874 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   6.7e-06    0.0034       3      61 ..      37     106 ..      36     123 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-06
                         AAA_33   3 llvGlpGsGKstlaerllkklgavllssdt.....lrrrlfg...tdqqskt....dytrvldrlyqilne 61 
                                    ll G+pG+GK+t+a+ l+ +++ +l +sd+     +r+r+++   t +++kt    +  ++++++  +l++
  gene193|gene193|rna193|rna193  37 LLYGPPGTGKTTFAHLLA-NRKLELNASDErgisvIRERIKVyasTLDKDKTiildECENLTSDAQHCLRR 106
                                    688***********9877.7788888888888887666666643433333333332223344445555554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00053      0.27      10      34 ..      33      57 ..      27      81 .. 0.76
   2 ?    4.6   0.0     0.076        39      97     129 ..      79     111 ..      50     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00053
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivall 34
                                   +++ll+ ++pGtGKT+  +   +  
  gene193|gene193|rna193|rna193 33 HPNLLLYGPPGTGKTTFAHLLANRK 57
                                   57899**********9766555544 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.076
                         AAA_19  97 ekklqeeellivDEfqdvdelqyrLlkallgek 129
                                     ++l + +++i DE  +++  +++ l+++ +++
  gene193|gene193|rna193|rna193  79 ASTLDKDKTIILDECENLTSDAQHCLRRVIEDS 111
                                    45674555***********99999999998766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0036       1.8      24      46 ..      38      60 ..      31      80 .. 0.76
   2 ?    4.1   0.1     0.054        28     119     143 ..      84     107 ..      76     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0036
                                   EE--TTSSTTHHHHHHHHHHHHT CS
                           PhoH 24 aiGpaGtGKtylavalavealkk 46
                                     Gp GtGKt +a  la + l+ 
  gene193|gene193|rna193|rna193 38 LYGPPGTGKTTFAHLLANRKLEL 60
                                   68************999887764 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.054
                                    -SEEEEE-SGGG--HHHHHHHHTTB CS
                           PhoH 119 ndafvilDEAQnttkeqmkmfltRl 143
                                    +d+ +ilDE  n+t+   + +l R+
  gene193|gene193|rna193|rna193  84 KDKTIILDECENLTSDA-QHCLRRV 107
                                    4789*********9875.4555555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.065       8      50 ..      21      75 ..      18     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                       ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdk............y 50
                                   lk++++  +    + +++YGp g GKt++   +++++++++              
  gene193|gene193|rna193|rna193 21 LKNILRKSDGRGHPNLLLYGPPGTGKTTFAHLLANRKLELNAsdergisvirerI 75
                                   77788888888888899*******************9998874444444433333 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002       0.1      25      57 ..      19      51 ..       2      55 .. 0.80
   2 ?   -1.5   0.0       2.5   1.3e+03     120     164 ..      57     101 ..      51     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                   ET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHH CS
                   FtsK_SpoIIIE 25 ei.sgnplvldlkkmashllvaGatgsGKStaln 57
                                   +   ++  ++d ++++ +ll+ G +g+GK+t+ +
  gene193|gene193|rna193|rna193 19 DHlKNILRKSDGRGHP-NLLLYGPPGTGKTTFAH 51
                                   454666778999****.**************977 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.5
                                    HHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-........... CS
                   FtsK_SpoIIIE 120 yalfreagvrsiaaydgeiaedpldifgdvflvlDnyddlaaene 164
                                    +  ++++  r i++ ++ i+ ++  +++d  ++lD+ ++l    +
  gene193|gene193|rna193|rna193  57 KLELNASDERGISVIRERIKVYASTLDKDKTIILDECENLTSDAQ 101
                                    555666667788888999999999999999999999998876655 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00066      0.34      42      68 ..      30      56 ..       1     134 [. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00066
                          Rad17 42 srkkriLLisGPsGCgkstvvkvLske 68
                                    r +  LL+ GP+G gk+t  + L+  
  gene193|gene193|rna193|rna193 30 GRGHPNLLLYGPPGTGKTTFAHLLANR 56
                                   33455689***********99999864 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013     0.065      37      54 ..      37      54 ..      18      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                         AAA_25 37 llaGapgtGKttlaldla 54
                                   ll+G+pgtGKtt+a  la
  gene193|gene193|rna193|rna193 37 LLYGPPGTGKTTFAHLLA 54
                                   89***********98776 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.073      19      41 ..      35      57 ..      19     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                         AAA_11 19 itliqGPPGtgKTktivellsql 41
                                     l+ GPPGtgKT++   l ++ 
  gene193|gene193|rna193|rna193 35 NLLLYGPPGTGKTTFAHLLANRK 57
                                   5799*********8776666654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00021      0.11      12     111 ..      21     122 ..      18     128 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                                    HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEE CS
                         ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllk.kgkee.kflflvprkslleqtleefkkflseaykeigkkv 89 
                                    ++n+l k + +++ ++l+  + GtGKT  a  l+ r l+ +++ e  + ++  r++++  tl++ k ++ ++    ++++
  gene193|gene193|rna193|rna193  21 LKNILRKSDGRGHPNLLLYGPPGTGKTTFAHLLANRKLElNASDErGISVIRERIKVYASTLDKDKTIILDE----CENL 96 
                                    6788888888899999**************6666555441333334899999999*****998877777765....4444 PP

                                    SSS-B--...........-SEEEEEH CS
                         ResIII  90 sgdkkka....kekdstnkkilvtti 111
                                    ++d ++      e + +++ i++t++
  gene193|gene193|rna193|rna193  97 TSDAQHClrrvIEDSVNTRFIFITNY 122
                                    44444333333455555556666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0012      0.62       3      21 ..      36      54 ..      35      62 .. 0.89
   2 ?    2.3   0.0      0.28   1.4e+02      57     126 ..      52     120 ..      50     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   ++l G++G GKTt+++ la
  gene193|gene193|rna193|rna193 36 LLLYGPPGTGKTTFAHLLA 54
                                   5899***********9887 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.28
                                    HHCCCCTS--SSS-C...CHHHHCCSCCCEE.....EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEE CS
                          NACHT  57 llfsqlpepaapvse...vwavllelperlL.....lilDglDelvtdlgqkekqpvrtlLselirkkllpeaslllt 126
                                    ll+   +e++a  ++   v+ +++++  ++L     +ilD  + l +d ++         L++ i+  ++ +  +++t
  gene193|gene193|rna193|rna193  52 LLANRKLELNASDERgisVIRERIKVYASTLdkdktIILDECENLTSDAQH--------CLRRVIED-SVNTRFIFIT 120
                                    5666667777777775555666666667777999999****9999998888........66666665.4455555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018     0.091       6      44 ..      19      57 ..      16     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                   HHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC  6 ekviekLlekdelqslvvalvGmgGvGKttlakqilnks 44
                                   +++++ L ++d+ +   + l+G +G GKtt a+   n  
  gene193|gene193|rna193|rna193 19 DHLKNILRKSDGRGHPNLLLYGPPGTGKTTFAHLLANRK 57
                                   578899999999*999***************98777664 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00024      0.12       2      50 ..      36      83 ..      35      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00024
                                   EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTB CS
                            Roc  2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvend 50
                                   ++l G  g+GKt++++ + ++k + + +   g+++++++++ +   + d
  gene193|gene193|rna193|rna193 36 LLLYGPPGTGKTTFAHLLANRKLELNASDERGISVIRERIK-VYASTLD 83
                                   6889********************************99984.4433333 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0017      0.86      22      37 ..      36      51 ..      29      70 .. 0.84
   2 ?    1.0   0.0      0.44   2.3e+02      98     145 ..      62     109 ..      51     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0017
                         ATPase 22 vlitGepGtGKtifal 37
                                    l++G pGtGKt+fa 
  gene193|gene193|rna193|rna193 36 LLLYGPPGTGKTTFAH 51
                                   689***********96 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                         ATPase  98 ekdkedleelieelaeaikeika.krvviDsitglayeekeavaReilr 145
                                    ++d+  ++ + e+++ + +++   k +++D  ++l +++ ++ +R+ + 
  gene193|gene193|rna193|rna193  62 ASDERGISVIRERIKVYASTLDKdKTIILDECENL-TSDAQHCLRRVIE 109
                                    46677777788888888888876699999******.8888888888776 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00082      0.42      20      41 ..      34      55 ..      10      63 .. 0.75
   2 ?   -2.0   0.0       6.4   3.3e+03      36      59 ..     233     256 ..     231     263 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00082
                                   EEEEEEESTTSSHHHHHHHHHH CS
                           TsaE 20 dvilLeGdLGaGKTtlvrglak 41
                                     +lL+G+ G+GKTt+++ la+
  gene193|gene193|rna193|rna193 34 PNLLLYGPPGTGKTTFAHLLAN 55
                                   3499*************98876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.4
                                    HHHHHHHTT------TTTTSEEEE CS
                           TsaE  36 vrglakalgveevkSPTFtlveeY 59 
                                    vr+l  + + +ev+S  F lv ++
  gene193|gene193|rna193|rna193 233 VRQLSGSNKGSEVQSAEFHLVLSF 256
                                    44444444444999*999999887 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00035      0.18     116     151 ..      19      55 ..       6     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                          T2SSE 116 ekiaevlrkav.rerglilvsGgTgsGKttllyallk 151
                                    ++++++lrk+  r + ++l+ G+ g+GKtt++  l +
  gene193|gene193|rna193|rna193  19 DHLKNILRKSDgRGHPNLLLYGPPGTGKTTFAHLLAN 55 
                                    56778888873145779*************9865543 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0012      0.61       2      21 ..      36      55 ..      35      74 .. 0.82
   2 ?   -0.2   0.0       1.6     8e+02      93     127 ..      82     117 ..      58     144 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                                   EEEE--TTSSHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvle 21
                                   +++ GppG+GKtT+ + +++
  gene193|gene193|rna193|rna193 36 LLLYGPPGTGKTTFAHLLAN 55
                                   6788***********98876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                                    HHHH-EEEE---STTGGG-HH.HHHHHHHHHTTTSE CS
                       NTPase_1  93 lseadviviDEiGkmElkskk.fkeaveevLksekp 127
                                    l +   i++DE+ ++   +++ +++ +e+ +++  +
  gene193|gene193|rna193|rna193  82 LDKDKTIILDECENLTSDAQHcLRRVIEDSVNTRFI 117
                                    244448899998655554443133344444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00088      0.45      22      40 ..      37      55 ..      23     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00088
                         AAA_30 22 vltGpAGtGKttalkalre 40
                                   +l Gp+GtGKtt    l++
  gene193|gene193|rna193|rna193 37 LLYGPPGTGKTTFAHLLAN 55
                                   789*********9877654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00039       0.2      20      42 ..      37      59 ..      32      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                         AAA_13 20 liYGwNGaGKTtLSrllrslelg 42
                                   l+YG  G+GKTt++ ll++ +l+
  gene193|gene193|rna193|rna193 37 LLYGPPGTGKTTFAHLLANRKLE 59
                                   68***************986543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.53
# Mc/sec: 1613.19
//
Query:       gene194|gene194|rna194|rna194  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-11   43.3   0.5    1.2e-10   41.4   0.1    2.0  2  DnaJ       DnaJ domain
    0.00044   20.7   3.2     0.0036   17.8   0.7    2.5  3  HSCB_C     HSCB C-terminal oligomerisation domain
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.31   11.1   0.0    1.7  1  Hormone_3  Pancreatic hormone peptide


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.1   1.9e-14   1.2e-10       2      62 ..       7      69 ..       6      69 .. 0.92
   2 ?   -0.7   0.0      0.26   1.6e+03       7      23 ..      95     111 ..      92     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.9e-14
                                   HHHHHTSSTTG..-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHH CS
                           DnaJ  2 yYeiLgvskda..sedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqY 62
                                   y++i g++++   ++ ++k++Y ++++++HPDk + +p      +ein+Ay+vL ++  R++Y
  gene194|gene194|rna194|rna194  7 YFDIFGLKPSFsiDKHDLKERYFEISKRIHPDKARPSPGEGTSIEEINKAYDVLRNDLARARY 69
                                   89*******96225777*******************************************999 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.26
                                    TSSTTG-HHHHHHHHHH CS
                           DnaJ   7 gvskdasedeIkkaYrk 23 
                                    gvs+d ++ +I++  +k
  gene194|gene194|rna194|rna194  95 GVSNDEDKRNIREDLQK 111
                                    78899999999887666 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.6   1.6e+04      26      39 ..      22      35 ..      19      37 .. 0.56
   2 ?    2.6   0.0     0.033     2e+02      50      72 ..      53      74 ..      46      75 .. 0.78
   3 !   17.8   0.7     6e-07    0.0036       3      49 ..      80     123 ..      79     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.6
                                   HHHHHHHHHHHHHH CS
                         HSCB_C 26 eeleelkaeveeri 39
                                    +l+e   e+++ri
  gene194|gene194|rna194|rna194 22 HDLKERYFEISKRI 35
                                   55555555555555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.033
                                   HHTT-HHHHHHHHHHHHHHHHHH CS
                         HSCB_C 50 fekkdleaaadllrrlrYlekik 72
                                   + +k ++ ++  l r rYl+++k
  gene194|gene194|rna194|rna194 53 I-NKAYDVLRNDLARARYLSSTK 74
                                   4.4578999999******99876 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 6e-07
                                    HHHHHHHHHHHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         HSCB_C   3 pefLmevMelrEeleeaeeaadkeeleelkaeveerieeleaeleea 49 
                                    ++fLme+++   e+  +  ++d e+ +++++++++ri+++   ++e+
  gene194|gene194|rna194|rna194  80 KQFLMEILDYEQEISGV--SND-EDKRNIREDLQKRIDHCKLHINEE 123
                                    58***************..546.99***************9888876 PP

>> Hormone_3  Pancreatic hormone peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.2e-05      0.31       6      25 ..      43      62 ..      40      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.2e-05
                                   XXXTTS-HHHHHHHHHHHHH CS
                      Hormone_3  6 rPgedaspEeLakYyaaLrh 25
                                   +Pge +s+Ee++k y+ Lr+
  gene194|gene194|rna194|rna194 43 SPGEGTSIEEINKAYDVLRN 62
                                   7************9999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 951.90
//
Query:       gene195|gene195|rna195|rna195  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2423.07
//
Query:       gene196|gene196|rna196|rna196  [L=658]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-12   47.1   5.8    5.8e-06   27.0   0.0    6.8  7  WD40         WD domain, G-beta repeat
    1.8e-09   37.7   0.0     0.0038   17.5   0.0    4.2  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
     0.0002   20.8   0.2     0.0013   18.2   0.1    2.2  2  WD40_like    WD40-like domain
     0.0017   18.2   0.4     0.0045   16.8   0.4    1.7  1  CHIPS        Chemotaxis-inhibiting protein CHIPS


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.037   1.7e+02      13      38 .]      18      41 ..       2      41 .. 0.63
   2 !   27.0   0.0   1.3e-09   5.8e-06       2      37 ..      45      81 ..      44      82 .. 0.92
   3 !    6.2   0.2    0.0046        21       4      38 .]      88     121 ..      85     121 .. 0.81
   4 ?    0.5   0.0       0.3   1.3e+03      10      34 ..     134     159 ..     128     160 .. 0.72
   5 ?    4.1   0.0     0.022        98      16      37 ..     185     210 ..     173     211 .. 0.76
   6 ?   -0.6   0.0      0.65   2.9e+03       6      37 ..     219     258 ..     215     259 .. 0.60
   7 ?    0.1   0.0      0.39   1.8e+03      13      32 ..     277     296 ..     270     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.037
                                   EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40 13 vtslafspdgawlasGsdDgtvriWd 38
                                   + s+++s dg+ ++++s  g +++W+
  gene196|gene196|rna196|rna196 18 IFSIDVS-DGH-IVTSSLGGEIKLWN 41
                                   6666333.333.457888*******8 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 1.3e-09
                                   EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40  2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriW 37
                                   +c+rt++ H + v +++fs dg+++asG+dDg v ++
  gene196|gene196|rna196|rna196 45 ECIRTIKKHqGTVLCVRFSVDGDLFASGGDDGMVFVY 81
                                   79*******777**********************987 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0046
                                    EEEEESS.SSEEEEEEETTSSE....EEEEETTSEEEEEE CS
                           WD40   4 lrtltGH.ssvtslafspdgaw....lasGsdDgtvriWd 38 
                                    +++ + H ++v+ +       w    l+s ++Dg v ++d
  gene196|gene196|rna196|rna196  88 VGSTSEHeNDVSNV------IWtdrfLVSVGYDGYVVLYD 121
                                    677789*999*999......888887777677*****998 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.3
                                    S.SSEEEEEEETTSSEEEEEETTSEE CS
                           WD40  10 H.ssvtslafspdgawlasGsdDgtv 34 
                                    H + + +++++++ +++++ +dDg v
  gene196|gene196|rna196|rna196 134 HeGQIKGICVDKSFRYMCTQGDDGIV 159
                                    64448888889999998765779987 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.022
                                    EEEETTSSEEEEE.E...TTSEEEEE CS
                           WD40  16 lafspdgawlasG.s...dDgtvriW 37 
                                    +++ pdg ++asG s     +tv ++
  gene196|gene196|rna196|rna196 185 MSWTPDGEFFASGlSfnrNYNTVEVF 210
                                    68**********97533236666665 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.65
                                    EEESS.SS..EEEEE...EETTSSE..EEEEETTSEEEEE CS
                           WD40   6 tltGH.ss..vtsla...fspdgaw..lasGsdDgtvriW 37 
                                    +l GH  +  v +++   + +d ++   a +s D ++ +W
  gene196|gene196|rna196|rna196 219 SLIGHaAPceVVAFSpvlYKKDRKYyvAAVSSQDLSLSLW 258
                                    5678865555666666665556666522345778888777 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 0.39
                                    EEEEEEETTSSEEEEEETTS CS
                           WD40  13 vtslafspdgawlasGsdDg 32 
                                    v +++++ +g+ l+ +s+ g
  gene196|gene196|rna196|rna196 277 VLDMCWNESGTRLLVCSYGG 296
                                    7899********99998555 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.8e-05      0.08      31      91 ..      49     105 ..      22     106 .. 0.83
   2 !   17.5   0.0   8.5e-07    0.0038       3      82 ..      62     137 ..      60     146 .. 0.90
   3 ?    3.5   0.0     0.019        87      43      60 ..     184     201 ..     165     227 .. 0.79
   4 !   11.0   0.0   8.7e-05      0.39      38      81 ..     274     317 ..     249     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                    ANAPC4_WD40  31 tleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWge 91 
                                    t+  +k++++v +++++ dg l+a + +dg v +++  +g+vv s s ++++ v+ + W++
  gene196|gene196|rna196|rna196  49 TI--KKHQGTVLCVRFSVDGDLFASGGDDGMVFVYK-RNGDVVGSTSEHEND-VSNVIWTD 105
                                    34..7999***********************98886.689999998888885.**999986 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 8.5e-07
                    ANAPC4_WD40   3 wcptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksek 82 
                                    ++   DL+A + +dg + v+  ng  v ++  +++++ v+++ W   +++L+ +  dg v l+d +s +v ++++ ++ +
  gene196|gene196|rna196|rna196  62 FSVDGDLFASGGDDGMVFVYKRNGDVVGST--SEHENDVSNVIWT--DRFLVSVGYDGYVVLYDQKSLDVAKKMRPHEGQ 137
                                    67778********************99998..89999*******6..79***********************99999875 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.019
                    ANAPC4_WD40  43 sLaWkpdgklLavaysdg 60 
                                     ++W pdg+++a + s +
  gene196|gene196|rna196|rna196 184 RMSWTPDGEFFASGLSFN 201
                                    799**********99865 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 8.7e-05
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                    +  v +++W+++g+ L v    gev  +d+e+g+  ++++ +++
  gene196|gene196|rna196|rna196 274 ELPVLDMCWNESGTRLLVCSYGGEVVQIDVEDGDFGKAYEEEED 317
                                    678999***************************98887776655 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.9e-07    0.0013      47     196 ..      19     173 ..      17     181 .. 0.81
   2 ?   -0.9   0.0      0.18   8.1e+02     103     127 ..     206     230 ..     201     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-07
                      WD40_like  47 fvklldddlilvvtlDGtillslleneeevenekieedistv..kviddklliGtnkGsiyvfskdlqleevllgqsseI 124
                                    f+  ++d +i+  +l G i l     e +  ++k +  + +v  +v++d ++ G++ G ++v++++  ++  ++ ++ ++
  gene196|gene196|rna196|rna196  19 FSIDVSDGHIVTSSLGGEIKLWNPDYECIRTIKKHQGTVLCVrfSVDGDLFASGGDDGMVFVYKRNGDVVGSTSEHENDV 98 
                                    55557788999999999994444444444445566667777633578999***************9999999******** PP

                      WD40_like 125 keikiennkiysLsesafiv.fdlfsqnieykisvkdiktfeiienkdilligtege..ililkknvilqkidve 196
                                     +++ ++ ++ s   + ++v +d +s +  +k+  +++++  i  +k    ++t+g+  i+++ + ++++k+d  
  gene196|gene196|rna196|rna196  99 SNVIWTDRFLVSVGYDGYVVlYDQKSLDVAKKMRPHEGQIKGICVDKSFRYMCTQGDdgIVLYEEFKVVKKVDAS 173
                                    *************998887559******************99999999988888764449999999999999864 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.18
                      WD40_like 103 siyvfskdlqleevllgqsseIkei 127
                                    ++ vf+kdl +e  l+g+ ++ + +
  gene196|gene196|rna196|rna196 206 TVEVFNKDLRNECSLIGHAAPCEVV 230
                                    6789**************9886544 PP

>> CHIPS  Chemotaxis-inhibiting protein CHIPS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4     1e-06    0.0045       6      70 ..     579     643 ..     574     647 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-06
                          CHIPS   6 ttlgklderlrnylkkgtknsaqfekmviltenkgyytvylntplaedrknvellgkmyktyffk 70 
                                    + l k  er+   lk+ tk +++++km  + e k    + +     e  k ve+lgkm   y+++
  gene196|gene196|rna196|rna196 579 SHLVKDKERMIRALKRITKAACKMKKMEDFIELKLKNIITMLLEAGERSKAVEILGKMNTNYVLQ 643
                                    6688999********************99999988888888888899************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3936.51
//
Query:       gene197|gene197|rna197|rna197  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-12   45.1   2.1    1.3e-11   44.6   2.1    1.3  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    2.2e-08   34.5   0.1    2.7e-08   34.2   0.1    1.2  1  Histone        Core histone H2A/H2B/H3/H4
    8.1e-06   25.9   0.2    1.1e-05   25.5   0.2    1.1  1  TAFII28        hTAFII28-like protein conserved region
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.029   13.9   0.0    1.1  1  Peptidase_C3G  Tungro spherical virus-type peptidase
       0.15   12.4   0.1       0.23   11.8   0.1    1.3  1  CENP-X         CENP-S associating Centromere protein X


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   2.1   3.6e-15   1.3e-11       6      65 .]      28      86 ..      23      86 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3.6e-15
                                   HHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                  CBFD_NFYB_HMF  6 arvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                   +++kkImk+     +i+kdA + ++ cv   i+e+++ A  +++ +++K ++++hi +A+
  gene197|gene197|rna197|rna197 28 SQIKKIMKDR-TRMRISKDALVAVSACVMYLISEITDGAKNVANTDGKKKVMPKHINHAI 86
                                   68********.5555******************************************997 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   7.6e-12   2.7e-08      71     129 ..      30      87 ..       9      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 7.6e-12
                                    HHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                        Histone  71 vreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                    +++i+k +++ +ris++a++a+ + + +l+ e++  A ++a+   ++ ++pk+i  A++
  gene197|gene197|rna197|rna197  30 IKKIMK-DRTRMRISKDALVAVSACVMYLISEITDGAKNVANTDGKKKVMPKHINHAIC 87 
                                    688998.**************************************************99 PP

>> TAFII28  hTAFII28-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.2     3e-09   1.1e-05      15      83 ..      18      85 ..      10      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3e-09
                        TAFII28 15 evfrrsklnkaavkklvnsvlsqsvsqnvaivvaglaKvFvgeiveeArevqeeweesgplqpehlrea 83
                                   e  ++s ++ +++kk+++  +   +s+  +++v+++    + ei   A++v ++ + ++ ++p+h+++a
  gene197|gene197|rna197|rna197 18 EEHHKSIVKLSQIKKIMKDRTRMRISKDALVAVSACVMYLISEITDGAKNVANTDG-KKKVMPKHINHA 85
                                   5578888999******************************************9984.56899***9988 PP

>> Peptidase_C3G  Tungro spherical virus-type peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.9e-06     0.029       3      72 ..      32     102 ..      30     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.9e-06
                  Peptidase_C3G   3 gldkdlnmvsllddklakiscvivnvlpnrta.ylnvlrliGtyvvlpahylealeeedtlyficfslvik 72 
                                     + kd + + + +d l+ +s+ ++ ++++ t    nv    G   v+p h  +a+ ++ +l+f+    +ik
  gene197|gene197|rna197|rna197  32 KIMKDRTRMRISKDALVAVSACVMYLISEITDgAKNVANTDGKKKVMPKHINHAICNDTELHFVGHDWLIK 102
                                    6789999999**********9999999988762679999*************************9877776 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.4e-05      0.23       8      53 ..      34      76 ..      22      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.4e-05
                                   HCCC-SS.TT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SE CS
                         CENP-X  8 Lqesfkd.ektkItkdalelvaeylklFvrEavaRaaeeaeeegkee 53
                                   ++    d  +++I+kdal +v+  +  +++E    a + a+++gk++
  gene197|gene197|rna197|rna197 34 MK----DrTRMRISKDALVAVSACVMYLISEITDGAKNVANTDGKKK 76
                                   33....3378*********************9998888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 766.57
//
Query:       gene198|gene198|rna198|rna198  [L=505]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-93  312.6   0.0    1.8e-93  312.1   0.0    1.2  1  PAP_central   Poly(A) polymerase central domain
    2.9e-20   72.6   0.9    9.9e-15   54.6   0.1    2.5  2  PAP_RNA-bind  Poly(A) polymerase predicted RNA binding domain
    2.6e-11   43.7   0.0    6.6e-11   42.4   0.0    1.7  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0017   18.2   0.0     0.0034   17.2   0.0    1.5  1  Nrap_D2       Nrap protein PAP/OAS-like domain


Domain annotation for each model (and alignments):
>> PAP_central  Poly(A) polymerase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.1   0.0   4.1e-97   1.8e-93       1     246 [.      11     349 ..      11     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 312.1 bits;  conditional E-value: 4.1e-97
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                    PAP_central   1 GvtepislakptekdlklteeLieeLkeqnlfeseeetkkreevlekleklvkefvkk...................... 58 
                                    Gvt p+s++++te+d+kl+ee+   L+e + fe++ee ++re+vl+kl+ +vkefv +                      
  gene198|gene198|rna198|rna198  11 GVTGPLSMKESTEEDVKLSEEMDMYLQERGFFEDDEEGQTRERVLGKLNFMVKEFVARmaknkgngdgekayggkiftfg 90 
                                    9******************************************************************************* PP

                                    .........................................................................xxxxxxx RF
                    PAP_central  59 .........................................................................lkevped 65 
                                                                                                             ++ v++ 
  gene198|gene198|rna198|rna198  91 syrlgvhgkgtdidalcivprhvtrndfftyfyeelkgdpnikgvtkiedafvpiikfefqgipidlvfarlnVPVVKDG 170
                                    ******************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    PAP_central  66 ldlkddslLknldekevrslnGvRvtdeilrlvpnketFrlaLraiklWAkrraiysnvlgflgGvawAllvariCqlyP 145
                                    ++l +d+lLk++dek++ slnG+Rvtde+l+lvpn++ F+ aLr+ik+WAkrr +y+n +g++gGva++l var+CqlyP
  gene198|gene198|rna198|rna198 171 INLLNDTLLKSMDEKCILSLNGSRVTDEMLNLVPNVKAFHSALRCIKYWAKRRCVYGNPYGYFGGVAFSLCVARVCQLYP 250
                                    ******************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    PAP_central 146 naaastlvskfFlvlskWkwpqpvlLkeieekeeplrvWdpkvnksdrahlmpiitpaypsmnstynvsrstlevlkeel 225
                                    na++ t+v kfF+++s+Wkwp+pv+L+++ + + +l+vWdpkv++sd++h+mp+itpaypsm++t+nvs+st++v++ e+
  gene198|gene198|rna198|rna198 251 NASSFTIVCKFFELFSSWKWPTPVILRPVVDLNYNLKVWDPKVYPSDKYHRMPVITPAYPSMCATHNVSNSTQHVITMEF 330
                                    *******************************997799******************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxx RF
                    PAP_central 226 krgleiteeiesgkakwekLf 246
                                    +r++ei++++e+++  ++++f
  gene198|gene198|rna198|rna198 331 SRAHEILSNLEKND--FRRIF 349
                                    ********998764..55555 PP

>> PAP_RNA-bind  Poly(A) polymerase predicted RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   2.2e-18   9.9e-15       1      57 [.     353     409 ..     353     415 .. 0.96
   2 !   16.1   0.1   1.5e-06    0.0067     102     159 ..     427     482 ..     413     492 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 2.2e-18
                   PAP_RNA-bind   1 tFFskYkyYLsvvassktkeaqkkWsglVESkvRlLvqkLeavesialahpfnkgfe 57 
                                    +FF +Yk +++v a s+ +e  +kW+g+VES++R+L +k eav++i +a pf+k f 
  gene198|gene198|rna198|rna198 353 DFFGRYKLFVEVLAMSTLEEGFTKWEGYVESRIRILASKFEAVDDILYAIPFPKAFR 409
                                    7******************************************************97 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.5e-06
                   PAP_RNA-bind 102 ytttfYIGLeleekakskkldlsypvqeFkelckswekykeelmsltvkhvknfdLpd 159
                                     +t f+I++++ + + +kk+ ++++v+eF+e +k+ e  ke+ m ++++ +k++d+  
  gene198|gene198|rna198|rna198 427 RCTAFFIAIDVIPVK-GKKVVVEQQVKEFMEFVKEYEG-KESNMWIEINSLKRKDVQG 482
                                    6899*********99.6********************9.99999********998765 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.5e-14   6.6e-11      11      93 ..      80     162 ..      73     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.5e-14
                                    HTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEEEEEEC CS
                   NTP_transf_2  11 lepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpllvksile 90 
                                    + ++ k+++fGSy+ G ++kg DiD l+++p++v r++ +++ ++  +   +++ ++++e  +v++ k+e++++++++++
  gene198|gene198|rna198|rna198  80 KAYGGKIFTFGSYRLGVHGKGTDIDALCIVPRHVTRNDFFTYFYEELKGDPNIKGVTKIEDAFVPIIKFEFQGIPIDLVF 159
                                    45589********************************777777888888888888899*************999999999 PP

                                    EEE CS
                   NTP_transf_2  91 erp 93 
                                     r+
  gene198|gene198|rna198|rna198 160 ARL 162
                                    885 PP

>> Nrap_D2  Nrap protein PAP/OAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.6e-07    0.0034       1     149 [.     208     349 ..     208     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.6e-07
                                    THHHHHHHHHHHHHHTT--SS--T.S-S-SHHHHHHHHHHHTSBBSTTS-BSS-TT--HHHHHHHHHHHHHHS--SS-EE CS
                        Nrap_D2   1 afkdAclLlkvWlrqRgfgssirk.aggfggfewamllalllqgggkkgrkklskslssyqlfkavlqfLastdltkkpi 79 
                                    af +A+  +k W+++R + +   + +g fgg+ +++++a +          +l ++ ss+ ++ ++++ ++s+++  +p+
  gene198|gene198|rna198|rna198 208 AFHSALRCIKYWAKRRCVYG---NpYGYFGGVAFSLCVARVC---------QLYPNASSFTIVCKFFELFSSWKW-PTPV 274
                                    689999***********994...4589***************.........9**********************9.7799 PP

                                    EE.......-------BEEES-.--SS...--EEETTT--BTTTT--HHHHHHHHHHHHHHHHHHT-SSS--HHHHH CS
                        Nrap_D2  80 fl.......gaskseeskkeseeefskafepvlvdpsgklNllakmtassydlLqqeAketlelLddsssdqFdslF 149
                                    +l        + k  + k ++++++++   pv++    ++   +++++s+ + +  e +++ e+L++ +++ F  +F
  gene198|gene198|rna198|rna198 275 ILrpvvdlnYNLKVWDPKVYPSDKYHR--MPVITPAYPSMCATHNVSNSTQHVITMEFSRAHEILSNLEKNDFRRIF 349
                                    998888876333334455666667666..899999999999************************999*****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2905.53
//
Query:       gene199|gene199|rna199|rna199  [L=77]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-34  117.3   0.3      2e-34  117.2   0.3    1.0  1  ubiquitin    Ubiquitin family
    2.7e-16   59.2   0.4    2.9e-16   59.0   0.4    1.0  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
    1.4e-05   25.5   0.1    5.5e-05   23.5   0.1    1.8  1  Ubiquitin_2  Ubiquitin-like domain
     0.0013   19.1   0.0     0.0015   18.9   0.0    1.1  1  Ubiquitin_5  Ubiquitin-like domain
     0.0046   17.0   0.0     0.0092   16.1   0.0    1.6  1  Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
     0.0048   16.9   0.3        2.3    8.3   0.0    2.0  2  Ubiquitin_4  Ubiquitin-like domain
     0.0081   16.1   0.0      0.009   15.9   0.0    1.2  1  TBK1_ULD     TANK binding kinase 1 ubiquitin-like domain
  ------ inclusion threshold ------
      0.061   13.9   0.1      0.075   13.6   0.1    1.2  1  DUF2407      DUF2407 ubiquitin-like domain
      0.092   13.5   0.0       0.11   13.3   0.0    1.2  1  Big_7        Bacterial Ig domain
      0.096   12.5   0.0       0.11   12.3   0.0    1.1  1  Sde2_N_Ubi   Silencing defective 2 N-terminal ubiquitin domai
       0.12   12.9   0.0       0.12   12.8   0.0    1.1  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.3   1.2e-37     2e-34       1      72 []       3      74 ..       3      74 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 1.2e-37
                                   EEEEETTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEESSC CS
                      ubiquitin  1 itvktldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlvlrlr 72
                                   i+vktl+gk+itleve sd++e++K+ki++kegip++qqrLi++Gk+Led rtl++y+iq++stlhlvlrlr
  gene199|gene199|rna199|rna199  3 IFVKTLTGKTITLEVEASDSIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74
                                   9********************************************************************986 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.4   1.8e-19   2.9e-16       1      72 []       1      71 [.       1      71 [. 0.98

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 1.8e-19
                                   EEEEEEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEEEEEEX CS
                      Rad60-SLD  1 ikiilkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdtidvvi 72
                                   ++i++k+ +gk+++++V+++  +++++ + ++k+gip+ +++rLiF G++L++  t+ d+ i++++t+++v+
  gene199|gene199|rna199|rna199  1 MQIFVKTLTGKTITLEVEASDSIENVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
                                   89************************************.******************************996 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   3.4e-08   5.5e-05      15      80 ..      12      69 ..       1      70 [. 0.85

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.4e-08
                                   EEEEEEETTSBHHHHHHHHHHHH---TTCEEEEEE.-SSSSEEECSSGCCSBCCCCT--TTEEEEE CS
                    Ubiquitin_2 15 sserrfsksltieelKekLelitGtspasmrLqlyddkkdnevsklddddalLgsYgvkdgmrihV 80
                                     +  ++ s++ie++K+k++   G++p+++rL +          k  +d ++L++Y+++  +++h 
  gene199|gene199|rna199|rna199 12 TITLEVEASDSIENVKAKIQDKEGIPPDQQRLIFA--------GKQLEDGRTLSDYNIQKESTLHL 69
                                   5566788999***********************99........5667899***********99995 PP

>> Ubiquitin_5  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   8.9e-07    0.0015      33      93 ..      12      73 ..       4      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.9e-07
                    Ubiquitin_5 33 kklletkLdvtgkelvskiaeefglkensiKlilngklleldktLeeQgvknnskv.mvLkl 93
                                     +le++ + + +++ +ki ++ g+  ++ +li  gk+le ++tL + +++++s + +vL+l
  gene199|gene199|rna199|rna199 12 TITLEVEASDSIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLhLVLRL 73
                                   55677777778889999999*****99***********************999875467765 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.6e-06    0.0092      16      87 ..      13      71 ..       1      74 [. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.6e-06
                                   EEEEEETT-BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-TTSBCCCCS-TTTTTTTS-EEEEEEE CS
                    Rad60-SLD_2 16 gpvkfsdaatvaelkekviaqWPkdkeekpksvndlklilaGkiLennktlkelrlplgevkggvtvmHvvv 87
                                     ++ +++++++++k+k+     +dke  p  +++ +li aGk Le+ +tl++++++        +++H+v+
  gene199|gene199|rna199|rna199 13 ITLEVEASDSIENVKAKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLSDYNIQKE------STLHLVL 71
                                   555666677777777777.....4555533..34569****************965433......3566666 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0029       4.8       1      33 [.       1      33 [.       1      37 [. 0.94
   2 !    8.3   0.0    0.0014       2.3      58      86 ..      43      70 ..      38      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0029
                    Ubiquitin_4  1 lkvtvkkldgeslevvvkqnatvkdLkkaierk 33
                                   +++ vk l g+++ ++v+ + +++++k+ i+ k
  gene199|gene199|rna199|rna199  1 MQIFVKTLTGKTITLEVEASDSIENVKAKIQDK 33
                                   7899*************************9975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                    Ubiquitin_4 58 LsfegekLkddkaklkeygirnkselsFv 86
                                   L+f g++L+ d  +l++y i+++s+l+ v
  gene199|gene199|rna199|rna199 43 LIFAGKQLE-DGRTLSDYNIQKESTLHLV 70
                                   899999986.6789************976 PP

>> TBK1_ULD  TANK binding kinase 1 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.5e-06     0.009      19      53 ..      17      51 ..       3      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                       TBK1_ULD 19 ihpyntvaifqeevakqTkiaaekQellfeghrll 53
                                   +++ + ++++  +++++  i++++Q l+f g++l 
  gene199|gene199|rna199|rna199 17 VEASDSIENVKAKIQDKEGIPPDQQRLIFAGKQLE 51
                                   67789999************************973 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.6e-05     0.075      15      64 ..      14      59 ..       5      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                        DUF2407 15 eLdipdpntttvagLkqliRerlpaelasrrLrLIyaGrlLedttslass 64
                                   +L+++  ++ +++++k  i ++    +   + rLI+aG+ Led  +l++ 
  gene199|gene199|rna199|rna199 14 TLEVE--ASDSIENVKAKIQDKE--GIPPDQQRLIFAGKQLEDGRTLSDY 59
                                   55565..5567778888888876..66667779*************9874 PP

>> Big_7  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.4e-05      0.11      13      43 ..       7      35 ..       6      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-05
                                   -EBTSEEEEEEEEE-SS-EEEEEEEETTEE. CS
                          Big_7 13 tvsggtvtisasAsddggvskVefyvdgtlg 43
                                   t++g+t+t++++Asd+  +++V+  +++++g
  gene199|gene199|rna199|rna199  7 TLTGKTITLEVEASDS--IENVKAKIQDKEG 35
                                   67899***********..9999999998874 PP

>> Sde2_N_Ubi  Silencing defective 2 N-terminal ubiquitin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.7e-05      0.11       2      88 ..       2      76 ..       1      77 [] 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-05
                     Sde2_N_Ubi  2 nvlvssfdgltlpstlsltlpstatvsdlvdklserlpeslkesliLttvsnkqlllssdvslssllassadsellslrllv 83
                                   +++v+++ g+    t++l++  + +++++ +k++++      +   L  + + ql  ++  +ls++  ++++    +l+l++
  gene199|gene199|rna199|rna199  2 QIFVKTLTGK----TITLEVEASDSIENVKAKIQDKEGIPPDQ-QRLIFAGK-QL--EDGRTLSDYNIQKES----TLHLVL 71
                                   8999*99996....999999999**********9998877555.45555554.66..99999****999999....99**** PP

                     Sde2_N_Ubi 84 rlrGG 88
                                   rlrGG
  gene199|gene199|rna199|rna199 72 RLRGG 76
                                   ****9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.6e-05      0.12      23      64 ..       9      52 ..       2      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.6e-05
                                   TTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCS.TTCHH CS
                      HATPase_c 23 kageieveikase..ddlvisveDnGiGipkedlkklfe.kfsqd 64
                                   ++++i++e++as+  ++++ +++D   Gip++++ ++f+ k  +d
  gene199|gene199|rna199|rna199  9 TGKTITLEVEASDsiENVKAKIQD-KEGIPPDQQRLIFAgKQLED 52
                                   56788888887556789999***9.78***********9876662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 465.43
//
Query:       gene2|gene2|rna2|rna2  [L=333]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     6e-110  367.3   0.0   6.8e-110  367.1   0.0    1.0  1  Glycolytic  Fructose-bisphosphate aldolase class-I


Domain annotation for each model (and alignments):
>> Glycolytic  Fructose-bisphosphate aldolase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  367.1   0.0  3.8e-114  6.8e-110       3     328 ..      10     332 ..       8     333 .] 0.98

  Alignments for each domain:
  == domain 1  score: 367.1 bits;  conditional E-value: 3.8e-114
                            HHHHHHHT-TT-EEEEE---HHHHHHHHHCTT----HHHHHHHHHHHHT-TT.GGGTEEEEEE-HHHHT-B-TTS-BHHHHHHHTT-E CS
             Glycolytic   3 aetakaivapGkGiLaaDestgtigkrlasigventeenrrayrelLfttdkeleeyisGvilfeetlyqkaddgkplvellkekgii 90 
                              +ak+i ++GkGiLaaDes gt+gkrl+++g+enteenrr++re+Lf+t++ le+yi+Gvil +et+ q+++dg+pl++llk++gi 
  gene2|gene2|rna2|rna2  10 GMMAKKILENGKGILAADESPGTLGKRLERLGIENTEENRRKFREILFSTKE-LERYIGGVILNQETFGQTNEDGVPLTKLLKKRGIE 96 
                            578************************************************9.*********************************** PP

                            EEEE----EEE-TTSSS-EEE---TTHHHHHHHHHHTT--EEEEEEEE--BTTBS-HHHHHHHHHHHHHHHHHHHHTT-EEEEEEEE- CS
             Glycolytic  91 pGiKvdkgvvplagtegetttqGldglaercaqykkdGarFaKWravlkisektpselaiqenanvLarYasicqenglvpivepeil 178
                            +GiK+dkg+++    e+e    Gl++l+ rc++   + a FaKWr+ +   +  pse +i+en +vLa+Ya icq+nglvpivepei+
  gene2|gene2|rna2|rna2  97 IGIKLDKGLIDY--KEKEKISVGLEDLDLRCKSSTFKDATFAKWRSLFYFYDGIPSEDCINENCSVLAKYAIICQKNGLVPIVEPEIF 182
                            *********765..5679********************************************************************** PP

                            --SS--HHHHHHHHHHHHHHHHHHHHHTT--GGG-EE--B-----TT-S----HHHHHHHHHHHHHTT--TTS-EEEEB-TT--HHHH CS
             Glycolytic 179 ldGdhdlercqkvtekvlaavykalsdhhvlleGtllkpnmvtpGaecskkatpeevaeatvtalrrtvPpavpgvvflSGgqseeea 266
                            l+Gd ++e + kv +++l++  k+l+ + v++ G+l+k++ vt+G  + +k+tp++va++t +al  tvP+ vpg+vflSGg s e+a
  gene2|gene2|rna2|rna2 183 LEGDYTIEGSYKVFRQILSTLVKYLNYESVYIPGVLIKTSYVTSGILSDEKYTPKKVATYTFRALLSTVPCGVPGIVFLSGGHSSEKA 270
                            **************************************************************************************** PP

                            HHHHHHHHHTS-.-SSEEEEEESHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHHHHHTTT- CS
             Glycolytic 267 tvnLnainklekkkpwaltfsygralqasvlkaWkGkkenvkaaqeellkrakanslaalgk 328
                             + Lnain  + ++ w+l+fs+gral   vl+aW+G++ n+++aq++ll+++ +  +aa+gk
  gene2|gene2|rna2|rna2 271 IAFLNAINMERGCRTWTLSFSFGRALTDDVLEAWRGEDPNIEEAQRVLLETSFKAYKAAEGK 332
                            ****************************************************9999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2070.66
//
Query:       gene20|gene20|rna20|rna20  [L=236]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-05   24.0   6.8    2.7e-05   23.5   6.8    1.3  1  BAR_2       Bin/amphiphysin/Rvs domain for vesicular traffick
  ------ inclusion threshold ------
      0.052   13.0   6.1      0.065   12.7   4.1    1.8  2  Pil1        Eisosome component PIL1
       0.06   12.6   7.4      0.069   12.4   3.5    2.0  2  TMPIT       TMPIT-like protein
      0.087   12.8   3.2       0.44   10.6   2.6    2.2  2  Laminin_II  Laminin Domain II
      0.089   13.0   3.5       0.19   12.0   3.5    1.4  1  MPM1        Mitochondrial peculiar membrane protein 1
       0.25   11.4   2.9       0.73    9.9   0.7    2.3  2  DUF1664     Protein of unknown function (DUF1664)
       0.42   11.1   2.5       0.51   10.8   0.1    2.2  2  SspO        Small acid-soluble spore protein O family
       0.61   10.3   6.5        1.7    8.9   0.0    3.2  3  XhlA        Haemolysin XhlA
       0.77   10.2   5.1        1.9    8.9   2.8    2.6  3  Goodbye     fungal STAND N-terminal Goodbye domain
        5.9    7.4   7.1        5.9    7.4   0.8    3.7  5  FlaC_arch   Flagella accessory protein C (FlaC)
        6.1    7.4   5.9        7.4    7.1   0.6    2.5  2  PP2C_C      Protein serine/threonine phosphatase 2C, C-termin


Domain annotation for each model (and alignments):
>> BAR_2  Bin/amphiphysin/Rvs domain for vesicular trafficking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   6.8   1.6e-08   2.7e-05      67     281 ..       4     233 ..       2     236 .] 0.56

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.6e-08
                      BAR_2  67 esisdwwksigaklke..lknvs.....sleedeivllgkkkkekskeeke.........sqatsallprtlaqalskaakdss 134
                                e ++d+ +si+ kl+   +++vs     s  ed   ++ ++ k       +         + ++ ++  ++l++ +  +++ s 
  gene20|gene20|rna20|rna20   4 ETVKDIQRSIAMKLNRvdYTEVSlisgySEAEDCYKKFRDNLK-------KisdsitwlmTYEHGGSKMKSLYSKMDMITSTSR 80 
                                6677777778777764113333311111222222222222222.......1223455566666667777788888877777776 PP

                      BAR_2 135 lilqele...............ekdedlepLikvleqvssaykeiaeakleqDslivkefnkkLeellnqefkkvhelrkk... 200
                                  l + +                +    ++++ + +++s+a+ +i++ k+e+            ++ l+q++kk++elr     
  gene20|gene20|rna20|rna20  81 --LGHFKnydiyelnglvglelSRIGLGSNVSDIGKKYSKAHMDISRYKVEM------------NRKLEQQIKKISELRDHsna 150
                                ..44443222444444444443333334444444445555555555555555............55555555555555532122 PP

                      BAR_2 201 VeesRlkfdtlrseveek...ekpeteeedkklleklEDefvsateeAvvvmkeildssklisllklfqkaqleYfekcvkkle 281
                                + ++R k   +r+++e     ++p+  ++++k  e++E  f +  +eA  +m++ + ++ +   l+++++a  e+ ek+ k l 
  gene20|gene20|rna20|rna20 151 IDKKRKKISNIRYDLEMMkrsKDPKAPDAVSK-EEEMERTFKETSKEALKEMERFIGNDGVCGVLQSVAQAHGEFSEKSSKVLG 233
                                45555555555555544322245555564444.488999****************************************99885 PP

>> Pil1  Eisosome component PIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.31   5.1e+02     137     167 ..      35      65 ..       4      81 .. 0.68
   2 ?   12.7   4.1     4e-05     0.065      97     181 ..     108     193 ..      95     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.31
                       Pil1 137 EasvqpsRdkkekladeiaklkakepqserl 167
                                E   +  Rd+ +k+ d+i  l + e    ++
  gene20|gene20|rna20|rna20  35 EDCYKKFRDNLKKISDSITWLMTYEHGGSKM 65 
                                4444555666666666666655555555444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4e-05
                       Pil1  97 dvsDvsDklgvllselgeledayadrldqsRatlKsirniEasvqpsRdkkekladeiakl.kakepqserlvvlEqeLvraea 179
                                +vsD+  k +   ++++  + ++  +l+q   ++ ++r+  + ++ +R+k + +  +++++ ++k+p+ +  v+ E+e+ r  +
  gene20|gene20|rna20|rna20 108 NVSDIGKKYSKAHMDISRYKVEMNRKLEQQIKKISELRDHSNAIDKKRKKISNIRYDLEMMkRSKDPKAPDAVSKEEEMERTFK 191
                                79***********************************************************557**************999876 PP

                       Pil1 180 es 181
                                e 
  gene20|gene20|rna20|rna20 192 ET 193
                                64 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.057        92      12      75 ..       4      72 ..       1      91 [. 0.75
   2 ?   12.4   3.5   4.2e-05     0.069      16      89 ..     129     205 ..     113     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.057
                      TMPIT 12 keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.....eeeeeeveelkeel 75
                               +++++ ++++  kl+++   + ++ +  ++ +  +k+++++lkk++ s++     e+  +++++l +++
  gene20|gene20|rna20|rna20  4 ETVKDIQRSIAMKLNRVDYTEVSLISGYSEAEDCYKKFRDNLKKISDSITwlmtyEHGGSKMKSLYSKM 72
                               678888899999999999999999999999999999999999999988666655544444444444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.2e-05
                      TMPIT  16 etakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelker.kkvlkevesll 89 
                                e +++++q+++++s+l +  s++i+k++k++++++ +l+ +k+s++    +  ++ ee+++++ke+ k+ lke+e ++
  gene20|gene20|rna20|rna20 129 EMNRKLEQQIKKISELRD-HSNAIDKKRKKISNIRYDLEMMKRSKDpkaPDAVSKEEEMERTFKETsKEALKEMERFI 205
                                456788888888888776.5789********************98833333444556788887765256778998876 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.39   6.3e+02      27      71 ..      32      75 ..       3     103 .. 0.67
   2 ?   10.6   2.6   0.00027      0.44      47      96 ..     113     162 ..      98     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.39
                               XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTT CS
                 Laminin_II 27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqL 71
                               ++ ++ +++++++++++ + +  +++  +  ++++k L  +++ +
  gene20|gene20|rna20|rna20 32 SEAEDCYKKFRDNLKKISDSITWLMT-YEHGGSKMKSLYSKMDMI 75
                               45566677777777777777765443.445566666666666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00027
                                XXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                 Laminin_II  47 vkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96 
                                 k+++ka  d +r  ++++++++q ++k++el+ +++a     ++is+i+
  gene20|gene20|rna20|rna20 113 GKKYSKAHMDISRYKVEMNRKLEQQIKKISELRDHSNAIDKKRKKISNIR 162
                                468999999************99999999999988888777888999998 PP

>> MPM1  Mitochondrial peculiar membrane protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.5   0.00011      0.19      77     161 ..     125     212 ..     107     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                       MPM1  77 nWksemkelikekreeeikkkkee...ekkkkesektkedlmlkkssekdskkkvvssssktsvntteegneeklkevkt.yfd 156
                                 +k em+++++++ ++  + + ++   +kk+k+ ++ + dl++ k s++ +  + vs++++++ + +e  ++e lke+++ + +
  gene20|gene20|rna20|rna20 125 RYKVEMNRKLEQQIKKISELRDHSnaiDKKRKKISNIRYDLEMMKRSKDPKAPDAVSKEEEMERTFKET-SKEALKEMERfIGN 207
                                68999999988887765444333300044444445788899999999988999*****99998766555.55********8889 PP

                       MPM1 157 dgtvk 161
                                dg + 
  gene20|gene20|rna20|rna20 208 DGVCG 212
                                99876 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.28   4.6e+02      55     104 ..       4      53 ..       2      77 .. 0.70
   2 ?    9.9   0.7   0.00045      0.73      38     107 ..     104     169 ..     100     174 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.28
                    DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedve 104
                                e++++ +r ++ +++rvd +  + +   +e ++  ++ r++l++i++ ++
  gene20|gene20|rna20|rna20   4 ETVKDIQRSIAMKLNRVDYTEVSLISGYSEAEDCYKKFRDNLKKISDSIT 53 
                                56677777777777777777777777777777777777777777776665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00045
                    DUF1664  38 slsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                +l + v++++k+  +   ++++ k ++++++++  kk+ e  + s++i+++    r+++s+i+ d+e +k
  gene20|gene20|rna20|rna20 104 GLGSNVSDIGKKYSKAHMDISRYKVEMNRKLEQQIKKISELRDHSNAIDKK----RKKISNIRYDLEMMK 169
                                667778888888888888888888777777777666666666666555443....555555555555444 PP

>> SspO  Small acid-soluble spore protein O family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3       1.6   2.7e+03      43      48 ..     152     157 ..     144     158 .. 0.85
   2 ?   10.8   0.1   0.00031      0.51      17      43 ..     181     206 ..     176     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                       SspO  43 nkKrKk 48 
                                 kKrKk
  gene20|gene20|rna20|rna20 152 DKKRKK 157
                                69***9 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00031
                       SspO  17 sqgkgagsrfyeEesqeplteaeRqnn 43 
                                s +++ + r+++E s+e l+e+eR+ +
  gene20|gene20|rna20|rna20 181 SKEEEME-RTFKETSKEALKEMERFIG 206
                                5566666.9***************865 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0011       1.7      29      53 ..      33      57 ..       4      62 .. 0.90
   2 ?    2.6   1.8     0.098   1.6e+02       8      44 ..     133     168 ..     109     173 .. 0.75
   3 ?   -1.5   0.1       1.9   3.1e+03      22      42 ..     182     202 ..     174     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                       XhlA 29 eaeekiknleedlkklesnqkWlir 53
                               eae   k   ++lkk+ ++++Wl++
  gene20|gene20|rna20|rna20 33 EAEDCYKKFRDNLKKISDSITWLMT 57
                               7788889999*************87 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.098
                       XhlA   8 rietkldnlee.rvdkleekaaeaeekiknleedlkkl 44 
                                ++e+++++++e r  +  +  ++ ++ki n+  dl+ +
  gene20|gene20|rna20|rna20 133 KLEQQIKKISElR--DHSNAIDKKRKKISNIRYDLEMM 168
                                4567777777744..66666677777777777776665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.9
                       XhlA  22 kleekaaeaeekiknleedlk 42 
                                k ee +++++e +k++ ++++
  gene20|gene20|rna20|rna20 182 KEEEMERTFKETSKEALKEME 202
                                445555555565655555544 PP

>> Goodbye  fungal STAND N-terminal Goodbye domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.3   5.4e+03      44      47 ..      41      44 ..       5      58 .. 0.59
   2 ?    8.9   2.8    0.0012       1.9       5      53 ..     123     170 ..     116     218 .. 0.93
   3 ?   -0.2   0.1      0.82   1.3e+03       7      50 ..     189     230 ..     183     234 .. 0.58

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.3
                    Goodbye 44 frek 47
                               fr +
  gene20|gene20|rna20|rna20 41 FRDN 44
                               2222 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                    Goodbye   5 lkeyekeTgkdlkdealkelssvedllkqieaekdkfeefrekkeklke 53 
                                + +y+ e +++l ++++k++s++ d ++ i+++++k ++ r + e +k+
  gene20|gene20|rna20|rna20 123 ISRYKVEMNRKL-EQQIKKISELRDHSNAIDKKRKKISNIRYDLEMMKR 170
                                579*********.*************************99977766665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.82
                    Goodbye   7 eyekeTgkdlkdealkelssvedllkqieaekdkfeefrekkek 50 
                                ++++++++ l  ++++++   + +   +++ ++++ ef+ek++k
  gene20|gene20|rna20|rna20 189 TFKETSKEAL--KEMERFIGNDGVCGVLQSVAQAHGEFSEKSSK 230
                                5666666666..55555555555555555555555555555554 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.8   6.2e+03      29      37 ..       5      13 ..       3      32 .. 0.57
   2 ?    1.0   0.0      0.35   5.7e+02      19      41 ..      34      56 ..      12      60 .. 0.72
   3 ?   -2.8   0.1       5.3   8.6e+03       8      19 ..      64      75 ..      63      79 .. 0.48
   4 ?    0.3   0.1      0.57   9.2e+02      10      34 ..     117     142 ..     109     143 .. 0.51
   5 ?    7.4   0.8    0.0036       5.9       6      35 ..     135     170 ..     132     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                  FlaC_arch 29 sveelkenV 37
                               +v+++++++
  gene20|gene20|rna20|rna20  5 TVKDIQRSI 13
                               333333333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.35
                  FlaC_arch 19 vkkeneelsksveelkenVkdll 41
                               +++  ++ +++++++ +++  l+
  gene20|gene20|rna20|rna20 34 AEDCYKKFRDNLKKISDSITWLM 56
                               55556667777777777776665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.3
                  FlaC_arch  8 klsklsteletv 19
                               k+++l ++++++
  gene20|gene20|rna20|rna20 64 KMKSLYSKMDMI 75
                               444444444443 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.57
                  FlaC_arch  10 sklsteletvkke.neelsksveelk 34 
                                sk  + ++  k e n +l+++++++ 
  gene20|gene20|rna20|rna20 117 SKAHMDISRYKVEmNRKLEQQIKKIS 142
                                55555555555441335555555554 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.0036
                  FlaC_arch   6 Enklsklst......eletvkkeneelsksveelke 35 
                                E++++k+s        ++  +k++++++ ++e++k+
  gene20|gene20|rna20|rna20 135 EQQIKKISElrdhsnAIDKKRKKISNIRYDLEMMKR 170
                                555555555555555*******************97 PP

>> PP2C_C  Protein serine/threonine phosphatase 2C, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.6     0.094   1.5e+02      23      42 ..     129     148 ..     118     178 .. 0.63
   2 ?    7.1   0.6    0.0045       7.4      15      43 ..     177     203 ..     171     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.094
                     PP2C_C  23 eldekleervkeiiekeekk 42 
                                e+++kle+++k i e +++ 
  gene20|gene20|rna20|rna20 129 EMNRKLEQQIKKISELRDHS 148
                                67788888888887722222 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0045
                     PP2C_C  15 eeavkkEkeldekleervkeiiekeekke 43 
                                ++av+kE+e++++ +e  ke+++  e + 
  gene20|gene20|rna20|rna20 177 PDAVSKEEEMERTFKETSKEALK--EMER 203
                                79********************9..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1752  (0.0977188); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1675.08
//
Query:       gene200|gene200|rna200|rna200  [L=206]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-17   61.6   0.1    9.9e-17   60.5   0.1    1.6  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.1   5.5e-21   9.9e-17      15      84 ..      92     161 ..      79     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 5.5e-21
                                    EEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEE CS
                 Ribosomal_L7Ae  15 klvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsala 84 
                                     ++ Glk+vt ++e ++aklv+++++v+p+e + +l++lc++++v y +v++   LG+lv++k ++++++
  gene200|gene200|rna200|rna200  92 LVKFGLKHVTNLIETKKAKLVLISASVDPIEVVIFLPTLCRKMGVSYAIVEDSTILGRLVNLKSTSCVCL 161
                                    5899***********************************************************9855544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1376.36
//
Query:       gene201|gene201|rna201|rna201  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-08   34.3   0.0    2.5e-08   33.8   0.0    1.3  1  Peptidase_S24  Peptidase S24-like
     0.0043   17.0   0.0      0.011   15.7   0.0    1.7  1  Cu_bind_like   Plastocyanin-like domain


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   2.8e-12   2.5e-08       2      66 ..      56     119 ..      55     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.8e-12
                                    XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SSTT.STEEE CS
                  Peptidase_S24   2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnne.ypply 66 
                                    v ++SM p+++ Gd+++   + +   Gd  vf+  +e    ++r+i++ g+r+l++ +n+ ++++ 
  gene201|gene201|rna201|rna201  56 VLSESMSPGFERGDILWLA-NKDFSVGDMTVFKFGKEI-PCVHRCIKQFGGRYLTKGDNNlDDDVS 119
                                    88****************7.99***************6.********************7799886 PP

>> Cu_bind_like  Plastocyanin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-06     0.011      11      39 ..      71      99 ..      66     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                   Cu_bind_like 11 kWaesktFrvGDtLlFkydsevhsvvevs 39
                                    W  +k F+vGD+ +Fk+ +e+  v++  
  gene201|gene201|rna201|rna201 71 LWLANKDFSVGDMTVFKFGKEIPCVHRCI 99
                                   59******************988887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1250.73
//
Query:       gene202|gene202|rna202|rna202  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-35  122.1   3.2    1.4e-35  121.8   3.2    1.0  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   3.2     8e-40   1.4e-35       1     111 [.       1     111 [.       1     117 [. 0.98

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 8e-40
                                    XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHHTTSS--SS---HHHHHHHHH CS
                 Ribosomal_S17e   1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkriqkgpvrgislklqeeerer 80 
                                    mg v++k+vK+aar+i eky+++l n F++n  v+++va+++skkl+n+iaGy t l k+i kg+   + +k  eeerer
  gene202|gene202|rna202|rna202   1 MGSVKNKIVKRAARTIAEKYFQRLDNTFDHNLLVVQDVAVVESKKLKNEIAGYLTSLYKKILKGTYNRVYIKSHEEERER 80 
                                    99****************************************************************************** PP

                                    HH-----------------HHHHHHHHHH-X CS
                 Ribosomal_S17e  81 rdnyvpevsaldqeaievdkdtkemlkslgf 111
                                    ++n+ p++s ld++ +evdk t++m+k+ g+
  gene202|gene202|rna202|rna202  81 KENVIPKESMLDVDCVEVDKVTMDMIKRYGY 111
                                    ***************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       993  (0.0553851); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 789.59
//
Query:       gene203|gene203|rna203|rna203  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-15   56.7   0.0    3.8e-15   55.8   0.0    1.5  1  TFIIF_beta    TFIIF, beta subunit HTH domain
      9e-10   39.4   0.1    1.6e-09   38.6   0.1    1.6  1  TFIIF_beta_N  TFIIF, beta subunit N-terminus


Domain annotation for each model (and alignments):
>> TFIIF_beta  TFIIF, beta subunit HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   4.3e-19   3.8e-15       2      65 .]     165     227 ..     164     227 .. 0.98

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 4.3e-19
                     TFIIF_beta   2 RmprqelldalfelFeeyqYWslkdLkaetrqPeayLkevLeeIAvlhrsGpfknkweLkpeyk 65 
                                    R+ ++e++d++f++Fe+y  W++kdL +   qP a+++e+ ++I vl+++ + kn++eL+peyk
  gene203|gene203|rna203|rna203 165 RLGKNEVIDMVFKAFEKYPSWTVKDLADFCGQPVAFIQEIVSDICVLNKK-DLKNTYELRPEYK 227
                                    899*********************************************99.99**********8 PP

>> TFIIF_beta_N  TFIIF, beta subunit N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   1.8e-13   1.6e-09       1      88 [.       9      89 ..       9     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.8e-13
                   TFIIF_beta_N  1 erkvWLvKvPkfLaekWekeeddeegielGklrikkdtskenkkqrvklklnedlsesekiPkeYelevtnervqntyVFsE 82
                                   + k+WL KvP fLae+       +e++ +G+l i+k+  ++++ + + lkl+++   +   P  +++++ + r +n yV + 
  gene203|gene203|rna203|rna203  9 NTKIWLAKVPLFLAERIL---SRNEETVVGELDITKA--TPTEPAVLNLKLSKE-FCEGGFPSSFDVKI-KARDNNMYVVKA 83
                                   579***************...66699**********9..777889*******55.67889*********.999*******65 PP

                   TFIIF_beta_N 83 kdlkga 88
                                   ++ ++ 
  gene203|gene203|rna203|rna203 84 HENNAD 89
                                   555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1428.11
//
Query:       gene204|gene204|rna204|rna204  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-09   37.3   0.1    1.3e-07   32.2   0.0    2.3  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   7.2e-12   1.3e-07       1      76 []      11      83 ..      11      83 .. 0.93
   2 !    3.3   0.1    0.0077   1.4e+02      12      56 ..     105     149 ..      95     173 .. 0.58

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.2e-12
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-.CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                   Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltrei.pegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                   +P++++vs +g ++ ++ Gpkg++  ++ ++ +t+++   +++++   ++g++k+ + l  tv sl +n ik Vt g
  gene204|gene204|rna204|rna204 11 VPENCTVSQEG-KVFTFEGPKGSIVEDCtRHPLTFDIY--EGNIRIRLWNGKRKAAA-LAITVESLLRNAIKAVTVG 83
                                   7*********8.***********9999824669***88..99***************.****************976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0077
                                    TTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH CS
                   Ribosomal_L6  12 gqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv 56 
                                    g+++lv+ + ge +++i +   v+    ++ ++ iv++g +  +v
  gene204|gene204|rna204|rna204 105 GKILLVKNFLGEKSVKIFKMRGVARVRLDERKDTIVIEGPSLPDV 149
                                    455555555555555555444444444447888888888776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1127.38
//
Query:       gene205|gene205|rna205|rna205  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-30  102.7   6.5    1.6e-29  101.9   6.5    1.4  1  Ribosomal_L24e  Ribosomal protein L24e
    0.00016   21.5   4.3    0.00035   20.4   4.3    1.6  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   6.5   1.8e-33   1.6e-29       1      64 [.       1      64 [.       1      66 [. 0.97

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 1.8e-33
                                   XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT--GGGSTTSTTT-XXXXXXXX CS
                 Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrnPrklkWTkayRrahkkelt 64
                                   m++ekC+F++++iy GhG+++vrnD+kvfrF++sKc+k+f+++ nPr++kWTk++R++++kel 
  gene205|gene205|rna205|rna205  1 MRIEKCWFCSSNIYQGHGTVYVRNDAKVFRFCRSKCRKFFERRVNPRRVKWTKIARKMANKELC 64
                                   9************************************************************976 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   4.3   3.9e-08   0.00035       5      39 ..       5      38 ..       3      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.9e-08
                         zf-FCS  5 rCwfCkkyikgkpeftyvlendgvvgqFCStsCld 39
                                   +CwfC+ +i+ ++  t+++ nd +v +FC + C++
  gene205|gene205|rna205|rna205  5 KCWFCSSNIYQGH-GTVYVRNDAKVFRFCRSKCRK 38
                                   8************.7**************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1059.21
//
Query:       gene206|gene206|rna206|rna206  [L=442]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   12.5   0.2        5.9    5.1   0.0    2.8  2  CDC45     CDC45-like protein


Domain annotation for each model (and alignments):
>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0   0.00033       5.9      11      31 ..      30      50 ..      20      51 .. 0.87
   2 ?    4.2   0.1   0.00059        11     232     265 ..     108     143 ..     103     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.00033
                          CDC45 11 alCAariLtsLLkkdliphki 31
                                   + CAa+i+t++L+k+li +++
  gene206|gene206|rna206|rna206 30 SFCAAKIITEILHKELIRFEV 50
                                   89***************9986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.00059
                          CDC45 232 slmYsLaselgredndlLW..lAIvGltslelseri 265
                                    +l YsLa++++  +nd+LW  +++ G  ++++++ +
  gene206|gene206|rna206|rna206 108 ILAYSLAKAMNYITNDILWpiITCFGFYKMFTKNTM 143
                                    678999999999999999955566677777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2991.06
//
Query:       gene207|gene207|rna207|rna207  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 673.14
//
Query:       gene208|gene208|rna208|rna208  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   13.3   0.3       0.92    9.0   0.1    2.7  2  DUF3153   Protein of unknown function (DUF3153)
      0.046   13.5   0.1      0.046   13.5   0.1    2.4  2  DUF3449   Domain of unknown function (DUF3449)
        6.7    6.8  15.3       0.28   11.2   6.9    2.3  2  YL1       YL1 nuclear protein


Domain annotation for each model (and alignments):
>> DUF3153  Protein of unknown function (DUF3153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00015      0.92      15      89 ..      31     107 ..      21     153 .. 0.86
   2 ?    1.2   0.0      0.04   2.4e+02      39      61 ..     298     321 ..     248     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00015
                        DUF3153  15 qelssasgeqlpwqeeleqrlaelggkveerdeeelrltipflngeeleellnrlvsrase..aaglslpepelrlv 89 
                                    +e +++ +++l +++ +e ++++  g++++r eee+rl+    + e+ +++ n+ ++r+s+    +l++  p +r v
  gene208|gene208|rna208|rna208  31 KEYEENEANSLKLRNFVEDEFYQSDGQMQYRGEEEMRLRYGRKKKEKRKKKKNDENKRPSNrkIVNLPASPPYVRFV 107
                                    66778889999**********************************************99996656666666655544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.04
                        DUF3153  39 ggkve.erdeeelrltipflngee 61 
                                    ++k+e +++++el ++i fln e+
  gene208|gene208|rna208|rna208 298 KSKWEsHNADNELAVKIAFLNVEN 321
                                    567778999***********9986 PP

>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.4      0.11   6.7e+02      28      57 ..      63      87 ..      19     102 .. 0.39
   2 ?   13.5   0.1   7.8e-06     0.046     101     165 ..     296     362 ..     292     367 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
                                   T--HHHHHHH.....................HH--SS--B-XX CS
                        DUF3449 28 altaeereeeeeeeeeek.............keeeedeeeeee 57
                                                    +             +++++++e+  +
  gene208|gene208|rna208|rna208 63 E----------------EemrlrygrkkkekRKKKKNDEN--K 87
                                   1................01122222211111111222222..1 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.8e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXX.XXXXXXXXX CS
                        DUF3449 101 kGrkaFekHFseerHaeglkcLgientklfkeitkiedaleLweklkkekkk..ekakeeeeveveD 165
                                    +G+ ++e+H  ++  a ++  L++ent+ ++ i  +++ + L + +++ k+k  e +++e+++e+ D
  gene208|gene208|rna208|rna208 296 FGKSKWESHNADNELAVKIAFLNVENTSFWNAIKALDKTTVLKKAIEAYKQKrdEYVSSEDDTEISD 362
                                    699*******************************************876555004455555666655 PP

>> YL1  YL1 nuclear protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   6.9   4.8e-05      0.28      24      98 ..      18      89 ..       4     141 .. 0.60
   2 ?    0.1   1.2      0.12   7.3e+02      19      53 ..     275     352 ..     260     368 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.8e-05
                                   xxxxxxxxxxxx...xxxxxxxxxxxx.....xxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                            YL1 24 lellFaEeedDe...efeseeeeeeee.....nsDsdfdsdeedee.sdeeedeeegekele.rqerkkrkkekkkrkaqkk 95
                                   ++  F+E+ dD    e+e++e +   +     +         ede  +++++ + +ge+e++ r  rkk++k+ kk+k++++
  gene208|gene208|rna208|rna208 18 IY-QFQEDSDDLgekEYEENEAN---SlklrnF--------VEDEFyQSDGQMQYRGEEEMRlRYGRKKKEKR-KKKKNDEN 86
                                   34.4****999732355544333...2233442........33333344444555666666654444444222.33333322 PP

                                   xxx RF
                            YL1 96 ksk 98
                                   k  
  gene208|gene208|rna208|rna208 87 KRP 89
                                   222 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
                                    xxxxxxxx...xxxxxxxxxxxxxxxxxxxxx........................................xxxxxx RF
                            YL1  19 eeedelel...lFaEeedDeefeseeeeeeee........................................nsDsdf 53 
                                    + +de++    +F ++ dD  f +++ e  +                                         + D+ +
  gene208|gene208|rna208|rna208 275 KIDDEFKSrfsVFMDDFDDTSFGKSKWESHNAdnelavkiaflnventsfwnaikaldkttvlkkaieaykqKRDEYV 352
                                    337777777777888888888776655554435556666666666666666666666666666555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1312  (0.0731775); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2262.96
//
Query:       gene209|gene209|rna209|rna209  [L=499]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-18   65.1   0.0    1.2e-12   47.8   0.0    2.5  2  Thioredoxin    Thioredoxin
    1.3e-06   28.5   4.3      0.016   15.1   0.0    3.5  4  Thioredoxin_6  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.037   14.3   0.3        1.3    9.4   0.0    3.2  3  Thioredoxin_8  Thioredoxin-like
       0.15   11.8   0.1       0.27   10.9   0.1    1.3  1  Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal regi


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   2.6e-16   1.2e-12      18     101 ..      23     105 ..      10     107 .. 0.89
   2 !   14.7   0.0   5.1e-06     0.023      40      82 ..     159     201 ..     140     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.6e-16
                                    SSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT...TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HH CS
                    Thioredoxin  18 kklvlveFyApwCghCkalaPeleklaeelkd...kvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarek 94 
                                    +   l +++ +wC++C+++aP++e++++++     ++k+   d+d++    +  +++++Ptl l k+g+   ++eg++  
  gene209|gene209|rna209|rna209  23 EGYALTKYFTQWCPSCQSIAPVIEEISNKIDRhgaNLKIRSADCDKC----SCPNIKSYPTLELSKDGEVLGRLEGGHGY 98 
                                    5678999***********************99888999999999887....5567************************* PP

                                    HHHHHHH CS
                    Thioredoxin  95 eklaafl 101
                                    +++++f+
  gene209|gene209|rna209|rna209  99 DAIVEFI 105
                                    ***9998 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.1e-06
                                    HHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETT CS
                    Thioredoxin  40 leklaeelkdkvklakvdvdenedlakkyevegiPtlklfkng 82 
                                    +++la+ + +k+ + ++d  e+++ +++y+++++P +  + ng
  gene209|gene209|rna209|rna209 159 FKELAKIYDGKLNIGEIDSAESAEFVNRYDIRSYPSISGIFNG 201
                                    7899999999**************************9866666 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.5e-06     0.016      95     184 .]     141     224 ..     122     224 .. 0.81
   2 !   14.2   0.4     7e-06     0.031       4     105 ..     151     258 ..     147     278 .. 0.76
   3 !   11.3   0.3   5.4e-05      0.24      63     105 ..     333     375 ..     310     446 .. 0.72
   4 ?   -0.3   0.0      0.19   8.6e+02      40      81 ..     419     466 ..     415     481 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.5e-06
                                    --EEEEEEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHTT--GGG-SEEEEEESSSS-EEEET.TSS- CS
                  Thioredoxin_6  95 lppllllflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleylglsssdlPvivivdsashkykypp.kdef 173
                                     p +++lf+     e++k++++++++ak + +k+n+  +d  + ++++++++++  + P i  +      + ++  + e+
  gene209|gene209|rna209|rna209 141 GP-YVVLFYS---REDDKYREIFKELAKIYDGKLNIGEIDSAESAEFVNRYDIR--SYPSISGIF-NGLVVPFIEkEREP 213
                                    34.8899994...5789**********************************999..999997333.24567788777799 PP

                                    -HHHHHHHHHH CS
                  Thioredoxin_6 174 speklkeFlkd 184
                                    s+ +l eF+++
  gene209|gene209|rna209|rna209 214 SVLSLIEFCDK 224
                                    99999999985 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7e-06
                                    STSTHHHHHHHHTTT-T.TSEEEEE--HH...HHHHTT--S.SEEEEEETTTTEEEEEETH..T--HHHHHHHHHHH--- CS
                  Thioredoxin_6   4 kdkeeseiFekvakelkgdvrfgvtkske...vadklgvke.pavllfrkfdeekvkydge..kitvddlkkfieknslp 77 
                                    +d++++eiF++ ak + g++  g + s+e   +++ +++++ p++  + +     v + ++  + +v +l +f++k + p
  gene209|gene209|rna209|rna209 151 EDDKYREIFKELAKIYDGKLNIGEIDSAEsaeFVNRYDIRSyPSISGIFNGLV--VPFIEKerEPSVLSLIEFCDKLIEP 228
                                    689999*****************9999886668888***99999985554233..33333335569999*********** PP

                                    SEEE-SHHHHHHHHTS..S--EEEEEEE-T CS
                  Thioredoxin_6  78 lvreltpenaeelfee..glppllllflkk 105
                                     +  lt+e +++l ++  +  p++++f+k+
  gene209|gene209|rna209|rna209 229 SFSNLTFEKFNDLASNlePGEPIYVVFHKN 258
                                    ***********9987522445677777754 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 5.4e-05
                                    -HHHHHHHHHHH---SEEE-SHHHHHHHHTSS--EEEEEEE-T CS
                  Thioredoxin_6  63 tvddlkkfieknslplvreltpenaeelfeeglppllllflkk 105
                                    +  +++++i    + + ++++  n+  +f+  +p+++ll + +
  gene209|gene209|rna209|rna209 333 DEVKITDWIFHTHYKYLTKVDNRNFYSIFHGLKPVMILLTRGE 375
                                    55689***************************99666665533 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.19
                                    -SSEEEEEET....TTTEEEEEETH..T--HHHHHHHHHHH---SEEE CS
                  Thioredoxin_6  40 kepavllfrk....fdeekvkydge..kitvddlkkfieknslplvre 81 
                                    ++pa+++f +    f  +kvk++++     + d    ++knslpl++ 
  gene209|gene209|rna209|rna209 419 STPALIVFEPwanlFRHKKVKLTEDnfISAAMDTYALYQKNSLPLYPP 466
                                    668888888655667778888888876557788888899999999986 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00029       1.3       8      36 ..      30      59 ..      25      68 .. 0.83
   2 ?   -0.5   0.0      0.35   1.6e+03       4      28 ..     143     167 ..     141     185 .. 0.83
   3 ?   -1.4   0.0       0.7   3.1e+03      37      62 ..     249     271 ..     226     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00029
                                   E--SSSHHHHHHHHHHHHHHHHHHH.TTSE CS
                  Thioredoxin_8  8 fgaswcppckaftpklkelyeklkk.kkkv 36
                                   +++ wcp+c+ + p + e+++k+   + ++
  gene209|gene209|rna209|rna209 30 YFTQWCPSCQSIAPVIEEISNKIDRhGANL 59
                                   6789******************98655555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                                    EEEEE--SSSHHHHHHHHHHHHHHH CS
                  Thioredoxin_8   4 vlLyfgaswcppckaftpklkelye 28 
                                    +++ f++ ++++ +++ ++l ++y+
  gene209|gene209|rna209|rna209 143 YVVLFYSREDDKYREIFKELAKIYD 167
                                    5677888889999999999999986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.7
                                    EEEEEE-SS-HHHHHHHGGGS-TTSE CS
                  Thioredoxin_8  37 eivyvsldkkeeefekylkknkkpwl 62 
                                    e +yv ++k+    ++y++ +    +
  gene209|gene209|rna209|rna209 249 EPIYVVFHKNVALANAYFQRM---AH 271
                                    678888888888888999988...22 PP

>> Cytochrom_NNT  NapC/NirT cytochrome c family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1     6e-05      0.27      36      75 ..      32      73 ..      23      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6e-05
                  Cytochrom_NNT 36 eeFCvsCHemednveeykesi..HysnrsgvraeCsdCHvPk 75
                                   +++C sC ++ + +ee+++ i  H +n +   a+C  C  P+
  gene209|gene209|rna209|rna209 32 TQWCPSCQSIAPVIEEISNKIdrHGANLKIRSADCDKCSCPN 73
                                   689*************9987655999999999******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2796.44
//
Query:       gene21|gene21|rna21|rna21  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-12   47.6  37.0    2.7e-05   23.9   0.4    5.0  5  zf-CCCH    Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    2.6e-08   34.5  25.4    0.00032   21.4   2.5    4.2  4  Torus      Torus domain
    5.3e-08   32.7  42.2      2e-05   24.5   2.9    5.9  5  zf_CCCH_4  Zinc finger domain
    8.4e-06   25.5   0.5    8.4e-06   25.5   0.5    4.5  5  zf-CCCH_4  CCCH-type zinc finger
     0.0014   18.9  24.9      0.013   15.7  10.4    3.5  3  zf-CCCH_3  Zinc-finger containing family
  ------ inclusion threshold ------
      0.039   13.7   0.7      0.039   13.7   0.7    5.0  5  zf-C3H1    Putative zinc-finger domain
        1.3    9.6  44.1       0.48   11.0   3.4    6.0  6  zf-CCCH_2  RNA-binding, Nab2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4      0.32   8.2e+02       6      22 ..      26      40 ..      22      45 .. 0.66
   2 !   23.9   0.4   1.1e-08   2.7e-05       5      25 ..      51      70 ..      49      72 .. 0.94
   3 !   13.9   0.9   1.5e-05     0.039       3      25 ..      77      98 ..      75     100 .. 0.93
   4 !   13.6   3.8   1.8e-05     0.047       4      26 ..     106     127 ..     104     128 .. 0.80
   5 !   15.9   5.0   3.5e-06    0.0089       4      27 .]     130     152 ..     128     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.32
                               BCHHHHHS--TTGGG-S CS
                    zf-CCCH  6 CrffmrtGyCkyGdrCk 22
                               C  ++   +Ck  ++C+
  gene21|gene21|rna21|rna21 26 CIPYQT-NSCKD-PNCS 40
                               555555.88987.7776 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.1e-08
                               CBCHHHHHS--TTGGG-SSBS CS
                    zf-CCCH  5 lCrffmrtGyCkyGdrCkFaH 25
                                C++++r G Ck G +C F+H
  gene21|gene21|rna21|rna21 51 VCKHWLR-GLCKKGIKCEFMH 70
                               7******.************* PP

  == domain 3  score: 13.9 bits;  conditional E-value: 1.5e-05
                               CHCBCHHHHHS--TTGGG-SSBS CS
                    zf-CCCH  3 telCrffmrtGyCkyGdrCkFaH 25
                               +++C ff+ +G+C   + C+++H
  gene21|gene21|rna21|rna21 77 MPECYFFSSYGECMN-PECNYIH 98
                               799************.******* PP

  == domain 4  score: 13.6 bits;  conditional E-value: 1.8e-05
                                HCBCHHHHHS--TTGGG-SSBSC CS
                    zf-CCCH   4 elCrffmrtGyCkyGdrCkFaHg 26 
                                ++C+ ++ +G+C+ G++Ck  H+
  gene21|gene21|rna21|rna21 106 KECP-WYNRGFCRNGASCKNKHV 127
                                5799.5555*********97775 PP

  == domain 5  score: 15.9 bits;  conditional E-value: 3.5e-06
                                HCBCHHHHHS--TTGGG-SSBSCS CS
                    zf-CCCH   4 elCrffmrtGyCkyGdrCkFaHgq 27 
                                +lC +++  G+C++G++C + H++
  gene21|gene21|rna21|rna21 130 KLCYNYFL-GFCPRGPTCDYGHPK 152
                                79******.*********999985 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   2.5   1.2e-07   0.00032      53      92 ..      31      71 ..      13      79 .. 0.81
   2 !    7.0   0.4    0.0036       9.3      72      97 ..      79     104 ..      73     107 .. 0.78
   3 !   12.3   0.5   8.2e-05      0.21      69      91 ..     104     126 ..     100     128 .. 0.87
   4 !   12.2   1.8     9e-05      0.23      66      91 ..     125     150 ..     123     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-07
                               --HHHH----HHH.HSTT--B-HHHHHT--SSGGG-SSB-S CS
                      Torus 53 cnikkdsGytkad.kekesyfClfFarGlCakGkkCeylHr 92
                                n  kd    k++ k +++++C ++ rGlC+kG kCe++H+
  gene21|gene21|rna21|rna21 31 TNSCKDPNCSKQHvKLSTAVVCKHWLRGLCKKGIKCEFMHE 71
                               5555666666666467788*********************7 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0036
                                B-HHHHH.T--SSGGG-SSB-S---SS CS
                      Torus  72 fClfFar.GlCakGkkCeylHrlPtee 97 
                                 C+fF+  G C++  +C+y+H  P+++
  gene21|gene21|rna21|rna21  79 ECYFFSSyGECMN-PECNYIHIDPNSS 104
                                5999975388886.79*****988765 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 8.2e-05
                                T--B-HHHHHT--SSGGG-SSB- CS
                      Torus  69 esyfClfFarGlCakGkkCeylH 91 
                                +s  C ++ rG+C +G++C+  H
  gene21|gene21|rna21|rna21 104 SSKECPWYNRGFCRNGASCKNKH 126
                                5678****************999 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 9e-05
                                HSTT--B-HHHHHT--SSGGG-SSB- CS
                      Torus  66 kekesyfClfFarGlCakGkkCeylH 91 
                                k+ ++ +C+ +  G+C++G  C+y H
  gene21|gene21|rna21|rna21 125 KHVRKKLCYNYFLGFCPRGPTCDYGH 150
                                5667899*****************99 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.21   5.4e+02       1      10 [.      26      35 ..      26      36 .. 0.87
   2 !   24.5   2.9   7.7e-09     2e-05       1      19 []      52      70 ..      52      70 .. 0.99
   3 ?    2.7   1.6     0.056   1.4e+02       1      19 []      80      98 ..      80      98 .. 0.66
   4 !   11.4   6.0   9.9e-05      0.25       4      19 .]     110     126 ..     108     126 .. 0.86
   5 !   11.3   4.9   0.00011      0.28       1      19 []     132     150 ..     132     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                  zf_CCCH_4  1 CkfflqGtCk 10
                               C  +++++Ck
  gene21|gene21|rna21|rna21 26 CIPYQTNSCK 35
                               778999***8 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 7.7e-09
                  zf_CCCH_4  1 CkfflqGtCkkGdkCrFaH 19
                               Ck++l+G CkkG kC F+H
  gene21|gene21|rna21|rna21 52 CKHWLRGLCKKGIKCEFMH 70
                               ******************* PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.056
                  zf_CCCH_4  1 Ckfflq.GtCkkGdkCrFaH 19
                               C ff   G C +   C+++H
  gene21|gene21|rna21|rna21 80 CYFFSSyGECMN-PECNYIH 98
                               888888888874.4555555 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 9.9e-05
                  zf_CCCH_4   4 flq.GtCkkGdkCrFaH 19 
                                + + G C++G++C+  H
  gene21|gene21|rna21|rna21 110 WYNrGFCRNGASCKNKH 126
                                6666**********988 PP

  == domain 5  score: 11.3 bits;  conditional E-value: 0.00011
                  zf_CCCH_4   1 CkfflqGtCkkGdkCrFaH 19 
                                C ++  G C++G  C + H
  gene21|gene21|rna21|rna21 132 CYNYFLGFCPRGPTCDYGH 150
                                ***************9988 PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.88   2.2e+03       6      12 ..      29      35 ..      26      35 .. 0.82
   2 !   25.5   0.5   3.3e-09   8.4e-06       1      22 []      50      71 ..      50      71 .. 0.95
   3 ?   -1.3   0.0       0.8     2e+03      17      21 ..      94      98 ..      92      98 .. 0.91
   4 !    6.0   4.0     0.004        10       3      21 ..     108     126 ..     106     127 .. 0.88
   5 ?    4.3   5.4     0.014        37       1      22 []     130     151 ..     130     151 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.88
                  zf-CCCH_4  6 fakGsCr 12
                               ++++sC+
  gene21|gene21|rna21|rna21 29 YQTNSCK 35
                               7899996 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 3.3e-09
                  zf-CCCH_4  1 rlCpyfakGsCrfGdnCrFsHd 22
                               ++C+++++G C+ G +C F H+
  gene21|gene21|rna21|rna21 50 VVCKHWLRGLCKKGIKCEFMHE 71
                               59*******************6 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.8
                  zf-CCCH_4 17 CrFsH 21
                               C++ H
  gene21|gene21|rna21|rna21 94 CNYIH 98
                               99*99 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.004
                  zf-CCCH_4   3 CpyfakGsCrfGdnCrFsH 21 
                                Cp + +G Cr G  C+ +H
  gene21|gene21|rna21|rna21 108 CPWYNRGFCRNGASCKNKH 126
                                99999**********8666 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.014
                  zf-CCCH_4   1 rlCpyfakGsCrfGdnCrFsHd 22 
                                +lC +++ G C  G+ C + H+
  gene21|gene21|rna21|rna21 130 KLCYNYFLGFCPRGPTCDYGHP 151
                                68999999***********997 PP

>> zf-CCCH_3  Zinc-finger containing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7  10.4     5e-06     0.013       6      91 ..      22     105 ..      16     108 .. 0.77
   2 !   11.9  10.9   7.5e-05      0.19       8      69 ..      52     113 ..      49     128 .. 0.77
   3 !    7.8   2.3    0.0015       3.8       5      28 ..     129     152 ..     125     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5e-06
                  zf-CCCH_3   6 ddcyffyyst.ctkGdscpfrheeaalGsetvctlWqegrclre.vckfrhmeidkkrkeipcywenqpaGcqklhcaflhekp 87 
                                d+ y   y t   k  +c+ +h +  l + +vc+ W +g c +  +c+f h e d  r    cy+ +  + c+ ++c ++h  p
  gene21|gene21|rna21|rna21  22 DEVYCIPYQTnSCKDPNCSKQHVK--LSTAVVCKHWLRGLCKKGiKCEFMH-EYDLSR-MPECYFFSSYGECMNPECNYIHIDP 101
                                55666655541457789**99987..7889***********9863699988.455554.4589******************998 PP

                  zf-CCCH_3  88 ravd 91 
                                ++ +
  gene21|gene21|rna21|rna21 102 NSSS 105
                                8655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.5e-05
                  zf-CCCH_3   8 cyffyystctkGdscpfrheeaalGsetvctlWq.egrclrevckfrhmeidkkrkeipcywe 69 
                                c  +    c+kG +c f he   l     c ++   g+c++  c++ h++ +  +ke p y  
  gene21|gene21|rna21|rna21  52 CKHWLRGLCKKGIKCEFMHEY-DLSRMPECYFFSsYGECMNPECNYIHIDPNSSSKECPWYNR 113
                                66667778**********976.577778888875269***********999999999988854 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0015
                  zf-CCCH_3   5 gddcyffyystctkGdscpfrhee 28 
                                ++ cy ++   c +G +c + h +
  gene21|gene21|rna21|rna21 129 KKLCYNYFLGFCPRGPTCDYGHPK 152
                                567*****************9976 PP

>> zf-C3H1  Putative zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   1.5e-05     0.039      10      22 .]      33      45 ..      31      45 .. 0.92
   2 ?    4.6   0.3     0.011        28       7      20 ..      57      70 ..      51      70 .. 0.82
   3 ?    4.3   0.0     0.013        32       9      21 ..      87      99 ..      85     100 .. 0.88
   4 ?    1.6   0.8     0.091   2.3e+02       8      22 .]     114     128 ..     108     128 .. 0.79
   5 ?   -2.2   0.2       1.4   3.6e+03      14      18 ..     144     148 ..     139     150 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                    zf-C3H1 10 vCnDpsCefQHFr 22
                                C+Dp+C+ QH++
  gene21|gene21|rna21|rna21 33 SCKDPNCSKQHVK 45
                               5**********86 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                    zf-C3H1  7 aGGvCnD.psCefQH 20
                               +G  C++  +Cef+H
  gene21|gene21|rna21|rna21 57 RG-LCKKgIKCEFMH 70
                               56.7888889***** PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.013
                    zf-C3H1  9 GvCnDpsCefQHF 21
                               G C +p+C + H+
  gene21|gene21|rna21|rna21 87 GECMNPECNYIHI 99
                               69******99885 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.091
                    zf-C3H1   8 GGvCnD.psCefQHFr 22 
                                G  C +  sC++ H+r
  gene21|gene21|rna21|rna21 114 G-FCRNgASCKNKHVR 128
                                3.7888899**99998 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.4
                    zf-C3H1  14 psCef 18 
                                p+C +
  gene21|gene21|rna21|rna21 144 PTCDY 148
                                56766 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.8      0.05   1.3e+02       7      17 ..      33      43 ..      28      43 .. 0.83
   2 ?    9.1   1.9   0.00076       1.9       2      17 ..      52      70 ..      52      70 .. 0.98
   3 ?   11.0   3.4   0.00019      0.48       2      17 ..      80      98 ..      79      98 .. 0.85
   4 ?   -2.3   0.0         3   7.6e+03      11      15 ..     106     110 ..     105     111 .. 0.78
   5 ?    7.3   1.1    0.0026       6.8       2      11 ..     116     125 ..     116     126 .. 0.94
   6 ?    3.0   4.9      0.06   1.5e+02       4      18 .]     135     151 ..     131     151 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.05
                  zf-CCCH_2  7 nCtnpkCpFaH 17
                                C+ p+C+  H
  gene21|gene21|rna21|rna21 33 SCKDPNCSKQH 43
                               3******9888 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00076
                  zf-CCCH_2  2 Crffpn..C.tnpkCpFaH 17
                               C+++    C ++ kC F H
  gene21|gene21|rna21|rna21 52 CKHWLRglCkKGIKCEFMH 70
                               *****************99 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00019
                  zf-CCCH_2  2 Crffpn...CtnpkCpFaH 17
                               C ff     C+np+C ++H
  gene21|gene21|rna21|rna21 80 CYFFSSygeCMNPECNYIH 98
                               567777788********** PP

  == domain 4  score: -2.3 bits;  conditional E-value: 3
                  zf-CCCH_2  11 pkCpF 15 
                                ++Cp+
  gene21|gene21|rna21|rna21 106 KECPW 110
                                69996 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0026
                  zf-CCCH_2   2 CrffpnCtnp 11 
                                Cr+++ C+n+
  gene21|gene21|rna21|rna21 116 CRNGASCKNK 125
                                *********8 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.06
                  zf-CCCH_2   4 ffpn.C.tnpkCpFaHP 18 
                                +f   C ++p C + HP
  gene21|gene21|rna21|rna21 135 YFLGfCpRGPTCDYGHP 151
                                78889***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1358.65
//
Query:       gene210|gene210|rna210|rna210  [L=422]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-19   70.6   0.0    1.6e-19   70.3   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
     0.0038   15.8   0.0     0.0053   15.3   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.8e-23   1.6e-19      21     358 ..      97     414 ..      80     419 .. 0.80

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.8e-23
                                    HHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEE CS
                  Aminotran_1_2  21 pevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvp 99 
                                    +e+++  ++ g++ +g++ +yg+ d++ +lee++ k lg        +ea++v+ + ++a++++++ ++k   +d ++ +
  gene210|gene210|rna210|rna210  97 EEIIEVIRKyGVGTCGPRGFYGTLDIHLDLEETISKELG--------AEASIVYPNSFTAVNSIIACFCK--QQDIVFYH 166
                                    44555555579****************************........*************9998888887..******** PP

                                    ESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHH CS
                  Aminotran_1_2 100 dptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakk 179
                                    + + + + +++ ls+++ +++           + +l+ +l+ +++ ++ + +++ve+ + +tG + +   + kl    +k
  gene210|gene210|rna210|rna210 167 EDSNEAILRGIGLSKSKNIEFG---------SVSDLKIKLEYFTKPSV-RNFVIVEGLSRNTGRIVDIRMILKL---RDK 233
                                    *****************99999.........89999999999999999.9************************...*** PP

                                    TTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT....EEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHH CS
                  Aminotran_1_2 180 ynlllfvDeaYagfvfgsldavatranveeepn....llivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssl 255
                                    yn+++++De Y++  +++ +    +++++        +++ gsls  + ++G   ++ +g+   v++++   +++++s++
  gene210|gene210|rna210|rna210 234 YNFRIILDESYSIPLLNKRG----VCGMNGI-SlreiDIVIGSLSGGLCSTG---AFSTGTYYTVDYQKLSGSSYCFSAS 305
                                    ****************9554....4444442.335568**************...**********************999 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHH....CHHHHHHH.......H CS
                  Aminotran_1_2 256 lqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsae....takelskk.......L 324
                                    ++   a+a     +++ e+ee r+++++ ++++r++  e  +++l s+  ++ ++  ++     ++++l k+       L
  gene210|gene210|rna210|rna210 306 MPGGMAKAGILNIKRDFEHEELRDKVKAFHTSFRSKTYE-IISHLLSP--IIIVVKKKEIrrsmSKEALLKEvldirseL 382
                                    999888888887776669999999999999999988644.44444443..333322222233454444444456666668 PP

                                    HHTCTEEEEEGGGGTSTTEEEEEC.TTS-HHHHHH CS
                  Aminotran_1_2 325 leevgvyvtpgtsftvpgrlRitv.Aglteeelee 358
                                    le+ g+++   ++  +p+ lR ++     ee++ +
  gene210|gene210|rna210|rna210 383 LEN-GIIIGF-NHNPCPS-LRACLkTDILEEDIAR 414
                                    887.665543.6666677.7777755555555555 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     6e-07    0.0053      57     183 ..     126     251 ..     121     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-07
                                    HHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT CS
                Cys_Met_Meta_PP  57 leeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaike 136
                                    lee+i++  g+ea+++++   +A++++i  ++k+ d +  ++d  +   r +    +k +ie+  v   ++ +le   k+
  gene210|gene210|rna210|rna210 126 LEETISKELGAEASIVYPNSFTAVNSIIACFCKQQDIVFYHEDSNEAILRGIGLSKSK-NIEFGSVSDLKI-KLEYFTKP 203
                                    899999999***************9999999999999999999988888888766555.477777766544.68888888 PP

                                    TEE.EEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS- CS
                Cys_Met_Meta_PP 137 ntk.lvylEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqr 183
                                     ++  v +E ++  + ++vDi+ i+kl  k +  +++D +++ pll +
  gene210|gene210|rna210|rna210 204 SVRnFVIVEGLSRNTGRIVDIRMILKLRDKYNFRIILDESYSIPLLNK 251
                                    7652899*************************************8754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 2505.91
//
Query:       gene211|gene211|rna211|rna211  [L=626]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00017   21.0   0.0    0.00046   19.6   0.0    1.7  2  Mcl1_mid   Minichromosome loss protein, Mcl1, middle region
  ------ inclusion threshold ------
        0.1   12.8   0.1       0.69   10.2   0.1    2.3  2  AMPK1_CBM  Glycogen recognition site of AMP-activated protein
       0.13   12.8   0.2        1.6    9.4   0.0    3.0  5  PQQ_3      PQQ-like domain


Domain annotation for each model (and alignments):
>> Mcl1_mid  Minichromosome loss protein, Mcl1, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.73   4.4e+03     154     178 ..     150     176 ..     136     230 .. 0.48
   2 !   19.6   0.0   7.7e-08   0.00046       7     164 ..     366     500 ..     363     536 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.73
                       Mcl1_mid 154 askdklavvyhegap..lngnqeleys 178
                                    +    ++v+  +++   + ++ +++++
  gene211|gene211|rna211|rna211 150 SDGTEVFVADLRNKItvYPSKRTYDIR 176
                                    444444444433333233333333222 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 7.7e-08
                       Mcl1_mid   7 stplgeegdrryLawNsiGvvttveedeeensieveFhDtslhrevhftdsfgftlasLseeglllAskaskseekkpst 86 
                                    s+p+ +e+ +  L +Ns G++++++ ++    +ev +hD s +r++++    g+ l+s  ++ ++ +     +      +
  gene211|gene211|rna211|rna211 366 SSPMPKEEAENLLYYNSEGYMICIRGES-FDRVEVIYHDIS-RRKIEVPRICGCVLGSFCKDNVVVG-----D----GKK 434
                                    6677777789**************9876.999*********.899*********************7.....2....247 PP

                       Mcl1_mid  87 lyyrpleswasnseWsvkLpegEevtavalgkkwvavaTskrylRiFslsGvqlavlslpgpvVtlaaskdklavvyh 164
                                    +yy    ++   s+W+++++    ++ v++++k v+v +  + l +F l G+++    +p +v +++++   +av  +
  gene211|gene211|rna211|rna211 435 IYYTG--KF---SRWEKEIE----AKMVSVSEKMVVVFS--GILQVFGLDGTEVFNCLVP-DVHAMCCHLGIIAVFCR 500
                                    99865..34...789****9....89************9..************6666666.99999999988888775 PP

>> AMPK1_CBM  Glycogen recognition site of AMP-activated protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.53   3.1e+03      31      58 ..     197     224 ..     187     232 .. 0.80
   2 ?   10.2   0.1   0.00012      0.69       9      30 ..     430     451 ..     428     470 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.53
                      AMPK1_CBM  31 ksekdfsvilkLpeGthqykFiVDgewr 58 
                                    ++++ f + l++++    y F  +g + 
  gene211|gene211|rna211|rna211 197 RTRNAFATYLTVEKPINSYTFSMNGGIL 224
                                    77899999******99****99999765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00012
                      AMPK1_CBM   9 ggGkkVyvtGsfnnWkkkipLk 30 
                                    g+Gkk+y tG+f++W+k+i+ k
  gene211|gene211|rna211|rna211 430 GDGKKIYYTGKFSRWEKEIEAK 451
                                    68***************98754 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00026       1.6      21      36 ..      82      97 ..      65     100 .. 0.81
   2 ?   -2.9   0.0       1.9   1.1e+04      19      34 ..     149     165 ..     140     167 .. 0.61
   3 ?   -2.6   0.0       1.5   8.9e+03      17      32 ..     217     231 ..     207     238 .. 0.66
   4 ?   -4.0   0.1         3   1.8e+04      24      34 ..     427     436 ..     425     437 .. 0.56
   5 ?   -3.3   0.0       2.5   1.5e+04       4      25 ..     443     461 ..     443     474 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00026
                          PQQ_3 21 gglvyvgtgdGtlyAl 36
                                   +g vy+g++dGt++ +
  gene211|gene211|rna211|rna211 82 DGFVYCGSEDGTIHVY 97
                                   9************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.9
                          PQQ_3  19 vdggl.vyvgtgdGtly 34 
                                     ++g+ v+v++  ++++
  gene211|gene211|rna211|rna211 149 CSDGTeVFVADLRNKIT 165
                                    34555599998776665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.5
                          PQQ_3  17 pavdgglvyvgtgdGt 32 
                                      + gg++++ +  + 
  gene211|gene211|rna211|rna211 217 FSMNGGILFAQCR-ND 231
                                    4788999998765.44 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 3
                          PQQ_3  24 vyvgtgdGtly 34 
                                    v+vg+g  ++y
  gene211|gene211|rna211|rna211 427 VVVGDG-KKIY 436
                                    666665.5554 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 2.5
                          PQQ_3   4 lWsvqlpgpvnsspavdgglvy 25 
                                    +W++++ ++    + v++  v+
  gene211|gene211|rna211|rna211 443 RWEKEIEAKM---VSVSEKMVV 461
                                    6998888765...355555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3865.91
//
Query:       gene213|gene213|rna213|rna213  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-39  135.8   1.1    1.2e-39  135.6   1.1    1.1  1  Ribosomal_S8e  Ribosomal protein S8e
  ------ inclusion threshold ------
      0.098   12.7   0.0        0.2   11.7   0.0    1.5  1  GlgS           Glycogen synthesis protein


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.6   1.1   1.4e-43   1.2e-39       1     137 []       1     152 [.       1     152 [. 0.99

  Alignments for each domain:
  == domain 1  score: 135.6 bits;  conditional E-value: 1.4e-43
                                    XXXBXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                  Ribosomal_S8e   1 mgisrdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                    mgi++++ hkr++tG+ka + rkkr+++ g +++atk+g++rv  vrvrgG+rk++alrl+ +++   ++++ + +k+l+
  gene213|gene213|rna213|rna213   1 MGINHRGDHKRRKTGAKAVISRKKRNNRAGSQPSATKIGERRVMPVRVRGGNRKHKALRLDVGHFRFITTGKIRPAKLLQ 80 
                                    899***************************************************************************** PP

                                    EECSSSTCHHHHTTC--TTEEEEEESHH...............HHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                  Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvse...............LgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                    V+++ps+n++vr+++ltK+++++++++                L+e +++g ++A +tsrPgq G + + +L
  gene213|gene213|rna213|rna213  81 VVYHPSSNDLVRTNTLTKSSVVKISAEGfkedikavasnvdpeLHESFEKGYLYAIITSRPGQIGAATGHVL 152
                                    **************************99**************************************999886 PP

>> GlgS  Glycogen synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.2e-05       0.2      17      50 ..      99     132 ..      93     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                                    HHHHHHHHHT----HHHHHHH--TTHHHHHHHHH CS
                           GlgS  17 rsFaRmhaeGrrvDidavtGnmdeahraWFckRY 50 
                                    +s  ++ aeG + Di+av  n+d +  + F k Y
  gene213|gene213|rna213|rna213  99 SSVVKISAEGFKEDIKAVASNVDPELHESFEKGY 132
                                    5778999****************99888898887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1220.83
//
Query:       gene214|gene214|rna214|rna214  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-05   23.4  10.0    6.4e-05   22.8  10.0    1.4  1  PHD       PHD-finger
  ------ inclusion threshold ------
      0.023   14.8   0.4      0.039   14.0   0.4    1.3  1  RAG2_PHD  RAG2 PHD domain


Domain annotation for each model (and alignments):
>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8  10.0   7.2e-09   6.4e-05       2      50 ..      11      58 ..      10      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.2e-09
                                   BTTTTSTTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSS.TBSSTTTH CS
                            PHD  2 CavCkkksdeeeelvqCdgCkrwfHqkClkppleseekpeg.ewlCekCk 50
                                   C  C+     + +++ C +C++w H+ C+++  +++++ ++  + C  C 
  gene214|gene214|rna214|rna214 11 C-HCRL-IGRDPHMIHCSSCGNWLHTVCCGFFSNEDKRISKeTFSCFYCL 58
                                   7.8888.77899******************9877666666669***9995 PP

>> RAG2_PHD  RAG2 PHD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   4.4e-06     0.039      27      65 ..      19      57 ..      15      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-06
                       RAG2_PHD 27 kpamifcskgeGhwvhaqcmdlseslllrlseenkkyf.c 65
                                    p mi+cs+  G w+h+ c  +  +   r+s+e+  +f c
  gene214|gene214|rna214|rna214 19 DPHMIHCSS-CGNWLHTVCCGFFSNEDKRISKETFSCFyC 57
                                   599****97.59*********9999999999988766415 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1010.68
//
Query:       gene215|gene215|rna215|rna215  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-27   94.4   0.3    4.3e-27   94.1   0.3    1.1  1  Ribosomal_L35Ae  Ribosomal protein L35Ae
  ------ inclusion threshold ------
      0.071   13.3   0.1        2.7    8.3   0.0    2.2  2  RimM             RimM N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L35Ae  Ribosomal protein L35Ae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.3   4.8e-31   4.3e-27       4      94 ..      17     103 ..      15     104 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 4.8e-31
                                    EEEEEEEE--SSSSS-EEEEEEESS--SHHHHHCCTT-EE..EEE-......TTT-EEEEEEEEECTTTTEEEEEETT-- CS
                Ribosomal_L35Ae   4 kavflgykrgkrnqrentaLlkiegvkskeeaefylGkrvayvykakkkkkgskvrviwGkvtrahGnsgvvrakFkknL 83 
                                    +a+f+++krg+r+ +++ aLlki++v sk+ea++y+G+ v++++++    ++ kv  ++G vtr+hGnsg+vra+F++nL
  gene215|gene215|rna215|rna215  17 PATFVSFKRGQRRLHPRYALLKINNVASKDEASKYIGNGVICYKTS----NKGKVYPVHGVVTRIHGNSGAVRARFARNL 92 
                                    79**************************************875555....45788899********************** PP

                                    SSS-TT-EEEE CS
                Ribosomal_L35Ae  84 ppkaigarvrv 94 
                                     pk++g++v +
  gene215|gene215|rna215|rna215  93 DPKMLGTHVFI 103
                                    ********976 PP

>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0003       2.7      40      76 ..      18      54 ..       1      61 [. 0.75
   2 ?    3.1   0.1     0.012   1.1e+02       3      17 ..      72      86 ..      70      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0003
                                   TEEEEE-EEEEEEETTEEEEEETT--SHHHHHTTTT- CS
                           RimM 40 getreltvesvrvhkkgvivklegvddrdaAealkga 76
                                   ++  +++  + r+h +  ++k+ +v + d+A ++ g 
  gene215|gene215|rna215|rna215 18 ATFVSFKRGQRRLHPRYALLKINNVASKDEASKYIGN 54
                                   45555666777799*******************9986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.012
                                   EEEEEEETTTTEEEE CS
                           RimM  3 GkIvgahGlkGevkV 17
                                   G +++ hG  G v+ 
  gene215|gene215|rna215|rna215 72 GVVTRIHGNSGAVRA 86
                                   99***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 669.26
//
Query:       gene216|gene216|rna216|rna216  [L=109]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 760.93
//
Query:       gene217|gene217|rna217|rna217  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-17   61.2   7.9    9.9e-16   57.3   7.9    2.1  1  MAD             Mitotic checkpoint protein
  ------ inclusion threshold ------
      0.012   15.9   2.2        4.2    7.8   0.1    3.0  3  TSC22           TSC-22/dip/bun family
      0.014   15.0   2.7        1.2    8.8   0.7    2.4  2  PikAIV_N        Narbonolide/10-deoxymethynolide synthase PikA
      0.043   14.0   9.0       0.13   12.5   1.3    2.1  2  ATG16           Autophagy protein 16 (ATG16)
       0.06   13.8   3.7       0.11   12.9   3.7    1.4  1  Fez1            Fez1
      0.067   13.6   3.7       0.11   12.9   3.7    1.4  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
       0.11   12.8   0.1       0.29   11.5   0.1    1.6  1  Chordopox_E11   Chordopoxvirus E11 protein
       0.12   13.1   2.9        4.6    7.9   0.7    2.3  2  YabA            Initiation control protein YabA
       0.25   11.5   5.6         13    5.9   0.1    3.2  3  NYD-SP28_assoc  Sperm tail C-terminal domain
       0.38   11.0   3.7         11    6.3   0.4    2.4  2  HALZ            Homeobox associated leucine zipper
       0.43   10.7   6.1        3.8    7.7   0.9    2.6  3  bZIP_1          bZIP transcription factor
       0.48   10.3   3.8         16    5.5   0.2    2.7  3  GIT_CC          GIT coiled-coil Rho guanine nucleotide exchan
       0.58   10.3   6.3       0.93    9.6   6.2    1.5  1  BRE1            BRE1 E3 ubiquitin ligase
        1.8    9.5   9.3         38    5.2   9.8    2.6  2  PRKG1_interact  cGMP-dependent protein kinase interacting dom
        4.9    7.3   6.6    4.5e+02    1.0   6.6    2.6  1  Swi5            Swi5
        9.2    6.5   9.6        1.5    9.0   0.6    2.8  2  Cnn_1N          Centrosomin N-terminal motif 1


Domain annotation for each model (and alignments):
>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   7.9   8.8e-19   9.9e-16     504     661 .]      50     196 ..       1     196 [. 0.83

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 8.8e-19
                            MAD 504 eqlekLqaEierlkellkkleedkekkvaslpessltlafkevleLrkelesaelkiqrlKevFkakiqEFRevvYmLlG 583
                                    +++e L++E++rl++   k  +    + ++++ +  t a ke  e  ++  +    +  l+ + ++     Re v  L+G
  gene217|gene217|rna217|rna217  50 KKIESLEQENKRLRDAADKDGHRIY-EGENMNPN--TPASKERTESIAQASEEKDPNNELRQYLRT----IREYVTGLTG 122
                                    57899***********997775544.45677777..8899999999999999999999***99876....588899**** PP

                            MAD 584 YkidittnsqyRltSmYaeekedallfklsesnesklkLletpfSrtleelidlhlaeqksiPaflsalTLeLfsrqt 661
                                    Yk+++  +++    S+Ya ++ed+++f   +s+  +++L++++f+ +    i+ +l + ksiPafl+a+TLeLf+++t
  gene217|gene217|rna217|rna217 123 YKMEFR-DGEIIFHSLYAFDSEDVFIF-RYKSG--SMELVNNEFAASWASEIQNYLIAGKSIPAFLAAVTLELFNKKT 196
                                    ****95.89999***************.44444..5****************************************97 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.025        28      18      34 ..      17      33 ..       2      35 .. 0.55
   2 ?    6.6   0.2    0.0085       9.5      18      41 ..      17      40 ..       9      44 .. 0.87
   3 ?    7.8   0.1    0.0037       4.2      23      46 ..      45      68 ..      42      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                          TSC22 18 vLkekIkeLeernsele 34
                                    L+ +I++L++  +  e
  gene217|gene217|rna217|rna217 17 ALRHQIVDLQSALASKE 33
                                   35666666666555555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0085
                          TSC22 18 vLkekIkeLeernseleeENslLk 41
                                    L+ +I++L++  +  e+E s+ +
  gene217|gene217|rna217|rna217 17 ALRHQIVDLQSALASKEQELSMAR 40
                                   69*************999988766 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0037
                          TSC22 23 IkeLeernseleeENslLkalasp 46
                                   I+  +++++ le+EN+ L+  a +
  gene217|gene217|rna217|rna217 45 ITHHLKKIESLEQENKRLRDAADK 68
                                   5566789************98876 PP

>> PikAIV_N  Narbonolide/10-deoxymethynolide synthase PikA4 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0084       9.4      13      23 ..      11      21 ..      10      28 .. 0.87
   2 ?    8.8   0.7    0.0011       1.2      14      30 .]      49      65 ..      49      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0084
                       PikAIV_N 13 SLkEnERLRqq 23
                                    LkEn  LR+q
  gene217|gene217|rna217|rna217 11 TLKENTALRHQ 21
                                   69*******99 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                       PikAIV_N 14 LkEnERLRqqNrrLtAA 30
                                   Lk +E L q+N rL++A
  gene217|gene217|rna217|rna217 49 LKKIESLEQENKRLRDA 65
                                   899***********998 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.3      0.01        12      90     121 ..       8      39 ..       2      43 .. 0.83
   2 ?   12.5   1.3   0.00012      0.13      25      93 ..      46     120 ..      42     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.01
                          ATG16  90 laelyksrgelaqrllelneelqkleeklked 121
                                     ae++k+++ l  ++++l+++l+ +e++l+  
  gene217|gene217|rna217|rna217   8 FAETLKENTALRHQIVDLQSALASKEQELSMA 39 
                                    58999999999999999999999999998765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                          ATG16  25 nrLldrtsaleaenaklekaaasaks......sksskksakekeasasqsnskqsakiqsleqklaqlreelael 93 
                                    +++l+++++le+en++l+ aa +  +      + +++++a+++++++ +++s++++  ++l q l ++re ++ l
  gene217|gene217|rna217|rna217  46 THHLKKIESLEQENKRLRDAADKDGHriyegeNMNPNTPASKERTESIAQASEEKDPNNELRQYLRTIREYVTGL 120
                                    6899*************9999999889*99775555556666666666688899999999999999999977765 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.7   9.9e-05      0.11      29     100 ..      11     107 ..       2     133 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                           Fez1  29 klseivalkaqlrelrakleekeeeikeleesl..eektlelevcenelqrk........................ksea 82 
                                     l+e  al+ q+ +l+++l +ke+e++ ++es+  +++ +++e +e+e +r                         k+++
  gene217|gene217|rna217|rna217  11 TLKENTALRHQIVDLQSALASKEQELSMARESSgiTHHLKKIESLEQENKRLrdaadkdghriyegenmnpntpasKERT 90 
                                    45666677777777777777777776666665421445556666666666663333322222222222222222211111 PP

                           Fez1  83 ellrekvekleeelkelr 100
                                    e + + +++ +++ +elr
  gene217|gene217|rna217|rna217  91 ESIAQ-ASEEKDPNNELR 107
                                    11111.222222222222 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.7   9.9e-05      0.11       7      80 ..      26     100 ..      20     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-05
                                    THHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   V-ATPase_G_2   7 lkeLaerEaeLdqrlEaA.rkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeaea 80 
                                     + La++E+eL+   E   + +  +++e  e+e +r+  +A+++ +++ +  + + ++  +++r e  a+a++e 
  gene217|gene217|rna217|rna217  26 QSALASKEQELSMARESSgITHHLKKIESLEQENKRLRDAADKDGHRIYEGENMNPNTPASKERTESIAQASEEK 100
                                    578*********9888752777889**********************9999999999999999999999998875 PP

>> Chordopox_E11  Chordopoxvirus E11 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00025      0.29      57      78 ..     142     163 ..     133     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                  Chordopox_E11  57 dkdiFyykcdkGrvspvenefy 78 
                                     +d+F ++++ G++ +v+nef 
  gene217|gene217|rna217|rna217 142 SEDVFIFRYKSGSMELVNNEFA 163
                                    469*****************96 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.7    0.0041       4.6      24      63 ..       1      40 [.       1      52 [. 0.73
   2 ?    5.8   0.1     0.018        21      31      53 ..      45      86 ..      37     115 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0041
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXX CS
                           YabA 24 leelkeelaelleenaeLeleneklrerleeeekkekekk 63
                                   +eel +++ae+l+en++L+ +   l++ l+++e++ +  +
  gene217|gene217|rna217|rna217  1 MEELYRKFAETLKENTALRHQIVDLQSALASKEQELSMAR 40
                                   5789999**********************65555443333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHHHHHHH...................X CS
                           YabA 31 laelleenaeLeleneklrerl...................e 53
                                   +++ l++ ++Le en++lr+                     +
  gene217|gene217|rna217|rna217 45 ITHHLKKIESLEQENKRLRDAAdkdghriyegenmnpntpaS 86
                                   556677788899999999998877777767666665554431 PP

>> NYD-SP28_assoc  Sperm tail C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1     0.063        70      36      56 ..       9      29 ..       4      32 .. 0.87
   2 ?    5.9   0.1     0.012        13      39      54 ..      49      64 ..      44      65 .. 0.85
   3 ?    3.2   0.2     0.087        97      33      57 ..      87     111 ..      87     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.063
                 NYD-SP28_assoc 36 aklieetesLekqNeeLrnlL 56
                                   a++++e+++L++q   L++ L
  gene217|gene217|rna217|rna217  9 AETLKENTALRHQIVDLQSAL 29
                                   678999********9999988 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.012
                 NYD-SP28_assoc 39 ieetesLekqNeeLrn 54
                                   ++++esLe++N+ Lr+
  gene217|gene217|rna217|rna217 49 LKKIESLEQENKRLRD 64
                                   67899*******9996 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.087
                 NYD-SP28_assoc  33 teRaklieetesLekqNeeLrnlLk 57 
                                    +eR + i++ ++ +  N+eLr+ L+
  gene217|gene217|rna217|rna217  87 KERTESIAQASEEKDPNNELRQYLR 111
                                    6899999999999999******997 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.018        20      21      42 ..       8      29 ..       2      30 .. 0.79
   2 ?    6.3   0.4      0.01        11      17      32 ..      49      63 ..      47      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.018
                           HALZ 21 ydsLkkenekLkaelqeLkekl 42
                                   +   +ken +L+ ++  L + l
  gene217|gene217|rna217|rna217  8 FAETLKENTALRHQIVDLQSAL 29
                                   556689**********998765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.01
                           HALZ 17 LksdydsLkkenekLk 32
                                   Lk + +sL++en++L+
  gene217|gene217|rna217|rna217 49 LK-KIESLEQENKRLR 63
                                   56.78**********7 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9    0.0034       3.8      28      63 ..       1      36 [.       1      37 [. 0.91
   2 ?    5.3   0.0     0.018        21      34      50 ..      51      67 ..      48      74 .. 0.86
   3 ?   -2.6   0.1       5.3     6e+03      42      53 ..     103     114 ..      87     120 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63
                                   +eeL r++++  keN++L+ ++  l+   +++++++
  gene217|gene217|rna217|rna217  1 MEELYRKFAETLKENTALRHQIVDLQSALASKEQEL 36
                                   699**********************99999888875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                                   HHHHHHHHHHHHHHHHH CS
                         bZIP_1 34 rvkaLekeNksLksele 50
                                   + + Le+eNk L++ ++
  gene217|gene217|rna217|rna217 51 KIESLEQENKRLRDAAD 67
                                   8899******9998776 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.3
                                    HHHHHHHHHHHH CS
                         bZIP_1  42 NksLkseleelk 53 
                                    N +L++ l +++
  gene217|gene217|rna217|rna217 103 NNELRQYLRTIR 114
                                    444666666555 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.014        16      31      59 ..       7      35 ..       3      42 .. 0.82
   2 ?    5.4   0.2     0.015        16      48      65 ..      47      64 ..      39      65 .. 0.82
   3 ?   -2.5   0.0       4.4     5e+03      39      52 ..     103     116 ..      94     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                         GIT_CC 31 kiqqLlkvNtslsdelrlLQskvqkLqae 59
                                   k  + lk Nt l  ++  LQs + + ++e
  gene217|gene217|rna217|rna217  7 KFAETLKENTALRHQIVDLQSALASKEQE 35
                                   56677999*************98775555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                         GIT_CC 48 lLQskvqkLqaeNaqlrd 65
                                   +  +k+++L++eN+ lrd
  gene217|gene217|rna217|rna217 47 HHLKKIESLEQENKRLRD 64
                                   55589***********97 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.4
                         GIT_CC  39 NtslsdelrlLQsk 52 
                                    N++l + lr + + 
  gene217|gene217|rna217|rna217 103 NNELRQYLRTIREY 116
                                    78888888776555 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   6.2   0.00083      0.93       6      81 ..       2      79 ..       1     100 [. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00083
                           BRE1  6 vklekafeelseqlskkvkeltileekklrleaekakadq..kyfaamrskdalenelkkLnkllsKsselieqLkel 81
                                   ++l + f e+ +++ ++  ++ +l++ ++  e+e + a++   +    +++++le+e+k+L+   +K    i + +++
  gene217|gene217|rna217|rna217  2 EELYRKFAETLKENTALRHQIVDLQSALASKEQELSMAREssGITHHLKKIESLEQENKRLRDAADKDGHRIYEGENM 79
                                   6788999***************************87665511677888999****************99888777774 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   9.8     0.034        38       7      88 ..       9      64 ..       2     115 .. 0.66
   2 ?   -0.7   0.0       2.4   2.7e+03       8      27 ..      98     117 ..      96     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.034
                 PRKG1_interact  7 eeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkeleeLraenqrLkd 88
                                    e ++en  L++++ +l+  l++ ++el+                          + r+ s + + lk++e L +en+rL+d
  gene217|gene217|rna217|rna217  9 AETLKENTALRHQIVDLQSALASKEQELS--------------------------MARESSGITHHLKKIESLEQENKRLRD 64
                                   34444455555555555555555555444..........................555555555555555555555555554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                 PRKG1_interact   8 eekeenerLkreLeelekel 27 
                                    eek+ n++L++ L+++++ +
  gene217|gene217|rna217|rna217  98 EEKDPNNELRQYLRTIREYV 117
                                    68889999999999988765 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   6.6       0.4   4.5e+02      21      46 ..      91     116 ..       7     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.4
                                    HHHHHHHHHH.HHHHHHHHHHHHHHH CS
                           Swi5  21 elkeelkekkdpeetvkrhIklLheY 46 
                                    e  ++  e+kdp+++++++++ ++eY
  gene217|gene217|rna217|rna217  91 ESIAQASEEKDPNNELRQYLRTIREY 116
                                    22222233346888888888888888 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.6    0.0014       1.5      40      69 ..      10      39 ..       2      43 .. 0.89
   2 ?   -0.0   2.8       0.9     1e+03      22      22 ..      72      72 ..      49     121 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                         Cnn_1N 40 ellkenielkveveslqkelkekkkllrea 69
                                   e+lken+ l+ ++ +lq  l +k+++l  a
  gene217|gene217|rna217|rna217 10 ETLKENTALRHQIVDLQSALASKEQELSMA 39
                                   799**********************99876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.9
                         Cnn_1N 22 r 22
                                   r
  gene217|gene217|rna217|rna217 72 R 72
                                   1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1338  (0.0746277); expected 358.6 (0.02)
Passed bias filter:                      743  (0.0414412); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1179.08
//
Query:       gene218|gene218|rna218|rna218  [L=493]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-08   34.6   0.1      2e-08   34.6   0.1    3.4  3  Suf       Suppressor of forked protein (Suf)
  ------ inclusion threshold ------
      0.066   13.5   0.2        3.3    8.2   0.0    3.0  2  TPR_8     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Suf  Suppressor of forked protein (Suf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   5.8     0.066   5.9e+02      56     123 ..      68     140 ..      15     199 .. 0.70
   2 ?   -0.1   0.1      0.08   7.1e+02      70      97 ..     214     240 ..     208     265 .. 0.84
   3 !   34.6   0.1   2.3e-12     2e-08      15     128 ..     300     405 ..     288     485 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.066
                            Suf  56 tkIFelGlKkFpedee.fvl..kYldyLislnddn....naRvlfekvvsklskekeakelykkfleyestfgdl 123
                                     +++e  l +F++  + +vl  +Y++ L +++d++    ++R  + ++++++++   ++el+k f ++e + + +
  gene218|gene218|rna218|rna218  68 YEVYEFTLGQFENYWDsYVLykEYIEELGKIEDEQtrieKIRNGYMRALQTPMNS--LSELWKDFENFELELNKI 140
                                    4577778888877644155433566667777666411113555555555555544..599*****9999887765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.08
                            Suf  70 eefvlkYldyLislnddnnaRvlfekvv 97 
                                    e++  +Y +yLi +  +++a+ ++++ +
  gene218|gene218|rna218|rna218 214 EAY-FFYSEYLIGIGQKERAKKVIQRGI 240
                                    454.4799****************9977 PP

  == domain 3  score: 34.6 bits;  conditional E-value: 2.3e-12
                            Suf  15 eGikgaRkvFkkARkkprltyevyvasAllEyyiskdkkvAtkIFelGlKkFpedeefvlkYldyLislnddnnaRvlfe 94 
                                    +G+++ Rk F +    + ++ +v++  A +Eyy +   ++  +IF  Gl k p++     ++  +L+++ d++naR+lf 
  gene218|gene218|rna218|rna218 300 RGLESFRKLFIELGG-EGIGPHVFIYCAFVEYYATGSRATPYNIFSSGLLKHPTSTLLKEEFFLFLLKIGDEENARALFK 378
                                    678888888887654.45899**********************************************************9 PP

                            Suf  95 kvvsklskekeakelykkfleyestfgdlssilk 128
                                    ++      ek ++ +++ ++eye   g+++   +
  gene218|gene218|rna218|rna218 379 RL------EK-TSRMWDSMIEYEFMVGSMELFRE 405
                                    85......55.67999999999999998876655 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00037       3.3       2      31 ..     214     243 ..     213     245 .. 0.93
   2 ?    1.9   0.0     0.036   3.2e+02      11      26 ..     364     379 ..     362     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00037
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleld 31 
                                    eay+  +  ++  g++e Ak+++++ + ++
  gene218|gene218|rna218|rna218 214 EAYFFYSEYLIGIGQKERAKKVIQRGIGMN 243
                                    79**********************999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.036
                                    HHHTT-HHHHHHHHHH CS
                          TPR_8  11 ylklgdyeeAkeyyek 26 
                                    +lk gd e+A + +++
  gene218|gene218|rna218|rna218 364 LLKIGDEENARALFKR 379
                                    6799********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3043.89
//
Query:       gene219|gene219|rna219|rna219  [L=309]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-45  154.9   1.2      3e-45  154.7   1.2    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.5e-21   77.0   0.1    1.6e-20   73.6   0.1    1.9  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    3.2e-13   50.0   1.3    6.1e-12   45.9   0.3    2.6  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.4e-05   23.1   0.3       0.44    9.6   0.0    4.0  4  GIDA           Glucose inhibited division protein A
    0.00049   19.3   1.0       0.57    9.2   0.0    3.7  4  FAD_binding_2  FAD binding domain
    0.00053   18.8   0.2      0.085   11.5   0.0    3.4  4  HI0933_like    HI0933-like protein
     0.0015   18.2   1.2     0.0025   17.5   0.0    2.0  3  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.059   13.4   0.2       0.27   11.2   0.1    2.0  2  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.7   1.2   1.3e-48     3e-45       2     294 .]       3     295 ..       2     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 1.3e-48
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.........evvkklnqgiel 69 
                                    +vv+iG+GpA+++aal+        +l+e    +++ ++g+   ++a+ +++++++ ++         ++   ++qg+++
  gene219|gene219|rna219|rna219   3 KVVIIGSGPAAYNAALYTMS--RSPLLFEggyIGNNGPGGQLTTTTAVDNYPGFPDGIEgpvltslmkDH--AVSQGLRV 78 
                                    8**************99877..5677887778899999999999************999*9999998754..67888888 PP

                                    CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC...TTBEECCSECHHHHHHCCSS-TSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv..aenvgklvrtldsaealklkllpkrivv 147
                                     ++ ++ +i +  + +++     +++ ++ ++++++AtG+s+r+l +pG    e ++k+v++++ ++++ + ++   ++v
  gene219|gene219|rna219|rna219  79 AKE-TISDIRKRDGVFVVV----SEKGEYRAEAVIVATGASARRLFVPGTgdDEFWQKGVSSCAVCDGFIYMNKI--TCV 151
                                    877.899998888888883....45569*****************99955559****************999988..9** PP

                                    ES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEE.EEETT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.xxxxx RF
                    Pyr_redox_2 148 vGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge....kle.vvled 222
                                    +GgG  ++E A +l+ ++k+v+++++r+++      +  +++++a  +e++e+++  + +++ g ++    +++ v++++
  gene219|gene219|rna219|rna219 152 IGGGDAAMEEALYLSGIAKKVYIIHRRNTFR-----ARNDMVKKAKAAENIEIMTPYVLERASGTKKveeiSIRnVETGE 226
                                    ******************************7.....66999*************************99966666999999 PP

                                    SCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 223 geeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                                     + i++  v++++G  p+t++l +++++ ld++g++vv++  +t++pg++a+GDv+  ++++++a++A ++G
  gene219|gene219|rna219|rna219 227 VKIIPMNGVFFGIGHDPNTSFL-KNINVDLDPNGYVVVKDEACTSIPGLFAAGDVC--DKRYRQAVTAAASG 295
                                    999*******************.*********************************..99999999999877 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.073   1.6e+02     165     184 ..       2      21 ..       1      26 [. 0.78
   2 !   73.6   0.1     7e-24   1.6e-20      98     305 .]      78     278 ..      61     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.073
                    Pyr_redox_3 165 qkvvViGgknSavDaAlelv 184
                                    +kvv+iG +  a  aAl ++
  gene219|gene219|rna219|rna219   2 EKVVIIGSGPAAYNAALYTM 21 
                                    68888888888888888665 PP

  == domain 2  score: 73.6 bits;  conditional E-value: 7e-24
                    Pyr_redox_3  98 iklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek.....lvkhyskvkefhkyagqkvvViGg 172
                                    + ++e++ ++ k d+ f+v ++k++y+A+ vi+AtG     ++l +pG  +     + + +  v +   y ++  +ViGg
  gene219|gene219|rna219|rna219  78 V-AKETISDIRKRDGVFVVVSEKGEYRAEAVIVATGA--SARRLFVPGTGDdefwqKGVSSCAVCDGFIYMNKITCVIGG 154
                                    4.4689******************************9..7888888888752343345555566666689999******* PP

                    Pyr_redox_3 173 knSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedg 252
                                    ++ a++ Al l    ++V +++r+++ +++++ ++    + + + +  +v  e  ++  +++v+ei+ +    +v+t + 
  gene219|gene219|rna219|rna219 155 GDAAMEEALYLSGIAKKVYIIHRRNTFRARNDMVKKAKAAENIEIMTPYVL-E--RASGTKKVEEISIR----NVETGEV 227
                                    *************************99999866665555555555555554.4..57788888888865....5677774 PP

                    Pyr_redox_3 253 kkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                     k+   + v++ +G +p++sflk+  ++ld +g++v+++e + t +pglf aG
  gene219|gene219|rna219|rna219 228 -KIIPMNGVFFGIGHDPNTSFLKNINVDLDPNGYVVVKDEAC-TSIPGLFAAG 278
                                    .56667888999*************************99988.56******99 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.14   3.2e+02       1      16 [.       3      18 ..       3      22 .. 0.85
   2 ?   -3.1   0.0       5.4   1.2e+04      43      61 ..      64      82 ..      55      96 .. 0.70
   3 !   45.9   0.3   2.7e-15   6.1e-12       4      79 ..     151     220 ..     149     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.14
                                   EEEEECSSHHHHHHHH CS
                      Pyr_redox  1 kvvvvGgGyiglElAg 16
                                   kvv++G+G  +  +A 
  gene219|gene219|rna219|rna219  3 KVVIIGSGPAAYNAAL 18
                                   79******99988775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.4
                                   HHHHHHHHHHTTEEEECSE CS
                      Pyr_redox 43 skilqeklekngievllnt 61
                                    ++++++   +g +v  +t
  gene219|gene219|rna219|rna219 64 TSLMKDHAVSQGLRVAKET 82
                                   5667777777777776554 PP

  == domain 3  score: 45.9 bits;  conditional E-value: 2.7e-15
                                    EECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEEEE CS
                      Pyr_redox   4 vvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvklk 79 
                                    v+GgG+ ++E+A +l+ ++kkV++++r+++++      a++ + +k ++  +ie+++  ++e+  g+++ ve++ ++
  gene219|gene219|rna219|rna219 151 VIGGGDAAMEEALYLSGIAKKVYIIHRRNTFR------ARNDMVKKAKAAeNIEIMTPYVLERASGTKK-VEEISIR 220
                                    9*******************************......9999999997777**************9998.9999876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.049   1.1e+02       1      18 [.       3      20 ..       3      24 .. 0.88
   2 !    9.6   0.0    0.0002      0.44     109     150 ..      74     113 ..      63     132 .. 0.78
   3 ?    2.8   0.0     0.022        50       3      33 ..     150     179 ..     148     218 .. 0.84
   4 !    4.0   0.0    0.0096        21     353     389 ..     269     307 ..     263     309 .] 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.049
                                   CEEEE-SSHHHHHHHHHH CS
                           GIDA  1 dviViGgGhAGceAAlaa 18
                                   +v++iG G A + AAl +
  gene219|gene219|rna219|rna219  3 KVVIIGSGPAAYNAALYT 20
                                   69*************865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0002
                                    TTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 109 pnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                    + l + +e+++++    +    vv +++ +++a+av++atG+
  gene219|gene219|rna219|rna219  74 QGLRVAKETISDIRK--RDGVFVVVSEKGEYRAEAVIVATGA 113
                                    579999*******54..444556666777899*********9 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.022
                                    EEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkld 33 
                                     ViGgG A +e Al ++    kv +i h+ +
  gene219|gene219|rna219|rna219 150 CVIGGGDAAMEEALYLSGIAKKVYII-HRRN 179
                                    69**************9999999998.3333 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.0096
                                    SSSBTEEE-CGGGTB-SH...HHHHHHHHHHHHHHHHHHC CS
                           GIDA 353 kkvkgLflAGqinGteGY...eEaaaqGllAGinaarkak 389
                                     +++gLf+AG++     Y   + aaa+G ++G+ a   ++
  gene219|gene219|rna219|rna219 269 TSIPGLFAAGDVCDKR-YrqaVTAAASGAISGMKAMEFLD 307
                                    4699********9997.622256789*******9987665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0    0.0081        18       2      16 ..       4      18 ..       3      24 .. 0.90
   2 ?    0.8   0.0     0.089     2e+02     185     204 ..      97     116 ..      63     130 .. 0.77
   3 ?    0.0   0.0      0.15   3.4e+02       4      35 ..     151     182 ..     149     187 .. 0.88
   4 !    9.2   0.0   0.00026      0.57     379     402 ..     256     281 ..     252     295 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0081
                                   EEEE--SHHHHHHHH CS
                  FAD_binding_2  2 viViGsGlAGLaAAl 16
                                   v++iGsG A + AAl
  gene219|gene219|rna219|rna219  4 VVIIGSGPAAYNAAL 18
                                   9*************8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.089
                                    TCEEEEEESEEEE-----GG CS
                  FAD_binding_2 185 grevrirakavvlatgGfgr 204
                                    +++ ++ra av++atg+  r
  gene219|gene219|rna219|rna219  97 SEKGEYRAEAVIVATGASAR 116
                                    34457999*******98766 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.15
                                    EE--SHHHHHHHHHHHHTTT-EEEEESSSGGG CS
                  FAD_binding_2   4 ViGsGlAGLaAAleaaeaGlkvavvekeqefg 35 
                                    ViG+G A +  Al ++   +kv ++   + f+
  gene219|gene219|rna219|rna219 151 VIGGGDAAMEEALYLSGIAKKVYIIHRRNTFR 182
                                    9***************9999999998776665 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00026
                                    ETTSBE..STTEEESSBTEEE-STCE CS
                  FAD_binding_2 379 dengrv..ldadgqpipGLYAaGeva 402
                                    d+ng v  +d++++ ipGL+AaG v 
  gene219|gene219|rna219|rna219 256 DPNGYVvvKDEACTSIPGLFAAGDVC 281
                                    7777777799*************997 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.039        87       2      18 ..       3      19 ..       2      31 .. 0.81
   2 !   11.5   0.0   3.8e-05     0.085     125     178 ..      77     131 ..      54     138 .. 0.71
   3 ?    0.8   0.0      0.07   1.6e+02       4      34 ..     150     180 ..     147     184 .. 0.89
   4 ?   -1.5   0.0      0.35   7.8e+02     373     386 ..     269     282 ..     264     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.039
                                   SEEEE--SHHHHHHHHH CS
                    HI0933_like  2 dviviGgGaAGlmaAis 18
                                   +v++iG G+A   aA+ 
  gene219|gene219|rna219|rna219  3 KVVIIGSGPAAYNAALY 19
                                   79********8888865 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.8e-05
                                    EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS....-GGGT--SHHHH CS
                    HI0933_like 125 klrletevksvekeedgkfrvktkseeeleadklvlAtGGlS....iPklGstgkgyk 178
                                    +   ++++++++ ++dg+f v   +++e++a+++++AtG  +    +P +G ++++ k
  gene219|gene219|rna219|rna219  77 R-VAKETISDIR-KRDGVFVVVS-EKGEYRAEAVIVATGASArrlfVPGTGDDEFWQK 131
                                    2.3456688885.5777788887.9**************9876666899999999976 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.07
                                    EEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                    HI0933_like   4 iviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                     viGgG A +  A+ ++   k+V ++ + ++
  gene219|gene219|rna219|rna219 150 CVIGGGDAAMEEALYLSGIAKKVYIIHRRNT 180
                                    79**********************9988776 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.35
                                    TTSTTEEE-GGGBS CS
                    HI0933_like 373 kkvpgLffaGEvlD 386
                                     ++pgLf aG v D
  gene219|gene219|rna219|rna219 269 TSIPGLFAAGDVCD 282
                                    679********988 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       0.9     2e+03       1      18 [.       3      20 ..       3      40 .. 0.75
   2 !   17.5   0.0   1.1e-06    0.0025     146     207 ..      61     119 ..      45     135 .. 0.77
   3 ?   -3.2   0.0       2.1   4.7e+03       3      29 ..     150     178 ..     149     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.9
                                   EEEEECTSHHHHHHHHHH CS
                            DAO  1 dvviiGGGiiGlstAyeL 18
                                   +vviiG+G +   +A++ 
  gene219|gene219|rna219|rna219  3 KVVIIGSGPAAYNAALYT 20
                                   59******8877777775 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.1e-06
                                    HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HH CS
                            DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.ll 207
                                      lt  + + a ++G ++ ++ ++ +++++dg    v + ++ge + a+av++a+Ga ++ l+
  gene219|gene219|rna219|rna219  61 PVLTSLMKDHAVSQGLRVAKE-TISDIRKRDGV-FVV-VSEKGEYR-AEAVIVATGASARrLF 119
                                    5577778888**********9.99***776644.444.34448765.599********99655 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.1
                                    EEECTSHHHHHHHHHHHHTT....EEEEESS CS
                            DAO   3 viiGGGiiGlstAyeLarrg....Vtllekg 29 
                                    ++iGGG + +  A++L+  g    V ++ ++
  gene219|gene219|rna219|rna219 150 CVIGGGDAAMEEALYLS--GiakkVYIIHRR 178
                                    89999988777788884..222257777666 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.54   1.2e+03       1      14 [.       5      18 ..       5      26 .. 0.79
   2 ?   11.2   0.1   0.00012      0.27     105     155 ..      64     113 ..      61     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.54
                  NAD_binding_9  1 aivGaGprGlavle 14
                                   +i+G Gp++  ++ 
  gene219|gene219|rna219|rna219  5 VIIGSGPAAYNAAL 18
                                   79*****9988776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                  NAD_binding_9 105 eellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                    ++l+++   +  ++v ++++ d+++r dg+ v+ +++ +++a+aV++A+G 
  gene219|gene219|rna219|rna219  64 TSLMKDHAVSQGLRVAKETISDIRKR-DGVFVVVSEKGEYRAEAVIVATGA 113
                                    5566666666679999********88.566788999999**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2021.42
//
Query:       gene22|gene22|rna22|rna22  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.9   0.8      0.039   14.0   0.7    1.5  1  Med9      RNA polymerase II transcription mediator complex su
      0.089   12.4   0.4       0.12   11.9   0.3    1.2  1  LepB_N    LepB N-terminal domain
        3.4    7.6   8.0        1.4    8.8   5.2    1.9  2  NUFIP1    Nuclear fragile X mental retardation-interacting pr


Domain annotation for each model (and alignments):
>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.7   6.6e-06     0.039      14      67 ..      56     116 ..      48     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.6e-06
                       Med9  14 ekdpnlsskdletktgelrhkLkkareli..relpg.....idrsveeqeaeieeleeqla 67 
                                ek++n   + ++++++++r k +ka+e+   ++++g      d s+e+ e+ iee +++la
  gene22|gene22|rna22|rna22  56 EKGKNMLYTRIKNAMSSIRSKSEKAKEVAgsENMQGseeeaFDLSPEDIEKLIEEVKKKLA 116
                                67777778899****************9533788889999999999999999999999886 PP

>> LepB_N  LepB N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3     2e-05      0.12      85     154 ..      55     126 ..      39     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                     LepB_N  85 ftkgYilnykkikglfpaiaekakklkekldekllkdivskalkkipadl..ldketkkelakylgidsfke 154
                                f kg  + y  ik+ +++i +k++k ke    + ++   ++a++  p+d+  l +e kk+la y+ + + k+
  gene22|gene22|rna22|rna22  55 FEKGKNMLYTRIKNAMSSIRSKSEKAKEVAGSENMQGSEEEAFDLSPEDIekLIEEVKKKLAGYMDVAEEKN 126
                                5566677899*************************************998445799*********8876554 PP

>> NUFIP1  Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.49     3e+03      44      47 ..      75      78 ..      59      92 .. 0.60
   2 ?    8.8   5.2   0.00024       1.4      17      50 ..     100     133 ..      86     134 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.49
                     NUFIP1 44 keee 47
                               ++ e
  gene22|gene22|rna22|rna22 75 SKSE 78
                               2222 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00024
                     NUFIP1  17 TpeeIakWreERkKnyPtkaniekkkkkeeekkk 50 
                                +pe+I+k +eE kK+      ++++k++eeekk+
  gene22|gene22|rna22|rna22 100 SPEDIEKLIEEVKKKLAGYMDVAEEKNEEEEKKE 133
                                8******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1547  (0.0862848); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 999.06
//
Query:       gene220|gene220|rna220|rna220  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-65  219.9  13.2    3.1e-65  219.7  13.2    1.0  1  DUF5089   Domain of unknown function (DUF5089)


Domain annotation for each model (and alignments):
>> DUF5089  Domain of unknown function (DUF5089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.7  13.2   1.7e-69   3.1e-65       2     193 .]      23     210 ..      22     210 .. 0.97

  Alignments for each domain:
  == domain 1  score: 219.7 bits;  conditional E-value: 1.7e-69
                        DUF5089   2 eileeakkiEeqnyetakkarkkLesaartqkkTtkelrkQgekLekakqsaikvhknaekgeelakkikregkvfvfks 81 
                                    +++eea+++E qnye+ak++r++L+++a +qk+Tt+el++Qge+Le+a+++ai +++na++g++++++i+reg+vf++++
  gene220|gene220|rna220|rna220  23 DVIEEAERVEDQNYERAKGVRMQLDETALKQKATTEELMRQGETLENARKAAIGINTNARRGSDITEDIEREGRVFSCEL 102
                                    799***************************************************************************** PP

                        DUF5089  82 pvvdkikkwfkkdkkaeeeveeiknkeeeakeeeedkkeeeefipedkelvpgeektdkeLekilnglkslkkeaevQnk 161
                                    p+v+ ik+wf++d+    ++++i +k++e++ e e+ +e+ ef++ ++e+++g++ktd+e++ +ln+++++++ea++Qnk
  gene220|gene220|rna220|rna220 103 PCVRAIKRWFRGDRG---NIDDIVSKKQEEEGEREYVPEHVEFEE-GEEYIKGQNKTDREMVGVLNTVRQIRAEADKQNK 178
                                    *************66...************999999877777765.********************************** PP

                        DUF5089 162 eikkqkskikdItkvneksekevkkteeelkk 193
                                    e+ ++ks ++dI+++ne+s+k++k+t++elkk
  gene220|gene220|rna220|rna220 179 EAVRHKSIVNDISMINERSSKVIKETDQELKK 210
                                    *******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1637  (0.0913046); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1359.30
//
Query:       gene221|gene221|rna221|rna221  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-14   52.3   0.9    7.3e-14   52.1   0.9    1.0  1  EMP24_GP25L  emp24/gp25L/p24 family/GOLD


Domain annotation for each model (and alignments):
>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.9   4.1e-18   7.3e-14      19     182 .]      18     195 ..      14     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 4.1e-18
                    EMP24_GP25L  19 kkgtlltgsyqvtdgg...........aaldvdlsvkdpdgngerlvkkkdrese..gdfsftakesgeykvCfdnsfst 85 
                                    +++  ++++++v++ +           +++ +++ ++  +++g +++++++   +    fsf+ +e+   ++ ++++  +
  gene221|gene221|rna221|rna221  18 RRNRNIEIEFDVIENKickgylkpincKNSSFKAVLA--SDTGSVYLSNENLPVDteTHFSFNISEPKVLSMVLTPIVID 95 
                                    67899999*****999999999999998999******..9999******997755448********************99 PP

                    EMP24_GP25L  86 kss......kkvsfdievgseasdykdsakkekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwws 159
                                     s+      ++v+f+ ++      +kd+akk ++e+    + kl++ l+++ +e +yl  r  +       ++s v+++s
  gene221|gene221|rna221|rna221  96 DSQphtfgeIEVDFSTQFDT---FKKDVAKKVSVEPAMAAMTKLDNLLHELNSESEYLAHRMGSIDYEHRRMFSFVTVFS 172
                                    999999*6666666666644...5788***************************************************** PP

                    EMP24_GP25L 160 ilqllvlvlvavlqvyyLkrfFk 182
                                    +++l++  +v  + +y+Lk+fF+
  gene221|gene221|rna221|rna221 173 VVTLVIYFGVNSYELYSLKKFFQ 195
                                    **********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1180.10
//
Query:       gene222|gene222|rna222|rna222  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-08   32.8   0.0    1.1e-07   31.6   0.0    1.5  1  TRAPP           Transport protein particle (TRAPP) component
  ------ inclusion threshold ------
      0.096   12.2   0.0       0.13   11.8   0.0    1.1  1  Glyco_hydro_76  Glycosyl hydrolase family 76


Domain annotation for each model (and alignments):
>> TRAPP  Transport protein particle (TRAPP) component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   1.3e-11   1.1e-07       1     119 [.      14     123 ..      14     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.3e-11
                          TRAPP   1 fafllgelvsylqrdskdveevekrLekmGyrvGlrllelllarer.pretdilevlkfickdlWkllfgkqidnlktnh 79 
                                    fa+++++ ++ +++  + v + ++++ ++G+r+G rl++++++ ++  +++ + e+ k ++++++ ++f   ++     +
  gene222|gene222|rna222|rna222  14 FALVYTSFINKVVK--DGVGKDREKMFRIGVRIGERLADDFFFTASpGKPMSLAEISKDVSETFFPHYFSFRPT----YN 87 
                                    67889999999988..57888999********************996689999999999999999999988775....45 PP

                          TRAPP  80 rgeyvltdnefpltrfvelpkelsylaflcGiirGaLenl 119
                                    +g   l+    p+ +++   ke ++l ++cGi++G+ +++
  gene222|gene222|rna222|rna222  88 QGIIALKKF--PMLQYT--RKEKKCLEMICGILKGVYNHV 123
                                    677777665..888887..34577***********98766 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.4e-05      0.13     218     268 ..      85     135 ..      80     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHHHHHHHHHH.--HHHHHHHHHHHHHHHHHCEECTTEEEEEE-T CS
                 Glyco_hydro_76 218 tYnqGtylsgaaylynaT.gdekWldrvkgllnatlstffpdgnilyevace 268
                                    tYnqG++      + ++T +++k l+ + g+l+++ ++  ++ +i +e++  
  gene222|gene222|rna222|rna222  85 TYNQGIIALKKFPMLQYTrKEKKCLEMICGILKGVYNHVSKE-DIWFEASED 135
                                    9*****************9999*******************9.9***96544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1152.91
//
Query:       gene223|gene223|rna223|rna223  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-19   68.6   0.0    8.2e-19   68.2   0.0    1.1  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   4.6e-23   8.2e-19       2     138 .]      21     150 .]      21     150 .] 0.88

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 4.6e-23
                                    EE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S----E CS
                       Archease   2 eyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkevk 81 
                                    e+ldh ADv+++++++ l  ++e a++++++y ++  +v +    ++e+++ + e+ ++++L +++ l++ e fv+ ev+
  gene223|gene223|rna223|rna223  21 EFLDHLADVQMHCTAPCLPLLYETAVKGMMSYAVKAPTVAKGG-GRVELSEGSNEMNMVALLTHFIDLMYGEGFVAIEVS 99 
                                    79*********************************99998884.9**********************************4 PP

                                    EEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                       Archease  82 vdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                        ++ ++  l +       d +k +   e+KA+T+ +lri e+d+ ++ y+++Di
  gene223|gene223|rna223|rna223 100 ----VALKNGLLVCDYSTA--DGSKCQSLCEIKAITLCDLRIFEKDGVFHSYCIFDI 150
                                    ....444566666654443..445555459**************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1035.32
//
Query:       gene224|gene224|rna224|rna224  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   12.9   1.7       0.12   12.4   0.2    1.8  2  DHR10     Designed helical repeat protein 10 domain
       0.25   10.7   5.3       0.66    9.3   0.7    2.1  2  GAS       Growth-arrest specific micro-tubule binding


Domain annotation for each model (and alignments):
>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.25   2.2e+03      42      57 ..      93     108 ..      89     119 .. 0.58
   2 ?   12.4   0.2   1.3e-05      0.12       8      76 ..     147     215 ..     145     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.25
                          DHR10  42 leeieaelakleeakk 57 
                                    le i++e++k ++a+ 
  gene224|gene224|rna224|rna224  93 LESISDEVEKKNTAST 108
                                    4555555555555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.3e-05
                          DHR10   8 keelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrel 76 
                                    k+e+a +++  +e+++ ++al+++ kdl+s+ +  + +++ +   e+++k +k   d l+ + ie+ e 
  gene224|gene224|rna224|rna224 147 KKEIALTQAEVKEIKEGLKALDKISKDLESLKARFQSVSKRILGSEKEEKGAKPPTDLLNYNFIEVTET 215
                                    899**********************************************99999999999999998886 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3    0.0044        39     133     163 ..      71     105 ..      64     119 .. 0.75
   2 ?    9.3   0.7   7.4e-05      0.66      61     106 ..     148     193 ..     143     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0044
                            GAS 133 iqevqqktglknllLe....kklkalqeelEkkea 163
                                    +  + ++++ k+++L     +kl+++++e+Ekk+ 
  gene224|gene224|rna224|rna224  71 VIVLEEDSEKKSMILNpkmgQKLESISDEVEKKNT 105
                                    55567778888888764444889999999999985 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 7.4e-05
                            GAS  61 epLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                    +++   ++ev+e ++ lk  +k  ++l++lkar +++ k +   + 
  gene224|gene224|rna224|rna224 148 KEIALTQAEVKEIKEGLKALDKISKDLESLKARFQSVSKRILGSEK 193
                                    67778899*************************9999988765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1638.54
//
Query:       gene225|gene225|rna225|rna225  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.2   0.0      0.086   13.1   0.0    1.6  1  AAA_22    AAA domain
       0.05   14.0   0.0      0.084   13.3   0.0    1.3  1  AAA_16    AAA ATPase domain
      0.075   12.8   0.0       0.11   12.2   0.0    1.2  1  AAA_30    AAA domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.086       5      49 ..      21      64 ..      17      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlps 49
                                    +++vv+G++G+ KT+++rr ++ l   ++  + e+++v++  lp+
  gene225|gene225|rna225|rna225 21 TTVVVVYGPPGSSKTHSIRRTADALSLTIE--YiEDVGVYRGMLPV 64
                                   5789******************99954332..25455555444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.084      10      49 ..      10      46 ..       7      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                         AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellrale 49
                                   ++L++a++++  g + +v+++G++G+ K+  +r+ ++al+
  gene225|gene225|rna225|rna225 10 KELRTAFQKL--G-TTVVVVYGPPGSSKTHSIRRTADALS 46
                                   5677777755..3.379****************9998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05      0.11       5      42 ..       8      45 ..       5      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                         AAA_30  5 eQaaavealltsgdrvavltGpAGtGKttalkalreaw 42
                                   +Q+++ +a+ + g  v+v+ Gp+G+ Kt++++  ++a+
  gene225|gene225|rna225|rna225  8 KQKELRTAFQKLGTTVVVVYGPPGSSKTHSIRRTADAL 45
                                   79999999999999*****************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1545.28
//
Query:       gene226|gene226|rna226|rna226  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-07   31.3   0.1    3.8e-07   29.8   0.0    1.9  2  LisH       LisH
    5.1e-06   26.5   2.6    1.7e-05   24.8   2.6    1.8  1  CLTH       CTLH/CRA C-terminal to LisH motif domain
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.16   11.3   0.0    1.4  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   6.4e-11   3.8e-07       2      26 ..      28      52 ..      27      53 .. 0.95
   2 ?   -2.9   0.1       1.4   8.1e+03       2       9 ..      98     105 ..      98     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 6.4e-11
                                   HHHHHHHHHHHHCT-HHHHHHHHHH CS
                           LisH  2 eLNrLIydYLvkeGyeetAeaFekE 26
                                   +LNrL++dYLv+eG+ + A +F+k+
  gene226|gene226|rna226|rna226 28 DLNRLVLDYLVHEGLGDVATEFAKD 52
                                   8*********************995 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                                    HHHHHHHH CS
                           LisH   2 eLNrLIyd 9  
                                    eL++ I++
  gene226|gene226|rna226|rna226  98 ELYYFIME 105
                                    79999985 PP

>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   2.6   2.8e-09   1.7e-05       3      91 ..      64     167 ..      63     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.8e-09
                           CLTH   3 kerqkIiklilegdlseaiewinenkpellesnsnLeFkLkllqfielirg.....ktkd.........ieealeyaren 68 
                                    + r +I+++i+eg+++ ai++in++++e+ +sn +L++ +  ++  e  +      +  +         +ee+le++r +
  gene226|gene226|rna226|rna226  64 NHRTRIRNAIEEGNIDMAISRINDLNSEIIDSNIELYYFIMEQKACEQAQAirndsE--SigeqkvfvlLEEVLEFVRSE 141
                                    6799*****************************999977777776666554433540..1444568899**********9 PP

                           CLTH  69 le...fendehlkelekamsLLafsd 91 
                                    l+    en +   + e+     +f++
  gene226|gene226|rna226|rna226 142 LSsivEENPSLGLHFEDFLEFVVFNS 167
                                    96243333355555555555555555 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.8e-05      0.16      27      67 ..      44      86 ..      43     218 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHCT-EEEEEE-.SGGGHH.HHHHTTSSSEEESSEB CS
                                   xxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxx RF
                      SBP_bac_3 27 dlakaiakrlgvkvefvpv.swdeli.palksgkvDiaiaait 67
                                   d+a ++ak+ g+ +++  + +  ++i +a+++g++D+ai+ i 
  gene226|gene226|rna226|rna226 44 DVATEFAKDVGIPFTVSSFlNHRTRIrNAIEEGNIDMAISRIN 86
                                   99*************9995555555549***********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.54
# Mc/sec: 1266.65
//
Query:       gene227|gene227|rna227|rna227  [L=73]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-05   23.3   0.3    0.00012   21.7   0.3    2.0  1  LSM             LSM domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.13   12.0   0.0    1.1  1  Cyclophil_like  Cyclophilin-like


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.3   1.3e-08   0.00012      20      40 ..      34      54 ..      16      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-08
                                   EEEEEEEEEETTSEEEEEEEE CS
                            LSM 20 elrGtLkgfDqfmNlvLedve 40
                                   + +G+++gfD++mNlv+++ +
  gene227|gene227|rna227|rna227 34 KHKGRIVGFDEYMNLVIDNGT 54
                                   568**************9965 PP

>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05      0.13      24      80 ..      13      70 ..       3      73 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                                   HHHHC-SEEEEEEECTTEEEEE-S.-----SSSEESSB-TTEEEEECCCTEEEEESS- CS
                 Cyclophil_like 24 aikealPiesrvntWgeEiYfstp.vklekeenakevveagdiaywppGkalclffGk 80
                                   ++++ l    +v+ W+++i  + +   ++ +e  + v++ g+  y  +G  +c+ fG+
  gene227|gene227|rna227|rna227 13 KLYDFLSKSIDVEIWEKDIRVKHKgRIVGFDEYMNLVIDNGTKRYILKGDCICVIFGR 70
                                   566666667789999999988765156788999999*********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 499.42
//
Query:       gene228|gene228|rna228|rna228  [L=509]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-09   37.7   7.4      0.027   15.2   0.4    3.8  3  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.8e-06     0.032       6      35 ..     183     210 ..     179     213 .. 0.87
   2 !    9.7   0.1   7.7e-05       1.4       6      33 ..     388     413 ..     386     416 .. 0.88
   3 !   15.2   0.4   1.5e-06     0.027       1      30 [.     419     446 ..     419     448 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                           Sel1   6 rLGmfylylnGlgvpkDpekAiewyekAAe 35 
                                     LG  ++y++G gv++  ++A++++ k  e
  gene228|gene228|rna228|rna228 183 YLG--EIYYHGIGVKRSLDQAMYFFSKGKE 210
                                    599..999*****************99765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 7.7e-05
                           Sel1   6 rLGmfylylnGlgvpkDpekAiewyekA 33 
                                    r G   +y++G gv+k ++ A+ +y  A
  gene228|gene228|rna228|rna228 388 RIG--DAYFYGSGVEKSYRDAFAFYISA 413
                                    789..778****************9888 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.5e-06
                           Sel1   1 aeAmyrLGmfylylnGlgvpkDpekAiewy 30 
                                    +e +y++   y+y++G gv+k   +A+++ 
  gene228|gene228|rna228|rna228 419 PEGCYNVS--YMYEHGYGVKKSLLLAYKYI 446
                                    689*****..999**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3318.60
//
Query:       gene229|gene229|rna229|rna229  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-35  121.8   0.5    7.2e-32  110.9   0.1    2.1  2  Gti1_Pac2  Gti1/Pac2 family


Domain annotation for each model (and alignments):
>> Gti1_Pac2  Gti1/Pac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.1     4e-36   7.2e-32       1      79 [.       6      83 ..       6      89 .. 0.96
   2 !    9.8   0.0   4.3e-05      0.77     159     180 ..      88     109 ..      84     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 4e-36
                                   SEES---SHHHHHHHHHHHHTTSS---SS---HHHHHHHSSTTEEEEEEHHHH--SS---S--B---EEETTEEEEEB- CS
                      Gti1_Pac2  1 tfkgyiettkdalllieavlegilkrvtrRlkekErkeliksGsvFvfeeeesgikRWTDGvsWSpSrilgnfLvYrel 79
                                   +f g +e++ d l+li+ +++g+++r++rRl++kErk +i+ Gs+F++ eeesgi+RWTDG+sW pSr++g fL+Y++l
  gene229|gene229|rna229|rna229  6 SFYGSVENESDCLVLIDLARRGLIPRIQRRLTSKERK-QIRHGSIFIYCEEESGIRRWTDGMSWTPSRVQGVFLMYKQL 83
                                   599**********************************.***************************************98 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 4.3e-05
                                    --EEEEEEEEEETTTEEEEEEE CS
                      Gti1_Pac2 159 gLvKkTisvtlkgkelhlisYy 180
                                     ++K+T+s+t+ +k++h++ Y 
  gene229|gene229|rna229|rna229  88 PMIKRTYSATCGDKNFHIVGYI 109
                                    58*******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 988.02
//
Query:       gene23|gene23|rna23|rna23  [L=396]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-13   50.2   0.3    1.2e-12   47.5   0.1    2.5  2  BHD_1     Rad4 beta-hairpin domain 1
    1.8e-06   28.2   0.0    4.1e-06   27.1   0.0    1.5  1  BHD_3     Rad4 beta-hairpin domain 3
     0.0044   17.9   0.4        1.6    9.7   0.0    2.5  2  BHD_2     Rad4 beta-hairpin domain 2


Domain annotation for each model (and alignments):
>> BHD_1  Rad4 beta-hairpin domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.1     2e-16   1.2e-12       3      51 .]     191     238 ..     190     238 .. 0.96
   2 ?   -1.2   0.0      0.32   1.9e+03      16      26 ..     346     356 ..     344     357 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 2e-16
                      BHD_1   3 pmPenlqdfKnhplYvLerhLkrnEvlhpdakpvgvfkkkepVYrRsdV 51 
                                 +P+++  +K+hp Y++e+ L+  ++++p++   g f+ +e VY+R++V
  gene23|gene23|rna23|rna23 191 TIPNSVEKMKRHPKYIVESMLRWDQCIYPKRPVFGIFR-GEAVYPRENV 238
                                58*****************************9999**6.********98 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.32
                      BHD_1  16 lYvLerhLkrn 26 
                                lYvL  +L+++
  gene23|gene23|rna23|rna23 346 LYVLSNFLSQY 356
                                7*******998 PP

>> BHD_3  Rad4 beta-hairpin domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   6.8e-10   4.1e-06      10      69 ..     292     345 ..     291     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.8e-10
                                E-SSGGGS-TTEEEEE-TTHHHHHHHCT---EEEEEEEEE-SS-EE..EEEEEEEEEGGG CS
                      BHD_3  10 eifkpsmlPegavhislkgaakaakklgidyapAvvGFefkgrrgkgiPvidGivVaeed 69 
                                + f+p+ +P+++v+i +k+a+ +a ++gi y  ++ GF  +      iP+ +Gi +++++
  gene23|gene23|rna23|rna23 292 DYFHPNFIPQDCVYIDNKNAKDVAYLIGIPYRICFHGFSGR------IPINRGIFIEKKN 345
                                679***********************************766......7******999987 PP

>> BHD_2  Rad4 beta-hairpin domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0023        14       1      25 [.     242     265 ..     242     268 .. 0.83
   2 !    9.7   0.0   0.00027       1.6      47      61 ..     266     280 ..     262     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
                      BHD_2   1 rSaerWyrlGReVkpgelPvKrvks 25 
                                r++e++y++G+eV+ ++ P+++vk+
  gene23|gene23|rna23|rna23 242 RTKEQFYKEGKEVRSSK-PYRIVKR 265
                                89***********9864.7777776 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00027
                      BHD_2  47 egevpLYgewQTelY 61 
                                ++++ LY++wQT+++
  gene23|gene23|rna23|rna23 266 DKMIRLYAPWQTCEI 280
                                57999*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2646.63
//
Query:       gene231|gene231|rna231|rna231  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-05   23.0   0.2    9.7e-05   22.3   0.2    1.3  1  NAC       NAC domain


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.2   5.4e-09   9.7e-05      10      55 ..      19      63 ..      16      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.4e-09
                            NAC 10 klglkeipgieeVtirksdgkvlvfdnPkVqkspgsntyvvfGeae 55
                                   k gl+ei+gie V  ++ +     ++n  V+k +g+++  +fG+ e
  gene231|gene231|rna231|rna231 19 KVGLEEIEGIEGVSVITGN-IRCSVENSVVYKIKGTESLLIFGKQE 63
                                   99*****************.***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 933.29
//
Query:       gene232|gene232|rna232|rna232  [L=386]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-16   58.0   6.8    5.5e-07   29.1   0.1    4.6  4  PPTA      Protein prenyltransferase alpha subunit repeat
  ------ inclusion threshold ------
       0.16   12.5   0.1       0.33   11.5   0.1    1.5  1  Sod_Ni    Nickel-containing superoxide dismutase


Domain annotation for each model (and alignments):
>> PPTA  Protein prenyltransferase alpha subunit repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   1.3e-10   1.1e-06       2      27 ..     128     153 ..     128     154 .. 0.92
   2 !   29.1   0.1   6.2e-11   5.5e-07       4      27 ..     169     192 ..     166     193 .. 0.88
   3 ?    1.0   0.0     0.044     4e+02       8      21 ..     217     230 ..     215     230 .. 0.90
   4 ?   -0.9   0.0      0.17   1.6e+03       5      13 ..     349     357 ..     346     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.3e-10
                                    HHHHHHHHHH-TT-CHHHHHHHHHHC CS
                           PPTA   2 LeltekliekdpkNYsaWnyRrwlle 27 
                                    L+ +e+ ++ +pk+Y+ W++R++ ++
  gene232|gene232|rna232|rna232 128 LKVCENSLRSNPKSYQPWHHRKFMMK 153
                                    789*******************9877 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 6.2e-11
                                    HHHHHHHH-TT-CHHHHHHHHHHC CS
                           PPTA   4 ltekliekdpkNYsaWnyRrwlle 27 
                                    lt+ l++ dp+N+++WnyR+ +l 
  gene232|gene232|rna232|rna232 169 LTKLLLDSDPRNFHCWNYRMSILN 192
                                    67888899************9986 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.044
                                    HHHH-TT-CHHHHH CS
                           PPTA   8 liekdpkNYsaWny 21 
                                    +i++dp + + W y
  gene232|gene232|rna232|rna232 217 IIYTDPLDPTSWEY 230
                                    89**********77 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.17
                                    HHHHHHH-T CS
                           PPTA   5 tekliekdp 13 
                                    +ek+i++dp
  gene232|gene232|rna232|rna232 349 IEKIISLDP 357
                                    899****96 PP

>> Sod_Ni  Nickel-containing superoxide dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.6e-05      0.33      43      84 ..      74     117 ..      45     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                         Sod_Ni  43 aakqnqlsRlv..aiKEehaekvkeeilvlwtdYfkaqrlekyp 84 
                                    +++++ + Rl+    KEe  ek ke ++++  dYf  ++l++y 
  gene232|gene232|rna232|rna232  74 IEDNDAFDRLLklRSKEESIEKHKEIVQLVSDDYFSWNKLKEYL 117
                                    566777888752258*************************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2276.42
//
Query:       gene233|gene233|rna233|rna233  [L=493]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00017   21.6   3.2     0.0049   16.8   0.4    3.1  3  BOP1NT    BOP1NT (NUC169) domain


Domain annotation for each model (and alignments):
>> BOP1NT  BOP1NT (NUC169) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   2.7e-07    0.0049      23     155 ..       2     121 ..       1     140 [. 0.72
   2 !    3.7   0.2    0.0028        50     242     260 .]     165     183 ..     150     183 .. 0.83
   3 ?   -2.3   0.0      0.19   3.4e+03       7      22 ..     368     383 ..     365     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.7e-07
                         BOP1NT  23 deldkllekiddpkawrtvkDkktgkevkLsdeelelikrlqkgelpdeeydpyedvvelftseeeihplseapepkrrf 102
                                    d+++++l +    k+ r+v  k+ gke+ +++++++li++ +k+ + d ++d y ++   f+++++ + ++++     r 
  gene233|gene233|rna233|rna233   2 DRIERFLGRR-PTKKCRKV--KSGGKEFLVTKKDVKLIRSYRKNVCMDPDVDLYRPLNLSFSRKTMDEGIETR-----RK 73 
                                    5677777763.44456676..57899*************************************9988888744.....33 PP

                         BOP1NT 103 ipskweakkvaklvrairkgriklekkekeeeekvydlWedeeeeeeekrkke 155
                                    +p  + ++  +   r+ir+gr k+ +  ++++++++d+We+e  ee +  +++
  gene233|gene233|rna233|rna233  74 TPAPQSRRWPK---RKIRNGRRKVIE--ERNKNEIVDIWEEEGLEELNDYEQD 121
                                    44444443333...466777777543..3344789****99877665555444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0028
                         BOP1NT 242 dpesLlPkLPspkdLkPFP 260
                                    +  +L+ +LP+++ LkPFP
  gene233|gene233|rna233|rna233 165 KLRDLIKDLPRAETLKPFP 183
                                    56799*************9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.19
                         BOP1NT   7 iGYdidgkkimkeakk 22 
                                    i Yd+  +ki++eak+
  gene233|gene233|rna233|rna233 368 IVYDLVSRKIAREAKE 383
                                    78**********8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3287.70
//
Query:       gene234|gene234|rna234|rna234  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-33  113.0   0.2    5.6e-33  112.5   0.2    1.2  1  ubiquitin      Ubiquitin family
    1.9e-15   56.4   0.3    2.8e-15   55.9   0.3    1.3  1  Rad60-SLD      Ubiquitin-2 like Rad60 SUMO-like
      9e-05   22.9   0.1    0.00036   20.9   0.1    1.9  1  Ubiquitin_2    Ubiquitin-like domain
     0.0035   17.4   0.1     0.0076   16.3   0.1    1.6  1  Rad60-SLD_2    Ubiquitin-2 like Rad60 SUMO-like
     0.0039   17.3   2.1     0.0079   16.3   2.1    1.4  1  Ribosomal_S27  Ribosomal protein S27a
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.025   14.9   0.0    1.5  1  Ubiquitin_5    Ubiquitin-like domain
      0.023   15.3   0.1      0.029   14.9   0.1    1.2  1  DUF2407        DUF2407 ubiquitin-like domain
      0.032   14.1   0.0      0.047   13.6   0.0    1.3  1  TBK1_ULD       TANK binding kinase 1 ubiquitin-like domain
      0.077   13.1   0.6        8.9    6.4   0.0    2.4  2  Ubiquitin_4    Ubiquitin-like domain
       0.13   12.3   0.1        0.2   11.7   0.1    1.3  1  Svf1           Svf1-like N-terminal lipocalin domain


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.2   3.1e-36   5.6e-33       1      72 []       3      74 ..       3      74 .. 0.99

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 3.1e-36
                                   EEEEETTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEESSC CS
                      ubiquitin  1 itvktldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlvlrlr 72
                                   i+vktl+gk+itlev  sdt++++K+ki++kegip++qqrLi++Gk+Led rtl++y+iq++stlhlvlrlr
  gene234|gene234|rna234|rna234  3 IFVKTLTGKTITLEVGASDTIDSVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLR 74
                                   9********************************************************************986 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.3   1.6e-18   2.8e-15       1      72 []       1      71 [.       1      71 [. 0.98

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1.6e-18
                                   EEEEEEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEEEEEEX CS
                      Rad60-SLD  1 ikiilkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdtidvvi 72
                                   ++i++k+ +gk+++++V ++ t+  ++ + ++k+gip+ +++rLiF G++L++  t+ d+ i++++t+++v+
  gene234|gene234|rna234|rna234  1 MQIFVKTLTGKTITLEVGASDTIDSVKAKIQDKEGIPP-DQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVL 71
                                   89************************************.******************************986 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1     2e-07   0.00036      19      80 ..      16      69 ..       2      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                                   EEETTSBHHHHHHHHHHHH---TTCEEEEEE.-SSSSEEECSSGCCSBCCCCT--TTEEEEE CS
                    Ubiquitin_2 19 rfsksltieelKekLelitGtspasmrLqlyddkkdnevsklddddalLgsYgvkdgmrihV 80
                                    +  s+ti+++K+k++   G++p+++rL +          k  +d ++L++Y+++  +++h 
  gene234|gene234|rna234|rna234 16 EVGASDTIDSVKAKIQDKEGIPPDQQRLIFA--------GKQLEDGRTLSDYNIQKESTLHL 69
                                   567899***********************99........5667899*********9999995 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.2e-06    0.0076      25      99 ..      22      83 ..       2      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-06
                                   BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-TTSBCCCCS-TTTTTTTS-EEEEEEE---SS----.XX CS
                    Rad60-SLD_2 25 tvaelkekviaqWPkdkeekpksvndlklilaGkiLennktlkelrlplgevkggvtvmHvvvrenlsekksekk 99
                                   t++++k+k+     +dke  p  +++ +li aGk Le+ +tl++++++        +++H+v+r      k++kk
  gene234|gene234|rna234|rna234 22 TIDSVKAKI-----QDKEGIP--PDQQRLIFAGKQLEDGRTLSDYNIQKE------STLHLVLRLRGGGAKKKKK 83
                                   555555555.....3444433..34569*****************54433......5799999877666665555 PP

>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.1   4.4e-06    0.0079       5      43 ..     106     142 ..     103     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.4e-06
                                    CCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTT CS
                  Ribosomal_S27   5 YkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCg 43 
                                    + + + +kv+  +  C   CG +vf  +      CGkC 
  gene234|gene234|rna234|rna234 106 FTITE-DKVKVNNVSCEA-CGVEVFCRKISSGFKCGKCY 142
                                    56667.9***********.*******************5 PP

>> Ubiquitin_5  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.4e-05     0.025      36      93 ..      15      73 ..       5      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                    Ubiquitin_5 36 letkLdvtgkelvskiaeefglkensiKlilngklleldktLeeQgvknnskv.mvLkl 93
                                   le+  + t + + +ki ++ g+  ++ +li  gk+le ++tL + +++++s + +vL+l
  gene234|gene234|rna234|rna234 15 LEVGASDTIDSVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLhLVLRL 73
                                   4444445667788899999999999**********************999875467765 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.6e-05     0.029      22      72 ..      19      82 ..       7     117 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                        DUF2407 22 ntttvagLkqliRerlpaelasrrLrLIyaGrlLedttslasslklpees...............v 72
                                   ++ t+ ++k  i ++    +   + rLI+aG+ Led  +l++   ++e++               +
  gene234|gene234|rna234|rna234 19 ASDTIDSVKAKIQDKE--GIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTlhlvlrlrgggakkkK 82
                                   5678899999999887..67777789**************98655554445777777665544332 PP

>> TBK1_ULD  TANK binding kinase 1 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.6e-05     0.047      21      53 ..      19      51 ..       5      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                       TBK1_ULD 21 pyntvaifqeevakqTkiaaekQellfeghrll 53
                                   + +t++ +  +++++  i++++Q l+f g++l 
  gene234|gene234|rna234|rna234 19 ASDTIDSVKAKIQDKEGIPPDQQRLIFAGKQLE 51
                                   679999************************973 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.017        30       1      32 [.       1      32 [.       1      36 [. 0.93
   2 ?    6.4   0.0     0.005       8.9      58      86 ..      43      70 ..      39      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.017
                    Ubiquitin_4  1 lkvtvkkldgeslevvvkqnatvkdLkkaier 32
                                   +++ vk l g+++ ++v  + t+  +k+ i+ 
  gene234|gene234|rna234|rna234  1 MQIFVKTLTGKTITLEVGASDTIDSVKAKIQD 32
                                   7899************************9997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.005
                    Ubiquitin_4 58 LsfegekLkddkaklkeygirnkselsFv 86
                                   L+f g++L+ d  +l++y i+++s+l+ v
  gene234|gene234|rna234|rna234 43 LIFAGKQLE-DGRTLSDYNIQKESTLHLV 70
                                   889999986.6789************976 PP

>> Svf1  Svf1-like N-terminal lipocalin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00011       0.2      46     122 ..      81     151 ..      60     152 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                           Svf1  46 keknlWkstklenfeidkasfyadnlsielkneegeqykikssvnkelkvdltvtrlapGfklgedgttyfgddiee 122
                                    k+k++ +  k+++ ++++     dn++i+ +     ++k+++  ++ + v++ ++++++Gfk g+   t++g+di++
  gene234|gene234|rna234|rna234  81 KKKDFSTPKKVKKPHVKRGLSWLDNFTITED-----KVKVNNVSCEACGVEVFCRKISSGFKCGK-CYTVYGKDIAS 151
                                    4447778888999999888888899999984.....588999999*******************9.9******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 921.12
//
Query:       gene235|gene235|rna235|rna235  [L=678]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-53  180.8   0.1    7.5e-53  179.2   0.0    1.8  2  Helicase_C_2  Helicase C-terminal domain
    5.7e-49  166.1   0.0    9.1e-49  165.4   0.0    1.3  1  DEAD_2        DEAD_2
    0.00069   19.7   0.0     0.0086   16.1   0.0    2.5  2  ResIII        Type III restriction enzyme, res subunit
      0.003   17.4   0.1       0.28   10.9   0.0    2.6  2  DEAD          DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.061   13.1   0.0    2.0  2  AAA_11        AAA domain
       0.13   11.9   0.1       0.33   10.6   0.0    1.7  2  HBB           Helical and beta-bridge domain


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   4.4e+03      12      44 ..      92     124 ..      85     147 .. 0.69
   2 !  179.2   0.0   2.5e-56   7.5e-53       9     170 ..     492     655 ..     484     656 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                   Helicase_C_2  12 vlvffpSyklleevverlkeeleskkieifvee 44 
                                    +++    +k+l++++++l+++  + +i+i+ ++
  gene235|gene235|rna235|rna235  92 IIICSRTHKQLDQLIDQLRKTQYKPRISILASR 124
                                    566666778888888888888777777776654 PP

  == domain 2  score: 179.2 bits;  conditional E-value: 2.5e-56
                   Helicase_C_2   9 p..ggvlvffpSyklleevverlkeeleskkieifvee...keesrekvleeykek..kkkgaillavcrGklsEGidfs 81 
                                    +  gg+lvf+pSy++le++ +r+  +       i++e+     +++ekv+++yk++   k+ a++++v+rGk sEGidf+
  gene235|gene235|rna235|rna235 492 KghGGTLVFVPSYSFLENLQKRMGGTNP----GILTEPkngAGNEFEKVMKRYKNRiaMKQSAVFMCVYRGKASEGIDFK 567
                                    4449*******************99875....566666666778***********666********************** PP

                   Helicase_C_2  82 ddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeRfakeeir 161
                                    d  +ravi vg+P+p+++dp+ve+k+e++d++++  +g+ wy+ +a+ravnQa+GR+iRhkdD+g+++llD+R+++++++
  gene235|gene235|rna235|rna235 568 DSFARAVIAVGIPYPSLHDPQVELKKEFNDRYKS-FNGRLWYEAQAFRAVNQALGRAIRHKDDWGIVMLLDNRYSEKRVQ 646
                                    **********************************.********************************************* PP

                   Helicase_C_2 162 eklpkwlre 170
                                    ++l+kw+ e
  gene235|gene235|rna235|rna235 647 NHLSKWVAE 655
                                    ******986 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.0     3e-52   9.1e-49       1     174 [.      94     248 ..      94     250 .. 0.94

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 3e-52
                                    EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTTTTT-SCC CS
                         DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeekeekCsffenl 80 
                                    +csRTh+ql+q++++l+k+ +yk      ++ iL+SR+++C+++++++   +++ n+ C+el+k+       +C +f+ +
  gene235|gene235|rna235|rna235  94 ICSRTHKQLDQLIDQLRKT-QYKP-----RISILASRSQYCVSPKLRE---VTDKNTGCNELVKSG------NCAYFTGK 158
                                    6*****************9.7998.....9**************9999...789999********9......6****999 PP

                                    CCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEEECTCCCHH CS
                         DEAD_2  81 eelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslkgislknsivilDEAhNie 160
                                     +   l k++ ++v+die+l+  g++++ CPYy+sr l eda++i++pY+yL+d++ire++  i l+ns+vi+DEAhNie
  gene235|gene235|rna235|rna235 159 DR---LAKRVGDRVFDIEELKGEGRRCGGCPYYASRILNEDAEVIFAPYNYLIDPRIRENTG-IGLENSVVIIDEAHNIE 234
                                    44...4579****************************************************6.***************** PP

                                    HHHHHCC-EEEECH CS
                         DEAD_2 161 dvceeaasveisee 174
                                    dvc+++ s+e+ ++
  gene235|gene235|rna235|rna235 235 DVCRSSGSIELGSR 248
                                    *********99765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.9e-06    0.0086       2     146 ..      15     235 ..      14     258 .. 0.65
   2 ?   -3.1   0.0       2.3   6.9e+03      56      80 ..     496     520 ..     483     554 .. 0.56

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.9e-06
                                    -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.............................-E CS
                         ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee........................kf 57 
                                    +e+++ Q+  +++l++ l     + gl++ +TGtGK+l ++ ++  ++++ k+                         k+
  gene235|gene235|rna235|rna235  15 FEPYPAQIITMTKLISCL--MTGTSGLVESPTGTGKSLSILCAALGYSEHLKRGirsgcgkrregggmkgeevkeeklKI 92 
                                    577888999999999998..48999************98877777777766655779********************999 PP

                                    EEEESSHHHHHHHHHHG...........................................GGGTGG....GEEEESSS-B CS
                         ResIII  58 lflvprkslleqtleef...........................................kkflseaykeigkkvsgdkk 94 
                                    ++   + + l+q+++++                                           +                   
  gene235|gene235|rna235|rna235  93 IICSRTHKQLDQLIDQLrktqykprisilasrsqycvspklrevtdkntgcnelvksgncA------------------- 153
                                    99999999******99945455555555555544444443333333333333333332221................... PP

                                    --..........................................-SEEEEEHHHHHHTH........HHHTTT-SEEEEE CS
                         ResIII  95 ka...................................kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiD 139
                                                                         +++ +++++++++ ++ l  ++      +++    ++ v+iiD
  gene235|gene235|rna235|rna235 154 -YftgkdrlakrvgdrvfdieelkgegrrcggcpyyaSRILNEDAEVIFAPYNYLIDPR----IRENTGIGLENSVVIID 228
                                    .0222222223333333333333333344466666666666666666666666666666....344444555555***** PP

                                    TGGGTTS CS
                         ResIII 140 EaHrlga 146
                                    EaH++ +
  gene235|gene235|rna235|rna235 229 EAHNIED 235
                                    ***9876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.3
                                    -EEEEESSHHHHHHHHHHGGGGTGG CS
                         ResIII  56 kflflvprkslleqtleefkkflse 80 
                                     +l++vp+ s le +++++  + + 
  gene235|gene235|rna235|rna235 496 GTLVFVPSYSFLENLQKRMGGTNPG 520
                                    5788888888888887766333332 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   9.4e-05      0.28       7      73 ..      28     115 ..      23     149 .. 0.75
   2 ?    3.4   0.0     0.019        57     123     137 ..     223     238 ..     189     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.4e-05
                                    HHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS......................TTSTS-EEEEEESSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   7 aiplilgggdvlvaaeTGsGKTlaflipvlqivyet......................kgktgpkalivePtreLaeqtl 64 
                                     i ++++g + lv+ +TG+GK+l  l ++l    e+                       ++++ k++i + t++   q +
  gene235|gene235|rna235|rna235  28 LISCLMTGTSGLVESPTGTGKSLSILCAALGYS-EHlkrgirsgcgkrregggmkgeeVKEEKLKIIICSRTHKQLDQLI 106
                                    67888899999***************9999444.3346677777777777777666654566688888888888888888 PP

                                    HHHHHHTTT CS
                                    xxxxxxxxx RF
                           DEAD  65 nnlkkfkky 73 
                                    ++l+k   +
  gene235|gene235|rna235|rna235 107 DQLRKTQYK 115
                                    888776554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.019
                                    EEEEEETHHHHHHT.T CS
                                    xxxxxxxxxxxxxx.x RF
                           DEAD 123 rflVlDEadrlldq.g 137
                                    +++++DEa+++ d   
  gene235|gene235|rna235|rna235 223 SVVIIDEAHNIEDVcR 238
                                    589*******998743 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05     0.061      15      91 ..      33     119 ..      24     174 .. 0.75
   2 ?   -0.4   0.0      0.26   7.8e+02     195     226 ..     196     230 ..     188     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                         AAA_11  15 seseitliqGPPGtgKTktivellsqllsr.................rkseeeksakpriLvCapSNaAvDellerllrg 77 
                                     +    l++ P GtgK+  i+       ++                  k ee k++k +i +C+ +++  D+l+++l + 
  gene235|gene235|rna235|rna235  33 MTGTSGLVESPTGTGKSLSILCAALGYSEHlkrgirsgcgkrregggMKGEEVKEEKLKIIICSRTHKQLDQLIDQLRK- 111
                                    4555589**********7776666555433555666666666666554478999**********************988. PP

                         AAA_11  78 lldsegekykpkiv 91 
                                           +ykp+i 
  gene235|gene235|rna235|rna235 112 ------TQYKPRIS 119
                                    ......55666554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.26
                         AAA_11 195 eaeivltTlsgagsklleklak...kfdvviIDEA 226
                                    +ae++++  +    +++++ ++   +  vviIDEA
  gene235|gene235|rna235|rna235 196 DAEVIFAPYNYLIDPRIRENTGiglENSVVIIDEA 230
                                    56777777777777777777666667789*****9 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         2     6e+03     119     146 ..     343     367 ..     323     368 .. 0.67
   2 ?   10.6   0.0   0.00011      0.33     133     172 ..     406     446 ..     397     457 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                                    .EECCCCS-TCCHHHHHHHCHCCCCCCT CS
                            HBB 119 esLeavcldPskalrflkerlssllmsg 146
                                      L+ + l    +l+ l  +ls+++ sg
  gene235|gene235|rna235|rna235 343 DLLNVSTLH---VLEGLDSVLSAIHFSG 367
                                    455555555...8888899999999887 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00011
                                    HHHHHCHCCCCCCTS-SSHHHHHHHHT.....EEE.S..S. CS
                            HBB 133 rflkerlssllmsgtltpleeysdiiGle.aklkkfpspfp 172
                                    +f+ +++s++l sgtltp+  +s+ +G e a     p+++ 
  gene235|gene235|rna235|rna235 406 SFVGKVRSVVLLSGTLTPFSSFSSELGHEfAHSIVAPHLIT 446
                                    68999********************9988766666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.82u 0.39s 00:00:01.21 Elapsed: 00:00:00.60
# Mc/sec: 3430.36
//
Query:       gene236|gene236|rna236|rna236  [L=686]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.4e-141  473.0  23.4   1.6e-141  472.7  23.4    1.1  1  HSP90        Hsp90 protein
    5.4e-11   42.5   0.0    5.4e-11   42.5   0.0    1.9  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.6e-08   35.0   0.0    3.6e-08   33.9   0.0    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
  ------ inclusion threshold ------
        5.3    5.8   7.2       0.28   10.0   0.4    2.0  2  EP400_N      E1A-binding protein p400, N-terminal


Domain annotation for each model (and alignments):
>> HSP90  Hsp90 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.7  23.4  3.6e-145  1.6e-141       1     488 [.     204     674 ..     204     686 .] 0.92

  Alignments for each domain:
  == domain 1  score: 472.7 bits;  conditional E-value: 3.6e-145
                                    GGGSHHHHHHHHHHCCTTSSS-EEEEEEEEXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXEEEEEE CS
                          HSP90   1 eyleekklkelvkkySeFinfpiyllkekeeekeveeeeeeeeeeeeeeeeeakveeeeeeeeekkktkkvketvkewel 80 
                                    e+l+ k++ e+vkkyS F+ +piy ++eke+e+ +e++ee   e+  ee++e+kvee++e+     + kkv    +e e+
  gene236|gene236|rna236|rna236 204 EFLDPKRISEIVKKYSLFVFYPIYTYVEKEVEEAEEKKEE---EKAVEETNEPKVEEVQEK-----RLKKV----TEREQ 271
                                    89*************************9987765443333...333447889999998864.....45555....5569* PP

                                    ESXXSXGGGSXGGGSXHHHHHHHHHHTTTTTSXXSEEEEEEEXSSSXEEEEEEEXSSXXTTTTTTTTTSXXTTEEEEETT CS
                          HSP90  81 lNkqkpiWlrkpkevteeeYkeFYkslskdsedplavkhfsaegevefkaiLfvPkrapsdlfekykkkkknnikLYvrr 160
                                    +N +kp+W r+ k+v eee k+FYk++s d++d lav  +++eg ++++ ++f+Pkra++d+f++  +kk+nnikLY+++
  gene236|gene236|rna236|rna236 272 INVEKPLWKRNIKDVPEEELKSFYKTISGDWDDFLAVDFWHIEGLLSIELLMFIPKRARFDMFNR--NKKNNNIKLYCKN 349
                                    ****************************************************************8..79*********** PP

                                    EEEESXXTTSSXGGGTTXEEEEEESSSXSSSTHHHHHTCHHHHHHHHHHHHHHHHHHHTSXHHH..HHTHHHHHHHHHHH CS
                          HSP90 161 VfitdefedllPkyLsFvkGvvdsddLPLNvsREtlqqnkilkvikkklvrKvlemlkklaeekeeykkfykefsknlkl 240
                                    Vf+td+f d +P+++sFv Gvv sdd+P+N+sRE++q ++++k++kk+l +K++em+ kla ++e+yk+fykef++ lk+
  gene236|gene236|rna236|rna236 350 VFVTDDFGDCIPEWMSFVSGVVASDDIPMNISREMIQGTNVMKLVKKTLPQKIFEMVGKLAMDTEKYKTFYKEFGNCLKM 429
                                    ******************************************************************************** PP

                                    HHHHXGG.GHHHHHTTXEEEETTEEEEEEEHHHHHHHSXTTXXEEEEEEXSSHHHHHTSGGGHHHHHTTXXEEEEXSTTH CS
                          HSP90 241 Giiedsa.nrkklakLlrfksskseeeltsLedYvermkekqksiYyiageskeevekspflerlkkkgyevlylvdpiD 319
                                    +i + s+ +++  ak lr+ ++ks+e+++sL++Yverm  +qk+iY ++g  k++v+++p l++++k  yev+y++d +D
  gene236|gene236|rna236|rna236 430 AIGDASEgQQDGYAKCLRYFTTKSGEDMISLDTYVERMAANQKQIYVVTGLGKNQVKSNPALDAFQK--YEVIYMYDVMD 507
                                    ***999856788****************************************************986..8********** PP

                                    HHHHHTXSEETTEEEEETTBSTXXXXXXHHHHHHHHHHHHHHHHHHHHHHHTTTTTESEEEEXSSXSSXSEEEEBXTTSX CS
                          HSP90 320 eyvvqqlkeyegkklvnvakegleleeeeeekkkkeelkkkfeeltkllkevlkdkvekvkvserlvdsPcvlvtseygw 399
                                    e++++ +k+y+g+ ++ ++ eg+el+e+e   +++ee+ k+fee++k +k++l++kvekv+v  rlv+ P+v+ t++y +
  gene236|gene236|rna236|rna236 508 EVMLRGFKKYKGHAIQRITSEGVELPEDE---ENNEEVVKSFEEFCKKVKDILSNKVEKVTVNPRLVSVPAVISTTKYSL 584
                                    *************************8765...5678999***************************************** PP

                                    XHHHHHHHHHHHHHHHSSTSSSSS..XEEEEEXTTSHHHHHHHHHHHHTTTXHHHHHHHHHHHHHHHHHTTXXXSXHHHH CS
                          HSP90 400 sanmerimkaqalrdkskssymss..kktleinprhpiikeLkkkveedkedeeakdlaellyetallesGfsledpasf 477
                                    s++me imk+q +++++  + m++  kk++e+np+h+++k+Lk  ++++ e e+++++ el++et l++ Gf+l++p++f
  gene236|gene236|rna236|rna236 585 SGTMENIMKSQPVTEANPFAAMTAvsKKIFELNPNHKLVKNLKAFFDNN-EIEKMSKILELFFETVLIHNGFMLSEPKEF 663
                                    *************9666655555444******************99998.5688999*********************** PP

                                    HHHHHHHHTTT CS
                          HSP90 478 akrierllkls 488
                                     +++ ++l ++
  gene236|gene236|rna236|rna236 664 CANVFDFLCSE 674
                                    ****9988654 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   1.2e-14   5.4e-11       3      97 ..      41     165 ..      39     190 .. 0.79
   2 ?   -4.1   0.5         3   1.3e+04     112     127 ..     243     258 ..     234     271 .. 0.46

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.2e-14
                    HATPase_c_3   3 l.ekAlaelvdNsldAdaen.....................vkievnknrgktgeivieDdGkGmseeelknal.rlats 59 
                                    + e  l elv Ns dA  +                      ++i  nk    + +++i+D+G Gm++++l+n++ ++a+s
  gene236|gene236|rna236|rna236  41 SkELFLRELVSNSSDACDKLkalyfqlrekgcsldpvtslgIEIIPNKG---NRTLTIKDNGIGMTKADLMNFIgTIASS 117
                                    4466789********977667999***************6666665554...68******************66379999 PP

                    HATPase_c_3  60 skeakr...........kstslGkkGiGlklAslslgkkltvitkkege 97 
                                     +++ r            s+ +G++G+G + +s  ++++++vitk+ ++
  gene236|gene236|rna236|rna236 118 GTKKFReemkekgnstdASNLIGQFGLG-FYSSYLVAERVDVITKHPED 165
                                    888665344443333333555*******.****************9754 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3
                    HATPase_c_3 112 nekvleeltveeieev 127
                                    +ek +ee+++ ++eev
  gene236|gene236|rna236|rna236 243 EEKAVEETNEPKVEEV 258
                                    3344444443333322 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     8e-12   3.6e-08       2      94 ..      42     158 ..      41     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 8e-12
                                    HHHHHHHHHHHHHHHHHHH.........HSTTT.......EEEEEEEEEETEEEEEEEESSSSSTTHHHT.......GTC CS
                      HATPase_c   2 dekrLrqiisnlvdNavkf.........atkag.......eieveikaseddlvisveDnGiGipkedlk.......klf 58 
                                    +e +Lr+++sn +d+ +k          +   g       ++ +ei +++++ +++++DnGiG++k+dl         ++
  gene236|gene236|rna236|rna236  42 KELFLRELVSNSSDACDKLkalyfqlreK---GcsldpvtSLGIEIIPNKGNRTLTIKDNGIGMTKADLMnfigtiaSSG 118
                                    6889**************98888754431...2233333355889998789*******************9999999888 PP

                                    S.TTCH......HCSTCHT.STSSSHHHHHHHHHHHHTTTEEEE CS
                      HATPase_c  59 e.kfsq......ddstkrg.gggtGlGlsivkklvelmgGeiwv 94 
                                    + kf +      +++++++  g++GlG++ +  ++e+++    v
  gene236|gene236|rna236|rna236 119 TkKFREemkekgNSTDASNlIGQFGLGFYSSYLVAERVD----V 158
                                    888888998886333334435999999999977777433....2 PP

>> EP400_N  E1A-binding protein p400, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.5      0.23   1.1e+03     402     431 ..     223     252 ..     215     269 .. 0.76
   2 ?   10.0   0.4   6.2e-05      0.28     302     396 ..     572     672 ..     557     680 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.23
                        EP400_N 402 cvplqaylrqndldleeeeeeeeesevind 431
                                    + p+++y+ ++  + ee++eee+  e  n+
  gene236|gene236|rna236|rna236 223 FYPIYTYVEKEVEEAEEKKEEEKAVEETNE 252
                                    579*****9999999999999987776664 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 6.2e-05
                        EP400_N 302 gitssipptspsrasvp.qGlsslpltstgnatsvkkvpkkleeiapatpeiaqlrkqcldhhtkkmeslkevfke.yli 379
                                    ++++ i  t  s++ +  + + s+p+t +   +++  v+kk+ e+ p  + + +l+    +   +km  + e f e +li
  gene236|gene236|rna236|rna236 572 SVPAVISTTKYSLSGTMeNIMKSQPVTEANPFAAMTAVSKKIFELNPNHKLVKNLKAFFDNNEIEKMSKILELFFEtVLI 651
                                    66677777777777555045689*******9********************9999999999999***9999987762566 PP

                        EP400_N 380 el.ffl...qhlqGnlmdfla 396
                                       f+l   + +  n++dfl 
  gene236|gene236|rna236|rna236 652 HNgFMLsepKEFCANVFDFLC 672
                                    541555433467788888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1575  (0.0878465); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.82u 0.38s 00:00:01.20 Elapsed: 00:00:00.57
# Mc/sec: 3645.45
//
Query:       gene237|gene237|rna237|rna237  [L=835]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00026   20.7   0.0    0.00096   18.9   0.0    2.0  2  NUC173    NUC173 domain
  ------ inclusion threshold ------
       0.28   11.5   4.0        4.1    7.8   0.1    4.1  5  COMMD1_N  COMMD1 N-terminal domain


Domain annotation for each model (and alignments):
>> NUC173  NUC173 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-07   0.00096     154     203 ..     389     437 ..     375     438 .. 0.88
   2 ?   -2.9   0.0      0.48   4.3e+03     172     203 ..     665     697 ..     662     698 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-07
                         NUC173 154 iWslLPsfcelptDlkesfkklaklLsnaLyeqpeLrltickaLrkLves 203
                                    + ++LP+fc++ tD ++s+k+l +++++ + +  ++ ++ic+++rkL++s
  gene237|gene237|rna237|rna237 389 LLNCLPAFCNYGTDRNNSIKTLLQVMKANMGDA-NVFNSICTGIRKLIHS 437
                                    5689**********************9999875.67789*********87 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.48
                         NUC173 172 fkklaklLsnaLyeq.peLrltickaLrkLves 203
                                    f+  ++l+ + ++++  +Lr  i++a ++L+e+
  gene237|gene237|rna237|rna237 665 FDFYSRLMIAGMESEsMDLRCGILEASTSLIEN 697
                                    56667788888888779**********999985 PP

>> COMMD1_N  COMMD1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.095   8.5e+02       8      57 ..      10      59 ..       6      69 .. 0.79
   2 ?    7.8   0.1   0.00046       4.1      27      62 ..     177     212 ..     171     219 .. 0.89
   3 ?   -2.6   0.0      0.77   6.9e+03      51      72 ..     274     295 ..     266     299 .. 0.74
   4 ?   -3.4   0.0       1.4   1.3e+04       5      30 ..     422     447 ..     419     458 .. 0.78
   5 ?    0.1   0.1      0.11   9.7e+02      40      78 ..     754     794 ..     749     827 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.095
                       COMMD1_N  8 sgllngiakrkyygeeeiteellkeelypdvsedefaalvekmksLlksi 57
                                   s +l +i ++   ++ eit+e + ++      e   ++ ++k+++Ll+ i
  gene237|gene237|rna237|rna237 10 SKVLDAIRQSITSERMEITPENIASAAICTFLEMSRRNDHSKVQELLQII 59
                                   679999999999999******99998887776666777777777777655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00046
                       COMMD1_N  27 eellkeelypdvsedefaalvekmksLlksiasadm 62 
                                    ee+++  +++d+ +de +al + + +Ll +   + m
  gene237|gene237|rna237|rna237 177 EEFVRPTIFSDMDSDEARALYSECCDLLYNYTVMRM 212
                                    89*************************998877666 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.77
                       COMMD1_N  51 ksLlksiasadmdlaQLeafLt 72 
                                    k+++k+i +  +   Q+ +f++
  gene237|gene237|rna237|rna237 274 KEVVKEICESKLKNDQIYEFIR 295
                                    5678888888888888887776 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.4
                       COMMD1_N   5 kslsgllngiakrkyygeeeiteell 30 
                                    + ++++++gi k  + +e +i + l+
  gene237|gene237|rna237|rna237 422 NVFNSICTGIRKLIHSHEGNIKNTLI 447
                                    56888999999998888888887776 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.11
                       COMMD1_N  40 edefaalvek.mksLlksiasadmdl.aQLeafLtaqtkkq 78 
                                    +d f+  + k +ks++    s d+++   L+a L++++k++
  gene237|gene237|rna237|rna237 754 ADRFKRRHGKdIKSIVLRLMSRDVEIpKSLKALLKEKKKRK 794
                                    56666665443788888888999986256899999777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1125  (0.0627475); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.49
# Mc/sec: 5083.86
//
Query:       gene238|gene238|rna238|rna238  [L=603]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-07   28.8   1.9    8.8e-07   28.8   1.9    3.2  3  MIF4G     MIF4G domain


Domain annotation for each model (and alignments):
>> MIF4G  MIF4G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.08   1.4e+03       6      65 ..      28      87 ..      23     103 .. 0.65
   2 !   28.8   1.9   4.9e-11   8.8e-07      74     198 ..     302     407 ..     253     416 .. 0.77
   3 ?   -0.1   0.1     0.033   5.9e+02      92     117 ..     485     510 ..     445     551 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.08
                                   HHHHCHT...TTTHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHH CS
                          MIF4G  6 gilnkls...kenfevlikqllklamdddknelkevielifekaveepsfsplyarlcgklns 65
                                   +i++k+    +e+++++  +l +  m+      +e++ ++    v++ +++  ++r++++l++
  gene238|gene238|rna238|rna238 28 SIIKKIRnigSEDVDTIRNDLASEDMSK---FTSEIVPSLLLAKVQSGDDIKNVVRVTSALMA 87
                                   5555555555888888888888888887...55555555555555556666666666666655 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 4.9e-11
                                    HHHHHHHHHHHHHC-S-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEHHHHHHHHHHHHHGGCCCCSCCHSCHHHHHHH CS
                          MIF4G  74 kllnklqeefekryeleneleenedgnrrrrlglvrflgelfklkmltskilldclkellssltketaddppqdleeiei 153
                                    k+ ++l++e          +++ + + ++ + ++ ++++e++k+  ++ + +++ l++l++              ++ie+
  gene238|gene238|rna238|rna238 302 KIAATLFKE----------IYQSKNIGHNDVVSNCLLISEMCKFREVSPDEMFVLLDHLFKI-------------KNIEA 358
                                    444444444..........44478888899999**************************987.............689** PP

                                    HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCH....CSSSSHHH CS
                          MIF4G 154 lltllttigktlennekakkeldqffkriqkiledat....rqelssri 198
                                    ++ +l+ ig+++  ne+++ ++++f++ri++++ ++      +++ sr+
  gene238|gene238|rna238|rna238 359 YCACLNGIGRYFLLNESTSHRIREFIERIRNYKASKMdfihANNCLSRV 407
                                    **********************************976888855555554 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.033
                                    HHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          MIF4G  92 eleenedgnrrrrlglvrflgelfkl 117
                                    ++e++ + +r ++++lvr+ + l  l
  gene238|gene238|rna238|rna238 485 SIEIMYEHSRHKCIALVRLYSSLMLL 510
                                    45555555555555555554444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (603 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3630.32
//
Query:       gene239|gene239|rna239|rna239  [L=1810]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-42  145.4   0.0    7.1e-42  143.9   0.0    1.9  1  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
    3.7e-07   29.8   0.0    7.5e-07   28.9   0.0    1.6  1  FATC            FATC domain
  ------ inclusion threshold ------
      0.091   11.6   0.1       0.94    8.3   0.1    2.2  2  Nucleo_P87      Nucleopolyhedrovirus capsid protein P87
       0.19   12.0   1.9         12    6.3   0.1    3.6  3  RGS             Regulator of G protein signaling domain


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.0   1.6e-45   7.1e-42       4     249 ..    1527    1759 ..    1524    1760 .. 0.91

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 1.6e-45
                                     EEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHHHHHHHHCTTST CS
                 PI3_PI4_kinase    4 giykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvassetaaslldeklekkgvpp 81  
                                      ++k++ddlr+d++++ +  +++ +l+k+++ +     ++ty vip+++++giie+++   +++ + d ++ k+g+ +
  gene239|gene239|rna239|rna239 1527 WLCKNQDDLRKDSRFMDLNFIINSILKKQSSENY----IRTYTVIPFSHESGIIEWIDGLSSLKVICDSYYAKDGISI 1600
                                     589******************************9....*********************************8864433 PP

                                     CHHHHHHHHHCHCHCCHHHHHCCHHHHHHTSSTTHHHHHHHHHSSSHHHHHHHHHHHHHHHHHHHHHHHHHT-TT--T CS
                 PI3_PI4_kinase   82 tasveslrvaldkkklkkekklkfekrtalkpksgllqeFvkkspsaeewlearkqFvrslaklsvldyilgngDRhl 159 
                                          + r+ ++kk   +     + ++  lk+    + +F +++p +  wl ar++++r +a + ++++ +g+gDRh+
  gene239|gene239|rna239|rna239 1601 SET-AC-RFVSNKKIGMR-----EWHKVILKFHPKFHLWFSDNFPHPYGWLVARNNYTRTYAIMNIVGWFMGLGDRHA 1671
                                     222.22.23444444433.....446788899999******************************************* PP

                                     TTEEEETTTSEEEESSTTTCCTCSHCSSSS-.SSSSSS-THHHHHHTSTTCCHHHHHHHHHHHHHHHHHTHHHHHHHH CS
                 PI3_PI4_kinase  160 dNilvdktsgklihIDfGlilpdewkllpfpqekvPfrltrelvlaidpskdeglfresceealealrrdqnlltrll 237 
                                     +Nil d  +g  +h+D + i+  ++k l++p e+vP+rlt+++v+a++ ++ eg ++ +++ +le++ ++ n+l++ l
  gene239|gene239|rna239|rna239 1672 ENILFDSNTGDTVHVDLNCIF-GKGKELQVP-ERVPYRLTQNIVDAFGVLGLEGSYNATLCATLELFLKNRNILVSNL 1747
                                     *********************.8999*****.********************************************** PP

                                     HHHHHHHCCSSC CS
                 PI3_PI4_kinase  238 kkavkdglilwe 249 
                                       +v+d+l++w+
  gene239|gene239|rna239|rna239 1748 LSFVYDPLFEWR 1759
                                     ***********7 PP

>> FATC  FATC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.7e-10   7.5e-07       2      31 ..    1780    1809 ..    1779    1810 .] 0.90

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.7e-10
                           FATC    2 LsveqQVdrLIkeATdpeNLaqmyiGWcPw 31  
                                     L+ +   d L +eAT  eNL+ myiGW P+
  gene239|gene239|rna239|rna239 1780 LDASSKCDLLNEEATKDENLSTMYIGWLPF 1809
                                     566677899********************9 PP

>> Nucleo_P87  Nucleopolyhedrovirus capsid protein P87
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00021      0.94     449     515 ..     792     858 ..     780     868 .. 0.84
   2 ?    0.4   0.0     0.051   2.3e+02     133     186 ..    1043    1097 ..    1023    1113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00021
                     Nucleo_P87 449 lelskyagvneRlekivqvtkamqrlYdYCnCkntiegtPsaanfekLLkrLntYnLshve.mtvnFY 515
                                    l+++k     eR+e iv+  ++ q  Y++   ++t +   +  +f+k L+r+  Y L  +e  ++n Y
  gene239|gene239|rna239|rna239 792 LKFIKGP-LSERIEEIVEQFRSTQYSYEHMPSHSTERVYEKTYTFKKFLQRVYRYSLGEIErANMNDY 858
                                    6677766.89***********************************************99984355543 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.051
                     Nucleo_P87  133 aealykeirkkkikkflkdleaqareraeaek.ssaeqvvaeplrdaeiieavkn 186 
                                      ++   e +++++ kf++d ++ +r+ +e +   s +++  + ++d e++++ +n
  gene239|gene239|rna239|rna239 1043 LSEIIDECQDDEVIKFMDDCKRIERDFSEWKSlVSRNEIFRHFIKDCELVSKSGN 1097
                                     3566788999***************988755515666777788889998887776 PP

>> RGS  Regulator of G protein signaling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       3.1   1.4e+04      72     102 ..     799     829 ..     786     845 .. 0.52
   2 ?    6.3   0.1    0.0026        12       4      60 ..    1032    1088 ..    1030    1103 .. 0.86
   3 ?    3.0   0.0     0.026   1.2e+02      67     113 ..    1376    1420 ..    1310    1424 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.1
                                    HHHHHHHHHCSSSTTTTTTHHHHHHHHHHHH CS
                            RGS  72 lreelekrlekeqpsrklfeeaqeevfelle 102
                                    l e++e+ +e+ + ++  +e++ ++  e   
  gene239|gene239|rna239|rna239 799 LSERIEEIVEQFRSTQYSYEHMPSHSTERVY 829
                                    4555555555554455555444444333332 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0026
                                     HHHTSHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTST CS
                            RGS    4 slledqpgrslFreFlesefseenlsFwlaveefkkakeqeelkkkakeIyneylap 60  
                                     s+++d  ++ l+ e +++ +++e ++F ++++++++  ++ + +   +eI+++++++
  gene239|gene239|rna239|rna239 1032 SVIQDLELKALLSEIIDECQDDEVIKFMDDCKRIERDFSEWKSLVSRNEIFRHFIKD 1088
                                     6778888999999999999999***************888888999*********53 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.026
                                     TS-HHHHHHHHHHHCSSSTTTTTTHHHHHHHHHHHHHHHHHHHHTSH CS
                            RGS   67 nidkklreelekrlekeqpsrklfeeaqeevfellekdsypkFlkse 113 
                                     ++     +++ +rl++  p++++ e + + v+el+e+ + + F +s 
  gene239|gene239|rna239|rna239 1376 SLLPPYYNQILSRLSH--PNQDVAEVVSRTVLELMENYPSKTFWRSL 1420
                                     4445566777777777..*************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1810 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 1.01u 0.32s 00:00:01.33 Elapsed: 00:00:00.52
# Mc/sec: 10409.65
//
Query:       gene24|gene24|rna24|rna24  [L=375]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     4e-144  480.2   0.0     2e-143  477.9   0.0    1.8  1  Actin     Actin


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  477.9   0.0  1.1e-147    2e-143       4     407 .]       5     375 .]       2     375 .] 0.98

  Alignments for each domain:
  == domain 1  score: 477.9 bits;  conditional E-value: 1.1e-147
                      Actin   4 vsavVlDnGssttraGyagedaPkavipslvgkprgrkvea.....klyvgdealtkrpelevrspvedGvvedwdaveelweh 82 
                                v+a+V+D Gs++++ G+ag+daP+av+ps+vg+p+++ v+      + yvgdea+tkr+ l++++p+e+G+v++wd++e++w+h
  gene24|gene24|rna24|rna24   5 VQALVIDIGSGVVKSGFAGDDAPRAVFPSIVGSPKHKGVMVgmgqkDAYVGDEAQTKRGILHIKYPIEHGIVNNWDDMEKIWHH 88 
                                89***********************************999999**9************************************** PP

                      Actin  83 vlkeelkvdpeehpllltepplnppkqrekalEivfEkfkvpalylaksavlsafasgkstglvvDsGasvtsvvpVldGyvLk 166
                                ++++el+v peehp+llte+plnp+++rek+++i+fE+f+vp++y++ +avls++asg++tg+v DsG++v++vvp+++Gy+L 
  gene24|gene24|rna24|rna24  89 TFYNELRVAPEEHPVLLTEAPLNPKANREKITQIMFETFNVPSFYISIQAVLSLYASGRTTGIVFDSGDGVSHVVPIYEGYSLP 172
                                ************************************************************************************ PP

                      Actin 167 kairrsdlgGkaLteqlkellssknvevtprylikkkkvveaessaekeelekltesyktleeeevleeiKesvcevsedpegd 250
                                +ai r dl+G++Lt++l+ +l+++                              ++s++t++e+e++++iKe++c+vs + e+d
  gene24|gene24|rna24|rna24 173 YAINRIDLAGRDLTDYLQLILTES------------------------------GNSFTTTAEREIVRDIKEKLCYVSLNYEED 226
                                ***********************7..............................99*************************996 PP

                      Actin 251 eekss..sspeksYeLPDgseiklgeeRfkvpEiLFdpsligsesaleeekskllgiselivaainacdvdlrpeLlanivvtG 332
                                 ++ +  +s++k+Ye+PDg++i +g+eRf++pE+LF+p+l g e +         g+++ i+++i++cdvd+r+eL+ niv++G
  gene24|gene24|rna24|rna24 227 MRNTEhlASITKTYEMPDGQVISIGNERFRAPELLFQPKLRGLELK---------GVHQNIYDSIMKCDVDIRKELYGNIVLSG 301
                                66555679********************************999877.........***************************** PP

                      Actin 333 GnsllpglteRlekelaqlaskgvkvkiiapeeerkysaWiGGSiLAslgtfqqlwvskqEYeEqGssvverkck 407
                                G++++pgl eR+ +e+++la++ +k+ ++ap+ erkys+WiGGSiLAsl+tfqq+wvsk+EY+E+G+s+v+rkc+
  gene24|gene24|rna24|rna24 302 GTTMYPGLAERILNEIKALAPPVIKIGVVAPP-ERKYSVWIGGSILASLSTFQQMWVSKAEYQEHGPSIVHRKCF 375
                                ********************************.*****************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2499.03
//
Query:       gene240|gene240|rna240|rna240  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-23   83.9   1.3    1.7e-23   83.2   1.3    1.4  1  SPC25     Microsomal signal peptidase 25 kDa subunit (SPC25)
  ------ inclusion threshold ------
      0.016   15.1   1.0      0.034   14.0   1.0    1.6  1  DUF5412   Family of unknown function (DUF5412)
      0.041   14.0   0.3      0.049   13.8   0.3    1.1  1  GWT1      GWT1


Domain annotation for each model (and alignments):
>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   1.3   2.8e-27   1.7e-23       1     161 [.      48     192 ..      48     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.8e-27
                          SPC25   1 elKntlDdalkeyltdl.gfkeshtltdvrLalGylavaiaavaflydykveFeeskpvlaiavvlYfilsgiltlystf 79 
                                    elK +lDd++++++++  + ++s + td+++++G++++aia v+ +++ + eFe ++ ++a++ +lYfi++++  +y ++
  gene240|gene240|rna240|rna240  48 ELKIILDDVIRDFMEKVrNSRQSKASTDIKIVIGLISTAIASVVAYLSVTSEFEYHRRIIAVLTLLYFIINILGEVYFRY 127
                                    79*************9999************************************************************* PP

                          SPC25  80 vekntifvgkrktgskriekitissslkklsptytltvsykdksnkgkslkakeleksvgewFdedGylveeefeqwlak 159
                                    +   ++f+ +            +s+++   +pty + v+ k+k  ++      + +ksv ++Fd++G+lv+eef  +l+ 
  gene240|gene240|rna240|rna240 128 IGFSMVFEDR-----------VVSTNISAPDPTYVILVYNKNKLIPS------KYTKSVFDLFDSNGRLVHEEFLDDLQA 190
                                    ******9873...........3566667799********97777663......467788*****************9988 PP

                          SPC25 160 ll 161
                                    l+
  gene240|gene240|rna240|rna240 191 LF 192
                                    75 PP

>> DUF5412  Family of unknown function (DUF5412)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   5.8e-06     0.034       5      57 ..     107     159 ..     102     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                        DUF5412   5 ivllililllviliaiviywkffdlerlpkgellke.skSPdgtYtlnaYlvng 57 
                                    i++l ++l ++i i+  +y++   ++++ +++++++ ++ Pd tY++ +Y  n 
  gene240|gene240|rna240|rna240 107 IAVL-TLLYFIINILGEVYFRYIGFSMVFEDRVVSTnISAPDPTYVILVYNKNK 159
                                    3344.446666666667***********999999762667**********9885 PP

>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   8.2e-06     0.049      38     136 ..      63     161 ..      10     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.2e-06
                           GWT1  38 kkkkkkkkesketlkllikllllsilllllllllelyvefvSRrlaNlpYvlwvvalnltllllflliellfvekeeeke 117
                                    k +++++++ ++ +k++i l++++i+ ++++l +++ +e+  R++a l+   +++ +   + + ++ ++++f ++ ++++
  gene240|gene240|rna240|rna240  63 KVRNSRQSKASTDIKIVIGLISTAIASVVAYLSVTSEFEYHRRIIAVLTLLYFIINILGEVYFRYIGFSMVFEDRVVSTN 142
                                    55666778888999**************************9999999998888888888888888888887778888888 PP

                           GWT1 118 rkekatstvleainrngLl 136
                                     +    + v+  +n+n+L+
  gene240|gene240|rna240|rna240 143 ISAPDPTYVILVYNKNKLI 161
                                    888899999999****996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1327.76
//
Query:       gene241|gene241|rna241|rna241  [L=709]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.3e-100  334.3   0.3      1e-99  332.2   0.0    2.0  2  MCM              MCM P-loop domain
    1.6e-33  115.2   1.6    1.6e-33  115.2   1.6    2.0  2  MCM_OB           MCM OB domain
    5.9e-27   93.9   1.2    1.9e-26   92.3   1.2    2.0  1  MCM_lid          MCM AAA-lid domain
    4.7e-07   29.4   0.0    1.4e-05   24.6   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.2e-06   29.0   0.2    5.9e-06   26.8   0.1    2.3  2  MCM_N            MCM N-terminal domain
    4.3e-05   23.4   0.0    0.00015   21.6   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
    0.00011   22.2   0.0    0.00033   20.7   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0023   17.7   0.1      0.073   12.8   0.0    2.9  2  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  332.2   0.0  4.6e-103     1e-99       3     224 .]     308     528 ..     306     528 .. 0.99
   2 ?   -0.5   0.2      0.24   5.3e+02     124     147 ..     666     689 ..     625     693 .. 0.79

  Alignments for each domain:
  == domain 1  score: 332.2 bits;  conditional E-value: 4.6e-103
                                    HHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSS CS
                            MCM   3 eeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklap 82 
                                    ++i++l+k+++++e+l++siaps++g+ed kka+llqlfggv+k+le+ ++lrgdin+ll gdpg++KsqlL +++++++
  gene241|gene241|rna241|rna241 308 DKINDLRKRPELYEILANSIAPSVCGMEDTKKALLLQLFGGVRKELES-SRLRGDINILLAGDPGISKSQLLSFIHRTSE 386
                                    799*****************************************9987.9****************************** PP

                                    SEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE CS
                            MCM  83 ravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLn 162
                                    r++ytsg+gssa+gLta+v++d++tg+f+le+Galvl+d+GvcciDefdkm++++rs+lhE+mEqqt+s+aKaGi++tLn
  gene241|gene241|rna241|rna241 387 RGMYTSGRGSSAVGLTASVTKDPDTGQFILESGALVLSDNGVCCIDEFDKMSDTTRSVLHEVMEQQTVSVAKAGIITTLN 466
                                    ******************************************************************************** PP

                                    --EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                            MCM 163 artsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                    ar+s+la++np++++y+++ks++eninl+++lLsrFD++++l Dk+de +D+++ +hivsl+
  gene241|gene241|rna241|rna241 467 ARCSILASCNPIESKYNPRKSIVENINLPPTLLSRFDVVCLLIDKSDELQDRAIGDHIVSLY 528
                                    ***********************************************************875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.24
                                    EEEEESGGGSTCHHHHHHHHHHHH CS
                            MCM 124 vcciDefdkmkeedrsalhEamEq 147
                                     + + e+ km+ +d+++++Ea+E+
  gene241|gene241|rna241|rna241 666 KVEVSEIVKMTGADEKMVLEALEE 689
                                    467889999999999999999997 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.92   2.1e+03      67      88 ..      40      61 ..      18      64 .. 0.80
   2 !  115.2   1.6   7.3e-37   1.6e-33       2     125 ..     145     270 ..     144     271 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.92
                                   E-GGGSEEEEEEEEEEE----- CS
                         MCM_OB 67 letekskfvdfqklklQEspee 88
                                   +ete+ k++   ++++QE++e+
  gene241|gene241|rna241|rna241 40 VETERVKVIWGTTINIQETSEH 61
                                   667788888888999***9987 PP

  == domain 2  score: 115.2 bits;  conditional E-value: 7.3e-37
                                    XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH-EEE-GGGSEEEE CS
                         MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskdpfkletekskfvd 76 
                                    +R+++ ++i+k+v+++G+v+r+s+v p++++a+f+c+kc+++  v      +eeP+kC   eC+ k +++l+++ s+f d
  gene241|gene241|rna241|rna241 145 IRNINPNDIDKIVQITGMVIRSSSVIPEIVRAFFKCSKCQHECFVesvrnVIEEPNKC---ECGGKYTHQLVHNASEFED 221
                                    8****************************************8887666655677****...9**999************* PP

                                    EEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                         MCM_OB  77 fqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                    +q  ++QE pe +p G++P  ++++++++ vd + PGdrv+v+G+++a+
  gene241|gene241|rna241|rna241 222 KQIARVQELPEGIPDGTTPMAMTIVCRNEFVDGLVPGDRVKVIGVLKAT 270
                                    *********************************************9876 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   1.2   8.5e-30   1.9e-26       2      87 .]     542     623 ..     541     623 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 8.5e-30
                                    HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                        MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                    ll++Y++ a+ +i Pkl+ e++++l++aYv+lR++++    ++i++t+RqLesliRLseA+A++r+s++v+ +dv+ea+r
  gene241|gene241|rna241|rna241 542 LLKAYVREAK-RIVPKLTSESMKMLTQAYVDLRQMDN---GRTITATTRQLESLIRLSEAHARMRFSSTVDGKDVREAVR 617
                                    69********.***********************995...569************************************* PP

                                    HHHHHH CS
                        MCM_lid  82 llkesl 87 
                                    +++esl
  gene241|gene241|rna241|rna241 618 IIRESL 623
                                    ***985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.062   1.4e+02      21      41 ..     360     380 ..     350     387 .. 0.86
   2 !   24.6   0.0   6.4e-09   1.4e-05      94     162 ..     413     481 ..     402     493 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.062
                   Mg_chelatase  21 GgHnlllvGppGsGKtmlakr 41 
                                    G  n+ll+G pG  K+ l + 
  gene241|gene241|rna241|rna241 360 GDINILLAGDPGISKSQLLSF 380
                                    788*************98765 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 6.4e-09
                   Mg_chelatase  94 gskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcg 162
                                    + + + G++ l+ nGv  +DE+ +++ ++  vL e +e+++v++++a   ++  ar+ ++a+ Np  + 
  gene241|gene241|rna241|rna241 413 QFILESGALVLSDNGVCCIDEFDKMSDTTRSVLHEVMEQQTVSVAKAGIITTLNARCSILASCNPIESK 481
                                    557889***********************************************************8764 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.1   2.7e-09   5.9e-06       2      86 ..      60     131 ..      59     160 .. 0.85
   2 ?   -3.7   0.0         8   1.8e+04      65      82 ..     438     455 ..     432     473 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.7e-09
                          MCM_N   2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklep 81 
                                    e F++F+++           + Y + l++m  +++  + ++++dL+   +eL  ++  +p+e+lp+l+  l+e++ + +p
  gene241|gene241|rna241|rna241  60 EHFKEFIRKN----------RDYYSILEQMDLTQEFVFDLNCEDLY---DELRSQLAMYPQEVLPILQGSLQEIYTENFP 126
                                    7899999976..........89***********************6...58***************************99 PP

                          MCM_N  82 sykdd 86 
                                    s++  
  gene241|gene241|rna241|rna241 127 SFNGS 131
                                    87755 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8
                          MCM_N  65 lplleealkevvkkleps 82 
                                     +  +++l+ev+++ + s
  gene241|gene241|rna241|rna241 438 SDTTRSVLHEVMEQQTVS 455
                                    555677888888776654 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   6.7e-08   0.00015       2     116 ..     364     481 ..     363     487 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.7e-08
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdi..lGtevfeekekefefkkGpvfan...llladeinrapp 76 
                                    +ll g PG++k +l + + +    + +r  +t+    s +  + +   + ++ +f +++G+++ +   +   de ++ + 
  gene241|gene241|rna241|rna241 364 ILLAGDPGISKSQLLSFIHR----TSERGMYTSGRGSSAVglTASVTKDPDTGQFILESGALVLSdngVCCIDEFDKMSD 439
                                    68888888888877665554....44555666665544432144455567789*******987432449999******** PP

                          AAA_3  77 ktqsalleameerqvtvege..thklpepflvlatqnPieqe 116
                                     t+s l e+me+++v+v+++   ++l+    +la  nPie++
  gene241|gene241|rna241|rna241 440 TTRSVLHEVMEQQTVSVAKAgiITTLNARCSILASCNPIESK 481
                                    **************99986522679**************975 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.5e-07   0.00033       1     124 [.     363     479 ..     363     502 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.5e-07
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEverae 78 
                                    ++lL G+pG+ Ks+l   + +    e  ++   r+ ++  l+ ++  +   g+  l+ ++lv       ++++DE+++++
  gene241|gene241|rna241|rna241 363 NILLAGDPGISKSQLLSFIHRTS--ERGMYTSGRGSSAVGLTASVTKDpdTGQFILESGALV--LSDNGVCCIDEFDKMS 438
                                    689**********9987665544..3334444555666666666654455666778999999..9999************ PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                    + + ++L+ ++e++++++++ g  +  ++       +++a++np +
  gene241|gene241|rna241|rna241 439 DTTRSVLHEVMEQQTVSVAKAGIITTLNAR-----CSILASCNPIE 479
                                    *****************9999988888775.....89999999987 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.3e-05     0.073      20     141 ..     359     475 ..     348     492 .. 0.82
   2 ?   -2.5   0.0       1.6   3.7e+03     135     150 ..     578     593 ..     573     601 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                    TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEE CS
                Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfL 99 
                                    + d+++l+ G+ G  K+ l + ih++s+r    + +   ++ +  l +s    ++k   tG    ++G++  +d+G+  +
  gene241|gene241|rna241|rna241 359 RGDINILLAGDPGISKSQLLSFIHRTSERG---MYTSGRGSSAVGLTAS----VTKDPDTGQFILESGALVLSDNGVCCI 431
                                    567999******************999864...5577788888889888....67788888888999************* PP

                                    ETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEE CS
                Sigma54_activat 100 DeigelplelQekLlrvlqegev..ervGsskeikvdvriiaat 141
                                    De  +++ ++ + L +v+++++v   + G  ++ ++ + i+a+ 
  gene241|gene241|rna241|rna241 432 DEFDKMSDTTRSVLHEVMEQQTVsvAKAGIITTLNARCSILASC 475
                                    ******************99976115677777777777777665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                    EEEEEEESS-HHHHHH CS
                Sigma54_activat 135 vriiaatnedleeave 150
                                     r i+at+++le+ ++
  gene241|gene241|rna241|rna241 578 GRTITATTRQLESLIR 593
                                    5899*******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (709 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 4135.46
//
Query:       gene242|gene242|rna242|rna242  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-07   30.8   0.0    6.2e-07   29.1   0.0    1.9  2  KH_1      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.11   2.1e+03      47      55 ..      68      76 ..      60      86 .. 0.82
   2 !   29.1   0.0   3.5e-11   6.2e-07       7      65 ..      88     149 ..      77     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.11
                                   EEEEEESHH CS
                           KH_1 47 evtisGspe 55
                                    vtisGs++
  gene242|gene242|rna242|rna242 68 NVTISGSMY 76
                                   699999887 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 3.5e-11
                                    G.GGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT....T.-EEEEEE.SHHHHHHHHHHHH CS
                           KH_1   7 P.sslvgriIGkgGsnIkeIreetgakIkvpksedeg.sderevtisG.speavekAkelie 65 
                                    P s++vg+iIG++Gs+ k++++ t ++I + +s +++  ++  + i+  ++e+  +A + ie
  gene242|gene242|rna242|rna242  88 PeSNFVGLIIGPRGSTQKQLERITRTRIYIRGSYKDKyAEPLHCYITAdTQESLLNATAVIE 149
                                    43569************************875666669999999999999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1591.43
//
Query:       gene243|gene243|rna243|rna243  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1525.42
//
Query:       gene244|gene244|rna244|rna244  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-16   58.9   0.4    9.7e-16   57.4   0.5    1.7  2  FYRN      F/Y-rich N-terminus


Domain annotation for each model (and alignments):
>> FYRN  F/Y-rich N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.5   5.4e-20   9.7e-16       3      51 .]      74     127 ..      72     127 .. 0.95
   2 ?   -2.5   0.0      0.27   4.8e+03       5      13 ..     180     188 ..     179     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 5.4e-20
                           FYRN   3 ltvlslGelvpds.pkfhteryIyPvGYkstRlYw....stkdprkrclYtceI 51 
                                    l+++++G+l++d+ + fhte++IyPvGY+++++Y+      +++++r+lY+c++
  gene244|gene244|rna244|rna244  74 LSLIDIGKLPTDNiDMFHTETAIYPVGYTCRKKYKkhntYKRKAKDRILYICSV 127
                                    899**********************************98889999*******97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.27
                           FYRN   5 vlslGelvp 13 
                                    + slG l p
  gene244|gene244|rna244|rna244 180 IESLGDLSP 188
                                    899**9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1349.44
//
Query:       gene245|gene245|rna245|rna245  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.026   14.2   0.1       0.05   13.2   0.1    1.5  1  Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (
      0.062   13.9   0.1       0.23   12.0   0.0    2.0  1  Syntaxin-6_N   Syntaxin 6, N-terminal
       0.89    9.6   3.4        1.7    8.7   0.1    2.1  2  DUF1640        Protein of unknown function (DUF1640)


Domain annotation for each model (and alignments):
>> Mt_ATP-synt_B  Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.4e-06      0.05      64     158 ..      22     117 ..       5     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.4e-06
                                    HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHC CS
                  Mt_ATP-synt_B  64 lkerieqekklqslveltkslfevskeqvaleaeaferelqaklareikkkld.tlvnaessrrqrlQdelvkgvissVl 142
                                    ++ + e e+kl  + ++++ l+e   ++ +l+ +++e++++ + ++  +k ld  +  ++  ++ + ++++++ v  sV+
  gene245|gene245|rna245|rna245  22 VDASKERESKLEDMFRICDRLVECGQQSPKLVGQYNELKNRYRCIARPYKELDdEISACKMHMEVLSRKDTINEVARSVQ 101
                                    678999*************************************9999999997256778889999*************** PP

                                    CHCTCCCCHHHHHHHH CS
                  Mt_ATP-synt_B 143 kelsspkfkkevlqes 158
                                    + ++ ++  +  ++ +
  gene245|gene245|rna245|rna245 102 EIIAVSDYINYAINDA 117
                                    *998777666666655 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.8e-05      0.23      16      97 ..      31     102 ..      18     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                   Syntaxin-6_N  16 kaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafveevreev 95 
                                    k+e ++r   rl e +++  s++l  + +eL++ +r i    ++L++ +++ +           e+ +r++ ++ev + v
  gene245|gene245|rna245|rna245  31 KLEDMFRICDRLVECGQQ--SPKLVGQYNELKNRYRCIARPYKELDDEISACKM--------HMEVLSRKDTINEVARSV 100
                                    556666666777766654..89***************************55544........356777778888888777 PP

                   Syntaxin-6_N  96 ke 97 
                                    +e
  gene245|gene245|rna245|rna245 101 QE 102
                                    76 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   0.00028       1.7     129     167 ..      57     106 ..      12     108 .. 0.75
   2 ?    1.2   0.9     0.055   3.3e+02     150     173 ..     152     174 ..     147     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00028
                        DUF1640 129 qelnnk..........idrevsalrteiE.svKldvikyliglvvgilav 167
                                    +el+n+          +d e+sa ++++E  ++ d+i  ++ +v  i+av
  gene245|gene245|rna245|rna245  57 NELKNRyrciarpykeLDDEISACKMHMEvLSRKDTINEVARSVQEIIAV 106
                                    4555555555555555*************999******999999888887 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.055
                        DUF1640 150 KldvikyliglvvgilavglavvR 173
                                    K+ +i+ ++ +v++++a+ + v R
  gene245|gene245|rna245|rna245 152 KVRIIRSMLLIVFTLAAIFMVV-R 174
                                    8999*****9*99999998865.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1115.96
//
Query:       gene246|gene246|rna246|rna246  [L=130]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-10   39.2   0.4    9.3e-10   38.2   0.3    1.6  1  Homeodomain  Homeodomain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.3   5.2e-14   9.3e-10       6      57 .]      36      87 ..      31      87 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 5.2e-14
                                   SS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                    Homeodomain  6 tftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakekk 57
                                   + t+ q+ +L++ Fe ++ ps++++ +LA  +++  + ++ WFqN R+  +k
  gene246|gene246|rna246|rna246 36 RKTRLQTCVLNRIFEISKFPSSKTIIDLALLINVHPKSIQKWFQNTRQAIRK 87
                                   56899******************************************98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 796.93
//
Query:       gene247|gene247|rna247|rna247  [L=642]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.3e-101  338.9   0.0   3.2e-101  338.3   0.0    1.2  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    1.1e-37  129.5   1.5    1.9e-37  128.8   1.5    1.4  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
     0.0026   17.3   0.1     0.0062   16.1   0.1    1.6  1  STAR_dimer      Homodimerisation region of STAR domain protei
     0.0038   16.8   0.5     0.0079   15.8   0.5    1.5  1  RE_LlaMI        LlaMI restriction endonuclease


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.3   0.0  7.2e-105  3.2e-101       2     313 ..     149     451 ..     148     452 .. 0.98

  Alignments for each domain:
  == domain 1  score: 338.3 bits;  conditional E-value: 7.2e-105
                                    -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHH CS
                   tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdel 81 
                                    V+tRf+PeP+G LHiGha+aalln++fA + +Gk+++R++DT+pe+e+e +e+ iledlk+lgi+  +++ ++sd+f+++
  gene247|gene247|rna247|rna247 149 VVTRFPPEPNGRLHIGHARAALLNWYFASKGKGKLLVRFDDTNPEKEEERFEKGILEDLKLLGIEE-YTLSHTSDYFEKI 227
                                    99***************************************************************9.************* PP

                                    HHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.GGGSS CS
                   tRNA-synt_1c  82 kkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.vefrD 160
                                     ++a  Li +GkAY +++++e +++er++   ++s  r+ + ee+++ f eem +gka+g  +++R+kid+++   ++rD
  gene247|gene247|rna247|rna247 228 IDLAFFLIDEGKAYTDNTPQEVMRDERGK--GIESRCRNTSAEESRRTF-EEMINGKASG--YCLRAKIDMSNCnKAMRD 302
                                    *****************************..888889************.99*9999887..9*********999***** PP

                                    TEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEET CS
                   tRNA-synt_1c 161 lvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrlnle 240
                                    +v+ r + +p   h+++++k+++yPtYdfa++++D+le++t +lrt+e++d++++y+w++++l+l  +p ih ++rln+e
  gene247|gene247|rna247|rna247 303 PVIFRTNGSP---HHRTGDKYKVYPTYDFACPVVDSLEGVTLSLRTNEYRDRNQQYYWFIDNLQLSNRPKIHDFSRLNFE 379
                                    **********...******************************************************************* PP

                                    TSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHHHHHH CS
                   tRNA-synt_1c 241 kkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdrkkLe 313
                                    +++lSKRkl+  vd+  v +wdd+r+a++ ++ rlG+++e  re + ++++++++  ++++++++a+++kk++
  gene247|gene247|rna247|rna247 380 NTVLSKRKLKYYVDNGFVSGWDDPRLATVAGIKRLGMSMEVLREYILMQGVSQKT-CTISWDKVWAMNKKKID 451
                                    *******************************************************.***************97 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   1.5   4.2e-41   1.9e-37       1     174 []     454     624 ..     454     624 .. 0.92

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 4.2e-41
                 tRNA-synt_1c_C   1 ApRymaVl..dpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveeve 78 
                                    A Ry++V+  + v+v+ien++   e  +evp+h+kn +lg ++v +s+  ++++eD k l+++ee++L++++n+ v++  
  gene247|gene247|rna247|rna247 454 AARYFCVQqrNVVEVSIENMS---EYMMEVPKHKKNGNLGVKEVLYSNLMLLSQEDGKVLQDDEEFTLMNWGNAIVKKK- 529
                                    89******999*******998...589*************************************************886. PP

                 tRNA-synt_1c_C  79 kdesgevte..lkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeee.de.dfllnpdslkvleeglaepa 153
                                    +  +g vt+  + l+++g ++    k+++ +i Wvs++ +v +e+ +Y +L+++e+ d+ d  +n+ds k+ e ++ae+a
  gene247|gene247|rna247|rna247 530 TVVDGIVTKmsIVLNLEG-DF----KQTKnKISWVSKRGSVIVELTEYGNLMNDEDtDDlDMKFNKDSIKK-EYCYAESA 603
                                    455999999777788887.77....55555*********************998887775777******97.9******* PP

                 tRNA-synt_1c_C 154 lanlkkgdivQfeRiGyfrvd 174
                                    + n k+gd++QfeR+G++++d
  gene247|gene247|rna247|rna247 604 VVNIKEGDVIQFERNGFYYCD 624
                                    ******************998 PP

>> STAR_dimer  Homodimerisation region of STAR domain protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.4e-06    0.0062       8      27 ..      94     113 ..      90     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-06
                     STAR_dimer   8 YLaqLLkdKKqlaafpnvft 27 
                                     L  L+kdKK +++fp+v++
  gene247|gene247|rna247|rna247  94 VLNRLMKDKKEMEKFPEVCR 113
                                    6999**************96 PP

>> RE_LlaMI  LlaMI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   1.8e-06    0.0079      78     138 ..     536     596 ..     523     619 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                       RE_LlaMI  78 verrdsflkvfGkfdrdknryswsGevcikiknsnrsGqilrieenkdisiiynfsedkrq 138
                                    v +    l++ G+f+++kn+ sw  +    i   +++G +++ e+++d+ + +n +  k++
  gene247|gene247|rna247|rna247 536 VTKMSIVLNLEGDFKQTKNKISWVSKRGSVIVELTEYGNLMNDEDTDDLDMKFNKDSIKKE 596
                                    44445566777***************************************99998765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.54
# Mc/sec: 3596.12
//
Query:       gene248|gene248|rna248|rna248  [L=589]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-57  193.8   0.6    4.5e-57  193.0   0.6    1.4  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    2.6e-35  122.3   0.0    4.4e-35  121.6   0.0    1.4  1  DNA_ligase_A_N   DNA ligase N terminus
    2.8e-22   79.2   0.0    6.3e-22   78.0   0.0    1.6  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
  ------ inclusion threshold ------
       0.13   12.3   0.5         11    6.1   0.0    2.6  2  DNA_ligase_OB_2  DNA ligase OB-like domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0   0.6     1e-60   4.5e-57       1     204 []     230     429 ..     230     429 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 1e-60
                                    -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEE CS
                 DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGEl 80 
                                    pmLA++ k++ +a+k++e k f +E+KyDGeR+q+h+ g++++ fSR++++ t+++p+l+  + ++++k   ++i+DGE+
  gene248|gene248|rna248|rna248 230 PMLANPSKDLTSAFKRVEDKRFACEYKYDGERVQIHRFGNNIETFSRNSEKTTEKYPDLMDLY-NIADK---DFIIDGEI 305
                                    9**********************************************************8777.44444...5******* PP

                                    EEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEE CS
                 DNA_ligase_A_M  81 vavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaesle 160
                                    va+d+++ +ilpfq+l++rk+k+++ +++   +++c+f FD++y+dg++++de l+eRr++L++ +ke ++r+++ae ++
  gene248|gene248|rna248|rna248 306 VAYDRKECKILPFQVLTTRKRKRVESSKI--DVHVCVFGFDLIYFDGKTYIDELLEERRRVLHNSFKEMKGRFQFAEFKD 383
                                    *******************9999988888..9************************************************ PP

                                    ESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 161 vkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                    +++ e++e++++ ++++g EG++vK+   d++Y p++rs++w+K+K
  gene248|gene248|rna248|rna248 384 CETPEDAEAFFNTSVEKGFEGMMVKTlgSDATYLPSQRSNKWIKIK 429
                                    **************************999****************9 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6   0.0   9.7e-39   4.4e-35       2     172 ..       6     179 ..       5     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 9.7e-39
                                    CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--HH CS
                 DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglskk 77 
                                    F+++++++eki+  t+krle+++il+n++++v ++ p +l+pal+L    ++P+y ++e+g+ge++l+ ++ae +g s k
  gene248|gene248|rna248|rna248   6 FSDFCATLEKINL-TTKRLEIQSILTNYLKEVCETHPPSLAPALYLstgmVYPEYFNKELGVGENALVGVVAEFTGKSIK 84 
                                    9************.899************999999999****************************************99 PP

                                    HHHHHHHHHS-HHHHHHHHHCCHHHH------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHC CS
                 DNA_ligase_A_N  78 kikdalakvgDlgevaeevlskrstlakkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriil 156
                                    +i++++ k gDlg++a++++ ++    +k++l + +v+  ++++ ++ g +s   kk+i+ +++ ++sp+E kylir+++
  gene248|gene248|rna248|rna248  85 SIRNEYSKEGDLGTIAMKCRVSQLF-IPKTQLEVMDVFLGMRRIVNEgGPKSSSSKKRIILGMMVKCSPLESKYLIRLVE 163
                                    9*****************9988877.9*****************9899999***************************** PP

                                    T---SS--HHHHHHHH CS
                 DNA_ligase_A_N 157 kdlriglsektvldal 172
                                    ++l+igl+ ktvl  l
  gene248|gene248|rna248|rna248 164 GRLKIGLALKTVLISL 179
                                    ************9876 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0   1.4e-25   6.3e-22       1      99 []     454     562 ..     454     562 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 1.4e-25
                                    GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG.GGEECTTCESS---HHHHTTEEE-TT-EEEEEESEE CS
                 DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk.elerkkppfaekvpeeekrdvWvePelvveVkfaei 77 
                                    r+g +g +llgvy+  ++k+e ++k+gtGf+d+ l +l+++l+ +l  +++++  + +e+ k+dvWve ++v+eV++a +
  gene248|gene248|rna248|rna248 454 RAGFYGGFLLGVYNdeEEKFEALCKIGTGFDDNILSKLYEQLSsNLCGAPKNY--SYKESIKPDVWVEAKYVWEVRAAGM 531
                                    57899*********98888***********************85666666666..555556678**************** PP

                                    ECTSSSTT.........EECT-EEEEE-TTS CS
                 DNA_ligase_A_C  78 tasgkyka.........slRfPrfkrlReDk 99 
                                    + s+ y+a         slRfPrf+r R+Dk
  gene248|gene248|rna248|rna248 532 SLSPIYNAggsrngkgiSLRFPRFIRERDDK 562
                                    ******************************8 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0025        11       2      32 ..     450     486 ..     449     510 .. 0.82
   2 ?    3.7   0.1     0.014        62      54      66 .]     546     559 ..     537     559 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0025
                                    ...EEEEEEEEEEEEE.TTEE......EEE-SS--HH CS
                DNA_ligase_OB_2   2 GkGkykgmlGallvetkkgkr......fkiGsGlsda 32 
                                    GkGk +g+ G +l    ++++       kiG+G++d+
  gene248|gene248|rna248|rna248 450 GKGKRAGFYGGFLLGVYNDEEekfealCKIGTGFDDN 486
                                    9*********9998775433223456689*****996 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.014
                                    SSS.-EEEEEEEE- CS
                DNA_ligase_OB_2  54 kgv.pRfPsflrvR 66 
                                    kg+ +RfP+f r R
  gene248|gene248|rna248|rna248 546 KGIsLRFPRFIRER 559
                                    44479******988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3628.20
//
Query:       gene249|gene249|rna249|rna249  [L=705]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-18   65.6   0.0    2.9e-17   63.1   0.0    2.3  1  Sec23_trunk     Sec23/Sec24 trunk domain
    3.8e-11   42.8   3.5    7.7e-11   41.9   3.5    1.6  1  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
    6.8e-11   42.8   0.1    1.3e-10   41.9   0.1    1.5  1  Sec23_BS        Sec23/Sec24 beta-sandwich domain
    4.4e-09   36.1   0.1    9.5e-09   35.0   0.1    1.6  1  Sec23_helical   Sec23/Sec24 helical domain
     0.0084   16.0   0.0      0.026   14.4   0.0    1.8  1  Gelsolin        Gelsolin repeat


Domain annotation for each model (and alignments):
>> Sec23_trunk  Sec23/Sec24 trunk domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0     8e-21   2.9e-17       1     240 [.     160     374 ..     160     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 8e-21
                                    SS--EEEEEEE-SHHHHHHTHHHHHHHHHHHHCTTSSTSTT-EEEEEEESSSEEEEETSTTSSSSEEEEECHTTSCCSST CS
                    Sec23_trunk   1 pkppvflFviDvsleaikegelkalkeslkqsLdllPeepralvglitfdsvvhffelkselrqpkelvvsdlqdvflpl 80 
                                    p+pp  +F+i v++e++k   ++a+++s+   L+  + +pr++  +  fds v  + lk + +     v+sd + +   l
  gene249|gene249|rna249|rna249 160 PSPPLICFLIEVTFESMKYRAVDAVMRSIFGGLNPKSFDPRSRMMFAFFDSSV--YLLKKNGD--F-SVISDATYIPFFL 234
                                    78********************************999**************86..77877433..3.3445544444445 PP

                                    SSSSSEETTTTHHHHHHHHHHHHHHSTT-TTC-----HHHHHHHHHHHHCHCTS-EEEEEEESS---SSTTTSS-SBTTS CS
                    Sec23_trunk  81 adrlLvplseseavledlLeelpemfavtagkrperalgpalkaavellkavetggkiivfvgslptvgaggklksrede 160
                                    ++++L+pl +  +     ++ ++++f ++  k + + +g al++ +++l+  +tgg ii f  + p+vg+ g ++     
  gene249|gene249|rna249|rna249 235 EEDFLLPLDHH-FD----IDGIEKFFIEN--KPTRNNYGDALRVVQNILG--TTGGCIISFLATHPNVGP-GSVD----- 299
                                    699****9864.44....5789*******..99999**************..899***************.5443..... PP

                                    CCTSSTTCHHCHSCSSSCHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHHHHTTT-EEEEETTTC..CHHHHHHHHHH CS
                    Sec23_trunk 161 slldidkekaklvkkadkfYkkLakecvkqgisvDlFlfsldyvdlaelkqlaeltgGqvvlydsFs..aekdasklkqd 238
                                           ++ +l  k+  fYk+++  ++kqgisv  Flf+   ++l +l++l+++tgG++++y++F   ++  a kl +d
  gene249|gene249|rna249|rna249 300 ------ANQYELRCKSV-FYKEMSVHLSKQGISVTQFLFPRLGIELPTLSVLSKYTGGMLYYYPNFDgsDPAFATKLAND 372
                                    ......33445666666.************************************************96555666777777 PP

                                    HH CS
                    Sec23_trunk 239 lk 240
                                    l+
  gene249|gene249|rna249|rna249 373 LA 374
                                    76 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   3.5   2.2e-14   7.7e-11       1      36 [.      72     107 ..      72     110 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.2e-14
                 zf-Sec23_Sec24   1 PirCrrCraylNpfckidfggkrwiCnfCnhknevp 36 
                                    +irC  C++ylNpf++i+  g +w+Cn C + n++ 
  gene249|gene249|rna249|rna249  72 IIRCECCKSYLNPFVEIIPPGLKWKCNVCLSINDLA 107
                                    79*******************************986 PP

>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.1   3.6e-14   1.3e-10       4      93 ..     385     462 ..     382     465 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 3.6e-14
                                    EEEEEEE-TTEEEEEEESSSEECSTBESSEESECSESEEEEEEEETT--EEEEEEESSBTCTTSEEEEEEEEEEEETTSE CS
                       Sec23_BS   4 atlevrtSkelkvsgliGncvslsnvsekeiGeggtsewklcsldpdstlavyfdideklksgkqayiQfatlYthssge 83 
                                    ++++vr Sk + +++++G  + +s          ++  ++++++ p++++++++d++   + ++ +++Q+a+l t  +ge
  gene249|gene249|rna249|rna249 385 GMCRVRASKSVFIKEYFGSLHHRS---------ADL--ISFSTFFPSHSFSFEIDVS-REEGTRGVCFQVAILRTLRTGE 452
                                    679*********************.........99*..******************9.66778***************** PP

                                    EEEEEEEEEE CS
                       Sec23_BS  84 rrlRVttval 93 
                                    rr+RV+++++
  gene249|gene249|rna249|rna249 453 RRIRVVNFCI 462
                                    ********97 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   2.7e-12   9.5e-09      25      96 ..     497     563 ..     474     568 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2.7e-12
                                    HHHHHHHHHHHHHHHHHHH-------------GGGTTHHHHHHHHHTSTTTS--TT--HHHHHHHHHHHHH- CS
                  Sec23_helical  25 arealdtslvdllsayrkvgasgsspsqlqlpeslklLPlyilallKspafrggnsvpaDervfalslllsl 96 
                                    + e l++s+ d++++y++ ++      ++ lp++l+ LP++il+l Ks  +r+ + +p D +++++ ll + 
  gene249|gene249|rna249|rna249 497 GNEYLNKSMKDIVKSYKQLSN-----TTTLLPATLEVLPMLILSLSKSIPLRPASYTPMDYKSYYIYLLANS 563
                                    67899***************5.....479************************99***********999876 PP

>> Gelsolin  Gelsolin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   7.3e-06     0.026       7      35 ..     587     615 ..     583     623 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.3e-06
                                    EBSSSGGGEETTSEEEEEESSEEEEEEHT CS
                       Gelsolin   7 vvklsssslesgdcyLLdngftiflWiGk 35 
                                    + +l+   le+++ yLLd+g tif+++ +
  gene249|gene249|rna249|rna249 587 PLNLTLNCLETNGLYLLDTGVTIFFFVAR 615
                                    567777889****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4869.73
//
Query:       gene25|gene25|rna25|rna25  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-32  109.7   0.9    6.1e-32  109.7   0.9    1.8  2  Forkhead        Forkhead domain
  ------ inclusion threshold ------
      0.029   14.7   0.9      0.053   13.9   0.1    1.8  2  Linker_histone  linker histone H1 and H5 family
       0.11   12.4   0.0       0.18   11.8   0.0    1.5  1  RepA_C          Plasmid encoded RepA protein


Domain annotation for each model (and alignments):
>> Forkhead  Forkhead domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.9     1e-35   6.1e-32       2      84 ..      41     123 ..      40     125 .. 0.93
   2 ?   -2.2   0.1      0.87   5.2e+03      34      58 ..     135     159 ..     131     164 .. 0.64

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 1e-35
                                -----HHHHHHHHHHT-TTT-B-HHHHHHHHHCC-HHHHCC.-CCHHHHHHHHHHHHC--EEETT.-T.TSS--EEE--TTHHH CS
                   Forkhead   2 kPpysYaaLIaqAiksspekkltLseIyefieenfpyyrtaakkgWqnSirhnLslnkcFekvpreee.egkgslwtidpesee 84 
                                +P +sYa LI++Ai+ss+e++ltL+eIy++i+++ py++ + k+gWqnSirhnLslnk+F kvpr++  +gkgs+w+i+ e ++
  gene25|gene25|rna25|rna25  41 RPGISYADLITEAIESSSEGMLTLKEIYSYISSKHPYFSLK-KTGWQNSIRHNLSLNKSFYKVPRTSVnPGKGSFWKINYEFQN 123
                                899*************************************5.**********************955438********998776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.87
                                CC-HHHHCC.-CCHHHHHHHHHHHH CS
                   Forkhead  34 enfpyyrtaakkgWqnSirhnLsln 58 
                                +++++ ++++ ++  nSi + L  +
  gene25|gene25|rna25|rna25 135 NKYSFNSHRDAEKNVNSISELLGPQ 159
                                5566666655666678887776655 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       1.8   1.1e+04      15      22 ..      18      25 ..      17      27 .. 0.80
   2 ?   13.9   0.1   8.8e-06     0.053       3      41 ..      45      82 ..      44      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
             Linker_histone 15 lkerkGsS 22
                                +erkG S
  gene25|gene25|rna25|rna25 18 ANERKGFS 25
                               589***99 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.8e-06
             Linker_histone  3 sykdMikeAIkalkerkGsSrqaIkkyikakykvvdvsk 41
                               sy+d+i+eAI++  e    ++  I  yi++k+++ + +k
  gene25|gene25|rna25|rna25 45 SYADLITEAIESSSE-GMLTLKEIYSYISSKHPYFSLKK 82
                               8***********887.779*************9875554 PP

>> RepA_C  Plasmid encoded RepA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.1e-05      0.18      59     126 ..     107     175 ..      39     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                     RepA_C  59 vsriaaceltvrwedaeslgdektailedkilfederdseqgslfeselvlsea.ffkhlaehpvPide 126
                                v+   ++++++++e +++ g +kt    +k +f+++rd+e++    sel+  ++ ff ++    vP + 
  gene25|gene25|rna25|rna25 107 VNPGKGSFWKINYEFQNNKGSQKTYRSRNKYSFNSHRDAEKNVNSISELLGPQQgFFDNIGVTEVPFER 175
                                5555799**********99***********************999999886554499999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1271.70
//
Query:       gene250|gene250|rna250|rna250  [L=917]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-19   70.8   9.8    2.4e-16   60.2   1.2    4.7  5  Cnd1       non-SMC mitotic condensation complex subunit 1
    2.4e-08   33.6   1.9       0.31   11.4   0.1    5.9  6  HEAT       HEAT repeat
    3.2e-05   22.7  13.1    0.00014   20.6   1.6    3.6  4  Adaptin_N  Adaptin N terminal region
    3.8e-05   23.0   1.9    0.00039   19.7   1.2    2.8  2  Cnd3       Nuclear condensing complex subunits, C-term domain
      0.002   18.5   0.1       0.32   11.4   0.1    4.2  5  HEAT_2     HEAT repeats


Domain annotation for each model (and alignments):
>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.6   2.2e+03      71     131 ..      51     110 ..      31     121 .. 0.58
   2 !    8.1   0.0   0.00072       2.6      66     147 ..     167     248 ..     158     251 .. 0.85
   3 !    4.5   0.0    0.0093        33      22      52 ..     278     308 ..     269     373 .. 0.86
   4 ?   -2.8   0.1       1.5   5.6e+03      73      88 ..     552     567 ..     534     616 .. 0.54
   5 !   60.2   1.2   6.6e-20   2.4e-16       2      96 ..     753     848 ..     752     879 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.6
                           Cnd1  71 nprVvanalaalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdk 131
                                      +V  +  ++ +++  +s++++++   d i     +  e sew  + il ++l+ +++++
  gene250|gene250|rna250|rna250  51 PVEVAPLLFTFTSKLEPESDEELLSRITDFIRGCRGDSRETSEWMVK-ILFLILEKVKEKR 110
                                    44444444444444444466777777777777777788888888654.4445554444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00072
                           Cnd1  66 lleDenprVvanalaalteiseksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdkq..eaeslveklcp 143
                                    +++ +np   +n  ++l+ +sek+  + + ++ + +  l+d+   + ++++ +i+  L++y  k+    +++ +++++++
  gene250|gene250|rna250|rna250 167 AMKQDNPVLLKNLSTVLSLLSEKD--ISLFVNYEFFDELLDSEYFFMRNCFLEICVNLMEYFRKKGMlgKTNGIINRVVE 244
                                    467889999999999999999999..5555667999999988777*****************9998767899******** PP

                           Cnd1 144 rlqh 147
                                    rl+ 
  gene250|gene250|rna250|rna250 245 RLSD 248
                                    *975 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0093
                           Cnd1  22 lvepLrkrLkDedpyVRktaaivvakLilnd 52 
                                    ++ ++  r+ D+   VRk a+ +++ L+ + 
  gene250|gene250|rna250|rna250 278 VIREIGGRVADKTVVVRKKAISICSGLLMKH 308
                                    567788899****************995443 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 1.5
                           Cnd1  73 rVvanalaalteisek 88 
                                    +Vv+ +++++  is+ 
  gene250|gene250|rna250|rna250 552 QVVEITVSVIYSISRF 567
                                    3333333333333333 PP

  == domain 5  score: 60.2 bits;  conditional E-value: 6.6e-20
                           Cnd1   2 iRalairtlg..cirvpnlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanal 79 
                                    iRa+a++++g   ++++++ e  +  L ++L+D ++ VRk+a++v+ +L+ +++ k kg+  +la ll De+ ++ ++a 
  gene250|gene250|rna250|rna250 753 IRANAVVAMGdfLLNYNTTAERHSHLLLESLRDANADVRKNALLVIHNLLMKNILKIKGHGTKLALLLMDESMEIKEMAE 832
                                    9******************************************************************************* PP

                           Cnd1  80 aalteiseksenaiynl 96 
                                    ++l++is+k++++++ l
  gene250|gene250|rna250|rna250 833 NLLMQISKKENMMAV-L 848
                                    *********954443.3 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.012        43       1      25 [.     238     262 ..     238     267 .. 0.89
   2 ?   -2.6   0.0       2.8     1e+04      11      24 ..     288     301 ..     286     305 .. 0.77
   3 ?   -1.3   0.0       1.1   3.9e+03       5      27 ..     705     727 ..     703     728 .. 0.82
   4 !    7.2   0.0     0.002         7       4      28 ..     741     765 ..     739     768 .. 0.89
   5 !   11.4   0.1   8.7e-05      0.31       4      27 ..     778     801 ..     777     802 .. 0.91
   6 ?    3.5   0.0      0.03   1.1e+02       8      29 ..     819     840 ..     815     841 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.012
                                    HHHHHHHHHT-SSHHHHHHHHHHHH CS
                           HEAT   1 llPlllkllsDpspeVReaAakaLg 25 
                                    +++ +++ lsD+    R+ A++aL 
  gene250|gene250|rna250|rna250 238 IINRVVERLSDTYFLTRYKALQALE 262
                                    688999*****************96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                    -SSHHHHHHHHHHH CS
                           HEAT  11 DpspeVReaAakaL 24 
                                    D+   VR+ A+  +
  gene250|gene250|rna250|rna250 288 DKTVVVRKKAISIC 301
                                    778889**998765 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.1
                                    HHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   5 llkllsDpspeVReaAakaLgal 27 
                                    + + +++++ e+  aA  +L +l
  gene250|gene250|rna250|rna250 705 VEEGCHSSDEEIQVAAYVSLYRL 727
                                    67889999****99998888776 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.002
                                    HHHHHHT-SSHHHHHHHHHHHHHHH CS
                           HEAT   4 lllkllsDpspeVReaAakaLgala 28 
                                    l+++ ++++ +++R++A+ a+g+++
  gene250|gene250|rna250|rna250 741 LFVRSMNHSVSRIRANAVVAMGDFL 765
                                    789999****************986 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 8.7e-05
                                    HHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   4 lllkllsDpspeVReaAakaLgal 27 
                                    lll+ l+D +++VR++A++ + +l
  gene250|gene250|rna250|rna250 778 LLLESLRDANADVRKNALLVIHNL 801
                                    699***************999877 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.03
                                    HHT-SSHHHHHHHHHHHHHHHH CS
                           HEAT   8 llsDpspeVReaAakaLgalae 29 
                                    ll+D+s+e+ e+A + L ++++
  gene250|gene250|rna250|rna250 819 LLMDESMEIKEMAENLLMQISK 840
                                    68***********999999987 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1   0.00028         1     340     431 ..      57     148 ..       5     153 .. 0.70
   2 ?   -0.9   0.0      0.13   4.7e+02      93     137 ..     251     300 ..     225     318 .. 0.54
   3 ?   -1.1   0.8      0.15   5.3e+02     405     475 ..     525     598 ..     508     641 .. 0.62
   4 !   20.6   1.6   3.9e-08   0.00014      34     187 ..     691     846 ..     668     861 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00028
                                    HHHHHHHHTTSSXXHHHHHHHHHHHHHHHHHSCCHHHHHHHHHHHHHTTXXHHH.HHHHHHHHHHHHHHSTTTSTTCHHH CS
                      Adaptin_N 340 ivkeLkkyvkevadedfksklvkaIgrlaekfatdaewvldvllellslsgesv.kdeivevirdliqkvpelheeiiek 418
                                    ++ ++++ ++  +de++ s++ + I+ +   + +  ew++++l+ +l+   e+  ++ i  ++++ i+++ e   + +++
  gene250|gene250|rna250|rna250  57 LLFTFTSKLEPESDEELLSRITDFIRGCRGDSRETSEWMVKILFLILEKVKEKRkDSGIRLRLLECIRMYGED-ISLVNH 135
                                    55555566666678889999999999999999****************9666653777888999999999998.568*** PP

                                    HCCTCCGXXSHHH CS
                      Adaptin_N 419 Laellekieseea 431
                                    +++l+++ +s  +
  gene250|gene250|rna250|rna250 136 MIDLMCTKNSGDI 148
                                    *****99887666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHCCC-.-CCCH....HHHHHHHHHHHT-SSHHHHHHHHHH CS
                      Adaptin_N  93 qlirglALrvLssir.vpela....edlapaikkllkdrspyvrkkAala 137
                                     l r  AL++L ++   ++++      + ++i   + d++ +vrkkA+ +
  gene250|gene250|rna250|rna250 251 FLTRYKALQALECFFqKNSISverrHEVIREIGGRVADKTVVVRKKAISI 300
                                    34444444444333323333343334444455555555555555555544 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.15
                                    HHHSTTTSTTCHHHHCCTCCG.....XXSHHHHHHHHHHHHHTTTTXTT...HHHHHHCTTTTTTTSXHHHHHHHH CS
                      Adaptin_N 405 iqkvpelheeiiekLaellek.....ieseearaaaiWllGeygelvsntesasdllrslaekfvlesekvklqil 475
                                    i+++ e  +ei+e+L++ l k      ++ e+  ++i+ +  + e+ s   ++ + l  + +++ ++  +v +  l
  gene250|gene250|rna250|rna250 525 IRERVEFDGEIVETLIKNLAKmtffeHQVVEITVSVIYSISRFPEKSSI--MLLEKLCMMEKNILKAVSVVGCIGL 598
                                    4445555566667776666665555556666777777777777777766..5555555555555555555555444 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 3.9e-08
                                    HHCT---GHHHHHHHCCCC.SS-CHHHHHHHHHHHHHCTTSCCHHCCCCHHHHHHCCSSSHHHHHHHHHHHCCC-..-CC CS
                      Adaptin_N  34 ialGedvsflffevvklva.skdfelKrlvYlylellaeesedlalLvtnslqkDlkdpnqlirglALrvLssir..vpe 110
                                    +++G+++   f ++v+    s+d e+    Y+ l +l+  s +        + ++++++ + ir++A+ +++++    ++
  gene250|gene250|rna250|rna250 691 MLYGKSILSIFKQIVEEGChSSDEEIQVAAYVSLYRLMCVSFEFFSEHYELFVRSMNHSVSRIRANAVVAMGDFLlnYNT 770
                                    6788888888888887665588888889999999999999999999999***********************9987799* PP

                                    CHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-SSHHHHHHHHHHHHHHHCCCCCCC CS
                      Adaptin_N 111 laedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdkdpgvvlaAvalleeikkndrlll 187
                                    +ae   + + + l+d ++ vrk+A+l i  l+ k+   ++     ++  ll d+++ ++  A +ll +i k++++++
  gene250|gene250|rna250|rna250 771 TAERHSHLLLESLRDANADVRKNALLVIHNLLMKNILKIKGH-GTKLALLLMDESMEIKEMAENLLMQISKKENMMA 846
                                    ********************************9999998876.**************************55544433 PP

>> Cnd3  Nuclear condensing complex subunits, C-term domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.58   2.1e+03     179     209 ..     259     289 ..     236     360 .. 0.60
   2 !   19.7   1.2   1.1e-07   0.00039      22     150 ..     696     804 ..     688     855 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.58
                                    HHHHHHHHHHHCC-HHHHHHHHHHHHHHHHH CS
                           Cnd3 179 QcLsvffpvYafsspknqellaeiflptlrt 209
                                    Q+L  ff+  + s +++ e ++ei + +  +
  gene250|gene250|rna250|rna250 259 QALECFFQKNSISVERRHEVIREIGGRVADK 289
                                    5666666666666665555555555544443 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.1e-07
                                    HHHHHHHHTHHHHHC-SSHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHH-CGGGGG CS
                           Cnd3  22 sleslleslilpavrskeaairelglkcLglfclldkklakenlklflqalskgneelkiialkaifDllllhglevldk 101
                                    s+ s++++++  + +s++++i+ ++ ++L  +++++ ++  e+ +lf+++++++ +++++ a+ a+ D+ll + ++    
  gene250|gene250|rna250|rna250 696 SILSIFKQIVEEGCHSSDEEIQVAAYVSLYRLMCVSFEFFSEHYELFVRSMNHSVSRIRANAVVAMGDFLLNYNTTAE-- 773
                                    677788888888888888888888888888888888888888888888888888888888888888888888877332.. PP

                                    GHH..............HHHHHHHHHHC-TT-HHHHHHHHHHHHHHHHH CS
                           Cnd3 102 ekkedsdeeeeesessksllkllykaLdsednpelqaiaaeglcKLlla 150
                                                     +  +ll++ L+++ n++++  a   +  Ll+ 
  gene250|gene250|rna250|rna250 774 -----------------RHSHLLLESLRDA-NADVRKNALLVIHNLLMK 804
                                    .................2333444444333.344444444444444444 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         4   1.4e+04       8      37 ..      27      59 ..      25      63 .. 0.58
   2 ?   -2.9   0.0       2.6   9.2e+03      11      44 ..     110     144 ..     103     149 .. 0.78
   3 ?    1.0   0.0      0.15   5.5e+02      34      56 ..     240     262 ..     232     301 .. 0.53
   4 ?   -1.9   0.0       1.3   4.6e+03      20      44 ..     589     615 ..     582     649 .. 0.81
   5 !   11.4   0.1     9e-05      0.32      34      82 ..     740     794 ..     710     801 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4
                         HEAT_2  8 lendpdpevrr.aairaLgrignp..ealpaLv 37
                                   l++++d+++ + ++ + L +++np  e+ p+L+
  gene250|gene250|rna250|rna250 27 LVSCADKYTNKaKIFELLRSKNNPpvEVAPLLF 59
                                   666677766441455555556666566666665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                         HEAT_2  11 dpdpevrraairaLgrignp.ealpaLvelleded 44 
                                     +d  +r + ++++  +g++ ++++ +++l+ +++
  gene250|gene250|rna250|rna250 110 RKDSGIRLRLLECIRMYGEDiSLVNHMIDLMCTKN 144
                                    56778999999999999887788888888886555 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.15
                         HEAT_2  34 paLvellededpavRraaaeaLg 56 
                                    + +ve l+d+   +R+ a +aL 
  gene250|gene250|rna250|rna250 240 NRVVERLSDTYFLTRYKALQALE 262
                                    44555555555555555555553 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.3
                         HEAT_2  20 airaLg..rignpealpaLvelleded 44 
                                    a+ + g   +++ e+l++L +l+++  
  gene250|gene250|rna250|rna250 589 AVSVVGciGLKHMEYLEMLERLVKSNR 615
                                    666666667788999999999998754 PP

  == domain 5  score: 11.4 bits;  conditional E-value: 9e-05
                         HEAT_2  34 paLvellededpavRraaaeaLgai......gdpealpaLkellddddddvvRea 82 
                                    +++v+ ++++ +++R++a+ a+g +        ++   +L+e+l+d + dv+++a
  gene250|gene250|rna250|rna250 740 ELFVRSMNHSVSRIRANAVVAMGDFllnyntTAERHSHLLLESLRDANADVRKNA 794
                                    5677888888888899999999876555443358888888888887777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (917 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 5761.88
//
Query:       gene251|gene251|rna251|rna251  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-31  107.8   0.0      3e-31  107.4   0.0    1.2  1  TAFII28   hTAFII28-like protein conserved region
  ------ inclusion threshold ------
       0.09   12.8   0.0       0.22   11.5   0.0    1.6  1  DUF1932   Domain of unknown function (DUF1932)


Domain annotation for each model (and alignments):
>> TAFII28  hTAFII28-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.0   3.3e-35     3e-31       4      86 .]      48     130 ..      45     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 3.3e-35
                        TAFII28   4 enfdeeqlnRYevfrrsklnkaavkklvnsvlsqsvsqnvaivvaglaKvFvgeiveeArevqeeweesgplqpehlrea 83 
                                     +++ee+l+RYe fr s ++kaa+kk+++sv++q+v+ n++i+v+glaKvFvge++e A+ vqee++e+gpl+p+h++ea
  gene251|gene251|rna251|rna251  48 GAMSEEELHRYEKFRGSGFPKAAIKKYISSVIGQAVNPNFVIAVCGLAKVFVGEMIEIAKIVQEERQEEGPLLPSHIHEA 127
                                    589***************************************************************************** PP

                        TAFII28  84 yrr 86 
                                    yrr
  gene251|gene251|rna251|rna251 128 YRR 130
                                    *97 PP

>> DUF1932  Domain of unknown function (DUF1932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.4e-05      0.22      39      69 ..      98     134 ..      95     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                                    HHHHHHHHHHHHHCTT......S--HHHHHHHHHHHH CS
                        DUF1932  39 wveEMeeiaetlaeeg......lepqmfraiaevyrl 69 
                                    +v EM eia+ ++ee       l++ + +a +++y++
  gene251|gene251|rna251|rna251  98 FVGEMIEIAKIVQEERqeegplLPSHIHEAYRRLYKR 134
                                    699*************998888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 993.91
//
Query:       gene252|gene252|rna252|rna252  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2010.73
//
Query:       gene253|gene253|rna253|rna253  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-42  143.7   0.2      3e-42  143.6   0.2    1.0  1  DIM1      Mitosis protein DIM1


Domain annotation for each model (and alignments):
>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.2   1.7e-46     3e-42       1     132 [.       1     132 [.       1     133 [. 0.98

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 1.7e-46
                                    TS-EE-SHHHHHHHHHH-SSSEEEEEEE-TT-HHHHHHHHHHHHHHHHTTTTEEEEEEETTT--TTSCCCTT-SSSEEEE CS
                           DIM1   1 llpkLetkeevdqailseeerlvviRFGrdedaeClklDelLakiaeklknfaviylvdidevpdfnkmyeledpvtilf 80 
                                    +++ L++ +ev++++ ++ +rlvviRFG+++d+ C+++D +L++i+ +l++++ iy++++ +v++++++++l++p++i++
  gene253|gene253|rna253|rna253   1 MVNVLDSLDEVNRVVGDTLCRLVVIRFGDRDDPLCIHVDAVLERICPTLSKYVDIYTCERASVRELVDVMKLDSPLNIMC 80 
                                    57899*************************************************************************** PP

                                    EETTEEEEEE-SSS--SSB-S----HHHHHHHHHHHHHHHHHT-SEEE-SS- CS
                           DIM1  81 fyrnkhmkvDfgtgdnnKlnfvledkqelidiietiyrgakkgkglvvspid 132
                                    f +++h+k+D+++gdn+K+nf+++d ++li+++++ y+++ +gkg+++sp++
  gene253|gene253|rna253|rna253  81 FLNRRHIKIDCSSGDNDKINFLVDDPEMLIELFTLAYKAGVRGKGIIRSPFK 132
                                    **************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1023.05
//
Query:       gene254|gene254|rna254|rna254  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.7   0.1         20    5.4   0.0    2.4  2  DUF2802   Protein of unknown function (DUF2802)


Domain annotation for each model (and alignments):
>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1    0.0016        28       2      28 ..       1      27 [.       1      42 [. 0.83
   2 ?    5.4   0.0    0.0011        20      42      57 ..     127     142 ..     124     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0016
                        DUF2802  2 mgqrlaelekrlkqleerleeleqqdp 28
                                   m++rl+e+ + +k+++ +le++ q+  
  gene254|gene254|rna254|rna254  1 MDERLKEVSRLMKEIKGKLEAIIQNSM 27
                                   89******************9966654 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0011
                        DUF2802  42 qGasveelaeecgLsr 57 
                                    +Ga +ee++++ g+sr
  gene254|gene254|rna254|rna254 127 EGAALEEIIKTTGISR 142
                                    7**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1231.29
//
Query:       gene255|gene255|rna255|rna255  [L=446]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-51  176.4  14.6    7.8e-31  107.5   2.0    4.7  5  Cnd2      Condensin complex subunit 2
     0.0037   17.5   0.1      0.009   16.2   0.1    1.6  1  CNDH2_N   Condensin II complex subunit CAP-H2 or CNDH2, N-ter
  ------ inclusion threshold ------
      0.047   14.0   0.2       0.11   12.9   0.2    1.5  1  PcF       Phytotoxin PcF protein


Domain annotation for each model (and alignments):
>> Cnd2  Condensin complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   2.0   1.3e-34   7.8e-31      82     168 ..       7      93 ..       3      99 .. 0.93
   2 !   10.0   0.2   3.9e-05      0.23     189     225 ..      82     118 ..      76     124 .. 0.75
   3 !   29.2   0.1   6.1e-11   3.7e-07     433     537 ..     226     321 ..     174     347 .. 0.67
   4 !    7.7   0.1    0.0002       1.2     655     682 ..     354     381 ..     342     388 .. 0.86
   5 !   37.6   0.1   1.8e-13   1.1e-09     711     758 ..     385     432 ..     380     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.3e-34
                           Cnd2  82 eewmklatdNKInakNsWnlaLIDyfhdmsLLkegdsvNFqkAsctLDgcvKIYtsRVDSvatetgkllsgLadstekkk 161
                                    ++w+k a++NKI++kN+W  +LID+f ++   +e++++NFqkAsctLDgc+K+Y++RVD v +++++ll g +++++kkk
  gene255|gene255|rna255|rna255   7 RTWLKAAAENKITTKNTWRSTLIDHFTNIDEFREKQGINFQKASCTLDGCAKVYSTRVDDVSENAVRLLEGFGREESKKK 86 
                                    68*************************************************************************99888 PP

                           Cnd2 162 kdneeee 168
                                    +++++ +
  gene255|gene255|rna255|rna255  87 QSRKQTK 93 
                                    8877544 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 3.9e-05
                           Cnd2 189 kkkkkKkqrsseatlaksfeslqlkklelefavDPLF 225
                                    + kkk+ +++ ++t++k++ +l++k    + +vDP F
  gene255|gene255|rna255|rna255  82 ESKKKQSRKQTKTTIEKNIFNLNIKVNASRKSVDPKF 118
                                    23334444556789*********************88 PP

  == domain 3  score: 29.2 bits;  conditional E-value: 6.1e-11
                           Cnd2 433 dqalq...knWagPehWrirrikdvnkseeaakkkrkekepfeidFeapldesvaealftqassnsaislpkkqlkkksr 509
                                    ++a     k WagP+hW+i+++k  n        ++k ke+  +dF + +d   +e++   ++ n+    p+  ++ + +
  gene255|gene255|rna255|rna255 226 KEASVshfKGWAGPNHWKIQAKKGRN-------GSQKPKETSFLDFTEVID---HESIT--EPGNTLFD-PSFIVERREN 292
                                    3333235699************9944.......467899********9999...88888..44444444.5555554444 PP

                           Cnd2 510 n.lLPddkhfnskqLlklflkPkarlsrr 537
                                    + +LP+d+  + ++L+k+ ++ +   ++ 
  gene255|gene255|rna255|rna255 293 RhILPQDFRLDVEDLYKYLIRDGSFYGKD 321
                                    45****************98877655555 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0002
                           Cnd2 655 vrkeyvqYArvAKkvDvrrLKeelWkli 682
                                    ++k  +++ ++ Kkv++++LK+++   +
  gene255|gene255|rna255|rna255 354 IQKNPIPFRKTSKKVNIKKLKDNVFDSV 381
                                    678899****************998754 PP

  == domain 5  score: 37.6 bits;  conditional E-value: 1.8e-13
                           Cnd2 711 alkFtevmnnLkkvypkqmmediStslaFiclLHLANEkgLklekqed 758
                                    +++  +++++++k+y  ++++diS++l+Fi+lLHLAN+++ +l+   +
  gene255|gene255|rna255|rna255 385 NTTLLSIFESVPKIYGDDESKDISVHLCFISLLHLANDNNIQLKGVGN 432
                                    56677899**********************************998765 PP

>> CNDH2_N  Condensin II complex subunit CAP-H2 or CNDH2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.5e-06     0.009      36      90 ..      39      94 ..      22     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                        CNDH2_N 36 ggkttlnFaeAaLliqgsavvYsrKveyLyslvyqtlellskkkk.kkqkesesek 90
                                    +k+ +nF +A+  + g a+vYs +v+ + +  ++ le   ++++ kkq+++++++
  gene255|gene255|rna255|rna255 39 REKQGINFQKASCTLDGCAKVYSTRVDDVSENAVRLLEGFGREESkKKQSRKQTKT 94
                                   46777*********************************665554413333333333 PP

>> PcF  Phytotoxin PcF protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.8e-05      0.11       4      22 ..      51      69 ..      48      71 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                            PcF  4 CtatGCaslYseanievSk 22
                                   Ct +GCa++Ys   ++vS+
  gene255|gene255|rna255|rna255 51 CTLDGCAKVYSTRVDDVSE 69
                                   9*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2985.19
//
Query:       gene256|gene256|rna256|rna256  [L=670]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-58  198.1  13.7    1.7e-58  198.1  13.7    1.7  2  PMT       Dolichyl-phosphate-mannose-protein mannosyltransfer
    8.4e-43  146.3  12.0    8.4e-43  146.3  12.0    2.2  2  PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltra
    8.4e-17   61.6   0.2    1.4e-16   60.9   0.2    1.3  1  MIR       MIR domain


Domain annotation for each model (and alignments):
>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.1  13.7   2.8e-62   1.7e-58       3     244 ..      16     253 ..      14     254 .. 0.96
   2 ?   -4.6   2.4       2.2   1.3e+04     139     155 ..     606     622 ..     579     641 .. 0.70

  Alignments for each domain:
  == domain 1  score: 198.1 bits;  conditional E-value: 2.8e-62
                            PMT   3 ltllallirlwrlslpnsvvfdevhfgkfasdYlehsffmdvhpplgkmllalggyLagkdgnftfesigaeyypenvpy 82 
                                    +++l+++i  +++ + n vv+de+hfgkfa +Yl ++f++dvhpplgk l +lggyL+  + +f+f+s   e++p++ +y
  gene256|gene256|rna256|rna256  16 IFALSIIIKTYKIENGNFVVWDEAHFGKFAEKYLSRKFYFDVHPPLGKILTSLGGYLFNQPLDFEFNSG--EKFPQGFDY 93 
                                    78999***************************************************************9..9******** PP

                            PMT  83 vslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkferkapfsr 162
                                    +++R f+ +  s+++++ yl+l+e+g+s +   + +l++++en++  ++r+illds Ll ft++  y++++++  +   r
  gene256|gene256|rna256|rna256  94 SGMRRFHSIIASFTPVIGYLMLKEMGYSYRRRTILSLMFIFENGFTSIGRLILLDSHLLTFTAAVAYFMTRMY-FRSKKR 172
                                    ************************************************************************9.345678 PP

                            PMT 163 swwlwllltgvalglavsvKwvglftvllvgllliwelwqllgdkslllksivkhllaralaliviPvtlylavftvhfw 242
                                      + + +l+g++lg+++svKw+g++t++lvg+ +i++lw  +  k   l+  +k +l++a++li++P +ly++ f++hf+
  gene256|gene256|rna256|rna256 173 VDIPSIFLLGITLGCVMSVKWIGFLTTSLVGVFTIYHLWCNITSKESILA-FMKLFLVKAFFLIGVPSFLYILLFYIHFE 251
                                    8899**************************************97777776.89**************************9 PP

                            PMT 243 ll 244
                                    ++
  gene256|gene256|rna256|rna256 252 IV 253
                                    87 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 2.2
                            PMT 139 pLlfftllsmyclvkfe 155
                                    p lff l s+++++kf 
  gene256|gene256|rna256|rna256 606 PALFFALFSLCYVMKFV 622
                                    44666666666666654 PP

>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   4.1       1.1   6.8e+03      51     180 ..     178     215 ..     150     252 .. 0.47
   2 !  146.3  12.0   1.4e-46   8.4e-43       1     199 []     476     664 ..     476     664 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.1
                       PMT_4TMC  51 iyllGNpvlwwlstiallvfvllllalllrrqrgvkdleeeetrllnsglflllgwalhylPfflmgRvlflhhYlpAll 130
                                    i+llG  ++ ++s+  + +++                                                           
  gene256|gene256|rna256|rna256 178 IFLLGITLGCVMSVKWIGFLTT---------------------------------------------------------- 199
                                    4444444444444333332222.......................................................... PP

                       PMT_4TMC 131 failllaalldfllkslkkslkkkklvklivvvvllvlviavFiffsplt 180
                                                                       lv v+ ++ +++ +t
  gene256|gene256|rna256|rna256 200 ----------------------------------SLVGVFTIYHLWCNIT 215
                                    ..................................2333344444444333 PP

  == domain 2  score: 146.3 bits;  conditional E-value: 1.4e-46
                       PMT_4TMC   1 Flkkflelqkamltsnnalte.s....hpyaSepyeWplllrgisywtkneekkqiyllGNpvlwwlstiallvfvllll 75 
                                    F+kkf+e +kam+ +n+++++ +    +++ S+pyeW +l+rg++++ ++ +++++y++GNp++w++s i++++  +lll
  gene256|gene256|rna256|rna256 476 FIKKFIEHNKAMFITNASFVQdEdlepERIVSKPYEWFILRRGMRMTAWDGRNEKFYMFGNPLVWYSSGICVILSPFLLL 555
                                    99*******************559*999**************************************************** PP

                       PMT_4TMC  76 alllrrqrgvkdleeeetrllnsglflllgwalhylPfflmgRvlflhhYlpAllfailllaalldfllkslkkslkkkk 155
                                      ++ r+r+ k l +  ++  + +++ ++gw++hy+Pff+++Rvl++hhY+pAl+fa++ l+++++f+            
  gene256|gene256|rna256|rna256 556 SRVIIRKRKGKPL-TFLKNEGYMVFLSCCGWLFHYVPFFFVKRVLYFHHYYPALFFALFSLCYVMKFVR----------- 623
                                    ********99999.333333455668899**************************************93........... PP

                       PMT_4TMC 156 lvklivvvvllvlviavFiffspltyGlpgtseevkklkwlssW 199
                                         +v+v++++vi++F+++s ltyG++ ++  +++  ++++W
  gene256|gene256|rna256|rna256 624 ---FRFVAVFMSAVIISFFLYSRLTYGFTEETPFLRRISMIPTW 664
                                    ...6799*************************999999999999 PP

>> MIR  MIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.2   2.4e-20   1.4e-16       2     179 ..     300     446 ..     299     452 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 2.4e-20
                            MIR   2 yLkggdvvRLfHshqdeyltiseqqqkqevflritlypsadaanssraLWeievvqkdawrgglikwgkvyRlkHlaTgr 81 
                                    yL         Hsh ++y+ ++++q         t+y+++d++n     W  + v++d    ++i+ g+++ l H+ T++
  gene256|gene256|rna256|rna256 300 YL---------HSHDHKYPDGKNNQV--------TIYHHKDENNG----WVFQKVTDDLEDAKFIESGDTVVLLHMETKK 358
                                    55.........*********988776........***********....******************************* PP

                            MIR  82 yLaseeekksplseseddqkevsayglegfegdnDkveifekksttgmksaklvprdsyvrlqHvvtgcwLhstsvklkk 161
                                     L + ++  s++s+  +++  +s  +  +      k+ei+   ++  +k++++++ ++++rl  ++ +c+L  +s k ++
  gene256|gene256|rna256|rna256 359 HLDVPNN-PSFISSGLRAESSGSHLSDTNL----FKIEIV---DDALKKESRVKTLTTKFRLLNIKHNCYLKPSSRKYPS 430
                                    ******9.9999988776665554433222....248888...5999********************************* PP

                            MIR 162 ekfekvqqkvicakeked 179
                                    ++fe  q +vica  k +
  gene256|gene256|rna256|rna256 431 WGFE--QGEVICAARKDE 446
                                    ****..*******98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (670 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4535.36
//
Query:       gene257|gene257|rna257|rna257  [L=293]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1872.77
//
Query:       gene258|gene258|rna258|rna258  [L=552]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-23   83.2   8.5    3.4e-05   24.1   0.2    6.5  6  BRCT           BRCA1 C Terminus (BRCT) domain
    9.5e-15   54.8   1.6    3.7e-09   36.9   0.0    4.4  5  BRCT_2         BRCT domain, a BRCA1 C-terminus domain
    1.2e-14   54.0   3.4    3.9e-07   29.9   0.0    4.8  6  RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRC
    1.5e-14   53.7   5.5     0.0018   18.2   0.0    5.3  6  PTCB-BRCT      twin BRCT domain
    0.00083   19.6   0.1       0.14   12.5   0.0    3.5  3  LIG3_BRCT      DNA ligase 3 BRCT domain


Domain annotation for each model (and alignments):
>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.2   9.4e-09   3.4e-05      10      77 ..      13      78 ..       6      79 .. 0.79
   2 !   15.7   0.1   4.2e-06     0.015       4      71 ..      89     150 ..      87     155 .. 0.89
   3 !   12.6   0.0   3.7e-05      0.13       4      79 .]     177     245 ..     175     245 .. 0.87
   4 !   12.3   0.0   4.8e-05      0.17      27      79 .]     287     335 ..     266     335 .. 0.89
   5 !    9.2   0.0   0.00043       1.6      23      76 ..     388     441 ..     373     443 .. 0.77
   6 !    8.4   0.1   0.00078       2.8      18      53 ..     498     533 ..     492     546 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.4e-09
                                   EEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHH CS
                           BRCT 10 kfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlld 77
                                   +fv+t++ +  + + +++ + +h   + + +s +t++l+  +    ++ky +alk+ni+i+h +wl+d
  gene258|gene258|rna258|rna258 13 IFVCTTGISRDEQELIKSQLPKHAV-LEDILSITTDYLISYKA-MMTEKYIQALKWNIKILHVKWLYD 78
                                   5666666666666666666666643.36778999*****9999.999*******************98 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.2e-06
                                    TTTTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEE CS
                           BRCT   4 llfhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivh 71 
                                     +++gc+f +    ++   ++l +   ++G+++t+ ++ +t++l++++    + k +  +k +ipi++
  gene258|gene258|rna258|rna258  89 APLEGCSFTV----SEVSNESLINYHCLLGATFTQNLMVWTDFLITDSK--SNDKTEFCKKYGIPIIT 150
                                    6899999999....77777888888899*********************..99999999******997 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 3.7e-05
                                    TTTTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHHH CS
                           BRCT   4 llfhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldci 79 
                                     +f+ ++f++  +l ++  + l++li ++GG+ ++ v+++++++ ++++          +k   ++ h ++++dci
  gene258|gene258|rna258|rna258 177 SVFNEKVFFLDPSLPQILFNRLRRLIISNGGTRVSVVDRDVDFIMTQSY-------GDFKKYDGKVFHYQYVFDCI 245
                                    6899999999888888888889************************999.......56778888888888888887 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 4.8e-05
                                    HHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHHH CS
                           BRCT  27 elikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldci 79 
                                    ++++ +G+ v ++v+  +thl+v +      ++ e  +   ++v  +w+ +c+
  gene258|gene258|rna258|rna258 287 NKLRALGAIVKEDVDASCTHLIVRDG----RECREGRRMPCKVVLYSWVDQCL 335
                                    68999******************988....68999999999999999999997 PP

  == domain 5  score: 9.2 bits;  conditional E-value: 0.00043
                                    HHHHHHHHHTTCEE.ESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHH CS
                           BRCT  23 deleelikehGGkv.ttevskktthlvvgepesrslkylealklnipivheewll 76 
                                    +++ e+ +++  ++  t+  +k+thl++g+   +s+k+l  l ++ +i++++++ 
  gene258|gene258|rna258|rna258 388 KKAIEKFENLSIRYsDTDRYEKCTHLIMGTI-CTSEKFLSCLCNGGWILRPDFID 441
                                    44444555555555788999***********.577******************96 PP

  == domain 6  score: 8.4 bits;  conditional E-value: 0.00078
                                    SSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSS.H CS
                           BRCT  18 dnftrdeleelikehGGkvttevskktthlvvgep.e 53 
                                    ++ +r+++ ++i++ GG+v te ++ t ++v +++ e
  gene258|gene258|rna258|rna258 498 EGQKRESYVRVIENGGGRV-TEGNEYTHCFVSKTYkE 533
                                    7889**************9.88888899999888831 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.71   2.5e+03      54      76 ..      58      83 ..      34      90 .. 0.71
   2 !   36.9   0.0     1e-12   3.7e-09       3      80 ..     177     252 ..     175     257 .. 0.85
   3 ?    4.1   0.0     0.017        60      32      84 ..     293     346 ..     282     347 .. 0.73
   4 ?   -3.1   0.0         3   1.1e+04      50      70 ..     417     441 ..     395     442 .. 0.65
   5 !    9.3   0.0   0.00041       1.5      18      53 ..     499     534 ..     491     551 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.71
                         BRCT_2 54 e...laekrkrrvvspkyIkdCikkg 76
                                   e   +a k + +++++k+++d  ++ 
  gene258|gene258|rna258|rna258 58 EkyiQALKWNIKILHVKWLYDTEENT 83
                                   3556777788999999**99976665 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 1e-12
                         BRCT_2   3 klFeglrFYindaepspsreklkklIeknGGevvetitsavyiviaesneeelaekrkrrvvspkyIkdCikkgkllp 80 
                                     +F++  F++  + p+   ++l++lI++nGG+ v++ +++v +++++s    + +k + +v++++y++dCi++g +l 
  gene258|gene258|rna258|rna258 177 SVFNEKVFFLDPSLPQILFNRLRRLIISNGGTRVSVVDRDVDFIMTQSYG--DFKKYDGKVFHYQYVFDCIEAGAVLL 252
                                    68********87888899*******************9997776666653..46999*****************9874 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.017
                         BRCT_2  32 GGevvetitsavyiviaesneee.laekrkrrvvspkyIkdCikkgkllpleny 84 
                                    G  v+e+ + + +++i+    e  + ++   +vv +++++ C++  + ++ ++y
  gene258|gene258|rna258|rna258 293 GAIVKEDVDASCTHLIVRDGRECrEGRRMPCKVVLYSWVDQCLHLLRRVNEDKY 346
                                    55665666555666666665544566666778999*********9999999999 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 3
                         BRCT_2  50 sneee....laekrkrrvvspkyIk 70 
                                    + +++    +   ++ ++++p++I+
  gene258|gene258|rna258|rna258 417 TICTSekflSCLCNGGWILRPDFID 441
                                    4444444455556677888888886 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.00041
                         BRCT_2  18 spsreklkklIeknGGevvetitsavyiviaesnee 53 
                                    +++re + ++Ie+ GG+v+e  + ++ +v  +++ee
  gene258|gene258|rna258|rna258 499 GQKRESYVRVIENGGGRVTEGNEYTHCFVSKTYKEE 534
                                    4799**************998864444444333332 PP

>> RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   2.2e-06    0.0079      16      86 ..      11      79 ..       3      91 .. 0.77
   2 ?   -2.6   0.0       1.5   5.3e+03      21      48 ..     123     150 ..     118     155 .. 0.69
   3 ?   -2.4   0.0       1.2   4.3e+03      76      94 ..     234     252 ..     219     258 .. 0.75
   4 ?    3.1   0.0     0.024        85      32      58 ..     282     309 ..     259     313 .. 0.77
   5 ?    0.8   0.0      0.12   4.3e+02      76      99 ..     324     347 ..     319     348 .. 0.82
   6 !   29.9   0.0   1.1e-10   3.9e-07       8      86 ..     365     443 ..     358     456 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-06
                                   --EEEEESSS.TT..SSHHHHHHHHHTTEEE-SGCCT-SEEE-SS---SHHHHHHCCCTTEEE-CHHHHHH CS
                  RTT107_BRCT_5 16 vkiravlTgceeevnkedsdkkkLrklGikivqeakkcntliApkilRTeKFLksLskapkilspdfiedv 86
                                    +i +++Tg++++  +++  k++L k  +       ++++li+ k + TeK++++L  + kil+++++ d 
  gene258|gene258|rna258|rna258 11 PNIFVCTTGISRD--EQELIKSQLPKHAVLEDILSITTDYLISYKAMMTEKYIQALKWNIKILHVKWLYDT 79
                                   5677888888888..667777777776543333444589*****************************986 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                    EESSS.TT..SSHHHHHHHHHTTEEE-S CS
                  RTT107_BRCT_5  21 vlTgceeevnkedsdkkkLrklGikivq 48 
                                    v T +  +++k++++++  +k Gi i++
  gene258|gene258|rna258|rna258 123 VWTDFLITDSKSNDKTEFCKKYGIPIIT 150
                                    5566665655777777778888888876 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                    EEE-CHHHHHHHHHTS--- CS
                  RTT107_BRCT_5  76 kilspdfiedvLkkkklld 94 
                                    k+ + +++ d+++ + +l 
  gene258|gene258|rna258|rna258 234 KVFHYQYVFDCIEAGAVLL 252
                                    788999*****99876655 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.024
                                    SHHHHHHHHHTTEEE-SGCCT.-SEEE- CS
                  RTT107_BRCT_5  32 edsdkkkLrklGikivqeakk.cntliA 58 
                                    + +  +kLr lG  + ++ +  c++li 
  gene258|gene258|rna258|rna258 282 KVEMFNKLRALGAIVKEDVDAsCTHLIV 309
                                    4556789**********99888****95 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.12
                                    EEE-CHHHHHHHHHTS---SGGGB CS
                  RTT107_BRCT_5  76 kilspdfiedvLkkkklldleeyl 99 
                                    k++  ++++++L+  + +++++y 
  gene258|gene258|rna258|rna258 324 KVVLYSWVDQCLHLLRRVNEDKYS 347
                                    79999********77778999987 PP

  == domain 6  score: 29.9 bits;  conditional E-value: 1.1e-10
                                    HTSSSXXX--EEEEESSS.TT..SSHHHHHHHHHTTEEE-S..GCCT-SEEE-SS---SHHHHHHCCCTTEEE-CHHHHH CS
                  RTT107_BRCT_5   8 kkkkskpevkiravlTgceeevnkedsdkkkLrklGikivq..eakkcntliApkilRTeKFLksLskapkilspdfied 85 
                                    +kk++k +  +   +Tg +    ++++ ++k ++l i+  +  +++kc++li   i   eKFL++L  +  il pdfi++
  gene258|gene258|rna258|rna258 365 SKKTKKASKPMMFQFTGLSPL--LKKKAIEKFENLSIRYSDtdRYEKCTHLIMGTICTSEKFLSCLCNGGWILRPDFIDK 442
                                    677778888888999***999..9999************99878899*******************************97 PP

                                    H CS
                  RTT107_BRCT_5  86 v 86 
                                     
  gene258|gene258|rna258|rna258 443 F 443
                                    5 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   7.4e-07    0.0026       3      63 .]      15      75 ..      13      75 .. 0.95
   2 !   13.8   0.0   1.2e-05     0.043      13      60 ..     103     150 ..      94     152 .. 0.88
   3 ?   -3.0   0.0       2.1   7.4e+03      15      34 ..     197     216 ..     196     225 .. 0.76
   4 !   18.2   0.0   5.1e-07    0.0018       8      62 ..     277     329 ..     270     330 .. 0.74
   5 ?    2.1   0.0     0.054   1.9e+02      32      40 ..     407     415 ..     399     424 .. 0.76
   6 ?   -2.7   0.0       1.6   5.8e+03       9      29 ..     498     518 ..     496     524 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.4e-07
                                   EEEECB-TTCHHHHHHHHHHTT-EEESSEETT-SEEEE.CSS-CHHHHHHHHCT-EEE-CHH CS
                      PTCB-BRCT  3 icvtgysgddrkslqklieamGaeyskdltksvTHLic.ksgeGekyekAkkwgipvVsveW 63
                                   +c+tg+s d+ + ++ ++ ++ a   + l+ ++ +Li+ k +  eky  A kw+i++  v+W
  gene258|gene258|rna258|rna258 15 VCTTGISRDEQELIKSQLPKH-AVLEDILSITTDYLISyKAMMTEKYIQALKWNIKILHVKW 75
                                   8*******************9.999999**********788899****************** PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHTT-EEESSEETT-SEEEECSS-CHHHHHHHHCT-EEE- CS
                      PTCB-BRCT  13 rkslqklieamGaeyskdltksvTHLicksgeGekyekAkkwgipvVs 60 
                                     +sl +    +Ga+++++l+  + +Li  s + +k e+ kk gip+++
  gene258|gene258|rna258|rna258 103 NESLINYHCLLGATFTQNLMVWTDFLITDSKSNDKTEFCKKYGIPIIT 150
                                    66777888889***********************************98 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.1
                                    HHHHHHHHTT-EEESSEETT CS
                      PTCB-BRCT  15 slqklieamGaeyskdltks 34 
                                    +l++li ++G++ +  + ++
  gene258|gene258|rna258|rna258 197 RLRRLIISNGGTRVSVVDRD 216
                                    68899999999876666555 PP

  == domain 4  score: 18.2 bits;  conditional E-value: 5.1e-07
                                    B-TTCHHHHHHHHHHTT-EEESSEETT-SEEEECSS-CHHHHHHHHCT-EEE-CH CS
                      PTCB-BRCT   8 ysgddrkslqklieamGaeyskdltksvTHLicksgeGekyekAkkwgipvVsve 62 
                                      ++ + ++ + + a+Ga +++d+  s+THLi+++g  + ++  +++ ++vV   
  gene258|gene258|rna258|rna258 277 SLKECKVEMFNKLRALGAIVKEDVDASCTHLIVRDG--RECREGRRMPCKVVLYS 329
                                    4445577888999********************985..56666666666666555 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.054
                                    ETT-SEEEE CS
                      PTCB-BRCT  32 tksvTHLic 40 
                                     +++THLi 
  gene258|gene258|rna258|rna258 407 YEKCTHLIM 415
                                    689*****8 PP

  == domain 6  score: -2.7 bits;  conditional E-value: 1.6
                                    -TTCHHHHHHHHHHTT-EEES CS
                      PTCB-BRCT   9 sgddrkslqklieamGaeysk 29 
                                    +g++r+s  + ie  G+ +++
  gene258|gene258|rna258|rna258 498 EGQKRESYVRVIENGGGRVTE 518
                                    577799999999999999886 PP

>> LIG3_BRCT  DNA ligase 3 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.052   1.9e+02       5      49 ..     178     223 ..     177     249 .. 0.65
   2 !   12.5   0.0   3.9e-05      0.14      32      77 ..     293     336 ..     267     340 .. 0.81
   3 ?   -1.6   0.0      0.97   3.5e+03      40      57 ..     519     536 ..     505     545 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.052
                      LIG3_BRCT   5 iFtgvklfipksved..ykklrRYfiAydGdlvkeekekeaTHvvvs 49 
                                    +F + + f+ +s+++  +++lrR +i ++G+ v+     ++  ++++
  gene258|gene258|rna258|rna258 178 VFNEKVFFLDPSLPQilFNRLRRLIISNGGTRVS-VVDRDVDFIMTQ 223
                                    67888889999997733579**********9887.334445555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.9e-05
                      LIG3_BRCT  32 GdlvkeekekeaTHvvvskkeeskkekeksknakaVtaewiwesIk 77 
                                    G +vke+  +++TH +v++    + +       k+V  +w++++ +
  gene258|gene258|rna258|rna258 293 GAIVKEDVDASCTHLIVRDG--RECREGRRMPCKVVLYSWVDQCLH 336
                                    55****************66..66777788899***********86 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.97
                      LIG3_BRCT  40 ekeaTHvvvskkeeskke 57 
                                     +e TH  vsk  +++  
  gene258|gene258|rna258|rna258 519 GNEYTHCFVSKTYKEEVD 536
                                    567788888855433322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4029.78
//
Query:       gene259|gene259|rna259|rna259  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-06   29.1   9.1    1.4e-06   28.8   9.1    1.0  1  V-ATPase_G  Vacuolar (H+)-ATPase G subunit
  ------ inclusion threshold ------
      0.054   13.4   3.3      0.062   13.1   3.3    1.0  1  PIN_8       PIN like domain
       0.71   10.2   7.5        1.5    9.2   0.4    2.1  2  KxDL        Uncharacterized conserved protein
        7.5    6.5  11.6        4.1    7.4   5.7    1.9  2  Sds3        Sds3-like


Domain annotation for each model (and alignments):
>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   9.1     3e-10   1.4e-06       4     103 ..       4     101 ..       2     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3e-10
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHH CS
                     V-ATPase_G   4 qgIqqLLqAEkeAaeivkeArkrkakrlkqAkeeAekEieeyrakkekefkekeaeklgseeelekkieketeekikelk 83 
                                    ++I+ L q E eA+e ++ Ar++ +++  qA+++A+  ++  ++++e ++   e+e+    + + +k+++e e kikel+
  gene259|gene259|rna259|rna259   4 ESIKRLVQCENEAKERLEIARREFEEMRVQARNDAKLMVDGLKKENESKLLLLEKEVEEYIKIVDEKLKSELEMKIKELR 83 
                                    689****************************************************************************9 PP

                                    HHHHHHHHHHHHHHHHHHTS CS
                     V-ATPase_G  84 esvkknkeavvkellklvld 103
                                    +   +n+++vv  l+k+v  
  gene259|gene259|rna259|rna259  84 NI--RNRKDVVLALVKHVSG 101
                                    86..68899*******9975 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.3   1.4e-05     0.062      50     134 ..      11      95 ..       3     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                          PIN_8  50 sviskekkayedlekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeelkaeleelkksskadkeedp 129
                                    +  ++ k+++e +++e+e+++ +a ++ + +++  +k+++ +   l+ke+++ ++ ++e+lk ele++ k+ ++++++++
  gene259|gene259|rna259|rna259  11 QCENEAKERLEIARREFEEMRVQARNDAKLMVDGLKKENESKLLLLEKEVEEYIKIVDEKLKSELEMKIKELRNIRNRKD 90 
                                    4456778888999999**********999999999*************************************99998866 PP

                          PIN_8 130 ilkkl 134
                                    ++ +l
  gene259|gene259|rna259|rna259  91 VVLAL 95 
                                    66554 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00033       1.5      30      54 ..       7      31 ..       4      40 .. 0.86
   2 ?    4.2   2.9     0.012        54      26      76 ..      36      87 ..      30      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00033
                           KxDL 30 reLlelnalsqerlaklrarfkqgt 54
                                   ++L ++ ++++erl+ +r +f++  
  gene259|gene259|rna259|rna259  7 KRLVQCENEAKERLEIARREFEEMR 31
                                   5799*****************9976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.012
                           KxDL 26 nkknreLlelnalsqerlaklrarfkqgtkllke.vkkdLesifkkirslka 76
                                   n+ + ++  l ++ +++l  l++++++++k + e +k++Le+  k +r+++ 
  gene259|gene259|rna259|rna259 36 NDAKLMVDGLKKENESKLLLLEKEVEEYIKIVDEkLKSELEMKIKELRNIRN 87
                                   6667788999999999999**********998653899***99999999975 PP

>> Sds3  Sds3-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.6    0.0068        30      56      95 ..       8      47 ..       4      54 .. 0.70
   2 ?    7.4   5.7   0.00091       4.1      59     117 ..      33      91 ..      32     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0068
                           Sds3 56 eLkrlrlreeyqlkriekefkadiekakqeheklvkllke 95
                                   +L++ ++  + +l+  ++ef++ + +a ++ + +v+ lk+
  gene259|gene259|rna259|rna259  8 RLVQCENEAKERLEIARREFEEMRVQARNDAKLMVDGLKK 47
                                   6677777777777777777777777777777777776665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00091
                           Sds3  59 rlrlreeyqlkriekefkadiekakqeheklvkllkeklyeelekkikrLkeeklllDl 117
                                    ++r+  +  ++ ++ke + ++   ++e e+ +k + ekl +ele kik+L   ++  D+
  gene259|gene259|rna259|rna259  33 QARNDAKLMVDGLKKENESKLLLLEKEVEEYIKIVDEKLKSELEMKIKELRNIRNRKDV 91 
                                    5677777888899999999*******************************988888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1474  (0.0822132); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 760.54
//
Query:       gene26|gene26|rna26|rna26  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-29  102.5   0.4    2.8e-29  102.2   0.4    1.0  1  EMG1       EMG1/NEP1 methyltransferase
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.015   14.8   0.0    1.1  1  CSS-motif  CSS motif domain associated with EAL


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.4   3.1e-33   2.8e-29      46     194 .]      29     174 ..      25     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3.1e-33
                                HHHHHHHHCSCHHCTT.EEEEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC.SE CS
                       EMG1  46 HqcLlalldspLnkagllqvyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlppgsk 129
                                H+++  l+dspLnk+ +++vy+htt nvlIe++  + +P +  +F+ +m  LL++l +++++g  +L kviknpi++hlpp+s+
  gene26|gene26|rna26|rna26  29 HKAIQLLMDSPLNKSRKIHVYVHTTSNVLIELSHLLEVPESPIEFSDVMSYLLRRLVVKSSDGA-VLAKVIKNPIEKHLPPNST 111
                                889999*********************************************************9.****************999 PP

                                EEEE-TTSEE-..............EEEE-SSSS....---HHEEESSSS---HHHHHHHHHHHCH CS
                       EMG1 130 iillsesaekk.lvdleefvvkpvvfvigamskgsvkidykeeeisisnypLsaavvcskiltafE 194
                                +++ls ++ +    d+e ++++ +vf+i     g+v+ +  e ++++sn +Ls + +c+k+++ fE
  gene26|gene26|rna26|rna26 112 KVVLSSRGCRMsPKDFEPYIERGLVFFINI---GKVEKKEGEVTMKVSNFKLSPVSCCTKLTNMFE 174
                                999999988553445666679999999988...544555566699*****************9998 PP

>> CSS-motif  CSS motif domain associated with EAL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.7e-06     0.015      88     178 ..      25     111 ..       9     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-06
                  CSS-motif  88 tsrdgvrlwllrgtplvpdrpalvlrrgnyavvispgvfidgqyl.pelllavsssdgeqlalvvgpaallldgrvlslaelia 170
                                 +r+  ++ ll+++pl++ r+  v+ ++ ++v+i ++++++++    e+++++s+  + +l+++++++a l+    ++++++i+
  gene26|gene26|rna26|rna26  25 FNRSHKAIQLLMDSPLNKSRKIHVYVHTTSNVLIELSHLLEVPESpIEFSDVMSYLLR-RLVVKSSDGAVLA----KVIKNPIE 103
                                567788899*********************************9999999888888877.7788888888765....45566666 PP

                  CSS-motif 171 searssga 178
                                 + +++++
  gene26|gene26|rna26|rna26 104 KHLPPNST 111
                                66665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1262.17
//
Query:       gene260|gene260|rna260|rna260  [L=420]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-53  180.3   0.2    5.4e-53  179.9   0.2    1.1  1  ThiF             ThiF family
     0.0071   16.3   0.4          3    7.7   0.1    2.2  3  UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
     0.0094   16.4   0.2       0.05   14.0   0.1    2.3  2  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.016   15.5   0.1      0.035   14.4   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.02   15.1   0.1      0.055   13.7   0.0    1.7  1  TrkA_N           TrkA-N domain
       0.19   11.3   0.0        0.3   10.7   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.9   0.2   1.8e-56   5.4e-53      19     219 ..       4     312 ..       2     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 179.9 bits;  conditional E-value: 1.8e-56
                                    SEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-CC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  19 skvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavterit 98 
                                     +vl++G+Gg+G+ellk+La+  ++++tl+D D+i+lsNlnRqflf+++diGk+Ka vaa+  +++n ++ v +++++it
  gene260|gene260|rna260|rna260   4 GRVLVIGCGGIGCELLKLLAKQNLRSITLIDCDTIDLSNLNRQFLFNRDDIGKNKAVVAARTFKKLNKKCRVLPICADIT 83 
                                    79*****************************************************************************9 PP

                                    G.CCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EECCCCEE CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  99 d.etvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeCldpsstedptekkvp 177
                                    + ++    ++ ++ +V  +lDn ear +vn++c  + +pl+++g+ gf+gq++ ++ ++++c++C +      +  k++ 
  gene260|gene260|rna260|rna260  84 EfDA---MFFARYKVVYSCLDNAEARSYVNQRCLISNTPLVDGGCGGFKGQAYYFD-YNSECFDCIP-----RKFSKEYL 154
                                    9664...8***********************************************6.8********6.....45567788 PP

                                    HHH............................................................................. CS
                                    xxx............................................................................. RF
                           ThiF 178 lct............................................................................. 180
                                    +ct                                                                             
  gene260|gene260|rna260|rna260 155 MCTirsrptrfehciiwakyvllemrlkvdensqdfyqrflkdviencedmstadklekfrnsedykertkkiveilgkl 234
                                    888889999999999***************************************************************** PP

                                    ......................................HHHCT.E-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEE CS
                                    ......................................xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 181 ......................................siagn.ipaiatttavvaglaalellkllsgkeklensll 219
                                                                           +agn ip+++t++++va+l++l +   ++  +  ++++ 
  gene260|gene260|rna260|rna260 235 dsilfnkdnrdileyiynaayirgrcagiepisfdeavTVAGNiIPSLSTINSIVASLMMLSVRNKCNYYSVDNGNVI 312
                                    ************************************************************998877766665555555 PP

>> UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.3    0.0012       3.7       1      58 [.     162     220 ..     162     233 .. 0.68
   2 !    7.7   0.1   0.00099         3     195     247 ..     212     267 ..     178     271 .. 0.63
   3 !    6.0   0.0    0.0032       9.6     116     145 ..     237     266 ..     235     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                UBA_e1_thiolCys   1 PneieHtieWArdkFeglFekkpeevnkfl.kdkekfleelekekeeekletlekvlkl 58 
                                    P++ eH+i WA+    ++  k  e+ ++f     ++++e+ e++++++kle +++ +++
  gene260|gene260|rna260|rna260 162 PTRFEHCIIWAKYVLLEMRLKVDENSQDFYqRFLKDVIENCEDMSTADKLEKFRNSEDY 220
                                    8999********87776666666666666633345688888888888776655555544 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00099
                UBA_e1_thiolCys 195 aeeleklakkessla.....lklkpieFeKDddtnfhidfitaasNlRArnYkIkead 247
                                    ++  ++ + ke++++      kl +i F+KD+ +   +++i+ a+ +R r+ +I++++
  gene260|gene260|rna260|rna260 212 EKFRNSEDYKERTKKiveilGKLDSILFNKDNRD--ILEYIYNAAYIRGRCAGIEPIS 267
                                    2222222222222224455567899999999988..7899999999999999998875 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0032
                UBA_e1_thiolCys 116 lefdlenelhleFvvaaanLraqvygikge 145
                                    + f+ +n++ le++++aa +r  + gi++ 
  gene260|gene260|rna260|rna260 237 ILFNKDNRDILEYIYNAAYIRGRCAGIEPI 266
                                    679999********************9994 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   1.7e-05      0.05       8      77 ..       4      72 ..       1     121 [. 0.57
   2 ?   -2.6   0.0       2.5   7.6e+03      52      82 ..     224     254 ..     189     258 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                  NAD_binding_7  8 kkvlvvGgGevAarkvrklleag.akvtvvapevkeeleelvklaeeel..ekdlegadlviaatddrelner 77
                                    +vlv+G G ++ + ++ l++++   +t+++ ++     +l +l+++ l  ++d+ + + v+aa + ++ln++
  gene260|gene260|rna260|rna260  4 GRVLVIGCGGIGCELLKLLAKQNlRSITLIDCDTI----DLSNLNRQFLfnRDDIGKNKAVVAARTFKKLNKK 72
                                   58*****************9999678****99942....3344444443444444444444444444444443 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                  NAD_binding_7  52 eeelekdlegadlviaatddrelneriaeaa 82 
                                     +++ + l + d ++   d+r++ e i++aa
  gene260|gene260|rna260|rna260 224 TKKIVEILGKLDSILFNKDNRDILEYIYNAA 254
                                    2223333566677777777777777777665 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.2e-05     0.035       1      43 [.       6      46 ..       6      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCH CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaak 43
                                   vl+iG+G++G  +++lla+++     it++d +   l +l  +
  gene260|gene260|rna260|rna260  6 VLVIGCGGIGCELLKLLAKQNLR--SITLIDCDTIDLSNLNRQ 46
                                   89*****************9865..9****9988877776555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.055       1      38 [.       6      44 ..       6      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                   EEEES-SHHHHHHHHHHHHTT.EEEEEEESSHHHHHHHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLsegg.kdvvvidkdeerveelr 38
                                   +++iG+G +G +l++ L +++ +++++id d   + +l 
  gene260|gene260|rna260|rna260  6 VLVIGCGGIGCELLKLLAKQNlRSITLIDCDTIDLSNLN 44
                                   68*****************66688*****9976666665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0001       0.3       1      48 [.       6      55 ..       6      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                                   EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHCEEEEETTC CS
                           ApbA  1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkknGlrltsegg 48
                                   ++++G+G+iG+ l   Lak + + +tli+ +   l +l+++ l  +++ g
  gene260|gene260|rna260|rna260  6 VLVIGCGGIGCELLKLLAKqNLRSITLIDCDTiDLSNLNRQFLFNRDDIG 55
                                   68*****************66666****9999888888887764444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      641  (0.0357521); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2538.47
//
Query:       gene261|gene261|rna261|rna261  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-18   64.4   0.1    1.5e-17   63.4   0.1    1.5  1  E2F_TDP    E2F/DP family winged-helix DNA-binding domain
      6e-16   58.6   0.0    1.2e-15   57.7   0.0    1.4  1  E2F_CC-MB  E2F transcription factor CC-MB domain


Domain annotation for each model (and alignments):
>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.1   1.6e-21   1.5e-17       2      71 .]      16      79 ..      15      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.6e-21
                        E2F_TDP  2 dksLgvltkkfvellkesakgtlslneaakeLvdkkdekvkkRRiYDilNVLealglieKeskneikWig 71
                                   ++sL +lt++f++l++ s+++++s+++a+ eL+      v kRRiYDi+NVLe+lgl++K s ++ kW+g
  gene261|gene261|rna261|rna261 16 ENSLYNLTRRFLKLISMSPDRNVSIHQASIELN------VGKRRIYDITNVLEGLGLLSKWSVSNAKWVG 79
                                   79**************9****************......*****************************98 PP

>> E2F_CC-MB  E2F transcription factor CC-MB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   1.3e-19   1.2e-15      13      94 ..     109     190 ..     102     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.3e-19
                      E2F_CC-MB  13 qkLDelieklteqlknltedekn.qlaYvtyedirsiasfkeqtviaikAppgtqlevpdpeeekryqiyLkStsgpiev 91 
                                    + LDe +  l+e++  l+++ekn  +aYvty+d++s++s+ +++v+a+kAp++t++e p+ e +  y++ L+S++g i +
  gene261|gene261|rna261|rna261 109 DDLDETLCRLNEEISMLSQSEKNlANAYVTYSDLQSLPSLGGNLVFAVKAPSETTMEYPRYE-KGFYKLKLSSEKGAISI 187
                                    68***************99999967**********************************998.899************** PP

                      E2F_CC-MB  92 ylv 94 
                                    ++v
  gene261|gene261|rna261|rna261 188 FYV 190
                                    998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1350.93
//
Query:       gene262|gene262|rna262|rna262  [L=511]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-22   79.1   0.0    6.4e-22   77.6   0.1    1.9  2  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
    1.4e-20   74.0   0.0    3.1e-20   72.9   0.0    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    4.9e-17   61.9   0.1    1.2e-16   60.6   0.1    1.7  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.057   13.3   0.0       0.11   12.4   0.0    1.3  1  DUF5021         Domain of unknown function (DUF5021)


Domain annotation for each model (and alignments):
>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.8     8e+03      35      53 ..     361     383 ..     346     391 .. 0.78
   2 !   77.6   0.1   1.4e-25   6.4e-22       1      69 []     432     511 .]     432     511 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                                    EEEEEESSB....-SSCCCSB-T CS
                      ProRS-C_1  35 kslcipfdq....epseegtkCi 53 
                                    +++++p+      + +e+ + C+
  gene262|gene262|rna262|rna262 361 EIRGVPLRLevgfKDMEGAEACL 383
                                    68999997445667778888886 PP

  == domain 2  score: 77.6 bits;  conditional E-value: 1.4e-25
                                    HHHHHHHHHTT-EEEEEESSGHHHHHHHHHHH............S-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B CS
                      ProRS-C_1   1 weefkealekkgfvlapWcgeeecEekIkeet............gakslcipfdqepseegtkCivcgkpakkwvlfgrs 68 
                                    +e+f  al++k++++apWcg +ecE  Ik ++            gak+lcip d+ +  +g +C+ cgk+a +++lfgrs
  gene262|gene262|rna262|rna262 432 FEDFISALDNKNIIMAPWCGIDECESTIKSRStklgpngsvistGAKTLCIPYDS-KPCSGLECVSCGKQAIHYTLFGRS 510
                                    699***************************************************7.67899******************* PP

                                    - CS
                      ProRS-C_1  69 Y 69 
                                    Y
  gene262|gene262|rna262|rna262 511 Y 511
                                    * PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   6.8e-24   3.1e-20       9     176 ..     116     286 ..     109     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 6.8e-24
                                    EEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                   tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdlika 86 
                                    +  +++Pt+e+ ++  ++++ +rs ++LPlk+ q +++ R E   + + +R++eF +++g+   + ++++d+++  ++ +
  gene262|gene262|rna262|rna262 116 DPVAIRPTSETIIYPSFSKW-IRShRDLPLKINQWCSVLRWELHGTLPFIRGKEFLWQEGHTAFLtKEESDEEVLAILDL 194
                                    56789*************99.***555****************9788**************86665999*********** PP

                                    HHHHHHHTT.SCEEEEEE..GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  87 isriferlglefraiiel..msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimica 164
                                    +sri+e+l+  + +i++    s+k   +++++ +ea  + +++g++ +t ++lg+++s+ ++++v   +++e+s ++ + 
  gene262|gene262|rna262|rna262 195 YSRIYEELL-AVPVIKGRktESEKFGGADYTTSIEAFIPGSGRGVQAATSHFLGQNFSRMFDIKVDTDEGSENSSFVYQN 273
                                    *******97.44566666523333345778999********************************999999999999999 PP

                                    EEE.HHHHHHHHH CS
                                    xxx.xxxxxxxxx RF
                   tRNA-synt_2b 165 aig.veRllsail 176
                                    + g ++R +++++
  gene262|gene262|rna262|rna262 274 SWGiTTRSIGIAV 286
                                    9998899998876 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.1   2.7e-20   1.2e-16       1      91 [.     305     403 ..     305     406 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2.7e-20
                                    SEEEEESSSS.......HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEE CS
                 HGTP_anticodon   1 qvvviplnek.......aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvr 72 
                                    qvv+ip++ +       ae+l+ y  k++++L+  girv +dd +n ++g+k+++++  g+p++++vG+k++e  +  + 
  gene262|gene262|rna262|rna262 305 QVVIIPCGITsssskddAERLKMYIGKIQAQLKSSGIRVYVDDrNNVTVGFKFNHWEIRGVPLRLEVGFKDMEGAEACLV 384
                                    8****************999****************************************************9999**** PP

                                    ETTTCEEEEEETTHHHHHH CS
                 HGTP_anticodon  73 drdtreqervsldelvekl 91 
                                    +rdtr+++++s++ + + +
  gene262|gene262|rna262|rna262 385 RRDTRAKRQISVEGIDQTV 403
                                    ***********99776665 PP

>> DUF5021  Domain of unknown function (DUF5021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05      0.11      78     119 ..     314     355 ..     303     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                        DUF5021  78 skasskrdteLLsiyLasvfpelksayieanvekgkvvsvay 119
                                    + +ssk+d e L +y+ ++  +lks+ i+++v   + v+v +
  gene262|gene262|rna262|rna262 314 TSSSSKDDAERLKMYIGKIQAQLKSSGIRVYVDDRNNVTVGF 355
                                    7899****************************9998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3571.98
//
Query:       gene263|gene263|rna263|rna263  [L=646]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   5.2e-138  461.1   0.3   6.3e-138  460.8   0.3    1.1  1  Trehalase  Trehalase


Domain annotation for each model (and alignments):
>> Trehalase  Trehalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.8   0.3  3.5e-142  6.3e-138      72     512 .]     156     603 ..      61     603 .. 0.86

  Alignments for each domain:
  == domain 1  score: 460.8 bits;  conditional E-value: 3.5e-142
                                    HHHHHCTGGHH.EECCHHCCTTC.CCCHTTTS-SCE-TTECEEE-TT-EE-SBTTB-S-BCCHHHHHHHHHHHTT-HHHH CS
                      Trehalase  72 flkkaedeelrleaeelnklwka.lvrkikkkvgllpeassllplpkpfvVPGgRFrElYyWDsYfvilGLleskkvdla 150
                                    + +  + e+l ++a +ln++wk+ +v+   +++ ++ ++++++++++pf++PG+RF+E YyWDsY+vi+GL+ +++ ++a
  gene263|gene263|rna263|rna263 156 YNQ--KLENLLRVARQLNSEWKNiYVK---QRDLDEGNHTTMIKVENPFIIPGDRFKEAYYWDSYWVIEGLVRNGMQKVA 230
                                    333..56777789**********6666...9************************************************* PP

                                    HHHHHHHHHHHHHHSS--SBSBGGGTT---S--HHHHHHHHHHHC...HCCHHHHHHHHHHHHHHHCCTTTCCETTCCC- CS
                      Trehalase 151 kgmvenfiyliekYGkilNgnRsYYlsRSQPPlltdmvlrvyekt...eddallravlaalkkeyefwmaeqrldevtkl 227
                                    kgmvenfi+lie+ G+i+Ng R YYl+RSQPP++ +m+ ++y+++   e++ ++++ l+a   e+ef+m  +++++v+k+
  gene263|gene263|rna263|rna263 231 KGMVENFISLIENIGFIPNGLRKYYLNRSQPPYFPQMLFTLYRHLpweEIEDVIKRGLNAAVVEHEFFM-REKSENVVKD 309
                                    ***********************************************9*********************.8999999999 PP

                                    CTC-EEE--SSSTTS-TCCCHHHHHHHHHCTT.....HCCHHHHHCCCCHHHHHCCHHCHHHHCCCCTT-S.TCCCCTGG CS
                      Trehalase 228 skryllnrygvpeetprpesyledketaeklk.....kerkkeevyrelkaaaesgwdlssRwlresghdtgellelrta 302
                                     k++ ln+y+v + tpr+esy+ed+ t e++k     ++r++ee+y+elka+aesgwd+s+Rwl      +g+l+++rt+
  gene263|gene263|rna263|rna263 310 GKTHILNVYKVRDTTPRAESYSEDRMTTEENKareekYRRRSEEIYSELKAGAESGWDFSTRWLGL----HGQLDSIRTS 385
                                    99***************************999999988999*************************....5789****** PP

                                    GEE-HHHHHHHHHHHHHHHHCCCHCC-..CCHHHHHHHHHHHHHHHHHHHCEETTTTEE--EETTTT.EE----BGGGGH CS
                      Trehalase 303 klvpvDLNallyklekdiaefedklgd..setseefeekaekrkkaidkvLWneeagvylDYdlkkk.kqtnyesatnlv 379
                                      +p DLNa++y++e +i+++++ ++   s++s++f++k+e+r +ai++vLW + +gv++DYd+ +k ++++ ++a+n++
  gene263|gene263|rna263|rna263 386 RRIPADLNAMMYANECIISKLYEIVEGkdSRNSQDFKRKSEERIDAINSVLWCDREGVWNDYDIDTKeHTSSGFYASNIM 465
                                    *******************998887655699*********************************988466788******* PP

                                    HHHCT-S-HHHHHHHHHHCHHHHCCCCCEESCCCC-SBSSS...-SSTTSTTEEEHHHHHHHHHHHHHTT-HHHHHHHHH CS
                      Trehalase 380 pLwaglaskeqaaklvakvlekleesgllvaegglgtsllk...sgrQWDyPngWaPlqilaveglerygeeelaerlae 456
                                    p+++g+  +e ++ +v + l+ + e      +gg++ s+ k   s+ QWDyPn+W+Pl++ +  +ler+ge+e+a ++a+
  gene263|gene263|rna263|rna263 466 PMCYGIKPPEGKDVTVYNILNMFVEDMFGH-PGGMPVSGAKnknSTLQWDYPNVWPPLVHAVALFLERIGEREMALHMAK 544
                                    ***********7777777777776666666.*******998788999********************************* PP

                                    HHHHHHHHHHH..HC..TSEBSCEETTSTSTTBTT-SSSSTTCSBHHHHHHHHHHHCCH. CS
                      Trehalase 457 rwlktvtkafs..de..gklvEKYdvtreaeygGgggeyvlqeGFGWvNgvvlelLellg 512
                                    ++l++++ ++s  de  + ++EKY +++++  g ++gey +q+GFGW+Ngv++++L+ +g
  gene263|gene263|rna263|rna263 545 SFLENISISTSvvDEekRGIFEKYSCENAGCPG-YKGEYMAQKGFGWTNGVAIHFLDIFG 603
                                    ****987655322335799********777777.**********************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4129.95
//
Query:       gene264|gene264|rna264|rna264  [L=411]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-43  147.7   0.0    7.3e-43  146.6   0.0    1.5  2  Peptidase_M48    Peptidase family M48
    1.6e-37  129.2   8.6    1.6e-37  129.2   8.6    1.8  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra
    6.6e-05   22.2   2.6    9.9e-05   21.7   2.6    1.2  1  Peptidase_M56    BlaR1 peptidase M56
  ------ inclusion threshold ------
       0.04   13.8   0.1      0.072   12.9   0.1    1.4  1  SprT-like        SprT-like family


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.96   4.3e+03     131     164 ..      44      77 ..       7      88 .. 0.66
   2 !  146.6   0.0   1.6e-46   7.3e-43       3     194 ..     203     405 ..     201     407 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.96
                                    HHHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 131 alSRkrEyqADeagvellkrakdlvraliklakd 164
                                     + +++Ey+ D++++++ + +  l+r l+ ++++
  gene264|gene264|rna264|rna264  44 QIKKTKEYNRDKLSMSIFELTLLLARDLYLINQG 77 
                                    5667888888888888777666666666666655 PP

  == domain 2  score: 146.6 bits;  conditional E-value: 1.6e-46
                                    -SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT....-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48   3 reaelkevveelakeaglpkpltkvyvvnspkr....NAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhr 78 
                                    +e +lk+++eelak++g+    +k++v++++kr    NA+++g++k+kr+v++d+Ll +  +eee++a+l HE GH+k +
  gene264|gene264|rna264|rna264 203 EESDLKTKIEELAKKVGF--CAKKILVMDASKRsghsNAYFIGITKEKRVVIYDTLL-KQTDEEEVLAILCHEFGHWKYN 279
                                    7899**************..*************************************.99******************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT............HHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxx RF
                  Peptidase_M48  79 hsvvslivsllasillllglallisraeedaagafldalavliglliillfl............alSRkrEyqADeagve 146
                                    h+++++++ ll ++++l++l + +++++ ++   + + l+ l+  + +l+ +            ++SR++E qAD+++v+
  gene264|gene264|rna264|rna264 280 HVMKMASIVLLIQLFYLYVLNISLNSKSFERLVLA-GDLPLLVRCIYFLMIIgalsvpidtlrnFISRYFEGQADRFAVS 358
                                    **************999999988888877766555.5677776666666666888************************* PP

                                    TTT.HHHHHHHHHHHHHHTT--S---HHHHHHS-SS--HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 147 llkrakdlvraliklakdlerqdvsaslrsellstHPplleRiqalke 194
                                    l++  k+l + likl+++++++ + + l+s++++tHP l eR++ +++
  gene264|gene264|rna264|rna264 359 LGY-GKKLSSGLIKLFEKNSSNMEPDPLYSAVVHTHPTLIERMKLIEN 405
                                    ***.***************************************98876 PP

>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.2   8.6   3.6e-41   1.6e-37       4     182 .]      24     198 ..      21     198 .. 0.92
   2 ?   -2.0   0.3      0.62   2.8e+03      63      64 ..     300     301 ..     271     344 .. 0.40

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 3.6e-41
                Peptidase_M48_N   4 klketkkvP.eeladaitkekfdksraYgldksrfglvsslyslilllallllgllpflwklsgkllgldaeseilqslv 82 
                                     l++ +k+P  +  ++ t ++ +k+++Y++dk+++++++ ++ l+ +l l+  g l+++++           ++++  ++
  gene264|gene264|rna264|rna264  24 ELRQLSKPPsRTYLKLATPDQIKKTKEYNRDKLSMSIFELTLLLARDLYLINQGTLEKVYSSKY------FMNNWYGDAL 97 
                                    566677755245568899**************************************99876443......3699****** PP

                Peptidase_M48_N  83 fllllslistlislPfslYstFviEekhGfnkqtlklfikdklkslllalviglpllaallwiie.wggeyfylylwlfl 161
                                    fl+ ++ ++ l +lP+++ stF+iE+khGfnk+tl++f++d+lk+ l+ +vi +p+ ++  +ii+ +  ++fylylw+f+
  gene264|gene264|rna264|rna264  98 FLMGYAHFQRLCDLPLEVISTFYIEAKHGFNKTTLSTFLMDFLKMSLVITVIFGPFSYVATKIIRiYHKTSFYLYLWVFM 177
                                    *****************************************************************555899********* PP

                Peptidase_M48_N 162 lvfslllmtiyPtlIaPLFnK 182
                                    ++f+++l+++yP++I+PLFnK
  gene264|gene264|rna264|rna264 178 AIFQIVLVVVYPIVIQPLFNK 198
                                    ********************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.62
                Peptidase_M48_N  63 kl 64 
                                    ++
  gene264|gene264|rna264|rna264 300 NI 301
                                    22 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.6   2.2e-08   9.9e-05      91     214 ..     158     283 ..     112     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-08
                  Peptidase_M56  91 tdvkkvewktilkillliWivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemq.lkrnikir...lss 166
                                    t++  +  kt   + l++W+++a+   + l+ ++ ++ + ++ k ++++++ lk +++e  ++++   ++i ++   + s
  gene264|gene264|rna264|rna264 158 TKIIRIYHKT--SFYLYLWVFMAIF-QIVLVVVYPIVIQPLFNKFEEMEESDLKTKIEELAKKVGfCAKKILVMdasKRS 234
                                    5555444444..47899**998876.888899999999899************************867777665222445 PP

                  Peptidase_M56 167 sidsPavlgllk.prIvlPadflkklsdeeleyillHElaHlkrkDllv 214
                                      ++  ++g+ k  r+v+ + +lk+ ++ee   il HE  H k + ++ 
  gene264|gene264|rna264|rna264 235 GHSNAYFIGITKeKRVVIYDTLLKQTDEEEVLAILCHEFGHWKYNHVMK 283
                                    678999***998469**************************99764443 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.6e-05     0.072      40      75 ..     225     276 ..     193     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                      SprT-like  40 r................atvrhhasIeLseklldsrsedrllntLaHElcHl 75 
                                                         +++++ +  +ll++ +e+++l +L+HE+ H 
  gene264|gene264|rna264|rna264 225 IlvmdaskrsghsnayfIGITKEKRVVIYDTLLKQTDEEEVLAILCHEFGHW 276
                                    44555555555555555667889999*************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2776.11
//
Query:       gene265|gene265|rna265|rna265  [L=486]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-19   68.6   1.9    4.4e-18   66.0   0.1    2.3  2  ERCC4     ERCC4 domain
    3.2e-05   24.2   0.0    0.00014   22.2   0.0    2.1  2  HHH_8     Helix-hairpin-helix domain
    0.00045   20.8   0.1       0.52   11.0   0.0    2.8  2  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.048   13.8   0.3        1.2    9.3   0.1    2.9  2  HHH_2     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3     0.063   2.8e+02      62     110 ..      13      66 ..      10      93 .. 0.69
   2 !   66.0   0.1   9.8e-22   4.4e-18       1     151 [.     231     356 ..     231     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.063
                                    EEHHHHHHHHCC.....SHHHHHHHHHHH.H-SEEEEEEES-GGGTT....... CS
                          ERCC4  62 ksaddlvasikd.....grleeqvsrlkrngykkpillvegldqykrknknsrn 110
                                    ksa+d+ + +++     +r+  ++   + n ++ p++ ++gl++ k   ++ + 
  gene265|gene265|rna265|rna265  13 KSAVDFLSHLSSsrnmkSRYSYKKIAQELNRIEEPLYSLDGLKSIKGAGSKTIK 66 
                                    8999998888553335356666444443378999*******9999886554433 PP

  == domain 2  score: 66.0 bits;  conditional E-value: 9.8e-22
                                    EEGGGCTSH.....HHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSH CS
                          ERCC4   1 iDsrelksg.....ieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgr 75 
                                    iD+re+ks+      +ey +e++++++ ++ l++gd+ lw   ++ e+  +          +++erk+ +d+v+si+dgr
  gene265|gene265|rna265|rna265 231 IDAREIKSRkfrlfFQEY-FESKKIRHDTRILEVGDF-LW---IRGEKVCG----------FIIERKKGSDFVSSIMDGR 295
                                    899**9955455555555.******************.99...55555555..........******************* PP

                                    HHHHHHHHHH.H-SEEEEEEES-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHH CS
                          ERCC4  76 leeqvsrlkrngykkpillvegldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetae 151
                                    + eq++rlk++g+kk++++vegl++ + +               + +  ++s L+++ l  g+ ++ t++  +t  
  gene265|gene265|rna265|rna265 296 FKEQKNRLKSTGIKKIFYIVEGLKSTHMQS--------------VGKGLVMSCLATTKLE-GFIVIETKDITQTGS 356
                                    **********************99998875..............6666666666666666.666666666666655 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   3.1e-08   0.00014      26      67 ..      32      72 ..      16      73 .. 0.93
   2 ?   -2.2   0.0       1.2   5.4e+03      49      66 ..     426     443 ..     419     445 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.1e-08
                                   HHHHHHHCCCCC-SS-HHHHTTHCTTSTT--HHHHHHHHHHH CS
                          HHH_8 26 raYrrAaraiealpeeitsleeeltklpgiGkkiaakieeil 67
                                    +Y++ a+ + + +e++ sl++ l++++g G k+ ++i+e++
  gene265|gene265|rna265|rna265 32 YSYKKIAQELNRIEEPLYSLDG-LKSIKGAGSKTIKRIQEFV 72
                                   48*******************9.******************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                    CTTSTT--HHHHHHHHHH CS
                          HHH_8  49 ltklpgiGkkiaakieei 66 
                                    l +++g+G k a  ++e+
  gene265|gene265|rna265|rna265 426 LLSIKGMGHKKAWALAEF 443
                                    7899****9888777776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0023        10      34      53 ..      51      70 ..      25      82 .. 0.78
   2 !   11.0   0.0   0.00012      0.52       3      53 ..     425     482 ..     423     485 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0023
                                   HHHHHTSTTS-HHHHHHHHH CS
                          HHH_5 34 veeLakipGiGkktAeriil 53
                                    + L +i+G G kt +ri +
  gene265|gene265|rna265|rna265 51 LDGLKSIKGAGSKTIKRIQE 70
                                   456999************87 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS....-HHHHHTS..TT..S-HHHHHHHHH CS
                          HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaa....dveeLaki..pG..iGkktAeriil 53 
                                    +Lls++G+G k A al++  ++++ +l+ +     + +L +    G  i+ k A+ ii+
  gene265|gene265|rna265|rna265 425 SLLSIKGMGHKKAWALAEF-YKTIGELIGKvknnGPGKLYEFevEGkkISRKNADDIIE 482
                                    69*****************.****99987633325788998444555599999999997 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.094   4.2e+02      33      59 ..      50      76 ..      35      80 .. 0.82
   2 ?    9.3   0.1   0.00027       1.2       3      30 ..     424     451 ..     421     486 .] 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.094
                          HHH_2 33 sleeLlevddiGeeiAqsivefFenek 59
                                   sl+ L ++++ G ++ + i+ef +++ 
  gene265|gene265|rna265|rna265 50 SLDGLKSIKGAGSKTIKRIQEFVDKKV 76
                                   6788999*************9988765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00027
                          HHH_2   3 lfaLGIrhVGektAklLakrFksldaLk 30 
                                    ++ L+I+  G k A +La+ +k++ +L 
  gene265|gene265|rna265|rna265 424 ISLLSIKGMGHKKAWALAEFYKTIGELI 451
                                    4559********************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.48
# Mc/sec: 3029.44
//
Query:       gene266|gene266|rna266|rna266  [L=408]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-35  119.3  12.5    1.6e-06   28.7   0.3    7.3  7  WD40         WD domain, G-beta repeat
    1.4e-17   63.8   2.0      0.049   13.9   0.1    6.1  6  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    5.2e-07   29.7   0.2      0.045   13.6   0.0    2.6  2  eIF2A        Eukaryotic translation initiation factor eIF2A
     0.0023   17.3   0.0       0.28   10.5   0.0    2.3  2  WD40_like    WD40-like domain
  ------ inclusion threshold ------
      0.052   12.5   0.0       0.51    9.2   0.0    2.5  3  Ge1_WD40     WD40 region of Ge1, enhancer of mRNA-decapping p


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.012        45      12      38 .]      99     125 ..      84     125 .. 0.72
   2 !   17.0   0.0   2.2e-06    0.0078       5      31 ..     133     158 ..     129     166 .. 0.86
   3 !   28.7   0.3   4.5e-10   1.6e-06       2      38 .]     171     208 ..     170     208 .. 0.93
   4 !   23.8   0.1   1.6e-08   5.6e-05       5      38 .]     216     250 ..     212     250 .. 0.92
   5 !   16.5   0.0   3.2e-06     0.011       4      36 ..     257     290 ..     254     292 .. 0.88
   6 ?    4.4   0.0     0.021        76       5      37 ..     300     334 ..     297     335 .. 0.78
   7 !   25.8   0.1   3.7e-09   1.3e-05       8      37 ..     347     377 ..     340     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.012
                                    SEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  12 svtslafspdgawlasGsdDgtvriWd 38 
                                    +v+ +++ pdg+ l+sG+  g   +W+
  gene266|gene266|rna266|rna266  99 PVNIVRWTPDGRRLMSGTATGEFTLWN 125
                                    255566***********8777777776 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.2e-06
                                    EEEESS.SSEEEEEEETTSSEEEEEETT CS
                           WD40   5 rtltGH.ssvtslafspdgawlasGsdD 31 
                                    ++l +H s+v+++a+sp+g++l+s s D
  gene266|gene266|rna266|rna266 133 TILQAHeSPVRGMAWSPSGSFLIS-S-D 158
                                    5789**999*************96.5.4 PP

  == domain 3  score: 28.7 bits;  conditional E-value: 4.5e-10
                                    EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    ++++++ GH   v++l+fs++ + ++s+sdD t+++Wd
  gene266|gene266|rna266|rna266 171 NNIQIIQGHaEAVRDLSFSHNDSKFCSASDDSTIKVWD 208
                                    678999***777*************************9 PP

  == domain 4  score: 23.8 bits;  conditional E-value: 1.6e-08
                                    EEEESSSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   5 rtltGHss.vtslafspdgawlasGsdDgtvriWd 38 
                                     +l+GH++ v++ +++++++++as+++D+ v++Wd
  gene266|gene266|rna266|rna266 216 SVLRGHNWdVRAAQWHKYKSLIASAGKDNLVKMWD 250
                                    689***667*************************9 PP

  == domain 5  score: 16.5 bits;  conditional E-value: 3.2e-06
                                    EEEEESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40   4 lrtltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                    l tl  H + + +l++  d ++l++G++D+ +++
  gene266|gene266|rna266|rna266 257 LCTLHHHkNTILALKWMGDENYLLTGGKDQVIKM 290
                                    6788889888**********************97 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.021
                                    EEEESS.SSEEEEEEETTSSE......EEEEETTSEEEEE CS
                           WD40   5 rtltGH.ssvtslafspdgaw......lasGsdDgtvriW 37 
                                     t++ H + vts+     g+       ++sG+  g +++W
  gene266|gene266|rna266|rna266 300 FTYKNHrKEVTSI-----GTHpcipdmFVSGGTEGGIYFW 334
                                    6899999999988.....5556666667899889999999 PP

  == domain 7  score: 25.8 bits;  conditional E-value: 3.7e-09
                                    ESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   8 tGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                    +GH + v+sl+++p g+ lasGs D++vr+W
  gene266|gene266|rna266|rna266 347 EGHeGTVWSLDYHPVGHILASGSVDQSVRFW 377
                                    59*888************************* PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0002      0.73      34      66 ..      93     125 ..      82     138 .. 0.84
   2 !    9.9   0.0   0.00025      0.89      35      65 ..     136     166 ..     129     176 .. 0.83
   3 !    8.2   0.0   0.00081       2.9      36      71 ..     178     213 ..     169     221 .. 0.87
   4 !   13.6   0.2   1.7e-05     0.063      38      90 ..     222     273 ..     216     273 .. 0.92
   5 !   13.9   0.1   1.4e-05     0.049      36      87 ..     262     312 ..     255     315 .. 0.90
   6 !    9.1   0.0   0.00045       1.6      33      64 ..     345     376 ..     330     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                    ANAPC4_WD40  34 edkedsevrsLaWkpdgklLavaysdgevrlld 66 
                                     +k +  v+ ++W pdg+ L+ +++ ge  l +
  gene266|gene266|rna266|rna266  93 VNKVKCPVNIVRWTPDGRRLMSGTATGEFTLWN 125
                                    56778999*******************998876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
                    ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrll 65 
                                    ++++s vr++aW+p+g++L  + + g ++  
  gene266|gene266|rna266|rna266 136 QAHESPVRGMAWSPSGSFLISSDNFGIIKYW 166
                                    45899***************99998888765 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00081
                    ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesgk 71 
                                    ++ + vr+L+++++++ ++ a +d+++++ d+ ++k
  gene266|gene266|rna266|rna266 178 GHAEAVRDLSFSHNDSKFCSASDDSTIKVWDSIEAK 213
                                    56789************************9987766 PP

  == domain 4  score: 13.6 bits;  conditional E-value: 1.7e-05
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                    +  vr+ +W++  +l+a a +d+ v++ d  +++ + +l+ +++ ++  l+W+
  gene266|gene266|rna266|rna266 222 NWDVRAAQWHKYKSLIASAGKDNLVKMWDPRTAEELCTLHHHKN-TILALKWM 273
                                    5679999********************************99999.6******5 PP

  == domain 5  score: 13.9 bits;  conditional E-value: 1.4e-05
                    ANAPC4_WD40  36 kedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtcl 87 
                                    ++++++ +L+W  d++ L  + +d  ++++d+ +   v +++ ++++ vt++
  gene266|gene266|rna266|rna266 262 HHKNTILALKWMGDENYLLTGGKDQVIKMVDIRTMVDVFTYKNHRKE-VTSI 312
                                    67899*****************************9999999999985.8877 PP

  == domain 6  score: 9.1 bits;  conditional E-value: 0.00045
                    ANAPC4_WD40  33 eedkedsevrsLaWkpdgklLavaysdgevrl 64 
                                     e++++++v sL ++p g++La +  d +vr+
  gene266|gene266|rna266|rna266 345 IEEGHEGTVWSLDYHPVGHILASGSVDQSVRF 376
                                    5778999********************99986 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.3e-05     0.045      86     160 ..      82     156 ..      76     161 .. 0.84
   2 !   13.3   0.2   1.6e-05     0.058      53     162 ..     175     283 ..     161     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                    EEEECSCEEEEEEE.EES--EEEE-TTSSEEEEE-TTSSS-EEEEEETT..TTEEEEEEE-TT--EEEE-TTSSEEEE CS
                          eIF2A  86 slfdlkvkviskle.eqkrNtiffspkgklvllaGfgnlaGeleiwdvk..kkkkiakaeaanatlvewspdgryvlT 160
                                    slf +k++ is  + + + N + + p g+ ++ +      Ge  +w+    ++++i +a+++    + wsp+g++++ 
  gene266|gene266|rna266|rna266  82 SLFTTKIEHISVNKvKCPVNIVRWTPDGRRLMSG---TATGEFTLWNGYgcNFETILQAHESPVRGMAWSPSGSFLIS 156
                                    6788887777644327899**********99875...5689******9989999*******************99875 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.6e-05
                                    ECCEESSS.EEEEEE-TTSS-EEEEESSSSCEEEEEEC...SCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEE CS
                          eIF2A  53 vvelkkegpihdvaWspkskefaviyGkmpakvslfdl...kvkviskleeqkrNtiffspkgklvllaGfgnlaGelei 129
                                    +++ + e  + d++ s + ++f+      +++++++d+   k + + + ++    +  +++   l++ aG  nl   +++
  gene266|gene266|rna266|rna266 175 IIQGHAE-AVRDLSFSHNDSKFC--SASDDSTIKVWDSieaKEESVLRGHNWDVRAAQWHKYKSLIASAGKDNL---VKM 248
                                    4444444.588999999999996..55677888888886445677777777888899*****************...*** PP

                                    EETTTTEEEEEEE-TT--E..EEE-TTSSEEEEEE CS
                          eIF2A 130 wdvkkkkkiakaeaanatl..vewspdgryvlTat 162
                                    wd  + +++ ++++ + t   ++w  d +y+lT  
  gene266|gene266|rna266|rna266 249 WDPRTAEELCTLHHHKNTIlaLKWMGDENYLLTGG 283
                                    *********99998887752368*********975 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0044        16      75     144 ..      92     162 ..      78     210 .. 0.78
   2 !   10.5   0.0   7.8e-05      0.28      10     109 ..     232     336 ..     224     375 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0044
                      WD40_like  75 evenekieedistvkviddklliGtnkGsiyvfsk.dlqleevllgqsseIkeikiennkiysLsesafiv 144
                                    +v++ k   +i   + ++ +l+ Gt +G+  +++    ++e++l  ++s+++ +  + +  + +s+++f +
  gene266|gene266|rna266|rna266  92 SVNKVKCPVNIVRWTPDGRRLMSGTATGEFTLWNGyGCNFETILQAHESPVRGMAWSPSGSFLISSDNFGI 162
                                    3455555555555556677999*********98852578999*************9999999999998844 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.8e-05
                      WD40_like  10 kkgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd.lilvvtlDGtillsllenee.evenekieedist 87 
                                    k  sli+  gkd+ +++ + ++ e+   +++ ++ ++  k + d+  +l +  D  i + +++    +   ++   +++ 
  gene266|gene266|rna266|rna266 232 KYKSLIASAGKDNLVKMWDPRTAEELCTLHHHKNTILALKWMGDEnYLLTGGKDQVIKMVDIRTMVdVFTYKNHRKEVTS 311
                                    5568999*********************************9977636677899*99988888877643344444555555 PP

                      WD40_like  88 v...kviddklliGtnkGsiyvfsk 109
                                    +     i d ++ G+++G iy ++ 
  gene266|gene266|rna266|rna266 312 IgthPCIPDMFVSGGTEGGIYFWQA 336
                                    51115789*************9765 PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00014      0.51      45     102 ..     160     217 ..     145     235 .. 0.80
   2 ?   -2.1   0.0      0.39   1.4e+03     256     285 ..     233     262 ..     221     271 .. 0.72
   3 ?   -0.5   0.0      0.13   4.7e+02     188     214 ..     351     377 ..     334     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00014
                       Ge1_WD40  45 eglvrvvnketeeraLlkglkgevldlafahvsskillavdekgslfvy.kveeveskl 102
                                     g+++  + ++++  +++g  ++v+dl+f+h +sk   a d+ + + v+ ++e++e+ +
  gene266|gene266|rna266|rna266 160 FGIIKYWHPSMNNIQIIQGHAEAVRDLSFSHNDSKFCSASDD-STIKVWdSIEAKEESV 217
                                    68999999999********************99998777665.5677772466655555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.39
                       Ge1_WD40 256 WrfaitgadnnselklWscelWtClqtikf 285
                                    ++ +i++a +++ +k+W   + + l t++ 
  gene266|gene266|rna266|rna266 233 YKSLIASAGKDNLVKMWDPRTAEELCTLHH 262
                                    566788888888888888877777777765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.13
                       Ge1_WD40 188 sliveaafspdGtalatasedGevkff 214
                                     ++ +  + p G  la  s d  v+f+
  gene266|gene266|rna266|rna266 351 GTVWSLDYHPVGHILASGSVDQSVRFW 377
                                    46777778899***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.54
# Mc/sec: 2276.64
//
Query:       gene267|gene267|rna267|rna267  [L=429]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-90  303.6   0.8    2.2e-90  303.3   0.8    1.0  1  GDI        GDP dissociation inhibitor
  ------ inclusion threshold ------
      0.032   14.8   0.0       0.21   12.2   0.0    2.2  2  Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.3   0.8   2.5e-94   2.2e-90       2     424 ..       4     425 ..       3     428 .. 0.92

  Alignments for each domain:
  == domain 1  score: 303.3 bits;  conditional E-value: 2.5e-94
                                    XXEECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCGGG-EE-HHHHHHHH-TTHHHHHHH--GGG--EESS--BEE CS
                            GDI   2 deeydvivlGtGlkecilsGllsvdgkkvlhldrndyyGgesasltleqlyerfkleekpeeklGkdrdwnvdlipkfll 81 
                                    d+eyd ++lGtGl ec +  +l+ ++kkv+ +drn+ yG++ a+l  ++l   f++ ++ +e    d ++++dl pk++l
  gene267|gene267|rna267|rna267   4 DHEYDFVILGTGLVECAVGCILAGKNKKVILIDRNPMYGSDFATLRYTELETYFRNLNTIPELKTYDSEFSIDLTPKLFL 83 
                                    78*******************************************************99999999*************** PP

                                    TTSHHHHHHHHTTGGGCS-EEE-SEEEEEETCEEEE--SSHHHHHC-TTS-HHHHHHHHHHHHHHHH-BTTBGGGSTT-- CS
                            GDI  82 anGelvkiliktdvtrylefkaveGsyvykegkiakvpanelealaspllglfekrrakkfleyvseyeeddpktyedld 161
                                    a+ ++ k+l++  + +ylef  + Gs+++k +k++ vp+ne +++++ l+g+ +k ++ +f+  v++y     k      
  gene267|gene267|rna267|rna267  84 ADSKMLKMLVRYGIDEYLEFCRIPGSFLWK-KKLYSVPTNEAQSMTTGLIGIWQKPKVMRFFWNVRDYARAAMKGK--PY 160
                                    ****************************98.589**********************************98877653..23 PP

                                    TTTSBHHHHHHHCT--HHHHHHHHHHTS--SSSGGGGSBCHHHHHHHHHHHHHHCCCS...S-SEEEETT-TTHHHHHHH CS
                            GDI 162 lkkatmkevykkfdlsedtkdfiGhalalyrdddylkqpaletleriklyaeslaryg...kspylyplyGlGelpqgfa 238
                                      k+tm+e +k+++l+e+++++iGh +al +dd+yl++  +et+++i  y+ s+  y+   +spylyp+yGl e+ qgfa
  gene267|gene267|rna267|rna267 161 KFKNTMREEFKEYGLTEESMELIGHGIALNLDDSYLDRDPRETFDKIVTYVRSIICYEnsmESPYLYPRYGLSEIAQGFA 240
                                    5699*****************************************************955559***************** PP

                                    HHHHHTT-EEETS--ECEEEE-TTS-EEEEEE..TTEE..EEECEEEE-GGG-CCCEEEEEEEEEEEEEES.S--TTSTT CS
                            GDI 239 rlsaiyGGtymlnkpvdevvldedgkvvGvks..eeev..akakkvicdpsylpekvrkvgkviraicils.hpipntdd 313
                                    r +   GG  m+n ++ e+  ++    + v+   +++v  +ka k+i+d sy+++ v    ++ir ic++  +    t  
  gene267|gene267|rna267|rna267 241 RSCCTKGGEIMINAEILEINEENM--EIHVQEpvNKKVlkIKAGKIISDQSYFQKSV-VLYEIIRGICVIRgDAACVTRG 317
                                    *****************9976444..3334332355551167889********8777.5779******997245668999 PP

                                    -SSEEEEE-GGGCTSSS-EEEEEEEGGGTSS-TT-EEEEEEEE--SS-HHHHTHHHHHTT-SECEEEEEEEEEEEESSSS CS
                            GDI 314 adsvqiiipqkqlgrksdiyvalvssahnvaakgkylaivsttvetenpevelepalellgpieekfvkisdlyepvedg 393
                                    a+s qii  +  lgrk+di+v+++    + +++g+ +ai+st+ et++pe e++  le lg i + fv+++ +y + +  
  gene267|gene267|rna267|rna267 318 ASSAQIIFLKGELGRKNDIFVVILGPEEKSTPEGYKVAIISTVKETDDPEGEIRVVLEKLGDIVRYFVDVKPVYRAED-- 395
                                    **************************************************************************8754.. PP

                                    TTTSEEE-----S-SBSHHHHHHHHHHHHHH CS
                            GDI 394 skdnifisksydatshfettvedvkdiykrl 424
                                      +ni  +k++d + hfe + e++  i k+l
  gene267|gene267|rna267|rna267 396 -MENIIFTKGVDESPHFEDVYEEIERICKKL 425
                                    .679999*****************9998875 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05      0.21       3      35 ..      10      42 ..       8      62 .. 0.85
   2 ?   -0.6   0.0      0.23   2.1e+03      45      76 ..     238     266 ..     233     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                                   EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   v++G G++ + ++++la  +kkV +++r+++  
  gene267|gene267|rna267|rna267 10 VILGTGLVECAVGCILAGKNKKVILIDRNPMYG 42
                                   9***************************99766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.23
                                    HHHHHHHHTTEEEECSEEEEEEEEETTSEEEE CS
                      Pyr_redox  45 ilqeklekngievllntkveeiegsedgvesv 76 
                                     ++++   +g e++ n+++ ei++++ +   +
  gene267|gene267|rna267|rna267 238 GFARSCCTKGGEIMINAEILEINEENME---I 266
                                    5555666678899999999999988775...4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2802.93
//
Query:       gene268|gene268|rna268|rna268  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-07   29.7   1.5    0.00017   22.1   0.9    2.8  2  RNase_PH  3' exoribonuclease family, domain 1


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.9   9.3e-09   0.00017       5     127 ..       1      99 [.       1     104 [. 0.66
   2 ?   -0.3   0.0     0.077   1.4e+03      25      47 ..     107     129 ..     101     186 .. 0.48

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9.3e-09
                                    EEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHH CS
                       RNase_PH   5 lsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsrller 84 
                                    ++i+tg++ +a  S+yl+ ++t+ ++ ++ + +    e+ d  +    vev++++++  e+r           + + + +
  gene268|gene268|rna268|rna268   1 MEIKTGLVGKALSSCYLKTNKTSAICCIHFEQKG---ET-D--P---WVEVNFSEMIPLEIR---------SPI-SSIAN 61 
                                    689*****************************65...33.4..3...345555555533331.........111.12333 PP

                                    HHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHH CS
                       RNase_PH  85 alrpsillekkpkstididitvlssdggslldalinaaslALa 127
                                    +l++s        ++i+++ ++l +    ll++lin+ s   +
  gene268|gene268|rna268|rna268  62 SLLSSKAR----STKIKVSFHTLRHGE-DLLSCLINSFSICVI 99 
                                    44443332....367888888888877.888888888776555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.077
                                    CEEEEEEEEEEEEEE-TCCG.--C CS
                       RNase_PH  25 dtkvlasvtgpieerpseer.dda 47 
                                    dt++  +v++++   ++ ++ +d 
  gene268|gene268|rna268|rna268 107 DTICSSTVYAGKDR-IALTEgPDL 129
                                    67777777777765.222222333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1169.41
//
Query:       gene269|gene269|rna269|rna269  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-54  185.5   0.1    2.5e-54  184.6   0.1    1.4  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    1.6e-05   24.8   0.1       0.36   10.7   0.0    3.1  3  RsgA_GTPase      RsgA GTPase
    0.00015   21.4   0.0    0.00084   18.9   0.0    2.0  1  GTP_EFTU         Elongation factor Tu GTP binding domain
    0.00022   21.3   0.0     0.0019   18.3   0.0    2.1  1  MMR_HSR1         50S ribosome-binding GTPase
    0.00037   20.8   0.0    0.00095   19.5   0.0    1.9  2  AAA_22           AAA domain
    0.00097   18.8   0.0        1.3    8.8   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.001   18.7   0.1     0.0058   16.2   0.1    2.1  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0012   18.3   0.0        1.5    8.2   0.0    2.2  2  SRPRB            Signal recognition particle receptor beta su
     0.0013   18.4   0.0      0.018   14.7   0.0    2.1  2  SRP54            SRP54-type protein, GTPase domain
     0.0029   17.5   0.0      0.035   14.0   0.0    2.4  3  NTPase_1         NTPase
     0.0031   17.7   0.0     0.0041   17.3   0.0    1.3  1  AAA_33           AAA domain
     0.0053   17.3   0.0      0.012   16.1   0.0    1.7  1  AAA_18           AAA domain
     0.0055   16.6   0.0     0.0094   15.9   0.0    1.3  1  NACHT            NACHT domain
     0.0066   15.7   0.0      0.014   14.6   0.0    1.5  1  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
       0.01   15.5   0.1          1    8.9   0.0    2.2  2  Ras              Ras family
      0.011   14.8   0.0      0.055   12.5   0.0    1.9  2  T2SSE            Type II/IV secretion system protein
      0.013   15.3   0.3       0.15   11.8   0.0    2.3  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.014   15.8   0.0      0.048   14.0   0.0    1.8  2  AAA_16           AAA ATPase domain
      0.015   14.8   0.0        4.9    6.6   0.0    2.2  2  Arf              ADP-ribosylation factor family
      0.017   14.9   0.0      0.035   13.8   0.0    1.4  1  AAA_30           AAA domain
      0.018   14.9   0.0      0.031   14.2   0.0    1.4  1  MobB             Molybdopterin guanine dinucleotide synthesis
       0.02   14.2   0.3       0.81    9.0   0.0    2.6  3  ATPase           KaiC
      0.022   14.2   0.0          2    7.8   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.031   14.0   0.0      0.047   13.4   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.052   13.3   0.3       0.68    9.7   0.3    2.1  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.054   13.2   0.2       0.15   11.7   0.2    1.9  1  AAA_24           AAA domain
      0.061   13.8   0.0       0.69   10.4   0.0    2.2  2  AAA_23           AAA domain
      0.077   12.7   0.0       0.16   11.6   0.0    1.5  1  Thymidylate_kin  Thymidylate kinase
       0.11   12.6   0.0       0.29   11.2   0.0    1.9  1  AAA_14           AAA domain
       0.13   12.3   0.0       0.68    9.9   0.0    2.1  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.14   11.7   0.0        0.5    9.9   0.0    1.9  2  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.6   0.1   4.4e-57   2.5e-54       1     240 [.      21     264 ..      21     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 4.4e-57
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsv..........avvNLDPAaeelpYeaavdirelitledvmedlglgpngalvv 70 
                                    vvG+aGsGKttf+++l++++++ + +v          + +NLDPA+ + + + ++dir+++++ + me+++lgpng++++
  gene269|gene269|rna269|rna269  21 VVGMAGSGKTTFCQRLYSWISQDNCRVnpdtglnsyiYSINLDPAVVNAKMPLNLDIRDVVDYHETMEKYNLGPNGGITT 100
                                    89****************998875443222222222268***************************************** PP

                     ATP_bind_1  71 aleflresldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsals 150
                                    +l+++  ++    e ++k +++y+++DtPGQie ft+s+ +  ++e+L++ ++++ vy+vDs  + + + fis++++a s
  gene269|gene269|rna269|rna269 101 CLNLFLLNI---GEYIDKIKEEYVIIDTPGQIEAFTWSSPGYMLIETLKTIGNVILVYVVDSVSSHKHAVFISNMMYAAS 177
                                    *********...677755599*********************************************************** PP

                     ATP_bind_1 151 amlrlelPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesied 230
                                     m+r+e+  +  +nk Dl +  +e   e+++d e+++  l+++ + ++    ++a ++eef+   + + +ss+++++ +d
  gene269|gene269|rna269|rna269 178 LMCRYEVEALCLFNKKDLSR--SEVLEEWISDYESFRDSLNED-NIFSPILGSMALYFEEFYNSVKSVSISSHTGSGRSD 254
                                    ******************55..888899**********99988.66788999**************************** PP

                     ATP_bind_1 231 llslidealq 240
                                    ++++++++l+
  gene269|gene269|rna269|rna269 255 FFDAVNQLLE 264
                                    *****99876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0027       1.6      98     124 ..      15      41 ..       2      53 .. 0.79
   2 ?    1.7   0.0      0.36   2.1e+02     148     160 ..     115     127 ..     109     134 .. 0.83
   3 !   10.7   0.0   0.00062      0.36      12      75 ..     147     211 ..     139     267 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0027
                                    TTSEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpele 124
                                    k k+ v+vG  G GK+t+  +l +  +
  gene269|gene269|rna269|rna269  15 KRKIFVVVGMAGSGKTTFCQRLYSWIS 41 
                                    5699***************99987544 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                                    EETTTEEEESS-S CS
                    RsgA_GTPase 148 elaegglliDtPG 160
                                    +++e+ ++iDtPG
  gene269|gene269|rna269|rna269 115 KIKEEYVIIDTPG 127
                                    5678899****** PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00062
                                    TEES--EEEEEEESTTTT--HHHHHHHHHHHH...HTT-EEEEEEE-GGG--HHHHHHHHHHHHHHT CS
                    RsgA_GTPase  12 kvaNvdqllivvslkepelslnlldrfLvlae...ekgiepvivlnKiDlleeeeeleelkeeleal 75 
                                    ++ Nv  + +v s+++++ +  +++ ++ +a    + ++e + ++nK Dl  +e  lee+ +++e++
  gene269|gene269|rna269|rna269 147 TIGNVILVYVVDSVSSHK-HAVFISNMMYAASlmcRYEVEALCLFNKKDLSRSEV-LEEWISDYESF 211
                                    478999999999999555.55667777766542227899**************99.******99986 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.5e-06   0.00084       6     193 ..      19     264 ..      15     265 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-06
                                    EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHH.HST..............................HCHSHHHHHHTS CS
                       GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaee.erv..............................lDtlkeErergi 54 
                                    ++++g   +GKtT++ rL    ++++ + + +++ +++                              + + +   + gi
  gene269|gene269|rna269|rna269  19 FVVVGMAGSGKTTFCQRLYSWISQDNCRVNPDTGlNSYiysinldpavvnakmplnldirdvvdyhetMEKYNLGPNGGI 98 
                                    78999999999999999998888877766655442333889999999999999999999999999999999999999999 PP

                                    CSSCEEEEEE...T.TCSSEEEEEEEESSSGG.GH.....HHHHHHHHT-SEEEE..EEETTTB.....STHHHHHHHHH CS
                       GTP_EFTU  55 Tiksaaisle...k.etkkylinliDtPGHvd.Fs.....kevirglrvlDgavl..vvdaveG.....vepqteevlrl 117
                                    T   +   l+     ++ k ++ +iDtPG ++ F+        i++l+++  ++l  vvd+v+        ++    + l
  gene269|gene269|rna269|rna269  99 TTCLNLFLLNigeYiDKIKEEYVIIDTPGQIEaFTwsspgYMLIETLKTIGNVILvyVVDSVSShkhavFISNMMYAASL 178
                                    999999988888625889999*********98776333323467888988888772257777666666666677777888 PP

                                    HHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH..........HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHH CS
                       GTP_EFTU 118 alkegvpiivfiNKmDrlkaelkeiveevkqklsrk..........eeklekygekgekevpvvfgSalkgegvktllea 187
                                    + +++v+  ++ NK D  ++e+ e     +++++++           +++  y e+  + v+ v +S+ +g g +++++a
  gene269|gene269|rna269|rna269 179 MCRYEVEALCLFNKKDLSRSEVLEEWISDYESFRDSlnednifspiLGSMALYFEEFYNSVKSVSISSHTGSGRSDFFDA 258
                                    9999**************7776666666666885556666777777444444443333789******************9 PP

                                    HHHHSH CS
                       GTP_EFTU 188 lvellp 193
                                    + +ll+
  gene269|gene269|rna269|rna269 259 VNQLLE 264
                                    998875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.3e-06    0.0019       3      92 ..      20     164 ..      18     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-06
                                    EEEESTTSSHHHHHHHHHT...S.TEEESSSTTSSSSEEEEEEEETTEE............................... CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltg...e.kaivsdkpgtTrdinegrvklkgke............................... 47 
                                    ++vG+  +GK+t+ ++l     + +++v+   g    i  ++++                                    
  gene269|gene269|rna269|rna269  20 VVVGMAGSGKTTFCQRLYSwisQdNCRVNPDTGLNSYIYSINLDPA--Vvnakmplnldirdvvdyhetmekynlgpngg 97 
                                    79***************86443235666555555555555544422..12344556666666666677777777777777 PP

                                    ......................EEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHH CS
                       MMR_HSR1  48 ......................ielvDtpGlie...gaseekglgkaflaleeadlillvvdaseeklkp 92 
                                                          ++++DtpG ie    +s + +l ++++ + +  ++++vvd+ ++  ++
  gene269|gene269|rna269|rna269  98 ittclnlfllnigeyidkikeeYVIIDTPGQIEaftWSSPGYMLIETLKTIGN-VILVYVVDSVSS--HK 164
                                    7777777777777777777777********88755455666689998888777.899999996622..22 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.6e-06   0.00095       4      32 ..      15      43 ..      11     158 .. 0.90
   2 ?   -2.2   0.0         8   4.6e+03      45      65 ..     242     264 ..     226     267 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldee 32
                                   +++i vv+G +G+GKTt ++rl ++  ++
  gene269|gene269|rna269|rna269 15 KRKIFVVVGMAGSGKTTFCQRLYSWISQD 43
                                   58999*******************98654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8
                         AAA_22  45 vtlpsst..sskdllrellralg 65 
                                    v ++s t  +++d++ ++ + l+
  gene269|gene269|rna269|rna269 242 VSISSHTgsGRSDFFDAVNQLLE 264
                                    33333333356666666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0056       3.2      23      38 ..      17      32 ..       6      37 .. 0.80
   2 !    8.8   0.0    0.0022       1.3      25      46 ..     242     263 ..     233     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0056
                         AAA_29 23 gatlltGpsGsGKSTl 38
                                    +++++G  GsGK+T+
  gene269|gene269|rna269|rna269 17 KIFVVVGMAGSGKTTF 32
                                   37899**********7 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0022
                         AAA_29  25 tlltGpsGsGKSTllDAiqalL 46 
                                    + ++ ++GsG S ++DA++ lL
  gene269|gene269|rna269|rna269 242 VSISSHTGSGRSDFFDAVNQLL 263
                                    5677899***********9998 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     1e-05    0.0058       2     145 ..      18     179 ..      17     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                                    EEEEEESTTCCHHHHHHHHH......CT--SS-EEEEESS-SSCHCCCCCCHCCCT..................EEEETT CS
                           cobW   2 vtvltGflGsGKTtLlnhll......enraglklavivNefgevsiDaellretgve.................ivelen 58 
                                    ++v++G  GsGKTt+ ++l       ++r + ++  +   ++++++D ++++++                     +  + 
  gene269|gene269|rna269|rna269  18 IFVVVGMAGSGKTTFCQRLYswisqdNCRVNPDTG-LNSYIYSINLDPAVVNAKMPLnldirdvvdyhetmekyNLGPNG 96 
                                    579****************9887754444444433.45557789999999955533344555555665655543444444 PP

                                    TTECCHCTT-HHHHHHHHHHHHTT-SEEEEEECTTTTHHHH.HTT...SHHHHHCCCECEEEEEEETTTH.CCHCCHHHH CS
                           cobW  59 GciCctlredllkelealeereerldviliEttGlaePapv.aft...eeelksdltldavvavvDaknleaeeekieek 134
                                    G   c   + +l ++ ++ ++  + ++++i t G  e+ ++         e+ + +   ++v+vvD+     +++k +  
  gene269|gene269|rna269|rna269  97 GITTCL--NLFLLNIGEYIDKI-KEEYVIIDTPGQIEAFTWsS-PgymLIETLKTIGNVILVYVVDS----VSSHKHAVF 168
                                    555666..88999999999999.89**************9941.23446666677888889999999....455666666 PP

                                    HHHHHHTSSEE CS
                           cobW 135 aedqlaaadll 145
                                    + +++ aa+l+
  gene269|gene269|rna269|rna269 169 ISNMMYAASLM 179
                                    66666666665 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0032       1.8       2      24 ..      15      37 ..      14      50 .. 0.87
   2 !    8.2   0.0    0.0026       1.5      48     124 ..     117     195 ..     107     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0032
                                   ---EEEEE-STTSSHHHHHHHHH CS
                          SRPRB  2 skpavllvGlsdsGKTslftrLt 24
                                   +++++++vG+  sGKT++ +rL 
  gene269|gene269|rna269|rna269 15 KRKIFVVVGMAGSGKTTFCQRLY 37
                                   57899*************99996 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                                    GTT-SEEEETT-GC.C.....SHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE- CS
                          SRPRB  48 gskltliDfPGhek.l.....rqklleklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnK 121
                                    +++  +iD PG+ + +      + l+e+lk+  ++  lv+vvDS    k++  +  ++y   l     + +v+ l   nK
  gene269|gene269|rna269|rna269 117 KEEYVIIDTPGQIEaFtwsspGYMLIETLKTIGNV-ILVYVVDSVSSHKHAVFISNMMYAASLMC---RYEVEALCLFNK 192
                                    56677888888743131111146789997777776.69************999999999755443...355666666666 PP

                                    TTS CS
                          SRPRB 122 qel 124
                                    ++l
  gene269|gene269|rna269|rna269 193 KDL 195
                                    666 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-05     0.018       2      30 ..      17      45 ..      16      48 .. 0.87
   2 ?    1.4   0.0      0.37   2.1e+02      83      97 ..     117     131 ..     108     177 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS CS
                          SRP54  2 nvillvGlqGaGKTttlaKLaallkkegk 30
                                   +++++vG+ G+GKTt + +L  ++++++ 
  gene269|gene269|rna269|rna269 17 KIFVVVGMAGSGKTTFCQRLYSWISQDNC 45
                                   5789****************999998875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.37
                                    TSSEEEEEE--SSTT CS
                          SRP54  83 kidvvlvDTaGrlqn 97 
                                    k ++v++DT G+ + 
  gene269|gene269|rna269|rna269 117 KEEYVIIDTPGQIEA 131
                                    45789*****99875 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     6e-05     0.035       2      30 ..      19      47 ..      18      49 .. 0.92
   2 ?   -2.2   0.0       5.9   3.4e+03      97     112 ..     119     134 ..     104     172 .. 0.61
   3 ?    0.1   0.0       1.1   6.6e+02       2      27 ..     242     267 ..     241     268 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                   +++ G+ G+GKtT+++++++ +++++++v
  gene269|gene269|rna269|rna269 19 FVVVGMAGSGKTTFCQRLYSWISQDNCRV 47
                                   5789**********************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.9
                                    -EEEE---STTGGG-H CS
                       NTPase_1  97 dviviDEiGkmElksk 112
                                    + ++iD  G++E ++ 
  gene269|gene269|rna269|rna269 119 EYVIIDTPGQIEAFTW 134
                                    5677888888887653 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.1
                                    EEEE--TTSSHHHHHHHHHHHH...G CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssg 27 
                                    v i+ + G+G + +++ v +ll++++
  gene269|gene269|rna269|rna269 242 VSISSHTGSGRSDFFDAVNQLLEEKD 267
                                    6789999*************999875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     7e-06    0.0041       2      32 ..      19      51 ..      18     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7e-06
                         AAA_33  2 vllvGlpGsGKstlaerllkklg..avllssdt 32
                                   +++vG++GsGK+t+ +rl+       ++++ dt
  gene269|gene269|rna269|rna269 19 FVVVGMAGSGKTTFCQRLYSWISqdNCRVNPDT 51
                                   689**************9754444466666666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.2e-05     0.012       3      33 ..      21      58 ..      20     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-05
                         AAA_18  3 ltGtpGvGKttlakeL....skrlgf....gvnlrdvak 33
                                   + G++G+GKtt++++L    s+  ++     + l+++++
  gene269|gene269|rna269|rna269 21 VVGMAGSGKTTFCQRLyswiSQD-NCrvnpDTGLNSYIY 58
                                   89**************6555332.234456444444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.6e-05    0.0094       3      29 ..      19      45 ..      17      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                    ++ G aGsGKTt+ q+l + + ++++
  gene269|gene269|rna269|rna269 19 FVVVGMAGSGKTTFCQRLYSWISQDNC 45
                                   6899**************999888876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.4e-05     0.014      17      42 ..      13      38 ..       6      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                                   TSCSEEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlakqiln 42
                                   + ++ +  +vGm+G+GKtt  +  ++
  gene269|gene269|rna269|rna269 13 GAKRKIFVVVGMAGSGKTTFCQRLYS 38
                                   45677999************998876 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.042        24       2      44 ..      19      63 ..      17      81 .. 0.66
   2 ?    8.9   0.0    0.0018         1      49     122 ..     119     201 ..     107     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                                   EEEEESTTSSHHHHHHHHHH..SSCSSSCTTTSSEEEEEEEEEET CS
                            Ras  2 lvlvGdsavGKtslllrfvk..dkFkeeyesTigvdfytkeievd 44
                                   +v+vG  + GKt++  r  +  ++ + + ++  g ++y+ +i++d
  gene269|gene269|rna269|rna269 19 FVVVGMAGSGKTTFCQRLYSwiSQDNCRVNPDTGLNSYIYSINLD 63
                                   59************8876541122233345555666666666666 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0018
                                    EEEEEEETTS.GGGHHHHHHHH.....TTESEEEEEEETTBHHHHHT...HHHHHHHHHHHSTTTSEEEEEEETTTGGGG CS
                            Ras  49 kleiwDTAGq.eefkslrelyy.....rdaegillvyditsresfen...vkkwveeikrvaeenvpivLvGnKvDleek 119
                                    +  i DT Gq e f+   + y+     ++   ++lvy ++s +s ++   +++++   + +++ +v+ + + nK Dl+++
  gene269|gene269|rna269|rna269 119 EYVIIDTPGQiEAFTWSSPGYMlietlKTIGNVILVYVVDSVSSHKHavfISNMMYAASLMCRYEVEALCLFNKKDLSRS 198
                                    567899999978888877777633222566679***********998333457777788888889************986 PP

                                    -SS CS
                            Ras 120 rav 122
                                    +++
  gene269|gene269|rna269|rna269 199 EVL 201
                                    554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.5e-05     0.055     128     158 ..      15      45 ..       7      48 .. 0.87
   2 ?   -0.6   0.0      0.96   5.6e+02     131     156 ..     241     266 ..     225     268 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                          T2SSE 128 erglilvsGgTgsGKttllyallkeinksde 158
                                    +r++++v G  gsGKtt+   l ++i +++ 
  gene269|gene269|rna269|rna269  15 KRKIFVVVGMAGSGKTTFCQRLYSWISQDNC 45 
                                    699****************999999998855 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.96
                          T2SSE 131 lilvsGgTgsGKttllyallkeinks 156
                                    ++ +s  TgsG++ +  a+ + ++++
  gene269|gene269|rna269|rna269 241 SVSISSHTGSGRSDFFDAVNQLLEEK 266
                                    5668999******9999998888776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00026      0.15       2      21 ..      17      36 ..      15      42 .. 0.85
   2 ?    1.1   0.1       0.5   2.9e+02      37      46 ..     119     128 ..     111     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                      PduV-EutP  2 kkilliGkvgsGKttLtqal 21
                                   k  +++G  gsGKtt +q+l
  gene269|gene269|rna269|rna269 17 KIFVVVGMAGSGKTTFCQRL 36
                                   445689************99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.5
                      PduV-EutP  37 sdeviDtPGe 46 
                                    +  +iDtPG+
  gene269|gene269|rna269|rna269 119 EYVIIDTPGQ 128
                                    4568*****8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   8.3e-05     0.048      25      55 ..      17      47 ..       9      79 .. 0.82
   2 ?   -1.2   0.0         4   2.3e+03      26     127 ..     241     263 ..     192     266 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.3e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggif 55
                                    + +++G++G+GK++  ++l+  +++d++ +
  gene269|gene269|rna269|rna269 17 KIFVVVGMAGSGKTTFCQRLYSWISQDNCRV 47
                                   6899****************98888775544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4
                         AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleeal 105
                                    +v                                                                              
  gene269|gene269|rna269|rna269 241 SV------------------------------------------------------------------------------ 242
                                    33.............................................................................. PP

                         AAA_16 106 aavpelagaeasrllellkrll 127
                                     ++++ +g+++s++++++++ll
  gene269|gene269|rna269|rna269 243 -SISSHTGSGRSDFFDAVNQLL 263
                                    .444444455555555555554 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0085       4.9      15      36 ..      17      38 ..       6      61 .. 0.68
   2 ?    6.0   0.0     0.012       7.1      84     131 ..     152     199 ..     147     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0085
                                   EEEEEEESTTSSHHHHHHHHHH CS
                            Arf 15 lrilllGLDnaGKtTilkklkl 36
                                      +++G+ ++GKtT  ++l +
  gene269|gene269|rna269|rna269 17 KIFVVVGMAGSGKTTFCQRLYS 38
                                   345899**********988854 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                                    EEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS CS
                            Arf  84 avifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpeal 131
                                     +++vvDs+ +++ +   +++    +     ev  l l NK+Dl+ + 
  gene269|gene269|rna269|rna269 152 ILVYVVDSVSSHKHAVFISNMMYAASLMCRYEVEALCLFNKKDLSRSE 199
                                    589*******998887777666666666666999*********98764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     6e-05     0.035      16      46 ..      14      44 ..       8      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6e-05
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaag 46
                                    ++++ v++G AG+GKtt  + l   + +++
  gene269|gene269|rna269|rna269 14 AKRKIFVVVGMAGSGKTTFCQRLYSWISQDN 44
                                   567899************9998877777665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.4e-05     0.031       1      31 [.      18      48 ..      18      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                           MobB  1 vlgivgksgsGKTtLleklipelkarglrvg 31
                                   ++ +vg+ gsGKTt+ ++l +++++ ++rv+
  gene269|gene269|rna269|rna269 18 IFVVVGMAGSGKTTFCQRLYSWISQDNCRVN 48
                                   5789*********************999985 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0014      0.81      18      38 ..      15      35 ..      13      44 .. 0.88
   2 ?    2.2   0.0      0.16        94     107     128 ..     105     126 ..      79     152 .. 0.84
   3 ?    1.1   0.1      0.36   2.1e+02     111     129 ..     109     127 ..     108     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                         ATPase 18 egrvvlitGepGtGKtifalq 38
                                   ++++  ++G +G+GKt+f+++
  gene269|gene269|rna269|rna269 15 KRKIFVVVGMAGSGKTTFCQR 35
                                   578999*************86 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.16
                         ATPase 107 lieelaeaikeikakrvviDsi 128
                                    ++ ++ e+i++ik++ v+iD+ 
  gene269|gene269|rna269|rna269 105 FLLNIGEYIDKIKEEYVIIDTP 126
                                    567899**************74 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.36
                         ATPase 111 laeaikeikakrvviDsit 129
                                    + e+i++ik++ v+iD+ +
  gene269|gene269|rna269|rna269 109 IGEYIDKIKEEYVIIDTPG 127
                                    5677777777777777533 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0034         2      16      44 ..       8      36 ..       4      90 .. 0.80
   2 ?    4.4   0.0     0.039        22      28      50 ..     243     265 ..     233     268 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0034
                                   EEEEEETTSSEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 16 ktvilpfsksftaivGpNGSGKsnlldAi 44
                                   k+ ++  ++++ ++vG  GSGK+ +++ +
  gene269|gene269|rna269|rna269  8 KKEEVGAKRKIFVVVGMAGSGKTTFCQRL 36
                                   555666788999***********998776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                                    EEEESTTSSHHHHHHHHHHHCTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnlldAilFvLGe 50 
                                    +i  + GSG+s ++dA+  +L e
  gene269|gene269|rna269|rna269 243 SISSHTGSGRSDFFDAVNQLLEE 265
                                    577788***********887765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.1e-05     0.047       2      29 ..      20      45 ..      19      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.1e-05
                Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnr 29
                                   vv G++G+GK+t +++l++   i + n+
  gene269|gene269|rna269|rna269 20 VVVGMAGSGKTTFCQRLYSW--ISQDNC 45
                                   899*************9976..444444 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0012      0.68       1     139 [.      23     159 ..      23     175 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                         CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpi.......dveegfsldaplvyffGdts. 72 
                                    G   sGK+T+++ L  ++ + +   + v+ D G +++ +   +  a+v+ ++       dv + +++++  +y  G +  
  gene269|gene269|rna269|rna269  23 GMAGSGKTTFCQRLYSWISQDN---CRVNPDTGLNSYIYSINLDPAVVNAKMplnldirDVVDYHETME--KYNLGPNGg 97 
                                    5578999999999999986666...45678888888777777766666666633543333323322222..234443321 PP

                         CLP1_P  73 psdnpslylalvkelareveekleenkkakasgliIntpGwvk.....glgaellleliealepdvvvvldq 139
                                    +++ ++l+l  + e +          +k k++ +iI+tpG ++     + g+ l++ l  + ++ +v+v+d+
  gene269|gene269|rna269|rna269  98 ITTCLNLFLLNIGEYI----------DKIKEEYVIIDTPGQIEaftwsSPGYMLIETLKTIGNVILVYVVDS 159
                                    2222223333333333..........3455789999999999744444557766666666667777777666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00027      0.15       4      37 ..      18      55 ..      15     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                         AAA_24  4 kiliyGpsgiGKTtlakel....gpkplfidtekGlks 37
                                    ++++G +g+GKTt++ +l     ++   ++ + Gl+s
  gene269|gene269|rna269|rna269 18 IFVVVGMAGSGKTTFCQRLyswiSQDNCRVNPDTGLNS 55
                                   5799*************996666555555566666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0012      0.69      15      35 ..      12      32 ..       6      37 .. 0.84
   2 ?    0.7   0.0       1.1   6.5e+02      22      43 ..     242     263 ..     230     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                         AAA_23 15 idFskgltlItGpNGaGKTTi 35
                                   +  ++++++++G+ G+GKTT+
  gene269|gene269|rna269|rna269 12 VGAKRKIFVVVGMAGSGKTTF 32
                                   555789**************7 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                         AAA_23  22 tlItGpNGaGKTTildAiklaL 43 
                                    + I+ ++G+G + ++dA+   L
  gene269|gene269|rna269|rna269 242 VSISSHTGSGRSDFFDAVNQLL 263
                                    568899***********98665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00027      0.16       3      24 ..      23      44 ..      21      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                                   ESTTSSHHHHHHHHHHHHHHTT CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeeg 24
                                   G+ G+GKtt+++ l++++++  
  gene269|gene269|rna269|rna269 23 GMAGSGKTTFCQRLYSWISQDN 44
                                   899**************99876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0005      0.29       2      24 ..      16      38 ..      15      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0005
                         AAA_14  2 rkilvitGaRrvGKTtllkqlik 24
                                   rki v++G+  +GKTt++++l++
  gene269|gene269|rna269|rna269 16 RKIFVVVGMAGSGKTTFCQRLYS 38
                                   79****************99974 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0012      0.68      19      43 ..      16      40 ..       4      52 .. 0.76
   2 ?   -1.3   0.0       3.5     2e+03      47      61 ..     133     147 ..     122     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                                   TEEEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglakal 43
                                   +++++  G  G+GKTt+++ l + +
  gene269|gene269|rna269|rna269 16 RKIFVVVGMAGSGKTTFCQRLYSWI 40
                                   4578999************998765 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.5
                                    ----TTTTSEEEEEE CS
                           TsaE  47 evkSPTFtlveeYel 61 
                                    + +SP + l+e+ ++
  gene269|gene269|rna269|rna269 133 TWSSPGYMLIETLKT 147
                                    568999999998765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00086       0.5      32      64 ..      15      47 ..      10      61 .. 0.87
   2 ?   -2.5   0.0       5.4   3.1e+03      26      55 ..     232     261 ..     227     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00086
                          AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekyls 64
                                   ++k +++vG +G+GKt+ +++l + ++++++ +
  gene269|gene269|rna269|rna269 15 KRKIFVVVGMAGSGKTTFCQRLYSWISQDNCRV 47
                                   6778899**************999998888765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.4
                          AAA_7  26 lelllknkkpvllvGptGtGKtviikdllk 55 
                                    +e + ++ k+v +  +tG+G++     + +
  gene269|gene269|rna269|rna269 232 FEEFYNSVKSVSISSHTGSGRSDFFDAVNQ 261
                                    566667778888888899998877666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.54
# Mc/sec: 1494.05
//
Query:       gene27|gene27|rna27|rna27  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   10.8   0.0       0.18   10.5   0.0    1.1  1  Tweety    Tweety


Domain annotation for each model (and alignments):
>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   9.8e-06      0.18     113     197 ..     138     234 ..     121     235 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.8e-06
                     Tweety 113 seteesleekleeeLtkleeifak.rtdlletlrlvqeqveevvqqlselpflkkk...........dvsltelaeqvelvely 184
                                 ++ e+++e l++eL k+e+ +++ + +l e+++++++    + ++l++++  k++           + s ++  e  +++e+ 
  gene27|gene27|rna27|rna27 138 LNVLEDIKELLSNELFKVETYISRgKGHLCESIKKLRRYDGILKKYLKKISSAKAAkskhnyatkytEFSEKAHEEAKSYYETK 221
                                45667899999999****99877526779999999999999999999999966555455666444334444444455679999* PP

                     Tweety 185 RWlaylllllldl 197
                                +Wl ++ +l   l
  gene27|gene27|rna27|rna27 222 KWLQTIVTLFRSL 234
                                ****999997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1022  (0.0570026); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1587.28
//
Query:       gene270|gene270|rna270|rna270  [L=544]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-38  133.5   1.6    1.5e-38  132.9   1.6    1.2  1  RIBIOP_C   40S ribosome biogenesis protein Tsr1 and BMS1 C-te
  ------ inclusion threshold ------
       0.35   10.6   3.4         11    5.8   0.3    2.5  2  DUF1281_C  Ferredoxin-like domain in Api92-like protein


Domain annotation for each model (and alignments):
>> RIBIOP_C  40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   1.6   1.6e-42   1.5e-38      13     291 ..     283     540 ..     274     541 .. 0.89

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 1.6e-42
                       RIBIOP_C  13 fakyrglkslrtsewdpkenlpeeyarifefenfketkkrvlkealeeregvegGtyvrleiknvpeelveeknfdekkp 92 
                                    ++ yrg+++l t++   + n pe+y+r++ f++fk+++k v  ++      +   ++vr++++  +  l e      ++ 
  gene270|gene270|rna270|rna270 283 YSGYRGIRNLSTCNF-RSCNFPEHYKRLVFFDDFKRAEKLVSGQNSI----IPNNQMVRIKLR-YE-GLLE------EQI 349
                                    6779***********.7889***************999999887666....899********8.44.3444......469 PP

                       RIBIOP_C  93 livfgllphEekvsvvnvrikrhreyekpikskdplifsvGfRrfqakPifsqedtknnkhklerylkpghtcvatfygp 172
                                     ++fg +++E+++++ n+ ++ ++        ++++++++G + + ++P+ + +     +hk+ +  k+ ++ v++f+gp
  gene270|gene270|rna270|rna270 350 CVLFGCYEYEDQKTIHNFYFEGQEALG-----EEDMVVDLGHKIINVRPMITRNL----NHKVFKRQKELESGVISFIGP 420
                                    **********************99976.....59****************65555....56666666666889******* PP

                       RIBIOP_C 173 itfpntpvlafkelsskeasfrlvatGsvlevdpsriivkrivLtGhpfkihkktaviryMFfnpedvawFkpveLrTk. 251
                                    i+f+ + vl++k++   e s++ +a   +  +  +rii + +vL G pf+ +k+   ++ MF ++e+v +F++++L+ + 
  gene270|gene270|rna270|rna270 421 IAFGLSRVLIYKKSVLGELSASTFASVGMNGFVGDRIIFEEAVLQGIPFRNKKRYSLVKRMFSSKEEVMYFRNIQLYMRn 500
                                    ************9866567777777777788889******************************************9873 PP

                       RIBIOP_C 252 sGrrGhIkeslgthGyfkatFddklkqsDiVlmslYkrvf 291
                                      ++G+Ik+++gt+G fk +F +++k+ D V+mslYkrvf
  gene270|gene270|rna270|rna270 501 KKITGFIKKPIGTKGTFKGYFTQPIKSGDKVMMSLYKRVF 540
                                    689************************************8 PP

>> DUF1281_C  Ferredoxin-like domain in Api92-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3    0.0012        11      52      85 ..     210     243 ..     201     248 .. 0.80
   2 ?    5.0   0.2    0.0022        20      46      85 ..     346     383 ..     334     385 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0012
                      DUF1281_C  52 ncGyreyknGelieeylpeeefeealdeerkvyd 85 
                                    + G r+yk G+l++ ++   +f+ +++  ++ yd
  gene270|gene270|rna270|rna270 210 VLGDRVYKGGDLCSGTDLRGTFHTDVERSEEEYD 243
                                    58*********************55555555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0022
                      DUF1281_C  46 eegiglncGyreyknGelieeylpeeefeealdeerkvyd 85 
                                    ee+i++  G +ey++ + i+  ++e +  eal ee  v+d
  gene270|gene270|rna270|rna270 346 EEQICVLFGCYEYEDQKTIHNFYFEGQ--EALGEEDMVVD 383
                                    8999988******************88..78777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3519.06
//
Query:       gene271|gene271|rna271|rna271  [L=308]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-62  211.2   0.0    6.2e-62  209.3   0.0    1.7  1  Pkinase         Protein kinase domain
    8.7e-29  100.6   0.0    1.1e-28  100.2   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
  ------ inclusion threshold ------
      0.014   14.8   0.0      0.017   14.4   0.0    1.2  1  Kinase-like     Kinase-like
      0.039   12.9   0.0      0.049   12.6   0.0    1.2  1  Haspin_kinase   Haspin like kinase domain
       0.07   12.7   0.1      0.099   12.2   0.1    1.2  1  RIO1            RIO1 family
      0.079   11.7   0.1      0.098   11.4   0.1    1.2  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3   0.0   2.1e-65   6.2e-62       2     264 .]       5     294 ..       4     294 .. 0.90

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 2.1e-65
                                    EEEEEEEEESSEEEEEEEETT.............TTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEE CS
                        Pkinase   2 ekleklGeGsfGkVykaveke.............tgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfe 68 
                                     k+++lGeG+++++y ++++              ++  vA+K++k  k ++ +e +++rEik lk+++++++v+l+++f 
  gene271|gene271|rna271|rna271   5 IKEKRLGEGTYAVIYLGYRALpqdkpfvntgtriEDTPVAIKRVKPTKYTQGHEISAIREIKALKRISSKYVVKLLDAFI 84 
                                    56778888888888777654311111111111114567****************************************** PP

                                    ESSEEEEEEE--TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEE CS
                        Pkinase  69 ekdelylvleyveggeladlle.rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlake 147
                                    +++ +++vleyve++ l+++++ +++++ + ++k ++  il+g+  +H+  iiHrD+Kp+NiLi  +g++K++DFGl + 
  gene271|gene271|rna271|rna271  85 HDKCVHIVLEYVETN-LENVIRnTDKIIMPGDIKAWMLMILRGVYECHKLFIIHRDIKPNNILITAEGMVKLADFGLTRG 163
                                    *************66.*****966777***************************************************** PP

                                    SSSSCSBCTTTSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCT.SHH. CS
                        Pkinase 148 lessskltsfvgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilg.etke 225
                                    ++++  +t + +t++Y+APE+l ++++y++++D+Ws+G++++el+ + p+f    g++    +++ql +i++ lg +t++
  gene271|gene271|rna271|rna271 164 IRNK--MTPQAVTRWYRAPELLmGSRDYGSPSDMWSVGCVFAELFLRVPLFG---GDT----DIHQLDMIFRALGtPTEK 234
                                    **95..799*************999***************************...666....8999999*****988999 PP

                                    ..HHHTTS.....................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 226 klpeasei.....................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                    ++p  s++                     s++a+dll++ll+ +p +R+ ++++++hpy+
  gene271|gene271|rna271|rna271 235 EWPGVSTLpeflefqqyakislgslfsaaSSDALDLLERLLTLNPCNRINCDDAIKHPYF 294
                                    9**********************************************************8 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   3.8e-32   1.1e-28       4     200 ..       7     207 ..       4     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 3.8e-32
                                    EEEEEEESSEEEEEEEEET.........TTTSSEEEEEEEEEST.TSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESS CS
                    Pkinase_Tyr   4 gkklGeGafGkVvegtlkg.........ekekkevkVavKtlke.eateeekeelleeakimkklkhpnivkllgvctke 73 
                                    +k+lGeG+++ ++ g+             ++ +++ Va+K +k  ++t+ ++ + ++e+k +k+++ + +vkll + +++
  gene271|gene271|rna271|rna271   7 EKRLGEGTYAVIYLGYRALpqdkpfvntGTRIEDTPVAIKRVKPtKYTQGHEISAIREIKALKRISSKYVVKLLDAFIHD 86 
                                    689************98877889998776777899*******8625677778999************************* PP

                                    SSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEET CS
                    Pkinase_Tyr  74 epllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardi 153
                                    + + iv+eyv+  +L++ +r++ ++ +   d+  ++l + +G+   ++  ++Hrd+   N+L++ + +vk++DfGL+r i
  gene271|gene271|rna271|rna271  87 KCVHIVLEYVET-NLENVIRNT-DKIIMPGDIKAWMLMILRGVYECHKLFIIHRDIKPNNILITAEGMVKLADFGLTRGI 164
                                    **********86.8*******9.9999999************************************************** PP

                                    TTSSEEEETTSSTSGGGGS.-HHHHHHSE.EEHHHHHHHHHHHHHHHHT CS
                    Pkinase_Tyr 154 ekddeyvkkeeaklpvkWm.apEslkekk.ftsksDvWsfGvllwEift 200
                                          ++k + +   +W+ apE l+ ++ + s sD+Ws G +  E+f 
  gene271|gene271|rna271|rna271 165 ------RNKMTPQAVTRWYrAPELLMGSRdYGSPSDMWSVGCVFAELFL 207
                                    ......55566666677766****998777****************995 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.7e-06     0.017     153     238 ..     123     200 ..      52     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-06
                    Kinase-like 153 lirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlsevekgfaPpEllgsrggytrknktkmthkld 232
                                    ++r + + +++ ++h +++++n+l   +g ++l +f+  +   +k+    v + +  pEll     y+         + d
  gene271|gene271|rna271|rna271 123 ILRGVYECHKLFIIHRDIKPNNILITAEGMVKLADFGLTRGIRNKMTPQAVTRWYRAPELLMGSRDYG--------SPSD 194
                                    467777788899************************9888888888879999*******986644444........3556 PP

                    Kinase-like 233 aWqlGl 238
                                     W +G 
  gene271|gene271|rna271|rna271 195 MWSVGC 200
                                    666665 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.049     227     280 ..     134     189 ..      60     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                  Haspin_kinase 227 eFEHRdLhldniLvdknlnvtlidlklsRle.ssegkvlytrld.dpllFqGggDy 280
                                       HRd++ +niL+ +++ v l d+ l R   ++    + tr    p+l  G +Dy
  gene271|gene271|rna271|rna271 134 FIIHRDIKPNNILITAEGMVKLADFGLTRGIrNKMTPQAVTRWYrAPELLMGSRDY 189
                                    456**************************654444444444444377788887777 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.3e-05     0.099      41     149 ..      47     158 ..      27     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                                    G--GS-HHHHHHHHHHHHHHHHHHHHHTT.--S--EEEEETTE.EEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHH CS
                           RIO1  41 rksktnprklvklwaekEfrnLkrleeag.vpvPkpielkrhv.lvmefigedgvaapklkdve.eeeeaeelyeevlee 117
                                    r + t+  +  +++a +E+++Lkr++++  v+  ++  + + v +v+e+++++  ++ +  d   +  +++  + ++l+ 
  gene271|gene271|rna271|rna271  47 RVKPTKYTQGHEISAIREIKALKRISSKYvVKLLDAFIHDKCVhIVLEYVETNLENVIRNTDKIiMPGDIKAWMLMILRG 126
                                    55556666778899***********998646676766666665599*****65555555444443466666666666664 PP

                                    HHHHHHTSTEEESS-STTSEEEETT.EEEE--G CS
                           RIO1 118 mrklykeaglvHaDLSeyNvlvded.kvviIDv 149
                                    +     +  ++H D+   N+l++ +  v + D+
  gene271|gene271|rna271|rna271 127 VYECH-KLFIIHRDIKPNNILITAEgMVKLADF 158
                                    44433.4557************99955556665 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.3e-05     0.098     308     343 ..     120     150 ..      61     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                 Pkinase_fungal 308 llealrDaIkghrsLflkagiLHrDiSenNilitds 343
                                    +l  lr + + h +Lf    i+HrDi  nNilit +
  gene271|gene271|rna271|rna271 120 MLMILRGVYECH-KLF----IIHRDIKPNNILITAE 150
                                    555555555555.367....9************933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2164.33
//
Query:       gene272|gene272|rna272|rna272  [L=713]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-10   39.5   0.2    2.3e-09   37.8   0.2    2.0  1  Sec23_BS        Sec23/Sec24 beta-sandwich domain
    3.8e-08   33.1   0.3    1.2e-07   31.5   0.3    1.8  1  Sec23_helical   Sec23/Sec24 helical domain
    1.5e-06   28.0   0.0    3.1e-06   27.0   0.0    1.5  1  Gelsolin        Gelsolin repeat
    1.8e-06   27.9   4.2    1.8e-06   27.9   4.2    1.8  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger


Domain annotation for each model (and alignments):
>> Sec23_BS  Sec23/Sec24 beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.2   5.2e-13   2.3e-09       2      94 ..     393     474 ..     392     476 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.2e-13
                                    EEEEEEEEE-TTEEEEEEESSSEECSTBESSEESECSESEEEEEEEETT--EEEEEEESSBTCTTSEEEEEEEEEEEETT CS
                       Sec23_BS   2 fnatlevrtSkelkvsgliGncvslsnvsekeiGeggtsewklcsldpdstlavyfdideklksgkqayiQfatlYthss 81 
                                    +++++e +tS+ ++  +++Gn   ++          g    +++++d ++t++++f+ +e+lk+++++y+Q+++++   +
  gene272|gene272|rna272|rna272 393 YKVRVEAKTSDAIRKLSFYGNTAFEH---------LGF--QDFAQMDDKTTFGITFSLEESLKNKSKVYVQMILSFYCFD 461
                                    8899*********************9.........555..678************************************* PP

                                    SEEEEEEEEEEEE CS
                       Sec23_BS  82 gerrlRVttvalp 94 
                                    g++r+ V++++++
  gene272|gene272|rna272|rna272 462 GSSRVLVMNTSFE 474
                                    *********9975 PP

>> Sec23_helical  Sec23/Sec24 helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.3   2.6e-11   1.2e-07      17      80 ..     501     563 ..     488     572 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.6e-11
                                    TTTS-HHHHHHHHHHHHHHHHHHHHHH-------------GGGTTHHHHHHHHHTSTTTS--TT CS
                  Sec23_helical  17 alesgladarealdtslvdllsayrkvgasgsspsqlqlpeslklLPlyilallKspafrggns 80 
                                    ++e+++++  +++ +s+++ l++yr+ + +++s+sq++lpes+kl+Pl   ++lK+ +f ++  
  gene272|gene272|rna272|rna272 501 MDENTVKEHSKKVENSISRSLKYYRNSCCKEASSSQFVLPESIKLIPLIYQSMLKNSCFSNS-A 563
                                    45678999***************************************************864.2 PP

>> Gelsolin  Gelsolin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     7e-10   3.1e-06       6      44 ..     603     643 ..     599     681 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 7e-10
                                    EEBSSSGGGEETTSEEEEEESSEEEEEEHTT..SHHHHHHH CS
                       Gelsolin   6 kvvklsssslesgdcyLLdngftiflWiGke..ssqeeknf 44 
                                    k  kl+ +sl+s+ +y+Ldn ++i+++iG++   s+ e+ f
  gene272|gene272|rna272|rna272 603 KALKLTAESLNSEEIYVLDNSQKIYIYIGENvdTSLKEAIF 643
                                    66799**************************9666666554 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.1       3.7   1.7e+04      10      15 ..     100     105 ..     100     106 .. 0.80
   2 !   27.9   4.2     4e-10   1.8e-06       2      36 ..     119     151 ..     119     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.7
                 zf-Sec23_Sec24  10 ylNpfc 15 
                                    +lNpf 
  gene272|gene272|rna272|rna272 100 VLNPFN 105
                                    79**96 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 4e-10
                 zf-Sec23_Sec24   2 irCrrCraylNpfckidfggkrwiCnfCnhknevp 36 
                                    +rC +C++y+N+f++i   g  + Cn+C +kn+v 
  gene272|gene272|rna272|rna272 119 VRCWQCQSYVNIFTRI--EGTVFYCNICDSKNQVK 151
                                    7***************..669***********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (713 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 4062.56
//
Query:       gene273|gene273|rna273|rna273  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-17   62.9   0.3      3e-17   62.6   0.3    1.0  1  PRA1      PRA1 family protein


Domain annotation for each model (and alignments):
>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.3   1.7e-21     3e-17      10     142 ..      26     154 ..      19     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.7e-21
                           PRA1  10 sefldlsrfslPkslskatsRvkkNllyfrtNYlivvllvlllslltnplslivllllvlawlflyflrseplvlfgrel 89 
                                    ++f+++++ s+P++l++a+ R+ +Nl  f+ +Y++++ ++ l+ +l++  +li+l+ ++++ ++ y+++  p  lf+ e+
  gene273|gene273|rna273|rna273  26 KDFFNIRKASVPRDLNDAKRRILTNLDRFKFHYFAMASILTLIYVLYRL-ELIILIGIISITAYAYKTK--PT-LFNIEM 101
                                    79***********************************999999888876.8888888899999998873..33.69**** PP

                           PRA1  90 .sdrvvlivllvvsvlllfltgavlvllwalliglllvllHAsfrkrndkfkde 142
                                      ++v++++++ + ++++f+ +a++ ll   +i  +++l+HA+  ++ d+ kde
  gene273|gene273|rna273|rna273 102 ePRSVCIAGIVGILIFFIFFKEAIVGLLAISAICGIIILIHAASLEE-DLQKDE 154
                                    5566888889999999999999********************99855.444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 877.97
//
Query:       gene274|gene274|rna274|rna274  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-06   28.4   0.8    1.5e-06   28.4   0.8    2.2  2  Spc24     Spc24 subunit of Ndc80
  ------ inclusion threshold ------
      0.029   12.6   3.7      0.037   12.3   3.7    1.0  1  Vinculin  Vinculin family
       0.13   11.7   5.1       0.06   12.8   1.0    2.0  2  CENP_C_N  Kinetochore assembly subunit CENP-C N-terminal
       0.17   11.1   0.0       0.18   11.1   0.0    1.1  1  DUF2398   Protein of unknown function (DUF2398)
        1.2    8.9   8.7        4.6    7.1   0.6    2.4  2  DivIC     Septum formation initiator


Domain annotation for each model (and alignments):
>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.4      0.16   5.7e+02      43      71 ..      33      63 ..       1      78 [. 0.48
   2 !   28.4   0.8   4.2e-10   1.5e-06       2     105 .]      80     182 ..      79     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.16
                          Spc24 43 ekeser....vedetllklklYrsLGielekdv 71
                                   e  +++    v ++    ++l+++  i+le +v
  gene274|gene274|rna274|rna274 33 E--ERMkmetVTKALQDNVQLFKKKNIQLEGEV 63
                                   2..222212111222244555555555555553 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 4.2e-10
                          Spc24   2 ldnekfriakelsdleselesleselaelkeeleeleeeseekeserve.detllklklYrsLGiel.ekd.vnkvlirn 78 
                                    + nek+++ak++ +le+e e+++       + ++e ee        ++    + + l++ + +Gie+ e d  + + i+n
  gene274|gene274|rna274|rna274  80 INNEKLKLAKKIVELEDENEKIKVGIIMADKSIQEKEERLRT----LSRpSFNEIYLEIVKGFGIEFlEGDgRKYCRIKN 155
                                    679999****************99999999998888888888....4444778899**********8555577899**** PP

                          Spc24  79 kekgdvnvlnlddklseffianyiWdk 105
                                    k+  dv ++++ ++ s f i+n iW+k
  gene274|gene274|rna274|rna274 156 KKMSDVFTIDVGSSASMFEITNSIWEK 182
                                    *************************96 PP

>> Vinculin  Vinculin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.7     1e-05     0.037     774     868 ..      26     124 ..       7     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                                    XSSSHCCHHHT.XHCHHCHHHHHHHHHHHHHHHHHHHHTTEC...XTTSC.HHHHHHHHHHHHHHHHHHCCTXCGCHHHH CS
                       Vinculin 774 eeetdeeeerrlfeeekakiaaqvqpilaaarklhrEvakWs...skgNd.IiaaAkrmallmaelselvrgkggtkrdl 849
                                    +  ++++eer  +e+  +  + +vq++++++ +l+ Ev+k+s   sk Nd  i + ++   l  ++ el   + + k  +
  gene274|gene274|rna274|rna274  26 ALDSQRKEERMKMETVTKALQDNVQLFKKKNIQLEGEVRKYSythSKKNDaFIEINNEKLKLAKKIVELEDENEKIKVGI 105
                                    4455666666678888999**********************866678999457788888999999*****9999****** PP

                                    HHHHHHHHHHHHHHHHHHH CS
                       Vinculin 850 iqaakkIaeaseevtrLak 868
                                    i a k I e  e++  L++
  gene274|gene274|rna274|rna274 106 IMADKSIQEKEERLRTLSR 124
                                    ************9999976 PP

>> CENP_C_N  Kinetochore assembly subunit CENP-C N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.13   4.5e+02     226     247 ..      29      50 ..      13      60 .. 0.81
   2 ?   12.8   1.0   1.7e-05      0.06     212     267 ..      78     137 ..      65     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.13
                                    XXX.XXXXXXXXXXXXXXXXXX CS
                       CENP_C_N 226 serqqerkqsetsqkriqdsey 247
                                    s+r++er + et  k +qd  +
  gene274|gene274|rna274|rna274  29 SQRKEERMKMETVTKALQDNVQ 50 
                                    6789999999999999999765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.7e-05
                                    XXXXXXXXXXXXXXXXX...XXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       CENP_C_N 212 veienkvsevedkvserq..qerkqse..tsqkriqdseyeiqpqakksFStLfLEtvkr 267
                                    +ei+n++ +  +k+ e +  +e+++ +   ++k+iq++e++ ++ ++ sF +++LE vk+
  gene274|gene274|rna274|rna274  78 IEINNEKLKLAKKIVELEdeNEKIKVGiiMADKSIQEKEERLRTLSRPSFNEIYLEIVKG 137
                                    79999999999999875500455555433589**************************96 PP

>> DUF2398  Protein of unknown function (DUF2398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.9e-05      0.18      89     134 ..       3      48 ..       1     122 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                        DUF2398  89 geqftLseLaervraaaaeaalaafdlesraeRraLvaalrlLvel 134
                                    + +++L++L+e+ +  a+++ l a d ++ +eR+++ ++ + L + 
  gene274|gene274|rna274|rna274   3 ETKTLLQDLCEKFKNPAEKNILMALDSQRKEERMKMETVTKALQDN 48 
                                    7799**********999999999*****************999875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.6    0.0013       4.6      21      51 ..      37      67 ..      29      79 .. 0.80
   2 ?    6.2   2.4    0.0023       8.4      17      45 ..      75     103 ..      67     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdLk 51
                                   +++   +alq++++  k++n +Le ev++++
  gene274|gene274|rna274|rna274 37 KMETVTKALQDNVQLFKKKNIQLEGEVRKYS 67
                                   555667899********************95 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0023
                                    XHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          DivIC  17 laykqlkqeiaalqaelaklkaeneeLea 45 
                                     a+ ++++e  +l +++++l +ene+ + 
  gene274|gene274|rna274|rna274  75 DAFIEINNEKLKLAKKIVELEDENEKIKV 103
                                    5778999******************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1830  (0.102069); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 991.24
//
Query:       gene276|gene276|rna276|rna276  [L=864]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   6.3e-175  582.8   0.1   1.1e-174  582.0   0.1    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    1.3e-11   44.4   4.0    1.4e-11   44.3   1.7    2.5  2  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  582.0   0.1  1.2e-178  1.1e-174       2     536 ..       8     531 ..       7     541 .. 0.93

  Alignments for each domain:
  == domain 1  score: 582.0 bits;  conditional E-value: 1.2e-178
                                    HHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS CS
                   tRNA-synt_2c   2 irekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGktar 81 
                                    +r++Fld+F++k H+vv sssv+p +d+tllf+n+gm+qfk+ +lg++  ++l+ra++ Q+ciRagGkhnDl++VGk+++
  gene276|gene276|rna276|rna276   8 LRRSFLDYFTSKSHKVVSSSSVIPYEDDTLLFTNSGMVQFKKNLLGER--NDLRRACSVQRCIRAGGKHNDLDDVGKDTY 85 
                                    79********************************************99..99**************************** PP

                                    --SEEEEEEEEESSSS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH.HHHHHHHHTTTTEGGGEEEE-HHHHEEESS CS
                   tRNA-synt_2c  82 HhTfFeMlGnfsfgdYfkeeaiefawelltkelgldkerlyvtvfeedd.eaveiweklvgvpeerilrfgekdnfwemg 160
                                    HhT+FeM+Gn+sfgdYfkeeai fawe+l   l+l+k++lyvt++ e d e ++iw k+  +p++ri++ + kdnfwemg
  gene276|gene276|rna276|rna276  86 HHTYFEMMGNWSFGDYFKEEAIGFAWEFLVGILKLSKDKLYVTYYDELDkESRRIWLKY--LPSNRIIPASYKDNFWEMG 163
                                    *********************************************88666*********..7****************** PP

                                    SSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHHHHHHHTTHSS CS
                   tRNA-synt_2c 161 dtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtGmglerlvavLqevrs 240
                                    dtgpcgpc+ei+ydr   ig+r+a++ v+ dd++v+eiwn+vf+++nr+    l pL++k+idtG+glerl ++L +v+s
  gene276|gene276|rna276|rna276 164 DTGPCGPCTEIHYDR---IGNRDASELVNKDDPNVIEIWNIVFIEYNRT-ASGLVPLERKCIDTGIGLERLLSILIDVKS 239
                                    ***************...*******************************.66689************************* PP

                                    GGGSCCTHHHHHHHHHHHT--T.CSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHHHHHH.HHTT-S CS
                   tRNA-synt_2c 241 nydtdlfvpvieaieeisgaty.edkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRravrha.kkLglk 318
                                    ny  d f ++i+aie ++  +y +++++ d+a+rviaDH+r++a+ + d v +sn+g gYvlRr+lRravr+a + L+l+
  gene276|gene276|rna276|rna276 240 NYLIDSFSTIIKAIEGCCTSKYkDSEESEDVAFRVIADHCRTIAVCIHDKVDFSNDGVGYVLRRILRRAVRYAhEVLKLE 319
                                    **********************65666789*******************************************999**** PP

                                    STHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHHHHHHCHXXXH CS
                   tRNA-synt_2c 319 ekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkkkkelsgedafkLydtyGfPv 398
                                    e++l++lv + +  +g    +l+++     + +++Ee+ F kTl++G + +++ +++   ++++sged+f LydtyGfP+
  gene276|gene276|rna276|rna276 320 EGVLEELVRIAAGTIG---IDLESA-----DCVSREEALFMKTLKKGIERFNKIVEN---NDKISGEDLFLLYDTYGFPI 388
                                    **********998888...777664.....68899********************97...789***************** PP

                                    HHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEE. CS
                   tRNA-synt_2c 399 dltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallkdkefve. 477
                                    dlt+++a+e+++k+d ++fe+ ++++ e skk+k  k  i+ d++ +++++ t+++ +ye+ +++  +l  + +k +v+ 
  gene276|gene276|rna276|rna276 389 DLTELMARERNIKIDYTNFENFRQKAIEVSKKSKGMK--ISIDMDMCSKFPPTDDSSKYEKNNINVVLLFAIVGKDIVTe 466
                                    ******************************7666553..699*******************9999988888888877761 PP

                                    ..EEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESS.....EEEEESEEEEETTEEEEEXSS.XS CS
                   tRNA-synt_2c 478 ..eveegeevgvvLdrTpfYaesGGqigDeGliekeg.....aefrvkdvqkakgvvlhkgkleeg 536
                                      e+ e +evg+v+d+T+fYae GGq gD+G+i+  +     + f+v+d+q +k +v+hkg+le g
  gene276|gene276|rna276|rna276 467 psEIPEKTEVGLVFDKTCFYAECGGQVGDTGKITFYDgekitGVFNVTDTQAIKRFVVHKGTLE-G 531
                                    11566788899********************8875544456688*****************997.4 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.3   1.1e+04      19      33 ..     513     527 ..     513     528 .. 0.80
   2 !   44.3   1.7   1.6e-15   1.4e-11       1      44 []     640     686 ..     640     686 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.3
                                    -SBGGGC-SEEEECC CS
                       tRNA_SAD  19 vpnTgeIgafkilse 33 
                                    v  T  I+ f++ ++
  gene276|gene276|rna276|rna276 513 VTDTQAIKRFVVHKG 527
                                    667999****98665 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 1.6e-15
                                    EEEEEETT....EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                       tRNA_SAD   1 vrvvsiGd...isvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                    vrv+++ +   +  e+CgGtHv n+++Ig f+i++e +++++ rRI+
  gene276|gene276|rna276|rna276 640 VRVITMKNdglVIEEMCGGTHVTNVSDIGRFRIINETGVSANTRRIV 686
                                    89****65477777********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (864 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 4922.17
//
Query:       gene277|gene277|rna277|rna277  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-06   27.6   1.1    4.6e-06   27.0   1.1    1.2  1  TFIID_20kDa    Transcription initiation factor TFIID subunit 
    1.3e-05   25.3   0.0    1.4e-05   25.1   0.0    1.1  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
    0.00047   20.3   0.1    0.00055   20.0   0.1    1.2  1  CENP-T_C       Centromere kinetochore component CENP-T histon
     0.0014   18.5   0.0     0.0022   17.9   0.0    1.3  1  TFIID_30kDa    Transcription initiation factor TFIID 23-30kDa
     0.0042   17.3   0.1     0.0059   16.9   0.1    1.2  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.017   15.2   0.3    1.2  1  FANCI_S1-cap   FANCI solenoid 1 cap
      0.034   14.5   0.0      0.047   14.0   0.0    1.2  1  Histone        Core histone H2A/H2B/H3/H4
      0.047   13.7   0.1      0.069   13.2   0.1    1.3  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu


Domain annotation for each model (and alignments):
>> TFIID_20kDa  Transcription initiation factor TFIID subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   1.1     2e-09   4.6e-06      15      67 ..      18      70 ..      14      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2e-09
                                   S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHHS- CS
                    TFIID_20kDa 15 etkldedvedlLleiaddFvesvtkfacklakhRksdklevrDiqlhlernyn 67
                                   ++k+d++v   L  + + F ++++++++ l kh+  +++++ Di++ +e++++
  gene277|gene277|rna277|rna277 18 NKKIDKEVMRNLQLLTEKFLSDIIHRSALLCKHKGKSVVDSSDIRFVIEKDFD 70
                                   789***********************************************985 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   6.4e-09   1.4e-05      22      79 ..      20      85 ..      11     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 6.4e-09
                    TFIID-31kDa 22 eyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqsrlekqfkep........p 79
                                   +++++V+  L  ++ ++ s++++ + +l +h++k+ v+ +d+r+ i++ ++++f +         p
  gene277|gene277|rna277|rna277 20 KIDKEVMRNLQLLTEKFLSDIIHRSALLCKHKGKSVVDSSDIRFVIEKDFDYSFGGReiqgstalP 85
                                   67899*************************************************887555555554 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.4e-07   0.00055      27      76 ..      18      67 ..      11      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.4e-07
                       CENP-T_C 27 kaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkr 76
                                   ++k++ke +  l+  ++kf++ + +  +   kH g+  +d+sD+   + +
  gene277|gene277|rna277|rna277 18 NKKIDKEVMRNLQLLTEKFLSDIIHRSALLCKHKGKSVVDSSDIRFVIEK 67
                                   689****************************************9988766 PP

>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.8e-07    0.0022      21      49 ..      22      50 ..      13      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.8e-07
                    TFIID_30kDa 21 DprlarlvsLaaqKFisdiaadAyqyski 49
                                   D+++ r + L ++KF+sdi++ +   +k 
  gene277|gene277|rna277|rna277 22 DKEVMRNLQLLTEKFLSDIIHRSALLCKH 50
                                   999*****************999888886 PP

>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.6e-06    0.0059      13      64 ..      15      64 ..      11      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.6e-06
                                   HCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                  CBFD_NFYB_HMF 13 ksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                   +    ++ki k++   ++  +e f++++  ++a +ck++++  +   +i+ +
  gene277|gene277|rna277|rna277 15 RLC--NKKIDKEVMRNLQLLTEKFLSDIIHRSALLCKHKGKSVVDSSDIRFV 64
                                   555..789*****************************************976 PP

>> FANCI_S1-cap  FANCI solenoid 1 cap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.3   7.7e-06     0.017       4      44 ..      12      52 ..      10      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.7e-06
                   FANCI_S1-cap  4 kIlsLaaedsteeLqkfLqtLkedeLtelitnsAlKGkevG 44
                                   k l L +++  +e  + Lq L+e+ L+++i +sAl  k  G
  gene277|gene277|rna277|rna277 12 KLLRLCNKKIDKEVMRNLQLLTEKFLSDIIHRSALLCKHKG 52
                                   8899999999*************************666554 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.1e-05     0.047      81     128 ..      18      65 ..      11      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                    SXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHH CS
                        Histone  81 dlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlAr 128
                                    +++i++e +  lq ++E +l ++  +++ll+kh  ++ + + Di++++
  gene277|gene277|rna277|rna277  18 NKKIDKEVMRNLQLLTEKFLSDIIHRSALLCKHKGKSVVDSSDIRFVI 65 
                                    57899***************************************9987 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.1e-05     0.069      26      67 ..      27      68 ..      11      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXXXX CS
                    TFIID-18kDa 26 qlledlvrgyliellqqaakvaklrgsrkitlEDllfliRkD 67
                                     l+ l +++l ++++++a + k++g+ ++   D+ f+i kD
  gene277|gene277|rna277|rna277 27 RNLQLLTEKFLSDIIHRSALLCKHKGKSVVDSSDIRFVIEKD 68
                                   556778899********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 672.57
//
Query:       gene278|gene278|rna278|rna278  [L=376]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.8   0.6      0.059   13.6   0.6    1.6  1  DUF4362   Domain of unknown function (DUF4362)
      0.041   13.5   1.1       0.88    9.2   0.3    2.4  2  Rpn9_C    Rpn9 C-terminal helix
      0.098   12.6   0.1        0.6   10.0   0.1    2.2  1  Utp13     Utp13 specific WD40 associated domain


Domain annotation for each model (and alignments):
>> DUF4362  Domain of unknown function (DUF4362)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6   9.9e-06     0.059      26      72 ..      20      68 ..       3      88 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.9e-06
                        DUF4362 26 qkkkdkirivsyTeeGdpiledleyd..gkklkyilDnrrDe.fasdekd 72
                                   +k kd+i+ ++yT+e d i+e l  d  +++l ++ D+  De f +   +
  gene278|gene278|rna278|rna278 20 AKMKDRIQEIKYTDEMDYIVEGLDNDeiDESLRLVIDSITDErFKT-YMK 68
                                   4567*******************999555899*****999973443.333 PP

>> Rpn9_C  Rpn9 C-terminal helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3   0.00015      0.88       6      14 ..      18      26 ..      16      28 .. 0.89
   2 ?    2.7   0.0     0.017        99      10      19 ..     175     184 ..     172     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                                   HHHHHHHHH CS
                         Rpn9_C  6 QInkMKdrL 14
                                   QI kMKdr+
  gene278|gene278|rna278|rna278 18 QIAKMKDRI 26
                                   ********8 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.017
                                    HHHHHHHHHH CS
                         Rpn9_C  10 MKdrLVeWde 19 
                                    M  r+V W+e
  gene278|gene278|rna278|rna278 175 MSKRIVKWNE 184
                                    889******8 PP

>> Utp13  Utp13 specific WD40 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1    0.0001       0.6      22      83 ..       5      65 ..       2     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                                   HSSSTHHHHHHHHHHHS-SS--STSSSSSHHHHHHHHC--HHHHHHHHHHHHHHHTSTTTHH CS
                          Utp13 22 kldqpkrllkllkevleseeeeeesitgskevdevlkslskeqleklLkyirdWntnartse 83
                                    +++  +l+ l +++++++ ++ ++i+  +e+d +++ l+++++ + L+ + d  t +r+ +
  gene278|gene278|rna278|rna278  5 GMQNMAKLFPLHSQIAKMK-DRIQEIKYTDEMDYIVEGLDNDEIDESLRLVIDSITDERFKT 65
                                   5677788888889998665.57888888889*************999999999999888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2341.88
//
Query:       gene279|gene279|rna279|rna279  [L=424]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-30  104.0   1.3    1.2e-29  103.3   1.3    1.4  1  DEAD          DEAD/DEAH box helicase
    5.3e-26   91.2   0.1      4e-25   88.3   0.0    2.4  3  Helicase_C    Helicase conserved C-terminal domain
    5.1e-05   23.3   0.0    0.00011   22.3   0.0    1.5  1  ResIII        Type III restriction enzyme, res subunit
     0.0031   17.7   0.1      0.039   14.1   0.2    2.5  2  Helicase_C_2  Helicase C-terminal domain
     0.0062   16.9   0.2      0.014   15.7   0.2    1.7  1  AAA_19        AAA domain
     0.0085   15.8   0.2      0.015   15.0   0.2    1.4  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.085   12.8   0.0       0.15   12.0   0.0    1.3  1  Flavi_DEAD    Flavivirus DEAD domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   1.3   4.9e-33   1.2e-29       3     175 ..      76     232 ..      74     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 4.9e-33
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                    iQ++aip+il+g++v+v+ + G+GKT a+   +l +    +  +g++al+v+PtreL  q+ + ++ + k ++++v + +
  gene279|gene279|rna279|rna279  76 IQKSAIPHILRGHNVVVQSKSGTGKTIAYTCGILGNT---RAGEGTQALVVTPTRELSTQVTEVISGLAKSLGMKVFSAL 152
                                    9*********************************666...789999***************************9998887 PP

                                    TTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTSTTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  83 ggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqitcdgklqrq 161
                                    +++a+    s++    +ivvg pg +++l++ gkln +++r++VlDEad lld+  ++ +  ril+ +       +   q
  gene279|gene279|rna279|rna279 153 KNKAT---DSVM---GEIVVGSPGTILKLIDLGKLNHKEIRTIVLDEADILLDKdMMGTQTFRILKLV-------S-GAQ 218
                                    77666...4555...678************************************88899999999999.......3.345 PP

                                    EEEEESSBSHHHHH CS
                                    xxxxxxxxxxxxxx RF
                           DEAD 162 vivlSATlpkdvkk 175
                                    ++++SAT +++vk+
  gene279|gene279|rna279|rna279 219 IVFFSATYSEQVKQ 232
                                    *********99986 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.9   2.3e+03       6      35 ..     105     137 ..     100     161 .. 0.65
   2 ?   -0.9   0.0       0.8     2e+03      14      58 ..     214     270 ..     206     279 .. 0.56
   3 !   88.3   0.0   1.6e-28     4e-25       6     111 .]     271     380 ..     265     380 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.9
                                    HHHHH..HHTTTTSEEEEEESSHHHHHH.HHHH CS
                     Helicase_C   6 llell..kleeeggkilifvntidrlek.vkll 35 
                                     + +l  ++  eg ++l++++t++   + ++++
  gene279|gene279|rna279|rna279 105 TCGILgnTRAGEGTQALVVTPTRELSTQvTEVI 137
                                    555556666778999999999999443333333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.8
                                    TTTSEEEEEESSHH.HHHH.........HHHHHHHT..TSTEEEESTTSTHHHHHHH CS
                     Helicase_C  14 eeggkilifvntid.rlek.........vklllekk..gikvavlhgelpqnereei 58 
                                    ++g +i+ f+ t + ++++         +k+ +e++    ++  ++ el+ ++++++
  gene279|gene279|rna279|rna279 214 VSGAQIVFFSATYSeQVKQtiefyapdaIKMYEERNgkPDEIKLFYIELEGDNKRKA 270
                                    578888888888885443343334444455556666542344445555555555555 PP

  == domain 3  score: 88.3 bits;  conditional E-value: 1.6e-28
                                    HHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                     Helicase_C   6 llellkleeeggkilifvntidrlekvklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                    l+ l+ +  + ++++ifv ++ ++   ++l++k      +v +lhg+l+ +ere+++e+f++ +s++L++tdv +rG+di
  gene279|gene279|rna279|rna279 271 LKSLY-EYLSISQMIIFVSSKATV---NYLRKKLeddLHSVSCLHGDLEIEERERAVEEFRSSKSKILLTTDVFSRGMDI 346
                                    44443.555899************...6663333444799**************************************** PP

                                    TTESEEEESSSS.....SSHHHHHHHHTTSSSTT CS
                     Helicase_C  83 pkvnlVinfdlp.....rnvtsyiqriGRtgRag 111
                                    p+vnl++n+dlp      ++++yi+riGR gR+g
  gene279|gene279|rna279|rna279 347 PQVNLIVNYDLPiykgiASTQTYIHRIGRSGRFG 380
                                    *************9999999************86 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   4.2e-08   0.00011      23     169 ..      86     226 ..      58     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.2e-08
                                    TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                         ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                                    r ++++++   GtGKT+ ++  i   +++g+  ++l++ p+++l  q  e ++ ++++     +k++s  k+ka   ds 
  gene279|gene279|rna279|rna279  86 RGHNVVVQSKSGTGKTIAYTCGILGNTRAGEGTQALVVTPTRELSTQVTEVISGLAKSL---GMKVFSALKNKA--TDSV 160
                                    5678999************98888888999999*****************999999988...677788888887..8889 PP

                                    .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T....TTHHHHHT---SEEEEEESS- CS
                         ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk....swreilekfkeavllglTATp 169
                                      +i+v +  ++ + +     +  +l ++++  i+ DEa  l +k+    +  +il+ ++ a ++ ++AT 
  gene279|gene279|rna279|rna279 161 MGEIVVGSPGTILKLI-----DLGKLNHKEIRTIVLDEADILLDKDmmgtQTFRILKLVSGAQIVFFSATY 226
                                    9***************.....77888889999********999974555477778999999********97 PP

>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.34   8.7e+02      11      58 ..     119     166 ..     113     182 .. 0.83
   2 !   14.1   0.2   1.5e-05     0.039      10      84 ..     281     350 ..     208     361 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.34
                   Helicase_C_2  11 gvlvffpSyklleevverlkeeleskkieifveekeesrekvleeyke 58 
                                    ++lv++p  +l ++v+e+++   +s ++++f   k++ +++v+ e+  
  gene279|gene279|rna279|rna279 119 QALVVTPTRELSTQVTEVISGLAKSLGMKVFSALKNKATDSVMGEIVV 166
                                    67999999999********999999999***99899999999887665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.5e-05
                   Helicase_C_2  10 ggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfsddl 84 
                                     ++++f++S ++++ ++++l++ l+s +    +  + e+re+ +ee+++  +k +ill +    +s G+d+++ +
  gene279|gene279|rna279|rna279 281 SQMIIFVSSKATVNYLRKKLEDDLHSVSCLHGDL-EIEERERAVEEFRS--SKSKILLTTD--VFSRGMDIPQVN 350
                                    689********************97555444443.899***********..*********9..9******98654 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   5.5e-06     0.014       1      75 [.      77     152 ..      77     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae..atTiHrl 75 
                                    q++a+   l+ ++++v    GtGKT   ++ +    ++g  +  + l+v++t+    +++e +++l ++   + + +l
  gene279|gene279|rna279|rna279  77 QKSAIPhILRGHNVVVQSKSGTGKTIAYTCGILGNTRAG--EGTQALVVTPTRELSTQVTEVISGLAKSlgMKVFSAL 152
                                    788886699999************977776666666666..559*****************99777666653333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   5.9e-06     0.015       6     104 ..      77     202 ..      74     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.9e-06
                         AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalk..alreaweaaggrviglAptgkaAkvLaeelgieastia.kllkrlk. 81 
                                    Q++a+ ++l +++  +v++   GtGKt a +   l ++ + +g + ++++pt + + +++e +   a+++  k+ ++lk 
  gene279|gene279|rna279|rna279  77 QKSAIPHILRGHN--VVVQSKSGTGKTIAYTcgILGNTRAGEGTQALVVTPTRELSTQVTEVISGLAKSLGmKVFSALKn 154
                                    99*******9997..9***********8765214566666669***************9985554333322022222223 PP

                         AAA_30  82 ........................grarlepgtllivDEagmv.dtkq 104
                                                            g+ + ++ + ++ DEa  + d ++
  gene279|gene279|rna279|rna279 155 katdsvmgeivvgspgtilklidlGKLNHKEIRTIVLDEADILlDKDM 202
                                    346667777779999999999987544455559999999987633333 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     6e-05      0.15       6     135 ..      89     225 ..      85     232 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                                    EEEEE--TTS-TTTTHHHHHHHHH.HHTT--EEEEESSHHHHHHHHHHTTTS-EEE--...-----------SEEEEEHH CS
                     Flavi_DEAD   6 ltvldlhPGaGktrkvlpelvkea.ierrlrtlvLaPtrvvlaemeealkglevrykt...savkeektgrelvdvmcha 81 
                                      v++ + G+Gkt  +   ++ ++ + +  ++lv++Ptr   + ++e ++gl  +      sa+k+++t+  + +++  +
  gene279|gene279|rna279|rna279  89 NVVVQSKSGTGKTIAYTCGILGNTrAGEGTQALVVTPTRELSTQVTEVISGLAKSLGMkvfSALKNKATDSVMGEIVVGS 168
                                    56899999********99999765267899*********99988888888765444330113344444444333343333 PP

                                    ..H.HHHHHHHT------SEEEEETTT--.SHHHHHHHHHHHHHHHTTS-EEEEEESS CS
                     Flavi_DEAD  82 ..t.ftkrllspvrkknyeliimDeahfl.DPasiaarGyletkaeegeaalilltat 135
                                      t +    l + ++k+   i++Dea  l D   + ++ +   k  +g a++++++at
  gene279|gene279|rna279|rna279 169 pgTiLKLIDLGKLNHKEIRTIVLDEADILlDKDMMGTQTFRILKLVSG-AQIVFFSAT 225
                                    003033344557777888899999998641555555554444444433.667777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2636.42
//
Query:       gene28|gene28|rna28|rna28  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-34  118.7   0.9    1.8e-34  118.4   0.9    1.1  1  Med6      MED6 mediator sub complex component
  ------ inclusion threshold ------
       0.09   12.5   0.0        4.1    7.2   0.0    2.1  2  G2F       G2F domain


Domain annotation for each model (and alignments):
>> Med6  MED6 mediator sub complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4   0.9     2e-38   1.8e-34       1     132 [.       8     139 ..       8     140 .. 0.95

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2e-38
                       Med6   1 iqwkspewlqalgLtennvldYFaespFydktsnNevlkmqrqfnqaaeealLkkmkGleyvla.hvqepdlfvirkqerksat 83 
                                i++ ++++l++  L+++n+l+YF+ spFydk++nNe+lkmq+qf+   ++++L++m G+ y +  +++e +lfvirk   + + 
  gene28|gene28|rna28|rna28   8 ISFFDQRFLSSKSLDTTNILEYFSGSPFYDKSCNNEILKMQTQFRGLDQKSKLSSMIGIFYEVEsSNNERTLFVIRKAYNHGD- 90 
                                68999**********************************************************9556778********97665. PP

                       Med6  84 evtvlaaYyiiggniYqapslysvvqsrllsalsslskalkelsslakf 132
                                ++++l +Yy+i+g++Y ap+ ys+ + r+  ++  l+++++++ + ++f
  gene28|gene28|rna28|rna28  91 TTETLGMYYVIHGHVYAAPTNYSIYRCRMGDSMWLLNSFIEKMMEKRRF 139
                                899****************************************999888 PP

>> G2F  G2F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00045       4.1      93     118 ..      41      66 ..      38      79 .. 0.85
   2 ?    3.7   0.0    0.0054        48      95     130 ..      78     113 ..      66     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00045
                                SSS-EEEEEEEEEE-TTS-EEEEEEE CS
                        G2F  93 tgekltitqefeGldeedqLkvdtei 118
                                ++e l+++ +f+Gld++ +L+  + i
  gene28|gene28|rna28|rna28  41 NNEILKMQTQFRGLDQKSKLSSMIGI 66 
                                6899***************9987655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0054
                                S-EEEEEEEEEE-TTS-EEEEEEEEEEE----TT-E CS
                        G2F  95 ekltitqefeGldeedqLkvdteieGevpeipagak 130
                                  + i++ ++  d  ++L +  +i+G+v + p++ +
  gene28|gene28|rna28|rna28  78 TLFVIRKAYNHGDTTETLGMYYVIHGHVYAAPTNYS 113
                                446789999999****************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1174.33
//
Query:       gene280|gene280|rna280|rna280  [L=705]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-14   52.9   1.1      0.026   15.4   0.0    6.2  6  WD40         WD domain, G-beta repeat
    2.1e-06   27.9   0.2       0.37   11.1   0.0    4.8  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    1.4e-05   24.5   1.2     0.0048   16.2   0.1    2.8  3  NUP214       Nucleoporin or Nuclear pore complex subunit NUP2
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.34   11.0   0.1    1.7  1  Kazal_1      Kazal-type serine protease inhibitor domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.94   4.2e+03      13      34 ..      64      83 ..      57      86 .. 0.67
   2 !   10.1   0.0   0.00026       1.2       4      38 .]      90     123 ..      87     123 .. 0.79
   3 !   14.3   0.1   1.3e-05     0.058       6      38 .]     132     163 ..     127     163 .. 0.80
   4 ?   -1.5   0.0       1.3   5.8e+03      23      38 .]     383     396 ..     369     396 .. 0.65
   5 !    5.2   0.0    0.0093        42       4      38 .]     402     436 ..     399     436 .. 0.84
   6 !   15.4   0.0   5.8e-06     0.026       3      37 ..     441     477 ..     439     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.94
                                   EEEEEEETTSSEEEEEETTSEE CS
                           WD40 13 vtslafspdgawlasGsdDgtv 34
                                   +ts+  + + ++l+ G ++g v
  gene280|gene280|rna280|rna280 64 ITSF--DFSDDLLVIGYENGAV 83
                                   6766..5556666668777766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00026
                                    EEEEESSSS....EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   4 lrtltGHss....vtslafspdgawlasGsdDgtvriWd 38 
                                    + +++ Hs     +t +     g++++s+s Dg++ ++d
  gene280|gene280|rna280|rna280  90 IISFRPHSRrvtkITKI-----GDYILSSSADGSIILYD 123
                                    56788994475556666.....*******99*****998 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1.3e-05
                                    EEESSSSEEEEE.EETTSSEEEEE.ETTSEEEEEE CS
                           WD40   6 tltGHssvtsla.fspdgawlasG.sdDgtvriWd 38 
                                    +++G  ++ ++  f +d++ ++ G + D+t+riWd
  gene280|gene280|rna280|rna280 132 SYEGN-DI-CVEgFFSDSKIVV-GvCADNTLRIWD 163
                                    46777.78.8888899999987.6666*******9 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.3
                                    SEEEEEETTSEEEEEE CS
                           WD40  23 awlasGsdDgtvriWd 38 
                                      l+ G  D+t+ ++d
  gene280|gene280|rna280|rna280 383 E-LIIGK-DNTILFYD 396
                                    3.44477.****9998 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0093
                                    EEEEESSSSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   4 lrtltGHssvtslafspdgawlasGsdDgtvriWd 38 
                                    l+tl+  ss++s+  s+dg++l+ G  + +v+i++
  gene280|gene280|rna280|rna280 402 LKTLDVESSISSIEISKDGSLLCVGLLNSKVHIYN 436
                                    666766678*************9997799999987 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 5.8e-06
                                    EEEE.EESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   3 clrt.ltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                    cl++ l GH  +v+s++ s d++ +++++ D+tv++W
  gene280|gene280|rna280|rna280 441 CLKVaLYGHaLPVRSMKLSLDNSEILTCGADKTVKMW 477
                                    5666578**777*****8888888888888******* PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0021       9.2      38      68 ..      61      89 ..      46     107 .. 0.74
   2 ?    0.2   0.0      0.21   9.2e+02      50      77 ..     107     134 ..      89     143 .. 0.84
   3 ?    3.0   0.0     0.029   1.3e+02      48      73 ..     145     170 ..     132     183 .. 0.82
   4 !   11.1   0.0   8.3e-05      0.37      27      67 ..     399     437 ..     384     457 .. 0.84
   5 ?   -1.6   0.0      0.77   3.4e+03      38      81 ..     450     493 ..     441     499 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                    ANAPC4_WD40 38 dsevrsLaWkpdgklLavaysdgevrlldae 68
                                   +++++s+ +  ++ lL+++y++g+v++++ e
  gene280|gene280|rna280|rna280 61 KKKITSFDF--SDDLLVIGYENGAVQIHSEE 89
                                   556666555..577*************8865 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.21
                    ANAPC4_WD40  50 gklLavaysdgevrlldaesgkvvhsls 77 
                                    g  +  + +dg++ l+d+  g+v  s++
  gene280|gene280|rna280|rna280 107 GDYILSSSADGSIILYDIIGGEVRVSYE 134
                                    777888999*********9999987765 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.029
                    ANAPC4_WD40  48 pdgklLavaysdgevrlldaesgkvv 73 
                                     d k+ + +++d+++r+ d e++++ 
  gene280|gene280|rna280|rna280 145 SDSKIVVGVCADNTLRIWDFEDKHIK 170
                                    577888999***********998764 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 8.3e-05
                    ANAPC4_WD40  27 qrvwtleedkedsevrsLaWkpdgklLavaysdgevrllda 67 
                                     +v ++   + +s+++s++ ++dg+lL+v+  +++v+++++
  gene280|gene280|rna280|rna280 399 YKVLKT--LDVESSISSIEISKDGSLLCVGLLNSKVHIYNM 437
                                    455555..577899************************986 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 0.77
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvkse 81 
                                       vrs++ + d++ +    +d +v++   + g++ +s+  +s+
  gene280|gene280|rna280|rna280 450 ALPVRSMKLSLDNSEILTCGADKTVKMWGTQFGECRKSFIGDSK 493
                                    56799999999999999999999999999999999998866655 PP

>> NUP214  Nucleoporin or Nuclear pore complex subunit NUP214=Nup159
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0016       7.3     119     166 ..      36      87 ..      21     106 .. 0.83
   2 !   16.2   0.1   1.1e-06    0.0048      32     137 ..     145     254 ..     140     278 .. 0.75
   3 ?   -1.3   0.1      0.22   9.9e+02      82     157 ..     428     506 ..     368     578 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0016
                                    EEETTSEEEEEETT........EEEECSEEEEEE-SSEEEEEETTS-EEEEE CS
                         NUP214 119 lldsnnqLsaldlskkel....kslaenvasfDvledkLvvllkdksvqvfe 166
                                     ++  +qL++++++ +e+     +l+++++sfD  +d Lv+  ++  vq+++
  gene280|gene280|rna280|rna280  36 YISVGKQLNGWNIRFSEIersiPTLKKKITSFDFSDDLLVIGYENGAVQIHS 87 
                                    5677789999999988776655789****************99999999875 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.1e-06
                                    ETTEEEEEEHHHHHHHHHS...SS-----SEEEE-TTEEEEEEETTE.EEEEESSEEEEEESSSTT.EEEEEE-SS-EE. CS
                         NUP214  32 sGekvviGdlqkLrdvits..edkaelefkwekeikdviavkflndevvlvstksellsldleelseleeihklekdlve 109
                                    s +k+v+G   +    i +  +++++  +++ek ikdv av   +de v+  +++e + +dle+ ++ +   k++ +l +
  gene280|gene280|rna280|rna280 145 SDSKIVVGVCADNTLRIWDfeDKHIKSLHMFEKPIKDVFAV---GDEAVIFFKDGECIYYDLED-KTSRPFNKFK-KLRN 219
                                    667888888766555555543667778889********998...7999****************.4447777786.5888 PP

                                    .EEETTEEEEEETTSEEEEEETT............E CS
                         NUP214 110 lkllkstlllldsnnqLsaldlskkel........k 137
                                    +k+ ++++ +l+++++L+++++s+++          
  gene280|gene280|rna280|rna280 220 IKIKEDKV-FLQNKSKLHIYEISRRDRiilkhqetV 254
                                    99999886.5788999******98776343333333 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.22
                                    ESSEEEEEESSSTT...EEEEEE-SS-EE..EEETTEEEEEETTSEEEEEETT.....EEEECSEEEEEE-SSEEEEEE CS
                         NUP214  82 tksellsldleels..eleeihklekdlvelkllkstlllldsnnqLsaldlskkel.kslaenvasfDvledkLvvll 157
                                     +s+++ ++++ l        h l ++ ++l+l +s++l   ++++++++  +  e  ks+  +  s++ l++ L ++ 
  gene280|gene280|rna280|rna280 428 LNSKVHIYNMDGLClkVALYGHALPVRSMKLSLDNSEILTCGADKTVKMWGTQFGECrKSFIGDSKSVEYLNKDLFMFA 506
                                    2333444444444410222333344444444445556666666666665555554545555555566666655555554 PP

>> Kazal_1  Kazal-type serine protease inhibitor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   7.6e-05      0.34      16      49 .]     303     339 ..     301     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.6e-05
                                    EEETTSEEESSHHHH....HHHHHTTSSS--EEECS-- CS
                        Kazal_1  16 vCGtDgkTYsneCll....CaengkkgtklqlehdGeC 49 
                                    vCG  g+T+s eC++     ++++k+  ++q+ ++G+C
  gene280|gene280|rna280|rna280 303 VCGEKGITFSKECIMfwmlDKKTMKRIGSIQI-RNGKC 339
                                    9************9987655555677777776.35666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (705 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 4525.38
//
Query:       gene281|gene281|rna281|rna281  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-10   38.9   1.3    9.9e-10   38.6   1.3    1.1  1  DUF2463   Protein of unknown function (DUF2463)
  ------ inclusion threshold ------
      0.047   13.9   4.5      0.047   13.9   4.5    1.6  2  BofA      SigmaK-factor processing regulatory protein BofA


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   1.3   1.1e-13   9.9e-10     152     208 ..      11      67 ..       1      69 [. 0.86

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.1e-13
                        DUF2463 152 yllyfaiissiliLvrllkekylpskksslptakwrvaifvliLilavliYvflale 208
                                     l yfai+s  l+L+r+lk+ky+ s k     + wr+ i+++iLi+ v+ +++ +++
  gene281|gene281|rna281|rna281  11 ILSYFAITSIALVLIRSLKQKYSQSPKHEGLYTWWRLTILTIILIIIVYGFLISVCQ 67 
                                    678*********************9999999999***********988888777765 PP

>> BofA  SigmaK-factor processing regulatory protein BofA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.39   3.5e+03       5       8 ..      20      23 ..      10      31 .. 0.50
   2 ?   13.9   4.5   5.3e-06     0.047      13      54 ..      43      84 ..      40      85 .] 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.39
                           BofA  5 llll 8 
                                   ++l+
  gene281|gene281|rna281|rna281 20 IALV 23
                                   2222 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.3e-06
                           BofA 13 lkkplkillkllinavlGlvlLflvNllgavfglhipiNlit 54
                                    ++ l il+ +li +v G+++ ++ N+l ++f+l+i++Nl +
  gene281|gene281|rna281|rna281 43 TWWRLTILTIILIIIVYGFLISVCQNALYTYFNLYIKCNLTN 84
                                   579999*********************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1028  (0.0573373); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 515.19
//
Query:       gene282|gene282|rna282|rna282  [L=391]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.34   10.9   0.0    1.6  1  2H-phosphodiest  Domain of unknown function (DUF1868)
       0.69    9.8   8.0        7.1    6.6   0.3    3.6  4  MtrG             Tetrahydromethanopterin S-methyltransferase,
          3    8.1   6.4       0.32   11.2   0.9    2.3  3  Lge1             Transcriptional regulatory protein LGE1


Domain annotation for each model (and alignments):
>> 2H-phosphodiest  Domain of unknown function (DUF1868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.6e-05      0.34      37      96 ..      78     135 ..      50     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.6e-05
                                    HHTSGGGGGEEE--GGG-EEEEEEEEETT--STTSS-TTS-TT--HHHHHHHHHHHGGG- CS
                2H-phosphodiest  37 lqaspeadklallPpsSlHmTvfegvieerrktdlWpadLpldaplqkitallaerLeqf 96 
                                    +++  e   l+ + ++S+HmT+f+  +e  +  ++ p++Lp +      +++++++L+++
  gene282|gene282|rna282|rna282  78 VNTLGEERALLKTREESFHMTMFQVCVEFFK-DGYDPNTLPWNI-FSVFDDYIKKKLDKM 135
                                    556667778888999*********9998776.788888888553.556667777777665 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.079   4.7e+02      15      30 ..     128     143 ..     124     160 .. 0.73
   2 ?    6.6   0.3    0.0012       7.1       3      27 ..     161     185 ..     159     190 .. 0.92
   3 ?   -2.9   0.1       1.1   6.6e+03      10      25 ..     276     291 ..     273     294 .. 0.64
   4 ?    5.0   0.2    0.0037        22      15      34 ..     339     358 ..     327     362 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.079
                           MtrG  15 vkkrLdeieekvefvn 30 
                                    +kk+Ld++   v+  +
  gene282|gene282|rna282|rna282 128 IKKKLDKMTSSVDVPS 143
                                    89******99998765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0012
                           MtrG   3 PsvvvdpddfnevkkrLdeieekve 27 
                                    Ps vv + + +++k+ +d+i ek++
  gene282|gene282|rna282|rna282 161 PSHVVARVELKTIKEEMDKIKEKLN 185
                                    999********************86 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                           MtrG  10 ddfnevkkrLdeieek 25 
                                    +++ne ++ L++ +e 
  gene282|gene282|rna282|rna282 276 EEINEKTEELNKANEN 291
                                    5666666667666665 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0037
                           MtrG  15 vkkrLdeieekvefvnsEia 34 
                                    + ++L +i+ek e +++E +
  gene282|gene282|rna282|rna282 339 ISSKLSDIQEKAEKTKGEEV 358
                                    889**************965 PP

>> Lge1  Transcriptional regulatory protein LGE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.59   3.5e+03       9      22 ..     170     184 ..     162     187 .. 0.49
   2 ?   11.2   0.9   5.3e-05      0.32      15      43 ..     275     303 ..     263     325 .. 0.81
   3 ?   -3.8   0.1       2.6   1.5e+04      33      41 ..     344     352 ..     339     359 .. 0.46

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.59
                           Lge1   9 lnd.estlkkieskl 22 
                                    l+  +++++ki++kl
  gene282|gene282|rna282|rna282 170 LKTiKEEMDKIKEKL 184
                                    333333444555544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.3e-05
                           Lge1  15 lkkiesklkeiesldkqleelklkvlkle 43 
                                    +++i++k++e+++++++++  +l+++ le
  gene282|gene282|rna282|rna282 275 REEINEKTEELNKANENICRKLLEKFELE 303
                                    489*******************9999886 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.6
                           Lge1  33 eelklkvlk 41 
                                    ++ + k +k
  gene282|gene282|rna282|rna282 344 SDIQEKAEK 352
                                    333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2394.07
//
Query:       gene283|gene283|rna283|rna283  [L=344]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-19   69.7   0.0    6.6e-19   68.3   0.0    1.6  1  Choline_kinase  Choline/ethanolamine kinase
    1.9e-09   37.8   0.0    4.3e-09   36.7   0.0    1.4  1  APH             Phosphotransferase enzyme family
    2.5e-05   23.7   0.0    3.9e-05   23.1   0.0    1.3  1  EcKinase        Ecdysteroid kinase
     0.0012   17.8   0.0     0.0021   17.0   0.0    1.3  1  DUF1679         Protein of unknown function (DUF1679)
     0.0079   15.6   0.0      0.016   14.6   0.0    1.4  1  Pkinase         Protein kinase domain
  ------ inclusion threshold ------
      0.086   12.4   0.0        0.2   11.2   0.0    1.6  1  RIO1            RIO1 family
       0.14   11.5   0.0       0.54    9.6   0.0    1.8  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   2.6e-22   6.6e-19      68     197 ..     123     265 ..     107     277 .. 0.72

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 2.6e-22
                                    HHHHHHHHHHHTTCHH.....TTSSSS-HHHHHHHHHHHCCS.TT..ECHHGGCCHCCCTHHHHHH.HHHTHHHHHH... CS
                 Choline_kinase  68 skkiAkklaelHslel....eseskespslwktmqkwllnkeaqtkakkekkkkqlklinledlek.elekleklle... 139
                                    +++iA +l+++H++++    + e   ++++ k++++  + ++ +   + ++ ++++k ++ +d      ++   ++    
  gene283|gene283|rna283|rna283 123 LRRIAPELRKFHDTHVegirSYEELVESMMVKCIREM-VAGSGRGDMSLSSIEEKMKRMRASDAGWcSGDDCVFWILmka 201
                                    789*************555544445556666666666.555555555555555555555555543212333333332334 PP

                                    ........CHGG-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEHHHHHHHHHHHTTEEHHHC CS
                 Choline_kinase 140 ........elespvvfcHnDlqegNillnkeekklvlIDFEYagynyrgfDlanhfiEwagdyeee 197
                                            +   + v+cHnDlq+gNil+  +++++vlIDFE+a++   + ++an f+E+ +dy+  
  gene283|gene283|rna283|rna283 202 rdrvfevpKGGFKAVMCHNDLQPGNILV--SKDEVVLIDFEFAAMGSPVIEIANLFCEAGYDYSRY 265
                                    4566655566666***************..9*******************************9875 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   1.7e-12   4.3e-09     158     209 ..     207     255 ..     179     291 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.7e-12
                                    HH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH CS
                            APH 158 allpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll 209
                                    +   g +++v +H+Dl pgN+lv   d  v  +iDfe+a +g p+ ++a l 
  gene283|gene283|rna283|rna283 207 EVPKGGFKAVMCHNDLQPGNILVS-KDEVV--LIDFEFAAMGSPVIEIANLF 255
                                    444448899***************.66777..****************9987 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.5e-08   3.9e-05     200     261 ..     199     255 ..     106     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.5e-08
                       EcKinase 200 ferllelveekeeef.nvlnHGDlwvnNimfkydeegepedvilvDFQlsrygSpalDLlyfl 261
                                    ++   +++e +++ f +v++H+Dl   Ni+++ d      +v+l+DF ++ +gSp++ ++ ++
  gene283|gene283|rna283|rna283 199 MKARDRVFEVPKGGFkAVMCHNDLQPGNILVSKD------EVVLIDFEFAAMGSPVIEIANLF 255
                                    334444555445555279*************887......89***************998876 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.2e-07    0.0021     265     315 ..     212     256 ..     194     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.2e-07
                        DUF1679 265 GikkvlvhgDlwsaNiLfseeeegklklkkviDyQlvslgnpaeDlvrlll 315
                                    G+k v++h Dl   NiL s++e        +iD+  +++g+p   ++ l++
  gene283|gene283|rna283|rna283 212 GFKAVMCHNDLQPGNILVSKDEV------VLIDFEFAAMGSPVIEIANLFC 256
                                    99******************776......79***************99997 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.4e-06     0.016     118     147 ..     216     244 ..     213     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.4e-06
                                    TEE-SS-SGGGEEEETTTEEEE-SGTTSEE CS
                        Pkinase 118 giiHrDlKpeNiLidekgelKitDFGlake 147
                                     ++H Dl p NiL++ k+e+ ++DF +a+ 
  gene283|gene283|rna283|rna283 216 VMCHNDLQPGNILVS-KDEVVLIDFEFAAM 244
                                    579************.99999*****9986 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.7e-05       0.2     125     149 ..     215     239 ..     202     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.7e-05
                                    STEEESS-STTSEEEETTEEEE--G CS
                           RIO1 125 aglvHaDLSeyNvlvdedkvviIDv 149
                                    a + H DL   N+lv++d+vv+ID+
  gene283|gene283|rna283|rna283 215 AVMCHNDLQPGNILVSKDEVVLIDF 239
                                    5678********************8 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.49   1.2e+03     121     139 ..     120     138 ..     112     139 .. 0.86
   2 ?    9.6   0.0   0.00021      0.54     137     167 ..     215     240 ..     213     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.49
                            Kdo 121 rallkavgrliaklhragv 139
                                    r+ l++++   +k+h+ +v
  gene283|gene283|rna283|rna283 120 REDLRRIAPELRKFHDTHV 138
                                    688999*********9987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00021
                            Kdo 137 agvnHadlyaknillqqeeeeeaeiwliDld 167
                                    a ++H dl + nil+ ++e     ++liD++
  gene283|gene283|rna283|rna283 215 AVMCHNDLQPGNILVSKDE-----VVLIDFE 240
                                    5689*************97.....******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2242.43
//
Query:       gene284|gene284|rna284|rna284  [L=537]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-13   49.4   4.4    8.1e-13   48.6   4.4    1.4  1  DUF1686       Protein of unknown function (DUF1686)
     0.0047   16.9   0.7      0.025   14.6   0.7    2.3  1  HTH_Mga       M protein trans-acting positive regulator (MGA)
     0.0068   16.5   0.8        0.2   11.7   0.1    3.0  3  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
  ------ inclusion threshold ------
      0.028   13.0   0.1       0.06   11.9   0.0    1.6  2  GDI           GDP dissociation inhibitor
      0.034   14.0   2.9      0.035   14.0   1.7    1.6  2  EC042_2821    EC042_2821-lke REase
      0.081   13.4   3.4        8.2    7.0   0.1    2.9  2  PhoU          PhoU domain
      0.099   12.5   1.0        1.8    8.4   0.0    2.5  2  STAT_alpha    STAT protein, all-alpha domain
       0.17   11.9   5.4       0.25   11.4   1.9    2.6  3  Laminin_II    Laminin Domain II
       0.52   10.7   8.6       0.21   11.9   1.0    3.4  4  GAT           GAT domain
       0.98    9.8   3.3        1.9    8.9   0.9    2.5  3  DUF3510       Domain of unknown function (DUF3510)
        1.2    8.2   4.6          5    6.1   4.6    1.9  1  APG17         Autophagy protein Apg17
        1.7    8.2  10.7        9.9    5.7   3.8    2.3  3  DUF4795       Domain of unknown function (DUF4795)
        2.7    8.4   9.0         13    6.2   0.1    3.5  4  BLOC1_2       Biogenesis of lysosome-related organelles compl


Domain annotation for each model (and alignments):
>> DUF1686  Protein of unknown function (DUF1686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   4.4   5.9e-16   8.1e-13       8     136 ..     345     485 ..     338     530 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 5.9e-16
                        DUF1686   8 talyvlavaGtiiyqiwvLakey...rdkgveevlreeWsvvgcmvPmlvgl...lnagvirssvysvtvag........ 73 
                                     +++v+++ G+iiy++w++ ++y   rd+g ++ ++++  v+ cm+P+++g+    ++g ir   +s  + g        
  gene284|gene284|rna284|rna284 345 YISFVISILGPIIYGVWIIWNSYrldRDNGLKGAIGRNLGVLVCMFPVMTGVvdiGKGGRIR--IDSRWMDGrnneiaga 422
                                    5799***************8888333589**********************97664455544..4444444444555557 PP

                        DUF1686  74 igivmlyvQslvkk..kmsrrqvcvvvlgnillasaclagdklllpgvedrsslvcvglvvfaal 136
                                    + i m+  Q l+++  k s  ++ vv++g i+la       k ++    d++ + ++g++++ + 
  gene284|gene284|rna284|rna284 423 MCIMMMHLQILMNEnrKTSYIELGVVAIGDIILAFSRYF--KEFIVCLPDKYDFTWIGYIMVGLG 485
                                    ************988899***************966555..445555669999999999998554 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.7   1.8e-05     0.025      12      46 ..      52      85 ..      47      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.8e-05
                        HTH_Mga 12 elLteneksltldelakeLglseltlqsdiseLne 46
                                   e++t+  k+ + d+++k+L+ s ++++++++ L+e
  gene284|gene284|rna284|rna284 52 EIVTK-IKEYSSDDICKQLDESLKKIKKILQSLRE 85
                                   78999.*************************9986 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00014       0.2      41      90 ..      44      99 ..       7     111 .. 0.81
   2 ?    0.3   0.0      0.48   6.6e+02      41      81 ..     172     208 ..     164     213 .. 0.49
   3 ?    0.3   0.0      0.47   6.4e+02      19      50 ..     276     306 ..     242     314 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                   Baculo_PEP_C 41 daietqLnalsedlksll.aeldtrldtlltnLtdalnalq.....dtlrneLtnl 90
                                   ++ie++L+++ +++k+ +  ++ ++ld++l+++++ l++l      ++++ne + +
  gene284|gene284|rna284|rna284 44 KTIEKVLEEIVTKIKEYSsDDICKQLDESLKKIKKILQSLRewansQDIKNEVDKT 99
                                   6899**********9865167999****************9999999999998876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.48
                   Baculo_PEP_C  41 daietqLnalsedlksllaeldtrldtlltnLtdalnalqd 81 
                                    d i+++Ln+  ++l ++ +e+ ++l +     +d lnalq+
  gene284|gene284|rna284|rna284 172 DIIQSSLNKGYKALLKMNKEVGSKLRK----CSDDLNALQE 208
                                    555555555555444444444444433....3344444443 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.47
                   Baculo_PEP_C  19 tnvLnairlqnvqilaqlatlldaietqLnal 50 
                                     + L +i   +  + +ql++++ +i  ++ +l
  gene284|gene284|rna284|rna284 276 ETYLRSIEGESYRL-NQLNSTIHDIRHRFANL 306
                                    44444444444444.44444444444444443 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.2     3e+03     374     410 ..      67     102 ..      42     123 .. 0.59
   2 ?   11.9   0.0   4.4e-05      0.06     152     198 ..     208     254 ..     189     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.2
                                    -SECEEEEEEEEEEEESSSSTTTSEEE-----S-SBS CS
                            GDI 374 gpieekfvkisdlyepvedgskdnifisksydatshf 410
                                    + ++e++ ki+++++++ + ++++  i + +d ts +
  gene284|gene284|rna284|rna284  67 KQLDESLKKIKKILQSLREWANSQ-DIKNEVDKTSAL 102
                                    445555555555555555555444.244555555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.4e-05
                                    TBGGGSTT--TTTSBHHHHHHHCT--HHHHHHHHHHTS--SSSGGGG CS
                            GDI 152 ddpktyedldlkkatmkevykkfdlsedtkdfiGhalalyrdddylk 198
                                    +d  t +++  +    +++y+k+++ +  +d+iG+ lal ++d+ ++
  gene284|gene284|rna284|rna284 208 EDLLTSDGFSWESLGFQDLYRKYNIISYNQDLIGKELALALNDSVIN 254
                                    678899999999*******************************8765 PP

>> EC042_2821  EC042_2821-lke REase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.7   2.5e-05     0.035      25     144 ..      31     140 ..      24     149 .. 0.84
   2 ?   -3.7   0.0       6.8   9.4e+03      30      52 ..     187     209 ..     183     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                     EC042_2821  25 deikakyskeiaek.llkfaneikelieetesdkfaigidvnlqivKkkekadlvvaidkeadakvkivkelkDpnkthp 103
                                    +ei  ++s+e +ek ++k+ +ei+  i+e++sd +  ++d +l+ +Kk+ ++  + a +++ +++v  +  lk++n+ h 
  gene284|gene284|rna284|rna284  31 EEIGRRVSYEFNEKtIEKVLEEIVTKIKEYSSDDICKQLDESLKKIKKILQSLREWANSQDIKNEVDKTSALKAINDLHR 110
                                    56788888888887356789******************************999999999999****************** PP

                     EC042_2821 104 YtykevikkvnerLkkkniklkkkkkfnsydfqlfikfyki 144
                                    + y +v+ + ++ L+           ++s+  + ++k y++
  gene284|gene284|rna284|rna284 111 WVYPQVFGCKKK-LEL----------IRSILKNMICKGYSL 140
                                    ******987666.543..........556666666666665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.8
                     EC042_2821  30 kyskeiaekllkfaneikeliee 52 
                                    k++ke+  kl k + +++ l+e+
  gene284|gene284|rna284|rna284 187 KMNKEVGSKLRKCSDDLNALQED 209
                                    77899999999999999998887 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0     0.016        22      15      77 ..      37     110 ..      24     111 .. 0.64
   2 ?    7.0   0.1     0.006       8.2       3      44 ..     169     210 ..     167     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                                    HHHHHHCT-HHHH.HHHHHH..HHHHHHHHHHHHHHHHHHH.HHHGG-SH.........HHHHHHHHHHHHHHHHH CS
                           PhoU  15 alealeekdtela.revier..ddeidrlekeierslleal.akrqplae.........dlrellsllriardlER 77 
                                    +   + ek  e + +e++ +  + + d+++k++++s l+++ ++ q+l+e         +++  +s+l++++dl R
  gene284|gene284|rna284|rna284  37 VSYEFNEKTIEKVlEEIVTKikEYSSDDICKQLDES-LKKIkKILQSLREwansqdiknEVDK-TSALKAINDLHR 110
                                    44445455444444555544789999*******999.67773669998888866655433333.678888888876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.006
                                    HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekei 44 
                                    ++++i+++ l++ ++al + ++e   ++++  d++++l++++
  gene284|gene284|rna284|rna284 169 DIKDIIQSSLNKGYKALLKMNKEVGSKLRKCSDDLNALQEDL 210
                                    6899*****************9999************98877 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.11   1.5e+02      63     171 ..      48      79 ..      20     111 .. 0.56
   2 ?    8.4   0.0    0.0013       1.8      54     101 ..     167     218 ..     122     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                     STAT_alpha  63 qmlnaLdqkRkelvdklkellnlleslqeklldeeLieWKrrQqlagiGapfnesLDqlqkwfealaeliwqlrqqlkkl 142
                                    + l++                                                                           
  gene284|gene284|rna284|rna284  48 KVLEE--------------------------------------------------------------------------- 52 
                                    33333........................................................................... PP

                     STAT_alpha 143 eelrqkl.tyeedpeltdqlpqlneqvtel 171
                                      + +k+ +y++d  +++ql++ +++++++
  gene284|gene284|rna284|rna284  53 --IVTKIkEYSSDD-ICKQLDESLKKIKKI 79 
                                    ..333332222222.333333333333322 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                     STAT_alpha  54 lkkqkellqqmlna....LdqkRkelvdklkellnlleslqeklldeeLieW 101
                                    +k  k+ +q++ln+    L ++ ke+ +kl++  + l+ lqe ll+    +W
  gene284|gene284|rna284|rna284 167 YKDIKDIIQSSLNKgykaLLKMNKEVGSKLRKCSDDLNALQEDLLTSDGFSW 218
                                    666678899999999999**************************98766666 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.9   0.00018      0.25      61     121 ..      43     102 ..      35     106 .. 0.89
   2 ?   -0.9   0.0       1.1   1.5e+03       7      39 ..     177     209 ..     171     214 .. 0.78
   3 ?   -0.5   0.0      0.83   1.1e+03      46      81 ..     288     309 ..     272     344 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                    XXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHT---EEEEES--EE CS
                     Laminin_II  61 vkkLeklapqLldklkelkqleeassslsdniseikelIaqARkaAnkikvsvsfdgdsiv 121
                                     k++ek++++++ k+ke       ++ l +++++ik++ +  R+ An+  +  + d+ s++
  gene284|gene284|rna284|rna284  43 EKTIEKVLEEIVTKIKEYSSDDICKQ-LDESLKKIKKILQSLREWANSQDIKNEVDKTSAL 102
                                    5899**********999988888866.*********************9999999988876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrs 39 
                                    + n+  k+ l+  +++  +l + +++l+ ++++
  gene284|gene284|rna284|rna284 177 SLNKGYKALLKMNKEVGSKLRKCSDDLNALQED 209
                                    556777888888889999999999999888877 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.83
                                    XXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                     Laminin_II  46 kvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                     +++              L+ ++ ++  ++ +l+ l
  gene284|gene284|rna284|rna284 288 RLNQ--------------LNSTIHDIRHRFANLESL 309
                                    3444..............444444444444444444 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   0.00015      0.21       5      62 ..      48     107 ..      44     109 .. 0.80
   2 ?   -1.3   0.0       2.1   2.9e+03      10      58 ..     129     151 ..     120     165 .. 0.55
   3 ?   -2.9   0.0       6.3   8.7e+03      55      66 ..     194     205 ..     166     213 .. 0.62
   4 ?    1.7   0.1      0.23   3.2e+02      57      76 ..     245     264 ..     223     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                            GAT   5 klLsemLsstepdeellenellkeLyetckamqpriqklieetadeed......llaelLqlND 62 
                                    k+L+e++++ ++    +++++ k+L e++k++++ +q l e   + +d      ++  l  +ND
  gene284|gene284|rna284|rna284  48 KVLEEIVTKIKE---YSSDDICKQLDESLKKIKKILQSLREWA-NSQDiknevdKTSALKAIND 107
                                    79*******994...478******************9999984.33333344448888888888 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                            GAT  10 mLsst.......epdeellenellkeLyetckamqpriqklieetadeedllaelL 58 
                                    +L+++       +                                +dee +l+e++
  gene284|gene284|rna284|rna284 129 ILKNMickgyslN--------------------------------PDEE-VLEEII 151
                                    4444443333333................................3444.444444 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.3
                            GAT  55 aelLqlNDeLnn 66 
                                     +l +++D+Ln 
  gene284|gene284|rna284|rna284 194 SKLRKCSDDLNA 205
                                    334445555554 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.23
                            GAT  57 lLqlNDeLnnvlerYerlkk 76 
                                     L lND++ nv   Y  +k+
  gene284|gene284|rna284|rna284 245 ALALNDSVINVTDVYGTFKD 264
                                    799*********99988875 PP

>> DUF3510  Domain of unknown function (DUF3510)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.9    0.0014       1.9      54     113 ..      37      94 ..      21     103 .. 0.50
   2 ?   -0.3   0.0      0.98   1.4e+03      59      95 ..     170     206 ..     119     210 .. 0.63
   3 ?   -2.7   0.0       5.2   7.2e+03      72      92 ..     319     339 ..     305     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                        DUF3510  54 lseevleewlaevleevtsrYletisevlssvkkteesLkrlkkarkgaaasanggeeas 113
                                    +s e+ e+ +++vlee++++  e  s+ +   k+ +esLk++kk  ++  + an+++ ++
  gene284|gene284|rna284|rna284  37 VSYEFNEKTIEKVLEEIVTKIKEYSSDDI--CKQLDESLKKIKKILQSLREWANSQDIKN 94 
                                    33344444444444444444444444422..56667777777766664443344444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.98
                        DUF3510  59 leewlaevleevtsrYletisevlssvkkteesLkrl 95 
                                    +++++++ l++  ++ l++ +ev s+ +k  + L+ l
  gene284|gene284|rna284|rna284 170 IKDIIQSSLNKGYKALLKMNKEVGSKLRKCSDDLNAL 206
                                    3555566666666666666666666666666666655 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.2
                        DUF3510  72 srYletisevlssvkkteesL 92 
                                     +Yl +i+ v+s++ kt e L
  gene284|gene284|rna284|rna284 319 CAYLLIIAMVISNMLKTSEKL 339
                                    578999999999999999987 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.6    0.0036         5      58     160 ..      46     192 ..      34     217 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0036
                                    IIIIIIIIIIIIII.IIIHHHHHHHHHHHHHHHHHHHHHTSS-TTS..............STGGGCS-......-TTTTH CS
                          APG17  58 irkslerklekgke.efkdlikeldaanerLektlekLrktkvepsfrpegee.......ktLlDFvd......edsvee 123
                                    i+k le+ ++k+ke   +d+ k+ld++ ++++k+l++Lr+  + +++++e  +         L+ +v       +++ e 
  gene284|gene284|rna284|rna284  46 IEKVLEEIVTKIKEySSDDICKQLDESLKKIKKILQSLREWANSQDIKNEVDKtsalkaiNDLHRWVYpqvfgcKKKLEL 125
                                    44444444433333144688999***********************9999866888988866766665333333555566 PP

                                    HHHHHHHH..............................HHHHHHHHHHHHTTHH...HHHHHHHHHHH CS
                          APG17 124 lkealkes..............................idelqaaqkkldssll.efdtdlrelkkel 160
                                    +++ lk++                               + ++++++ ++ssl+  ++  l +++ke+
  gene284|gene284|rna284|rna284 126 IRSILKNMickgyslnpdeevleeiinvigsdllkgddEKWYKDIKDIIQSSLNkGYK-ALLKMNKEV 192
                                    6666655566666666666666666666666666666655555555555555553333.444555555 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.8    0.0072       9.9      92     154 ..      25      85 ..      23      99 .. 0.77
   2 ?    5.2   9.5      0.01        14      12     170 ..      50     211 ..      42     214 .. 0.81
   3 ?   -3.6   0.0       4.9   6.8e+03       9      26 ..     289     306 ..     283     311 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0072
                        DUF4795  92 eLekmleellekle..eqeealkkaldtLqeelkekldrlelepLkeqleerlkelqkelqeame 154
                                     +e++lee+  +++   +e+ ++k+l+++     +k+ + + +++ +ql+e lk+++k lq+  e
  gene284|gene284|rna284|rna284  25 VMERILEEIGRRVSyeFNEKTIEKVLEEIV----TKIKEYSSDDICKQLDESLKKIKKILQSLRE 85 
                                    588999999888775577888888887777....9999999999999999999999988886544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                        DUF4795  12 lqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq..fDea 89 
                                    l+e ++k++e+      +  ++ k+l +  kk++ + ++++e  ++ + k+ev++  a+ka  ++L + v  +     ++
  gene284|gene284|rna284|rna284  50 LEEIVTKIKEY------SSDDICKQLDESLKKIKKILQSLREWANSQDIKNEVDKTSALKA-INDLHRWVYPQVfgCKKK 122
                                    34445555533......45677888888889999999999999999999999999999999.899999997777444566 PP

                        DUF4795  90 kkeLekmleellek...leeqeealkkaldtLqeelkekldrlelepLkeqle....erlkelqkelqeamekedk.ede 161
                                    +++++ +l+ ++ k   l+  ee l+++++ + ++l +  d++  +++k+ ++    +  k+l k+ +e  +k++k  d+
  gene284|gene284|rna284|rna284 123 LELIRSILKNMICKgysLNPDEEVLEEIINVIGSDLLKGDDEKWYKDIKDIIQsslnKGYKALLKMNKEVGSKLRKcSDD 202
                                    6778888888888888899**********************88888888887777769999*************999889 PP

                        DUF4795 162 aaglrkkLl 170
                                      +l++ Ll
  gene284|gene284|rna284|rna284 203 LNALQEDLL 211
                                    999998887 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.9
                        DUF4795   9 lkklqeaieklqeelekl 26 
                                    l++l+++i ++  + ++l
  gene284|gene284|rna284|rna284 289 LNQLNSTIHDIRHRFANL 306
                                    566666666666665554 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.8     0.015        20      23      76 ..      28      85 ..      11      95 .. 0.79
   2 ?    6.2   0.1    0.0092        13       9      50 ..     172     210 ..     164     214 .. 0.79
   3 ?   -0.7   0.0       1.3   1.8e+03      50      78 ..     279     307 ..     272     311 .. 0.45
   4 ?   -3.3   0.1       8.5   1.2e+04      21      36 ..     429     442 ..     422     448 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                        BLOC1_2 23 klLeklNeaasekykk..lkdvaaslekkleklnekye..elqpylqqidqiekqvte 76
                                   ++Le++ +++s+++++  +++v++++ +k++++++ +   +l++ l++i++i ++++e
  gene284|gene284|rna284|rna284 28 RILEEIGRRVSYEFNEktIEKVLEEIVTKIKEYSSDDIckQLDESLKKIKKILQSLRE 85
                                   5778888888888754338899999999999998876555999999999999988765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0092
                        BLOC1_2   9 kyleaeleatvedyklLeklNeaasekykklkdvaaslekkl 50 
                                    +++++ l+   + yk L k+N+++ +k  k +d ++ l+++l
  gene284|gene284|rna284|rna284 172 DIIQSSLN---KGYKALLKMNKEVGSKLRKCSDDLNALQEDL 210
                                    55555554...459*******************999998875 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.3
                        BLOC1_2  50 leklnekyeelqpylqqidqiekqvteLe 78 
                                    l  ++ ++  l+++ + i +i  + + Le
  gene284|gene284|rna284|rna284 279 LRSIEGESYRLNQLNSTIHDIRHRFANLE 307
                                    33333444444444444444444444444 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 8.5
                        BLOC1_2  21 dyklLeklNeaaseky 36 
                                    ++++L + N++  + y
  gene284|gene284|rna284|rna284 429 HLQILMNENRK--TSY 442
                                    55555555555..445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1911  (0.106587); expected 358.6 (0.02)
Passed bias filter:                     1175  (0.0655363); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.82u 0.35s 00:00:01.17 Elapsed: 00:00:00.54
# Mc/sec: 3013.22
//
Query:       gene285|gene285|rna285|rna285  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00017   21.8  38.5     0.0024   18.0  17.1    2.1  2  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0  13.4   4.2e-05      0.75       4     132 ..       7     135 ..       4     137 .. 0.79
   2 !   18.0  17.1   1.4e-07    0.0024       2     134 ..     147     281 ..     146     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.2e-05
                           EamA   4 illallaalfwaiyfvls.killrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllf 82 
                                    +l+a l  lf++i ++ls k++l+++   +   +    ++ +++ +++l++ +l +++l+++   ++ +ll tv+  +  
  gene285|gene285|rna285|rna285   7 ELMASLTYLFSSIITTLSnKYILSNLGFKMQYLLVAAQSFTIVMGLLVLRGMRLIEFKLTNFRKWMIPSLLLTVMI-FSG 85 
                                    688999999*********9999**9988855555555566666666777777775777777555555555444444.367 PP

                           EamA  83 fyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGv 132
                                     ++l +++ s  +l+ + + v++++l  +l+ ++++ +++l+++l++++ 
  gene285|gene285|rna285|rna285  86 SKSLYYLPISLYTLFKNSSIVVVALLEQYLFEKRIGALSYLSFILMIISS 135
                                    8**********************************************985 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.4e-07
                           EamA   2 lgillallaalfwaiyfvlskillrkvspl...tltfvrfliagillliiallkegkl.aklslkdwllllllgllgtvl 77 
                                    +g+ ++l+  l+  +y +  k++  ++++    + + ++ li+  +l +++ ++++k+ +++  k ++++l+ + l+ ++
  gene285|gene285|rna285|rna285 147 IGYAWILINILSTTAYVLSLKVV-VDMNSKaktESVYYSNLISLPILTFLSIFFDEKDaSVFGFKVFIWILISS-LCAFF 224
                                    68888777777666666666665.5555544659999*********************8999999999988888.56677 PP

                           EamA  78 afllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                    + +   + l+ +s++  s+i +l   +  + ++++lge ++  ++l+++l+ l+ ++
  gene285|gene285|rna285|rna285 225 TSFSTAWTLNVLSSTALSMIGALNKSLGSFAGIFVLGEIINAQKILSLLLGSLASAI 281
                                    7789**********************************************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1680.65
//
Query:       gene286|gene286|rna286|rna286  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.031   14.0   0.8      0.031   14.0   0.8    2.1  2  DUF745        Protein of unknown function (DUF745)
       0.42   10.1   4.8       0.53    9.8   4.8    1.3  1  Exonuc_VII_L  Exonuclease VII, large subunit
        2.6    8.2  11.8       0.78    9.9   7.1    2.3  2  CREPT         Cell-cycle alteration and expression-elevated p
        2.7    7.2   9.1        2.3    7.5   6.4    1.9  2  CorA          CorA-like Mg2+ transporter protein
        2.9    7.9   6.8         15    5.7   0.9    2.3  2  DUF1664       Protein of unknown function (DUF1664)


Domain annotation for each model (and alignments):
>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.8   8.6e-06     0.031     104     157 ..      43      96 ..      29     110 .. 0.82
   2 ?    1.7   0.8      0.05   1.8e+02      72     134 ..      98     161 ..      89     176 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.6e-06
                         DUF745 104 qqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlke 157
                                    +q e l ++l+++k++l++++++ ++a+++++e ++l+ +A++++ + ++ lk 
  gene286|gene286|rna286|rna286  43 RQNEDLLTILNQSKSQLKDVKSIGKEASKSISELSELIYEARNKLSRYEEMLKY 96 
                                    567788899999999999999999999999999999999999999988877764 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.05
                         DUF745  72 reaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqva.agaqqel 134
                                    +e e+ ++ee +  +s  +n+k+  +  +q  + ++ ++  +++++   e++  ++ ++a++el
  gene286|gene286|rna286|rna286  98 TEREKSLKEECTRFESLDENLKVYDELTAQFDRGCKEMQVNIEKINVLKEEIAMMStNEAEEEL 161
                                    5677777777777777777777777777777777777777777777766666665413344444 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.8   0.00015      0.53     161     255 ..      56     167 ..      18     226 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                   Exonuc_VII_L 161 krlleekkqrleklasrlkspeellerkrqrldeleerleralkkq..lkkkrerleelkerlk.............ekl 225
                                    k++l++ k+  +++++++++ +el+ ++r++l+++ee l+ +++++  lk++ +r+e+l e+lk             +++
  gene286|gene286|rna286|rna286  56 KSQLKDVKSIGKEASKSISELSELIYEARNKLSRYEEMLKYETEREksLKEECTRFESLDENLKvydeltaqfdrgcKEM 135
                                    22222222222222233333444444444444444444433322222244444444444444433332222222233112 PP

                   Exonuc_VII_L 226 eekkerlkklkerle..lleekkerleeleek 255
                                    + + e+++ lke+++  +++e++e+l++++++
  gene286|gene286|rna286|rna286 136 QVNIEKINVLKEEIAmmSTNEAEEELKSIKNR 167
                                    22222222222222222233333333333333 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.1   0.00022      0.78      32     117 ..      57     150 ..      35     155 .. 0.76
   2 ?    0.3   0.3       0.2   7.2e+02      90     113 ..     152     175 ..     147     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                          CREPT  32 sdvslleki..kdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledf......leaqkellakaeekleelk 103
                                    s+++ +++i  + +++  +l++ + ea + l+ Y + L+ e+e  k+l++  + f      l++  el a+ ++ ++e++
  gene286|gene286|rna286|rna286  57 SQLKDVKSIgkEASKSISELSELIYEARNKLSRYEEMLKYETEREKSLKEECTRFesldenLKVYDELTAQFDRGCKEMQ 136
                                    555566666433567889******************************98766661111114556678888888899999 PP

                          CREPT 104 eklekvksvrkelk 117
                                      +ek++  ++e+ 
  gene286|gene286|rna286|rna286 137 VNIEKINVLKEEIA 150
                                    99999999888875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.2
                          CREPT  90 ellakaeekleelkeklekvksvr 113
                                    ++ ++aee+l+++k++ +k+  ++
  gene286|gene286|rna286|rna286 152 MSTNEAEEELKSIKNRRDKLCGKQ 175
                                    56789999*******999987665 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   6.4   0.00064       2.3     117     230 ..      42     157 ..      22     164 .. 0.78
   2 ?    0.5   0.1     0.086   3.1e+02     172     234 ..     159     220 ..     152     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00064
                           CorA 117 deivdrlfellekleeeldeledel.edstkkeilrelaq.lrrrlvklrralapnrevlkrlla.kaddkllddedkey 193
                                    d+ +++l+++l + +++l+++ +   e s++ ++l+el++  r +l +++++l++ +e  k+l++ +++ + ld e+ + 
  gene286|gene286|rna286|rna286  42 DRQNEDLLTILNQSKSQLKDVKSIGkEASKSISELSELIYeARNKLSRYEEMLKYETEREKSLKEeCTRFESLD-ENLKV 120
                                    456666777777777777766655587778888888876648888***************99999544444444.55588 PP

                           CorA 194 lrdlldelerllemlealrerleslqdtyssllserl 230
                                    +++l  +++r  +++++  e++++l+++++ +++++ 
  gene286|gene286|rna286|rna286 121 YDELTAQFDRGCKEMQVNIEKINVLKEEIAMMSTNEA 157
                                    *****************************99998875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.086
                           CorA 172 evlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssllserlNrvm 234
                                    e lk++++ ++dkl  +++++ l ++++ +e+++++     e + +++ +   ++ +++N+  
  gene286|gene286|rna286|rna286 159 EELKSIKN-RRDKLCGKQKRPSLITMESYIENSYNWYRKALEFIKNVFGISLVTIEQENNEMY 220
                                    55655555.666777777777799999999999999999999999999999999999998865 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.6    0.0057        20      59     121 ..      29      91 ..      26      94 .. 0.91
   2 ?    5.7   0.9    0.0041        15      66     120 ..     109     164 ..      98     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0057
                        DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                    +tk  L + +   d++ ++   i ++ k+++++v++  +e ++ +++++e++ +  +kl+r e
  gene286|gene286|rna286|rna286  29 TTKTLLLQSLRPEDRQNEDLLTILNQSKSQLKDVKSIGKEASKSISELSELIYEARNKLSRYE 91 
                                    688899999999999999*******************9************9999999999877 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0041
                        DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav.egleskleri 120
                                     r +++d++l+   e++++ ++  +e++ ++++i+   e++  +  ++ e++l++i
  gene286|gene286|rna286|rna286 109 TRFESLDENLKVYDELTAQFDRGCKEMQVNIEKINVLKEEIAMMStNEAEEELKSI 164
                                    58899****************************99888888766413455666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1488  (0.082994); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1834.62
//
Query:       gene287|gene287|rna287|rna287  [L=467]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-31  107.0  26.4    1.1e-21   77.3  11.6    2.2  2  Mg_trans_NIPA  Magnesium transporter NIPA


Domain annotation for each model (and alignments):
>> Mg_trans_NIPA  Magnesium transporter NIPA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   6.8   3.2e-13   5.7e-09       3     161 ..     135     284 ..     133     293 .. 0.85
   2 !   77.3  11.6   6.1e-26   1.1e-21     169     289 ..     321     441 ..     316     447 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.2e-13
                  Mg_trans_NIPA   3 fliGvlLavssslfigssfilkkkgllrlarkgevrageGGyaylkevlWwaGlltmavGeaanfaayafaPatLvtPLG 82 
                                    +++Gv L++s+++ i   ++l+kk++++     ++r        ++   ++aG    ++G +  + +y+f   +L++ L 
  gene287|gene287|rna287|rna287 135 WIFGVFLSISGNIGINVGINLQKKSYKQS----HIRL-----FNMNLQTFYAGCFIYGLGKIFGYCSYIFGNQSLMAVLS 205
                                    589**********************9864....4555.....345667899***************************** PP

                  Mg_trans_NIPA  83 alsvivsavlasllLkekLkllgllGcllailGstvlvihaPkeeeieslkevadllvdpaflvyvilvvvvvlvlily 161
                                    a  ++  +++a ++ +e +   +   ++  ++G+t++v+ +   +++ +l e++++ +  + l++   ++ +++vl ++
  gene287|gene287|rna287|rna287 206 ATGLVSNSIFAPMINEEIFTWKDFCAIFFVFAGTTLIVMNTTTSHKVYTLCELMKMYRRVETLLWFGFIILIIVVLFVF 284
                                    ***************************************************9999999888777544333222222222 PP

  == domain 2  score: 77.3 bits;  conditional E-value: 6.1e-26
                  Mg_trans_NIPA 169 tnilvyitlcsllgsltvisvkalgiaikltlaGkaqlkyalawilllvlvicvvlqinyLnkaldifntsivtPvyyvl 248
                                    t +l y+ l s ++s+t +svk+lg +i +t+aG +q+   +++++++vlvic  +qi +Ln+al  +++ +v P+++v 
  gene287|gene287|rna287|rna287 321 TMVLAYVCLSSFIASFTTLSVKSLGEMIDKTIAGDNQFIFLTTYFFIIVLVICTFFQIYWLNRALRHYDALLVIPMFHVT 400
                                    67999*************************************************************************** PP

                  Mg_trans_NIPA 249 fttlvivasailfkefleasvddvlgelsGfllvllgvfll 289
                                    +t l i+++ i f+ef + +  ++   + G+ l+++g ++l
  gene287|gene287|rna287|rna287 401 WTLLSILTAGIYFREFEQYTSYQLGVFVGGIGLIFIGSIFL 441
                                    ********************999999999998888875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2776.71
//
Query:       gene288|gene288|rna288|rna288  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-19   67.2   3.1    8.6e-19   67.2   3.1    2.0  2  Chromo         Chromo (CHRromatin Organisation MOdifier) doma
    1.1e-13   51.1   0.4    3.6e-10   39.8   0.0    2.3  2  Chromo_shadow  Chromo shadow domain
  ------ inclusion threshold ------
      0.045   13.9   0.1      0.082   13.1   0.1    1.5  1  Mtf2_C         Polycomb-like MTF2 factor 2


Domain annotation for each model (and alignments):
>> Chromo  Chromo (CHRromatin Organisation MOdifier) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   3.1   1.4e-22   8.6e-19       1      53 [.       7      55 ..       7      56 .. 0.95
   2 ?   -1.6   0.0      0.45   2.7e+03       3      12 ..      96     105 ..      95     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.4e-22
                                   EEEEEEEEEEEETTEECEEEEEEETTSTGGGTEEEEGGGCSSHSHHHHHHHHH CS
                         Chromo  1 yeVerIidhrtdkdgleleYlVKWkglpysentWEpeenlekcfqelideFkk 53
                                   y+V++I++hr +++++  +YlVKW+g+++sentWE+e+n+ ++  +li+e+++
  gene288|gene288|rna288|rna288  7 YTVDKIVGHRRRRGTK--QYLVKWEGYSDSENTWEDEKNIFCK--KLIKEYEE 55
                                   78**************..**********************955..9*****97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.45
                                    EEEEEEEEEE CS
                         Chromo   3 VerIidhrtd 12 
                                    V+rI++++++
  gene288|gene288|rna288|rna288  96 VDRIVSVEKN 105
                                    99**998876 PP

>> Chromo_shadow  Chromo shadow domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1   0.00017         1       2      25 ..       9      32 ..       8      55 .. 0.85
   2 !   39.8   0.0     6e-14   3.6e-10       2      53 .]      92     146 ..      91     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                                   TTTTEEEEEETS-EEEEEEETTS- CS
                  Chromo_shadow  2 pekiigavdtsgelmflikWknge 25
                                   ++ki+g+  ++g   +l+kW++  
  gene288|gene288|rna288|rna288  9 VDKIVGHRRRRGTKQYLVKWEGYS 32
                                   79******************9844 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 6e-14
                                    TTTTEEEEEE...TS.-EEEEEEETTS-EEE.EEHHHHHHHSHHHHHHHHHCT-XX CS
                  Chromo_shadow   2 pekiigavdt...sg.elmflikWkngekaelvpskeanqkcPqkvikFYEerltw 53 
                                    ++++++ + +   +g  l++++ +k+g+k +  p++e++ +cP  ++++YE++l++
  gene288|gene288|rna288|rna288  92 WDELVDRIVSvekNGpILVVWLLFKDGKKDR-FPASEIHIRCPLHLLEYYESNLVF 146
                                    6666666544455999***************.**********************98 PP

>> Mtf2_C  Polycomb-like MTF2 factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.4e-05     0.082      34      47 ..      18      31 ..       4      32 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                         Mtf2_C 34 pnGkvqYLieWeGa 47
                                     G+ qYL+ WeG+
  gene288|gene288|rna288|rna288 18 RRGTKQYLVKWEGY 31
                                   47999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1408  (0.078532); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 913.14
//
Query:       gene289|gene289|rna289|rna289  [L=334]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   11.6   0.0       0.43   10.3   0.0    1.6  1  Cupin_2   Cupin domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.4e-05      0.43      23      68 ..     283     328 ..     282     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.4e-05
                                    EEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEE CS
                        Cupin_2  23 fyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparll 68 
                                    ++ ++G++ ++++  +++l++G + ++++ t   + N   + + +l
  gene289|gene289|rna289|rna289 283 IFMIKGTACIEMGQDKIILKRGSICVIEKETVYSISNSFGTGCTIL 328
                                    6899******************************999877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2172.68
//
Query:       gene29|gene29|rna29|rna29  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-51  174.1   0.0    1.6e-51  173.8   0.0    1.0  1  NifU_N    NifU-like N terminal domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.8   0.0   8.8e-56   1.6e-51       2     126 ..      14     136 ..      13     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 173.8 bits;  conditional E-value: 8.8e-56
                                SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSBHHHH CS
                     NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgktleea 85 
                                y   v+dh++nPrnvG+l+++d++vg+g vgapacGD+++Lqikv ++ ++iedakFktfGCgsaiAsssl+te++k ktl+e 
  gene29|gene29|rna29|rna29  14 YDASVVDHFENPRNVGSLDKADPRVGTGIVGAPACGDVMKLQIKVGKD-NVIEDAKFKTFGCGSAIASSSLATEWIKKKTLDES 96 
                                8999******************************************97.9********************************** PP

                                CCCCHHHHHHHHTCSCSSSCHCSCHHHHHHHHHHHHHHHHC CS
                     NifU_N  86 lkitnkeiaeelgglpkeklhcsvlaedalkaavkkYkakk 126
                                lki+n++ia++l+ lp+ klhcs+laeda+k a+k++  k+
  gene29|gene29|rna29|rna29  97 LKISNRDIAKKLS-LPPIKLHCSMLAEDAIKSAIKDFLDKN 136
                                *************.***********************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 910.56
//
Query:       gene290|gene290|rna290|rna290  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-48  165.7   0.0    1.5e-48  165.4   0.0    1.0  1  TatD_DNase  TatD related DNase


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   0.0   8.4e-53   1.5e-48       1     254 [.       3     260 ..       3     261 .. 0.93

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 8.4e-53
                                    EEEEE-TTSCCCTTT...HHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH CS
                     TatD_DNase   1 iDaHcHldskefeed...reeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel 77 
                                    iD +++++++++++d    ee+++r+++++v  +  vg+++++sk+++ la+ky+   + ++G+HP+++ +   + ++e+
  gene290|gene290|rna290|rna290   3 IDIAVNITDRLLARDegsVEEVIKRCKDSKVLPI-FVGLDHNTSKRCVSLARKYKT--VSTVGVHPTSSSR--YKNIDEI 77 
                                    8********88855555599************99.69*****************97..9*******99997..5777888 PP

                                    HHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT- CS
                     TatD_DNase  78 kelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsf 157
                                      l  ++++ vvaiGe+GLDy + e ++k  q+++F+ ql+l  ++   +++H+r++++d++e +++++    ++v+Hsf
  gene290|gene290|rna290|rna290  78 IPL--INDDVVVAIGECGLDYDRLEFADKTSQKRIFRSQLDLKGDC---YFLHSRSCHRDFMETISDYEI---RGVVHSF 149
                                    888..*************************************9888...9*****************965...67***** PP

                                    -S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEE................CCCTTSE--G CS
                     TatD_DNase 158 sgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltp................kpyrgkrnep 221
                                    +g++eeak+++k+g++i+++g++++  + e +++++++pl++lLiETD+Py++                 ++  +k+nep
  gene290|gene290|rna290|rna290 150 TGDIEEAKELIKKGLFIGVNGCSVK--TPEGIDVIRSLPLESLLIETDSPYCKIrksyagfkyvttdfggEKVLKKKNEP 227
                                    *********************9999..779************************999999999999999966778***** PP

                                    GGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                     TatD_DNase 222 anvayvveklaelkaltleelaeitaeNakrlf 254
                                    +++ +++e ++ +++ ++  + +++ eN+ rl+
  gene290|gene290|rna290|rna290 228 CCIIQMAEIISSITERDYSYVVNTLFENTIRLY 260
                                    *******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 1547.63
//
Query:       gene291|gene291|rna291|rna291  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-29  100.0   1.5    1.1e-28   99.3   0.5    1.8  2  PSP1      PSP1 C-terminal conserved region


Domain annotation for each model (and alignments):
>> PSP1  PSP1 C-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.14   2.6e+03      32      51 ..      83     102 ..      36     108 .. 0.69
   2 !   99.3   0.5   6.3e-33   1.1e-28       1      86 []     145     230 ..     145     230 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.14
                           PSP1  32 klkelnlnmklldaefqfdr 51 
                                    ++++ +l++ ++d+++++ +
  gene291|gene291|rna291|rna291  83 QFESKRLDVAFVDVNINVKK 102
                                    34455566666666666555 PP

  == domain 2  score: 99.3 bits;  conditional E-value: 6.3e-33
                           PSP1   1 kqvlrlatpedvstnlenkqdeekalhiaqeklkelnlnmklldaefqfdrkkltfyYvaeervDFreLvkeLfkfyktR 80 
                                    k+++rlat  d++ +++++  +++al++++e++   +l+m+++ +e+q+d +k+tfy+ ++ervDFreLvkeL ++yktR
  gene291|gene291|rna291|rna291 145 KRIYRLATLLDLEALERKRSMQARALEFCRERAMLGGLDMEVVGCEYQWDLNKITFYFASDERVDFRELVKELYRVYKTR 224
                                    79****************************************************************************** PP

                           PSP1  81 IwLcai 86 
                                    Iw+cai
  gene291|gene291|rna291|rna291 225 IWMCAI 230
                                    ****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1447.51
//
Query:       gene292|gene292|rna292|rna292  [L=700]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.6e-152  508.6  11.5     2e-152  508.2  11.5    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.014   15.5   1.2        1.6    8.8   0.8    2.5  2  Jagunal     Jagunal, ER re-organisation during oogenesis


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  508.2  11.5  2.3e-156    2e-152       2     487 ..     194     691 ..     193     694 .. 0.96

  Alignments for each domain:
  == domain 1  score: 508.2 bits;  conditional E-value: 2.3e-156
                                    HHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   2 adivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                     + +kt++GP G+dKm v+++g+v +TnDGatil+++ +++Paak+lv++a++qd+evGDGTt+vv++a++L+e++++li
  gene292|gene292|rna292|rna292 194 YNSIKTSFGPLGLDKMCVDSAGEVSITNDGATILQNMVVDDPAAKILVDLATQQDHEVGDGTTSVVLIAASLIEKGARLI 273
                                    5789**************************************************************************** PP

                                    HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCS.... CS
                     Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieene.... 157
                                    a+gvhp+++++gy++a++++++++k+  ++ +  +   ++L++v++ts+ssk++++e+e ++ +v+dA+k+ie+ +    
  gene292|gene292|rna292|rna292 274 ASGVHPSVVVSGYKMAFNECVQFIKKS-MSKNALNLGPKALKNVVKTSISSKVINSENEPFCGIVIDALKCIESIRenkk 352
                                    ************************544.3444447899*******************************99987667778 PP

                                    EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHH CS
                     Cpn60_TCP1 158 keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekae 237
                                    + + ++ i+++k  ggs+++s l +G++l+++++s+ m+k+++++k+l++d++L+  k+  ++++v++d+++le+++k+e
  gene292|gene292|rna292|rna292 353 NVYPIEDINILKHPGGSIKESFLYQGYALNCSLASSFMKKQIKKPKILCIDFGLQKYKNPLTVNIVVDDPNKLEDIRKKE 432
                                    88999*************************************************************************** PP

                                    HHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC....-EEEE CS
                     Cpn60_TCP1 238 ekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpee....lGtak 313
                                     +++++++++ii+sg++vv++++gidd+++++la++gi ++rr+kk+dl  +akatG+++++s++dl+  +    lG+a+
  gene292|gene292|rna292|rna292 433 LEITKKQVKAIIDSGADVVLTTRGIDDMCTKILAEAGIAGIRRCKKEDLVVIAKATGTSLINSISDLNGGDsittLGSAD 512
                                    ********************************************************************8666999***** PP

                                    EEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCT CS
                     Cpn60_TCP1 314 kveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaks 393
                                    k+e+  ig+e++++i++ +++k+a+i+lrga+ + lde++r+++dA++v+k+++e+++vvpGGG++e++l+ +l+++a +
  gene292|gene292|rna292|rna292 513 KFEVVLIGEEECIFING-LKRKMASIILRGANSQLLDEMQRSVHDAICVLKRTLESNHVVPGGGSVECALSLMLEKFAFT 591
                                    ****************9.99************************************************************ PP

                                    SXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHH......HTTXTTEEEETTTTCEEECCCCTXEEEHHHHH CS
                     Cpn60_TCP1 394 vsgeeqlaieafakALevipktLaeNaGldpievlaklraah......nkgekelgidvesgeiidlveagvvDplkvkr 467
                                    v+++e++ai+ +a++L++ipk+La+NaGld++e++a+l++++      ++++  lgidv +g+i+d +e g+++p   k+
  gene292|gene292|rna292|rna292 592 VNSKEHVAIHRYAESLLSIPKILATNAGLDSNEIVASLMSSQskeassSSSQRFLGIDVMTGKIQDNFEFGIIEPSMNKM 671
                                    ****************************************9977777745557*************************** PP

                                    HHHHHHHHHHHHHHCEEEEE CS
                     Cpn60_TCP1 468 qalksAteaastiLrideii 487
                                    ++lk+Ateaa +iLri+e+i
  gene292|gene292|rna292|rna292 672 KSLKAATEAAISILRINEVI 691
                                    *******************9 PP

>> Jagunal  Jagunal, ER re-organisation during oogenesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.8   0.00018       1.6      88     166 ..      32     108 ..      26     119 .. 0.82
   2 ?    4.2   0.0    0.0044        39      90     122 ..     174     206 ..     168     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00018
                        Jagunal  88 Sivpsllgllalkknkikllklyligtlvlgllpllygaveylkevleylkskeaseeitllqgfplvvlwyifvlial 166
                                     + ++llg+  +++  +kll+  +i+t +++l    +++++ l+ + +++ +++ ++   ll+   + ++w+  +l  +
  gene292|gene292|rna292|rna292  32 TLTLTLLGIFLVPRECMKLLSSLVIATPIFSLKCFCISLFNILTALSAFFVQGRREH--ILLRFTVISTVWFSSILDHI 108
                                    677899************************************************998..33333334556666555555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0044
                        Jagunal  90 vpsllgllalkknkikllklyligtlvlgllpl 122
                                      s+ g++a++kn   ++k+y  + + +g l l
  gene292|gene292|rna292|rna292 174 GESYSGISAVEKNAKAMMKVYNSIKTSFGPLGL 206
                                    56789****************999998886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (700 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 4247.54
//
Query:       gene293|gene293|rna293|rna293  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-11   44.5   2.7    1.7e-11   44.2   2.7    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   2.7   9.4e-16   1.7e-11       4      74 ..      10      81 ..       7      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 9.4e-16
                 Ribosomal_L31e  4 treytInihkrihgvgfkkraprAlkeikkfamkemgtp.dvridtrLnkavwakgirnvpyrirvrlsrkr 74
                                   t e+t+n+ + + +   +k+a +A+k++k+ ++k+++ +  v i ++Ln+++ ++g +++p ++rvr+++ +
  gene293|gene293|rna293|rna293 10 TVEMTVNLRRICSRLPWTKKADKAVKMLKREIQKHFKEKiGVAITSELNNFIHSRGTKKIPSKVRVRVTKES 81
                                   88***********************************65378*************************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1018  (0.0567795); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 786.28
//
Query:       gene294|gene294|rna294|rna294  [L=584]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-27   97.3   0.0    1.8e-27   96.5   0.0    1.4  1  ABC_tran      ABC transporter
    6.6e-19   68.6   7.9    9.3e-19   68.1   7.9    1.1  1  ABC_membrane  ABC transporter transmembrane region
    2.4e-06   27.2   2.1    0.00049   19.6   2.1    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00072   19.4   0.7      0.021   14.6   0.0    2.5  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0017   18.1   0.0     0.0037   17.0   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0024   17.8   0.0     0.0048   16.8   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.003   17.9   0.1      0.009   16.4   0.0    1.9  1  RNA_helicase  RNA helicase
      0.004   17.1   0.0      0.087   12.7   0.0    2.3  2  NTPase_1      NTPase
     0.0088   16.1   0.0      0.033   14.3   0.0    2.0  2  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.016   14.9   0.1       0.15   11.7   0.0    2.3  2  AAA_24        AAA domain
      0.024   15.1   5.4      0.024   15.1   1.5    2.4  2  AAA_23        AAA domain
      0.025   13.9   0.0      0.043   13.1   0.0    1.4  1  Septin        Septin
       0.03   13.7   0.0      0.053   12.9   0.0    1.3  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.052   13.9   0.0      0.093   13.1   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.061   12.4   0.0      0.096   11.7   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
      0.064   13.5   0.0       0.23   11.7   0.0    2.0  1  AAA_22        AAA domain
      0.092   12.2   0.0       0.19   11.2   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
      0.093   12.5   0.0       0.18   11.6   0.0    1.4  1  AAA_11        AAA domain
      0.096   11.5   0.0       0.16   10.7   0.0    1.4  1  PPV_E1_C      Papillomavirus helicase
      0.097   12.4   0.0       0.41   10.4   0.0    2.0  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.15   11.3   0.0       0.28   10.4   0.0    1.4  1  Zeta_toxin    Zeta toxin
       0.19   11.9   0.0       0.79    9.9   0.0    2.1  2  AAA_33        AAA domain
       0.28   10.9   1.1        3.8    7.2   0.1    2.6  2  IstB_IS21     IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.0   2.3e-30   1.8e-27       1     137 []     356     504 ..     356     504 .. 0.87

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 2.3e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ v+++l++gek+ai G+nGaGKSt+++ l++ l+  +Gei +dg ++++ +++s r+ i+++pq++++ +++ v +n 
  gene294|gene294|rna294|rna294 356 LRGVNFTLRKGEKLAIAGPNGAGKSTFINSLLRFLD-YSGEIFIDGVEMRKYTRRSIRHIIAYVPQDNCILDDT-VLKNl 433
                                    678********************************8.7*****************************9999999.88888 PP

                                    ......HHHTCHHHHHHHSTTGG........TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ......xxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ......esdeeiekalsklglke........lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                           s e+i+++ +++g +e           + +++++ +LS Gq+q ++l+ra++k++++++lDE+t+
  gene294|gene294|rna294|rna294 434 qygnkdISFEKIKEICKRYGTHEvfssleggY-LKEAGQQGCELSVGQRQYLSLMRAIIKDSPIFILDEATS 504
                                    99988855566666666666666666655532.33335688*****************************96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   7.9   1.2e-21   9.3e-19       4     246 ..      32     276 ..      28     297 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 1.2e-21
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHSS...TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   4 iillailagvlsplfplvlgrildtlldk...gdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrkl 80 
                                    i+   ++a+++++l  +v + i++ + ++   +d +      + + +++ g++ +i++++  +++  + + + ++  r++
  gene294|gene294|rna294|rna294  32 IFPIVLMATFANILYDYVPSVIIPRIAEHikaNDLSL--HMNLVYGFFFYGVLATIFEYFPIFVMALIIQDIYRDCYRDV 109
                                    5555677888888888888888888888844344444..444556677889999************************** PP

                                    HHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH.HHHHHSHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  81 fkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvggli.vmfylgwkltlvllailpliilvsa 159
                                    f   ++++   f + s+G++ sr+ + +  + +++   + +++ s + +++++i ++  +g+ ++l+ ++i + +i +++
  gene294|gene294|rna294|rna294 110 FIEYMSLEYNTFHSISPGDMESRIYRKCKAVGEAVDVVIPTLMNSTIFVLVAMIdIYRSFGPIVSLMFFVIPVSYISITV 189
                                    *********************************************99999999967778********************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 160 viakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsy 239
                                    +++++ ++++ k++ a +k+++ + ++l+++++Vk+fg ee++ ekf+ +l +  + g  +  +++++   + l + +  
  gene294|gene294|rna294|rna294 190 FLTSRRNRIRGKYNAAKDKSTKKLGDILNNYEVVKSFGLEERESEKFHASLIDRVSTGTVYSCSENIITFLQKLSSAIPH 269
                                    *************************************************************9999999999999998888 PP

                                    HHHHHHH CS
                   ABC_membrane 240 alalwfG 246
                                    + +l+++
  gene294|gene294|rna294|rna294 270 IGILYLS 276
                                    8887755 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.1   6.3e-07   0.00049      27     209 ..     369     544 ..     357     552 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.3e-07
                                    EEEEESTTSSHHHHHHHHHHHCTT.........TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  27 taivGpNGSGKsnlldAilFvLGer........sakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevs 98 
                                     ai GpNG+GKs +++++l  L  +        +++k  +++++++i +  + +++   +v   ++  +k+     +  +
  gene294|gene294|rna294|rna294 369 LAIAGPNGAGKSTFINSLLRFLDYSgeifidgvEMRKYTRRSIRHIIAYVPQDNCILDDTVLKNLQYGNKD----ISFEK 444
                                    5899*************987775441112211134444445555555554444444444444444444444....11122 PP

                                    EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                    i+   kr g+       +ev ++     l++ag +  +LS G+++   l+L+ Ai  +k +p+++lDe  +  D k  ++
  gene294|gene294|rna294|rna294 445 IKEICKRYGT-------HEVFSSLEGGYLKEAGQQGCELSVGQRQY--LSLMRAI--IKDSPIFILDEATSDVDYKTETE 513
                                    3333333333.......233333334577888888889******86..6677777..5799******************* PP

                                    HHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 179 vaellkeksknaQfivislreemlekadklv 209
                                    + +++ +  ++  +i+i +++ +l+k d+++
  gene294|gene294|rna294|rna294 514 LIDYVMSVLSDRTIIMIVHNHSLLSKFDNIL 544
                                    *************************999876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.7e-05     0.021       3      39 ..     370     411 ..     369     448 .. 0.78
   2 ?    2.5   0.1      0.13     1e+02     236     302 ..     475     537 ..     475     538 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                         AAA_21   3 vliGpNgsGKSnLLdaldllarl.....drdvegltdelsgg 39 
                                    ++ GpNg+GKS+++  l  + ++     ++ ve+++++++++
  gene294|gene294|rna294|rna294 370 AIAGPNGAGKSTFINSLLRFLDYsgeifIDGVEMRKYTRRSI 411
                                    689**************8887766666666666665555544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                                    elS G++++l l  a++ +    +++++DE  +  ++k  ++l++ + + ls+    +i+  H+ +ll
  gene294|gene294|rna294|rna294 475 ELSVGQRQYLSLMRAIIKDS---PIFILDEATSDVDYKTETELIDYVmSVLSD--RTIIMIVHNHSLL 537
                                    57999999988888888877...**************9999999555377777..8888877776665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.7e-06    0.0037      16      43 ..     360     387 ..     352     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.7e-06
                         AAA_29  16 tieidlkg.atlltGpsGsGKSTllDAiq 43 
                                     ++++  g    ++Gp+G+GKST++ ++ 
  gene294|gene294|rna294|rna294 360 NFTLRK-GeKLAIAGPNGAGKSTFINSLL 387
                                    566664.44999************98765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.2e-06    0.0048      65     121 ..     331     388 ..     320     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.2e-06
                                    HHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  65 leelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                      ++ke  ++++++ + ++  ++  l+ ++  l++ +  +++G+ G+GKSt+in+ll 
  gene294|gene294|rna294|rna294 331 QADIKEFNQDIEVRDIGIKRGNNIILRGVNFTLRKgEKLAIAGPNGAGKSTFINSLLR 388
                                    45666777777777888888888888999999998899*****************975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05     0.009       3      75 ..     371     446 ..     369     462 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkkl...klkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdee.npsdlaelir 75 
                                    + Gp+g GKSt++++L + l  +     +  + + y+   +  +   Y  q+ ++ dD   ++ ++ n+++ +e+i+
  gene294|gene294|rna294|rna294 371 IAGPNGAGKSTFINSLLRFLDYSGeifIDGVEMRKYT-RRSIRHIIAYVPQDNCILDDTVLKNLQYgNKDISFEKIK 446
                                    78*************8887763332232223333444.455678899*************99999999996666664 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00011     0.087       2      42 ..     369     410 ..     368     448 .. 0.82
   2 ?    2.5   0.0      0.15   1.2e+02      54     136 ..     452     535 ..     410     552 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                    EEEE--TTSSHHHHHHHHHHHH...G.GGEEEEEEEEE---- CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssg.vkvgGfyteevregg 42 
                                    ++i Gp G GK+T+++ +l+ l+ sg + ++G+  ++++++ 
  gene294|gene294|rna294|rna294 369 LAIAGPNGAGKSTFINSLLRFLDYSGeIFIDGVEMRKYTRRS 410
                                    789*******************98852778998666555444 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                                    T--EEEEEETT---SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT..TTSEEEEE CS
                       NTPase_1  54 sgeegiLarveakreprvgkyvvdvesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk..sekpvlav 131
                                     g+++ +++ e+    + g+   ++   ++  l+ +r  ++++ ++++DE  +  +  k+  e ++ v++  s++ ++++
  gene294|gene294|rna294|rna294 452 YGTHEVFSSLEGGYLKEAGQQGCELSVGQRQYLSLMRAIIKDSPIFILDEATS-DVDYKTETELIDYVMSvlSDRTIIMI 530
                                    47888888888888889999999998888999999998889999******754.55555555666666666666778888 PP

                                    --SS- CS
                       NTPase_1 132 ihrrk 136
                                    +h+++
  gene294|gene294|rna294|rna294 531 VHNHS 535
                                    88774 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.2e-05     0.033       2      22 ..     369     395 ..     368     447 .. 0.70
   2 ?   -2.0   0.0       4.7   3.7e+03      47      86 ..     511     550 ..     482     571 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                                    EEEEESTTSSHHHHHHHHHT......S CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg......e 22 
                                     ai+G   +GKSt+in+l++      e
  gene294|gene294|rna294|rna294 369 LAIAGPNGAGKSTFINSLLRfldysgE 395
                                    69****************974444332 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.7
                                    EEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT CS
                       MMR_HSR1  47 eielvDtpGliegaseekglgkaflaleeadlillvvdas 86 
                                    e el+D +  + ++++  ++ ++   l + d il++ d +
  gene294|gene294|rna294|rna294 511 ETELIDYVMSVLSDRTIIMIVHNHSLLSKFDNILFLKDKT 550
                                    4444444432212222223334444445566667766644 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0002      0.15       3      24 ..     367     387 ..     365     415 .. 0.86
   2 ?    0.2   0.1      0.69   5.4e+02     121     176 ..     490     552 ..     479     569 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                         AAA_24   3 lkiliyGpsgiGKTtlakelgp 24 
                                     k++i Gp+g+GK+t++++l  
  gene294|gene294|rna294|rna294 367 EKLAIAGPNGAGKSTFINSL-L 387
                                    699**************999.4 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.69
                         AAA_24 121 lrk.nvifiahektrkdedpegeakytrlepklgkkt......anelkeevDlvlranlkred 176
                                      k   ifi  e t  ++ ++++  ++++ + l+++t         l +++D +l+++ k+ +
  gene294|gene294|rna294|rna294 490 IIKdSPIFILDEATSDVDYKTETELIDYVMSVLSDRTiimivhNHSLLSKFDNILFLKDKTMK 552
                                    455578999999999999999998888888888888888888888888899999998866554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.58   4.5e+02     109     198 ..     225     340 ..     162     345 .. 0.44
   2 ?   15.1   1.5   3.1e-05     0.024      23      40 ..     370     387 ..     355     574 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.58
                         AAA_23 109 lelleideleqfisellgskki......ilnlilflgqer................feefelkdkkerleelekelee.l 165
                                     ++le++e+e+f  +l+++         + n+i fl++ +                    ++ dk  +l++l   l+e l
  gene294|gene294|rna294|rna294 225 SFGLEERESEKFHASLIDRVSTgtvyscSENIITFLQKLSsaiphigilylslntnI---LTFDKAIKLNSLHFILKErL 301
                                    222222444444444433332244444444444444444445566666555553330...22222224444444333323 PP

                         AAA_23 166 edekkllekl......eqekekekeleeleeeleeilke 198
                                    +++ k++ +l           +eke +e + +++e +++
  gene294|gene294|rna294|rna294 302 TEFSKEFTELyeyyydYSTSTYEKEDDEGQADIKEFNQD 340
                                    333333333344445422223344444444444444444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.1e-05
                         AAA_23  23 lItGpNGaGKTTildAik 40 
                                    +I GpNGaGK+T+++ + 
  gene294|gene294|rna294|rna294 370 AIAGPNGAGKSTFINSLL 387
                                    7*************9886 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.5e-05     0.043       7      74 ..     369     437 ..     357     454 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
                                    EEEEEBTTSSCCCCCCTTSSSS------------.------S-EEEEEEEEETTCEEEEEEEE---BSS CS
                         Septin   7 lmvvGesglGkttlintlfetdlieeekleease.kkkktveikkkkvvieedgvklnltviDtpgfGd 74 
                                    l ++G +g Gk+t+in+l++  +++ e + +  e +k +  +i++  + + +d+  l  tv+    +G+
  gene294|gene294|rna294|rna294 369 LAIAGPNGAGKSTFINSLLRFLDYSGEIFIDGVEmRKYTRRSIRHIIAYVPQDNCILDDTVLKNLQYGN 437
                                    6799***************99999887766665535556667777777777777777777777777776 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-05     0.053      19      60 ..     347     387 ..     333     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                                    EEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE  19 pvalgkeisgnplvldlkkmashllvaGatgsGKStalntLi 60 
                                     +++g +i+ + + + l+k +  l +aG  g GKSt++n+L+
  gene294|gene294|rna294|rna294 347 GIKRGNNIILRGVNFTLRKGE-KLAIAGPNGAGKSTFINSLL 387
                                    577888888888999999999.******************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00012     0.093      25      63 ..     367     405 ..     355     529 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                         AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    e + + G+ G GKs+ +++llr l  +g if+ g   + 
  gene294|gene294|rna294|rna294 367 EKLAIAGPNGAGKSTFINSLLRFLDYSGEIFIDGVEMRK 405
                                    44789******************9999888876655554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012     0.096     119     159 ..     356     395 ..     329     413 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                          T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyallkeinksder 159
                                     + ++  +r+   + ++G+ g GK+t++++ll +++ s  +
  gene294|gene294|rna294|rna294 356 LRGVNFTLRKGEKLAIAGPNGAGKSTFINSLLRFLDYS-GE 395
                                    444555556668899*******************9987.33 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0003      0.23       8      38 ..     369     409 ..     364     531 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.............e 38 
                                    l++ G+ G+GK+t ++ ll+ ld      e             +
  gene294|gene294|rna294|rna294 369 LAIAGPNGAGKSTFINSLLRFLDYS--G-EifidgvemrkytrR 409
                                    7899*****************9732..2.124455666665432 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00024      0.19      27      59 ..     360     393 ..     336     413 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                          AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkld.k 59 
                                    +  l+++ ++ + Gp G GK++ i++ll+ ld +
  gene294|gene294|rna294|rna294 360 NFTLRKGEKLAIAGPNGAGKSTFINSLLRFLDyS 393
                                    5678899999******************999833 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.18      10      97 ..     359     456 ..     351     506 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                         AAA_11  10 iksalseseitliqGPPGtgKTktivellsqllsr..........rkseeeksakpriLvCapSNaAvDellerllr.gl 78 
                                    ++++l++ e   i GP G gK+++i +ll+ l  +           ++ +++s  + i +  + N   D+++++ l+ g 
  gene294|gene294|rna294|rna294 359 VNFTLRKGEKLAIAGPNGAGKSTFINSLLRFLD-YsgeifidgveMRKYTRRSIRHIIAYVPQDNCILDDTVLKNLQyGN 437
                                    56788888899*********************6.3366666665423588888899999999999999999999999888 PP

                         AAA_11  79 ldsegekykpkivRvgnee 97 
                                    +d + ek+k  + R g +e
  gene294|gene294|rna294|rna294 438 KDISFEKIKEICKRYGTHE 456
                                    8888888888888887776 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00021      0.16     261     287 ..     365     391 ..     317     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                       PPV_E1_C 261 kknclvllGppntGkslfamslikfLk 287
                                    k + l + Gp  +Gks+f +sl++fL+
  gene294|gene294|rna294|rna294 365 KGEKLAIAGPNGAGKSTFINSLLRFLD 391
                                    667799*******************96 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.5   2.8e+03     195     233 ..     204     242 ..     190     246 .. 0.77
   2 ?   10.4   0.0   0.00053      0.41       1      23 [.     371     393 ..     371     397 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.5
                     ATP_bind_1 195 ekykklaeaiaelleefalvlrflplssekeesiedlls 233
                                     +  k+++++ ++l++++ v +f   ++e+e+    l++
  gene294|gene294|rna294|rna294 204 AAKDKSTKKLGDILNNYEVVKSFGLEERESEKFHASLID 242
                                    456789999999*******98888888888877766666 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00053
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelr 23 
                                    ++Gp G+GK+tf+++l  +l+ +
  gene294|gene294|rna294|rna294 371 IAGPNGAGKSTFINSLLRFLDYS 393
                                    79**************9998765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00036      0.28      21      60 ..     371     409 ..     362     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                     Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60 
                                    ++G  GAGKs+ ++ l + l+ +++ + +d+ ++R++ ++
  gene294|gene294|rna294|rna294 371 IAGPNGAGKSTFINSLLRFLD-YSGEIFIDGVEMRKYTRR 409
                                    89******************6.9999*********99765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.2     4e+03     112     142 ..     193     222 ..     181     223 .. 0.66
   2 ?    9.9   0.0     0.001      0.79       4      24 ..     371     391 ..     369     434 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.2
                         AAA_33 112 keRlakRaangddrsevpeealdrqkarfer 142
                                     +R++ R +  +++ +  ++ l + ++++e+
  gene294|gene294|rna294|rna294 193 SRRNRIRGKY-NAAKDKSTKKLGDILNNYEV 222
                                    4555556553.34567888888888888875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.001
                         AAA_33   4 lvGlpGsGKstlaerllkklg 24 
                                    + G++G+GKst++ +ll+ l+
  gene294|gene294|rna294|rna294 371 IAGPNGAGKSTFINSLLRFLD 391
                                    57**************98766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0048       3.8      38      66 ..     356     385 ..     335     458 .. 0.84
   2 ?    1.4   0.1      0.31   2.4e+02      99     158 ..     483     544 ..     474     553 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0048
                      IstB_IS21  38 Latlsf.iekkenivllGpsGvGKshlaia 66 
                                    L++ +f ++k e +++ Gp G+GKs +  +
  gene294|gene294|rna294|rna294 356 LRGVNFtLRKGEKLAIAGPNGAGKSTFINS 385
                                    677777347789************987665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.31
                      IstB_IS21  99 laralkrllkv.dllilDdlgllpldqa.eaellfeviekryerrsiiitsnlp.faewdevl 158
                                    + + +++++k   + ilD+    ++d + e+el+  v++   +r+ i+i  n + ++++d++l
  gene294|gene294|rna294|rna294 483 YLSLMRAIIKDsPIFILDEATS-DVDYKtETELIDYVMSVLSDRTIIMIVHNHSlLSKFDNIL 544
                                    5555556555436888888654.5555405555555777777788888887776257788775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.79u 0.36s 00:00:01.14 Elapsed: 00:00:00.53
# Mc/sec: 3287.52
//
Query:       gene295|gene295|rna295|rna295  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-19   70.7  16.3    2.1e-19   70.0  16.3    1.3  1  Chs7      Chitin synthase export chaperone


Domain annotation for each model (and alignments):
>> Chs7  Chitin synthase export chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0  16.3   1.2e-23   2.1e-19       6     276 ..       5     258 ..       2     266 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.2e-23
                           Chs7   6 dsiCrktalplCnllksskseteakegiepeCyargielantiifnlgsilihivalivtlililrvrskktAvGRkEil 85 
                                    d++C+ + +p+C+ l+++       ++      +rg  l +t +  + ++++ ++ ++ ++ +i +v++  ++vGRkE+l
  gene295|gene295|rna295|rna295   5 DKVCSVSNFPMCEHLSDE-----ICKD-----VSRGSLLFKTKVSSPTTVILLVMVMLSAVRMIRHVKALCSSVGRKEML 74 
                                    689999999999999988.....2333.....4789999***************************************** PP

                           Chs7  86 lflllyllleilelvvdggviplsskvypyfvavqiglisatlwiLllnglvgfqlleDGtplSllllrlsslvlfivtf 165
                                    +f+ ly+    le v++g     s+++  +++++q+ l ++ + +L++ ++    ++      + +ll++s++++ ++  
  gene295|gene295|rna295|rna295  75 VFFNLYFGSAALEAVLVGFKESISKQTHLFLTSIQLSLYTSGFFSLFVGSITVDMFTGILGFRAATLLKISTAIYSVG-- 152
                                    ******************99999***********************98776665555444445555555555555444.. PP

                           Chs7 166 lialdtfkswtaelsstktiaLfvllyllnlvllvvyvvlqlilvlrvLeerwplgalllgvllfvigqvllyvlskkiC 245
                                     i  + f+ +ta  ++  +i +fvl    n +++++y+v q+    ++ +e+w+ g+l++++  f i+  +l+v s+ i 
  gene295|gene295|rna295|rna295 153 -IGTVIFTGLTAPAKEIASIPFFVL----NPLFFFLYMVFQIKRLRKTDGEVWAYGTLVISTTCFLIANTVLFVGSRMIG 227
                                    .444455556667777788888875....77899********************************************** PP

                           Chs7 246 egvkhyidGlffetlcnllavmmvykfWdsi 276
                                      +++y d lff  ++ l++ +m++k+W s+
  gene295|gene295|rna295|rna295 228 LMTDRYFDNLFFYHFFILCTFIMIHKYWLSV 258
                                    ****************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1734.69
//
Query:       gene296|gene296|rna296|rna296  [L=135]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-12   46.0   1.3    5.2e-12   45.7   1.3    1.2  1  SKIP_SNW  SKIP/SNW domain


Domain annotation for each model (and alignments):
>> SKIP_SNW  SKIP/SNW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   1.3   2.9e-16   5.2e-12      31     146 ..      20     131 ..       4     135 .] 0.75

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2.9e-16
                       SKIP_SNW  31 DPleppkfkhkkvpagpesppvpvl.hspprkltkeeqekwkIPpaiSnwkNpkGytipLdkRlaadgrglqeveind.k 108
                                    DPl+ +  + +k  ++     + v  +++prkl  ++++k k   ++S wkNp    ipL++R+a d+ ++ + ein  +
  gene296|gene296|rna296|rna296  20 DPLKITCKRGTKKHRK-----EGVGdKDKPRKLY-KNKSKVKLVKCVSMWKNPTSQIIPLEMRVAHDRFRSIQPEINLgR 93 
                                    5555544443332222.....2333034566665.568899***************************888889***99* PP

                       SKIP_SNW 109 FaklseaLeeAerkareevklraelkkklaekekeeke 146
                                    F +l ++L+ Ae    +e k++a  k++++e+++  k 
  gene296|gene296|rna296|rna296  94 FGELKSSLDSAEGLYSQETKKKAIKKERIEETKRTDKS 131
                                    ******************99998777777776666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 1013.47
//
Query:       gene297|gene297|rna297|rna297  [L=762]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-35  120.1  17.0    2.3e-26   92.4   9.0    2.1  2  Adaptin_N        Adaptin N terminal region
    1.5e-06   28.4  10.7    0.00034   20.7   2.3    3.9  3  Cnd1             non-SMC mitotic condensation complex subunit
      7e-06   26.2   1.5    3.4e-05   24.0   0.0    2.6  3  COP-gamma_platf  Coatomer gamma subunit appendage platform su
    1.1e-05   25.7   0.0        0.4   11.1   0.0    3.5  3  HEAT_2           HEAT repeats
    0.00043   20.3   0.2        1.8    9.0   0.1    3.8  2  HEAT             HEAT repeat
     0.0017   18.0   0.1        0.1   12.2   0.0    3.0  2  UTP15_C          UTP15 C terminal
     0.0024   18.4   2.3        1.4    9.6   0.0    4.3  4  Vac14_Fab1_bd    Vacuolar 14 Fab1-binding region
  ------ inclusion threshold ------
       0.05   13.7   0.1       0.21   11.7   0.0    2.1  2  Coatomer_g_Cpla  Coatomer subunit gamma-1 C-terminal appendag
       0.38    9.7   4.9        1.2    8.1   2.0    2.7  2  Rif1_N           Rap1-interacting factor 1 N terminal
        3.8    7.9   5.9         15    6.0   0.2    3.6  4  SporV_AA         Stage V sporulation protein AA


Domain annotation for each model (and alignments):
>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   1.0   1.9e-11   3.3e-08       7     155 ..      16     167 ..      10     172 .. 0.87
   2 !   92.4   9.0   1.3e-29   2.3e-26     245     522 ..     236     507 ..     206     509 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.9e-11
                                    HHHHHHCCSSS-SCHHHHHHHHHHHHHHHCT-....--GHHHHHHHCCCCSS-CHHHHHHHHHHHHHCTTSCCHHCCCCH CS
                      Adaptin_N   7 qelaeilnsnkdddekkkeavkkliylialGe....dvsflffevvklvaskdfelKrlvYlylellaeesedlalLvtn 82 
                                    +e+ e l++++++ ++  +a++ l y++ + +    ++  + ++ +k ++skd+ lK  +Y ++e +++  ++  l+ +n
  gene297|gene297|rna297|rna297  16 EEMNESLTKSPVSTRSAVKALNNLFYMLSTRKlseaTIRNVYVALLKGFQSKDLYLKLCIYSAIEKMSKLTDE-GLVGIN 94 
                                    345555666668888888899999998887666666777******************************9988.99**** PP

                                    HHHHHCCSSSH.HHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHH CS
                      Adaptin_N  83 slqkDlkdpnq.lirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlve 155
                                     l++Dl+ + +   ++++Lr+L si+  e++ d+ ++i ++ +++s   r  +++ +++l+  +  +++k+ +e
  gene297|gene297|rna297|rna297  95 VLMNDLNGKIPdDAKAMTLRTLFSIIPFEMVYDFRKYINQAFVSTSMARRDMSVVVAYRLLCDNFTQVKKW-LE 167
                                    *******98752679***********************************************999999996.65 PP

  == domain 2  score: 92.4 bits;  conditional E-value: 1.3e-29
                                    CHHHHHHHHHCCHCCCCST..HHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCCCSXXTTSXHHHHH CS
                      Adaptin_N 245 naVlletvnlivelapkne..livlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlkifllktdddvsirl 322
                                    + V +e+++ +  l+++     + + ++ L  +l+s +  l++ a+r ++++++k p++v+  + +i+ l ++++ si++
  gene297|gene297|rna297|rna297 236 EVVFMEAAKIVSGLSEEYGsqFVDQTIQSLRIFLRSTNMVLQFTAMRIISQLAQKYPQKVSVANKEIEDLVSSENKSISM 315
                                    6799*********9999777799**************************************99999999999******** PP

                                    HHHHHHCCCXXTTTHHHHHHHHHHHTTSSXXHHHHHHHHHHHHHHHHHSCCHHHHHHHHH.HHHHTTXXHHHHHHHHHHH CS
                      Adaptin_N 323 kaldlllklvdesNvkeivkeLkkyvkevadedfksklvkaIgrlaekfatdaewvldvl.lellslsgesvkdeivevi 401
                                     a++ llk+++e+ ++++v+ + + v++++d+ fk+ +++++ +l+  f++ ++ ++d+l   ll+  +  +k+ i++vi
  gene297|gene297|rna297|rna297 316 FAITSLLKTGTEETIDKLVNLIPSMVHDMSDG-FKKIAIETLESLSNLFESRKTLYIDFLgSSLLQKGELEFKKYIIDVI 394
                                    ********************************.***************************44566666666799999999 PP

                                    HHHHHHSTTTSTTCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTTXTT...HHHHHHCTTTTTTTSXHHHHHHHHHHHHHH CS
                      Adaptin_N 402 rdliqkvpelheeiiekLaellekieseearaaaiWllGeygelvsntesasdllrslaekfvlesekvklqiltalvKl 481
                                     +  +   + +e+i+e L+ ++e+ ++ ++   ++ +l  + ++ +    +++++ +++++++le++ v++ +l+ l   
  gene297|gene297|rna297|rna297 395 SRATRDD-DTRERILEILCTYIEDSQYYQITLDILGILSREIPRSKT---PAKYVVHVLNRLILENNHVRAGALQCLYNI 470
                                    8887665.56699*********************9999999999998...**************************9999 PP

                                    HHCXGCC.THXHHHHHHHHHHHXXSHHHHHHHHHHHHHHCC CS
                      Adaptin_N 482 yltspdketqekliqlvlslatssdlevrdRaveylqllss 522
                                    + + +       + + ++++++++d ++r+ a ++l+ +++
  gene297|gene297|rna297|rna297 471 SSVVS---PL-TVENAMKRCLNDQDESIREIAAFLLRNMKL 507
                                    98886...33.799********99********999987765 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.82   1.5e+03      89     126 ..      28      63 ..      10      84 .. 0.68
   2 !   20.7   2.3   1.9e-07   0.00034      17     150 ..     256     420 ..     247     432 .. 0.82
   3 !   10.4   0.1   0.00028      0.49      34      85 ..     456     505 ..     427     514 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.82
                           Cnd1  89 senaiynllpdiisklsdalnecsewgqitilefLlsy 126
                                    s++ +++ l ++++ ls+   ++se++ ++++ +Ll+ 
  gene297|gene297|rna297|rna297  28 STRSAVKALNNLFYMLST--RKLSEATIRNVYVALLKG 63 
                                    335556666666666664..489999999999999874 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.9e-07
                           Cnd1  17 nlveylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteisek.senaiyn 95 
                                    ++v+++++ Lr  L+ +++  + ta+ ++++L ++   k++   +e+++l++ en++++  a+++l +  ++ + ++++n
  gene297|gene297|rna297|rna297 256 QFVDQTIQSLRIFLRSTNMVLQFTAMRIISQLAQKYPQKVSVANKEIEDLVSSENKSISMFAITSLLKTGTEeTIDKLVN 335
                                    79******************************999999999999**********************99999955599*** PP

                           Cnd1  96 llpdiisklsd.................alne................csewgqitilefLlsyipkdkqeaeslveklc 142
                                    l p++++ +sd                 +  +                 + +  ++i++++++ + +d+   e ++e lc
  gene297|gene297|rna297|rna297 336 LIPSMVHDMSDgfkkiaietleslsnlfE--SrktlyidflgssllqkGELEFKKYIIDVISRATRDDDT-RERILEILC 412
                                    ***********888777766665555550..055555555555555546667778899999998888888.899999999 PP

                           Cnd1 143 prlqhans 150
                                      ++ ++ 
  gene297|gene297|rna297|rna297 413 TYIEDSQY 420
                                    88877665 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00028
                           Cnd1  34 dpyVRktaaivvakL.ilndmvkekgflselaklleDenprVvanalaaltei 85 
                                    + +VR  a+ ++ ++     +v    + + ++++l+D+++++++ a ++l ++
  gene297|gene297|rna297|rna297 456 NNHVRAGALQCLYNIsS---VVSPLTVENAMKRCLNDQDESIREIAAFLLRNM 505
                                    55555555555555521...222223334566666666666666666666544 PP

>> COP-gamma_platf  Coatomer gamma subunit appendage platform subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   4.5e+03      82     103 ..      41      62 ..      18      77 .. 0.67
   2 ?   -0.6   0.1       0.7   1.3e+03      45      87 ..     271     319 ..     262     333 .. 0.61
   3 !   24.0   0.0   1.9e-08   3.4e-05      18      87 ..     543     610 ..     537     633 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                COP-gamma_platf  82 fiipiekLkynepgsvyvvlkr 103
                                    ++++ +kL+  + ++vyv+l +
  gene297|gene297|rna297|rna297  41 YMLSTRKLSEATIRNVYVALLK 62 
                                    4557778888888888887764 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.7
                COP-gamma_platf  45 kehiVlqfn...ikNtledqvLenvsvqlepeeee...lfeevfiipie 87 
                                    + ++Vlqf+   i   l+++  ++vsv+ ++ e+    + + +++ +i+
  gene297|gene297|rna297|rna297 271 STNMVLQFTamrIISQLAQKYPQKVSVANKEIEDLvssENKSISMFAIT 319
                                    5689999963335667777888899996666333322233333333444 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 1.9e-08
                COP-gamma_platf  18 kllksskpveLTesetEYvVsvvKhifkehiVlqfnikNtledqvLenvsvqlepeeeelfeevfiipie 87 
                                    +l+k ++++ LTe++ + +++v+K ++++++V+ f+ kN le  ++ +  ++l +++  +++   +i+i+
  gene297|gene297|rna297|rna297 543 PLIKNCRELVLTEANGDVQIKVIKKVYEDKLVFSFSLKNNLEGIQICDGMLNLVSSD--CEKRSLSIKID 610
                                    7899*************************************9877776666555522..34444445544 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00035      0.63      18      71 ..     281     337 ..     262     357 .. 0.73
   2 !   11.1   0.0   0.00022       0.4       3      85 ..     410     500 ..     400     503 .. 0.72
   3 ?   -3.7   0.0       9.1   1.6e+04      32      52 ..     544     565 ..     521     566 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                         HEAT_2  18 raairaLgrignpea...lpaLvellededpavRraaaeaLgaigdpealpaLkell 71 
                                     ++i +L+++ ++++    + + +l+++e+  + + a+++L + g++e+++ L  l 
  gene297|gene297|rna297|rna297 281 MRIISQLAQKYPQKVsvaNKEIEDLVSSENKSISMFAITSLLKTGTEETIDKLVNLI 337
                                    45666666655554444489999***********************99998887653 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                         HEAT_2   3 aLlqalendpdpevrraairaLg.ri.gnpealpaLvelled...edpavRraaaeaLgaig...dpealpaLkellddd 74 
                                     L+ ++e++  +++   ++  L  +i ++++  +++v +l+    e+ +vR+ a + L  i    +p +++   +++++d
  gene297|gene297|rna297|rna297 410 ILCTYIEDSQYYQITLDILGILSrEIpRSKTPAKYVVHVLNRlilENNHVRAGALQCLYNISsvvSPLTVENAMKRCLND 489
                                    577777767777777777777776352334445666665532244*************9998444599998888888899 PP

                         HEAT_2  75 dddvvReaAae 85 
                                    +d+ +Re Aa 
  gene297|gene297|rna297|rna297 490 QDESIREIAAF 500
                                    99999999875 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.1
                         HEAT_2  32 alpaLvell.ededpavRraaa 52 
                                    +++ ++el+ + ++ +v+  ++
  gene297|gene297|rna297|rna297 544 LIKNCRELVlTEANGDVQIKVI 565
                                    4667777666777888887776 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0056        10      12      30 ..     455     473 ..     450     474 .. 0.92
   2 !    9.0   0.1   0.00099       1.8       6      26 ..     484     504 ..     481     505 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0056
                                    SSHHHHHHHHHHHHHHHHC CS
                           HEAT  12 pspeVReaAakaLgalaev 30 
                                    ++ +VR+ A+++L ++++v
  gene297|gene297|rna297|rna297 455 ENNHVRAGALQCLYNISSV 473
                                    6889************987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00099
                                    HHHHT-SSHHHHHHHHHHHHH CS
                           HEAT   6 lkllsDpspeVReaAakaLga 26 
                                     ++l+D++ ++Re Aa  L +
  gene297|gene297|rna297|rna297 484 KRCLNDQDESIREIAAFLLRN 504
                                    5789************99976 PP

>> UTP15_C  UTP15 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   5.8e-05       0.1      69     102 ..     398     431 ..     394     457 .. 0.87
   2 ?    2.0   0.0     0.086   1.5e+02      52      92 ..     472     511 ..     468     515 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                        UTP15_C  69 grdeeslepiLkfllkhitdpryvsllvdvanvl 102
                                     rd+++ e+iL++l+ +i+d +y+++ +d++ +l
  gene297|gene297|rna297|rna297 398 TRDDDTRERILEILCTYIEDSQYYQITLDILGIL 431
                                    79**************************987655 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.086
                        UTP15_C  52 tlleeLrhRgalraALagrdeeslepiLkfllkhitdpryv 92 
                                    +++  L   +a++++L+++de s+  i  fll++++  r++
  gene297|gene297|rna297|rna297 472 SVVSPLTVENAMKRCLNDQDE-SIREIAAFLLRNMKLSRVY 511
                                    6777788889*******9987.79999******99988776 PP

>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.025        44       8      63 ..     313     371 ..     309     378 .. 0.63
   2 ?   -0.2   0.0      0.84   1.5e+03      21      44 ..     383     406 ..     374     416 .. 0.82
   3 !    9.6   0.0   0.00078       1.4      27      96 ..     443     506 ..     425     507 .. 0.85
   4 ?   -3.1   0.0       7.1   1.3e+04      64      82 ..     730     748 ..     724     760 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                  Vac14_Fab1_bd   8 igLaavaialekkikeyleeivkpv...lkcfsDkdsrvRyyacEslyniakvakgevl 63 
                                    i++ a++  l++ ++e ++++v+ +   ++ +sD  +++   + Esl n+    k+  +
  gene297|gene297|rna297|rna297 313 ISMFAITSLLKTGTEETIDKLVNLIpsmVHDMSDGFKKIAIETLESLSNLFESRKTLYI 371
                                    55666777778888888887776651115555555566666666777777666666555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.84
                  Vac14_Fab1_bd  21 ikeyleeivkpvlkcfsDkdsrvR 44 
                                      e+ + i++++ ++ +D+d+r R
  gene297|gene297|rna297|rna297 383 ELEFKKYIIDVISRATRDDDTRER 406
                                    55788999************9988 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00078
                  Vac14_Fab1_bd  27 eivkpvlkcfsDkdsrvRyyacEslyniakvakgevlkllneifdalvklvaDsdesvksgaelldrllk 96 
                                    + v  vl+ +  ++++vR  a  +lyni+ v+    ++      +a+ + + D+des+++ a++l r +k
  gene297|gene297|rna297|rna297 443 KYVVHVLNRLILENNHVRAGALQCLYNISSVVSPLTVE------NAMKRCLNDQDESIREIAAFLLRNMK 506
                                    5567789999999***************9998877665......67889999********9999999887 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 7.1
                  Vac14_Fab1_bd  64 kllneifdalvklvaDsde 82 
                                     ++n ++++ +k v D+  
  gene297|gene297|rna297|rna297 730 IHVNLVHNVACKCVVDVYC 748
                                    5778888888888888744 PP

>> Coatomer_g_Cpla  Coatomer subunit gamma-1 C-terminal appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         4   7.2e+03      23      57 ..     310     346 ..     302     352 .. 0.66
   2 ?   11.7   0.0   0.00012      0.21      24     113 ..     679     759 ..     666     761 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4
                                    T-EEEEEEESS-..--HHHHHHHHHHHHT-EE-TTTT CS
                Coatomer_g_Cpla  23 aeavetfaLssv..ksleeavdkliellgmqplegsd 57 
                                    +++++ fa++s   +  ee +dkl++l+  ++ + sd
  gene297|gene297|rna297|rna297 310 NKSISMFAITSLlkTGTEETIDKLVNLIPSMVHDMSD 346
                                    5556666664431145789999999988777666665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00012
                                    -EEEEEEESS---HHHHHHHHHHHHT-EE-TTTT---SS-SEEEEEEEEEETTS-EEEEEEEEEE..SS.EEEEEEEEES CS
                Coatomer_g_Cpla  24 eavetfaLssvksleeavdkliellgmqplegsdkvpenassHtLklaGkfvggekvlvrarlalssskgvtlkltvRse 103
                                    +++ tf+L  + ++ +a +k+++ll+m+ + + +    ++++ +++l G++  ++ +++ ++l+++    + + + v ++
  gene297|gene297|rna297|rna297 679 KNEITFNL--QGDIYSAGKKVLDLLNMKIISQET----EKNTMIVLLHGEYY-KTPIAIHVNLVHNV--ACKCVVDVYCD 749
                                    44556666..68****************887766....777889*****986.689*********76..68888899999 PP

                                    SHHHHHHHHH CS
                Coatomer_g_Cpla 104 deevaelvls 113
                                    de va+ + +
  gene297|gene297|rna297|rna297 750 DEHVAQKITK 759
                                    9999999976 PP

>> Rif1_N  Rap1-interacting factor 1 N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.4   2.6e+03     337     361 ..      24      48 ..      12      60 .. 0.59
   2 ?    8.1   2.0   0.00067       1.2      71     136 ..     238     308 ..     236     465 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                                    TSHHHHHHHHHHHHHHHHHHHTT-T CS
                         Rif1_N 337 sakelreavlsslcnllyyalrpla 361
                                    +++  ++ +++ l+nl+y + +   
  gene297|gene297|rna297|rna297  24 KSPVSTRSAVKALNNLFYMLSTRKL 48 
                                    5566666677777777666544444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00067
                                    HHHSSHHHHHHHTTHHHTHHHHHHTTTTTS..TT--HHHHHHHHHHHHH..--THHHH.S-HHHHHHHHTT CS
                         Rif1_N  71 tllsnpaiastLsddfkvfiidhsirsled..sstpKniithllsvlsq..QkFsski.mtservkrllsa 136
                                    +++   +i+s Ls++ ++ ++d++i+sl+    st+  +  ++++++sq  Qk+++k+ + +++++ l+s+
  gene297|gene297|rna297|rna297 238 VFMEAAKIVSGLSEEYGSQFVDQTIQSLRIflRSTNMVLQFTAMRIISQlaQKYPQKVsVANKEIEDLVSS 308
                                    799999*********************99722566666667899999977799999984566777777764 PP

>> SporV_AA  Stage V sporulation protein AA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.087   1.6e+02      49      71 ..     271     293 ..     234     301 .. 0.75
   2 ?   -2.0   0.0       2.7   4.8e+03      21      61 ..     390     430 ..     367     437 .. 0.73
   3 ?   -2.9   0.0       4.9   8.8e+03      21      54 ..     684     716 ..     676     718 .. 0.57
   4 ?    6.0   0.2    0.0084        15      11      40 ..     729     759 ..     723     761 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.087
                       SporV_AA  49 kkkkrvvisvlkvieaIkkeypn 71 
                                    +++ +  ++++ +i+++ ++yp+
  gene297|gene297|rna297|rna297 271 STNMVLQFTAMRIISQLAQKYPQ 293
                                    45557889*************97 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.7
                       SporV_AA  21 lgdvaevycsdkkvekklkaikvykikekkkkrvvisvlkv 61 
                                    + dv +  ++d++ ++++ +i  + i++++  ++ +++l +
  gene297|gene297|rna297|rna297 390 IIDVISRATRDDDTRERILEILCTYIEDSQYYQITLDILGI 430
                                    55777778888888999988888888877766777777665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 4.9
                       SporV_AA  21 lgdvaevycsdkkvekklkaikvykikekkkkrv 54 
                                     +   ++y+  kkv++   ++k+++ +++k++++
  gene297|gene297|rna297|rna297 684 FNLQGDIYSAGKKVLDL-LNMKIISQETEKNTMI 716
                                    55556677777776654.4566666654444444 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.0084
                       SporV_AA  11 nvevk.kkeVtlgdvaevycsdkkvekklka 40 
                                     + v+   +V  + v++vyc+d++v++k+ +
  gene297|gene297|rna297|rna297 729 AIHVNlVHNVACKCVVDVYCDDEHVAQKITK 759
                                    57788888999999**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (762 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.81u 0.34s 00:00:01.15 Elapsed: 00:00:00.54
# Mc/sec: 4230.06
//
Query:       gene298|gene298|rna298|rna298  [L=492]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.6e-174  579.3   0.1   4.2e-174  579.0   0.1    1.0  1  UDPGP     UTP--glucose-1-phosphate uridylyltransferase
     0.0057   15.5   0.5        0.2   10.5   0.2    2.7  3  DUF4301   Domain of unknown function (DUF4301)
  ------ inclusion threshold ------
      0.066   13.2   0.1       0.15   12.0   0.1    1.6  1  DUF4298   Domain of unknown function (DUF4298)
       0.11   12.5   0.1        1.2    9.1   0.0    2.2  2  MSA-2c    Merozoite surface antigen 2c


Domain annotation for each model (and alignments):
>> UDPGP  UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  579.0   0.1  9.4e-178  4.2e-174       2     413 .]      56     457 ..      55     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 579.0 bits;  conditional E-value: 9.4e-178
                          UDPGP   2 esFkklferyleekskqekidwdkieplpeeevvdyedlkekeeekkellnklavlkLnGglGtsmGckgpKslieVrdg 81 
                                    ++F++lferyl++++  eki w++i++++ +++++y+d+ e++e++kell+kla+lkLnGglGt+mGc+gpKs+i V+dg
  gene298|gene298|rna298|rna298  56 DEFYRLFERYLRTRN--EKIVWERIRSPK-DKIIQYSDIPEPTERSKELLKKLAILKLNGGLGTTMGCVGPKSAITVKDG 132
                                    79**********977..9*********98.789******999999*********************************** PP

                          UDPGP  82 ktfLdlivqqieelnkkynvdvPlvlmnSfnTdedtekilkkykkkkvdiltfnqsryPriskesllpvekkakkeekee 161
                                    k+f+dliv+q+++ln+kyn+dvPl+lmnSfnT+++t ki+ +y+     i+ f+qs++Pris+e+llpv+ ++    ++ 
  gene298|gene298|rna298|rna298 133 KNFIDLIVKQVRHLNSKYNIDVPLILMNSFNTESMTDKIIFRYDR----IRKFSQSKFPRISSETLLPVSPEHG---DKG 205
                                    *******************************************99....********************98886...589 PP

                          UDPGP 162 wyPpGhGdlyesLknsglldkllaeGkeyiFvsniDNlgatvDlkilnllvekkaeflmevtektradvkgGtlieyegk 241
                                    +yPpGhGdl+ sLknsg+l++ll+eG+ey+FvsniDNl++tvDlk+l++++++++ flmevt+ktradvkgGtliey+g 
  gene298|gene298|rna298|rna298 206 MYPPGHGDLFYSLKNSGMLEELLSEGYEYLFVSNIDNLASTVDLKLLEYFATNGLGFLMEVTDKTRADVKGGTLIEYKGG 285
                                    ******************************************************************************** PP

                          UDPGP 242 lrlleiaqvpkehveefksvkkfkifntnniwinlkalkrlveekelkleiivnkktldegekviqletavgaaiksFkk 321
                                    lrlleiaqvp+++++ef+s kkf ifntnniwinlk +k+ +ee+ ++l+ii+nkktl  +e+viqleta+g+aik+F++
  gene298|gene298|rna298|rna298 286 LRLLEIAQVPSSKKSEFTSFKKFTIFNTNNIWINLKDMKKKLEEGFFDLDIIENKKTLG-DETVIQLETAIGSAIKYFPN 364
                                    **********************************************************8.888***************** PP

                          UDPGP 322 avginVpRsrflpvkttsdlLlvksdlysleegslvlnpkrsfktvplvkLg.sefkkveefqkrfksipslleldhltv 400
                                    ++g+ VpRsrflpvkt+sdl+lv+s+l+  ++g+l+l+p+r  kt p++kL  ++f+k+e+++k fk ip++leld ltv
  gene298|gene298|rna298|rna298 365 SCGVVVPRSRFLPVKTCSDLFLVESNLFIEKNGTLQLHPSRVPKTCPIIKLIgKNFSKIENYEKCFKGIPDILELDILTV 444
                                    ***************************************************99*************************** PP

                          UDPGP 401 sGdvtfgknvtLk 413
                                    sG+v fgknv+Lk
  gene298|gene298|rna298|rna298 445 SGNVIFGKNVVLK 457
                                    ***********98 PP

>> DUF4301  Domain of unknown function (DUF4301)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.78   3.5e+03     311     349 ..      34      72 ..      25      84 .. 0.74
   2 ?    1.9   0.0     0.017        78     262     313 ..     208     268 ..     196     275 .. 0.58
   3 !   10.5   0.2   4.4e-05       0.2     399     502 ..     286     385 ..     280     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.78
                        DUF4301 311 lqekifeylkklekekvseeeleeieeflekelniklee 349
                                    l +++ e l+k++k++ +  +l+e  +++e+ l +++e+
  gene298|gene298|rna298|rna298  34 LLKEMKETLEKIKKDHPNPVDLDEFYRLFERYLRTRNEK 72 
                                    556677778888888888888888888888777777665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.017
                        DUF4301 262 PgGHGaLieNLnd.........ldadivfikNiDNvvpdrlkeetvkykkvlagvlvelqe 313
                                    P GHG L   L++            + +f+ NiDN+ ++   +    +     g+l+e+ +
  gene298|gene298|rna298|rna298 208 PPGHGDLFYSLKNsgmleellsEGYEYLFVSNIDNLASTVDLKLLEYFATNGLGFLMEVTD 268
                                    66777765544431111111104567899******98665555444444445566666555 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 4.4e-05
                        DUF4301 399 lqivEsaqidledkeqkeileeathFNPvdlvcavkdykgekfdLkkfvdkktgfiseKskeGkelkalElPGLWNGama 478
                                    l+++E aq+  ++k++ + +++ t FN  ++ + +kd+k +    + f d +  +i +K + G e   +    +   a+ 
  gene298|gene298|rna298|rna298 286 LRLLEIAQVPSSKKSEFTSFKKFTIFNTNNIWINLKDMKKKLE--EGFFDLD--IIENKKTLGDETVIQLETAI-GSAIK 360
                                    7899*********************************997632..4688865..79999999988654433344.34444 PP

                        DUF4301 479 dW.ntvfvevpletFnPVKtvndLl 502
                                     + n++ v vp + F PVKt  dL+
  gene298|gene298|rna298|rna298 361 YFpNSCGVVVPRSRFLPVKTCSDLF 385
                                    4348999****************96 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.4e-05      0.15      12      40 ..      32      60 ..      24      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                                   HHHHHHHHHHHHHHHHTHHHHHHHHHHHT CS
                        DUF4298 12 sallqqLeealeqwkklqkklakLdeYYq 40
                                   ++ll++++e+le++kk  ++  +Lde+Y 
  gene298|gene298|rna298|rna298 32 CKLLKEMKETLEKIKKDHPNPVDLDEFYR 60
                                   789*************************5 PP

>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.11     5e+02       2      46 ..      26      72 ..      25      87 .. 0.80
   2 ?    9.1   0.0   0.00026       1.2     108     176 ..     137     209 ..     124     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                         MSA-2c  2 meddkakdtlkaLkkvkalikeea..pfetslfdaevleelstkdde 46
                                    +d+++ + lk +k+ +  ik++   p++ + f  +  ++l t+++ 
  gene298|gene298|rna298|rna298 26 FDDKCTCKLLKEMKETLEKIKKDHpnPVDLDEFYRLFERYLRTRNEK 72
                                   58899999999***999999999722577788888888899888875 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00026
                         MSA-2c 108 vkvckeflddesefy..klvelykafatdiaalkdv..teeLlkelqekkPsrtssaetP.aPsdaesaaaqPP 176
                                      + k+    +s+++      l ++f+t++ + k++  ++ + k+ q+k P  +s++  P +P+ ++  +  PP
  gene298|gene298|rna298|rna298 137 DLIVKQVRHLNSKYNidVPLILMNSFNTESMTDKIIfrYDRIRKFSQSKFPRISSETLLPvSPEHGDK-GMYPP 209
                                    4455666666677774322346789******99996558********************999999955.45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2926.02
//
Query:       gene299|gene299|rna299|rna299  [L=1515]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.5e-103  346.5   0.0   3.3e-103  345.3   0.0    1.6  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    4.8e-90  301.6   1.4    5.6e-90  301.4   0.1    1.7  2  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    7.6e-74  247.4   0.1      2e-73  246.1   0.1    1.8  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
      6e-48  162.7   0.8    1.6e-47  161.4   0.2    2.0  2  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    4.2e-38  129.6   0.2    1.1e-37  128.3   0.2    1.8  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    2.9e-26   92.1   0.1    1.3e-25   89.9   0.0    2.1  2  RNA_pol_Rpb1_7  RNA polymerase Rpb1, domain 7
    4.1e-16   59.4   5.5      1e-14   54.8   0.8    3.1  2  RNA_pol_Rpb1_6  RNA polymerase Rpb1, domain 6
  ------ inclusion threshold ------
        7.2    7.2  34.4       0.32   11.4  16.2    3.1  3  RNA_pol_Rpb1_R  RNA polymerase Rpb1 C-terminal repeat


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.3   0.0  1.5e-106  3.3e-103       1     312 []       7     311 ..       7     311 .. 0.93

  Alignments for each domain:
  == domain 1  score: 345.3 bits;  conditional E-value: 1.5e-106
                                    BE---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   1 ekkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPv 80 
                                    +k+ik+iqfg++speeir+ S++ + ++e++e +   P+ gGl+D r+gt+d+ + C+ Cg ++ +C+ghfGhieL+kP+
  gene299|gene299|rna299|rna299   7 KKQIKSIQFGLFSPEEIRNGSAALIVHPEVMEGG--VPKVGGLIDLRMGTTDRMYLCQSCGGDNFSCPGHFGHIELTKPI 84 
                                    589******************************9..9******************************************* PP

                                    E-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCCCCHHHHHHHHCCS-BE-.........SSSSB-EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxx RF
                 RNA_pol_Rpb1_1  81 fhigffklilkilecvckecskllldeekkkllsklkkrekleelkkrlkaieelckkinlce.........kCgavqpk 151
                                    fh+g++++i+k+lecvc++csk+ + ++                 ++ l+++++++k +++ce         +Cg++qp 
  gene299|gene299|rna299|rna299  85 FHVGYISKIKKVLECVCFYCSKIKVPKRGV---------------RSTLNNVWSMSKGKSVCEgevvgdgrsGCGNRQPV 149
                                    ************************998754...............334444555555555555555555555******** PP

                                    EEEETTEEEEEESSSST.SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEE CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 152 leeegeklkaalkkske.eekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrs 230
                                    +++eg +l+a +k +++ e k +l+ e+v +++k+i+ded++ +gf+ ++srPew+i+tvl+VpPp++RPs++++g+ r+
  gene299|gene299|rna299|rna299 150 VKKEGLTLVAFMKGEESnEGKVMLNGERVYSIFKKISDEDCVYMGFDLKYSRPEWMIFTVLLVPPPSVRPSIVMEGSLRG 229
                                    *************988747789********************************************************** PP

                                    BECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 231 edDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRg 310
                                    edDlt+kl+diik N  Lkk e+egap +i+++ ++lLQ+hvatl+dn+i g+++a qks+rplksls+rLkGKeGr+Rg
  gene299|gene299|rna299|rna299 230 EDDLTHKLADIIKSNGYLKKYEQEGAPGHIVRDYEQLLQFHVATLIDNDIGGQPQALQKSGRPLKSLSARLKGKEGRIRG 309
                                    ******************************************************************************** PP

                                    CT CS
                                    xx RF
                 RNA_pol_Rpb1_1 311 nL 312
                                    nL
  gene299|gene299|rna299|rna299 310 NL 311
                                    *9 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.94   2.1e+03     110     170 ..     666     726 ..     630     761 .. 0.61
   2 !  301.4   0.1   2.5e-93   5.6e-90       1     264 [.     801    1357 ..     801    1360 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.94
                                    HHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSECBTTEEEEEEEEEEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 110 rlkeilnvskniksksltvllvdeeakelekakkvkkaiekgikkikrilvkeaekgkeee 170
                                      k +++v+++i++++ +v+++ e+a++ + ++ +  ++++++++  ++++++a++   ++
  gene299|gene299|rna299|rna299 666 DAKTVKMVKEAIRKAKEEVSVIIENARQNRLERLPGMTMKESFESHLNLVLNRARDVSGTS 726
                                    3344477888888888888888888777777777777777777777777777655443333 PP

  == domain 2  score: 301.4 bits;  conditional E-value: 2.5e-93
                                     B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS............ CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                 RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg............ 66  
                                     GL+++efffh+mggReGLiDtA+kTae+GY+qRrlvkaled +v++d++vr+ +g ++q++ygedg            
  gene299|gene299|rna299|rna299  801 GLDPEEFFFHAMGGREGLIDTAIKTAETGYIQRRLVKALEDAIVRQDESVRSGNGLMYQIKYGEDGfdatflesqkvd 878 
                                     9***************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5   67 .............................................................................. 66  
                                                                                                                   
  gene299|gene299|rna299|rna299  879 vknftkryyidmfgsgelaikqdqvseevygmlssdvdlqklldqeyewlvseifegpsllstgeididhdyqvrdiy 956 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5   67 .............................................................................. 66  
                                                                                                                   
  gene299|gene299|rna299|rna299  957 knavmspcnftrllvtakrafhlstgdvspyyiletqkslmtsnkilnvlirtnlnvkrvllehklnteafnwvvemi 1034
                                     ****************************************************************************** PP

                                     .......B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSC CS
                                     .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   67 .......lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeake 137 
                                             ++p e+vG++aaQS+GeP+TQ+tlnTFH+aGv+s+ vt Gvprlkei nv+kn+k++s++++l +++ k 
  gene299|gene299|rna299|rna299 1035 nakilqaRITPNEMVGTLAAQSVGEPATQMTLNTFHLAGVSST-VTMGVPRLKEIFNVTKNLKTPSMKIYLDKDHCKT 1111
                                     ****************************************875.7********************************* PP

                                     HHHCHHHHHHHSE................................................................. CS
                                     xxxxxxxxxxxxx................................................................. RF
                 RNA_pol_Rpb1_5  138 lekakkvkkaiek................................................................. 150 
                                      e+ak ++++ie                                                                  
  gene299|gene299|rna299|rna299 1112 IESAKVIQNEIEClcvkdlclsseiyydpeitsteiaedkdfvetyfefpdddvdfsclspflmrlivdraklvgrga 1189
                                     ************9***************************************************************** PP

                                     ...........................................................CBTTEEEEEEEEEEEEEEE CS
                                     ...........................................................xxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  151 ...........................................................gikkikrilvkeaekgkee 169 
                                                                                                g k++k++++ e++++   
  gene299|gene299|rna299|rna299 1190 nleyvaesirkelgsgahvicsdenavhmvirirvgksedeslnfymtilnsllklqlrGYKSVKKVYISEDKDK--- 1264
                                     ********************************************************9999999999999965543... PP

                                     TEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTT CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  170 ekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtk 247 
                                      ke+ l+t+g+ l +vl ++  v+ + ++snd+ ei+e+lgieaar+ +l+e+ +v+  +g++vn+rH++l++d+mt 
  gene299|gene299|rna299|rna299 1265 -KEWYLQTDGTCLPQVLGNPA-VNSRLTISNDLIEIAETLGIEAARESILRELAMVIDGNGSYVNYRHMSLLADVMTM 1340
                                     .5799****************.******************************************************** PP

                                     TSS---SSTTCHCCSSS CS
                                     xxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  248 kgeivavnrsGinkael 264 
                                     +g++  ++r+G+nka  
  gene299|gene299|rna299|rna299 1341 RGYLCGITRHGVNKAGA 1357
                                     *************9865 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.1   0.1   8.9e-77     2e-73       1     166 []     313     476 ..     313     476 .. 0.99

  Alignments for each domain:
  == domain 1  score: 246.1 bits;  conditional E-value: 8.9e-77
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SC CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkrk 80 
                                    Gkrvd+saR+vi+pdpn++l+evgvP +vak++t+pe+vt++ni+kl+klv++gp+++Pga+yv r+dg++ +l+ +  k
  gene299|gene299|rna299|rna299 313 GKRVDFSARTVITPDPNISLEEVGVPLEVAKVHTFPEKVTSFNIDKLEKLVRTGPNEHPGANYVLRSDGQKIDLNFN--K 390
                                    9****************************************************************************..6 PP

                                    HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHH CS
                 RNA_pol_Rpb1_2  81 lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEa 160
                                    ++ +le+g+iverh+++gdvvl+NRqPsLhk+s+mah+++v++ kt+rlnlsvt++yNaDFDGDemnlh+pqs++++aE+
  gene299|gene299|rna299|rna299 391 SDIRLEEGYIVERHMQTGDVVLFNRQPSLHKMSMMAHYARVMDDKTFRLNLSVTSPYNADFDGDEMNLHMPQSYTSKAEL 470
                                    69****************************************************************************** PP

                                    HHCSBT CS
                 RNA_pol_Rpb1_2 161 eelllv 166
                                    eel+lv
  gene299|gene299|rna299|rna299 471 EELALV 476
                                    **9875 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.4   0.2     7e-51   1.6e-47       1     157 []     479     663 ..     479     663 .. 0.92
   2 ?   -2.1   0.0       1.4   3.2e+03      58      96 ..     989    1020 ..     950    1059 .. 0.72

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 7e-51
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCC....................SSSSSSSSSBES CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsd....................sktvtlrpailk 60 
                                    +i+spqs+kPv+givQD+l+G++l+T +d+f+++ e++ lly ++ +                       +v+ rpai k
  gene299|gene299|rna299|rna299 479 QIISPQSNKPVMGIVQDTLTGLRLFTLRDTFLNEREVMLLLYAVNIEFcdtppggtsymelrrtkdydIMKVLKRPAIAK 558
                                    79******************************************777799999999998888776655366899****** PP

                                    SSEBEEHHHHHHCCCHCCCCEEEE...SSSS........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHH CS
                 RNA_pol_Rpb1_3  61 pkelwtgkqtfsrilpneinyerk...neek........dgkvlikngelikGvidkkvvgkksqgslihvlakeygike 129
                                    p +lwtgkq++s++lp ++ny ++   +  +        d+kv+i++g + +Gvidkk+ g ++qg+l+h++++++g+k+
  gene299|gene299|rna299|rna299 559 PMKLWTGKQILSFVLP-NMNYVGFsseH--NdndnenisDTKVIIQDGYIHSGVIDKKAAG-ATQGGLVHIIFNDFGPKR 634
                                    *88*************.9*****97652..1457889************************.9***************** PP

                                    HHHHHHHHHHHHHHHHHHHC.EB-TGGGG CS
                 RNA_pol_Rpb1_3 130 tvrfldslqrlgfkyllqsg.ftigigDt 157
                                    +++f++ +qr+++ +++  + f+igigDt
  gene299|gene299|rna299|rna299 635 AAQFFNGVQRMINVFMTGIHtFSIGIGDT 663
                                    *****************8888*******7 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                     BESS.SEBEEHHHHHHCCCHCCCCEEEESSSSSTSEEECS CS
                 RNA_pol_Rpb1_3   58 ilkp.kelwtgkqtfsrilpneinyerkneekdgkvlikn 96  
                                     il + k+l t + ++ +++  ++n++r         l+++
  gene299|gene299|rna299|rna299  989 ILETqKSLMTSNKILNVLIRTNLNVKRV--------LLEH 1020
                                     6666677888888888888888888874........3322 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.3   0.2   4.9e-41   1.1e-37       3     108 .]     689     794 ..     687     794 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.3 bits;  conditional E-value: 4.9e-41
                                    HHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBS CS
                 RNA_pol_Rpb1_4   3 eaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkr 82 
                                    e+ r+++le+lpg++++e+fe+  n +ln+ard +g++a++sl+++N++++Mv +G+KGs+inisq+++c+Gqqnvegkr
  gene299|gene299|rna299|rna299 689 ENARQNRLERLPGMTMKESFESHLNLVLNRARDVSGTSAQRSLSENNNMKTMVLAGSKGSFINISQVTACVGQQNVEGKR 768
                                    45566***************************************99********************************** PP

                                    S--SSTSCSSTTSSSSESSTTTSSEE CS
                 RNA_pol_Rpb1_4  83 ipkgfsgrtlphfkkidespesrGFv 108
                                    ip+gfs+rtlphf k+d++ +srGFv
  gene299|gene299|rna299|rna299 769 IPFGFSHRTLPHFVKDDYTGRSRGFV 794
                                    *************************8 PP

>> RNA_pol_Rpb1_7  RNA polymerase Rpb1, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.2   2.8e+03      32      69 ..     986    1026 ..     984    1041 .. 0.66
   2 !   89.9   0.0   5.9e-29   1.3e-25       5     106 ..    1129    1230 ..    1126    1254 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                                     TTS--------..-----SBEEEEEE-SHHH.HHTT--HHH CS
                 RNA_pol_Rpb1_7   32 eyyelpdedve..ksrlspWlLRieLdrkkm.tdkkltmee 69  
                                      yy l+ ++    ++++ + l+R +L+ k++ +++kl++e 
  gene299|gene299|rna299|rna299  986 PYYILETQKSLmtSNKILNVLIRTNLNVKRVlLEHKLNTEA 1026
                                     566665554443258999999*****988762578888654 PP

  == domain 2  score: 89.9 bits;  conditional E-value: 5.9e-29
                                     GTEEEEEEEB---TTS-SSGGGGHHHHTTS-------------SBEEEEEE-SHHHHHTT--HHHHHHHHHHHHTTTE CS
                 RNA_pol_Rpb1_7    5 kvtaateiyYDPdprntvieeDrefveeyyelpdedveksrlspWlLRieLdrkkmtdkkltmeevaekikeefkndl 82  
                                     +++ ++eiyYDP++++t i+eD++fve+y+e+pd+dv+ s lsp+l+R+ +dr+k++ +  ++e vae i +e ++  
  gene299|gene299|rna299|rna299 1129 DLCLSSEIYYDPEITSTEIAEDKDFVETYFEFPDDDVDFSCLSPFLMRLIVDRAKLVGRGANLEYVAESIRKELGSGA 1206
                                     567789*******************************99*************************************** PP

                                     EEEE--TTSSSEEEEEEE------ CS
                 RNA_pol_Rpb1_7   83 kvifsddnaeklvlririvkeeke 106 
                                     +vi+sd+na ++v+rir+ k+e+e
  gene299|gene299|rna299|rna299 1207 HVICSDENAVHMVIRIRVGKSEDE 1230
                                     ******************996443 PP

>> RNA_pol_Rpb1_6  RNA polymerase Rpb1, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3         2   4.4e+03      56     113 ..     677     736 ..     665     741 .. 0.66
   2 !   54.8   0.8   4.6e-18     1e-14       2     189 ..     868    1039 ..     867    1041 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                    HHHHHHHHHHHHHHHHHHHHTT-T..T.--.-EEE..EES-HHHHHHHHHHHTT--SSS- CS
                 RNA_pol_Rpb1_6  56 qelldeEyeqLkedRellrkeifpdee.kd.ekvklqLPvNikRlienaqkefkidkrke 113
                                     ++ +eE   ++e+ ++ r e +p  + k+  + +l+L++N +R ++ + ++ +++++++
  gene299|gene299|rna299|rna299 677 IRKAKEEVSVIIENARQNRLERLPGMTmKEsFESHLNLVLNRARDVSGTSAQRSLSENNN 736
                                    455667777777766666666666544433377788899999999988888888766665 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 4.6e-18
                                     -GGGEEEEE-TTSSS-HHHHHHHH---TTSSSSS--T.TTSSSHH..HHTT-TTHHHHHHHHHHHHHHH....HHHHH CS
                 RNA_pol_Rpb1_6    2 dgafiEkQkidllklsdekfekkYkldlddekkselk.elleeevveeiredaelqelldeEyeqLked....Rellr 74  
                                     d++f+E+Qk+d+     ++f k+Y +d+  +++  +k + ++eev+ ++++d++lq+lld+Eye L+++      ll 
  gene299|gene299|rna299|rna299  868 DATFLESQKVDV-----KNFTKRYYIDMFGSGELAIKqDQVSEEVYGMLSSDVDLQKLLDQEYEWLVSEifegPSLLS 940 
                                     899999999865.....88*********97777777779*************************98866222245555 PP

                                     H.TT-T..T...--.-EEE..EES-HHHHHHHHHHHTT--SSS-B---HHHHHHHHHHHHTT--SS-SSSHHHHHHHH CS
                 RNA_pol_Rpb1_6   75 k.eifpdee...kd.ekvklqLPvNikRlienaqkefkidkrkesdlspveviekvkelldklvvvrgddklskeaqe 147 
                                     + ei  d++   +d  k  +  P+N+ Rl+ +a++ f++   +  d+sp +++e  k+l+++  +             
  gene299|gene299|rna299|rna299  941 TgEIDIDHDyqvRDiYKNAVMSPCNFTRLLVTAKRAFHL---STGDVSPYYILETQKSLMTSNKI------------- 1002
                                     4255555556675555556678*****************...5689************9976665............. PP

                                     HTTTHHHHHHHHTS-HHHHHHTS---HHHHHHHHHHHHHHHH CS
                 RNA_pol_Rpb1_6  148 natllfkillrstLasKrvleeyrLskeaFdwllgeiesrFk 189 
                                          +++l+r++L+ Krvl e++L++eaF+w+++ i+++  
  gene299|gene299|rna299|rna299 1003 -----LNVLIRTNLNVKRVLLEHKLNTEAFNWVVEMINAKIL 1039
                                     .....459****************************998865 PP

>> RNA_pol_Rpb1_R  RNA polymerase Rpb1 C-terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.7   8.4e+03       7      12 ..     441     446 ..     440     446 .. 0.82
   2 ?   11.4  16.2   0.00014      0.32       1      14 []    1467    1480 ..    1467    1480 .. 0.98
   3 ?    3.3   6.9     0.056   1.2e+02       1      10 [.    1481    1490 ..    1481    1494 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.7
                 RNA_pol_Rpb1_R   7 ySPtSP 12 
                                    +S tSP
  gene299|gene299|rna299|rna299 441 LSVTSP 446
                                    799999 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00014
                 RNA_pol_Rpb1_R    1 SPTSPaySPtSPgY 14  
                                     SPTSP+ySPtSP+Y
  gene299|gene299|rna299|rna299 1467 SPTSPSYSPTSPSY 1480
                                     9************9 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.056
                 RNA_pol_Rpb1_R    1 SPTSPaySPt 10  
                                     SPTSP+yS +
  gene299|gene299|rna299|rna299 1481 SPTSPSYSIS 1490
                                     9******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.99u 0.36s 00:00:01.35 Elapsed: 00:00:00.56
# Mc/sec: 8202.39
//
Query:       gene3|gene3|rna3|rna3  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.6e-11   42.3   2.7    9.2e-11   41.9   2.7    1.3  1  DUF866         Eukaryotic protein of unknown function (DUF866
  ------ inclusion threshold ------
       0.12   12.6   0.8       0.48   10.6   0.8    2.0  1  Zn-ribbon_8    Zinc ribbon domain
       0.13   12.8   4.9        3.5    8.2   2.3    2.2  2  Ribosomal_L44  Ribosomal protein L44


Domain annotation for each model (and alignments):
>> DUF866  Eukaryotic protein of unknown function (DUF866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   2.7   1.5e-14   9.2e-11       4     131 ..       7     142 ..       4     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.5e-14
                            EEEEEESEEEEE--T...T--EEEEEEETTSS.-EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEEEEE-............. CS
                 DUF866   4 ikaelenvtslepadeeedfeytfkvkctsCreehpkevsisreekveisgsrgeanfvvkcklckressisikke............ 79 
                            ++ e++n++ + +     d+ y ++++ct+C+  h+k v++s  ++v   + ++++n++v+c++ckr ++++i k             
  gene3|gene3|rna3|rna3   7 VEGEFNNIKGVFI-----DQSYPLRIRCTNCGAPHEKVVVLSD-DSVAEGDFKEKVNLSVNCRSCKRMMTLKILKLkeakkhmlptkf 88 
                            7889*********.....579***********88887776655.55555899*********************997555444433332 PP

                            ..-TTTTEEEGGTS-E............EEEEEEEESEEEEEE---S-EEEEETTS-EEEEE--TS CS
                 DUF866  80 ..teksytaedsgkfk............tilefdcrGlelvefkpeggwkvesasgtkfedvdLse 131
                              +           fk             + ++++ G e++  +    ++++s +   f++ d+++
  gene3|gene3|rna3|rna3  89 edE-----------FKevwftdmeksrfLVSRIETNGAEVMSIESC-ILNMVSNQDVLFTNADFED 142
                            221...........22222233333334778889999888877744.4555555555577777775 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8     8e-05      0.48       7      33 ..      28      66 ..      26      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8e-05
            Zn-ribbon_8  7 rCeeCghefevlqsisdap...........lta.CPeCg 33
                           rC++Cg  +e+++  sd++           l + C +C+
  gene3|gene3|rna3|rna3 28 RCTNCGAPHEKVVVLSDDSvaegdfkekvnLSVnCRSCK 66
                           8*********88877766656666666676555577775 PP

>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0066        39      52      65 ..      25      38 ..      22      41 .. 0.84
   2 ?    8.2   2.3   0.00058       3.5      48      72 ..      54      78 ..      51      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0066
                           EEEEETTT--EEE- CS
          Ribosomal_L44 52 lrleCteCkkkrlk 65
                           lr++Ct+C+  + k
  gene3|gene3|rna3|rna3 25 LRIRCTNCGAPHEK 38
                           8********88766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00058
                           BB--EEEEETTT--EEE----BBS- CS
          Ribosomal_L44 48 KKivlrleCteCkkkrlkalkRakk 72
                            K++l ++C  Ck++ ++++ ++k+
  gene3|gene3|rna3|rna3 54 EKVNLSVNCRSCKRMMTLKILKLKE 78
                           59******************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 959.25
//
Query:       gene30|gene30|rna30|rna30  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1509.69
//
Query:       gene300|gene300|rna300|rna300  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-10   39.2   2.5    1.5e-09   37.8   2.5    1.8  1  Skp1      Skp1 family, dimerisation domain
    0.00016   21.8   0.4    0.00036   20.6   0.4    1.6  1  Skp1_POZ  Skp1 family, tetramerisation domain
  ------ inclusion threshold ------
      0.093   12.6   0.2       0.24   11.3   0.0    1.7  2  DUF3385   Domain of unknown function (DUF3385)


Domain annotation for each model (and alignments):
>> Skp1  Skp1 family, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   2.5   2.6e-13   1.5e-09       2      48 .]     102     148 ..     101     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.6e-13
                           Skp1   2 gLldltcktvAdmikgktpeeiReiFnIenDftpEEeeeirkEneWa 48 
                                    +Ll+l+ck ++ ++k k++ e+ e+ ++e+ +t+EE  +i++E eW+
  gene300|gene300|rna300|rna300 102 YLLELCCKIISEKMKHKNTRELAEFIGVECNITDEELMKIEREFEWI 148
                                    6********************************999999*******6 PP

>> Skp1_POZ  Skp1 family, tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   6.1e-08   0.00036       2      57 ..       1      53 [.       1      57 [. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 6.1e-08
                                   EEEEEETTSCEEEEEHHHHTTSHHHHHHHHCTCCCGTTCEEETTS-HHHHHHHHHH CS
                       Skp1_POZ  2 sivLqSsDgesfeveeavakkSktikhmiedlgdddkpriplpnvtskiLekvieY 57
                                   +i +++ Dg +f++ee+ a kS++ik++      +++  i l +v+s+i e +  Y
  gene300|gene300|rna300|rna300  1 MIEIETTDGRIFKIEEKQAYKSVLIKNVCTSTTYKNP--IAL-QVSSFIFEIIQRY 53
                                   7999************************998888877..877.6999999887666 PP

>> DUF3385  Domain of unknown function (DUF3385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.4   2.4e+03     119     119 ..      39      39 ..      10      68 .. 0.52
   2 ?   11.3   0.0     4e-05      0.24       5      36 ..      97     128 ..      95     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                        DUF3385 119 g 119
                                     
  gene300|gene300|rna300|rna300  39 A 39 
                                    1 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4e-05
                        DUF3385   5 yleypqLLelLlnilkteqsqsirrevikllG 36 
                                    yleyp LLel ++i+ ++++ +  re +  +G
  gene300|gene300|rna300|rna300  97 YLEYPYLLELCCKIISEKMKHKNTRELAEFIG 128
                                    9*****************87777778777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1016.88
//
Query:       gene301|gene301|rna301|rna301  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-19   68.0   0.1    7.5e-19   67.9   0.1    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.1   4.2e-23   7.5e-19       1      78 [.       7      93 ..       7      95 .] 0.97

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 4.2e-23
                                   EEEEESHHHHHHHHHTTCEEEE..........CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEE CS
                     ATP-synt_F  1 iavIGdedtvtgfrlaGvgeve..........vtdeeeieealkelleredigiilitekiaeeirelideykeealPaile 72
                                   i++IGde+t+tgf+ aGv+ v           +t e+++++++ +l+ r+d +iil+++  ae+++e+id+y+e + Pa+l 
  gene301|gene301|rna301|rna301  7 IGIIGDEETLTGFLIAGVESVHdnpnlvqvtpNTAEDDLKRIFCSLTGRKDLAIILVCDFAAEKLKEEIDAYNE-VVPAVLV 87
                                   89***************************9999999**************************************.******* PP

                                   ESCSCC CS
                     ATP-synt_F 73 IPskeg 78
                                   I sk++
  gene301|gene301|rna301|rna301 88 IASKNK 93
                                   **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 627.05
//
Query:       gene302|gene302|rna302|rna302  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-22   79.6   0.0    2.9e-22   79.4   0.0    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16
  ------ inclusion threshold ------
      0.055   13.4   0.1       0.07   13.1   0.1    1.1  1  DUF2677       Protein of unknown function (DUF2677)
      0.085   12.8   0.0       0.14   12.1   0.0    1.3  1  DUF4265       Domain of unknown function (DUF4265)
        0.1   12.7   0.1       0.17   12.1   0.1    1.3  1  DUF1244       Protein of unknown function (DUF1244)


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4   0.0   6.5e-26   2.9e-22       1     121 []      12     145 .]      12     145 .] 0.83

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 6.5e-26
                                    EECTTEEEEEEEE.ESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSS....SEEEEEEEESS-HHHHHHHHHHHHH CS
                   Ribosomal_S9   1 GrrKesvArvwik.egkgkilvngksleeYfkeeaarekvleplkltgllg....kfdvfvkvkgGGlsgqaeAirlgia 75 
                                    Gr+K++vA++ ++ +g+ +i++n+++++  ++++ + +k++e + +++  +    +fd++  +k GG +++++A+r++++
  gene302|gene302|rna302|rna302  12 GRKKRAVATCVCTySGEFSIRINKVPFKL-ITNTLMIAKLKEIICIVEHANikdlSFDIT--CKVGGDVSRVYAVRMAFS 88 
                                    9********999735699***********.88899**********999988875555555..555*************** PP

                                    HHHHHHHH.....HHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                   Ribosomal_S9  76 raLvalek.....eekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                    +a++a++       +k+e++      ++  l++D+R++E+kK+g ++AR++yq+s+R
  gene302|gene302|rna302|rna302  89 KAILAFYGtyydeWKKQEIQkrlldfDRFSLVADSRKREPKKFGGPGARARYQKSYR 145
                                    ******854444422334433333577999*************************99 PP

>> DUF2677  Protein of unknown function (DUF2677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.6e-05      0.07      88     148 ..      32      94 ..      12     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                        DUF2677  88 tinat.lrllirdgmygrgekelciahlptlrdir...tcrvdadlgllyavclilsfsivtaal 148
                                     in   ++l+    m  + ++ +ci     ++d+    tc+v  d+  +yav + +s +i+  a+
  gene302|gene302|rna302|rna302  32 RINKVpFKLITNTLMIAKLKEIICIVEHANIKDLSfdiTCKVGGDVSRVYAVRMAFSKAIL--AF 94 
                                    55554145555556777777779**99999999855559*************987776665..44 PP

>> DUF4265  Domain of unknown function (DUF4265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.1e-05      0.14      32      97 ..       9      74 ..       6      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                        DUF4265 32 evdedeerlafervvkesGnstirvlvdekaelgesevreeLealgceveglsakllavdvpadvd 97
                                   +++ +++r +   v + sG++ ir+   + +   +  ++++L+++ c ve  + k l++d+  +v+
  gene302|gene302|rna302|rna302  9 TTQGRKKRAVATCVCTYSGEFSIRINKVPFKLITNTLMIAKLKEIICIVEHANIKDLSFDITCKVG 74
                                   556677888889999**************99988899**********************9987664 PP

>> DUF1244  Protein of unknown function (DUF1244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.8e-05      0.17      29      53 ..      82     106 ..      71     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                                    T----HHHHHHHHHSS-HHHHCHCH CS
                        DUF1244  29 gvelskdearelvYgmpyeeWkakh 53 
                                     v++   +a  ++Yg+ y+eWk++ 
  gene302|gene302|rna302|rna302  82 AVRMAFSKAILAFYGTYYDEWKKQE 106
                                    577888899999**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 928.44
//
Query:       gene303|gene303|rna303|rna303  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-38  132.2   1.9    2.1e-38  132.0   1.9    1.1  1  Ribosomal_L13e  Ribosomal protein L13e


Domain annotation for each model (and alignments):
>> Ribosomal_L13e  Ribosomal protein L13e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   1.9   1.2e-42   2.1e-38       2     131 ..       7     135 ..       6     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 1.2e-42
                 Ribosomal_L13e   2 ipnnhfrKdwqrrvktwfdqparkkrRrearqakaakvaprpvekLrPvVrcptvrYntkvraGrGFtleElkaagiskk 81 
                                    +pnnhfrK+   ++k++ d +++ +  +e++ +ka++++p p++kLrP++rcp+++Yn+  r+GrGFt +E+ +ag++ +
  gene303|gene303|rna303|rna303   7 LPNNHFRKTS-LKIKVHHDPETKLRIMEEKKLRKAKSMFPIPLKKLRPIIRCPSIKYNRNERLGRGFTPAECEKAGLDYR 85 
                                    89******76.67******************************************************************* PP

                 Ribosomal_L13e  82 lArtiGIavDhRrknkseeslkaNveRLkeYkskLilfprkakkpkkgda 131
                                     Ar +GIavD Rr+++++e+l++N +R+k+Y sk+ +++  +++ +kg +
  gene303|gene303|rna303|rna303  86 HARRLGIAVDLRRRDTNQETLEKNADRIKTYLSKITIYESVKEAKEKGAK 135
                                    **************************************999888888844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1052.49
//
Query:       gene305|gene305|rna305|rna305  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-56  189.7   3.2    1.3e-53  182.0   3.2    2.2  1  PIP5K     Phosphatidylinositol-4-phosphate 5-Kinase


Domain annotation for each model (and alignments):
>> PIP5K  Phosphatidylinositol-4-phosphate 5-Kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.0   3.2   7.4e-58   1.3e-53      10     272 ..      73     291 ..      65     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 182.0 bits;  conditional E-value: 7.4e-58
                                    ---SSS--EEEETTSSEEEEEE-HHHHHHHHHHHHHHHHHHTT-TT--S--EEEEEEEE.ETTEEEEEEEEE-SS-TTS- CS
                          PIP5K  10 seGkSgsffylteDkkfiiKtitksevkflrkllpeYyehvkenpnsLltrfyglhrvklkggkkvrfvVmenlfptdke 89 
                                      GkSgsf+++teD kf++Kti+kse+ ++r++++eY  h+ +np sLl++++g++++  ++g++ +f+Vme+++ +   
  gene305|gene305|rna305|rna305  73 IHGKSGSFLFFTEDLKFVVKTIRKSEFYCIRRMVEEYKIHILQNPMSLLCKILGCYSL-CTRGDEEYFIVMESML-KRSG 150
                                    57********************************************************.5699999*********.7899 PP

                                    -SEEEEE-S--TT-S--HHHHTSSS-EEEHHHHHHHST.EEE-HHHHHHHHHHHHHHHHHHHHTTB-S-EEEEEEEB--- CS
                          PIP5K  90 iheryDLKGstvgReakkkeeekkektlkDlDliekkeklklgkekreelleqlekDvefLeslnimDYSLLlGihnsek 169
                                    ++e yDLKG +v+R+  +         lk+ D+i +++++ lg++ +e++++q+++DvefL++++imDYS+++ +  +++
  gene305|gene305|rna305|rna305 151 MQEIYDLKGASVKRKGYS------VSSLKEIDWIGNSKRIDLGNR-KEAIISQIKNDVEFLKRHRIMDYSFFVSFGWKKR 223
                                    9************98775......3459**************986.999************************9966653 PP

                                    -----------------------------------------SEEEEESSSSEEEEEEEEE----B--------------- CS
                          PIP5K 170 eekeekkesessssekesekseeeaseeeeeseeeedeegekakeensedgkevyylgiIDiLqkynlkKklehalkslk 249
                                    e+                                   +  +  k++n+ +++e + +gi+DiL+++++kK++e+++  ++
  gene305|gene305|rna305|rna305 224 ESV----------------------------------DPFSLCKDHNHMPENEDVHFGIVDILTQWTFKKRMERLFHIFC 269
                                    332..................................34445667888999999*************************7 PP

                                    -------TTHHHHHHHHHHHHHH CS
                          PIP5K 250 kdkksisavpPkeYaeRFlkfie 272
                                     ++ ++s+++P+ Y +RFl +ie
  gene305|gene305|rna305|rna305 270 CKS-NSSCLNPDAYMDRFLIMIE 291
                                    777.69*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1802.84
//
Query:       gene306|gene306|rna306|rna306  [L=564]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-27   95.5   0.0    4.4e-27   94.5   0.0    1.5  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.9e-15   57.3   0.0    8.6e-15   55.2   0.0    2.0  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    4.3e-14   52.7   0.0    7.8e-14   51.8   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
     0.0004   20.5   0.0     0.0011   19.0   0.0    1.8  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   9.7e-31   4.4e-27       2     135 ..      64     193 ..      63     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 9.7e-31
                                    GGBBTTCEEEECCHCT..BSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-H CS
                      PGM_PMM_I   2 qkfgtsGlRgkvgege..ltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllpt 79 
                                    +kfgt G+Rg +  g   +++ +   +g  +++ +++      +v+G D+R+ s   a  l +++  nG ++ l+  + t
  gene306|gene306|rna306|rna306  64 MKFGTGGMRGPMRSGFngINEVTCNLIGTELCKRFSS------IVIGCDGRYNSLNYAILLREIFRLNGKKADLYPEVVT 137
                                    69***********998888888888888888888886......************************************* PP

                                    HHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT- CS
                      PGM_PMM_I  80 PavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiiekee 135
                                    P ++f++ kl+a+agim+taSHnp+eyng+Kvy+s+G +i p+ +++Ie+++++ +
  gene306|gene306|rna306|rna306 138 PFLAFLTCKLGAEAGIMVTASHNPKEYNGFKVYTSKGSQIGPPLDREIEESMRALD 193
                                    **************************************************998876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   1.9e-18   8.6e-15      17      99 ..     266     351 ..     253     356 .. 0.85
   2 ?   -1.5   0.0      0.86   3.9e+03      15      46 ..     442     475 ..     431     508 .. 0.72

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.9e-18
                                    HHHT-E.EEEE-TT-TTHHHHHHHHHHTT-....EEEES-----TT-TT.SS----TT-TTTTHHHHGGGGG-SEEEEE- CS
                     PGM_PMM_II  17 kksglk.vvidplhGaggeilkellkelgv....dvvelnaepdpdfpt.kapnpeekealkllielvkkegadlglafD 90 
                                    + s+l  +v++ l G++ge++k++l+ +++     ++ ++++p+pdfp+  +pnpe +e+l++     +++ ad+++++D
  gene306|gene306|rna306|rna306 266 NTSPLVpIVFTGLCGVSGEFVKKALEFYNLdgtvYFIDEECNPNPDFPNlPFPNPEVAETLARS---KESNLADIIFSCD 342
                                    4444444*************************999999*******************8888888...566677******* PP

                                    TTS-BEEEE CS
                     PGM_PMM_II  91 gDaDRlgvv 99 
                                    +D+DR+g+ 
  gene306|gene306|rna306|rna306 343 PDGDRFGLS 351
                                    ******986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.86
                                    HHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-..E CS
                     PGM_PMM_II  15 aikksglkvvidplhGaggeilkellkelgv..d 46 
                                     ++k+g+k v+  ++ + +e+ +++lk++++   
  gene306|gene306|rna306|rna306 442 GKEKDGIKCVVLMAYMVQKELPSKILKKMEMygS 475
                                    5677888888888888888888889988877552 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.7e-17   7.8e-14       1     107 [.     362     467 ..     362     473 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.7e-17
                                    HHHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTT..ECEEEETTCEEEETT CS
                    PGM_PMM_III   1 dgdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeeg..avlGgEeSghiifld 78 
                                    +g++++a++   + ++  + + + v+t  +++++e+v+ ++gi++++t +G+k+v + +++ +   v+++E S +++f++
  gene306|gene306|rna306|rna306 362 NGNEIAAMFMYFFVKNFSPSDLAFVNTYLCNDLMEKVCSAHGIEYLKTETGFKNVSRGVDSVKgkKVFAYEDSLGFLFGN 441
                                    79*********999984444559*************************************986669*************7 PP

                                    TBSS--HHHHHHHHHHHHHHHTS-HHHHH CS
                    PGM_PMM_III  79 eattkDGilaallvleilaetgkslsell 107
                                      ++kDGi  ++l++ +++++   +s++l
  gene306|gene306|rna306|rna306 442 G-KEKDGIKCVVLMAYMVQKE--LPSKIL 467
                                    7.69************99876..355555 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.6e-07    0.0011       4      72 ..     483     553 ..     481     556 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.6e-07
                                    CCHCC-TT...EECCCCCTTHHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEES..SHHHHHHHHHHHHHH CS
                     PGM_PMM_IV   4 vrveekak.vvaalaallkvasikeglkilledGrrlavRpSGTepllrvyvEak..sdeelarlaeevael 72 
                                    vr+ ++++   +al++l  v+ + +  ++++ +  ++ +R SGTe++++vy  ++  +++ la++a +++++
  gene306|gene306|rna306|rna306 483 VRCSNPDNvLERALRKLPNVKTEGKRSAVKFDNYKVI-LRVSGTESMVKVYTSSTalDKKSLAKVANDFIDK 553
                                    6667766655555666655555566667888888999.**************99889999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4088.00
//
Query:       gene307|gene307|rna307|rna307  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-19   68.4   5.1    1.6e-18   67.1   5.1    1.7  1  DUF4451   Domain of unknown function (DUF4451)
  ------ inclusion threshold ------
      0.093   12.9   0.6        2.3    8.4   0.0    2.2  2  PHF5      PHF5-like protein


Domain annotation for each model (and alignments):
>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   5.1   1.8e-22   1.6e-18       5     122 .]      75     170 ..      72     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.8e-22
                        DUF4451   5 dlYeprvvrgekdknekkeglCpiCeeevekkekflklknssyekhlsfeHGvlsngslvpePillrskkrrkakekeke 84 
                                    d+Y+pr vrg   +++ +eg C iC+        ++klk+ssy++h++++HG++s+g+++peP + ++         +k 
  gene307|gene307|rna307|rna307  75 DMYKPRKVRG---VGRLREGCCGICN-------SWFKLKTSSYWYHMNYKHGISSKGIKYPEPQIRYT--------GDKV 136
                                    89********...9************.......8*****************************98843........3345 PP

                        DUF4451  85 givCpkCneiievslsknkkekkvnellayfrHfkkch 122
                                      +C  C e+i++++++n+k+++    + +frH +k h
  gene307|gene307|rna307|rna307 137 DGFCMICDEWITLGYKSNRKSTR----FGWFRHCQKKH 170
                                    568***********999999984....56******998 PP

>> PHF5  PHF5-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.016   1.4e+02      24      41 ..      87     104 ..      76     108 .. 0.75
   2 ?    8.4   0.0   0.00026       2.3      12      38 ..     122     148 ..     111     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.016
                           PHF5  24 ekcdgkcpicdslvkpat 41 
                                    +  +g c ic+s +k +t
  gene307|gene307|rna307|rna307  87 RLREGCCGICNSWFKLKT 104
                                    556899999999887655 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00026
                           PHF5  12 rkqpGtaigklcekcdgkcpicdslvk 38 
                                     k p  +i +  +k dg c+icd  ++
  gene307|gene307|rna307|rna307 122 IKYPEPQIRYTGDKVDGFCMICDEWIT 148
                                    577788899999***********9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.54
# Mc/sec: 985.42
//
Query:       gene309|gene309|rna309|rna309  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-13   48.6   0.7      6e-13   48.3   0.7    1.1  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.7   3.3e-17     6e-13       3      66 ..       7      69 ..       5      70 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 3.3e-17
                                   HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                            LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                   l+ ++nk+v +elkn+  lrG L  +D  mNl+L+ v+  ++d+ ++ ++++++++G++i l+ 
  gene309|gene309|rna309|rna309  7 LRISRNKIVELELKNNDHLRGLLYKCDMAMNLHLKSVTIQKEDG-SSIFINECYLKGTSIKLVK 69
                                   77799***************************************.****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 529.96
//
Query:       gene31|gene31|rna31|rna31  [L=545]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-22   79.7   0.1    1.1e-19   71.1   0.0    2.3  2  GRASP55_65  GRASP55/65 PDZ-like domain
    1.7e-10   40.6   0.0    8.9e-09   35.1   0.0    2.5  2  PDZ_6       PDZ domain
    2.4e-07   31.0   0.0    5.2e-05   23.5   0.0    2.4  2  PDZ_2       PDZ domain
      1e-05   25.8   0.1    0.00056   20.2   0.0    2.5  2  PDZ         PDZ domain


Domain annotation for each model (and alignments):
>> GRASP55_65  GRASP55/65 PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0019       8.5      44     103 ..      10      69 ..       4      80 .. 0.88
   2 !   71.1   0.0   2.5e-23   1.1e-19      24     136 ..      81     187 ..      65     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0019
                                -EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTTTSSS-EEEEEEETTT CS
                 GRASP55_65  44 vwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselveaheekelkLlvYnses 103
                                  ++l+v egs  +k g++p+   i+ ++ + +++++d   + +++e+k+l+L + +  +
  gene31|gene31|rna31|rna31  10 SLQILKVSEGSVSHKNGVLPFIHSIVSFNGKAIESKDDALAMNKEWESKALNLELIDMRT 69 
                                568**********************************************99997766655 PP

  == domain 2  score: 71.1 bits;  conditional E-value: 2.5e-23
                                SSSSSSEEEEEEE-TTTTTS-EEEEEEBTTSHHHHHT--TTTEEEEEEE.SSSSSTSCSHHHHTTTSSS-EEEEEEETTTTEEE CS
                 GRASP55_65  24 gqgllGlslrlaslekaaeevwhvldvlegsPaakagLvpksDYiiGldkgllkgeedlselveaheekelkLlvYnsesdevr 107
                                +++ lG+s+++ +   a+   + vl v++gsPa+kag+v   DYi+G+++   k+e+dl + +e ++ + + LlvYn++ + vr
  gene31|gene31|rna31|rna31  81 DKTRLGISVKFHQSM-ASLLSMEVLRVNPGSPAEKAGIV-VGDYILGIENIYSKDEDDLLRFLELNRRRVVPLLVYNNDLEYVR 162
                                5689********999.888899***************98.68****************************************** PP

                                EEEE---TTSSSSTTTSEEEE-SGGGS-- CS
                 GRASP55_65 108 evtvkpsrewGgegalGcdvgyGlLhriP 136
                                 v +    ++G + +lGc++g+G L ++P
  gene31|gene31|rna31|rna31 163 VVPL----QVGMDVLLGCQIGMGELYKVP 187
                                ****....9*******************9 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.022        98      22      41 ..      34      51 ..      15      64 .. 0.88
   2 !   35.1   0.0     2e-12   8.9e-09       2      54 ..     103     153 ..     102     155 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.022
                      PDZ_6 22 ilsvNGqpveglsladvaal 41
                               i+s+NG+ +  +s +d+ a+
  gene31|gene31|rna31|rna31 34 IVSFNGKAI--ESKDDALAM 51
                               99*******..999998765 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 2e-12
                      PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlvv 54 
                                V  V pgsPA++AG+ vGD+il + ++    ++ +d+ + l+ + ++ v l+v
  gene31|gene31|rna31|rna31 103 VLRVNPGSPAEKAGIVVGDYILGIENIYS--KDEDDLLRFLELNRRRVVPLLV 153
                                778**************************..***********88888888877 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0075        33      15      53 ..      10      49 ..       5      65 .. 0.86
   2 !   23.5   0.0   1.2e-08   5.2e-05       3      56 ..      85     141 ..      83     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0075
                               -EEEEEE-TTSGGGGT..--TT-EEEEETTB--SSHHHHH CS
                      PDZ_2 15 gvlvvsVkeggPaakag.lkagDvilkvdgkkvksledli 53
                                + + +V eg+ ++k g l     i++++gk+++s +d  
  gene31|gene31|rna31|rna31 10 SLQILKVSEGSVSHKNGvLPFIHSIVSFNGKAIESKDDAL 49
                               578999***********7777999*********9999875 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.2e-08
                                ..XX------.....-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHH CS
                      PDZ_2   3 lGvsvsdeed...tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlisll 56 
                                lG+sv+ +++      + v  V++g+Pa+kag+  gD il +++   k+++dl + l
  gene31|gene31|rna31|rna31  85 LGISVKFHQSmasLLSMEVLRVNPGSPAEKAGIVVGDYILGIENIYSKDEDDLLRFL 141
                                788888888855433445667**************************9999998755 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.029   1.3e+02      26      75 ..       9      57 ..       2      65 .. 0.81
   2 !   20.2   0.0   1.3e-07   0.00056       6      55 ..      79     128 ..      74     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.029
                               SSEEEEEECTTSHHHHHT.SSTTEEEEEETTEETTTSHHHHHHHHHHTTTS CS
                        PDZ 26 kgifvsevlpggaaeadg.lkvGDkIlsvNgvdvenvsheeavqaikgskg 75
                               k++ + +v++g+  ++ g l   + I+s Ng+ +e+   ++a +++k+  +
  gene31|gene31|rna31|rna31  9 KSLQILKVSEGSVSHKNGvLPFIHSIVSFNGKAIESK--DDALAMNKEWES 57
                               6788999***************************975..777777777655 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.3e-07
                                TSTTSESSEEEEEETTSSSSSSEEEEEECTTSHHHHHTSSTTEEEEEETT CS
                        PDZ   6 kegrgglGfslkggsdqrgdkgifvsevlpggaaeadglkvGDkIlsvNg 55 
                                ++ + +lG+s+k  ++     +  v +v+pg++ae++g+ vGD Il++ +
  gene31|gene31|rna31|rna31  79 RKDKTRLGISVKFHQSMASLLSMEVLRVNPGSPAEKAGIVVGDYILGIEN 128
                                5577899999999888889999*************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 3148.12
//
Query:       gene310|gene310|rna310|rna310  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00096   18.9  15.7     0.0027   17.4  12.2    2.4  3  DUF4203   Domain of unknown function (DUF4203)
     0.0069   15.9   3.5      0.016   14.7   3.5    1.5  1  GPI2      Phosphatidylinositol N-acetylglucosaminyltransferas


Domain annotation for each model (and alignments):
>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.011        97       3      25 ..      39      62 ..      37      96 .. 0.77
   2 ?   -0.8   1.7      0.11     1e+03      17      40 ..     108     131 ..     102     145 .. 0.68
   3 !   17.4  12.2   3.1e-07    0.0027      62     201 .]     118     253 ..     111     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.011
                        DUF4203  3 gailillG.lvlcffGyrlfkltl 25
                                   ga++illG ++++f+G r+ +++l
  gene310|gene310|rna310|rna310 39 GAWAILLGsFFVTFYGSRFPRISL 62
                                   788888884578999****99987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.11
                        DUF4203  17 Gyrlfkltlflsgfllgsllvlvl 40 
                                    G  +  +tl+++ f+l+s+l+++l
  gene310|gene310|rna310|rna310 108 GSNNDPATLCFISFVLASILMWAL 131
                                    555556677777777777777765 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.1e-07
                        DUF4203  62 vvGllgGllallfwelglfllgalgGlllallilsllegglitslpskaiflvivvlgllgavlslkl...qklllivat 138
                                    ++ ++++ ++++  e+++ ll +  Gl + + ++  l+   +++++   +f  ++ l + +++l+ +    +k+ll++ +
  gene310|gene310|rna310|rna310 118 FISFVLASILMWALEVASSLLFI-IGLYIVYRMFFHLGFETYKESNP-GVF--YILLFVSFGILYYVTrrtTKYLLLILF 193
                                    55566677766666666666644.55555555555553344444444.455..5666666666665555789******** PP

                        DUF4203 139 svvGaaavvlgiDyfvgaglkefll.nlfpratvalltypltrgdwvllalwivlalvGvlvQf 201
                                    s+ G+ ++   i +++++   e+   +l+ ++++  ++y+  +     +a+wi+ a++G+++Q+
  gene310|gene310|rna310|rna310 194 SITGSLILLTSIELITENN--ELGFyDLILDFED--TQYLELSSASTPIAVWIITAFIGMFWQW 253
                                    ******************8..4333466666666..688877888999***************9 PP

>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.5   1.7e-06     0.016     179     259 ..     118     197 ..     102     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-06
                           GPI2 179 mastvLASRLpstlqVFslllfsievfglfPvfrrslrhrswrlhvvltvllvllagagvgiilklllavvlllllalim 258
                                    + s vLAS L   l+V s llf i ++++ ++f +   +++ + + +++ +l+++++++++ + +   + +lll+l+ i+
  gene310|gene310|rna310|rna310 118 FISFVLASILMWALEVASSLLFIIGLYIVYRMFFHLGFETYKESNPGVFYILLFVSFGILYYVTR-RTTKYLLLILFSIT 196
                                    789*********************************99999999888888888888877777776.33333333333332 PP

                           GPI2 259 g 259
                                    g
  gene310|gene310|rna310|rna310 197 G 197
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1571.92
//
Query:       gene311|gene311|rna311|rna311  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-22   77.5   0.7    6.9e-22   77.3   0.7    1.0  1  SPC12     Microsomal signal peptidase 12 kDa subunit (SPC12)


Domain annotation for each model (and alignments):
>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.7   3.8e-26   6.9e-22       1      69 [.      13      81 ..      13      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 3.8e-26
                          SPC12  1 iDFeGQklaekllqvilvlsaviafivGyitqdlkltlyillagvvltllvvvPpWpfYnrnplkWlkp 69
                                   iD+ GQkla +l+++i+ +++++a+i+G  +++l +t+yi + ++v++++vvvP+W fY+rnplk+++p
  gene311|gene311|rna311|rna311 13 IDYVGQKLASDLMYLIFGVGYTAALIFGVSLNNLVYTMYISITTLVISAIVVVPSWGFYRRNPLKFRPP 81
                                   9*****************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 601.97
//
Query:       gene312|gene312|rna312|rna312  [L=591]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-39  134.9  23.9    2.5e-39  134.9  23.9    1.9  2  ABC2_membrane    ABC-2 type transporter
    2.3e-24   86.5   0.0    3.6e-24   85.8   0.0    1.3  1  ABC_tran         ABC transporter
    0.00023   21.1   0.8     0.0004   20.3   0.2    1.7  1  RsgA_GTPase      RsgA GTPase
    0.00062   19.0  24.2    0.00062   19.0  24.2    2.2  2  ABC2_membrane_3  ABC-2 family transporter protein
      0.002   17.6   0.0     0.0038   16.7   0.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.007   16.7   0.4      0.058   13.7   0.4    2.4  1  AAA_22           AAA domain
     0.0081   15.9   0.9      0.019   14.7   0.9    1.6  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.044   14.2   0.0    1.6  1  RNA_helicase     RNA helicase
      0.027   14.3   0.5       0.75    9.5   0.0    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.033   14.3   0.1      0.092   12.8   0.1    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
      0.036   14.6   0.0      0.087   13.4   0.0    1.7  1  AAA_18           AAA domain
      0.037   14.4   0.0      0.062   13.7   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.055   13.7   0.2        0.1   12.8   0.2    1.4  1  AAA_28           AAA domain
      0.077   12.7   0.0       0.36   10.5   0.0    2.1  2  AAA_24           AAA domain
      0.083   12.5   0.1       0.16   11.5   0.1    1.4  1  AAA_25           AAA domain
       0.15   12.2   0.0       0.26   11.4   0.0    1.4  1  AAA_33           AAA domain
       0.17    9.4   0.4       0.24    8.9   0.4    1.1  1  DUF3584          Protein of unknown function (DUF3584)
       0.34   11.4   1.9        1.6    9.2   2.1    1.8  1  AAA_23           AAA domain


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9  23.9   2.6e-42   2.5e-39       3     210 .]     314     523 ..     313     523 .. 0.97
   2 ?    0.8   0.1      0.27   2.7e+02      31      86 ..     523     585 ..     518     588 .. 0.67

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 2.6e-42
                  ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnrpgllffsvlflafsaltsvapvferergv 81 
                                    + +ll+r++++++r+  ++   + +q ++++lvfg+++ ++g + e++++r+g + f+++++ f     + +vf +er v
  gene312|gene312|rna312|rna312 314 FSLLLNRNLKNYIRNVDYL-KIKGFQKVFFMLVFGLAYLQMGySIESIYTRIGGITFILTNVLFGVSNPIFNVFSSERQV 392
                                    6789***************.88********************8888888******************************* PP

                  ABC2_membrane  82 lerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaasslgllisalapsfe 159
                                    + re++s++ys  + ++ak+l+e  +++l+ + +++++y+++gl  +   f+ fl ++  ++l++++++l+i+a+++++ 
  gene312|gene312|rna312|rna312 393 ILRERRSGMYSGIVAFMAKYLSETFINFLIEMPYVVTIYWMIGLSSDvsTFLVFLTIMGSLILFSIAYSLAIGAITSTQN 472
                                    ***********************************************9888999999999999999************** PP

                  ABC2_membrane 160 dasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnlf 210
                                    + ++l+s+ ll++l++sG f +++++p+wl+w+ +++P++ya++a ++n++
  gene312|gene312|rna312|rna312 473 NSQVLGSMGLLVFLIYSGSFNNPNTIPSWLRWVVWVSPMYYATKASVQNQL 523
                                    *********************************************999985 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                  ABC2_membrane  31 llalvfgtvfgnlg.nsedglnr.......pgllffsvlflafsaltsvapvferergvlerel 86 
                                    l ++vf + + ++  +++ ++ r       p ++f+++ +++f +++++ ++  +++ +++ el
  gene312|gene312|rna312|rna312 523 LNGVVFESSNIRITgEEQIRI-RgldgtgvPLCIFILLGMNFFWIVSGALALHLTTKNNMKMEL 585
                                    555566666655442222222.256788889999999999999999999888888888877666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0   3.6e-27   3.6e-24       1     137 []      30     178 ..      30     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 3.6e-27
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                    lk vs ++++++++a++G +GaGK+tL++ lag        +Geill++++ ++     + + +g+++qe +  +  tv 
  gene312|gene312|rna312|rna312  30 LKGVSGSIEPSTMTALMGTSGAGKTTLMNSLAGRIPSsmvLKGEILLNSHPRSK---DTWPNTVGYVEQEFHGYEYQTVF 106
                                    789*******************************98777789****99888777...99***********7777777799 PP

                                    HH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    e+                + +++ie++++ lgl++ k+t +     +LSgG+++rv++   ll +p++l++DEpt+
  gene312|gene312|rna312|rna312 107 ETllfaskikmryeeveqKIKNRIEEIIALLGLNNAKNTYI----VNLSGGERKRVSIGVELLGDPSILFCDEPTS 178
                                    999*********99888888888*****************9....*****************************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2     4e-07    0.0004      85     122 ..      25      63 ..       2      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 4e-07
                                    TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    ++k+ l+ ++  ++   +++l+G SG+GK+tL+n+l+++
  gene312|gene312|rna312|rna312  25 TNKTVLKGVSGSIEPsTMTALMGTSGAGKTTLMNSLAGR 63 
                                    5556666677777776899*****************986 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   5.5       0.2     2e+02     243     288 ..     341     383 ..     337     389 .. 0.72
   2 !   19.0  24.2   6.3e-07   0.00062     172     342 ..     374     566 ..     364     574 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.2
                ABC2_membrane_3 243 llfllfglayialgyllsslfknsetaqilifivilllsgffgglf 288
                                    +++l+fglay+ +gy + s+ ++ +    +++ v   l+g++ ++f
  gene312|gene312|rna312|rna312 341 FFMLVFGLAYLQMGYSIESIYTRIGGITFILTNV---LFGVSNPIF 383
                                    799*****************99986654433333...445555554 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 6.3e-07
                ABC2_membrane_3 172 ifitasfiavsi.veEkesrikelqlvsgvsplqywlskilgdflvyllqlllill.l..afglgipfgnlglllllfll 247
                                    +++++s+ ++++  +E++  ++e+   +  s +  +++k+l+  ++ +l+ + +++ +  ++g  ++ + + +l++l ++
  gene312|gene312|rna312|rna312 374 VLFGVSNPIFNVfSSERQVILRERRSGM-YSGIVAFMAKYLSETFINFLIEMPYVVtIywMIG--LSSDVSTFLVFLTIM 450
                                    4444444444444788888888888888.8888899999999888888887655554335999..777755555555555 PP

                ABC2_membrane_3 248 f..glayialgyllsslfknsetaqilifivilllsgffgglfp.ledlpsalkwifsiiPffapglgllrli.tgdplw 323
                                    +  +l +ia +++++++++++ + q+l ++ +l  ++++ g+f   +++ps+l+w+ ++ P+++ +++ ++   +g+  +
  gene312|gene312|rna312|rna312 451 GslILFSIAYSLAIGAITSTQNNSQVLGSMGLL-VFLIYSGSFNnPNTIPSWLRWVVWVSPMYYATKASVQNQlNGV-VF 528
                                    52366788888999*******999998877776.8888888888799999******************999863444.66 PP

                ABC2_membrane_3 324 e...................illsliilalfavvylll 342
                                    e                   ++ +l i +l++  ++++
  gene312|gene312|rna312|rna312 529 EssniritgeeqirirgldgTGVPLCIFILLGMNFFWI 566
                                    67888888888888888888555555555555555554 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.8e-06    0.0038      25     202 ..      41     211 ..      27     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.8e-06
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                     +ta++G  G+GK+ l++++   +   s+  l+ e l +   +sk+    + ++ve  f+  + + ++ ++ +  s+ ++
  gene312|gene312|rna312|rna312  41 TMTALMGTSGAGKTTLMNSLAGRIP--SSMVLKGEILLNSHPRSKDTWPNTVGYVEQEFHGYEYQ-TVFETLLFASKIKM 117
                                    589*****************66666..4446777766555555888889999******9998888.77778888888889 PP

                                    TTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                    r +e e ki+++  +   +  l + ++ ++ +LSgGe++ v++ +          ++ + De  + LD  n  ++ +llk
  gene312|gene312|rna312|rna312 118 RYEEVEQKIKNRIEEIIALLGLNNAKNTYIVNLSGGERKRVSIGVE----LLGDPSILFCDEPTSGLDSFNALNILSLLK 193
                                    9999999**99999999999999999*************9998754....5666677788******************** PP

                                    HHCTTSEEEEE-SSHHHC CS
                                    xxxxxxxxxxxxxxxxxx RF
                          SMC_N 185 eksknaQfivislreeml 202
                                       +    + +++++  +
  gene312|gene312|rna312|rna312 194 DLANMGKTVLVTIHQPSY 211
                                    *99998888888776544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.4   5.9e-05     0.058       6      31 ..      41      66 ..      37     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqlde 31
                                   ++++++G sG+GKTtl++ l+ + + 
  gene312|gene312|rna312|rna312 41 TMTALMGTSGAGKTTLMNSLAGRIPS 66
                                   789****************9988754 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.9   1.9e-05     0.019      15      41 ..      33      59 ..      25      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDA 41
                                    + +i+++ +t l+G+sG+GK+Tl+ +
  gene312|gene312|rna312|rna312 33 VSGSIEPSTMTALMGTSGAGKTTLMNS 59
                                   5667888899**************966 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.4e-05     0.044       3      53 ..      45      98 ..      43     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                   RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfw...dgYtgqevv 53
                                   l G sg GK+tl+++La ++ +++ lk +  + s++ ++d w    gY +qe++
  gene312|gene312|rna312|rna312 45 LMGTSGAGKTTLMNSLAGRIPSSMVLKGEILLNSHPRSKDTWpntVGYVEQEFH 98
                                   78*******************999666666666666666666433355555544 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3      0.11   1.1e+02       1      19 [.      42      60 ..      42      67 .. 0.88
   2 ?    9.5   0.0   0.00075      0.75     224     299 ..     137     209 ..     102     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
                         AAA_21  1 lnvliGpNgsGKSnLLdal 19
                                   +++l G  g+GK++L+  l
  gene312|gene312|rna312|rna312 42 MTALMGTSGAGKTTLMNSL 60
                                   58999**********9766 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00075
                         AAA_21 224 lengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                    l  ++ +++ + +lS G ++   + + ll ++   s+l+ DEp +gL+      +l llk+l++ g  v++t H+p
  gene312|gene312|rna312|rna312 137 LGLNNAKNTYIVNLSGGERKRVSIGVELLGDP---SILFCDEPTSGLDSFNALNILSLLKDLANMGKTVLVTIHQP 209
                                    45567888999999999999999999999988...*****************************999999998887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.3e-05     0.092       3      22 ..      44      63 ..      42      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-05
                                   EEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                   a++G + +GK+tL+n+l g+
  gene312|gene312|rna312|rna312 44 ALMGTSGAGKTTLMNSLAGR 63
                                   89***************997 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.7e-05     0.087       3      57 ..      45      98 ..      44     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.7e-05
                         AAA_18  3 ltGtpGvGKttlakeLskrl.gfgvnlrdvakenglllevdpealdeskrldedkl 57
                                   l+Gt+G+GKttl + L+ r   + v  ++++ +++++  ++++  +    ++++++
  gene312|gene312|rna312|rna312 45 LMGTSGAGKTTLMNSLAGRIpSSMVLKGEILLNSHPRSKDTWP--NTVGYVEQEFH 98
                                   89**************988644466666666666666666666..55555555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.2e-05     0.062      24      52 ..      39      78 ..      27     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.2e-05
                         AAA_16 24 p.elvllsGesGvGKsslvrellralekd..........g 52
                                   p  ++ l G sG GK++l+++l+ ++  +           
  gene312|gene312|rna312|rna312 39 PsTMTALMGTSGAGKTTLMNSLAGRIPSSmvlkgeillnS 78
                                   257899*****************99998844444444440 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2    0.0001       0.1       3      22 ..      44      63 ..      42      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                         AAA_28  3 vitGgestGKTtlleaLaar 22
                                   +++G++++GKTtl++ La r
  gene312|gene312|rna312|rna312 44 ALMGTSGAGKTTLMNSLAGR 63
                                   799**************976 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00036      0.36       4      23 ..      42      64 ..      40     138 .. 0.85
   2 ?   -1.2   0.0       1.4   1.4e+03     111     131 ..     188     208 ..     185     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                         AAA_24  4 kiliyGpsgiGKTtlakel...g 23
                                   + +++G sg+GKTtl+++l    
  gene312|gene312|rna312|rna312 42 MTALMGTSGAGKTTLMNSLagrI 64
                                   6789*************995443 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                         AAA_24 111 frrllkklqelrknvifiahe 131
                                    + +llk+l +++k+v ++ h+
  gene312|gene312|rna312|rna312 188 ILSLLKDLANMGKTVLVTIHQ 208
                                    5689999***********996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00016      0.16      26      56 ..      33      63 ..      12      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                         AAA_25 26 vkgllpagelallaGapgtGKttlaldlala 56
                                   v g +   + ++l+G +g+GKttl  +la  
  gene312|gene312|rna312|rna312 33 VSGSIEPSTMTALMGTSGAGKTTLMNSLAGR 63
                                   678889999****************999865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00026      0.26       3      38 ..      44      80 ..      42     176 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                         AAA_33  3 llvGlpGsGKstlaerllkklg.avllssdtlrrrlf 38
                                    l G +G+GK+tl  +l+ + +   +l   +l++ + 
  gene312|gene312|rna312|rna312 44 ALMGTSGAGKTTLMNSLAGRIPsSMVLKGEILLNSHP 80
                                   578**************99998766666666444433 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4   0.00024      0.24       6      36 ..      29      59 ..      25      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00024
                        DUF3584  6 flkGrvaeldldghtnieGtNaaGKTtLlrL 36
                                    lkG+ + ++++  t + Gt +aGKTtL+  
  gene312|gene312|rna312|rna312 29 VLKGVSGSIEPSTMTALMGTSGAGKTTLMNS 59
                                   58999999********************975 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.1    0.0016       1.6      20      40 ..      41      61 ..      34     160 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                         AAA_23 20 gltlItGpNGaGKTTildAik 40
                                    +t++ G  GaGKTT+++ + 
  gene312|gene312|rna312|rna312 41 TMTALMGTSGAGKTTLMNSLA 61
                                   6899*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 3559.15
//
Query:       gene313|gene313|rna313|rna313  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.065   13.2   0.6       0.37   10.8   0.3    2.4  2  BSD       BSD domain


Domain annotation for each model (and alignments):
>> BSD  BSD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   2.1e-05      0.37       9      44 ..      99     133 ..      94     133 .. 0.85
   2 ?   -1.5   0.0      0.15   2.6e+03      17      39 ..     161     184 ..     158     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.1e-05
                            BSD   9 kteeiaqsllkedpeLrklynelVPskvseeqFWsr 44 
                                    ++++i + +l++dp++r l+n+l    vs + FWs+
  gene313|gene313|rna313|rna313  99 TDQDITKKILESDPAMRVLFNNLKQW-VSPSKFWSI 133
                                    899******************99555.777999985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.15
                            BSD  17 llkedpeLrklynel.VPskvsee 39 
                                    + + dp L ++++++ ++  ++++
  gene313|gene313|rna313|rna313 161 ISSLDPVLLNIFEQMnCSINQFYN 184
                                    567799999999999898888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2248.95
//
Query:       gene314|gene314|rna314|rna314  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   18.8   0.7     0.0029   17.4   0.7    1.7  1  Cyclin_N  Cyclin, N-terminal domain


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7   1.6e-07    0.0029      48     126 ..      24     122 ..      18     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-07
                                    -TTHHHHHHHHHHHHHH...HS---CC.CHHHHHHHHHHHHHHHHSSS---HHHHHHHT...............TT..SS CS
                       Cyclin_N  48 tpetlflavnyldRfls...kksvpkd.klqlvgatcLllAaKveeisppkledlvyit...............de..af 106
                                    t+++++l+++y  R+ +     +++++ ++  ++++++llA+K+ee  + +l++++y+                +     
  gene314|gene314|rna314|rna314  24 TESCVLLSLSYQSRYKAlilFYNFNEEiDFAGLCMASVLLASKLEEE-VCTLKKVIYVFnylytryeskptpltNRlsIR 102
                                    67899999999999987333345555589999************999.9*********9999999999998885224344 PP

                                    -HHHHHHHHHHHHHHTTT-- CS
                       Cyclin_N 107 teeeilemErliLetLnfdl 126
                                     +e  + +E +iL+ L fd+
  gene314|gene314|rna314|rna314 103 LKEGCILAETQILKSLGFDV 122
                                    46667788999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1573.96
//
Query:       gene315|gene315|rna315|rna315  [L=854]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-27   96.7   1.3    2.7e-27   95.8   0.3    2.0  2  SPT16            FACT complex subunit (SPT16/CDC68)
    3.5e-13   49.7   1.6    1.3e-12   47.9   0.0    2.7  3  FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe d
    8.7e-11   42.1   1.1    5.8e-10   39.4   0.6    2.6  2  Rtt106           Histone chaperone Rttp106-like
    2.9e-06   27.1   0.0    6.3e-06   26.0   0.0    1.5  1  Peptidase_M24    Metallopeptidase family M24
  ------ inclusion threshold ------
       0.56   10.2   4.0       0.68    9.9   0.8    2.8  3  UCH_N            N-terminal of ubiquitin carboxyl-terminal hy
       0.62    8.3  10.9          1    7.6  10.9    1.3  1  CDC45            CDC45-like protein


Domain annotation for each model (and alignments):
>> SPT16  FACT complex subunit (SPT16/CDC68)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   4.9e+03      69      88 ..      84     103 ..      65     112 .. 0.72
   2 !   95.8   0.3   9.2e-31   2.7e-27       1     151 []     399     542 ..     399     542 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                          SPT16  69 eltfrskdekklqevfreik 88 
                                    ++  r+kd+++++e+++ +k
  gene315|gene315|rna315|rna315  84 NVVVRNKDNSNMDEIYKILK 103
                                    45678888888888877766 PP

  == domain 2  score: 95.8 bits;  conditional E-value: 9.2e-31
                          SPT16   1 iyvdkkketillPifGiavPFhistiknvskseegdytylrinFnvpgsavgkke..ealfknpeaifikeltfrskdek 78 
                                    ++vd  ke++++Pi ++avPFhis ik+v +++e+   +lrinF+++ +  ++ +  e  + ++ +  ik+++ r ++++
  gene315|gene315|rna315|rna315 399 VVVDFSKESVVIPIGSYAVPFHISNIKSVAVTDEK---ILRINFKAETKGKEEGQdtECEQGENLLSTIKSISVRGSNSR 475
                                    58********************************6...9******99555444441033444455599**********87 PP

                          SPT16  79 klqevfreikelkkkvkkreaekkekedlveqekLilskskrkprLkdlyirpnieg...kklaGtleaheNGlRy 151
                                       ++++ei++lkk ++ r++     e++   e+L ++   r+ +L+d+y++++++g   ++  G+le+heNG+R+
  gene315|gene315|rna315|rna315 476 ---DLAEEINNLKKVHSARKT----VEEVEISEELKVNP--RPLSLTDVYMKTDMKGgsrRRKIGSLELHENGFRF 542
                                    ...888999999999877765....45556689999885..589************66999**************9 PP

>> FACT-Spt16_Nlob  FACT complex subunit SPT16 N-terminal lobe domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   4.2e-16   1.3e-12      31     143 ..      26     122 ..       6     135 .. 0.79
   2 ?   -1.7   0.1      0.74   2.2e+03      73     119 ..     318     362 ..     307     370 .. 0.66
   3 ?   -2.5   0.0       1.3   3.9e+03      93     133 ..     721     766 ..     693     774 .. 0.64

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 4.2e-16
                                    EEEEE-S--TT----HHHHHHHHHHSS--SSEEEEEESSEEEEEEEHHHHHTTGGGCTSTT-.SSEEEEEEE-S-HHHHH CS
                FACT-Spt16_Nlob  31 llvvlGksdeenpykKstalqtWLlGyefpdtlilltkkkiviltskkKaklLeplkekkeeekvevellvreKdadenk 110
                                    l+ +lGks++  +++ ++al ++LlGyefp+t++ +  + ++++ts+kK ++L++++  +        ++vr+K    ++
  gene315|gene315|rna315|rna315  26 LIAMLGKSQDVLEFRINSALFIYLLGYEFPETIL-IIDDACTVITSQKKSEILRQIRCLN--------VVVRNK----DN 92 
                                    77899***************************86.6699****************98765........899***....45 PP

                                    HHHHHHHHHHHTTTSEEEE-TT----SHHHHHH CS
                FACT-Spt16_Nlob 111 knfeklieaikeagkkvGvlaKdkseGkfveew 143
                                    +n++++ +++k++     +   ++ +G+f+ + 
  gene315|gene315|rna315|rna315  93 SNMDEIYKILKDSY---YIAGSEEMQGDFCRKI 122
                                    88888888888875...3444566677776655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.74
                                    EEEEHHHH.HTTGGGCTSTT-.SSEEEEEEE-S-HHHHHHHHHHHHHH CS
                FACT-Spt16_Nlob  73 iltskkKa.klLeplkekkeeekvevellvreKdadenkknfekliea 119
                                     lts+  a ++L++ k+  ++++ e e+  r +  +++k++++klie+
  gene315|gene315|rna315|rna315 318 YLTSQDTAlDFLDK-KSRFRDKTKEYEMNIRRR--EHQKELLDKLIEE 362
                                    56666555144444.444444567777777777..7899999999986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.3
                                    ......SSEEEEEEE-S-.HHHHHHHHHHHHHHHHTTTSEEEE-TT- CS
                FACT-Spt16_Nlob  93 e.....kvevellvreKd.adenkknfeklieaikeagkkvGvlaKd 133
                                          +v+v+ + + K+  d+n+ +f +    i+ ++  +G ++Kd
  gene315|gene315|rna315|rna315 721 LlvsilSVDVQSVNKLKEyLDSNNVLFMETSASIRWNN-VIGSIMKD 766
                                    23444456666666655413667777777777777776.88888888 PP

>> Rtt106  Histone chaperone Rttp106-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.8   2.4e+03       7      45 ..     526     562 ..     524     619 .. 0.77
   2 !   39.4   0.6     2e-13   5.8e-10       2      85 ..     652     745 ..     651     749 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.8
                         Rtt106   7 rkakeGlLyflekgllfgfkkPllfiplediesvsfeRv 45 
                                    r+ k G L + e+g+ f  k   ++i +++i ++ f+  
  gene315|gene315|rna315|rna315 526 RRRKIGSLELHENGFRF--KEENVVILFSNIRHIFFSEG 562
                                    55677778888888877..77889999999999999833 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 2e-13
                         Rtt106   2 gVkasrkakeGlLyflekgllfgfkkPllfiplediesvsfeRvsvtsrtfdlvvel.............kkeeveFsmi 68 
                                    gV+++   +++++  ++++l+ +++ P ++++led+e v+feRv  t +t+d+ + l             +k  v++ ++
  gene315|gene315|rna315|rna315 652 GVPFR---ESVMIKQTHECLVSLDETPYFVLTLEDVEVVNFERVVLTVKTVDVLFILknkypldvvmknkSKLLVSILSV 728
                                    67777...8999999******************************************999999999976333778***** PP

                         Rtt106  69 dqeelegidefvkskgi 85 
                                    d +++++++e+++s+++
  gene315|gene315|rna315|rna315 729 DVQSVNKLKEYLDSNNV 745
                                    **************987 PP

>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.1e-09   6.3e-06      80     186 ..     208     297 ..     206     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.1e-09
                                    EEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESS CS
                  Peptidase_M24  80 dagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGl 159
                                     +g++y+gy+s ++rT++          ++e +  aqe ++ +++pG++ + ++   ++++ ++gl +f p +  + vGl
  gene315|gene315|rna315|rna315 208 RIGVRYNGYCSEVSRTIVT---------NMEEAYMAQEYILGLIRPGADSGFVYSETEKYFSENGL-EFDPDF-VYTVGL 276
                                    68***************99.........6788899******************************9.665554.677887 PP

                                    SSSEEEEEESSSTTCSSB--TTBEEEE CS
                  Peptidase_M24 160 evhdegpsvsresndgrkleeGmvfti 186
                                       +  ++ +    ++  le+G vf i
  gene315|gene315|rna315|rna315 277 MSQER-SF-K----NTFCLEKGCVFVI 297
                                    55543.32.2....3566666666665 PP

>> UCH_N  N-terminal of ubiquitin carboxyl-terminal hydrolase 37
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5   7.4e+03      51      70 ..     419     433 ..     412     442 .. 0.67
   2 ?   -1.3   0.1       0.7   2.1e+03      49      78 ..     546     576 ..     539     580 .. 0.67
   3 ?    9.9   0.8   0.00023      0.68      57     101 ..     696     742 ..     673     745 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                          UCH_N  51 FqLnnNiksvvlrsygekqn 70 
                                    F++  Niksv ++ +    +
  gene315|gene315|rna315|rna315 419 FHI-SNIKSVAVTDE----K 433
                                    555.69999999843....3 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.7
                          UCH_N  49 ktFqLnnNiksvvlrsygek.qnrLhLtlkd 78 
                                    ++  L  Ni+++ +++ + + ++ Lh  l++
  gene315|gene315|rna315|rna315 546 NVVILFSNIRHIFFSEGNVEtNCILHFHLWN 576
                                    36667899**999987665515557777776 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00023
                          UCH_N  57 iksvvlrsygekqnrLhLtlkdnsflfidklss..kdaeklkefLdk 101
                                    +k+v +    ++++ L +++k++s l++  ls   + ++klke+Ld+
  gene315|gene315|rna315|rna315 696 VKTVDVLFILKNKYPLDVVMKNKSKLLVSILSVdvQSVNKLKEYLDS 742
                                    77787777889999************999888522789********7 PP

>> CDC45  CDC45-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  10.9   0.00034         1      78     193 ..     743     853 ..     714     854 .] 0.48

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00034
                          CDC45  78 vevyViDshRPwnleNlfgsseekerivvfDDgdieeeleeereayealeeeeesdeedeeeeeeddddeeeeeeeeede 157
                                     +v  + +   +  +N++gs   k+ i  ++Dg  +e +  + e+  + e+e e++ee++ +e e+ +++e+ ++ ++  
  gene315|gene315|rna315|rna315 743 NNVLFMETSASIRWNNVIGS-IMKDPISFYEDGAWSELMVGDSEE-GSEESEGEVTEESSTSETENISTDEDVSDISS-- 818
                                    46666677777888999865.5799999999*9975555554443.33333333332222111111111111111111.. PP

                          CDC45 158 edeeedeeeskkkrksksdeeeesddddersrkrrr 193
                                     +ee +e+es  +++++ +e+++++++de++rkrr+
  gene315|gene315|rna315|rna315 819 -EEELEEDESYYDSSDDYEEDDSDEESDEEPRKRRK 853
                                    .11111112112222222333335566666777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (854 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1437  (0.0801495); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.87u 0.34s 00:00:01.21 Elapsed: 00:00:00.51
# Mc/sec: 5017.87
//
Query:       gene316|gene316|rna316|rna316  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-32  110.5  23.5    2.1e-05   25.2   1.0    8.0  8  WD40         WD domain, G-beta repeat
    1.3e-11   44.4   5.3    1.4e-05   24.6   0.2    2.9  3  WD40_like    WD40-like domain
    3.3e-07   30.3   1.4     0.0042   17.1   0.0    4.8  7  BBS2_Mid     Ciliary BBSome complex subunit 2, middle region
    4.1e-07   30.2   0.1          1    9.7   0.0    5.3  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
      0.011   15.8   0.4       0.29   11.3   0.1    2.5  2  DUF3718      Protein of unknown function (DUF3718)
      0.019   15.5   1.1         12    6.5   0.0    4.7  5  PQQ_3        PQQ-like domain
      0.049   14.2   0.6        0.1   13.1   0.6    1.6  1  NLE          NLE (NUC135) domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   1.0   8.1e-09   2.1e-05       2      38 .]      85     119 ..      84     119 .. 0.92
   2 !   15.0   0.3   1.4e-05     0.035       9      37 ..     133     160 ..     124     161 .. 0.81
   3 !   19.4   0.1   5.3e-07    0.0014       2      38 .]     165     200 ..     164     200 .. 0.84
   4 !   15.7   0.0   7.8e-06      0.02       9      37 ..     210     237 ..     203     238 .. 0.83
   5 !   17.4   0.3   2.3e-06    0.0058       6      38 .]     245     276 ..     240     276 .. 0.89
   6 !   19.5   0.0   5.2e-07    0.0013      10      38 .]     286     315 ..     280     315 .. 0.88
   7 !    8.7   0.0    0.0013       3.4      22      37 ..     338     353 ..     319     354 .. 0.72
   8 ?   -0.2   0.1      0.86   2.2e+03      13      36 ..     370     392 ..     362     394 .] 0.76

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 8.1e-09
                                    EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                     c  +++GH ++v ++   ++g+ +++G+ D tvr+Wd
  gene316|gene316|rna316|rna316  85 HCSSSFSGHeGPVLCV---KNGDVIVTGGGDSTVRFWD 119
                                    5899*****999****...99999****88*******9 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-05
                                    SSSSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   9 GHssvtslafspdgawlasGsdDgtvriW 37 
                                    GH +  sl+ s+dg+++asG  Dg+v ++
  gene316|gene316|rna316|rna316 133 GH-WTLSLDISSDGKYVASGALDGSVNLY 160
                                    66.435999***********99****997 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 5.3e-07
                                    EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    + +r++ GH ++v sl + + g+++ +Gs+D++v +W+
  gene316|gene316|rna316|rna316 165 EYIRSFPGHkKGVVSL-VFHKGNLV-TGSRDNSVIMWS 200
                                    6799*****99999**.66666665.8**********5 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 7.8e-06
                                    SS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   9 GH.ssvtslafspdgawlasGsdDgtvriW 37 
                                    +H   vt++  ++  +++asGs+Dg ++++
  gene316|gene316|rna316|rna316 210 AHtMAVTCI--CSGEDYIASGSKDGRIKVY 237
                                    78555****..9999*************98 PP

  == domain 5  score: 17.4 bits;  conditional E-value: 2.3e-06
                                    EEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   6 tltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    +l+GH s+++ +  + +g++++sG+d g v iW+
  gene316|gene316|rna316|rna316 245 ELRGHsSGINTI--DCNGNYMVSGCDGGDVIIWK 276
                                    799**777*999..99*****************6 PP

  == domain 6  score: 19.5 bits;  conditional E-value: 5.2e-07
                                    SSS.EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  10 Hss.vtslafspdgawlasGsdDgtvriWd 38 
                                    H+  v s++ sp+  + asGs D+tvr+W+
  gene316|gene316|rna316|rna316 286 HNAeVISVSISPNRLYAASGSFDKTVRLWS 315
                                    7445779**********************5 PP

  == domain 7  score: 8.7 bits;  conditional E-value: 0.0013
                                    SSEEEEEETTSEEEEE CS
                           WD40  22 gawlasGsdDgtvriW 37 
                                    +++++s+s+D+t++++
  gene316|gene316|rna316|rna316 338 NDLIVSCSKDKTIKMF 353
                                    34599*********86 PP

  == domain 8  score: -0.2 bits;  conditional E-value: 0.86
                                    EEEEEEETTSSEEEEEETTSEEEE CS
                           WD40  13 vtslafspdgawlasGsdDgtvri 36 
                                    v++++   dg ++ +G++   v++
  gene316|gene316|rna316|rna316 370 VYCFDIKGDGGLV-CGTKSSRVYF 392
                                    9999999999997.6987666665 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.31     8e+02      10      38 ..     101     129 ..      97     133 .. 0.84
   2 !   20.7   0.6   8.1e-08   0.00021       5     136 ..     138     265 ..     136     287 .. 0.86
   3 !   24.6   0.2   5.3e-09   1.4e-05       2     108 ..     289     394 .]     288     394 .] 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.31
                      WD40_like  10 kkgslilyGgkddkctvlkleslesvsiv 38 
                                    k+g++i+ Gg d +++  + +++++  +v
  gene316|gene316|rna316|rna316 101 KNGDVIVTGGGDSTVRFWDPRTKTQSKVV 129
                                    8999***********99998888876665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 8.1e-08
                      WD40_like   5 sidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslleneeevenekieed 84 
                                    s+dis +g++++ G+ d  + ++++ s+e + ++ + +  v+   + +++ ++ ++ D  +++  l+ e  v+      +
  gene316|gene316|rna316|rna316 138 SLDISSDGKYVASGALDGSVNLYSI-SGEYIRSFPGHKKGVVSLVFHKGN-LVTGSRDNSVIMWSLSGEVLVSY-AHTMA 214
                                    89**********************9.6789999********988776666.578999*9998999988876665.55689 PP

                      WD40_like  85 istvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiys 136
                                    +++++  +d ++ G++ G i v+++ l++   l g+ss I+ i  + n++ s
  gene316|gene316|rna316|rna316 215 VTCICSGEDYIASGSKDGRIKVYKN-LKFFDELRGHSSGINTIDCNGNYMVS 265
                                    ***********************87.6999999**********999988765 PP

  == domain 3  score: 24.6 bits;  conditional E-value: 5.3e-09
                      WD40_like   2 eiYsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslleneeeveneki 81 
                                    e+ s+ is++  + + G+ d+++++ +++s+++  i+ +  d v  v  + +dli+ ++ D ti +  ++++++v+    
  gene316|gene316|rna316|rna316 289 EVISVSISPNRLYAASGSFDKTVRLWSMDSGQQLLIFRHV-DLVYKV-RMMNDLIVSCSKDKTIKMFRVSKKKIVSDLVC 366
                                    899********************************99876.555555.55689*************************** PP

                      WD40_like  82 eedistvkvidd.klliGtnkGsiyvfs 108
                                    ++++ + ++ +d  l+ Gt+   +y f+
  gene316|gene316|rna316|rna316 367 DDEVYCFDIKGDgGLVCGTKSSRVYFFN 394
                                    ********986626999********997 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.9   1.2e+04      70      88 ..      58      76 ..      52      85 .. 0.67
   2 ?   -0.9   0.0      0.65   1.7e+03      58      81 ..     101     129 ..      96     163 .. 0.59
   3 ?    1.3   0.0      0.13   3.3e+02      13      46 ..     185     219 ..     178     220 .. 0.80
   4 !   17.1   0.0   1.7e-06    0.0042      10      85 ..     220     295 ..     212     304 .. 0.91
   5 !    5.7   0.0    0.0057        15      63     102 ..     305     346 ..     303     349 .. 0.83
   6 ?    3.0   0.0     0.039     1e+02      13      41 ..     338     369 ..     331     377 .. 0.68
   7 ?   -2.1   0.0       1.5   3.9e+03       5      27 ..     373     393 ..     369     394 .] 0.60

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.9
                       BBS2_Mid 70 rlWrvksknevvalaaydi 88
                                   ++ +++s +evv++ + ++
  gene316|gene316|rna316|rna316 58 KIQNISSAEEVVKIRMSEE 76
                                   5556677777777776665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.65
                       BBS2_Mid  58 eNGtvgvy...ekkerlW..rvksknevv 81 
                                    +NG v v    +++ r W  r+k++++vv
  gene316|gene316|rna316|rna316 101 KNGDVIVTgggDSTVRFWdpRTKTQSKVV 129
                                    55555443222455666633334444444 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.13
                       BBS2_Mid  13 neLvvgsddfeirvfkee.elvaeitetekvvsla 46 
                                     +Lv gs d+++ +++   e++     t +v++++
  gene316|gene316|rna316|rna316 185 GNLVTGSRDNSVIMWSLSgEVLVSYAHTMAVTCIC 219
                                    579********999885438888888888888776 PP

  == domain 4  score: 17.1 bits;  conditional E-value: 1.7e-06
                       BBS2_Mid  10 dgeneLvvgsddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvksknevvalaa 85 
                                     ge+++  gs+d +i+v+k+ +   e++ ++  ++ ++ +++ ++ + + G v ++++   + r+k + ev+++  
  gene316|gene316|rna316|rna316 220 SGEDYIASGSKDGRIKVYKNLKFFDELRGHSSGINTIDCNGNYMVSGCDGGDVIIWKGFSLYKRMKHNAEVISVSI 295
                                    58999***************************************************************99998865 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0057
                       BBS2_Mid  63 gvyekkerlWrvksknevvalaaydin..gdgtkelivgwsn 102
                                    g ++k+ rlW++ s ++++ +  +d+    + +++liv++s+
  gene316|gene316|rna316|rna316 305 GSFDKTVRLWSMDSGQQLLIFRHVDLVykVRMMNDLIVSCSK 346
                                    5699*************9999999986335677899999886 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.039
                       BBS2_Mid  13 neLvv.gsddfeirvfk..eeelvaeitetek 41 
                                    n+L+v +s+d +i++f+  ++++v+++   ++
  gene316|gene316|rna316|rna316 338 NDLIVsCSKDKTIKMFRvsKKKIVSDLVCDDE 369
                                    45555389********8224466666665555 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 1.5
                       BBS2_Mid   5 advdgdgeneLvvgsddfeirvf 27 
                                    +d++gd    Lv g++  ++  f
  gene316|gene316|rna316|rna316 373 FDIKGD--GGLVCGTKSSRVYFF 393
                                    344444..677777777776655 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.47   1.2e+03      48      71 ..     101     124 ..      62     136 .. 0.80
   2 !    9.7   0.0   0.00041         1      43      88 ..     138     181 ..     121     219 .. 0.86
   3 ?    0.8   0.0      0.24     6e+02       4      19 ..     219     234 ..     187     240 .. 0.54
   4 ?    4.0   0.0     0.024        62      29      73 ..     274     322 ..     216     338 .. 0.77
   5 !    8.2   0.0    0.0012       3.1       7      53 ..     338     382 ..     335     393 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.47
                    ANAPC4_WD40  48 pdgklLavaysdgevrlldaesgk 71 
                                    ++g +++ +  d++vr+ d  +++
  gene316|gene316|rna316|rna316 101 KNGDVIVTGGGDSTVRFWDPRTKT 124
                                    589999999999999998876654 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00041
                    ANAPC4_WD40  43 sLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                    sL  + dgk  a +  dg+v+l+++ sg+ ++s++ +++  v++l 
  gene316|gene316|rna316|rna316 138 SLDISSDGKYVASGALDGSVNLYSI-SGEYIRSFPGHKKG-VVSLV 181
                                    788899*****************98.79999999999886.55444 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.24
                    ANAPC4_WD40   4 cptmDLiAlatedgel 19 
                                    c+  D iA +++dg++
  gene316|gene316|rna316|rna316 219 CSGEDYIASGSKDGRI 234
                                    3334444444444444 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.024
                    ANAPC4_WD40  29 vwtl....eedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvv 73 
                                    +w++    ++ k++ ev s++ +p+    a +  d +vrl ++ sg+ +
  gene316|gene316|rna316|rna316 274 IWKGfslyKRMKHNAEVISVSISPNRLYAASGSFDKTVRLWSMDSGQQL 322
                                    5666666777888899999999999999999999999999999988865 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.0012
                    ANAPC4_WD40   7 mDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklL 53 
                                    +DLi   ++d+ + +fR++ +++++      d ev ++  k dg l 
  gene316|gene316|rna316|rna316 338 NDLIVSCSKDKTIKMFRVSKKKIVSD--LVCDDEVYCFDIKGDGGLV 382
                                    69999999999999999999998876..5677777777777777654 PP

>> DUF3718  Protein of unknown function (DUF3718)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   2.7e+02      27      39 ..     252     264 ..     227     266 .. 0.81
   2 ?   11.3   0.1   0.00011      0.29      15      36 ..     348     369 ..     347     371 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                        DUF3718  27 vaegivCNGesll 39 
                                      + i CNG+ ++
  gene316|gene316|rna316|rna316 252 GINTIDCNGNYMV 264
                                    56889****9876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                        DUF3718  15 kklkesrlkkrrvaegivCNGe 36 
                                    k++k +r++k+++++ +vC++e
  gene316|gene316|rna316|rna316 348 KTIKMFRVSKKKIVSDLVCDDE 369
                                    89******************97 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0048        12      20      40 .]     102     122 ..      89     122 .. 0.84
   2 ?    1.5   0.0      0.18   4.6e+02      12      34 ..     175     197 ..     143     201 .. 0.77
   3 ?    0.7   0.0      0.32   8.1e+02      16      33 ..     292     311 ..     282     317 .. 0.81
   4 ?   -0.2   0.0       0.6   1.5e+03      30      38 ..     367     375 ..     360     376 .. 0.74
   5 ?   -2.7   0.1       3.8   9.8e+03      21      35 ..     378     392 ..     377     394 .] 0.57

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0048
                          PQQ_3  20 dgglvyvgtgdGtlyAlDaet 40 
                                     g+++++g+gd t++  D++t
  gene316|gene316|rna316|rna316 102 NGDVIVTGGGDSTVRFWDPRT 122
                                    48999**************98 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.18
                          PQQ_3  12 pvnsspavdgglvyvgtgdGtly 34 
                                    +++ s+++  g +++g+ d+++ 
  gene316|gene316|rna316|rna316 175 KGVVSLVFHKGNLVTGSRDNSVI 197
                                    44456688999999999998875 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.32
                          PQQ_3  16 spavdgglvyvgtg..dGtl 33 
                                    s+ ++ +++y+++g  d t+
  gene316|gene316|rna316|rna316 292 SVSISPNRLYAASGsfDKTV 311
                                    6789999******9777666 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.6
                          PQQ_3  30 dGtlyAlDa 38 
                                    d  +y++D 
  gene316|gene316|rna316|rna316 367 DDEVYCFDI 375
                                    899*****7 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 3.8
                          PQQ_3  21 gglvyvgtgdGtlyA 35 
                                    +g +++gt   ++y 
  gene316|gene316|rna316|rna316 378 DGGLVCGTKSSRVYF 392
                                    445556666666665 PP

>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6     4e-05       0.1       1      65 []       5      57 ..       5      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4e-05
                            NLE  1 vqvrFvtkdedeslavpgtplsvPasltrkqLselvnkLlkeekpvpFdFlidgellrtsLeehL 65
                                   v+v+F +++   ++      l++P+++ r+qL+ l n+ l+        ++i+g+ +  +Lee+L
  gene316|gene316|rna316|rna316  5 VLVEFEDQEG-RKV---SDRLQIPTKILRSQLQLLANTTLS--------LYINGQPVLETLEETL 57
                                   7889999944.588...999*****************9998........8899888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2770.40
//
Query:       gene317|gene317|rna317|rna317  [L=1046]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   3.6e-105  352.2   0.9    6.9e-74  249.2   0.1    2.2  2  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    6.2e-23   81.4   0.0    7.1e-23   81.2   0.0    1.2  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    6.6e-23   80.9   0.1    1.3e-22   80.0   0.1    1.6  1  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    8.6e-20   70.7   0.0    1.8e-19   69.6   0.0    1.6  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
    5.6e-14   52.2   0.0    1.6e-13   50.7   0.0    1.8  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
     0.0024   18.1   0.0     0.0083   16.4   0.0    2.0  2  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.25   11.4   0.0    1.6  1  RNA_pol_Rpa2_4  RNA polymerase I, Rpa2 specific domain
        0.5   10.4   3.0       0.22   11.5   0.3    1.7  2  OMP_b-brl_2     Outer membrane protein beta-barrel domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.7   0.1     2e-32   4.5e-29       2     122 ..     621     730 ..     620     759 .. 0.93
   2 !  249.2   0.1   3.1e-77   6.9e-74     195     390 .]     761     959 ..     739     959 .. 0.91

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 2e-32
                                    HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEEEE CS
                 RNA_pol_Rpb2_6   2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGqna 81 
                                    a l+p+++h+qspr+++q++m+kqa+g+ ++n   r+++++y++++ q P+v+t+  +++++          +++ G n+
  gene317|gene317|rna317|rna317 621 AGLTPYSDHNQSPRNMYQCQMAKQAIGLPAYNIKARVDSSMYTINYLQSPIVRTK-GYDLVK----------DYPVGVNC 689
                                    889****************************************************.999988..........9******* PP

                                    EBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE- CS
                 RNA_pol_Rpb2_6  82 vVAvmsyeGYniEDaiilnerlvdrdvftsihikeyevear 122
                                    +VAv+sy+ Y++EDa++++++++dr++ft +++k+ +v+ +
  gene317|gene317|rna317|rna317 690 MVAVLSYTAYDMEDALVISKNSIDRGLFTGYVYKTEKVSLE 730
                                    ***********************************766654 PP

  == domain 2  score: 249.2 bits;  conditional E-value: 3.1e-77
                                    ---EE--TT-EEEEEEEEE.......EE-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS--- CS
                 RNA_pol_Rpb2_6 195 dtslrvksgeegvVdkvkvfsrekgdelkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivv 274
                                    +   ++ + e g++d+v+vf        ++ +++++  +++  R++++GDKf+srhGqKGv+s+ +p+ DmPf+e+G v+
  gene317|gene317|rna317|rna317 761 EYESKYYEAEGGIIDSVRVF-------DNDIGERCATFTIRIVRNPSIGDKFSSRHGQKGVCSMHWPTVDMPFTESGYVP 833
                                    44456667789********6.......55667899********************************************* PP

                                    SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSSS--B--TT-.............-HHHHHHHHHTTS-TT-EE-EEETTTS CS
                 RNA_pol_Rpb2_6 275 DivlNPlgvPSRmtigqllEtllgkaaalegkkvdatvFdg..........akeeeikelLeeagleasGkevlydGrtG 344
                                    Di++NP+++PSRmtig+l+E+++gk+++l+g+  d+t+F++          +++e+++e+L+++g++++G+e +y+G++G
  gene317|gene317|rna317|rna317 834 DIIINPHAFPSRMTIGMLIESIAGKVGCLSGSIQDGTAFEKsffsgedengKEKEYLCEELQRHGFNYYGNEPMYSGISG 913
                                    ****************************************85655555443337************************** PP

                                    -B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGGG CS
                 RNA_pol_Rpb2_6 345 ekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGkaq 390
                                    ++++ ++fvGv+Yy++Lkh+v dK+++R+tGp+   tqQP+gGk++
  gene317|gene317|rna317|rna317 914 NEFRVDVFVGVVYYQRLKHMVGDKFQVRTTGPVVSTTQQPIGGKKK 959
                                    ********************************************86 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   0.0   3.2e-26   7.1e-23      40     156 ..      37     230 ..       7     712 .. 0.82

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 3.2e-26
                                    CEEEEEEEEEEESCSSECTT..SCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTS CS
                                    xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1  40 elelkfvsirlgkPvvdesd..asereiyPkearlrnltYsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskac 117
                                    + ++ +++i ++ P+ ++ d   ++r+++P+e+r+r+ltY++++  ++ l      ++++ + e+ + G  P+M+rsk c
  gene317|gene317|rna317|rna317  37 RTKIVVEEIHISPPFLSDRDhiSVDRRLFPRECRERGLTYKGKMVARVSLFY----DNKHVMTEDKFAGYFPIMVRSKLC 112
                                    478999************8866789*************************99....8999999999************** PP

                                    SSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE.......................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                 RNA_pol_Rpb2_1 118 vlseaseeelvelkEcpldqGGyFiinGtekvivaqek.......................................... 155
                                    +l +++  ++ +++E++ ++GGyFi+nG++k i+  +                                           
  gene317|gene317|rna317|rna317 113 HLRNVE--NMNKVGEDEGEVGGYFIVNGIDKFIRLGIIqkrnhifafkqrkkenfltgygvsircvgkdeighlnslyyc 190
                                    **9985..799*********************986554455666666666666666666666666666666666666666 PP

                                    .......................................X CS
                                    .......................................x RF
                 RNA_pol_Rpb2_1 156 .......................................l 156
                                                                            
  gene317|gene317|rna317|rna317 191 tdgnviikifyrrstflfplvlilralinttdeelfealG 230
                                    5555555555555555555555555555555555555550 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.1   5.9e-26   1.3e-22       1      85 [.     961    1045 ..     961    1046 .] 0.97

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 5.9e-26
                                     BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHHHT CS
                 RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqeLqsl 78  
                                     GG+rfGEMErdali++Ga++lL++rl++ SD +  + cg ck +  +n+   v ++++++ ve+p+ fk L+ eL ++
  gene317|gene317|rna317|rna317  961 GGIRFGEMERDALISHGASHLLQDRLLKCSDGTIFEYCGVCKSILFTNNGDCVCGSNDLKIVEMPYVFKYLCYELLAM 1038
                                     9***********************************************999999************************ PP

                                     TBEEEEE CS
                 RNA_pol_Rpb2_7   79 gialkll 85  
                                     +i++k++
  gene317|gene317|rna317|rna317 1039 NIKVKID 1045
                                     ***9985 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.0   8.2e-23   1.8e-19       2      68 .]     425     488 ..     424     488 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 8.2e-23
                 RNA_pol_Rpb2_3   2 vldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                    +++r+n++++l +lr+++  rg++ + +  t++R+l+p++wG+iCpv+TP+G++cG++ ++a  a+v
  gene317|gene317|rna317|rna317 425 TAERINFYRYLCNLRSIN--RGSYIS-SLVTDIRKLRPESWGFICPVHTPDGAPCGILLHMAKGAEV 488
                                    69****************..998866.679********************************98876 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   7.3e-17   1.6e-13       2     188 ..     151     323 ..     150     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 7.3e-17
                                    TSCEEEEE-SSSSSE.......SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHT CS
                 RNA_pol_Rpb2_2   2 sngiyvekekdknki.......satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIleric 74 
                                    +n+i ++k+++k+++       ++ v +++i   +s+++ +++  ++ +  +  +   p+v++l+Al  ++d+e +e++ 
  gene317|gene317|rna317|rna317 151 RNHIFAFKQRKKENFltgygvsIRCVGKDEIGHLNSLYYCTDGNVIIKIFYRRSTFLFPLVLILRALINTTDEELFEALG 230
                                    7***************************************999999988888888899********************** PP

                                    SSSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH CS
                 RNA_pol_Rpb2_2  75 ydsedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenk 154
                                    +     + +++l+     + ++ +++e+ldyig+++ ++ +  ++++ a+e+l          +++   hl+++ +    
  gene317|gene317|rna317|rna317 231 G---GEKAIHLLKCF--AEYNVFSRAECLDYIGSRFSAAINVGTKVEAAKELLS---------KYVAS-HLTSNLD---- 291
                                    8...55555555444..456789*****************************94.........67666.*******.... PP

                                    ..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEE CS
                 RNA_pol_Rpb2_2 155 rlkaqdilymidrLlslklgrrevDDiDhlgnkR 188
                                      k+ +++ ++++L+s   +++++DD D+ gn +
  gene317|gene317|rna317|rna317 292 --KFNFLVLAAKKLFSFVDNEIVEDDFDSPGNHE 323
                                    ..9**************************99977 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       6.8   1.5e+04      16      25 ..     449     458 ..     445     460 .. 0.85
   2 !   16.4   0.0   3.7e-06    0.0083       1      56 [.     518     574 ..     518     577 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.8
                                    CHHHHHHHHC CS
                 RNA_pol_Rpb2_4  16 klvetlRelR 25 
                                    +lv+++R+lR
  gene317|gene317|rna317|rna317 449 SLVTDIRKLR 458
                                    7999****99 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.7e-06
                                    EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT...T--EEEE-SSEEB-E CS
                 RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek...qkevkiatDgGRvcR 56 
                                    V v+G+++G t++p+ +v+ lRe++ k+++  +++iv++e      +v +++  GR++R
  gene317|gene317|rna317|rna317 518 VLVDGKVIGSTSSPHTFVRMLREYKVKNNL--KIEIVYSEGpkmFPSVCVFNSMGRFTR 574
                                    78************************9997..688888887333445999999999998 PP

>> RNA_pol_Rpa2_4  RNA polymerase I, Rpa2 specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.25      11      58 .]     533     574 ..     526     574 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                 RNA_pol_Rpa2_4  11 avaktLRrlKvegekkvpltlEIglvppskggqYpGLYlftspaRmmR 58 
                                    ++++ LR +Kv+++    l++EI++ +    + +p + +f s +R+ R
  gene317|gene317|rna317|rna317 533 TFVRMLREYKVKNN----LKIEIVYSEGP--KMFPSVCVFNSMGRFTR 574
                                    7899********96....89*****8877..8**************99 PP

>> OMP_b-brl_2  Outer membrane protein beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       4.4   9.9e+03      95     124 ..     715     743 ..     707     772 .. 0.66
   2 ?   11.5   0.3   9.9e-05      0.22      19      62 ..     898     943 ..     896     951 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.4
                    OMP_b-brl_2  95 PllakykikksnvrlflfaGpyfgylle.sk 124
                                     l+ +y  k +  +++l+ G yf yll+ +k
  gene317|gene317|rna317|rna317 715 GLFTGYVYKTE--KVSLEKGHYFTYLLSvGK 743
                                    55566666663..788888888888888555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.9e-05
                    OMP_b-brl_2  19 Gfnasklspsaeseensqsnprlgfsvgvvveyrlee....gwglqpg 62 
                                    Gfn+++ +p  +++++s +++r+ ++vgvv+ +rl++    +++++++
  gene317|gene317|rna317|rna317 898 GFNYYGNEP--MYSGISGNEFRVDVFVGVVYYQRLKHmvgdKFQVRTT 943
                                    9********..************************8766667888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1046 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 6229.99
//
Query:       gene318|gene318|rna318|rna318  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-12   47.8   7.6    6.7e-12   46.2   7.6    1.9  1  DUF1764   Eukaryotic protein of unknown function (DUF1764)


Domain annotation for each model (and alignments):
>> DUF1764  Eukaryotic protein of unknown function (DUF1764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   7.6   3.8e-16   6.7e-12      32      99 ..      23     101 ..       1     102 [] 0.60

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 3.8e-16
                        DUF1764  32 e.............ekekkkkskkkkkkkkkkeeekkfedseskkrrktedGlpvYteeeLgigkadgGgtplCPFdCeC 98 
                                    +             + +  k  k k+ k+++++++ ++ +   +  r++++GlpvYt eeL++g+  gG+t++CP  C+C
  gene318|gene318|rna318|rna318  23 KghktendieaifsKVDSPKICKVKEGKEDEESDKGRYFSV-GEGGRRYHEGLPVYTLEELQLGD-GGGDTEDCPIYCDC 100
                                    03332222222222334444444444444444444444444.58999*****************9.9************* PP

                        DUF1764  99 C 99 
                                    C
  gene318|gene318|rna318|rna318 101 C 101
                                    * PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 687.12
//
Query:       gene319|gene319|rna319|rna319  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-34  117.4   0.0    1.1e-33  116.7   0.0    1.3  1  SIR2      Sir2 family


Domain annotation for each model (and alignments):
>> SIR2  Sir2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   5.9e-38   1.1e-33       1     176 [.      26     232 ..      26     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 5.9e-38
                                    -GGGGGGGT---SSSTTSHHHHSCHHHHSSHHHHHHHHHHHHH.......HHHHHHHHHHCCTSS--HHHHHHHHHHHTT CS
                           SIR2   1 GAGiStesGipdfRskeGlyaklakeelaspealfskkllvee.......vfyniarellaeeaepnaaHkalkklekkg 73 
                                    GAGiS++sGipdfRs++G+++ ++k+   s ++lf++++ +++       ++++  ++++  +a+p+++H++l+   + +
  gene319|gene319|rna319|rna319  26 GAGISVSSGIPDFRSRSGIFNDIKKNLGISGSDLFTYSTSMSKemrkdylKYMSKLKDMID-RAAPSPTHEFLSLYSDVS 104
                                    9**********************99874444444443333332244423444444444444.8***************** PP

                                    CEEEEEES-SSSHHHHTT-S.......SEEETTEEEEEEEETTTSBEEECCGGH.CHHHCCTT.B-TTTCC......... CS
                           SIR2  74 kllrliTQNiDgLekkaGsk.......kvvelHGslakakcvkcekkldkeelq.eeieaekvpecekcgk......... 136
                                    k +r++TQNiDgLe+kaG+        +vv lHG+++k+ c  c++k+d  +++ ++  + ++  c+ c +         
  gene319|gene319|rna319|rna319 105 KKFRMYTQNIDGLEEKAGLVatkdrsaTVVYLHGNMKKLGCLYCGYKVDFGDTErDTYGKGEEIVCSACIRrnekrgkdt 184
                                    ******************8666677889********************97666505556778889999999999****** PP

                                    ......BEEEEE--CTSB-S.HHHHHHHH.HHHH-SEEEEES--STST CS
                           SIR2 137 ......llkpdvvfFGealp.dklkklie.kveeadlllviGtSlkVa 176
                                          + +++++ + ++ p +++ + ++    ++dl++v+GtSlkV 
  gene319|gene319|rna319|rna319 185 rkrpvgVFHTTIIHYNQSHPdSSFISKMTqYDCDCDLFIVMGTSLKVF 232
                                    *******************986666666636669************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2248.59
//
Query:       gene32|gene32|rna32|rna32  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-13   49.8   0.1    2.8e-13   49.5   0.1    1.1  1  RRM_1         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
    9.3e-05   22.3   0.0    0.00027   20.9   0.0    1.7  2  Nup35_RRM_2   Nup53/35/40-type RNA recognition motif
     0.0067   16.3   0.1      0.008   16.0   0.1    1.2  1  RRM_occluded  Occluded RNA-recognition motif
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.049   13.6   0.0    1.3  1  RL            RL domain


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.1   6.2e-17   2.8e-13       1      69 [.      28      93 ..      28      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.2e-17
                               EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                      RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69
                               ++V+nL  +vt++++ ++F+ +G i+ i++++  t++++++a+V+F+s+ + e  l  +ng  l+g+++
  gene32|gene32|rna32|rna32 28 VYVKNLDASVTNSDIAAHFRSCGNISGINVIT--TKNTRKYAIVDFTSEKSVEMSLL-FNGSVLKGKKI 93
                               8*******************************..8**********************.********997 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.46   2.1e+03      34      42 ..      23      31 ..      13      38 .. 0.73
   2 !   20.9   0.0   5.9e-08   0.00027      15      51 ..      40      79 ..      34      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.46
                Nup35_RRM_2 34 kevsvmyvk 42
                               k vs++yvk
  gene32|gene32|rna32|rna32 23 KPVSSVYVK 31
                               458999998 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.9e-08
                Nup35_RRM_2 15 elVlehFasfGeIvkhyvp...kevsvmyvkfesekdaek 51
                               +++++hF+s+G+I  ++v    + + +++v f sek+ e+
  gene32|gene32|rna32|rna32 40 SDIAAHFRSCGNISGINVIttkNTRKYAIVDFTSEKSVEM 79
                               68999*************999999************9987 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.8e-06     0.008       4      70 ..      28      95 ..      25     104 .] 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
               RRM_occluded  4 isllplsDtvnkariralveekegeikkivLvpdheG...AivefkdekiagkasLaLdgsefegkklrc 70
                               + + +l   v+++ i a++ +  g+i  i + + ++    Aiv f++ek++  +sL  +gs ++gkk+ +
  gene32|gene32|rna32|rna32 28 VYVKNLDASVTNSDIAAHFRSC-GNISGINVITTKNTrkyAIVDFTSEKSV-EMSLLFNGSVLKGKKIIV 95
                               667789999*************.77666666665554444********987.89*************976 PP

>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05     0.049      20      65 ..      32      80 ..      19      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                         RL 20 scpskisekkllkylsqhGkinkhFfYeskgv..yavvEFsekesi.as 65
                               ++ + +++ ++ +++ + G+i      ++k +  ya+v+F ++ s+  s
  gene32|gene32|rna32|rna32 32 NLDASVTNSDIAAHFRSCGNISGINVITTKNTrkYAIVDFTSEKSVeMS 80
                               467889999*************999999998888************445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 711.73
//
Query:       gene320|gene320|rna320|rna320  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.5e-39  134.5   0.0    3.1e-39  134.2   0.0    1.1  1  Arf         ADP-ribosylation factor family
    9.5e-12   45.2   0.0    1.3e-11   44.7   0.0    1.2  1  Roc         Ras of Complex, Roc, domain of DAPkinase
    1.5e-10   40.9   0.0    1.9e-10   40.6   0.0    1.1  1  Ras         Ras family
      6e-08   32.2   0.6    0.00067   18.9   0.1    2.3  2  G-alpha     G-protein alpha subunit
    2.7e-06   26.9   0.0    3.3e-06   26.6   0.0    1.1  1  Gtr1_RagA   Gtr1/RagA G protein conserved region
    9.3e-06   25.2   0.0    1.2e-05   24.8   0.0    1.2  1  SRPRB       Signal recognition particle receptor beta subunit
    1.4e-05   25.2   0.0    3.2e-05   24.0   0.0    1.6  2  MMR_HSR1    50S ribosome-binding GTPase
    8.4e-05   22.2   0.1     0.0083   15.7   0.0    2.2  2  GTP_EFTU    Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.078   12.7   0.1       0.34   10.7   0.0    1.8  2  ATP_bind_1  Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.0   1.6e-42   3.1e-39       2     172 ..       4     167 ..       3     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 1.6e-42
                                    HHHHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTT CS
                            Arf   2 lsilaklklkkkelrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfek 81 
                                     +i++++k+++ +lril+lGLDnaGKtTil+k+ ++ ++++ PT g+++ ++++k  ++ + D+GGq+   ++W++Y+e+
  gene320|gene320|rna320|rna320   4 NKIVRRIKKERAQLRILVLGLDNAGKTTILHKILSKPIEDVHPTFGYQIYDVSYKATSLIILDIGGQSMFIEYWSSYYED 83 
                                    68999999999********************************************************************* PP

                                    ESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTT CS
                            Arf  82 tdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkg 161
                                    +d+v+fv Ds+d++ + e    ++++l      + ++l+laNK Dl+   + ++  +    e lk k++++++kc+ +kg
  gene320|gene320|rna320|rna320  84 VDGVVFVFDSSDSRSFVEHIGHIRSILV-----STPMLILANKSDLNPMFNPNQFGKDFC-ELLK-KKDVKLIKCCGIKG 156
                                    **********************999986.....5799****************9987653.3355.99************ PP

                                    BTHHHHHHHHH CS
                            Arf 162 eglkeglewls 172
                                    +gl+ g++w+ 
  gene320|gene320|rna320|rna320 157 DGLEAGFDWML 167
                                    *********86 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   6.7e-15   1.3e-11       1     119 [.      18     123 ..      18     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 6.7e-15
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    +++++G  ++GKt++l++++++ ++ + ++t+g+++++ ++            k  +l i D++Gq  f +  ++y+++ 
  gene320|gene320|rna320|rna320  18 RILVLGLDNAGKTTILHKILSKPIE-DVHPTFGYQIYDVSY------------KATSLIILDIGGQSMFIEYWSSYYEDV 84 
                                    689*****************99996.5679*****987543............345799********************* PP

                                    CEEEEEEEGHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  81 alailvydsrssenlkeWlkelkkvagkspvilvgnkiD 119
                                    + +++v+ds++s+++ e + ++++   ++p+++++nk D
  gene320|gene320|rna320|rna320  85 DGVVFVFDSSDSRSFVEHIGHIRSILVSTPMLILANKSD 123
                                    **************99*********************99 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   9.4e-14   1.9e-10       2     154 ..      19     164 ..      18     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 9.4e-14
                                    EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                    ++++G  + GKt++l++  ++   e+ ++T g + y    +v+ k  +l i+D  Gq  f +  ++yy+d++g++ v+d 
  gene320|gene320|rna320|rna320  19 ILVLGLDNAGKTTILHKILSKPI-EDVHPTFGYQIY----DVSYKATSLIILDIGGQSMFIEYWSSYYEDVDGVVFVFDS 93 
                                    899**************887765.67799*976655....56678889******************************** PP

                                    TBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHH...HHHTSEEEEEBTTTTCTHHHHHH CS
                            Ras  82 tsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeela...kelglkfletSAktnenveeafe 154
                                    ++++sf +    + +i+++   ++p+++++nK+Dl+      ++ g++++   k++++k +++   +  ++e  f+
  gene320|gene320|rna320|rna320  94 SDSRSFVEH---IGHIRSILV-STPMLILANKSDLNP-MFNPNQFGKDFCellKKKDVKLIKCCGIKGDGLEAGFD 164
                                    ******764...556666666.4789*********96.33334444444433356667777777666666666665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   5.6e-05      0.11      19      43 ..      11      36 ..       4      44 .. 0.80
   2 !   18.9   0.1   3.4e-07   0.00067     187     236 ..      46      94 ..      38      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.6e-05
                                   XE...EEEEEEEESTTSSHHHHHHHH CS
                        G-alpha 19 kk.krevkllllGqseSGKsTilkql 43
                                   kk + ++++l+lG +  GK+Til ++
  gene320|gene320|rna320|rna320 11 KKeRAQLRILVLGLDNAGKTTILHKI 36
                                   3335689***************9876 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 3.4e-07
                                    ---SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGG CS
                        G-alpha 187 ktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvsls 236
                                    +t G + ++++++  +++ i+d+gGq    + W ++++dvd ++F+   s
  gene320|gene320|rna320|rna320  46 PTFGYQIYDVSYK-ATSLIILDIGGQSMFIEYWSSYYEDVDGVVFVFDSS 94 
                                    5899999999999.99*****************************98766 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   1.6e-09   3.3e-06       1     112 [.      18     113 ..      18     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.6e-09
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvl 80 
                                    ++L +G  ++GKt++     +++l + +  +  t   +  +v  ++   l ++D+gGq+ f+e       ++ +++v+ +
  gene320|gene320|rna320|rna320  18 RILVLGLDNAGKTTI----LHKILSKPIEDVHPTFGYQIYDV-SYKATSLIILDIGGQSMFIEYW-----SSYYEDVDGV 87 
                                    589**********96....567778889999***********.688999***********99975.....678999**** PP

                      Gtr1_RagA  81 iyVfDvesreleedletlkeilealrqyspea 112
                                    ++VfD++++      ++++e + ++r +    
  gene320|gene320|rna320|rna320  88 VFVFDSSDS------RSFVEHIGHIRSILVST 113
                                    *****9944......44444444444444444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   6.1e-09   1.2e-05       4     124 ..      17     124 ..      14     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 6.1e-09
                                    -EEEEE-STTSSHHHHHHHHHHS...S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEE CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttd...svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglv 80 
                                     ++l++Gl ++GKT+++++++++    v++t   q   ++      k ++l ++D+ G+  +    +    + + + g+v
  gene320|gene320|rna320|rna320  17 LRILVLGLDNAGKTTILHKILSKpieDVHPTFGYQIYDVS-----YKATSLIILDIGGQSMFIEYWSS---YYEDVDGVV 88 
                                    589*******************944444444444444444.....46699******998776555544...5788***** PP

                                    EEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTS CS
                          SRPRB  81 fvvDStidpkevkevAEllyeilliteklkdavdiliACnKqel 124
                                    fv DS+ d++   e    + +il+ t       ++li  nK++l
  gene320|gene320|rna320|rna320  89 FVFDSS-DSRSFVEHIGHIRSILVST-------PMLILANKSDL 124
                                    *****8.5555555444455554443.......46666666665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   1.6e-08   3.2e-05       1     114 []      18     121 ..      18     121 .. 0.68
   2 ?   -2.9   0.0       3.6   7.1e+03      45      70 ..     143     171 ..     135     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.6e-08
                                    EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adl 78 
                                    +++++G  N+GK+t++ +++ +    v      T   + + v++k ++++++D+ G  +      ++ + + +  e +d 
  gene320|gene320|rna320|rna320  18 RILVLGLDNAGKTTILHKILSKpIEDVHP----TFGYQIYDVSYKATSLIILDIGG-QS------MFIEYWSSYYEdVDG 86 
                                    689*****************984445544....445566666666789********.44......6777777766559** PP

                                    EEEEEETT.TTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
                       MMR_HSR1  79 illvvdas.eeklkpldeeleellee..akkplilvlnk 114
                                    +++v+d+s +   +   e++  ++ +     p+++++nk
  gene320|gene320|rna320|rna320  87 VVFVFDSSdS---RSFVEHIGHIR-SilVSTPMLILANK 121
                                    ******7741...22223333332.12345677777776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.6
                                    TEEEEEEECGGCSS....HHHHHHHHHHHH CS
                       MMR_HSR1  45 gkeielvDtpGlie....gaseekglgkaf 70 
                                    +k+++l+ + G i+    +a  +++lg+a+
  gene320|gene320|rna320|rna320 143 KKDVKLIKCCG-IKgdglEAGFDWMLGRAM 171
                                    46677777778.543334455555666665 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.011        22       5      26 ..      18      39 ..      14      46 .. 0.85
   2 !   15.7   0.0   4.2e-06    0.0083      66     180 ..      56     158 ..      45     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.011
                                   EEEEEESTTSSHHHHHHHHHHH CS
                       GTP_EFTU  5 nigiighvDhGKtTLtdrLlyk 26
                                    i ++g  ++GKtT++ ++l k
  gene320|gene320|rna320|rna320 18 RILVLGLDNAGKTTILHKILSK 39
                                   688999999*********9965 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.2e-06
                                    TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHH..TTTEEEEEEESCGST.HHHHHHH CS
                       GTP_EFTU  66 etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalk..egvpiivfiNKmDrl.kaelkei 142
                                    ++k + + ++D  G   F++  +  ++ +Dg+v+v+d+++       e++ ++++  + +p+ ++ NK D     + ++ 
  gene320|gene320|rna320|rna320  56 SYKATSLIILDIGGQSMFIEYWSSYYEDVDGVVFVFDSSDSRSF--VEHIGHIRSilVSTPMLILANKSDLNpMFNPNQF 133
                                    47889999*******************************98654..455555555115666*********9776666666 PP

                                    HHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBT CS
                       GTP_EFTU 143 veevkqklsrkeeklekygekgekevpvvfgSalkgeg 180
                                     ++  + l            k+ k+v+++ ++++kg+g
  gene320|gene320|rna320|rna320 134 GKDFCELL------------KK-KDVKLIKCCGIKGDG 158
                                    66666555............22.245555555555555 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.43   8.7e+02       1      16 [.      21      36 ..      21      45 .. 0.84
   2 ?   10.7   0.0   0.00017      0.34      90     170 ..      59     126 ..      47     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.43
                     ATP_bind_1  1 vvGpaGsGKttfvgal 16
                                   v+G   +GKtt+ +++
  gene320|gene320|rna320|rna320 21 VLGLDNAGKTTILHKI 36
                                   7888899****99876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
                     ATP_bind_1  90 eddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDll 169
                                     ++++++D+ GQ  +  +++s          e   +vv+++Ds  +++ ++ i +        + +++P+++  nk Dl 
  gene320|gene320|rna320|rna320  59 ATSLIILDIGGQSMFIEYWSSYY--------EDVDGVVFVFDSSDSRSFVEHIGH-----IRSILVSTPMLILANKSDLN 125
                                    4589*******************........66779******9988885555555.....66677899**********94 PP

                     ATP_bind_1 170 k 170
                                     
  gene320|gene320|rna320|rna320 126 P 126
                                    3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.35s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1020.70
//
Query:       gene321|gene321|rna321|rna321  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-13   49.9   0.1    6.5e-13   48.9   0.1    1.6  1  SF3A2          Pre-mRNA-splicing factor SF3a complex subunit 
  ------ inclusion threshold ------
      0.023   15.0   2.0      0.023   15.0   2.0    2.5  2  zf-C2H2_jaz    Zinc-finger double-stranded RNA-binding
      0.083   12.0   0.3       0.13   11.4   0.3    1.3  1  Peptidase_C62  Gill-associated viral 3C-like peptidase
      0.085   13.3   2.2       0.22   12.0   2.2    1.7  1  zf-met         Zinc-finger of C2H2 type
        7.4    6.3   6.2       0.98    9.1   1.0    2.2  2  zf-SCNM1       Zinc-finger of sodium channel modifier 1


Domain annotation for each model (and alignments):
>> SF3A2  Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   1.8e-16   6.5e-13      17      96 .]      96     170 ..      57     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.8e-16
                          SF3A2  17 eqvgllvevkypeikeevkPlhrimsaleqkleekpdkkvqyLliaaePYetiafkipskeidksedklwtfwdkdkkey 96 
                                    +++g  + ++y+ ++e   P++r++++leq +e+  d+ + yL++ ++PYe+++fk++sk++dk+  + ++  d+++ +y
  gene321|gene321|rna321|rna321  96 DRKGYGIVIDYKLAEEM--PQYRFVNSLEQAVED-YDECFGYLVFICKPYENVGFKFESKKVDKD--SIYEDIDEETGTY 170
                                    67788888999866666..**************6.***************************998..6677777766655 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.9      0.22     8e+02      19      27 .]       8      18 ..       7      18 .. 0.86
   2 ?   15.0   2.0   6.3e-06     0.023       2      27 .]      46      71 ..      45      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.22
                                   CCTTS..HHHH CS
                    zf-C2H2_jaz 19 nHlkS..KkHK 27
                                   +H  S  KkHK
  gene321|gene321|rna321|rna321  8 AHTASeiKKHK 18
                                   6889999***9 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 6.3e-06
                                   CBBTTTTBBBSSHHHHHCCTTSHHHH CS
                    zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHlkSKkHK 27
                                   + C++C+    +e ++ +H  +KkH+
  gene321|gene321|rna321|rna321 46 YICIICKTKHLTEMSYVKHREGKKHR 71
                                   89*****999***************7 PP

>> Peptidase_C62  Gill-associated viral 3C-like peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   3.6e-05      0.13      10      88 ..       3      77 ..       1      89 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                  Peptidase_C62 10 vrtgnattvedlnkhpynkyrknivrvygergdlngflsgkslhfprhifdtctdntltrhirvtkgeethdiellsee 88
                                   +r gna t  +++kh  ++ r+  +  yg   d n  ls  s+   r+i   c  + lt    v + e  +  e ls +
  gene321|gene321|rna321|rna321  3 LRMGNAHTASEIKKHKRERSRRLFLEAYGLTADQN--LSKDSV--GRYICIICKTKHLTEMSYVKHREGKKHREKLSAK 77
                                   699******************************98..888875..7999999*99999999999888888777777755 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.2   6.1e-05      0.22       1      25 []      46      70 ..      46      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.1e-05
                         zf-met  1 fyCelCnvtfnsesqlksHlqGKkH 25
                                   + C +C++++  e ++  H  GKkH
  gene321|gene321|rna321|rna321 46 YICIICKTKHLTEMSYVKHREGKKH 70
                                   78*********************** PP

>> zf-SCNM1  Zinc-finger of sodium channel modifier 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4      0.54   1.9e+03       1       5 [.      48      52 ..      48      54 .. 0.85
   2 ?    9.1   1.0   0.00027      0.98      18      26 ..      63      71 ..      61      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.54
                       zf-SCNM1  1 ClVCs 5 
                                   C++C 
  gene321|gene321|rna321|rna321 48 CIICK 52
                                   ****7 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00027
                       zf-SCNM1 18 vHrkGkkHl 26
                                    Hr GkkH+
  gene321|gene321|rna321|rna321 63 KHREGKKHR 71
                                   6*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1091.32
//
Query:       gene322|gene322|rna322|rna322  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-18   65.9   4.0      2e-18   65.9   4.0    2.7  3  TFIIS_C          Transcription factor S-II (TFIIS)
    1.2e-06   28.3   0.7    1.2e-06   28.3   0.7    2.7  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
     0.0022   17.6   1.1     0.0022   17.6   1.1    2.6  3  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
  ------ inclusion threshold ------
       0.08   13.3   5.6       0.37   11.2   2.0    2.4  2  Lar_restr_allev  Restriction alleviation protein Lar
        0.1   13.2   1.0       0.28   11.8   1.0    1.8  1  Trm112p          Trm112p-like protein
       0.33   11.1   0.1       0.33   11.1   0.1    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.2   5.9e+02       3      12 ..       4      13 ..       2      16 .. 0.74
   2 ?   -0.8   0.0      0.47   1.4e+03      31      36 ..      24      29 ..      22      32 .. 0.64
   3 !   65.9   4.0   6.8e-22     2e-18       2      39 .]      63     103 ..      62     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                        TFIIS_C  3 CpkCgsreay 12
                                   Cp C+s  ++
  gene322|gene322|rna322|rna322  4 CPLCSSMLVV 13
                                   ****987665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.47
                        TFIIS_C 31 CtkCgh 36
                                   C  Cg+
  gene322|gene322|rna322|rna322 24 CRMCGY 29
                                   666665 PP

  == domain 3  score: 65.9 bits;  conditional E-value: 6.8e-22
                        TFIIS_C   2 kCpk...CgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                    kC k   Cgs+e++f++lQtRsaDEpmt+fykC+ C++ Wr
  gene322|gene322|rna322|rna322  63 KCGKrceCGSEEVSFVELQTRSADEPMTIFYKCIRCKKVWR 103
                                    6777777*********************************8 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.7   3.9e-10   1.2e-06       1      34 [.       1      34 [.       1      36 [. 0.91
   2 ?   -1.6   0.6      0.88   2.6e+03       2       8 ..      59      65 ..      58      72 .. 0.67
   3 ?   -0.7   0.1      0.45   1.4e+03      20      28 ..      90      99 ..      83     101 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.9e-10
                                   EEBESTTTSBEEEEECSCCCEEEESSSS-EEESS CS
                 RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepad 34
                                   + FCp C ++L +k+   g+ + Cr CgY + ++
  gene322|gene322|rna322|rna322  1 MLFCPLCSSMLVVKRQPVGNELSCRMCGYLYAIS 34
                                   67*****************77********99776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.88
                                   EBESTTT CS
                 RNA_POL_M_15KD  2 kFCpkCg 8 
                                   kF +kCg
  gene322|gene322|rna322|rna322 59 KFVSKCG 65
                                   5666776 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.45
                                   CE.EEESSSS CS
                 RNA_POL_M_15KD 20 kn.feCrqCg 28
                                   ++ + C  C+
  gene322|gene322|rna322|rna322 90 TIfYKCIRCK 99
                                   5678899896 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.46   1.4e+03      36      41 ..      23      28 ..      22      29 .. 0.84
   2 ?   -1.0   0.5       0.5   1.5e+03      32      39 ..      59      66 ..      54      71 .. 0.62
   3 !   17.6   1.1   7.4e-07    0.0022      16      40 ..      74      98 ..      66     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.46
                  Baculo_LEF5_C 36 yCskCg 41
                                    C+ Cg
  gene322|gene322|rna322|rna322 23 SCRMCG 28
                                   5****9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.5
                  Baculo_LEF5_C 32 sfvryCsk 39
                                    fv  C k
  gene322|gene322|rna322|rna322 59 KFVSKCGK 66
                                   56777754 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 7.4e-07
                  Baculo_LEF5_C 16 dfvtiEiQnRagDEivsfvryCskC 40
                                   + + +E Q+R+ DE   +   C +C
  gene322|gene322|rna322|rna322 74 EVSFVELQTRSADEPMTIFYKCIRC 98
                                   4459********************* PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.0   0.00012      0.37       6      37 ..       4      37 ..       1      92 [. 0.73
   2 ?    2.2   1.7     0.078   2.3e+02       9      32 ..      70      99 ..      63     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga.......s 37
                                   CP C +  v++r++ + +      +C  Cg+        
  gene322|gene322|rna322|rna322  4 CPLCSSMLVVKRQPVGNE-----LSCRMCGYlyaiskeI 37
                                   *************99985.....7888888755532221 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.078
                Lar_restr_allev  9 Cggravlersqrvvaeigq......cvyCa 32
                                   Cg+++v + + ++++  ++      c+ C+
  gene322|gene322|rna322|rna322 70 CGSEEVSFVELQTRSADEPmtifykCIRCK 99
                                   777777666666665555567766777775 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.0   9.4e-05      0.28       8      67 ..       2      35 ..       1      36 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                                   -B-TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEET CS
                        Trm112p  8 LaCpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIkd 67
                                   L Cp+c + L                           ++ + + +eL C+ cg  Y I++
  gene322|gene322|rna322|rna322  2 LFCPLCSSML--------------------------VVKRQPVGNELSCRMCGYLYAISK 35
                                   6777777777..........................47899*****************86 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00011      0.33       2      31 ..       4      36 ..       3      41 .. 0.87
   2 ?   -0.1   0.7      0.34     1e+03      11      22 ..      87      98 ..      42     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                       zf-Mss51  2 CPvpkhkqt...apkhvdfeCpdCGiptycsee 31
                                   CP++++      +p   ++ C  CG+ +  s+e
  gene322|gene322|rna322|rna322  4 CPLCSSMLVvkrQPVGNELSCRMCGYLYAISKE 36
                                   99998777687899999***********99998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
                       zf-Mss51 11 apkhvdfeCpdC 22
                                   +p  + ++C +C
  gene322|gene322|rna322|rna322 87 EPMTIFYKCIRC 98
                                   677777888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 704.47
//
Query:       gene323|gene323|rna323|rna323  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-34  119.1   3.6    3.5e-34  118.8   3.6    1.0  1  V-ATPase_C  V-ATPase subunit C


Domain annotation for each model (and alignments):
>> V-ATPase_C  V-ATPase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.8   3.6     2e-38   3.5e-34       3     322 ..       4     306 ..       2     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 118.8 bits;  conditional E-value: 2e-38
                     V-ATPase_C   3 Lisvpg.ektseqtleelnkalskksknselykfeipdlkvgtLDsLvalsddLgKldafvesvvkKvartlaevledqk 81 
                                    L+ +p  e t + t  +++++ +      +++++ +p++   +L+ +v++ + L+ l++++e+++k  + + +       
  gene323|gene323|rna323|rna323   4 LVGLPVeEDTPHPTEGQIQEEYG-----VHSSRILLPSFTGVSLEGIVNQVERLNSLEKSCEGLLKTFVGYSGGDN---- 74 
                                    56666633333334444444443.....6778999******************************99999877652.... PP

                     V-ATPase_C  82 dkleenllvngkslesYltkFqWdeakypvkqslkelvdiiskevtqidedlktksaaYnelksslqalerkktgnLltr 161
                                       + n+  + + ++++l   +Wd++ + + +s+ +++  +++e ++i++ + +k +++ne+k++   l++ + gnL   
  gene323|gene323|rna323|rna323  75 -MGKGNVCNSAERMKEFL---KWDSQSFMT-NSIDKVILLLEEEYKRINKAYEEKAEEFNEAKKECDRLQKLTRGNLCDI 149
                                    .234567777899*****...9*****976.69*********************************************** PP

                     V-ATPase_C 162 sLadlvkkedfvldseyLttllViVpknsekewlk.sYekltdmVVPrSakklaeDneyaLftVtlfkkvveefkakare 240
                                    +L+ +v+k++     e+L+ + V+V k++ +e+++  Ye+    +     +k+ +D+++ Lf+  ++  + ee ++ + e
  gene323|gene323|rna323|rna323 150 NLNIIVEKQEKY---EFLKVMYVVVQKSKSSEFNRiVYES--PHISSDAVEKINSDEDHDLFKLYILHHSEEEIRNMMHE 224
                                    *********988...******************9845885..789999******************************** PP

                     V-ATPase_C 241 kkfivReFsydeeeleeekeeltkleaekkkqegelvrllkvnFsevfvawiHlkalrvFvEsvLRYGlpvnFqalllqp 320
                                    ++f +++ + +  + +e   e+ k+e++ +  e  l+  ++++  e++ +++H+k lr+FvEsv RYGlp ++++++ + 
  gene323|gene323|rna323|rna323 225 EGFLIKDLDENMISSKEMITERRKAEERFSAIERILMTFVHIHLVEALKILVHVKLLRLFVESVYRYGLPTEYMFFVTNG 304
                                    *******9999999999999999999999999******************************************887775 PP

                     V-ATPase_C 321 ek 322
                                    ek
  gene323|gene323|rna323|rna323 305 EK 306
                                    33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2494.94
//
Query:       gene324|gene324|rna324|rna324  [L=1238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   24.8   1.2    5.1e-05   23.0   0.1    2.5  3  DCB       Dimerisation and cyclophilin-binding domain of Mon2
  ------ inclusion threshold ------
      0.092   13.7   0.5       0.33   11.9   0.5    2.0  1  Pup       Pup-like protein


Domain annotation for each model (and alignments):
>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   5.7e-09   5.1e-05      29     172 ..      22     162 ..      12     166 .. 0.88
   2 ?   -3.4   0.0      0.71   6.4e+03      80     109 ..     263     292 ..     259     298 .. 0.79
   3 ?   -2.8   0.0      0.49   4.4e+03      48      72 ..    1079    1103 ..    1065    1109 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.7e-09
                            DCB  29 keasekgilkLktikssseeeeqslaeaseeilkPlllacetknpkivqiaLgslqrLisheviseeaiskiietlwkll 108
                                    +e sek+   Lk+i++ +ee+ +++++++ +++  ++++ + k +  + + ++ +  ++  +++  + i++ii+ + + +
  gene324|gene324|rna324|rna324  22 SEISEKCRKLLKEIDKLEEENIKDFIRNTRDVVDVFMQGLKAKRQAPI-FVIDFIYTFLVNDLLGLNDINEIIDVISAGV 100
                                    556666666677777777666**********************99876.569**************************** PP

                            DCB 109 elgveielkvLqtllllvttssvvhgdtlakalvlCfrLhfskdnvvqntAaAtlrQlvsvvFe 172
                                     +++  ++k+Lq+   ++ +++  +gd+ + ++    r+ + +++ vq+tA+    +lv+v F 
  gene324|gene324|rna324|rna324 101 WCESS-KMKILQMSYYII-RYENFRGDLALALFKSIVRMVDDRSKQVQTTAKPIAMHLVDVTFG 162
                                    ****9.******988766.67889*****************************99999999986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.71
                            DCB  80 LgslqrLisheviseeaiskiietlwklle 109
                                    ++ l+ Li+ ++ s+ ++ k+i++l++ ++
  gene324|gene324|rna324|rna324 263 MELLKGLIKKGCSSKGNVYKVISILVERHN 292
                                    567888899999999999999998887665 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.49
                            DCB   48 eeeqslaeaseeilkPlllacetkn 72  
                                     +   +++ + ++il+ +  ac++ +
  gene324|gene324|rna324|rna324 1079 RIVLEFLMFYHDILTKFASACSSLQ 1103
                                     3345556667899999999998855 PP

>> Pup  Pup-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.5   3.7e-05      0.33      31      60 ..      19      48 ..       5      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                            Pup 31 erkeelsedvDdlLDeIDevLEeNAeeFVr 60
                                   +++ e+se    lL eID++ EeN  +F+r
  gene324|gene324|rna324|rna324 19 AEDSEISEKCRKLLKEIDKLEEENIKDFIR 48
                                   456789999********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.91u 0.32s 00:00:01.23 Elapsed: 00:00:00.51
# Mc/sec: 7273.97
//
Query:       gene325|gene325|rna325|rna325  [L=682]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     3e-166  554.1   7.5      9e-90  301.6   0.1    2.8  2  HSP70           Hsp70 protein
    1.4e-10   40.5   0.2     0.0026   16.6   0.1    3.2  3  MreB_Mbl        MreB/Mbl protein
    0.00011   21.6   1.1        1.8    7.7   0.0    3.2  3  Hydantoinase_A  Hydantoinase/oxoprolinase
     0.0026   17.5   0.0     0.0064   16.2   0.0    1.7  1  FGGY_C          FGGY family of carbohydrate kinases, C-termin
  ------ inclusion threshold ------
      0.025   14.5   0.4        4.4    7.2   0.1    2.5  2  DeoRC           DeoR C terminal sensor domain
       0.46    9.5   3.4       0.74    8.8   3.4    1.2  1  Membralin       Tumour-associated protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.6   0.1     3e-93     9e-90       1     317 [.      13     361 ..      13     371 .. 0.84
   2 !  252.1   3.7   2.9e-78   8.6e-75     324     596 ..     393     673 ..     381     676 .. 0.93

  Alignments for each domain:
  == domain 1  score: 301.6 bits;  conditional E-value: 3e-93
                                    EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSHHHH CS
                          HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfsdpevq 79 
                                    +iGiDLGtt s+va   +gk+evi+n+ g+rttPsvv+F+++   +vG+aAk+ +  +p+ ++f++KrliGr+f+dp +q
  gene325|gene325|rna325|rna325  13 AIGIDLGTTFSCVAGYISGKVEVITNADGERTTPSVVSFDENnCTVVGTAAKNMVGLDPTSVLFDAKRLIGREFDDPRIQ 92 
                                    59***************************************966899********************************* PP

                                    HHHTTXSSEEEEETT.................SBEEEEEEETTE..EEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEE CS
                          HSP70  80 keikelpykvvkken.................gkavveveaage..kftpeqisamvLkklketaeaylgkkvtdavitv 140
                                    + ++ +p+k+v+ ++                 +++  +v+  g+   ++p ++s++vL +lk+ aea lg +v+ av+tv
  gene325|gene325|rna325|rna325  93 NSMSGWPFKIVRYNHrekreetskvpegsnsyDNIAYKVTKDGKvkYYAPVEVSGKVLLYLKSAAEARLGGTVDSAVVTV 172
                                    **********96432111111111111111113445567777879889******************************** PP

                                    XTTXXHHHHHHHHHHHHHTTX..EEEEEEEHHHHHHHHHHTCCSS......SCEEEEEEEEXSSXEEEEEEEEE....TT CS
                          HSP70 141 PaYfndaqRqatkdAgkiAGL..nvlRivNepTAaalaYGldkkd......kernvlvyDlGggtfdvSilele....kG 208
                                    PaYf++ q+  tk A++iAG+  n +R++ epTAaa+aYG  +++       ++ vlv+DlGggtfdvS+l++e     G
  gene325|gene325|rna325|rna325 173 PAYFEEPQKDVTKAAATIAGFdpNKVRLLAEPTAAAMAYGHIQTQknanfsAKEDVLVFDLGGGTFDVSVLDFEfngaAG 252
                                    *********************55569**************877776889988899*****************98745556 PP

                                    EEE.EEEEEEETTXSHHHHHHHHHHHHHHHHHHHH.SX.XGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETT CS
                          HSP70 209 vfe.vkaTagDthlGGedfDealvehlveefkkke.gi.dlskdkkalqrlkeaaekaKkeLSsskqteinleietvded 285
                                     +  vka  gDt lGG+dfD+ l++h+++ef kk+ +i     ++ al rl+ ++ ++K  LSs++++ i +++  ++e 
  gene325|gene325|rna325|rna325 253 SLGiVKAIDGDTFLGGQDFDNLLINHCISEFLKKNpSIkKSDLKESALLRLRAECTRVKAVLSSATSSAIYVPCFHMTE- 331
                                    775489*************************777424523334567******************666666655555555. PP

                                    TEEEEEEEEHHHHHHHHHHHHHHTHHHHHHHH CS
                          HSP70 286 gkdlseklsRakfeelvedllertlepvekal 317
                                      dl+++++Ra+fe l+++l+++++e ++ +l
  gene325|gene325|rna325|rna325 332 --DLNVQITRARFELLCDHLFKKCMERTKGCL 361
                                    ..9**********************9998776 PP

  == domain 2  score: 252.1 bits;  conditional E-value: 2.9e-78
                                    GGGCSEEEEESGGGGSHHHHHHHHHHTT.CHHBSSSHTTTHHHHHHHHHHH.HHCTC.GCSHCCEEEEBESS-EEEEETT CS
                          HSP70 324 keeidevvlvGGstRiPkvqelvkelfg.kepsktvnpDeavaiGAAvqag.vlsge.eevkdllllDvtpLslgietlg 400
                                     + i++v+lvGGs+RiPkv+ ++ e+fg ++  + vn+Deava+GAA qa+ ++s +    + lll D +pL l+iet+g
  gene325|gene325|rna325|rna325 393 RNSISKVLLVGGSSRIPKVKAMLAEYFGaHKVVEPVNADEAVAYGAAYQAAsIYSDAvDAGSSLLLIDCVPLNLSIETAG 472
                                    5789************************999******************8747777634557899*************** PP

                                    TEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEE CS
                          HSP70 401 gvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGilt 480
                                    gv+t l +  + ip kk+++f+t++dnqtav+i+v++g+r + kdnk++gsf+ldgi paprGvp+ieVtfd+d nGil 
  gene325|gene325|rna325|rna325 473 GVATPLVNCGDNIPIKKTETFTTYEDNQTAVTINVYEGNRPMCKDNKKIGSFNLDGIIPAPRGVPKIEVTFDVDHNGILI 552
                                    ******************************************************************************** PP

                                    EEEEETTTCCEEEEEEECCSS.SBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..GGGSTHHHH CS
                          HSP70 481 vsakdketgkeeeitieaseg.lseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleee..aekvseaek 557
                                    v+a+dk+tgke++it+++s++ ls+eeie+m k+a++++++d+++ke++ ++ + ++ + s ++ le++  +++ +++++
  gene325|gene325|rna325|rna325 553 VTAQDKQTGKENKITVTNSQNrLSQEEIERMAKEARDNEQRDNETKEKMTKRMSFDQAIFSFKSLLEKSniSQEKKDEAQ 632
                                    ********************99********************************************99976555555666 PP

                                    HHHHHHHHHHHCHTTSSC..HHHHHHHHHHHHHHHHHHHHH CS
                          HSP70 558 ekvesaieeLkeeleeee..keeieakteelkkvvekiaek 596
                                    + +++++e+L ++   ++  ++e+e++ +el++ +++i+++
  gene325|gene325|rna325|rna325 633 KIIKENEEWLLRAQGPDDfeVDELERRSNELQSFMNDIMKE 673
                                    889999***999875555679***************99986 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   8.8e-07    0.0026       2      56 ..      12      73 ..      11      77 .. 0.79
   2 !   15.2   0.0   2.3e-06    0.0069      71     164 ..     143     245 ..     124     285 .. 0.74
   3 !    4.8   0.0    0.0035        10     261     318 ..     385     441 ..     379     449 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.8e-07
                                   SEEEEEE-SSEEEE..EETTTEEEEEE.......ES-EEEETTT--EEEESHHHHTTTTS-GTT CS
                       MreB_Mbl  2 kdlgiDLGtantlv..yvkgkgivlne.......psvvAikkktkkvlavGeeAkkmlgktpgn 56
                                   + +giDLGt+   v  y++gk  v+++       psvv +++++   + vG+ Ak+m+g  p++
  gene325|gene325|rna325|rna325 12 RAIGIDLGTTFSCVagYISGKVEVITNadgerttPSVVSFDENN--CTVVGTAAKNMVGLDPTS 73
                                   679*******999999*****98885333334449**9998765..6679*********88876 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.3e-06
                                    HHHHHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT..-SEEEEEEHHHHHHHHTT.......--T CS
                       MreB_Mbl  71 levaeellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaG..arevllieeplaAAiGag.......lpv 141
                                    +ev  ++l y+ + ++ +   + ++ v++vP   +e ++   k aa+ aG   ++v l+ ep aAA+  g        + 
  gene325|gene325|rna325|rna325 143 VEVSGKVLLYLKSAAEARLGGTVDSAVVTVPAYFEEPQKDVTKAAATIAGfdPNKVRLLAEPTAAAMAYGhiqtqknANF 222
                                    45666677777666666767788899************99999999999944579***********98762111111345 PP

                                    TSSS-EEEEEE-SS-EEEEEEET CS
                       MreB_Mbl 142 eepsgnmvvdiGggttevavisl 164
                                    ++ +  +v d+Gggt +v+v+ +
  gene325|gene325|rna325|rna325 223 SAKEDVLVFDLGGGTFDVSVLDF 245
                                    5556679*************964 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0035
                                    HHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-.EEE-SSTTTHHHHHHHHT CS
                       MreB_Mbl 261 LektppeLaadivdrgivltGGgallkgldkllseetglp.vkvaedpltcvakGtgkv 318
                                    Lekt  e    i +  ++l+GG++ +  ++ +l e +g + v    ++ ++va G++  
  gene325|gene325|rna325|rna325 385 LEKTLNEVRNSISK--VLLVGGSSRIPKVKAMLAEYFGAHkVVEPVNADEAVAYGAAYQ 441
                                    77777777777754..899******************9751555568899999998765 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.013        38      75     112 ..       7      44 ..       1      72 [. 0.77
   2 !    7.7   0.0   0.00061       1.8      62      97 ..     204     244 ..     194     252 .. 0.68
   3 !    7.2   0.0   0.00086       2.6     189     283 ..     332     439 ..     324     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
                 Hydantoinase_A  75 lagekkvItfDmGGTstDvslikdgevevsleteiagv 112
                                    + + +++I++D+G T   v+ +++g+vev ++    + 
  gene325|gene325|rna325|rna325   7 KSNTSRAIGIDLGTTFSCVAGYISGKVEVITNADGERT 44 
                                    556789**********************9888774444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00061
                 Hydantoinase_A  62 PaaGvvgaaat.....sklagekkvItfDmGGTstDvslik 97 
                                    P a ++++ ++     ++   +++v++fD+GG ++Dvs+++
  gene325|gene325|rna325|rna325 204 PTAAAMAYGHIqtqknANFSAKEDVLVFDLGGGTFDVSVLD 244
                                    555555555542111133345689**************986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.00086
                 Hydantoinase_A 189 kldvelarrafeelakelnlk.................veevAegilsvavenmanavrklsvergldpkeltlvvfGGa 251
                                     l+v+++r+ fe l ++l +k                 ve  A+g   +++  + + ++++    +  ++++ l  +GG+
  gene325|gene325|rna325|rna325 332 DLNVQITRARFELLCDHLFKKcmertkgcllrsagvpeVEYSADGSKLLLNPSLEKTLNEV----RNSISKVLL--VGGS 405
                                    6888999999999999998889999999999999999999999999999999999999999....555555555..5777 PP

                 Hydantoinase_A 252 G..aqhaaalaeelgvkkvivppyagvlsalGma 283
                                    +  + + a+lae +g +kv++p  a  ++a+G+a
  gene325|gene325|rna325|rna325 406 SriPKVKAMLAEYFGAHKVVEPVNADEAVAYGAA 439
                                    756889**************************98 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.1e-06    0.0064     147     195 ..     393     443 ..     382     446 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.1e-06
                         FGGY_C 147 gkpldrlavdGGgskndllmqllAdilg.vpVerpkt.aeatalGaAilAa 195
                                    +  +++++++GG s+ + +  +lA+ +g  +V+ p + +ea+a GaA+ Aa
  gene325|gene325|rna325|rna325 393 RNSISKVLLVGGSSRIPKVKAMLAEYFGaHKVVEPVNaDEAVAYGAAYQAA 443
                                    56799***********************9666666666***********98 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0015       4.4      21      50 ..      12      39 ..       9      41 .. 0.92
   2 ?    4.7   0.0    0.0085        26      81     118 ..     595     632 ..     586     642 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                          DeoRC 21 dtifldaGtTtlelaraLaekknltvvTns 50
                                    +i +d GtT   +a +++ k  + v+Tn 
  gene325|gene325|rna325|rna325 12 RAIGIDLGTTFSCVAGYISGK--VEVITNA 39
                                   5799****************9..*****95 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0085
                          DeoRC  81 gplaeealrqfnvdkaflgangidaegglttsdeeeae 118
                                    ++++e++ +++++d+a+++ +++ +++++++++ +ea+
  gene325|gene325|rna325|rna325 595 NETKEKMTKRMSFDQAIFSFKSLLEKSNISQEKKDEAQ 632
                                    5678999**********************999999986 PP

>> Membralin  Tumour-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.4   0.00025      0.74      75     175 ..     535     633 ..     530     659 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                      Membralin  75 Gilrveivrnlkksevllessekeeesekkisisenkkvllkeasvtlleesvlevsleaeeeeke.ssslkkeeelrsv 153
                                    G+ ++e++ +++++ +l ++++ +++ +++ ++  n++  l++++ +++ ++ ++ +++++e +++ +++++  +++   
  gene325|gene325|rna325|rna325 535 GVPKIEVTFDVDHNGILIVTAQDKQTGKENKITVTNSQNRLSQEEIERMAKEARDNEQRDNETKEKmTKRMSFDQAI--- 611
                                    9999***********98888887777666666666666666666655555555544444333332202223223332... PP

                      Membralin 154 eliensslktnlklledleise 175
                                    + +++   k+n+++ ++ e ++
  gene325|gene325|rna325|rna325 612 FSFKSLLEKSNISQEKKDEAQK 633
                                    2233333333333222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1578  (0.0880138); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.87u 0.36s 00:00:01.23 Elapsed: 00:00:00.56
# Mc/sec: 3676.29
//
Query:       gene326|gene326|rna326|rna326  [L=176]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-08   31.7   0.3    2.9e-07   30.2   0.3    1.8  1  Synaptobrevin  Synaptobrevin
  ------ inclusion threshold ------
      0.022   14.8   0.0       0.04   14.0   0.0    1.5  1  Longin         Regulated-SNARE-like domain


Domain annotation for each model (and alignments):
>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.3   3.2e-11   2.9e-07       2      56 ..     117     171 ..     116     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.2e-11
                                    XXHHHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHH CS
                  Synaptobrevin   2 ndklakikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkqark 56 
                                    +++l +i++ev+e+k+ + + +  vler++kl++Lv k+e+L  +++   k+a+k
  gene326|gene326|rna326|rna326 117 KHTLLQIQNEVEETKGALSKTLMAVLERNDKLEDLVAKSEHLCYETKLLFKSAKK 171
                                    57899*************************************9999888888876 PP

>> Longin  Regulated-SNARE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.4e-06      0.04      20      56 ..      64     100 ..      42     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-06
                         Longin  20 hdsytfhylaedgltylviadesyprrlaFafLeeik 56 
                                    ++ y    l++++++y+  ad++yp  +a  +L+e +
  gene326|gene326|rna326|rna326  64 EKTYKLFSLVHNDYAYIACADDNYPGIVALKLLQEAR 100
                                    6668888999************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1086.01
//
Query:       gene327|gene327|rna327|rna327  [L=714]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-60  202.9   0.1    8.3e-60  202.0   0.1    1.4  1  MutS_V    MutS domain V
    1.1e-18   68.1   0.1    3.4e-18   66.6   0.1    1.8  1  MutS_III  MutS domain III
  ------ inclusion threshold ------
      0.071   12.8   0.0       0.15   11.7   0.0    1.6  1  CDPS      Cyclodipeptide synthase
       0.12   11.3   1.4       0.37    9.7   1.4    1.7  1  IFT57     Intra-flagellar transport protein 57
       0.14   12.5   1.3       0.48   10.8   1.3    2.0  1  MutS_IV   MutS family domain IV


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.1   2.3e-63   8.3e-60       2     185 ..     540     713 ..     539     714 .] 0.95

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 2.3e-63
                                    EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TTSEE CS
                         MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatekslv 81 
                                    ++tGpnm+Gkst+l+  ++i+lla++G++vpae+a+i+i+d i+ Rvga+D   +g+stFm+Em+++a+i + ++ +slv
  gene327|gene327|rna327|rna327 540 VVTGPNMGGKSTFLKTCGVIALLAHMGCYVPAEYASIPILDGIYVRVGAADCSFTGSSTFMMEMADIARICRLSSPESLV 619
                                    8******************************************************************************* PP

                                    EEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEEES--SS- CS
                         MutS_V  82 ilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvkegaaeks 161
                                    i+DElGRGts+ dGl+ia+av e+l++ +k+ +l atH+ el+  +  +++vk         +e   ++y++ +g+++ s
  gene327|gene327|rna327|rna327 620 IIDELGRGTSAIDGLSIAQAVKEHLVQ-KKSLCLCATHFPELCGDDVLNKKVK---------NEGTLLMYELVDGVCDTS 689
                                    **************************9.79*************9886655554.........5678899*********** PP

                                    -HHHHHHHTT--HHHHHHHHHHHH CS
                         MutS_V 162 yGikvaklaglPesvverArevlk 185
                                    +Gi va+ +g+P +v+++A+e ++
  gene327|gene327|rna327|rna327 690 FGIMVAEKVGFPVEVIQMAKEYME 713
                                    ********************9875 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.1   9.5e-22   3.4e-18      23     191 .]     229     493 ..     213     493 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 9.5e-22
                                    HHH---SSHHHHHHHHHHHH--BS-HHHHHHHHHHHHHT..TT.HHHHHHHHTT---HHHHHHHHHTT---HHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III  23 gvldrTvTamGaRlLrewllqPltdleeInaRldaVeeleneelreelrellrrlpDleRllsrislgkakardlkalle 102
                                    +   ++ T++G RlL++ llqPl+++eeI++Rl+ ++ l+         + lr++pDl Rl +ris g+++ r++++l++
  gene327|gene327|rna327|rna327 229 SKTFCCYTNQGWRLLHRMLLQPLRNKEEIERRLNTIDSLKT-----LNLSILRKFPDLLRLSRRISGGRVSLREILRLVQ 303
                                    4445799******************************9733.....335779**************************** PP

                                    HHHHHHTTTTT---SSTHHHHH............................................HHHHHHHHHHB-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxx............................................xxxxxxxxxxxxxx RF
                       MutS_III 103 alkaleelvallekeklaesee............................................eslaelleeaidee 138
                                    +++a+++l+   +++ +                                                  +l+e l+e +dee
  gene327|gene327|rna327|rna327 304 TIDAIPDLISSFSTSLPL-T-RdvgeplkkifsafepikaevarvvdleaaeenvyrimpdvsprlYKLNEALKE-VDEE 380
                                    ***999998888655443.2.246888888888887777777777777777777777776665444223355555.5555 PP

                                    --SSGGGS--B-T............................................................HHHHHHH CS
                                    xxxxxxxxxxxxx............................................................xxxxxxx RF
                       MutS_III 139 plalekegedlra............................................................iealeqe 158
                                      ++ +++ +                                                                +++e+e
  gene327|gene327|rna327|rna327 381 MDKEYRRVCETFPklkidrilgvfkttkteyqktrdifrkegfvelnlvkggvslttrtlsslnerktslkekVDDEEKE 460
                                    5555555555444889999999999999999999999999******************************9998888899 PP

                                    HHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III 159 lfqelleeveealerlrrlaealaeLDvllSlA 191
                                    +++ +   ++++++ +++l  + a +Dv+ +++
  gene327|gene327|rna327|rna327 461 IMDGMKTMLKNYISYIESLNYLTALIDVFSAFS 493
                                    99999999999******************9995 PP

>> CDPS  Cyclodipeptide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.2e-05      0.15      27      69 ..     130     172 ..     128     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.2e-05
                                    TBTTS-HHHHHHHHHHHHHHSSEEEEEE--TTHHHHHHHTT-- CS
                           CDPS  27 gnsyfsedrlaalirwaareFaqvdvvvadtevaellealGys 69 
                                    + s f++d + + + w+ +e + v+vv+  +++ + l++lG s
  gene327|gene327|rna327|rna327 130 YTSNFEDDEIFSSLYWILNEVNAVEVVYDNKKLTDFLNKLGIS 172
                                    6799*************************************97 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.4    0.0001      0.37     234     333 ..     354     466 ..     344     478 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0001
                          IFT57 234 ksieeslpetksqlkklhedisktlekiesrEkyl.....nsqleellqeyreaqeelsevke........kykqlsegv 300
                                    +++   +p++++ l kl e ++++ e++ +  +++       +++  l  ++++++e++++++        +++ +++gv
  gene327|gene327|rna327|rna327 354 ENVYRIMPDVSPRLYKLNEALKEVDEEMDKEYRRVcetfpKLKIDRILGVFKTTKTEYQKTRDifrkegfvELNLVKGGV 433
                                    55556666666666666666666666666655555222223344444555666666666665422222223678899*** PP

                          IFT57 301 seltrelaeiseelekvkqemeergssmtDgsp 333
                                    s  tr+l++++e+ +++k+++++ ++++ Dg  
  gene327|gene327|rna327|rna327 434 SLTTRTLSSLNERKTSLKEKVDDEEKEIMDGMK 466
                                    ******************************976 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.3   0.00013      0.48       4      91 ..     365     452 ..     362     453 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHHHHHHHHHHHHCCCCCCCT-TTBEECCCSSSEEEEEE-TCCCTTT--.....SEEEEEECTCEEEEECCC CS
                        MutS_IV   4 eeLdelrdrleelekeleeleekereklgikslkveynkvlGyylevtrseakkvpk.....efirlqtlknseryttae 78 
                                    ++L +l+++l+e+ +e++++ +++ e +  ++lk++++   G +++ t++e++k ++      f++l   k+++  tt +
  gene327|gene327|rna327|rna327 365 PRLYKLNEALKEVDEEMDKEYRRVCETF--PKLKIDRIL--G-VFKTTKTEYQKTRDifrkeGFVELNLVKGGVSLTTRT 439
                                    6666777777777777766666665544..789999766..3.7*********9999888899***************** PP

                                    HHHHHHHHHHHHH CS
                        MutS_IV  79 lkkleaelleaee 91 
                                    l++l+++  +++e
  gene327|gene327|rna327|rna327 440 LSSLNERKTSLKE 452
                                    ******9888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.52
# Mc/sec: 4146.94
//
Query:       gene328|gene328|rna328|rna328  [L=795]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-23   83.8   1.5    1.7e-23   83.8   1.5    1.7  2  RhoGEF     RhoGEF domain
    1.7e-20   73.8   0.1    2.8e-20   73.1   0.1    1.4  1  CNH        CNH domain
  ------ inclusion threshold ------
      0.032   14.8   1.8      0.073   13.6   1.8    1.6  1  SIN1       Stress-activated map kinase interacting protein 1 
       0.11   13.2   0.3       0.36   11.5   0.3    1.9  1  PBECR1     phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease
       0.19   11.8   3.3       0.12   12.4   1.2    1.7  2  Rootletin  Ciliary rootlet component, centrosome cohesion
        3.5    8.3   8.0       0.33   11.6   0.8    2.6  2  Com_YlbF   Control of competence regulator ComK, YlbF/YmcA


Domain annotation for each model (and alignments):
>> RhoGEF  RhoGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   1.5   5.7e-27   1.7e-23       2     181 ..      11     216 ..      10     221 .. 0.86
   2 ?   -3.8   0.0       4.2   1.3e+04      90     106 ..     437     453 ..     407     475 .. 0.57

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 5.7e-27
                                    HHHHHHHHHHHHHHHHHHHHHTH.....CCCHHCTCCHHHHHHHHCTTHHHHHHHHHHHHHHHHHHHH............ CS
                         RhoGEF   2 ikElleTErsYvrdLkvlvevyl.....kplselevlseeeikiiFsnieeilelhrsflleeLeerl............ 64 
                                    i E++++E+sY++dL v  + ++      pl +   ++ e  + iF+n++ i +lh +++ e+++ ++            
  gene328|gene328|rna328|rna328  11 IGEIFKSEKSYIQDLLVWEKDFRvwilgYPLFSTPKIKYEICDRIFINLDRIQRLH-KKIYEDMKRVNlgiyseitggnv 89 
                                    78*********************888884444344688888889************.99999999999999****99999 PP

                                    .............HHHTTSS-S-SHHHHHHHHSTHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSGGGTT--H CS
                         RhoGEF  65 ............keseeqkeaqsigdvflkfadkfkkYseYcsnypnalkllkelskknkkfkafleeaeerpecskldL 132
                                                + ++   ++ +  +++++++++f+ Y eY+++ p+a+  l++l ++ ++f++ +e+  + +++  l +
  gene328|gene328|rna328|rna328  90 lrntdeyiidkiDVENPGLRKLEYVSIYERYIEEFDLYNEYVRRLPKAEFELEKLVHRYPEFAKGVENFLKGKNAAFLGI 169
                                    9988877776552446666778899******************************************************* PP

                                    HHHTTHHHHHHHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHHHH CS
                         RhoGEF 133 eslLikPvqRlprYpLLLkellkntpeshpdyealkkaleaikevasei 181
                                    +++L +P q+l rYpLLLk+++kn + +   +++ ++ +e++k +a+++
  gene328|gene328|rna328|rna328 170 KHFLYRPSQKLARYPLLLKAVVKNEEGNL--KKEYERLIEKFKAIAKNV 216
                                    *************************8873..345566666666666655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.2
                                    HHHHHHCHHHHHHHHHH CS
                         RhoGEF  90 YseYcsnypnalkllke 106
                                     ++ ++n++++ k + +
  gene328|gene328|rna328|rna328 437 VTKLINNFHRIRKDVAS 453
                                    44444444444444444 PP

>> CNH  CNH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.1   9.3e-24   2.8e-20     131     271 ..     625     766 ..     548     769 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 9.3e-24
                            CNH 131 klrefqvpaevfsisvlkpklcvgvakgFelvnldegaaeslldpedns..ldfaarkenlkplaviqisedefLlcyde 208
                                    + r++++  +v+ + ++++k+++g +k Fe+v++++  +e+ll++ d+     +    +n+++ +++ +s  efLlc+++
  gene328|gene328|rna328|rna328 625 LSRKLYIGLQVYNVFFCSEKIVIG-CKDFEIVDMETLRTEELLQVYDPFipI-LFHGLKNITARSIFPVSPHEFLLCFNT 702
                                    567899999***************.899********************9963.45889********************** PP

                            CNH 209 favyvdlqGrrsr.dseleWegkPesvaclepyllafhknfieirsvetgelvqeisgkklrfl 271
                                    ++++vd  G+ +r d ++ W+ +P  + ++++y++    + i+i++++tg lv + +  klrf+
  gene328|gene328|rna328|rna328 703 MGFVVDDTGKLKRtDIIFLWNCNPLGFKVVKNYVICLGRYIINIFDLKTGLLVFTKCQSKLRFV 766
                                    **********9999************************************************98 PP

>> SIN1  Stress-activated map kinase interacting protein 1 (SIN1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.8   2.4e-05     0.073      56     124 ..     403     478 ..     377     493 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                           SIN1  56 ersevefsdypglDlsddedvgssqsydIqsysevg.....ihrfrsnTaqklErldiakrka..akiksikyedr 124
                                      s  + + y +  ls+++  +s+++++ + +++v+     +hr r   a k+E+ld++  +   +k k++++++r
  gene328|gene328|rna328|rna328 403 SLSSSDSLEYSTGTLSEESSPDSTEYSEMFKDQDVTklinnFHRIRKDVASKEEKLDSEESQEgdEKSKEVSSRKR 478
                                    344568899*************************96555559***************7654431155555555553 PP

>> PBECR1  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00012      0.36      43     106 ..     188     256 ..     157     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                         PBECR1  43 k....ekaeklinkleeiiekgk.vkeeeevntielkkeeeeykvglskgfkgkgdnkwvitayekkke 106
                                    k    +++ +l ++ e  iek k + ++ +++  ++  + + yk+g++  +k++ +n++ ++ ++kk++
  gene328|gene328|rna328|rna328 188 KavvkNEEGNLKKEYERLIEKFKaIAKNVDKEFNKFGTQFAMYKLGINFRYKQNVKNQYCLALFQKKRK 256
                                    044435567889999999***997777777777777777799***********************9975 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.7   8.1e+03     105     128 ..     196     219 ..     190     227 .. 0.64
   2 ?   12.4   1.2     4e-05      0.12     108     157 ..     434     484 ..     396     487 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
                      Rootletin 105 eaLtedlqkltkdwerlreeleqk 128
                                     +L+++ ++l ++++ ++++++++
  gene328|gene328|rna328|rna328 196 GNLKKEYERLIEKFKAIAKNVDKE 219
                                    467777777777777766666554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4e-05
                      Rootletin 108 tedlqkltkdwerlreeleqkekewreeeeafneylsse.hsrllsLWrev 157
                                     +d++kl ++++r+r+++ +ke+++ +ee +  +  s+e  sr  sLW+++
  gene328|gene328|rna328|rna328 434 DQDVTKLINNFHRIRKDVASKEEKLDSEESQEGDEKSKEvSSRKRSLWKSF 484
                                    369**********************9999876665555527899****986 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   1.2      0.78   2.3e+03      32      57 ..     200     226 ..     186     265 .. 0.59
   2 ?   11.6   0.8   0.00011      0.33      26      74 ..     429     474 ..     426     485 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.78
                                    HHHHHHHHHHHHHHHHHHH.HHHTT-- CS
                       Com_YlbF  32 eelqklikefkklqkelqe.kqmkgee 57 
                                    +e  +li++fk++ k++ + + ++g +
  gene328|gene328|rna328|rna328 200 KEYERLIEKFKAIAKNVDKeFNKFGTQ 226
                                    455566666666666554424444433 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00011
                                    HHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHHH CS
                       Com_YlbF  26 ealeedeelqklikefkklqkelqekqmkgeelkeeekkelqelkeeld 74 
                                    +++ +d+++ kli++f++++k+++ k+   e+l+ ee +e +e  +e+ 
  gene328|gene328|rna328|rna328 429 SEMFKDQDVTKLINNFHRIRKDVASKE---EKLDSEESQEGDEKSKEVS 474
                                    5799*****************998877...4555555556666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 5037.07
//
Query:       gene329|gene329|rna329|rna329  [L=336]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-33  116.6   0.6    3.6e-33  115.0   0.6    1.7  1  RabGAP-TBC  Rab-GTPase-TBC domain
  ------ inclusion threshold ------
      0.079   12.5   0.1       0.13   11.9   0.1    1.3  1  DUF4843     Domain of unknown function (DUF4843)


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.6     4e-37   3.6e-33       2     208 ..      45     290 ..      44     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 4e-37
                     RabGAP-TBC   2 elRgevWklllgyep....evkrlkksekkqeksekeksklekseeskelsqIkkDvprtfp............es.... 61 
                                    +lR++ Wk++lgy++    +++   +++++++ +   + +++ + +++ ++ I++Dv+rtf             e+    
  gene329|gene329|rna329|rna329  45 SLRPKYWKVFLGYYSknkfRTEMFLRNMRNSYSFYAGRVGNKFEGKEECYKVIENDVSRTFIkprvdyegpgekERycef 124
                                    69*************8865444444455555556666777888888888************9999998888875116666 PP

                     RabGAP-TBC  62 ....esfknkqgqnqLeriLkaysiynpevgYcqGmndivapll.lvsl..deee.......aFwcfvsLlekyklrdly 127
                                        ++ +++  +++++riLk+y++ n  v Y+qGmn ++  ++ +++l  dee+       +F+cf sL+    + d++
  gene329|gene329|rna329|rna329 125 ldgtSENSEETHRDVIKRILKCYAMSNSSVRYVQGMNLVLIAIYyVLYLsdDEEDrkyceedSFFCFNSLM--AEIGDNF 202
                                    777566666689999**********************8765444433433255559***************..99***** PP

                     RabGAP-TBC 128 tsslpg....lkrklkvleellkkkdpklykhlkeegldlelfaikwfltlflrefpletvlrlwD.lllege..kfvll 200
                                    + +l++    +  ++ v+ e++kk d +ly  + ++gl+ e f +kw+l +f+++f +e v+ lwD ll   +  ++vl+
  gene329|gene329|rna329|rna329 203 IRDLDRcnggIMHRMSVVMEIVKKADGELYGVMRRKGLTEEGFHMKWILLMFMSCFEIEDVIWLWDrLLSDTYrfEMVLY 282
                                    ****875556555556**************************************************66665557778666 PP

                     RabGAP-TBC 201 rvalailk 208
                                     +a ai+ 
  gene329|gene329|rna329|rna329 283 CCASAIII 290
                                    66666663 PP

>> DUF4843  Domain of unknown function (DUF4843)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.4e-05      0.13     128     159 ..      37      65 ..      13      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                        DUF4843 128 lkilltnrlekPawWeelalelGeYSrvKhel 159
                                    +   ++n   +P++W+    +lG YS+ K++ 
  gene329|gene329|rna329|rna329  37 CYYGFSNASLRPKYWKV---FLGYYSKNKFRT 65 
                                    445699*********66...7********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1887.15
//
Query:       gene33|gene33|rna33|rna33  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-14   52.8   0.1    4.4e-14   51.9   0.1    1.5  1  LSM       LSM domain
    0.00034   20.7   0.2    0.00052   20.1   0.2    1.3  1  DUF150_C  RimP C-terminal SH3 domain
  ------ inclusion threshold ------
      0.031   14.4   0.0       0.04   14.0   0.0    1.3  1  SM-ATX    Ataxin 2 SM domain
       0.09   12.6   0.1       0.13   12.1   0.1    1.4  1  DUF2642   Protein of unknown function (DUF2642)


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1   9.9e-18   4.4e-14       1      66 [.       5      64 ..       5      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 9.9e-18
                               HHHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                        LSM  1 kflkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                               +flkk++++kv ve+k gr+++G+++++D+ mN+ +ed+++           +++ +RG++i++i 
  gene33|gene33|rna33|rna33  5 RFLKKCKGEKVKVETKEGRKIEGRITSVDKTMNVEMEDAVV------DGVPASTYTVRGSSIRYIM 64
                               59*************************************97......34678************95 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   1.2e-07   0.00052       9      45 ..       9      40 ..       5      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-07
                   DUF150_C  9 rflGelVkvklklpvegrkkftGkivevdeetitlev 45
                               +  Ge+Vkv++k    +++k++G+i +vd+++  +e+
  gene33|gene33|rna33|rna33  9 KCKGEKVKVETK----EGRKIEGRITSVDKTM-NVEM 40
                               668*********....*************554.4444 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     9e-06      0.04       4      44 ..       3      41 ..       1      67 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9e-06
                               -HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEE CS
                     SM-ATX  4 llflltslvGkevevtvknGevyeGifstvslekdfsvvLk 44
                               l+ +l+++ G++v+v++k G ++eG  ++v+    ++v ++
  gene33|gene33|rna33|rna33  3 LIRFLKKCKGEKVKVETKEGRKIEGRITSVDK--TMNVEME 41
                               6778999******************8888887..6665555 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     3e-05      0.13      11      38 ..       4      32 ..       3      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3e-05
                    DUF2642 11 yqtlqsllgqevvvqttrgsv.rGiLkdv 38
                               +  l++ +g++v v+t++g+  +G++++v
  gene33|gene33|rna33|rna33  4 IRFLKKCKGEKVKVETKEGRKiEGRITSV 32
                               56799*************9754***9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 650.30
//
Query:       gene330|gene330|rna330|rna330  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-38  131.8   0.4    2.1e-38  131.7   0.4    1.0  1  Vac_ImportDeg  Vacuolar import and degradation protein


Domain annotation for each model (and alignments):
>> Vac_ImportDeg  Vacuolar import and degradation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.4   1.2e-42   2.1e-38       2     154 ..       9     163 ..       8     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 1.2e-42
                  Vac_ImportDeg   2 lrpgakfkGeqqsgkkkyevkvelktvdleeslltGfleikglteekpeittffegeiidekysfltkkkkwkaseetDl 81 
                                    l++gak++Geq ++  +++++++++ +d+++++++G++ei++lt++++ +tt+fegei+ + y f+t+  ++ + ++ D+
  gene330|gene330|rna330|rna330   9 LENGAKYRGEQLTNGGSFKIEMNVDIIDTRQEFICGTFEIHNLTDRYELLTTYFEGEIVGNIYPFTTE--EY-SMANPDI 85 
                                    789********************************************************999******..67.67799** PP

                  Vac_ImportDeg  82 ehWkkleafkkllak.....dlenkelifmrwkekflvpdervksiegasfeGfYYivldqstgsieGlYyhkksekf 154
                                     hWk ++++k  +       d++++++++++ ke fl+pd r k+i gas++G+YY+++ ++ + + G Yy k+++++
  gene330|gene330|rna330|rna330  86 IHWKLFPEWKGEYVYrkgsyDIRKSNFMYIKIKELFLLPDPRLKTIPGASIDGHYYCCYYKNLDCFAGHYYYKNTSNL 163
                                    *********987666889999***********************************************9999987643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1191.40
//
Query:       gene331|gene331|rna331|rna331  [L=934]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-38  131.6   0.0    1.1e-37  129.9   0.0    1.9  1  UCH            Ubiquitin carboxyl-terminal hydrolase
    7.4e-12   45.5   0.0    4.4e-08   33.1   0.0    2.3  2  UCH_1          Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.087   12.5   0.0    2.0  2  Orthopox_35kD  35kD major secreted virus protein
        3.4    8.0   7.4         17    5.8   0.1    4.0  5  DUF3912        Protein of unknown function (DUF3912)


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.9   0.0   2.4e-41   1.1e-37       1     257 []     111     411 ..     111     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 2.4e-41
                                    -EES-SSSTHHHHHHHHHHHTSHHHH.HHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE--H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH   1 tGlsNlGntCymnsvlQcLfsipelr.dyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskavsPk 79 
                                    +Gl+NlG+tCy+ns++Q+Lf+i+++r d++         +                  +  l++lfke++  ++ av ++
  gene331|gene331|rna331|rna331 111 VGLRNLGATCYVNSLMQSLFNIAKFRnDVFSL-------EPSG--------------RVLLLQKLFKEMQ-VEEHAVDTT 168
                                    69************************777666.......2111..............24579********.478999999 PP

                                    HHHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCC............HCCCHHHHHHCCCTTSHHHHHH-EEEEE.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                            UCH  80 klkktlsklaksfsgykqqDaqEflaflLdqlhedlnr............evaeekwkkhlkrndslitdlfegqlks.. 145
                                     ++     +  +      qD +Ef ++ +d+l++d++r                                       +  
  gene331|gene331|rna331|rna331 169 DFVVNN--IWVD-DVHVHQDIHEFSKVFFDSLEKDSKRkdfiedliqgelV--------------------------Tyi 219
                                    996443..4444.34789********************5555555555550..........................555 PP

                                    ................................................................EEEEEEB-SEEEEEEE CS
                                    ................................................................xxxxxxxxxxxxxxxx RF
                            UCH 146 ................................................................klklkrlPeiLiihlk 161
                                                                                                     + + +lP+++++ lk
  gene331|gene331|rna331|rna331 220 dgkcgcvrrirekfqdiqveirdffnnklssnlseslkryvkaevldgnnkynceehglvdakkGVVFGSLPPVMFVLLK 299
                                    555555555555555555555555555555599999999************************99*************** PP

                                    SEEETEE...EEE--SEEB--SEEE-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEECTTTTEEEEEETTE CS
                                    xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 162 Rfsynss...ksKlntkvefpeeldlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayiknekngkWykydDet 238
                                    Rf+ + +     K+n+ +efp ++d+s+++++++ k++ + + YeL++v+vH+G +++GH+++y k   +g+W+k++D+ 
  gene331|gene331|rna331|rna331 300 RFNVDFEtgnGYKINDYFEFPSSIDMSPFMDKDDGKEKGDDEMYELYSVIVHKGDHDEGHFYVYLK--IDGRWLKFNDTI 377
                                    ****77777899******************************************************..89********** PP

                                    EEEE-HH..............CCCTT.CEEEEEE CS
                                    xxxxxxx..............xxxxx.xxxxxxx RF
                            UCH 239 vkevkee..............eevls.sayiLfY 257
                                    v+e  e               ++++  s+y L+Y
  gene331|gene331|rna331|rna331 378 VTEAGEMealehnyggrhpykDKIRDhSGYYLVY 411
                                    ****977566666555555544444489999988 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   9.8e-05      0.44       1      27 [.     111     137 ..     111     163 .. 0.88
   2 !   33.1   0.0   9.8e-12   4.4e-08     100     319 ..     184     377 ..     155     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.8e-05
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1   1 sGLEnhivnsYlNslLQvlyfipplrn 27 
                                    +GL n  +++Y+Nsl+Q l+ i  +rn
  gene331|gene331|rna331|rna331 111 VGLRNLGATCYVNSLMQSLFNIAKFRN 137
                                    7********************999996 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 9.8e-12
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 100 sliqsfnrflldqlekelketkknsseeesaieqllgtkaettirclkCgseksrksstlvldlkyPkpsnekkeakvtf 179
                                    + i +f ++++d lek++k+        ++ ie+l++ +++t i  + Cg  ++ ++ +  +++     +  +++ ++++
  gene331|gene331|rna331|rna331 184 QDIHEFSKVFFDSLEKDSKR--------KDFIEDLIQGELVTYIDGK-CGCVRRIREKFQDIQVEI--RDFFNNKLSSNL 252
                                    44567999999999999877........489*************999.999999999998887755..222233444555 PP

                                    xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx..xxxxxxxxxxxxxxx RF
                          UCH_1 180 asilkssler...ekttrawCekCkryqpteqrktvknlPpvLalnakleee..eelelwktk..nwlpleiklsldedk 252
                                    ++ lk+ ++    + ++++ Ce+ +     +++ ++ +lPpv+ + +k+++   e+ + +k +    +p++i++s   d 
  gene331|gene331|rna331|rna331 253 SESLKRYVKAevlDGNNKYNCEE-HGLVDAKKGVVFGSLPPVMFVLLKRFNVdfETGNGYKINdyFEFPSSIDMSPFMD- 330
                                    55555555553334788888877.6677888888888***********9976342233333341255668888843332. PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 253 nleeklkeerekakaekeikvYeLqsvvvhigdskesghLvslvkvaekelerdppesqWylFNDfl 319
                                           +++   k++ +  +YeL sv+vh gd++ +gh + + k+          +++W++FND  
  gene331|gene331|rna331|rna331 331 -------KDD--GKEKGDDEMYELYSVIVHKGDHD-EGHFYVYLKI----------DGRWLKFNDTI 377
                                    .......233..35566788************887.*********9..........469******75 PP

>> Orthopox_35kD  35kD major secreted virus protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.22   9.9e+02     175     210 ..     225     266 ..     193     272 .. 0.65
   2 ?   12.5   0.0   1.9e-05     0.087      29     118 ..     519     610 ..     501     652 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.22
                  Orthopox_35kD 175 Cvksl.....dltvelgdmC..keasdLslkdslkykdGelve 210
                                    Cv+ +     d++ve++d    k +s+Ls     +y+  e+++
  gene331|gene331|rna331|rna331 225 CVRRIrekfqDIQVEIRDFFnnKLSSNLSESL-KRYVKAEVLD 266
                                    454443333499******98778889988543.3466666666 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.9e-05
                  Orthopox_35kD  29 dkvCqalrdieesasdednsvekeddsastedvdd.vstyyaiiGgGlsvt....lgftglPsvksisesadGrtvyvrl 103
                                    d++ + +++ +   ++++   ++e+ s ++e+v    +  ++++ +G+  t    + +t  P+v    ++ +Gr +++++
  gene331|gene331|rna331|rna331 519 DRPSKRVKEDIHGLTEPEVGRDEENASRTIEYVRLsHQKKVSLVRDGIVNTdadyFIYTCYPEV----DFEKGRLIFLKV 594
                                    5555666666666777777778899999999998525678999*99997654555788988***....99********** PP

                  Orthopox_35kD 104 ssdaPw.qdtndlsin 118
                                     s+ Pw  dt++ s+ 
  gene331|gene331|rna331|rna331 595 FSNMPWcEDTLPTSLR 610
                                    ************9986 PP

>> DUF3912  Protein of unknown function (DUF3912)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0038        17      28      60 ..      65      97 ..      61     106 .. 0.82
   2 ?   -2.4   0.3       1.3     6e+03      41      49 ..     179     187 ..     161     209 .. 0.50
   3 ?   -2.4   0.0       1.4   6.2e+03      42      50 ..     234     242 ..     217     247 .. 0.56
   4 ?   -3.6   0.0       3.1   1.4e+04      23      39 ..     349     366 ..     348     374 .. 0.70
   5 ?    3.9   0.0     0.014        64      17      67 ..     555     603 ..     549     605 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0038
                        DUF3912 28 eqedddhftvviddqdidvelkdillvdvDvgk 60
                                   +qe + +f +   d+ i +e kd  ++ vDvg 
  gene331|gene331|rna331|rna331 65 KQEYQYQFSMFNTDIGIYIEDKDSYVIRVDVGV 97
                                   4666677777788999**************985 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                        DUF3912  41 dqdidvelk 49 
                                    d ++  +  
  gene331|gene331|rna331|rna331 179 DVHVHQDIH 187
                                    333333333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                        DUF3912  42 qdidvelkd 50 
                                    qdi+ve +d
  gene331|gene331|rna331|rna331 234 QDIQVEIRD 242
                                    445555444 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 3.1
                        DUF3912  23 vvkkkeqedddhftvv..i 39 
                                    +v+k +++d+ hf v   i
  gene331|gene331|rna331|rna331 349 IVHK-GDHDEGHFYVYlkI 366
                                    4455.99999999987445 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.014
                        DUF3912  17 yrnklGvvkkkeqedddhftvviddqdidvelkdillvdvDvgkfhewceq 67 
                                    ++ k+ +v+    + d  + +     ++d+e++ ++ ++v       wce+
  gene331|gene331|rna331|rna331 555 HQKKVSLVRDGIVNTDADYFIYTCYPEVDFEKGRLIFLKVFSNM--PWCED 603
                                    9999*****966666777888888999********999986555..78885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (934 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.52
# Mc/sec: 5402.47
//
Query:       gene332|gene332|rna332|rna332  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-08   33.7  14.4    3.7e-08   33.3  14.4    1.2  1  Yip1      Yip1 domain


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3  14.4   2.1e-12   3.7e-08      18     157 ..      61     177 ..      38     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.1e-12
                           Yip1  18 ilrapdlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllgllllalllhliakllggkgsf 97 
                                      ++ dl ++++++  + lgl++                   ++++g+++++ l++ l+ ++l  +l+        ++ f
  gene332|gene332|rna332|rna332  61 FVKNADLSGPIVFIGLYTLGLILN-----------------YKIHFGYVYFISLLTALSMYFLLNVLDT------KHIGF 117
                                    56789*******************.................9999**9888888655555555555555......9**** PP

                           Yip1  98 kqtlsvvgyallPlilgaliaillllllgtllllvgllaliWslvllylglkaahnlskk 157
                                     ++ sv+gy++lP++++++i+il+  ++ +  ++ gl++++Ws++  ++ + +   ls+k
  gene332|gene332|rna332|rna332 118 LECCSVLGYSFLPVVFFSFINILMGRIGVGFKVFYGLVFALWSSYTASVVFCRYLSLSNK 177
                                    ******************************9****************9999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1386.66
//
Query:       gene333|gene333|rna333|rna333  [L=125]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.8e-13   48.3   0.3      1e-12   47.7   0.3    1.2  1  Homeodomain  Homeodomain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.024   14.6   0.0    1.3  1  Homeobox_KN  Homeobox KN domain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.3   1.1e-16     1e-12       4      55 ..      34      85 ..      32      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 1.1e-16
                                   SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHH CS
                    Homeodomain  4 RttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRake 55
                                   Rt+ t+ q+ +L+++F+  ++ps+ ++++LA  ++L+ + V++WFqN R ++
  gene333|gene333|rna333|rna333 34 RTRKTTFQMMVLKEVFKIAPHPSTLTKTDLALMIKLPLKAVQIWFQNERSRK 85
                                   9************************************************986 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.6e-06     0.024       9      40 .]      53      84 ..      51      84 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-06
                    Homeobox_KN  9 PYPseedKeeLlkeTglsvkqitnWFINaRrR 40
                                   P Ps   K+ L+   +l  k ++ WF N R R
  gene333|gene333|rna333|rna333 53 PHPSTLTKTDLALMIKLPLKAVQIWFQNERSR 84
                                   99****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 744.07
//
Query:       gene334|gene334|rna334|rna334  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-10   38.8   0.0    9.4e-10   38.2   0.0    1.2  1  Homeodomain  Homeodomain
     0.0024   17.7   0.1      0.004   17.0   0.1    1.5  1  Homeobox_KN  Homeobox KN domain
     0.0096   14.9   0.0      0.011   14.7   0.0    1.1  1  ECM1         Extracellular matrix protein 1 (ECM1)
  ------ inclusion threshold ------
      0.099   12.7   0.0       0.12   12.5   0.0    1.4  1  DnaB         DnaB-like helicase N terminal domain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   2.1e-13   9.4e-10       6      53 ..      27      74 ..      23      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.1e-13
                                   SS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHH CS
                    Homeodomain  6 tftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRa 53
                                   + +k q e+L k ++ ++yp+ e + ++   + L+ r V +WFqN+R 
  gene334|gene334|rna334|rna334 27 RKSKFQKEVLRKIYQITPYPTWENKIDIGILISLSPRAVDIWFQNKRH 74
                                   66899*****************************************95 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   8.9e-07     0.004       9      38 ..      44      73 ..      30      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.9e-07
                    Homeobox_KN  9 PYPseedKeeLlkeTglsvkqitnWFINaR 38
                                   PYP+ e K  +     ls + ++ WF N R
  gene334|gene334|rna334|rna334 44 PYPTWENKIDIGILISLSPRAVDIWFQNKR 73
                                   *****************************9 PP

>> ECM1  Extracellular matrix protein 1 (ECM1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.5e-06     0.011     278     324 ..      15      62 ..      11      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.5e-06
                           ECM1 278 ayscckqrGea.rfscfqeeaprpdyqlracPshqpgissGlelpfPP 324
                                    + +c k+ Ge+ r s fq+e  r  yq  ++P+ +++i  G+ +++ P
  gene334|gene334|rna334|rna334  15 PERCLKRPGEKvRKSKFQKEVLRKIYQITPYPTWENKIDIGILISLSP 62 
                                    778******9659*****************************999887 PP

>> DnaB  DnaB-like helicase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.6e-05      0.12      10      46 ..       4      42 ..       2     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHHS..TTHHHHHHCC--GGGSSSHHHHHHHHH CS
                           DnaB 10 qavLgalLld..peaidevadilkpedFyepahrliFea 46
                                   qavLg +Ll   ++++++  +++++  F ++  r+i+++
  gene334|gene334|rna334|rna334  4 QAVLGMILLFhpERCLKRPGEKVRKSKFQKEVLRKIYQI 42
                                   89******9754559**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 696.67
//
Query:       gene335|gene335|rna335|rna335  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-47  160.5   0.0    5.5e-47  160.3   0.0    1.0  1  Pkinase         Protein kinase domain
    1.4e-25   90.1   0.0    1.8e-25   89.7   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    0.00014   21.3   0.0     0.0002   20.7   0.0    1.3  1  Kinase-like     Kinase-like
    0.00025   19.9   0.0    0.00029   19.7   0.0    1.0  1  Pkinase_fungal  Fungal protein kinase
      0.001   19.0   0.0     0.0017   18.3   0.0    1.3  1  APH             Phosphotransferase enzyme family
     0.0012   18.2   0.0     0.0019   17.6   0.0    1.2  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.064   12.9   0.0       0.32   10.6   0.0    1.9  2  FTA2            Kinetochore Sim4 complex subunit FTA2
      0.076   12.6   0.0       0.15   11.6   0.0    1.4  1  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   0.0   2.4e-50   5.5e-47       1     197 [.      29     223 ..      29     224 .] 0.95

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 2.4e-50
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE-- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyv 80 
                                    ye +e+l +Gs++k+ kav    +++ AvK i+k +++ ++   +lrE ki+ +l+hpniv++++++e+ +++++v+ + 
  gene335|gene335|rna335|rna335  29 YELQETLASGSTAKIKKAV-VVGNEKCAVKLISKGDMSLQM---FLREAKIHGSLRHPNIVEFVDSYEDRERYCIVMKLG 104
                                    7788999************.7999**********9988755...8*********************************99 PP

                                    TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS...BCTT CS
                        Pkinase  81 eggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk...ltsf 157
                                      ge+ +++   + l++  a ++++q++++++ylHskg++HrD+KpeN+Lid +g+l ++DFG+++ + ++ +   l+sf
  gene335|gene335|rna335|rna335 105 Y-GEVGNMIWSGVGLDPLLAHFYFRQLVSAVKYLHSKGVCHRDIKPENMLIDGNGNLLLSDFGFSTLFFHKGRrrrLRSF 183
                                    9.568888888889****************************************************9988877899**** PP

                                    TSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-ST CS
                        Pkinase 158 vgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppf 197
                                    vg+ eY+APEv ++   ++ +D+Ws+G+ l+ +ltg+ p 
  gene335|gene335|rna335|rna335 184 VGSLEYMAPEVFEGDYDGSLADIWSCGISLVVFLTGTLPV 223
                                    ************99999*******************9986 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   7.8e-29   1.8e-25       2     198 ..      30     216 ..      29     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 7.8e-29
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivte 81 
                                    el+++l++G+ +k+ ++ +       ++k+avK ++++ ++   +++l+eaki  +l+hpniv+++  + ++e+++iv++
  gene335|gene335|rna335|rna335  30 ELQETLASGSTAKIKKAVVV-----GNEKCAVKLISKGDMSL--QMFLREAKIHGSLRHPNIVEFVDSYEDRERYCIVMK 102
                                    6899****************.....8999******7776665..9*****************************999999 PP

                                    --TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEE CS
                    Pkinase_Tyr  82 yvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvk 161
                                    +  +G++ +++ +     l+      +  q+ ++++yL+sk + Hrd+   N+L++ n    +sDfG +    ++ + ++
  gene335|gene335|rna335|rna335 103 L-GYGEVGNMIWSG--VGLDPLLAHFYFRQLVSAVKYLHSKGVCHRDIKPENMLIDGNGNLLLSDFGFSTLFFHKGRRRR 179
                                    6.79*******997..7788777788999*************************************************** PP

                                    TTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHH CS
                    Pkinase_Tyr 162 keeaklpvkWmapEslkekkftsksDvWsfGvllwEi 198
                                     ++   ++++mapE+++     s +D+Ws G+ l   
  gene335|gene335|rna335|rna335 180 LRSFVGSLEYMAPEVFEGDYDGSLADIWSCGISLVVF 216
                                    ********************************98744 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.1e-08    0.0002     152     212 ..     129     194 ..     121     224 .] 0.73

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.1e-08
                    Kinase-like 152 qlirlaanLqakglvhgkftvdnllldekgglmlggf..taL.vragtkvvl.seve.kgfaPpEl 212
                                    ql+  + +L++kg+ h +++++n+l d +g l l +f  + L + +g + +l s v    +  pE+
  gene335|gene335|rna335|rna335 129 QLVSAVKYLHSKGVCHRDIKPENMLIDGNGNLLLSDFgfSTLfFHKGRRRRLrSFVGsLEYMAPEV 194
                                    89999*****************************98733445146666666655555434555554 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.3e-07   0.00029     281     388 ..      71     197 ..      23     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.3e-07
                 Pkinase_fungal 281 r...................lenrvhrrlvis....pvGkpiekaespkellea..lrDaIkghrsLflkagiLHrDiSe 335
                                    r                   +e+r   ++v++    +vG+ i+       ll+   +r+ + + + L+  +g+ HrDi  
  gene335|gene335|rna335|rna335  71 ReakihgslrhpnivefvdsYEDRERYCIVMKlgygEVGNMIWSGVGLDPLLAHfyFRQLVSAVKYLH-SKGVCHRDIKP 149
                                    0334444444557777777788888889998766667999999999999999862269**********.*********** PP

                 Pkinase_fungal 336 nNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkg 388
                                    +N+li      g+ + lL+D+ + +   ++ +++  r  +G le+ma ev +g
  gene335|gene335|rna335|rna335 150 ENMLID-----GNGNLLLSDFGFSTLFFHKGRRRRLRSFVGSLEYMAPEVFEG 197
                                    *****9.....88999********9999888888889**********999886 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   7.7e-07    0.0017     163     197 ..     137     169 ..     118     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7.7e-07
                                    SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                            APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                      +++++H+D++p N+l+d +++ +  + Df++++
  gene335|gene335|rna335|rna335 137 LHSKGVCHRDIKPENMLIDGNGNLL--LSDFGFST 169
                                    55799**************666666..77888876 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.4e-07    0.0019     125     173 ..     128     179 ..     117     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.4e-07
                            Kdo 125 kavgrliaklhragvnHadlyaknillqqee...eeeaeiwliDldkarlrl 173
                                    +++  +++ lh+ gv+H+d+ + n+l++ ++     ++ ++ + ++k+r+r 
  gene335|gene335|rna335|rna335 128 RQLVSAVKYLHSKGVCHRDIKPENMLIDGNGnllLSDFGFSTLFFHKGRRRR 179
                                    67778999*********************99888789999999999999985 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.15   3.3e+02      15      62 ..      20      67 ..      19      98 .. 0.69
   2 ?   10.6   0.0   0.00014      0.32     177     205 ..     126     155 ..      63     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.15
                           FTA2 15 pFdfsaekdiefleyLgkglhsiVlkvkirgk.eYALKlFrfleaeele 62
                                   pF  s  +++e+ e L +g ++ + k+ + g+ + A+Kl  +  +++l+
  gene335|gene335|rna335|rna335 20 PFLVSIMEKYELQETLASGSTAKIKKAVVVGNeKCAVKLISKG-DMSLQ 67
                                   5677777899999999999999999987655548999986665.33444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                           FTA2 177 qlpkllrdlkklhklgIvvrDlkeenyi.d 205
                                    ++++l++ +k lh+ g+ +rD+k+en++ d
  gene335|gene335|rna335|rna335 126 YFRQLVSAVKYLHSKGVCHRDIKPENMLiD 155
                                    7899*********************98643 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.6e-05      0.15     147     175 ..     142     169 ..     126     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                                    EE-S--SGGGEEE.-CTTEEEE--GTT-E CS
                 Choline_kinase 147 fcHnDlqegNillnkeekklvlIDFEYag 175
                                     cH D+ ++N+l  + +++l l DF +++
  gene335|gene335|rna335|rna335 142 VCHRDIKPENMLI-DGNGNLLLSDFGFST 169
                                    7************.999********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1420.45
//
Query:       gene336|gene336|rna336|rna336  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1615.27
//
Query:       gene337|gene337|rna337|rna337  [L=390]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-41  140.8   0.0    8.3e-41  140.1   0.0    1.3  1  Pkinase          Protein kinase domain
    3.2e-18   65.9   0.0    6.2e-18   65.0   0.0    1.4  1  Pkinase_Tyr      Protein tyrosine kinase
  ------ inclusion threshold ------
      0.034   13.8   0.1      0.065   12.9   0.1    1.4  1  FTA2             Kinetochore Sim4 complex subunit FTA2
      0.049   13.0   0.1      0.097   12.0   0.1    1.4  1  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
       0.15   11.8   0.5       0.33   10.8   0.5    1.5  1  Antimicrobial12  Pleurocidin family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.1   0.0   2.3e-44   8.3e-41      46     264 .]     134     358 ..     125     358 .. 0.92

  Alignments for each domain:
  == domain 1  score: 140.1 bits;  conditional E-value: 2.3e-44
                                    HHHHHHHHHHSCTTB--EEEEEEE.........SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHH CS
                        Pkinase  46 lrEikilkklkhpnivrlyevfee.........kdelylvleyveggeladllerkgslseeeakkiakqilegleylHs 116
                                    l+E +i+k+l+h+++v+++++f+e         ++ +++++e+++ +  +d+++     +e+++++iak il+gl+ylH 
  gene337|gene337|rna337|rna337 134 LEEDEIMKSLDHDHVVKFLKSFREkyvnlreeeETIIWIFMEHMDSKVSQDVVK----GNENKIREIAKGILHGLKYLHG 209
                                    57999**************************9888899*******998888887....69******************** PP

                                    TTEE-SS-SGGGEEEETTTE...EEE-SGTTSEESSSSCS......BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHH CS
                        Pkinase 117 kgiiHrDlKpeNiLidekge...lKitDFGlakelesssk......ltsfvgtseYlAPEvlkeneyskkvDvWslGvil 187
                                    +gi H DlK +N++ +e+++    Ki+DFG+a++le+ s+       ++  gt  Y +PE  + n+++ k D+W lG i+
  gene337|gene337|rna337|rna337 210 MGIAHLDLKISNVMGKETKDgivYKIIDFGFARKLEHPSDnaeiqiPSKSFGTYPYKPPETSQLNMHGVKGDIWCLGAIV 289
                                    ****************88888999*************9999*****9********************************* PP

                                    HHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 188 yelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdllkkllkkdpkkRltaeellqhpyl 264
                                    + l  +++pf+ ++g++    +l++      ++   ++ +  + + s+ ++d++kk+++ d+  R+ a++ll+hp++
  gene337|gene337|rna337|rna337 290 WFLSRRQTPFYFDDGRK----NLEEWR----MFIRGRLPISFKPNSSPALRDFVKKCMNFDRFARPNASDLLEHPFI 358
                                    ***********666665....777722....22345788999999******************************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   1.7e-21   6.2e-18      49     257 ..     134     354 ..     131     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.7e-21
                                    HHHHHHHHTS-BTTB--EEEEEE......SSSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHT CS
                    Pkinase_Tyr  49 leeakimkklkhpnivkllgvct......keepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLesk 122
                                    lee +imk+l+h+++vk+l          +ee+  i+  ++++  +++ + ++   k + +++ ++a  + +G++yL+ +
  gene337|gene337|rna337|rna337 134 LEEDEIMKSLDHDHVVKFLKSFRekyvnlREEEETIIWIFMEH--MDSKVSQD-VVKGNENKIREIAKGILHGLKYLHGM 210
                                    57899*************9987766666666777888888876..67777777.7788899999**************** PP

                                    TEEEST-SGGGEEEEETT...EEEE-STTTHEETTTSSEE...EETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHH CS
                    Pkinase_Tyr 123 klvHrdlaarNvLlsenk...vvkisDfGLardiekddey...vkkeeaklpvkWmapEslkekkftsksDvWsfGvllw 196
                                     + H dl   Nv+ +e+k   v ki DfG ar++e+ ++    +  +++   + + +pE+ + +   +k D+W+ G ++w
  gene337|gene337|rna337|rna337 211 GIAHLDLKISNVMGKETKdgiVYKIIDFGFARKLEHPSDNaeiQIPSKSFGTYPYKPPETSQLNMHGVKGDIWCLGAIVW 290
                                    *************9985444489***********6655443446677888999*************************** PP

                                    HHHTTSSGT.T..TTS.HHHHHHHHHHTTEES-BBTTSBHHHHHHHHHHT-SSGGGS--HHHHHH CS
                    Pkinase_Tyr 197 Eiftlgesp.y..pgl.kneevleklkegkrlekpekcpeelyelmkkcweedpeeRptfselve 257
                                     +    ++p y   g  + ee   +++ +  ++   + +++l +++kkc++ d   Rp+ s+l+e
  gene337|gene337|rna337|rna337 291 FLSR-RQTPfYfdDGRkNLEEWRMFIRGRLPISFKPNSSPALRDFVKKCMNFDRFARPNASDLLE 354
                                    7766.6666332223324455556667778899999***********************999976 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.8e-05     0.065     142     206 ..     155     225 ..     134     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                           FTA2 142 drsralgeedgkkrpiraIVKel......ellkeqeelevsqlpkllrdlkklhklgIvvrDlkeenyidg 206
                                     r++++  ++++++ i+ +   +      +++k++e+++ ++++ +l+ lk lh  gI + Dlk +n+++ 
  gene337|gene337|rna337|rna337 155 FREKYVNLREEEETIIWIFMEHMdskvsqDVVKGNENKIREIAKGILHGLKYLHGMGIAHLDLKISNVMGK 225
                                    46677777888888888888777889988899*********************************999875 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.7e-05     0.097     116     167 ..     189     239 ..     162     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.7e-05
                            Kdo 116 aeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDld 167
                                    +e++ r++ k +    + lh +g+ H dl + n++ ++++ +++   +iD+ 
  gene337|gene337|rna337|rna337 189 NENKIREIAKGILHGLKYLHGMGIAHLDLKISNVMGKETK-DGIVYKIIDFG 239
                                    466677777777788899*********************8.*********96 PP

>> Antimicrobial12  Pleurocidin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   9.1e-05      0.33      25      41 ..     194     210 ..     190     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                                    HHHHHHHHHHHHHHHHH CS
                Antimicrobial12  25 ghlikGivHggkaIHgl 41 
                                      + kGi+Hg k +Hg+
  gene337|gene337|rna337|rna337 194 REIAKGILHGLKYLHGM 210
                                    5689************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2673.38
//
Query:       gene338|gene338|rna338|rna338  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   16.0   0.1      0.018   15.3   0.1    1.5  1  Rpr2      RNAse P Rpr2/Rpp21/SNM1 subunit domain


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1     1e-06     0.018      40      90 .]      37      74 ..      23      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-06
                                   SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                           Rpr2 40 ppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                                   + + k  +C +C +++ip v++++r                vl+++Cl Cg
  gene338|gene338|rna338|rna338 37 DSWGKAMFCGRCLHLYIPVVNSRIRYDG-------------VLTIECLGCG 74
                                   4455999******************952.............4567777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 626.97
//
Query:       gene339|gene339|rna339|rna339  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-37  126.0   2.0      1e-36  125.7   2.0    1.1  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   2.0   5.6e-41     1e-36       2     110 .]      15     132 ..      14     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 5.6e-41
                  Ribosomal_S11   2 vahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........pG 72 
                                    vahi+a+ n+t+++itd++G e+++k++Gg+ vka+r + sPyaa+laa+++aek+l +G+k ++ k++g         G
  gene339|gene339|rna339|rna339  15 VAHIKATKNDTFVHITDMTGSETIAKITGGMRVKAQRdEGSPYAAMLAAQDVAEKILGRGVKILHFKLRGaggvkpmaLG 94 
                                    89***********************************9*************************************9999* PP

                  Ribosomal_S11  73 pGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                    pG+++a+r+l raGlk+griedvtP+ +d +r+++++r
  gene339|gene339|rna339|rna339  95 PGAQTAIRTLIRAGLKVGRIEDVTPVARDRVRKRGGHR 132
                                    ********************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1061.94
//
Query:       gene34|gene34|rna34|rna34  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1618.17
//
Query:       gene340|gene340|rna340|rna340  [L=576]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-29  101.3   0.6    9.5e-29  100.7   0.6    1.3  1  UCH           Ubiquitin carboxyl-terminal hydrolase
    1.5e-14   54.0   6.5    1.5e-14   54.0   6.5    3.3  3  zf-UBP        Zn-finger in ubiquitin-hydrolases and other pro
      1e-05   25.3   2.1    0.00059   19.5   2.1    2.1  1  UCH_1         Ubiquitin carboxyl-terminal hydrolase
    0.00011   21.9  10.1      0.017   14.9   4.6    2.7  2  zf-UBP_var    Variant UBP zinc finger
  ------ inclusion threshold ------
      0.057   13.5   0.2       0.16   12.1   0.2    1.7  1  V-ATPase_H_C  V-ATPase subunit H


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.6   2.7e-32   9.5e-29       1     257 []     249     575 ..     249     575 .. 0.76

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 2.7e-32
                                    -EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHH....SH-CCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxx RF
                            UCH   1 tGlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkell....kskskav 76 
                                    +G++N GntCy++svlQ++  + +  ++  +        ++ + +  +npl+    ++++l ++f+++     + + + +
  gene340|gene340|rna340|rna340 249 VGIINSGNTCYISSVLQMIGYVVSKEEFDMD--------QHFEICCVKNPLEC---FFCQLMRVFNKMKeardRIEINRI 317
                                    69****************9886644433333........33323333455555...*************77664445689 PP

                                    --HHHHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCC..............HCCCHHHHHHCCCTTSHHHHHH-EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH  77 sPkklkktlsklaksfsgykqqDaqEflaflLdqlhedlnr..............evaeekwkkhlkrndslitdlfegq 142
                                    s   l+  + +  ++fs++ qqDa+Efl flL++++e  ++                                       
  gene340|gene340|rna340|rna340 318 SILDLIMLIWRDMPMFSKFVQQDAHEFLLFLLEKIKEGESSyliphitscfefevG------------------------ 373
                                    9999**********************************999777777777777440........................ PP

                                    EEE...................................................EEEEEEB-SEEEEEEESEEETEE.EE CS
                                    xxx...................................................xxxxxxxxxxxxxxxxxxxxxxx.xx RF
                            UCH 143 lks...................................................klklkrlPeiLiihlkRfsynss.ks 170
                                                                                          +  ++  P++Lii++ R+syn+   +
  gene340|gene340|rna340|rna340 374 --ReifcsgcsdksvgyesmmmmctclkgdirksvemffssdewdckcggkksvRRFVTMPPKYLIIQVGRYSYNNYkVE 451
                                    ..333333333333333333333333344444488888888***********999999999*************999999 PP

                                    E--SEEB--SEEE-GGGBSS-BTTS-TCS-B..........................................EEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................................xxxxxxx RF
                            UCH 171 Klntkvefpeeldlssylaeekkkkteekkk..........................................YeLiavv 208
                                    K+++k+ ++ +++l+s++ +++ +k   k k                                          Y+ ++ +
  gene340|gene340|rna340|rna340 452 KIKSKIGMK-SVKLESFIRKNDVEKALVK-KlvddgyaeedaektlsifcndeskardflknrltmhhrsdlkYRVVGCI 529
                                    999999999.7888877776655553322.2467777777777788888888888888888888888888888******* PP

                                    EEES.CTTSEEEEEEEECTTTTEEEEEETTEEEEE-HHCCCTTCEEEEEE CS
                                    xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 209 vHsG.slssGHYvayiknekngkWykydDetvkevkeeeevlssayiLfY 257
                                    +HsG + + GHY+ ++   +++k yk+dD++v +++   evl+++yi+++
  gene340|gene340|rna340|rna340 530 NHSGdNIKAGHYTWWVY--DDEKCYKIDDTNVLSSNV--EVLEDGYIFLF 575
                                    ************99999..777889999999999984..6899***9975 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   3.1         1   3.7e+03      17      46 ..      29      54 ..      13      57 .. 0.76
   2 !   54.0   6.5   4.3e-18   1.5e-14       1      60 [.     124     192 ..     124     196 .. 0.92
   3 ?   -2.8   0.1       2.3   8.4e+03      50      58 ..     376     384 ..     364     388 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1
                                   T--EEE-TTTT-HHHHHHHHH---EEEETT CS
                         zf-UBP 17 CghvgCgrksnghalkHyeetrHplavdls 46
                                   Cg  +C     +h+  H+ + +++++++++
  gene340|gene340|rna340|rna340 29 CGLSFCR----KHIDIHLGKAECHIVFEIK 54
                                   4555554....6******999998888776 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 4.3e-18
                                    -TTTH--.SSEEEETTT--EEE-TTT.....T-HHHHHHHHH---EEEETTT--.....EEETTTTEEBE CS
                         zf-UBP   1 CseCnsenknlWlCLkCghvgCgrks.....nghalkHyeetrHplavdlstls.....vycyscddeve 60 
                                    C+ C+   ++lW+C +Cg+vgCgr +     ngha+ Hye+t+H ++v + +l      v+cy cd+ + 
  gene340|gene340|rna340|rna340 124 CKLCDIR-TRLWICFSCGYVGCGRVQygtegNGHAKLHYEQTQHNVFVLIPSLLrescdVFCYLCDSSIR 192
                                    999**88.***************988999989****************99888888899*******9886 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                                    EEETTTTEE CS
                         zf-UBP  50 vycyscdde 58 
                                    ++c  c d+
  gene340|gene340|rna340|rna340 376 IFCSGCSDK 384
                                    888888775 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.1   1.6e-07   0.00059       1     292 [.     249     541 ..     249     557 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-07
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                          UCH_1   1 sGLEnhivnsYlNslLQvlyfipplrnlalshlak.eckke..hcLlcElgflfdmldkakgl.ncqasnFlralssipe 76 
                                    +G  n  +++Y+ s+LQ+  ++    ++++ +  +  c k+  +c +c+l  +f+ +++a+ + ++     l  +  i  
  gene340|gene340|rna340|rna340 249 VGIINSGNTCYISSVLQMIGYVVSKEEFDMDQHFEiCCVKNplECFFCQLMRVFNKMKEARDRiEINRISILDLIMLIW- 327
                                    57778899**************8888777754444367666668**********9999998664555444444444332. PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1  77 asalglileeeeetekssaislssliqs....fnrflldqlekelketkknsseeesaieqllgtkaettirclkCgsek 152
                                       + +               +s+ +q+    f  fll+++++ +++           i++++++++  +i c+ C+ ++
  gene340|gene340|rna340|rna340 328 -RDMPM---------------FSKFVQQdaheFLLFLLEKIKEGESSY------LIPHITSCFEFEVGREIFCSGCSDKS 385
                                    .22222...............444444223339999999998887775......4678********************** PP

                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 153 srksstlvl.dlkyPkpsnekkeakvtfasilksslerekttrawCekCkryqpteqrktvknlPpvLalnakleeeeel 231
                                    +  +s++++               k ++ + +++++++      w  kC  ++  + r+ v+  P+ L++++++ + +++
  gene340|gene340|rna340|rna340 386 VGYESMMMMcTC-----------LKGDIRKSVEMFFSS----DEWDCKCGGKK--SVRRFVTMPPKYLIIQVGRYSYNNY 448
                                    777777774033...........347899999999999....99998996644..568999999*********9966644 PP

                                    xxxxx............xxxxxxxxxxxxxxxxxx....................................xxxxxxxxx RF
                          UCH_1 232 elwkt............knwlpleiklsldedknl....................................eeklkeere 263
                                    ++ k             +                +                                    ++++  ++ 
  gene340|gene340|rna340|rna340 449 KVEKIkskigmksvkleS----------------FirkndvekalvkklvddgyaeedaektlsifcndesKARDFLKNR 512
                                    444443333333333330................1333334566666677777777777777788888874333334444 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 264 kakaekeikvYeLqsvvvhigdskesghL 292
                                     + ++++  +Y +++++ h gd+ ++gh+
  gene340|gene340|rna340|rna340 513 LTMHHRSDLKYRVVGCINHSGDNIKAGHY 541
                                    4556667789***********9988***9 PP

>> zf-UBP_var  Variant UBP zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   4.6   4.8e-06     0.017      11      60 ..       9      55 ..       6      58 .. 0.92
   2 !    9.3   0.2   0.00026      0.94      28      58 ..     133     172 ..     122     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.8e-06
                     zf-UBP_var 11 yKdECvycFdtpesedGlyvcLkcFlgfckkhaekhaektghpvylnikr 60
                                   +++ C+yc+++    +G+ vc  c l+fc+kh++ h  k++  ++  ik+
  gene340|gene340|rna340|rna340  9 FREKCCYCYRDV--AEGISVC-GCGLSFCRKHIDIHLGKAECHIVFEIKE 55
                                   799******965..78*****.9******************999999997 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00026
                     zf-UBP_var  28 lyvcLkc.Flgfck........khaekhaektghpvylni 58 
                                    l +c +c + g ++         ha++h+e+t+h v++ i
  gene340|gene340|rna340|rna340 133 LWICFSCgYVGCGRvqygtegnGHAKLHYEQTQHNVFVLI 172
                                    77888886777777888888889**************977 PP

>> V-ATPase_H_C  V-ATPase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.4e-05      0.16      40     102 ..     474     537 ..     459     539 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                   V-ATPase_H_C  40 nfkllkkLiklleeskd.ktvlavalnDigelvkllpegkkvleklkaKekimellehedeevk 102
                                    + +l+kkL++  ++++d +++l++ +nD ++  ++l++  ++ ++ + K +++ +++h+ +++k
  gene340|gene340|rna340|rna340 474 EKALVKKLVDDGYAEEDaEKTLSIFCNDESKARDFLKNRLTMHHRSDLKYRVVGCINHSGDNIK 537
                                    35678888887766666579***************************************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 3418.97
//
Query:       gene341|gene341|rna341|rna341  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.1e-39  133.4   0.0    1.1e-38  133.1   0.0    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0     6e-43   1.1e-38       1     198 []      20     215 ..      20     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 6e-43
                                    EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH....SEEEEEEE-HHHHH.HHTTTS- CS
                      RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik....kkiekrklvaeeikyasenein 76 
                                    +GiDEaGrGpv+G +v+ a + +k +   lk  g+kDSK L++ +r   ++ ik     ++ + +   +  + ++  + +
  gene341|gene341|rna341|rna341  20 VGIDEAGRGPVVGYMVYGALVAPKSA---LKSTGFKDSKVLTHAQRHTFFQTIKekglGYVYHCTHPDYITEMMQLGSTS 96 
                                    6****************887777665...59***********************99997777777777777779999*** PP

                                    HHHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHH CS
                      RNase_HII  77 lneikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverdeelell 156
                                    l ei ++++ ++ +++++++ +v+ ++vd+ ++ e++k  l++  +  ++vek+ad+++ +v+ ASi+Akv+rd+++   
  gene341|gene341|rna341|rna341  97 LDEISVNSVFRILDEIKAKCENVEGVYVDALGNCEKYKARLKKKYPYMFVVEKRADSRFQIVSGASIVAKVQRDLMISEF 176
                                    **********************************************99****************************9877 PP

                                    HHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHHH CS
                      RNase_HII 157 krkpgtldkgsGyasdektrallkkgats..klpdivrlsfktv 198
                                     ++      gsGy+sd+ t  +lk+++      p  vr+s+ tv
  gene341|gene341|rna341|rna341 177 GND-----LGSGYPSDPSTIRWLKRNTNAvfGFPPGVRYSWSTV 215
                                    666.....68******************9999999******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1473.69
//
Query:       gene342|gene342|rna342|rna342  [L=895]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   3.6e-176  584.3   3.3   1.3e-109  366.0   2.2    2.1  2  PFK            Phosphofructokinase
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.073   12.8   0.0    2.2  2  Lactamase_B_4  tRNase Z endonuclease
      0.038   13.9   0.0         13    5.8   0.0    2.6  2  PriA_3primeBD  3′ DNA-binding domain (3′BD)
       0.04   13.8   0.0       0.17   11.8   0.0    2.0  2  SfsA           Sugar fermentation stimulation protein RE doma
      0.043   13.0   0.0        0.1   11.8   0.0    1.6  1  NAD_kinase     ATP-NAD kinase
        0.1   12.2   0.1        1.2    8.7   0.0    2.7  2  DAGK_cat       Diacylglycerol kinase catalytic domain
       0.17   12.1   0.5        1.9    8.7   0.1    2.8  3  EF1_GNE        EF-1 guanine nucleotide exchange domain


Domain annotation for each model (and alignments):
>> PFK  Phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.0   2.2  4.9e-113  1.3e-109       1     284 []     103     478 ..     103     478 .. 0.99
   2 !  217.6   0.0   7.9e-68     2e-64       1     284 []     568     844 ..     568     844 .. 0.94

  Alignments for each domain:
  == domain 1  score: 366.0 bits;  conditional E-value: 4.9e-113
                                    EEEEEEESS--TTHHHHHHHHHHHHHHTT-EEEEETTHHHHHHTT-EEEE-SGGGTT-TT--S-TT-----GGGGSHHHH CS
                            PFK   1 riailtsGGdapGmNaairavvrtaikkglevygireGfeGlieeeiekltledvsgilsegGtiLgsaRskefkeregr 80 
                                    riai+tsGGdapGmN+ai++++rt+ik+g++vyg+++G++Gli+++i++l++++ ++++s+gGt+L saRs++f+er+gr
  gene342|gene342|rna342|rna342 103 RIAIVTSGGDAPGMNSAIKSIIRTGIKWGASVYGVYNGYDGLINDNIRRLSWDTETHCSSQGGTVLLSARSQKFMERNGR 182
                                    7******************************************************************************* PP

                                    HHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T............................................ CS
                            PFK  81 kkaaenlkklgidaLvviGGdgslkganklseerkgllee........................................ 120
                                    k+a+ n+++++i++++v+GGdgs+kga +l++e+k++l++                                        
  gene342|gene342|rna342|rna342 183 KQAVLNMVQKRINCMIVLGGDGSMKGAMTLRDEFKEHLRDliregrismkvlrkikmdktgpqdeekiqattdtsvvgys 262
                                    **********************************998888**************************************** PP

                                    ..................................................--EEEEEEETT---TT-S--EEHHHHHHHH CS
                            PFK 121 ..................................................lkivgiPkTidNDipgtdytiGfdTAlnti 150
                                                                                      lki+giP+TidNDi+g  +++G dTA++++
  gene342|gene342|rna342|rna342 263 dfygkpecykevptvyhelnssdgiedfqdndecsgesidlndiesyvydLKIIGIPATIDNDICGASISLGEDTAVHRV 342
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHT-EEEEEES-TT-THHHHHHHHHHT-SEEE-TTS---HH.HHHHHHHHHHT.T-S-EEEEEESSS. CS
                            PFK 151 veaidklkstakshkrvfvvEvmGrncGwlAlmaglaggadvilipEepfdie.eliekikklrkkgkkksiivvaEgak 229
                                    +e id+l st+ksh r+fv+EvmGr+cGw+Alm++la+ ad++l+pE p +++ e+ie++ ++++ gk++++++vaEga+
  gene342|gene342|rna342|rna342 343 IEGIDHLISTMKSHTRTFVIEVMGRKCGWIALMSALASAADYALLPETPTEWRkEMIEALMTAKRYGKSGTFVIVAEGAI 422
                                    ****************************************************99**********99************** PP

                                    .S-.....HHHHHHHHHHHHSS-EEEEE-GGGGG-S---HHHHHHHHHHHHHHHHHH CS
                            PFK 230 dkeg..iiaeelakeieektgievrvtvlGhlqrGgspsafDrilatrlGikavell 284
                                    +++g  i+a+++++ei++ +gievr+++lGh+qrGg++sa+Dri++t+lG+kave+l
  gene342|gene342|rna342|rna342 423 EEDGtaITASQVVEEISK-SGIEVRLLKLGHIQRGGPTSAQDRIYGTLLGVKAVEIL 478
                                    877788**********77.79*********************************975 PP

  == domain 2  score: 217.6 bits;  conditional E-value: 7.9e-68
                                    EEEEEEESS--TTHHHHHHHHHHHHHHTT-EEEEETTHHHHHHTT-EEEE-SGGGTT-TT--S-TT-----GGGGSHHHH CS
                            PFK   1 riailtsGGdapGmNaairavvrtaikkglevygireGfeGlieeeiekltledvsgilsegGtiLgsaRskefkeregr 80 
                                    ri+il+   +++GmN+a++a++++++  g+e+y+i +GfeGli +++ k    ++ g  ++gG+ +g   s+e     ++
  gene342|gene342|rna342|rna342 568 RIGILQFERRSSGMNTALNAATQYSLMVGAEPYYIPNGFEGLIGGRLVKPRPYEFFGDVNNGGSAIGIGDSEEV----DI 643
                                    79******************************************999999999****************99886....49 PP

                                    HHHHHHHHHHT--EEEEEESHHHHHHHHHHHHT..T....--EEEEEEETT---TT-S--EEHHHHHHHHHHHHHHHHHH CS
                            PFK  81 kkaaenlkklgidaLvviGGdgslkganklseerkglleelkivgiPkTidNDipgtdytiGfdTAlntiveaidklkst 160
                                      + ++++++++d L+viGG+++l++++ l+    +    + iv+iP++  N+ipg d++iG+dTAlnti+++ d  k  
  gene342|gene342|rna342|rna342 644 GLVQKKVEEYKLDSLIVIGGSKALNIIKGLK----N----IDIVLIPASSYNNIPGIDISIGADTALNTILKISDVSKLN 715
                                    99***************************99....6....89************************************** PP

                                    HHHH.T-EEEEEES-TT-THHHHHHHHHHT-SEEE-TTS---HHHHHHHHHHHH....T.T-S-EEEEEESSS..S-... CS
                            PFK 161 aksh.krvfvvEvmGrncGwlAlmaglaggadvilipEepfdieeliekikklr....kkgkkksiivvaEgakdkegii 235
                                    + +  +++fv+Ev G+ncG+l lm+g+a+ga  ++ipE+++ i +l+e+ ++lr    +k +++++i+++E++++  +i 
  gene342|gene342|rna342|rna342 716 SFAYkNNAFVIEVGGKNCGYLSLMGGIAAGAFEVFIPERKYLIGHLSEAAQRLRvkfrEKVRRGIVIFRNEKTFR--SIP 793
                                    *9999*************************************************98765567888********96..589 PP

                                    HHHHHHHHHHHHSS..-EEEEE-GGGGG-S---HHHHHHHHHHHHHHHHHH CS
                            PFK 236 aeelakeieektgi..evrvtvlGhlqrGgspsafDrilatrlGikavell 284
                                    +e++++ ++  ++   e+++++lG lq+G +ps++Dri at lGi+av+l+
  gene342|gene342|rna342|rna342 794 TESFCEILKTDSQDlfETNYCILGDLQQGLNPSPIDRINATILGIEAVDLC 844
                                    ********55444246********************************975 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.9   4.8e+03      10      25 ..     162     177 ..     158     177 .. 0.84
   2 ?   12.8   0.0   2.9e-05     0.073      17      39 ..     749     771 ..     746     782 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.9
                  Lactamase_B_4  10 tsgPlllLqldskrYl 25 
                                    ++g ++lL+ +s++++
  gene342|gene342|rna342|rna342 162 SQGGTVLLSARSQKFM 177
                                    45689********996 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.9e-05
                  Lactamase_B_4  17 LqldskrYlfGkvgEgtQRavne 39 
                                    +++++++Yl+G+++E  QR+ ++
  gene342|gene342|rna342|rna342 749 VFIPERKYLIGHLSEAAQRLRVK 771
                                    57899**************8665 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.005        13      16      60 ..      79     125 ..      78     127 .. 0.86
   2 ?    5.1   0.0    0.0084        21      23      60 ..     763     802 ..     746     817 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.005
                  PriA_3primeBD  16 vpeelevkiGsrVlVpfgkr...klvGiVvalkeeseveeeklkpiee 60 
                                    vp e+++ +G r++V f ++   ++++iV++  + +   ++ +k+i++
  gene342|gene342|rna342|rna342  79 VPLEMMDMMGNRIVVTFSGQgrmNRIAIVTSGGDAPG-MNSAIKSIIR 125
                                    788999999********888777999***99999988.7889999875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0084
                  PriA_3primeBD  23 kiGsrVlVpfgkrklvGiVvalkee..seveeeklkpiee 60 
                                    ++ +r +V+f+++ + GiV+  +e+   ++++e+  +i++
  gene342|gene342|rna342|rna342 763 EAAQRLRVKFREKVRRGIVIFRNEKtfRSIPTESFCEILK 802
                                    5679****************99988666666776666665 PP

>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.85   2.2e+03      66      97 ..     336     367 ..     330     370 .. 0.84
   2 ?   11.8   0.0   6.5e-05      0.17      48      95 ..     371     418 ..     344     451 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.85
                                    SS--HHHHHHHHHHHHHHHTT-EEEEEEEE-S CS
                           SfsA  66 dapteRgqkhleeLaelvkegyravvlfvvqr 97 
                                    d+   R ++ +++L++ +k++ r++v+ v+ r
  gene342|gene342|rna342|rna342 336 DTAVHRVIEGIDHLISTMKSHTRTFVIEVMGR 367
                                    66667899999*************99988766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.5e-05
                                    EEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHHHTT-EEEEEEEE CS
                           SfsA  48 yvEVKsvtleeggialfPdapteRgqkhleeLaelvkegyravvlfvv 95 
                                    ++ + s+  +   +al P +pte+ ++++e L+ +++ g+    ++v+
  gene342|gene342|rna342|rna342 371 WIALMSALASAADYALLPETPTEWRKEMIEALMTAKRYGKSGTFVIVA 418
                                    55555555565459************************9988877765 PP

>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05       0.1      67      97 ..     182     212 ..     156     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                                    EECCC-TTTTTSSSEEEEEE-HHHHHHHHHH CS
                     NAD_kinase  67 trkaleafadagvdliivvGGDGTaldvarl 97 
                                     ++a+ +++++++ ++iv+GGDG +  +++l
  gene342|gene342|rna342|rna342 182 RKQAVLNMVQKRINCMIVLGGDGSMKGAMTL 212
                                    567999*******************998775 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00048       1.2      35      72 ..     173     210 ..     139     221 .. 0.80
   2 ?   -0.6   0.1      0.37   9.4e+02      49      97 ..     648     690 ..     639     710 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00048
                                    EEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHH CS
                       DAGK_cat  35 lieteepgdakelakeakeegvdlivvaGGDGtvsevl 72 
                                     ++  e++  k+ + ++ ++++++ +v+GGDG ++ ++
  gene342|gene342|rna342|rna342 173 SQKFMERNGRKQAVLNMVQKRINCMIVLGGDGSMKGAM 210
                                    44555677789999999999************998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.37
                                    HHHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-SS--HHH CS
                       DAGK_cat  49 keakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlGtgNdla 97 
                                    k+++e + d ++v+GG    s++ln + +   +++ + +iP+ + N++ 
  gene342|gene342|rna342|rna342 648 KKVEEYKLDSLIVIGG----SKALNIIKG--LKNIDIVLIPASSYNNIP 690
                                    5566677799999999....666666666..667999999999988875 PP

>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.61   1.6e+03      18      34 ..     116     132 ..     111     140 .. 0.84
   2 ?   -3.5   0.1       4.8   1.2e+04      53      80 ..     489     511 ..     472     514 .. 0.60
   3 ?    8.7   0.1   0.00074       1.9      10      53 ..     638     681 ..     636     692 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.61
                                    HHHHHHH.HS-TSEE-- CS
                        EF1_GNE  18 lekkvksikleglvwge 34 
                                    +  ++ksi   g++wg 
  gene342|gene342|rna342|rna342 116 MNSAIKSIIRTGIKWGA 132
                                    7889************5 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.8
                                    EESSS-GGGGHHHHHHTTS-S.....SE CS
                        EF1_GNE  53 vieddkvstdeleekieeiegeledlVq 80 
                                     i  d++s  el+e ie      +dlV 
  gene342|gene342|rna342|rna342 489 SIFRDEISEVELKEVIE-----RNDLVR 511
                                    44455555566666666.....244455 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00074
                                    SS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEE CS
                        EF1_GNE  10 ddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscv 53 
                                    ++e+d+  ++kkv++ kl+  +v+g  sk   i  Glk + i ++
  gene342|gene342|rna342|rna342 638 SEEVDIGLVQKKVEEYKLDSlIVIG-GSKALNIIKGLKNIDIVLI 681
                                    89******************99999.5************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (895 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.50
# Mc/sec: 5394.51
//
Query:       gene343|gene343|rna343|rna343  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.019   15.0   1.0      0.038   14.0   1.0    1.5  1  zf-BED     BED zinc finger
      0.092   13.6   2.7      0.092   13.6   2.7    1.8  2  zf-C2H2_4  C2H2-type zinc finger
       0.95   10.1   4.7        2.1    8.9   4.7    1.6  1  zf-C2H2    Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.0   6.3e-06     0.038      12      43 ..      80     108 ..      71     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-06
                                    GGSS--EETTTTEE----SSTHHHHHHHHHS- CS
                         zf-BED  12 lkeqkavCryCgkilsrgggttnLkrHLrrkH 43 
                                    ++++  +C +C + + ++    +L +HL + H
  gene343|gene343|rna343|rna343  80 EDRNGFICAHCDARYVYK---RCLVNHLIKSH 108
                                    789999************...*******9998 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         3   1.8e+04       5       9 ..      34      37 ..      34      43 .. 0.53
   2 ?   13.6   2.7   1.5e-05     0.092       1      24 []      85     108 ..      85     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                      zf-C2H2_4  5 iCgks 9 
                                   +C k+
  gene343|gene343|rna343|rna343 34 YC-KV 37
                                   46.33 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.5e-05
                      zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                    f+C +C++++  k+ L +Hl + H
  gene343|gene343|rna343|rna343  85 FICAHCDARYVYKRCLVNHLIKSH 108
                                    89******************9998 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.7   0.00036       2.1       1      23 []      85     108 ..      85     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00036
                                    EEETTTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                    + C +C+ ++  k  L++H+ + H
  gene343|gene343|rna343|rna343  85 FICAHCDARYVYKRCLVNHLIKsH 108
                                    78******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 865.23
//
Query:       gene344|gene344|rna344|rna344  [L=835]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-88  294.8   0.0    1.3e-87  294.2   0.0    1.3  1  RNB         RNB domain
    1.4e-20   73.1   0.0    2.7e-20   72.2   0.0    1.5  1  OB_Dis3     Dis3-like cold-shock domain 2 (CSD2)
    4.3e-06   26.5   0.0      1e-05   25.3   0.0    1.6  1  Rrp44_CSD1  Rrp44-like cold shock domain
    1.3e-05   25.3   0.6    0.00023   21.3   0.0    2.6  2  CSD2        Cold shock domain
     0.0001   22.2   1.3    0.00057   19.8   1.3    2.1  1  Rrp44_S1    S1 domain
  ------ inclusion threshold ------
      0.044   13.5   0.2       0.13   12.0   0.2    1.8  1  OB_RNB      Ribonuclease B OB domain
      0.072   12.9   0.0        0.2   11.5   0.0    1.7  1  NifT        NifT/FixU protein


Domain annotation for each model (and alignments):
>> RNB  RNB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.2   0.0     5e-91   1.3e-87       1     325 [.     390     699 ..     390     700 .. 0.92

  Alignments for each domain:
  == domain 1  score: 294.2 bits;  conditional E-value: 5e-91
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RNB   1 RkdlrdllvitIdpedakdlDdAisieklpngnyelgVhIADvshyvkegspldkearkratsvyLpekvvpMLPqelse 80 
                                    R+d+r+l +++Idp++++d+DdA++ + lpngn e+gVhIADv++yv+++s++dk+a+ r+t+vyLpe  + MLP++ls+
  gene344|gene344|rna344|rna344 390 REDFRELVIMSIDPPGCEDIDDALHWRVLPNGNLEVGVHIADVAYYVHKDSKVDKIAADRGTTVYLPEWRIDMLPPNLST 469
                                    99****************************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RNB  81 dlcSLnpgedrlalsvlidvdekgevlsveiylsvIkskarltydevqdlleqkdekeekktaedLellyelakalrkkR 160
                                    d+cSL +g+dr+a+sv+++++++ ++l +++ +s I+s++ ++y+e+ d++++++++  + t ++L  l e++++lr+ R
  gene344|gene344|rna344|rna344 470 DICSLVAGKDRPAFSVVWEMSKDAKILRTHFCRSLIRSRKAFSYKEAYDVIKGATDNG-DGTSDSLVGLLEISRILRNGR 548
                                    ***************************************************8877654.46******************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RNB 161 lkkgalefdspeikllldedkgnrielkveeetkahslveelmllANelvArfl.seleipailriheepsnekledlik 239
                                    l+kg+l++  +++++++ e       ++v+e    + lvee+m+lAN  vA f+ +++++  +lr h++ps   l+  ++
  gene344|gene344|rna344|rna344 549 LSKGSLDL--STKQVMFRE-----GGFEVKEYFPTNFLVEEFMILANISVALFIyHHHPDSSLLRKHPPPS--VLDMPVD 619
                                    *****999..688999988.....34999999**********************9999**********999..2222222 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RNB 240 lakklglklednsskknlqeslekleeeeaeqllselllrllkeakyssep....vgHfgLaleeYthfTSPirRYpDlv 315
                                    +           s+ k l e+l +++  + ++l++++l++++++a+y  +     + H+gLa++ YthfTSPirRY+D+v
  gene344|gene344|rna344|rna344 620 IGT---------STSKGLGEVLGRMDGIK-KDLMKRMLVKSMNQAVYVISGeasnFYHYGLATPMYTHFTSPIRRYADIV 689
                                    222.........33457888888887777.999**************97777777************************* PP

                                    xxxxxxxxxx RF
                            RNB 316 vhrllkalla 325
                                    vhr+l  +l+
  gene344|gene344|rna344|rna344 690 VHRILGSILQ 699
                                    *****99986 PP

>> OB_Dis3  Dis3-like cold-shock domain 2 (CSD2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0     1e-23   2.7e-20       2      77 .]     287     354 ..     286     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1e-23
                                    EEE--SSTTS--EEEETTSSTTTHHHHTTTTTT--EEEEE----TT-SS-EEEEEEE-HHHHHHHHHHHHHHHHTT CS
                        OB_Dis3   2 vlfkPldkrlPriliptkelpeeflenpeelegklfvvkidsWsetsryPlGeivksLGeagdieaeteaiLleng 77 
                                    vl++P+dkr+P ++i+t+++        eel +k+++v+id W+ ts+yP+G++ k LG++gd +ae+eaiL++ng
  gene344|gene344|rna344|rna344 287 VLVIPIDKRIPAVRIRTSQV--------EELVNKRLCVEIDGWERTSNYPIGHYYKRLGNIGDKKAEMEAILVANG 354
                                    89******************........*********************************************996 PP

>> Rrp44_CSD1  Rrp44-like cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0     4e-09     1e-05      21      73 ..     180     230 ..     163     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 4e-09
                                    SEEEEEEEEESSBTTEEEEE-SSSSS-EEEESHHHHTS--TT-EEEEEE--GG CS
                     Rrp44_CSD1  21 vlyqgniqiseynflegsvslprfskpvlivgqknlnrafngdqvivellpqs 73 
                                     ly+g +++s yn   g v        +l+vg+kn+nra+ gd+v ve++ + 
  gene344|gene344|rna344|rna344 180 GLYKGTLEVSMYNCYSGFVIDGD--VKILVVGKKNMNRAISGDEVYVEVVDEC 230
                                    49***************997654..569********************98765 PP

>> CSD2  Cold shock domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.15   3.7e+02      14      36 ..     206     229 ..     200     239 .. 0.81
   2 !   21.3   0.0   8.9e-08   0.00023       2      71 ..     289     357 ..     288     358 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.15
                           CSD2  14 f.ipkeklkgakdGdkVvveitey 36 
                                    + + k++ + a +Gd V ve+++ 
  gene344|gene344|rna344|rna344 206 LvVGKKNMNRAISGDEVYVEVVDE 229
                                    437799999***********9875 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 8.9e-08
                           CSD2   2 VvpddkrlkqdifipkeklkgakdGdkVvveiteypdkkn.peGevievLGkkgdpgveilsilakhglpe 71 
                                    V+p dkr++  + i  ++ ++++ ++   vei  ++   n p+G+  + LG+ gd+++e+++il ++g+ +
  gene344|gene344|rna344|rna344 289 VIPIDKRIPA-VRIRTSQVEELV-NKRLCVEIDGWERTSNyPIGHYYKRLGNIGDKKAEMEAILVANGITY 357
                                    8999999995.778877777676.566789*****965667*************************99975 PP

>> Rrp44_S1  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.3   2.2e-07   0.00057       3      39 ..     770     806 ..     769     830 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.2e-07
                                    EEEEEEEEESSEEEEEETTTTEEEEEEHHHCBS-GGG CS
                       Rrp44_S1   3 eegyvikvfsNGvvvlvprfGiEglirledlaeeees 39 
                                    +eg+v+ + sNGvvv+vp + +E +i  e+  e  ++
  gene344|gene344|rna344|rna344 770 TEGFVTSIKSNGVVVYVPEYNLEEVIVSEESFEMFQK 806
                                    69************************98876665555 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2     5e-05      0.13      11      44 ..     196     228 ..     192     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5e-05
                                    EEEEECT.TEEEEE-HHHHTTS-TT-EEEEEEEE CS
                         OB_RNB  11 GFlipdegkeDifippeqmkkamhGDrVlvritk 44 
                                    GF+i d++ + + + +++m++a+ GD V v++  
  gene344|gene344|rna344|rna344 196 GFVI-DGDVKILVVGKKNMNRAISGDEVYVEVVD 228
                                    5654.556888999*****************976 PP

>> NifT  NifT/FixU protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.8e-05       0.2      10      38 ..     780     807 ..     774     822 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                                    S-E.EEEETTTTEEEEEEEESSSSS-SSE CS
                           NifT  10 eGklsvYvpKkDLEekvveeekeekwGge 38 
                                    + +++vYvp   LEe +v+ee+ e++ ++
  gene344|gene344|rna344|rna344 780 N-GVVVYVPEYNLEEVIVSEESFEMFQKI 807
                                    4.589**************9999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 5181.86
//
Query:       gene345|gene345|rna345|rna345  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-28   97.3   8.8    5.8e-28   97.0   8.8    1.1  1  Ribosomal_L34e  Ribosomal protein L34e
  ------ inclusion threshold ------
      0.014   15.5   0.9      0.018   15.2   0.9    1.2  1  Mut7-C          Mut7-C RNAse domain
       0.16   10.5   0.2       0.17   10.4   0.2    1.0  1  DUF629          Protein of unknown function (DUF629)


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   8.8   9.7e-32   5.8e-28       3      94 .]       2      93 ..       1      93 [. 0.98

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 9.7e-32
                 Ribosomal_L34e  3 qrltyrrrlsYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGgslcakc 84
                                   +++ +++  +Y+trsn+++ v+tp+gklv +++kk +k+++C++c++ L +i+++rp+e+sr + ++++v+RaYG ++c++c
  gene345|gene345|rna345|rna345  2 KNVLIHKGSTYKTRSNRRVRVRTPSGKLVNRRTKKYSKKHRCHECNAVLGSIARMRPAEFSRQKVSARRVNRAYGATHCGRC 83
                                   6788999*************************************************************************** PP

                 Ribosomal_L34e 85 vkerivrafl 94
                                   v+e+i+ afl
  gene345|gene345|rna345|rna345 84 VREKIIGAFL 93
                                   ********97 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.9   2.9e-06     0.018      88     131 ..      38      85 ..       4      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-06
                         Mut7-C  88 pelsrCvaCngeleevekee....vkervpekvyeeadeftrCekCrk 131
                                     + +rC +Cn++l ++ + +     +++v+++  ++a  +t+C +C +
  gene345|gene345|rna345|rna345  38 SKKHRCHECNAVLGSIARMRpaefSRQKVSARRVNRAYGATHCGRCVR 85 
                                    3368*******88777665511113456888888888889*****976 PP

>> DUF629  Protein of unknown function (DUF629)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   2.8e-05      0.17     349     418 ..      15      83 ..       5      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.8e-05
                         DUF629 349 ksnqgvavLralekefrkleslyekklehlsyeeaLqavenLcleEdkrRenvqedqarstYeslLrkrc 418
                                    +sn+ v v     k ++   ++y+kk++  + +++L ++ ++   E+ r++ + + ++r  Y +  + rc
  gene345|gene345|rna345|rna345  15 RSNRRVRVRTPSGKLVNRRTKKYSKKHRCHECNAVLGSIARMRPAEFSRQKVSARRVNRA-YGATHCGRC 83 
                                    566666666666677888899********************************9988865.*99999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 674.73
//
Query:       gene346|gene346|rna346|rna346  [L=273]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.4e-31  106.9   2.4    1.7e-14   53.4   0.2    2.4  2  RRM_1         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
    0.00017   21.7   0.2       0.15   12.2   0.0    2.5  2  RRM_7         RNA recognition motif
      0.009   16.0   0.8       0.39   10.8   0.1    2.6  2  RRM_3         RNA binding motif
  ------ inclusion threshold ------
      0.016   15.2   0.5        7.3    6.7   0.0    2.5  2  Nup35_RRM_2   Nup53/35/40-type RNA recognition motif
      0.033   14.6   0.6         14    6.2   0.0    3.0  3  Phage_TAC_13  Phage tail assembly chaperone, TAC
      0.075   12.8   0.0       0.35   10.7   0.0    2.0  2  RRM_Rrp7      Rrp7 RRM-like N-terminal domain


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.1   5.9e-18   1.8e-14       1      69 [.      69     137 ..      69     138 .. 0.98
   2 !   53.4   0.2   5.6e-18   1.7e-14       1      58 [.     153     211 ..     153     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 5.9e-18
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklggrel 69 
                                    +f++++++d+te +Lk  ++k+G++ ++ ++ +   +++kgf++VeF ++ed +kAl+ l+g+ + gre+
  gene346|gene346|rna346|rna346  69 VFIKGISYDLTEYDLKSEMEKIGKVARVGIPMTnDYKRNKGFGYVEFCKEEDVKKALK-LDGTVFLGREV 137
                                    8********************************9************************.*********97 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 5.6e-18
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHH CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlea 58 
                                    ++++n+p+ +++++Lk++F++ G+++ ++ ++d e+++ kg++f++F +ked ek l++
  gene346|gene346|rna346|rna346 153 IYISNIPFGCDKRKLKKYFEEMGEVVGVSFPYDkENDRLKGYGFIDFGNKEDYEKVLKK 211
                                    8******************************************************9985 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   4.9e-05      0.15       2      67 ..      67     125 ..      66     149 .. 0.82
   2 !    7.2   0.1    0.0018       5.5       4      68 ..     153     210 ..     150     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                          RRM_7   2 rkvFvGGlPiDiteeelkatfkefgkv.lvdwPkkaeskkkaaenskaakgyvflvfedeksvkaLl 67 
                                      vF+ G+  D+te +lk+ +++ gkv +v  P  + +k++        kg+ ++ f +e+ vk+ l
  gene346|gene346|rna346|rna346  67 LTVFIKGISYDLTEYDLKSEMEKIGKVaRVGIPMTNDYKRN--------KGFGYVEFCKEEDVKKAL 125
                                    679**********************9835888887666433........588888888888887655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                          RRM_7   4 vFvGGlPiDiteeelkatfkefgkvl.vdwPkkaeskkkaaenskaakgyvflvfedeksvkaLle 68 
                                    +++  +P   ++++lk+ f+e g+v+ v +P  +e+++         kgy f+ f +++  +++l+
  gene346|gene346|rna346|rna346 153 IYISNIPFGCDKRKLKKYFEEMGEVVgVSFPYDKENDRL--------KGYGFIDFGNKEDYEKVLK 210
                                    78999******************98669***88776433........5777777766666555554 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00013      0.39       4      55 ..      69     126 ..      67     138 .. 0.91
   2 ?    3.0   0.1     0.036   1.1e+02      15      57 ..     164     212 ..     155     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                    EEEEE-SSS--HHHHHHHCHCCS-ECEE......EE-TTSSEEEEEESSHHHHHHHHH CS
                          RRM_3   4 lklsGlnkelsredikellsklgevayv......dyekgdkegevrFkedeeakkale 55 
                                    ++++G++ +l+  d+k  ++k+g+va v      dy++++  g+v F ++e+ kkal+
  gene346|gene346|rna346|rna346  69 VFIKGISYDLTEYDLKSEMEKIGKVARVgipmtnDYKRNKGFGYVEFCKEEDVKKALK 126
                                    899***********************9977777789999999*************986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.036
                                    HHHHHHHCHCCS-ECEEEE-TTSSE......EEEEESSHHHHHHHHHHH CS
                          RRM_3  15 redikellsklgevayvdyekgdke......gevrFkedeeakkaleka 57 
                                    ++++k+ ++++gev  v +  ++++      g + F ++e+ +k+l+k 
  gene346|gene346|rna346|rna346 164 KRKLKKYFEEMGEVVGVSFPYDKENdrlkgyGFIDFGNKEDYEKVLKKK 212
                                    7899********9999988766655333433667788888888887765 PP

>> Nup35_RRM_2  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0024       7.3      20      53 .]      86     125 ..      66     125 .. 0.77
   2 ?    6.6   0.1    0.0026       7.7      19      49 ..     168     205 ..     150     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0024
                    Nup35_RRM_2  20 hFasfGeIvkhyvp......kevsvmyvkfesekdaekAL 53 
                                     ++ +G++ +  +p      +++ + yv+f +e d +kAL
  gene346|gene346|rna346|rna346  86 EMEKIGKVARVGIPmtndykRNKGFGYVEFCKEEDVKKAL 125
                                    578899999988888888888899***************8 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0026
                    Nup35_RRM_2  19 e.hFasfGeIvkhyvp......kevsvmyvkfesekda 49 
                                      +F++ Ge+v  ++p      + + + ++ f ++ d 
  gene346|gene346|rna346|rna346 168 KkYFEEMGEVVGVSFPydkendRLKGYGFIDFGNKEDY 205
                                    34*************99888776677777777766665 PP

>> Phage_TAC_13  Phage tail assembly chaperone, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0047        14      24      58 ..      61      95 ..      35      98 .. 0.76
   2 ?    4.9   0.0     0.012        35      11      52 ..     134     173 ..     123     180 .. 0.73
   3 ?   -0.6   0.1      0.61   1.8e+03       7      23 ..     254     270 ..     250     273 .] 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
                   Phage_TAC_13 24 egeeltatvyvrklsfktaeadlkalkkkedkvAa 58
                                   ++e+   tv+++ +s++ +e dlk+  +k  kvA+
  gene346|gene346|rna346|rna346 61 KKENPSLTVFIKGISYDLTEYDLKSEMEKIGKVAR 95
                                   4466789****************999998888875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                   Phage_TAC_13  11 gkpvekeikwkqgegeeltatvyvrklsfktaeadlkalkkk 52 
                                    g+ v  +    +  ++++  t+y+  ++f+  +++lk++ ++
  gene346|gene346|rna346|rna346 134 GREVVVNM--AHPRENKQRHTIYISNIPFGCDKRKLKKYFEE 173
                                    55554444..44556899****************99998766 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.61
                   Phage_TAC_13   7 glfvgkpvekeikwkqg 23 
                                    g ++++  +k++k++ +
  gene346|gene346|rna346|rna346 254 GESQNRNNNKKVKFNSD 270
                                    5566999*******983 PP

>> RRM_Rrp7  Rrp7 RRM-like N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.33   9.8e+02      36      47 ..      61      72 ..       2     106 .. 0.58
   2 ?   10.7   0.0   0.00012      0.35      34      66 ..     145     175 ..     139     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.33
                       RRM_Rrp7 36 ndeessrslFlv 47
                                   ++e+ s ++F+ 
  gene346|gene346|rna346|rna346 61 KKENPSLTVFIK 72
                                   112222333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                       RRM_Rrp7  34 knndeessrslFlvNlPiettletlkkffqkva 66 
                                    ++n++   +++++ N+P      +lkk+f+++ 
  gene346|gene346|rna346|rna346 145 RENKQ--RHTIYISNIPFGCDKRKLKKYFEEMG 175
                                    44443..48********************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1797.92
//
Query:       gene347|gene347|rna347|rna347  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-11   41.4   0.4    7.1e-07   28.9   0.1    2.4  2  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom
  ------ inclusion threshold ------
       0.11   12.7   0.5          3    8.0   0.0    2.3  2  PHM7_cyt  Cytosolic domain of 10TM putative phosphate transpo


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   4.3e-05      0.39      15      69 ..      28      79 ..      10      80 .. 0.76
   2 !   28.9   0.1     8e-11   7.1e-07       1      57 [.     102     153 ..     102     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.3e-05
                                   HHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                          RRM_1 15 LkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69
                                   L  l   f +i +ik++++   +  g afV + + e  +++l++lng+ + g+++
  gene347|gene347|rna347|rna347 28 LALLVTRFSKILKIKMSNK--PRLLGQAFV-YLDGEVTNEILSNLNGRFFLGNVI 79
                                   4446667999*99***997..999*****9.7889999*************9998 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 8e-11
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHH CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAle 57 
                                    l V+++p+ vt+++++++F+ f++ ++i+ ++      k  afV+F s+  A  A +
  gene347|gene347|rna347|rna347 102 LLVTDIPSLVTRDDIEDIFKSFEGLENIRFIKV-----KSLAFVDFLSSQKASIAYS 153
                                    6799****************************8.....**********999988866 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00034         3       2      27 ..     100     124 ..      99     134 .. 0.73
   2 ?    3.1   0.1     0.011        99     122     150 ..     135     162 ..     126     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00034
                       PHM7_cyt   2 rTvlvtgiPkelrseeklkeffeely 27 
                                    +T+lvt+iP+ ++ +++++++f+++ 
  gene347|gene347|rna347|rna347 100 KTLLVTDIPSLVT-RDDIEDIFKSFE 124
                                    6**********99.556777776643 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.011
                       PHM7_cyt 122 lgaaFvtfesersaaavakqakcaaqiqq 150
                                    ++ aFv f s+++a  ++ ++  + qi++
  gene347|gene347|rna347|rna347 135 KSLAFVDFLSSQKASIAY-SHFADGQIRH 162
                                    678*******99999887.4444456654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1099.47
//
Query:       gene348|gene348|rna348|rna348  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-11   42.6   0.0    6.8e-11   41.8   0.0    1.4  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom
  ------ inclusion threshold ------
       0.12   12.6   0.1         11    6.2   0.0    2.2  2  PHM7_cyt  Cytosolic domain of 10TM putative phosphate transpo


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   7.6e-15   6.8e-11       1      69 [.      39     108 ..      39     109 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 7.6e-15
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrd.etgkskgfafVeFeskedAekAlealngkklggrel 69 
                                    +f++n+p +v ee + elF  +G++k++ +  + +t +  gf+fVeF +  +A+ A++  ng  l++++l
  gene348|gene348|rna348|rna348  39 VFISNIPISVREERIWELFLLCGEVKRVIMGLNrNTLRFCGFCFVEFYTVHSADMAVKYINGFRLDQSPL 108
                                    8**************************************************************9998876 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0013        11       2      24 ..      37      58 ..      36      75 .. 0.75
   2 ?    5.2   0.0    0.0025        22     118     142 ..      74      98 ..      55     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0013
                       PHM7_cyt  2 rTvlvtgiPkelrseeklkeffe 24
                                    Tv++++iP ++r ee++ e+f 
  gene348|gene348|rna348|rna348 37 STVFISNIPISVR-EERIWELFL 58
                                   6************.777888774 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0025
                       PHM7_cyt 118 kkkplgaaFvtfesersaaavakqa 142
                                    + ++ g +Fv+f + +sa+ ++k++
  gene348|gene348|rna348|rna348  74 TLRFCGFCFVEFYTVHSADMAVKYI 98 
                                    457899************9998743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 987.33
//
Query:       gene349|gene349|rna349|rna349  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0079   15.9   0.4       0.02   14.6   0.4    1.7  1  ubiquitin    Ubiquitin family
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.023   14.8   0.0    1.3  1  Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.4   2.2e-06      0.02       2      58 ..      10      72 ..       7      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-06
                                   EEEETTSE.EEEEEEETTSBHHHHHHHHHHHHT.....SSGGGEEEEETTEEE-TTSBHGGHT CS
                      ubiquitin  2 tvktldgk.kitleveesdtveelKekiaekeg.....ipaeqqrLiysGkvLedertleeyg 58
                                   t+++ +g+ ++t e+e++ t++++Ke + ++ +        + +++i++Gk+ +d   l  +g
  gene349|gene349|rna349|rna349 10 TLRSRNGEyTYTKEFESDHTILHVKEYLKSQIEeysieSTEKGIKIILNGKIVSDAVQLHTLG 72
                                   5565444458888***********99888888667776888899***********99998775 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.6e-06     0.023       6      70 ..      10      72 ..       6      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                                   EEEETTS-EEEEEEEETT-BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-TTSBCCCCS CS
                    Rad60-SLD_2  6 kfrlvdGsDigpvkfsdaatvaelkekviaqWPkdkeekpksvndlklilaGkiLennktlkelr 70
                                    +r  +G+ +  ++f++  t+ ++ke + +q  +   +  ++ + +k+il+Gki  ++++l+ l+
  gene349|gene349|rna349|rna349 10 TLRSRNGEYTYTKEFESDHTILHVKEYLKSQIEE--YSIESTEKGIKIILNGKIVSDAVQLHTLG 72
                                   5788899999999***************998644..44458999****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1338.74
//
Query:       gene35|gene35|rna35|rna35  [L=589]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.013   15.6   9.9      0.013   15.6   9.9    8.5  8  Cnn_1N       Centrosomin N-terminal motif 1
      0.014   15.3   0.4      0.014   15.3   0.4    4.5  3  Shugoshin_N  Shugoshin N-terminal coiled-coil region
        2.3    8.7   5.2         24    5.5   0.0    4.5  5  NPV_P10      Nucleopolyhedrovirus P10 protein


Domain annotation for each model (and alignments):
>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   9.9   2.2e-06     0.013       1      60 [.      18      88 ..      18     102 .. 0.63
   2 ?   -2.1   3.1      0.77   4.6e+03      26      60 ..     105     141 ..      84     154 .. 0.64
   3 ?   -1.7  10.8      0.57   3.4e+03      31      71 ..     141     190 ..     104     192 .. 0.70
   4 ?   -0.7   1.4      0.27   1.6e+03      36      60 ..     229     253 ..     201     265 .. 0.52
   5 ?    1.3   8.9     0.065   3.9e+02      33      68 ..     262     303 ..     234     309 .. 0.67
   6 ?    2.6   1.7     0.026   1.6e+02      36      68 ..     330     362 ..     313     367 .. 0.61
   7 ?    0.3   0.7      0.13     8e+02      36      60 ..     389     413 ..     365     441 .. 0.53
   8 ?    0.7   3.6     0.097   5.8e+02      39      64 ..     530     555 ..     478     561 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-06
                     Cnn_1N  1 TlrEqeeqidkLkKENFdLKLriyfLeerleklse...........eqkeellkenielkveveslqkelk 60
                               T++++e++i++L++ENF  K ++ + +     + +           ++++ l+ en el  ++e +   + 
  gene35|gene35|rna35|rna35 18 TVKDYEKEIEELRNENFEIKHQLSHYKASSGGNIQediqkllldskRSIDILEGENEELNKQMERMNEMVR 88
                               89******************999777765444444133334444445555555555555555555554444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.77
                     Cnn_1N  26 Leerleklse..eqkeellkenielkveveslqkelk 60 
                                L+e l+k+s   e++  llk + ++   +++l+ e++
  gene35|gene35|rna35|rna35 105 LQEYLNKISMleEENGRLLKHLENVNGINAKLREENE 141
                                5566666665555566666666655555555555554 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.57
                     Cnn_1N  31 eklse.........eqkeellkenielkveveslqkelkekkkllreaek 71 
                                e l+e         +++++l+++    k+e  + +kel ++k+ l +++k
  gene35|gene35|rna35|rna35 141 EVLGEcfnrskntiDEQKSLIEKIAHEKEEKSQVEKELMSYKNALLNSNK 190
                                3333355555558899****************************999988 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.27
                     Cnn_1N  36 eqkeellkenielkveveslqkelk 60 
                                 +++++ +    +++e +++ ++++
  gene35|gene35|rna35|rna35 229 AEMNQMREHYKSMEDEYKEMYRQKQ 253
                                2333333333334444444444444 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.065
                     Cnn_1N  33 lse......eqkeellkenielkveveslqkelkekkkllre 68 
                                ++e      ++k+el   n el+ eve+l+ +   +kk+l+ 
  gene35|gene35|rna35|rna35 262 MGEnymretRDKQELALRNEELRREVEQLKTSRSDLKKRLEV 303
                                333333345677888888999999999999999999988875 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.026
                     Cnn_1N  36 eqkeellkenielkveveslqkelkekkkllre 68 
                                e+ e++ +e+  l +eve l+k+  e++  l++
  gene35|gene35|rna35|rna35 330 EELEKAKRERNSLMEEVEGLKKKCLECTSDLER 362
                                455566666666666666666666666555544 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.13
                     Cnn_1N  36 eqkeellkenielkveveslqkelk 60 
                                e++ +++++ i+l  ++   +++++
  gene35|gene35|rna35|rna35 389 EKMADTIDSKIDLARKMLGERRSVD 413
                                4555555555555544444444433 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 0.097
                     Cnn_1N  39 eellkenielkveveslqkelkekkk 64 
                                e+  ken elk  +  l+k+ +e++k
  gene35|gene35|rna35|rna35 530 EKKGKENKELKASNLVLEKKFNECRK 555
                                55568999999999999999999988 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.4   2.3e-06     0.014      22      44 ..      18      40 ..      11      41 .. 0.83
   2 ?   -1.6   0.4      0.42   2.5e+03      28      37 ..     110     119 ..     105     128 .. 0.61
   3 ?   -1.0   0.9      0.28   1.7e+03      19      34 ..     276     291 ..     270     301 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                Shugoshin_N 22 kirelekevseLlsENlnLReli 44
                               +++++eke++eL++EN +++ ++
  gene35|gene35|rna35|rna35 18 TVKDYEKEIEELRNENFEIKHQL 40
                               499**************999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.42
                Shugoshin_N  28 kevseLlsEN 37 
                                +++s L  EN
  gene35|gene35|rna35|rna35 110 NKISMLEEEN 119
                                5555555555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.28
                Shugoshin_N  19 lslkirelekevseLl 34 
                                l l+  el+ ev++L+
  gene35|gene35|rna35|rna35 276 LALRNEELRREVEQLK 291
                                3444445555555554 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2     0.067     4e+02      38      56 ..      74      92 ..      49     104 .. 0.54
   2 ?    5.5   0.0    0.0041        24      12      54 ..     104     146 ..      99     165 .. 0.85
   3 ?   -1.4   0.0      0.55   3.3e+03      16      35 ..     206     225 ..     203     243 .. 0.73
   4 ?   -1.1   0.1      0.47   2.8e+03      25      58 ..     285     315 ..     274     351 .. 0.61
   5 ?   -2.6   0.0       1.3     8e+03      42      63 ..     383     404 ..     372     410 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.067
                    NPV_P10 38 telnekLdaqsaqLaelet 56
                               +eln++++++++ + ++ t
  gene35|gene35|rna35|rna35 74 EELNKQMERMNEMVRKIRT 92
                               3444444444444444444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0041
                    NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLael 54 
                                d ++  +k++ l+++  ++ + l++v+ +n+kL + ++ L e 
  gene35|gene35|rna35|rna35 104 DLQEYLNKISMLEEENGRLLKHLENVNGINAKLREENEVLGEC 146
                                67777899**************************999999875 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.55
                    NPV_P10  16 vddkVdalqqqvddvqenlp 35 
                                 ++k++ lq  v + +e+++
  gene35|gene35|rna35|rna35 206 YSNKISQLQGIVGSFEEKMN 225
                                67899999999988777654 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.47
                    NPV_P10  25 qqvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                 +v+++++   d   l+++L+   ++  +l+ kv
  gene35|gene35|rna35|rna35 285 REVEQLKTSRSD---LKKRLEVCENEKRALSYKV 315
                                555555555555...4455554444444444443 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 1.3
                    NPV_P10  42 ekLdaqsaqLaeletkvenIqd 63 
                                 +L ++ +  +++++k++   +
  gene35|gene35|rna35|rna35 383 RRLGEIEKMADTIDSKIDLARK 404
                                4455555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3065  (0.170952); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); expected 17.9 (0.001)
Passed Fwd filter:                        71  (0.00396006); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.93u 0.43s 00:00:02.36 Elapsed: 00:00:00.76
# Mc/sec: 2354.36
//
Query:       gene350|gene350|rna350|rna350  [L=1115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.86u 0.35s 00:00:01.21 Elapsed: 00:00:00.58
# Mc/sec: 5822.96
//
Query:       gene351|gene351|rna351|rna351  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.4e-20   69.9  60.6    3.3e-05   24.1   1.7    7.0  7  zf-C2H2       Zinc finger, C2H2 type
    1.2e-12   47.5  65.2     0.0046   17.7   1.8    6.9  7  zf-C2H2_4     C2H2-type zinc finger
    0.00034   20.9   1.7    0.00034   20.9   1.7    7.2  6  zf-H2C2_2     Zinc-finger double domain
     0.0012   17.9   0.9     0.0015   17.5   0.9    1.2  1  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0032   17.5   3.3     0.0032   17.5   3.3    4.7  5  zf-BED        BED zinc finger
  ------ inclusion threshold ------
        0.3   11.4   8.5        5.9    7.2   8.3    2.3  2  FpoO          F420H2 dehydrogenase subunit FpoO
        3.7    7.6   9.7        9.2    6.4   0.1    3.7  3  YyzF          YyzF-like protein
        6.1    6.4  13.7         13    5.3   0.9    4.5  4  zf-ribbon_3   zinc-ribbon domain
        6.4    7.3  36.3        5.6    7.5   0.3    6.4  7  zf-met        Zinc-finger of C2H2 type


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.49   9.7e+02       1       9 [.       6      14 ..       6      16 .. 0.85
   2 !   24.1   2.3   1.7e-08   3.4e-05       1      23 []      17      41 ..      17      41 .. 0.99
   3 !   18.1   4.5   1.3e-06    0.0026       1      23 []      47      69 ..      47      69 .. 0.99
   4 !   13.5   3.8   3.9e-05     0.078       1      22 [.      74      95 ..      74      95 .. 0.96
   5 !   17.2   2.6   2.7e-06    0.0053       1      23 []      99     121 ..      99     122 .. 0.95
   6 !   24.1   1.7   1.7e-08   3.3e-05       1      23 []     133     156 ..     133     156 .. 0.97
   7 !    6.3   2.2    0.0075        15       6      22 ..     166     182 ..     162     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.49
                                   EEETTTTEE CS
                        zf-C2H2  1 ykCpdCgks 9 
                                   + C+ C++s
  gene351|gene351|rna351|rna351  6 FFCSNCPWS 14
                                   77****976 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.7e-08
                                   EEET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2  1 ykCp..dCgksFkrksnLkrHirtH 23
                                   ++C+  +C ksF+r+s L+ H++tH
  gene351|gene351|rna351|rna351 17 FQCHfeGCEKSFPRRSKLNDHLNTH 41
                                   89**********************9 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.3e-06
                                   EEETTTTEEESSHHHHHHHHHCC CS
                        zf-C2H2  1 ykCpdCgksFkrksnLkrHirtH 23
                                   ykC+ C ks+  +s+L +H +tH
  gene351|gene351|rna351|rna351 47 YKCDMCEKSYMKNSHLSVHKKTH 69
                                   9*********************9 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 3.9e-05
                                   EEETTTTEEESSHHHHHHHHHC CS
                        zf-C2H2  1 ykCpdCgksFkrksnLkrHirt 22
                                   ++Cp Cg+++ +++ L +H++t
  gene351|gene351|rna351|rna351 74 FECPRCGRMCHTRDKLSKHQKT 95
                                   89*****************986 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 2.7e-06
                                    EEETTTTEEESSHHHHHHHHHCC CS
                        zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                                    ykC+ Cgk++k ks + +H  +H
  gene351|gene351|rna351|rna351  99 YKCDTCGKKYKKKSWFDAHVESH 121
                                    9*******************995 PP

  == domain 6  score: 24.1 bits;  conditional E-value: 1.7e-08
                                    EEETTTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                                    ++C++C+  F+rk nL +Hir+ H
  gene351|gene351|rna351|rna351 133 HVCEYCKFEFSRKGNLLTHIRSvH 156
                                    79*******************999 PP

  == domain 7  score: 6.3 bits;  conditional E-value: 0.0075
                                    TTEEESSHHHHHHHHHC CS
                        zf-C2H2   6 CgksFkrksnLkrHirt 22 
                                    Cgk + ++ +L +H ++
  gene351|gene351|rna351|rna351 166 CGKEYAHNTSLHSHKKR 182
                                    **************875 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.5       1.7   3.5e+03       1       8 [.       6      13 ..       6      16 .. 0.72
   2 !   16.0   1.7   8.2e-06     0.016       1      23 [.      17      41 ..      17      42 .. 0.96
   3 !   15.6   3.7   1.1e-05     0.021       1      23 [.      47      69 ..      47      70 .. 0.96
   4 !   13.5   5.0   5.1e-05       0.1       1      22 [.      74      95 ..      74      97 .. 0.95
   5 !   16.9   2.7     4e-06     0.008       1      24 []      99     122 ..      99     122 .. 0.96
   6 !   17.7   1.8   2.3e-06    0.0046       1      24 []     133     156 ..     133     156 .. 0.95
   7 ?    3.6   4.9     0.079   1.6e+02       1      22 [.     162     182 ..     162     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.7
                      zf-C2H2_4  1 fkCpiCgk 8 
                                   f C+ C+ 
  gene351|gene351|rna351|rna351  6 FFCSNCPW 13
                                   67999954 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.2e-06
                      zf-C2H2_4  1 fkCpi..CgksFsskkaLlrHlkth 23
                                   f+C++  C ksF+++++L++Hl+th
  gene351|gene351|rna351|rna351 17 FQCHFegCEKSFPRRSKLNDHLNTH 41
                                   89**********************9 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 1.1e-05
                      zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkth 23
                                   +kC+ C ks+  +++L+ H kth
  gene351|gene351|rna351|rna351 47 YKCDMCEKSYMKNSHLSVHKKTH 69
                                   8*********************9 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 5.1e-05
                      zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkt 22
                                   f+Cp Cg+ ++++++L++H kt
  gene351|gene351|rna351|rna351 74 FECPRCGRMCHTRDKLSKHQKT 95
                                   89*****************997 PP

  == domain 5  score: 16.9 bits;  conditional E-value: 4e-06
                      zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                    +kC+ Cgk ++ k+ +  H+++hH
  gene351|gene351|rna351|rna351  99 YKCDTCGKKYKKKSWFDAHVESHH 122
                                    89********99999999****** PP

  == domain 6  score: 17.7 bits;  conditional E-value: 2.3e-06
                      zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkthH 24 
                                    + C++C+  Fs+k +Ll+H++++H
  gene351|gene351|rna351|rna351 133 HVCEYCKFEFSRKGNLLTHIRSVH 156
                                    58*********************9 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.079
                      zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkt 22 
                                    fkC +Cgk +  +++L +H k+
  gene351|gene351|rna351|rna351 162 FKC-LCGKEYAHNTSLHSHKKR 182
                                    788.9**************986 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.9   6.3         9   1.8e+04      15      24 ..      17      28 ..       4      30 .. 0.59
   2 !   20.9   1.7   1.7e-07   0.00034       2      24 ..      34      56 ..      33      56 .. 0.95
   3 !    7.1   5.6    0.0041       8.2       1      22 [.      61      81 ..      59      85 .. 0.70
   4 ?    3.5   9.4     0.053   1.1e+02      13      26 .]      88     110 ..      81     110 .. 0.68
   5 !    7.3   2.5    0.0034       6.8       4      25 ..     116     143 ..     114     144 .. 0.70
   6 !    5.9   1.3    0.0096        19       1      24 [.     147     170 ..     147     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 9
                      zf-H2C2_2 15 yeCp..lCdkaF 24
                                   ++C    C k+F
  gene351|gene351|rna351|rna351 17 FQCHfeGCEKSF 28
                                   556643366666 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.7e-07
                      zf-H2C2_2  2 LrrHirkHtgekpyeCplCdkaF 24
                                   L+ H+ +Ht+ +py+C+ C k++
  gene351|gene351|rna351|rna351 34 LNDHLNTHTKNRPYKCDMCEKSY 56
                                   899******************97 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0041
                      zf-H2C2_2  1 nLrrHirkHtgekpyeCplCdk 22
                                   +L+ H ++H ++ ++eCp C+ 
  gene351|gene351|rna351|rna351 61 HLSVHKKTHFPP-EFECPRCGR 81
                                   456666666665.3******86 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.053
                      zf-H2C2_2  13 k.........pyeCplCdkaFkt 26 
                                    k         +y+C+ C+k++k+
  gene351|gene351|rna351|rna351  88 KlskhqktclEYKCDTCGKKYKK 110
                                    33333334667**********96 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.0034
                      zf-H2C2_2   4 rHirkHtge.k.....pyeCplCdkaFk 25 
                                     H  +H+++ +     ++ C++C+  F+
  gene351|gene351|rna351|rna351 116 AHVESHHVKiFnvrklRHVCEYCKFEFS 143
                                    578888855334444459******9997 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.0096
                      zf-H2C2_2   1 nLrrHirk.HtgekpyeCplCdkaF 24 
                                    nL  Hir+ H   kp++C lC+k +
  gene351|gene351|rna351|rna351 147 NLLTHIRSvHFLVKPFKC-LCGKEY 170
                                    6888***659988*****.666666 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.9   7.7e-07    0.0015     164     210 ..      63     109 ..      22     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.7e-07
                   tRNA-synt_1f 164 eereetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeee 210
                                    +  ++t +p +  c++cgr+ +t+ +  +++++ +eYkc+ cG++ +
  gene351|gene351|rna351|rna351  63 SVHKKTHFPPEFECPRCGRMCHTRDKLSKHQKTCLEYKCDTCGKKYK 109
                                    3367889999**************9999999************9876 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.8   1.6e+03      22      41 ..      24      40 ..      19      45 .. 0.75
   2 ?   -0.5   3.6      0.65   1.3e+03      13      29 ..      43      59 ..      28      70 .. 0.73
   3 ?    1.8   3.5      0.12   2.4e+02      18      42 ..     100     121 ..      87     123 .. 0.78
   4 !   17.5   3.3   1.6e-06    0.0032       6      43 ..     122     156 ..     120     157 .. 0.92
   5 ?   -2.3   2.6       2.3   4.7e+03      21      34 ..     165     175 ..     163     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.8
                                   TTEE----SSTHHHHHHHHH CS
                         zf-BED 22 CgkilsrgggttnLkrHLrr 41
                                   C+k + r+   + L  HL++
  gene351|gene351|rna351|rna351 24 CEKSFPRR---SKLNDHLNT 40
                                   77777777...777777754 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.65
                                   GSS--EETTTTEE---- CS
                         zf-BED 13 keqkavCryCgkilsrg 29
                                   k+   +C  C+k +  +
  gene351|gene351|rna351|rna351 43 KNRPYKCDMCEKSYMKN 59
                                   555578******99876 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                                    EETTTTEE----SSTHHHHHHHHHS CS
                         zf-BED  18 vCryCgkilsrgggttnLkrHLrrk 42 
                                    +C  Cgk+++ +   + + +H ++ 
  gene351|gene351|rna351|rna351 100 KCDTCGKKYKKK---SWFDAHVESH 121
                                    8*********98...5566665555 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 1.6e-06
                                    SS----GGSS--EETTTTEE----SSTHHHHHHHHHS- CS
                         zf-BED   6 yftpvslkeqkavCryCgkilsrgggttnLkrHLrrkH 43 
                                    ++++ + ++ + vC yC++++sr+    nL +H+r+ H
  gene351|gene351|rna351|rna351 122 HVKIFNVRKLRHVCEYCKFEFSRK---GNLLTHIRSVH 156
                                    88888889999*************...8*******999 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 2.3
                                    TTTEE----SSTHH CS
                         zf-BED  21 yCgkilsrgggttn 34 
                                     Cgk+++ +   t 
  gene351|gene351|rna351|rna351 165 LCGKEYAHN---TS 175
                                    599999986...33 PP

>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.11   2.1e+02      49      69 ..      35      55 ..      16      70 .. 0.71
   2 ?    7.2   8.3     0.003       5.9      37      98 ..      76     139 ..      49     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                           FpoO 49 delskeeasgtaGkcdlcgkk 69
                                   +++ +++++ +  kcd+c k 
  gene351|gene351|rna351|rna351 35 NDHLNTHTKNRPYKCDMCEKS 55
                                   445556677788899999764 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.003
                           FpoO  37 cekclkaakktydelskeeasgtaGkcdlcgkktr...lydvevqvPsfskgsekktaklckrcl 98 
                                    c++c     +t d+lsk+++++ + kcd cgkk +    +d +v+    +   ++k +++c+ c 
  gene351|gene351|rna351|rna351  76 CPRCGRM-CHTRDKLSKHQKTCLEYKCDTCGKKYKkksWFDAHVESHHVKIFNVRKLRHVCEYCK 139
                                    5666443.46899******************875422279999*9999999999*******9996 PP

>> YyzF  YyzF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0046       9.2      28      41 ..      41      54 ..      26      56 .. 0.77
   2 ?    0.8   1.4      0.25   4.9e+02      30      42 ..      93     107 ..      86     109 .. 0.69
   3 ?    3.7   0.1     0.032        63      25      40 ..     124     139 ..     121     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0046
                           YyzF 28 eveklsktCefCek 41
                                   ++++ + +C++Cek
  gene351|gene351|rna351|rna351 41 HTKNRPYKCDMCEK 54
                                   4458899*****97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.25
                           YyzF  30 e..klsktCefCekp 42 
                                    +   l+ +C+ C k+
  gene351|gene351|rna351|rna351  93 QktCLEYKCDTCGKK 107
                                    33347899****875 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.032
                           YyzF  25 kleeveklsktCefCe 40 
                                    k+ +v kl + Ce+C+
  gene351|gene351|rna351|rna351 124 KIFNVRKLRHVCEYCK 139
                                    5667778999*****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4       0.1     2e+02       4       8 ..       7      11 ..       4      14 .. 0.78
   2 ?    5.3   0.9    0.0067        13       2       9 ..      73      80 ..      72      87 .. 0.87
   3 ?    4.5   0.2     0.012        25       2      10 ..      98     106 ..      97     111 .. 0.82
   4 ?    1.0   0.0      0.15     3e+02      18      24 ..     134     140 ..     127     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.1
                    zf-ribbon_3  4 rCPnC 8 
                                   +C+nC
  gene351|gene351|rna351|rna351  7 FCSNC 11
                                   78888 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0067
                    zf-ribbon_3  2 tvrCPnCG 9 
                                   + +CP+CG
  gene351|gene351|rna351|rna351 73 EFECPRCG 80
                                   679****9 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.012
                    zf-ribbon_3   2 tvrCPnCGa 10 
                                    +++C  CG+
  gene351|gene351|rna351|rna351  98 EYKCDTCGK 106
                                    689999998 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.15
                    zf-ribbon_3  18 vCpyCGt 24 
                                    vC yC  
  gene351|gene351|rna351|rna351 134 VCEYCKF 140
                                    8****76 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   5.6e+03      15      22 ..      16      23 ..      15      23 .. 0.78
   2 ?    6.0   0.0    0.0085        17       6      22 ..      24      40 ..      22      42 .. 0.91
   3 ?    6.1   3.5    0.0076        15       1      20 [.      47      66 ..      47      69 .. 0.89
   4 ?   -0.6   0.3         1     2e+03       1      10 [.      74      83 ..      74      87 .. 0.86
   5 ?    6.5   1.4    0.0059        12       1      23 [.      99     121 ..      99     121 .. 0.91
   6 ?    7.5   0.3    0.0028       5.6       3      22 ..     135     154 ..     133     155 .. 0.93
   7 ?    1.6   1.4       0.2   4.1e+02       5      20 ..     165     180 ..     164     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                         zf-met 15 qlksHlqG 22
                                   ++++H+ G
  gene351|gene351|rna351|rna351 16 TFQCHFEG 23
                                   68999876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0085
                         zf-met  6 CnvtfnsesqlksHlqG 22
                                   C ++f  +s l++Hl+ 
  gene351|gene351|rna351|rna351 24 CEKSFPRRSKLNDHLNT 40
                                   ***************96 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0076
                         zf-met  1 fyCelCnvtfnsesqlksHl 20
                                   + C++C +++   s+l  H 
  gene351|gene351|rna351|rna351 47 YKCDMCEKSYMKNSHLSVHK 66
                                   78**************9996 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1
                         zf-met  1 fyCelCnvtf 10
                                   f+C+ C +++
  gene351|gene351|rna351|rna351 74 FECPRCGRMC 83
                                   78*9998877 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.0059
                         zf-met   1 fyCelCnvtfnsesqlksHlqGK 23 
                                    + C+ C ++++ +s +++H  ++
  gene351|gene351|rna351|rna351  99 YKCDTCGKKYKKKSWFDAHVESH 121
                                    78***********9999998885 PP

  == domain 6  score: 7.5 bits;  conditional E-value: 0.0028
                         zf-met   3 CelCnvtfnsesqlksHlqG 22 
                                    Ce C+  f+ +++l +H ++
  gene351|gene351|rna351|rna351 135 CEYCKFEFSRKGNLLTHIRS 154
                                    999**************998 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.2
                         zf-met   5 lCnvtfnsesqlksHl 20 
                                    lC + + + ++l sH 
  gene351|gene351|rna351|rna351 165 LCGKEYAHNTSLHSHK 180
                                    8**************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1045  (0.0582855); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 978.96
//
Query:       gene352|gene352|rna352|rna352  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   47.4   0.1    2.1e-12   47.3   0.1    1.1  1  Urm1      Urm1 (Ubiquitin related modifier)


Domain annotation for each model (and alignments):
>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   1.1e-16   2.1e-12       5      96 .]       4      96 .]       1      96 [] 0.83

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.1e-16
                                   EEETTCGGGCTT-SEEEEEE-SSSSS.-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTE CS
                           Urm1  5 eflgGlelllekkkkhkveleiesee.vnleeliayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkD 85
                                   +f g  ++ l++k+ +  + e+e  + ++ ee ++y+ +++++ r++ F +++++  G +++in +Dwe++g+++  +k +D
  gene352|gene352|rna352|rna352  4 KFNGASNVELNNKEIELTKEEMEGLPiTTAEEALKYLFDRHMEVRDSYFDSHGELVYGTICIINKMDWEITGKEKSPVKYGD 85
                                   666666666666555544444444441467899************************************************* PP

                                   EEEEEETTT-- CS
                           Urm1 86 kivFistlhGG 96
                                   + v ist+hGG
  gene352|gene352|rna352|rna352 86 HAVLISTIHGG 96
                                   **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 555.89
//
Query:       gene353|gene353|rna353|rna353  [L=129]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-06   27.4   0.0    3.2e-06   27.3   0.0    1.1  1  Sedlin_N  Sedlin, N-terminal conserved region


Domain annotation for each model (and alignments):
>> Sedlin_N  Sedlin, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.8e-10   3.2e-06       1     104 [.       7      99 ..       7     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.8e-10
                       Sedlin_N   1 iigkkdnplyelefssskekeekelkeL.nqfilhasLDivedlqwktnnlylgkvdkfeklsvsayvtnskikflllhe 79 
                                    ii++k+  +y+  +s+++++e     +  +  +++ s+Di+  ++ +t++ y   ++k  ++ +say+ +s+ k+l +h+
  gene353|gene353|rna353|rna353   7 IISEKNDIVYQRMYSRASNEE-----YCrLIILIYGSIDILIWKMASTSSNYFDCLEKHGEMRISAYIMPSGYKLLFIHT 81 
                                    899999999999998888775.....44355788********************************************** PP

                       Sedlin_N  80 sssskkkdekikqffqevhelyvkt 104
                                            ++++ f++ +h ++  +
  gene353|gene353|rna353|rna353  82 -------RKDVRPFLEGIHRMFAPV 99 
                                    .......555666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 860.19
//
Query:       gene354|gene354|rna354|rna354  [L=439]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-69  232.0   0.0    1.3e-68  231.1   0.0    1.4  1  Tubulin          Tubulin/FtsZ family, GTPase domain
      3e-42  143.8   0.2    4.8e-42  143.1   0.2    1.3  1  Tubulin_C        Tubulin C-terminal domain
    1.4e-05   25.4   0.0    2.8e-05   24.4   0.0    1.5  1  Misat_Tub_SegII  Misato Segment II tubulin-like domain
  ------ inclusion threshold ------
      0.093   12.4   0.0       0.18   11.4   0.0    1.5  1  Tubulin_3        Tubulin domain
       0.12   11.5   0.0       0.22   10.7   0.0    1.3  1  Tubulin_2        Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.1   0.0   3.6e-72   1.3e-68       1     196 [.       3     211 ..       3     212 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 3.6e-72
                                    EEEEEEEHHHHHHHHHHHHH...HHHCH..............HHHT.....TTEEEEE....EEESBHHHHHTS-GS... CS
                        Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdg..........dslesfFsesgkveyiprsvaidtdpqvlneikags.. 68 
                                    eii+++ GqcGnq+g+++we++  ehgi+++g          ++++ +++e ++++y+pr+v+id++p +++++++g+  
  gene354|gene354|rna354|rna354   3 EIIHLQTGQCGNQVGCKFWETISGEHGIDQTGryvgtsdnqlERVNIYYNEASSKKYVPRAVLIDLEPGTMDAVRQGPfg 82 
                                    79**************************98889*********************************************** PP

                                    .....EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTS CS
                        Tubulin  69 elfnpnklllgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypka 148
                                    +lf+p+++++g++gagnn+a+g+++ g+e+++++++ +rke+e++d+lqgf+it+slgGGTG G+g+++l++++e++p++
  gene354|gene354|rna354|rna354  83 DLFRPDNFVFGQSGAGNNWAKGHYTEGAELIDSVMDVVRKEAESSDCLQGFQITHSLGGGTGAGMGTLLLSKIREDFPDR 162
                                    ******************************************************************************** PP

                                    EEEEEEEE--.GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                        Tubulin 149 lvvtvvvlPs.efsevvvepynailalkelieesdavividNdaLlkil 196
                                    +++t++v+Ps + s+ vvepyna l++++l+e++d +++idN+aL++i+
  gene354|gene354|rna354|rna354 163 MICTFSVVPSpKVSDTVVEPYNATLSIHQLVENADETFCIDNEALYDIC 211
                                    ************************************************8 PP

>> Tubulin_C  Tubulin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.1   0.2   1.3e-45   4.8e-42       1     125 [.     261     382 ..     261     383 .. 0.99

  Alignments for each domain:
  == domain 1  score: 143.1 bits;  conditional E-value: 1.3e-45
                                    TTC-EEEEEEESSSCTTTTTCS-HHHHHHHHHTCSGGGBSSSTSTTTSSEEEEEEEEEESSSHHHHHHHHHHHHHTTTS- CS
                      Tubulin_C   1 PrlhFlltsyaPlvsaekaavektsvqdvtrallepknimvkvdprkgkylaiallirGdvepkevnkavqrikekkkaq 80 
                                    PrlhF+++++aPl++  ++++++ sv+++t++++++kn+m ++dprkg+yl++ +++rG++++k+v+++++ +++k+++ 
  gene354|gene354|rna354|rna354 261 PRLHFFVVGFAPLIAIGTQKFKTYSVSELTQQMFDSKNMMTACDPRKGRYLTVTAIFRGKISMKDVDEQMSMVQSKNSSL 340
                                    9******************************************************************************* PP

                                    BSTTSTTTEEEEEEECECT-TTTSSCEEEEEEEEGGGHHHHHHHH CS
                      Tubulin_C  81 fveWiptgikvalnkkspyvkkqskvsvlmlaNttsiaelfkrll 125
                                    fveWip+++k+a+++ +p++ ++s   +++++Nttsi+elfkr++
  gene354|gene354|rna354|rna354 341 FVEWIPSNVKTAVCDIAPTGLEMS---ATFVGNTTSIQELFKRIS 382
                                    **********************99...****************96 PP

>> Misat_Tub_SegII  Misato Segment II tubulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   7.8e-09   2.8e-05       1      68 [.       2      71 ..       2      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 7.8e-09
                Misat_Tub_SegII  1 rEivtlqlGnyaNyvgtHfWNtQesyftydeeeeesevdhdvlfreget..kqgqvtytPRllivDlkgs 68
                                   rEi+ lq G+  N vg  fW t       d++  +    ++ l r ++   +  + +y+PR++++Dl+ +
  gene354|gene354|rna354|rna354  2 REIIHLQTGQCGNQVGCKFWETISGEHGIDQTGRYVGTSDNQLERVNIYynEASSKKYVPRAVLIDLEPG 71
                                   8*********************98888777777763343334444433322678999*********9854 PP

>> Tubulin_3  Tubulin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.1e-05      0.18      64     144 ..     120     194 ..     102     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.1e-05
                      Tubulin_3  64 lrpfaeecdqlrglqvftgvddaWG.GfaakylerlrdeygkksilvWvlaleeklkkkkkaklerklkklnkarslkel 142
                                    +r+ ae +d l+g+q+  +     G G ++  l ++r++++ + i+++ +  + k+++         ++  n + s+++l
  gene354|gene354|rna354|rna354 120 VRKEAESSDCLQGFQITHSLGGGTGaGMGTLLLSKIREDFPDRMICTFSVVPSPKVSD-------TVVEPYNATLSIHQL 192
                                    68999**************99877769****************998886543322222.......223344555555555 PP

                      Tubulin_3 143 se 144
                                     e
  gene354|gene354|rna354|rna354 193 VE 194
                                    55 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.1e-05      0.22     137     202 ..     111     175 ..      98     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.1e-05
                      Tubulin_2 137 ealrdaikrlrgsage.eeglnvfVvgSLaGGTGSGiflDvayllrkilkeekqkvkiiglvllPdv 202
                                    e ++++++ +r++a++ + +  + +  SL GGTG+G+   ++  +r+ +++      ++ +v++P+v
  gene354|gene354|rna354|rna354 111 ELIDSVMDVVRKEAESsDCLQGFQITHSLGGGTGAGMGTLLLSKIREDFPDRMI--CTFSVVPSPKV 175
                                    566677777777655544446678999**********99999999988888775..46666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2844.74
//
Query:       gene355|gene355|rna355|rna355  [L=233]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-43  148.2   8.5    4.8e-34  117.6   2.1    2.1  2  DUF5092   Domain of unknown function (DUF5092)
     0.0062   16.3   0.1       0.01   15.6   0.1    1.3  1  DUF4118   Domain of unknown function (DUF4118)
      0.007   16.4   0.3      0.016   15.3   0.3    1.5  1  DUF3671   Protein of unknown function


Domain annotation for each model (and alignments):
>> DUF5092  Domain of unknown function (DUF5092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   2.1     8e-38   4.8e-34       1      91 [.      45     135 ..      45     137 .. 0.98
   2 !   35.5   0.5   1.4e-12   8.5e-09     126     163 .]     136     176 ..     134     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 8e-38
                        DUF5092   1 vEtftleefrklilesrkkkkdfilArVttkdpedqsslynvyYdAeelnkvlFevvieserrllhrkkvkdPlnnmkIk 80 
                                    vE+ft+++f+++i e++ k++d++lArV+++ + ++ ++++++YdA++l+k++Fe+vi++e+r++++k++kdP+n+++I+
  gene355|gene355|rna355|rna355  45 VEPFTQKQFADMIKEAHAKSQDYYLARVQCRSNPEDGKNIYYCYDARQLCKYIFEMVISTEGRKIRIKNFKDPINQEQIH 124
                                    59*****************************9999999****************************************** PP

                        DUF5092  81 qvyyYkltvee 91 
                                    +++++kl++++
  gene355|gene355|rna355|rna355 125 EISFFKLRYDS 135
                                    *********97 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 1.4e-12
                        DUF5092 126 klilkaeyfasdddFLeksevre..yfkenaldad.dnFlF 163
                                    +++lkaey++++ +FLe++++r+  +++enalda+ +nF+F
  gene355|gene355|rna355|rna355 136 DTPLKAEYVGNQVNFLENNCFRSkiFYQENALDALsVNFQF 176
                                    689*************************************9 PP

>> DUF4118  Domain of unknown function (DUF4118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.7e-06      0.01      53     101 ..     167     215 ..     165     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                        DUF4118  53 lsvllfnyfftpPyftltiadpeylltlvvflvvallvstlvararrqa 101
                                    l +l +n+ f p   ++ i +++ l+t++++++  ++++tlva +++++
  gene355|gene355|rna355|rna355 167 LDALSVNFQFGPQKKKIPIINRRKLFTVFMMVILVFVIGTLVAMVAERE 215
                                    6789****************************************98876 PP

>> DUF3671  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3   2.6e-06     0.016      14      68 ..     159     215 ..     151     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-06
                        DUF3671  14 kiFdkidkidelakkkn..ndkkkfkkkvlkkyglllilpvllpliglivpilfeak 68 
                                    kiF++ + +d l+ +++   +kkk++ +  +k + ++++++l+++ig++v++++e +
  gene355|gene355|rna355|rna355 159 KIFYQENALDALSVNFQfgPQKKKIPIINRRKLFTVFMMVILVFVIGTLVAMVAERE 215
                                    8999999999999887733589****************************9997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1526.16
//
Query:       gene356|gene356|rna356|rna356  [L=87]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-16   57.8   0.0    7.7e-16   57.5   0.0    1.1  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.043   14.0   0.0    1.1  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   8.6e-20   7.7e-16       2      66 ..       9      71 ..       8      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 8.6e-20
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                   +l++ ++ +vt+e+ ng  +rG++k++D++mN+vL++v++t+ +  +    ++ +iRG++i++ +
  gene356|gene356|rna356|rna356  9 LLHEAQGFIVTIETSNGDMYRGRMKEIDDYMNVVLDEVTVTSFG--SCSPRKEAIIRGSSIRFFV 71
                                   7999**************************************99..69999***********976 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.8e-06     0.043       7      51 ..       9      51 ..       7      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.8e-06
                                   HHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                         SM-ATX  7 lltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                   ll    G  v+++++nG+ y+G  + ++    ++vvL+ + +++ 
  gene356|gene356|rna356|rna356  9 LLHEAQGFIVTIETSNGDMYRGRMKEIDD--YMNVVLDEVTVTSF 51
                                   566677888********************..******99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 588.77
//
Query:       gene357|gene357|rna357|rna357  [L=532]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.082   12.6   1.6       0.14   11.8   1.6    1.3  1  Amidoligase_2  Putative amidoligase enzyme


Domain annotation for each model (and alignments):
>> Amidoligase_2  Putative amidoligase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.6   7.7e-06      0.14     147     203 ..     353     403 ..     348     424 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.7e-06
                  Amidoligase_2 147 klldvdlarrlnpyckpldeeyvervrleasksatldeliddylkrnptrnraldll 203
                                    k+ +++  r+  ++c++++++y+++ + +  + ++ + ++d+++   ++rn++  + 
  gene357|gene357|rna357|rna357 353 KEEPIHQ-RKSVRFCDRFTPRYKKMKIYSRYYMENTKGVQDCWY---EKRNED--MK 403
                                    5667885.*****************999999*************...666666..32 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1108  (0.0617993); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3311.39
//
Query:       gene358|gene358|rna358|rna358  [L=118]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 745.82
//
Query:       gene359|gene359|rna359|rna359  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   13.5   0.2       0.16   11.7   0.0    2.0  2  DUF4525   Domain of unknown function (DUF4525)
      0.081   12.9   0.0       0.29   11.2   0.0    1.9  2  SNARE     SNARE domain


Domain annotation for each model (and alignments):
>> DUF4525  Domain of unknown function (DUF4525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.23   2.1e+03      77      99 ..      83     105 ..      59     113 .. 0.71
   2 ?   11.7   0.0   1.8e-05      0.16      55     119 ..     129     193 ..     119     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.23
                        DUF4525  77 yadlkrtiavllddilqrlvkle 99 
                                    +  +kr i + l  i +rl  l+
  gene359|gene359|rna359|rna359  83 FEGIKRIILMKLQGIERRLRALK 105
                                    55678888888888888887775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.8e-05
                        DUF4525  55 vkalaeenknvmdgengaslagyadlkrt...iavllddilqrlvklenkvdylvvngsaanttnstt 119
                                    v+ + eenk++++g n   + gy   +r    +  l d i+q l   ++++d+++   s a t  s +
  gene359|gene359|rna359|rna359 129 VQVMEEENKKLVEGYN---MEGYRLTRRRlleVEALQDTIFQHLILQDERIDNIIDLTSKAGTYVSGG 193
                                    78899*******9876...889955554422245699****************986666655544443 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.41   3.7e+03       4      18 ..      28      42 ..      28      43 .. 0.86
   2 ?   11.2   0.0   3.2e-05      0.29       3      52 ..     176     225 ..     174     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.41
                                   HHHHHHHHHHHHHHH CS
                          SNARE  4 DrIdtnVenaqsnve 18
                                   D+I +++e ++ +++
  gene359|gene359|rna359|rna359 28 DTINSKIEKIEARLR 42
                                   899999999999886 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTXXXXXXXXXXXXXXXXXXX CS
                          SNARE   3 vDrIdtnVenaqsnveraqkeLkkavkyqksnRklkciillilviillvv 52 
                                    +D+I +    a ++v+++++ L +  ++ +  R++++i+ll+l ++ll++
  gene359|gene359|rna359|rna359 176 IDNIIDLTSKAGTYVSGGNEALGRITNSGRFFRRFLFILLLCLSFVLLFL 225
                                    6666677777889**********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1422.72
//
Query:       gene36|gene36|rna36|rna36  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-10   38.7   0.0    2.4e-09   37.2   0.0    1.8  1  DnaJ         DnaJ domain
    2.8e-07   30.6  15.8    9.9e-06   25.7   7.8    3.0  3  zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
    1.7e-05   25.2   7.8       0.06   14.2   3.0    2.9  2  zf-C2H2_4    C2H2-type zinc finger
    2.3e-05   24.6  11.6      0.048   14.1   0.1    2.6  2  zf-met       Zinc-finger of C2H2 type
    0.00037   20.4   4.8      0.081   12.9   0.3    2.6  2  zf-C2H2_6    C2H2-type zinc finger
      0.003   17.9   5.3      0.055   13.8   1.5    2.8  2  zf-C2H2_2    C2H2 type zinc-finger (2 copies)
      0.004   17.5  10.4      0.042   14.3   0.1    2.9  2  zf-C2H2      Zinc finger, C2H2 type
  ------ inclusion threshold ------
       0.11   12.6   5.5       0.47   10.5   1.6    2.4  2  Mut7-C       Mut7-C RNAse domain
       0.12   12.0   1.2        6.7    6.4   0.0    2.5  2  zf_UBZ       Ubiquitin-Binding Zinc Finger
          1    9.9   6.4        2.9    8.5   1.6    3.1  2  zf-H2C2_2    Zinc-finger double domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.3e-12   2.4e-09       2      52 ..      12      63 ..      11      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.3e-12
                               HHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHH.HHHHHHHHHHHHHHH CS
                       DnaJ  2 yYeiLgvskdasedeIkkaYrklalkyHPDknpkdp.eaeekFkeineAyev 52
                               ++e+Lg+s+ ++++e+k  Yr+l+lk+HPD ++ ++ +a ++  ei eAy  
  gene36|gene36|rna36|rna36 12 PHEVLGLSPVSTKKEVKDCYRTLILKVHPDAQKVHSsKAPKEAMEIMEAYTS 63
                               579***************************77666669999999*****975 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.8   6.9e+03      11      18 ..     121     128 ..     120     131 .. 0.68
   2 !   25.7   7.8   5.5e-09   9.9e-06       2      26 ..     180     204 ..     179     205 .. 0.97
   3 !    9.5   0.1   0.00067       1.2       4      22 ..     273     291 ..     272     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.8
                                BSSHHHHH CS
                zf-C2H2_jaz  11 Fksenald 18 
                                F +++++d
  gene36|gene36|rna36|rna36 121 FRTQKVFD 128
                                67777776 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 5.5e-09
                                CBBTTTTBBBSSHHHHHCCTTSHHH CS
                zf-C2H2_jaz   2 fYCvlCdKyFksenaldnHlkSKkH 26 
                                + C +C+K F+s+n+   H++SKkH
  gene36|gene36|rna36|rna36 180 YNCDHCSKGFHSHNQIIDHFRSKKH 204
                                89*********************** PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00067
                                BTTTTBBBSSHHHHHCCTT CS
                zf-C2H2_jaz   4 CvlCdKyFksenaldnHlk 22 
                                C +C+  F+s   l +Hlk
  gene36|gene36|rna36|rna36 273 CAECKAVFNSRAELLTHLK 291
                                99***************98 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.0   3.3e-05      0.06       1      22 [.     180     201 ..     180     203 .. 0.93
   2 !   12.7   0.2    0.0001      0.18       2      22 ..     272     292 ..     271     294 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                  zf-C2H2_4   1 fkCpiCgksFsskkaLlrHlkt 22 
                                + C++C+k F+s++++ +H+++
  gene36|gene36|rna36|rna36 180 YNCDHCSKGFHSHNQIIDHFRS 201
                                78*****************997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                  zf-C2H2_4   2 kCpiCgksFsskkaLlrHlkt 22 
                                +C  C+++F+s+ +Ll+Hlk+
  gene36|gene36|rna36|rna36 272 TCAECKAVFNSRAELLTHLKM 292
                                699***************985 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   7.2    0.0001      0.18       1      25 []     180     204 ..     180     204 .. 0.97
   2 !   14.1   0.1   2.7e-05     0.048       2      21 ..     272     291 ..     271     291 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                     zf-met   1 fyCelCnvtfnsesqlksHlqGKkH 25 
                                + C+ C + f s +q ++H+++KkH
  gene36|gene36|rna36|rna36 180 YNCDHCSKGFHSHNQIIDHFRSKKH 204
                                67*********************** PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.7e-05
                     zf-met   2 yCelCnvtfnsesqlksHlq 21 
                                +C  C+ +fns++ l +Hl+
  gene36|gene36|rna36|rna36 272 TCAECKAVFNSRAELLTHLK 291
                                699***************96 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.5   0.00092       1.6       2      13 ..     180     191 ..     180     198 .. 0.95
   2 !   12.9   0.3   4.5e-05     0.081       4      24 ..     273     294 ..     271     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00092
                  zf-C2H2_6   2 heCsvCsksFps 13 
                                ++C+ Csk F+s
  gene36|gene36|rna36|rna36 180 YNCDHCSKGFHS 191
                                99********99 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.5e-05
                  zf-C2H2_6   4 CsvCsksFpslqaLggHkks.H 24 
                                C +C+++F+s  +L +H+k  H
  gene36|gene36|rna36|rna36 273 CAECKAVFNSRAELLTHLKMgH 294
                                *****************99666 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   1.5   3.1e-05     0.055      46      86 ..     176     216 ..     167     230 .. 0.77
   2 ?    4.8   0.1     0.019        34      52      75 ..     272     294 ..     242     297 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                  zf-C2H2_2  46 kieekleClyCekefkslealreHmkkkgHckine.eeeeek 86 
                                k+   ++C +C+k f+s +++ +H ++k+H +     +e+ k
  gene36|gene36|rna36|rna36 176 KLYP-YNCDHCSKGFHSHNQIIDHFRSKKHFERIRlVSEDPK 216
                                5555.79***********************875322444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                  zf-C2H2_2  52 eClyCekefkslealreHmkkkgH 75 
                                +C  C+  f+s+++l +H+k  gH
  gene36|gene36|rna36|rna36 272 TCAECKAVFNSRAELLTHLK-MGH 294
                                67777777777777777775.344 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   6.0     0.029        51       1      23 []     180     204 ..     180     204 .. 0.88
   2 !   14.3   0.1   2.3e-05     0.042       2      23 .]     272     294 ..     272     294 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.029
                                EEETTTTEEESSHHHHHHHHHC..C CS
                    zf-C2H2   1 ykCpdCgksFkrksnLkrHirt..H 23 
                                y C++C+k F +  +   H r+  H
  gene36|gene36|rna36|rna36 180 YNCDHCSKGFHSHNQIIDHFRSkkH 204
                                89**********9999999887555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.3e-05
                                EETTTTEEESSHHHHHHHHHC.C CS
                    zf-C2H2   2 kCpdCgksFkrksnLkrHirt.H 23 
                                +C +C+ +F+++ +L +H+++ H
  gene36|gene36|rna36|rna36 272 TCAECKAVFNSRAELLTHLKMgH 294
                                7*******************999 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.045        80     110     135 ..     164     191 ..     141     199 .. 0.82
   2 ?   10.5   1.6   0.00026      0.47      60     133 ..     206     280 ..     191     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.045
                     Mut7-C 110 ervpekvyeeade..ftrCekCrkvfWk 135
                                + +p+kv+e++++   ++C++C+k f +
  gene36|gene36|rna36|rna36 164 HPAPPKVREKKTKlyPYNCDHCSKGFHS 191
                                568999999999976789******9965 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00026
                     Mut7-C  60 kgvlltsrdveeqlreviarlglklslkpelsrCvaCngeleevekeevkervpekvyeeade..ftrCekCrkvf 133
                                ++++l s+d+++ +++ ++++ ++   + + + C++   e++e +k+e  ++vp+k+ +  +   f +C +C+ vf
  gene36|gene36|rna36|rna36 206 ERIRLVSEDPKKYIEKQLQEITCQDLSEITQEPCTEKELEIVEDHKAEE-QSVPKKTGHIREPapFRTCAECKAVF 280
                                3466677777777777667777666555556779987777777666665.779999888888789********999 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4     0.024        42       3      15 ..     180     192 ..     179     198 .. 0.82
   2 ?    6.4   0.0    0.0037       6.7       4      20 ..     272     289 ..     270     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.024
                     zf_UBZ   3 ylCerCgkeipes 15 
                                y C+ C k + ++
  gene36|gene36|rna36|rna36 180 YNCDHCSKGFHSH 192
                                89******99887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0037
                     zf_UBZ   4 lCerCgkeipes.elqEH 20 
                                +C++C++ + +  el  H
  gene36|gene36|rna36|rna36 272 TCAECKAVFNSRaELLTH 289
                                8********999999999 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.6    0.0016       2.9      13      24 ..     175     189 ..     164     191 .. 0.77
   2 ?    2.5   0.2      0.13   2.3e+02      13      25 ..     268     281 ..     248     282 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0016
                  zf-H2C2_2  13 k...pyeCplCdkaF 24 
                                +   py+C+ C+k F
  gene36|gene36|rna36|rna36 175 TklyPYNCDHCSKGF 189
                                14449********99 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                  zf-H2C2_2  13 kpy.eCplCdkaFk 25 
                                 p+ +C +C+ +F+
  gene36|gene36|rna36|rna36 268 APFrTCAECKAVFN 281
                                35579*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1009  (0.0562775); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1885.42
//
Query:       gene360|gene360|rna360|rna360  [L=263]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1639.94
//
Query:       gene361|gene361|rna361|rna361  [L=442]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-53  181.1   0.2    3.7e-53  180.8   0.2    1.1  1  Haspin_kinase   Haspin like kinase domain
    5.8e-07   29.1   0.0    1.2e-06   28.1   0.0    1.5  1  Pkinase         Protein kinase domain
    0.00078   19.4   0.0     0.0012   18.8   0.0    1.3  1  APH             Phosphotransferase enzyme family
      0.001   18.7   0.1     0.0026   17.4   0.0    1.8  2  Choline_kinase  Choline/ethanolamine kinase
     0.0035   16.7   0.0      0.038   13.3   0.0    2.1  2  Pkinase_Tyr     Protein tyrosine kinase
     0.0041   16.8   0.0     0.0097   15.5   0.0    1.6  2  RIO1            RIO1 family
  ------ inclusion threshold ------
      0.025   14.0   0.0      0.039   13.3   0.0    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family


Domain annotation for each model (and alignments):
>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.8   0.2   1.4e-56   3.7e-53     108     322 ..     182     415 ..     102     440 .. 0.87

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 1.4e-56
                  Haspin_kinase 108 d....seklssevyqtkekdkevvlKvipl..........evledvtiskelsl....kelkslklvkgtypglllllqd 169
                                    +    +e+ +sev+   +    +v+K+ipl            l++ ti k +s      +lk + lvkg yp   l ++d
  gene361|gene361|rna361|rna361 182 NirkiGEATFSEVFAHGT----LVYKIIPLgntsdetslpSFLKESTIFKAISEedgvCKLKDVFLVKGRYPREYLKAWD 257
                                    1334699*******9999....********98888888887777777777777577779********************* PP

                  Haspin_kinase 170 kvlkek...pdfyseqqlflvlllkdkGtdLeevklkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnv 246
                                     + +e+   p  y++ q + v++++d+G++Le ++++ +++a +    ++ +L+  E+k+eFEHRdLh++niL++ ++++
  gene361|gene361|rna361|rna361 258 DYGEEEnerPSKYEDSQEYGVIVMEDGGESLESIRFQGIEEADRFIRTVIRTLARLEEKYEFEHRDLHWGNILIK-QGHI 336
                                    **9999899*****************************************************************7.599* PP

                  Haspin_kinase 247 tlidlklsRlessegkvlytrld.dpllFqGgg..DyqfeiYrlMrsllskswaefePrtNllwlhyLavkLlkkkn.kk 322
                                    +lid++lsRl+ + ++v++++l+  + lF+G +  D qf +Yr Mr+l+s +w++f+P++N+lw++yL++k + k++ k 
  gene361|gene361|rna361|rna361 337 NLIDFSLSRLK-NGNTVIFNDLNdRQWLFEGDEevDVQFKVYRDMRELCSGHWERFTPQSNVLWIRYLVEKTFGKNKfKG 415
                                    **********8.99********944679***864479**********************************999988432 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   4.7e-10   1.2e-06       4     151 ..     183     350 ..     181     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.7e-10
                                    EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHS.CTTB--EEEEEEE............ CS
                        Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklk.hpnivrlyevfee............ 69 
                                    ++k+Ge +f++V+         + + K+i   ++++++   ++l+E +i+k ++  + +++l++vf              
  gene361|gene361|rna361|rna361 183 IRKIGEATFSEVFAHG------TLVYKIIPLGNTSDETSlPSFLKESTIFKAISeEDGVCKLKDVFLVkgrypreylkaw 256
                                    6788888888888655......7899999999999988889999*******9998999******9998899999999999 PP

                                    .................SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEE CS
                        Pkinase  70 .................kdelylvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLi 131
                                                     +++ ++v+e  +gge  + ++       eea ++++++++ l+ l  + ++ HrDl   NiLi
  gene361|gene361|rna361|rna361 257 ddygeeenerpskyedsQEYGVIVME--DGGESLESIR---FQGIEEADRFIRTVIRTLARLEeKYEFEHRDLHWGNILI 331
                                    99999999999999876666667777..4554444444...35678999*************95667************* PP

                                    ETTTEEEE-SGTTSEESSSS CS
                        Pkinase 132 dekgelKitDFGlakeless 151
                                    + +g++ ++DF l++  + +
  gene361|gene361|rna361|rna361 332 K-QGHINLIDFSLSRLKNGN 350
                                    *.************987765 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.8e-07    0.0012     145     197 ..     296     345 ..     264     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.8e-07
                                    HHHHHHHHHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                            APH 145 leeleeqvlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                    +ee+++ +++++ ++l++ e++  + H+Dlh gN+l++  +g++  +iDf +++
  gene361|gene361|rna361|rna361 296 IEEADR-FIRTVIRTLARlEEKYEFEHRDLHWGNILIK--QGHI-NLIDFSLSR 345
                                    678888.89999999999999*****************..9998.9****8876 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.4   8.8e+03      17      42 ..     126     151 ..     123     154 .. 0.73
   2 !   17.4   0.0     1e-06    0.0026     115     172 ..     284     342 ..     216     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.4
                                    CCHHHHHHHHHHHHHHTTSSS-EEEE CS
                 Choline_kinase  17 lidretElvvfallserglgpklygi 42 
                                     i+re+ +++++   ++g++ +l+g 
  gene361|gene361|rna361|rna361 126 EIKRESKMQNITFRRKKGIDHHLHGQ 151
                                    57777777888888888888888876 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1e-06
                                    GGCCHCCCTHHHHHHHHHTHHHHHH...CHGG-EEEE-S--SGGGEEE.-CTTEEEE--GT CS
                 Choline_kinase 115 kkkqlklinledlekelekleklle...elespvvfcHnDlqegNillnkeekklvlIDFE 172
                                      ++l++i+++ +e+    ++ ++    +le++  f H Dl  gNil   +++++ lIDF 
  gene361|gene361|rna361|rna361 284 GGESLESIRFQGIEEADRFIRTVIRtlaRLEEKYEFEHRDLHWGNILI--KQGHINLIDFS 342
                                    456677777777777777777666445599999***************..9*********6 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.08     2e+02     184     205 ..     190     211 ..     173     255 .. 0.72
   2 !   13.3   0.0   1.5e-05     0.038     108     153 ..     302     347 ..     264     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.08
                                    HHHHHHHHHHHHHHHHTTSSGT CS
                    Pkinase_Tyr 184 sksDvWsfGvllwEiftlgesp 205
                                    + s v++ G+l++ i+ lg+++
  gene361|gene361|rna361|rna361 190 TFSEVFAHGTLVYKIIPLGNTS 211
                                    5578888888888888888765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHHHHHT.TEEEST-SGGGEEEEETTEEEE-STTTHEET CS
                    Pkinase_Tyr 108 falqvAkGmeyLesk.klvHrdlaarNvLlsenkvvkisDfGLardi 153
                                    f+  v + ++ Le+k ++ Hrdl   N+L++ + ++ + Df L+r  
  gene361|gene361|rna361|rna361 302 FIRTVIRTLARLEEKyEFEHRDLHWGNILIK-QGHINLIDFSLSRLK 347
                                    5666667777777663699***********9.78899*******977 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.7   9.4e+03      18      39 ..      16      37 ..       8      45 .. 0.69
   2 !   15.5   0.0   3.8e-06    0.0097      81     150 ..     277     342 ..     267     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.7
                                   E-S---SS-HHHHCTTTSTTST CS
                           RIO1 18 yktstteFkkrkkyvsgekrfk 39
                                   y   ++ F+++++++ ++ r +
  gene361|gene361|rna361|rna361 16 YEEVRKAFEDIRRKIADTGRLS 37
                                   5566677888888877777754 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.8e-06
                                    TEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GT CS
                           RIO1  81 hvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvs 150
                                     v+vme  g + ++  + + +e   ea++  ++v++++++l ++ +  H DL   N+l++++++ +ID+s
  gene361|gene361|rna361|rna361 277 GVIVMEDGG-ESLESIRFQGIE---EADRFIRTVIRTLARLEEKYEFEHRDLHWGNILIKQGHINLIDFS 342
                                    688888766.777777777777...9999***************************************98 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.039     121     184 ..     300     358 ..     272     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                            Kdo 121 rallkavgrliaklh.ragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLa 184
                                     + ++ v r+ a+l  + + +H+dl   nil++q++     i liD+  +rl+  ++    +dL+
  gene361|gene361|rna361|rna361 300 DRFIRTVIRTLARLEeKYEFEHRDLHWGNILIKQGH-----INLIDFSLSRLKN-GNTVIFNDLN 358
                                    45567777777777624689**************96.....*******999998.7776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3017.34
//
Query:       gene362|gene362|rna362|rna362  [L=521]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-73  247.0   3.7    6.9e-73  246.8   3.7    1.0  1  Sec1      Sec1 family


Domain annotation for each model (and alignments):
>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.8   3.7   3.8e-77   6.9e-73       1     575 []      22     513 ..      22     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 3.8e-77
                                    EEEEE-HHHHHHHHTT--HHHHHTTTEEETT..T.--S-.....BTTSEEEEEE-S-HHHHHHHHHHHHSS-SBS-EEEE CS
                           Sec1   1 KvLvlDkelskilssvlkvsdlleegVtkieklk.krepskrealphlkaiyflrptkenidrlakdfisarrykeyhif 79 
                                    +vLvl ++ ++i+ +++kv++l+e g+t  + ++  r+p     +++ +a+yf++ t+  id ++k+      y+ey+++
  gene362|gene362|rna362|rna362  22 RVLVLSERAQQIIAPLMKVNELRECGITAHFLVTqGRHP-----ISNTPAVYFVESTDGIIDDVLKEL-----YSEYYLN 91 
                                    59*********************88***44434336888.....*************99999999876.....******* PP

                                    ESS---HHHHHHHHH..SG......GGGEEEEE----SEEEETTEEE-STTHHHHSTTG.....GG.......--HHHHH CS
                           Sec1  80 ftprlseslleglakadee.....vvkkvklkelnldfvplesdlfslnpelplsfrdlyldndnsaleeeieslldria 154
                                    ft ++++  +e++    +e      v++v+  ++++df++l +d+f+l   +++sf  +           e+ ++ ++++
  gene362|gene362|rna362|rna362  92 FTTSVKRREIEEMGLRLSErglglRVRSVF--DQFVDFIALQDDMFTL--GMKDSFAGM-----------ENPDIWRETV 156
                                    ******999995443233346788999999..****************..776666654...........345666779* PP

                                    HHHHHHHHHH-..--EEEE-TT-HHHHHHHH..........HHHHTTT..--SS--EEEEE-GGG-SSTTTS---BHHHH CS
                           Sec1 155 kgLlsvllslekkiPiirykgsaasmvakkladelkekidskknfese..ssrqrpvLiIlDRsvDlvtpllhqwTYqal 232
                                     +++sv++++ + iP i+ + ++ s    ++a++l+ ki++   +     ++++rp+Li++ R+ D  tp+ h w Y al
  gene362|gene362|rna362|rna362 157 MSIMSVFVTI-GEIPFIVTIDDEES---MQIARMLEAKIKN---TG-VikKTSKRPLLILVNRNYDVSTPVQHVWSYSAL 228
                                    **********.77******876655...5999999999987...22.2479***************************** PP

                                    HHHHS--BTEEEEEE--SSSEEEEEE--TT..-TTHHHHTTSBHHHHHHHHHHHHHHHHHHHHTTT...-TTHHHHHHHH CS
                           Sec1 233 iddllgglnnnnvvleeepkeekeaelvesssDeffaelrhlnfgevgeklkkeakeyqeenekkrngakesiadlkkfv 312
                                     +dl++ l++n++ l++      ++ +++  +De+++ + ++ f+ v ek++ke+ ey++e++ ++   k++ + +++++
  gene362|gene362|rna362|rna362 229 MNDLFK-LESNKITLKS-----GKVFDLDP-QDELWKGNSNEYFPVVVEKVEKELLEYRKEMALRSIDEKTDKKVIQEAL 301
                                    *****8.9888888865.....46666666.*******************************55555555799******* PP

                                    HH-GGGHHHHHHHHHHHHHHHHHHHHS-HHH.HHHHHHHHHHHHSS--.B--..-HHHHHHHH-TTS-H.HHHHHHHHHH CS
                           Sec1 313 aklpelqeekkklskHtnlaeellkevkkrkldellelEqdlatgesdkkikekkvieeliaddeptseledklRLllly 392
                                    +k pel ++ +++  H+++++e+++ +k+r +d+++++E   +t+  +      + ++el +++++    ed+lRL++l+
  gene362|gene362|rna362|rna362 302 DKAPELAKRNESVNAHISICSEMVEVIKERAIDDFYKVEKGGCTS--Q------E-LMELSEKGDD----EDILRLAILL 368
                                    *****************************************9865..2......3.5599988666....6********* PP

                                    HH...-B.-HT--GG....GGHHHHGGGGG........---.BGGG-------.......---------S...TT----- CS
                           Sec1 393 slvegglkekelkellrelvqsalygleylktlrsleklgllkkrkgkksskkksslklikeeedeesnydlsgvsryaP 472
                                      ++      +++ +   l+q+   + +++         ++++k+ +++s k+        +  +++ ++ + +v++ +P
  gene362|gene362|rna362|rna362 369 LNTK------DFDLI-DPLLQKRKIKSKVI---------EFFRKHRNTHSEKS-------GTFYSQVVTSLMGNVKKLLP 425
                                    8863......33322.11233221223333.........34433333222222.......22233333322556889999 PP

                                    H.....HHHHHHHHTTT-S-TTTS-BSS-GGGS--------------------------S-EEEEEEEEEE-HHHHHHHH CS
                           Sec1 473 l.....lvrlvealikgkklssespslskkdpsqeesssslrsakktnsaskesaekkkkqrviVffvGGvTysEiralr 547
                                          +  lve+++  +  s  +++++ +dp               +s+++  +e     r++Vf +GG+Ty+E+++l+
  gene362|gene362|rna362|rna362 426 VkektpVSSLVESIYG-DIKSRIYSNFKVFDP--------------MGSEDIYANEI---SRIVVFGIGGGTYTELKTLK 487
                                    999999*********8.888888888877764..............56777777777...99****************** PP

                                    HHT...TSSSEEEEEEEEE--HHHHHH. CS
                           Sec1 548 llskqekknkeiiigttsilnpksflee 575
                                    ll+++    + +i+g+t+iln+++fl++
  gene362|gene362|rna362|rna362 488 LLEERM--DVPVIYGSTEILNAREFLRQ 513
                                    ***866..888**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2994.49
//
Query:       gene363|gene363|rna363|rna363  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-27   94.6   0.3    7.6e-27   94.3   0.3    1.0  1  Pkinase         Protein kinase domain
    9.1e-15   54.6   0.1    1.1e-14   54.4   0.1    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    2.2e-07   30.0   0.0    2.7e-07   29.7   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase
     0.0014   18.6   0.1      0.028   14.3   0.1    2.3  2  APH             Phosphotransferase enzyme family
     0.0081   15.5   0.2      0.022   14.1   0.0    1.7  2  Kinase-like     Kinase-like
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.16   11.6   0.0    1.4  1  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.3   2.5e-30   7.6e-27       3     208 ..      10     223 ..       8     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.5e-30
                                    EEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHS...CTTB--EEEEEEESSEEE.EEEE CS
                        Pkinase   3 kleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklk...hpnivrlyevfeekdely.lvle 78 
                                     ++k+ +G+fG ++ + +++t+++vAvK  kk + ++ k+     E  + k l     p+i ++ ++++e+ ++  lv+e
  gene363|gene363|rna363|rna363  10 LVQKIASGAFGDIFIGQNTTTNQTVAVKLEKKAHYSQLKH-----EYGVYKALGgtrTPKIYEYGKILYENVYVNgLVME 84 
                                    6799*************************99999999887.....7777777665559*************99999**** PP

                                    --TTEBHHHHHH.HHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTEEEE-SGTTSEESSSSCS... CS
                        Pkinase  79 yveggeladlle.rkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekgelKitDFGlakelesssk... 153
                                    ++  ++l++l    ++ +s +++  + ++++  +eylH+++ +HrD+Kp+N+ +d + ++l ++D+Glake+++  +   
  gene363|gene363|rna363|rna363  85 LMG-KSLEQLFVtCNRRFSLKTVLMLGEKMVDNVEYLHHRNYVHRDIKPDNFVFDlRGDKLYLIDYGLAKEFRNPMTfkh 163
                                    **9.5588887746677**************************************66666**************999999 PP

                                    .....BCTTTSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHH CS
                        Pkinase 154 .....ltsfvgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvek 208
                                          +s +gt +Y + +  ++ e s+  D+ s+G  ++ +l g+ p++g k k+k+ek
  gene363|gene363|rna363|rna363 164 remrtDKSLTGTARYASLRTHQGYEQSRRDDLESIGFCMVYFLKGRLPWQGLKAKTKQEK 223
                                    **999999*********999999999************************8777664443 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.1   3.7e-18   1.1e-14       1     217 [.       8     223 ..       8     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 3.7e-18
                                    EEEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSS.EEEE CS
                    Pkinase_Tyr   1 lelgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeep.lliv 79 
                                    ++l +k+++GafG+++ g+ +    +++++VavK  k+ + ++  ++ +  +k +  ++ p+i ++  + +++     +v
  gene363|gene363|rna363|rna363   8 IKLVQKIASGAFGDIFIGQNT----TTNQTVAVKLEKKAHYSQ-LKHEYGVYKALGGTRTPKIYEYGKILYENVYvNGLV 82 
                                    57899*************999....8999*****986655555.6666778888999999***9998888866554789* PP

                                    EE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEE.ETTEEEE-STTTHEET..... CS
                    Pkinase_Tyr  80 teyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLls.enkvvkisDfGLardi..... 153
                                    +e++ + +L++   +  +++++lk++l +  ++ + +eyL+++++vHrd+   N + + ++++  + D+GLa++      
  gene363|gene363|rna363|rna363  83 MELMGK-SLEQLFVTC-NRRFSLKTVLMLGEKMVDNVEYLHHRNYVHRDIKPDNFVFDlRGDKLYLIDYGLAKEFrnpmt 160
                                    ***977.788877777.8************************************999835779**********9832211 PP

                                    TTSSEEEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHH CS
                    Pkinase_Tyr 154 ekddeyvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevlek 217
                                     k+ e++++++ +   ++ ++ + +  + + + D  s G ++   ++ g+ p++glk+++  ek
  gene363|gene363|rna363|rna363 161 FKHREMRTDKSLTGTARYASLRTHQGYEQSRRDDLESIGFCMVYFLK-GRLPWQGLKAKTKQEK 223
                                    23445577777788999999999999999999999999999998777.9999999866554333 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   8.9e-11   2.7e-07     281     406 ..      51     204 ..      18     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 8.9e-11
                 Pkinase_fungal 281 r.....................lenrvhrrlvispvGkpieka.......espkellealrDaIkghrsLflkagiLHrD 332
                                                          +en  ++ lv++ +Gk++e+         s k +l   +  +   + L+ + +++HrD
  gene363|gene363|rna363|rna363  51 YgvykalggtrtpkiyeygkilYENVYVNGLVMELMGKSLEQLfvtcnrrFSLKTVLMLGEKMVDNVEYLH-HRNYVHRD 129
                                    0555555555555556666666666666666777777766653111111134555566667788888999*.******** PP

                 Pkinase_fungal 333 iSenNilitdskkegerkglLiDLDlakelsddssesga.....rertGTleFmaievlkgeeHsyrhDLESffyvllw 406
                                    i  +N ++      +++k  LiD  lake  ++ + +++     +  tGT+ + +++  +g e s r+DLES+ + +++
  gene363|gene363|rna363|rna363 130 IKPDNFVFD----LRGDKLYLIDYGLAKEFRNPMTFKHRemrtdKSLTGTARYASLRTHQGYEQSRRDDLESIGFCMVY 204
                                    ******998....89***************9876655334445599**************************9777766 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.1   3.1e+02      18      79 ..      29      87 ..      23     100 .. 0.78
   2 !   14.3   0.1   9.5e-06     0.028     168     196 ..     125     152 ..     112     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.1
                                   ETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE---- CS
                            APH 18 tpagryvlrrnpparaaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpg 79
                                   t+++++++++  +a  + ++  e+ ++++L ++  ++P+++ +++  +e+ ++  l+  + g
  gene363|gene363|rna363|rna363 29 TTNQTVAVKLEKKA-HYSQLKHEYGVYKALGGT--RTPKIYEYGKILYENVYVNGLVMELMG 87
                                   44489999999999.999999999999999999..789**9998888888775555544455 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.5e-06
                                    EE-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 168 llHgDlhpgNllvdpddgrvtGviDfeda 196
                                     +H+D++p+N+++d +++++ ++iD ++a
  gene363|gene363|rna363|rna363 125 YVHRDIKPDNFVFDLRGDKL-YLIDYGLA 152
                                    69************999999.9***9988 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.43   1.3e+03      12      45 ..       6      39 ..       3      57 .. 0.78
   2 !   14.1   0.0   7.4e-06     0.022     124     186 ..      83     147 ..      71     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.43
                    Kinase-like 12 rtlvrgellkkgdrsvvfevkdqetgeplavkvf 45
                                   r+ + ++ +  g ++ +f  ++  t++ +avk  
  gene363|gene363|rna363|rna363  6 RNIKLVQKIASGAFGDIFIGQNTTTNQTVAVKLE 39
                                   6778888899999999999999999999998864 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.4e-06
                    Kinase-like 124 leilnkvlqkrset.hkkletiarlllTlqlirlaanLqakglvhgkftvdnllldekg.glmlg 186
                                    +e+++k l++  +t +++      l+l  +++  + +L+++  vh ++++dn+++d +g +l+l 
  gene363|gene363|rna363|rna363  83 MELMGKSLEQLFVTcNRRFSLKTVLMLGEKMVDNVEYLHHRNYVHRDIKPDNFVFDLRGdKLYLI 147
                                    5777777777777765666666668888999999**********************998335555 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.3e-05      0.16     107     171 ..      83     149 ..      26     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                                    TT..ECHHGGCCHCCCTHHHHHHHHHTHHHHHHCHGG-..EEEE-S--SGGGEEE.-CTTEEEE--G CS
                 Choline_kinase 107 qtkakkekkkkqlklinledlekelekleklleelesp..vvfcHnDlqegNillnkeekklvlIDF 171
                                    +    k+ ++  +++ +  +l+  l+  ek++++ e+    ++ H D+ + N++++   +kl+lID+
  gene363|gene363|rna363|rna363  83 MELMGKSLEQLFVTCNRRFSLKTVLMLGEKMVDNVEYLhhRNYVHRDIKPDNFVFDLRGDKLYLIDY 149
                                    555556667777888888899999999999997655544599************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2061.91
//
Query:       gene364|gene364|rna364|rna364  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-17   63.6   0.1    1.6e-17   63.4   0.1    1.1  1  tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal
  ------ inclusion threshold ------
       0.17   12.8   0.0       0.26   12.2   0.0    1.2  1  DUF3306        Protein of unknown function (DUF3306)


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.1   1.8e-21   1.6e-17       4      77 ..       8      78 ..       5      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 1.8e-21
                                   HHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                  tRNA_int_endo  4 kyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77
                                   + a  r + e+G+vv +Glk+G d++vY+++ps++hs+y V++   d + ++ d+++a r+++sv+K+l++a+ 
  gene364|gene364|rna364|rna364  8 REALRRMFEEEGFVVGDGLKYGVDLLVYTDKPSRVHSRYGVLI---DRRHSFLDIVGAQRTCTSVNKTLVVAFF 78
                                   5677799************************************...99999*********************87 PP

>> DUF3306  Protein of unknown function (DUF3306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05      0.26      88     109 ..       6      27 ..       3      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                        DUF3306  88 vkraALrklFadphfnvmdgld 109
                                     kr+ALr++F+++ f v dgl+
  gene364|gene364|rna364|rna364   6 EKREALRRMFEEEGFVVGDGLK 27 
                                    69******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 719.11
//
Query:       gene365|gene365|rna365|rna365  [L=989]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-84  281.5   0.0    4.5e-57  193.2   0.0    2.5  2  ThiF             ThiF family
    1.5e-58  198.7   6.9      3e-41  142.0   1.6    2.4  2  UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
    9.1e-06   26.3   0.0      5e-05   23.9   0.0    2.3  1  E1_UFD           Ubiquitin fold domain
    0.00021   21.4   0.2    0.00061   19.9   0.2    1.8  1  E1_FCCH          Ubiquitin-activating enzyme E1 FCCH domain
  ------ inclusion threshold ------
      0.057   13.6   0.0       0.13   12.4   0.0    1.6  1  E1_4HB           Ubiquitin-activating enzyme E1 four-helix bu
       0.31   11.3   1.2       0.65   10.3   0.1    2.1  2  Mrpl_C           54S ribosomal protein L8 C-terminal domain


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   1.2e-27   3.7e-24       1     231 [.      14     385 ..      14     393 .. 0.89
   2 !  193.2   0.0   1.5e-60   4.5e-57       8     240 ..     403     890 ..     393     898 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1.2e-27
                                    THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaea 80 
                                    ysrql+++g+d ++k+ +skvl++G+ glG+e++kn+ l+Gv+k+ l+D+ +++ ++l   f+ r+ediGkp+  ++  +
  gene365|gene365|rna365|rna365  14 YSRQLYVVGKDAMKKMMSSKVLVMGLDGLGQEIVKNICLAGVSKVGLFDDRVVSEEDLCTGFYLRREDIGKPRDSSVVSR 93 
                                    89****************************************************************************** PP

                                    HHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-EC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  81 lqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcy 160
                                     +++n +v+v+ v e         + +e++D+Vv +   +  +  +n++++k +  +i  ++ g+ +qv++ +    + +
  gene365|gene365|rna365|rna365  94 FRSMNEYVDVNVVSEV--------KSFEEYDVVVVCNECYGEQIRLNEMARKDKCMFIGCQVRGLFSQVFCDF---GAEF 162
                                    **********988653........4589********************************************7...3344 PP

                                    TSS-TGGS.EECCCCEEHHH............................................................ CS
                                    xxxxxxxxxxxxxxxxxxxx............................................................ RF
                           ThiF 161 eCldpsstedptekkvplct............................................................ 180
                                     C d  + e p   +++ +                                                             
  gene365|gene365|rna365|rna365 163 ICVDR-TGEIPVSGMINDISedgvmtvvdgqrhnledydiikitqceeyegrhfrvkvisptqvmlqsvdgvrmfeeeae 241
                                    44442.2233333333333333333444888888888888889999999999999999999999999999********** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           ThiF 181 ................................................................................ 180
                                                                                                                    
  gene365|gene365|rna365|rna365 242 fkaekfkavyggdfeqqkkpvmisfkplgrtidepsilgfnheveernlvvhkcfvalgeymeqdkqevdgegflsffvr 321
                                    ******************************************************************************** PP

                                    .................HHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEE CS
                                    .................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 181 .................siagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfen 231
                                                     + +g    + ++++vv+g +a+e+lk + +k +   +++ ++d+++ + ++
  gene365|gene365|rna365|rna365 322 kykshfefeglirsfgkQCMG---TLMPMCSVVGGFVAQEILKGVGSKFTPLHQFF-YFDAADAIPKD 385
                                    **********99766666666...9********************99999999999.89988776655 PP

  == domain 2  score: 193.2 bits;  conditional E-value: 1.5e-60
                                    HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTT...EEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   8 lgedgqekLrdskvllvGaGglGsellknLalsGvg...kltlvDnDkielsNlnRqflfreediGkpKaevaaealqei 84 
                                    lg++  e+L + +v++vGaG++G+e lkn++++G+g   ++ ++D+D ie sNlnRqflfr+ d+   Kaeva + ++++
  gene365|gene365|rna365|rna365 403 LGKECVERLFNLHVFMVGAGAIGCEHLKNMVMCGIGhngRISVTDMDAIEQSNLNRQFLFRSGDVSSMKAEVAVREAMAL 482
                                    788999*****************************98889**************************************** PP

                                    -TTS.EEEEEES-C.............................CGCC...S-HHHHTT-SEEEEESSSHHHHHHHHHHHH CS
                                    xxxx.xxxxxxxxx.............................xxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  85 npdv.eveavteri.............................tdet...vleellesvDlVvdalDniearrlvnracv 131
                                    n d  +v+  ++++                             ++et   +++ +++svD+V+ alDn++ar++++ +cv
  gene365|gene365|rna365|rna365 483 NQDFlQVSSDEKKVeekgvsevtngmsnnessqsnlvyynlkvGKETegvFSDRFFQSVDAVATALDNVDARMYMDGRCV 562
                                    ***88************************************9944334679***************************** PP

                                    HHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EECCCCEEHHH............................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                           ThiF 132 kkgiplieagtlgfegqvvviipgktgcyeCldpsstedptekkvplct............................... 180
                                     +++ +++agt+g++g+v+v++p     ++ + + s++dp+ek++plct                               
  gene365|gene365|rna365|rna365 563 VNRKFMVDAGTSGTKGNVQVVVP-----FHTESYGSSQDPPEKSIPLCTiknfpyaiehtiewarsefefkfhdeillik 637
                                    *********************98.....5555566779****************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           ThiF 181 ................................................................................ 180
                                                                                                                    
  gene365|gene365|rna365|rna365 638 eylskektnteserkedqsneiiedvvekiptnakecirngillfvklfhtsiknlitafppdsktkegqvfwmppkrap 717
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           ThiF 181 ................................................................................ 180
                                                                                                                    
  gene365|gene365|rna365|rna365 718 rtinfdvnndlhilfvqstanifslnfgikqhiskemvaefvkneilveefstvadsicaeesskpyvdpsiitpcifek 797
                                    ******************************************************************************** PP

                                    .................................HHHCT.E-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTT CS
                                    .................................xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 181 .................................siagn.ipaiatttavvaglaalellkllsgkeklenslltqvdlle 226
                                                                     +iag+ ipaiatttavv+gla+le++k+  g e   + ++++++l++
  gene365|gene365|rna365|rna365 798 dddtnfhvdflyaaanlrainykikqadrltvkGIAGRiIPAIATTTAVVSGLAILEMIKYALGVE-HIKHKNSFLNLAL 876
                                    *************************************************************97666.78888889***** PP

                                    TEEEEECCEEEEEE CS
                                    xxxxxxxxxxxxxx RF
                           ThiF 227 srfenvelerakks 240
                                    ++f ++ +++++k+
  gene365|gene365|rna365|rna365 877 PFFASTDPVEPAKQ 890
                                    ******99998876 PP

>> UBA_e1_thiolCys  Ubiquitin-activating enzyme active site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.0   1.6     1e-44     3e-41       1     167 [.     611     772 ..     611     787 .. 0.86
   2 !   60.2   0.4   9.2e-20   2.7e-16     209     252 .]     783     830 ..     765     830 .. 0.81

  Alignments for each domain:
  == domain 1  score: 142.0 bits;  conditional E-value: 1e-44
                UBA_e1_thiolCys   1 PneieHtieWArdkFeglFekkpeevnkflkdkekfleelekekeeekletlekvlkllvkerpktfedCvkwArekfek 80 
                                    P++ieHtieWAr++Fe  F++++  ++++l+++++ +e+ +k ++     + +++ + +v++ p++ ++C++ +++ f k
  gene365|gene365|rna365|rna365 611 PYAIEHTIEWARSEFEFKFHDEILLIKEYLSKEKTNTESERK-ED-----QSNEIIEDVVEKIPTNAKECIRNGILLFVK 684
                                    9*****************************774443333222.22.....2445666666888***************** PP

                UBA_e1_thiolCys  81 lFnnkikqLlynfPkdsktsdGapFWsgpKraPkplefdlenelhleFvvaaanLraqvygikgerdeeaiaklls.kvk 159
                                    lF+++ik+L+++fP+dskt++G+ FW  pKraP+ ++fd++n+lh+ Fv ++an++  ++gik++ ++e +a++++ ++ 
  gene365|gene365|rna365|rna365 685 LFHTSIKNLITAFPPDSKTKEGQVFWMPPKRAPRTINFDVNNDLHILFVQSTANIFSLNFGIKQHISKEMVAEFVKnEIL 764
                                    ****************************************************************9999999997774777 PP

                UBA_e1_thiolCys 160 vpefkpke 167
                                    v+ef+  +
  gene365|gene365|rna365|rna365 765 VEEFSTVA 772
                                    88887655 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 9.2e-20
                UBA_e1_thiolCys 209 a....lklkpieFeKDddtnfhidfitaasNlRArnYkIkeadrlkvK 252
                                           ++p+ FeKDddtnfh+df +aa+NlRA nYkIk+adrl+vK
  gene365|gene365|rna365|rna365 783 PyvdpSIITPCIFEKDDDTNFHVDFLYAAANLRAINYKIKQADRLTVK 830
                                    1344567899***********************************998 PP

>> E1_UFD  Ubiquitin fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.7e-08     5e-05       1      86 [.     904     980 ..     904     984 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.7e-08
                         E1_UFD   1 WDrlevegeitlkelldyfkekkklevsmislgvsllYasflpkkkdkerlklklselveevtkkkipphqkyldlevsv 80 
                                    W rle + +  l  +l+ f+ ++k ++sm++ +++l+Y +f   +k +++l++++ elv        +p++ +++l+v+ 
  gene365|gene365|rna365|rna365 904 WNRLEYK-DSKLGTILRAFEIQFKRKISMVTAESALIYWDFD--SKYADNLEKTVGELVD------RKPDELFVVLDVIT 974
                                    9******.*********************************4..6***************......457899******** PP

                         E1_UFD  81 edeege 86 
                                    +d+ege
  gene365|gene365|rna365|rna365 975 DDDEGE 980
                                    *99876 PP

>> E1_FCCH  Ubiquitin-activating enzyme E1 FCCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2     2e-07   0.00061       2      52 ..     182     228 ..     181     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2e-07
                                    TTSEEEESTT--S---TT-EEEEES-BT-CCGGGS--EE-EE-SSSEEE-- CS
                        E1_FCCH   2 npgvVtvleesrhgledgDyVtFseveGmtelNgkeprkikvlgpytFeIg 52 
                                    ++gv tv++ +rh+led D++++++    +e++g++ +++kv++p +  ++
  gene365|gene365|rna365|rna365 182 EDGVMTVVDGQRHNLEDYDIIKITQC---EEYEGRH-FRVKVISPTQVMLQ 228
                                    789*******************9987...8999998.*******9987666 PP

>> E1_4HB  Ubiquitin-activating enzyme E1 four-helix bundle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.5e-05      0.13       1      48 [.     261     307 ..     261     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                                    -EEE----HHHHTTS-.-BE-S-GGGTTCHHHHHHHHHHHHHHHHCTT CS
                         E1_4HB   1 PktlsFksleesleePeeflisDfakfdrpeqlHlafqALhaFeeehg 48 
                                    P ++sFk+l   + eP ++l  + +  +r+  +H +f AL ++ e+ +
  gene365|gene365|rna365|rna365 261 PVMISFKPLGRTIDEP-SILGFNHEVEERNLVVHKCFVALGEYMEQDK 307
                                    889*************.**************************99865 PP

>> Mrpl_C  54S ribosomal protein L8 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.7     5e+03      41      89 ..     455     508 ..     448     523 .. 0.51
   2 ?   10.3   0.1   0.00022      0.65      53      94 ..     628     668 ..     601     678 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                         Mrpl_C  41 nLkKmlkfkskeq..llkeilavrkflkeeq...elewdee.eekeavkalldqv 89 
                                    nL++++ f+s +   +++e+ avr+ +  +q   +++ de+  e++ v+++++ +
  gene365|gene365|rna365|rna365 455 NLNRQFLFRSGDVssMKAEV-AVREAMALNQdflQVSSDEKkVEEKGVSEVTNGM 508
                                    66666666665543366666.4666666666222222233203444444444444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00022
                         Mrpl_C  53 qllkeilavrkflkeeqelewdeeeekeavkalldqvakktl 94 
                                    +++ eil ++++l++e+  +  e++e++  + +++ v++k  
  gene365|gene365|rna365|rna365 628 KFHDEILLIKEYLSKEKTNTESERKEDQSNE-IIEDVVEKIP 668
                                    699***********99966544444444433.3333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (989 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.78u 0.29s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 6205.43
//
Query:       gene366|gene366|rna366|rna366  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-08   32.1   7.5     0.0029   18.0   2.0    2.6  2  zf-C2H2        Zinc finger, C2H2 type
    2.7e-06   27.7   8.8     0.0083   16.3   0.9    2.4  2  zf-C2H2_aberr  Aberrant zinc-finger
    9.6e-06   26.0   5.2      0.063   14.2   1.1    2.6  2  zf-C2H2_4      C2H2-type zinc finger
    4.7e-05   23.0   0.5       0.37   10.5   0.1    2.3  2  zf_Hakai       C2H2 Hakai zinc finger domain
    0.00012   22.4   1.0    0.00012   22.4   1.0    3.3  3  zf-H2C2_2      Zinc-finger double domain
  ------ inclusion threshold ------
      0.022   14.8   2.9        1.7    8.7   0.3    2.4  2  zf-BED         BED zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   2.1e-06    0.0062       1      23 []     132     157 ..     132     157 .. 0.95
   2 !   18.0   2.0   9.6e-07    0.0029       1      23 []     168     193 ..     168     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                                    EEET..TTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirt.H 23 
                                    y C+  +C+k+++++  Lk H++  H
  gene366|gene366|rna366|rna366 132 YACEieGCTKKYTSSFGLKYHMKEgH 157
                                    789999*****************988 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9.6e-07
                                    EEET..TTTEEESSHHHHHHHHHC.C CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirt.H 23 
                                    y+Cp  +C+k++k++  Lk Hi+  H
  gene366|gene366|rna366|rna366 168 YVCPfdGCDKKYKNNNGLKYHIKHyH 193
                                    99*********************988 PP

>> zf-C2H2_aberr  Aberrant zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.9   2.8e-06    0.0083     139     164 ..     130     155 ..     108     168 .. 0.80
   2 !   14.8   2.5   7.7e-06     0.023     141     166 ..     168     193 ..     157     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                  zf-C2H2_aberr 139 dliyCripGCgkrfkslmaYkYhckk 164
                                     ++ C+i+GC k++ s  + kYh k+
  gene366|gene366|rna366|rna366 130 RVYACEIEGCTKKYTSSFGLKYHMKE 155
                                    6889*******************986 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.7e-06
                  zf-C2H2_aberr 141 iyCripGCgkrfkslmaYkYhckkfl 166
                                    + C+  GC+k++k+  + kYh k+++
  gene366|gene366|rna366|rna366 168 YVCPFDGCDKKYKNNNGLKYHIKHYH 193
                                    57*******************99985 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   4.3e-05      0.13       1      21 [.     132     154 ..     132     155 .. 0.94
   2 !   14.2   1.1   2.1e-05     0.063       1      24 []     168     193 ..     168     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                      zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlk 21 
                                    + C+i  C+k ++s+ +L+ H+k
  gene366|gene366|rna366|rna366 132 YACEIegCTKKYTSSFGLKYHMK 154
                                    7899999***************8 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.1e-05
                      zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlkthH 24 
                                    + Cp+  C+k ++++++L+ H+k  H
  gene366|gene366|rna366|rna366 168 YVCPFdgCDKKYKNNNGLKYHIKHYH 193
                                    79********************9988 PP

>> zf_Hakai  C2H2 Hakai zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00012      0.37       1      30 [.     129     157 ..     129     159 .. 0.93
   2 !   10.5   0.0   0.00013      0.38       4      30 ..     168     193 ..     167     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00012
                       zf_Hakai   1 GtvFmCtvvegCrRTYLSqRDLqAHIkhRH 30 
                                    G v+ C + egC   Y S   L+ H k  H
  gene366|gene366|rna366|rna366 129 GRVYACEI-EGCTKKYTSSFGLKYHMKEGH 157
                                    88******.****************99887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00013
                       zf_Hakai   4 FmCtvvegCrRTYLSqRDLqAHIkhRH 30 
                                    ++C + +gC   Y  +  L+ HIkh H
  gene366|gene366|rna366|rna366 168 YVCPF-DGCDKKYKNNNGLKYHIKHYH 193
                                    89***.*******************99 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.16   4.7e+02      11      26 .]     128     145 ..     117     145 .. 0.68
   2 !   22.4   1.0   3.9e-08   0.00012       1      26 []     148     181 ..     148     181 .. 0.91
   3 ?    3.3   0.2     0.041   1.2e+02       1      13 [.     184     197 ..     184     198 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.16
                      zf-H2C2_2  11 gekpyeCp..lCdkaFkt 26 
                                    g + y C+   C k++++
  gene366|gene366|rna366|rna366 128 GGRVYACEieGCTKKYTS 145
                                    44559999877***9985 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.9e-08
                      zf-H2C2_2   1 nLrrHirk.Htgek.....pyeCp..lCdkaFkt 26 
                                    +L++H+++ H  ek     py Cp   Cdk++k+
  gene366|gene366|rna366|rna366 148 GLKYHMKEgHSEEKmnifkPYVCPfdGCDKKYKN 181
                                    69*****99**999999999****666*****97 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.041
                      zf-H2C2_2   1 nLrrHirk.Htgek 13 
                                    +L++Hi+  H  ++
  gene366|gene366|rna366|rna366 184 GLKYHIKHyHDDQT 197
                                    69*****6697666 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0036        11      22      44 .]     139     158 ..     130     158 .. 0.82
   2 ?    8.7   0.3   0.00056       1.7      22      43 ..     175     193 ..     169     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0036
                                    TTEE----SSTHHHHHHHHHS-H CS
                         zf-BED  22 CgkilsrgggttnLkrHLrrkHp 44 
                                    C k+++++    +Lk+H++ +H+
  gene366|gene366|rna366|rna366 139 CTKKYTSS---FGLKYHMKEGHS 158
                                    66666665...99*********6 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00056
                                    TTEE----SSTHHHHHHHHHS- CS
                         zf-BED  22 CgkilsrgggttnLkrHLrrkH 43 
                                    C k+++++   ++Lk+H++++H
  gene366|gene366|rna366|rna366 175 CDKKYKNN---NGLKYHIKHYH 193
                                    88888887...9*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1365.17
//
Query:       gene367|gene367|rna367|rna367  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-18   65.5   2.7    7.7e-17   60.9   2.8    2.2  2  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.049   13.4   1.4      0.092   12.5   1.4    1.4  1  DUF5105        Domain of unknown function (DUF5105)
       0.11   11.6   0.0       0.18   10.9   0.0    1.3  1  ChpXY          CO2 hydration protein (ChpXY)
       0.25   11.4   0.2       0.25   11.4   0.2    1.7  2  DUF591         Protein of unknown function


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   2.8   1.7e-20   7.7e-17       2      51 .]      83     132 ..      82     132 .. 0.97
   2 ?    2.2   0.0     0.038   1.7e+02      28      51 .]     153     181 ..     150     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.7e-20
                                    EEEE-S-STTS-HHHHHHHHHTT-SSTT.EEEE--SSHHHHHHHHHCCCGE CS
                  Ribosomal_L30   2 fVtrirsiigvppkvrktLqlLgLrkin.gtvvklntpsirGmLkkVkhlV 51 
                                     V++irs  +++pkvrk+L+l++L++in +++v++n+ +++ mL+++k++V
  gene367|gene367|rna367|rna367  83 VVILIRSKCKCSPKVRKVLELFRLKRINnCVFVRNNKSTKK-MLHIIKDYV 132
                                    69***************************************.********9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.038
                                    TT.EEEE--SSHHHHHH....HHHCCCGE CS
                  Ribosomal_L30  28 in.gtvvklntpsirGm....LkkVkhlV 51 
                                    +n +t vkl++  i  m    +k +++lV
  gene367|gene367|rna367|rna367 153 RNgRTRVKLTNEFIEDMfdgkIKCIEELV 181
                                    5779*******999999999999999998 PP

>> DUF5105  Domain of unknown function (DUF5105)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4     2e-05     0.092      40      88 ..      23      70 ..      15      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2e-05
                                   HHHHHHHHHHHHHHHHHHTT--GGGGGSHHHHHHHHHHHHHHHHH-EEE CS
                        DUF5105 40 sevveeveesfkksfkralgyssssvtdkeldnlfkalkealkekakve 88
                                   s +   +e++f +  k+ + y  ++vt+k ld ++++ +e+l++ka++e
  gene367|gene367|rna367|rna367 23 SGIRRRQEKEFMERKKSNAKYA-EEVTEKLLDRYYQQEREVLEKKASME 70
                                   5567789999*99988888866.***********************987 PP

>> ChpXY  CO2 hydration protein (ChpXY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.1e-05      0.18     127     184 ..     131     188 ..     104     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.1e-05
                          ChpXY 127 eklfpeflleqvrqlayysaLGqfWrvmsdiflelsdrydegeiksipdvvefikdgl 184
                                    +  f  + +e +r+l y+++ G+  r   ++  e+ +   +g+ik+i++ v++i +g 
  gene367|gene367|rna367|rna367 131 YVAFGTIDMELLRELMYTKGTGRNGRTRVKLTNEFIEDMFDGKIKCIEELVHHIYNGT 188
                                    346888889***************************9999***************984 PP

>> DUF591  Protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   5.6e-05      0.25       7      26 ..       8      29 ..       3      41 .. 0.77
   2 ?   -3.5   0.2       2.6   1.2e+04      36      42 ..     152     158 ..     148     161 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.6e-05
                         DUF591  7 ePPdrirr..keArGgGLRRRt 26
                                    P   irr   eA+ +G+RRR+
  gene367|gene367|rna367|rna367  8 APQSSIRRkeYEAKMSGIRRRQ 29
                                   355689994447*********9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                         DUF591  36 Gratrik 42 
                                    Gr +r +
  gene367|gene367|rna367|rna367 152 GRNGRTR 158
                                    5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1308  (0.0729544); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1637.44
//
Query:       gene368|gene368|rna368|rna368  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 2601.48
//
Query:       gene369|gene369|rna369|rna369  [L=487]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.52
# Mc/sec: 2839.62
//
Query:       gene37|gene37|rna37|rna37  [L=202]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       861  (0.0480228); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1355.21
//
Query:       gene370|gene370|rna370|rna370  [L=566]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-71  239.0   0.0    9.8e-71  238.2   0.0    1.4  1  Pkinase         Protein kinase domain
    5.1e-32  111.2   0.0    1.1e-31  110.1   0.0    1.6  1  Pkinase_Tyr     Protein tyrosine kinase
    1.3e-10   41.1   0.0    2.9e-10   39.9   0.0    1.6  2  Kinase-like     Kinase-like
    7.2e-06   25.2   0.6    1.7e-05   24.0   0.6    1.6  1  Haspin_kinase   Haspin like kinase domain
    4.5e-05   22.9   0.1    0.00011   21.6   0.0    1.6  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00027   20.9   0.4     0.0022   18.0   0.4    2.1  2  APH             Phosphotransferase enzyme family
    0.00099   18.8   0.1     0.0023   17.6   0.1    1.5  1  RIO1            RIO1 family
  ------ inclusion threshold ------
      0.028   13.2   0.0      0.047   12.5   0.0    1.3  1  Pkinase_fungal  Fungal protein kinase
       0.27   10.8   2.5        0.3   10.6   0.8    1.9  2  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.2   0.0   4.9e-74   9.8e-71       1     264 []      58     316 ..      58     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 238.2 bits;  conditional E-value: 4.9e-74
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.......HHHHHHHHHHHHHSCTTB--EEEEEEESSEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.......kkvlrEikilkklkhpnivrlyevfeekdel 73 
                                    y+ +++lG Gs++kV+ +++ ++g++vA+K+i ++ + +++        ++++rE+ i   ++hp+ivrl++++++++++
  gene370|gene370|rna370|rna370  58 YRFVRQLGIGSSSKVVLGCDVHSGEKVAIKVIPRRMNGDETSgvemrcdQRIFREVIISSVVNHPHIVRLKNFLYSPTHY 137
                                    67889******************************999999899999*9******************************* PP

                                    EEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                        Pkinase  74 ylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                    +l++eyv+g++l d++  +g l+e+e +++++qil++++y+H+++i+HrDlK eNiLide++++K++DFGl++ +++++ 
  gene370|gene370|rna370|rna370 138 FLIFEYVKGKQLYDIIISNGPLKEKEGQRYFRQILSAIDYIHRNSIVHRDLKIENILIDENDNVKLIDFGLSNFYDNKTL 217
                                    ******************************************************************************** PP

                                    BCTTTSCGGGS-HHHHTTSCB.SHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTT CS
                        Pkinase 154 ltsfvgtseYlAPEvlkeney.skkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpease 232
                                    l++f+g+ ++ APE+l++++y ++++DvWslGv+ly +l+g+ pf +e+ +  ++k              ++ +++  ++
  gene370|gene370|rna370|rna370 218 LNTFCGSLYFAAPELLQGQRYcGPEIDVWSLGVVLYAILCGCVPFDDENVQGLQAK-------------IKDADFKFCKT 284
                                    ******************9999************************4444442222.............245699***** PP

                                    S-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 233 iseeakdllkkllkkdpkkRltaeellqhpyl 264
                                    is+ea++l++ ++  +p++R++ ++++ ++++
  gene370|gene370|rna370|rna370 285 ISKEAQELIRGMIVAQPSSRMGLDQVIGSEWV 316
                                    **************************999995 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.1   0.0   5.5e-35   1.1e-31       3     255 ..      60     310 ..      58     313 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 5.5e-35
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHH........HHHHHHHHHHHHTS-BTTB--EEEEEESSS CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateee........keelleeakimkklkhpnivkllgvctkee 74 
                                    + ++lG G+ +kVv g       ++ +kVa+K++ ++++ +e         +++++e+ i + ++hp+iv+l  + ++  
  gene370|gene370|rna370|rna370  60 FVRQLGIGSSSKVVLGCDV----HSGEKVAIKVIPRRMNGDEtsgvemrcDQRIFREVIISSVVNHPHIVRLKNFLYSPT 135
                                    6799***********9988....67788888888654443332223334468899999999999**************** PP

                                    SEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETT CS
                    Pkinase_Tyr  75 pllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardie 154
                                    ++++++eyvkg +L + + ++   +l+ k+  ++  q+ ++++y++++++vHrdl   N+L++en+ vk+ DfGL++   
  gene370|gene370|rna370|rna370 136 HYFLIFEYVKGKQLYDIIISN--GPLKEKEGQRYFRQILSAIDYIHRNSIVHRDLKIENILIDENDNVKLIDFGLSNFY- 212
                                    ********************9..9*****************************************************99. PP

                                    TSSEEEETTSSTSGGGGS-HHHHHHSEE.EHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBHH CS
                    Pkinase_Tyr 155 kddeyvkkeeaklpvkWmapEslkekkf.tsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcpee 233
                                      d+ +  ++   ++ + apE l+ +++   + DvWs Gv+l+ i++ g  p+ + + + + +k+k+    +  +++++e
  gene370|gene370|rna370|rna370 213 --DNKTLLNTFCGSLYFAAPELLQGQRYcGPEIDVWSLGVVLYAILC-GCVPFDDENVQGLQAKIKDA-DFKFCKTISKE 288
                                    ..445555666778999*******999626799*************9.99***999998888888765.57777889999 PP

                                    HHHHHHHHT-SSGGGS--HHHH CS
                    Pkinase_Tyr 234 lyelmkkcweedpeeRptfsel 255
                                     +el++    ++p++R  + ++
  gene370|gene370|rna370|rna370 289 AQELIRGMIVAQPSSRMGLDQV 310
                                    *****99999999999988876 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.7   5.4e+03      20      44 ..      64      88 ..      61      92 .. 0.88
   2 !   39.9   0.0   1.5e-13   2.9e-10     155     285 ..     173     301 ..     149     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.7
                    Kinase-like 20 lkkgdrsvvfevkdqetgeplavkv 44
                                   l+ g +s+v++  d+  ge++a+kv
  gene370|gene370|rna370|rna370 64 LGIGSSSKVVLGCDVHSGEKVAIKV 88
                                   78889999**************998 PP

  == domain 2  score: 39.9 bits;  conditional E-value: 1.5e-13
                    Kinase-like 155 rlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve..kgfaPpEllgsrggytrknktkmthkld 232
                                      + +++ + +vh +++ +n+l de+  ++l +f+    + +k  l++ +    fa pEll  + +           ++d
  gene370|gene370|rna370|rna370 173 SAIDYIHRNSIVHRDLKIENILIDENDNVKLIDFGLSNFYDNKTLLNTFCgsLYFAAPELLQGQ-R-------YCGPEID 244
                                    45679999***************************99999999999999966779*****9873.3.......35679** PP

                    Kinase-like 233 aWqlGlviyriwclklPltlateeakeew....kfklckkipekvkaLlkkfLqlsq 285
                                    +W lG+v y i c  +P++    ++ ++     +fk ck i+++ + L+++++  + 
  gene370|gene370|rna370|rna370 245 VWSLGVVLYAILCGCVPFDDENVQGLQAKikdaDFKFCKTISKEAQELIRGMIVAQP 301
                                    ******************9876544333335559******************97765 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.6   8.3e-09   1.7e-05     228     261 ..     183     215 ..      62     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 8.3e-09
                  Haspin_kinase 228 FEHRdLhldniLvdknlnvtlidlklsRlesseg 261
                                      HRdL+++niL+d+n nv lid+ ls + ++ +
  gene370|gene370|rna370|rna370 183 IVHRDLKIENILIDENDNVKLIDFGLSNFYDN-K 215
                                    56*************************99733.2 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.6e-08   0.00011      95     166 ..     140     206 ..     132     213 .. 0.81
   2 ?   -2.9   0.0       1.8   3.7e+03      42      80 ..     339     378 ..     318     384 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.6e-08
                            Kdo  95 lterlegaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                    + e ++g q L d++ +   l+e+  ++ ++++  +i  +hr  + H+dl + nil+++++    ++ liD+
  gene370|gene370|rna370|rna370 140 IFEYVKGKQ-LYDIIISNGPLKEKEGQRYFRQILSAIDYIHRNSIVHRDLKIENILIDEND----NVKLIDF 206
                                    555555544.4444444344788899999*******************************9....999***9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                            Kdo  42 gklskdlyrfk.lgrtravrEfrllkrLeeagvavpkpva 80 
                                    +k +k+  r+  ++ + + rE+r  ++  ++ + +++ ++
  gene370|gene370|rna370|rna370 339 EKYIKSISRAVrFQFPNMEREIRRFHKICKEEIGTLEQIY 378
                                    4555555555557777778888888888888887777766 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.27   5.4e+02      70      95 ..     137     168 ..     118     182 .. 0.72
   2 !   18.0   0.4   1.1e-06    0.0022     165     196 ..     180     209 ..     167     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.27
                                    EEEEEE----EE-SS......HHHHHHHHHHH CS
                            APH  70 lfalieyvpgrsllr......klsaaqlpell 95 
                                    +f+++eyv g++l++      +l +++ ++++
  gene370|gene370|rna370|rna370 137 YFLIFEYVKGKQLYDiiisngPLKEKEGQRYF 168
                                    89***********9977666655555555555 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.1e-06
                                    -EEEE-SS-SGGGEEEC..TTEEEEE---TT- CS
                            APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfeda 196
                                    + +++H+Dl+  N+l+d++d+    +iDf+++
  gene370|gene370|rna370|rna370 180 RNSIVHRDLKIENILIDENDNVK--LIDFGLS 209
                                    6789*************888887..****986 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.1e-06    0.0023      83     150 ..     139     207 ..     132     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                                    EEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GT CS
                           RIO1  83 lvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvs 150
                                    l+ e+++ +++    +++ + +e+e +++++++l++ +  ++++ +vH DL   N+l+de+ +v +ID++
  gene370|gene370|rna370|rna370 139 LIFEYVKGKQLYDIIISNGPlKEKEGQRYFRQILSA-IDYIHRNSIVHRDLKIENILIDENdNVKLIDFG 207
                                    889999955555555666665589999999999996.55666******************99******97 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05     0.047     322     389 ..     178     236 ..     162     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                 Pkinase_fungal 322 LflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkge 389
                                     +    i+HrD  ++Nili      ++++  LiD+ l   +++   +   ++  G l+F a e+l+g+
  gene370|gene370|rna370|rna370 178 IH-RNSIVHRDLKIENILID-----ENDNVKLIDFGLSNFYDN---KTLLNTFCGSLYFAAPELLQGQ 236
                                    45.788*************9.....567889*******99995...3334679999999999999975 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   0.00015       0.3     147     174 ..     183     209 ..     161     222 .. 0.81
   2 ?   -2.1   0.0       1.2   2.4e+03     117     140 ..     346     369 ..     322     377 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                                    EE-S--SGGGEEE.-CTTEEEE--GTT- CS
                 Choline_kinase 147 fcHnDlqegNillnkeekklvlIDFEYa 174
                                      H Dl  +Nil  +e++++ lIDF  +
  gene370|gene370|rna370|rna370 183 IVHRDLKIENILI-DENDNVKLIDFGLS 209
                                    45***********.999********766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                    CCHCCCTHHHHHHHHHTHHHHHHC CS
                 Choline_kinase 117 kqlklinledlekeleklekllee 140
                                    +++  +++ ++e+e+ +++k+++e
  gene370|gene370|rna370|rna370 346 SRAVRFQFPNMEREIRRFHKICKE 369
                                    455566777888888888888843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3547.46
//
Query:       gene371|gene371|rna371|rna371  [L=569]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-13   51.9   0.0    2.8e-13   50.8   0.0    1.6  1  CAP       Cysteine-rich secretory protein family


Domain annotation for each model (and alignments):
>> CAP  Cysteine-rich secretory protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   1.6e-17   2.8e-13       1     126 []      20     138 ..      20     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 1.6e-17
                                    HHHHHHHHHHTT----EE-HHHHHHHHHHHHHHHHH...T---S-GGG--HHHHHHTT-T.......EEEEEES--CCCH CS
                            CAP   1 leahNeyRaaaglppLkwdatLekaAqdhardcaash..sdsssspeggdllkyaenagk.......eniaaaseaaeda 71 
                                    l+++N++R ++ +  L+  ++L kaA  ++ +++++    ++++s+ g++l ++ ++++          +++++++++++
  gene371|gene371|rna371|rna371  20 LRYTNKFRNEHSMEELYSLPSLQKAADLQVLHMCKKAklTHDGPSGLGSSLSGRLKKFDFvglnigeNIAKQENDDYKEV 99 
                                    789******************************99999*************************9985588888889**** PP

                                    HHHHHTSHH.............HHHHHT-SS--EEEEEEEEBTTS-E..EEEEEE CS
                            CAP  72 vdsWysepgtynkgketegsighftnllwpkstkvGcavatcgngsftfivvcny 126
                                    v+ W+++++             h++n+l  ++ + G+a   +++g+   ++v+++
  gene371|gene371|rna371|rna371 100 VKLWMKSEK-------------HRNNIL-GDYVYSGVATCIGKDGNR--YWVQVF 138
                                    *********.............****99.****************77..****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3542.13
//
Query:       gene372|gene372|rna372|rna372  [L=549]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.5e-10   38.4   0.2    2.2e-09   37.1   0.2    1.6  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.055   13.6   0.0    1.9  2  DUF5340     Family of unknown function (DUF5340)
       0.32   10.5   1.7       0.72    9.3   1.7    1.6  1  Spo7        Spo7-like protein


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.2   3.7e-13   2.2e-09      53     152 ..     394     492 ..     376     542 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 3.7e-13
                                    HHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS..SSEEEEEEEEEE-TTS-.. CS
                     MS_channel  53 iillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvtsnieNlsr.esgtrrikvsigvtyssdvk 131
                                    +++ + kpf++GD v i +i  +V d+gl+ t++   ++++++iPn ++++++i+Nl++ ++ ++r++++++ t + + +
  gene372|gene372|rna372|rna372 394 VFIFLVKPFDVGDKVLIDGILHKVYDMGLLYTSFV-VEKKVTVIPNTKIMDKTIVNLRKaRTSQKRFEFTFSNTPEFK-E 471
                                    688899************************99986.5677*******************9999999999999998888.8 PP

                                    .HHHHHHHHHHHHHH-TTB-T CS
                     MS_channel 132 klekvleelkealkekpevlk 152
                                    k+ ++   + +++ ++p+v +
  gene372|gene372|rna372|rna372 472 KAGELSAAIEKEVGSDPNVYT 492
                                    899999999999888888876 PP

>> DUF5340  Family of unknown function (DUF5340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.98   5.8e+03      11      22 ..      58      69 ..      56      78 .. 0.80
   2 ?   13.6   0.0   9.2e-06     0.055      37      60 ..     442     465 ..     425     469 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.98
                        DUF5340 11 HYEllLqlLErq 22
                                   HY l+L  LE +
  gene372|gene372|rna372|rna372 58 HYSLILPKLEAN 69
                                   9*****999865 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.2e-06
                        DUF5340  37 vqqliitLRKAlaqQkqLEesceq 60 
                                    + + i++LRKA + Qk++E ++++
  gene372|gene372|rna372|rna372 442 MDKTIVNLRKARTSQKRFEFTFSN 465
                                    5789***************98875 PP

>> Spo7  Spo7-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.7   0.00012      0.72      31      98 ..      82     149 ..      67     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00012
                           Spo7  31 ytlflllLalviafflyalflapredgsgvggsvywvve.vvekvlliggvvTl.vLfwlsGeyertivi 98 
                                     ++fl+  +++ ++ l   +l+     ++vg+++  + + ++++  +i+ v Tl vL ++ G y+r+i i
  gene372|gene372|rna372|rna372  82 LMCFLIGVMVWFVLELTLTYLSI--TLKKVGEKQGFLQStLIKNGWFISLVLTLlVLSFIMGSYSRGIEI 149
                                    45677777777777777777733..444555555555551556667777777753799*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 3015.34
//
Query:       gene373|gene373|rna373|rna373  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-84  282.5   7.0    2.5e-84  282.2   7.0    1.1  1  14-3-3     14-3-3 protein
  ------ inclusion threshold ------
      0.066   12.6   1.1       0.13   11.6   1.1    1.5  1  RNase_E_G  Ribonuclease E/G family
      0.089   13.3   0.6       0.44   11.1   0.0    2.2  2  TPR_19     Tetratricopeptide repeat
       0.31   10.4   5.6       0.48    9.7   3.6    1.9  2  PhoU_div   Protein of unknown function DUF47


Domain annotation for each model (and alignments):
>> 14-3-3  14-3-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.2   7.0   5.6e-88   2.5e-84       1     222 []      12     239 ..      12     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 282.2 bits;  conditional E-value: 5.6e-88
                                    HHHHHHHCCHHHHHHHHHCHHHHC....SS---HCHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCTCCHHHHHHHHHHH CS
                         14-3-3   1 laklaeqaeryddmveymkkvvel....keeLskeernlLsvayKnvvgarRaswrvlssieqkeeskeekkvelikeyr 76 
                                    +a l++ aeryddm++ mk++v l    k+ L++  rnl+svayKn+v++rR+swr+l+s +qk e k+ + v++i+e  
  gene373|gene373|rna373|rna373  12 KANLSDMAERYDDMAKEMKHAVMLaheeKHTLNVMARNLFSVAYKNLVSSRRSSWRMLCSERQKLEGKDPSVVHVIDEKI 91 
                                    5899*****************9999999999******************************99999999999******** PP

                                    HHHHHHHHHHHHHHHHHHHHCCH.CH....-SHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHHHHTT CS
                         14-3-3  77 ekiekeLkeiceevlelldktli.pka...tseeskvfylkmkgDyyRYlaEfaegeekkeaaekakeaYeeAleiakke 152
                                    + +e+eL ++c+evl+++ ++++       ++ e ++f+lkmkgDyyRY+aE+ +g+e++e++++a e+Y+eA+e a k+
  gene373|gene373|rna373|rna373  92 KMVEEELLRFCDEVLDIITTYILsL-EdakKNIEYNIFFLKMKGDYYRYKAEVITGSEHSEVSKHAAESYREATEKA-KT 169
                                    ***********************53.2245788********************************************.88 PP

                                    TGCC-HHHHHHHHHHHHHHHCTT--HHHHHHHHHHHHHCCHCCCCCS.TTTHHHHHHHHHHHHHHHHHHC CS
                         14-3-3 153 lqpthpirLglaLNySVflyeilnspekAcelakkafdeaiaeldelseesykdstlilqlLrdnltlWt 222
                                    l+pt+pi+LglaLNySVf+yeiln++ekAc++ak afdeai+eld+lsee+y+dstli+qlLrdnltlWt
  gene373|gene373|rna373|rna373 170 LPPTNPIKLGLALNYSVFHYEILNDSEKACSIAKGAFDEAIKELDTLSEEHYRDSTLIMQLLRDNLTLWT 239
                                    *********************************************************************8 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1     3e-05      0.13      53     142 ..       4      92 ..       1     113 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                      RNase_E_G  53 gaseeel.ekdleelkkkweeilekakkrkapsllyeeedlllrvlrdllnedieeivvddkelyeeikeyleevapele 131
                                    ++ ee+l +++l+ ++++++++ +++k  +a  l +ee++ l+ + r+l++  ++++v + +++++++++  ++++ +  
  gene373|gene373|rna373|rna373   4 KQYEEALqKANLSDMAERYDDMAKEMK--HAVMLAHEEKHTLNVMARNLFSVAYKNLVSSRRSSWRMLCSERQKLEGKDP 81 
                                    44444451568999***********98..77999999999****************************999988888888 PP

                      RNase_E_G 132 ekvelyeeeep 142
                                    + v++ +e+ +
  gene373|gene373|rna373|rna373  82 SVVHVIDEKIK 92 
                                    77777744434 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.36   1.6e+03       3      12 ..       2      11 ..       1      28 [. 0.64
   2 ?   11.1   0.0   9.9e-05      0.44      34      59 ..     199     224 ..     198     231 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.36
                         TPR_19  3 aegdyaeAla 12
                                   a+++y+eAl+
  gene373|gene373|rna373|rna373  2 ASKQYEEALQ 11
                                   5556666633 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.9e-05
                         TPR_19  34 allalgqldeAealLdalpeedpdda 59 
                                    + +a g +deA++ Ld+l ee   d+
  gene373|gene373|rna373|rna373 199 CSIAKGAFDEAIKELDTLSEEHYRDS 224
                                    7799****************998875 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.6   0.00011      0.48      78     187 ..      13     128 ..      10     133 .. 0.83
   2 ?    0.1   0.0     0.091   4.1e+02     129     151 ..     205     227 ..     189     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                       PhoU_div  78 edllelveslDeildvlediamlvtlrkvefpeelkdeflallkktveaiealaevieeleklletalskk...diveei 154
                                    ++l++++e  D+++ ++++++ml    k  ++   ++ f +  k +v + +   +++ +  + le+    +   +i e+i
  gene373|gene373|rna373|rna373  13 ANLSDMAERYDDMAKEMKHAVMLAHEEKHTLNVMARNLFSVAYKNLVSSRRSSWRMLCSERQKLEGKDP-SvvhVIDEKI 91 
                                    6899*************************************************9999877766665433.3455666789 PP

                       PhoU_div 155 eslEde....iDqlqrklikklfsredasnplevlll 187
                                    + +E+e    +D++   + +  +s eda   +e+ ++
  gene373|gene373|rna373|rna373  92 KMVEEEllrfCDEVLDIITTYILSLEDAKKNIEYNIF 128
                                    9999865555899999999999999998888888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.091
                       PhoU_div 129 alaevieeleklletalskkdiv 151
                                    a +e+i+el++l e+ ++ + ++
  gene373|gene373|rna373|rna373 205 AFDEAIKELDTLSEEHYRDSTLI 227
                                    57899999999999999977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1527.25
//
Query:       gene374|gene374|rna374|rna374  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2321.38
//
Query:       gene375|gene375|rna375|rna375  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-12   45.6   0.0    2.1e-11   44.2   0.0    1.7  2  AAA_22           AAA domain
    8.4e-12   45.7   0.0    5.5e-11   43.0   0.0    2.2  3  AAA              ATPase family associated with various cellul
    3.1e-07   30.9   0.0    1.1e-05   25.9   0.0    2.4  2  AAA_16           AAA ATPase domain
    4.7e-06   26.5   0.0    1.1e-05   25.3   0.0    1.6  1  Cdc6_C           CDC6, C terminal winged helix domain
    0.00028   21.4   0.0     0.0047   17.5   0.0    2.5  3  AAA_18           AAA domain
     0.0016   18.2   0.0     0.0031   17.3   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0035   17.4   0.0       0.11   12.5   0.0    2.5  2  AAA_14           AAA domain
      0.007   16.5   0.2      0.014   15.5   0.2    1.4  1  AAA_lid_10       AAA lid domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.026   14.5   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
      0.012   15.8   0.0      0.033   14.3   0.0    1.8  2  AAA_33           AAA domain
       0.02   14.7   0.0      0.038   13.8   0.0    1.5  1  AAA_11           AAA domain
      0.027   13.9   0.1       0.11   11.9   0.0    2.0  2  TniB             Bacterial TniB protein
      0.045   13.7   0.6         16    5.4   0.0    3.0  3  NTPase_1         NTPase
      0.045   13.0   0.0      0.081   12.2   0.0    1.3  1  Zeta_toxin       Zeta toxin
      0.046   13.6   0.0       0.18   11.7   0.0    2.0  1  NACHT            NACHT domain
       0.15   12.4   0.1       0.71   10.2   0.0    1.9  2  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.9e-14   2.1e-11       5     117 ..      26     127 ..      23     148 .. 0.80
   2 ?   -2.5   0.0       5.1   5.7e+03      55      85 ..     244     274 ..     206     285 .. 0.52

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.9e-14
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                     gi+++ G +G+GKT+++ +l+e+          +++++f +++++   +++++++l +l   +++  +s++  l  l+q
  gene375|gene375|rna375|rna375  26 GGIVYISGVPGAGKTHTVLELMERR---------QVSYLFLNATELRMKREVYKWILTNLP--CSS--GSKRMHLMNLQQ 92 
                                    799*********************9.........9************************99..888..555555588999 PP

                         AAA_22  85 alraravielliiDEaqhlr..seealeeLrslln 117
                                    ++ ++  +++++iDE++ l   ++e+l ++ ++  
  gene375|gene375|rna375|rna375  93 HFMECTLPHVIVIDEVDILVgkTQEVLYNVFDMPY 127
                                    99999999**********97655777777755544 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.1
                         AAA_22  55 dllrellralglelkaerlsseellealeqa 85 
                                    +++++   +l +e ++er +  el+e +   
  gene375|gene375|rna375|rna375 244 SFYQKAILFLFNESERERMKVNELYEEFISF 274
                                    3444433333333333344444444444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   4.9e-14   5.5e-11       1     118 [.      29     148 ..      29     161 .. 0.89
   2 ?   -0.9   0.0       1.8     2e+03      21      51 ..     175     205 ..     168     227 .. 0.60
   3 ?   -2.7   0.0       6.8   7.6e+03      78      99 ..     256     277 ..     254     294 .. 0.71

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.9e-14
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.............STTHHHHHHHHHHHHHHHTSTSEEEEEETG CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk.............yvgesekkirelfkeakekakpsilfiDEi 67 
                                    v+++G pG GKT ++  +++  +v++l ++++el+ k               g + +++ +l ++  e   p++++iDE+
  gene375|gene375|rna375|rna375  29 VYISGVPGAGKTHTVLELMERRQVSYLFLNATELRMKrevykwiltnlpcSSGSKRMHLMNLQQHFMECTLPHVIVIDEV 108
                                    6899*******************************778**********998899999988888886666568******** PP

                                    GGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHH CS
                            AAA  68 dalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpa 118
                                    d l+++            +++L++++d    k+skv++ +++n+++ +++ 
  gene375|gene375|rna375|rna375 109 DILVGKT-----------QEVLYNVFDMPYLKNSKVLLFVISNTINLPERL 148
                                    *******...........**************************8766654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.8
                                    HHTHEEEEEETTTCSSSSTTHHHHHHHHHHH CS
                            AAA  21 elgvefleisgsellskyvgesekkirelfk 51 
                                     ++ + ++ ++ el+sk +g+ + ++r++ +
  gene375|gene375|rna375|rna375 175 MAEGHRMKRKCIELISKRIGAISGDVRKVKD 205
                                    5555566677788888866666665555433 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.8
                                    CCHHHHHHHHHHHHHHHHTTTS CS
                            AAA  78 eseeeervvnqLlteldgvkkk 99 
                                    ese e+  vn+L++e+  + k+
  gene375|gene375|rna375|rna375 256 ESERERMKVNELYEEFISFCKR 277
                                    6777888899999988777664 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   9.8e-09   1.1e-05       2      51 ..       3      53 ..       2      80 .. 0.78
   2 ?    2.8   0.0      0.12   1.3e+02     122     162 ..      90     126 ..      59     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 9.8e-09
                         AAA_16  2 lvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd 51
                                   ++GReee  +L+++l+  +++  +++v++sG +G GK+  v el+++ + +
  gene375|gene375|rna375|rna375  3 VIGREEEYLKLERYLDiFLSTEAGGIVYISGVPGAGKTHTVLELMERRQVS 53
                                   58**************65555555********************9854433 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                         AAA_16 122 llkrllallsrderplvlvlDdlqwadeaslqllaaLlrll 162
                                    l ++++   ++   p v+v+D+++ +   ++++l++ ++ +
  gene375|gene375|rna375|rna375  90 LQQHFM---EC-TLPHVIVIDEVDILVGKTQEVLYNVFDMP 126
                                    333333...33.3367********99999999999988875 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   9.8e-09   1.1e-05       3      61 ..     249     307 ..     248     316 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9.8e-09
                                    HHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE CS
                         Cdc6_C   3 alvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgilelekss 61 
                                    a++ l+++s++e +++ e+ye++ s C++ +v+ +   e++dl+  L  +gil +++s+
  gene375|gene375|rna375|rna375 249 AILFLFNESERERMKVNELYEEFISFCKRSDVKEVGFFEYLDLIEALVGYGILGCRNSG 307
                                    78889999************************************************994 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.2e-06    0.0047       2      94 ..      30     120 ..      29     147 .. 0.81
   2 ?   -2.7   0.0       7.5   8.4e+03      78      82 ..     206     210 ..     175     233 .. 0.52
   3 ?    0.9   0.0      0.57   6.4e+02       3      22 ..     300     319 ..     299     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.2e-06
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlv 78 
                                     ++G+pG+GKt    eL +r ++     n +++  +++ + +   + l+ s   +++ l++l++ ++e+      ++++v
  gene375|gene375|rna375|rna375  30 YISGVPGAGKTHTVLELMERRQVsylFLNATELRMKREVYKWILTN-LPCSSGSKRMHLMNLQQHFMECTL----PHVIV 104
                                    699**************99975556888888888888888887777.777777777778889999999987....9999* PP

                         AAA_18  79 idghlaeleseaakdi 94 
                                    id +     +++ + +
  gene375|gene375|rna375|rna375 105 IDEVDILVGKTQEVLY 120
                                    *998876666665555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.5
                         AAA_18  78 vidgh 82 
                                    vid +
  gene375|gene375|rna375|rna375 206 VIDRV 210
                                    22222 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.57
                         AAA_18   3 ltGtpGvGKttlakeLskrl 22 
                                    + G+  +GK  la  L+++ 
  gene375|gene375|rna375|rna375 300 ILGCRNSGKEVLAMVLKEEV 319
                                    88999********9998873 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.7e-06    0.0031       2      70 ..      30     107 ..      29     111 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.7e-06
                Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegk............pklpnlsvrtvdsflmalvkstkgkililD 69 
                                    +++GvpG+GK++ + +l++ + +     +++el+ ++             + +++ +  ++++  m ++     +++++D
  gene375|gene375|rna375|rna375  30 YISGVPGAGKTHTVLELMERRQVSYLFLNATELRMKREvykwiltnlpcsSGSKRMHLMNLQQHFMECTL---PHVIVID 106
                                    699***************9994444566667777777766666776644444444444444444444444...4788888 PP

                Viral_helicase1  70 E 70 
                                    E
  gene375|gene375|rna375|rna375 107 E 107
                                    7 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0    0.0001      0.11       3      76 ..      27     111 ..      25     145 .. 0.68
   2 ?    2.1   0.0      0.16   1.8e+02       6      27 ..     299     319 ..     297     339 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd.................kkladpe.....kllelilekl 60 
                                     i+ i+G+  +GKT  + +l++++     s+l++n  + r                  +     +     +l + ++e  
  gene375|gene375|rna375|rna375  27 GIVYISGVPGAGKTHTVLELMERRQ---VSYLFLNATELRMkrevykwiltnlpcssgS-----KrmhlmNLQQHFMECT 98 
                                    6899*****************8888...7888888888777555555555554444332.....0332335667777763 PP

                         AAA_14  61 keekktylflDEiqev 76 
                                         +++++DE+  +
  gene375|gene375|rna375|rna375  99 ---LPHVIVIDEVDIL 111
                                    ...4589999999754 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                         AAA_14   6 vitGaRrvGKTtllkqlikell 27 
                                     i G+R +GK +l+  l ke+ 
  gene375|gene375|rna375|rna375 299 GILGCRNSGKEVLAMVL-KEEV 319
                                    589*******9996444.5554 PP

>> AAA_lid_10  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.2e-05     0.014      43      76 ..     179     212 ..     174     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                                    --------HHHHHHHHHHT-TTTTHHHHHHHHHH CS
                     AAA_lid_10  43 lkisddaieiasrkvAsvsgdarrAlkiCkrAvE 76 
                                    ++++ + ie++s+++  +sgd r+   + +r  E
  gene375|gene375|rna375|rna375 179 HRMKRKCIELISKRIGAISGDVRKVKDVIDRVRE 212
                                    89**********************9888887766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-05     0.026       4      91 ..      31     125 ..      28     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                                    EE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.............--------...G-SEEEEESGGG CS
                          AAA_5   4 LvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik....ngttslvdsplvraar...egeilvlDEver 76 
                                    + G pG gK+  + +l ++ + +++  + t+   ++++   + ++    +g ++++   l + +     ++++v+DEv+ 
  gene375|gene375|rna375|rna375  31 ISGVPGAGKTHTVLELMERRQVSYLFLNATELRMKREVYKWILTNlpcsSGSKRMHLMNLQQHFMectLPHVIVIDEVDI 110
                                    77**********************999999987778876666666999977777776666555445559**********9 PP

                                    --HHHHHHHHHHHHS CS
                          AAA_5  77 aesevlnsLlsllee 91 
                                    +  +++++L ++++ 
  gene375|gene375|rna375|rna375 111 LVGKTQEVLYNVFDM 125
                                    99*******999885 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-05     0.033       2      37 ..      29      66 ..      28      98 .. 0.85
   2 ?   -2.7   0.0       5.3   5.9e+03      24      39 ..     218     233 ..     209     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrl 37
                                   v++ G+pG+GK++ + +l+++++  + +l+  +lr + 
  gene375|gene375|rna375|rna375 29 VYISGVPGAGKTHTVLELMERRQvsYLFLNATELRMKR 66
                                   8999****************999999999988877654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                         AAA_33  24 gavllssdtlrrrlfg 39 
                                    +a++l+ d ++r++++
  gene375|gene375|rna375|rna375 218 DAEVLDVDGIMRKMYA 233
                                    3889999999999886 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-05     0.038      15      41 ..      24      50 ..      14     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                         AAA_11 15 seseitliqGPPGtgKTktivellsql 41
                                   +  +i+ i+G PG gKT+t++el+++ 
  gene375|gene375|rna375|rna375 24 EAGGIVYISGVPGAGKTHTVLELMERR 50
                                   3445999****************9886 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.11      66     136 ..      48     115 ..      29     137 .. 0.79
   2 ?   -1.3   0.0       1.1   1.2e+03      88     121 ..     248     281 ..     242     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                           TniB  66 daekvpvlvvqappkpdekrlyaaiLealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsa 136
                                    ++++v  l ++a +   +++ y+ iL++l     +  +  +l +   ++++ + ++v++iDE++ l+ g+ 
  gene375|gene375|rna375|rna375  48 ERRQVSYLFLNATELRMKREVYKWILTNLPCS--SGSKRMHLMNLQQHFMECTLPHVIVIDEVDILV-GKT 115
                                    566778888999999999*********99666..566666777777799**************8665.544 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
                           TniB  88 aaiLealgaplkararvskleqqvlrllrelkvr 121
                                    +aiL  +++  ++r +v++l+++ ++++++ +v+
  gene375|gene375|rna375|rna375 248 KAILFLFNESERERMKVNELYEEFISFCKRSDVK 281
                                    5799999999999999*****9999999998886 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.014        16       2      22 ..      29      49 ..      28      67 .. 0.83
   2 ?    4.6   0.1     0.024        27      86     135 ..      87     141 ..      77     154 .. 0.75
   3 ?   -0.5   0.0      0.88   9.9e+02      68     135 ..     190     257 ..     153     273 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                                   EEEE--TTSSHHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                   v+i+G pG GKt  v  ++e 
  gene375|gene375|rna375|rna375 29 VYISGVPGAGKTHTVLELMER 49
                                   79**********888777664 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                                    HHHHHHHHHHH-...EEEE---STTGGG-HHHHHHHHHH..HTTTSEEEEE--SS CS
                       NTPase_1  86 lealrkalsead...viviDEiGkmElkskkfkeaveev..Lksekpvlavihrr 135
                                    l +l++ + e+    viviDE+  +  k++++   v ++  Lk++k++l+vi ++
  gene375|gene375|rna375|rna375  87 LMNLQQHFMECTlphVIVIDEVDILVGKTQEVLYNVFDMpyLKNSKVLLFVISNT 141
                                    555666665554455*******999999999999998765588999999999876 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.88
                                    SSEETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS CS
                       NTPase_1  68 eprvgkyvvdvesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk.sekpvlavihrr 135
                                    + r+g +  dv +++++ ++ +r++ +++d  v+D  G m    + + +   + L+  +k +l+ + ++
  gene375|gene375|rna375|rna375 190 SKRIGAISGDVRKVKDV-IDRVRESEKGEDAEVLDVDGIMRKMYAPVYTYCLQGLSfYQKAILFLFNES 257
                                    45677777777777775.566666666666666666666666666666666666665566666555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.2e-05     0.081      18      56 ..      28      64 ..      15      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-05
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                   ++ ++G pGAGK+++  +l ++   q +++ l++++lR 
  gene375|gene375|rna375|rna375 28 IVYISGVPGAGKTHTVLELMERR--QVSYLFLNATELRM 64
                                   6889**********999998885..999*****999996 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.18       3     142 ..      29     151 ..      27     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvsevwavllelper 82 
                                    v + G +G GKT+ + +l++  + ++         +fl+  el+ +     + + +  +lp +++  +    +l+ l++ 
  gene375|gene375|rna375|rna375  29 VYISGVPGAGKTHTVLELMERRQVSY---------LFLNATELRMKR---EVYKWILTNLPCSSGSKRM---HLMNLQQH 93 
                                    7899********98877776544444.........455666666653...5677777777777777766...56666666 PP

                                    EE.......EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE CS
                          NACHT  83 lL.......lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeqleea 142
                                     +       +++D +D lv + ++        +L + +   +l+++++ll v +++  +l+e l e+
  gene375|gene375|rna375|rna375  94 FMectlphvIVIDEVDILVGKTQE--------VLYNVFDMPYLKNSKVLLFVISNTI-NLPERLFEP 151
                                    666667777**********97777........9*************99999999888.666655544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00063      0.71      10      34 ..      26      50 ..      19      64 .. 0.86
   2 ?   -0.7   0.0       1.4   1.6e+03      98     117 ..      97     114 ..      77     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00063
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivall 34
                                    +++ + + pG GKT+++ + ++  
  gene375|gene375|rna375|rna375 26 GGIVYISGVPGAGKTHTVLELMERR 50
                                   57899*************9998865 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                         AAA_19  98 kklqeeellivDEfqdvdel 117
                                     +l    ++++DE+  +   
  gene375|gene375|rna375|rna375  97 CTL--PHVIVIDEVDILVGK 114
                                    333..558999*99876633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 2056.12
//
Query:       gene376|gene376|rna376|rna376  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-23   81.1   0.7      4e-23   81.1   0.7    1.6  2  Myb_DNA-bind_7   Myb DNA-binding like
    5.6e-06   26.5   0.0    1.4e-05   25.2   0.0    1.6  1  Myb_DNA-binding  Myb-like DNA-binding domain
  ------ inclusion threshold ------
      0.057   12.7   0.0      0.062   12.6   0.0    1.1  1  PAD_porph        Porphyromonas-type peptidyl-arginine deimina
      0.066   13.5   0.2       0.12   12.7   0.2    1.5  1  Myb_DNA-bind_6   Myb-like DNA-binding domain
        0.2   11.9   1.7       0.22   11.8   0.1    2.1  2  CotJB            CotJB protein


Domain annotation for each model (and alignments):
>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.95   3.4e+03      51      54 ..      32      35 ..      11      66 .. 0.64
   2 !   81.1   0.7   1.1e-26     4e-23       1      78 [.      77     154 ..      77     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.95
                 Myb_DNA-bind_7 51 kEer 54
                                   +Eer
  gene376|gene376|rna376|rna376 32 SEER 35
                                   3333 PP

  == domain 2  score: 81.1 bits;  conditional E-value: 1.1e-26
                 Myb_DNA-bind_7   1 sfrkrkktkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKFkkEerknpeliekalkkrkeldleefkee 78 
                                    +f+k+k + +Wsk+e e+FYkaL+ +G +Fsli++lfp+++r+++K+K+ kE + npe+i++ l++ k +d   +++ 
  gene376|gene376|rna376|rna376  77 TFSKKKGALRWSKKEIELFYKALEICGIEFSLISSLFPNKERKHIKAKYIKEAKVNPERINEVLNEYKTFDQVAYNKL 154
                                    699********************************************************************9988876 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.9e-09   1.4e-05       3      44 ..      86     127 ..      85     129 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.9e-09
                                    SSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHH CS
                Myb_DNA-binding   3 kWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrn 44 
                                    +W++ E el+++a++  G  +++I++ ++++ +k+++ ++ +
  gene376|gene376|rna376|rna376  86 RWSKKEIELFYKALEICGIEFSLISSLFPNKERKHIKAKYIK 127
                                    7**************************************975 PP

>> PAD_porph  Porphyromonas-type peptidyl-arginine deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.062     176     266 ..      37     132 ..      15     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                    SEEEEESS-.STTTT....SSS-GGGTEEEEETTEEEEEE-S-TTSTTHHHHHHHHHHHHTTB-TTSSB-EEEEEEB-S- CS
                      PAD_porph 176 ekviwlkeG.lagdd....tdgHiDtlarfvapgtvllareddeedenyealkealeiLkaatdakgrklevvelplpee 250
                                    e+++++k+G ++ +d     d H D  + ++++++++++++ ++++   + +k+  e   +a +  g ++ ++   +p++
  gene376|gene376|rna376|rna376  37 EEILMIKDGeIVVNDanmyVDTHKDMEMEVMEDDRIVTSSTFSKKKGALRWSKKEIELFYKALEICGIEFSLISSLFPNK 116
                                    78999999995555559999**********************************************************99 PP

                                    -EEEE--BTT--EEET CS
                      PAD_porph 251 vrerlpasYaNflivn 266
                                    +r+ ++a Y+    vn
  gene376|gene376|rna376|rna376 117 ERKHIKAKYIKEAKVN 132
                                    9999999998665555 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   3.3e-05      0.12       1      51 [.      87     137 ..      87     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                 Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkLrpkisrkk 51 
                                    W++ E e+  k  e +g ++++I++ ++++  k+++ +++++ +++++r++
  gene376|gene376|rna376|rna376  87 WSKKEIELFYKALEICGIEFSLISSLFPNKERKHIKAKYIKEAKVNPERIN 137
                                    888888888888899999*********88************9988888876 PP

>> CotJB  CotJB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   6.1e-05      0.22       6      28 ..      41      63 ..      36     103 .. 0.86
   2 ?   -1.6   0.1      0.93   3.3e+03      39      39 ..     134     134 ..     114     157 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                          CotJB  6 eiqelsFavvdlnLYLDthPddk 28
                                    i+  + +v+d n+Y Dth d +
  gene376|gene376|rna376|rna376 41 MIKDGEIVVNDANMYVDTHKDME 63
                                   5778889************9866 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                          CotJB  39 k 39 
                                    +
  gene376|gene376|rna376|rna376 134 E 134
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 961.48
//
Query:       gene377|gene377|rna377|rna377  [L=229]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-23   82.2  15.1    3.7e-23   81.9  15.1    1.1  1  Far-17a_AIG1  FAR-17a/AIG1-like protein


Domain annotation for each model (and alignments):
>> Far-17a_AIG1  FAR-17a/AIG1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9  15.1   2.1e-27   3.7e-23       7     197 ..      18     208 ..      13     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.1e-27
                   Far-17a_AIG1   7 lstlcsyaalfypfhsekelanea..ayGgkfkyLtfiglvlqalfftlallaDeltlsallk.lrdnllavlafPvevl 83 
                                    l+++c+y a++y   +e  + + +    Gg+  y+t ++l++++++  l++   ++ +s +++ +rd+l   +++P+e l
  gene377|gene377|rna377|rna377  18 LLIFCVYGATDYSQPKE--WVDFVnnLAGGSHIYITQLSLYMTIITLVLSYCVKHMGVSSIKEiYRDFL--SITLPMEGL 93 
                                    67788888888877764..444444599**********************9999898887766157777..7778***** PP

                   Far-17a_AIG1  84 vsvlFWgLyliDrelvypklldel...ipdWlnhsmHtvvlvailleifllkhkypsrlaalalsaafallYliwierva 160
                                    v+++FW+L  iD++l+++k+l+++    p   ++s+H+  +++i+l +++   +  ++++   +  +f++ Y+i i+++ 
  gene377|gene377|rna377|rna377  94 VTTVFWTLNSIDPTLLKNKELYTAgvrTPLICEVSLHL--FPFIVLLVDQVGVNIYEKKRHYWFFGIFGFTYFIVIHHFQ 171
                                    *********************99985555566666666..88888888888888888888888889************** PP

                   Far-17a_AIG1 161 qfngvwvYPvlealslegrvlffalsavvmallylll 197
                                    + n++w YP+l+ +++  r ++ + ++++++++y+l 
  gene377|gene377|rna377|rna377 172 KLNDYWIYPFLGYMTILMRAVLVFTAVLLVVGYYKLF 208
                                    *********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1511.60
//
Query:       gene378|gene378|rna378|rna378  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-34  117.7   7.9    4.7e-34  117.5   7.9    1.0  1  Far-17a_AIG1  FAR-17a/AIG1-like protein
      0.004   16.7   0.8      0.004   16.7   0.8    1.7  2  4HB_MCP_1     Four helix bundle sensory module for signal tra
  ------ inclusion threshold ------
       0.25   10.1   5.2        1.2    7.8   0.1    2.1  2  DUF2207       Predicted membrane protein (DUF2207)
        7.2    6.8   7.8        1.8    8.8   0.9    2.7  3  Pox_A14       Poxvirus virion envelope protein A14


Domain annotation for each model (and alignments):
>> Far-17a_AIG1  FAR-17a/AIG1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5   7.9     1e-37   4.7e-34       5     198 ..      16     210 ..      12     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 1e-37
                   Far-17a_AIG1   5 vhlstlcsyaalfypfhsekelaneaayGgkfkyLtfiglvlqalfftlallaDeltlsallklrdnllavlafPvevlv 84 
                                    + ++++c+ya++++    e  ++++a++Ggkf yLt+i l+l+++ + l++++  +  ++l ++ + +l +++f++e +v
  gene378|gene378|rna378|rna378  16 LVFLGFCVYATTDFSLPPEIVEMSNATSGGKFVYLTIITLYLTIISTVLGYISKTRVGKRLEEIYKDML-AVTFSLEGIV 94 
                                    568899****9999999888888888****************************666666666777664.6689****** PP

                   Far-17a_AIG1  85 svlFWgLyliDrelvypklldel.ipd..WlnhsmHtvvlvailleifllkhkypsrlaalalsaafallYliwiervaq 161
                                    ++lFW+Ly+i+++l+++k l++  i++  ++++s H+  +++ill i++ + ++++r++++ ++++f++lY+++i+++ +
  gene378|gene378|rna378|rna378  95 TTLFWSLYFINPTLLKNKSLYKRgIREsfLTELSAHL--FPIILLLICQADVRLQKRKRCIYFIFGFGALYFLEICYFSF 172
                                    ******************9988768887788899998..9999999*******************************998 PP

                   Far-17a_AIG1 162 fn.gvwvYPvlealslegrvlffalsavvmallyllle 198
                                    +n g w+YP+++++++ +r+lf  +++++ +l y+ l 
  gene378|gene378|rna378|rna378 173 VNnGKWAYPIFRKMGWVQRILFVLIACFIGTLFYMGLL 210
                                    7626******************************9875 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.8   8.9e-07     0.004       5      53 ..      44      92 ..      40      98 .. 0.87
   2 ?   -3.2   1.2       1.2   5.3e+03      11      31 ..     193     213 ..     189     217 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.9e-07
                      4HB_MCP_1  5 rkKLillflllallliivGvvGlyslkkinknletmYedrllpikdlge 53
                                   + K++ l ++ + l+ii+ v+G++s +++ k le++Y+d l  +  l+ 
  gene378|gene378|rna378|rna378 44 GGKFVYLTIITLYLTIISTVLGYISKTRVGKRLEEIYKDMLAVTFSLEG 92
                                   6799************************************987766665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                      4HB_MCP_1  11 lflllallliivGvvGlyslk 31 
                                    lf+l+a +++ +  +Gl+ ++
  gene378|gene378|rna378|rna378 193 LFVLIACFIGTLFYMGLLATN 213
                                    455555555555566666555 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00027       1.2     378     445 ..       4      83 ..       1      87 [. 0.81
   2 ?    3.9   1.5     0.004        18     379     436 ..     148     212 ..     142     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00027
                        DUF2207 378 kklkklsalglgliilglilillallllvll............lvfllilllillliaiivlllfsrllgrrteeGaell 445
                                    +k+ ++   +l l++lg+++   + ++l +             +v+l i++l l +i+ ++ +++++++g+r ee ++ +
  gene378|gene378|rna378|rna378   4 RKTRSVLKEALKLVFLGFCVYATTDFSLPPEivemsnatsggkFVYLTIITLYLTIISTVLGYISKTRVGKRLEEIYKDM 83 
                                    45555556666777777777777777766669999*************************************99988766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.004
                        DUF2207 379 klkklsalglgliilglilillallllvll.......lvfllilllillliaiivlllfsrllgr 436
                                    k+k+ +++++g++ l+++ i+++ ++ ++         ++++  +l++l++++i +l++ +ll  
  gene378|gene378|rna378|rna378 148 KRKRCIYFIFGFGALYFLEICYFSFVNNGKwaypifrKMGWVQRILFVLIACFIGTLFYMGLLAT 212
                                    5667777777888888888888877777779*****99999999999999999999998777665 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1      0.29   1.3e+03      25      53 ..      21      48 ..       3      56 .. 0.60
   2 ?    8.8   0.9    0.0004       1.8      11      61 ..      47      98 ..      36     107 .. 0.84
   3 ?    1.3   0.4     0.083   3.7e+02      18      65 ..     160     206 ..     145     222 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                        Pox_A14 25 acifafvdfskststtdkawralsivsFi 53
                                    c++a  dfs   +  + +  a s+  F+
  gene378|gene378|rna378|rna378 21 FCVYATTDFSLPPEIVE-MSNATSGGKFV 48
                                   49999999997655443.55566665555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0004
                        Pox_A14 11 ystvliaGiiLLilacifafvdfskststtdkawralsivsFil.givillg 61
                                   + ++ i+ + L i++ ++ ++   ++++  +++++ +  v+F l giv +l 
  gene378|gene378|rna378|rna378 47 FVYLTIITLYLTIISTVLGYISKTRVGKRLEEIYKDMLAVTFSLeGIVTTLF 98
                                   667788899999*****************999*********97747777764 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.083
                        Pox_A14  18 GiiLLilacifafvdfskststtdkawralsivsFilg..ivillglllf 65 
                                    G +     c f fv+  k       ++r +  v  il   i+  +g+l +
  gene378|gene378|rna378|rna378 160 GALYFLEICYFSFVNNGKWAY---PIFRKMGWVQRILFvlIACFIGTLFY 206
                                    334444455666665555554...44555544444433003344555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1582.47
//
Query:       gene379|gene379|rna379|rna379  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-18   67.1   3.0    1.7e-14   54.6   0.8    2.0  2  TFIIA     Transcription factor IIA, alpha/beta subunit


Domain annotation for each model (and alignments):
>> TFIIA  Transcription factor IIA, alpha/beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   4.5e-06      0.08       1      42 [.       4      45 ..       4      60 .. 0.89
   2 !   54.6   0.8   9.7e-19   1.7e-14     370     415 .]     109     157 .]      97     157 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-06
                          TFIIA  1 vYrsvIedVIesvredFeeeGvdeqvLeeLkqlWesKllqsk 42
                                   +Y+ +I +VI++  +   e    ++ + eL++ W+++l++  
  gene379|gene379|rna379|rna379  4 IYEDIISEVISKLEQAGDEINMGKSAIHELRNEWRERLIEYT 45
                                   6*************************************9865 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 9.7e-19
                          TFIIA 370 tdn...vivCqYDKvhRsKNKWKftLKDGvmtvnGkdYVFsKAiGeaEW 415
                                    +dn    +vC+Y Kv+ sK KWK+t+K G +++++ d+VF+ A+Ge EW
  gene379|gene379|rna379|rna379 109 KDNvgnCMVCLYVKVNMSKGKWKCTFKQGFISIGNIDFVFNSAQGELEW 157
                                    5666669****************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1169.78
//
Query:       gene38|gene38|rna38|rna38  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1155.10
//
Query:       gene380|gene380|rna380|rna380  [L=345]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-29  100.8   0.0    1.2e-28   99.3   0.0    1.9  1  XPG_I       XPG I-region
    1.5e-28   99.2   0.0    2.6e-28   98.5   0.0    1.4  1  XPG_N       XPG N-terminal domain
    0.00015   22.3   0.0    0.00037   21.1   0.0    1.7  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.018   14.4   0.0    1.3  1  XRN_N       XRN 5'-3' exonuclease N-terminus
      0.048   14.3   0.0       0.14   12.8   0.0    1.8  1  HHH_5       Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   3.3e-32   1.2e-28       2      94 .]     146     232 ..     145     232 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 3.3e-32
                                    HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT.ECECTT..EEECEEEEEEHHHHHHHHT--H CS
                          XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnlskkkskkkkekekkkvevidlekvlkelgltr 81 
                                    lmgip+ +Ap+EAEA ca L+kk  v++v++eD+D+l+FG+p+vlrn+s     +k    k +v +++l+++l+ l+l++
  gene380|gene380|rna380|rna380 146 LMGIPFETAPSEAEAYCALLCKKRAVYGVATEDMDSLTFGSPVVLRNFS--GTRSK----KLPVVEYNLRQLLEDLSLDQ 219
                                    7***********************************************8..43444....689***************** PP

                                    HHHHHHHHHHCET CS
                          XPG_I  82 eqlidlaillgcD 94 
                                    +++idl+illgcD
  gene380|gene380|rna380|rna380 220 DEFIDLCILLGCD 232
                                    ************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.5   0.0   7.2e-32   2.6e-28       1     100 [.       1     105 [.       1     106 [. 0.93

  Alignments for each domain:
  == domain 1  score: 98.5 bits;  conditional E-value: 7.2e-32
                                    X--TTHHHHHHHH-..GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS....-HHHHHHHHHHHHHHHTTEE CS
                          XPG_N   1 MGikgLlkllkeva..airsvsiealegkklaiDaslwlyrfliavreqlgnalen....tshlmglfsrllrlldfgik 74 
                                    MGik L kllke    +i++  +  ++ k++aiDas+++y+fliavr+ +g  l n    tshl+glf+r++r++++gi+
  gene380|gene380|rna380|rna380   1 MGIKQLSKLLKENSvkGIKERPLAYYSSKRVAIDASMSIYQFLIAVRS-DGSTLGNgdttTSHLVGLFYRTIRMVELGIT 79 
                                    ***********99888*******************************5.55566666777******************** PP

                                    EEEEE--S--GGGHHHHHHHHHHHHH CS
                          XPG_N  75 PifVFdgkapdlkkeelekrserrqe 100
                                    P++VFdg +p++k +el kr+err+ 
  gene380|gene380|rna380|rna380  80 PVYVFDGVPPEVKMKELGKRNERRAT 105
                                    ***********************986 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     1e-07   0.00037       5      88 ..     221     297 ..     217     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1e-07
                     5_3_exonuc   5 qiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenldelkekklkekLeenkeearlskkLatiktdvplel 84 
                                    ++idl  L G   D     +giG+k+A  L+k++ s+e il++ + l++    ++  ++++  +++++La+i +  ++++
  gene380|gene380|rna380|rna380 221 EFIDLCILLG--CDYCDTLKGIGPKKALGLIKKHRSIERILQEEN-LET---PDEW-RYEDAQKIFRNLAEIGDAKEFNI 293
                                    6777777777..466667799*********************443.222...2222.33455677888888877777776 PP

                     5_3_exonuc  85 eled 88 
                                    ++++
  gene380|gene380|rna380|rna380 294 SWKS 297
                                    6665 PP

>> XRN_N  XRN 5'-3' exonuclease N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.1e-06     0.018       1     136 [.       1     132 [.       1     258 [. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                                    XXX-HHHHHHHHHSGGGEEE------SSSS-EEEEEEETHHHHHHHHS-SSS-......--SSHHHHHHHHHHHHHHHHH CS
                          XRN_N   1 mGvpklfrwlserypkivkevieeeeeeekefdnLYlDmNgiihkcshkedkeekelskkpkteeeifkkifkyidrlvk 80 
                                    mG+++l + l+e+  k +ke          +   + +D    i++         +++ ++  + ++  ++++    r ++
  gene380|gene380|rna380|rna380   1 MGIKQLSKLLKENSVKGIKERP---L-AYYSSKRVAIDASMSIYQFLIA----VRSDGSTLGNGDTTTSHLVGLFYRTIR 72 
                                    7777777777776654444443...2.2225667777878788887755....344455566666667777777777777 PP

                                    HH-EEEEEEEE------HHHHHH...HHHHHHHHHHHHHHHHHH.HHHHHHHHHHHT-BB CS
                          XRN_N  81 ivrprkllylavDGvaPraKmnq...qRsRRfrsakeakeekee.keelkeelekeekee 136
                                    +v+   + ++  DGv P+ Km++   + +RR  + ke k+++e+ +++l e ++k+++++
  gene380|gene380|rna380|rna380  73 MVELGITPVYVFDGVPPEVKMKElgkRNERRATADKEYKDASEAgDKRLMEMYDKRKTKV 132
                                    787777777779*********973313345555555555555544555555555554444 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.9e-05      0.14       6      32 ..     236     261 ..     232     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.9e-05
                                    TSTT--HHHHHHHHTTT--SHHHHHHS CS
                          HHH_5   6 svsGiGpktAlallsaGiesvedlaaa 32 
                                    +++GiGpk Al l+++  +s+e ++++
  gene380|gene380|rna380|rna380 236 TLKGIGPKKALGLIKK-HRSIERILQE 261
                                    689***********99.8999999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2431.69
//
Query:       gene381|gene381|rna381|rna381  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0012   18.7   0.0        0.4   10.6   0.0    2.5  2  CutA1     CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
      0.016   15.5   1.9       0.61   10.5   0.1    2.4  2  PsiE      Phosphate-starvation-inducible E


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0017        15      49      75 ..      34      61 ..      31      64 .. 0.85
   2 !   10.6   0.0   4.5e-05       0.4      38      93 ..      89     144 ..      83     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0017
                                   EEEE.EEEEEEGGGHHHHHHHHHHHSSS CS
                          CutA1 49 kEvl.lliktreekveelekrvkelhpy 75
                                   +E+l ++ik+ ++++e+++++v ++hp 
  gene381|gene381|rna381|rna381 34 QEILaMVIKSLKRHAERISRTVVDIHPT 61
                                   5654289*******************95 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.5e-05
                                    EEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEEEEEESEEEHHHH CS
                          CutA1  38 vYrWkgkieedkEvllliktreekveelekrvkelhpyevpeiialpieagseaYl 93 
                                    +Y++ +k  +++ +l+l+ t+ + v++le+rvk+  +  v  i  lp e+  + Y 
  gene381|gene381|rna381|rna381  89 IYHYLEKTRRHSCCLVLVSTSCTSVDRLERRVKSRFNHRVFFIGFLPFESYRALYS 144
                                    799**************************************999999998877775 PP

>> PsiE  Phosphate-starvation-inducible E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2    0.0065        59      12      34 ..      35      58 ..      34      59 .. 0.91
   2 ?   10.5   0.1   6.8e-05      0.61      17      58 ..     145     189 ..     139     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0065
                           PsiE 12 Ellrtivaylkeh.riavrlviea 34
                                   E+l+++++ lk+h +   r+v+++
  gene381|gene381|rna381|rna381 35 EILAMVIKSLKRHaERISRTVVDI 58
                                   89***********98889999986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.8e-05
                           PsiE  17 ivaylkeh.riavrlvieaaiiavaRklIil..dlkdggyltllg 58 
                                    +++++ e+ +i+ ++ i+  i a+++k+Ii+  +l++++ +tl+ 
  gene381|gene381|rna381|rna381 145 QLTGIDEDeEIQRQYSIDPSISALSKKIIIKkyELPEYTIETLYT 189
                                    4588999999*********************88888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1959.94
//
Query:       gene383|gene383|rna383|rna383  [L=711]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-30  105.8   1.2    1.4e-28  100.4   1.2    2.4  1  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase


Domain annotation for each model (and alignments):
>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   1.2   7.9e-33   1.4e-28       3     240 ..     456     650 ..     455     656 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 7.9e-33
                                    EEEEECSSCHHHHHHHHHHHHHHHHHHHHTTTTCCCT-------EEESSSSEEEEE--TTEEEHHHHHHHHHHHCTTSTC CS
                 PI3_PI4_kinase   3 agiykvgddlrqdelivqvfklmdeelskennpkrrklalktysviplgrkcgiielvassetaaslldeklekkgvppt 82 
                                    ++i+k g++l+q+ +  q++  m +++++en+p++    +++y+++   + +gi+e v  +++++++ ++ +++      
  gene383|gene383|rna383|rna383 456 SIIVKTGESLKQELMAHQILLEMRKIWKEENSPLW----VNPYQIYLVNDTSGIVETVVDATSIHKIKKKMMSE------ 525
                                    5899*******************************....****************************9998844...... PP

                                    HHHHHHHHHCHCHCCHHHHHCCHHHHHHTSSTTHHHHHHHHHSSSH.HHHHHHHHHHHHHHHHHHHHHHHHT-TT--TTT CS
                 PI3_PI4_kinase  83 asveslrvaldkkklkkekklkfekrtalkpksgllqeFvkkspsa.eewlearkqFvrslaklsvldyilgngDRhldN 161
                                               +k                    +l+++Fv++++   e++ + +++F  sl ++s ++yil++ DRh++N
  gene383|gene383|rna383|rna383 526 -----------NK------------------NYSLKNYFVESFELNsEKYKSCLRNFLYSLVGYSLATYILQVKDRHNGN 576
                                    ...........33..................3689********9664899999*************************** PP

                                    EEEETTTSEEEESSTTTCCTCSHCSSSS-.SSSSSS-THHHHHHTSTTCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                 PI3_PI4_kinase 162 ilvdktsgklihIDfGlilpdewkllpfpqekvPfrltrelvlaidpskdeglfresceealealrrdqnlltrllkka 240
                                    i++ +++g+++h+DfG+i+++ + ++ +  e  Pf+  +e+ +++     +  f+++  + + alr+++  l r+++ +
  gene383|gene383|rna383|rna383 577 IMI-DEQGHIVHVDFGFIMGSHPGFYCV--EAAPFKFSKEYLELL--GDLMDEFKSLFLQGYMALRKHSSRLFRIMETM 650
                                    ***.*********************997..69*************..777889***************99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 4155.02
//
Query:       gene384|gene384|rna384|rna384  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1946.33
//
Query:       gene385|gene385|rna385|rna385  [L=84]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0064   16.5   0.2       0.25   11.4   0.0    2.1  2  HTH_19    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.9   0.0    0.0031        56      44      58 ..      22      36 ..       8      49 .. 0.72
   2 !   11.4   0.0   1.4e-05      0.25      14      44 ..      50      80 ..      45      84 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0031
                         HTH_19 44 lllkiaealgidley 58
                                   +++ i+e+lgi +e+
  gene385|gene385|rna385|rna385 22 VYYLICEELGIAEEE 36
                                   44889******9874 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.4e-05
                         HTH_19 14 tqeelaerlgisrskisaiEngkkdvpsael 44
                                   +q++ ++++g+ r++i+ i ++++d+++ ++
  gene385|gene385|rna385|rna385 50 GQDKFSGEIGFLRNYIMRIKKERRDKHGEWD 80
                                   799*********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 553.37
//
Query:       gene386|gene386|rna386|rna386  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-05   24.7  24.7     0.0001   22.6   6.3    2.2  2  ATP-synt_C     ATP synthase subunit C
  ------ inclusion threshold ------
        1.6    8.4   6.6        6.2    6.5   0.2    2.2  2  Baculo_11_kDa  Baculovirus 11 kDa family


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2  10.5   0.00036       3.2       3      60 .]      26      84 ..      21      84 .. 0.77
   2 !   22.6   6.3   1.1e-08    0.0001       2      60 .]     102     160 ..     101     160 .. 0.97

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00036
                                   HHHHH.GGGHHHHHHHHHHHHHHHH.HHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C  3 aglavGlsalgsGigiGkagsagir.avarnpklftksliilafaeaialygLivalil 60
                                   +gla+ ++    G + G+a s+g++   +rn ++ + +  i++++ +i+   ++vali+
  gene386|gene386|rna386|rna386 26 IGLAIEMALAVYGACEGMASSGGASiLCSRNRSILGPTYFIMIMVSTIFFSSFLVALII 84
                                   456655555555666666666666636677889*************************8 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.1e-08
                                    HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C   2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                                     a+l+vG++a  sG  + ++g  g r+++++p+    ++i+++++e + +  L +al++
  gene386|gene386|rna386|rna386 102 SACLMVGITAAISGKVCSTLGRRGFRILSEKPSFLPILIILFGMIEFVIIVVLSCALLM 160
                                    79******************************************************997 PP

>> Baculo_11_kDa  Baculovirus 11 kDa family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2   0.00069       6.2      25      66 ..      52      95 ..      48     103 .. 0.81
   2 ?    4.3   2.0    0.0032        29      37      61 ..     139     163 ..     127     166 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00069
                  Baculo_11_kDa 25 lvsrNrsfl..rdFvLvicglvvfvvivlfilLlvvilknaeae 66
                                   l srNrs+l  + F++++ + + f   ++ +++  +i ++ +++
  gene386|gene386|rna386|rna386 52 LCSRNRSILgpTYFIMIMVSTIFFSSFLVALIIATNIDEKLDMA 95
                                   679*****9666799*9999999998888888888887776655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0032
                  Baculo_11_kDa  37 vLvicglvvfvvivlfilLlvvilk 61 
                                    ++++ g++ fv+iv++   l+++ +
  gene386|gene386|rna386|rna386 139 LIILFGMIEFVIIVVLSCALLMVYQ 163
                                    6788999*9***9999887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1055.55
//
Query:       gene387|gene387|rna387|rna387  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-08   34.0   0.1    3.7e-07   29.7   0.1    2.1  1  Rad51     Rad51
    1.7e-05   24.5   0.2      0.032   13.8   0.0    2.1  2  AAA_25    AAA domain
    0.00013   22.3   0.3    0.00026   21.3   0.3    1.5  1  AAA_22    AAA domain
     0.0002   20.8   1.4      0.048   13.0   0.0    2.3  2  ATPase    KaiC
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.043   13.7   0.0    1.3  1  NACHT     NACHT domain
      0.041   13.1   0.1      0.055   12.7   0.1    1.2  1  TIP49     TIP49 P-loop domain
      0.042   13.6   0.1      0.072   12.8   0.1    1.4  1  AAA_24    AAA domain
        0.1   13.0   0.4       0.25   11.8   0.4    1.6  1  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   1.6e-10   3.7e-07      76     252 ..      22     192 ..       2     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.6e-10
                                    EEESSS---GGGGHHHH...HHTT--HHHHGGGEEEEE--STTHHHHHHH.HTHHHHHHS-EEEEEEETTTGGGCH---- CS
                          Rad51  76 yidtegtfrperlveia...erykldkeevlenvayaRaytiehqeellq.qaaallaedkfallivDsvtalyRtdfsg 151
                                     ++    + +  +++      ryk  ++ev++++ +  + +ie  ++++  ++   ++e + +l+i+Ds+  l  t+  g
  gene387|gene387|rna387|rna387  22 AVEESKELATIYITTTTfciGRYKGASKEVMDRIIVKYIPSIEYLASFVMnSMERIIVERRTGLVIIDSLDHLLATEGMG 101
                                    4444444444444444444589***********************9988757888999******************9877 PP

                                    ---THHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEE CS
                          Rad51 152 rgelakRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivk 231
                                     +    R+  +  ++++L+++ ++++v +++      +    +a+       P++Gl +  ++ tR +   + g++R ++
  gene387|gene387|rna387|rna387 102 MD----RGILF-GVVNRLKRMNQKYGVNILVVTYHYGSWTI-GAFC---IPNPMLGLQWMYMVNTRYVC-SRAGDKRTLR 171
                                    65....77655.58899**********99876554444433.2333...44699************765.56799***** PP

                                    EES-SSS-S-EEEEEEETTEE CS
                          Rad51 232 vvdsPnlpeleavfaigeeGi 252
                                    +v sP +  +   f+ig++ +
  gene387|gene387|rna387|rna387 172 LVRSPFMKSKAWEFVIGSSAV 192
                                    ****************99877 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2   0.00052       1.2      35      58 ..       7      30 ..       2      38 .. 0.87
   2 !   13.8   0.0   1.4e-05     0.032     130     186 ..      71     128 ..      54     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00052
                         AAA_25 35 lallaGapgtGKttlaldlalava 58
                                   ++ l+G +gtGKt++a++++ ++a
  gene387|gene387|rna387|rna387  7 VTELTGKSGTGKTAIAVEESKELA 30
                                   6779*************9987776 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.4e-05
                         AAA_25 130 vdaleaaieevegvrlvviDplsralgg.densnsdv.galvealeriarrtgaavllv 186
                                    ++ +e+ i e  + +lv+iD+l+++l+  +   ++ +   +v++l+r+ +++g+ +l+v
  gene387|gene387|rna387|rna387  71 MNSMERIIVE-RRTGLVIIDSLDHLLATeGMGMDRGIlFGVVNRLKRMNQKYGVNILVV 128
                                    5678999999.67***********99997777777778****************99887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3   1.2e-07   0.00026       6     128 ..       6     128 ..       2     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst......sskdllrellralglelkaerlsseell 79 
                                    g++ +tG sGtGKT  + +  ++l            ++++t +  +       sk+++ ++  ++  + ++     + ++
  gene387|gene387|rna387|rna387   6 GVTELTGKSGTGKTAIAVEESKEL-----------ATIYITTTTFCigrykgASKEVMDRIIVKYIPSIEY---LASFVM 71 
                                    67789**********998877777...........333333333333333349999999999999988888...888888 PP

                         AAA_22  80 ealeqalraravielliiDEaqhlr...s........eealeeLrsllnlsrkgvqliLv 128
                                    + +e+ + +r++ +l+iiD  +hl               +++ L+++    ++gv +++v
  gene387|gene387|rna387|rna387  72 NSMERIIVERRT-GLVIIDSLDHLLateGmgmdrgilFGVVNRLKRMNQ--KYGVNILVV 128
                                    ************.**********76565155667888889999987777..888887665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.3    0.0013       2.9      21      37 ..       7      23 ..       2      38 .. 0.82
   2 !   13.0   0.0   2.2e-05     0.048     107     165 ..      70     131 ..      45     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                         ATPase 21 vvlitGepGtGKtifal 37
                                   v+ +tG++GtGKt +a 
  gene387|gene387|rna387|rna387  7 VTELTGKSGTGKTAIAV 23
                                   7899*********9885 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.2e-05
                         ATPase 107 lieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkklgv...Tailvseks 165
                                    ++++++++i e +   v+iDs++ l  +e   + R il+ +v++lk +++   ++ilv   +
  gene387|gene387|rna387|rna387  70 VMNSMERIIVERRTGLVIIDSLDHLLATEGMGMDRGILFGVVNRLKRMNQkygVNILVVTYH 131
                                    6788999999999999*********9999999**********99987665222566666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.043       5      98 ..      10      99 ..       7     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                   EEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C...CHHHHCCSCCCE CS
                          NACHT  5 lqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse...vwavllelperl 83
                                   l+G++G GKT+ + +   ++a+ +           ++ ++ +  +++  +++++++  p ++   s     ++ ++  ++  
  gene387|gene387|rna387|rna387 10 LTGKSGTGKTAIAVEESKELATIYITTT------TFCIGRYKGASKE-VMDRIIVKYIPSIEYLASFvmnSMERIIVERRTG 84
                                   79*********************98886......59999**999999.9********9999999988333334455556778 PP

                                   EEEEE-STT-SS-TC CS
                          NACHT 84 LlilDglDelvtdlg 98
                                   L i+D+lD l +  g
  gene387|gene387|rna387|rna387 85 LVIIDSLDHLLATEG 99
                                   8*******9987655 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.4e-05     0.055      55      76 ..      10      31 ..       6      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                                   XXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 55 laGpsgtGktalaiaiskelge 76
                                   l+G+sgtGkta+a+  skel++
  gene387|gene387|rna387|rna387 10 LTGKSGTGKTAIAVEESKELAT 31
                                   79*****************984 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.2e-05     0.072       7      78 ..      10      95 ..       7     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                         AAA_24  7 iyGpsgiGKTtlakel.........gpkplfi......dtekGlksldadkfpdieswedfldevvelaaeladyktlviDt 73
                                   ++G+sg+GKT +a e          + ++++i        e  ++++ ++ +p+ie ++ f+    e    +++   ++iD+
  gene387|gene387|rna387|rna387 10 LTGKSGTGKTAIAVEEskelatiyiTTTTFCIgrykgaSKEV-MDRIIVKYIPSIEYLASFVMNSMERIIVERRTGLVIIDS 90
                                   78***********99866555556555555556655544444.677777788888888888888888899999999****** PP

                         AAA_24 74 idele 78
                                   +d+l 
  gene387|gene387|rna387|rna387 91 LDHLL 95
                                   **995 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00011      0.25       3      74 ..      10      98 ..       9     136 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                   EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SS..................STTHHHHHHHHHHHHHHHTS...TSEEE CS
                            AAA  3 lyGppGtGKTllakavakelgvefleisgsell.sk..................yvgesekkirelfkeakeka...kpsil 62
                                   l+G  GtGKT++a    kel +  + i  ++++                          e   + +++++++     ++  +
  gene387|gene387|rna387|rna387 10 LTGKSGTGKTAIAVEESKELAT--IYITTTTFCiGRykgaskevmdriivkyipS---IEYLASFVMNSMERIIverRTGLV 86
                                   78***********999999742..2222222221221112223334444443331...222222222222222244345788 PP

                                   EEETGGGHHHHH CS
                            AAA 63 fiDEidalaksr 74
                                   +iD +d l  ++
  gene387|gene387|rna387|rna387 87 IIDSLDHLLATE 98
                                   888888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1252.04
//
Query:       gene388|gene388|rna388|rna388  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 850.02
//
Query:       gene389|gene389|rna389|rna389  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-17   63.9   0.6    1.9e-17   63.4   0.6    1.2  1  CH        Calponin homology (CH) domain
    0.00051   20.3   0.5    0.00095   19.4   0.5    1.4  1  CDC24     CDC24 Calponin


Domain annotation for each model (and alignments):
>> CH  Calponin homology (CH) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.6   2.1e-21   1.9e-17       2     108 ..       3     106 ..       2     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 2.1e-21
                                    HHHHHHHHHHHHHHTTSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGGSTTTHHHHHHHHHHHHHHHHHHTTCHTT CS
                             CH   2 eqkkellrWinshleeagpkvkvedfeedlrDGvlLckLlnklapglvdkkklnksefkkleNinlaldvaekklgvpkv 81 
                                    +q+ke++ Wi+++l+e+        f++ ++DGv Lc++lnk+ p  v++k+   + f ++eNi  +++ ++ kl+++++
  gene389|gene389|rna389|rna389   3 KQQKEVTLWIEAVLGEKFGP---GTFHDLFKDGVKLCRFLNKVSPLNVKYKESR-QIFVQRENICSFINGLK-KLNMNEY 77 
                                    699***********998665...57**************************995.49************888.******* PP

                                    SS.-HHHHHTTSHH.HHHHHHHHHHHHHH CS
                             CH  82 li.eaedlvegknk.svltllaqLfrafq 108
                                    ++ +++dl+e k+  +v+ +l++L+r  q
  gene389|gene389|rna389|rna389  78 ELfQTNDLFEAKDLkQVVICLYALSRQLQ 106
                                    **********66666*********99765 PP

>> CDC24  CDC24 Calponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.5   1.1e-07   0.00095       8      73 ..      27      88 ..      23     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                          CDC24  8 kllrqGspLlalfNalkpeeklevdevksddlkvcKksvydFllackkeLgfedeelftisdlfse 73
                                    l++ G  L+   N ++p   l+v+ ++s +  v ++ +  F++++k +L++++ elf   dlf+ 
  gene389|gene389|rna389|rna389 27 DLFKDGVKLCRFLNKVSP---LNVKYKESRQIFVQRENICSFINGLK-KLNMNEYELFQTNDLFEA 88
                                   79************9986...99*99******************986.7**************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1216.52
//
Query:       gene39|gene39|rna39|rna39  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-19   68.7   0.0    8.9e-19   67.9   0.0    1.4  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    7.4e-13   47.7   0.0    1.1e-12   47.2   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0     1e-22   8.9e-19       3     112 .]      75     187 ..      73     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 1e-22
                                EEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC....EEGGGCBES.......SSS CS
              RNA_pol_A_bac   3 ieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge....vtagdlkle.......dad 75 
                                ++en+sv+ DE++aHrlglipl ++++++      e    e+e +e++s+ + Lnv ++++    v++ d+k+           
  gene39|gene39|rna39|rna39  75 LKENESVFPDEFIAHRLGLIPLEADPEMF------EF--VEKELNERNSLRFVLNVTNESKdvmnVYSDDIKWIpfggqreA-- 148
                                679***********************999......55..3467899999********99999999********988666431.. PP

                                CEES.....STTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
              RNA_pol_A_bac  76 veiv.....npdilIakLrkgqeleleakvkkGiGkehakfs 112
                                   +       ++l +kL+ gq+++ e+ + k+iG++hak+s
  gene39|gene39|rna39|rna39 149 ---LrnakfCSGVLMFKLARGQKINAELVCTKNIGRVHAKWS 187
                                ...233345799*****************************8 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   1.2e-16   1.1e-12       1      68 [.      43     291 ..      43     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.2e-16
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................................... RF
                  RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea...................................................... 30 
                                ef+l +vd++++NaLRril ++vp++a+                                                        
  gene39|gene39|rna39|rna39  43 EFDLVNVDCSFANALRRILCNDVPTMAVKDvflkenesvfpdefiahrlglipleadpemfefvekelnernslrfvlnvtnes 126
                                79*******************************************************999999999999999999999999999 PP

                                .......................................................................xx........... RF
                  RNA_pol_L  31 .......................................................................pv........... 32 
                                                                                                       p            
  gene39|gene39|rna39|rna39 127 kdvmnvysddikwipfggqrealrnakfcsgvlmfklargqkinaelvctknigrvhakwspvcpatyrlmPLieigdvfdeda 210
                                999999999999999999999999988888888888888888888888888888888888866655555550055555555555 PP

                                ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  RNA_pol_L  33 ..............................................vkvntdkdklilevetdgslkPeealkeAlkiLkek 68 
                                                                              v + +  d + +++ +   l+P  +lk+A+ iL+ek
  gene39|gene39|rna39|rna39 211 yklqkcfsegvidvrlsdgrmkayvvnprldtmsrealrheefkdkVFIGRRSDYFLFTINS-VFLDPLYLLKKAVSILIEK 291
                                55555555555555555555555555555655665555555555556777***********4.467**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2219.25
//
Query:       gene390|gene390|rna390|rna390  [L=529]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-45  153.7   0.2    1.1e-44  153.1   0.2    1.2  1  Syja_N    SacI homology domain


Domain annotation for each model (and alignments):
>> Syja_N  SacI homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.2     6e-49   1.1e-44       1     300 [.      55     300 ..      55     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 6e-49
                         Syja_N   1 ygilGlirllsgsyllvitkreevgtlkgkkeiykitevellplsseeeaekalkslkaktekkkeekeleekllkllek 80 
                                    yg++G+++++++syl+++ ++   g + ++  +y+i++ve+++l++e   + ++             k+ e k    + +
  gene390|gene390|rna390|rna390  55 YGVYGIVTISKSSYLILVVDAIMRGMMYDH-VVYEIKDVEIIQLKRE---RMESF------------KN-EMK---AV-R 113
                                    79********9**********999998676.************9433...22222............12.232...33.4 PP

                         Syja_N  81 lfessgsfYFsydlDltrslqrqlekssesskslplweraderFvWNrhllkpli...eaeldswllpviqGfveqsklk 157
                                     f  ++++YFs  + l ++l  + +               d++F++N+  l++++    ++ + + ++ iqGf+++ ++ 
  gene390|gene390|rna390|rna390 114 RFLGNSGVYFST-YPLHKTLAVKKD--------D------DTDFLFNALPLEKFLkytGDQGSLFSVSCIQGFFGSVDVG 178
                                    4557888***97.689999886654........3......668**********995542367889999******666664 PP

                         Syja_N 158 lsksqkekekkevtltlisRrsrkraGtRylrRGiddeGnvANfvEtEqilevessekeskilSfvqiRGSiPlfWsqep 237
                                               ++ l lisRrs++r G+Ry+ RG +  G+v+N+vEtEqi+++      +k++Sf+q+RGSiPl+W+   
  gene390|gene390|rna390|rna390 179 -----------SICLRLISRRSWRRVGARYFCRGSNAIGYVSNYVETEQIVYE-----GEKTTSFLQVRGSIPLIWEHVL 242
                                    ...........388**************************************3.....4589****************** PP

                         Syja_N 238 tlkykpkirierseeenleafkkHfekllkrYgkvvvvnLlekkgrEkkLgeayekavkklnk 300
                                      +y+p+i i   +++ l+ ++   + + ++Yg+v ++nL+ ++g E+ L  +yek +   nk
  gene390|gene390|rna390|rna390 243 GREYNPRIIIS--NKKVLHIAD---KVMRDKYGDVLYLNLIRNTGYEGMLHCEYEKELLGNNK 300
                                    **********6..333333333...334679*************************9887763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3731.82
//
Query:       gene391|gene391|rna391|rna391  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-19   68.6   2.4    5.9e-19   67.7   2.4    1.5  1  Homeodomain  Homeodomain
  ------ inclusion threshold ------
      0.035   14.2   0.7      0.048   13.7   0.7    1.1  1  TERB2        Telomere-associated protein TERB2


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   2.4   6.6e-23   5.9e-19       2      57 .]      32      87 ..      31      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 6.6e-23
                                   T-SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
                    Homeodomain  2 rkRttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakekk 57
                                   ++R + tk ql++Le+ Fe n  p+a++r++L ++lg++ r V+vWFqNrRak kk
  gene391|gene391|rna391|rna391 32 KHRKRTTKAQLKVLEETFETNIRPDANMRKKLGEQLGMTPRSVQVWFQNRRAKIKK 87
                                   789**************************************************997 PP

>> TERB2  Telomere-associated protein TERB2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   5.3e-06     0.048      63     175 ..      26     145 ..      19     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-06
                          TERB2  63 FhssylsaaknekskksvalgkyvLppakvqeeirkkigrfiweqdnqslveqssevhsaeepeiakdslleekeeqask 142
                                    F+++++++ k ++  +   l++   +  +  +++rkk+g+ ++    +++v  +++ +  ++ +++k  ++e++ + +  
  gene391|gene391|rna391|rna391  26 FDPYFVKHRKRTTKAQLKVLEETFETNIRPDANMRKKLGEQLGMTPRSVQVWFQNRRAKIKKLTQKKMMQQENTDNTKGP 105
                                    99******9999999999999999999999***************99999988888666666666666666665555544 PP

                          TERB2 143 laksaeksatstsksekqlcselk.......eyPvnnvvt 175
                                    +a+ +++   +   s+ +++++l+        yP +n v 
  gene391|gene391|rna391|rna391 106 EASRSSSPSKDRKYSNYHPYVPLQapleefnVYPRDNSVY 145
                                    4444444444555556666777755555555999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1686.00
//
Query:       gene392|gene392|rna392|rna392  [L=529]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-10   41.2   1.7    2.5e-10   40.1   1.2    1.5  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   1.2   1.4e-14   2.5e-10     146     268 ..     342     436 ..     330     453 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 1.4e-14
                                    HHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 146 ainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgniv 225
                                    +++r   ++g++vv+ aGN +       + s  ++p++s+++i vg++++ + ++ fS++G ++       i a G++  
  gene392|gene392|rna392|rna392 342 IVDRIS-SRGIIVVTPAGNFH-------DQSCNYSPGSSRSAINVGSVNKHAGVSKFSNHGDCV------RIFALGEE-- 405
                                    888888.99************.......6666799****************************9......6******9.. PP

                                    CCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 226 stwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkl 268
                                      +  +s          ++ GTS +++ +a+++Al l+a p  
  gene392|gene392|rna392|rna392 406 --VLGNS----------NIVGTSLSAAIVASSIALFLEASPRA 436
                                    ..55555..........699******************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3233.95
//
Query:       gene393|gene393|rna393|rna393  [L=177]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.1e-28   96.8   0.0    1.1e-27   96.4   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
      5e-11   42.5   0.0    5.8e-11   42.3   0.0    1.1  1  Redoxin     Redoxin
     0.0012   18.7   0.0      0.002   18.0   0.0    1.3  1  SCO1-SenC   SCO1/SenC
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.28   11.1   0.0    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.4   0.0   2.4e-31   1.1e-27      12     118 ..      16     129 ..       5     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 2.4e-31
                                    STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H........SS CS
                       AhpC-TSA  12 nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes.......lnf 84 
                                    +++ +++sl+dykgk+vv++fyp d+++vC+te+ +l++l eef +r++ v+ vs+ds+++hk+++   +       + +
  gene393|gene393|rna393|rna393  16 DGEIKEISLQDYKGKYVVVVFYPLDFTFVCPTEINRLSDLKEEFLKRNAVVLLVSCDSVYTHKAWASIPRekggvlgVSW 95 
                                    78899*************************************************************9888899******* PP

                                    EEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TT CS
                       AhpC-TSA  85 pllsDeegkvakaygvlkeekglalratfvidke 118
                                    p+++D +++++ ++ +++ee+g ++r+t++++k+
  gene393|gene393|rna393|rna393  96 PMIWDAKRELCSQFSMFDEENGHPMRGTVLLSKD 129
                                    ******************************9987 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.3e-14   5.8e-11      16     126 ..      17     131 ..       6     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.3e-14
                                    TCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH........TT-TS CS
                        Redoxin  16 tdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk........eglkf 87 
                                     + +++sl+++kgk vvv+f+p  f+ +C +e++ l +l+e++ +++  v  +v+ ++ +  ++w++        +g+++
  gene393|gene393|rna393|rna393  17 GEIKEISLQDYKGKYVVVVFYPLDFTFVCPTEINRLSDLKEEFLKRNAVV-LLVSCDSVYTHKAWASiprekggvLGVSW 95 
                                    67899*************************************88886655.66677778899999999************ PP

                                    EEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTE CS
                        Redoxin  88 pvlsDgsaaftkalGlrleedaseglrtpryavidedgk 126
                                    p++ D++ ++ +++   +  d ++g  ++ ++++ +d  
  gene393|gene393|rna393|rna393  96 PMIWDAKRELCSQFS--M-FDEENGHPMRGTVLLSKDLS 131
                                    ***************..4.46677778888888888755 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.6e-07     0.002       6      66 ..      14      72 ..      10      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.6e-07
                      SCO1-SenC  6 lvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvD 66
                                   +vd + ++++ +d++gk+++v f     + vCpt++++++++ +++ ++  +  +l +++D
  gene393|gene393|rna393|rna393 14 FVDGEIKEISLQDYKGKYVVVVFYPLDFTFVCPTEINRLSDLKEEFLKR--NAVVLLVSCD 72
                                   68888899****************99999****************9998..4455555655 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.3e-05      0.28       1      18 [.     155     172 ..     155     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.3e-05
                                    HHHHHHHHT-BB-TTT.T CS
                     1-cysPrx_C   1 ALQladkhgvatPAnWkp 18 
                                    AL + +++g+ +P+ W++
  gene393|gene393|rna393|rna393 155 ALAFNEENGEICPVEWRK 172
                                    8899************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1156.20
//
Query:       gene394|gene394|rna394|rna394  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.061   13.5   0.1          2    8.6   0.0    2.2  2  DUF3960   Domain of unknown function (DUF3960)


Domain annotation for each model (and alignments):
>> DUF3960  Domain of unknown function (DUF3960)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00011         2      34      76 ..      13      55 ..       2      61 .. 0.87
   2 ?    2.9   0.0    0.0069   1.2e+02       6      37 ..      87     118 ..      83     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00011
                        DUF3960 34 hpkgegkertilvwkekefykeenlaafivygmnkaknlpqfh 76
                                     k e +er++l+   ++  k+ n+ +f+ y +++  nl  ++
  gene394|gene394|rna394|rna394 13 IKKSEDHERAMLLMEYNKALKDLNVGSFLRYKVKHDVNLGLYK 55
                                   5799*****************************9999997665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0069
                        DUF3960   6 rdpnwnlvtdtyiepnnfaelfsllvpchpkg 37 
                                    r+  +n+     ie nnf     ll  +  kg
  gene394|gene394|rna394|rna394  87 RESLFNMARRNIIERNNFVRARKLLNIAREKG 118
                                    667789999999******99988887777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 893.30
//
Query:       gene395|gene395|rna395|rna395  [L=383]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.2e-125  418.5   3.3   2.6e-125  418.3   3.3    1.0  1  Ribosomal_L3  Ribosomal protein L3
  ------ inclusion threshold ------
       0.65   10.0   0.1       0.65   10.0   0.1    2.9  3  DUF1639       Protein of unknown function (DUF1639)


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.3   3.3  2.9e-129  2.6e-125       1     369 []       1     357 [.       1     357 [. 0.94

  Alignments for each domain:
  == domain 1  score: 418.3 bits;  conditional E-value: 2.9e-129
                                    XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEE.CHHTTSCCCCCEEEEEEEEE CS
                   Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVre.vdkpgskldkkevveavtvv 79 
                                    ms rkf+aprhgsl f prkR++  r+   +fP+dd+s+pv+lt+f+GyKaGmth++r+ ++ +  k+  +ev++avtv+
  gene395|gene395|rna395|rna395   1 MSCRKFSAPRHGSLQFCPRKRSKTIRPSPGAFPADDSSQPVHLTGFMGYKAGMTHVIRTkIQAAKNKQLSREVMDAVTVL 80 
                                    999******************************************************9626667788889********** PP

                                    EC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSC CS
                   Ribosomal_L3  80 etppmvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasv 159
                                    e ppmv+ gvvgy+ t  Glr l  v a  +s+ v rr++ n +  +       sk++     ++  e  ++eikk+a  
  gene395|gene395|rna395|rna395  81 EAPPMVVYGVVGYERTVTGLRRLPIVLAPYVSDGVLRRMFGNKHVERE-----NSKRF---CASEETESRISEIKKKAEC 152
                                    ***************************************998765543.....34444...23344566799******** PP

                                    EEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT-- CS
                   Ribosomal_L3 160 vrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvk 239
                                    vrv++ t+ + +k l  Kkah+ EiqvngG+i+ek+++  ++lek +++ +vF+++e iDvigvtkGkGf+G+vkR+gv+
  gene395|gene395|rna395|rna395 153 VRVLVQTQPGLIKKLGLKKAHIAEIQVNGGSISEKVEWCLDMLEKEIHIGEVFKENENIDVIGVTKGKGFQGTVKRFGVR 232
                                    ******************************************************************************** PP

                                    --STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB. CS
                   Ribosomal_L3 240 klprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGe 319
                                    k+prk  +g Rkva+igaw+p+rV+++varaGq+G+h+Rte nk++y +g+   + + +tefdltek i+PmGGf+hyGe
  gene395|gene395|rna395|rna395 233 KQPRKSRKGIRKVACIGAWHPSRVMYSVARAGQMGFHRRTEKNKRVYMVGN--GNSSIRTEFDLTEKFISPMGGFPHYGE 310
                                    ***************************************************..556789********************* PP

                                    .TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                   Ribosomal_L3 320 vkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                    vkndfi+vkG+v+Gp+kr+v+lrksl  q   +  ee+  kf+dt+sk g
  gene395|gene395|rna395|rna395 311 VKNDFIMVKGAVVGPRKRVVTLRKSLDQQ---RPSEELVIKFVDTSSKIG 357
                                    *************************9754...6678888********976 PP

>> DUF1639  Protein of unknown function (DUF1639)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.3      0.14   1.2e+03      22      30 ..      18      26 ..      17      28 .. 0.88
   2 ?   -1.6   0.8       0.3   2.7e+03      17      29 ..     233     245 ..     229     247 .. 0.70
   3 ?   10.0   0.1   7.3e-05      0.65       5      42 ..     310     345 ..     308     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                        DUF1639 22 PKKRpknVq 30
                                   P+KR+k+++
  gene395|gene395|rna395|rna395 18 PRKRSKTIR 26
                                   9*****985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.3
                        DUF1639  17 kpprRPKKRpknV 29 
                                    k pr+++K  + V
  gene395|gene395|rna395|rna395 233 KQPRKSRKGIRKV 245
                                    6778888866655 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 7.3e-05
                        DUF1639   5 EieeDflamtGkkpprRPKKRpknVqkqldslfPGlwL 42 
                                    E+++Df++++G      P+KR  +++k+ld+  P   L
  gene395|gene395|rna395|rna395 310 EVKNDFIMVKGAVVG--PRKRVVTLRKSLDQQRPSEEL 345
                                    9**********9998..*************98887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2420.15
//
Query:       gene396|gene396|rna396|rna396  [L=329]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00025   21.8   0.0          1   10.3   0.0    3.1  3  WD40       WD domain, G-beta repeat
    0.00026   20.4   2.5     0.0052   16.2   1.0    2.7  2  WD40_like  WD40-like domain
     0.0023   17.2   0.0     0.0023   17.2   0.0    1.6  2  NUP214     Nucleoporin or Nuclear pore complex subunit NUP214
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.48   10.5   0.0    2.1  1  EPTP       EPTP domain
       0.18   12.3   0.3        7.5    7.2   0.1    3.3  4  PQQ_3      PQQ-like domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0016       5.6       7      38 .]     138     168 ..     133     168 .. 0.84
   2 !   10.3   0.0   0.00029         1      10      36 ..     252     277 ..     244     279 .. 0.83
   3 ?   -3.5   0.0         5   1.8e+04       4      11 ..     295     303 ..     293     309 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0016
                                    EESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    l+GH   v s+  s+dg ++ sGs D t+  Wd
  gene396|gene396|rna396|rna396 138 LKGHeEAVLSI-ESRDGILF-SGSLDSTIIEWD 168
                                    789*7779999.88899996.8*******9998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00029
                                    S.SSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40  10 H.ssvtslafspdgawlasGsdDgtvri 36 
                                    H +s+t+l++  d+ +  +Gs Dgt+++
  gene396|gene396|rna396|rna396 252 HeDSITGLDTLGDNVY--TGSLDGTIKV 277
                                    9788****76666666..9*******98 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5
                                    EEEEESS.S CS
                           WD40   4 lrtltGH.s 11 
                                    + +l++H +
  gene396|gene396|rna396|rna396 295 VFSLRAHeD 303
                                    667889953 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.024        87     111     155 ..     132     177 ..     111     205 .. 0.74
   2 !   16.2   1.0   1.4e-06    0.0052      51     113 ..     220     283 ..     190     307 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.024
                      WD40_like 111 lqleevllgqsseIkeikiennkiysLsesafiv.fdlfsqnieyk 155
                                    +  + +l g++  +++i++ +++++s s +  i+ +d +    + +
  gene396|gene396|rna396|rna396 132 ILPQVLLKGHEEAVLSIESRDGILFSGSLDSTIIeWDTEKALAKNR 177
                                    566788999*****************99665554155555444333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.4e-06
                      WD40_like  51 ldddlilvvtlDGtillsllenee..evenekieedistvkviddklliGtnkGsiyvfskdlql 113
                                    + ++ +lv    Gt+  ++l++    ++e++  e+ i+  ++++d+++ G+  G+i v s d ++
  gene396|gene396|rna396|rna396 220 IRENAMLVSNTTGTLRCYDLRKMTevIIEKRIHEDSITGLDTLGDNVYTGSLDGTIKVVSLD-TF 283
                                    67889999999999999999887654455555566799999999999999999999999998.44 PP

>> NUP214  Nucleoporin or Nuclear pore complex subunit NUP214=Nup159
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.8      0.77   2.8e+03     186     234 ..      24      70 ..      13      78 .. 0.67
   2 !   17.2   0.0   6.6e-07    0.0023      83     168 ..     192     281 ..     159     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.77
                                    TS-TTTSEEEEEEESSSSEEEEEEES---SS-SS----EEEEEEEEETT CS
                         NUP214 186 eelkdeyeplsikvLskqeylvvfGnkvseteedvsyDhklyivkkkde 234
                                    e++++  + l+i v++k++  v f  +++e+ee +  D  ++   ++d+
  gene396|gene396|rna396|rna396  24 EDIHQSLNYLNIPVVDKEK--VPFDDDIDESEEIMENDIVVFCTPNEDD 70 
                                    4445555567777777775..6788888888888888887777665554 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.6e-07
                                    SSEEEEEESSSTT.EEEEEE-SS-EE..EEETTEEEEEETTSEEEEEETT........EEEE.CSEEEEEE-SSEEEEEE CS
                         NUP214  83 ksellsldleelseleeihklekdlvelkllkstlllldsnnqLsaldlskkel....ksla.envasfDvledkLvvll 157
                                    +s ++s++ ++l  l+e  k+e ++ +++++++++l+ +++++L+++dl+k       k +  + ++ +D l d++++ +
  gene396|gene396|rna396|rna396 192 SSVVYSVE-NSLYCLDEEIKFEGEVERIRIRENAMLVSNTTGTLRCYDLRKMTEviieKRIHeDSITGLDTLGDNVYTGS 270
                                    44555554.7888889999*******************************876557776665156999***999999999 PP

                                    TTS-EEEEEEE CS
                         NUP214 158 kdksvqvfele 168
                                     d +++v++l+
  gene396|gene396|rna396|rna396 271 LDGTIKVVSLD 281
                                    99999988775 PP

>> EPTP  EPTP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.48      12      43 ..      97     167 ..      86     168 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                           EPTP  12 galdwehFtiggdvfLavAns.......................................sksgfSviYkW 43 
                                       d e++tigg+ ++a+A +                                       s s +S+i +W
  gene396|gene396|rna396|rna396  97 TICDSEYLTIGGEMYVALATFekdimvfdpfmrnpilpqvllkgheeavlsiesrdgilfSGSLDSTIIEW 167
                                    556779*************9966666665555555555555555555555555555555555555555555 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.7   1.3e+04      21      33 ..     152     164 ..     151     165 .. 0.82
   2 ?   -0.4   0.0      0.51   1.8e+03      31      37 ..     200     206 ..     183     208 .. 0.78
   3 ?    0.0   0.0      0.37   1.3e+03      29      39 ..     230     240 ..     222     241 .. 0.81
   4 ?    7.2   0.1    0.0021       7.5       9      38 ..     251     280 ..     248     282 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.7
                          PQQ_3  21 gglvyvgtgdGtl 33 
                                    +g+++ g+ d t+
  gene396|gene396|rna396|rna396 152 DGILFSGSLDSTI 164
                                    8999999988776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.51
                          PQQ_3  31 GtlyAlD 37 
                                    ++ly+lD
  gene396|gene396|rna396|rna396 200 NSLYCLD 206
                                    789**99 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.37
                          PQQ_3  29 gdGtlyAlDae 39 
                                    + Gtl+++D +
  gene396|gene396|rna396|rna396 230 TTGTLRCYDLR 240
                                    46*******75 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0021
                          PQQ_3   9 lpgpvnsspavdgglvyvgtgdGtlyAlDa 38 
                                    ++++  +++ + g+ vy+g+ dGt+  +  
  gene396|gene396|rna396|rna396 251 IHEDSITGLDTLGDNVYTGSLDGTIKVVSL 280
                                    5565666777779***********976655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2160.43
//
Query:       gene397|gene397|rna397|rna397  [L=314]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-18   65.0   0.0    1.1e-17   64.3   0.0    1.3  1  ATP_bind_3     PP-loop family
    2.4e-05   23.3   0.4    3.8e-05   22.6   0.0    1.5  2  tRNA_Me_trans  tRNA methyl transferase
    0.00037   20.1   0.1    0.00068   19.3   0.1    1.3  1  ThiI           Thiamine biosynthesis protein (ThiI)
     0.0066   16.5   0.0       0.01   15.9   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
  ------ inclusion threshold ------
      0.041   13.0   0.1      0.064   12.4   0.1    1.3  1  NAD_synthase   NAD synthase
      0.067   13.2   7.5       0.29   11.2   0.1    3.3  3  DZR            Double zinc ribbon
       0.14   12.4   1.0        1.3    9.3   0.1    2.6  2  CTU2           Cytoplasmic tRNA 2-thiolation protein 2


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   4.5e-21   1.1e-17       2     176 ..      51     245 ..      50     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 4.5e-21
                                    EEEE--SCHHHHHHHHHHHHHCTTTTT..EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H..HHCTTSTCC CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi..klvaihvdhglreeskeeaelvkelckklnikleiekvdv..akkkgknle 77 
                                    v +++SgG DS++L ++l  l+k+ g   +lv++ vd g+    ++    v++ +++l++kl+i +++   +++  k + 
  gene397|gene397|rna397|rna397  51 VGIGMSGGKDSTVLAYVLDLLNKRHGYgvELVLLGVDEGITGYRDQSIMSVCKNSSRLGLKLKIVSFEEtfGTTMDKVVR 130
                                    779**************99998888777799************************************9888444445555 PP

                                    CHHHH........HHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEE......TTCCEE-. CS
                     ATP_bind_3  78 eaARe........lRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeasei......asirlvR. 142
                                    +  R+        +R ++l+ a++k g++v++++h+adD aEt+ll++ rg   +   ++ ++++         i l R 
  gene397|gene397|rna397|rna397 131 KVGRRgnctycgvFRRQALEDAARKMGVDVIVTGHNADDMAETVLLNIVRGDISRLRRCTLARTKPqrsedgRMISLSRl 210
                                    55553333333338*************************************99865555444333334445422455444 PP

                                    .CCCT--HHHHHHHHHHTT---B--CGGGCTTSHH CS
                     ATP_bind_3 143 .PlLkvskeeleeylkekkikwveDesNadekyeR 176
                                     P+ +++++e+  y+ +kk++++  e  ++   +R
  gene397|gene397|rna397|rna397 211 kPFKHIYQKEIVLYAFHKKLEYFSTECTYSPGASR 245
                                    4*********************9877666655555 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.5e-08   3.8e-05       2     131 ..      50     172 ..      49     195 .. 0.77
   2 ?   -3.4   0.1       1.3   3.2e+03      90      99 ..     281     290 ..     276     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.5e-08
                  tRNA_Me_trans   2 kvvvalSgGVDSsvaaall....keqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykek 77 
                                    kv +++SgG DS+v a++l    k++gy v+ v l + e       +   ++ +  + + +++lg++l++v+fe+++ ++
  gene397|gene397|rna397|rna397  50 KVGIGMSGGKDSTVLAYVLdllnKRHGYGVELVLLGVDEG----I-TGYRDQSIMSVCKNSSRLGLKLKIVSFEETFGTT 124
                                    899*************998333345566666666555444....2.4566888999999999***************876 PP

                  tRNA_Me_trans  78 vfeefleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHYarvsle 131
                                     +++++++   Gr  n +  C    + +al ++a + +g+d ++tGH a  + e
  gene397|gene397|rna397|rna397 125 -MDKVVRK--VGRRGN-CTYCGVF-RRQALEDAARK-MGVDVIVTGHNADDMAE 172
                                    .6778875..466655.9999754.55677777777.**********9987765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                  tRNA_Me_trans  90 rTPnPdvlCN 99 
                                    r P P+vlC 
  gene397|gene397|rna397|rna397 281 RSPIPCVLCG 290
                                    679******5 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   2.7e-07   0.00068       9     129 ..      54     178 ..      46     183 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.7e-07
                           ThiI   9 LlSgGiDSpVaayll..l..kRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkev....lkeil 80 
                                     +SgG DS V ay+l  l  + G  v+lv l  +    e  ++ + +    + ++++ l +kl +v+f+e+    +++++
  gene397|gene397|rna397|rna397  54 GMSGGKDSTVLAYVLdlLnkRHGYGVELVLLGVD----EGITGYRDQSIMSVCKNSSRLGLKLKIVSFEETfgttMDKVV 129
                                    58***********754333356*******99644....444555545455555555566677777777665111156667 PP

                           ThiI  81 ekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNl 129
                                    +kv  +  +  +     ++ e  a+++g++ +vtG +    a   l N+
  gene397|gene397|rna397|rna397 130 RKVGRRGNCTYCGVFRRQALEDAARKMGVDVIVTGHNADDMAETVLLNI 178
                                    777777778888777777889999************9999998888886 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.1e-06      0.01       6     155 ..      55     232 ..      50     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.1e-06
                                    --SSCTCHHH...HHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S- CS
                    PAPS_reduct   6 vsgGkdslVl...lhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinaekhgs 75 
                                    +sgGkds+Vl   l+L+ k    +      ++ vd g +   ++ i  v + ++r+gl+lk+++ ee++   + +     
  gene397|gene397|rna397|rna397  55 MSGGKDSTVLayvLDLLNKRH--GygvelVLLGVDEGITgyRDQSIMSVCKNSSRLGLKLKIVSFEETFGTTMDKVV--- 129
                                    79*******833344444444..1446656777897765224566667778899*****999999999877766665... PP

                                    THHHC....HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-S...................CEE CS
                    PAPS_reduct  76 slyee....aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfek...................slr 132
                                    +++ +     ++ + + ++l+ a +k++ d+++tG  +d+ ++   l+iv+ d +  +                     r
  gene397|gene397|rna397|rna397 130 RKVGRrgncTYCGVFRRQALEDAARKMGVDVIVTGHNADDMAETVLLNIVRGDISRLRrctlartkpqrsedgrmisLSR 209
                                    3444447789***************************************9999886668999999999999999997778 PP

                                    E-CCCT--HHHHHHHHHHCT--B CS
                    PAPS_reduct 133 vfPllnWteedvwqyilrenipy 155
                                    + P  +  ++++  y+  ++++y
  gene397|gene397|rna397|rna397 210 LKPFKHIYQKEIVLYAFHKKLEY 232
                                    88999999999999998888877 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.5e-05     0.064      19     132 ..      49     168 ..      34     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                    SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--..SSST.....THHHHHHHHHHHHHHTSEEEE---HHHHHHHHHH CS
                   NAD_synthase  19 kgvvlGlSGGvDSslvaalavkalgkenvlalllP..ssvs.....seedvedalalaenlgievktidikpivrafeqe 91 
                                    ++v +G+SGG DS++ a++  ++l+k +  ++ l   ++ +      ++++    +   +lg++ k ++ +++  +  ++
  gene397|gene397|rna397|rna397  49 DKVGIGMSGGKDSTVLAYVL-DLLNKRHGYGVELVllGVDEgitgyRDQSIMSVCKNSSRLGLKLKIVSFEETFGTTMDK 127
                                    67889************986.56667666665543212222010113333444444444566666666666666655555 PP

                                    HHHHH-HHHHHH..HHHHHHHHHHHHHHHHHTEEEB---BHHH CS
                   NAD_synthase  92 lkeakedlakgN..lkaRiRmailyaianklnllvlgTgnksE 132
                                    +  +    ++gN   +   R ++l + a k++  v+ Tg++++
  gene397|gene397|rna397|rna397 128 VVRKVG--RRGNctYCGVFRRQALEDAARKMGVDVIVTGHNAD 168
                                    555543..44551156778888888888888888888888775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.0     0.025        64       1      18 [.       3      26 ..       1      29 [. 0.52
   2 ?   -0.0   0.0      0.36   9.1e+02      45      49 .]     138     142 ..     123     148 .. 0.73
   3 ?   11.2   0.1   0.00011      0.29      27      49 .]     280     304 ..     252     304 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.025
                            DZR  1 CpqCgee......lppdarfCseC 18
                                   C +C++        +++a++C+ C
  gene397|gene397|rna397|rna397  3 CVRCNTSqaivirAKDRAKVCKSC 26
                                   444444444444445555555555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.36
                            DZR  45 CpeCG 49 
                                    C +CG
  gene397|gene397|rna397|rna397 138 CTYCG 142
                                    44443 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00011
                            DZR  27 a..edrCpsCgekvdpearfCpeCG 49 
                                    +  ++ C+ Cg+++++++++C+ C+
  gene397|gene397|rna397|rna397 280 HrsPIPCVLCGHSTSSRDAICNGCT 304
                                    155889***************9995 PP

>> CTU2  Cytoplasmic tRNA 2-thiolation protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.13   3.4e+02      23      57 ..     120     147 ..      25     212 .. 0.77
   2 ?    9.3   0.1   0.00051       1.3      10      56 ..     252     294 ..     248     308 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.13
                           CTU2  23 tvvrTgeKLvknksseeaeletsekCalCglpldd 57 
                                    t   T +K+v +       + ++ +C+ Cg+  ++
  gene397|gene397|rna397|rna397 120 TFGTTMDKVVRK-------VGRRGNCTYCGVFRRQ 147
                                    333344444444.......4467889999876644 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00051
                           CTU2  10 ilklekdfpstvstvvrTgeKLvknksseeaeletsekCalCglpld 56 
                                    +++le++ p+++  v+r+g+ +++++s++    ++   C lCg + +
  gene397|gene397|rna397|rna397 252 MKQLEREDPKVILDVIRSGDIIQQEDSTH----RSPIPCVLCGHSTS 294
                                    789**********************9975....57889999998763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2025.73
//
Query:       gene398|gene398|rna398|rna398  [L=280]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-13   50.1  13.4    4.8e-13   49.2  13.4    1.4  1  GPI2      Phosphatidylinositol N-acetylglucosaminyltransferas


Domain annotation for each model (and alignments):
>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2  13.4   2.7e-17   4.8e-13       1     266 [.       3     266 ..       3     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.7e-17
                           GPI2   1 WkKlLwvkqsypDnYtdetFleeLqrnprvkpydfwplvadstvivqhvcsviifvlvFvgiyqervspvsvvllssilt 80 
                                    Wk+ L+ +q+yp nY++      ++r    +++d+ ++  d+ ++v ++++v++f+ +F  ++ e     s  ++ s+++
  gene398|gene398|rna398|rna398   3 WKRCLYLQQEYPINYME------VRRV--YRRRDVNEIYEDINRMVIRISIVMLFLSLFKVMMLEDKPGMSKSSWFSLFL 74 
                                    ***************85......4444..467899************************999988877776666666666 PP

                           GPI2  81 vlgwllwelwaskeesrssraqqrlktiksalliyftllglSPiLksLTkstssDSIw...alsfwlllinifffdysie 157
                                         ++e           +++++  ++k  ++++++ ++lSP++++LT  +  ++ +   a++ +l++i  ++++   +
  gene398|gene398|rna398|rna398  75 HSTQNFLE-----------NREDKGINLKPGFMLLTFAYLLSPLIRTLTLEIHPNTLYiyfAITQILFIIDSVSASIYNT 143
                                    65555552...........455667899****************************974457888888888887775544 PP

                           GPI2 158 kkkskekeek................lvaslStnaalmastvLASRLpstlqVFslllfsievfglfPvfrrslrhrswr 221
                                    +++ + k+e+                 ++ l ++  +++ ++L+SR ++  +VF ll++    ++   ++ ++++h +++
  gene398|gene398|rna398|rna398 144 RSSMEVKDEQtplsleesinipkrisSNQILGLTSYFLGFILLSSRFNEPSSVFNLLCLTFMGYI---ILLNHIEHLEVH 220
                                    444444444489********99999888899999999********************99877777...555666665566 PP

                           GPI2 222 lhvvltvllvllagag.vgiilklllavvlllllali.mgvcpwwli 266
                                     +++ t+l+ ++++++ ++  ++ +++++ +++++++ +  +++w++
  gene398|gene398|rna398|rna398 221 RSTAATALMYVFVSMMtLLPDIR-IFCIYSCIVTFVYsVSHISVWFL 266
                                    65555555555433330333333.34444444444431334677775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1828.42
//
Query:       gene399|gene399|rna399|rna399  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-09   38.3   0.3    1.5e-09   38.1   0.3    1.1  1  EMP24_GP25L  emp24/gp25L/p24 family/GOLD


Domain annotation for each model (and alignments):
>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.3   8.4e-14   1.5e-09       3     172 ..      14     168 ..      12     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.4e-14
                    EMP24_GP25L   3 tfklpageekCfyeelkkgtlltgsyqvtdggaaldvdlsvkdpdgngerlvkkkdresegdfsfta.kesgeykvCfdn 81 
                                    ++kl+++e+  f ++++++++ ++ yq+   +   +++l+ +  d +g+++ k+  r+   ++ ++  +e+ge+ + ++n
  gene399|gene399|rna399|rna399  14 RIKLEPKEQFTFRDKVVANQMYKFMYQTPRTS---KIELTMF--DTKGRQMTKT--RDPY-SVIYSKiAEDGEIVISVKN 85 
                                    589************************98866...9******..5555888888..5566.6666666************ PP

                    EMP24_GP25L  82 sfstksskkvsfdievgseasdykdsakkekletlese.lkkleekldsikreqkylrereerlrdtnestnsrvvwwsi 160
                                    ++s    k+v+f  +       +++ + +  l ++ +  + +l++ l+ + + q+ + +++e++ +++    ++v++  i
  gene399|gene399|rna399|rna399  86 NSS----KSVKFGYRCP-----DTSNKAQGGLGPISVDlVSELQNVLETVVQAQRVHIKKHEEHARMVAGSRKWVTRLLI 156
                                    877....89*****993.....34456689999987751678************************************** PP

                    EMP24_GP25L 161 lqllvlvlvavl 172
                                    +++l+ ++v ++
  gene399|gene399|rna399|rna399 157 FETLFFIGVLYF 168
                                    *******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1289.71
//
Query:       gene4|gene4|rna4|rna4  [L=127]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.8e-13   48.2   0.0    1.3e-12   47.8   0.0    1.2  1  Dynein_light  Dynein light chain type 1


Domain annotation for each model (and alignments):
>> Dynein_light  Dynein light chain type 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   7.3e-17   1.3e-12      25      85 ..      60     121 ..      44     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 7.3e-17
                            HHH-SSHH...HHHHHHHHHHHHHH-S-EEEEEEEEEEEEEEEETTEEEEEEETTEEEEEEE CS
           Dynein_light  25 lekfkkeke.kdiaayikkeldkkygptWhciVgksfgssvthekghfiyfyigklaillfK 85 
                            l  f++e+  + i++ +k  ld+k+g++W ++ g +f+ s+t+e+++f+++++g ++i +f+
  gene4|gene4|rna4|rna4  60 LAMFTDETPpTRICEALKSMLDSKFGKGWCVFAGAHFAGSCTFEEKYFAQISFGTYSITVFR 121
                            333444444589*************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 933.00
//
Query:       gene40|gene40|rna40|rna40  [L=646]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-25   88.2  14.5    3.2e-05   24.6   0.1    9.1  9  WD40          WD domain, G-beta repeat
    7.7e-09   35.7   0.1      0.012   15.8   0.0    4.8  6  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
     0.0028   16.7   0.1        6.3    5.6   0.0    3.8  4  Ge1_WD40      WD40 region of Ge1, enhancer of mRNA-decapping 
  ------ inclusion threshold ------
      0.081   11.4   1.3       0.55    8.7   1.3    2.1  2  Cytochrom_D1  Cytochrome D1 heme domain
       0.14   12.3   0.4       0.31   11.1   0.4    1.6  1  UPF0270       Uncharacterised protein family (UPF0270)


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7     6e+03      14      35 ..     126     145 ..     118     147 .. 0.63
   2 !   13.5   0.1   2.8e-05       0.1       5      37 ..     157     192 ..     155     193 .. 0.84
   3 !   16.5   0.9   3.2e-06     0.011       2      37 ..     202     237 ..     201     238 .. 0.87
   4 ?    5.4   0.0     0.011        38       7      36 ..     285     313 ..     278     314 .. 0.76
   5 ?    3.9   0.0     0.031   1.1e+02       3      21 ..     437     456 ..     435     468 .. 0.73
   6 !   18.4   0.0     8e-07    0.0029       9      38 .]     487     517 ..     479     517 .. 0.87
   7 !   24.6   0.1   8.8e-09   3.2e-05       5      37 ..     526     559 ..     522     560 .. 0.87
   8 ?   -0.1   0.0      0.57     2e+03      14      31 ..     577     594 ..     570     599 .. 0.80
   9 ?    5.1   0.0     0.013        46       9      36 ..     615     643 ..     608     644 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                                EEEEEETTSSEEEE....EETTSEEE CS
                       WD40  14 tslafspdgawlas....GsdDgtvr 35 
                                t+l      + ++s    Gs++g++ 
  gene40|gene40|rna40|rna40 126 TCL------TTICSrtfaGSRKGSIF 145
                                666......44432223299999885 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.8e-05
                                EEEESS.SSEEEEE..EETTSSEEEEEETTSEEEEE CS
                       WD40   5 rtltGH.ssvtsla..fspdgawlasGsdDgtvriW 37 
                                ++ +GH +s+ +++    +  a++a++s D t++iW
  gene40|gene40|rna40|rna40 157 HEVEGHkDSIQDIKstLIDGEAYVATSSQDETIKIW 192
                                6789**777999987767777779************ PP

  == domain 3  score: 16.5 bits;  conditional E-value: 3.2e-06
                                EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                       WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                ++++tl GH ++v+++ +   g++l+s s D+++  W
  gene40|gene40|rna40|rna40 202 KHIQTLNGHtDWVYGVFWTGKGDLLSS-SADKSIIYW 237
                                57899****777************975.55****999 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.011
                                EESS.SSEEEEEEETTSSE....EEEEETTSEEEE CS
                       WD40   7 ltGH.ssvtslafspdgaw....lasGsdDgtvri 36 
                                ++GH ++v s+      +w    l+++s D t r+
  gene40|gene40|rna40|rna40 285 ISGHlDGVKSI------DWrgefLLTSSLDMTSRM 313
                                47**999****......666666889998988775 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.031
                                EEEEEESS.SSEEEEEEETT CS
                       WD40   3 clrtltGH.ssvtslafspd 21 
                                 +r+  GH ++v+++a+s+d
  gene40|gene40|rna40|rna40 437 EIRKVYGHyFDVSDVAVSKD 456
                                567778**999****87766 PP

  == domain 6  score: 18.4 bits;  conditional E-value: 8e-07
                                SS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                       WD40   9 GH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                 H  ++  l fs+dg++la++s+D+tv ++d
  gene40|gene40|rna40|rna40 487 VHdYGIERLVFSRDGRYLAAASKDKTVSVYD 517
                                57334999*********************98 PP

  == domain 7  score: 24.6 bits;  conditional E-value: 8.8e-09
                                EEEESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                       WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                r l+GH   v++++fs+d+++la++s+D++v ++
  gene40|gene40|rna40|rna40 526 RRLEGHrRIVWDCSFSHDSRYLATCSRDRSVLVY 559
                                6789**4448*********************997 PP

  == domain 8  score: -0.1 bits;  conditional E-value: 0.57
                                EEEEEETTSSEEEEEETT CS
                       WD40  14 tslafspdgawlasGsdD 31 
                                tsl+fsp   +la G + 
  gene40|gene40|rna40|rna40 577 TSLCFSPREYLLAIGLES 594
                                89*****99999988444 PP

  == domain 9  score: 5.1 bits;  conditional E-value: 0.013
                                SS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                       WD40   9 GH.ssvtslafspdgawlasGsdDgtvri 36 
                                 H + v+ ++f+ dg+  a+G+ Dg v++
  gene40|gene40|rna40|rna40 615 EHsKRVNVISFNEDGSGYATGGGDGMVKM 643
                                69777999*********999988****97 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.1   3.9e+03      49      66 ..      37      54 ..      32      61 .. 0.82
   2 ?    1.8   0.2     0.082   2.9e+02      11      61 ..     181     234 ..     178     254 .. 0.72
   3 !   10.9   0.0   0.00012      0.43      35      69 ..     486     520 ..     458     536 .. 0.83
   4 ?   -1.0   0.0      0.64   2.3e+03      41      79 ..     535     575 ..     524     580 .. 0.73
   5 !   13.8   0.0   1.5e-05     0.053      10      90 ..     547     626 ..     538     628 .. 0.76
   6 !   15.8   0.0   3.5e-06     0.012       2      65 ..     580     644 ..     579     646 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                ANAPC4_WD40 49 dgklLavaysdgevrlld 66
                               ++k+L v y d+ v+ ++
  gene40|gene40|rna40|rna40 37 EEKVLSVIYMDNDVNAIE 54
                               689999999999998776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.082
                ANAPC4_WD40  11 AlatedgellvfRl..ng...qrvwtleedkedsevrsLaWkpdgklLavaysdge 61 
                                A  ++d+ + + R+  ++   +++ t   +++   v ++ W  +g lL  + +++ 
  gene40|gene40|rna40|rna40 181 ATSSQDETIKIWRVtdEWpwiKHIQT--LNGHTDWVYGVFWTGKGDLLSSSADKSI 234
                                66778888888888433433333333..3677888999999999999988776654 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00012
                ANAPC4_WD40  35 dkedsevrsLaWkpdgklLavaysdgevrlldaes 69 
                                + +d  ++ L ++ dg+ La a +d +v+++d+ +
  gene40|gene40|rna40|rna40 486 EVHDYGIERLVFSRDGRYLAAASKDKTVSVYDVGK 520
                                6788899************************9965 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.64
                ANAPC4_WD40  41 vrsLaWkpdgklLavaysdgevrlldaes..gkvvhslsvk 79 
                                v + ++++d + La    d +v +++a +   k v++++++
  gene40|gene40|rna40|rna40 535 VWDCSFSHDSRYLATCSRDRSVLVYEAPEfrVKYVSKFDCE 575
                                55678999999999999999999999865114556666665 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 1.5e-05
                ANAPC4_WD40  10 iAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksek.avtclgWg 90 
                                +A  + d ++lv+     rv  +  +k d e +sL+++p + lLa++ + g v + +   +++  + + k+++ +v+ ++++
  gene40|gene40|rna40|rna40 547 LATCSRDRSVLVYEAPEFRVKYV--SKFDCEATSLCFSPREYLLAIGLESGDVLIAKLGGAEIKIKRRSKEHSkRVNVISFN 626
                                56666666777777666677666..78899*************************999999886666555544378888776 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 3.5e-06
                ANAPC4_WD40   2 swcptmDLiAlatedgellvfRlngqrvwtl.eedkedsevrsLaWkpdgklLavaysdgevrll 65 
                                +++p   L+A++ e+g++l+  l g ++     +++++++v+ +++++dg+  a +  dg v+++
  gene40|gene40|rna40|rna40 580 CFSPREYLLAIGLESGDVLIAKLGGAEIKIKrRSKEHSKRVNVISFNEDGSGYATGGGDGMVKMF 644
                                799**********************99965547899999*********************99975 PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.14   5.1e+02     200     216 ..     178     194 ..     146     208 .. 0.71
   2 !    5.6   0.0    0.0018       6.3     189     216 ..     491     518 ..     457     527 .. 0.84
   3 ?    0.5   0.0     0.065   2.3e+02     186     214 ..     530     559 ..     523     566 .. 0.79
   4 !    4.6   0.0    0.0037        13     185     215 ..     614     645 ..     592     646 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                   Ge1_WD40 200 talatasedGevkffqv 216
                                + +at+s+d ++k ++v
  gene40|gene40|rna40|rna40 178 AYVATSSQDETIKIWRV 194
                                34777777777777776 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0018
                   Ge1_WD40 189 liveaafspdGtalatasedGevkffqv 216
                                 i   +fs dG  la+as+d +v  + v
  gene40|gene40|rna40|rna40 491 GIERLVFSRDGRYLAAASKDKTVSVYDV 518
                                577889*****************99987 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.065
                   Ge1_WD40 186 ehs.liveaafspdGtalatasedGevkff 214
                                 h   + + +fs d   lat+s d  v  +
  gene40|gene40|rna40|rna40 530 GHRrIVWDCSFSHDSRYLATCSRDRSVLVY 559
                                554367789999999999999999888766 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0037
                   Ge1_WD40 185 eehs.liveaafspdGtalatasedGevkffq 215
                                +ehs  +   +f  dG   at   dG+vk+f 
  gene40|gene40|rna40|rna40 614 KEHSkRVNVISFNEDGSGYATGGGDGMVKMFL 645
                                45554588899******************996 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.3   0.00015      0.55      41      93 ..     495     549 ..     484     566 .. 0.79
   2 ?    2.3   0.1     0.014        49      30      62 ..     527     559 ..     518     582 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00015
                                EE-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE-SSEEEEEEE-..-TTSEEEE CS
               Cytochrom_D1  41 rvfasdgRyvyvigRDgkvtliDLwakeivaevkiGlnarsvavS..qddryviv 93 
                                 vf++dgRy+  +++D +v+++D+ +     +   G   +  + S  +d ry+++
  gene40|gene40|rna40|rna40 495 LVFSRDGRYLAAASKDKTVSVYDVGKSIRFSRRLEGHRRIVWDCSfsHDSRYLAT 549
                                589********************98776555555677777666666577777664 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.014
                                EEE-STTEEEEEE-TT.SSEEEEEETTSEEEEE CS
               Cytochrom_D1  30 vletgyalHisrvfasdgRyvyvigRDgkvtli 62 
                                +le++  +     f+ d Ry+ + +RD  v ++
  gene40|gene40|rna40|rna40 527 RLEGHRRIVWDCSFSHDSRYLATCSRDRSVLVY 559
                                566666666667899999999999999888766 PP

>> UPF0270  Uncharacterised protein family (UPF0270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   8.7e-05      0.31      20      65 ..     145     192 ..     143     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-05
                                HHH-------..-.---HHHHHHHHHHHHHTTSEEEEE-TTT--EEEE CS
                    UPF0270  20 fvlregtDyG..eqelsleekveqvkqqLksgeavivfselhesvniv 65 
                                fvl e++D     +    ++ ++++k  L +gea +  s+++e+++i 
  gene40|gene40|rna40|rna40 145 FVLDEIEDDIkwHEVEGHKDSIQDIKSTLIDGEAYVATSSQDETIKIW 192
                                899999998874334467899*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3878.91
//
Query:       gene400|gene400|rna400|rna400  [L=220]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-60  203.7   0.7    3.1e-60  203.5   0.7    1.0  1  Cytidylate_kin   Cytidylate kinase
    6.2e-09   36.5   0.1      5e-08   33.6   0.1    2.1  1  AAA_18           AAA domain
    9.2e-07   29.4   0.7     0.0058   17.0   0.0    2.4  2  AAA_17           AAA domain
    1.5e-06   28.5   0.9      2e-06   28.1   0.9    1.2  1  Cytidylate_kin2  Cytidylate kinase-like family
    0.00012   22.0   0.1    0.00019   21.4   0.1    1.4  1  dNK              Deoxynucleoside kinase
    0.00072   19.7   0.0     0.0023   18.1   0.0    1.8  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.071   13.2   0.0       0.19   11.8   0.0    1.8  2  ADK              Adenylate kinase


Domain annotation for each model (and alignments):
>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.5   0.7   1.2e-63   3.1e-60       1     210 [.       6     214 ..       6     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 203.5 bits;  conditional E-value: 1.2e-63
                                    EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHHHT..T--TT-HHHHHHHHHT--EEEEEEEEEETTEE-TT CS
                 Cytidylate_kin   1 iaiDGPagsGKssvaralaeklglkyldtgalYRalalaalrr..kvdlldeaalvelakevelsfeaekvllngedvee 78 
                                    ia+DGPa+sGKss + ++a+klg++ l +g+lYRa+++a + +  +v++ de++  +++  +++++++++v+lng+d+++
  gene400|gene400|rna400|rna400   6 IAVDGPAASGKSSASDLVAKKLGFSHLISGNLYRAVTYALVSQfeEVQPKDEEQ-KRFVLGLDMEIRNNRVFLNGKDISD 84 
                                    8*************************************9988755899999876.68999******************** PP

                                    GGGSHHHHHHHHHHTTSHHHHHHHHHHHHTT-B..SSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT- CS
                 Cytidylate_kin  79 elrsdevekavSavaaipavRailvkklrelvk..karvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgt 156
                                     lr ++++  v  +a+ + vR+++   +++ +k  k++++v+GRDi+t+++p+a+lKifl+As+e+RakRR+k+    ++
  gene400|gene400|rna400|rna400  85 YLRGEKIDYHVTSIAKEKYVREKVSVIQKSTIKleKKGIIVDGRDIATKIMPEADLKIFLTASPETRAKRRYKE----SK 160
                                    *******************************998899*************************************....66 PP

                                    ---HHHHHHHHHHHHHHHHCTSSS-S---TT-EEEETTTS-HHHHHHHHHHHHH CS
                 Cytidylate_kin 157 svsleellaeikeRDklDkerevgpLklaedaliidtskltieevvekilelik 210
                                    s+s+eell+ +++RD+ D++re gpL++ae+ +ii+ +++t+ee  ++i++l+k
  gene400|gene400|rna400|rna400 161 SESYEELLEAMIKRDRGDRTREHGPLVAAEGSIIIENDCMTLEETADEIVRLFK 214
                                    789***********************************************9987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   1.9e-11     5e-08       1     117 [.       6     162 ..       6     174 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.9e-11
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf..........................gvnlrdvakenglllevdpealdeskrlde 54 
                                    I++ G++++GK++ ++ ++k+lgf                                                +e+kr++ 
  gene400|gene400|rna400|rna400   6 IAVDGPAASGKSSASDLVAKKLGFshlisgnlyravtyalvsqfeevqpkD---------------------EEQKRFVL 64 
                                    8899********************999987744444444444444444440.....................45555555 PP

                         AAA_18  55 dkldklldaleenss.....................................aleegknlvidghlaeleseaakdikkv 97 
                                    + ++++ ++    +                                      +  e k +++dg+      +   d+k +
  gene400|gene400|rna400|rna400  65 GLDMEIRNNRVFLNGkdisdylrgekidyhvtsiakekyvrekvsviqkstiK-LEKKGIIVDGRDIATKIMPEADLK-I 142
                                    55444444444444455556666666666666666665555555555555533.345666999999999988888989.* PP

                         AAA_18  98 vLtaspeelleRlekRgyee 117
                                    +Ltaspe++++R  k +++e
  gene400|gene400|rna400|rna400 143 FLTASPETRAKRRYKESKSE 162
                                    ***********998888766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   2.3e-06    0.0058       2      53 ..      10      59 ..      10      83 .. 0.76
   2 !   10.3   0.3   0.00027      0.69      65     126 ..      98     162 ..      80     173 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
                                   E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHH CS
                         AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklplee 53
                                   G+  sGK+ +++ +++k+gf+hl  G l r++     l+++++e++  ++e+
  gene400|gene400|rna400|rna400 10 GPAASGKSSASDLVAKKLGFSHLISGNLYRAVT--YALVSQFEEVQPKDEEQ 59
                                   7889**************************985..45566666666544443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00027
                                    HHHHH..HSSEEEEEE-SEEEETTEEEESSHHHHHHHH....SEEEEEE--HHHHHHHHHHHTTST CS
                         AAA_17  65 iaeea..kkkgvlvdghprikeqagfldglpkevleelkp..daiilleadpeeilerrlkdrtrg 126
                                    ia+e+  ++k  ++ +     e++g++ +  +++ +++ p  d+ i+l a+pe+  +rr k+ +++
  gene400|gene400|rna400|rna400  98 IAKEKyvREKVSVIQKSTIKLEKKGIIVD-GRDIATKIMPeaDLKIFLTASPETRAKRRYKESKSE 162
                                    33333333334344444444455555443.345677776655889****************97765 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.9   7.8e-10     2e-06       2     153 ..       6     178 ..       5     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.8e-10
                Cytidylate_kin2   2 ITIsreyGsgGetigeaLAekLgl.pfydreiieevakelglseeeveevdersrlssflskllaarvagdtl....... 73 
                                    I++++  +sg++   + +A+kLg+ ++++ ++ ++v   l  + eev+  de+   ++f+  l ++   ++ +       
  gene400|gene400|rna400|rna400   6 IAVDGPAASGKSSASDLVAKKLGFsHLISGNLYRAVTYALVSQFEEVQPKDEE--QKRFVLGLDMEIRNNRVFlngkdis 83 
                                    777888899**************9568888*****************999993..3578888888877777778999*** PP

                Cytidylate_kin2  74 ............deklddelfeaqervirela...aeesvVivGR.gadliLkdrpnvlrvfltapledrvkr.vaereg 136
                                                ++  ++++++ + +vi++     +++++++ GR  a  i+ + +  l++flta+ e r+kr ++e+++
  gene400|gene400|rna400|rna400  84 dylrgekidyhvTSIAKEKYVREKVSVIQKSTiklEKKGIIVDGRdIATKIMPEAD--LKIFLTASPETRAKRrYKESKS 161
                                    ****9999999855555555555555555543345677999****44777888855..*************987999999 PP

                Cytidylate_kin2 137 lseeearekiketDkrr 153
                                     s ee+ e++ ++D+  
  gene400|gene400|rna400|rna400 162 ESYEELLEAMIKRDRGD 178
                                    99999999999998865 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   7.3e-08   0.00019       1     153 [.       6     165 ..       6     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 7.3e-08
                                    EEEEESTTSSHHHHHHHHHCCSTCEEEE-..........HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHH....H CS
                            dNK   1 ivveGnIgaGKstlvklLskklgvkvfeE..........pvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrl....k 66 
                                    i+v+G+ ++GKs+  +l +kklg+ ++            +v+++     + ++   ++ +r+ + l++++ ++r+    k
  gene400|gene400|rna400|rna400   6 IAVDGPAASGKSSASDLVAKKLGFSHLISgnlyravtyaLVSQF-----EEVQPKDEEQKRFVLGLDMEIRNNRVflngK 80 
                                    89*********************998877677755555555555.....88888899***************99833333 PP

                                    HHHCHHSSS-EEEEES-HHHHHHTHHHHH.HHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTT CS
                            dNK  67 qqlealatkqvvvleRsiysdryiFakal.aekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgr 145
                                     + + l+ ++++    si +++y+  k+  ++k t++ e+  i  + +d +++ +++ dl i+L as+et  +r +k ++
  gene400|gene400|rna400|rna400  81 DISDYLRGEKIDYHVTSIAKEKYVREKVSvIQKSTIKLEKKGIIVDGRDIATKIMPEADLKIFLTASPETRAKRRYKESK 160
                                    34444477788888889999****99985268999**********************************97777666555 PP

                                    CCCTTS-H CS
                            dNK 146 eeekkiel 153
                                    +e     +
  gene400|gene400|rna400|rna400 161 SE---SYE 165
                                    44...444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   9.1e-07    0.0023       5      78 ..       9     115 ..       6     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 9.1e-07
                         AAA_33   5 vGlpGsGKstlaerllkklgavllssdtlrrrlfg......tdqqskt...........................dytrv 51 
                                     G+++sGKs  ++ ++kklg+ +l s +l+r++++      +++q+k                            dy r 
  gene400|gene400|rna400|rna400   9 DGPAASGKSSASDLVAKKLGFSHLISGNLYRAVTYalvsqfEEVQPKDeeqkrfvlgldmeirnnrvflngkdisDYLRG 88 
                                    69**************************9999998666666333333244445555555555555555555554444443 PP

                         AAA_33  52 ldrlyqilnelarkal.sagrnvildat 78 
                                     +++ +++  +a+++  +++ +vi  +t
  gene400|gene400|rna400|rna400  89 -EKIDYHVTSIAKEKYvREKVSVIQKST 115
                                    .345555555554433255555555555 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.6e-05      0.19       3      35 ..      10      42 ..       8      64 .. 0.90
   2 ?   -2.4   0.0       1.8   4.7e+03      31      81 ..     104     127 ..      88     137 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                                   ESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  3 GaPgaGKGtqaeklvkkyglahlstGdllRaev 35
                                   G+ ++GK   ++ ++kk+g+ hl +G+l Ra +
  gene400|gene400|rna400|rna400 10 GPAASGKSSASDLVAKKLGFSHLISGNLYRAVT 42
                                   8899**************************965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                                    HHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  31 lRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllDG 81 
                                    +R++v+                        v + k++++   +kkg ++DG
  gene400|gene400|rna400|rna400 104 VREKVS------------------------V-IQKSTIKL--EKKGIIVDG 127
                                    333332........................1.22222222..244444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1175.77
//
Query:       gene401|gene401|rna401|rna401  [L=426]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.06   13.4   0.0       0.12   12.4   0.0    1.5  1  Peptidase_S49_N  Peptidase family S49 N-terminal


Domain annotation for each model (and alignments):
>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.9e-06      0.12      92     134 ..     335     377 ..     311     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.9e-06
                Peptidase_S49_N  92 eeekkrvfvldFkGdikAsevesLreeitavLsvakpeDevll 134
                                    ++++kr+ +  F+G i+  +v++ +  ++++ +v++++Dev+l
  gene401|gene401|rna401|rna401 335 RSSDKRILIGGFDGTIRNAKVNKRKARVKTLFQVVRKGDEVIL 377
                                    56788999999******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2549.02
//
Query:       gene402|gene402|rna402|rna402  [L=329]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-44  150.0   0.0      9e-44  149.7   0.0    1.1  1  ThiF       ThiF family
    1.3e-07   32.1   0.0    3.1e-07   30.9   0.0    1.6  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0     1e-47     9e-44      35     243 ..       1     194 [.       1     197 [. 0.91

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 1e-47
                                    HHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  35 knLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavteritdetvleellesvDlVv 114
                                    ++L+ +G+g+l lvD+D++e+ Nl+Rq++++e+d  ++K+ +a  ++++ n+ +ev+ ++e +++e+ +e +++ +D+++
  gene402|gene402|rna402|rna402   1 MYLVSCGIGRLGLVDFDRVEIHNLQRQIIYTEADLSQYKVVAALSFARRANSCIEVVGYNEFLNKEN-VERIISPYDVIL 79 
                                    589**************************************************************99.68********** PP

                                    EESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 115 dalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgcyeCldpsstedptekkvplctsiagnipaiattta 194
                                    d++D+i +r+l+ + c   +++li +++l++egq++       +cy+Cl+p     + +    +c + ag   +++++++
  gene402|gene402|rna402|rna402  80 DCTDSIHTRYLLSDHCKALSKSLICGSVLRWEGQLYKLT-PSGPCYRCLFP-----NMKGRTLTC-EDAG---VVGPVCG 149
                                    **************************************7.59********9.....445566899.99**...******* PP

                                    HHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEEEC-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 195 vvaglaalellkllsgkeklenslltqvdllesrfenvelerakkskcl 243
                                    v+++l+ale++k++ g +     ++t +++ +s + +++l++ +k++c+
  gene402|gene402|rna402|rna402 150 VIGSLQALEAIKIITGDT---RPKMTIYNGMTSDLMDFQLRA-PKPDCR 194
                                    **************7666...555556788888888888855.445665 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   3.4e-11   3.1e-07       7     105 ..     235     316 ..     229     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.4e-11
                      Rhodanese   7 ellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaall 86 
                                    ++l++  + l+D+R+p++Ye  +++g+vn+             pl +l ++++    + +k+v v+c+ g +++  a ++
  gene402|gene402|rna402|rna402 235 KNLKS--YLLIDIRSPVQYEMFRVKGSVNI-------------PLVNLEDKVRTI-ETGGKRVGVVCRRGISSKKGALIF 298
                                    44533..35*********************.............555555555544.347********************* PP

                      Rhodanese  87 kklGyknvsvldGGfkawk 105
                                    k+ G  + + ++GG+++ k
  gene402|gene402|rna402|rna402 299 KANG-IDAFSVNGGIDGLK 316
                                    *9**.8*********9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2067.65
//
Query:       gene403|gene403|rna403|rna403  [L=165]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1128.43
//
Query:       gene405|gene405|rna405|rna405  [L=370]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.13   11.3   7.3       0.02   14.1   1.5    2.2  2  AI-2E_transport  AI-2E family transporter
       0.29   10.9   1.2       0.54   10.1   0.2    2.0  2  DDDD             Putative mitochondrial precursor protein


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.5   2.2e-06      0.02      75     170 ..     218     305 ..     200     318 .. 0.57
   2 ?   -0.6   0.5     0.063   5.6e+02     147     166 ..     320     339 ..     307     359 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-06
                AI-2E_transport  75 liaqltqlvkslpayidslqnilnelpslleele.nliqalkqslskilsnilssilnsllsllasllglilslvlvlll 153
                                    + + +++l+       +s+++ +  +++++  ++ +   ++ +   k l  + s++ +     +++ll +il+ ++ +++
  gene405|gene405|rna405|rna405 218 ISKETSSLI------ESSVLERIIRHTNIYFSKKhPETTPNSDIQKKFLDFLKSELSSK---SMSYLLATILTPFFCIFM 288
                                    333333333......33344444444444444421223344444444444444444443...3455666779******** PP

                AI-2E_transport 154 lffllldgeklrqgilk 170
                                    ++fll+  ek+ q++++
  gene405|gene405|rna405|rna405 289 TYFLLKTTEKFEQMVYR 305
                                    **************987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.063
                AI-2E_transport 147 lvlvllllffllldgeklrq 166
                                    +++++++  fll+  +++++
  gene405|gene405|rna405|rna405 320 VLTIIFIILFLLYAYHEILT 339
                                    34444444444444444444 PP

>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1         1   9.3e+03      32      40 ..     110     118 ..     109     126 .. 0.69
   2 ?   10.1   0.2     6e-05      0.54      36      63 ..     201     228 ..     196     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1
                           DDDD  32 tpFgLlrvi 40 
                                    ++FgLl ++
  gene405|gene405|rna405|rna405 110 MTFGLLILV 118
                                    678888554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6e-05
                           DDDD  36 LlrvilvVipgllvGtliSknvAnlLee 63 
                                    +++vi+ Vi + ++ t+iSk+  +l+e 
  gene405|gene405|rna405|rna405 201 VIEVIVRVIGYWIITTTISKETSSLIES 228
                                    689*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2294.81
//
Query:       gene406|gene406|rna406|rna406  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.3   5.0      0.081   12.8   1.5    1.9  2  DUF4271   Domain of unknown function (DUF4271)
        2.8    7.8   4.9         11    5.9   0.2    3.1  3  DUF2976   Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.12   1.1e+03     155     174 ..      10      28 ..       3      61 .. 0.60
   2 ?   12.8   1.5   9.1e-06     0.081       1      99 [.      67     171 ..      67     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.12
                        DUF4271 155 lililiillliklllllyks 174
                                    l+++ +++ +i +l+ ++k 
  gene406|gene406|rna406|rna406  10 LMFVKAVFHFIVILR-IIKE 28 
                                    333334444444444.3333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.1e-06
                        DUF4271   1 itillllcflllalaksrfrkf..fsrllklf...fnnkereslfkee.tksesrfqlflllltclllglllylllsefg 74 
                                    it++l+  +++la+  +r +kf  ++  l++f   +++  +es+ k+  ++ e+   +fl+   ++l + ll+ + ++f 
  gene406|gene406|rna406|rna406  67 ITSILISTMMMLAINAIRKKKFesMESVLRPFidfLSHGLSESTQKKVsSSLENIIPVFLVGHLVVLASGLLLGIEKRFT 146
                                    689999999999888777766544556666666636666677777776899999999************99999999977 PP

                        DUF4271  75 slfgsylassllllliiflilllyl 99 
                                    +  +   ++ l+++++i++il +y+
  gene406|gene406|rna406|rna406 147 KYVRHPRDKLLFVYGLILFILGFYI 171
                                    7666545599999998888888775 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0012        11      35      76 ..      13      54 ..       7      56 .. 0.86
   2 ?    1.9   0.0     0.021   1.9e+02      28      55 ..      65      92 ..      61     104 .. 0.81
   3 ?   -0.4   0.5      0.11     1e+03      29      51 ..     126     148 ..     117     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0012
                        DUF2976 35 laavaflaVakaalkkfneisegkaewgkfgltlvvGvvllv 76
                                   + av  + V+  ++k++n + + k ++  +  +++   vll+
  gene406|gene406|rna406|rna406 13 VKAVFHFIVILRIIKEWNHVPDYKMNFETVSKIVLASYVLLL 54
                                   566777889999********************9999999985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.021
                        DUF2976 28 villgLvlaavaflaVakaalkkfneis 55
                                     +  ++++++++la+     kkf+ ++
  gene406|gene406|rna406|rna406 65 SSITSILISTMMMLAINAIRKKKFESME 92
                                   5678899999999999999999998765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.11
                        DUF2976  29 illgLvlaavaflaVakaalkkf 51 
                                    +++ Lv+ a ++l  +++ ++k+
  gene406|gene406|rna406|rna406 126 LVGHLVVLASGLLLGIEKRFTKY 148
                                    45556666666665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1578.44
//
Query:       gene407|gene407|rna407|rna407  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-42  143.0   0.0    1.9e-41  141.6   0.0    1.8  1  AAA              ATPase family associated with various cellul
    6.4e-10   38.7   0.4    1.4e-09   37.6   0.4    1.5  1  AAA_lid_3        AAA+ lid domain
    4.9e-07   29.8   0.0    1.9e-06   27.9   0.0    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
    2.7e-05   24.6   0.1    0.00067   20.1   0.0    2.4  2  AAA_16           AAA ATPase domain
    0.00012   21.3   0.0    0.00018   20.8   0.0    1.2  1  DUF815           Protein of unknown function (DUF815)
    0.00021   21.6   0.1     0.0067   16.7   0.0    2.3  2  AAA_22           AAA domain
    0.00026   20.8   0.0     0.0023   17.7   0.0    2.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00063   19.9   0.0     0.0015   18.7   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
     0.0012   19.4   0.0     0.0028   18.2   0.0    1.7  1  AAA_18           AAA domain
     0.0024   18.2   0.0     0.0041   17.4   0.0    1.5  1  AAA_28           AAA domain
     0.0043   17.2   0.0     0.0087   16.2   0.0    1.5  1  AAA_33           AAA domain
      0.005   16.4   0.0      0.013   15.0   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
     0.0055   17.1   0.0      0.019   15.3   0.0    1.9  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.019   14.7   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
      0.013   14.7   0.0      0.027   13.7   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.013   14.9   0.0      0.026   13.9   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.016   14.9   0.1      0.064   13.0   0.1    1.9  2  AAA_24           AAA domain
      0.017   15.0   0.1      0.055   13.4   0.0    1.9  2  NTPase_1         NTPase
      0.041   13.8   0.4       0.79    9.6   0.0    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
      0.048   13.5   0.0       0.11   12.4   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.071   12.7   0.0       0.26   10.8   0.0    1.9  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.071   12.8   0.0       0.15   11.8   0.0    1.6  1  Sigma54_activat  Sigma-54 interaction domain
      0.083   12.9   0.0       0.17   11.9   0.0    1.5  1  AAA_14           AAA domain
        0.1   12.2   0.0       0.51    9.9   0.0    2.0  2  AAA_25           AAA domain
       0.14   11.2   0.0       0.26   10.3   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.15   12.0   0.0       0.27   11.2   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.17   11.5   0.1       0.67    9.6   0.0    1.8  2  AAA_30           AAA domain
       0.18   11.6   0.0       0.31   10.8   0.0    1.3  1  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0   2.9e-44   1.9e-41       1     131 [.     196     326 ..     196     327 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 2.9e-44
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgses 79 
                                    vllyGppGtGKTlla+ava+ +++ f+++ gsel++kyvge+++ +re+f+ ak k+  +i+f+DE+da++++r +++++
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTNACFIRVIGSELVQKYVGEGARMVREIFAMAKGKK-ACIIFFDEVDAFGGTRfDDEDD 274
                                    79***************************************************9997.9***************999999 PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +e +r++ +L+++ldg++ + +++ v++atnrpd+ldpallr gR+drk+e++
  gene407|gene407|rna407|rna407 275 NEVQRTMLELINQLDGFDPR-GNIKVLMATNRPDTLDPALLRpGRLDRKVEFG 326
                                    999****************7.66***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.4   2.1e-12   1.4e-09       3      44 ..     351     392 ..     346     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 2.1e-12
                      AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                     ++ +A+++++ +GA+l ++c eA++ A+r+ +k  t++df 
  gene407|gene407|rna407|rna407 351 RFDLIARLCNNATGAELRSVCTEAGMFAIRERRKIATEADFL 392
                                    5788************************************96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     3e-09   1.9e-06       1      76 [.     195     263 ..     195     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3e-09
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEver 76 
                                    +vlL GppGtgK+ la+ +a ++n+ +  v +++      l++++   +g +  ++  ++ ++++++i+++DEv+ 
  gene407|gene407|rna407|rna407 195 GVLLYGPPGTGKTLLARAVANRTNACFIRVIGSE------LVQKYV-GEGARMVREIFAMAKGKKACIIFFDEVDA 263
                                    59**********************9999998876......999999.588888999999999************95 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     1e-06   0.00067      24      47 ..     193     216 ..     165     232 .. 0.82
   2 ?    1.7   0.0      0.46     3e+02     127     151 ..     245     273 ..     236     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-06
                         AAA_16  24 pelvllsGesGvGKsslvrellra 47 
                                    p  vll+G++G+GK+ l+r+++++
  gene407|gene407|rna407|rna407 193 PKGVLLYGPPGTGKTLLARAVANR 216
                                    489*****************9974 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.46
                         AAA_16 127 lallsrderplvlvlDdlq.....wadeas 151
                                    +a + ++++  ++++D+++     ++d+++
  gene407|gene407|rna407|rna407 245 FAMA-KGKKACIIFFDEVDafggtRFDDED 273
                                    3444.44777*********77777666644 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.8e-07   0.00018      16     116 ..     147     261 ..     139     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-07
                         DUF815  16 lepveevdevklddLvgidkqkealve.......nteqfle..glpannvLLwGarGtGKSslvkallneyaeegLrli. 85 
                                    l  vee   v+ +d+ g +++ e++ e       n e+f++    p + vLL+G  GtGK  l +a+ n++++  +r+i 
  gene407|gene407|rna407|rna407 147 LMQVEERPDVTYNDIGGCKEEIEKIREvveapllNPERFVAlgIDPPKGVLLYGPPGTGKTLLARAVANRTNACFIRVIg 226
                                    5566666666666666666655555432223333777887632368999******************************8 PP

                         DUF815  86 .evekedlkelpklvellr...erperfilfvDDL 116
                                     e+ ++ + e  ++v+++    + ++ +i+f D +
  gene407|gene407|rna407|rna407 227 sELVQKYVGEGARMVREIFamaKGKKACIIFFDEV 261
                                    8888999998888888765232667899***9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     1e-05    0.0067       8      29 ..     196     217 ..     191     234 .. 0.86
   2 ?    2.6   0.0      0.23   1.5e+02      76     126 ..     238     300 ..     217     305 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G++GtGKT+l+r ++++ 
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRT 217
                                    689***************9987 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.23
                         AAA_22  76 eellealeqalraravielliiDEaqhlr..s..........eealeeLrsllnl.srkgvqli 126
                                     ++++ +   ++ +++  ++  DE++ +   +           ++le + +l  +  r +++++
  gene407|gene407|rna407|rna407 238 ARMVREIFAMAKGKKA-CIIFFDEVDAFGgtRfddeddnevqRTMLELINQLDGFdPRGNIKVL 300
                                    5555666666667777.9999*******776155556666767888877766666677777776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.5e-06    0.0023      35      71 ..     195     232 ..     187     265 .. 0.70
   2 ?    0.2   0.0      0.87   5.6e+02      26      60 ..     312     347 ..     301     359 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvk.lkitsgPvlek 71 
                                     vllyGpPG Gkt la+ +a+  ++  +++  +  ++k
  gene407|gene407|rna407|rna407 195 GVLLYGPPGTGKTLLARAVANRTNACfIRVIGSELVQK 232
                                    59*******************99876145544444444 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.87
                         RuvB_N  26 akkreealdhvllyGpPGl.Gkttlakiiakelgvk 60 
                                    a  r   ld  + +G P l G+t++ +i ak + v+
  gene407|gene407|rna407|rna407 312 ALLRPGRLDRKVEFGLPDLeGRTSILRIHAKTMSVD 347
                                    666777899999999999989*********999886 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.4e-06    0.0015       6     104 ..     196     286 ..     191     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.4e-06
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHH...HHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlv...srligappgyvgaeegGivllDEidKihp 82 
                                    +ll gp g+Gkt+la+a+a+  ++     +ir+  sel +     ++v   +r + +  ++ + ++  i+++DE+d    
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTNA----CFIRVIGSELVQ-----KYVgegARMVREIFAMAKGKKACIIFFDEVDAFGG 266
                                    6899******************96....999999999999.....33311123333333344444556********9999 PP

                                    ----------HHHHHHHHHHHH CS
                          AAA_2  83 kessgadvSregVqrdLLqile 104
                                      +   d   ++Vqr +L ++ 
  gene407|gene407|rna407|rna407 267 --TRFDDEDDNEVQRTMLELIN 286
                                    ..888899999*******9986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.4e-06    0.0028       1      45 [.     196     262 ..     196     304 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.4e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevdpe.a 45 
                                    +ll G+pG+GKt la+++++r+ ++                    ++++  +ak +  ++ +++e +
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTnACfirvigselvqkyvgegarmVREIFAMAKGKKACIIFFDEvD 262
                                    799******************9666998888666666666666666666666666666665555554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.4e-06    0.0041       2      40 ..     196     239 ..     195     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.4e-06
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv.pEaareileekla 40 
                                    + + G+++tGKT l++a a+r     ++v+  E + +++ e+++
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRtnacFIRVIgSELVQKYVGEGAR 239
                                    6799***************9865555666666666666655543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-05    0.0087       2      29 ..     196     223 ..     196     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavlls 29 
                                    vll G+pG+GK+ la+ +++++ a++++
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTNACFIR 223
                                    7899***************999955544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     2e-05     0.013      31     111 ..     191     263 ..     181     284 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                          AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDln 110
                                    +  k vll+Gp GtGKt++++ + ++ +          f     ++ +q+ + +     r+   +++g+k +++F D+++
  gene407|gene407|rna407|rna407 191 DPPKGVLLYGPPGTGKTLLARAVANRTN--------ACFIRVIGSELVQKYVGEGARMVREIFAMAKGKKACIIFFDEVD 262
                                    55688****************9999888........56667778899999999998888888888888899999999887 PP

                          AAA_7 111 m 111
                                     
  gene407|gene407|rna407|rna407 263 A 263
                                    6 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     3e-05     0.019       1      64 [.     196     250 ..     196     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkde 64 
                                    ++lyGp+g+GK++la+            ++++ +++r   ++ +++Y g+ + ++ ++ ++ ++
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARA---------VANRTNACFIRVIGSELVQKYVGEGARMVREIFAMAKG 250
                                    689**************.........34666888889999999999999999888888888776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     3e-05     0.019      47      70 ..     193     216 ..     187     259 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgve 70 
                                     ++++l Gp+G+GK+ la a++ +
  gene407|gene407|rna407|rna407 193 PKGVLLYGPPGTGKTLLARAVANR 216
                                    57899***************9875 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.3e-05     0.027      51      90 ..     194     231 ..     191     248 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevys 90 
                                    ++vLl Gp+gtGkt la a+++  +    f+ + gse+ +
  gene407|gene407|rna407|rna407 194 KGVLLYGPPGTGKTLLARAVANRTN--ACFIRVIGSELVQ 231
                                    89*******************9866..7899999999865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-05     0.026      25      43 ..     196     214 ..     185     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt+la++++
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVA 214
                                    89*************9875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1    0.0001     0.064       5      22 ..     196     213 ..     193     265 .. 0.88
   2 ?   -1.7   0.0       3.1     2e+03      31      66 ..     372     405 ..     358     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    +l+yGp+g+GKT la+  
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAV 213
                                    89*************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                         AAA_24  31 tekGlksldadkfpdieswedfldevvelaaelady 66 
                                    te+G+ ++  ++  +i + +dfl++v+++ + +a++
  gene407|gene407|rna407|rna407 372 TEAGMFAIRERR--KIATEADFLKAVDKVIKGYAKF 405
                                    788998888888..8899999999999998888777 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       3.4   2.2e+03      18      50 ..     101     134 ..      99     172 .. 0.76
   2 ?   13.4   0.0   8.5e-05     0.055       2      61 ..     196     256 ..     195     287 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.4
                                    HHHHHH...GGGEEEEEEEE.E-------EEEEE CS
                       NTPase_1  18 kvlellkssgvkvgGfytee.vreggrrigFkiv 50 
                                     +++ +  +g +v+G + +e +r g  r  ++i+
  gene407|gene407|rna407|rna407 101 MIAKFIVGKGKRVDGSLIQEgMRVGVDRNKYQII 134
                                    5677778888888886655525666677777765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.5e-05
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEE.EEEEE-------EEEEEET.T--EEEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf.yteevreggrrigFkivdlasgeegiLa 61 
                                    v++ GppG+GKt l + v++  +   ++v G  +++++  +g r+  +i ++a+g+++ + 
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTNACFIRVIGSeLVQKYVGEGARMVREIFAMAKGKKACII 256
                                    6788*******************999***9974688899*****************98765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012      0.79      23      45 ..     196     218 ..     187     234 .. 0.82
   2 ?    1.6   0.0      0.34   2.2e+02     114     135 ..     248     269 ..     226     289 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                       ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                    +++YGp g GKt L + ++++ +
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTN 218
                                    789**********9999999875 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.34
                       ATPase_2 114 kkkgkkiiiiiDelqklidlgl 135
                                     k +k  ii++De+   +   +
  gene407|gene407|rna407|rna407 248 AKGKKACIIFFDEVDAFGGTRF 269
                                    4444559*******88775554 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00017      0.11       2      30 ..     196     224 ..     195     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                    vll g PG++ktll++a+a+  ++ f r+
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTNACFIRV 224
                                    7999********************99998 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.3   2.7e+03      91     121 ..      55      89 ..      53     103 .. 0.72
   2 ?   10.8   0.0   0.00041      0.26       4      65 ..     197     256 ..     195     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.3
                                    CTTTTHHHH.HTT...SHHHHHCCCECEEEEEEET CS
                           cobW  91 tGlaePapv.aft...eeelksdltldavvavvDa 121
                                    tGla P+ + ++      + + +l++  v  v+D+
  gene407|gene407|rna407|rna407  55 TGLAPPMCWdLLGdrnRIQSEPNLQVARVCKVLDG 89 
                                    89999999964435444444557888888888887 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00041
                                    EEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SS..CHCCCCCCHCCCT.EEEETTTTECCHC CS
                           cobW   4 vltGflGsGKTtLlnhllenraglklavivNefge..vsiDaellretgveivelenGciCctl 65 
                                    +l G++G+GKT L +++ ++++   + vi  e+ +  v++ a+++r +   i+ +++G+  c +
  gene407|gene407|rna407|rna407 197 LLYGPPGTGKTLLARAVANRTNACFIRVIGSELVQkyVGEGARMVR-E---IFAMAKGKKACII 256
                                    688*****************************98643444444443.3...7888999888874 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00023      0.15      23      47 ..     194     218 ..     177     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                                    S-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheask 47 
                                      vl+ G  GtGK+llara+ ++++
  gene407|gene407|rna407|rna407 194 KGVLLYGPPGTGKTLLARAVANRTN 218
                                    679***************9976543 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00026      0.17       5      76 ..     196     264 ..     193     295 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00026
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT l++ ++++         +i +   ++  k   + +++ ++i++++k++k  ++f+DE+   
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTN-----ACFIRVIGSELvqKYVGEGARMVREIFAMAKGKKACIIFFDEVDAF 264
                                    7899***********99996655.....4444444433311333333356777777766677888*****9765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00079      0.51      36      53 ..     196     213 ..     167     217 .. 0.88
   2 ?   -0.7   0.0       1.4   9.2e+02     143     173 ..     253     289 ..     236     303 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                         AAA_25  36 allaGapgtGKttlaldl 53 
                                    +ll+G+pgtGKt la  +
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAV 213
                                    69***********99665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                         AAA_25 143 vrlvviDplsralgg..densnsdv....galveale 173
                                    +  + +D ++++ g   d +++++v     +l+++l+
  gene407|gene407|rna407|rna407 253 ACIIFFDEVDAFGGTrfDDEDDNEVqrtmLELINQLD 289
                                    5567778887777777766666665311134445554 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00041      0.26     117     137 ..     196     216 ..     191     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00041
                      Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                    v++yGp+ tGkt la+a a+ 
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANR 216
                                    89***************9985 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00042      0.27      21      46 ..     195     220 ..     165     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00042
                                    EEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE  21 vilLeGdLGaGKTtlvrglakalgve 46 
                                     +lL+G+ G+GKT l+r++a+  +  
  gene407|gene407|rna407|rna407 195 GVLLYGPPGTGKTLLARAVANRTNAC 220
                                    49*****************9987654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0     0.001      0.67      21      48 ..     196     223 ..     189     232 .. 0.82
   2 ?   -1.4   0.0       2.5   1.6e+03      91     113 ..     368     390 ..     339     397 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                         AAA_30  21 avltGpAGtGKttalkalreaweaaggr 48 
                                    ++l Gp+GtGKt + +a+++  +a   r
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTNACFIR 223
                                    5789************998876665555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                         AAA_30  91 llivDEagmvdtkqlaallkaae 113
                                      +  Eagm ++++ ++++++a+
  gene407|gene407|rna407|rna407 368 RSVCTEAGMFAIRERRKIATEAD 390
                                    45667999999999999988875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00048      0.31      20      42 ..     196     218 ..     183     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00048
                         AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                    +l+ GPPGtgKT    ++ ++ +
  gene407|gene407|rna407|rna407 196 VLLYGPPGTGKTLLARAVANRTN 218
                                    699*********88888777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2650.13
//
Query:       gene408|gene408|rna408|rna408  [L=850]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (850 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 5426.66
//
Query:       gene409|gene409|rna409|rna409  [L=355]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-36  125.0   0.0    3.7e-36  124.4   0.0    1.3  1  NMT             Myristoyl-CoA:protein N-myristoyltransferase,
      4e-30  104.9   0.0    6.5e-30  104.2   0.0    1.3  1  NMT_C           Myristoyl-CoA:protein N-myristoyltransferase,
    4.2e-05   23.8   0.8    0.00048   20.3   0.1    2.5  2  Acetyltransf_1  Acetyltransferase (GNAT) family
  ------ inclusion threshold ------
      0.071   13.3   0.1       0.77    9.9   0.0    2.5  3  GHL6            Hypothetical glycosyl hydrolase 6
       0.08   13.0   0.0       0.16   12.1   0.0    1.5  1  Acetyltransf_9  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> NMT  Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   0.0     1e-39   3.7e-36      17     158 ..      33     167 ..      27     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 1e-39
                                    --STTEEEEE--TTSHHHHHHHHHHHHHHSSCTTTSTEEE---HHHHHHHCTSTT--GGGEEEEEETTTTEEEEEEEEEE CS
                            NMT  17 klpkgfewvtvdledeeelkevyelLsenYvedddamfrfkyskeflkWalkppgykkewhvgvrvkkskkLvafisaip 96 
                                    klp+gf++ ++       ++ev e+L++nYved +a   ++ys++flkW +   g kk++++ +r    +++v+fi + +
  gene409|gene409|rna409|rna409  33 KLPDGFRFEDLR-----CIEEVTEFLEKNYVEDVHAEHMLRYSSNFLKWVIDCGGEKKKYCIVLRL--CGRMVGFIFGKE 105
                                    677777776665.....799*********************************************8..89********** PP

                                    EEEEETTEEEEEEEEEEEEE-GGGTTSSHHHHHHHHHHHHHHTTT--EEEEEESSTSSSESE CS
                            NMT  97 vklrvrkkvlklveinfLcvhkklRskrlapvlikEitRrvnlkgifqavytagvvlpkpvs 158
                                    +++ +r ++ ++  +nfLcv +++R +rlap+likEitRr n++gif+ v+t+g+ l   vs
  gene409|gene409|rna409|rna409 106 HHVVIRGEKNRAIGVNFLCVAQEMRGRRLAPILIKEITRRANVDGIFKGVFTSGTELFFNVS 167
                                    *******************************************************9988877 PP

>> NMT_C  Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   1.8e-33   6.5e-30      20     189 ..     191     344 ..     177     350 .. 0.91

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 1.8e-33
                                    H---SS-SSTTEEE--CCCHHHHHHHHHHHHTTSSEEEE--HHHHHHHHC-SSTTSBTTTEEEEEEEETTS.EEEEEEEE CS
                          NMT_C  20 yklpeetktkglremeekDveavtellekylkrfdlaqvfseeeveHwllskkkkreeqvvwsYVvedeetkkitDfvSF 99 
                                    +k+ e+   +g r  ee+D++++++l+ +  kr+ l++++ + ++   l +      ++vv++YV ed+    i  f +F
  gene409|gene409|rna409|rna409 191 MKIRETRVRRGTRIAEERDMKEIERLYMEESKRYMLYEEMGSSDIISALKP-----VKNVVYTYVHEDDG--CIDGFGAF 263
                                    6777888889***************************************99.....9**********876..69999999 PP

                                    EE--EEETT-SS-SEEEEEEEEEEEECCCTTHHHHHHHHHHHHHHHHHHCTESEEEEESSTTGGGCTTTTT-EEEEEEEE CS
                          NMT_C 100 YslpstvlknpkhktlkaAYlfyyastetkklkkrlkeLvkdalilakkakfDvfnaltlmdnklfleelkFgagdgkLn 179
                                      ++   ++++++++++  Yl+y   + +       +++v+d++ +a+k+++Dvfn+l++m+n+lfle l F +g g+L+
  gene409|gene409|rna409|rna409 264 LIIE--TIEKKSRRSVQGGYLYYRGGKDN-------TKMVEDLIYFAQKEGCDVFNCLDIMENSLFLEGLGFFPGSGELR 334
                                    8776..47899999*********998887.......89****************************************** PP

                                    EEEETEEE.- CS
                          NMT_C 180 YYLyNyrvap 189
                                    YYLyN+   +
  gene409|gene409|rna409|rna409 335 YYLYNWSSGE 344
                                    ******9755 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.3e-07   0.00048       5      98 ..      50     156 ..      46     177 .. 0.70
   2 ?    1.4   0.0     0.097   3.5e+02      36      96 ..     249     308 ..     207     326 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.3e-07
                                    HHHHHHHTHHHHHHHHHHH....HHHHHHS...TTC.EEEEEEETTEEEEEEEEEEEET....TSTTEEEEEEEEESGGG CS
                 Acetyltransf_1   5 vellvesffppnedaseee....feesfsl...eae.gllvaeedgeliGfisllkipd....ekggvayieslaVspey 72 
                                     e+l++ + +  + +++ +    f ++ ++   e + +++v +  g+ +Gfi ++        ek++ + +++l V+ e 
  gene409|gene409|rna409|rna409  50 TEFLEKNYVEDVHAEHMLRyssnFLKWVIDcggEKKkYCIVLRLCGRMVGFIFGKEHHVvirgEKNRAIGVNFLCVAQEM 129
                                    555555555444444444445566666444322333355557777*******6666666999999*************** PP

                                    TTSSHHHHHHHHHHHHHHHTTE.SEEE CS
                 Acetyltransf_1  73 rgkGlGsaLlealeerareegi.kkiv 98 
                                    rg+ l+  L++++ +ra   gi k ++
  gene409|gene409|rna409|rna409 130 RGRRLAPILIKEITRRANVDGIfKGVF 156
                                    ****************99888866654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.097
                                    EEEEETTEEEEEEEEEEEET.TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESE CS
                 Acetyltransf_1  36 lvaeedgeliGfisllkipd.ekggvayieslaVspeyrgkGlGsaLlealeerareegikk 96 
                                    +v e+dg + Gf  +l+i   ek+ +  + + +    yrg    ++++e+l+ +a +eg++ 
  gene409|gene409|rna409|rna409 249 YVHEDDGCIDGFGAFLIIETiEKKSRRSVQGGYL--YYRGGKDNTKMVEDLIYFAQKEGCDV 308
                                    5566666666666666665552222222211111..14444444666777777777777765 PP

>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00021      0.77      92     134 ..     108     152 ..      96     155 .. 0.85
   2 ?   -2.4   0.0       1.4   4.9e+03      54      98 ..     196     240 ..     162     256 .. 0.63
   3 ?   -0.3   0.0       0.3   1.1e+03      24      42 ..     278     292 ..     274     315 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
                           GHL6  92 iiiegervgepgwptlCinsgyq.eklaeel.eealkrldlDGif 134
                                    ++i ge+ ++ g + lC+ ++ +  +la+ l +e+ +r ++DGif
  gene409|gene409|rna409|rna409 108 VVIRGEKNRAIGVNFLCVAQEMRgRRLAPILiKEITRRANVDGIF 152
                                    578889999999999********767777666************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                           GHL6  54 achregikvvvrvdfskaderiyeqhpeWaavkenGeviiieger 98 
                                       r+g ++    d++ +++  +e+    +  +e G+  ii + +
  gene409|gene409|rna409|rna409 196 TRVRRGTRIAEERDMKEIERLYMEESKRYMLYEEMGSSDIISALK 240
                                    444667777777777777777777666666666666666555555 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.3
                           GHL6  24 aggvvyYrtkldfvtehpk 42 
                                    +gg++yYr+ +d    + k
  gene409|gene409|rna409|rna409 278 QGGYLYYRGGKD----NTK 292
                                    466999999984....333 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05      0.16      41     103 ..      85     147 ..      44     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                    TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHH CS
                 Acetyltransf_9  41 esrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleemr 103
                                    ++ +++++  g+ vg +    +++ ++G++ +a gv   +va e rgr ++  L+++  ++++
  gene409|gene409|rna409|rna409  85 KKYCIVLRLCGRMVGFIFGKEHHVVIRGEKNRAIGVNFLCVAQEMRGRRLAPILIKEITRRAN 147
                                    445556666899999999999*****************************9999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2425.48
//
Query:       gene41|gene41|rna41|rna41  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-12   45.7   0.8    4.7e-11   43.3   0.8    2.0  2  CTD_bind  RNA polymerase II-binding domain.


Domain annotation for each model (and alignments):
>> CTD_bind  RNA polymerase II-binding domain.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.8   2.6e-15   4.7e-11       1      63 []      56     122 ..      56     122 .. 0.87
   2 ?   -0.6   0.0      0.14   2.5e+03      24      39 ..     145     160 ..     132     164 .. 0.58

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 2.6e-15
                   CTD_bind   1 kLnllYLaNdvlqnskrkq..kdefapaFapvlpeafadayk..kapekikkklkrllniWeernvf 63 
                                +LnllYLaN+v+q +k       e++  +++v++e+f+ ++k   +++++ kk+++l n+W +rnv+
  gene41|gene41|rna41|rna41  56 RLNLLYLANEVVQTTKDVDpdSIELKILLKKVVNEVFEETKKmaMKNPSLYKKYCELENVWIQRNVM 122
                                8************65322244578899*****************77888****************96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.14
                   CTD_bind  24 apaFapvlpeafaday 39 
                                + ++++vl++a++ + 
  gene41|gene41|rna41|rna41 145 KAKLSAVLEDALSRVR 160
                                5567788888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1044.45
//
Query:       gene410|gene410|rna410|rna410  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-90  301.4   0.0    1.1e-89  301.3   0.0    1.0  1  UPF0160   Uncharacterised protein family (UPF0160)


Domain annotation for each model (and alignments):
>> UPF0160  Uncharacterised protein family (UPF0160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.3   0.0     6e-94   1.1e-89       2     317 .]       3     297 ..       2     297 .. 0.96

  Alignments for each domain:
  == domain 1  score: 301.3 bits;  conditional E-value: 6e-94
                        UPF0160   2 igTHngkFhaDevlAvalLrllpeykdaelvRtrdpevleecdivvDVggvyDpakkryDHHqrefnetfsekaktklSS 81 
                                    ++TH+++Fh+DevlA ++L ++  y+dae++Rtrd++++e+ div+DVggv++pa++r+DHHqr+f+etfs+k+++klSS
  gene410|gene410|rna410|rna410   3 LVTHDERFHYDEVLASCVLLRI--YPDAEIMRTRDNAIIEQGDIVYDVGGVFNPATRRFDHHQRTFSETFSSKYNVKLSS 80 
                                    79********************..******************************************************** PP

                        UPF0160  82 aGLvYkhfgkeiikkllkleldeeevellyeklyeefveaiDaiDnGisvyeevekkykiktslssrvgrlnpewneeek 161
                                    +GL++k+f+k++++ +  +e +   ++++++k+y+ef+ + DaiDnG ++y e++++     +++++vg +n++   + +
  gene410|gene410|rna410|rna410  81 SGLIFKYFHKQLLSLY-GIEDTCGIYNMVVDKIYSEFFLYADAIDNGQDIYGEIRPR-----TMADLVGLFNTD---TPD 151
                                    **************99.88889999**************************987777.....99*********4...456 PP

                        UPF0160 162 eedederFekAselvgeeflekvkylakswlpareivkealekrkevdesgrilvleesvpwkehllelekelkiekkvl 241
                                    e  e++ F k +e+v++++++++k+ +k w++  e+v++  ++      +g ilvl+++  +++ +le+e++ +  k+++
  gene410|gene410|rna410|rna410 152 EGLENRGFYKVLEIVSTDLDNYMKR-IKIWVNNYEHVEKKARE-----TNGPILVLDKH-YTTDLILEIESQNG--KDFK 222
                                    999*********************9.8************9999.....79*******98.77889999999988..9*** PP

                        UPF0160 242 yvlyedeeekwrvqavpvskesfesrkpLpeeWrGlrdeeLsevsgiegavFvHasgFiggnktkegalemAkkaL 317
                                    +++++ +++ +rv a+p++++sfe++ pL++eWrGl +eeL ++sgieg++FvH+sgF+g n+t+e+al+m++++L
  gene410|gene410|rna410|rna410 223 FMVFP-HRNAYRVIAIPKRRGSFETKNPLKKEWRGLVNEELVRASGIEGCIFVHSSGFMGINSTFENALKMCEESL 297
                                    ****9.8******************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1836.07
//
Query:       gene411|gene411|rna411|rna411  [L=415]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-82  276.5   0.0      4e-82  276.1   0.0    1.1  1  Hist_deacetyl    Histone deacetylase domain
  ------ inclusion threshold ------
       0.16   12.9   0.4         16    6.5   0.0    2.4  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  276.1   0.0   4.4e-86     4e-82       1     305 [.      23     312 ..      23     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: 276.1 bits;  conditional E-value: 4.4e-86
                                    SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskllddd 80 
                                    hp++p R++ ++++l   ++l  +++++ +p +a+ e l+++H  +Y+++l+s+s+e  ++  +k+   ++ +     dd
  gene411|gene411|rna411|rna411  23 HPMKPLRVK-MTHTLLVGYELY-KYMDVLRPFQASYENLTNFHAVDYINFLSSVSSENMEEM-IKDL--HKFN---IRDD 94 
                                    8999*****.999999999988.56778************************9998876665.3333..3333...5689 PP

                                    THCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETT.SS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  81 tpvspktlkaallavgavleavdavlsgsvkaafvlv.rPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDv 159
                                    +pv+p+++++++l+ g+++ a++++ sg  k +++++  ++ HHak+seasGFC+vN+++++i +l + ++ krv+++D+
  gene411|gene411|rna411|rna411  95 CPVFPGLYDYCKLTSGGSIYAAQKINSG--KYDVAINwAGGLHHAKRSEASGFCYVNDIVLGILELLK-YN-KRVLYIDI 170
                                    ****************************..99999999****************************99.55.7******* PP

                                    SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 160 DvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkP 239
                                    DvHhG+G+eeafy +++v+t+S+H+y++ ++Pgtg ++d+g +kgkg+++nvpl++g++de+y ++f+ ++ +v+e ++P
  gene411|gene411|rna411|rna411 171 DVHHGDGVEEAFYTTDRVMTVSFHKYGD-YFPGTGMVTDIGLAKGKGYSVNVPLRDGIDDESYFSIFKPVVSKVIEVYRP 249
                                    *************************966.9************************************************** PP

                                    SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 240 dlilvsaGfDalkgdplgelnlsvegykeltkklaeladkvkkvvllleGGYnlealaravtavls 305
                                    d+i+++ G+D+l+gd+lg +nls  g+++++k + ++     +++ll++GGY++ ++++a+++ +s
  gene411|gene411|rna411|rna411 250 DAIVLQSGADSLSGDKLGCFNLSHLGHSRCIKFVQSFNI---PLILLGGGGYTIGNVSKAWAYGTS 312
                                    ************************************998...99*****************99776 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0018        16      31      59 ..      63      94 ..      32     107 .. 0.70
   2 ?    4.1   0.1      0.01        90      36      59 ..     345     368 ..     342     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0018
                Ribosomal_L18_c 31 qFskyik..kgieaddleelykkaha.aIred 59
                                   +  +yi+  ++++++++ee+ k+ h+ +Ir+d
  gene411|gene411|rna411|rna411 63 HAVDYINflSSVSSENMEEMIKDLHKfNIRDD 94
                                   44567777789**************9678877 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.01
                Ribosomal_L18_c  36 ikkgieaddleelykkahaaIred 59 
                                    +k++ + ++le++ +k+h+++r  
  gene411|gene411|rna411|rna411 345 MKNQNTKESLEDIVAKVHENLRGV 368
                                    5788899*************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2884.40
//
Query:       gene412|gene412|rna412|rna412  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-28   97.7   2.9    8.5e-28   96.9   2.9    1.4  1  eRF1_1          eRF1 domain 1
    2.2e-15   57.1   0.1    6.7e-15   55.6   0.1    1.9  1  eRF1_3          eRF1 domain 3
  ------ inclusion threshold ------
        0.2   12.1   2.1        1.5    9.3   0.1    2.8  3  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   2.9   1.4e-31   8.5e-28       1     128 [.       1     125 [.       1     126 [. 0.96

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1.4e-31
                                    HEEEEECTB.TTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTTSS CS
                         eRF1_1   1 mkllkrdle.kdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkdag 79 
                                    mkl k+ ++ +  sgs+++ +e ++d++ l+ +i+ gd v ++t+rk+q +     +++ r+ l L+ik+e++++d +++
  gene412|gene412|rna412|rna412   1 MKLEKNRIDqRCMSGSLRMTAEHQDDIYILSSVIDVGDMVTSTTTRKIQID----GKTQYRMSLVLKIKIESINVDLESS 76 
                                    8999999987889***********************************884....56699******************** PP

                                    EEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECEESHHHHHHHHHH CS
                         eRF1_1  80 vlrisGkvieenehvklgafhtldlelkrpftiikeewdsfalerLkea 128
                                    ++ ++Gk++  ne+v+lg++ht+d+ l++ f+++keew+++ ++ Lkea
  gene412|gene412|rna412|rna412  77 TIYLKGKTVLINEYVRLGSYHTIDVTLGQSFELEKEEWQEMSIKLLKEA 125
                                    ***********************************************98 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.1   1.1e-18   6.7e-15       2     112 ..     248     345 ..     247     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.1e-18
                                    HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSH.HHHHS-HHH-HHHHHHHHHHHHHHHHH CS
                         eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdt.lkekvketgeelelvelieelvenvee 80 
                                    i++ k +++f+ + ak++++++ G+e +++a+ +gA+++L++++e  + +d+ ++++             +e ++++++ 
  gene412|gene412|rna412|rna412 248 IDDLKEIDNFFVKFAKGSDLICIGMESIREAMDYGALDKLMITDEKIKPNDVeERRE-------------MEVFCKEIQA 314
                                    678899***************************************999988856665.............89******** PP

                                    TT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                         eRF1_3  81 sgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                    +++k+ ii+  + +Ge+l k++gGi ++L+++
  gene412|gene412|rna412|rna412 315 MNCKISIIPVAHFSGERL-KEMGGICGLLKFN 345
                                    ******************.***********97 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   7.3e+03      56      81 ..      95     120 ..      62     122 .. 0.64
   2 ?    1.0   0.1     0.096   5.7e+02      39      62 ..     206     232 ..     194     244 .. 0.75
   3 ?    9.3   0.1   0.00025       1.5      42      84 ..     279     321 ..     260     323 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                                    SSSEEEEEEEHHHHHHHHHHHHTTBE CS
                 RNA_pol_Rpb2_7  56 eekiekveipeafklLlqeLqslgia 81 
                                    + ++ +v++ ++f+l  +e q + i+
  gene412|gene412|rna412|rna412  95 SYHTIDVTLGQSFELEKEEWQEMSIK 120
                                    34445555667777777777777665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.096
                                    SSSSSCCCEE...EBTTTTCSSSEEEE CS
                 RNA_pol_Rpb2_7  39 grckllaaan...eCkivkseekiekv 62 
                                    + c+ + +++   eC+ +++++ i++v
  gene412|gene412|rna412|rna412 206 KACGSFCVIKvppECRGCSNSKVINMV 232
                                    45555555555669******9999887 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00025
                                    SSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTBEEEE CS
                 RNA_pol_Rpb2_7  42 kllaaaneCkivkseekiekveipeafklLlqeLqslgialkl 84 
                                      + a ++ +i++++ k+++ve ++ ++++++e+q+++ ++++
  gene412|gene412|rna412|rna412 279 MDYGALDKLMITDEKIKPNDVEERREMEVFCKEIQAMNCKISI 321
                                    2344455899999999**********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2030.65
//
Query:       gene413|gene413|rna413|rna413  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-36  124.8   0.0    1.2e-22   80.6   0.0    2.0  2  Carb_kinase  Carbohydrate kinase


Domain annotation for each model (and alignments):
>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.0   6.8e-27   1.2e-22       2     133 ..      31     160 ..      30     166 .. 0.89
   2 !   42.6   0.0   2.8e-15   4.9e-11     159     242 ..     169     257 ..     161     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 6.8e-27
                                    EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT-SS.. CS
                    Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGLgr.. 79 
                                    l+igGs+ ytGA+++a laa ++g+ lv ++ e+ea  +lk+ lpe iv  ++         +l++++  ++GpGLgr  
  gene413|gene413|rna413|rna413  31 LIIGGSKYYTGAPYFASLAAFHSGSELVYIFSEPEATVSLKTLLPESIVCGIEY-----QEWILKKVSCCIMGPGLGRps 105
                                    8****************************************************3.....3347999***********832 PP

                                    SHCHHH...HCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHC CS
                    Carb_kinase  80 dekikk...lleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLl 133
                                    +e+ k+   +l +   +d p+viD+dg+ l ++        + vi+TP+  E k++ 
  gene413|gene413|rna413|rna413 106 EETCKEitrILSYLGRRDIPIVIDGDGIRLASKLD--IGDLKTVIITPNTNEQKYIG 160
                                    3444448889***********************85..889999*********98875 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 2.8e-15
                                    EEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTS......SHHHHHHHHHHHHHHHHHHHCCCT-TS CS
                    Carb_kinase 159 llkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqne......asyeaaiaaawlhgaasdeaaekkgvg 232
                                    +lkg++dvi  +++ev+in++g + ++ GG+GD+LaG i++l +  +      + + + i +++++++a+++a ek++ +
  gene413|gene413|rna413|rna413 169 VLKGSNDVILWKDKEVKINNEGCP-KRIGGQGDILAGTIASLVSKCKppssdkEVFGSIILGCVMVRKAGRLAYEKYWKS 247
                                    8*****************998876.799***************9999898888889999********************9 PP

                                    -HCHHHHHHH CS
                    Carb_kinase 233 mlatelskii 242
                                    + + ++++ +
  gene413|gene413|rna413|rna413 248 LITRDILEML 257
                                    9999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1863.26
//
Query:       gene414|gene414|rna414|rna414  [L=97]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.9e-15   54.8   0.5    8.2e-15   54.4   0.5    1.2  1  Homeodomain  Homeodomain
    2.8e-06   27.1   2.7    0.00026   20.9   1.3    2.1  2  Homeobox_KN  Homeobox KN domain
  ------ inclusion threshold ------
      0.014   16.1   0.1      0.017   15.8   0.1    1.2  1  HOCHOB       Homeobox-cysteine loop-homeobox


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.5   1.4e-18   8.2e-15       8      56 ..      14      62 ..       9      63 .. 0.96

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.4e-18
                                   -HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    Homeodomain  8 tkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56
                                   +k q + L+++Fe n++p+ +er+ +A +  ++e+++++WFqNrRa+e+
  gene414|gene414|rna414|rna414 14 SKAQKDFLNTYFEVNPNPNIQERAYIACQSLISEKKIRNWFQNRRARER 62
                                   799********************************************98 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.0    0.0021        13      14      34 ..       2      25 ..       1      26 [. 0.90
   2 !   20.9   1.3   4.3e-08   0.00026       8      40 .]      28      60 ..      26      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0021
                    Homeobox_KN 14 edKeeLlkeTglsvkq...itnWF 34
                                   + K++L+k +gls++q   ++++F
  gene414|gene414|rna414|rna414  2 QAKRRLIKNSGLSKAQkdfLNTYF 25
                                   679************988898888 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 4.3e-08
                    Homeobox_KN  8 nPYPseedKeeLlkeTglsvkqitnWFINaRrR 40
                                   nP P+ ++++ ++ ++++s k i nWF N R+R
  gene414|gene414|rna414|rna414 28 NPNPNIQERAYIACQSLISEKKIRNWFQNRRAR 60
                                   899****************************99 PP

>> HOCHOB  Homeobox-cysteine loop-homeobox
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.1   2.9e-06     0.017       3      47 ..      23      67 ..      21      92 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-06
                         HOCHOB  3 elfeknrHPsiqemikiseetgvkYeqvfkRfselRllkkekCek 47
                                   ++fe n  P iqe   i++++ ++ +++ + f++ R+ ++  C++
  gene414|gene414|rna414|rna414 23 TYFEVNPNPNIQERAYIACQSLISEKKIRNWFQNRRARERGDCKA 67
                                   69*****************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 633.41
//
Query:       gene415|gene415|rna415|rna415  [L=503]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-08   35.5   3.0    1.1e-06   29.1   0.1    3.2  4  TPR_19      Tetratricopeptide repeat
    5.8e-07   30.1   1.6    5.6e-05   23.7   0.1    3.2  4  TPR_16      Tetratricopeptide repeat
    1.6e-06   28.3   5.6    4.2e-05   23.7   0.3    2.6  2  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    4.5e-06   27.0   1.4      0.036   14.9   0.2    3.6  3  TPR_14      Tetratricopeptide repeat
    4.4e-05   23.0   0.5    7.6e-05   22.3   0.5    1.3  1  Coatomer_E  Coatomer epsilon subunit
    0.00011   22.3   0.0       0.12   12.6   0.0    3.1  3  TPR_9       Tetratricopeptide repeat
    0.00016   21.3   8.5      0.042   13.5   0.0    4.8  5  TPR_11      TPR repeat
     0.0012   18.8  18.5       0.08   13.1   0.0    5.5  5  TPR_2       Tetratricopeptide repeat
      0.003   16.5   0.3     0.0062   15.5   0.3    1.5  1  NARP1       NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.013   15.8   5.9       0.96    9.8   0.2    4.0  4  TPR_12      Tetratricopeptide repeat
      0.025   14.4  17.8       0.24   11.3   1.7    5.4  6  TPR_1       Tetratricopeptide repeat
      0.078   13.2   9.9         13    6.3   0.0    5.0  4  TPR_8       Tetratricopeptide repeat
        1.5    9.7   8.0         63    4.5   0.2    4.4  4  TPR_6       Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.5   7.6e+03      30      46 ..     238     254 ..     234     260 .. 0.73
   2 ?   -1.3   0.0       2.3   3.2e+03      32      46 ..     266     280 ..     262     286 .. 0.83
   3 !   29.1   0.1   7.8e-10   1.1e-06       2      57 ..     339     394 ..     338     398 .. 0.96
   4 !   15.0   0.4   1.9e-05     0.026       5      57 ..     376     428 ..     375     436 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.5
                         TPR_19  30 lLAeallalgqldeAea 46 
                                    lL +a+++   +++A  
  gene415|gene415|rna415|rna415 238 LLGDAYYSYSAYEKALV 254
                                    57888888888888865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                         TPR_19  32 AeallalgqldeAea 46 
                                    +++l++l++  eA +
  gene415|gene415|rna415|rna415 266 INCLVNLNRGSEAAE 280
                                    589999999999865 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 7.8e-10
                         TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                    l++g  + A++ le+al   p+n e++ l+A al +++++ eA a+ ++l ++d++
  gene415|gene415|rna415|rna415 339 LKAGAVEKAINSLEKALNIVPGNTEIQFLYASALTSAKRFSEAAAVYERLVADDQK 394
                                    899***************************************************98 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 1.9e-05
                         TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                    +++ eA+a +e++ ++d kn   + +LA + ++l +++     L+++   d++
  gene415|gene415|rna415|rna415 376 KRFSEAAAVYERLVADDQKNTMFLRNLAMCRIQLEDIKNGLTSLKKASIYDQN 428
                                    6899***********************************99999999999888 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.32   4.4e+02      39      60 ..     238     259 ..     231     265 .. 0.85
   2 ?   -2.6   0.3       6.7   9.2e+03      18      27 ..     316     325 ..     315     328 .. 0.52
   3 !   23.7   0.1   4.1e-08   5.6e-05       2      62 ..     333     390 ..     332     396 .. 0.93
   4 !   13.9   0.2   4.8e-05     0.066      10      54 ..     375     416 ..     374     422 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.32
                         TPR_16  39 llgdaalrqgrlaeAaalyraa 60 
                                    llgda++  + +++A+ +++++
  gene415|gene415|rna415|rna415 238 LLGDAYYSYSAYEKALVYFEKY 259
                                    79**************999887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.7
                         TPR_16  18 aaleaalkrd 27 
                                    a+++aal+++
  gene415|gene415|rna415|rna415 316 AYFDAALDAY 325
                                    3445555544 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 4.1e-08
                         TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                    a++ ++l+ag  ++A++ le al      P + e ++l++ a+  ++r+ eAaa+y+++++
  gene415|gene415|rna415|rna415 333 AKGIYFLKAGAVEKAINSLEKALNIV---PGNTEIQFLYASALTSAKRFSEAAAVYERLVA 390
                                    67999*********************...*****************************974 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 4.8e-05
                         TPR_16  10 agdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa 54 
                                    a+++ +Aaa++e+++++d     +  +l +l+ ++ ++ + +  +
  gene415|gene415|rna415|rna415 375 AKRFSEAAAVYERLVADD---QKNTMFLRNLAMCRIQLEDIKNGL 416
                                    689***************...**************9999987665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   1.0     0.008        11      28      59 ..     238     269 ..     232     282 .. 0.86
   2 !   23.7   0.3   3.1e-08   4.2e-05       4      81 ..     343     421 ..     340     422 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.008
                                    HHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHH CS
                         ANAPC3  28 llAlclylngqykrAyellrkaklnskslgcr 59 
                                    ll+ ++y+ + y++A+ +++k+k nsk ++c+
  gene415|gene415|rna415|rna415 238 LLGDAYYSYSAYEKALVYFEKYKCNSKAINCL 269
                                    68899999999999999999998888888887 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.1e-08
                                    -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    + ++Ai  +e++l+  + + e  +l+A +l +++++ +A  +++++   + k+   +  +A c ++L+ ++ +++ L+k
  gene415|gene415|rna415|rna415 343 AVEKAINSLEKALNIVPGNTEIQFLYASALTSAKRFSEAAAVYERLvADDQKNTMFLRNLAMCRIQLEDIKNGLTSLKK 421
                                    67899***********************************************************************998 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       5.6   7.8e+03       6      26 ..     238     258 ..     234     259 .. 0.83
   2 !   14.0   0.0   4.9e-05     0.068       4      43 ..     331     370 ..     329     371 .. 0.92
   3 !   14.9   0.2   2.6e-05     0.036       3      42 ..     364     403 ..     362     405 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.6
                         TPR_14   6 alaeallalGdpdeAiallrr 26 
                                    +l++a++    +++A+ ++++
  gene415|gene415|rna415|rna415 238 LLGDAYYSYSAYEKALVYFEK 258
                                    688999999999999999986 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.9e-05
                         TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaq 43 
                                    l+a + ++l +G  ++Ai+ l++al   P++ e+++l+a 
  gene415|gene415|rna415|rna415 331 LRAKGIYFLKAGAVEKAINSLEKALNIVPGNTEIQFLYAS 370
                                    56778999*****************************995 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 2.6e-05
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                     + ++a+al  + ++ eA+a+++r++a++ ++  +++ la
  gene415|gene415|rna415|rna415 364 IQFLYASALTSAKRFSEAAAVYERLVADDQKNTMFLRNLA 403
                                    5678*************************99999998887 PP

>> Coatomer_E  Coatomer epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.5   5.5e-08   7.6e-05      64     232 ..     261     427 ..     234     437 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.5e-08
                                    HHHHHHHHHHHHHH-STTHHHHHHHHHHHHHS----S-HH....HHHHHHHHHHHTT-HHHHHHHHTT--SHHHHHHHHH CS
                     Coatomer_E  64 telqAvrllaeylnspsrkeeilaelkeeladseiesnev....lrllaaivflkegdfddalkllkksenLeavAlkvq 139
                                     +++A+  l +     ++ e++l+e+k      +   +++    ++++ +++  ke  fd+al++  + e L a    ++
  gene415|gene415|rna415|rna415 261 CNSKAINCLVNLNRGSEAAERALEEIKSIGVPTNR-RSKIrlcsMNIILGTIIGKEAYFDAALDAYYSYEPLRAK--GIY 337
                                    56778888888888888888888888875444443.3333222267899999******************98655..555 PP

                                    HHHHTT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHTT-HHH CS
                     Coatomer_E 140 illklhrvdlAekelkkmqdidedatltQLAqawvklavggekiqdAyyifqelsekykstplllngkAvvslllgryee 219
                                     +lk   v+ A + l k+ +i   +t  Q   a  +  ++++++ +A  +++ l    +++++ l   A++ ++l++ ++
  gene415|gene415|rna415|rna415 338 -FLKAGAVEKAINSLEKALNIVPGNTEIQFLYA--SALTSAKRFSEAAAVYERLVADDQKNTMFLRNLAMCRIQLEDIKN 414
                                    .99***********************9998554..45566799***********9999********************** PP

                                    HHHHHHHHHHH-T CS
                     Coatomer_E 220 AeslLkeaLdkda 232
                                      ++Lk+a   d+
  gene415|gene415|rna415|rna415 415 GLTSLKKASIYDQ 427
                                    ******9965555 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         6   8.3e+03      36      55 ..     240     259 ..     239     263 .. 0.80
   2 !    6.2   0.0     0.008        11      30      61 ..     329     360 ..     326     372 .. 0.87
   3 !   12.6   0.0   8.4e-05      0.12       5      56 ..     372     423 ..     367     437 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6
                          TPR_9  36 GlllaqlGclsaAladLeay 55 
                                    G +++   ++++Al  +e y
  gene415|gene415|rna415|rna415 240 GDAYYSYSAYEKALVYFEKY 259
                                    67788888888888888877 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.008
                          TPR_9  30 eerrdRGlllaqlGclsaAladLeaylalapd 61 
                                    e +r  G+   + G++++A++ Le +l + p 
  gene415|gene415|rna415|rna415 329 EPLRAKGIYFLKAGAVEKAINSLEKALNIVPG 360
                                    67899*********************988775 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 8.4e-05
                          TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                    + +++++++a av+erl++ + +    +r  ++++ ql++++ +l  L  + 
  gene415|gene415|rna415|rna415 372 LTSAKRFSEAAAVYERLVADDQKNTMFLRNLAMCRIQLEDIKNGLTSLKKAS 423
                                    56899***************************************99998765 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.7   2.3e+03      17      25 ..     202     210 ..     200     214 .. 0.86
   2 ?    2.3   0.6     0.097   1.3e+02       1      14 [.     240     253 ..     240     258 .. 0.89
   3 !   13.5   0.0   3.1e-05     0.042       5      32 ..     339     366 ..     337     372 .. 0.86
   4 !    6.3   0.0    0.0057       7.9       3      34 ..     371     402 ..     369     403 .. 0.85
   5 ?   -0.1   0.0      0.56   7.7e+02      11      33 ..     413     435 ..     407     436 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.7
                         TPR_11  17 YkkAlkldP 25 
                                    Y  Al+ldP
  gene415|gene415|rna415|rna415 202 YLMALNLDP 210
                                    788*****9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.097
                         TPR_11   1 GdayyeqGkyeeAi 14 
                                    Gdayy+   ye+A+
  gene415|gene415|rna415|rna415 240 GDAYYSYSAYEKAL 253
                                    9************8 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3.1e-05
                         TPR_11   5 yeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                     + G  e+Ai++++kAl++ P n e+ +
  gene415|gene415|rna415|rna415 339 LKAGAVEKAINSLEKALNIVPGNTEIQF 366
                                    567999***************9999987 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0057
                         TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayynL 34 
                                    a+++  ++ eA ++Y++ ++ d++n  ++ nL
  gene415|gene415|rna415|rna415 371 ALTSAKRFSEAAAVYERLVADDQKNTMFLRNL 402
                                    6788899****************997776666 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.56
                         TPR_11  11 eeAieaYkkAlkldPdnaeayyn 33 
                                    ++ ++++kkA  +d++   ay+ 
  gene415|gene415|rna415|rna415 413 KNGLTSLKKASIYDQNMIQAYFL 435
                                    5558999*********9999985 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.4     2e+03      22      33 ..     200     211 ..     199     212 .. 0.86
   2 ?    5.5   1.9     0.015        21       6      26 ..     238     258 ..     233     259 .. 0.91
   3 !   13.1   0.0   5.8e-05      0.08       4      34 .]     331     361 ..     328     361 .. 0.91
   4 !    7.4   0.1    0.0039       5.4       3      31 ..     364     392 ..     362     395 .. 0.85
   5 ?    1.2   0.0      0.37   5.1e+02       4      27 ..     399     422 ..     397     428 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.4
                          TPR_2  22 eafekAleldPn 33 
                                    +++  Al ldP+
  gene415|gene415|rna415|rna415 200 NYYLMALNLDPR 211
                                    69999*****96 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.015
                          TPR_2   6 nlGlayyklgdyeeAleafek 26 
                                     lG+ayy    ye+Al +fek
  gene415|gene415|rna415|rna415 238 LLGDAYYSYSAYEKALVYFEK 258
                                    69*****************98 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 5.8e-05
                          TPR_2   4 lynlGlayyklgdyeeAleafekAleldPnn 34 
                                    l + G   +k+g  e+A++ +ekAl + P+n
  gene415|gene415|rna415|rna415 331 LRAKGIYFLKAGAVEKAINSLEKALNIVPGN 361
                                    778999*********************9987 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0039
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleld 31 
                                    + +  + a+  ++++ eA++ +e+ ++ d
  gene415|gene415|rna415|rna415 364 IQFLYASALTSAKRFSEAAAVYERLVADD 392
                                    6788999999**************98766 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.37
                          TPR_2   4 lynlGlayyklgdyeeAleafekA 27 
                                    l nl+++ ++l d +  l  ++kA
  gene415|gene415|rna415|rna415 399 LRNLAMCRIQLEDIKNGLTSLKKA 422
                                    789***********9999999998 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.3   4.5e-06    0.0062      15      87 ..     339     415 ..     334     447 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.5e-06
                                    HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT......SSS CS
                          NARP1  15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak....klske 87 
                                     +ag +e+A++ Le++ + +  + +++   a+ l+  +r++eA+a+ye+L+   + n+ + ++l  ++    +++++
  gene415|gene415|rna415|rna415 339 LKAGAVEKAINSLEKALNIVPGNTEIQFLYASALTSAKRFSEAAAVYERLVADDQKNTMFLRNLAMCRiqleDIKNG 415
                                    589**************************************************************999655423332 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.044        60      50      70 ..     238     258 ..     235     259 .. 0.91
   2 ?    5.8   0.0     0.012        17      48      74 ..     331     357 ..     315     360 .. 0.82
   3 ?    9.8   0.2    0.0007      0.96      12      73 ..     337     390 ..     330     394 .. 0.81
   4 ?    1.6   0.0      0.26   3.5e+02       6      29 ..     399     422 ..     393     427 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.044
                         TPR_12  50 nLgrlyralgryeeAlellee 70 
                                     Lg++y+    ye+Al ++e+
  gene415|gene415|rna415|rna415 238 LLGDAYYSYSAYEKALVYFEK 258
                                    69****************997 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.012
                         TPR_12  48 lrnLgrlyralgryeeAlelleealai 74 
                                    lr+ g++++++g  e+A++ le+al+i
  gene415|gene415|rna415|rna415 331 LRAKGIYFLKAGAVEKAINSLEKALNI 357
                                    567788889999999999999999987 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0007
                         TPR_12  12 vlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                      +++g  ++A+  lekal+i+   +G  +    ++++ ++ ++  ++r+ eA + +e+ +a
  gene415|gene415|rna415|rna415 337 YFLKAGAVEKAINSLEKALNIV---PG--N---TEIQFLYASALTSAKRFSEAAAVYERLVA 390
                                    4567899999***********9...44..4...358999999999999*******9999765 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.26
                         TPR_12   6 lnnlaavlrrlgrydeAlelleka 29 
                                    l+nla++  +l++    l+ l+ka
  gene415|gene415|rna415|rna415 399 LRNLAMCRIQLEDIKNGLTSLKKA 422
                                    449**********99999999998 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.69   9.5e+02      23      32 ..     201     210 ..     197     212 .. 0.89
   2 ?   11.3   1.7   0.00017      0.24       6      26 ..     238     258 ..     235     259 .. 0.94
   3 ?   -3.2   0.9       6.8   9.4e+03      17      24 ..     318     325 ..     318     326 .. 0.88
   4 ?    9.2   0.0   0.00082       1.1       7      34 .]     334     361 ..     329     361 .. 0.89
   5 ?   -0.1   0.0      0.69   9.6e+02       9      26 ..     370     387 ..     369     388 .. 0.86
   6 ?    0.6   0.0      0.42   5.7e+02       5      27 ..     400     422 ..     398     428 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.69
                                    HHHHHHHHST CS
                          TPR_1  23 yyekALelnP 32 
                                    yy  AL l+P
  gene415|gene415|rna415|rna415 201 YYLMALNLDP 210
                                    9********9 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00017
                                    HHHHHHHHTT-HHHHHHHHHH CS
                          TPR_1   6 nlGnayfklgkydeAleyyek 26 
                                     lG ay++   y++Al y+ek
  gene415|gene415|rna415|rna415 238 LLGDAYYSYSAYEKALVYFEK 258
                                    69*****************98 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.8
                                    HHHHHHHH CS
                          TPR_1  17 ydeAleyy 24 
                                    +d Al++y
  gene415|gene415|rna415|rna415 318 FDAALDAY 325
                                    799***99 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00082
                                    HHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                          TPR_1   7 lGnayfklgkydeAleyyekALelnPnn 34 
                                    +G  ++k g  ++A+   ekAL + P n
  gene415|gene415|rna415|rna415 334 KGIYFLKAGAVEKAINSLEKALNIVPGN 361
                                    788999****************987765 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.69
                                    HHHHHTT-HHHHHHHHHH CS
                          TPR_1   9 nayfklgkydeAleyyek 26 
                                     a+ + +++ eA + ye+
  gene415|gene415|rna415|rna415 370 SALTSAKRFSEAAAVYER 387
                                    578899*******99997 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.42
                                    HHHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_1   5 ynlGnayfklgkydeAleyyekA 27 
                                     nl+++  +l++ +  l   +kA
  gene415|gene415|rna415|rna415 400 RNLAMCRIQLEDIKNGLTSLKKA 422
                                    69**********99999999988 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.5       0.6   8.2e+02       7      27 ..     239     259 ..     238     260 .. 0.83
   2 ?    6.3   0.0    0.0093        13      12      30 ..     339     357 ..     334     361 .. 0.83
   3 ?    4.9   0.1     0.026        36       2      28 ..     363     389 ..     362     390 .. 0.90
   4 ?    2.6   0.1      0.15   2.1e+02       6      27 ..     401     422 ..     401     428 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.6
                                    HHHHHHHTT-HHHHHHHHHHH CS
                          TPR_8   7 lgsiylklgdyeeAkeyyeka 27 
                                    lg++y +   ye+A  y+ek+
  gene415|gene415|rna415|rna415 239 LGDAYYSYSAYEKALVYFEKY 259
                                    788888888899999999995 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0093
                                    HHTT-HHHHHHHHHHHHHH CS
                          TPR_8  12 lklgdyeeAkeyyekalel 30 
                                    lk g  e+A+ ++ekal +
  gene415|gene415|rna415|rna415 339 LKAGAVEKAINSLEKALNI 357
                                    677888***********87 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.026
                                    CHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          TPR_8   2 eayynlgsiylklgdyeeAkeyyekal 28 
                                    e+ ++ +s++ + +++ eA ++ye+ +
  gene415|gene415|rna415|rna415 363 EIQFLYASALTSAKRFSEAAAVYERLV 389
                                    678999******************975 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.15
                                    HHHHHHHHTT-HHHHHHHHHHH CS
                          TPR_8   6 nlgsiylklgdyeeAkeyyeka 27 
                                    nl+++ ++l+d+++   +++ka
  gene415|gene415|rna415|rna415 401 NLAMCRIQLEDIKNGLTSLKKA 422
                                    799999**************99 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.09   1.2e+02       6      26 ..     239     259 ..     238     260 .. 0.88
   2 ?    3.2   0.1      0.12   1.7e+02      10      31 ..     337     359 ..     315     361 .. 0.81
   3 ?    4.5   0.2     0.045        63       3      28 ..     365     390 ..     363     392 .. 0.87
   4 ?   -1.4   0.0       3.6     5e+03       5      24 ..     401     420 ..     400     422 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.09
                                    HHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   6 lalsyrklgdtdkAlealerl 26 
                                    l+ +y++   ++kAl ++e+ 
  gene415|gene415|rna415|rna415 239 LGDAYYSYSAYEKALVYFEKY 259
                                    899****66*********985 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                                    HHH.HHHHHHHHHHHHHHHHH-T CS
                          TPR_6  10 yrk.lgdtdkAlealerlikeYP 31 
                                    y+  +g  +kA+  le+ ++  P
  gene415|gene415|rna415|rna415 337 YFLkAGAVEKAINSLEKALNIVP 359
                                    4433799**********999877 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.045
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   3 lyklalsyrklgdtdkAlealerlik 28 
                                    +++ a ++ ++++ ++A + +erl+ 
  gene415|gene415|rna415|rna415 365 QFLYASALTSAKRFSEAAAVYERLVA 390
                                    678888999989************96 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.6
                                    HHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   5 klalsyrklgdtdkAleale 24 
                                    +la+++++l d  + l+ l+
  gene415|gene415|rna415|rna415 401 NLAMCRIQLEDIKNGLTSLK 420
                                    69****99768777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3292.72
//
Query:       gene416|gene416|rna416|rna416  [L=678]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-54  181.9   0.0    5.1e-40  137.0   0.0    2.5  2  AAA              ATPase family associated with various cellul
    4.2e-10   40.0   0.0    3.6e-05   24.1   0.0    3.5  3  AAA_22           AAA domain
    4.6e-10   39.2   0.0    1.3e-09   37.7   0.0    1.9  1  AAA_lid_3        AAA+ lid domain
    7.3e-09   36.2   0.0      0.014   15.8   0.1    3.4  3  AAA_16           AAA ATPase domain
    1.3e-08   34.9   0.0     0.0011   19.0   0.0    3.1  2  AAA_5            AAA domain (dynein-related subfamily)
    3.1e-08   33.7   0.1    0.00057   19.9   0.1    2.7  2  AAA_14           AAA domain
    6.2e-08   32.9   0.0    1.8e-05   24.9   0.0    2.7  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.3e-07   32.0   0.0     0.0071   16.7   0.0    2.8  2  RNA_helicase     RNA helicase
    2.5e-07   31.3   0.0      0.016   15.8   0.0    3.0  2  AAA_18           AAA domain
    1.2e-06   28.4   0.0      0.018   14.8   0.0    2.6  2  AAA_24           AAA domain
    1.2e-06   28.0   0.2     0.0029   17.0   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.2e-05   25.1   0.2       0.15   11.8   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.5e-05   24.8   0.0       0.25   11.1   0.0    2.8  2  IstB_IS21        IstB-like ATP binding protein
    1.7e-05   25.0   0.0      0.075   13.2   0.0    2.4  2  AAA_33           AAA domain
    2.6e-05   23.6   0.2      0.053   12.7   0.0    3.4  3  NB-ARC           NB-ARC domain
    3.9e-05   23.3   2.4       0.27   10.8   0.1    3.2  3  AAA_25           AAA domain
    4.2e-05   23.5   0.0        0.2   11.7   0.0    2.7  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      6e-05   22.9   0.0      0.048   13.5   0.0    2.4  2  AAA_3            ATPase family associated with various cellul
    0.00012   21.5   0.7      0.066   12.6   0.0    3.1  3  ATPase           KaiC
     0.0002   21.3   0.1        2.1    8.3   0.0    3.8  4  NACHT            NACHT domain
    0.00089   18.8   0.1       0.64    9.5   0.0    2.4  2  AAA_7            P-loop containing dynein motor region
     0.0014   19.1   0.8       0.84   10.1   0.0    3.7  3  AAA_17           AAA domain
     0.0016   17.7   0.0        1.5    8.0   0.0    2.3  2  TIP49            TIP49 P-loop domain
     0.0017   17.9   0.0        2.4    7.6   0.0    2.7  2  PhoH             PhoH-like protein
     0.0045   17.3   0.0       0.88    9.8   0.0    2.4  2  AAA_28           AAA domain
     0.0062   16.9   0.0        2.9    8.2   0.1    2.9  2  AAA_19           AAA domain
     0.0065   16.5   0.0       0.21   11.5   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
     0.0067   16.2   0.0       0.15   11.8   0.0    2.6  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0078   16.7   0.2        0.6   10.6   0.0    2.6  2  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.017   14.9   0.0        1.5    8.6   0.0    2.3  2  AAA_11           AAA domain
      0.027   14.2   0.0       0.81    9.4   0.0    2.3  2  AAA_30           AAA domain
       0.03   14.0   0.0         10    5.8   0.0    2.5  2  Sigma54_activat  Sigma-54 interaction domain
      0.031   14.2   1.4        3.2    7.6   0.0    2.9  2  NTPase_1         NTPase
       0.04   13.2   0.2        1.3    8.2   0.2    2.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.05   13.0   0.1         21    4.4   0.0    3.2  3  TniB             Bacterial TniB protein
      0.098   12.3   0.1        7.8    6.1   0.0    2.5  2  SRP54            SRP54-type protein, GTPase domain
       0.26   11.4   1.4         22    5.1   0.1    2.9  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   0.0   1.1e-42   5.1e-40       1     131 [.     227     366 ..     227     367 .. 0.93
   2 !   42.6   0.0   1.5e-13   7.5e-11       1     113 [.     508     617 ..     508     635 .. 0.88

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 1.1e-42
                                    EEEESSTTSSHHHHHHHHHHHHT.HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.......TSEEEEEETGGGHHH CS
                            AAA   1 vllyGppGtGKTllakavakelg.vefleisgsellskyvgesekkirelfkeakeka.......kpsilfiDEidalak 72 
                                    ++lyGppGtGKTl+a+ + + l+ ++   ++g+e+l+kyvg+se++ir+lfk+a+e+        + +i+++DEida+++
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNaRPPKIVNGPEILNKYVGQSEENIRNLFKDAEEEWkvkkedsNLHIIIFDEIDAICR 306
                                    79********************9455699*************************6666677788677************* PP

                                    HH.TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  73 sr.sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +r +++ ++++++vvnqLl+++dgv++ e+ ++vig+tnr d +d+allr gRf++++ei+
  gene416|gene416|rna416|rna416 307 RRgNSNGTGVGDQVVNQLLSKMDGVESIEN-ILVIGMTNRLDLIDEALLRpGRFEIHLEIS 366
                                    **9999*********************755.**************************9986 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1.5e-13
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsell.skyvgesekkirelfkeakekakpsilfiDEidalaksrsgses 79 
                                    +l+yG pG+GKT+la   a+++ ++f++i  ++ +      e+ + i+e f +a +++  si+++D+i+ l+    +   
  gene416|gene416|rna416|rna416 508 LLFYGSPGVGKTTLAVKAARSSMFPFIKIISPRDIiGLSEYEKVNYIKEKFMDAYKSE-ESIIILDDIEGLIDFV-NIGP 585
                                    69************************99888776647777788889999999998876.8***********9988.7799 PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGG CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpd 113
                                    +++++v+++L  +++++++k  k++v g+t +++
  gene416|gene416|rna416|rna416 586 RFSNSVLQALKIFIKEESRK--KMFVFGTTSSVE 617
                                    9****************995..799999998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   7.4e-08   3.6e-05       8      71 ..     227     310 ..     223     352 .. 0.70
   2 !    9.4   0.0    0.0025       1.2       5      26 ..     505     526 ..     500     536 .. 0.86
   3 ?    2.1   0.0      0.45   2.2e+02      82     131 ..     558     613 ..     540     618 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.4e-08
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelka................ 70 
                                    ++++G++GtGKT+ +r+l + l++++    ++pe++ ++  +s+++ ++l+++  +++++++++                
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNARPPKIVNGPEILnKYVGQSEENIRNLFKDAEEEWKVKKEDsnlhiiifdeidaicr 306
                                    689*******************76544444999999999999999***************99995555555555555555 PP

                         AAA_22  71 ...e 71 
                                       +
  gene416|gene416|rna416|rna416 307 rrgN 310
                                    5430 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0025
                         AAA_22   5 agilvvtGesGtGKTtllrrll 26 
                                     ++l+ +G +G+GKTtl+ + +
  gene416|gene416|rna416|rna416 505 TSSLLFYGSPGVGKTTLAVKAA 526
                                    67899************97765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.45
                         AAA_22  82 leqalraravielliiDEaqhlr.........seealeeLrsllnlsrkgvqliLvGtp 131
                                    + +a ++    +++i+D+++ l+         s+ +l+ L+++ + +++  +++++Gt+
  gene416|gene416|rna416|rna416 558 FMDAYKSE--ESIIILDDIEGLIdfvnigprfSNSVLQALKIFIK-EESRKKMFVFGTT 613
                                    33444444..56*********887887765444888888888877.7888888888887 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.0   2.7e-12   1.3e-09       1      36 [.     393     428 ..     393     454 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.7e-12
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik 36 
                                    +vdl+++A+++++y+GA++ a+++ A+  Al+r+ +
  gene416|gene416|rna416|rna416 393 SVDLNKVAKLSKNYTGAEITAVVKSAVSFALERKVH 428
                                    69*******************************754 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.4e-05     0.036      25      51 ..     225     251 ..     203     340 .. 0.83
   2 !   15.8   0.1   2.9e-05     0.014      12      45 ..     493     526 ..     490     532 .. 0.83
   3 ?    1.5   0.0      0.71   3.4e+02     119     165 ..     551     605 ..     537     610 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.4e-05
                         AAA_16  25 elvllsGesGvGKsslvrellralekd 51 
                                      ++l+G++G+GK+ ++r+l   l+++
  gene416|gene416|rna416|rna416 225 KGMILYGPPGTGKTLIARKLGSLLNAR 251
                                    7899**************998655554 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.9e-05
                         AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrell 45 
                                    Ll+ l++++  +++++l++G +GvGK++l+ +++
  gene416|gene416|rna416|rna416 493 LLQKLRKTNLYSTSSLLFYGSPGVGKTTLAVKAA 526
                                    6777888888899****************95555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.71
                         AAA_16 119 llellkrllallsrderplvlvlDdlq..........wadeaslqllaaLlrllesk 165
                                    +++   ++++ +++ e+  +++lDd++          ++  + lq+l+ + ++ ++k
  gene416|gene416|rna416|rna416 551 VNYIKEKFMDAYKS-EE-SIIILDDIEglidfvnigpRFSNSVLQALKIFIKEESRK 605
                                    55666677777777.44.5********988888888888889999888888877665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-06    0.0011       2      34 ..     227     260 ..     226     307 .. 0.70
   2 !   12.3   0.0   0.00026      0.12       2      75 ..     508     575 ..     507     579 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                                    EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltr 34 
                                    ++L GppGtgK+ +a++l ++l  r+  +v++++
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLnARPPKIVNGPE 260
                                    89********************666666666655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00026
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGG CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEve 75 
                                    +l  G pG+gK++la + a+       +  + + ++++d++g  e+  ++  + + ++++a + e +i++lD++e
  gene416|gene416|rna416|rna416 508 LLFYGSPGVGKTTLAVKAARS-----SMFPFIKIISPRDIIGLSEY--EKVNYIKEKFMDAYKsEESIIILDDIE 575
                                    7999***********998864.....5666677788999***9998..8888999999*999999999****997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00074      0.36       5      76 ..     227     304 ..     224     341 .. 0.71
   2 !   19.9   0.1   1.2e-06   0.00057       7     102 ..     510     614 ..     504     622 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00074
                         AAA_14   5 lvitGaRrvGKTtllkqlikell......vkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT ++++l + l       v+  +il   + + ++  ++ +++ +e+++ k ++++ +++++DEi  +
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNarppkiVNGPEILNKYVGQSEENIRNLFKDAEEEWKVKKEDSNLHIIIFDEIDAI 304
                                    6899**************966556566655555555444444444333445555555555544467889******876 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.2e-06
                         AAA_14   7 itGaRrvGKTtllkqlikellvkkesilyinldderd....kkladpekllelileklke...ekktylflDEiqev... 76 
                                      G   vGKTtl+ + +++++     + +i++ ++rd    +   ++ +  ++i+ek+++   +++++++lD i  +   
  gene416|gene416|rna416|rna416 510 FYGSPGVGKTTLAVKAARSSM-----FPFIKIISPRDiiglS---EY-EKVNYIKEKFMDaykSEESIIILDDIEGLidf 580
                                    567789***********9999.....8888888888843332...33.234555555322233699***********999 PP

                         AAA_14  77 ........pewekalkslvdegknldvivtGSns 102
                                            +++ +alk +++e+++ +++v G  s
  gene416|gene416|rna416|rna416 581 vnigprfsNSVLQALKIFIKEESRKKMFVFGTTS 614
                                    9999999888999999999977555555555444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   3.7e-08   1.8e-05       6     103 ..     227     328 ..     223     334 .. 0.71
   2 ?    5.1   0.0     0.047        23       3      78 ..     505     575 ..     503     590 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.7e-08
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---......----THHHHHHHHHTTT-HHHHTTS..EEEEETG CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle......eeevehlvsrligappgyvgaeegG..ivllDEi 77 
                                    ++l gp g+Gkt++a++l +ll++   ++  +++  e+l       ee++++l +  + + +  ++       i+ +DEi
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNA---RPPKIVNGPEILNkyvgqsEENIRNLFKDAEEEWKVKKEDS--NlhIIIFDEI 301
                                    5678******************95...88888888888887754444455555544444444444444..366******* PP

                                    GG----..---------HHHHHHHHHHH CS
                          AAA_2  78 dKihpk..essgadvSregVqrdLLqil 103
                                    d i+++  +s+g  v  + V++ LL  +
  gene416|gene416|rna416|rna416 302 DAICRRrgNSNGTGVGDQ-VVNQLLSKM 328
                                    ******977777777665.555555545 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.047
                                    ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGG CS
                          AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEid 78 
                                    ++s+l+ g+ gvGkt la + a+       k +   d   l e e+v    +  i ++ ++  + e+ i+ lD+i+
  gene416|gene416|rna416|rna416 505 TSSLLFYGSPGVGKTTLAVKAARSSMFPFIKIISPRDIIGLSEYEKV----N-YIKEKFMDAYKSEESIIILDDIE 575
                                    5799************9887777654422233333333333332222....1.22222233334455566666666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00038      0.18       2      48 ..     228     266 ..     227     301 .. 0.69
   2 !   16.7   0.0   1.5e-05    0.0071       2      59 ..     509     575 ..     508     582 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00038
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYt 48 
                                    +lyGp+g+GK+++a++L + l       + ++++   +  +++++Y 
  gene416|gene416|rna416|rna416 228 ILYGPPGTGKTLIARKLGSLLNA-----RPPKIV---NGPEILNKYV 266
                                    79**************7776663.....333443...2444444444 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1.5e-05
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl............klkkkdsvysrnpeddfwdgYt.gqevvvidDfg 59 
                                    ++yG++g+GK+tla + a++ +  +            +l + ++v  +  +++f+d Y+ ++ +++ dD+ 
  gene416|gene416|rna416|rna416 509 LFYGSPGVGKTTLAVKAARSSM--FpfikiisprdiiGLSEYEKV--NYIKEKFMDAYKsEESIIILDDIE 575
                                    79**************555555..155888899988855554555..3369********778888889975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.3e-05     0.016       2      69 ..     228     306 ..     227     339 .. 0.62
   2 !   12.2   0.0   0.00041       0.2       3      44 ..     510     549 ..     508     584 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.3e-05
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf...................gvnlrdvakenglllevdpealdeskrldedkldklld 62 
                                    +l G+pG+GKt +a+ L ++l+                     +n+r ++k+ + +         + k++d + +  ++d
  gene416|gene416|rna416|rna416 228 ILYGPPGTGKTLIARKLGSLLNArppkivngpeilnkyvgqsEENIRNLFKDAEEE--------WKVKKEDSNLHIIIFD 299
                                    799****************9966799777776666555333333333333332222........3344445555555555 PP

                         AAA_18  63 aleenss 69 
                                    +++++++
  gene416|gene416|rna416|rna416 300 EIDAICR 306
                                    5555444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00041
                         AAA_18   3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44 
                                      G pGvGKttla   +++    +  +++++ +++    + e
  gene416|gene416|rna416|rna416 510 FYGSPGVGKTTLAVKAARSS--MFPFIKIISPRDIIGLSEYE 549
                                    6799************9986..67777777766666666666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.7e-05     0.018       5      78 ..     227     305 ..     224     310 .. 0.66
   2 !   10.9   0.0   0.00059      0.28       4      22 ..     507     525 ..     504     579 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.7e-05
                         AAA_24   5 iliyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdieswedfldevvel...aaeladyktlviDtide 76 
                                    +++yGp+g+GKT +a++l        p +++  + l++  +   +   ++ ++ ++++e    ++e+++++++++D id 
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLgsllnARPPKIVNGPEILNKYVGQSEE---NIRNLFKDAEEEwkvKKEDSNLHIIIFDEIDA 303
                                    789***************777774444455555534333333333...34444444444467788888888888888887 PP

                         AAA_24  77 le 78 
                                    ++
  gene416|gene416|rna416|rna416 304 IC 305
                                    76 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00059
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                    ++l yG++g+GKTtla ++
  gene416|gene416|rna416|rna416 507 SLLFYGSPGVGKTTLAVKA 525
                                    5789************988 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   5.9e-06    0.0029      25      48 ..     227     250 ..     221     263 .. 0.90
   2 !    8.6   0.0    0.0023       1.1      24      41 ..     507     524 ..     490     550 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.9e-06
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpp 48 
                                    ++l+GppG+GKt++a++l sll +
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNA 250
                                    89******************9965 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                   Mg_chelatase  24 nlllvGppGsGKtmlakr 41 
                                    +ll++G+pG GKt la +
  gene416|gene416|rna416|rna416 507 SLLFYGSPGVGKTTLAVK 524
                                    79*************965 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0014      0.68      36      68 ..     227     260 ..     217     266 .. 0.77
   2 !   11.8   0.0    0.0003      0.15      34      55 ..     506     527 ..     492     542 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                         RuvB_N  36 vllyGpPGlGkttlakiiakelgvk.lkitsgPv 68 
                                    ++lyGpPG Gkt +a+ + + l+++  ki  gP 
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNARpPKIVNGPE 260
                                    79************99988888775246666665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0003
                         RuvB_N  34 dhvllyGpPGlGkttlakiiak 55 
                                      +l+yG+PG+Gkttla   a+
  gene416|gene416|rna416|rna416 506 SSLLFYGSPGVGKTTLAVKAAR 527
                                    5689************986665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00051      0.25      46      69 ..     223     246 ..     199     256 .. 0.84
   2 !   10.4   0.0   0.00081      0.39      20      72 ..     479     530 ..     470     580 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                      IstB_IS21  46 kkenivllGpsGvGKshlaialgv 69 
                                    + ++++l Gp+G+GK+ +a  lg 
  gene416|gene416|rna416|rna416 223 HVKGMILYGPPGTGKTLIARKLGS 246
                                    56789**************99985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00081
                      IstB_IS21  20 edidfraarsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveav 72 
                                    e+  f++  +  k+ +++L++++   +  ++++ G +GvGK+ la+  +++ +
  gene416|gene416|rna416|rna416 479 ETPIFTQGIEHGKNLLQKLRKTNLY-STSSLLFYGSPGVGKTTLAVKAARSSM 530
                                    5556777777788888999888755.567899*************97776655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00015     0.075       3      50 ..     228     278 ..     227     310 .. 0.79
   2 !    9.4   0.0    0.0024       1.1       3      21 ..     509     527 ..     508     558 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
                         AAA_33   3 llvGlpGsGKstlaerl...lkklgavllssdtlrrrlfgtdqqsktdytr 50 
                                    +l G+pG+GK+  a++l   l++++  +++ ++++++++g+ +++++++ +
  gene416|gene416|rna416|rna416 228 ILYGPPGTGKTLIARKLgslLNARPPKIVNGPEILNKYVGQSEENIRNLFK 278
                                    789*************877788888********999999976666665444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0024
                         AAA_33   3 llvGlpGsGKstlaerllk 21 
                                    l+ G pG+GK+tla + ++
  gene416|gene416|rna416|rna416 509 LFYGSPGVGKTTLAVKAAR 527
                                    799**********988776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.027        13      23      39 ..     227     243 ..     218     249 .. 0.88
   2 !   12.7   0.0   0.00011     0.053       7      43 ..     492     528 ..     488     532 .. 0.84
   3 ?    1.4   0.0       0.3   1.5e+02      87     122 ..     549     584 ..     541     631 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.027
                                    EEEEESTTSSHHHHHHH CS
                         NB-ARC  23 valvGmgGvGKttlakq 39 
                                    + l+G +G GKt +a++
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARK 243
                                    889***********997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                                    HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC   7 kviekLlekdelqslvvalvGmgGvGKttlakqilnk 43 
                                    ++ +kL + +   +  + ++G +GvGKttla ++ ++
  gene416|gene416|rna416|rna416 492 NLLQKLRKTNLYSTSSLLFYGSPGVGKTTLAVKAARS 528
                                    678899987777888999*************999887 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.3
                                    -STTSHHHHHHHHCCCTTEEEEEEEE-SHHHH.... CS
                         NB-ARC  87 eeveslkrklvrlLltkrfllvlDDVweeedwdkig 122
                                    e+v+ +k+k + + ++  ++++lDD+    d+ +ig
  gene416|gene416|rna416|rna416 549 EKVNYIKEKFMDAYKSEESIIILDDIEGLIDFVNIG 584
                                    44444899999999999********96665554444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0048       2.3      36      53 ..     227     244 ..     220     247 .. 0.85
   2 ?    2.8   0.0      0.16        77     139     172 ..     289     324 ..     268     329 .. 0.79
   3 !   10.8   0.1   0.00055      0.27      34      56 ..     506     528 ..     493     532 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                         AAA_25  36 allaGapgtGKttlaldl 53 
                                     +l+G+pgtGKt +a  l
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKL 244
                                    59**********998665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.16
                         AAA_25 139 evegvrlvviDplsralggdensnsd.v.galveal 172
                                    e  +++ +++D ++++++   nsn   v +++v++l
  gene416|gene416|rna416|rna416 289 EDSNLHIIIFDEIDAICRRRGNSNGTgVgDQVVNQL 324
                                    334599*************88888663589999998 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00055
                         AAA_25  34 elallaGapgtGKttlaldlala 56 
                                    +  l++G pg+GKttla+  a +
  gene416|gene416|rna416|rna416 506 SSLLFYGSPGVGKTTLAVKAARS 528
                                    56799*************99865 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0029       1.4      21      59 ..     219     265 ..     195     277 .. 0.70
   2 !   11.7   0.0   0.00041       0.2      12      61 ..     491     550 ..     483     602 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                                    E.......EEEEESTTSSHHHHHHHHHHHTT--...----TTTTSEEEE CS
                           TsaE  21 v.......ilLeGdLGaGKTtlvrglakalgve...evkSPTFtlveeY 59 
                                    +       ++L+G+ G+GKT ++r+l + l+ +    v+ P   ++++Y
  gene416|gene416|rna416|rna416 219 FgiphvkgMILYGPPGTGKTLIARKLGSLLNARppkIVNGP--EILNKY 265
                                    0344445599****************999988765446666..455665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00041
                                    HHHHHCH.......TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTS.EEEEEE CS
                           TsaE  12 kklakal.......gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtl.veeYel 61 
                                    k+l ++l       ++ +l++G  G+GKTtl+ + a++  +   ++ SP   + ++eYe+
  gene416|gene416|rna416|rna416 491 KNLLQKLrktnlysTSSLLFYGSPGVGKTTLAVKAARSSMFPfiKIISPRDIIgLSEYEK 550
                                    44444443222444455*******************999887889999975554566654 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.8e-05     0.048       2      72 ..     227     302 ..     226     312 .. 0.84
   2 ?    6.9   0.0     0.011       5.5       2      50 ..     508     551 ..     507     579 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.8e-05
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGt.....evfeekekefefkkGpvfanllladein 72 
                                    ++l g PG++ktl++++l++ l+++  +i   p++l   +  +     ++f+++e+e+++kk     ++++ dei+
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNARPPKIVNGPEILNKYVGQSeenirNLFKDAEEEWKVKKEDSNLHIIIFDEID 302
                                    578999******************************887644322223689999999****999999999999997 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeek 50 
                                    +l+ g PG++kt+l+ + a++    f +i     + P di+G + +e+ 
  gene416|gene416|rna416|rna416 508 LLFYGSPGVGKTTLAVKAARSSMFPFIKI-----ISPRDIIGLSEYEKV 551
                                    577899*********99999887777666.....568888888877765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00014     0.066      10      37 ..     215     242 ..     205     244 .. 0.87
   2 ?    5.6   0.0     0.018       8.6      12      38 ..     498     524 ..     464     531 .. 0.86
   3 ?   -1.3   0.0       2.3   1.1e+03     102     176 ..     549     624 ..     524     630 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         ATPase  10 eilkgGipegrvvlitGepGtGKtifal 37 
                                     i k Gip+ + + ++G pGtGKt++a 
  gene416|gene416|rna416|rna416 215 VIRKFGIPHVKGMILYGPPGTGKTLIAR 242
                                    44478********************986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.018
                         ATPase  12 lkgGipegrvvlitGepGtGKtifalq 38 
                                     k  +++ ++ l +G+pG GKt++a +
  gene416|gene416|rna416|rna416 498 RKTNLYSTSSLLFYGSPGVGKTTLAVK 524
                                    4567889999**************975 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.3
                         ATPase 102 edleelieelaeaikeikakrvviDsitgl..ayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygv 176
                                    e+++ ++e++++a k+ +++ +++D i+gl    +  +    + l+ l+ ++k+     ++v   +ss e a + g+
  gene416|gene416|rna416|rna416 549 EKVNYIKEKFMDAYKS-EESIIILDDIEGLidFVNIGPRFSNSVLQALKIFIKEESRKKMFVFGTTSSVEVARECGI 624
                                    5566666666666554.557888899999964444455556666666777778888888888877776666665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0043       2.1       3      26 ..     227     250 ..     225     257 .. 0.87
   2 ?   -1.2   0.0       3.5   1.7e+03      83     102 ..     294     318 ..     266     341 .. 0.64
   3 ?    6.3   0.0     0.017         8       3      19 ..     508     524 ..     506     528 .. 0.84
   4 ?    1.2   0.0      0.61     3e+02      85     153 ..     569     640 ..     546     651 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0043
                                    EEEEC-TTTCHHHHHHHHHHHHCT CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                    +il G++G GKT  ++kl +++ +
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNA 250
                                    799**************9888765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.5
                                    EEEEEE-STT-SS-TCH........ CS
                          NACHT  83 lLlilDglDelvtdlgq.....kek 102
                                      +i+D +D +++  g+      + 
  gene416|gene416|rna416|rna416 294 HIIIFDEIDAICRRRGNsngtgVGD 318
                                    3489999999988877753333333 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.017
                                    EEEEC-TTTCHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqk 19 
                                    ++  G +G+GKTtL+ k
  gene416|gene416|rna416|rna416 508 LLFYGSPGVGKTTLAVK 524
                                    5778**********976 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.61
                                    EEEE-STT-SS-TCH...........HHHHHCTTTTT--EEEEEEECCCHHH...HCTTSSCE..EEEE--TCC CS
                          NACHT  85 lilDglDelvtdlgq..kekqpvrtlLselirkkllpeasllltvrpralrd...leeqleeaivlevegfses 153
                                    +ilD+++ l +  +      ++v + L+  i++++ ++  ++ t+++  + +   + e++++a  +eve ++ +
  gene416|gene416|rna416|rna416 569 IILDDIEGLIDFVNIgpRFSNSVLQALKIFIKEESRKKMFVFGTTSSVEVARecgIYECFQSA--YEVEKIGFP 640
                                    78888887776433355667899999999******************9998889999999999..666655544 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0013      0.64      31      57 ..     222     248 ..     212     257 .. 0.82
   2 ?    6.6   0.0      0.01       4.9      27      52 ..     499     524 ..     482     536 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                          AAA_7  31 knkkpvllvGptGtGKtviikdllkkl 57 
                                     + k ++l+Gp GtGKt+i+++l + l
  gene416|gene416|rna416|rna416 222 PHVKGMILYGPPGTGKTLIARKLGSLL 248
                                    5678899************99976655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                          AAA_7  27 elllknkkpvllvGptGtGKtviikd 52 
                                    ++ l +  ++l++G+ G+GKt+++ +
  gene416|gene416|rna416|rna416 499 KTNLYSTSSLLFYGSPGVGKTTLAVK 524
                                    5667778899***********99876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       2.2   1.1e+03      48      94 ..       9      53 ..       6      89 .. 0.61
   2 ?    4.2   0.2      0.11        55       1      15 [.     230     244 ..     230     283 .. 0.89
   3 !   10.1   0.0    0.0017      0.84       1      24 [.     511     534 ..     511     566 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 2.2
                                   TSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHH CS
                         AAA_17 48 klpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpk 94
                                   k +++ek ++ k+ + k  e + ++ vlvdg++ +k   +f  g  +
  gene416|gene416|rna416|rna416  9 KIEQVEKGKINKIYIPKTSELDPSEFVLVDGKYAFKF--EFTNGCNA 53
                                   5567777788888888999988888899999998853..33333333 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                                    EE-TTSSHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqcekl 15 
                                    +G+PG GK+ +++kl
  gene416|gene416|rna416|rna416 230 YGPPGTGKTLIARKL 244
                                    7********999998 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0017
                                    EE-TTSSHHHHHHHHHHHHTEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthl 24 
                                    +G PG+GK+t++ k ++   f+++
  gene416|gene416|rna416|rna416 511 YGSPGVGKTTLAVKAARSSMFPFI 534
                                    799*************99988877 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0045       2.2      51     102 ..     225     275 ..     213     293 .. 0.80
   2 !    8.0   0.0     0.003       1.5      39      85 ..     494     538 ..     488     609 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0045
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltqa 102
                                    ++++l Gp+gtGkt +a  +   l++  p  +++g e+    v ++e  +++
  gene416|gene416|rna416|rna416 225 KGMILYGPPGTGKTLIARKLGSLLNA-RPPKIVNGPEILNKYVGQSEENIRN 275
                                    7899*************999988875.5668899999999888887755544 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  39 ivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsg 85 
                                    + +l k++  +  ++L+ G +g Gkt la+  +++  +  pf+++ +
  gene416|gene416|rna416|rna416 494 LQKLRKTNLYSTSSLLFYGSPGVGKTTLAVKAARS--SMFPFIKIIS 538
                                    55666777778899****************99986..5588876543 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0055       2.7      22      40 ..     227     245 ..     213     256 .. 0.85
   2 !    7.6   0.0    0.0049       2.4       5      44 ..     491     530 ..     488     597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0055
                                    EEEE--TTSSTTHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavala 40 
                                    ++  Gp GtGKt++a  l+
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLG 245
                                    6789**********98765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0049
                                    -SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHH CS
                           PhoH   5 ktkeQkeylealkkndivfaiGpaGtGKtylavalaveal 44 
                                    k+  Qk   ++l + + +   G+ G GKt lav +a + +
  gene416|gene416|rna416|rna416 491 KNLLQKLRKTNLYSTSSLLFYGSPGVGKTTLAVKAARSSM 530
                                    555666666777777778889************9996654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0018      0.88       3      37 ..     228     268 ..     227     297 .. 0.74
   2 ?    5.0   0.0     0.055        27       4      16 ..     510     522 ..     507     535 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                         AAA_28   3 vitGgestGKTtlleaLa....argypvv..pEaareilee 37 
                                    ++ G+++tGKT ++++L     ar  ++v  pE+  +++ +
  gene416|gene416|rna416|rna416 228 ILYGPPGTGKTLIARKLGsllnARPPKIVngPEILNKYVGQ 268
                                    689************99955544444455567777777744 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.055
                         AAA_28   4 itGgestGKTtll 16 
                                    + G ++ GKTtl+
  gene416|gene416|rna416|rna416 510 FYGSPGVGKTTLA 522
                                    89*********98 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1     0.006       2.9      12      31 ..     226     245 ..     221     257 .. 0.81
   2 ?    5.3   0.0     0.047        23      11      30 ..     506     525 ..     498     575 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.006
                         AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                     +++ ++pGtGKT + ++  
  gene416|gene416|rna416|rna416 226 GMILYGPPGTGKTLIARKLG 245
                                    5899*********9877655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.047
                         AAA_19  11 kvllvtaGpGtGKTrvlkhi 30 
                                    + ll  + pG GKT++ +++
  gene416|gene416|rna416|rna416 506 SSLLFYGSPGVGKTTLAVKA 525
                                    567889********987765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00044      0.21      16     115 ..     216     305 ..     202     352 .. 0.79
   2 ?    2.4   0.0      0.29   1.4e+02      14      46 ..     492     527 ..     482     621 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00044
                                    T......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B- CS
                         ResIII  16 leklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkk 95 
                                    + k+ + + k +++  + GtGKTl+a kl   l    ++     +v++ ++l++   + ++ + + +k+++++++ +k++
  gene416|gene416|rna416|rna416 216 IRKFGIPHVKGMILYGPPGTGKTLIARKLGSLLNARPPK-----IVNGPEILNKYVGQSEENIRNLFKDAEEEWKVKKED 290
                                    55555566778889999************9999997664.....9**********************99******99999 PP

                                    -.......-SE.EEEEHHHHH CS
                         ResIII  96 akekdstnkki.lvttiqsld 115
                                    +      n +i ++ +i+++ 
  gene416|gene416|rna416|rna416 291 S------NLHIiIFDEIDAIC 305
                                    9......44440444555554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.29
                                    HHT.........TTSEEEEEESTTSTHHHHHHHHHH CS
                         ResIII  14 nlleklks...krdkrglikmaTGtGKTlvaaklie 46 
                                    nll+kl +   +    +l+    G+GKT +a+k+++
  gene416|gene416|rna416|rna416 492 NLLQKLRKtnlYSTSSLLFYGSPGVGKTTLAVKAAR 527
                                    66666665554556688899999*******999876 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.69   3.3e+02       5      71 ..     231     301 ..     227     304 .. 0.56
   2 ?   -1.6   0.0       3.8   1.9e+03      47      77 ..     328     357 ..     318     366 .. 0.80
   3 !   11.8   0.0   0.00031      0.15       5      81 ..     512     580 ..     508     594 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.69
                Viral_helicase1   5 GvpGcGKStlirkllrts..liltvnrptaelltegkpklpnlsvrtvdsflmalvks...tkgkililDEy 71 
                                    G pG GK+ + rkl +    +   ++++  e+l++ + +++ +  + ++++++  + +    + +i+i+DE+
  gene416|gene416|rna416|rna416 231 GPPGTGKTLIARKLGSLLnaR-PPKIVNGPEILNKYVGQSEENIRNLFKDAEEEWKVKkedSNLHIIIFDEI 301
                                    789****99888876663431.22233335666666644444444444444443322222346788888886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.8
                Viral_helicase1  47 vrtvdsflmalvkstkgkililDEylllhaG 77 
                                      +v+s+++ lv ++++++ ++DE+ll + G
  gene416|gene416|rna416|rna416 328 MDGVESIENILVIGMTNRLDLIDEALLRP-G 357
                                    567888889899999999*******8876.5 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00031
                Viral_helicase1   5 GvpGcGKStlirkllrtsliltvnrptaelltegk..pklpnlsvrtvdsflmalvkstkgkililDEylllhaGyill 81 
                                    G pG GK+tl +k++r+     +  p +++++++     ++ ++v+++++  m + ks +  i+ilD++     G+i++
  gene416|gene416|rna416|rna416 512 GSPGVGKTTLAVKAARS-----SMFPFIKIISPRDiiGLSEYEKVNYIKEKFMDAYKS-EESIIILDDI----EGLIDF 580
                                    89***************.....444558888888888999999999999999999997.79******98....344555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0012       0.6       6      80 ..     219     310 ..     217     404 .. 0.77
   2 ?    3.5   0.1      0.19        93       8      28 ..     502     522 ..     498     529 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                                    EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...... 79 
                                    + + + + + + G+ G+GK+ +++ l  ll+    +i ++g ++ ++   +++++i+ l+++++   +++ +++      
  gene416|gene416|rna416|rna416 219 FGIPHVKGMILYGPPGTGKTLIARKLGSLLNARPPKI-VNGPEILNKYVGQSEENIRNLFKDAEEEWKVKKEDSnlhiii 297
                                    56666677889**************************.9*****999999999999999999555444432222566655 PP

                                    ............H CS
                                    ............x RF
                       ABC_tran  80 ............e 80 
                                                +
  gene416|gene416|rna416|rna416 298 fdeidaicrrrgN 310
                                    5555555555440 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.19
                                    EETTSEEEEEESTTSSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLl 28 
                                    l+  + + + G+ G GK+tL+
  gene416|gene416|rna416|rna416 502 LYSTSSLLFYGSPGVGKTTLA 522
                                    5566778899*********96 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0     0.003       1.5      20      42 ..     227     249 ..     214     296 .. 0.75
   2 ?    3.9   0.0     0.081        39      12      41 ..     501     529 ..     491     566 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.003
                         AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                     ++ GPPGtgKT    +l s l+
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLN 249
                                    5789********98888887775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.081
                         AAA_11  12 salseseitliqGPPGtgKTktivellsql 41 
                                    + +s+s+  l+ G PG gKT+  v+  ++ 
  gene416|gene416|rna416|rna416 501 NLYSTSS-LLFYGSPGVGKTTLAVKAARSS 529
                                    5566666.899**********999987765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0017      0.81      21      49 ..     227     255 ..     214     301 .. 0.89
   2 ?    2.3   0.0      0.25   1.2e+02      21      36 ..     508     523 ..     495     534 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0017
                         AAA_30  21 avltGpAGtGKttalkalreaweaaggrv 49 
                                    ++l Gp+GtGKt + ++l  +++a+  ++
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNARPPKI 255
                                    6899************9999998876554 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                         AAA_30  21 avltGpAGtGKttalk 36 
                                     +  G +G GKtt+  
  gene416|gene416|rna416|rna416 508 LLFYGSPGVGKTTLAV 523
                                    56789*******9754 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.021        10      25      44 ..     227     246 ..     214     303 .. 0.87
   2 ?    5.6   0.0     0.025        12      10      43 ..     492     526 ..     485     538 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                                    EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  25 vlitGesGtGKellaraihe 44 
                                    +++ G  GtGK+l+ar++ +
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGS 246
                                    6799***********98755 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                                    HHHHHHHHHCTSS.S-EEEECSTTSSHHHHHHHHH CS
                Sigma54_activat  10 elleqikkvaktd.lsvlitGesGtGKellaraih 43 
                                    +ll++++k+  ++ +s+l  G  G+GK++la +  
  gene416|gene416|rna416|rna416 492 NLLQKLRKTNLYStSSLLFYGSPGVGKTTLAVKAA 526
                                    5667777766665488999**********997655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.056        27       3      24 ..     228     249 ..     226     258 .. 0.85
   2 ?    7.6   0.0    0.0066       3.2       6      21 ..     512     527 ..     507     530 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.056
                                    EEE--TTSSHHHHHHHHHHHH. CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvlellk 24 
                                    ++ GppG+GKt + +k+ +ll+
  gene416|gene416|rna416|rna416 228 ILYGPPGTGKTLIARKLGSLLN 249
                                    788************9988886 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0066
                                    --TTSSHHHHHHHHHH CS
                       NTPase_1   6 GppGvGKtTlvkkvle 21 
                                    G+pGvGKtTl  k+++
  gene416|gene416|rna416|rna416 512 GSPGVGKTTLAVKAAR 527
                                    99*********99876 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0026       1.3       5      96 ..     228     300 ..     225     341 .. 0.65
   2 ?    1.6   0.0      0.27   1.3e+02       6      23 ..     510     527 ..     506     560 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0026
                        DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekk 84 
                                    +  G +GtGKt+++ +l   l      + +   +vN+p++l   + + ++e  +++++ f++ ++  +          kk
  gene416|gene416|rna416|rna416 228 ILYGPPGTGKTLIARKLGSLL------NARPPKIVNGPEILN--KYVGQSE--ENIRNLFKDAEEEWK---------VKK 288
                                    6789**********9998777......222333566666543..3333333..334444444443333.........334 PP

                        DUF2075  85 eepkedvvivDE 96 
                                    e+ +++++i+DE
  gene416|gene416|rna416|rna416 289 EDSNLHIIIFDE 300
                                    667777777777 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.27
                        DUF2075   6 VtGvaGtGKtvvllnlla 23 
                                      G +G GKt ++++++ 
  gene416|gene416|rna416|rna416 510 FYGSPGVGKTTLAVKAAR 527
                                    57***********99876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.057        28      35      55 ..     224     244 ..     213     258 .. 0.84
   2 ?   -0.6   0.0       1.5   7.4e+02     117     133 ..     290     306 ..     268     314 .. 0.81
   3 ?    4.4   0.0     0.044        21      25      56 ..     492     526 ..     474     532 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.057
                           TniB  35 mpnlllvGdsnnGKtmivekF 55 
                                    ++ ++l+G++ +GKt i++k 
  gene416|gene416|rna416|rna416 224 VKGMILYGPPGTGKTLIARKL 244
                                    67899************9985 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                           TniB 117 elkvrvLiiDEihnlla 133
                                    + +++++i+DEi+ + +
  gene416|gene416|rna416|rna416 290 DSNLHIIIFDEIDAICR 306
                                    57889*******99875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.044
                           TniB  25 eLleypkrkrm...pnlllvGdsnnGKtmivekFa 56 
                                    +Ll++ +++     ++ll++G + +GKt+++ k a
  gene416|gene416|rna416|rna416 492 NLLQKLRKTNLystSSLLFYGSPGVGKTTLAVKAA 526
                                    4444444443222289*************987765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0       0.1        50       4      28 ..     227     251 ..     224     256 .. 0.85
   2 ?    6.1   0.0     0.016       7.8       3      23 ..     507     527 ..     505     534 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.1
                                    EEEEESTTSSHHHHHHHHHHHHHHT CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkke 28 
                                    ++l G+ G+GKT  + KL  ll+++
  gene416|gene416|rna416|rna416 227 MILYGPPGTGKTLIARKLGSLLNAR 251
                                    6899**************9998876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.016
                                    EEEEEESTTSSHHHHHHHHHH CS
                          SRP54   3 villvGlqGaGKTttlaKLaa 23 
                                     +l+ G  G+GKTt + K a+
  gene416|gene416|rna416|rna416 507 SLLFYGSPGVGKTTLAVKAAR 527
                                    5799************99887 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.062        30       9      26 ..     234     251 ..     227     501 .. 0.93
   2 ?    5.1   0.1     0.045        22       8      21 ..     514     527 ..     508     529 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.062
                                    TSSHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxx RF
                           CbiA   9 GvGKTtlaanLaralarr 26 
                                    G+GKT +a +L+ +l+ r
  gene416|gene416|rna416|rna416 234 GTGKTLIARKLGSLLNAR 251
                                    9************99875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.045
                                    TTSSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxx RF
                           CbiA   8 GGvGKTtlaanLar 21 
                                     GvGKTtla++ ar
  gene416|gene416|rna416|rna416 514 PGVGKTTLAVKAAR 527
                                    59********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              37  [number of targets reported over threshold]
# CPU time: 0.82u 0.36s 00:00:01.18 Elapsed: 00:00:00.52
# Mc/sec: 3943.92
//
Query:       gene417|gene417|rna417|rna417  [L=624]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.3   0.9        8.4    6.2   0.1    2.3  2  Tipalpha  TNF-alpha-Inducing protein of Helicobacter
      0.066   12.8   5.1      0.075   12.7   0.3    2.2  2  Wzy_C     O-Antigen ligase


Domain annotation for each model (and alignments):
>> Tipalpha  TNF-alpha-Inducing protein of Helicobacter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0016        14     116     147 ..     256     286 ..     235     289 .. 0.82
   2 ?    6.2   0.1   0.00094       8.4      43      93 ..     485     535 ..     477     545 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0016
                                    -HHHHHHHHHHT.T--HHHHHHHHHHHHHHHH CS
                       Tipalpha 116 dkerlekrllkidaldadtvklilakvkeifk 147
                                     +e+l+k+ll++++++a+ v++il++  +ifk
  gene417|gene417|rna417|rna417 256 TDENLQKHLLNFRSIEAQ-VSKILEEFSKIFK 286
                                    4678***********987.8999********9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00094
                                    HHHHHHHHHHHHHHHHHHHHHSTT----S---HHHHHHTHHHHHHHEEEEE CS
                       Tipalpha  43 rerarirvaihiankikeiykssqnaekkkiddeifkqitqaiaasldkev 93 
                                    r  a+i v  ++ nki  +y    n +k+k+d+  f +  + +   l++  
  gene417|gene417|rna417|rna417 485 RVNAKISVFSNLFNKILFVYDDFDNLTKRKVDKSTFYNYIKMMSRLLENIA 535
                                    557999******************************998888777777665 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   8.4e-06     0.075      21     110 ..      43     129 ..      27     151 .. 0.68
   2 ?    1.9   0.6     0.017   1.5e+02      24      59 ..     374     437 ..     362     537 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-06
                          Wzy_C  21 gllvalivlliifykrripfllllgilvgvilliilfvlstnletlknitkafgkldkk..kgkdksgssRlyiwkralp 98 
                                     ll+++i + i+++  r p+ + + +l   i++++l++ s nl+++   +   +   k+  + + + +++ ++ w ++++
  gene417|gene417|rna417|rna417  43 FLLLLMICFGIVLIFFRSPRDRSSTLLY--IVGFLLIFCSYNLQKVIEANRTLN---KSvvQPNTTKNTWSWASWMSSWR 117
                                    4555555555555555554556666444..566666666777777765544444...43449999999999********* PP

                          Wzy_C  99 likdspilGtG.v 110
                                    + + +p +G+G  
  gene417|gene417|rna417|rna417 118 ARLTNP-FGIGhK 129
                                    ******.****41 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.017
                          Wzy_C  24 valivlliifykrri.........pfllllgilvgvilliilfv.....................l 59 
                                    v +i+ l++f+  +          + ++ +g++v+++l +i  +                      
  gene417|gene417|rna417|rna417 374 VEMILSLLLFLSVLAkleiaayilKPVVSVGLIVVTLLSVI--FllngqmldrtcksgaikgcsfT 437
                                    44444444444444444456554322222223333333333..23466666666666666666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4222.39
//
Query:       gene418|gene418|rna418|rna418  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-51  172.0   1.2    8.7e-51  171.7   1.2    1.0  1  Ras          Ras family
    9.1e-36  122.7   0.3    1.4e-35  122.1   0.3    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    5.5e-20   71.5   0.2    7.1e-20   71.2   0.2    1.0  1  Arf          ADP-ribosylation factor family
    4.7e-10   39.2   0.8    5.7e-10   38.9   0.8    1.1  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    1.5e-07   31.0   0.0    3.1e-07   30.0   0.0    1.3  1  SRPRB        Signal recognition particle receptor beta subuni
    1.9e-07   30.8   0.5    1.6e-06   27.8   0.5    2.0  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.1e-06   28.7   0.1    1.4e-06   28.3   0.1    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
    0.00065   19.5   1.4     0.0047   16.7   1.4    2.1  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0012   19.2   0.1     0.0033   17.8   0.1    1.7  1  AAA          ATPase family associated with various cellular a
     0.0026   18.0   0.0     0.0047   17.2   0.0    1.5  1  AAA_22       AAA domain
      0.006   16.5   0.7      0.054   13.4   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.022   14.0   0.0    1.4  1  Septin       Septin
      0.012   15.2   0.0      0.025   14.1   0.0    1.5  1  FeoB_N       Ferrous iron transport protein B
      0.014   15.4   0.4      0.034   14.2   0.2    1.7  1  AAA_14       AAA domain
      0.016   14.7   0.1      0.032   13.7   0.1    1.5  1  AAA_7        P-loop containing dynein motor region
      0.029   14.4   0.0       0.15   12.1   0.0    1.9  2  AAA_5        AAA domain (dynein-related subfamily)
      0.032   14.2   0.3      0.063   13.3   0.3    1.4  1  DUF2481      Protein of unknown function (DUF2481)
       0.06   13.1   0.8       0.12   12.1   0.8    1.8  1  AAA_24       AAA domain
       0.13   12.8   0.5       0.25   11.8   0.5    1.7  1  ABC_tran     ABC transporter
       0.14   12.5   0.0       0.24   11.8   0.0    1.4  1  HA           Helicase associated domain
       0.15   12.2   0.0       0.17   12.1   0.0    1.4  1  AAA_33       AAA domain


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.7   1.2     1e-53   8.7e-51       1     160 [.      10     172 ..      10     174 .. 0.97

  Alignments for each domain:
  == domain 1  score: 171.7 bits;  conditional E-value: 1e-53
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K++l+G+s+vGKt+l+ r+++++++ ++ sTigvdf++k++ev+g++vkl+iwDTAGqe+f+++ ++yyr+a+gi++v+d
  gene418|gene418|rna418|rna418  10 KMILIGNSGVGKTCLMKRYTDETYSFTQSSTIGVDFKIKSLEVEGEKVKLQIWDTAGQERFRAIISNYYRGAHGIIMVFD 89 
                                    89****************************************************************************** PP

                                    TTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT...SEEEEEBTTTTCTHHHHHHHHH CS
                            Ras  81 itsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelg...lkfletSAktnenveeafeell 157
                                    + s+esf+n+ +w+ e+++ ++env+i+++GnKvD +ek +v++ee e++ +e+g     f+ tSAk+n  v++ fe l+
  gene418|gene418|rna418|rna418  90 MGSKESFDNLGDWLAEVRKNTNENVEIIILGNKVDDKEKIVVTEEEIERFLSENGiekSSFYMTSAKDNICVNDSFEYLT 169
                                    ***************************************************999833347*******************9 PP

                                    HHH CS
                            Ras 158 rei 160
                                    r++
  gene418|gene418|rna418|rna418 170 RKL 172
                                    987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.1   0.3   1.7e-38   1.4e-35       1     119 [.      10     124 ..      10     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.1 bits;  conditional E-value: 1.7e-38
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K++l+G+sgvGKt+l+kr++++++s +++stigvdf+ k++ +++g       +kvkl+iWDtaGqerfr++ + y+r+a
  gene418|gene418|rna418|rna418  10 KMILIGNSGVGKTCLMKRYTDETYSFTQSSTIGVDFKIKSL-EVEG-------EKVKLQIWDTAGQERFRAIISNYYRGA 81 
                                    89**********************************99886.4554.......5799*********************** PP

                                    CEEEEEEE...GHHHHCHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                            Roc  81 alailvyd...srssenlkeWlkelkkvagks.pvilvgnkiD 119
                                    + +i+v+d   ++s++nl +Wl e++k+++++  +i++gnk+D
  gene418|gene418|rna418|rna418  82 HGIIMVFDmgsKESFDNLGDWLAEVRKNTNENvEIIILGNKVD 124
                                    ********98666889**********9987653899******9 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.2   8.3e-23   7.1e-20      15     172 ..       9     169 ..       3     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 8.3e-23
                                    EEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSS..EEEEEEEE..TTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEE CS
                            Arf  15 lrilllGLDnaGKtTilkklkleelvt.tvPTig..fnveelei..knlkftvwDvGGqeklRplWknYfektdavifvv 89 
                                    ++++l+G  + GKt ++k++++e  +  ++ Tig  f++++le+  +++k+++wD  Gqe+ R + +nY++  +++i v 
  gene418|gene418|rna418|rna418   9 FKMILIGNSGVGKTCLMKRYTDETYSFtQSSTIGvdFKIKSLEVegEKVKLQIWDTAGQERFRAIISNYYRGAHGIIMVF 88 
                                    799******************999875156787644788887775589******************************** PP

                                    ETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS..-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHH CS
                            Arf  90 DsadreRleeakeeLkalleeeelkevallvlaNKqDlpeal..seeelrellgleelkgkrkleiqkcsavkgeglkeg 167
                                    D   +e +++  + L+++ +++++++v +++l+NK D +e +  +eee+++ l+ + ++   k +  ++sa  +  ++++
  gene418|gene418|rna418|rna418  89 DMGSKESFDNLGDWLAEV-RKNTNENVEIIILGNKVDDKEKIvvTEEEIERFLSENGIE---KSSFYMTSAKDNICVNDS 164
                                    ***************996.78899*************9997523789999999999999...556667777777777777 PP

                                    HHHHH CS
                            Arf 168 lewls 172
                                    +e l+
  gene418|gene418|rna418|rna418 165 FEYLT 169
                                    77776 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.8   6.6e-13   5.7e-10       1     176 [.      10     173 ..      10     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 6.6e-13
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsi.iFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k++L+G+sg GKt++ +    + y+ ++  ++g+  +++  ev   ++++l++wD  Gqe+f +       ++ +r    
  gene418|gene418|rna418|rna418  10 KMILIGNSGVGKTCLMKRyTDETYSFTQSSTIGVDFKIKSLEV-EGEKVKLQIWDTAGQERFRAII-----SNYYRGAHG 83 
                                    799***********7666155679999*************999.5899*************99886.....78899999* PP

                      Gtr1_RagA  80 liyVfDvesreleedletlkeilealrq.yspeakvfvlihKmDliqedereeifeerkeeireeieklekeeiqffaTS 158
                                    +i VfD+ s   +e++++l + l ++r+ +++++++ +l +K+D       e+ +   +eei++ +++ + e+ +f++TS
  gene418|gene418|rna418|rna418  84 IIMVFDMGS---KESFDNLGDWLAEVRKnTNENVEIIILGNKVDDK-----EK-IVVTEEEIERFLSENGIEKSSFYMTS 154
                                    ********5...55666677777776651678999********964.....23.334567888888888999999****9 PP

                      Gtr1_RagA 159 iwde.slykAfssivqkli 176
                                      d+  + + f    +kli
  gene418|gene418|rna418|rna418 155 AKDNiCVNDSFEYLTRKLI 173
                                    9887335556666666666 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   3.6e-10   3.1e-07       6     123 ..      11     124 ..       7     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.6e-10
                                    EEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG.....GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEE CS
                          SRPRB   6 vllvGlsdsGKTslftrLttdsvkktvtSq.essaalkv..ksekgskltliDfPGheklrqklleklkaksslkglvfv 82 
                                    ++l+G s  GKT l++r t +++  t+ S     +  k    + ++ kl++ D  G+e++r  ++++    + ++g++ v
  gene418|gene418|rna418|rna418  11 MILIGNSGVGKTCLMKRYTDETYSFTQSSTiGVDFKIKSleVEGEKVKLQIWDTAGQERFRAIISNY---YRGAHGIIMV 87 
                                    89***************************97677777773334455667789*********998888...7899****** PP

                                    EETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TT CS
                          SRPRB  83 vDStidpkevkevAEllyeilliteklkdavdiliACnKqe 123
                                     D    +    +  ++l e+  +t    ++v+i+i  nK +
  gene418|gene418|rna418|rna418  88 FDMGS-KESFDNLGDWLAEVRKNTN---ENVEIIILGNKVD 124
                                    **764.4567888999999988777...8999999999976 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.5   1.9e-09   1.6e-06      51     191 ..      40     171 ..       6     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.9e-09
                                    HHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB....STHHHHHHHHHHHHTTTEEE CS
                       GTP_EFTU  51 ergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG....vepqteevlrlalkegvpii 126
                                      g+  k++  ++e  ++k ++++ Dt G + F   +++ +r ++g ++v+d  +             +r   +e+v+ii
  gene418|gene418|rna418|rna418  40 TIGVDFKIKSLEVE--GEKVKLQIWDTAGQERFRAIISNYYRGAHGIIMVFDMGSKesfdNLGDWLAEVRKNTNENVEII 117
                                    44555667777777..************************************9855444444555566778889999*** PP

                                    EEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHH CS
                       GTP_EFTU 127 vfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvel 191
                                    ++ NK+D   +++  + ee++ ++      l++ g ++    +++++Sa+++ +v++ +e+l+++
  gene418|gene418|rna418|rna418 118 ILGNKVDDK-EKIVVTEEEIE-RF------LSENGIEK---SSFYMTSAKDNICVNDSFEYLTRK 171
                                    *******85.56777778888.56......56666555...48************9998888765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   1.7e-09   1.4e-06       2     110 ..      11     118 ..      10     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.7e-09
                                    EEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adl 78 
                                    ++++G++ vGK+ L+++ t+e      s++ g+  +i+  +v+ ++ +++++Dt+G  e  + +  +  ++    + a+ 
  gene418|gene418|rna418|rna418  11 MILIGNSGVGKTCLMKRYTDEtySFTQSSTIGVDFKIKSLEVEGEKVKLQIWDTAG-QE--RFR-AIISNYY---RgAHG 83 
                                    689*****************9544466778888888888888866799********.44..222.3333333...3399* PP

                                    EEEEEETT.TTCSHHHHHHHHHHHHH..TTSEEEE CS
                       MMR_HSR1  79 illvvdas.eeklkpldeeleellee..akkplil 110
                                    i++v+d+  +e++++l   l+e++++  ++ ++i+
  gene418|gene418|rna418|rna418  84 IIMVFDMGsKESFDNLGDWLAEVRKNtnENVEIII 118
                                    ******88544455554445555443333333444 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.4   5.6e-06    0.0047       3      53 ..      10      62 ..       8     170 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.6e-06
                      PduV-EutP  3 killiGkvgsGKttLtqalkgeelkYkk..tqaiefsdeviDtPGeylenrkl 53
                                   k++liG++g+GKt L+++ ++e+ ++++  t  ++f+ + ++  Ge ++ + +
  gene418|gene418|rna418|rna418 10 KMILIGNSGVGKTCLMKRYTDETYSFTQssTIGVDFKIKSLEVEGEKVKLQIW 62
                                   789******************99877651144567777778888887765544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.9e-06    0.0033       1      66 [.      11      89 ..      11     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.9e-06
                                   EEEESSTTSSHHHHHHHHHHHH.............THEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                            AAA  1 vllyGppGtGKTllakavakel.............gvefleisgsell.skyvgesekkirelfkeakekakpsilfiDE 66
                                   ++l+G+ G+GKT l+k    e+             +++ le++g ++  + +  ++++++r+++++  + a + i+++ +
  gene418|gene418|rna418|rna418 11 MILIGNSGVGKTCLMKRYTDETysftqsstigvdfKIKSLEVEGEKVKlQIWDTAGQERFRAIISNYYRGA-HGIIMVFD 89
                                   79*******************64444444444444577888888888866699999**********99998.86666544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.5e-06    0.0047       8      29 ..      11      32 ..      10      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.5e-06
                         AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                   ++++G sG+GKT l++r++++ 
  gene418|gene418|rna418|rna418 11 MILIGNSGVGKTCLMKRYTDET 32
                                   589****************985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   6.4e-05     0.054     102     123 ..      11      32 ..       4      83 .. 0.86
   2 ?    1.6   0.1      0.26   2.2e+02      44      87 ..     111     158 ..      84     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-05
                                    EEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                    ++l+G+SGvGK+ L+++ + e+
  gene418|gene418|rna418|rna418  11 MILIGNSGVGKTCLMKRYTDET 32 
                                    689************9998874 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.26
                                    HTT-EEEEEEE-GGG--HHH....HHHHHHHHHHHTTSEEEE--TTTH CS
                    RsgA_GTPase  44 ekgiepvivlnKiDlleeee....eleelkeelealgyevllvsaktk 87 
                                    ++++e++i+ nK+D  e+      e+e++ +e      +++++sak++
  gene418|gene418|rna418|rna418 111 NENVEIIILGNKVDDKEKIVvteeEIERFLSENGIEKSSFYMTSAKDN 158
                                    567888888888886555443111233333333333334455555555 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.022       5      71 ..       9      66 ..       6      77 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                   EEEEEEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE--- CS
                         Septin  5 ftlmvvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpg 71
                                   f ++++G+sg+Gkt l++    ++  +       +++++  v++k k+ ++e  g k++l++ Dt g
  gene418|gene418|rna418|rna418  9 FKMILIGNSGVGKTCLMKRYTDETY-SF------TQSSTIGVDFKIKSLEVE--GEKVKLQIWDTAG 66
                                   899*************987544332.22......223334555555555555..5577788889877 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.9e-05     0.025       2      56 ..      10      66 ..       9      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEE..EEEE--- CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkev..eivDlPG 56
                                   +++l+Gn  vGkt l+ + t+ + +    + + v+ k  +l+++g++v  +i D  G
  gene418|gene418|rna418|rna418 10 KMILIGNSGVGKTCLMKRYTDETYSFTQSSTIGVDFKIKSLEVEGEKVklQIWDTAG 66
                                   689************************999999999998888877655116677666 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2     4e-05     0.034       6     101 ..      12     122 ..      10     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                         AAA_14   6 vitGaRrvGKTtllkqlikell.vkkesilyinldderd........kkladpe........kllelileklkeekktyl 68 
                                    ++ G   vGKT l+k++ +e +  +++s++ ++++ +++              +        ++  +i + +++ +  ++
  gene418|gene418|rna418|rna418  12 ILIGNSGVGKTCLMKRYTDETYsFTQSSTIGVDFKIKSLevegekvkL-----QiwdtagqeRFRAIISNYYRGAHGIIM 86 
                                    7889999****************9999*******99988555543320.....122232332333333333444677888 PP

                         AAA_14  69 flDEiqe..vpewekalkslvdeg.knldvivtGSn 101
                                    ++D  ++   +++ ++l ++ +++ +n+++i+ G +
  gene418|gene418|rna418|rna418  87 VFDMGSKesFDNLGDWLAEVRKNTnENVEIIILGNK 122
                                    888554311688888888888877678888888865 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   3.8e-05     0.032      34      63 ..       9      37 ..       1      53 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldkekyl 63
                                    +++l+G++G+GKt+++k+++++   + ++
  gene418|gene418|rna418|rna418  9 FKMILIGNSGVGKTCLMKRYTDETY-SFTQ 37
                                   6799***************887765.3333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.15       2      21 ..      11      30 ..      10      43 .. 0.84
   2 ?   -0.4   0.0       1.2     1e+03     104     127 ..     105     128 ..      90     139 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                   EEEE--SSSSHHHHHHHGGG CS
                          AAA_5  2 vlLvGppGtgKselaerlaa 21
                                   ++L+G++G+gK+ l++r+  
  gene418|gene418|rna418|rna418 11 MILIGNSGVGKTCLMKRYTD 30
                                   79**************9976 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                    E---......-EEEEEESS--..-T CS
                          AAA_5 104 kaknddllerfrviatanpld.rsl 127
                                     +++++  e++ +i ++n++d +++
  gene418|gene418|rna418|rna418 105 EVRKNT-NENVEIIILGNKVDdKEK 128
                                    333332.344999999999995444 PP

>> DUF2481  Protein of unknown function (DUF2481)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   7.3e-05     0.063       5      69 ..     106     169 ..     103     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.3e-05
                        DUF2481   5 itkskarqreiisyianndvel.dellklqkelnqlmnentiekqktywtktfdrivkkkkwaeit 69 
                                    + k    + eii  i  n v+  ++++  + e+++++ en iek   y t + d i  +  +  +t
  gene418|gene418|rna418|rna418 106 VRKNTNENVEII--ILGNKVDDkEKIVVTEEEIERFLSENGIEKSSFYMTSAKDNICVNDSFEYLT 169
                                    556666666666..556666650556677899***********************98877765555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00014      0.12       4      25 ..      10      31 ..       9     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                         AAA_24  4 kiliyGpsgiGKTtlakelgpk 25
                                   k++++G sg+GKT l+k+++++
  gene418|gene418|rna418|rna418 10 KMILIGNSGVGKTCLMKRYTDE 31
                                   799***************9332 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5    0.0003      0.25      13      62 ..      10      58 ..       2     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                                   EEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGGB-HHHCCHCEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkp..teGeilldgkdlkeqeleslrkeig 62
                                   k+ ++G++G GK+ L+k  + ++    ++ +i   g d+k ++le+  ++++
  gene418|gene418|rna418|rna418 10 KMILIGNSGVGKTCLMKRYTDETYSftQSSTI---GVDFKIKSLEVEGEKVK 58
                                   5789*************999988877677777...34444444444444444 PP

>> HA  Helicase associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.24      15      57 ..      78     138 ..      55     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                             HA  15 ykaehGhlnvP..ekteenpsLgkWvakqRqqykkgk................lteeriel 57 
                                    y+ +hG   v+    +e+  +Lg W+a  R++ +++                  tee ie+
  gene418|gene418|rna418|rna418  78 YRGAHGIIMVFdmGSKESFDNLGDWLAEVRKNTNENVeiiilgnkvddkekivVTEEEIER 138
                                    788899999999866788889************5554899888888888888778888876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.17       3      45 ..      12      58 ..      11     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                         AAA_33  3 llvGlpGsGKstlaerllkklg....avllssdtlrrrlfgtdqqsk 45
                                   +l+G +G+GK+ l +r+  ++       ++  d  ++ l++++++ k
  gene418|gene418|rna418|rna418 12 ILIGNSGVGKTCLMKRYTDETYsftqSSTIGVDFKIKSLEVEGEKVK 58
                                   89**************9966555555555555555555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1100.34
//
Query:       gene419|gene419|rna419|rna419  [L=464]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-25   88.8   0.0    7.1e-25   87.9   0.0    1.5  1  PolyA_pol        Poly A polymerase head domain
      2e-05   24.2   0.0      5e-05   23.0   0.0    1.7  1  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym


Domain annotation for each model (and alignments):
>> PolyA_pol  Poly A polymerase head domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   7.9e-29   7.1e-25       2     126 .]      31     165 ..      30     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 7.9e-29
                                    EEETHHHHHHHTT---CEEEEEEC.S-HHHHHHHHHHHHT-EEEEETTTTCCCCEECCEE....EEECCEECEEEEEE-- CS
                      PolyA_pol   2 ylvGGaVRDlllgkepkDvDlatd.aapeelakllrkkvkeallsgeefqtiavlekkql....levatfRlekdesdar 76 
                                    +++GG+VRD+++g+++ D+D+a++  ++ ++a  l k++ +     ++   ++v++++++    le+a +R++  + d++
  gene419|gene419|rna419|rna419  31 RVAGGWVRDKIMGNPSFDMDIALEnISGYKFAAGLVKSATG-----QKLTEVHVIKDNPDkskhLETAVVRINGFCVDFV 105
                                    689*******************9846677777777766666.....677777777766444557**************** PP

                                    -SSHHH............HHHHHHCTSSBGGGS-EEECTTTCEE-TTS.HHHHHHTTEE- CS
                      PolyA_pol  77 npesekste.........sleeDlkrRDftiNalaynlnkgkvlDlfg.GikdLkskvir 126
                                    n ++e+++e         + +eD+ rRD+tiN+l+ynl + +++D++g Gi+d+k k++r
  gene419|gene419|rna419|rna419 106 NLRNETYSEtripninpgTPQEDAFRRDLTINSLFYNLFTRRIEDYTGrGIDDIKGKILR 165
                                    ********9**********************************************99986 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   5.6e-09     5e-05       1      58 [.     192     253 ..     192     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.6e-09
                PolyA_pol_RNAbd   1 gFtIepeTaaairklap...lLkkispeRifeEllKlLlsghpeaglelLretgLlkylf.P 58 
                                    gF+I++++ +a+ +      l kk+s eRi  E+ K+L++++++ gl + ++ g  +++f P
  gene419|gene419|rna419|rna419 192 GFKIDEKIDEALLDERIktaLGKKVSNERIHIEIFKILHYPRGQYGLLEIIRRGYVNPIFkP 253
                                    78999999998877655455889*******************************99999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2992.69
//
Query:       gene42|gene42|rna42|rna42  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-71  241.4   0.1    1.3e-71  241.0   0.1    1.2  1  Pkinase         Protein kinase domain
    5.5e-43  147.1   0.0    7.5e-43  146.7   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
      9e-10   38.6   0.1    1.5e-06   28.2   0.0    2.7  2  POLO_box        POLO box duplicated region
    5.2e-09   35.8   0.0    7.8e-07   28.7   0.0    2.3  2  Kinase-like     Kinase-like
    0.00048   19.2   0.3    0.00075   18.5   0.3    1.3  1  Haspin_kinase   Haspin like kinase domain
     0.0037   16.1   0.0     0.0061   15.4   0.0    1.3  1  Pkinase_fungal  Fungal protein kinase
     0.0083   16.1   0.1       0.24   11.3   0.1    2.7  3  APH             Phosphotransferase enzyme family
  ------ inclusion threshold ------
      0.027   14.1   1.7       0.97    9.0   0.4    2.3  2  RIO1            RIO1 family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.0   0.1   5.9e-75   1.3e-71       2     264 .]      25     279 ..      24     279 .. 0.94

  Alignments for each domain:
  == domain 1  score: 241.0 bits;  conditional E-value: 5.9e-75
                                EEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEB CS
                    Pkinase   2 ekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvleyvegge 84 
                                  ++ lG+G+++++y a   e+g+++A+K+++ +++k++k  +k+ +Ei+i+ kl+ pniv++y++f++++++++vle++e g 
  gene42|gene42|rna42|rna42  25 ILKKLLGRGAYAQCYLAE-IENGEQYAMKVVRLKDIKSRKVhEKLESEISIHSKLDNPNIVKMYRSFRNEEYVFMVLELCERGA 107
                                56899***********98.9*****************998889***************************************** PP

                                HHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBCTTTSCGGGS-HH CS
                    Pkinase  85 ladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgelKitDFGlakelessskltsfvgtseYlAPE 167
                                l+ ll+r+g+l+e+++ +++kq++egl ylH s +++HrDlK  N+++d+k ++Ki+DFGl++ ++ ++k+ +++gt++Y+APE
  gene42|gene42|rna42|rna42 108 LDALLKRNGKLKERHVARFVKQTVEGLMYLHdSVNVVHRDLKLGNLFLDSKFNVKIGDFGLSAVIKDGEKKITMCGTPNYIAPE 191
                                *******************************8889************************************************* PP

                                HH..TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHHHHHHHHT-SSG CS
                    Pkinase 168 vl..keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeakdllkkllkkdp 249
                                vl  k++++s ++D+WslGvi+y+ll g ppf++        k+++++   +k+++ ++  +pe+ ++s+ea+dl++++l+ +p
  gene42|gene42|rna42|rna42 192 VLfgKASGHSFEADIWSLGVIIYTLLVGVPPFQK--------KNVEDI---YKMIKLNNYIFPENCDLSSEAIDLITQILNTNP 264
                                ***999***************************2........345553...33444457899********************** PP

                                CCSTTHHHHHTSGGG CS
                    Pkinase 250 kkRltaeellqhpyl 264
                                 +R+t e++l h++l
  gene42|gene42|rna42|rna42 265 LERPTLEHILGHKFL 279
                                ************996 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   0.0   3.3e-46   7.5e-43       3     256 ..      26     274 ..      24     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 3.3e-46
                                EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE--TTE CS
                Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivteyvkgG 86 
                                l+k lG+Ga+++ + ++++ + e+  +k  v  lk+ ++++ +e+l +e++i +kl++pnivk++    +ee +++v+e+++ G
  gene42|gene42|rna42|rna42  26 LKKLLGRGAYAQCYLAEIE-NGEQYAMK--VVRLKDIKSRKVHEKLESEISIHSKLDNPNIVKMYRSFRNEEYVFMVLELCERG 106
                                6789***************.33333333..33455666777789**************************************** PP

                                BHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHH.TTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEEEETTSSTSGG CS
                Pkinase_Tyr  87 dLlkfLrkkekekltlkdllsfalqvAkGmeyLes.kklvHrdlaarNvLlsenkvvkisDfGLardiekddeyvkkeeaklpv 169
                                 L+  L+++   kl+ +++ +f+ q  +G+ yL++  ++vHrdl   N +l+++  vki+DfGL+  i  +d  +kk +     
  gene42|gene42|rna42|rna42 107 ALDALLKRN--GKLKERHVARFVKQTVEGLMYLHDsVNVVHRDLKLGNLFLDSKFNVKIGDFGLSAVI--KD-GEKKITMCGTP 185
                                ********9..9*********************96269******************************..33.33344445566 PP

                                GGS-HHHHHHSE..EEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHH.HTTEES-BBTTSBHHHHHHHHHHT-SSGGGS- CS
                Pkinase_Tyr 170 kWmapEslkekk..ftsksDvWsfGvllwEiftlgespypglkneevlekl.kegkrlekpekcpeelyelmkkcweedpeeRp 250
                                +++apE+l+ k    + ++D+Ws Gv+++ ++  g  p+++ + e++++++  +++  +++ + ++e  +l+++ ++++p eRp
  gene42|gene42|rna42|rna42 186 NYIAPEVLFGKAsgHSFEADIWSLGVIIYTLLV-GVPPFQKKNVEDIYKMIkLNNYIFPENCDLSSEAIDLITQILNTNPLERP 268
                                9*******998877999**************99.*****************6678889999999******************** PP

                                -HHHHH CS
                Pkinase_Tyr 251 tfselv 256
                                t+++++
  gene42|gene42|rna42|rna42 269 TLEHIL 274
                                **9986 PP

>> POLO_box  POLO box duplicated region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   6.9e-10   1.5e-06       5      46 ..     319     363 ..     315     380 .. 0.83
   2 !    7.5   0.0    0.0021       4.7       4      37 ..     412     445 ..     410     460 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 6.9e-10
                                EEEEEETTS-EEEEETTTEEEEEETTTTEEEEE-T...T--EEEE CS
                   POLO_box   5 gigyqLsdgtvgVnFnDhtkiilspdgkavtyidr...qgersty 46 
                                gigy L +g  g++F Dh  ++l p++k+v y ++    g+r+ y
  gene42|gene42|rna42|rna42 319 GIGYVLKSGVYGIYFSDHRNLMLKPNKKSVIYLSSameSGKRVFY 363
                                9********************************996665555544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0021
                                SEEEEEETTS-EEEEETTTEEEEEETTTTEEEEE CS
                   POLO_box   4 ygigyqLsdgtvgVnFnDhtkiilspdgkavtyi 37 
                                 g+++ + d t+ + F D+ +++ls  g++v  +
  gene42|gene42|rna42|rna42 412 CGFLFVMADSTIVFDFVDGWRVVLSRCGERVSCY 445
                                69***********************999999654 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0065        15      12      63 ..      22      72 ..      13      90 .. 0.81
   2 !   28.7   0.0   3.5e-10   7.8e-07     143     259 ..     122     232 ..     107     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0065
                Kinase-like 12 rtlvrgellkkgdrsvvfevkdqetgeplavkvfllpseaskkdlerlkeqe 63
                                 ++ ++ll++g    +++++ ++ ge+ a+kv  l++  s+k  e+l+ + 
  gene42|gene42|rna42|rna42 22 TRYILKKLLGRGAYAQCYLAEIEN-GEQYAMKVVRLKDIKSRKVHEKLESEI 72
                               567999*************98777.**********************98764 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.5e-10
                Kinase-like 143 tiarlllTlqlirlaanLqa.kglvhgkftvdnllldekgglmlggf..taLvragtkvvl.sevekgfaPpEllgsrggytrk 222
                                ++ar +   q +    +L++   +vh +++  nl+ld k+ +++g+f  +a +++g+k      +++  aP  l+g++ g    
  gene42|gene42|rna42|rna42 122 HVARFVK--QTVEGLMYLHDsVNVVHRDLKLGNLFLDSKFNVKIGDFglSAVIKDGEKKITmCGTPNYIAPEVLFGKASG---- 199
                                5555444..55666667775258**********************9844699****998854677788888888898777.... PP

                Kinase-like 223 nktkmthkldaWqlGlviyriwclklPltlateeake 259
                                     +++ d W lG+ iy +   + P++++  e + 
  gene42|gene42|rna42|rna42 200 ----HSFEADIWSLGVIIYTLLVGVPPFQKKNVEDIY 232
                                ....79***************9999999987665544 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   3.4e-07   0.00075     143     257 ..      52     172 ..       8     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.4e-07
              Haspin_kinase 143 kelslkelkslklvkgtypglllllqdkvlkek.....pdfyseqqlflvlllkdkGt..dLeev..klkswkqalsifwqivk 217
                                k+++lk+ ks k+ +    +  + +++k+ + +       f++e+ +f+vl+l ++G    L +   kl + +++ +   q+v+
  gene42|gene42|rna42|rna42  52 KVVRLKDIKSRKVHEKL--ESEISIHSKLDNPNivkmyRSFRNEEYVFMVLELCERGAldALLKRngKL-KERHVARFVKQTVE 132
                                44455555554444444..333344444444445555568899999***********632454442333.45778899999*** PP

              Haspin_kinase 218 iLyvaEtkfeFEHRdLhldniLvdknlnvtlidlklsRle 257
                                 L     + +  HRdL+l+n  +d++ nv + d+ ls + 
  gene42|gene42|rna42|rna42 133 GLMYLHDSVNVVHRDLKLGNLFLDSKFNVKIGDFGLSAVI 172
                                **********************************999765 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.7e-06    0.0061     312     399 ..     127     208 ..     117     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-06
             Pkinase_fungal 312 lrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkgee..Hsy 393
                                +++ ++g+  L+   +++HrD   +N+ +      ++ +  + D+ l   ++d    +++ +  GT++++a evl g+   Hs+
  gene42|gene42|rna42|rna42 127 VKQTVEGLMYLHDSVNVVHRDLKLGNLFLD-----SKFNVKIGDFGLSAVIKDG---EKKITMCGTPNYIAPEVLFGKAsgHSF 202
                                678899**********************99.....789999**********973...344679*************86567*** PP

             Pkinase_fungal 394 rhDLES 399
                                  D+ S
  gene42|gene42|rna42|rna42 203 EADIWS 208
                                ***977 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.2   4.5e+02       5      44 ..      30      75 ..      28     110 .. 0.60
   2 !   11.3   0.1   0.00011      0.24     140     183 ..     111     158 ..      86     172 .. 0.67
   3 ?    0.1   0.0      0.28   6.3e+02     176     201 ..     291     313 ..     291     317 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                               E--.SSCEEEEEEETT.--EEEEEE-TT.....S-HHHHHHHHHHH CS
                        APH  5 lsggasnrtylvttpa.gryvlrrnppa.....raaeeirrevall 44
                               l+ ga+ + yl + ++  +y++++++ +     + +e++++e  + 
  gene42|gene42|rna42|rna42 30 LGRGAYAQCYLAEIENgEQYAMKVVRLKdiksrKVHEKLESEISIH 75
                               678999999*******55***9997777432334444444444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                                CTCCHHHHHHHH.HHHHHHHH--S....SS-EEEE-SS-SGGGEEEC.. CS
                        APH 140 elldlleeleeq.vlaalaallpg....elptvllHgDlhpgNllvdpd 183
                                +l+    +l e+ v++ +++++ g    +++  ++H+Dl++gNl +d+ 
  gene42|gene42|rna42|rna42 111 LLKR-NGKLKERhVARFVKQTVEGlmylHDSVNVVHRDLKLGNLFLDSK 158
                                3333.4455555555556666666666699999**************33 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.28
                                GGEEEC..TTEEEEE---TT-EEEEC CS
                        APH 176 gNllvdpddgrvtGviDfedaglgpp 201
                                +Nl+++  +++  GviD +++  + p
  gene42|gene42|rna42|rna42 291 RNLMIN--KTQ-EGVIDTDYVLFSIP 313
                                5*****..888.59***999877665 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4   0.00043      0.97       3      62 ..      39      98 ..      37     106 .. 0.91
   2 ?    4.5   0.0      0.01        23      85     150 ..     100     167 ..      96     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00043
                               EEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHH CS
                       RIO1  3 yhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnL 62
                               y a  e+g+++a+K+ +++  + +k++++ + e   +++  + n  k+ +   + E+  +
  gene42|gene42|rna42|rna42 39 YLAEIENGEQYAMKVVRLKDIKSRKVHEKLESEISIHSKLDNPNIVKMYRSFRNEEYVFM 98
                               889999*****************************9999999999999999999998665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                                EE--EETTEEGGBHHHCG-..HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GT CS
                       RIO1  85 mefigedgvaapklkdvee..eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvs 150
                                +e+++ +g   + lk   +  e++ ++ +++++e +  l   +++vH DL   N+++d++ +v i D++
  gene42|gene42|rna42|rna42 100 LELCE-RGALDALLKRNGKlkERHVARFVKQTVEGLMYLHDSVNVVHRDLKLGNLFLDSKfNVKIGDFG 167
                                55555.3444444554443247788899999999999999**************999999888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2962.49
//
Query:       gene420|gene420|rna420|rna420  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1659.31
//
Query:       gene421|gene421|rna421|rna421  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-44  149.1   0.2    9.7e-44  148.9   0.2    1.0  1  Histone   Core histone H2A/H2B/H3/H4
    1.8e-05   25.4   2.9    2.1e-05   25.1   2.9    1.2  1  PAF       PCNA-associated factor histone like domain
     0.0013   18.9   0.0     0.0024   18.0   0.0    1.4  1  CENP-T_C  Centromere kinetochore component CENP-T histone fol
     0.0022   18.3   0.0     0.0036   17.7   0.0    1.2  1  CENP-S    CENP-S protein
  ------ inclusion threshold ------
       0.16   12.4   0.0       0.34   11.3   0.0    1.5  1  PH_2      Plant pleckstrin homology-like region


Domain annotation for each model (and alignments):
>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   0.2   2.7e-47   9.7e-44       1     131 []       1     135 [.       1     135 [. 0.99

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 2.7e-47
                                    XXEESXEEEXXXXEEXXXXXXXXXXHT..TS-SSSSB--TTT-XTTHHHHHHHHHHHHXXSXXSXHHHHHHHHHHHH... CS
                        Histone   1 marekekarkesektapekkvsakker..kasskskkkkkrryrpgtvalkeirkyqkstdlliqklpfaRvvreivk.. 76 
                                    mar+k++ark+++++ap+k++sak++r  +++++s  +kk ryrpg+valkeir+yqkstd+li++lpf+R +r +vk  
  gene421|gene421|rna421|rna421   1 MARTKQSARKTTGGKAPRKQLSAKSARkaVSPASSGGAKKSRYRPGSVALKEIRRYQKSTDFLIRRLPFQRACRSVVKec 80 
                                    9******************************************************************************* PP

                                    TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHHHT CS
                        Histone  77 sekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArrlr 131
                                    s+ +d+r+++ a+  +qealE +lv lfe+A+l+a haKRvT++pkDi l+++lr
  gene421|gene421|rna421|rna421  81 SNATDIRFQGPALASIQEALEVYLVGLFEDAMLCACHAKRVTVFPKDISLVLKLR 135
                                    ****************************************************986 PP

>> PAF  PCNA-associated factor histone like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   2.9   5.8e-09   2.1e-05       1      62 [.       1      59 [.       1      92 [. 0.80

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.8e-09
                            PAF  1 mVRTkAdvssarkavaakAprkslgasssssssssssp.kkkkkkyvGGNpvcpRptPaWQKp 62
                                   m RTk ++   rk  ++kAprk+l+a+s  +++s  s+   kk+ y +G +v  +++   QK 
  gene421|gene421|rna421|rna421  1 MARTKQSA---RKTTGGKAPRKQLSAKSARKAVSPASSgGAKKSRYRPG-SVALKEIRRYQKS 59
                                   99*****9...*******************9999888845556666666.7888888888887 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.6e-07    0.0024      24      81 ..      82     140 ..      64     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.6e-07
                       CENP-T_C  24 sgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmk.rqrkvt 81 
                                    +++  + +  al+++++a++ ++  + eD    a Ha+R t+  +D+ l +k r r+v+
  gene421|gene421|rna421|rna421  82 NATDIRFQGPALASIQEALEVYLVGLFEDAMLCACHAKRVTVFPKDISLVLKlRSRHVK 140
                                    34788889999************************************999996788886 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0     1e-06    0.0036       9      71 ..      71     133 ..      67     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1e-06
                         CENP-S   9 ysvgkiveeeaaekeveatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLlaR 71 
                                     +++++v+e ++ +++++   ++a++ e     l  l +D  + a HAkR t+ ++D+ L+++
  gene421|gene421|rna421|rna421  71 RACRSVVKECSNATDIRFQGPALASIQEALEVYLVGLFEDAMLCACHAKRVTVFPKDISLVLK 133
                                    5678999****************************************************9976 PP

>> PH_2  Plant pleckstrin homology-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.6e-05      0.34      10      36 ..     115     140 ..     107     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.6e-05
                           PH_2  10 klhwktVsvyinkksqVvlklkskhvg 36 
                                    ++h k+V+v+ +    +vlkl+s+hv+
  gene421|gene421|rna421|rna421 115 ACHAKRVTVFPKDI-SLVLKLRSRHVK 140
                                    69*******99776.99********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 888.26
//
Query:       gene422|gene422|rna422|rna422  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1007.70
//
Query:       gene423|gene423|rna423|rna423  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 682.06
//
Query:       gene424|gene424|rna424|rna424  [L=200]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-38  129.9   0.6    8.5e-38  129.6   0.6    1.1  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
    0.00011   22.9   0.7    0.00021   21.9   0.7    1.5  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.6   0.6   9.5e-42   8.5e-38      12     176 ..      18     180 ..       8     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.6 bits;  conditional E-value: 9.5e-42
                  Ribosomal_L18  12 skrkapksenvylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrl 91 
                                    s+rk+pks+n+yl+ L   y  +a  t+    k + krL ms++ r+p+ +s++v++++++  e+k+avvv++v+dD r+
  gene424|gene424|rna424|rna424  18 SRRKEPKSKNIYLRALSDFYTKVADNTSVLAIKKISKRLKMSKSDRQPVKISKIVSELENS--EGKVAVVVAKVLDDDRI 95 
                                    689********************************************************87..9**************** PP

                  Ribosomal_L18  92 levPklsvaALrftetararilkaGGeiltlDqLalraPtGkntvLlrGkkkareavkhfgaapgvphshkkpyvrskgr 171
                                    +e+P+++v AL+ ++ ++++i++ GG i tlDqL    P+ ++  L+  +k ar++ k++g apg+ +s++ p+ ++k +
  gene424|gene424|rna424|rna424  96 MEIPAIKVIALQWSKGVKEKIERYGGSIGTLDQLFELCPNMDDIKLISTDKFARKSAKFWGPAPGEKGSTTYPRANQKCH 175
                                    ******************************************************************************99 PP

                  Ribosomal_L18 172 kfeka 176
                                    + ek 
  gene424|gene424|rna424|rna424 176 NREKR 180
                                    98863 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.7   2.4e-08   0.00021      46     126 ..      41     123 ..      10     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.4e-08
                                    .---EEEEHHHHHHTTTTGTTS------EEEGGGTTTTSSS........SE.EEE--S---..-.-EEEESEE-HHHHHH CS
                 Ribosomal_L27A  46 kkeykvvnlkdLdelideerleladeaeeidleelaeaglikk....kdgv.Kvlgkgeltk.k.lkvkaskfSkkAkek 118
                                    + +++v+ +k++ + ++  +    ++++++++++++++    +       v Kvl + ++ + + +kv a + Sk  kek
  gene424|gene424|rna424|rna424  41 ADNTSVLAIKKISKRLKMSK----SDRQPVKISKIVSELEN-SegkvAVVVaKVLDDDRIMEiPaIKVIALQWSKGVKEK 115
                                    46678888888885444444....47789999999443333.2577777778*****98866556*************** PP

                                    HHHTT-EE CS
                 Ribosomal_L27A 119 IeaaGGkv 126
                                    Ie+ GG++
  gene424|gene424|rna424|rna424 116 IERYGGSI 123
                                    ******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1322.29
//
Query:       gene425|gene425|rna425|rna425  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-07   29.6   0.0    1.2e-06   28.6   0.0    1.4  1  DnaJ      DnaJ domain
  ------ inclusion threshold ------
       0.23   11.2   6.7       0.41   10.4   6.7    1.5  1  zf-CSL    CSL zinc finger


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.3e-10   1.2e-06       3      51 ..       4      49 ..       3      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-10
                                   HHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHH CS
                           DnaJ  3 YeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAye 51
                                   +++L + k a+++e++ +Y +  +++HPD+n   + +  ++ ++ +Aye
  gene425|gene425|rna425|rna425  4 FSLLRLRKGATKEEVRIRYLRRLIQIHPDRN---KGNGAEYTKLRNAYE 49
                                   689****************************...555677889999987 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.7   4.6e-05      0.41      21      56 ..      75     102 ..      65     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.6e-05
                                    ETTSSEEEEEHHHHHTT....--EEEETTSSEEEEE CS
                         zf-CSL  21 CRCgdeFelteedleegaegaevvvqCssCSLwikV 56 
                                    CRCg++++++ e   ++        +C+ CS +i++
  gene425|gene425|rna425|rna425  75 CRCGGKYKISHEVDGRI--------ECEFCSCFIEI 102
                                    **************998........9*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 718.59
//
Query:       gene426|gene426|rna426|rna426  [L=134]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.15   12.2   0.0    1.2  1  DUF3314   Protein of unknown function (DUF3314)


Domain annotation for each model (and alignments):
>> DUF3314  Protein of unknown function (DUF3314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-06      0.15      19      72 ..      21      75 ..      13      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-06
                        DUF3314 19 hfliGqvqlgslkvsifryckptpylasletglykr.mrWnverekeeeeegese 72
                                    f+i   +l+ +++  f +++  py++s+++ ly r  r++ e ++e  e+++s 
  gene426|gene426|rna426|rna426 21 AFIITTRTLSPYRLDSFPFSQVGPYKTSTDPILYSRpSRFETETSTEVGERKNSV 75
                                   689999999*************************885799999755544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1022.65
//
Query:       gene427|gene427|rna427|rna427  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.3e-22   77.6   1.4    1.4e-21   76.9   1.4    1.4  1  CBFB_NFYA  CCAAT-binding transcription factor (CBF-B/NF-YA) s


Domain annotation for each model (and alignments):
>> CBFB_NFYA  CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   1.4   7.6e-26   1.4e-21       1      56 []      68     121 ..      68     121 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 7.6e-26
                      CBFB_NFYA   1 eplyVNakQynrIlkRReaRakleaelklrkarkkylheSRhkhAmrRpRgpgGRF 56 
                                    +plyVNakQ+n I kR+++R+ l++ +   +++++ylheSRhkhAm+R R+p+GRF
  gene427|gene427|rna427|rna427  68 QPLYVNAKQLNWIKKRKARRDMLDTLMV--TSKRNYLHESRHKHAMKRLRAPSGRF 121
                                    69*********************88654..55668********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 962.23
//
Query:       gene428|gene428|rna428|rna428  [L=369]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-17   62.8   5.1    0.00037   21.2   0.1    5.3  6  WD40          WD domain, G-beta repeat
      4e-05   23.8   0.1       0.03   14.6   0.0    3.5  3  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
  ------ inclusion threshold ------
       0.04   13.8   0.1        1.7    8.5   0.0    3.0  4  eIF2A         Eukaryotic translation initiation factor eIF2A
      0.068   11.7   0.0       0.14   10.7   0.0    1.5  2  Cytochrom_D1  Cytochrome D1 heme domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.8   8.1e+03      12      25 ..     111     126 ..     102     131 .. 0.72
   2 !    7.4   0.0    0.0019       8.7       7      36 ..     148     176 ..     142     178 .. 0.71
   3 !   16.0   0.0   3.9e-06     0.017       8      38 .]     189     220 ..     182     220 .. 0.88
   4 !   21.2   0.1   8.3e-08   0.00037       3      38 .]     227     266 ..     225     266 .. 0.81
   5 ?   -1.8   0.0       1.6   7.1e+03      13      28 ..     289     305 ..     280     313 .. 0.63
   6 !   15.9   0.1     4e-06     0.018       7      37 ..     325     356 ..     316     357 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.8
                                    S..EEEEEEETTSSEE CS
                           WD40  12 s..vtslafspdgawl 25 
                                    s  +ts++ +p  + +
  gene428|gene428|rna428|rna428 111 SlgITSVKCNPTTSTV 126
                                    3449999988887766 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0019
                                    EESS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvri 36 
                                    ++ H s + ++  s + +  ++Gs+D++++i
  gene428|gene428|rna428|rna428 148 YSFHrSRI-GVIESENTNI-ITGSRDRKIKI 176
                                    66676667.6655555555.68********9 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 3.9e-06
                                    ESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   8 tGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                      H + v++l+ s+d ++lasG+ D+ ++i+d
  gene428|gene428|rna428|rna428 189 LNHrQEVCGLSISKDLRFLASGGNDNRLYIYD 220
                                    469888************************98 PP

  == domain 4  score: 21.2 bits;  conditional E-value: 8.3e-08
                                    EEEEEESS.SSEEEEEEETTSSEEE.EEE..TTSEEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgawla.sGs..dDgtvriWd 38 
                                    +l+ ++ H   v ++++sp ++ l+ sG+   D+t+++Wd
  gene428|gene428|rna428|rna428 227 PLKQCSNHkAAVKAISWSPLSPNLLvSGGgtADKTIKLWD 266
                                    67888999555************753875447*******9 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 1.6
                                    EEEEEEETTSSEEEE.E CS
                           WD40  13 vtslafspdgawlas.G 28 
                                    ++ l++ ++++ l++ G
  gene428|gene428|rna428|rna428 289 ICNLRWLKSNKILSThG 305
                                    77777777777775444 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 4e-06
                                    EESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                    + GH + v +++ s+d ++++sGs D ++ +W
  gene428|gene428|rna428|rna428 325 FLGHkNRVIHFSCSDDEKYFVSGSSDSNINFW 356
                                    56**777879999**********99******* PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   6.8e-06      0.03      16      90 ..     171     244 ..     160     246 .. 0.81
   2 !    4.5   0.0    0.0096        43      37      74 ..     285     323 ..     263     337 .. 0.81
   3 ?   -0.2   0.0      0.29   1.3e+03      38      66 ..     329     357 ..     326     362 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.8e-06
                    ANAPC4_WD40  16 dgellvfRlng.qrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaes.gkvvhslsvksekavtclgWg 90 
                                    d ++ +  l   + v t+   ++ +ev +L+ ++d ++La + +d+++ ++d  + ++ ++++s ++  av+ ++W+
  gene428|gene428|rna428|rna428 171 DRKIKITDLRSeKAVATI--LNHRQEVCGLSISKDLRFLASGGNDNRLYIYDYRNlAHPLKQCSNHKA-AVKAISWS 244
                                    556666666441445555..7999****************************9885788999988888.6******6 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0096
                    ANAPC4_WD40  37 edsevrsLaWkpdgklLav.aysdgevrlldaesgkvvh 74 
                                     +s++ +L+W +++k+L   +ys+  +rl +++s kv +
  gene428|gene428|rna428|rna428 285 YGSQICNLRWLKSNKILSThGYSKDDIRLSQMSSFKVER 323
                                    678999***********75499*******9999887755 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.29
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlld 66 
                                    +++v +++ + d+k ++ + sd+++++ +
  gene428|gene428|rna428|rna428 329 KNRVIHFSCSDDEKYFVSGSSDSNINFWE 357
                                    67788888899999999999999998765 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.3   5.7e+03     147     162 ..      76      91 ..      70     128 .. 0.68
   2 ?   -1.1   0.0      0.32   1.5e+03      72      99 ..     161     189 ..     157     212 .. 0.71
   3 ?    8.5   0.0   0.00038       1.7      38      91 ..     213     268 ..     198     301 .. 0.82
   4 ?    1.1   0.0     0.069   3.1e+02      38      93 ..     308     361 ..     286     367 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                                    -EEEE-TTSSEEEEEE CS
                          eIF2A 147 tlvewspdgryvlTat 162
                                    +l++ws +  +++  +
  gene428|gene428|rna428|rna428  76 SLIDWSGENVFFTADS 91 
                                    5666666555554433 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.32
                                    S-EEEEESSSSCEEEEEECS.CEEEEEEE CS
                          eIF2A  72 kefaviyGkmpakvslfdlk.vkviskle 99 
                                    ++  +i G  ++k+++ dl+  k+++++ 
  gene428|gene428|rna428|rna428 161 ENTNIITGSRDRKIKITDLRsEKAVATIL 189
                                    5667999*******999998334444444 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00038
                                    EEEEEESSSTT--EEECCEESSS..EEEEEE-TTSS-EEEEES.SSSCEEEEEECS CS
                          eIF2A  38 etelyliklkkkksevvelkkegp.ihdvaWspkskefaviyG.kmpakvslfdlk 91 
                                     + ly+ + ++      + +++   +++++Wsp s +++v  G  ++++++l+d  
  gene428|gene428|rna428|rna428 213 DNRLYIYDYRNLAHPLKQCSNHKAaVKAISWSPLSPNLLVSGGgTADKTIKLWDIS 268
                                    56778887777777777776554449*************99876888899999975 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.069
                                    EEEEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEESSSSCEEEEEECSCE CS
                          eIF2A  38 etelyliklkkkksevvelkkegpihdvaWspkskefaviyGkmpakvslfdlkvk 93 
                                    + ++ l ++++ k+e+  l +++ ++ ++ s ++k f  + G +++++++++l+++
  gene428|gene428|rna428|rna428 308 KDDIRLSQMSSFKVERYFLGHKNRVIHFSCSDDEKYF--VSGSSDSNINFWELDGE 361
                                    4445555566666667777777777777666666555..68888888888887765 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.1e-05      0.14      33     118 ..     146     234 ..     139     268 .. 0.78
   2 ?   -2.8   0.0      0.38   1.7e+03      75      94 ..     326     347 ..     298     357 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.1e-05
                                    -STTEEEEEE..-TT.SSEEEEEETTSEEEEEESSSSSEEEEEE.-SSEEEEEEE--TTSEEEEEEEETTEEEEEETTT- CS
                   Cytochrom_D1  33 tgyalHisrv..fasdgRyvyvigRDgkvtliDLwakeivaevk.iGlnarsvavSqddryvivgnYlPgqlvildaetL 109
                                    t+y  H sr+    s++  + + +RD k+++ DL  ++ va++     +  ++ +S+d r+++ g      l i d ++L
  gene428|gene428|rna428|rna428 146 TRYSFHRSRIgvIESENTNIITGSRDRKIKITDLRSEKAVATILnHRQEVCGLSISKDLRFLASGGN-DNRLYIYDYRNL 224
                                    78888888852245567888899***************99998515678999*********998864.456677777777 PP

                                    .-EEEEEE-- CS
                   Cytochrom_D1 110 .elvkvisar 118
                                     +++k+ s  
  gene428|gene428|rna428|rna428 225 aHPLKQCSNH 234
                                    3356665555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.38
                                    -SSEEEEEEE-..-TTSEEEEE CS
                   Cytochrom_D1  75 iGlnarsvavS..qddryvivg 94 
                                    +G   r +  S  +d++y + g
  gene428|gene428|rna428|rna428 326 LGHKNRVIHFScsDDEKYFVSG 347
                                    4555555544444666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2342.73
//
Query:       gene429|gene429|rna429|rna429  [L=1256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-45  154.4   0.0    8.4e-45  153.0   0.0    1.6  1  SNF2_N      SNF2 family N-terminal domain
    6.3e-19   68.4   0.0    2.4e-18   66.5   0.0    2.1  1  Helicase_C  Helicase conserved C-terminal domain
      0.008   16.6   0.0      0.049   14.0   0.0    2.2  2  HEAT_2      HEAT repeats
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.088   12.6   0.0    2.3  1  DEAD        DEAD/DEAH box helicase
      0.072   13.4   0.1    1.7e+02    2.9   0.0    4.6  4  HEAT        HEAT repeat


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.0   0.0   2.3e-48   8.4e-45      51     303 ..     811    1033 ..     789    1043 .. 0.88

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 2.3e-48
                                     HHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE-- CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N   51 akqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlv 128 
                                     +++ + +GiLaD+mGLGKT+qvl+++  + +   k ++k         +L+++P+sl  +W++e++++ +  a +++ 
  gene429|gene429|rna429|rna429  811 LHSFNLNGILADDMGLGKTLQVLTFLCSEIY---KTNRK---------ILVICPSSLTGHWKSEVKKFFPLVAAEIYK 876 
                                     5666789********************4444...33333.........9**************************999 PP

                                     SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  129 yggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLsts 206 
                                      +g++               +y  +i +Y++ +++         + +++w++vv+DEgh l+n+++ ++  ++ ++  
  gene429|gene429|rna429|rna429  877 REGKS---------------KYSFLISSYETFRNDY------LNFIEKDWFYVVVDEGHVLRNKQTILYSRMNMIKCP 933 
                                     99953...............799**********666......899999****************************** PP

                                     -EEEE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH...HHHHHHHHHHHTT-STTEE---GGGT--S-- CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  207 nrwiltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie...aqaekgrsrLlqllqrlmlrrakkdveknlP 281 
                                     ++++ltGTP+ ns+edl++L++fL+++  g+ + + +l  + +    ++++++ + L++ + +++lrr k dv k+lP
  gene429|gene429|rna429|rna429  934 RKIVLTGTPVHNSVEDLVSLFNFLMPNYIGSEKEYGSLNVKMSDteiEKTQERLNLLHKKVLPFVLRRLKIDVLKDLP 1011
                                     ******************************98866655433333445699999999999999**************** PP

                                     -EEEEEEEEE--HHHHHHHH.. CS
                                     xxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  282 pkteeiiflklskverksYnrl 303 
                                     pk+ + i ++l +v++k+Y ++
  gene429|gene429|rna429|rna429 1012 PKIIRDITVELGPVQEKLYREI 1033
                                     *******************965 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.0   6.7e-22   2.4e-18      11     111 .]    1096    1198 ..    1084    1198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 6.7e-22
                                     HHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEE.EESGGGTSSSTSTTES CS
                     Helicase_C   11 kleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvL.iatdvaerGidipkvn 86  
                                       e  ++k+lif +++++++  +k +  k ++k+ +l+g+ p++ r +i e+fn g++++L ++t+v++ G+++++++
  gene429|gene429|rna429|rna429 1096 GGEDLRNKMLIFFQFKSSIDLvIKDIMAKYKFKYSRLDGSVPSSARAKIAEDFNTGTTQILfLTTQVGGLGLNLTGAD 1173
                                     5567799**********99888666667779****************************6669*************** PP

                                     EEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C   87 lVinfdlprnvtsyiqriGRtgRag 111 
                                     +V++++ ++n+ +  q+++R++R+g
  gene429|gene429|rna429|rna429 1174 TVVMYEHDWNPFNDLQAMDRAHRIG 1198
                                     ***********************97 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.4e-05     0.049      16      81 ..     222     295 ..     201     302 .. 0.77
   2 ?   -1.5   0.0      0.96   3.5e+03      14      52 ..     367     406 ..     355     410 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                         HEAT_2  16 vrraairaLg....rignpealpaLvellededpavRraaaeaLgaig.....dpealpaLkellddddddvvRe 81 
                                    vr aa+  L      ig+ ++++ L+++l++ed+ ++     aLg ++     ++   + L  lld++d+d+ + 
  gene429|gene429|rna429|rna429 222 VRDAAAYLLSciypLIGPNDIIEQLLRFLDSEDWQIQFSGLIALGYLKefvedRDGLRKKLISLLDSPDEDI-KL 295
                                    888999999999888999999999999999999999999999999886333323667899999887766654.54 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.96
                         HEAT_2  14 pevrraairaLgrignpealpaLve.ll.ededpavRraaa 52 
                                    pevr+ ++    ++ + e+++ Lv  ++   e+ ++R++a+
  gene429|gene429|rna429|rna429 367 PEVRISILNMVENLSE-ESIDFLVAeVIlIEEKDEIREMAI 406
                                    5666666666665555.345555543333556666666665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.5e-05     0.088      19     175 ..     820     949 ..     800     950 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.5e-05
                                    EEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  19 vaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngv 98 
                                    +a + G GKTl  l  +++++y    kt+ k+l+++P+ +L+    +++kkf+      +  i++  + ++++s l    
  gene429|gene429|rna429|rna429 820 LADDMGLGKTLQVLTFLCSEIY----KTNRKILVICPS-SLTGHWKSEVKKFFPL---VAAEIYK-REGKSKYSFL---- 886
                                    56678****************8....68899******8.69*************4...3333444.4444445555.... PP

                                    SEEEEEHHHHHH.HHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.HHHHH CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                           DEAD  99 divvgtpgrldd.llstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.kdvkk 175
                                       ++  + + +  l+   +  ++  ++V+DE + l ++  +  + + +n +   +c      + ivl+ T+  ++v++
  gene429|gene429|rna429|rna429 887 ---ISSYETFRNdYLN---FIEKDWFYVVVDEGHVLRNK--QTILYSRMNMI---KCP-----RKIVLTGTPVhNSVED 949
                                    ...5555555542332...22478899*******99998..66666658888...343.....3588888876566665 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.053   1.9e+02      13      28 ..     219     234 ..     210     237 .. 0.82
   2 ?    2.9   0.0     0.047   1.7e+02       1      27 [.     242     268 ..     242     272 .. 0.88
   3 ?    0.1   0.0      0.38   1.4e+03       5      26 ..     282     303 ..     278     304 .. 0.88
   4 ?    0.0   0.0      0.39   1.4e+03       7      22 ..     360     375 ..     357     383 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.053
                                    SHHHHHHHHHHHHHHH CS
                           HEAT  13 speVReaAakaLgala 28 
                                     + VR+aAa+ L  ++
  gene429|gene429|rna429|rna429 219 VAPVRDAAAYLLSCIY 234
                                    577********98876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.047
                                    HHHHHHHHHT-SSHHHHHHHHHHHHHH CS
                           HEAT   1 llPlllkllsDpspeVReaAakaLgal 27 
                                    ++  ll+ l ++++++  + + aLg l
  gene429|gene429|rna429|rna429 242 IIEQLLRFLDSEDWQIQFSGLIALGYL 268
                                    68899**************99999976 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.38
                                    HHHHHT-SSHHHHHHHHHHHHH CS
                           HEAT   5 llkllsDpspeVReaAakaLga 26 
                                    l++ll +p+ ++   +a+ L++
  gene429|gene429|rna429|rna429 282 LISLLDSPDEDIKLLSAELLCH 303
                                    8999*************99986 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.39
                                    HHHT-SSHHHHHHHHH CS
                           HEAT   7 kllsDpspeVReaAak 22 
                                     + ++p peVR + ++
  gene429|gene429|rna429|rna429 360 PCFMSPVPEVRISILN 375
                                    57799******98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.28s 00:00:01.08 Elapsed: 00:00:00.43
# Mc/sec: 8699.85
//
Query:       gene43|gene43|rna43|rna43  [L=457]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   4.5e-140  467.7   0.7   5.2e-140  467.5   0.7    1.0  1  DUF5098      Domain of unknown function (DUF5098)
  ------ inclusion threshold ------
       0.18   11.9   4.0        2.7    8.2   0.0    3.2  3  T3SchapCesA  Type III secretion system filament chaperone Ces


Domain annotation for each model (and alignments):
>> DUF5098  Domain of unknown function (DUF5098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.5   0.7  5.8e-144  5.2e-140       1     463 []      11     454 ..      11     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 467.5 bits;  conditional E-value: 5.8e-144
                    DUF5098   1 ykllkeKvkwikaflehvetvskraaellfratqiPrntawkDpliiellemsdkqravfdeltrlyeitvvkeldallkkled 84 
                                yk+lk+K+ ++k++leh+ +vskr+++llfra+qiP++taw+Dpl+++++ems++qravfde   ly++t++keld+l+++++ 
  gene43|gene43|rna43|rna43  11 YKMLKCKCVYLKSYLEHIIIVSKRSSDLLFRALQIPQDTAWNDPLLMHCIEMSERQRAVFDEAGLLYGETLFKELDGLIATIVS 94 
                                89********************************************************************************** PP

                    DUF5098  85 kiaelneeekkfekklkellkelkaardshleAwtegkaDpWlteleLkkaikkylkedeesnellkaeisksdkelqelkkkY 168
                                +i++++ee+k++ +k++e lkel+ ar++h+eAwt+gk+DpWltel+Lk+a+kk+l +d+e+n+ +  +i+ + ++lq + +++
  gene43|gene43|rna43|rna43  95 DIRMIDEEVKRVSEKPAEGLKELRIARNKHMEAWTYGKHDPWLTELGLKRAVKKVLLMDDEANHVMYDKIGGFAESLQGAGERF 178
                                ************************************************************************************ PP

                    DUF5098 169 keillnflkiqkahyknlleevdid..rf.....lfdevselkkeifydfpeseeeklqekeekeelkekeetkfeelveqIvk 245
                                ke ll+ + iq+++y++l ++ d +   +     +fd+vse++ke              e +++e+lkek++ +fe++ve+I+k
  gene43|gene43|rna43|rna43 179 KEALLSLVRIQRQKYQKLRDSTDVEikGYdeidrFFDTVSESPKE-----------MKAEVNKEEKLKEKVDSSFETFVEGISK 251
                                *******************9998887666888888**********...........56666777799***************** PP

                    DUF5098 246 elkkkrkqfikkklevkkcgifkvkk.nksdiktlfiivtetnfiHafdldsiveelesLsdeekallkkLndgsykklisfFd 328
                                el   ++++++k+lev++++i+kvkk ++ d+ t+++ +t+t++ H+fd++ +++e e+L    ++++++Ln g  k lis+Fd
  gene43|gene43|rna43|rna43 252 EL-IGKGITVRKNLEVVRSSICKVKKgYTGDWVTAYLTITSTGYGHFFDISGLLNETEDL----RNIVERLNGGVGKSLISIFD 330
                                **.9******************************************************99....89****************** PP

                    DUF5098 329 kskkealntteekelkeisaavlneidvlssvlkgfpiklkdklvkLdkekreiiitekksntlksiFvsntikiksFtlkdiy 412
                                +  k++++  e++ ++e++ +v + i++lss  ++++i l+d++++Ld+e+r+i+ +++++n+++s+F ++++kik+Ftl++++
  gene43|gene43|rna43|rna43 331 A-GKHKKEPGEDRMVFEVNSKVGEMIETLSS--PVISIYLNDNTYELDRERRQISASNRHQNGFASFFGVSEVKIKLFTLSNAI 411
                                *.999**************************..*************************************************** PP

                    DUF5098 413 elffalldknkkeeseekeeesdeeeedndsvekekeeekiissiedeNPW 463
                                e+f+a+ d+n+ ees ++++es e++ d++   k++++e        eNPW
  gene43|gene43|rna43|rna43 412 EIFHAFKDRNQPEESIDDFSESPEKVLDEGIGLKVLLQE--------ENPW 454
                                ****************************99988888877........9999 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0003       2.7      24      67 ..      89     133 ..      76     152 .. 0.82
   2 ?    1.5   1.3     0.038   3.4e+02      14      72 ..     197     255 ..     183     276 .. 0.73
   3 ?    0.4   0.0      0.08   7.1e+02      65      86 ..     339     359 ..     335     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0003
                T3SchapCesA  24 ikkiiaefdvvkesvnilsekakt.dpqaaeklnkliegytygee 67 
                                i  i++++ ++ e+v+ +sek      +     nk +e +tyg+ 
  gene43|gene43|rna43|rna43  89 IATIVSDIRMIDEEVKRVSEKPAEgLKELRIARNKHMEAWTYGKH 133
                                678999***************655055566788**********75 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.038
                T3SchapCesA  14 dkkirseieaikkiiaefdvvkesvnilsekaktdpqaaeklnkliegytygeerklyd 72 
                                      ei+    i   fd v es +++    + + +  ek++   e +  g  + l  
  gene43|gene43|rna43|rna43 197 RDSTDVEIKGYDEIDRFFDTVSESPKEMKAEVNKEEKLKEKVDSSFETFVEGISKELIG 255
                                44456688888888888999999999998888888888999988888888887777665 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.08
                T3SchapCesA  65 geerklydsalskieklietlk 86 
                                ge+r +++   sk+  +ietl+
  gene43|gene43|rna43|rna43 339 GEDRMVFE-VNSKVGEMIETLS 359
                                77887776.569********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2955.63
//
Query:       gene430|gene430|rna430|rna430  [L=329]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.6e-09   35.6   9.0    1.4e-08   34.9   9.0    1.4  1  zf-RING_2     Ring finger domain
    6.8e-07   28.9   5.6    1.3e-06   28.0   5.6    1.5  1  zf-RING_11    RING-like zinc finger
    6.1e-05   23.2   6.3    0.00012   22.3   6.3    1.5  1  zf-rbx1       RING-H2 zinc finger domain
    0.00069   19.5   7.6     0.0011   18.8   7.6    1.4  1  zf-RING_5     zinc-RING finger domain
    0.00074   19.3   7.6     0.0013   18.6   7.6    1.4  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    0.00096   18.9   8.8     0.0017   18.2   8.8    1.4  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
      0.001   19.0   5.4     0.0023   17.9   5.4    1.6  1  zf-RING_UBOX  RING-type zinc-finger
     0.0026   17.8   3.3      0.005   16.9   3.3    1.5  1  Zf_RING       KIAA1045 RING finger
     0.0079   16.0   5.6      0.012   15.4   5.6    1.3  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.017   15.2   5.8      0.072   13.1   5.9    1.9  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
      0.028   14.0   4.8      0.049   13.2   4.8    1.4  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
      0.055   13.6   9.6        1.7    8.8   9.6    2.5  1  FANCL_C       FANCL C-terminal domain
      0.094   12.6   5.5       0.21   11.5   5.4    1.6  1  Prok-RING_4   Prokaryotic RING finger family 4
        0.2   11.3   1.4         69    3.3   0.0    3.7  3  Spore_YhaL    Sporulation protein YhaL
        4.9    7.2   7.7        2.8    7.9   2.8    2.2  2  Prok-RING_1   Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   9.0   1.2e-11   1.4e-08       3      44 .]     238     281 ..     236     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.2e-11
                      zf-RING_2   3 CpICleelssadsvlllpCgHvfhreClerw..lrssstCPlCr 44 
                                    C+IC+ +++ +d++++l C H+fh++C++ w  l +++ CP+C+
  gene430|gene430|rna430|rna430 238 CMICTRSFDGSDRIHTLVCTHSFHEDCIKGWclLGKKPFCPYCK 281
                                    ***************889*************65666666****7 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   5.6   1.1e-09   1.3e-06       2      29 .]     238     265 ..     238     265 .. 0.99

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.1e-09
                     zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                    C+IC  +f  ++++ +l C H FH +CI
  gene430|gene430|rna430|rna430 238 CMICTRSFDGSDRIHTLVCTHSFHEDCI 265
                                    ***************************9 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   6.3     1e-07   0.00012      12      55 .]     236     281 ..     231     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1e-07
                        zf-rbx1  12 eacieckapgdeecpvvlGeCgHaFHlhCiskW..lktrkvCPlcr 55 
                                    + c+ c+++ d +  + +  C+H+FH +Ci+ W  l ++  CP c+
  gene430|gene430|rna430|rna430 236 SLCMICTRSFDGSDRIHTLVCTHSFHEDCIKGWclLGKKPFCPYCK 281
                                    67888888777765666667*************54456999****6 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   7.6   9.5e-07    0.0011       2      44 .]     238     282 ..     237     282 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.5e-07
                      zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkll..ekeavCpiCrk 44 
                                    C +C +++ ++++++++ C+H+f+e+C+k     +k+  Cp C+k
  gene430|gene430|rna430|rna430 238 CMICTRSFDGSDRIHTLVCTHSFHEDCIKGWCllGKKPFCPYCKK 282
                                    99***************************988899********97 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   7.6   1.1e-06    0.0013       1      41 []     238     280 ..     238     280 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                                    -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                    C iC+  +   +   +l C+Hsf+++Ci+ +    kk  CP C
  gene430|gene430|rna430|rna430 238 CMICTRSFDGSDriHTLVCTHSFHEDCIKGWCLLGKKPFCPYC 280
                                    99****9998888899*****************888888***9 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   8.8   1.4e-06    0.0017       2      40 .]     238     280 ..     237     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                     zf-C3HC4_2   2 CpiCldmlkdpsvvt..pCgHvfCqkCilr..sLeekneCPlC 40 
                                    C iC  ++    ++    C H+f+++Ci+    L +k  CP C
  gene430|gene430|rna430|rna430 238 CMICTRSFDGSDRIHtlVCTHSFHEDCIKGwcLLGKKPFCPYC 280
                                    9*******8554444459***********954477777***** PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.4   1.9e-06    0.0023       1      39 []     238     278 ..     238     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                   zf-RING_UBOX   1 CpIClelft.....dPlvlpCGHtFCreClwelskslegafkCP 39 
                                    C IC  +f+     + lv  C H+F+++C+ + +  l+++  CP
  gene430|gene430|rna430|rna430 238 CMICTRSFDgsdriHTLV--CTHSFHEDCI-KGWCLLGKKPFCP 278
                                    99*******996543344..**********.5666677776676 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.3   4.2e-06     0.005       3      35 ..     233     266 ..     231     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.2e-06
                        Zf_RING   3 eedelCeiC.evytaeelypCRvCtkvfHegClr 35 
                                    +++ lC iC   + +++ +   vCt+ fHe+C++
  gene430|gene430|rna430|rna430 233 NNNSLCMICtRSFDGSDRIHTLVCTHSFHEDCIK 266
                                    5899*****889********************97 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   5.6     1e-05     0.012       2      49 ..     235     286 ..     234     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1e-05
                                    GSB-TTTSSS...BS-EEETTEEEEEE-HHHHHHHHH..TT-B-TTT--B--E CS
                     zf-C3HC4_3   2 deeCviCler...prnvvllpCgHlvlCeeCaekllk..rkkkCpiCrrpiek 49 
                                    +++C+iC ++      +  l C H  + e+C + +    +k+ Cp+C+++ie+
  gene430|gene430|rna430|rna430 235 NSLCMICTRSfdgSDRIHTLVCTHS-FHEDCIKGWCLlgKKPFCPYCKKKIES 286
                                    689*****9765566688889****.********98899************97 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   5.9   6.1e-05     0.072      32      81 ..     235     284 ..     228     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                                    TS--TTCSTTTTTS-EEEBT.TS-EEEHHHHHHHHHHHSTSSB-TTTSSB- CS
                     zf-ANAPC11  32 dGtcpsckfpGddcplvlGk.ckhnfhlhcilkwletetskglcpmcrqtf 81 
                                    +  c  c+   d    +    c+h+fh+ ci  w      k  cp c++++
  gene430|gene430|rna430|rna430 235 NSLCMICTRSFDGSDRIHTLvCTHSFHEDCIKGWCLL-GKKPFCPYCKKKI 284
                                    556777777777666555555*************865.6799*****9876 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.8   4.1e-05     0.049       4      46 ..     235     278 ..     232     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                   Zn_ribbon_17   4 lksCayCelavkgr.vvlcgvCeHvlHasCarewfenddlaeCp 46 
                                    +  C++C  +  g+  +   vC H  H++C++ w   ++++ Cp
  gene430|gene430|rna430|rna430 235 NSLCMICTRSFDGSdRIHTLVCTHSFHEDCIKGWCLLGKKPFCP 278
                                    66799999999997357789**************8888888888 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.6    0.0015       1.7       4      68 ..     237     287 ..     234     289 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                    S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG CS
                        FANCL_C   4 eCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrslkesrqsfdvlfGeCPyCkkkisvk 68 
                                     C iC   ++ s+++ + +C     +++fH+ C+k W      +++ f      CPyCkkki+++
  gene430|gene430|rna430|rna430 237 LCMICTRSFDGSDRIHTLVC-----THSFHEDCIKGWCL---LGKKPF------CPYCKKKIESS 287
                                    59999999999999999886.....689*********64...455555......********986 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   5.4   0.00018      0.21       1      43 [.     238     287 ..     238     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                    Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk....dlssCPlCqrrisks 43 
                                    C++C+++      +    C H + ++C +++    +   CP C+++i++s
  gene430|gene430|rna430|rna430 238 CMICTRSfdgSDRIHTLVCTHSFHEDCIKGWcllgKKPFCPYCKKKIESS 287
                                    9*****998655556678*************65544449*******9765 PP

>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.27   3.3e+02      23      46 ..      16      40 ..      14      46 .. 0.75
   2 ?    3.3   0.0     0.057        69       5      23 ..      80      98 ..      78     102 .. 0.85
   3 ?    3.2   0.1      0.06        72      11      24 ..     128     141 ..     122     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.27
                     Spore_YhaL 23 akeEreldqefIEkE.Gevylerle 46
                                    keE+ +dq+ ++k  G+ +   +e
  gene430|gene430|rna430|rna430 16 GKEEKVFDQAKVDKDdGDSFFDDIE 40
                                   599********99843777766555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.057
                     Spore_YhaL  5 vYlviagIlfSgymavkta 23
                                   vY++++  +fS+++ ++  
  gene430|gene430|rna430|rna430 80 VYALVIQTFFSAWKKINKK 98
                                   9***********9988765 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.06
                     Spore_YhaL  11 gIlfSgymavktak 24 
                                     +lfS +m+++t+k
  gene430|gene430|rna430|rna430 128 WLLFSSFMLLNTLK 141
                                    589*******9987 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.8    0.0024       2.8       3      36 ..     234     266 ..     232     274 .. 0.85
   2 ?    1.8   0.2       0.2   2.4e+02       6      16 ..     276     286 ..     271     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                    Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCgtpyHraCye 36 
                                    +++ C +C + ++   D +   +C  ++H +C +
  gene430|gene430|rna430|rna430 234 NNSLCMICTRSFDGS-DRIHTLVCTHSFHEDCIK 266
                                    5789********876.7888899*********75 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                    Prok-RING_1   6 kCpvCgkelke 16 
                                     Cp C+k++++
  gene430|gene430|rna430|rna430 276 FCPYCKKKIES 286
                                    6******9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.59
# Mc/sec: 1678.60
//
Query:       gene431|gene431|rna431|rna431  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-08   34.3   6.8    2.8e-08   33.7   5.1    2.1  2  bZIP_1    bZIP transcription factor
    5.5e-05   23.2   4.5    5.5e-05   23.2   4.5    1.8  2  bZIP_2    Basic region leucine zipper
    8.1e-05   23.1   1.4    0.00015   22.2   1.4    1.5  1  bZIP_Maf  bZIP Maf transcription factor
    0.00052   19.7   0.6      0.013   15.2   0.9    2.1  2  BAR       BAR domain
  ------ inclusion threshold ------
        0.3   10.6   1.5       0.51    9.8   1.5    1.3  1  SieB      Super-infection exclusion protein B


Domain annotation for each model (and alignments):
>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.56     2e+03      32      47 ..       2      17 ..       1      23 [. 0.80
   2 !   33.7   5.1   7.7e-12   2.8e-08       2      57 ..      84     139 ..      83     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.56
                                   HHHHHHHHHHHHHHHH CS
                         bZIP_1 32 errvkaLekeNksLks 47
                                   e+r + ++ eN++++ 
  gene431|gene431|rna431|rna431  2 EDREENIDYENEQMQA 17
                                   6788899999999976 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 7.7e-12
                                    XXXXXXXXX--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1   2 kelKrekrkqkNReaArrsRqRKqaeieeLerrvkaLekeNksLkseleelkkeve 57 
                                    +++K   +k++NR+aA+r+R+++ a+ +eLer+  a+  e ++Lk+ +  + +  e
  gene431|gene431|rna431|rna431  84 ERIKSIWKKERNRIAAKRCREKRIARLKELERKEHAMIYEISELKEAIHDYDNILE 139
                                    7899999**************************************99998887666 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.4     5e+03      33      46 ..       4      17 ..       1      20 [. 0.58
   2 !   23.2   4.5   1.5e-08   5.5e-05       8      48 ..      91     131 ..      87     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                                   HHHHHHHHHHHHHH CS
                         bZIP_2 33 rvkeLeeeNaqLrq 46
                                   r ++   eN+q ++
  gene431|gene431|rna431|rna431  4 REENIDYENEQMQA 17
                                   44555567777665 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.5e-08
                                    XXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2   8 rRrkNreAarrsRekkkakeeeleervkeLeeeNaqLrqkv 48 
                                    ++++Nr+Aa+r+Rek+ a+ +ele++   +  e+++L++ +
  gene431|gene431|rna431|rna431  91 KKERNRIAAKRCREKRIARLKELERKEHAMIYEISELKEAI 131
                                    678***********************999999999998866 PP

>> bZIP_Maf  bZIP Maf transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.4   4.1e-08   0.00015      26      72 ..      83     129 ..      65     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.1e-08
                       bZIP_Maf  26 verLKqrRRrlKNrgyakscrkrrlqqkeelekekeeleeelerlqq 72 
                                    +er+K + ++ +Nr +ak+cr++r+ + +ele+++  +  e ++l++
  gene431|gene431|rna431|rna431  83 QERIKSIWKKERNRIAAKRCREKRIARLKELERKEHAMIYEISELKE 129
                                    68999999************************999888777777765 PP

>> BAR  BAR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.9   3.6e-06     0.013     109     217 ..      61     164 ..      55     171 .. 0.77
   2 ?    2.3   0.0      0.03   1.1e+02      15      54 ..     171     210 ..     168     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.6e-06
                            BAR 109 aqteeelekrvetnfldplrellekefkeiqkerkkl.ehkrlDyDaakarlkklktkkskkakde...ekaeeelrkAq 184
                                    +++e+++ +++et+  +pl+  + + +k i k+ +++ + kr    +  +r+ +lk+  ++k  ++   ++   el++A 
  gene431|gene431|rna431|rna431  61 GEQENQFYQQIETHGYSPLQVDQ-ERIKSIWKKERNRiAAKR----CREKRIARLKE-LERK--EHamiYE-ISELKEAI 131
                                    7899****************999.888888665544414444....34456666663.2233..2234444.589***** PP

                            BAR 185 qkfeesneelkaeLpnllalevefvnqlqafve 217
                                      +++  e+l + +++ l+le+  +++++++++
  gene431|gene431|rna431|rna431 132 HDYDNILEILLRYIQGYLDLEIGKHESFVSLFD 164
                                    *****************************9986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.03
                            BAR  15 kvgkaekTkLDedFeelerrldvteklieklvkelkeylq 54 
                                    kvg+   T L ++   l ++l+vt + i+k+ ++++++l 
  gene431|gene431|rna431|rna431 171 KVGTPNPTYLRDVSHFLSKKLNVTNEGIDKITEAIRGWLN 210
                                    6666667777777777899******************997 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.5   0.00014      0.51      52      89 ..      87     124 ..      84     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00014
                           SieB  52 skllaeikekikkkreqkkvekklknLteeekavLref 89 
                                     +++++ +++i+ kr  +k++++lk L ++e a++ e+
  gene431|gene431|rna431|rna431  87 KSIWKKERNRIAAKRCREKRIARLKELERKEHAMIYEI 124
                                    578999****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1416.92
//
Query:       gene432|gene432|rna432|rna432  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-41  140.4   0.0    4.4e-41  140.2   0.0    1.0  1  Ras          Ras family
    3.4e-18   66.0   0.0    4.6e-18   65.6   0.0    1.2  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      1e-05   25.6   0.0    1.6e-05   25.0   0.0    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
    1.7e-05   24.5   0.0    3.5e-05   23.4   0.0    1.5  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.7e-05   22.9   0.0    5.3e-05   22.7   0.0    1.1  1  Arf          ADP-ribosylation factor family
  ------ inclusion threshold ------
      0.018   15.3   0.0       0.94    9.7   0.0    2.2  2  AAA_22       AAA domain
      0.031   13.8   0.0       0.11   12.0   0.0    1.9  3  AAA_7        P-loop containing dynein motor region
      0.034   14.5   0.0      0.055   13.8   0.0    1.3  1  DrsE         DsrE/DsrF-like family
      0.054   13.0   0.1       0.12   11.9   0.1    1.8  1  FeoB_N       Ferrous iron transport protein B
      0.071   13.0   0.1        3.9    7.4   0.0    2.1  2  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   0.0   2.4e-44   4.4e-41       1     160 [.       5     161 ..       5     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 2.4e-44
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K+vlvGd +vGK+ l+  ++++k +e y++T+ +++++k ++v +k++++++wDTAG ee+++lr+l++++++++l++y+
  gene432|gene432|rna432|rna432   5 KCVLVGDPSVGKSWLISTYITGKNPEGYIPTL-FNNHSKVVNVGDKKYNMTLWDTAGSEEYNKLRSLSFQETDVFLICYA 83 
                                    89******************************.*********************************************** PP

                                    TTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras  81 itsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelg.lkfletSAktnenveeafeellre 159
                                    +++  sf+n k+w++e+ ++   nvp++L+G+K+D+ + + v++e   +l+ke+g + f+e+S  +  nv+++f+ +l++
  gene432|gene432|rna432|rna432  84 VNNILSFHNSKRWIDELAEY---NVPMILCGTKCDIIDGNIVDKELPTKLSKEYGlYGFVECSSVELINVKKVFDVALEA 160
                                    ****************9876...589*****************************999****************999887 PP

                                    H CS
                            Ras 160 i 160
                                    +
  gene432|gene432|rna432|rna432 161 A 161
                                    6 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   2.6e-21   4.6e-18       1     119 [.       5     115 ..       5     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.6e-21
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K vlvGd +vGK+ l++ ++++k  e + +t+  +  +k v+++         kk+++ +WDtaG e++++l++l ++e 
  gene432|gene432|rna432|rna432   5 KCVLVGDPSVGKSWLISTYITGKNPEGYIPTLFNNH-SK-VVNVGD-------KKYNMTLWDTAGSEEYNKLRSLSFQET 75 
                                    889****************************97665.34.333322.......5689*********************** PP

                                    CEEEEEEEGH...HHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  81 alailvydsr...ssenlkeWlkelkkvagkspvilvgnkiD 119
                                    ++++++y  +   s++n k+W++el ++  + p+il+g+k+D
  gene432|gene432|rna432|rna432  76 DVFLICYAVNnilSFHNSKRWIDELAEY--NVPMILCGTKCD 115
                                    *******844234789*********998..58*********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   8.7e-09   1.6e-05       2     113 ..       6     112 ..       5     113 .. 0.56

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.7e-09
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE...ETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk...lkgkeielvDtpGliegaseekglgkaflaleeadl 78 
                                    +++vG p vGKS Li++ +  k   + +p  T+  n+ +v     k+ +++l+Dt+G  e    e +  +++   +e+d+
  gene432|gene432|rna432|rna432   6 CVLVGDPSVGKSWLISTYITGKNPEGYIP--TLFNNHSKVVnvgDKKYNMTLWDTAG-SE----EYNKLRSLS-FQETDV 77 
                                    79**************9987655555555..444444443332244589********.55....333333333.445677 PP

                                    EEEEEETT..TTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                       MMR_HSR1  79 illvvdas..eeklkpldeeleelleeakkplilvln 113
                                    +l++  ++    ++++ ++ + el  e + p+il+ +
  gene432|gene432|rna432|rna432  78 FLICYAVNniL-SFHNSKRWIDEL-AEYNVPMILCGT 112
                                    66666544231.233332222222.234578887755 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.7   3.1e+03       4      22 ..       4      22 ..       2      30 .. 0.79
   2 !   23.4   0.0     2e-08   3.5e-05      58     150 ..      41     130 ..      35     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                                   EEEEEEESTTSSHHHHHHH CS
                       GTP_EFTU  4 rnigiighvDhGKtTLtdr 22
                                   ++++++g+   GK+ L+ +
  gene432|gene432|rna432|rna432  4 IKCVLVGDPSVGKSWLIST 22
                                   67899999999**998865 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 2e-08
                                    CEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBST.HHHHHHHHHHHHTTTEEEEEEESCGSTH CS
                       GTP_EFTU  58 saaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGve.pqteevlrlalkegvpiivfiNKmDrlk 136
                                    s+++++    kky+++l Dt G ++++k  + + + +D+ ++  ++++    +++++ +  + +++vp+i++ +K+D ++
  gene432|gene432|rna432|rna432  41 SKVVNVG--DKKYNMTLWDTAGSEEYNKLRSLSFQETDVFLICYAVNNILSfHNSKRWIDELAEYNVPMILCGTKCDIID 118
                                    5666677..89***************************999888888775427899999******************995 PP

                                    HHHHHHHHHHHHHH CS
                       GTP_EFTU 137 aelkeiveevkqkl 150
                                     ++  + +e+ +kl
  gene432|gene432|rna432|rna432 119 GNI--VDKELPTKL 130
                                    544..233333333 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     3e-08   5.3e-05      14     140 ..       3     130 ..       1     163 [. 0.79

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3e-08
                                    EEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE...TTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEE CS
                            Arf  14 elrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei...knlkftvwDvGGqeklRplWknYfektdavifvv 89 
                                     ++++l+G  + GK+ ++  + +++  +  +PT+  n  ++     k++++t+wD  G e+  +l +  f++td+ + + 
  gene432|gene432|rna432|rna432   3 TIKCVLVGDPSVGKSWLISTYITGKNPEgYIPTLFNNHSKVVNvgdKKYNMTLWDTAGSEEYNKLRSLSFQETDVFLICY 82 
                                    589****************99888776659***96665554433449***************************999998 PP

                                    ETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTST.TSS-HHHHHHHT CS
                            Arf  90 DsadreRleeakeeLkalleeeelkevallvlaNKqDlp.ealseeelrell 140
                                     +++   ++++k+ +++l e     +v++++ + K D+  + + ++el ++l
  gene432|gene432|rna432|rna432  83 AVNNILSFHNSKRWIDELAE----YNVPMILCGTKCDIIdGNIVDKELPTKL 130
                                    88999999999998888865....4688888888888641455556665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00053      0.94       9      40 ..       7      41 ..       5      61 .. 0.76
   2 ?    3.5   0.0     0.043        78     109     131 ..      84     113 ..      62     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00053
                         AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee...erp 40
                                   v++G + +GK++l+ ++   ++ e ++ +   +++
  gene432|gene432|rna432|rna432  7 VLVGDPSVGKSWLISTYITGKNPEGYIPTlfnNHS 41
                                   89***************998865555555555444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.043
                         AAA_22 109 leeLrsllnl.......srkgvqliLvGtp 131
                                    ++++ s++n        ++++v++iL+Gt 
  gene432|gene432|rna432|rna432  84 VNNILSFHNSkrwidelAEYNVPMILCGTK 113
                                    567777777777777899**********97 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.3e-05      0.11      34      71 ..       4      41 ..       1      45 [. 0.88
   2 ?   -2.8   0.0       2.1   3.8e+03      24      41 ..      95     112 ..      91     114 .. 0.83
   3 ?   -2.4   0.0       1.6   2.9e+03     142     161 ..     149     168 ..     143     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsltinfsa 71
                                    +++lvG+  +GK+ +i+++++  ++e y+++ +n ++
  gene432|gene432|rna432|rna432  4 IKCVLVGDPSVGKSWLISTYITGKNPEGYIPTLFNNHS 41
                                   5789**************************99988655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                          AAA_7  24 yllelllknkkpvllvGp 41 
                                     +++ l + + p++l+G+
  gene432|gene432|rna432|rna432  95 RWIDELAEYNVPMILCGT 112
                                    578999999999999997 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.6
                          AAA_7 142 efkeikdvqlvaamgppggg 161
                                    ++k++ dv l aa +p++++
  gene432|gene432|rna432|rna432 149 NVKKVFDVALEAALKPKKSK 168
                                    78899999999999998765 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.055      31      79 ..      66     112 ..      41     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                                    T......-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHH CS
                           DrsE  31 g......hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgq 79 
                                    +      +e  vf+++ +v+++l+ +        n + ++ +l+ey+v++++Cg+
  gene432|gene432|rna432|rna432  66 KlrslsfQETDVFLICYAVNNILSFH--------NSKRWIDELAEYNVPMILCGT 112
                                    04444468999*************44........4677***************96 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.9e-05      0.12       2      57 ..       5      61 ..       4     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.9e-05
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSE.EEEEEEEETTEEEEEEE---- CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtve.kkegklklkgkeveivDlPGi 57
                                   +++lvG+p vGk+ l+ +    k+  g  p    +  k +++  k++++++ D  G 
  gene432|gene432|rna432|rna432  5 KCVLVGDPSVGKSWLISTYITGKNPEGYIPTLFNNhSKVVNVGDKKYNMTLWDTAGS 61
                                   789*************97555555556666554430344445555567777777765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.022        40     102     121 ..       6      25 ..       1      47 [. 0.87
   2 ?    7.4   0.0    0.0022       3.9      15      63 ..      74     121 ..      61     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
                                    EEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallp 121
                                    +vlvG   vGKS Li + + 
  gene432|gene432|rna432|rna432   6 CVLVGDPSVGKSWLISTYIT 25 
                                    69************988665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0022
                                    S--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH CS
                    RsgA_GTPase  15 NvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee 63 
                                      d  li+ +++ + ls +  +r + ++ e +++++++ +K+D+++ + 
  gene432|gene432|rna432|rna432  74 ETDVFLICYAVN-NILSFHNSKRWIDELAEYNVPMILCGTKCDIIDGNI 121
                                    567778888888.999****************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1225.50
//
Query:       gene433|gene433|rna433|rna433  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-09   36.2   3.4     0.0006   19.5   0.3    2.5  2  EF-hand_6   EF-hand domain
    4.2e-09   36.7   0.6    0.00024   21.5   0.0    2.2  2  EF-hand_7   EF-hand domain pair
    5.8e-07   28.6   8.5     0.0033   16.9   0.5    2.9  3  EF-hand_1   EF hand
    0.00076   19.3   3.7       0.19   11.6   0.2    2.8  3  EF-hand_8   EF-hand domain pair
     0.0018   17.7   6.7      0.026   14.0   1.0    2.6  2  EF-hand_5   EF hand
  ------ inclusion threshold ------
       0.91    9.8   3.2         17    5.7   3.1    2.3  1  Dockerin_1  Dockerin type I domain


Domain annotation for each model (and alignments):
>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   1.3e-06     0.004       1      29 [.      23      50 ..      23      52 .. 0.92
   2 !   19.5   0.3     2e-07    0.0006       2      27 ..      93     118 ..      92     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                      EF-hand_6  1 elreaFklfDkdgdGkidaeElrkalrka 29
                                   elreaF+ +D++ d ++d+ +l ++l  +
  gene433|gene433|rna433|rna433 23 ELREAFNFMDVNSDTFVDRGDLESFLA-S 50
                                   79**********************997.5 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2e-07
                      EF-hand_6   2 lreaFklfDkdgdGkidaeElrkalr 27 
                                    +  a k+fD +gdG+id + lr++l 
  gene433|gene433|rna433|rna433  93 IFNALKEFDDNGDGTIDEKVLRAWLM 118
                                    567889*****************997 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     8e-08   0.00024       3      52 ..      23      66 ..      22      71 .. 0.92
   2 !   13.6   0.1   2.3e-05      0.07       2      50 ..      91     133 ..      90     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8e-08
                      EF-hand_7  3 klkeaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellfke 52
                                   +l+eaF+ +D++ d ++d+ +l+++l       + gs++s+ee+ +++ e
  gene433|gene433|rna433|rna433 23 ELREAFNFMDVNSDTFVDRGDLESFLA------SIGSPFSSEEISEMMAE 66
                                   589***********************9......9*******999988876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.3e-05
                      EF-hand_7   2 eklkeaFkelDtdgdgyldkeellrllrkifqgagegsklsdeelellf 50 
                                    ++++ a ke+D +gdg +d+  l+  l       + g+ +  e ++ll+
  gene433|gene433|rna433|rna433  91 KDIFNALKEFDDNGDGTIDEKVLRAWLM------EKGDQMAGEDVDLLL 133
                                    689999****************998766......777777777777665 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   1.5e-06    0.0044       1      28 [.      23      50 ..      23      51 .. 0.94
   2 ?   -2.1   0.1       1.3   3.9e+03      20      27 ..      58      65 ..      56      66 .. 0.66
   3 !   16.9   0.5   1.1e-06    0.0033       2      20 ..      93     111 ..      92     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-06
                                   HHHHHHHHHTTTSSSEEEHHHHHHHHHH CS
                      EF-hand_1  1 elkeiFrefDkDgdGkIdfeEfkellkk 28
                                   el+e+F+ +D++ d ++d+ ++ ++l++
  gene433|gene433|rna433|rna433 23 ELREAFNFMDVNSDTFVDRGDLESFLAS 50
                                   79********************999986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                   HHHHHHHH CS
                      EF-hand_1 20 eEfkellk 27
                                   eE  e+++
  gene433|gene433|rna433|rna433 58 EEISEMMA 65
                                   77777775 PP

  == domain 3  score: 16.9 bits;  conditional E-value: 1.1e-06
                                    HHHHHHHHTTTSSSEEEHH CS
                      EF-hand_1   2 lkeiFrefDkDgdGkIdfe 20 
                                    + ++ +efD +gdG+Id +
  gene433|gene433|rna433|rna433  93 IFNALKEFDDNGDGTIDEK 111
                                    66899************86 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       3.2   9.4e+03      27      36 ..      23      32 ..      23      34 .. 0.75
   2 !    8.2   0.0   0.00075       2.2       4      32 ..      38      64 ..      35      67 .. 0.89
   3 !   11.6   0.2   6.5e-05      0.19      25      45 ..      90     110 ..      76     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.2
                      EF-hand_8 27 evdilfrefD 36
                                   e+++ f+ +D
  gene433|gene433|rna433|rna433 23 ELREAFNFMD 32
                                   6677888888 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00075
                      EF-hand_8  4 kItreelrrilrilglkkglseeevdilf 32
                                    ++r +l ++l+++g +  +s ee+ +++
  gene433|gene433|rna433|rna433 38 FVDRGDLESFLASIGSP--FSSEEISEMM 64
                                   689********999*99..********98 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 6.5e-05
                      EF-hand_8  25 eeevdilfrefDtdgdGkisf 45 
                                    e+++   ++efD +gdG+i+ 
  gene433|gene433|rna433|rna433  90 EKDIFNALKEFDDNGDGTIDE 110
                                    6679999************96 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.5    0.0022       6.6       1      23 [.      24      46 ..      24      48 .. 0.77
   2 !   14.0   1.0   8.7e-06     0.026       2      17 ..      95     109 ..      94     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                                   HHHHHHHH-SS-SSCE-HHHHHH CS
                      EF-hand_5  1 lkdtFqaiDlNgDGkIskeELkt 23
                                   l+++F+ +D+N D ++++  L+ 
  gene433|gene433|rna433|rna433 24 LREAFNFMDVNSDTFVDRGDLES 46
                                   6788********97777766665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.7e-06
                                    HHHHHHH-SS-SSCE- CS
                      EF-hand_5   2 kdtFqaiDlNgDGkIs 17 
                                    ++ ++++D NgDG+I+
  gene433|gene433|rna433|rna433  95 NA-LKEFDDNGDGTID 109
                                    56.89**********9 PP

>> Dockerin_1  Dockerin type I domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.1    0.0058        17       3      46 ..      32     109 ..      30     111 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0058
                                    ETTSSSC-SHHHHHHHHHHCT..................................SSEBTTSCCCHGGGSTT-SSCES CS
                     Dockerin_1   3 DVNgDgkVnalDalliinyln..................................qregqssssngkaaDvNgDGrvn 46 
                                    DVN D  V+  D+      +                                   +++++   +  k +D NgDG+++
  gene433|gene433|rna433|rna433  32 DVNSDTFVDRGDLESFLASIGspfsseeisemmaesgdnmtymlfltmigerlscTDPEKDIFNALKEFDDNGDGTID 109
                                    999999999999987777777666666666666666666666666666666666655555555666666777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 975.68
//
Query:       gene434|gene434|rna434|rna434  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0095   16.0   0.3       0.03   14.4   0.0    1.9  2  TLE_N     Groucho/TLE N-terminal Q-rich domain
  ------ inclusion threshold ------
        3.1    7.6   5.7        5.5    6.8   0.3    3.2  3  IDEAL     IDEAL domain


Domain annotation for each model (and alignments):
>> TLE_N  Groucho/TLE N-terminal Q-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.4e-06      0.03      19      51 ..      80     112 ..      69     129 .. 0.88
   2 ?   -1.6   0.1      0.29   2.6e+03      14      31 ..     191     208 ..     178     210 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-06
                          TLE_N  19 tvlescdrikeefqflqaqyhsLklecekLase 51 
                                      +++c ri + ++fl++++  L++  ekL s+
  gene434|gene434|rna434|rna434  80 LQMDACKRINDSYDFLRKKIGGLRMRSEKLKSK 112
                                    5689**************************985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.29
                          TLE_N  14 qslkftvlescdrikeef 31 
                                     + +  +l+ +d+++e f
  gene434|gene434|rna434|rna434 191 RQKQTVILNELDKVQEPF 208
                                    233344556677776666 PP

>> IDEAL  IDEAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.4     0.086   7.7e+02       9      19 ..       6      16 ..       3      17 .. 0.84
   2 ?    1.1   0.0     0.038   3.4e+02      10      20 ..     105     115 ..     103     118 .. 0.84
   3 ?    6.8   0.3   0.00061       5.5      12      28 ..     178     194 ..     177     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.086
                          IDEAL  9 frrekLlreID 19
                                   ++ ++Ll++ID
  gene434|gene434|rna434|rna434  6 QKDQELLTLID 16
                                   56789*****9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.038
                          IDEAL  10 rrekLlreIDe 20 
                                    r ekL+ +ID 
  gene434|gene434|rna434|rna434 105 RSEKLKSKIDG 115
                                    789*******7 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.00061
                          IDEAL  12 ekLlreIDeALdnrDke 28 
                                    ek+l+e D AL++r k+
  gene434|gene434|rna434|rna434 178 EKILKEVDNALQERQKQ 194
                                    79***********9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1161.65
//
Query:       gene435|gene435|rna435|rna435  [L=450]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-12   46.6   0.0    6.7e-07   29.8   0.0    2.4  2  Ank_2     Ankyrin repeats (3 copies)
    2.9e-10   40.5   1.8    1.3e-07   32.0   0.1    3.7  4  Ank_4     Ankyrin repeats (many copies)
    1.2e-07   31.9   1.3     0.0031   17.9   0.1    4.5  5  Ank       Ankyrin repeat
    2.5e-06   27.4   3.9       0.18   12.4   0.2    5.4  5  Ank_3     Ankyrin repeat
    0.00042   20.5   0.1     0.0081   16.5   0.0    3.0  3  Ank_5     Ankyrin repeats (many copies)


Domain annotation for each model (and alignments):
>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.3e-05     0.048       4      64 ..     110     182 ..     107     189 .. 0.71
   2 !   29.8   0.0   1.9e-10   6.7e-07      19      81 ..     267     337 ..     248     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                          Ank_2   4 AakngnlelvklLl.eg..adpn.k......ngktaLhyAakngnleivklLleh.....adndgrtpLhyAarsg 64 
                                    +akn+ +e+v  +l +g  +++n        +  t  h+A+   + +i++ +l++     +  +g tp ++A+++g
  gene435|gene435|rna435|rna435 110 MAKNN-PEIVYSMLsKGfpNNINaPvfrsqmF-PTYFHLACAMHH-DILSVFLKFspnysLCWNGLTPQMIASFNG 182
                                    56665.89*****9866334444514554444.688999999865.*******97755444488*********987 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.9e-10
                          Ank_2  19 gadpnk..ngktaLhyAakngnleivklLle...h...adndgrtpLhyAarsghleivklLlekgadinl 81 
                                     + +++  ng ++Lh++ ++gn e++ ++++   h    d+ g+tp+hy+a  +h+++++lL+  g ++++
  gene435|gene435|rna435|rna435 267 QTSVHQefNGISPLHVSSISGNFETLVAFIAlgsHinsRDKLGNTPMHYCAMLKHFRCLELLIRLGGNMTM 337
                                    344553589************998866666544456666699*********99**********66767665 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.19     7e+02      11      47 ..     112     152 ..      96     161 .. 0.76
   2 ?   -1.1   0.0       0.9   3.2e+03      15      45 ..     153     181 ..     142     186 .. 0.45
   3 ?    4.1   0.0      0.02        71       5      30 ..     221     246 ..     220     257 .. 0.89
   4 !   32.0   0.1   3.7e-11   1.3e-07       3      55 .]     278     329 ..     276     329 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                          Ank_4  11 sgrlelvrlLlekgad..inaqdnrsGe..talhiAakrgn 47 
                                    +++ e+v + l+kg    ina   rs++  t +h A+ + +
  gene435|gene435|rna435|rna435 112 KNNPEIVYSMLSKGFPnnINAPVFRSQMfpTYFHLACAMHH 152
                                    66777777777777333599988899999999999998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.9
                          Ank_4  15 elvrlLlekgadinaqdnrsGetalhiAakr 45 
                                    +++   l +  ++n+++  +G+t+  iA  +
  gene435|gene435|rna435|rna435 153 DILSVFLKF--SPNYSLCWNGLTPQMIASFN 181
                                    333333322..33343333366665555555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.02
                          Ank_4   5 LhyaaisgrlelvrlLlekgadinaq 30 
                                    ++ +++++++e++r +l++++++ ++
  gene435|gene435|rna435|rna435 221 IDFLCMKSDMESARKILNRNPELSRV 246
                                    7899******************9988 PP

  == domain 4  score: 32.0 bits;  conditional E-value: 3.7e-11
                          Ank_4   3 taLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    ++Lh   isg++e++   ++ g  in + ++ G+t++h++a+  ++++l+lL+
  gene435|gene435|rna435|rna435 278 SPLHVSSISGNFETLVAFIALGSHINSR-DKLGNTPMHYCAMLKHFRCLELLI 329
                                    6899999*********************.***********************8 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.68   2.5e+03      10      18 ..     111     118 ..      75     133 .. 0.38
   2 ?    2.3   0.0     0.072   2.6e+02       7      22 ..     145     159 ..     142     166 .. 0.80
   3 ?   -2.0   0.0       1.6   5.8e+03       1      14 [.     170     183 ..     170     190 .. 0.78
   4 !    6.5   0.0    0.0034        12       1      31 [.     275     306 ..     275     307 .. 0.76
   5 !   17.9   0.1   8.7e-07    0.0031       2      31 ..     309     339 ..     308     340 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.68
                                    HHHTTHHHH CS
                            Ank  10 atngkkrii 18 
                                    a  ++++i+
  gene435|gene435|rna435|rna435 111 A-KNNPEIV 118
                                    2.3445555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.072
                                    HHHHHHTTHHHHHHHH CS
                            Ank   7 HlAatngkkriiklLL 22 
                                    HlA+   +++i++ +L
  gene435|gene435|rna435|rna435 145 HLAC-AMHHDILSVFL 159
                                    **99.78888***999 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.6
                                    TSBBHHHHHHHHTT CS
                            Ank   1 dGnTPLHlAatngk 14 
                                    +G TP ++A+ ngk
  gene435|gene435|rna435|rna435 170 NGLTPQMIASFNGK 183
                                    68899899997775 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0034
                                    TSBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   1 dGnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    +G +PLH+ +  g+ + + +++  G+ +n++d
  gene435|gene435|rna435|rna435 275 NGISPLHVSSISGNFETLVAFIaLGSHINSRD 306
                                    79*****9776677667767885588899988 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 8.7e-07
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    GnTP H++a+ ++ r+++lL+  G n ++++
  gene435|gene435|rna435|rna435 309 GNTPMHYCAMLKHFRCLELLIrLGGNMTMVN 339
                                    9*******************95466877766 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.2     8e+03      11      30 ..     111     129 ..     106     130 .. 0.77
   2 ?    0.7   0.0      0.35   1.2e+03       4      23 ..     142     160 ..     141     166 .. 0.76
   3 !    9.5   0.0   0.00047       1.7       1      30 [.     275     303 ..     275     304 .. 0.89
   4 !   12.4   0.2   5.1e-05      0.18       2      26 ..     309     332 ..     308     334 .. 0.90
   5 ?   -0.5   0.0      0.85   3.1e+03       5      23 ..     393     410 ..     390     418 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.2
                          Ank_3  11 rsgnleivkfLlenkgadvn 30 
                                      +n+eiv  +l  kg + n
  gene435|gene435|rna435|rna435 111 AKNNPEIVYSMLS-KGFPNN 129
                                    5788999999999.787777 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.35
                          Ank_3   4 tpLhlAarsgnleivkfLle 23 
                                    t +hlA+   +   +  +l+
  gene435|gene435|rna435|rna435 142 TYFHLACAMHHDI-LSVFLK 160
                                    779****998875.777776 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00047
                          Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvn 30 
                                    nG +pLh+   sgn+e + +++   g  +n
  gene435|gene435|rna435|rna435 275 NGISPLHVSSISGNFETLVAFIA-LGSHIN 303
                                    799************98999998.888877 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 5.1e-05
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkg 26 
                                    G+tp+h++a+  ++  +++L++  g
  gene435|gene435|rna435|rna435 309 GNTPMHYCAMLKHFRCLELLIR-LG 332
                                    9*************99*****9.66 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.85
                          Ank_3   5 pLhlAarsgnleivkfLle 23 
                                      h+ ++ ++++i   Ll+
  gene435|gene435|rna435|rna435 393 SNHTIVKKNRFTI-TSLLN 410
                                    67999999***95.44444 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.75   2.7e+03       1      25 [.     121     149 ..     121     153 .. 0.77
   2 !   16.5   0.0   2.3e-06    0.0081      12      56 .]     272     316 ..     269     316 .. 0.92
   3 ?   -1.1   0.0      0.71   2.6e+03      28      50 ..     321     344 ..     317     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.75
                          Ank_5   1 Llehg.padvnrldgggn...tpLhvAak 25 
                                    +l++g p+++n++  +++   t +h+A+ 
  gene435|gene435|rna435|rna435 121 MLSKGfPNNINAPVFRSQmfpTYFHLACA 149
                                    67788888888887777778899999985 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.3e-06
                          Ank_5  12 ldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    ++ +g +pLhv++  g+++ +  ++a g+++n +d+ G+t+++++
  gene435|gene435|rna435|rna435 272 QEFNGISPLHVSSISGNFETLVAFIALGSHINSRDKLGNTPMHYC 316
                                    5667779***********************************995 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.71
                          Ank_5  28 aadvvrlLlargadlnltdsrG.l 50 
                                    ++++++lL+  g + ++ + +G +
  gene435|gene435|rna435|rna435 321 HFRCLELLIRLGGNMTMVNREGvS 344
                                    778889999889998888888855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2958.36
//
Query:       gene436|gene436|rna436|rna436  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-19   68.6   0.8    4.9e-19   68.1   0.8    1.3  1  YEATS     YEATS family


Domain annotation for each model (and alignments):
>> YEATS  YEATS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.8   2.7e-23   4.9e-19       1      79 [.      29      99 ..      29     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 2.7e-23
                          YEATS  1 thkWtvavrsaasddlsefikkVqFkLhetyanptrvvekpPFevtetGwGeFeiqikiffkpeaekpltlehdLklhp 79
                                   th+W+ +v+ +      e++kkV+FkLhe+++n     ++ PFev e+GwGeF+iq+ki + +   +++t+ h L+lh 
  gene436|gene436|rna436|rna436 29 THEWKAYVKAPP-----EIVKKVEFKLHESFSNRLV-SKEHPFEVVERGWGEFSIQMKILLFNG--EKITTSHFLQLHG 99
                                   8**********8.....5**************9984.7999******************99977..48*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1142.82
//
Query:       gene437|gene437|rna437|rna437  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-07   30.1  29.8       0.01   16.3   9.9    3.1  3  YtxH            YtxH-like protein
    5.7e-06   26.3  42.5    0.00071   19.6  13.9    4.3  4  LEA_4           Late embryogenesis abundant protein
    0.00032   21.3  12.5      0.079   13.6   3.2    3.0  3  DUF883          Bacterial protein of unknown function (DUF883
    0.00035   20.5   7.0    0.00046   20.1   7.0    1.1  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
     0.0037   17.4   3.7     0.0037   17.4   3.7    2.4  2  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
  ------ inclusion threshold ------
       0.75    9.8  18.2        1.1    9.2   1.1    4.1  3  ApoC-I          Apolipoprotein C-I (ApoC-1)
        2.3    7.7  16.4        2.1    7.8  15.3    1.5  2  PET10           Petite colonies protein 10


Domain annotation for each model (and alignments):
>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   8.8   2.5e-05     0.064      21      75 .]      27      81 ..      26      81 .. 0.95
   2 !   16.3   9.9     4e-06      0.01      27      74 ..      77     124 ..      74     131 .. 0.62
   3 !   11.0   0.4   0.00018      0.47      24      56 ..     130     162 ..     124     169 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                           YtxH 21 ksGketRkdlkekaddlkekakelleeakekakekaedlkekvkekadelkekvk 75
                                   ++G+e++++ k++++++  k+ke ++e+  ++ + a++ ke+ k+ka+el +k+k
  gene437|gene437|rna437|rna437 27 RKGSEMKDKTKNTTSNAMGKTKEKTNETMGRTGDAANETKEQTKNKASELGDKTK 81
                                   79**********************99999999******************99875 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 4e-06
                           YtxH  27 Rkdlkekaddlkekakelleeakekakekaedlkekvkekadelkekv 74 
                                     ++ k++a+d+  k+ke ++e+ke+ak+ka+ + +k keka+ +k+++
  gene437|gene437|rna437|rna437  77 GDKTKDTANDTMGKTKEKTNETKEQAKNKASSMGDKTKEKANNVKSSI 124
                                    455566666666666666666666667777777777777776666654 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00018
                           YtxH  24 ketRkdlkekaddlkekakelleeakekakeka 56 
                                    +e+ + +ke  +++++k+ke++ ++k+  k+ +
  gene437|gene437|rna437|rna437 130 NEVYENIKEGGNKAWNKTKEVASSMKDGLKDLT 162
                                    78999********************66655443 PP

>> LEA_4  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   7.1   0.00017      0.44       6      43 ..      27      64 ..      22      65 .. 0.93
   2 !   19.6  13.9   2.8e-07   0.00071       1      43 [.      66     108 ..      66     109 .. 0.96
   3 !   14.7   4.1   9.3e-06     0.024       1      23 [.      99     121 ..      99     127 .. 0.90
   4 ?    2.9   0.4     0.046   1.2e+02       1      23 [.     129     151 ..     129     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                          LEA_4  6 eKakeaKDataeKageyKDyAaeKAgeaKDkaaekage 43
                                   +K  e+KD+t++ + ++   ++eK+ e+ + + ++a e
  gene437|gene437|rna437|rna437 27 RKGSEMKDKTKNTTSNAMGKTKEKTNETMGRTGDAANE 64
                                   6999******************************9988 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.8e-07
                          LEA_4   1 kdyaaeKakeaKDataeKageyKDyAaeKAgeaKDkaaekage 43 
                                    k+ +++Ka e  D+t++ a ++   ++eK+ e+K+ a +ka+ 
  gene437|gene437|rna437|rna437  66 KEQTKNKASELGDKTKDTANDTMGKTKEKTNETKEQAKNKASS 108
                                    899*************************************975 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 9.3e-06
                          LEA_4   1 kdyaaeKakeaKDataeKageyK 23 
                                    k+ a++Ka  + D+t+eKa ++K
  gene437|gene437|rna437|rna437  99 KEQAKNKASSMGDKTKEKANNVK 121
                                    799****************9999 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.046
                          LEA_4   1 kdyaaeKakeaKDataeKageyK 23 
                                    k++ +e +ke   ++ +K++e++
  gene437|gene437|rna437|rna437 129 KNEVYENIKEGGNKAWNKTKEVA 151
                                    67889999999999999999975 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   3.2   3.1e-05     0.079      12      70 ..      27      85 ..      20      87 .. 0.92
   2 !   12.5   6.8   6.9e-05      0.18      15      67 ..      63     115 ..      61     129 .. 0.66
   3 ?    4.9   0.1     0.016        41      22      57 ..     126     161 ..     115     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                         DUF883 12 adleellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaaddyVr 70
                                    +  e+ +++++++ + + + +e+ +e++ r+ +++++++e+ +++a+e  ++++d + 
  gene437|gene437|rna437|rna437 27 RKGSEMKDKTKNTTSNAMGKTKEKTNETMGRTGDAANETKEQTKNKASELGDKTKDTAN 85
                                   56789999**********************************************99876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.9e-05
                         DUF883  15 eellkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                    +e  ++++++a e  ++ ++ +++++ +++e++++++e+++++a+++ +++++
  gene437|gene437|rna437|rna437  63 NETKEQTKNKASELGDKTKDTANDTMGKTKEKTNETKEQAKNKASSMGDKTKE 115
                                    45566666666666677777777777777777777777777777777666665 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.016
                         DUF883  22 adeageeaeelRerleerlerarerlrdaeeavaer 57 
                                    +++ +e +e+++e  +++ ++++e ++ +++ +++ 
  gene437|gene437|rna437|rna437 126 NKDKNEVYENIKEGGNKAWNKTKEVASSMKDGLKDL 161
                                    56778889999**99999999999999999887765 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   7.0   1.8e-07   0.00046      45     176 ..      28     160 ..      23     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.8e-07
                                    HHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHH CS
                 Apolipoprotein  45 eleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyve 124
                                    + +e +++ ++ ++++  + ++++ e   r   +++e +e+ + +a el ++ +  a++   ++++++ ++k++ +  + 
  gene437|gene437|rna437|rna437  28 KGSEMKDKTKNTTSNAMGKTKEKTNETMGRTGDAANETKEQTKNKASELGDKTKDTANDTMGKTKEKTNETKEQAKNKAS 107
                                    55788899999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    HHHHHHHHHHHHHHH-----...-----SSSHHHHHHHTS-TTSHHHHHS--X CS
                 Apolipoprotein 125 elrqklaerleelkeslaphae.eveerlssrveelrekleeqaeelrerlea 176
                                    ++ +k +e++ ++k+s++++ + ev e++ +  + +  k +e a+ +++ l  
  gene437|gene437|rna437|rna437 108 SMGDKTKEKANNVKSSIDNKDKnEVYENIKEGGNKAWNKTKEVASSMKDGLKD 160
                                    99999999999999999999655888999999999999999999999888765 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  10.7     0.065   1.7e+02      26      91 ..      31     101 ..      17     109 .. 0.64
   2 !   17.4   3.7   1.5e-06    0.0037       3      54 ..     112     163 ..     110     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.065
                      ApoLp-III  26 tiKensenlvdql.kqvikslqeelkkksdeleealkevkkkieetadklse....enPevkkkaqelqek 91 
                                    ++K++++n  +++  ++ ++++e + ++ d+++e+ +++k+k +e  dk +         +k+k +e++e+
  gene437|gene437|rna437|rna437  31 EMKDKTKNTTSNAmGKTKEKTNETMGRTGDAANETKEQTKNKASELGDKTKDtandTMGKTKEKTNETKEQ 101
                                    56666666665541456667777777777777777777777777766665554333455556666665554 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.5e-06
                      ApoLp-III   3 aieelqksvkkqlnlpsqeevvetiKensenlvdqlkqvikslqeelkkksd 54 
                                    +++e +++vk ++  ++++ev e iKe+ +++ ++ k+v++s+++ lk+ ++
  gene437|gene437|rna437|rna437 112 KTKEKANNVKSSIDNKDKNEVYENIKEGGNKAWNKTKEVASSMKDGLKDLTN 163
                                    6889999******9**********************************9554 PP

>> ApoC-I  Apolipoprotein C-I (ApoC-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.9    0.0016       4.1      34      60 ..      28      54 ..      25      55 .. 0.92
   2 ?    9.2   1.1   0.00043       1.1      34      60 ..      72      98 ..      59      99 .. 0.86
   3 ?    1.1   2.7      0.14   3.7e+02      19      39 ..     106     125 ..      96     160 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0016
                                   CTTSSSSCCHHHHHHHHHHHHHHSSSX CS
                         ApoC-I 34 kqSelpaktrnWfsetfekvkeklket 60
                                   k Se+  kt+n  s+++ k kek +et
  gene437|gene437|rna437|rna437 28 KGSEMKDKTKNTTSNAMGKTKEKTNET 54
                                   679********************9887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00043
                                   CTTSSSSCCHHHHHHHHHHHHHHSSSX CS
                         ApoC-I 34 kqSelpaktrnWfsetfekvkeklket 60
                                   k Sel  kt++  ++t+ k kek +et
  gene437|gene437|rna437|rna437 72 KASELGDKTKDTANDTMGKTKEKTNET 98
                                   78*********************9877 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                                    HHHHHHHHCCHCCCHCTTSSS CS
                         ApoC-I  19 gktledKaraaieeIkqSelp 39 
                                    ++ + dK+++  +++k S + 
  gene437|gene437|rna437|rna437 106 ASSMGDKTKEKANNVKSS-ID 125
                                    555566666666666543.33 PP

>> PET10  Petite colonies protein 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.9      0.22   5.5e+02     176     210 ..      21      55 ..       4      71 .. 0.67
   2 ?    7.8  15.3   0.00083       2.1     134     240 ..      53     163 ..      35     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.22
                          PET10 176 kdkalekydslvkPtadklqseyvdptkekinetY 210
                                    +dk +e+  s +k  +++  s+ + +tkek net 
  gene437|gene437|rna437|rna437  21 NDKSYERKGSEMKDKTKNTTSNAMGKTKEKTNETM 55 
                                    55555555566666666666777777777777765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00083
                          PET10 134 e.....aktskktesknLPhvkeLsstTkslskdlqskvksdyieptkdkalekydslvkPtadklqseyvdptkekine 208
                                    e      + +++t++++  + +eL + Tk   +d   k  ++  ++tk++a++k  s+ + t++k+++      ++  ne
  gene437|gene437|rna437|rna437  53 EtmgrtGDAANETKEQTKNKASELGDKTKDTANDTMGKT-KEKTNETKEQAKNKASSMGDKTKEKANNVKSSIDNKDKNE 131
                                    123333456667777777899*****************6.77789**********************988888889999* PP

                          PET10 209 tYktvsetYesnLnksesvprAivsTgvdlgn 240
                                    +Y+ + e  ++  nk++ v+  + +   dl n
  gene437|gene437|rna437|rna437 132 VYENIKEGGNKAWNKTKEVASSMKDGLKDLTN 163
                                    *******************9988777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3130  (0.174578); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.91u 0.39s 00:00:01.30 Elapsed: 00:00:00.56
# Mc/sec: 909.61
//
Query:       gene438|gene438|rna438|rna438  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 703.44
//
Query:       gene439|gene439|rna439|rna439  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 595.44
//
Query:       gene44|gene44|rna44|rna44  [L=530]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-20   70.9   0.0    1.3e-08   34.6   0.0    2.5  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
      2e-10   41.2   0.1    7.4e-10   39.4   0.0    2.1  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.2e-10   38.7   0.0    2.2e-09   37.3   0.0    1.7  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
    0.00052   20.2   0.0      0.001   19.2   0.0    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   2.9e-12   1.3e-08      92     120 ..      54      82 ..      29      95 .. 0.84
   2 !   33.7   0.0   5.5e-12   2.5e-08      39      95 ..     121     177 ..     102     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.9e-12
                                CEEEEE--TTS-TTCCCEEEEETTTCE-- CS
                  PGM_PMM_I  92 dagimitaSHnppeyngiKvylsnGgpis 120
                                  g+mitaSHnp eyngiK++++nG  ++
  gene44|gene44|rna44|rna44  54 IVGVMITASHNPIEYNGIKIIDHNGDMLD 82 
                                579*********************97765 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 5.5e-12
                                TS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEE CS
                  PGM_PMM_I  39 kkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagi 95 
                                 ++ vv+GrD+R s++el +++ ++l + ++ v ++g+++tP+++f++rk ++++ +
  gene44|gene44|rna44|rna44 121 VRGHVVLGRDARDSGEELCNNIKSVLSKLNCVVDDYGVVTTPELHFLVRKCNVENKV 177
                                5789**********************************************9998766 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.7e-13   7.4e-10       1     103 []     181     291 ..     181     291 .. 0.92
   2 ?   -4.0   0.0         4   1.8e+04      23      33 ..     511     521 ..     505     522 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.7e-13
                                .HHHHHGGGTS-.HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-........EEEE.S-----TT-TT.SS----TT-TTTT CS
                 PGM_PMM_II   1 eaYiealkekvd.seaikksglkvvidplhGaggeilkellkelgv........dvve.lnaepdpdfpt.kapnpeekealkl 73 
                                e+Y+++++ ++     ++k +lk++id+++G++g+ +k l ++l+         d++  ln ++ +df++ k   p+  e++++
  gene44|gene44|rna44|rna44 181 EEYLKNIARNFTkLLSLTKGNLKMMIDTANGVAGMKIKNLDEMLEGklnceilnDPKGiLNLDCGADFVKtKKRAPKL-EVFDS 263
                                58**********977888999********************999988999********************86666666.78999 PP

                                HHHHGGGGG-SEEEEE-TTS-BEEEEETTE CS
                 PGM_PMM_II  74 lielvkkegadlglafDgDaDRlgvvderG 103
                                    +++  + ++++fDgD+DRl+++++ G
  gene44|gene44|rna44|rna44 264 G--RFSRPPNGICASFDGDVDRLIFFTGPG 291
                                9..99*********************9876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4
                                EEEE-TT-TTH CS
                 PGM_PMM_II  23 vvidplhGagg 33 
                                 v+d + G+g+
  gene44|gene44|rna44|rna44 511 HVYDMCSGVGD 521
                                58999***997 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0     5e-13   2.2e-09      23      71 ..     464     510 ..     438     512 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 5e-13
                                HHCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHH CS
                 PGM_PMM_IV  23 asikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevae 71 
                                ++++++ + l   Gr++ vRpSGTe+++rvy+E ++++ ++ l  +va 
  gene44|gene44|rna44|rna44 464 QDRIDV-EALSLGGRSF-VRPSGTEDVVRVYAECSTEADADLLCLKVAQ 510
                                255555.778889****.*****************99999888877765 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.3e-07     0.001       6      76 ..     305     376 ..     297     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.3e-07
                                HHHHHHHHHCH.CSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEE CS
                PGM_PMM_III   6 lallakyllee.klkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiif 76 
                                l l ++ lle+   k + gvv +  +++a  +++ +   k+v++++G k+++   ++ ++ + +E +gh+++
  gene44|gene44|rna44|rna44 305 LGLYIRSLLEKiGSKLSIGVVLSYYSNNAAVDALPSSSFKVVMAQTGVKNFVSPARKFDVGIYFEPNGHGSV 376
                                3455555566554444468**************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3179.27
//
Query:       gene441|gene441|rna440|rna440  [L=138]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-18   64.7   0.0    8.9e-18   64.3   0.0    1.1  1  GTP_cyclohydroI  GTP cyclohydrolase I


Domain annotation for each model (and alignments):
>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0     5e-22   8.9e-18      20     111 ..      45     138 .]      36     138 .] 0.87

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 5e-22
                                    TTTTHHHHHHHHH.HHHTGG.GGS-G.GGGGSSEEETT--S-EEEEEEEEEEEETTT--EEEEEEEEEEE-..TTEEE-H CS
                GTP_cyclohydroI  20 glketpkRvakay.eelfkg.leedpkekvlkkvfeeekdemvlvkdiefsSlCeHHllpfigkahvaYiP..kkkviGl 95 
                                    ++ +tp Rv + + +++ ++ ++  p+ ++++++    + ++++   i+++S+C+HH  pf+g+a +aYiP  +++ +Gl
  gene441|gene441|rna440|rna440  45 HTVDTPLRVSRLWvSDIAASfYAPPPRITTFDNTRG--YGDLLFRGPIPIKSICSHHHSPFVGEAYIAYIPqrEGRTVGL 122
                                    6789*********88888883555557777777776..*********************************7669***** PP

                                    HHHHHHHHHHHSSEE- CS
                GTP_cyclohydroI  96 SklaRivdvvarrlqv 111
                                    S+l+Ri+++++r +q+
  gene441|gene441|rna440|rna440 123 SNLNRIAKFYSRMPQL 138
                                    *************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 892.62
//
Query:       gene442|gene442|rna441|rna441  [L=561]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-09   37.4   0.0      6e-09   35.6   0.0    1.9  2  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
       0.03   14.2   0.1      0.066   13.1   0.1    1.5  1  GCV_T_C       Glycine cleavage T-protein C-terminal barrel do
        0.2   11.1   0.0        8.5    5.7   0.0    2.3  2  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.49   2.9e+03      97     118 ..     342     363 ..     336     364 .. 0.78
   2 !   35.6   0.0     1e-12     6e-09      14     114 ..     376     481 ..     368     495 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.49
                                    ESSSHHHHHHHHHHHCC-BSEE CS
                   Pribosyltran  97 ldtGgTllaalelLkekgpeev 118
                                    l+ G++++++ +lL + + +++
  gene442|gene442|rna441|rna441 342 LKGGTSVEYVKKLLNSTKSKSI 363
                                    567888999999**99999887 PP

  == domain 2  score: 35.6 bits;  conditional E-value: 1e-12
                                    EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS......TT-EE-EEEEEE-TTT--EE........EE----TT CS
                   Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeL......evplayvrkvkyrpdgseeaargssdesrlledpag 87 
                                    +  +la++i++e ++ pdv+    rgG  +++ ++ ++      ++ +a+v++ +y + g ++ ++ +   ++++ +++g
  gene442|gene442|rna441|rna441 376 NGIKLAHRIYKE-GFIPDVIYVAVRGGTYLGNVISGYFnavcgrKILYAVVSAHSYTDIGENGNIQINGWTHHPSNLKEG 454
                                    5679999*****.999************************9999999***********99999999888888******** PP

                                    SEEEEE-SEESSSHHHHHHHHHHHCC- CS
                   Pribosyltran  88 kkVliVDDildtGgTllaalelLkekg 114
                                    +kVl+VDDi d+G+T++   e++ ++g
  gene442|gene442|rna441|rna441 455 EKVLLVDDIFDSGKTINCLSEIILNEG 481
                                    ****************98888666665 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.1e-05     0.066      22      66 ..     398     443 ..     388     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                        GCV_T_C  22 lrdgevvGhvTSgaysptlgksialAyvk.aelaklgtevevevrg 66 
                                    +r+g+ +G v Sg++ + +g+ i +A+v+   + ++g++ ++++ g
  gene442|gene442|rna441|rna441 398 VRGGTYLGNVISGYFNAVCGRKILYAVVSaHSYTDIGENGNIQING 443
                                    579999***********************77789999999999987 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.012        70      78     146 ..     285     356 ..     280     371 .. 0.68
   2 ?    5.7   0.0    0.0014       8.5     116     154 ..     448     487 ..     430     491 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.012
                        UPRTase  78 GegmeealrellpearvghlglqreeetlepveyynkLPkki....aertvlllDpviaTGgsaaaaiqlLke 146
                                    G gm+  l +++ +++v+h+ l+ree  l     + k  ++     ++    ++D +   Gg+ ++ +++L++
  gene442|gene442|rna441|rna441 285 GVGMVVRLANICGDVNVYHV-LKREEVRLGVADDLWKSRHEGgkmiEDMMKNVVDNMSLKGGTSVEYVKKLLN 356
                                    899*****************.7888877554333333332221122444466777777777777777777776 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0014
                        UPRTase 116 Pkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekI 154
                                    P+++ + ++vll+D +  +G+++    ++++++g++ ++ 
  gene442|gene442|rna441|rna441 448 PSNLkEGEKVLLVDDIFDSGKTINCLSEIILNEGIPRSDL 487
                                    667767789***********************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3384.20
//
Query:       gene443|gene443|rna442|rna442  [L=492]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-13   49.4   3.1    2.4e-12   46.8   2.6    2.8  2  DnaJ        DnaJ domain
    1.9e-06   28.3   0.0      0.047   14.2   0.0    3.4  3  TPR_19      Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.048   13.9   2.6         10    6.6   0.0    4.4  4  PPR         PPR repeat
        0.1   12.2   0.0       0.53    9.9   0.0    2.0  2  HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
       0.11   12.4   0.0       0.66    9.9   0.0    2.2  3  Wzy_C_2     Virulence factor membrane-bound polymerase, C-ter


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.96   3.4e+03      35      56 ..     104     125 ..     103     129 .. 0.75
   2 !   46.8   2.6   6.8e-16   2.4e-12       2      63 .]     375     440 ..     374     440 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.96
                                    CHHHHHHHHHHHHHHHHHHTSH CS
                           DnaJ  35 kdpeaeekFkeineAyevLsdp 56 
                                    kdpe +ek k+ ne  ++L  +
  gene443|gene443|rna442|rna442 104 KDPEMKEKVKRANECLSILVSN 125
                                    5778888888888888888665 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 6.8e-16
                                    HHHHHTSSTTG..-HHHHHHHHHHHHHHHSTT.TSCCHH.HHHHHHHHHHHHHHHHTSHHHHHHHH CS
                           DnaJ   2 yYeiLgvskda..sedeIkkaYrklalkyHPD.knpkdp.eaeekFkeineAyevLsdpekRkqYD 63 
                                    yY+ Lg ++    +e+eIkkaYrkl+++     knp+++ e ee+Fk++n+A+ vL d++kR++YD
  gene443|gene443|rna442|rna442 375 YYKTLGFKEGErpDEKEIKKAYRKLVVENKKKkKNPQEEkEWEENFKKLNKAFGVLRDKKKREMYD 440
                                    9********96347888***********9887555555569999*********************9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.3e-05     0.047       3      43 ..      57      97 ..      55     108 .. 0.94
   2 ?    4.0   0.0      0.02        70      21      59 ..     137     175 ..     127     205 .. 0.67
   3 !    6.0   0.0    0.0047        17      22      46 ..     289     313 ..     280     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                         TPR_19  3 aegdyaeAlalleqalqedpknaearllLAeallalgqlde 43
                                   ++gd+  A ++++++ q+  +n+  r  +Ae l+a g++ e
  gene443|gene443|rna442|rna442 57 KNGDLLKAESIYKEISQYFRDNDVFRKKYAEFLMAKGEYGE 97
                                   79************************************965 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.02
                         TPR_19  21 dpknaearllLAeallalgqldeAealLdalpeedpdda 59 
                                    +p +  ++ ++++++l    l+eAe+ +++    +p+++
  gene443|gene443|rna442|rna442 137 SPYSKLVLEAYIQVCLVDEKLEEAEKFVKKSRSLFPNEP 175
                                    554444444667777777777777777777666666643 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0047
                         TPR_19  22 pknaearllLAeallalgqldeAea 46 
                                     +n++  +l++ al+  g+++eAe+
  gene443|gene443|rna442|rna442 289 RNNEDTMYLYIMALILDGNIKEAEE 313
                                    5899*******************97 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0028        10      11      26 ..      56      71 ..      53      74 .. 0.90
   2 ?    1.8   0.0     0.097   3.5e+02       7      25 ..     148     166 ..     146     170 .. 0.85
   3 ?    2.1   0.1     0.078   2.8e+02       7      27 ..     299     319 ..     297     323 .. 0.84
   4 ?   -3.6   0.0         5   1.8e+04      15      28 ..     422     435 ..     421     437 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0028
                            PPR 11 cknGkleeAlelfkeM 26
                                   +knG+l +A++++ke+
  gene443|gene443|rna442|rna442 56 VKNGDLLKAESIYKEI 71
                                   69************97 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.097
                            PPR   7 IsgycknGkleeAlelfke 25 
                                    I+++    kleeA+++ k+
  gene443|gene443|rna442|rna442 148 IQVCLVDEKLEEAEKFVKK 166
                                    78899999*******9887 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.078
                            PPR   7 IsgycknGkleeAlelfkeMk 27 
                                    I+++   G+++eA+e f+  k
  gene443|gene443|rna442|rna442 299 IMALILDGNIKEAEEKFNLFK 319
                                    7888999********998765 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 5
                            PPR  15 kleeAlelfkeMke 28 
                                    kl +A+ ++++ k+
  gene443|gene443|rna442|rna442 422 KLNKAFGVLRDKKK 435
                                    67899999987655 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.32   1.1e+03      48      73 ..      48      73 ..      45      93 .. 0.75
   2 ?    9.9   0.0   0.00015      0.53      18      82 ..     148     212 ..     135     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                     HrpB1_HrpK 48 dllegvlliergrweeAlrlLrevea 73
                                   +++ + + +++g++  A  + +e+++
  gene443|gene443|rna442|rna442 48 EVFKADISVKNGDLLKAESIYKEISQ 73
                                   6889999***********99999984 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00015
                     HrpB1_HrpK  18 lslalasedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyak 82 
                                    + + l +e+ e+ae+ ++  r L P+ + ++  e +l+  rg ++ ++++L+++e ++    +a+
  gene443|gene443|rna442|rna442 148 IQVCLVDEKLEEAEKFVKKSRSLFPNEPGFAHQEMQLYFLRGMFSPGIKALNSLEYKEMASSFAS 212
                                    4567899************************************************8777766666 PP

>> Wzy_C_2  Virulence factor membrane-bound polymerase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.43   1.5e+03     155     183 ..      57      85 ..      52      87 .. 0.83
   2 ?    9.9   0.0   0.00018      0.66     132     181 ..     129     179 ..     122     184 .. 0.84
   3 ?   -3.9   0.0       3.1   1.1e+04     146     163 ..     295     312 ..     292     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.43
                        Wzy_C_2 155 llGdedeAeqilararalfpeedakwvql 183
                                     +Gd  +Ae i+++   +f ++d  ++++
  gene443|gene443|rna442|rna442  57 KNGDLLKAESIYKEISQYFRDNDVFRKKY 85 
                                    689999*************9998766555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00018
                        Wzy_C_2 132 larklihlsPepa.vierlilslallGdedeAeqilararalfpeedakwv 181
                                    l   li+ sP+ + v+e +i+   +  + +eAe+ +++ r lfp+e   ++
  gene443|gene443|rna442|rna442 129 LIATLIKESPYSKlVLEAYIQVCLVDEKLEEAEKFVKKSRSLFPNEPGFAH 179
                                    556789999*97637899***************************987764 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.1
                        Wzy_C_2 146 ierlilslallGdedeAe 163
                                    ++ +i++l l G  +eAe
  gene443|gene443|rna442|rna442 295 MYLYIMALILDGNIKEAE 312
                                    678999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1745  (0.0973284); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 2695.47
//
Query:       gene444|gene444|rna443|rna443  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-08   34.5   3.6    1.6e-08   34.2   3.6    1.1  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
       0.18   10.5   0.2       0.24   10.1   0.2    1.1  1  p450           Cytochrome P450


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   3.6   1.8e-12   1.6e-08      12      51 ..      27      63 ..      20      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.8e-12
                                   CTTT---SSS--SSSEE-GGG-EHHHHHHHTTT...TT-E CS
                  Ribosomal_S14 12 trirnrCrvtGrprGvirkfgLsRicfRelAlkgelpGvk 51
                                   +++++ C+ +   rG+irk  ++R cfRe+A++   +G++
  gene444|gene444|rna443|rna443 27 GKGSRSCVSCYTFRGIIRKLMMCRRCFREYASD---IGFT 63
                                   789******************************...9986 PP

>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   2.7e-05      0.24     391     413 ..      13      34 ..      10      34 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 2.7e-05
                                    TTSCTESSCTT--TTEEGGGS-T CS
                           p450 391 ekgnskrksfaflPFGaGpRnCi 413
                                    +++  ++++   +PFG G R+C+
  gene444|gene444|rna443|rna443  13 KNE-RSGPHSHRMPFGKGSRSCV 34 
                                    444.45899999**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 422.14
//
Query:       gene445|gene445|rna444|rna444  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.33   10.0   1.0       0.48    9.5   1.0    1.3  1  Tmemb_55A  Transmembrane protein 55A
       0.51   10.2   5.7        0.2   11.6   2.5    1.8  2  DUF1275    Protein of unknown function (DUF1275)


Domain annotation for each model (and alignments):
>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.0   5.4e-05      0.48     189     246 .]      87     144 ..      75     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 5.4e-05
                      Tmemb_55A 189 llllllglillviaigltlgtlkqakkykgiyvsyvllillalvllaraiyyltlkvs 246
                                     +l + + i+ vi+ g +l tlk+ +k   +++++ +++ ++ vl+ + ++  ++kvs
  gene445|gene445|rna444|rna444  87 RILWISTAIFPVIGRGFMLITLKNNNKPFHLVIAWLMALEMSGVLMQKLLFNKRMKVS 144
                                    3455778899***********************************************8 PP

>> DUF1275  Protein of unknown function (DUF1275)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.5   2.2e-05       0.2      44     111 ..      60     128 ..      44     145 .. 0.70
   2 ?   -0.7   0.1      0.13   1.2e+03     157     186 ..     149     178 ..     130     185 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                        DUF1275  44 akaalaalvsllaFvlGaalagllarrggrrrrlvllleallllaaallvpagsvsp.....lalallafamG 111
                                    +k+a  + +sl+++++G+++++++     + r l++ + +  ++  ++++ ++++++     ++  l+a+ m+
  gene445|gene445|rna444|rna444  60 YKQAELSRMSLISYFIGIIIFSIFS----QMRILWISTAIFPVIGRGFMLITLKNNNkpfhlVIAWLMALEMS 128
                                    377778889***************5....67777887778888888888776665557677555555555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                        DUF1275 157 aiilafllGavvGallvks.aaalwlaaall 186
                                    + i++++lG  +G  l++   ++++l++ l+
  gene445|gene445|rna444|rna444 149 GEIFILILGLGLGR-LYRLpDYTMMLVVFLV 178
                                    45666777777776.4555544444433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1405.99
//
Query:       gene446|gene446|rna445|rna445  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-31  106.6   1.2    1.3e-30  106.0   1.2    1.2  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   1.2   7.2e-35   1.3e-30      17     149 .]     100     241 .]      88     241 .] 0.95

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 7.2e-35
                                    STTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE- CS
                   Ribosomal_S7  17 kynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevr 92 
                                    k++ ++ e+++  lm+    +Gkk lA +i+++a  ii++ tkk+pl+vl++A+ n+ Pr+++ ++   G++ + +v+v+
  gene446|gene446|rna445|rna445 100 KARIPIAERFVCSLMRhgrnNGKKRLAINIFEDACFIIHSMTKKNPLQVLVDAIINSGPREDTARIGRAGSMRRTSVDVS 179
                                    577899**********9999************************************************************ PP

                                    HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                   Ribosomal_S7  93 pkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                    p +r ++A+ ++ ++    ++r+  ++ae++a+El++A+ g+  ++av+k++e++r+A++nr
  gene446|gene446|rna445|rna445 180 PLKRISIAIANLSTGIrsaSFRNRITLAEAIANELMAASTGSqnSYAVNKKKEIERIAQSNR 241
                                    ************8887666899999***************9999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1439.32
//
Query:       gene447|gene447|rna446|rna446  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 659.43
//
Query:       gene448|gene448|rna447|rna447  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.063   13.0   0.6       0.14   11.9   0.6    1.5  1  Oxidored-like  Oxidoreductase-like protein, N-terminal
      0.091   13.0   1.3       0.22   11.8   1.3    1.6  1  Ribosomal_L36  Ribosomal protein L36


Domain annotation for each model (and alignments):
>> Oxidored-like  Oxidoreductase-like protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   1.5e-05      0.14      15      24 ..      98     107 ..      95     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.5e-05
                  Oxidored-like  15 dnCCmSGCvn 24 
                                    d+CCm GCv 
  gene448|gene448|rna447|rna447  98 DECCMFGCVT 107
                                    8*******96 PP

>> Ribosomal_L36  Ribosomal protein L36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.3   2.4e-05      0.22      15      29 ..     108     122 ..      93     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                  Ribosomal_L36  15 kvvrRkgrvyviCkk 29 
                                     v+r+k ++yviC++
  gene448|gene448|rna447|rna447 108 EVIRKKDSIYVICSS 122
                                    358999*******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 879.83
//
Query:       gene450|gene450|rna449|rna449  [L=325]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-24   85.5   3.5    2.8e-20   72.8   3.5    3.0  1  ERO1      Endoplasmic Reticulum Oxidoreductin 1 (ERO1)


Domain annotation for each model (and alignments):
>> ERO1  Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   3.5   1.5e-24   2.8e-20      88     352 ..      51     272 ..      14     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 1.5e-24
                           ERO1  88 d.............yceledeeeeeavyvdLlenperfTgYk.GesaervWkaiYeencfkeeseseeseekeleelcle 153
                                    d              c +++++  + +y++Lle  e +Tg+k G+ ++++W+ i+e                     + e
  gene450|gene450|rna449|rna449  51 DlgefhskskctllSCLITKKSIFNEEYINLLEIREAYTGFKtGDGSAEIWRRIWE--------------------ISNE 110
                                    22222222334444778888888899***************758999*******94....................2457 PP

                           ERO1 154 krvfyrliSGlhasisihlaaeylnqetgewepnlelfkervgkhperlenlYfnyalvlrAvaklapyleelefstgee 233
                                      ++  l+SGl+ si +hl+a +++   g++ pn +lf++r+++++ rl n Y++y+lv   v  ++       ++  e+
  gene450|gene450|rna449|rna449 111 DPLLPILVSGLQFSILTHLSAFHKK-FFGTYLPNPTLFQKRFQDKH-RL-NFYLTYLLVRNCVGNIT-------ID--EQ 178
                                    78999***************99888.5789************8765.55.9*******988776553.......22..23 PP

                           ERO1 234 eedeetkellkeelakellsalsskekafdesklfkdkeeaeelkeefrerfrnisrimdCVgCekCrLwGKlqttGlgt 313
                                    e de  ++          ++++     +f+ s+ +   +++ +l++ + +r++++ r++  ++CekC+LwG +q++Gl  
  gene450|gene450|rna449|rna449 179 EMDEGLSAV---------IQTI-----KFQGSTNWV--TQSVDLEKTI-QRVEEMARLLKHISCEKCQLWGTIQLKGLRA 241
                                    444433333.........3322.....588888888..5677777766.6899*************************** PP

                           ERO1 314 AlkilfeeeekeeekklkLernevvALintlerlseSie 352
                                    Al+++  ++        +Ler e   Lin + rls S++
  gene450|gene450|rna449|rna449 242 ALRVFSGST--------NLERLERFFLINLFMRLSVSVK 272
                                    ***987773........599*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 1770.92
//
Query:       gene45|gene45|rna45|rna45  [L=414]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-49  167.5   0.4    5.4e-49  167.1   0.4    1.2  1  Tfb2          Transcription factor Tfb2
    3.2e-21   75.5   0.1    7.5e-21   74.3   0.1    1.7  1  Tfb2_C        Transcription factor Tfb2 (p52) C-terminal doma
     0.0034   17.5   0.0     0.0063   16.7   0.0    1.5  1  Helicase_C_3  Helicase conserved C-terminal domain


Domain annotation for each model (and alignments):
>> Tfb2  Transcription factor Tfb2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.1   0.4     9e-53   5.4e-49       1     353 [.      17     333 ..      17     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 9e-53
                       Tfb2   1 eyleklpettlerLYkspatclaifrlLpslakqlvmrllylekpvplsdlekwvkkeskkekeealkkLkelhilkekklkek 84 
                                ey+  lp++   +LY  p  +++ ++  ++ +  +++ ll+++++++          +  +  +e+l++L +++++++k     
  gene45|gene45|rna45|rna45  17 EYFGMLPDHSKAQLYGAPIFAVSFLKIFDEKTTRFIFDLLLMSHSISS--------LRDIEGIKETLRTLLKIQMIEKK----- 87 
                                6888999************************************55543........2334567899**********554..... PP

                       Tfb2  85 kqelklnptFkkslrkaltgggeeksfgvpseeedkekvdvefLdkyakekWesilhflvgseeeeepskevlelLkasglvee 168
                                ++++ l++ F++sl++ ++  + ek+ +  s+      + +e  ++ ++ k+e+il  +v+ e +     ++ e+L  +gl+++
  gene45|gene45|rna45|rna45  88 GDNIYLDASFRRSLMEGFCILKMEKHYK--ST-----GKGLEIDENESNGKFEAILRSIVNREYR-IQAFGIGEVLMFGGLLRK 163
                                579******************9777777..21.....2334445788999***********9887.34669***********55 PP

                       Tfb2 169 keskkslkItseGFqFlLqdinaQiwtlllqylkaleergmdlvevlsflfqLsslelgkaYsvealsetqkemledLrdlGLv 252
                                ++     +It++GF+FlL++ ++Q+w l+l  lk+  ++  ++  +l+ lf+Ls+ +++ a + +       ++l+ L  lG++
  gene45|gene45|rna45|rna45 164 DR-----NITNRGFEFLLKTKKEQLWCLVLLSLKYFLRSVEEEIYALEALFELSTKTIETAHHQDGR--MDGRLLKYLEALGIL 240
                                55.....5****************************9888899*****************9998874..456799********* PP

                       Tfb2 253 yqrkkkskrFypTrlattLtssssessseskeegfiivETNfrvyAYtssplqialLslFvklkyrfpnlvvgkitresvreAl 336
                                       +r  + r +++L +     +se++++ fiivETN ++yAYt+s+++ ++++lF+++++ +pnl+ g+it+esv+ A+
  gene45|gene45|rna45|rna45 241 RVCG---ERLAIGRSFVQLFE-----ASERNRREFIIVETNNKIYAYTNSEYEKSVIHLFCNVSVSLPNLIKGSITEESVNVAF 316
                                6655...579***********.....588999**************************************************** PP

                       Tfb2 337 knGItadqIisyLesha 353
                                ++GIt +qIi++Le+  
  gene45|gene45|rna45|rna45 317 DKGITGKQIIHFLEASV 333
                                *************9875 PP

>> Tfb2_C  Transcription factor Tfb2 (p52) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.1   1.2e-24   7.5e-21       2      68 .]     345     411 ..     344     411 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 1.2e-24
                     Tfb2_C   2 QIrLWekernRlkaeegvlyddFesqadfeevleyakelgvllwedeekrllvvkeeghesvkefik 68 
                                QI +We++rnR+ + +g++y++F + +d+++vle++ e+ +l+ +d  kr++vvk eghe v+efik
  gene45|gene45|rna45|rna45 345 QIMIWESKRNRIFMVPGYIYSNFLNLSDYQRVLEFCTERSYLIESDVGKRMIVVKLEGHELVREFIK 411
                                9*****************************************************************8 PP

>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0063      43      82 ..     307     347 ..     269     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
               Helicase_C_3  43 ltplSlrrAldaGltaeeiiefLerls.kypvPqaleylir 82 
                                +t++S+  A+d G+t ++ii fLe+     ++P a++ +i 
  gene45|gene45|rna45|rna45 307 ITEESVNVAFDKGITGKQIIHFLEASVkPGSLPPAITSQIM 347
                                9************************997779****999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 2438.06
//
Query:       gene451|gene451|rna450|rna450  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-22   79.8   2.4      2e-22   79.8   2.4    1.7  2  TFIIS_M   Transcription factor S-II (TFIIS), central domain
    2.5e-17   62.4   8.2    7.8e-17   60.8   7.1    2.3  2  TFIIS_C   Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> TFIIS_M  Transcription factor S-II (TFIIS), central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.81   7.3e+03      49      62 ..      47      60 ..      22      78 .. 0.55
   2 !   79.8   2.4   2.2e-26     2e-22       3     111 ..      97     200 ..      95     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.81
                                   -HHHHHHHHHHHHH CS
                        TFIIS_M 49 kkykqkvrslvfNL 62
                                   k++++ +r++ + +
  gene451|gene451|rna450|rna450 47 KRIQALIRTRHLEI 60
                                   33444444444444 PP

  == domain 2  score: 79.8 bits;  conditional E-value: 2.2e-26
                                    HHHHHHHHHHHHTT---...-.--THHHHHHHHHHHHHHHT------HHHHHHHHHHHHHS-TT-HHHHHTSSSS--STT CS
                        TFIIS_M   3 vRdkcrelLaealeedsseaeeeedveelaaeiEealfekekkstdkkykqkvrslvfNLkdkkNpeLrrrvlsgeispe 82 
                                     +d+ +++++ea+++ +s+++ +++++ la++i +++fe    +++ ++ + vrs ++NLkdk+Np L+r v+ geisp+
  gene451|gene451|rna450|rna450  97 QKDRSIKMFFEAFKTSISDCS-NRYAALLAKQITNEIFE----RNSADIAKLVRSKCLNLKDKNNPVLCRMVYDGEISPS 171
                                    57899************9999.99***************....57899******************************** PP

                                    TTS---TTTSS-HHHHHHHHHHHHHHHHT CS
                        TFIIS_M  83 klvkmspeElaseelkeereklekealee 111
                                    + v m++eE++se+l++e+ k+ + +l e
  gene451|gene451|rna450|rna450 172 RYVDMTSEEMKSESLRNEEVKMIEVSLYE 200
                                    *******************9998877765 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.15   1.4e+03       5      18 ..     115     128 ..     114     130 .. 0.84
   2 !   60.8   7.1   8.7e-21   7.8e-17       1      39 []     213     250 ..     213     250 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.15
                        TFIIS_C   5 kCgsreayffqlQt 18 
                                     C++r a    +Q+
  gene451|gene451|rna450|rna450 115 DCSNRYAALLAKQI 128
                                    59999999999987 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 8.7e-21
                        TFIIS_C   1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                    +kC++Cg+r++++ qlQtRs+DEpmt+f++C +Cg++Wr
  gene451|gene451|rna450|rna450 213 FKCNRCGERKCSYRQLQTRSGDEPMTTFVTC-ECGNKWR 250
                                    69*****************************.******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1104  (0.0615762); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 1417.53
//
Query:       gene452|gene452|rna451|rna451  [L=204]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-08   31.9   4.6    2.8e-07   30.3   1.5    2.5  2  KH_1      KH domain
  ------ inclusion threshold ------
      0.025   14.4   1.8      0.038   13.8   0.2    2.2  3  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.019   1.7e+02      27      38 ..      80      92 ..      58     117 .. 0.60
   2 !   30.3   1.5   3.1e-11   2.8e-07       5      64 ..     137     195 ..     133     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.019
                                   HHHT-EEEEES.S CS
                           KH_1 27 eetgakIkvpk.s 38
                                   +e +++I ++k +
  gene452|gene452|rna451|rna451 80 QEANVSISIDKfN 92
                                   2235555555444 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 3.1e-11
                                    EEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT...T.-EEEEEE.SHHHHHHHHHHH CS
                           KH_1   5 lvPsslvgriIGkgGsnIkeIreetgakIkvpk.sedegsderevtisG.speavekAkeli 64 
                                     +P +    +IGk+G nI +++++ +  I+v++ ++   s+ + ++isG ++ +v++A++++
  gene452|gene452|rna451|rna451 137 DIPPESEDIVIGKNGVNIYKLQKDFKIIIRVIDgNR---SGIKALVISGdDKSQVQEACNHV 195
                                    677777778**************99*******7444...59*****************9987 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.4   3.6e+03      14      28 ..      24      38 ..      16      42 .. 0.59
   2 ?   -2.2   0.0      0.43   3.8e+03      38      40 ..      65      67 ..      54      94 .. 0.56
   3 ?   13.8   0.2   4.3e-06     0.038      37      63 ..     144     170 ..     128     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.4
                                   TEEEEEEECCSCEEE CS
                           KH_2 14 gvskveIertanrvi 28
                                   g+ k e++r++n++i
  gene452|gene452|rna451|rna451 24 GKYKKEVRREHNKII 38
                                   344445555555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.43
                                   HHH CS
                           KH_2 38 ivI 40
                                   ivI
  gene452|gene452|rna451|rna451 65 IVI 67
                                   444 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 4.3e-06
                                    HHHHTGGGHHHHHHHHHHHHHHHHHHT CS
                           KH_2  37 givIGkgGsnikkigkelrkdiekleg 63 
                                     ivIGk+G ni k++k+++ +i+++ g
  gene452|gene452|rna451|rna451 144 DIVIGKNGVNIYKLQKDFKIIIRVIDG 170
                                    69***************9999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1252.54
//
Query:       gene454|gene454|rna453|rna453  [L=254]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-17   62.2   2.3    4.5e-17   62.1   2.3    1.0  1  B56       Protein phosphatase 2A regulatory B subunit (B56 fa
  ------ inclusion threshold ------
       0.16   12.2   0.0       0.36   11.1   0.0    1.7  1  DUF3970   Protein of unknown function (DUF3970)


Domain annotation for each model (and alignments):
>> B56  Protein phosphatase 2A regulatory B subunit (B56 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   2.3   5.1e-21   4.5e-17     149     402 ..       2     250 ..       1     254 [] 0.94

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 5.1e-21
                            B56 149 fdseDprERdylktilhriygkfldlrsfirkainniflrfiyeterhngiaelLeilgsiingfalplkeehkkflerv 228
                                    +++eD +ER+ + ++l+ i    +++ + i+  ++n f++fi++++ h g  e+L+++  +i++ ++   e ++ f  +v
  gene454|gene454|rna453|rna453   2 TRTEDVEERKGISELLTCIS-DYPGCLNTIFFGLANEFISFINNNRTHIGLEEILKVVLVVIRKRSIA-YEDMVVFHYQV 79 
                                    6789************9998.8999999************************************8888.566677***** PP

                            B56 229 llpLhkvkslslyhqqLaycvvqfiekdpklaeevikgllkyWPitnsqKevlFLneleeileviepeefqkilkplfkr 308
                                    +l  ++++++   ++++++++  ++ + p+l+  +ik   k++    s+ +v+ +  + e ++v+ +e++  + +++++ 
  gene454|gene454|rna453|rna453  80 ILGMIRTRFCGE-SKEISNVIKAICRNYPELIPLTIKHFKKVFGEVWSNTKVVIVHAMGETFSVMGDEMYLCLENEICEL 158
                                    *********998.899**************************************************************** PP

                            B56 309 lakcissphfqVaeralylwnnekivnlisenseeilpilfpaleknskkHWnktvrglalnvlkllmeldpelfdecaa 388
                                    +  + +s+h+ V e +  ++  +   + i +++e+ +p +f+ ++++s+k W  +  + +l +l  + e+d +lf++c +
  gene454|gene454|rna453|rna453 159 IGMSFDSNHHLVIEDMAEILLLN--YRSILRHKETFVPKVFEPIYRASQKFWRIEGVNKILRILHAILEMDCRLFERCLK 236
                                    ***************99999888..578999************************************************* PP

                            B56 389 kykeekekekekkk 402
                                     y+ ++ +++ k +
  gene454|gene454|rna453|rna453 237 AYNVKRWRNRWKRE 250
                                    99998877766555 PP

>> DUF3970  Protein of unknown function (DUF3970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     4e-05      0.36       1      24 [.      83     106 ..      83     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                        DUF3970   1 MirvRlaGkqeEieeflkslekny 24 
                                    Mir R  G  +Ei +++k + +ny
  gene454|gene454|rna453|rna453  83 MIRTRFCGESKEISNVIKAICRNY 106
                                    9******************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 1446.53
//
Query:       gene455|gene455|rna454|rna454  [L=398]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-39  134.6  32.7    3.7e-23   82.1   9.4    2.1  2  Sugar_tr  Sugar (and other) transporter
    2.2e-11   43.3  60.7    7.4e-10   38.3  34.2    2.3  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1  14.9   3.9e-20   3.5e-16       2     189 ..      17     190 ..      16     200 .. 0.91
   2 !   82.1   9.4   4.1e-27   3.7e-23     239     443 ..     203     393 ..     191     394 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 3.9e-20
                                    HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                       Sugar_tr   2 alvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslli 81 
                                    a +a+++++lfg  + ++g +    ++  ++++++++ +      l+g++ s  ++G++++ ++a++   r   k +l+ 
  gene455|gene455|rna454|rna454  17 AAMASMSSVLFGISLTIMGCMHPYVSKMWRETMDQTEVD-----NLWGIVSSNIFLGCLASNILASI--IRPNMKGALIL 89 
                                    5799**********************9999999988853.....38********************5..57788****** PP

                                    HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  82 aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl 161
                                     ++l+  g +  ++++   s+  ++ gR+++G++ G+++++vP+y+s i+p + Rg l s++ l+it+Gi ++  +  + 
  gene455|gene455|rna454|rna454  90 NNILYTMGYITFFFSQ---SFGSIFSGRFIIGLASGITCAIVPIYTSLISPIECRGLLLSFHPLGITVGITLGNALSCF- 165
                                    ****************...***************************************************999877653. PP

                                    HTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
                       Sugar_tr 162 nktsnadgwrillglqlvpallllilll 189
                                       + +++w+i+l ++l++  l li+ll
  gene455|gene455|rna454|rna454 166 ---NTESTWKIPLIITLFLIGLSLIGLL 190
                                    ...33457**********9999999887 PP

  == domain 2  score: 82.1 bits;  conditional E-value: 4.1e-27
                                    ...HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHH CS
                       Sugar_tr 239 kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfvaiflvdrfGRRt 318
                                     +s+  l++++  r+ +++++++++ q l+G+ +i+ +   +f    +s++ ++ ++++   +v+t ++   vdr+GR++
  gene455|gene455|rna454|rna454 203 DISLYALIKNRRARRSVFLVMLVHVSQHLCGVDYITLFLRDLFPADMYSPK-ITAVLISLASVVITAFSGRYVDRIGRKP 281
                                    6777788888889**************************************.**************************** PP

                                    HHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHH CS
                       Sugar_tr 319 llllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwla 398
                                    l +++++++  ++++++  +           i  +++ +lf+a +++g+ ++pw++ +E+fp++  s+a  + v +nw++
  gene455|gene455|rna454|rna454 282 LIIISSLVAGGATAMFT--FG----------IYPTAAALLFVAGYNMGLCSIPWFITAEIFPPKYASAAGLLGVSLNWVS 349
                                    *****999999999997..44..........4455589****************************************** PP

                                    HHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT- CS
                       Sugar_tr 399 nflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgr 443
                                     + +      ++ ++g   vf +++++++lf+  + +f+ etk++
  gene455|gene455|rna454|rna454 350 AYTTLAALYPLHIKYG-RIVFSFYTICMALFAGLMAVFFKETKNK 393
                                    ***9999999999999.**************************86 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3  34.2   8.3e-14   7.4e-10      35     346 ..      59     346 ..      14     353 .. 0.72
   2 !   18.8  18.5   6.8e-08   0.00061      39     176 ..     257     391 ..     253     397 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 8.3e-14
                          MFS_1  35 gllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.fasslw.lllvlrvlqGlgagalfpagaalia 111
                                    g++ +  +lg+++++++++ +  +    +  l+l  +l+  g ++ + f s+++  ++ +r++ Gl++g+  +++ ++++
  gene455|gene455|rna454|rna454  59 GIVSSNIFLGCLASNILASIIRPN---MKgALILNNILYTMG-YITFfF-SQSFgSIFSGRFIIGLASGITCAIVPIYTS 133
                                    334444566666666666666333...35599**********.777746.88888************************* PP

                          MFS_1 112 dwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgt 191
                                     ++p e rg+ +++  +g+ +G+ lg +l+ + ++s  W  + +i  ++  l+  l++ll  ++p   +++s++ +    
  gene455|gene455|rna454|rna454 134 LISPIECRGLLLSFHPLGITVGITLGNALSCFNTES-TWKIPLIITLFLIGLS--LIGLLGITDPFYQEKPSDISL---- 206
                                    *****************************9998866.6***********9999..667999999999999999999.... PP

                          MFS_1 192 gpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls..glllaglllallalvgailallagrlsd 269
                                            + ++++++   ++++++l+    +   + +++l+l++ +  +  +  ++++l++l+++v+     ++gr++d
  gene455|gene455|rna454|rna454 207 --------YALIKNRRARRSVFLVMLVHVSQHLCGVDYITLFLRDLFPADmySPKITAVLISLASVVI---TAFSGRYVD 275
                                    ........333333331112222222222233337777777777777777663477777777777777...889****** PP

                          MFS_1 270 rlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntags 346
                                    r+gr++ ++++ l++  a++++ +   +     ++++l+++G  +g+++++++  a  +    + ++a+gl ++  +
  gene455|gene455|rna454|rna454 276 RIGRKPLIIISSLVAGGATAMFTFGIYP----TAAALLFVAGYNMGLCSIPWFITAEIFP--PKYASAAGLLGVSLN 346
                                    ***8655555555555555555555555....5555667777788888777776666665..566678888886555 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.8e-08
                          MFS_1  39 tlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpke 117
                                    +l +l+++v + + Gr +dr+Gr+++++++ l+ + ++++++f  +++ + ++l +++G  +g+       ++a++fp+ 
  gene455|gene455|rna454|rna454 257 VLISLASVVITAFSGRYVDRIGRKPLIIISSLVAGGATAMFTF--GIYpTAAALLFVAGYNMGLCSIPW-FITAEIFPP- 332
                                    567999*******************666666666666366666..355589999999999987776666.799******. PP

                          MFS_1 118 ergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeep 176
                                    + ++a gll+++ +  ++ + l++ + ++    r vf + +i ++l++ l+++++ e++
  gene455|gene455|rna454|rna454 333 KYASAAGLLGVSLNWVSAYTTLAALYPLHIKYGRIVFSFYTICMALFAGLMAVFFKETK 391
                                    ********************999999997777789988888888888778888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2383.71
//
Query:       gene456|gene456|rna455|rna455  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-05   23.1   0.1     0.0003   20.9   0.0    2.3  2  Myb_DNA-binding  Myb-like DNA-binding domain
  ------ inclusion threshold ------
       0.81    9.9   9.1       0.36   11.0   5.7    2.1  3  zf-B_box         B-box zinc finger
        6.3    6.7   8.3         31    4.5   8.3    2.0  1  ZZ               Zinc finger, ZZ type


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     5e-08    0.0003       2      36 ..      71     104 ..      70     114 .. 0.85
   2 ?   -3.5   0.0       2.1   1.2e+04       1      12 [.     306     317 ..     306     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5e-08
                                    SSSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HH CS
                Myb_DNA-binding   2 gkWteeEdelLleavkkhG.nrWkkIaerlggRtek 36 
                                     kWt  E+ l++e++   G ++W+ +++++gg  e 
  gene456|gene456|rna455|rna455  71 EKWTLMEEILFIEGLSVSGiGNWSGVSKYVGG--ER 104
                                    69*****************************5..33 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.1
                                    CSSSBHHHHHHH CS
                Myb_DNA-binding   1 rgkWteeEdelL 12 
                                    ++++t+e+ ++L
  gene456|gene456|rna455|rna455 306 KKRFTKEDFNRL 317
                                    679999986666 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3       0.1   6.2e+02      24      29 ..      14      19 ..       4      25 .. 0.64
   2 ?   11.0   5.7   5.9e-05      0.36       6      40 ..      16      59 ..      11      61 .. 0.81
   3 ?   -3.7   0.0       2.3   1.4e+04       5      10 ..     281     286 ..     278     288 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.1
                       zf-B_box 24 plCeeC 29
                                    lC++C
  gene456|gene456|rna455|rna455 14 ILCDNC 19
                                   466666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.9e-05
                       zf-B_box  6 CpeHk...nkpatlfCedCqqplCeeC.....stgeHrg.Hevv 40
                                   C+++    +  + + C +C+  lC +C      t+ H++ H++ 
  gene456|gene456|rna455|rna455 16 CDNCFvemTTLTYIKCSECEIDLCLSCfvnqvETSLHSKyHKYR 59
                                   666665445666778***************99999***889986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.3
                       zf-B_box   5 kCpeHk 10 
                                     C+ H+
  gene456|gene456|rna455|rna455 281 LCETHG 286
                                    577775 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   8.3    0.0052        31       7      37 ..      16      45 ..      12      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0052
                                   -TTT-S..EESSEEEESSSSS-EE-HHHHHH CS
                             ZZ  7 CdgCseapligvRyhclrcsdYDLCqsCfst 37
                                   Cd C    +  +  +c  c + DLC sCf  
  gene456|gene456|rna455|rna455 16 CDNCFVEMTTLTYIKCSEC-EIDLCLSCFVN 45
                                   9999997777777799999.69*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1834.67
//
Query:       gene457|gene457|rna456|rna456  [L=406]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-46  157.1   1.2    3.4e-46  156.5   1.2    1.3  1  Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
    3.7e-06   26.9   0.6    6.8e-06   26.1   0.6    1.4  1  Mad3_BUB1_I    Mad3/BUB1 homology region 1


Domain annotation for each model (and alignments):
>> Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.5   1.2   3.8e-50   3.4e-46       1     127 [.      16     143 ..      16     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.5 bits;  conditional E-value: 3.8e-50
                  Mad3_BUB1_I_2   1 llrkidipyfrnnpsyiekwkelYkktkdlkilfLmklKkIskfyyfvYlelsryFlkkgkkeaalfiLqegiknkvydk 80 
                                    ll++idipyfrnnpsyi++w+++Y+kt+d+ +lfLmk+KkIs++y+++Y+elsr+F++ g  ++ +++L+ gi++++y++
  gene457|gene457|rna456|rna456  16 LLNYIDIPYFRNNPSYISLWQRYYYKTNDPSVLFLMKYKKISQYYHWIYVELSRFFMRNGRYGVCKAVLNVGIACNAYER 95 
                                    689***************************************************************************** PP

                  Mad3_BUB1_I_2  81 eilkeelksikklekklseeeakkllkpkkirlfGkeWve.ievnyla 127
                                    e+l++el++i+ ++++  e+e+++ll+pk+++++Gk+W++ +ev +++
  gene457|gene457|rna456|rna456  96 EVLEDELQRIPMVTNPSPEHEINTLLNPKGFTALGKVWNSyQEVLFYN 143
                                    ****************************************88888875 PP

>> Mad3_BUB1_I  Mad3/BUB1 homology region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.6   7.5e-10   6.8e-06      47     124 .]      12      88 ..       8      88 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7.5e-10
                                    HHHHHHHTTTSGGGTT-HHHHHHHHHHHTTSS-HHHHHHHHHHHTTSTTBHHHHHHHHHHHHHTT-HHHHHHHHHHH. CS
                    Mad3_BUB1_I  47 lerclkkfkdderYknDpRylklwlkyadlveepreifkflaskkiGtklalfYeewAellekkgrfkeAeevyelGi 124
                                    le++l ++ d + ++n+p y++lw +y   +++p  +f  +  kki + +  +Y e ++++ ++gr+  +++v++ Gi
  gene457|gene457|rna456|rna456  12 LENALLNYIDIPYFRNNPSYISLWQRYYYKTNDPSVLF-LMKYKKISQYYHWIYVELSRFFMRNGRYGVCKAVLNVGI 88 
                                    899999****************************9999.68999********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2662.98
//
Query:       gene458|gene458|rna457|rna457  [L=605]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-10   40.7   0.1    5.2e-09   36.4   0.0    3.1  3  Helicase_C       Helicase conserved C-terminal domain
    1.7e-06   28.3   0.0    3.9e-06   27.1   0.0    1.6  1  OB_NTP_bind      Oligonucleotide/oligosaccharide-binding (OB)
     0.0012   18.9   0.3       0.16   12.0   0.3    2.8  2  ResIII           Type III restriction enzyme, res subunit
     0.0017   18.2   0.1     0.0067   16.2   0.1    1.9  1  DEAD             DEAD/DEAH box helicase
     0.0022   18.0   0.0     0.0061   16.6   0.0    1.7  1  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.022   14.0   1.1          5    6.3   0.1    3.2  3  ERCC3_RAD25_C    ERCC3/RAD25/XPB C-terminal helicase
      0.025   14.3   0.0      0.074   12.8   0.0    1.8  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.06   12.4   0.0        0.1   11.6   0.0    1.3  1  T2SSE            Type II/IV secretion system protein


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         1   2.3e+03      12      35 ..     137     160 ..     102     184 .. 0.72
   2 !   36.4   0.0   2.3e-12   5.2e-09      14     111 .]     210     321 ..     196     321 .. 0.85
   3 ?   -0.5   0.0      0.68   1.5e+03      19      62 ..     461     508 ..     442     560 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                                    HTTTTSEEEEEESSHHHHHHHHHH CS
                     Helicase_C  12 leeeggkilifvntidrlekvkll 35 
                                     ++++gk+++++ t+d+ + ++++
  gene458|gene458|rna457|rna457 137 IKNIKGKVILMSATVDTGKLADYF 160
                                    356777777777777744323555 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 2.3e-12
                                    TTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEES CS
                     Helicase_C  14 eeggkilifvntidrlek.vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinf 91 
                                     ++++il+f++  +++++   ll++    +k+ ++ + l+ +e+++i e      ++v+++t++ e++++ip++ +Vi+ 
  gene458|gene458|rna457|rna457 210 IKNKDILVFLPGEEDINElYVLLRK-LpVVKIYKIFSALSDKEQNKIYEPS--SLRKVILSTNICETSLTIPGIGYVIDT 286
                                    57899*********99874455544.359********************99..6889*********************** PP

                                    SSSSSH...............HHHHHHHTTSSSTT CS
                     Helicase_C  92 dlprnv...............tsyiqriGRtgRag 111
                                    +l +                 +s+ qr GR+ R g
  gene458|gene458|rna457|rna457 287 GLYKVKiydqmsclgiqaisrESADQRLGRCNRTG 321
                                    *99442345567777788888**********9975 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.68
                                    EEEEESSHHHHHHHHHHHHHT.......TSTEEEESTTSTHHHHHHHHHHH CS
                     Helicase_C  19 ilifvntidrlekvklllekk.......gikvavlhgelpqnereeileqf 62 
                                    il+ + ++d++   ++l+ k+       g+ v+ l g l++++ ++   ++
  gene458|gene458|rna457|rna457 461 ILVSLISQDSC---NFLKYKNkpqgtdlGFLVCLLEGYLEAEDPKQYCIKY 508
                                    33333444466...4553333455777788888888888888777655554 PP

>> OB_NTP_bind  Oligonucleotide/oligosaccharide-binding (OB)-fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.7e-09   3.9e-06      11      67 ..     546     597 ..     516     600 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.7e-09
                                    TCEEEEEETTCCEEETTTCEEEEE-TTSTTTTT...TSSSEEEEEEEEESSSEEEEE CS
                    OB_NTP_bind  11 pqiarkdpskkdyktartktrvfihpsSvlaknekekepewvvytelvettklylrd 67 
                                     +++++++ ++ y++++ ++ v ihpsS+++k     +++++v+     ttk y+r 
  gene458|gene458|rna457|rna457 546 HNLCERAKDGS-YRHLKSNEVVWIHPSSCFFK----RKDRFIVFVDVFYTTKAYARI 597
                                    45665655555.999999*************9....*******************96 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.3   7.1e-05      0.16     122     169 ..     100     151 ..      10     153 .. 0.68
   2 ?   -2.1   0.0       1.5   3.3e+03      22      77 ..     499     560 ..     480     581 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.1e-05
                                    .....HHHTTT-SEEEEETGGGTTS.T.....TTHHHHHT---SEEEEEESS- CS
                         ResIII 122 eeeseellrdrfdviiiDEaHrlgakk.....swreilekfkeavllglTATp 169
                                     +  +e  + +fd+ii+DE+H  +  +      +++ ++++k + ++ ++AT 
  gene458|gene458|rna457|rna457 100 GSFLNEVAEREFDYIIVDEVHERSIRTdvilgLFKNSIKNIKGK-VILMSATV 151
                                    34456668999**********88876445666677767777744.55569996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S..........-EEEEESSHHHHHHHH.HHGGGG CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkee.....kflflvprkslleqtl.eefkkf 77 
                                    ++ k+++ik + G+    +a k+  +l +k++ +     +++ ++ + +l+e+++   ++++
  gene458|gene458|rna457|rna457 499 EDPKQYCIKYEVGMKHMNIAKKIFLELNRKKGGDietveRIFSFAYQHNLCERAKdGSYRHL 560
                                    66777888887777555555666667776666557777788888888888888884345444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     3e-06    0.0067      10     170 ..      20     152 ..      12     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3e-06
                                    HHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  10 lilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaard 89 
                                     i + + ++++++TG GK++   +p l ++    + +  ++ i+eP r  +   ++ l+  ++ ++           ++ 
  gene458|gene458|rna457|rna457  20 GIRRSKVCIIKGATGCGKSTY--VPYLLSL----SFPSCRIAIIEPRRIAVTSLHRILSGAMEGVG-----------YKM 82 
                                    455668899*********998..6777566....68999*********999999988888888644...........333 PP

                                    HHHHH.HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESS CS
                                    xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  90 qlskl.dngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSAT 168
                                      +k  +++++ ++ t g +++ +       +++ ++++DE+++ +       +    n++++i    k   +vi++SAT
  gene458|gene458|rna457|rna457  83 RFNKCiESNTKTIIYTDGSFLNEVA-----EREFDYIIVDEVHERSIR-TDVILGLFKNSIKNI----KG--KVILMSAT 150
                                    3333325678899999999999775.....3569*********98887.555555555666433....43..3******* PP

                                    BS CS
                                    xx RF
                           DEAD 169 lp 170
                                    + 
  gene458|gene458|rna457|rna457 151 VD 152
                                    96 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06    0.0061       2      92 ..      24     139 ..      23     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                         AAA_14   2 rkilvitGaRrvGKTtllkqlikell.......vkkesilyinldderd...............kkladpe.......kl 52 
                                    +k+++i+Ga  +GK+t++  l++ ++       +++++i   +l +                        e         
  gene458|gene458|rna457|rna457  24 SKVCIIKGATGCGKSTYVPYLLSLSFpscriaiIEPRRIAVTSLHRILSgamegvgykmrfnkcI-----EsntktiiYT 98 
                                    6899*****************98888999999999999999999998888888887554443321.....0212222222 PP

                         AAA_14  53 lelileklkeekktylflDEiqevpewekalkslvdeg.kn 92 
                                    +  +l+++ e++  y++ DE++e +   +++ +l++++ kn
  gene458|gene458|rna457|rna457  99 DGSFLNEVAEREFDYIIVDEVHERSIRTDVILGLFKNSiKN 139
                                    344444443478899********999888888888876544 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.17   3.8e+02      58     118 ..      89     153 ..      73     167 .. 0.68
   2 ?    3.9   0.0     0.012        27     134     185 ..     303     355 ..     226     361 .. 0.84
   3 ?    6.3   0.1    0.0022         5      58      84 ..     576     602 ..     570     604 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                  ERCC3_RAD25_C  58 krgDkiivfsDnvfaLkeyakklkkpyiyGetse.aerlk.ilqkfkkn...pkvntiflskvgDt 118
                                    + + k i+++D  f L+e+a++     i+ e++e + r++ il  fk++    k ++i++s   Dt
  gene458|gene458|rna457|rna457  89 ESNTKTIIYTDGSF-LNEVAEREFDYIIVDEVHErSIRTDvILGLFKNSiknIKGKVILMSATVDT 153
                                    568899*****999.677777766666666665515576526788887631145678888887776 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.012
                  ERCC3_RAD25_C 134 hfgsrrqeaqrlGriLrakkksneeefnaffY.sLvskDtkemaystkrqqfl 185
                                    ++ sr    qrlGr  r+  ++  + +  + Y +L s+   e+  s+  q+fl
  gene458|gene458|rna457|rna457 303 QAISRESADQRLGRCNRTGPGTCYRLYTEHMYnALPSHQSPEICRSDLCQAFL 355
                                    567899999**********9999888887777368899999999999999997 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0022
                  ERCC3_RAD25_C  58 krgDkiivfsDnvfaLkeyakklkkpy 84 
                                    kr+D+ ivf D  ++ k+ya+ + + +
  gene458|gene458|rna457|rna457 576 KRKDRFIVFVDVFYTTKAYARIVGRYF 602
                                    89******************9988766 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05     0.074       2      71 ..      28     119 ..      27     125 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                Viral_helicase1   2 vvhGvpGcGKStlirkllrts...liltvnrptaelltegk....................pklpnlsvrtvdsflmalv 58 
                                    +++G+ GcGKSt +  ll+ s   + + ++ p+ +++t  +                    + +++  ++t  sfl+   
  gene458|gene458|rna457|rna457  28 IIKGATGCGKSTYVPYLLSLSfpsCRIAIIEPRRIAVTSLHrilsgamegvgykmrfnkciESNTKTIIYTDGSFLNEVA 107
                                    89****************99888855555555555555444567777888888888888887788888888888888877 PP

                Viral_helicase1  59 kstkgkililDEy 71 
                                    ++ +++++i+DE 
  gene458|gene458|rna457|rna457 108 ER-EFDYIIVDEV 119
                                    76.7888888886 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.6e-05       0.1     119     164 ..      15      58 ..       3      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                          T2SSE 119 aevlrkavrerglilvsGgTgsGKttll.yallkeinksderivtvE 164
                                    +++l   +r+ ++ ++ G+Tg GK+t + y l   ++++  ri ++E
  gene458|gene458|rna457|rna457  15 DRILDG-IRRSKVCIIKGATGCGKSTYVpYLLSLSFPSC--RIAIIE 58 
                                    455544.488899**************956666666666..888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.72u 0.33s 00:00:01.05 Elapsed: 00:00:00.53
# Mc/sec: 3410.48
//
Query:       gene459|gene459|rna458|rna458  [L=306]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-30  105.9  17.4    1.6e-30  105.9  17.4    2.2  2  DHHC      DHHC palmitoyltransferase
  ------ inclusion threshold ------
      0.011   16.0   0.5       0.11   12.8   0.2    2.5  2  UPF0122   Putative helix-turn-helix protein, YlxM / p13 like
       0.21   11.7   0.2       0.21   11.7   0.2    2.8  4  UL41A     Herpesvirus UL41A


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   4.4       0.5     3e+03      57     104 ..      19      62 ..       7      79 .. 0.41
   2 !  105.9  17.4   2.7e-34   1.6e-30       6     132 ..     111     228 ..     107     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.5
                           DHHC  57 ylllllilalvlllialvklveeekkseflavtllkkllsilllvlsl 104
                                    y +l     l+++++++  l+ e++++  ++++ l  ++++++++ ++
  gene459|gene459|rna458|rna458  19 YPTLE----LYIYFVFVGLLCLEDTEFNSWTIFALFVAYHVIVTYKAM 62 
                                    33333....333333333333333333333332222222222222222 PP

  == domain 2  score: 105.9 bits;  conditional E-value: 2.7e-34
                           DHHC   6 kfCstcniykpprskHcrvCnrcvlrfDHhCpwlnnciGerNykyFllfllylllllilalvlllialvklveeekksef 85 
                                    k Cs+c++ykppr++Hc +C+rc l++DHhC  ln+ciG++Nyk+F++f++  l+++i+++v+++i++   ++++++  +
  gene459|gene459|rna458|rna458 111 KLCSKCKTYKPPRAHHCGTCKRCYLKYDHHCALLNTCIGFHNYKFFYQFMVLNLVSVIFFIVTISIYMMLHTPKSTTHYV 190
                                    78*****************************************************9999999999999888888888644 PP

                           DHHC  86 lavtllkkllsilllvlsllfllllgllllfhlylilrnlTtieamk 132
                                    +          i+++ l  + +++ ++ll+fh++li  n Ttie++ 
  gene459|gene459|rna458|rna458 191 N---------YIVSISLLGVEFIFNLSLLIFHTWLIGMNETTIEHYA 228
                                    4.........278888889999999*******************985 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.8e-05      0.11       5      39 ..      44      78 ..      42     118 .. 0.90
   2 ?    0.3   0.0      0.14   8.2e+02      25      41 ..     228     244 ..     221     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                        UPF0122  5 lrlnaLfdiYqsLLTekqanylelyyadDlSlsEi 39
                                   + + aLf  Y+ ++T k + y++l++++  S  Ei
  gene459|gene459|rna458|rna458 44 WTIFALFVAYHVIVTYKAMFYMKLFINEGVSTLEI 78
                                   56679**************************9998 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                        UPF0122  25 ylelyyadDlSlsEiAe 41 
                                     l+ y++ D S+s i +
  gene459|gene459|rna458|rna458 228 ALNDYINGDHSFSHIFQ 244
                                    5899********99965 PP

>> UL41A  Herpesvirus UL41A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   1.0       1.7     1e+04      44      44 ..      40      40 ..      13      68 .. 0.60
   2 ?   -1.9   0.1      0.63   3.8e+03      29      52 ..      63      87 ..      45     100 .. 0.65
   3 ?   -0.6   0.3      0.25   1.5e+03      18      51 ..     145     176 ..     140     183 .. 0.46
   4 ?   11.7   0.2   3.5e-05      0.21       5      41 ..     180     215 ..     174     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                          UL41A 44 a 44
                                    
  gene459|gene459|rna458|rna458 40 E 40
                                   1 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.63
                          UL41A 29 fvfgvfilifcstlkaf.yvrqkty 52
                                   f + +fi   +stl  f  v q  y
  gene459|gene459|rna458|rna458 63 FYMKLFINEGVSTLEIFpDVPQEGY 87
                                   4555666666677776633556555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.25
                          UL41A  18 nvcigmigvvcfvfgvfilifcstlkafyvrqkt 51 
                                    n cig+     f +  ++l ++s +  f v    
  gene459|gene459|rna458|rna458 145 NTCIGFHNYK-FFYQFMVLNLVSVI-FFIVTISI 176
                                    6677765443.33333333333322.33344344 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 3.5e-05
                          UL41A   5 crtanstagyvdmnvcigmigvvcfvfgvfilifcst 41 
                                      t +st+ yv+  v i ++gv  f+f + +lif + 
  gene459|gene459|rna458|rna458 180 LHTPKSTTHYVNYIVSISLLGV-EFIFNLSLLIFHTW 215
                                    57899****************7.6*********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1257  (0.0701099); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.60
# Mc/sec: 1533.41
//
Query:       gene460|gene460|rna459|rna459  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-08   34.4   8.3    3.2e-08   33.6   8.3    1.5  1  zf-AN1    AN1-like Zinc finger
  ------ inclusion threshold ------
       0.36   10.6   6.6        2.2    8.1   2.2    2.5  2  zf-CSL    CSL zinc finger


Domain annotation for each model (and alignments):
>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   8.3   3.6e-12   3.2e-08       1      40 []      77     115 ..      69     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.6e-12
                         zf-AN1   1 CsfksCkkkdflp..fkCryCgkvFClkHrlpedHdCkklak 40 
                                    C   +C+k++ l   + Cr Cg+++C  Hr+ ++H+C++++k
  gene460|gene460|rna459|rna459  77 CG--KCGKRLRLTnnYSCR-CGNTYCIMHRFHDQHGCTFDYK 115
                                    55..8*****87788****.*******************996 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1    0.0037        33      12      30 ..      68      87 ..      60      90 .. 0.68
   2 ?    8.1   2.2   0.00024       2.2      19      31 ..      90     102 ..      88     113 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0037
                                   TTTTEEEEEE.TTSSEEEEE CS
                         zf-CSL 12 eeeesyyypC.RCgdeFelt 30
                                   e++es +++C  Cg++  lt
  gene460|gene460|rna459|rna459 68 EKKESGVMSCgKCGKRLRLT 87
                                   55667788888888877666 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00024
                                    EEETTSSEEEEEH CS
                         zf-CSL  19 ypCRCgdeFelte 31 
                                    y+CRCg+++ +  
  gene460|gene460|rna459|rna459  90 YSCRCGNTYCIMH 102
                                    99******99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 849.51
//
Query:       gene46|gene46|rna46|rna46  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00081   18.7   0.1     0.0011   18.2   0.1    1.2  1  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
     0.0044   16.3   0.7      0.023   13.9   0.0    2.0  2  Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.041   12.6   0.5        5.6    5.6   0.0    2.1  2  HI0933_like  HI0933-like protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.9e-07    0.0011       2      99 ..       3      98 ..       2     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-07
                               SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......HHHHCHHHHCCCCHCCTCEEEEES CS
                               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx RF
                Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......evvkklnqgielllgeevvkidpg 81
                               +vv++G Gp+++ + +++ +a++  +++ +       + + s++++gv++ ++ ++      +  ++ n gie++ + e+++i ++
  gene46|gene46|rna46|rna46  3 NVVILGQGPGAYMCGIYAHTANLSPIII-KACKKSMTDFSGSEKVVGVKGIQSPEElvglveR--QSKNMGIEVREE-EILNISKK 84
                               79**************************.6666677779999999999999988889977632..355667888888.8****999 PP

                               CEEEEETEEECTCEEEEE CS
                               xxxxxxxxxxxxxxxxxx RF
                Pyr_redox_2 82 kkkvklekkkegdeekia 99
                               + ++++e++++      +
  gene46|gene46|rna46|rna46 85 QNHFEIETNTG-T---HE 98
                               99999966553.2...23 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.033     2e+02       1      27 [.       5      30 ..       5      48 .. 0.85
   2 !   13.9   0.0   3.9e-06     0.023      98     130 ..      73     104 ..      52     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.033
                Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                               +I G GP    ++i +  a+l+  +i+
  gene46|gene46|rna46|rna46  5 VILGQGPGAYMCGIYAHTANLS-PIII 30
                               799******************6.5565 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.9e-06
                Pyr_redox_3  98 iklfeeVesvkkedegfevetsketyeAkkvii 130
                                +  +ee+ +++k++++fe+et+++t e+++++i
  gene46|gene46|rna46|rna46  73 V-REEEILNISKKQNHFEIETNTGTHETRSLVI 104
                                3.3689************************998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0   0.00094       5.6       2      34 ..       3      35 ..       2      43 .. 0.88
   2 ?    5.5   0.1   0.00098       5.8     109     160 ..      56     104 ..      52     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00094
                               SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                               +v+++G G+   m+ i a++++ + +++ + kk
  gene46|gene46|rna46|rna46  3 NVVILGQGPGAYMCGIYAHTANLSPIIIKACKK 35
                               79********************99999987776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.00098
                                HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE CS
                HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvl 160
                                e++v + +++ k+ g+++r  +e+ +++k++++ f+++t ++++ e+++lv+
  gene46|gene46|rna46|rna46  56 EELVGLVERQSKNMGIEVRE-EEILNISKKQNH-FEIET-NTGTHETRSLVI 104
                                67788888899999999985.689999888877.*****.999*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 1018.69
//
Query:       gene461|gene461|rna460|rna460  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-25   87.6   0.0    1.4e-24   87.0   0.0    1.2  1  Ssl1            Ssl1-like
     0.0025   18.1   0.1      0.021   15.1   0.1    2.0  1  VWA             von Willebrand factor type A domain
     0.0036   16.9   5.0     0.0036   16.9   5.0    2.1  2  Tfb4            Transcription factor Tfb4
  ------ inclusion threshold ------
      0.016   15.4  17.1      0.019   15.2   8.4    2.5  2  C1_4            TFIIH C1-like domain
      0.052   13.6   4.0       0.83    9.7   0.0    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.41   10.7  21.9        1.1    9.3   4.2    2.5  2  DZR             Double zinc ribbon
        1.8    8.1  15.5       0.13   11.7   4.8    2.9  2  zf-ribbon_3     zinc-ribbon domain
        3.8    7.5  31.0        0.5   10.3   3.9    3.8  4  zf-HIT          HIT zinc finger


Domain annotation for each model (and alignments):
>> Ssl1  Ssl1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.0   6.2e-28   1.4e-24       1     193 []      48     229 ..      48     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 6.2e-28
                                    EEE-SGGGGSSSSSS-HHHHHHHHHHHHHHHHHHHSTT-EEEEEEEETTEEEEEEEEES-HHHHHHHHHHHTTS---S-- CS
                           Ssl1   1 vlDlsrameekdlkpsrlavviklleefveeffdqnPisqlgliavkdkkaekltelsGnprkhikaLkslreveakgep 80 
                                    ++D+s+a+ + d+ p+  + v++ leef+  f++ nP+s l+ ++++d   + ++++  + + ++ +  s+        +
  gene461|gene461|rna460|rna460  48 IIDVSEAIDKSDFLPTFRTNVARILEEFIPSFYNENPLSTLSFLSTRDVCVKYISSMDMDVHAFLGQTGSKW-------F 120
                                    69**************999**************************************988877776666666.......* PP

                                    -HHHHHHHHHHHHSSS-TTSEEEEEEEE-SS----SS-HHHHHHHHHHTT-EEEEEEESS--HHHHHHHHHTTTTEEEE- CS
                           Ssl1  81 sLqnaLelalasLkkvpshasrevliifsslstcDPgdiyetidelkkekirvsvigLsaevavckelaketkgtysvvl 160
                                    sL n+Le + + +++      +e+l+i++s st DP    e++++lk+ +i+v+ i+L  e+++ k ++k+t+g + v +
  gene461|gene461|rna460|rna460 121 SLLNGLEGSIEIMRNT--MHVKEILVIVASTSTRDPHGYTEVLNKLKTYNIKVHFISLCGELTLYKSISKATGGRFYVPV 198
                                    *******999988764..4468********************************************************** PP

                                    SHHHHHHHHHHHHS------------EEEEE-- CS
                           Ssl1 161 dethlkelllehvsPppaakskkeaslikmGfP 193
                                    d  hl  +++e  +P   + ++   sl+k+GfP
  gene461|gene461|rna460|rna460 199 DVGHLSMIMKELSHPTDFNGTT--LSLVKIGFP 229
                                    *******999999998888777..********9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   9.3e-06     0.021       3     162 ..      46     196 ..      44     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.3e-06
                                    EEEEE-STTSCHHHHH.HHHHHHHHHHHHHTBTTTTEE.EEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGSSC- CS
                            VWA   3 vfvlDgSgsmgeenfe.kvkefikklveklevgpegtr.vglvqfssevktefslndysskeellsalnnlkysgggttn 80 
                                     +++D+S+ +++++f  ++++ + +++e+++ + ++ + ++ ++f s+  + +++ +  +  +++  l +    g+++ +
  gene461|gene461|rna460|rna460  46 HVIIDVSEAIDKSDFLpTFRTNVARILEEFIPSFYNENpLSTLSFLSTRDVCVKYISSMD-MDVHAFLGQ---TGSKWFS 121
                                    6899***********999999999999999943333333566666555555555544332.566666666...4777776 PP

                                    HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEE.SSSHHHHHHHHHSSSSCHH CS
                            VWA  81 tgkalkyaleklfkssagaRenakkviilltdGksndg.dpkeaaneakeqgikvfavGv.gnadekelLnkiasepgeg 158
                                    +  +l+  +e + + +     ++k +++++++  + d   ++e++n++k ++ikv+ +   g+ +  +   +i++ +g g
  gene461|gene461|rna460|rna460 122 LLNGLEGSIEIMRNTM-----HVKEILVIVASTSTRDPhGYTEVLNKLKTYNIKVHFISLcGELTLYK---SISKATG-G 192
                                    6666666555333333.....468888888888888845*****************998765554433...6655555.5 PP

                                    CEEE CS
                            VWA 159 hvft 162
                                    +++ 
  gene461|gene461|rna460|rna460 193 RFYV 196
                                    5555 PP

>> Tfb4  Transcription factor Tfb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   5.0   1.6e-06    0.0036     145     276 .]     140     269 ..     117     269 .. 0.78
   2 ?   -4.1   2.1         4   8.9e+03     254     266 ..     308     320 ..     305     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                           Tfb4 145 ksRilv..vsaskdsalqyipimNviFaaqklkipidvvklggkdsafLqQasdaTkGvylk...vkepkgllqyLltaf 219
                                    k  ilv   s+s+ +++ y  ++N +   +  +i +  ++l g + ++ +  s+aT+G +     v + + +++ L+   
  gene461|gene461|rna460|rna460 140 KE-ILVivASTSTRDPHGYTEVLNKL---KTYNIKVHFISLCG-ELTLYKSISKATGGRFYVpvdVGHLSMIMKELSHPT 214
                                    43.444346778889999******87...66899999****99.99999*********8753122566778888888777 PP

                           Tfb4 220 lidqssRsllvlptrvsVdfRasCfchrkvvdiGfvCSvCLsilceispenkCktCe 276
                                      + ++ sl+++  +      + C ch ++ +iG+ C vC +++c   p+ +C+ C+
  gene461|gene461|rna460|rna460 215 DFNGTTLSLVKIGFPLPTIESSVCSCHLEMKSIGYECPVCKTMVCSL-PT-SCPICG 269
                                    77777777666655555555688************************.54.7****6 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 4
                           Tfb4 254 fvCSvCLsilcei 266
                                    + C +C s +c +
  gene461|gene461|rna460|rna460 308 YQCELCKSTFCSY 320
                                    7899*******98 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.4     0.015        34      21      36 ..     244     259 ..     230     261 .. 0.82
   2 ?   15.2   8.4   8.5e-06     0.019      23      54 ..     305     336 ..     289     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                           C1_4  21 ltssryrCekCkndFC 36 
                                    + s+ y+C+ Ck++ C
  gene461|gene461|rna460|rna460 244 MKSIGYECPVCKTMVC 259
                                    67889********999 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.5e-06
                           C1_4  23 ssryrCekCkndFCiDCDvFiHesLHnCpGCe 54 
                                    +  y+Ce Ck++FC  C    H++L  C+ Ce
  gene461|gene461|rna460|rna460 305 KGAYQCELCKSTFCSYCNGLAHNTLSFCIYCE 336
                                    568****************************8 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   2.5     0.062   1.4e+02       1       8 [.     250     257 ..     250     260 .. 0.82
   2 ?    9.7   0.0   0.00037      0.83       2      12 ..     265     275 ..     264     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.062
                 DNA_ligase_ZBD   1 hCPvCGsa 8  
                                    +CPvC + 
  gene461|gene461|rna460|rna460 250 ECPVCKTM 257
                                    5****985 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00037
                 DNA_ligase_ZBD   2 CPvCGsavvRe 12 
                                    CP+CG+ +v +
  gene461|gene461|rna460|rna460 265 CPICGTQLVST 275
                                    ********976 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.2   0.00049       1.1       3      38 ..     239     272 ..     237     281 .. 0.76
   2 ?    5.1  20.8      0.01        23       1      49 []     251     336 ..     251     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00049
                            DZR   3 qCgeelppdarfCseCgtklkavaaedrCpsCgekv 38 
                                    +C+ e+++    C+ C+t +   + ++ Cp Cg+++
  gene461|gene461|rna460|rna460 239 SCHLEMKSIGYECPVCKTMVC--SLPTSCPICGTQL 272
                                    688888888888999999987..4588999999885 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.01
                            DZR   1 CpqCgeelppdarfCseCgtklkavaa.....................................edrCpsCgekvdpear 43 
                                    Cp C++ + +    C+ Cgt+l ++ +                                     +++C+ C+  ++++ +
  gene461|gene461|rna460|rna460 251 CPVCKTMVCSLPTSCPICGTQLVSTLNlskslrflyplkpfiekaegicricrdkgayqcelckSTFCSYCNGLAHNTLS 330
                                    9********************9866669999************************************************* PP

                            DZR  44 fCpeCG 49 
                                    fC +C+
  gene461|gene461|rna460|rna460 331 FCIYCE 336
                                    *****5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.8   5.8e-05      0.13       3      26 .]     249     272 ..     248     272 .. 0.91
   2 ?    0.8   2.9      0.15   3.4e+02       4      23 ..     317     336 ..     315     338 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.8e-05
                    zf-ribbon_3   3 vrCPnCGaplssddnvCpyCGtkl 26 
                                    ++CP C++ + s  + Cp CGt+l
  gene461|gene461|rna460|rna460 249 YECPVCKTMVCSLPTSCPICGTQL 272
                                    68******66************97 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.15
                    zf-ribbon_3   4 rCPnCGaplssddnvCpyCG 23 
                                    +C++C+ ++    ++C yC 
  gene461|gene461|rna460|rna460 317 FCSYCNGLAHNTLSFCIYCE 336
                                    78888877777777777775 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.9   0.00022       0.5      14      26 ..     249     261 ..     237     262 .. 0.90
   2 ?   -0.6   0.2      0.56   1.2e+03      16      21 ..     265     270 ..     263     272 .. 0.66
   3 ?    9.2   9.6   0.00048       1.1       3      25 ..     297     319 ..     295     321 .. 0.94
   4 ?   -1.1   0.1      0.83   1.9e+03       4      12 ..     331     339 ..     329     340 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                    EE-TTT--EESSH CS
                         zf-HIT  14 YkCpkCntryCSL 26 
                                    Y Cp C+t++CSL
  gene461|gene461|rna460|rna460 249 YECPVCKTMVCSL 261
                                    9***********9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.56
                                    -TTT-- CS
                         zf-HIT  16 CpkCnt 21 
                                    Cp C+t
  gene461|gene461|rna460|rna460 265 CPICGT 270
                                    777766 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00048
                                    -B-TTT-SB-SEE-TTT--EESS CS
                         zf-HIT   3 klCgvCgfpakYkCpkCntryCS 25 
                                    ++C +C  ++ Y C  C+  +CS
  gene461|gene461|rna460|rna460 297 GICRICRDKGAYQCELCKSTFCS 319
                                    78********************9 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 0.83
                                    B-TTT-SB- CS
                         zf-HIT   4 lCgvCgfpa 12 
                                    +C+ C  p+
  gene461|gene461|rna460|rna460 331 FCIYCELPH 339
                                    899998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2337.40
//
Query:       gene462|gene462|rna461|rna461  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0084   16.2   0.3      0.016   15.3   0.3    1.5  1  DUF2318   Predicted membrane protein (DUF2318)


Domain annotation for each model (and alignments):
>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.3     9e-07     0.016      41      78 ..      47      88 ..       8     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9e-07
                        DUF2318 41 ekkgYvqegeelvCkn....CgvrfaldsigekkGGCnpipl 78
                                    +k+++ +++++ Ck     C  r+++ +i++++G+Cn + +
  gene462|gene462|rna461|rna461 47 FPKEFILKENRIFCKIriegCYRRLKIVKIERMSGSCNAYTV 88
                                   578999********744444******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1030.59
//
Query:       gene463|gene463|rna462|rna462  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-19   70.7   0.0    2.6e-17   63.2   0.0    2.1  1  Y_phosphatase    Protein-tyrosine phosphatase
    3.6e-05   23.6   0.0    6.7e-05   22.7   0.0    1.5  1  DSPc             Dual specificity phosphatase, catalytic doma
    4.2e-05   23.6   0.0    5.8e-05   23.2   0.0    1.3  1  Y_phosphatase3   Tyrosine phosphatase family
     0.0015   18.6   0.2      0.012   15.8   0.0    2.3  3  PTPlike_phytase  Inositol hexakisphosphate


Domain annotation for each model (and alignments):
>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   5.8e-21   2.6e-17      22     234 ..      62     243 ..      42     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 5.8e-21
                                    TTTTTTTEEEEEEEEECTEEEEEEEEE---GGGHHHHHHHHHHTT--EEEEESBSEETTEESS---S-SSTSSEEEETTE CS
                  Y_phosphatase  22 ssegpsdYInAnyikgykkekkyIatQgPlkstvedFWrmvwqekvkvivmLtsleekgrekcaqYwpeeeeesleygki 101
                                    ++ g ++Y+nA+++ +   +  +Ia+Q P ++  + F    ++++++++v+L ++ +        Y++   ee l++ k+
  gene463|gene463|rna462|rna462  62 EKYGVKEYVNASFVPTP--RTLFIAAQNPKDEKRDVFLDFLMKSNTNLVVSLINDPK--------YFE---EEWLQNRKV 128
                                    3566678*******555..589*******************************9987........9**...888887776 PP

                                    EEEEE.EEEEEESSEEEEEEEEEETTTTEEEEEEEEEEESSS-SSSSGSCCHHHHHHHHHHHHHHSTTSS-EEEECSSSS CS
                  Y_phosphatase 102 kvtlkekekedekeyvlrelevkkkkeeseerevkqlqytnWpdhgvpesaksllklirkvekskeaksgpvvVhCsaGv 181
                                      ++       ++ ++ +  +v+        r+++ l y nW d +v   +++ ++++++   s   +s pvvVhC aGv
  gene463|gene463|rna462|rna462 129 IKHVG------KDLFIDEAYNVQ---G----RSIRRLRYINWVDFSVI--TREEMETFHSYFDSI--RSDPVVVHCVAGV 191
                                    55555......223444444444...3....47899**********87..333344444444444..4789********* PP

                                    HHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHHTTSTTSS-SHHHHHHHHHHHH CS
                  Y_phosphatase 182 gRtgtfvaldillqqleaeeevdvlqivkelrkqRpgmvqtleqyiflyevil 234
                                    gRtgtf++ dil + +++      ++++ +lr++R+++v++  q+ fl +++l
  gene463|gene463|rna462|rna462 192 GRTGTFIMYDIL-KGMKDITLDAFVNVFLSLRSKRAHLVTNKVQLEFLKNIFL 243
                                    **********86.455553446777999*******************998876 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.5e-08   6.7e-05      73     123 ..     180     234 ..     142     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-08
                                    T-EEEEEESSSSSHHHHHHHHHHHHHHTS.CHHHHHHHH...HHHSTT-SSTHHH CS
                           DSPc  73 gkkvlVHCqaGisRSatliiaYlmktknl.slneayefl...kerrpaispnagf 123
                                       v+VHC aG+ R++t+i+  ++k ++  +l+ +++++   +++r +++ n  +
  gene463|gene463|rna462|rna462 180 SDPVVVHCVAGVGRTGTFIMYDILKGMKDiTLDAFVNVFlslRSKRAHLVTNKVQ 234
                                    568******************9*99776526666666557779999999988554 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.3e-08   5.8e-05      98     139 ..     153     199 ..      86     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-08
                 Y_phosphatase3  98 lYrelle......sakkayrkvfealadeepvlfHCtaGKDRTGvlaa 139
                                     Y ++++      +  ++++ +f+ +++ +pv++HC aG  RTG +++
  gene463|gene463|rna462|rna462 153 RYINWVDfsvitrEEMETFHSYFDSIRS-DPVVVHCVAGVGRTGTFIM 199
                                    56777777777667889***********.***************9876 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.9   4.1e+03     104     125 ..      79     100 ..      24     110 .. 0.57
   2 !   15.8   0.0   2.6e-06     0.012      85     149 ..     137     198 ..      85     204 .. 0.68
   3 ?    0.1   0.0      0.17   7.6e+02     115     137 ..     208     231 ..     204     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.9
                                    EEEE-TTS---HHHHHHHHHHH CS
                PTPlike_phytase 104 Ripitdekapeeedfdalvsil 125
                                    R  + + + p++e+ d ++++l
  gene463|gene463|rna462|rna462  79 RTLFIAAQNPKDEKRDVFLDFL 100
                                    3333344555555555555555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.6e-06
                                    ...EE-HHHHHHHTT-EEEEEEE-TTS---HHHHHHHHHHHHTS-TT-EEEEE-SSSSHHHHHHH CS
                PTPlike_phytase  85 tpeevyerelaeelslrYaRipitdekapeeedfdalvsilkeapektalvfnCqmGrgRTTtam 149
                                      +e y+ + ++  +lrY  i   d   ++ e+++++ s++ +  +++++v++C +G+gRT t++
  gene463|gene463|rna462|rna462 137 FIDEAYNVQGRSIRRLRY--INWVDFSVITREEMETFHSYFDSI-RSDPVVVHCVAGVGRTGTFI 198
                                    555555555555555555..455666777778888888888877.4789************9875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHHHTS.-TT-EEEEE CS
                PTPlike_phytase 115 eedfdalvsilkea.pektalvfn 137
                                    + ++da+v++++++ ++++ lv n
  gene463|gene463|rna462|rna462 208 DITLDAFVNVFLSLrSKRAHLVTN 231
                                    5689**********7777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1533.26
//
Query:       gene464|gene464|rna463|rna463  [L=795]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-38  133.0   0.1    2.6e-38  132.2   0.1    1.3  1  RPN1_RPN2_N  RPN1/RPN2 N-terminal domain
    3.4e-12   46.1   1.7     0.0045   17.4   0.0    7.0  8  PC_rep       Proteasome/cyclosome repeat
      4e-07   30.0   0.0    7.7e-07   29.1   0.0    1.5  1  RPN1_C       26S proteasome non-ATPase regulatory subunit RPN
  ------ inclusion threshold ------
      0.013   15.5   0.2      0.051   13.6   0.1    2.0  2  Cnd1         non-SMC mitotic condensation complex subunit 1
      0.021   15.1   0.1      0.056   13.7   0.1    1.8  1  ANAPC3       Anaphase-promoting complex, cyclosome, subunit 3
      0.091   13.2   0.0         17    5.9   0.0    3.2  3  HEAT_2       HEAT repeats


Domain annotation for each model (and alignments):
>> RPN1_RPN2_N  RPN1/RPN2 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.2   0.1   8.6e-42   2.6e-38       1     305 [.       6     283 ..       6     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 132.2 bits;  conditional E-value: 8.6e-42
                    RPN1_RPN2_N   1 LellverlkdadaelaklaLeaLkeeirtsts.smTSvPkPLKfLrphyetlkeiyetlkkskakklladilsvlamtls 79 
                                    L+++ver++d+d++++++aL++L + +++s s s+ ++   + +L      l++++++++  +++++l+di+s +++  +
  gene464|gene464|rna463|rna463   6 LKIIVERIRDPDPDIQNNALSMLFDITKSSHSkSIDTI--NFQYLADNLPVLEDVCREVT-GDTRRRLCDIISAICVIDD 82 
                                    6899************************9977355555..69****************98.5678899******998755 PP

                    RPN1_RPN2_N  80 degkresLkyrlegskedigsWGheYvrhLaaeiaeeyqerqeeekeeetkekkkkvkellelvkeivpfllkhnaeaeA 159
                                       +r+ L+yr+eg+  d+++WGh Yv++L+  ia++   +++              ++   + ++++ fl+khnae eA
  gene464|gene464|rna463|rna463  83 ---ERKLLAYRVEGNVIDLKEWGHLYVKKLTECIANAKGGKMDFP-----------FEKTEYVGRKCIDFLFKHNAEFEA 148
                                    ...5******************************99877777666...........4555556799************** PP

                    RPN1_RPN2_N 160 vDLllEvekleklvklvdeenyqrvclYLlscakylaepddvellrvafeiyrklkkyseaLrvalrlndkelvkevfka 239
                                    +D l+E+  +e+++++vd++ny+r++lYL  ++++++      l +v++ iy+k++++s+ ++  +r +  +   e +++
  gene464|gene464|rna463|rna463 149 IDFLVEIGGIEMILDYVDTHNYNRIVLYLEDMCSFIE------LSDVILGIYLKMNDHSRYVVGLIRRQRIREAIEYVRN 222
                                    ***********************************85......77799************9999999999999999999* PP

                    RPN1_RPN2_N 240 aedklvkkQlayllarqqvkleleeledededlneilsneklsehfkaLakdLdvlepktpediYK 305
                                     edk  kkQ  y+lar  + +e++     d++ ++ilsn ++++ +++ a +L++  p + + i K
  gene464|gene464|rna463|rna463 223 IEDKDYKKQCLYILARCDLYYETS-----DRKERHILSNGHVKDVYRSVAAELEIDKPSKMDGILK 283
                                    ******************999999.....567789***********************99998877 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   9.6e+03      15      31 ..      22      37 ..      21      40 .. 0.74
   2 ?    1.8   0.0      0.13   3.8e+02       7      17 ..     302     312 ..     298     315 .. 0.83
   3 ?    0.9   0.0      0.25   7.6e+02       5      30 ..     344     369 ..     344     370 .. 0.81
   4 ?   -2.0   0.0       2.1   6.2e+03      17      30 ..     392     405 ..     377     406 .. 0.75
   5 !    7.7   0.0    0.0017         5      10      33 ..     420     443 ..     418     444 .. 0.89
   6 !    9.3   0.0   0.00056       1.7       6      33 ..     451     478 ..     448     480 .. 0.91
   7 !   17.4   0.0   1.5e-06    0.0045       2      33 ..     625     656 ..     624     658 .. 0.83
   8 ?   -2.5   0.1       2.9   8.8e+03       4      14 ..     664     674 ..     664     677 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                                   CHHHHHHHHHHHHHHSS CS
                         PC_rep 15 neeaislLkpylsdtsa 31
                                   n+ a+s+L ++ +++ +
  gene464|gene464|rna463|rna463 22 NN-ALSMLFDITKSSHS 37
                                   66.9****999876654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                                    HHHCTTSTCHH CS
                         PC_rep   7 GlihaGsgnee 17 
                                    G +h+G+g+++
  gene464|gene464|rna463|rna463 302 GFVHMGYGRDP 312
                                    99*******97 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.25
                                    HHHHHCTTSTCHHHHHHHHHHHH.HHS CS
                         PC_rep   5 ALGlihaGsgneeaislLkpyls.dts 30 
                                    ++G+i  + ++e +++ L++++  dts
  gene464|gene464|rna463|rna463 344 SIGVIESW-NSEKVMETLQEHIFaDTS 369
                                    68888899.999********9764666 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.1
                                    HHHHHHHHHHHHHS CS
                         PC_rep  17 eaislLkpylsdts 30 
                                    ++++lL++ l++ts
  gene464|gene464|rna463|rna463 392 AILALLSNNLQSTS 405
                                    78899999998886 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0017
                                    CTTSTCHHHHHHHHHHHHHHSSHH CS
                         PC_rep  10 haGsgneeaislLkpylsdtsaev 33 
                                    + G+ +ee+++lL+p++ ++s+ev
  gene464|gene464|rna463|rna463 420 FSGTQSEEVRELLQPLMFSDSSEV 443
                                    5699*************9999987 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.00056
                                    HHHHCTTSTCHHHHHHHHHHHHHHSSHH CS
                         PC_rep   6 LGlihaGsgneeaislLkpylsdtsaev 33 
                                    LG +++Gs +e+++sl+++   +++ e+
  gene464|gene464|rna463|rna463 451 LGSVFCGSADEDLTSLMLQTFVEKEKES 478
                                    8******************999998876 PP

  == domain 7  score: 17.4 bits;  conditional E-value: 1.5e-06
                                    HHHHHHHHCTTSTCHHHHHHHHHHHHHHSSHH CS
                         PC_rep   2 AllALGlihaGsgneeaislLkpylsdtsaev 33 
                                     + +LGli+aG+ n++++++L+++ s+++ ++
  gene464|gene464|rna463|rna463 625 TIVSLGLIGAGTLNSRITKILDQQYSYYYKDS 656
                                    5779******************8877666555 PP

  == domain 8  score: -2.5 bits;  conditional E-value: 2.9
                                    HHHHHHCTTST CS
                         PC_rep   4 lALGlihaGsg 14 
                                    +A+Gl+ +G g
  gene464|gene464|rna463|rna463 664 IAQGLVSLGKG 674
                                    699***99976 PP

>> RPN1_C  26S proteasome non-ATPase regulatory subunit RPN1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.6e-10   7.7e-07       1      51 [.     748     795 .]     748     795 .] 0.91

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.6e-10
                         RPN1_C   1 VgqaGkpktItGfqThttPVlLaageRAELateeYiplssvLEgivilkkn 51 
                                    Vg  G pk+ +  q ht+PV+L+ + RAE  ++    +ss +E++ ilkkn
  gene464|gene464|rna463|rna463 748 VGMVGEPKKLSSVQIHTSPVVLNEKTRAETDEN---VCSSYIEDVLILKKN 795
                                    899*************************95544...47899*********9 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.7e-05     0.051      59     128 ..       5      79 ..       1      95 [. 0.74
   2 ?   -1.9   0.0         1   3.1e+03      99     132 ..     337     369 ..     333     373 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                           Cnd1  59 flselaklleDenprVvanalaalteisekse.....naiynllpdiisklsdalnecsewgqitilefLlsyip 128
                                     l+ + + ++D++p +++nal++l +i + s      ++ ++ l d +  l d   e++ ++++  +++++    
  gene464|gene464|rna463|rna463   5 ELKIIVERIRDPDPDIQNNALSMLFDITKSSHsksidTINFQYLADNLPVLEDVCREVTGDTRRRLCDIISAICV 79 
                                    566778899********************9442333344566777777778877788999999999998887544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                           Cnd1  99 diisklsdalnecsewgqitilefLlsyipkdkq 132
                                    d+is +  ++  ++ w+  +++e+L ++i  d++
  gene464|gene464|rna463|rna463 337 DLISIFG-SIGVIESWNSEKVMETLQEHIFADTS 369
                                    5666666.5677899999******9999877765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.9e-05     0.056       2      69 ..     167     243 ..     166     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                    TT-HHHHHHHHHHHH............HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHT CS
                         ANAPC3   2 qnnyknAiflaerll..........a.aetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkL 69 
                                    ++ny+ +++++e ++            + + ++ ++y  +  l ++++  +A+e++r+ + ++  ++c+y++A+c l +
  gene464|gene464|rna463|rna463 167 THNYNRIVLYLEDMCsfielsdvilGiYLKMNDHSRYVVG--LIRRQRIREAIEYVRNIEDKDYKKQCLYILARCDLYY 243
                                    6888888888888887777665554157788888888844..679999***********9999999*********8876 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0056        17      33      80 ..       6      68 ..       2      77 .. 0.68
   2 ?   -2.0   0.0       1.7     5e+03      25      71 ..     349     401 ..     344     409 .. 0.56
   3 ?    3.4   0.0     0.034     1e+02      20      58 ..     410     454 ..     390     475 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0056
                         HEAT_2 33 lpaLvellededpavRraaaeaLgai.........g......dpealpaLkellddddddvvR 80
                                   l+++ve ++d+dp+++ +a   L  i         +      + ++lp+L++ +++ + d +R
  gene464|gene464|rna463|rna463  6 LKIIVERIRDPDPDIQNNALSMLFDItksshsksiDtinfqyLADNLPVLEDVCREVTGDTRR 68
                                   6789999*************9996553222222221333333577888888888776666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                         HEAT_2  25 grignpealpaLvell..ededpavRraaaeaLgaig....dpealpaLkell 71 
                                     ++++++++++L e +  +++++ +      aL+ ++    +p+ l++L   l
  gene464|gene464|rna463|rna463 349 ESWNSEKVMETLQEHIfaDTSHRKTGSLLGLALSGLKnfeeRPAILALLSNNL 401
                                    46777788888887665233445565555566655542222355555555555 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.034
                         HEAT_2  20 airaLg......rignpealpaLvellededpavRraaaeaLgai 58 
                                    ++  Lg        +++e++++L +l+ +++++v    a +Lg +
  gene464|gene464|rna463|rna463 410 IATLLGiesmfsGTQSEEVRELLQPLMFSDSSEVVFFTAFTLGSV 454
                                    445555666665678999*********777777777777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5055.54
//
Query:       gene465|gene465|rna464|rna464  [L=595]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-18   65.7   0.0    5.9e-18   65.1   0.0    1.3  1  Lipase_3       Lipase (class 3)
    0.00038   20.2   0.0     0.0006   19.5   0.0    1.2  1  Abhydrolase_1  alpha/beta hydrolase fold
     0.0079   15.5   0.0      0.012   14.8   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
  ------ inclusion threshold ------
      0.012   15.3   0.0       0.02   14.6   0.0    1.3  1  PGAP1          PGAP1-like protein
      0.014   16.0   0.0      0.024   15.3   0.0    1.3  1  Abhydrolase_6  Alpha/beta hydrolase family


Domain annotation for each model (and alignments):
>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   1.7e-21   5.9e-18       1     139 [.     352     479 ..     352     482 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 1.7e-21
                                    EEEE----------------EEE-HHHH-GTT-EEEHHHHHHHHS-HHHHHHHHHHHHHHHTT-EEEEEEEETHHHHHHH CS
                       Lipase_3   1 vvafRGtesakdwltdldfslteakellekeggkvhsgfleayeeslreqvlkelkrllekypeysivvtGHSLGgalAl 80 
                                    vv+f+Gt++ +++++d++++  e+ +      g vh+gf ++++  + ++  + ++r l+k  + ++ + GHSLGga+++
  gene465|gene465|rna464|rna464 352 VVSFKGTTNSEETIQDINCEYAEFGT------GFVHNGFKKLAT-YFIDNHINAIERTLTKLGTKKLLLLGHSLGGAISM 424
                                    79*****************9999988......689*********.99999999*************************** PP

                                    HHHHHHHHTT-SS---EEEEEES----B-HHHHHHHHT-TTEEEEEEEETT--GGG-S- CS
                       Lipase_3  81 LaaldlvengenekkkvtvvtfGqPrvgnkefaklvdsqlnkkvlrvvntnDivPrlpp 139
                                    L+ +++ e++  +  +v++++f++P v ++e+a++++    + ++ + + nDi+Pr+++
  gene465|gene465|rna464|rna464 425 LVKIMVEEMKLLKGMDVEAIVFSSPPVVSEEIASRFS----DGITVINYGNDIIPRMSY 479
                                    ************************************9....67999**********987 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.7e-07    0.0006      39      89 ..     357     425 ..     350     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.7e-07
                                    TSTTSSSTTTGB...................CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHH CS
                  Abhydrolase_1  39 GvgySspapacin..................ddygtasvaddldrildalgddkltlvGhSmGGmiala 89 
                                    G   S+  +  in                   +y ++++ + ++r l +lg +kl l+GhS+GG+i++ 
  gene465|gene465|rna464|rna464 357 GTTNSEETIQDINceyaefgtgfvhngfkklATYFIDNHINAIERTLTKLGTKKLLLLGHSLGGAISML 425
                                    6666777777777777666666666666555666777888888888********************975 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.5e-06     0.012      59     112 ..     392     452 ..     376     489 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.5e-06
                    Hydrolase_4  59 vdDlaafvekvkeehpelplfllGhSmGGliallyllrypd.......kvaglilsaPalk 112
                                    +d    ++e+  ++ ++++l llGhS+GG+i++l+  + ++       +v+++++s+P + 
  gene465|gene465|rna464|rna464 392 IDNHINAIERTLTKLGTKKLLLLGHSLGGAISMLVKIMVEEmkllkgmDVEAIVFSSPPVV 452
                                    555566777888888899***************9984444444566668999999999764 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.7e-06      0.02      71     132 ..     391     454 ..     370     465 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-06
                          PGAP1  71 ylndaIkyIlslysssekeptsviliGHSmGGivaraaltlkn....yikqsvntiltlasPhalp 132
                                    ++++ I+ I +    ++  +++++l+GHS+GG ++ ++ ++ +    ++  +v+ i+  + P+++ 
  gene465|gene465|rna464|rna464 391 FIDNHINAIERTL--TKLGTKKLLLLGHSLGGAISMLVKIMVEemklLKGMDVEAIVFSSPPVVSE 454
                                    6677778877777..7778999***********997765544444556677899999888888765 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   6.6e-06     0.024      52      97 ..     398     450 ..     357     494 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.6e-06
                                    HHHHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC..............EE.EEES-.. CS
                  Abhydrolase_6  52 dlaalldelaagggpvvlvGHSlGGalalaaapla............lvvg.vlldppp 97 
                                    +++++l++l  g+++  l+GHSlGGa++++   +             +v++ v+ +p p
  gene465|gene465|rna464|rna464 398 AIERTLTKL--GTKKLLLLGHSLGGAISML---VKimveemkllkgmDVEAiVFSSP-P 450
                                    335566666..69999*************9...665556667666655555344444.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3640.62
//
Query:       gene466|gene466|rna465|rna465  [L=126]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-09   36.6   2.0      5e-09   36.4   1.4    1.5  1  Ribosomal_L27e  Ribosomal L27e protein family
    0.00035   20.4   1.6     0.0006   19.7   1.6    1.4  1  KOW             KOW motif
  ------ inclusion threshold ------
       0.03   14.1   0.0       0.05   13.4   0.0    1.3  1  DNA_pol3_delta  DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> Ribosomal_L27e  Ribosomal L27e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   1.4   8.4e-13     5e-09      12      85 .]      54     126 .]      39     126 .] 0.82

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.4e-13
                 Ribosomal_L27e  12 akrskikpFvKvvnynhlmpTRYtvdvedlkelvkkealkdpakrkeakkevkkkfeeryksgknkwffkkLrF 85 
                                    +++sk+ + +K +n++hl++TRY+ d+  l+++  +   ++++ ++ +  ++k+ + +  k++k k++f+ L F
  gene466|gene466|rna465|rna465  54 RRNSKFYVVLKKYNISHLIATRYKADL-GLSSIDYSGIEQNAETKRVLTDKTKDFMMKAWKESKAKFLFSSLSF 126
                                    4567889999*************9999.4444444444468889999999999999999*************99 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.6     1e-07    0.0006       5      27 ..       9      38 ..       8      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-07
                                   EEESSSTTTTCEEEEEEEETTT.......T CS
                            KOW  5 VkVvsGphkGktGkVvkvdqhk.......v 27
                                   V V+sG+++Gk+++V k  +++       v
  gene466|gene466|rna465|rna465  9 VVVTSGKNAGKKAVVIKQLDERyvltacvV 38
                                   9****************9999965555555 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.4e-06      0.05      95     155 ..       7      72 ..       3      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.4e-06
                                    EEEEEES.S--HHHH.HHHHHTT....TEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHH CS
                 DNA_pol3_delta  95 lLiliapkklderkk.lvklLkk....katvveaktlkeeelkkwiqkraqelglkiekealelLl 155
                                    ++++++++k + +k  ++k+L++    +a+vv++ + +e+  +kwi++r ++  + ++k  ++ L+
  gene466|gene466|rna465|rna465   7 MIVVVTSGKNAGKKAvVIKQLDEryvlTACVVRVPKDSEDHQPKWIKRRNSKFYVVLKKYNISHLI 72 
                                    6777777677766666*******999999***************************9999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 862.81
//
Query:       gene467|gene467|rna466|rna466  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0079   16.9   0.1      0.012   16.3   0.1    1.3  1  PMC2NT    PMC2NT (NUC016) domain


Domain annotation for each model (and alignments):
>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   6.8e-07     0.012      25      82 ..       6      59 ..       3      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.8e-07
                         PMC2NT 25 faksldeqserllslinsllklaaskseisassklededdvee...kfksvvdvvDsllEk 82
                                   + ks+++++er+l+  +++l+++ s++++ ++      d+v++     + vv++vDs lE 
  gene467|gene467|rna466|rna466  6 LVKSIEANAERILEDFTEILQYLRSEGSD-KC------DEVQNllfATRRVVNLVDSALEI 59
                                   56899***********************9.33......555555448999*********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 706.97
//
Query:       gene468|gene468|rna467|rna467  [L=1144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.6e-122  409.5   0.0   2.9e-122  408.6   0.0    1.4  1  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    1.5e-47  161.0   0.4    1.5e-47  161.0   0.4    2.2  2  TOPRIM_C       C-terminal associated domain of TOPRIM
    9.5e-21   74.0   0.8    2.2e-20   72.8   0.8    1.6  1  DNA_gyraseB    DNA gyrase B
      8e-14   52.1   0.0    1.8e-13   51.0   0.0    1.7  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    1.4e-08   34.9   0.0    5.1e-08   33.1   0.0    2.0  1  Toprim         Toprim domain


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.6   0.0  8.2e-126  2.9e-122       1     426 []     663    1067 ..     663    1067 .. 0.96

  Alignments for each domain:
  == domain 1  score: 408.6 bits;  conditional E-value: 8.2e-126
                  DNA_topoisoIV    1 RaiPsvrDGlKPvqRriLyamfkllnldkkekKvaqlvGev..lgkYhPHGdaslydaivrlaqdfvg..niplldpq 74  
                                     R+iPs++DGlKP+qR++++++fk +nl ++e+KvaqlvG+v  +++Yh HG++sl+++iv+laqdfvg  ni+ll p 
  gene468|gene468|rna467|rna467  663 RSIPSLVDGLKPGQRKVMFSCFK-RNL-RSEIKVAQLVGYVseQSAYH-HGEQSLCSTIVNLAQDFVGsnNINLLLPI 737 
                                     9**********************.999.***************9****.***************************** PP

                  DNA_topoisoIV   75 GnfGsildgdkd.AaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatki 151 
                                     G+fGs+l+g+kd A++RYi+t Ls+++r +++e d+ +++y ++ D+ ++EPe+++piiP++LvnGaeGI++G++t+i
  gene468|gene468|rna467|rna467  738 GQFGSRLQGGKDaASPRYIFTSLSPLTRLIFNENDDAILNYLND-DNLSIEPEFYVPIIPMVLVNGAEGIGTGWSTSI 814 
                                     ********************************************.********************************* PP

                  DNA_topoisoIV  152 pphnlkeiidaliallkgeeaellelvlgPdfptgggiigkeeikeayetgrGkikvrakveiee.ktivitElPigv 228 
                                     p++n+ +++++++++++ge++    +++ P++++++g i+        + g+Gk++v++ ++  +   ++itElP+g+
  gene468|gene468|rna467|rna467  815 PNFNPIDVVENIRRMIRGEDP----VEMVPYYRNFRGSIE--------KIGEGKFQVSGVYK--GdMDLEITELPVGT 878 
                                     *******************99....469***********4........46689999999966..4499********** PP

                  DNA_topoisoIV  229 ntskliekieelvkkkkikisdirde.sdrgvrivielkrgaseekvleklykktkLessisvnnlvlfdkk...pky 302 
                                     +t +++e++e+lv+++ +k  d++++ ++++v+++++l++           ++++kL+++i++nn+v+fd++   +ky
  gene468|gene468|rna467|rna467  879 WTLNYKEFLESLVQAGVVK--DFKEYhTEKTVNFTVKLAK----------HVSNLKLSNTITINNMVCFDENlgiKKY 944 
                                     *******************..*****8889*******994..........345699***************779**** PP

                  DNA_topoisoIV  303 lslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskk.ekkakkeLieelse..... 374 
                                      ++k+il++f++vrl++y+ rk+ +++ ++++l +le      nk+++++ev  + +  ++++k+e+i +l++     
  gene468|gene468|rna467|rna467  945 STPKDILRDFYDVRLRYYSMRKDNMMKVMKDELVKLE------NKVKFIKEVSTGGLIiNRRRKAEIIFDLESrgyar 1016
                                     *************************************......***************9************9999999 PP

                  DNA_topoisoIV  375 .eqaeyllemrlrrLtkeeveklekeieelekeikelekllaklkklikeeld 426 
                                      +++eyll m++ +Lt e++ekl++e+++  +e ++l  +++k   l+ e+ld
  gene468|gene468|rna467|rna467 1017 vDDYEYLLGMSILSLTVERIEKLNNEHAKRLEEYNKLAGKTPK--VLWLEDLD 1067
                                     999****************************************..99999985 PP

>> TOPRIM_C  C-terminal associated domain of TOPRIM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       3.7   1.3e+04      34      56 ..     162     184 ..     151     196 .. 0.68
   2 !  161.0   0.4   4.2e-51   1.5e-47       1     128 []     538     661 ..     538     661 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.7
                       TOPRIM_C  34 lkkwkikYYkGLgtstskeakey 56 
                                    +k +k kY   +g +++ e ++y
  gene468|gene468|rna467|rna467 162 KKYYKQKYRNNMGAKEEPEISRY 184
                                    45677777777777777666655 PP

  == domain 2  score: 161.0 bits;  conditional E-value: 4.2e-51
                       TOPRIM_C   1 FitPivkvtkkkkeeisffslpeyeewkestenlkkwkikYYkGLgtstskeakeyfsnldkhlkefkleeeedkeaiel 80 
                                    FitPi+++tkk  ++++ff+lpeyee+k+s+   ++w+ikYYkGLgtsts++ak+yfsnl  h+k+f+   +edke+i+l
  gene468|gene468|rna467|rna467 538 FITPIIRATKKG-QVRDFFTLPEYEEFKRSE---EGWNIKYYKGLGTSTSADAKQYFSNLPIHVKHFTPLVDEDKELIDL 613
                                    9********875.89*************998...79******************************************** PP

                       TOPRIM_C  81 aFskkkaderkewlkklepgtyldkkkkkisysdFvnkeLilfsmadn 128
                                    aF+kkkad+rk+wl ++epgt+ld++ ++is+sdFvnkeLilfsmadn
  gene468|gene468|rna467|rna467 614 AFNKKKADARKTWLLSFEPGTFLDQSLSHISISDFVNKELILFSMADN 661
                                    ***********************************************8 PP

>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.8   6.3e-24   2.2e-20      29     166 ..     261     391 ..     226     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 6.3e-24
                    DNA_gyraseB  29 veevievevalqwtssyse.nilsFvNniatpeGGtHvdgfksaltktlneyakkkkllkkkeekisgediregltavvs 107
                                    +++++e  val  t+s+++ +++sFvN i t++GG+Hv+++ + +++ l+e+++kk++   +  ++++ +i++ ++++v+
  gene468|gene468|rna467|rna467 261 INDRWE--VAL--TTSEEQfQQVSFVNAICTTKGGSHVNHVVERIVEPLSEAIQKKEK---GL-SVKPFQIKSCMFIFVN 332
                                    355444..455..4445555**********************************9885...55.9*************** PP

                    DNA_gyraseB 108 vkipepqFeGQTKekLgnsevk..sivekvvseeleafleenkeeakkilekaveaakare 166
                                    + i++p F++QTKe+L+ + ++  s +e +    + + + +n+++++k++++a++++  ++
  gene468|gene468|rna467|rna467 333 CLIENPAFDSQTKENLTLRVSAfgSKCEPI--ADFVKSVIKNTSIVQKVASFAKARQSLQL 391
                                    *****************9988854666633..45666777778888888887777666555 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   5.1e-17   1.8e-13       4     111 ..      54     199 ..      51     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.1e-17
                                    HHHHHHHHHHHHHHHHH...HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT........GTCSTTCH.....HCST CS
                      HATPase_c   4 krLrqiisnlvdNavkf...atkageieveikaseddlvisveDnGiGipkedlk........klfekfsq.....ddst 67 
                                    ++L++i+++++ Na+++    +k++ i+v+i+ +e +++isv +nG+Gip+ ++k        ++f+++ +     d+++
  gene468|gene468|rna467|rna467  54 PGLYKIFDEIIVNAADNkirDPKMDVIKVSID-PE-KNEISVYNNGKGIPVRIHKeenvyvpeLIFGNLLTssnynDEEK 131
                                    6899999999999999977667**********.44.9**************************99997777799999999 PP

                                    CHTSTSSSHHHHHH..............HHHHHHTTTEEEE..............EEET.......TTEEEEEEEEESS CS
                      HATPase_c  68 krggggtGlGlsiv..............kklvelmgGeiwv..............esep.......grGttftftlple 111
                                    k++gg++G+G++++              +           v              ++ep       g  t++tf+++l+
  gene468|gene468|rna467|rna467 132 KVTGGRNGYGAKLCnifskefivetadcE-----------VkkyykqkyrnnmgaKEEPeisrytkGDFTRITFKPDLR 199
                                    **************444422222222220...........233444444444444222223333446688899998875 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.4e-11   5.1e-08       2      88 ..     424     522 ..     423     533 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.4e-11
                                    EEEESSHHHHHHHHHTHT...STEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH......HHHHHHHHSEEEEE CS
                         Toprim   2 lvivEgpsdaktiakalg...sgfqavtaslGhildlet.efkpvye..eiedkkkvlka......lkelakradeiila 69 
                                    l++ Eg+s+   + + l+   ++++ v++++G++l++ + + k+++e  ei ++kk+l+        + +++r+ +++++
  gene468|gene468|rna467|rna467 424 LILTEGDSAKTLAVSGLSvvgRDTYGVFPLRGKLLNVREaSHKQIMEnsEISSIKKILGLqhnkvyEDTSSLRYGHVMIM 503
                                    8999***97777777777888******************76666666999999999999888886455555********* PP

                                    CSSSHHHHHHHHHHHHHHT CS
                         Toprim  70 tDpDreGeaiawellevlk 88 
                                    tD D +G++i+ +++++l+
  gene468|gene468|rna467|rna467 504 TDQDHDGSHIKGLIINFLD 522
                                    ***************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.84u 0.29s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 6759.34
//
Query:       gene469|gene469|rna468|rna468  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1216.06
//
Query:       gene470|gene470|rna469|rna469  [L=401]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0066   14.1   0.1       0.01   13.4   0.1    1.2  1  INTS2     Integrator complex subunit 2


Domain annotation for each model (and alignments):
>> INTS2  Integrator complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   5.8e-07      0.01     908     952 ..     299     343 ..     287     376 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-07
                          INTS2 908 licshlHQvFIadpslakLvHFQgYpseLlpltvagipSmHiCld 952
                                    l+   +HQ+ ++ p l+k +    +p +L+  +v+ +pS H+  +
  gene470|gene470|rna469|rna469 299 LLKEVIHQLILDTPILVKVIVMRRFPCNLVRKMVECVPSFHLAYE 343
                                    566689***********************************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2438.85
//
Query:       gene47|gene47|rna47|rna47  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00027   19.9   0.2    0.00032   19.7   0.2    1.0  1  Trehalase  Trehalase
  ------ inclusion threshold ------
       0.43   10.3   4.3       0.14   12.0   1.1    1.6  2  PAW        PNGase C-terminal domain, mannose-binding module P


Domain annotation for each model (and alignments):
>> Trehalase  Trehalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   3.5e-08   0.00032     202     290 ..      25     113 ..      13     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-08
                                HHHHHHHHHHHHCCTTTCCETTCCC-CTC-EEE--SSSTTS-TCCCHHHHHHHHHCTTHCCHHHHHCCCCHHHHHCCHHCHHHH CS
                  Trehalase 202 ravlaalkkeyefwmaeqrldevtklskryllnrygvpeetprpesyledketaeklkkerkkeevyrelkaaaesgwdlssRw 285
                                ++v ++ ++e+++w ++ r+ ++ + ++ + l+ + ++++ p ++ +++    a k +++r  +++y++ k+a+e+  d+  R 
  gene47|gene47|rna47|rna47  25 SKVSKKKEEEKSMWKKNVRHYKILSVDQISALEDFFISKQLPITKTNIKHASKALKIPYQRSVNYLYNKYKKAQENAEDFYHRC 108
                                567778899**************************************************************************9 PP

                                CCCCT CS
                  Trehalase 286 lresg 290
                                ++e g
  gene47|gene47|rna47|rna47 109 IHEFG 113
                                98855 PP

>> PAW  PNGase C-terminal domain, mannose-binding module PAW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.16   1.5e+03      55      66 ..      30      41 ..      19      58 .. 0.60
   2 ?   12.0   1.1   1.5e-05      0.14      25      83 ..      65     125 ..      54     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.16
                               GTTEEEESGGGG CS
                        PAW 55 kneeeikgwesa 66
                               k+eee++ w++ 
  gene47|gene47|rna47|rna47 30 KKEEEKSMWKKN 41
                               223444445444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.5e-05
                                -EB---HHHHHHTEEEEEEETTTT.EEEECCGTTEEEES.GGGG-SSEESEEEEEETTTTE CS
                        PAW  25 yvfkptekekkekllelrYsivkD.kYvrvskneeeikg.wesavfevenifrkvEeDWkm 83 
                                  ++ t+ ++ +k l++ Y+ + +  Y +++k +e++++ ++++++e+  i++ vE+ W+m
  gene47|gene47|rna47|rna47  65 LPITKTNIKHASKALKIPYQRSVNyLYNKYKKAQENAEDfYHRCIHEFGLIMQNVEKCWEM 125
                                556788899999*******976552688888877776661678999999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 922.29
//
Query:       gene471|gene471|rna470|rna470  [L=392]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-17   61.6  31.4    9.7e-12   45.4  10.7    3.0  3  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4  10.7   5.4e-16   9.7e-12       4     119 ..      58     181 ..      55     188 .. 0.76
   2 ?   -0.9   0.2      0.11     2e+03      75      85 ..     200     210 ..     181     250 .. 0.53
   3 !   25.2   8.3   9.4e-10   1.7e-05       2     123 ..     261     377 ..     260     378 .. 0.64

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 5.4e-16
                                    HHHHHHHHHHHHHHHHHHHHHTTSS.-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-........CTSHH.HHHHH CS
                           MgtE   4 ilglgGnlgaqlasristalhlgel.ekklkkvllkelrvvlllgvilgllifllalllgw.......slllal.vvgla 74 
                                    il+++Gn++ ++a+ +s++ h  ++ +k+++ +++ +  +vl +++i+gl i+l+ ++ g        +  l+l +v+ +
  gene471|gene471|rna470|rna470  58 ILSFKGNIEVIFAMYLSSMSHSPLFiYKNYFIYVFDNSNLVLAQSAIIGLTIGLVGII-GTtlsgelhT-GLGLaIVTGS 135
                                    899********************995666999********************999665.3346666742.3333145555 PP

                                    HHHHHHHHHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHH CS
                           MgtE  75 lvlvllaaall.ilgvllplllwklglDPdnaaiPlltalgDllgt 119
                                    lv ++l+++l+ il v+ + +++ lg++Pdn+++P ++++gD + +
  gene471|gene471|rna470|rna470 136 LVSCILTTILFiILLVISIEVSKILGINPDNIILPTISSFGDYMNV 181
                                    55555555555666666668**********************9544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHH CS
                           MgtE  75 lvlvllaaall 85 
                                    l++++l+ +++
  gene471|gene471|rna470|rna470 200 LICIFLSISII 210
                                    33333333332 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 9.4e-10
                                    HHHHHHHHHHHHHHHHHHHHHHHTTSS-GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHH CS
                           MgtE   2 PvilglgGnlgaqlasristalhlgelekklkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvlvlla 81 
                                    Pv++g++ +++ + +  i t+++ ++++++       + +++++++v+++l  +++a+l+g +    +++ +++++v+ +
  gene471|gene471|rna470|rna470 261 PVFSGMSVSIAFIYLHKIFTSINNQTIHNS-----KESYITLVFISVLMSLTYLVIAILMGLQYSHEFCILFMIFFVFHV 335
                                    9999***********************777.....223333333344444444444443333222222233333333333 PP

                                    HHHH...HHHHHHHHHHTTS-GGGSHHHHHHHHHHHHHHHHHH CS
                           MgtE  82 aall.ilgvllplllwklglDPdnaaiPlltalgDllgtlllv 123
                                    ++ll  + +l+   l k++ D  ++a+Pl+++++D+l+ ++l+
  gene471|gene471|rna470|rna470 336 TILLrGISILV-EYLDKKEEDTGVMALPLIASISDVLSAGFLL 377
                                    33333334555.89***********************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2159.23
//
Query:       gene472|gene472|rna471|rna471  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-17   62.2   0.1    9.6e-17   61.4   0.1    1.5  1  HSF_DNA-bind   HSF-type DNA-binding
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.016   15.2   0.0    1.2  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> HSF_DNA-bind  HSF-type DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.1   1.1e-20   9.6e-17       1      95 [.      16     111 ..      16     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.1e-20
                                    HHHHHHHHHCTTTT..SEESSSSSEEEES-HHHHHHHTHHHHSTT--HHHHHHHHHHTTEEE---SSBTTB--TTSEEEE CS
                   HSF_DNA-bind   1 FlkkLyklledeel..isWsedgksfvvkdkeefakevlpkyfkhsnfssFvrqLnlYgFrkvkrkeekkkkkskvweFs 78 
                                    F+ kLyk  +de++  i+W++dg +++++d++ f ke+lp + k+++f +F+r Ln YgF k k+        ++   ++
  gene472|gene472|rna471|rna471  16 FIMKLYKATSDEKYkgICWTSDGLKIHIYDRDVFVKETLPLISKTREFGTFIRMLNSYGFVKSKD-------IEEEDIYY 88 
                                    9********9966566**********************************************774.......345668** PP

                                    ESS--XXXX......XXXXXXXX CS
                   HSF_DNA-bind  79 henFkrgkp......elLkkikr 95 
                                    ++nF++g++      ++L+ ikr
  gene472|gene472|rna471|rna471  89 NKNFRKGREdllgidDSLRMIKR 111
                                    ********933333344666666 PP

>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-06     0.016      22      94 ..      59     131 ..      44     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                                    XXXXESXEEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXCEEXXSXXXXEEEEE-SS-TTTSSSSXEEEEEEE CS
                  Ribosomal_L16  22 tklefgdygLvalekgqltaealeaariainrylkkkrgkklwirvfphhpvtkkagedRmgkGkGkpegwva 94 
                                    ++ efg++  + +++g ++++ +e   i  n++++k r++ l i     ++ +kk ++ Rm  G G+ +++v 
  gene472|gene472|rna471|rna471  59 KTREFGTFIRMLNSYGFVKSKDIEEEDIYYNKNFRKGREDLLGIDDSLRMIKRKKSNDIRMRIGDGSLKEVVE 131
                                    56678888778889*********************99999**************************9998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1587.56
//
Query:       gene473|gene473|rna472|rna472  [L=771]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 5022.44
//
Query:       gene474|gene474|rna473|rna473  [L=260]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      2e-23   82.6   0.0    3.4e-23   81.9   0.0    1.3  1  JAB         JAB1/Mov34/MPN/PAD-1 ubiquitin protease
    2.2e-17   63.5   0.0      4e-17   62.6   0.0    1.4  1  MitMem_reg  Maintenance of mitochondrial structure and functi
  ------ inclusion threshold ------
      0.013   15.7   0.0       0.03   14.5   0.0    1.6  1  SPATA19     Spermatogenesis-associated protein 19, mitochondr


Domain annotation for each model (and alignments):
>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0   5.6e-27   3.4e-23       5     117 ..       5     106 ..       2     107 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 5.6e-27
                                    EEEEEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCTT CS
                            JAB   5 avhleslvllkildhalrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklrgr 84 
                                    +v++++lvll+ +dh++r++++  +v+G+l+G  +++  ++it++fa +fee+e+    +++d +y++++ el++k++ +
  gene474|gene474|rna473|rna473   5 SVIVHPLVLLSAVDHYKRKGTK--RVAGILLGNEDGE--IHITESFACIFEEDEDG---WFIDTSYIRSMFELFYKVNHK 77 
                                    799*******************..********98888..*****************...********************* PP

                                    SEEEEEEEESSSS-SS--HHHHHHHHHHHHHST CS
                            JAB  85 ervvGWYhshpditvwlsevdvrtqalyqrmde 117
                                    +++ GWYh++p +     e+d+++  ++ ++ e
  gene474|gene474|rna473|rna473  78 LKIMGWYHTGPRM----YENDLDITRSLSKFVE 106
                                    *************....9999999999888765 PP

>> MitMem_reg  Maintenance of mitochondrial structure and function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   6.7e-21     4e-17       1     110 [.     146     246 ..     146     248 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 6.7e-21
                     MitMem_reg   1 Eaeeigvehllkpsiqdas.stlstglnrqyyslkilqerldlikdYlkkveegelpvnheilrnlqkllnllPhletee 79 
                                    Eaee+gvehl + +i++++ +++++++n   +sl   +  l +i++Yl++v++g + +++ei+   q+++n++P+le+  
  gene474|gene474|rna473|rna473 146 EAEEVGVEHLIR-DIREEAsGSIAAKINGIKESLLVYKGVLGEIRSYLEDVIKGHISPSQEIIDLCQEIINSIPKLEK-- 222
                                    9***********.99988899********************************************************9.. PP

                     MitMem_reg  80 lekefnvetnDvllvvyLasltrsilalnel 110
                                            + + l   y+++l ++++aln+l
  gene474|gene474|rna473|rna473 223 -------PLDENLSDCYVSALAKTVIALNDL 246
                                    .......556666678*************98 PP

>> SPATA19  Spermatogenesis-associated protein 19, mitochondrial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.1e-06      0.03       3      72 ..     141     215 ..     139     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-06
                        SPATA19   3 dievveseavsvvqhwlkkteeeasqdikeklsins......ppthgqdvhvtrdvvkhhlsksdllanqsqevle 72 
                                     ie +e+e v  v+h ++   eeas +i  k+            + g+      dv+k h+s s+ + +  qe+++
  gene474|gene474|rna473|rna473 141 SIEAEEAEEVG-VEHLIRDIREEASGSIAAKINGIKesllvyKGVLGEIRSYLEDVIKGHISPSQEIIDLCQEIIN 215
                                    58899999997.59****************997555455555667777777899*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1585.34
//
Query:       gene475|gene475|rna474|rna474  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   21.4   6.5    0.00021   21.4   6.5    1.8  2  Gpi1      N-acetylglucosaminyl transferase component (Gpi1)


Domain annotation for each model (and alignments):
>> Gpi1  N-acetylglucosaminyl transferase component (Gpi1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   6.5   1.2e-08   0.00021      82     183 ..     153     263 ..     121     267 .. 0.65
   2 ?   -1.4   0.1      0.11   2.1e+03      98     131 ..     272     306 ..     264     316 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.2e-08
                           Gpi1  82 llesllsllelll.................kllallsll.GltfalsllsDlls.lltlhiylfyvlsariyrlqlevlk 142
                                    ++          +                 + +++++ + G+ + l + + ++  ++ + +++   +++  +++  + l+
  gene475|gene475|rna474|rna474 153 YI----------VncsteekriitikttlgTYIKFFCSIqGAFLRLGFPIVFIDeIFVVPTTMYLSAFSYACSFLARSLI 222
                                    33..........23333333333566666677777777778877777755555424444444444555666677777777 PP

                           Gpi1 143 sLfqlfrGkkyNvLrnrvDsldyeldqlllGtllFtvlvfL 183
                                      ++l+    yN+L++r Ds+  ++dq++++ l+F +++++
  gene475|gene475|rna474|rna474 223 ESIHLLNNSSYNPLKRRRDSVILNTDQIFMSALIFSFILLI 263
                                    7789999****************************988775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.11
                           Gpi1  98 allsllGlt.falsllsDllslltlhiylfyvlsa 131
                                     l+s++ l  + l ++ D++ ++ + i  + +++ 
  gene475|gene475|rna474|rna474 272 ILCSFMSLClVGLKFITDFIDFVLMDISKCRTYTL 306
                                    34444433213356677777777777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2021.05
//
Query:       gene476|gene476|rna475|rna475  [L=631]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-10   38.5   4.0    9.2e-09   34.3   0.9    2.2  2  Sec10     Exocyst complex component Sec10


Domain annotation for each model (and alignments):
>> Sec10  Exocyst complex component Sec10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.9   5.2e-13   9.2e-09      96     274 ..     151     317 ..     105     366 .. 0.80
   2 !    5.1   0.1   0.00035       6.3     578     683 ..     492     598 ..     481     624 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5.2e-13
                          Sec10  96 kaentrekiekyaerlEkelLkeFdkayrkedfermkeiAkvLqefnggasvvqlfvnqhdffidkdkldeangiessei 175
                                    k    + ++++y + +E+++L+ F+++ ++++ ++m+++ + L e   ++  v +++ + d+f       e  ++  +  
  gene476|gene476|rna475|rna475 151 KIGDDNGELQEYNKAVEDKMLSVFETGNKQNNKTMMQSAYNSLLEMGKESFLVHSYIYSLDLFK------EPVSM--EYR 222
                                    556666789***********************99999999************************......33332..355 PP

                          Sec10 176 wekladpdeapskveeslqalfseiretvkeeaeiikrVFpnpekVmqtFlqrvfaqviqqrlealLdkassisqlayLr 255
                                    +e + d+d  + ++  +  +l+++ir+++  + + i  +F n + V ++  ++v+ +vi+  l  +L+++       +L 
  gene476|gene476|rna475|rna475 223 KESIIDLDF-HTTSHSTFVELIDKIRDAYDSKFRDIGDIFVNTKDVYKIIHKKVYGDVISTALGDYLKDTG---PCMFLL 298
                                    788999999.56777789**********************************************9999876...555555 PP

                          Sec10 256 aLhslysstlkLvkdLkey 274
                                     L s y+ ++ L   ++++
  gene476|gene476|rna475|rna475 299 GLESCYKNLRILGSFIETI 317
                                    5555555554444444444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.00035
                          Sec10 578 eaCkeivefL.ssvhsalkeslsgsnlesflteiGlrlhklLleHlkkftvsseGGlmltkDlneYqdavksfkipelse 656
                                    e C++++e++  ++++a + s++g+n + +   i   lh++L+  + + t++ + +      +++  ++ k+++  +  +
  gene476|gene476|rna475|rna475 492 EGCERVIEVVrHEIVKASEASIKGENFRILINRILCLLHSALYGRILQLTFDEKQSRNMVEYVTKILEFAKELGSADAIQ 571
                                    79********6678888899999******************************99988888888889999999******* PP

                          Sec10 657 kFelLrelgnlfiVqpevlkslvrega 683
                                    kF++L+ l+ l  +   + +s  ++  
  gene476|gene476|rna475|rna475 572 KFSDLQNLAILISISEGDFESFYNSLV 598
                                    *********999888777777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 4049.79
//
Query:       gene477|gene477|rna476|rna476  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-18   65.2   0.4    3.5e-08   32.9   0.0    2.2  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0     2e-12   3.5e-08       2      97 ..      23     117 ..      22     123 .. 0.88
   2 !   30.5   0.3   1.1e-11     2e-07     149     208 ..     124     183 ..     119     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2e-12
                   Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIygern..gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakra 79 
                                    + +++h+G     +n+++++y yg+r+  +i+iid++   ++l  a++++ ++ ++ ++i  v+tk   ++ v + ++ +
  gene477|gene477|rna476|rna476  23 ILSQAHLGGTS--TNKNFSRYMYGTRSqdKISIIDINAMWEKLIIAARAFCGI-KHPSSIAVVSTKTFGRKPVVKFCEAV 99 
                                    66899999654..68899999999996348*******************9987.67899********************* PP

                   Ribosomal_S2  80 ngyyvnerWlgGtLTNfk 97 
                                    ++  ++ r+++G++TN +
  gene477|gene477|rna476|rna476 100 GATPITGRFIPGSFTNSE 117
                                    ****************54 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 1.1e-11
                   Ribosomal_S2 149 PdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvl 208
                                    P l++v d+  +k a+ E +  + p+ia+v+ + +   vd++Ip+N+ s  +i   + +l
  gene477|gene477|rna476|rna476 124 PRLLIVSDTYADKQAILESQYCNLPTIAFVNADNSLIGVDIAIPMNNRSPSAIAAGFFIL 183
                                    99************************************************9998655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1586.80
//
Query:       gene479|gene479|rna478|rna478  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-55  188.3   0.0    1.6e-55  188.1   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.2e-07   31.5   0.0      5e-07   30.3   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    5.8e-06   27.0   0.0    1.4e-05   25.8   0.0    1.6  1  Methyltransf_12  Methyltransferase domain
     0.0015   19.1   0.0     0.0032   18.1   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0035   16.7   0.0     0.0055   16.0   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
     0.0054   16.6   0.0     0.0072   16.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0061   16.1   0.0      0.011   15.3   0.0    1.4  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.026   14.3   0.0      0.043   13.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.097   12.4   0.0        0.2   11.4   0.0    1.4  1  AAA_lid_4        RuvB AAA lid domain
       0.14   11.4   0.0       0.22   10.8   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.1   0.0   8.7e-59   1.6e-55       3     228 ..       5     220 ..       3     245 .. 0.96

  Alignments for each domain:
  == domain 1  score: 188.1 bits;  conditional E-value: 8.7e-59
                                    CCXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT....TCCCE CS
                         RrnaAD   3 klrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls....kdekl 78 
                                    k++k+ gq++lkn  vi+ I++ + +++++ vle+g G+G+lT +L++ ak+v  +E+d+rLa++l k+++     ++k 
  gene479|gene479|rna478|rna478   5 KFNKQHGQHILKNLGVIDTIIERARIKPTDVVLEVGGGTGNLTMKLLQKAKKVICYEIDPRLAAELAKRVNgvpgMAQKF 84 
                                    89***********************************************************************999**** PP

                                    EEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHH CS
                         RrnaAD  79 kvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrls 158
                                    ++   D+lk ++p +           l++ nlPy+is++++++ll+ + f  + +++++q+ef  rl+arpg+ +++rls
  gene479|gene479|rna478|rna478  85 QLFVGDALKHDFPHFD----------LCITNLPYQISSPFMFKLLK-YNF--KCAYIMFQREFSDRLVARPGNPEYCRLS 151
                                    **************77..........9******************6.888..9*************************** PP

                                    HHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCT CS
                         RrnaAD 159 vlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksl 228
                                    v +++++++ +v+kv k++f Pppkv+s+ v++e++ ++ p  d +++++++++++ rk+ktl++++k+ 
  gene479|gene479|rna478|rna478 152 VGAQMLAQIDHVLKVSKNSFVPPPKVESSFVRIEPRIPR-PPIDFEEFDRFLKICFLRKNKTLRANFKNS 220
                                    **************************************9.89************************9964 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.8e-10     5e-07       1      71 [.      36     105 ..      36     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.8e-10
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.....TEEEEESBCCGBSSSTTTEEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.....nvefvqgdaedlpfedgsfDlvvss 71 
                                    vL++G GtG+lt++l+++   +kv++ +i++++ ++ ++r++   +     ++++ +gda + +f++  fDl++ +
  gene479|gene479|rna478|rna478  36 VLEVGGGTGNLTMKLLQKA--KKVICYEIDPRLAAELAKRVNG--VpgmaqKFQLFVGDALKHDFPH--FDLCITN 105
                                    9*****************6..9*****************9955..4455889999*******99996..***9985 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   7.7e-09   1.4e-05       1      72 [.      37     104 ..      37     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.7e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                    Le+G+GtG+l++ ll+k   +++++++i+p+  +  +++ +   +  +++++l++ d+l++d + +fDl + 
  gene479|gene479|rna478|rna478  37 LEVGGGTGNLTMKLLQK--AKKVICYEIDPRLAAELAKRVNGVPG-MAQKFQLFVGDALKHDFP-HFDLCIT 104
                                    8****************..**************999999999886.88999********99999.***9775 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.8e-06    0.0032       1      68 [.      37     105 ..      37     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-06
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCTSS-TT-EEEEEEE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaeklpfednsfDlvvss 68 
                                    L+vG GtG l+ +l +++++v++ ++++++ +   +++++ +    k+++ v+da k  f+   fDl++ +
  gene479|gene479|rna478|rna478  37 LEVGGGTGNLTMKLLQKAKKVICYEIDPRLAAELAKRVNGVPGmaqKFQLFVGDALKHDFPH--FDLCITN 105
                                    89****************************96666666665556999999*******99998..9998765 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     3e-06    0.0055      36     132 ..       7     103 ..       2     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3e-06
                                    HHHHHHHHHTTHHHHHHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS.-----TTEE CS
                 Methyltransf_2  36 rakfnkglqessslvakkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehl.sageeerve 114
                                    +++  + + ++  +  ++++e   +++  ++++vGGGtG l  +  ++  ++ +   D    +e Ak+   ++g +++++
  gene479|gene479|rna478|rna478   7 NKQHGQHILKNLGV-IDTIIERARIKPTDVVLEVGGGTGNLTMKLLQKAKKVICYEIDPRLAAELAKRVNgVPGMAQKFQ 85 
                                    55555555444444.578999999***********************99998888888777777788877899******* PP

                                    EEES-TTTS-----SEEE CS
                 Methyltransf_2 115 fvgGdffkdslPeaDail 132
                                       Gd  k+  P+ D+ +
  gene479|gene479|rna478|rna478  86 LFVGDALKHDFPHFDLCI 103
                                    *************99987 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     4e-06    0.0072      20      62 ..      30     117 ..      12     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4e-06
                Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...................................... 61 
                                     ++   vL++G GtG+l+  l ++ ++v+ ++++p++ ++++                                      
  gene479|gene479|rna478|rna478  30 IKPTDVVLEVGGGTGNLTMKLLQKAKKVICYEIDPRLAAELAkrvngvpgmaqkfqlfvgdalkhdfphfdlcitnlpyq 109
                                    677789**********999999999*********9988877766666666666666666555555555555555555555 PP

                Methyltransf_23  62 .......k 62 
                                           k
  gene479|gene479|rna478|rna478 110 isspfmfK 117
                                    55555554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   6.1e-06     0.011      31     108 ..      32     109 ..      20     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.1e-06
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHH.HHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE---S CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdar.Alesakenleankle..vevvasdvleeveekkfdlivsNPPf 107
                                     ++ vl +G G+G l+++l+++ ++  v ++++d r A e+ak+     +++   +++  d+l++    +fdl ++N P+
  gene479|gene479|rna478|rna478  32 PTDVVLEVGGGTGNLTMKLLQKAKK--VICYEIDPRlAAELAKRVNGVPGMAqkFQLFVGDALKHDF-PHFDLCITNLPY 108
                                    45679****************9998..777777754477888876666666557999****999988.8********998 PP

                                    T CS
                            MTS 108 h 108
                                    +
  gene479|gene479|rna478|rna478 109 Q 109
                                    6 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.4e-05     0.043      65     121 ..      24      77 ..      11      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.4e-05
                                    HHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHC CS
                           PCMT  65 alellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkl 121
                                    ++e  ++k+ + vLevG+G+G lt    +l+++  +v+  e  ++l++e  ++++  
  gene479|gene479|rna478|rna478  24 IIERARIKPTDVVLEVGGGTGNLTM---KLLQKAKKVICYEIDPRLAAELAKRVNGV 77 
                                    6677789**************9985...77888889999999999999999988764 PP

>> AAA_lid_4  RuvB AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011       0.2       8      42 ..      49      83 ..      44      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                      AAA_lid_4  8 eivkrsakilgveieeegaaeiarRsRGTPRianr 42
                                   ++++++ k++  ei++  aae+a+R  G P +a++
  gene479|gene479|rna478|rna478 49 KLLQKAKKVICYEIDPRLAAELAKRVNGVPGMAQK 83
                                   6789999***********************99986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.22      39      98 ..      24      80 ..      11     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                   HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS CS
                Ubie_methyltran 39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki 98
                                   ++++   k+   vl+v gGtg+l++kl+++++   kv+  +i++ +  +  k+++    +
  gene479|gene479|rna478|rna478 24 IIERARIKPTDVVLEVGGGTGNLTMKLLQKAK---KVICYEIDPRLAAELAKRVNGVPGM 80
                                   5556667788899**************98776...6788888888877777777665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1765.88
//
Query:       gene480|gene480|rna479|rna479  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1886.76
//
Query:       gene48|gene48|rna48|rna48  [L=429]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.9e-25   87.4   0.4    5.5e-24   84.8   0.4    2.0  1  GTP_EFTU     Elongation factor Tu GTP binding domain
      6e-23   80.9   0.1    1.9e-22   79.3   0.0    2.0  2  eIF2_C       Initiation factor eIF2 gamma, C terminal
      1e-08   35.4   0.2    2.5e-08   34.2   0.2    1.7  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00028   20.8   0.8     0.0039   17.1   0.1    2.1  2  RsgA_GTPase  RsgA GTPase
     0.0015   18.6   0.0     0.0027   17.7   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.4   1.5e-27   5.5e-24       3     193 ..      13     212 ..      11     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 1.5e-27
                                EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE...................... CS
                   GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle...................... 64 
                                ++nig+ighv hGK+T++ ++   + +               + k+E er iTik   ++ +                      
  gene48|gene48|rna48|rna48  13 TLNIGTIGHVAHGKSTIVKAISGISTI---------------KFKAELERNITIKLGYANAKiykcdskcirpncyqsfgssnp 81 
                                68****************999833333...............4578888999999888877777899999999999999***** PP

                                ..........TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGST. CS
                   GTP_EFTU  65 ..........ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDrl. 135
                                          + +  ++++++D+PGH   + ++ +g++++D ++l+++a+e  ++pqt e+l  +  ++++ + v+ NK+D + 
  gene48|gene48|rna48|rna48  82 dqlpckkcggTLKLVRHVSFVDCPGHDVLMATMLNGTAIMDSVLLLIAANEPcPQPQTTEHLFAVEIMDLKkVLVVQNKIDLVs 165
                                *****99887688899**********************************9879*****************888888******7 PP

                                HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                   GTP_EFTU 136 kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                +++  e+ ++++ k+      l+   ++     pv++++a  g ++ +ll+ +v+++p
  gene48|gene48|rna48|rna48 166 REQALEQYDQIQ-KF------LRTSNVS----GPVIPTAAQVGVNIPALLDFIVNYIP 212
                                777888888888.66......5555555....59**********************99 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.4   1.2e+04       7      30 ..     148     175 ..     144     192 .. 0.56
   2 !   79.3   0.0   5.4e-26   1.9e-22       2      86 .]     337     417 ..     336     417 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.4
                                EEE-SBESSSSSC....CC-----TTEE CS
                     eIF2_C   7 yellerlvgvkee....kkveklkkkEv 30 
                                +  l++++ v+++    ++ ++l++ ++
  gene48|gene48|rna48|rna48 148 IMDLKKVLVVQNKidlvSREQALEQYDQ 175
                                5556777777776333222444555444 PP

  == domain 2  score: 79.3 bits;  conditional E-value: 5.4e-26
                                EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEEEEEE CS
                     eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLiGwGe 85 
                                ++++ey+l+ +   + +     klk++E+++lniGs++tg+v+  + +   +++L kP+c+e+ge+ia+sR+++++WrLiG+Ge
  gene48|gene48|rna48|rna48 337 KITVEYSLFPKTTVQGSF----KLKEGEHVLLNIGSTTTGSVIGGIGETRGEFDLVKPACCEIGERIAISRKINNHWRLIGHGE 416
                                789999999998887765....9************************************************************9 PP

                                E CS
                     eIF2_C  86 i 86 
                                i
  gene48|gene48|rna48|rna48 417 I 417
                                8 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.2   6.8e-12   2.5e-08       1      66 [.     244     318 ..     244     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 6.8e-12
                                EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS..G CS
                GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikgled..a 66 
                                G+v++g++++G l++Gd+++i++ +  ++ +       v++i sl ++  d++ea++g+ +Gv++ +++  +  +
  gene48|gene48|rna48|rna48 244 GGVIGGSLVTGMLRVGDRIEIRPgLVMKRNNrfvcrpFVSEIVSLKAESTDLEEAYPGGLIGVGTTMDPSFCkaD 318
                                89*********************99875555***********************************998766553 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.043   1.5e+02      93     124 ..       4      38 ..       1      48 [. 0.63
   2 !   17.1   0.1   1.1e-06    0.0039      13      76 ..     118     184 ..      95     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.043
                                HHHHCTTSEEEE...ECSTTSSHHHHHHHHCTT-- CS
                RsgA_GTPase  93 lkellkdktsvl...vGqSGvGKStLinallpele 124
                                ++e +k++ ++    +G+   GKSt+++a+ +  +
  gene48|gene48|rna48|rna48   4 VSEIMKKQATLNigtIGHVAHGKSTIVKAISGIST 38 
                                455555555554000455567*******9988554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-06
                                EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH...HHHHHHHHHHHTT CS
                RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee...eleelkeelealg 76 
                                 a +d +l++++++ep  ++++ +  L+++e  ++ ++++v nKiDl+++e+   +++++++ l++ +
  gene48|gene48|rna48|rna48 118 TAIMDSVLLLIAANEPCPQPQTTEH-LFAVEIMDLkKVLVVQNKIDLVSREQaleQYDQIQKFLRTSN 184
                                5778**********99999988776.5666666663788888**********5555555555555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   7.6e-07    0.0027       2     113 ..      16     159 ..      15     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 7.6e-07
                                EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEEETTEE..................................E CS
                   MMR_HSR1   2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvklkgke..................................i 48 
                                ++ +G+   GKSt+++a++g    k +++ +   T++  +++ k+ + +                                  +
  gene48|gene48|rna48|rna48  16 IGTIGHVAHGKSTIVKAISGIstiKFKAELERNITIKLGYANAKIYKCDskcirpncyqsfgssnpdqlpckkcggtlklvrhV 99 
                                889****************9544566777777888888888777433113566667777777777888888888888888888* PP

                                EEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT......TTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                   MMR_HSR1  49 elvDtpGliegaseekglgkaflalee.adlillvvdas......eeklkpldeeleelleeakkplilvln 113
                                 +vD+pG  +       l  ++l+    +d +ll++ a+      +       e+l ++   + k++++v n
  gene48|gene48|rna48|rna48 100 SFVDCPG-HD------VLMATMLNGTAiMDSVLLLIAANepcpqpQ-----TTEHLFAVEIMDLKKVLVVQN 159
                                *******.44......577777765555799999998774333220.....122222222224455666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2793.75
//
Query:       gene481|gene481|rna480|rna480  [L=557]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-25   88.6   0.0    9.9e-25   87.6   0.0    1.5  1  ABC_tran      ABC transporter
    1.2e-11   44.8  13.0    1.2e-11   44.8  13.0    1.5  2  ABC_membrane  ABC transporter transmembrane region
    6.6e-08   32.2   3.5    4.9e-06   26.2   3.5    2.3  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0038   17.1   3.1       0.84    9.4   1.0    3.0  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   2.2e-28   9.9e-25       1     136 [.     360     507 ..     360     508 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 2.2e-28
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+nv++ +++gek++i G+nG GK++++++l+g l+  +G+il+dg +l++ ++e lr+ i++ pqe+qlf+++ v +n 
  gene481|gene481|rna480|rna480 360 LRNVDMRIRRGEKIGISGDNGGGKTSFARALLGFLD-YSGSILIDGIELSTLNKEGLRSMISYSPQESQLFNKS-VLSNi 437
                                    789********************************8.7************************************.99999 PP

                                    ......HHHTC.........HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ......xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ......esdee.........iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                           sdee         ++++ ++l++ +  +t v+++++ LSgGq+q+v l+ra++k+++++++D  t
  gene481|gene481|rna480|rna480 438 rdgnkyLSDEEiveyckrygMDEVFRNLSDGY--QTSVGDGGNRLSGGQRQKVNLMRAVVKDAPIYIFDQVT 507
                                    99999844555333334445666666666665..99999999***************************877 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8  13.0   2.7e-15   1.2e-11       3     272 ..      32     300 ..      30     302 .. 0.92
   2 ?   -2.5   0.0       0.7   3.1e+03     201     238 ..     505     542 ..     504     544 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 2.7e-15
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane   3 liillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfk 82 
                                    ++il +i+a +++    +++ +il+++ + +d+    +n  + ++l+++l + +l+l++ + ++   e ++++   +l+k
  gene481|gene481|rna480|rna480  32 VMILPIIVALIVAGYGEILITQILNDIQERADNTE-IVNGKIRVYLIVALSSYVLGLVSLFAMSSYVEAICRDYIIDLYK 110
                                    57888999999999999999*******99555554.999999999999999999999999999999************** PP

                                    HHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHH.HSHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane  83 kilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfy.lgwkltlvllailpliilvsavi 161
                                      + ++   f +  vG+++s +++ v +lr++l +++ +f++sl+ +++++i + + +  +  l++ ++++ + ++ ++i
  gene481|gene481|rna480|rna480 111 EHICMSFLHFKKIGVGDMISFMNRKVLSLRWILESTIKCFIMSLCCIIITMIKIRVgVESYYGLLMGGVVLAYGVCVIII 190
                                    ********************************************************9999******************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 162 akilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyal 241
                                    ++  ++++ k++ +++   +  + s+ ++  +k++++ee + ++  k    + + g+++  +  + + i + ++  ++++
  gene481|gene481|rna480|rna480 191 NHYRNTIRLKMNREIDMTERKRYNSILNYDIIKSYNNEELEADELYKRMGAETRYGKMYWSWLQAGNFIGENIFIMAMFI 270
                                    ***********************************************999999999999999999988888888888888 PP

                                    HHHHHHHHHHTTSSTHHHHHHHHHHHHHHHH CS
                   ABC_membrane 242 alwfGttlvisgelsvgdlvvflslfailfg 272
                                    ++   ++  +++++s++d++ ++sl+++l +
  gene481|gene481|rna480|rna480 271 MTI-QFSNGDAKNISFKDYTLIISLSNQLRM 300
                                    844.445555569**************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.7
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 201 yflekfekaleeakkagikkaianglligitqllglls 238
                                    +++++ +k++e+a   +i+k++++  +i+i+q  glls
  gene481|gene481|rna480|rna480 505 QVTSHLDKESENAIVDMIMKNLSDKTVIMIMQNSGLLS 542
                                    67788999999999999999999999999999988876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   3.5   1.1e-09   4.9e-06      28     209 ..     374     548 ..     350     555 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.1e-09
                                    EEEESTTSSHHHHHHHHHHHCTT.........TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnlldAilFvLGer........sakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                     i G NG GK+++  A+l  L  +        + ++l +e l+++i++s +++++ + +v   +++ +k    ++e  +i
  gene481|gene481|rna480|rna480 374 GISGDNGGGKTSFARALLGFLDYSgsilidgiELSTLNKEGLRSMISYSPQESQLFNKSVLSNIRDGNKY--LSDE--EI 449
                                    5889999999999999865554331111111133455555555555554444444444444444444443..2222..23 PP

                                    EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                        kr g  e++ n ++  ++ v       g   + LSgG+++ v   L+ A+  vk ap+y++D + ++LD++  +++
  gene481|gene481|rna480|rna480 450 VEYCKRYGMDEVFRNLSDGYQTSV-------GDGGNRLSGGQRQKV--NLMRAV--VKDAPIYIFDQVTSHLDKESENAI 518
                                    333333333344444444443333.......334568*****9855..555554..799********************* PP

                                    HHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 180 aellkeksknaQfivislreemlekadklv 209
                                    ++++ ++ ++  +i+i  ++++l+k d+++
  gene481|gene481|rna480|rna480 519 VDMIMKNLSDKTVIMIMQNSGLLSKFDRVY 548
                                    *******99**************9999987 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.063   2.8e+02      71     117 ..     210     254 ..     191     265 .. 0.85
   2 !    9.4   1.0   0.00019      0.84       4      29 ..     375     408 ..     373     452 .. 0.65
   3 !    5.0   0.0    0.0042        19     237     293 ..     480     532 ..     416     542 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.063
                         AAA_21  71 ryryglrlersqveeklssvetllesgllldkrsleeedvfnpearg 117
                                    r ry+  l+++++  k +++e+l+ + l+++  ++ ++ + ++ +  
  gene481|gene481|rna480|rna480 210 RKRYNSILNYDII--KSYNNEELEADELYKRMGAETRYGKMYWSWLQ 254
                                    6689999999999..99*********************999999875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00019
                         AAA_21   4 liGpNgsGKSnLLdaldllarl........drdv 29 
                                    + G+Ng GK+++ +al ++ ++        +  +
  gene481|gene481|rna480|rna480 375 ISGDNGGGKTSFARALLGFLDYsgsilidgIELS 408
                                    569*************999887666655332222 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0042
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvi 293
                                    lS G+++   l  a+  ++   +++++D + ++L+ +    +++++ k+ls+    vi
  gene481|gene481|rna480|rna480 480 LSGGQRQKVNLMRAVVKDA---PIYIFDQVTSHLDKESENAIVDMImKNLSD--KTVI 532
                                    4777777777777777777...*********************999888887..5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3410.40
//
Query:       gene482|gene482|rna481|rna481  [L=114]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-16   58.4   0.0      1e-15   58.1   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   5.6e-20     1e-15       2     116 ..       4     110 ..       3     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 5.6e-20
                                    EEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHT.TTSEEEEEESSHHHHHHHHHHHHHTT-SEEE CS
                           PTH2   2 kmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeee.gqkkivlkveseeeLlelaakakalglpaal 80 
                                    ++++++r+DL+ s+G+++aq++h +v  ++++++++   ++++  ++   ++k+vlk++  ++  e+ +++ ++++++++
  gene482|gene482|rna481|rna481   4 VQYILLRNDLNFSRGALIAQACHSSVYSIERYRDHP---DTVEYLRNVrLMTKVVLKIKG-KDVGEIIDHLVSKNIDHTV 79 
                                    699*******************************94...45555555559*********5.6789*************** PP

                                    EEETSSSSSST.TCEEEEEEEEEEHHHHHHHHTTSEB CS
                           PTH2  81 irDagrtqiep.gtkTvlaigPapksivdkvtgkLkl 116
                                    + +      ep  ++T++ ++P+ k+++  v++ +k 
  gene482|gene482|rna481|rna481  80 WVE------EPeSITTCISLRPYAKDKIADVVEYFKR 110
                                    ***......885778*****************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 680.55
//
Query:       gene483|gene483|rna482|rna482  [L=744]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-82  276.7   0.2    4.9e-82  275.8   0.2    1.4  1  HECT      HECT-domain (ubiquitin-transferase)


Domain annotation for each model (and alignments):
>> HECT  HECT-domain (ubiquitin-transferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.8   0.2   2.7e-86   4.9e-82       2     305 ..     453     742 ..     451     744 .] 0.95

  Alignments for each domain:
  == domain 1  score: 275.8 bits;  conditional E-value: 2.7e-86
                                    HHHHHHT-GGGSSEEESSTTSSSEEE-TTHHHHS....HHHHHHHHHHHHHTT--BSS-B-HHHHHHHTT-.---TCHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HECT   2 llskelldpklglfeeesedsgtlypkpssseeellklfeflGkvlGkaiyeeilldlpfsraflkfllgeekitledle 81 
                                    lls+e ++++ +lf   ++ ++ ++++p   +ee    +e +G+++++a+y++++l++pf+++f+k+llg ++ +l+dl+
  gene483|gene483|rna482|rna482 453 LLSQE-IKEDGRLF---EHTENRIWIRPHEGDEEE---YEAIGRIIAIALYNNVVLNIPFPSLFFKKLLG-RRPSLDDLR 524
                                    56666.56788999...467778999998766666...********************************.7******** PP

                                    HH-HHHHHHHHHHH..HS-GGG...GT-BSEEEEE.TTEEEEEESSTTGGGSB--TTTHHHHHHHHHHHHHTGGGHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HECT  82 eidpelakslkellslesnteevedlaLtFtipen.agasatieLipnGanipVtnenkkeYiklyvnyllkksvekqle 160
                                    ei + +a sl++l++l++++  +++l+L+F+ ++n  g+++t  L++nG+ni++t+en++++i++y+++++++ +++q+e
  gene483|gene483|rna482|rna482 525 EISSGIATSLRNLRKLSKDE--INELDLRFVAEHNvDGTTKTYPLVKNGKNIRLTSENMRLFIEKYIEFHTDTLIKPQFE 602
                                    **************886665..***********9988******************************************* PP

                                    HHHHHHHTTS-HHHHTTS-HHHHHHHHBCSSS.--HHHHHHTEEEETT--TTSHHHHHHHHHHHHS-HHHHHHHHHHHHS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HECT 161 aflkGfsevipskalklfdaeelellisGedelidvedlrrnteykggynaesetiewlweilkefspeekrlfLqFvTg 240
                                    a++kGf+++i+++++  +d++ele+++ G++  +d++ +r+ t+y+g ++++s++i ++wei+++f++++++++LqF+Tg
  gene483|gene483|rna482|rna482 603 AIRKGFYSIIDKDKMMYLDPKELEKIMMGSNT-FDIKAIRSSTTYSG-FKEDSPIIIYFWEIFEGFNRKKRKKLLQFITG 680
                                    *******************************6.************75.******************************** PP

                                    SSS--TTCGGG-B--EEEEE-S..-TTS--EEEGGGTEEEE---SSHHHHHHHHHHHHHHHH--X CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HECT 241 ssrlPlgGfaelhpkftierkskedetrLPtahTCfnlLklpdYsskeilkekLltAieetegFe 305
                                     +r+P++G a+l  k++i r++  d++rLP+++TCfn+L lp+Yssk++l++kL+tA+e t+gF 
  gene483|gene483|rna482|rna482 681 NDRIPVSGPASL--KLVIMRNG-CDTDRLPSSQTCFNTLLLPEYSSKNKLEKKLETALELTAGFF 742
                                    ************..******88.9**************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.62
# Mc/sec: 3605.17
//
Query:       gene484|gene484|rna483|rna483  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.029   14.3   0.0    1.1  1  Tcp10_C   T-complex protein 10 C-terminus


Domain annotation for each model (and alignments):
>> Tcp10_C  T-complex protein 10 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.6e-06     0.029      10      96 ..       4      91 ..       1     115 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-06
                                   EEE-TTS-EEEE-TTSS-EEEE-TTS-EEEE-TTS-EEEEE.TTTTEEEEE-TTS-EEEE-TTS-EEEE-TTS-EEEE-TTS CS
                        Tcp10_C 10 vityanGtvkevsadgktvtvsffNgDvketledgrviYyy.aeaqtthttypdglevlefpngqiekhykdgskeivfpdg 90
                                   + +y++G  k+  +  k+++v+   +D+   ++ +++iY y + ++ +   +++g++ + ++ +++ + +++++ke +   g
  gene484|gene484|rna483|rna483  4 KASYPKGMSKTDAQGPKMMVVRIKRKDIPLHKKSNKLIYEYsVWDNKVTLLMSEGYNKVLYECKRMPRICPEEEKEFEVELG 85
                                   679**************************************777788888999*********************99887766 PP

                                   -EEEE- CS
                        Tcp10_C 91 tvkslk 96
                                     + l 
  gene484|gene484|rna483|rna483 86 EDEALL 91
                                   666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 904.27
//
Query:       gene485|gene485|rna484|rna484  [L=281]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-31  108.2   0.7    3.9e-31  107.0   0.7    1.7  1  KH_8      Krr1 KH1 domain
  ------ inclusion threshold ------
      0.048   13.5   4.2      0.076   12.8   0.6    2.6  2  KH_1      KH domain
       0.12   12.7   1.6        5.4    7.4   0.0    2.5  2  Img2      Mitochondrial large subunit ribosomal protein (Img2
       0.13   12.8   0.6       0.74   10.4   0.1    2.2  2  PCI       PCI domain


Domain annotation for each model (and alignments):
>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.7   8.7e-35   3.9e-31       2      81 .]      21     100 ..      20     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 8.7e-35
                           KH_8   2 sfevlfpkyrekylkeveekikklleekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvleD 81 
                                    s  v+fpkyreky+ +++++i k+le kk+++++dl++r++ v+T++ TrDP+i++ka +++kL+srgv +eea+kvleD
  gene485|gene485|rna484|rna484  21 SEAVMFPKYREKYIEQTQKYIIKALEGKKISCKIDLEKRVIDVETNKSTRDPFIFIKAVNFVKLVSRGVGVEEAMKVLED 100
                                    5579***************************************************************************9 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.084   3.8e+02      21      37 ..      41      58 ..      37      77 .. 0.79
   2 ?   12.8   0.6   1.7e-05     0.076      11      64 ..     123     168 ..     117     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.084
                                   HHHHHHHHH.T-EEEEES CS
                           KH_1 21 nIkeIreet.gakIkvpk 37
                                    Ik ++ ++  +kI+++k
  gene485|gene485|rna484|rna484 41 IIKALEGKKiSCKIDLEK 58
                                   699***9999****9774 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 1.7e-05
                                    HHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                           KH_1  11 vgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                      r+IG++  ++k I+  t++++ v  +       ++v i+Gs  ++e+ k+ +
  gene485|gene485|rna484|rna484 123 RDRLIGPKEMTLKAIQILTKCYVLVH-G-------KTVSIIGSFRGIEEVKKIV 168
                                    569*************99******98.5.......48******999**999876 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.013        58      11      58 ..      24      69 ..      16     169 .. 0.76
   2 ?    7.4   0.0    0.0012       5.4      25      60 ..     182     217 ..     173     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                           Img2 11 gslPVYtdvkrggtkkltvirkieGDiaalredLrkaleelvkvnevt 58
                                    ++P Y++   ++t+k  +i+  eG    ++ dL+k +   v+ n+ t
  gene485|gene485|rna484|rna484 24 VMFPKYREKYIEQTQK-YIIKALEGKKISCKIDLEKRVI-DVETNKST 69
                                   6788888888877776.579**************99988.45555533 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                           Img2  25 kkltvirkieGDiaalredLrkaleelvkvnevtgk 60 
                                    kkl++ rk eGDi++  ed +++l e+ k n++++k
  gene485|gene485|rna484|rna484 182 KKLVEKRKLEGDITKEGEDWSRFLPEIKKSNKKSKK 217
                                    789999*******************87777766655 PP

>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00017      0.74      65     103 ..      19      63 ..      10      65 .. 0.86
   2 ?    0.2   0.0      0.24   1.1e+03      44      87 ..     130     174 ..     107     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                    HHHHHHTSSH......HHHHHHHHHHHHTTSSSEEEETTTTEEEE CS
                            PCI  65 rlaklldlsv......devEkilvklIrdgeirakidqesgivvf 103
                                    + ++++ +++      ++++k+++k+ + ++i++kid e++++ +
  gene485|gene485|rna484|rna484  19 MSSEAVMFPKyrekyiEQTQKYIIKALEGKKISCKIDLEKRVIDV 63 
                                    55677777778889999***********************99866 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
                                    HHHHHHHHHHHHHCESEEEHHHHHHHHTSSH.HHHHHHHHHHHHT CS
                            PCI  44 kkvrerllrqvskiyssislerlaklldlsv.devEkilvklIrd 87 
                                    k++++++++ ++k y  ++ ++++    + + +ev ki+++++++
  gene485|gene485|rna484|rna484 130 KEMTLKAIQILTKCYVLVHGKTVSIIGSFRGiEEVKKIVIDCMNN 174
                                    567777777777777777777777777777789999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1948.04
//
Query:       gene486|gene486|rna485|rna485  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.0   0.0       0.11   12.4   0.0    1.8  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.9e-06      0.11      29      51 ..     302     324 ..     302     334 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-06
                                    CCCTTSSCHCHHHHHHHHHHCTS CS
                           TrmB  29 aeelgvprskvYevLrsLedkGl 51 
                                    ae +g++++ vY+vLr+L + G+
  gene486|gene486|rna485|rna485 302 AELSGISQNGVYRVLRRLFKNGM 324
                                    6889******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2189.09
//
Query:       gene487|gene487|rna486|rna486  [L=315]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-34  119.2  20.4    2.4e-34  118.9  20.4    1.1  1  UAA       UAA transporter family
    3.8e-06   26.5  11.7    5.2e-06   26.0  11.7    1.2  1  TPT       Triose-phosphate Transporter family
     0.0016   18.6  25.3     0.0081   16.3  11.3    3.0  3  EamA      EamA-like transporter family


Domain annotation for each model (and alignments):
>> UAA  UAA transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9  20.4   4.1e-38   2.4e-34       4     299 ..      12     304 ..       9     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 4.1e-38
                            UAA   4 lavslvfvgccsnvvllElivkeep.kafg.....nlltfvqflfvalegllesid...ilkkrkiPlktYvilvalffi 74 
                                    l + +++  +++ +v  E++ ++++ ++         l++  +  +a+   + s +      + k  l +Y+ l++l +i
  gene487|gene487|rna486|rna486  12 LHAMGIYAFFLVFGVYGEKLTTTTYnGR-KyesalFPLVLQSLGGIAVGRTMMSYSkeaEGAPGKRVLCHYACLALLSLI 90 
                                    5667888888888888888888766422.23343222333335555554444443322224444555668********** PP

                            UAA  75 tsvlnnealkydisvPvhiifrssklipvmilGililgkrYsllqylsvllltlGviiftllsakdkkedskeslnkfll 154
                                    +  l   +lky +s+P+ ii++s+kl+p  ++  li++++ s ++ ls+ l+++ v  f+l+++      s+++  ++++
  gene487|gene487|rna486|rna486  91 SAQLGFISLKY-LSYPTLIIAKSCKLLPIALMNFLIYRRTLSHRKCLSLSLISISVLSFSLFDK-----RSTSTSGFSFI 164
                                    ***********.*************************************************776.....444566789** PP

                            UAA 155 Giallvlallldavlglvqeklykkygkhskealfyshllslplfl...llqgellsavkflsesedvallslpsklfyl 231
                                    Gi++l+ +ll+d++++  q++l++ ++ +s  +++y++l+ +++ +   ll+++l   ++f+++ +++          +l
  gene487|gene487|rna486|rna486 165 GILILITSLLADGIINSAQDHLFRTFKISSFHMMYYTNLFRFLISFtaiLLTDNLKYSIAFIKSTPEIV--------PDL 236
                                    **********************************************9*9****************9999........8** PP

                            UAA 232 llnvltqyvcikgVlilisefgaltvtlvltlRKfvslllSillFknpltlqhlvgtllVflglllys 299
                                    +l+++   +++ +++ ++++ g+lt+t+v  +RK++s+ lS+++F++ +   + ++ l V+++++l++
  gene487|gene487|rna486|rna486 237 FLYSTFNIFGQIVIYSMVQSHGSLTLTTVNLTRKMLSIFLSLIVFGHRIKKVQALSILGVLGSIALEM 304
                                    ***************************************************************99987 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0  11.7   8.7e-10   5.2e-06      67     278 ..      80     292 ..      19     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 8.7e-10
                            TPT  67 ailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasv......tEl 140
                                        lal+ +++  l+ +sl+  +     + K+++ +  +++  l+++ +ls  + lsL  i   v   s+         
  gene487|gene487|rna486|rna486  80 HYACLALLSLISAQLGFISLKYLSYPTLIIAKSCKLLPIALMNFLIYRRTLSHRKCLSLSLISISVLSFSLfdkrstSTS 159
                                    555688899999999999999876666667799999999********************999888877766222221334 PP

                            TPT 141 sFnligfisAlisnltfslrnifsKkllkklkdldalnlfaiitilslllllPvallvegvlktpsllkstkvslkevll 220
                                     F +ig++  ++s l++ + n     l+++ k +++ +++ ++ ++ +l+++ ++ll+++++ +++ +kst     e++ 
  gene487|gene487|rna486|rna486 160 GFSFIGILILITSLLADGIINSAQDHLFRTFK-ISSFHMMYYTNLFRFLISFTAILLTDNLKYSIAFIKST----PEIVP 234
                                    599999999999******************87.***************************99999999999....9**** PP

                            TPT 221 llllsgvlfhlynqvaymvLervspvthsvantvKrvvvIvlsvlvfknpvsllnaiG 278
                                    +l+l + ++ + ++v y++++    +t +  n ++++++I ls++vf+ +++ ++a+ 
  gene487|gene487|rna486|rna486 235 DLFLYSTFNIFGQIVIYSMVQSHGSLTLTTVNLTRKMLSIFLSLIVFGHRIKKVQALS 292
                                    *************************************************999998863 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.034     2e+02      94     122 ..       8      36 ..       5      39 .. 0.86
   2 !    8.1   2.4   0.00047       2.8      57     134 ..      70     147 ..      38     150 .. 0.77
   3 !   16.3  11.3   1.4e-06    0.0081       2     134 ..     164     302 ..     163     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.034
                           EamA  94 aslitslePvftlilsvlllgekltlkql 122
                                    +sl+++ + +++ +l + ++geklt +++
  gene487|gene487|rna486|rna486   8 VSLALHAMGIYAFFLVFGVYGEKLTTTTY 36 
                                    78999999999999999999999998775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00047
                           EamA  57 aklslkdwlll.lllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                    +  + k +l+  + l+ll+ + a  l f++lk++s  +  ++ s   + ++++ +l+++ +l+ ++ l++ li ++vl 
  gene487|gene487|rna486|rna486  70 EGAPGKRVLCHyACLALLSLISA-QLGFISLKYLSYPTLIIAKSCKLLPIALMNFLIYRRTLSHRKCLSLSLISISVLS 147
                                    35666666666355555555555.58899********************************************999986 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.4e-06
                           EamA   2 lgillallaalfwaiyfvlskillrkv..spltltfvrfliagillliiallkegkl...aklslkd..wllllllgllg 74 
                                    +gil+++++ l  +i   ++++l+r++  s++++  ++ l+ +++ +  +ll+++ +   a ++ ++  +  l+l++++ 
  gene487|gene487|rna486|rna486 164 IGILILITSLLADGIINSAQDHLFRTFkiSSFHMMYYTNLFRFLISFTAILLTDNLKysiAFIKSTPeiVPDLFLYSTF- 242
                                    7999999999999**********99987777777777777777777777777777777775555555226666666665. PP

                           EamA  75 tvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                    ++++++++++ +++ ++ + + ++++  +++++ls +++g ++++ q l+i+ +l +++l
  gene487|gene487|rna486|rna486 243 NIFGQIVIYSMVQSHGSLTLTTVNLTRKMLSIFLSLIVFGHRIKKVQALSILGVLGSIAL 302
                                    56677888888888888899999*****************************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2239.73
//
Query:       gene488|gene488|rna487|rna487  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-13   49.9   0.5    4.6e-13   49.4   0.5    1.2  1  Fcf1      Fcf1


Domain annotation for each model (and alignments):
>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.5   2.6e-17   4.6e-13       2      97 ..      50     142 ..      49     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 2.6e-17
                                    HCTS-EEEEEEHHHHHHHHHCT..-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHHHT CS
                           Fcf1   2 tLqakvkpliTqCviaeleklgkklkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrlrk 81 
                                    +++++ k++iT+Cv+++l+++g++  +   i + +e l+C+hk+ +++ +Cl +v++ k+nk++yi+A++ ++++  + +
  gene488|gene488|rna487|rna487  50 LFKSQPKLFITKCVYKKLKEIGRD--HKEGISRYLEILHCDHKEVKEPLSCLRRVMR-KSNKNHYILASNCTEITDLIGT 126
                                    678999****************88..455667789*******8888**********9.55*****************999 PP

                                    STT--EEEEE--EEEE CS
                           Fcf1  82 ipgvPilyikrsvmvl 97 
                                       +P++ ++  ++v+
  gene488|gene488|rna487|rna487 127 QRKIPVVSCRGGTLVI 142
                                    9999999988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1121.41
//
Query:       gene489|gene489|rna488|rna488  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-80  270.1   0.2    2.5e-80  269.9   0.2    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    5.6e-09   35.8   0.6    0.00033   20.2   0.1    2.5  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    3.1e-06   27.1   0.1    5.3e-06   26.3   0.1    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.9   0.2   4.2e-84   2.5e-80       2     313 ..      86     437 ..      85     438 .. 0.92

  Alignments for each domain:
  == domain 1  score: 269.9 bits;  conditional E-value: 4.2e-84
                                    CCHHHHTHHHHC.CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SH CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2   2 eelrlknryldl.rtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspq 80 
                                     e+ ++ ry+dl  +++ ++ ++ r+++++++r++l+++gf+e+etP++    ++++a++F+++++e + +++ +++sp+
  gene489|gene489|rna488|rna488  86 AETIYRRRYMDLlINKESKERFQKRTQIIRYIRRFLDSRGFLEVETPMMNLIPGGAAAKPFVTHHNELKLDLY-MRVSPE 164
                                    578899******9*******************************************************88999.****** PP

                                    HHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  81 lylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrn 160
                                    lyl+ l+++g+drv++i+++FR+E ++ ++++ EFt++e++m++ +++d+m ++eel++ +vke+  ++ + +++ ++r+
  gene489|gene489|rna488|rna488 165 LYLKKLVIGGLDRVYEIGKQFRNEGIDLTHNP-EFTSCEFYMAYGDYNDLMVMTEELMSGMVKEM-FGTDTIVYSPKKRE 242
                                    ********************************.********************************.55556666555555 PP

                                    S......EE-SSS-EEEEHHHHHHHHHTS.....................-SS--HHHHHHHHH...........HS--S CS
                                    x......xxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxx...........xxxxx RF
                    tRNA-synt_2 161 s......kdlkkpfkrltykeaieklnei.....................gkdldkaderalvk...........kekne 202
                                    +       ++k+pf+ ++  e ++   +                      +++++ ++ r l++            +  +
  gene489|gene489|rna488|rna488 243 ErsesveLSFKRPFRVISIIEELNSRLGLdlsgetldspetleklleaceKEGIHVEKPRTLTRvldklighviePQCVN 322
                                    56888889999*******99999994444888888877777777777777666666666666669999*****9988899 PP

                                    EEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHH.....SSSGGGGHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx RF
                    tRNA-synt_2 203 pvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgld.....eeaeekfswyleal 277
                                    p+f+ d+P +++p++++++++ + lte+++l+in  E++++++++++p e++e++ ++  d     +ea+ +++++++al
  gene489|gene489|rna488|rna488 323 PTFIKDYPIAMSPLAKNHRSK-PGLTERFELFINCKEVCNAYTELNNPFEQRERFIQQAQDmnagdDEAMMNDEDFCTAL 401
                                    *********************.9***********************************99999***************** PP

                                    HCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 278 eyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                    eyG+pp++G+glG+dRl+m+l+++ +Irdvi+FP +
  gene489|gene489|rna488|rna488 402 EYGLPPTAGWGLGIDRLIMYLTNAANIRDVIFFPTM 437
                                    **********************************87 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.55   3.3e+03      13      42 ..     104     133 ..      96     135 .. 0.78
   2 !   20.2   0.1   5.6e-08   0.00033     104     160 ..     178     235 ..     176     258 .. 0.78
   3 !   13.2   0.0   7.9e-06     0.047     211     234 ..     408     431 ..     393     434 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.55
                                    HSB-SHHHHHHHHHHHHHHCTTCEESSTTS CS
                   tRNA-synt_2d  13 agklhpltkvleeikeiflelgfeevegpe 42 
                                    + + +  t++++ i++++ + gf eve p 
  gene489|gene489|rna488|rna488 104 KERFQKRTQIIRYIRRFLDSRGFLEVETPM 133
                                    556667789999999999999999999875 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.6e-08
                                    EEEEEEEEBSST-SSSB-SEEEEEEEEEE..ETT--HHHHHHHHHHHHHHHCTSTEEEE CS
                   tRNA-synt_2d 104 iisigrvfRrdavDathlaeFhqveglvv..denvsladlkgvleellkklfgaevkvr 160
                                    +  ig+ fR++ +D th +eF+++e+ ++  d n  +     +++ ++k++fg++ ++ 
  gene489|gene489|rna488|rna488 178 VYEIGKQFRNEGIDLTHNPEFTSCEFYMAygDYNDLMVMTEELMSGMVKEMFGTD-TIV 235
                                    6679*********************998722444456666777888889999988.544 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 7.9e-06
                                    EEEEEEEHHHHHHHHHT-SSGHHH CS
                   tRNA-synt_2d 211 gfafGlGveRlamlkygieDiRel 234
                                     +++GlG++Rl m  ++  +iR++
  gene489|gene489|rna488|rna488 408 TAGWGLGIDRLIMYLTNAANIRDV 431
                                    678*******************97 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   8.9e-10   5.3e-06       9      75 ..       2      68 ..       1      69 [. 0.94

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.9e-10
                                   EEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                tRNA_anti-codon  9 sisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75
                                   si  r +++++f+ ++ +  ++q+v++    +++++ + lk+Gd+v+ tG+++r+++ e ++ v+e+ +
  gene489|gene489|rna488|rna488  2 SI--RLHARFCFFMVTSNGENLQLVIDAkeVGKDQIIKFLKRGDIVGFTGKPGRTKTLESSVFVSEVII 68
                                   77..999*************************************************9999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2727.79
//
Query:       gene490|gene490|rna489|rna489  [L=587]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-38  131.4   0.0    5.7e-38  130.7   0.0    1.3  1  Peptidase_M24    Metallopeptidase family M24
    2.9e-28   99.0   0.2    3.5e-27   95.5   0.0    2.3  2  Creatinase_N_2   Creatinase/Prolidase N-terminal domain
    4.3e-15   55.5   0.1    2.8e-14   52.9   0.1    2.3  2  Peptidase_M24_C  C-terminal region of peptidase_M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.7   0.0   9.5e-42   5.7e-38      16     208 ..     325     519 ..     318     520 .. 0.90

  Alignments for each domain:
  == domain 1  score: 130.7 bits;  conditional E-value: 9.5e-42
                                    HHHHH....HHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEEEEETTEEEE CS
                  Peptidase_M24  16 avlea....ikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlidagaeydgyasD 91 
                                    +++e+    + +g++e+ + + ++  + +  g+ +++f+ iv+ g+n+a++h+ ++drv+ +++++lid+g +y   ++D
  gene490|gene490|rna489|rna489 325 ELFEWvdlsLDKGISEKVIKERLDGIKKRFSGYVQPSFESIVGGGPNGAIVHHKASDRVVSRNEVILIDSGSQYMFGTTD 404
                                    455552223669************99888999************************************************ PP

                                    EEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-.STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEES..SSSSEEEEEE CS
                  Peptidase_M24  92 itrTvlvGkftpeqrelyeavleaqeaaikav.kpGvtlseidaaarevlesaglakffphglGHgvG..levhdegpsv 168
                                    +trT+++G++tpe+++ y+ vl++q + +++  k  +  s +d   r  l++ ++ +++ h +GHgvG  l vh++ p++
  gene490|gene490|rna489|rna489 405 TTRTLHFGEPTPEEKKSYTRVLKGQLRSMRMRfKSSMQPSVLDSLSRIDLWN-EM-EDYGHATGHGVGhfLCVHESPPTI 482
                                    *****************************966266****************7.68.888*********988****96668 PP

                                    SSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                  Peptidase_M24 169 sresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                    s  +++++ l++ +vf+iEpg+y  +ge+g+rie++v+++
  gene490|gene490|rna489|rna489 483 S--YSSDQLLKPRQVFSIEPGFY-KEGEYGIRIENLVYLK 519
                                    7..678*****************.78**********9876 PP

>> Creatinase_N_2  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.066   3.9e+02      81     107 ..     101     126 ..      50     166 .. 0.80
   2 !   95.5   0.0   5.9e-31   3.5e-27      14     161 .]     180     308 ..     170     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.066
                                    EE-GGG-..-HHHHHHHTTEEEE-GGG CS
                 Creatinase_N_2  81 Fvdeeklteevkehleengveikpyee 107
                                    F++++k  e++k++le+ g+++kp+e+
  gene490|gene490|rna489|rna489 101 FIRSRKY-EDLKNKLESRGITLKPFEN 126
                                    7777875.6788888888888888874 PP

  == domain 2  score: 95.5 bits;  conditional E-value: 5.9e-31
                                    -HHHHSS-HHHHHHHHHHHHHHTT-SEEEE-SHHHHHHHTTEE--SBTTB----EEEEEES.S-EEEEE-GGG-..-HHH CS
                 Creatinase_N_2  14 peeyaGesvaeKlerlrkelkkkkadalvlsaldeiAWllNlRGsDipynPvflsyaivtkdekatLFvdeeklteevke 93 
                                    ++++ G+ +++Kl+++r+ l+   ++ lv+++ld iAW++NlRGsDi ynPvf+syaiv+kd +a LF++e+++      
  gene490|gene490|rna489|rna489 180 DTSVVGRAFKDKLKEIRSILEP--DQTLVITELDTIAWIFNLRGSDILYNPVFYSYAIVSKD-SAKLFTNEKNI------ 250
                                    56789***************95..69*********************************875.*******9987...... PP

                                    HHHHTTEEEE-GGGHHHHHHHHHHHH----EEE-TTSBHHHHHHH-GGGEEE-S-HHHHHHHC--HHH CS
                 Creatinase_N_2  94 hleengveikpyeevvsdlkalasaskkkvlldpsktsyalasalkekkvveeespiallKavKNevE 161
                                    ++  ++v+i py+++v++++ l+     +++++  ++++++ + ++  +     + i ll + K evE
  gene490|gene490|rna489|rna489 251 KM--DDVDIYPYDDFVRHATGLK----GRIVIS-GECNAYVKDLFEGIE---YCDKIRLLQSQKAEVE 308
                                    55..56*********99999996....689998.89**99999885444...3467788888877776 PP

>> Peptidase_M24_C  C-terminal region of peptidase_M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.37   2.2e+03       8      19 ..     119     130 ..     114     131 .. 0.86
   2 !   52.9   0.1   4.7e-18   2.8e-14       1      63 []     524     585 ..     524     585 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.37
                                    S------STT-- CS
                Peptidase_M24_C   8 lTlvPidrklId 19 
                                    +Tl P++ +l+d
  gene490|gene490|rna489|rna489 119 ITLKPFENDLVD 130
                                    8*********99 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 4.7e-18
                                    -EEEEEES------STT--GGGS-HHHHHHHHHHHHHHHHHHHHHHHHT-H.HHHHHHHT--- CS
                Peptidase_M24_C   1 kfleFetlTlvPidrklIdvslLtpeEiawLnaYhakvreklsplLeeeneeleWLkraTrpl 63 
                                    kf+e  +lTlvP++ +lId+s++++eE+  Ln+ ++++r +l+p ++++   +++L+++T p+
  gene490|gene490|rna489|rna489 524 KFYEITNLTLVPYHLRLIDTSMMSEEEVSHLNRINEEIRSTLEPFMKGK-IGYRYLMENTVPI 585
                                    699*******************************************887.669*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.33s 00:00:00.99 Elapsed: 00:00:00.51
# Mc/sec: 3464.27
//
Query:       gene49|gene49|rna49|rna49  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.046   14.0   0.7      0.046   14.0   0.7    2.4  4  BLOC1_2   Biogenesis of lysosome-related organelles complex-1
      0.091   12.7   0.0       0.21   11.5   0.0    1.6  1  MarR      MarR family
       0.41   11.3   4.3       0.91   10.2   4.3    1.7  1  Ead_Ea22  Ead/Ea22-like protein
       0.54   10.7   5.3       0.77   10.2   0.5    2.8  3  YgaB      YgaB-like protein


Domain annotation for each model (and alignments):
>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   7.1e+03      49      60 ..      40      51 ..      38      53 .. 0.75
   2 ?   -0.7   0.1       0.4   1.8e+03      46      59 ..      85      98 ..      59     101 .. 0.59
   3 ?   14.0   0.7     1e-05     0.046      31      84 ..      97     151 ..      84     153 .. 0.86
   4 ?   -3.4   0.0       2.9   1.3e+04      70      77 ..     188     195 ..     176     200 .. 0.47

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                    BLOC1_2 49 kleklnekyeel 60
                               +le+lne+y e+
  gene49|gene49|rna49|rna49 40 SLEDLNELYREM 51
                               678888888876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.4
                    BLOC1_2 46 lekkleklnekyee 59
                               ++++l++l++k+ee
  gene49|gene49|rna49|rna49 85 ISSELDELRKKQEE 98
                               34555555555555 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1e-05
                    BLOC1_2  31 aasekykklkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeavseL 84 
                                + ++ y++++++++ le++l ++++kye + +  + +i ++  +++eL ++ + +
  gene49|gene49|rna49|rna49  97 EEIALYDEYERECDILEVELANMKQKYEeTWKYSCHEISDLRHRLDELRKMFNDM 151
                                55678***********************44555689************9998776 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 2.9
                    BLOC1_2  70 iekqvteL 77 
                                  + ++++
  gene49|gene49|rna49|rna49 188 TREYLNSM 195
                                22222222 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.8e-05      0.21      14      53 ..     221     260 ..     214     262 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                                HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET CS
                       MarR  14 eqgplsvseLakklgvskstvtrvldrLekkGlieRsksp 53 
                                +++++ + +L+k lgv+++ + r++  L  kG i   +s+
  gene49|gene49|rna49|rna49 221 HEESIELDKLGKILGVDRTVLLRIVYGLLSKGIIAFDRSE 260
                                56789999**************************999984 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.3    0.0002      0.91      71     138 ..      87     144 ..      62     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                   Ead_Ea22  71 aLLDelekkqqrikeleeeaenedialtvgklrveleaaekrlekenveqadaaeveitalrqriael 138
                                + LDel kkq++i++++e       +   + l+vel ++++       e  ++   ei++lr r+ el
  gene49|gene49|rna49|rna49  87 SELDELRKKQEEIALYDEY------ERECDILEVELANMKQKY----EETWKYSCHEISDLRHRLDEL 144
                                67***************66......889999999999988866....233334445566666666555 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2     0.059   2.7e+02       3      46 ..      58     102 ..      57     108 .. 0.75
   2 ?   10.2   0.5   0.00017      0.77      24      64 ..     106     149 ..      99     152 .. 0.80
   3 ?   -1.9   0.0      0.99   4.4e+03       8      19 ..     190     201 ..     185     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.059
                       YgaB   3 erLVseQmktmdkLLflQselerC.qeiekeLlklekeaklesiq 46 
                                er+ ++ m ++d L +l  e +r    i +eL +l+k+ +   + 
  gene49|gene49|rna49|rna49  58 ERMLDDHMALLDVLNNLSIEYNRYgLIISSELDELRKKQEEIALY 102
                                678889999999999999999996245788888888877655555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00017
                       YgaB  24 er.CqeiekeLlkleke..aklesiqeeikrkkkeLkeiqkvFe 64 
                                er C  +e eL++++++    ++   +ei+ ++++L e++k+F+
  gene49|gene49|rna49|rna49 106 EReCDILEVELANMKQKyeETWKYSCHEISDLRHRLDELRKMFN 149
                                555999999999887751156888999****************7 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.99
                       YgaB   8 eQmktmdkLLfl 19 
                                e ++ m+k+L l
  gene49|gene49|rna49|rna49 190 EYLNSMEKMLVL 201
                                567788888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1089  (0.0607396); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1592.24
//
Query:       gene491|gene491|rna490|rna490  [L=246]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-13   49.6   7.0    3.5e-13   49.6   7.0    1.6  1  zf-RING_2      Ring finger domain
    1.1e-10   41.2   7.8    1.1e-10   41.2   7.8    1.8  2  zf-C3HC4_2     Zinc finger, C3HC4 type (RING finger)
    2.2e-09   37.5   5.0    5.2e-09   36.3   5.0    1.6  1  zf-rbx1        RING-H2 zinc finger domain
    2.6e-08   33.7   4.0      3e-08   33.6   2.3    2.0  2  zf-RING_UBOX   RING-type zinc-finger
    2.9e-08   33.4   5.6    2.9e-08   33.4   5.6    1.7  2  zf-C3HC4       Zinc finger, C3HC4 type (RING finger)
    4.4e-08   33.0   4.7    4.4e-08   33.0   4.7    1.7  2  zf-RING_5      zinc-RING finger domain
    5.1e-08   32.5   7.5      1e-07   31.6   7.5    1.5  1  zf-RING_11     RING-like zinc finger
    4.3e-07   29.7   2.6    4.3e-07   29.7   2.6    1.7  2  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
    3.7e-06   26.7   4.6    3.7e-06   26.7   4.6    1.6  1  Prok-RING_4    Prokaryotic RING finger family 4
    0.00011   22.1   1.7    0.00022   21.2   1.7    1.4  1  zf-ANAPC11     Anaphase-promoting complex subunit 11 RING-H2 
     0.0076   15.8   3.9      0.017   14.7   3.9    1.6  1  Zn_ribbon_17   Zinc-ribbon, C4HC2 type
     0.0099   16.0   7.2       0.13   12.4   7.2    2.5  1  FANCL_C        FANCL C-terminal domain
  ------ inclusion threshold ------
      0.089   13.0   6.5       0.58   10.4   6.7    2.1  2  zf-C3HC4_4     zinc finger of C3HC4-type, RING
      0.096   12.8   2.8       0.19   11.9   2.1    1.9  1  zf-RING_10     zinc RING finger of MSL2
       0.25   11.2   3.6       0.59   10.0   3.6    1.6  1  zf-RING_4      RING/Ubox like zinc-binding domain
          5    7.3  11.2        1.7    8.8   7.0    2.4  2  RINGv          RING-variant domain
          6    7.3   7.9       0.33   11.3   2.3    1.9  2  zf-RING-like   RING-like domain
          8    6.6   9.0         12    6.0   0.9    3.0  3  TssO           Type VI secretion system, TssO


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   7.0   3.6e-16   3.5e-13       2      44 .]     187     229 ..     186     229 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.6e-16
                      zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                     C+IC++++ ++ ++ llpCgH+fh+eC+++wl  + tCPlC+
  gene491|gene491|rna490|rna490 187 HCTICFDNYIPGIKLKLLPCGHHFHQECIDEWLDLKDTCPLCK 229
                                    5*****************************************7 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.2       5.6   5.6e+03      23      28 ..     124     129 ..     122     131 .. 0.72
   2 !   41.2   7.8   1.1e-13   1.1e-10       2      40 .]     188     228 ..     187     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.6
                     zf-C3HC4_2  23 CqkCil 28 
                                    C++C  
  gene491|gene491|rna490|rna490 124 CEDCST 129
                                    999965 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 1.1e-13
                     zf-C3HC4_2   2 CpiCldmlkdpsvvt..pCgHvfCqkCilrsLeekneCPlC 40 
                                    C+iC+d +  ++ ++  pCgH f+q+Ci+++L+ k+ CPlC
  gene491|gene491|rna490|rna490 188 CTICFDNYIPGIKLKllPCGHHFHQECIDEWLDLKDTCPLC 228
                                    *********99999999************************ PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   5.0   5.2e-12   5.2e-09      23      55 .]     197     229 ..     178     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5.2e-12
                        zf-rbx1  23 eecpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55 
                                      ++++l  CgH+FH++Ci++Wl+ +++CPlc+
  gene491|gene491|rna490|rna490 197 PGIKLKLLPCGHHFHQECIDEWLDLKDTCPLCK 229
                                    446677779***********************6 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   2.3     3e-11     3e-08       1      39 []     188     226 ..     188     226 .. 0.83
   2 ?   -0.1   0.2         1     1e+03       1       9 [.     225     233 ..     225     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3e-11
                   zf-RING_UBOX   1 CpIClelftdP...lvl.pCGHtFCreClwelskslegafkCP 39 
                                    C+IC++ +  P   l+l pCGH F++eC+   +++l+ + +CP
  gene491|gene491|rna490|rna490 188 CTICFDNY-IPgikLKLlPCGHHFHQECI---DEWLDLKDTCP 226
                                    ********.889964455***********...77777777777 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1
                   zf-RING_UBOX   1 CpIClelft 9  
                                    Cp C+   +
  gene491|gene491|rna490|rna490 225 CPLCKRNIN 233
                                    ****98655 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       6.6   6.6e+03      22      26 ..     124     128 ..     122     130 .. 0.69
   2 !   33.4   5.6   2.9e-11   2.9e-08       1      41 []     188     228 ..     188     228 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.6
                                    -CHHH CS
                       zf-C3HC4  22 CskCi 26 
                                    C++C 
  gene491|gene491|rna490|rna490 124 CEDCS 128
                                    78886 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 2.9e-11
                                    -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                    C iC++++      +ll+C+H f+++Ci+++l+   k +CPlC
  gene491|gene491|rna490|rna490 188 CTICFDNYIPGIklKLLPCGHHFHQECIDEWLD--LKDTCPLC 228
                                    ********9877779******************..8899**** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.4       7.2   7.2e+03      25      29 ..     124     128 ..     123     131 .. 0.50
   2 !   33.0   4.7   4.4e-11   4.4e-08       1      44 []     187     230 ..     187     230 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 7.2
                      zf-RING_5  25 CekCl 29 
                                    Ce+C 
  gene491|gene491|rna490|rna490 124 CEDCS 128
                                    44443 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 4.4e-11
                      zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44 
                                    hC +Cf+++ +  k  l++CgH f+++C+++ l  +++Cp+C++
  gene491|gene491|rna490|rna490 187 HCTICFDNYIPGIKLKLLPCGHHFHQECIDEWLDLKDTCPLCKR 230
                                    9*****************************************95 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   7.5     1e-10     1e-07       2      29 .]     188     215 ..     187     215 .. 0.99

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1e-10
                     zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                    C+IC +++ pg +l +lpC+H FH++CI
  gene491|gene491|rna490|rna490 188 CTICFDNYIPGIKLKLLPCGHHFHQECI 215
                                    ***************************9 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4       5.9   5.9e+03      26      31 ..     124     129 ..     122     130 .. 0.78
   2 !   29.7   2.6   4.3e-10   4.3e-07       4      48 ..     187     233 ..     184     235 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.9
                                    -HHHHH CS
                     zf-C3HC4_3  26 CeeCae 31 
                                    Ce+C++
  gene491|gene491|rna490|rna490 124 CEDCST 129
                                    999975 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 4.3e-10
                                    B-TTTSSS...BS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B-- CS
                     zf-C3HC4_3   4 eCviCler...prnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpie 48 
                                     C iC+++     +  llpCgH  + +eC +++l+ k++Cp+C+r+i+
  gene491|gene491|rna490|rna490 187 HCTICFDNyipGIKLKLLPCGHH-FHQECIDEWLDLKDTCPLCKRNIN 233
                                    7******96666778999*****.*********************996 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   4.6   3.7e-09   3.7e-06       1      41 [.     188     233 ..     188     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 3.7e-09
                    Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk.dls.sCPlCqrris 41 
                                    C +C  +   + k  l pCgH + +eC d++ dl+ +CPlC+r+i+
  gene491|gene491|rna490|rna490 188 CTICFDNyipGIKLKLLPCGHHFHQECIDEWlDLKdTCPLCKRNIN 233
                                    99999998889999*****************98888*******996 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.7   2.2e-07   0.00022      35      82 ..     191     233 ..     171     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.2e-07
                                    -TTCSTTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB-- CS
                     zf-ANAPC11  35 cpsckfpGddcplvlGkckhnfhlhcilkwletetskglcpmcrqtfk 82 
                                    c +  +pG +    l  c h fh+ ci +wl+    k+ cp+c+++++
  gene491|gene491|rna490|rna490 191 CFDNYIPGIKLK--LLPCGHHFHQECIDEWLDL---KDTCPLCKRNIN 233
                                    555566665544..447**************86...789****98765 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.9   1.7e-05     0.017       4      46 ..     185     226 ..     182     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                   Zn_ribbon_17   4 lksCayC.elavkgrvvlcgvCeHvlHasCarewfenddlaeCp 46 
                                    +++C++C +  + g  +    C+H  H++C++ew++ +d   Cp
  gene491|gene491|rna490|rna490 185 TYHCTICfDNYIPGIKLKLLPCGHHFHQECIDEWLDLKD--TCP 226
                                    678888855667888888889***************999..887 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   7.2   0.00013      0.13       3      43 ..     186     221 ..     184     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                    -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHH CS
                        FANCL_C   3 veCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrs 43 
                                     +C iC+ + +     p i      C+++fH++C+ eWl  
  gene491|gene491|rna490|rna490 186 YHCTICFDNYI-----PGIKLKLLPCGHHFHQECIDEWLDL 221
                                    68999996655.....999999999*************964 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.1   1.1e+03      32      42 .]     181     191 ..     174     191 .. 0.68
   2 ?   10.4   6.7   0.00058      0.58      14      42 .]     204     228 ..     188     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                     zf-C3HC4_4  32 pdgeqllCplC 42 
                                     ++  + C+ C
  gene491|gene491|rna490|rna490 181 VSDDTYHCTIC 191
                                    4445599*999 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00058
                     zf-C3HC4_4  14 leCGhsfClsCisslqkepdgeqllCplC 42 
                                    l+CGh f ++Ci+++   +d     CplC
  gene491|gene491|rna490|rna490 204 LPCGHHFHQECIDEWLDLKDT----CPLC 228
                                    78************9888754....9999 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.1   0.00019      0.19       3      45 ..     188     230 ..     186     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                     zf-RING_10   3 CvvCckLLvdPlepkekeCqHyvCrlCvgkkkklkpsCsqCkd 45 
                                    C++C       ++ k   C+H+  + C+ +   lk +C+ Ck 
  gene491|gene491|rna490|rna490 188 CTICFDNYIPGIKLKLLPCGHHFHQECIDEWLDLKDTCPLCKR 230
                                    888888888888889999***********************94 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.6   0.00059      0.59       3      46 ..     190     231 ..     188     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                      zf-RING_4   3 lCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCree 46 
                                    +C+++    + +lk  +Cg+++ + C ++ l + +  CP C+++
  gene491|gene491|rna490|rna490 190 ICFDNY-IPGIKLKLLPCGHHFHQECIDEWL-DLKDTCPLCKRN 231
                                    555554.445566666899999999*99999.5799******85 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       6.3   6.2e+03      14      20 ..     120     127 ..     118     133 .. 0.57
   2 ?    8.8   7.0    0.0017       1.7      25      48 .]     208     228 ..     188     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.3
                                    -B-SS-.- CS
                          RINGv  14 lispCk.C 20 
                                    ++++C+ C
  gene491|gene491|rna490|rna490 120 WVQECEdC 127
                                    55555324 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                                    CSB-HHHHHHHHHHTCT-SB-TTT CS
                          RINGv  25 klvHesClekWldekeantqCeiC 48 
                                    + +H++C+++Wld    + +C +C
  gene491|gene491|rna490|rna490 208 HHFHQECIDEWLDL---KDTCPLC 228
                                    679***********...8899999 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       8.7   8.7e+03      40      43 .]     124     127 ..     121     130 .. 0.53
   2 ?   11.3   2.3   0.00034      0.33       1      43 []     188     228 ..     188     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.7
                   zf-RING-like  40 CpkC 43 
                                    C+ C
  gene491|gene491|rna490|rna490 124 CEDC 127
                                    4433 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00034
                   zf-RING-like   1 CeaCkeivtqGvrCsnesCnvrlHvdCfqhyirthsskkCpkC 43 
                                    C++C +  + G++ +   C  ++H++C+++ +  +   +Cp C
  gene491|gene491|rna490|rna490 188 CTICFDNYIPGIKLKLLPCGHHFHQECIDEWLDLKD--TCPLC 228
                                    99999999999999999**************94443..6**99 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.6   1.6e+03       8      24 ..      32      48 ..      30      50 .. 0.83
   2 ?    6.0   0.9     0.012        12       2      43 ..      50      90 ..      49     110 .. 0.75
   3 ?    5.1   0.1     0.023        23       8      33 ..     144     169 ..     142     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                           TssO  8 sgflyflllFlvtvlll 24
                                   +gfl++l +++++++l+
  gene491|gene491|rna490|rna490 32 EGFLKVLKILVTLTVLF 48
                                   799*****999999876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                           TssO  2 nkkErrsgflyflllFlvtvlllflivffffkssplqekeil 43
                                   +++E+ +  l+++ll  +++++  +++f++++ +p+++ + +
  gene491|gene491|rna490|rna490 50 TRNEKCEVPLKLFLLVYMVITVAKFGIFMSKN-IPFFRINRI 90
                                   6788888888888888888888888*****99.999998776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.023
                           TssO   8 sgflyflllFlvtvlllflivffffk 33 
                                     gf+ f++ ++++vlllfli f + k
  gene491|gene491|rna490|rna490 144 LGFVAFIAPLIAIVLLLFLITFVKPK 169
                                    589***************99888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1462.33
//
Query:       gene492|gene492|rna491|rna491  [L=360]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-47  160.2   0.0    1.3e-46  158.8   0.0    1.6  2  Met_10           Met-10+ like-protein
    8.4e-07   28.9   0.0    1.6e-06   28.0   0.0    1.5  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0031   17.1   0.0     0.0054   16.3   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0079   16.0   0.0      0.016   15.0   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.013   14.6   0.0      0.018   14.1   0.0    1.3  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.014   14.8   0.0      0.041   13.3   0.0    1.7  1  TehB             Tellurite resistance protein TehB
      0.016   14.8   0.0      0.031   13.8   0.0    1.5  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.017   14.5   0.0      0.036   13.4   0.0    1.5  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.058   13.2   0.0      0.098   12.5   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      0.063   14.0   0.0       0.24   12.1   0.0    2.0  1  Methyltransf_25  Methyltransferase domain
       0.11   12.3   0.0         11    5.9   0.0    2.6  2  Arc              Arc-like DNA binding domain


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.3     2e+03      17      50 ..      22      54 ..      10      73 .. 0.62
   2 !  158.8   0.0   8.2e-50   1.3e-46       2     199 .]     109     307 ..     108     307 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                                   TSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTT CS
                         Met_10 17 elkeykkvigevildktkvktvlrkvsevegefR 50
                                   e++e  + ++e i ++ ++ +v++ +++ +++fR
  gene492|gene492|rna491|rna491 22 EASECIQRVKESIRKVPRIPSVIKVKKR-YTTFR 54
                                   4444445555555555566666655555.55555 PP

  == domain 2  score: 158.8 bits;  conditional E-value: 8.2e-50
                                    EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS CS
                         Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskv 81 
                                    +fei+G +v+lnl+ee  +yk +ig+v++dkt  ktv++k+++++ e+R f+lev+ G++ +etihkE  + f +D+++v
  gene492|gene492|rna491|rna491 109 SFEIVGSIVHLNLDEEQIKYKDIIGQVVYDKTG-KTVITKTGQISNEYRSFDLEVIGGEGILETIHKEGDILFYIDYKNV 187
                                    79****************************985.9********************************************* PP

                                    ---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-T.TCEEEEES-G CS
                         Met_10  82 yfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkve.kvvkpileDg 160
                                    y+ skl++Er  l+++ ++g+v +d f G+Gp ++++ k  k+ +v+++dlnP+++  l++ ++ Nk++ + +++++  +
  gene492|gene492|rna491|rna491 188 YWCSKLQNERLDLVQKLRDGDVLCDPFCGVGPVSLAALK--KGCKVYSNDLNPHAISCLRKSMEINKLDpRNIEVFNLPA 265
                                    **************************************9..***************************8467******** PP

                                    GG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                         Met_10 161 revir...eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                     e+++     ++d++ +nlp+++ ++l k+ a   d  v++y
  gene492|gene492|rna491|rna491 266 SEFLEkiaGRKIDHFFLNLPDHSLDYLRKISAWDDDSLVHCY 307
                                    ***986767889*****************************9 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   9.9e-10   1.6e-06      17      63 ..     202     249 ..     191     309 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 9.9e-10
                                    -...--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCC CS
                MethyltransfD12  17 pkd.kgktfvepFaGggaVffeakkqgkkvlinDinedlinlykalik 63 
                                     k  +g+++++pF+G g V+++a+k+g kv++nD+n++ i++ ++ ++
  gene492|gene492|rna491|rna491 202 QKLrDGDVLCDPFCGVGPVSLAALKKGCKVYSNDLNPHAISCLRKSME 249
                                    4445889***********************************997665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.3e-06    0.0054      29     108 ..     206     287 ..     185     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.3e-06
                                    CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC......EEEEE-STTTTSTTS-EEEEE CS
                            MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle......vevvasdvleeveekkfdliv 102
                                    +   + + D  cG+G++++a++k+  +  v   d + +A+ + ++ +e nkl+       ++ as+ le+++ +k+d+  
  gene492|gene492|rna491|rna491 206 D--GDVLCDPFCGVGPVSLAALKKGCK--VYSNDLNPHAISCLRKSMEINKLDprnievFNLPASEFLEKIAGRKIDHFF 281
                                    3..33456889*******999997776..9**********************9999555555578999999999999999 PP

                                    E---ST CS
                            MTS 103 sNPPfh 108
                                     N P h
  gene492|gene492|rna491|rna491 282 LNLPDH 287
                                    887766 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   9.9e-06     0.016       3      81 ..     206     283 ..     204     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.9e-06
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld..nveFeqgdiee.leklledekfDlil 79 
                                    +g +++D+ CG G  ++++ ++   +++v++ D +++ai+  r+  + ++ld  n+e+   ++ e lek ++ +k+D  +
  gene492|gene492|rna491|rna491 206 DGDVLCDPFCGVGPVSLAALKK---GCKVYSNDLNPHAISCLRKSMEINKLDprNIEVFNLPASEfLEK-IAGRKIDHFF 281
                                    67889**************955...689****************7777777777***********8887.6668999877 PP

                Methyltransf_31  80 sn 81 
                                     n
  gene492|gene492|rna491|rna491 282 LN 283
                                    76 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.018     193     269 ..     196     276 ..      77     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                tRNA_U5-meth_tr 193 Walevtqe.skgdll.elycGnGnfslalarnfekvlateiakssveaaqyniaankid..nvqiirlsaeeltealkkk 268
                                      l+++q+ ++gd+l + +cG G  sla  ++  kv + ++   +++  ++ ++ nk+d  n+++  l a e+ e ++++
  gene492|gene492|rna491|rna491 196 ERLDLVQKlRDGDVLcDPFCGVGPVSLAALKKGCKVYSNDLNPHAISCLRKSMEINKLDprNIEVFNLPASEFLEKIAGR 275
                                    555666651455765389***************************************98779***********9988875 PP

                tRNA_U5-meth_tr 269 r 269
                                    +
  gene492|gene492|rna491|rna491 276 K 276
                                    4 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.5e-05     0.041       9      92 ..     184     268 ..     180     275 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                    HHHHHT-----HHHHHHCCCS-S-EEE.EES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--G CS
                           TehB   9 fskkynltathsevveavkivkpgkvl.dlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydi 87 
                                    +++ y  ++  +e ++ v+ ++ g vl d  cg g  sl    +g +v + d n ++i+ l++ +e+++l+  + +++++
  gene492|gene492|rna491|rna491 184 YKNVYWCSKLQNERLDLVQKLRDGDVLcDPFCGVGPVSLAALKKGCKVYSNDLNPHAISCLRKSMEINKLDPRNIEVFNL 263
                                    566788888999999*********9987899****************************************999999988 PP

                                    GG--- CS
                           TehB  88 neakl 92 
                                     + ++
  gene492|gene492|rna491|rna491 264 PASEF 268
                                    77766 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.031       3      88 ..     209     293 ..     207     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgv.sdkitlvlgdvfellaklklekikvdlvflSpPw 81 
                                    v+ D+f+G G  + +  ++++kv++ + n++ + c  +  e+      +i +      e l+k+  +ki  d  fl  P 
  gene492|gene492|rna491|rna491 209 VLCDPFCGVGPVSLAALKKGCKVYSNDLNPHAISCLRKSMEINKLdPRNIEVFNLPASEFLEKIAGRKI--DHFFLNLPD 286
                                    678********99999999**********************9977445677777777777777777777..999999998 PP

                Methyltransf_15  82 GGpsYkk 88 
                                       +Y +
  gene492|gene492|rna491|rna491 287 HSLDYLR 293
                                    8888876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.1   5.1e+03      54      79 ..       9      34 ..       4      41 .. 0.71
   2 ?   13.4   0.0   2.2e-05     0.036     159     218 ..     204     264 ..     193     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.1
                           PrmA 54 eevkvkalfkeeteakeliaqlkese 79
                                   + +++kal ++++ea e+i+++kes+
  gene492|gene492|rna491|rna491  9 SVICLKALGTSDKEASECIQRVKESI 34
                                   45667777777888888888887766 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.2e-05
                           PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.kleva.ls 218
                                    ++ g+ + D  +G G  ++aa+k g  kv+  D+++ A++  ++ +e+Nk++  ++ev+ l+
  gene492|gene492|rna491|rna491 204 LRDGDVLCDPFCGVGPVSLAALKKGC-KVYSNDLNPHAISCLRKSMEINKLDPrNIEVFnLP 264
                                    45555666999************997.69***********************9899995243 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     6e-05     0.098       8      62 ..     192     252 ..     183     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
                Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......k 62 
                                    +l+ +++ l++klr g  ++d  cG+G ++  + ++g++v+  Dl+p+a++ ++      k
  gene492|gene492|rna491|rna491 192 KLQNERLDLVQKLRDGDVLCDPFCGVGPVSLAALKKGCKVYSNDLNPHAISCLRksmeinK 252
                                    466778889999*************************************998776555540 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.24       5      57 ..     214     267 ..     211     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                    T-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCG CS
                Methyltransf_25   5 GcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaed 57 
                                     cG G ++la++k++  +kv+  D+++ ++   r+ +e ++l   n+e+ +  a++
  gene492|gene492|rna491|rna491 214 FCGVGPVSLAALKKG--CKVYSNDLNPHAISCLRKSMEINKLdprNIEVFNLPASE 267
                                    6*************5..*******************98877777788877766655 PP

>> Arc  Arc-like DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0069        11      32      46 ..      24      38 ..      23      41 .. 0.86
   2 ?    3.4   0.0     0.041        67       2      22 ..     275     295 ..     274     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0069
                                   HHHHHHHHHHHHHCT CS
                            Arc 32 SEilqrveeslkkeg 46
                                   SE +qrv+es+ k  
  gene492|gene492|rna491|rna491 24 SECIQRVKESIRKVP 38
                                   9*********99965 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.041
                                    CCSEEEEEECEHHHHHHHHHH CS
                            Arc   2 rkapkFnlRlPeevrekvkev 22 
                                    rk ++F l lP   ++ +++ 
  gene492|gene492|rna491|rna491 275 RKIDHFFLNLPDHSLDYLRKI 295
                                    899**********99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2353.52
//
Query:       gene493|gene493|rna492|rna492  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-45  153.7   0.0    2.6e-45  153.5   0.0    1.0  1  UQ_con    Ubiquitin-conjugating enzyme


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.5   0.0   1.5e-49   2.6e-45       2     138 ..      12     159 ..      11     161 .. 0.96

  Alignments for each domain:
  == domain 1  score: 153.5 bits;  conditional E-value: 1.5e-49
                                    HHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBETTSBB CS
                         UQ_con   2 lqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvdksGev 81 
                                    l k++k++++++++ +s++lvd  ++++w+vli+gp+ tpYe+g+Fk ++ fp dYP +pPk++f +k++HPn+d++G+v
  gene493|gene493|rna492|rna492  12 LLKDYKRIQENPNEYYSVGLVDG-DIYTWEVLIFGPRATPYENGIFKGRMVFPIDYPGSPPKFRFCSKMWHPNIDENGNV 90 
                                    789*******************7.******************************************************** PP

                                    -CGGGS............TTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHH CS
                         UQ_con  82 cldiLk............eekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvke 138
                                    c++iL+             ++W p+ t esv+lsi+ Ll++pn esp+n++aa++l+++++eyk+kv e
  gene493|gene493|rna492|rna492  91 CISILHnpgedeygyeslGDRWLPVRTPESVILSIITLLTSPNCESPANVDAAQHLRENEKEYKRKVME 159
                                    ******999999998888556*********************************************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1141.32
//
Query:       gene494|gene494|rna493|rna493  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-23   80.7   4.5    9.5e-23   80.1   4.5    1.3  1  Ribosomal_S17    Ribosomal protein S17
    1.3e-19   70.4   0.8    1.3e-19   70.4   0.8    1.7  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   4.5   1.1e-26   9.5e-23       1      67 [.      70     139 ..      70     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 1.1e-26
                                    EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS...--TT-EEEEEEECECSSSEEEEEE CS
                  Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns...vkvGDiVrieecrPlSktkrfvvv 67 
                                    GvV ++k +kT+vV v++ ++ +kyk+y +r++++++h ++++   ++vGD+V+++e+rPlSktk+ vv+
  gene494|gene494|rna493|rna493  70 GVVKKMKAEKTIVVVVNYVHYSKKYKRYSRRHTNFSVHMSPCFegmINVGDVVMCGETRPLSKTKSSVVL 139
                                    899999************************************************************9996 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.8   1.4e-23   1.3e-19       2      69 .]       6      68 ..       5      68 .. 0.87
   2 ?   -2.5   0.1      0.81   7.2e+03      24      31 ..      92      96 ..      75     106 .. 0.52

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.4e-23
                                   -SSS----SS--------------....--------TT----GGGGS-----TTSSSSSS----S-EE CS
                Ribosomal_S17_N  2 terafqkQetvflnkkkskeekkkkkkkkryvknvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                   + +++++Q++v+ ++++s  e +k     r v++  +gfk+P++A++++YiDkKCPFtG+v++rGri+
  gene494|gene494|rna493|rna493  6 KLKVYPRQTGVYAKPYAS--EDEK---PARKVREEVCGFKAPETAYTRQYIDKKCPFTGDVNVRGRIF 68
                                   5699************33..3333...268899999*******************************7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.81
                                   --....-- CS
                Ribosomal_S17_N 24 kkkkkkkr 31
                                   kk    kr
  gene494|gene494|rna493|rna493 92 KKY---KR 96
                                   222...22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1021.57
//
Query:       gene495|gene495|rna494|rna494  [L=116]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-19   68.0   1.3    8.6e-19   67.4   1.3    1.3  1  Swi5      Swi5
  ------ inclusion threshold ------
      0.038   14.1   0.1      0.059   13.4   0.1    1.3  1  DUF5072   Domain of unknown function (DUF5072)


Domain annotation for each model (and alignments):
>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   1.3   9.6e-23   8.6e-19      15      78 ..      52     114 ..      40     116 .] 0.85

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 9.6e-23
                                    HHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHCGGGHHHCT-X CS
                           Swi5  15 lekelaelkeelkekkdpeetvkrhIklLheYNEiKDvgqgLigliAeargvrikevfeefGve 78 
                                    ++k   el e l+ k d ++++kr I lL+ YNEiKD+gq+Lig+iA+ r+++ k+v+ee+G+e
  gene495|gene495|rna494|rna494  52 WKKVNHELAEYLDIK-DIDKEIKRFIFLLNSYNEIKDIGQELIGKIANLRQTTAKDVHEELGME 114
                                    455556666677765.6*********************************************97 PP

>> DUF5072  Domain of unknown function (DUF5072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   6.6e-06     0.059      55     108 ..      59     115 ..      42     116 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.6e-06
                        DUF5072  55 vtdlanvekvdellteyirlPeGy...kliavvesGkislvkepqtkeihaklsflv 108
                                     +++ +++ +d+ ++ +i l + y   k i++   Gki+++++  +k +h  l++++
  gene495|gene495|rna494|rna494  59 LAEYLDIKDIDKEIKRFIFLLNSYneiKDIGQELIGKIANLRQTTAKDVHEELGMEI 115
                                    57899******************94334579999*****************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 766.61
//
Query:       gene496|gene496|rna495|rna495  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.1e-05   22.0   0.0    0.00012   21.4   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00011   21.9   0.0    0.00037   20.2   0.0    1.6  2  Abhydrolase_1  alpha/beta hydrolase fold
    0.00079   19.4   0.0     0.0012   18.8   0.0    1.2  1  UPF0227        Uncharacterised protein family (UPF0227)
     0.0013   18.7   0.1     0.0036   17.2   0.1    1.7  1  Lipase_3       Lipase (class 3)
     0.0053   17.4   0.0     0.0077   16.9   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.19   11.9   0.0    1.2  1  DUF4030        Protein of unknown function (DUF4030)
       0.16   11.7   0.0       0.29   10.8   0.0    1.3  1  PGAP1          PGAP1-like protein


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.7e-08   0.00012      58     109 ..     146     195 ..     134     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.7e-08
                    Hydrolase_4  58 yvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaP 109
                                    y  D  ++v+ vk++++e + +l+GhS+GG+ia l++ ry    +++ +s+P
  gene496|gene496|rna495|rna495 146 YFSDGLKIVDYVKRTYHEDKPILIGHSLGGTIASLLGIRYNL--SAVAFSSP 195
                                    667778899**********9*******************988..89999988 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.45   1.1e+03     108     147 ..      60      99 ..      40     106 .. 0.71
   2 !   20.2   0.0   1.4e-07   0.00037      35      95 ..     103     186 ..      96     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.45
                                    SSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCC CS
                  Abhydrolase_1 108 dpaaslieaqrqqaksfpdffdgyaadcarnpagpllade 147
                                    +++  ++++ ++++ +f +  dg++a+ +r ++ + +a++
  gene496|gene496|rna495|rna495  60 ASNTYHSHDLDTILDKFGYDGDGVRAKAFRYNGRVAIAFK 99 
                                    6666677777888888888888888888888887777765 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.4e-07
                                    EEETTSTTSSSTTTGB...CHH......................SHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHH CS
                  Abhydrolase_1  35 lDlrGvgySspapacin..ddy......................gtasvaddldrildalgddkltlvGhSmGGmialay 90 
                                    l ++Gvg +++++                                + +  +++d+++  +  dk++l+GhS+GG+ia+ +
  gene496|gene496|rna495|rna495 103 LSVMGVGIGRTSKKDKLldR-IlysickdkgceeekirefdsigYFSDGLKIVDYVKRTYHEDKPILIGHSLGGTIASLL 181
                                    66777777777777544540.14444444444444555556666666678999*************************99 PP

                                    HHHHG CS
                  Abhydrolase_1  91 aaeyp 95 
                                      +y+
  gene496|gene496|rna495|rna495 182 GIRYN 186
                                    98884 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   4.6e-07    0.0012      54      88 ..     159     193 ..     134     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.6e-07
                        UPF0227  54 aelgddnillvGssLGGyyatrlgerfglrqvlln 88 
                                      + +d+++l+G sLGG  a  lg r+ l +v + 
  gene496|gene496|rna495|rna495 159 RTYHEDKPILIGHSLGGTIASLLGIRYNLSAVAFS 193
                                    4566778************************9884 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.4e-06    0.0036      56      87 ..     155     186 ..     146     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                    HHHHHHTT-EEEEEEEETHHHHHHHHHHHHHH CS
                       Lipase_3  56 krllekypeysivvtGHSLGgalAlLaaldlv 87 
                                    + +++ y e + ++ GHSLGg++A+L+++ + 
  gene496|gene496|rna495|rna495 155 DYVKRTYHEDKPILIGHSLGGTIASLLGIRYN 186
                                    556667777788999***********998754 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     3e-06    0.0077      62      95 ..     159     194 ..     130     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-06
                                    ....TTSEEEEEETCHHHHHHHHHHCC..EEEEES- CS
                  Abhydrolase_6  62 a..gggpvvlvGHSlGGalalaaaplalvvgvlldp 95 
                                         ++++l+GHSlGG++a++++    +++v+ ++
  gene496|gene496|rna495|rna495 159 RtyHEDKPILIGHSLGGTIASLLGIRYNLSAVAFSS 194
                                    34456789************9955555445555555 PP

>> DUF4030  Protein of unknown function (DUF4030)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.5e-05      0.19      32     101 ..      39     109 ..      32     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                        DUF4030  32 dirpytinisqrdmevvkkekrwnkvlssileevftkngykGfeiqqvnveseqpvtlaik.tkissadsG 101
                                      + y +n+ +r + +   e   n   s+ l+ ++ k gy+G ++++  ++ +  v++a k t++s   +G
  gene496|gene496|rna495|rna495  39 AFQEYDLNLIDRVRLMELVEMASNTYHSHDLDTILDKFGYDGDGVRAKAFRYNGRVAIAFKgTTLSVMGVG 109
                                    5678999*999887777778888999****************************99999874556665555 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.29      89     108 ..     162     181 ..     148     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                          PGAP1  89 eptsviliGHSmGGivaraa 108
                                    ++ + iliGHS+GG +a ++
  gene496|gene496|rna495|rna495 162 HEDKPILIGHSLGGTIASLL 181
                                    445569**********9664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 1686.98
//
Query:       gene497|gene497|rna496|rna496  [L=311]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-05   23.4   3.0    6.3e-05   22.9   3.0    1.3  1  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   3.0   3.5e-09   6.3e-05      35     192 ..      81     252 ..      61     289 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.5e-09
                                    HHHHHHHHTT--SHHHHHHHHH....HHHHHHHHHHTTTSSSHHHHHHHHHHHHHHHHHH---...HHHHHHHHHHHHHH CS
                   CTP_transf_1  35 lalkElirlvrlkkrekrllll.llslvlllllllflylesliallklvlllvlvllllvlkvlkskskklervilalla 113
                                    + + E+i  +  ++++ +++++ ++ ++l  ll+ ++ ++s ++ lk  ++ ++ +l+++++   + s +l + +l++l 
  gene497|gene497|rna496|rna496  81 VNIPEYIFRTIDEMKQEPYAFIeVVCISLGCLLMQTFLFRSSWTNLKRKTFHFFAFLVFYKE--YRMSLVLGEGLLLVLG 158
                                    55555554444444444444444333344444444444444444444444444444443443..2444455555555555 PP

                                    HHHTHHHH........................TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH---B-S-TTS-- CS
                   CTP_transf_1 114 llyvvlll.......................qslllienikeglllvllllalvvaaDigaYffGklfGktkllpkiSPk 170
                                    ll  +  +                        s+ ++ + +  ++  + +l+ + + D++a ++G ++Gkt        +
  gene497|gene497|rna496|rna496 159 LLSSCKYVnslfkpylskndkgrtvlshiylLSACIYPRLFIRHVEYVSVLVSICFQDSMASIIGEWLGKT--------E 230
                                    554444449999**************99999899999999*******************************........* PP

                                    -BHHHHHHHHHHHHHHHHHHHH CS
                   CTP_transf_1 171 KTveGfigGlvaavvvglllal 192
                                    K+++G+igG+v+ ++v + l+ 
  gene497|gene497|rna496|rna496 231 KSIQGSIGGTVSGTMVYFTLYR 252
                                    **********998887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2154.67
//
Query:       gene498|gene498|rna497|rna497  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-54  183.3   0.9      3e-54  183.0   0.9    1.1  1  Ras          Ras family
    4.4e-31  107.6   0.3      7e-31  107.0   0.3    1.3  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    9.4e-17   61.0   0.1    1.3e-16   60.6   0.1    1.1  1  Arf          ADP-ribosylation factor family
    8.4e-06   25.8   0.1    1.4e-05   25.1   0.1    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    4.3e-05   23.1   0.2    0.00095   18.8   0.2    2.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
     0.0012   18.3   0.2     0.0018   17.8   0.2    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
     0.0013   18.7   0.2        1.5    8.7   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.016   15.0   0.0      0.032   14.0   0.0    1.5  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.017   14.5   0.1      0.025   13.9   0.1    1.3  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.027   14.7   0.0        0.6   10.4   0.0    2.3  1  AAA_22       AAA domain
      0.091   12.5   0.1       0.36   10.6   0.0    1.9  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.12   11.9   0.1       0.17   11.4   0.1    1.5  1  FeoB_N       Ferrous iron transport protein B
       0.14   12.0   0.9       0.27   11.0   0.9    1.8  1  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
       0.16   11.4   0.0        2.8    7.3   0.0    2.6  3  TniB         Bacterial TniB protein


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.0   0.9   2.4e-57     3e-54       1     161 [.      37     198 ..      37     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.0 bits;  conditional E-value: 2.4e-57
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K+vl+GdsavGKt+ll + ++++F +++++Tigv+f t ++++ +  vk +iwDTAGqe+++++ ++yyr+++g+++vyd
  gene498|gene498|rna497|rna497  37 KIVLIGDSAVGKTNLLAKLTRNEFYKDSKATIGVEFGTITFKIGEDIVKAQIWDTAGQERYQAIVQAYYRGTSGAVIVYD 116
                                    9******************************************************************************* PP

                                    TTBHHHHHTHH.HHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras  81 itsresfenvk.kwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellre 159
                                    it+++s+++++  w++++k+  ++++pivL+GnK Dle+ ra+ te+g+e a  ++l f+etSA t env+eaf el+++
  gene498|gene498|rna497|rna497 117 ITNKDSLKKATsLWLKQLKDFSPSEIPIVLIGNKKDLEDYRAIATEKGKEEAVANELSFFETSALTGENVREAFFELAKT 196
                                    *********9989******************************************************************9 PP

                                    HH CS
                            Ras 160 il 161
                                    i+
  gene498|gene498|rna497|rna497 197 IH 198
                                    86 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.3   5.4e-34     7e-31       1     119 [.      37     152 ..      37     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 5.4e-34
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K+vl+Gds+vGKt ll ++++++f +++k+tigv+f t ++ ki      +  + vk +iWDtaGqer++++ + y+r+ 
  gene498|gene498|rna497|rna497  37 KIVLIGDSAVGKTNLLAKLTRNEFYKDSKATIGVEFGTITF-KIG-----E--DIVKAQIWDTAGQERYQAIVQAYYRGT 108
                                    9***********************************99776.333.....2..24889********************** PP

                                    CEEEEEEEGHHHHCHHH....HHHHHHHHCS.SS-EEEEEE-TT CS
                            Roc  81 alailvydsrssenlke....Wlkelkkvag.kspvilvgnkiD 119
                                    + a++vyd +++++lk+    Wlk+lk+ ++ ++p++l+gnk D
  gene498|gene498|rna497|rna497 109 SGAVIVYDITNKDSLKKatslWLKQLKDFSPsEIPIVLIGNKKD 152
                                    ********6666544322334********983569********9 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.1   9.8e-20   1.3e-16      15     174 ..      36     196 ..      27     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 9.8e-20
                                    EEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE....TTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEE CS
                            Arf  15 lrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei....knlkftvwDvGGqeklRplWknYfektdavifvv 89 
                                    ++i+l+G  + GKt +l kl+ +e+ +  + Tig +  ++++      +k ++wD  Gqe+   + + Y++ t + + v 
  gene498|gene498|rna497|rna497  36 FKIVLIGDSAVGKTNLLAKLTRNEFYKdSKATIGVEFGTITFkigeDIVKAQIWDTAGQERYQAIVQAYYRGTSGAVIVY 115
                                    79*****999*************99765899******999985554469******************************* PP

                                    ETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHH CS
                            Arf  90 DsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkegle 169
                                    D ++++ l++a +   + l++   +e+++++++NK+Dl++    + ++++ g ee   +++l+ +++sa++ge++ e++ 
  gene498|gene498|rna497|rna497 116 DITNKDSLKKATSLWLKQLKDFSPSEIPIVLIGNKKDLEDY---RAIATEKGKEEAV-ANELSFFETSALTGENVREAFF 191
                                    *************999999*******************975...4555555655555.58899***************99 PP

                                    HHHHH CS
                            Arf 170 wlses 174
                                     l+++
  gene498|gene498|rna497|rna497 192 ELAKT 196
                                    98876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   1.1e-08   1.4e-05       1     114 []      37     150 ..      37     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.1e-08
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE....ETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCT CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk....lkgkeielvDtpGliegaseekglgkaflaleea 76 
                                    +++++G + vGK+ L+ +lt+++    +   +T+ +++g+++    ++  + +++Dt+G  e   + + + +a+ +   +
  gene498|gene498|rna497|rna497  37 KIVLIGDSAVGKTNLLAKLTRNE--FYKDSKATIGVEFGTITfkigEDIVKAQIWDTAG-QE---RYQAIVQAYYR--GT 108
                                    589*****************974..455555666666666664432333778*******.54...34467777775..36 PP

                                    SEEEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                       MMR_HSR1  77 dlillvvdaseeklkpldeeleellee......akkplilvlnk 114
                                    + +++v d++++  + l++    +l++      +++p++l+ nk
  gene498|gene498|rna497|rna497 109 SGAVIVYDITNK--DSLKKATSLWLKQlkdfspSEIPIVLIGNK 150
                                    788888887744..334444444444444466688888888776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   7.4e-07   0.00095      53     183 ..      67     188 ..      34     203 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.4e-07
                                    TSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETT..TBSTHHHHHHHHHHHH...TTTEEEE CS
                       GTP_EFTU  53 giTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvdav..eGvepqteevlrlalk...egvpiiv 127
                                     i ++  +i+++  ++  + ++ Dt G + ++  v + +r + gav+v d++  +  +  t   l+++++    ++pi++
  gene498|gene498|rna497|rna497  67 TIGVEFGTITFKIGEDIVKAQIWDTAGQERYQAIVQAYYRGTSGAVIVYDITnkDSLKKATSLWLKQLKDfspSEIPIVL 146
                                    45556666666656777889999***************************984456999999999998872225788999 PP

                                    EEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHH CS
                       GTP_EFTU 128 fiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvkt 183
                                    + NK D  + +   + +  ++ +               +e +++ +Sal+ge+v++
  gene498|gene498|rna497|rna497 147 IGNKKDLEDYRAIATEKGKEEAV------------A--NELSFFETSALTGENVRE 188
                                    99****98555544444444344............1..246777788888887774 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   1.4e-06    0.0018       5     128 ..      37     157 ..      34     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                                    EEEEE-STTSSHHHHHHHHHHS.S---B---S...S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttd.svkktvtSq...essaalkvksekgskltliDfPGheklrqklleklkaksslkglv 80 
                                    +++l+G s  GKT l+ +Lt +  +k++ + +     +++ k+ +e+  k ++ D  G+e+ +  +++   + +   g v
  gene498|gene498|rna497|rna497  37 KIVLIGDSAVGKTNLLAKLTRNeFYKDSKATIgveFGTITFKI-GEDIVKAQIWDTAGQERYQA-IVQA--YYRGTSGAV 112
                                    589*****************99534445555531245667777.889999**********9754.5555..566777888 PP

                                    EEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT-- CS
                          SRPRB  81 fvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelflak 128
                                     v D t ++  +k+   l  + l +    + +++i++  nK++l   +
  gene498|gene498|rna497|rna497 113 IVYDITNKD-SLKKATSLWLKQLKDFS--PSEIPIVLIGNKKDLEDYR 157
                                    888877544.45555555555555555..8899999999999986555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0012       1.5     102     123 ..      38      59 ..      35      98 .. 0.87
   2 !    8.2   0.0    0.0017       2.1      35      99 ..     130     195 ..      93     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                    EEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpel 123
                                    +vl+G S vGK+ L+ +l+ ++
  gene498|gene498|rna497|rna497  38 IVLIGDSAVGKTNLLAKLTRNE 59 
                                    69***************99874 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                                    HHHHHHHHHHTT-EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                    RsgA_GTPase  35 ldrfLvlaeekgiepvivlnKiDlleeee.eleelkeelealgyevllvsaktkegleelkellkd 99 
                                      + L  +  ++i++v++ nK Dl + +  ++e+ kee  a +++++ +sa t+e+++e   +l++
  gene498|gene498|rna497|rna497 130 WLKQLKDFSPSEIPIVLIGNKKDLEDYRAiATEKGKEEAVANELSFFETSALTGENVREAFFELAK 195
                                    446677778899*************99998889999999999************999887666665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.6   2.1e+03       2      17 ..      41      56 ..      40      70 .. 0.73
   2 ?   14.0   0.0   2.5e-05     0.032      69     209 ..      67     198 ..      52     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                     ATP_bind_1  2 vGpaGsGKttfvgals 17
                                   +G   +GKt +  +l+
  gene498|gene498|rna497|rna497 41 IGDSAVGKTNLLAKLT 56
                                   788999***9999885 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2.5e-05
                     ATP_bind_1  69 vvaleflresldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsa 148
                                    ++ +ef+++++ ++ e++     +  + Dt GQ +   ++++          +++ ++v + D +  ++  k  s  l  
  gene498|gene498|rna497|rna497  67 TIGVEFGTITF-KIGEDI----VKAQIWDTAGQERYQAIVQAYY--------RGTSGAVIVYDITNKDSLKKATSLWLKQ 133
                                    56889999999.888888....6889****************99........9**************999999999999* PP

                     ATP_bind_1 149 lsamlrlelPhvvvlnkfDllkek...lekeleffedvealslllekee..ekykklaeaiaelle 209
                                    l+     e+P v + nk Dl + +   +ek  e     ++ls  +++    e +++ + ++a+++ 
  gene498|gene498|rna497|rna497 134 LKDFSPSEIPIVLIGNKKDLEDYRaiaTEKGKEEAV-ANELSFFETSALtgENVREAFFELAKTIH 198
                                    ********************6644664222222211.22222222222244555555555555554 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     2e-05     0.025       1     139 [.      37     167 ..      37     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrf...lgnltlnlwDcgGqeafveeylssqkeeifrnv 77 
                                    k++L+G s  GKt +   +  n   +d    +ati ve  ++ f    + ++ ++wD  Gqe++++     q    +r  
  gene498|gene498|rna497|rna497  37 KIVLIGDSAVGKTNLLAKLTRNEFYKDS---KATIGVEFGTITFkigEDIVKAQIWDTAGQERYQAIV---Q--AYYRGT 108
                                    799***********99999888888887...467766666665522245679************9886...3..344444 PP

                      Gtr1_RagA  78 gvliyVfDvesreleedletlkeilealrqyspeakvfvli.hKmDliqedereeifeerkee 139
                                    +  + V D+++++  ++ ++    l++l+++sp     vli +K Dl   d r+ + e+ kee
  gene498|gene498|rna497|rna497 109 SGAVIVYDITNKDSLKKATS--LWLKQLKDFSPSEIPIVLIgNKKDLE--DYRAIATEKGKEE 167
                                    44455669996664444443..36889999999877777774677764..5555444444433 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00047       0.6       8     135 ..      38     155 ..      37     156 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00047
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka....erlsseelleale 83 
                                    +v++G s +GKT ll++l+++          +++ +++ +         +  +  ++g++  +     ++ +e++ + ++
  gene498|gene498|rna497|rna497  38 IVLIGDSAVGKTNLLAKLTRNEF-------YKDSKATIGVE--------FGTITFKIGEDIVKaqiwDTAGQERYQAIVQ 102
                                    7899*********9999999851.......13332222222........3444444444444444445666677777777 PP

                         AAA_22  84 qalraravielliiD..EaqhlrseealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                     + r ++  ++++ D  + + l +++   +L++l ++s + ++++L+G   +l++
  gene498|gene498|rna497|rna497 103 AYYRGTSG-AVIVYDitNKDSL-KKATSLWLKQLKDFSPSEIPIVLIGNKkDLED 155
                                    77777777.5555553366666.67777777777777888888888887766665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00028      0.36       3      27 ..      37      61 ..      35      77 .. 0.82
   2 ?   -1.1   0.0       1.1   1.4e+03     116     137 ..     166     189 ..     137     195 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                      PduV-EutP  3 killiGkvgsGKttLtqalkgeelk 27
                                   ki+liG + +GKt L  +l+ +e+ 
  gene498|gene498|rna497|rna497 37 KIVLIGDSAVGKTNLLAKLTRNEFY 61
                                   89*****************998863 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                      PduV-EutP 116 ksaGaeki..fevsavekegieel 137
                                    ++a a+++  fe+sa++ e++ e 
  gene498|gene498|rna497|rna497 166 EEAVANELsfFETSALTGENVREA 189
                                    444444433499999999999875 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00014      0.17       2      56 ..      37      93 ..      36     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT..EEEEEEE--- CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg..keveivDlPG 56
                                   +++l+G+  vGkt l+ +lt  + +    + + ve  + ++k+ +   +++i D  G
  gene498|gene498|rna497|rna497 37 KIVLIGDSAVGKTNLLAKLTRNEFYKDSKATIGVEFGTITFKIGEdiVKAQIWDTAG 93
                                   799*****************9988777777777777777777654344556666655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.9   0.00021      0.27       3      49 ..      39      79 ..      37     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                   vliG+ ++GK+nLL  l       r+ +   ++++ g++++ i++++
  gene498|gene498|rna497|rna497 39 VLIGDSAVGKTNLLAKL------TRNEFYKDSKATIGVEFGTITFKI 79
                                   9*************888......666666666665555555555554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0022       2.8      38      63 ..      38      63 ..      31     104 .. 0.85
   2 ?    0.1   0.0      0.36   4.6e+02     152     164 ..     139     151 ..     117     163 .. 0.70
   3 ?   -0.6   0.0      0.58   7.5e+02     137     164 ..     185     212 ..     178     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0022
                           TniB 38 lllvGdsnnGKtmivekFarlhppek 63
                                   ++l+Gds++GKt ++ k +r++  ++
  gene498|gene498|rna497|rna497 38 IVLIGDSAVGKTNLLAKLTRNEFYKD 63
                                   789************99998875444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                           TniB 152 elkipivlvGtee 164
                                      +ipivl+G ++
  gene498|gene498|rna497|rna497 139 PSEIPIVLIGNKK 151
                                    358*******876 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.58
                           TniB 137 rkqreflnalksLgnelkipivlvGtee 164
                                    + +++f+++ k+++ ++k p   +G ++
  gene498|gene498|rna497|rna497 185 NVREAFFELAKTIHKKMKAPKASAGKRR 212
                                    4578999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1564.12
//
Query:       gene499|gene499|rna498|rna498  [L=2386]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.4e-21   75.8   9.7    1.4e-19   70.6   1.0    2.9  3  VPS13_C    Vacuolar-sorting-associated 13 protein C-terminal
    6.2e-20   71.5   0.8    2.7e-19   69.4   0.4    2.3  2  Chorein_N  N-terminal region of Chorein or VPS13
  ------ inclusion threshold ------
      0.032   14.0   1.4       0.13   12.0   1.4    2.1  1  Toxin_31   Scorpion acidic alpha-KTx toxin family
      0.052   12.9   0.1       0.19   11.1   0.1    2.0  1  SHR-BD     SHR-binding domain of vacuolar-sorting associated 


Domain annotation for each model (and alignments):
>> VPS13_C  Vacuolar-sorting-associated 13 protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0         1   4.6e+03     139     160 ..    1090    1111 ..    1087    1113 .. 0.91
   2 !   70.6   1.0     3e-23   1.4e-19      38     170 ..    2034    2159 ..    1987    2165 .. 0.88
   3 !    9.8   0.5   0.00014      0.62     106     165 ..    2201    2260 ..    2197    2264 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1
                        VPS13_C  139 kGaksLvkktvfGvadsvskit 160 
                                     +Ga+s++ + v+G +++ s it
  gene499|gene499|rna498|rna498 1090 NGAESFFLSMVGGWYEANSLIT 1111
                                     7***************999998 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 3e-23
                        VPS13_C   38 slllllnslgvtltniddapikLnalelenvflslesliekikkhYsqqllkqlykilgsldvlGNPvglfnnissGv 115 
                                     +++   n++g+ + ni+d ++++  ++ + ++++ e+l + ++ +Y +ql k+lyk+++ ld++GN   + +++s G+
  gene499|gene499|rna498|rna498 2034 DFI--SNVMGLLINNISDFSLEIDGMKESCLYTTFEELKDVLTIFYMTQLKKNLYKVITHLDLIGNIGSFTESVSMGI 2109
                                     444..8999*********************************************************8889999***** PP

                        VPS13_C  116 kdlfyePiqglvkgpeefgeglakGaksLvkktvfGvadsvskitgsvskglaal 170 
                                     kdl+ eP         ++++g+ kG ks++k+t++Gv+++v k+++s+++g+  +
  gene499|gene499|rna498|rna498 2110 KDLLTEPTL-----DTSVTHGIVKGGKSFLKNTIYGVSNTVGKFSKSIGTGARFV 2159
                                     *******75.....46789******************************998665 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00014
                        VPS13_C  106 glfnnissGvkdlfyePiqglvkgpeefgeglakGaksLvkktvfGvadsvskitgsvsk 165 
                                     ++f +i+ G++ +  +P++g+ +g   +++gl kG    ++  +  vad ++ i++ +++
  gene499|gene499|rna498|rna498 2201 NFFDSITRGMAGIAISPVEGASQGVAGVVKGLGKGLLGAFTRPIAEVADLITDISDVIKT 2260
                                     5899************************************************99998876 PP

>> Chorein_N  N-terminal region of Chorein or VPS13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.4   5.9e-23   2.7e-19       2      88 ..      11      96 ..      10     100 .. 0.95
   2 ?   -2.0   0.0      0.84   3.8e+03       8      43 ..     762     796 ..     760     798 .. 0.85

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 5.9e-23
                      Chorein_N  2 eslvskllnryLgeyvenldrdqlkvslwsGeveLenlkLkkealdklelPfevkegvigklrlkipwsnlkskpvvieied 83
                                   ++++ k+ln++Lg+yven+d+ ql++++++G v+  nl++k ++++ l +  +v++ +ig+lr+ +pw+++++kp++i+i+d
  gene499|gene499|rna498|rna498 11 KKILLKTLNKFLGSYVENIDKHQLELGIFKGYVSVSNLRIKSSVISRL-FEGRVISNCIGTLRVLVPWKSFSRKPIEIYIKD 91
                                   788999*****************************************8.99******************************* PP

                      Chorein_N 84 vylla 88
                                   + + +
  gene499|gene499|rna498|rna498 92 IDIKL 96
                                   *9866 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.84
                      Chorein_N   8 llnryLgeyvenldrdqlkvslwsGeveLenlkLkk 43 
                                    +ln  ++ey+e+l r+ +++sl ++ + +e+l++ +
  gene499|gene499|rna498|rna498 762 TLNISVSEYFEGLARS-VNMSLDESMADIEDLEVGE 796
                                    7888999******776.99***99999999999766 PP

>> Toxin_31  Scorpion acidic alpha-KTx toxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   2.9e-05      0.13       4      26 ..    1569    1592 ..    1568    1594 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                       Toxin_31    4 PkesCsDemCviY..CkGeeYstGv 26  
                                     P  sCsDe+ viY  C G eYst v
  gene499|gene499|rna498|rna498 1569 PGTSCSDEIKVIYklCAG-EYSTDV 1592
                                     6679*********98988.6**987 PP

>> SHR-BD  SHR-binding domain of vacuolar-sorting associated protein 13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.3e-05      0.19     169     260 ..    1714    1794 ..    1652    1801 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                         SHR-BD  169 nsqwSggfnisdvgsl.yvklrrqnseqvllkveiiledatifikiedaeknewPfsirNeseveilfyqrdpelnsd 245 
                                     +   Sg+f   d++++ y+kl  q+se+vll+v+     + ++ +i +++ n wP+ + N+++ ++ f+q+   ++ d
  gene499|gene499|rna498|rna498 1714 SLRSSGAFIPLDIKTTeYFKL--QGSETVLLSVNKSRSFGQYVFSIRTET-N-WPYMLCNDTDIDLKFTQNHDTVEHD 1787
                                     445677777777754438888..78999******9999999999998765.5.9****************94444443 PP

                         SHR-BD  246 eskplkytlppksvm 260 
                                             +   sv+
  gene499|gene499|rna498|rna498 1788 --------VLRDSVY 1794
                                     ........3334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 1.05u 0.31s 00:00:01.36 Elapsed: 00:00:00.53
# Mc/sec: 13599.71
//
Query:       gene500|gene500|rna499|rna499  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-39  134.9   0.2    6.2e-39  134.6   0.2    1.1  1  Metallophos  Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.032   14.7   0.1    1.6  1  STPPase_N    Serine-threonine protein phosphatase N-terminal 


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.2   6.9e-43   6.2e-39       2     201 ..      43     234 ..      42     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 6.9e-43
                                    EEEEEESBTBTTCCTHHHHHHHHHHHH.HHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-TTS... CS
                    Metallophos   2 rilvigDlHlalgggqlddllkllddl.lreekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGNHe... 75 
                                    +++++gD+H     gq++dl++l++   l++  ++l++  GD+vdrg  ++e+ +  ll+ +vkyp++v+ll+GNHe   
  gene500|gene500|rna499|rna499  43 PVTICGDVH-----GQFYDLMELFKVGgLPPYTNYLFM--GDYVDRGyhSVET-ISILLCLKVKYPDRVWLLRGNHEsrq 114
                                    799******.....**********88888889******..*******555555.55559********************* PP

                                    .....CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSCHHHHCC.. CS
                    Metallophos  76 .....gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnleleapepg.. 147
                                         gf++e+ +kyg     s +wr++++ f++lp+a+ +++  +++++hGg sp + ++ld+l+ +++  e+p++g  
  gene500|gene500|rna499|rna499 115 itqvyGFYDECVRKYGT----SLVWRYFTDLFDYLPVAAVVGN--DTFCCHGGlSPSF-DTLDQLKAIDRKVEIPHEGpm 187
                                    **************997....99********************..********99999.********************* PP

                                    .HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                    Metallophos 148 .dewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHt 201
                                     d++++d        ++  lg+ p +rg+g +fg + ++ + +++g+++++++H+
  gene500|gene500|rna499|rna499 188 cDLLWSD--------PDEKLGWGPSPRGAGFTFGKDITDSFNERNGLKMICRAHQ 234
                                    *******........***************************************7 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.5e-06     0.032      21      41 ..      13      34 ..       7      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-06
                      STPPase_N 21 q.LseaEIrqlCakareiFLsQ 41
                                   + L+eaE+r+lC +a e+++++
  gene500|gene500|rna499|rna499 13 NlLTEAEVRHLCDTATEMLMKE 34
                                   559****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1941.80
//
Query:       gene5|gene5|rna5|rna5  [L=438]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.54
# Mc/sec: 2453.32
//
Query:       gene50|gene50|rna50|rna50  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-08   34.4   0.0    2.3e-08   34.0   0.0    1.2  1  Thioredoxin  Thioredoxin
    0.00068   18.7   0.2     0.0042   16.1   0.2    1.8  1  Phosducin    Phosducin


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   2.5e-12   2.3e-08      15      93 ..      43     121 ..      33     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.5e-12
                                TT.TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-H CS
                Thioredoxin  15 ak.ekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegare 93 
                                +k ++ +++v Fy p    Ck +  +le++ + +   +++++v+++ ++ + kk+e++ +P l +fk+g  v++++g ++
  gene50|gene50|rna50|rna50  43 EKtKSLKMIVHFYKPEFNRCKIMDRRLEEIRDYFP-GIQFYRVNAEMCPVVTKKLEIRVLPFLGFFKDGYFVDQVVGFEK 121
                                44345689**************************9.9**********************************999999765 PP

>> Phosducin  Phosducin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   4.6e-07    0.0042     138     224 ..      40     125 ..       9     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-07
                                HHHHSS-TT-EEEEEEE-TTSTTHHHHHHHHHHHHHH-TTSEEEEEEHHHH-.-TTSS-TTT-SEEEEEETTEEEEEETTGGGG CS
                  Phosducin 138 dtidkeqkitlivvhiyedgvkgtealnssliclaaeyptvkfckvkasvig.asdrfsrdvlpallvykagellsnfvrvtdq 220
                                ++i+k  k+  ++vh y+   + ++ ++  l  +   +p ++f +v+a      ++++   vlp l  +k g ++ + v   ++
  gene50|gene50|rna50|rna50  40 ELIEKT-KSLKMIVHFYKPEFNRCKIMDRRLEEIRDYFPGIQFYRVNAEMCPvVTKKLEIRVLPFLGFFKDGYFVDQVVG-FEK 121
                                667775.788899***********************************998625788999************99988775.466 PP

                                S-TT CS
                  Phosducin 221 laed 224
                                l++d
  gene50|gene50|rna50|rna50 122 LGDD 125
                                6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1035.60
//
Query:       gene501|gene501|rna500|rna500  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-11   44.4   0.0      5e-11   43.1   0.0    1.7  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   2.8e-15     5e-11       5     106 ..     136     231 ..     132     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.8e-15
                      Rhodanese   5 lkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr.aaaaa 83 
                                    + e + + ++ ++D+R+p+eY+ ghI +Avn+             ++   +  l ++     k ++++c+ ++  a ++a
  gene501|gene501|rna500|rna500 136 VIEGMYNIDYLVIDCRFPYEYQGGHIMNAVNI-------------SSTRELGLLFRK----PKALIFHCEFSSIrAPRLA 198
                                    555554444559********************.............666666666665....899*********9888889 PP

                      Rhodanese  84 allk........k..lGyknvsvldGGfkawke 106
                                    + l+        +  l  ++v+v++GG++++++
  gene501|gene501|rna500|rna500 199 QHLRnmdrmknpYplLTIPEVYVMEGGYRKFYS 231
                                    99997776655426677899***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1653.63
//
Query:       gene502|gene502|rna501|rna501  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-30  104.1   0.0    6.4e-30  103.9   0.0    1.1  1  PTH2      Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.052   13.4   0.0      0.092   12.6   0.0    1.3  1  Alba      Alba


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.0   7.1e-34   6.4e-30       3     117 .]      45     155 .]      43     155 .] 0.95

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 7.1e-34
                                    EEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEEEE CS
                           PTH2   3 mvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaalir 82 
                                    m +++++D +mskGk+++q++h++  ++  l ++  e ell+eW+++g++kivlk++  +e++e+ + ak++g+ ++ + 
  gene502|gene502|rna501|rna501  45 MNIIINMDYSMSKGKVISQICHGMSCVMYYLFRN--E-ELLHEWKRNGEAKIVLKAS-GNEIQEIIRLAKKNGIYYHKVC 120
                                    89*********************98888888886..6.7****************98.789******************* PP

                                    ETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                           PTH2  83 DagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                    Dagrtq++pg +Tvl +gPa +s + ++ g+Lkl+
  gene502|gene502|rna501|rna501 121 DAGRTQVPPGANTVLILGPALRSNLSPISGHLKLY 155
                                    **********************************8 PP

>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     1e-05     0.092      11      47 ..      71     110 ..      66     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                                    HHHHHHHHHHHH...THTTESEEEEEEETTHHHHHHHHHH CS
                           Alba  11 imsyvkralklL...snkkeeeVvlkatGraIskAvsvae 47 
                                    +m y  r  +lL   + ++e  +vlka G+ I+  +++a+
  gene502|gene502|rna501|rna501  71 VMYYLFRNEELLhewKRNGEAKIVLKASGNEIQEIIRLAK 110
                                    7888888889999998899***************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 983.59
//
Query:       gene503|gene503|rna502|rna502  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.099   12.7   2.4        0.2   11.7   2.4    1.5  1  Ac76      Orf76 (Ac76)


Domain annotation for each model (and alignments):
>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.4   1.1e-05       0.2       4      55 ..      72     126 ..      69     133 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                           Ac76   4 illlialivlafildknekl.sellltllllfvlFiil..lnvyyikteStpadl 55 
                                    + l++ li+la+ + + +k  ++ +l++ ++++lF+    + v y+ ++ ++++l
  gene503|gene503|rna502|rna502  72 LPLMVKLILLALTFKRSDKKdNNAFLWVHMILMLFLTFadMIVLYTYDQDKTKNL 126
                                    557899*******988765415566655444444443311344555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1190.10
//
Query:       gene504|gene504|rna503|rna503  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-21   75.1   0.0    1.2e-20   74.4   0.0    1.3  1  Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phospho


Domain annotation for each model (and alignments):
>> Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.0   6.5e-25   1.2e-20      26     199 ..      23     173 ..       5     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 6.5e-25
                                    S-EEEEE--SHCHHHHHHHHHCSG.GGGGS-GGGEEEEESEEESS-TTSTT-HHHHHHHHTGGGS---GGGEE-S-TTSS CS
                Glucosamine_iso  26 graslalsGGstpkalyealaeeeeaaaaldwskvhvflgDERfVpaddpdsNaklareallskvkipeanvhpikesaa 105
                                    ++ +l++sGGs+ + l ++        ++ld s++++f++DER   +d++  N+++    ++sk    + +v++i +s  
  gene504|gene504|rna503|rna503  23 KNLALMISGGSLLQCLDDKRY------TDLDTSRWKIFYSDER---EDQNYLNYTAS-MGFISK---TNGKVYKICTSR- 88 
                                    568999****98776666555......359*************...44444444433.334444...6889****8644. PP

                                    THHHHHHHHHHHHHHHHCCSSSSSESEEEE---TTS-BTTB-TTCHHHHCSSSSEEEESSBSTSSS-EEEE-HHHHTT.C CS
                Glucosamine_iso 106 eapeaaaaayeeelkellakelpvfDlvlLGmGpDGHtaSLFPgspeleetdrlvvavedspkpppeRitlTlpvlns.a 184
                                     ++e+aa+ y++el++        +D++lLG+G DGH++SL Pg +el ++d+ vva+e +    p+R+++T +++n+  
  gene504|gene504|rna503|rna503  89 -PLEEAARMYSTELTD--------IDVCLLGIGGDGHICSLPPGCKEL-DSDDYVVALEGNFPVSPKRVSITPRFINKkI 158
                                    .58************7........9**********************6.55577888877767789***********978 PP

                                    SEEEEEEESHHHHHH CS
                Glucosamine_iso 185 revlflvaGeeKaea 199
                                    ++++f+v  ++K+ +
  gene504|gene504|rna503|rna503 159 KKLYFVVPNSKKKGV 173
                                    899999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1136.43
//
Query:       gene505|gene505|rna504|rna504  [L=112]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-24   85.6   0.0    3.1e-24   85.4   0.0    1.0  1  Ribosomal_L22e  Ribosomal L22e protein family


Domain annotation for each model (and alignments):
>> Ribosomal_L22e  Ribosomal L22e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   1.7e-28   3.1e-24       1     108 [.       7     112 .]       7     112 .] 0.89

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1.7e-28
                 Ribosomal_L22e   1 kkklkftidcskpvedkildvaefekfLkerikv.ngktgnlgdkveieregks.kvtvtsevkfskrylkyltkkyLkk 78 
                                    k+++kft+dc+kp++d++++++++ +fL+++ik+  gk+++l   ++i+ +g+  +++vt    +sk+ lk+ t ++L+ 
  gene505|gene505|rna504|rna504   7 KTTRKFTVDCTKPASDSLISPSDLGAFLQQKIKCnMGKKEKL---LQINVNGNIvEISVT-GGFISKQGLKWQTGRFLHM 82 
                                    6799******************************66999999...555555443366666.6899*************** PP

                 Ribosomal_L22e  79 kqlrdwlrvvasskesYeLryfnieedeee 108
                                    k+lr +++++a+  + +eL y+n+ee +ee
  gene505|gene505|rna504|rna504  83 KKLRAFIKIFAQGPDGFELGYINVEEGKEE 112
                                    *************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 735.71
//
Query:       gene506|gene506|rna505|rna505  [L=429]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-34  117.0   0.3    1.6e-33  116.2   0.3    1.4  1  tRNA-synt_2b   tRNA synthetase class II core domain (G, H, P,
    3.2e-19   69.1   8.9    6.9e-19   68.1   8.9    1.6  1  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
     0.0015   18.9   1.0     0.0015   18.9   1.0    1.7  2  zf-C4H2        Zinc finger-containing protein
  ------ inclusion threshold ------
      0.041   13.1   0.3       0.13   11.5   0.0    1.9  2  tRNA-synt_His  Histidyl-tRNA synthetase
      0.063   13.3   1.9       0.16   12.0   1.9    1.6  1  DUF4446        Protein of unknown function (DUF4446)
       0.07   13.7   4.8       0.17   12.5   4.8    1.7  1  Com_YlbF       Control of competence regulator ComK, YlbF/Ymc
      0.083   13.2   5.5      0.092   13.1   3.9    1.8  2  OmpH           Outer membrane protein (OmpH-like)
      0.084   11.9   0.2       0.23   10.5   0.2    1.9  1  tRNA-synt_2    tRNA synthetases class II (D, K and N)
       0.67    9.4   4.6       0.33   10.4   2.2    1.6  2  Z1             Z1 domain
        1.6    8.3   4.5       0.68    9.5   1.4    1.9  2  Fzo_mitofusin  fzo-like conserved region
        2.9    7.7  11.4        8.2    6.3   4.3    2.6  2  DivIC          Septum formation initiator


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.3   9.7e-37   1.6e-33       8     179 .]     226     404 ..     220     404 .. 0.94

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 9.7e-37
                                    SEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                    +++++L++t+e+++++l+ de + +++ P kl   + ++R+E+     d  GL+Rv++F++ +++v++ +++++   +++
  gene506|gene506|rna505|rna505 226 EDDLYLIATSEQALAALYMDERMIPQEVPKKLCGQSLCFRKEAGahgkDNAGLFRVHQFEKIEQFVICEPSESRKHHEEM 305
                                    5789*****************888888****************77897888***************************** PP

                                    HHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTE..EEECTTSSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
                   tRNA-synt_2b  84 ikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlga..tvldennreksvim 161
                                    i++ ++++++l +++ ++  + ++ +  ++ k+++ea+++  +k++e+++++++ +++s++l++   v++ennr+  v++
  gene506|gene506|rna505|rna505 306 IRVCEEFYQSLDISYNVVSIVSGELNDAAAIKYDLEAYFPNADKYRELVSCSNCTDYQSRELEIryGVVKENNRKVYVHL 385
                                    **************99998889999999************************************66689*********** PP

                                    EEEE.EEHHHHHHHHHHHH CS
                                    xxxx.xxxxxxxxxxxxxx RF
                   tRNA-synt_2b 162 icaa.igveRllsaileqn 179
                                    ++ + ++++R l++i+e++
  gene506|gene506|rna505|rna505 386 LNGTmCAIQRALCCIVENY 404
                                    ****888**********96 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   8.9   4.2e-22   6.9e-19       1     107 [.       1     114 [.       1     115 [. 0.97

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 4.2e-22
                                    ---HHHHHH..-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.....S-TCCCC CS
                   Seryl_tRNA_N   1 MLDiklire..npeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.....edaeeli 73 
                                    M+Di+lir+    e+v e+ kkR++d   v + +eld+kr e+ ++l++++a+ N+l++e+++  k++     e+ ++ i
  gene506|gene506|rna505|rna505   1 MIDINLIRDpkTREEVVESEKKRFRDGTAVGKAYELDRKRIETAFKLDQINARVNQLNREVKSGYKQGkkkedEELAKKI 80 
                                    9*********9***************************************************999999898889999999 PP

                                    CCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                   Seryl_tRNA_N  74 aevkelkeelkaleaelkeleaeleklllaiPNi 107
                                    +e+k+l +e k+l+++   +e+el+k++  i+Ni
  gene506|gene506|rna505|rna505  81 DEIKNLYDEAKNLKEDSGRIEEELNKVMKGIGNI 114
                                    *********************************9 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.0   9.3e-07    0.0015      40     155 ..      33     152 ..      10     249 .. 0.79
   2 ?   -1.9   0.0       2.1   3.4e+03      67      93 ..     291     317 ..     281     367 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.3e-07
                        zf-C4H2  40 lelLeqEkmaHveeLrlIhaDinalEsvikea.eeekekslekakklyeeykklkeevnelrselgl..ekledleeeee 116
                                      +L++ + + + +L +I+a +n+l + +k+  ++ k+k+ e+  k+++e+k+l +e  +l++++g   e+l++  +   
  gene506|gene506|rna505|rna505  33 AYELDRKRIETAFKLDQINARVNQLNREVKSGyKQGKKKEDEELAKKIDEIKNLYDEAKNLKEDSGRieEELNKVMKGIG 112
                                    45788888899999****************973667888889999*******************6642268999999999 PP

                        zf-C4H2 117 ellkeeifekqklkaaavelkkessta.pappapptslls 155
                                    ++++ee++ ++ +k++ +  + +s  + +  p+p ++l++
  gene506|gene506|rna505|rna505 113 NIISEEVVVSNDEKDNLIVRSYRSGRSiQRNPQPFSMLMK 152
                                    9***999998888866555444443330344444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                        zf-C4H2  67 vikeaeeekekslekakklyeeykklk 93 
                                    vi e  e++++++e+++   e y+ l 
  gene506|gene506|rna505|rna505 291 VICEPSESRKHHEEMIRVCEEFYQSLD 317
                                    455666666666667666666666654 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.85   1.4e+03     207     246 ..      49      84 ..      19     115 .. 0.48
   2 ?   11.5   0.0   8.2e-05      0.13      10     102 ..     176     268 ..     171     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.85
                                    HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHHHHHHHHHHH CS
                  tRNA-synt_His 207 elygdaevleealealaaapalqaaldeleelaalleala 246
                                    +++ + ++l+++ ++  ++      ++e eela+ +++++
  gene506|gene506|rna505|rna505  49 QINARVNQLNREVKSGYKQ----GKKKEDEELAKKIDEIK 84 
                                    4444433333333322221....12222223333333222 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.2e-05
                                    HHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTS.TCCHH.HS-EEE-TTSSEEEE-SSSHHHHHHHHHHHHHTSS CS
                  tRNA-synt_His  10 aekieelrrrlldlfeswGYelVspPllEyldslltga.gedld.qtfklvDqsgrllglRaDiTpqvaRiaahrlnrer 87 
                                    a+ +++l r  +d++e++GY ++ +P++ + d++ +++  +d d q++k+ D+    l   ++     + ++ +++ +e 
  gene506|gene506|rna505|rna505 176 ARLAQALTRYAIDFLENKGYTYIQTPVMLRRDVMAKTSqLSDFDdQLYKVEDD--LYLIATSEQALAALYMDERMIPQEV 253
                                    777889999***********************99998854554459****975..3444556677777777777777777 PP

                                    -EEEEEEEEEEESS- CS
                  tRNA-synt_His  88 plRlcYaGsvlrtrp 102
                                    p +lc    ++r+++
  gene506|gene506|rna505|rna505 254 PKKLCGQSLCFRKEA 268
                                    777777766666665 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.9   9.7e-05      0.16      21      83 ..      51     112 ..      43     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.7e-05
                        DUF4446  21 lvklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqkvg 83 
                                    ++++++l++++k+  k+ ++k  +e l++k++e+++l +e ++l+++  ++ee+l+k ++ +g
  gene506|gene506|rna505|rna505  51 NARVNQLNREVKSGYKQGKKK-EDEELAKKIDEIKNLYDEAKNLKEDSGRIEEELNKVMKGIG 112
                                    678889999998888755544.45667899**************************9998765 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.8    0.0001      0.17      22     104 ..      35     119 ..      28     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                    HHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT.----HHHHHHHHHHHHHHHTSHHHHH.HHHHHHHHHHHHHHHHHH CS
                       Com_YlbF  22 keaeealeedeelqklikefkklqkelqekqmkg.eelkeeekkelqelkeeldknplvke.yleaeqelnellqevnki 99 
                                    +  ++++e   +l +  +++++l+ e+    ++g ++++ee +k+++e+k+ +d+ +++ke     e+eln++++ + +i
  gene506|gene506|rna505|rna505  35 ELDRKRIETAFKLDQINARVNQLNREVKSGYKQGkKKEDEELAKKIDEIKNLYDEAKNLKEdSGRIEEELNKVMKGIGNI 114
                                    555666777777777778888888888775556666667777779999999998888887526789************** PP

                                    HHHHH CS
                       Com_YlbF 100 iaeai 104
                                    i+e++
  gene506|gene506|rna505|rna505 115 ISEEV 119
                                    **987 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.9   5.7e-05     0.092      22     102 ..      32     115 ..      22     133 .. 0.61
   2 ?   -2.4   0.0       3.3   5.5e+03      96     115 ..     180     199 ..     174     217 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS....-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHH CS
                           OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakkl.e..keekeqelqkkeqelqqkqqqkaqelqkkqqe...llkpil 95 
                                    + +e ++k+++++++   +++++ +++l+++ k++ +  k+++ +el+kk +e++++++ +a++l++ +     +l++++
  gene506|gene506|rna505|rna505  32 KAYELDRKRIETAFK--LDQINARVNQLNREVKSGyKqgKKKEDEELAKKIDEIKNLYD-EAKNLKEDSGRieeELNKVM 108
                                    555555566666555..55666666666666666655657778888**********555.55565555533000233344 PP

                                    HHHHHHH CS
                           OmpH  96 dkinkai 102
                                    + i ++i
  gene506|gene506|rna505|rna505 109 KGIGNII 115
                                    4444443 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.3
                                    HHHHHHHHHHHHHTT-SEEE CS
                           OmpH  96 dkinkaikevakekgydlvl 115
                                    + ++    ++ + kgy+++ 
  gene506|gene506|rna505|rna505 180 QALTRYAIDFLENKGYTYIQ 199
                                    45555555667899999994 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00014      0.23      20      59 ..     174     213 ..     171     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                                    HHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  20 kvlrlrstvtkavrkyleengfieietPiLsksdteegar 59 
                                    k+ rl + +t++  ++le++g++ i+tP++ + d+ ++  
  gene506|gene506|rna505|rna505 174 KMARLAQALTRYAIDFLENKGYTYIQTPVMLRRDVMAKTS 213
                                    5677888999999*****************9998655443 PP

>> Z1  Z1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.2    0.0002      0.33      40     116 ..      48     127 ..      39     141 .. 0.63
   2 ?   -2.3   0.0       1.6   2.6e+03      63      79 ..     300     316 ..     282     387 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                             Z1  40 ekvaelieelleelkkelkes...aeekkeellkeleklwekektstkseeeelsfeevkeelkealeki......evvv 110
                                    +++++++++l +e+k+ +k+    ++e+ +++++e+++l+++       ++ + +  +++eel+++++ i      evvv
  gene506|gene506|rna505|rna505  48 DQINARVNQLNREVKSGYKQGkkkEDEELAKKIDEIKNLYDEA------KNLKEDSGRIEEELNKVMKGIgniiseEVVV 121
                                    4566666666666666666663224444455555666666666......4555566677777777777776667768888 PP

                             Z1 111 vNsskk 116
                                     N +k+
  gene506|gene506|rna505|rna505 122 SNDEKD 127
                                    888776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                             Z1  63 ekkeellkeleklweke 79 
                                    +++ee+++ +e+ +++ 
  gene506|gene506|rna505|rna505 300 KHHEEMIRVCEEFYQSL 316
                                    33444444444444443 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4   0.00042      0.68     100     156 ..      51     108 ..      42     110 .. 0.82
   2 ?   -2.5   0.1         2   3.2e+03      40      57 ..     231     248 ..     230     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00042
                  Fzo_mitofusin 100 sstfarlcqqvde.tekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                    +  +++l+++v+   ++  ++e +el k+i++++++  +ak l++   ++e+eL+k  
  gene506|gene506|rna505|rna505  51 NARVNQLNREVKSgYKQGKKKEDEELAKKIDEIKNLYDEAKNLKEDSGRIEEELNKVM 108
                                    5556777778876245556788999*****************************9865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                  Fzo_mitofusin  40 vialslalygllYlyErl 57 
                                    +ia s  + ++lY+ Er+
  gene506|gene506|rna505|rna505 231 LIATSEQALAALYMDERM 248
                                    799999999******997 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.9     0.014        23      19      49 ..      33      63 ..      29      67 .. 0.91
   2 ?    6.3   4.3     0.005       8.2      27      59 ..      70     102 ..      65     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.014
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                          DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkd 49
                                    ++l++++ +   +l++++a+ ++L++evk 
  gene506|gene506|rna505|rna505 33 AYELDRKRIETAFKLDQINARVNQLNREVKS 63
                                   68999************************85 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.005
                                    HHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                          DivIC  27 aalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                    ++  +elak+ +e+++L +e k+Lk d  +iee
  gene506|gene506|rna505|rna505  70 KKEDEELAKKIDEIKNLYDEAKNLKEDSGRIEE 102
                                    566789*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1353  (0.0754643); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2708.94
//
Query:       gene507|gene507|rna506|rna506  [L=1990]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-93  312.4  11.9    1.4e-88  297.3   6.0    2.2  2  PROCN           PROCN (NUC071) domain
    8.6e-70  233.8   0.8    1.7e-69  232.9   0.8    1.5  1  U6-snRNA_bdg    U6-snRNA interacting domain of PrP8
    5.8e-39  133.5   0.8    5.8e-39  133.5   0.8    2.0  2  PRO8NT          PRO8NT (NUC069), PrP8 N-terminal domain
    1.1e-36  125.9   0.0    2.4e-36  124.8   0.0    1.6  1  U5_2-snRNA_bdg  U5-snRNA binding site 2 of PrP8
    1.7e-22   79.6   1.2    4.4e-22   78.2   1.2    1.7  1  RRM_4           RNA recognition motif of the spliceosomal PrP
    2.1e-14   53.7   0.1    4.8e-14   52.6   0.1    1.6  1  PRP8_domainIV   PRP8 domain IV core
    1.2e-06   28.5   0.3    2.5e-06   27.4   0.3    1.6  1  PROCT           PROCT (NUC072) domain
  ------ inclusion threshold ------
      0.058   13.1   0.0       0.13   12.0   0.0    1.5  1  Herpes_teg_N    Herpesvirus tegument protein, N-terminal cons


Domain annotation for each model (and alignments):
>> PROCN  PROCN (NUC071) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.3   6.0   6.4e-92   1.4e-88      23     334 ..     229     517 ..     217     528 .. 0.91
   2 !   18.2   0.3   3.7e-07   0.00084     341     401 ..     605     658 ..     602     662 .. 0.87

  Alignments for each domain:
  == domain 1  score: 297.3 bits;  conditional E-value: 6.4e-92
                          PROCN  23 ktkraedvplikkwykeraekeePvkvrvsyqkllkkyvlnelkkkkkkkkkkkkllkelketkffqktkldwveaGlqv 102
                                    k k  +d+pl+k ++ ++ +  eP kvr    +ll++y  n  +k+k+  +  +++lkelk+t++fq+t++dwveaGlq+
  gene507|gene507|rna506|rna506 229 KEKHPVDIPLLKGYCFQERPGGEP-KVR----NLLRNYTRNIERKRKR--RPSTRILKELKNTRYFQRTEIDWVEAGLQL 301
                                    4566789******99999999888.665....79****9887665554..577899************************ PP

                          PROCN 103 vrqgfnmlnllihrksltylhldynfnlkPtktlttkerkksrlGnafhlirellrlvkllvdahvqyrlgkidayqlad 182
                                    v qg+ ml  +++rk+l+yl ld+nfnlkP++ lttkerkksr+G ++hl re+l++vk lvd+hv +r g+id+y+l  
  gene507|gene507|rna506|rna506 302 VYQGHRMLSEILRRKKLSYLVLDWNFNLKPIRQLTTKERKKSRVGTSYHLTREMLKFVKHLVDIHVLFRQGNIDCYELMG 381
                                    ******************************************************************************** PP

                          PROCN 183 glqyifnhvgqltGiyrykykvmrqirackdlkhvi.ysrfntgevgkGPGvGfwaPswrvwvfflrGiiPllerwlgnl 261
                                     + ++fn vg +tGiyrykykvmrqi++ck  k +  y + +            w+ +wr w f++rG iPll r+++ l
  gene507|gene507|rna506|rna506 382 NVDHVFNNVGVITGIYRYKYKVMRQIKQCKSWKRLSsYVKIEG-----------WGEQWRTWCFMFRGHIPLLGRYISGL 450
                                    *********************************9842444433...........99************************ PP

                          PROCN 262 larqfeGrkskevaktitkqrveseydlelraavlhdildmlPegvkqskaktilqhlseafrcwkanipwkv 334
                                    ++r  eGr    + k +++qr es yd+ l+ ++++++  +l    ++s++k +lqh+ ea+rcwkan+p+++
  gene507|gene507|rna506|rna506 451 VTRIAEGRDY--NPKPLSRQRSESGYDIALKRQIVEEVSSVL----HHSQVKRLLQHFGEAWRCWKANVPYHI 517
                                    ********55..6799***************99999988775....78999*******************986 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.7e-07
                          PROCN 341 ienlilryvkakadewisvahynrerikrgatvdktvvkknlGrltrlylkeeqerqaeyl 401
                                    ++++i +y+++k++++i++a    ++ k+         kk lG+++rly+ke    q eyl
  gene507|gene507|rna506|rna506 605 LQEIIDKYIRLKSEWYIESATNMEKKSKK-------EEKKRLGKISRLYMKERMAEQVEYL 658
                                    789***************99877666544.......4689*****************9997 PP

>> U6-snRNA_bdg  U6-snRNA interacting domain of PrP8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.9   0.8   7.4e-73   1.7e-69       7     157 ..    1233    1379 ..    1228    1381 .. 0.97

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 7.4e-73
                   U6-snRNA_bdg    7 lksekfawtsarhdgkllnleryradviealGgveailehtlfkatsfksweglvwdkasgfeeslkakkltnaqrsG 84  
                                      k ++f++t+++hdgkl+++ery+ad ++ +Ggve+i +htlf at+f+s+++++w+++s    +  +++ltnaqr+G
  gene507|gene507|rna506|rna506 1233 GKPDWFWFTDTKHDGKLWSMERYTADCLKSFGGVEGIASHTLFGATYFRSFSKVFWEDMS----VEGNRRLTNAQRMG 1306
                                     5889******************************************************88....7789********** PP

                   U6-snRNA_bdg   85 lsqiPnrrftlWWsPtinranvyvGfqvqldltGvfmhgklptlkisliqifrahlWqkihesvvmdllqvld 157 
                                     lsq+Pnrrf+lWWsPtinr+nvyvG+qvqld+tGv+mhgklptlkis+iqifr+hlW++ihes+  dl+ v++
  gene507|gene507|rna506|rna506 1307 LSQVPNRRFILWWSPTINRGNVYVGYQVQLDQTGVLMHGKLPTLKISFIQIFRNHLWRRIHESITEDLCGVFK 1379
                                     ***********************************************************************98 PP

>> PRO8NT  PRO8NT (NUC069), PrP8 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   0.8   2.6e-42   5.8e-39       1     142 [.       7     139 ..       7     147 .. 0.96
   2 ?   -3.9   0.0       5.3   1.2e+04      28      89 ..     341     403 ..     336     413 .. 0.58

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 2.6e-42
                                    -----HHHHHHHHHHHTTT-SGGGTTTHHHHHHHHTTSHHHHHHHHTT---TT-S--B--EEEETTT--EEE-----B-H CS
                         PRO8NT   1 keelPpehlRkiikdhgdlsskkfksdkrvylgalkylPhavlkllenmpmpweevrevkvlyhvtgaitfvneiprvie 80 
                                    ke++PpehlR+iik ++d++         +++ga++y+P a+++l+++mpmpwe++r+v+vlyhv+g+itfvne++rv  
  gene507|gene507|rna506|rna506   7 KERMPPEHLRRIIKVSRDMHP--------SFMGAMRYVPYALHNLMRSMPMPWESIRYVDVLYHVSGLITFVNEKRRVDV 78 
                                    789*****************9........9************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHTTS------SS-S-SSS----H.HHHHHH-----------TTT CS
                         PRO8NT  81 pvylaqwstmwiamrrekrdrrhfkrlrfppfddeeppldyadnildvepleaiqleldeee 142
                                    + +  +ws  ++ +++e ++r  ++ lr+p+fdd++p++dy+ +i+++ ++ ai  e +e  
  gene507|gene507|rna506|rna506  79 KEHRMRWSHASARFSSEMKKRGFVRVLRYPVFDDDDPVVDYG-SIMGLPVPAAIGDEGKEWR 139
                                    *****************************************9.9**********99877655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5.3
                                    HHHHHHHHTTSHHHHHHHHTT---TT-S--B--E.EEETTT--EEE-----B-HHHHHHHHHH CS
                         PRO8NT  28 krvylgalkylPhavlkllenmpmpweevrevkv.lyhvtgaitfvneiprviepvylaqwst 89 
                                    k++ +g+  +l + +lk+++ ++      r+ ++  y+  g +  v +   vi  +y  ++  
  gene507|gene507|rna506|rna506 341 KKSRVGTSYHLTREMLKFVKHLVDIHVLFRQGNIdCYELMGNVDHVFNNVGVITGIYRYKYKV 403
                                    555555555555666666666665555555555544666666666655556666666665554 PP

>> U5_2-snRNA_bdg  U5-snRNA binding site 2 of PrP8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.8   0.0   1.1e-39   2.4e-36      18     131 ..    1043    1156 ..    1032    1159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 1.1e-39
                 U5_2-snRNA_bdg   18 kaflkvseeeiekfenrirqillssgsttftkiaakwntalialltyfreavvsteelldvlvkaetkiqtrvklgln 95  
                                      a l vsee ie+fe++i +i+ +sgs+tf k+a++wnt ++a++ y+re++ +t+ l + l ++e  iq+ +k g+n
  gene507|gene507|rna506|rna506 1043 YASLAVSEEGIEMFESNISHIVSTSGSATFLKVATRWNTQILAFVGYYRECIHDTKGLGERLRRSEGLIQNVIKKGIN 1120
                                     57899************************************************************************* PP

                 U5_2-snRNA_bdg   96 skmpsrfPpavfytPkelGGlGmlsaghvliPasdl 131 
                                     skmp rfPp++fy+Pke+GGlGmls+g   + + dl
  gene507|gene507|rna506|rna506 1121 SKMPVRFPPVMFYAPKEMGGLGMLSVGGARVFRDDL 1156
                                     **************************9988887777 PP

>> RRM_4  RNA recognition motif of the spliceosomal PrP8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   1.2     2e-25   4.4e-22       4      71 ..     834     901 ..     831     917 .. 0.96

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2e-25
                          RRM_4   4 dltllnrllrlivdknladyitaknnvvltykdmshvnsyGlirGlqfssfvvqyyglvldllllGle 71 
                                    d +ll++l++li+d++ladyi+++nn ++ ykdm+++n++G+i+G+q+s+fv+++y++++dl +lG +
  gene507|gene507|rna506|rna506 834 DNNLLSKLFKLILDPTLADYIISRNNCQVFYKDMAYTNHVGFIKGFQLSPFVYKFYSFIIDLCVLGED 901
                                    889***************************************************************75 PP

>> PRP8_domainIV  PRP8 domain IV core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.1   2.2e-17   4.8e-14      47     230 .]    1557    1714 ..    1548    1714 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.2e-17
                  PRP8_domainIV   47 avfilnPktGqlflkvihtsvwagqkrlsqlakwkaaeevaalvrslPveeqPkqiivtrkglldplevhlldfPniv 124 
                                     +vfi++P++G+l++k    s +   k++ q ++   a +v      l  ee  k+ +v ++++++++e+ ++d+P i 
  gene507|gene507|rna506|rna506 1557 TVFIFDPHSGNLYFK----SYYGESKKIRQ-TRLLVARDVF-----LMGEELNKRNVVVSESMINAMENLIIDHPSIC 1624
                                     79***********97....67777777766.6778888886.....4579999999********************** PP

                  PRP8_domainIV  125 ikgselkLPfkavlkiekladlvlkatepkmvlfnlyddWlesissytafsrlililralkinkekakkilkpdkevv 202 
                                     +k+   ++P+  + ++ k++++    +e ++   nly+ W+e+   +t f r++l++ ++++++ k k++        
  gene507|gene507|rna506|rna506 1625 VKTCP-SIPL--FSNVAKIKEI---GMEKNVRSINLYEGWKET-GRFTNFCRVLLVMHGMDVDEAKVKDL-------- 1687
                                     **986.5554..3455666665...467888899******987.78*******************99864........ PP

                  PRP8_domainIV  203 vkehhlwptlsdeeWvevevklrdlila 230 
                                        + +wp  sd+eW++ e++l+dli++
  gene507|gene507|rna506|rna506 1688 -GINSIWPEISDDEWIKKEIQLKDLIVD 1714
                                     .34679********************85 PP

>> PROCT  PROCT (NUC072) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.3   1.1e-09   2.5e-06      59     112 ..    1931    1982 ..    1908    1990 .] 0.82

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.1e-09
                          PROCT   59 GfflvPeegvWnysfmgakfsekmkyelkldiPkeFydelHRpthFlqfaelee 112 
                                     G+f +P  g+Wnysf    ++++ +y  k++ P++Fyd + R+ hF +f + + 
  gene507|gene507|rna506|rna506 1931 GVFYTP--GMWNYSFARPFYDDRLEYVWKVGAPHRFYDGTCRVGHFSEFWKEQG 1982
                                     556565..79***************************************99854 PP

>> Herpes_teg_N  Herpesvirus tegument protein, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.7e-05      0.13     118     136 ..    1548    1566 ..    1480    1575 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                   Herpes_teg_N  118 aiailikddkyylFDpHst 136 
                                     + a+++k++++++FDpHs 
  gene507|gene507|rna506|rna506 1548 TKALFRKEKTVFIFDPHSG 1566
                                     789**************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1990 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.17u 0.35s 00:00:01.52 Elapsed: 00:00:00.55
# Mc/sec: 10927.71
//
Query:       gene508|gene508|rna507|rna507  [L=347]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2216.94
//
Query:       gene509|gene509|rna508|rna508  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-73  245.7   2.1    3.9e-73  245.1   2.1    1.3  1  eIF-6     eIF-6 family


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.1   2.1   2.2e-77   3.9e-73       1     196 [.      11     208 ..      11     209 .. 0.99

  Alignments for each domain:
  == domain 1  score: 245.1 bits;  conditional E-value: 2.2e-77
                                    .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHH CS
                          eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklk 80 
                                    r+++egsseiG +++ltn+y++v ++ ++++ k ++e++++++vetti+++r vGs + gN++gllvp+t+td+e+ +++
  gene509|gene509|rna508|rna508  11 RIDFEGSSEIGAYMTLTNTYCVVGRSQSNNVLKFLQENVSIPIVETTINSIRSVGSQCRGNRHGLLVPHTITDQEIMHIR 90 
                                    799***********************9999************************************************** PP

                                    HHHH---..EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT- CS
                          eIF-6  81 eslklev..erleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpka 158
                                    + l+++v  +r+ee+l+AlGNvil+ND+vA++h dl++e++++i+dvL+v+v+r++i+++++vG++++++n+g+lvhp +
  gene509|gene509|rna508|rna508  91 NTLPENVivRRIEERLNALGNVILCNDHVAIIHADLDEESENLIKDVLQVPVYRHNIGHEPLVGTFGALNNQGMLVHPLT 170
                                    ****99888*********************************************************************** PP

                                    -HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS- CS
                          eIF-6 159 teeeleeleellkveveagTvNrGsklvgsglvaNdkg 196
                                    ++e ++el+ell+v+v agTvN Gs+++g+g+v Nd++
  gene509|gene509|rna508|rna508 171 NQECQKELSELLEVNVIAGTVNGGSPCIGGGVVTNDWM 208
                                    ************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1680.60
//
Query:       gene510|gene510|rna509|rna509  [L=81]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-17   63.1   0.4    1.7e-17   62.9   0.4    1.1  1  LSM       LSM domain
     0.0017   18.4   0.1     0.0021   18.2   0.1    1.3  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.4   1.9e-21   1.7e-17       2      66 ..      17      79 ..      16      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 1.9e-21
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                   fl+ ++n++v v lk+g++++G+L+  D++ N+ L++++e   +  +++k+g+v iR+nni +is
  gene510|gene510|rna509|rna509 17 FLQRMKNRNVSVCLKWGQVYEGVLVTSDNYFNVLLDECVEKEGE--TSTKVGEVSIRCNNIKSIS 79
                                   9***************************************9977..7****************98 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.3e-07    0.0021      14      51 ..      24      59 ..      17      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-07
                                   SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                         SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                   ++v+v +k G vyeG++ t++    f+v L+   +++ 
  gene510|gene510|rna509|rna509 24 RNVSVCLKWGQVYEGVLVTSDN--YFNVLLDECVEKEG 59
                                   589*******************..9*999998777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 570.95
//
Query:       gene51|gene51|rna51|rna51  [L=316]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-05   24.2   0.0    0.00012   21.9   0.0    2.1  1  PRK         Phosphoribulokinase / Uridine kinase family
     0.0012   19.2   0.0     0.0042   17.3   0.0    2.0  1  AAA_22      AAA domain
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.026   15.1   0.0    1.6  1  AAA_18      AAA domain
      0.017   14.2   0.0      0.026   13.6   0.0    1.2  1  T2SSE       Type II/IV secretion system protein
      0.032   14.2   0.0       0.13   12.2   0.0    1.9  1  NACHT       NACHT domain
      0.042   14.1   0.2      0.069   13.4   0.2    1.3  1  AAA_28      AAA domain
      0.052   13.6   0.7        2.6    8.1   0.4    3.4  2  AAA_14      AAA domain
      0.062   13.5   0.0      0.095   12.9   0.0    1.3  1  AAA_33      AAA domain
      0.084   13.3   0.4       0.78   10.2   0.4    2.2  1  AAA         ATPase family associated with various cellular ac
      0.086   12.6   0.0       0.13   12.0   0.0    1.4  1  AAA_24      AAA domain
       0.16   11.9   0.0       0.27   11.1   0.0    1.4  1  APS_kinase  Adenylylsulphate kinase


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   7.3e-08   0.00012       1     121 [.      38     150 ..      38     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7.3e-08
                        PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyevlkelkeg 84 
                                +I + g+   Gktt+ar+l+ ++ r ++ a        l ld+ + +     + +  e++++f++p a d+ +++ vlk+l++ 
  gene51|gene51|rna51|rna51  38 IICIQGPTSTGKTTFARRLHGLLSRGGISA------YALGLDSYYFKP--L-NPDLDEEDYDFDNPGALDWRNIFDVLKALRDR 112
                                89**********************888883......344444444332..2.23455689**********************98 PP

                        PRK  85 kk.vdkpiYsheteeaapdkeeliegadvlviEGlhal 121
                                +  ++  +Ys ++   +   +e    ++v++i+G+ a+
  gene51|gene51|rna51|rna51 113 EPfIEHNVYSASSYGEVSVVREPNTMPNVIIIDGVQAF 150
                                75389999*98887777767888888999****99876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.6e-06    0.0042       4     105 ..      35     155 ..      32     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-06
                     AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...............erpevv..fvtlpsst..sskdllrellralglel 68 
                                +++i+++ G++ tGKTt +rrl+  l +    ++                        ++  +++  ++++++  l    ++e 
  gene51|gene51|rna51|rna51  35 RRYIICIQGPTSTGKTTFARRLHGLLSRGGISAYalgldsyyfkplnpdL----DeeDYDFDNPGalDWRNIFDVLKALRDREP 114
                                689***********************888777779998888888755333....233555555555588888776666666666 PP

                     AAA_22  69 kaerlsseellealeqalrarav..ielliiDEaqhlr...s 105
                                   +++     ++ e  + +     + ++iiD +q ++   s
  gene51|gene51|rna51|rna51 115 FI-EHNVYSASSYGEVSVVREPNtmPNVIIIDGVQAFNtinS 155
                                66.888888888888888888889999999999999975531 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.6e-05     0.026       1      82 [.      39     147 ..      39     215 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                     AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss.............. 69 
                                I++ G+  +GKtt+a++L  +l   g+    +  ++++  + +p+  +e   +d +    + ++++   +              
  gene51|gene51|rna51|rna51  39 ICIQGPTSTGKTTFARRLHGLLSRgGISAYALGLDSYYFKPLNPDLDEEDYDFDNPGALDWRNIFDVLKAlrdrepfiehnvys 122
                                9*****************666533544444443333333333333222223333333333333333332233333355555555 PP

                     AAA_18  70 ............aleegknlvidgh 82 
                                             ++ +++++idg+
  gene51|gene51|rna51|rna51 123 assygevsvvrePNTMPNVIIIDGV 147
                                5555555555554555556666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.026     127     148 ..      34      55 ..      20      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                      T2SSE 127 rerglilvsGgTgsGKttllya 148
                                ++r++i + G+T++GKtt++  
  gene51|gene51|rna51|rna51  34 SRRYIICIQGPTSTGKTTFARR 55 
                                5899**************9865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.9e-05      0.13       2      32 ..      38      68 ..      37     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                               CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                      NACHT  2 lvilqGeaGsGKTtLlqklalawaegklpqg 32
                               ++++qG+   GKTt++++l+ ++ +g   + 
  gene51|gene51|rna51|rna51 38 IICIQGPTSTGKTTFARRLHGLLSRGGISAY 68
                               589******************9999987665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.3e-05     0.069       2      20 ..      39      57 ..      38      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                     AAA_28  2 ivitGgestGKTtlleaLa 20
                               i+i G+ stGKTt +++L+
  gene51|gene51|rna51|rna51 39 ICIQGPTSTGKTTFARRLH 57
                               89****************8 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0016       2.6       3      23 ..      37      57 ..      35     223 .. 0.84
   2 ?    0.3   0.0      0.42   6.9e+02      55      79 ..     288     312 ..     244     314 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
                     AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                i++i+G+  +GKTt++++l 
  gene51|gene51|rna51|rna51 37 YIICIQGPTSTGKTTFARRLH 57
                               6899************99885 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.42
                     AAA_14  55 lilek.lkeekktylflDEiqevpew 79 
                                ++  +  +  +k +++lD    vp+w
  gene51|gene51|rna51|rna51 288 ECTGEcEY-GGKACIVLDDKIAVPQW 312
                                22222122.46777777777777766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.8e-05     0.095       2      36 ..      39      78 ..      38     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.8e-05
                     AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssdtlrrr 36
                               + + G+  +GK+t+a+rl+  l      a+ l  d+++++
  gene51|gene51|rna51|rna51 39 ICIQGPTSTGKTTFARRLHGLLSrggisAYALGLDSYYFK 78
                               5678**************8766666677666777766654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00048      0.78       2     117 ..      40     202 ..      39     216 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00048
                                EEESSTTSSHHHHHHHHHHHH............THEEEEEETTTCSSS.................................STT CS
                        AAA   2 llyGppGtGKTllakavakel............gvefleisgsellsk.................................yvg 40 
                                ++ Gp  tGKT++a+ +   l            ++++++   ++l ++                                 y  
  gene51|gene51|rna51|rna51  40 CIQGPTSTGKTTFARRLHGLLsrggisayalglDSYYFKPLNPDLDEEdydfdnpgaldwrnifdvlkalrdrepfiehnvYSA 123
                                789*************99997333222222222233444444444433677777777777777777776666666555554444 PP

                                HHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH.......TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGST CS
                        AAA  41 esekkirelfkeakeka.kpsilfiDEidalaksr.......sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkld 116
                                 s  +++ + +     +  p +++iD + a+++ +       + +  + e+ + n+++  + ++++   k++ i++tn  +++ 
  gene51|gene51|rna51|rna51 124 SSYGEVSVVREP----NtMPNVIIIDGVQAFNTINskifnikEFDPYDTEKAISNEFVDNFLRMDDF--KILKILMTNCASRIL 201
                                444444443333....234688888888888888877877754445566666777777776666664..577788888765554 PP

                                H CS
                        AAA 117 p 117
                                +
  gene51|gene51|rna51|rna51 202 S 202
                                4 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.7e-05      0.13       3      22 ..      37      56 ..      35     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.7e-05
                     AAA_24  3 lkiliyGpsgiGKTtlakel 22
                               + i+i Gp  +GKTt+a++l
  gene51|gene51|rna51|rna51 37 YIICIQGPTSTGKTTFARRL 56
                               779***************98 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.27       3      52 ..      37      87 ..      35     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                               EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTT.TTTT--SS CS
                 APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhg.LnkdLgfs 52
                                ++ + G +++GK+t a++l+  L + gis+y L  d+  ++ Ln dL  +
  gene51|gene51|rna51|rna51 37 YIICIQGPTSTGKTTFARRLHGLLSRGGISAYALGLDSYYFKpLNPDLDEE 87
                               578999***************************988876543377777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2486.30
//
Query:       gene511|gene511|rna510|rna510  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.061   12.9   0.5       0.11   12.1   0.4    1.4  1  Pox_VP8_L4R  Poxvirus nucleic acid binding protein VP8/L4R
       0.13   12.2   0.0       0.17   11.8   0.0    1.2  1  EMP24_GP25L  emp24/gp25L/p24 family/GOLD


Domain annotation for each model (and alignments):
>> Pox_VP8_L4R  Poxvirus nucleic acid binding protein VP8/L4R
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   1.2e-05      0.11      59     120 ..     116     177 ..      98     187 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                    Pox_VP8_L4R  59 aiekyyLdknndvltLivnntdlselgvprkksrrkknpvifrkgsaPlllvfesrkkvdiy 120
                                    ai + +Ld +  +++L   nt l+++  +   + ++    ++   ++P++ v+    k+++ 
  gene511|gene511|rna510|rna510 116 AIKNLFLDLEAKLMSLYRTNTRLKTIQENNIAEAKRIRNGLYIMFAIPIMYVIIGLAKLHTT 177
                                    57889*********************666655554455568999******999877776665 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17      63     146 ..      74     154 ..      19     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                    EMP24_GP25L  63 gdfsftakesgeykvCfdnsfstksskkvsfdievgseasdykdsakkekletleselkkleekldsikreqkylreree 142
                                     d ++t+  +g yk+ ++n  s k+s++v+ d++ + ++ d ++ a k+   +le +l  l +  + +k+ q+   +  +
  gene511|gene511|rna510|rna510  74 VDLRYTT--PGAYKIEVYNDGSEKASISVYTDVMSS-GDVDNDNLAIKNLFLDLEAKLMSLYRTNTRLKTIQENNIAEAK 150
                                    2566666..9**************999999999995.4456677777888888888888887777777777776666666 PP

                    EMP24_GP25L 143 rlrd 146
                                    r r+
  gene511|gene511|rna510|rna510 151 RIRN 154
                                    6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1123.19
//
Query:       gene512|gene512|rna511|rna511  [L=184]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-08   34.5   1.4    2.2e-05   24.8   0.3    2.5  2  EF-hand_7     EF-hand domain pair
    3.8e-08   32.3   3.5    3.3e-06   26.2   0.1    4.1  4  EF-hand_1     EF hand
    1.3e-07   31.0   0.4    0.00049   19.8   0.0    3.8  4  EF-hand_6     EF-hand domain
    1.9e-07   30.8   1.5    5.5e-06   26.1   0.1    3.0  3  EF-hand_8     EF-hand domain pair
    0.00039   19.8   0.2     0.0019   17.6   0.1    2.3  2  EF-hand_5     EF hand
  ------ inclusion threshold ------
      0.016   15.6   0.1      0.038   14.3   0.0    1.5  1  SPARC_Ca_bdg  Secreted protein acidic and rich in cysteine Ca


Domain annotation for each model (and alignments):
>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00099         3      16      70 ..      40      89 ..      39      90 .. 0.90
   2 !   24.8   0.3   7.5e-09   2.2e-05       2      67 ..      99     166 ..      98     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00099
                      EF-hand_7 16 dgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGvisfdEFlkly 70
                                   +gy++ ++l+ ++r +f + g   ++s+    +lf+ ++ +++  i+f E+l +y
  gene512|gene512|rna511|rna511 40 TGYMTSDDLETIFRDFFPF-GSPTNFSK----RLFETINISQSEAIDFHELLIAY 89
                                   69************99877.88888898....******************99888 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 7.5e-09
                      EF-hand_7   2 eklkeaFkelDtdgdgyldkeellrllrkifqga..gegsklsdee.lellfkefDtdkdGvisfdEFl 67 
                                    ekl+++F+ +D+d+dg ++k e+ ++++ + +++    ++++++e   +++f  + t k+  ++f++F+
  gene512|gene512|rna511|rna511  99 EKLRWIFRFYDKDNDGVVSKKEIVEVIQYLADMTshTLDVSIDSEGiADEIFASVGTVKS-FLTFEDFK 166
                                    79********************999***99888876444444443357788888888885.78888886 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18   5.3e+02      15      28 ..      41      54 ..      40      55 .. 0.80
   2 ?    2.2   0.0     0.053   1.6e+02       4      24 ..      67      87 ..      65      91 .. 0.80
   3 !   26.2   0.1   1.1e-09   3.3e-06       2      26 ..     101     125 ..     100     126 .. 0.92
   4 ?    0.2   0.1      0.24   7.1e+02      16      24 ..     159     167 ..     158     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                   SEEEHHHHHHHHHH CS
                      EF-hand_1 15 GkIdfeEfkellkk 28
                                   G+++ +++ +++++
  gene512|gene512|rna511|rna511 41 GYMTSDDLETIFRD 54
                                   89999999998875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.053
                                   HHHHHHTTTSSSEEEHHHHHH CS
                      EF-hand_1  4 eiFrefDkDgdGkIdfeEfke 24
                                   ++F+ +   ++  Idf E++ 
  gene512|gene512|rna511|rna511 67 RLFETINISQSEAIDFHELLI 87
                                   6777778888999*****975 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 1.1e-09
                                    HHHHHHHHTTTSSSEEEHHHHHHHH CS
                      EF-hand_1   2 lkeiFrefDkDgdGkIdfeEfkell 26 
                                    l++iFr +DkD+dG ++++E +e++
  gene512|gene512|rna511|rna511 101 LRWIFRFYDKDNDGVVSKKEIVEVI 125
                                    899******************9986 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.24
                                    EEEHHHHHH CS
                      EF-hand_1  16 kIdfeEfke 24 
                                    +++fe+fk 
  gene512|gene512|rna511|rna511 159 FLTFEDFKV 167
                                    69*****96 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.032        95      14      27 ..      40      53 ..      36      60 .. 0.88
   2 ?    3.2   0.0     0.036   1.1e+02       4      27 ..      67      90 ..      65      93 .. 0.84
   3 !   19.8   0.0   1.7e-07   0.00049       5      27 ..     104     126 ..     102     128 .. 0.93
   4 ?   -2.7   0.0       2.7   8.1e+03      16      23 ..     159     166 ..     158     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.032
                      EF-hand_6 14 dGkidaeElrkalr 27
                                   +G+ + ++l  ++r
  gene512|gene512|rna511|rna511 40 TGYMTSDDLETIFR 53
                                   8**********999 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.036
                      EF-hand_6  4 eaFklfDkdgdGkidaeElrkalr 27
                                   ++F+ +  + +  id++El  a++
  gene512|gene512|rna511|rna511 67 RLFETINISQSEAIDFHELLIAYS 90
                                   6788888888999******99986 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1.7e-07
                      EF-hand_6   5 aFklfDkdgdGkidaeElrkalr 27 
                                    +F+ +Dkd+dG ++++E++ +++
  gene512|gene512|rna511|rna511 104 IFRFYDKDNDGVVSKKEIVEVIQ 126
                                    7*****************99886 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.7
                      EF-hand_6  16 kidaeElr 23 
                                    ++++e+++
  gene512|gene512|rna511|rna511 159 FLTFEDFK 166
                                    78999996 PP

>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.19   5.7e+02       1      13 [.      39      51 ..      39      56 .. 0.78
   2 !   26.1   0.1   1.8e-09   5.5e-06       4      50 ..      79     123 ..      76     126 .. 0.90
   3 ?    1.3   0.1       0.1   3.1e+02      43      53 ..     160     170 ..     157     172 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.19
                      EF-hand_8  1 ekgkItreelrri 13
                                   ++g++t ++l +i
  gene512|gene512|rna511|rna511 39 PTGYMTSDDLETI 51
                                   6899999999876 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.8e-09
                      EF-hand_8   4 kItreelrrilrilglkkglseee.vdilfrefDtdgdGkisfeEFcv 50 
                                     I+++el  +++il +k   s++e ++++fr  D d+dG++s++E ++
  gene512|gene512|rna511|rna511  79 AIDFHELLIAYSIL-IK--GSDHEkLRWIFRFYDKDNDGVVSKKEIVE 123
                                    69*********995.78..999999********************875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.1
                      EF-hand_8  43 isfeEFcvlle 53 
                                    ++fe+F vl +
  gene512|gene512|rna511|rna511 160 LTFEDFKVLSV 170
                                    46666666655 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.7   5.1e+03      16      21 ..      80      85 ..      79      86 .. 0.84
   2 !   17.6   0.1   6.5e-07    0.0019       5      22 ..     105     122 ..     102     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                                   E-HHHH CS
                      EF-hand_5 16 IskeEL 21
                                   I++ EL
  gene512|gene512|rna511|rna511 80 IDFHEL 85
                                   999998 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.5e-07
                                    HHHH-SS-SSCE-HHHHH CS
                      EF-hand_5   5 FqaiDlNgDGkIskeELk 22 
                                    F+  D+++DG +sk E  
  gene512|gene512|rna511|rna511 105 FRFYDKDNDGVVSKKEIV 122
                                    9***************75 PP

>> SPARC_Ca_bdg  Secreted protein acidic and rich in cysteine Ca binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.038      54      86 ..      99     131 ..      93     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                   SPARC_Ca_bdg  54 epvawkFsklDtnsdkvlsksELaplraplvkl 86 
                                    e+++w F   D+++d+v+sk+E+ ++ + l  +
  gene512|gene512|rna511|rna511  99 EKLRWIFRFYDKDNDGVVSKKEIVEVIQYLADM 131
                                    7899********************998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1207.97
//
Query:       gene513|gene513|rna512|rna512  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-73  246.0   0.2    4.3e-73  245.6   0.2    1.2  1  Nop       snoRNA binding domain, fibrillarin


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.6   0.2   2.4e-77   4.3e-73       1     229 [.     146     376 ..     146     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 245.6 bits;  conditional E-value: 2.4e-77
                                    HHHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT....HHHHHHHHHHHHCHHHH-SS CS
                            Nop   1 lldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkee...deelakevimaakvtastsmg 77 
                                    lld++dk+in  ++r++ewY+ hFpEL+s+ ++n eY+k+v +ig ++ +++++++   ++ + ++  +++k  a+tsmg
  gene513|gene513|rna512|rna512 146 LLDDMDKDINLHCMRLKEWYGFHFPELSSITDNNREYLKLVVAIG-RKGSIDEEKKrmlRDMVGDDCEKIVKL-AETSMG 223
                                    689******************************************.789997775555522266667777777.788*** PP

                                    S-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HH CS
                            Nop  78 aelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaek 157
                                    + ++eed+ ni+e ++ vl+  e+r+el eY++ +m+ +APN+++LvGe ++a++is+aG+L+nLa+mP s iq++Gaek
  gene513|gene513|rna512|rna512 224 VAMDEEDVLNILEDAKGVLRSFEFRDELVEYIRVKMEGLAPNITSLVGEVIGAKMISKAGSLSNLARMPGSSIQMMGAEK 303
                                    ******************************************************************************** PP

                                    HHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT---.-SHHHHHHHHHHHHHH CS
                            Nop 158 alfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekd.gslGkklreeiekklk 229
                                    alf+alk k+ntpkyG+iy ++l++ ++  ++k++iaR la+K+a+aaRiD+++e++ +++G ++re+ie+++k
  gene513|gene513|rna512|rna512 304 ALFQALKsKTNTPKYGIIYGCSLLG-QVASQNKGRIARSLASKIAMAARIDSYGEERtNKVGIRMREKIERRIK 376
                                    *******888***************.66***********************9998888**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2960.11
//
Query:       gene514|gene514|rna513|rna513  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-22   78.0   0.8    5.2e-10   39.0   1.4    3.6  2  PAXNEB    PAXNEB protein


Domain annotation for each model (and alignments):
>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   1.4   2.9e-14   5.2e-10      14     125 ..      11     103 ..       4     121 .. 0.70
   2 !   31.8   0.0   4.5e-12   8.1e-08     204     347 ..     139     267 ..     106     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 2.9e-14
                         PAXNEB  14 dgqlltStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlreLPgpltdke 93 
                                     g    StG++ LD +Lg  +  G+++l+ Ed++++ ++++lk+Fl+eG+ ++ + l++               +  d e
  gene514|gene514|rna513|rna513  11 RGMEKLSTGISGLDAILGECFTRGTSILLLEDENSRIHSTILKVFLSEGIYNQESTLAVVK-------------EGGDVE 77 
                                    566668***********99*******************************98876555544.............111112 PP

                         PAXNEB  94 eekeqrkeekkaeeekeendlkIAWRYekelp 125
                                    + ++ ++ e  +e   +e+ + IAWRY+k l+
  gene514|gene514|rna513|rna513  78 VYDTGSSME--QE---NEDRMVIAWRYSK-LS 103
                                    222222221..11...3456*******99.44 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 4.5e-12
                         PAXNEB 204 tkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieLes 283
                                     +++ lRi++ sL+sp+++    +  +++++++FL  Lr l r +n + +++ p  ++++      ++ + +Dtv e  s
  gene514|gene514|rna513|rna513 139 REERELRIAVFSLGSPAWRL---SGYEEKKMMRFLFELRRLSRINNHIYMVSAPGFMMPDA-----NFSLYFDTVAEFDS 210
                                    334569************66...688999*****************************543.....45678999999877 PP

                         PAXNEB 284 fagseketepalkseeyqGlLkihklpalnelavgmpetedlafklsrkkfvIekfhLPPelse 347
                                       s     +     +y+G+L+ +k+  +  l +++ e+ ++  k+++  +++ek  +PPe+  
  gene514|gene514|rna513|rna513 211 NIFS-----RFCP--NYNGVLEFKKIGGYGCLRINSLESLKYGVKIRKESICVEKVAMPPEDVK 267
                                    4332.....2334..789***************99999***********************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1783.93
//
Query:       gene515|gene515|rna514|rna514  [L=472]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-21   76.4   0.0    7.6e-10   39.0   0.0    2.3  2  Asn_synthase  Asparagine synthase
  ------ inclusion threshold ------
      0.048   13.6   0.0       0.13   12.2   0.0    1.8  1  GATase_7      Glutamine amidotransferase domain
       0.16   12.2   0.0       0.33   11.2   0.0    1.5  1  GATase_6      Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.3e-13   7.6e-10       3     141 ..     230     375 ..     228     381 .. 0.73
   2 !   35.9   0.0   1.1e-12   6.6e-09     206     292 ..     377     463 ..     374     471 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.3e-13
                   Asn_synthase   3 relLedaVkrrlradvpvGalLSGGlDSSliaalaarqsk..splktFsigfeekgsdeakyakevaehlgte..htelv 78 
                                     ++++++V+rr+ ++  +++++SGG+DS l++ ++   ++  +++      f    s +++  k+  e l ++   + ++
  gene515|gene515|rna514|rna514 230 GKAFRKSVERRV-SEGNICVFFSGGVDSMLVTIFLHYSTDpcQRIYLINTSF--GPSWDRDTGKRGFESLCSRfrERAFI 306
                                    5789*****887.9***********************999777777777777..78888888888777777775544444 PP

                   Asn_synthase  79 l.teeelldalpdviyhlee...pfadrsai....plyllsrlakrkgvkvvLsGeGaDElfgGYpyfyka 141
                                    + ++e  ++++++  +h+ +   p ++r+++     l++ +r+  rk +k+   G GaDE+fgGY+ +yk 
  gene515|gene515|rna514|rna514 307 FvSNEVSIEEVRAFKEHIYKlihPKCGRMDFnigaTLFFTARES-RKYSKIGYLGSGADEMFGGYH-RYKG 375
                                    40444444444444444444455777777652222689999999.666******************.9985 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 1.1e-12
                   Asn_synthase 206 elhrelyldlktllpgdllrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegylPeeileRpK 285
                                    e++  +++dl t+ + ++ r Dr    + +E R+PflD   ve+ lr+  ++ + +g  K + Re+l++   e + + pK
  gene515|gene515|rna514|rna514 377 EFRGDMLFDLFTISHHNVCRDDRVISDNQVECRFPFLDSGMVEYSLRVGRDILMMNGDRKFVIREVLRREGFECVSKVPK 456
                                    6778899*************************************************************987777777777 PP

                   Asn_synthase 286 egfsapv 292
                                    +++++++
  gene515|gene515|rna514|rna514 457 KAMQYGS 463
                                    7777655 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05      0.13      10      37 ..      48      72 ..      40     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                       GATase_7 10 eagaQPmvssedgrlvivfnGeiyNyke 37
                                   e+ +QP+v   ++r+++ +nGe+yN++ 
  gene515|gene515|rna514|rna514 48 ESIKQPVV---GHRYILLYNGEVYNKEP 72
                                   5668****...699***********875 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.5e-05      0.33      30      54 ..      49      71 ..      29      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                       GATase_6 30 egaqPfpsedgrlllvhNGeiynyk 54
                                   + +qP+     r++l +NGe+yn +
  gene515|gene515|rna514|rna514 49 SIKQPV--VGHRYILLYNGEVYNKE 71
                                   345***..***************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 2806.70
//
Query:       gene516|gene516|rna515|rna515  [L=784]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-97  324.7   1.0    4.7e-97  323.5   0.2    1.9  2  MCM              MCM P-loop domain
    3.2e-37  127.2   0.0    5.5e-37  126.4   0.0    1.3  1  MCM_OB           MCM OB domain
    3.8e-26   91.3   0.4    1.3e-25   89.7   0.0    2.1  2  MCM_lid          MCM AAA-lid domain
      2e-11   44.4   0.2    4.8e-11   43.2   0.2    1.6  1  MCM_N            MCM N-terminal domain
    4.6e-09   36.0   0.3    1.7e-07   30.8   0.0    2.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.3e-06   25.7   0.1    3.4e-05   23.8   0.0    2.0  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0011   18.8   0.0     0.0037   17.1   0.0    1.9  1  AAA_3            ATPase family associated with various cellul
     0.0041   16.8   0.0       0.69    9.6   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.14   12.3   1.0       0.35   11.0   1.0    1.7  1  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.5   0.2  2.4e-100   4.7e-97       2     224 .]     366     587 ..     365     587 .. 0.99
   2 ?   -0.9   0.0      0.35     7e+02      12      52 ..     660     701 ..     652     707 .. 0.72

  Alignments for each domain:
  == domain 1  score: 323.5 bits;  conditional E-value: 2.4e-100
                                    HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                            MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla 81 
                                    ++eik++a++++i +++++siaps+yghe+vk+a++l+++ggv+k++++ +++rgdinvll+gdpg+aKsq+L+yve+++
  gene516|gene516|rna515|rna515 366 IREIKKIARHPEIKRIVINSIAPSVYGHEEVKRAVALAMLGGVAKESTS-HRIRGDINVLLLGDPGMAKSQFLRYVENTS 444
                                    789*****************************************98877.****************************** PP

                                    SSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEE CS
                            MCM  82 pravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatL 161
                                    +rav ++g+g+s++gLta+v++d+  +e++le+GalvladkG+c+iDefdkm+e+dr+++hEamEqq+isi+KaGivatL
  gene516|gene516|rna515|rna515 445 HRAVLATGQGASSVGLTASVRKDPVVKEWTLEGGALVLADKGICLIDEFDKMNEHDRTSIHEAMEQQSISISKAGIVATL 524
                                    ******************************************************************************** PP

                                    E--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                            MCM 162 nartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                    +ar+sv+aAanp+ gry+ + ++++n+nls++++srFD+++v +D++d+ +De+ a++i+++h
  gene516|gene516|rna515|rna515 525 HARCSVIAAANPIRGRYNGSLTFSQNVNLSDPIISRFDILCVTKDNIDAGEDEKTARFIIDSH 587
                                    ************************************************************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.35
                                    STHHHHHHHHSSTTSSS-HHHHHHHHHHH..H---EBBBSSSS CS
                            MCM  12 kdiieklvksiapsiyghedvkkaillql..fggvkkkledkt 52 
                                     +i e ++k+   si+  ed+ +ai + l  f g +k + + +
  gene516|gene516|rna515|rna515 660 VRISEAFAKMRLSSIVSAEDIDEAISVVLdsFMGAQKYSMS-K 701
                                    5677888899999**********986554338888887655.3 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.0   2.8e-40   5.5e-37       2     124 ..     205     328 ..     204     330 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 2.8e-40
                                    XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EE.E..S----SB-..TTT-HHH-EEE-GGGSEEEEEE CS
                         MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktve.v..eleePrkCeekeCeskdpfkletekskfvdfq 78 
                                    +R+lr++h+g+lv+v+G+vtr+s v+p  + ++f c kc+++ + +  +  +P++C   eC+s++pf+++t+++ ++dfq
  gene516|gene516|rna515|rna515 205 IRSLRNSHLGRLVRVSGVVTRRSGVFPLYSIVKFSCLKCKSVFGpFvaSSFKPTHC--FECQSRGPFTVNTSETIYKDFQ 282
                                    8***************************************988854455667****..99******************** PP

                                    EEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                         MCM_OB  79 klklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                    kl++QE p++vp+G+lPrs+ev+l  dl+d++kPG++vevtGiy++
  gene516|gene516|rna515|rna515 283 KLTIQEVPGSVPPGSLPRSKEVLLFYDLIDCAKPGEEVEVTGIYKN 328
                                    ********************************************86 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       3.5   6.9e+03      37      48 ..     152     170 ..     125     180 .. 0.45
   2 !   89.7   0.0   6.4e-29   1.3e-25       1      87 []     608     691 ..     608     691 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.5
                                    H.......TSSTSSSST-- CS
                        MCM_lid  37 e.......edskrksipit 48 
                                    +       +++++ +i + 
  gene516|gene516|rna515|rna515 152 SmdlirllNQHAEMTIEVM 170
                                    3333333322233344444 PP

  == domain 2  score: 89.7 bits;  conditional E-value: 6.4e-29
                                    HHHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHH CS
                        MCM_lid   1 ellrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeai 80 
                                    +ll+kYi yar+++ P++++ + +k+s+ Y+elRke+     + +p+tvR++es++R+seA+Ak+rls++v++ed++eai
  gene516|gene516|rna515|rna515 608 DLLKKYILYARTNVMPVFNDVDIDKISSLYLELRKESL---PSGLPVTVRHVESIVRISEAFAKMRLSSIVSAEDIDEAI 684
                                    58*********************************884...569************************************ PP

                                    HHHHHHH CS
                        MCM_lid  81 rllkesl 87 
                                    +++ +s+
  gene516|gene516|rna515|rna515 685 SVVLDSF 691
                                    **98875 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.2   2.4e-14   4.8e-11       2      86 ..     112     188 ..     111     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.4e-14
                          MCM_N   2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklep 81 
                                    +kF  F++ef        + kkY +++++m+ ++ +++ev++ d+++ + +L + + ++ +  ++++++al +vv+ ++p
  gene516|gene516|rna515|rna515 112 KKFVCFFNEF--------KGKKYAAKIRKMCSENLESIEVSYLDIEEESMDLIRLLNQHAEMTIEVMDKALSDVVRMHFP 183
                                    68999*****........68************************************************************ PP

                          MCM_N  82 sykdd 86 
                                    +y+  
  gene516|gene516|rna515|rna515 184 NYYLI 188
                                    99765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.067   1.3e+02      19      38 ..     417     436 ..     388     443 .. 0.67
   2 !   30.8   0.0   8.6e-11   1.7e-07      98     196 ..     476     564 ..     471     573 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.067
                   Mg_chelatase  19 aaGgHnlllvGppGsGKtml 38 
                                    + G  n+ll+G pG  K+  
  gene516|gene516|rna515|rna515 417 IRGDINVLLLGDPGMAKSQF 436
                                    44667999999999999865 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 8.6e-11
                   Mg_chelatase  98 kpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekectcseke 177
                                    + G++ la +G+ ++DE+ +++++   ++ e +e+++++is+a   ++  ar+ ++aa+Np +  + ++ +         
  gene516|gene516|rna515|rna515 476 EGGALVLADKGICLIDEFDKMNEHDRTSIHEAMEQQSISISKAGIVATLHARCSVIAAANPIRGRYNGSLT----F---- 547
                                    57999********************************************************9865444221....1.... PP

                   Mg_chelatase 178 ierYlsklsgplldRidlq 196
                                      +   +ls+p++ R+d+ 
  gene516|gene516|rna515|rna515 548 --SQNVNLSDPIISRFDIL 564
                                    ..11235677777777665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.7e-08   3.4e-05       1     125 [.     422     541 ..     422     561 .. 0.83
   2 ?   -2.1   0.1       1.8   3.6e+03      57      86 ..     663     692 ..     651     695 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.7e-08
                                    EEEEE--SSSSHHHHHHHGGGGB.......S--EEEEE--TT--HHHHH--B--.........--------G-SEEEEES CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal.......nreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDE 73 
                                    +vlL+G+pG +Ks++ +++           ++    v lt++ +++ ++ ++ +       + ++lv     + i+++DE
  gene516|gene516|rna515|rna515 422 NVLLLGDPGMAKSQFLRYVENTShravlatGQGASSVGLTASVRKDPVVKEWTL-------EGGALV--LADKGICLIDE 492
                                    69*************999876655556788888899999999999999999996.......889999..88999****** PP

                                    GGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--... CS
                          AAA_5  74 veraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld..r 125
                                    +++++ +   s +  +e++ +++ + g +    +       +via+anp +  +
  gene516|gene516|rna515|rna515 493 FDKMNEHDRTSIHEAMEQQSISISKAGIVATLHAR-----CSVIAAANPIRgrY 541
                                    **********************9888888877764.....9********98541 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                                    --------G-SEEEEESGGG--HHHHHHHH CS
                          AAA_5  57 splvraaregeilvlDEveraesevlnsLl 86 
                                    s++  ++r ++i+  +++++a s vl+s++
  gene516|gene516|rna515|rna515 663 SEAFAKMRLSSIVSAEDIDEAISVVLDSFM 692
                                    566678999999999****99999999875 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.8e-06    0.0037       2     114 ..     423     538 ..     422     550 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke..kefefkkGpvf...anllladeinrapp 76 
                                    vll g PG+ak ++ + + ++   + + +  t     s  l ++v ++    ke++++ G+++   + + l de ++ + 
  gene516|gene516|rna515|rna515 423 VLLLGDPGMAKSQFLRYVENT---SHRAVLATGQGASSVGLTASVRKD-PvvKEWTLEGGALVladKGICLIDEFDKMNE 498
                                    677788888888777665543...334444444433332222333222.13489999999876333359*********** PP

                          AAA_3  77 ktqsalleameerqvtvege..thklpepflvlatqnPie 114
                                    + ++++ eame++ ++++++    +l+    v+a+ nPi 
  gene516|gene516|rna515|rna515 499 HDRTSIHEAMEQQSISISKAgiVATLHARCSVIAAANPIR 538
                                    *************999976521679*************96 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.013        26      15      49 ..     413     447 ..     406     458 .. 0.86
   2 !    9.6   0.0   0.00035      0.69      86     142 ..     477     535 ..     472     545 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.013
                                    HHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTT CS
                Sigma54_activat  15 ikkvaktdlsvlitGesGtGKellaraiheaskrk 49 
                                    +++ ++ d++vl++G+ G  K+ + r + ++s+r+
  gene516|gene516|rna515|rna515 413 TSHRIRGDINVLLLGDPGMAKSQFLRYVENTSHRA 447
                                    556678899******************99999885 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00035
                                    EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEES CS
                Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatn 142
                                     G++  ad+G+ ++De  +++ +  + + +++++++  +++ G  ++ ++ + +iaa+n
  gene516|gene516|rna515|rna515 477 GGALVLADKGICLIDEFDKMNEHDRTSIHEAMEQQSisISKAGIVATLHARCSVIAAAN 535
                                    49999***************************9997225799**************987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   0.00017      0.35       6      34 ..     238     265 ..     231     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                    Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs 34 
                                    + C +C+++f +++++s + +t+C eC+s
  gene516|gene516|rna515|rna515 238 FSCLKCKSVFGPFVASSFK-PTHCFECQS 265
                                    77************98853.477****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (784 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 4526.84
//
Query:       gene517|gene517|rna516|rna516  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1753.99
//
Query:       gene518|gene518|rna517|rna517  [L=685]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.011   15.8   0.2       0.38   10.8   0.0    3.1  2  Cnd1      non-SMC mitotic condensation complex subunit 1


Domain annotation for each model (and alignments):
>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.017     3e+02      96     130 ..      56      88 ..      42     108 .. 0.75
   2 ?   10.8   0.0   2.1e-05      0.38       2      65 ..     144     210 ..     143     334 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.017
                           Cnd1  96 llpdiisklsdalnecsewgqitilefLlsyipkd 130
                                      ++ii++++   n+c+ ++ +++++++++y +++
  gene518|gene518|rna517|rna517  56 DIIKIIKSIH--VNQCKMKKLCKVFNSVSNYNTDS 88 
                                    3445555555..78999999999999999998765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.1e-05
                           Cnd1   2 iRalairtlg..cirvpnlve..ylvepLrkrLkDedpyVRktaaivvakLilndmvkekgflselak 65 
                                    iR+ ++  ++   +  p++    ++++ +  +L+D++  VR+  + +++kL++++ v  + f+s++++
  gene518|gene518|rna517|rna517 144 IRSICVGFMCewIVSAPEIFNfpCYLKYIGWSLSDKNDNVRRKGVGACIKLVRKK-VDIQTFVSRFKN 210
                                    8999999999999999999865589**************************8776.455556666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4418.18
//
Query:       gene519|gene519|rna518|rna518  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1291.40
//
Query:       gene520|gene520|rna519|rna519  [L=345]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-14   54.0   0.0    4.9e-09   36.6   0.0    2.4  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-06     0.023       5      68 ..      11      76 ..       7     107 .. 0.67
   2 !   36.6   0.0   2.8e-13   4.9e-09       2      68 ..     182     248 ..     181     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-06
                PseudoU_synth_1  5 lvGthdfg.sfckqkqek..kntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.fav 68
                                   ++G+++ g +f +++ ++  k+ v  +l+++    ++++++  ++++k+s+++d++V+a  +++ +++
  gene520|gene520|rna519|rna519 11 YDGSRYHGlQF-NKELDTieKRVVECLLQVEAIS-ERNADDPKKIHIKSSSRTDKGVHAALNLIsVKI 76
                                   77777777555.3333334577777777777663.33334445****************998876555 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 2.8e-13
                PseudoU_synth_1   2 akelvGthdfgsfckqkqek..kntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfav 68 
                                     ++++Gt+df +f+k ++ek  k+++++i+  +      e  e+++++++g++Fl hq+R mv  +++ 
  gene520|gene520|rna519|rna519 182 LQKYIGTKDFHNFTKLNNEKgsKRYIKSITVTDPYVS--EGVEYVRISITGQSFLLHQIRKMVLFAVLL 248
                                    689**********999999988999999999988833..335788*****************9776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2312.47
//
Query:       gene52|gene52|rna52|rna52  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 712.56
//
Query:       gene521|gene521|rna520|rna520  [L=557]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-33  114.9   0.0    5.3e-33  114.3   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    1.4e-22   79.6   0.1    3.7e-22   78.4   0.1    1.7  1  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
    1.6e-17   63.8   0.0    3.1e-17   62.8   0.0    1.4  1  B3_4             B3/4 domain
    2.1e-17   63.2   0.3    4.1e-12   46.2   0.1    2.5  2  B5               tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   1.2e-36   5.3e-33       5     214 .]     354     546 ..     351     546 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 1.2e-36
                tRNA_synthFbeta   5 lPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLe 84 
                                    lP+  t++  + + +++++klr +++++G+ E++t ++ s++e+  +    d ++ v l nP s+ ++++RtsL+pgl++
  gene521|gene521|rna520|rna520 354 LPSLFTVGS-EVPLNRFSDKLRVEVSMMGFDEALTLTLLSHEEN-II----DADRGVVLMNPKSAGYEMCRTSLIPGLMK 427
                                    666666666.7799****************************94.44....78999************************ PP

                tRNA_synthFbeta  85 vlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekve 163
                                    ++a+Nl+ +++ +rlFEi++++l d ++e +++++r+lai+++g++              +++ g +  lle++g+ + +
  gene521|gene521|rna520|rna520 428 TVASNLHMKIP-FRLFEISDIVLLDkENECGARNSRRLAILYSGHS-----------PCLEEIQGSLSLLLEKCGM-QPS 494
                                    ***********.*************889999***************...........9******************.999 PP

                tRNA_synthFbeta 164 fep.aehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                    ++p ++   + +++ A + v++ ++G +G  +pe+++ f++++ ++++E+d+
  gene521|gene521|rna520|rna520 495 YSPyDDPVRYLKNQGALVIVRNIVIGSIGVCNPEICRTFKVPYAASFLEIDI 546
                                    9**888889*****************************************96 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.1   8.2e-26   3.7e-22       1      81 [.       1      72 [.       1      74 [. 0.98

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 8.2e-26
                      PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralkvFl 81
                                   MPt+  +k+++ ++l+ el+++++e  lf+fGlElD ++eee          + +y+idipAnryDLLc+egl+ alk Fl
  gene521|gene521|rna520|rna520  1 MPTLVAEKQRIKDLLQMELDDSQFERTLFDFGLELDGVTEEEG---------KAVYRIDIPANRYDLLCTEGLCYALKAFL 72
                                   9******************************************.........99*************************97 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.0   6.9e-21   3.1e-17      35     134 ..     116     245 ..     102     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 6.9e-21
                                    --HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEE.EEE--TTEEEEBTTS-EEEE.-T................... CS
                           B3_4  35 innvVDitNyvmlelgq.....PlhafDldkiqgdiv.vrlakegeklvtldgkerel.de................... 88 
                                    +++++D +++++l +g+      ++++Dldkiqg++  +   +++  + +l+g++    +e                   
  gene521|gene521|rna520|rna520 116 YKSFIDYQDKLHLTIGRnrtlvSMGTHDLDKIQGPVFyKSEVPDKIIFKPLNGDKEMSaQElgtffppgskigkymklne 195
                                    899*******************************7773666667779****9884444255******************* PP

                                    ...TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHH CS
                           B3_4  89 ...edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirk 134
                                       +++ ++ds++ v sl++v++++++k+s +Tkn+f+ +++ d  +++ 
  gene521|gene521|rna520|rna520 196 kneKYPYFSDSKGTVlSLPPVINSDATKISPETKNIFIDITGTDFHRVNT 245
                                    *****************************************988766655 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.3e-06     0.028       4      55 ..       7      62 ..       4      65 .. 0.91
   2 !   46.2   0.1   9.1e-16   4.1e-12       3      67 .]     283     347 ..     281     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-06
                                   EHHHHHHHHTS---HHHHHHHHHHTT-E.....EESSTTCEEEE--TT-TT--SHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                             B5  4 rvekinkllGidlseeeiikiLkrlgce....riekdkdlllVtvPswRsDleree 55
                                   + ++i+ ll ++l++++ +++L   g+e    ++e++k ++++ +P+ R+Dl+  e
  gene521|gene521|rna520|rna520  7 EKQRIKDLLQMELDDSQFERTLFDFGLEldgvTEEEGKAVYRIDIPANRYDLLCTE 62
                                   5689************************99998899999*************8765 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 9.1e-16
                                    EEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             B5   3 lrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                    + +e+ink lG+d+s e    +++++ + ++  ++++l+V+v   RsD+ +++DliE+va ++G+
  gene521|gene521|rna520|rna520 283 IGLEEINKKLGLDISLEVARGYMEKMMHCASVVNENTLRVKVHDVRSDVIHKCDLIEDVAVAHGF 347
                                    5689*********************997779********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3722.80
//
Query:       gene522|gene522|rna521|rna521  [L=933]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-43  146.7   0.0      1e-42  145.6   0.0    1.6  1  DSHCT           DSHCT (NUC185) domain
    5.7e-16   58.8   0.0    1.4e-15   57.5   0.0    1.6  1  DEAD            DEAD/DEAH box helicase
    3.3e-06   27.4   0.0    1.3e-05   25.5   0.0    2.2  1  Helicase_C      Helicase conserved C-terminal domain
      5e-05   23.4   0.0    0.00011   22.2   0.0    1.6  1  ResIII          Type III restriction enzyme, res subunit
     0.0015   18.5   0.0     0.0033   17.4   0.0    1.6  1  rRNA_proc-arch  rRNA-processing arch domain
  ------ inclusion threshold ------
      0.023   13.8   0.0        0.1   11.7   0.0    1.9  2  T2SSE           Type II/IV secretion system protein
      0.027   14.4   0.4       0.15   12.0   0.0    2.4  2  ATPase_2        ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.6   0.0   3.9e-46     1e-42       3     164 .]     760     928 ..     758     928 .. 0.84

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 3.9e-46
                          DSHCT   3 tvtlkGrvaaeirsedeLlltellfsgvlddlepeelaAllsalvfeekredeeeke......pkl.seeleealeelke 75 
                                    +v +kGr+a+ei+s+deL+lte++f+g + ++ +e+ + lls++vfee  +d+ + +       kl s+ +e+ +  lk 
  gene522|gene522|rna521|rna521 760 SVLIKGRMACEISSGDELVLTEMIFNGDFAGIPVEHFVPLLSCIVFEEWDSDNFVLSdenklyYKLlSSSVEKVCGVLKS 839
                                    6899********************************************98776554344444433334444444433333 PP

                          DSHCT  76 iaeriakvs........vesrldlglvevvyaWakgasfaellektdldeGdiVRllrrleellrqlakaakvigneeLk 147
                                            +        + +r+ ++l++vv  W++g +f ++++ t+++eG+i+R+++rleellrql++aa+vign+eL+
  gene522|gene522|rna521|rna521 840 --------CsidvdpaaYLRRFSYELMDVVRMWVCGHTFVSICSRTNIFEGSIIRTFKRLEELLRQLSSAARVIGNTELE 911
                                    ........13444444455689********************************************************** PP

                          DSHCT 148 kkaeeaielikRdiVfa 164
                                    + +   i++ikRdiVfa
  gene522|gene522|rna521|rna521 912 NMFALGIAKIKRDIVFA 928
                                    ***************96 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   5.3e-19   1.4e-15       2     172 ..      73     220 ..      72     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 5.3e-19
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    d Q+ ++  + ++++vlv+a+T sGKT ++  ++  ++     k++ ++++ +P ++L +q +++l + +      v l+
  gene522|gene522|rna521|rna521  73 DFQKISVCSLERDESVLVSAHTSSGKTVVAEYAIAMSL-----KSKQRVVYTSPIKALSNQKYRELLSEFGD----VGLM 143
                                    57888888899999*********************777.....88999*****************9777774....4466 PP

                                    ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                    +g+v+ +        ++ ++v+t++ l ++l +g   ++++ ++++DE++ + d++++  +++ +  l       + + +
  gene522|gene522|rna521|rna521 144 TGDVTINP-------TATCLVMTTEILRNMLYKGGEVVREIHWIIFDEIHYMRDKERGVVWEETIILL-------PRHVR 209
                                    77777643.......35677*********99878879**************************99999.......56678 PP

                                    EEEEESSBSHH CS
                                    xxxxxxxxxxx RF
                           DEAD 162 vivlSATlpkd 172
                                    +++lSAT+p+ 
  gene522|gene522|rna521|rna521 210 MVFLSATIPNA 220
                                    ********955 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   5.1e-09   1.3e-05      21     111 .]     330     435 ..     296     435 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 5.1e-09
                                    EEESSHHHHHH....HHHHHHHT.....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEES CS
                     Helicase_C  21 ifvntidrlek....vklllekk.....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinf 91 
                                    if+n i +l k    + ++  ++        + ++h+ l    +e +   f++g  +vL at   + G+++p  ++V+  
  gene522|gene522|rna521|rna521 330 IFTNAIMSLRKedreIPII--QNilpllMRGIGIHHSGLLPIIKEVVEILFQEGLLKVLFATETFSIGLNMPAKSVVFTA 407
                                    7777777666665552223..2223444566778999999999999999***********************77777754 PP

                                    SSS........SSHHHHHHHHTTSSSTT CS
                     Helicase_C  92 dlp........rnvtsyiqriGRtgRag 111
                                      +         +  +yiq++GR+gR g
  gene522|gene522|rna521|rna521 408 LKKfdgesmrlVSSGEYIQMSGRAGRRG 435
                                    44444434444445************75 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.4e-08   0.00011      21     170 ..      73     218 ..      56     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.4e-08
                                    ...........TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEES CS
                         ResIII  21 s.........krdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvs 90 
                                    +         +rd+ +l+ + T +GKT+va ++++ +l++k   ++++   p k+l +q ++e+ + + +      + ++
  gene522|gene522|rna521|rna521  73 DfqkisvcslERDESVLVSAHTSSGKTVVAeYAIAMSLKSK---QRVVYTSPIKALSNQKYRELLSEFGDV-----GLMT 144
                                    2444566667899*****************77777777776...58*************999999999875.....7899 PP

                                    SS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHH.HHHT---SEEEEEE CS
                         ResIII  91 gdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swre.ilekfkeavllglT 166
                                    gd  ++      ++  lv+t++ l + +     ++      ++  ii+DE H +++k+    w+e i+   ++  ++ l+
  gene522|gene522|rna521|rna521 145 GDVTIN-----PTATCLVMTTEILRNML-----YKGGEVVREIHWIIFDEIHYMRDKErgvVWEEtIILLPRHVRMVFLS 214
                                    999998.....89999********9999.....88888889999************758889*9977877788999999* PP

                                    SS-S CS
                         ResIII 167 ATpe 170
                                    AT++
  gene522|gene522|rna521|rna521 215 ATIP 218
                                    *986 PP

>> rRNA_proc-arch  rRNA-processing arch domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.3e-06    0.0033       2      81 ..     490     561 ..     490     607 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                    HHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHGGG--TTEEEEE CS
                 rRNA_proc-arch   2 yMlerSFsqfqnqkslpelekklkeleeelksitiedeedieeyyklrqqleelreeirkiltkpknilpfLqpGRlvrv 81 
                                    y++ rSF++fq++k++ + e+ l  +  +l++i+   ++ i   y +r++ +  r+++ +     +   ++L+ GR+v +
  gene522|gene522|rna521|rna521 490 YLISRSFHHFQSYKKALAEEETLYSMHRQLENIC---PNGIVTLYRIREEKKVERNKRLS-----EEFSKYLKKGRVVDL 561
                                    89******************************88...56899999999998888888764.....566678888888865 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.9e-05       0.1     125     161 ..      81     117 ..      50     120 .. 0.79
   2 ?   -1.6   0.0      0.42   1.1e+03     213     251 ..     857     899 ..     855     919 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                          T2SSE 125 avrerglilvsGgTgsGKttll.yallkeinksderiv 161
                                    ++++  ++lvs  T+sGKt+++ ya+   ++++ +r+v
  gene522|gene522|rna521|rna521  81 SLERDESVLVSAHTSSGKTVVAeYAIAMSLKSK-QRVV 117
                                    5677899**************956666666665.7766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.42
                          T2SSE 213 tleilkAvnTGHl....gslsTlHansaagalerLeqlgaeve 251
                                     +++++ +  GH     +s + +  +s + +++rLe+l  +++
  gene522|gene522|rna521|rna521 857 LMDVVRMWVCGHTfvsiCSRTNIFEGSIIRTFKRLEELLRQLS 899
                                    56788899999964333667889999**********9997743 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.7e-05      0.15      14      73 ..      79     138 ..      70     198 .. 0.79
   2 ?   -1.5   0.1      0.76   1.9e+03      93     122 ..     317     348 ..     225     352 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.7e-05
                       ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeee 73 
                                    +++ e++e +++    +sGKt +   +i  +++++++v+y ++++  s++k++e + e  
  gene522|gene522|rna521|rna521  79 VCSLERDESVLVSAHTSSGKTVVAEYAIAMSLKSKQRVVYTSPIKALSNQKYRELLSEFG 138
                                    56667777788888899************************************9977544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.76
                       ATPase_2  93 eilk.eksklvfkaielllekikkkgkk.iii 122
                                      l  ++ k v+  +++++++++k+ ++ +ii
  gene522|gene522|rna521|rna521 317 SYLGdSEAKMVQTIFTNAIMSLRKEDREiPII 348
                                    23335677888888899999999988884443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (933 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.27s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 6064.24
//
Query:       gene524|gene524|rna523|rna523  [L=314]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2146.34
//
Query:       gene525|gene525|rna524|rna524  [L=102]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0033   18.0   0.1     0.0044   17.6   0.1    1.2  1  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
       0.36   10.9   6.2        3.3    7.9   6.2    2.0  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.9e-07    0.0044      18      57 .]      15      53 ..       6      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.9e-07
                                   HHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                          HHH_5 18 llsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                   +++  ++  e++++ d+e L +i+G    +Aer+i+e+k+
  gene525|gene525|rna524|rna524 15 IYKI-YRKAEKVMKNDEEYLMRITGYTRGLAERMIDEAKK 53
                                   6666.78899****************************97 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.2   0.00036       3.3      17      66 ..      27      76 ..       3      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00036
                                   ...TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                         DUF357 17 pdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDa 66
                                   +++e+ l++    +  +ae+ + +ak   + ++++ +   f Ya+ +LD+
  gene525|gene525|rna524|rna524 27 KNDEEYLMRITGYTRGLAERMIDEAKKHSRDKEYELSAEYFYYAYKYLDS 76
                                   367777777778888899******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 745.77
//
Query:       gene526|gene526|rna525|rna525  [L=1159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-54  183.6   0.0    6.2e-54  182.7   0.0    1.4  1  SMC_N          RecF/RecN/SMC N terminal domain
      4e-25   88.4   0.0    7.9e-25   87.4   0.0    1.5  1  SMC_hinge      SMC proteins Flexible Hinge Domain
    1.3e-12   48.1  10.1    6.1e-07   29.5   0.1    3.5  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.9e-11   44.9  18.2    1.9e-11   44.9  18.2    5.6  3  AAA_23         AAA domain
    9.3e-11   42.0  10.1    9.3e-11   42.0  10.1    3.3  3  AAA_15         AAA ATPase domain
    2.9e-07   30.1   0.0    5.5e-07   29.2   0.0    1.5  1  AAA_29         P-loop containing region of AAA domain
     0.0075   15.8   1.7     0.0075   15.8   1.7    4.9  5  Fzo_mitofusin  fzo-like conserved region
  ------ inclusion threshold ------
      0.068   12.9   0.2       0.91    9.2   0.0    2.6  2  AAA_30         AAA domain
      0.088   13.1   0.1         10    6.4   0.0    3.6  3  AAA_22         AAA domain
       0.93   10.0   0.0       0.93   10.0   0.0    5.2  4  ABC_tran       ABC transporter


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.7   0.0   3.5e-57   6.2e-54       2     214 ..       3    1144 ..       2    1149 .. 0.99

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 3.5e-57
                                     EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaev 79  
                                     l+r+e+enFksy g++vi+pf++ ft+i+GpNGSGKsn++dA+ F+LG   a++lr+++++ li++     + ++a+v
  gene526|gene526|rna525|rna525    3 LERIEVENFKSYVGRHVIGPFDR-FTCIIGPNGSGKSNIMDAVTFCLGI-GARHLRASNAKGLINS-----KCTHASV 73  
                                     79*******************99.************************7.777************8.....899**** PP

                                     EEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...................... CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                          SMC_N   80 eitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske...................... 135 
                                     +++++ ++++          +r+v ++g+s y+i+ ++v ++  +e +e +++ ++                      
  gene526|gene526|rna525|rna525   74 TLYIELDGER-------KGFKRHVNNDGRSLYFIDLENVGYERFREAVEGMNLLIDarnflvfqgdvnaigsmmpmel 144 
                                     **87777776.......7899********************************************************* PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  145 trlfeemsgsiklkevyeekqreqakavsecsslyeekkevmsrmkeaeevreqegmfkrlverkheiqkeivlhelm 222 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  223 errsrrkdindevirleleskevqelidskekevemyrnkineirreyfevdalmskekevvaerrawkyeaeqerek 300 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  301 rriliveaemeikskeemingkrreidrrrkemkgiegeyaelckeeeerrrrlgsvkeekevieekekellemcged 378 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  379 kenmntldlemfshrmmrddykrkvkelrekdeelkskikekkvirgntkvkidalersevelsrkilhheerykrlv 456 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  457 seekqkneelswilgeilrikgkrridgrrsmivstvetlkgmfpgvygrvvdlveptqnkyeiglsvllgrhsqsvv 534 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  535 vdsettamscinfikekrlckmtflpiqnirdgdemrgiedviqeygggvrrgvdtirydgryrkvmsfllkeklivd 612 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  613 nleiardicygkgtkvsvctldgiyihgggylisggeigrnkfqeedldelvkrrtrilddvrriqdskndlsyveic 690 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  691 keriemwrrsramemevmkdldicieelesevaenskllkeaeeslrhvleememcegkmkelrqkveevecslfcgv 768 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  769 fpnawfksfeeykeardcesfelkrmeyesvrgrielrigtlereveglekeirvlrerveelrvvegndgedmsedt 846 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  847 selailsekrkrkleafekardefkeineefkrlmgkkneldqgiiycasakerieeeikntlsfavleeieipcagr 924 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene526|gene526|rna525|rna525  925 kcvgkvsideidfsglersveelrreleeinqkissqaplirvgekdgdcsryvkisaeyerqkaaaisaknefneik 1002
                                     ****************************************************************************** PP

                                     .................................................................CS-HHHHHHHHHH CS
                                     .................................................................xxxxxxxxxxxxx RF
                          SMC_N  136 .................................................................lLSgGektLvala 148 
                                                                                                      lLSgGe+t++ l+
  gene526|gene526|rna525|rna525 1003 krrthifmecfekvnkelsriykcltmtetsegnaylalentsepfkegvrfhlmppnkrfrevrLLSGGERTMAVLS 1080
                                     ****************************************************************************** PP

                                     HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkv 214 
                                     Llf+ ++++pap+yl+De+d+aLD++nv+++++++ +++  aQfi i+l+  ++++ d lvgv+k 
  gene526|gene526|rna525|rna525 1081 LLFSFHAYRPAPFYLFDEVDSALDKANVSRIVSFIISST--AQFILITLKPSLFQHGDGLVGVYKD 1144
                                     ************************************999..***********************84 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   4.4e-28   7.9e-25       2     116 ..     501     620 ..     500     621 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 4.4e-28
                      SMC_hinge   2 kgvlGrladlievd.egyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns.. 78 
                                    +gv+Gr++dl+e++ ++ye+ +++ lg + q++vv++e ta ++i+f+k+k++ ++tflp+++i++  +  g +d+ +  
  gene526|gene526|rna525|rna525 501 PGVYGRVVDLVEPTqNKYEIGLSVLLGRHSQSVVVDSETTAMSCINFIKEKRLCKMTFLPIQNIRDGDEMRGIEDVIQey 580
                                    79****************************************************************9999999888889* PP

                      SMC_hinge  79 ..gavplidlvevddelrkalryllgdtlvvdsldeAeel 116
                                      g+++ +d +++d ++rk++ +ll++ l+vd+l+ A+++
  gene526|gene526|rna525|rna525 581 ggGVRRGVDTIRYDGRYRKVMSFLLKEKLIVDNLEIARDI 620
                                    *************************************998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   3.4e-10   6.1e-07       1      38 [.      26      64 ..      26     126 .. 0.85
   2 ?   -2.0   0.4       1.4   2.5e+03      99     158 ..     410     469 ..     395     483 .. 0.79
   3 ?   -3.6   0.3       4.1   7.4e+03      71     129 ..     816     874 ..     795     911 .. 0.60
   4 !   24.1   0.0   1.5e-08   2.7e-05     219     296 ..    1043    1126 ..     928    1131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.4e-10
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarl.drdvegltdelsg 38
                                   ++++iGpNgsGKSn++da  +  ++ +r+++ ++ +   
  gene526|gene526|rna525|rna525 26 FTCIIGPNGSGKSNIMDAVTFCLGIgARHLRASNAKGLI 64
                                   89*********************9998888888877654 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                         AAA_21  99 lldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawslllll 158
                                        +s+++e++++      ++++ ++s+ els+++ + ++++k+l++  +++++ l++ 
  gene526|gene526|rna525|rna525 410 DEELKSKIKEKKVIRGNTKVKIDALERSEVELSRKILHHEERYKRLVSEEKQKNEELSWI 469
                                    455677888888888888888999999999999999999999999999999888888876 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.1
                         AAA_21  71 ryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslke 129
                                      + ++r+ r++vee   + ++++e++  + ++ ++   +   + + + + +++f++++
  gene526|gene526|rna525|rna525 816 GLEKEIRVLRERVEELRVVEGNDGEDMSEDTSELAILSEKRKRKLEAFEKARDEFKEIN 874
                                    44445555555555555555555555555555555555555555555555555555554 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 1.5e-08
                         AAA_21  219 r........gvvflengdgqelparelSdGtkrll..alltallralkkgsllliDEpEngLHPkllrrllellkels 286 
                                     +          ++l +++ + + +r lS G + ++   ll ++++ ++  +++l+DE+++ L+ + ++r++ ++ + +
  gene526|gene526|rna525|rna525 1043 NtsepfkegVRFHLMPPNKRFREVRLLSGGERTMAvlSLLFSFHAYRPA-PFYLFDEVDSALDKANVSRIVSFIISST 1119
                                     044444444666777788899999999*******555666666666666.************************6666 PP

                         AAA_21  287 rngaQviltT 296 
                                     +   Q+il T
  gene526|gene526|rna525|rna525 1120 A---QFILIT 1126
                                     6...999988 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9  18.2   1.1e-14   1.9e-11       1     195 [.       5     266 ..       5     334 .. 0.48
   2 ?  -14.6  33.6        10   1.8e+04      75     199 ..     306     466 ..     278     473 .. 0.61
   3 ?  -20.5  33.8        10   1.8e+04     153     199 ..     790     877 ..     645    1025 .. 0.55

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.1e-14
                         AAA_23   1 kLkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks.....grgfeksdveiesegkvkay 74 
                                    ++++enf+s+ ++  i   + +t+I+GpNG+GK+ i+dA++++L+  ++ l+ ++     ++++ +++v++  e ++++ 
  gene526|gene526|rna525|rna525   5 RIEVENFKSYvGRHVIGPFDRFTCIIGPNGSGKSNIMDAVTFCLGIGARHLRASNakgliNSKCTHASVTLYIELDGERK 84 
                                    799*******77778*****************************877777877773344433444444444444333333 PP

                         AAA_23  75 .veltfenkdgry................................................................... 86 
                                     +++ ++n+++ +                                                                   
  gene526|gene526|rna525|rna525  85 gFKRHVNNDGR-Slyfidlenvgyerfreavegmnllidarnflvfqgdvnaigsmmpmeltrlfeemsgsiklkevyee 163
                                    34444433333.25788877666667888888888888887777777777777777766665555555554443222222 PP

                         AAA_23  87 .....trsiererelskkkgktt....kkaklellei.......deleqfisellgskkiilnlilflgqer........ 142
                                                      k+++     +++k+e ++        +e+e ++++l+++k +i + i+++   +        
  gene526|gene526|rna525|rna525 164 kqreqA------------KAVSEcsslYEEKKEVMSRmkeaeevREQEGMFKRLVERKHEIQKEIVLHELMErrsrrkdi 231
                                    222220............22222111111122222221111111222222222333333322222222222222222222 PP

                         AAA_23 143 feefelkdkke................rleelekeleeledekkllekleqekekekeleeleeeleei 195
                                    +         +                                          +keke e  +++++ei
  gene526|gene526|rna525|rna525 232 N---------DevirleleskevqeliD-------------------------SKEKEVEMYRNKINEI 266
                                    0.........122222221111111220.........................2222222222222222 PP

  == domain 2  score: -14.6 bits;  conditional E-value: 10
                         AAA_23  75 veltfenkdgry.trsiererelskkkgkttkkaklellei....deleqfisellgskki.....ilnlilflgqerfe 144
                                    ve + e k++++     +re+ +++k++k + ++  el+++    + +   ++e+     +     + +l+ ++g+++++
  gene526|gene526|rna525|rna525 306 VEAEMEIKSKEEmINGKRREIDRRRKEMKGIEGEYAELCKEeeerRRRLGSVKEEK----EvieekEKELLEMCGEDKEN 381
                                    44444444443331112345566666666677777777766322233333344444....24444588**********76 PP

                         AAA_23 145 efel..............kdkkerleelekeleeledekkllekl................eqekekekeleeleeelee 194
                                    ++ l              k+k ++l+e  +el+ + +ekk ++ +                 +++  e++++ l +e ++
  gene526|gene526|rna525|rna525 382 MNTLdlemfshrmmrddyKRKVKELREKDEELKSKIKEKKVIRGNtkvkidalersevelsRKILHHEERYKRLVSEEKQ 461
                                    66666666666777777777777888888888888888887666666776666776777764555555566655555555 PP

                         AAA_23 195 ilkel 199
                                     ++el
  gene526|gene526|rna525|rna525 462 KNEEL 466
                                    55554 PP

  == domain 3  score: -20.5 bits;  conditional E-value: 10
                         AAA_23 153 e...............rleelekeleeledekkllekl..........................eqekekekeleeleee 191
                                    e               r+  le+e e le+e++ l+++                          e++k k +++e+ ++e
  gene526|gene526|rna525|rna525 790 ElkrmeyesvrgrielRIGTLEREVEGLEKEIRVLRERveelrvvegndgedmsedtselailsEKRKRKLEAFEKARDE 869
                                    23334444455555553333333333333333333333333333355555555555555555444444444455555555 PP

                         AAA_23 192 leeilkel 199
                                    ++ei++e 
  gene526|gene526|rna525|rna525 870 FKEINEEF 877
                                    55554443 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0  10.1   5.2e-14   9.3e-11       1     274 [.       1     429 [.       1     467 [. 0.61
   2 ?   -3.2   0.0         3   5.3e+03     231     254 ..     725     748 ..     676     769 .. 0.54
   3 ?    3.9   4.7      0.02        37      57     288 ..     783    1073 ..     771    1119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 5.2e-14
                         AAA_15   1 MkIkkikikNFRsl..kdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdik 78 
                                    M +++i+++NF+s+  ++v  +++  +t++iG+N+sGKS+i++a  + l    ++   + + +    +++ + s    i+
  gene526|gene526|rna525|rna525   1 MGLERIEVENFKSYvgRHVIGPFDR-FTCIIGPNGSGKSNIMDAVTFCLGIGARHL-RASNAKGLINSKCTHASVTLYIE 78 
                                    889***********55568889***.************************998877.34445555555555555555666 PP

                         AAA_15  79 Idvef........................................................................... 83 
                                    +d e                                                                            
  gene526|gene526|rna525|rna525  79 LDGERkgfkrhvnndgrslyfidlenvgyerfreavegmnllidarnflvfqgdvnaigsmmpmeltrlfeemsgsiklk 158
                                    65555666666666666666666666777777777777777777777999999999999999999999999999999999 PP

                         AAA_15  84 ..................................................................aekekakeyektlk 97 
                                                                                                      +           ++
  gene526|gene526|rna525|rna525 159 evyeekqreqakavsecsslyeekkevmsrmkeaeevreqegmfkrlverkheiqkeivlhelmerR-----------SR 227
                                    9999999999999998888888888888888888888888888777777766654444443333320...........33 PP

                         AAA_15  98 skekkkadlllkkkesdlkkti..kdkklklkknelsdekisvekkkskkelpkekeeklekekeelkidkedlkklikk 175
                                    +k+++ + + l+ ++++ +++i  k+k+ + + n+++  + ++++  + ++ +ke   ++   k+e + + e+ + li +
  gene526|gene526|rna525|rna525 228 RKDINDEVIRLELESKEVQELIdsKEKEVEMYRNKINEIRREYFEVDALMSKEKEVVAERRAWKYEAEQEREKRRILIVE 307
                                    33333333334444444444331133333344444444444444444455555555555555555555555555555555 PP

                         AAA_15 176 leeslkkee.........................elknvlksaiiklllisakRnvsdedsekkssllgklkekileeal 230
                                     e  +k++e                         el +  ++  + l   ++++           ++++++ +++le ++
  gene526|gene526|rna525|rna525 308 AEMEIKSKEemingkrreidrrrkemkgiegeyaELCKEEEERRRRLGSVKEEK-----------EVIEEKEKELLEMCG 376
                                    555555555666666677777665433333322222222223333333333333...........444444444444444 PP

                         AAA_15 231 qekl...........eeelteklkeiqeklkeidkklaeelk.kilkkkidkikkf 274
                                    ++k            + +++++ k+  ++l+e+d++l++++k k   k i    k+
  gene526|gene526|rna525|rna525 377 EDKEnmntldlemfsHRMMRDDYKRKVKELREKDEELKSKIKeK---KVIRGNTKV 429
                                    44444444455667877888888888888888888887777742...222222222 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3
                         AAA_15 231 qekleeelteklkeiqeklkeidk 254
                                    ++kl +e +e l +++e+ +  ++
  gene526|gene526|rna525|rna525 725 NSKLLKEAEESLRHVLEEMEMCEG 748
                                    112233333333333333333333 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.02
                         AAA_15   57 vikiekedleifeniseskdikIdvef................................aekekakeyektlkskekk 102 
                                     + ++e+ +l+ +e++s   +i++++                                  +   ++++ e +  s+++k
  gene526|gene526|rna525|rna525  783 ARDCESFELKRMEYESVRGRIELRIGTlereveglekeirvlrerveelrvvegndgedM---SEDTSELAILSEKRK 857 
                                     566777777777777777777777777788888888888888888888888877764321...222222333333333 PP

                         AAA_15  103 kadlllkkkesdlkktikdkklklkknelsde.kisvekkks.kkelpkekeeklekekeelkidkedlkklikklee 178 
                                      +   ++k ++++k++ +++k    k++  d+ +i++   k+ + e  k++ +++ +e+ e+     ++    +  e 
  gene526|gene526|rna525|rna525  858 RKLEAFEKARDEFKEINEEFKRLMGKKNELDQgIIYCASAKErIEEEIKNTLSFAVLEEIEIPCAGRKCVGKVSIDEI 935 
                                     333368888899999988888777655555441444444444266677777788888888888888888888888888 PP

                         AAA_15  179 slkkee...........elknvlksaiiklllisakRnvsd.....edsekkssllgklkekileealqekleeelte 240 
                                      +++ e           e++++++s+++++++ +++ + s       ++e ++ + +++k++++e   +++ +    e
  gene526|gene526|rna525|rna525  936 DFSGLErsveelrreleEINQKISSQAPLIRVGEKDGDCSRyvkisAEYERQKAAAISAKNEFNEI--KKRRTHIFME 1011
                                     8888889999999*9999999999999999999999999988877777888888888888888884..4444444567 PP

                         AAA_15  241 klkeiqeklkeidkklaeelk.........kilkkkidkikkfnykgkkneeieik.....d 288 
                                      +++++++l+ i+k l++ ++         ++  +++++ + f+ ++ ++ ++e++     +
  gene526|gene526|rna525|rna525 1012 CFEKVNKELSRIYKCLTMTETsegnaylalENTSEPFKEGVRFHLMPPNKRFREVRllsggE 1073
                                     78888888888888887777777888788877888888888888888888777776665440 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   3.1e-10   5.5e-07       1      46 [.       3      48 ..       3      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.1e-10
                         AAA_29  1 LkrlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                   L+r+++ N  ++ g h+i    + +t ++Gp+GsGKS ++DA+++ L
  gene526|gene526|rna525|rna525  3 LERIEVENFKSYVGrHVIGPF-DRFTCIIGPNGSGKSNIMDAVTFCL 48
                                   799***********8888665.358******************9876 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   2.2       1.6   2.8e+03     112     151 ..     226     269 ..     203     276 .. 0.61
   2 ?   -1.0   1.8      0.64   1.1e+03     115     154 ..     380     419 ..     339     436 .. 0.69
   3 !   15.8   1.7   4.2e-06    0.0075      87     152 ..     699     764 ..     684     766 .. 0.89
   4 ?   -0.2   0.1      0.35   6.3e+02     116     139 ..     809     832 ..     790     849 .. 0.64
   5 ?   -2.3   0.0       1.5   2.8e+03     103     125 ..     937     959 ..     934     966 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                  Fzo_mitofusin 112 etekeleeeikele...keiekl.eevqkkakllrnkasllese 151
                                      +k++++e+ +le   ke+++l ++ +k+ ++ rnk +++++e
  gene526|gene526|rna525|rna525 226 SRRKDINDEVIRLElesKEVQELiDSKEKEVEMYRNKINEIRRE 269
                                    34566666666654111455554256667788889998888776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.64
                  Fzo_mitofusin 115 keleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                    +++++   e+ ++  + ++ ++k k lr+k ++l+s++++
  gene526|gene526|rna525|rna525 380 ENMNTLDLEMFSHRMMRDDYKRKVKELREKDEELKSKIKE 419
                                    4444433334444444567777788888888777777654 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 4.2e-06
                  Fzo_mitofusin  87 tsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseL 152
                                     s +++  v ++l+  +++l+++v e++k l+e  ++l++ +e++e  + k+k lr+k +++e +L
  gene526|gene526|rna525|rna525 699 RSRAMEMEVMKDLDICIEELESEVAENSKLLKEAEESLRHVLEEMEMCEGKMKELRQKVEEVECSL 764
                                    688999****************************************************99988665 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.35
                  Fzo_mitofusin 116 eleeeikelekeiekleevqkkak 139
                                    +le+e++ lekei+ l e  ++++
  gene526|gene526|rna525|rna525 809 TLEREVEGLEKEIRVLRERVEELR 832
                                    455556666666655555544444 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 1.5
                  Fzo_mitofusin 103 farlcqqvdetekeleeeikele 125
                                    f+ l+++v+e ++elee  ++++
  gene526|gene526|rna525|rna525 937 FSGLERSVEELRRELEEINQKIS 959
                                    55666666666666665444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00051      0.91      11     188 ..      17     196 ..      13     200 .. 0.58
   2 ?   -4.1   0.1       6.2   1.1e+04     155     184 ..     392     420 ..     378     426 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00051
                         AAA_30  11 ealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Laeelgieastiakllkrlk....grar 85 
                                    +++++  dr++++ Gp G+GK+ ++ a++  +    +++      +  Ak  ++ ++  ++ t+   l+  +    ++++
  gene526|gene526|rna525|rna525  17 RHVIGPFDRFTCIIGPNGSGKSNIMDAVTFCLGIGARHLR-----ASNAKGlINSKCTHASVTLYIELDGERkgfkRHVN 91 
                                    56777778999***************99877664433222.....22233314445555555555555444466653334 PP

                         AAA_30  86 lepgtllivD..EagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlveaagigtaeLtevvRqkeseer 163
                                     + ++l+ +D   +g   ++++ + ++ + +a   +++ GD +  +s  + ++ r+   ++  g+++L+ev+  k+ e++
  gene526|gene526|rna525|rna525  92 NDGRSLYFIDleNVGYERFREAVEGMNLLIDARNFLVFQGDVNAIGSMMPMELTRLF--EEMSGSIKLKEVYEEKQREQA 169
                                    444577777642234445555555555555566667777777777777777776666..566777777777777776666 PP

                         AAA_30 164 aaalalregdae..ealealadrgrih 188
                                    +a+ + ++  +e  e+++++++ + ++
  gene526|gene526|rna525|rna525 170 KAVSECSSLYEEkkEVMSRMKEAEEVR 196
                                    666666543333334555555555555 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 6.2
                         AAA_30 155 vRqkeseeraaalalregdaeealealadr 184
                                    +R+ ++++++ +++lre d+e + ++ +++
  gene526|gene526|rna525|rna525 392 HRMMRDDYKRKVKELREKDEELK-SKIKEK 420
                                    78888999999999999998833.344444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0057        10       6      25 ..      25      44 ..      24      84 .. 0.82
   2 ?   -1.2   0.0       1.3   2.3e+03      80     128 ..     915     967 ..     865     971 .. 0.67
   3 ?    1.6   0.0      0.17   3.1e+02      88     128 ..    1087    1125 ..     981    1132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0057
                         AAA_22  6 gilvvtGesGtGKTtllrrl 25
                                   ++++++G+ G+GK+  +  +
  gene526|gene526|rna525|rna525 25 RFTCIIGPNGSGKSNIMDAV 44
                                   689***********888766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                         AAA_22  80 ealeqalraravielliiDEaqhlrs.eealeeL.rsllnl...srkgvqliLv 128
                                    e +e  +  r+ ++ + iDE+++    e+ +eeL r+l ++    +++ +li v
  gene526|gene526|rna525|rna525 915 EEIEIPCAGRKCVGKVSIDEIDFS-GlERSVEELrRELEEInqkISSQAPLIRV 967
                                    555555555555667789999986.55777777744444434455555555555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
                         AAA_22   88 aravielliiDEaqh.lrseealeeLrsllnlsrkgvqliLv 128 
                                     a++  ++ + DE++  l  +++++ ++s+    ++  q+iL+
  gene526|gene526|rna525|rna525 1087 AYRPAPFYLFDEVDSaL-DKANVSRIVSFII--SSTAQFILI 1125
                                     333378999******99.9999999999999..999999998 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00052      0.93      14      31 ..      27      44 ..      24      48 .. 0.86
   2 ?   -6.5   7.9        10   1.8e+04      91      91 ..     234     234 ..     137     426 .. 0.64
   3 ?   -1.6   0.1         2   3.6e+03      38      94 ..     799     872 ..     792     892 .. 0.54
   4 ?    4.5   0.0     0.026        47      40     119 ..     928    1079 ..     908    1099 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00052
                                   EEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkll 31
                                   + i+G+nG+GKS ++ ++
  gene526|gene526|rna525|rna525 27 TCIIGPNGSGKSNIMDAV 44
                                   679*********999876 PP

  == domain 2  score: -6.5 bits;  conditional E-value: 10
                                    H CS
                                    x RF
                       ABC_tran  91 k 91 
                                    +
  gene526|gene526|rna525|rna525 234 E 234
                                    1 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                    SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH....................HHHTC...HHHHHHHSTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxx...xxxxxxxxxx RF
                       ABC_tran  38 teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren....................esdee...iekalsklgl 94 
                                      G+i+l+   l++ e e l+kei+vl +  +  + +  + n                        +   +eka+++++ 
  gene526|gene526|rna525|rna525 799 VRGRIELRIGTLER-EVEGLEKEIRVLRERVEELRVV--EGNdgedmsedtselailsekrkR---KleaFEKARDEFKE 872
                                    55666666445555.6777888888888773333322..222456666666666666543321...13334444444444 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.026
                                     EEEEETTCEGGG..B-HHHCCHCEEEE-SS.--S-TTSBHHHH................................... CS
                                     xxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxxxxxxxx................................... RF
                       ABC_tran   40 Geilldgkdlke..qeleslrkeigvlpqe.pqlfpeltvren................................... 79  
                                     G++ +d+ d++   ++ e+lr+e++ + q+ ++  p ++v+e+                                   
  gene526|gene526|rna525|rna525  928 GKVSIDEIDFSGleRSVEELRRELEEINQKiSSQAPLIRVGEKdgdcsryvkisaeyerqkaaaisaknefneikkrr 1005
                                     788888888877888899999999999999777788888999999999999999986655555555555555544444 PP

                                     ........................HHHTCHHHHHHHSTTGG..........................TTCBGESTTSG CS
                                     ........................xxxxxxxxxxxxxxxxx..........................xxxxxxxxxxx RF
                       ABC_tran   80 ........................esdeeiekalsklglke..........................lkdtvvkssps 107 
                                                             +               e                           ++++  ++ +
  gene526|gene526|rna525|rna525 1006 thifmecfekvnkelsriykcltmT---------------EtsegnaylalentsepfkegvrfhlmPPNKRF-REVR 1067
                                     4444444443332222222222220...............133344444444444444555555554333333.4446 PP

                                     GS-HHHHHHHHH CS
                                     xxxxxxxxxxxx RF
                       ABC_tran  108 sLSgGqkqrval 119 
                                      LSgG++ + +l
  gene526|gene526|rna525|rna525 1068 LLSGGERTMAVL 1079
                                     677777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2066  (0.115232); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 1.16u 0.30s 00:00:01.46 Elapsed: 00:00:00.53
# Mc/sec: 6529.72
//
Query:       gene527|gene527|rna526|rna526  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-11   42.8   0.8    5.5e-11   42.4   0.8    1.2  1  Sec66     Preprotein translocase subunit Sec66


Domain annotation for each model (and alignments):
>> Sec66  Preprotein translocase subunit Sec66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.8   3.1e-15   5.5e-11      11     151 ..       6     136 ..       1     163 [. 0.82

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 3.1e-15
                          Sec66  11 vavligslatfsslyrkrkakklaelepwFpenlqrdiYlsllhlekkkeekvpekvlkAALLrravedirrilklresk 90 
                                     ++l +++++fs + r ++ k+  e     ++n++ ++Y+  ++      e +p +vl   L++ a+    r++kl ++ 
  gene527|gene527|rna526|rna526   6 AMILSTMILMFSFIKRINRRKTPIEE----NPNTELEMYFL-QKS-----EGAPSSVLLKQLVKAAACFKERVMKLEKDM 75 
                                    56778888889998888887777766....67889999984.333.....3689999999******************** PP

                          Sec66  91 palevllqkGsvgddlwqrfqraekeleeElkdvvqeaealkpgWgqtifqsaneilanea 151
                                    + l +l+++  ++++ w+r++++ k+ e E   + +ea+ +kpg g+ if+ a+ i   ++
  gene527|gene527|rna526|rna526  76 EILGTLYEDRMISEEHWERINEESKNCEVERICIESEANIIKPGYGEEIFKDASKISITNT 136
                                    ******************************************************9965433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      692  (0.0385967); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 992.02
//
Query:       gene528|gene528|rna527|rna527  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-20   71.2   0.3    6.4e-20   71.0   0.3    1.0  1  TFIID-18kDa  Transcription initiation factor IID, 18kD subuni


Domain annotation for each model (and alignments):
>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.3   3.6e-24   6.4e-20       2      92 ..       8      96 ..       7      97 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 3.6e-24
                                   --CCCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    TFIID-18kDa  2 lfrkelqsmlyalGdvkePlqetvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliRkDkkKlnRlkellslkel 83
                                   +f k+++ m+y++Gdv  P  +t++ l   v +y+  ll+++ ++a+ +   k + EDll+ +++D+kK +R+++ll ++e+
  gene528|gene528|rna527|rna527  8 SFMKDIKVMMYGYGDVIAPRYDTAEALHGYVLDYMSILLTNTHNMAQVK--GKTKTEDLLYYLKRDRKKYSRVRHLLITNEE 87
                                   699*********************************************9..57789************************** PP

                                   XXXXXXXXX CS
                    TFIID-18kDa 84 lkkakKqfd 92
                                   +k akK+fd
  gene528|gene528|rna527|rna527 88 IKLAKKAFD 96
                                   *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 586.39
//
Query:       gene529|gene529|rna528|rna528  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 651.72
//
Query:       gene530|gene530|rna529|rna529  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-13   50.4   1.7    2.2e-13   49.8   1.7    1.3  1  Homeodomain  Homeodomain
    2.2e-06   27.5   0.8    3.3e-06   26.9   0.8    1.3  1  Homeobox_KN  Homeobox KN domain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   1.7   2.5e-17   2.2e-13       1      56 [.      28      83 ..      28      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 2.5e-17
                                   ST-SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    Homeodomain  1 rrkRttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56
                                   +r+R  + + q  +Le  F+ n+yp++ e+  L  k++++ +++k+WFqNrRa+ek
  gene530|gene530|rna529|rna529 28 KRSRILLHEWQSMMLEHSFRINPYPDRIEKYNLFLKTKVPIKNIKIWFQNRRAREK 83
                                   799999*************************************************9 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.8   3.7e-10   3.3e-06       8      40 .]      49      81 ..      42      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.7e-10
                    Homeobox_KN  8 nPYPseedKeeLlkeTglsvkqitnWFINaRrR 40
                                   nPYP++ +K  L  +T+  +k i+ WF N R+R
  gene530|gene530|rna529|rna529 49 NPYPDRIEKYNLFLKTKVPIKNIKIWFQNRRAR 81
                                   9******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 868.94
//
Query:       gene53|gene53|rna53|rna53  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-36  123.5   0.1    9.9e-36  123.3   0.1    1.1  1  TK            Thymidine kinase
      0.007   16.6   0.0      0.013   15.8   0.0    1.4  1  AAA_22        AAA domain
  ------ inclusion threshold ------
       0.12   11.6   0.0       0.16   11.2   0.0    1.1  1  Ribosomal_S2  Ribosomal protein S2
       0.18   11.5   0.0       0.24   11.1   0.0    1.2  1  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3   0.1   2.2e-39   9.9e-36       2     177 .]       5     187 ..       4     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 2.2e-39
                         TK   2 sielilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRysegkvvthdgisleakksktssleeikeeleeedvdvvlvDE 85 
                                 ++++ +pm+ GK+t++l r+kr++    kv++ k+++d+R+s + ++++ g  +e + +   +++ +k+++ + dvd+++vDE
  gene53|gene53|rna53|rna53   5 VLKFVASPMNGGKTTNMLLRAKRASVLGWKVLLAKPQIDTRHSSTIIKSRCGAEMECNLCIDPQFNFMKDISYK-DVDILFVDE 87 
                                689*******************************************************7666667766666666.9******** PP

                         TK  86 aqFfe.qdivelseklanegkivivagLdtdFerklFenilkllalaekvkklkavCmkCgkkAsftkrln.....kekevili 163
                                aqF++ ++i+el e+++ +++ + ++gL tdF+++lFe++ +l+ l++k+ +l+  C +C +   f  + +       +  i++
  gene53|gene53|rna53|rna53  88 AQFLStRQIEELREVVDVHKVSIWCYGLLTDFKKNLFEGSRRLVELCDKMYELDVLCCFCSESGRFHLKYTdgkasLSGPSIEV 171
                                *********************************************************************997777733344444 PP

                         TK 164 G..gkekYvsvCrkcy 177
                                    ++k+vsvC  c+
  gene53|gene53|rna53|rna53 172 TtpENDKFVSVCHMCW 187
                                312699*********8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.8e-06     0.013      92     126 ..      80     111 ..      69     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.8e-06
                     AAA_22  92 ielliiDEaqhlrseealeeLrsllnlsrkgvqli 126
                                + +l +DEaq+l s +++eeLr+ ++   ++v++ 
  gene53|gene53|rna53|rna53  80 VDILFVDEAQFL-STRQIEELREVVD--VHKVSIW 111
                                489*********.*************..8877765 PP

>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.6e-05      0.16      45     102 ..      68     125 ..      60     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.6e-05
               Ribosomal_S2  45 aykvvkevaakggkilfvgtkk.qakeavkeaakrangyyvnerWlgGtLTNfktikks 102
                                 ++++k+++ k+  ilfv   +    + ++e  + ++ + v + W  G+LT fk+   +
  gene53|gene53|rna53|rna53  68 QFNFMKDISYKDVDILFVDEAQfLSTRQIEELREVVDVHKV-SIWCYGLLTDFKKNLFE 125
                                679*****************996677788888887777777.88********9976555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.4e-05      0.24      85     123 ..      76     114 ..      11     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.4e-05
                     AAA_30  85 rlepgtllivDEagmvdtkqlaallkaaekagakvilvG 123
                                ++++ ++l vDEa  ++t+q+++l + ++ +++++++ G
  gene53|gene53|rna53|rna53  76 SYKDVDILFVDEAQFLSTRQIEELREVVDVHKVSIWCYG 114
                                4455699*******************9999888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1394.70
//
Query:       gene531|gene531|rna530|rna530  [L=466]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-67  227.1   0.2    2.1e-67  226.6   0.2    1.3  1  SRP54        SRP54-type protein, GTPase domain
    7.9e-28   97.0   1.0      2e-26   92.5   0.0    2.9  2  SRP_SPB      Signal peptide binding domain
      1e-11   44.9   0.0    3.3e-11   43.2   0.0    1.9  1  SRP54_N      SRP54-type protein, helical bundle domain
    4.4e-07   29.7   0.3    7.3e-06   25.7   0.3    2.2  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
    0.00052   19.1   0.1     0.0022   17.0   0.0    1.9  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00063   19.5   0.0     0.0014   18.4   0.0    1.6  1  AAA_30       AAA domain
     0.0026   17.6   0.0     0.0061   16.5   0.0    1.6  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
  ------ inclusion threshold ------
       0.01   15.0   0.1       0.38    9.9   0.0    2.3  2  ArsA_ATPase  Anion-transporting ATPase
      0.015   15.4   0.0      0.025   14.7   0.0    1.5  1  AAA_33       AAA domain
      0.031   14.7   0.1      0.083   13.3   0.0    1.8  2  AAA_16       AAA ATPase domain
      0.045   13.5   0.4       0.46   10.2   0.1    2.5  3  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.047   13.1   0.2        9.2    5.7   0.0    2.9  3  SRPRB        Signal recognition particle receptor beta subuni
      0.064   13.5   0.1       0.17   12.2   0.1    1.9  1  AAA_22       AAA domain
      0.079   12.9   0.2       0.24   11.3   0.2    1.8  1  NTPase_1     NTPase
       0.12   12.4   0.2       0.46   10.6   0.2    2.1  1  SapB_1       Saposin-like type B, region 1


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.6   0.2   1.8e-70   2.1e-67       2     196 .]     100     293 ..      99     293 .. 0.98

  Alignments for each domain:
  == domain 1  score: 226.6 bits;  conditional E-value: 1.8e-70
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                    nv+++vGlqG+GKTt++ K a+ +kk+g+kv +v+aDtfRa+A++Q+k++a k++vp+++++ e dp++va ++ve++++
  gene531|gene531|rna530|rna530 100 NVVVFVGLQGSGKTTSICKYANFYKKKGYKVGIVCADTFRAGAFDQVKQNALKIKVPFFGSS-EVDPVKVAGAGVERFRK 178
                                    79*********************************************************766.889************** PP

                                    TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHH CS
                          SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaals 161
                                    ek++++lvDT+Gr+ +++el+ e+k+i + v p+++++v+da +gq+a  qa  Fk+av+++++ ltk+Dg++k+G+als
  gene531|gene531|rna530|rna530 179 EKFELILVDTSGRHTQESELFLEMKDIIREVGPNSIVFVMDAGIGQSAEDQAVGFKRAVDVGSILLTKIDGTSKAGGALS 258
                                    ******************************************************************************** PP

                                    HHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                          SRP54 162 iaaelklPikfigvGekiedleefdperlvsrllg 196
                                     +a++k Pi f+g+Ge +edle fd++r+vsr+lg
  gene531|gene531|rna530|rna530 259 SVAATKCPIEFVGTGEGMEDLEMFDARRFVSRMLG 293
                                    ********************************995 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.28   3.3e+02       4      31 ..     281     308 ..     278     320 .. 0.74
   2 !   92.5   0.0   1.7e-29     2e-26       2      99 .]     323     419 ..     322     419 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.28
                                    THHHHHHHHHHHCCCCCCHHHHCCC... CS
                        SRP_SPB   4 lrdlleqlqqikkmGplskllsmiPgms 31 
                                    + d +  ++++  mG+++ l++++  ++
  gene531|gene531|rna530|rna530 281 MFDARRFVSRMLGMGDVEGLMEKVGSLG 308
                                    6688888999***********9987643 PP

  == domain 2  score: 92.5 bits;  conditional E-value: 1.7e-29
                                    SCTHHHHHHHHHHHCCCCCCHHHHCCC.....H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..H..HHHHHHHHHTT CS
                        SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsaeakaeeeaekklkrieaiidSMTkeErdspekllke..sRkrRiArGsG 79 
                                    ftl d+++q+q+i ++Gp+skll+miPg+s      +  e+++k++ +++dSM++ E+ds+++++++  +R+ R+ArGsG
  gene531|gene531|rna530|rna530 323 FTLGDFYDQFQKILSLGPISKLLEMIPGFSGLSL-PD--EESFKKLIYVFDSMSRGELDSTGQIFERepTRVVRVARGSG 399
                                    9***************************875532.33..689***********************9568*********** PP

                                    S-HHHHHHHHHHHHHHHHHT CS
                        SRP_SPB  80 tsvqevnellkqfeqmkkmm 99 
                                    tsvq v e+l+qf++++ mm
  gene531|gene531|rna530|rna530 400 TSVQGVTEILSQFKKVHAMM 419
                                    ******************98 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   2.8e-14   3.3e-11       1      75 []       5      81 ..       5      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 2.8e-14
                                   HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS.....S-HHHHHHHHHHHHH CS
                        SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk.....lkpkqqvkkivkdeL 75
                                   Lg++++++l++l ++ + +++d++ a+ke++++L+ ++V+ k+v +l ++++  ++   k      +++++v+++v++ L
  gene531|gene531|rna530|rna530  5 LGRSITNTLSNLLSSHT-TDQDIDTAIKEICNSLILSNVNPKYVNDLKNSLRA-ELD-PKgmppgFNKAKMVQNAVYERL 81
                                   7999*******999975.99*******************************88.888.445999999**********976 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.3   6.1e-09   7.3e-06       2     158 ..     101     256 ..     100     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.1e-09
                                    EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeer 79 
                                    v+v++G  GsGKTt ++++    +++g+k+ ++  +    +     ++++   +++++      + + d +k++ a +er
  gene531|gene531|rna530|rna530 101 VVVFVGLQGSGKTTSICKYAnfYKKKGYKVGIVCADTFRAGAFD-QVKQN---ALKIKVPFFGSS-EVDPVKVAGAGVER 175
                                    7899****************99999***********99544333.34444...455544444444.34444444444443 PP

                                    H..TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                           cobW  80 e..erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee 156
                                       e++++il+ t+G   +  ++ ++ +++ +++  +++v+v+Da  + ++ e+++  +++ + + + ++l+K+D  +++
  gene531|gene531|rna530|rna530 176 FrkEKFELILVDTSGrHTQESELFLEMKDIIREVGPNSIVFVMDA-GIGQSAEDQAVGFKRAVDVGS-ILLTKIDGTSKA 253
                                    23467**********777777776779******************.666888888888888888876.7899***99887 PP

                                    ... CS
                           cobW 157 .al 158
                                       
  gene531|gene531|rna530|rna530 254 gGA 256
                                    554 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.8e-06    0.0022      25      66 ..      95     136 ..      89     144 .. 0.93
   2 ?   -1.8   0.0         1   1.2e+03     204     234 ..     391     421 ..     376     425 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                                    G-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                           MeaB  25 kaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                    + G+++vv + G+ G+Gk t + + +  ++++G++v+++  D
  gene531|gene531|rna530|rna530  95 EKGKTNVVVFVGLQGSGKTTSICKYANFYKKKGYKVGIVCAD 136
                                    569***********************************9988 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                                    --EEEEEBCCCTBSHHHHHHHHHHHHHHHHH CS
                           MeaB 204 rpkvlktsavegeGidelvdaieehrevlkk 234
                                      +v + s++  +G+ e++++ ++ + +++k
  gene531|gene531|rna530|rna530 391 VVRVARGSGTSVQGVTEILSQFKKVHAMMQK 421
                                    4578888999999999999999988887775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.2e-06    0.0014      17      58 ..      98     140 ..      92     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrv.iglAptgka 58 
                                    +  v+v +G  G+GKtt++ ++++ ++++g++v i++A t +a
  gene531|gene531|rna530|rna530  98 KTNVVVFVGLQGSGKTTSICKYANFYKKKGYKVgIVCADTFRA 140
                                    56799***************************95577777666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   5.1e-06    0.0061       1      33 [.     101     133 ..     101     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                           MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                    v+ +vg +gsGKTt + k  +  k++g++vg++
  gene531|gene531|rna530|rna530 101 VVVFVGLQGSGKTTSICKYANFYKKKGYKVGIV 133
                                    6889***************************98 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00031      0.38       2      81 ..     100     181 ..      99     206 .. 0.79
   2 ?    2.8   0.0     0.046        54      81     112 ..     402     433 ..     360     446 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00031
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEET.SSEEEEE--HH....HHHHHH CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvk.eNLsavEidpe....veleea 76 
                                    +v+++ G  G GKtt+ +  a    +kg+kv ++  D     + +fdq +++++ k+k       E+dp       +e+ 
  gene531|gene531|rna530|rna530 100 NVVVFVGLQGSGKTTSICKYANFYKKKGYKVGIVCADTFR--AGAFDQ-VKQNALKIKvPFFGSSEVDPVkvagAGVERF 176
                                    68999999****************************9765..689999.999999**98888899999985555444444 PP

                                    HCCHH CS
                    ArsA_ATPase  77 kqevq 81 
                                    ++e +
  gene531|gene531|rna530|rna530 177 RKEKF 181
                                    44444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.046
                                    HGGGSCCH.HHHHHHHHHHHHHTSSTTHHHHHH CS
                    ArsA_ATPase  81 qkeeeall.gleeledvlaeelaslPGideils 112
                                     +  +++l ++++++ ++++ +++ PGi++++ 
  gene531|gene531|rna530|rna530 402 VQGVTEILsQFKKVHAMMQKFSSI-PGIENMMG 433
                                    444444542667777777777666.****9985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.1e-05     0.025       1      40 [.     101     145 ..     101     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                         AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlfgt 40 
                                    +v++vGl+GsGK+t + ++   +kk g  + ++  dt+r   f +
  gene531|gene531|rna530|rna530 101 VVVFVGLQGSGKTTSICKYanfYKKKGykVGIVCADTFRAGAFDQ 145
                                    89************9877744466666544457777777766654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.9e-05     0.083      19      52 ..      94     131 ..      76     219 .. 0.74
   2 ?   -2.5   0.0       4.7   5.6e+03       8      39 ..     194     226 ..     189     227 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.9e-05
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd....g 52 
                                    + +g +++v+++G +G+GK++ + + ++ ++k+    g
  gene531|gene531|rna530|rna530  94 IEKGKTNVVVFVGLQGSGKTTSICKYANFYKKKgykvG 131
                                    566777*****************999988888844322 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                         AAA_16   8 eleqL.lsalervrsgrpelvllsGesGvGKss 39 
                                    + ++L l++ + +r+ +p++++++ ++G+G s+
  gene531|gene531|rna530|rna530 194 QESELfLEMKDIIREVGPNSIVFVMDAGIGQSA 226
                                    444553555556667778899999999999886 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.62   7.4e+02     189     236 ..      39      86 ..      12      90 .. 0.76
   2 ?   10.2   0.1   0.00038      0.46       2      33 ..     105     136 ..     104     140 .. 0.92
   3 ?   -3.5   0.0         6   7.1e+03     211     237 ..     345     371 ..     341     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.62
                     ATP_bind_1 189 llekeeekykklaeaiaelleefalvlrflplssekeesiedllslid 236
                                    l + + +++++l++++++ l+  ++ + f  ++  ++  +e+l++l+d
  gene531|gene531|rna530|rna530  39 LSNVNPKYVNDLKNSLRAELDPKGMPPGFNKAKMVQNAVYERLVDLLD 86 
                                    33333389999********************99999999999999887 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00038
                     ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                    vG  GsGKtt + + +++++++g++v +v  D
  gene531|gene531|rna530|rna530 105 VGLQGSGKTTSICKYANFYKKKGYKVGIVCAD 136
                                    89************************999766 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6
                     ATP_bind_1 211 falvlrflplssekeesiedllslide 237
                                     ++++ f  ls  +ees+++l+ + d+
  gene531|gene531|rna530|rna530 345 LEMIPGFSGLSLPDEESFKKLIYVFDS 371
                                    567888999999999999999987765 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0077       9.2       3      20 ..      99     116 ..      97     136 .. 0.85
   2 ?    3.9   0.0     0.027        32      45      89 ..     177     224 ..     167     236 .. 0.78
   3 ?   -1.5   0.0       1.2   1.5e+03      73      86 ..     359     372 ..     355     378 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0077
                                    --EEEEE-STTSSHHHHH CS
                          SRPRB   3 kpavllvGlsdsGKTslf 20 
                                    ++ v++vGl+ sGKT+ +
  gene531|gene531|rna530|rna530  99 TNVVVFVGLQGSGKTTSI 116
                                    6899***********855 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.027
                                    ..GGTT-SEEEETT-GCCSHHHHHHHHHHGG...EEEEEEEEETTS-H CS
                          SRPRB  45 sekgskltliDfPGheklrqklleklkakss...lkglvfvvDStidp 89 
                                     +++++l l+D  G +   ++l+ ++k+  +     ++vfv+D+ i +
  gene531|gene531|rna530|rna530 177 RKEKFELILVDTSGRHTQESELFLEMKDIIRevgPNSIVFVMDAGIGQ 224
                                    567889999*****99999999877655322213789******99876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.2
                                    HGGEEEEEEEEETT CS
                          SRPRB  73 ksslkglvfvvDSt 86 
                                    ++s k+l++v DS 
  gene531|gene531|rna530|rna530 359 EESFKKLIYVFDSM 372
                                    6789********95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.17       5      32 ..      99     126 ..      94     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldee 32 
                                     +++v +G  G+GKTt++ ++++ +++ 
  gene531|gene531|rna530|rna530  99 TNVVVFVGLQGSGKTTSICKYANFYKKK 126
                                    578899*****************99643 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2    0.0002      0.24       3      38 ..     103     138 ..     101     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                                    EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE CS
                       NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteev 38 
                                    +  G +G+GKtT + k ++  k++g+kvg + +   
  gene531|gene531|rna530|rna530 103 VFVGLQGSGKTTSICKYANFYKKKGYKVGIVCADTF 138
                                    556999*********************964444444 PP

>> SapB_1  Saposin-like type B, region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00038      0.46      10      37 ..      10      37 ..       8      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                                   HHHHHHHH-SS--HHHHHHHHHHHHHHS CS
                         SapB_1 10 VkeveklLkdNkTeeeIieaLekvCskL 37
                                    + + +lL++ +T ++I +a++++C+ L
  gene531|gene531|rna530|rna530 10 TNTLSNLLSSHTTDQDIDTAIKEICNSL 37
                                   67889********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2654.04
//
Query:       gene532|gene532|rna531|rna531  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.1   0.0      0.068   12.5   0.0    1.3  1  DUF5066   Domain of unknown function (DUF5066)


Domain annotation for each model (and alignments):
>> DUF5066  Domain of unknown function (DUF5066)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.8e-06     0.068      46     109 ..      43     108 ..      30     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-06
                        DUF5066  46 aelpeslkallaydcdlkspygqkvleylvdsid..eegvilsyspdeeayygsgldiagvdledl 109
                                    + +p+ l      d dl  +y  k+l+ ++  ++  +eg     + +e+a+y +++ i+  d+e +
  gene532|gene532|rna531|rna531  43 SCFPKRLWIKRDVDYDLDLSYCDKILNRFIFHVNtlKEGGTYERDINEDAFYYKYMPISPCDIETI 108
                                    5567777777777888888999***9988776664467888999*******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1290.74
//
Query:       gene533|gene533|rna532|rna532  [L=1679]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-250  833.3   6.2   1.3e-250  833.3   6.2    1.8  2  Myosin_head   Myosin head (motor domain)
    4.1e-06   26.5   2.7      1e-05   25.3   2.7    1.6  1  Myosin_N      Myosin N-terminal SH3-like domain
     0.0078   16.3   3.2     0.0078   16.3   3.2   10.8 11  Cep57_CLD_2   Centrosome localisation domain of PPC89
  ------ inclusion threshold ------
      0.053   13.8   0.0      0.053   13.8   0.0    4.1  5  AAA_22        AAA domain
      0.064   13.0   0.1        0.3   10.8   0.1    2.2  1  Get5_C        Get5 C-terminal domain
       0.11   12.9   0.7         23    5.4   0.0    3.6  3  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> Myosin_head  Myosin head (motor domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  833.3   6.2  4.3e-254  1.3e-250       2     677 .]      86     742 ..      85     742 .. 0.97
   2 ?   -5.3   2.8       2.6   7.7e+03     277     358 ..    1122    1205 ..    1115    1264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 833.3 bits;  conditional E-value: 4.3e-254
                                    SBGCGSSS-SHHHHHHHHHHHHHTT--EEEETTEEEEE--SS--STSSHHHHHHHTTS-GGGSSSSHHHHHHHHHHHHHH CS
                    Myosin_head   2 edlveLsllneasvlenlkkRykkdliYtysglvlvavnPykklkiysedvikaykgkkreelpPHifaiadeayrslle 81 
                                    +dl+eLs+lne+ vl+nl++Ry++  iYtysgl+l+a+nPyk l iy e+ i++y+  k++el+PHifa+a+eay+ +++
  gene533|gene533|rna532|rna532  86 DDLAELSYLNEPGVLHNLRRRYQNGRIYTYSGLFLLAINPYKDLRIYGEKDIRKYTLSKKYELEPHIFAVANEAYKLMVS 165
                                    8******************************************************************************* PP

                                    HTSEEEEEEESSTTSSHHHHHHHHHHHHHHHSSSSSCTCTTHHHHHHHHHHHHHHHHHEEEESSETTEESSEEEEEEEEE CS
                    Myosin_head  82 dkenqsilisGEsGAGKteatKkvlqylasvaeskekveeeeleekilqsnPilEafGnAktvrndnssRFGKfieiefd 161
                                    ++enqsili+GEsGAGKte+tK+v+++la+v + +   ee+++++ki+++nPilEafGnA+tv+ndnssRFGKfi+i+f+
  gene533|gene533|rna532|rna532 166 NRENQSILITGESGAGKTENTKRVVEFLATVGGCRG--EEASIDRKIIDANPILEAFGNAQTVKNDNSSRFGKFIKIKFN 243
                                    *********************************999..789**************************************9 PP

                                    TTSSEEEEEEEEECE-GGGGT---TT--SBHHHHHHHHCSTHHHHHHTT--.TCCGSTTTTTTSSSSBTTS-HHHHHHHH CS
                    Myosin_head 162 akgkiagakietYLLEksRvvkqakeERnyHiFYqllagaseeekkelkle.dvkdyaylsqsgeltvdgiddseefket 240
                                      g+i ga+ie+YLLEksRv +q+++ERnyHiFYqll   +  +kk+l l+ d+kdy++l + ++++++ idd+eef+ +
  gene533|gene533|rna532|rna532 244 G-GNICGAHIEKYLLEKSRVTNQSRDERNYHIFYQLLGCDDLGLKKQLLLDgDPKDYRFLRN-SRFKIQDIDDAEEFRRL 321
                                    5.89**********************************************************.69*************** PP

                                    HHHHHHHT--HHHHHHHHHHHHHHHHHCTSSEEEECTTSSEEESSHHHHHHHHHHHTS-HHHHHHHHHSEEEEETTEEEE CS
                    Myosin_head 241 kkaldilglseeeqkeifrivaailhlGniefkkeakdeqavledeeklekaaellgvdaeelekalvkrriktgkevvs 320
                                    +k++d+l++++eeq + f+iv+ailhlGnief++++   +a++++ e +ek+++ll +  +e+ k l+++ ik+g+e+v+
  gene533|gene533|rna532|rna532 322 RKSMDVLNIKKEEQIGYFEIVSAILHLGNIEFREKD--GAAEIANLEVAEKVCKLLSIPLTEFIKRLIHPMIKAGNEYVA 399
                                    ********************************9876..5689999999******************************** PP

                                    EE-BHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-S-SEEEEEEEEE-B---SSB-HHHHHHHHHHHHHHHHHHH CS
                    Myosin_head 321 kalnveqaevardalakaiyerlFdwlverinkslekkkeekksfiGvLDiaGFEifeknsFEqlcinyvnEkLqqlFne 400
                                    ++ n+eqa  ++d la+ +y+++Fd +++rin sl++ +  k +fiGvLDiaGFEif knsFEqlciny+nEkLqq+Fn+
  gene533|gene533|rna532|rna532 400 HSRNKEQALKIVDGLARILYDKMFDNVIDRINMSLSSPH--KGNFIGVLDIAGFEIFGKNSFEQLCINYTNEKLQQFFNH 477
                                    ************************************999..9************************************** PP

                                    HHCHHHHHHHHHTTSSGCGS-GGGCCHHHHHHHHS.SSTSHHHHHHHHHTSTTS-HHHHHHHHHHHHTTSTTEEETTSTT CS
                    Myosin_head 401 lvlklEqeeYvrEgiewkfidfgldnqaiidLiek.kplGilslLdeecllpkatdetfleklvkafskhakfeksrlkk 479
                                    ++++lEqe Y +E iew+fidfgld+q++idLiek +p+Gils Ldeec++p at++tfl kl+k+  +h+kfe  +   
  gene533|gene533|rna532|rna532 478 HMFILEQEVYRQERIEWDFIDFGLDLQPTIDLIEKsNPIGILSYLDEECVMPMATEKTFLRKLMKNI-RHEKFEVDK--- 553
                                    ***********************************99***************************997.578887776... PP

                                    TTTEEEEEETTCEEEEE-TTHHHHHH----HHHHHHHHTSSSHHHHHHCCSHCHB--.........CSSSECCCCCSBHH CS
                    Myosin_head 480 geakFiikHyAgkveYevegfleKnkDtlnedlvellksskkkllaelfkeeekeakaeakksekkkkkkkkkkkfktvg 559
                                     +++F+++HyAg+veY+v+++l+KnkD+ +e l++l++ s+++ +++l  eee                + kk  f+tv+
  gene533|gene533|rna532|rna532 554 IKDAFVLNHYAGDVEYTVDDWLSKNKDSHSEALTSLIRMSNSETVSRLSLEEE----------------TIKKGFFRTVS 617
                                    599********************************************988744................477889***** PP

                                    HHHHHHHHHHHHHHCTSEEEEEEEE-SSSS--TT---HHHHHHHHHHTTHHHHHHHHHHSSSEEEEHHHHHHHHGGGSTT CS
                    Myosin_head 560 skfkeslaeLmktlestnphfvRCikpnekkkakkldeslvleqlrclGvlegirirraGfpnRitfeefvqrYkllakk 639
                                    +k+ke+l++Lm +l+ tnphfvRCi+pn +k+  +ld+ +vl ql+c+Gvlegiri+r+Gfp+R+ ++efv+rY++++k+
  gene533|gene533|rna532|rna532 618 QKHKEQLGSLMCELRGTNPHFVRCIIPNLEKNGDRLDNGVVLGQLKCNGVLEGIRISRQGFPSRMGYQEFVRRYRIMMKD 697
                                    ******************************************************************************** PP

                                    SS-SS........SSSHHHHHHHHHHHTTS-GCGEEECSSEEEET CS
                    Myosin_head 640 elkkl.......lkedakkaveailkeleldkeeykiGktKiFfr 677
                                    ++ ++       + e  k++ e+il+ + +++++y++G+tK+Ffr
  gene533|gene533|rna532|rna532 698 KVRETeswdddmCMEVCKEMGEQILSGIGISANQYRMGRTKVFFR 742
                                    9988778665654555678889999999****************8 PP

  == domain 2  score: -5.3 bits;  conditional E-value: 2.6
                                     TTSSEEESSHHHHHHHHHHHTS-HHHHHHHHHSEEEEETTEEEEEE-BHHHHHHHHHHHHHHHHHH..HHHHHHHHHH CS
                    Myosin_head  277 kdeqavledeeklekaaellgvdaeelekalvkrriktgkevvskalnveqaevardalakaiyer..lFdwlverin 352 
                                     k++q+  +++e+l + ++ l   +++l++ l +++i+ ++ +  k   ++q ++ +++   +i++r  +F+ + +++ 
  gene533|gene533|rna532|rna532 1122 KEKQSRDSTQESLLEKTRNLERRVKSLSEKLKSEEIANKQLMNEKDEMYKQIHILQQSKLDEIFDReaMFNSVKKNLQ 1199
                                     555555566666666666666666666666666666666666666666666666666666666654335555555554 PP

                                     HHHTTS CS
                    Myosin_head  353 kslekk 358 
                                       +++ 
  gene533|gene533|rna532|rna532 1200 MEIQRL 1205
                                     444444 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   2.7   3.3e-09     1e-05       1      30 [.      33      62 ..      33      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.3e-09
                                   SEEEEETTSTTS-EEEEEEEEESSEEEEEE CS
                       Myosin_N  1 KklVWVpDpkegyvkGeIkeeeGdkvtVet 30
                                   K++VWVp  k+gyv G +++eeGd +++ +
  gene533|gene533|rna532|rna532 33 KRWVWVPKSKDGYVSGFVVKEEGDVLEIDC 62
                                   9***********************888766 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   8.9      0.38   1.1e+03       5      64 ..     881     940 ..     878     942 .. 0.92
   2 ?   -2.3   7.4       1.7     5e+03       2      59 ..     948    1003 ..     947    1011 .. 0.80
   3 ?   -1.1   5.1      0.71   2.1e+03      17      61 ..    1002    1049 ..     994    1058 .. 0.84
   4 ?  -10.7  15.8         6   1.8e+04       4      60 ..    1063    1123 ..    1056    1136 .. 0.70
   5 !   16.3   3.2   2.6e-06    0.0078       7      42 ..    1140    1175 ..    1134    1184 .. 0.90
   6 ?   -3.8   0.2       4.7   1.4e+04      46      57 ..    1201    1212 ..    1196    1218 .. 0.51
   7 ?   -1.6   2.5         1   3.1e+03      31      59 ..    1245    1273 ..    1238    1284 .. 0.80
   8 ?   -1.9   4.2       1.2   3.6e+03       4      59 ..    1348    1403 ..    1346    1414 .. 0.83
   9 ?   -1.6   1.9      0.98   2.9e+03      43      66 ..    1493    1517 ..    1487    1545 .. 0.71
  10 !    5.1   2.2    0.0078        23      47      64 ..    1616    1633 ..    1586    1638 .. 0.69
  11 ?   -2.4   0.5       1.8   5.4e+03      39      58 ..    1643    1662 ..    1639    1664 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.38
                    Cep57_CLD_2   5 vktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELkeq 64 
                                     ++L+ + d + ++++    e ++   E   ++ qL++A+e l+   +e   l+kE +eq
  gene533|gene533|rna532|rna532 881 LMALRYKADEMGQEIERIRKEADNICDEKKLSEDQLREAIEMLERKESEISKLKKEVEEQ 940
                                    67899999999999999999999*********************************9988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                    Cep57_CLD_2    2 eaevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeeln.eLkaevealrk 59  
                                     e+e+++L+++   +++k ++ +   +++ +ERd+ +  L +++ e + e k+ +e+ +k
  gene533|gene533|rna532|rna532  948 EREISSLREE---VVSKSSEKDAMVEKMLRERDREVCLLKEKIKEKDcEVKNILERMKK 1003
                                     6788888876...689999*****************99999999876566666666665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.71
                    Cep57_CLD_2   17 rklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkE...L 61  
                                      k +v +ee++r  kE ++ +  L   +    + k+e   lrk+    
  gene533|gene533|rna532|rna532 1002 KKSEVEDEERRRELKEKEMIIDELKANCISMKKWKDECGELRKDyevM 1049
                                     48999999999999****************************995441 PP

  == domain 4  score: -10.7 bits;  conditional E-value: 6
                    Cep57_CLD_2    4 evktLqnrLdsltrklqvheeelkrLnk....ERdsalrqLgvAyeeln.eLkaevealrkE 60  
                                     e+ +L n+   ++ + ++ e+  k+L+     ER++  ++L  A++el+ e  a  e l+kE
  gene533|gene533|rna532|rna532 1063 ENDRLHNEIRKMEKEREELESMQKKLRDdlefERNRG-KKLEKAFQELRgEYLAAEEQLQKE 1123
                                     6677777777788888888877777777777788774.778888887743555555666666 PP

  == domain 5  score: 16.3 bits;  conditional E-value: 2.6e-06
                    Cep57_CLD_2    7 tLqnrLdsltrklqvheeelkrLnkERdsalrqLgv 42  
                                      L+ r +sl++kl + e+++k+L++E d++ +q+++
  gene533|gene533|rna532|rna532 1140 NLERRVKSLSEKLKSEEIANKQLMNEKDEMYKQIHI 1175
                                     6999*****************************986 PP

  == domain 6  score: -3.8 bits;  conditional E-value: 4.7
                    Cep57_CLD_2   46 elneLkaeveal 57  
                                     e++ L  e+ +l
  gene533|gene533|rna532|rna532 1201 EIQRLEMENQRL 1212
                                     334444444443 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 1
                    Cep57_CLD_2   31 kERdsalrqLgvAyeelneLkaevealrk 59  
                                     + R +a++q+++    +  L++eve lr+
  gene533|gene533|rna532|rna532 1245 RKRKEAEHQISEQENKNVILSSEVEMLRE 1273
                                     55778888888888888899999998886 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 1.2
                    Cep57_CLD_2    4 evktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrk 59  
                                     ++++L +r  sl++++++   + +++n   ++ ++q  +A +e+ +L a+ ++l+ 
  gene533|gene533|rna532|rna532 1348 AIEELNDRILSLSHEVEERRATEDEMNVKVEELMKQYNSAMSEVASLGAKCNSLEM 1403
                                     68889999999999999999999999999999999999999999999999888875 PP

  == domain 9  score: -1.6 bits;  conditional E-value: 0.98
                    Cep57_CLD_2   43 Ayeeln.eLkaevealrkELkeqra 66  
                                     A+ee+n +L+ + + l++E ++ ++
  gene533|gene533|rna532|rna532 1493 ALEEINgQLMKRFDDLQEEHQSLLD 1517
                                     3444333788888888888444433 PP

  == domain 10  score: 5.1 bits;  conditional E-value: 0.0078
                    Cep57_CLD_2   47 lneLkaevealrkELkeq 64  
                                     + +L++eve+lr+E +e+
  gene533|gene533|rna532|rna532 1616 NKKLRDEVERLRGEIDES 1633
                                     689***********9987 PP

  == domain 11  score: -2.4 bits;  conditional E-value: 1.8
                    Cep57_CLD_2   39 qLgvAyeelneLkaevealr 58  
                                     +Lg  ++ +n L++e+e  r
  gene533|gene533|rna532|rna532 1643 KLGCQLLAVNRLSRELEEER 1662
                                     56666666666666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05     0.053       4      29 ..     168     193 ..     165     212 .. 0.89
   2 ?   -3.4   0.0       3.6   1.1e+04      76     117 ..     388     431 ..     366     441 .. 0.70
   3 ?   -2.1   0.1       1.5   4.4e+03      44      86 ..     795     839 ..     768     855 .. 0.67
   4 ?   -2.8   0.1       2.3   6.9e+03      35      70 ..    1011    1052 ..     997    1089 .. 0.59
   5 ?   -3.3   0.0       3.5     1e+04      38      88 ..    1574    1625 ..    1555    1631 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleql 29 
                                    + +++++tGesG+GKT   +r++e l
  gene533|gene533|rna532|rna532 168 ENQSILITGESGAGKTENTKRVVEFL 193
                                    6789******************9987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
                         AAA_22  76 eellealeqalrarav..ielliiDEaqh.lrseealeeLrslln 117
                                    + +++a ++++ + +   ++l i+D   + l  ++++ ++ ++ n
  gene533|gene533|rna532|rna532 388 HPMIKAGNEYVAHSRNkeQALKIVDGLARiL-YDKMFDNVIDRIN 431
                                    4455666677777766788999999999966.7888888887777 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.5
                         AAA_22  44 fvtlpsst.sskdllrellralglelka.erlsseellealeqal 86 
                                    ++++  +  ++ +l++++   l++++ + e +++e++++   + l
  gene533|gene533|rna532|rna532 795 RICCELQRwNWWKLYQKIKPLLDVRKRDsEMKEKEAMIQEYIRML 839
                                    455555556688999999999999888855555555555444444 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.3
                         AAA_22   35 aee..erpevv....fvtlpsstsskdllrellralglelka 70  
                                      ++  +++e +    + ++ s +++kd + el +++++ + +
  gene533|gene533|rna532|rna532 1011 RRRelKEKEMIidelKANCISMKKWKDECGELRKDYEVMQRK 1052
                                     444553333333555667777777777777777776665555 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 3.5
                         AAA_22   38 erpevvfvtlpsstsskdllrellralglelkaerlsseell.ealeqalra 88  
                                     er++ v +t+ +++ ++  ++++  + +l + + +++s+  + ++l++ +++
  gene533|gene533|rna532|rna532 1574 ERSPSVIYTCDKEKYQALDRKRMIAEHELAKAKDEKKSQMAInKKLRDEVER 1625
                                     6777788888888855555666666666666663444444444555555554 PP

>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0001       0.3      12      32 ..     982    1003 ..     980    1004 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                         Get5_C   12 LLknkfkn.daearavleRLqK 32  
                                     LLk+k+k+ d e++++leR++K
  gene533|gene533|rna532|rna532  982 LLKEKIKEkDCEVKNILERMKK 1003
                                     9*******88***********9 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.036   1.1e+02       1      22 [.     172     193 ..     172     208 .. 0.83
   2 ?    5.4   0.0    0.0076        23      18      82 ..     536     598 ..     530     611 .. 0.77
   3 ?   -1.9   0.0       1.4   4.3e+03      40      79 ..     802     841 ..     780     845 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.036
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakal 22 
                                    i+++G+sg GK+  +k++++ l
  gene533|gene533|rna532|rna532 172 ILITGESGAGKTENTKRVVEFL 193
                                    689**********999966544 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0076
                   RNA_helicase  18 Lakallkklklkkkdsvysrnpeddfw.dgYtgqevvvidDfgqvkdeenpsdlaelirlvsstpy 82 
                                    + ++l+k++   +++++ + + +d f+ + Y g     +dD+ +++++++ + l+ lir+ +s ++
  gene533|gene533|rna532|rna532 536 FLRKLMKNI---RHEKFEVDKIKDAFVlNHYAGDVEYTVDDWLSKNKDSHSEALTSLIRMSNSETV 598
                                    445555444...6677777666666655*************999998856669*********9876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.4
                   RNA_helicase  40 eddfwdgYtgqevvvidDfgqvkdee.nps.dlaelirlvss 79 
                                    + ++w+ Y+  ++    D+ ++ +e+ +++ +++e ir+ + 
  gene533|gene533|rna532|rna532 802 RWNWWKLYQ--KIKPLLDVRKRDSEMkEKEaMIQEYIRMLDA 841
                                    456666665..6777778888888877777799999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2974  (0.165877); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                       175  (0.00976072); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 2.46u 0.39s 00:00:02.85 Elapsed: 00:00:00.72
# Mc/sec: 7064.64
//
Query:       gene534|gene534|rna533|rna533  [L=137]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 934.54
//
Query:       gene535|gene535|rna534|rna534  [L=85]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-12   46.0   5.3    3.7e-12   45.8   5.3    1.1  1  Ribosomal_S27e  Ribosomal protein S27
  ------ inclusion threshold ------
      0.017   15.2   0.5      0.017   15.2   0.5    2.0  2  DUF2752         Protein of unknown function (DUF2752)


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   5.3   4.1e-16   3.7e-12       2      53 ..      27      78 ..      26      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.1e-16
                                   S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEE CS
                 Ribosomal_S27e  2 rskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqiler 53
                                   +++F+ v+C +C ++t  +sh++t + C  Cg ++ +  GG+a ++ ++ + 
  gene535|gene535|rna534|rna534 27 NGFFMYVRCGGCRHTTCCYSHSQTNISCPGCGDIILTSSGGRAVVSPNCEFK 78
                                   789**********************************************996 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.8      0.14   1.3e+03      10      21 ..      34      45 ..      30      47 .. 0.76
   2 ?   15.2   0.5   1.8e-06     0.017       1      15 [.      44      58 ..      44      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.14
                        DUF2752 10 pCPGCGltRavh 21
                                    C GC  t++++
  gene535|gene535|rna534|rna534 34 RCGGCRHTTCCY 45
                                   688998888776 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.8e-06
                        DUF2752  1 CpfkaltGipCPGCG 15
                                   C  ++ t+i+CPGCG
  gene535|gene535|rna534|rna534 44 CYSHSQTNISCPGCG 58
                                   9999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 562.82
//
Query:       gene536|gene536|rna535|rna535  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.8e-36  124.4   0.8    5.9e-36  124.1   0.8    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.12   13.2   0.0       0.23   12.2   0.0    1.5  1  RraB        Regulator of ribonuclease activity B


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   0.8   6.6e-40   5.9e-36       3     259 ..      35     274 ..      34     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 6.6e-40
                                    HHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   3 divkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaeklia 82 
                                    ++vk+ +G + ++K++vn +g+v ++++  +i  +++++hP++kll++ ++++d  vGDG t+ v+L++eL++e+ ++i 
  gene536|gene536|rna535|rna535  35 NLVKSLYGRSHRTKLIVNGYGQVLLSSQPGVIYDNIKMNHPLVKLLQDYVKKMD-VVGDGATFFVVLVSELIQETIDIIG 113
                                    68999999999******************************************8.5************************ PP

                                    CTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCSEECSC CS
                     Cpn60_TCP1  83 agvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieenekeldl 162
                                    +g++pt +   +++  +++ +  k   ve+ ++ +dre++ kv r +l+         +l k+v + ++l+    ++++ 
  gene536|gene536|rna535|rna535 114 KGMKPTYLSHMLREVHKEVEDLTKGLRVEHIIRFEDRESISKVLRGILKDS-------NLEKMVSEGISLT----RSFNS 182
                                    **************999999999999999999999*************988.......899*******555....58*** PP

                                    CCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHH CS
                     Cpn60_TCP1 163 grikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqle 242
                                    ++i+v+k+  gs+eds +v+G+v+++++ ++   k++ + k  +++++L+i +te k+tv +++a+el +++k+e+k ++
  gene536|gene536|rna535|rna535 183 ENIRVCKVACGSVEDSYVVQGMVFNRSPEGE--VKHVLKGKTSIYNCPLDISRTELKGTVLMRTASELLSFSKDENKRTK 260
                                    *******************************..9*******************************************999 PP

                                    HHHHHHHHTTECEEEES CS
                     Cpn60_TCP1 243 ellekiiksgvnvvvcq 259
                                    + +e++   + +vv+c 
  gene536|gene536|rna535|rna535 261 KAVESM---DGDVVICS 274
                                    998864...55555554 PP

>> RraB  Regulator of ribonuclease activity B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.5e-05      0.23       6      41 ..     123     158 ..     120     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                           RraB   6 evldalledGddldkpreiehhfyfedeedlekfae 41 
                                     +l++ +++ +dl+k +++eh + fed+e + k++ 
  gene536|gene536|rna535|rna535 123 HMLREVHKEVEDLTKGLRVEHIIRFEDRESISKVLR 158
                                    5899*************************9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1835.02
//
Query:       gene537|gene537|rna536|rna536  [L=212]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-18   66.1   0.3    6.2e-17   61.4   0.1    2.0  2  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.1   3.5e-21   6.2e-17     263     404 ..       6     148 ..       1     156 [. 0.84
   2 !    3.3   0.0    0.0014        26     456     485 ..     160     189 ..     154     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 3.5e-21
                                    -HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEE.EECCETTCCEEEEECESSSSXEEEEE CS
                     Cpn60_TCP1 263 ddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkv.eeekigsekttiieevksgkiatill 341
                                    d++ l+fl+k++ l+ r ++k dl+r+ +++G++++ssl++ ++e++G +++v + ++   e+t +i++  s+k+ t++l
  gene537|gene537|rna536|rna536   6 DKIYLDFLNKSRKLVFRITSKYDLRRIRELLGGHILSSLGSQSEESMGFVEEVvTFTEGICEYTKFISG--SKKVYTLVL 83 
                                    67789************************************************4444444466666888..********* PP

                                    EESTCCCHHHHHHHHHHHHHHHHHHHHHHEE..EETTTCHHHHHHHHHHCCCCTSXCCHHHHHHH CS
                     Cpn60_TCP1 342 rgatdtvldeieraiedAlnvvknaiedekv..vpGGGatelelakklkeyaksvsgeeqlaiea 404
                                    +++ + +lde er ++ Alnv+++ ++++k+  v G+G +e +l+k   e +   ++ + l++++
  gene537|gene537|rna536|rna536  84 KNSVQAELDEQERMVQKALNVLSKNTKENKIdlVDGAGRFEKRLSKIFLERSAASKEGKGLVYKC 148
                                    **********************999998985559***********97555555555555555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0014
                                    CCTXEEEHHHHHHHHHHHHHHHHHHHCEEE CS
                     Cpn60_TCP1 456 eagvvDplkvkrqalksAteaastiLride 485
                                    +a ++D ++ k +alk + e  st+ ++++
  gene537|gene537|rna536|rna536 160 DAEIYDVYNSKVKALKYSIEFISTLFETSD 189
                                    689*******************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      741  (0.0413297); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1336.76
//
Query:       gene538|gene538|rna537|rna537  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-16   59.7   0.1    3.4e-16   58.8   0.1    1.5  1  Homeodomain  Homeodomain
  ------ inclusion threshold ------
      0.016   15.0   0.6      0.018   14.8   0.6    1.1  1  Use1         Membrane fusion protein Use1


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.1   3.8e-20   3.4e-16       1      56 [.      35      90 ..      35      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 3.8e-20
                                   ST-SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    Homeodomain  1 rrkRttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56
                                   +r+R  ++ +q+++Le+ F+ +++p++ ++  LA+ l ++ +++++WFqNrRakek
  gene538|gene538|rna537|rna537 35 KRSRLKLSGHQIDILESNFKIDSHPNSTTKSLLANTLSIPFKNIQIWFQNRRAKEK 90
                                   799****************************************************9 PP

>> Use1  Membrane fusion protein Use1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.6     2e-06     0.018      22      90 ..       8      86 ..       2     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-06
                           Use1 22 senewrLekyvkaleemleeLkkesskpskevlkeYsekveaLkllleaeklssteekalanqllapg...........e 90
                                   +++e ++ k++ ++ee ++ L+k +s  +  +lk    +++ L++  + ++  +++ k l  + l+             +
  gene538|gene538|rna537|rna537  8 NKDEKKVVKFIDSTEEIIKHLNKTDS-NKRSRLKLSGHQIDILESNFKIDSHPNSTTKSLLANTLSIPfkniqiwfqnrR 86
                                   45589******************998.888899999999999*9999998877666666555555444355555544321 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 871.84
//
Query:       gene539|gene539|rna538|rna538  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0001   21.3   0.2     0.0036   16.2   0.1    2.6  3  RNA_pol_I_A49  A49-like RNA polymerase I associated factor


Domain annotation for each model (and alignments):
>> RNA_pol_I_A49  A49-like RNA polymerase I associated factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0     0.035   6.2e+02      17      41 ..      16      40 ..       9      55 .. 0.83
   2 !    2.3   0.0    0.0034        61     158     194 ..     118     154 ..     107     191 .. 0.71
   3 !   16.2   0.1     2e-07    0.0036     271     348 ..     192     267 ..     164     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.035
                                   E-----EEEEEE-SSEEEEEE--HH CS
                  RNA_pol_I_A49 17 krkkselllvgeterleYvgknege 41
                                   ++ + +  l+g+ e +eY+g++ ++
  gene539|gene539|rna538|rna538 16 SKVNGRVFLKGDFEGIEYKGSEWNS 40
                                   55678999*************9976 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0034
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  RNA_pol_I_A49 158 ssrplPpanldAtepedVYplsdlissaelealevka 194
                                    ++++lPp++ +A+ p++   l+ + ++++l++ e+ +
  gene539|gene539|rna538|rna538 118 KDQILPPMDEEAECPKKRFVLERMFPKEVLSSFEEIK 154
                                    4689************************998755433 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 2e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  RNA_pol_I_A49 271 svpeiiidkllrkFteessnnkgkskrlskshkdkLlayilalaLhldnfsvdltdLaedLklkpkklnelfkelGck 348
                                     +++ + d+  + F+   +n+  ++k+l++  +dkL+  + +l L +++fsv+ + L  d+k ++kk+ ++ + +Gc 
  gene539|gene539|rna538|rna538 192 ITNDCLNDSGYSSFFAVIENE-VENKMLTPLCRDKLAILCYILFLQIQGFSVKYEVLP-DFKFSKKKVISMHRLIGCL 267
                                    566666666677777776644.44456***************************9995.9*****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1880.47
//
Query:       gene540|gene540|rna539|rna539  [L=182]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.7   0.0      0.074   12.8   0.0    1.5  1  DUF4423   Domain of unknown function (DUF4423)


Domain annotation for each model (and alignments):
>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-06     0.074      38      81 ..       7      50 ..       1      68 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-06
                        DUF4423 38 dpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqtek 81
                                   +++ +++  ++ i++eeve++l+  ++++++++de gk+++ e+
  gene540|gene540|rna539|rna539  7 EMRLIERYGTGVIPKEEVESILNEAVESNVIERDEIGKWEKEEE 50
                                   566677777789****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1342.54
//
Query:       gene54|gene54|rna54|rna54  [L=335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-09   37.5  12.9    4.8e-09   36.4  12.9    1.6  1  zf-RING_2     Ring finger domain
    2.4e-05   24.5  16.2    0.00031   21.0  16.2    2.4  1  zf-rbx1       RING-H2 zinc finger domain
    3.2e-05   23.8   7.2    3.9e-05   23.6   4.2    2.4  2  zf-RING_UBOX  RING-type zinc-finger
    0.00022   21.0  13.9     0.0005   19.9  13.9    1.7  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    0.00032   20.5  13.9    0.00071   19.4  13.9    1.7  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
     0.0013   18.5   7.0     0.0013   18.5   7.0    2.4  2  zf-RING_11    RING-like zinc finger
     0.0025   17.7   9.5      0.005   16.7   9.5    1.5  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.021   14.9   9.3      0.074   13.1   9.3    1.9  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
      0.052   13.5  13.9      0.069   13.1  13.1    1.7  1  zf-RING_5     zinc-RING finger domain
       0.19   11.9  13.2        0.2   11.8  10.5    2.4  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING
        2.2    8.2  13.3          2    8.4  11.6    1.8  2  Prok-RING_4   Prokaryotic RING finger family 4
          4    7.5   9.3         13    5.9   8.2    2.0  1  TerY_C        TerY-C metal binding domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4  12.9   3.2e-12   4.8e-09       3      44 .]     269     307 ..     267     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.2e-12
                  zf-RING_2   3 CpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44 
                                C+IC ++++ ++++    CgH+fh eCl+ w+++++tCP+C+
  gene54|gene54|rna54|rna54 269 CAICRDDMEIGKKLA---CGHCFHIECLKMWCERQQTCPICK 307
                                ********9999988...***********************7 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  16.2   2.1e-07   0.00031      31      55 .]     283     307 ..     267     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.1e-07
                    zf-rbx1  31 eCgHaFHlhCiskWlktrkvCPlcr 55 
                                +CgH+FH +C++ W +++++CP+c+
  gene54|gene54|rna54|rna54 283 ACGHCFHIECLKMWCERQQTCPICK 307
                                7***********************6 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   4.2   2.6e-08   3.9e-05       1      39 []     269     304 ..     269     304 .. 0.88
   2 ?    3.5   0.2      0.05        74       1       8 [.     303     310 ..     303     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.6e-08
               zf-RING_UBOX   1 CpIClelftdPlvlpCGHtFCreClwelskslegafkCP 39 
                                C IC+++++  ++l CGH+F+ eCl   + + e++ +CP
  gene54|gene54|rna54|rna54 269 CAICRDDMEIGKKLACGHCFHIECL---KMWCERQQTCP 304
                                ********7444578**********...89999999999 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.05
               zf-RING_UBOX   1 CpIClelf 8  
                                CpIC++++
  gene54|gene54|rna54|rna54 303 CPICKSTL 310
                                *****876 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9  13.9   3.3e-07    0.0005       1      41 []     269     306 ..     269     306 .. 0.98

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-07
                                -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                   zf-C3HC4   1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41 
                                C+iC + +++ +  l C+H f+ +C++ + +  ++++CP+C
  gene54|gene54|rna54|rna54 269 CAICRDDMEIGK-KLACGHCFHIECLKMWCE--RQQTCPIC 306
                                ************.******************..8899**** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4  13.9   4.8e-07   0.00071       2      40 .]     269     306 ..     268     306 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.8e-07
                 zf-C3HC4_2   2 CpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40 
                                C+iC d ++ +    +CgH f+ +C++ + e+++ CP+C
  gene54|gene54|rna54|rna54 269 CAICRDDMEIG-KKLACGHCFHIECLKMWCERQQTCPIC 306
                                *********99.8889*********************** PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   7.0   8.5e-07    0.0013       2      29 .]     269     293 ..     269     293 .. 0.96
   2 ?   -1.7   0.2       1.7   2.5e+03       2       8 ..     303     309 ..     303     313 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.5e-07
                 zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                C+IC ++++ g++l    C+H+FH +C+
  gene54|gene54|rna54|rna54 269 CAICRDDMEIGKKL---ACGHCFHIECL 293
                                ***********999...9*********6 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                 zf-RING_11   2 CsICLee 8  
                                C IC ++
  gene54|gene54|rna54|rna54 303 CPICKST 309
                                9***765 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   9.5   3.3e-06     0.005       3      45 ..     267     308 ..     265     311 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.3e-06
                                SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT-- CS
                 zf-C3HC4_3   3 eeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCrr 45 
                                  C iC +  +    l CgH+ +  eC++ + +r+++CpiC++
  gene54|gene54|rna54|rna54 267 GFCAICRDDMEIGKKLACGHC-FHIECLKMWCERQQTCPICKS 308
                                67******9777777777777.777****************97 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   9.3   4.9e-05     0.074      33      83 ..     267     312 ..     242     314 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                                S--TTCSTTTTTS-EEEBT.TS-EEEHHHHHHHHHHHSTSSB-TTTSSB--B CS
                 zf-ANAPC11  33 GtcpsckfpGddcplvlGk.ckhnfhlhcilkwletetskglcpmcrqtfkl 83 
                                G c  c+   dd  +     c h+fh  c+  w e+   ++ cp+c+ t+ +
  gene54|gene54|rna54|rna54 267 GFCAICR---DDMEIGKKLaCGHCFHIECLKMWCER---QQTCPICKSTLAF 312
                                4454444...6666544436*************987...578****998876 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  13.1   4.6e-05     0.069       2      43 ..     269     307 ..     268     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.6e-05
                  zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43 
                                C +C++ +   e    ++CgH f+ +Clk   e++++CpiC+
  gene54|gene54|rna54|rna54 269 CAICRDDM---EIGKKLACGHCFHIECLKMWCERQQTCPICK 307
                                99999999...889999************9999********8 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.7e+03      20      28 ..     150     158 ..     147     161 .. 0.81
   2 ?   11.8  10.5   0.00013       0.2       1      42 []     269     306 ..     269     308 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                 zf-C3HC4_4  20 fClsCissl 28 
                                f lsCiss+
  gene54|gene54|rna54|rna54 150 FTLSCISSI 158
                                7899**986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                 zf-C3HC4_4   1 CPiCldYLekPvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                C iC+d +e    l+CGh f ++C++ +++ ++    +Cp C
  gene54|gene54|rna54|rna54 269 CAICRDDMEIGKKLACGHCFHIECLKMWCERQQ----TCPIC 306
                                99************************9999884....59999 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.6   8.9e+02      23      39 ..     259     275 ..     253     281 .. 0.75
   2 ?    8.4  11.6    0.0013         2       1      40 [.     269     310 ..     269     315 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.6
                Prok-RING_4  23 eCfdskdlssCPlCqrr 39 
                                +C +++    C +C+  
  gene54|gene54|rna54|rna54 259 KCVEGSGDGFCAICRDD 275
                                57777777789999865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0013
                Prok-RING_4   1 CvlCgeqekkailepCgHlvCkeCfdsk..dlssCPlCqrri 40 
                                C +C+   +      CgH +  eC++ +    ++CP+C++ +
  gene54|gene54|rna54|rna54 269 CAICRDDMEIGKKLACGHCFHIECLKMWceRQQTCPICKSTL 310
                                8888888444444567777777777777544458****9876 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   8.2    0.0088        13      73     122 ..     265     319 ..     255     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0088
                     TerY_C  73 GapgCPhCgnala....favCeCgkllCidg..eeeatCpwCgkevkfgeaseegf 122
                                G + C  C + +     +a  +C ++ C++   e ++tCp C+++++f+   +e+f
  gene54|gene54|rna54|rna54 265 GDGFCAICRDDMEigkkLACGHCFHIECLKMwcERQQTCPICKSTLAFD-VRKESF 319
                                666788888776511225667899999998766999************9.555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2083.99
//
Query:       gene541|gene541|rna540|rna540  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-29  103.6   0.0    1.2e-29  103.3   0.0    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
      9e-12   45.4   0.0    1.1e-11   45.1   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.028   13.9   0.0      0.043   13.3   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0     2e-33   1.2e-29       2     168 ..       4     167 ..       3     169 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 2e-33
                                    EEEEESS-...TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                Glycos_transf_2   2 vviptyNe...ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                    v+iptyNe    k ll+++  + +  + + f+iivvDD+S+D+t+ ++e+   + p+v+++ r+++ G+++a++++l ++
  gene541|gene541|rna540|rna540   4 VIIPTYNErenIKVLLRMVSDVMKE-EGKPFKIIVVDDNSPDGTRVVVESM--GLPNVCLLSRKKKLGLGSAYRTALGHC 80 
                                    9*******88888888888888888.*************************..69************************* PP

                                    -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCC CS
                Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsa 158
                                       + +++D D+ +dp +++ ++e   k ga +v+g+r++ +g+ + ++  ++    + + +   + +l++n+s+++gs+
  gene541|gene541|rna540|rna540  81 EYPFTIVMDGDLSHDPMYIKTMIELQRK-GAEIVVGSRYAEGGGVYGWSMKRK--IISLGANNLARTFLNINVSDVTGSF 157
                                    ****************************.********************9997..7************************ PP

                                    CEEEEHHHHH CS
                Glycos_transf_2 159 allrrealee 168
                                    +l++ ea++ 
  gene541|gene541|rna540|rna540 158 RLYKTEAFRA 167
                                    ******9975 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.8e-15   1.1e-11       5     199 ..       3     192 ..       1     203 [. 0.80

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.8e-15
                Glyco_tranf_2_3   5 avlVptfneed...vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                     v++pt+ne +   vl++++ ++ + e  +++++vv+d+s ++t+ v+e +   lp+v   ++ ++++lg +++ r    
  gene541|gene541|rna540|rna540   3 NVIIPTYNEREnikVLLRMVSDVMKEEGKPFKIIVVDDNSPDGTRVVVESM--GLPNV--CLLSRKKKLGLGSAYR---T 75 
                                    59*******999999999******9999********************986..88885..788999999*999977...* PP

                Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstl.vsalgal.efaerhlrflaarralgvlt 159
                                    al ++++ +++++D+D   +P ++k +  + +++++++v ++++++ +  + +s+  ++  ++ ++l   ++ + ++v  
  gene541|gene541|rna540|rna540  76 ALGHCEYPFTIVMDGDLSHDPMYIKTMIEL-QRKGAEIVVGSRYAEGGGVYgWSMKRKIiSLGANNL--ARTFLNINVSD 152
                                    **************************9999.5**************877554887655436555555..34447888999 PP

                Glyco_tranf_2_3 160 lnGsgslirrevlkelegldplflltdDyelglrlrragf 199
                                    ++Gs+ l+ +e +++l     +       el   ++r+gf
  gene541|gene541|rna540|rna540 153 VTGSFRLYKTEAFRALVEKSVSTGYSFQMELMCLAKRHGF 192
                                    9999999999999999322222222233444444455666 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.1e-06     0.043      28     116 ..      79     168 ..      63     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-06
                Glyco_transf_21  28 aakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqa.kls.glgfavGks 105
                                      +y+++++ D d   +p y++++ +  ++ ++++V++  ++ +    +  +++ +++ +a+ l++ +l   ++ ++G++
  gene541|gene541|rna540|rna540  79 HCEYPFTIVMDGDLSHDPMYIKTMIELQRK-GAEIVVGSRYAEGGGVYGWSMKRKIISLGANNLARtFLNiNVSDVTGSF 157
                                    478*********************998885.999999999877777655556666665555555553332366889**** PP

                Glyco_transf_21 106 malrreaLeai 116
                                     ++++ea++a+
  gene541|gene541|rna540|rna540 158 RLYKTEAFRAL 168
                                    *****999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1571.81
//
Query:       gene542|gene542|rna541|rna541  [L=622]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.4e-111  373.5   0.0   1.8e-111  373.1   0.0    1.1  1  Topoisom_bac  DNA topoisomerase
    2.3e-15   56.4  28.3    4.3e-08   33.1   8.2    2.9  3  zf-GRF        GRF zinc finger
      3e-06   27.4   0.0    8.3e-06   26.0   0.0    1.8  1  Toprim        Toprim domain
  ------ inclusion threshold ------
       0.14   12.3   0.2         12    6.0   0.0    2.7  2  DUF4513       Domain of unknown function (DUF4513)


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.1   0.0  3.9e-115  1.8e-111       1     412 [.      53     457 ..      53     458 .. 0.93

  Alignments for each domain:
  == domain 1  score: 373.1 bits;  conditional E-value: 3.9e-115
                   Topoisom_bac   1 einenlvdaaeaRrelDwliGinlsrlltk...klkg.kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkke 76 
                                    eine++++a+++R elD++iG +++rl+t+   k+ + kk+ls+G++q+ptL+++veR re+e+Fvpe +w++++++  +
  gene542|gene542|rna541|rna541  53 EINEAEAEAVDVRMELDLRIGSAFTRLQTLslgKVGQeKKILSFGPCQVPTLGFVVERARERESFVPEMFWTLKFKV--R 130
                                    5899**************************777666689***********************************996..4 PP

                   Topoisom_bac  77 kkekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYe 156
                                    +k+ e+++++++++++dk+++  + + l  ++ak++  e ke+ k++plp++t++Lqk++s++++ls +k++++a+ LY+
  gene542|gene542|rna541|rna541 131 NKKLEDEFTWRRGSVFDKNCVIYFHKGLVGEKAKIVLKEMKERIKYRPLPLRTVELQKKCSSYFRLSGHKVMEVAEGLYN 210
                                    44444579********************7778************************************************ PP

                   Topoisom_bac 157 kaglitYpRTdstrlseeaelkailealakkygk.eylefaekllkktkkksvvknkkveaHeAIrPteelpklkelsdd 235
                                    + g+i+YpRT+++++++++++k il++l+k+++  ey+e   +++k +++    kn++ +aH +I+P +e      ls++
  gene542|gene542|rna541|rna541 211 R-GYISYPRTETDVFDKKFDFKYILNKLSKDSKVgEYAERLGRVFKYPRN---GKNND-MAHLPIYPLKEGV---GLSGS 282
                                    7.****************99**********86656777777777776653...45656.*********8865...89999 PP

                   Topoisom_bac 236 ekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeevkvkevel 315
                                    ++++Y++I+rrfl ++++dak  et+++l+v+ e+f++sg +++ek++++vy+++k++++e  ++++  +e+v  +++ +
  gene542|gene542|rna541|rna541 283 DRDIYDFICRRFLGCISEDAKGLETRYELKVGMETFDLSGIRVVEKNYLEVYYYDKWDNKE--VSDFVMEEIV-SGDLHI 359
                                    99********************************************************987..*********9.5889** PP

                   Topoisom_bac 316 eekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTael 394
                                    +e+kT++pk+++ea+Li++m+k+giGt+aT++e+i+k++ergY+ + +++++p  lG+al++++e+f  ++ +p+l+++l
  gene542|gene542|rna541|rna541 360 SEGKTTAPKYLSEAELISLMDKNGIGTDATIHEHIQKIQERGYAIKVGEEIRPLGLGMALIDGYERFgLNVSKPSLRKNL 439
                                    **********************************************99******************************** PP

                   Topoisom_bac 395 eekLdeIaegkadakevl 412
                                    e +L++I++g++d ++v+
  gene542|gene542|rna541|rna541 440 EINLKRISHGEIDGRSVV 457
                                    *************99987 PP

>> zf-GRF  GRF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       1.7   7.7e+03      16      24 ..      10      18 ..       9      18 .. 0.86
   2 !   33.1   8.2   9.5e-12   4.3e-08       2      43 ..     533     572 ..     532     574 .. 0.92
   3 !   32.5   7.7   1.5e-11   6.8e-08       2      42 ..     583     621 ..     582     622 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                         zf-GRF 16 ktgpNkGRk 24
                                   ++g+N GR+
  gene542|gene542|rna541|rna541 10 REGENIGRQ 18
                                   48******7 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 9.5e-12
                         zf-GRF   2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWad 43 
                                     C c  +a++l v+ +g N G++FY C     k+C FF+W++
  gene542|gene542|rna541|rna541 533 ECDCKAEAKVLKVK-KGDNAGKEFYSCGRTP-KSCYFFQWCE 572
                                    5************5.9***********9988.59*******7 PP

  == domain 3  score: 32.5 bits;  conditional E-value: 1.5e-11
                         zf-GRF   2 lCkcgrlavlltvrktgpNkGRkFYkCpkgkekqCgFFkWa 42 
                                     C cg + +ll+++ t  N+GRkFYkC k+  k C FF+W+
  gene542|gene542|rna541|rna541 583 KCFCGFEPQLLVAN-TENNRGRKFYKCKKAY-KPCKFFQWE 621
                                    69***999999997.************9998.59******8 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.9e-09   8.3e-06      66     101 ..       2      37 ..       1      39 [. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.9e-09
                                    EEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEES CS
                         Toprim  66 iilatDpDreGeaiawellevlkellenkigrvefs 101
                                    ++++tD+DreGe+i+ ++++ + +  + +++r++fs
  gene542|gene542|rna541|rna541   2 VVIWTDCDREGENIGRQIRDIVLKVKNVNVKRARFS 37 
                                    89*****************9998555559*****98 PP

>> DUF4513  Domain of unknown function (DUF4513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0026        12      55      79 ..      24      48 ..      20      62 .. 0.91
   2 ?    3.2   0.0      0.02        90      55     113 ..     125     183 ..     111     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0026
                        DUF4513 55 mkfrnvnlkkaevsgiyagpledsl 79
                                   +k +nvn+k+a  sgi    +e++l
  gene542|gene542|rna541|rna541 24 LKVKNVNVKRARFSGITLKDIEEAL 48
                                   799**************99999987 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                        DUF4513  55 mkfrnvnlkkaevsgiyagpledslflnyserlchgedrkvvlkkgpleikiadmplhs 113
                                    +kf+  n k  +      g + d   + y  +   ge+ k+vlk     ik   +pl +
  gene542|gene542|rna541|rna541 125 LKFKVRNKKLEDEFTWRRGSVFDKNCVIYFHKGLVGEKAKIVLKEMKERIKYRPLPLRT 183
                                    44544455555555666777777777777777788****************99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3908.18
//
Query:       gene543|gene543|rna542|rna542  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   12.0   0.2      0.088   11.9   0.2    1.1  1  DUF444    Protein of unknown function (DUF444)


Domain annotation for each model (and alignments):
>> DUF444  Protein of unknown function (DUF444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   4.9e-06     0.088     201     249 ..      38      85 ..       8      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-06
                         DUF444 201 keseeleeleeeieeleerikripfidelDlRYrrvekepkpesnaVmf 249
                                     + ++++  +e++e+le++ k ip++  lD++++++++++++++++V++
  gene543|gene543|rna542|rna542  38 VNVKDIMMYAENMEKLESK-KLIPYVVYLDEQFKEIVQKRRKDAKVVLI 85 
                                    3444666677777777665.78*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1234  (0.068827); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 674.18
//
Query:       gene544|gene544|rna543|rna543  [L=341]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-30  106.4   1.6      3e-24   85.4   0.3    3.6  2  Actin     Actin
    2.2e-05   23.4   4.1    5.4e-05   22.2   4.1    1.5  1  MreB_Mbl  MreB/Mbl protein
  ------ inclusion threshold ------
      0.087   11.7   0.2       0.13   11.1   0.2    1.3  1  EutA      Ethanolamine utilisation protein EutA


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   5.4e-06     0.032       3      35 ..       6      38 ..       4      55 .. 0.86
   2 !   85.4   0.3     5e-28     3e-24      93     405 ..      68     332 ..      41     335 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.4e-06
                          Actin  3 evsavVlDnGssttraGyagedaPkavipslvg 35
                                   +v++ V+D Gs+t+++Gy++   P++ ++s+  
  gene544|gene544|rna543|rna543  6 DVTTGVVDIGSETVKIGYSDGLLPTVFCSSMTW 38
                                   57788********************99998765 PP

  == domain 2  score: 85.4 bits;  conditional E-value: 5e-28
                          Actin  93 eehpllltepplnppkqrekalEivfEkfkvpalylaksavlsafasgkstglvvDsGasvtsvvpVldGyvLkkairrs 172
                                    + ++l+++e++++    ++++l  ++E   ++++ +++s +l af++gk+tg+vv++G +++ ++ V+dG++     r+ 
  gene544|gene544|rna543|rna543  68 DAQSLVISENTMEAGGVKKEILGYLMEGRLCESVLFVRSGILDAFSYGKTTGVVVNLGGGSSQICSVVDGLITC--RRQI 145
                                    5679******************************************************************8865..5899 PP

                          Actin 173 dlgGkaLteqlkellssknvevtprylikkkkvveaessaekeelekltesyktleeeevleeiKesvcevsedpegdee 252
                                    d+gG +Lt +++++l+s   ++                    ++ e+l e   ++e++e  +++Kesv++ +        
  gene544|gene544|rna543|rna543 146 DVGGMDLTLEFMRILESFGSDLGKFID--------------VKNGETLYERRVEFEKKEFSRHVKESVLRLR-------- 203
                                    *****************6444422222..............2333344455556677777777777777764........ PP

                          Actin 253 ksssspeksYeLPDgseiklgeeRfkvpEiLFdpsligsesaleeekskllgiselivaainacdvdlrpeLlanivvtG 332
                                      s++++  Y+LPDg+ei+ +e   k+         ++ +         l g+ ++iv+ i+   +++r+ L  ni+v G
  gene544|gene544|rna543|rna543 204 --SEEANGRYVLPDGKEIDAEEY-CKA---------MEIK---------LGGVIKMIVEVIESNGMEIRSVLSGNILVGG 262
                                    ..4456789********997653.233.........2333.........45***************************** PP

                          Actin 333 GnsllpglteRlekelaqlaskgvkvkiiapeeerkysaWiGGSiLAslgtfqqlwvskqEYeEqGssvverk 405
                                    G   + g+ + +  e+ +      kvk+  +    ++s++ GG + +s+g+++++ +  ++YeE+G+s+ +rk
  gene544|gene544|rna543|rna543 263 GCGGIGGIDSFICDEIGK-ERGRWKVKVSVER--SRFSTFQGGCVIGSMGSARSFHIGVRDYEEYGESILDRK 332
                                    ******************.7777888888776..89*********************************9987 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   4.1     9e-09   5.4e-05     146     298 ..     118     279 ..     114     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9e-09
                                    -EEEEEE-SS-EEEEEEETTEEEEEEEES-SHHHHH...........HHHHHHHHHHHSEE--HHHHHHHHHHH-BSS-- CS
                       MreB_Mbl 146 gnmvvdiGggttevavislggivtsksvrvaGdeld...........eaiikyirkkynlliGertaekikieigsavke 214
                                      +vv++Ggg++++  +  g i+  +++ v+G +l            +++ k+i  k   ++ er +e  k+e +  vke
  gene544|gene544|rna543|rna543 118 TGVVVNLGGGSSQICSVVDGLITCRRQIDVGGMDLTlefmrilesfgSDLGKFIDVKNGETLYERRVEFEKKEFSRHVKE 197
                                    5689****************************776511111111111455567777777778888888889999999988 PP

                                    HHHH..EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHH CS
                       MreB_Mbl 215 eeee..kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkl 292
                                    +  +  + e +Gr +   lp   e+++ee  +a++ ++  +++++ ev+e+   e+ + ++   i++ GG++ + g+d++
  gene544|gene544|rna543|rna543 198 SVLRlrSEEANGRYV---LPDGKEIDAEEYCKAMEIKLGGVIKMIVEVIESNGMEIRS-VLSGNILVGGGCGGIGGIDSF 273
                                    877666888999975...8************************************976.7778899************** PP

                                    HHHHHS CS
                       MreB_Mbl 293 lseetg 298
                                    + +e+g
  gene544|gene544|rna543|rna543 274 ICDEIG 279
                                    *99986 PP

>> EutA  Ethanolamine utilisation protein EutA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   2.1e-05      0.13     124     269 ..      99     240 ..      94     260 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.1e-05
                           EutA 124 EsiiagkGagaaalskekstrvlniDiGGGtsnlalfkeGevidtacldvGGrlikidkdtkkityispklkkiieelgl 203
                                    Es++  +    +a+s  k+t v+ +++GGG s +  + +G +++   +dvGG  + ++   + +++    l k i+ ++ 
  gene544|gene544|rna543|rna543  99 ESVLFVRSGILDAFSYGKTTGVV-VNLGGGSSQICSVVDGLITCRRQIDVGGMDLTLEF-MRILESFGSDLGKFIDVKNG 176
                                    56666666666778888877766.789*************************9999997.55555556666665555555 PP

                           EutA 204 elevgeklekeelkkiveemaellvevvgl.kkesel.aelllttkslkekkeievvtls.GGvadliy 269
                                    e     +l +++++   +e+++ ++e+v   ++e+ +    l  +k++ +++ ++++ +  GGv ++i 
  gene544|gene544|rna543|rna543 177 E-----TLYERRVEFEKKEFSRHVKESVLRlRSEEANgRYVLPDGKEIDAEEYCKAMEIKlGGVIKMIV 240
                                    4.....444444444455566666655543032222203334455666666666665553366666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2318.12
//
Query:       gene545|gene545|rna544|rna544  [L=470]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-41  142.1   0.1    1.9e-41  141.8   0.1    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    8.1e-12   45.4   0.1    2.1e-11   44.1   0.1    1.7  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
      6e-05   22.5   1.2       0.29   10.4   0.2    2.6  2  Gtr1_RagA    Gtr1/RagA G protein conserved region
     0.0002   21.7   2.8    0.00029   21.2   0.3    2.6  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00037   20.5   0.6     0.0021   18.1   0.4    2.4  2  MMR_HSR1     50S ribosome-binding GTPase
     0.0012   18.7   0.2        1.8    8.5   0.1    2.5  2  RsgA_GTPase  RsgA GTPase
     0.0027   17.5   0.9     0.0064   16.3   0.9    1.6  1  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0041   17.0   0.8      0.019   14.9   0.3    2.4  2  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.063   12.6   0.1       0.13   11.5   0.1    1.5  1  Septin       Septin
       0.11   12.0   0.4       0.78    9.2   0.4    2.3  1  SRPRB        Signal recognition particle receptor beta subuni
       0.12   11.5   0.0       0.87    8.7   0.0    2.0  2  G-alpha      G-protein alpha subunit


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.8   0.1   1.2e-44   1.9e-41       3     182 ..      12     204 ..      10     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 141.8 bits;  conditional E-value: 1.2e-44
                                    EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHST............HCHSHHHHHHTSCSSCEEEEEETTCSS CS
                       GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeerv............lDtlkeErergiTiksaaisleketkk 69 
                                     +n+++ighvD+GK+T+++ L ++ g i+k++ ++ e+e++            +D++++Er+rgiTi+++ ++l   t+k
  gene545|gene545|rna544|rna544  12 RLNVCFIGHVDSGKSTTVGMLSHQMGVIDKRELEKyEKEAAmnnkdtfylaylTDKTEAERKRGITITTTLVTLP--TEK 89 
                                    68*****************************999963333369999*****************************..*** PP

                                    EEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETT.....TBSTHHHHHHHHHHHHTTTE.EEEEEESCGST.HHHHHHH CS
                       GTP_EFTU  70 ylinliDtPGHvdFskevirglrvlDgavlvvdav.....eGvepqteevlrlalkegvp.iivfiNKmDrl.kaelkei 142
                                    +++n++D+PGH+dF+k++ +g++++D+av++v a+      Gv    ++++ +   +g++ +i+++NKmD++ +++ ke 
  gene545|gene545|rna544|rna544  90 FNVNILDCPGHKDFVKNMVTGASQADVAVVIVPASgfescIGVGGMLKTHIMISGILGCEkLIICVNKMDMIsEDKRKEK 169
                                    **********************************98877778*****************99***********95555555 PP

                                    HHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH CS
                       GTP_EFTU 143 veevkqklsrkeeklekygekgekevpvvfgSalkgegvk 182
                                     +ev++++    + ++  + ++  +  ++++S+l g +++
  gene545|gene545|rna544|rna544 170 FKEVSDEM---LRIVTRSHKDK--NPIILPISGLMGLNLT 204
                                    55555555...22233333332..4567788888888776 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   1.3e-14   2.1e-11      10     110 ..     345     440 ..     338     441 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.3e-14
                                    EEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE--TTTHC CS
                    GTP_EFTU_D3  10 AqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpialekgseyp 89 
                                     +++++ek  ++ +  gY+p++ +      ++v+++lsk+ kk++++   +pe + +G++ i  v  +kp++++k++ ++
  gene545|gene545|rna544|rna544 345 VKIIVVEK--PNGMEVGYTPQINFGICRSPARVAKILSKVVKKKGHE---NPEKIINGEAFIGIVVFQKPLVIDKMERFQ 419
                                    35666666..**************************99999888877...9***************************** PP

                                    CCCEEEEECTTCEEEEEEEEE CS
                    GTP_EFTU_D3  90 qlGrFaiReggrTvaaGvvte 110
                                    +l +Fa+ + +  va+G v+e
  gene545|gene545|rna544|rna544 420 NLSKFALMDSNGVVAIGNVME 440
                                    *****************9975 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00021      0.34      33      68 ..      76     110 ..      14     122 .. 0.64
   2 !   10.4   0.2   0.00018      0.29     113     146 ..     150     183 ..     137     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                      Gtr1_RagA  33 atidveksevrflgnltlnlwDcgGqeafveeylss 68 
                                    +ti ++  ++  +++ ++n++Dc+G ++fv+++++ 
  gene545|gene545|rna544|rna544  76 ITITTTLVTL-PTEKFNVNILDCPGHKDFVKNMVTG 110
                                    3334444444.367899***************8764 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                      Gtr1_RagA 113 kvfvlihKmDliqedereeifeerkeeireeiek 146
                                    k+ + ++KmD+i+ed+r+e f+e ++e+ + +++
  gene545|gene545|rna544|rna544 150 KLIICVNKMDMISEDKRKEKFKEVSDEMLRIVTR 183
                                    567889*****************99999887664 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.8   4.5e+03      22      43 ..      18      37 ..      14      53 .. 0.73
   2 !   21.2   0.3   1.8e-07   0.00029       1      63 [.     260     317 ..     260     330 .. 0.84
   3 ?   -3.7   0.0       9.9   1.6e+04      45      58 ..     336     349 ..     331     354 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.8
                                   EC.TCTTSEEEEEEEEEEEEETE CS
                    GTP_EFTU_D2 22 lg.ndtskkeivtrissletfhe 43
                                   +g +d++k+   t+++ l   ++
  gene545|gene545|rna544|rna544 18 IGhVDSGKS---TTVGMLSHQMG 37
                                   466899999...99998888777 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.8e-07
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSC CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgl 63 
                                    G + +grv+ Gt+ ++ ++ i  ++    + v++i+s+e ++++     +g+n+Gv +++  +
  gene545|gene545|rna544|rna544 260 GKIFTGRVEYGTITPNLKISI--QPA---GVVGEIRSVEIHNKPRSMIPCGENCGVALKGGVT 317
                                    7889*****************..554...467**************************98644 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.9
                                    ESEEETTSEEEEEE CS
                    GTP_EFTU_D2  45 edeavaganaGviv 58 
                                    + +a++ga + +iv
  gene545|gene545|rna544|rna544 336 KAIAYPGAKVKIIV 349
                                    44556666666665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   1.3e-06    0.0021       1      87 [.      14     128 ..      14     193 .. 0.74
   2 ?   -3.8   0.0       8.2   1.3e+04      46      58 ..     422     434 ..     412     455 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
                                    EEEEEESTTSSHHHHHHHHHT...............................STEEESSSTTSSSSEEEEEEEETTEEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg...............................ekaivsdkpgtTrdinegrvklkgkeie 49 
                                    +v+++G+  +GKSt +  l+                                +k ++++k g T++++  ++ +++ +++
  gene545|gene545|rna544|rna544  14 NVCFIGHVDSGKSTTVGMLSHqmgvidkrelekyekeaamnnkdtfylayltDKTEAERKRGITITTTLVTLPTEKFNVN 93 
                                    599****************9444455555555555666666677777766646999999************9999999** PP

                                    EEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT...T CS
                       MMR_HSR1  50 lvDtpGliegaseekglgkaflaleeadlillvvdas...e 87 
                                    ++D+pG  +       +++ +    +ad+++++v as   +
  gene545|gene545|rna544|rna544  94 ILDCPG-HK-----DFVKNMVTGASQADVAVVIVPASgfeS 128
                                    ******.33.....235555555667899999998775540 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.2
                                    EEEEEEECGGCSS CS
                       MMR_HSR1  46 keielvDtpGlie 58 
                                    +++ l+D  G++ 
  gene545|gene545|rna544|rna544 422 SKFALMDSNGVVA 434
                                    5788888888642 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0019       3.1     102     163 ..      15     102 ..       3     105 .. 0.87
   2 !    8.5   0.1    0.0011       1.8      48      86 ..     150     187 ..     138     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                                    EEEECSTTSSHHHHHHHHCTT.........................-----S-----------.---SEEEEEETTTEEE CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpe.........................lelktgevseklgrGkh.TTtavellelaeggll 155
                                    ++++G+   GKSt + +l  +                         l   t ++ ++ +rG   TTt v+l   + +  +
  gene545|gene545|rna544|rna544  15 VCFIGHVDSGKSTTVGMLSHQmgvidkrelekyekeaamnnkdtfyLAYLTDKTEAERKRGITiTTTLVTLPTEKFNVNI 94 
                                    6899****************99*********************9999999***********76266666666666699** PP

                                    ESS-SSSS CS
                    RsgA_GTPase 156 iDtPGfre 163
                                     D PG + 
  gene545|gene545|rna544|rna544  95 LDCPGHKD 102
                                    *****876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                                    EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTT CS
                    RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealgyevllvsakt 86 
                                    +++i++nK+D+++e+++ e++ke   ++ +++++ s k+
  gene545|gene545|rna544|rna544 150 KLIICVNKMDMISEDKRKEKFKEVSDEM-LRIVTRSHKD 187
                                    679*************777777766665.6666666665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.9   3.9e-06    0.0064       2     185 ..      18     175 ..      17     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.9e-06
                     ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresldw 81 
                                    +G++ sGK+t vg ls  +  + ++          e+ + eaa++ ++++ l+ + ++++ + ++++++   +++     
  gene545|gene545|rna544|rna544  18 IGHVDSGKSTTVGMLSHQMGVIDKR--------ELEKYEKEAAMNNKDTFYLAYLTDKTEAERKRGITITTTLVTLPT-- 87 
                                    8999************999988333........247778899**************************9999777776.. PP

                     ATP_bind_1  82 ldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltd..ptkfisgllsalsamlrlelPh 159
                                      e+      +  ++D+PG   +++ +  +a        + a v+v++v +   ++   +  + ++++ +s +l +e   
  gene545|gene545|rna544|rna544  88 --EKF-----NVNILDCPGHKDFVKNMVTGA--------SQADVAVVIVPASGFESciGVGGMLKTHIMISGILGCE-KL 151
                                    ..444.....6677****************9........66777777777777777353444444455555555555.48 PP

                     ATP_bind_1 160 vvvlnkfDllkek.lekeleffedvea 185
                                    ++++nk+D+++e+ ++++++ ++   +
  gene545|gene545|rna544|rna544 152 IICVNKMDMISEDkRKEKFKEVS---D 175
                                    99*********665444444444...3 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.3   1.1e-05     0.019      21      82 ..     264     326 ..     250     330 .. 0.84
   2 ?   -2.7   0.0       3.5   5.8e+03      36      50 ..     350     364 ..     339     365 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                    EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT..S--TT CS
                    GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr..qikeg 82 
                                     G +v  G+i+p++k+  +    vGei++++ ++k  +++  G++ +++++g + G   +++ g
  gene545|gene545|rna544|rna544 264 TG-RVEYGTITPNLKISIQPAGVVGEIRSVEIHNKPRSMIPCGENCGVALKGGVTGDlsKVDAG 326
                                    56.99**********96655559*******************************9952255555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.5
                                    EEETTE.EEEEEEEE CS
                    GTP_EFTU_D4  36 likedGrevGeilqi 50 
                                    + k++G+evG   qi
  gene545|gene545|rna544|rna544 350 VEKPNGMEVGYTPQI 364
                                    346789999987776 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.2e-05      0.13       5      79 ..      13     107 ..       9     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.2e-05
                                    EEEEEEEBTTSSCCCCCCTTSSSS.----...................--------------S-EEEEEEEEETTCEEEE CS
                         Septin   5 ftlmvvGesglGkttlintlfetd.liee...................ekleeasekkkktveikkkkvvieedgvklnl 64 
                                    +++  +G+   Gk+t +  l ++  +i++                     + + + +++++  i+ +++++     k+n+
  gene545|gene545|rna544|rna544  13 LNVCFIGHVDSGKSTTVGMLSHQMgVIDKrelekyekeaamnnkdtfyLAYLTDKTEAERKRGITITTTLVTLPTEKFNV 92 
                                    7899999999999999999987652444488999999999999998884455555666777778888888888888**** PP

                                    EEEE---BSSSSSHH CS
                         Septin  65 tviDtpgfGdavdns 79 
                                    +++D pg+ d+v n 
  gene545|gene545|rna544|rna544  93 NILDCPGHKDFVKNM 107
                                    ************995 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4   0.00048      0.78      39     174 ..      80     212 ..      10     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00048
                                    EETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEE CS
                          SRPRB  39 aalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDStidpkevkevAEllyeilliteklkdavdiliA 118
                                    ++l +  +++++++++D PGh+ + +++++     s++   v +v ++ ++  +     l ++i++  ++     +++i 
  gene545|gene545|rna544|rna544  80 TTLVTLPTEKFNVNILDCPGHKDFVKNMVTG---ASQADVAVVIVPASGFESCIGVGGMLKTHIMISGIL--GCEKLIIC 154
                                    33333445999*****************999...444445555666666665554444444445444443..33456666 PP

                                    EE-TTSTT.---HHHHHHHHHHHHHHHHHC..HHHHHH------T....T--------G CS
                          SRPRB 119 CnKqelfl.akspklikdaLEkElnkiier..rskalkeldeeedksavlakkgkdFkf 174
                                     nK ++    k +++ k+ +  E+ +i+ r  + k++  l  +     +l+kkg+ Fk+
  gene545|gene545|rna544|rna544 155 VNKMDMISeDKRKEKFKE-VSDEMLRIVTRshKDKNPIILPISGLMGLNLTKKGDSFKW 212
                                    688876541444555554.5566666655511334444445555555677777777776 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00053      0.87      20      47 ..       9      34 ..       2      65 .. 0.67
   2 ?    0.0   0.0      0.23   3.7e+02     198     240 ..      83     128 ..      65     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00053
                                   E..EEEEEEEESTTSSHHHHHHHHHHHC CS
                        G-alpha 20 kkrevkllllGqseSGKsTilkqlklly 47
                                   +k  +++ ++G+ +SGKsT++  l   +
  gene545|gene545|rna544|rna544  9 NKPRLNVCFIGHVDSGKSTTVGMLS--H 34
                                   345689**************87666..2 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.23
                                    C...T-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT- CS
                        G-alpha 198 v...dsklefrivdvgGqrserkkWvpffddvdaiiFlvslsefdq 240
                                    v   ++k +++i+d+ G+++  k+ v+  +++d+ + +v+ s+f  
  gene545|gene545|rna544|rna544  83 VtlpTEKFNVNILDCPGHKDFVKNMVTGASQADVAVVIVPASGFES 128
                                    2346668888888888888888888888888888888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2768.94
//
Query:       gene546|gene546|rna545|rna545  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   44.6   0.6    2.2e-11   43.6   0.6    1.6  1  TP6A_N    Type IIB DNA topoisomerase
     0.0021   18.0   0.0     0.0038   17.2   0.0    1.3  1  DUF2399   Protein of unknown function C-terminus (DUF2399)


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.6   2.5e-15   2.2e-11       5      62 .]      30      87 ..      26      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.5e-15
                                   HHHHHHHHHHHHHHTT--EEHHHHHHHGGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                         TP6A_N  5 qllkvlelihelleegkvvTkRdiYYrdvelFksQaesdrliddievllgvsReeLnv 62
                                   + +++ e+i e+ e+g +   R+i+Y+dv++F++Q ++ r+i  i++ l+vs+ eL+v
  gene546|gene546|rna545|rna545 30 VRIRLHEIIIEMQESGISRNEREIFYMDVNVFRTQTTVKRMISSIASELRVSKYELGV 87
                                   567899**************************************************98 PP

>> DUF2399  Protein of unknown function C-terminus (DUF2399)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.2e-07    0.0038      20      83 ..     136     202 ..     122     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.2e-07
                        DUF2399  20 ravyVvENpavlaaaadrlga....kaaplvctsGqpsaaalelldklaaagarlrYhGDfDwpGlai 83 
                                    ++v VvE   +l+ +a+++g     + + lvc  G p + ++ ll+ + ++ ++++   DfD+ G++i
  gene546|gene546|rna545|rna545 136 KKVLVVEKDTILQRIASEIGRerclEGVLLVCGRGYPCKNTMLLLKMIENK-TTISGFFDFDPFGIHI 202
                                    45****************99977777789***********99999887665.6788888*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1782.94
//
Query:       gene547|gene547|rna546|rna546  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1009.50
//
Query:       gene548|gene548|rna547|rna547  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.3e-112  374.9  10.9   4.1e-112  374.6  10.9    1.0  1  Glyco_transf_15  Glycolipid 2-alpha-mannosyltransferase


Domain annotation for each model (and alignments):
>> Glyco_transf_15  Glycolipid 2-alpha-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.6  10.9  2.3e-116  4.1e-112      55     324 ..      14     283 ..       9     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: 374.6 bits;  conditional E-value: 2.3e-116
                Glyco_transf_15  55 nenAtllalvrnselakilrsikkvekrFnkkfnYpyvfindepftekfkekieklveeadvefgeipkeewsyPefide 134
                                    +enA++l+l+rns+ + i+++ik++e+ Fnk+f Ypyvf+nde+fte+fk++i+ +++ + vefg++ +eew+ P +id 
  gene548|gene548|rna547|rna547  14 KENAVILILCRNSDKNGITETIKNFEEMFNKNFGYPYVFLNDEEFTEDFKKSIKGITS-SSVEFGKLDPEEWEVPPWIDM 92 
                                    68******************************************************99.********************* PP

                Glyco_transf_15 135 ekaakareelad..iaygdsesyrhmcRyysGlfykhellkkydyYwRvePdiklycdieyDvfkymkdekkiygFtlsl 212
                                    eka++ +++l +  i+yg s syr mcR++sG+fyk +l++kydyYwR+ePd+k+ c+ieyD f y+++++k ygF++sl
  gene548|gene548|rna547|rna547  93 EKAKQGMKNLEErkIIYGGSLSYRKMCRFFSGFFYKNKLVQKYDYYWRIEPDVKFLCQIEYDPFTYLRENNKQYGFVISL 172
                                    **********9999****************************************************************** PP

                Glyco_transf_15 213 keieetiktlWdstkkflkenkefieeknslsflsdddqdtynlCeFwsnfeigdldffrseayekfFeylDskGgffYe 292
                                     e  eti++l+++  kf+ +n ++i++ n  +f+ ++d+ +yn C+Fwsnfei+++ ffrse+y+k+F++lD++GgffYe
  gene548|gene548|rna547|rna547 173 VEFMETIPSLFGEAIKFATKNLNLIKKANGNRFILNKDG-SYNGCHFWSNFEIANFGFFRSETYQKYFDWLDRAGGFFYE 251
                                    **********************************77665.7*************************************** PP

                Glyco_transf_15 293 rWgdapvhsiavslllpkdkihffedigyshd 324
                                    rWgdapvhsia+sl+l+kd+ihff+digy+h 
  gene548|gene548|rna547|rna547 252 RWGDAPVHSIAASLFLDKDEIHFFSDIGYEHP 283
                                    *****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2123.64
//
Query:       gene549|gene549|rna548|rna548  [L=927]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.6e-183  610.6   0.0   5.4e-182  606.2   0.0    2.0  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    1.6e-25   89.9   0.8    3.2e-25   88.9   0.8    1.4  1  Anticodon_1      Anticodon-binding domain of tRNA
    1.4e-17   63.5   2.2    1.8e-10   40.2   0.0    4.5  5  tRNA-synt_1g     tRNA synthetases class I (M)
    8.2e-10   38.5   3.6    3.9e-09   36.3   0.0    3.1  4  tRNA-synt_1_2    Leucyl-tRNA synthetase, Domain 2
    0.00015   21.2   0.2       0.47    9.7   0.0    2.6  3  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
  ------ inclusion threshold ------
        0.1   11.9   0.0        3.2    7.0   0.0    2.4  2  tRNA-synt_1b     tRNA synthetases class I (W and Y)
       0.14   11.9   3.6       0.35   10.7   3.6    1.7  1  Selenoprotein_S  Selenoprotein S (SelS)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  606.2   0.0  2.1e-185  5.4e-182       1     602 []      57     679 ..      57     679 .. 0.93

  Alignments for each domain:
  == domain 1  score: 606.2 bits;  conditional E-value: 2.1e-185
                    tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                    k+y  Wee+++fk+     +  +++i++++PP+vtG+lHiGha+  +++d+++rykrm G+evly pG+DhaG+a++ +v
  gene549|gene549|rna548|rna548  57 KWYRYWEEKGLFKPV----EGGPKYIIPIPPPNVTGNLHIGHAMMVSIQDTLCRYKRMCGYEVLYIPGTDHAGIATQNVV 132
                                    69*************....779********************************************************** PP

                    tRNA-synt_1  81 ekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgk 160
                                     k++ +++      + re f +k +ewk +  ++i +q+krlG+svDf+re++Tld++++eav+ +fv l++kgliyr  
  gene549|gene549|rna548|rna548 133 SKQMEKEG----IRVDREMFLKKAWEWKGKHGSRIYEQFKRLGTSVDFSRERFTLDPGMNEAVVDAFVSLYEKGLIYREL 208
                                    ***84444....6889**************************************************************** PP

                    tRNA-synt_1 161 klvnwstklktalselEveykdkk..............dalihvafpladkee........vklviaTTtPeTllgdtav 218
                                    k+vnw+ kl+t++s+lEv+++++               ++++h+++p++ ++e         ++++aTT+PeT+lgdt++
  gene549|gene549|rna548|rna548 209 KIVNWCGKLSTTISDLEVNHEEVMpntylqvdggkyefGVIYHFRYPVTTDKEfsgdylslPTIEVATTRPETILGDTGI 288
                                    ************************************************999999999999999***************** PP

                    tRNA-synt_1 219 avnpeldyvitkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPah 298
                                    +vn        ++++             e  ++i  d+  +     +  +pl+ + ip+i ddy+d+ +GtG+Vki+Pah
  gene549|gene549|rna548|rna548 289 CVNRK------DRRF-----------SPEGIREIFGDVPCEC--NIYGVNPLTREVIPVIFDDYADMSFGTGIVKITPAH 349
                                    ***99......2222...........2223346777777664..345579****************************** PP

                    tRNA-synt_1 299 dedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrate 378
                                    d++D+ v+k++nl    +lde+ ++  e +ef+g+k+f+ark+vv++lk+ gl+++++  +  +p c+rs+++i++ +++
  gene549|gene549|rna548|rna548 350 DANDFDVSKRHNLACKAVLDEQNKVISE-GEFKGMKRFEARKAVVSKLKDIGLFIEKKGYSQVIPRCSRSNDIIEPIIKS 428
                                    **********************999877.69************************************************* PP

                    tRNA-synt_1 379 qWfvrvkeladaalkave..kvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagre 456
                                    qW+ + ke+a+ a++av   k+++ p+ +e+++++wleni+dWc+SRq+wWGhrip++++ e    +v +++++   +++
  gene549|gene549|rna548|rna548 429 QWWLNCKEMAKRAIEAVVdgKIRILPEGAERQWYRWLENIRDWCLSRQLWWGHRIPAYRTPEGR-WYVGRSKMDAFSKMK 507
                                    ****************9989***************************************99966.777444444443222 PP

                    tRNA-synt_1 457 eeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlil 536
                                     e  e++           ++ +e+ +dedvlD+WFsSg+wpf++lg+p++ t+++ +++p  +l++G+Di+++Wvar+++
  gene549|gene549|rna548|rna548 508 SECLESS-----------CNLDEFCQDEDVLDTWFSSGLWPFAILGWPKK-TDDFLRYYPNTLLETGSDILFFWVARMVM 575
                                    2222222...........344899**************************.99*************************** PP

                    tRNA-synt_1 537 lslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvik..................................... 579
                                    l+l+lt ++Pf +v++hg+vrd++GrKmSKslgNvidp+ vi+                                     
  gene549|gene549|rna548|rna548 576 LGLELTVKAPFSQVFLHGIVRDAHGRKMSKSLGNVIDPIFVIDgcslenlistmrsgnldekemkraeaalrqdfpngip 655
                                    ******************************************************************************** PP

                    tRNA-synt_1 580 kygadalRltli.lsdvgrdinls 602
                                    ++gadalR+tl+ +++ ++d+nl+
  gene549|gene549|rna548|rna548 656 RCGADALRFTLLsYTSGMKDVNLD 679
                                    ************9********986 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.8   1.2e-28   3.2e-25       3     142 ..     742     865 ..     741     873 .. 0.86

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 1.2e-28
                    Anticodon_1   3 wilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmP 82 
                                    wil++ n++++++++ +++++f  a +a+++ff+ dlcd+++e+vk+  +        +  ++ll v+   +++l+PfmP
  gene549|gene549|rna548|rna548 742 WILKKRNEAIETIRRMLDSFNFMAATQAIHQFFIYDLCDVFIEVVKKNRDE-------RYISTLLSVFIDSMKMLHPFMP 814
                                    *********************************************987532.......2559****************** PP

                    Anticodon_1  83 fitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselki 142
                                    fitEe++        +++si+++++p+ +      e+ e+++++  +ivk ir++ ++++ 
  gene549|gene549|rna548|rna548 815 FITEEVFS-----NYSNDSISVSSYPKvD----GSEH-ENKFSMTLQIVKYIRAKAESNGW 865
                                    *******3.....356799*******733....4444.778888889*****998877765 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.3       1.2   3.2e+03     184     228 ..      13      38 ..       4      45 .. 0.58
   2 !   40.2   0.0     7e-14   1.8e-10       6     136 ..      82     227 ..      77     235 .. 0.76
   3 !   12.2   0.1   2.1e-05     0.055     176     242 ..     424     490 ..     406     506 .. 0.76
   4 !    6.4   0.0    0.0013       3.2     310     347 ..     583     622 ..     544     640 .. 0.75
   5 ?   -0.2   0.0      0.12   3.2e+02     344     367 ..     656     679 ..     648     687 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.2
                                    EEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-E CS
                   tRNA-synt_1g 184 lffklskfekklkewieeeekeleenvkkivkewlkegLkdlais 228
                                     ++                   +ee+ k++++++l +  +++++s
  gene549|gene549|rna548|rna548  13 RML-------------------KEEKRKQKLEKFLAKKTQEVSVS 38 
                                    233...................55666666667776666666666 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 7e-14
                                    --B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHH....HHHHHTTS-HHH..HHH.......HHHH CS
                   tRNA-synt_1g   6 alpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpie....lkAekegvtpee..lve.......kvhe 72 
                                    + p ++g+lH+Gh++ v + D ++Rykr++g+evl++ gtD+ G++++     + ekeg+ ++   + +       k  +
  gene549|gene549|rna548|rna548  82 PPPNVTGNLHIGHAMMVSIQDTLCRYKRMCGYEVLYIPGTDHAGIATQnvvsKQMEKEGIRVDRemFLKkawewkgKHGS 161
                                    557789*********99999************************997622225778899987531133311111113445 PP

                                    HHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                   tRNA-synt_1g  73 eikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                    +i e+fk+l+ s d      t +   +e+v + f  l+ekgliy++   + +c k +++++d +v+
  gene549|gene549|rna548|rna548 162 RIYEQFKRLGTSVDfsRERFTLDPGMNEAVVDAFVSLYEKGLIYRELKIVNWCGKLSTTISDLEVN 227
                                    6778888876555410555688999999999999************99999999999999998775 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 2.1e-05
                                    .EEE.EEEEEE-GGGGHHHHHHHH.HH-TT.SHHHHHHHH.HHHHT----EE-ESS-SSS-EET..TECC CS
                   tRNA-synt_1g 176 pevketehlffklskfekklkewieeeeke.leenvkkivkewlkegLkdlaisrdldwGipvP..gaek 242
                                    p++  +++++++ ++++k+  e +   + + l+e ++++   wl++ ++d+++sr+l wG ++P   +++
  gene549|gene549|rna548|rna548 424 PII--KSQWWLNCKEMAKRAIEAVVDGKIRiLPEGAERQWYRWLEN-IRDWCLSRQLWWGHRIPayRTPE 490
                                    344..478999999888766555545555569*************9.*****************554444 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0013
                                    ---.S-EEEE--EE.E--------------HHHHHHHH-H CS
                   tRNA-synt_1g 310 klp.kkvvaheylt.vegkKlSkSrgvvvkakealerlda 347
                                    k+p ++v+ h+ +   +g+K+SkS g+v+++  +++ ++ 
  gene549|gene549|rna548|rna548 583 KAPfSQVFLHGIVRdAHGRKMSKSLGNVIDPIFVIDGCSL 622
                                    33337889999885378************99777766655 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.12
                                    HH-HHHHHHHHHHHS-TTS-EEE- CS
                   tRNA-synt_1g 344 rldadllRYylaaeapekkDldfs 367
                                    r+ ad+lR+ l++ ++ +kD+++ 
  gene549|gene549|rna548|rna548 656 RCGADALRFTLLSYTSGMKDVNLD 679
                                    6789****************9975 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       1.3   3.4e+03      50      78 ..      16      44 ..       9      50 .. 0.70
   2 ?    1.5   0.0      0.07   1.8e+02      22      40 ..     271     289 ..     251     295 .. 0.80
   3 !   36.3   0.0   1.5e-12   3.9e-09      86     146 ..     314     374 ..     310     398 .. 0.88
   4 ?   -3.9   0.0       3.2   8.2e+03     102     146 ..     816     862 ..     806     874 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                  tRNA-synt_1_2 50 klaekkkelaafieevkkksesereletk 78
                                   k +++k++l++f+++ +++ + ++ +++ 
  gene549|gene549|rna548|rna548 16 KEEKRKQKLEKFLAKKTQEVSVSKPKRDY 44
                                   55789999999999888877666655554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.07
                  tRNA-synt_1_2  22 klevfttrpdtlfGvtfva 40 
                                    ++ev ttrp+t+ G t + 
  gene549|gene549|rna548|rna548 271 TIEVATTRPETILGDTGIC 289
                                    799**********987665 PP

  == domain 3  score: 36.3 bits;  conditional E-value: 1.5e-12
                  tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                    +++ ++P+t e ip+   +y  m++gtg v   Pahd +Df+ +k++nl  k v+ ++++ 
  gene549|gene549|rna548|rna548 314 NIYGVNPLTREVIPVIFDDYADMSFGTGIVKITPAHDANDFDVSKRHNLACKAVLDEQNKV 374
                                    7899***************************************************987764 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 3.2
                  tRNA-synt_1_2 102 vanyvlmeygt..gavmavPahdqrDfeFakkynlpikqvikpedee 146
                                    +++ v+++y     +v + P  d  ++e      l+i + i+ + e+
  gene549|gene549|rna548|rna548 816 ITEEVFSNYSNdsISVSSYPKVDGSEHENKFSMTLQIVKYIRAKAES 862
                                    56666666654225677888888888887777778888888766554 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00019      0.47      18      51 ..      85     118 ..      79     151 .. 0.92
   2 !    8.6   0.0   0.00041       1.1     235     263 ..     584     612 ..     571     641 .. 0.86
   3 ?   -4.0   0.0       2.9   7.3e+03      89     120 ..     677     708 ..     668     725 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00019
                                    BTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                   tRNA-synt_1e  18 tvydashlGhaRslvafDilrrilqalgYdvqfv 51 
                                     v  + h+Gha  + + D l r+ ++ gY+v ++
  gene549|gene549|rna548|rna548  85 NVTGNLHIGHAMMVSIQDTLCRYKRMCGYEVLYI 118
                                    688899**************************98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00041
                                    S--EEEEEEE--EEETTBE--TTTT---B CS
                   tRNA-synt_1e 235 kqlvkyflhnghlkiegekmsksLknfit 263
                                     ++ + flh  +   +g+kmsksL+n+i 
  gene549|gene549|rna548|rna548 584 APFSQVFLHGIVRDAHGRKMSKSLGNVID 612
                                    568899***999999***********985 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 2.9
                                    HTT----SB--BGGGGHHHHHHHHHHHHHTTS CS
                   tRNA-synt_1e  89 aLnvlkptleprvsekvdeiielvekliekgy 120
                                    +L+vl+ +   r  +k+ +  ++v+ ++++ +
  gene549|gene549|rna548|rna548 677 NLDVLRVEGYRRFCNKIWNAHKFVKMMVDEIM 708
                                    57788888888888888888888888877644 PP

>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.042   1.1e+02      15      62 ..      87     137 ..      85     157 .. 0.66
   2 ?    7.0   0.0    0.0013       3.2     185     209 ..     589     611 ..     576     619 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.042
                                    SSS-BGG..GHHHHHHHHHHHH..TTSEEEEEEEHHHHHTTTTT-SSHHHHH CS
                   tRNA-synt_1b  15 TgklHlG..ylvplkklvelqk..aghevffliaDlhAiigdpskaeerklr 62 
                                    Tg+lH+G   +v+++  +  +k   g+ev+ + +  hA i  ++   +++++
  gene549|gene549|rna548|rna548  87 TGNLHIGhaMMVSIQDTLCRYKrmCGYEVLYIPGTDHAGIATQN-VVSKQME 137
                                    9******4334555544333335579999999888888887777.3344443 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0013
                                    EEEET-BBSTTSSSBTTCETTCGC- CS
                   tRNA-synt_1b 185 gltvplltgldGekKmSKSagnsaI 209
                                    ++++ ++ ++ G  KmSKS gn +I
  gene549|gene549|rna548|rna548 589 VFLHGIVRDAHGR-KMSKSLGN-VI 611
                                    5677799******.********.66 PP

>> Selenoprotein_S  Selenoprotein S (SelS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.6   0.00014      0.35      97     127 ..       2      32 ..       1      57 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                Selenoprotein_S  97 dakaekfkekkkqleeekRrqkiemWesmke 127
                                    d++ e+ +ekk++l+eekR+qk+e++   k 
  gene549|gene549|rna548|rna548   2 DSEKEALREKKRMLKEEKRKQKLEKFLAKKT 32 
                                    6677899*****************9865554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (927 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.58
# Mc/sec: 4830.71
//
Query:       gene550|gene550|rna549|rna549  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-11   41.6   7.7    1.6e-10   40.8   7.7    1.4  1  UPF0121   Uncharacterised protein family (UPF0121)
  ------ inclusion threshold ------
        0.4   10.1   7.7       0.21   11.1   4.7    1.9  2  DUF3959   Protein of unknown function (DUF3959)


Domain annotation for each model (and alignments):
>> UPF0121  Uncharacterised protein family (UPF0121)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   7.7   1.8e-14   1.6e-10      91     238 ..      71     209 ..      64     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.8e-14
                        UPF0121  91 lysliFlfsaPvtlallPvflfallHaasytktlldvlgsnslvvarllkvislvesqaeniLrliAlieivlmpllivl 170
                                    +y+++ ++  P+ + llP+ l +++H++s++++  ++++ +    a ++     +++ + ++ rl+ ++e + +pl +++
  gene550|gene550|rna549|rna549  71 IYCIMVFLTFPHEILLLPFYLLSIYHLSSFVLSNKKIFERTVIYPACVS-----LSAYHVSLGRLALFTEALTVPLSFLM 145
                                    7******************************999888887776443333.....4455566678999************* PP

                        UPF0121 171 lllgkaslllpllYyqfLklRYsSrrnPytreafseLrvlletlanhpscPavirslieklialvsrl 238
                                    ++l k+sl++   +  +++  Y    nP++r +f e+rv+l++ +   scP+ +++ +++ ++++  +
  gene550|gene550|rna549|rna549 146 IFLRKSSLVTFTAFIAMVRQQYF--NNPSMRSVFGEIRVSLDRWIL--SCPRDVQEYYRRGRDFLVST 209
                                    ***********************..******************986..79********9999998655 PP

>> DUF3959  Protein of unknown function (DUF3959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   4.7   2.4e-05      0.21       6     105 ..      35     135 ..      20     140 .. 0.89
   2 ?   -0.7   0.0     0.094   8.5e+02      47      70 ..     152     172 ..     145     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.4e-05
                        DUF3959   6 lfpiagilkqiplelslflggllfftslgsyytkktssricswlaytifitll.lgiwdqyvtassllanakiaaciavi 84 
                                    ++p+   ++ + l  s+ +  l  f+s+g   ++     i+ +l++   i ll + +   y   s +l+n ki     + 
  gene550|gene550|rna549|rna549  35 IYPLPNFVNILCLISSYSISLLPHFSSIGEILSQPNIYCIMVFLTFPHEILLLpFYLLSIYHLSSFVLSNKKIFERTVIY 114
                                    567777777788888999999999**********9999********99888774678899999***************** PP

                        DUF3959  85 plilrfrtyaitlgllalwga 105
                                    p+ + + +y ++lg lal+  
  gene550|gene550|rna549|rna549 115 PACVSLSAYHVSLGRLALFTE 135
                                    ******************975 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.094
                        DUF3959  47 swlaytifitlllgiwdqyvtass 70 
                                    s +++t fi    ++++qy    s
  gene550|gene550|rna549|rna549 152 SLVTFTAFI---AMVRQQYFNNPS 172
                                    555555555...578899977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1432.75
//
Query:       gene55|gene55|rna55|rna55  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-07   30.9   0.7    5.8e-07   29.6   0.7    1.7  1  Myb_DNA-binding  Myb-like DNA-binding domain
  ------ inclusion threshold ------
      0.018   15.3   0.2      0.035   14.4   0.2    1.5  1  Myb_DNA-bind_6   Myb-like DNA-binding domain
      0.025   14.6   0.0      0.046   13.8   0.0    1.4  1  SLIDE            SLIDE


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.7   9.7e-11   5.8e-07       2      30 ..      45      74 ..      44      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.7e-11
                               SSSBHHHHHHHHHHHHHHT.TCHHHHHHHH CS
            Myb_DNA-binding  2 gkWteeEdelLleavkkhG.nrWkkIaerl 30
                               ++W+ eE+e Ll+++k++G ++Wk+I+e++
  gene55|gene55|rna55|rna55 45 KPWSLEEEEALLRGIKELGhGKWKEILEKY 74
                               69************************9976 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   5.8e-06     0.035       1      28 [.      47      75 ..      47      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.8e-06
             Myb_DNA-bind_6  1 WteeEdeiLlklvekygn.dWknIaealn 28
                               W+ eE+e+Ll++ ++ g  +Wk+I e ++
  gene55|gene55|rna55|rna55 47 WSLEEEEALLRGIKELGHgKWKEILEKYK 75
                               9***************855*****87776 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.7e-06     0.046      29      80 ..      22      75 ..       5      80 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.7e-06
                      SLIDE 29 eqyknplqelkikyp...psnkgkkeyteeeDrfllvllakyGygnyekikkeir 80
                                + k+  +++ ++     p  k k  ++ ee+++ll  ++++G+g++++i ++ +
  gene55|gene55|rna55|rna55 22 PKKKHVRENVVVRSYtknPRRKPKP-WSLEEEEALLRGIKELGHGKWKEILEKYK 75
                               5555555555544331323344455.************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1227.18
//
Query:       gene551|gene551|rna550|rna550  [L=327]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-43  146.1   0.0    1.3e-42  145.5   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    8.5e-34  116.1   0.2    2.4e-32  111.4   0.1    2.1  2  Transketolase_C  Transketolase, C-terminal domain
    0.00091   19.5   0.0     0.0019   18.5   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.0   2.2e-46   1.3e-42       3     176 ..       2     176 ..       1     177 [. 0.99

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 2.2e-46
                                    EEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEE CS
                   Transket_pyr   3 iawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaq 80 
                                    i++r+a+++a++e++++d++v+++g++v+  gg++ v+kgl ++ g+ rv+d++isE +++g avGa+  g l++ive++
  gene551|gene551|rna550|rna550   2 ITVREALNQAIDEEMERDERVFVLGEEVGvsGGNNEVTKGLYEKYGKWRVLDTPISEMGFTGLAVGASYLG-LRPIVEFM 80 
                                    899**************************99****************************************.9******* PP

                                    EHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHH CS
                   Transket_pyr  81 FgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrai 158
                                      +Fa ++  +i+++ a++ ++++gk+ ++vv+r p g+    ++++ +   +++ ++pglkvv+P+++ + k+ll+ ai
  gene551|gene551|rna550|rna550  81 TWNFALQSidHIINSCAKTLYMSGGKISCPVVFRGPNGFNPGYAAQHTQDFCNYYGAVPGLKVVAPCTARDHKGLLKCAI 160
                                    ******************************************************************************** PP

                                    HSSS.SEEEEEE-SSEEC CS
                   Transket_pyr 159 rredrkPvvlrlpksllr 176
                                    r  d++Pvv++++++l++
  gene551|gene551|rna550|rna550 161 R--DDNPVVFLENETLYN 176
                                    *..89*********9997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.016        98      44     100 ..       2      60 ..       1      70 [. 0.78
   2 !  111.4   0.1   4.1e-36   2.4e-32       2     120 ..     192     309 ..     191     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.016
                                    SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCC..CTTCSSEEEEEE CS
                Transketolase_C  44 rtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeea..fdgldapvkrvg 100
                                    +tv+    + i+e +++ +r+ v+ e v   G   ev++ l+e++  +  ld+p++ +g
  gene551|gene551|rna550|rna550   2 ITVREALNQAIDEEMERDERVFVLGEEVGVSGGNNEVTKGLYEKYgkWRVLDTPISEMG 60 
                                    566666678999999999***9999999999999*******994423666666766665 PP

  == domain 2  score: 111.4 bits;  conditional E-value: 4.1e-36
                                    EEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHH CS
                Transketolase_C   2 kaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigseva 81 
                                    +a+i+ eg+d+tl++ +  v++++eAae+L++ gis+eV++l +++p+Dk+t+l+s+kkt+++ vv+  +++++++sev+
  gene551|gene551|rna550|rna550 192 RAVIEVEGNDITLIGISLSVKVCMEAAEALKDVGISCEVINLVSIRPIDKKTLLSSAKKTKHVFVVDFSWPSFSVASEVS 271
                                    68999*************************************************************************** PP

                                    HHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-S CS
                Transketolase_C  82 aalaeeafdgldapvkrvggpdviepgsaeelekafgld 120
                                    a++ e++f +l +pv+r+ g dv++p+s ee+e+++ ++
  gene551|gene551|rna550|rna550 272 AIIHEQCFGDLAVPVQRINGEDVPTPYS-EEVERMAFPT 309
                                    ****************************.99****9997 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   3.1e-07    0.0019       2      97 ..     201     294 ..     200     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.1e-07
                                    SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGG CS
                        PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkks 81 
                                    ++ ++++  +++++ +a+++l++ gi+  ++ l ++rP  ++ l + +kk+k v+v+d +     +  +++ev+a ++++
  gene551|gene551|rna550|rna550 201 DITLIGISLSVKVCMEAAEALKDVGISCEVINLVSIRPIDKKTLLSSAKKTKHVFVVDFSWP---SFSVASEVSAIIHEQ 277
                                    677888888999***********************************************992...346788888888877 PP

                                    .TSEEEEEE--GGG--- CS
                        PFOR_II  82 .kvkvvnfvaglgGrdi 97 
                                       ++   v++++G+d+
  gene551|gene551|rna550|rna550 278 cFGDLAVPVQRINGEDV 294
                                    65566667777877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2030.61
//
Query:       gene552|gene552|rna551|rna551  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-12   44.9   0.2    1.2e-11   44.3   0.2    1.4  1  eIF-1a    Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.2   6.5e-16   1.2e-11       2      61 ..      22      80 ..      21      83 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 6.5e-16
                                   EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEE CS
                         eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrI 61
                                   +v+g++i  lg+++f+V ++d g  ++a+++g+  +++++ +Gd+Vl  +++ d ++++I
  gene552|gene552|rna551|rna551 22 TVYGQIICPLGQGQFKVSCSD-GIYRTAKVRGRDYRRVRMIPGDIVLLRVRDGDEKRADI 80
                                   79*****************85.*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 886.92
//
Query:       gene553|gene553|rna552|rna552  [L=192]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      7e-34  117.4   0.1    7.9e-34  117.2   0.1    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.1   4.4e-38   7.9e-34       1     186 [.       4     179 ..       4     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 4.4e-38
                                    EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BSSSHHHHHHHHHHHHHH.H..TS-EEEEEEEEEEGGGTTTB CS
                     Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtqgtfeenalkKaraaae.a..glpvladDsgLevdaLnglP 77 
                                    i+faT+N +Kl+ev++ +++++++++         ++E+q++ e ++ +K  ++++ +  + +v++dD+g+++d L g+P
  gene553|gene553|rna552|rna552   4 IYFATTNLKKLKEVRRPFNTDIVHMN-------VSMVEIQASQERVVHNKLDQVMAlIskEDAVIVDDTGVFLDSLCGFP 76 
                                    89***************976555554.......345699999999999999997764344555***************** PP

                                    GGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEET..TTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEE CS
                     Ham1p_like  78 GvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladp..eeeeellfeGeveGeiveeprgeggfGyDpiFv 155
                                    Gvy++ f++ g++   ++ ++l+++e    d++A++  +l++a+   ++  ++ f+Ge++G+i+e +++eg    D iF+
  gene553|gene553|rna552|rna552  77 GVYIKDFLKIGSQ---KILEILKKVE----DNNATVSYTLGIAHYkdGQIAKKAFSGEIKGTIME-SKEEGSAELDGIFI 148
                                    *******877766...5555555553....46666666654444433788889**********96.899999999***** PP

                                    ETT-SS.BTTTS.CHHHHHHSHHHHHHHHHHH CS
                     Ham1p_like 156 peegek.tfaelskeeknaiShRgkAleklle 186
                                    p+e  k ++  +s +ekn iShR+ A e+l +
  gene553|gene553|rna552|rna552 149 PDE-FKaSLKSMSIDEKNCISHRRIATENLTD 179
                                    *76.666*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1177.20
//
Query:       gene554|gene554|rna553|rna553  [L=403]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.1e-34  117.4  35.2    9.9e-34  116.7  35.2    1.3  1  Aa_trans    Transmembrane amino acid transporter protein


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7  35.2   5.5e-38   9.9e-34       3     408 ..       5     401 ..       3     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 5.5e-38
                       Aa_trans   3 ssalsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrllGpkg 82 
                                     s++sa+++++++++G+G+  +PyAfk+ G+  G++l+  v++l++++l+ ++ ++ +  s++ + +Y+ l    +++++
  gene554|gene554|rna553|rna553   5 LSVKSAIVTMVTSMMGTGINYMPYAFKSVGYARGILLINGVGILTFFSLYAISIAANM--SKDPSPTYSSL-STRISKYL 81 
                                    699*****************************************************98..468999*****.78899*** PP

                       Aa_trans  83 kliidlailvqlfGvgvsyliligdllpaifesffdt.lllsnvyfilisaliiipLslipnlskLsylSllalvsslyy 161
                                    k+++dl+i+ ++fGv +++    + l+  +f+ +     ++ + +++ + a+ +++Lsl+++ls+L+++S++ + s++y 
  gene554|gene554|rna553|rna553  82 KILVDLSIFSSCFGVNIVFYRYLTGLITVMFPMNRYVdPEVWRKIIVGVLAVPFLLLSLKKDLSSLKVTSYITVASVTY- 160
                                    *******************999999999999986655899*************************************98. PP

                       Aa_trans 162 ivilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkkmtkvlllsiilatvl 241
                                      +++l+   +++  ++ v+e ++ k+ +  ++++ i+ ++ A +++a++++ ++el++ s   ++ kv   +  l t++
  gene554|gene554|rna553|rna553 161 --LAMLMGGYYLFIGERCVEE-PARKFES--QFSSGISCFMLALSCQANMVKTYTELEHKSP-GNIIKVAMGASFLGTLI 234
                                    ..3444444444444444444.4445555..9***************************888.78*************** PP

                       Aa_trans 242 yilvGlvGYltFGnevkgnillnlpkss................ilivivnlllvlhlilsfplqlhplrqvvenllikk 305
                                    y +vGl+GY++FGn+++++i+  l + +                 +  i+ +  +l l+++fp+q+ pl  +    +i++
  gene554|gene554|rna553|rna553 235 YGSVGLCGYFVFGNTIESSIIDILINPKaginvylmnstidkyaLSSKIACIGAMLVLFGAFPVQMNPLAGIPLSYFIQE 314
                                    ******************999988766678899999999999999999**********************9999999874 PP

                       Aa_trans 306 eavagasekeapkskllrlvirlllvvityliA.lsvpslakvlslvGatsstplsfilPalfhlkliktekksleklvk 384
                                               +++ l r  + + l++++++++ +   +++ vl +vGat++ + sf++P++++l   k        l  
  gene554|gene554|rna553|rna553 315 ----------GRNTDLIRKKVVFVLMLMFLFLGmMEKLNIDTVLQMVGATAINLVSFTYPSIYYLYFRKRMD-----L-- 377
                                    ..........3344444555556777778888856677**************************99988763.....3.. PP

                       Aa_trans 385 kkildlicivlglllvfyglavli 408
                                     +il++++i+ ++l ++y ++ +i
  gene554|gene554|rna553|rna553 378 MSILSIAVIIGSILSMIYMSYNII 401
                                    368899999********9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2661.10
//
Query:       gene555|gene555|rna554|rna554  [L=350]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   53.8   0.0    3.5e-14   52.4   0.0    1.8  1  SWIB      SWIB/MDM2 domain
  ------ inclusion threshold ------
      0.021   14.5   0.0        0.4   10.4   0.0    2.3  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
        0.1   12.8   1.1        1.1    9.4   0.1    2.6  3  DUF4279   Domain of unknown function (DUF4279)


Domain annotation for each model (and alignments):
>> SWIB  SWIB/MDM2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   5.9e-18   3.5e-14       2      74 .]     170     240 ..     169     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 5.9e-18
                           SWIB   2 pvklspeLaellgekelsrpevvkklweYIkennLqdpedkreilcDekLkklfggkdrvkffempkllkkHl 74 
                                     ++ls +L++ll + ++++p+vv +lw Y++ n+L    d  ++ cD  Lk+++g  +r++f+++p+l+ +Hl
  gene555|gene555|rna554|rna554 170 IFRLSTKLSNLLMKYTDTKPNVVTHLWRYVNRNGLMSI-DSDIVECDLPLKDILGV-ERFEFPQLPDLIVPHL 240
                                    589********************************776.99*************87.6**************7 PP

>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.7e-05       0.4      71     120 ..     130     179 ..     125     187 .. 0.86
   2 ?    1.5   0.0     0.037   2.2e+02      65      94 ..     280     309 ..     268     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.7e-05
                                    EHHHHHHHHTTSTTTSEEEEEEETTSSEEEEEEEECTSSEEEEEEEEEEE CS
                         PCNA_N  71 nlnslskilkcannedsvtlkaedeadtlalvfesekkdkiaeydlklkl 120
                                    +++ +    kc+++++   ++++ ++ +++l+f+ e+  +i   + kl +
  gene555|gene555|rna554|rna554 130 SMEGFFEWTKCCGDTEAFEINSDKKPKNIKLLFDLENPREIFRLSTKLSN 179
                                    555556668****************************9999999998875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.037
                                    -EEEEEEHHHHHHHHTTSTTTSEEEEEEET CS
                         PCNA_N  65 nlalgvnlnslskilkcannedsvtlkaed 94 
                                      al+ ++++l  +lk ++n++ v+ + e 
  gene555|gene555|rna554|rna554 280 IYALDRKIEALKHLLKRCENREDVLSEFEK 309
                                    567888999999***999999988765554 PP

>> DUF4279  Domain of unknown function (DUF4279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00019       1.1      51     104 ..      10      61 ..       2      66 .. 0.81
   2 ?   -2.1   0.0      0.73   4.4e+03      30      43 ..     186     199 ..     166     212 .. 0.77
   3 ?    0.9   0.0     0.088   5.2e+02      54      76 ..     288     310 ..     282     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00019
                        DUF4279  51 dleeqldk..lldrlepkaekikelakkygleiylqvviyiedgeqpelhldkevl 104
                                    ++ee +d+  l ++l+  ae++k+++ k  l++y+qv i+     ++ ++ld++v+
  gene555|gene555|rna554|rna554  10 SIEEEVDRlcLARKLNMEAEYLKRIKCKKYLRCYVQVAIKK----GTFIRLDSRVI 61 
                                    6777888877889************************8876....34458888777 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.73
                        DUF4279  30 dptkkrkegsWels 43 
                                    d++++ +++ W+++
  gene555|gene555|rna554|rna554 186 DTKPNVVTHLWRYV 199
                                    44477888889887 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.088
                        DUF4279  54 eqldklldrlepkaekikelakk 76 
                                    e l++ll+r e+ ++ + e+ k+
  gene555|gene555|rna554|rna554 288 EALKHLLKRCENREDVLSEFEKD 310
                                    57899*********999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2384.89
//
Query:       gene556|gene556|rna555|rna555  [L=804]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-44  151.5  20.1    4.9e-33  114.7   6.7    3.4  5  Ufd2P_core   Ubiquitin elongating factor core
    2.2e-14   53.3   0.3    4.9e-14   52.2   0.3    1.5  1  U-box        U-box domain
    0.00033   20.5   0.1    0.00072   19.4   0.1    1.5  1  Phage_GP20   Phage minor structural protein GP20
  ------ inclusion threshold ------
      0.037   14.0   0.4      0.037   14.0   0.4    2.1  2  GerD         Spore germination GerD central core domain
      0.086   12.8   0.1       0.21   11.5   0.1    1.6  1  Nipped-B_C   Sister chromatid cohesion C-terminus
      0.086   12.4   0.1        0.2   11.2   0.1    1.5  1  CAMP_factor  CAMP factor (Cfa)
      0.088   12.8   0.1       0.28   11.2   0.1    1.8  1  Rep-A_N      Replication factor-A protein 1, N-terminal domai
       0.34   10.8   5.4        5.4    6.9   0.0    3.1  3  CemA         CemA family


Domain annotation for each model (and alignments):
>> Ufd2P_core  Ubiquitin elongating factor core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.63   1.4e+03      97     117 ..     183     203 ..     182     211 .. 0.83
   2 !   44.0   1.0   5.3e-15   1.2e-11      47     128 ..     235     314 ..     207     323 .. 0.89
   3 ?   -0.5   0.0      0.16   3.5e+02     164     258 ..     322     403 ..     314     454 .. 0.81
   4 ?   -1.6   0.0      0.34   7.6e+02     562     593 ..     471     508 ..     468     515 .. 0.89
   5 !  114.7   6.7   2.2e-36   4.9e-33     436     625 .]     516     717 ..     504     717 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.63
                                    HHHHHHHHHHHHHHHGGGGST CS
                     Ufd2P_core  97 dgfmlNllavLlrLcepflda 117
                                    +gf++N+   L  ++epf+ +
  gene556|gene556|rna555|rna555 183 YGFLCNFPCFLDGFFEPFIYK 203
                                    89****************732 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 5.3e-15
                                    HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHT-GGGGSSS--GGGS--HHHHHHHHHHHHHHHGGGGSTT-TTGGGS- CS
                     Ufd2P_core  47 tiqenlveiiknllkassesRervlkwlakilnlNekrakiqvdpskvssdgfmlNllavLlrLcepfldatfskidkid 126
                                     +  ++++ii +++k+s+e R ++++++ +++++ ++r+k+  + +   sdgf +N+++v+ r+ ++++d ++  idki+
  gene556|gene556|rna555|rna555 235 DHSYKMHHIIYSIIKSSKELRTNFMRYVCNVISVSKERSKTIFNWRVSISDGFAYNMSMVMSRFNRKIIDGNM--IDKIN 312
                                    4566899**************************************************************9988..****9 PP

                                    TT CS
                     Ufd2P_core 127 pn 128
                                    p+
  gene556|gene556|rna555|rna555 313 PE 314
                                    97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.16
                                    --HHHHHHHHHHHHHHHTHHHHHHHHHTHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHH CS
                     Ufd2P_core 164 pnFiteiFfltlkalhlglkpaisefkrllqelkrlqdeleeleaeaaqleeqlkklkkelekllseklaleavlldpel 243
                                    ++F+t ++f  +++l  +  +  +++k l+ e + l+ +            e+l+ ++k+++   s++ al+++l+ +++
  gene556|gene556|rna555|rna555 322 TSFPTFCYFSKIHLLFTSCVKFGEYIKSLAYEYRLLEGDGG----------ERLEAYRKRID---SKISALNGLLYMTDF 388
                                    58999999999999988888888888899988888888554..........56777888888...889999999999999 PP

                                    HHHHHHHHHHHHHHH CS
                     Ufd2P_core 244 lqellkFlrlvaawl 258
                                     ++   F ++++++ 
  gene556|gene556|rna555|rna555 389 FADEKAFTDFMTEYT 403
                                    998888888888876 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.34
                                    HHHHHHHHHHHHCTT-......HHHHHHHHH-TTT--H CS
                     Ufd2P_core 562 elLssiveiYlnLske......eeFvkavakDgRsYkk 593
                                    ++L+++++ Y +L k+       + +  + k+gR ++ 
  gene556|gene556|rna555|rna555 471 TMLNKVIDYYNSLGKDetrmepRSIIHSIFKEGRVFSR 508
                                    5899*********88889999999************97 PP

  == domain 5  score: 114.7 bits;  conditional E-value: 2.2e-36
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...........---....-----.......HHHHHHHHHHHHHHHHH CS
                     Ufd2P_core 436 vrFinlllNDvtflldealskLkeikelqeele...........dqeewsslseee.......rqekeesleqlerqaks 497
                                    + Fin ++ D  + l e ls++k+ike  +  e           +++e +     +         + ++s++ ++++a++
  gene556|gene556|rna555|rna555 516 ITFINCMMKDFEYSLSEGLSSIKDIKEDMKTVEdltkeleevkkNNAEME-----KaesiserIGSIKKSIRFSKNKARN 590
                                    78**********************99877777755545443333222222.....122344345678899999******* PP

                                    HHHHHHHHHHHHHHHHHH-GGGGCSHHHHHHHHHHHHHHHHHHHSHHHHT---SSGGGGT--HHHHHHHHHHHHHHCTT- CS
                     Ufd2P_core 498 ylqlanetvkllklltkeipepfltpeivdrlaamLnynLdqLvGpkcknLkVknpekynFrPkelLssiveiYlnLske 577
                                    +  +     +l+  +  e p+ fl +e+++  +  Ln+nL+ + Gp+c++L +++pe+y+F+ k+lL+++v iY+++ ++
  gene556|gene556|rna555|rna555 591 SFLYVDGCFDLFMHILDEKPDLFLVNEMISNFVRVLNCNLKVITGPRCTDLVIRSPEQYGFDAKNLLRRMVMIYIKI-RS 669
                                    *****************************************************************************.55 PP

                                    HHHHHHHHH-TTT--HHHHHHHHHHHTTSTSSTHHHHHHHHHHHHHHH CS
                     Ufd2P_core 578 eeFvkavakDgRsYkkelFekavrilkregllseeelekfkelaqkve 625
                                    ++Fv+ va+D  +++ e+F+ a ri++ + l++e+++e++++l++k+e
  gene556|gene556|rna555|rna555 670 DKFVEMVASDKMYFDIEFFRTALRICESKYLINESQMEELRSLISKLE 717
                                    6*******************************************9975 PP

>> U-box  U-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.3   2.2e-17   4.9e-14       1      67 [.     728     794 ..     728     799 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.2e-17
                                    SSGGGB-TTT-SB-SSEEEETTT.EEEEHHHHHHHHTT.SSB-TTT-SB--GGGSEE-HHHHHHHHHH CS
                          U-box   1 iPdefldpitlelmkdPvilpsg.vvvdrstiekhllsrdktdPftrepltqdqlipnlelKekIdef 67 
                                    +Pdef+dp+t+  ++ Pv l  + v+vd+st +  + + +  dPf+r+plt+d+++ ++elKekId+ 
  gene556|gene556|rna555|rna555 728 VPDEFIDPLTFNPIRNPVKLLTSkVTVDKSTYDMLMMN-GGIDPFNRMPLTEDMVVEDTELKEKIDKH 794
                                    8*****************998888**************.**************************985 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   3.2e-07   0.00072      17      71 ..     513     567 ..     497     597 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.2e-07
                     Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakae 71 
                                    k +++ ++   ++++ +l +  ++++d+k++ k++e+L+k++ee++++n++ ++ 
  gene556|gene556|rna555|rna555 513 KRNITFINCMMKDFEYSLSEGLSSIKDIKEDMKTVEDLTKELEEVKKNNAEMEKA 567
                                    66666677778999999********************************996653 PP

>> GerD  Spore germination GerD central core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   1.6e-05     0.037      72     111 ..     421     462 ..     420     465 .. 0.92
   2 ?   -2.2   0.2       1.8     4e+03      52      78 ..     521     549 ..     510     567 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                           GerD  72 mekqllellkskeyrkqlekviqetle..sPlfkaklqellk 111
                                    m++++++l+ks+++ + l+kv++  ++  sP+fk+++ ++l+
  gene556|gene556|rna555|rna555 421 MQEMTIDLIKSSTISSSLNKVMETIMDwrSPMFKKEVVKILS 462
                                    899*********************996669********9997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                           GerD  52 dLmkDpeYq..kmlleilkdpemekqlle 78 
                                     +mkD eY   + l +i    e +k++++
  gene556|gene556|rna555|rna555 521 CMMKDFEYSlsEGLSSIKDIKEDMKTVED 549
                                    56666666311223333333333333333 PP

>> Nipped-B_C  Sister chromatid cohesion C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.5e-05      0.21     110     151 ..     232     270 ..     203     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.5e-05
                                    ...GG---HHHHHHHHH--SHHHHHHHHHHHHHHH.HHTSST CS
                     Nipped-B_C 110 setesptallsslysllrsnkqsrrkflsslvklfdfesesd 151
                                    +  ++ +++++ +ys+++s+k+ r+ f++ +++++++   s+
  gene556|gene556|rna555|rna555 232 ALCDHSYKMHHIIYSIIKSSKELRTNFMRYVCNVISV---SK 270
                                    5678899999*************************63...22 PP

>> CAMP_factor  CAMP factor (Cfa)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   8.9e-05       0.2      33      80 ..     534     581 ..     516     590 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.9e-05
                    CAMP_factor  33 adyekeiekllktakelkealeaiakgkvtlydlksIlaRvellvdiv 80 
                                        k i++ +kt+++l+++le++ k++  +  ++sI  R+  + +++
  gene556|gene556|rna555|rna555 534 LSSIKDIKEDMKTVEDLTKELEEVKKNNAEMEKAESISERIGSIKKSI 581
                                    56678999********************************98877765 PP

>> Rep-A_N  Replication factor-A protein 1, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00012      0.28      22      68 ..     261     307 ..     242     311 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                    EEEEEEEE--..SSSS-EEEEEEESSSEEEEEEESGGGHHHHHTTSS CS
                        Rep-A_N  22 QvvelkkinskaeesseRyrlllsDgknkakamlatqLnslvksgkl 68 
                                     v ++ +++++ +++   +r+++sDg ++  +m+ +  n ++ +g++
  gene556|gene556|rna555|rna555 261 YVCNVISVSKERSKTIFNWRVSISDGFAYNMSMVMSRFNRKIIDGNM 307
                                    5666666666777888899***********************99986 PP

>> CemA  CemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0024       5.4     191     220 ..     183     212 ..     178     221 .. 0.88
   2 ?   -2.3   0.0       1.5   3.4e+03      47      86 ..     448     490 ..     418     523 .. 0.57
   3 ?    4.4   1.2     0.014        31      58     152 ..     535     633 ..     495     643 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0024
                           CemA 191 llfiatfPVildtvfKywiFryLnrisPsa 220
                                    + f++ fP +ld+ f  +i++    +sP+ 
  gene556|gene556|rna555|rna555 183 YGFLCNFPCFLDGFFEPFIYKKCDYSSPAQ 212
                                    679*********************999975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                           CemA  47 flnkeleeealeelkefeekleleel...igeapelseeeiee 86 
                                      +  +++e+++ l++  + +++ +l   i+ +++l ++e++ 
  gene556|gene556|rna555|rna555 448 WRSPMFKKEVVKILSHRSNAIKFTMLnkvIDYYNSLGKDETRM 490
                                    3455667888888888888888766533244444455555444 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.014
                           CemA  58 eelkefeekle....leeligeape.lseeeieeelkekaeelakeyreesseaiknifadlvsliafvvllllskeele 132
                                    +++k ++e ++    l + ++e ++   e e  e+++e++  ++k++r ++++a +n f  +  ++ +++ +l +k +l 
  gene556|gene556|rna555|rna555 535 SSIKDIKEDMKtvedLTKELEEVKKnNAEMEKAESISERIGSIKKSIRFSKNKA-RNSFLYVDGCFDLFMHILDEKPDLF 613
                                    445555555441111334444444423366777899999999999999876655.7777788889999999********* PP

                           CemA 133 ilksfldevlygLsDsaKaf 152
                                    ++++++++++  L+ + K +
  gene556|gene556|rna555|rna555 614 LVNEMISNFVRVLNCNLKVI 633
                                    **********9999888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (804 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1312  (0.0731775); expected 358.6 (0.02)
Passed bias filter:                      739  (0.0412181); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 4927.39
//
Query:       gene557|gene557|rna556|rna556  [L=191]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-38  131.4   0.0    3.6e-38  131.1   0.0    1.0  1  Thymidylate_kin  Thymidylate kinase
    0.00045   20.5   0.0    0.00059   20.1   0.0    1.3  1  AAA_28           AAA domain
     0.0029   17.6   0.6      0.009   16.1   0.0    2.1  2  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.017   14.6   0.1      0.047   13.1   0.0    1.7  2  Arf              ADP-ribosylation factor family
      0.028   14.3   0.1        0.7    9.7   0.1    2.1  1  dNK              Deoxynucleoside kinase
      0.075   13.5   0.1       0.15   12.5   0.1    1.6  1  DUF4367          Domain of unknown function (DUF4367)
        0.1   13.1   0.1       0.18   12.4   0.0    1.6  1  AAA_18           AAA domain
       0.16   11.3   0.0       0.38   10.1   0.0    1.5  2  FtsK_SpoIIIE     FtsK/SpoIIIE family


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.0   1.6e-41   3.6e-38       1     181 [.       9     181 ..       9     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 1.6e-41
                                    EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT CS
                Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqg 80 
                                    +EGlD++GKtt++++l+e l        ++++++++ +G++i+e+l+k+  l+++t++llf+adr+eh +  i+ +l ++
  gene557|gene557|rna556|rna556   9 FEGLDRSGKTTIVNTLYESLLPTVSVNKIRFPNRNGCVGKVIDEYLQKKISLKNETIHLLFSADRYEHKA-MIE-ELRKD 86 
                                    8******************999986689*************************************66655.555.59999 PP

                                    -EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTS.E-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHH CS
                Thymidylate_kin  81 ktvivdRylfSslaYqgakegvdldlvlslnedvll.kPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrery 159
                                     +v +dRy +S++aY+ ak+   l+l ++   + ll kPdlt+++dv+ ++  +R ++++e    +  +++fl+kv   y
  gene557|gene557|rna556|rna556  87 SIVLCDRYSMSGVAYSVAKG---LSLDWCAMSESLLpKPDLTVFIDVPMDEICRRKEFGKE----IHDSITFLKKVFLAY 159
                                    *****************988...99999988888888************************....999************ PP

                                    HHHHHTTSTEEEEETTS-HHHH CS
                Thymidylate_kin 160 lelakederiliidasksieev 181
                                    + l+ke+++++i+d + +i+e+
  gene557|gene557|rna556|rna556 160 QILLKEEKNVFIVDGTLPIDEI 181
                                    ******************9987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.6e-07   0.00059       2     121 ..       7     135 ..       6     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.6e-07
                         AAA_28   2 ivitGgestGKTtlleaLaar..........gyp....vvpEaareileeklakgedalpwvedllafaervleeqleee 67 
                                    +v+ G   +GKTt+++ L +            +p    +v  +  e+l++k   ++++++     l f + + e+++  e
  gene557|gene557|rna556|rna556   7 VVFEGLDRSGKTTIVNTLYESllptvsvnkiRFPnrngCVGKVIDEYLQKKISLKNETIH-----LLFSADRYEHKAMIE 81 
                                    677777789**********6556666666562224557999999****999988887555.....567777777776666 PP

                         AAA_28  68 aaaaankvlfcDrglldtlaYarayggeaeaeleaaarekrydl.vfllppapei 121
                                    +  +++ +++cDr ++  +aY+ a g   +    ++    + dl vf+  p+ ei
  gene557|gene557|rna556|rna556  82 EL-RKDSIVLCDRYSMSGVAYSVAKGLSLDWCAMSESLLPKPDLtVFIDVPMDEI 135
                                    66.489******************9999444444577788888877776678777 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     4e-06     0.009       2      42 ..       4      43 ..       3      92 .. 0.71
   2 ?   -0.6   0.1      0.54   1.2e+03      77      82 ..     153     158 ..     125     187 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                         AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldder 42
                                   +k +v +G+ r+GKTt++++l+++ll +  s+  i + + +
  gene557|gene557|rna556|rna556  4 GKFVVFEGLDRSGKTTIVNTLYESLL-PTVSVNKIRFPNRN 43
                                   688999****************9999.55555555554433 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.54
                         AAA_14  77 peweka 82 
                                    ++++ a
  gene557|gene557|rna556|rna556 153 KKVFLA 158
                                    222222 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.047      17      37 ..       7      27 ..       1      43 [. 0.80
   2 ?   -1.4   0.0       0.6   1.4e+03      88     115 ..      49      76 ..      36      87 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                   EEEEESTTSSHHHHHHHHHHS CS
                            Arf 17 illlGLDnaGKtTilkklkle 37
                                   +++ GLD +GKtTi++ l + 
  gene557|gene557|rna556|rna556  7 VVFEGLDRSGKTTIVNTLYES 27
                                   6788************99654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.6
                                    EEETT-CTTHHHHHHHHHHHCTSGCCTT CS
                            Arf  88 vvDsadreRleeakeeLkalleeeelke 115
                                    v+D + +++++  +e ++ l++ ++ ++
  gene557|gene557|rna556|rna556  49 VIDEYLQKKISLKNETIHLLFSADRYEH 76 
                                    7888888888888888888888877665 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00031       0.7       4     169 ..      10     165 ..       7     188 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
                                    EESTTSSHHHHHHHHHCCSTCEEEE-HHHHCCSSSS...HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS-EEEE CS
                            dNK   4 eGnIgaGKstlvklLskklgvkvfeEpvdkwtnvqk...nlLekfYkdpsrwsfalqtyvllsrlkqqlealatkqvvvl 80 
                                    eG   +GK+t+v++L + l  ++++    ++ n ++   ++++ + ++  + s++ +t  ll   +++++        ++
  gene557|gene557|rna556|rna556  10 EGLDRSGKTTIVNTLYESL-LPTVSVNKIRFPNRNGcvgKVIDEYLQK--KISLKNETIHLLFSADRYEH------KAMI 80 
                                    5555677777777776666.3333333334434333445555554432..33444333333333333311......1222 PP

                                    ES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHH CS
                            dNK  81 eRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekLh 160
                                    e    +d  + +   + +g++  ++     ++  +  + l+kpdl ++++++++++ +r   ++  +e + ++ +l+k+ 
  gene557|gene557|rna556|rna556  81 EE-LRKDSIVLCDRYSMSGVAYSVAKGLSLDWCAMSESLLPKPDLTVFIDVPMDEICRR---KEFGKEIHDSITFLKKVF 156
                                    21.22333344443444444444444444444444445568899999999999998876...444455566666777777 PP

                                    HHHHHHHTS CS
                            dNK 161 ekyeewlkk 169
                                      y+  lk+
  gene557|gene557|rna556|rna556 157 LAYQILLKE 165
                                    777777666 PP

>> DUF4367  Domain of unknown function (DUF4367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   6.6e-05      0.15      78     108 ..     156     186 ..     129     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.6e-05
                        DUF4367  78 dgeyvlvwedegvvytlsgniskeelikiae 108
                                       y+++ ++e+ v+ + g+++ +e+i+i++
  gene557|gene557|rna556|rna556 156 FLAYQILLKEEKNVFIVDGTLPIDEIIEIVK 186
                                    33399************************98 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.9e-05      0.18       1      39 [.       7      61 ..       7     149 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf...............gvnlrdvakenglll 39
                                   ++  G  ++GKtt+ + L ++l                  g ++ ++++++ +l 
  gene557|gene557|rna556|rna556  7 VVFEGLDRSGKTTIVNTLYESLlPTvsvnkirfpnrngcvGKVIDEYLQKKISLK 61
                                   5789**************9996322533333333333333333333333333222 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00017      0.38      46      74 ..      11      39 ..       5      40 .. 0.89
   2 ?   -3.2   0.0       1.9   4.4e+03     228     237 ..      61      70 ..      43      85 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                                   --TTSSHHHHHHHHHHHHHTT--TTTEEE CS
                   FtsK_SpoIIIE 46 GatgsGKStalntLilSlatthtPeeVql 74
                                   G   sGK+t +ntL  Sl+ t + +++++
  gene557|gene557|rna556|rna556 11 GLDRSGKTTIVNTLYESLLPTVSVNKIRF 39
                                   6678****************999998887 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.9
                                    GGGTEEEEEE CS
                   FtsK_SpoIIIE 228 raaglHllla 237
                                    +++ +Hll+ 
  gene557|gene557|rna556|rna556  61 KNETIHLLFS 70 
                                    2444555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1214.55
//
Query:       gene558|gene558|rna557|rna557  [L=328]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-09   35.9   0.3    1.3e-08   34.7   0.3    1.7  1  HUN       HPC2 and ubinuclein domain
  ------ inclusion threshold ------
        0.6   10.3   4.0          8    6.7   0.6    3.2  4  HTH_17    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HUN  HPC2 and ubinuclein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.3   1.5e-12   1.3e-08       2      51 ..      23      70 ..      22      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 1.5e-12
                            HUN  2 rrkrdddgddtgsgYDieDpFIDDsElydelvpdilktktgGFYvnqgel 51
                                   ++++ ++++++ ++YD++DpFI   E+ + +v  +++  +++F+v++gel
  gene558|gene558|rna557|rna557 23 KKEKQKKRRQRTDEYDYNDPFIEPFEGETQMV--MIESSLEDFFVYKGEL 70
                                   67899999********************9999..77788899******98 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.2   1.1e+04      22      31 ..      65      75 ..      64      78 .. 0.69
   2 ?    6.7   0.6   0.00089         8      27      42 ..     114     128 ..     108     128 .. 0.82
   3 ?   -2.0   0.1      0.47   4.2e+03      36      50 ..     159     173 ..     156     174 .. 0.87
   4 ?    3.0   0.0     0.013   1.2e+02       5      22 ..     191     208 ..     189     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.2
                         HTH_17 22 irrgelpaa.k 31
                                   + +gelp+  k
  gene558|gene558|rna557|rna557 65 VYKGELPYSaK 75
                                   67899*76654 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00089
                         HTH_17  27 lpaakiGrrwriprsd 42 
                                    +  +++Grr+rip+sd
  gene558|gene558|rna557|rna557 114 I-SVGKGRRRRIPKSD 128
                                    4.569*********98 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.47
                         HTH_17  36 wriprsdleewlekr 50 
                                    ++++ + le++ ++r
  gene558|gene558|rna557|rna557 159 YYVSLKVLEAFQKER 173
                                    8999999****9986 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.013
                         HTH_17   5 eEaAelLgvsrstvyrli 22 
                                    eE+A++L+ s+s   +l 
  gene558|gene558|rna557|rna557 191 EEIARYLKKSESAMNELF 208
                                    8*********99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1246  (0.0694963); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2184.22
//
Query:       gene559|gene559|rna558|rna558  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-08   33.7   0.4      8e-08   32.6   0.3    1.4  1  Brix            Brix domain
  ------ inclusion threshold ------
      0.075   12.6   0.0       0.15   11.7   0.0    1.5  1  Abhydro_lipase  Partial alpha/beta-hydrolase lipase region


Domain annotation for each model (and alignments):
>> Brix  Brix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.3   8.9e-12     8e-08      30     193 .]      41     181 ..      29     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 8.9e-12
                                    CT-TTTHHHHHHH-HHHHHHHHHCTCSEEEEEE..S.....STTE....EEEEEEEECECTGGGSTTTSTS-TT---EEE CS
                           Brix  30 nsnklkdlvelagvthlellsekndcslfvfelskk.....rPng....ptlefkvenyslmkdlkkakktefgsrPllv 100
                                    + n+++       ++++e l +k++ ++f++ ++       r  +    +++efk+++y +  d++   ++e  ++  +v
  gene559|gene559|rna558|rna558  41 KVNPFDC------AEQIEKLMKKKKSGMFISITKDSllvigRTFNdeiiDMVEFKINRYLSVTDFECV-GPELHMKYFVV 113
                                    3367776......667888888888899999994447665544448999****************988.99999999999 PP

                                    EES.HHHHHHHHHHHHHH..SEEEG..-B-GG-SEEEEEEES.CCTTTECEEEEEEEEEEE..STTTTECT..T..EEEE CS
                           Brix 101 fngkenfkllksllqdlFrvpkislkspklsglrrvvlftaaenqetdktisfRhYaiklkksgkklpnlekekkerveL 180
                                    ++ + n k+l +l+ d+F+  k s  ++ l+g+r+  +ft   ++e++   ++  Y  +       l+           +
  gene559|gene559|rna558|rna558 114 LQ-NINNKRLENLIVDFFN--KKSS-KVCLEGIRYSWVFT---KTEDG---YVLKYVRV-------LK--------DLNV 168
                                    99.5555***********5..3333.34669*********...56644...22233332.......33........6778 PP

                                    EEESEEEEEEEEE CS
                           Brix 181 eEiGPrfdLklrk 193
                                    e++GP ++++l++
  gene559|gene559|rna558|rna558 169 EDCGPLLEMELVR 181
                                    8888888888875 PP

>> Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.7e-05      0.15      17      35 ..     149     167 ..     140     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                 Abhydro_lipase  17 VqTeDGYiLtlhRipaknk 35 
                                     +TeDGY+L+  R+++  +
  gene559|gene559|rna558|rna558 149 TKTEDGYVLKYVRVLKDLN 167
                                    58************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1365.88
//
Query:       gene560|gene560|rna559|rna559  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.7e-23   80.8  11.1    1.7e-06   28.6   0.1    6.4  6  WD40         WD domain, G-beta repeat
    1.5e-14   54.1   3.7    9.1e-06   25.9   0.1    4.4  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    1.6e-08   33.9   0.1    0.00013   21.0   0.0    2.8  2  Ge1_WD40     WD40 region of Ge1, enhancer of mRNA-decapping p
    7.1e-05   22.3   0.2     0.0025   17.2   0.0    2.2  2  Nbas_N       Neuroblastoma-amplified sequence, N terminal
  ------ inclusion threshold ------
      0.096   10.7   0.0       0.16    9.9   0.0    1.4  1  IKI3         IKI3 family


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.1    0.0033        12      10      38 .]     106     135 ..      98     135 .. 0.75
   2 !    8.3   0.1    0.0013       4.7       2      33 ..     140     168 ..     139     172 .. 0.73
   3 !   28.6   0.1   4.7e-10   1.7e-06       7      37 ..     184     215 ..     179     216 .. 0.90
   4 !   20.1   0.1   2.4e-07   0.00084       3      38 .]     221     260 ..     219     260 .. 0.73
   5 ?    2.6   0.0     0.077   2.8e+02       6      38 .]     269     303 ..     264     303 .. 0.74
   6 !   16.4   0.0   3.4e-06     0.012       3      38 .]     309     345 ..     307     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0033
                                    SSS...EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  10 Hss...vtslafspdgawlasGsdDgtvriWd 38 
                                    Hs+   ++s+   ++g+ l+ G  Dgt r+ d
  gene560|gene560|rna559|rna559 106 HSGenyISSV--KSNGDILCIGASDGTMRLID 135
                                    6223459999..99*****99955****9865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                    EEEEEEESSSS.EEEEEEETTSSEEEEEETTSE CS
                           WD40   2 qclrtltGHss.vtslafspdgawlasGsdDgt 33 
                                    + ++t + H+  v+sl  s +g+ + s++ D+t
  gene560|gene560|rna559|rna559 140 KEVHTMRNHNArVSSL--SWNGNVI-SSG-DKT 168
                                    6799*****555****..4466665.667.776 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 4.7e-10
                                    EESS.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvriW 37 
                                     +GH + +++l +s d ++lasG+ D+ +riW
  gene560|gene560|rna559|rna559 184 VEGHsQEICGLEWSTDTKYLASGGNDNVIRIW 215
                                    58**666************************* PP

  == domain 4  score: 20.1 bits;  conditional E-value: 2.4e-07
                                    EEEEEESS.SSEEEEEEETTSSE.EEEEE..TTSEEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgaw.lasGs..dDgtvriWd 38 
                                    + +tl+GH s v +la++p  +  l+sG+  +D t+++Wd
  gene560|gene560|rna559|rna559 221 NPQTLSGHkSAVKALAWCPWRSGiLTSGGgaKDMTIKFWD 260
                                    5689****666****65555555455664458*******9 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.077
                                    EEESSSSEEEEEEETTSSEEEEEET..TSEEEEEE CS
                           WD40   6 tltGHssvtslafspdgawlasGsd..DgtvriWd 38 
                                    +++++s v+ l + p  + ++s++    + +riW+
  gene560|gene560|rna559|rna559 269 SIDTQSQVCTLTYLPKYKEIISSHGyiENDIRIWK 303
                                    5555666899988888888998853469******6 PP

  == domain 6  score: 16.4 bits;  conditional E-value: 3.4e-06
                                    EEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    ++ ++  H s v ++a spdg+ las s D ++++W+
  gene560|gene560|rna559|rna559 309 LISSFGKHgSRVLHVALSPDGSELASVSADENLKFWK 345
                                    6788999*777**************9999*******6 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   2.5e-09   9.1e-06      47      90 ..     116     158 ..      78     160 .. 0.84
   2 !   16.9   0.1   1.6e-06    0.0059      32      89 ..     184     237 ..     160     238 .. 0.79
   3 !    4.8   0.1    0.0096        34      36      89 ..     227     281 ..     215     284 .. 0.79
   4 !    7.0   0.0     0.002         7      28      68 ..     300     347 ..     291     356 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.5e-09
                    ANAPC4_WD40  47 kpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                    k +g +L+++ sdg++rl+d++  k vh+++ ++  +v++l+W+
  gene560|gene560|rna559|rna559 116 KSNGDILCIGASDGTMRLIDISVNKEVHTMRNHNA-RVSSLSWN 158
                                    789******************************99.6******8 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.6e-06
                    ANAPC4_WD40  32 leedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                    +  +++++e+ +L+W+ d k La + +d+ +r+ +  + +    +  ks  av+ l W
  gene560|gene560|rna559|rna559 184 V--EGHSQEICGLEWSTDTKYLASGGNDNVIRIWQLGNNNPQTLSGHKS--AVKALAW 237
                                    4..67899**************************999888755544443..4888888 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0096
                    ANAPC4_WD40  36 kedsevrsLaWkpdgk.lLav..aysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                    +++s v++LaW p  + +L    + +d ++++ d+ + k+ +s++++s+  v++l++
  gene560|gene560|rna559|rna559 227 GHKSAVKALAWCPWRSgILTSggGAKDMTIKFWDVAENKLERSIDTQSQ--VCTLTY 281
                                    678999*****99654156553346899****************99998..888876 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.002
                    ANAPC4_WD40  28 rvwtl.......eedkedsevrsLaWkpdgklLavaysdgevrlldae 68 
                                    r+w++       +  k++s+v ++a +pdg+ La + +d ++++ ++ 
  gene560|gene560|rna559|rna559 300 RIWKAstmnlisSFGKHGSRVLHVALSPDGSELASVSADENLKFWKIF 347
                                    67777677777666899**********************999877665 PP

>> Ge1_WD40  WD40 region of Ge1, enhancer of mRNA-decapping protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   9.2e-05      0.33     157     218 ..     156     219 ..      96     230 .. 0.81
   2 !   21.0   0.0   3.8e-08   0.00013     161     225 ..     286     355 ..     222     357 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.2e-05
                       Ge1_WD40 157 iwsvdmiaskygsgelsveeieegllk.ieehs.liveaafspdGtalatasedGevkffqvyl 218
                                     w+ ++i+s  ++g+l + +i++g +  +e hs +i    +s+d   la   +d +++ +q+  
  gene560|gene560|rna559|rna559 156 SWNGNVISSGDKTGKLCNFDIRSGRISmVEGHSqEICGLEWSTDTKYLASGGNDNVIRIWQLGN 219
                                    48889999999************999725778879999***********************854 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 3.8e-08
                       Ge1_WD40 161 dmiaskygsgelsveeieegll....kieeh.sliveaafspdGtalatasedGevkffqvyledeeepr 225
                                    + i+s +g +e +    + +++     + +h s + + a+spdG  la  s+d  +kf++++ +++ + r
  gene560|gene560|rna559|rna559 286 KEIISSHGYIENDIRIWKASTMnlisSFGKHgSRVLHVALSPDGSELASVSADENLKFWKIFNSEKPSTR 355
                                    3455555554444444443333000134445368****************************99987655 PP

>> Nbas_N  Neuroblastoma-amplified sequence, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.014        51     186     262 ..     104     180 ..      79     217 .. 0.82
   2 !   17.2   0.0   6.9e-07    0.0025     186     260 ..     277     348 ..     259     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.014
                         Nbas_N 186 rvlsgspyykqvtsyeddvgalakkrgllkllslklysrkaeekdgvfkm.slspdgtllavihfsgklsiwdipslk 262
                                     + sg  y   v s++d ++      g ++l+++ +     + ++   ++ sls +g +++    +gkl+ +di s +
  gene560|gene560|rna559|rna559 104 DIHSGENYISSVKSNGDILC-IGASDGTMRLIDISVNKEVHTMRNHNARVsSLSWNGNVISSGDKTGKLCNFDIRSGR 180
                                    56789999999999887666.6678899999999998776655555555427999****9999999999999998865 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 6.9e-07
                         Nbas_N 186 rvlsgspyykqvtsyeddvgalakkrgllkllslklysrkaeekdgvfkmslspdgtllavihfsgklsiwdips 260
                                     +l+ +p yk++ s +  +    +   ++k  +++l s  ++    v++++lspdg+ la +    +l  w+i  
  gene560|gene560|rna559|rna559 277 CTLTYLPKYKEIISSHGYIE---NDIRIWKASTMNLISSFGKHGSRVLHVALSPDGSELASVSADENLKFWKIFN 348
                                    578889********999998...4578999*****************************************9954 PP

>> IKI3  IKI3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   4.4e-05      0.16     292     335 ..     177     220 ..     175     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.4e-05
                                    XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                           IKI3 292 rhgefslrlekeeeevqsLaWsadSevLavrledr.vqlwtisNy 335
                                    r g +s+  e +++e+  L+Ws+d + La   +d+ +++w  +N+
  gene560|gene560|rna559|rna559 177 RSGRISMV-EGHSQEICGLEWSTDTKYLASGGNDNvIRIWQLGNN 220
                                    55667775.5899*****************6655449******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2217.13
//
Query:       gene561|gene561|rna560|rna560  [L=585]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.4e-51  173.1   0.5    1.3e-50  172.5   0.5    1.3  1  SAC3_GANP  SAC3/GANP family


Domain annotation for each model (and alignments):
>> SAC3_GANP  SAC3/GANP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.5     7e-55   1.3e-50       1     292 [.      26     293 ..      26     294 .. 0.94

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 7e-55
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-----HHHHHHHHHHHHHHTG..G. CS
                      SAC3_GANP   1 GtCedmCPekEraeRevqkdlsrfEkekkktkkvdpskaVKeysRsaagqeeplpsdlRppevLkkTldYLlkeildree 80 
                                    G C+++CPe E  eR  ++d+s +E          ++ ++K+y++ +  ++  lp+d+Rp+evL++++++ + ++++++ 
  gene561|gene561|rna560|rna560  26 GECMTFCPELEGLERVLNNDVSPYE----------TEVMIKKYRKVSSETPCILPEDIRPMEVLLSVINHVI-RLCASD- 93 
                                    89***********************..........479**********************************.777444. PP

                                    .GTTTCHHHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHHHHHHTTS.---CHHHHHHHHHHHHHHHHHHHHH CS
                      SAC3_GANP  81 eelaevydFiwDRtRaiRqDltiqnlskaeaveilerivrfhilslhrlceepessfdeqqnleqLqkclqsLlelYddl 160
                                     +  ++y F ++RtRai  D++iq  ++++a+e+le+ivrf+i+ +++l ++p  +f++ +nl qL+ ++ sL +lYd  
  gene561|gene561|rna560|rna560  94 -QSLQMYRFAENRTRAIISDMKIQGERGKDAIEVLEKIVRFYIVFRYLLYDHP--HFNKDMNLGQLKVVMDSLVKLYDLE 170
                                    .7899************************************************..8*********************988 PP

                                    H....---TTHHHHHHHHHHHTTT-HHHHHHHCTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHTTS-HHHHHHHGG CS
                      SAC3_GANP 161 rkkk.eelpneaefrayylLlnlrdpdilrevqelpseilkspevqlalklvaalqennyvrffklvkevsylqacller 239
                                    ++ +  e ++++ef +y+++ ++++     ++q    ++ + p+v+l +++ + ++++n + ffkl++++  +  cl+++
  gene561|gene561|rna560|rna560 171 EA-GwCEKDRKEEFYCYHIIATMGERCPF-RIQ----RWDDGPRVRLSMEITRKYMQKNGAGFFKLLRKLDCIAFCLAQS 244
                                    84.44888899************987555.456....667889************************************* PP

                                    GHHHHHHHHHHHHHHHS-TT---EEHHHHHHHTT-SSHHHHHHHHHHTT--EE CS
                      SAC3_GANP 240 hfnevRrkalkalsraykskskkvpleeLaelLlfddeeeaeefceayglevs 292
                                    +  evR ++++++++++   ++kv++e L ++L     +eaeef++  g+ v+
  gene561|gene561|rna560|rna560 245 FAGEVRARCIQMFRKSL---AEKVSIEFLEDILWARG-SEAEEFLRRNGIVVK 293
                                    *****************...789*************9.9*******9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 3147.88
//
Query:       gene562|gene562|rna561|rna561  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1318.75
//
Query:       gene563|gene563|rna562|rna562  [L=282]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-10   40.3   0.0    3.4e-10   39.7   0.0    1.3  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   1.9e-14   3.4e-10       4     135 .]      67     222 ..      62     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.9e-14
                Acyltransferase   4 vtglenlpekgpailvaNHqsylDvlllwlllyksn.gprnvviiakkellsipllgflmrllgfifidRksnaraagsl 82 
                                    v+g+  +  ++ + +++NH   +D++l++ ++ ks+ +   v+ ++k+ l  +p++ +++  +gf  ++R s +++++ +
  gene563|gene563|rna562|rna562  67 VHGSIDIG-NESYFVISNHIGSVDFILINEIARKSGmI-SHVKYAVKDGLRVFPVFYQIIVYVGFLVLKR-SFEKDKKKI 143
                                    56644455.58899******************999955.99999999999999*****************.888888888 PP

                Acyltransferase  83 eniselleeg..kl.vviFPEGtrsre...................gellpfkkGlvrlaakak....kgvpivPvais 135
                                     +++e ++ +  ++  v++PEG r++e                     l+p +kG++ + +++k    k++++v++++s
  gene563|gene563|rna562|rna562 144 IRYLEFFNTSgiPIwFVFYPEGSRFSEelklkswkysdekgmarlnNVLFPRYKGFKLICENLKnsriKKIVDVTFSYS 222
                                    888897777745444889************************9975555**************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1801.71
//
Query:       gene564|gene564|rna563|rna563  [L=869]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-39  135.2   0.1    3.3e-39  134.2   0.1    1.6  1  DSHCT           DSHCT (NUC185) domain
    1.5e-19   70.4   0.0    3.9e-19   69.1   0.0    1.7  1  DEAD            DEAD/DEAH box helicase
    1.7e-06   28.3   0.0    1.7e-05   25.2   0.0    2.7  1  Helicase_C      Helicase conserved C-terminal domain
    3.1e-06   27.3   0.0    5.9e-06   26.4   0.0    1.4  1  ResIII          Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.061   13.6   0.0    1.7  1  AAA_22          AAA domain
      0.032   14.1   0.0      0.087   12.7   0.0    1.7  1  ATPase_2        ATPase domain predominantly from Archaea
      0.045   13.7   1.7      0.097   12.6   0.0    2.1  2  rRNA_proc-arch  rRNA-processing arch domain


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.2   0.1   1.3e-42   3.3e-39       2     163 ..     702     863 ..     701     864 .. 0.87

  Alignments for each domain:
  == domain 1  score: 134.2 bits;  conditional E-value: 1.3e-42
                          DSHCT   2 ntvtlkGrvaaeirsedeLlltellfsgvlddlepeelaAllsalvfeekredeeekepkl.seeleealeelkeiaeri 80 
                                    + +t+kGr+aaei++ +e+l+ e++fs+++ +++  ++++l+s+++ ee  e+e  ++ ++  ++++e ++el    +++
  gene564|gene564|rna563|rna563 702 EAITMKGRAAAEIHTVNEVLVVEMIFSNEFREMDGRKIISLMSSMIHEEPDEQEPGETLYVeCKKMKEYFAEL---SKDL 778
                                    579**********************************************977666654555555566555555...5555 PP

                          DSHCT  81 akvs...vesrldlglvevvyaWakgasfaellektdldeGdiVRllrrleellrqlakaakvigneeLkkkaeeaieli 157
                                    ++++   + + l ++lve+vy+W++g s+a+++++  + eG++VRl++rlee++r+l  ++ +ig+++L++k+++a+  +
  gene564|gene564|rna563|rna563 779 EELMippFAP-LTFSLVEAVYDWCSGSSLAKIVSNHGVLEGTFVRLILRLEECCRELMGVSAMIGDKALEEKIRDASMSM 857
                                    5554444564.69******************************************************************* PP

                          DSHCT 158 kRdiVf 163
                                    kRdi+f
  gene564|gene564|rna563|rna563 858 KRDIIF 863
                                    *****8 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.0   1.5e-22   3.9e-19       3     172 ..      56     202 ..      54     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.5e-22
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                     Q++a+  + ++ +v+v+a+T sGKTl++  ++   +    +k+g+++++ +P ++L +q ++++k+  + ++     ii
  gene564|gene564|rna563|rna563  56 FQKQAFYFLSRESSVFVSAHTSSGKTLVAEYAIS--L---SQKHGTRTIYTSPIKALSNQKYHDFKQKYDDVG-----II 125
                                    699999999999*****************99999..5...3799***********************999644.....55 PP

                                    TTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  83 ggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                    +g+ +      ++ +++++v+t++ l +l+ ++   l++ +f+V+DE++ + d++++  +++++  lp        +  +
  gene564|gene564|rna563|rna563 126 TGDVQ------VNPTAKCLVMTTEILRNLVYRNGDLLRDTEFVVFDEVHYINDSERGVVWEECIIMLP-------RNISF 192
                                    55444......23447789*********99544446*******************************4.......5566* PP

                                    EEEESSBSHH CS
                                    xxxxxxxxxx RF
                           DEAD 163 ivlSATlpkd 172
                                    i+lSAT+p++
  gene564|gene564|rna563|rna563 193 IMLSATIPNS 202
                                    *******965 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   6.5e-09   1.7e-05      42     111 .]     350     427 ..     272     427 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.5e-09
                                    TEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.........SSHHHHHHHHTTSSSTT CS
                     Helicase_C  42 kvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp.........rnvtsyiqriGRtgRag 111
                                     +av+hg+l    +e +   f  + +++Liat   ++G+++p ++++++++l           +  +yiq++GR+gR g
  gene564|gene564|rna563|rna563 350 GIAVHHGSLLPFVKECVELLFSMNLVKLLIATETFAMGVNMP-AKCCVFLSLSkidsgvfryVSSGEYIQMSGRAGRRG 427
                                    57889************************************9.6666666666566555444445************75 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.3e-09   5.9e-06      21     170 ..      58     200 ..      36     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.3e-09
                                    ........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B CS
                         ResIII  21 s......krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkk 94 
                                    +       r+  +++ + T +GKTlva  +i   +k+g   +++   p k+l +q +++fk+ +++      ++++gd +
  gene564|gene564|rna563|rna563  58 KqafyflSRESSVFVSAHTSSGKTLVAEYAISLSQKHGT--RTIYTSPIKALSNQKYHDFKQKYDDV-----GIITGDVQ 130
                                    244445567788899999********9666665555444..9******************9988864.....88999988 PP

                                    --.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT-.--SEEEEEESS-S CS
                         ResIII  95 kakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilekf.keavllglTATpe 170
                                     +      ++k lv+t++ l +       +++  l    +++++DE+H +++++    w+e++ ++ ++   + l+AT++
  gene564|gene564|rna563|rna563 131 VN-----PTAKCLVMTTEILRNLV-----YRNGDLLRDTEFVVFDEVHYINDSErgvVWEECIIMLpRNISFIMLSATIP 200
                                    88.....89*************99.....888888888999***********85888****7666625567789999986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.061       5     116 ..      67     186 ..      64     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsst...sskdllrellralglelka.....erl 73 
                                    +++++v +++ +GKT++++   +  +++      + +++    +++ s     + k+ + ++  ++g+ + +        
  gene564|gene564|rna563|rna563  67 ESSVFVSAHTSSGKTLVAEYAISLSQKH------GTRTIytsPIKALSNQkyhDFKQKYDDVGIITGDVQVNptakcLVM 140
                                    678899999************9998766......6666633322222222122444444555555554444465677777 PP

                         AAA_22  74 sseellealeqalraravielliiDEaqhlr...seealeeLrsll 116
                                    ++e l+++++++ +  +++e+++ DE+++++   +  ++ee+ ++l
  gene564|gene564|rna563|rna563 141 TTEILRNLVYRNGDLLRDTEFVVFDEVHYINdseRGVVWEECIIML 186
                                    888888888888888888************9854488888875554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.4e-05     0.087      24     131 ..      71     171 ..      64     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                       ATPase_2  24 fiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk...eksk 100
                                    f+    +sGKt +   +i+ +++++ + iy ++++  s++k+ +f   ++      + +gi ++ ++++   k    +++
  gene564|gene564|rna563|rna563  71 FVSAHTSSGKTLVAEYAISLSQKHGTRTIYTSPIKALSNQKYHDF---KQ----KYDDVGIITGDVQVNPTAKclvMTTE 143
                                    5566679**************************************...22....23334444444444433332212222 PP

                       ATPase_2 101 lvfkaielllekikkkgkkiiiiiDelqkli 131
                                       +++ +   ++ ++     +++De+ ++ 
  gene564|gene564|rna563|rna563 144 I-LRNLVYRNGDLLRDT--EFVVFDEVHYIN 171
                                    2.222222222222222..356666666665 PP

>> rRNA_proc-arch  rRNA-processing arch domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.8e-05     0.097       1      51 [.     480     529 ..     480     545 .. 0.86
   2 ?   -0.9   0.7      0.47   1.2e+03     224     265 ..     633     673 ..     626     677 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.8e-05
                                    HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHTC--TT.HHHHHHHHHHHHH CS
                 rRNA_proc-arch   1 EyMlerSFsqfqnqkslpelekklkeleeelksitied.eedieeyyklrqq 51 
                                    E++++rS+ ++ +q++  +  k+l ele e++ ++  +   d+++y ++ ++
  gene564|gene564|rna563|rna563 480 EDLMRRSYGEHRSQRNYEKDMKRLSELERERDDTC--NvCGDLTNYIDAVEE 529
                                    99*******************************76..335578888776655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.47
                                    HHHHHHHHHHHTSGG.GSSSHHHHHHHHHHHHHHHHHHHHHH CS
                 rRNA_proc-arch 224 kkiealesrlaknpllhspnleelyalyekkvalqeeikelk 265
                                    +++++l   l + +   +++++ +y+   k  + ++ei+e+k
  gene564|gene564|rna563|rna563 633 RRLRSLYDSLISEKK-DCKEFDLHYSNALKTSHKRKEIEEIK 673
                                    566677777766554.59********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (869 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 5614.31
//
Query:       gene565|gene565|rna564|rna564  [L=304]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-16   59.5   3.1    9.3e-08   31.8   0.1    3.1  3  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.21   3.8e+03      14      26 ..      89     101 ..      85     104 .. 0.77
   2 !   26.9   0.1   1.8e-10   3.1e-06       3      50 ..     145     192 ..     144     209 .. 0.91
   3 !   31.8   0.1   5.2e-12   9.3e-08       2      61 ..     221     281 ..     221     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.21
                                    HHHHHHHTTSCEE CS
                          RRM_1  14 eLkelFskfGpik 26 
                                    ++k+ F++f ++k
  gene565|gene565|rna564|rna564  89 DIKKTFKNFKDMK 101
                                    8999999997765 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1.8e-10
                                    EESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHH CS
                          RRM_1   3 VgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeske 50 
                                    ++nL++  ++e ++++F+k+G+i++i++ +++++ s+g a+++F+++ 
  gene565|gene565|rna564|rna564 145 LTNLSYKEDKESISKVFKKYGEIERITIKKNKDNISTGKAIITFKKRA 192
                                    589*****************************************9875 PP

  == domain 3  score: 31.8 bits;  conditional E-value: 5.2e-12
                                    EEESETTTSSHHHHHHHHHTTSCE.EEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTT CS
                          RRM_1   2 fVgnLppdvteeeLkelFskfGpi.ksiklvrdetgkskgfafVeFeskedAekAlealng 61 
                                    f+g L+++++  e++++F k++   k+i++ + e+++++g++f+e++++ dA+  +e++ +
  gene565|gene565|rna564|rna564 221 FLGKLTKSLSIVEIRKIFAKVECKpKDIRILYGENKRNRGYGFIEYANEKDANVFIERFEK 281
                                    78999***************88666****************************99997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2021.77
//
Query:       gene566|gene566|rna565|rna565  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-43  145.4   0.5    9.4e-43  145.0   0.5    1.1  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.0   0.5   5.3e-47   9.4e-43       2     108 .]      22     128 ..      21     128 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.0 bits;  conditional E-value: 5.3e-47
                                    -----TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..EE CS
                 Ribosomal_L32e   2 kkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksyaa 81 
                                    kkFirh+sdry+++k swrkp+Gid++vr+r+kgq++mp+i Y++pk++r+llp+G++kv + n+++L+ l   n+ y+ 
  gene566|gene566|rna565|rna565  22 KKFIRHHSDRYKRVKPSWRKPHGIDSKVRKRCKGQREMPSIKYKKPKEIRHLLPNGLRKVRIFNINDLTPLASLNRFYCG 101
                                    8******************************************************************************* PP

                                    EE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                 Ribosomal_L32e  82 eiahsVsskkrkeiverAaelgikVtN 108
                                    eiah+V+++kr++iv+rA+elgi ++N
  gene566|gene566|rna565|rna565 102 EIAHAVGARKRIAIVNRAKELGICLLN 128
                                    ***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 807.37
//
Query:       gene567|gene567|rna566|rna566  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.7   0.0        7.3    6.8   0.1    3.5  3  NHL       NHL repeat


Domain annotation for each model (and alignments):
>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1   0.00041       7.3      13      26 ..      79      94 ..      73      95 .. 0.90
   2 ?    4.3   0.0    0.0027        48       2      24 ..     106     128 ..     105     131 .. 0.80
   3 ?   -0.9   0.0      0.12   2.1e+03       3      13 ..     179     190 ..     177     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00041
                                   TEEEEEE..CCCTEEE CS
                            NHL 13 GdiyVaD..senhrvq 26
                                   +++yVaD     hr++
  gene567|gene567|rna566|rna566 79 NEVYVADrfGDVHRIR 94
                                   89******99999996 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0027
                                    SSEEEEEEETTTEEEEEE.CCCTE CS
                            NHL   2 nyPhGvavdsnGdiyVaD.senhr 24 
                                    +y +G a+  nG+i+ +D +++ r
  gene567|gene567|rna566|rna566 106 SYLTGMAIH-NGRILLSDkYGRIR 128
                                    677899996.********777655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.12
                                    SEEEEEEE.TTT CS
                            NHL   3 yPhGvavd.snG 13 
                                     P+G++v+ s+G
  gene567|gene567|rna566|rna566 179 LPEGTSVVkSMG 190
                                    6******98877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1424.13
//
Query:       gene568|gene568|rna567|rna567  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0027   17.5   0.1       0.01   15.6   0.1    2.1  1  BCIP      p21-C-terminal region-binding protein


Domain annotation for each model (and alignments):
>> BCIP  p21-C-terminal region-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.8e-07      0.01      38     137 ..      65     150 ..      38     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.8e-07
                           BCIP  38 eLadlileqktvGsvvkvdgeesDpvygllsvlnlkkhkekecikqlkeyllekakksasskkklkklLssskdkkvgll 117
                                     +++  l++ t+ +v+       D +++++ +l l +       k+lk+ l++ +++s s     k++++ +   kv  +
  gene568|gene568|rna567|rna567  65 PFSEEFLSSFTISKVLTS----GDTILSFCGFLQLSRMLG-IPQKKLKKALNTLISTSGS-----KEIIK-D---KVYVF 130
                                    555555555555555544....466677777777766653.4556777777777776666.....56663.3...5**** PP

                           BCIP 118 iseRliNiPvevvpplykmL 137
                                     +eR  NiP+e +  lyk+L
  gene568|gene568|rna567|rna567 131 CTERAANIPLEMILDLYKSL 150
                                    ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1419.57
//
Query:       gene569|gene569|rna568|rna568  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-05   23.8   0.0    6.5e-05   23.0   0.0    1.4  1  CBF       CBF/Mak21 family
  ------ inclusion threshold ------
      0.056   12.3   0.1       0.06   12.2   0.1    1.2  1  DUF3384   Domain of unknown function (DUF3384)


Domain annotation for each model (and alignments):
>> CBF  CBF/Mak21 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   7.2e-09   6.5e-05      25      99 ..     117     191 ..     103     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7.2e-09
                            CBF  25 dRFyraLYrkLldpelltsskralllnlly...kalkadkpvkrvaAFvKRllqlalhappsfalgllallsellk.hp 99 
                                    d F+++L+ ++++ ++ +  +++ll+ l++    +     p++ ++AF+K+l+ ++l++++s +  +l  +  +++ hp
  gene569|gene569|rna568|rna568 117 DGFHSTLFDCITSRNIEEDIEKKLLFILMTledGST----PLAVAKAFIKKLCNISLQVKSSHCHKILWTILWIMRfHP 191
                                    88*********9999999999999998888765555....************************999999999998555 PP

>> DUF3384  Domain of unknown function (DUF3384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   6.7e-06      0.06     178     242 ..     122     184 ..      17     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-06
                                    HHHHHHCS-S-HHHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHHHHH-GG....GHHHHHHHH CS
                        DUF3384 178 saleicigtsnaddlrsclklldaiiryghlPsasldvvikvLCsiycridsndddlqkevwril 242
                                     +++++++ + ++d+++ l ++ +++  g+ P a  + +ik LC i  +++s  ++++k  w il
  gene569|gene569|rna568|rna568 122 TLFDCITSRNIEEDIEKKLLFILMTLEDGSTPLAVAKAFIKKLCNISLQVKS--SHCHKILWTIL 184
                                    567788888899**********************************666665..89999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1574.09
//
Query:       gene570|gene570|rna569|rna569  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.08   12.6   0.0       0.16   11.6   0.0    1.6  1  Terpene_synth  Terpene synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Terpene_synth  Terpene synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   8.9e-06      0.16      97     131 ..      89     124 ..      44     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.9e-06
                                    BHHHHHHHHHHHHHTT----GGGGGGGE.ETT...E CS
                  Terpene_synth  97 dletvAlaFrLLRqhGydvssdvFkkFkdeeg.nfk 131
                                    + +  A+ + +LR h y +s + ++ F+++ + +fk
  gene570|gene570|rna569|rna569  89 NDKILAIIYNVLRRHQYPISYSDLEPFTEKTSsRFK 124
                                    44668**********************986541455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1469.59
//
Query:       gene57|gene57|rna57|rna57  [L=431]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-06   26.2   7.2    5.2e-06   26.2   7.2    4.7  5  zf-C3HC4_3   Zinc finger, C3HC4 type (RING finger)
    0.00048   20.4   7.4    0.00048   20.4   7.4    4.7  5  zf-RING_2    Ring finger domain
     0.0054   16.6   7.4     0.0054   16.6   7.4    5.4  5  zf-C3HC4     Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.024   14.5   5.7      0.024   14.5   5.7    3.9  3  Prok-RING_4  Prokaryotic RING finger family 4


Domain annotation for each model (and alignments):
>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   7.2   1.2e-09   5.2e-06       5      49 ..       3      48 ..       1      49 [. 0.94
   2 ?    2.0   1.1     0.043   1.9e+02      28      46 ..      80     100 ..      79     104 .. 0.85
   3 ?    0.8   6.5       0.1   4.5e+02       3      34 ..      92     127 ..      90     133 .. 0.76
   4 ?   -1.9   6.8       0.7   3.1e+03      21      43 ..     156     187 ..     155     193 .. 0.74
   5 ?   -6.2   2.7         4   1.8e+04      26      26 ..     214     214 ..     210     225 .. 0.47

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.2e-09
                               -TTTSSSBS-EEETTEEEEEE-HHHHHHHHH..TT-B-TTT--B--E CS
                 zf-C3HC4_3  5 CviClerprnvvllpCgHlvlCeeCaekllk..rkkkCpiCrrpiek 49
                               C++C  +   ++ ++C+H  +C  C+ +l    ++++Cp+Cr+p e+
  gene57|gene57|rna57|rna57  3 CQVCTGSMDVFARYDCNHR-ICMVCSMRLVFlyMQPTCPLCRKPAEE 48
                               *******************.*********8799**********9886 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.043
                                HHHHHHHH..TT-B-TTT--B CS
                 zf-C3HC4_3  28 eCaekllk..rkkkCpiCrrp 46 
                                eC++k+++   ++kC  C+ +
  gene57|gene57|rna57|rna57  80 ECVKKMMEdlLSNKCQKCHNK 100
                                799999989999999999876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.1
                                SB-TTTSSS....BS-EEETTEEEEEE-HHHHHHHH CS
                 zf-C3HC4_3   3 eeCviCler....prnvvllpCgHlvlCeeCaekll 34 
                                ++C+ C+++    ++    + C  ++lC eC ++ +
  gene57|gene57|rna57|rna57  92 NKCQKCHNKfgtlKELSKHYSCHGVILCLECIKNRK 127
                                689999997444344467778*999******99874 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.7
                                EEEEE-HHHHHHHHH..........TT-B-TTT CS
                 zf-C3HC4_3  21 gHlvlCeeCaekllk..........rkkkCpiC 43 
                                gH+ lC +C   l +          +++ C++C
  gene57|gene57|rna57|rna57 156 GHV-LCVHCKIYLFDsddakqhcnlKHELCHVC 187
                                788.99999999988788666666666666666 PP

  == domain 5  score: -6.2 bits;  conditional E-value: 4
                                - CS
                 zf-C3HC4_3  26 C 26 
                                C
  gene57|gene57|rna57|rna57 214 C 214
                                2 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   7.4   1.1e-07   0.00048       3      44 .]       3      43 ..       1      43 [. 0.84
   2 ?    4.0   3.8     0.014        64       1      32 [.      92     125 ..      92     133 .. 0.82
   3 ?   -6.0   9.0         4   1.8e+04      22      43 ..     156     187 ..     155     188 .. 0.49
   4 ?   -6.2   5.4         4   1.8e+04      25      25 ..     227     227 ..     204     249 .. 0.54
   5 ?   -3.7   0.0       3.6   1.6e+04       2      13 ..     255     267 ..     254     271 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-07
                  zf-RING_2  3 CpICleelssadsvlllpCgHvfhreClerw..lrssstCPlCr 44
                               C +C+ +++      + +C+H ++  C +r+  l  ++tCPlCr
  gene57|gene57|rna57|rna57  3 CQVCTGSMD---VFARYDCNHRICMVCSMRLvfLYMQPTCPLCR 43
                               ****97774...444557************777999*******9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                  zf-RING_2   1 deCpICleelssadsvlll.pCgH.v.fhreCler 32 
                                ++C  C +++ + +++ +   C H v  + eC+++
  gene57|gene57|rna57|rna57  92 NKCQKCHNKFGTLKELSKHySC-HgViLCLECIKN 125
                                58999*****99999996668*.54659****965 PP

  == domain 3  score: -6.0 bits;  conditional E-value: 4
                  zf-RING_2  22 gHvfhreCl..........erwlrssstCPlC 43 
                                gHv + +C           ++ + +++ C +C
  gene57|gene57|rna57|rna57 156 GHVLCVHCKiylfdsddakQHCNLKHELCHVC 187
                                57788888544455444322223333336666 PP

  == domain 4  score: -6.2 bits;  conditional E-value: 4
                  zf-RING_2  25 f 25 
                                f
  gene57|gene57|rna57|rna57 227 F 227
                                1 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 3.6
                  zf-RING_2   2 eCpIC.leelssa 13 
                                +C I  +++++++
  gene57|gene57|rna57|rna57 255 KCNIPvMDPFKKK 267
                                6999977888765 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   7.4   1.2e-06    0.0054       1      41 []       3      42 ..       3      42 .. 0.97
   2 ?    1.4   1.6     0.069   3.1e+02      24      41 .]      80      97 ..      79      99 .. 0.79
   3 ?   -5.0   6.9         4   1.8e+04      13      28 ..     109     125 ..      94     134 .. 0.61
   4 ?   -7.4  10.7         4   1.8e+04      19      38 ..     157     177 ..     156     187 .. 0.52
   5 ?   -6.0   2.6         4   1.8e+04       4       9 ..     213     218 ..     210     225 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-06
                               -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                   zf-C3HC4  1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41
                               C++C+  +       +C+H++C  C  +++   ++ +CPlC
  gene57|gene57|rna57|rna57  3 CQVCTGSMDVFA-RYDCNHRICMVCSMRLVFLYMQPTCPLC 42
                               9*****999999.9*****************9999****** PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.069
                               HHHHHHHHCTSSB--TTT CS
                   zf-C3HC4 24 kCirkilksrkkvkCPlC 41
                               +C++k++++  ++kC +C
  gene57|gene57|rna57|rna57 80 ECVKKMMEDLLSNKCQKC 97
                               6*******9566677777 PP

  == domain 3  score: -5.0 bits;  conditional E-value: 4
                                .E-TTS--.B-CHHHHH CS
                   zf-C3HC4  13 elleCkHs.fCskCirk 28 
                                +   C+   +C +Ci++
  gene57|gene57|rna57|rna57 109 KHYSCHGViLCLECIKN 125
                                55566666689999987 PP

  == domain 4  score: -7.4 bits;  conditional E-value: 4
                                --B-CHHHHHHHHC.TSSB-- CS
                   zf-C3HC4  19 HsfCskCirkilks.rkkvkC 38 
                                H +C +C   + +s + k+ C
  gene57|gene57|rna57|rna57 157 HVLCVHCKIYLFDSdDAKQHC 177
                                777777777666666333333 PP

  == domain 5  score: -6.0 bits;  conditional E-value: 4
                                T-S--S CS
                   zf-C3HC4   4 Cleeak 9  
                                C++ ++
  gene57|gene57|rna57|rna57 213 CCTFQT 218
                                333333 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   5.7   5.4e-06     0.024       1      39 [.       3      45 ..       3      51 .. 0.87
   2 ?   -2.5   4.4       1.1   4.9e+03      15      27 ..     112     125 ..      94     129 .. 0.77
   3 ?   -6.9   8.9         4   1.8e+04      17      24 ..     156     163 ..     156     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.4e-06
                Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeCfdskdls....sCPlCqrr 39
                               C +C+ +  + +   C+H +C  C     +     +CPlC++ 
  gene57|gene57|rna57|rna57  3 CQVCTGSMDVFARYDCNHRICMVCSMRLVFLymqpTCPLCRKP 45
                               999**********************9995555568******85 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                Prok-RING_4  15 pCgHl.vCkeCfds 27 
                                +C  + +C eC ++
  gene57|gene57|rna57|rna57 112 SCHGViLCLECIKN 125
                                7876669****876 PP

  == domain 3  score: -6.9 bits;  conditional E-value: 4
                Prok-RING_4  17 gHlvCkeC 24 
                                gH++C +C
  gene57|gene57|rna57|rna57 156 GHVLCVHC 163
                                79999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.52
# Mc/sec: 2477.99
//
Query:       gene571|gene571|rna570|rna570  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-14   52.0   0.0    6.4e-14   51.8   0.0    1.0  1  S10_plectin  Plectin/S10 domain


Domain annotation for each model (and alignments):
>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   3.6e-18   6.4e-14       1      85 [.       3      86 ..       3      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 3.6e-18
                                   --HCHHHHHHHHCCCCSCEEEE--SS----SSS---HHHHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHHHHXXXX CS
                    S10_plectin  1 ipkknrkaiyeylfkegvlvakkdfelkkheelnvpnlqvikalqSLksrgyvkeqfaWrhyYytLtneGieylreylhlpe 82
                                   ip+ n+ +i + l+++  l+ + d+ l +h++l++pnlq   +++ + s gyv++   Wrh Y++Lt+ G + lre+l +++
  gene571|gene571|rna570|rna570  3 IPTPNKYKIKRRLLEKKALLLE-DTVLGNHRDLEIPNLQLKVFMKTMISHGYVQKVHIWRHSYFLLTSLGESRLREELVFTD 83
                                   7889999**********99998.66679**************************************************9988 PP

                                   SXH CS
                    S10_plectin 83 eiv 85
                                   e +
  gene571|gene571|rna570|rna570 84 EGM 86
                                   765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.34s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 569.43
//
Query:       gene572|gene572|rna571|rna571  [L=66]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 418.28
//
Query:       gene573|gene573|rna572|rna572  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-32  109.2   1.6    7.9e-32  109.0   1.6    1.0  1  CutA1     CutA1 divalent ion tolerance protein


Domain annotation for each model (and alignments):
>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   1.6   4.4e-36   7.9e-32       2      97 ..       6     100 ..       5     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 4.4e-36
                                    EEEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                          CutA1   2 lvlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81 
                                    +v++t+p++e+a+k++ +l+++kla C++i + + S+Y Wkg +e+++E++l+ikt+++ +++++++++e hpyevpeii
  gene573|gene573|rna572|rna572   6 IVFTTYPTKESAEKVSYELLARKLAVCCQISQ-VASIYSWKGSVEKETEYKLTIKTSSSLFDKIQRFMEESHPYEVPEII 84 
                                    89***************************999.*********************************************** PP

                                    EEEESEEEHHHHHHHH CS
                          CutA1  82 alpieagseaYlkWie 97 
                                     +++ ++s++Yl+W++
  gene573|gene573|rna572|rna572  85 GIEARSASKEYLEWLH 100
                                    **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 746.89
//
Query:       gene574|gene574|rna573|rna573  [L=338]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-07   30.5   0.1      6e-07   29.6   0.1    1.4  1  Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein
    0.00015   21.0   0.0    0.00033   19.9   0.0    1.6  1  Rad21_Rec8    Conserved region of Rad21 / Rec8 like protein


Domain annotation for each model (and alignments):
>> Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   6.7e-11     6e-07      23      87 ..      23      85 ..      14      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.7e-11
                   Rad21_Rec8_N 23 lekklskkeilevniekaveeIlnpeaplaLrlsgqLllGvvriyskkvkyllsDceealekikk 87
                                   +e++lsk+++ ev+i+ +v +++++  +++ +  g  +lG++ri+ +k+kyl+++c+++++ki +
  gene574|gene574|rna573|rna573 23 MERRLSKHNLKEVSISAIVLKVMDE--SVSVKDGGLVVLGLTRIFVRKLKYLQDECSDTVHKIYQ 85
                                   599********************97..89999*****************************9965 PP

>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.7e-08   0.00033       6      47 ..     292     333 ..     289     337 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.7e-08
                                    TT----------HHHHHHHHHHHHHHHHTSEEEEESSTT--E CS
                     Rad21_Rec8   6 dslsllpagktRkeAArlFyelLvLatkgvIkvkQeaPYgdI 47 
                                    +++++l+ g +R e  r+F +lL L   gv+++ Q++ Y++I
  gene574|gene574|rna573|rna573 292 FIFNELTIGHSRHEKGRMFLSLLKLLGDGVLQAYQDRSYSNI 333
                                    6789*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1888.55
//
Query:       gene575|gene575|rna574|rna574  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0019   18.4   1.9       0.34   11.2   0.0    2.7  3  Ribosomal_L13  Ribosomal protein L13
  ------ inclusion threshold ------
       0.12   12.7   7.5       0.25   11.6   7.5    1.5  1  DUF349         Domain of Unknown Function (DUF349)


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   3.8e-05      0.34       3      23 ..       7      27 ..       5      34 .. 0.89
   2 !    6.2   0.0    0.0013        12      80     114 ..      72     107 ..      35     113 .. 0.83
   3 ?   -1.6   0.1      0.35   3.1e+03      87      87 ..     173     173 ..     142     198 .] 0.46

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                                   EEEEETTSBHHHHHHHHHHHH CS
                  Ribosomal_L13  3 yviDAegqvlgrlaskiakvL 23
                                   ++iDA+gqv g+la+k+ k+L
  gene575|gene575|rna574|rna574  7 VIIDATGQVAGKLAAKVTKLL 27
                                   79***************9987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0013
                                    HCCSHHHHHHHHHHCCS-SSH.HHHHHGCTEEEESS CS
                  Ribosomal_L13  80 lekkpeeilekaVkgmLpknk.lgrrrlkrLkvyag 114
                                    + ++p++ l k +++m+  +k  g+  +++L  y+g
  gene575|gene575|rna574|rna574  72 HFREPRMHLAKIIRRMISYKKaRGKIAMSKLATYEG 107
                                    6689999***********6661566667******98 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.35
                                    H CS
                  Ribosomal_L13  87 i 87 
                                    +
  gene575|gene575|rna574|rna574 173 V 173
                                    2 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   7.5   2.8e-05      0.25      15      50 ..     150     185 ..     147     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                         DUF349  15 errkahfeeqdaereenlekKealieeaealakstt 50 
                                    e+ k   ee+++ +++++ kKe+ ++eae+l+k+++
  gene575|gene575|rna574|rna574 150 EAAKSLTEELREREKQAFLKKEEVCKEAEKLKKDKS 185
                                    5667789************************88742 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1236  (0.0689386); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1291.38
//
Query:       gene576|gene576|rna575|rna575  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-13   49.7   0.8    3.5e-13   49.1   0.8    1.4  1  YL1_C     YL1 nuclear protein C-terminal domain


Domain annotation for each model (and alignments):
>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.8   1.9e-17   3.5e-13       1      29 []      52      80 ..      52      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.9e-17
                          YL1_C  1 yCdITGlpAkYrDPkTgLpYanveaykvI 29
                                   +Cd TGlpA+Y++P T+L Y+n++++k I
  gene576|gene576|rna575|rna575 52 LCDLTGLPAPYTCPNTRLFYYNSSVFKRI 80
                                   6**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 633.77
//
Query:       gene577|gene577|rna576|rna576  [L=1396]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-79  267.1   0.0    5.8e-79  265.3   0.0    2.0  2  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    4.8e-60  202.5   0.0    7.9e-60  201.8   0.0    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
      1e-33  117.0   5.6    1.2e-33  116.7   1.0    2.5  2  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
      2e-27   96.0   3.3      4e-27   95.1   0.0    2.9  4  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    5.9e-19   68.0   0.0    2.5e-18   66.0   0.0    2.1  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.78   2.8e+03     206     253 ..     135     182 ..     127     221 .. 0.72
   2 !  265.3   0.0   1.6e-82   5.8e-79       1     263 [.     827    1337 ..     827    1341 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.78
                                    HHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS--- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 206 leilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeiva 253
                                    + + + e++ +++++ +++  k++  s  +rH e++ + +  +g+  +
  gene577|gene577|rna576|rna576 135 YMVEEEEELYRIVTEKVESSKKRKTASSTERHQEVVHKFLSNTGSRRK 182
                                    555556667777777777777777777777887777777766665444 PP

  == domain 2  score: 265.3 bits;  conditional E-value: 1.6e-82
                                     B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS............ CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                 RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg............ 66  
                                     G++  ++ffh+m+gReGLiDtAvkTa+sGYlqR+lvk++e+v v+yd + r+ g ++vqf+ygedg            
  gene577|gene577|rna576|rna576  827 GIDLPQYFFHCMAGREGLIDTAVKTANSGYLQRCLVKHMEEVKVEYDMSARM-GSKVVQFIYGEDGldctkssylddi 903 
                                     89999********************************************975.789********************** PP

                                     ......................................................B--TT-BHHHHHHHHHHHHHHCCC CS
                                     ......................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   67 ......................................................lvepGeavGiiaaQSiGePgTQlt 90  
                                                                                           l +pGe+vGiiaaQS+GeP+TQ+t
  gene577|gene577|rna576|rna576  904 effrkntvlfkekesgisklgdiskgflskkfkdqieklddelkrfltsryvcsLADPGESVGIIAAQSVGEPSTQMT 981 
                                     ****************************************************************************** PP

                                     SSTTSSTCSSTSSSSSSHHHHHHHHTT.-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE................. CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                 RNA_pol_Rpb1_5   91 lnTFHfaGvasknvtlGvprlkeilnv.skniksksltvllvdeeakelekakkvkkaiek................. 150 
                                     lnTFH+aGv++knvtlGvprl+eil v s+ ik++ + v + +++  + +    +kk + k                 
  gene577|gene577|rna576|rna576  982 LNTFHLAGVGAKNVTLGVPRLREILLVaSRSIKTPLIVVPIKRNVGFDIAGC--LKKVTLKdcvkkfgvaeeivmidg 1057
                                     ************************99889***************99988763..333333334557999********* PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5  151 .............................................................................. 150 
                                                                                                                   
  gene577|gene577|rna576|rna576 1058 vfqkkvkivfelsnfvdlasealnkkflklfgkkmrglckakyklgvsevgkkglpevdenkenesedqnesdsdkes 1135
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5  151 .............................................................................. 150 
                                                                                                                   
  gene577|gene577|rna576|rna576 1136 itksddlcvevtsnesnekdsddnttaypdidredeqmdepsnpseeeimnftknsrnvlsfemlyptglnevissai 1213
                                     ****************************************************************************** PP

                                     ..........CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTT..TBETTTEEESSHHHHHHHHCHHHHHH CS
                                     ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  151 ..........gikkikrilvkeaekgkeeekelvletegvnlsevlkvee..vvdageilsndiaeileilgieaark 216 
                                               +ik+++++ v  ++   e+++ +   t  ++ s  + ++   ++d+ +  sndi +++++lgieaar 
  gene577|gene577|rna576|rna576 1214 esilptiivrEIKGVEKASVSGDMLFVESSSIF-SLTRRIETSPGVYEDLmsFLDIYKAESNDIYNVYSTLGIEAARY 1290
                                     **********9*******999999777774444.445666666655544457999*********************** PP

                                     HHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSS CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  217 allkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkae 263 
                                     a+++ei +v+ v+g++++ rHl l++d+mt+kg++ +++r+G+  ++
  gene577|gene577|rna576|rna576 1291 AIINEIVKVFDVYGITIDSRHLLLVADYMTRKGSYSPFSRHGFGDED 1337
                                     ******************************************87665 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.8   0.0   2.2e-63   7.9e-60       1     165 [.     347     515 ..     347     516 .. 0.91

  Alignments for each domain:
  == domain 1  score: 201.8 bits;  conditional E-value: 2.2e-63
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTS..SEEETTTT- CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredg..sekklkakk 78 
                                    Gkrv++++R+vispdpnl++ e+g+P  +a+ lt+pe vt++n+++l+k+v ngp +yPg+ y+++ +   s k++  +k
  gene577|gene577|rna576|rna576 347 GKRVNFAGRTVISPDPNLETREIGIPSIFAEALTFPEGVTSFNVSRLKKAVVNGP-IYPGSLYLQDGNVmlSLKHMADEK 425
                                    9*****************************************************9.69******8877511455666666 PP

                                    S.CHHCCTTTTS.EEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESS.SSEEEEGGGHCCCT--SSS-EEEEE--SSHH CS
                 RNA_pol_Rpb1_2  79 r.klakelekgd.iverhvkdgdvvllNRqPsLhklsimahrvkvlek.ktlrlnlsvttayNaDFDGDemnlhlpqsee 155
                                    r +la++l  g+ +v rh+ dgdvvl+NRqP+Lh+ simah+ +vl++ +t+r++++++++yNaDFDGDemn+h+pq+  
  gene577|gene577|rna576|rna576 426 RyALANQLLDGKkVVWRHLVDGDVVLVNRQPTLHRPSIMAHKCRVLKGeRTIRMHYANCKSYNADFDGDEMNIHFPQTCV 505
                                    6567777777663778*******************************99******************************* PP

                                    HHHHHHHCSB CS
                 RNA_pol_Rpb1_2 156 araEaeelll 165
                                    + aEa+++++
  gene577|gene577|rna576|rna576 506 SEAEARHIVM 515
                                    *******986 PP

>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   1.0   3.5e-37   1.2e-33       5     311 ..       8     344 ..       6     345 .. 0.77
   2 ?    1.5   0.2     0.042   1.5e+02      73     168 ..    1072    1182 ..    1037    1215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 3.5e-37
                                    -EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE-HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   5 keiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfhig 84 
                                    k+i+fg+ s+eei + S++ev  +  ++     P +gGl D r+g +d + +C+tC+ +  +C+ghfGhi+L +Pvf+  
  gene577|gene577|rna576|rna576   8 KKISFGLYSDEEIERASCMEVVIPASFDRFG-HPVQGGLYDLRMGPTDLSSNCKTCNLSLLSCPGHFGHIKLPRPVFNPM 86 
                                    79**************************984.9*********************************************** PP

                                    HHHHHHHHCTTCETTTTEBSS-TT.......................................SH....HHHHHHCSSSC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1  85 ffklilkilecvckecskllldee.......................................kkkllsklkkrekleel 125
                                     f++ l+i++c c++c++  +++                                        k + ++k k ++ +e+ 
  gene577|gene577|rna576|rna576  87 LFDTLLSIVKCCCFQCKHFRITNYdrlilfcklsllkngeeingldelymveeeeelyrivteKVESSKKRKTASSTERH 166
                                    ***********************988888886666666666666666666666666665554433333344444444444 PP

                                    CCCHHHHHHHHCCS-BE-SSSSB-EEE.EEETTEEEEEESSSST....SCE.EEE-HHHHHHHHHCSTHHHHHHTTSBTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 126 kkrlkaieelckkinlcekCgavqpkl.eeegeklkaalkkske....eek.eklsaekvkkllkriededvevlgfkss 199
                                    ++ +++  +   + ++c  Cg ++p + + +++k+ +++++++e    e++ e l ++ +k+l++++  +++ ++    s
  gene577|gene577|rna576|rna576 167 QEVVHKFLSNTGSRRKCVRCGHSNPWItKGSNMKILKNFRNKEEkeeeEKDfELLLPDVIKELIENLFLNEADLIESIFS 246
                                    477777777777778889*******9955567888888888887666433458899**********99888888888888 PP

                                    TB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 200 gsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdne 279
                                       P  + ++++PV+P++ RP+  ++g ++ e+     l di+k+  ++ k ++           +  LQ +v + fdn+
  gene577|gene577|rna576|rna576 247 TRDPGFFFMSNIPVIPNRFRPINIVNG-KKIENPQSIYLNDILKICISMVKDLS----------YWPELQGAVLSSFDNS 315
                                    99*******************877766.77777777888888877766655543..........3556666666666666 PP

                                    SSSSSEEBSTTSSS--THHHHHTSSSSCCCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 280 isglkpatqkskrplkslsqrLkGKeGrfRgn 311
                                      +  + +++s+    + +q L  K G fR n
  gene577|gene577|rna576|rna576 316 NIK--KWHHSST-IPPGHKQILERKDGLFRRN 344
                                    533..3333333.3345556666666666665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.042
                                     EEEEECEEE-HHHHHHHHHHCTTCETTTTEBSS-TT...........SH....HHHHHHCSSSCCCCHHHHHHHHCCS CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   73 hieLakPvfhigffklilkilecvckecskllldee...........kkkllsklkkrekleelkkrlkaieelckki 139 
                                     +++La+  ++  f+kl  k ++  ck + kl ++e            k    ++ + +++ ++ k+ +++  +lc ++
  gene577|gene577|rna576|rna576 1072 FVDLASEALNKKFLKLFGKKMRGLCKAKYKLGVSEVgkkglpevdenK---ENESEDQNESDSDKESITKSDDLCVEV 1146
                                     688999999999*******************99998666666664331...222333333333334555555555555 PP

                                     -BE-SSSS.......B-EEEEEETTEEEEEESSSST CS
                                     xxxxxxxx.......xxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1  140 nlcekCga.......vqpkleeegeklkaalkkske 168 
                                     +  e+ +        + p +++e e++ +  ++s+e
  gene577|gene577|rna576|rna576 1147 TSNESNEKdsddnttAYPDIDREDEQMDEPSNPSEE 1182
                                     553321113333333666667776666666666665 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17   6.1e+02      92     149 ..     120     178 ..      77     179 .. 0.73
   2 !   95.1   0.0   1.1e-30     4e-27       1     157 []     519     685 ..     519     685 .. 0.90
   3 ?   -4.1   0.0       3.8   1.4e+04     101     141 ..     842     879 ..     835     883 .. 0.75
   4 ?   -3.2   0.2       1.9     7e+03      57     119 ..    1017    1074 ..    1005    1101 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                    EEECSSEEEES--SHHHHS.SSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHC CS
                 RNA_pol_Rpb1_3  92 vlikngelikGvidkkvvg.kksqgslihvlakeygiketvrfldslqrlgfkyllqsg 149
                                     l+knge i+G  + ++v+ +++++ ++ + ++  +  +t+    + q+++ k+l + g
  gene577|gene577|rna576|rna576 120 SLLKNGEEINGLDELYMVEeEEELYRIVTEKVESSKKRKTASSTERHQEVVHKFLSNTG 178
                                    68999999999888888875566677777777777778888888899999999998865 PP

  == domain 2  score: 95.1 bits;  conditional E-value: 1.1e-30
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHC... CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpn... 77 
                                    n+l p +g P+ g++QD+++ + +lT ++ f+++e++  l+++g   + ++v+ +p ilkp +l++gkq++s i+ n   
  gene577|gene577|rna576|rna576 519 NYLAPTDGNPIRGLTQDHIIVATILTMKGSFFSEEDYFTLVNSGLNGK-RIVLDKPCILKPIRLYSGKQVISTIIKNlgl 597
                                    89******************************************7664.678999******88**************999 PP

                                    ..CCCEEEE.SSSS........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
                 RNA_pol_Rpb1_3  78 ..einyerk.neek........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyll 146
                                      ++ +e k             +++  i++g +i+G++dk+ +g  + +sl h + +  g  +  ++l  + r+ +++l+
  gene577|gene577|rna576|rna576 598 avNVEIETKiP--AdtwkehseESTLRINEGDIITGILDKNSLG-PTFKSLAHACGEVKGFAASNDLLTYVGRVSNRFLQ 674
                                    66444444331..24455667799********************.777******************************** PP

                                    HHCEB-TGGGG CS
                 RNA_pol_Rpb1_3 147 qsgftigigDt 157
                                    ++gft+gi+D+
  gene577|gene577|rna576|rna576 675 MYGFTVGIDDL 685
                                    **********6 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 3.8
                                    ES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHH CS
                 RNA_pol_Rpb1_3 101 kGvidkkvvgkksqgslihvlakeygiketvrfldslqrlg 141
                                    +G id +v   ++ g l  +l+k+   +e++   d   r+g
  gene577|gene577|rna576|rna576 842 EGLIDTAVKT-ANSGYLQRCLVKHM--EEVKVEYDMSARMG 879
                                    4788888888.77799999999998..66666666555555 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.9
                                     SBESSSEBEEHHHHHHCCCHCCCCEEEESSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHH CS
                 RNA_pol_Rpb1_3   57 ailkpkelwtgkqtfsrilpneinyerkneekdgkvlikngelikGvidkkvvgkksqgslih 119 
                                      i++p +  +g ++++++    + +++  + k ++ + ++ + i Gv +kkv    ++++ ++
  gene577|gene577|rna576|rna576 1017 LIVVPIKRNVGFDIAGCLKK--VTLKD--CVK-KFGVAEEIVMIDGVFQKKVKIVFELSNFVD 1074
                                     56666445566666666554..44444..333.455556666667777777665555555555 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   6.9e-22   2.5e-18      18     108 .]     730     820 ..     721     820 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 6.9e-22
                                    HHHHHHHHHHHHHHHHHHH.HHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS--SSTSCSSTTSS CS
                 RNA_pol_Rpb1_4  18 leelfeakinkilnkardk.agkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkripkgfsgrtlphfk 96 
                                    l+ +++a++nk+   + d+ + +  +ks + +N +  ++  GaKGsi+n+sqi+g lGqq++egkr+p ++sg+tlp+fk
  gene577|gene577|rna576|rna576 730 LDSVMRAEMNKVTTSIVDAsVPSGLKKSFP-NNGMELIITVGAKGSIVNLSQISGALGQQELEGKRVPIMISGKTLPCFK 808
                                    677888999999988888844555666655.7************************************************ PP

                                    SSESSTTTSSEE CS
                 RNA_pol_Rpb1_4  97 kidespesrGFv 108
                                    + d +p s G++
  gene577|gene577|rna576|rna576 809 SLDFGPSSGGYI 820
                                    **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 1.06u 0.31s 00:00:01.37 Elapsed: 00:00:00.51
# Mc/sec: 8201.99
//
Query:       gene579|gene579|rna578|rna578  [L=598]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1472  (0.0821016); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3762.74
//
Query:       gene58|gene58|rna58|rna58  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.076   13.1   0.3       0.14   12.2   0.3    1.4  1  COPI_assoc  COPI associated protein


Domain annotation for each model (and alignments):
>> COPI_assoc  COPI associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3     8e-06      0.14      80     113 ..     175     208 ..     172     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-06
                 COPI_assoc  80 lvsyggvlsilialllflvGLvyillhlvpsiee 113
                                ++ y ++++++++++l+ +G v+++l ++++  +
  gene58|gene58|rna58|rna58 175 MILYNSIFKLINGVVLLKIGTVFVTLLYINKKTK 208
                                8999************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.55
# Mc/sec: 1188.95
//
Query:       gene581|gene581|rna580|rna580  [L=346]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.079   12.7   0.3       0.14   11.9   0.3    1.3  1  Glyco_transf_10  Glycosyltransferase family 10 (fucosyltransf


Domain annotation for each model (and alignments):
>> Glyco_transf_10  Glycosyltransferase family 10 (fucosyltransferase) C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   7.7e-06      0.14      67     136 ..     156     223 ..     153     240 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.7e-06
                Glyco_transf_10  67 ickDYiTeKlwnaleagavPvvlGparenyerfvppdsfihvddFkspkelaeyLkkldkneeeYleYfe 136
                                     c+D++  Kl++  ea  v +++  + +++++++ +d++ih    k+  +l +   ++ + e +Y  Y++
  gene581|gene581|rna580|rna580 156 ACQDFLAGKLFEDGEARRVNIII--KDSTINSLLKKDAYIHFYVKKKDGKLYAVFDEVYTREIKYYDYLS 223
                                    6**********************..556***************9999*************9999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2181.46
//
Query:       gene582|gene582|rna581|rna581  [L=336]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00076   19.4   1.2     0.0015   18.4   1.2    1.5  1  CLTH          CTLH/CRA C-terminal to LisH motif domain
     0.0025   17.9   0.6     0.0074   16.4   0.2    2.1  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING
  ------ inclusion threshold ------
      0.015   15.3   0.2      0.039   14.0   0.2    1.7  1  zf-RING_UBOX  RING-type zinc-finger
      0.018   14.4   0.2      0.037   13.4   0.2    1.5  1  Rtf2          Rtf2 RING-finger
      0.039   14.2   0.0       0.07   13.4   0.0    1.4  1  TPR_5         Tetratrico peptide repeat
       0.13   11.3   0.0       0.17   10.9   0.0    1.1  1  XK-related    XK-related protein


Domain annotation for each model (and alignments):
>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.2   5.1e-07    0.0015      18     144 ..     121     242 ..     108     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.1e-07
                           CLTH  18 seaiewinenkpelles......nsnLeFkLkllqfielirgktkdieealeyarenlefendehlkelekamsLLafsd 91 
                                    +e++ +i+e + +lle+      ++ Le  L   +f+ li  + + ++eal+ + ++l+++  +++++++++   L+ + 
  gene582|gene582|rna581|rna581 121 KEIVFEISEDSTRLLENflesypSKMLELYLVSHEFLLLIH-N-GRYDEALKLCLKKLKSFVPTYIRDVKPLLKFLVNPV 198
                                    5666677788888888877767779999*************.9.**************999999**********999888 PP

                           CLTH  92 peskelssplknlldpsrrekvakefnsailkllglskespLeillsaglsal 144
                                            ++++ l+ + re +++ f s++l+  g++++  Le l   g+sa+
  gene582|gene582|rna581|rna581 199 --------NVEEALE-KNRERLIENFKSEYLEVTGIPNRCYLEELFETGTSAF 242
                                    ........4666666.568************************9999999876 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         2   6.1e+03       6      15 ..     192     201 ..     191     201 .. 0.84
   2 !   16.4   0.2   2.5e-06    0.0074      11      42 .]     291     322 ..     288     322 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                     zf-C3HC4_4   6 dYLekPvsle 15 
                                    ++L +Pv +e
  gene582|gene582|rna581|rna581 192 KFLVNPVNVE 201
                                    799****986 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 2.5e-06
                     zf-C3HC4_4  11 PvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                    Pv leCGh++ l+  + l++e   +++ Cp C
  gene582|gene582|rna581|rna581 291 PVMLECGHVISLEAANVLSQEGVLNSFKCPYC 322
                                    9**********************99******9 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.3e-05     0.039       1      39 []     278     320 ..     278     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                   zf-RING_UBOX   1 CpIClelft...dPlv.lpCGHtFCreClw.elskslegafkCP 39 
                                    Cp+ + l      P v l+CGH++  e     ++++  ++fkCP
  gene582|gene582|rna581|rna581 278 CPVLKTLCVgenIP-VmLECGHVISLEAANvLSQEGVLNSFKCP 320
                                    55555544455479.4369**********6688999999****9 PP

>> Rtf2  Rtf2 RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.3e-05     0.037     110     164 ..     271     330 ..     250     335 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                           Rtf2 110 tkeapfiCpltglemngktkfvalrkCGcVfsekalkevksev......ClvCgkeykeed 164
                                    + ++ fiCp+ +    g++   ++ +CG+V+s +a   + +e       C+ C +    e+
  gene582|gene582|rna581|rna581 271 NYHSLFICPVLKTLCVGEN-IPVMLECGHVISLEAANVLSQEGvlnsfkCPYCPEMSRYEN 330
                                    56789*****998877765.667889*********99987443455555999987665555 PP

>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.3e-05      0.07      55     113 ..     129     188 ..     124     194 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                          TPR_5  55 eealaLLraelea.psdelddalaaflaLvLsdlgrereavsivllalaehlprYqRsvt 113
                                    e++ +LL++ le+ ps+ l+  l +   L L+  gr  ea+++ l+ l   +p Y R v+
  gene582|gene582|rna581|rna581 129 EDSTRLLENFLESyPSKMLELYLVSHEFLLLIHNGRYDEALKLCLKKLKSFVPTYIRDVK 188
                                    8999*****999989999999***********************************9886 PP

>> XK-related  XK-related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.9e-05      0.17     108     151 ..     114     155 ..      65     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.9e-05
                     XK-related 108 eeereyyerkllkeeadlsmlrlleaflesaPqlvLqlyillqt 151
                                    + ++ + ++ +++ + d   +rlle fles P  +L ly++ ++
  gene582|gene582|rna581|rna581 114 RDDHARFKEIVFEISED--STRLLENFLESYPSKMLELYLVSHE 155
                                    44444444444444444..479*****************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2264.88
//
Query:       gene583|gene583|rna582|rna582  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-65  216.8   1.0    8.4e-32  109.0   0.3    2.1  2  TBP       Transcription factor TFIID (or TATA-binding protein
      6e-06   26.3   0.1      0.025   14.7   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.084   12.7   0.3       0.66    9.8   0.0    2.4  2  DUF4295   Domain of unknown function (DUF4295)


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0   0.3   1.4e-35   8.4e-32       3      84 ..      24     103 ..      23     104 .. 0.97
   2 !  106.7   0.0   7.1e-35   4.2e-31       1      84 [.     112     194 ..     112     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 1.4e-35
                                    EEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHH CS
                            TBP   3 kiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapil 82 
                                    + qNvva++nl+++ldL+++al+a  rnaeY+p+rf ++++r+repk+taliF+sGk+vitGakse+ ++ aa+++a+i+
  gene583|gene583|rna582|rna582  24 TLQNVVATVNLNCKLDLKNIALRA--RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVITGAKSEKSSKMAAQRYAKII 101
                                    68*******************998..****************************************************** PP

                                    HH CS
                            TBP  83 kk 84 
                                     k
  gene583|gene583|rna582|rna582 102 HK 103
                                    98 PP

  == domain 2  score: 106.7 bits;  conditional E-value: 7.1e-35
                                    EEEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                            TBP   1 dfkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80 
                                    dfkiqN+v s++++++++Le+la+  +++ ++Yepe fpgl+yr+ +pk+++liF+sGk+v+tGak ++++++a+++i+p
  gene583|gene583|rna582|rna582 112 DFKIQNIVSSCDIKFSIRLEGLAYA-HSNYCSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKVRDDIYQAFNNIYP 190
                                    69********************988.79**************************************************** PP

                                    HHHH CS
                            TBP  81 ilkk 84 
                                    +l +
  gene583|gene583|rna582|rna582 191 VLIQ 194
                                    9965 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.2e-06     0.025      27      63 ..      57      93 ..      29     103 .. 0.85
   2 !    9.5   0.0   0.00017         1      24      55 ..     145     176 ..     135     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-06
                        DUF3378 27 ppyavfaakkndttItaYtSgKVlFQGknaeaeAskw 63
                                      +++++++++tt  ++ SgK ++ G++ e+ +++ 
  gene583|gene583|rna582|rna582 57 FAAVIMRIREPKTTALIFASGKMVITGAKSEKSSKMA 93
                                   556899*************************998765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
                        DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGkn 55 
                                     +  p+ +++  k++++  ++ SgK+++ G++
  gene583|gene583|rna582|rna582 145 PELFPGLIYRMVKPKIVLLIFVSGKIVLTGAK 176
                                    56689***********************9986 PP

>> DUF4295  Domain of unknown function (DUF4295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00011      0.66       9      35 ..      47      75 ..      41      82 .. 0.78
   2 ?    0.0   0.2      0.13   7.8e+02      27      29 ..      87      89 ..      78     103 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00011
                        DUF4295  9 kkga..sgkkytKvIkmvKspKTGaYtFk 35
                                   + +a  + k+++ vI  ++ pKT a +F 
  gene583|gene583|rna582|rna582 47 ARNAeyNPKRFAAVIMRIREPKTTALIFA 75
                                   44444588*****************9996 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.13
                        DUF4295 27 pKT 29
                                   +K+
  gene583|gene583|rna582|rna582 87 EKS 89
                                   443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.57
# Mc/sec: 1044.38
//
Query:       gene584|gene584|rna583|rna583  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 807.93
//
Query:       gene585|gene585|rna584|rna584  [L=685]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-09   36.9   1.4    6.7e-09   36.0   1.4    1.5  1  DENN      DENN (AEX-3) domain


Domain annotation for each model (and alignments):
>> DENN  DENN (AEX-3) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   1.4   3.7e-13   6.7e-09      92     184 ..     243     327 ..     225     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 3.7e-13
                           DENN  92 cLsienilqlfeavLlErriillSeklarLtsvaealvallyPlkWqhiyiPvlpaslldvleaPtPfiiGvessllele 171
                                    c  ++ +l+++++vLlE+ri+++S+  + L   +  +++l+ P++W hi    l   + ++le+P+Pfi  + ++     
  gene585|gene585|rna584|rna584 243 CYPPKFLLEVISLVLLEERIVFYSSTDSSLR--VLQIMELMKPFRWPHIICLPLLSGMEEILESPLPFITCLSKR----- 315
                                    5667889*******************99997..45799**********875445568************755544..... PP

                           DENN 172 ekpledvvlvDld 184
                                      + e v+lvDld
  gene585|gene585|rna584|rna584 316 -LKIEGVTLVDLD 327
                                    .446899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 4304.58
//
Query:       gene586|gene586|rna585|rna585  [L=421]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-34  119.0  33.2    2.5e-34  118.7  33.2    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7  33.2   1.4e-38   2.5e-34       9     378 ..      16     393 ..       7     395 .. 0.86

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.4e-38
                                    HHHHH....HHHHTTSXHHHHHHHHHHHHTTTTTS.........HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHH CS
                 Na_H_Exchanger   9 llvgl....larrlklpeivgliiaGlllGpsglglieps....eedlevlselglilllFlaGleldlrelrknlksil 80 
                                    ll+g+    + + l l+e+++ +++G++lG +gl++++ +    ++    +s+++l+++   ++++l+ +++  ++ si+
  gene586|gene586|rna585|rna585  16 LLFGMiskyIKNNLFLSESLISVLVGIVLGHHGLNVFDTNyvysKIMMYNFSRIVLCIQTMTVAMSLPKNYVVVKWQSIF 95 
                                    222222332466666********************7777788888*********************************** PP

                                    HHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC....CCCTSTCCCCCCHHHHHHHHHHHCCC CS
                 Na_H_Exchanger  81 llallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailk...eegrvperlgtlllgesvlnDavavv 157
                                     l +++ +i + + ++ l + l+ +++ + +  ++++l++tdp++ ++i      ++ vper++ ll +es++nD+++++
  gene586|gene586|rna585|rna585  96 FLVIVVGIIKCSF-SFCLVY-LFTNYNKSISWSLASCLTPTDPILSSSIIHgklAMKMVPERIRLLLAAESGINDGMGIF 173
                                    *************.998886.699**************************9999999*********************** PP

                                    CCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS....CTHHHHHHHHHHHHHHHHHHHHHTS CS
                 Na_H_Exchanger 158 llavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft....dddrelevllvlllallaallaell 233
                                    ll++ l l+ ++  ++  +  ++ ++l+ ++++ ++gl +g l+r  ++++        e++++  ++la ++ +l+e +
  gene586|gene586|rna585|rna585 174 LLFLGLDLL-GHGLENGIYPFIINSILIRVLFSAVIGLSVGILSRQGLKYCytrrLVGVESFLAHGIILAVFSMALMEFI 252
                                    ********9.66666666778888899999999999999999999999999876555567888888889999999***** PP

                                    XXXHHHHHHHHHHHHH.HHHHHTTHHHH.HHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHHHHHTHHHHHH CS
                 Na_H_Exchanger 234 gvsgilgaflaGlvls.eyefsnklsek.lesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilvaillgrilav 311
                                    g s ++ +f+aG++++ + +f  ++  + l  + + ++ + fF+++G  +d     ++ + l  v+++lv+i+++r++  
  gene586|gene586|rna585|rna585 253 GGSELICIFFAGIMFPfDEWFVLETKNSsLQEITDTILSTSFFLFFGSRID-----FGRFTLSNVIVSLVIIFIRRPVIC 327
                                    ****************7777766666667778888****************.....4577999***************** PP

                                    HHHTTTX..SSXHHHHHHCC.CCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHHHHHH CS
                 Na_H_Exchanger 312 flllrll..glslrealiig.fgglqrgavalalaalgpalgllarel.yallivvvlftvlvqGlslkpl 378
                                     l  r +    s+real++g fg++++ga+++al+   +++  ++++l + ++ ++v+++v ++Gl+++++
  gene586|gene586|rna585|rna585 328 CLTYRQIpeLRSRREALFVGwFGPIGVGALYYALL---TDK--IQETLtIDFVSCTVFLSVMIHGLTVPIY 393
                                    *****99755899*******566666666666554...344..566777******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2353.49
//
Query:       gene587|gene587|rna586|rna586  [L=216]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-22   78.7   2.1    5.3e-22   78.4   2.1    1.1  1  zf-ZPR1         ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.099   12.8   3.5        1.4    9.1   0.6    2.4  2  Ribosomal_L37e  Ribosomal protein L37e
       0.98    8.9   5.4        1.9    8.0   0.1    3.0  3  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   2.1   8.9e-26   5.3e-22       2     158 ..      21     184 ..      20     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 8.9e-26
                        zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekG.kritlkveseedlnrqvlkSetatvei 80 
                                    +C sCg+     +++++++  ++e +i++f+C++Cg k+ ++   ++ +++G +ri++  +++edl+r+v  S+ a+vei
  gene587|gene587|rna586|rna586  21 KCASCGW---SGKMKIVDLSDVTENVICAFVCKKCGDKSVNF-LEKTCDPRGsVRIECFFDDKEDLSREVNLSQLASVEI 96 
                                    8****84...599**************************999.56666777769************************** PP

                        zf-ZPR1  81 peleleippgtlegrlttvEGlLeqikeele....ke.....egdqaer.......edeekekieeflekleeliegeep 144
                                     + +l+++ +++  ++++vE +L q k++++    ke     +              d +ke++e+ l+++++l++ + +
  gene587|gene587|rna586|rna586  97 ISDDLSFKLSSTYPSIQNVESFLIQGKDQIKnlcgKEditsgA-----GggnvladGDISKETCEKKLDDFQKLMA-NPK 170
                                    *****999999*******************8666522445441.....134444324469***************9.889 PP

                        zf-ZPR1 145 ftlildDpagnSfi 158
                                    f+li++D +g S +
  gene587|gene587|rna586|rna586 171 FKLIIEDDFGLSRV 184
                                    ***********987 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.01        61      32      40 ..      20      28 ..      16      34 .. 0.76
   2 ?    9.1   0.6   0.00024       1.4      18      35 ..      48      65 ..      42      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.01
                 Ribosomal_L37e 32 ktCascGyp 40
                                    +CascG+ 
  gene587|gene587|rna586|rna586 20 MKCASCGWS 28
                                   58*****94 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00024
                 Ribosomal_L37e 18 lCrrCgkrsyhvqkktCa 35
                                   +C++Cg +s ++ +ktC 
  gene587|gene587|rna586|rna586 48 VCKKCGDKSVNFLEKTCD 65
                                   8****************6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1   0.00031       1.9      10      23 ..      13      26 ..      12      27 .. 0.89
   2 ?    2.4   0.2     0.018   1.1e+02      18      23 ..      48      53 ..      46      56 .. 0.86
   3 ?   -3.9   0.1       1.8   1.1e+04       8      10 ..     130     132 ..     130     138 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00031
                    zf-ribbon_3 10 aplssddnvCpyCG 23
                                   +++s++ ++C++CG
  gene587|gene587|rna586|rna586 13 NNISESSMKCASCG 26
                                   578**********9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.018
                    zf-ribbon_3 18 vCpyCG 23
                                   vC++CG
  gene587|gene587|rna586|rna586 48 VCKKCG 53
                                   7****9 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.8
                    zf-ribbon_3   8 CGa 10 
                                    CG+
  gene587|gene587|rna586|rna586 130 CGK 132
                                    555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1384.00
//
Query:       gene588|gene588|rna587|rna587  [L=512]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-07   28.8   0.4    2.2e-06   27.4   0.4    1.8  1  LisH      LisH
  ------ inclusion threshold ------
      0.074   12.1   0.0       0.12   11.4   0.0    1.4  1  LisH_2    LisH


Domain annotation for each model (and alignments):
>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.4   2.5e-10   2.2e-06       3      26 ..      17      40 ..      15      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.5e-10
                                   HHHHHHHHHHHCT-HHHHHHHHHH CS
                           LisH  3 LNrLIydYLvkeGyeetAeaFekE 26
                                   LN+L+ydYL+k+ ye +A+ F  E
  gene588|gene588|rna587|rna587 17 LNMLVYDYLLKMKYEGSAKIFFGE 40
                                   9********************766 PP

>> LisH_2  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.3e-05      0.12       1      28 []      17      44 ..      17      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.3e-05
                         LisH_2  1 lnsLvaeYLqsqgYnYTLSVFlPEsGla 28
                                   ln+Lv +YL + +Y+ + ++F  E Gl+
  gene588|gene588|rna587|rna587 17 LNMLVYDYLLKMKYEGSAKIFFGEAGLG 44
                                   7****************99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3189.21
//
Query:       gene589|gene589|rna588|rna588  [L=359]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-63  210.1   1.9    1.2e-11   45.1   0.0    7.3  7  RCC1      Regulator of chromosome condensation (RCC1) repeat
    2.3e-33  113.3  26.2    7.4e-09   35.2   0.8    6.9  8  RCC1_2    Regulator of chromosome condensation (RCC1) repeat
  ------ inclusion threshold ------
      0.017   14.9   0.0        1.1    8.9   0.0    2.9  3  Hira      TUP1-like enhancer of split


Domain annotation for each model (and alignments):
>> RCC1  Regulator of chromosome condensation (RCC1) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   2.2e-11   1.3e-07       4      50 .]       3      50 ..       2      50 .. 0.93
   2 !   45.1   0.0     2e-15   1.2e-11       1      50 []      53      98 ..      53      98 .. 0.97
   3 !   20.5   0.0   8.9e-08   0.00053       1      50 []     101     150 ..     101     150 .. 0.92
   4 !   31.7   0.0     3e-11   1.8e-07       3      50 .]     155     210 ..     153     210 .. 0.93
   5 !   26.5   0.1   1.2e-09   7.5e-06       1      50 []     213     259 ..     213     259 .. 0.79
   6 !   28.4   0.1   3.2e-10   1.9e-06       1      31 [.     262     291 ..     262     305 .. 0.89
   7 !   18.1   0.0   5.3e-07    0.0032       3      49 ..     312     356 ..     311     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.2e-11
                                   EEEEE--GGGTTSSSS-.--EEEEEE-GGGTTS-EEEEEEETTEEEEE CS
                           RCC1  4 VysWGrndyGqLGlgtt.esvlvPtkveglsgnrvvkvacGddhtval 50
                                   V+ +G+n   qLGlg +  s +vPt++++++g    kv cG+ ht+ l
  gene589|gene589|rna588|rna588  3 VFVFGSNAISQLGLGEDeGSTHVPTRLSFFDGLSPAKVRCGSLHTLIL 50
                                   9****************767799**********************975 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 2e-15
                                   TTEEEEEE--GGGTTSSSS---EEEEEE-GGGTTS-EEEEEEETTEEEEE CS
                           RCC1  1 dGrVysWGrndyGqLGlgttesvlvPtkveglsgnrvvkvacGddhtval 50
                                   dG +ysWG+nd+G LG+  +es   P+kv + +  +vv++ cG++ ++al
  gene589|gene589|rna588|rna588 53 DGTLYSWGCNDEGALGRDGDEST--PKKVCLRE--KVVDMDCGASISAAL 98
                                   8**********************..****9977..*************97 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 8.9e-08
                                    TTEEEEEE..--GGGTTSSSS---E.EEEEE-GGGTTS-EEEEEEETTEEEEE CS
                           RCC1   1 dGrVysWG..rndyGqLGlgttesv.lvPtkveglsgnrvvkvacGddhtval 50 
                                    +G+Vy WG  r+++G  Gl ++es   vP kv++    ++ + ++G+++ +al
  gene589|gene589|rna588|rna588 101 SGHVYVWGtfRSTNGAFGLTPRESIsFVPIKVPLK---NIRALSAGQSFIAAL 150
                                    59********************998799****884...8*********99986 PP

  == domain 4  score: 31.7 bits;  conditional E-value: 3e-11
                                    EEEEEE--GGGTTSSSS---E....EEEEE-GGGTTS....-EEEEEEETTEEEEE CS
                           RCC1   3 rVysWGrndyGqLGlgttesv....lvPtkveglsgn....rvvkvacGddhtval 50 
                                     ++++G+n++G LG+ t+e++    l+P  v++++++    r++++ cG +h +al
  gene589|gene589|rna588|rna588 155 AIFTFGSNEFGELGRRTSERNklraLIPDAVTTPRKRlqnyRFKSIGCGLNHLIAL 210
                                    69****************888788899********99***************9986 PP

  == domain 5  score: 26.5 bits;  conditional E-value: 1.2e-09
                                    TTEEEEEE--GGGTTSSSS-...--EEEEEE-GGGTTS-EEEEEEETTEEEEE CS
                           RCC1   1 dGrVysWGrndyGqLGlgtt...esvlvPtkveglsgnrvvkvacGddhtval 50 
                                    dG+ y+WG+n yGqLG+ +     ++    kv++     +v+++ G +h++++
  gene589|gene589|rna588|rna588 213 DGEAYCWGSNLYGQLGHDKAestFNK---YKVPLD---GIVQAVGGENHSLFI 259
                                    8****************666333333...455553...7***********997 PP

  == domain 6  score: 28.4 bits;  conditional E-value: 3.2e-10
                                    TTEEEEEE--GGGTTSSSS---EEEEEE-GG CS
                           RCC1   1 dGrVysWGrndyGqLGlgttesvlvPtkveg 31 
                                    dG++y++Grn +GqLG+++tes   P+++ g
  gene589|gene589|rna588|rna588 262 DGSLYGCGRNKEGQLGIQSTESIRSPVRL-G 291
                                    9**************************98.3 PP

  == domain 7  score: 18.1 bits;  conditional E-value: 5.3e-07
                                    EEEEEE--GGGTTSSSS---EEEEEE-GGGTTS.-EEEEEEETTEEEE CS
                           RCC1   3 rVysWGrndyGqLGlgttesvlvPtkveglsgn.rvvkvacGddhtva 49 
                                    ++ysWG + +G LG+  +     P+k+++      v++   G+d++v 
  gene589|gene589|rna588|rna588 312 ELYSWGTGFNGALGHEEETLF-SPKKIPFD--FpSVIDFDVGNDFSVI 356
                                    69*************877444.79999873..3499999999999986 PP

>> RCC1_2  Regulator of chromosome condensation (RCC1) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.1   6.5e+03      20      26 ..       3       9 ..       3      10 .. 0.88
   2 !   30.8   0.7     3e-11   1.8e-07       3      29 ..      39      65 ..      38      66 .. 0.92
   3 !   19.2   1.5   1.3e-07   0.00078       1      24 [.      85     108 ..      85     116 .. 0.88
   4 !   13.2   0.0   9.5e-06     0.057       1      29 [.     137     165 ..     137     166 .. 0.95
   5 !   35.2   0.8   1.2e-12   7.4e-09       2      30 .]     198     226 ..     197     226 .. 0.97
   6 !   26.1   0.1   8.9e-10   5.3e-06       2      30 .]     247     275 ..     246     275 .. 0.91
   7 ?    2.4   0.2     0.024   1.4e+02      18      29 ..     311     322 ..     309     323 .. 0.80
   8 ?   -1.9   0.0      0.54   3.2e+03       1      15 [.     344     358 ..     344     359 .] 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.1
                         RCC1_2 20 VlcWGsN 26
                                   V+ +GsN
  gene589|gene589|rna588|rna588  3 VFVFGSN 9 
                                   899***9 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 3e-11
                         RCC1_2  3 svsaGdyHscaLtedGeVlcWGsNsdG 29
                                   +v +G+ H+++L++dG++++WG+N+ G
  gene589|gene589|rna588|rna588 39 KVRCGSLHTLILDSDGTLYSWGCNDEG 65
                                   5779********************988 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.3e-07
                         RCC1_2   1 VksvsaGdyHscaLtedGeVlcWG 24 
                                    V+++ +G++ s aLt++G+V+ WG
  gene589|gene589|rna588|rna588  85 VVDMDCGASISAALTSSGHVYVWG 108
                                    89999******************* PP

  == domain 4  score: 13.2 bits;  conditional E-value: 9.5e-06
                         RCC1_2   1 VksvsaGdyHscaLtedGeVlcWGsNsdG 29 
                                    ++++saG ++  aL+  ++++++GsN++G
  gene589|gene589|rna588|rna588 137 IRALSAGQSFIAALDLKDAIFTFGSNEFG 165
                                    6789***********************99 PP

  == domain 5  score: 35.2 bits;  conditional E-value: 1.2e-12
                         RCC1_2   2 ksvsaGdyHscaLtedGeVlcWGsNsdGQ 30 
                                    ks+ +G +H +aL +dGe +cWGsN +GQ
  gene589|gene589|rna588|rna588 198 KSIGCGLNHLIALNADGEAYCWGSNLYGQ 226
                                    89**************************9 PP

  == domain 6  score: 26.1 bits;  conditional E-value: 8.9e-10
                         RCC1_2   2 ksvsaGdyHscaLtedGeVlcWGsNsdGQ 30 
                                    ++   G +Hs+++t+dG ++++G+N  GQ
  gene589|gene589|rna588|rna588 247 VQAVGGENHSLFITRDGSLYGCGRNKEGQ 275
                                    6666799*********************9 PP

  == domain 7  score: 2.4 bits;  conditional E-value: 0.024
                         RCC1_2  18 GeVlcWGsNsdG 29 
                                    +e+++WG   +G
  gene589|gene589|rna588|rna588 311 NELYSWGTGFNG 322
                                    68*****87665 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 0.54
                         RCC1_2   1 VksvsaGdyHscaLt 15 
                                    V++   G+++s+++t
  gene589|gene589|rna588|rna588 344 VIDFDVGNDFSVIVT 358
                                    667778*****9987 PP

>> Hira  TUP1-like enhancer of split
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.12     7e+02      17      37 ..      40      60 ..      34      67 .. 0.80
   2 ?    8.9   0.0   0.00019       1.1       8      38 ..      79     109 ..      74     123 .. 0.90
   3 ?    1.5   0.0     0.035   2.1e+02      19      36 ..     202     219 ..     194     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.12
                           Hira 17 LessgsyLlavtsvgllyvWn 37
                                   + + + + l++ s+g+ly W 
  gene589|gene589|rna588|rna588 40 VRCGSLHTLILDSDGTLYSWG 60
                                   5677778899**********6 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00019
                           Hira   8 lvlespasfLessgsyLlavtsvgllyvWnv 38 
                                    ++l+ +++ +++  s  +a+ts+g++yvW +
  gene589|gene589|rna588|rna588  79 VCLREKVVDMDCGASISAALTSSGHVYVWGT 109
                                    789999999********************76 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.035
                           Hira  19 ssgsyLlavtsvgllyvW 36 
                                    +  ++L+a+ ++g+ y+W
  gene589|gene589|rna588|rna588 202 CGLNHLIALNADGEAYCW 219
                                    55599************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2314.91
//
Query:       gene590|gene590|rna589|rna589  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-18   66.4   0.4    3.3e-18   65.6   0.4    1.4  1  tRNA_bind  Putative tRNA binding domain
  ------ inclusion threshold ------
       0.14   12.3   0.1       0.21   11.7   0.1    1.2  1  DUF4760    Domain of unknown function (DUF4760)


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.4   3.7e-22   3.3e-18       1      95 [.     130     221 ..     130     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 3.7e-22
                                    EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESS CS
                      tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldek 80 
                                    ++vG+++++ ++++ dkL+ ++v vG+++ +qi sg++ ++ +e l+++k   v n+kp+k++G+ SeGMil++++ +++
  gene590|gene590|rna589|rna589 130 IQVGEIVNIGDVQGLDKLYSEEV-VGKKK-MQILSGLRGHVRKEGLLGNKFLFVTNMKPAKFKGQVSEGMILCVKD-KDG 206
                                    68*********************.99999.*********************************************5.*** PP

                                    CEEEEEESST--TTC CS
                      tRNA_bind  81 evgilelpadveaGe 95 
                                    + + +e+ +d+ +G+
  gene590|gene590|rna589|rna589 207 NIEPIEISKDIINGS 221
                                    ***********9997 PP

>> DUF4760  Domain of unknown function (DUF4760)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.4e-05      0.21      31      99 ..      45     112 ..      20     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                        DUF4760  31 qealkqlrkvldsgkslakftlleekksekgeeeserekiltvlNflEfvavgiesgildEdmikelsv 99 
                                     + l  l k+ +++++ ++++  ++k   ++e  +    i++++ f+++++ +i +g+l  +++ + +v
  gene590|gene590|rna589|rna589  45 DDVLGALYKMYEQDCDYKNIK-EAKKLRANPEVRKVEVSISNLISFYGLYCQMITQGVLKNKLFIDQMV 112
                                    555666777788999999999.6777778899999999************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1875.62
//
Query:       gene59|gene59|rna59|rna59  [L=459]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.3e-140  466.6   0.4   1.7e-139  465.5   0.4    1.5  1  Glyco_transf_20  Glycosyltransferase family 20
     0.0014   18.4   0.8     0.0027   17.5   0.3    1.7  2  Glyco_transf_5   Starch synthase catalytic domain
      0.008   15.7   0.0      0.025   14.1   0.0    1.9  1  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  465.5   0.4  2.9e-143  1.7e-139       2     470 ..       2     447 ..       1     451 [. 0.95

  Alignments for each domain:
  == domain 1  score: 465.5 bits;  conditional E-value: 2.9e-143
                                -EEEEEEE-SECEEE-S.SCG..EEECCGSSHHHHHCCCHHCCC-EEEEEE.ECCES-CCC..HCCCCHHHCCCCCEEEEEE-H CS
            Glyco_transf_20   2 klvvvsnrlplklereseeekeeyelkkssgglvsalkglkeetevvwvgw.lgvevdeseeakekvskeleekfsvvpvflsd 84 
                                kl+v+snrlpl++++ +    + +e+++ sgglv+ lk+++ + +++w+g  +gve +e+e  k+ + k+  ekf+++pvf++ 
  gene59|gene59|rna59|rna59   2 KLLVISNRLPLTIKKGK----NGFEYTRTSGGLVTGLKSINDRIRFKWLGNiSGVELNEEE--KDIIRKDCWEKFHSIPVFIDP 79 
                                6799******9987765....5799************************962567777777..9999***************** PP

                                HHHHHHCCCHHHHCHHHHHTT-GG....G----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEESGGGTTHHHHHHHCCTT.SE CS
            Glyco_transf_20  85 ekveeyyngfsksvLWpllHYklpdsseekefersawdaYvkvnklFAdkiveeikdgdliwvhDYhLmllPellRkkled.ak 167
                                e     y+gf++++LWp++H    + +++ +f  ++++aYv+ n++F+dk++e ++dgd++wvhDYhLm+lPe+l+kk ++  k
  gene59|gene59|rna59|rna59  80 ELNSDCYDGFCNAILWPIIH----SFKDDVAFTIKNYNAYVEYNRIFCDKVCEALEDGDIVWVHDYHLMMLPEMLKKKSKKdFK 159
                                ********************....7889************************************************997766** PP

                                EEEEE-S----HHHHTTSTTHHHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSSEEEECTTEEEEETTEEEEEEE------HHH CS
            Glyco_transf_20 168 igfflHiPFPsseifriLpvreeilegllgadliGFhtedyarhFlsccsrllgleveskrggveykgrkvsvkalpigidver 251
                                + fflH+PFP++ei  +L+ r+ei+ g+ ++dl++Fh +dya +F ++c     +e             k++++a+pigid+e 
  gene59|gene59|rna59|rna59 160 VMFFLHTPFPPAEIMETLACRKEIVSGMAHSDLVAFHSFDYAINFHDTCIANH-IE------------VKTKLDAIPIGIDPEM 230
                                ************************************************96433.33............345699********** PP

                                HHHHCCSCHHHHHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGTTTEEEEEEEEB-STTSHHHHHHHHHH CS
            Glyco_transf_20 252 lesalkkesvsekvkelkerfenkkklilgvDrlDyikGvkqkllaferfLeeypelrgkvvlvqiavpsredveeyqelekev 335
                                ++++lk++++ e++ke+k+ f++k k++lgvDr DyikG++++++ f rfLe+ype+ gkvv++q+ vpsr++v+ey ++++++
  gene59|gene59|rna59|rna59 231 FRKILKEKKTVERIKEIKQMFKGK-KILLGVDRTDYIKGMPHRFKGFHRFLEKYPEFVGKVVFLQVGVPSRTNVKEYSSYTNKL 313
                                *********************996.*********************************************************** PP

                                HHHHHHHHHHH-BTTB-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT-TTTS CS
            Glyco_transf_20 336 eelvgrINgefgtldytPvvylersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqsLkdaa 419
                                +el+ ++N++ g ++ t +++l+rs++f+el+al+aa+dvllvtsl dGmnlva+eyv cq+e+kgvL+LSe aGa+  L+ aa
  gene59|gene59|rna59|rna59 314 NELASEVNSKIGPIEATHIHFLNRSVEFDELCALYAASDVLLVTSLIDGMNLVALEYVSCQDENKGVLLLSESAGASTTLS-AA 396
                                *********************************************************************************.78 PP

                                EEE-TT-HHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHT-HHHHHHHHHH CS
            Glyco_transf_20 420 ilvNPwdieevaeaikeaLkmseeerkkrekkllkqvskhdvqsWaesfls 470
                                + +N w++ee+a+ i++a+ m+ eer++r++   k+v   ++ +Wae  l+
  gene59|gene59|rna59|rna59 397 LEINSWNTEEIADGIQKAIMMPMEERSERHEINKKAVDVFTSVEWAERNLD 447
                                **********************************************98776 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   4.5e-07    0.0027     115     170 ..     119     165 ..     100     211 .. 0.76
   2 ?   -2.3   0.0      0.47   2.8e+03      44      95 ..     232     287 ..     228     327 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-07
             Glyco_transf_5 115 falfsraalelleklgwkpdvihahDWhtalvpallkelykerglfkkiktvftiH 170
                                  +f+  ++e+le      d++ +hD+h +++p +lk+  k     k+ k++f +H
  gene59|gene59|rna59|rna59 119 NRIFCDKVCEALED----GDIVWVHDYHLMMLPEMLKKKSK-----KDFKVMFFLH 165
                                4589999*****99....5*******************864.....5699999999 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.47
             Glyco_transf_5  44 gaikeekkeleevaelskaaed.evevev...ekvkvaklkkdgvdvyfldnpeff 95 
                                ++i +ekk++e+++e+++ +++ ++ ++v    ++k + ++ +g ++++ + pef 
  gene59|gene59|rna59|rna59 232 RKILKEKKTVERIKEIKQMFKGkKILLGVdrtDYIKGMPHRFKGFHRFLEKYPEFV 287
                                56666677777777777777777777664234444444444466666666666654 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   4.2e-06     0.025       5     116 ..     244     374 ..     240     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.2e-06
                                HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCC...HCSCEEEEEES..........STTHHHHHHHHHHHCTT.... CS
            Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkq...lnpnvklviaG.........ngeeekelkklaeelels.... 72 
                                +++ ++  ++kki+l v r ++ Kg  +  k f+++ ++      +v+++ +G           ++ ++l +la e + +    
  gene59|gene59|rna59|rna59 244 IKEIKQMFKGKKILLGVDRTDYIKGMPHRFKGFHRFLEKypeFVGKVVFLQVGvpsrtnvkeYSSYTNKLNELASEVNSKigpi 327
                                566666778999999999999999999999999999998666666777777889999999997888888888888887542222 PP

                                ..CGGGEEECCH.SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT CS
            Glycos_transf_1  73 ..dnviflgevs.redleellknadifvlpsisEgfGivllEAmaag 116
                                   +++fl ++   ++l +l+ ++d+++++s  +g+ +v+lE+ ++ 
  gene59|gene59|rna59|rna59 328 eaTHIHFLNRSVeFDELCALYAASDVLLVTSLIDGMNLVALEYVSCQ 374
                                2257777777767889****************************994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2766.44
//
Query:       gene591|gene591|rna590|rna590  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.38   10.8   1.9       0.83    9.7   0.6    2.2  2  Toxin_25  Hefutoxin family


Domain annotation for each model (and alignments):
>> Toxin_25  Hefutoxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.6   4.7e-05      0.83       8      14 ..      43      49 ..      42      50 .. 0.96
   2 ?   -1.9   0.0      0.19   3.4e+03       2       9 ..     136     143 ..     136     143 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 4.7e-05
                       Toxin_25  8 CWREGND 14
                                   CWR+GND
  gene591|gene591|rna590|rna590 43 CWRDGND 49
                                   ******9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.19
                       Toxin_25   2 HACYRNCW 9  
                                    H  Y+N W
  gene591|gene591|rna590|rna590 136 HKIYKNMW 143
                                    677***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1645.62
//
Query:       gene592|gene592|rna591|rna591  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-32  112.2   0.7    2.6e-32  112.2   0.7    1.5  2  RabGAP-TBC  Rab-GTPase-TBC domain


Domain annotation for each model (and alignments):
>> RabGAP-TBC  Rab-GTPase-TBC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1      0.23   4.1e+03       2      20 ..      31      49 ..      30      68 .. 0.55
   2 !  112.2   0.7   1.4e-36   2.6e-32      43     214 ..     106     280 ..      92     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.23
                     RabGAP-TBC  2 elRgevWklllgyep..evkr 20
                                   e+R+ +W+++ ++    +  +
  gene592|gene592|rna591|rna591 31 EYRCIAWRIIFQVIGlrK--Q 49
                                   789999999998865332..2 PP

  == domain 2  score: 112.2 bits;  conditional E-value: 1.4e-36
                     RabGAP-TBC  43 eskelsqIkkDvprtfpesesfknkqgqnqLeriLkaysiynpevgYcqGmndivaplllvsldeee......aFwcfvs 116
                                    ++k+ +qI++D++r  p  +  +  +++ + ++iL  ++ ++p++gY+qGm di+ p+ lv+ de+       a++c ++
  gene592|gene592|rna591|rna591 106 PEKIAHQIDLDIKRIDPRYKTYSGIDISYMYYHILWLIARRRPQLGYVQGMADILVPFVLVFSDESVetaesnAYFCYAR 185
                                    67889************545555569999******************************9*99999999*********** PP

                     RabGAP-TBC 117 LlekyklrdlytsslpglkrklkvleellkkkdpklykhlkeegldlelfaikwfltlflrefpletvlrlwD.lll.eg 194
                                    Ll  + ++++ ++ + g   ++k ++ +l+++dp+++k+lk++gl++ +fa++wf++ f+ref++ ++l+++D +++   
  gene592|gene592|rna591|rna591 186 LL--DEIQHNIIDLQAG---MIKGVDLVLQTVDPDFHKFLKDIGLEIHMFAFRWFNCFFAREFKIPILLKVLDtVFAsD- 259
                                    **..99******98855...556699***********************************************777743. PP

                     RabGAP-TBC 195 e.kfvllrvalailklleeel 214
                                    + + +ll++++a+l +l++ l
  gene592|gene592|rna591|rna591 260 NiNESLLYFGVALLMRLKPVL 280
                                    35566*********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2363.53
//
Query:       gene593|gene593|rna592|rna592  [L=191]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   13.4   0.1       0.33   11.4   0.0    1.9  2  DUF836    Glutaredoxin-like domain (DUF836)


Domain annotation for each model (and alignments):
>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.8e-05      0.33       5      44 ..      39      78 ..      36     114 .. 0.78
   2 ?   -0.8   0.0      0.12   2.1e+03       2      11 ..     133     142 ..     132     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.8e-05
                                   EE-TT..-HHHHHHHHHHHHHCCCTTEEEEEEETTT-CCCHC CS
                         DUF836  5 yskpg..ChlCeqakekLkelkleegleleviDIakdeelea 44
                                   ys+p+  C+ Ce+ +  ++  kl++ +++++i+  +d++  +
  gene593|gene593|rna592|rna592 39 YSRPNvhCPACESFNRNIS--KLQKYIPVKKINFFEDPKVAS 78
                                   6776444************..88999*******999988655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.12
                                    EEEEE-TT-H CS
                         DUF836   2 ltLyskpgCh 11 
                                    + Lys+ +C 
  gene593|gene593|rna592|rna592 133 INLYSTANCA 142
                                    679******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1315.34
//
Query:       gene594|gene594|rna593|rna593  [L=222]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-19   68.0   4.8    3.5e-10   40.0   2.8    2.1  2  mRNA_triPase  mRNA capping enzyme, beta chain
  ------ inclusion threshold ------
      0.089   12.8   0.0       0.16   12.0   0.0    1.4  1  DUF5529       Family of unknown function (DUF5529)


Domain annotation for each model (and alignments):
>> mRNA_triPase  mRNA capping enzyme, beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   5.8e-11   5.2e-07      25      89 ..      30      93 ..      13     108 .. 0.84
   2 !   40.0   2.8   3.9e-14   3.5e-10     113     219 .]      91     197 ..      84     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.8e-11
                                   CCEEEEEEEEEEEETTTSSB---SBSS-EEE-TT.CTEEEEE-B-HHHHHHHHHHHHHHHH..HTT CS
                   mRNA_triPase 25 sqiEiEaklGlivdkstkeRlklpvsteaivenn.adskfesgvdedqfkelnnfLnelsrrneee 89
                                   +  E+E++lG+i++k+++ R+++ ++ ++++ +  +d++fes vd ++f+ l++    l+   e++
  gene594|gene594|rna593|rna593 30 ERKELEIRLGKIISKEDGSRMRVDTVAPVVFRSIpMDYRFESAVDLSDFNILKKQFSTLKS--EAK 93
                                   4559*****************************99******************99998773..333 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 3.9e-14
                                    SSS--EEEEEEETT...T--EEEEEEE.EEEEEEEEE-TTSSSEEEEEEEEEEE-SSSHHHCTTS--SEEEEEEEEEEEE CS
                   mRNA_triPase 113 keekskirvskdse...nqevlkkieK.eriadlniylPnsklDyriSinlElpvseskaklskktpvseRlkeRlSyih 188
                                    + +++ + + +d +   +  vlkk+eK  r ++l+i++P +k+D+r+ ++ E +     +  skk+p+ +R + R +y  
  gene594|gene594|rna593|rna593  91 EAKNDVVIINEDGRetyEDGVLKKVEKkTRSQKLDIFIPGKKYDVRLVLSEENEGF---KRASKKKPIVKRVRRRETYFI 167
                                    455555556666666667778888865168999*******************9944...67999**************** PP

                                    CCGTEEEEEEEE.SSS---S--EEEEEEEEEE CS
                   mRNA_triPase 189 kksgiqfDLtkv.ektektkkteekyElEiEi 219
                                    +   + fD t    ++ k++k+++k+E+E+E+
  gene594|gene594|rna593|rna593 168 EP--YGFDFTEAiLSGDKDEKEKRKFEIEVEV 197
                                    **..******98555599*************7 PP

>> DUF5529  Family of unknown function (DUF5529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.8e-05      0.16      13      47 ..      57      93 ..      48     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                        DUF5529 13 plyfpsl.yd.rgisssplsdfniwkklfvplkagga 47
                                   p+ f s+  d r  s+  lsdfni kk f  lk+ + 
  gene594|gene594|rna593|rna593 57 PVVFRSIpMDyRFESAVDLSDFNILKKQFSTLKSEAK 93
                                   555555422325668889***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1411.06
//
Query:       gene595|gene595|rna594|rna594  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-40  138.0   0.2    3.2e-40  137.4   0.2    1.2  1  Ras          Ras family
    3.8e-29  101.3   0.1    5.3e-29  100.9   0.1    1.2  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    9.5e-13   48.0   0.0    1.2e-12   47.7   0.0    1.1  1  Arf          ADP-ribosylation factor family
    2.8e-06   27.4   0.0    4.2e-06   26.8   0.0    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
    6.6e-06   26.1   0.2       0.12   12.2   0.2    2.4  3  RsgA_GTPase  RsgA GTPase
    0.00016   21.2   0.1    0.00023   20.6   0.1    1.3  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.001   18.9   1.2        0.8    9.4   0.0    2.4  3  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0076   16.2   0.2      0.019   14.9   0.1    1.7  2  NTPase_1     NTPase
  ------ inclusion threshold ------
      0.015   14.6   0.4      0.072   12.4   0.0    2.0  2  Septin       Septin
      0.016   15.0   0.4      0.044   13.5   0.4    1.8  1  AAA_24       AAA domain
      0.039   13.5   0.0       0.11   12.0   0.0    1.7  1  AAA_7        P-loop containing dynein motor region
      0.072   12.6   0.2        2.7    7.5   0.1    2.2  2  FeoB_N       Ferrous iron transport protein B
       0.14   12.4   0.0       0.22   11.8   0.0    1.5  1  AAA_22       AAA domain


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.4   0.2   2.3e-43   3.2e-40       1     158 [.       9     167 ..       9     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 137.4 bits;  conditional E-value: 2.3e-43
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEET.TEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievd.gkevkleiwDTAGqeefkslrelyyrdaegillvy 79 
                                    K+ l+Gd++vGKt+ ++r  +++F+++y++T+g+ ++  ++  d g+ +k+++wDTAGqe+   l++ yy +a+g++ ++
  gene595|gene595|rna594|rna594   9 KICLIGDGGVGKTTYINRVLDGRFEKNYNATVGAVNHPVTFLDDqGNVIKFNVWDTAGQEKKAVLKDVYYIGASGAIFFF 88 
                                    899*****************************9887776655544999******************************** PP

                                    ETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHH CS
                            Ras  80 ditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktnenveeafeellr 158
                                    d+tsr + +n+++wv+e++ v+ ++ piv+++nK+D+++++++s++ + e+ k ++++++e+SAkt++n+   f +l+r
  gene595|gene595|rna594|rna594  89 DVTSRITCQNLARWVKEFQAVVGNEAPIVICANKIDIKNRQKISKKLVMEVLKGKNYEYFEISAKTAHNFGLPFLHLAR 167
                                    ***********************************************************************99999987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.1   3.9e-32   5.3e-29       1     119 [.       9     124 ..       9     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 3.9e-32
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K++l+Gd+gvGKt+ ++r+++++f++++++t+g+  +  ++  +     d++ + +k+n+WDtaGqe+   l+++y+ +a
  gene595|gene595|rna594|rna594   9 KICLIGDGGVGKTTYINRVLDGRFEKNYNATVGAVNHPVTF--L-----DDQGNVIKFNVWDTAGQEKKAVLKDVYYIGA 81 
                                    9********************************97765544..2.....3456789************************ PP

                                    CEEEEEEE..GH.HHHCHHHHHHHHHHHCSSS.-EEEEEE-TT CS
                            Roc  81 alailvyd..sr.ssenlkeWlkelkkvagks.pvilvgnkiD 119
                                    + ai+++d  sr + +nl +W+ke+++v+g++ p+++++nkiD
  gene595|gene595|rna594|rna594  82 SGAIFFFDvtSRiTCQNLARWVKEFQAVVGNEaPIVICANKID 124
                                    ********54333569***********9876449********9 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   8.4e-16   1.2e-12      13     160 ..       6     154 ..       1     166 [. 0.82

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 8.4e-16
                                    TEEEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEEEEEEEE.....TTEEEEEEEE-SSGGGGGGGGGGCTTESEEE CS
                            Arf  13 kelrilllGLDnaGKtTilkklkleelvt.tvPTigfnveelei.....knlkftvwDvGGqeklRplWknYfektdavi 86 
                                      ++i l+G  + GKtT ++++ ++++++    T+g   + +++     + +kf+vwD  Gqek   l + Y+    + i
  gene595|gene595|rna594|rna594   6 LTYKICLIGDGGVGKTTYINRVLDGRFEKnYNATVGAVNHPVTFlddqgNVIKFNVWDTAGQEKKAVLKDVYYIGASGAI 85 
                                    5689********************999764789*****9*999988887789**************************** PP

                                    EEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTT CS
                            Arf  87 fvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavk 160
                                    f  D++ r   ++  + +k++ +    +e+++++ aNK+D+++   +++++++l +e lk  ++ e ++ sa +
  gene595|gene595|rna594|rna594  86 FFFDVTSRITCQNLARWVKEF-QAVVGNEAPIVICANKIDIKN---RQKISKKLVMEVLK-GKNYEYFEISAKT 154
                                    *****9876555555444443.33334589**********986...67899999999999.6667777666655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.1e-09   4.2e-06       1     114 []       9     122 ..       9     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.1e-09
                                    EEEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTS CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseekglgkaflaleead 77 
                                    +++++G   vGK+t in+ ++   +   +++ g+  +++++  + ++  +++++Dt+G  e    +k + k++   + a+
  gene595|gene595|rna594|rna594   9 KICLIGDGGVGKTTYINRVLDGrfEKNYNATVGAVNHPVTFLDDQGNvIKFNVWDTAG-QE----KKAVLKDVY-YIGAS 82 
                                    689*****************873444667777777777777444444678********.54....443444444.35589 PP

                                    EEEEEEETTTTCSHHHHHHHHHHHHH......TTSEEEEEEES CS
                       MMR_HSR1  78 lillvvdaseeklkpldeeleellee......akkplilvlnk 114
                                     +++ +d++ + +    ++l+++ +e      ++ p+++++nk
  gene595|gene595|rna594|rna594  83 GAIFFFDVT-SRI--TCQNLARWVKEfqavvgNEAPIVICANK 122
                                    99999**77.424..3356677766667778899999999998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00017      0.23     102     121 ..      10      29 ..       4      46 .. 0.80
   2 ?   -1.5   0.0       1.5     2e+03      51     100 ..      57     106 ..      55     114 .. 0.62
   3 !   12.2   0.2   8.8e-05      0.12      43      89 ..     110     157 ..      90     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                    EEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallp 121
                                    ++l+G  GvGK+t in++l 
  gene595|gene595|rna594|rna594  10 ICLIGDGGVGKTTYINRVLD 29 
                                    589*************9875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                    EEEE-GGG--HHHHHHHHHHH..HHHTTSEEEE--TTTHTTHHHHHHHCTTS CS
                    RsgA_GTPase  51 ivlnKiDlleeeeeleelkee..lealgyevllvsaktkegleelkellkdk 100
                                    i +n  D + +e+  +++ ++  +  +  ++++ +++++ ++++l++++k+ 
  gene595|gene595|rna594|rna594  57 IKFNVWDTAGQEK--KAVLKDvyYIGASGAIFFFDVTSRITCQNLARWVKEF 106
                                    5566666666666..3344440034444578888899999999999998873 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 8.8e-05
                                    HHTT-EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTT CS
                    RsgA_GTPase  43 eekgiepvivlnKiDlleeee.eleelkeelealgyevllvsaktkeg 89 
                                      +++++vi+ nKiD+ ++++ + + ++e l+  +ye + +sakt ++
  gene595|gene595|rna594|rna594 110 VGNEAPIVICANKIDIKNRQKiSKKLVMEVLKGKNYEYFEISAKTAHN 157
                                    5578899*************9777788999*************99876 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   1.7e-07   0.00023       1     125 [.       9     127 ..       9     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnl.tlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k+ L+G +g GKt+  + + d    ++      ++++  + +   gn+ ++n+wD  Gqe+         k+  +   + 
  gene595|gene595|rna594|rna594   9 KICLIGDGGVGKTTYINRVLDGRFEKNYNATVGAVNHPVTFLDDQGNViKFNVWDTAGQEKKAVL-----KDVYYIGASG 83 
                                    789***********99999999888877654444444445454455544**********975433.....4444445567 PP

                      Gtr1_RagA  80 liyVfDvesreleedletlkeilealrqyspeakvfvlihKmDliq 125
                                     i+ fDv+sr   ++l+++++ ++a++ +  ea + +  +K+D  +
  gene595|gene595|rna594|rna594  84 AIFFFDVTSRITCQNLARWVKEFQAVVGN--EAPIVICANKIDIKN 127
                                    79******9999999******99999865..677788889998643 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1    0.0011       1.5       2      27 ..      13      38 ..      12      46 .. 0.80
   2 !    9.4   0.0   0.00058       0.8      97     183 ..      63     139 ..      37     160 .. 0.65
   3 ?   -3.1   0.0       3.9   5.3e+03      29      42 ..     180     193 ..     170     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0011
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsv 27
                                   +G  G+GKtt+++++ + + +++++ 
  gene595|gene595|rna594|rna594 13 IGDGGVGKTTYINRVLDGRFEKNYNA 38
                                   7999***********98877776655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00058
                     ATP_bind_1  97 DtPGQielfthseslakiveeLesefalvvvyLvDsq.rltd..ptkfisgllsalsamlrlelPhvvvlnkfDllkekl 173
                                    Dt GQ +   + ++           +a ++++ +D++ r+t    + ++++     +a++  e P v++ nk+D+ k+++
  gene595|gene595|rna594|rna594  63 DTAGQEKKAVLKDVYY--------IGASGAIFFFDVTsRITCqnLARWVKE----FQAVVGNEAPIVICANKIDI-KNRQ 129
                                    5555555555555555........678888888886523333224555555....9999****************.5454 PP

                     ATP_bind_1 174 ekeleffedv 183
                                    +   + + +v
  gene595|gene595|rna594|rna594 130 KISKKLVMEV 139
                                    4444444444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.9
                     ATP_bind_1  29 vvNLDPAaeelpYe 42 
                                     vNL P   +  Y+
  gene595|gene595|rna594|rna594 180 NVNLEPTDVNYDYH 193
                                    46777766666664 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.4e-05     0.019       2      59 ..      10      71 ..       9     113 .. 0.78
   2 ?   -0.9   0.0      0.94   1.3e+03     134     155 ..     127     150 ..      95     157 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE.EEEEEEE-...------EEEEEET.T--EEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg.Gfyteevr...eggrrigFkivdlasgeegi 59
                                   +++ G  GvGKtT +++vl+   +++++ + G + + v+   ++g+ i F++ d a +e++ 
  gene595|gene595|rna594|rna594 10 ICLIGDGGVGKTTYINRVLDGRFEKNYNATvGAVNHPVTfldDQGNVIKFNVWDTAGQEKKA 71
                                   7889***************99888888753377777777777999*******9996555544 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.94
                                    SS-..-SHHHHHHHT-TT-EEEE- CS
                       NTPase_1 134 rrk..dlalveeirerkdvkvfev 155
                                    +r+  +++lv e+ + k+ ++fe+
  gene595|gene595|rna594|rna594 127 NRQkiSKKLVMEVLKGKNYEYFEI 150
                                    222345555555555555555555 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.2e-05     0.072       2      71 ..       5      66 ..       4      76 .. 0.78
   2 ?   -0.1   0.1      0.32   4.4e+02     146     181 ..     115     151 ..      98     159 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                                   EEEEEEEEEEBTTSSCCCCCCTTSSSS------------------S-EEEEEEEEETTCEEEEEEEE--- CS
                         Septin  2 gieftlmvvGesglGkttlintlfetdlieeekleeasekkkktveikkkkvvieedgvklnltviDtpg 71
                                   ++++ + ++G+ g+Gktt+in ++  +  ++   +      ++   +++  + ++++g  ++++v Dt g
  gene595|gene595|rna594|rna594  5 ELTYKICLIGDGGVGKTTYINRVLDGRFEKNY--N------ATVGAVNHPVTFLDDQGNVIKFNVWDTAG 66
                                   5678899**************99987765553..2......22345667777888889999999999987 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                                    EEESSGGGS-HHHHHH.HHHHHHHHHHHTT------- CS
                         Septin 146 PviaKaDtltkeElke.fKkkireeleeeeikiyklp 181
                                    P++  a+ +  ++ ++  Kk ++e l+ ++ +++++ 
  gene595|gene595|rna594|rna594 115 PIVICANKIDIKNRQKiSKKLVMEVLKGKNYEYFEIS 151
                                    5555555555444444168899999999999999844 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   3.2e-05     0.044       3      22 ..       8      27 ..       6      78 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                         AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                   +ki+++G+ g+GKTt +++ 
  gene595|gene595|rna594|rna594  8 YKICLIGDGGVGKTTYINRV 27
                                   8**************99987 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.1e-05      0.11      34      64 ..       8      38 ..       5      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldkekyls 64
                                   ++++l+G+ G+GKt++i+++l+   +++y+ 
  gene595|gene595|rna594|rna594  8 YKICLIGDGGVGKTTYINRVLDGRFEKNYNA 38
                                   5789***************888777677765 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0019       2.7       2      23 ..       9      30 ..       8      71 .. 0.81
   2 ?    3.4   0.0     0.036        50      89     124 ..      97     132 ..      89     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
                                   EEEEEESTTSSHHHHHHHHHTT CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltga 23
                                   +++l+G+  vGktt +n++ + 
  gene595|gene595|rna594|rna594  9 KICLIGDGGVGKTTYINRVLDG 30
                                   799**************98765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.036
                                    GGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEE CS
                         FeoB_N  89 tnlernLyLtlqllelgvpvvlalnmideaekkgie 124
                                    +nl r +  +  ++  ++p+v++ n+id  ++++i+
  gene595|gene595|rna594|rna594  97 QNLARWVKEFQAVVGNEAPIVICANKIDIKNRQKIS 132
                                    567777777777888899**********98877654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.22       8      36 ..      10      38 ..       4     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                         AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakae 36
                                   ++++G  G+GKTt ++r+l+   e ++ +
  gene595|gene595|rna594|rna594 10 ICLIGDGGVGKTTYINRVLDGRFEKNYNA 38
                                   789***************99875554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1323.53
//
Query:       gene596|gene596|rna595|rna595  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.059   13.5   0.1      0.098   12.8   0.1    1.4  1  DUF2977   Protein of unknown function (DUF2977)


Domain annotation for each model (and alignments):
>> DUF2977  Protein of unknown function (DUF2977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   5.5e-06     0.098       2      22 ..      68      88 ..      67     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-06
                        DUF2977  2 kiqindkneiigyvvvGglen 22
                                   k+ +n+kn ++g++v+G ++n
  gene596|gene596|rna595|rna595 68 KVILNKKNGVVGFIVTGKAQN 88
                                   6889*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 767.33
//
Query:       gene597|gene597|rna596|rna596  [L=294]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-07   31.8   1.1      0.012   16.4   0.2    4.8  6  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.99   1.8e+04      19      35 ..      29      44 ..      24      47 .. 0.57
   2 !   16.4   0.2   6.7e-07     0.012       3      33 ..      91     122 ..      89     126 .. 0.87
   3 ?    2.4   0.0     0.018   3.2e+02      11      28 ..     140     157 ..     130     166 .. 0.78
   4 !    6.4   0.0     0.001        18      18      35 ..     187     212 ..     175     212 .. 0.77
   5 ?   -0.1   0.0      0.11     2e+03      18      36 ..     225     242 ..     222     244 .. 0.72
   6 ?   -1.8   0.0       0.4   7.2e+03      18      32 ..     266     278 ..     237     283 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.99
                                   ETTSSEEEEEETTSEEE CS
                           WD40 19 spdgawlasGsdDgtvr 35
                                   s dg  l s++  + +r
  gene597|gene597|rna596|rna596 29 STDGLVL-SSTQGNVLR 44
                                   5666665.566455555 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.7e-07
                                    EEEEEESS.SSEEEEEEETTSSEEEEEETTSE CS
                           WD40   3 clrtltGH.ssvtslafspdgawlasGsdDgt 33 
                                     + t++GH s +++l+++p  + ++s+s+D t
  gene597|gene597|rna596|rna596  91 YVSTFSGHkSQINALSVCPGEDTVLSSSYDST 122
                                    5789****666***************998865 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.018
                                    SSEEEEEEETTSSEEEEE CS
                           WD40  11 ssvtslafspdgawlasG 28 
                                    +s+++l+ s d a l+ G
  gene597|gene597|rna596|rna596 140 NSISCLSLSNDYAILING 157
                                    78*********9999866 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.001
                                    EETTSSEEEE.........EETTSEEE CS
                           WD40  18 fspdgawlas.........GsdDgtvr 35 
                                    +spdg+++++         +s Dgt+r
  gene597|gene597|rna596|rna596 187 YSPDGSFIIAseekshlflSS-DGTIR 212
                                    89*****88645555555556.99998 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.11
                                    EETTSSEEEEEETTSEEEE CS
                           WD40  18 fspdgawlasGsdDgtvri 36 
                                      pd+++++++    ++ +
  gene597|gene597|rna596|rna596 225 ITPDSKFFLCCE-SSSILV 242
                                    489****99763.666655 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 0.4
                                    EETTSSEEEEEETTS CS
                           WD40  18 fspdgawlasGsdDg 32 
                                    f+p  a ++s s  +
  gene597|gene597|rna596|rna596 266 FNPCYAQFVS-S-SN 278
                                    7777777775.4.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2269.18
//
Query:       gene598|gene598|rna597|rna597  [L=194]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1282.64
//
Query:       gene599|gene599|rna598|rna598  [L=283]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 2084.79
//
Query:       gene600|gene600|rna599|rna599  [L=609]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-18   67.4   7.9    3.4e-18   66.1   7.9    1.7  1  MIF4G       MIF4G domain
  ------ inclusion threshold ------
       0.83   10.0   4.1        3.1    8.2   0.1    3.1  3  ATP-synt_E  ATP synthase E chain


Domain annotation for each model (and alignments):
>> MIF4G  MIF4G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   7.9   3.8e-22   3.4e-18       8     210 ..     194     411 ..     189     412 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 3.8e-22
                                    HHCHTTTTHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSH...........HHHHHHHH CS
                          MIF4G   8 lnklskenfevlikqllklamdddknelkevielifekaveepsfsplyarlcgklnsrfq...........qnFrikll 76 
                                    +n+l+ +n+   ik l  +   +  +e+ke+ +++f+ka++ep+f+ +ya ++  l +  q           + F   ll
  gene600|gene600|rna599|rna599 194 FNRLTAKNVGFVIKNLKGIRVGT-IEEMKEIANILFDKAISEPTFVKYYALVVLDLKKVWQseeektrdinqTVFFGTLL 272
                                    57788777777777777777777.589*********************************9******************* PP

                                    HHHHHHHHHHC.....................-S-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEHHHHHHHHHHHHHG CS
                          MIF4G  77 nklqeefekry.....................eleneleenedgnrrrrlglvrflgelfklkmltskilldclkellss 135
                                    + +++ fe+++                     e+ +e e ++++++rr+lg+v fl+ l+ l++++   +  c+++l++s
  gene600|gene600|rna599|rna599 273 TLTLKTFENKEkwgdeyerkkemtfkermayeEKLEEAETERYIKKRRTLGTVDFLSSLYSLNVISYVHMNACINTLMRS 352
                                    *********99********************************************************9999********* PP

                                    GCCCCSCCHSCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCHCSSSSHHHHHHHHHHHHHHH CS
                          MIF4G 136 ltketaddppqdleeieilltllttigktlennekakkeldqffkriqkiledatrqelssrirfmlkdlielkk 210
                                     +           e+ie+l++l+++ig++l    + k+ +  +++    +++d    +++ rir+m+++l+e k+
  gene600|gene600|rna599|rna599 353 SDS----------ESIEVLCYLIENIGEKLV--VSGKEHIISMICSRLVQKKD----NYANRIRYMIENLLEKKN 411
                                    999..........******************..88888877777766666664....9*************9887 PP

>> ATP-synt_E  ATP synthase E chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2      0.26   2.3e+03      50      67 ..      96     113 ..      73     136 .. 0.54
   2 ?    8.2   0.1   0.00035       3.1      22      76 ..     266     320 ..     265     335 .. 0.87
   3 ?    1.4   0.1     0.047   4.2e+02      22      79 ..     373     430 ..     373     448 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.26
                     ATP-synt_E  50 kliekakaayakkkqaks 67 
                                     + ++ ka+y+ ++  ++
  gene600|gene600|rna599|rna599  96 DVHKETKAEYKDERPIQK 113
                                    233445555544444433 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00035
                     ATP-synt_E  22 vvyGakrqrslkseekkeekereleaqekliekakaayakkkqakseakslaegs 76 
                                    v++G     +lk  e+ke+   e+e+++++  k++ ay+ k ++ + ++++ +  
  gene600|gene600|rna599|rna599 266 VFFGTLLTLTLKTFENKEKWGDEYERKKEMTFKERMAYEEKLEEAETERYIKKRR 320
                                    7889999999**99************************99999888888877765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.047
                     ATP-synt_E  22 vvyGakrqrslkseekkeekereleaqekliekakaayakkkqakse.akslaegssak 79 
                                    vv G+ +  s+  + +  +k+ +++++     +   ++++++++k+  a+++ +  +++
  gene600|gene600|rna599|rna599 373 VVSGKEHIISMI-CSRLVQKKDNYANRIRYMIENLLEKKNSWKPKEMkARNVFSCLEVE 430
                                    566777777777.7777788889999988888999999999999883244444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3737.90
//
Query:       gene6|gene6|rna6|rna6  [L=151]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0036   17.5   3.8     0.0068   16.7   3.8    1.4  1  zf-C2H2_jaz   Zinc-finger double-stranded RNA-binding
  ------ inclusion threshold ------
       0.01   16.1   1.5      0.019   15.3   1.4    1.6  1  zf-C2H2_2     C2H2 type zinc-finger (2 copies)
      0.019   15.6   0.2      0.028   15.0   0.2    1.4  1  FRP           Photoprotection regulator fluorescence recovery
      0.039   14.1   0.3      0.068   13.4   0.3    1.4  1  FliG_C        FliG C-terminal domain
      0.099   13.3   0.1       0.13   13.0   0.1    1.3  1  zf-C2H2_3rep  Zinc finger C2H2-type, 3 repeats
       0.18   12.3   2.6       0.32   11.5   2.6    1.4  1  zf-met        Zinc-finger of C2H2 type


Domain annotation for each model (and alignments):
>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.8   2.3e-06    0.0068       3      26 ..       2      25 ..       2      26 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                           BBTTTTBBBSSHHHHHCCTTSHHH CS
            zf-C2H2_jaz  3 YCvlCdKyFksenaldnHlkSKkH 26
                           +C+ C+K F++ na++ H+ + +H
  gene6|gene6|rna6|rna6  2 FCIPCQKKFSTKNAYKCHILTSSH 25
                           7******************99999 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.4   6.3e-06     0.019      52      82 ..       2      32 ..       1      57 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-06
              zf-C2H2_2 52 eClyCekefkslealreHmkkkgHckineee 82
                            C+ C+k+f++++a++ H+ + +H k + e 
  gene6|gene6|rna6|rna6  2 FCIPCQKKFSTKNAYKCHILTSSHAKAEDEY 32
                           6*************************86644 PP

>> FRP  Photoprotection regulator fluorescence recovery protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   9.3e-06     0.028       7      60 ..      33      84 ..      27     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.3e-06
                    FRP  7 kiarealekayereiealiaevkekaeslsdlddlWq.lhdfLsakRydidgkyd 60
                           ki r+    a er++ + i+++++ ++++++ +++ q  +++L+++R++i+g   
  gene6|gene6|rna6|rna6 33 KINRK---VAIERNTVNFITDFHSYISQIAEYKEIGQaYREYLTKNRFRIEGTRF 84
                           55554...599************************98358***********9543 PP

>> FliG_C  FliG C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   2.3e-05     0.068      65     108 .]      66     109 ..      59     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                            HHHHHHHHHHHHHC-S--HHHHHHHHHHHHHHHHHHHCTTSS-B CS
                 FliG_C  65 kraaemlreelealgpvrlsdveeaqkeivaiirrleeeGeIel 108
                            +  +e l ++  +++  r + veea ++i ++i  ++eeG+I++
  gene6|gene6|rna6|rna6  66 QAYREYLTKNRFRIEGTRFKSVEEAVDKIAKRISVMKEEGRIMI 109
                            566677777777888999************************97 PP

>> zf-C2H2_3rep  Zinc finger C2H2-type, 3 repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.2e-05      0.13      34      75 ..       2      44 ..       1      97 [. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
           zf-C2H2_3rep 34 qcipcgshfgnaeelwlhvls.vhpsdfklskvaqkknlsase 75
                            cipc+ +f+ ++    h+l+  h++   + k+++k +++ + 
  gene6|gene6|rna6|rna6  2 FCIPCQKKFSTKNAYKCHILTsSHAKAEDEYKINRKVAIERNT 44
                           6*****************9962677776777777766555443 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   2.6   0.00011      0.32       3      20 ..       3      20 ..       2      25 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                 zf-met  3 CelCnvtfnsesqlksHl 20
                           C  C+++f+ ++++k+H 
  gene6|gene6|rna6|rna6  3 CIPCQKKFSTKNAYKCHI 20
                           778**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1058.86
//
Query:       gene60|gene60|rna60|rna60  [L=183]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.5    7.8   7.2        1.1    9.4   0.1    2.3  2  Popeye    Popeye protein conserved region


Domain annotation for each model (and alignments):
>> Popeye  Popeye protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   6.2e-05       1.1      18      71 ..      46      99 ..      34     115 .. 0.79
   2 ?    0.4   2.7     0.037   6.6e+02      10      46 ..     129     166 ..     121     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.2e-05
                               xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Popeye 18 lapsgvlgllvlrsllvlGflllalwawlvvCaldiflWnlllvlinlaqllyl 71
                                  +gv+  l+ +s+ ++Gf+l ++ ++  +C  d +   ++ +   +++++ +
  gene60|gene60|rna60|rna60 46 SDAKGVFCFLFSFSTTIIGFMLETMRSTAKICKNDRMKYRVMKAQRGFTYMTLI 99
                               34556688899999*********************9988887766666665555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.037
                                xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                     Popeye  10 nillllaflapsgvlgllvlrsll.vlGflllalwawl 46 
                                 ++ ++af++ +     ++l +++  lG+lll++ a +
  gene60|gene60|rna60|rna60 129 ICCSFTAFIGMDMLNTFFYLTFVIsNLGVLLLTYVAGF 166
                                47889999999999877777766525899999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1116.57
//
Query:       gene601|gene601|rna600|rna600  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.2   3.6    2.3e-07   30.8   3.6    1.2  1  CLTH      CTLH/CRA C-terminal to LisH motif domain


Domain annotation for each model (and alignments):
>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   3.6   1.3e-11   2.3e-07       1     144 [.      57     191 ..      57     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.3e-11
                           CLTH   1 sikerqkIiklilegdlseaiewinenkpelles..nsnLeFkLkllqfielirgktkdieealeyarenlefendehlk 78 
                                    si  r++I +li+++ ++ a + ++++k   l +    +++ +L  l f+  +r   ++  ea+e+ar+ ++ en+    
  gene601|gene601|rna600|rna600  57 SISTRKRILSLIEKKCTNDAFKICEDLKLFDLGIenEASVKETLSKLVFVDFLR-A-RKHIEAIEFARTFINDENE---- 130
                                    5889**********************887666553269999*************.9.9***********8875555.... PP

                           CLTH  79 elekamsLLafsdpeskelssplknlldpsrrekvakefnsailkllglskespLeillsaglsal 144
                                       k+++L+ ++d ++    +++ ++ d+ +rekv++++n+ +       + s L+++l++  s+l
  gene601|gene601|rna600|rna600 131 -NDKLFTLIGYEDIND----ARFLEIADSIKREKVVEILNKHLFGKEVGRQLSLLSLALNHYNSIL 191
                                    .469*********998....8********************9998888888888888888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1289.12
//
Query:       gene602|gene602|rna601|rna601  [L=64]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   19.2   1.0     0.0018   18.4   1.0    1.5  1  Cir_N     N-terminal domain of CBF1 interacting co-repressor 


Domain annotation for each model (and alignments):
>> Cir_N  N-terminal domain of CBF1 interacting co-repressor CIR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.0     1e-07    0.0018       2      33 ..      11      41 ..      10      46 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1e-07
                                   S-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Cir_N  2 WHPgllkNqerVWkaEqkaleEkkkieerkke 33
                                   WHP+ ++ q rV++aE++  e+ k +e+ ++e
  gene602|gene602|rna601|rna601 11 WHPSRYETQIRVREAEKA-IEKSKIQEDTRRE 41
                                   ***************965.5555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 390.58
//
Query:       gene603|gene603|rna602|rna602  [L=428]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.029   15.0   1.0         14    6.4   0.2    2.8  2  SPT6_acidic  Acidic N-terminal SPT6


Domain annotation for each model (and alignments):
>> SPT6_acidic  Acidic N-terminal SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2   0.00076        14      11      46 ..     122     157 ..     120     161 .. 0.63
   2 ?    6.1   0.0   0.00092        16      52      70 ..     360     378 ..     333     386 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00076
                    SPT6_acidic  11 eeerkvregFIvddd..eeeeeeeeseeeeekkrrkkk 46 
                                    e+  k+re FIv+ +  ee+ + ++s+    ++ +kkk
  gene603|gene603|rna602|rna602 122 EDFLKIRERFIVETEglEEDMNLSHSD--LMERMKKKK 157
                                    566799*******98666655555554..223333333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00092
                    SPT6_acidic  52 eeedaLdedDldLieentg 70 
                                    +e++++de Dl+Li+    
  gene603|gene603|rna602|rna602 360 DEKKEVDEADLELIQKSFS 378
                                    56689*********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2684.60
//
Query:       gene604|gene604|rna603|rna603  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.023   14.1   1.5      0.063   12.6   0.4    1.9  2  Gtr1_RagA  Gtr1/RagA G protein conserved region


Domain annotation for each model (and alignments):
>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.019   3.4e+02      83     113 ..      64      94 ..      60     118 .. 0.59
   2 ?   12.6   0.4   3.5e-06     0.063      70     121 ..     124     175 ..     107     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.019
                      Gtr1_RagA  83 VfDvesreleedletlkeilealrqyspeak 113
                                    +fD++ +++ee+  + +++l+ l++   +a 
  gene604|gene604|rna603|rna603  64 IFDATLESFEEASLRVQKTLTSLKELIYKAD 94 
                                    5666655555555555555555554433333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.5e-06
                      Gtr1_RagA  70 keeifrnvgvliyVfDvesreleedletlkeilealrqyspeakvfvlihKm 121
                                    ++ei r+ + l+  +D++++e+e+d++++ke+++++    +  ++  l++K 
  gene604|gene604|rna603|rna603 124 EDEIERELKELVVFLDIQNEEVEKDVAYYKEMVSRAGIRTKLENISYLVNKK 175
                                    6889999999************************999888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1083.02
//
Query:       gene605|gene605|rna604|rna604  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-31  108.1   4.0    6.4e-31  107.9   4.0    1.1  1  DUF2463   Protein of unknown function (DUF2463)
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.023   14.3   0.0    1.5  1  HARP      HepA-related protein (HARP)
      0.043   13.8   1.8       0.33   10.9   0.4    2.2  2  LrgA      LrgA family
       0.13   12.1   0.0       0.16   11.8   0.0    1.1  1  VirB8     VirB8 protein


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   4.0   1.4e-34   6.4e-31      82     203 ..       3     123 ..       1     130 [. 0.94

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 1.4e-34
                        DUF2463  82 idkwesdddlliysiilPslvvpltyLlstscnlvpgqisftdtginilidlliLlllivslvllleeseyllyfaiiss 161
                                    i +w ++d + i+s+++Ps++v + yLlstsc+l p ++ ftdtgi+il+ ll+Ll + +++ ll+  ++y lyfai+s+
  gene605|gene605|rna604|rna604   3 IYEWANED-PNIFSMVIPSILVLPPYLLSTSCDLKPCKFFFTDTGIDILLSLLVLLHIPLGVGLLCGGTKYQLYFAITSF 81 
                                    67896666.699******************************************************************** PP

                        DUF2463 162 iliLvrllkekylpskksslptakwrvaifvliLilavliYv 203
                                       L+++lke +lps+k   +t kwr+ai+++iL+ a++i  
  gene605|gene605|rna604|rna604  82 FATLAKSLKEVCLPSRKYEDSTRKWRLAILIFILLSAAIICG 123
                                    ************************************999855 PP

>> HARP  HepA-related protein (HARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.2e-06     0.023      18      33 ..      94     109 ..      77     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-06
                           HARP  18 ipSrnYdpktkkWnFs 33 
                                    +pSr+Y+  t+kW ++
  gene605|gene605|rna604|rna604  94 LPSRKYEDSTRKWRLA 109
                                    7************987 PP

>> LrgA  LrgA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   7.3e-05      0.33      31      62 ..      35      66 ..      12      87 .. 0.78
   2 ?    2.2   0.1     0.038   1.7e+02      69      93 ..     104     128 ..      97     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.3e-05
                           LrgA 31 tkivklekveeaadfllkhlallFvPagvgvm 62
                                   +k +k    +++ d+ll+ l ll +P gvg++
  gene605|gene605|rna604|rna604 35 LKPCKFFFTDTGIDILLSLLVLLHIPLGVGLL 66
                                   55566666788999****************97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.038
                           LrgA  69 kaellailvalvvstllvlvvtglv 93 
                                    ++  lail+ +++s +++  +t +v
  gene605|gene605|rna604|rna604 104 RKWRLAILIFILLSAAIICGITIFV 128
                                    5566889999999999999998877 PP

>> VirB8  VirB8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.5e-05      0.16      14      62 ..     100     148 ..      96     150 .] 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX.XXXX CS
                          VirB8  14 rvqarnwrlvafvslliavlavgavvlllplktvePyvvevdkttGeve 62 
                                    + ++r wrl+ ++++l++++ + ++++ + l+t++ y  +++kt+G+++
  gene605|gene605|rna604|rna604 100 EDSTRKWRLAILIFILLSAAIICGITIFVFLETFKNYSTSIKKTSGNLR 148
                                    568899****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1057.04
//
Query:       gene606|gene606|rna605|rna605  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0045   16.9   4.5     0.0058   16.5   4.5    1.2  1  DUF2463   Protein of unknown function (DUF2463)


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.5   3.2e-07    0.0058       1      68 [.      51     118 ..      51     119 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-07
                        DUF2463   1 fpvlmyfifekdsfeeslllrfitlllpfsys...avqyllllhtnwkssnkpesilhkilyyllnlllla 68 
                                    +p+++y+   k++++++lllr+it+ +p+      ++ y+ l+ +n   ++   s+l  + ++l +llll 
  gene606|gene606|rna605|rna605  51 LPIVVYLLAGKKTIKNNLLLRLITIFFPVHTQqrnTLTYF-LILGN--PNIGLYSTLFLMAFFLHSLLLLF 118
                                    69**************************987611144454.33333..44444455666666655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 759.01
//
Query:       gene607|gene607|rna606|rna606  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-58  196.3  25.8    6.4e-58  196.1  25.8    1.0  1  DUF2463   Protein of unknown function (DUF2463)
  ------ inclusion threshold ------
       0.39   11.1   8.5        2.8    8.3   3.3    2.5  2  2TM       2TM domain


Domain annotation for each model (and alignments):
>> DUF2463  Protein of unknown function (DUF2463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.1  25.8   7.1e-62   6.4e-58       1     210 []      23     225 ..      23     225 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 7.1e-62
                        DUF2463   1 fpvlmyfifekdsfeeslllrfitlllpfsysavqyllllhtnwkssnkpesilhkilyyllnllllaFaiisilSiial 80 
                                    fp++m f++   s+++slll+fit+llpfsysa+q++ll++ n+  ++k++s+lh+ily+llnl l++Fa+i  +S++++
  gene607|gene607|rna606|rna606  23 FPAIMHFTL-GPSIKDSLLLKFITVLLPFSYSAAQHFLLFRINRSLDYKSSSLLHSILYFLLNLFLFVFAVIDGISTVTF 101
                                    9*******9.789******************************************************************* PP

                        DUF2463  81 tidkwesdddlliysiilPslvvpltyLlstscnlvpgqisftdtginilidlliLlllivslvllleeseyllyfaiis 160
                                    t+dkw  ddd + +si+lPs+vvp+tyLlst c l+pg+i+f dtg+n lid+liLl ++v++++ l++s y +y+a+ s
  gene607|gene607|rna606|rna606 102 TLDKW--DDD-VSFSILLPSFVVPSTYLLSTACILTPGSIQFPDTGFNFLIDILILLRIVVGIMFPLHNSSY-IYIAVPS 177
                                    *****..444.569*********************************************************9.99***** PP

                        DUF2463 161 siliLvrllkekylpskksslptakwrvaifvliLilavliYvflalesi 210
                                    +iliL+r+l+  y+   +s    a wr +i +li+ ++ +i++++a+ si
  gene607|gene607|rna606|rna606 178 FILILLRSLNLGYSS--SSVTEYAVWRQLIVFLIFGISLFIHTIIACMSI 225
                                    *********987766..67788899**********************997 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0026        23      16      39 ..      76     101 ..      62     129 .. 0.75
   2 ?    8.3   3.3   0.00031       2.8      17      53 ..     169     219 ..     163     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0026
                            2TM  16 hlvvYlivniflilinl..gsswflw 39 
                                    h ++Y++ n+fl+++ +  g+s + +
  gene607|gene607|rna606|rna606  76 HSILYFLLNLFLFVFAVidGISTVTF 101
                                    8899********99976664433333 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00031
                            2TM  17 lvvYlivniflili....nl......gsswflw....pilfWgiglllhal 53 
                                     ++Y++v +f++++    nl        ++++w    + l+ gi l++h +
  gene607|gene607|rna606|rna606 169 SYIYIAVPSFILILlrslNLgyssssVTEYAVWrqliVFLIFGISLFIHTI 219
                                    578888888555554655557776664444466665477889*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1475.44
//
Query:       gene608|gene608|rna607|rna607  [L=813]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.6e-85  284.8   4.3    7.6e-85  284.8   4.3    1.7  2  Kinesin       Kinesin motor domain
      3e-19   69.4   3.0    4.8e-19   68.8   0.9    2.5  2  Microtub_bd   Microtubule binding
    4.1e-06   27.4   6.9        1.1   10.3   0.2    5.6  5  WD40          WD domain, G-beta repeat
     0.0033   17.5  14.2      0.011   15.8   9.2    2.9  2  Cnn_1N        Centrosomin N-terminal motif 1
     0.0061   16.8   1.1        2.6    8.4   0.0    3.8  4  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domai
  ------ inclusion threshold ------
       0.01   16.3   0.0        7.2    7.2   0.0    3.9  4  PQQ_3         PQQ-like domain
       0.44   11.3   3.8       0.52   11.0   0.5    2.9  3  DnaI_N        Primosomal protein DnaI N-terminus
       0.54   10.4   5.6        1.7    8.8   5.6    1.9  1  Herpes_BLRF2  Herpesvirus BLRF2 protein
        4.7    7.7   9.3    1.4e+02    3.1   9.4    2.6  1  ZapB          Cell division protein ZapB


Domain annotation for each model (and alignments):
>> Kinesin  Kinesin motor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.8   4.3   3.8e-88   7.6e-85      12     333 .]       5     299 ..       1     299 [. 0.91
   2 ?   -3.5   0.2       1.9   3.9e+03     231     255 ..     452     479 ..     436     505 .. 0.62

  Alignments for each domain:
  == domain 1  score: 284.8 bits;  conditional E-value: 3.8e-88
                                    TTTEBCEEEECTCTCEEEEEEEEECTTSCEEEEESEEEETTS-HHHHHHHHHHHHHHHHHTTSEEEEEEEESTTSSHHHH CS
                        Kinesin  12 eeeeeeveveeekkeeekkskkenkeeeekkfkFdkvfdeeatqeevyeetakplvesvleGynatifaYGqtgsGKTyT 91 
                                    +++ ++ ++++ + ++ ++s+ ++ +  +k++ F++v   +++q ++y++ +++l es+leGyn+t++aYGqtgsGKTyT
  gene608|gene608|rna607|rna607   5 RNTIQVEVRINPRLDNVIESTPTALTVGTKTYGFNRVHL-TTSQMQMYDRSVRHLTESFLEGYNCTVMAYGQTGSGKTYT 83 
                                    344444445557888899999999999*********976.77899*********************************** PP

                                    HTBCTTTSBSHHHHHHHHHHHHHHHCTTTHEEEEEEEEEEEEEETTEEEETTSTTTTSTSSEBEEEECTTSCCEEETTS- CS
                        Kinesin  92 megkeeeeeGiipraleelFesikkekeekekefsvkvsylEiYneeiyDLLeskkskkkkklkiredskkgevyvkglt 171
                                    m  ++e+ +Gi+p++l+++F+s+++          ++++++E+Ynee+ DL++++    k +l++re +   e++++g t
  gene608|gene608|rna607|rna607  84 MGMTHEDMTGIVPQSLNHIFKSCQE----------INCTFIEVYNEEVIDLFSKH----KMPLSLREVNG--EITIAGAT 147
                                    ****9******************65..........899***************88....45799999665..69****** PP

                                    -EEESSHHHHHHHHHHHHHHHTSTTSSCTSHHCCSEEEEEEEEEEEETTTTTCEEEEEEEEEEEEEEECCCHHHHSSTCH CS
                        Kinesin 172 evevksaeevlellekgeknrkvaetklneeSSRSHavftitleqknlkeeteekvkisklnLvDLAGsErasktgaaeg 251
                                    ev ++s+++ +e l+kg+ +r++++t++n++SSRSHa+f +  +++  +   +    +sk+++vDLAGsEr+++t    g
  gene608|gene608|rna607|rna607 148 EVALRSYQDGIEALKKGSLERTTKSTNMNSKSSRSHAIFILSHRREI-D--GS--FVTSKFSFVDLAGSERLKRTLC-AG 221
                                    ***************************************88654443.3..33..679******************5.69 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHTCCTSTSCGGGSHHHHHTGGGHSSSSEEEEEEEE-TBGGGHHHHHHHHHHHHHHC CS
                        Kinesin 252 erlkEaaniNkSLlaLgrvisaLaekkkskhipYRdSkLTrlLqdsLgGnsktlmivtvspssenleetlstlkfaerak 331
                                    +r kE+ +iN  LlaLg+visaL +k  s+hip+RdSkLTr+Lq++L+G   +lmi++vs s+ +++et++tlk+a+ra 
  gene608|gene608|rna607|rna607 222 DRAKEGISINSGLLALGNVISALFKK--SSHIPFRDSKLTRILQSCLSGY--VLMIACVSSSHADISETHNTLKYASRAA 297
                                    99************************..********************95..8*************************98 PP

                                    TT CS
                        Kinesin 332 ei 333
                                    +i
  gene608|gene608|rna607|rna607 298 SI 299
                                    76 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                                    EEEE.EEEEECCCHHHHSS..TCHHHHH CS
                        Kinesin 231 klnL.vDLAGsErasktga..aegerlk 255
                                    +ln+ vDL  sE++ ++++  +e++  +
  gene608|gene608|rna607|rna607 452 HLNIsVDLDKSEEMFNRNKiqSESQGKE 479
                                    3444477777777766665432233233 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.9   2.4e-22   4.8e-19      16     148 ..       2     124 ..       1     125 [. 0.88
   2 ?   -1.7   0.0       1.2   2.4e+03      72      91 ..     259     278 ..     246     331 .. 0.74

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 2.4e-22
                                    HHHCTB-EEEEEEECCCS-T.EEEETTT...TTTEEEE-SEEEECTTHCCCCCCCCHHHHHHHHTT--EEEEEEES.... CS
                    Microtub_bd  16 qelkGniRvfarvrpelesekakikfpeeekkkkkefsFdrvfeseseqeevfeeisqlvqsaldgynvcifaygqTGsG 95 
                                    +e + +i v +r++p+l++     ++p+  +  +k++ F+rv  ++s+ ++    +++l++s l+gyn++++aygqTGsG
  gene608|gene608|rna607|rna607   2 EERRNTIQVEVRINPRLDNV--IESTPTALTVGTKTYGFNRVHLTTSQMQMYDRSVRHLTESFLEGYNCTVMAYGQTGSG 79 
                                    67788888888888888883..344445677899********************************************** PP

                                    .............ST-HCHHHHHHHHHHCCTSCCCCEEEEEEEEEEESS-EEET CS
                    Microtub_bd  96 KtyTmeg.eeeeagmipraveeifetiselkekgwkyeielqfveiynekvqDl 148
                                    KtyTm   +e+ +g +p+++++if+ ++e          +++f+e+yne+v Dl
  gene608|gene608|rna607|rna607  80 KTYTMGMtHEDMTGIVPQSLNHIFKSCQEI---------NCTFIEVYNEEVIDL 124
                                    *****986788899**********999876.........99************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHTT--EEEEEEES CS
                    Microtub_bd  72 sqlvqsaldgynvcifaygq 91 
                                    + ++qs+l+gy   i ++++
  gene608|gene608|rna607|rna607 259 TRILQSCLSGYVLMIACVSS 278
                                    56789999999999888887 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.68   1.4e+03      25      38 .]     567     579 ..     555     579 .. 0.76
   2 !    6.6   0.0     0.008        16      11      36 ..     625     648 ..     615     650 .. 0.73
   3 !    7.4   0.1    0.0045       8.9       8      37 ..     661     689 ..     654     690 .. 0.70
   4 ?    0.6   0.0      0.63   1.3e+03      10      37 ..     700     726 ..     692     727 .. 0.63
   5 !   10.3   0.2   0.00053       1.1      23      38 .]     751     766 ..     730     766 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.68
                                    EEEEETTSEEEEEE CS
                           WD40  25 lasGsdDgtvriWd 38 
                                    ++ +s D+++r Wd
  gene608|gene608|rna607|rna607 567 VF-ASIDNKIRSWD 579
                                    44.688*******9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.008
                                    SSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40  11 ssvtslafspdgawlasGsdDgtvri 36 
                                    s v++l fs+d+  l +G++Dgt+ i
  gene608|gene608|rna607|rna607 625 SEVSAL-FSRDNYIL-TGHEDGTLSI 648
                                    457666.77777776.8******987 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0045
                                    ESS.SSEEEEEEETTSSE....EEEEETTSEEEEE CS
                           WD40   8 tGH.ssvtslafspdgaw....lasGsdDgtvriW 37 
                                    ++H + v ++            + +Gs+D+tvr +
  gene608|gene608|rna607|rna607 661 KAHsGTVFCI------EKigsdIYTGSRDHTVRCY 689
                                    6894449999......333444679********87 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.63
                                    S.SSEEEEEEETTSSEEEEEETTSEEEEE CS
                           WD40  10 H.ssvtslafspdgawlasGsdDgtvriW 37 
                                    H +sv +l    +++ l+s ++D+++r W
  gene608|gene608|rna607|rna607 700 HlDSVQGL--LCYNDNLISFGRDCSIRRW 726
                                    55556666..223333455467*****98 PP

  == domain 5  score: 10.3 bits;  conditional E-value: 0.00053
                                    SEEEEEETTSEEEEEE CS
                           WD40  23 awlasGsdDgtvriWd 38 
                                    + +++Gs+Dg +r+Wd
  gene608|gene608|rna607|rna607 751 DSFVTGSKDGMLRFWD 766
                                    33679**********9 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   9.2   5.8e-06     0.011      12      68 ..     319     375 ..     317     377 .. 0.96
   2 ?    3.2   0.2     0.051     1e+02      38      63 ..     383     408 ..     375     413 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-06
                         Cnn_1N  12 LkKENFdLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllre 68 
                                    LkKE   LK + ++L+er+ k s  ++e+l++en  lk +ve l  e++ k++ + +
  gene608|gene608|rna607|rna607 319 LKKEIQKLKVENQMLKERFRKESRVNIEDLISENRMLKSKVEALSFEKDDKREDIIQ 375
                                    89*************************************************998765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.051
                         Cnn_1N  38 keellkenielkveveslqkelkekk 63 
                                    +++l++en  lk+ v +  k+l++ k
  gene608|gene608|rna607|rna607 383 VQNLIDENQRLKDMVGKISKDLERQK 408
                                    7899*****************99987 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.9   3.8e+03      56      80 ..     105     129 ..     100     135 .. 0.83
   2 ?   -1.9   0.0       2.1   4.1e+03      23      51 ..     342     369 ..     335     370 .. 0.79
   3 !    8.4   0.0    0.0013       2.6      50      87 ..     634     670 ..     625     673 .. 0.88
   4 ?    4.1   0.0     0.028        55      27      64 ..     770     805 ..     750     812 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                    ANAPC4_WD40  56 aysdgevrlldaesgkvvhslsvks 80 
                                    ++++ ++ ++++++++v+  +s ++
  gene608|gene608|rna607|rna607 105 SCQEINCTFIEVYNEEVIDLFSKHK 129
                                    67888999*********99988765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.1
                    ANAPC4_WD40  23 RlngqrvwtleedkedsevrsLaWkpdgk 51 
                                    R+n + + +  +   +s+v++L++++d+k
  gene608|gene608|rna607|rna607 342 RVNIEDLISE-NRMLKSKVEALSFEKDDK 369
                                    6666666665.7788999******99987 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0013
                    ANAPC4_WD40  50 gklLavaysdgevrlldaesgkvvhslsvksekavtcl 87 
                                    ++ +  +++dg++++ld  + k+v s +++s  +v c+
  gene608|gene608|rna607|rna607 634 DNYILTGHEDGTLSILDQRNSKLVFSEKAHSG-TVFCI 670
                                    567889************************99.59998 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.028
                    ANAPC4_WD40  27 qrvwtleedkedsevrsLaWkpdgklLavaysdgevrl 64 
                                    + v+ + + k ++ ++sL W  +g++  v++++ e+  
  gene608|gene608|rna607|rna607 770 NSVFCVGKLKAGGAINSLVW--NGEVVYVGCQNKEILA 805
                                    67888889999*********..699*******998865 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         5   9.9e+03      15      37 ..     557     579 ..     550     581 .. 0.77
   2 ?    1.9   0.0      0.17   3.4e+02      21      39 ..     634     652 ..     613     653 .. 0.83
   3 ?    1.5   0.0      0.22   4.4e+02      24      36 ..     677     689 ..     664     691 .. 0.91
   4 ?    7.2   0.0    0.0036       7.2       9      36 ..     780     806 ..     771     807 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5
                          PQQ_3  15 sspavdgglvyvgtgdGtlyAlD 37 
                                    +++++ g ++++++ d+++++ D
  gene608|gene608|rna607|rna607 557 TALTLFGSHLVFASIDNKIRSWD 579
                                    55677789999999999998877 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.17
                          PQQ_3  21 gglvyvgtgdGtlyAlDae 39 
                                    ++++ +g +dGtl  lD +
  gene608|gene608|rna607|rna607 634 DNYILTGHEDGTLSILDQR 652
                                    89999********999965 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.22
                          PQQ_3  24 vyvgtgdGtlyAl 36 
                                    +y+g+ d+t++++
  gene608|gene608|rna607|rna607 677 IYTGSRDHTVRCY 689
                                    8**********97 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0036
                          PQQ_3   9 lpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                     +g++  s++  g +vyvg+ +  + A+
  gene608|gene608|rna607|rna607 780 AGGAI-NSLVWNGEVVYVGCQNKEILAI 806
                                    56667.689*************999986 PP

>> DnaI_N  Primosomal protein DnaI N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.5     9e+03      58      81 ..      42      68 ..       2      75 .. 0.53
   2 ?   11.0   0.5   0.00026      0.52      19      47 ..     368     395 ..     344     405 .. 0.78
   3 ?   -2.9   0.0       5.6   1.1e+04      40      82 ..     515     557 ..     501     561 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.5
                                   HHHHHS-SS-TT...TTS--SSTTEEE CS
                         DnaI_N 58 yeyveekkkcea...eecknlakGYeP 81
                                       ++ + +++   +  +++++GY+ 
  gene608|gene608|rna607|rna607 42 HLTTSQMQMYDRsvrHLTESFLEGYNC 68
                                   444444444444444444555555554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00026
                                    HHHHHHHHHHTTXHHHHHHHHHSTTTC-H CS
                         DnaI_N  19 kryeklkeevlsdpeVqaFlqehqeelte 47 
                                    ++ e++++e+l++p Vq++++e+q+ l++
  gene608|gene608|rna607|rna607 368 DKREDIIQEILKHPFVQNLIDENQR-LKD 395
                                    67899*******************6.765 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.6
                                    HSTTTC-HHHHHHTHHHHHHHHHS-SS-TT.TTS--SSTTEEEE CS
                         DnaI_N  40 ehqeelteeaierslskLyeyveekkkcea.eecknlakGYePk 82 
                                    +h+ ++ + ++er+ +k   +   k+k++     +  + GY P+
  gene608|gene608|rna607|rna607 515 AHK-RVVSFDLERNTKKYALFTPRKEKITMaTTVEDKLVGYLPT 557
                                    344.4777778888888888888888887766777777788876 PP

>> Herpes_BLRF2  Herpesvirus BLRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.6   0.00087       1.7       7      79 ..     319     389 ..     314     424 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00087
                   Herpes_BLRF2   7 laaelakLkvENkaLkkklkssvspkdeeLTaaekeavltstvgrlsskaakkieervrkevlkvvtknevee 79 
                                    l++e++kLkvEN+ Lk++ +++   + e L  +++  +l s v++ls +  +k e+ ++ ++++   +n ++e
  gene608|gene608|rna607|rna607 319 LKKEIQKLKVENQMLKERFRKESRVNIEDLISENR--MLKSKVEALSFEKDDKREDIIQEILKHPFVQNLIDE 389
                                    789*****************999999999998877..899999999999999888888877777666666665 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   9.4     0.068   1.4e+02      22      69 ..     318     400 ..     314     408 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.068
                           ZapB  22 lLqmeieeLkeeneelkeenrele........eeneqlk...........................eereawqerlkkLL 66 
                                    lL++ei++Lk en+ lke+ r+ +        +en  lk                           ++    ++rlk ++
  gene608|gene608|rna607|rna607 318 LLKKEIQKLKVENQMLKERFRKESrvniedliSENRMLKskvealsfekddkrediiqeilkhpfvQNLIDENQRLKDMV 397
                                    7999***********99998877777788888677666666666666666666666666666666666666666666666 PP

                           ZapB  67 gkl 69 
                                    gk+
  gene608|gene608|rna607|rna607 398 GKI 400
                                    665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.80u 0.32s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 4926.83
//
Query:       gene609|gene609|rna608|rna608  [L=904]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-21   77.4   0.0    3.3e-21   76.4   0.0    1.5  1  Patatin       Patatin-like phospholipase
    3.2e-11   43.2   0.1    6.1e-05   23.0   0.0    3.4  3  cNMP_binding  Cyclic nucleotide-binding domain
  ------ inclusion threshold ------
      0.063   13.5   0.1       0.45   10.7   0.1    2.4  2  CENP-C_C      Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   5.5e-25   3.3e-21       1     203 [.     610     773 ..     610     774 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 5.5e-25
                        Patatin   1 LvlsGGGsrgafslgalkaLkkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllirelaanla 80 
                                    Lvl+GGG+rg++++g+++aL +e+g+ +d i+GtS GA+i+   al+   a++  +++ + ++k f+r+     +++ + 
  gene609|gene609|rna608|rna608 610 LVLGGGGARGLAHIGVIQAL-EEEGIPIDCIGGTSMGAFIG---ALY---AKECNNYYVFKQAKKFSRK-----MSNIWL 677
                                    8*******************.********************...555...5568889999999999999.....89999* PP

                        Patatin  81 arlsgllgkgglfdaealrellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglyteddd 160
                                     +l+ ++   ++f+++a+ + l  v++d+ +++l    +++                           +++ + y e+  
  gene609|gene609|rna608|rna608 678 LLLDLTYPICSMFSGNAFNRSLHSVFGDGLIQDLWLEYFCI---------------------------TTNISNYEEEVH 730
                                    *****************************************...........................99********** PP

                        Patatin 161 ddvdladavraSsafPglfppvsldgelyvDGGilsNvPilaa 203
                                    +++ +++ vraS+ + g++pp   + +l+vDGG l+NvP++++
  gene609|gene609|rna608|rna608 731 RNGMVWRYVRASMGLCGYLPPICDNKRLLVDGGYLNNVPADVM 773
                                    *********************999999*************987 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.067     4e+02      22      78 ..      94     145 ..      81     150 .. 0.76
   2 !   23.0   0.0     1e-08   6.1e-05       3      82 ..     224     298 ..     222     303 .. 0.80
   3 !   14.7   0.0     4e-06     0.024       3      80 ..     331     398 ..     329     407 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.067
                                    EEEES-EEEEEEETTS.EEEEEEE-TTEEE.SHHHHHHTS--SSEEEESSTEEEEEEE CS
                   cNMP_binding  22 ivlsGevrvyrlsedgkevvlavlgpGdlf.GelalltgeprtatvvAltdsellalp 78 
                                    ++l+G+v+++   +d    ++ +  +G+++ G ++ll+  +   t +A++ +e+l ++
  gene609|gene609|rna608|rna608  94 FILQGSVEIW--YKDR---LVCIKERGSFLnGSMELLG-YRTIGTKRAKGFVEVLLVD 145
                                    899******6..3333...7888899999779999996.5677788888888888765 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1e-08
                                    EE-TT-EEE-TTSB.-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHHH CS
                   cNMP_binding   3 sfkagevifrqGdp.adslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprdd 81 
                                    +f+  + +++ +++ +d++ +v+sGe+ v+  +++ +      +g+G++fG  +l+ ++ ++ t++A++ds +l  + + 
  gene609|gene609|rna608|rna608 224 RFASKDEVLKGNEEsMDYILYVVSGEILVM--AGENAF----SFGSGSIFGYFSLFFDSYSSVTIQAREDSSILICSSSV 297
                                    56666667777755499************5..333333....69************99*************999777666 PP

                                    H CS
                   cNMP_binding  82 f 82 
                                    +
  gene609|gene609|rna608|rna608 298 L 298
                                    5 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4e-06
                                    EE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEEHH CS
                   cNMP_binding   3 sfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalprd 80 
                                    ++++g +++++G + ++++++  G+v+             ++l++G  +G  +++ ge+++ + +A   + ++++p  
  gene609|gene609|rna608|rna608 331 RLSPGGMVVQKGAASKEIFYIAAGRVKSA-----S-----KELSSGTAIGGKECIFGENWPESFIATRITDVVQIPSL 398
                                    789*************************2.....2.....3699999999999999999*******999999999975 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   7.6e-05      0.45      29      61 ..     235     267 ..     225     271 .. 0.89
   2 ?   -1.8   0.0      0.62   3.7e+03      35      46 ..     347     358 ..     330     368 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.6e-05
                                    E--SEEEEEEEEESEEEEEETTEEEEEETT-EE CS
                       CENP-C_C  29 nskkatlvFyViqGrvevtvsktsfvigkgsvF 61 
                                    n +++ ++ yV+ G++ v   ++ f+ g+gs+F
  gene609|gene609|rna608|rna608 235 NEESMDYILYVVSGEILVMAGENAFSFGSGSIF 267
                                    456788999**********************99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.62
                                    EEEEEEESEEEE CS
                       CENP-C_C  35 lvFyViqGrvev 46 
                                     +Fy+ +Grv+ 
  gene609|gene609|rna608|rna608 347 EIFYIAAGRVKS 358
                                    479999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (904 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 5545.88
//
Query:       gene610|gene610|rna609|rna609  [L=641]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4147.21
//
Query:       gene61|gene61|rna61|rna61  [L=348]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.15   11.1   0.0        0.2   10.6   0.0    1.1  1  TED_complement  A-macroglobulin TED domain


Domain annotation for each model (and alignments):
>> TED_complement  A-macroglobulin TED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   1.1e-05       0.2     192     250 ..      25      83 ..      12     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.1e-05
                                HHHS---HHHHHHHHHHHHHTT-THHHHHHHHHHHTTEEEETTEEEE--TTSSSGGGTS CS
             TED_complement 192 qaeelesvyalAilaYalalakseekaeellksLkaeakeegnsvyWeedekskeeekl 250
                                + e+  ++y++ + a ++a a + ++ +e+++ Lka+  e+  ++yW+++   +++ +l
  gene61|gene61|rna61|rna61  25 NCEQELKPYNAVLDAKCMAFALNGSNINEAIRYLKAMNIEKAYVLYWNDHDLRQNPMVL 83 
                                567788999999999999999999999**********************9988887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2191.40
//
Query:       gene611|gene611|rna610|rna610  [L=104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 698.32
//
Query:       gene612|gene612|rna611|rna611  [L=221]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-34  118.0   0.0    3.4e-34  117.8   0.0    1.1  1  Arf          ADP-ribosylation factor family
    2.6e-09   37.3   0.0    6.4e-09   36.1   0.0    1.7  1  Roc          Ras of Complex, Roc, domain of DAPkinase
    3.2e-08   33.3   0.0    5.1e-08   32.7   0.0    1.4  1  Ras          Ras family
    3.9e-08   33.4   0.0      6e-08   32.8   0.0    1.3  1  MMR_HSR1     50S ribosome-binding GTPase
    6.9e-08   32.1   0.0    8.9e-08   31.8   0.0    1.2  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
    2.4e-07   30.4   0.0    3.6e-07   29.8   0.0    1.2  1  SRPRB        Signal recognition particle receptor beta subuni
    2.8e-07   30.0   0.2    0.00085   18.6   0.0    2.6  2  G-alpha      G-protein alpha subunit
    2.5e-05   23.9   0.3     0.0034   17.0   0.0    2.1  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00022   20.8   0.2     0.0012   18.4   0.2    1.9  1  FeoB_N       Ferrous iron transport protein B
     0.0036   17.2   0.1       0.46   10.4   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
     0.0064   16.1   0.0       0.39   10.3   0.0    2.1  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.074   12.8   0.0    1.7  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.12   12.1   0.0          2    8.1   0.0    2.1  2  ATP_bind_1   Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   2.4e-37   3.4e-34       4     134 ..      27     153 ..      22     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 2.4e-37
                                    HHHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTES CS
                            Arf   4 ilaklklkkkelrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektd 83 
                                     +++l++  k   il+lG+DnaGKtT+++klk+++++  +PT ++ +  +ei nlk +v D+GG++ +R  W++Yf + +
  gene612|gene612|rna611|rna611  27 FVKSLFG--KPSSILFLGIDNAGKTTLVNKLKSDSTDVYMPTHHPSTSYIEIGNLKAQVIDLGGHTAARLAWRDYFYDCH 104
                                    4556666..8889******************************************************************* PP

                                    EEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HH CS
                            Arf  84 avifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealsee 134
                                    +++f+vD+ d eR++e +e  +++ + e  k+++++vl NK+Dl++   e+
  gene612|gene612|rna611|rna611 105 GIVFIVDVHDVERFSEVREAYETVKSLE--KKAPVVVLMNKIDLEGHTPET 153
                                    ******************9999875554..689***********9877654 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   4.7e-12   6.4e-09       2     120 .]      38     146 ..      37     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4.7e-12
                                    EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSC CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaa 81 
                                    ++++G  ++GKt+l++++ +d+ +  + +t+  +++  e+             ++k ++ D++G++  r   + y+ + +
  gene612|gene612|rna611|rna611  38 ILFLGIDNAGKTTLVNKLKSDSTD-VYMPTHHPSTSYIEI------------GNLKAQVIDLGGHTAARLAWRDYFYDCH 104
                                    789***************988775.667777666544333............2466899**********98888888888 PP

                                    EEEEEEE...GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                            Roc  82 lailvyd...srssenlkeWlkelkkvagkspvilvgnkiDl 120
                                     +++++d    +++++++e ++ +k+  +k+pv++++nkiDl
  gene612|gene612|rna611|rna611 105 GIVFIVDvhdVERFSEVREAYETVKSLEKKAPVVVLMNKIDL 146
                                    8888877544668899************************95 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   3.7e-11   5.1e-08       2     119 ..      38     167 ..      37     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.7e-11
                                    EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                    ++++G  + GKt+l+++  +d+ ++ y +T     + ++  ++  ++k ++ D  G    +   + y+ d++gi+ + d+
  gene612|gene612|rna611|rna611  38 ILFLGIDNAGKTTLVNKLKSDS-TDVYMPTH----HPSTSYIEIGNLKAQVIDLGGHTAARLAWRDYFYDCHGIVFIVDV 112
                                    678999**********987665.899****9....677777888899********************************* PP

                                    TBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG..................G CS
                            Ras  82 tsresfenvkkwveeikrvaeenvpivLvGnKvDlee..................k 119
                                    ++ e f++v++ +e +k+  + + p+v++ nK+Dle                   +
  gene612|gene612|rna611|rna611 113 HDVERFSEVREAYETVKSLEK-KAPVVVLMNKIDLEGhtpetaeadyqwkswlsqE 167
                                    ****************99999.59***********985666555555555544444 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   4.3e-11     6e-08       2     114 .]      38     143 ..      37     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.3e-11
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHH.HHCTSEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkafla.leeadlil 80 
                                    ++++G  N+GK+tL+n+l    +  +d    T ++ +  +++++ + +++D+ G           + a+++   +++ i+
  gene612|gene612|rna611|rna611  38 ILFLGIDNAGKTTLVNKLK---SDSTDVYMPTHHPSTSYIEIGNLKAQVIDLGG-HT------AARLAWRDyFYDCHGIV 107
                                    7899**************5...5688888999999999999989999*******.33......2333333312369**** PP

                                    EEEETT.....TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  81 lvvdas.....eeklkpldeeleelleeakkplilvlnk 114
                                    ++vd++     + ++++  e++++l   +k p+++++nk
  gene612|gene612|rna611|rna611 108 FIVDVHdverfS-EVREAYETVKSLE--KKAPVVVLMNK 143
                                    ****77743322.2333334444442..67899999998 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   6.5e-11   8.9e-08       2     128 ..      38     151 ..      37     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.5e-11
                      Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvli 81 
                                    +L++G  ++GKt++     +++    t     t + + s +   gnl+ +++D+gG +a           + f ++  ++
  gene612|gene612|rna611|rna611  38 ILFLGIDNAGKTTLV----NKLKSDSTDVYMPTHHPSTSYI-EIGNLKAQVIDLGGHTAARLA-----WRDYFYDCHGIV 107
                                    899*********985....4555555555667788888888.69************9876544.....5788******** PP

                      Gtr1_RagA  82 yVfDvesreleedletlkeilealrqyspeakvfvlihKmDliqede 128
                                    +++Dv+  ++ e +++ +e+ e+++  +++a v vl++K+Dl  +  
  gene612|gene612|rna611|rna611 108 FIVDVH--DV-ERFSEVREAYETVKSLEKKAPVVVLMNKIDLEGHTP 151
                                    ******..54.4577888999999999**************976443 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.6e-10   3.6e-07       5     104 ..      37     130 ..      34     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.6e-10
                                    EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvD 84 
                                    ++l++G+ ++GKT+l ++L +ds+   +   ++s+++   +  + k ++iD+ Gh   r    ++       +g+vf+vD
  gene612|gene612|rna611|rna611  37 SILFLGIDNAGKTTLVNKLKSDSTDVYMPTHHPSTSYI--EIGNLKAQVIDLGGHTAARLAWRDY---FYDCHGIVFIVD 111
                                    79*******************98766555556666553..468999*************999998...55689******* PP

                                    TTS-HHHHHHHHHHHHHHHH CS
                          SRPRB  85 StidpkevkevAEllyeill 104
                                       d  +  ev E + ++ +
  gene612|gene612|rna611|rna611 112 VH-DVERFSEVREAYETVKS 130
                                    64.55556666666555544 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00028      0.39      23      45 ..      35      57 ..      22      74 .. 0.78
   2 !   18.6   0.0   6.1e-07   0.00085     182     280 ..      60     145 ..      56     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00028
                                   EEEEEEEESTTSSHHHHHHHHHH CS
                        G-alpha 23 evkllllGqseSGKsTilkqlkl 45
                                   + ++l+lG +  GK+T++++lk 
  gene612|gene612|rna611|rna611 35 PSSILFLGIDNAGKTTLVNKLKS 57
                                   4589****************993 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 6.1e-07
                                    HCS-----SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT-B-SS-TTSBHHHHHHHHHHCC CS
                        G-alpha 182 lkarlktvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvslsefdqvlyedekvnrleeslklFkei 261
                                      + ++t   s   +e++ +l+ +++d+gG+ + r +W  +f d   i+F+v + +          v r+ e  + ++++
  gene612|gene612|rna611|rna611  60 TDVYMPTHHPSTSYIEIG-NLKAQVIDLGGHTAARLAWRDYFYDCHGIVFIVDVHD----------VERFSEVREAYETV 128
                                    555667777788888888.99******************************98654..........55666666777766 PP

                                    CC-GGGTTSEEEEEEE-HH CS
                        G-alpha 262 cnnkllkntpiiLflnKlD 280
                                     +  l k++p+++++nK+D
  gene612|gene612|rna611|rna611 129 KS--LEKKAPVVVLMNKID 145
                                    55..557777777777777 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0087        12       7      32 ..      39      64 ..      36      75 .. 0.79
   2 !   17.0   0.0   2.5e-06    0.0034      69     176 ..      78     193 ..      66     216 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0087
                                   EEEESTTSSHHHHHHHHHHHTTSSCH CS
                       GTP_EFTU  7 giighvDhGKtTLtdrLlyktgaisk 32
                                    ++g  ++GKtTL+ +L  ++ ++ +
  gene612|gene612|rna611|rna611 39 LFLGIDNAGKTTLVNKLKSDSTDVYM 64
                                   56666689*********998877665 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.5e-06
                                    SEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE..EEEEEESCGSTHHHHHHHHHH CS
                       GTP_EFTU  69 kylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp..iivfiNKmDrlkaelkeivee 145
                                    + + ++iD  GH             ++g v++vd+++    +  +e  + +++++ +  ++v++NK+D  +++ +    +
  gene612|gene612|rna611|rna611  78 NLKAQVIDLGGHTAARLAWRDYFYDCHGIVFIVDVHDVeRFSEVREAYETVKSLEKKapVVVLMNKIDLEGHTPETAEAD 157
                                    6677899999999988888899999*********9965345566777776666555555***********7777666666 PP

                                    HHHHHHHH.HHHHHHHHHTTT........TTEEEEEEBTT CS
                       GTP_EFTU 146 vkqklsrk.eeklekygekge........kevpvvfgSal 176
                                    ++ k   + e+ +e++    e        k++ v  +S+ 
  gene612|gene612|rna611|rna611 158 YQWKSWLSqETGIEDQ----EdpergqvvKIFYVTITSGS 193
                                    5543311112222222....12223435544444444444 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   8.7e-07    0.0012       3     117 ..      38     146 ..      36     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.7e-07
                                    EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEE CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvv 82 
                                    + ++G  n+Gkttl+n+l   +++v      t   ++ ++++ + +++++Dl G       +      rd++++   + +
  gene612|gene612|rna611|rna611  38 ILFLGIDNAGKTTLVNKLKSDSTDVY---MPTHHPSTSYIEIGNLKAQVIDLGGH------TAARLAWRDYFYDC--HGI 106
                                    7889***************9999994...3588889999999999*******995......55667778888854..455 PP

                                    EEEEEGGGHH.....HHHHHHHHHHHTTSSEEEEEETHHH CS
                         FeoB_N  83 vnvvdatnle.....rnLyLtlqllelgvpvvlalnmide 117
                                    v +vd + +e     r+ y t++ le ++pvv+ +n+id 
  gene612|gene612|rna611|rna611 107 VFIVDVHDVErfsevREAYETVKSLEKKAPVVVLMNKIDL 146
                                    55555555551114468999******************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00034      0.46      99     123 ..      34      59 ..       4      95 .. 0.74
   2 ?    5.2   0.0     0.013        18      42      71 ..     130     159 ..     105     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                                    T.SEEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpel 123
                                    + + ++++G   +GK+tL+n+l+++ 
  gene612|gene612|rna611|rna611  34 KpSSILFLGIDNAGKTTLVNKLKSDS 59 
                                    34678899**************9973 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.013
                                    HHHTT-EEEEEEE-GGG--HHHHHHHHHHH CS
                    RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelkee 71 
                                      ek++++v+++nKiDl  ++ e+ e   +
  gene612|gene612|rna611|rna611 130 SLEKKAPVVVLMNKIDLEGHTPETAEADYQ 159
                                    5678999**********8877744444444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.028        38      11      22 ..      46      57 ..      38      64 .. 0.76
   2 !   10.3   0.0   0.00029      0.39     110     160 ..     101     154 ..      73     168 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.028
                                   CCHHHHHHHHHC CS
                           cobW 11 sGKTtLlnhlle 22
                                   +GKTtL+n+l +
  gene612|gene612|rna611|rna611 46 AGKTTLVNKLKS 57
                                   9*******9865 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00029
                                    CCECEEEEEEETTTH...CCHCCHHHHHHHHHHTSS.EEEEE-HHHHCHC...HH CS
                           cobW 110 ltldavvavvDaknl..eaeeekieekaedqlaaad.llvlnKtDlldee.alle 160
                                    +   ++v++vD++ +   +e ++  e++++  ++a  ++++nK+Dl  ++ ++ +
  gene612|gene612|rna611|rna611 101 YDCHGIVFIVDVHDVerFSEVREAYETVKSLEKKAPvVVLMNKIDLEGHTpET-A 154
                                    55678888888877755344455555555555566515678*****9998444.3 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.3e-05     0.074       3      48 ..      37      91 ..      35     170 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                      PduV-EutP  3 killiGkvgsGKttLtqalkg......eelkYkktqaief...sdeviDtPGeyl 48
                                    il++G  ++GKttL ++lk          +  +t +ie+   + +viD  G  +
  gene612|gene612|rna611|rna611 37 SILFLGIDNAGKTTLVNKLKSdstdvyMPTHHPSTSYIEIgnlKAQVIDLGGHTA 91
                                   69*****************995555444456667777765222456777766544 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.12   1.6e+02       2      17 ..      41      56 ..      40      65 .. 0.84
   2 ?    8.1   0.0    0.0015         2     125     173 ..     105     154 ..     102     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.12
                     ATP_bind_1  2 vGpaGsGKttfvgals 17
                                   +G   +GKtt+v++l 
  gene612|gene612|rna611|rna611 41 LGIDNAGKTTLVNKLK 56
                                   577789*******986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0015
                     ATP_bind_1 125 vvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllkek...l 173
                                    ++v++vD++ ++  ++  ++  +     l+ + P vv +nk+Dl  +    +
  gene612|gene612|rna611|rna611 105 GIVFIVDVHDVERFSEVREA--YETVKSLEKKAPVVVLMNKIDLEGHTpetA 154
                                    68999999999998887777..888889999*************65445333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1485.46
//
Query:       gene613|gene613|rna612|rna612  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-66  220.8   0.2    9.4e-66  220.6   0.2    1.0  1  DUF5091   Domain of unknown function (DUF5091)


Domain annotation for each model (and alignments):
>> DUF5091  Domain of unknown function (DUF5091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.6   0.2   5.2e-70   9.4e-66       2     146 ..       5     148 ..       4     149 .. 0.99

  Alignments for each domain:
  == domain 1  score: 220.6 bits;  conditional E-value: 5.2e-70
                        DUF5091   2 lkklnnllkkptleeilkiFeadgyiRlnmvyisPislkhlkaklenlglvsweltenglkFifknfilkFkGsltitvk 81 
                                    ++k+nnllk+p+le+il++Fe+dgyiRln+vyisP+sl++l  +l+ l+lvsw++t++gl F+f+ f+lkF+Gs++i+vk
  gene613|gene613|rna612|rna612   5 IHKINNLLKNPRLEDILSVFEIDGYIRLNRVYISPFSLRQLLIRLAGLDLVSWQMTPSGLFFQFRAFCLKFYGSVNIVVK 84 
                                    79****************************************************************************** PP

                        DUF5091  82 edkifsieidfdpeidsevgieilkeiekylkgcDalfFmtyfvdidkeiLknpLaesveflekr 146
                                    + k+f+ieidfdp+id   g+++l+e+e+ylkgcDalfFmty +didkeiL+npL+es++fl+++
  gene613|gene613|rna612|rna612  85 Q-KVFCIEIDFDPSIDGGAGVPVLRELERYLKGCDALFFMTYYTDIDKEILHNPLSESLDFLYRK 148
                                    *.*************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 886.39
//
Query:       gene614|gene614|rna613|rna613  [L=325]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2295.73
//
Query:       gene615|gene615|rna614|rna614  [L=656]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (656 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 4033.23
//
Query:       gene616|gene616|rna615|rna615  [L=323]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   15.1   1.5      0.036   14.2   0.4    2.0  2  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4     2e-06     0.036      21      84 ..      72     145 ..      60     147 .. 0.70
   2 ?   -1.2   0.0      0.12   2.1e+03      63      75 ..     234     246 ..     168     248 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-06
                                    HHHHHHHCTT---HHHHBSSSS-EEET..TTT........EE--HHHHHHHHS---HHHHHHHHHHHSEEE--H CS
                           SBDS  21 nklleyregkeidLsevlqsekiFtna..skG........etaskselekafgteskdeiikeILkkGeiqvsa 84 
                                    nk+l+  +  + +L +vl  ++i +++  +kG          a  +  + +fg ++++e i++ILkkG+++  +
  gene616|gene616|rna615|rna615  72 NKILKSLKSADNNLIRVLCCNEILEKEaeEKGngereahvRNAIIEARNLMFGVSNSKETIEKILKKGNEKSGE 145
                                    566666667777788888888888766557774444433333333334456699***************98766 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.12
                                    S---HHHHHHHHH CS
                           SBDS  63 gteskdeiikeIL 75 
                                    ++e + ++i++IL
  gene616|gene616|rna615|rna615 234 NKEISMSVIEHIL 246
                                    2223557888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1155  (0.0644208); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2168.19
//
Query:       gene617|gene617|rna616|rna616  [L=244]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1512.96
//
Query:       gene618|gene618|rna617|rna617  [L=408]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-28   98.0  42.4    6.5e-28   97.6  42.4    1.2  1  Aa_trans  Transmembrane amino acid transporter protein
  ------ inclusion threshold ------
        6.2    6.7   6.3        1.1    9.1   0.6    2.4  2  DUF412    Protein of unknown function, DUF412


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6  42.4   7.3e-32   6.5e-28       6     398 ..       8     394 ..       3     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 7.3e-32
                       Aa_trans   6 lsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrllGpkgkli 85 
                                     sa++++i++++Ga + + P+Af+  G+i G i++++vall++++l+ ++  +  +   +   +Y+ l   +++pk+k +
  gene618|gene618|rna617|rna617   8 YSATVTMITSMMGASIYFTPVAFRFVGYIYGWIIIFIVALLTSFSLYCISYSAMNM---PVGPTYSSL-GACISPKLKNV 83 
                                    589**************************************************976...5999*****.89********* PP

                       Aa_trans  86 idlailvqlfGvgvsyliligdllpaifesffdt...lllsnvyfilisaliiipLslipnlskLsylSllalvsslyyi 162
                                     d+  +v+ + + +      ++l++a f+ ++     +++ +  ++++  + +++Ls+ +nls+L+y+Sl  +vs++y+ 
  gene618|gene618|rna617|rna617  84 LDAFVIVNSLTANICLYRYLSELIVAAFPVLLLVfpsYETARKGVVVVLLIPLLTLSFHKNLSSLRYVSLAMVVSIVYF- 162
                                    *****************************9876677899**************************************95. PP

                       Aa_trans 163 vilvlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkkmtkvlllsiilatvly 242
                                     il l+++ l+++ +++  e t  ++ +  g+f +++i++ A +++ +++++ +e+ + s   k+++v+++s +   ++y
  gene618|gene618|rna617|rna617 163 -ILLLISYNLLFYPGRSNYETT--PFGN--GFFFSVPIFITAMACQSNMVKVLDEMASYSV-RKVKFVSIWSGVGGGLIY 236
                                    .888888888888888777776..5888..****************************999.77**************** PP

                       Aa_trans 243 ilvGlvGYltFGnevkgnillnlpkss...............ilivivnlllvlhlilsfplqlhplrqvvenllikkea 307
                                     ++G +GY  FGn   g +l  +  ++               ++  i+    +l  i+sfp+ql pl+  + n++ ++  
  gene618|gene618|rna617|rna617 237 GSIGHLGYSLFGNGLDGDLLGIFADKNsvinaqlagtidrylVSSKIAVYGSMLIFIGSFPMQLNPLITTLFNIFPER-- 314
                                    ********************9998777799999*******99999999999************************554.. PP

                       Aa_trans 308 vagasekeapkskllrlvirlllvvityliAlsvp.slakvlslvGatsstplsfilPalfhlkliktekksleklvkkk 386
                                             + +   rl++ ++l+++   +Al+   s + v+s+ Gat + ++sf +P +f + ++k+ ++s+     + 
  gene618|gene618|rna617|rna617 315 ---------RRTENIRLILMVFLMILCFSLALIRDlSAGLVISIAGATVTNFISFLFPFVFFISAKKKFSTSTFLALVS- 384
                                    .........5555569999999999999999665437899*********************999988776554333322. PP

                       Aa_trans 387 ildlicivlgll 398
                                      +++ci  ++ 
  gene618|gene618|rna617|rna617 385 --MVACISSSIY 394
                                    ..3444444443 PP

>> DUF412  Protein of unknown function, DUF412
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.7      0.09   8.1e+02      24      87 ..     117     179 ..     100     210 .. 0.68
   2 ?    9.1   0.6   0.00013       1.1      12      57 ..     298     343 ..     289     391 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.09
                         DUF412  24 lfpenrvikatrfaikvmpalavltlvlqlylagsealpqailtalfllsLPlQGlywlGkrak 87 
                                    +fp +   +   +++  + +l +l++  +l    + +l+  + ++ f+l L    l++   r++
  gene618|gene618|rna617|rna617 117 VFPSYETARKGVVVVL-LIPLLTLSFHKNLSSLRYVSLAMVVSIVYFILLLISYNLLFYPGRSN 179
                                    5555555444433333.33445566666666666668888888888888776666666666655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00013
                         DUF412  12 lktwPlekeLaalfpenrvikatrfaikvmpalavltlvlqlylag 57 
                                    +++ Pl   L ++fpe r ++ +r+   v+ ++ +++l+l   l +
  gene618|gene618|rna617|rna617 298 MQLNPLITTLFNIFPERRRTENIRLILMVFLMILCFSLALIRDLSA 343
                                    8889999*****************************9987655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 2343.37
//
Query:       gene619|gene619|rna618|rna618  [L=490]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-05   24.0   0.5    5.8e-05   22.7   0.5    1.7  1  SWIM         SWIM zinc finger
    0.00084   19.3   0.0     0.0031   17.5   0.0    2.0  2  DBD_Tnp_Mut  MuDR family transposase


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.5   6.5e-09   5.8e-05      10      32 ..     401     423 ..     386     425 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6.5e-09
                           SWIM  10 vrlnkatCsCpefqkngipCkHa 32 
                                    v+l+  tC+C++fq + ipC Ha
  gene619|gene619|rna618|rna618 401 VDLENLTCTCGRFQEFLIPCSHA 423
                                    7788******************9 PP

>> DBD_Tnp_Mut  MuDR family transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.5e-07    0.0031       5      66 ..       5      68 ..       2      69 .. 0.90
   2 ?   -3.1   0.0      0.88   7.9e+03      23      30 ..     172     179 ..     169     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.5e-07
                    DBD_Tnp_Mut  5 rvGleFksleelrkalkkyaIahhrefrvvksdksrytvrCe...kegCpWrvhaskrsekklfe 66
                                    vG +F+  ee  k l  +a++   ++ ++++ ks + v C+   + gC  r+ a +r++++ f 
  gene619|gene619|rna618|rna618  5 SVGDVFPTKEEAEKVLISHAVQSNLNYDLEETPKS-VAVLCKgrkEFGCEARIVAQVRKKDGVFV 68
                                   699****************************9987.689999765569************99986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.88
                    DBD_Tnp_Mut  23 yaIahhre 30 
                                     aIahhre
  gene619|gene619|rna618|rna618 172 SAIAHHRE 179
                                    69****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 2719.05
//
Query:       gene620|gene620|rna619|rna619  [L=727]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-13   50.5   8.6     0.0097   16.7   0.2    6.5  6  WD40         WD domain, G-beta repeat
    9.9e-12   44.8  11.4      2e-07   30.6   0.3    4.7  4  WD40_like    WD40-like domain
    6.5e-10   39.2   0.3     0.0053   17.0   0.0    6.3  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    0.00031   21.0   0.0    0.00055   20.2   0.0    1.4  1  Utp12        Dip2/Utp12 Family
    0.00036   19.3   5.9      0.036   12.7   0.0    4.0  5  Nup160       Nucleoporin Nup120/160
     0.0011   18.6   0.5       0.04   13.5   0.0    2.9  3  CNH          CNH domain
     0.0063   16.3   0.0        4.6    6.9   0.0    2.5  2  Hira         TUP1-like enhancer of split
  ------ inclusion threshold ------
      0.028   14.7   0.3        4.6    7.6   0.0    3.6  4  PH_8         Pleckstrin homology domain
      0.065   13.1   0.0       0.11   12.3   0.0    1.4  1  Maf          Maf-like protein
       0.12   11.3   0.0       0.19   10.6   0.0    1.3  1  Spc7         Spc7 kinetochore protein


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.6   2.9e+03      18      37 ..      87     105 ..      79     106 .. 0.84
   2 !   16.7   0.2   5.4e-06    0.0097       7      38 .]     123     153 ..     117     153 .. 0.82
   3 ?    5.6   0.0     0.018        33      23      38 .]     298     313 ..     266     313 .. 0.85
   4 ?    5.5   0.4     0.019        35       2      38 .]     316     353 ..     315     353 .. 0.70
   5 !   12.7   0.1    0.0001      0.18       2      38 .]     400     435 ..     399     435 .. 0.87
   6 !    8.7   0.0    0.0019       3.3      11      36 ..     498     523 ..     490     525 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.6
                                    EETTSSEEEEEETTSEEEEE CS
                           WD40  18 fspdgawlasGsdDgtvriW 37 
                                     s +++++a G   + + iW
  gene620|gene620|rna619|rna619  87 ISVNKDLIAVGF-SNVLEIW 105
                                    3779999*9999.9999999 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.4e-06
                                    EESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   7 ltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    l GH  ++ts++f +d++ +++ s+D+tvr++d
  gene620|gene620|rna619|rna619 123 L-GHfLDITSVRFMDDNTVVTT-SRDCTVRLFD 153
                                    4.99767************865.66******98 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.018
                                    SEEEEEETTSEEEEEE CS
                           WD40  23 awlasGsdDgtvriWd 38 
                                     ++a G+ D++vri+d
  gene620|gene620|rna619|rna619 298 EMIAVGCADKKVRIYD 313
                                    56899999*******8 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.019
                                    EEEEEEE....SSSSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtlt....GHssvtslafspdgawlasGsdDgtvriWd 38 
                                    +c++t++    +H  +  +   +++ + + +  Dg v iWd
  gene620|gene620|rna619|rna619 316 RCIHTFSdpniAH-AIFNVHLLQNSVLCL-CL-DGRVSIWD 353
                                    7999998777788.566664455555555.67.*******9 PP

  == domain 5  score: 12.7 bits;  conditional E-value: 0.0001
                                    EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    + + tl+GH ++v  ++++ d+ + + +  D+t+r W+
  gene620|gene620|rna619|rna619 400 KEIDTLKGHdGPVFKMKWDADSLYTL-SY-DNTIRRWN 435
                                    67889****888************55.57.*****998 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.0019
                                    SSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40  11 ssvtslafspdgawlasGsdDgtvri 36 
                                    ++v sl+f  d+++++sG++ +t+++
  gene620|gene620|rna619|rna619 498 KPVESLDFTFDNRFIVSGGEANTIKV 523
                                    5799***************9999997 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.016        28     115     181 ..      35     102 ..      18     118 .. 0.64
   2 !    6.1   0.2    0.0034       6.1      11      77 ..     136     202 ..     127     217 .. 0.71
   3 !   30.6   0.3   1.1e-10     2e-07       4     184 ..     291     471 ..     289     480 .. 0.79
   4 !    8.4   0.0   0.00068       1.2       2      37 ..     499     534 ..     498     540 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.016
                      WD40_like 115 evllgqsseIkeikiennki..ysLsesafivfdlfsq.nieykisvkdiktfeii.enkdilligtegei 181
                                    +   g++++I ++    ++i  +s se+ fiv ++    n e k+     + f++i  nkd++++g+++ +
  gene620|gene620|rna619|rna619  35 KASKGKYTKICDVG---GTImdFSVSEKLFIVTEERMYmNNESKMLGSLKRRFSCIsVNKDLIAVGFSNVL 102
                                    44445555555554...333339999999999987654133344433445678888679999999998765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0034
                      WD40_like  11 kgslilyGgkddkctvlkleslesvsivesfedSvifvkllddd..lilvvtlDGtillslleneeeve 77 
                                    + + ++  ++d ++++++++ + s+ i   ++  +  + ++d++  +++vv  DG++l  ++e e+ ++
  gene620|gene620|rna619|rna619 136 DDNTVVTTSRDCTVRLFDIQAHRSIRICSTMSVPIA-AYFIDEEkkKLVVVCEDGALLYFTIEGEN-IS 202
                                    444566677888888888888888888888866654.66888776678888889998776666665.44 PP

  == domain 3  score: 30.6 bits;  conditional E-value: 1.1e-10
                      WD40_like   4 YsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslleneeevenekiee 83 
                                     s+d+  k ++i++G  d+k+++++ +  +   +  ++   +  v ll++  +l+  lDG ++  +++n+   ++ +i  
  gene620|gene620|rna619|rna619 291 ISMDV--KKEMIAVGCADKKVRIYDGRRCIHTFSDPNIAHAIFNVHLLQN-SVLCLCLDGRVSIWDIKNGVCYRSFQIAV 367
                                    45666..7789*****************9999999999999988888876.579999*********************** PP

                      WD40_like  84 distvkviddklliGtnkGsiyv.fskdlq..le.evllgqsseIkeikiennkiysLsesafiv.fdlfsqnieykisv 158
                                     +s  +v dd+ll+     s y     dlq   e  +l g+  ++ ++k + + +y+Ls ++ i  ++++s ++  ++++
  gene620|gene620|rna619|rna619 368 RMSASEVSDDNLLLFIADFSNYSiRVVDLQrgKEiDTLKGHDGPVFKMKWDADSLYTLSYDNTIRrWNVYS-QTVEELQI 446
                                    **********98876554444431233444113315788********************999985389999.56667778 PP

                      WD40_like 159 kdiktfeiienkdilligtegeilil 184
                                    k++ t  ++ n+  l+++t +e+ i+
  gene620|gene620|rna619|rna619 447 KKMATGFSVRNRK-LCVSTVNELTIY 471
                                    7777655564544.678887777776 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.00068
                      WD40_like   2 eiYsidiskkgslilyGgkddkctvlkleslesvsi 37 
                                    ++ s+d+ +++ +i+ Gg+ ++++v++++++++v+ 
  gene620|gene620|rna619|rna619 499 PVESLDFTFDNRFIVSGGEANTIKVISVDTGDVVQT 534
                                    5779***************************99975 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.49   8.8e+02      39      77 ..     127     164 ..      87     174 .. 0.70
   2 ?   -0.3   0.0      0.76   1.4e+03      50      79 ..     179     208 ..     172     220 .. 0.76
   3 ?    5.1   0.0     0.016        28      49      67 ..     296     314 ..     289     330 .. 0.83
   4 ?    5.2   0.0     0.014        25      52      90 ..     380     418 ..     333     420 .. 0.80
   5 !   17.0   0.0   2.9e-06    0.0053      38      82 ..     497     541 ..     482     568 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.49
                    ANAPC4_WD40  39 sevrsLaWkpdgklLavaysdgevrlldaesgkvvhsls 77 
                                      ++s+++  d +  +    d +vrl+d++  + ++ +s
  gene620|gene620|rna619|rna619 127 LDITSVRFMDD-NTVVTTSRDCTVRLFDIQAHRSIRICS 164
                                    56777777554.555667789999999998877776555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.76
                    ANAPC4_WD40  50 gklLavaysdgevrlldaesgkvvhslsvk 79 
                                     k L+v+++dg++  + +e +++ ++  ++
  gene620|gene620|rna619|rna619 179 KKKLVVVCEDGALLYFTIEGENISSKGIIH 208
                                    57799******9999988887776665555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.016
                    ANAPC4_WD40  49 dgklLavaysdgevrllda 67 
                                    + +++av+++d +vr++d 
  gene620|gene620|rna619|rna619 296 KKEMIAVGCADKKVRIYDG 314
                                    5689************995 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.014
                    ANAPC4_WD40  52 lLava.ysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                    lL +a +s+ ++r++d + gk + +l+ ++   v +++W 
  gene620|gene620|rna619|rna619 380 LLFIAdFSNYSIRVVDLQRGKEIDTLKGHDGP-VFKMKWD 418
                                    34444156668999999999999999999884.9999996 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 2.9e-06
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksek 82 
                                    ++ v+sL +  d+++++ + + ++++++++ +g+vv++l+v+++k
  gene620|gene620|rna619|rna619 497 EKPVESLDFTFDNRFIVSGGEANTIKVISVDTGDVVQTLRVSDNK 541
                                    678************************************998875 PP

>> Utp12  Dip2/Utp12 Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.1e-07   0.00055       1      59 [.     630     687 ..     630     721 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.1e-07
                                    HHHHHHH.HHHSS-TTTHHHHHHCS-CTCHHHHHHHHHHHH.HTTTTHHHHHHHHHHHH CS
                          Utp12   1 ndeelleevlekippsdirltvlrLpssyvlkLLeflaerlaeksphlelllrwlkall 59 
                                    n++e+++ev+ ++p++ i+ +v+ L+ ++v+ L   ++++l ++s+     +rwlk+++
  gene620|gene620|rna619|rna619 630 NEYEIVKEVVVSCPTEKIEGVVKHLDMELVVGLRSMISRML-DNSMYHLVAIRWLKFIV 687
                                    899************************************88.6666556899*****98 PP

>> Nup160  Nucleoporin Nup120/160
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.019        33     229     259 ..     136     166 ..     114     229 .. 0.61
   2 ?   -2.5   0.0      0.84   1.5e+03     226     246 ..     291     313 ..     287     328 .. 0.78
   3 !   12.7   0.0     2e-05     0.036     229     265 ..     336     371 ..     319     402 .. 0.73
   4 !    3.9   0.1    0.0097        17     229     251 ..     418     440 ..     411     470 .. 0.84
   5 ?   -4.0   0.0       2.4   4.3e+03      99     119 ..     519     540 ..     502     576 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.019
                                    TTTEEEEEETT-EEEEEETTTTEEEEEEE-- CS
                         Nup160 229 gqtylfalsrdgkLrvWnlltgkclatidll 259
                                    +++++++ srd ++r+ +++  + ++ +++ 
  gene620|gene620|rna619|rna619 136 DDNTVVTTSRDCTVRLFDIQAHRSIRICSTM 166
                                    6666667777777776666665555553332 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.84
                                    .....TTTEEEEEETT-EEEEEE CS
                         Nup160 226 vei..gqtylfalsrdgkLrvWn 246
                                    +++  ++ ++++ + d+k+r+ +
  gene620|gene620|rna619|rna619 291 ISMdvKKEMIAVGCADKKVRIYD 313
                                    55556899*************95 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 2e-05
                                    TTTEEEEEETT-EEEEEETTTTEEEEEEE--..-SSST CS
                         Nup160 229 gqtylfalsrdgkLrvWnlltgkclatidll.rdeeaq 265
                                     q+ ++ l++dg++ +W++++g c +++++  r  +++
  gene620|gene620|rna619|rna619 336 LQNSVLCLCLDGRVSIWDIKNGVCYRSFQIAvR--MSA 371
                                    68999**********************999952..222 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.0097
                                    TTTEEEEEETT-EEEEEETTTTE CS
                         Nup160 229 gqtylfalsrdgkLrvWnlltgk 251
                                    + + l++ls d+++r Wn+ +++
  gene620|gene620|rna619|rna619 418 DADSLYTLSYDNTIRRWNVYSQT 440
                                    67889*************98765 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 2.4
                                    SEEEEEEEESSS-EEEEEEE.H CS
                         Nup160  99 dvlivivtttsvhlyvlrls.s 119
                                    +++ vi+++t  ++ +lr+s  
  gene620|gene620|rna619|rna619 519 NTIKVISVDTGDVVQTLRVSdN 540
                                    3455555555555555555531 PP

>> CNH  CNH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.35   6.2e+02     183     241 ..     161     223 ..     131     260 .. 0.60
   2 ?    0.9   0.0      0.16   2.9e+02     139     165 ..     288     315 ..     228     409 .. 0.62
   3 !   13.5   0.0   2.2e-05      0.04      83     191 ..     437     557 ..     373     565 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                            CNH 183 aarkenlkplaviqised...efLlcydefavyvdlqGr.rsrdseleWegkPesvaclepyl 241
                                    +    +  p+a++ i+e+    + +c d    y + +G+  s++ +++ ++k+ +  +  +++
  gene620|gene620|rna619|rna619 161 RICSTMSVPIAAYFIDEEkkkLVVVCEDGALLYFTIEGEnISSKGIIHLDSKVLATSYHLGFV 223
                                    444445556666666654444555566666666666666444466666555555555544443 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                            CNH 139 aevfsisvlkpklcvgv.akgFelvnld 165
                                    + ++s+ v k++++vg+  k+  +++ +
  gene620|gene620|rna619|rna619 288 PRIISMDVKKEMIAVGCaDKKVRIYDGR 315
                                    6678888889999999954555555555 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 2.2e-05
                            CNH  83 ltqklpetkgchffairngyskekfLvvavkskivllewneplkkfk......kklrefqvp.aevfsisvl.kpklcvg 154
                                    ++q ++e+ ++ ++a    + +++ L+v++ + + ++ ++ + +++       +k +e+ ++  +v s+ ++ +++++v+
  gene620|gene620|rna619|rna619 437 YSQTVEEL-QIKKMA-TGFSVRNRKLCVSTVNELTIYDPDFNYEREIkvslkaRKRNEIFISeKPVESLDFTfDNRFIVS 514
                                    44455554.333334.45566899*****************9988889*****9****9998688889999999999998 PP

                            CNH 155 v..akgFelvnldegaaeslldpedns....ldfaarkenlkp 191
                                       a++++++++d+g++ + l ++dn+     + +  ke++kp
  gene620|gene620|rna619|rna619 515 GgeANTIKVISVDTGDVVQTLRVSDNKewenYKEVLGKESFKP 557
                                    888**************99999*99997766444566666666 PP

>> Hira  TUP1-like enhancer of split
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0027       4.9       3      43 ..     161     201 ..     160     217 .. 0.92
   2 !    6.9   0.0    0.0026       4.6      21      57 ..     337     372 ..     326     444 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0027
                           Hira   3 rllPplvlespasfLessgsyLlavtsvgllyvWnvkkkkv 43 
                                    r+++++ ++ +a f++ ++++L++v ++g l  + ++ +++
  gene620|gene620|rna619|rna619 161 RICSTMSVPIAAYFIDEEKKKLVVVCEDGALLYFTIEGENI 201
                                    89********************************9987665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                           Hira  21 gsyLlavtsvgllyvWnvkkkkvllppvslapllsss 57 
                                    ++ +l++  +g++++W++k+  +   + ++a  +s+s
  gene620|gene620|rna619|rna619 337 QNSVLCLCLDGRVSIWDIKNGVCYR-SFQIAVRMSAS 372
                                    5789**************9988876.66666666554 PP

>> PH_8  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.089   1.6e+02      31      70 ..      69     107 ..      59     113 .. 0.85
   2 ?   -3.3   0.0       6.5   1.2e+04      43      61 ..     166     184 ..     147     204 .. 0.63
   3 ?   -2.2   0.0       2.9   5.3e+03      36      69 ..     211     245 ..     179     252 .. 0.69
   4 ?    7.6   0.0    0.0026       4.6      57      87 ..     522     552 ..     509     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.089
                           PH_8  31 yrddnssalrgkiplslaiisaneekreiiidsGaevWeL 70 
                                    y  +n+s++ g++  + + is+n++   +      e+W++
  gene620|gene620|rna619|rna619  69 YM-NNESKMLGSLKRRFSCISVNKDLIAVGFSNVLEIWHI 107
                                    55.4667888******************999999****97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.5
                           PH_8  43 iplslaiisaneekreiii 61 
                                    +++ +a+  ++eek+++++
  gene620|gene620|rna619|rna619 166 MSVPIAAYFIDEEKKKLVV 184
                                    4444444445555555444 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.9
                           PH_8  36 ssalrgkiplslaiisaneek.reiiidsGaevWe 69 
                                    s++l  +  l   +is ++e+  ++ i  G e+ +
  gene620|gene620|rna619|rna619 211 SKVLATSYHLGFVAISLDKESgENMLIYNGQEIVH 245
                                    45566666667777777766514577788887765 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0026
                           PH_8  57 reiiidsGaevWeLkasnekdfqeWvealek 87 
                                    + i++d+G  v +L+ s++k++++++e+l k
  gene620|gene620|rna619|rna619 522 KVISVDTGDVVQTLRVSDNKEWENYKEVLGK 552
                                    6799**********************99865 PP

>> Maf  Maf-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.3e-05      0.11      20     142 ..     468     636 ..     446     651 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-05
                                    EEEE------HHHHHHHHHHHHHHHHH...........................TCEEEEEE.....EEEE........C CS
                            Maf  20 fevvpsdvdeaeelvlrlAeaKaeava...........................alvigaDt.....vvvl........i 59 
                                    +++  +d++ ++e+ + l  +K ++++                           + vi+ Dt     +  l        +
  gene620|gene620|rna619|rna619 468 LTIYDPDFNYEREIKVSLKARKRNEIFisekpvesldftfdnrfivsggeantiK-VISVDTgdvvqT--LrvsdnkewE 544
                                    4444444444555566666666666666777777777777776666666666533.888888553330..1333333320 PP

                                    .........E---SSHHHHHHHHHHH...TTSEEEEEE..EEEEEEEEE..EEEEEEEEEE-.---HHHHHHHHHCTSGC CS
                            Maf  60 .........lgKPkdeeealemLkkl...sgrthevvT..gvavlkekevksfvettevtfk.elsdeeieaYvatgepl 124
                                               KP d+ + +e+Lk +   s+r+  v+T  gv++++     sf++   ++++ +l+ e i++Y++tge+l
  gene620|gene620|rna619|rna619 545 nykevlgkeSFKPFDKTKIIEVLKIVhssSQREFYVLTreGVSIYEP----SFIKFMPLHLDvSLTPESIRRYLDTGEYL 620
                                    33334334477999999999999877433566668888334666553....45666666774489*************99 PP

                                    CST.TS--TTCGGGGGCEE CS
                            Maf 125 dkA.Gaygiqgllglalve 142
                                    ++A G+++i++     +v+
  gene620|gene620|rna619|rna619 621 KAAiGSLKINEY---EIVK 636
                                    977699999997...2344 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.19       7      32 ..     122     150 ..     117     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                           Spc7   7 sLqdFLnmtgIrFmdl...tttkrrstia 32 
                                    +L  FL+ t++rFmd+   +tt+r  t+ 
  gene620|gene620|rna619|rna619 122 NLGHFLDITSVRFMDDntvVTTSRDCTVR 150
                                    6889***********98988888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (727 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.78u 0.32s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 4057.16
//
Query:       gene62|gene62|rna62|rna62  [L=346]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-17   62.3  19.6    3.1e-09   36.5   4.4    3.3  3  zf-CCCH    Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    2.5e-08   33.7  17.4    6.5e-06   26.0   4.5    3.1  3  zf_CCCH_4  Zinc finger domain
    1.1e-05   25.0  16.8     0.0019   18.0   1.8    3.1  3  zf-CCCH_4  CCCH-type zinc finger
  ------ inclusion threshold ------
      0.087   13.5  13.4       0.82   10.4   2.2    2.4  2  Torus      Torus domain
       0.09   12.9   0.0       0.19   11.9   0.0    1.5  1  DUF3378    Domain of unknown function (DUF3378)
       0.61   10.7  14.0       0.48   11.0   2.1    3.0  2  zf-CCCH_2  RNA-binding, Nab2-type zinc finger


Domain annotation for each model (and alignments):
>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   4.4   1.1e-12   3.1e-09       1      27 []     113     139 ..     113     139 .. 0.97
   2 !   32.2   4.6   2.3e-11   6.8e-08       1      26 [.     151     176 ..     151     177 .. 0.96
   3 ?   -0.4   0.0       0.4   1.2e+03       5      13 ..     312     320 ..     308     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.1e-12
                                -HCHCBCHHHHHS--TTGGG-SSBSCS CS
                    zf-CCCH   1 yktelCrffmrtGyCkyGdrCkFaHgq 27 
                                ykte Cr + + GyCkyGd+C+FaH++
  gene62|gene62|rna62|rna62 113 YKTEMCRSHTEIGYCKYGDKCQFAHSK 139
                                8************************96 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 2.3e-11
                                -HCHCBCHHHHHS--TTGGG-SSBSC CS
                    zf-CCCH   1 yktelCrffmrtGyCkyGdrCkFaHg 26 
                                ykte C++f + G+C+yG rC+F+H 
  gene62|gene62|rna62|rna62 151 YKTETCKTFWEEGSCPYGKRCCFIHI 176
                                9************************5 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.4
                                CBCHHHHHS CS
                    zf-CCCH   5 lCrffmrtG 13 
                                +Cr ++r+G
  gene62|gene62|rna62|rna62 312 PCRKQSRGG 320
                                799999988 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   4.5   2.2e-09   6.5e-06       1      19 []     118     137 ..     118     137 .. 0.98
   2 !   14.9   2.2   6.7e-06      0.02       3      19 .]     159     175 ..     158     175 .. 0.94
   3 ?   -2.2   0.0       1.7   5.1e+03       3      11 ..     307     315 ..     307     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.2e-09
                  zf_CCCH_4   1 Ckfflq.GtCkkGdkCrFaH 19 
                                C+   + G+Ck+GdkC+FaH
  gene62|gene62|rna62|rna62 118 CRSHTEiGYCKYGDKCQFAH 137
                                9999**************** PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.7e-06
                  zf_CCCH_4   3 fflqGtCkkGdkCrFaH 19 
                                f+ +G+C++G +C F+H
  gene62|gene62|rna62|rna62 159 FWEEGSCPYGKRCCFIH 175
                                9************9988 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.7
                  zf_CCCH_4   3 fflqGtCkk 11 
                                f+l+G C+k
  gene62|gene62|rna62|rna62 307 FYLEGPCRK 315
                                899998987 PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.8   6.4e-07    0.0019       3      21 ..     118     137 ..     116     138 .. 0.82
   2 !   14.3   4.5   9.1e-06     0.027       2      21 ..     155     175 ..     154     175 .. 0.89
   3 ?   -3.2   0.0       2.7   8.2e+03       5      12 ..     307     314 ..     307     314 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.4e-07
                  zf-CCCH_4   3 Cpyfa.kGsCrfGdnCrFsH 21 
                                C++ +  G C++Gd+C F+H
  gene62|gene62|rna62|rna62 118 CRSHTeIGYCKYGDKCQFAH 137
                                666665588*********** PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.1e-06
                  zf-CCCH_4   2 lCpyfa.kGsCrfGdnCrFsH 21 
                                +C+ f  +GsC +G +C F H
  gene62|gene62|rna62|rna62 155 TCKTFWeEGSCPYGKRCCFIH 175
                                698888688**********99 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.7
                  zf-CCCH_4   5 yfakGsCr 12 
                                ++++G Cr
  gene62|gene62|rna62|rna62 307 FYLEGPCR 314
                                57788887 PP

>> Torus  Torus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.7    0.0013       3.7      51      92 ..      94     138 ..      65     147 .. 0.68
   2 ?   10.4   2.2   0.00027      0.82      66      95 ..     150     178 ..     138     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                                ----HHHH----HHH..HSTT--B-HHHHH.T--SSGGG-SSB-S CS
                      Torus  51 trcnikkdsGytkad..kekesyfClfFar.GlCakGkkCeylHr 92 
                                 + + +   G ++++  +  ++ +C  ++  G+C++G kC++ H+
  gene62|gene62|rna62|rna62  94 IQTHFSSARGSHTNKkyQLYKTEMCRSHTEiGYCKYGDKCQFAHS 138
                                3444444444444431266677888777654*************6 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00027
                                HSTT--B-HHHHHT--SSGGG-SSB-S--- CS
                      Torus  66 kekesyfClfFarGlCakGkkCeylHrlPt 95 
                                k k++++  f+  G C++Gk+C ++H +P+
  gene62|gene62|rna62|rna62 150 KYKTETCKTFWEEGSCPYGKRCCFIH-IPN 178
                                455556667899*************9.665 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.3e-05      0.19      34      55 ..      41      62 ..      37      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                    DUF3378 34 akkndttItaYtSgKVlFQGkn 55
                               a k+ +++t ++S+K lFQG+ 
  gene62|gene62|rna62|rna62 41 ASKPRNVCTCFKSNKKLFQGNV 62
                               78999***************85 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.1   0.00016      0.48       7      17 ..     126     137 ..     118     137 .. 0.84
   2 ?    4.0   4.4     0.025        75       7      17 ..     162     175 ..     156     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                  zf-CCCH_2   7 nC.tnpkCpFaH 17 
                                +C +++kC FaH
  gene62|gene62|rna62|rna62 126 YCkYGDKCQFAH 137
                                4*********** PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.025
                  zf-CCCH_2   7 n..C.tnpkCpFaH 17 
                                   C ++++C F+H
  gene62|gene62|rna62|rna62 162 EgsCpYGKRCCFIH 175
                                355*********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2175.98
//
Query:       gene621|gene621|rna620|rna620  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-13   50.6  13.5    4.9e-13   49.6  13.5    1.5  1  zinc_ribbon_15  zinc-ribbon family
     0.0032   17.5   6.3     0.0032   17.5   6.3    2.7  2  DZR             Double zinc ribbon
     0.0034   18.0   0.7     0.0034   18.0   0.7    2.5  3  zinc-ribbon_6   zinc-ribbon domain
  ------ inclusion threshold ------
      0.025   14.7   3.8      0.025   14.7   3.8    3.3  3  Zn-ribbon_8     Zinc ribbon domain
      0.034   13.6  21.8      0.064   12.7   5.0    3.9  4  zf-ribbon_3     zinc-ribbon domain
       0.16   12.6   6.2       0.22   12.1   3.1    2.2  2  Cript           Microtubule-associated protein CRIPT
       0.21   11.7  12.7        4.4    7.5   0.3    3.2  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.29   11.1  19.7        7.7    6.6   7.0    3.6  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.95   10.2  13.6        4.1    8.1   0.4    4.0  4  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        1.3    6.8   3.1        1.4    6.7   3.1    1.1  1  PolC_DP2        DNA polymerase II large subunit DP2
        1.6    8.9   5.3        1.4    9.1   0.8    2.5  3  Acetone_carb_G  Acetone carboxylase gamma subunit
        1.9    8.5  14.3        8.3    6.5   8.0    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
        2.1    7.0   5.7       0.28    9.9   1.8    1.5  2  NRDD            Anaerobic ribonucleoside-triphosphate reducta
        3.1    7.4  17.1        4.4    6.9   0.1    3.7  4  TF_Zn_Ribbon    TFIIB zinc-binding
        4.1    7.2  26.5        1.1    9.1   0.7    4.6  5  zinc_ribbon_2   zinc-ribbon domain
        9.6    6.2  17.3        2.9    7.9   0.8    3.2  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6  13.5   4.4e-16   4.9e-13       2      86 .]      34     105 ..      33     105 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 4.4e-16
                 zinc_ribbon_15   2 lCpkCgklskaelvkkkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeveeefky 81 
                                    lCp+Cg l+++e++++k+ + ++fip+++w+++ pyl cs+Ck +l++                ++C++Cg +++ e++ 
  gene621|gene621|rna620|rna620  34 LCPYCGYLTDSEYRHDKYSFCICFIPCIPWGNSYPYLSCSHCKRNLGSIG-------------DYRCQKCGVATTFESSN 100
                                    7************************************************9.............9**************** PP

                 zinc_ribbon_15  82 CpkCg 86 
                                    Cp+Cg
  gene621|gene621|rna620|rna620 101 CPNCG 105
                                    ****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.9     0.037        42      27      41 ..      25      45 ..       2      56 .. 0.64
   2 !   17.5   6.3   2.8e-06    0.0032      14      49 .]      71     105 ..      65     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.037
                            DZR 27 a......edrCpsCgekvdpe 41
                                          +  Cp Cg+ +d+e
  gene621|gene621|rna620|rna620 25 GypeppkKFLCPYCGYLTDSE 45
                                   155555566788888777765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.8e-06
                            DZR  14 fCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                     Cs+C+ +l      +rC +Cg +++ e++ Cp+CG
  gene621|gene621|rna620|rna620  71 SCSHCKRNLG-SIGDYRCQKCGVATTFESSNCPNCG 105
                                    5*******96.5559********************9 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       8.3   9.3e+03       4       8 ..      35      39 ..      32      55 .. 0.56
   2 ?    1.6   0.1      0.41   4.6e+02      17      26 ..      71      80 ..      65      83 .. 0.80
   3 !   18.0   0.7     3e-06    0.0034       2      27 ..      85     110 ..      84     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.3
                  zinc-ribbon_6  4 CeqCg 8 
                                   C  Cg
  gene621|gene621|rna620|rna620 35 CPYCG 39
                                   55454 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.41
                  zinc-ribbon_6 17 sClkCgaalg 26
                                   sC +C+++lg
  gene621|gene621|rna620|rna620 71 SCSHCKRNLG 80
                                   7999998887 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 3e-06
                  zinc-ribbon_6   2 feCeqCgqllffenssClkCgaalgf 27 
                                    ++C++Cg    fe+s+C +Cg++ g+
  gene621|gene621|rna620|rna620  85 YRCQKCGVATTFESSNCPNCGEEKGH 110
                                    99*******************98876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.4     0.022        24       8      33 ..      13      39 ..      11      43 .. 0.75
   2 ?   -0.3   0.2       1.1   1.2e+03      29      34 ..      72      77 ..      66      79 .. 0.62
   3 ?   14.7   3.8   2.2e-05     0.025       5      34 ..      84     106 ..      84     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                    Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCg 33
                                   C++  ++ ++     ++p++  CP Cg
  gene621|gene621|rna620|rna620 13 CRSSAEKVDKPEGYPEPPKKFlCPYCG 39
                                   6666666666666669999999****9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                    Zn-ribbon_8 29 CPeCgs 34
                                   C +C+ 
  gene621|gene621|rna620|rna620 72 CSHCKR 77
                                   666654 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.2e-05
                    Zn-ribbon_8   5 eYrCeeCghefevlqsisdapltaCPeCgs 34 
                                    +YrC++Cg + + + s++      CP+Cg+
  gene621|gene621|rna620|rna620  84 DYRCQKCG-VATTFESSN------CPNCGE 106
                                    8*******.888787555......****97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.7   1.9e+03      22      26 .]       3       7 ..       3       7 .. 0.81
   2 ?    8.2   0.6    0.0014       1.6      19      24 ..      35      40 ..      34      42 .. 0.83
   3 ?    3.7   4.6      0.04        44       4      23 ..      71      91 ..      68      92 .. 0.88
   4 ?   12.7   5.0   5.7e-05     0.064       3      24 ..      85     106 ..      83     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
                    zf-ribbon_3 22 CGtkl 26
                                   CGt+l
  gene621|gene621|rna620|rna620  3 CGTDL 7 
                                   99986 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
                    zf-ribbon_3 19 CpyCGt 24
                                   CpyCG+
  gene621|gene621|rna620|rna620 35 CPYCGY 40
                                   999998 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.04
                    zf-ribbon_3  4 rCPnCGa.plssddnvCpyCG 23
                                   +C++C+  + s +d  C +CG
  gene621|gene621|rna620|rna620 71 SCSHCKRnLGSIGDYRCQKCG 91
                                   8******77899999999999 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 5.7e-05
                    zf-ribbon_3   3 vrCPnCGaplssddnvCpyCGt 24 
                                    +rC +CG   + + ++Cp+CG+
  gene621|gene621|rna620|rna620  85 YRCQKCGVATTFESSNCPNCGE 106
                                    69******66***********7 PP

>> Cript  Microtubule-associated protein CRIPT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.47   5.3e+02      68      79 ..      31      42 ..      11      52 .. 0.76
   2 ?   12.1   3.1    0.0002      0.22      45      78 ..      70     107 ..      61     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.47
                          Cript 68 kkgiCamCGkkl 79
                                   kk +C  CG  +
  gene621|gene621|rna620|rna620 31 KKFLCPYCGYLT 42
                                   677899999654 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0002
                          Cript  45 skCkiCktkveqkgakYCqkC....aYkkgiCamCGkk 78 
                                     +C+ Ck ++ + g   CqkC     ++   C  CG +
  gene621|gene621|rna620|rna620  70 LSCSHCKRNLGSIGDYRCQKCgvatTFESSNCPNCGEE 107
                                    38**********99999****5544588999*****86 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3     0.004       4.4      11      26 ..      27      42 ..      11      52 .. 0.74
   2 ?    5.0   6.8     0.024        27       2      27 ..      72      95 ..      71     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.004
                       zf-Mss51 11 apkhvdfeCpdCGipt 26
                                   ++ + +f Cp CG+ t
  gene621|gene621|rna620|rna620 27 PEPPKKFLCPYCGYLT 42
                                   556779*******866 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.024
                       zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGipty 27
                                   C ++k +    +  d+ C++CG+ t 
  gene621|gene621|rna620|rna620 72 CSHCKRNL--GSIGDYRCQKCGVATT 95
                                   99998888..9999*********986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   7.0    0.0069       7.7      16      45 ..      30      77 ..      26      78 .. 0.85
   2 ?    2.3   8.1      0.15   1.7e+02      15      44 ..      63      91 ..      54      93 .. 0.85
   3 ?    6.2   0.6    0.0094        10      20      28 ..     100     108 ..      94     119 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0069
                  Zn_Tnp_IS1595 16 pngfvCPhCgsrkayrikt..................rglfqCkeCrk 45
                                   p +f CP+Cg+ +  ++++                    ++ C++C++
  gene621|gene621|rna620|rna620 30 PKKFLCPYCGYLTDSEYRHdkysfcicfipcipwgnsYPYLSCSHCKR 77
                                   56799*******777777777999999999999999988999999997 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                  Zn_Tnp_IS1595 15 Wpng...fvCPhCgsrkayriktrglfqCkeCr 44
                                   W+n      C hC+ r + +i +   ++C++C+
  gene621|gene621|rna620|rna620 63 WGNSypyLSCSHCK-RNLGSIGD---YRCQKCG 91
                                   888887777****9.78888877...******7 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0094
                  Zn_Tnp_IS1595  20 vCPhCgsrk 28 
                                     CP+Cg +k
  gene621|gene621|rna620|rna620 100 NCPNCGEEK 108
                                    6*****983 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4    0.0037       4.1       4      19 ..      34      51 ..      31      59 .. 0.83
   2 ?   -0.1   0.1       1.4   1.6e+03       4       9 ..      71      76 ..      69      79 .. 0.79
   3 ?    1.0   0.3      0.61   6.9e+02       4       9 ..      86      91 ..      85      95 .. 0.61
   4 ?    7.8   0.2    0.0047       5.2       5      17 ..     101     113 ..      97     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0037
                        zf-ISL3  4 rCPnCgsktv..vkhgkk 19
                                    CP+Cg  t+  ++h+k+
  gene621|gene621|rna620|rna620 34 LCPYCGYLTDseYRHDKY 51
                                   6*******5545999986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.4
                        zf-ISL3  4 rCPnCg 9 
                                    C +C+
  gene621|gene621|rna620|rna620 71 SCSHCK 76
                                   599997 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.61
                        zf-ISL3  4 rCPnCg 9 
                                   rC +Cg
  gene621|gene621|rna620|rna620 86 RCQKCG 91
                                   466666 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0047
                        zf-ISL3   5 CPnCgsktvvkhg 17 
                                    CPnCg+ + +  g
  gene621|gene621|rna620|rna620 101 CPNCGEEKGHSGG 113
                                    ******9987765 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.1    0.0012       1.4     632     664 ..      71     107 ..      40     115 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                       PolC_DP2 632 rCeeCgektee..klvCkkceeeve..eekcekceke 664
                                     C++C+++  +   ++C+kc+ +++  +++c++c++e
  gene621|gene621|rna620|rna620  71 SCSHCKRNLGSigDYRCQKCGVATTfeSSNCPNCGEE 107
                                    4444444332211344444444332112224444443 PP

>> Acetone_carb_G  Acetone carboxylase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.8    0.0012       1.4      77      98 ..      32      53 ..      17      63 .. 0.84
   2 ?    1.5   0.1      0.28   3.2e+02      65      90 ..      72      97 ..      61     102 .. 0.78
   3 ?   -1.8   0.1       3.1   3.5e+03      80      85 ..     101     106 ..      97     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                                   EEE-TTT--EEEEEEE-TT--- CS
                 Acetone_carb_G 77 EyycPecgtllevEaltpgyPv 98
                                    ++cP cg l + E+    y  
  gene621|gene621|rna620|rna620 32 KFLCPYCGYLTDSEYRHDKYSF 53
                                   69*************9888765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.28
                                   TTS--TTT-EEEEEE-TTT--EEEEE CS
                 Acetone_carb_G 65 llapdpewqrirEyycPecgtllevE 90
                                     +++ +   i +y c +cg     E
  gene621|gene621|rna620|rna620 72 CSHCKRNLGSIGDYRCQKCGVATTFE 97
                                   4567777888999******9887666 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.1
                                    -TTT-- CS
                 Acetone_carb_G  80 cPecgt 85 
                                    cP+cg+
  gene621|gene621|rna620|rna620 101 CPNCGE 106
                                    ****97 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.8     0.041        46      67      94 ..      29      77 ..      11      84 .. 0.82
   2 ?    6.5   8.0    0.0074       8.3      70      96 ..      84     108 ..      69     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.041
                                   E--EEEETTTS-EEECHHH.HH....................S-TTTSS CS
                           HypA 67 vpvkvrCreCgkefeleek.al....................rCpkCgs 94
                                    p k+ C  Cg+ +++e + +                     +C +C++
  gene621|gene621|rna620|rna620 29 PPKKFLCPYCGYLTDSEYRhDKysfcicfipcipwgnsypylSCSHCKR 77
                                   678899999*998887763322478999999999999999999999987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0074
                                    EEEETTTS-EEECHHHHHS-TTTSSS- CS
                           HypA  70 kvrCreCgkefeleekalrCpkCgsad 96 
                                     +rC++Cg  ++ e+   +Cp+Cg+++
  gene621|gene621|rna620|rna620  84 DYRCQKCGVATTFES--SNCPNCGEEK 108
                                    579*****8888774..48*****986 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.6   1.7e+03     520     526 ..      33      39 ..      11      51 .. 0.69
   2 ?    9.9   1.8   0.00025      0.28     509     529 ..      86     108 ..      84     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                                    SB-TTT- CS
                           NRDD 520 ekCpkCg 526
                                    + Cp+Cg
  gene621|gene621|rna620|rna620  33 FLCPYCG 39 
                                    4577777 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
                                    EETT.--..EESSSB-TTT--BE CS
                           NRDD 509 vCnecgy..kgeiekCpkCgsee 529
                                    +C++cg   + e  +Cp+Cg+e+
  gene621|gene621|rna620|rna620  86 RCQKCGVatTFESSNCPNCGEEK 108
                                    7******76666699*****665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5    0.0041       4.6      20      31 ..      33      44 ..      28      56 .. 0.77
   2 ?   -2.7   0.2       3.9   4.3e+03       3       7 ..      72      76 ..      70      79 .. 0.59
   3 ?    6.9   0.1    0.0039       4.4      18      27 ..      83      92 ..      81      98 .. 0.86
   4 ?    4.0   1.7     0.031        35       3       9 ..     101     107 ..     100     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0041
                                   EEESSSSBEEEE CS
                   TF_Zn_Ribbon 20 lvCtdCGlVled 31
                                   ++C+ CG++ + 
  gene621|gene621|rna620|rna620 33 FLCPYCGYLTDS 44
                                   788888887654 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.9
                                   ETTTT CS
                   TF_Zn_Ribbon  3 CPnCg 7 
                                   C  C+
  gene621|gene621|rna620|rna620 72 CSHCK 76
                                   55555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0039
                                   TCEEESSSSB CS
                   TF_Zn_Ribbon 18 gelvCtdCGl 27
                                   g+++C +CG+
  gene621|gene621|rna620|rna620 83 GDYRCQKCGV 92
                                   89******97 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.031
                                    ETTTTCE CS
                   TF_Zn_Ribbon   3 CPnCgst 9  
                                    CPnCg +
  gene621|gene621|rna620|rna620 101 CPNCGEE 107
                                    9999975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.5   1.7e+03      19      23 .]       3       7 ..       3       7 .. 0.67
   2 ?    9.1   0.7   0.00099       1.1      14      21 ..      32      40 ..      29      41 .. 0.85
   3 ?   -3.1   0.1       6.6   7.4e+03      13      16 ..      51      54 ..      49      55 .. 0.65
   4 ?    4.4   3.9     0.029        32       2      20 ..      72      91 ..      71      92 .. 0.87
   5 ?    7.9   1.5    0.0023       2.6       2       8 ..     101     107 ..      99     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                  zinc_ribbon_2 19 CGtpl 23
                                   CGt l
  gene621|gene621|rna620|rna620  3 CGTDL 7 
                                   88765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00099
                  zinc_ribbon_2 14 kF.CpyCGt 21
                                   kF CpyCG+
  gene621|gene621|rna620|rna620 32 KFlCPYCGY 40
                                   566*****7 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 6.6
                  zinc_ribbon_2 13 akFC 16
                                     FC
  gene621|gene621|rna620|rna620 51 YSFC 54
                                   5688 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.029
                  zinc_ribbon_2  2 CpnCGaelqd.nakFCpyCG 20
                                   C++C + l   ++  C +CG
  gene621|gene621|rna620|rna620 72 CSHCKRNLGSiGDYRCQKCG 91
                                   99999999655999999999 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0023
                  zinc_ribbon_2   2 CpnCGae 8  
                                    CpnCG+e
  gene621|gene621|rna620|rna620 101 CPNCGEE 107
                                    7777765 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5     0.034        39      41      57 ..      27      43 ..      12      56 .. 0.70
   2 ?    4.2   3.0     0.036        40      30      54 ..      71      92 ..      66      97 .. 0.87
   3 ?    7.9   0.8    0.0026       2.9      27      40 ..      97     110 ..      92     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.034
                 OrfB_Zn_ribbon 41 alsgrtfkCpnCgfead 57
                                   +  +++f Cp Cg+  d
  gene621|gene621|rna620|rna620 27 PEPPKKFLCPYCGYLTD 43
                                   55677778888877555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.036
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgf 54
                                   +Cs+C +++        ++C++Cg+
  gene621|gene621|rna620|rna620 71 SCSHCKRNLGS---IGDYRCQKCGV 92
                                   58999888888...99*******97 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0026
                 OrfB_Zn_ribbon  27 TSktCseCgsknke 40 
                                     S++C++Cg+++ +
  gene621|gene621|rna620|rna620  97 ESSNCPNCGEEKGH 110
                                    599******99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 661.89
//
Query:       gene622|gene622|rna621|rna621  [L=425]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2682.08
//
Query:       gene623|gene623|rna622|rna622  [L=779]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-14   52.0   3.5    4.7e-05   24.1   0.6    6.4  5  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0055        98       5      38 .]     398     430 ..     391     430 .. 0.79
   2 !    6.0   0.0    0.0013        24      23      38 .]     467     481 ..     449     481 .. 0.85
   3 !    3.9   0.0    0.0061   1.1e+02       9      36 ..     491     519 ..     485     521 .. 0.87
   4 !   24.1   0.6   2.6e-09   4.7e-05       2      38 .]     525     560 ..     524     560 .. 0.91
   5 !    8.1   0.0   0.00028       5.1       2      38 .]     565     602 ..     564     602 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0055
                                    EEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    +++ +H   + sl  s + ++l++ s+D++  +W+
  gene623|gene623|rna622|rna622 398 HIIPAHgEAIMSL--SIHEDFLMTVSRDKKAILWK 430
                                    5556774449999..7799999999********95 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0013
                                    SEEEEEETTSEEEEEE CS
                           WD40  23 awlasGsdDgtvriWd 38 
                                     ++++Gs D+ + iWd
  gene623|gene623|rna622|rna622 467 IFVLAGS-DQILQIWD 481
                                    46889**.*******9 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0061
                                    SS.SSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40   9 GH.ssvtslafspdgawlasGsdDgtvri 36 
                                     H + ++++  + +  ++a++s D++ ++
  gene623|gene623|rna622|rna622 491 VHdKEINGVEINEERGLIATCSQDKKAKV 519
                                    59778999999999999*******99886 PP

  == domain 4  score: 24.1 bits;  conditional E-value: 2.6e-09
                                    EEEEEEESS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                    + l++l+GH ++v+s+     ++++a++s D tv++W+
  gene623|gene623|rna622|rna622 525 RILHVLSGHtKGVWSV--GFGKNLMATCSADTTVKVWK 560
                                    679******999****..7788889************6 PP

  == domain 5  score: 8.1 bits;  conditional E-value: 0.00028
                                    EEEEEEESS.SSE..EEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   2 qclrtltGH.ssv..tslafspdgawlasGsdDgtvriWd 38 
                                    +c++tltGH s+v   ++ +  d ++ +sG+  g  ++Wd
  gene623|gene623|rna622|rna622 565 ECIGTLTGHrSGVlkGGF-YKNDEKF-ISGCATGEMKVWD 602
                                    8********999954455.6666666.58999*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 4583.80
//
Query:       gene624|gene624|rna623|rna623  [L=117]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   13.5   2.0       0.14   12.5   1.7    1.7  2  DUF4467   Domain of unknown function with cystatin-like fold 


Domain annotation for each model (and alignments):
>> DUF4467  Domain of unknown function with cystatin-like fold (DUF4467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.7   8.1e-06      0.14      19      72 ..      18      72 ..       3      92 .. 0.75
   2 ?   -0.0   0.0     0.065   1.2e+03      26      46 ..      71      92 ..      68     113 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-06
                        DUF4467 19 lakkgndvevd.ikkedanvyVyedgKlivlaykllknreevtyvaYeikdkkve 72
                                   l  k+  ++v+ ik+ +a v +++    i l ykl+   ++  +v Y+ +  k  
  gene624|gene624|rna623|rna623 18 LRPKEIRKQVEeIKRMKATVVIFDFCGKIPLVYKLFAGVKKEVFVVYDASKCKER 72
                                   444555677777************99999*********99*******98876643 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.065
                        DUF4467 26 vevd.ikkedanvyVyedgKli 46
                                    ++d i ++   +yV ed + +
  gene624|gene624|rna623|rna623 71 ERIDeISRDHDLIYVLEDIQAV 92
                                   5677788888888888875544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 811.31
//
Query:       gene625|gene625|rna624|rna624  [L=509]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-22   80.1   0.0    3.2e-20   72.8   0.0    2.3  1  Flavodoxin_1   Flavodoxin
    1.7e-07   31.1   0.0    2.7e-05   23.9   0.0    2.2  1  FAD_binding_1  FAD binding domain
      4e-06   27.4   0.0    2.3e-05   25.0   0.0    2.2  2  NAD_binding_1  Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.8   0.0   5.3e-24   3.2e-20       1     143 []       4     159 ..       4     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.8 bits;  conditional E-value: 5.3e-24
                                    EEEETSSSHHHHHHHHHHHHHHHTTTEE.EEEEEEGTTSC................GGGGGTHSEEEEEEEEETTTBEEG CS
                   Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfna.dvvslsdydes................lseieeealllvvtsTfgnGdppe 63 
                                    ilYgS+tG++  + k + + +   g +a ++++l+ ++ s                +++i + +++++v+sT+g+G  p 
  gene625|gene625|rna624|rna624   4 ILYGSQTGTSIYVSKLIERAIL-YGYDArTIYNLESFSSSqdqrsmsivvemdlfdIEKIIDVDFIIFVCSTHGDGTEPF 82 
                                    6777777777777777777666.45544134555555544555566666666666689********************** PP

                                    GGHHHHHHHHHHHCHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEETTSTHGHHHHHHHH CS
                   Flavodoxin_1  64 ngesffqdllelkgdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegdednqegqeeafrkW 143
                                    n+  +f+++l +++ + +   ls ++favfglGds+ye+F++  k+l ++l+ lG++ + + + gd +++eg+  ++r W
  gene625|gene625|rna624|rna624  83 NMT-KFWSFLSNDSLPST--ILSHLSFAVFGLGDSSYEKFNYCSKRLFNRLKMLGGRPVIRRGCGDSQDKEGYLSDLRPW 159
                                    *99.********976555..6************************************************99999999998 PP

>> FAD_binding_1  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   4.4e-09   2.7e-05     100     222 .]     254     373 ..     180     373 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.4e-09
                                    HHHHTB--SS---HHHHHHHGGG-SSH..HHHHHHHHHHH-.HHHHHTTTTT--HHHHHHHHHTT---TTS-HHHHHHHS CS
                  FAD_binding_1 100 alkyylditgppskqlleaLaefasee..eekqkLekLssd.egakeykelklneartllevleefpsvklplefLlevl 176
                                    ++++ +d+ ++p++ ++ aL +f  ++   e + L k+ +  e  + y +  ++ +rt+ evl++ + vk+ ++fL    
  gene625|gene625|rna624|rna624 254 LVRQVIDFNSQPHQPFFFALGHFLRQKidVEEEILLKVEEIaEDYDLYYDYIIKPKRTVFEVLKDLK-VKVDIAFLRRFG 332
                                    45677899999*****999999976641134444444443344577788999999**********98.79********** PP

                                    -B---EEEEB-S-TTTTTTEEEEEEE--EE---SSS--EE-HHHHH CS
                  FAD_binding_1 177 pqLkpRyYSiSssskvhpdevhltvvVveyetdgegrirkGvcsny 222
                                    p L pR++S+      ++   h+t+ +v y+t   ++ rkGvcs+y
  gene625|gene625|rna624|rna624 333 PTLYPRFFSVTK----KEGLYHITASIVRYKT-LLAQPRKGVCSEY 373
                                    *********975....55667**********8.9**********98 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       0.6   3.6e+03      30      64 ..       4      38 ..       2      73 .. 0.58
   2 !   25.0   0.0   3.8e-09   2.3e-05       1     107 [.     401     490 ..     401     492 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.6
                                   EEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEES CS
                  NAD_binding_1 30 lvyGnrteedllyreeleelakklpgrlkvvavvs 64
                                   ++yG +t  ++++++ +e++     ++ ++++ +s
  gene625|gene625|rna624|rna624  4 ILYGSQTGTSIYVSKLIERAILYGYDARTIYNLES 38
                                   78999999999999988887544444456666622 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 3.8e-09
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGC.GSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrtee.dllyreeleelakklpgrlkvvavvsreeagweggkgrvqd 79 
                                    +i++GtGia  r+ ++++ +     +++v++yG r+++ d+ly++e+++       +++++++    ++++   k++vqd
  gene625|gene625|rna624|rna624 401 FICTGTGIALPRACVHEFKD-----KEMVIFYGFRHRHkDFLYSDEWNNK------NVRIITA---ASRDD---KVYVQD 463
                                    7********88888887776.....58*********999*******9865......4566666...33344...889999 PP

                                    HHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                  NAD_binding_1  80 alleellslkkeethvyvCGppgMikav 107
                                     ++++ ++   ++ +++v G  ++ k v
  gene625|gene625|rna624|rna624 464 IFRKNPVE-GIDQYLIFVSGSSRLNKVV 490
                                    99999998.7899999999988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2934.57
//
Query:       gene626|gene626|rna625|rna625  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-62  210.3   4.5    2.7e-62  210.0   4.5    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
      0.028   12.4   0.0      0.043   11.7   0.0    1.2  1  V_ATPase_I      V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   4.5     3e-66   2.7e-62       2     200 ..      19     221 ..      17     222 .. 0.97

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 3e-66
                                    S----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESS CS
                 Ribosomal_S3Ae   2 kkkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgk 81 
                                    kkk  +D+f++KeWy++++Ps+f ++  Gktlv++ +g+ +a   ++gr ++v+ aDLt+++ + a+rk+++ki +v+g 
  gene626|gene626|rna625|rna625  19 KKKTGQDSFARKEWYNLRSPSIFPSNINGKTLVSKATGK-NAHMRAIGRRYDVNHADLTKNN-DVAHRKFIFKIGDVKGA 96 
                                    68889****************************888885.89999**************996.889************** PP

                                    EEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STT......B---HHHHHHHHHHHHHHHHH CS
                 Ribosomal_S3Ae  82 naltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrn......sYakssqkkaIrkkmveilte 155
                                    +++  F gmelt+Dk + +++kw+slIea+ d+  kD  ++rvfv+a+Tk+ +      +Y+k+s +k+Irk+m+++++e
  gene626|gene626|rna625|rna625  97 DCIGFFDGMELTSDKHKAMIKKWHSLIEAQKDIVAKDQSVFRVFVMAVTKRPHgytkktCYVKHSDEKRIRKIMFDVIEE 176
                                    ***************************************************96699************************ PP

                                    HHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE CS
                 Ribosomal_S3Ae 156 easeldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlk 200
                                    e+   +++++++kl +e++gk+ie+  ++I+pl+n+++rKvk +k
  gene626|gene626|rna625|rna625 177 ELGGRSVDDIMSKLSNETVGKRIEELGSEIFPLQNCCVRKVKTIK 221
                                    ******************************************998 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.8e-06     0.043     263     346 ..     106     191 ..      99     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-06
                     V_ATPase_I 263 eqteealkevleeiakeleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateess..ssvps 340
                                    e t+++ k++++++ + +e+ k +v k ++++ ++ +  +++ + +    ++v+++++++i+k++ ++ ee+   +sv  
  gene626|gene626|rna625|rna625 106 ELTSDKHKAMIKKWHSLIEAQKDIVAKDQSVFRVFVMAVTKRPHGYTKKTCYVKHSDEKRIRKIMFDVIEEELggRSVDD 185
                                    66889999******************************9*************************9998876655677777 PP

                     V_ATPase_I 341 ilneie 346
                                    i+++++
  gene626|gene626|rna625|rna625 186 IMSKLS 191
                                    777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1562.53
//
Query:       gene627|gene627|rna626|rna626  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-92  307.5   4.8    6.5e-92  307.3   4.8    1.0  1  PMM              Eukaryotic phosphomannomutase
    1.3e-09   38.2   0.1    2.5e-09   37.3   0.1    1.4  1  Hydrolase_3      haloacid dehalogenase-like hydrolase
      4e-07   29.8   0.0      0.023   14.2   0.0    2.1  2  S6PP             Sucrose-6F-phosphate phosphohydrolase
     0.0014   18.7   0.7     0.0081   16.3   0.1    2.1  2  HAD_2            Haloacid dehalogenase-like hydrolase
     0.0022   18.3   1.0     0.0022   18.3   1.0    2.1  2  DUF1497          Protein of unknown function (DUF1497)
  ------ inclusion threshold ------
      0.037   14.1   0.8      0.095   12.8   0.0    2.0  3  DUF600           Protein of unknown function, DUF600
       0.04   13.0   0.0       0.06   12.5   0.0    1.3  1  Trehalose_PPase  Trehalose-phosphatase
       0.12   12.5   0.4       0.27   11.3   0.1    1.6  2  SKI              Shikimate kinase
       0.13   12.5   0.0        0.7   10.1   0.0    2.0  2  Hydrolase        haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> PMM  Eukaryotic phosphomannomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.3   4.8   3.2e-95   6.5e-92       1     219 [.      28     245 ..      28     247 .. 0.98

  Alignments for each domain:
  == domain 1  score: 307.3 bits;  conditional E-value: 3.2e-95
                                    HHHHHHHHCTTSEEEEE-SS-HHHHHHHHS.TTHHHH-SEEEEGGGTEEEETTEEEEE--HHHHH-HHHHHHHHHHHHHH CS
                            PMM   1 lkeflqklrkkveigvvgGsdlekikeqlagdevldefdyvfsenGlvaykkgkelasqsiiealgeeklkklinfvlry 80 
                                    ++e+l+kl+kkv+ig+vgGsdlek+ eq+ gd++l+ f+y f+enG+  yk+g   ++ +ii+ lge+ +k+++ fvl+y
  gene627|gene627|rna626|rna626  28 MREMLKKLKKKVHIGFVGGSDLEKQREQI-GDDLLELFEYGFPENGVSFYKNGTLKSQEKIINVLGEKFYKEFVGFVLEY 106
                                    789**************************.7************************************************* PP

                                    HHCS--S---S-SEEEESSEEEE-SS-TTSSHHHHHHHHHHHHHHTHHHHHHHHHHHHTTTSSEEEEEETTTEEEEEETT CS
                            PMM  81 ladldlPvkrGtfiefrngllnvsPiGrnasqeernefeeydkkekireklvealkeefadlgltfsiGGqisfdvfPkg 160
                                    l+++d+P+krG+fie+rn+++n+sPiGrn+s+eer+ef e+dkkek r+ +v+a++e+f++  l fsiGGqis+d fPkg
  gene627|gene627|rna626|rna626 107 LSKMDIPIKRGNFIEYRNSMINISPIGRNCSREERKEFFELDKKEKFRKSMVAAMRERFKNSCLVFSIGGQISIDCFPKG 186
                                    ******************************************************************************** PP

                                    -SGGGGGGGCTTST-SEEEEEESS-STTSTTHHHHHSTTCEEEE-SSHHHHHHHHHHHH CS
                            PMM 161 WdktyclqhvekdsfdeihffGdktaeGGndyeiyadprtighsvtspddtvkkleell 219
                                    Wdktycl+h+ ++++++++ffGd t+eGGndyei++++++ g +v++pddt +k+++ l
  gene627|gene627|rna626|rna626 187 WDKTYCLRHIRDEGIKNVYFFGDMTMEGGNDYEIFNHQDVHGVTVENPDDTYRKVSQKL 245
                                    *****************************************************998766 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   1.2e-12   2.5e-09       2     239 ..      10     242 ..       9     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 1.2e-12
                                    EEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHH..HCCCCSEEEEGGGTEEECTTTEEEEE--B CS
                    Hydrolase_3   2 alDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvle..elgldlpvialNGaliddekgkilyksti 79 
                                     +D+DGTL  s  +++ek +e +kklk k +++ +  G  l++ ++ +    l+l  +    NG    +++g + ++++i
  gene627|gene627|rna626|rna626  10 LFDVDGTLSESRASMTEKMREMLKKLK-KKVHIGFVGGSDLEKQREQIGddLLELFEYGFPENGVSF-YKNGTLKSQEKI 87 
                                    69*************************.889999999987776666665233444499999****99.777777766666 PP

                                    -HHHHHHHHHHHHHTTCEEEEEESSEEEESTT.THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES-HHHHHHHHH CS
                    Hydrolase_3  80 skedvkeiikllkennveillytedkvyvlnkeksekkkkeeektkkkkeeidseeeledeeiakililkdkekldelek 159
                                     +   ++++k +    v ++l+  +k+ +  k  + + ++++++  + +++ ++ + +e++e++ +  +k+++  +++ +
  gene627|gene627|rna626|rna626  88 INVLGEKFYKEF----VGFVLEYLSKMDIPIK--RGNFIEYRNSMINISPIGRNCSREERKEFFEL--DKKEKFRKSMVA 159
                                    655555555555....5555555555555555..33555555555555555555555555555555..333333444577 PP

                                    HHHHHCTTTE.EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEES....SGGGHHHHHHSS.EEEEETTS-H CS
                    Hydrolase_3 160 elksklnkll.titssskgyleimpkgvsKgtalkklakelnisleeviafGD....geNDieMLeaag.lgvAmgnase 233
                                    ++++++++    ++  ++ +++  pkg++K   l+++    +   ++v+ fGD    g ND+e +++ + +gv ++n ++
  gene627|gene627|rna626|rna626 160 AMRERFKNSClVFSIGGQISIDCFPKGWDKTYCLRHIR---DEGIKNVYFFGDmtmeGGNDYEIFNHQDvHGVTVENPDD 236
                                    77777766654777788999*****************9...67899*******444457*******996479****9998 PP

                                    HHHHHS CS
                    Hydrolase_3 234 evkkaA 239
                                    +  k++
  gene627|gene627|rna626|rna626 237 TYRKVS 242
                                    877765 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.2e-05     0.023       3     106 ..       7     109 ..       5     116 .. 0.89
   2 !   13.7   0.0   1.7e-05     0.034     128     212 ..     149     237 ..     137     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                    EEEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEEEE..TTEE-H CS
                           S6PP   3 lllvsdLDntlvdgdnealarlnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGteiyygeelvpdk 82 
                                     +++ d+D+tl ++ ++ +++++e+l+ + +k+v ++f+ G  l++++e + +  l   ++   + G++ y+  +l++++
  gene627|gene627|rna626|rna626   7 TIFLFDVDGTLSESRASMTEKMREMLK-KLKKKVHIGFVGGSDLEKQREQIGDDLLELFEYGFPENGVSFYKNGTLKSQE 85 
                                    68999*******9999999********.99**********************9999999999999999999988999999 PP

                                    HHHHHHHTT--HHHHHHHHHT-TT CS
                           S6PP  83 aweeildekwdrqavvealaklpe 106
                                    +  ++l ek+ ++ v  +l+ l +
  gene627|gene627|rna626|rna626  86 KIINVLGEKFYKEFVGFVLEYLSK 109
                                    999999999998888777777765 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.7e-05
                                    S-THHHHHHHHHHHTTTS-EEEEEETTTE..EEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-S....GGGHHHH.TSS CS
                           S6PP 128 kaaevlkeleqlLekreldvkviyssgkd..lDvlPkraskgeAlryLakkleleleqilvcGds....gnDeell.ign 200
                                    k ++  k++ +++++r  +  +++s g +  +D  Pk+ +k + lr++ +      +++ + Gd     gnD e++  ++
  gene627|gene627|rna626|rna626 149 KKEKFRKSMVAAMRERFKNSCLVFSIGGQisIDCFPKGWDKTYCLRHIRDE---GIKNVYFFGDMtmegGNDYEIFnHQD 225
                                    4444567778888888888999999876522799*************9986...5788888888544449******99** PP

                                    SEEEE-TT--HH CS
                           S6PP 201 vlgVvVgnaqee 212
                                    v+gV V n +  
  gene627|gene627|rna626|rna626 226 VHGVTVENPDDT 237
                                    ********8876 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.1e-06    0.0081       2      61 ..      10      83 ..       9     115 .. 0.74
   2 ?    1.2   0.1      0.18   3.5e+02      30      57 ..     133     161 ..      79     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                          HAD_2  2 iFDlDgTlldteeliiqafnelleey.......glselseeelrkliglslrellrklgeseeeee.......k 61
                                   +FD+DgTl  ++  + + ++e+l++         ++  ++e+ r+ ig +l el+++ ++++ ++        +
  gene627|gene627|rna626|rna626 10 LFDVDGTLSESRASMTEKMREMLKKLkkkvhigFVGGSDLEKQREQIGDDLLELFEYGFPENGVSFykngtlkS 83
                                   8************************999999954448999****************999998877766664432 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.18
                          HAD_2  30 s.elseeelrkliglslrellrklgesee 57 
                                    + + s+ee +++++l+ +e +rk+ +   
  gene627|gene627|rna626|rna626 133 GrNCSREERKEFFELDKKEKFRKSMVAAM 161
                                    44678899999999999999999887644 PP

>> DUF1497  Protein of unknown function (DUF1497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.1   4.2e+03      41      56 ..      23      38 ..       5      39 .. 0.68
   2 !   18.3   1.0   1.1e-06    0.0022       7      51 ..     123     166 ..     118     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.1
                        DUF1497 41 emqaefhekikklGek 56
                                    m   + e +kkl  k
  gene627|gene627|rna626|rna626 23 SMTEKMREMLKKLKKK 38
                                   5666677777887655 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.1e-06
                        DUF1497   7 rnearrisklasqnisseqtkkefeldrqskfnqemqaefhekik 51 
                                    rn    is +  +n s e  k  feld++ kf + m a + e+ k
  gene627|gene627|rna626|rna626 123 RNSMINISPI-GRNCSREERKEFFELDKKEKFRKSMVAAMRERFK 166
                                    6666666665.5799***************************988 PP

>> DUF600  Protein of unknown function, DUF600
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       3.5     7e+03      69      82 ..      25      38 ..      19      40 .. 0.57
   2 ?   -2.0   0.0       1.7   3.5e+03      77      93 ..     151     167 ..     125     181 .. 0.59
   3 ?   12.8   0.0   4.8e-05     0.095      13      65 ..     180     231 ..     172     250 .. 0.58

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.5
                                   HHHHHHHHHHHHHH CS
                         DUF600 69 lkeLyelikeLree 82
                                   +++++e++k+L+++
  gene627|gene627|rna626|rna626 25 TEKMREMLKKLKKK 38
                                   34555555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                                    HHHHHHHHHHHSS--SE CS
                         DUF600  77 keLreefkkeeqeaWtn 93 
                                    +++r+ +  + +e  +n
  gene627|gene627|rna626|rna626 151 EKFRKSMVAAMRERFKN 167
                                    33344444444444444 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 4.8e-05
                                    HHH--S-EEEEEEEEEE-TT--EEEEEEEEETTT-EEEGGGGGGT--S-HHHH CS
                         DUF600  13 ldmiPeeWekvylyaevledsgevyFyylkkesekliysheipekynvseeey 65 
                                    +d  P+ W+k y + ++ +++ + ++++      +  +++ei ++ +v     
  gene627|gene627|rna626|rna626 180 IDCFPKGWDKTYCLRHIRDEGIKNVYFFGDMTM-EGGNDYEIFNHQDVHGVTV 231
                                    5788***************97666666644433.3444455544444433222 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     3e-05      0.06       1      52 [.      10      54 ..      10      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                                   EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHH CS
                Trehalose_PPase  1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeel 52
                                   ++D dGTls+       a ++++++++LkkL ++++  + +v G++l+++++
  gene627|gene627|rna626|rna626 10 LFDVDGTLSESR-----ASMTEKMREMLKKLKKKVH--IGFVGGSDLEKQRE 54
                                   69******9865.....59*****************..999***99999443 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.2     1e+04      74     123 ..      24      34 ..      15      42 .. 0.47
   2 ?   11.3   0.1   0.00014      0.27      33      73 ..     139     179 ..     132     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.2
                                    GSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHH CS
                            SKI  74 lseenrellkekgiviyLdvsleellerlkadkeRPllqekskeeellee 123
                                    ++e++re+lk                                       +
  gene627|gene627|rna626|rna626  24 MTEKMREMLK---------------------------------------K 34 
                                    2233333333.......................................2 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00014
                                    S-HHHHHHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGG CS
                            SKI  33 ksiaeifeeegeegFrelEsevlkelleeeglViatGGGav 73 
                                     + +e+fe + +e+Fr+   ++++e  ++  lV++ GG + 
  gene627|gene627|rna626|rna626 139 EERKEFFELDKKEKFRKSMVAAMRERFKNSCLVFSIGGQIS 179
                                    6779*********************************9875 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00035       0.7       3      44 ..       8      58 ..       6     126 .. 0.72
   2 ?    0.0   0.0      0.44   8.7e+02     174     198 ..     184     209 ..     152     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
                                   EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHH.........HHCHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxx RF
                      Hydrolase  3 tvvfDkdGTLttgepsvedvivsaalalaaaletg.........sehpigk 44
                                    ++fD+dGTL +++ s ++ +++  ++l++  ++g          +  ig 
  gene627|gene627|rna626|rna626  8 IFLFDVDGTLSESRASMTEKMREMLKKLKKKVHIGfvggsdlekQREQIGD 58
                                   689***********9999999999666666666665566555554444444 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.44
                                    TSHHHHHHHHHHHTST.GGGEEEEES CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      Hydrolase 174 pspegkvaaireLqgk.peevamVGD 198
                                    p+ ++k + +r ++ + +++v ++GD
  gene627|gene627|rna626|rna626 184 PKGWDKTYCLRHIRDEgIKNVYFFGD 209
                                    78899999999998545999*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      804  (0.0448435); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 1483.43
//
Query:       gene628|gene628|rna627|rna627  [L=345]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-41  139.6   0.1    1.6e-40  138.7   0.1    1.5  1  NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogen
    1.4e-37  129.1   0.0      2e-37  128.6   0.0    1.2  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.002   18.5   0.0      0.008   16.6   0.0    1.9  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
  ------ inclusion threshold ------
      0.073   13.7   0.0       0.39   11.3   0.0    2.3  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.1   3.5e-44   1.6e-40       1     140 [.     191     334 ..     191     336 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 3.5e-44
                                    -HHHHHHHHHHHHHHHHHHHHHHHTTH-HHHHHHHHHHHHHHHHHHHHHHTSS...GGGGGSTTTHHHHHHHHHSCT.HH CS
                 NAD_Gly3P_dh_C   1 DviGvelagalKNviAiaaGivdglglgdntkaalitrglaEmarlakalgak...petflglaglgDlivtctsgksRN 77 
                                    Dv+Gve+ galKNv+++a+G+++glg+ +ntk a++++g+aEm+++ k + ++   +e++++++g+gDl+v+c+sg  RN
  gene628|gene628|rna627|rna627 191 DVYGVEISGALKNVVSMAYGFAEGLGYCTNTKVAIFRNGFAEMRKFFKFF-YPmatTESLFQSSGVGDLLVSCMSG--RN 267
                                    9************************************************8.4434588999***************..** PP

                                    HHHHHHHHC.T--HHHHHHHHC.C--HHHHHHHHHHHHHHHTT...G.HHHHHHHHHHHS---HHHH CS
                 NAD_Gly3P_dh_C  78 rrfGeelgk.gesleeiekeln.qvleGvetakevyellkkkgv..emplleavykilyegkspeel 140
                                    + +++++++ ++sl+e+e +++ ++l+G+ ta  vy++lk+++   e+pl+++vy+i+ye++  +++
  gene628|gene628|rna627|rna627 268 FGCAKMMAEkRMSLKEAEGTMRfTKLQGPTTALIVYNYLKRQKRidEFPLMSTVYRICYENEAYDAI 334
                                    ********98889*****9***9***************99997669***************988776 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6   0.0   4.5e-41     2e-37       1     156 [.       4     171 ..       4     172 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 4.5e-41
                                    -EEEE--SHHHHHHHHHHHTTT.......--EEEE-S-H.....HHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHT CS
                 NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaeng.......hevrlwvree.....elieeineehenvkyLpgiklpenlvattdlaealk 68 
                                    k++++G G+wGta+ ++la+n+       ++vr+w+ +e     +l + in+++ n kyLpgi+lpenl+a++d+++ l+
  gene628|gene628|rna627|rna627   4 KVSIIGNGNWGTAIGRLLANNTiessifeKDVRMWGCREefegrALNDIINSDNINPKYLPGIHLPENLKAVDDIRT-LA 82 
                                    79**********************************99999999999***************************975.66 PP

                                    T--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE...ET.TTEEHHHHHHHHH-S--EEEEESS--HHHHHTT--E CS
                 NAD_Gly3P_dh_N  69 gadiivlvvPsqalrevlkklkgllkkkailvsliKGi...eegtlkllsevieeelkeekvavlsGpslAeEvakgkpt 145
                                    ++d++v+++P+q+++  ++ lkgl+k++ i vsl+KG+   e+g  +l+s  i+++l+++ v+v++G+++A  va+++++
  gene628|gene628|rna627|rna627  83 DSDVLVFALPHQYIE-AIEPLKGLVKNNCIGVSLTKGFidaEDGDIDLVSRSIHRILDIN-VSVMMGANIADQVARDMIS 160
                                    7************96.579*********************99******************.******************* PP

                                    EEEEEES-HHH CS
                 NAD_Gly3P_dh_N 146 avviaskdkea 156
                                    + +++++d++a
  gene628|gene628|rna627|rna627 161 EGTLGYTDEDA 171
                                    ******99876 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.8e-06     0.008       1      99 [.       4     118 ..       4     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.8e-06
                                    EEEEETTTSHHHHHHHHHHHC....T..SSEEEEEEEESTTTTTSBHHHHSG..........GGTTTECEBEEEGGGGGC CS
                 Semialdhyde_dh   1 kvaivGatGyvGqellrlLee....h..pevelvvllsssrsaGkklaeavk..........aleegkdlkvedvdeeel 64 
                                    kv+i+G  G+ G+++ rlL++    +  +e ++     +++ +G++l++  +           +   ++lk  d d+  l
  gene628|gene628|rna627|rna627   4 KVSIIG-NGNWGTAIGRLLANntieSsiFEKDVRMWGCREEFEGRALNDIINsdninpkylpGIHLPENLKAVD-DIRTL 81 
                                    689999.9999999999999854421223444555666777899999999989999888877777788888888.99999 PP

                                    TT-SEEEE-SCHHHHHHHHHHH..HHTTSEEEESSST CS
                 Semialdhyde_dh  65 kevdivflalpagvskelapkl..aeagvkviDlssd 99 
                                    ++ d++++alp+++ ++++p    ++++++ ++l++ 
  gene628|gene628|rna627|rna627  82 ADSDVLVFALPHQYIEAIEPLKglVKNNCIGVSLTKG 118
                                    ******************9853339999988888865 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.6e-05      0.39       1      76 [.       4      98 ..       4     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.6e-05
                                   EEEEETTSHHHHHHHHHHHHTTS....-GGCEEEEEESSCCCHHHHHHHHC...............-EEECECHHHHHHH-S CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaaga....qpheivvansrnpekaeelaeelg...............vkvtavdneeaaeead 63
                                   k+ iiG Gn g a+ + l+++       ++++++ + r++ + ++l + ++                +++avd   +++++d
  gene628|gene628|rna627|rna627  4 KVSIIGNGNWGTAIGRLLANNTIessiFEKDVRMWGCREEFEGRALNDIINsdninpkylpgihlpENLKAVDDIRTLADSD 85
                                   689**********999887776566555677777777777777788888879999999999999998888889999999999 PP

                                   EEEE-S-HHHHHH CS
                  F420_oxidored 64 vvvlavkpedvee 76
                                   v+v+a++ +++e+
  gene628|gene628|rna627|rna627 86 VLVFALPHQYIEA 98
                                   9999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2403.54
//
Query:       gene629|gene629|rna628|rna628  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-17   60.9   0.1    8.5e-17   60.7   0.1    1.1  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    0.00058   19.2   0.0    0.00081   18.8   0.0    1.3  1  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.095   12.5   0.0       0.12   12.2   0.0    1.2  1  Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1   1.4e-20   8.5e-17       2      71 ..      19      88 ..      18      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 1.4e-20
                                   EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHH CS
                    RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicde 71
                                   ++++i+gE+hTLgnlL +++l+++++ f +Y+++HP  +++ lri  +++ + ++ L + lk++++++ +
  gene629|gene629|rna628|rna628 19 MELKIEGETHTLGNLLCEEMLEDKRCLFSAYRVEHPTDNHVFLRITADKDCQVRDLLLETLKRIEEDTVS 88
                                   689*************************************************************998765 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.4e-07   0.00081       2      67 ..      21      84 ..      20      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-07
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  2 fllrgvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlkiLke 67
                                     ++g++htlgN L   +l e   + + a     p+      +++ +l++  d   +++++l+e lk ++e
  gene629|gene629|rna628|rna628 21 LKIEGETHTLGNLLCEEML-EDKRCLFSAyrvehPT------DNHVFLRITADKDCQVRDLLLETLKRIEE 84
                                   6799***************.9999999998777777......99***********************9986 PP

>> Cofilin_ADF  Cofilin/tropomyosin-type actin-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.9e-05      0.12      21      71 ..      11      60 ..       3      78 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                                   EECTT...TEEEEEESS-HHHH.HHHHH.HTTT-EEEEEEEEEECCSECCEEEEEE CS
                    Cofilin_ADF 21 idddk...eeivveeegetyee.lreel.peseprYavydveyehddeskrsklvf 71
                                   + +++    e+++e e  t+ + l+ee+ +++++ +  y+ve+ +d+       vf
  gene629|gene629|rna628|rna628 11 YAGNTrntMELKIEGETHTLGNlLCEEMlEDKRCLFSAYRVEHPTDN------HVF 60
                                   55544422666666633334443555543899**********98886......444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 614.16
//
Query:       gene630|gene630|rna629|rna629  [L=121]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-10   38.7   0.0    2.1e-09   37.2   0.0    1.6  1  dUTPase   dUTPase
  ------ inclusion threshold ------
       0.22   11.3   0.5       0.33   10.7   0.5    1.3  1  TSP_3     Thrombospondin type 3 repeat


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   2.3e-13   2.1e-09      16     107 ..      24     109 ..      18     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.3e-13
                                    EEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-E CS
                        dUTPase  16 yDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdR 95 
                                    y l++++   v+ ++  ++p + ++k+p+ + + i      +   +  ++gv+dsdyrGe+ v ++n t++d+ ++kgd 
  gene630|gene630|rna629|rna629  24 YKLYSSSSGRVPSRSGARIPAGFMMKIPKYYFGKI------QSTRIKKLGGVVDSDYRGEICVLVYNDTDEDFVYEKGDE 97 
                                    77788888888888888888888888888887776......3445667899***************************** PP

                                    EEEEEEEEBECG CS
                        dUTPase  96 iAqLifarilta 107
                                    i  +++ +i  +
  gene630|gene630|rna629|rna629  98 IGEMVICKISMP 109
                                    *****9888764 PP

>> TSP_3  Thrombospondin type 3 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5   3.7e-05      0.33       4      25 ..      71      95 ..      70      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.7e-05
                          TSP_3  4 DsDgvGDaC...dkDfDnDgvqddl 25
                                   DsD +G +C    +D+D+D v  + 
  gene630|gene630|rna629|rna629 71 DSDYRGEICvlvYNDTDEDFVYEKG 95
                                   9******************887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 801.93
//
Query:       gene63|gene63|rna63|rna63  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-09   36.3   0.0    4.5e-08   32.8   0.0    2.1  2  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.021   3.8e+02      20      36 ..      20      35 ..      16      39 .. 0.81
   2 !   32.8   0.0   2.5e-12   4.5e-08       3      63 ..      88     151 ..      86     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.021
                               HTTSCEEEEEEEEETTT CS
                      RRM_1 20 skfGpiksiklvrdetg 36
                               + fG+ ++i++v+ +t 
  gene63|gene63|rna63|rna63 20 KTFGDTSRIRVVK-STA 35
                               68**********9.455 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 2.5e-12
                                EESETTTSSHHHHHHHHHTTSCE..EEEEEEEE.TTTSEEEEEEEEESSHHHHHHHHHHHTTEE CS
                      RRM_1   3 VgnLppdvteeeLkelFskfGpi..ksiklvrd.etgkskgfafVeFeskedAekAlealngkk 63 
                                ++nLp d+t++ L+ + +   ++   s +lv + etg  +gfafV+ esk+dA + ++ l g  
  gene63|gene63|rna63|rna63  88 LSNLPLDMTRDRLYSIIKSHTSVffMSPNLVMNrETGVFRGFAFVTLESKDDAIRFIKDLRGVA 151
                                68*****************99997888888888**************************99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1100.45
//
Query:       gene631|gene631|rna630|rna630  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-23   83.6   0.1    1.4e-23   83.4   0.1    1.1  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.1   7.9e-28   1.4e-23       3     188 ..       6     193 ..       4     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 7.9e-28
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                    +Gt+v+ +k+kdgv+++ad+r ++g     +  ++++fk  d+++++++G+++D+++lv+ ++   ++ +    r i ++
  gene631|gene631|rna630|rna630   6 TGTSVISFKYKDGVMMGADTRGSYGRLAKYSG-IQRMFKFGDQTLIGISGEVSDMQYLVKTLSILTEEDN----RGIDPK 80 
                                    7**********************999996666.9*****************************9999998....777777 PP

                                    HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTT.......EEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH. CS
                     Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeg.......gpeLyqidpsGsyieekdavaiGsgseaaktalekey. 154
                                       ++++++++   +rs+ rp+ +s++++g   ++       +  L ++d  G+++  + ++++G gs+ a ++l++++ 
  gene631|gene631|rna630|rna630  81 -GYHKIVQRMLYS-ARSKIRPLNLSVCVGGTRCDDdsmthceRKMLGCVDRLGNFYFSD-VICTGIGSYIALPFLRSKVe 157
                                    .445566666543.45558**********998666678888889**************6.******************** PP

                                    ..STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                     Proteasome 155 ..kedltleeavelavkalkealerdklsgknieva 188
                                      ++++t+ee++ l++++++ + +rd+  +++i+++
  gene631|gene631|rna630|rna630 158 grEDEITREEGINLIEETMRILCYRDCNASNEIQIG 193
                                    *8899****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1682.75
//
Query:       gene632|gene632|rna631|rna631  [L=564]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-23   82.1   0.1    4.8e-23   81.1   0.1    1.5  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai
    1.1e-20   74.2   2.0    4.4e-11   42.7   0.0    3.5  3  Mlh1_C          DNA mismatch repair protein Mlh1 C-terminus
    6.5e-10   39.0   0.1    1.6e-09   37.7   0.1    1.7  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    0.00025   21.5   0.1    0.00051   20.5   0.1    1.6  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l


Domain annotation for each model (and alignments):
>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.1   1.1e-26   4.8e-23      29     118 ..     243     331 ..     226     332 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 1.1e-26
                                    EE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSSSSB-EEEEEEEESSGGEE-TSSTT----EETTHHCHHH CS
                 DNA_mis_repair  29 iskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpkgrypvvvLnleidpeevDvNvhPtKreVrfqdeeevie 108
                                    +s+p+++ +k    +lfvNgRlv s+e+k+++ ++Yk+l+p++r+p+++L+l+++ + vDvNvhP+KreV f de+ v++
  gene632|gene632|rna631|rna631 243 FSTPQFNLKK-GVFVLFVNGRLVVSQEMKETLFKVYKDLIPAQRQPFIYLELNVEKSMVDVNVHPSKREVLFADEKLVTQ 321
                                    5677777766.8899***************************************************************** PP

                                    HHHHHHHHHH CS
                 DNA_mis_repair 109 aieealkeal 118
                                     + + +++ l
  gene632|gene632|rna631|rna631 322 ELCKCITNRL 331
                                    ***9999877 PP

>> Mlh1_C  DNA mismatch repair protein Mlh1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.0   9.8e-15   4.4e-11      21      79 ..     396     454 ..     383     459 .. 0.92
   2 !   13.3   0.1   8.9e-06      0.04     122     188 ..     463     522 ..     457     529 .. 0.77
   3 !   16.0   0.1   1.4e-06    0.0061     234     270 .]     530     564 .]     524     564 .] 0.94

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9.8e-15
                                    HHHHHT-EEEEEEETTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHTT--EEEE-G-.- CS
                         Mlh1_C  21 teilanltfVGlvderlaliQhgtkLylvdygalskelfyqllLtdFgnfgeikLeepl 79 
                                    t ++++l +VG+ de  +l+Qhg +L+ ++++ l+ke++yq l++dFgnf++ k + pl
  gene632|gene632|rna631|rna631 396 TTFFRSLNYVGMKDEDTILVQHGSSLLCCKTAPLVKEYLYQTLINDFGNFERKKTSIPL 454
                                    679************************************************98877776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.9e-06
                                    HHHHHHHH--EETT-EEEEEEEE-STT----STTHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHS CS
                         Mlh1_C 122 aemLeeyFsieidedgellslPlllkgytpslekLPlfllrLateVdWeeekeCfetilrelAlfya 188
                                    +++L++yFsiei  +++++++P++   y+   e      l L+ +V+   e e +++i+++++++y+
  gene632|gene632|rna631|rna631 463 RALLDDYFSIEI-VEKHIVAIPVISTIYIDTPE------LWLGFDVKKGLEYETLKSIIETISTLYS 522
                                    899*********.6688********99986654......4577777777777777777777777777 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.4e-06
                                    HHHHHHHH---BGGGGG..GEEEEEEHHHHHHHS--- CS
                         Mlh1_C 234 lfpaikarllppksllkdgtvvevasledLYkVFERC 270
                                    lf+ ik+r++ + + l+  ++  v++l++LYk FERC
  gene632|gene632|rna631|rna631 530 LFNIIKRRMIGTPKALE--CFGLVTTLKELYKNFERC 564
                                    99***************..9***************** PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   0.1   3.5e-13   1.6e-09       5      99 ..      25     118 ..      20     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.5e-13
                    HATPase_c_3   5 kAlaelvdNsldAdaenvkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGi.GlklAsl 82 
                                      l e ++NsldA+++++ i+++ +     ++ ieDdG+G+ e+++     ++ ts+  ++++  sl ++G+ G  l+s+
  gene632|gene632|rna631|rna631  25 NILKETIENSLDANSTRIVIKIELD---GLSLIIEDDGDGIHENDFGLLCkQYCTSKLHKEEDLFSLPSYGFrGEALSSI 101
                                    5689*************99988886...48*****************96625777766666777779999999999**** PP

                    HATPase_c_3  83 slgkkltvitkkegess 99 
                                    s +++++v +kk+ ++ 
  gene632|gene632|rna631|rna631 102 SRCSRIKVKSKKRANEI 118
                                    **********9986554 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   1.1e-07   0.00051       4      63 ..      21      76 ..      18     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH CS
                      HATPase_c  4 krLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq 63
                                   +r + i+++ ++N++++  ++++i ++i+   d l++ +eD+G Gi ++d  +l + + +
  gene632|gene632|rna631|rna631 21 TRPYNILKETIENSLDA--NSTRIVIKIE--LDGLSLIIEDDGDGIHENDFGLLCKQYCT 76
                                   68899***********7..6777777777..449***************99955555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3361.94
//
Query:       gene633|gene633|rna632|rna632  [L=632]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-78  264.8   0.0    1.2e-78  264.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    9.4e-19   67.1   3.4      2e-18   66.0   3.4    1.6  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
    2.2e-16   60.6   0.3    4.2e-16   59.7   0.3    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
      0.039   13.7   0.0      0.075   12.8   0.0    1.5  1  Peptidase_C28  Foot-and-mouth virus L-proteinase
      0.089   12.7   0.0       0.26   11.2   0.0    1.8  1  DUF1967        Domain of unknown function (DUF1967)


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.6   0.0   3.5e-82   1.2e-78       2     422 ..      62     506 ..      61     507 .. 0.87

  Alignments for each domain:
  == domain 1  score: 264.6 bits;  conditional E-value: 3.5e-82
                                    HHHHHHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                    AMP-binding   2 eeqaaktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                    +++aa  pdkva+++   +ge  ++T++++ ++v r++a+L++ G++kgd+Va+++ +sp  v+++la++++G+v+  + 
  gene633|gene633|rna632|rna632  62 DRHAACDPDKVAIIYdgnDGESVRYTFKDVLDEVIRISAVLKEQGLEKGDTVAMYMAMSPYAVFSALACARLGLVHNAIF 141
                                    689999************99**********************99************************************ PP

                                    TTS-HHHHHHHHHHHTESEEE..E.TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS...... CS
                    AMP-binding  79 ptltaeelayiledseakvli..a.tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekae...... 148
                                     ++++  +a  l+ds+a++li  +  v ++  ++ l++++++le++ + +++ +  l++e+ l+e ++ ++k        
  gene633|gene633|rna632|rna632 142 GGFSPSSVALRLDDSDARLLIvqDvVVRQDStINFLENTRKALESRPTPVLVFDTLLNEEKILNELDGIKSKVLvwskvm 221
                                    *********************86255555666777777777777777777777777788878888777775542567889 PP

                                    ....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHH CS
                    AMP-binding 149 ....kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifglilelll 223
                                        +  + ++++++d ++ +YTSG+TG+PKG+++++ +++v+++ +   + +f+l++ddv+ +++++ +i+g+++ +++
  gene633|gene633|rna632|rna632 222 kkknEFIPCVPVNSEDRLFYLYTSGSTGRPKGIIHTTgGYMVYATLTS--KICFDLQKDDVFACTADIGWITGHTYVIYG 299
                                    999944466779*************************88889888885..56799999********************** PP

                                    HHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHH CS
                    AMP-binding 224 allsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrf 302
                                    +l++G t v++ ++++ ++  +l++++ek+++t ++++P+v++ l +  + +   ++++l slr++ ++gep+++++  +
  gene633|gene633|rna632|rna632 300 PLSNGITTVVFGGTPFyPSYLRLFKMVEKHRITQLYTAPTVIRTLRKYFSTTPLNHRYNLTSLRILGSVGEPINKQAYLW 379
                                    ****************66688999*********************77433332445669********************* PP

                                    HHHHHTC.EEEEEEEEGGGSSECEECHCTTTCT.STTS-BEE-TTEEEEEE..-TTTSCBEE..TTSEEEEEEEET..TS CS
                    AMP-binding 303 fralfge.evlegYGlTEttgvvtvlpleedkk.klgsvGkplpgvevkiv..Deetgepvp..dgeeGellvrgp..gv 374
                                    f++ f + +v+++Y++TE +g+++  p +   + k+  +  p+ g ev i+  D ++g  ++  d e G +l++g   g+
  gene633|gene633|rna632|rna632 380 FSENFNGcPVVDTYWQTESGGILIA-PIPYTVErKPECACLPFLGLEVVIAssDSKDGHVIEakDYELGRILFKGSwpGI 458
                                    *****999***************85.434444405555568999*******87777777775547777*******8668* PP

                                    -SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 375 mkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                    ++g l++ e+ ++ ++ + ++++ TGD g+ d  G++++ gR++d+i++
  gene633|gene633|rna632|rna632 459 ARGILGDAERFKKGYF-PyKGFYFTGDEGYKDSSGHVWVRGRADDVINV 506
                                    ***************9.7678**************************98 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   3.4   5.6e-22     2e-18       1      55 []       6      60 ..       6      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 5.6e-22
                                   HHHHHHHHHH-HHHHHHHHHCC.S--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N  1 ykelykeSiedpeaFWaeqake.ldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                   y++ly++S+ed e+FW+eqak  l+W+k f++v++  + ++ kWF+GG lN+cyNc
  gene633|gene633|rna632|rna632  6 YEKLYRKSVEDKEGFWGEQAKAlLKWDKIFNEVYNN-NFESSKWFDGGMLNACYNC 60
                                   99*******************99************9.66789************** PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.3   1.2e-19   4.2e-16       1      76 []     515     593 ..     515     593 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.2e-19
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..---.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea.leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    evEsa    p Vaeaa+v+ +de++G+al+ fVvlkd   s++ ++  L+  +r ++g++   k+++f++ +pkt++GK
  gene633|gene633|rna632|rna632 515 EVESAACMDPHVAEAAAVAESDEITGQALCFFVVLKDRkvSKEkVKTSLRVTLRNRIGKFVNAKNIYFCEGIPKTATGK 593
                                    8**********************************96554233599********************************9 PP

>> Peptidase_C28  Foot-and-mouth virus L-proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.1e-05     0.075     110     180 ..     241     310 ..     224     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                  Peptidase_C28 110 llytgigtasrpsevcmvdgtdmcladfhagiflkgqdhavfacvtsdgwyaiddedfypwtpnpadvlvf 180
                                     lyt  g++ rp  ++   g  m+ a + + i +  q   vfac +  gw +     +y    n    +vf
  gene633|gene633|rna632|rna632 241 YLYT-SGSTGRPKGIIHTTGGYMVYATLTSKICFDLQKDDVFACTADIGWITGHTYVIYGPLSNGITTVVF 310
                                    3555.48899****************************************987777777666666666665 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.4e-05      0.26      22      64 ..      72     116 ..      67     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.4e-05
                                    HHTTEEE-TGGGHHH.HHHHHHH.TTHHHHHHTTT--TT-EEEET CS
                        DUF1967  22 lvkqtnfeneeavrr.farrLkk.lGvedaLrkaGakeGdtVrIg 64 
                                    ++  ++ ++ e+vr+ f+++L + + +   L+++G ++GdtV ++
  gene633|gene633|rna632|rna632  72 VAIIYDGNDGESVRYtFKDVLDEvIRISAVLKEQGLEKGDTVAMY 116
                                    55567778889998779999987479****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 3621.38
//
Query:       gene634|gene634|rna633|rna633  [L=388]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-95  320.4   0.0    1.6e-95  320.2   0.0    1.0  1  PGK          Phosphoglycerate kinase
  ------ inclusion threshold ------
      0.056   13.2   0.0      0.092   12.5   0.0    1.3  1  Hydrolase_3  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.2   0.0   1.8e-99   1.6e-95       1     377 [.       4     375 ..       4     376 .. 0.92

  Alignments for each domain:
  == domain 1  score: 320.2 bits;  conditional E-value: 1.8e-99
                                    GGGS--TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-E.EEEEE--S--TT.S-GGG-SHHHHHHHHHH CS
                            PGK   1 vkdldlkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgak.vvllsHlgrpkg.ekeklslkpvaerLsel 78 
                                    +++++++gk v++RvDfNvp+++  ++ +d +i + lpTik+l +kg k v++ sHlgrpkg  ++++sl pv + L++l
  gene634|gene634|rna633|rna633   4 IDEVSIEGKSVFLRVDFNVPISN-LVVLNDFKIASVLPTIKFLHSKGPKkVIIGSHLGRPKGkYSKEFSLIPVYSVLKKL 82 
                                    68999****************87.**********************9877***********9556*************** PP

                                    HTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.....HHHHHHHHT-SEEEE--GGGTTS--TTTTH CS
                            PGK  79 lgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.....elakklasladvyVnDAFgtahrahaStvg 153
                                    lgke+ +    + +     +++  +   +lLeN+rf + Ee++d+     + ++ + + +d+ V DAFg+ hr+  S++ 
  gene634|gene634|rna633|rna633  83 LGKEIGVELA-FCD--IWDVENT-HHTWILLENLRFCSAEEREDDrdlveRYRNAFIKNMDIAVIDAFGCLHRECGSIQR 158
                                    *997766322.222..2334454.4899************99887655544888889999*****************998 PP

                                    HHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-SEEEEETCHHHHHHHH.TT-B-TTSS CS
                            PGK 154 iakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekvdkliigGgmantFlka.qgleigksl 232
                                        l+++ G+l++kE++ ++++ e  e+  ++ilGG+k+sdkik++++L ++  +l+++Gg+a+ F+k   g e+g+s+
  gene634|gene634|rna633|rna633 159 TG--LPSYSGFLVQKEIDSIREIAE--ENIDLMILGGKKISDKIKLLKSLGQRTKNLFVTGGLAFPFIKYiLGKEVGDSV 234
                                    77..4569***************97..555699************************************99********* PP

                                    --GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHHHHHHHCC-SEEEEES- CS
                            PGK 233 veedklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktielfaeaikeaktvvwnGp 312
                                    +ee + e +k++ e ++++g+++l+pvD++v +     +++v+++++ip++  a+Digp+tie++++++++a++ +wnGp
  gene634|gene634|rna633|rna633 235 CEEVSKEEVKKIHEICESHGTRMLFPVDFTVLH-----NGRVQKSRTIPSEGTAMDIGPETIEMLKKEVSRANVAFWNGP 309
                                    *******************************97.....47999************************************* PP

                                    SS-TTSGCCCHHHHHHHHHHHHHCH.TSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHCT CS
                            PGK 313 mGvfeiekfakGTkaiakalaeatk.galsivGGgdsaaaveklgladkvshvStGGgAsLelLeg 377
                                     Gvfe ++f++GT+a++++l + +k g  s++GGg++a a++ +g  d +++vStGGg +++lL++
  gene634|gene634|rna633|rna633 310 PGVFEEKNFSDGTRALVNILESLKKrGGKSFCGGGETAGAIKLFGNYDGFTYVSTGGGVLMKLLSN 375
                                    **********************999999***********************************975 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     1e-05     0.092      18     110 ..     170     268 ..     161     305 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1e-05
                                    HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE....ECTTTEEE...EE--B-HHHHHHHHHH CS
                    Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali....ddekgkil...ykstiskedvkeiikl 90 
                                    +k ++ i+++ e++i ++i  G ++++ +++l++lg  +  + + G+l     ++  gk +     +++ske+vk+i+++
  gene634|gene634|rna633|rna633 170 QKEIDSIREIAEENIDLMILGGKKISDKIKLLKSLGQRTKNLFVTGGLAfpfiKYILGKEVgdsVCEEVSKEEVKKIHEI 249
                                    78899*******************************9977777778877777644444444244578999********** PP

                                    HHHTTCEEEEEESSEEEEST CS
                    Hydrolase_3  91 lkennveillytedkvyvln 110
                                    +++++ ++l+   d ++ +n
  gene634|gene634|rna633|rna633 250 CESHGTRMLFP-VDFTVLHN 268
                                    ***99776644.33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 2182.82
//
Query:       gene635|gene635|rna634|rna634  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    0.00088   19.1   0.6     0.0013   18.5   0.6    1.2  1  DUF4201      Domain of unknown function (DUF4201)
      0.003   16.9   0.0      0.011   15.1   0.0    1.9  1  DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B


Domain annotation for each model (and alignments):
>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.6   1.5e-07    0.0013      82     155 ..      28     101 ..      18     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-07
                        DUF4201  82 lkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekve 155
                                    + + + ml++ +se + +  ++ ++++++r+ +++  +++d +   n+++k++++ll++ +Ll+  d+ +  ++
  gene635|gene635|rna634|rna634  28 NVKSEAMLKAISSEYRRRNGQRLADINSIREVVESFDAKKDTYNILNQEFKEKNELLKYKHLLEKIDRIVTPIY 101
                                    556678999******************************************************99998776665 PP

>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-06     0.011      80     178 ..     248     335 ..     239     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-06
                                    TSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHHHS-H CS
                    DNA_pol_E_B  80 kttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesntdver 159
                                    + +++l P ++D   s  lP++      ++ ++++ k +k ++NP  +e+ +  ++++++di+    + ++  +n     
  gene635|gene635|rna634|rna634 248 TPDIILCPDADDTYPS-FLPKE------IEVPREYGKFIKAASNPFILETYGYSIGVIREDIFRYKEQGTFIGKN----Y 316
                                    5567888888888888.77764......3444444456999*********************9988888888888....7 PP

                                    HHHHHHHHHHHTBS---SS CS
                    DNA_pol_E_B 160 lrklvktildqrhlaPlap 178
                                    ++ +++ il+q ++ P+  
  gene635|gene635|rna634|rna634 317 VDSFAREILSQHSFNPFGI 335
                                    9***************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2858.57
//
Query:       gene636|gene636|rna635|rna635  [L=199]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-13   50.4  12.7    2.4e-11   43.6  12.4    2.3  1  Bap31     Bap31/Bap29 transmembrane region


Domain annotation for each model (and alignments):
>> Bap31  Bap31/Bap29 transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6  12.4   1.4e-15   2.4e-11       1     130 [.       1     116 [.       1     124 [. 0.88

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.4e-15
                          Bap31   1 msLqytlvaalLvaeivvvllLvlPlpsavrkklfksllvsklsaklqialkillifllllflDavrrvrkvseeeeeaa 80 
                                    m +  +lv  + + e+ ++++++lP+ ++ +kk++k+  +sk+ + +  ++++l++++l++f+D+  +++  +++ +   
  gene636|gene636|rna635|rna635   1 MGITTQLVQSIVFGEMCMFTFMLLPISKNLKKKVIKLFQTSKFYRGFLHIIYVLFAMILIMFVDSAYKIYTGEDQINP-- 78 
                                    778899***********************************************************9999877655544.. PP

                          Bap31  81 aklkleaesevqarkFyaQRNlYlsGftLfLslvlrrlvtliselaklea 130
                                                  ++ a RN+Yl+GftLfL +++r ++  +  l + e+
  gene636|gene636|rna635|rna635  79 ------------FVLYQAERNMYLTGFTLFLGVIFRMFIRTMCLLFREEE 116
                                    ............46899*****************9988777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2105  (0.117408); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1171.92
//
Query:       gene637|gene637|rna636|rna636  [L=400]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-12   46.6   0.0    7.8e-12   45.4   0.0    1.7  1  SWIRM            SWIRM domain
    8.4e-11   41.9   0.1    1.5e-10   41.1   0.1    1.4  1  Myb_DNA-binding  Myb-like DNA-binding domain
    4.7e-05   23.6   0.1    9.9e-05   22.5   0.1    1.5  1  Myb_DNA-bind_6   Myb-like DNA-binding domain
     0.0051   16.7   0.5     0.0099   15.8   0.5    1.4  1  SWIRM-assoc_1    SWIRM-associated region 1


Domain annotation for each model (and alignments):
>> SWIRM  SWIRM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.7e-15   7.8e-12       4      89 .]      54     130 ..      51     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.7e-15
                          SWIRM   4 ewFdpdslhpiEkellselfngkdktpeeYlkiRnkiialyrenpkeyltvteaqkalkrrrltgidvnllsrihefLer 83 
                                    +wF+  +++p E++ +se+++   + pe+Y+++R+ ii++y e  ++ +tv +a  ++        d+ l+++i++f er
  gene637|gene637|rna636|rna636  54 NWFKKGEVSPLEQNGMSEVIQ--AIGPEKYVQSRDCIISSYEEG-NRPMTVGKAFTLVD------VDMGLMLKIFSFIER 124
                                    5*******************5..49******************7.677******77776......6************** PP

                          SWIRM  84 wGlINf 89 
                                    w++IN+
  gene637|gene637|rna636|rna636 125 WRIINY 130
                                    *****8 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.1   3.3e-14   1.5e-10       1      44 [.     220     263 ..     220     265 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.3e-14
                                    CSSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHH CS
                Myb_DNA-binding   1 rgkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrn 44 
                                    r+ W+  E+ lLle+++k+G+ W++++++++++t++qc  ++++
  gene637|gene637|rna636|rna636 220 RNMWSRKEEFLLLEGIRKFGDEWDSVSRYVQTKTKEQCVFHFLR 263
                                    678***************************************86 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.2e-08   9.9e-05       1      43 [.     223     264 ..     223     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.2e-08
                 Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknkL 43 
                                    W+  E+ +Ll++ +k+g++W ++++    +t++qc +++++ +
  gene637|gene637|rna636|rna636 223 WSRKEEFLLLEGIRKFGDEWDSVSRYVQTKTKEQCVFHFLR-I 264
                                    9**************************88**********99.3 PP

>> SWIRM-assoc_1  SWIRM-associated region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   2.2e-06    0.0099       9      66 ..     334     391 ..     329     394 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-06
                  SWIRM-assoc_1   9 akAkvlasqeereiqrlvaqlvetqlkKlelKLkqfeelEklleaerrelekqrqqLl 66 
                                     kA+   + e r+i+rl + + e+ l+K+ +K   ++el    ++ r el   r+ L 
  gene637|gene637|rna636|rna636 334 EKAREQRDLERRKIERLGSVICEALLNKIKMKIGTYKELYLSTQRVRSELVALRRGLA 391
                                    58999999***************************************99998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2495.93
//
Query:       gene638|gene638|rna637|rna637  [L=386]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-34  117.6   0.1    8.6e-34  116.7   0.1    1.5  1  eRF1_2          eRF1 domain 2
    9.4e-32  109.8   0.3    2.1e-31  108.7   0.3    1.6  1  eRF1_3          eRF1 domain 3
    1.4e-13   51.0   0.0    2.7e-13   50.0   0.0    1.5  1  eRF1_1          eRF1 domain 1
    6.7e-07   29.7   0.0    1.1e-06   29.0   0.0    1.3  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
      2e-05   24.9   0.0      3e-05   24.3   0.0    1.2  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.043   14.5   0.0        1.4    9.6   0.0    2.6  2  VWA_2           von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.1   2.9e-37   8.6e-34       1     133 []     138     266 ..     138     266 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 2.9e-37
                                    EEEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEE CS
                         eRF1_2   1 kvglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgi 80 
                                    k+g+iv+d++ + +++l+g+++++l++i v++PkKh+rGgqs+ rf+Rlr ek++ ++kkv+e a + fl++ + +++g+
  gene638|gene638|rna637|rna637 138 KYGFIVMDGHSTIFATLQGNVKTILQQIHVDLPKKHGRGGQSSVRFARLRVEKRNAYVKKVGEIAGNLFLTNCIMNVEGV 217
                                    69****************************************************************************** PP

                                    EEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                         eRF1_2  81 ilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                    ilag ++ k+e+ +   ld +   kvik+vd++ygge gln+++e  ++ lkd
  gene638|gene638|rna637|rna637 218 ILAGQSDLKNELSRV--LDSR--IKVIKTVDTNYGGEGGLNQAIELCEDILKD 266
                                    ************864..5554..589***********************9997 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   0.3   6.9e-35   2.1e-31       2     113 .]     270     367 ..     269     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 6.9e-35
                                    HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHH.HHHHHHHHHHH CS
                         eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelve.lieelvenvee 80 
                                    ++ekk+l++f++e+++++gk +++++e++++lemgAvetL+v+e+l + rd+               e ++++++en+++
  gene638|gene638|rna637|rna637 270 SKEKKVLQKFFNEINTESGKFCFTMKETMQCLEMGAVETLIVYENLSDVRDE---------------ElFVDWIAENYKN 334
                                    69**********************************************9854...............2279********* PP

                                    TT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                         eRF1_3  81 sgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                    +g++++++s++s+eG+q++++fgGi++iLRy+v
  gene638|gene638|rna637|rna637 335 FGCTLVFVSDKSAEGTQFIEGFGGIGGILRYRV 367
                                    *******************************97 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   9.1e-17   2.7e-13       2     125 ..      12     129 ..      10     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 9.1e-17
                                    EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT.. CS
                         eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd.. 77 
                                    kll+   d +++g++++++i++++++++ ++++++++++++++++++v+r          +v+ ++t+ + k++ + +  
  gene638|gene638|rna637|rna637  12 KLLRGlrDSRGNGTSMISIIIPPKDQISRVSKMLTDEYGTASNIKSRVNR---------LSVLGAITSAQSKLKQYSKtp 82 
                                    5555566999**************************************99.........9*************9888879 PP

                                    .SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHH CS
                         eRF1_1  78 .agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerL 125
                                     +g+  + G+v +e++   +++++++ +e+ +p++++ +  +++f+++ L
  gene638|gene638|rna637|rna637  83 pNGLGIFVGTVLMEQN---KEKKVSVGVEPIKPVNTSLYMcDSKFHVDDL 129
                                    99*************9...9******************999******987 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   3.6e-10   1.1e-06      16      92 ..     152     232 ..     138     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.6e-10
                        acVLRF1  16 gvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarll....aeesaevvlgGdrslvaevle 91 
                                    ++++g+  +  ++ + d  +++ +GG+S  RfaR r ++ +a +++v e a +l+      +++ v+l+G+  l +e+  
  gene638|gene638|rna637|rna637 152 ATLQGNVKTILQQIHVDLPKKHGRGGQSSVRFARLRVEKRNAYVKKVGEIAGNLFltncIMNVEGVILAGQSDLKNELSR 231
                                    566677777778889999*************************************4443355555*******99999876 PP

                        acVLRF1  92 d 92 
                                     
  gene638|gene638|rna637|rna637 232 V 232
                                    5 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     1e-08     3e-05       2     113 ..     125     238 ..     125     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1e-08
                 baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAella 81 
                                    ++  Ll++ ++  +yg +++d +   +++ ++      +++  + p+++ +gg+ s  rf+r + e++ +++k+v+e++ 
  gene638|gene638|rna637|rna637 125 HVDDLLALFEDEVKYGFIVMDGHSTIFATLQGNVKTILQQIHVDLPKKHGRGGQ-SSVRFARLRVEKRNAYVKKVGEIAG 203
                                    57889****************9887666666555555999999***9999****.************************* PP

                 baeRF_family10  82 klleerg...verlvlgGdeeetaalldrlpkalr 113
                                    +l+ ++    ve ++l+G+ + +++l   l  +++
  gene638|gene638|rna637|rna637 204 NLFLTNCimnVEGVILAGQSDLKNELSRVLDSRIK 238
                                    *****97777*************999999988765 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00046       1.4      28      93 ..     126     192 ..     116     202 .. 0.81
   2 ?    1.7   0.0      0.13     4e+02      66      99 ..     240     275 ..     216     286 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00046
                          VWA_2  28 veallkslp.gdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaaaLqlarkalkkrr 93 
                                    v +ll+ +  ++++g ++++++++++++l  + ++il+ ++   +k+ g   ++ +++ar  ++kr+
  gene638|gene638|rna637|rna637 126 VDDLLALFEdEVKYGFIVMDGHSTIFATLQGNVKTILQQIHVDLPKKHGRGGQSSVRFARLRVEKRN 192
                                    556666665489*****************************98888777777777777777777766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                          VWA_2  66 lrnleak....gggtnlaaaLqlarkalkkrr.kgekrv 99 
                                    ++         gg+  l++a++l++++lk+ + ++ek+v
  gene638|gene638|rna637|rna637 240 IKT---VdtnyGGEGGLNQAIELCEDILKDVKlSKEKKV 275
                                    333...244578899999999999999998887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2636.57
//
Query:       gene639|gene639|rna638|rna638  [L=247]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-09   37.4   0.7    2.6e-08   34.0   0.1    2.6  3  TPR_12    Tetratricopeptide repeat
    7.8e-07   28.8   3.2    2.5e-06   27.3   1.4    2.7  2  TPR_8     Tetratricopeptide repeat
      3e-06   26.9   1.6     0.0004   20.3   1.0    3.5  3  TPR_2     Tetratricopeptide repeat
      9e-06   25.3   3.1    2.4e-05   24.0   1.2    2.7  3  TPR_1     Tetratricopeptide repeat
    0.00092   19.1   0.7     0.0039   17.1   0.2    2.3  2  TPR_7     Tetratricopeptide repeat
    0.00099   18.6   1.1     0.0021   17.6   0.6    1.8  2  SNAP      Soluble NSF attachment protein, SNAP
      0.001   19.7   0.1        2.6    9.1   0.0    2.9  2  TPR_14    Tetratricopeptide repeat
     0.0017   17.8   0.6      0.011   15.2   0.0    2.6  3  SHNi-TPR  SHNi-TPR
      0.003   18.1   0.3       0.48   11.0   0.0    3.4  3  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.042   13.7   0.4       0.33   10.9   0.1    2.7  4  TPR_10    Tetratricopeptide repeat
       0.11   12.9   1.0        1.1    9.8   0.0    2.9  2  TPR_17    Tetratricopeptide repeat
       0.44   10.9   4.3        1.2    9.5   4.3    1.7  1  DUF349    Domain of Unknown Function (DUF349)


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.39   5.8e+02      17      33 ..       2      18 ..       1      37 [. 0.67
   2 ?   -1.1   0.0       1.6   2.4e+03      15      31 ..      19      35 ..      10      55 .. 0.77
   3 !   34.0   0.1   1.7e-11   2.6e-08       8      76 ..     117     185 ..     109     186 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.39
                         TPR_12 17 grydeAlellekaleia 33
                                   ++++eA+ +l +a++ +
  gene639|gene639|rna638|rna638  2 EDLAEAFPMLSEARASI 18
                                   56777777777776654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                         TPR_12 15 rlgrydeAlellekale 31
                                   ++g+++  +e++ + l+
  gene639|gene639|rna638|rna638 19 AQGEFEHGIEIYSEILD 35
                                   57888888888877775 PP

  == domain 3  score: 34.0 bits;  conditional E-value: 1.7e-11
                         TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                      +++++   ++ + l  + ++++++ +++++d   +a +++ L+ +y+ l+++e+ +e++e+a+ i++
  gene639|gene639|rna638|rna638 117 LQGEICLLNNNFRDGLHEFIECVAVMDKIYEKDCFRYADVYQSLANCYEFLEDFEKSREYYEKAIGIYK 185
                                    579999999********************************************************9998 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   1.7e+03       9      27 ..      15      33 ..      11      35 .. 0.79
   2 !   27.3   1.4   1.7e-09   2.5e-06       1      32 [.     154     185 ..     154     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                                   HHHHHTT-HHHHHHHHHHH CS
                          TPR_8  9 siylklgdyeeAkeyyeka 27
                                   ++ + +g++e  +e y + 
  gene639|gene639|rna638|rna638 15 RASIAQGEFEHGIEIYSEI 33
                                   6677899999999999765 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.7e-09
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldp 32 
                                    a++y+ l+++y+ l+d+e++ eyyeka+ + +
  gene639|gene639|rna638|rna638 154 ADVYQSLANCYEFLEDFEKSREYYEKAIGIYK 185
                                    689*************************9976 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.27     4e+02       8      28 ..      14      34 ..      10      36 .. 0.86
   2 ?    0.7   0.0       0.5   7.5e+02       4      26 ..     115     137 ..     112     143 .. 0.80
   3 !   20.3   1.0   2.7e-07    0.0004       1      28 [.     154     181 ..     154     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.27
                          TPR_2  8 GlayyklgdyeeAleafekAl 28
                                   ++a +++g++e  +e + + l
  gene639|gene639|rna638|rna638 14 ARASIAQGEFEHGIEIYSEIL 34
                                   788999*****9999998876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.5
                          TPR_2   4 lynlGlayyklgdyeeAleafek 26 
                                     + +G++++ ++++ + l+ f +
  gene639|gene639|rna638|rna638 115 RFLQGEICLLNNNFRDGLHEFIE 137
                                    5889**********998887755 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 2.7e-07
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAl 28 
                                    a+++  l+++y+ l d+e+ +e++ekA+
  gene639|gene639|rna638|rna638 154 ADVYQSLANCYEFLEDFEKSREYYEKAI 181
                                    688999*********************8 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.5   2.2e+03      13      28 ..      19      34 ..      16      35 .. 0.83
   2 ?   -2.4   0.0       3.4     5e+03       2      18 ..     113     129 ..     112     132 .. 0.76
   3 !   24.0   1.2   1.6e-08   2.4e-05       1      30 [.     154     183 ..     154     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                                   HTT-HHHHHHHHHHHH CS
                          TPR_1 13 klgkydeAleyyekAL 28
                                    +g+++  +e y++ L
  gene639|gene639|rna638|rna638 19 AQGEFEHGIEIYSEIL 34
                                   6999*99999998766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                                    HHHHHHHHHHHHTT-HH CS
                          TPR_1   2 kalynlGnayfklgkyd 18 
                                    ++ +  G +++ ++++ 
  gene639|gene639|rna638|rna638 113 RTRFLQGEICLLNNNFR 129
                                    56667899999999986 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 1.6e-08
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                    a+++  l+n+y  l+++++  eyyekA+ +
  gene639|gene639|rna638|rna638 154 ADVYQSLANCYEFLEDFEKSREYYEKAIGI 183
                                    7999***********************966 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.2   6.3e+03       2      14 ..     108     120 ..     108     120 .. 0.81
   2 !   17.1   0.2   2.6e-06    0.0039       2      35 ..     157     190 ..     156     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.2
                          TPR_7   2 LlnLarlysrlGd 14 
                                    ++ Lar+++ +G+
  gene639|gene639|rna638|rna638 108 YSMLARTRFLQGE 120
                                    5789**9998886 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 2.6e-06
                          TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                    +  La++y+ l d+e+  e+ye+++++ k+++++
  gene639|gene639|rna638|rna638 157 YQSLANCYEFLEDFEKSREYYEKAIGIYKAEQER 190
                                    678********************99888887765 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.82   1.2e+03      84     181 ..      10      33 ..       2      38 .. 0.53
   2 !   17.6   0.6   1.4e-06    0.0021     112     163 ..     152     202 ..      98     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.82
                                    HHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           SNAP  84 cykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAe 163
                                    ++++ +++ A                                                                      
  gene639|gene639|rna638|rna638  10 MLSEARASIAQ--------------------------------------------------------------------- 20 
                                    44444444444..................................................................... PP

                                    HHHHTT-HHHHHHHHHHH CS
                           SNAP 164 lsaelekyekAieiyekv 181
                                         +++e+ ieiy+++
  gene639|gene639|rna638|rna638  21 -----GEFEHGIEIYSEI 33 
                                    .....5555555555554 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.4e-06
                                    HHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           SNAP 112 raAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAe 163
                                    r A+ ++++a++ye   +d+ek+ e+YekA  +y+ e+   ++++ + ++ +
  gene639|gene639|rna638|rna638 152 RYADVYQSLANCYEFL-EDFEKSREYYEKAIGIYKAEQERKESEEEKNEICD 202
                                    458999********87.********************987777666665555 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0017       2.6       8      37 ..      14      44 ..       5      54 .. 0.79
   2 !    7.5   0.1    0.0055       8.3       3      32 ..     156     185 ..     154     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                         TPR_14  8 aeallalGdpdeAiallrralal.aPddaea 37
                                   a+a  a+G+++  i+++ ++l++ +Pdd+ +
  gene639|gene639|rna638|rna638 14 ARASIAQGEFEHGIEIYSEILDDmNPDDEKI 44
                                   667789****************779999763 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0055
                         TPR_14   3 allalaeallalGdpdeAiallrralalaP 32 
                                    +++ la  ++ l+d++++++++++a+  + 
  gene639|gene639|rna638|rna638 156 VYQSLANCYEFLEDFEKSREYYEKAIGIYK 185
                                    67889999*****************97665 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.1e-06     0.011       6      30 ..     117     141 ..     112     149 .. 0.84
   2 ?   -0.9   0.0      0.78   1.2e+03       1       9 [.     154     162 ..     154     163 .. 0.89
   3 ?   -2.4   0.1       2.3   3.5e+03      21      32 ..     167     178 ..     167     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.1e-06
                       SHNi-TPR   6 lLGEislEnenFpqAveDlrkaLeL 30 
                                    l+GEi+l n+nF + ++++ ++++ 
  gene639|gene639|rna638|rna638 117 LQGEICLLNNNFRDGLHEFIECVAV 141
                                    89********************975 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.78
                       SHNi-TPR   1 AdvydlLGE 9  
                                    Advy  L++
  gene639|gene639|rna638|rna638 154 ADVYQSLAN 162
                                    9*****995 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.3
                       SHNi-TPR  21 veDlrkaLeLre 32 
                                    +eD++k+ e++e
  gene639|gene639|rna638|rna638 167 LEDFEKSREYYE 178
                                    589999977766 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   1.6e+03       4      17 ..       1      14 [.       1      17 [. 0.85
   2 !   11.0   0.0   0.00032      0.48       2      39 ..      18      59 ..      17      61 .. 0.84
   3 ?    2.7   0.0      0.13   1.9e+02      24      47 ..     153     176 ..     141     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                         TPR_19  4 egdyaeAlalleqa 17
                                   ++d+aeA ++l++a
  gene639|gene639|rna638|rna638  1 MEDLAEAFPMLSEA 14
                                   5799*******998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00032
                         TPR_19  2 laegdyaeAlalleqalqe.dpknaearllL...Aeallalg 39
                                   +a+g ++  +++++++l++ +p+++ + +l+   A+al+++ 
  gene639|gene639|rna638|rna638 18 IAQGEFEHGIEIYSEILDDmNPDDEKIPYLYieyADALIKSS 59
                                   79**************97779998888886666699999975 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.13
                         TPR_19  24 naearllLAeallalgqldeAeal 47 
                                    +a++   LA+++  l ++++ ++ 
  gene639|gene639|rna638|rna638 153 YADVYQSLANCYEFLEDFEKSREY 176
                                    7888889*******9999998876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.8   5.7e+03      25      37 ..      23      35 ..      18      40 .. 0.72
   2 ?   -2.3   0.1       3.1   4.7e+03      16      26 ..      79      89 ..      77     101 .. 0.72
   3 ?   -2.3   0.0         3   4.5e+03      18      37 ..     128     147 ..     125     149 .. 0.69
   4 ?   10.9   0.1   0.00022      0.33       2      34 ..     154     186 ..     154     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.8
                         TPR_10 25 leealairrrllG 37
                                   +e+ ++i+ ++l 
  gene639|gene639|rna638|rna638 23 FEHGIEIYSEILD 35
                                   6778888888875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.1
                         TPR_10 16 grydeAealle 26
                                    ++++Ae++le
  gene639|gene639|rna638|rna638 79 EERKGAEDDLE 89
                                   56788888877 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3
                         TPR_10  18 ydeAealleealairrrllG 37 
                                    + + +  ++e++a+  ++++
  gene639|gene639|rna638|rna638 128 FRDGLHEFIECVAVMDKIYE 147
                                    55566778999998877766 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00022
                         TPR_10   2 AsslnNLanalrqrgrydeAealleealairrr 34 
                                    A  +  Lan +  + +++++++++e+a+ i+++
  gene639|gene639|rna638|rna638 154 ADVYQSLANCYEFLEDFEKSREYYEKAIGIYKA 186
                                    56688899999999*****************96 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.3   1.9e+03       9      25 ..      38      57 ..      35      61 .. 0.79
   2 ?    9.8   0.0   0.00075       1.1      12      33 ..     153     174 ..     152     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                         TPR_17  9 dPnn...adaynnLAelllk 25
                                   +P++   +++y ++A +l k
  gene639|gene639|rna638|rna638 38 NPDDekiPYLYIEYADALIK 57
                                   77777779999999999865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00075
                         TPR_17  12 nadaynnLAelllknGdlmtAr 33 
                                    +ad+y+ LA++++ + d+++ r
  gene639|gene639|rna638|rna638 153 YADVYQSLANCYEFLEDFEKSR 174
                                    79**************999877 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.3   0.00077       1.2      23      60 ..     185     222 ..     167     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00077
                         DUF349  23 eqdaereenlekKealieeaealaksttdwksatkrlk 60 
                                    + ++er+e  e+K+++++ + +l+++tt++k + ++l+
  gene639|gene639|rna638|rna638 185 KAEQERKESEEEKNEICDVITELLQKTTELKYKKEKLE 222
                                    4578899999***************9889998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1606  (0.0895755); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1495.79
//
Query:       gene640|gene640|rna639|rna639  [L=192]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1155.21
//
Query:       gene64|gene64|rna64|rna64  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-06   27.2   0.0      1e-05   26.0   0.0    1.7  1  PCI       PCI domain
  ------ inclusion threshold ------
      0.096   12.5   0.2        3.6    7.5   0.0    2.8  2  OST-HTH   OST-HTH/LOTUS domain


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.1e-09     1e-05       6     105 .]     239     342 ..     234     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.1e-09
                                HHHHHHHTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHH...CESEEEHHHHHHHH.TSSHHHHHHHHHHHH CS
                        PCI   6 llkalrsgnlsgfseelkdleeelladdglaqllesLekkvrerllrqvsk...iyssislerlakll.dlsvdevEkilvklI 85 
                                +++ +r g +++++ + ++ ++ + ++   + +   +   +  +l+ ++++     s++++++++++l d++ +e+ ++l+++I
  gene64|gene64|rna64|rna64 239 VVSVVRGGFYMEVDDAIRSASKGVVNHNLCRIISAHCPLICFNNLVNRTYLqygCDSRLDIQKISEALpDIDFKEIVCLLSNAI 322
                                556666666888888888888888888888899999999999999999999666669********98835888*********** PP

                                HTTSSSEEEETTTTEEEECS CS
                        PCI  86 rdgeirakidqesgivvfkk 105
                                ++g++r++i+   ++vvf+k
  gene64|gene64|rna64|rna64 323 ESGRLRGYISISRRVVVFSK 342
                                ******************86 PP

>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.027   2.4e+02      32      50 ..     181     205 ..     178     207 .. 0.85
   2 ?    7.5   0.0    0.0004       3.6      29      53 ..     216     240 ..     214     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.027
                                HHHHSST-S......TCCCTSSSHH CS
                    OST-HTH  32 kkkygksfd......prkyGfskLs 50 
                                 k+y +sf+       r +G++k++
  gene64|gene64|rna64|rna64 181 IKMYQESFKesylalERAFGYKKWR 205
                                5888889999999999*******86 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0004
                                HHHHHHHSST-STCCCTSSSHHHHH CS
                    OST-HTH  29 slykkkygksfdprkyGfskLseLl 53 
                                sl+ +k++k++  +++G+  Lse +
  gene64|gene64|rna64|rna64 216 SLLVNKFPKDIYLKRFGCDYLSEVV 240
                                6889******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2459.21
//
Query:       gene641|gene641|rna640|rna640  [L=639]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-29  102.0   0.0    6.7e-29  100.7   0.0    1.7  1  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
    4.8e-05   23.6   0.0    8.6e-05   22.8   0.0    1.3  1  CPSF100_C        Cleavage and polyadenylation factor 2 C-term
     0.0013   18.6   0.0      0.012   15.5   0.0    2.3  2  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
  ------ inclusion threshold ------
      0.022   14.0   0.4      0.097   11.9   0.0    2.2  3  Beta_lactamase3  Putative beta-lactamase-like family


Domain annotation for each model (and alignments):
>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   1.5e-32   6.7e-29       1     176 [.      22     177 ..      22     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.5e-32
                  Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGr 80 
                                    lLe+dnvkiL+++G   + +++ s+  ++   i + d+iLL+   +++ Ga+++++++    +    +v++++p++ LG+
  gene641|gene641|rna640|rna640  22 LLEIDNVKILVNCGAPYT-MDM-SIYTPILPQILSCDAILLTSFGVNYAGALPYILQNN---Y--YNKVFSSVPIKTLGK 94 
                                    89**************87.665.6788888888899****************9999874...3..369************ PP

                  Lactamase_B_6  81 vslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYav 160
                                    ++l ++ +  g + ++d+           f++i+++kYsQ++ ++    ++ + ayn+G+++GG+++kisk+ ekiv   
  gene641|gene641|rna640|rna640  95 ICLDEHLKGMGKELEVDTG---------LFERISEIKYSQPTVIN----NVEVCAYNSGNSIGGCLYKISKGAEKIVVGF 161
                                    **99999888777666655.........89***********8776....69***************************** PP

                  Lactamase_B_6 161 dwnhakeshLngaall 176
                                    ++nh+ke+hL+g+ ++
  gene641|gene641|rna640|rna640 162 NMNHRKENHLDGIGFS 177
                                    ************9875 PP

>> CPSF100_C  Cleavage and polyadenylation factor 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.9e-08   8.6e-05     103     168 ..     571     634 ..     561     635 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.9e-08
                      CPSF100_C 103 plfvGdlrLadLkkallssgikAEFrgeGtLvidgaVaVrKsakGrieiegvvletfyeVrkaiYe 168
                                     + +G  ++++L+++++++++++E + +G  +++++V +r +  G + i+g  +  fy+Vr+++Y 
  gene641|gene641|rna640|rna640 571 RMMIGHTDINELRRMIIERNMRVEQEENGL-LVEDSVWIRINPDG-LTIDGKDTGVFYAVRDVVYR 634
                                    679*********************999885.56889****99999.*******************7 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.7e-06     0.012       2      46 ..     456     499 ..     455     503 .. 0.89
   2 ?   -0.0   0.0      0.19   8.5e+02      15      26 ..     575     586 ..     575     592 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-06
                          RMMBL   2 ipvkarieeidfSgHadknellelirklkprnvilvHGeeeatsa 46 
                                    i++k ri+++d+ g +d n+ +++i++l+pr+++ + Ge + t++
  gene641|gene641|rna640|rna640 456 IELKYRIAKMDLMGISDLNSSKMIIETLSPRKLVCI-GEDRDTER 499
                                    899*****************************9998.66666665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
                          RMMBL  15 gHadknelleli 26 
                                    gH d nel+++i
  gene641|gene641|rna640|rna640 575 GHTDINELRRMI 586
                                    8********998 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.2e-05     0.097     130     171 ..     117     158 ..      94     172 .. 0.87
   2 ?   -2.0   0.1      0.39   1.7e+03     130     149 ..     288     307 ..     276     310 .. 0.85
   3 ?   -3.4   0.0       1.1   4.7e+03      93     128 ..     355     392 ..     353     396 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                Beta_lactamase3 130 nvkfiryneliyfddltieakaagtflGWvnyllevekkkil 171
                                    ++  i+y + + ++++++ a  +g ++G + y++  + +ki+
  gene641|gene641|rna640|rna640 117 RISEIKYSQPTVINNVEVCAYNSGNSIGGCLYKISKGAEKIV 158
                                    68889********************************99965 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.39
                Beta_lactamase3 130 nvkfiryneliyfddltiea 149
                                    ++ fi++ + i++ d++i +
  gene641|gene641|rna640|rna640 288 KIEFIEHYQNISEFDVMIAV 307
                                    799*******9999999986 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                Beta_lactamase3  93 lllrlkellslqvvyeeeeekqdlkive..eidierlk 128
                                    l++r  e ++++v    e++++d+  ve  e+d  +++
  gene641|gene641|rna640|rna640 355 LVERTDEKRGMNVSDVAEDVTEDVSDVEgaEADWSEIR 392
                                    77888888999999999999999999996666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 4111.35
//
Query:       gene642|gene642|rna641|rna641  [L=554]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-13   48.7   0.0    2.4e-07   29.7   0.0    2.3  2  Actin     Actin
     0.0029   16.7   0.1       0.54    9.2   0.0    2.2  2  PilM_2    Type IV pilus assembly protein PilM;
  ------ inclusion threshold ------
      0.034   12.9   0.0        4.8    5.9   0.0    2.4  2  MreB_Mbl  MreB/Mbl protein
      0.044   14.4   1.9      0.072   13.7   0.0    2.2  2  DUF5499   Family of unknown function (DUF5499)
       0.11   13.0   3.5        1.7    9.1   0.3    2.5  2  Imm42     Immunity protein 42


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   6.8e-11   2.4e-07       3     190 ..      19     190 ..      17     287 .. 0.80
   2 !   16.9   0.0   5.3e-07    0.0019     269     375 ..     430     518 ..     329     523 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.8e-11
                          Actin   3 evsavVlDnGssttraGyagedaPkavipslvgkprgrkveaklyvgdealtkrpelevrspvedGvvedwdaveelweh 82 
                                    ++ ++V+DnG++ ++aGy+g+  P++v+ +++ + +  +          ++++ ++ + + + +  vv++ ++ e ++++
  gene642|gene642|rna641|rna641  19 KTDTIVIDNGTYECKAGYSGD-GPQMVFKNVLYRHKAVS----------SIENFQGASPKTMFDGDVVTNFEVLEYIIDE 87 
                                    5789***************97.6********98888874..........45566677777778999*************9 PP

                          Actin  83 vlkeelkvdpeehpllltepplnppkqrekalEivfEkfkvpalylaksavls.afasgkstglvvDsGasvtsvvpVld 161
                                    +l+  lk + + + l++te+ ++p++  ++++  +f+ ++++ + ++ +   s +++   +  +++D+ +s t+   +  
  gene642|gene642|rna641|rna641  88 ILEY-LKPE-RLKNLIFTEKIFSPSH--TELVKFLFDVYGFERIQIGVDSYYSyLWNLDHEDCMIIDMSHSATTCLVIQA 163
                                    9977.5544.55689********987..689***************998887736788888999********99998888 PP

                          Actin 162 GyvLkkairrsdlgGkaLteqlkellssk 190
                                     +++   + + ++gGka  ++l ++l +k
  gene642|gene642|rna641|rna641 164 EQIVD--VYKINFGGKAAGDYLSAVLFNK 190
                                    88874..7788888888888877766554 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.3e-07
                          Actin 269 eiklgeeRfkvpEiLFdpsligsesaleeekskllgiselivaainacdvdlrpeLlanivvtGGnsllpglteRlekel 348
                                    +++++ +  k+pEi+F ps+ig ++          g+ e++ ++++      r+  ++++++tGG s ++g+  R+++e+
  gene642|gene642|rna641|rna641 430 RMNVNVDLLKIPEIIFSPSIIGLDQM---------GLTEIM-DSVS------RKYQVKKVLLTGGFSQIKGIDVRIKNEM 493
                                    56777778899**********99988.........999974.4444......6666799********************* PP

                          Actin 349 aqlaskgvkvkiiapeeerkysaWiGG 375
                                    +  +s   +v +i+++ ++   ++ G+
  gene642|gene642|rna641|rna641 494 RS-MSFVGEVEVIRAS-DPTSDSFKGA 518
                                    **.7777789999998.8888888776 PP

>> PilM_2  Type IV pilus assembly protein PilM;
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0026       9.5     180     215 ..     144     179 ..     112     194 .. 0.83
   2 !    9.2   0.0   0.00015      0.54     269     299 ..     464     494 ..     458     502 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0026
                         PilM_2 180 kvvaivdigasrttlsvlrdgkivYtreqafGgeql 215
                                    +  +i+d+++s tt  v+++++iv   + +fGg++ 
  gene642|gene642|rna641|rna641 144 EDCMIIDMSHSATTCLVIQAEQIVDVYKINFGGKAA 179
                                    44689*******************999******976 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00015
                         PilM_2 269 ssqqnkvdkilLaGGtaslpgleelleeelg 299
                                     s++ +v+k+lL+GG ++++g++  +++e+ 
  gene642|gene642|rna641|rna641 464 VSRKYQVKKVLLTGGFSQIKGIDVRIKNEMR 494
                                    57788*********************99875 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0    0.0037        13     147     180 ..     146     179 ..     141     191 .. 0.88
   2 ?    5.9   0.0    0.0013       4.8     275     314 ..     471     517 ..     449     526 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0037
                                    EEEEEE-SS-EEEEEEETTEEEEEEEES-SHHHH CS
                       MreB_Mbl 147 nmvvdiGggttevavislggivtsksvrvaGdel 180
                                     m++d+   +t + vi + +iv    +  +G++ 
  gene642|gene642|rna641|rna641 146 CMIIDMSHSATTCLVIQAEQIVDVYKINFGGKAA 179
                                    6**************************9999865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0013
                                    H-EEEESGGGGSBTHHHHHHHHH.......SS-EEE-SSTTTHHHHH CS
                       MreB_Mbl 275 rgivltGGgallkgldkllseet.......glpvkvaedpltcvakG 314
                                    + ++ltGG +++kg+d  +++e+       +++v+ a+dp++   kG
  gene642|gene642|rna641|rna641 471 KKVLLTGGFSQIKGIDVRIKNEMrsmsfvgEVEVIRASDPTSDSFKG 517
                                    6799***************9998222222235566666666555555 PP

>> DUF5499  Family of unknown function (DUF5499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       1.5   5.3e+03      17      50 ..     329     364 ..     318     393 .. 0.56
   2 ?   13.7   0.0     2e-05     0.072      16      77 ..     453     515 ..     448     519 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                        DUF5499  17 yfgkrkapdgvshk..dmvenifrsdkwrrmkgids 50 
                                    ++gk+ka     ++  +m  ++ r  k r+    + 
  gene642|gene642|rna641|rna641 329 FIGKKKAELQAVKRelEMRSKLRRDAKNRKTYEFQV 364
                                    557777764443331245555555556665555544 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2e-05
                        DUF5499  16 dyfgkrkapdgvshkdmvenifrsdkwrrmkgidsevkdelnr.qlrgevrklkksvyidddf 77 
                                    d +g  +  d vs+k  v++++ +  + ++kgid  +k+e+    + gev  ++ s    d f
  gene642|gene642|rna641|rna641 453 DQMGLTEIMDSVSRKYQVKKVLLTGGFSQIKGIDVRIKNEMRSmSFVGEVEVIRASDPTSDSF 515
                                    778888999*******************************97526889999888887666665 PP

>> Imm42  Immunity protein 42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.2     0.015        55      34     133 ..      71     160 ..      66     177 .. 0.72
   2 ?    9.1   0.3   0.00048       1.7      37     111 ..     223     295 ..     217     341 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.015
                          Imm42  34 dgeiypd.ykltttLrsevnslkdnksalinkkidkelfnldakeafkllvdaegaekgddeddleedeeesyrydlspe 112
                                    dg+ + + ++l++++   +++lk   + l+n  +++++f+    e++k+l d  g e+++   d +      y+y  +  
  gene642|gene642|rna641|rna641  71 DGDVVTNfEVLEYIIDEILEYLKP--ERLKNLIFTEKIFSPSHTELVKFLFDVYGFERIQIGVDSY------YSYLWN-- 140
                                    677777767788888888888888..99*************************7777777776665......444444.. PP

                          Imm42 113 eifDdgfyiFlvsndenirii 133
                                     +  +++ i  +s++  ++++
  gene642|gene642|rna641|rna641 141 -LDHEDCMIIDMSHSATTCLV 160
                                    .22233566666666666665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00048
                          Imm42  37 iypdykltttLrsevnslkdnksalinkkidkelfnldakeafkllvdaegaekgddeddleedeeesyrydlsp 111
                                     ++dy+++++L  e++ lk++  + + k+++  + +  + e+   l+++  a++  d ++++e++++ + y+ ++
  gene642|gene642|rna641|rna641 223 KIGDYSRNYFLDEELEALKEKPMDKKHKVYAAPSASNSMPEIDIGLLNT--ADTELDAERIKEKKKQKILYHSTL 295
                                    689*****************9999999**********************..899999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 3480.50
//
Query:       gene643|gene643|rna642|rna642  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-20   71.9  13.0    8.1e-20   71.1  13.0    1.4  1  vATP-synt_E  ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
      0.047   13.5   0.4       0.11   12.4   0.1    1.7  2  DUF1364      Protein of unknown function (DUF1364)


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1  13.0     9e-24   8.1e-20       1     199 []      15     187 ..      15     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 9e-24
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    vATP-synt_E   1 fIrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfee 80 
                                    fI+ eA ek +e k ka++e++ eka++ +ee+ +ie+ + +k+K++e ++  a  +  n  +++ L+ + ++l+e+ +e
  gene643|gene643|rna642|rna642  15 FINHEADEKIKEMKIKATQEYNTEKARIIKEETFRIENGFVMKQKEIEKKRVMAENSLINTYKQRYLEEKVKILDEIYNE 94 
                                    8*****************************************************************************98 PP

                                    HHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTTS CS
                    vATP-synt_E  81 aekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedfledv 160
                                    a   L+  +++      l  +Li q+ +k+  +e +v+++k+D+++v +       eyk++   + v +++ e       
  gene643|gene643|rna642|rna642  95 A---LSICSKEP-----LNPSLIAQCTEKIS-GEFVVYCNKKDKKVVLS-------EYKNA---E-VREMVSE------G 148
                                    7...66666666.....888*********96.689************99.......99996...3.3344444......6 PP

                                    SSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCHC CS
                    vATP-synt_E 161 lGGvvleaadgkikvnnTlearLelvleqllpeirkaLF 199
                                    +GGv+l ++d    v+n++ +rLe+v+ +  +ei k  F
  gene643|gene643|rna642|rna642 149 VGGVILCSKDCSTIVDNSFASRLETVKSSFEAEINKIIF 187
                                    9*********************************98776 PP

>> DUF1364  Protein of unknown function (DUF1364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.1   9.5e+03      69      85 ..      61      77 ..      56      81 .. 0.62
   2 ?   12.4   0.1   1.2e-05      0.11      11      62 ..     111     165 ..     110     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHH CS
                        DUF1364 69 aeeaelvhaegvlrTqe 85
                                    e+++ ++ ++++ T++
  gene643|gene643|rna642|rna642 61 IEKKRVMAENSLINTYK 77
                                   55666666666666765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.2e-05
                                    --S---TT....T----GGG-EEEE--------------SSSEEEE-H.HHHHHHTT CS
                        DUF1364  11 eCtvripg....vCNgnpeTtvlahyrlaglagvglksddllaafaCs.achdaidr 62 
                                    +Ct +i+g    +CN+  + +vl+ y+ a++   ++ s+++ +++ Cs +c   +d 
  gene643|gene643|rna642|rna642 111 QCTEKISGefvvYCNKKDKKVVLSEYKNAEVR--EMVSEGVGGVILCSkDCSTIVDN 165
                                    6888887766558*************777766..56899********9458877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1814  (0.101177); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1366.42
//
Query:       gene644|gene644|rna643|rna643  [L=362]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-34  118.5   0.0    2.3e-34  117.6   0.0    1.5  1  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
    3.8e-20   72.1   0.0    8.4e-20   71.0   0.0    1.6  1  MMR_HSR1        50S ribosome-binding GTPase
    1.7e-18   66.4   0.0    3.1e-18   65.6   0.0    1.5  1  TGS             TGS domain
    6.1e-10   38.8   0.1    1.8e-09   37.3   0.0    1.8  2  FeoB_N          Ferrous iron transport protein B
     0.0029   16.6   0.3      0.006   15.6   0.3    1.5  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
  ------ inclusion threshold ------
      0.085   12.8   0.0       0.16   11.9   0.0    1.3  1  Ploopntkinase3  P-loop Nucleotide Kinase3
        0.1   12.6   2.0        4.6    7.3   0.0    2.6  3  Dynamin_N       Dynamin family
       0.14   11.6   0.3       0.82    9.1   0.0    2.0  2  KTI12           Chromatin associated protein KTI12


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.0     1e-37   2.3e-34       2     106 .]     185     285 ..     184     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 1e-37
                   MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelarepn 81 
                                    gG++++++    +ld +tvk++l e++i naev+ ++ +t+Ddlidviegnr+Y+pc+yvlNKiD+is eeld l++ p+
  gene644|gene644|rna643|rna643 185 GGVTLIGD----SLDLATVKAVLGEFRISNAEVITNGPCTIDDLIDVIEGNRKYVPCIYVLNKIDSISVEELDLLHKIPH 260
                                    77777766....5899**************************************************************** PP

                   MMR_HSR1_Xtn  82 svviSaekelnldeLkekiweeLnL 106
                                    sv+++a+ ++n+d+L++k+w++L+L
  gene644|gene644|rna643|rna643 261 SVPVCAHLGWNFDSLLSKMWDYLDL 285
                                    ***********************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   3.7e-23   8.4e-20       1      99 [.      64     165 ..      64     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 3.7e-23
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adli 79 
                                    +v++vG p vGKStL+++ltg+ + v+++ +tT++++ g ++++g +i+++D+pG+iega+++kg gk++la+ + ++li
  gene644|gene644|rna643|rna643  64 RVGFVGFPSVGKSTLMSKLTGTFSAVAAYEFTTLTTVPGVLSYNGAKIQILDLPGIIEGAKDGKGRGKQVLAVARtCSLI 143
                                    69**********************************************************************99978*** PP

                                    EEEEETT....TTCSHHHHHHHHH CS
                       MMR_HSR1  80 llvvdas....eeklkpldeelee 99 
                                    ++++d+     ++  + +++ele 
  gene644|gene644|rna643|rna643 144 IVCLDVLkpvsHK--AVIERELEG 165
                                    *****65443211..123344444 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   0.0   1.4e-21   3.1e-18       1      60 []     286     360 ..     286     360 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.4e-21
                                    EEEEE.TTSSEEE......EETTB-.HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEEE CS
                            TGS   1 irvyt.PdGkvpd......lprgat.veDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIvt 60 
                                    +r+y  P+G+ +d      l++ +  v Df+++Ihr++  kf++AlV+G       q+vg +h L+d dvv+Iv+
  gene644|gene644|rna643|rna643 286 VRIYPkPKGQPIDyeepviLRSSRRsVSDFCNAIHRGILAKFKHALVWGtsvkhnpQKVGKEHILNDSDVVQIVK 360
                                    79*****************9999988***********************************************97 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   8.1e-13   1.8e-09       2      57 ..      64     119 ..      63     149 .. 0.94
   2 ?   -2.2   0.0       1.1   2.6e+03     106     122 ..     235     251 ..     227     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 8.1e-13
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE---- CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGi 57 
                                    +v +vG p vGk+tl+ +ltg+ + v+ +  +t     g l+++g +++i+DlPGi
  gene644|gene644|rna643|rna643  64 RVGFVGFPSVGKSTLMSKLTGTFSAVAAYEFTTLTTVPGVLSYNGAKIQILDLPGI 119
                                    5789***************************************************8 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                    SSEEEEEETHHHHHHTT CS
                         FeoB_N 106 vpvvlalnmideaekkg 122
                                    vp++ +ln+id ++ ++
  gene644|gene644|rna643|rna643 235 VPCIYVLNKIDSISVEE 251
                                    57889999999887665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   2.7e-06     0.006      25      54 ..      59      87 ..      56     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-06
                                   G-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                           MeaB 25 kaGraqvvGltGvPGaGkstlvealglelr 54
                                   k+G a +vG+ G+P +Gkstl+++l+ ++ 
  gene644|gene644|rna643|rna643 59 KTGIA-RVGFVGFPSVGKSTLMSKLTGTFS 87
                                   55554.89*****************98765 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     7e-05      0.16       8      31 ..      67      90 ..      63     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7e-05
                 Ploopntkinase3  8 lvGqPGaGkstlmaeltkgfdrsk 31
                                   +vG P  Gkstlm++lt +f+   
  gene644|gene644|rna643|rna643 67 FVGFPSVGKSTLMSKLTGTFSAVA 90
                                   69***************9998655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1         2   4.5e+03      70      89 ..       8      26 ..       3      53 .. 0.59
   2 ?    4.0   0.3      0.02        45       1      21 [.      65      85 ..      65     107 .. 0.80
   3 ?    7.3   0.0     0.002       4.6      97     142 ..     105     153 ..      99     169 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                                   HHHHHHHHHHHTSSSS--SS CS
                      Dynamin_N 70 eeieketekiagankgiskk 89
                                   +eie+e+++ + +nk++s++
  gene644|gene644|rna643|rna643  8 KEIENEMARTQ-KNKATSNH 26
                                   44555555444.44444444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.02
                                   EEEEEBTTTTHHHHHHHHHTS CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlge 21
                                   + +vG  S GKS+++ +L+g 
  gene644|gene644|rna643|rna643 65 VGFVGFPSVGKSTLMSKLTGT 85
                                   5789999**********9996 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.002
                                    ETTS-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-C CS
                      Dynamin_N  97 sllvkgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdl 142
                                    s +  ++ ++DlPG+++ +k  +   + v   ++ +++i++ ++  + +
  gene644|gene644|rna643|rna643 105 SYNGAKIQILDLPGIIEGAKDGKgrgKQVLAVARTCSLIIVCLDVLKPV 153
                                    5667899**********99999888888888888888777766665555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.16   3.7e+02     175     214 ..      10      49 ..       1      58 [. 0.63
   2 ?    9.1   0.0   0.00037      0.82       6      28 ..      67      90 ..      63     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                                    S--SSSTT-------HHHHHHHHHHHHHHHHHHH....HT CS
                          KTI12 175 lkpnqatlskplaeanflqeLdketseivkeileaqksav 214
                                     +++ a  +k++a++n l  L+++  +  +e+++  ks++
  gene644|gene644|rna643|rna643  10 IENEMARTQKNKATSNHLGILKAKLAKLRRELMSVSKSSS 49 
                                    3445556666777777777777777777777777555554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00037
                                   EE--TTSSHHHHHHHHHHHHHH.T CS
                          KTI12  6 ltGlPssGKstrakeLakalee.e 28
                                   + G+Ps+GKst+ ++L  ++++  
  gene644|gene644|rna643|rna643 67 FVGFPSVGKSTLMSKLTGTFSAvA 90
                                   79***************9999852 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2224.32
//
Query:       gene645|gene645|rna644|rna644  [L=407]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.001   18.4   8.2     0.0047   16.2   0.0    3.6  4  Sin_N     Sin-like protein conserved region


Domain annotation for each model (and alignments):
>> Sin_N  Sin-like protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1     0.017     3e+02       5      60 ..       3      52 ..       2      73 .. 0.71
   2 !    3.1   1.1    0.0024        43     173     214 ..     124     165 ..     117     181 .. 0.87
   3 !   16.2   0.0   2.6e-07    0.0047     278     373 ..     185     265 ..     173     276 .. 0.85
   4 ?   -0.4   0.0     0.029   5.2e+02     278     330 ..     355     404 ..     344     407 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.017
                          Sin_N  5 VveeidVylskslsd.kLyllQYPlrpadrpyddeqvkevrvkpkqqklelelaidt 60
                                   +v e+d+ ls+++++  Ly l  P +       + ++  vr+k++ + le+e+++ +
  gene645|gene645|rna644|rna644  3 IVSEYDIKLSRESEPvALYRL--PSSEG-----NLRIGTVRYKHQFKYLEIEMKLPK 52
                                   777888888777776555544..55544.....457788999999999999998755 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.0024
                          Sin_N 173 kfkraeterqkkareqSyallkkkeeeEpWiklevheqesse 214
                                    +f++aet ++k+ r +  +++ kk + E  +++e++ +e s+
  gene645|gene645|rna644|rna644 124 QFRKAETREEKEHRTKNINFQIKKMNLEGFTTMEYKRKEMSQ 165
                                    89*********************************9855444 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 2.6e-07
                          Sin_N 278 qvkalLkkakvlsfsklrelvapesdeavseeqlleaLqqvAvlvqGnWVvkselvypkdngvsaellaaaRdyiLllFs 357
                                    qv+    +akv++fs+l  l ++   +    + +  aL+++  +vqG+ ++ s++ y       ++ l+ +Rd iL lF+
  gene645|gene645|rna644|rna644 185 QVRNSIINAKVVNFSELILLYRD---Q----NVVKTALSRYTSFVQGRYIL-SNVFY-------EKSLHGIRDKILELFK 249
                                    999999**************988...2....34889************876.78888.......566************* PP

                          Sin_N 358 rdakvsrkelaaatkl 373
                                    + +kv  k++ a+++ 
  gene645|gene645|rna644|rna644 250 EREKVPCKDIYALVGD 265
                                    *****99999888765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.029
                          Sin_N 278 qvkalLkkakvlsfsklrelvapesdeavseeqlleaLqqvAvlvqGnWVvks 330
                                    ++  +L   k  + +++++++++e+ +    e+   +L +++ l   +WV+k 
  gene645|gene645|rna644|rna644 355 KIVEILVTKKSWKKTEMLRIAQNEPGK---IEDFFDVLCEYCELKGNVWVIKE 404
                                    788899999999999999999996666...569***********999***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2494.12
//
Query:       gene646|gene646|rna645|rna645  [L=434]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-05   21.6  16.5    7.9e-05   21.6  16.5    2.5  2  MAP65_ASE1   Microtubule associated protein (MAP65/ASE1 famil
  ------ inclusion threshold ------
      0.021   15.5   0.4      0.069   13.9   0.4    1.9  1  LTXXQ        LTXXQ motif family protein
      0.043   13.8   1.2         11    5.9   0.8    3.0  2  DUF1796      Putative papain-like cysteine peptidase (DUF1796
        0.7   10.2   5.4        1.1    9.6   0.9    3.5  3  TSC22        TSC-22/dip/bun family
        5.7    7.5   8.0         25    5.4   3.6    3.5  2  Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II


Domain annotation for each model (and alignments):
>> MAP65_ASE1  Microtubule associated protein (MAP65/ASE1 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?  -10.1  22.6         5   1.8e+04      33     220 ..     116     311 ..      39     311 .. 0.59
   2 !   21.6  16.5   2.2e-08   7.9e-05     296     395 ..     298     396 ..     271     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: -10.1 bits;  conditional E-value: 5
                                    HHHHHHHHHHHHHH........HHST-----....-SS--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MAP65_ASE1  33 neIaelraeasglk........siLheepvdvpqsekkelsLlqkkkkldtaleelrkekaerlaeflelleqlqklcee 104
                                     +  ++r+e++++k         ++   +++ +++e++++sL +  k+l++++++lr +k+   ++   l+e+l  ++++
  gene646|gene646|rna645|rna645 116 GRMITIREEIEKIKedifdvetMEIDCIELK-TMDEESCVSLANL-KELEMRRDFLRSKKEGMERNRDRLYEELCVFLSQ 193
                                    3344455555555554444434222222233.4668888888765.5688888888888888888888888888888888 PP

                                    HTS---SS--TSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHT----SHHHHHH......H CS
                     MAP65_ASE1 105 lgeeplsllidslpkleeleslrkhleelkeekerRleeikelkkq.......IkslmeeLglepktsieedl......l 171
                                    l ++ l+ +     k   le+l+k+    kee+erR  e+  l+ +       + + ++e +++++++    +      l
  gene646|gene646|rna645|rna645 194 LSKNDLDVA--IGQKIFVLEQLHKK---YKEEIERRDLEFRRLEIEirrregyLGTPCKEIEMDLSDENLGMMrsyekyL 268
                                    877333222..22333334444443...2334444444444444440000011555555555555555444337654432 PP

                                    CT-TTTS-....TSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     MAP65_ASE1 172 kesednskklkpltretikkLkllkkeleeqksereeklkdlrekikeL 220
                                      +e++++      +e+ +k ++++kel ++  e++e  k+ +e i+e+
  gene646|gene646|rna645|rna645 269 -REEQERQ-----LDEIYEKKRSQLKELLDIFGENMEDYKKTEEGIEEM 311
                                    .2333333.....478888888888888888888888888888888775 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.2e-08
                                    STSS-....SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-GGGGTSSTSH..HHHHHHHHHHH CS
                     MAP65_ASE1 296 feele....deelLelhElelkqLkeelesnKeilelvekfeslwedeeeLEakskDpsRlnnRGghkiLLkEEKeRkri 371
                                    +   e    +ee  e + + +++L+++     +i +l+ek+++l+++++e+E+ ++Dp Rl  R +   LL EEK R   
  gene646|gene646|rna645|rna645 298 M---EdykkTEEGIEEMAMTISKLESKKDLFLSIRSLMEKRSELISKMSEFEKIASDPKRLF-RSSL-QLLSEEKFRNSA 372
                                    2...24447888888888******************************************98.5555.6*********** PP

                                    HHHHHHHHHHHHHHHHHHHHHCTS CS
                     MAP65_ASE1 372 skhlPkveqeLtekveaweeefgr 395
                                      +l ++e+++ +++ ++e++f++
  gene646|gene646|rna645|rna645 373 YPNLIRIEEAIFKLLDEYEDRFEK 396
                                    *********************976 PP

>> LTXXQ  LTXXQ motif family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   1.9e-05     0.069      15      58 ..     268     317 ..     267     349 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                    --HHHHHHHHHHHHHHHHHS---.............-HHHHHHHHHHH..TSSS--H CS
                          LTXXQ  15 LtdaQkaalkalaeaaraeakpl...........kakkeemramrkkv..laanfde 58 
                                    L ++Q+++l+++ e+ r++ k+l           k+++e        +  +a+++++
  gene646|gene646|rna645|rna645 268 LREEQERQLDEIYEKKRSQLKELldifgenmedyKKTEEG-------IeeMAMTISK 317
                                    78*********************88884444444444444.......3445555443 PP

>> DUF1796  Putative papain-like cysteine peptidase (DUF1796)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0046        17      25      53 ..      31      59 ..       7     115 .. 0.85
   2 ?    5.9   0.8    0.0031        11      92     153 ..     288     351 ..     186     363 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0046
                        DUF1796 25 slPfDwvrssldglveliangFssfldpe 53
                                     PfD++ s +++++e +   F+s l+++
  gene646|gene646|rna645|rna645 31 DHPFDYFDSEIECIIESVDAVFKSILSRR 59
                                   68**********************99875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0031
                        DUF1796  92 fthhDl.anneevkakfrrrirrfeallsspe.rkvlFirtviaenkakellellpqleqalre 153
                                        D+  +n e+++k +++i++    +s+ e +k lF+ + + ++k++el++ ++++e++ ++
  gene646|gene646|rna645|rna645 288 KELLDIfGENMEDYKKTEEGIEEMAMTISKLEsKKDLFLSIRSLMEKRSELISKMSEFEKIASD 351
                                    55555556789999999********99999776999***9999999999********9998655 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.9   0.00031       1.1       9      27 ..     118     136 ..     117     152 .. 0.89
   2 ?   -1.4   0.0      0.83     3e+03      21      36 ..     306     321 ..     303     330 .. 0.74
   3 ?   -1.1   0.0      0.69   2.5e+03      19      34 ..     331     346 ..     326     351 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                          TSC22   9 mfAVrEeVevLkekIkeLe 27 
                                    m+++rEe+e  ke I + e
  gene646|gene646|rna645|rna645 118 MITIREEIEKIKEDIFDVE 136
                                    99*************9975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.83
                          TSC22  21 ekIkeLeernseleeE 36 
                                    e I e+ +++s+le+ 
  gene646|gene646|rna645|rna645 306 EGIEEMAMTISKLESK 321
                                    4577888888888765 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.69
                          TSC22  19 LkekIkeLeernsele 34 
                                    L ek  eL++++se e
  gene646|gene646|rna645|rna645 331 LMEKRSELISKMSEFE 346
                                    4555667777777766 PP

>> Arc_PepC_II  Archaeal Peptidase A24 C-terminus Type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.56     2e+03      36      36 ..     222     222 ..     154     284 .. 0.63
   2 ?    5.4   3.6    0.0071        25      10      48 ..     283     336 ..     279     425 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.56
                    Arc_PepC_II  36 k 36 
                                    +
  gene646|gene646|rna645|rna645 222 E 222
                                    2 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0071
                    Arc_PepC_II  10 yrvkvkellkkflflleefeekdgkikrkfisvekeld...............e 48 
                                    +r ++kell+ f+  +e++++++++i+++ ++++k  +               +
  gene646|gene646|rna645|rna645 283 KRSQLKELLDIFGENMEDYKKTEEGIEEMAMTISKLESkkdlflsirslmekrS 336
                                    577899999****************99999988753334556666666665552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1281  (0.0714485); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 2416.53
//
Query:       gene647|gene647|rna646|rna646  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 1225.46
//
Query:       gene648|gene648|rna647|rna647  [L=457]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-26   94.4   0.5    1.9e-26   93.8   0.5    1.3  1  Metallophos  Calcineurin-like phosphoesterase
    5.8e-05   22.9   0.2       0.33   11.2   0.1    3.0  3  TPR_2        Tetratricopeptide repeat
    0.00099   18.8   1.3       0.31   10.9   0.1    3.2  3  TPR_1        Tetratricopeptide repeat
     0.0024   18.1   0.0        2.9    8.3   0.0    2.7  2  TPR_12       Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.03   14.6   0.7        7.2    7.0   0.4    2.6  2  PRD          PRD domain
      0.066   13.9   0.1    1.2e+02    3.7   0.0    3.7  3  TPR_6        Tetratricopeptide repeat
       0.33   11.3   3.1         13    6.3   0.1    3.9  3  PPR          PPR repeat


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.5   7.4e-30   1.9e-26       3     201 ..     193     384 ..     191     387 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 7.4e-30
                                    EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-TTS..... CS
                    Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGNHe..... 75 
                                    +lv+gD+H     gq+ d++ +l+++ + e++ ++   GD+vdrg  ++e+ ++ l++ ++ +p +v+l++GNHe     
  gene648|gene648|rna647|rna647 193 VLVFGDTH-----GQYFDVVGVLNKVFDGERIFIFN--GDYVDRGthSVEN-FVLLISLKILFPGKVHLTRGNHElmdin 264
                                    8*******.....*************7776666666..*******999999.88999*********************** PP

                                    ...CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.HHHH CS
                    Metallophos  76 ...gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg.dewl 151
                                       gf +e+++ky+++   + ++++++ vf +lp++ +++   kv++ hGg p+    ++k++ l+   + ++   de+l
  gene648|gene648|rna647|rna647 265 kayGFFDEVKRKYPFSS--GSVYQKFQAVFRALPISIIVNE--KVFITHGGLPGT---PTKIDELQESYRMTDAHtDELL 337
                                    **************999..89********************..********8888...6666666666666666669999 PP

                                    HHHHHHTTCSEEEEEESSESS.........CSSSCSCCHHHHHHHHHHTTESEEEEESS CS
                    Metallophos 152 kdlekrekadwvivlgHsply.........rgsgylfgdealedllkkygvdlvisGHt 201
                                    k             + +s ++         r++g +fg + ++ +l+ +g+dl +++H+
  gene648|gene648|rna647|rna647 338 KG------------FLWSDPEeitgieeskRRAGVVFGIDIVDQFLQGNGLDLLVRSHQ 384
                                    99............5555555588888888****************************8 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00013      0.33       5      27 ..      10      32 ..       9      34 .. 0.90
   2 !    8.3   0.0    0.0011       2.7       4      34 .]      57      87 ..      54      87 .. 0.90
   3 ?   -2.2   0.0       2.5   6.5e+03       3      19 ..      89     105 ..      88     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                          TPR_2  5 ynlGlayyklgdyeeAleafekA 27
                                    + +++++k+++ +eAl++++k+
  gene648|gene648|rna647|rna647 10 RQEANSLFKNQRIDEALDLYKKS 32
                                   5789****************996 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                          TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                                    yn+  +yyk++++ + l +  ++l+ + n+
  gene648|gene648|rna647|rna647 57 AYNICIVYYKRKNFPKSLTFGLESLKRCKND 87
                                   6999****************99999998875 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.5
                          TPR_2   3 alynlGlayyklgdyee 19 
                                    +l+ +  +y+++g ++e
  gene648|gene648|rna647|rna647  89 VLHKICTIYLRMGMLKE 105
                                    67888899***998876 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00012      0.31       8      26 ..      13      31 ..       9      33 .. 0.92
   2 !    5.0   0.0    0.0088        23       5      21 ..      58      74 ..      56      76 .. 0.90
   3 ?   -1.2   0.0       0.8     2e+03       7      19 ..      93     105 ..      88     112 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                   HHHHHHTT-HHHHHHHHHH CS
                          TPR_1  8 GnayfklgkydeAleyyek 26
                                   +n +fk+++ deAl+ y+k
  gene648|gene648|rna647|rna647 13 ANSLFKNQRIDEALDLYKK 31
                                   899***************9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0088
                                   HHHHHHHHHTT-HHHHH CS
                          TPR_1  5 ynlGnayfklgkydeAl 21
                                   yn+  +y+k +++ + l
  gene648|gene648|rna647|rna647 58 YNICIVYYKRKNFPKSL 74
                                   9************9976 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.8
                                    HHHHHHHTT-HHH CS
                          TPR_1   7 lGnayfklgkyde 19 
                                    +  +y+++g+++e
  gene648|gene648|rna647|rna647  93 ICTIYLRMGMLKE 105
                                    5567888887765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1     0.003       7.7       8      29 ..      11      32 ..       4      33 .. 0.79
   2 !    8.3   0.0    0.0011       2.9       5      63 ..      56     112 ..      52     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                         TPR_12  8 nlaavlrrlgrydeAlelleka 29
                                   + a+ l++ +r deAl+l++k+
  gene648|gene648|rna647|rna647 11 QEANSLFKNQRIDEALDLYKKS 32
                                   5588999999999999999987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                         TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryee 63 
                                    +++n+  v+++++++ ++l++  ++l ++++   +  +  +t++  +g+l ++ + ye+
  gene648|gene648|rna647|rna647  56 LAYNICIVYYKRKNFPKSLTFGLESLKRCKND--KVLHKICTIYLRMGMLKEYVEMYEQ 112
                                    4559*************************766..5555799999999988877777765 PP

>> PRD  PRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4    0.0028       7.2      28      64 ..     122     157 ..     102     159 .. 0.77
   2 ?    5.1   0.0     0.011        27      41      84 ..     265     308 ..     253     309 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0028
                                    HHHHHHHHHTT.--HHHHHHHHHHHHTHHHHHHHHHHH CS
                            PRD  28 lkfaieRlkeg.itienplleeikekypkefeiakeil 64 
                                    +k +++R+k g +tie  l + i    +k++e+ kei 
  gene648|gene648|rna647|rna647 122 IKVLLNRMKLGsQTIEKYLENRITL--EKLYEMSKEIS 157
                                    8899*******55555555555555..*********96 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTST--HHHHHHHH CS
                            PRD  41 ienplleeikekypkefeiakeileeleeeldielpedEiayla 84 
                                      + +++e+k+kyp     + + ++ + ++l i++  +E ++++
  gene648|gene648|rna647|rna647 265 KAYGFFDEVKRKYPFSSGSVYQKFQAVFRALPISIIVNEKVFIT 308
                                    556689************************************98 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.11   2.7e+02       7      25 ..      13      31 ..      11      31 .. 0.84
   2 ?    3.0   0.0     0.076     2e+02       9      29 ..      96     116 ..      89     117 .. 0.89
   3 ?    3.7   0.0     0.046   1.2e+02      12      32 ..     260     279 ..     257     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.11
                                   HHHHHHHHHHHHHHHHHHH CS
                          TPR_6  7 alsyrklgdtdkAlealer 25
                                   a s++k ++ d+Al+++++
  gene648|gene648|rna647|rna647 13 ANSLFKNQRIDEALDLYKK 31
                                   67899955********986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.076
                                    HHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   9 syrklgdtdkAlealerlike 29 
                                     y+++g   + +e++e+++++
  gene648|gene648|rna647|rna647  96 IYLRMGMLKEYVEMYEQIVDK 116
                                    699999***********9986 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.046
                                    HHHHHHHHHHHHHHHHHH-TT CS
                          TPR_6  12 klgdtdkAlealerlikeYPd 32 
                                     + d  kA   ++++ ++YP 
  gene648|gene648|rna647|rna647 260 LM-DINKAYGFFDEVKRKYPF 279
                                    47.8899*************6 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.005        13       8      25 ..      14      31 ..      13      37 .. 0.87
   2 ?    2.0   0.1      0.12   3.1e+02      10      31 .]      97     118 ..      95     118 .. 0.89
   3 ?    0.4   0.0       0.4     1e+03      15      29 ..     262     276 ..     260     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.005
                            PPR  8 sgycknGkleeAlelfke 25
                                   +++ kn +++eAl+l+k+
  gene648|gene648|rna647|rna647 14 NSLFKNQRIDEALDLYKK 31
                                   6899************98 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                            PPR  10 ycknGkleeAlelfkeMkekGi 31 
                                    y + G+l+e +e+++++++k +
  gene648|gene648|rna647|rna647  97 YLRMGMLKEYVEMYEQIVDKSC 118
                                    99*************9998876 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.4
                            PPR  15 kleeAlelfkeMkek 29 
                                    ++ +A  +f+e k+k
  gene648|gene648|rna647|rna647 262 DINKAYGFFDEVKRK 276
                                    5789*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3232.86
//
Query:       gene649|gene649|rna648|rna648  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-17   63.9   0.2    2.3e-17   63.0   0.2    1.5  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    1.3e-08   35.3   0.5      2e-08   34.7   0.5    1.3  1  Histone        Core histone H2A/H2B/H3/H4
  ------ inclusion threshold ------
       0.03   13.8   0.4      0.061   12.9   0.4    1.5  1  Corona_NS1     Coronavirus nonstructural protein NS1


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.2   3.8e-21   2.3e-17       2      65 .]      38     101 ..      37     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 3.8e-21
                                    XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                  CBFD_NFYB_HMF   2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65 
                                     LP+ar+k++mk  +++r++a+++++l++ ++e fieel+ +A+  ++++kr+++++ ++  Av
  gene649|gene649|rna648|rna648  38 NLPLARIKRLMKIEEGVRMVASEVPVLFSMITEKFIEELTLRAWINTEENKRRILQKSDLTAAV 101
                                    69**********************************************************9998 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.5   3.3e-12     2e-08      60     129 ..      34     102 ..      15     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.3e-12
                                    XXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                        Histone  60 lliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                    l+  +lp aR ++ ++k e+   ++ +e ++++ +++E +++el+ +A++ ++++KR+ +++ D+ +A++
  gene649|gene649|rna648|rna648  34 LKDLNLPLAR-IKRLMKIEEGVRMVASEVPVLFSMITEKFIEELTLRAWINTEENKRRILQKSDLTAAVK 102
                                    677889****.9*****9999***********************************************97 PP

>> Corona_NS1  Coronavirus nonstructural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4     1e-05     0.061      13      22 ..     117     126 ..     102     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                     Corona_NS1  13 DDILHPsNHV 22 
                                     D LHP+NH 
  gene649|gene649|rna648|rna648 117 NDLLHPFNHL 126
                                    69*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1445.32
//
Query:       gene650|gene650|rna649|rna649  [L=397]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-11   42.5   0.0    8.9e-11   41.9   0.0    1.3  1  DHH       DHH family
    4.4e-09   36.6   0.0    9.6e-09   35.6   0.0    1.6  1  DHHA2     DHHA2 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   9.9e-15   8.9e-11       3      85 ..      25     184 ..      23     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 9.9e-15
                                    EE.E-ECSSSHHHHHHHHHHHH.......................................................... CS
                                    xx.xxxxxxxxxxxxxxxxxxx.......................................................... RF
                            DHH   3 li.vghknpDtDsigSaialan.......................................................... 23 
                                    l+ +g + +D+Ds+ S++++a+                                                          
  gene650|gene650|rna649|rna649  25 LVaMGNEACDLDSFISSLVVAYaegavhvvnmrkevfvakgeimwvckefgidvddliflvkptlhfsskarkigayfds 104
                                    5559************9999997788888888888887777777777777777777777777777777777776666666 PP

                                    ..............CECS--TCGGCGCCHHCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHH..... CS
                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                            DHH  24 ..............llvDhneksqavegeakeeaedviiiDHHrlgeefetlapilflnepvgstaeivaellee..... 84 
                                                  ll Dhn+++++ e+     +e+ +iiDHH ++++++   + ++++ +vgs+ ++v ++l e     
  gene650|gene650|rna649|rna649 105 gekeypvcgkkiklLLTDHNQPAEELED-----CEIELIIDHHMVERSVSPA-KRIYIDLDVGSATTLVSKYLGEdlark 178
                                    666666666666666*******999855.....************9555555.788999************998877665 PP

                                    .....T CS
                                    .....x RF
                            DHH  85 .....k 85 
                                         +
  gene650|gene650|rna649|rna649 179 nhslpS 184
                                    444441 PP

>> DHHA2  DHHA2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.1e-12   9.6e-09       2     140 ..     246     380 ..     245     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.1e-12
                                    HHHHHHT-STTS-HHHHTTTTEEEEE.ETTEEEEEEEEEES-HHHHHT.THHH...........HHHHHHHHH.HHT-SE CS
                          DHHA2   2 elkkaksdlsglsledllrrDyKeftgeggvkvgiasvpvslsewleekrkge...........llaalekfaeerkldl 70 
                                    +lk+a+++ sg  +  +l++D+K+f+ +++  +g ++v  ++++w +++ ++            l+ ++e+f+++ +ld+
  gene650|gene650|rna649|rna649 246 ALKNARKNDSGQETGLILQKDFKTFH-YRDFFFGGSTVKYPFEDWADREGRNIsripeekagiaLMVEIESFRKAMGLDF 324
                                    6899**********************.*********************66555********************9999*** PP

                                    EEEEEE.....ETTTEEEEEE...STTHHHHHT---BT.EEET...............T---HHHHTHHHH CS
                          DHHA2  71 lvlmttfeeegdirrelllaaldaaeklaealekasee.leLeewkegaewrrvykqgnvkasRKqvaPll 140
                                    +++ t      +  r +++a + +a+++a++ +++s +  +Le           y  +  + +RK ++P +
  gene650|gene650|rna649|rna649 325 FFVATK----AKGSRNIIFANFPFARQIAAKNQMKSIDyKGLE-----------YYSASKNLTRKLLVPEI 380
                                    ******....789999999988777776664444433436666...........66667788888888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2357.67
//
Query:       gene65|gene65|rna65|rna65  [L=265]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-09   36.7   0.0    1.6e-05   24.4   0.0    2.3  2  HAT_KAT11        Histone acetylation protein
  ------ inclusion threshold ------
       0.21   10.7   0.0       0.34   10.0   0.0    1.2  1  PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subuni


Domain annotation for each model (and alignments):
>> HAT_KAT11  Histone acetylation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.8e-09   1.6e-05     125     169 ..      66     125 ..      40     142 .. 0.74
   2 !   10.8   0.0   2.4e-05      0.22     218     272 ..     143     190 ..     124     251 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-09
                  HAT_KAT11 125 v...............klsLFtraqdqYLFPnssknpkKHvLddkgLlkWWikvldkilr 169
                                                  ++F  ++++Y+F +ss n++K +  +++Ll+ Wi v ++i  
  gene65|gene65|rna65|rna65  66 YarefimsilrvlspdLSCCFSIPKNEYIFNGSSLNKEKKIRGPRELLEYWIGVFEEIYD 125
                                0444455555555555569***********************************999983 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 2.4e-05
                  HAT_KAT11 218 avyeiPlFpDDPKgrfleelieEgrlksvsldqfweelafrqEfslgrlvgfigl 272
                                 + ei +F+DDPK r  ++ +         l++    l  r +f+ g+lv    +
  gene65|gene65|rna65|rna65 143 HMDEIVYFEDDPKDRLRKHFVGG-------LEEMFAALLCRTDFTNGSLVYGRSC 190
                                5679***************9887.......7777777777777777777766666 PP

>> PHA_synth_III_E  Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   3.7e-05      0.34     227     255 ..     101     129 ..      97     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.7e-05
            PHA_synth_III_E 227 ekgkqiksaralfdlWveaaeevyaevva 255
                                +k+k+i   r+l ++W+ + ee+y +v +
  gene65|gene65|rna65|rna65 101 NKEKKIRGPRELLEYWIGVFEEIYDNVHV 129
                                6899********************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1612.16
//
Query:       gene651|gene651|rna650|rna650  [L=186]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-07   31.0   0.0    4.1e-07   29.9   0.0    1.6  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    3.8e-07   30.2   2.3    1.3e-06   28.5   0.2    2.2  2  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   4.6e-11   4.1e-07      34      70 ..     125     161 ..     101     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.6e-11
                   RL10P_insert  34 lptklkkGkivleedylvckkGetltseqaqlLklLg 70 
                                    lp+ +k+ k  l+edy+vc++Get++ ++a++Lk +g
  gene651|gene651|rna650|rna650 125 LPVTMKDEKMQLNEDYVVCEAGETVDERKAKILKFFG 161
                                    899*******************************997 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   1.4e-10   1.3e-06       1      59 [.       7      64 ..       7      74 .. 0.95
   2 ?    1.5   0.1     0.035   3.2e+02       4      26 ..     151     172 ..     109     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.4e-10
                                   SSCCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCC CS
                  Ribosomal_L10  1 ktkekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmr 59
                                   k+kek+++  +++++ ++ky  v+v++  g+++  l+++R++++++ +++ + ++++++
  gene651|gene651|rna650|rna650  7 KNKEKRQAEMEKIRNYAEKYPLVAVIENPGIPNVILKKIREDFKGT-SKILFTRKKMAS 64
                                   689******************************************9.*********987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.035
                                    CCHCCCCCCCCCCCTTSSEEEEE CS
                  Ribosomal_L10   4 ekKeelvkelkellkkyksvvvv 26 
                                    e+K++++k + ++lkk + vv +
  gene651|gene651|rna650|rna650 151 ERKAKILKFFGKRLKKKNLVV-F 172
                                    567777777777777764443.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1180.47
//
Query:       gene652|gene652|rna651|rna651  [L=735]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.0   0.1      0.073   13.1   0.0    2.1  2  Xpo1      Exportin 1-like protein


Domain annotation for each model (and alignments):
>> Xpo1  Exportin 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.1e-06     0.073       6      50 ..      86     134 ..      84     183 .. 0.84
   2 ?   -4.1   0.0      0.83   1.5e+04      40      53 ..     394     407 ..     388     412 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.1e-06
                                    HHHHHHHHHHHHHHTTTTSTTHHHHHHHHHCT.....HHHHHHHHHHHH CS
                           Xpo1   6 nklaealaelflqeypnnWpsffddllsllsss....psglelllriLk 50 
                                    +k a+++a l + e+p+n+p+ff+ +++lls       + le++l +++
  gene652|gene652|rna651|rna651  86 DKAAQVFALLGIYEWPSNFPQFFSIIIDLLSHRkemgYKILENFLYLCN 134
                                    689***************************9965555445566665554 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.83
                                    HHHHHHHHHHHHHH CS
                           Xpo1  40 sglelllriLkvlp 53 
                                    +++ l+++iL ++p
  gene652|gene652|rna651|rna651 394 EACRLVIKILEMFP 407
                                    67899999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (735 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 4502.74
//
Query:       gene653|gene653|rna652|rna652  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.35s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 647.58
//
Query:       gene654|gene654|rna653|rna653  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-09   36.9   0.1    2.6e-09   36.7   0.1    1.0  1  Synaptobrevin    Synaptobrevin
  ------ inclusion threshold ------
      0.038   13.3   0.0      0.038   13.3   0.0    1.1  1  AmpE             Regulatory signalling modulator protein AmpE
      0.051   13.9   0.9      0.051   13.9   0.9    1.5  1  DUF4164          Domain of unknown function (DUF4164)
       0.06   13.5   0.1      0.068   13.3   0.1    1.1  1  MCU              Mitochondrial calcium uniporter
      0.078   12.9   1.3        0.1   12.5   0.8    1.5  1  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
       0.11   12.4   0.4        0.2   11.7   0.1    1.6  2  DUF5345          Family of unknown function (DUF5345)
       0.18   11.7   2.6        2.4    8.1   0.1    2.4  2  AvrM_N           Flax-rust effector AvrM N-terminal domain
        0.2   11.6   3.9       0.24   11.4   3.9    1.1  1  DUF1151          Protein of unknown function (DUF1151)
        9.2    6.2   8.9         20    5.1   8.9    1.7  1  Ferlin_C         Ferlin C-terminus


Domain annotation for each model (and alignments):
>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   1.3e-12   2.6e-09       5      86 ..       6      87 ..       2      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.3e-12
                                   HHHHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXX CS
                  Synaptobrevin  5 lakikaevdevkdimkeNidkvlergekldeLvdktenLqssaqqFkkqarklkrkmwwknmkliiililvvlililiiiiv 86
                                   ++ki++ev++ ++ +ke ++   + g+   +L+++t +L++++++ k  + + k+k  wkn+k+ +i +++++++++ i+  
  gene654|gene654|rna653|rna653  6 TQKIEKEVEDLQGALKEQLKAQRDLGDLETNLKSETFTLEKTTEEHKAATEEAKNKLFWKNFKYFLIAGILIILVLFGIFGN 87
                                   689************************99***********************************************999865 PP

>> AmpE  Regulatory signalling modulator protein AmpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.038     121     160 ..      46      88 ..       7      90 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                           AmpE 121 vdase.kerlrelqnallwinfryyl..aplfwfvvagpygpv 160
                                      ++e k+  +e +n l+w nf+y+l  + l+ +v+ g +g +
  gene654|gene654|rna653|rna653  46 KTTEEhKAATEEAKNKLFWKNFKYFLiaGILIILVLFGIFGNI 88 
                                    3444415567899************942346778888999876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.9   2.5e-05     0.051       7      42 ..       3      38 ..       2      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                        DUF4164  7 eaaltrLeaaldsLEkavdrrleaerkrdeleaeie 42
                                   +++++++e+ ++ L +a++++l+a+r+ ++le++++
  gene654|gene654|rna653|rna653  3 DEVTQKIEKEVEDLQGALKEQLKAQRDLGDLETNLK 38
                                   689*****************************9885 PP

>> MCU  Mitochondrial calcium uniporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.4e-05     0.068      31     105 ..       5      76 ..       2      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                    XXXXXXXXXXXXX-SSSSSSTSSSSSHHHHHHHHHHHHH-SHHHHHHHHTCCCGGGCHHHHGGGHHHHHHHHTHH CS
                            MCU  31 vllrvkqlvkalesalnveeeqlkkereleekleelreelepleekkeeidekAerrtrrllwagLallavqlgi 105
                                    v +++++ v++l+ al   +eqlk +r+l + + +l++e   le++ ee +++ e+ +++l w  + ++ +   +
  gene654|gene654|rna653|rna653   5 VTQKIEKEVEDLQGAL---KEQLKAQRDLGDLETNLKSETFTLEKTTEEHKAATEEAKNKLFWKNFKYFLIAGIL 76 
                                    5566666777777777...6789999999999999****************************999888765544 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   5.2e-05       0.1      16      50 ..       3      36 ..       2      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.2e-05
                HU-CCDC81_bac_2 16 eeAlqkiekeveelkqeLeeegrveleniGeLsln 50
                                   +e++qkiekeve+l+ +L+e+ + +  ++G+L +n
  gene654|gene654|rna653|rna653  3 DEVTQKIEKEVEDLQGALKEQLKAQ-RDLGDLETN 36
                                   5899**************9998776.667777766 PP

>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.78   1.6e+03      20      33 ..      14      27 ..       3      30 .. 0.51
   2 ?   11.7   0.1   9.8e-05       0.2       4      59 ..      29      85 ..      26      90 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.78
                        DUF5345 20 eeleqllaeekerk 33
                                   e+l+  l+e+ +++
  gene654|gene654|rna653|rna653 14 EDLQGALKEQLKAQ 27
                                   44454554444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.8e-05
                        DUF5345  4 glerlDqlievetPsleel.eqllaeekerkrkrlrrElllFlliAllilsllllal 59
                                   +l  l+++++ et +le+  e++ a+++e+k k +++ +  Fl++ +li+ +l+ ++
  gene654|gene654|rna653|rna653 29 DLGDLETNLKSETFTLEKTtEEHKAATEEAKNKLFWKNFKYFLIAGILIILVLFGIF 85
                                   66678888888885555550455556666666778**************98887665 PP

>> AvrM_N  Flax-rust effector AvrM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.025        50      41      62 ..       7      28 ..       3      30 .. 0.88
   2 ?    8.1   0.1    0.0012       2.4      38      64 ..      32      58 ..      27      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.025
                         AvrM_N 41 tnvekmarkLykaakeykkaek 62
                                   +++ek++ +L+ a ke  ka++
  gene654|gene654|rna653|rna653  7 QKIEKEVEDLQGALKEQLKAQR 28
                                   579***********99999987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
                         AvrM_N 38 erdtnvekmarkLykaakeykkaekkA 64
                                   + +tn++ ++  L+k  +e+k a ++A
  gene654|gene654|rna653|rna653 32 DLETNLKSETFTLEKTTEEHKAATEEA 58
                                   6689*******************9987 PP

>> DUF1151  Protein of unknown function (DUF1151)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.9   0.00012      0.24      49     104 ..       9      62 ..       3      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                        DUF1151  49 lekrkeeqvlkqkkeeeeakkkkseLeqelekraqrleelekeeekqkeeqekape 104
                                    +ek  e  ++ + ke+ +a++   +Le++l+     le++++e++ ++ee++++  
  gene654|gene654|rna653|rna653   9 IEKEVE-DLQGALKEQLKAQRDLGDLETNLKSETFTLEKTTEEHKAATEEAKNK-L 62 
                                    455553.66777889999********************9999988888886654.4 PP

>> Ferlin_C  Ferlin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   8.9    0.0098        20     115     139 ..      60      84 ..       7      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0098
                       Ferlin_C 115 iffiWkkykkyiiallilallalfl 139
                                     +++Wk++k ++ia ++++l+ + +
  gene654|gene654|rna653|rna653  60 NKLFWKNFKYFLIAGILIILVLFGI 84 
                                    579**********866655554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1967  (0.109711); expected 358.6 (0.02)
Passed bias filter:                     1081  (0.0602934); expected 358.6 (0.02)
Passed Vit filter:                       145  (0.00808746); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 595.42
//
Query:       gene655|gene655|rna654|rna654  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-26   90.5   0.0    2.5e-12   46.7   0.0    2.3  2  TFIIB         Transcription factor TFIIB repeat
    1.1e-08   35.4   5.2    1.2e-08   35.2   3.0    2.2  2  BRF1          Brf1-like TBP-binding domain
    1.3e-06   27.8   0.8    3.4e-06   26.4   0.8    1.8  1  TF_Zn_Ribbon  TFIIB zinc-binding
     0.0062   16.3   0.0      0.055   13.2   0.0    2.4  3  Cyclin_N      Cyclin, N-terminal domain
     0.0087   15.8   0.4       0.03   14.1   0.4    2.0  1  HTH_38        Helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   14.4   0.2      0.072   12.7   0.0    2.0  2  HTH_24        Winged helix-turn-helix DNA-binding
      0.023   14.4   0.1      0.073   12.8   0.1    1.8  1  Sigma70_r4_2  Sigma-70, region 4
      0.028   14.2   0.2       0.41   10.5   0.1    2.6  2  HTH_23        Homeodomain-like domain
        0.1   12.6   0.1       0.23   11.4   0.1    1.5  1  HTH_11        HTH domain
       0.15   12.0   0.1       0.51   10.3   0.0    1.9  2  HTH_5         Bacterial regulatory protein, arsR family
       0.16   11.4   0.0       0.34   10.3   0.0    1.6  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
       0.21   11.2   1.5       0.32   10.6   0.2    2.0  2  Sigma70_r4    Sigma-70, region 4


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   5.8e-14   8.6e-11       1      68 [.      77     144 ..      77     147 .. 0.94
   2 !   46.7   0.0   1.6e-15   2.5e-12       2      71 .]     172     242 ..     171     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 5.8e-14
                                    HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--S CS
                          TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVse 68 
                                    i+ +++ l+L     ++ + ++kl l+ ++ kG+s    ++Ac+yi cr+e++ +++ ++s+ l++ +
  gene655|gene655|rna654|rna654  77 ISGICASLGLGIDHVECSFRWYKLLLQYNLSKGKSILYTLSACIYIVCRQEKTPHMLMDFSNALHIDV 144
                                    667999*****99999*************************************************976 PP

  == domain 2  score: 46.7 bits;  conditional E-value: 1.6e-15
                                    HHHHHHTT--H.HHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   2 krfadaleLpe.kVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    +rf+++l +   +V      l+ ++++++++ Gr+p+++ +A+l+iA+r  +++r+  ei+++++Vs+ ti
  gene655|gene655|rna654|rna654 172 PRFVSRLRFESsEVLGLSLRLISRMKRDWIVVGRRPNNLCGAALLIASRIVGEERSIYEIAKIVHVSVSTI 242
                                    788888888776888889999***********************************************998 PP

>> BRF1  Brf1-like TBP-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       5.2   7.7e+03      35      43 ..     282     290 ..     260     306 .. 0.48
   2 !   35.2   3.0   8.2e-12   1.2e-08       4     101 .]     313     393 ..     308     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.2
                           BRF1  35 eqeekrlke 43 
                                    e+++k+++e
  gene655|gene655|rna654|rna654 282 EMAKKQECE 290
                                    222333333 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 8.2e-12
                           BRF1   4 dddeideyllseeevkiKeriWvelnkeyLeeqeekrlkeeaeeaeadkkkkkkkrkrkkkekkkgepetaaeavkkmle 83 
                                    d +ei+  +ls+ee+k +e++W+e+  e+++e+e++ +   ++ ++       ++r   +  ++     + +ea +++  
  gene655|gene655|rna654|rna654 313 DSEEIERNILSPEETKRREIVWEEMYGEFMREREKRVKSSVKKGKR-------RRR---N--EEF---GSIVEAFRSL-- 375
                                    566***************************9876655443333222.......222...2..122...5889999886.. PP

                           BRF1  84 kkklskkINydaLekLfd 101
                                     +k+s k+Ny+a+e++fd
  gene655|gene655|rna654|rna654 376 DRKISGKLNYQAIESIFD 393
                                    5679************96 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.8   2.3e-09   3.4e-06       2      37 ..       3      38 ..       2      44 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.3e-09
                                   EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCC CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsideg 37
                                   +C nC+s ++ eD+++g ++Ct CG V e+n i+  
  gene655|gene655|rna654|rna654  3 ICSNCSSGDFAEDTAQGAVYCTTCGMVQEENAIVAS 38
                                   6******99***********************9865 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.2   1.8e+03     109     126 ..      26      43 ..      16      44 .. 0.82
   2 ?   -1.7   0.0       1.6   2.3e+03      77      98 ..     116     136 ..      97     148 .. 0.74
   3 !   13.2   0.0   3.7e-05     0.055      48     108 ..     182     244 ..     170     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHTTT-- CS
                       Cyclin_N 109 eeilemErliLetLnfdl 126
                                      +++ E+ i+  Lnf+ 
  gene655|gene655|rna654|rna654  26 CGMVQEENAIVASLNFNT 43 
                                    568899**********95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHSSS---HHHH CS
                       Cyclin_N  77 gatcLllAaKveeisppkledl 98 
                                      +c+++ ++ e++ p  l d+
  gene655|gene655|rna654|rna654 116 LSACIYIVCRQEKT-PHMLMDF 136
                                    57899999999877.6666555 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 3.7e-05
                                    -TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH..HSSS---HHHHHHHTTTSS-H CS
                       Cyclin_N  48 tpetlflavnyldRflskksvpkdklqlvgatcLllAaKv..eeisppkledlvyitdeafte 108
                                    ++e+l l+++++ R+ +  +v  ++ + ++ ++Ll+A+++  ee s+ ++ ++v+++ +++++
  gene655|gene655|rna654|rna654 182 SSEVLGLSLRLISRMKRDWIVVGRRPNNLCGAALLIASRIvgEERSIYEIAKIVHVSVSTINK 244
                                    468999**********************************999999*********98765544 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.4     2e-05      0.03      20      42 ..     225     247 ..     217     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                         HTH_38  20 GlslreIArrLgrspsTIsRElk 42 
                                      s++eIA+++++s sTI++ lk
  gene655|gene655|rna654|rna654 225 ERSIYEIAKIVHVSVSTINKRLK 247
                                    679***************99776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.4   3.6e+03      24      36 ..     183     195 ..     183     196 .. 0.81
   2 ?   12.7   0.0   4.8e-05     0.072      22      40 ..     230     248 ..     227     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                         HTH_24  24 AerlglSpstvnr 36 
                                    +e lglS+  ++r
  gene655|gene655|rna654|rna654 183 SEVLGLSLRLISR 195
                                    6889**9988877 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 4.8e-05
                         HTH_24  22 eLAerlglSpstvnrrlkr 40 
                                    e+A+ +++S+st+n+rlk+
  gene655|gene655|rna654|rna654 230 EIAKIVHVSVSTINKRLKE 248
                                    9****************96 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.9e-05     0.073      25      48 ..     224     247 ..     220     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                                    S---HHHHHHHHT--HHHHHHHHH CS
                   Sigma70_r4_2  25 eglsykEIAellgisegtVksrls 48 
                                    e+ s+ EIA++ ++s++t+++rl+
  gene655|gene655|rna654|rna654 224 EERSIYEIAKIVHVSVSTINKRLK 247
                                    78899****************995 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.38   5.6e+02      24      41 ..     183     200 ..     181     209 .. 0.90
   2 ?   10.5   0.1   0.00027      0.41      18      39 ..     226     247 ..     213     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.38
                         HTH_23  24 AreLgvsrrTvyrwlkry 41 
                                    ++ Lg s r ++r ++ +
  gene655|gene655|rna654|rna654 183 SEVLGLSLRLISRMKRDW 200
                                    689**********99988 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00027
                         HTH_23  18 lsvreIAreLgvsrrTvyrwlk 39 
                                     s+ eIA++ +vs +T+ + lk
  gene655|gene655|rna654|rna654 226 RSIYEIAKIVHVSVSTINKRLK 247
                                    5889*************97666 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00015      0.23      17      39 ..     227     249 ..     221     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                         HTH_11  17 sgeeLAeeLnvSrrtvrrdIkaL 39 
                                    s+ e+A+  +vS +t+ +++k++
  gene655|gene655|rna654|rna654 227 SIYEIAKIVHVSVSTINKRLKEI 249
                                    899*****************987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       6.7     1e+04      17      27 ..      76      86 ..      75      86 .. 0.86
   2 ?   10.3   0.0   0.00034      0.51      14      37 ..     224     247 ..     215     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6.7
                                   EHHHHHHHHTS CS
                          HTH_5 17 cvcelaeelgl 27
                                   +++ +++ lgl
  gene655|gene655|rna654|rna654 76 TISGICASLGL 86
                                   7899***9986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00034
                                    SSEEHHHHHHHHTS-HHHHHHHHH CS
                          HTH_5  14 gelcvcelaeelglsqstvShHLk 37 
                                    +e+++ e+a+++++s st+   Lk
  gene655|gene655|rna654|rna654 224 EERSIYEIAKIVHVSVSTINKRLK 247
                                    689***************976665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00023      0.34      26      50 ..     224     248 ..     216     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                   HTH_Tnp_ISL3  26 esrsvkavArqlgvSwtTVwrildr 50 
                                    e rs+ ++A++++vS +T++ +l++
  gene655|gene655|rna654|rna654 224 EERSIYEIAKIVHVSVSTINKRLKE 248
                                    447999**************99986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1         4     6e+03      28      40 ..     184     196 ..     183     199 .. 0.75
   2 ?   10.6   0.2   0.00021      0.32      16      43 ..     220     248 ..     214     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4
                                    HHHTS-HHHHHHH CS
                     Sigma70_r4  28 erlgiSrerVrqi 40 
                                    e+lg+S+  +++ 
  gene655|gene655|rna654|rna654 184 EVLGLSLRLISRM 196
                                    7899999888775 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00021
                                    HH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4  16 rf.geglTleEIgerlgiSrerVrqiekr 43 
                                    r  ge+++  EI+++ ++S +++  ++k+
  gene655|gene655|rna654|rna654 220 RIvGEERSIYEIAKIVHVSVSTINKRLKE 248
                                    4469*******************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2451.67
//
Query:       gene656|gene656|rna655|rna655  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-45  152.2   0.1    9.6e-45  151.6   0.1    1.3  1  Bromo_TP_like  Histone-fold protein
    5.2e-07   29.6   0.0    9.7e-07   28.7   0.0    1.4  1  Bromo_TP       Bromodomain associated


Domain annotation for each model (and alignments):
>> Bromo_TP_like  Histone-fold protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.6   0.1   1.1e-48   9.6e-45       1     118 [.       8     125 ..       8     126 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.6 bits;  conditional E-value: 1.1e-48
                  Bromo_TP_like   1 KilklvivEillQvGferiseqslniltdllkyyiekillkikkevdkdlleeilikllleeslgedsYkrnELlsFLky 80 
                                    Kilkl++vE+l+Q+Gf+++++q+ln+ltd+l+yyie++ +++k++ +k+++ e+++++l+ee++ge++Y+  ELlsFL+y
  gene656|gene656|rna655|rna655   8 KILKLAVVEVLSQSGFDKTADQALNVLTDVLRYYIEQLGCRMKRRHGKGVVPEMMCRILVEETYGECEYQVPELLSFLRY 87 
                                    9******************************************************************************* PP

                  Bromo_TP_like  81 qlnlkkqlktkeaveedeslleiLkvlpknhllervlr 118
                                    q+++k++l +++ v+++es+l+iL+vlpkn++l++v+r
  gene656|gene656|rna655|rna655  88 QVTVKNYLSDRYNVGSEESILHILRVLPKNAQLRMVMR 125
                                    ************************************98 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.1e-10   9.7e-07       5      49 ..       7      51 ..       3      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-10
                                   HHHHHHHHHHHHHHHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Bromo_TP  5 rsllkvvvsqileeaGfdsaeesaLEtLteiaqkYirelgeqaks 49
                                   ++ lk +v  +l ++Gfd++ + aL+ Lt+++  Yi++lg  +k+
  gene656|gene656|rna655|rna655  7 TKILKLAVVEVLSQSGFDKTADQALNVLTDVLRYYIEQLGCRMKR 51
                                   67899***********************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1508.27
//
Query:       gene657|gene657|rna656|rna656  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-24   85.0   2.6    4.5e-24   85.0   2.6    2.8  2  TAFII55_N   TAFII55 protein conserved region
  ------ inclusion threshold ------
        1.8    7.9   8.1        2.4    7.5   8.1    1.2  1  DltD        DltD protein
        5.5    6.6   6.5         12    5.4   0.0    2.1  2  GCD14       tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> TAFII55_N  TAFII55 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   2.6   7.5e-28   4.5e-24       1     159 [.       1     134 [.       1     135 [. 0.83
   2 ?    0.1   0.2       0.1   6.1e+02      12      26 ..     191     205 ..     158     231 .. 0.62

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 7.5e-28
                      TAFII55_N   1 lEeqfiLRlppeeaeklreaiesgdvnkdklsiklekderravvkidgklyaaklvDLPtiiEslKtiDkknlyKtaDis 80 
                                    +E qfiLRl +    +++++++ ++      ++++  +++ +v+  +gk y + +v LP+i+Es+Kt+D ++ yK+aDis
  gene657|gene657|rna656|rna656   1 MERQFILRLHE----TIKHVVDLKSS-----TLDV-CNDKSVVLVHNGKRYPGIIVRLPCIVESQKTMDGRQHYKVADIS 70 
                                    68999999975....88888988874.....5566.345667777899******************************** PP

                      TAFII55_N  81 qmllvkeeeeakkeeeleeekskkkkkekkkekkfqyphGitpPlknvrkrRFrkrlkk.keieavekevkrLlraDaea 159
                                     +++v  ++ +   +++            +ke++++   G+ pPlk v+ rRFrk+ +k +++e++e++v++Ll++D +a
  gene657|gene657|rna656|rna656  71 TLVVV-YPHGD---FDF------------DKEREMHELSGLCPPLKYVKARRFRKKNSKvEYVEEIERKVNELLEKDMKA 134
                                    *****.33333...332............2567888899***************88877478899************987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.1
                      TAFII55_N  12 eeaeklreaiesgdv 26 
                                    +e+e+l+++ie+++ 
  gene657|gene657|rna656|rna656 191 AEVERLEKSIEEKRK 205
                                    223333333333332 PP

>> DltD  DltD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.1    0.0004       2.4     114     240 ..     107     229 ..      99     240 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0004
                                    HHHH--.SSHHHHHHHHHHHHH.-TT-T....THHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHHTTC-HHHHHTTT CS
                           DltD 114 llknpkiseetkryiakrllelekskkskee.lkkllkkyangkklsklqklllkikkallekedklksklkkkekkiek 192
                                    + k+++ + e+ ++i++++ el  +k++k+  ++ + k  ++++  ++l+ l+ +i+++l+++e+  +  ++    + ++
  gene657|gene657|rna656|rna656 107 FRKKNS-KVEYVEEIERKVNEL-LEKDMKAIsVEVVTK--EEKEDSDDLDVLAAEIENKLADHEELHQEEVQACPPEADE 182
                                    444444.78899999*******.334443330344444..55566799999999**************999988999999 PP

                                    HCTTS-SS--HHHHHHHHHHHHHHCTTTTSSS--HHHHHHHTSTTCCT CS
                           DltD 193 kakklpkeidwdelrkkaekegkksttnNefgiknkyYkkrlkpklkk 240
                                    k++++p++ ++++l+k +e++ k+  +     i +k ++++l   +k+
  gene657|gene657|rna656|rna656 183 KKEEKPRNAEVERLEKSIEEKRKQMES-ALNPILQKRFESQLGVLMKE 229
                                    999*************99988776554.33345555555555555555 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0021        12     146     176 ..      48      78 ..      14     115 .. 0.75
   2 ?   -0.1   5.6     0.098   5.9e+02     149     235 ..     117     203 ..     112     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0021
                          GCD14 146 sPCieqvqrtceaLrelgfteietlevllrt 176
                                     PCi   q+t++  ++ +  +i+tl v + +
  gene657|gene657|rna656|rna656  48 LPCIVESQKTMDGRQHYKVADISTLVVVYPH 78 
                                    5************************998754 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.098
                          GCD14 149 ieqvqrtceaLrelgfteietlevllrtyevrkskleeidl.aekrleenerkriekakrrkaskdakvedkssksstev 227
                                    +e + r +++L e++ + i+ +ev +++ +    +l+++    e++l ++e+ + e+++    + d+k+e+k  +++ e 
  gene657|gene657|rna656|rna656 117 VEEIERKVNELLEKDMKAIS-VEVVTKEEKEDSDDLDVLAAeIENKLADHEELHQEEVQACPPEADEKKEEKPRNAEVER 195
                                    78999999999999988885.79999998888888888776466667777777777777777788999998888887777 PP

                          GCD14 228 llkPvsel 235
                                    l k ++e 
  gene657|gene657|rna656|rna656 196 LEKSIEEK 203
                                    77777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2254  (0.125718); expected 358.6 (0.02)
Passed bias filter:                      708  (0.0394891); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1619.52
//
Query:       gene658|gene658|rna657|rna657  [L=124]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 924.87
//
Query:       gene659|gene659|rna658|rna658  [L=3441]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-39  135.7   0.1    2.9e-38  132.0   0.0    2.4  2  FAT             FAT domain
     0.0025   17.7   0.1     0.0069   16.2   0.1    1.7  1  PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase


Domain annotation for each model (and alignments):
>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   0.0   3.3e-42   2.9e-38       6     345 ..    2380    2736 ..    2376    2737 .. 0.95
   2 ?    0.5   0.3      0.03   2.7e+02     164     250 ..    2780    2853 ..    2773    2871 .. 0.82

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 3.3e-42
                                     CCCCTSSSGHH...CCCCT......TSSSS--CCCHCCCCHH--CCHCHHCCCHCCCCCCCCCTS---SCCCCCHHH. CS
                            FAT    6 eaaWrlgqWds...meeylsvlk..kdspdkaffeailalhrnqfdeakeliekarqlldtelsalvgesynraygv. 77  
                                     e+ W+l+++ s   +e++ +v++  ++ ++k+f++++ +      + +k+++ek++++l +++++l+++ +++   + 
  gene659|gene659|rna658|rna658 2380 ESLWHLSSFTSqeaIEKFKDVIDrgRNVFEKEFYNTFAS------TFMKYSAEKIKDILAKNIAELRNYPAESGARSr 2451
                                     789****9777688899999999****************......99**********************999988777 PP

                                     .HHCCCCCHHHCHHCCHHCSS-.---TTTTTTT----TTS-TTTGCCCTTTCCCCTCCCH...CCCHC.......... CS
                            FAT   78 .lvrvQmlaEleeiiqykqkls.sseklksllktWrkRlpgcqdnvevwqdiltvRslvl...spied.......... 140 
                                      l ++Q+++E+ e+  + +++   +e l+s+l +W+++ p++ d++e+w+ + t+R++v+   ++ie+          
  gene659|gene659|rna658|rna658 2452 lLTYLQIIIEMVEAEPILNDRLdAAEALTSILFRWKDKEPSTYDSFEQWSLFRTWRRHVYsrlGMIEKvdneemmfkl 2529
                                     7******************877899***********************************7777888899******** PP

                                     ........................................HCCS-STTCCC..CCCCCHCHHHHCCSTTHHCCCCCHC CS
                            FAT  141 ........................................llkgvkaemwl..kfanlarksgrlslAekaLkellee 176 
                                                                             + kg+++ +++   f++ a + g+++ A  +Lke+   
  gene659|gene659|rna658|rna658 2530 sgggyleetvgpsggggptgsslfspkevvessiktrkelVSKGASELAKIlnAFSKAAIDRGYYDAALFHLKEV--- 2604
                                     ****************************************9999999999999**********************... PP

                                     TT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCCSS-SS---............HH.HHCCCTCCC CS
                            FAT  177 dpeewlprappevvyaylKylwssgeqkealqkLreftsellekkeelqsgleaqkeptnleeftkll.arcylkkGe 253 
                                                        +++ss+++ +a+qk+ +++ + l kk e++ g +++  + n+++f++++ + ++++kG 
  gene659|gene659|rna658|rna658 2605 -------------------FDLSSVKVGDAFQKVVYELLCFLGKK-EYKIGADQC-VSANIQHFSDSQsSILFNLKGL 2661
                                     ...................************************98.*********.************999******* PP

                                     CCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHHSSSS.S-TCCHHHHCCT..CCHHHH CS
                            FAT  254 wqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeqkeeeepedlqeyvvpavkgflksis 331 
                                     + e+l+k       +++++++y+++++i++ + ++w tw+ f f +  ke+ +     p       ++a+ + l++i+
  gene659|gene659|rna658|rna658 2662 FSEKLGK-------VSDAEKFYLQSAQICNVVGENWLTWGSFLFGRADKESGG-----P------KEDAFVALLQAIA 2721
                                     *******.......9***********************************777.....4......5789********* PP

                                     TTTS.STTTCHHHHH CS
                            FAT  332 lsse.nslqdtlRLL 345 
                                     ++s+ +++  +l+++
  gene659|gene659|rna658|rna658 2722 YCSGrKARRGILKMI 2736
                                     ***********9986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.03
                                     CSTTHHCCCCCHCTT.....TT.TSSCCCHHHHHHHCCHHHHHSSCCHHHHCCTSSCCCSS-SS---........... CS
                            FAT  164 slAekaLkelleedpeewlprappevvyaylKylwssgeqkealqkLreftsellekkeelqsgleaqkeptnleeft 241 
                                     +lA+  L+++ e         ++p+ v+  lK   +++++k +l+  +e t++++++ +++ ++++ +   +++  ++
  gene659|gene659|rna658|rna658 2780 ELAQVILSKISE---------EHPQAVMGPLK--AAKERIKRTLYPRKEDTECKMQRYKKMENNHNGI---SKVRPNE 2843
                                     567777777733.........45688888888..57888999***************99888888766...8999999 PP

                                     .HH.HHCCCT CS
                            FAT  242 kll.arcylk 250 
                                     +ll  rc+++
  gene659|gene659|rna658|rna658 2844 QLLeKRCFFL 2853
                                     9999999987 PP

>> PI3_PI4_kinase  Phosphatidylinositol 3- and 4-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.6e-07    0.0069      79     172 ..    3211    3318 ..    3193    3328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.6e-07
                                     TSTCHHHHH..........HHHHCHCHCCHHHHHCC....HHHHHHTSSTTHHHHHHHHHSSSHHHHHHHHHHHHHHH CS
                 PI3_PI4_kinase   79 vpptasves..........lrvaldkkklkkekklk....fekrtalkpksgllqeFvkkspsaeewlearkqFvrsl 142 
                                     + ++ +++           +++a++  k+++ k+ k    ++++ ++k  + l +++ + +   + ++++ ++  +s+
  gene659|gene659|rna658|rna658 3211 YVSNLKQNKveclgcnekgEGIAPCTYKYEASKRQKyiayEKMYNTFKVCNFLDEYLRSIYGCLGGYFRFKDRLLSSY 3288
                                     4444444444447777778888999999988888889988888888888899999999999999************** PP

                                     HHHHHHHHHHT-TT--TTTEEEETTTSEEE CS
                 PI3_PI4_kinase  143 aklsvldyilgngDRhldNilvdktsgkli 172 
                                     ++ s   y+l + DR + Ni + k sg+++
  gene659|gene659|rna658|rna658 3289 SVNSAFLYMLSIVDRRPRNIVITKASGQFM 3318
                                     **************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (3441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.45u 0.33s 00:00:01.78 Elapsed: 00:00:00.57
# Mc/sec: 18334.12
//
Query:       gene660|gene660|rna659|rna659  [L=353]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.8   0.0      0.031   14.8   0.0    1.6  1  NLE       NLE (NUC135) domain
       0.03   14.3   0.0      0.074   13.1   0.0    1.6  1  BBS2_Mid  Ciliary BBSome complex subunit 2, middle region


Domain annotation for each model (and alignments):
>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.4e-06     0.031       1      63 [.       4      61 ..       4      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-06
                            NLE  1 vqvrFvtkdedeslavpgtplsvPasltrkqLselvnkLlk.eekpvpFdFlidgellrtsLee 63
                                   v+v++v++   ++l v+  pl v  s+ +++L+  + ++l+ +     + F+i+g+ll   L++
  gene660|gene660|rna659|rna659  4 VLVKLVDR---SHLDVEHDPLHVSPSFCVEDLERYLRSVLSgD---GGYRFYIEGRLLEGCLQK 61
                                   789*****...379***************************44...56*********9988875 PP

>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.3e-06     0.074      17      76 ..     185     242 ..     175     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-06
                       BBS2_Mid  17 vgsddfeirvfkeeelvaeitetekvvslarlekerfayaleNGtvgvyekkerlWrvks 76 
                                    vg+++ e  vfk+  +  ++++ ++++s++ ++k++ ++    G++gv+e ++   r+k 
  gene660|gene660|rna659|rna659 185 VGTHEGECYVFKGRLM--KVHKFKACISVTIIDKDEVMFVCMDGSMGVFETSTNAFRTKD 242
                                    899999*****99866..5678899*****************************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2106.55
//
Query:       gene66|gene66|rna66|rna66  [L=717]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-31  106.8   0.0    1.5e-30  106.0   0.0    1.4  1  Trehalose_PPase  Trehalose-phosphatase
    8.9e-13   47.7   0.0    1.9e-10   40.0   0.0    2.3  2  Glyco_transf_20  Glycosyltransferase family 20
  ------ inclusion threshold ------
      0.082   12.6   0.0      0.082   12.6   0.0    2.7  3  Hydrolase_3      haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0   2.6e-34   1.5e-30       2     204 ..     506     687 ..     505     706 .. 0.91

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 2.6e-34
                                EETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EEE-HHHHTT CS
            Trehalose_PPase   2 lDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedwenqaeved 85 
                                +DydGTl++i+ +p  a p++e+ +lL +L + ++  v+i +Grs++++++++ + e+ + aeHGa +r +++  w++     +
  gene66|gene66|rna66|rna66 506 MDYDGTLTDIAVHPSMAAPTQEIKDLLVRLNKVCR--VIISTGRSVEDSDKFF-PREIEVFAEHGACRRVNGE--WKE---GVA 581
                                8**********************************..**************95.799**************99..997...888 PP

                                HHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT....THHHHHHHHHHHHHHH.--EEEE-SSEEEEE-S---HHHH CS
            Trehalose_PPase  86 lewlkevkeileektertpGsyiEekkfalsvHyrnadde..elqakelaehlesvltdkpdlevtqgkkvvevrpqgvsKGka 167
                                ++ ++ + ++ e +  rtpGs +E+k++ +++H+rna +   + qak+l e l ++ +d+    v++g+++vevr++++s    
  gene66|gene66|rna66|rna66 582 FPQKDLAWRVAEFFHLRTPGSELEKKRTGYAFHFRNASPLvgVKQAKALFELLMRICRDN----VKEGNHIVEVRSSKKS---- 657
                                8888888888888889************************9999***********99999....****************.... PP

                                HHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT CS
            Trehalose_PPase 168 verlleslgsadseddfvlciGDdrtDedmFsvlrkt 204
                                   ++++ g+      f+lc+GDd+ De++F+  +  
  gene66|gene66|rna66|rna66 658 --CVMKEVGEG-----FILCAGDDVADEEAFDLCNGY 687
                                ..99*****98.....***************988754 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   3.3e-14   1.9e-10      40     213 ..      67     227 ..      35     304 .. 0.78
   2 !    5.3   0.0    0.0011       6.6     420     455 ..     379     414 ..     364     425 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 3.3e-14
                                CHHCCC-EEEEEEECCES-CCC...HCCCCHHHCCCCCEEEEEE-HHHHHHHCCCHHHHCHHHHHTT-GG....G----HHHHH CS
            Glyco_transf_20  40 glkeetevvwvgwlgvevdesee.akekvskeleekfsvvpvflsdekveeyyngfsksvLWpllHYklpdsseekefersawd 122
                                 +  + e+ +vg++g  + e  + +  k  +e   ++ ++pvf++    +  y+ + +++L+        +  +++ ++ s ++
  gene66|gene66|rna66|rna66  67 DMLDDGEMFFVGTPGFYSSEAFDdEDCKRIEESMRHYRCYPVFQT----KGEYSRMIERILRKNTY----EFVQKDLNHASMFE 142
                                44556788999**99988887754333344566678889999998....8999999******9886....4558999******* PP

                                HHHHHHHHHHHHHHCC--TT-EEEEESGGGTTHHHHHHHCCTTSEEEEEE-S----HHHHTTSTTHHHHHHHHTTSSEEEESSH CS
            Glyco_transf_20 123 aYvkvnklFAdkiveeikdgdliwvhDYhLmllPellRkkledakigfflHiPFPsseifriLpvreeilegllgadliGFhte 206
                                +Y+     +++ki+e++++gd++wv D +L+llP +l      +  g    +PF  s +f+++p  ee+  ++l +  i F  +
  gene66|gene66|rna66|rna66 143 RYKVYVTEYCKKIMEIYEEGDVVWVIDHSLLLLPGMLG----SVPTGMSFCAPF--SLLFKCIPFWEELFSSILCCKYIEFSEN 220
                                ***********************************985....566677777888..679*******************999877 PP

                                HHHHHHH CS
            Glyco_transf_20 207 dyarhFl 213
                                     F 
  gene66|gene66|rna66|rna66 221 LSEGSFN 227
                                6655555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0011
                                EEE-TT-HHHHHHHHHHHHC--HHHHHHHHHHHHHH CS
            Glyco_transf_20 420 ilvNPwdieevaeaikeaLkmseeerkkrekkllkq 455
                                +  NP+d  eva+ i+e L+   +  ++++++++ +
  gene66|gene66|rna66|rna66 379 VQSNPYDFFEVADEINEKLEQAGKSTEENSEEMVGK 414
                                445*********************999999999765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.44   2.7e+03      78     109 ..     118     149 ..      83     164 .. 0.48
   2 ?   -2.0   2.7       0.4   2.4e+03     112     152 ..     459     499 ..     438     505 .. 0.56
   3 ?   12.6   0.0   1.4e-05     0.082       2      51 ..     505     559 ..     504     576 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.44
                                -B-HHHHHHHHHHHHHTTCEEEEEESSEEEES CS
                Hydrolase_3  78 tiskedvkeiikllkennveillytedkvyvl 109
                                 i++   k+ ++++++   ++ +++  kvyv+
  gene66|gene66|rna66|rna66 118 MIERILRKNTYEFVQKDLNHASMFERYKVYVT 149
                                22333333334444444444444444444444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.4
                                .THHHHHHHHHCHCTCEEEESHHHHHCHCSESEEEEES-HH CS
                Hydrolase_3 112 eksekkkkeeektkkkkeeidseeeledeeiakililkdke 152
                                ++++k+++++++++kk+ ++ + + +ede++a ++ +++k+
  gene66|gene66|rna66|rna66 459 NAKKKSSTKKREDRKKEAIQIDLDSKEDENAARMVDDFKKS 499
                                24455555555555555555556666666666666444444 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 1.4e-05
                                EEEIIIIIS-.....TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHH.H CS
                Hydrolase_3   2 alDlDGTLln.....sdkkisektkeaikklkekgikvviATGRslravlpvle.e 51 
                                ++D DGTL +     s    ++++k+ + +l  k + v+i+TGRs+++  +++  e
  gene66|gene66|rna66|rna66 505 IMDYDGTLTDiavhpSMAAPTQEIKDLLVRLN-KVCRVIISTGRSVEDSDKFFPrE 559
                                79******998887666668899999999998.99***************999733 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (717 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1426  (0.0795359); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.50
# Mc/sec: 4322.34
//
Query:       gene661|gene661|rna660|rna660  [L=179]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-28   98.7   0.3    3.1e-28   98.1   0.3    1.3  1  Fcf1           Fcf1
    6.2e-13   49.1   0.1      9e-13   48.5   0.1    1.2  1  PIN_9          PIN like domain
    0.00045   20.8   0.2    0.00079   20.0   0.2    1.4  1  PIN_12         PIN domain
  ------ inclusion threshold ------
      0.013   15.4   0.0      0.021   14.7   0.0    1.3  1  RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRC
      0.021   15.1   0.2      0.073   13.4   0.1    1.7  2  PIN_4          PIN domain


Domain annotation for each model (and alignments):
>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.3   8.5e-32   3.1e-28       2      99 .]      78     173 ..      77     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 8.5e-32
                                    HCTS-EEEEEEHHHHHHHHHCT..-HHHHHHHT.T.SEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHH CS
                           Fcf1   2 tLqakvkpliTqCviaeleklgkklkealkiak.t.ferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrl 79 
                                    +++a++k+++ +Cviaeleklg+ ++ al++++ + ++rl+C+h k+t+addC+ ++v+    +++yivAt D++lr+r+
  gene661|gene661|rna660|rna660  78 VVNASIKICVPECVIAELEKLGRPFRVALALVRdNdVQRLECDH-KGTYADDCIFNRVS-A--HRCYIVATSDTALRQRI 153
                                    67899****************************978********.**************.4..9**************** PP

                                    HTSTT--EEEEE--EEEE-- CS
                           Fcf1  80 rkipgvPilyikrsvmvlEk 99 
                                    ++ipgvP++ ++ +++++E+
  gene661|gene661|rna660|rna660 154 KAIPGVPLITYRGQRCFIER 173
                                    **************999996 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.1   2.5e-16     9e-13       1     115 [.      54     166 ..      54     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.5e-16
                          PIN_9   1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaDda 79 
                                    vilDtn++   ++ + di e+l +++  s ++ vp+ v++ELe+l   g++   + a v  +  +r+e+ ++++ +aDd 
  gene661|gene661|rna660|rna660  54 VILDTNFINDCIRKKYDIREQLMKVVnASIKICVPECVIAELEKL---GRPFRVALALVRDNDVQRLEC-DHKGTYADDC 129
                                    8*************************999****************...444333333333333444444.333689**** PP

                          PIN_9  80 ilelakeldaavlvTnDreLkkrlle.kgipvilLRq 115
                                    i +  ++ ++ +++T+D++L++r++   g+p i+ R+
  gene661|gene661|rna660|rna660 130 IFNRVSAHRCYIVATSDTALRQRIKAiPGVPLITYRG 166
                                    ************************9736999999887 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   2.2e-07   0.00079       1      47 [.      54      97 ..      54      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.2e-07
                         PIN_12  1 ifiDTnifldeffrlseeealkklleliesgkiklivpdivldEflk 47
                                   +++DTn++ d   r++++ + ++l + +++  ik++vp+ v+ E++k
  gene661|gene661|rna660|rna660 54 VILDTNFIND-CIRKKYD-IREQLMKVVNAS-IKICVPECVIAELEK 97
                                   79*******9.9***9**.**********95.************987 PP

>> RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     6e-06     0.021      63      90 ..      38      68 ..      32      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6e-06
                                   -SHHHHHHCCCTT...EEE-CHHHHHHHHHT CS
                  RTT107_BRCT_5 63 RTeKFLksLskap...kilspdfiedvLkkk 90
                                    TeKFL s    p    il+++fi+d+++kk
  gene661|gene661|rna660|rna660 38 NTEKFLLSHTLRPpynVILDTNFINDCIRKK 68
                                   5************9999***********964 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1     2e-05     0.073       1      40 [.      54     101 ..      54     136 .. 0.83
   2 ?   -0.7   0.0      0.46   1.7e+03     102     119 ..     135     152 ..     107     160 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2e-05
                          PIN_4   1 fVlDTnvlLhdpealksf........keehdvviPitVleELdklKkg 40 
                                    ++lDTn++ ++++  + +        +  +++++P  V+ EL+kl + 
  gene661|gene661|rna660|rna660  54 VILDTNFINDCIRKKYDIreqlmkvvNASIKICVPECVIAELEKLGRP 101
                                    589***9988887777778889*********************98665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.46
                          PIN_4 102 kpdrkvvLvskDinlrik 119
                                      +r+ +  + D+ lr +
  gene661|gene661|rna660|rna660 135 SAHRCYIVATSDTALRQR 152
                                    335677788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1138.92
//
Query:       gene662|gene662|rna661|rna661  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-21   76.2   0.3    4.8e-21   75.3   0.3    1.4  1  Peptidase_C65  Peptidase C65 Otubain


Domain annotation for each model (and alignments):
>> Peptidase_C65  Peptidase C65 Otubain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.3   2.7e-25   4.8e-21      37     209 ..       2     162 ..       1     194 [. 0.83

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2.7e-25
                                    TTEEEEE-B--SSTHHHHHHHHHHHHHHHH-HH..HHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHTTSS CS
                  Peptidase_C65  37 ekYssiRrvrgDGnCfyRaflfsylellleskdkaevsrikerveklkealeslgfdeevvedfleaflellkkiekkte 116
                                    ++Y+++R++ +DGnC+y + ++ +  l+  s+ ++ ++ +    +k+++ l+   +de  ++ f++ f+++l ++ ++t+
  gene662|gene662|rna661|rna661   2 KSYTEFRECIRDGNCLYISYAVVLADLV-TSEGEPLLKTLTSAFAKTNSMLHLYNIDELGYKGFYDSFADILADMVNGTK 80 
                                    57*****************999877665.5555599999999**********************************7766 PP

                                    -HH....HHHHHHTSHHHHHHHHHHHHHHHHHHHHHTHHHHGGGS-TT--HHHHHHHHTSSTT--B-HHHHHHHHHHTT- CS
                  Peptidase_C65 117 eseekaeellkafneqeesdyivvflRlltsaelkthadeyepFldelstveeFceqevepvnkEaDnvqitaLaealgv 196
                                    + e   +  l+ + +       v++lRl++s e+k++ ++y+p++ e ++v+++c++ v+p+ + a  v+i aL++ + +
  gene662|gene662|rna661|rna661  81 KIE---DVPLYSLYD------CVAYLRLVVSTEIKSNPEKYQPYIPE-MDVDKYCTRFVDPFYQQAGCVEICALSNSIPI 150
                                    664...355555543......789***********************.****************************9999 PP

                                    -EEEEESSSSGBS CS
                  Peptidase_C65 197 kvrVeyldrsveg 209
                                    +++++ + +  ++
  gene662|gene662|rna661|rna661 151 RIHIVDITKE-NE 162
                                    9999888765.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1751.00
//
Query:       gene663|gene663|rna662|rna662  [L=385]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-51  174.0  31.1    4.9e-51  173.7  31.1    1.0  1  Aa_trans      Transmembrane amino acid transporter protein
    9.6e-05   21.6  15.0    9.6e-05   21.6  15.0    2.2  2  Trp_Tyr_perm  Tryptophan/tyrosine permease family


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7  31.1   5.4e-55   4.9e-51       6     402 ..      11     380 ..       8     385 .] 0.89

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 5.4e-55
                       Aa_trans   6 lsavlnlikaivGaGvLaLPyAfkqlGlivGlillllvallslytlllLvkcsktlasgkrnksYgdlgyrllGpkgkli 85 
                                    +s ++nlik+++G+G+L +P+ fk  G++   +l+l+ al+sl++l+l +++ +++  +++ ++      r++ p++  +
  gene663|gene663|rna662|rna662  11 RSIFINLIKTTIGSGILRYPFLFKMYGVWYTTALTLISALASLLGLWLYIDLNDFYGLDNSMSTI----ARYIYPSLQPV 86 
                                    57789*************************************************99744444444....4444455555* PP

                       Aa_trans  86 idlailvqlfGvgvsyliligdllpaifesffdtlllsnvyfilisaliiipLslipnlskLsylSllalvsslyyivil 165
                                    ++++  v++f v+++yl+l +++lp  ++s+f+  +++++  ++ ++l+++p+  + +++kL+y+S +++ + ++   ++
  gene663|gene663|rna662|rna662  87 VNVTVSVKCFLVCTAYLVLLKNNLPGTIKSIFGLEDTHQALCMAGVVLCVFPFVSMHKIDKLRYTSSFGFGAAIA---LV 163
                                    *************************************************************************74...56 PP

                       Aa_trans 166 vlvvaelvklelkgvseetvkkasklkglflaigiivFAftghavlleiqnelkdpskfkkmtkvlllsiilatvlyilv 245
                                     l+++ +v+ +++ +  e+      + +++  +g +vF ft+h +++++qne+k  +k  + +  +ll+ ++a ++yi +
  gene663|gene663|rna662|rna662 164 LLSIYRYVVCKEVPTYGEG-----RVGNYLGELGSFVFGFTCHQNIFSVQNEMKVSDK-AALKITVLLVLLMASLIYITF 237
                                    6666666666655555554.....36789**************************888.667777888888999****** PP

                       Aa_trans 246 GlvGYltFGnevkgnillnlpkssilivivnlllvlhlilsfplqlhplrqvvenllikkeavagasekeapkskllrlv 325
                                    Gl+ Yl+ G+   +n++ n p+   +++i+ +++ l +++s+plq hp+r ++  l+ ++       +  + k + lr+v
  gene663|gene663|rna662|rna662 238 GLTNYLVLGDGMSENFFENIPEG--MKNIIAMFYFLVVMMSIPLQTHPCRTYFLDLFDTR-------YSADGKYWHLRFV 308
                                    ********************955..8*******************************987.......99*********** PP

                       Aa_trans 326 irlllvvityliAlsvpslakvlslvGatsstplsfilPalfhlkliktekksleklvkkkildlicivlglllvfy 402
                                    + l++++++ +iA+ v++++++ +++G  +st+++f++ +l+++ ++++    ++k++      l+++  g+++++ 
  gene663|gene663|rna662|rna662 309 TSLFIILLSFMIAMNVSKMERLCEIIGGSFSTLMCFVFASLYYFIAFWNRGFEMKKITA-----LFVLLYGVAAFVS 380
                                    **************************************************999999963.....4555555555554 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  15.0   1.1e-08   9.6e-05      13     251 ..      18     257 ..      11     281 .. 0.77
   2 ?   -0.3   4.1     0.048   4.3e+02      83     135 ..     307     354 ..     291     384 .. 0.45

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-08
                   Trp_Tyr_perm  13 agtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaakeeasfttlakkllGkkgniivalvllflly 92 
                                    + t+iG+G+l  P      g  +++ l ++s++ +l+  +l+++++  +  + s++t+a+ + ++    +v++++ +  +
  gene663|gene663|rna662|rna662  18 IKTTIGSGILRYPFLFKMYGVWYTTALTLISALASLLGLWLYIDLNDFYGLDNSMSTIARYIYPSLQ-PVVNVTVSVKCF 96 
                                    679********************************************************99998765.566778888899 PP

                   Trp_Tyr_perm  93 iLlvAyisggGsilselleeasgialsarlavliftlvlgalvvlstkavdrinrvllflklvafvlllalllskvksdv 172
                                        Ay+    + l  ++++ +g++  ++ a ++  +vl ++  +s + +d++     f+   a++l+l ++   v  + 
  gene663|gene663|rna662|rna662  97 LVCTAYLVLLKNNLPGTIKSIFGLED-THQALCMAGVVLCVFPFVSMHKIDKLRYTSSFGFGAAIALVLLSIYRYVVCKE 175
                                    99********************8544.44444455566666777777888987666666666666655555555554444 PP

                   Trp_Tyr_perm 173 LlsaksdtskvslvlsalPvlllsfGFhgivpslvkyldkn.vkkvkkailiGtliaLvlyllW...elivlGn.lpree 247
                                      +       v   l  l  ++  f  h+++ s+ + +  + +  +k  +l+  l+a ++y+     +++vlG  ++++ 
  gene663|gene663|rna662|rna662 176 VPT--YGEGRVGNYLGELGSFVFGFTCHQNIFSVQNEMKVSdKAALKITVLLVLLMASLIYITFgltNYLVLGDgMSENF 253
                                    444..245899999999999**99999*******9999877355667788889999999999773335678886244444 PP

                   Trp_Tyr_perm 248 lari 251
                                    + +i
  gene663|gene663|rna662|rna662 254 FENI 257
                                    4444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.048
                   Trp_Tyr_perm  83 valvllfllyiLlvAyisggGsilselleeasgialsarlavliftlvlgalv 135
                                       +l ++l + ++A   +  + l+e++  ++      +l++++f+ +  ++ 
  gene663|gene663|rna662|rna662 307 FVTSLFIILLSFMIAMNVSKMERLCEIIGGSF-----STLMCFVFASLYYFIA 354
                                    33333333344444433333333333333333.....3444444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2619.29
//
Query:       gene664|gene664|rna663|rna663  [L=245]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1521.81
//
Query:       gene666|gene666|rna665|rna665  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-19   69.7   1.3    3.7e-19   69.3   1.3    1.1  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   1.3   2.1e-23   3.7e-19       2     201 ..      26     210 ..      23     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 2.1e-23
                                    HHHS-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHH CS
                   Ribosomal_L1   2 lkhakkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkky 81 
                                    ++ +  +++++++i++nl++++p+k d++ ++  + p ++++  ki +i+++ + +      +ag    +++++++  + 
  gene666|gene666|rna665|rna665  26 KENEDPEKTATIQIQVNLKGYDPRK-DNKLSKDMSFPYKVRRLDKIIVIADEAHIK---ACVDAG--LPHVSIEEIAGDD 99 
                                    55666678899***********777.8899**************************...99****..999******9999 PP

                                    T-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEE CS
                   Ribosomal_L1  82 ksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkv 161
                                    k + ++ ++lke + f+  +  ++++ + L ++++  +k+P+    k    +d+k+  e a++ ++++r+++ +++s++v
  gene666|gene666|rna665|rna665 100 K-KAKRDAVLKENKYFILCSG-YNKVFQ-LKNILRF-GKTPYIL--KD--DDDIKAVFEAAKR-SYKLRIKDFAVTSFPV 170
                                    7.4888899999999999977.577777.9999966.799****..53..5799999999999.9*************** PP

                                    EETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEET CS
                   Ribosomal_L1 162 GklsftaeelaeNieavvkalvekvpkkwkniksiylktt 201
                                    G+++++++++ eNi++ +  l++ ++k+ +n+k +++kt+
  gene666|gene666|rna665|rna665 171 GHTGMDSDHIYENIKTGMGLLISYLKKGTQNLKGVMIKTN 210
                                    **************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1417.78
//
Query:       gene667|gene667|rna666|rna666  [L=278]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-05   25.2   6.6     0.0019   18.6   2.5    2.7  2  zf-C2H2    Zinc finger, C2H2 type
    0.00058   20.5   4.6       0.19   12.6   1.2    2.9  2  zf-C2H2_4  C2H2-type zinc finger
     0.0036   17.7   2.1      0.013   15.9   2.1    2.0  1  zf-H2C2_2  Zinc-finger double domain
     0.0041   17.4   2.7     0.0092   16.3   2.7    1.5  1  zf-C2H2_8  C2H2-type zinc ribbon
  ------ inclusion threshold ------
        2.5    9.0   7.7       0.56   11.1   3.7    1.9  2  DUF1764    Eukaryotic protein of unknown function (DUF1764)
        4.4    8.1   6.9        1.6    9.5   1.5    2.7  3  zf-TRAF    TRAF-type zinc finger


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0015       4.5       1      23 []     217     241 ..     217     241 .. 0.96
   2 !   18.6   2.5   6.2e-07    0.0019       1      23 []     247     271 ..     247     271 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                                    EEET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                    y Cp  +C++  ++ s  krH+ +H
  gene667|gene667|rna666|rna666 217 YICPyeGCTMELPTLSRIKRHYIVH 241
                                    89*******************9998 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 6.2e-07
                                    EEET..TTTEEESSHHHHHHHHHCC CS
                        zf-C2H2   1 ykCp..dCgksFkrksnLkrHirtH 23 
                                    +kC   dC+k+F+rk+n+ +H+++H
  gene667|gene667|rna666|rna666 247 FKCLnkDCNKRFSRKDNMLQHYKIH 271
                                    899999*****************99 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0018       5.3       1      23 [.     217     241 ..     217     242 .. 0.94
   2 !   12.6   1.2   6.5e-05      0.19       5      23 ..     251     271 ..     247     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0018
                      zf-C2H2_4   1 fkCpi..CgksFsskkaLlrHlkth 23 
                                    ++Cp+  C+   ++ ++++rH   h
  gene667|gene667|rna666|rna666 217 YICPYegCTMELPTLSRIKRHYIVH 241
                                    89*******************9888 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.5e-05
                      zf-C2H2_4   5 i..CgksFsskkaLlrHlkth 23 
                                       C+k+Fs+k+++l+H k h
  gene667|gene667|rna666|rna666 251 NkdCNKRFSRKDNMLQHYKIH 271
                                    455***************998 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.1   4.4e-06     0.013       3      25 ..     235     259 ..     234     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.4e-06
                      zf-H2C2_2   3 rrHirkHtgekpyeCp..lCdkaFk 25 
                                    +rH  +Ht+ +p++C    C+k+F+
  gene667|gene667|rna666|rna666 235 KRHYIVHTKLRPFKCLnkDCNKRFS 259
                                    79**************988*****8 PP

>> zf-C2H2_8  C2H2-type zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.7   3.1e-06    0.0092      18      90 ..     198     272 ..     188     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.1e-06
                      zf-C2H2_8  18 aqhlrvhlsptqsleg.klfrcstascaetfpsmqelvahtklhykpnryfkcen..cllrfrthrslfkhlhvcs 90 
                                       +++ + p +s +g k + c    c+  +p++  +  h  +h k  r fkc n  c  rf  +  +++h ++ +
  gene667|gene667|rna666|rna666 198 FADFETSMFPYKSKNGiKSYICPYEGCTMELPTLSRIKRHYIVHTKL-RPFKCLNkdCNKRFSRKDNMLQHYKIHC 272
                                    456788999999*99978899***********************985.89***6655******9999999998744 PP

>> DUF1764  Eukaryotic protein of unknown function (DUF1764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1         3     9e+03      24      26 ..      82      84 ..      66     119 .. 0.50
   2 ?   11.1   3.7   0.00019      0.56       8      95 ..     131     222 ..     128     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3
                        DUF1764 24 eke 26
                                   +++
  gene667|gene667|rna666|rna666 82 QEN 84
                                   111 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                        DUF1764   8 keeideifseskkkkkekekeeeee....ekekkkkskkkkkkkkkkeeekkfedseskkrrktedGlpvYteeeLgigk 83 
                                    +ee+ +i+  + +k+ e +ke++e+    +++k++   + +k+++k+ ++ ++++++s +rr++ + ++ ++++    ++
  gene667|gene667|rna666|rna666 131 EEELRNIIRGRIEKHLEANKEANERkremKRRKREVLGEINKEESKEGNSPEISQEDSDSRREKIESFADFETSMFPYKS 210
                                    5566666666666665555555544344477777777788888888888999999999****************999999 PP

                        DUF1764  84 adgGgtplCPFd 95 
                                    ++g ++  CP++
  gene667|gene667|rna666|rna666 211 KNGIKSYICPYE 222
                                    99999*****97 PP

>> zf-TRAF  TRAF-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.96   2.9e+03      20      32 ..     136     148 ..     130     156 .. 0.80
   2 ?   -0.2   0.1      0.55   1.6e+03      40      54 ..     218     230 ..     214     237 .. 0.73
   3 ?    9.5   1.5   0.00053       1.6       8      37 ..     245     275 ..     237     278 .] 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.96
                                    EEETTTCCCCCCT CS
                        zf-TRAF  20 kilRkdlkdHlek 32 
                                     i+R  +++Hle+
  gene667|gene667|rna666|rna666 136 NIIRGRIEKHLEA 148
                                    589999****994 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.55
                                    XXSSXXXXSXXXXXH CS
                        zf-TRAF  40 kCkfkevGCkekvkr 54 
                                     C++   GC  ++++
  gene667|gene667|rna666|rna666 218 ICPY--EGCTMELPT 230
                                    5888..899887765 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00053
                                    SEEE-TT--S-BEEETTT.CCCCCCTTSTTS CS
                        zf-TRAF   8 apvpCpnecckkkilRkd.lkdHlekdCkka 37 
                                     p +C n++c+k  +Rkd + +H++  C++ 
  gene667|gene667|rna666|rna666 245 RPFKCLNKDCNKRFSRKDnMLQHYKIHCSYS 275
                                    6889************97699*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1785.18
//
Query:       gene668|gene668|rna667|rna667  [L=355]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-10   38.8   7.7        2.7    8.2   0.0    8.1  9  LRR_6     Leucine Rich repeat
      2e-09   37.5   0.5       0.19   12.2   0.0    5.5  6  LRR_4     Leucine Rich repeats (2 copies)
    3.8e-05   23.7  10.0        4.1    8.3   0.1    7.8  8  LRR_1     Leucine Rich Repeat


Domain annotation for each model (and alignments):
>> LRR_6  Leucine Rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0017       9.9       5      24 .]      32      51 ..      32      51 .. 0.90
   2 !    5.0   0.0    0.0049        29       4      18 ..      92     106 ..      90     106 .. 0.85
   3 ?    3.4   0.3     0.017        99       2      20 ..     118     136 ..     117     140 .. 0.86
   4 ?   -0.8   0.0      0.38   2.3e+03       3      14 ..     150     161 ..     148     162 .. 0.85
   5 ?    1.2   0.0     0.084     5e+02       4      15 ..     178     189 ..     177     192 .. 0.87
   6 !    7.4   0.2   0.00088       5.2       1      16 [.     202     217 ..     202     221 .. 0.83
   7 !    8.2   0.0   0.00046       2.7       4      23 ..     232     251 ..     232     252 .. 0.92
   8 ?    1.6   0.0     0.064   3.8e+02       8      18 ..     277     287 ..     276     292 .. 0.75
   9 ?   -2.6   0.0       1.4   8.2e+03       4      13 ..     300     309 ..     299     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0017
                          LRR_6  5 LteLdLsgNdIgDeGaeaLa 24
                                   L e+dLsgN+++ e +e ++
  gene668|gene668|rna667|rna667 32 LVEVDLSGNHFSEEAMEEIC 51
                                   6799********99999887 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0049
                          LRR_6   4 hLteLdLsgNdIgDe 18 
                                    ++++ dLs+N I+ e
  gene668|gene668|rna667|rna667  92 KIQKIDLSDNAISSE 106
                                    68899*******876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.017
                          LRR_6   2 nthLteLdLsgNdIgDeGa 20 
                                    +t L +L ++ +++g +G+
  gene668|gene668|rna667|rna667 118 STDLVHLKMNNCGLGKVGG 136
                                    67899***********997 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.38
                          LRR_6   3 thLteLdLsgNd 14 
                                    ++L+ +d++ N 
  gene668|gene668|rna667|rna667 150 SKLEVVDIAQNR 161
                                    79******9996 PP

  == domain 5  score: 1.2 bits;  conditional E-value: 0.084
                          LRR_6   4 hLteLdLsgNdI 15 
                                    +++eL +++N I
  gene668|gene668|rna667|rna667 178 NIKELRIQYNTI 189
                                    689*******99 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.00088
                          LRR_6   1 snthLteLdLsgNdIg 16 
                                    sn++L+ Ld+++N ++
  gene668|gene668|rna667|rna667 202 SNHSLEVLDIRDNFLS 217
                                    69***********555 PP

  == domain 7  score: 8.2 bits;  conditional E-value: 0.00046
                          LRR_6   4 hLteLdLsgNdIgDeGaeaL 23 
                                    +L+eL + ++ +g+eG++ +
  gene668|gene668|rna667|rna667 232 NLKELRVGDCMMGNEGVKEF 251
                                    69***************975 PP

  == domain 8  score: 1.6 bits;  conditional E-value: 0.064
                          LRR_6   8 LdLsgNdIgDe 18 
                                    Ld+s+N++  +
  gene668|gene668|rna667|rna667 277 LDISYNEFEQD 287
                                    9*****98655 PP

  == domain 9  score: -2.6 bits;  conditional E-value: 1.4
                          LRR_6   4 hLteLdLsgN 13 
                                    +++eL + gN
  gene668|gene668|rna667|rna667 300 TIKELGVFGN 309
                                    8999*99998 PP

>> LRR_4  Leucine Rich repeats (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.012        69      19      33 ..      25      40 ..      17      50 .. 0.77
   2 !   12.2   0.0   3.2e-05      0.19       2      37 ..      92     132 ..      91     141 .. 0.77
   3 !    8.1   0.0   0.00064       3.8       2      36 ..     151     189 ..     150     193 .. 0.77
   4 !    9.1   0.4   0.00031       1.8       2      40 ..     178     219 ..     177     228 .. 0.75
   5 !    5.0   0.1    0.0059        35       2      18 ..     205     220 ..     204     245 .. 0.63
   6 ?   -3.2   0.0       2.2   1.3e+04       8      20 ..     296     308 ..     295     310 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.012
                                   HHH.-TT--EEE-.-S CS
                          LRR_4 19 lek.lpnLkeLdLsgN 33
                                   ++k l+ L e+dLsgN
  gene668|gene668|rna667|rna667 25 IRKsLDELVEVDLSGN 40
                                   5555999******999 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.2e-05
                                    S--EEE--SS---.E-S-.HH....H-TT--EEE-.-S---- CS
                          LRR_4   2 nLevLdLsnNqlt.dipl.le....klpnLkeLdLsgNnlit 37 
                                    + +++dLs+N ++ ++p+ ++    + ++L +L ++++  ++
  gene668|gene668|rna667|rna667  92 KIQKIDLSDNAISsEFPPeFGefisSSTDLVHLKMNNC-GLG 132
                                    6799*********6666673366656999******555.555 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00064
                                    S--EEE--SS---E-S-.HH....H-TT--EEE-.-S--- CS
                          LRR_4   2 nLevLdLsnNqltdipl.le....klpnLkeLdLsgNnli 36 
                                    +Lev+d+++N+  ++p  l+    k+ n keL +  N  i
  gene668|gene668|rna667|rna667 151 KLEVVDIAQNRFFSFPKeLSdallKFENIKELRIQYN-TI 189
                                    8**********77777763344549*********777.33 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00031
                                    S--EEE--SS---E-S-...HH..H-TT--EEE-.-S-----GG CS
                          LRR_4   2 nLevLdLsnNqltdipl...le..klpnLkeLdLsgNnlitdld 40 
                                    n ++L ++ N + +      l+  ++ +L++Ld+ + n++ +l+
  gene668|gene668|rna667|rna667 178 NIKELRIQYNTIEEETMllfLRsfSNHSLEVLDI-RDNFL-SLE 219
                                    7899999999988866666544555777******.65587.665 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.0059
                                    S--EEE--SS---E-S- CS
                          LRR_4   2 nLevLdLsnNqltdipl 18 
                                    +LevLd+++N l+ +++
  gene668|gene668|rna667|rna667 205 SLEVLDIRDNFLS-LEG 220
                                    6888888888877.555 PP

  == domain 6  score: -3.2 bits;  conditional E-value: 2.2
                                    --SS---E-S-HH CS
                          LRR_4   8 LsnNqltdiplle 20 
                                    ++ N +++++ ++
  gene668|gene668|rna667|rna667 296 CRRNTIKELGVFG 308
                                    5678999888765 PP

>> LRR_1  Leucine Rich Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.083     5e+02       2      12 ..      32      42 ..      31      79 .. 0.74
   2 ?    3.5   0.0     0.026   1.6e+02       1      21 [.      92     112 ..      92     114 .. 0.84
   3 ?    0.5   0.1      0.25   1.5e+03       2      12 ..     121     131 ..     120     146 .. 0.76
   4 ?    4.0   0.0     0.018   1.1e+02       1      18 [.     151     168 ..     151     174 .. 0.86
   5 ?   -1.1   0.1      0.85   5.1e+03       1      12 [.     178     189 ..     178     203 .. 0.70
   6 !    8.3   0.1   0.00069       4.1       1      20 [.     205     224 ..     205     227 .. 0.80
   7 ?    1.0   0.0      0.18   1.1e+03       1      11 [.     232     242 ..     232     253 .. 0.81
   8 ?    1.1   0.0      0.17     1e+03       4      14 ..     276     286 ..     275     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.083
                          LRR_1  2 LrhLdLsnnpl 12
                                   L + dLs+n++
  gene668|gene668|rna667|rna667 32 LVEVDLSGNHF 42
                                   56789999998 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                          LRR_1   1 nLrhLdLsnnpllglppnsfq 21 
                                    + +++dLs+n +++  p+ f 
  gene668|gene668|rna667|rna667  92 KIQKIDLSDNAISSEFPPEFG 112
                                    5789*******9999998886 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.25
                          LRR_1   2 LrhLdLsnnpl 12 
                                    L hL ++n+ l
  gene668|gene668|rna667|rna667 121 LVHLKMNNCGL 131
                                    779999***98 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.018
                          LRR_1   1 nLrhLdLsnnpllglppn 18 
                                    +L++ d+ +n+++++p++
  gene668|gene668|rna667|rna667 151 KLEVVDIAQNRFFSFPKE 168
                                    79**********999876 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.85
                          LRR_1   1 nLrhLdLsnnpl 12 
                                    n ++L + +n +
  gene668|gene668|rna667|rna667 178 NIKELRIQYNTI 189
                                    679999999976 PP

  == domain 6  score: 8.3 bits;  conditional E-value: 0.00069
                          LRR_1   1 nLrhLdLsnnpllglppnsf 20 
                                    +L++Ld+++n+l+  +++++
  gene668|gene668|rna667|rna667 205 SLEVLDIRDNFLSLEGSRYL 224
                                    69*********976666665 PP

  == domain 7  score: 1.0 bits;  conditional E-value: 0.18
                          LRR_1   1 nLrhLdLsnnp 11 
                                    nL++L ++++ 
  gene668|gene668|rna667|rna667 232 NLKELRVGDCM 242
                                    8******9996 PP

  == domain 8  score: 1.1 bits;  conditional E-value: 0.17
                          LRR_1   4 hLdLsnnpllg 14 
                                     Ld+s+n +++
  gene668|gene668|rna667|rna667 276 ILDISYNEFEQ 286
                                    69*****9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.36s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 1944.49
//
Query:       gene669|gene669|rna668|rna668  [L=691]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-49  167.9   0.0    4.7e-49  167.1   0.0    1.4  1  Pkinase         Protein kinase domain
      3e-36  125.0   0.0    4.5e-36  124.5   0.0    1.2  1  Pkinase_Tyr     Protein tyrosine kinase
    7.2e-06   26.1   0.2    1.8e-05   24.9   0.2    1.7  1  OSR1_C          Oxidative-stress-responsive kinase 1 C-termin
     0.0064   15.3   0.0      0.014   14.2   0.0    1.6  2  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.1   0.0   1.1e-52   4.7e-49       4     264 .]      56     308 ..      52     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 1.1e-52
                                    EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH..HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--T CS
                        Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkke..kkvlrEikilkklkhpnivrlyevfeekdelylvleyve 81 
                                    ++ lGeG+f kVyka+++e+gk+vA  +ik +++ ++ +  + +++Ei +lk+++hpni+r+++++ ++d++++++e+++
  gene669|gene669|rna668|rna668  56 QTILGEGTFKKVYKAIDQEEGKEVAWNEIKISEKGQDCKerTLFANEIGLLKSISHPNILRILDYWFTPDSFIFITELMS 135
                                    4679*********************99998887766555457899*********************************** PP

                                    TEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTT..EE-SS-SGGGEEEE.TTTEEEE-SGTTSEESSSSCSBCTTT CS
                        Pkinase  82 ggeladllerkgslseeeakkiakqilegleylHskg..iiHrDlKpeNiLid.ekgelKitDFGlakelessskltsfv 158
                                    gg+l +++ + g l+ + +kk+ ++ilegl ylH ++  iiHrD+K eNi+++   ge+Ki+D+G+ake + +    ++v
  gene669|gene669|rna668|rna668 136 GGTLREYIAEIGDLNVKLIKKWGRSILEGLVYLHGQNppIIHRDIKCENIFVNaALGEVKIGDLGVAKERRMKR--YTVV 213
                                    **********************************99999**************88999**********998865..99** PP

                                    SCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HH.H CS
                        Pkinase 159 gtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseisee.a 237
                                    gt++++A E+ ++++y +k+Dv++ G+ l+e+ tg  p+++ ++  +v+k + q            +     s+i++  +
  gene669|gene669|rna668|rna668 214 GTPQFMAREMFEGEGYCEKIDVYAFGMCLIEMATGAYPYKECTTAAEVYKAIIQ-----------GVPPVALSSIKDIcL 282
                                    ****************************************77776666666666...........222334455544405 PP

                                    HHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 238 kdllkkllkkdpkkRltaeellqhpyl 264
                                    ++l+ ++l   +k+Rl   e+l+h+++
  gene669|gene669|rna668|rna668 283 RNLVMNCLV-SEKDRLRSVECLKHHFF 308
                                    677777774.56788988889988887 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0     1e-39   4.5e-36       3     246 ..      55     294 ..      54     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 1e-39
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE- CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivtey 82 
                                    l++ lGeG+f kV+++  + e+ k+     +K+ +++++ +e++ + +e+ ++k+++hpni+++l      ++ +++te+
  gene669|gene669|rna668|rna668  55 LQTILGEGTFKKVYKAIDQ-EEGKEVAWNEIKISEKGQDCKERTLFANEIGLLKSISHPNILRILDYWFTPDSFIFITEL 133
                                    5778************999.6666666667************************************************** PP

                                    -TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTT..EEEST-SGGGEEEEETT.EEEE-STTTHEETTTSSEE CS
                    Pkinase_Tyr  83 vkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskk..lvHrdlaarNvLlsenk.vvkisDfGLardiekddey 159
                                    ++gG+L++++ +     l++k + ++   + +G+ yL+ ++  ++Hrd+ + N++++     vki+D G+a++   + ++
  gene669|gene669|rna668|rna668 134 MSGGTLREYIAEI--GDLNVKLIKKWGRSILEGLVYLHGQNppIIHRDIKCENIFVNAALgEVKIGDLGVAKERRMKRYT 211
                                    ***********98..99*********************99888**************97659**********99433333 PP

                                    EETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTS.HHHHHHHHHHTTEES-BBTTSBH.HHHHH CS
                    Pkinase_Tyr 160 vkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypgl.kneevleklkegkrlekpekcpe.elyel 237
                                              ++ma E+++ + + +k Dv++fG++l+E++t g+ py+++ +++ev++++ +g    + +++++  l +l
  gene669|gene669|rna668|rna668 212 -----VVGTPQFMAREMFEGEGYCEKIDVYAFGMCLIEMAT-GAYPYKECtTAAEVYKAIIQGVPPVALSSIKDiCLRNL 285
                                    .....344679******************************.********8999******99887665555544156777 PP

                                    HHHHT-SSG CS
                    Pkinase_Tyr 238 mkkcweedp 246
                                    +++c+ +++
  gene669|gene669|rna668|rna668 286 VMNCLVSEK 294
                                    888876655 PP

>> OSR1_C  Oxidative-stress-responsive kinase 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.2     4e-09   1.8e-05      23      60 ..     361     398 ..     359     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4e-09
                         OSR1_C  23 IqFeFdlgkDtaeevaqelvkaglvdeeDvkvvaknlq 60 
                                    I+F+++l++Dt+e+va+e+ + + v+e+   +  k+l 
  gene669|gene669|rna668|rna668 361 IKFDYNLETDTVEDVANEMLEEEVVSEDQRDTLLKLLS 398
                                    9************************9987777777665 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.2e-06     0.014     327     388 ..     174     226 ..     159     238 .. 0.81
   2 ?   -3.5   0.1      0.75   3.3e+03     198     231 ..     371     407 ..     367     477 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-06
                 Pkinase_fungal 327 giLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkg 388
                                     i+HrDi  +Ni ++     +  +  + DL +ake        ++ + +GT++Fma e+ +g
  gene669|gene669|rna668|rna668 174 PIIHRDIKCENIFVN----AALGEVKIGDLGVAKERRM-----KRYTVVGTPQFMAREMFEG 226
                                    59*************....56778889********996.....334579*******999886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.75
                 Pkinase_fungal 198 gvegvarlvahedve..ekdddi.aeiRkgldvtkae 231
                                     ve+va  + +e+v   ++ d+  + + +g++  k++
  gene669|gene669|rna668|rna668 371 TVEDVANEMLEEEVVseDQRDTLlKLLSRGIERAKER 407
                                    5777777776666665666666666666666665553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 4669.65
//
Query:       gene670|gene670|rna669|rna669  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 492.46
//
Query:       gene67|gene67|rna67|rna67  [L=111]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 660.67
//
Query:       gene671|gene671|rna670|rna670  [L=507]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     4e-146  487.4   0.3   5.2e-146  487.1   0.3    1.1  1  PGI         Phosphoglucose isomerase
  ------ inclusion threshold ------
       0.14   12.4   3.7        7.7    6.8   0.4    2.4  2  Phi-29_GP4  Phi-29-like late genes activator (early protein G


Domain annotation for each model (and alignments):
>> PGI  Phosphoglucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  487.1   0.3  5.8e-150  5.2e-146       1     485 [.      33     498 ..      33     499 .. 0.94

  Alignments for each domain:
  == domain 1  score: 487.1 bits;  conditional E-value: 5.8e-150
                                    E-TTSS--HHHHHHHHHHHHHTTHHHHHHHHHTT---BTTTTB---HHHHT-TT----EETTEESHHH.....HHHHHHH CS
                            PGI   1 dysknkvddeilealvklaeeaklkaarealfaGekinstenravlhvalrnrsnkpilvdGkdvvpe.....vkevldk 75 
                                    d+sk ++++ei++ +  l + +++ ++++ +f+Gekin+te+r vlhvalr+++   ++  Gkdv  +     v + l k
  gene671|gene671|rna670|rna670  33 DFSKTHLTEEIIDGY--LEKMKDFGKKIDGMFSGEKINFTEDRKVLHVALRDKEVLRMVDGGKDVKLDedrrmVYDELMK 110
                                    9***********987..55778899******************************9999899999754222236667789 PP

                                    HHHHHHHHHTT-SB-TTS-B--EEEEE--GGGTHHHHHHHHHTGGG-TT.-EEEEE--SSHHHHHHHHTT--GGGEEEEE CS
                            PGI  76 mkefsekvrsGewkGatgkaitdvvniGiGGsdlGPvlvtealkkeser.lkvafvsnvdgthiaevlkkldpettlfiv 154
                                    +k f+e ++ G   G tgk +  +vniGiGGsdlGP +v +al ++ ++ ++  f+sn+d+t+  +v++k+dpe++lfiv
  gene671|gene671|rna670|rna670 111 IKRFVEDFDNGRICGVTGKRLATIVNIGIGGSDLGPRMVCDALSHYGRKgMETYFISNIDATDTIKVFEKIDPERALFIV 190
                                    **********************************************9988****************************** PP

                                    E-SSS--HHHHHHHHHHHHHHHHHH--.GGGG.GGTEEEESS-HHHHHHHT--GGGEEE--TTS-GGG-TTSGGGHHHHH CS
                            PGI 155 asktfttaetllnaesakewllkalke.dsav.akhfvalstnaekveefGideknmfefwdwvGGryslwsaiGlsval 232
                                    +sktftt et+ nae a+++l k+l++ +s++ +khfva+s+n e+v++  i  +++f++wd+vGGr+slwsa+G+s+al
  gene671|gene671|rna670|rna670 191 VSKTFTTLETIKNAELAMKFLEKRLGKsKSEIaSKHFVAVSSNVEEVKKHSI--SRVFSMWDFVGGRFSLWSAVGMSIAL 268
                                    *********************99987755555269****************9..589*********************** PP

                                    HH-HHHHHHHHHHHHHHHHHHHHS-GGG-HHHHHHHHHHHHHHTS---EEEEEES-GGGTTHHHHHHHHHHHHH---BBT CS
                            PGI 233 siGfenfeelleGaaaidkhfleaplekniPvllalvgvwyvnflgaeteailpydqylerlaaylqqldmesnGksvtk 312
                                    +iGf+nf +ll+Ga a+d+ f++     n+ ++ a+v+++y++  g++ + +++ydqy+e++  ylqq +mesnGk+ ++
  gene671|gene671|rna670|rna670 269 YIGFDNFMRLLKGASAVDEEFRKNKGKSNAEMVHAIVEIFYSE-NGYNNKCLVSYDQYMEKFYLYLQQAEMESNGKQSER 347
                                    *****************************************87.7*******************************9887 PP

                                    TS-B-SS--S-EEE---TTTGGGTSHHHHHHSSS---EEEEEEEE-S-GGGGHHHHHHHHHHHHHHHHHHH-B-HHHHHH CS
                            PGI 313 dgvlvdvetgeiifGeagtngqhafyqlihqGtkliPcdfiaavksqnieiadhhkillsnffaqtealmvGkseeevkk 392
                                           +tg ii+G+ gtn+qh+f+ql+hqGt+ i ++f++++k  + + ++ hk ++sn +aq+  lmvGk+      
  gene671|gene671|rna670|rna670 348 G------DTGLIIWGGLGTNTQHSFFQLLHQGTRKILVEFLMPLKPLH-SEEEYHKLVVSNCLAQSRGLMVGKK------ 414
                                    6......69*************************************99.788999******************9...... PP

                                    HHHHTHHHHHGGGG-B-----EEEEEEEE--HHHHHHHHHHHHHHHHHHHHHHTB-TT--GGGHHHHHHHHHHHHHHSSS CS
                            PGI 393 elakakveklvphktfeGnrPsnsillekltpaelGalialyehkilvqGviwginsfdqwGvelGkelakkilkeleas 472
                                    e          p k+feGn+Ps +i  + ltp +lG +ia yehki++ G+ wginsfdq Gv lGk++a ++l+ le++
  gene671|gene671|rna670|rna670 415 ES--------TPEKSFEGNKPSITICYSMLTPETLGGMIAHYEHKIFILGLYWGINSFDQPGVTLGKKIAIEVLETLESK 486
                                    33........699***************************************************************9876 PP

                                    ----SS-HHHHHH CS
                            PGI 473 ekvsdfdsstngl 485
                                     + +++d+stn +
  gene671|gene671|rna670|rna670 487 -EDGKYDGSTNEI 498
                                    .889******976 PP

>> Phi-29_GP4  Phi-29-like late genes activator (early protein GP4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0014        13      24      54 ..      30      60 ..      21      69 .. 0.84
   2 ?    6.8   0.4   0.00085       7.7      21      50 ..     302     331 ..     287     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0014
                                   EEEEESSHHHHHHHHHHHHHHHHHHHHHHHT CS
                     Phi-29_GP4 24 vtfffsselylnkfldgyqeyrkkfnkkier 54
                                   + + fs     ++++dgy e  k f kki+ 
  gene671|gene671|rna670|rna670 30 IYYDFSKTHLTEEIIDGYLEKMKDFGKKIDG 60
                                   4566788888899****************85 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00085
                                    -SSEEEEESSHHHHHHHHHHHHHHHHHHHH CS
                     Phi-29_GP4  21 ntdvtfffsselylnkfldgyqeyrkkfnk 50 
                                     + v +f+s + y nk l  y++y +kf  
  gene671|gene671|rna670|rna670 302 HAIVEIFYSENGYNNKCLVSYDQYMEKFYL 331
                                    456889*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3203.89
//
Query:       gene672|gene672|rna671|rna671  [L=231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-21   75.4   1.5    2.3e-17   63.4   0.3    2.2  2  BIR       Inhibitor of Apoptosis domain
  ------ inclusion threshold ------
      0.035   14.1   0.9       0.14   12.2   0.2    2.1  2  zf-C3HC   C3HC zinc finger-like
       0.38   10.8   4.2        6.9    6.8   1.3    2.9  2  Elf1      Transcription elongation factor Elf1 like


Domain annotation for each model (and alignments):
>> BIR  Inhibitor of Apoptosis domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.3   3.8e-21   2.3e-17       1      72 [.       7      75 ..       7      76 .. 0.93
   2 !   11.0   0.0   8.5e-05      0.51       1      47 [.      83     121 ..      83     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3.8e-21
                            BIR  1 RlatFkknWpeskkeakpsaeeLaeaGFyytptseskdnvqCfyCklaldgweedDdpleeHkkhspkCefl 72
                                   R++tF  +Wpe       ++e+L+ aGF++  t+e + +v+C+yC+++l+ we++D p++eH+ h +kC+++
  gene672|gene672|rna671|rna671  7 RMETFA-KWPEGY--GVATPERLSVAGFVCLSTEEGNLTVECVYCHKTLECWERTDLPVREHYLHMSKCPLF 75
                                   99***5.5**655..679999************************************************987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.5e-05
                            BIR   1 RlatFkknWpeskkeakpsaeeLaeaGFyytptseskdnvqCfyCkl 47 
                                    R++ F + W +      ++a++La+ GF+ ++   + d + C+ C+ 
  gene672|gene672|rna671|rna671  83 RVNMF-NGWDS------KEAKALARIGFVKYNL-GDADFIFCYKCGS 121
                                    67778.45883......45789*********99.899********85 PP

>> zf-C3HC  C3HC zinc finger-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   2.3e-05      0.14       6      54 ..       3      53 ..       1      71 [. 0.86
   2 ?   -0.2   0.0      0.16   9.4e+02      30      51 ..      97     121 ..      83     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                        zf-C3HC  6 dllrRlkTfkalkWtskpselselkcAkrGWkcvs....kdrlkCevCgaslv 54
                                   ++ +R++Tf   kW + +   ++ +++  G++c s    + +++C+ C+++l 
  gene672|gene672|rna671|rna671  3 SFKERMETFA--KWPEGYGVATPERLSVAGFVCLSteegNLTVECVYCHKTLE 53
                                   58899***96..7999*****************665566779********995 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.16
                        zf-C3HC  30 kcAkrGWkc...vskdrlkCevCga 51 
                                    ++A+ G++     ++d + C  Cg+
  gene672|gene672|rna671|rna671  97 ALARIGFVKynlGDADFIFCYKCGS 121
                                    6799999884445599999*99985 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.3    0.0011       6.9      37      72 ..      34      90 ..      29      94 .. 0.73
   2 ?    3.2   0.1     0.015        89      46      70 ..     114     146 ..     106     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                           Elf1 37 ldkkekiaevsCkvCge....................sfe.tkvnalsepvDvYskw 72
                                   l+++e++ +v+C +C++                    ++  ++vn+++++v++++ w
  gene672|gene672|rna671|rna671 34 LSTEEGNLTVECVYCHKtlecwertdlpvrehylhmsKCPlFNVNKIESRVNMFNGW 90
                                   78899999*********7777777777777777766544346677777777777766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.015
                           Elf1  46 vsCkvCge........sfetkvnalsepvDvYs 70 
                                    + C +Cg+        + + +v +l+ ++D+++
  gene672|gene672|rna671|rna671 114 IFCYKCGSidkghscrRKRGSVYNLERRIDIFF 146
                                    67999999888887766668899********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1443.50
//
Query:       gene673|gene673|rna672|rna672  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-48  162.7   0.2    6.6e-48  161.8   0.2    1.4  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   0.2   3.7e-52   6.6e-48       1     125 []       1     125 [.       1     125 [. 0.99

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 3.7e-52
                                    -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTS CS
                  Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskgg 80 
                                    mklni++p++g+qk +e++ ++  +l++k+ig+++dg++lGee++g +++itgg d qGfpm +g lt++rvr Llskg+
  gene673|gene673|rna672|rna672   1 MKLNIAYPTNGTQKIFEIERRNEVKLYDKKIGDQFDGGILGEEFEGAIMEITGGDDYQGFPMVKGHLTKKRVRPLLSKGD 80 
                                    9******************************************************************************* PP

                                    SSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TTTSS CS
                  Ribosomal_S6e  81 vgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdiegltd 125
                                     gyr+rrkG r+rksvrG+ivs++i++lnl++ + gek+i+glt+
  gene673|gene673|rna672|rna672  81 AGYRCRRKGVRRRKSVRGSIVSEEICVLNLIMLRPGEKEIDGLTN 125
                                    *******************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1517.14
//
Query:       gene674|gene674|rna673|rna673  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-25   88.5   0.0    7.6e-25   87.9   0.0    1.3  1  PseudoU_synth_2  RNA pseudouridylate synthase
    5.9e-05   23.5   0.0    9.6e-05   22.8   0.0    1.3  1  TruB_N           TruB family pseudouridylate synthase (N term


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   8.5e-29   7.6e-25       1     159 [.      91     227 ..      91     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 8.5e-29
                PseudoU_synth_2   1 dlvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkY 80 
                                    d++vvnKP g+p++p++         ++ +  ra  + k++  ++RLD ++sG+l++A+ +++++ l +    +   K Y
  gene674|gene674|rna673|rna673  91 DYIVVNKPPGIPCHPTG-------GYREYSITRALFDDKKVACINRLDMPVSGVLIIAT-KNYSRCLER---IKDAVKIY 159
                                    69***************.......66666777888999********************9.555555544...477***** PP

                PseudoU_synth_2  81 lalvfgapeeeegaikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkhQiRvhla 159
                                    +a v ++  +e   ++k+i+         ++   +++gk   t ++ l+++      ++slve++++tGr+hQiR+hl+
  gene674|gene674|rna673|rna673 160 VAKV-CGVFPERVDVDKSIKC-----TEGKNRCVNDEGKACLTLFRRLEYK-----DGYSLVECRPVTGRTHQIRIHLQ 227
                                    ****.8*************99.....4555555567899************.....*********************98 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.1e-08   9.6e-05       1      49 [.     116     164 ..     116     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-08
                                    HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEE CS
                         TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatir 49 
                                    + l++ kkv     LD  ++GvL++a+ ++ ++le +++a K Y+a++ 
  gene674|gene674|rna673|rna673 116 RALFDDKKVACINRLDMPVSGVLIIATKNYSRCLERIKDAVKIYVAKVC 164
                                    5678899**************************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2229.19
//
Query:       gene675|gene675|rna674|rna674  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-14   51.8   9.7    9.6e-14   51.8   9.7    3.3  3  GWT1      GWT1


Domain annotation for each model (and alignments):
>> GWT1  GWT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.061   1.1e+03      87     124 ..      43      80 ..      10      89 .. 0.63
   2 ?    0.2   2.8     0.042   7.6e+02      13      99 ..     115     194 ..      87     221 .. 0.60
   3 !   51.8   9.7   5.3e-18   9.6e-14       1     145 [.     234     349 ..     234     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.061
                           GWT1  87 Yvlwvvalnltllllflliellfvekeeekerkekats 124
                                    Y+ +++   + +l l+l+i   +++ +++ke+++++ts
  gene675|gene675|rna674|rna674  43 YCAIMFPNEIWILYLCLVILAKYPKIRRSKETTNEKTS 80 
                                    55555555555555555443323344444444444433 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.042
                           GWT1  13 laiyllgvslgkyvlkrekeaeeeekkkkkkkkesketlkllikllllsilllllllllelyvef.vSRrlaNlpYvlwv 91 
                                    l i l+ +++g++++++       + k++     +++ +k    l+ll ++ ++++ ++++ v++       N+ + l +
  gene675|gene675|rna674|rna674 115 LGISLMDIGVGSFIYNSGVV----RCKSR----FKRKHVKSYLILILLGFVRFFVVKWFNISVNPkEYGTHLNFYFLLAI 186
                                    55666777777777722221....11122....22223333333444444444444444444444333455666666666 PP

                           GWT1  92 valnltll 99 
                                    v + ++++
  gene675|gene675|rna674|rna674 187 VNFICSMV 194
                                    66666655 PP

  == domain 3  score: 51.8 bits;  conditional E-value: 5.3e-18
                           GWT1   1 aNkEGlfsliGylaiyllgvslgkyvlkrekeaeeeekkkkkkkkesketlkllikllllsilllllllllelyvefvSR 80 
                                    +NkEGl+ +i y++i+l+++++g++ l+                  + ++ + + ++l +s ++ +l++++ + +e  SR
  gene675|gene675|rna674|rna674 234 KNKEGLTAIISYVSIFLMATEVGRICLS------------------QGKIRRKALRVLGMSGIFACLYVTSCFSCEG-SR 294
                                    6**************************2..................2334566677777777777776666666666.** PP

                           GWT1  81 rlaNlpYvlwvvalnltllllflliellfvekeeekerkekatstvleainrngLlvFLlaNllt 145
                                    rl N+++v+w++al ++ + +++l+e           +    ++ v+  +++n++++FL++Nl++
  gene675|gene675|rna674|rna674 295 RLGNAAFVFWILALHTFHVGIYMLLES----------TIVMYNPLVVMFCSSNMMFIFLFSNLIV 349
                                    ***********************9999..........34578899999**************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2455.40
//
Query:       gene676|gene676|rna675|rna675  [L=540]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-18   67.0   0.1    3.2e-18   66.4   0.1    1.3  1  GCP_N_terminal  Gamma tubulin complex component N-terminal


Domain annotation for each model (and alignments):
>> GCP_N_terminal  Gamma tubulin complex component N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   1.8e-22   3.2e-18       1     262 [.      21     256 ..      21     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1.8e-22
                 GCP_N_terminal   1 lrdllylLqGisgklirfdekddervvkdvrlpgllppslr.slverllelgtlyrrlrkfveevsrsesglvlqalaaa 79 
                                    l+ l+ylL G++ ++i++  kd+       r++ + +p+   +lv  + +l+ ++r l+kf+ + s+++s  +++ + + 
  gene676|gene676|rna675|rna675  21 LENLFYLLCGVDTTHIKVGVKDK-------RYALTADPTYPpQLVLPFESLAINVRILNKFILR-SQYSSDTIKEIVGDY 92 
                                    6789*************877666.......5555556655558*******************88.899999********* PP

                 GCP_N_terminal  80 ldeelteyyrliaqlEsqlledsesiltLlrlevwlqetllllrvLanlveevekanlkggallsllheaaqhgdpkvrk 159
                                    ++e ++ey+  ++ l ++         ++  l+  l +++++++ + ++v+ ++  n+ g ++l+ l ++ +    ++ +
  gene676|gene676|rna675|rna675  93 FEEKVSEYLNTLMGLRNKG-------GSIETLMINLGNSIEEFDEMKEIVDGIR--NMSGVRILNWLEKRRSKAVRFL-D 162
                                    ********99999886543.......58999***********************..999**********999777776.9 PP

                 GCP_N_terminal 160 llsellervsrpflemlekWileGelsDpynEfFveenesvakeklkeddseklweekYtlrkemlPsflseelaekIle 239
                                    l+++l+  ++  + e +e+W+ eG +  p + f+v++ne  +       + e +w+++Yt+ +e++P fl e + e I++
  gene676|gene676|rna675|rna675 163 LYDRLIDPCVLRIKEEVESWVTEGLM--PSSGFMVKKNECLNG------FTECVWTHQYTIVEENVPYFLAE-HKELIYN 233
                                    ************************55..99********99965......9999*******************.******* PP

                 GCP_N_terminal 240 tGkslnflrescgdsewiektes 262
                                    +G+ +n+ +++ g++++  ++++
  gene676|gene676|rna675|rna675 234 CGRVINLGKRIQGKNTFHGSRRE 256
                                    **********9777665332333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3289.75
//
Query:       gene677|gene677|rna676|rna676  [L=287]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-26   93.4   0.2    1.8e-26   92.8   0.2    1.3  1  RhoGAP    RhoGAP domain


Domain annotation for each model (and alignments):
>> RhoGAP  RhoGAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.2   9.9e-31   1.8e-26       1     149 [.      91     253 ..      91     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 9.9e-31
                                    BHHHHHHHHHHHHHTTTSTTTTTS-S-HHHHHHHHHHHHHTGGGCT........TTTTSCHHHHHHHHHHHHHHSSSTTT CS
                         RhoGAP   1 PiivekcvefiekrgldtegiyRvsgskarvkelreafdkgkavds........dleeedvhavaslLKrfLrelpepLl 72 
                                    P  ++ ++e + + ++++ gi+Rv  s +++ke+ e ++ + + ++         +++++v ++++++K+ Lre+ + ++
  gene677|gene677|rna676|rna676  91 PRNFYILTETVLSLDCKVGGIFRVRNSITTIKECVETINMCVQRNLsygearriLIRDFNVIDLTTAFKEILREYSTTII 170
                                    56677889999999*****************************999********************************** PP

                                    TGGHHHHHHHHHTSSSHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHH......THHHH---HHHHHHHHHHHHHT- CS
                         RhoGAP  73 tkelyeelieaaksedeeerlealkellekLPkenrdtLryLlehLkrvae......nskenkMtaknLaivfaPtLlrp 146
                                    +++l+++++++ak e++e+++  +++l+ ++Pk+nr++L++ + +L+ +++      ++++++M+++ ++++++P+L+ +
  gene677|gene677|rna676|rna676 171 PESLIDTMFKIAKVESKEDQIILCQMLFISMPKPNRHVLEATIYFLYVIHDiatdkgKNHKDNMNMEGISTIMMPNLVIK 250
                                    **************************************************95444444455*****************99 PP

                                    TSS CS
                         RhoGAP 147 kse 149
                                    +++
  gene677|gene677|rna676|rna676 251 PHS 253
                                    986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1960.48
//
Query:       gene678|gene678|rna677|rna677  [L=356]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.015   15.1   0.0        2.1    8.2   0.0    3.1  3  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.025   4.5e+02      42      61 ..     103     121 ..      90     130 .. 0.81
   2 ?    1.8   0.0     0.012   2.1e+02       7      33 ..     163     189 ..     160     216 .. 0.82
   3 ?    8.2   0.0   0.00012       2.1      13      67 ..     280     338 ..     279     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.025
                                    EEEEESSHHHHHHHHHHHTT CS
                          RRM_1  42 afVeFeskedAekAlealng 61 
                                    a VeF  + dA+++l  l +
  gene678|gene678|rna677|rna677 103 AEVEFIERQDATECLY-LSN 121
                                    569***********98.554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.012
                                    TTTSSHHHHHHHHHTTSCEEEEEEEEE CS
                          RRM_1   7 ppdvteeeLkelFskfGpiksiklvrd 33 
                                    p +++ + L++ + ++ p +s++++r+
  gene678|gene678|rna677|rna677 163 PLNIDSNLLRDALDEISPLQSFRVCRN 189
                                    6789999******************96 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00012
                                    HHHHHHHHTTSCEEEEEEEEE..TTTSEEEE..EEEEESSHHHHHHHHHHHTTEEETTE CS
                          RRM_1  13 eeLkelFskfGpiksiklvrd..etgkskgf..afVeFeskedAekAlealngkklggr 67 
                                    ee+k   sk+ ++k++ ++rd  + g+  g    f+e ++ e  ek  ++l g  +++r
  gene678|gene678|rna677|rna677 280 EEIKSRCSKYKGVKDVMVPRDslRSGRQPGSsrVFIECKDLETSEKVYDELGGLIYKDR 338
                                    7899999****************666666642279****************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2680.80
//
Query:       gene679|gene679|rna678|rna678  [L=475]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-46  159.5   0.0    1.6e-46  159.2   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
     0.0009   18.6   0.0     0.0011   18.3   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.016   13.9   0.1      0.033   12.9   0.1    1.4  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.2   0.0   2.6e-50   1.6e-46       3     363 .]     107     462 ..     106     462 .. 0.91

  Alignments for each domain:
  == domain 1  score: 159.2 bits;  conditional E-value: 2.6e-50
                                    EEESSSSSTTSTTSS..HHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                  Aminotran_1_2   3 vinLgsneylgdsgk..ptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                    ++nLgs +ylg s++  p +++v++  ++  + ++ ++ e g +d+  +lee++a+fl         +e+  v++ G+g 
  gene679|gene679|rna678|rna678 107 LLNLGSYNYLGFSNNegPIVEKVVEVVRHyPLVMTAPTREVGCYDIVRTLEEEMASFLY--------QEDCMVFSIGYGT 178
                                    79***********9999999999999999*999999***********************........999********** PP

                                    HHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE.......TEEEE CS
                  Aminotran_1_2  80 liealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnk.......ktkvi 152
                                    + + ++ +++  +++ il++++++as ++++++s+g ++ ++       h+++e+le++l  + ++ +       k+ ++
  gene679|gene679|rna678|rna678 179 NSSNIPVICE--AETLILSDELNHASLITGAKISKGVIRVFE-------HNNMEDLENKLVFNISQGQplthrswKKIIV 249
                                    *********8..******************************.......***********999999999*********** PP

                                    EEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH....HGGSTTSTTEEEEEESSSTTSSGGG CS
                  Aminotran_1_2 153 lvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat....ranveeepnllivgslsKafGlaGe 228
                                    +ve+++++ Gt+ +l++l++l   +kky++++fvDea++++++g+++        +a+v+ +  ++ +g++ K+fG +G 
  gene679|gene679|rna678|rna678 250 IVEGIYSMEGTIVNLKKLVEL---KKKYKFYIFVDEAHSIGALGATG---RgvceYAGVDFKEIDIFMGTFTKSFGGMG- 322
                                    *********************...********************552...245568888877778**************. PP

                                    -EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHSTEEEECCS.C CS
                  Aminotran_1_2 229 RvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemr...qrlqkrrkelrdeLaelglkvlasq.s 304
                                      Gyi+g+++++ +lr  s   l+  + +++v   +  +l+ ++++e  r   ++l +++  +r++L ++g+ vl+ + s
  gene679|gene679|rna678|rna678 323 --GYIAGSKKLITWLRFYSDLSLYGDQIPPFVCSQILESLRCIKFTELGRlkiEKLRSNTVLMRQSLVNAGFFVLGDEfS 400
                                    ..**********************9999999999999999999955555501155566667899***999********** PP

                                    SSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHHHH CS
                  Aminotran_1_2 305 gmflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelveal 363
                                     ++++  +++ +  e+s+ +  e g+ v+ + ++ +   ++r+R+++ A++t+e++ ++ e +
  gene679|gene679|rna678|rna678 401 PVIPILIVCPGKLAEFSRLCMAE-GIGVVVVGYPATpilTSRVRLCIsASHTTEDVMRAFEVI 462
                                    ***********999999997777.555555558888899*****************9998876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.9e-07    0.0011      34     215 ..     153     332 ..     141     462 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-07
                                    HHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHH CS
                Beta_elim_lyase  34 vnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlek 113
                                    v++Le+++a  +  e  + +  G + ns  + ++++ ++ ++ +e +h    +   i   +gv  r +++++  +++ +k
  gene679|gene679|rna678|rna678 153 VRTLEEEMASFLYQEDCMVFSIGYGTNSSNIPVICEAETLILSDELNHASLITGAKI--SKGV-IRVFEHNNMEDLE-NK 228
                                    78999****9998888888888*************9999999999999999987666..5666.6666666645555.67 PP

                                    HHHHS--S-T...TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHH.... CS
                Beta_elim_lyase 114 leaaikevga...heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemf.... 186
                                    l   i + g+   h+   k+i++   + ++ G++v l++l    ++ kky+  +++D A  + a  + g  v e++    
  gene679|gene679|rna678|rna678 229 LVFNISQ-GQpltHRSWKKIIVIVEGIYSMEGTIVNLKKL---VELKKKYKFYIFVDEAHSIGALGATGRGVCEYAgvdf 304
                                    7777888.55599*********************976665...56668**************************998888 PP

                                    TTSSEEEEESSSTT--SS-EEEEE-HH.. CS
                Beta_elim_lyase 187 syvDsvtmslkKdllanvGgvlafrddel 215
                                    + +D+++  ++K  +  +Gg +a++++ +
  gene679|gene679|rna678|rna678 305 KEIDIFMGTFTKSFGG-MGGYIAGSKKLI 332
                                    99***********776.*********944 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.5e-06     0.033      85     207 ..     172     285 ..     154     288 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-06
                                    EEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHH.HHHHS-EEEEEE--E..B-TTS-BE---GGGGSHHHHHHHHH CS
                       OKR_DC_1  85 yfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSieh.alvlsgatPvylepe..rnalgiiggidlkefeeetlkekik 161
                                    +++  GT ssn  v   ++++  l+l d  +H S+ + a +  g+  v+ + +  + +  ++ +i +         + ++
  gene679|gene679|rna678|rna678 172 FSIGYGTNSSNIPV---ICEAETLILSDELNHASLITgAKISKGVIRVFEHNNmeDLENKLVFNISQ--------GQPLT 240
                                    45556777777554...57788888888888888888677777888888655421222223333333........34444 PP

                                    HSTTTGSESEEEEESS-T..TSEEE-HHHHHHHHTTSESEEEEE-TT- CS
                       OKR_DC_1 162 evpdakaprlavitnsTY..dGvlynakeivdkleklsdrilfDeAwv 207
                                      +     + +vi  + Y   G++ n+k++v++ +k++ +i++DeA+ 
  gene679|gene679|rna678|rna678 241 HRSW---KKIIVIVEGIYsmEGTIVNLKKLVELKKKYKFYIFVDEAHS 285
                                    4444...44599999999556*************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3132.49
//
Query:       gene680|gene680|rna679|rna679  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   7.6e-110  367.0  15.8   8.5e-110  366.8  15.8    1.0  1  WD40_like  WD40-like domain
  ------ inclusion threshold ------
      0.078   12.6   0.0       0.15   11.7   0.0    1.4  1  Big_3_3    Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  366.8  15.8  9.5e-114  8.5e-110       1     301 []       3     301 ..       3     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 366.8 bits;  conditional E-value: 9.5e-114
                      WD40_like   1 eeiYsidiskkgslilyGgkddkctvlkleslesvsivesfedSvifvklldddlilvvtlDGtillslleneeevenek 80 
                                    +e+Y id++ + ++++ Gg d+kctv ++e+++++sive+f+dSvif+k++dd+ ++v +lDGti  sl+++e e++n  
  gene680|gene680|rna679|rna679   3 SEVYGIDLNARRNILIHGGGDEKCTVTDIETGDVISIVEDFSDSVIFCKFIDDERFIVSSLDGTI--SLMTLEGEINNVC 80 
                                    69***************************************************************..9************ PP

                      WD40_like  81 ieedistvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiysLsesafivfdlfsqnieykisvkd 160
                                    ++edis +k+ +d+ll+Gt  Gs+++f  dl++++v++gq  eI+++++en+k+y+Ls+++f++fd+ s++++++++v++
  gene680|gene680|rna679|rna679  81 VNEDISQIKINGDRLLVGTVGGSVHLFTLDLCIQNVCIGQCNEIQDVCYENGKVYTLSKTNFVIFDALSHQKLMDVHVRG 160
                                    ******************************************************************************** PP

                      WD40_like 161 iktfeiienkdilligtegeililkknvilqkidvegkPecillvddylivGgsfkyllliNiklnvntfklrlevegis 240
                                    ++++++i+ +d++++g eg+i+++k+ ++l ki++eg+Pecil++++y+ivGg+f+ +lliNi++ ++tfk+   +e i 
  gene680|gene680|rna679|rna679 161 GSAMDKIPLSDVVCLGLEGCIVVRKNSHLLSKISIEGSPECILYMNNYFIVGGDFEDILLINIPMGMRTFKIPTGTERIL 240
                                    ******************************************************************************** PP

                      WD40_like 241 kikkisefvvafsTlcgkvgigDiRdketfkllesgvGviydmkfenntiyvgGeaGlkil 301
                                     ik   e++++fsT+ g+vg+gDiRd+++fkl+e+gvG+i+d++f++ ++yvgGe+G+++l
  gene680|gene680|rna679|rna679 241 SIKGDGENKIVFSTCSGVVGYGDIRDERSFKLIEGGVGCIFDLCFKDKMVYVGGEHGFNAL 301
                                    **********************************************************976 PP

>> Big_3_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.6e-05      0.15      58      98 ..     130     170 ..     116     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
                        Big_3_3  58 dgavvkglenlritladaldkskltsialsGGpasDkVels 98 
                                    ++  v++l + +  + dal + kl  + ++GG+a Dk+ ls
  gene680|gene680|rna679|rna679 130 ENGKVYTLSKTNFVIFDALSHQKLMDVHVRGGSAMDKIPLS 170
                                    567899********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1870.63
//
Query:       gene68|gene68|rna68|rna68  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1245.37
//
Query:       gene681|gene681|rna680|rna680  [L=119]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.9e-05   23.8   1.2     0.0024   17.7   0.4    2.3  2  EF-hand_8  EF-hand domain pair
     0.0074   16.7   1.0        1.3    9.5   0.9    2.3  2  EF-hand_7  EF-hand domain pair
  ------ inclusion threshold ------
      0.018   14.5   0.9       0.81    9.4   0.0    3.1  3  EF-hand_1  EF hand
      0.023   14.6   0.4        9.3    6.5   0.2    2.9  3  EF-hand_6  EF-hand domain


Domain annotation for each model (and alignments):
>> EF-hand_8  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0061        27      33      51 ..      11      29 ..      11      31 .. 0.90
   2 !   17.7   0.4   5.3e-07    0.0024       3      39 ..      73     107 ..      71     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0061
                      EF-hand_8 33 refDtdgdGkisfeEFcvl 51
                                   r+fD+ ++G +s+eE+  +
  gene681|gene681|rna680|rna680 11 RAFDIGKKGFLSYEEYKGY 29
                                   68*************9875 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5.3e-07
                      EF-hand_8   3 gkItreelrrilrilglkkglseeevdilfrefDtdg 39 
                                    ++I++++l++++++l +   +s+e++ ++++ +D ++
  gene681|gene681|rna680|rna680  73 DYISFQTLKKAISKLEMS--ISNEDIAMMLDMLDSNK 107
                                    78**********999888..*************9875 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0025        11      51      70 ..      11      30 ..       2      31 .. 0.86
   2 !    9.5   0.9   0.00029       1.3      15      60 ..      71     108 ..      11     118 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0025
                      EF-hand_7 51 kefDtdkdGvisfdEFlkly 70
                                   + fD  k G +s++E++ ++
  gene681|gene681|rna680|rna680 11 RAFDIGKKGFLSYEEYKGYC 30
                                   5799999********98776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00029
                      EF-hand_7  15 gdgyldkeellrllrkifqgagegsklsdeelellfkefDtdkdGv 60 
                                    g  y++ + l++++         + ++s e +  +++++D++k  +
  gene681|gene681|rna680|rna680  71 GEDYISFQTLKKAIS------KLEMSISNEDIAMMLDMLDSNK--Q 108
                                    344555555555555......7777888888888888888887..4 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00018      0.81       7      25 ..      11      29 ..      11      33 .. 0.87
   2 ?    1.7   0.0     0.053   2.4e+02      16      29 .]      74      87 ..      71      87 .. 0.88
   3 ?   -0.3   0.2      0.23     1e+03       2      13 ..      96     107 ..      95     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00018
                                   HHHTTTSSSEEEHHHHHHH CS
                      EF-hand_1  7 refDkDgdGkIdfeEfkel 25
                                   r fD  + G++++eE+k +
  gene681|gene681|rna680|rna680 11 RAFDIGKKGFLSYEEYKGY 29
                                   579************9976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.053
                                   EEEHHHHHHHHHHH CS
                      EF-hand_1 16 kIdfeEfkellkkl 29
                                   +I+f+ +k++++kl
  gene681|gene681|rna680|rna680 74 YISFQTLKKAISKL 87
                                   8*******999875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.23
                                    HHHHHHHHTTTS CS
                      EF-hand_1   2 lkeiFrefDkDg 13 
                                    +  + +++D ++
  gene681|gene681|rna680|rna680  96 IAMMLDMLDSNK 107
                                    66799999*997 PP

>> EF-hand_6  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0045        20       7      23 ..      11      27 ..      11      35 .. 0.87
   2 ?    6.5   0.2    0.0021       9.3       5      28 ..      64      86 ..      60     104 .. 0.80
   3 ?   -1.7   0.0      0.88     4e+03       7      13 ..     101     107 ..      94     116 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0045
                      EF-hand_6  7 klfDkdgdGkidaeElr 23
                                   ++fD  + G++++eE +
  gene681|gene681|rna680|rna680 11 RAFDIGKKGFLSYEEYK 27
                                   589***********965 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0021
                      EF-hand_6  5 aFklfDkdgdGkidaeElrkalrk 28
                                   +F+ f  +g  +i+++ l+ka++k
  gene681|gene681|rna680|rna680 64 VFDFF-SSGEDYISFQTLKKAISK 86
                                   56666.66777***********96 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.88
                      EF-hand_6   7 klfDkdg 13 
                                    +++D ++
  gene681|gene681|rna680|rna680 101 DMLDSNK 107
                                    4555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.57
# Mc/sec: 632.64
//
Query:       gene682|gene682|rna681|rna681  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-29  102.9   0.2      3e-29  102.4   0.2    1.1  1  Peptidase_C48  Ulp1 protease family, C-terminal catalytic dom
     0.0053   15.5   1.3      0.011   14.4   0.1    1.9  2  Peptidase_C57  Vaccinia virus I7 processing peptidase
  ------ inclusion threshold ------
      0.072   12.7   0.0       0.11   12.1   0.0    1.3  1  LupA           Legionella ubiquitin-specific protease A domai
       0.12   12.7   0.0       0.23   11.8   0.0    1.4  1  FAM195         FAM195 family


Domain annotation for each model (and alignments):
>> Peptidase_C48  Ulp1 protease family, C-terminal catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   0.2   6.8e-33     3e-29       3     203 ..      67     225 ..      66     232 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 6.8e-33
                                    -BHHHHHHHHHHHHHHHHHCCCTCCCEEE--THHHHHHC..........SS.......TCHCHHHCTTCCCCCS..-GGG CS
                  Peptidase_C48   3 lndtvidfylkllaerlesseskaervhflntffvskLtkavkdfkknkskkkfkeskkkdlyngvrrwtrkvnkedlfd 82 
                                    lnd++i++y +ll      +++++  v++++tff++ L+                    k+++  v+rwt       +f+
  gene682|gene682|rna681|rna681  67 LNDKIINVYFELL------AKHSKVGVYVFSTFFYTTLS--------------------KRGIPWVQRWTSGI---NIFE 117
                                    9************......89******************....................89************...**** PP

                                    -SEEEEEEEC.TTEEEEEEEETCCCEEEEE-TTS-SSH.HHHHHHHHHHHHHHHHHCCCCCSTT-.GGGEEEEEEE---- CS
                  Peptidase_C48  83 kdiiyiPinedgkHWvlliinlpdktililDSlislhtvkkenrpinnlkpyLleealkkkqkqldltpfeierltkvpq 162
                                    +  +yiP+ +   HW+l++ ++++k  +++DS+++ +t     ++++++++y+ +e++   ++++   + +++ + k+p 
  gene682|gene682|rna681|rna681 118 NRLVYIPVYI-PGHWMLIVFDVKKKVLEHYDSMGNAYT-----EVVHRILRYIRDEWSRVHKSEP---SLSVDIKRKIPL 188
                                    **********.***************************.....**************76555555...889999999*** PP

                                    -SSCCCHHHHHHHHHHHHHCTHHCHHHHHSS.HHHHHHHHH CS
                  Peptidase_C48 163 qknsgDCGiyvlkfiellaegapqessvtltekdvdsfrkk 203
                                    q n+ DCG++v++f ++ ++g++ +    l++  +++frk 
  gene682|gene682|rna681|rna681 189 QRNGRDCGVFVCMFGRYRLCGNEVW----LSSDRIPRFRKL 225
                                    *************************....888999999875 PP

>> Peptidase_C57  Vaccinia virus I7 processing peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   2.5e-06     0.011     232     273 ..     117     158 ..     106     179 .. 0.86
   2 ?   -0.8   0.1       0.1   4.7e+02     327     340 ..     189     202 ..     177     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.5e-06
                  Peptidase_C57 232 kkryvmfgfiYlshwkcvvfdkekklvlFydsgGniPeefkh 273
                                    ++r v +++    hw  +vfd +kk+   yds Gn  +e+ h
  gene682|gene682|rna681|rna681 117 ENRLVYIPVYIPGHWMLIVFDVKKKVLEHYDSMGNAYTEVVH 158
                                    6899999999999**********************9888765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.1
                  Peptidase_C57 327 qlleseCGmFisiF 340
                                    q    +CG+F+++F
  gene682|gene682|rna681|rna681 189 QRNGRDCGVFVCMF 202
                                    566689*******9 PP

>> LupA  Legionella ubiquitin-specific protease A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.6e-05      0.11      44     136 ..     115     204 ..      76     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                                    HT-TT--EEEEEEE.SSS-EEEEEE--------EEEEEE-TT-HHHHGG...GHHHHHHHHHHCT--GGGEEEEEE--SS CS
                           LupA  44 ifneeikhilipvg.pghwrgvyltkpadltdefdlelfdpygpegaaa...lddfilkllekcgidkeklnirhkgpvh 119
                                    if++++  + ipv  pghw  + +  ++++     le +d  g + + +   +  +i++   +   ++  l++  k  + 
  gene682|gene682|rna681|rna681 115 IFENRL--VYIPVYiPGHWMLIVFDVKKKV-----LEHYDSMGNAYTEVvhrILRYIRDEWSRVHKSEPSLSVDIKRKIP 187
                                    455544..5567633****99988888887.....666666666555541115579999999999999999999999999 PP

                                    ----GGGHHHHHHHHHH CS
                           LupA 120 pqgdayscgdftcaysh 136
                                     q+++  cg f c +  
  gene682|gene682|rna681|rna681 188 LQRNGRDCGVFVCMFGR 204
                                    99***********9865 PP

>> FAM195  FAM195 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.2e-05      0.23       7      54 ..     135     177 ..     132     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                         FAM195   7 vFhrvngkkslrasstkeseeevitpqheElikyindsWnevvaeles 54 
                                    vF     kk++   ++ +s+ +++t+    + +yi d+W++v ++++s
  gene682|gene682|rna681|rna681 135 VFD---VKKKV--LEHYDSMGNAYTEVVHRILRYIRDEWSRVHKSEPS 177
                                    664...34444..5889999999********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1784.83
//
Query:       gene683|gene683|rna682|rna682  [L=96]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.0   0.3      0.033   14.0   0.3    1.2  1  Rep_2     Plasmid replication protein
       0.89    9.8   8.3        1.2    9.4   8.3    1.2  1  DUF3886   Protein of unknown function (DUF3886)


Domain annotation for each model (and alignments):
>> Rep_2  Plasmid replication protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   3.7e-06     0.033     125     163 ..      31      70 ..       6      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-06
                          Rep_2 125 asedkeklleeiedlieendiielaelvdylreeese.ll 163
                                    +++  +++ e+++ +i++n i e++el++y   e+ + ++
  gene683|gene683|rna682|rna682  31 DENLRREMCEKVLRFIDKNAIDEIRELIRYGLYEDLQeFV 70 
                                    45556899**********************9999988643 PP

>> DUF3886  Protein of unknown function (DUF3886)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   8.3   0.00013       1.2      28      61 ..       2      36 ..       1      40 [. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00013
                        DUF3886 28 keeeekrkeeekarreeerkarek.nksfeelLee 61
                                   k++ ++++ e k + +ee++++e+ n+sf+e L  
  gene683|gene683|rna682|rna682  2 KKSPKRKEVEDKCEVIEEEREEEReNNSFDENLRR 36
                                   6666777778899******************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1421  (0.0792571); expected 358.6 (0.02)
Passed bias filter:                      738  (0.0411624); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 656.02
//
Query:       gene684|gene684|rna683|rna683  [L=715]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   8.5e-100  332.5   0.1    1.5e-99  331.6   0.1    1.4  1  MCM              MCM P-loop domain
      3e-37  127.3   0.1    5.9e-37  126.3   0.1    1.5  1  MCM_OB           MCM OB domain
    9.6e-25   86.8   4.4    9.6e-25   86.8   4.4    2.9  3  MCM_lid          MCM AAA-lid domain
    2.9e-10   39.9   0.0    3.5e-07   29.8   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.6e-08   34.7   0.7    1.6e-08   34.7   0.7    2.8  3  MCM6_C           MCM6 C-terminal winged-helix domain
    4.2e-08   33.3   0.1    1.9e-07   31.1   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
      2e-06   27.7   0.0      5e-06   26.4   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
    0.00013   21.8   0.1    0.00058   19.6   0.1    2.1  1  Sigma54_activat  Sigma-54 interaction domain
     0.0015   19.1   0.7     0.0043   17.6   0.7    1.8  1  MCM_N            MCM N-terminal domain
  ------ inclusion threshold ------
      0.053   13.0   0.0       0.13   11.7   0.0    1.6  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  331.6   0.1  8.3e-103   1.5e-99       5     224 .]     293     512 ..     289     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 331.6 bits;  conditional E-value: 8.3e-103
                                    HHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSE CS
                            MCM   5 ikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapra 84 
                                    i+e+++++d++ kl++s++psi+gh ++k+aill+l+ggv kk+e +t+lrgdinvllvgdpgtaKsq+Lk++++++pr+
  gene684|gene684|rna683|rna683 293 ISEMRSTPDLYYKLSQSMFPSIHGHYSIKNAILLLLVGGVGKKAEGGTSLRGDINVLLVGDPGTAKSQFLKQTSAFLPRS 372
                                    899***************************************************************************** PP

                                    EEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE-- CS
                            MCM  85 vytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnar 164
                                    vytsgk+ssaagLta+v +d etgef++eaGal+l+d+GvcciDefdkm+ +d++++hEamEqqti+i+KaG++atLnar
  gene684|gene684|rna683|rna683 373 VYTSGKSSSAAGLTASVIKDGETGEFTIEAGALMLSDTGVCCIDEFDKMNVKDQVSIHEAMEQQTITISKAGVNATLNAR 452
                                    ******************************************************************************** PP

                                    EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                            MCM 165 tsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                    +s+laAanp++grydkkk++ +ninlsa+++srFDl fvl D+++ e+D+++a hi+++h
  gene684|gene684|rna683|rna683 453 SSILAAANPIKGRYDKKKTLRQNINLSAPVMSRFDLYFVLIDDANVENDRNVAAHILNSH 512
                                    *********************************************************987 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.1   3.3e-40   5.9e-37       2     123 ..     101     227 ..     100     230 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 3.3e-40
                                    XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EE.E....S----SB-..TTT-HHH-EEE-GGGSEEEE CS
                         MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktve.v....eleePrkCeekeCeskdpfkletekskfvd 76 
                                    +R+l+s+++g+l + +G+vtr+++v+p+l+k +f ck c+++v+ +    +++eP  C+++ C++++ +kl+++ks+f +
  gene684|gene684|rna683|rna683 101 IRELKSDKLGQLLSFSGTVTRTTQVRPELSKGTFVCKVCSSVVSdIfqefKYTEPLVCPNHLCTNRRLWKLDIDKSEFLN 180
                                    8****************************************9997789889999************************** PP

                                    EEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEE CS
                         MCM_OB  77 fqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyr 123
                                    +qk+++QE++ee+p+G+lPrs++vi+++dlv+k+++Gd+v +tG   
  gene684|gene684|rna683|rna683 181 WQKIHIQENTEEIPPGSLPRSMDVIVRNDLVEKIRAGDKVVMTGYPI 227
                                    ********************************************765 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   2.2e+03      11      29 ..       2      20 ..       1      36 [. 0.81
   2 !   86.8   4.4   5.3e-28   9.6e-25       2      86 ..     529     611 ..     528     612 .. 0.94
   3 ?    0.4   0.1      0.48   8.6e+02      19      40 ..     654     675 ..     637     685 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                                   HHTT--BETCHHHHHHHHH CS
                        MCM_lid 11 rekikPklseeakeklsea 29
                                   rek+ Pk++ee+++k+ e+
  gene684|gene684|rna683|rna683  2 REKFYPKMTEEVHDKFLEF 20
                                   78999******99998776 PP

  == domain 2  score: 86.8 bits;  conditional E-value: 5.3e-28
                                    HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                        MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                    ++r Y++yar k +Pk++eeake+l + Y+++R+++   +++++++tvR+LesliRLseAlAk++ se vt+e+veea r
  gene684|gene684|rna683|rna683 529 QVRLYLRYAR-KRSPKMTEEAKEMLIKKYINIRQDSLI-HSNNYMMTVRHLESLIRLSEALAKIHDSELVTKEYVEEAHR 606
                                    6899******.***********************9943.4899************************************* PP

                                    HHHHH CS
                        MCM_lid  82 llkes 86 
                                    l+k+s
  gene684|gene684|rna683|rna683 607 LVKSS 611
                                    **998 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.48
                                    TCHHHHHHHHHHHHHHHHHTSS CS
                        MCM_lid  19 seeakeklseaYvelRkeeeds 40 
                                    +++ +++l+eaY++ R+++ +s
  gene684|gene684|rna683|rna683 654 EPMERHELVEAYLSERESSIES 675
                                    4567899*********988544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0016       2.8      20      49 ..     343     372 ..     334     383 .. 0.88
   2 !   29.8   0.0     2e-10   3.5e-07      93     197 ..     396     490 ..     378     500 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0016
                   Mg_chelatase  20 aGgHnlllvGppGsGKtmlakrlpsllppl 49 
                                     G  n+llvG pG+ K+   k+ ++ lp+ 
  gene684|gene684|rna683|rna683 343 RGDINVLLVGDPGTAKSQFLKQTSAFLPRS 372
                                    5888*********************99986 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 2e-10
                   Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekect 172
                                    g  +++ G++ l+ +Gv  +DE+ +++ k   ++ e +e++++tis+a  +++  ar  ++aa+Np +  ++++k     
  gene684|gene684|rna683|rna683 396 GEFTIEAGALMLSDTGVCCIDEFDKMNVKDQVSIHEAMEQQTITISKAGVNATLNARSSILAAANPIKG-RYDKK----- 469
                                    4457899***********************************************************985.44422..... PP

                   Mg_chelatase 173 csekeierYlsklsgplldRidlqv 197
                                        ++ r   +ls+p++ R+dl +
  gene684|gene684|rna683|rna683 470 ----KTLRQNINLSAPVMSRFDLYF 490
                                    ....233445578888888888865 PP

>> MCM6_C  MCM6 C-terminal winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.4      0.31   5.5e+02      30      63 ..     544     577 ..     525     612 .. 0.65
   2 !   34.7   0.7   8.9e-12   1.6e-08       4      80 ..     633     704 ..     630     709 .. 0.91
   3 ?   -2.2   0.0       2.6   4.7e+03     100     108 .]     707     715 .]     703     715 .] 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.31
                         MCM6_C  30 eegiekeeLvewYleqieeeleseeeleeekklv 63 
                                     ++  ke L++ Y++ ++++l   +++  + + +
  gene684|gene684|rna683|rna683 544 MTEEAKEMLIKKYINIRQDSLIHSNNYMMTVRHL 577
                                    4555677788888888888855554444444333 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 8.9e-12
                         MCM6_C   4 rityekYveianllvlklreeeeeeeeegiekeeLvewYleqieeeleseeeleeekklvekvlkrLvk.dkvLlevr 80 
                                     i+ ++Y +i+n ++  ++++e        e+ eLve+Yl+++e+++ese+ l ee++ +e+vl+ L+  ++vL   +
  gene684|gene684|rna683|rna683 633 MINSKDYIRITNSFIYLIKTREPM------ERHELVEAYLSERESSIESEKALIEEQSKAENVLSFLIGkEGVLFITD 704
                                    588899************998876......9*************************************9899997655 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.6
                         MCM6_C 100 lvvhPnyav 108
                                    + +hPny+v
  gene684|gene684|rna683|rna683 707 IHIHPNYDV 715
                                    679****86 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.1e-10   1.9e-07       1     125 [.     347     469 ..     347     486 .. 0.81
   2 ?   -2.1   0.1       1.9   3.4e+03      24      61 ..     560     597 ..     545     608 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.1e-10
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEverae 78 
                                    +vlLvG+pGt+Ks++ ++ +a+l r+v +    ++ +++ l+ ++  +   g+   + ++l+       ++++DE+++++
  gene684|gene684|rna683|rna683 347 NVLLVGDPGTAKSQFLKQTSAFLPRSVYTS--GKSSSAAGLTASVIKDgeTGEFTIEAGALM--LSDTGVCCIDEFDKMN 422
                                    69*********************9998765..455677888888775565688888899999..999************* PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--...... CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.....r 125
                                     + + s +  +e++++ + + g     ++       +++a+anp +     +
  gene684|gene684|rna683|rna683 423 VKDQVSIHEAMEQQTITISKAGVNATLNAR-----SSILAAANPIKgrydkK 469
                                    999**************9888887777775.....79999999998554330 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.9
                                    S--EEEEE--TT--HHHHH--B--.........----- CS
                          AAA_5  24 nreveyvqltrdtteedlkgrreikngttslvdsplvr 61 
                                    ++  ++  ++  +t ++l   +++++  ++ +ds+lv+
  gene684|gene684|rna683|rna683 560 RQDSLIHSNNYMMTVRHLESLIRLSEALAKIHDSELVT 597
                                    66667777788899999999999999999999999987 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.8e-09     5e-06       2     114 ..     348     463 ..     347     471 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.8e-09
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvf...anllladeinrappkt 78 
                                    vll g PG+ak ++ k+ +  l  ++           + ++ + + + ++ ef++++G+++   + +   de ++ + k 
  gene684|gene684|rna683|rna683 348 VLLVGDPGTAKSQFLKQTSAFLPRSVYTSGK--SSSAAGLTASVIKDGETGEFTIEAGALMlsdTGVCCIDEFDKMNVKD 425
                                    899999******9999999988766544333..33467899999999999*********9844456999*********** PP

                          AAA_3  79 qsalleameerqvtveg..ethklpepflvlatqnPie 114
                                    q ++ eame++++t+++   + +l+    +la+ nPi+
  gene684|gene684|rna683|rna683 426 QVSIHEAMEQQTITISKagVNATLNARSSILAAANPIK 463
                                    *************9976115778*************96 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   3.3e-07   0.00058      20     157 ..     343     475 ..     334     483 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.3e-07
                                    TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEE CS
                Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfL 99 
                                    + d++vl++G+ Gt K+ + ++  +  +r+   + +   ++ ++ l +s +   e G Ft     ++G++  +d G+  +
  gene684|gene684|rna683|rna683 343 RGDINVLLVGDPGTAKSQFLKQTSAFLPRS---VYTSGKSSSAAGLTASVIKDGETGEFT----IEAGALMLSDTGVCCI 415
                                    567999999999999999888777777655...445555566667778877777888887....578************* PP

                                    ETGGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS-HHHHHHTTSS-HH CS
                Sigma54_activat 100 DeigelplelQekLlrvlqegev..ervGsskeikvdvriiaatnedleeaveegkfred 157
                                    De  +++++ Q+ + ++++++++  ++ G +++ ++   i+aa+n    +  +++++r++
  gene684|gene684|rna683|rna683 416 DEFDKMNVKDQVSIHEAMEQQTItiSKAGVNATLNARSSILAAANPIKGRYDKKKTLRQN 475
                                    ******************999752279****************99766666677777775 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.7   2.4e-06    0.0043       3      66 ..      16      69 ..      14     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-06
                          MCM_N  3 kFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylp 66
                                   kF +FL++           +k r   ++ + r++  L +dl+d++a++ eL+  il+n  + ++
  gene684|gene684|rna683|rna683 16 KFLEFLDNT----------PKVRMDAEQAIYRNEGVLLIDLQDINAYSAELYTDILRNFSRDID 69
                                   788888887..........8999999********************************998665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.5e-05      0.13      31      68 ..     343     380 ..     339     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                          AAA_7  31 knkkpvllvGptGtGKtviikdllkkldkekylsltin 68 
                                    + + +vllvG+ Gt+K+  +k++   l+++ y+s + +
  gene684|gene684|rna683|rna683 343 RGDINVLLVGDPGTAKSQFLKQTSAFLPRSVYTSGKSS 380
                                    66789*****************9999998888876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 4338.29
//
Query:       gene685|gene685|rna684|rna684  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1649.22
//
Query:       gene686|gene686|rna685|rna685  [L=528]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-48  164.0   0.0    5.2e-48  163.0   0.0    1.5  1  NOG1_N          NOG1 N-terminal helical domain
    7.1e-22   77.0   0.2    1.4e-21   76.0   0.2    1.5  1  NOG1            Nucleolar GTP-binding protein 1 (NOG1)
    4.2e-17   62.3   0.0    1.5e-16   60.5   0.0    2.0  1  MMR_HSR1        50S ribosome-binding GTPase
    7.2e-13   48.3   1.9    2.2e-12   46.7   1.9    1.9  1  NOGCT           NOGCT (NUC087) domain
    1.4e-09   37.7   0.0    2.8e-09   36.7   0.0    1.5  1  FeoB_N          Ferrous iron transport protein B
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.044   13.4   0.0    1.6  1  Ras             Ras family
      0.033   14.2   0.5       0.21   11.6   0.0    2.5  3  Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
      0.066   13.3   2.0          6    6.9   0.0    3.1  3  Dynamin_N       Dynamin family
       0.08   13.0   1.9       0.13   12.2   0.2    2.3  3  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
       0.38   11.2   4.6       0.19   12.1   1.7    2.0  2  AvrM-A          Flax-rust effector AvrM-A


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.0   0.0   2.9e-51   5.2e-48       1     160 []       5     164 ..       5     164 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.0 bits;  conditional E-value: 2.9e-51
                         NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldv 80 
                                    F  i+ vp   elid++l++++r+++t+ + +++i ++r +++rkv+ a n++s +L +i+++fP+++++hpFy +l++v
  gene686|gene686|rna685|rna685   5 FGYITPVPLNMELIDTSLSKTQRKTPTIIHPQYNIIKIRMFYMRKVKHAGNEFSSRLGTILTDFPRIEDIHPFYGDLINV 84 
                                    667999************************************************************************** PP

                         NOG1_N  81 lvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpaiD 160
                                    l+d+d++k +L++v+ a++ i+k +ke+v++lk ad++ ++k+l+r+a+gr+as++k+ +k l++Le+vr ++ +Lp+iD
  gene686|gene686|rna685|rna685  85 LYDRDHYKLALGHVNAAKNGIEKTSKEFVKLLKFADSLYRCKQLKRAALGRMASTVKRLGKTLEYLEEVRMHMSRLPSID 164
                                    *******************************************************************************9 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.2   7.8e-25   1.4e-21       1      58 []     234     290 ..     234     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 7.8e-25
                           NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                    +IE+++i+AL+h++++vl+++D+se+cgys+eeQ++L++++ +l++   +++vl+K+D
  gene686|gene686|rna685|rna685 234 TIEMLSITALAHIKAVVLYFIDLSETCGYSIEEQIDLFNTLNPLLN-STMVIVLSKSD 290
                                    6********************************************9.89********9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   8.1e-20   1.5e-16       3     113 ..     171     287 ..     169     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 8.1e-20
                                    EEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS....HHHHHHHHHHHHHHHHCTSE CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie....gaseekglgkaflaleeadl 78 
                                    ++ G pNvGKS+++++ +++ ++v+ +p+tT+    g++++k  +++++DtpG+++    + ++ ++l+ + la+++  +
  gene686|gene686|rna685|rna685 171 LVCGFPNVGKSSFVRKVSRADVEVQPYPFTTKSLYVGHFDYKYLQWQVIDTPGILDqpleNRNTIEMLSITALAHIK-AV 249
                                    689*************************************999**********874444244555599999999999.99 PP

                                    EEEEEETT....TTCSHHHHHHHHHHHHH.TTSEEEEEEE CS
                       MMR_HSR1  79 illvvdas....eeklkpldeeleellee.akkplilvln 113
                                    +l+ +d+s      ++++ + +l ++l+   +  +++vl+
  gene686|gene686|rna685|rna685 250 VLYFIDLSetcgY-SIEE-QIDLFNTLNPlLNSTMVIVLS 287
                                    ******9954321.2222.244444443334455666665 PP

>> NOGCT  NOGCT (NUC087) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   1.9   1.2e-15   2.2e-12      22      54 .]     383     414 ..     379     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.2e-15
                          NOGCT  22 kkkYllkndewkyDiiPEildGkNvaDFidpdI 54 
                                    +++Yl+  +e kyDi+PEi+dGkNvaDF+dpdI
  gene686|gene686|rna685|rna685 383 QERYLV-PEEYKYDIVPEIMDGKNVADFFDPDI 414
                                    667755.67***********************9 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   1.5e-12   2.8e-09       3     153 ..     170     327 ..     168     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.5e-12
                                    EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SS..SSSSSHHHHHHHHHHHCTSSS CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYs..lsayseeekvardflleeepd 80 
                                    + ++G pnvGk++++ +++ a+ +v  +p +t     g++++k  + +++D PGi +  l++ ++ e ++ + l++ +  
  gene686|gene686|rna685|rna685 170 LLVCGFPNVGKSSFVRKVSRADVEVQPYPFTTKSLYVGHFDYKYLQWQVIDTPGILDqpLENRNTIEMLSITALAHIK-A 248
                                    6789***************************************************76337888888888888887665.4 PP

                                    EEEEEEE.....GGGHHHHHHHHHHHHH.TTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHH CS
                         FeoB_N  81 vvvnvvd.....atnlernLyLtlqlle.lgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieell 153
                                    vv+  +d       ++e ++ L+  l   l+  +v++l ++d+++ +++e  ++ +s   g + +++s +++e+i++++
  gene686|gene686|rna685|rna685 249 VVLYFIDlsetcGYSIEEQIDLFNTLNPlLNSTMVIVLSKSDVVRLSEVENKEAIMSFLEGKKYMEMSCEREENIDAVK 327
                                    56666662222234799*****99998725899*****************99999999999999*******99999886 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.5e-05     0.044       3     152 ..     171     326 ..     169     335 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.5e-05
                                    EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT...S..GGGHHHHHHHHT...TESE CS
                            Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG...q..eefkslrelyyr...daeg 74 
                                    ++ G  +vGK+s++ +  + + + +  +      y+ +  +d k ++ ++ DT G   q  e+ ++++ l+++   + ++
  gene686|gene686|rna685|rna685 171 LVCGFPNVGKSSFVRKVSRADVEVQPYPFTTKSLYVGH--FDYKYLQWQVIDTPGildQplENRNTIEMLSITalaHIKA 248
                                    67788899999999998888877665554424444444..4567888899999995552445555555555441104444 PP

                                    EEEEEETTBHHHH.HTHHHHHHHHHHHST.TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHH CS
                            Ras  75 illvyditsresf.envkkwveeikrvae.envpivLvGnKvDleekravsteegeelakelglkfletSAktnenveea 152
                                     +++y i+ +e+   ++++ ++ +++  +  n ++v+v  K+D+ +  +v+++e+  ++   g k++e+S + +en++ +
  gene686|gene686|rna685|rna685 249 -VVLYFIDLSETCgYSIEEQIDLFNTLNPlLNSTMVIVLSKSDVVRLSEVENKEAI-MSFLEGKKYMEMSCEREENIDAV 326
                                    .45555554444314556555555555556557999999**************998.7777889************9876 PP

>> Lip_prot_lig_C  Bacterial lipoate protein ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.21      32      85 .]      63     116 ..      62     116 .. 0.93
   2 ?   -3.7   0.0       6.8   1.2e+04      44      57 ..     301     314 ..     296     321 .. 0.67
   3 ?   -1.3   0.0       1.2   2.2e+03      45      65 ..     413     433 ..     398     450 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                    EEEESBSSSSHCHHHHHHHTTSBSSHHHHHHHHHTSCHHHHCCTHHHHHHHHHH CS
                 Lip_prot_lig_C  32 kiyGDffgpkdieeleekLigvkyekeaieealekidlseyfggieleellell 85 
                                    +i +Df   +di+ +   Li+v y++++ + al +++  +   + + +e+++ll
  gene686|gene686|rna685|rna685  63 TILTDFPRIEDIHPFYGDLINVLYDRDHYKLALGHVNAAKNGIEKTSKEFVKLL 116
                                    5899*********************************88888899999999987 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.8
                                    HHHHHHHTTSBSSH CS
                 Lip_prot_lig_C  44 eeleekLigvkyek 57 
                                    e++ + L+g+ky +
  gene686|gene686|rna685|rna685 301 EAIMSFLEGKKYME 314
                                    56666777777754 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.2
                                    HHHHHHTTSBSSHHHHHHHHH CS
                 Lip_prot_lig_C  45 eleekLigvkyekeaieeale 65 
                                    ++e++L  ++ e+e++ ++ +
  gene686|gene686|rna685|rna685 413 DIEKRLSEIEKEEEDMLAMYN 433
                                    577888888877777766655 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.022        40       2      33 ..     171     201 ..     170     213 .. 0.80
   2 ?    6.9   0.0    0.0033         6     103     160 ..     216     274 ..     206     289 .. 0.74
   3 ?   -0.6   0.2      0.69   1.2e+03      30      90 ..     371     428 ..     365     467 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.022
                                    EEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
                      Dynamin_N   2 avvGsqSsGKSSvlnaLlgedilprgpnptTr 33 
                                    +v+G  + GKSS++ ++ ++d+  ++p p T 
  gene686|gene686|rna685|rna685 171 LVCGFPNVGKSSFVRKVSRADV-EVQPYPFTT 201
                                    799999**********999995.555655554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0033
                                    EEEEE---B-SSSGTTSHHHHHHH.STTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTT CS
                      Dynamin_N 103 ltlvDlPGldsvnkrdqelvkeyi.kkadiilavtsanhdlsnsealflarevdpkgkr 160
                                      ++D+PG+ +++ ++ + ++ +  +  + i av+ +  dls++  + +++++d  ++ 
  gene686|gene686|rna685|rna685 216 WQVIDTPGILDQPLENRNTIEMLSiTALAHIKAVVLYFIDLSETCGYSIEEQIDLFNTL 274
                                    578**********9999888877667778888888888888888888888887755554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.69
                                    S---S-EEEEECCT---CCS...SSEEEE.T-EB--CHHHHHHHHHHHHHHHTSSSS--SS- CS
                      Dynamin_N  30 ptTrrplelqlgeeeeaseravkeelkek.ekkledfsevreeieketekiagankgiskkv 90 
                                    +++r ++e++ ++e +     v ee+k +   ++ d ++v++ ++   ek  ++ ++  +++
  gene686|gene686|rna685|rna685 371 ICSREITEIENEQERYL----VPEEYKYDiVPEIMDGKNVADFFDPDIEKRLSEIEKEEEDM 428
                                    78999999999998884....34444443444444444444444443333333333333333 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.4   9.7e+03      44      63 ..      80      99 ..      78     115 .. 0.78
   2 ?   12.2   0.2   7.5e-05      0.13      56      98 ..     280     328 ..     247     334 .. 0.78
   3 ?   -2.6   0.0       3.1   5.6e+03      58      78 ..     428     448 ..     426     466 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.4
                   MMR_HSR1_Xtn 44 dlidviegnrvYipclyvlN 63
                                   dli+v+ +   Y+ +l  +N
  gene686|gene686|rna685|rna685 80 DLINVLYDRDHYKLALGHVN 99
                                   79999999999998887777 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.5e-05
                   MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare......pnsvviSaekelnldeLke 98 
                                      +++vl K D ++l+e+++ +        ++++ +S+e+e n+d++k 
  gene686|gene686|rna685|rna685 280 STMVIVLSKSDVVRLSEVENKEAImsflegKKYMEMSCEREENIDAVKG 328
                                    457899**********9999887567888789*************9986 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.1
                   MMR_HSR1_Xtn  58 clyvlNKi.Dlisleeldelar 78 
                                    +l ++NK+ D +s ee   +++
  gene686|gene686|rna685|rna685 428 MLAMYNKTyDVLSPEERA-MKE 448
                                    578899963667766653.333 PP

>> AvrM-A  Flax-rust effector AvrM-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.1   7.4e+03      81     110 ..     361     392 ..     326     397 .. 0.47
   2 ?   12.1   1.7   0.00011      0.19      20      82 ..     407     469 ..     402     515 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.1
                         AvrM-A  81 kakgkpidekavqrqf..iKeqaklylkdeel 110
                                    k+  +  +  +  r++  i +++++yl+ ee 
  gene686|gene686|rna685|rna685 361 KEVREKAEAFICSREIteIENEQERYLVPEEY 392
                                    22222223333333332255555555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
                         AvrM-A  20 AalfDkkvarklaqWeaaEkrlddllkelykkqllefkkkkgekklkkkidviaeklkekaka 82 
                                    A +fD +++++l + e+ E+ +  + ++ y+  + e + +k e  +    + i+++l+ek k 
  gene686|gene686|rna685|rna685 407 ADFFDPDIEKRLSEIEKEEEDMLAMYNKTYDVLSPEERAMKEEVTVGIERRRIINRLNEKKKL 469
                                    88*******************************999988888888888888999999888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 3159.96
//
Query:       gene687|gene687|rna686|rna686  [L=367]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2568.56
//
Query:       gene688|gene688|rna687|rna687  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.33   11.2   4.8       0.44   10.8   4.8    1.1  1  MutS_III  MutS domain III


Domain annotation for each model (and alignments):
>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.8   2.4e-05      0.44      69     189 ..      40     201 ..      26     203 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.4e-05
                                    HHHHHHTT---HHHHHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHHHHHHHHHHHHB-SS--SSGGGS-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III  69 elrellrrlpDleRllsrislgkakardlkallealkaleelvallekeklaeseeeslaelleeaideeplalekeged 148
                                    +  +++ r+ D eR+  +++l+ +k +  ++l+ ++++++ l   ++++++a s + +l+ ++++ + + +++l++  ++
  gene688|gene688|rna687|rna687  40 RTLSEISRMLDKERVYESFTLQ-SKIDRASELVGKMRDVARLEMRCRNDQEAASYA-NLEGMIKNRVSRYSIKLKEFINK 117
                                    3334444555777777777662.233334445555555544444444343332222.33344444222222222222222 PP

                                    B-T...........................................HHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHH CS
                                    xxx...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III 149 lra...........................................iealeqelfqelleeveealerlrrlaealaeLD 185
                                     ++                                           + ++  ++++e+  +v+ + e +rr+ +++a+ D
  gene688|gene688|rna687|rna687 118 RNErrqaiserrkefdsecslehqdtvlmerevvterikerqkismQISEIGQIMEEISMHVSLQEESFRRIDDLMATSD 197
                                    222444444444445555777777777777788888888888778788888999999999997778************** PP

                                    HHHH CS
                                    xxxx RF
                       MutS_III 186 vllS 189
                                     l+S
  gene688|gene688|rna687|rna687 198 SLIS 201
                                    **99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1294  (0.0721736); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1412.84
//
Query:       gene689|gene689|rna688|rna688  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1206.96
//
Query:       gene690|gene690|rna689|rna689  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-15   56.9   0.4    2.1e-15   56.7   0.4    1.1  1  PX        PX domain


Domain annotation for each model (and alignments):
>> PX  PX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.4   1.2e-19   2.1e-15       8      96 ..      11      95 ..       4     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.2e-19
                                   EEEEEEETTSSEEEEEEEEEETTS.....SSEEEEEEEHHHHHHHHHHHHHHHTTSTSTSSSTSGSSSSSCTTSHHHHHHHH CS
                             PX  8 vleretsgskkhsyylyevelktg.....akewtvkRrYsdFeeLhskLlrkfprvkiPplPkkvlfgsvrkkdeefiekrr 84
                                   +  ++   + +++y+ yev + t+     + + +v RrY+dF+ Lhs+L+ + +  ++P++P+k++     k+d+++ie+r 
  gene690|gene690|rna689|rna689 11 IPGSR---NVQDRYTEYEVVCITNnksfgKCYTKVFRRYRDFHMLHSRLKCFLK--VLPEFPRKRWN----KMDKDVIEERM 83
                                   44433...6677888888888888888*99*******************99888..*********54....69********* PP

                                   HHHHHHHHHHHT CS
                             PX 85 kgLeeyLqrlln 96
                                   ++L++yL+ ++ 
  gene690|gene690|rna689|rna689 84 RMLTVYLKFVCD 95
                                   ********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.55
# Mc/sec: 662.63
//
Query:       gene69|gene69|rna69|rna69  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 903.92
//
Query:       gene691|gene691|rna690|rna690  [L=298]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.019   14.6   0.7      0.019   14.6   0.7    2.6  3  RPW8          Arabidopsis broad-spectrum mildew resistance pr
       0.23   11.7   2.5          3    8.2   1.3    2.8  3  ABC_tran_CTD  ABC transporter C-terminal domain
       0.32   11.2   4.7        1.8    8.8   0.2    2.6  2  K-box         K-box region


Domain annotation for each model (and alignments):
>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   3.2e-06     0.019      62     115 ..       2      53 ..       1      76 [. 0.86
   2 ?    0.3   0.2     0.087   5.2e+02      94     119 ..     133     158 ..     121     178 .. 0.74
   3 ?   -2.3   0.1      0.54   3.2e+03      62      73 ..     235     246 ..     226     259 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-06
                           RPW8  62 reeieeLkklLekaekLVekcsklkrynvlkkyrYkkklkeLekslrkfvqvel 115
                                    +e+i++L+k+L  ae+L +kc   k +n  +   Yk +l++L+  +r  +++++
  gene691|gene691|rna690|rna690   2 EEKIKSLEKKLLAAEQLHRKCEGFKLMNS-RIKEYKSRLEALDSRIRS-IDTQI 53 
                                    689**********************9886.55589**********998.77665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.087
                           RPW8  94 yrYkkklkeLekslrkfvqvelqvqq 119
                                    + ++  +k L++sl+  +qv++   +
  gene691|gene691|rna690|rna690 133 PNFTEFIKLLDESLVYRIQVKILQSR 158
                                    66777899999999999998876544 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.54
                           RPW8  62 reeieeLkklLe 73 
                                     e++e+Lk++Le
  gene691|gene691|rna690|rna690 235 MEDLESLKNRLE 246
                                    455666666665 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.3    0.0005         3      13      56 ..       1      45 [.       1      49 [. 0.81
   2 ?    5.5   0.0    0.0035        21      11      36 ..      33      58 ..      28      76 .. 0.69
   3 ?    0.4   0.0      0.13   7.8e+02      17      33 ..     235     251 ..     229     268 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                   ABC_tran_CTD 13 leaeIeaLEeeiaeleaeladpelysdp.eklaelsaeleeleae 56
                                   +e++I +LE+++ + e+   + e ++    +++e   +le+l++ 
  gene691|gene691|rna690|rna690  1 MEEKIKSLEKKLLAAEQLHRKCEGFKLMnSRIKEYKSRLEALDSR 45
                                   588899999999999998888888877778888888888888876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0035
                   ABC_tran_CTD 11 eeleaeIeaLEeeiaeleaeladpel 36
                                   +e  +++eaL+ +i ++++++a  +l
  gene691|gene691|rna690|rna690 33 KEYKSRLEALDSRIRSIDTQIAGYDL 58
                                   55566777777777777777776655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.13
                   ABC_tran_CTD  17 IeaLEeeiaeleaelad 33 
                                    +e LE  +  le+ l++
  gene691|gene691|rna690|rna690 235 MEDLESLKNRLETDLES 251
                                    56666666666666654 PP

>> K-box  K-box region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.7     0.013        75      12      59 ..       2      49 ..       1      75 [. 0.83
   2 ?    8.8   0.2   0.00031       1.8      36      57 ..     229     250 ..     224     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.013
                          K-box 12 kqEvskLkkeieklqrsqRkllGedleslslkeLqqLEqqLekslkki 59
                                   ++ +++L+k++   ++ +Rk+ G +l +  +ke ++  + L++ +++i
  gene691|gene691|rna690|rna690  2 EEKIKSLEKKLLAAEQLHRKCEGFKLMNSRIKEYKSRLEALDSRIRSI 49
                                   678999999999999******999999999999877555565555554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00031
                          K-box  36 dleslslkeLqqLEqqLekslk 57 
                                      es+++++L++L ++Le+ l+
  gene691|gene691|rna690|rna690 229 FFESCTMEDLESLKNRLETDLE 250
                                    569***************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 1645.54
//
Query:       gene692|gene692|rna691|rna691  [L=452]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-86  288.0   0.0    9.7e-86  287.7   0.0    1.1  1  6PGD            6-phosphogluconate dehydrogenase, C-terminal 
    9.5e-43  146.1   0.0    1.6e-42  145.4   0.0    1.3  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    2.7e-06   27.5   0.0      1e-05   25.6   0.0    1.9  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
    9.6e-06   26.1   0.2    3.6e-05   24.3   0.0    2.1  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0019   18.1   0.3     0.0036   17.2   0.0    1.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0083   16.4   0.0      0.016   15.4   0.0    1.5  1  NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobut
  ------ inclusion threshold ------
       0.12   11.9   0.0        0.3   10.6   0.0    1.7  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


Domain annotation for each model (and alignments):
>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.7   0.0   3.8e-89   9.7e-86       1     289 []     172     451 ..     172     451 .. 0.96

  Alignments for each domain:
  == domain 1  score: 287.7 bits;  conditional E-value: 3.8e-89
                           6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkvlglsneeiaevFeeWnkgelesyLieitakilrkkdeedgkplvdkilDka 80 
                                    Gh+VKm+HNGieygdm +i E+y +l++ lgl+n ei+++F++W++ e esyL++i+++ilr k+e+   +++d+i D++
  gene692|gene692|rna691|rna691 172 GHFVKMIHNGIEYGDMAVITETYLVLRS-LGLDNLEISSLFDSWDRMESESYLLRISSNILRMKNEK--GSVIDQIIDVS 248
                                    9*************************96.89********************************9973..49********* PP

                           6PGD  81 gqkGTgkwtvqealelgvpvptiaeavfaRllSslkeervkaskllkeeeekeeedkeefiedlrkAlyaskivsYaqgl 160
                                    +qkGTgk tv++a+e+g ++p+i+eav++R++S++k++r  +s+ lk++    +  k+   e++rk +y+++ivsY+qg+
  gene692|gene692|rna691|rna691 249 EQKGTGKETVISAMEIGEAIPAITEAVTSRMVSHMKDKRCWLSSRLKGS----RGGKRIPEETIRKGFYLARIVSYIQGF 324
                                    **********************************************763....3445556699***************** PP

                           6PGD 161 ellkaaskeygwnlnlaeiariWrgGCiIrakfldkikeafeknpelenllldpefakelkealealrrvvalaveagip 240
                                    +ll +a k+ygw+ ++++i r+W +GCi+r k+l+ ++   e++   e++ l++ f +  +++  +l+++v ++ve++++
  gene692|gene692|rna691|rna691 325 NLLMKARKKYGWTYTIKDITRVWSNGCILRGKLLNVVEGLGEER--EEDFELTSGFVSLYDRCSVDLKEMVLYSVENEVA 402
                                    **************************************999997..88999999************************** PP

                           6PGD 241 vpalsaalaYldslrserlpanliqaqrDyFGahtyervdkegkfhteW 289
                                    +p++s++l Yl+++++++   n+iqa+rDyFG+ht   + +++++h+eW
  gene692|gene692|rna691|rna691 403 IPTISSCLMYLNGMKEKEGGGNMIQAMRDYFGSHTVVMKGESQSVHIEW 451
                                    ************************************************* PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.4   0.0   6.1e-46   1.6e-42       1     157 [.       2     166 ..       2     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 6.1e-46
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT..EEE-SSHHHHHHHC....SEEEE-SSSHHHHHHHHH CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg..akaaesieelvasl....dvvitmvkagkavdevie 74 
                                    +ig+iGlGvMG+n+aln++++gyk++v+nrt++k+++l++e   + +++s++++v ++    +++i+m+++g+ vd+++e
  gene692|gene692|rna691|rna691   2 EIGLIGLGVMGHNLALNIVSKGYKLHVFNRTSSKTDRLAEESndVYPHYSVQDMVMGIktspKIIILMLTSGEVVDAFLE 81 
                                    59**************************************98889*********************************** PP

                                    SHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEE... CS
                  NAD_binding_2  75 gllealkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaiga... 151
                                    +l ++l k+di+idg++ss++dt+++++     +++f+++++SGGeegA++G+ simvG+s+ a+e+vk +l++i+a   
  gene692|gene692|rna691|rna691  82 ELGKYLGKDDIVIDGGNSSFRDTIRRNN----CKFRFVGCGISGGEEGARHGP-SIMVGCSKGAWEEVKGLLTDISAisa 156
                                    *************************975....69*******************.*********************99777 PP

                                    .....EEEEE- CS
                  NAD_binding_2 152 .....kvthvi 157
                                         +++ ++
  gene692|gene692|rna691|rna691 157 srndrCCV-WL 166
                                    77776665.55 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     4e-09     1e-05      15      76 ..       3      62 ..       1      78 [. 0.85
   2 ?   -1.2   0.0      0.73   1.9e+03      63      81 ..      77      95 ..      61     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4e-09
                                   EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT- CS
                   Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaea 76
                                   + liG G m++ +a ++++kg+k + v+NRt ++ ++laee +++ +   +++++   ++ +
  gene692|gene692|rna691|rna691  3 IGLIGLGVMGHNLALNIVSKGYK-LHVFNRTSSKTDRLAEESNDV-YPHYSVQDMVMGIKTS 62
                                   789********************.******************998.8888888888777765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.73
                                   EEEGCGHHHHHHT-SEEEE CS
                   Shikimate_DH 63 alkleelkellaeadvvis 81
                                      leel ++l + d+vi 
  gene692|gene692|rna691|rna691 77 DAFLEELGKYLGKDDIVID 95
                                   556999***********96 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.4e-08   3.6e-05       2      94 ..       3      96 ..       2      99 .. 0.75
   2 ?   -2.6   0.1       3.4   8.7e+03       6      15 ..     421     430 ..     421     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.4e-08
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...-EEECECHHHHHH.H-SEEEE-S.-HHHHHHHH CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...vkvtavdneeaae.eadvvvlav.kpedveevl 78
                                   ig+iG G mg+ la++++++g   +++ v  +r+ +k + laee +   +  +  d    ++ + ++++l +   e+v+++l
  gene692|gene692|rna691|rna691  3 IGLIGLGVMGHNLALNIVSKG---YKLHVF-NRTSSKTDRLAEESNdvyPHYSVQDMVMGIKtSPKIIILMLtSGEVVDAFL 80
                                   9********************...888855.888888888888777444444444444444446666666551568899999 PP

                                   HHCGHHHHTTSEEEEE CS
                  F420_oxidored 79 selakdalkgklvisv 94
                                   +el k + k+ +vi+ 
  gene692|gene692|rna691|rna691 81 EELGKYLGKDDIVIDG 96
                                   99999999*****995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.4
                                    TTSHHHHHHH CS
                  F420_oxidored   6 GaGnmgeala 15 
                                    G+Gnm++a+ 
  gene692|gene692|rna691|rna691 421 GGGNMIQAMR 430
                                    99*****985 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.4e-06    0.0036       2      44 ..       3      45 ..       2      78 .. 0.88
   2 ?   -3.2   0.1       2.6   6.6e+03     146     170 ..     244     268 ..     239     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                   ++ iG G+mG+ +a  ++s+g++ +++++++++ ++ +e+ ++
  gene692|gene692|rna691|rna691  3 IGLIGLGVMGHNLALNIVSKGYKLHVFNRTSSKTDRLAEESND 45
                                   899**************************99999988887665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.6
                                    EEEEEE-TT--HHHHHHHHHHHHHT CS
                        3HCDH_N 146 LvEvvrgekTseetvatvvelakki 170
                                    +++v +++ T +etv  ++e+ ++i
  gene692|gene692|rna691|rna691 244 IIDVSEQKGTGKETVISAMEIGEAI 268
                                    6778888888888888888877665 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.2e-06     0.016       1      35 [.     170     204 ..     170     242 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
                 NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldp 35 
                                    GaG+ vK+++n +    +a+++E  ++++ +Gld 
  gene692|gene692|rna691|rna691 170 GAGHFVKMIHNGIEYGDMAVITETYLVLRSLGLDN 204
                                    9********************************96 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012       0.3       6      48 ..       2      44 ..       1      93 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                   -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT CS
                           IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeeg 48
                                   +i +iG G  Gh+ aln+   g ++ v +r++sk+ + A+e++
  gene692|gene692|rna691|rna691  2 EIGLIGLGVMGHNLALNIVSKGYKLHVFNRTSSKTDRLAEESN 44
                                   5899****************************99888887643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2815.23
//
Query:       gene693|gene693|rna692|rna692  [L=224]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-18   66.3   0.0    4.1e-18   66.0   0.0    1.1  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   2.3e-22   4.1e-18       2     158 ..      39     184 ..      38     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2.3e-22
                                    EEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BSSSHHHHHHHHHHHHHH..H.TS-EEEEEEEEEEGGGTTTBG CS
                     Ham1p_like   2 vfaTgNkgKlrevkeilaeellevkslkelelpeveEtqgtfeenalkKaraaae..a.glpvladDsgLevdaLnglPG 78 
                                    vf+T+   K++ ++e+l+   +e++ l      +++E+qg+ ee++++K ++++   +    +++dD+++++  L+g+PG
  gene693|gene693|rna692|rna692  39 VFITSSVYKYEAFREFLN-APVELVVL------DIKEIQGSKEEIIMDKLQKVSHlvTeSTITFIDDTSIHMSGLGGFPG 111
                                    79**************95.45555555......889***************988743344459***************** PP

                                    GGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEET..TTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEE CS
                     Ham1p_like  79 vysarfagegaedeenlaklleeleeeeedrsArfvcvlaladp..eeeeellfeGeveGeiveeprgeggfGyDpiFvp 156
                                     y + f++ ga+      ++le  +++   r++ + +++++++   ++ ++++f+Gev+G i+++++ge +  +  iFvp
  gene693|gene693|rna692|rna692 112 QYAKDFLKIGAS------RILEIASKVG--RECLYSTIIGVMRMeeGKIVTKIFTGEVRGDIIQRSEGEPKT-FSDIFVP 182
                                    ******877766......5565555446..99******99988876777889***********999999876.89***** PP

                                    TT CS
                     Ham1p_like 157 ee 158
                                    +e
  gene693|gene693|rna692|rna692 183 KE 184
                                    63 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1376.37
//
Query:       gene694|gene694|rna693|rna693  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   14.1   0.3       0.41   11.3   0.1    2.4  2  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.3e-05      0.41      11      47 ..      74     110 ..      69     130 .. 0.85
   2 ?   -0.0   0.0     0.077   1.4e+03      24      41 ..     190     207 ..     162     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                          ACT_4  11 veaedrkglLaditqviseekanivsvnaktrkkdgl 47 
                                    v+ e++ ++L+d+++ isee++  +++ +k++ k+ +
  gene694|gene694|rna693|rna693  74 VINENEENALNDVSEEISEEDGICSNILIKDEAKKRI 110
                                    7889**********************99999875544 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.077
                          ACT_4  24 tqviseekanivsvnakt 41 
                                    t+v++++k+++++v+ + 
  gene694|gene694|rna693|rna693 190 TEVLNSSKVDVREVQRSV 207
                                    578888888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1784.18
//
Query:       gene696|gene696|rna695|rna695  [L=72]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   40.9   0.0    1.6e-10   40.8   0.0    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   8.8e-15   1.6e-10       2      54 ..      13      65 ..      12      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 8.8e-15
                                   HCHHHHHHHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHH CS
                           SecE  2 kFfkevkaElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfskli.nll 54
                                   +++k v+ + kK+++P+ kE+  + +  ++++ ++g+++++++l++ ++i n++
  gene696|gene696|rna695|rna695 13 DYLKSVRLFTKKCVKPSGKEFAMSVKRHAIGIGFLGILGYAIKLIH-IPInNII 65
                                   69*******************************************9.***7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 495.12
//
Query:       gene697|gene697|rna696|rna696  [L=209]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-32  109.5   3.0    3.8e-31  107.6   0.2    2.0  2  Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport 


Domain annotation for each model (and alignments):
>> Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.2     0.007   1.2e+02      67      89 ..      42      64 ..      33      71 .. 0.74
   2 !  107.6   0.2   2.1e-35   3.8e-31       2     126 ..      81     204 ..      80     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.007
                  Brr6_like_C_C 67 leekCeewekCmnrdpeskvera 89
                                    +e+C++  kC n   +  ++++
  gene697|gene697|rna696|rna696 42 AKESCTQMVKCLNDRRKVATKKV 64
                                   5789********96655544444 PP

  == domain 2  score: 107.6 bits;  conditional E-value: 2.1e-35
                  Brr6_like_C_C   2 sylqllfnlllvllllylvisfvltikkDiekkleekkaellaeieeCkkeYeeNkCdpetrvpaleekCeewekCmnrd 81 
                                     yl+l++n++++ +++y++++++  +++Di+ k+ +++++++++iee k+ Y+ NkCdp trvpa+e+ C++we C+ ++
  gene697|gene697|rna696|rna696  81 GYLHLVLNFVVIGFVCYVIMYVLIGLERDIRYKIINRRTQIRHQIEEAKTFYKVNKCDPATRVPAIEDLCNKWE-CVIKN 159
                                    69***********************************************************************9.999** PP

                  Brr6_like_C_C  82 peskverakvsaetlaeiinsfvepislktllfllllllivlfvs 126
                                       ++++++++ae++++++++f++++s+++ l++ ++++++l++ 
  gene697|gene697|rna696|rna696 160 GYWSIGYTRIIAEVFGDVMDGFIRKFSIRSSLTIGFFFVLFLVFR 204
                                    *999****************************9999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1120.56
//
Query:       gene698|gene698|rna697|rna697  [L=160]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-40  135.3   6.3    1.1e-39  134.4   5.1    1.8  2  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4   5.1     6e-44   1.1e-39       3     101 .]       2     100 ..       1     100 [. 0.99
   2 ?   -0.0   0.0     0.044     8e+02      15      49 ..     114     150 ..     105     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 6e-44
                                    -S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEETT CS
                 Ribosomal_L21e   3 nskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvgg 82 
                                    +skg+rrgtr+lfs++ rk+gvp++s+yl++y+ Gd+Vdi ++p++ kgmphk+yhG+tgrvy+v++r+v + ++k+v+g
  gene698|gene698|rna697|rna697   2 RSKGYRRGTRSLFSQDHRKHGVPHVSKYLEKYEIGDMVDILVNPAIMKGMPHKYYHGRTGRVYDVKPRSVNIALYKRVRG 81 
                                    89****************************************************************************** PP

                                    E..EEEEEE-GGGEEE--. CS
                 Ribosomal_L21e  83 kileKriivriehlkksks 101
                                    k++ K++i+rieh++ks++
  gene698|gene698|rna697|rna697  82 KYVIKKVIARIEHVRKSRC 100
                                    *****************97 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.044
                                    TS--GGG-S..S--SHHHH----TT-EEEE---TT-- CS
                 Ribosomal_L21e  15 fskkfrkkg..vpplstylreykkGdkVdikidpsvq 49 
                                    ++k+   +g  +pp+++ ++  +kG ++++k +  ++
  gene698|gene698|rna697|rna697 114 LAKSAEARGmvLPPIKRKIEGPRKGMEISLKNNQPIE 150
                                    6677777773345999999999999999988876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 974.14
//
Query:       gene699|gene699|rna698|rna698  [L=69]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-12   45.4   0.0    5.9e-12   45.1   0.0    1.2  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.067   13.3   0.0      0.077   13.1   0.0    1.1  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   6.6e-16   5.9e-12       2      62 ..       8      62 ..       7      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 6.6e-16
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnni 62
                                    l++l++k+v+v+  +g++l+G L+g+D fmN+vL++++e ++ +      g  +iRG+ +
  gene699|gene699|rna698|rna698  8 NLASLLHKNVIVRVDGGHVLKGLLMGYDAFMNIVLSKITEPSEVG------GSAIIRGEFV 62
                                   5899************************************99887......9999999988 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.6e-06     0.077      10      69 ..      11      66 ..       4      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-06
                                   TTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS...........-EEEEEE CS
                         SM-ATX 10 slvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkanskssspssgeipdtli 69
                                   sl  k+v v+v  G v +G++ +++    +++vL    + ++     s + +ge+++ + 
  gene699|gene699|rna698|rna698 11 SLLHKNVIVRVDGGHVLKGLLMGYDA--FMNIVLSKITEPSE--VGGSAIIRGEFVEDIT 66
                                   555589********************..9*****98888877..6666777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       149  (0.00831056); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 537.22
//
Query:       gene700|gene700|rna699|rna699  [L=185]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-06   27.1   0.2    4.8e-06   26.2   0.2    1.5  1  S4            S4 domain
  ------ inclusion threshold ------
      0.027   15.4   0.1      0.065   14.2   0.0    1.8  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   5.3e-10   4.8e-06       1      44 [.     112     155 ..     112     158 .. 0.96

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.3e-10
                                    EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-T CS
                             S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkp 44 
                                    rRL+  ++++gla+s  +Ar lI+++ + +  +vv+ p+++V++
  gene700|gene700|rna699|rna699 112 RRLQFRVFAAGLAKSVHHARVLIKGRCISIKDQVVDVPGFMVRA 155
                                    79****************************************96 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.2e-06     0.065      33      80 ..      11      59 ..       2     135 .. 0.85
   2 ?   -1.4   0.0      0.51   4.6e+03      11      22 ..     112     129 ..     107     178 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-06
                                   -----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                   Ribosomal_S4 33 rkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                   ++   +++k +l ++ +l + Ygl+ + +++ + k+ ++ + + ++ Ll+
  gene700|gene700|rna699|rna699 11 NTPRDPFEKeRLIREIQLVGVYGLKnKHELWVMEKMFSKDK-ERARMLLT 59
                                   4556689999*******************************.99999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.51
                                    CHCTS-STSSS......S CS
                   Ribosomal_S4  11 Rrvgfklflkg......r 22 
                                    Rr++f +f  g      +
  gene700|gene700|rna699|rna699 112 RRLQFRVFAAGlaksvhH 129
                                    555555555444333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1247.72
//
Query:       gene7|gene7|rna7|rna7  [L=91]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.47   10.2   3.4        5.7    6.7   0.0    2.4  2  Spore_YhaL  Sporulation protein YhaL


Domain annotation for each model (and alignments):
>> Spore_YhaL  Sporulation protein YhaL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0   0.00032       5.7      35      50 ..       7      22 ..       1      23 [. 0.84
   2 ?    3.0   1.6    0.0045        80       4      16 ..      70      82 ..      68      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00032
             Spore_YhaL 35 EkEGevylerleeere 50
                           E EG+v+  rl+  r+
  gene7|gene7|rna7|rna7  7 EDEGQVFTSRLKTLRN 22
                           89*********98775 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0045
             Spore_YhaL  4 WvYlviagIlfSg 16
                           W Y++  gI +S 
  gene7|gene7|rna7|rna7 70 WLYFILGGIGLSF 82
                           *********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.38s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 491.86
//
Query:       gene70|gene70|rna70|rna70  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1040.23
//
Query:       gene701|gene701|rna700|rna700  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-52  176.6   6.7    7.3e-52  176.4   6.7    1.0  1  IP_trans      Phosphatidylinositol transfer protein
  ------ inclusion threshold ------
       0.13   12.8   0.0       0.37   11.3   0.0    1.7  2  Phage_tail_T  Minor tail protein T


Domain annotation for each model (and alignments):
>> IP_trans  Phosphatidylinositol transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   6.7   8.2e-56   7.3e-52       4     244 ..       6     244 ..       4     247 .. 0.96

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 8.2e-56
                                    EEEEEEESS-HHHHHHHHHHHHHHHHTT-SSTTTTEEEEEEEEEE-TTS-EEEEEEEEEE-GGGS-HHHHTTS-TTTTEE CS
                       IP_trans   4 keYriilPltveeyqiaqlYmvakaskeetgggegvevlknepyedeeggkgqytekiyhlesklPswlrallpkkaltv 83 
                                    k Y  +lP+t +ey +++ ++v+ ++++e  g+  ve++k e++ +e+ gk++ t+ki++l+s+ P++l +l+p++a+ v
  gene701|gene701|rna700|rna700   6 KIYVTVLPMTTDEYAVGHFHTVSSMTESENAGDLKVEMIKAETVVHETLGKANKTHKIMYLKSRFPQVLHSLIPEDACIV 85 
                                    67999*************************************************************************** PP

                                    EEEEEEETTEEEEEEEET.TTGGGEEEEEEEEEESSSS--SSTT---HHHHTT-EEEEE-TT-GGG-GGG--GGG-TTT- CS
                       IP_trans  84 eekawnaypytkTvytnp.lmkekfsikietvhkedngtqeNvfnlskeelkkreveviDivndkisskdykeeedptlf 162
                                    ee ++nay +++T y+n  + +e+f++  +t+ +++++  eN f+ ++e +++ e   +D+ +++     +++  dp+++
  gene701|gene701|rna700|rna700  86 EEISYNAYTKCHTFYKNRyFSNETFNMAFNTINRDGAEILENPFEHDPEHIRNIEKINLDLHSSP-----INPMFDPSVY 160
                                    ******************9999*****************************************88.....79******** PP

                                    --TTT------T.HHH...TST---EEEEEEEEEEE--SS-HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTT--HHHHH CS
                       IP_trans 163 ksektgrgpLkegWrk...ksekpvmcaYKlvtvefkvwglqtkveefihkalrklflkfhrqafcwideWygltmedir 239
                                     +e++grg L+e W++   ++  p+m++YK +tve++ + +++   e i k +r +++++ +++fc++d+Wyg t+++ir
  gene701|gene701|rna700|rna700 161 YHEESGRGRLDEHWMEgykNKGIPMMVSYKHLTVEINNYMMGWISAE-IEKVMRGVITSVQQRIFCTMDKWYGKTIDEIR 239
                                    ****************9988889****************99987655.77****************************** PP

                                    HHHHH CS
                       IP_trans 240 elEee 244
                                    + +e+
  gene701|gene701|rna700|rna700 240 KENEN 244
                                    98765 PP

>> Phage_tail_T  Minor tail protein T
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.83   7.4e+03      52      78 ..      10      38 ..       6      50 .. 0.50
   2 ?   11.3   0.0   4.2e-05      0.37      14      54 ..      84     124 ..      78     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.83
                   Phage_tail_T 52 lsl.vtdkeldaddfslls.apeaveeke 78
                                   + l +t +e    +f  +s  +e+ +  +
  gene701|gene701|rna700|rna700 10 TVLpMTTDEYAVGHFHTVSsMTESENAGD 38
                                   44555555556666665552444444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.2e-05
                   Phage_tail_T  14 mlaemsstelgewaeffsensfsdalldaefstlkalvlsl 54 
                                    +++e+s   +++ ++f+++ +fs+  +++ f t++     +
  gene701|gene701|rna700|rna700  84 IVEEISYNAYTKCHTFYKNRYFSNETFNMAFNTINRDGAEI 124
                                    67899999*************************98765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1751.67
//
Query:       gene702|gene702|rna701|rna701  [L=1335]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-17   63.8   0.0    4.5e-17   62.4   0.0    1.8  2  DEAD        DEAD/DEAH box helicase
    1.4e-12   48.0   0.2    1.5e-11   44.6   0.0    2.6  2  ResIII      Type III restriction enzyme, res subunit
    4.1e-09   36.8   0.1    1.9e-08   34.6   0.0    2.3  2  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
       0.14   11.6   0.2        2.3    7.6   0.0    2.9  3  PhoH        PhoH-like protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0     1e-20   4.5e-17       4     170 ..     518     671 ..     515     675 .. 0.84
   2 ?   -3.5   0.0       1.7   7.6e+03      43      90 ..     923     973 ..     912     998 .. 0.62

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1e-20
                                    HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                    Q + ++l+ ++++ +++a+T +GKT + + ++ +i+   k+++++++++  Pt++L++q+  ++  ++   +++ + +++
  gene702|gene702|rna701|rna701 518 QVRLLDLVDQNKSAVISAPTSAGKTFICFYAIEKIL---KESDTNMVIFCLPTKALVNQVSADIYARFTA-KVNSKTFLQ 593
                                    77778888999****************988888888...689999******************9888883.444555555 PP

                                    TSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH.CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  84 gvaardqlskldngvdivvgtpgrlddllstgkln.lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                    g +  ++ s    ++++++  p+ l ++l+t     l++v+++++DE++++++++++  i+ri++  p      +    +
  gene702|gene702|rna701|rna701 594 G-SLMKEFSIAPWNCQVLIVIPSLLESVLNTPPKGfLERVKYIIIDEVHKISSEEMGIPIERIIHLSP-----CP----M 663
                                    5.666788888789*************996554334**************************888883.....33....9 PP

                                    EEEESSBS CS
                                    xxxxxxxx RF
                           DEAD 163 ivlSATlp 170
                                    +vlSATl 
  gene702|gene702|rna701|rna701 664 LVLSATLG 671
                                    ******95 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                                    TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEET..TSSHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx..xxxxxxx RF
                           DEAD  43 kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liig..gvaardq 90 
                                     +k++ k  ++ P+++L+   l++ +kf+k+++ +   +i+   gv   + 
  gene702|gene702|rna701|rna701 923 SDKKNIKYTFLDPLTKLTDYELSEETKFIKNTSFEFIdMIYRgiGVHHAHM 973
                                    467777888888888888888888888888777555544444233333333 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   3.3e-15   1.5e-11      22     169 ..     526     670 ..     489     672 .. 0.81
   2 ?   -0.7   0.6      0.28   1.2e+03      67     108 ..     888     932 ..     854     991 .. 0.69

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3.3e-15
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--..... CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekds 101
                                    +++k ++i ++T +GKT++++ +ie++lk+ + + ++f  p+k+l++q   ++   +  +++  +++++g   k+++++ 
  gene702|gene702|rna701|rna701 526 DQNKSAVISAPTSAGKTFICFYAIEKILKESDTNMVIFCLPTKALVNQVSADIYARFTAKVN-SKTFLQGSLMKEFSIAP 604
                                    7999**********************************************777666666665.78889999888888889 PP

                                    ..-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHHHHHT---SEEEEEESS- CS
                         ResIII 102 tnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swreilekfkeavllglTATp 169
                                     n+++l++  + l + +    ++  +   +r ++iiiDE+H++++++    +++i+   +++ +l l+AT+
  gene702|gene702|rna701|rna701 605 WNCQVLIVIPSLLESVL----NTPPKGFLERVKYIIIDEVHKISSEEmgiPIERIIHL-SPCPMLVLSATL 670
                                    99999999888888888....566666677777************7556677776655.88999999**97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.28
                                    HHHHHHHGGGGTGG.......GEEEESSS-B--.......-SEEE CS
                         ResIII  67 leqtleefkkflseayke...igkkvsgdkkkakekdstnkkilv 108
                                    +e++++e k++ + ++++   i++++  +k  + ++d++n+k+++
  gene702|gene702|rna701|rna701 888 IEKMKKEAKRTRDAEKTKeswIEESIAAEKSFQMRSDKKNIKYTF 932
                                    445555555555444444556666666666666666666666655 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.8   1.7e+04       9      27 ..     552     568 ..     545     590 .. 0.65
   2 !   34.6   0.0   4.3e-12   1.9e-08      41     111 .]     964    1035 ..     936    1035 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.8
                                    HHHHTTTTSEEEEEESSHH CS
                     Helicase_C   9 llkleeeggkilifvntid 27 
                                    +  l+e++ +++if+  ++
  gene702|gene702|rna701|rna701 552 I--LKESDTNMVIFCLPTK 568
                                    3..4778888888886555 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 4.3e-12
                                     STEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.SSHHHHHHHHTTSSSTT CS
                     Helicase_C   41 ikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp.rnvtsyiqriGRtgRag 111 
                                       + v+h+ ++ + r  +   f++++ +vL at  ++ Gi++p+ ++V+  d    ++ +y+q++GR+gR g
  gene702|gene702|rna701|rna701  964 RGIGVHHAHMNRKYRSLVEILFRQKHLQVLFATETLALGINMPCRTVVFAGDSLqLDPMNYKQMAGRAGRRG 1035
                                     457789*************************************99999999877467*************75 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0005       2.3       8      58 ..     517     567 ..     513     577 .. 0.86
   2 ?   -0.8   0.0       0.2   8.9e+02     121     143 ..     633     655 ..     631     659 .. 0.89
   3 ?   -1.9   0.2      0.42   1.9e+03      70     114 ..     878     922 ..     873     935 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0005
                                    HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S CS
                           PhoH   8 eQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriiltrpa 58 
                                     Q ++l+ +++n+  ++ +p+ +GKt++   +  ++lk+++ + +i+  p+
  gene702|gene702|rna701|rna701 517 WQVRLLDLVDQNKSAVISAPTSAGKTFICFYAIEKILKESDTNMVIFCLPT 567
                                    588999999*******************99887888888999999987765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.2
                                    EEEEE-SGGG--HHHHHHHHTTB CS
                           PhoH 121 afvilDEAQnttkeqmkmfltRl 143
                                    +++i+DE   +++e+m + + R+
  gene702|gene702|rna701|rna701 633 KYIIIDEVHKISSEEMGIPIERI 655
                                    68**************9888887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.42
                                    --------TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGT CS
                           PhoH  70 gdleekvdpylrplydaLkdllgaekvekllekgkievaplaymR 114
                                     d+e+k d +++ +  + k + +aek+++ + ++ i   +   mR
  gene702|gene702|rna701|rna701 878 MDMEKKKDKFIEKMKKEAKRTRDAEKTKESWIEESIAAEKSFQMR 922
                                    68999**************************99999999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1352  (0.0754086); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 1.00u 0.33s 00:00:01.33 Elapsed: 00:00:00.52
# Mc/sec: 7697.15
//
Query:       gene703|gene703|rna702|rna702  [L=248]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-12   46.0   0.0    9.5e-12   45.4   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.5e-10   41.6   0.0    2.7e-10   40.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.7e-09   38.3   3.2    2.7e-09   37.7   3.2    1.4  1  WBS_methylT      Methyltransferase involved in Williams-Beure
      2e-07   31.0   0.0    4.2e-07   29.9   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    1.2e-06   28.4   0.0    1.5e-06   28.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.3e-06   28.0   0.0    1.6e-06   27.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    1.1e-05   26.0   0.0      2e-05   25.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    0.00062   19.2   0.0    0.00093   18.6   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.001   18.9   0.0     0.0032   17.2   0.0    1.7  2  N6_N4_Mtase      DNA methylase
     0.0033   17.1   0.0     0.0059   16.2   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
     0.0044   16.8   0.0     0.0065   16.2   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.059   13.7   0.0      0.097   13.0   0.0    1.4  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
      0.096   12.3   0.0       0.17   11.6   0.0    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.24   10.7   0.1       0.33   10.3   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   7.4e-15   9.5e-12       1      95 [.      52     154 ..      52     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 7.4e-15
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC.TSS-TT-EEEEEEES-CCC-.C... CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek.lpfednsfDlvvssevlhhv.e... 75 
                                    LdvGcG+G+    la++g+  +g+D+s  mlkl  +k+++ g    ++++d+ + l f+ ++fD vvs ++++++ +   
  gene703|gene703|rna702|rna702  52 LDVGCGSGLSGSVLAENGHPWIGIDISMDMLKLGAAKKEGVG----YIRMDMGRgLEFQPGTFDGVVSVSAIQWLfHsys 127
                                    8******************************99977776655....8******879*******************93456 PP

                                    .......CHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  76 .......dpekalkeiaRvLkpgGllv 95 
                                           +++ ++  ++ ++kp+ ++v
  gene703|gene703|rna702|rna702 128 sddhpvrRLRTFFTALYSICKPDARCV 154
                                    6677787999*************9998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   2.1e-13   2.7e-10       2      77 ..      52     123 ..      51     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.1e-13
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTEEEEEEESTGGG.S CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsfDlvvssgalhh.l 77 
                                    Ld+GcG+G     la+++  + ++g+Dis +ml+  +++ e     v ++++d+ + l+f+ g+fD vvs+ a+++ +
  gene703|gene703|rna702|rna702  52 LDVGCGSGLSGSVLAENG--HPWIGIDISMDMLKLGAAKKE----GVGYIRMDMgRGLEFQPGTFDGVVSVSAIQWlF 123
                                    9****************5..9**************999884....699******777*************76676422 PP

>> WBS_methylT  Methyltransferase involved in Williams-Beuren syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   3.2   2.1e-12   2.7e-09      39      81 ..     205     246 ..     163     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.1e-12
                    WBS_methylT  39 kkrkkkkkkavksreWilkKKerrrkkGkeVkrdSKYTGRkRk 81 
                                    k +++kkkk   + + il++Ke+ r +G eV++d+KYTGRkR 
  gene703|gene703|rna702|rna702 205 K-KRGKKKKGMGRIDAILRRKEKLRLRGVEVPKDTKYTGRKRS 246
                                    2.344445555588****************************6 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   3.3e-10   4.2e-07       6     132 ..      32     170 ..      27     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.3e-10
                Methyltransf_23   6 eeelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq....eaaepqg 81 
                                    ++el +  ++ll+  + gg +Ld+GcG+G   +vl+eng+  +g+D+s  + ++   a k + + + ++      +++ g
  gene703|gene703|rna702|rna702  32 QRELTERCLELLE-PKDGGLLLDVGCGSGLSGSVLAENGHPWIGIDISMDMLKLG--AAKKEGVGYIRMdmgrGLEFQPG 108
                                    6777777778886.8999******************************9988884..55555555544444446677888 PP

                Methyltransf_23  82 kfdlIvlrevlehvpdpp...........ellrqiatllkpgGylllseplaslkedrllld 132
                                    +fd +v+   + ++ +               ++ +++++kp+++++l+ +l+s+ + ++++ 
  gene703|gene703|rna702|rna702 109 TFDGVVSVSAIQWLFHSYssddhpvrrlrTFFTALYSICKPDARCVLQFYLKSQGQIEMMKA 170
                                    *****99998887763222455556666566666666***************9988877654 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.2e-09   1.5e-06       6     109 ..      50     155 ..      45     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnev 83 
                                     +lD+GCG+G  + +lae+    ++  +GiDis ++++l  ++ +  g+      + d+   le  +++ +fD ++s ++
  gene703|gene703|rna702|rna702  50 LLLDVGCGSGLSGSVLAEN----GHpWIGIDISMDMLKLGAAKKEGVGYI-----RMDMGRgLE--FQPGTFDGVVSVSA 118
                                    58***************55....344*************99986655554.....667777788..88999****99988 PP

                Methyltransf_31  84 l...........naladpdkileeiervlkpggilli 109
                                    +           + +  +  ++  + +  kp+ ++++
  gene703|gene703|rna702|rna702 119 IqwlfhsyssddHPVRRLRTFFTALYSICKPDARCVL 155
                                    8777766666665555555555566666666666555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.3e-09   1.6e-06      46     171 ..      31     162 ..      12     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.3e-09
                                    HHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-- CS
                           CMAS  46 AqlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedld 125
                                     q++ +++ le le k+G  lLd+GcG G      +e+ +   +g+ +S +  kl  ++ + ++  r    + l+++  +
  gene703|gene703|rna702|rna702  31 IQRELTERCLELLEPKDGGLLLDVGCGSGLSGSVLAEN-GHPWIGIDISMDMLKLGAAKKEGVGYIRMDMGRGLEFQ--P 107
                                    577777889999999**************998888888.*****************999999998777766666665..6 PP

                                    ---SEEEEES-GGGT.........SGGGHHHHHHHHHHHS-TT-EEEEEEEEE-- CS
                           CMAS 126 ekvdrvvsvgafehv.........gkenydtffkklkkllkedGllllhtitslh 171
                                    + +d vvsv a++ +          ++++ tff +l+++ k+d + +l+   + +
  gene703|gene703|rna702|rna702 108 GTFDGVVSVSAIQWLfhsyssddhPVRRLRTFFTALYSICKPDARCVLQFYLKSQ 162
                                    7***********999899999988889*****************99998766554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.6e-08     2e-05       1      98 [.      52     152 ..      52     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.6e-08
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl. 79 
                                    L++GcG+G   ++l+e+  +   +g+Dis +++     kl + +++ +  ++ +    l+ ++g +fD vv+ +++++l 
  gene703|gene703|rna702|rna702  52 LDVGCGSGLSGSVLAEN--GHPWIGIDISMDML-----KLGAAKKEGVGYIRMDMGRGLEFQPG-TFDGVVSVSAIQWLf 123
                                    8****************..9999**********.....66666665666677777776655555.**************9 PP

                Methyltransf_12  80 ..........kdirevldnirklLkpgGr 98 
                                              + +r ++  +++ +kp++r
  gene703|gene703|rna702|rna702 124 hsyssddhpvRRLRTFFTALYSICKPDAR 152
                                    99999999999999999999999999986 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.3e-07   0.00093      39     120 ..      39     113 ..      17     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.3e-07
                                    HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EE CS
                Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfD 118
                                      +l  +k g  +lDv +G+g     l++   +    +++Di+ +mLk g +k +  g+i++++    +  L+f+ ++fD
  gene703|gene703|rna702|rna702  39 CLELLEPKDGGLLLDVGCGSGLSGSVLAE---NGHPWIGIDISMDMLKLGAAKKEGVGYIRMDM----GRGLEFQPGTFD 111
                                    344556778889********976666554...4446799*************999999998875....677999999999 PP

                                    EE CS
                Ubie_methyltran 119 vv 120
                                     v
  gene703|gene703|rna702|rna702 112 GV 113
                                    54 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.5e-06    0.0032     178     227 ..      33      83 ..      29      89 .. 0.91
   2 ?   -1.3   0.0       1.2   1.5e+03      32      63 ..     133     164 ..     120     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.5e-06
                                    HHHHHHHHHHHS-T.T-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHH CS
                    N6_N4_Mtase 178 vallerlIklstkk.gdivlDpFaGSGtTavaakelgrkfiGieieeeyve 227
                                    ++l er+++l+ +k g++ lD  +GSG  + + +e g  +iGi+i+   ++
  gene703|gene703|rna702|rna702  33 RELTERCLELLEPKdGGLLLDVGCGSGLSGSVLAENGHPWIGIDISMDMLK 83 
                                    6899*******99989*****************************987766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT CS
                    N6_N4_Mtase  32 leflekvlkevrrvLkddgsifiniddseikk 63 
                                    +++l+ ++  ++ + k+d   ++++  + + +
  gene703|gene703|rna702|rna702 133 VRRLRTFFTALYSICKPDARCVLQFYLKSQGQ 164
                                    67899999999999999999999887777665 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.6e-06    0.0059      13      87 ..      47     121 ..      33     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.6e-06
                           MetW  13 pgsrvldlGcGdGellellkeekqvdgrGleldeegva..ecvakGlsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                    +g  +ld+GcG G   ++l+e ++    G++++ + ++  ++ + G+  i+ d+ ++le f+  +fd vv   ++q 
  gene703|gene703|rna702|rna702  47 DGGLLLDVGCGSGLSGSVLAE-NGHPWIGIDISMDMLKlgAAKKEGVGYIRMDMGRGLE-FQPGTFDGVVSVSAIQW 121
                                    46679**************87.56666777776665541177778*************8.67789****99988885 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.1e-06    0.0065      43      93 ..      13      67 ..       7      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.1e-06
                                   TSSS-EEEETT..EEE..--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHH CS
                           PCMT 43 Yedaplsigyn..ati..SaphmvalalellelkkgarvLevGsGsGyltavlar 93
                                   Y d   s+ y   + i   +  +  ++lelle k+g   L+vG+GsG    vla+
  gene703|gene703|rna702|rna702 13 YYDEETSLKYTqnSRIvyIQRELTERCLELLEPKDGGLLLDVGCGSGLSGSVLAE 67
                                   55555555554222221135567889************************99986 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-05     0.097      62      89 ..      51      78 ..      27      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-05
                   AdoMet_MTase 62 fvdvgcgngllvyvlaaegykgygidlr 89
                                   + dvgcg gl   vla +g+   gid+ 
  gene703|gene703|rna702|rna702 51 LLDVGCGSGLSGSVLAENGHPWIGIDIS 78
                                   57************************85 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.17      35      70 ..      45      80 ..      21      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                   -S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HH CS
                           TPMT 35 akaglrvlvPlCGkaldlvwlAeqgrevvGvelsel 70
                                    k g+  l  +CG++l  + lAe+g+  +G+++s  
  gene703|gene703|rna702|rna702 45 PKDGGLLLDVGCGSGLSGSVLAENGHPWIGIDISMD 80
                                   45555556669**********************965 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00026      0.33     148     174 ..      36      60 ..      32      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                           PrmA 148 TklclealeklvkegeevlDvGtGSGi 174
                                    T+ cle+le   k g  +lDvG+GSG+
  gene703|gene703|rna702|rna702  36 TERCLELLEP--KDGGLLLDVGCGSGL 60 
                                    899*****96..78899*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1847.28
//
Query:       gene704|gene704|rna703|rna703  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1569.39
//
Query:       gene705|gene705|rna704|rna704  [L=357]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.3e-33  113.9   0.0    1.2e-32  113.5   0.0    1.1  1  Fe_hyd_lg_C  Iron only hydrogenase large subunit, C-terminal 


Domain annotation for each model (and alignments):
>> Fe_hyd_lg_C  Iron only hydrogenase large subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.0   6.9e-37   1.2e-32      20     243 .]      77     305 ..      56     305 .. 0.80

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 6.9e-37
                                    T--T-S-HHHHHHHHHH.TT-SEEEETHHHHHHHHHHHHHHHHHHHHHTS-SSEE----HHHHHHHHHH-GGGGGGB--B CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Fe_hyd_lg_C  20 glsvaattgklvaalrk.lGfdkVfdtafgadltimeeasellerleeeeklpmitScCPgwvkyvekkypellpnlssv 98 
                                    ++s ++++  l+++l++ + + k++dt++ +  + +e  +e+l+         ++ S+CPg+v+yve++ p+l+ +ls v
  gene705|gene705|rna704|rna704  77 DMSYRKFESALSSFLKTkFNIYKIVDTSCMRSRIYEEVYREYLTTN------HLVISACPGVVTYVERTAPHLIGYLSRV 150
                                    456699999*******99****************999889998865......5899************************ PP

                                    --HHHHHHHHHHTHHHHHGGEEEEEEES-SSHHHHHTSTT-BBTBBSS-EEEEHHHHHHHHHHTT--G.........GGS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxx RF
                    Fe_hyd_lg_C  99 kSPqqilgaliKkylaekekivvVsimPCtaKklEaareefksagrdvDavlTtrElaellkeagidl.........akl 169
                                    kSPqq++ +l+K          ++s+mPC++KklE  r+ +     + D+vl trE+ ++l+e g++           ++
  gene705|gene705|rna704|rna704 151 KSPQQMAFSLVKGS-------RTISVMPCYDKKLENGRDGV-----NFDFVLATREFRQVLDELGFEAfiksrtmnlCDM 218
                                    ***********886.......58*****************9.....78**************777666543322222222 PP

                                    -----.--TTSSSSSTSS-...............TTEEEEEEEE-TSEEEEEEEESHHHHHHHHHHHHTTSS--SEEEEE CS
                                    xxxxx.xxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Fe_hyd_lg_C 170 eeeel.dnplgessgagki...............egvkeaevelegktlkvavvnGlknikklleklkageakydfiEvm 233
                                    e++e+ ++ +g+ssg  +                +g+ke  v+ +g+   + +++Gl+n  + +++ k + a y++ E+ 
  gene705|gene705|rna704|rna704 219 EKTEIsQWNIGTSSGGYSEsilrrycsievvkdrNGIKEYVVD-DGS--IISQITGLENSINYFRRSKIKGARYKMAEIF 295
                                    332220233444444444499*******999888888888776.566..5899*************************** PP

                                    SSTTSGGG-T CS
                                    xxxxxxxxxx RF
                    Fe_hyd_lg_C 234 aCpgGCigGg 243
                                     C++ CigG+
  gene705|gene705|rna704|rna704 296 LCKSSCIGGP 305
                                    *********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2260.72
//
Query:       gene706|gene706|rna705|rna705  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-30  104.4   0.1    6.3e-30  104.2   0.1    1.0  1  ANAPC10   Anaphase-promoting complex, subunit 10 (APC10)
  ------ inclusion threshold ------
      0.092   12.3   0.2       0.19   11.3   0.0    1.6  2  Relaxase  Relaxase/Mobilisation nuclease domain


Domain annotation for each model (and alignments):
>> ANAPC10  Anaphase-promoting complex, subunit 10 (APC10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.1   7.1e-34   6.3e-30      31     162 ..       3     129 ..       1     135 [. 0.94

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 7.1e-34
                        ANAPC10  31 wsvsSakpgngvellrddnldtyWqsdgsqPHlvniqfqkktevkavalyvdyklDeSYtPskirvraGtgfndlkevkk 110
                                    + +sS k    +++l+ +++  yW +d ++PH ++i f k   v++v l++ ++ D+SYtP+ki +r+G   + +ke+  
  gene706|gene706|rna705|rna705   3 IRLSSFKREHSLKELLSKDMSEYWATDDVLPHSIQISFDKVKYVQSVQLFLSFTQDDSYTPEKIAIRSGLARECIKEISS 82 
                                    569***************************************************************************** PP

                        ANAPC10 111 vdleeptGWvkislkdarekllrvfllqiavlsnhqnGrdthvrqikiy.gPv 162
                                    v+l ep G + + +        +   +qi + snhq+G+d+h+r++k++ +P+
  gene706|gene706|rna705|rna705  83 VELVEPEGLLTLNVGR------KCLYIQIVINSNHQEGKDSHIRHLKVLeSPT 129
                                    **********999998......67789********************983454 PP

>> Relaxase  Relaxase/Mobilisation nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.1e-05      0.19      46      83 ..      37      78 ..      15      85 .. 0.82
   2 ?   -1.8   0.1      0.21   1.9e+03     106     119 ..     104     116 ..      96     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                       Relaxase 46 relydkvdkdqvhhiiqSFspge.ltp...eqineigrelak 83
                                   +  +dkv+++q+ ++++SF  ++  tp   +    ++re +k
  gene706|gene706|rna705|rna705 37 QISFDKVKYVQSVQLFLSFTQDDsYTPekiAIRSGLARECIK 78
                                   6789***********************444334456666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.21
                       Relaxase 106 HiviNrvnletgkk 119
                                     iviN+ ++e gk 
  gene706|gene706|rna705|rna705 104 QIVINSNHQE-GKD 116
                                    6999999999.554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 827.24
//
Query:       gene707|gene707|rna706|rna706  [L=947]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-97  325.9   0.0    4.9e-97  325.5   0.0    1.1  1  DNA_pol_B  DNA polymerase family B


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.5   0.0  2.7e-101   4.9e-97       4     456 ..     357     790 ..     354     793 .. 0.90

  Alignments for each domain:
  == domain 1  score: 325.5 bits;  conditional E-value: 2.7e-101
                                    HHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTT CS
                      DNA_pol_B   4 srvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcytt 83 
                                    +r+l++ +++r+e+ Ll+++ e+g+  p    ++++ +  Y G++Vl+P+ g+y++ vl+lDF+SLYPsiiq++N+c++t
  gene707|gene707|rna706|rna706 357 NRALQNLRAERIEYTLLHELYERGYLFP-CVASRREVK--YTGGLVLSPQVGFYEDLVLLLDFNSLYPSIIQEFNVCFST 433
                                    6899999*********************.555546666..**************************************** PP

                                    CE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHH CS
                      DNA_pol_B  84 lvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQlalKvta 163
                                    +   + + +  ++ + +le+  e++       s+ +g lpk+L+ ++ +Rka+k  +k +k ++e ++l+++Q alK+ta
  gene707|gene707|rna706|rna706 434 IGMFNGRISGDMDGE-KLEMLTEKS------RSSGRGFLPKILEGFVGRRKAVKDLMKRCKGKEEIKVLEIRQRALKLTA 506
                                    *99999988655544.455544443......6788********************************************* PP

                                    HHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-....S- CS
                      DNA_pol_B 164 NsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfiel....kv 239
                                    Ns+YG++G+a sr+  + +Aa +T++GR+ L+++k++ e+ +                ++k+iYGDTDSv++++    ++
  gene707|gene707|rna706|rna706 507 NSIYGCLGFAGSRFCNYTMAAYITNKGRDLLLEAKRIAEEGC----------------GMKIIYGDTDSVMVHTglggEM 570
                                    ***************************************772................9***************777677 PP

                                    SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHH CS
                      DNA_pol_B 240 kdveellkigkelaeevseklfkkplklefekvykkllLisKKkYaglkvektskanklliKGvdlvRrdncklvkevik 319
                                    ++++++l++   l+  +++ ++kk +++e++kv+kkllL +KKkYagl++++ + +++++ KG+dlvR+d c+ +++v++
  gene707|gene707|rna706|rna706 571 SNYKKALEMSVRLKDAINS-RYKK-IEIEVDKVFKKLLLYKKKKYAGLYITE-EGKSSIEYKGLDLVRKDFCEASRRVCR 647
                                    99*****************.9999.**************************4.444458********************* PP

                                    HHHHHHSSS................S-HHHHHHHHHHHHHHHHHHHHTT-S..-GGGG-EEEEESS.CCCS.SGCCSHHH CS
                      DNA_pol_B 320 kvlelllkdet............eersleeglealksilkdvleeleenkv..plekfvlskelskepeny.ksknlphl 384
                                    +vlelll d +             +r l++g  ++++ + d l++l +n    p ++fv+ ++lsk peny  s +lph+
  gene707|gene707|rna706|rna706 648 SVLELLLTDFEdprtyarfyedePKRVLNDGNSKIRRAVYDELKKLSSNLEglPTKDFVIYNTLSKAPENYdPSVALPHV 727
                                    *********889*********996677777777777777777777777654459*****************999****** PP

                                    HHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHHH CS
                      DNA_pol_B 385 evakrlkkrneeapevgdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarll 456
                                    ++a rlk+  + +   gd+  Yvi +        n+      + + y l+++  id+eyY+s q+l+++ r++
  gene707|gene707|rna706|rna706 728 SLALRLKEA-GMKFDQGDVACYVIGKGGP-----NE----APHKRAYHLNEDFAIDYEYYISnQILPPLLRIV 790
                                    ******988.799***********99986.....33....3444478899*******************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (947 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 5838.12
//
Query:       gene708|gene708|rna707|rna707  [L=207]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-21   75.1   0.1    4.4e-21   75.1   0.1    1.4  1  Arf        ADP-ribosylation factor family
    7.1e-08   32.0   0.2    0.00045   19.5   0.1    2.3  2  G-alpha    G-protein alpha subunit
    9.3e-08   32.1   0.0    2.6e-07   30.7   0.0    1.7  2  MMR_HSR1   50S ribosome-binding GTPase
    2.1e-06   27.9   0.2    7.4e-06   26.2   0.2    1.9  1  Roc        Ras of Complex, Roc, domain of DAPkinase
    0.00055   19.6   0.0    0.00092   18.8   0.0    1.3  1  Ras        Ras family
    0.00093   18.7   0.0     0.0012   18.4   0.0    1.1  1  SRPRB      Signal recognition particle receptor beta subunit
  ------ inclusion threshold ------
       0.01   15.2   0.1      0.029   13.7   0.1    1.8  1  Gtr1_RagA  Gtr1/RagA G protein conserved region
      0.031   14.3   0.0       0.47   10.5   0.0    2.2  2  Dynamin_N  Dynamin family
      0.069   13.2   0.0       0.11   12.5   0.0    1.4  1  AAA_14     AAA domain
      0.074   12.8   0.0      0.091   12.5   0.0    1.3  1  AAA_24     AAA domain
       0.12   12.1   0.1        1.5    8.6   0.1    2.4  1  PduV-EutP  Ethanolamine utilisation - propanediol utilisation


Domain annotation for each model (and alignments):
>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   2.7e-24   4.4e-21      14     174 ..      23     183 ..      12     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.7e-24
                                    EEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEETT- CS
                            Arf  14 elrilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvvDsad 93 
                                     +r+ +lG +++GK+Ti++++ +++l        +   +     +++ v+Dv G+++ R  W+ ++++ d+++++vD++ 
  gene708|gene708|rna707|rna707  23 RVRVAVLGPEKSGKSTIVNRMFKDRLRYLGSQKDMCLYKYDEDYINYVVYDVCGKRSSRVRWDYFYKRCDVILYCVDASS 102
                                    58999*************************999********************************************876 PP

                                    .CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHHHHHH CS
                            Arf  94 .reRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeglkeglewls 172
                                     +e+  ea+eeLk++l ++   +  +lvl+ K + ++al   e+ ++l+l +++   k++ +++sa k+++++  ++w+ 
  gene708|gene708|rna707|rna707 103 tEEKWVEAREELKSMLYRNPWIKRSILVLGTKNEKKSALGCMEIIRKLELFDIN-GLKVSCFSVSAKKNTNIECIMSWIR 181
                                    1569**************************************************.999********************99 PP

                                    HH CS
                            Arf 173 es 174
                                    ++
  gene708|gene708|rna707|rna707 182 DQ 183
                                    87 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00013      0.21      24      43 ..      24      43 ..       6      55 .. 0.87
   2 !   19.5   0.1   2.8e-07   0.00045     195     239 ..      61     104 ..      44     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                                   EEEEEEESTTSSHHHHHHHH CS
                        G-alpha 24 vkllllGqseSGKsTilkql 43
                                   v++ +lG ++SGKsTi++ +
  gene708|gene708|rna707|rna707 24 VRVAVLGPEKSGKSTIVNRM 43
                                   799*************9987 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.8e-07
                                    EEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT CS
                        G-alpha 195 kfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvslsefd 239
                                    k++ d  +++ ++dv G+rs r  W  f++  d+i+++v  s   
  gene708|gene708|rna707|rna707  61 KYDED-YINYVVYDVCGKRSSRVRWDYFYKRCDVILYCVDASSTE 104
                                    44445.78999****************************988655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.6e-10   2.6e-07       1     104 [.      25     124 ..      25     134 .. 0.81
   2 ?   -2.0   0.0       2.3   3.8e+03      46      58 ..     148     159 ..     134     179 .. 0.64

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.6e-10
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlil 80 
                                    +va++G   +GKSt++n++++++    ++ g  +d+  ++++++  +++++D+ G  +   ++ +++ ++   +++d+il
  gene708|gene708|rna707|rna707  25 RVAVLGPEKSGKSTIVNRMFKDRL---RYLGSQKDMCLYKYDEDYINYVVYDVCG--K---RSSRVRWDYF-YKRCDVIL 95 
                                    69*******************977...57999999999999988899********..3...2345666777.678***** PP

                                    EEEETT..TTCSHHHHHHHHHHHHH...T CS
                       MMR_HSR1  81 lvvdas..eeklkpldeeleellee...a 104
                                    ++vdas  eek+ + +eel+++l +    
  gene708|gene708|rna707|rna707  96 YCVDASstEEKWVEAREELKSMLYRnpwI 124
                                    ****9988778999999999999764432 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                                    EEEEEEECGGCSS CS
                       MMR_HSR1  46 keielvDtpGlie 58 
                                    +++el D+ Gl +
  gene708|gene708|rna707|rna707 148 RKLELFDINGL-K 159
                                    46788888884.2 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   4.5e-09   7.4e-06       1     104 [.      25     113 ..      25     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 4.5e-09
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    +v ++G +++GK+++++r+ +d+ +   ++    d++  ++        d+  + +++ ++D++G+   r   ++++++ 
  gene708|gene708|rna707|rna707  25 RVAVLGPEKSGKSTIVNRMFKDRLRYLGSQ---KDMCLYKY--------DE--DYINYVVYDVCGKRSSRVRWDYFYKRC 91 
                                    5889****************9998543322...23332222........22..36899********************** PP

                                    CEEEEEEEGHHHHCHHHHHHHHHH CS
                            Roc  81 alailvydsrssenlkeWlkelkk 104
                                    +++++++d++s e+  +W++  ++
  gene708|gene708|rna707|rna707  92 DVILYCVDASSTEE--KWVEAREE 113
                                    ********654432..34443332 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   5.7e-07   0.00092       2     158 ..      26     182 ..      25     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.7e-07
                                    EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEET CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydi 81 
                                    + ++G +  GK+++++r  kd+ +      +g ++ +   ++d+  ++  ++D  G+   +   + +y+ +++il +  +
  gene708|gene708|rna707|rna707  26 VAVLGPEKSGKSTIVNRMFKDRLRY-----LGSQKDMCLYKYDEDYINYVVYDVCGKRSSRVRWDYFYKRCDVILYC--V 98 
                                    789*************998887654.....588899999*****************999888888889888877655..6 PP

                                    TBHHHHHTHHHHHHHHHHHST....TTSEEEEEEETTTGGG....G-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHHH CS
                            Ras  82 tsresfenvkkwveeikrvae....envpivLvGnKvDlee....kravsteegeelakelglkfletSAktnenveeaf 153
                                    + +++ e+  +  ee+k++       + +i+++G+K   ++     + +++ e  +  + l++  + +SAk+n+n+e ++
  gene708|gene708|rna707|rna707  99 DASSTEEKWVEAREELKSMLYrnpwIKRSILVLGTKNEKKSalgcMEIIRKLELFD-INGLKVSCFSVSAKKNTNIECIM 177
                                    666666666666677776666555655789999***99988655444444444332.345668999**********9988 PP

                                    HHHHH CS
                            Ras 154 eellr 158
                                      + +
  gene708|gene708|rna707|rna707 178 SWIRD 182
                                    77655 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   7.1e-07    0.0012       5     128 ..      25     141 ..      22     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7.1e-07
                                    EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvD 84 
                                    +v ++G+ +sGK ++ +r+ +d  +    Sq+ ++ +k+ +e+  +  + D+ G+ + r +   +    ++   +++ vD
  gene708|gene708|rna707|rna707  25 RVAVLGPEKSGKSTIVNRMFKDRLR-YLGSQKDMCLYKY-DEDYINYVVYDVCGKRSSRVRWD-Y--FYKRCDVILYCVD 99 
                                    67899***************99876.5789*9*******.8888999999*****99998864.4..4567889****** PP

                                    TTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTSTT-- CS
                          SRPRB  85 StidpkevkevAEllyeilliteklkdavdiliACnKqelflak 128
                                    ++  + +  e  E l ++l  +  +k +  il+   K+e   a 
  gene708|gene708|rna707|rna707 100 ASSTEEKWVEAREELKSMLYRNPWIKRS--ILVLGTKNEKKSAL 141
                                    999999999999*9***99999977765..55556666665555 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.8e-05     0.029       2     118 ..      26     130 ..      25     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                      Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvli 81 
                                    v  +G+++sGK+++ + +F+       ++lg+  d+   +    + ++  + D+ G+++          ++ +++++v++
  gene708|gene708|rna707|rna707  26 VAVLGPEKSGKSTIVNRMFKD----RLRYLGSQKDMCLYKY-DEDYINYVVYDVCGKRSSRV-----RWDYFYKRCDVIL 95 
                                    5679*********99999986....5799***999999999.58999*********986544.....5699********* PP

                      Gtr1_RagA  82 yVfDvesreleedletlkeilealrqyspeakvfvli 118
                                    y +D++  + ee+  + +e l+ +   +p +k  +l+
  gene708|gene708|rna707|rna707  96 YCVDAS--STEEKWVEAREELKSMLYRNPWIKRSILV 130
                                    ******..55666666666666666666666655555 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00029      0.47       1      22 [.      26      47 ..      26      58 .. 0.87
   2 ?    1.9   0.0      0.12     2e+02     124     142 ..      85     104 ..      53     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                                   EEEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                   +av+G  +sGKS+++n + +++
  gene708|gene708|rna707|rna707 26 VAVLGPEKSGKSTIVNRMFKDR 47
                                   79**************998876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                                    HHH.STTEEEEEEEETTS-C CS
                      Dynamin_N 124 eyi.kkadiilavtsanhdl 142
                                     y  k++d+il+ ++a++  
  gene708|gene708|rna707|rna707  85 DYFyKRCDVILYCVDASSTE 104
                                    677799*******9999854 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.7e-05      0.11       5      33 ..      26      58 ..      23     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.7e-05
                         AAA_14  5 lvitGaRrvGKTtllkqlikell....vkkesi 33
                                   +++ G+ ++GK+t++++++k++l     +k+ +
  gene708|gene708|rna707|rna707 26 VAVLGPEKSGKSTIVNRMFKDRLrylgSQKDMC 58
                                   6799*****************997764333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.6e-05     0.091       3      58 ..      24      93 ..      22     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.6e-05
                         AAA_24  3 lkiliyGpsgiGKTtlakel.gpkplfi..dtekGlksldadkfpdie...........swedfldevve 58
                                   +++++ Gp+++GK+t+++++ +++  ++  + ++ l + d d ++++             w+ f++ ++ 
  gene708|gene708|rna707|rna707 24 VRVAVLGPEKSGKSTIVNRMfKDRLRYLgsQKDMCLYKYDEDYINYVVydvcgkrssrvRWDYFYKRCDV 93
                                   689*****************96666666335666666666666666656666666666666666666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00093       1.5       3      33 ..      25      55 ..      23     182 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00093
                      PduV-EutP  3 killiGkvgsGKttLtqalkgeelkYkktqa 33
                                   ++ ++G+ +sGK t+ +++ +++l+Y   q 
  gene708|gene708|rna707|rna707 25 RVAVLGPEKSGKSTIVNRMFKDRLRYLGSQK 55
                                   68899*******************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.34s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1281.74
//
Query:       gene709|gene709|rna708|rna708  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-06   29.0   3.9     0.0096   16.8   0.1    4.3  4  WD40         WD domain, G-beta repeat
    9.7e-05   22.6   0.0      0.026   14.8   0.0    2.8  2  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.28   11.5   0.0    1.7  1  CAF1C_H4-bd  Histone-binding protein RBBP4 or subunit C of CA


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1    0.0056        33       6      34 ..     175     202 ..     170     206 .. 0.75
   2 ?    4.3   0.0     0.014        83      12      36 ..     221     244 ..     212     246 .. 0.85
   3 !   16.8   0.1   1.6e-06    0.0096       8      38 .]     256     285 ..     250     285 .. 0.78
   4 ?   -0.4   0.0      0.43   2.6e+03      13      35 ..     310     330 ..     297     332 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0056
                                    EEESS.SSEEEEEEETTSSEEEEEETTSEE CS
                           WD40   6 tltGH.ssvtslafspdgawlasGsdDgtv 34 
                                     ++ H +s+ +l+++++  +  sGs D+++
  gene709|gene709|rna708|rna708 175 MISVHeDSIEGLCYQDNMIF--SGSCDHSI 202
                                    56789888*99977666655..9*99**98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                                    SEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40  12 svtslafspdgawlasGsdDgtvri 36 
                                    ++++++f+ d+ + + G+d+g +r+
  gene709|gene709|rna708|rna708 221 DINAVDFNGDNMLAF-GDDNGVIRL 244
                                    499**9999999987.*99*99997 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.6e-06
                                    ESS.SSEEEEEEETTSSE.....EEEEETTSEEEEEE CS
                           WD40   8 tGH.ssvtslafspdgaw.....lasGsdDgtvriWd 38 
                                    + H +++++l+      w     lasGs D  v iWd
  gene709|gene709|rna708|rna708 256 SRHkTPISCLK------WrdgdiLASGS-DEQVCIWD 285
                                    569788****5......44444489***.*******9 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.43
                                    EEEEEEETTSSEEEEEETTSEEE CS
                           WD40  13 vtslafspdgawlasGsdDgtvr 35 
                                    +t +    d++++++ s Dg + 
  gene709|gene709|rna708|rna708 310 ITFC--RGDNNYVITTSIDGLCV 330
                                    6555..67899999999998775 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0023        14      12      88 ..     156     226 ..     154     230 .. 0.87
   2 !   14.8   0.0   4.4e-06     0.026      41      90 ..     222     268 ..     213     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0023
                    ANAPC4_WD40  12 latedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                    ++t +ge+ ++  n++++  +  + ++ ++++L+++  ++++  +  d ++ + d+  +k v + + + +  ++ ++
  gene709|gene709|rna708|rna708 156 FGTRSGEVSMNDWNFNEISMI--SVHEDSIEGLCYQ--DNMIFSGSCDHSIGITDIRAKKSVFQKKFEYD--INAVD 226
                                    578899999999999999999..89999******97..57999******************999988877..66665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.4e-06
                    ANAPC4_WD40  41 vrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                    ++++ ++  +++La++ ++g +rl+d+ +  v +++s +++  ++cl+W 
  gene709|gene709|rna708|rna708 222 INAVDFNG-DNMLAFGDDNGVIRLMDIRNYSV-EEISRHKT-PISCLKWR 268
                                    56666665.479***************99876.55556655.3******7 PP

>> CAF1C_H4-bd  Histone-binding protein RBBP4 or subunit C of CAF1 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.7e-05      0.28       1      49 [.      31      69 ..      31     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHHHHHHHEEEEEEEE-SS--S-EEE-S-B---EEEEEEEE--- CS
                    CAF1C_H4-bd  1 eeylewkknapfLYdmlhshslewPsLsfdwlPdtvsslskqrllvGtq 49
                                   +e+le+ + a   Y+ +  +sl+wP  s+d++   +       +++Gt+
  gene709|gene709|rna708|rna708 31 DEELEVSEDA---YNVMEYISLDWPAQSIDIFRGFT-------VVLGTN 69
                                   799*******...******************87643.......455664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2079.54
//
Query:       gene710|gene710|rna709|rna709  [L=357]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-28   98.9   0.0    3.5e-28   97.4   0.1    1.8  2  DKCLD     DKCLD (NUC011) domain
      2e-22   80.2   0.1    9.6e-19   68.2   0.1    3.1  1  TruB_N    TruB family pseudouridylate synthase (N terminal do
    4.6e-21   74.7   0.3    8.6e-21   73.9   0.3    1.5  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
      3e-18   65.5   0.4    6.3e-18   64.5   0.4    1.6  1  PUA       PUA domain
  ------ inclusion threshold ------
       0.07   13.4   0.0       0.28   11.5   0.0    2.1  2  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.4   0.1   9.8e-32   3.5e-28       2      58 .]      18      74 ..      17      74 .. 0.98
   2 ?   -2.2   0.0       1.3   4.6e+03       4      28 ..     255     279 ..     253     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 9.8e-32
                                   XXXX....XXX-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                          DKCLD  2 sewpllLknydkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                   ++w+llL ++dk++vrt+hytpl +Gs+Pl+R+i eyikyG++nLDK+snPsSHEVV
  gene710|gene710|rna709|rna709 18 ETWDLLLADMDKMVVRTNHYTPLGCGSMPLNRKIGEYIKYGIVNLDKSSNPSSHEVV 74
                                   68******************************************************9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                                    XX....XXX-EEESS-----TTSS- CS
                          DKCLD   4 wpllLknydkllvrtehytplpaGs 28 
                                    ++ lL  y +++++ +  + + +G 
  gene710|gene710|rna709|rna709 255 LESLLVGYPRIMIKDSCVNAICYGA 279
                                    5678889999999999999888885 PP

>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.1   2.7e-22   9.6e-19       1     149 []      78     193 ..      78     193 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 2.7e-22
                                    HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHH CS
                         TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleev 80 
                                    k++lk +k Gh+GtLDp+++GvL +++++aT+l+++ ++  KeY+++i++ +e ++                  ++++++
  gene710|gene710|rna709|rna709  78 KEILKCEKTGHSGTLDPQVSGVLTICIDRATRLTKSQQSLGKEYVCVIEFLEEPNE------------------AEFHKI 139
                                    789**********************************************9876554..................558899 PP

                                    HHHC-EEE---------------------------------EEEEEEEEEEEEEE..EEEEEEEESTTTTH CS
                         TruB_N  81 lkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveep..evelevecskGtYi 149
                                     k++ G++ q+pp ++Avk                 r+ r  +iy++++le++++     ++v+c++GtY+
  gene710|gene710|rna709|rna709 140 SKRLIGSLLQRPPLMCAVK-----------------RELRVRNIYNIDILEFSKEkrVGLFKVSCEAGTYV 193
                                    99*****************.................899*************888667789*********8 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.3   2.4e-24   8.6e-21       1      63 [.     194     259 ..     194     260 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 2.4e-24
                                    HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                       TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                    RtLc+++G ++gcgA ++eLRRtr+g  +e+d++tl+dL dav++++   de+ ++r+++Ples+l
  gene710|gene710|rna709|rna709 194 RTLCTHMGILMGCGAKMKELRRTRSGRTSEKDIFTLHDLLDAVHIFNSekDETvIRRVIRPLESLL 259
                                    9*******************************************999986666***********97 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.4   1.8e-21   6.3e-18       1      74 []     263     336 ..     263     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 1.8e-21
                                    CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                            PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                    +r+ ++d++v+a+++ga+L + Gv++++ ++  g +++i++++ge+va+G+a++ss e+  i++g + +++rv+
  gene710|gene710|rna709|rna709 263 PRIMIKDSCVNAICYGAKLSVTGVLRFDRNIDVGKEIVIITTKGEAVALGIALVSSPEMSIIDHGLVCRTKRVI 336
                                    69*****************************************************************9999985 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.8   1.4e+04      37      51 ..      31      45 ..      27      50 .. 0.68
   2 ?   11.5   0.0   7.9e-05      0.28       3      59 ..     266     319 ..     264     334 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.8
                        UPF0113 37 vVlnengeplGiGki 51
                                   vV     +plG G +
  gene710|gene710|rna709|rna709 31 VVRTNHYTPLGCGSM 45
                                   554445589999976 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.9e-05
                        UPF0113   3 vvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdtkasp 59 
                                    ++k +  + + YG ++  +++l+++++++ ++ +v+  ++ge++++G++  ++   p
  gene710|gene710|rna709|rna709 266 MIKDSCVNAICYGAKLSVTGVLRFDRNIDVGKEIVIITTKGEAVALGIALVSS---P 319
                                    67778888999*************************************98855...3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2544.60
//
Query:       gene71|gene71|rna71|rna71  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-14   53.8   1.9    1.6e-14   53.4   1.9    1.2  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   1.9   9.1e-19   1.6e-14       2      83 ..      18      98 ..      17     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 9.1e-19
                               HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEE CS
             Ribosomal_L7Ae  2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsal 83
                               a+++v k+++   kl +G++e+tk +  g+  +v lA+d+ep+  k  ++ l+k+k++p+++v+s+ eLG++vg + ++s+ 
  gene71|gene71|rna71|rna71 18 ALSKVCKVSRTYCKLSRGARETTKKILAGNMRFVMLAKDAEPKIAKL-VTLLAKKKDIPIISVESRLELGKIVGVENASSSG 98
                               6788999999999****************************988777.***************************9875443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 894.14
//
Query:       gene711|gene711|rna710|rna710  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-21   75.8   1.6    3.3e-21   75.3   0.8    1.6  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    6.9e-15   55.4   0.3    2.7e-14   53.4   0.0    2.0  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    6.7e-06   25.7   0.1    9.9e-06   25.2   0.1    1.3  1  Rad9      Rad9
    0.00051   19.2   0.1     0.0007   18.7   0.1    1.3  1  Rad1      Repair protein Rad1/Rec1/Rad17


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3   0.8   7.3e-25   3.3e-21       4     122 ..      16     134 ..      15     137 .. 0.88
   2 ?   -3.1   0.0       1.4   6.1e+03      83     107 ..     175     198 ..     169     208 .. 0.65

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 7.3e-25
                                    EEESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTST CS
                         PCNA_N   4 arleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcan 83 
                                    a+++  sl+k++le++ ++v+ a +++ ++G+s+q++D +hva+  + l s  f kyrCDr+l++gv+l++++ki+k + 
  gene711|gene711|rna710|rna710  16 AQIDSLSLMKRVLESLNEIVETADIKVTEKGLSIQVMDVTHVAFADIFLSSAMFTKYRCDRELVIGVQLKTFTKIIKGMS 95 
                                    5677889**********************************************************************999 PP

                                    TTSEEEEEEETTSSEEEEEEEECTSSEEEEEEEEEEEBG CS
                         PCNA_N  84 nedsvtlkaedeadtlalvfesekkdkiaeydlklklid 122
                                     e   +++ e ++ t  l +++ ++ ++ +++lkl + d
  gene711|gene711|rna710|rna710  96 VEGGGVFRLECDDATTDLNVKNIREGNVLSFKLKLFSSD 134
                                    998888887777777888889999999986666655444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.4
                                    TTTSEEEEEEETTSSEEEEEEEECT CS
                         PCNA_N  83 nnedsvtlkaedeadtlalvfesek 107
                                    +n+  + +++ ++ad+l + fe++ 
  gene711|gene711|rna710|rna710 175 ENKTLIFFQTGEHADSL-MSFEESP 198
                                    56677777788888887.5555544 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.39   1.7e+03      20      43 ..      26      49 ..      20      72 .. 0.62
   2 !   53.4   0.0     6e-18   2.7e-14       2     128 .]     140     262 ..     139     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.39
                                   HHHHHHTTT-SEEEEEEETTEEEE CS
                         PCNA_C 20 ricrdlsqlsdsvvisvtkegvkf 43
                                   r+   l ++ ++  i+vt +g+  
  gene711|gene711|rna710|rna710 26 RVLESLNEIVETADIKVTEKGLSI 49
                                   555666666666666666666543 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 6e-18
                                    ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEE CS
                         PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltf 81 
                                    +p+ e+da  ++p+ ef  + + + +++d v ++v  +++ f   G+   +   l  ++++    +  k+e+kep+t   
  gene711|gene711|rna710|rna710 140 VPEFEFDASATIPAGEFIYVPKLVGSFGDVVGVQVENKTLIFFQTGEHADS---LMSFEESPA-RKELKIEAKEPITQEI 215
                                    79*********************************************8887...444544443.44589*********** PP

                                    EHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-BS CS
                         PCNA_C  82 alkYlaeftkatsLservtlslssevPlvveykikdvgllayllakk 128
                                    a+kY++ + k  +L + v++sl s  P+ +  +++d  +++ ++a+k
  gene711|gene711|rna710|rna710 216 AMKYVNLISKVVPLCKDVKISLGSGKPVFFGLHMDDFSHMKLYVAPK 262
                                    ********************************************996 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   2.2e-09   9.9e-06       2      76 ..      25      97 ..      24     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.2e-09
                           Rad9  2 aralqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsak 76
                                    r+l++l  i +   ++ +e+gl+++ ++ ++ a+a + l++++F ky  + + ++ + +++K++ ++++++s +
  gene711|gene711|rna710|rna710 25 KRVLESLNEIVETADIKVTEKGLSIQVMDVTHVAFADIFLSSAMFTKY--RCDRELVIGVQLKTFTKIIKGMSVE 97
                                   58999999999999**********************************..999*****************99855 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.6e-07    0.0007       4      61 ..      16      75 ..      15     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.6e-07
                           Rad1  4 AtlsnvseLatlLksia.fkdkalvqissdGlkfiv.ednrvlqaqafldkalFtsYtfe 61
                                   A+ +++s +  +L+s++ +++ a ++++++Gl++ v + ++v  a  fl++a+Ft+Y+ +
  gene711|gene711|rna710|rna710 16 AQIDSLSLMKRVLESLNeIVETADIKVTEKGLSIQVmDVTHVAFADIFLSSAMFTKYRCD 75
                                   5667778888999999736679************773679999**************993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1751.76
//
Query:       gene712|gene712|rna711|rna711  [L=251]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1709.80
//
Query:       gene713|gene713|rna712|rna712  [L=404]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-06   25.8   0.1    1.5e-05   24.9   0.1    1.4  1  POT1      Telomeric single stranded DNA binding POT1/CDC13
    0.00023   21.1   0.0      0.027   14.3   0.0    3.4  4  POT1PC    ssDNA-binding domain of telomere protection protein


Domain annotation for each model (and alignments):
>> POT1  Telomeric single stranded DNA binding POT1/CDC13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.7e-09   1.5e-05       9      83 ..      17      84 ..      10     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-09
                                   CTTEEEEEEEEEEEEEECCCSCCEEEEECCCCCTTTSCCHCTTTEEEEEEEECCCCCCCCGGCCCCEEECCCCEE CS
                           POT1  9 aekkvvnviGvVidasfpkktggsdyvctfkivDpsknkgdendglrvvlFsknfedLpivkkvgdiirlhrakl 83
                                   + +++ +++Gv++d+   k+++g+d+++t+ ++D+s       ++l+v++Fs++ + +++   vg+++r+ ++kl
  gene713|gene713|rna712|rna712 17 ERNRYHTIYGVIVDWLEWKRCKGRDFMMTLDVIDES------MKKLSVKVFSPK-KIFSEGFCVGEVVRIGNIKL 84
                                   789999******************************......999999999999.66788888888888888876 PP

>> POT1PC  ssDNA-binding domain of telomere protection protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.15   1.3e+03       2      19 ..      13      30 ..      12      52 .. 0.86
   2 ?   -1.9   0.0      0.31   2.8e+03      82     108 ..      59      84 ..      55     121 .. 0.71
   3 !   14.3   0.0   3.1e-06     0.027       2      41 ..     136     175 ..     135     184 .. 0.92
   4 ?    2.0   0.0     0.019   1.7e+02      74     121 ..     185     229 ..     177     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.15
                                   GGG--SSSEEEEEEEEEE CS
                         POT1PC  2 lkdvqegeffDligqvvk 19
                                   ++d++ +++++++g +v+
  gene713|gene713|rna712|rna712 13 ISDMERNRYHTIYGVIVD 30
                                   78999*********9987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.31
                                    EE-HHHHHHHTTT--TT-EEEEEEEEE CS
                         POT1PC  82 tlydehaefarenlkpgdfvrLrNvhi 108
                                     ++ +   f +    +g++vr+ N+++
  gene713|gene713|rna712|rna712  59 KVFSPKKIFSEG-FCVGEVVRIGNIKL 84 
                                    555666666666.77899999999876 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 3.1e-06
                                    GGG--SSSEEEEEEEEEEEE-..SS-EEEEEE-S---TTS CS
                         POT1PC   2 lkdvqegeffDligqvvkkasddsgkvvLyvwDgtenpnl 41 
                                    +++++eg++fD  g++++k  +  + v+L++ D ++n+  
  gene713|gene713|rna712|rna712 136 ISEIEEGKYFDFNGELIDKQRERTNLVLLRLVDFSRNKLV 175
                                    899*********************************9875 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.019
                                    SBS-EEEEEE-HHHHHHHTTT--TT-EEEEEEEEEEE-TTS.-EEEEE CS
                         POT1PC  74 fgkltlqitlydehaefarenlkpgdfvrLrNvhiklgrkgsklegfl 121
                                     ++++l +  ++  a+ a++  + g + r+rN+++  ++ g +l  +l
  gene713|gene713|rna712|rna712 185 PKEMVLIVKAWGRFANEAEK-CEIGGWYRIRNLKA--DEVGHNLYASL 229
                                    45689999999999999999.************99..55555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2294.02
//
Query:       gene714|gene714|rna713|rna713  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-12   46.0   1.0    8.5e-12   45.5   1.0    1.2  1  RNA_pol_Rpb4  RNA polymerase Rpb4


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   1.0   4.7e-16   8.5e-12      31     119 ..      19     103 ..       3     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 4.7e-16
                                    CHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSH CS
                   RNA_pol_Rpb4  31 isekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfeLtkaEklqlvnlkPesavelktlieeleerfede 110
                                    i++  e+++++ + l+k+  y t + ++++    +  + ++l +++Lt++E++ql++  P+s+v l+++ie++eerf++e
  gene714|gene714|rna713|rna713  19 INRSLETHPGQAEFLEKVRLYCTSSMAKDQ----ALGIKQTLINIGLTEFEIIQLLDFNPKSIVCLQLVIEDMEERFTEE 94 
                                    556667899999999999889998666666....7788899*************************************** PP

                                    HHHHHHHHH CS
                   RNA_pol_Rpb4 111 qleeiLdel 119
                                     l +iLd+ 
  gene714|gene714|rna713|rna713  95 ALLRILDLF 103
                                    ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 614.69
//
Query:       gene715|gene715|rna714|rna714  [L=386]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-58  195.4   0.1    6.5e-58  195.4   0.1    2.3  3  RIO1      RIO1 family
     0.0033   17.4   0.0       0.19   11.6   0.0    2.2  2  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.28   2.5e+03      35      69 ..       7      38 ..       2      39 .. 0.70
   2 !  195.4   0.1   7.3e-62   6.5e-58      12     183 ..      87     256 ..      55     261 .. 0.94
   3 ?   -1.5   0.9      0.18   1.6e+03      97     121 ..     336     360 ..     328     377 .. 0.51

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.28
                                   STTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT CS
                           RIO1 35 ekrfkdrksktnprklvklwaekEfrnLkrleeag 69
                                   ekr   +k k+++  + k+  +k  r L++le++g
  gene715|gene715|rna714|rna714  7 EKR---KKDKSDRATVDKVLDKKTLRVLEKLEARG 38
                                   444...44567777777888899999999998765 PP

  == domain 2  score: 195.4 bits;  conditional E-value: 7.3e-62
                                    EEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EET CS
                           RIO1  12 evaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefiged 91 
                                     v++Ki+kts+ +Fk+r++y+  ekrf+ r++++nprkl+k+waekE+rnLkrl++a++p P+pi lk+++l+m+ ig+ 
  gene715|gene715|rna714|rna714  87 PVVVKIFKTSIMSFKDRERYIRSEKRFQ-RFCTSNPRKLIKVWAEKEVRNLKRLNNAEIPSPEPIYLKNNILIMSRIGNC 165
                                    799***********************99.77************************************************* PP

                                    TEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTHHHHHHHHHHHH CS
                           RIO1  92 gvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpnalefLerDveni 171
                                    +  apkl+d+   e+ + +y +++e +r +yk+aglvHaDLSe+N+l+  + v++IDv+Q+ve+dh na++fL +D++ni
  gene715|gene715|rna714|rna714 166 EEVAPKLRDAM-IEDVNGCYLQCVEIIRNMYKKAGLVHADLSEFNLLYFGGVVYVIDVGQSVEIDHANAQSFLIMDINNI 244
                                    **********9.7799**************************************************************** PP

                                    HHHHHTTC---- CS
                           RIO1 172 ikfFrrkgvekv 183
                                    ++fF++kgv+ +
  gene715|gene715|rna714|rna714 245 NNFFSKKGVDVI 256
                                    ********9855 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.18
                                    BHHHCG-HHHHHHHHHHHHHHHHHH CS
                           RIO1  97 klkdveeeeeaeelyeevleemrkl 121
                                    +++++e+ +e ++  +++++em+++
  gene715|gene715|rna714|rna714 336 EIENTEDAKEEKKKKKKTVKEMNRI 360
                                    4444443333333444444444433 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0058        52      37      61 ..     129     153 ..     102     162 .. 0.87
   2 !   11.6   0.0   2.2e-05      0.19     163     194 ..     195     223 ..     160     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0058
                                    HHHHHHHHHHHHHTT-B--B-CTTB CS
                            APH  37 irrevallrlLakagvpvPevlagd 61 
                                    +++ev+ l+ L++a++p Pe+++++
  gene715|gene715|rna714|rna714 129 AEKEVRNLKRLNNAEIPSPEPIYLK 153
                                    589*******************964 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.2e-05
                                    SS-EEEE-SS-SGGGEEEC..TTEEEEE---T CS
                            APH 163 elptvllHgDlhpgNllvdpddgrvtGviDfe 194
                                      +++l+H Dl+  Nll    +g v +viD +
  gene715|gene715|rna714|rna714 195 YKKAGLVHADLSEFNLLYF--GGVV-YVIDVG 223
                                    57899**************..7887.****76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1945  (0.108483); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 2265.52
//
Query:       gene716|gene716|rna715|rna715  [L=387]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-09   38.8   4.6    2.7e-09   37.5   1.3    2.7  2  PCI        PCI domain
    0.00037   20.5   2.2      0.001   19.1   2.2    1.7  1  RPN5_C     26S proteasome regulatory subunit RPN5 C-terminal 
  ------ inclusion threshold ------
      0.047   14.5   1.9      0.086   13.7   0.2    2.3  2  FERM_N_2   FERM N-terminal domain
       0.06   13.3   0.1       0.26   11.3   0.1    2.1  1  SOAR       STIM1 Orai1-activating region
       0.15   12.5   3.1       0.11   13.0   0.9    2.0  2  AbiJ_NTD4  AbiJ N-terminal domain 4


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.11   3.9e+02       4      49 ..     140     185 ..     137     201 .. 0.83
   2 !   37.5   1.3   7.6e-13   2.7e-09      26     105 .]     275     354 ..     215     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                                    HHHHHHHHHTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                            PCI   4 sdllkalrsgnlsgfseelkdleeelladdglaqllesLekkvrer 49 
                                    ++l  ++++ ++ +++ ++k+ +++++++ g+ +  +++++ + + 
  gene716|gene716|rna715|rna715 140 EQLRLCVKNHDWIRADITMKKIRRKYFEESGNVEEKTKFYELIVLL 185
                                    5666788889999****************99999888888777665 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 7.6e-13
                                    HHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSSSEEEETTTTEEEECS CS
                            PCI  26 eeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvklIrdgeirakidqesgivvfkk 105
                                    ++ +    +++ +l++L+  + e+++r v ++yssi++++++   + +v+++ k ++ ++++g+ r+ki+q+++iv+f+k
  gene716|gene716|rna715|rna715 275 QQAFSSVLDVSVYLNDLVSAIDEHNFRIVERFYSSITIQEISLVMQSPVEDIIKKISFMVNNGFTRCKINQKTEIVEFGK 354
                                    444455555677**************99999***********************************************86 PP

>> RPN5_C  26S proteasome regulatory subunit RPN5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.2   2.8e-07     0.001       7      29 ..     357     379 ..     356     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.8e-07
                         RPN5_C   7 WssninkLLelvekttHLInKEe 29 
                                    W  ++++ ++++ k++HLI+KE 
  gene716|gene716|rna715|rna715 357 WNESVDDVMNKLIKCNHLIHKER 379
                                    **********************5 PP

>> FERM_N_2  FERM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.4e-05     0.086      23      82 ..     104     169 ..      87     183 .. 0.72
   2 ?   -1.2   0.1       1.1   3.8e+03      29      47 ..     322     339 ..     295     378 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.4e-05
                       FERM_N_2  23 rhgdatdvraiiqki....vrlgkvik..fvscyglrlkhlkseevhwLhpdltvseveekyeqsh 82 
                                    r++++ d+++ +  i    v++  ++k  +v +y+l    l  +++ w+ +d+t++++++ky ++ 
  gene716|gene716|rna715|rna715 104 RYESSGDIKSALDVIinvpVETFTMVKesVVVNYQLEQLRLCVKNHDWIRADITMKKIRRKYFEES 169
                                    677777777755555554554444444117889999999999********************8753 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                       FERM_N_2  29 dvraiiqkivrlgkvikfv 47 
                                     v +ii+ki  + ++  f+
  gene716|gene716|rna715|rna715 322 PVEDIIKKISFMVNN-GFT 339
                                    455555555444333.222 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   7.3e-05      0.26      13      89 ..     223     301 ..     219     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                           SOAR  13 lTyelElkylnkkkqeaekqlqeAkeeveklkkkrssllgslrlahs..sslddvdkkileakqaleevtkelkerqeR 89 
                                    +T+e+E++ +  k+ +  k+l+e k++ e ++   + +l+ + l +s  +++++  +++l +   l+++ +++ e++ R
  gene716|gene716|rna715|rna715 223 TTCETEMEDVVCKRIDMLKKLSEDKNNDEVVRSIVNRFLSRIVLDKSmaNEIQQAFSSVLDVSVYLNDLVSAIDEHNFR 301
                                    7*****************************************9986522677788888888888888888888887765 PP

>> AbiJ_NTD4  AbiJ N-terminal domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.8   6.6e+03      92      92 ..     174     174 ..     124     205 .. 0.54
   2 ?   13.0   0.9     3e-05      0.11      56     134 ..     301     384 ..     223     387 .] 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                      AbiJ_NTD4  92 e 92 
                                    e
  gene716|gene716|rna715|rna715 174 E 174
                                    1 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3e-05
                      AbiJ_NTD4  56 elhkllaeelgldelpe....dtteawke....ienyffkcewyevyDfiEfvfrnredqeaeaneslereeelNerfee 127
                                    ++ ++++  + + e++       +++ k+    ++n f +c+++++  ++Ef+ r++++  ++  ++l    ++N++  +
  gene716|gene716|rna715|rna715 301 RIVERFYSSITIQEISLvmqsPVEDIIKKisfmVNNGFTRCKINQKTEIVEFGKRKWNESVDDVMNKL---IKCNHLIHK 377
                                    255555556777777777776455555557778*********************************99...79******* PP

                      AbiJ_NTD4 128 enagYrf 134
                                    e++++ +
  gene716|gene716|rna715|rna715 378 ERLKFSI 384
                                    *999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2513.78
//
Query:       gene717|gene717|rna716|rna716  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1119.80
//
Query:       gene718|gene718|rna717|rna717  [L=1052]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-07   30.6   8.1    6.4e-07   29.6   8.1    1.6  1  zf-RING_2     Ring finger domain
    0.00026   21.2   8.5     0.0016   18.7   8.9    2.0  2  zf-rbx1       RING-H2 zinc finger domain
    0.00027   20.9   4.5    0.00058   19.9   4.5    1.5  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
     0.0029   17.8   6.5     0.0083   16.3   6.5    1.8  1  FANCL_C       FANCL C-terminal domain
  ------ inclusion threshold ------
       0.02   14.8   9.2       0.11   12.4   9.4    2.2  2  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
      0.043   13.7   2.1      0.098   12.6   2.1    1.6  1  C1_1          Phorbol esters/diacylglycerol binding domain (C
      0.051   13.7   6.6      0.098   12.8   6.6    1.5  1  RINGv         RING-variant domain
       0.12   12.2   5.5       0.83    9.6   2.7    2.5  2  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
       0.21   11.5   7.9       0.56   10.1   7.9    1.8  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
       0.88    9.2   6.2          2    8.1   6.2    1.5  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
        2.1    8.2   6.6        4.3    7.2   6.6    1.6  1  zf-RING_4     RING/Ubox like zinc-binding domain
        9.3    6.7  10.9       0.59   10.5   5.4    1.9  2  zf-RING-like  RING-like domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   8.1   4.3e-10   6.4e-07       1      44 []     996    1045 ..     996    1045 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.3e-10
                      zf-RING_2    1 deCpICleelssads....vlllpCgHvfhreClerwlrssst..CPlCr 44  
                                     +eCpIC+  ++ +ds     +++ C+  fh  C+++w++s  +  CP+Cr
  gene718|gene718|rna717|rna717  996 KECPICYLVIDLHDSsfpnSQCKACKNKFHARCIAKWVASGTRsnCPICR 1045
                                     59****9888777774333334469999*********88887788****9 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.6   2.4e+03      46      54 ..     993    1001 ..     988    1002 .. 0.73
   2 !   18.7   8.9   1.1e-06    0.0016      29      55 .]    1017    1045 ..     996    1045 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                        zf-rbx1   46 ktrkvCPlc 54  
                                     + +k+CP+c
  gene718|gene718|rna717|rna717  993 SGHKECPIC 1001
                                     55789**99 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-06
                        zf-rbx1   29 lGeCgHaFHlhCiskWlkt..rkvCPlcr 55  
                                     + +C+ +FH  Ci kW+ +  r++CP+cr
  gene718|gene718|rna717|rna717 1017 CKACKNKFHARCIAKWVASgtRSNCPICR 1045
                                     347***************999*******8 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   4.5   3.9e-07   0.00058      17      81 ..     987    1048 ..     971    1051 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.9e-07
                                     .-SS....SSB-TTT-SBTTS--TTCSTTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB- CS
                     zf-ANAPC11   17 dvas....ddvcGicrvsfdGtcpsckfpGddcplvlGkckhnfhlhcilkwletetskglcpmcrqtf 81  
                                     ++ +    ++ c ic +  d    +  fp  +c      ck +fh+ ci kw+++  ++++cp+cr  +
  gene718|gene718|rna717|rna717  987 NIDEkisgHKECPICYLVIDL--HDSSFPNSQCK----ACKNKFHARCIAKWVAS-GTRSNCPICRMPM 1048
                                     444444447788899888884..67889999996....6*************975.67899*****765 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   6.5   5.6e-06    0.0083       3      47 ..     996    1039 ..     994    1050 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.6e-06
                                     -S-SSS--S.S-TT-----B--S-TT----B-SGGGHHHHHHHHSS CS
                        FANCL_C    3 veCgiCyay.rldsgevpdisCdnekCnkkfHsaCLkeWlrslkes 47  
                                     +eC+iCy    l++++ p+  C    C++kfH+ C+  W++s + s
  gene718|gene718|rna717|rna717  996 KECPICYLViDLHDSSFPNSQCK--ACKNKFHARCIAKWVASGTRS 1039
                                     79*****761568999******6..7**************987765 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.11   1.6e+02      31      40 .]     992    1001 ..     988    1001 .. 0.78
   2 ?   12.4   9.4   7.4e-05      0.11       1      40 []     997    1044 ..     997    1044 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                     zf-C3HC4_2   31 LeekneCPlC 40  
                                     ++ ++eCP+C
  gene718|gene718|rna717|rna717  992 ISGHKECPIC 1001
                                     66799****9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.4e-05
                     zf-C3HC4_2    1 kCpiCldmlk..dp....svvtpCgHvfCqkCilrsLeekn..eCPlC 40  
                                     +CpiC+ ++   d     s  ++C+ +f++ Ci+++  ++   +CP+C
  gene718|gene718|rna717|rna717  997 ECPICYLVIDlhDSsfpnSQCKACKNKFHARCIAKWVASGTrsNCPIC 1044
                                     6****98865223311114667*************999887679**** PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.1   6.6e-05     0.098      11      45 ..     995    1031 ..     983    1038 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-05
                                     --B-TTT-SB-.-S.SSS-EEEETTT--EE-CCCCTT CS
                           C1_1   11 ptfCkhCgefl.wg.kekqglkCswCkllvHkkChek 45  
                                      + C  C   +  +  +++  +C++Ck ++H +C+ k
  gene718|gene718|rna717|rna717  995 HKECPICYLVIdLHdSSFPNSQCKACKNKFHARCIAK 1031
                                     566778887777445889999*************987 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   6.6   6.6e-05     0.098       1      48 []     998    1044 ..     998    1044 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                                     ETTTTEE-SSSS--B-SS--STCCCSB-HHHHHHHHHHTCT-SB-TTT CS
                          RINGv    1 CriCleeeeeseplispCkCrGslklvHesClekWldekeantqCeiC 48  
                                     C iC+   + +++ + + +C+   + +H  C+ kW+ +    ++C iC
  gene718|gene718|rna717|rna717  998 CPICYLVIDLHDSSFPNSQCKACKNKFHARCIAKWVAS-GTRSNCPIC 1044
                                     8888888888888888889999999*************.999****** PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.089   1.3e+02      36      46 ..     994    1004 ..     988    1008 .. 0.74
   2 ?    9.6   2.7   0.00056      0.83      26      49 ..    1017    1050 ..    1009    1051 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.089
                                     TT-B-TTT--B CS
                     zf-C3HC4_3   36 rkkkCpiCrrp 46  
                                      +k+CpiC   
  gene718|gene718|rna717|rna717  994 GHKECPICYLV 1004
                                     68999999655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00056
                                     -HHHHHHHHH..........TT-B-TTT--B--E CS
                     zf-C3HC4_3   26 CeeCaekllk..........rkkkCpiCrrpiek 49  
                                     C++C +k+++           + +CpiCr p+e 
  gene718|gene718|rna717|rna717 1017 CKACKNKFHArciakwvasgTRSNCPICRMPMEN 1050
                                     666666666566666666999*********9986 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   7.9   0.00038      0.56       1      41 []     998    1044 ..     993    1044 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00038
                                     -TTT-S--SS-E.......E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4    1 CpiCleeakepn......elleCkHsfCskCirkilksrkkvkCPlC 41  
                                     CpiC  ++  ++      +   Ck +f+  Ci k++ s +  +CP+C
  gene718|gene718|rna717|rna717  998 CPICYLVIDLHDssfpnsQCKACKNKFHARCIAKWVASGTRSNCPIC 1044
                                     999999988888889999999****************988889**** PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.2    0.0013         2       5      46 ..     996    1042 ..     993    1045 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                   Zn_ribbon_17    5 ksCayCelav..kgrvvl...cgvCeHvlHasCarewfenddlaeCp 46  
                                     k+C +C l +  + + +    c++C+   Ha C+++w   +  ++Cp
  gene718|gene718|rna717|rna717  996 KECPICYLVIdlHDSSFPnsqCKACKNKFHARCIAKWVASGTRSNCP 1042
                                     7899998765225566533449******************999***9 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.6    0.0029       4.3       1      46 [.     998    1047 ..     998    1049 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0029
                      zf-RING_4    1 cplCdeeldetdkdl..kpC.eCgyqiClfCyhrile.eeegrCPaCree 46  
                                     cp+C   +d +d+++    C  C+ ++   C  + ++  +   CP Cr +
  gene718|gene718|rna717|rna717  998 CPICYLVIDLHDSSFpnSQCkACKNKFHARCIAKWVAsGTRSNCPICRMP 1047
                                     9*************95557977999******999888347999*****76 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       7.3   1.1e+04      37      43 .]     995    1001 ..     990    1001 .. 0.70
   2 ?   10.5   5.4   0.00039      0.59      13      43 .]    1016    1044 ..    1013    1044 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.3
                   zf-RING-like   37 skkCpkC 43  
                                     +k+Cp C
  gene718|gene718|rna717|rna717  995 HKECPIC 1001
                                     4679988 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00039
                   zf-RING-like   13 rCsnesCnvrlHvdCfqhyirthsskkCpkC 43  
                                     +C+   C+ ++H  C+++ + + ++ +Cp C
  gene718|gene718|rna717|rna717 1016 QCK--ACKNKFHARCIAKWVASGTRSNCPIC 1044
                                     588..9**************99999****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1052 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      685  (0.0382063); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.85u 0.27s 00:00:01.12 Elapsed: 00:00:00.50
# Mc/sec: 6375.00
//
Query:       gene719|gene719|rna718|rna718  [L=571]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-42  143.5   2.1    2.3e-41  141.6   0.0    2.7  3  AAA_12           AAA domain
    1.7e-36  126.4   0.9    3.5e-18   66.3   0.0    2.9  3  AAA_11           AAA domain
    2.3e-11   44.2   0.0    9.6e-11   42.2   0.0    2.1  2  AAA_19           AAA domain
    1.5e-09   38.0   0.0    3.7e-07   30.1   0.0    3.0  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    3.6e-07   30.1   0.0    4.6e-05   23.2   0.0    3.0  2  AAA_30           AAA domain
    1.5e-06   28.3   0.4    4.5e-06   26.8   0.1    1.9  2  ResIII           Type III restriction enzyme, res subunit
    1.2e-05   25.3   0.1    0.00024   21.0   0.1    2.8  2  Helicase_RecD    Helicase
    0.00023   20.8   4.1    0.00091   18.8   0.1    2.9  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
     0.0003   20.2   0.2      0.015   14.6   0.0    2.9  3  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0013   18.5   0.0     0.0028   17.4   0.0    1.6  1  UvrD_C_2         UvrD-like helicase C-terminal domain
     0.0038   17.2   0.0      0.036   14.1   0.0    2.4  3  AAA_5            AAA domain (dynein-related subfamily)
      0.008   16.1   2.0      0.012   15.5   0.3    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
       0.01   16.1   0.1      0.076   13.3   0.0    2.5  2  AAA_22           AAA domain
      0.023   14.6   0.0      0.064   13.2   0.0    1.7  1  Flavi_DEAD       Flavivirus DEAD domain
      0.039   14.4   0.3       0.19   12.2   0.3    2.3  1  AAA              ATPase family associated with various cellul
      0.069   13.3   1.4       0.59   10.3   0.0    2.4  2  DUF5618          Domain of unknown function (DUF5618)
       0.14   11.1   0.0       0.26   10.2   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.17   12.0   4.1        0.5   10.4   0.0    2.8  3  DUF87            Helicase HerA, central domain


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1         1     1e+03      44      83 ..     141     178 ..     100     214 .. 0.62
   2 ?   -0.6   0.1      0.85   8.4e+02      36      56 ..     277     302 ..     268     337 .. 0.70
   3 !  141.6   0.0   2.3e-44   2.3e-41      14     198 ..     362     520 ..     354     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                         AAA_12  44 kdaesvkkreleaqealeepleplvfidvekseeekekke 83 
                                    k +e+vkk++++   + +++ ++l f+d++ ++++k+  e
  gene719|gene719|rna718|rna718 141 KLDEEVKKSTKK--ARKTSKPKKLNFYDTSLNASQKKAVE 178
                                    334455555555..44455556688888876666665544 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.85
                         AAA_12  36 klfYkgkLkdaesvkkrele.....a 56 
                                    + fYk++++++++++k++ +      
  gene719|gene719|rna718|rna718 277 TNFYKDRIEKQKKFMKEKRDsspvvF 302
                                    67999999999999988887333330 PP

  == domain 3  score: 141.6 bits;  conditional E-value: 2.3e-44
                         AAA_12  14 kekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekseeekekkeksyiNeeEae 93 
                                    + +vvlL++qYRm +++++f++++fYkg++k+ ++   + ++         +p++f+d++  e  ++++  s++N  Ea 
  gene719|gene719|rna718|rna718 362 TLPVVLLNEQYRMPSNLLKFSNEMFYKGQIKSVAK---ECKP-----IFGENPILFVDTQYFEFYESDD-ISKSNIGEAM 432
                                    4689**************************98554...3333.....346899******9999888876.9********* PP

                         AAA_12  94 lvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGrekdviilslVRsnekkeig 173
                                    +v ++ve l         +++g+i+pY +qv ll+++++          +ev+tvdgfQG+e+d+ii++lVR n++k++g
  gene719|gene719|rna718|rna718 433 IVKSIVEILK----G---EEVGIIAPYTSQVLLLREMVD----------VEVSTVDGFQGQERDYIIITLVRCNDRKDFG 495
                                    9999998773....2...479*****************9..........9****************************** PP

                         AAA_12 174 flkderrlNValTRAkskliivGnk 198
                                    fl++e+rlNValTR k+ l++vG++
  gene719|gene719|rna718|rna718 496 FLSNEKRLNVALTRCKKGLVVVGDS 520
                                    ***********************97 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       1.6   1.6e+03     114     149 ..     114     149 ..      19     163 .. 0.49
   2 !   66.3   0.0   3.5e-21   3.5e-18       2     102 ..     169     255 ..     168     278 .. 0.82
   3 !   58.6   0.0   8.1e-19     8e-16     159     256 ..     261     352 ..     252     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                         AAA_11 114 ekrlekeekaqlakeiskeleklakelrafeeeeek 149
                                    + +   ++  + +k+ ++ ++ +ak+ + +ee++++
  gene719|gene719|rna718|rna718 114 NTKVLLSNLKRFMKSGKSFSNFIAKSWKLDEEVKKS 149
                                    222222222222222222222222222222222222 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 3.5e-21
                         AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrgllds 81 
                                    ln+sq++a++ +  +     i GPPGtgKT+t+ve++sql          ++++r+LvC+pSN+++D+++er l+   ++
  gene719|gene719|rna718|rna718 169 LNASQKKAVEMTRLNIP-YKILGPPGTGKTRTVVEIISQL---------LAKNKRVLVCGPSNVSIDNIIERFLK---SK 235
                                    8********99888888.89********************.........799**********************9...77 PP

                         AAA_11  82 egekykpkivRvgneeerise 102
                                       ++kp++ R+g++  +  +
  gene719|gene719|rna718|rna718 236 YFLRSKPSFYRLGSSL-KGLS 255
                                    799999******9987.3333 PP

  == domain 3  score: 58.6 bits;  conditional E-value: 8.1e-19
                         AAA_11 159 skskleqerrklkkerkelskeleeaeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPl 238
                                    s ++l+++  k kk  +++ k+  e++++ ++e  d++ +v++Tl ++    l++ +  fd+v+IDEA+qa Ep+++ + 
  gene719|gene719|rna718|rna718 261 SLAELHTNFMKEKKNDTNFYKDRIEKQKKFMKEKRDSSPVVFATLFSS----LKEKR-MFDWVLIDEACQASEPESFLAV 335
                                    5566777778888888888888888888889***************99....55554.8********************* PP

                         AAA_11 239 rlgakkvvLvGDpkQLpa 256
                                     +g k ++L+GDp QL +
  gene719|gene719|rna718|rna718 336 TKG-KMFILIGDPMQLCP 352
                                    ***.************88 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   9.7e-14   9.6e-11       1     144 [.     173     353 ..     173     355 .. 0.73
   2 ?   -2.9   0.0         8   7.9e+03     124     138 ..     506     520 ..     499     522 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 9.7e-14
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae........... 68 
                                    q++ave +  + +  ++++pGtGKTr++++i++ l++ +    +++l++ + + + +++ er   l+ +           
  gene719|gene719|rna718|rna718 173 QKKAVEmTRLNIPYKILGPPGTGKTRTVVEIISQLLAKN----KRVLVCGPSNVSIDNIIERF--LKSKyflrskpsfyr 246
                                    8999988999999***********************999....89****************99..444467888666666 PP

                         AAA_19  69 .atTiHrlal............................ldfddlltealelle...............eaeeekklqeee 104
                                                                            ++d+++++ ++++               +  +ek     +
  gene719|gene719|rna718|rna718 247 lG-------SslkglshlnleslaelhtnfmkekkndtNFYKDRIEKQKKFMKekrdsspvvfatlfsS-LKEKR---MF 315
                                    63.......344444445566666667677777777763345555555566668888888888777532.22233...34 PP

                         AAA_19 105 .llivDEfqdvdelqyrLlkallgekkklllvGDpdQliyv 144
                                     ++++DE+ + +e +  L  a++ ++k ++l+GDp Ql ++
  gene719|gene719|rna718|rna718 316 dWVLIDEACQASEPESFL--AVT-KGKMFILIGDPMQLCPE 353
                                    4*******9999766544..566.4545*********9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8
                         AAA_19 124 allgekkklllvGDp 138
                                    al+  kk l++vGD 
  gene719|gene719|rna718|rna718 506 ALTRCKKGLVVVGDS 520
                                    566556779****97 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.042        41       3      30 ..     188     213 ..     187     230 .. 0.82
   2 !   30.1   0.0   3.7e-10   3.7e-07      39     233 ..     284     517 ..     261     518 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.042
                Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrp 30 
                                    + G pG GK++ +++++++   l +n++
  gene719|gene719|rna718|rna718 188 ILGPPGTGKTRTVVEIISQ--LLAKNKR 213
                                    5689*************99..5555554 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 3.7e-10
                Viral_helicase1  39 k.......pklpnlsvrtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfll 111
                                            +++ ++s   + ++ ++l+++  ++ +++DE++++   + +  +a  k k++il+GDp Q    ++ +  + 
  gene719|gene719|rna718|rna718 284 IekqkkfmKEKRDSSPVVFATLFSSLKEKRMFDWVLIDEACQAS--EPESFLAVTKGKMFILIGDPMQL-CPETPSLYES 360
                                    3334455444455555556666666666677*********9998..5666557777789*********5.5555554455 PP

                Viral_helicase1 112 ahlpssl...shrvgrrttyllpsdvaeilsak.......................vgteveversgel.....kvetep 160
                                      lp+ l   + r + +  ++ ++ +++ + ++                       +++++ +++s+ +     k   ++
  gene719|gene719|rna718|rna718 361 LTLPVVLlneQYRMPSNLLKFSNEMFYKGQIKSvakeckpifgenpilfvdtqyfeFYESDDISKSNIGeamivK---SI 437
                                    555555577788888888888888888877777999999999999999888888776666666666666664332...22 PP

                Viral_helicase1 161 kgq.e..kvlvyltftqa..lkealgvr.evttvhevqGltfdkV..tlvllketdlelisesrenllvAlTRhrkslvi 232
                                    ++  +  +v ++ + t +  l++++  + ev+tv + qG++ d    tlv+ ++ ++  + +++  l vAlTR +k+lv+
  gene719|gene719|rna718|rna718 438 VEIlKgeEVGIIAPYTSQvlLLREMV-DvEVSTVDGFQGQERDYIiiTLVRCNDRKDFGFLSNEKRLNVALTRCKKGLVV 516
                                    22223445555555554410444443.269***********99761155666555555555889999**********997 PP

                Viral_helicase1 233 l 233
                                    +
  gene719|gene719|rna718|rna718 517 V 517
                                    6 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.6e-08   4.6e-05       2     130 ..     169     352 ..     168     396 .. 0.68
   2 ?    2.5   0.0       0.1     1e+02      34      82 ..     433     484 ..     428     519 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.6e-08
                         AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae................. 64 
                                    lna+Q++ave +  +      + Gp+GtGKt ++ ++   + a+++rv+++ p++   +++ e                 
  gene719|gene719|rna718|rna718 169 LNASQKKAVEMTRLNI--PYKILGPPGTGKTRTVVEIISQLLAKNKRVLVCGPSNVSIDNIIErflkskyflrskpsfyr 246
                                    899******8665555..57789********999999888888999***********99977444444444444444444 PP

                         AAA_30  65 .......elgieastiakllkrlk........................................grarlepg.tllivDE 96 
                                                  ++++l + ++                                        +  + ++  + +++DE
  gene719|gene719|rna718|rna718 247 lgsslkgL---SHLNLESLAELHTnfmkekkndtnfykdriekqkkfmkekrdsspvvfatlfsS-LKEKRMfDWVLIDE 322
                                    43332220...22222222222224445556777777777777778888999999**99999953.444555699***** PP

                         AAA_30  97 agmvdtkqlaallkaaekagakvilvGDerQlas 130
                                    a  ++  +  ++l+  +k g   il+GD+ Ql +
  gene719|gene719|rna718|rna718 323 ACQASEPE--SFLAV-TK-GKMFILIGDPMQLCP 352
                                    99888765..55544.44.7889999**999976 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                         AAA_30  34 alkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.....g 82 
                                    ++k+++e+++  g++v ++Ap   +   L+e +++e st++ +  + +      
  gene719|gene719|rna718|rna718 433 IVKSIVEILK--GEEVGIIAPYTSQVLLLREMVDVEVSTVDGFQGQERdyiiiT 484
                                    5566666666..889**************************9987776555551 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.4   3.4e+03      72      96 ..     130     147 ..      98     168 .. 0.48
   2 !   26.8   0.1   4.5e-09   4.5e-06       4     152 ..     169     334 ..     161     345 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                                    HHGGGGTGG....GEEEESSS-B-- CS
                         ResIII  72 eefkkflseaykeigkkvsgdkkka 96 
                                    + f++f       i k+++ d++ +
  gene719|gene719|rna718|rna718 130 KSFSNF-------IAKSWKLDEEVK 147
                                    222222.......333333333322 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 4.5e-09
                                    E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG......... CS
                         ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef......... 74 
                                    l+  Q++a+e ++ ++       + i  + GtGKT++ +++i +ll k+k  ++l+  p++  ++  +e+f         
  gene719|gene719|rna718|rna718 169 LNASQKKAVEMTRLNI------PYKILGPPGTGKTRTVVEIISQLLAKNK--RVLVCGPSNVSIDNIIERFlkskyflrs 240
                                    5566777777776555......79999********************966..9********7778888777555555655 PP

                                    ..........................GGGTGG.......GEEEESSS-B--.......-SEEEEEHHHHHHTH....... CS
                         ResIII  75 ..........................kkflseayke...igkkvsgdkkkakekdstnkkilvttiqsldadseeeeees 125
                                                              ++f++e++++    +  ++++kk   +++++++ ++++t              s
  gene719|gene719|rna718|rna718 241 kpsfyrlgsslkglshlnleslaelhTNFMKEKKNDtnfYKDRIEKQKKFM-KEKRDSSPVVFAT------------LFS 307
                                    555555555555555555555555554444444333222222222222222.4444445555544............444 PP

                                    .HHHTTT-SEEEEETGGGTTS.TTTHH CS
                         ResIII 126 eellrdrfdviiiDEaHrlgakkswre 152
                                      +++  fd ++iDEa  +++ +s+ +
  gene719|gene719|rna718|rna718 308 SLKEKRMFDWVLIDEACQASEPESFLA 334
                                    555558899999999987777666555 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.4e-07   0.00024       2     100 ..     188     324 ..     187     329 .. 0.82
   2 ?   -2.3   0.0       3.4   3.4e+03     110     131 ..     457     478 ..     376     499 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                  Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglke........................ 57 
                                    + + +G+GK+ ++  ++++l+a++k ++lv+ ps+ ++++++e++ k+   l+ k                         
  gene719|gene719|rna718|rna718 188 ILGPPGTGKTRTVVEIISQLLAKNK-RVLVCGPSNVSIDNIIERFLKSKYFLRSKPsfyrlgsslkglshlnleslaelh 266
                                    67899******************87.*****************9988887777777999********************9 PP

                  Helicase_RecD  58 ..............eekkkkaekaelrvr...........kqrieyiapdellklkeqadllvvDEAA 100
                                                  +++           +           ++ + + +  + lk+k+  d++++DEA 
  gene719|gene719|rna718|rna718 267 tnfmkekkndtnfyKDRI----------EkqkkfmkekrdSSPVVFATLFSSLKEKRMFDWVLIDEAC 324
                                    988877665555432222..........1224444445678899999999999999999*******96 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                  Helicase_RecD 110 llekfkrvvlatTvhGYEGtGr 131
                                    ll + +  v  +Tv G+ G  r
  gene719|gene719|rna718|rna718 457 LLLREMVDVEVSTVDGFQGQER 478
                                    2223333344666666666655 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   2.7      0.82   8.2e+02      70     178 ..      57     173 ..       6     180 .. 0.55
   2 !   18.8   0.1   9.1e-07   0.00091       1     116 [.     169     286 ..     169     314 .. 0.75
   3 ?    1.3   0.0       0.2   1.9e+02     255     294 ..     313     349 ..     303     351 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.82
                                    HHCCHHCTT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHH..........HCCHHHHHHHHH CS
                  UvrD-helicase  70 kkaeqessdderlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedee..........dlkqqellkell 139
                                    +k+++ ++  +  +l l++ +    +T+ ++ q ++k+  ++   d+nf+   + + +           +k+ + + + +
  gene719|gene719|rna718|rna718  57 EKNKVPRILRQEEKLFLETSNGPLLCTIVEVEQDMVKAIGYKNLKDSNFEATLDFKYNtkvllsnlkrFMKSGKSFSNFI 136
                                    44444444444444455555555566666666666666555555444444332222222334443444555555555555 PP

                                    SC..HSHTTTTHHHHHHHHHHHHHHCCCCCHHHHCCCHHHH CS
                  UvrD-helicase 140 ek..saddslnldkkkleklikelsksrnikkeelslsksk 178
                                     k  + d+    + kk  k++++ sk++++++ + sl++s+
  gene719|gene719|rna718|rna718 137 AKswKLDE----EVKKSTKKARKTSKPKKLNFYDTSLNASQ 173
                                    54222222....22223333334455555555554444444 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 9.1e-07
                                    SSHHHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT CS
                  UvrD-helicase   1 lnpeqreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessd 78 
                                    ln++q++a++   l+ p  ++  +G+GKT++++e i +l++++    +r+lv    n + + + eR  +    +++ +s+
  gene719|gene719|rna718|rna718 169 LNASQKKAVEMtrLNIPYKILGPPGTGKTRTVVEIISQLLAKN----KRVLVCGPSNVSIDNIIERFLKS---KYFLRSK 241
                                    6899****9997788899****************999999998....9******9999999998888774...3444444 PP

                                    -H..HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT.....SHT CS
                  UvrD-helicase  79 de..rlrlalqnlseanisTlHsfcqkilkkeanrig.....ldp 116
                                     +  rl  +l+ ls++n   l ++  +++k++ n+ +     +++
  gene719|gene719|rna718|rna718 242 PSfyRLGSSLKGLSHLNLESLAELHTNFMKEKKNDTNfykdrIEK 286
                                    445688889999999998888888888888887777755554333 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.2
                                    HHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG CS
                  UvrD-helicase 255 erykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQ 294
                                    + ++ +liDE+ + ++   + +  +++g+  ++++GDp Q
  gene719|gene719|rna718|rna718 313 RMFDWVLIDEACQASEP--ESFLAVTKGK-MFILIGDPMQ 349
                                    56999999999877764..3344556665.79*****998 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       4.5   4.5e+03     259     266 ..     139     147 ..      94     168 .. 0.53
   2 !   14.6   0.0   1.5e-05     0.015       6     102 ..     188     328 ..     186     344 .. 0.78
   3 ?    2.0   0.0     0.099        99     344     360 ..     501     517 ..     488     519 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.5
                        DUF2075 259 pWnleek.e 266
                                    +W l+e+ +
  gene719|gene719|rna718|rna718 139 SWKLDEEvK 147
                                    333333321 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.5e-05
                        DUF2075   6 VtGvaGtGKtvvllnllael............edde.........................................eer 32 
                                    + G +GtGKt   ++++ +l            +  +                                          e 
  gene719|gene719|rna718|rna718 188 ILGPPGTGKTRTVVEIISQLlaknkrvlvcgpS--NvsidniierflkskyflrskpsfyrlgsslkglshlnleslAEL 265
                                    6699****************8765555555551..055666777777777888888888888888888888888888999 PP

                        DUF2075  33 tavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrllt 102
                                    +++++   ++  + ++ +++k++ k  k+++ + +  f + +s      + ke++++d v++DEA  + +
  gene719|gene719|rna718|rna718 266 HTNFMKEKKNDTNFYKDRIEKQK-KFMKEKRDSSPVVFATLFS------SLKEKRMFDWVLIDEACQASE 328
                                    99999999999999999998888.6666666677777777777......889*************88877 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.099
                        DUF2075 344 NayrVLLtRGrkGlyiy 360
                                     +++V LtR  kGl+++
  gene719|gene719|rna718|rna718 501 KRLNVALTRCKKGLVVV 517
                                    479************96 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.8e-06    0.0028       3      52 .]     466     517 ..     464     517 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.8e-06
                       UvrD_C_2   3 yaltihkaQGsefpaVivfdpdlaaarmgel.....rrrlLYtavTRAreklilv 52 
                                     ++t+  +QG+e +++i++ +   +++   +     + + L +a+TR+++ l++v
  gene719|gene719|rna718|rna718 466 EVSTVDGFQGQERDYIIITLVRCNDRK---DfgflsNEKRLNVALTRCKKGLVVV 517
                                    589***************555433333...335678999999***********98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.6e-05     0.036       4      45 ..     188     231 ..     187     250 .. 0.83
   2 ?   -2.8   0.0       5.8   5.8e+03      77      94 ..     297     314 ..     260     336 .. 0.79
   3 ?   -1.0   0.0       1.6   1.6e+03      58     100 ..     505     547 ..     498     569 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                                    EE--SSSSHHH.HHHHGGGGB.S--EEEEE--TT--HHHHH--B CS
                          AAA_5   4 LvGppGtgKse.laerlaaal.nreveyvqltrdtteedlkgrr 45 
                                    ++GppGtgK++ ++e ++++l +++ + v ++++ + ++++ r 
  gene719|gene719|rna718|rna718 188 ILGPPGTGKTRtVVEIISQLLaKNKRVLVCGPSNVSIDNIIERF 231
                                    58*******97256777777799999999999999999998876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.8
                                    --HHHHHHHHHHHHSSEE CS
                          AAA_5  77 aesevlnsLlslleerrl 94 
                                     ++ v+++L s l e+r+
  gene719|gene719|rna718|rna718 297 SSPVVFATLFSSLKEKRM 314
                                    457788888888888876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.6
                                    -------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SS CS
                          AAA_5  58 plvraaregeilvlDEveraesevlnsLlslleerrllleegg 100
                                    ++ + +++g ++v D  +  +s+++++L + l ++ l l++ +
  gene719|gene719|rna718|rna718 505 VALTRCKKGLVVVGDSKTFKRSSIFQKLFNFLKTNSLCLDPET 547
                                    4555777777777777776679999999999999988776654 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.1   3.1e+03      68      71 ..     135     145 ..      84     180 .. 0.52
   2 !   15.5   0.3   1.2e-05     0.012      20     129 ..     183     325 ..     172     331 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.1
                       ATPase_2  68 fie.......e 71 
                                    fi+       e
  gene719|gene719|rna718|rna718 135 FIAkswkldeE 145
                                    22233322111 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                       ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal................. 82 
                                    n +y i Gp g GKt+ + eii++l+ k+k+v+   + + +  + +++f++    +k++ + +                 
  gene719|gene719|rna718|rna718 183 NIPYKILGPPGTGKTRTVVEIISQLLAKNKRVLVCGPSNVSIDNIIERFLK----SKYFLRSKpsfyrlgsslkglshln 258
                                    56899************************9998888888777778888844....4444444445567777778888877 PP

                       ATPase_2  83 ......................giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqk 129
                                                          +++++k++   ++kek+      ++ l+ ++k+k+    ++iDe+ +
  gene719|gene719|rna718|rna718 259 leslaelhtnfmkekkndtnfyKDRIEKQKK--FMKEKRDSSPVVFATLFSSLKEKRMFDWVLIDEACQ 325
                                    6665555555555555543333333333222..333555555555566666666666555666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.6e-05     0.076      10      62 ..     188     233 ..     185     332 .. 0.82
   2 ?   -1.8   0.0       3.5   3.4e+03      84     113 ..     505     537 ..     499     557 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.6e-05
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellr 62 
                                    + G++GtGKT+++ ++ +ql +       + + v+v+ ps  s +++ +++l+
  gene719|gene719|rna718|rna718 188 ILGPPGTGKTRTVVEIISQLLA-------KNKRVLVCGPSNVSIDNIIERFLK 233
                                    88******************75.......777777877777777777666654 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.5
                         AAA_22  84 qalraravielliiDEaqhlr.s...eealeeLr 113
                                     al ++++ +l+++ +   +  s   ++++++L+
  gene719|gene719|rna718|rna718 505 VALTRCKK-GLVVVGDSKTFKrSsifQKLFNFLK 537
                                    55555666.6666666555543134444444442 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.5e-05     0.064      13      53 ..     192     231 ..     186     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.5e-05
                                    TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHT CS
                     Flavi_DEAD  13 PGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeeal 53 
                                    PG+Gktr v +e++ + + +++r lv  P  v + ++ e +
  gene719|gene719|rna718|rna718 192 PGTGKTRTV-VEIISQLLAKNKRVLVCGPSNVSIDNIIERF 231
                                    9*****975.79********************999987754 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   0.00019      0.19       4      23 ..     189     210 ..     187     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                                    ESSTTSSHHHHHHHHHHHH..T CS
                            AAA   4 yGppGtGKTllakavakel..g 23 
                                     GppGtGKT ++  ++++l  +
  gene719|gene719|rna718|rna718 189 LGPPGTGKTRTVVEIISQLlaK 210
                                    7*********999999997442 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00059      0.59      55     114 ..     150     211 ..     139     216 .. 0.77
   2 ?    1.0   0.2      0.47   4.7e+02      55      81 ..     265     291 ..     256     301 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00059
                                    --S...SS-.--HHHHHHHHHCC-HHHH..HHHHHHHHHHIIIICCT---BHHHHHHHHHHH CS
                        DUF5618  55 kkglekkkrpksvetYkealkkldkkll..kefnsaydvLhlagyydGiksakvvkeglkaa 114
                                    +k+ +k+ +pk++++Y ++l+ ++kk++  +++n  y++L + g+ +  + ++++++ l + 
  gene719|gene719|rna718|rna718 150 TKKARKTSKPKKLNFYDTSLNASQKKAVemTRLNIPYKILGPPGTGKTRTVVEIISQLLAKN 211
                                    244556899****************99733579999****9999988888888888877665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.47
                                    --S...SS-.--HHHHHHHHHCC-HHH CS
                        DUF5618  55 kkglekkkrpksvetYkealkkldkkl 81 
                                      +  +k+++++ ++Yk +++k+ k +
  gene719|gene719|rna718|rna718 265 LHTNFMKEKKNDTNFYKDRIEKQKKFM 291
                                    455567889999*******99987655 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00026      0.26      20      49 ..     188     217 ..     178     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                  TrwB_AAD_bind  20 ivGttGsGKtqalekllrairargdraivl 49 
                                    i+G  G+GKt ++ +++ ++ a+++r++v 
  gene719|gene719|rna718|rna718 188 ILGPPGTGKTRTVVEIISQLLAKNKRVLVC 217
                                    899************************997 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.18   1.8e+02      92     151 ..      95     154 ..      40     184 .. 0.69
   2 ?   10.4   0.0    0.0005       0.5      28      57 ..     188     216 ..     186     219 .. 0.94
   3 ?   -3.0   0.1       6.4   6.4e+03     155     174 ..     270     289 ..     225     310 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                          DUF87  92 inpwsldpeelldlleeddkpaaavqrsvleealdqaka..keekeklssdepveklleelk 151
                                    i +++l+   ++  l+   k +++v+ s l++++++ k+  +   ++++ de v+k+ ++ +
  gene719|gene719|rna718|rna718  95 IGYKNLKDSNFEATLDF--KYNTKVLLSNLKRFMKSGKSfsNFIAKSWKLDEEVKKSTKKAR 154
                                    66677777777777777..7777777777777777777666555666666666666666666 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0005
                          DUF87  28 ilgsTGsGKSntvavLleellekkgatili 57 
                                    ilg  G+GK+ tv  ++++ll  k+ ++l+
  gene719|gene719|rna718|rna718 188 ILGPPGTGKTRTVVEIISQLL-AKNKRVLV 216
                                    89999****************.99999998 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.4
                          DUF87 155 eelrklknqaiarlldkled 174
                                     +++k++++  +  ++k ++
  gene719|gene719|rna718|rna718 270 MKEKKNDTNFYKDRIEKQKK 289
                                    22333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.53
# Mc/sec: 3267.76
//
Query:       gene720|gene720|rna719|rna719  [L=337]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-60  203.5   0.1    5.5e-60  203.2   0.1    1.0  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.2   0.1   3.1e-64   5.5e-60       3     288 ..      29     314 ..      27     318 .. 0.94

  Alignments for each domain:
  == domain 1  score: 203.2 bits;  conditional E-value: 3.1e-64
                                    HS--EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHH.HHTCH CS
                   tRNA-synt_1b   3 erplrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaql.akgld 81 
                                    er+l vy+G++ Tgk+H++ylvpl+k+ ++ +ag++v +l+aD h+++++ + a+ +k++ r  ++e++ika l   g+d
  gene720|gene720|rna719|rna719  29 ERELNVYWGTAITGKPHIAYLVPLMKVKDFADAGCNVKVLLADIHGFLDNLK-APIEKIKYRCVYYEKLIKASLkMLGVD 107
                                    7899************************************************.****************888883567** PP

                                    TTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHH.CCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGG CS
                   tRNA-synt_1b  82 pekaevvlqsewlehlelaellrdlgklgslnrmlqfks.vkkrleegegislgeftYplLqaaDilllkadlvpgGsDQ 160
                                    +++++++ +se + + e++++l ++ +++s ++  ++ + v+k++e+ +   ++ + Yp +qa+D+++l +d ++gG DQ
  gene720|gene720|rna719|rna719 108 LNRIQFIKGSEFQRSNEYTMDLYKILSITSEHDAKKAGAqVVKQVEN-P--MVSSLVYPAMQALDEVHLSVDAQFGGVDQ 184
                                    **************************************988888888.4..8**************************** PP

                                    HHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTCSHHHHHHHH CS
                   tRNA-synt_1b 161 kqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsdeevekllklk 240
                                    +++++ +r++++ +n+k    k+ +l+ p+l+gl+ e KmS+S++ s+I+L d+ke + kki+k++++ +++   l+k++
  gene720|gene720|rna719|rna719 185 RKIFTYARKYLPLLNYK----KRIHLMSPMLPGLNSE-KMSSSDDLSKIDLMDSKEVILKKIKKCFCEEGNKENGLMKIF 259
                                    ****************9....****************.*********************************777777776 PP

                                    HTHHH.......CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHH CS
                   tRNA-synt_1b 241 telsn.......elierleavsgkkpkreaeellaeevtklvhggdlkkalaeal 288
                                      +         e i + +  +++k  ++++e++ e+++k +h+gdlk ++a+ +
  gene720|gene720|rna719|rna719 260 SHIIFpifeakgEKIRIADRDGKEKVFEKYQEFEDEFSSKSIHPGDLKTNAARLI 314
                                    65544499999999999999999999999*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1978.10
//
Query:       gene72|gene72|rna72|rna72  [L=131]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-08   33.0   0.0    5.5e-08   32.7   0.0    1.2  1  Thioredoxin    Thioredoxin
    1.3e-06   28.7   0.0      0.065   13.6   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
    4.7e-06   27.0   0.1    0.00012   22.4   0.1    2.2  1  Thioredoxin_2  Thioredoxin-like domain
    0.00048   20.5   0.1     0.0007   20.0   0.1    1.4  1  DUF836         Glutaredoxin-like domain (DUF836)
  ------ inclusion threshold ------
      0.017   15.3   0.1       0.73   10.1   0.1    3.0  4  Glutaredoxin   Glutaredoxin
      0.071   13.3   0.0       0.19   11.9   0.0    1.8  1  Thioredoxin_7  Thioredoxin-like
      0.087   12.9   0.0       0.11   12.5   0.0    1.4  1  TrbC_Ftype     Type-F conjugative transfer system pilin assem
       0.11   12.4   0.1       0.23   11.3   0.1    1.6  1  HNH_repeat     Homing endonuclease repeat


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.5e-11   5.5e-08       7      92 ..      13     100 ..       8     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.5e-11
                                HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTE.EEEEE CS
                Thioredoxin   7 kenFeeevakekklvlveFyApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlklfkngk.evkky 88 
                                 e+ +++v++  ++ l++F ++ Cg+C  l+ +l + +++l+   + +++  + + ++l ++++++++Pt++l+ ++  e ++ 
  gene72|gene72|rna72|rna72  13 PEEIKAKVKELGRPSLLKFSSENCGPCEDLKEKLSQYSTDLEInVFEICRTRTASYPSLWDEFDITAFPTVVLVDKDMkELQDK 96 
                                56778889999999***************************98567899999999******************98876577777 PP

                                ESS- CS
                Thioredoxin  89 egar 92 
                                +g++
  gene72|gene72|rna72|rna72  97 NGSQ 100
                                7764 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.9e-05     0.065       2      38 ..      25      60 ..      24      61 .. 0.89
   2 !   12.9   0.0   4.6e-05       0.1      73      94 ..      70      91 ..      61      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                               SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEE CS
              Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkvei 38
                               +  lL f++++c pc++  +kl++++++l+  + +ei
  gene72|gene72|rna72|rna72 25 RPSLLKFSSENCGPCEDLKEKLSQYSTDLE-INVFEI 60
                               6779************************98.677776 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.6e-05
                               HHTT-S--TT-SEEEEE-TT-B CS
              Thioredoxin_8 73 klkkkynvkaiPtlvvldknge 94
                                l+++++++a+Pt+v++dk+++
  gene72|gene72|rna72|rna72 70 SLWDEFDITAFPTVVLVDKDMK 91
                               5899****************97 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   5.5e-08   0.00012       2      93 ..      21      93 ..      20     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.5e-08
              Thioredoxin_2  2 kgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfl 87
                               k+ g+p l+ f++++C+ C+ lk++l+++            + + e+ +++i +++          ++  l ++++++++Pt+v+ 
  gene72|gene72|rna72|rna72 21 KELGRPSLLKFSSENCGPCEDLKEKLSQY------------STDLEINVFEICRTRTA--------SYPSLWDEFDITAFPTVVLV 86
                               56699***********************9............45556666677666655........477899************** PP

              Thioredoxin_2 88 dgk.eiv 93
                               d++ +++
  gene72|gene72|rna72|rna72 87 DKDmKEL 93
                               **97443 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   3.1e-07    0.0007       5      58 ..      31      88 ..      28     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.1e-07
                               EE-TT-HHHHHHHHHHHHHCCCTTEEEEEEETT.....T-CCCHCCCCTT.TTEEEECTT CS
                     DUF836  5 yskpgChlCeqakekLkelkleegleleviDIa.....kdeeleakYgle.ipvlalegv 58
                               +s ++C+ Ce++kekL++ +++ +  + v  I      + ++l+++++ +  p ++l+++
  gene72|gene72|rna72|rna72 31 FSSENCGPCEDLKEKLSQYSTDLE--INVFEICrtrtaSYPSLWDEFDITaFPTVVLVDK 88
                               8899*************8776666..6666666443335555999999763577777773 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.5   1.1e+03      29      48 ..       6      26 ..       1      28 [. 0.70
   2 ?   10.1   0.1   0.00032      0.73       4      54 ..      31      84 ..      29      90 .. 0.68
   3 ?    0.1   0.0      0.44     1e+03      27      35 ..      82      90 ..      63     110 .. 0.70
   4 ?    0.5   0.0      0.32   7.2e+02      30      49 ..     110     129 ..     107     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.5
                               EEGCCSH..HHHHHHHHHHTSS CS
               Glutaredoxin 29 idvdkde..eireelkelsgvr 48
                               +d + ++  ei++++kel g++
  gene72|gene72|rna72|rna72  6 RDCSGMSpeEIKAKVKEL-GRP 26
                               566666446999999999.766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00032
                               EESTSSHHHHHHHHHHHHTT..GGEEEEEGCCSH.HHHHHHHHHHTSSSSSEEE CS
               Glutaredoxin  4 ftkptCpyCkkakrlLkelg..vkfeeidvdkde.eireelkelsgvrtvPqvf 54
                               f++ +C+ C   k+ L ++   +++ ++++     +    l +  ++ ++P+v+
  gene72|gene72|rna72|rna72 31 FSSENCGPCEDLKEKLSQYStdLEINVFEICRTRtASYPSLWDEFDITAFPTVV 84
                               899*************99994444556665554445555555555666666666 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.44
                               EEEEGCCSH CS
               Glutaredoxin 27 eeidvdkde 35
                               +++ vdkd+
  gene72|gene72|rna72|rna72 82 TVVLVDKDM 90
                               455555554 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.32
                                EGCCSHHHHHHHHHHHTSSS CS
               Glutaredoxin  30 dvdkdeeireelkelsgvrt 49 
                                ++ k ee+ +e+++l g+ t
  gene72|gene72|rna72|rna72 110 NIKKFEELVKEHRHLFGQNT 129
                                788999*********99987 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.5e-05      0.19       7      40 ..      14      47 ..      11      88 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.5e-05
                               HHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHH CS
              Thioredoxin_7  7 dealakaaergkpvlvffgaswcftCqalerdfl 40
                               +e +ak +e g+p l+ f++++c++C  l++ + 
  gene72|gene72|rna72|rna72 14 EEIKAKVKELGRPSLLKFSSENCGPCEDLKEKLS 47
                               566899*********************9999875 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.1e-05      0.11      61     100 ..      69     107 ..      38     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                 TrbC_Ftype  61 PllFrqfkitaVPalvlaeedkaseeddecaakakysvvy 100
                                P l ++f+ita P++vl+ +d ++ +d++ ++  + ++++
  gene72|gene72|rna72|rna72  69 PSLWDEFDITAFPTVVLVDKDMKELQDKNGSQ-GALTRIV 107
                                999****************9999987554443.3355555 PP

>> HNH_repeat  Homing endonuclease repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0001      0.23       5      17 ..      14      26 ..      14      26 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
                 HNH_repeat  5 ElvQkqAaELGRt 17
                               E ++++ +ELGR+
  gene72|gene72|rna72|rna72 14 EEIKAKVKELGRP 26
                               789*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 843.08
//
Query:       gene721|gene721|rna720|rna720  [L=373]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-23   82.2   0.2    1.6e-22   79.5   0.1    2.1  2  CLP1_N    N-terminal beta-sandwich domain of polyadenylation 
    6.1e-17   62.0   0.0    1.8e-16   60.5   0.0    1.8  1  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
    1.7e-06   28.5   0.0    2.7e-06   27.8   0.0    1.4  1  Clp1      Pre-mRNA cleavage complex II protein Clp1
  ------ inclusion threshold ------
      0.081   12.9   0.0       0.18   11.8   0.0    1.6  1  RHH_3     Ribbon-helix-helix domain
       0.15   12.0   0.0       0.25   11.2   0.0    1.5  1  AAA_31    AAA domain
       0.18   10.8   0.0       0.29   10.1   0.0    1.2  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB


Domain annotation for each model (and alignments):
>> CLP1_N  N-terminal beta-sandwich domain of polyadenylation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.1   5.4e-26   1.6e-22       2      83 ..       5      85 ..       4      90 .. 0.95
   2 ?   -0.3   0.0      0.42   1.3e+03      22      47 ..     165     190 ..     156     192 .. 0.79

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 5.4e-26
                                   E-TTEEEEEEE-SSS-EEEEEEEE--EETTEE--TT-EEEE-TT-EEEEEESS-EEEEEES-EEEEEEES--SHHHHHHHHH CS
                         CLP1_N  2 LekeselrfeveskeklkikllsGtaEifGtELaknkeytfskgtkfaiftwegcklevkgeaeseyvseetpmksylnlhl 83
                                   L +++e+r+ev++++klk+ ++sG aE++G+EL+++k+y f+ +tk+ ift++gckl+v+g ++ +yvs++t++  ++n+  
  gene721|gene721|rna720|rna720  5 LWPNQEFRIEVNETQKLKVMVVSGLAEVKGQELLNEKWYAFK-DTKTFIFTFSGCKLKVEGACDLQYVSDTTNVPLIFNILS 85
                                   6799**************************************.8*******************************9999865 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.42
                                    EEEE--EETTEE--TT-EEEE-TT-E CS
                         CLP1_N  22 llsGtaEifGtELaknkeytfskgtk 47 
                                     + G+ Ei  +EL   ++ ++++ +k
  gene721|gene721|rna720|rna720 165 FYYGSTEITNMELYDLQTTKLQEAIK 190
                                    45799999999999999999887666 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   6.1e-20   1.8e-16       6     151 ..     106     239 ..     103     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 6.1e-20
                         CLP1_P   6 GKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnpslylalvk 85 
                                    G+ST++ +L+N  +r+g+k+++ ++D+  ++i  Pg++s   v++ +d  eg++l++pl++++G+t + +n++ly  ++ 
  gene721|gene721|rna720|rna720 106 GRSTFCFTLINFFVRMGKKVLFTEVDPSRGNI-FPGALSTIHVDTLVDCIEGLRLKNPLSFYYGSTEI-TNMELYDLQTT 183
                                    9******************************5.89********************************9.79********* PP

                         CLP1_P  86 elareveekleenkkakasgliIntpGwvkglgaellleliealepdvvvvldqeellnelkrdlp 151
                                    +l +++++k      +++ +li    G          + li+ +e+d v+v+++e+l+++l   ++
  gene721|gene721|rna720|rna720 184 KLQEAIKSK-----GVEDLHLILCPEG-----TSAFYNTLIKRFEVDRVIVVGNERLYHSLDTIAE 239
                                    *******44.....3445666654444.....34577999*******************9987665 PP

>> Clp1  Pre-mRNA cleavage complex II protein Clp1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0     9e-10   2.7e-06       3     116 ..     271     371 ..     269     372 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 9e-10
                                    -EEEEEETTS-EEEEE-.------------.------TS-EEEE-.--GGGTTEEEEEESSSS....TCCTT--EEEEEE CS
                           Clp1   3 PysitvdfddlsiyrvgeeeaapssalPigeeekeseetklekveepsselqnsilavsqasakdseeevldssvlGFvy 82 
                                    P++++v+++  +i+r+ge   ap salP+g ++++    + ++ve      +ns+l +s+a +    e+v+ s+++G+v+
  gene721|gene721|rna720|rna720 271 PFTFNVKYK-WRIVRIGEMYVAPVSALPLG-STRKVGCVEASEVE----IGENSVLGISEARE---IEDVAGSPIIGYVV 341
                                    899999985.7999****************.66666666666664....569********977...8************* PP

                                    EEEEETTTTEEEEEESSSS.-S.-SEEEEEEEE-- CS
                           Clp1  83 VtevdeekkkltvLsPvpgrlp.skalilgslkwp 116
                                    V + +    ++++L+ +p+ lp  ++l+ g+lk+ 
  gene721|gene721|rna720|rna720 342 VIDAN----TFKILCTQPR-LPkYTFLVQGDLKHI 371
                                    *9875....6899999997.551566777777765 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     6e-05      0.18      10      34 ..     227     251 ..     218     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                          RHH_3  10 dpelaekLkaLSekTrIprSkllde 34 
                                    ++ l+ +L+++ ek++I+rS  ++e
  gene721|gene721|rna720|rna720 227 NERLYHSLDTIAEKLMINRSGFVEE 251
                                    899*****************99987 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.5e-05      0.25      12      85 ..     104     201 ..     103     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.5e-05
                         AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.........................glgiekne.......iektl 59 
                                    G G++T ++ l  ++ ++gkkvL  ++Dp     +                         +              ++ +l
  gene721|gene721|rna720|rna720 104 GNGRSTFCFTLINFFVRMGKKVLFTEVDPSRGNIFpgalstihvdtlvdcieglrlknplS------FyygsteiTNMEL 177
                                    7899*************************87776655555555555555544333333221......0221111133344 PP

                         AAA_31  60 yevlieeknikeaiiktkvenldlip 85 
                                    y++  ++++++eai+++ ve+l+li 
  gene721|gene721|rna720|rna720 178 YDL--QTTKLQEAIKSKGVEDLHLIL 201
                                    444..889999999988899988885 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   9.8e-05      0.29      38      69 ..     103     134 ..      96     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 9.8e-05
                                    TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                           MeaB  38 PGaGkstlvealglelrrrGkrvavlavDPss 69 
                                     G G+st+   l+  ++r Gk+v    vDPs 
  gene721|gene721|rna720|rna720 103 IGNGRSTFCFTLINFFVRMGKKVLFTEVDPSR 134
                                    599***************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2547.49
//
Query:       gene722|gene722|rna721|rna721  [L=506]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-59  197.7   0.0    3.3e-45  153.7   0.0    2.4  2  AAA              ATPase family associated with various cellul
    5.9e-14   51.6   0.3      1e-07   31.6   0.0    2.5  2  AAA_lid_3        AAA+ lid domain
    8.5e-13   49.0   5.6    0.00028   21.3   0.1    4.7  3  AAA_16           AAA ATPase domain
    2.2e-09   37.5   0.0    0.00012   22.1   0.0    2.7  2  AAA_14           AAA domain
    7.8e-08   32.7   2.2      0.019   15.2   0.1    4.0  3  AAA_22           AAA domain
    2.6e-07   30.7   0.8     0.0015   18.5   0.0    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
      4e-07   30.6   0.0      0.038   14.5   0.0    2.3  2  ABC_tran         ABC transporter
      6e-07   29.3   0.0     0.0034   17.1   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.6e-06   28.2   1.5       0.43   10.4   2.2    3.4  2  Bac_DnaA         Bacterial dnaA  protein
    2.3e-06   28.2   0.0     0.0036   17.9   0.0    2.4  2  AAA_18           AAA domain
      3e-06   27.5   0.0      0.041   14.0   0.0    2.4  2  AAA_33           AAA domain
    6.2e-06   26.1   0.0     0.0017   18.1   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    3.2e-05   24.1   0.0     0.0031   17.7   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.3e-05   24.3   0.0      0.072   13.5   0.0    2.5  2  AAA_17           AAA domain
    3.4e-05   23.8   2.1       0.42   10.5   0.0    3.9  3  NACHT            NACHT domain
    6.7e-05   22.2   0.2       0.28   10.3   0.0    2.2  2  DUF815           Protein of unknown function (DUF815)
    0.00013   21.9   1.0      0.025   14.5   0.0    3.0  2  Rad17            Rad17 P-loop domain
    0.00015   22.1   0.0      0.053   13.9   0.0    2.6  2  RNA_helicase     RNA helicase
    0.00016   21.0   0.0        2.1    7.5   0.0    3.4  3  NB-ARC           NB-ARC domain
    0.00025   21.0   0.0       0.24   11.4   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00036   20.3   0.0       0.35   10.6   0.0    3.3  3  AAA_24           AAA domain
    0.00047   19.5   0.3      0.051   12.8   0.0    2.8  3  KAP_NTPase       KAP family P-loop domain
     0.0005   19.5   0.6       0.31   10.3   0.0    3.4  4  ATPase           KaiC
    0.00056   19.4   0.1      0.089   12.2   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0011   18.8   0.1       0.75    9.5   0.0    2.8  2  IstB_IS21        IstB-like ATP binding protein
     0.0012   18.7   0.0       0.77    9.6   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
     0.0015   18.3   0.0        4.5    7.0   0.0    3.1  3  Sigma54_activat  Sigma-54 interaction domain
     0.0022   17.3   0.0       0.72    9.1   0.0    2.3  2  Zeta_toxin       Zeta toxin
     0.0026   17.7   0.1       0.07   13.0   0.0    2.7  2  RsgA_GTPase      RsgA GTPase
     0.0046   16.5   0.1        2.1    7.9   0.0    3.1  3  AAA_25           AAA domain
      0.005   16.4   0.0       0.74    9.3   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
     0.0054   16.2   0.0        1.7    8.0   0.0    3.4  4  TniB             Bacterial TniB protein
     0.0082   15.4   0.0       0.46    9.6   0.0    2.8  3  TIP49            TIP49 P-loop domain
     0.0099   15.8   2.6       0.25   11.2   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.015   15.0   0.0        7.2    6.4   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
      0.016   15.6   0.0        4.4    7.6   0.0    2.6  2  AAA_19           AAA domain
      0.029   14.6   0.0       0.18   12.0   0.0    2.1  2  AAA_28           AAA domain
      0.037   13.9   0.9        6.9    6.5   0.0    3.3  3  NTPase_1         NTPase
      0.041   13.7   0.0        6.6    6.5   0.0    2.3  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.069   12.9   0.0        9.7    5.9   0.0    2.4  2  AAA_30           AAA domain
        0.1   12.3   0.0       0.37   10.5   0.0    1.8  2  AAA_11           AAA domain
       0.26   10.9   0.8         14    5.3   0.0    2.8  2  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   3.6e-13   1.6e-10       1     127 [.      74     177 ..      74     182 .. 0.88
   2 !  153.7   0.0   7.8e-48   3.3e-45       1     131 [.     299     426 ..     299     427 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 3.6e-13
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +ll+G  G+GKT l++ + +e + ++++ s+          s k++re f++ +   + si++i++id l++++      
  gene722|gene722|rna721|rna721  74 LLLHGVSGVGKTFLVNCISQEYKLPIIRASLD---------SDKELRESFRKSSLL-ERSIILIEDIDVLGEDD------ 137
                                    69**********************99998764.........6779*****886555.48***********8888...... PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                                      ++v++qL + l++ k    k ivi+++ +p  +++ l   +fd  
  gene722|gene722|rna721|rna721 138 --KKVISQLSEYLENHKG---KSIVIATARNPAFINESLN--KFDNS 177
                                    ..9***************...57********999999988..67765 PP

  == domain 2  score: 153.7 bits;  conditional E-value: 7.8e-48
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +llyGppG+GKTll++av + ++ +fl+i+g+el+skyvg+sek+ir+lf++ak+ + p++lf+DEid+l+++r  + +e
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNFLSIKGPELISKYVGDSEKEIRKLFDKAKQLQ-PCVLFFDEIDSLCGER--NGNE 375
                                    69******************************************************9.****************..999* PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +++r+vnq+lt ldg++++ ++v vigatnr++++d+a+lr gRfd++++++
  gene722|gene722|rna721|rna721 376 FTSRIVNQILTLLDGLDDR-GDVYVIGATNRIESIDKAILRpGRFDKILKVP 426
                                    ******************7.66**************************9998 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.4e-06    0.0023       3      44 ..     205     246 ..     203     247 .. 0.95
   2 !   31.6   0.0   2.4e-10     1e-07      12      44 ..     457     493 ..     453     494 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.4e-06
                      AAA_lid_3   3 dlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                    d+ eLA++++G++  Dl+   + A+  A+ +g  +i m d+e
  gene722|gene722|rna721|rna721 205 DWTELAKLMPGFVARDLKRALKIASTKAVADGSSAIRMIDLE 246
                                    7889**********************************9997 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 2.4e-10
                      AAA_lid_3  12 eGySGADlaalcreAallAlrrgik...e.itmedfe 44 
                                    eG+SGA++a l+r Aa+l+l+++++     it+e+++
  gene722|gene722|rna721|rna721 457 EGFSGAEIAGLIRDAAILCLKHNFDsdsLvITKENII 493
                                    9*********************999765368888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.5   1.1e-06   0.00049      23      62 ..      70     106 ..      60     230 .. 0.81
   2 !   21.3   0.1   6.5e-07   0.00028      17      46 ..     289     318 ..     283     339 .. 0.83
   3 ?    4.1   0.1      0.12        53     122     146 ..     343     366 ..     329     400 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                     p+ +ll+G sGvGK+ lv+++ ++++      +r+  d+
  gene722|gene722|rna721|rna721  70 PPSTLLLHGVSGVGKTFLVNCISQEYKLP---IIRASLDS 106
                                    4689******************9988766...34444444 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 6.5e-07
                         AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellr 46 
                                    +++   rp+ +ll+G++G+GK+ lvr++ +
  gene722|gene722|rna721|rna721 289 RKLGITRPSGILLYGPPGCGKTLLVRAVSN 318
                                    55667799******************9974 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.12
                         AAA_16 122 llkrllallsrderplvlvlDdlqw 146
                                    ++++l++++++  +p vl++D+++ 
  gene722|gene722|rna721|rna721 343 EIRKLFDKAKQ-LQPCVLFFDEIDS 366
                                    6889999***9.566********93 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00024       0.1       5      49 ..      74     115 ..      71     180 .. 0.78
   2 !   22.1   0.0   2.8e-07   0.00012       5     126 ..     299     428 ..     296     433 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00024
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49 
                                    l++ G+  vGKT+l++ + +e+      i+  +ld++++ +++  
  gene722|gene722|rna721|rna721  74 LLLHGVSGVGKTFLVNCISQEYK---LPIIRASLDSDKELRESFR 115
                                    7899**********977776666...99*******9888654422 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.8e-07
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelileklkeekktylflDEiqev...... 76 
                                    +++ G+  +GKT l++ + +  +   +++ +++++ +++  k   d+ek ++ +++k+k+ +  +lf+DEi  +      
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSN--M---SHCNFLSIKGPELisKYVGDSEKEIRKLFDKAKQLQPCVLFFDEIDSLcgerng 373
                                    6899***********99974..4...456666666666622334455544555555556678899********99***** PP

                         AAA_14  77 ....pewekalkslvd..egknldvivtGSnskllskeiatslagrvaeielypls 126
                                        +++ + +  l+d  + +++dv+v G  + + s + a    gr ++i   pl 
  gene722|gene722|rna721|rna721 374 neftSRIVNQILTLLDglD-DRGDVYVIGATNRIESIDKAILRPGRFDKILKVPLP 428
                                    9888666666666666533.478********9999999888888888888777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   0.00065      0.28       7      49 ..      73     106 ..      68     159 .. 0.79
   2 !   15.2   0.1   4.5e-05     0.019       7      30 ..     298     321 ..     293     354 .. 0.76
   3 ?    2.9   0.0      0.29   1.3e+02      84     117 ..     349     389 ..     326     407 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00065
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49 
                                     l+++G sG+GKT+l++ + +++         + ++++  l s
  gene722|gene722|rna721|rna721  73 TLLLHGVSGVGKTFLVNCISQEY---------KLPIIRASLDS 106
                                    689*************9999988.........55555555554 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4.5e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqld 30 
                                     ++++G++G+GKT+l+r + +  +
  gene722|gene722|rna721|rna721 298 GILLYGPPGCGKTLLVRAVSNMSH 321
                                    589***************998863 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.29
                         AAA_22  84 qalraravielliiDEaqhlr...s.....eealeeLrslln 117
                                    + +++ +   +l  DE++ l    +      ++++++ +ll+
  gene722|gene722|rna721|rna721 349 DKAKQLQP-CVLFFDEIDSLCgerNgneftSRIVNQILTLLD 389
                                    34444444.9*********98654133444555555555444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4     0.011       4.7       2      23 ..      74      95 ..      73     155 .. 0.90
   2 !   18.5   0.0   3.6e-06    0.0015       2      75 ..     299     365 ..     298     415 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.011
                                   EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                   +lL G +G+gK++l+  +++ +
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCISQEY 95
                                   79************99888755 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 3.6e-06
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                    +lL GppG+gK+ l++ ++ +  ++++ + +++      l+ ++    g+ + +  +l ++a+  ++++l++DE++
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNFLSIKGPE------LISKYV---GDSEKEIRKLFDKAKqlQPCVLFFDEID 365
                                    89*******************999999988876......555555...5555555666666666677777777776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00014     0.059       7      45 ..      67     105 ..      64     194 .. 0.73
   2 !   14.5   0.0   8.8e-05     0.038      12      79 ..     297     363 ..     289     412 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilld 45 
                                     +++ +++ + G +G GK+ L++++++++k    +  ld
  gene722|gene722|rna721|rna721  67 GIHPPSTLLLHGVSGVGKTFLVNCISQEYKLPIIRASLD 105
                                    577788999*******************98743333333 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.8e-05
                                    SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    + + + G+ G+GK+ L+++++++++ +  +i  +g +l ++    ++kei+ l+ + +ql+p +   ++
  gene722|gene722|rna721|rna721 297 SGILLYGPPGCGKTLLVRAVSNMSHCNFLSI--KGPELISKYVGDSEKEIRKLFDKaKQLQPCVLFFDE 363
                                    567899*****************99755555..888888888999999999999998888887765555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0023      0.96      35      96 ..      73     133 ..      67     188 .. 0.75
   2 !   17.1   0.0     8e-06    0.0034      35      96 ..     298     367 ..     262     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0023
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaall..tnleekdvlfideihrl 96 
                                     +ll+G  G+Gkt l + i++e +  +  +s   l+  ++l   +  ++l e+ +++i++i  l
  gene722|gene722|rna721|rna721  73 TLLLHGVSGVGKTFLVNCISQEYKLPIIRAS---LDSDKELRESFrkSSLLERSIILIEDIDVL 133
                                    579*******************999887766...334444433221145666666666666655 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8e-06
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideihrl 96 
                                     +llyGpPG Gkt l + +++  + ++ +  gP l      + ++++  l+ + ++ +  vlf dei  l
  gene722|gene722|rna721|rna721 298 GILLYGPPGCGKTLLVRAVSNMSHCNFLSIKGPELiskyvgDSEKEIRKLFDKAKQLQpcVLFFDEIDSL 367
                                    58******************************97633222223455666666655543448999998766 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   2.2     0.001      0.43      37     167 ..      74     190 ..      61     232 .. 0.57
   2 !    8.0   0.0    0.0052       2.2      37      64 ..     299     326 ..     293     387 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.001
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHH.HHTT-SEEEEE-GGGGTT-HHH CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefke.klrkvDvLliDDiqflagkekt 115
                                    l+++g +G+Gkt L++ i++e +   p  r + l +++           +  e+f++ +l +  ++li+Di  l + +  
  gene722|gene722|rna721|rna721  74 LLLHGVSGVGKTFLVNCISQEYK--LPIIRAS-LDSDK-----------ELRESFRKsSLLERSIILIEDIDVLGEDD-- 137
                                    66777777777777777765432..2222221.22222...........22234544156688999******998776.. PP

                                    HHHHHHHHHHHHT..TT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE----- CS
                       Bac_DnaA 116 qeelfhtfnalle..egkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppd 167
                                     ++++  + + le  +gk +v+++ r+P  ++e  +++ + + + + ++ e+ +
  gene722|gene722|rna721|rna721 138 -KKVISQLSEYLEnhKGKSIVIATARNPAFINESLNKFDNSLLVKIPTAAERRE 190
                                    .444555555554125789*********98877655544444444444443333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0052
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSS CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenape 64 
                                    +++yg+ G Gkt L++a++n    n+ +
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNFLS 326
                                    79****************9976655544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0     0.009       3.8       2      88 ..      75     167 ..      74     195 .. 0.67
   2 !   17.9   0.0   8.3e-06    0.0036       1      79 [.     299     400 ..     299     415 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.009
                         AAA_18   2 lltGtpGvGKttlakeLskrlgf.........gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                    ll G++GvGKt l + +s++ ++           +lr+ ++++ ll+      +++ ++l ed  +k++++l e  + ++
  gene722|gene722|rna721|rna721  75 LLHGVSGVGKTFLVNCISQEYKLpiirasldsDKELRESFRKSSLLERSIIL-IEDIDVLGEDD-KKVISQLSEYLE-NH 151
                                    578**************99866677888888855555555555555555555.33333333333.333333333332.45 PP

                         AAA_18  73 egknlvidghlaeles 88 
                                    +gk++vi   ++  + 
  gene722|gene722|rna721|rna721 152 KGKSIVIATARNPAFI 167
                                    7899999877776665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 8.3e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.....aldeskrlde 54 
                                    Ill G+pG+GKt l +++s++ ++                      ++l d ak+ +++  +++e       ++ +++  
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCnflsikgpeliskyvgdsekeIRKLFDKAKQLQPCVLFFDEidslcGERNGNEFTS 378
                                    99****************99865566999999999999999999999999999999999999999999999999999999 PP

                         AAA_18  55 dkldklldaleenssaleegknlvi 79 
                                      ++++l++l++ ++    g+++vi
  gene722|gene722|rna721|rna721 379 RIVNQILTLLDGLDD---RGDVYVI 400
                                    999999999999875...6666666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00068      0.29       3      38 ..      75     114 ..      74     212 .. 0.77
   2 !   14.0   0.0   9.7e-05     0.041       2      79 ..     299     404 ..     299     424 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00068
                         AAA_33   3 llvGlpGsGKstlaerllkklg..avl..lssdtlrrrlf 38 
                                    ll+G++G+GK++l+  + ++ +   ++  l+sd+++r  f
  gene722|gene722|rna721|rna721  75 LLHGVSGVGKTFLVNCISQEYKlpIIRasLDSDKELRESF 114
                                    79************99988877765554477777666554 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.7e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt..........................dytrvld 53 
                                    +ll G+pG+GK+ l++ + +  +  +  +  ++l+++++g+ ++ ++                          + +++++
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHcnFLSIKGPELISKYVGDSEKEIRklfdkakqlqpcvlffdeidslcgerNGNEFTS 378
                                    6789**************66666447788899999988886666555445555555555555555555555554445555 PP

                         AAA_33  54 rlyqilnelarkalsagrnvildatn 79 
                                    r+ +++  l++    +g  +++ atn
  gene722|gene722|rna721|rna721 379 RIVNQILTLLDGLDDRGDVYVIGATN 404
                                    55555555555444444445555555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.021         9       2      22 ..      75      95 ..      74     166 .. 0.80
   2 !   18.1   0.0   4.1e-06    0.0017       4      71 ..     302     364 ..     299     370 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                Viral_helicase1  2 vvhGvpGcGKStlirkllrts 22
                                   + hGv G GK+ l+  + ++ 
  gene722|gene722|rna721|rna721 75 LLHGVSGVGKTFLVNCISQEY 95
                                   68**********999888773 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.1e-06
                Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pGcGK+ l+r + ++s +++ +++   el+++ + +++++  + +d++ + + +     +l++DE+
  gene722|gene722|rna721|rna721 302 YGPPGCGKTLLVRAVSNMShCNFLSIKG-PELISKYVGDSEKEIRKLFDKAKQLQPC-----VLFFDEI 364
                                    588*****************99999999.9*******************99887764.....8*****8 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.13        55       3      54 ..      71     158 ..      69     173 .. 0.69
   2 !   17.7   0.0   7.2e-06    0.0031       5     105 ..     298     390 ..     295     392 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                                    ---EEEE--TTSSHHHHHHHHHHHTT-........................................-EEEEEGGG---- CS
                          AAA_2   3 iisilllgptgvGktelakalaellfv....................................kkekkliradasellee 46 
                                     +++ll g +gvGkt+l + +++  ++                                    ++++k +++  se+le+
  gene722|gene722|rna721|rna721  71 PSTLLLHGVSGVGKTFLVNCISQEYKLpiirasldsdkelresfrkssllersiiliedidvlGEDDKKVISQLSEYLEN 150
                                    57889999********9988888888777777777777777666666666666666666666666666666666777766 PP

                                    ---THHHH CS
                          AAA_2  47 eevehlvs 54 
                                     + +++v 
  gene722|gene722|rna721|rna721 151 HKGKSIVI 158
                                    66666655 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 7.2e-06
                                    -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                          AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                     ill gp g+Gkt+l +a++++ ++    ++  +   el+     ++e+ + +l  +++      +  ++++DEid  + 
  gene722|gene722|rna721|rna721 298 GILLYGPPGCGKTLLVRAVSNMSHC----NFLSIKGPELISkyVGDSEKEIRKLFDKAKQ----LQPCVLFFDEIDSLCG 369
                                    5899********************8....9999999999883333445555555444433....3456************ PP

                                    ----------HHHHHHHHHHHH- CS
                          AAA_2  83 kessgadvSregVqrdLLqileg 105
                                     e++g++  +  +++ +L +l+g
  gene722|gene722|rna721|rna721 370 -ERNGNEFTS-RIVNQILTLLDG 390
                                    .555555555.466777778876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00017     0.072       2      76 ..      78     159 ..      77     199 .. 0.72
   2 !    8.4   0.0    0.0064       2.7       1      50 [.     302     352 ..     302     373 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00017
                                    E-TTSSHHHHHHHHHHHHTEEEEEHH....HHHHHHHHTTTSHSSHHHHC....TSHHHHHHHHHHHHHHHHHHHHHSSE CS
                         AAA_17   2 GgPGsGKgtqceklvekygfthlsaG....dllreeakrgglakardemr....klpleekkelqkeaaekiaeeakkkg 73 
                                    G+ G+GK+++++ + ++y+++++ a+      lre  ++++l  +r+ +     ++  e++k++  ++ e ++++++k+ 
  gene722|gene722|rna721|rna721  78 GVSGVGKTFLVNCISQEYKLPIIRASldsdKELRESFRKSSL-LERSIILiediDVLGEDDKKVISQLSEYLENHKGKSI 156
                                    99********************99954444689999999988.3444333223334446677778888777777655555 PP

                                    EEE CS
                         AAA_17  74 vlv 76 
                                    v+ 
  gene722|gene722|rna721|rna721 157 VIA 159
                                    544 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0064
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklp 50 
                                    +G+PG+GK+ +++ +    +  +ls  G  l++    ++ ++ r+ ++k++
  gene722|gene722|rna721|rna721 302 YGPPGCGKTLLVRAVSNMSHCNFLSIkGPELISKYVGDSEKEIRKLFDKAK 352
                                    7********999877766666666655655555554444455666666555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00098      0.42       2      24 ..      73      95 ..      72     103 .. 0.89
   2 ?   -1.4   0.0       4.6   1.9e+03      81     139 ..     121     171 ..      98     191 .. 0.62
   3 !    9.5   0.2    0.0021      0.88       3      21 ..     299     317 ..     297     398 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00098
                                   CEEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                   +++l+G +G+GKT L+  + ++ 
  gene722|gene722|rna721|rna721 73 TLLLHGVSGVGKTFLVNCISQEY 95
                                   899*************9998875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.6
                                    CCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEEECCCHHHHCTTS CS
                          NACHT  81 erlLlilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltvrpralrdleeql 139
                                    er  +++ ++D l +d+++     v   Lse ++  +  ++ +++t+r+ a   + e+l
  gene722|gene722|rna721|rna721 121 ERSIILIEDIDVLGEDDKK-----VISQLSEYLEN-HKGKSIVIATARNPAF--INESL 171
                                    3333666667777766666.....66666666655.4455555555555555..55555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0021
                                    EEEEC-TTTCHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                    ++l G++G+GKT L++ + 
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVS 317
                                    7899***********9875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1     0.001      0.44      54     164 ..      72     176 ..      66     200 .. 0.71
   2 !   10.3   0.0   0.00065      0.28      55      84 ..     298     327 ..     289     404 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfilfvDDLsFeeeeeeyksLksvLe 133
                                    + +LL G  G+GK  lv  + +ey+   L +i  + ++ kel + +++  +  er i+++ D+      e+ k++ s L 
  gene722|gene722|rna721|rna721  72 STLLLHGVSGVGKTFLVNCISQEYK---LPIIRASLDSDKELRESFRKS-SLLERSIILIEDIDVLG--EDDKKVISQLS 145
                                    678******************9997...666655555555555555543.44578888999986544..44467778888 PP

                         DUF815 134 GsleakpenvliyaTsNrRhLlpeklsdnee 164
                                      le++  + ++ aT+    +++e+l+  ++
  gene722|gene722|rna721|rna721 146 EYLENHKGKSIVIATARNPAFINESLNKFDN 176
                                    8889999999999999888888888776655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00065
                         DUF815  55 nvLLwGarGtGKSslvkallneyaeegLrl 84 
                                     +LL+G  G+GK  lv+a+ n  + + L +
  gene722|gene722|rna721|rna721 298 GILLYGPPGCGKTLLVRAVSNMSHCNFLSI 327
                                    69*****************99888777654 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.082        35      47      75 ..      73     101 ..      64     196 .. 0.74
   2 !   14.5   0.0   5.9e-05     0.025      48     112 ..     299     364 ..     267     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.082
                          Rad17  47 iLLisGPsGCgkstvvkvLskelgiklre 75 
                                     LL+ G sG gk+  v+ +s+e+   ++ 
  gene722|gene722|rna721|rna721  73 TLLLHGVSGVGKTFLVNCISQEYKLPIIR 101
                                    68999999999999999999998766554 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.9e-05
                          Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslke.pdnqksdfkgltekesrflsqiesfkel 112
                                    +L+ GP+GCgk+  v+ +s     ++     p ++ +     +++++ l++k +++++ +  f e+
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNFLSIKGPELISKyVGDSEKEIRKLFDKAKQLQPCVLFFDEI 364
                                    5789****************9999999988887764414559999999999999999999999997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.049        21       2      21 ..      75      94 ..      74     116 .. 0.86
   2 !   13.9   0.0   0.00012     0.053       1      35 [.     299     336 ..     299     385 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.049
                   RNA_helicase  2 wlyGpsgeGKStlakeLaka 21
                                   +l+G sg+GK+ l++ ++++
  gene722|gene722|rna721|rna721 75 LLHGVSGVGKTFLVNCISQE 94
                                   79************997766 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00012
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl...klkkkdsvy 35 
                                    i+lyGp+g+GK++l++ +++    ++   k ++  s y
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNFlsiKGPELISKY 336
                                    789*************9766655444333333333334 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.012       5.2      23      44 ..      74      95 ..      65     101 .. 0.87
   2 ?    2.8   0.0      0.13        55      32     101 ..     153     226 ..     150     233 .. 0.84
   3 !    7.5   0.0    0.0049       2.1      23      43 ..     299     319 ..     292     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                                   EEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC 23 valvGmgGvGKttlakqilnks 44
                                   + l+G  GvGKt l++ i +++
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCISQEY 95
                                   679***********99998775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                                    SHHHHHHHHCCSH..CCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS..HHHHHHHHCC CS
                         NB-ARC  32 GKttlakqilnks..devegrFdsvawvvvsktdkseeiletilkeLslseddleekeeves..lkrklvrlLl 101
                                    GK+++++ + n    +e  ++Fd    v +    + +eil ++  +++ +e d+ e ++  +   +r+l r+L+
  gene722|gene722|rna721|rna721 153 GKSIVIATARNPAfiNESLNKFDNSLLVKIPTAAERREILISLTDKMKCQETDWTELAKLMPgfVARDLKRALK 226
                                    788777777776311344459************************************99999999999999886 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0049
                                    EEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                    + l+G +G+GKt l++ + n 
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNM 319
                                    679************999876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.013       5.4      20      44 ..      72      96 ..      53     103 .. 0.81
   2 !   11.4   0.0   0.00055      0.24      19      51 ..     296     330 ..     275     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                                   EEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE 20 dvilLeGdLGaGKTtlvrglakalg 44
                                   +++lL+G  G+GKT lv  + ++++
  gene722|gene722|rna721|rna721 72 STLLLHGVSGVGKTFLVNCISQEYK 96
                                   4699**************9998875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00055
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                     + ilL+G+ G+GKT lvr++ +  +++  ++k P
  gene722|gene722|rna721|rna721 296 PSGILLYGPPGCGKTLLVRAVSNMSHCNflSIKGP 330
                                    3349****************998887776677776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.058        25       5      22 ..      74      91 ..      71     107 .. 0.86
   2 ?    1.1   0.0      0.64   2.7e+02      14      44 ..     153     187 ..     148     275 .. 0.71
   3 !   10.6   0.0   0.00081      0.35       5      29 ..     299     322 ..     295     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.058
                         AAA_24  5 iliyGpsgiGKTtlakel 22
                                   +l+ G sg+GKT l++ +
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCI 91
                                   789*********998766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                         AAA_24  14 GKTtlakelgpkplfi.....dtekGlksldadkfp 44 
                                    GK+ +++++  +p+fi      ++++l    ++  +
  gene722|gene722|rna721|rna721 153 GKSIVIATA-RNPAFIneslnKFDNSLLVKIPTAAE 187
                                    999999999.99999944444444444433333333 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00081
                         AAA_24   5 iliyGpsgiGKTtlakelgpkplfi 29 
                                    il+yGp+g GKT l++    +   +
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAV-SNMSHC 322
                                    89************9988.555544 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00012     0.051      18      88 ..      69     155 ..      50     255 .. 0.77
   2 ?    3.0   0.0      0.12        50      18      40 ..     294     316 ..     286     323 .. 0.85
   3 ?   -0.6   0.0       1.4   6.1e+02     163     189 ..     343     371 ..     324     387 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                     KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkefa.....................kpvrflfaefnawsfkggddavaellaa 76 
                                    ++p+++ L g  G+GK++l+n + +e+k  +                     +   +l+ +++ +  ++     ++++++
  gene722|gene722|rna721|rna721  69 HPPSTLLLHGVSGVGKTFLVNCISQEYKLPIirasldsdkelresfrkssllERSIILIEDIDVLGEDD-----KKVISQ 143
                                    899*************************99899999999999999999998766666666777777665.....777777 PP

                     KAP_NTPase  77 Ladaleeeygql 88 
                                    L++ le ++g+ 
  gene722|gene722|rna721|rna721 144 LSEYLENHKGKS 155
                                    888777777765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                     KAP_NTPase  18 atpivvgLygkWGsGKssllnkl 40 
                                    ++p+ + Lyg+ G+GK+ l+  +
  gene722|gene722|rna721|rna721 294 TRPSGILLYGPPGCGKTLLVRAV 316
                                    678889***********998765 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.4
                     KAP_NTPase 163 dmektLda..lqkrlVvviDdLDrcetee 189
                                    ++ k +d+  + ++ V++ D++D++  e+
  gene722|gene722|rna721|rna721 343 EIRKLFDKakQLQPCVLFFDEIDSLCGER 371
                                    455555657778899********997776 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.033        14      15      36 ..      67      88 ..      58     160 .. 0.82
   2 ?   -2.4   0.0       5.9   2.5e+03     109     135 ..     243     270 ..     184     280 .. 0.64
   3 !   10.3   0.0   0.00073      0.31      13      36 ..     290     313 ..     282     316 .. 0.86
   4 ?   -0.9   0.0         2   8.7e+02     102     152 ..     338     389 ..     325     393 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.033
                         ATPase 15 GipegrvvlitGepGtGKtifa 36
                                   Gi   ++ l+ G++G GKt+++
  gene722|gene722|rna721|rna721 67 GIHPPSTLLLHGVSGVGKTFLV 88
                                   78888999***********876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.9
                         ATPase 109 eelaeaikeika..krvviDsitglayee 135
                                     +l+ a+ke+k     +  Dsi++l ++ 
  gene722|gene722|rna721|rna721 243 IDLEVALKEMKWkgAEITFDSIGSL-EDV 270
                                    3455566666553356777888888.444 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00073
                         ATPase  13 kgGipegrvvlitGepGtGKtifa 36 
                                    k Gi + + +l++G pG+GKt+++
  gene722|gene722|rna721|rna721 290 KLGITRPSGILLYGPPGCGKTLLV 313
                                    6799******************96 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2
                         ATPase 102 edleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvlk 152
                                     d e+ i++l +  k+++   +  D i++l  +++ ++ + +i+ q+++ l 
  gene722|gene722|rna721|rna721 338 GDSEKEIRKLFDKAKQLQPCVLFFDEIDSLcGERNGNEFTSRIVNQILTLLD 389
                                    5667778888888888888999999999996666666777778888777765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.053        23      24      43 ..      73      92 ..      64     119 .. 0.86
   2 !   12.2   0.1   0.00021     0.089      25      44 ..     299     318 ..     291     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.053
                   Mg_chelatase 24 nlllvGppGsGKtmlakrlp 43
                                    lll G +G GKt l ++++
  gene722|gene722|rna721|rna721 73 TLLLHGVSGVGKTFLVNCIS 92
                                   69*************99886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00021
                   Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                    +ll+GppG+GKt+l +++++
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSN 318
                                    89************998865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.018       7.6      49      70 ..      73      94 ..      68     172 .. 0.91
   2 !    9.5   0.0    0.0017      0.75      44      68 ..     293     317 ..     288     365 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.018
                      IstB_IS21 49 nivllGpsGvGKshlaialgve 70
                                    ++l G sGvGK++l   +++e
  gene722|gene722|rna721|rna721 73 TLLLHGVSGVGKTFLVNCISQE 94
                                   68999**********9888775 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0017
                      IstB_IS21  44 iekkenivllGpsGvGKshlaialg 68 
                                    i++  +i+l Gp+G GK+ l  a++
  gene722|gene722|rna721|rna721 293 ITRPSGILLYGPPGCGKTLLVRAVS 317
                                    5677899*************99876 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.016       6.9       2      34 ..      74     106 ..      73     109 .. 0.86
   2 !    9.6   0.0    0.0018      0.77       2      31 ..     299     328 ..     298     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftp 34 
                                    +ll+gv G++kt lv+ +++  +l + r  + +
  gene722|gene722|rna721|rna721  74 LLLHGVSGVGKTFLVNCISQEYKLPIIRASLDS 106
                                    699****************99998887766655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0018
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    +ll g PG +ktllv+a++++ +++f  i+
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNFLSIK 328
                                    7999*****************999998775 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0      0.01       4.5      22      45 ..      71      94 ..      60     108 .. 0.86
   2 ?    6.9   0.0     0.011       4.5      21      47 ..     295     321 ..     284     331 .. 0.85
   3 ?   -0.3   0.0       1.7   7.4e+02      93     110 ..     355     372 ..     335     424 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                                   SS-EEEECSTTSSHHHHHHHHHHH CS
                Sigma54_activat 22 dlsvlitGesGtGKellaraihea 45
                                   ++++l++G sG+GK++l ++i ++
  gene722|gene722|rna721|rna721 71 PSTLLLHGVSGVGKTFLVNCISQE 94
                                   5789**************999775 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                                    SSS-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheask 47 
                                     ++ +l+ G  G+GK+ll ra+ + s+
  gene722|gene722|rna721|rna721 295 RPSGILLYGPPGCGKTLLVRAVSNMSH 321
                                    56789****************988775 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.7
                                    TTSEEEEETGGGS-HHHH CS
                Sigma54_activat  93 dgGtlfLDeigelplelQ 110
                                    +  +lf+Dei +l  e  
  gene722|gene722|rna721|rna721 355 QPCVLFFDEIDSLCGERN 372
                                    447899999998876554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.015       6.6      16      60 ..      71     116 ..      58     189 .. 0.71
   2 !    9.1   0.0    0.0017      0.72      14      49 ..     294     327 ..     285     334 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                     Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldpD...dlRelhPe 60 
                                    P  +ll G +G GK+ l + + +e   +  ++r + D   +lRe +++
  gene722|gene722|rna721|rna721  71 PSTLLLHGVSGVGKTFLVNCISQEY--KLPIIRASLDsdkELRESFRK 116
                                    88899*******************9..888888777722335555544 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                     rP  ill G pG+GK+ l +++ +    + n++ +
  gene722|gene722|rna721|rna721 294 TRPSGILLYGPPGCGKTLLVRAVSNMS--HCNFLSI 327
                                    68999****************998876..6666666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00016      0.07     100     131 ..      72     103 ..      59     123 .. 0.83
   2 ?    1.3   0.0      0.65   2.8e+02     102     122 ..     299     319 ..     262     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
                                    SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevs 131
                                    +t +l G SGvGK+ L+n + +e +l +   s
  gene722|gene722|rna721|rna721  72 STLLLHGVSGVGKTFLVNCISQEYKLPIIRAS 103
                                    67899****************99877665554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.65
                                    EEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                    ++l G+ G GK+ L+ a+ + 
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNM 319
                                    6899*********99988765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0       0.1        45      35      50 ..      73      88 ..      67      94 .. 0.86
   2 !    7.9   0.0     0.005       2.1      36      50 ..     299     313 ..     292     319 .. 0.87
   3 ?    0.7   0.0      0.76   3.3e+02     128     184 ..     342     400 ..     324     403 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                         AAA_25 35 lallaGapgtGKttla 50
                                   + ll G +g+GKt+l+
  gene722|gene722|rna721|rna721 73 TLLLHGVSGVGKTFLV 88
                                   679***********97 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.005
                         AAA_25  36 allaGapgtGKttla 50 
                                    +ll+G+pg+GKt l+
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLV 313
                                    79**********996 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.76
                         AAA_25 128 advdaleaaieevegvrlvviDplsralgg...densnsdvgalvealeriarrtgaavl 184
                                     ++++l +++++  ++ ++ +D +++++g    +e  ++ v+++++ l+ + +r ++ v+
  gene722|gene722|rna721|rna721 342 KEIRKLFDKAKQ-LQPCVLFFDEIDSLCGErngNEFTSRIVNQILTLLDGLDDRGDVYVI 400
                                    678999999999.579**********9998854555555579999999999888888776 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.052        22      35      56 ..      73      94 ..      67     102 .. 0.85
   2 !    9.3   0.0    0.0017      0.74      30      57 ..     293     320 ..     286     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.052
                          AAA_7 35 pvllvGptGtGKtviikdllkk 56
                                    +ll G +G+GKt +++ + ++
  gene722|gene722|rna721|rna721 73 TLLLHGVSGVGKTFLVNCISQE 94
                                   5799***********9976665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0017
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkl 57 
                                    +++   +ll+Gp G+GKt++++ + +  
  gene722|gene722|rna721|rna721 293 ITRPSGILLYGPPGCGKTLLVRAVSNMS 320
                                    5566779**************9876544 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.23     1e+02      36      54 ..      72      90 ..      63     105 .. 0.85
   2 ?   -2.9   0.0       9.1   3.9e+03      46      95 ..     152     200 ..     148     212 .. 0.58
   3 !    8.0   0.0    0.0039       1.7      30      58 ..     291     319 ..     282     333 .. 0.84
   4 ?    1.2   0.0       0.5   2.1e+02     113     137 ..     349     372 ..     326     392 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.23
                           TniB 36 pnlllvGdsnnGKtmivek 54
                                   + lll+G s +GKt +v+ 
  gene722|gene722|rna721|rna721 72 STLLLHGVSGVGKTFLVNC 90
                                   6799***********9985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.1
                           TniB  46 nGKtmivekFarlhppekdedaekv.pvlvvqappkpdekrlyaaiLealg 95 
                                     GK+ ++   +  +p+  +e+ +k+ + l+v++p+ ++ +++  ++ ++++
  gene722|gene722|rna721|rna721 152 KGKSIVIATAR--NPAFINESLNKFdNSLLVKIPTAAERREILISLTDKMK 200
                                    56666665432..33333333333335677777877777777776666655 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0039
                           TniB  30 pkrkrmpnlllvGdsnnGKtmivekFarl 58 
                                       +r++ +ll+G++ +GKt +v+  +++
  gene722|gene722|rna721|rna721 291 LGITRPSGILLYGPPGCGKTLLVRAVSNM 319
                                    567899****************9977655 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.5
                           TniB 113 rllrelkvrvLiiDEihnllagsar 137
                                       ++l++ vL +DEi++l  g+++
  gene722|gene722|rna721|rna721 349 DKAKQLQPCVLFFDEIDSLC-GERN 372
                                    445789999*******9986.5444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.18        77      52      75 ..      73      96 ..      70     140 .. 0.83
   2 ?   -1.7   0.0         3   1.3e+03     225     269 ..     126     174 ..     113     182 .. 0.62
   3 !    9.6   0.0    0.0011      0.46      52      98 ..     298     342 ..     290     367 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.18
                                   XXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 52 avLlaGpsgtGktalaiaiskelg 75
                                   ++Ll G sg Gkt l   is+e  
  gene722|gene722|rna721|rna721 73 TLLLHGVSGVGKTFLVNCISQEYK 96
                                   689******************976 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3
                                    XXXXXXXXXXXXXXXXXXX....XXXXXX..XXXXXXX..XXXXXXXXX CS
                          TIP49 225 tLhdlDvanarpqdllslllqllkskkte..iteklre..einkkvaky 269
                                     + d+Dv     + ++s l ++l+ +k+   + +  r+   in+ ++k+
  gene722|gene722|rna721|rna721 126 LIEDIDVLGEDDKKVISQLSEYLENHKGKsiVIATARNpaFINESLNKF 174
                                    4568888888888888888777766655322233333311456655555 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0011
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                    ++Ll Gp+g Gkt l  a+s+   ++  f +++g e+ s  v  +e 
  gene722|gene722|rna721|rna721 298 GILLYGPPGCGKTLLVRAVSNM--SHCNFLSIKGPELISKYVGDSEK 342
                                    79*****************974..4799*********9998887774 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5      0.93     4e+02      23      43 ..      74      94 ..      68     160 .. 0.67
   2 !   11.2   0.0   0.00058      0.25      23      42 ..     299     318 ..     293     328 .. 0.83
   3 ?    0.3   0.0       1.3   5.4e+02     101     137 ..     339     372 ..     318     400 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.93
                       ATPase_2 23 yfiYGpegsGKtaLlkeiien 43
                                   +++ G  g+GKt L++ i ++
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCISQE 94
                                   667788888888888766544 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00058
                       ATPase_2  23 yfiYGpegsGKtaLlkeiie 42 
                                    +++YGp g+GKt L++ + +
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSN 318
                                    689*********99997755 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.3
                       ATPase_2 101 lvfkaielllekikkkgkk...iiiiiDelqklidlglng 137
                                    + +k i +l++k k    +    ++++De+  l   g ++
  gene722|gene722|rna721|rna721 339 DSEKEIRKLFDKAK----QlqpCVLFFDEIDSLC--GERN 372
                                    33344444444433....35569999***99887..4444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.025        11      17      40 ..      66      89 ..      59      93 .. 0.79
   2 ?    6.4   0.0     0.017       7.2      21      43 ..     296     317 ..     287     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.025
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllD 40
                                   i i++ ++ ll G sG+GK+ l+ 
  gene722|gene722|rna721|rna721 66 IGIHPPSTLLLHGVSGVGKTFLVN 89
                                   5566667899*********98886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                         AAA_29  21 lkgatlltGpsGsGKSTllDAiq 43 
                                    ++g +ll Gp G GK+ l+ A++
  gene722|gene722|rna721|rna721 296 PSG-ILLYGPPGCGKTLLVRAVS 317
                                    456.9***********9998876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.063        27       9      34 ..      70      95 ..      65      99 .. 0.86
   2 ?    7.6   0.0      0.01       4.4      13      31 ..     299     317 ..     292     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.063
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivall 34
                                   + ++ll+ +  G GKT ++++i +++
  gene722|gene722|rna721|rna721 70 PPSTLLLHGVSGVGKTFLVNCISQEY 95
                                   668899**************998876 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.01
                         AAA_19  13 llvtaGpGtGKTrvlkhiv 31 
                                    +l+ ++pG+GKT +++++ 
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVS 317
                                    799*********9887754 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.6   1.1e+03       4      24 ..      76      97 ..      74     103 .. 0.78
   2 ?   12.0   0.0   0.00043      0.18       2      36 ..     299     338 ..     298     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.6
                         AAA_28  4 itGgestGKTtlleaLaar.gy 24
                                   + G ++ GKT l++ ++++ + 
  gene722|gene722|rna721|rna721 76 LHGVSGVGKTFLVNCISQEyKL 97
                                   67999********988865455 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00043
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareile 36 
                                    i + G++++GKT l++a +++   ++  +  pE   +++ 
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMshcNFLSIkgPELISKYVG 338
                                    7899***************765465555557777776664 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.27   1.1e+02       2      22 ..      74      94 ..      73      99 .. 0.85
   2 ?    1.1   0.1      0.74   3.2e+02      94     149 ..     120     175 ..     103     195 .. 0.67
   3 ?    6.5   0.0     0.016       6.9       2      27 ..     299     324 ..     298     346 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.27
                                   EEEE--TTSSHHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                   +++ G +GvGKt lv+ ++++
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCISQE 94
                                   578899*********999876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.74
                                    HHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT CS
                       NTPase_1  94 seadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkd 149
                                     e  +i+i  i  +    kk+++++ e L+++k   +vi  ++++a+++e  ++ d
  gene722|gene722|rna721|rna721 120 LERSIILIEDIDVLGEDDKKVISQLSEYLENHKGKSIVIATARNPAFINESLNKFD 175
                                    566699999999999999***********977655555555544455555444333 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.016
                                    EEEE--TTSSHHHHHHHHHHHH...G CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssg 27 
                                    +++ GppG GKt lv+ v+++ + + 
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNF 324
                                    6788************9998765555 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.016       6.6       4      36 ..      74     106 ..      72     145 .. 0.89
   2 ?    4.8   0.0     0.052        22       4      33 ..     299     328 ..     297     355 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHH CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDa 36 
                                    +lL+G+s  GK+ l++++ +  + p +   +D+
  gene722|gene722|rna721|rna721  74 LLLHGVSGVGKTFLVNCISQEYKLPIIRASLDS 106
                                    69****************999888887777665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.052
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEE CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlg 33 
                                    ilL G +  GK+ l+ra+ ++++  +l ++
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHCNFLSIK 328
                                    89*******************999999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.07        30      21      40 ..      74      93 ..      64      98 .. 0.85
   2 ?    5.9   0.0     0.023       9.7      22      41 ..     300     319 ..     292     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.07
                         AAA_30 21 avltGpAGtGKttalkalre 40
                                    +l+G+ G GKt++++ + +
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCISQ 93
                                   6899**********998866 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.023
                         AAA_30  22 vltGpAGtGKttalkalrea 41 
                                    +l Gp+G GKt +++a+ ++
  gene722|gene722|rna721|rna721 300 LLYGPPGCGKTLLVRAVSNM 319
                                    688*************9876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.7   1.6e+03      20      41 ..      74      95 ..      65     165 .. 0.75
   2 ?   10.5   0.0   0.00088      0.37      20      58 ..     299     359 ..     289     373 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                         AAA_11 20 tliqGPPGtgKTktivellsql 41
                                    l++G  G gKT+ +  + ++ 
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCISQEY 95
                                   5788888999997766555444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00088
                         AAA_11  20 tliqGPPGtgKTktivellsqll.............sr........rk.seeeksakpriL 58 
                                     l+ GPPG+gKT  + ++ ++ +             ++        rk  +++k+ +p++L
  gene722|gene722|rna721|rna721 299 ILLYGPPGCGKTLLVRAVSNMSHcnflsikgpelisKYvgdsekeiRKlFDKAKQLQPCVL 359
                                    6999********9999999999866666666555541133333333224555555566555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.16        69       3      23 ..      74      94 ..      72     158 .. 0.87
   2 ?    5.3   0.0     0.032        14       4      22 ..     300     318 ..     298     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.16
                                   EEEEESTTCCHHHHHHHHHCT CS
                           cobW  3 tvltGflGsGKTtLlnhllen 23
                                   ++l G  G GKT L+n + ++
  gene722|gene722|rna721|rna721 74 LLLHGVSGVGKTFLVNCISQE 94
                                   6789999******99987654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.032
                                    EEEESTTCCHHHHHHHHHC CS
                           cobW   4 vltGflGsGKTtLlnhlle 22 
                                    +l G++G GKT L++++ +
  gene722|gene722|rna721|rna721 300 LLYGPPGCGKTLLVRAVSN 318
                                    689***********98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 3262.70
//
Query:       gene723|gene723|rna722|rna722  [L=969]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-11   43.1   1.5    4.8e-10   39.3   0.4    3.0  3  CPSF_A    CPSF A subunit region
  ------ inclusion threshold ------
      0.065   12.8   0.0       0.28   10.8   0.0    2.1  1  DUF295    Protein of unknown function (DUF295)


Domain annotation for each model (and alignments):
>> CPSF_A  CPSF A subunit region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0     0.047   4.2e+02     130     204 ..      95     167 ..      61     175 .. 0.79
   2 ?   -1.8   0.0      0.17   1.5e+03     205     240 ..     531     570 ..     491     585 .. 0.78
   3 !   39.3   0.4   5.4e-14   4.8e-10      67     280 ..     727     914 ..     707     920 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.047
                                    -SS-EEEEEEETTEEEEEES.SS-EEEEEE-SSS--EEEEEEESS---EEEEEEE--SSS.EEEEEETTSEEEEEE- CS
                         CPSF_A 130 tqlyvvslkvlgnriivgDl.mkSvtfveydeenyklilfardtqkrwvtaaeflvdged.tvlvaDkfgnlfvlry 204
                                     ++y+  + +l+n+i+++ + + Sv  ++yd     +   a d+ + ++ ++    ++ d ++l+ D +g +f  ry
  gene723|gene723|rna722|rna722  95 PSTYTRCIRTLKNLIFIAESgIVSVAALSYDG--LIFGDDANDFGYYKILDCFSG-KN-DvGFLLEDISGDIFYSRY 167
                                    34599999*******99997359999999966..325677778888888888777.55.669999999999999998 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.17
                                    -TTSGGGTTTT.....EEEEEEEEE-SS----E...EEEE CS
                         CPSF_A 205 dpeasessdgdp....rleeraefhlgeivtslrkgslvp 240
                                    ++e + ssdg      rlee +e+ l +i  s+ +g++++
  gene723|gene723|rna722|rna722 531 KKESKASSDGISsileRLEEESEWELLDIKPSFFSGCMIE 570
                                    4455556666667778999999999999999999988887 PP

  == domain 3  score: 39.3 bits;  conditional E-value: 5.4e-14
                                    EEEEEEE-SS--EEEEEEEEEEEES----EEEETTEEEEE-SSEEEEEEE-TTS-EEEEEEEE-SS-EEEEEEETTEEEE CS
                         CPSF_A  67 lvfeiievpetnrkLklvhkeevkgavtalaefqGrllvgvgqkvrvydlgedktLlrkafldtqlyvvslkvlgnriiv 146
                                     +f  +     ++ +kl+h+   +g+v+al   +++l+     ++ +y+ + +  L++ + +++++++  +   ++ri++
  gene723|gene723|rna722|rna722 727 AMFSTK-----DNTIKLIHESIDEGIVYALDTNEDYLVTHRDHTIHIYKRQAQI-LVELCAMKIDFVPYRIVMDRDRIAC 800
                                    444444.....579****************************************.************************* PP

                                    EESSS-EEEEEE-SSS--EEEEEEESS---EEEEEEE--SSSEEEEEETTSEEEEEE--TTSGGGTTTT.EEEEEEEEE- CS
                         CPSF_A 147 gDlmkSvtfveydeenyklilfardtqkrwvtaaeflvdgedtvlvaDkfgnlfvlrydpeasessdgdprleeraefhl 226
                                    + +++S+ ++ +++e + l+l   +t+k +v ++ f   g  ++++a  +g ++ l  +              +   f l
  gene723|gene723|rna722|rna722 801 SCVYRSFGVFTFNQETNHLSLDFLSTSKEQVESMVFG-LG--SLIIATTDGKILFLDENY-------------KAEAFLL 864
                                    **************7777*******************.77..8**********9998883.............3457*** PP

                                    SS----E...EEEE.SSS--S-EEEEEE-TTS-EEEEEE..--HHHHHHHHHHHH CS
                         CPSF_A 227 geivtslrkgslvpgeaesssspqllyatldGsigllvPl.iseeeyrrlqaLqq 280
                                    g+ +ts+++g+l    ++s     + + t +G++g+l+P+ +++++ + l +L++
  gene723|gene723|rna722|rna722 865 GDRITSMCPGTLSLCRSDS-----IYFITRNGGVGILTPIdLNKKDLEALIELER 914
                                    ***********99976777.....9**************4356777777777775 PP

>> DUF295  Protein of unknown function (DUF295)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.1e-05      0.28       9      41 ..     860     891 ..     847     906 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                         DUF295   9 raLFlGrn.ssfsvsasdfgglkgNcIYFttddd 41 
                                    +a++lG+   s++  +  +  +++++IYF+t++ 
  gene723|gene723|rna722|rna722 860 EAFLLGDRiTSMCPGTLSL--CRSDSIYFITRNG 891
                                    5777777755777777766..9*******98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (969 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 6084.35
//
Query:       gene724|gene724|rna723|rna723  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-19   70.1   2.3    2.9e-19   69.0   2.4    1.5  2  SGS       SGS domain
     0.0058   16.7   0.2     0.0076   16.3   0.2    1.2  1  CRA       Circumsporozoite-related antigen (CRA)


Domain annotation for each model (and alignments):
>> SGS  SGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.76   6.8e+03      36      51 ..      50      65 ..      47      82 .. 0.61
   2 !   69.0   2.4   3.2e-23   2.9e-19       8      72 ..      90     153 ..      85     155 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.76
                            SGS 36 adadedtrrammKSyv 51
                                   +d  +d +    KS +
  gene724|gene724|rna723|rna723 50 KDVHPDIKLSESKSRI 65
                                   5555666555555544 PP

  == domain 2  score: 69.0 bits;  conditional E-value: 3.2e-23
                            SGS   8 kelekeekeekkeeegeaalnklFkklYadadedtrrammKSyveSnGtvLstnWeevkkkkvet 72 
                                    +  + e++e+++e+e+++++ +l +k+Y+ + ed+rram KS++eS+GtvLst+W++vk+kk++ 
  gene724|gene724|rna723|rna723  90 DGSK-ETTENDSEDEENTSVMDLLRKIYQRSGEDVRRAMEKSFYESEGTVLSTDWDQVKSKKITR 153
                                    4444.4455555678999*******************************************9975 PP

>> CRA  Circumsporozoite-related antigen (CRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   8.5e-07    0.0076      52     102 ..      92     141 ..      59     148 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.5e-07
                            CRA  52 vekaeekedeneedridvlkLikelekKeeeliivnKkkkkYksatfglat 102
                                     +++ e +d ++e+++ v++L+++++++  e ++   +k+ Y s  ++l+t
  gene724|gene724|rna723|rna723  92 SKETTE-NDSEDEENTSVMDLLRKIYQRSGEDVRRAMEKSFYESEGTVLST 141
                                    333334.3555566667**************999999*****999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1020.12
//
Query:       gene725|gene725|rna724|rna724  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.53   10.7   4.9         11    6.5   0.1    2.4  2  NBD94     Nucleotide-Binding Domain 94 of RH


Domain annotation for each model (and alignments):
>> NBD94  Nucleotide-Binding Domain 94 of RH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1   0.00059        11      69      89 ..      71      91 ..      45      93 .. 0.91
   2 ?    5.4   1.3    0.0013        24       2      42 ..     141     180 ..     140     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00059
                          NBD94 69 nlieeiekyienideikkkls 89
                                   +++e+iek+ +nide  kk +
  gene725|gene725|rna724|rna724 71 KIMETIEKTETNIDELLKKTK 91
                                   79*************999876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0013
                          NBD94   2 eKtknivtkidkkkkiyeniekllnEleeiekektsleevk 42 
                                    eK  +iv +  +  +iy+n   + +El ++++e   ++e++
  gene725|gene725|rna724|rna724 141 EKLYEIVIESRRSLNIYDNT-GIWKELIKVKNEMLESKEIE 180
                                    6788999999999*****95.79*************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1438.01
//
Query:       gene726|gene726|rna725|rna725  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.1e-10   39.3   0.0    1.3e-09   38.4   0.0    1.4  1  HAD_2      Haloacid dehalogenase-like hydrolase
     0.0011   19.3   0.0     0.0072   16.6   0.0    2.1  2  Hydrolase  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.5e-13   1.3e-09       2     173 ..     106     279 ..     105     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.5e-13
                          HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkevkpy 81 
                                    ++D+D+Tl+  ++ + ++ ++ lee  ls  ++  l+++ +  +  ll+ +   + +  ++ee+++   e  + ++++p 
  gene726|gene726|rna725|rna725 106 LYDIDDTLYHPSNNLQKMERKFLEEKYLSFKKDGTLETFKEELSLSLLYSSLFYNYVGISLEEYWEMLSEFDYLQYLSPD 185
                                    89**********************99887556666665554333344444444445556***********99999***** PP

                          HAD_2  82 dgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekk...KPdpeviekaleklklk.keeviy 157
                                     +++++L ++  ++++  + T++ r+ +e+ l++lg+ + F+v+++  +  k    KP  +++e + + l+++ + +v +
  gene726|gene726|rna725|rna725 186 VNLRNFLLSM--KNIRRCCFTNGPRDRAENILAKLGVLDCFEVVISIGKYDKTfccKPLIKSYEFVTKVLGIEsPGNVYF 263
                                    *******888..89*******************************98887777777****************83567788 PP

                          HAD_2 158 vGDsptDieaakkagi 173
                                    + Ds   i+ a+++g 
  gene726|gene726|rna725|rna725 264 FDDSEINIIKAREFGW 279
                                    9************995 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.1   9.2e+02       4      22 ..     105     123 ..     104     156 .. 0.79
   2 !   16.6   0.0     8e-07    0.0072     128     201 ..     193     269 ..     167     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.1
                                    EEEESBTTTBCHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   4 vvfDkdGTLttgepsvedv 22 
                                    ++ D+d TL++ ++ + + 
  gene726|gene726|rna725|rna725 105 FLYDIDDTLYHPSNNLQKM 123
                                    67899****9988776654 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8e-07
                                    HHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES...STTTSHHHHHHHHHHHTST.GGGEEEEESSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                      Hydrolase 128 asLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet...vakpspegkvaaireLqgk.peevamVGDgvn 201
                                     s   ++i+ +  t++ +  ae ++ +lG  d+f++vi++       + kp+ + ++ + + L+++ p +v +++D+  
  gene726|gene726|rna725|rna725 193 LSM--KNIRRCCFTNGPRDRAENILAKLGvLDCFEVVISIGKYDktfCCKPLIKSYEFVTKVLGIEsPGNVYFFDDSEI 269
                                    343..499**********************8888555444333335******************555*********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1902.27
//
Query:       gene727|gene727|rna726|rna726  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-15   54.7   4.7    1.1e-14   54.1   4.7    1.3  1  TB2_DP1_HVA22  TB2/DP1, HVA22 family
  ------ inclusion threshold ------
      0.067   12.6   3.2       0.16   11.4   2.4    1.7  2  DUF373         Domain of unknown function (DUF373)
       0.13   11.8   0.0       0.21   11.2   0.0    1.3  1  INTS5_N        Integrator complex subunit 5 N-terminus
       0.72   10.4   9.5       0.29   11.6   2.6    2.8  3  IBV_3C         IBV 3C protein


Domain annotation for each model (and alignments):
>> TB2_DP1_HVA22  TB2/DP1, HVA22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.1   4.7   2.4e-18   1.1e-14       4      75 ..      20      90 ..      14      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.1 bits;  conditional E-value: 2.4e-18
                  TB2_DP1_HVA22  4 aslkaleskeksdetkwltYWvvfafltvvesladvllswiPfYylfKllfllwlvlpqtqgatyvYekflr 75
                                   +++ka++++++   ++  +Y++v+a+++v+++l++++l +iPfY+lfKl+++ w+ +p + ga +vY+ +++
  gene727|gene727|rna726|rna726 20 QAFKACREDKRI-YRRYNKYFMVIAVFLVLDNLFSFVLDFIPFYQLFKLMVVAWISIPACTGAVFVYKFYIH 90
                                   456666555544.667****************************************************9998 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.4   3.6e-05      0.16     264     329 ..       4      71 ..       1      75 [. 0.77
   2 ?    5.3   0.3    0.0026        12     163     224 ..      54     114 ..      51     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                         DUF373 264 gavewlalailtaslgkiideylkreekdiarllllpflvlaiglvlygasaylls....lsilalslvv 329
                                     +++ ++++++++ + +++++    e+k+i+r ++ +f+v+a+ lvl ++++++l+    ++ + l++v+
  gene727|gene727|rna726|rna726   4 LLINAFVAMLVLYNVLQAFKACR--EDKRIYRRYNKYFMVIAVFLVLDNLFSFVLDfipfYQLFKLMVVA 71 
                                    56788899999999999998887..6689*************************9997553333333333 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0026
                         DUF373 163 lllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvty 224
                                    ++l ++++  l++l+ +a+++i ++ G++++++ f ++  ++++   l+e++e+ r  ++ y
  gene727|gene727|rna726|rna726  54 FVLDFIPFYQLFKLMVVAWISIPACTGAVFVYK-FYIHGFMDKYQGALEEMVEKARSAVFRY 114
                                    6677889999999*****************999.8899999999999999999999888877 PP

>> INTS5_N  Integrator complex subunit 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.7e-05      0.21      39      81 ..     107     157 ..     102     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                        INTS5_N  39 aRsaVleylaqlfeeaveryl....eevete....pilkesqinaeldeai 81 
                                    aRsaV+ y+++  ++a ++y     +eve+e    +++ e ++ + +d+ +
  gene727|gene727|rna726|rna726 107 ARSAVFRYFNECYDKAQKTYHgrkiSEVEEEalgiKNEGEGSKISPEDSNM 157
                                    9*******************6666688888877764444444444444444 PP

>> IBV_3C  IBV 3C protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2     0.079   3.5e+02      20      39 ..       5      24 ..       2      34 .. 0.83
   2 ?   11.6   2.6   6.4e-05      0.29      19      67 ..      40      88 ..      33     106 .. 0.82
   3 ?   -1.0   0.0      0.56   2.5e+03      65      81 ..     124     140 ..     118     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.079
                         IBV_3C 20 iivgflalyllgralqafvq 39
                                   +i  f+a+ +l   lqaf  
  gene727|gene727|rna726|rna726  5 LINAFVAMLVLYNVLQAFKA 24
                                   67889999999999**9965 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.4e-05
                         IBV_3C 19 yiivgflalyllgralqafvqaadacclfwytwvvipgakgtafvykyt 67
                                    +i  fl l  l   +  f+   +   l+  +w+ ip + g+ fvyk+ 
  gene727|gene727|rna726|rna726 40 MVIAVFLVLDNLFSFVLDFIPFYQLFKLMVVAWISIPACTGAVFVYKFY 88
                                   466678888877777888888888999999*****************74 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.56
                         IBV_3C  65 kytygrklnnpeleavi 81 
                                    k  +grk+ + e ea+ 
  gene727|gene727|rna726|rna726 124 KTYHGRKISEVEEEALG 140
                                    44569****99999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.54
# Mc/sec: 1089.24
//
Query:       gene728|gene728|rna727|rna727  [L=555]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-39  134.1   8.4    6.6e-22   78.5   0.2    3.7  3  ABC_tran       ABC transporter
    2.5e-23   81.9   0.9      6e-23   80.7   0.9    1.7  1  ABC_tran_Xtn   ABC transporter
      5e-17   62.7   1.2      0.002   18.0   0.0    4.4  4  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
      1e-09   38.2   3.5     0.0041   16.6   0.0    4.2  4  SMC_N          RecF/RecN/SMC N terminal domain
    2.6e-06   28.0   0.5     0.0043   17.6   0.0    3.2  2  AAA_18         AAA domain
      4e-06   26.8   0.3      0.025   14.5   0.0    2.5  2  RsgA_GTPase    RsgA GTPase
    5.9e-06   26.2   9.4      0.096   12.4   0.2    4.1  4  AAA_15         AAA ATPase domain
    2.1e-05   24.5   0.5        0.1   12.5   0.0    2.6  2  NACHT          NACHT domain
    5.2e-05   22.9   1.6       0.14   11.9   0.1    2.5  2  AAA_29         P-loop containing region of AAA domain
    0.00015   22.1   0.1      0.053   13.9   0.0    2.5  2  RNA_helicase   RNA helicase
     0.0002   21.6   3.4       0.68   10.2   0.1    3.5  2  AAA_22         AAA domain
    0.00029   21.3   0.0       0.44   11.0   0.0    2.7  2  AAA            ATPase family associated with various cellular
    0.00036   21.1   6.2       0.06   13.8   0.1    3.0  3  AAA_23         AAA domain
    0.00055   20.4   0.1        1.1    9.6   0.0    2.5  2  AAA_16         AAA ATPase domain
     0.0006   20.1   0.1       0.38   11.0   0.0    2.6  2  AAA_28         AAA domain
    0.00083   19.0   0.1       0.17   11.5   0.0    2.4  2  AAA_27         AAA domain
    0.00093   19.4   0.6       0.43   10.8   0.6    3.4  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
    0.00099   18.9   2.3       0.51   10.0   0.1    3.0  2  AAA_30         AAA domain
     0.0022   17.8   4.0       0.41   10.3   0.7    3.0  2  AAA_24         AAA domain
     0.0022   18.1   5.7       0.85    9.7   0.3    3.1  2  MMR_HSR1       50S ribosome-binding GTPase
     0.0036   17.5   0.6        2.3    8.4   0.1    2.6  2  Roc            Ras of Complex, Roc, domain of DAPkinase
     0.0045   16.9   0.3        2.4    8.0   0.0    2.8  2  ATPase_2       ATPase domain predominantly from Archaea
     0.0057   16.7   1.0      0.082   13.0   0.0    2.7  3  Dynamin_N      Dynamin family
      0.006   16.6   1.1        6.4    6.8   0.0    3.2  2  AAA_14         AAA domain
     0.0064   16.1   0.2        2.5    7.7   0.0    2.6  2  SRP54          SRP54-type protein, GTPase domain
     0.0079   16.4   0.9       0.81    9.8   0.0    2.6  2  AAA_33         AAA domain
  ------ inclusion threshold ------
      0.013   14.4   0.9       0.49    9.1   0.0    2.8  2  ABC_ATPase     Predicted ATPase of the ABC class
      0.015   15.2   0.3        1.6    8.7   0.0    2.5  2  MobB           Molybdopterin guanine dinucleotide synthesis p
      0.015   15.2   0.5        7.5    6.4   0.1    2.7  2  NTPase_1       NTPase
      0.019   14.2   0.8       0.59    9.3   0.1    2.3  2  NB-ARC         NB-ARC domain
      0.033   13.8   0.4       0.52    9.9   0.0    2.6  3  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      0.039   13.2   0.0      0.064   12.5   0.0    1.2  1  Abhydrolase_7  Abhydrolase family
      0.043   12.9   0.2       0.13   11.3   0.0    1.8  2  T2SSE          Type II/IV secretion system protein
      0.049   12.8   0.1       0.65    9.1   0.0    2.3  2  G-alpha        G-protein alpha subunit
      0.053   12.6   0.2        1.5    7.8   0.0    2.3  2  MCM            MCM P-loop domain
      0.056   13.2   0.9        1.8    8.3   0.1    2.5  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
      0.058   12.4   0.3        3.2    6.7   0.0    2.3  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.061   13.6   0.0       0.18   12.0   0.0    1.8  1  PhetRS_B1      Phe-tRNA synthetase beta subunit B1 domain
      0.062   13.3   0.4         16    5.5   0.2    2.5  2  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
      0.098   12.2   0.5        8.9    5.9   0.1    2.4  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.099   11.9   2.5        2.4    7.4   0.0    2.7  3  Septin         Septin
       0.11   11.8   1.3       0.33   10.3   0.1    2.2  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.12   12.0   1.5         11    5.5   0.0    3.5  4  AAA_25         AAA domain
       0.14   11.6   0.4        2.1    7.8   0.1    2.4  2  Arf            ADP-ribosylation factor family
       0.17   11.9   1.2         16    5.5   0.1    2.7  2  AAA_5          AAA domain (dynein-related subfamily)
       0.19   11.2   0.9         10    5.6   0.1    2.3  2  AAA_7          P-loop containing dynein motor region
        0.2   10.9   0.8        3.3    6.9   0.1    2.3  2  Zeta_toxin     Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.6     2e-08   7.5e-06       5      33 ..     110     138 ..     106     149 .. 0.91
   2 !   32.0   0.0   3.9e-10   1.5e-07      97     137 .]     179     219 ..     171     219 .. 0.85
   3 !   78.5   0.2   1.7e-24   6.6e-22       1     137 []     367     493 ..     367     493 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2e-08
                                    EEEEETTSEEEEEESTTSSHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   5 slklkegekvaivGenGaGKStLlkllag 33 
                                    sl++ +g+k+++vG+nG GK+tLlk++ +
  gene728|gene728|rna727|rna727 110 SLSIIRGKKYGLVGRNGIGKTTLLKAIRK 138
                                    89999*********************976 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 3.9e-10
                                    TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  97 lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    ++++ + ++ s LSgG++ r  la+a+ ++p+llllDEpt+
  gene728|gene728|rna727|rna727 179 FTKDMAVKKISDLSGGWRMRAHLAKAINTDPDLLLLDEPTN 219
                                    4456666888******************************8 PP

  == domain 3  score: 78.5 bits;  conditional E-value: 1.7e-24
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    lk +++k++ ++++++vG nG GKSt+lkllag+++ t+G+i           ++ +  ++g++ q+  + ++l+v en 
  gene728|gene728|rna727|rna727 367 LKGLNMKINSDSRIVVVGANGQGKSTFLKLLAGKMEATSGSI-----------IRNSGLRVGYFAQH--HIDHLKVNENv 433
                                    7899**************************************...........788999*******9..77777788888 PP

                                    .......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                           +s+ee  +al+ +gl+  +++++     +LSgGqk+r+  a +   kp+ll+lDEpt+
  gene728|gene728|rna727|rna727 434 ldfmmksYSQEESRRALAAFGLNV-DNQRI----GTLSGGQKSRLGFAIINGMKPSLLVLDEPTN 493
                                    999**9999999*********999.67777....9*****************************8 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.9   1.6e-25     6e-23       1      81 [.     257     336 ..     257     342 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.6e-25
                   ABC_tran_Xtn   1 velengklteYkGnYseyleekeerleqqqkayekqqkeikkleefIerfrakakkakqaqsrekaLeklekiekpeekk 80 
                                    ++l++ k+  YkGnY++++++++er+ +++++ye q + ++++++fI+rfr++ak+a+ +qs++kaL k+  + +p+++ 
  gene728|gene728|rna727|rna727 257 LHLNDLKIDVYKGNYESFVKQRRERMSKARREYESQLAVREHIQSFIDRFRYNAKRASLVQSKIKALAKMPALVPPKQD- 335
                                    589999******************************************************************9999555. PP

                   ABC_tran_Xtn  81 p 81 
                                    +
  gene728|gene728|rna727|rna727 336 A 336
                                    3 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2     9e-06    0.0034       3      20 ..     120     137 ..     119     179 .. 0.83
   2 !   10.9   0.0   0.00078       0.3     256     302 ..     207     249 ..     195     250 .. 0.82
   3 !   11.8   0.0    0.0004      0.15       3      20 ..     381     398 ..     380     438 .. 0.86
   4 !   18.0   0.0   5.1e-06     0.002     255     301 ..     480     523 ..     456     525 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9e-06
                         AAA_21   3 vliGpNgsGKSnLLdald 20 
                                    +l+G+Ng GK++LL+a++
  gene728|gene728|rna727|rna727 120 GLVGRNGIGKTTLLKAIR 137
                                    69***************4 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00078
                         AAA_21 256 kkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                      ++lll+DEp n L+  +l  l + +kel++    vi+++H+  +l
  gene728|gene728|rna727|rna727 207 TDPDLLLLDEPTNYLDINALNWLERKIKELKT----VIIVSHDRNFL 249
                                    4459*************888888888888877....******97666 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0004
                         AAA_21   3 vliGpNgsGKSnLLdald 20 
                                    v++G+Ng GKS++L++l 
  gene728|gene728|rna727|rna727 381 VVVGANGQGKSTFLKLLA 398
                                    89**************94 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 5.1e-06
                         AAA_21 255 lkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                      k+sll++DEp n+L+ + +  l++ l++    ++ v++++H+  +
  gene728|gene728|rna727|rna727 480 GMKPSLLVLDEPTNHLDMESIDALADALRRF---DGAVVCVSHDLNF 523
                                    3455*********************999888...55*******9765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0095       3.6      28      45 ..     120     137 ..     108     144 .. 0.90
   2 ?    5.6   0.0     0.025       9.6     161     207 ..     211     254 ..     186     264 .. 0.86
   3 ?    6.6   0.2     0.012       4.6      25      42 ..     378     395 ..     367     415 .. 0.81
   4 !   16.6   0.0   1.1e-05    0.0041     119     202 ..     442     524 ..     417     540 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0095
                                    EEEESTTSSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnlldAil 45 
                                     +vG+NG GK+ ll Ai+
  gene728|gene728|rna727|rna727 120 GLVGRNGIGKTTLLKAIR 137
                                    58**************95 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                                    EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadk 207
                                    l llDe    LD +  + + + +ke +    +i++s+++++l++  +
  gene728|gene728|rna727|rna727 211 LLLLDEPTNYLDINALNWLERKIKELK---TVIIVSHDRNFLNNTTE 254
                                    789**********************99...89**********99865 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                                    SEEEEEESTTSSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlld 42 
                                    s  ++vG+NG GKs +l 
  gene728|gene728|rna727|rna727 378 SRIVVVGANGQGKSTFLK 395
                                    45789*********9986 PP

  == domain 4  score: 16.6 bits;  conditional E-value: 1.1e-05
                                    -HHHHHHHHHCTT-STT.....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEE CS
                                    xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 119 tkkevsellesagiske.....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfi 193
                                    +++e ++ l+  g++ +     +LSgG+k+ +     fAi +  + +l +lDe   +LD + + ++a+ l++      ++
  gene728|gene728|rna727|rna727 442 SQEESRRALAAFGLNVDnqrigTLSGGQKSRLG----FAIINGMKPSLLVLDEPTNHLDMESIDALADALRRFD--GAVV 515
                                    44455555555555554555558******9655....555555566799*********************9987..7788 PP

                                    EE-SSHHHC CS
                                    xxxxxxxxx RF
                          SMC_N 194 vislreeml 202
                                    ++s++ +++
  gene728|gene728|rna727|rna727 516 CVSHDLNFI 524
                                    888877666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2     0.018       6.7       3      25 ..     121     149 ..     120     264 .. 0.80
   2 !   17.6   0.0   1.1e-05    0.0043       1      66 [.     380     443 ..     380     495 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.018
                         AAA_18   3 ltGtpGvGKttlakeLskrl.gf.....g 25 
                                    l G  G GKttl k+++kr  g+      
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRRfGIpkgmkI 149
                                    6788899***********97566775551 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.1e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldalee 66 
                                    I++ G+ G GK+t+ k L+ ++     ++++++++gl+ +++++ + ++++++e++ld  ++   +
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKM--EATSGSIIRNSGLRVGYFAQHHIDHLKVNENVLDFMMKSYSQ 443
                                    89****************9998..********************9999999999998877766554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0015      0.56      97     122 ..     114     139 ..     102     217 .. 0.77
   2 !   14.5   0.0   6.6e-05     0.025      87     133 ..     364     411 ..     310     430 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                                    CTTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpe 122
                                    +++k   lvG  G+GK+tL++a++ +
  gene728|gene728|rna727|rna727 114 IRGKKYGLVGRNGIGKTTLLKAIRKR 139
                                    67778889**************9986 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.6e-05
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S----- CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevsek 133
                                    ++ l+ l+ ++++ + +v+vG  G GKSt+++ l++++e+  g++ ++
  gene728|gene728|rna727|rna727 364 RNILKGLNMKINSdSRIVVVGANGQGKSTFLKLLAGKMEATSGSIIRN 411
                                    555666777777668899*******************99998887655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1    0.0003      0.12      28      44 ..     121     137 ..     114     151 .. 0.94
   2 ?    3.8   0.0       0.1        40     313     351 ..     200     236 ..     194     249 .. 0.83
   3 ?    1.6   0.6      0.49   1.9e+02     194     297 ..     236     357 ..     232     368 .. 0.51
   4 !   12.4   0.2   0.00025     0.096      17      43 ..     372     397 ..     364     398 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                         AAA_15  28 liGkNnsGKSsileald 44 
                                    l+G+N++GK+++l+a+ 
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIR 137
                                    8**************95 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.1
                         AAA_15 313 eaekkdekeeknvilliEEPEahLHpqaqkvlikllkel 351
                                    ++   + +++++++ll++EP ++L ++a + l +++kel
  gene728|gene728|rna727|rna727 200 HLA--KAINTDPDLLLLDEPTNYLDINALNWLERKIKEL 236
                                    333..45999**********************9999998 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.49
                         AAA_15 194 iiklllisakRnvsdedsekkssllgklkekileealqekl..............eeelteklkeiqeklkeidkklaee 259
                                    ++++ + s +Rn+ ++++e++  l + +++ ++ +  +e++                   e    + e ++ +++ +  +
  gene728|gene728|rna727|rna727 236 LKTVIIVSHDRNFLNNTTEVTLHLNDLKIDVYKGN--YESFvkqrrermskarreY----ESQLAVREHIQSFIDRFRYN 309
                                    55677778888888877776665555555555553..2333334335554432221....22222333333333332222 PP

                         AAA_15 260 lk..kilkkkidkikkfnykgkkneeieik........ddeelplnkn 297
                                    +k  + +++ki+ + k+ + + +++   ik         +  ++++++
  gene728|gene728|rna727|rna727 310 AKraSLVQSKIKALAKMPALVPPKQDAIIKfsfastasQGPLVEFSDV 357
                                    224466667777776666666666666555566666655555555555 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00025
                         AAA_15  17 veidlseeltvliGkNnsGKSsileal 43 
                                    ++i+ ++   v++G+N+ GKS++l++l
  gene728|gene728|rna727|rna727 372 MKINSDS-RIVVVGANGQGKSTFLKLL 397
                                    4566555.89***************98 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0021      0.81       5      20 ..     121     136 ..     119     139 .. 0.90
   2 !   12.5   0.0   0.00027       0.1       2      24 ..     379     401 ..     378     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                                    EEC-TTTCHHHHHHHH CS
                          NACHT   5 lqGeaGsGKTtLlqkl 20 
                                    l G++G+GKTtLl+ +
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAI 136
                                    68***********988 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00027
                                    CEEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalaw 24 
                                     +++ G++G+GK+t+l+ la ++
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLAGKM 401
                                    689**************998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0019      0.71      24      42 ..     118     136 ..     108     138 .. 0.83
   2 !   11.9   0.1   0.00037      0.14      16      39 ..     371     394 ..     365     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0019
                         AAA_29  24 atlltGpsGsGKSTllDAi 42 
                                     + l+G++G GK+Tll Ai
  gene728|gene728|rna727|rna727 118 KYGLVGRNGIGKTTLLKAI 136
                                    56699***********997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00037
                         AAA_29  16 tieidlkgatlltGpsGsGKSTll 39 
                                     ++i+ ++ ++++G++G GKST+l
  gene728|gene728|rna727|rna727 371 NMKINSDSRIVVVGANGQGKSTFL 394
                                    67888777999***********97 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.053        20       3      21 ..     121     139 ..     120     156 .. 0.72
   2 !   13.9   0.0   0.00014     0.053       1      46 [.     380     426 ..     380     452 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.053
                   RNA_helicase   3 lyGpsgeGKStlakeLaka 21 
                                    l+G++g+GK+tl k + k+
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKR 139
                                    68************96554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00014
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfwdg 46 
                                    i+++G++g+GKSt+ k La +++ +++++ ++s    +  ++ + d 
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKMEATSGSIIRNSGLRvGYFAQHHIDH 426
                                    789****************9999887554444433334444444454 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.6    0.0038       1.5      10     112 ..     121     229 ..     117     250 .. 0.58
   2 !   10.2   0.1    0.0018      0.68       6     104 ..     378     496 ..     373     524 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0038
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllr....ellralglelka..........erls 74 
                                    ++G  G+GKTtll+ ++++      + + ++   ++ +l ++++ +d+      ++l+ lg                   
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRR---FGIPKgMKIYMIKQDLVGDGTVEDFVGvdggRILNGLG----FtkdmavkkisDLSG 193
                                    79**************9986...22222555555555555555666654311112333333....223335543433333 PP

                         AAA_22  75 seellealeqalraravielliiDEaqh.lrseealeeL 112
                                      +++++l++a+++  +  ll++DE  + l   +al++L
  gene728|gene728|rna727|rna727 194 GWRMRAHLAKAINTDPD--LLLLDEPTNyL-DINALNWL 229
                                    44444555555555544..77777777767.67777777 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0018
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsst.........sskdll 57 
                                    + +vv+G  G GK+t l+ l+ + ++ +                               + +++          +s+  l
  gene728|gene728|rna727|rna727 378 SRIVVVGANGQGKSTFLKLLAGKMEATSGSIIrnsglrvgyfaqhhidhlkV-------NENVLDfmmksysqeESRRAL 450
                                    5699****************99875443333367777777777744444432.......222222222211012333333 PP

                         AAA_22  58 rellralglelka..erlsseellealeqalraravielliiDEaqh.lr 104
                                     ++  ++++++ +  +++++++l  a+ +     ++++ll++DE  + l+
  gene728|gene728|rna727|rna727 451 AAFGLNVDNQRIGtlSGGQKSRLGFAIIN----GMKPSLLVLDEPTNhLD 496
                                    44444444433333333333333333332....22246777777666564 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0012      0.44       3      38 ..     121     187 ..     119     234 .. 0.61
   2 ?    7.7   0.0     0.012       4.6       2      30 ..     381     412 ..     380     490 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0012
                                    EESSTTSSHHHHHHHHHHH.......HTHE..............EEEEETTTCSSS..........S CS
                            AAA   3 lyGppGtGKTllakavake.......lgve..............fleisgsellsk..........y 38 
                                    l+G  G+GKT+l ka+ k        ++++              f+ ++g ++l+            
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRrfgipkgMKIYmikqdlvgdgtvedFVGVDGGRILNGlgftkdmavkK 187
                                    89**************999655444423223333344444444455555555554445444444443 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.012
                                    EEESSTTSSHHHHHHHHHHHHTHE...EEEEE CS
                            AAA   2 llyGppGtGKTllakavakelgve...fleis 30 
                                    +++G  G GK+++ k +a +++++   +++ s
  gene728|gene728|rna727|rna727 381 VVVGANGQGKSTFLKLLAGKMEATsgsIIRNS 412
                                    789*****************964422233333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   0.00016      0.06      24      40 ..     121     137 ..     114     165 .. 0.92
   2 ?    0.1   0.5       2.5   9.4e+02     118     175 ..     246     302 ..     201     326 .. 0.47
   3 !    8.4   0.1    0.0074       2.8      23      38 ..     381     396 ..     364     400 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00016
                         AAA_23  24 ItGpNGaGKTTildAik 40 
                                    ++G NG GKTT+l Ai+
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIR 137
                                    79**************7 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.5
                         AAA_23 118 eqfise..llgskkiilnlilflgqer.feefelkdkkerleelekeleeledekkllekl 175
                                    ++f+++  +++   + l++ +++g  + f     k++ er+ ++++e+e + ++++ ++  
  gene728|gene728|rna727|rna727 246 RNFLNNttEVTLHLNDLKIDVYKGNYEsFV----KQRRERMSKARREYESQLAVREHIQSF 302
                                    333333221222222333333333333211....122223333333333333333333333 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0074
                         AAA_23  23 lItGpNGaGKTTildA 38 
                                    +++G NG GK+T+l  
  gene728|gene728|rna727|rna727 381 VVVGANGQGKSTFLKL 396
                                    899**********975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0078         3      29      47 ..     121     139 ..     115     157 .. 0.89
   2 !    9.6   0.0    0.0029       1.1      25      63 ..     378     427 ..     364     512 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0078
                         AAA_16  29 lsGesGvGKsslvrellra 47 
                                    l+G  G+GK++l+++++++
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKR 139
                                    7899**********99974 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0029
                         AAA_16  25 elvllsGesGvGKsslvrellralekd..........g.giflrgkcdql 63 
                                    + ++++G+ G GKs+ ++ l+  +e++          + g+f++ + d+l
  gene728|gene728|rna727|rna727 378 SRIVVVGANGQGKSTFLKLLAGKMEATsgsiirnsglRvGYFAQHHIDHL 427
                                    5678*****************98888877888888884477777777777 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.023       8.9       4      24 ..     121     143 ..     118     150 .. 0.83
   2 !   11.0   0.0     0.001      0.38       1      22 [.     379     400 ..     379     452 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.023
                         AAA_28   4 itGgestGKTtlleaLaar..gy 24 
                                    ++G  + GKTtll+a+ +r  g+
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRrfGI 143
                                    67889***********9875655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.001
                         AAA_28   1 kivitGgestGKTtlleaLaar 22 
                                    +iv++G+ + GK+t l+ La +
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLAGK 400
                                    79*****************943 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00044      0.17      32      55 ..     122     145 ..     115     154 .. 0.92
   2 ?    4.8   0.0     0.047        18      25      44 ..     376     395 ..     366     422 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00044
                         AAA_27  32 yGpNEAGKstalrAisdllfGipe 55 
                                    +G N  GK+t+l+Ai++ +fGip+
  gene728|gene728|rna727|rna727 122 VGRNGIGKTTLLKAIRKRRFGIPK 145
                                    8*********************97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.047
                         AAA_27  25 eadlhliyGpNEAGKstalr 44 
                                    +++  +++G+N  GKst l+
  gene728|gene728|rna727|rna727 376 SDSRIVVVGANGQGKSTFLK 395
                                    5555699**********986 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.44   1.7e+02      55      78 ..     202     223 ..     186     229 .. 0.79
   2 !   10.8   0.6    0.0011      0.43      29      89 ..     461     508 ..     440     509 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.44
                        SbcCD_C  55 ssaegrepalrlvfLDEAFsklDe 78 
                                     +a   +++++l++LDE  + lD 
  gene728|gene728|rna727|rna727 202 AKA--INTDPDLLLLDEPTNYLDI 223
                                    443..47899*******9999986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                        SbcCD_C  29 ssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    ++gtlSGG+k+ l   ++                +++l++LDE  + lD esi++l ++l+
  gene728|gene728|rna727|rna727 461 RIGTLSGGQKSRLGFAIIN-------------GMKPSLLVLDEPTNHLDMESIDALADALR 508
                                    6666666666333222222.............34689*******************99997 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.2     0.009       3.4      23      40 ..     121     138 ..     113     249 .. 0.75
   2 !   10.0   0.1    0.0013      0.51      20     120 ..     379     515 ..     371     522 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.009
                         AAA_30  23 ltGpAGtGKttalkalre 40 
                                    l+G+ G GKtt+lka+r+
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRK 138
                                    89**************75 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                         AAA_30  20 vavltGpAGtGKttalkalreaweaa.g.......grviglAptgkaAkvLae......elgieastiakllkrlk.... 81 
                                      v++G+ G GK+t lk l+  +ea  g        rv  +A  +    +++e          ++++ ++  ++l+    
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLAGKMEATsGsiirnsgLRVGYFAQHHIDHLKVNEnvldfmM---KSYSQEESRRALAafgl 455
                                    5799*****************999995677777665555555544444444432221110...11111111111112223 PP

                         AAA_30  82 ........................grarlepgtllivDEag.mvdtkqlaallkaaekagakvi 120
                                                            g     + +ll+ DE    +d+++++al++a+++ +  v+
  gene728|gene728|rna727|rna727 456 nvdnqrigtlsggqksrlgfaiinG----MKPSLLVLDEPTnHLDMESIDALADALRRFDGAVV 515
                                    3333333333334446665533321....33467777774414577777777777777554444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.7    0.0011      0.41       2      22 ..     116     136 ..     115     245 .. 0.87
   2 !    7.6   0.0    0.0075       2.9       4      22 ..     379     397 ..     376     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                         AAA_24   2 klkiliyGpsgiGKTtlakel 22 
                                    ++k+ ++G +giGKTtl+k +
  gene728|gene728|rna727|rna727 116 GKKYGLVGRNGIGKTTLLKAI 136
                                    68999*************998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0075
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                    +i+++G +g GK+t++k l
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLL 397
                                    89**************987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.8    0.0028       1.1       2      24 ..     119     141 ..     118     295 .. 0.70
   2 !    9.7   0.3    0.0022      0.85       1      25 [.     379     404 ..     379     412 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0028
                                    EEEEESTTSSHHHHHHHHHTSTE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgeka 24 
                                     ++vGr   GK+tL++a+ +++ 
  gene728|gene728|rna727|rna727 119 YGLVGRNGIGKTTLLKAIRKRRF 141
                                    589***************98754 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0022
                                    EEEEEESTTSSHHHHHHHHHTS.TEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge.kai 25 
                                    ++++vG    GKSt+++ l g+ +a 
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLAGKmEAT 404
                                    699****************9985444 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0061       2.3       3      24 ..     120     141 ..     118     156 .. 0.87
   2 ?    6.9   0.0     0.018         7       1      25 [.     379     402 ..     379     439 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0061
                                    EEESSTTSSHHHHHHCHCT-CC CS
                            Roc   3 vlvGdsgvGKtsllkrfvedkf 24 
                                     lvG +g+GKt+llk + +++f
  gene728|gene728|rna727|rna727 120 GLVGRNGIGKTTLLKAIRKRRF 141
                                    69**************999888 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.018
                                    EEEEESSTTSSHHHHHHCHCT-CCC CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfs 25 
                                    ++v+vG +g+GK+++lk +  +k++
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLA-GKME 402
                                    69*************98766.4444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0062       2.4      26      70 ..     122     167 ..     115     248 .. 0.69
   2 ?    5.8   0.0     0.029        11      19     107 ..     376     479 ..     365     486 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0062
                       ATPase_2  26 YGpegsGKtaLlkeiienledkdk.yviyyialreesiskldefie 70 
                                     G+ g+GKt+Llk i +++    k  +iy+i+   +   ++++f++
  gene728|gene728|rna727|rna727 122 VGRNGIGKTTLLKAIRKRRFGIPKgMKIYMIKQDLVGDGTVEDFVG 167
                                    599************9999665555789988877777777777755 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.029
                       ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdk........yviyyialreesiskldefie.......eeeekkklekalg 83 
                                    +++ +++ G  g GK+++lk ++ + e  +         +v y+ + + ++  k++e +         +ee++++  a+g
  gene728|gene728|rna727|rna727 376 SDSRIVVVGANGQGKSTFLKLLAGKMEATSGsiirnsglRVGYFAQ-HHIDHLKVNENVLdfmmksySQEESRRALAAFG 454
                                    46678999*************9999977666466666633444333.333333333332258888887888888888889 PP

                       ATPase_2  84 iavpkaeleeilk.eksklvfkaie 107
                                     +v ++++ +++  +ks+l f+ i+
  gene728|gene728|rna727|rna727 455 LNVDNQRIGTLSGgQKSRLGFAIIN 479
                                    9999999988888888888777776 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.74   2.8e+02       3      23 ..     121     141 ..     120     149 .. 0.87
   2 ?   -2.0   0.1       8.5   3.2e+03      43      66 ..     277     300 ..     240     327 .. 0.52
   3 !   13.0   0.0   0.00021     0.082       1      27 [.     380     406 ..     380     451 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.74
                                    EEEBTTTTHHHHHHHHHTS-- CS
                      Dynamin_N   3 vvGsqSsGKSSvlnaLlgedi 23 
                                    +vG    GK+++l a+ ++++
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRRF 141
                                    6999999*********99987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.5
                                    T---CCS...SSEEEET-EB--CH CS
                      Dynamin_N  43 eeeaseravkeelkekekkledfs 66 
                                    + +++ ++++ e++++ +  e+++
  gene728|gene728|rna727|rna727 277 QRRERMSKARREYESQLAVREHIQ 300
                                    222222333334444433333333 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00021
                                    EEEEEBTTTTHHHHHHHHHTS--S--- CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprg 27 
                                    i+vvG+  +GKS++l  L g+    +g
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKMEATSG 406
                                    89*****************98755554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.6     0.019       7.2       5      36 ..     119     151 ..     115     254 .. 0.85
   2 ?    6.8   0.0     0.017       6.4       5      28 ..     380     409 ..     376     453 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.019
                         AAA_14   5 lvitGaRrvGKTtllkqlikell.vkkesilyi 36 
                                    + ++G   +GKTtllk + k+++ ++k   +y+
  gene728|gene728|rna727|rna727 119 YGLVGRNGIGKTTLLKAIRKRRFgIPKGMKIYM 151
                                    56889999********99998888776666665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                         AAA_14   5 lvitGaRrvGKTtllkqlikell......v 28 
                                    +v++Ga   GK+t+lk l+ +        +
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKMEatsgsiI 409
                                    799**************9988774444432 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.025       9.4       6      23 ..     121     138 ..     117     165 .. 0.69
   2 !    7.7   0.0    0.0066       2.5       3      28 ..     379     404 ..     377     452 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.025
                                    EEESTTSSHHHHHHHHHH CS
                          SRP54   6 lvGlqGaGKTttlaKLaa 23 
                                    lvG +G+GKTt l  + +
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRK 138
                                    8**********9876655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0066
                                    EEEEEESTTSSHHHHHHHHHHHHHHT CS
                          SRP54   3 villvGlqGaGKTttlaKLaallkke 28 
                                     i++vG +G GK t l  La ++++ 
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLAGKMEAT 404
                                    589*************9999887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1       0.1        39       4      21 ..     121     138 ..     120     171 .. 0.87
   2 !    9.8   0.0    0.0021      0.81       2      30 ..     380     411 ..     380     458 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.1
                         AAA_33   4 lvGlpGsGKstlaerllk 21 
                                    lvG +G GK+tl++ + k
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRK 138
                                    699*********997654 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0021
                         AAA_33   2 vllvGlpGsGKstlaerllkklg...avllss 30 
                                    +++vG++G GKst+++ l+ k     + +++ 
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKMEatsGSIIRN 411
                                    689*************9976655444555555 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0013      0.49     249     350 ..     121     218 ..     109     236 .. 0.81
   2 ?    2.3   0.1      0.15        57     247     264 ..     380     397 ..     357     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                                    EEE-TTSSHHHHHHHHHHCCSEE-TTSS-TTEEE-TT-EEE---TT--EEEE--TTTB---CCC--STTEEESS--HHHH CS
                     ABC_ATPase 249 IvGggfhGKsTLLeAlekGvynhvpgDGRefvvtdktavkiraEdgrsvkgvDispFinnLPegkdttkfstedASGSts 328
                                    +vG++  GK+TLL+A+ k  +  +p   + +++ ++ +     Ed     gvD    +n L   kd      +d SG   
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRRFG-IPKGMKIYMIKQDLVGDGTVEDF---VGVDGGRILNGLGFTKDMAVKKISDLSGGWR 196
                                    6999999**********99986.66656777777776667777775...5666677799999999999999999999999 PP

                                    HHHHHHHHHHTT-SEEEEEGGG CS
                     ABC_ATPase 329 qAanimealeagakllLiDEDt 350
                                    + a++++a++ + +llL+DE t
  gene728|gene728|rna727|rna727 197 MRAHLAKAINTDPDLLLLDEPT 218
                                    9999999999999999999944 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                                    EEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 247 tlIvGggfhGKsTLLeAl 264
                                    +++vG + +GKsT L+ l
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLL 397
                                    689***********9966 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0041       1.6       3      36 ..     120     155 ..     119     165 .. 0.81
   2 ?    4.1   0.0      0.11        42       2      25 ..     380     403 ..     379     435 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0041
                           MobB   3 givgksgsGKTtLleklipe..lkarglrvgtiKha 36 
                                    g+vg++g GKTtLl+ + +      +g+++ +iK++
  gene728|gene728|rna727|rna727 120 GLVGRNGIGKTTLLKAIRKRrfGIPKGMKIYMIKQD 155
                                    689***********9886541146789999999976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                           MobB   2 lgivgksgsGKTtLleklipelka 25 
                                    + +vg +g+GK t+l+ l  +++a
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKMEA 403
                                    6799***********999876654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1      0.02       7.5       4      20 ..     121     137 ..     118     141 .. 0.85
   2 ?    6.1   0.1     0.024       9.3       1      25 [.     379     403 ..     379     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.02
                                    EE--TTSSHHHHHHHHH CS
                       NTPase_1   4 iTGppGvGKtTlvkkvl 20 
                                    + G+ G+GKtTl+k + 
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIR 137
                                    78***********9886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.024
                                    EEEEE--TTSSHHHHHHHHHHHH.. CS
                       NTPase_1   1 kvfiTGppGvGKtTlvkkvlellks 25 
                                    ++++ G  G+GK+T++k ++ +++ 
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLAGKMEA 403
                                    58999************99988754 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0015      0.59      24      42 ..     120     138 ..     112     145 .. 0.90
   2 ?    3.0   0.0      0.12        47       9      43 ..     367     400 ..     361     445 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                                    EEEESTTSSHHHHHHHHCC CS
                         NB-ARC  24 alvGmgGvGKttlakqiln 42 
                                    +lvG+ G+GKttl+k i +
  gene728|gene728|rna727|rna727 120 GLVGRNGIGKTTLLKAIRK 138
                                    79*************9976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.12
                                    HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC   9 iekLlekdelqslvvalvGmgGvGKttlakqilnk 43 
                                     + L  k +++   + +vG  G GK+t +k    k
  gene728|gene728|rna727|rna727 367 LKGLNMKINSD-SRIVVVGANGQGKSTFLKLLAGK 400
                                    55566555666.457799*********98866555 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       9.6   3.7e+03     121     137 ..      52      68 ..      51      74 .. 0.84
   2 ?    9.9   0.0    0.0014      0.52       9      37 ..     111     139 ..     106     324 .. 0.83
   3 ?    1.3   0.0      0.61   2.3e+02      15      46 ..     378     409 ..     358     439 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.6
                                    HHHHHHHTTTSBEGGGS CS
                                    xxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 121 lreislrlgempadqgy 137
                                    +r +s r +em ad++ 
  gene728|gene728|rna727|rna727  52 MRSMSERKEEMVADEAM 68 
                                    799999*****999986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                    S-EBTT-EEEEEESTTSSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   9 fpivqGqrtlipgafgvGktvisqslskq 37 
                                    ++i++G++ +++g +g+Gkt++++++ k 
  gene728|gene728|rna727|rna727 111 LSIIRGKKYGLVGRNGIGKTTLLKAIRKR 139
                                    6799********************99887 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.61
                                    -EEEEEESTTSSHHHHHHHHHHHSSTSSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  15 qrtlipgafgvGktvisqslskqsnsddaiiy 46 
                                     r++++ga+g Gk++ ++ l+ ++++++ +i+
  gene728|gene728|rna727|rna727 378 SRIVVVGANGQGKSTFLKLLAGKMEATSGSII 409
                                    57888899999998888888877665554444 PP

>> Abhydrolase_7  Abhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00017     0.064     205     267 ..     218     284 ..     215     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHHHCT-TTEEEEEEEEEE....EGGGHHHHHHHHHH-TT--EEEEES-B--HHHHHHH CS
                  Abhydrolase_7 205 tsyldkqvldwmktqslirkdriivsG....fslGteplmvlGaldesiyafvyndflcrtqeralv 267
                                    t yld + l+w+ ++    k  iivs     +   te  + l  l  ++y   y+ f+ + +er   
  gene728|gene728|rna727|rna727 218 TNYLDINALNWLERKIKELKTVIIVSHdrnfLNNTTEVTLHLNDLKIDVYKGNYESFVKQRRERMSK 284
                                    78***********************9644424568999*************************9653 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       3.2   1.2e+03     136     149 ..     123     136 ..     106     139 .. 0.84
   2 ?   11.3   0.0   0.00035      0.13      76     160 ..     322     408 ..     260     410 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.2
                          T2SSE 136 GgTgsGKttllyal 149
                                    G  g GKttll a+
  gene728|gene728|rna727|rna727 123 GRNGIGKTTLLKAI 136
                                    77899******987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00035
                          T2SSE  76 kgvrlrvvllPvvag.ealviR..kksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallke 152
                                      +++ ++++P   +  +++     ++   ++++d+g++   + +i + l+  +++   i+v G+ g GK+t+l  l  +
  gene728|gene728|rna727|rna727 322 ALAKMPALVPPKQDAiIKFSFAstASQGPLVEFSDVGFSYG-SRNILKGLNMKINSDSRIVVVGANGQGKSTFLKLLAGK 400
                                    44445555555544444444443233333445555555443.3678889999**********************999998 PP

                          T2SSE 153 inksderi 160
                                    +++++  i
  gene728|gene728|rna727|rna727 401 MEATSGSI 408
                                    88876665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.57   2.2e+02      28      45 ..     121     138 ..     106     150 .. 0.88
   2 ?    9.1   0.0    0.0017      0.65      17     119 ..     373     472 ..     362     550 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.57
                                    EEESTTSSHHHHHHHHHH CS
                        G-alpha  28 llGqseSGKsTilkqlkl 45 
                                    l+G ++ GK+T+lk +++
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRK 138
                                    8999**********9984 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                                    XXXE..EEEEEEEESTTSSHHHHHHHHH.HHCS--...--HHHHHC.CHHHHHHHHHHHHHHHHHHHHHTT.......HH CS
                        G-alpha  17 arkkkrevkllllGqseSGKsTilkqlk.llykkg...fseeelat.wraviqlnivrsiktilealesleselsesfel 91 
                                    + +  ++ +++++G+++ GKsT+lk l  +++  +   ++++ l+  + a  +   ++  +++l+ ++++ s      ++
  gene728|gene728|rna727|rna727 373 KIN--SDSRIVVVGANGQGKSTFLKLLAgKMEATSgsiIRNSGLRVgYFAQHHIDHLKVNENVLDFMMKSYS------QE 444
                                    333..4889****************98865553334568888777667777777777777777777777322......23 PP

                                    HC-SS-SCCCS-HCHHHH.......... CS
                        G-alpha  92 qelkerldplkkveasliaklssateee 119
                                    +++++ ++  ++v+++ i +ls++++++
  gene728|gene728|rna727|rna727 445 ESRRALAAFGLNVDNQRIGTLSGGQKSR 472
                                    3444444444666666666666666655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       0.2        76      59      79 ..     118     138 ..      94     150 .. 0.74
   2 ?    7.8   0.0     0.004       1.5      51      82 ..     371     402 ..     360     427 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                                    EEEEEESSTSTHHHHHHHHHH CS
                            MCM  59 nvllvgdpgtaKsqlLkyvek 79 
                                    +  lvg  g++K++lLk++ k
  gene728|gene728|rna727|rna727 118 KYGLVGRNGIGKTTLLKAIRK 138
                                    45689************9976 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.004
                                    SSBBCSS-EEEEEESSTSTHHHHHHHHHHHSS CS
                            MCM  51 ktklrgdinvllvgdpgtaKsqlLkyveklap 82 
                                    ++k+ +d  +++vg  g +Ks++Lk ++  ++
  gene728|gene728|rna727|rna727 371 NMKINSDSRIVVVGANGQGKSTFLKLLAGKME 402
                                    58899********************9875443 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0048       1.8       3      26 ..     118     141 ..     116     156 .. 0.82
   2 ?    2.8   0.1      0.23        87       2      24 ..     378     400 ..     377     404 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0048
                      PduV-EutP   3 killiGkvgsGKttLtqalkgeel 26 
                                    k  l+G+ g GKttL +a++++++
  gene728|gene728|rna727|rna727 118 KYGLVGRNGIGKTTLLKAIRKRRF 141
                                    5569***************98765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.23
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                    ++i+++G+ g GK t  + l g+
  gene728|gene728|rna727|rna727 378 SRIVVVGANGQGKSTFLKLLAGK 400
                                    69*************99998875 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.077        29      17      51 ..     104     138 ..      92     156 .. 0.78
   2 ?    6.7   0.0    0.0084       3.2      15      53 ..     363     401 ..     350     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.077
                                    HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHH CS
                           MeaB  17 ellerllakaGraqvvGltGvPGaGkstlvealgl 51 
                                    e++++ + +  r ++ Gl G  G Gk tl++a+  
  gene728|gene728|rna727|rna727 104 EIVREGSLSIIRGKKYGLVGRNGIGKTTLLKAIRK 138
                                    5666666666688999**************99864 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0084
                                    HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHH CS
                           MeaB  15 akellerllakaGraqvvGltGvPGaGkstlvealglel 53 
                                    ++++l+ l  k     ++ + G  G Gkst+++ l+ ++
  gene728|gene728|rna727|rna727 363 SRNILKGLNMKINSDSRIVVVGANGQGKSTFLKLLAGKM 401
                                    789999999999999****************99887655 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00048      0.18      10      82 ..     432     512 ..     427     513 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00048
                      PhetRS_B1  10 aLfkalgkelteeeledllfefGlElDeiveeee........kkkadkkseeviykidipAnryDLLcleglaralkvFl 81 
                                    ++++ + k++++ee    l+ fGl +D+    +           +  +  +  ++ +d p n  D+ +++ la al+ F 
  gene728|gene728|rna727|rna727 432 NVLDFMMKSYSQEESRRALAAFGLNVDNQRIGTLsggqksrlGFAIINGMKPSLLVLDEPTNHLDMESIDALADALRRFD 511
                                    445667899*******************9887766676543322566778899999*********************998 PP

                      PhetRS_B1  82 g 82 
                                    g
  gene728|gene728|rna727|rna727 512 G 512
                                    6 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.042        16      20      41 ..     117     138 ..     101     147 .. 0.80
   2 ?    5.3   0.0     0.049        19      19      46 ..     377     404 ..     362     450 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.042
                                    EEEEEEESTTSSHHHHHHHHHH CS
                           TsaE  20 dvilLeGdLGaGKTtlvrglak 41 
                                    +   L G  G GKTtl +++ k
  gene728|gene728|rna727|rna727 117 KKYGLVGRNGIGKTTLLKAIRK 138
                                    55679999**********9965 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.049
                                    TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve 46 
                                     + i+  G  G GK+t+ + la +++ +
  gene728|gene728|rna727|rna727 377 DSRIVVVGANGQGKSTFLKLLAGKMEAT 404
                                    4459999**************9998654 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.023       8.9       4      23 ..     120     139 ..     117     164 .. 0.78
   2 ?    4.3   0.0      0.07        27       3      34 ..     380     411 ..     378     426 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.023
                                    EEEESTTCCHHHHHHHHHCT CS
                           cobW   4 vltGflGsGKTtLlnhllen 23 
                                    +l+G  G GKTtLl+++ ++
  gene728|gene728|rna727|rna727 120 GLVGRNGIGKTTLLKAIRKR 139
                                    689999*********99744 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.07
                                    EEEEESTTCCHHHHHHHHHCT--SS-EEEEES CS
                           cobW   3 tvltGflGsGKTtLlnhllenraglklavivN 34 
                                    +v++G  G GK+t+l+ l  + +  +  +i N
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKMEATSGSIIRN 411
                                    799*************9998888888777777 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.088        33       9      25 ..     121     137 ..     118     146 .. 0.88
   2 ?   -2.2   0.2         5   1.9e+03     248     273 ..     255     283 ..     243     290 .. 0.67
   3 ?    7.4   0.0    0.0063       2.4       6      29 ..     379     402 ..     375     437 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.088
                                    EEEBTTSSCCCCCCTTS CS
                         Septin   9 vvGesglGkttlintlf 25 
                                    +vG++g+Gkttl++++ 
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIR 137
                                    69***********9875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5
                                    HHHCHHHHHHHHHHTHHHHH...HHHHH- CS
                         Septin 248 lkthledLkevteellYety...Rsekls 273
                                    ++ hl+dLk    +  Ye +   R+e++s
  gene728|gene728|rna727|rna727 255 VTLHLNDLKIDVYKGNYESFvkqRRERMS 283
                                    56799999999999999988333444444 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0063
                                    EEEEEEBTTSSCCCCCCTTSSSS- CS
                         Septin   6 tlmvvGesglGkttlintlfetdl 29 
                                     ++vvG++g Gk+t+++ l  +  
  gene728|gene728|rna727|rna727 379 RIVVVGANGQGKSTFLKLLAGKME 402
                                    589*************98876655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       2.4   9.2e+02      44      58 ..     121     135 ..     102     136 .. 0.90
   2 ?   10.3   0.1   0.00086      0.33      40      58 ..     378     396 ..     356     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.4
                                    EE--TTSSHHHHHHH CS
                   FtsK_SpoIIIE  44 vaGatgsGKStalnt 58 
                                    ++G+ g GK+t l++
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKA 135
                                    58**********987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00086
                                    .SEEEE--TTSSHHHHHHH CS
                   FtsK_SpoIIIE  40 shllvaGatgsGKStalnt 58 
                                    s ++v+Ga g GKSt+l+ 
  gene728|gene728|rna727|rna727 378 SRIVVVGANGQGKSTFLKL 396
                                    689*************986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.26        98      31      50 ..     114     133 ..     108     136 .. 0.85
   2 ?   -2.1   0.0       6.4   2.5e+03     126     146 ..     223     239 ..     194     244 .. 0.50
   3 ?    5.5   0.0     0.029        11      31      56 ..     375     400 ..     355     418 .. 0.85
   4 ?   -0.4   0.0         2   7.5e+02     118     186 ..     488     517 ..     442     519 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.26
                         AAA_25  31 pagelallaGapgtGKttla 50 
                                    ++g+   l+G+ g GKttl+
  gene728|gene728|rna727|rna727 114 IRGKKYGLVGRNGIGKTTLL 133
                                    56777779**********97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.4
                         AAA_25 126 ltadvdaleaaieevegvrlv 146
                                    +  ++++le++i+e +    v
  gene728|gene728|rna727|rna727 223 I-NALNWLERKIKELK---TV 239
                                    2.45677888877743...33 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.029
                         AAA_25  31 pagelallaGapgtGKttlaldlala 56 
                                      ++ ++++Ga g GK+t++  la +
  gene728|gene728|rna727|rna727 375 NSDSRIVVVGANGQGKSTFLKLLAGK 400
                                    567899*************9888765 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 2
                         AAA_25 118 akdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllv 186
                                     ++  ++l  + +dal++a+++                                       ++ av++v
  gene728|gene728|rna727|rna727 488 LDEPTNHLDMESIDALADALRR---------------------------------------FDGAVVCV 517
                                    4444444444445555555554.......................................44444444 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.71   2.7e+02      19      38 ..     121     140 ..     111     145 .. 0.83
   2 ?    7.8   0.1    0.0054       2.1       8      38 ..     370     401 ..     364     412 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.71
                                    EEESTTSSHHHHHHHHHHSS CS
                            Arf  19 llGLDnaGKtTilkklklee 38 
                                    l+G  + GKtT+lk +++ +
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRR 140
                                    6788999******9988765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0054
                                    GTT..TTEEEEEEEESTTSSHHHHHHHHHHSS CS
                            Arf   8 lklk.kkelrilllGLDnaGKtTilkklklee 38 
                                    l+ k + + ri+++G  + GK+T lk l  + 
  gene728|gene728|rna727|rna727 370 LNMKiNSDSRIVVVGANGQGKSTFLKLLAGKM 401
                                    444338899****************9887665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.041        16       4      34 ..     121     154 ..     120     160 .. 0.77
   2 ?    4.3   0.1       0.1        38       2      24 ..     380     402 ..     379     414 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.041
                                    EE--SSSSHHHHHHHGGGGB...S--EEEEE--T CS
                          AAA_5   4 LvGppGtgKselaerlaaal...nreveyvqltr 34 
                                    LvG  G+gK++l + + ++     + + ++++++
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKRRfgiPKGMKIYMIKQ 154
                                    89***********999887555555555555555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.1
                                    EEEE--SSSSHHHHHHHGGGGBS CS
                          AAA_5   2 vlLvGppGtgKselaerlaaaln 24 
                                    +++vG+ G gKs++ + la  ++
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKME 402
                                    578***************98874 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.096        36      32      53 ..     115     136 ..     100     146 .. 0.86
   2 ?    5.6   0.1     0.027        10      27      58 ..     371     402 ..     366     411 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.096
                          AAA_7  32 nkkpvllvGptGtGKtviikdl 53 
                                    ++k+  lvG  G GKt+++k +
  gene728|gene728|rna727|rna727 115 RGKKYGLVGRNGIGKTTLLKAI 136
                                    6778889**********99875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.027
                          AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkld 58 
                                    ++ ++++  +++vG  G GK++ +k l  k++
  gene728|gene728|rna727|rna727 371 NMKINSDSRIVVVGANGQGKSTFLKLLAGKME 402
                                    566788999**************998888777 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.28   1.1e+02      21      39 ..     121     139 ..     112     156 .. 0.85
   2 ?    6.9   0.1    0.0087       3.3      19      47 ..     380     409 ..     366     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.28
                     Zeta_toxin  21 lgGqpGAGKselaellkde 39 
                                    l+G  G GK++l+++++++
  gene728|gene728|rna727|rna727 121 LVGRNGIGKTTLLKAIRKR 139
                                    899************9886 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0087
                     Zeta_toxin  19 illgGqpGAGKselaellkdele.rqgnvv 47 
                                    i+++G+ G GKs+ ++ll+ ++e + g+++
  gene728|gene728|rna727|rna727 380 IVVVGANGQGKSTFLKLLAGKMEaTSGSII 409
                                    899*******************95556555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              47  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.45
# Mc/sec: 3741.01
//
Query:       gene729|gene729|rna728|rna728  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   11.9   0.3       0.15   11.5   0.3    1.2  1  LIM_bind  LIM-domain binding protein


Domain annotation for each model (and alignments):
>> LIM_bind  LIM-domain binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   8.6e-06      0.15       2      54 ..     143     195 ..     142     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.6e-06
                       LIM_bind   2 rllelierlsnrs..nedsdieyWrkfvaefFspdavlrltlkl....deqekepkqFe 54 
                                    rl+++i+  + ++  ++++  e+ ++f +efF +++v  +t+ +    +      ++Fe
  gene729|gene729|rna728|rna728 143 RLFQIIDACKAEEmnQNQNISEWIERFKKEFFDSECVKFITTRSivysS------HTFE 195
                                    89********999956666667889************999999844440......3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1579.60
//
Query:       gene730|gene730|rna729|rna729  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-51  175.8   2.1    1.4e-51  175.4   2.1    1.2  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
      0.031   14.4   0.1      0.083   13.0   0.1    1.7  1  DUF5338          Family of unknown function (DUF5338)
      0.031   13.9   1.3      0.041   13.5   0.2    1.6  2  DEAD_2           DEAD_2


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.4   2.1   2.4e-55   1.4e-51       3     266 .]     145     386 ..     143     386 .. 0.84

  Alignments for each domain:
  == domain 1  score: 175.4 bits;  conditional E-value: 2.4e-55
                                    EEEEHHHHHHHTT-GGS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--... CS
                DNA_primase_lrg   3 ykvpfedvldlvkrrrvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellealsesy 82 
                                    + v+f++v+dl+++r  + ++Gy+ l++e ++s+l++++r+ l + ++++ e   +   +++ der  ++ l  +l    
  gene730|gene730|rna729|rna729 145 VLVHFTKVIDLIGKRLAVPERGYLKLNDEGIKSMLVNEYRRYLDRRMDELVEV--S---LYDPDER--MKILSTELL--- 214
                                    78*********************************************996665..3...3678888..333333333... PP

                                    ..........TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHH CS
                DNA_primase_lrg  83 vaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekF 162
                                     ++ +  +++ ++s     k +++ fP+C++ ++++lk+n hlk++ r+ l+lFlkd+g+++d+ +++++++f+  +e F
  gene730|gene730|rna729|rna729 215 -TNSTRCKRNISFSL----KESEKYFPLCIQIIMQRLKRNRHLKYNDRQILCLFLKDCGMNVDDGIDFFRSSFKVGREVF 289
                                    .33333444444444....5589********************************************************* PP

                                    HHHTHCHCHHHCC-STT--------HHHHHHS....TT---S-HHHH.HHHHHHHHHHTT..HHHHHHHHHHHHTT.HHH CS
                DNA_primase_lrg 163 dkeyrynirhnyGkegkrtnyspysCekiltkpppgkgdahgCpfrhdpdklktlLqeyglseediedilesvkegeyqv 242
                                    dkey y+irhnyG egkr+nys++ C+ki +++  ++++ + Cpf +d++ +   ++  +  e+died+++    g ++ 
  gene730|gene730|rna729|rna729 290 DKEYLYSIRHNYGLEGKRANYSCFTCSKIANTT--NEERRSSCPFIEDKEYV---MKLAEGMEADIEDVMD---GGTFNG 361
                                    *****************************5555..6789999***9766666...3333467788888877...9***** PP

                                    HHHHHHHHHHS.-TTT-SSCHHHCC CS
                DNA_primase_lrg 243 aCtkvFelthk.cerdeikhPlqYy 266
                                     Ct+++e ++  ++++ +  P +Yy
  gene730|gene730|rna729|rna729 362 KCTRLLEKLTRkKQEKLVVTPIRYY 386
                                    ******998886788888******9 PP

>> DUF5338  Family of unknown function (DUF5338)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.4e-05     0.083      32      68 ..       4      37 ..       2      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                        DUF5338 32 ikealkaGyalktiwehLheegkitisYeTFlrYVkr 68
                                   ik + ++G++  t +++L ++   ++ YeTF+rY++r
  gene730|gene730|rna729|rna729  4 IKTMKENGWPGITFYTTLSKS---SVDYETFRRYAER 37
                                   7888899***********877...69********987 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.36   2.2e+03      27      74 ..     206     261 ..     186     303 .. 0.52
   2 ?   13.5   0.2   6.9e-06     0.041      58     136 ..     314     390 ..     297     396 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.36
                                    S---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH........TTTT CS
                         DEAD_2  27 ekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek........eekC 74 
                                    +k++ + L   +  C ++   + k++++   +C +   ++ +++        +  C
  gene730|gene730|rna729|rna729 206 MKILSTELLTNSTRCKRNISFSLKESEKYFPLCIQIIMQRLKRNrhlkyndrQILC 261
                                    45555555555555555444445555555555555544444444444444443333 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 6.9e-06
                                    HHHHHHCCHHCCHTTTTTT-SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHH.HCCTSEEEEEHHHHTSCC CS
                         DEAD_2  58 aCkelkkkkaeekeekCsffenleelkklkkllleevvdiedlvelgeklklCPYylsrel.ledadiiilpYqyLldek 136
                                    +C++  + ++ee+ ++C+f e++e +    kl+     died+++ g+ ++ C   l + +  ++ ++++ p  y l+ k
  gene730|gene730|rna729|rna729 314 TCSKIANTTNEERRSSCPFIEDKEYVM---KLAEGMEADIEDVMDGGTFNGKCTRLLEKLTrKKQEKLVVTPIRYYLEYK 390
                                    6999999999999*******9996555...57888889****************99998651456679999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.50
# Mc/sec: 2387.17
//
Query:       gene73|gene73|rna73|rna73  [L=159]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-39  135.3   0.2    1.3e-39  135.1   0.2    1.0  1  UQ_con     Ubiquitin-conjugating enzyme
    1.4e-05   24.8   0.0    1.7e-05   24.5   0.0    1.2  1  Prok-E2_B  Prokaryotic E2 family B
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.036   14.1   0.0    1.2  1  TIR_3      Toll/interleukin-1 receptor domain


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.1   0.2   2.1e-43   1.3e-39       1     138 [.       6     145 ..       6     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.1 bits;  conditional E-value: 2.1e-43
                                HHHHHHHHHHHSTTTTEEEEEEET...TEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBETTSBB CS
                     UQ_con   1 rlqkelkelakkkpsgisaklvdd...enlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvdksGev 81 
                                rl  e ++lak+++  ++a +  +   +n+++w++ i gp+d++Y+g++++l ++fp+dYP++pP+v f+ +++HPnv+++ +v
  gene73|gene73|rna73|rna73   6 RLLAEQENLAKNRKYKFYAIPLPEkpkRNITRWECGIPGPPDGVYKGAYYTLYVDFPDDYPFNPPQVMFKYPVYHPNVYPTNQV 89 
                                67889999999***9**99999855669******************************************************** PP

                                -CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHH CS
                     UQ_con  82 cldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvke 138
                                cldi+ ++ W+p+l++ +vl  +q+Ll+ pn++sp+n++a   +kkd e+y ++vke
  gene73|gene73|rna73|rna73  90 CLDIIGDR-WKPSLNVMNVLCGVQQLLEAPNTRSPANTDASLCFKKDLERYLENVKE 145
                                ******55.**************************************99***99986 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.9e-09   1.7e-05      33     113 ..      42     124 ..       6     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.9e-09
                  Prok-E2_B  33 t........sggtvdlrlvypdsfpllppavflqdpeqlkllpHintfggaLClleeeldldewdpngsvadvleqlqqvLn.e 107
                                         +g+ + l++ +pd++p+ pp+v  + p      p +++ ++ +Cl       d w+p  +v +vl  +qq+L+  
  gene73|gene73|rna73|rna73  42 IpgppdgvyKGAYYTLYVDFPDDYPFNPPQVMFKYPV---YHPNVYP-TNQVCL---DIIGDRWKPSLNVMNVLCGVQQLLEaP 118
                                245555666899***********************99...6799***.******...9999********************987 PP

                  Prok-E2_B 108 gisgde 113
                                + ++  
  gene73|gene73|rna73|rna73 119 NTRSPA 124
                                777765 PP

>> TIR_3  Toll/interleukin-1 receptor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.1e-06     0.036      78     131 .]      94     147 ..      85     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                      TIR_3  78 LervlkppekvvvLlCGVeeselleelfkdweewkelstddepeeYisavkeii 131
                                + +  kp+ +v  +lCGV++  +  ++ + +++   l    + e Y+++vke i
  gene73|gene73|rna73|rna73  94 IGDRWKPSLNVMNVLCGVQQLLEAPNTRSPANTDASLCFKKDLERYLENVKENI 147
                                555678999************555555555555569**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1058.92
//
Query:       gene731|gene731|rna730|rna730  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0028   17.6   0.0     0.0094   15.9   0.0    1.8  2  SNARE     SNARE domain
     0.0038   16.9   1.0        1.9    8.1   0.1    2.3  2  Syntaxin  Syntaxin
  ------ inclusion threshold ------
       0.11   12.7   2.7        6.8    6.9   0.1    3.4  3  COG5      Golgi transport complex subunit 5


Domain annotation for each model (and alignments):
>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         1   6.2e+03      16      29 ..      77      90 ..      72      91 .. 0.73
   2 !   15.9   0.0   1.6e-06    0.0094       2      51 ..     175     224 ..     175     225 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                                   HHHHHHHHHHHHHH CS
                          SNARE 16 nveraqkeLkkavk 29
                                   ++e++ +e++k+++
  gene731|gene731|rna730|rna730 77 RAEKGIEEIVKFSN 90
                                   57788888888765 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.6e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTXXXXXXXXXXXXXXXXXX CS
                          SNARE   2 mvDrIdtnVenaqsnveraqkeLkkavkyqksnRklkciillilviillv 51 
                                    ++Dr+d   ++++ ++e+a+keL k   + +   ++ +++ l+l i+l++
  gene731|gene731|rna730|rna730 175 QIDRLDFYLDSINFYLEGANKELGKIPGSHRRMKNKVIYFMLLLSIVLVL 224
                                    69*********************************************996 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.1   0.00032       1.9      10     111 ..      27     131 ..      24     138 .. 0.75
   2 !    7.4   0.1   0.00051       3.1     173     199 ..     146     172 ..     145     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00032
                       Syntaxin  10 eikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekks...gegsavd 86 
                                    +++ +++++++++++l+  +e+      + ++k k+++++  ++i+ + +  ++ +e++ k ++++  +    g  + + 
  gene731|gene731|rna730|rna730  27 SLRGSLDDVKQSISRLGIIQEKHCMPSFSPKKKKKDEIDEVKRHITDQIHRAEKGIEEIVKFSNSKVLTDcmhGYFAGQL 106
                                    6788899999999999988777665554445559************************9998887766555445556666 PP

                       Syntaxin  87 RirksqtaaLrkklkevmteynelr 111
                                          + +L++k+ + ++ y e+ 
  gene731|gene731|rna730|rna730 107 KAIIHDYRGLQQKFLKNIDIYDEID 131
                                    6666667777777777777777665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00051
                       Syntaxin 173 kevlelekslkeLhqlFldmavLVEeQ 199
                                    ++v++l ks+ +L  + ldm + V +Q
  gene731|gene731|rna730|rna730 146 ENVKDLRKSIYDLTSVLLDMKMAVGQQ 172
                                    579*********************999 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.015        92      73      91 ..      24      42 ..       8      49 .. 0.83
   2 ?    6.9   0.1    0.0011       6.8      33      94 ..      55     119 ..      45     129 .. 0.73
   3 ?    0.7   0.0     0.092   5.5e+02      73      95 ..     189     211 ..     134     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.015
                                   XXXXXXXXXXXXXXXXXXX CS
                           COG5 73 vlselksslesLsasyerl 91
                                   ++s+l++sl+++++s++rl
  gene731|gene731|rna730|rna730 24 STSSLRGSLDDVKQSISRL 42
                                   7899*************98 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0011
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-T CS
                           COG5  33 tplkrlnydiqeldkrlrqlitsnhleL..lehlskskslss.vlselksslesLsasyerlksk 94 
                                    +p k+ +  i+e++++++++i + ++ +  + ++s+sk l + +     ++l+++   y+ l++k
  gene731|gene731|rna730|rna730  55 SPKKKKKDEIDEVKRHITDQIHRAEKGIeeIVKFSNSKVLTDcMHGYFAGQLKAIIHDYRGLQQK 119
                                    578899999************99988773344556666666656666666666666666666665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.092
                                    XXXXXXXXXXXXXXXXXXXX-TT CS
                           COG5  73 vlselksslesLsasyerlkskv 95 
                                    +l+  +++l ++  s++r+k+kv
  gene731|gene731|rna730|rna730 189 YLEGANKELGKIPGSHRRMKNKV 211
                                    34444556666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1496.76
//
Query:       gene732|gene732|rna731|rna731  [L=140]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-47  158.4   2.4      1e-46  158.3   2.4    1.0  1  G10       G10 protein


Domain annotation for each model (and alignments):
>> G10  G10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   2.4   5.8e-51     1e-46      10     145 ..       6     138 ..       1     139 [. 0.94

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 5.8e-51
                            G10  10 kkppegfekiedtleeleaklreaekeskeskkkeeslWkiarinhersryvyelyykrkaiskelydyllkekyadaeL 89 
                                     +pp++fek++  le++ea++r+ae+++ +  ++ e++W+i++++h+rsr++y+l  k+ +is+ely yl  ++++d+eL
  gene732|gene732|rna731|rna731   6 VNPPKEFEKVRTFLENMEAEMRKAENAP-TVPNPPENYWPIFQLHHQRSRHIYNL-KKKGEISNELYRYLSLNQFVDHEL 83 
                                    579**********************998.5788999*******************.8999******************** PP

                            G10  90 iakWkkaGYekLcclrciqtkeanegstciCRvPkakleeekkfvecvkcGCrgca 145
                                    +  W+++GYe Lcclrc+q+ ++++g++ciCRvP+++++  +k+++c +cGCrgc+
  gene732|gene732|rna731|rna731  84 VCYWEREGYEGLCCLRCVQPIDSKHGNVCICRVPQRNIDV-NKAIKCDNCGCRGCS 138
                                    **************************************55.555***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 911.61
//
Query:       gene733|gene733|rna732|rna732  [L=511]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.8e-138  461.5   0.0   4.2e-138  461.3   0.0    1.0  1  G_glu_transpept  Gamma-glutamyltranspeptidase


Domain annotation for each model (and alignments):
>> G_glu_transpept  Gamma-glutamyltranspeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.3   0.0  2.4e-142  4.2e-138       6     512 .]       2     506 ..       1     506 [. 0.97

  Alignments for each domain:
  == domain 1  score: 461.3 bits;  conditional E-value: 2.4e-142
                                    TT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEE.EEEE--BB-TT--TTTTTSCBCCHHHHSSGGG-BB- CS
                G_glu_transpept   6 kGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkve.aldaretAPaaatkdmfdkegdsklsktgalavgVP 84 
                                    +GGnA+DAa+A+++c+g+++ +ssGiGGGgf+l++  +t+ v+ ++d+retAP++++ + +  +g   + ++ +l vgVP
  gene733|gene733|rna732|rna732   2 EGGNAMDAAIASTICIGIINSFSSGIGGGGFMLIKGPGTNGVLdMIDFRETAPRNLSDSGL--SGMGGANEK-GLKVGVP 78 
                                    7****************************************99899***************..666665555.578**** PP

                                    -HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TTSEE--HHHHH CS
                G_glu_transpept  85 GevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkagellkqpalAk 164
                                    Ge+ gl+eahkkyGklpw++l+   i +ar Gfp s+ l + +++ ++ +++dp+l+++++++g  lk+g+++ ++++Ak
  gene733|gene733|rna732|rna732  79 GEILGLYEAHKKYGKLPWRELFRENIMIAR-GFPASNLLVKKINKLKSYITSDPGLRDIYTRNGVLLKEGDIVARENYAK 157
                                    *****************************7.************************************************* PP

                                    HHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSHHHHHHHHHHHHCT CS
                G_glu_transpept 165 tLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssggivllqiLnileg 244
                                    tLe + ++ +e+FY+G+lA+ +v+ ++k+gG++ ++DL++ykv  r+ ++ +y  +y+vy+++ +++g+ +l +Lni e+
  gene733|gene733|rna732|rna732 158 TLEIIMRH-PESFYTGSLADLIVKAVRKKGGLIDKRDLEEYKVIHRDVIEGRY-HDYKVYTTNLPTSGPLVLKALNIFEK 235
                                    *****987.799*****************************************.9************************* PP

                                    TTGGGCTTTC.....HHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHTT.BTTB..SGGGCSCG CS
                G_glu_transpept 245 fdlkslssns.....aetlhllvEamklayadRsrylgDpdfvknptelveellskeyakeraklIkdkaatpsseyyka 319
                                    +dlk+l+ +s      +++hll+E++k+a+a R + lgDp f +  +e+v+e++sk+ a+e  ++I+  +  +  + y+ 
  gene733|gene733|rna732|rna732 236 YDLKKLKADSlrngnFNHMHLLIEVFKFAMARRGE-LGDPAFLPGWEEIVKEIISKKSAEEAYRKINLGKVLD-IKEYGM 313
                                    **9999998899999********************.*************************************.788888 PP

                                    GCSCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTTSTTB--TT----B- CS
                G_glu_transpept 320 aeaaeesggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldpspanaiePgkRplss 399
                                    + + +e++gTth++v+D+++++V lts+inl+FG++++ p+tG+++n+  ddf+  ++ a ++ ++++n +e gkR +ss
  gene733|gene733|rna732|rna732 314 KTKGTEDHGTTHINVIDKDNMVVLLTSSINLEFGAKFMDPETGVVFNDTIDDFH--ISHARDVHSKHPNNVEGGKRSFSS 391
                                    89999*************************************************..9999******************** PP

                                    ---EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEESSSSTEEEESTTS.HHHHHHHHHTTSE CS
                G_glu_transpept 400 maPtivlkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihhqllpdkvevEegfseevveeLearGhk 479
                                    m+P+++lk ++  l++GaaGG ri+++v+ ++++    g +l+ea+ + rih+ql p+ + vE+++++++ + L + Gh+
  gene733|gene733|rna732|rna732 392 MSPILLLK-EDEILAIGAAGGIRIPTSVISTIFHL-GTGENLREAIIETRIHNQLSPNITFVEHNIPKALERYLISIGHR 469
                                    *******9.7889*******************986.69****************************************** PP

                                    EEESSSTCCCEEEEEEEE....TTTEEEEEE-TTTTT CS
                G_glu_transpept 480 vkevedsssvvaavavak....ekgvleaasDprkdg 512
                                    ++++ +++ +++++ ++     ++  ++a+sDprk+g
  gene733|gene733|rna732|rna732 470 IEKSLQNTIFTSVQGIFLksvgGNRIIQAVSDPRKEG 506
                                    ****************9999*99************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.52
# Mc/sec: 2949.04
//
Query:       gene734|gene734|rna733|rna733  [L=413]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-38  130.9   0.0    8.4e-38  130.3   0.0    1.3  1  UCH       Ubiquitin carboxyl-terminal hydrolase
    7.7e-13   48.7   8.6    1.2e-12   48.1   2.5    2.9  2  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.0   9.4e-42   8.4e-38       2     255 ..     130     409 ..     129     410 .. 0.93

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 9.4e-42
                                    EES-SSSTHHHHHHHHHHHTSHHHH.HHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE--HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH   2 GlsNlGntCymnsvlQcLfsipelr.dyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskavsPkk 80 
                                    G+sNlGntCy+n++l +++++ ++r ++lls       +r +  ++       ++ +++a+k+l+ + ++  s +v ++k
  gene734|gene734|rna733|rna733 130 GFSNLGNTCYINAILSIMVNLSPIRdELLLS-------TRIRARCS------GSRCIICAMKSLIDSSYG--SGCVLTHK 194
                                    9************************999999.......45554443......22359**********995..89****** PP

                                    HHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCCHCCCHHHHHHCCCTTSHHHHHH-EEEEE............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                            UCH  81 lkktlsklaksfsgykqqDaqEflaflLdqlhedlnrevaeekwkkhlkrndslitdlfegqlks............... 145
                                    ++ t+  la+++++ +qqDa+Ef+  lL+++he+ +        + ++   ++l +++f g+++s               
  gene734|gene734|rna733|rna733 195 FIHTFWLLAPHLASPRQQDAHEFFICLLQKIHEAYSP------STIDDLVCRCLSHRIFFGTFSSttncrrcnlgrakee 268
                                    *************************************......577788999**************************** PP

                                    ...........................................EEEEEEB-SEEEEEEESEEETEEEEE--SEEB--SEE CS
                                    ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 146 ...........................................klklkrlPeiLiihlkRfsynssksKlntkvefpeel 182
                                                                               +l++k+ P+iL++h+kRfsy++ ++K++++v    +l
  gene734|gene734|rna733|rna733 269 afatisleclpsiqssldiffepedlkcemacntcktktlctrRLEVKKHPRILSLHMKRFSYDKVPRKIDSHVALSSTL 348
                                    ***************************************************************999***********999 PP

                                    E-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEECTTTTEEEEEETTEEEEE-HHCCCTT....CEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                            UCH 183 dlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayiknekngkWykydDetvkevkeeeevls....sayiL 255
                                    ++ +             + Y+  ++v+H+Gs + GHY +yi     gkW k+dDe+v+ v +  e+++    +ay L
  gene734|gene734|rna733|rna733 349 TIGK-------------RVYDILGFVSHYGSINCGHYLSYII--LGGKWHKIDDEKVDIVPHR-ELSTdglyTAYYL 409
                                    9985.............34***********************..89**************976.7777888888876 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4      0.12   1.1e+03     176     203 ..      27      55 ..       4     105 .. 0.60
   2 !   48.1   2.5   1.3e-16   1.2e-12       5     319 ..     133     389 ..     130     390 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.12
                                    xxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                          UCH_1 176 kvtfasilkss.lerekttrawCekCkry 203
                                    ++tf+ i+ +    +++  r+ C+kCk  
  gene734|gene734|rna733|rna733  27 EKTFKMIVSKLdCLKKRGVRPRCQKCKAT 55 
                                    45555555443122344556667777653 PP

  == domain 2  score: 48.1 bits;  conditional E-value: 1.3e-16
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1   5 nhivnsYlNslLQvlyfipplr.nlalshlak.eckkehcLlcElgflfdmldkakgl.ncqasnFlralssipeasalg 81 
                                    n  +++Y+N++L ++  + p+r +l+ls   + +c+   c++c +  l+d    + g+  ++++ F +++  +     l 
  gene734|gene734|rna733|rna733 133 NLGNTCYINAILSIMVNLSPIRdELLLSTRIRaRCSGSRCIICAMKSLIDS---SYGSgCVLTHKFIHTFWLLA--PHLA 207
                                    66789*****************98888766555*************99975...4555377999******9666..3333 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1  82 lileeeeetekssaislssliqsfnrflldqlekelketkknsseeesaieqllgtkaettirclkCgseksrksstlvl 161
                                      ++++                +f  +ll+++++ +++++ +        ++++  + ++t++c++C+  + +++ + ++
  gene734|gene734|rna733|rna733 208 SPRQQD--------------AHEFFICLLQKIHEAYSPSTIDDLVCRCLSHRIFFGTFSSTTNCRRCNLGRAKEEAFATI 273
                                    322221..............246***************988887777788889999************************ PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                          UCH_1 162 dlkyPkpsnekkeakvtfasilksslerektt.rawCekCkryqpteqrktvknlPpvLalnakle.eeeelelwktknw 239
                                    +l              +++s l  ++e e+ + +  C++Ck+++  ++r  vk+ P++L+l++k++  ++          
  gene734|gene734|rna733|rna733 274 SLEC----------LPSIQSSLDIFFEPEDLKcEMACNTCKTKTLCTRRLEVKKHPRILSLHMKRFsYDK---------- 333
                                    **44..........3689**********87664889****************************994444.......... PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 240 lpleiklsldedknleeklkeerekakaekeikvYeLqsvvvhigdskesghLvslvkvaekelerdppesqWylFNDfl 319
                                    +p++i+ ++  +             ++ + + +vY++ ++v h g s + gh+ s++             ++W++++D +
  gene734|gene734|rna733|rna733 334 VPRKIDSHVALS-------------STLTIGKRVYDILGFVSHYG-SINCGHYLSYIIL----------GGKWHKIDDEK 389
                                    566666544332.............245667889***********.666********97..........35788888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2439.01
//
Query:       gene735|gene735|rna734|rna734  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-50  171.6  20.1    3.2e-50  171.4  20.1    1.1  1  CTP_transf_1  Cytidylyltransferase family


Domain annotation for each model (and alignments):
>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4  20.1   1.8e-54   3.2e-50       3     266 .]      53     353 ..      51     353 .. 0.92

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 1.8e-54
                                    HHHHHHHHHHHHHHTTTSH.HHHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHH...........HHHHHHHHHHTTTSS CS
                   CTP_transf_1   3 RvitalvlilivliilllgglvflllvavvvilalkElirlvrlkkrekrllll........llslvlllllllflyles 74 
                                    R+++++v+i  +++i +  +++  +lv+++++ ++kE+i ++r+++ +  +l +         + l+l++ ++++ y+ +
  gene735|gene735|rna734|rna734  53 RMVLSIVMISGFFWICMNNKIYSYALVIFLTVSIIKEIIGITRKSDGKPFHLRVsiilgfavPIYLYLVFPSIMMMYFSE 132
                                    99****************************************99887765544444566655577888999999999999 PP

                                    SHHHHHHHHHHHHHHHHHH---........HHHHHHHHHHHHHHHHHTHHHH.TTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   CTP_transf_1  75 liallklvlllvlvllllvlkvl.....kskskklervilallallyvvlllqslllienikeglllvllllalvvaaDi 149
                                    + +++   l +++++  ++  ++     ++ + +l+  ++al+ l+   + + +   i n ++g ++++++ +lv+++Di
  gene735|gene735|rna734|rna734 133 VLRYFFRRLSSICFYSYVAAFMCfvgslRKGKLRLQLGLFALVNLSTYSMAMVAKCAIFNLNKGRFWFVFPALLVISNDI 212
                                    999999999999999888876558999988888888888888888877777779999*********************** PP

                                    HHHHHHHCH---B-S-TTS---BHHHHHHHHHHHHHHHHHHHHHHHCTS.........................---TTS CS
                   CTP_transf_1 150 gaYffGklfGktkllpkiSPkKTveGfigGlvaavvvglllalvlskal.........................alsllh 204
                                     aY +Gk++Gk+ +l ++SPkKT+eGfig++++++vvg++l ++  ++                          + +++h
  gene735|gene735|rna734|rna734 213 SAYAVGKSIGKR-PLYRLSPKKTLEGFIGAFIFTTVVGFILGYLHVNRGflrdeepiklrksmkfkvfsavfkiQSIYFH 291
                                    ************.*****************************999987789***************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHT-SSS-S-SSSSS-HHHHHHHHHHHHHHHHHHHHHH CS
                   CTP_transf_1 205 llllslllslvavfGDLveSglKRafgiKDsGkliPGhGGilDRlDsllfaapvvylllelf 266
                                    ++ + l++s+va+f ++++S+lKRa++ KD+G+ i GhGGi DR+D+++++a+++ +++++f
  gene735|gene735|rna734|rna734 292 IIPFILVASFVAPFSGFLASALKRAYKKKDFGEAISGHGGIADRMDCQVIIAIFTSTYISSF 353
                                    *********************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2372.05
//
Query:       gene736|gene736|rna735|rna735  [L=341]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2179.24
//
Query:       gene737|gene737|rna736|rna736  [L=425]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-33  114.0   0.0    1.5e-32  112.7   0.0    1.6  1  DEAD         DEAD/DEAH box helicase
    4.5e-28   97.8   0.4    1.1e-24   86.9   0.1    2.7  3  Helicase_C   Helicase conserved C-terminal domain
    3.9e-12   46.5   0.0      2e-11   44.2   0.0    1.9  2  ResIII       Type III restriction enzyme, res subunit
    0.00015   21.5   0.2    0.00037   20.2   0.0    1.6  2  SWI2_SNF2    SWI2/SNF2 ATPase
     0.0017   17.1   0.0     0.0025   16.6   0.0    1.3  1  SNF2_N       SNF2 family N-terminal domain
      0.002   17.7   0.0     0.0039   16.7   0.0    1.4  1  Terminase_3  Phage terminase large subunit


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   5.1e-36   1.5e-32       1     170 [.      79     233 ..      79     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 5.1e-36
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                    td+Q+ +ip+il ++++ v  +TGsGKTl +++p ++i+    +++ ++ l+++PtreL+ q+ + ++kf +  +l+v+ 
  gene737|gene737|rna736|rna736  79 TDVQRIVIPHILAKESIGVVSKTGSGKTLSYVLPYIHIL----ESEDKRLLVIVPTRELVSQVGQIFRKFSED-SLKVVE 153
                                    79**********************************999....57888************************6.699999 PP

                                    EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqr 160
                                    i+g+   ++q+ ++++  d++v+tpgrl +l++ ++  +  ++++V+DEadrl++ +f++++  il++       g   +
  gene737|gene737|rna736|rna736 154 ITGEMGIDSQRLQVSEPFDVIVSTPGRLKELVKLKS--IGGFEYVVIDEADRLMQHDFRNDVTFILEEA------GA--K 223
                                    ***99999999999777***************8777..9******************************......34..3 PP

                                    EEEEEESSBS CS
                                    xxxxxxxxxx RF
                           DEAD 161 qvivlSATlp 170
                                     + ++SAT+ 
  gene737|gene737|rna736|rna736 224 VISLFSATPF 233
                                    499*****85 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0011       3.3      10      71 ..     114     175 ..     105     178 .. 0.70
   2 ?   -1.7   0.0       1.2   3.5e+03       5      49 ..     180     230 ..     176     234 .. 0.71
   3 !   86.9   0.1   3.8e-28   1.1e-24      15     110 ..     291     381 ..     278     382 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                    H.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEE CS
                     Helicase_C  10 l.kleeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesdvLi 71 
                                    +  le+e+++ l++v+t++ +++  +++ +k+   ++kv+ ++ge+  ++++  +++     +dv++
  gene737|gene737|rna736|rna736 114 IhILESEDKRLLVIVPTRELVSQvGQIF-RKFsedSLKVVEITGEMGIDSQRLQVSEP----FDVIV 175
                                    246799*************887753333.4445568**********988776555444....35555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHTTTTSEEEEEESSHHHHHH......HHHHHHHTTSTEEEESTT CS
                     Helicase_C   5 allellkleeeggkilifvntidrlek......vklllekkgikvavlhge 49 
                                    +l+el+kl+++gg  ++++   drl +      v+++le+ g kv+ l + 
  gene737|gene737|rna736|rna736 180 RLKELVKLKSIGGFEYVVIDEADRLMQhdfrndVTFILEEAGAKVISLFSA 230
                                    567777888888888888888887744566667777788888888877665 PP

  == domain 3  score: 86.9 bits;  conditional E-value: 3.8e-28
                                    TTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS CS
                     Helicase_C  15 eggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp 94 
                                    e +ki++f+nti+++   + l++++   ++vlh++ + +er++++e+  ++e  vLiatd ++rGidi +v+lVin+dlp
  gene737|gene737|rna736|rna736 291 EIKKIVVFCNTIKTC---ESLHKRF-KGSLVLHSRRTMEERKAVVEAL-EEEKVVLIATDLGGRGIDIRDVDLVINYDLP 365
                                    569************...7887777.7788******************.66778************************** PP

                                    SSHHHHHHHHTTSSST CS
                     Helicase_C  95 rnvtsyiqriGRtgRa 110
                                    ++++ y++r GR+gR 
  gene737|gene737|rna736|rna736 366 KTIEVYVHRCGRAGRQ 381
                                    ***************6 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   6.8e-15     2e-11      26     170 ..      94     233 ..      76     234 .. 0.79
   2 ?   -0.4   0.0      0.34     1e+03      53      77 ..     291     315 ..     279     347 .. 0.71

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 6.8e-15
                                    EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG......GEEEESSS-B--....... CS
                         ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke..igkkvsgdkkkakekdstn 103
                                     + ++  TG+GKTl ++    ++l++++ ++ l++vp+++l++q  + f+kf+++  k   i++++  d++  + + s+ 
  gene737|gene737|rna736|rna736  94 SIGVVSKTGSGKTLSYVLPYIHILESED-KRLLVIVPTRELVSQVGQIFRKFSEDSLKVveITGEMGIDSQ--RLQVSEP 170
                                    5568999*********777777777644.6*************************9865443333222222..3466899 PP

                                    -SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHH.H...HHT---SEEEEEESS-S CS
                         ResIII 104 kkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswre.i...lekfkeavllglTATpe 170
                                     +++v+t  +l++         + ++ + f++++iDEa rl +   +r+ +   le   ++v+  ++ATp 
  gene737|gene737|rna736|rna736 171 FDVIVSTPGRLKELV-------KLKSIGGFEYVVIDEADRLMQH-DFRNdVtfiLEEAGAKVISLFSATPF 233
                                    999999999999999.......9999*****************5.444434444888888999999***96 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                                    ...-EEEEESSHHHHHHHHHHGGGG CS
                         ResIII  53 keekflflvprkslleqtleefkkf 77 
                                    +++k+++++++++ +e + ++fk  
  gene737|gene737|rna736|rna736 291 EIKKIVVFCNTIKTCESLHKRFKGS 315
                                    4569999999999999999999654 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.2e-07   0.00037      16     148 ..      91     220 ..      79     244 .. 0.73
   2 ?   -2.6   0.1       1.2   3.6e+03      48      95 ..     291     339 ..     279     345 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-07
                      SWI2_SNF2  16 gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageekpkqaesrkeL...kellek 92 
                                     +++ Gv+   +GSGK+l+ v+    +le   ++++++v++  ++L +Q+ + f+k++e++ k +e + e+    ++l+ 
  gene737|gene737|rna736|rna736  91 AKESIGVVSK-TGSGKTLSYVLPYIHILE--SEDKRLLVIVPTRELVSQVGQIFRKFSEDSLKVVEITGEMgidSQRLQV 167
                                    4578898865.6*********99888888..7899999999999***********9987776655555555223456654 PP

                      SWI2_SNF2  93 e.sekiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklrkalpna 148
                                    +   ++i++t  +++e    kl+ +   e  +v++DEa R  + ++++ ++ +l++a
  gene737|gene737|rna736|rna736 168 SePFDVIVSTPGRLKELV--KLKSIGGFE--YVVIDEADRLMQHDFRNDVTFILEEA 220
                                    437899999999996532..356666666..9999*****99999999999888875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
                      SWI2_SNF2  48 knpkvvvvtDRkdLdkQlsktfaka.geekpkqaesrkeLkellekese 95 
                                    + +k+vv        + l+k f+ +   ++ +++e+rk ++e le+e+ 
  gene737|gene737|rna736|rna736 291 EIKKIVVFCNTIKTCESLHKRFKGSlVLHSRRTMEERKAVVEALEEEKV 339
                                    5566666666666666666666665333344567777777777744333 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.5e-07    0.0025      98     215 ..     104     232 ..      10     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.5e-07
                                    -...................EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHHH-----------------EEEE-H CS
                                    x...................xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  98 p...................tLivvPa.slldqWeneierhvsssalrvlvyggqkkmkkkntkvapklladydvvittY 157
                                    +                    L++vP+ +l+ q + +i r  s+++l+v+  +g+       + +  ++ + +dv++ t 
  gene737|gene737|rna736|rna736 104 GktlsyvlpyihilesedkrLLVIVPTrELVSQ-VGQIFRKFSEDSLKVVEITGEM----GIDSQRLQVSEPFDVIVSTP 178
                                    033333333444444444448******666666.9999999*************74....3355688999********** PP

                                    HHHHHHT......TTS-S-S.-SEEEES-GGGT--T..TSHHHHHHHH---S-EEEE-S-- CS
                                    xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 158 dvlsreaelqkkrsvlkqve.wkrvvlDEghtlkns..tskaaeavskLstsnrwiltGTP 215
                                     +l++ +       +lk++   ++vv+DE+ +l ++   + ++ ++++  ++   + ++TP
  gene737|gene737|rna736|rna736 179 GRLKELV-------KLKSIGgFEYVVIDEADRLMQHdfRNDVTFILEEAGAKVISLFSATP 232
                                    ****666.......788887578**********9996667777777767676666777777 PP

>> Terminase_3  Phage terminase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.3e-06    0.0039       7     123 ..      97     217 ..      92     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                    Terminase_3   7 lvggrgssKsysialkivlkklkekrkalvl...RkvkntlkdSvfaeike.llselgltklfkilkskieielengskf 82 
                                    +v+  gs+K+ s +l  +  + +e+++ lv+   R+   ++ + +f ++ e  l+ +++t  + i +  ++++ +++ ++
  gene737|gene737|rna736|rna736  97 VVSKTGSGKTLSYVLPYIHILESEDKRLLVIvptRELVSQVGQ-IFRKFSEdSLKVVEITGEMGIDSQRLQVSEPFDVIV 175
                                    567789**********999999999999996344666666655.999998747999***********************9 PP

                    Terminase_3  83 lFkgl.ddpaklkSiknlsdlwlEEasevseedidelvetlr 123
                                       g  ++  klkSi  ++ ++++Ea  + ++d+ + v  + 
  gene737|gene737|rna736|rna736 176 STPGRlKELVKLKSIGGFEYVVIDEADRLMQHDFRNDVTFIL 217
                                    998876999************************987665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       784  (0.043728); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3500.75
//
Query:       gene738|gene738|rna737|rna737  [L=340]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-15   57.7   0.8    2.9e-15   57.3   0.8    1.2  1  Metallophos    Calcineurin-like phosphoesterase
    4.7e-13   49.7   0.0    2.6e-12   47.3   0.0    2.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.8   3.2e-19   2.9e-15       1     203 [.       1     221 [.       1     222 [. 0.71

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 3.2e-19
                                    EEEEEEESBTB.......TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH......... CS
                    Metallophos   1 lrilvigDlHl.......algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky......... 63 
                                    +ril+++D Hl        l + ++++++++l+ ++re k+dl+l  GDl++++ ++  +l+  +  l +y         
  gene738|gene738|rna737|rna737   1 MRILITSDNHLgykesdpVLLDDSYETFEEILKVAQRE-KVDLILQGGDLFHDNRPSRNCLNRaIGLLRSYcvgsersrl 79 
                                    89************999988889999999999888777.***************66666666657777777777777777 PP

                                    ...............TSEEEEEC-TTS...CHHH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEE...EETTE...EEEE CS
                    Metallophos  64 ...............pipvylllGNHe...gfee.ellnkygylgifsepwrsdaevfnnlplas...lgsgs...lkvl 118
                                                    ipv++++GNH+   g  + + l   +     s +  ++ ++++ +  ++   l        + +
  gene738|gene738|rna737|rna737  80 rsnrtlnshdqnitiSIPVVAIHGNHDdpsGINMvSPLDILQ-----SSGLVNYIGKYSLMERIDvfpL---LlekEYRV 151
                                    777888888888989************666322223333333.....3344344344444444442221...12233566 PP

                                    EEESE.CEEE..THHHHHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESE CS
                    Metallophos 119 llhGg.spel..lvsldklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkygvdl 195
                                     ++G   + +  l+     g+++++++++   d w++           +vl+   ++ +   + + + ++d+      dl
  gene738|gene738|rna737|rna737 152 AIYGLgHIKDrrLYRMFCEGKVVFHKPEDY--DSWYNI----------LVLHQNRVP-REKEHLSLDFIDDF-----FDL 213
                                    666664333368899999999******999..999999..........555555555.56666666666666.....9** PP

                                    EEEESSSS CS
                    Metallophos 196 visGHtHv 203
                                    vi+GH+H+
  gene738|gene738|rna737|rna737 214 VIYGHEHE 221
                                    *******7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   2.9e-16   2.6e-12       1     150 [.       1     241 [.       1     260 [. 0.70

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.9e-16
                  Metallophos_2   1 MklaiiSDlH............snldaleavlealkevgvdaiihaGD.....................leeeep..... 42 
                                    M+++i SD H            ++++  e++l+ +++++vd+i+  GD                     +          
  gene738|gene738|rna737|rna737   1 MRILITSDNHlgykesdpvlldDSYETFEEILKVAQREKVDLILQGGDlfhdnrpsrnclnraigllrsY----Cvgser 76 
                                    9***********************************************6555555555555555555550....055555 PP

                  Metallophos_2  43 .........evleellela.pvlaVrGNnD..............................................eev. 65 
                                             +++++ + +  pv+a++GN+D                                                + 
  gene738|gene738|rna737|rna737  77 srlrsnrtlNSHDQNITISiPVVAIHGNHDdpsginmvspldilqssglvnyigkyslmeridvfplllekeyrvaI-Yg 155
                                    55555443366666666669************************999999999888888655555555544333220.12 PP

                  Metallophos_2  66 ..veedvlreaaelgtdlpeeaelelagek.vlliHgdplgvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvv 141
                                      +++d+     ++++++  ++  + + +  +l++H+   +v+ + ++l  +  ++ + +v++GH H+ +v+ke ++l++
  gene738|gene738|rna737|rna737 156 lgHIKDRRLYRMFCEGKVVFHKPEDYDSWYnILVLHQN--RVPREKEHLSLDFIDDFFdLVIYGHEHESRVTKE-ERLIL 232
                                    22333333333333333333333333444379999999..8888888888886666667**************9.89*** PP

                  Metallophos_2 142 nPGsvgepr 150
                                     PGs  + +
  gene738|gene738|rna737|rna737 233 QPGSTVRTS 241
                                    ****87764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2298.96
//
Query:       gene739|gene739|rna738|rna738  [L=255]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-13   49.9   0.4    1.2e-12   48.4   0.0    1.9  2  Mre11_DNA_bind  Mre11 DNA-binding presumed domain
  ------ inclusion threshold ------
       0.38   11.7   3.0        2.4    9.1   0.1    2.6  2  Prp31_C         Prp31 C terminal domain


Domain annotation for each model (and alignments):
>> Mre11_DNA_bind  Mre11 DNA-binding presumed domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.0   1.4e-16   1.2e-12      59     166 ..      27     119 ..       3     122 .. 0.75
   2 ?   -1.4   0.1      0.28   2.5e+03     101     107 ..     154     160 ..     124     196 .. 0.56

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 1.4e-16
                                    STTS------EEEEEEE-TTT-----HHHHHHCCCTTBS-SSSSEEEE-S-XXXXXXXXXXXXXXX......XXXXXXXX CS
                 Mre11_DNA_bind  59 eaeeeepplPLiRLrVdysggfevenpqrfgqrFvgkVANpndvlqfyrkkkarkkkkkekaaakeeeellaeaekldkl 138
                                      +ee+   P+iRL+V+   g ++++ +rf+ +F g VANpnd+l + rk+ +r++ + ++ ++++             +
  gene739|gene739|rna738|rna738  27 YLHEEKSYIPMIRLKVELH-GNDMFDRHRFSTQFKGLVANPNDMLSISRKTGRREEIEVHQPDEEK-------------V 92 
                                    557888899**********.******************************9988876655444444.............5 PP

                                    XCHHHHHHHHHHS.XXTTSXHHHHHHHH CS
                 Mre11_DNA_bind 139 kvedlVkeyleaqekLkllpekglneAv 166
                                    ++  + +++l +  +  +l+   ++e++
  gene739|gene739|rna738|rna738  93 EITHILRKILGNV-EFGVLNRLCFSESL 119
                                    5555555555555.55555555555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.28
                                    SSEEEE- CS
                 Mre11_DNA_bind 101 dvlqfyr 107
                                    dv++ ++
  gene739|gene739|rna738|rna738 154 DVIKAMK 160
                                    3333333 PP

>> Prp31_C  Prp31 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00027       2.4      39      97 ..     110     170 ..      89     205 .. 0.63
   2 ?    2.3   0.3     0.035   3.1e+02      16      30 ..     229     243 ..     224     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                        Prp31_C  39 qNRmaFGkeeeevgqgdetgkglGmlgkk..a.sgriraaqvdkktkaklskklkkklqrss 97 
                                     NR+ F++  ee+  gd++   +Gm++k+  +    i  +++  +  +k+ kk +++  rs 
  gene739|gene739|rna738|rna738 110 LNRLCFSESLEEYVRGDSN-AFMGMIRKNieKvIDTIDHSSIVDEDVIKAMKKISREEDRSY 170
                                    59************98887.9*******9421223333322222223444444433333332 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.035
                        Prp31_C  16 kkRGGrraRkaKerl 30 
                                    +k  G+r+Rk Ke  
  gene739|gene739|rna738|rna738 229 RKYLGKRVRKNKEDS 243
                                    5666********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1685.43
//
Query:       gene740|gene740|rna739|rna739  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.56
# Mc/sec: 896.37
//
Query:       gene74|gene74|rna74|rna74  [L=162]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.19   11.5   0.0    1.3  1  DUF2153   Uncharacterized protein conserved in archaea (DUF21
       0.14   12.0   0.2         19    5.3   0.0    2.8  3  DUF1641   Protein of unknown function (DUF1641)


Domain annotation for each model (and alignments):
>> DUF2153  Uncharacterized protein conserved in archaea (DUF2153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.2e-05      0.19      40     121 ..      68     149 ..      57     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                    DUF2153  40 qhmmrtlkaFdqWLqdPviishmpremLldvketlrei.lekllelDieHtsevrelleklskegklnpllalekeaeeekee 121
                                  ++  lk+ d +    ++ s   r m +dv++  r++ + +ll++ i+H  ++  l+  l  e+k n + +lek  +ee+++
  gene74|gene74|rna74|rna74  68 PKLVGLLKDKDIYNASAFMLSDACRHM-EDVQNAFRALgVFELLDFTIDHYRATTSLVYSLCMENKPNTIYFLEKYYNEERDK 149
                                555666677777777777777778876.89999999986689*******************************9988888765 PP

>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0069        62      19      27 ..      36      44 ..      34      45 .. 0.93
   2 ?    5.3   0.0    0.0021        19      13      23 ..      69      79 ..      69      88 .. 0.81
   3 ?   -1.7   0.0      0.31   2.8e+03      25      27 ..     102     104 ..      95     110 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0069
                    DUF1641 19 rDPDVqrGL 27
                               +DP+V+ GL
  gene74|gene74|rna74|rna74 36 NDPEVRNGL 44
                               8******98 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0021
                    DUF1641 13 gLlraLrDPDV 23
                               +L+++L+D+D+
  gene74|gene74|rna74|rna74 69 KLVGLLKDKDI 79
                               599*******9 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.31
                    DUF1641  25 rGL 27 
                                r+L
  gene74|gene74|rna74|rna74 102 RAL 104
                                333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 986.91
//
Query:       gene741|gene741|rna740|rna740  [L=958]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   14.4   0.1      0.097   13.0   0.1    1.7  1  Fer2_BFD  BFD-like [2Fe-2S] binding domain


Domain annotation for each model (and alignments):
>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.4e-06     0.097      23      46 ..     186     210 ..     181     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-06
                       Fer2_BFD  23 ttveevkrrtkagtg.CggCrpaie 46 
                                     +ve + ++ ka+tg C++C+p++ 
  gene741|gene741|rna740|rna740 186 EEVERIGEAIKASTGdCKKCIPEAS 210
                                    6799******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (958 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.81u 0.31s 00:00:01.12 Elapsed: 00:00:00.53
# Mc/sec: 5433.73
//
Query:       gene742|gene742|rna741|rna741  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-16   58.1   0.2    6.7e-16   57.7   0.2    1.2  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.039   14.1   0.1      0.064   13.4   0.1    1.3  1  DUF150_C  RimP C-terminal SH3 domain
        0.1   12.3   0.0       0.16   11.6   0.0    1.3  1  Hfq       Hfq protein


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.2   1.1e-19   6.7e-16       3      66 ..      12      77 ..      10      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.1e-19
                                   HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTET..EEEEEEEEEEEGGGEEEEE CS
                            LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkk..ekrklglvliRGnnivlis 66
                                    +k+++++++v l++gr l G++k+fDqf  + L+ v+e++ + +   +rk +l++iRG+ni++i+
  gene742|gene742|rna741|rna741 12 YEKYLEQEIVVVLRDGRYLYGIMKSFDQFNSITLDRVIERIFHDEkyAERKHELFIIRGENITMIG 77
                                   689***************************************9999******************97 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.064       4      48 ..       9      50 ..       7      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                       DUF150_C  4 aedFarflGelVkvklklpvegrkkftGkivevdeet.itlevdgk 48
                                    +d++++l +++ v+l+    +++ + G+ +++d+ + itl+++ +
  gene742|gene742|rna741|rna741  9 TRDYEKYLEQEIVVVLR----DGRYLYGIMKSFDQFNsITLDRVIE 50
                                   59***************....*************8777*9998766 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.7e-05      0.16      15      37 ..      19      41 ..      13      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.7e-05
                                   EEEEEETTS-EEEEEEEEE-SSE CS
                            Hfq 15 pvtifLvnGiklkGviksfDnft 37
                                   ++++ L  G  l G++ksfD+f 
  gene742|gene742|rna741|rna741 19 EIVVVLRDGRYLYGIMKSFDQFN 41
                                   7999*****************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 633.58
//
Query:       gene743|gene743|rna742|rna742  [L=180]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-09   38.5   0.6    2.3e-09   38.0   0.6    1.3  1  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
    9.2e-07   28.5   0.0    2.7e-06   27.0   0.0    1.8  1  S4            S4 domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.6   2.5e-13   2.3e-09       2      81 ..       4      63 ..       3     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 2.5e-13
                                   T-S-CHHHHCHCTS-STSSSS-S-SSTTTTS-----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHHH CS
                   Ribosomal_S4  2 ykgpkckllRrvgfklflkgreyppGqhgkrrkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlql 81
                                   +k +++kll+rv+f                      e+++ ++ +++ ++ rYgl+ ++++ +y++++++ir k++e L++l
  gene743|gene743|rna742|rna742  4 LKFHEKKLLKRVDFL---------------------EWKNtNTAREHLAIVRYGLRdREEYVKYNRIVGKIR-KLAEALSRL 63
                                   689************.....................************************************.******984 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     3e-10   2.7e-06       1      43 [.     106     148 ..     106     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3e-10
                                    EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE- CS
                             S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVk 43 
                                    rRL  v++r+++++  + A +++ehG+V++  kv+ dps++++
  gene743|gene743|rna742|rna742 106 RRLPMVMKRIRMVPNFKDATRFVEHGHVRLGSKVIYDPSTIIS 148
                                    8**************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1148.91
//
Query:       gene744|gene744|rna743|rna743  [L=178]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-16   59.5   3.8    5.6e-16   58.4   3.8    1.7  1  zf-DBF       DBF zinc finger
     0.0077   16.4   0.6      0.015   15.5   0.1    1.7  2  Dfp1_Him1_M  Dfp1/Him1, central region


Domain annotation for each model (and alignments):
>> zf-DBF  DBF zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   3.8   6.2e-20   5.6e-16       2      44 ..      63     105 ..      62     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 6.2e-20
                         zf-DBF   2 ksGYCEnCrvkfedleeHlksekHrkFaenssnfeelDelisk 44 
                                    ++G+CE+C v+f+++eeH+++ +Hr+Fa+++sn+++lD +is+
  gene744|gene744|rna743|rna743  63 REGFCEICYVRFNNYEEHIEEFEHREFAKDNSNYKKLDIFIST 105
                                    68***************************************97 PP

>> Dfp1_Him1_M  Dfp1/Him1, central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.7e-06     0.015      73     113 ..       2      34 ..       1      53 [. 0.72
   2 ?   -1.9   0.0       0.4   3.6e+03      79     106 ..      68      95 ..      49     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-06
                    Dfp1_Him1_M  73 kdlhyFkgpyvlveDleqelrpiivreykkeakkekdgewP 113
                                    k++++Fk+py+l+eD++++ +p+  +ey +  ++      P
  gene744|gene744|rna743|rna743   2 KSYKVFKKPYILIEDCKNKCQPF-YKEYVN--SDA-----P 34 
                                    67899*****************7.689944..222.....3 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.4
                    Dfp1_Him1_M  79 kgpyvlveDleqelrpiivreykkeakk 106
                                    +  yv  + +e+++  +  re++k+ ++
  gene744|gene744|rna743|rna743  68 EICYVRFNNYEEHIEEFEHREFAKDNSN 95 
                                    5566666777777777777777765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1248.49
//
Query:       gene745|gene745|rna744|rna744  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-34  117.1   0.0    7.8e-34  116.8   0.0    1.1  1  Proteasome      Proteasome subunit
      0.002   17.8   0.0     0.0051   16.5   0.0    1.7  1  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
       0.09   12.8   0.0       0.34   11.0   0.0    1.9  3  DUF1106         Protein of unknown function (DUF1106)


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.0   1.3e-37   7.8e-34       1     176 [.      27     192 ..      27     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 1.3e-37
                                    HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC CS
                     Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpip 80 
                                    v+k++t++G  + dg+vl++ ++ +      ++  +eKi++++d+i++a++Gl++Da  + r+ar++aq+   ++g + p
  gene745|gene745|rna744|rna744  27 VSKAGTIIGYVCVDGIVLIGINKEP------TNGPMEKIYQLSDNIYCALCGLFGDAMRIKRYARVKAQEALEKFGVECP 100
                                    57899***************97777......66778******************************************** PP

                                    HHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH.STTBS CS
                     Proteasome  81 verlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey.kedlt 159
                                    + +l++++ +k+qa tq++g rpfg+s+l+agv   g++ L+++dpsG++ +++  ++ G+++ea+ + l++ + +e+++
  gene745|gene745|rna744|rna744 101 LTTLCKAIGQKKQAFTQYAGTRPFGASFLYAGVM-GGEYALFSTDPSGTLNRWR-GMCYGENEEAINGGLKNDMpEEEME 178
                                    **********************************.889***************5.*******************666666 PP

                                    HHHHHHHHHHHHHHHHH CS
                     Proteasome 160 leeavelavkalkeale 176
                                    ++ a      +lk + +
  gene745|gene745|rna744|rna744 179 MKMATIE---ILKLLGK 192
                                    6655444...4444444 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.5e-07    0.0051       6      22 ..       9      25 ..       6      25 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.5e-07
                 Proteasome_A_N  6 ttFSPdGRLfQVEYAmk 22
                                   +tF+ +GRL QVE A+k
  gene745|gene745|rna744|rna744  9 NTFTDEGRLPQVEFAIK 25
                                   8**************98 PP

>> DUF1106  Protein of unknown function (DUF1106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.6e-05      0.34      26      81 ..      22      77 ..      11      82 .. 0.89
   2 ?   -2.9   0.0       1.2   7.1e+03      67      86 ..     161     180 ..     150     183 .. 0.70
   3 ?   -3.0   0.0       1.3     8e+03      73      86 ..     192     205 ..     189     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.6e-05
                        DUF1106 26 fsilcgrlrgivltikcskgiiylsikvspnnrkhvllynkkeyvfdklkelfpde 81
                                   f+i      g ++ + c +gi+ + i+ +p n     +y+  + ++  l  lf d 
  gene745|gene745|rna744|rna744 22 FAIKNVSKAGTIIGYVCVDGIVLIGINKEPTNGPMEKIYQLSDNIYCALCGLFGDA 77
                                   5555566679999************************************9999884 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                        DUF1106  67 keyvfdklkelfpdeaiefs 86 
                                     e +   lk+ +p+e +e+ 
  gene745|gene745|rna744|rna744 161 EEAINGGLKNDMPEEEMEMK 180
                                    45566678888888888865 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.3
                        DUF1106  73 klkelfpdeaiefs 86 
                                    k++el p ea  + 
  gene745|gene745|rna744|rna744 192 KIRELGPKEADRME 205
                                    77777777775444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1501.90
//
Query:       gene746|gene746|rna745|rna745  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-11   42.0   0.8    9.8e-11   41.5   0.8    1.3  1  PUA       PUA domain
     0.0051   17.5   0.1      0.021   15.5   0.1    1.9  1  Pre-PUA   Pre-PUA-like domain
  ------ inclusion threshold ------
      0.047   14.0   1.1       0.17   12.2   1.1    2.0  1  DUF1947   Domain of unknown function (DUF1947)


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.8   1.6e-14   9.8e-11       2      72 ..      82     156 ..      81     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.6e-14
                                    EEEE-HHHHHHHHTT-EEEGGGEEEEETT-....-TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                            PUA   2 rvvvddgAvkallsgasLlapGvvevegdf....eegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                    ++ +ddgA   l++ga++++pG++++++ +    e+gd+V+i   +  +va+G a  s +e+ +   g++ve+ +
  gene746|gene746|rna745|rna745  82 EIFLDDGALGPLCRGADVMIPGILKYKDLIkkefEAGDTVVIRIVGKSIVAIGEAVISLQEMVSKGNGVGVEVYH 156
                                    6899*********************987555555******************************99999999866 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.6e-06     0.021      39      85 ..      31      75 ..       5      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                        Pre-PUA 39 ellpkkeevkvvklqgehvelyvvdgeplffqdregellPtlytlwk 85
                                   ell k+e  ++ +++ ++v+l++ +g  ++f + + +++Pt++ l k
  gene746|gene746|rna745|rna745 31 ELLEKNEAYMIHRCK-NKVSLVSLGGVAILFFF-NRKYFPTIRYLEK 75
                                   688999999999***.***********888888.789******9976 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   2.9e-05      0.17       5      66 .]      16      76 ..      15      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                                   --HHHHHHHHHHHHTTT---TT--...-EEEE-S.S-EEEEETTEEEEEE.SSSEEE-HHHHHHS CS
                        DUF1947  5 LSkKeakeileklkekyisislesdk.iEieeek.keklYlingvpilfe.eekliPtLklLlki 66
                                   L kK++k+i ++l  +     le+++   i   k k +l   +gv ilf+ + k +Pt+++L k+
  gene746|gene746|rna745|rna745 16 LGKKDKKDINKRLGYEL----LEKNEaYMIHRCKnKVSLVSLGGVAILFFfNRKYFPTIRYLEKH 76
                                   56888888888887777....333333557777746677889999999999***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1145.25
//
Query:       gene748|gene748|rna747|rna747  [L=364]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-07   28.8   0.0    1.6e-06   27.9   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
    4.3e-05   23.9   0.0    5.2e-05   23.6   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
      5e-05   22.9   8.1      0.041   13.6   2.8    2.7  2  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00016   20.8   2.0    0.00028   19.9   0.9    1.9  2  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
      0.016   14.8   0.1      0.032   13.8   0.1    1.6  1  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   4.6e-10   1.6e-06       4     138 ..       5     130 ..       3     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 4.6e-10
                                    EE--S--GGGTTC.CTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
                NTP_transferase   4 ILaGGsGtRLwPL.trtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                    I+  G Gt L+P+ + + +k  +p++++ ++i +t++ l + + +  +v l++e++ l++   ++++   v v+++  + 
  gene748|gene748|rna747|rna747   5 IILIGPGTELFPIvSEKFSKACLPIMNS-PMILHTMECLRSISKKFFVVGLNEEKEDLMNAIKGRID---VPVEYVGIDT 80 
                                    555589******8466677777888888.*******9998655555555577777777777777765...779******* PP

                                    --BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEE CS
                NTP_transferase  83 gkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfg 138
                                     +gt  +++ +   +  e+    vlv  gD++++++++++  +  ++++  + +++
  gene748|gene748|rna747|rna747  81 YDGTVASLLNVYPRISSED----VLVCKGDIVTNMDIQAMASNYFNEKK--MFMVI 130
                                    ****999999999999888....8*****************99999888..33322 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.5e-08   5.2e-05      15     118 ..      23     127 ..       5     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.5e-08
                                    THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTC......TS-EEE-TTSS-SHHHHHHHHHHHH.SSSC CS
                   NTP_transf_3  15 dKallplggkpllervldalraagvdevvvvggdeevlaalarl......gvrvvededpgkgplaslaaalraaadada 88 
                                     Ka lp+ + p++ ++++ lr+   ++ +vvg +ee ++ ++        +v++v   d + g++asl+    ++ +++ 
  gene748|gene748|rna747|rna747  23 SKACLPIMNSPMILHTMECLRSI-SKKFFVVGLNEEKEDLMNAIkgridvPVEYVGI-DTYDGTVASLLNVYPRI-SSED 99 
                                    7**********************.689999987766555443333225445666665.5799************9.8*** PP

                                    EEEEETT-TT--HHHHHHHHHCHHHHTSSE CS
                   NTP_transf_3  89 vlvlacDmPlltpelverllaaaaasgadv 118
                                    vlv+ +D+  +t   +++++ ++ ++++  
  gene748|gene748|rna747|rna747 100 VLVCKGDI--VTNMDIQAMASNYFNEKKMF 127
                                    *******9..68999999998876555443 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   4.9e-05      0.18       3      28 ..     277     306 ..     277     306 .. 0.95
   2 !   13.6   2.8   1.2e-05     0.041       2      33 ..     309     339 ..     308     342 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.9e-05
                                    EEETTEEE-T....TEEEETTEEE-TTEEE CS
                        Hexapep   3 vIGsnvlIgp....faviggnVkIGdnvkI 28 
                                    v+Gsn++ ++     ++ig+++ IG+ +kI
  gene748|gene748|rna747|rna747 277 VVGSNTKTDNvlllDSIIGSGCDIGEESKI 306
                                    69*************************998 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvv 33 
                                    +++ +nv Ig++++i ++ +IG ++ I +g++
  gene748|gene748|rna747|rna747 309 SIVMNNVSIGNGSHI-EGSVIGMGANIFSGST 339
                                    678899999999999.5555999998876666 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.19   6.7e+02      49      68 ..      97     116 ..      71     159 .. 0.63
   2 !   19.9   0.9   7.9e-08   0.00028     254     324 ..     273     334 ..     235     355 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.19
                     Fucokinase  49 kpGvlvtssDvlllfdseei 68 
                                    ++ vlv+ +D +  +d + +
  gene748|gene748|rna747|rna747  97 SEDVLVCKGDIVTNMDIQAM 116
                                    66777777777765532222 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 7.9e-08
                     Fucokinase 254 sltstafsaiknkkekkkesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslel 324
                                     l++ + s      ++k+++++ ++S++ s++++ge+s i +s + +nvsig++s + g  +  +++   +
  gene748|gene748|rna747|rna747 273 DLSNVVGS------NTKTDNVLLLDSIIGSGCDIGEESKIISSIVMNNVSIGNGSHIEGSVIGMGAN---I 334
                                    23333322......33477788888888888888888888888888888888888777777665544...3 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     9e-06     0.032      12      72 ..     120     179 ..     109     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9e-06
                                    SSSSESSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHH CS
                 RNA_pol_Rpb2_2  12 dknkisatvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIler 72 
                                    + n+  +++  +l+ +++ ++ l  +g++l++   + +++ip++++ k l l++d +Il+ 
  gene748|gene748|rna747|rna747 120 YFNEK-KMFMVILENSTSETSILGYKGDDLMFYSNDSNEEIPFHLLKKGLTLTKDLDILQL 179
                                    45555.88999999999999999*9******9999************************94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2456.16
//
Query:       gene749|gene749|rna748|rna748  [L=407]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-08   32.5   0.0      2e-07   31.0   0.0    1.6  2  Peptidase_M48  Peptidase family M48


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.16   2.9e+03      87     114 ..      74     101 ..      66     121 .. 0.65
   2 !   31.0   0.0   1.1e-11     2e-07      12     190 ..     217     399 ..     213     401 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHHHHTT-SHHHHHTT-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  87 sllasillllglallisraeedaagafl 114
                                    + +++++l++ ++lli + + +++ a l
  gene749|gene749|rna748|rna748  74 KEVKRFMLYISVVLLIFNSKFRRRVAEL 101
                                    5567777777777777666665555444 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 1.1e-11
                                    HHHHHHTT-..-EEEEEEE-GGGT.-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  12 eelakeaglpkpltkvyvvnspkr.NAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivslla 90 
                                    +e++k+ g+   +  +y+v+++k  NA  +g g  kri ++ +     ++ + l  +  HE+GH   +  +++ i  +l 
  gene749|gene749|rna748|rna748 217 QEIIKSEGM---EESIYEVKGSKEkNASQVGLGSFKRIEIYGDFS---KDAKKLYPISFHEMGHSIDNIILKRKILLHLI 290
                                    566666666...6788888877767********999*******99...55566666666**************9999999 PP

                                    HHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT..........HHHHHHHHHHHHHHHHTTT.HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  91 sillllglallisraeedaagafldalavliglliillfl..........alSRkrEyqADeagvellkrakdlvralik 160
                                     ++  l+l+++++ +++   +  +++ a++++++ + l++           +  ++E+ ADe+++  ++  ++l ++l +
  gene749|gene749|rna748|rna748 291 VVCEVLVLSFIYRKESRTFGFSDISSEAFVLIIVVMYLVIgrplvfipsnIYAQRSELFADEVAKINGY-GRELSQTLLD 369
                                    9999999999998888877777777777766666666666**********9******************.99******** PP

                                    HHHHTT--S---HHHHHHS-SS--HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 161 lakdlerqdvsaslrsellstHPplleRiq 190
                                    +  +++ + +++ l+++++s HP   eRi 
  gene749|gene749|rna748|rna748 370 MTLEHNATIDTTYLFNAITSLHPVARERID 399
                                    ****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2789.12
//
Query:       gene750|gene750|rna749|rna749  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-17   62.2   0.2    2.5e-11   43.6   0.0    2.9  3  Glutaredoxin  Glutaredoxin
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.22   11.9   0.0    1.4  1  GST_N         Glutathione S-transferase, N-terminal domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-06     0.015      16      58 ..      30      72 ..      27      74 .. 0.92
   2 ?   -1.3   0.0       0.3   2.7e+03      34      44 ..      79      89 ..      73      94 .. 0.74
   3 !   43.6   0.0   2.8e-15   2.5e-11       1      60 []     106     173 ..     106     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-06
                                   HHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTE CS
                   Glutaredoxin 16 krlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgk 58
                                     +Lk+  +++ e+d+   e++r e ++  +v ++P ++i g 
  gene750|gene750|rna749|rna749 30 YSTLKDIDIDYVEVDLGVSEKLRMEFMKHFDVAKLPALVIRGT 72
                                   57899***********************************996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
                                   SHHHHHHHHHH CS
                   Glutaredoxin 34 deeireelkel 44
                                   d+ ire++ke+
  gene750|gene750|rna749|rna749 79 DKGIREYIKER 89
                                   4599***9997 PP

  == domain 3  score: 43.6 bits;  conditional E-value: 2.8e-15
                                    EEEEES.....TSSHHHHHHHHHHHHTTGG...EEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
                   Glutaredoxin   1 vvlftk.....ptCpyCkkakrlLkelgvk...feeidvdkdeeireelkelsgvrtvPqvfidgkhv 60 
                                    vvlf k     p C++ +   ++L + gv    ++++dv+ de++r+ lk++++++t+Pqv+i+++++
  gene750|gene750|rna749|rna749 106 VVLFIKgspehPKCGFTRILMDVLLREGVTrdkIAYFDVLSDEDVRKGLKKINNWPTFPQVYIGNRFI 173
                                    89**************************98888********************************997 PP

>> GST_N  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.22      23      64 ..      33      74 ..      27      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                                   HTT-EEEEEEECSTTTCGGCHHHHHHCTTS-SSEEEETTEEE CS
                          GST_N 23 akgveyevvpldfeageekspellklnplgkvPaLedngkkl 64
                                    k++++ +v++d++ +e+ + e++k +  +k+PaL+++g ++
  gene750|gene750|rna749|rna749 33 LKDIDIDYVEVDLGVSEKLRMEFMKHFDVAKLPALVIRGTPV 74
                                   46778888888888888888*****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1430.24
//
Query:       gene75|gene75|rna75|rna75  [L=95]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-07   31.8   0.2    1.4e-07   31.5   0.2    1.2  1  HTH_3           Helix-turn-helix
    0.00032   21.0   0.0    0.00039   20.7   0.0    1.2  1  HTH_31          Helix-turn-helix domain
     0.0029   17.6   0.2      0.004   17.1   0.2    1.2  1  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   15.1   0.2       0.03   14.7   0.2    1.3  1  Linker_histone  linker histone H1 and H5 family
      0.029   14.2   0.0      0.037   13.9   0.0    1.2  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.037   13.9   0.0      0.051   13.4   0.0    1.2  1  HTH_25          Helix-turn-helix domain
      0.081   13.7   0.2       0.11   13.3   0.2    1.1  1  Ribosomal_L28e  Ribosomal L28e protein family
       0.17   12.6   0.0       0.23   12.1   0.0    1.1  1  RPA_C           Replication protein A C terminal


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.2   6.2e-11   1.4e-07       1      54 [.      41      94 ..      41      95 .] 0.93

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 6.2e-11
                               HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                      HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54
                               ++ +R  +g+s+++LA+kl   +s i  +E+Ge+  + +++ +++k L  ++ +
  gene75|gene75|rna75|rna75 41 IANARTRKGMSRKDLAQKLKKNVSVIDSWERGEAPYNEKIASEIEKLLEFKINW 94
                               6789*****************************************999877766 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.7e-07   0.00039       2      40 ..      37      75 ..      36      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-07
                     HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrg 40
                                G+  + +R+r G+s++++A+ l   +s +  +E+G+ +
  gene75|gene75|rna75|rna75 37 VGDAIANARTRKGMSRKDLAQKLKKNVSVIDSWERGEAP 75
                               5888899*****************************984 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   1.8e-06     0.004       1      50 [.      38      89 ..      38      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.8e-06
                     HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvps....aelllkiae 50
                               G+ +  aR  +g++ ++la++l+ + s i  +E g+   p+    a+++ k++e
  gene75|gene75|rna75|rna75 38 GDAIANARTRKGMSRKDLAQKLKKNVSVIDSWERGE--APYnekiASEIEKLLE 89
                               78899****************************993..2333344666677666 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   1.4e-05      0.03       8      44 ..      37      74 ..      31      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
             Linker_histone  8 ikeAIkalkerkGsSrqaIkkyikakykvv.dvskfks 44
                               + +AI++  +rkG+Sr  + + +k++ +v  + ++ + 
  gene75|gene75|rna75|rna75 37 VGDAIANARTRKGMSRKDLAQKLKKNVSVIdSWERGEA 74
                               669***********************999863344444 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.037      10      51 ..      51      92 ..      43      95 .] 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
             YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpaervpeIekatnGeV 51
                               ++k LA++l    + +  W +g+ + + +   eIek+ ++++
  gene75|gene75|rna75|rna75 51 SRKDLAQKLKKNVSVIDSWERGEAPYNEKIASEIEKLLEFKI 92
                               7899****************9*999************99998 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.3e-05     0.051       3      33 ..      42      72 ..      40      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                               HHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                     HTH_25  3 raaRearglsleevaketkIrkdylealEed 33
                                +aR ++g+s++++a+++k  ++++   E++
  gene75|gene75|rna75|rna75 42 ANARTRKGMSRKDLAQKLKKNVSVIDSWERG 72
                               68*****************888888777766 PP

>> Ribosomal_L28e  Ribosomal L28e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   4.7e-05      0.11      53     112 ..       3      66 ..       1      68 [. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
             Ribosomal_L28e  53 ekkgvvlvtkkkerahkpak.awekvkls...knsrkalkqiakllkky.rpdlrkaalaRlski 112
                                ++k ++l+ kk+e +++p+  + e v+++   k++  a+ + +++ k+  r+dl+++ ++ +s i
  gene75|gene75|rna75|rna75   3 DNKPIILTKKKPEGQNRPKGpNPEDVEVKmvsKEVGDAIANARTR-KGMsRKDLAQKLKKNVSVI 66 
                                5788999999**999999532556666661125555555555555.6677*******99988765 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001      0.23      27      84 ..      12      66 ..       5      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                               XXXXXXXXXXXXXXXXXX.XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHH CS
                      RPA_C 27 samgtdgalsgnqaklankgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndv 84
                               ++ ++++ ++g + ++++  ++ + ++v ++i + +++ +G++ + +aqkl+ +v+ +
  gene75|gene75|rna75|rna75 12 KKPEGQNRPKGPNPEDVE--VKMVSKEVGDAIAN-ARTRKGMSRKDLAQKLKKNVSVI 66
                               556788999999999999..9*************.****************6665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 585.78
//
Query:       gene751|gene751|rna750|rna750  [L=404]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-13   49.7   0.0    6.2e-13   49.0   0.0    1.4  1  Peptidase_M48  Peptidase family M48


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   3.4e-17   6.2e-13      33     193 ..     236     403 ..     211     404 .] 0.82

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 3.4e-17
                                    GGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHH.HHHHHHHHHHHHHHTT-SHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  33 pkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivs.llasillllglallisraeedaag 111
                                    +++NA  +g+g ++ri ++ +    + ++ +l+ +l HE+GH   r  +++++v  ll  + +l++++l  s+a+e+   
  gene751|gene751|rna750|rna750 236 KNVNAALIGIGNSERIEIYGKVE--NIDDGQLESILIHEVGHSYDRSLIKKISVFfLLLGLEMLFLIILYDSVAKEFVWD 313
                                    3449*******888*****9975..**************************66651455555556666666677777777 PP

                                    T--S---HHHHHHHHHHTT.........HHHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHHTT--S---HHHHHHS-SS CS
                                    xxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 112 afldalavliglliillfl.........alSRkrEyqADeagvellkrakdlvraliklakdlerqdvsaslrsellstH 182
                                    ++ ++  + +++   +  +           S + E++AD + +++ + +++l+++l+k++ d + +   ++l++ l s H
  gene751|gene751|rna750|rna750 314 NVSKEGSFTVLMCLYFASIrpwlfilynLTSQSAEMYADLLTKKYNY-NRTLASTLYKISVDSLDFLSPSWLYNSLNSLH 392
                                    7766666666666666666999999**99******************.******************************** PP

                                    --HHHHHHHHH CS
                                    xxxxxxxxxxx RF
                  Peptidase_M48 183 PplleRiqalk 193
                                    P++++Ri+ l+
  gene751|gene751|rna750|rna750 393 PSIMSRIEYLS 403
                                    *******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3045.86
//
Query:       gene752|gene752|rna751|rna751  [L=232]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-46  157.2   0.0    3.9e-46  156.9   0.0    1.1  1  Proteasome      Proteasome subunit
    3.7e-10   39.3   0.0    6.9e-10   38.4   0.0    1.4  1  Proteasome_A_N  Proteasome subunit A N-terminal signature
  ------ inclusion threshold ------
      0.073   13.1   0.1        0.2   11.7   0.1    1.7  1  Imm3            Immunity protein Imm3


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.9   0.0   6.5e-50   3.9e-46       1     190 []      27     215 ..      27     215 .. 0.96

  Alignments for each domain:
  == domain 1  score: 156.9 bits;  conditional E-value: 6.5e-50
                                    HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC CS
                     Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpip 80 
                                    ++ Gtt++G+++k++v+l+++k++   s+l+++++v K +ki+dhi+++f+G  +D++t+v+r r  + ++   yg++ +
  gene752|gene752|rna751|rna751  27 MNLGTTTIGVRTKEFVILCSEKKIL--STLQNPKSVVKHYKIYDHIVLGFSGISGDTKTIVKRSRDFCISHTHMYGENTS 104
                                    789**********************..***************************************************** PP

                                    HHHHHHHHHHHHHHHHHHC.....TTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHS CS
                     Proteasome  81 verlvarvaaklqaytqrs.....grrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyk 155
                                    verl+++++++ ++   ++      rrpfgvsl+iag+d ++ p+Ly++dpsGsy+++k a aiGsg e++ ++le+ey+
  gene752|gene752|rna751|rna751 105 VERLLKYLSSLSLRFGEEDeakmiFRRPFGVSLIIAGFD-TE-PRLYSLDPSGSYVSYK-ARAIGSGHEVVEGVLENEYE 181
                                    **************999875555578*************.55.***************8.******************** PP

                                    TTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                     Proteasome 156 edltleeavelavkalkealerdklsgknievavi 190
                                    e   l++ ++ a+++l+++++ d ++++n+evav+
  gene752|gene752|rna751|rna751 182 EYRGLDQSLRKALHTLSKVMK-DRINKDNVEVAVV 215
                                    *********************.99*********97 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.2e-13   6.9e-10       3      23 .]       6      26 ..       6      26 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.2e-13
                 Proteasome_A_N  3 rslttFSPdGRLfQVEYAmkA 23
                                   +s++t+S +GR++Q+EYAmkA
  gene752|gene752|rna751|rna751  6 QSVNTYSSEGRIHQIEYAMKA 26
                                   69******************9 PP

>> Imm3  Immunity protein Imm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.4e-05       0.2      12      51 ..     176     215 ..     169     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                           Imm3  12 ineeyeeykaeerslseaiartsdefenveklgeiekvvv 51 
                                    +++eyeey+  ++sl++a+  +s++ ++  + +++e +vv
  gene752|gene752|rna751|rna751 176 LENEYEEYRGLDQSLRKALHTLSKVMKDRINKDNVEVAVV 215
                                    5789************************999*****9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1604.25
//
Query:       gene753|gene753|rna752|rna752  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   12.2   0.8         13    6.7   0.1    3.6  4  TPR_6     Tetratricopeptide repeat
       0.25   11.7   2.5        1.8    9.0   0.1    3.3  4  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0015        13       6      24 ..      38      56 ..      37      56 .. 0.93
   2 ?   -0.0   0.0       0.2   1.8e+03      14      26 ..      79      91 ..      71      92 .. 0.77
   3 ?   -1.4   0.0      0.55   4.9e+03      20      33 .]     200     213 ..     198     213 .. 0.89
   4 ?   -0.1   0.0      0.21   1.9e+03      21      32 ..     216     228 ..     209     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHHHH CS
                          TPR_6  6 lalsyrklgdtdkAleale 24
                                   la  yr++++++kA++al+
  gene753|gene753|rna752|rna752 38 LASIYRRTKQKSKAIQALQ 56
                                   7999***99********98 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.2
                                   HHHHHHHHHHHHH CS
                          TPR_6 14 gdtdkAlealerl 26
                                   gd+d Ale  e+l
  gene753|gene753|rna752|rna752 79 GDYDGALERAESL 91
                                   6******988876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.55
                                    HHHHHHHHHH-TT- CS
                          TPR_6  20 lealerlikeYPdS 33 
                                    +eal+ ++ + P+S
  gene753|gene753|rna752|rna752 200 IEALRLIVHRNPKS 213
                                    789999******98 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.21
                                    HHHHHHHHH.-TT CS
                          TPR_6  21 ealerlike.YPd 32 
                                    ++++++i++ +P+
  gene753|gene753|rna752|rna752 216 RYFREFIERcFPT 228
                                    79******98886 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.38   3.4e+03      56      74 ..      35      53 ..      16      54 .. 0.63
   2 ?   -2.5   0.0      0.79     7e+03      46      67 ..      85     106 ..      83     112 .. 0.73
   3 ?    0.2   0.0      0.11   9.9e+02      54      70 ..     209     225 ..     166     227 .. 0.62
   4 ?    9.0   0.1    0.0002       1.8      11      31 ..     244     264 ..     243     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHHHHHHHHHH CS
                           CM_2 56 eeaierifreiisasralq 74
                                   ++ +++i+r   + s+a+q
  gene753|gene753|rna752|rna752 35 PSILASIYRRTKQKSKAIQ 53
                                   3467788888888888777 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.79
                                    HHHHHHHHS-HHHHHHHHHHHH CS
                           CM_2  46 lerleegaldeeaierifreii 67 
                                    ler e+ ++ +e ier++ +i+
  gene753|gene753|rna752|rna752  85 LERAESLSFRDEPIERLLLQIF 106
                                    5666666688888999988887 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.11
                                    S-HHHHHHHHHHHHHHH CS
                           CM_2  54 ldeeaierifreiisas 70 
                                     ++++ er fre i+ +
  gene753|gene753|rna752|rna752 209 RNPKSSERYFREFIERC 225
                                    45777777777777765 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0002
                                    HHHHHHHHHHHHHHHHHHHHH CS
                           CM_2  11 ileLLaeRaelakevgeyKke 31 
                                    + eLL+eR  l+++++++K+ 
  gene753|gene753|rna752|rna752 244 LFELLKERNSLTEDIMKVKEY 264
                                    789****************63 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2225.34
//
Query:       gene754|gene754|rna753|rna753  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-08   33.1   0.3    3.2e-06   27.3   0.0    2.5  3  Arrestin_N  Arrestin (or S-antigen), N-terminal domain
     0.0064   16.9   0.4        2.3    8.7   0.0    2.6  2  Arrestin_C  Arrestin (or S-antigen), C-terminal domain
  ------ inclusion threshold ------
      0.062   13.4   0.1        0.2   11.7   0.1    1.9  1  PP1         Phloem filament protein PP1 cystatin-like domain


Domain annotation for each model (and alignments):
>> Arrestin_N  Arrestin (or S-antigen), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   5.3e-10   3.2e-06       2     104 ..       4     102 ..       3     150 .. 0.81
   2 ?   -3.7   0.0       1.9   1.1e+04       3      24 ..     176     197 ..     175     205 .. 0.63
   3 ?    3.5   0.0     0.011        67      98     142 ..     248     292 ..     232     295 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.3e-10
                                    EEEES-SEEEEETT--EEEEEEE-CCCCTT.CEEEEEEEEEEEESSSSTTTTCCCEEEEEEEEEEEEESTSSSSS.SSSS CS
                     Arrestin_N   2 tieldkrdevyhpgetvdGkvlleteelkkarkvkielsgkartgweesevagktfrkdltlkkkqeyleteksllkskk 81 
                                    +i++d  +e+y +g +++G + ++ + ++ ++k+++ ls +++++ +e +++   + ++++++k  + ++ e +++++ +
  gene754|gene754|rna753|rna753   4 RIKIDLDKEIYESGSEIKGAIDIKMRCPLCITKINLILSKAMKMKIQEIDRK---EGSGEKFEKIYDGYRYEFEVYSN-D 79 
                                    5788888****************************************99965...55555555554556666666666.8 PP

                                    HHHHHHHH-TTEEEEEE---TTS CS
                     Arrestin_N  82 dsqekLpkGehafpFsfelPknl 104
                                    d   ++++G+h+fpF+f l k+ 
  gene754|gene754|rna753|rna753  80 DPLGEISSGHHKFPFRFLLRKED 102
                                    88899************997765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.9
                                    EEES-SEEEEETT--EEEEEEE CS
                     Arrestin_N   3 ieldkrdevyhpgetvdGkvll 24 
                                    i ++ +++ y++g+ ++ ++++
  gene754|gene754|rna753|rna753 176 IHFEVNKQFYYSGDYLTIEATI 197
                                    5666677788888776655555 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.011
                                    E---TTS--SECSGEEEEEEEEEEEEECCCE--C.CCEEEEEEEE CS
                     Arrestin_N  98 felPknlpsSfeGkaggvrYevkvtldrpwkidkkkkkvftVirk 142
                                    +++P+  ps+++G+  ++r  + v l+       + kk++ Vi+k
  gene754|gene754|rna753|rna753 248 LKIPSTTPSTVTGSEFSIRVVLFVNLELYRGTPVRVKKYIPVIKK 292
                                    78***************9988888888887777778888888876 PP

>> Arrestin_C  Arrestin (or S-antigen), C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00038       2.3       6      52 ..       4      50 ..       2      70 .. 0.88
   2 !    5.9   0.1    0.0028        17       5     103 ..     174     266 ..     171     290 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00038
                                   EEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEEEESS CS
                     Arrestin_C  6 sleaslpkkgyvpGetipvtvkidndskkkvkkikvslvqhvdvcaf 52
                                    +++ l+k+ y  G++i+  ++i+    + + ki++ l +  +++ +
  gene754|gene754|rna753|rna753  4 RIKIDLDKEIYESGSEIKGAIDIKMRCPLCITKINLILSKAMKMKIQ 50
                                   6899********************************99988777766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0028
                                    EEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEEEESS..SEEEEEEEEEEEEE---B-TTEE.EEEEEE CS
                     Arrestin_C   5 vsleaslpkkgyvpGetipvtvkidndskkkvkkikvslvqhvdvcafnrsnkkeknvvaksdsvkvtsaakdkleteve 84 
                                     ++   ++k+ y+ G+ ++++ +i   ++ k+k++++ + + ++v  ++r+  ++k +   +   +     ++ l   ++
  gene754|gene754|rna753|rna753 174 YNIHFEVNKQFYYSGDYLTIEATIP-SKNPKIKSMECFAYEILNVSVEGREILRTKYIGGGQAEHHA---GGRVL--RAT 247
                                    5677788999999999988888885.44557888888888888888885433333333333333332...33334..599 PP

                                    E.----B--.---S---EEE CS
                     Arrestin_C  85 lqiPeeltp.ssarnvelik 103
                                    l+iP ++tp + + + + i+
  gene754|gene754|rna753|rna753 248 LKIP-STTPsTVTGSEFSIR 266
                                    9999.666624443444444 PP

>> PP1  Phloem filament protein PP1 cystatin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.3e-05       0.2       5      34 ..      43      72 ..      39      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                            PP1  5 evakfaveefnvksGdsLkfeeiyeGWyle 34
                                   + +k+ ++e++ k+G + kfe+iy+G+  e
  gene754|gene754|rna753|rna753 43 KAMKMKIQEIDRKEGSGEKFEKIYDGYRYE 72
                                   668999********************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1989.90
//
Query:       gene755|gene755|rna754|rna754  [L=192]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-20   74.0  15.0    1.1e-20   74.0  15.0    2.0  2  PTPLA     Protein tyrosine phosphatase-like protein, PTPLA
  ------ inclusion threshold ------
        9.3    6.5  23.1       0.44   10.8  14.6    2.3  2  DUF3397   Protein of unknown function (DUF3397)


Domain annotation for each model (and alignments):
>> PTPLA  Protein tyrosine phosphatase-like protein, PTPLA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.6      0.54   4.9e+03     138     154 ..      16      32 ..       4      39 .. 0.53
   2 !   74.0  15.0   1.3e-24   1.1e-20       1     159 [.      44     177 ..      44     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.54
                          PTPLA 138 lllllyvpglyvlythm 154
                                    +++++ ++ +++ y  m
  gene755|gene755|rna754|rna754  16 IVCTIALFTSLMFYKTM 32 
                                    34444444455555544 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 1.3e-24
                          PTPLA   1 QtlavlEvlhallglvrspvlttamQvasRllvvwgvvelfpelqtkspavtllllaWsvtEviRYsfyalklslgkvpk 80 
                                    Qt+ ++Ev +++ +  +++ l+t+mQ +sR+l++w+v++ ++    + +++ +++  W +++++RY fy++++       
  gene755|gene755|rna754|rna754  44 QTFFLMEVANICAKKSNARYLPTVMQLVSRMLIIWVVFWYYEI--ID-WTFPIMTACWYLSDLVRYVFYMFRI------D 114
                                    99*************************************9966..55.99***********************......7 PP

                          PTPLA  81 lltwlRYtlfivLYPlGvasElvliyaalpvlkeskklsielpnklnfsfsykyflllllllyvpglyvlythmlkqRr 159
                                     +  +RY+lf+   P+G++ E+ ++    + +                   ++y+++l +lly+pg+++l++hml+qR+
  gene755|gene755|rna754|rna754 115 TIRIIRYNLFLLTSPIGFILEMCCLRTLYNLIG----------------NILSYLVALAALLYIPGFIFLFSHMLRQRK 177
                                    9********************988777666666................3468888888889****************8 PP

>> DUF3397  Protein of unknown function (DUF3397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  14.6   4.9e-05      0.44       9     105 ..      15     110 ..       6     113 .. 0.86
   2 ?    0.3   0.5     0.086   7.7e+02      12      33 ..     163     184 ..     152     186 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                        DUF3397   9 llvlllvyiivkkfslkkkkaklkalDvttpflilavhllseelfgksflpllllvllllaillliiqarkkgeisykrf 88 
                                    ++v  ++ + + +f++  k   lk++ +   f++++v+ ++ +  +  +lp ++ +++ ++i++++++++   + ++  +
  gene755|gene755|rna754|rna754  15 FIVCTIALFTSLMFYKTMKTKYLKMAGLCQTFFLMEVANICAKKSNARYLPTVMQLVSRMLIIWVVFWYYEIIDWTF-PI 93 
                                    56666777777888777788899***********************************9999999988777777666.68 PP

                        DUF3397  89 fklfwRllfLltfllYl 105
                                    ++++w l++L+  ++Y+
  gene755|gene755|rna754|rna754  94 MTACWYLSDLVRYVFYM 110
                                    99*************97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.086
                        DUF3397  12 lllvyiivkkfslkkkkaklka 33 
                                      ++++++++++ +k+ +k+ka
  gene755|gene755|rna754|rna754 163 PGFIFLFSHMLRQRKWSRKIKA 184
                                    2333445556656667777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1174.74
//
Query:       gene756|gene756|rna755|rna755  [L=296]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-15   56.2   0.6    5.8e-09   35.6   0.0    2.4  2  RRM_1         RNA recognition motif. (a.k.a. RRM, RBD, or RNP
     0.0001   22.3   0.1      0.012   15.7   0.1    2.4  1  RRM_7         RNA recognition motif
    0.00021   21.2   0.5       0.19   11.7   0.1    2.4  2  RL            RL domain
    0.00028   20.9   0.0       0.15   12.1   0.0    2.2  2  RRM_3         RNA binding motif
     0.0022   17.8   0.0        1.6    8.6   0.0    2.3  2  RRM_occluded  Occluded RNA-recognition motif
  ------ inclusion threshold ------
      0.032   13.8   0.0        3.2    7.3   0.0    2.2  2  DUF4283       Domain of unknown function (DUF4283)


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0     2e-12   5.8e-09       1      58 [.       3      53 ..       3      64 .. 0.89
   2 !   18.8   0.1   3.5e-07     0.001       4      70 .]     182     244 ..     179     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2e-12
                                   EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHH CS
                          RRM_1  1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlea 58
                                   +f+g +p+ v+ee++ke+F++fG++++++l  +       ++f +F+s+++ ++ l++
  gene756|gene756|rna755|rna755  3 IFIGKIPNHVNEEQIKEYFGQFGEVTDVSLKGT-------YGFLNFDSESSIARVLNQ 53
                                   8******************************95.......*************99994 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 3.5e-07
                                    ESETTTSSHHHHHHHHHTTSCE.EEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                          RRM_1   4 gnLppdvteeeLkelFskfGpi.ksiklvrdetgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                    +n++p++t ++ k +  + G   + ++l +     s ++a  eF++ ed ++ +++l+g +++g++lk
  gene756|gene756|rna755|rna755 182 ENIAPNTTIDDFKNFVHDHGFEpSYARLGY-----SGNHAVLEFKNIEDKDNVMKKLDGAEFNGHVLK 244
                                    588888888888888888888755555555.....8*****************************986 PP

>> RRM_7  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     4e-06     0.012       3      29 ..       2      28 ..       1      74 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4e-06
                          RRM_7  3 kvFvGGlPiDiteeelkatfkefgkvl 29
                                   ++F+G +P  ++ee++k+ f++fg+v+
  gene756|gene756|rna755|rna755  2 QIFIGKIPNHVNEEQIKEYFGQFGEVT 28
                                   69**********************985 PP

>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   6.3e-05      0.19      20      67 ..       7      51 ..       3      56 .. 0.87
   2 !    7.4   0.0    0.0014       4.3      19      61 ..     182     224 ..     167     234 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.3e-05
                             RL 20 scpskisekkllkylsqhGkinkhFfYeskgvyavvEFsekesiasLq 67
                                   ++p++++e+++ +y+ q+G+++       kg+y    F+++ sia + 
  gene756|gene756|rna755|rna755  7 KIPNHVNEEQIKEYFGQFGEVTDV---SLKGTYGFLNFDSESSIARVL 51
                                   5799******************97...679**************7654 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0014
                             RL  19 iscpskisekkllkylsqhGkinkhFfYeskgvyavvEFseke 61 
                                     ++++++++ ++ +++  hG   ++      g +av EF++ e
  gene756|gene756|rna755|rna755 182 ENIAPNTTIDDFKNFVHDHGFEPSYARLGYSGNHAVLEFKNIE 224
                                    578899*********************************9865 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0     5e-05      0.15      10      83 ..       9      84 ..       3      86 .. 0.85
   2 !    6.6   0.1    0.0026       7.8       5      71 ..     180     245 ..     177     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                                   SSS--HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC....-B-CCTSSEEEEE--HHHHHHHH CS
                          RRM_3 10 nkelsredikellsklgevayvdyekgdkegevrFkedeeakkalekatea....klkikdaevtlelLeGeeEkeyw 83
                                    +++  e+ike + ++gev   d++   + g + F+++++  ++l+++ ++     + ++ a+ + + L+Ge   +y+
  gene756|gene756|rna755|rna755  9 PNHVNEEQIKEYFGQFGEVT--DVSLKGTYGFLNFDSESSIARVLNQRSHTidgaPISVERANGRKRPLDGEYHDRYM 84
                                   567789*************8..55666899**********99999999888888889999999999999999888876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0026
                                    EEEE-SSS--HHHHHHHCHCCS.-ECEEEE-TTSSEEEEEESSHHHHHHHHHHHHHC-B-CCTSSEEE CS
                          RRM_3   5 klsGlnkelsredikellsklg.evayvdyekgdkegevrFkedeeakkalekateaklkikdaevtl 71 
                                     ++ +  +++++d+k++++ +g e  y  +    + + + Fk+ e+  ++++k+  a  + + + ++ 
  gene756|gene756|rna755|rna755 180 VFENIAPNTTIDDFKNFVHDHGfEPSYARLGYSGNHAVLEFKNIEDKDNVMKKLDGA--EFNGHVLKT 245
                                    5666778999*************9****************************99888..444444433 PP

>> RRM_occluded  Occluded RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00054       1.6       6      37 ..       5      35 ..       1      65 [. 0.83
   2 !    7.1   0.0    0.0017         5      41      70 ..     216     245 ..     186     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00054
                   RRM_occluded  6 llplsDtvnkariralveekegeikkivLvpd 37
                                   +  ++  vn+++i++ + +  ge++++ L   
  gene756|gene756|rna755|rna755  5 IGKIPNHVNEEQIKEYFGQF-GEVTDVSLKGT 35
                                   5679****************.******99765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0017
                   RRM_occluded  41 AivefkdekiagkasLaLdgsefegkklrc 70 
                                    A++efk+ ++   ++ +Ldg ef+g++l++
  gene756|gene756|rna755|rna755 216 AVLEFKNIEDKDNVMKKLDGAEFNGHVLKT 245
                                    999*************************97 PP

>> DUF4283  Domain of unknown function (DUF4283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0011       3.2      39      87 ..      25      73 ..       5      79 .. 0.81
   2 ?    4.3   0.0    0.0086        26      47      67 ..     212     232 ..     200     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                        DUF4283 39 ggvkikelgdglflfrfsseedlekvleggpwlingkplilkrwspkfk 87
                                   g+v+  +l+ ++  + f+se    +vl+++ ++i+g p+ ++r +++ +
  gene756|gene756|rna755|rna755 25 GEVTDVSLKGTYGFLNFDSESSIARVLNQRSHTIDGAPISVERANGRKR 73
                                   5566666777777899*************************99887655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0086
                        DUF4283  47 gdglflfrfsseedlekvleg 67 
                                    + ++ +++f++ ed+++v+++
  gene756|gene756|rna755|rna755 212 SGNHAVLEFKNIEDKDNVMKK 232
                                    56899**************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1849.78
//
Query:       gene757|gene757|rna756|rna756  [L=113]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 697.19
//
Query:       gene758|gene758|rna757|rna757  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-16   61.0  16.3    2.2e-16   60.1  15.9    1.8  1  MBOAT     MBOAT, membrane-bound O-acyltransferase family


Domain annotation for each model (and alignments):
>> MBOAT  MBOAT, membrane-bound O-acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1  15.9   1.2e-20   2.2e-16      82     297 ..     122     306 ..      19     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 1.2e-20
                          MBOAT  82 aallsklpslleylgYvffyplllvGPilsyseymsfvesplsrllytakrnfavalyalflgltylilieyvlskicak 161
                                    ++++ ++  +++ l Y++f+p+l +GP+ +++   +f+e+++ +  + +   f  ++++l l  ++++++++  s++   
  gene758|gene758|rna757|rna757 122 KEYNKRTNTIKDALSYILFIPGLMLGPVPTFK---DFMENKYEKPKKPPYETFLKSFGFLIL--FQALRVSVPRSHLLEE 196
                                    667788888999******************99...588888888877544455555555555..5566666555555555 PP

                          MBOAT 162 dftifkmlssaqllmrsvimrilllllllfllifdflglwlvalgedilsGlgvngarldrvadrniygdwenavsfsef 241
                                    +++ +  l         +i+++  + +++f++ + f++   +++  +              + + ++++ +e a+s+++ 
  gene758|gene758|rna757|rna757 197 NISLPMRL--------VYIYLFTVGNRIKFYFAWHFSH-GCFTFQNFP------------NLLNADFIK-VELATSVKDL 254
                                    55555555........6999999999*****9998887.677776332............3579*****.********** PP

                          MBOAT 242 wraWNipvhkWLlryvYkplgskkfklnkslatlatFlfsAvwHglalgyliwfvl 297
                                    + +WNi++  WL++ +++p++    k++ + a+lat ++sA+wHg+ ++yl+ f+ 
  gene758|gene758|rna757|rna757 255 STYWNICTGVWLKNCFFVPMK----KRSIFWASLATSAVSALWHGINPCYLVMFLS 306
                                    *******************95....8*************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2415.14
//
Query:       gene759|gene759|rna758|rna758  [L=228]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.037   13.3   0.1        4.9    6.4   0.0    2.1  2  Dcc1      Sister chromatid cohesion protein Dcc1


Domain annotation for each model (and alignments):
>> Dcc1  Sister chromatid cohesion protein Dcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0   0.00027       4.9      27      52 ..      23      48 ..       4      56 .. 0.77
   2 ?    5.0   0.0   0.00069        12     246     292 ..     172     217 ..     151     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00027
                                   SSXEEEEXSSXEEEEEEEEEEEEEEE CS
                           Dcc1 27 deeaVLctedkTyslkqvetSNslLL 52
                                   +++a + ++dk y +k+v+ SN+ ++
  gene759|gene759|rna758|rna758 23 TSQAYVLSSDKGYGVKRVSPSNTFIV 48
                                   567778899**************987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.00069
                                    HHHHHSSS-EEHHHHHHHHHHTS-TTSS----GGGGTTSEE-..... CS
                           Dcc1 246 lLkktkaekieleeFlekWkssvPegleseldlelLrGlalvdsssk 292
                                     L +  +e+ ++ +Fl++W++s P++++ e  + + ++ ++++++++
  gene759|gene759|rna758|rna758 172 CLLGC-DEENDMTSFLKRWEDSSPNEINIEGLVRQVNSTFIIQEKKA 217
                                    44444.3677899**************95566888888888855544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1391.78
//
Query:       gene760|gene760|rna759|rna759  [L=163]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0056   17.3   0.2      0.014   16.0   0.2    1.7  1  Sas10_Utp3      Sas10/Utp3/C1D family
     0.0083   16.6   4.3      0.016   15.7   4.3    1.5  1  Sas10           Sas10 C-terminal domain
  ------ inclusion threshold ------
       0.14   12.2   2.8        5.4    7.0   0.1    2.1  2  Cytomega_TRL10  Cytomegalovirus TRL10 protein


Domain annotation for each model (and alignments):
>> Sas10_Utp3  Sas10/Utp3/C1D family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   2.4e-06     0.014      32      82 ..      19      67 ..       4      72 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                     Sas10_Utp3 32 d..eklsegisllslKnelllaYllnlllylllklsgvelkdhpvvkeLvrlR 82
                                   +  +++++  ++l++K +ll+ Yl+nl++y    ++  + + + v + L +  
  gene760|gene760|rna759|rna759 19 EarSSMQN--EILDIKSDLLSVYLMNLVIY--KEMNEEDRAGSSVEEMLAKTS 67
                                   12334444..6*******************..447775555555555555555 PP

>> Sas10  Sas10 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   4.3   2.6e-06     0.016       3      38 ..     105     139 ..     103     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                          Sas10   3 gkRkityqIekNkGLtpkRkkenrnpRvkkrkkYek 38 
                                    gkR it +++kNk  ++kR+ e+r pR+k+++k +k
  gene760|gene760|rna759|rna759 105 GKRIITDKMKKNKF-VKKRNIEDRIPRLKYKNKARK 139
                                    8************5.67*************999665 PP

>> Cytomega_TRL10  Cytomegalovirus TRL10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0009       5.4      72     107 ..      38      73 ..      31     103 .. 0.82
   2 ?    5.3   1.1     0.003        18      98     127 ..     105     134 ..      81     153 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0009
                 Cytomega_TRL10  72 llvvffviyareeeknntgtevdqclayrsltrkkl 107
                                    + ++ +viy   +e++ +g+ v+++la  s+   k+
  gene760|gene760|rna759|rna759  38 VYLMNLVIYKEMNEEDRAGSSVEEMLAKTSILLEKI 73 
                                    455678****99***************999877665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.003
                 Cytomega_TRL10  98 ayrsltrkkleqhaakkqniyeripyrpsr 127
                                      r +t k  +++  kk+ni +rip    +
  gene760|gene760|rna759|rna759 105 GKRIITDKMKKNKFVKKRNIEDRIPRLKYK 134
                                    56788999899999***********65444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1214  (0.0677115); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1026.97
//
Query:       gene76|gene76|rna76|rna76  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-23   80.6   0.1    1.9e-22   79.0   0.1    1.9  1  TBPIP          TBPIP/Hop2 winged helix domain
    4.5e-05   23.5   0.8    4.5e-05   23.5   0.8    2.6  3  LZ3wCH         Leucine zipper with capping helix domain
  ------ inclusion threshold ------
      0.027   14.7   0.5      0.044   14.0   0.5    1.4  1  SesA           N-terminal domain on NACHT_NTPase and P-loop N
      0.063   12.8   3.9       0.12   11.9   3.9    1.5  1  MscS_porin     Mechanosensitive ion channel porin domain
      0.071   12.7   6.9       0.11   12.1   6.9    1.4  1  Paralemmin     Paralemmin
      0.086   13.1  11.1        4.8    7.5   2.5    3.0  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
       0.11   13.2   0.2        1.1    9.9   0.2    2.4  2  ThiS           ThiS family
       0.14   12.2   0.1       0.38   10.8   0.1    1.7  2  PilJ           Type IV pili methyl-accepting chemotaxis trans
       0.15   12.4   0.1       0.15   12.4   0.1    2.4  1  DUF3134        Protein of unknown function (DUF3134)
        0.3   10.8   2.2       0.49   10.1   2.2    1.4  1  DUF745         Protein of unknown function (DUF745)
       0.33   10.3   7.7       0.42    9.9   7.7    1.2  1  FAM76          FAM76 protein
       0.47    9.6   5.7       0.68    9.1   5.7    1.3  1  TMPIT          TMPIT-like protein
       0.53   10.1   8.1       0.97    9.2   8.1    1.5  1  DUF724         Protein of unknown function (DUF724)
       0.95    9.1   8.0       0.34   10.5   0.3    3.2  4  Trimer_CC      Trimerisation motif
        1.7    8.9   9.1       0.67   10.2   3.4    2.5  2  XhlA           Haemolysin XhlA
          2    8.0   5.8        2.2    7.8   2.8    2.3  3  Fzo_mitofusin  fzo-like conserved region
        2.6    7.0   6.7          3    6.8   6.7    1.1  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
        3.5    6.1  14.3         15    4.0   1.2    1.9  2  FapA           Flagellar Assembly Protein A
          4    7.9   5.6        5.5    7.5   2.2    2.6  2  DUF4094        Domain of unknown function (DUF4094)
        6.4    7.5   7.1        7.9    7.2   1.7    2.2  2  DUF2203        Uncharacterized conserved protein (DUF2203)
        7.8    6.7   8.9        3.4    7.8   2.9    2.2  2  Fib_alpha      Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.1   2.2e-25   1.9e-22       1      62 []       7      68 ..       7      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 2.2e-25
                      TBPIP  1 eaeelvleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiieKeyGKqkiYlan 62
                               + ee v+++++++nrP+s+++++a++++++g+ta+q++Ld L++ g++++K+yGK+kiYl+n
  gene76|gene76|rna76|rna76  7 DEEERVFQMMYKCNRPTSKSEIMAYFKGEIGGTAIQEILDYLESDGRLVTKTYGKSKIYLVN 68
                               57899*******************************************************97 PP

>> LZ3wCH  Leucine zipper with capping helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.3     8e+03      34      46 ..      86      98 ..      84      99 .. 0.74
   2 ?   -3.0   0.1       9.9   8.5e+03       3      48 ..     114     123 ..     110     129 .. 0.52
   3 !   23.5   0.8   5.3e-08   4.5e-05       3      49 ..     150     196 ..     145     197 .] 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.3
                     LZ3wCH 34 kfpkskkelneef 46
                                ++ ++k l+ee+
  gene76|gene76|rna76|rna76 86 EYGEKRKILEEEI 98
                               5788888888876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.9
                     LZ3wCH   3 ieekkkatkkakeaanrWtdnifdikswikekfpkskkelneefgI 48 
                                i                                     +l+e + I
  gene76|gene76|rna76|rna76 114 I------------------------------------NQLEESIKI 123
                                3....................................444444443 PP

  == domain 3  score: 23.5 bits;  conditional E-value: 5.3e-08
                     LZ3wCH   3 ieekkkatkkakeaanrWtdnifdikswikekfpkskkelneefgIe 49 
                                +e  kk+++ a++  +  ++++ ++++  +e++ ++k+el+ee+gIe
  gene76|gene76|rna76|rna76 150 MENAKKKYERAQSGLKKIRRIFNEVIERLSEGMDMKKSELYEEIGIE 196
                                45567777777777777777**************************8 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   5.2e-05     0.044       5      86 ..      98     177 ..      94     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.2e-05
                       SesA   5 iaiveaaiklydaikdikglpeaFrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeifekvapa 86 
                                i+ ++a ik+ d++ +i++l e+++   k +   qe Le++k+  ++ ++++ +  ++k+  e+ ++ ++k+ +if++v + 
  gene76|gene76|rna76|rna76  98 ISTLDAEIKMLDKMMSINQLEESIKILDKTVKDNQERLESFKNGGREVSKKDME--NAKKKYERAQSGLKKIRRIFNEVIER 177
                                7889999************************************88888777654..48*********************554 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.9   0.00015      0.12      40     136 ..      78     178 ..      53     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                 MscS_porin  40 eelqkaiddaPkelrelqqelealqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlns........qlvelqtrp 115
                                 +l+  ++++ ++ + l++e+++l    +++ k  ++ +s+++Le  ++     + ++qe+l ++++        +  ++    
  gene76|gene76|rna76|rna76  78 VKLNAELQEYGEKRKILEEEISTL----DAEIKMLDKMMSINQLEESIKILDKTVKDNQERLESFKNggrevskkDMENAKKKY 157
                                479999******************....***********************************998711111111344445555 PP

                 MscS_porin 116 eraqqqltearqrlqeirnrL 136
                                eraq+ l + r+  +e+  rL
  gene76|gene76|rna76|rna76 158 ERAQSGLKKIRRIFNEVIERL 178
                                666666666666655555555 PP

>> Paralemmin  Paralemmin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.9   0.00013      0.11       4      78 ..      84     159 ..      81     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                 Paralemmin   4 leedeakvrkLEesiqrLekeieeLeseesaisakee..vlaeklketeksvedlqksllstdkekkvslsksrkve 78 
                                l+e  +k + LEe+i+ L+ ei+ L++  s  + +e+  +l +++k++++ +e++++   + +k k++++ k++ ++
  gene76|gene76|rna76|rna76  84 LQEYGEKRKILEEEISTLDAEIKMLDKMMSINQLEESikILDKTVKDNQERLESFKNGGREVSK-KDMENAKKKYER 159
                                788899*********************9987775544113444445555555554443333333.222222222222 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   5.7      0.01       8.7      35      82 ..      83     129 ..      67     137 .. 0.57
   2 ?    7.5   2.5    0.0056       4.8      20      74 ..     119     174 ..     116     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                    BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                + +++ ++ + le++++ l++ + ++  ++ +i+q+e++++ L ++v+
  gene76|gene76|rna76|rna76  83 ELQEYGEKRKILEEEISTLDA-EIKMLDKMMSINQLEESIKILDKTVK 129
                                344444555555555555555.33333334445555555555555554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0056
                    BLOC1_2  20 edyklLeklNeaasekykklkdvaasle.kkleklnekyeelqpylqqidqiekqv 74 
                                e +k+L k  +  +e+ ++ k+   +++ k++e+ ++kye  q+ l++i +i ++v
  gene76|gene76|rna76|rna76 119 ESIKILDKTVKDNQERLESFKNGGREVSkKDMENAKKKYERAQSGLKKIRRIFNEV 174
                                5677888888888888888888777765168********************98887 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       1.2   1.1e+03      21      52 ..      38      71 ..      31      77 .. 0.70
   2 ?    9.9   0.2    0.0013       1.1       1      36 [.      78     113 ..      78     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                               TSBHHHHHHHHHHHTCHHG..TTTTEEEEETTEE CS
                       ThiS 21 gstvaelleaLgerypela..lerrvavavNgei 52
                               g+ ++e+l+ L+ ++   +    +  + +vN+++
  gene76|gene76|rna76|rna76 38 GTAIQEILDYLESDGRLVTktYGKSKIYLVNQDL 71
                               7889999999988774444665566666677665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                                EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTC CS
                       ThiS   1 vllfaelrelageeelelaegstvaelleaLgeryp 36 
                                v+l+ael+e  ++++++++e st+++ ++ L+++ +
  gene76|gene76|rna76|rna76  78 VKLNAELQEYGEKRKILEEEISTLDAEIKMLDKMMS 113
                                89********99******************998875 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.2   1.9e+03      40      61 ..      87     108 ..      77     116 .. 0.77
   2 ?   10.8   0.1   0.00044      0.38      39     101 ..     116     184 ..     103     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.2
                       PilJ  40 aaearaqlretiaqfdrtlaal 61 
                                  e+r+ l+e i+++d+ ++ l
  gene76|gene76|rna76|rna76  87 YGEKRKILEEEISTLDAEIKML 108
                                4578889999999999887765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00044
                       PilJ  39 daaearaqlretiaqfdrtlaalrlgdpapgllvpae......avraqleaveqlWqelkkpaeaalaq 101
                                + +e+ + l++t+++ +++l++ ++g+ + + +++++        ++ l+++++ ++e  + +   +  
  gene76|gene76|rna76|rna76 116 QLEESIKILDKTVKDNQERLESFKNGGREVSKKDMENakkkyeRAQSGLKKIRRIFNEVIERLSEGMDM 184
                                46899999************************9999667766666666666666666666666555555 PP

>> DUF3134  Protein of unknown function (DUF3134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017      0.15      23      45 ..      43      65 ..      38     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                    DUF3134 23 slLdWLessGRLiardeeeeeel 45
                                +Ld+Les GRL+ +   +++ +
  gene76|gene76|rna76|rna76 43 EILDYLESDGRLVTKTYGKSKIY 65
                               79***********9887766665 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.2   0.00057      0.49      68     144 ..      97     174 ..      78     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00057
                     DUF745  68 eqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaa.kenlenaeqvaagaqqelaektqlleaA 144
                                e +  +ae  + +   s+++ e+++k+  k++k+ q+ le++k+  +++ k+ +ena++  + aq+ l++ + + ++ 
  gene76|gene76|rna76|rna76  97 EISTLDAEIKMLDKMMSINQLEESIKILDKTVKDNQERLESFKNGGREVsKKDMENAKKKYERAQSGLKKIRRIFNEV 174
                                333446666666666677777777777777777777777777666544315566677777777766666655555554 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   7.7    0.0005      0.42     192     283 ..      85     180 ..      48     192 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0005
                      FAM76 192 eeeklaeekesnetskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekd...kkitelkaellekeke.lreklkele 271
                                +e + +++  ++e s+  ++ ++ d+++ ++qL+e i+ l k+++  ++ l + +   +++++   e+ +k+ e  ++ lk+++
  gene76|gene76|rna76|rna76  85 QEYGEKRKILEEEISTLDAEIKMLDKMMSINQLEESIKILDKTVKDNQERLESFKnggREVSKKDMENAKKKYErAQSGLKKIR 168
                                22233344444444445889999*********************9999998765512255666555555554331455677888 PP

                      FAM76 272 keakekieklek 283
                                + ++e ie+l++
  gene76|gene76|rna76|rna76 169 RIFNEVIERLSE 180
                                888888888765 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.7    0.0008      0.68      10      89 ..      90     171 ..      74     184 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0008
                      TMPIT  10 efkeleetakeykqkleelsk..lqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesll 89 
                                + k lee+ +++ ++++ l k  +++++ ++ik   k +k+ +++l+++k+  +e +++ +e+ k++ +++++ lk++  ++
  gene76|gene76|rna76|rna76  90 KRKILEEEISTLDAEIKMLDKmmSINQLEESIKILDKTVKDNQERLESFKNGGREVSKKDMENAKKKYERAQSGLKKIRRIF 171
                                4444555555555544444441134566666677777777777777777766666666677777777777666666665544 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   8.1    0.0011      0.97     103     184 ..      90     174 ..      70     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                     DUF724 103 eqtklleerkkl..ekkieeeesekrkleeeidelekkilelerqlallk.ekkeaadkeiarlkseaekleeeledveqeFea 183
                                +++ l+ee++ l  e k+ ++ ++ ++lee+i+ l+k++++ +++l+++k   +e ++k++ + k++ e+++  l+++++ F++
  gene76|gene76|rna76|rna76  90 KRKILEEEISTLdaEIKMLDKMMSINQLEESIKILDKTVKDNQERLESFKnGGREVSKKDMENAKKKYERAQSGLKKIRRIFNE 173
                                4555566666551156678999999*************************8455556666666666677777777776666666 PP

                     DUF724 184 v 184
                                v
  gene76|gene76|rna76|rna76 174 V 174
                                5 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.6      0.33   2.8e+02      25      49 ..      75      98 ..      74     100 .. 0.80
   2 ?    0.6   0.1      0.48   4.1e+02      24      38 ..      94     108 ..      92     113 .. 0.78
   3 ?   10.5   0.3    0.0004      0.34      21      43 ..     114     136 ..     108     140 .. 0.89
   4 ?   -2.5   0.0       4.4   3.8e+03      18      28 ..     172     182 ..     165     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.33
                               HHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Trimer_CC 25 EEelrkLqatVQelQkRLDrLEetv 49
                               EE++ kL+a  Qe  ++   LEe +
  gene76|gene76|rna76|rna76 75 EEDV-KLNAELQEYGEKRKILEEEI 98
                               6666.79*****9988888888877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                                HHHHHHHHHHHHHHH CS
                  Trimer_CC  24 LEEelrkLqatVQel 38 
                                LEEe+  L a +  l
  gene76|gene76|rna76|rna76  94 LEEEISTLDAEIKML 108
                                899999999877655 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0004
                                --HHHHHHHHHHHHHHHHHHHHH CS
                  Trimer_CC  21 vSRLEEelrkLqatVQelQkRLD 43 
                                +  LEE ++ L  tV + Q+RL 
  gene76|gene76|rna76|rna76 114 INQLEESIKILDKTVKDNQERLE 136
                                557******************96 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 4.4
                                XXX--HHHHHH CS
                  Trimer_CC  18 sdavSRLEEel 28 
                                ++++ RL E +
  gene76|gene76|rna76|rna76 172 NEVIERLSEGM 182
                                57888998866 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.4   0.00078      0.67       3      46 ..      95     140 ..      72     142 .. 0.96
   2 ?    1.3   0.3      0.48   4.1e+02      24      45 ..     147     168 ..     143     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00078
                       XhlA   3 kerlerietkldnlee..rvdkleekaaeaeekiknleedlkkles 46 
                                +e++ ++++++++l++   +++lee     ++ +k ++e+l+++++
  gene76|gene76|rna76|rna76  95 EEEISTLDAEIKMLDKmmSINQLEESIKILDKTVKDNQERLESFKN 140
                                799***************************************9885 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.48
                       XhlA  24 eekaaeaeekiknleedlkkle 45 
                                ++++++a++k + ++  lkk+ 
  gene76|gene76|rna76|rna76 147 KKDMENAKKKYERAQSGLKKIR 168
                                7888999999999999999986 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.8    0.0025       2.2     108     155 ..      85     131 ..      53     141 .. 0.76
   2 ?    1.6   0.4      0.22   1.8e+02     121     159 ..     114     157 ..     111     159 .. 0.57
   3 ?   -0.2   0.0      0.73   6.2e+02      95     121 ..     167     193 ..     159     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0025
              Fzo_mitofusin 108 qqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekf 155
                                q+  e +k leeei++l++ei++l+++ +  ++l +  ++l++ +++ 
  gene76|gene76|rna76|rna76  85 QEYGEKRKILEEEISTLDAEIKMLDKMMS-INQLEESIKILDKTVKDN 131
                                455678889***************99865.455666666665555544 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.22
              Fzo_mitofusin 121 ikelekeiekleev....qkkakllrnkaslle.seLekfeeqy 159
                                i++le++i+ l+++    q++++ ++n   +++ +++e+ +++y
  gene76|gene76|rna76|rna76 114 INQLEESIKILDKTvkdnQERLESFKNGGREVSkKDMENAKKKY 157
                                55566666555543111166777778777776414577776666 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.73
              Fzo_mitofusin  95 vqqelsstfarlcqqvdetekeleeei 121
                                +++ ++++++rl++  d+ ++el eei
  gene76|gene76|rna76|rna76 167 IRRIFNEVIERLSEGMDMKKSELYEEI 193
                                666778899999999****99999998 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.7    0.0036         3      65     151 ..      80     168 ..      48     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0036
                      Atg14  65 kkakleelksliadlrerlqelkdklsqlkk..eieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqk 146
                                ++a l+e   ++ +l+e++++l + ++ l+k  +i++  + ++ l++++k+ +++les +n  +e  kk +++  +++ r +  
  gene76|gene76|rna76|rna76  80 LNAELQEYGEKRKILEEEISTLDAEIKMLDKmmSINQLEESIKILDKTVKDNQERLESFKNGGREVSKKDMENAKKKYERAQSG 163
                                445555555566666666666666666665533455556666666666666666666666666666666666666666655555 PP

                      Atg14 147 lssls 151
                                l++++
  gene76|gene76|rna76|rna76 164 LKKIR 168
                                44443 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.2     0.018        15     326     359 ..      80     111 ..      38     115 .. 0.54
   2 ?    3.8  13.7     0.021        18     327     412 ..     102     182 ..      70     197 .] 0.56

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.018
                       FapA 326 ievgldepelkeklkeleeeleeleeeleklkkk 359
                                ++   + +e+ ek+k leee+  l +e+++l+k+
  gene76|gene76|rna76|rna76  80 LN--AELQEYGEKRKILEEEISTLDAEIKMLDKM 111
                                22..222233334444444444444444444443 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.021
                       FapA 327 evgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                 ++++ ++ + ++++lee ++ l + +++ +++++++++ +      +  k++++++++++e+ ++ l++++++++e+ e+l +
  gene76|gene76|rna76|rna76 102 DAEIKMLDKMMSINQLEESIKILDKTVKDNQERLESFKNGGR-----EVSKKDMENAKKKYERAQSGLKKIRRIFNEVIERLSE 180
                                333444444445566666666666666666666555555332.....2345666666666666666666666666666666666 PP

                       FapA 411 kk 412
                                + 
  gene76|gene76|rna76|rna76 181 GM 182
                                53 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.2    0.0064       5.5      48      76 ..      83     113 ..      51     141 .. 0.66
   2 ?    1.1   0.9      0.62   5.3e+02      66      82 ..     119     135 ..     114     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0064
                    DUF4094  48 kdaesr.skdilg.evskthkaiqtLdktis 76 
                                + +e+  +++il+ e+s+   +i+ Ldk +s
  gene76|gene76|rna76|rna76  83 ELQEYGeKRKILEeEISTLDAEIKMLDKMMS 113
                                2222224778888888888888888888665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.62
                    DUF4094  66 kaiqtLdktissLemeL 82 
                                + i+ Ldkt+   +  L
  gene76|gene76|rna76|rna76 119 ESIKILDKTVKDNQERL 135
                                55555555555444333 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.4       0.1        88      46      82 ..      75     111 ..      39     115 .. 0.73
   2 ?    7.2   1.7    0.0093       7.9       5      73 ..     114     181 ..     110     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                    DUF2203  46 seaaeleaeleeleaeieelveeieelGvevkdleag 82 
                                +e  +l+ael+e+ ++ + l eei+ l +e+k l+++
  gene76|gene76|rna76|rna76  75 EEDVKLNAELQEYGEKRKILEEEISTLDAEIKMLDKM 111
                                2267788889999999999999999999999988865 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0093
                    DUF2203   5 leeAnalLpllkelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelG 73 
                                +++ ++ +  l++++++ ++  + +++  +e++++  e++k++++++++ l++++  ++e++e+++e G
  gene76|gene76|rna76|rna76 114 INQLEESIKILDKTVKDNQERLESFKNGGREVSKKDMENAKKKYERAQSGLKKIRRIFNEVIERLSE-G 181
                                5555666777777777777777777777778888888888888999999999999999999998876.4 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.6     0.073        62      70     118 ..      78     128 ..      38     136 .. 0.50
   2 ?    7.8   2.9     0.004       3.4      36     102 ..     113     179 ..     109     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.073
                                HHHHHHHHHHHHHHHHHHHCCCHHHHHHH..CCHHHHHHHHHHHHHHHHHH CS
                  Fib_alpha  70 kskkdndnvikksskeleeeilrlketid..aqesnirvLqnvlesneqki 118
                                 + + + + + + +k leeei++l+++i+  +++ +i++L + ++ +++ +
  gene76|gene76|rna76|rna76  78 VKLNAELQEYGEKRKILEEEISTLDAEIKmlDKMMSINQLEESIKILDKTV 128
                                333333555666666666666666555431134455555555555444433 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.004
                                HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHCCHH CS
                  Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeilrlketidaqes 102
                                ++++le++++ + ++ k+ +e  ++ k+  re  k++ +n ++ +++ ++ l+ +i r+ +++++  s
  gene76|gene76|rna76|rna76 113 SINQLEESIKILDKTVKDNQERLESFKNGGREVSKKDMENaKKKYERAQSGLK-KIRRIFNEVIERLS 179
                                68999999999999999999999999999999988888887889999999999.88888888877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2305  (0.128563); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 1190.77
//
Query:       gene761|gene761|rna760|rna760  [L=108]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-10   38.6   0.0    7.7e-10   38.4   0.0    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   4.3e-14   7.7e-10       2      92 ..      10     101 ..       9     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 4.3e-14
                                    HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHH...HTTEEEEEESCHHHHHHHTTSSS CS
                 Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealck...ekevpyvkvkskkeLGelvgkkr 78 
                                    ++ ++l +a+++g  ++G k+++k++  ++ak+ +++++ +  + k+ le+++      ++ ++++++ +eLG +  + +
  gene761|gene761|rna760|rna760  10 NVTSALLLAMRTGECIVGFKQAIKSVIMKRAKCLVISSNFPSTKRKQ-LEYYSVlagGLPIIFHNANN-EELGNITERGH 87 
                                    67789999**************************************9.66666663377777777777.*********** PP

                                    ECSEEEEEESTTTH CS
                 Ribosomal_L7Ae  79 pvsalaikdegdsk 92 
                                    +  +++i+d+g+++
  gene761|gene761|rna760|rna760  88 RLGCISIIDQGEAE 101
                                    **********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 759.00
//
Query:       gene762|gene762|rna761|rna761  [L=433]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.8e-32  109.6   0.1    3.4e-30  103.7   0.0    3.0  3  BING4CT      BING4CT (NUC141) domain
    0.00019   21.7   0.1        6.6    7.1   0.0    4.2  5  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
    0.00069   20.4   0.3        1.8    9.6   0.0    4.4  4  WD40         WD domain, G-beta repeat
  ------ inclusion threshold ------
      0.066   13.5   0.0       0.16   12.3   0.0    1.6  1  CBM_35       Carbohydrate binding module (family 35)


Domain annotation for each model (and alignments):
>> BING4CT  BING4CT (NUC141) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.43   1.9e+03       8      31 ..     151     174 ..     146     181 .. 0.70
   2 ?    2.3   0.0     0.032   1.4e+02       7      41 ..     192     226 ..     186     242 .. 0.88
   3 !  103.7   0.0   7.5e-34   3.4e-30       2      79 .]     316     392 ..     315     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.43
                        BING4CT   8 pgskieslrFvpfeDvlgvghskg 31 
                                    ++s + ++++ p++ +l   +++g
  gene762|gene762|rna761|rna761 151 DNSDVFKMEYLPYHYLLVSVSRRG 174
                                    467788899999987776555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.032
                        BING4CT   7 lpgskieslrFvpfeDvlgvghskgissiivPGsG 41 
                                    ++++++ s++  p + ++  g++kg+ s+  P s 
  gene762|gene762|rna761|rna761 192 MKNQEVISIKQNPMNAIIHTGSTKGVVSLWSPSSK 226
                                    678899999********************999885 PP

  == domain 3  score: 103.7 bits;  conditional E-value: 7.5e-34
                        BING4CT   2 YlthklpgskieslrFvpfeDvlgvghskgissiivPGsGepnfdaleanpfetkkqrrereVrsLLeKlqpelItld 79 
                                    Y++hk+ gs ++s++F+++eD+l++gh++gissiivPG+G+p +d++e+ pf +kk+rre+eVr+L+eK+++elI+++
  gene762|gene762|rna761|rna761 316 YIKHKV-GSLVSSVDFCNHEDILCIGHANGISSIIVPGCGDPVYDSYEDSPFTSKKARREKEVRRLMEKIPYELISME 392
                                    999985.679*****************************************************************995 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.63   2.8e+03      48      60 ..     123     135 ..     113     147 .. 0.81
   2 !    5.0   0.0    0.0068        31      37      86 ..     151     199 ..     123     203 .. 0.84
   3 !    5.1   0.0    0.0062        28      38      88 ..     194     243 ..     192     247 .. 0.91
   4 ?    3.0   0.0     0.029   1.3e+02      38      70 ..     236     268 ..     233     292 .. 0.80
   5 !    7.1   0.0    0.0015       6.6      34      65 ..     318     349 ..     280     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.63
                    ANAPC4_WD40  48 pdgklLavaysdg 60 
                                    ++++++ava +++
  gene762|gene762|rna761|rna761 123 HNERFIAVAQKNN 135
                                    7999999998876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0068
                    ANAPC4_WD40  37 edsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtc 86 
                                    ++s v ++++ p   lL+ +   g +r  d+++g+ v+++ +k+++ v +
  gene762|gene762|rna761|rna761 151 DNSDVFKMEYLPYHYLLVSVSRRGFLRYQDISTGNFVSQILMKNQE-VIS 199
                                    567899999999999*************************999996.554 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0062
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclg 88 
                                    ++ev s++ +p + ++  +  +g v+l + +s++ + ++ ++++ a+++++
  gene762|gene762|rna761|rna761 194 NQEVISIKQNPMNAIIHTGSTKGVVSLWSPSSKEYLMKILCHKS-AISSIE 243
                                    789999************************************99.588876 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.029
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesg 70 
                                    +s ++s++ + dg+ ++    d+++++ d  ++
  gene762|gene762|rna761|rna761 236 KSAISSIEIERDGRSMVTMGMDNRINVWDLRNT 268
                                    688999*********************998765 PP

  == domain 5  score: 7.1 bits;  conditional E-value: 0.0015
                    ANAPC4_WD40  34 edkedsevrsLaWkpdgklLavaysdgevrll 65 
                                    ++k +s v+s+ + + + +L++++++g  +++
  gene762|gene762|rna761|rna761 318 KHKVGSLVSSVDFCNHEDILCIGHANGISSII 349
                                    6788999********************98886 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.082   3.7e+02      15      38 .]     199     222 ..     183     222 .. 0.79
   2 !    9.6   0.0   0.00039       1.8       6      38 .]     232     264 ..     227     264 .. 0.83
   3 ?   -0.5   0.0      0.61   2.7e+03      29      38 .]     295     304 ..     270     304 .. 0.61
   4 ?    2.1   0.2      0.09     4e+02      12      32 ..     323     344 ..     313     356 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.082
                                    EEEEETTSSEEEEEETTSEEEEEE CS
                           WD40  15 slafspdgawlasGsdDgtvriWd 38 
                                    s++ +p +a + +Gs +g v +W+
  gene762|gene762|rna761|rna761 199 SIKQNPMNAIIHTGSTKGVVSLWS 222
                                    5666667777669*99*******5 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00039
                                    EEESS.SSEEEEEEETTSSEEEE.EETTSEEEEEE CS
                           WD40   6 tltGH.ssvtslafspdgawlas.GsdDgtvriWd 38 
                                    +l  H s ++s+   +dg+ +++ G+ D+ + +Wd
  gene762|gene762|rna761|rna761 232 IL-CHkSAISSIEIERDGRSMVTmGM-DNRINVWD 264
                                    44.79666************997566.*******9 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.61
                                    ETTSEEEEEE CS
                           WD40  29 sdDgtvriWd 38 
                                    s+ g+v+iW+
  gene762|gene762|rna761|rna761 295 SYGGNVHIWK 304
                                    4489999995 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.09
                                    S.EEEEEEETTSSEEEEEETTS CS
                           WD40  12 s.vtslafspdgawlasGsdDg 32 
                                    s v+s++f+ + + l+ G+ +g
  gene762|gene762|rna761|rna761 323 SlVSSVDFCNHEDILCIGHANG 344
                                    3567777777777776666554 PP

>> CBM_35  Carbohydrate binding module (family 35)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.5e-05      0.16      20      86 ..      88     157 ..      75     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                         CBM_35  20 kavsgtGyvgefegagdavslnVnvekaGeynlnvtfsapy...gsKentlvvnGtavatvafae.sdevk 86 
                                    +  ++ Gy+ +f++++ ++ ++++v+    y  +  ++ ++   ++K+n ++ +G  v+t  + + sd +k
  gene762|gene762|rna761|rna761  88 LLRNDRGYLASFNTKSMNLHFEIDVNDK-MYDAIYLHNERFiavAQKNNVFIYDGCGVETHCVRDnSDVFK 157
                                    556889*******************976.78888888888755579*********9999987765155554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2638.65
//
Query:       gene763|gene763|rna762|rna762  [L=320]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.8e-64  216.0   0.5    6.8e-64  215.8   0.5    1.1  1  Pkinase         Protein kinase domain
    2.2e-29  102.6   0.1    3.5e-29  101.9   0.1    1.3  1  Pkinase_Tyr     Protein tyrosine kinase
    6.3e-06   26.3   0.0    0.00049   20.1   0.0    2.1  2  APH             Phosphotransferase enzyme family
     0.0021   17.7   1.6     0.0076   15.9   0.3    2.2  2  Choline_kinase  Choline/ethanolamine kinase
     0.0064   15.3   0.2       0.11   11.2   0.0    2.0  2  Pkinase_fungal  Fungal protein kinase
  ------ inclusion threshold ------
      0.028   14.5   0.2      0.066   13.3   0.2    1.6  1  zf-C2H2_7       Zinc-finger
      0.055   13.1   0.4       0.22   11.1   0.0    1.9  2  FTA2            Kinetochore Sim4 complex subunit FTA2
       0.08   11.6   0.4       0.17   10.5   0.1    1.7  2  AXE1            Acetyl xylan esterase (AXE1)
       0.21   10.3   0.0        0.3    9.7   0.0    1.2  1  HCV_NS1         Hepatitis C virus non-structural protein E2/N
       0.45   10.6   2.5        2.2    8.4   0.3    2.6  2  DUF4176         Domain of unknown function (DUF4176)


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.8   0.5   3.8e-67   6.8e-64       1     264 []      37     316 ..      37     316 .. 0.91

  Alignments for each domain:
  == domain 1  score: 215.8 bits;  conditional E-value: 3.8e-67
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEE.SSEEE.EEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfee.kdely.lvle 78 
                                    y+  +++G+G++++V++++  ++++++++K++k  ++ k     + rE+ ilk+l+h+ni++l++v+ + ++++y l++e
  gene763|gene763|rna762|rna762  37 YQIYQRMGRGKYSEVFEGR--KDKEKIVIKTLKPVRKAK-----ISREVLILKSLSHKNIIKLIDVVVDsESQIYsLIFE 109
                                    67889**************..79999*******998887.....668******************99885555657**** PP

                                    --TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEE.TTTEEEE-SGTTSEESSSSCSBCTT CS
                        Pkinase  79 yveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLid.ekgelKitDFGlakelessskltsf 157
                                    y+e++++a++ e+   ls  ++ ++ kqil++l+y+Hs+giiHrD+Kp+N+ i+ e++elKi+D+Gla+ ++ +++++ +
  gene763|gene763|rna762|rna762 110 YIEHEDYAKIFEK---LSYMDIIEYSKQILSALDYCHSMGIIHRDIKPQNMVINrERRELKIIDWGLAEFYHPKKEYSVR 186
                                    ***********95...**************************************88999********************* PP

                                    TSCGGGS-HHHH.TTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS... CS
                        Pkinase 158 vgtseYlAPEvl.keneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeasei... 233
                                    v++++Y +PE+l ++  y+ + D+Ws G++l+el+++k pf + ++      + dql+ki+++lg t++    ++     
  gene763|gene763|rna762|rna762 187 VASRYYKSPELLvDYPYYDYSLDIWSFGCVLAELIFKKRPFFHGES------NSDQLVKIARVLGYTDLRKYIEKYRiap 260
                                    ************777888************************4444......6699999999999655544444433488 PP

                                    .........................-HHHHHHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 234 .........................seeakdllkkllkkdpkkRltaeellqhpyl 264
                                                               +a+dll+k+l +d+++R+taee+l+hp +
  gene763|gene763|rna762|rna762 261 lspkhegtgervllssfvplgkanlYIHAIDLLEKILVYDHQSRPTAEECLRHPLF 316
                                    88999******************99999**************************87 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.1   1.9e-32   3.5e-29       3     211 ..      39     233 ..      37     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 1.9e-32
                                    EEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEE..SSSSEEEEE CS
                    Pkinase_Tyr   3 lgkklGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvct..keepllivt 80 
                                    + +++G+G++++V+eg+ +      ++k+++Ktlk   ++    ++ +e+ i+k+l+h+ni+kl+ v++  +++ + +++
  gene763|gene763|rna762|rna762  39 IYQRMGRGKYSEVFEGRKD------KEKIVIKTLKPVRKA----KISREVLILKSLSHKNIIKLIDVVVdsESQIYSLIF 108
                                    6789************999......99*******776555....599**********************54444488*** PP

                                    E--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETT.EEEE-STTTHEETTTSSEE CS
                    Pkinase_Tyr  81 eyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenk.vvkisDfGLardiekddey 159
                                    ey+++ d  k  +k     l++ d+++++ q+ ++++y +s+ ++Hrd+  +N+++++++   ki D GLa+  + ++ey
  gene763|gene763|rna762|rna762 109 EYIEHEDYAKIFEK-----LSYMDIIEYSKQILSALDYCHSMGIIHRDIKPQNMVINRERrELKIIDWGLAEFYHPKKEY 183
                                    *****999888766.....6************************************986549************888888 PP

                                    EETTSSTSGGGGS-HHHHHHSEEEHHH.HHHHHHHHHHHHHTTSSGTTTTSHH CS
                    Pkinase_Tyr 160 vkkeeaklpvkWmapEslkekkftsks.DvWsfGvllwEiftlgespypglkn 211
                                    +++  ++    + +pE l +  +   s D+WsfG +l E++ + +  ++g +n
  gene763|gene763|rna762|rna762 184 SVRVASR---YYKSPELLVDYPYYDYSlDIWSFGCVLAELIFKKRPFFHGESN 233
                                    7666544...577*****9999666655***********99754444444444 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.019        35       6      84 ..      44     118 ..      40     127 .. 0.77
   2 !   20.1   0.0   2.7e-07   0.00049     165     201 ..     144     179 ..     121     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.019
                                    --.SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS CS
                            APH   6 sggasnrtylvttpagryvlrrnpparaaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr 84 
                                    + g ++ +++   ++ + v +   p   +++i+rev +l+ L+  ++   ++++    d e+ ++++++ey++ ++++ 
  gene763|gene763|rna762|rna762  44 GRGKYSEVFEGRKDKEKIVIKTLKPV-RKAKISREVLILKSLSHKNI--IKLIDVV-VDSESQIYSLIFEYIEHEDYAK 118
                                    56677777777777888888888888.99**************9988..4666643.345555569*******999876 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.7e-07
                                    -EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEEC CS
                            APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfedaglgpp 201
                                    +++++H+D++p+N++++ +  ++  +iD+++a   +p
  gene763|gene763|rna762|rna762 144 SMGIIHRDIKPQNMVINRERREL-KIIDWGLAEFYHP 179
                                    5789*************555555.7*******88887 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   4.2e-06    0.0076     118     172 ..     116     172 ..      97     179 .. 0.69
   2 ?   -0.4   0.0      0.41   7.4e+02     168     195 ..     198     224 ..     194     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-06
                                    CHCCCTHHHHHHHHHTHHHHHHCHGG-..EEEE-S--SGGGEEE.-CTTEEEE--GT CS
                 Choline_kinase 118 qlklinledlekelekleklleelesp..vvfcHnDlqegNillnkeekklvlIDFE 172
                                     +k ++  ++++ +e  +++l+ l++   +   H D+ ++N++ n e+++l +ID+ 
  gene763|gene763|rna762|rna762 116 YAKIFEKLSYMDIIEYSKQILSALDYChsMGIIHRDIKPQNMVINRERRELKIIDWG 172
                                    3344444445555555555555444434488889**********************5 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.41
                                    E--GTT-EEEEHHHHHHHHHHHTTEEHH CS
                 Choline_kinase 168 lIDFEYagynyrgfDlanhfiEwagdye 195
                                    l+D+ Y  y+   + ++ +++E  ++ +
  gene763|gene763|rna762|rna762 198 LVDYPYYDYSLDIWSFGCVLAELIFK-K 224
                                    89********************9993.2 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.04        71     149     207 ..      40      97 ..      31     114 .. 0.75
   2 !   11.2   0.0   6.3e-05      0.11     323     375 ..     143     187 ..     114     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.04
                 Pkinase_fungal 149 rqraivgRgTtcwrarkegergkeyvvKdsWr..daerksEaelLkkaeergvegvarlva 207
                                     qr  +g+   ++++rk++e+   +v+K      +a+ ++E+ +Lk  +++++  +  +v 
  gene763|gene763|rna762|rna762  40 YQRMGRGKYSEVFEGRKDKEK---IVIKTLKPvrKAKISREVLILKSLSHKNIIKLIDVVV 97 
                                    56666778889******8776...9***986521455559*******98888877666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.3e-05
                 Pkinase_fungal 323 flkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarert 375
                                    +   gi+HrDi  +N++i+     ++r+  +iD  la  ++ +++ s+   r+
  gene763|gene763|rna762|rna762 143 H-SMGIIHRDIKPQNMVIN----RERRELKIIDWGLAEFYHPKKEYSV---RV 187
                                    4.78***************....4567778999999988886444443...44 PP

>> zf-C2H2_7  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.7e-05     0.066      17      40 ..      20      43 ..      16      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                      zf-C2H2_7 17 kPykykcfqcPftcnikshlynhm 40
                                   k ++y+c+  P  c +k  +y  m
  gene763|gene763|rna762|rna762 20 KYWNYECYNIPTGCIEKYQIYQRM 43
                                   789******************999 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.54   9.7e+02      24      62 ..      37      75 ..      31     120 .. 0.66
   2 ?   11.1   0.0   0.00012      0.22     175     204 ..     129     158 ..     119     161 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.54
                           FTA2 24 iefleyLgkglhsiVlkvkirgkeYALKlFrfleaeele 62
                                   +++ + +g+g  s V++ + ++++ ++K  + +++ + +
  gene763|gene763|rna762|rna762 37 YQIYQRMGRGKYSEVFEGRKDKEKIVIKTLKPVRKAKIS 75
                                   567778888888888888888888888877777554443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00012
                           FTA2 175 vsqlpkllrdlkklhklgIvvrDlkeenyi 204
                                    +++ +++l+ l+  h+ gI++rD+k++n++
  gene763|gene763|rna762|rna762 129 IEYSKQILSALDYCHSMGIIHRDIKPQNMV 158
                                    567899*********************986 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   9.7e-05      0.17     219     258 ..      99     135 ..      88     154 .. 0.84
   2 ?   -3.4   0.0       1.7     3e+03     229     254 ..     227     252 ..     225     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.7e-05
                                    S.STTCHHHHHHHHHSH-CCHHHHHHHHHHTT-HHHHHCC- CS
                           AXE1 219 l.eeaYdEitrylkldperekeeevletLsYiDvknlAkrv 258
                                      ++ Y+ i++y+     +e  ++++e+LsY+D+++  k++
  gene763|gene763|rna762|rna762  99 SeSQIYSLIFEYIE----HEDYAKIFEKLSYMDIIEYSKQI 135
                                    34788999999998....999*************9998876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.7
                                    HHHHSH-CCHHHHHHHHHHTT-HHHH CS
                           AXE1 229 ylkldperekeeevletLsYiDvknl 254
                                    +++ +++ ++  ++ + L+Y D+ + 
  gene763|gene763|rna762|rna762 227 FFHGESNSDQLVKIARVLGYTDLRKY 252
                                    67777788888889999999998765 PP

>> HCV_NS1  Hepatitis C virus non-structural protein E2/NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00017       0.3     204     250 ..     178     230 ..     174     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00017
                                    XXXXXX.XXXXSSXECCTTEEEXXTT.....HHHHXGGGCCXEEEEEEEEETT CS
                        HCV_NS1 204 hpeaty.lkcgsgpwltprclvdypy.....rlwhypctvnftifkvrmyvgg 250
                                    hp+  y +++ s  + +p  lvdypy      +w + c +   ifk r +  g
  gene763|gene763|rna762|rna762 178 HPKKEYsVRVASRYYKSPELLVDYPYydyslDIWSFGCVLAELIFKKRPFFHG 230
                                    56666625788888999********94444448*************9988766 PP

>> DUF4176  Domain of unknown function (DUF4176)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3    0.0012       2.2      27      70 ..      13      59 ..       1      63 [. 0.68
   2 ?    1.2   0.1      0.22   3.9e+02      30      47 ..     201     218 ..     180     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                        DUF4176 27 e...eekkiydYvgclYPeGildsektllfnhedIekvvflGyedee 70
                                   +   +++k+++Y     P+G +++ +++  +     + vf+G +d+e
  gene763|gene763|rna762|rna762 13 AnekKDEKYWNYECYNIPTGCIEKYQIYQRMGRGKYSEVFEGRKDKE 59
                                   22336666***************999987666665555666666655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.22
                        DUF4176  30 kkiydYvgclYPeGilds 47 
                                      +ydY+  ++  G + +
  gene763|gene763|rna762|rna762 201 YPYYDYSLDIWSFGCVLA 218
                                    349*******99998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 1945.37
//
Query:       gene764|gene764|rna763|rna763  [L=290]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-22   79.5   0.0    7.6e-22   78.8   0.0    1.3  1  4HBT_3         Thioesterase-like superfamily
    4.2e-07   29.9   0.0    0.00087   19.1   0.0    2.9  2  Acyl_CoA_thio  Acyl-CoA thioesterase


Domain annotation for each model (and alignments):
>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   8.4e-26   7.6e-22       4     247 ..      19     280 ..      17     281 .. 0.71

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 8.4e-26
                                    GGECTTC...-HHHHHHHHHHHHHHT.-S.SS.EEEEEEE-S---SE.EEEEEEEEEE--SS-EEEEEEEEETTEEEEEE CS
                         4HBT_3   4 pwtpgga.g.yGGyvlAlalraaqrtvpdprl.hslhvyFlrpgdag.pviyhvervrdGrsfstrtvelsqggrpifta 79 
                                    +w+p  + + +GG+++A+ l+aa +tv ++ +  ++++ F+++++++ +v y v+ ++dG  + +r+v  +q++  + +a
  gene764|gene764|rna763|rna763  19 LWSPFPGyPaFGGQLAAQSLAAAFATVGENSIpITMSILFINRCKSSqKVKYAVKSLKDGSIVDMRQVDCYQNDVLVSSA 98 
                                    6999999888*****************7766788********************************************** PP

                                    EEEEE---T....---EE----.......---.GGG.E---.--SSGGGS.GG..TEEEE-HHT---S........S-EE CS
                         4HBT_3  80 tasfgraestgwelepaaappp.......vpppdea.alaadeaplplfr.rvpgflepfeprpaeggkpd.spagpkrv 149
                                     +sf+r+++++++ e+   +p        +p   e  + ++  ++ p+++  ++ ++    + ++ +  ++  +  +k +
  gene764|gene764|rna763|rna763  99 HISFSRPDNNAHDYES---NPYkiyddtfIPF-SEYiSRSMATSSVPQAEvNAKFQILYDNMLMMLNVLDVdVGVENKDM 174
                                    ********83322222...2221111122222.22212222233333332222222222222222222222133334444 PP

                                    EE.EEEETTTS-SSH..HHHHHHHTT-....-GGGGTSS-......SB--EEEEEEEE-S--S-.....EEEEEE-SEEE CS
                         4HBT_3 150 rq.Wvrlreggepah..laaLaylsDs.f..pvprvhglrldaeasgwmpsldltiyfhrepae..deWllleaetpwag 221
                                    rq  ++ +e++e      + L ++sD+ +  +++++++l l   +     sl++ ++f +  ++  d  l++ ++++ ++
  gene764|gene764|rna763|rna763 175 RQiRIKIKEEQESIKgkASLLTLISDIlLveTALMTSNLTLFSSDLSLLTSLNHVVNFVNLEKDisDGYLYYIVKCKGIR 254
                                    43246666555655543555*******66999999999997766678999*********944346799************ PP

                                    TTEEEEEEEEE-TTS-EEEEEEEEEE CS
                         4HBT_3 222 dgrglvearlwdedGrlvAtstQegl 247
                                    +  + +e++l  edG l++++ Q+g+
  gene764|gene764|rna763|rna763 255 NSKAICEGQLIHEDGALICLTGQQGV 280
                                    ***********************997 PP

>> Acyl_CoA_thio  Acyl-CoA thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00049       4.4      79     127 ..      52      98 ..      24     102 .. 0.81
   2 !   19.1   0.0   9.7e-08   0.00087      50     132 .]     193     280 ..     168     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00049
                                    EEEEEEE-S--BTTS-EEEEEEEEEEETTEEEEEECCEE......ECTTEEEEEE CS
                  Acyl_CoA_thio  79 ldHsvyFlrpgdlnewilydvespsasggrgLrqGriFs......tqdgkliasv 127
                                    +  s+ F++  ++ +++ y+v+s        L++G i +      +q++ l++s+
  gene764|gene764|rna763|rna763  52 ITMSILFINRCKSSQKVKYAVKS--------LKDGSIVDmrqvdcYQNDVLVSSA 98 
                                    445999*****************........777777777777778999999875 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 9.7e-08
                                    CHHHHHTTSSSGGGGGGGGT..TTSTTEEE..EEEEEEEE-S--.BTTS.-EEEEEEEEEEETTEEEEEECCEEECTTEE CS
                  Acyl_CoA_thio  50 vllaYlSDltllltalttHe..lledslqv..sldHsvyFlrpg.dlne.wilydvespsasggrgLrqGriFstqdgkl 123
                                     ll+ +SD+ l++tal+t +  l    l+   sl+H v F++   d+ +  ++y v+     +++++ +G+     dg l
  gene764|gene764|rna763|rna763 193 SLLTLISDILLVETALMTSNltLFSSDLSLltSLNHVVNFVNLEkDISDgYLYYIVKCKGIRNSKAICEGQLI-HEDGAL 271
                                    568899**************986666777668*********97525555156666677677899********9.****** PP

                                    EEEEEEEEE CS
                  Acyl_CoA_thio 124 iasvqqeGl 132
                                    i+ + q+G+
  gene764|gene764|rna763|rna763 272 ICLTGQQGV 280
                                    ******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1780.79
//
Query:       gene765|gene765|rna764|rna764  [L=567]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-31  108.1   0.0    1.3e-30  106.7   0.0    1.8  1  RFC1             Replication factor RFC1 C terminal domain
    7.8e-16   58.7   0.0    2.2e-15   57.3   0.0    1.8  1  AAA              ATPase family associated with various cellul
    4.1e-14   52.7   0.0      1e-13   51.4   0.0    1.7  1  BRCT             BRCA1 C Terminus (BRCT) domain
    6.7e-07   29.4   0.0    1.5e-06   28.2   0.0    1.5  1  Rad17            Rad17 P-loop domain
    4.3e-06   26.6   0.0    9.5e-06   25.4   0.0    1.6  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    7.7e-06   26.0   0.1    6.4e-05   23.0   0.0    2.5  2  AAA_14           AAA domain
    2.2e-05   24.3   0.1      9e-05   22.4   0.0    2.0  2  PTCB-BRCT        twin BRCT domain
    2.2e-05   24.5   0.0    4.6e-05   23.4   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
    4.4e-05   22.9   0.0    8.8e-05   21.9   0.0    1.5  1  Zeta_toxin       Zeta toxin
    7.4e-05   22.7   0.3    0.00082   19.3   0.2    2.4  2  NTPase_1         NTPase
     0.0001   22.5   0.0    0.00026   21.1   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00018   21.4   0.4       0.23   11.3   0.2    2.6  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0003   21.2   0.0    0.00064   20.1   0.0    1.5  1  AAA_16           AAA ATPase domain
    0.00093   19.6   0.1     0.0035   17.7   0.0    2.0  1  RNA_helicase     RNA helicase
    0.00099   18.4   0.2     0.0065   15.7   0.1    2.2  2  TIP49            TIP49 P-loop domain
     0.0014   18.0   0.5       0.02   14.2   0.0    2.5  2  ATPase           KaiC
     0.0038   17.5   0.2      0.063   13.6   0.2    2.5  1  AAA_22           AAA domain
     0.0047   16.5   0.0      0.011   15.3   0.0    1.6  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.035   14.1   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.018   14.4   0.3      0.053   12.8   0.0    1.9  2  6PF2K            6-phosphofructo-2-kinase
      0.018   15.6   0.0       0.05   14.2   0.0    1.8  1  AAA_18           AAA domain
       0.02   13.7   0.0      0.036   12.9   0.0    1.3  1  PPV_E1_C         Papillomavirus helicase
      0.027   14.9   0.1       0.14   12.6   0.1    2.3  1  AAA_17           AAA domain
      0.057   13.1   0.1        0.2   11.4   0.0    1.9  2  AAA_24           AAA domain
      0.058   13.1   0.0       0.13   12.0   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.068   12.7   0.0       0.13   11.8   0.0    1.4  1  AAA_25           AAA domain
       0.07   12.3   0.1       0.18   10.9   0.1    1.7  1  DUF815           Protein of unknown function (DUF815)
       0.09   12.9   0.0       0.24   11.6   0.0    1.7  1  AAA_33           AAA domain
      0.096   12.6   0.1       0.19   11.6   0.1    1.5  1  RsgA_GTPase      RsgA GTPase
       0.11   11.9   0.3       0.25   10.7   0.3    1.5  1  KTI12            Chromatin associated protein KTI12
       0.12   12.2   0.0       0.28   11.0   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
       0.13   12.2   0.0       0.64    9.9   0.0    2.0  2  NACHT            NACHT domain
       0.13   12.0   0.3        5.5    6.7   0.0    2.5  2  DEAD             DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.0   2.4e-33   1.3e-30       1     157 []     387     534 ..     387     534 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 2.4e-33
                                    HHHHHHHHHHHTT.SS-GGGHHHHHHHHTHHHHHTT-EE-SS-----SHHHHHHHHHHHHHHHHHHHTTTTT------HH CS
                           RFC1   1 isdgDlvdkkirs.eqnWsLlpthavlssvlPaslvrgslegrisFpswLGknSktnKnkRllqelqshlrlktsaskse 79 
                                    is gD+v+k ir+ +q+WsL p+hav+s+v+P+      l+++++FpswLG+nSk++K +R+l   ++h ++k++ +++e
  gene765|gene765|rna764|rna764 387 ISLGDVVEKLIRGaDQDWSLAPLHAVYSVVIPT--KGRPLTKKMMFPSWLGQNSKHSKAERILYMASMHSSCKIRVNTEE 464
                                    89******************************6..4445788************************************** PP

                                    HHHTTTHHHHHHHHS---------HHHHHHTTT--SHHHHHHHHHH-X...XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           RFC1  80 lrldylpllkkklvkpLkeegkdgveevielmdeysLtkedvdslvelslvkgekkkedplkkidtkvKaaftrkynk 157
                                    lr + l+l++kk   +Lk+   + ++++i+ + +y++tked+  l ++      ++ +d++++++ k +  + ++y+k
  gene765|gene765|rna764|rna764 465 LRKYALELILKKHAYHLKT---HCIDKAIDDIADYDMTKEDITGLGSI--L---PGGADLFEGVERKARFLLDKEYKK 534
                                    *******************...57************************..5...67899***********99999997 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0     4e-18   2.2e-15       1     128 [.     147     262 ..     147     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 4e-18
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksrsgs 77 
                                    vll+G pG+GKT++a+ v+k lg +++e+++s+++sk  +e ++kir ++++ +  +   k+++l++DE+d + ++r   
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYLGLDVVEFNASDVRSK--SEISSKIRSFVNSQSVYSresKKKVLIMDEVDGMSSDR--- 221
                                    79*********************************77..89999999999987555566678***********9999... PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEE CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrki 128
                                            +++L++++++         +i+++n+ ++l+   l+ + +d ++
  gene765|gene765|rna764|rna764 222 ------GGIPELVNVIKEAMI-----PIICICNDRNNLKIRTLSnHCLDLRF 262
                                    ......779999999998866.....79999999888877777666666665 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0   1.9e-16     1e-13       4      79 .]       6      79 ..       4      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.9e-16
                                   TTTTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHHH CS
                           BRCT  4 llfhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldci 79
                                    +++g++fv+ ++   + rd++++++  +GG++tt  s+ktt+lv+ge+  + +k+++a++l+i+i++ee + ++i
  gene765|gene765|rna764|rna764  6 EPLKGKVFVF-TGDMKISRDDAKTKVMVLGGRCTTVPSSKTTFLVTGEN-PGASKMQKAKELGIEILNEEDFTKLI 79
                                   699*******.**************************************.********************998876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   2.8e-09   1.5e-06       8     102 ..     111     200 ..     106     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 2.8e-09
                          Rad17   8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn 87 
                                     W eky+P k++e+      +++++++l+ ++  ++    +L+sG +G gk+t+ +v+ k lg ++ e+ n+  +++ + 
  gene765|gene765|rna764|rna764 111 IWSEKYRPSKKNEIVGNVGIVKQLEDYLQGHTKYKA----VLLSGQPGVGKTTMAHVVCKYLGLDVVEF-NASDVRSKSE 185
                                    6*************99999999***99999875555....999************************96.88888***** PP

                          Rad17  88 qksdfkgltekesrf 102
                                      s +++ ++ +s +
  gene765|gene765|rna764|rna764 186 ISSKIRSFVNSQSVY 200
                                    9******99999955 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.7e-08   9.5e-06       2      82 ..     117     193 ..     116     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.7e-08
                         RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltn 81 
                                    rP++ +e +g   + ++l+ +++   k       vll+G PG+Gktt+a++++k lg ++    +  +  ++++++ + +
  gene765|gene765|rna764|rna764 117 RPSKKNEIVGNVGIVKQLEDYLQGHTK----YKAVLLSGQPGVGKTTMAHVVCKYLGLDVVEFNASDVRSKSEISSKIRS 192
                                    899999999999999999999887654....5579*********************999888777777777777665544 PP

                         RuvB_N  82 l 82 
                                    +
  gene765|gene765|rna764|rna764 193 F 193
                                    3 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.2e-07   6.4e-05       2      84 ..     144     232 ..     143     252 .. 0.77
   2 ?   -0.7   0.0       2.5   1.4e+03      29      64 ..     442     476 ..     432     508 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.2e-07
                         AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lke..ekktylflDEiqev.. 76 
                                    +k+++++G   vGKTt+++ + k l     +++++n  d r k++  + k+ +++ ++ +++  +kk++l++DE+  +  
  gene765|gene765|rna764|rna764 144 YKAVLLSGQPGVGKTTMAHVVCKYLG---LDVVEFNASDVRSKSEISS-KIRSFVNSQsVYSreSKKKVLIMDEVDGMss 219
                                    6899*************999987777...99********999765544.56666666664335689*********98755 PP

                         AAA_14  77 .....pewekalk 84 
                                         pe+ +++k
  gene765|gene765|rna764|rna764 220 drggiPELVNVIK 232
                                    5555555555555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                         AAA_14  29 kkesilyinldderdkkladpekllelileklkeek 64 
                                    k+e+ily++  + + k + ++e+l ++ le++ + k
  gene765|gene765|rna764|rna764 442 KAERILYMASMHSSCKIRVNTEELRKYALELILK-K 476
                                    5788888888887776655666677777766433.2 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.7e-07     9e-05      12      60 ..      19      71 ..      12      73 .. 0.87
   2 ?   -2.2   0.0       7.6   4.2e+03      34      42 ..     159     167 ..     157     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-07
                                   C...HHHHHHHHHHTT-EEESSEETT-SEEEE.CSS-CHHHHHHHHCT-EEE- CS
                      PTCB-BRCT 12 d...rkslqklieamGaeyskdltksvTHLic.ksgeGekyekAkkwgipvVs 60
                                       r+++++ +  +G+ +++  + ++T+L+  +++  +k +kAk+ gi++ +
  gene765|gene765|rna764|rna764 19 MkisRDDAKTKVMVLGGRCTTVPSSKTTFLVTgENPGASKMQKAKELGIEILN 71
                                   33449***************************888899***********9986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.6
                                    T-SEEEECS CS
                      PTCB-BRCT  34 svTHLicks 42 
                                    ++ H++ck 
  gene765|gene765|rna764|rna764 159 TMAHVVCKY 167
                                    567****96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   8.5e-08   4.6e-05       2      89 ..     147     231 ..     146     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.5e-08
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HH CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraese 80 
                                    vlL G+pG+gK+++a  +++ l+  v++ + ++  +++++  +++      s+v+s  v + + ++++l++DEv+ ++s+
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYLGLDVVEFNASDVRSKSEISSKIR------SFVNSQSVYSREsKKKVLIMDEVDGMSSD 220
                                    89**************************99999999999999998......677776665555699*********88865 PP

                                    ..HHHHHHHHH CS
                          AAA_5  81 ..vlnsLlsll 89 
                                       +++L +++
  gene765|gene765|rna764|rna764 221 rgGIPELVNVI 231
                                    11455555555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.6e-07   8.8e-05      10      56 ..     137     182 ..     129     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.6e-07
                     Zeta_toxin  10 ypsq.erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56 
                                    y ++  + k++ll+GqpG GK+++a+ + ++l  + +vv++++ d+R+
  gene765|gene765|rna764|rna764 137 YLQGhTKYKAVLLSGQPGVGKTTMAHVVCKYL--GLDVVEFNASDVRS 182
                                    555556779***********************..9*********9997 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   1.5e-06   0.00082       2      43 ..     147     185 ..     146     238 .. 0.84
   2 ?    1.1   0.1      0.58   3.2e+02      89     135 ..     199     245 ..     184     257 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE----- CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggr 43 
                                    v+++G+pGvGKtT+ + v++ l   g+ v  f +++vr++ +
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYL---GLDVVEFNASDVRSKSE 185
                                    789*******************...9*********9998653 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.58
                                    HHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS CS
                       NTPase_1  89 lrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrr 135
                                    +    s++ v+++DE+  m      + e v+ + +   p++ +   r
  gene765|gene765|rna764|rna764 199 VYSRESKKKVLIMDEVDGMSSDRGGIPELVNVIKEAMIPIICICNDR 245
                                    444558999*******9998877777777766666666776666655 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   4.9e-07   0.00026       5      82 ..     146     219 ..     142     230 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 4.9e-07
                                    -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                          AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                     +ll g+ gvGkt +a  + ++l +     ++ ++as++  + e+++ + +++ ++  y +  ++ ++ +DE+d  ++
  gene765|gene765|rna764|rna764 146 AVLLSGQPGVGKTTMAHVVCKYLGL----DVVEFNASDVRSKSEISSKIRSFVNSQSVYSRESKKKVLIMDEVDGMSS 219
                                    57899*******************8....899999999999999******************************7776 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0054       2.9       5      43 ..     130     168 ..     126     171 .. 0.89
   2 !   11.3   0.2   0.00041      0.23      86     161 ..     188     264 ..     170     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0054
                DNA_pol3_delta2   5 alkilskalksgrlahayLfeGdegigkkelalnlakal 43 
                                    ++k+l+  l+  +  +a L++G+ g+gk ++a  ++k l
  gene765|gene765|rna764|rna764 130 IVKQLEDYLQGHTKYKAVLLSGQPGVGKTTMAHVVCKYL 168
                                    578999999999999*****************9999876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00041
                DNA_pol3_delta2  86 dqirelieelsrkpreskkkiiiiedaekmtks..AaNalLktlEEPsenaifiLitsdtnkl.LktirSRcqelkfsp 161
                                     +ir++ ++ s  +reskkk++i+++++ m++       l  ++ E    + +i i +d n+l + t+   c  l+f++
  gene765|gene765|rna764|rna764 188 SKIRSFVNSQSVYSRESKKKVLIMDEVDGMSSDrgGIPELVNVIKEA--MIPIICICNDRNNLkIRTLSNHCLDLRFRK 264
                                    6899**************************87611445688888887..666777888888888888888888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.2e-06   0.00064       9      63 ..     131     180 ..     124     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-06
                         AAA_16   9 leqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    ++qL+++l+   +    +vllsG++GvGK++++  + ++l  d   +++ ++ + 
  gene765|gene765|rna764|rna764 131 VKQLEDYLQGHTKY--KAVLLSGQPGVGKTTMAHVVCKYLGLD---VVEFNASDV 180
                                    78899999855444..89****************999999888...455555554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.4e-06    0.0035       1      83 [.     147     237 ..     147     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.4e-06
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..........klkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenpsdl 70 
                                    ++l+G++g+GK+t+a+ ++k l  ++          k++ ++++ s  +++++++  ++++v+++d++  ++++     +
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYLGLDVvefnasdvrsKSEISSKIRSFVNSQSVYSRESKKKVLIMDEVDGMSSD--RGGI 224
                                    6799******************9666788888888866666777777777888888889999999999999877..3466 PP

                   RNA_helicase  71 aelirlvsstpyp 83 
                                     el+++++ + +p
  gene765|gene765|rna764|rna764 225 PELVNVIKEAMIP 237
                                    6666666665555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.2e-05    0.0065      50      91 ..     144     183 ..     128     214 .. 0.83
   2 ?    0.9   0.1      0.38   2.1e+02     251     322 ..     183     251 ..     181     260 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevysl 91 
                                     +avLl+G++g Gkt +a  + k lg d   v +++s+v s 
  gene765|gene765|rna764|rna764 144 YKAVLLSGQPGVGKTTMAHVVCKYLGLD--VVEFNASDVRSK 183
                                    59************************55..588899998764 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.38
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 251 kteiteklreeinkkvakyveegkaeivpGvlfiDevhml..DiecfsylnraleselaPivilatnrgiakir 322
                                    k+ei +k+r+ +n +   y  e k      vl +Dev  +  D      l  ++ + + Pi+ ++ +r   kir
  gene765|gene765|rna764|rna764 183 KSEISSKIRSFVNSQSV-YSRESKK----KVLIMDEVDGMssDRGGIPELVNVIKEAMIPIICICNDRNNLKIR 251
                                    56777777777776644.3333333....467788887662344556668888888888888888888888887 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.7e-05      0.02       5      36 ..     131     161 ..     127     168 .. 0.89
   2 ?    0.8   0.1      0.46   2.5e+02      92     154 ..     179     234 ..     169     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                         ATPase   5 IeglDeilkgGipegrvvlitGepGtGKtifa 36 
                                    ++ l++ l +G  ++++vl++G+pG GKt++a
  gene765|gene765|rna764|rna764 131 VKQLEDYL-QGHTKYKAVLLSGQPGVGKTTMA 161
                                    57788888.999*******************8 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                         ATPase  92 aeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkkl 154
                                    + + ++++ ++++++++++   + +e k k +++D ++g+      +  R  + +lv+v+k+ 
  gene765|gene765|rna764|rna764 179 DVR-SKSEISSKIRSFVNSQSVYSRESKKKVLIMDEVDGM------SSDRGGIPELVNVIKEA 234
                                    333.334788999999999999999*************99......33355555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   0.00012     0.063       7      76 ..     146     206 ..     141     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsse 76 
                                     +++ G++G+GKTt +  + + l         + +vv+++++   s +++ +++ ++++++  ++r s++
  gene765|gene765|rna764|rna764 146 AVLLSGQPGVGKTTMAHVVCKYL---------GLDVVEFNASDVRSKSEISSKIRSFVNSQSVYSRESKK 206
                                    67999************999999.........9***********************99988777444433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-05     0.011      32     116 ..     143     221 ..     131     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                          AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDlnm 111
                                    + k vll G+ G+GKt++++ ++k l    + ++ +n s   s +++ + i s ++ ++  vy    +kk+++ +D+++ 
  gene765|gene765|rna764|rna764 143 KYKAVLLSGQPGVGKTTMAHVVCKYLG---LDVVEFNASDVRSKSEISSKIRSFVNSQS--VYSRESKKKVLI-MDEVDG 216
                                    6689********************999...99999*******************99876..888887777766.787776 PP

                          AAA_7 112 pakek 116
                                       ++
  gene765|gene765|rna764|rna764 217 MSSDR 221
                                    66655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.4e-05     0.035      18      47 ..     138     172 ..     126     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.4e-05
                                    H.....TEEEEEEESTTSSHHHHHHHHHHHTT--- CS
                           TsaE  18 l.....gdvilLeGdLGaGKTtlvrglakalgvee 47 
                                    l      +++lL+G+ G+GKTt+++ ++k lg++ 
  gene765|gene765|rna764|rna764 138 LqghtkYKAVLLSGQPGVGKTTMAHVVCKYLGLDV 172
                                    333223457**********************9874 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.8e-05     0.053      12      97 ..     143     222 ..     133     265 .. 0.70
   2 ?   -2.6   0.0       5.2   2.8e+03      61      91 ..     466     496 ..     448     502 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.8e-05
                                    S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS---GGGGSTT-HHHHHHHHHHHHHHHHHHHHH CS
                          6PF2K  12 sklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaskalsdaeffrpdneealklreklalaalkdllay 91 
                                    +  +++l G p  gKt++++ +++yl   g++   Fn++++r + + + +  +f+   n++++  re   +  + d ++ 
  gene765|gene765|rna764|rna764 143 KYKAVLLSGQPGVGKTTMAHVVCKYL---GLDVVEFNASDVRSKSEISSKIRSFV---NSQSVYSRESKKKVLIMDEVDG 216
                                    55678999***************997...788889******98777665555555...5555666665555566666666 PP

                                    HHTS-- CS
                          6PF2K  92 lneeeg 97 
                                    ++++ g
  gene765|gene765|rna764|rna764 217 MSSDRG 222
                                    666666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.2
                                    --GGGGSTT-HHHHHHHHHHHHHHHHHHHHH CS
                          6PF2K  61 sdaeffrpdneealklreklalaalkdllay 91 
                                    +++  +    + a +l+ ++  +a++d+++y
  gene765|gene765|rna764|rna764 466 RKYALELILKKHAYHLKTHCIDKAIDDIADY 496
                                    5555556666788889999999999999988 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.2e-05      0.05       1      44 [.     147     193 ..     147     219 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.2e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpe 44 
                                    +ll+G pGvGKtt+a+ + k lg+    +n +dv ++++++     +
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYLGLdvvEFNASDVRSKSEISSKIRSF 193
                                    799**************988888888888888887777776665555 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.6e-05     0.036     243     296 ..     125     178 ..      99     185 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                       PPV_E1_C 243 velisfltalkefLkgvPkknclvllGppntGkslfamslikfLkGkvlsfvns 296
                                    v  +  + +l ++L+g  k ++++l G p  Gk+++a  + k+L   v+ f  s
  gene765|gene765|rna764|rna764 125 VGNVGIVKQLEDYLQGHTKYKAVLLSGQPGVGKTTMAHVVCKYLGLDVVEFNAS 178
                                    456778899****************************************99776 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00026      0.14       2      26 ..     151     175 ..     150     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00026
                                    E-TTSSHHHHHHHHHHHH.TEEEEEH CS
                         AAA_17   2 GgPGsGKgtqceklveky.gfthlsa 26 
                                    G PG+GK+t++ ++v ky g+ ++++
  gene765|gene765|rna764|rna764 151 GQPGVGKTTMA-HVVCKYlGLDVVEF 175
                                    99*********.55555548888643 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       8.6   4.7e+03      28      73 ..      48      96 ..      37     100 .. 0.65
   2 ?   11.4   0.0   0.00037       0.2       3      77 ..     145     217 ..     143     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.6
                         AAA_24 28 fidtek.Glksldadkfpdie..swedfldevvelaaeladyktlviDt 73
                                   ++  e+ G+ +++ +k   ie  + edf + ++ +++el++   + iDt
  gene765|gene765|rna764|rna764 48 LVTGENpGASKMQKAKELGIEilNEEDFTKLIKNNEKELDNVIEIGIDT 96
                                   4444444777777666666666677888888888888877766666666 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00037
                         AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel..aaeladyktlviDtidel 77 
                                    + +l+ G++g+GKTt+a     k l +d+ + +++ d++   +i+s   ++++v++   +  +++ k+l+ D +d +
  gene765|gene765|rna764|rna764 145 KAVLLSGQPGVGKTTMAHVV-CKYLGLDVVE-FNASDVRSKSEISSK--IRSFVNSQsvYSRESKKKVLIMDEVDGM 217
                                    568999***********999.8888888877.777777777777633..3333333333566666788888888876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.13      46     136 ..     143     233 ..     130     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                      IstB_IS21  46 kkenivllGpsGvGKshlaialgveavr.aglsvlfvrvedLveelkrarrdgklaralkrl...lkvdllilDdlgllp 121
                                    k ++++l G++GvGK+ +a  +    ++  gl v+ + ++d+ ++ ++  +  ++ + ++ +    k ++li+D++    
  gene765|gene765|rna764|rna764 143 KYKAVLLSGQPGVGKTTMAHVV----CKyLGLDVVEFNASDVRSKSEISSKIRSFVNSQSVYsreSKKKVLIMDEVDGMS 218
                                    557899**********877655....5547999999999999999999999999877766551115669******99888 PP

                      IstB_IS21 122 ldqaeaellfeviek 136
                                     d+    +l +vi++
  gene765|gene765|rna764|rna764 219 SDRGGIPELVNVIKE 233
                                    888888888888876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00024      0.13      21      51 ..     133     162 ..     129     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                         AAA_25  21 prrwlvkgllpagelallaGapgtGKttlal 51 
                                    +++++++g+  + + +ll G+pg+GKtt+a 
  gene765|gene765|rna764|rna764 133 QLEDYLQGH-TKYKAVLLSGQPGVGKTTMAH 162
                                    678889999.58999*************985 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00034      0.18      40     104 ..     130     192 ..     121     216 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00034
                         DUF815  40 lventeqfleglp.annvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellre 104
                                    +v+  e +l+g++  + vLL G+ G+GK ++ + + + +   gL ++e + +d+++ +++ +++r+
  gene765|gene765|rna764|rna764 130 IVKQLEDYLQGHTkYKAVLLSGQPGVGKTTMAHVVCKYL---GLDVVEFNASDVRSKSEISSKIRS 192
                                    567778899987515789************999887654...899***********9999999985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00043      0.24       2      28 ..     147     173 ..     147     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                         AAA_33   2 vllvGlpGsGKstlaerllkklgavll 28 
                                    vll G pG+GK+t a+ ++k lg  ++
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYLGLDVV 173
                                    6899****************9994444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00035      0.19      91     130 ..     136     175 ..     110     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                                    HHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  91 eelkellkdktsvlvGqSGvGKStLinallpelelktgev 130
                                    + l+ + k k ++l Gq GvGK+t+  ++   l l + e 
  gene765|gene765|rna764|rna764 136 DYLQGHTKYKAVLLSGQPGVGKTTMAHVVCKYLGLDVVEF 175
                                    3455566668899************998887766666555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00047      0.25       4     109 ..     147     254 ..     146     298 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.TTSSS--GGGHHHHHHHHH.HHHHHHHTT.SEEEE-S---S CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslgiekdsykdsakekalRsslr.savkrdLskekvVIvDslnyi 82 
                                    v+l+G+P +GK+t+a+ + k+l   + +vv  +   ++  +    +s+   ++Rs ++ ++v  + sk+kv I+D++  +
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYL---GLDVVEFNASDVR--S----KSEISSKIRSFVNsQSVYSRESKKKVLIMDEVDGM 217
                                    89*************9998888...4555555544444..3....33445556665541468888899999999988877 PP

                                    HHHHH...HHHHHHHHTT-EEEEEEEE--.......H CS
                          KTI12  83 kgfRY...eLyciakaakttlcvvyvvap.......l 109
                                     + R    eL ++ k+a+++ + +   ++       +
  gene765|gene765|rna764|rna764 218 SSDRGgipELVNVIKEAMIPIICICNDRNnlkirtlS 254
                                    7777522266666666666655544333344444443 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00051      0.28       2      27 ..     147     172 ..     146     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                          AAA_3   2 vllegvPGlaktllvkalakaldlef 27 
                                    vll g PG++kt++++ ++k l+l++
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCKYLGLDV 172
                                    89*******************99886 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0    0.0012      0.64       3      22 ..     147     166 ..     145     176 .. 0.87
   2 ?   -0.9   0.0       2.5   1.4e+03      80      99 ..     204     223 ..     184     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                                    EEEEC-TTTCHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                    v+l G++G+GKTt+++ ++ 
  gene765|gene765|rna764|rna764 147 VLLSGQPGVGKTTMAHVVCK 166
                                    89************998775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                                    CCCEEEEEE-STT-SS-TCH CS
                          NACHT  80 perlLlilDglDelvtdlgq 99 
                                     ++ +li+D +D +++d g 
  gene765|gene765|rna764|rna764 204 SKKKVLIMDEVDGMSSDRGG 223
                                    566789******99998776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.22   1.2e+02      15      33 ..     145     163 ..     132     169 .. 0.81
   2 ?    6.7   0.0      0.01       5.5     120     149 ..     204     235 ..     185     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.22
                                    CEEEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                           DEAD  15 gdvlvaaeTGsGKTlafli 33 
                                    + vl++++ G GKT+++ +
  gene765|gene765|rna764|rna764 145 KAVLLSGQPGVGKTTMAHV 163
                                    789***********99765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.01
                                    TTEEEEEEETHHHHHHT..TTHHHHHHHHHHS CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                           DEAD 120 sqvrflVlDEadrlldq..gfsdfinrilnql 149
                                    s+ ++l++DE+d+++++  g  + +n i +++
  gene765|gene765|rna764|rna764 204 SKKKVLIMDEVDGMSSDrgGIPELVNVIKEAM 235
                                    67799**********99655555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.74u 0.37s 00:00:01.10 Elapsed: 00:00:00.51
# Mc/sec: 3375.69
//
Query:       gene766|gene766|rna765|rna765  [L=376]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-14   52.7   0.7      1e-13   51.7   0.2    1.8  2  PCI              PCI domain
     0.0018   18.0   0.2      0.007   16.1   0.0    2.1  2  RPN7             26S proteasome subunit RPN7
  ------ inclusion threshold ------
      0.023   14.8   0.0       0.19   11.9   0.0    2.5  2  TPR_2            Tetratricopeptide repeat
        0.1   12.6   0.5       0.35   10.8   0.5    2.0  1  CSN8_PSD8_EIF3K  CSN8/PSMD8/EIF3K family
       0.13   12.3   1.5        1.3    9.1   0.1    2.9  3  Imm30            Immunity protein 30


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.9   1.1e+04      46      55 ..     137     146 ..     112     160 .. 0.55
   2 !   51.7   0.2   2.8e-17     1e-13       2      93 ..     231     321 ..     230     325 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.9
                                    HHHHHHHHHH CS
                            PCI  46 vrerllrqvs 55 
                                    v++++l  + 
  gene766|gene766|rna765|rna765 137 VITNCLLDML 146
                                    3333322222 PP

  == domain 2  score: 51.7 bits;  conditional E-value: 2.8e-17
                                    HHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHH CS
                            PCI   2 sysdllkalrsgnlsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkil 81 
                                    +y +l + +++ ++++f+e+l+  + + l  +gl+ +  +L ++v+++ +r++s  ys+is+ ++a lld++ +e+E+++
  gene766|gene766|rna765|rna765 231 TYFELASVVKKAEIKKFEETLENSK-DELMAQGLYFVARRLSQNVIQEGIRRISIVYSRISFVDIAYLLDINPEEAEYLV 309
                                    6899********************5.55555************************************************* PP

                                    HHHHHTTSSSEE CS
                            PCI  82 vklIrdgeirak 93 
                                     + Ir+g+i++k
  gene766|gene766|rna765|rna765 310 KRTIRKGLIKGK 321
                                    **********98 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.9e-06     0.007      88     141 ..     144     194 ..     135     217 .. 0.83
   2 ?   -1.9   0.0      0.66   2.4e+03      13      30 ..     241     258 ..     229     269 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                                    -HHHHHHHHHHHHCSSS---.HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-G CS
                           RPN7  88 dwdlvskylekakellekggdwerknrlkvyeGlallairkfkeAaellldils 141
                                    d+   +k  +++++++ +    + ++r++ y+G++++  +++++A ++++ +  
  gene766|gene766|rna765|rna765 144 DMLISNKIFQRIENTIAT---TSEQARYNYYNGIISMVEGDYESALKNFHTSII 194
                                    666677888999999999...899**************************9865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                                    HHHHHHHHHHHHHHHHTT CS
                           RPN7  13 ekeleeLdaelkdakenl 30 
                                    ++e++++++ l++ k++l
  gene766|gene766|rna765|rna765 241 KAEIKKFEETLENSKDEL 258
                                    455666666666655554 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.75   2.7e+03      16      26 ..      20      30 ..      18      30 .. 0.86
   2 ?   11.9   0.0   5.3e-05      0.19       1      31 [.     166     196 ..     166     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.75
                          TPR_2 16 dyeeAleafek 26
                                   + eeA e +e+
  gene766|gene766|rna765|rna765 20 NREEAMEQYER 30
                                   679*****997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.3e-05
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAleld 31 
                                    a+++y+ G + +  gdye Al+ f  ++ l 
  gene766|gene766|rna765|rna765 166 ARYNYYNGIISMVEGDYESALKNFHTSIILS 196
                                    6899********************9998776 PP

>> CSN8_PSD8_EIF3K  CSN8/PSMD8/EIF3K family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   9.8e-05      0.35      38     120 ..     226     310 ..     133     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.8e-05
                CSN8_PSD8_EIF3K  38 deeiqklltLetlLeeanyakfwstlks..ddlsadltadva.gleelvReeiaklvgkaYesIsadvlaelLglssdee 114
                                    ++++++ ++L+  + +a+ +kf +tl++  d+l a+  ++va  l+++v +e ++ ++  Y+ Is  ++a lL+++ +ee
  gene766|gene766|rna765|rna765 226 KPSLRTYFELASVVKKAEIKKFEETLENskDELMAQGLYFVArRLSQNVIQEGIRRISIVYSRISFVDIAYLLDIN-PEE 304
                                    78888889999999999988888888751134444444555426899*****************************.**9 PP

                CSN8_PSD8_EIF3K 115 lekfvk 120
                                    +e  vk
  gene766|gene766|rna765|rna765 305 AEYLVK 310
                                    998876 PP

>> Imm30  Immunity protein 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.33   1.2e+03      60      82 ..       4      26 ..       1      38 [. 0.74
   2 ?    9.1   0.1   0.00036       1.3      30      95 ..     102     167 ..      95     170 .. 0.82
   3 ?   -0.2   0.0      0.29     1e+03       8      24 ..     241     257 ..     235     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.33
                          Imm30 60 eeylkklvealpkllknakeWak 82
                                    ey+++lve+l +l  n +e ++
  gene766|gene766|rna765|rna765  4 REYVEELVEVLGQLSTNREEAME 26
                                   57899999999999888776555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00036
                          Imm30  30 ledlckafdDdtedeevmFglvHlledleveeylkklvealpkllknakeWakilnyRilnsekar 95 
                                    ++ +++a +++++d+  +F+l+ +  +l+ e  ++ + ++l ++l + k +++i n     se+ar
  gene766|gene766|rna765|rna765 102 VKFFYLARKNECQDNSTLFSLLVTNKELGNEYTISVITNCLLDMLISNKIFQRIENTIATTSEQAR 167
                                    5667788899**********************************9997777766555555555555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.29
                          Imm30   8 eeevelFesalekllke 24 
                                    + e++ Fe++le+   e
  gene766|gene766|rna765|rna765 241 KAEIKKFEETLENSKDE 257
                                    67999999999976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2758.54
//
Query:       gene767|gene767|rna766|rna766  [L=205]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1553.91
//
Query:       gene768|gene768|rna767|rna767  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1087.70
//
Query:       gene769|gene769|rna768|rna768  [L=172]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.061   12.9   0.3      0.092   12.3   0.3    1.3  1  PspA_IM30    PspA/IM30 family
      0.066   13.4   0.2       0.11   12.7   0.2    1.5  1  T3SchapCesA  Type III secretion system filament chaperone Ces


Domain annotation for each model (and alignments):
>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     1e-05     0.092      76     119 ..      60     107 ..      37     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                      PspA_IM30  76 aALtkg....eeeLArealaeikslekqaealetqlaqqrsaveqlrk 119
                                    + L+k+    ++eL re++ e +sl++++++l + + +++s+ e+l+ 
  gene769|gene769|rna768|rna768  60 ECLEKQvserAQELCRELIFEHESLKEKVARLGEAAGNSESSFEELKS 107
                                    455666666699**********************************97 PP

>> T3SchapCesA  Type III secretion system filament chaperone CesA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.2e-05      0.11      10      60 ..      59     110 ..      46     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                    T3SchapCesA  10 kelldkkirsei.eaikkiiaefdvvkesvnilsekaktdpqaaeklnklie 60 
                                    ke l+k++     e  + +i e + +ke+v  l e a  +  + e+l+ li 
  gene769|gene769|rna768|rna768  59 KECLEKQVSERAqELCRELIFEHESLKEKVARLGEAAGNSESSFEELKSLII 110
                                    899999997654277899*****************************99974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1059.36
//
Query:       gene770|gene770|rna769|rna769  [L=196]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-57  193.7   0.1    1.9e-57  193.5   0.1    1.0  1  Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)


Domain annotation for each model (and alignments):
>> Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.5   0.1     1e-61   1.9e-57       6     174 ..       4     183 ..       1     184 [. 0.96

  Alignments for each domain:
  == domain 1  score: 193.5 bits;  conditional E-value: 1e-61
                  Pur_DNA_glyco   6 dalevAkeLLGkvlvreleegkvagrivEtEAYlgeeDpAshayrgr.ternavmFgppgtlYvYliygihhclnvvtee 84 
                                    ++ e+A+eLLGk+l+r++e ++++g+ivEtEAY+g+eD+A+h y gr tern++m++++gt+YvY iyg++ c+n+++ e
  gene770|gene770|rna769|rna769   4 PCIELARELLGKILCRRMEGKTMKGMIVETEAYVGREDKACHGYGGRrTERNSAMYMRAGTCYVYKIYGMYECFNISSVE 83 
                                    7899***************99*************************99******************************66 PP

                  Pur_DNA_glyco  85 egeasaVLiRalevveglelmrarrg.......lanGPgkLcqaLgidke.lngadlleseelvle.keeaeeeeivagp 155
                                    +  +++VLiRa+e++ g++lmr++rg       +anGP+kLc a+gi+++  +++ +++s+++++e + e+++++++ g+
  gene770|gene770|rna769|rna769  84 D--GAGVLIRAVEPLCGISLMRRHRGgrvkdrdIANGPSKLCIAMGITRKeIDKEWIMSSSKIWIEeGMEVADTSVIVGK 161
                                    6..89********************************************9999****99*******877999******** PP

                  Pur_DNA_glyco 156 RiGiskaae...lpwRfyikgn 174
                                    RiGi++ +e   + +Rfyik+n
  gene770|gene770|rna769|rna769 162 RIGIRNCGEweeKELRFYIKDN 183
                                    ******777777********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 1120.87
//
Query:       gene77|gene77|rna77|rna77  [L=301]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-47  162.6   0.0    5.5e-47  160.4   0.0    1.8  1  Aldo_ket_red  Aldo/keto reductase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   0.0   3.1e-51   5.5e-47       2     292 ..      17     283 ..      16     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 3.1e-51
                                EEEE-SSS-ST.TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH....-TTTGGG-EEEEEE--SSSTTSSSS CS
               Aldo_ket_red   2 lglGtwqlgskeeiskeealellrraleaGinffDtAevYgkgqseellGealkk....srkkreeviiatKvdlrdaeiksgl 81 
                                +glGtw l++     +++  + +r a++ G++++DtA +Y    +e+++G++lkk      ++r++++i++K+     ++ +++
  gene77|gene77|rna77|rna77  17 VGLGTWGLED-----ESSLEASIRNAISLGYRHIDTAFIY---GNEKMIGNILKKlfneGVVQRKDLFITSKL-----WNTFHH 87 
                                89****9995.....5777777******************...9*************9999************.....999999 PP

                                -HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-...................HHHHHHHHHHHHHTTSEEEEEEES--HHHHH CS
               Aldo_ket_red  82 skeniresleeslkrLgtdyvDllllHrpdpslp..................sieevldaleelvkeGkiraiGvSnfsveqle 147
                                ++e+   +l+++l  L+t+yvDl+l+H+p    p                  +   v++ +eelv+ G++++iG+Snf  e  e
  gene77|gene77|rna77|rna77  88 CPED---ALRQTLDDLQTSYVDLYLIHWPVTFEPapngsvescgkkynigefDAVSVWKKMEELVDLGLAKSIGISNFGKENTE 168
                                9986...67889******************9999************************************************** PP

                                HHHHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHH CS
               Aldo_ket_red 148 kakkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaee 231
                                k++k   ++++++q e +++  l++++l+e+++ +++++i ys lg+G  +++++                          +++
  gene77|gene77|rna77|rna77 169 KVLKACRIRPAVSQFELHPY--LNQKELVEFMQSEKIQVISYSSLGSGHDSSQKV------------------------REDKT 226
                                ********************..************************998775555........................67889 PP

                                HHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
               Aldo_ket_red 232 lselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                ++++ak++ ++++q+ l+y++  +++++vip +++ e+l++n+d    +l +e+++ +d l
  gene77|gene77|rna77|rna77 227 IKAIAKKYECTPSQIILSYIV--SRNICVIPRSKSKEHLKENIDLK--ELAKEDISIIDGL 283
                                *********************..9**********************..*******999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 1761.07
//
Query:       gene771|gene771|rna770|rna770  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.084   11.6   0.0        0.1   11.3   0.0    1.1  1  Aa_trans  Transmembrane amino acid transporter protein


Domain annotation for each model (and alignments):
>> Aa_trans  Transmembrane amino acid transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.6e-06       0.1     162     223 ..      44     106 ..      23     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.6e-06
                       Aa_trans 162 ivilvlvvaelvklelkgvseetv.kkasklkglflaigiivFAftghavlleiqnelkdpsk 223
                                    +++lv+ +++ + ++ +++++ ++  ++++  + f  +  i+F+f+   +l+ i+n+l++  +
  gene771|gene771|rna770|rna770  44 LIVLVIQKVHSILYSSYNIEYIEIlLDIIHSEEAFDELFRIIFSFENRPCLPRIINKLRNKNE 106
                                    567888888889999999999998888999999999***********************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 847.34
//
Query:       gene772|gene772|rna771|rna771  [L=624]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-90  303.5   0.0    2.1e-90  303.1   0.0    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    4.1e-36  124.3   0.0    2.7e-34  118.4   0.0    2.1  2  Transket_pyr     Transketolase, pyrimidine binding domain
    0.00071   19.4   0.0     0.0052   16.6   0.0    2.2  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
     0.0018   18.2   0.0      0.013   15.4   0.0    2.2  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.16   11.6   0.2       0.35   10.5   0.2    1.5  1  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.1   0.0   5.9e-94   2.1e-90       5     310 ..       3     293 ..       1     313 [. 0.95

  Alignments for each domain:
  == domain 1  score: 303.1 bits;  conditional E-value: 5.9e-94
                                    HHHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--HHH CS
                Transketolase_N   5 avnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsled 84 
                                     +n iR L  D+v+ka+sGhPGaplgla+  ++l++++   +P+d++w++RD f+LsnGha++l+Y++ +L G  l++ed
  gene772|gene772|rna771|rna771   3 NINNIRTLCADMVQKARSGHPGAPLGLAPFVYILYTEFISFDPDDENWVGRDIFLLSNGHACALQYVVNYLIG-RLDIED 81 
                                    589**********************************************************************.69**** PP

                                    HTTTTSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHH CS
                Transketolase_N  85 lksfrqlgsktpGhPelghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvssea 164
                                    l +frq++ +tpGhPe ++++g e  tGPLGqG+anavg a+  k+l       ++  + + +y+i gDgc +eG+s+e+
  gene772|gene772|rna771|rna771  82 LMNFRQINGRTPGHPE-KKHPGTESSTGPLGQGVANAVGYAISLKKL-------DHLQLGNRVYCIFGDGCYQEGISQES 153
                                    ****************.7889*********************99887.......45567899****************** PP

                                    HHHHHHTT-TTEEEEEEESSEETTEEGGGT--S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EEEEEE-- CS
                Transketolase_N 165 sslagtlkLgkLivlyDdnkisidGeteisftedvakrfeaygWhvievedgedveaikaaieeakaekdkPsliklrtv 244
                                     sl + lkL++++ +yD nk +idG t+ s++edv +rf + g++v  v +g+d+  i++a+++   +  +P +i l+tv
  gene772|gene772|rna771|rna771 154 FSLVASLKLDNIVFIYDFNKTTIDGPTSLSMNEDVVQRFLSLGFEVE-VVNGDDLDGIRKALNK---KVSRPMVIILETV 229
                                    *********************************************95.68999********985...3369********* PP

                                    TTTTSTTTTTSGGGTSS---HHHHHHHHHHTTS-TT-TS---HHHHHHHHHHHHHHHHHHHHHHHH CS
                Transketolase_N 245 iGygspakagtedvhGapLgedevaalkkklGfdpeksfevpeevydaykekvaegakaeeeWeek 310
                                    iG gs   +g++++hG+pLge+ v++lk+k+G+  e  f++ + +++++k+   + +k+++eW++k
  gene772|gene772|rna771|rna771 230 IGRGS-IVEGSCKAHGSPLGEEGVRKLKEKFGIP-EVDFYISSSLVEKFKNLNDRKRKIRAEWNTK 293
                                    *****.9*************************96.****************************986 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.012        43      64     168 ..     119     225 ..     113     229 .. 0.79
   2 !  118.4   0.0   7.6e-38   2.7e-34       3     176 ..     325     492 ..     321     494 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
                                    HHHHHHHCT.TEEEEEEEEHHHHGGG.HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSS...HHHHHHTSTT CS
                   Transket_pyr  64 avGaalagp.llviveaqFgdFangA.qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsae...leaflrlipg 138
                                     ++++l++   l +    +  F +g+ q  ++q  +s++a  kl  +v++ +   +  dGp+  s++     +fl l  +
  gene772|gene772|rna771|rna771 119 GYAISLKKLdHLQLGNRVYCIFGDGCyQEGISQESFSLVASLKLDNIVFIYDFNKTTIDGPTSLSMNedvVQRFLSLGFE 198
                                    445555555667777788999******99999999****************************99973334678888888 PP

                                    EEEE--SSHHHHHHHHHHHHHSSS.SEEEE CS
                   Transket_pyr 139 lkvvrPsdpaetkhllrrairredrkPvvl 168
                                    + vv+  d   ++++l + + r+    v++
  gene772|gene772|rna771|rna771 199 VEVVNGDDLDGIRKALNKKVSRP---MVII 225
                                    99999999999999999888843...3444 PP

  == domain 2  score: 118.4 bits;  conditional E-value: 7.6e-38
                                    EEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGT..TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEE CS
                   Transket_pyr   3 iawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqg..egrvidsgisEqavlgfavGaalagpllviveaq 80 
                                     a+rk + eal+ l ke   ++++ aD++ ++++++ +  ++++  +gr+i++gi+E+ ++g+ +G+a +g ++ ++ ++
  gene772|gene772|rna771|rna771 325 KATRKHFSEALKDL-KETRYLIGGAADLQSSVLTKIGEDDFNSEnyNGRYINFGIREHCMCGTINGIASHG-YFLPYTGT 402
                                    57888888888875.6778899**************9999999999*************************.8******* PP

                                    EHHHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHH CS
                   Transket_pyr  81 FgdFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrair 159
                                    F++F++    y ++ +r +    +l+   v+t+++ig+gedGp+hq++e ++ lr++p+l ++rP+d  e+++ l+ a++
  gene772|gene772|rna771|rna771 403 FLNFIS----YGFPSVR-LGCMDNLNLFyVLTHDSIGLGEDGPTHQPIEVLSTLRATPNLITMRPCDGTEVRASLYVALT 477
                                    ******....*******.99999999999*************************************************** PP

                                    SSS.SEEEEEE-SSEEC CS
                   Transket_pyr 160 redrkPvvlrlpksllr 176
                                    re  +  +++l++++++
  gene772|gene772|rna771|rna771 478 RE--GSKAVMLSRQNVP 492
                                    66..699********97 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.5e-06    0.0052      24      80 ..     104     169 ..      89     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                                    ETTTS-TTTHHHHHHHHHH.......HSTTSEEEEEEEHHHHHHT.GGG.HHHHHHTT-SEEEEEE CS
                   TPP_enzyme_C  24 sgglgtmGyglpaAiGakl.......akpdrevvaivGDGgflmi.lqe.latavrrnlpitvvvl 80 
                                    ++ +g +G g++ A+G ++       ++ +++v++i GDG+++    qe ++ ++  +l+ +v+++
  gene772|gene772|rna771|rna771 104 ESSTGPLGQGVANAVGYAIslkkldhLQLGNRVYCIFGDGCYQEGiSQEsFSLVASLKLDNIVFIY 169
                                    5678999*********999866544324478************98666624444445665555555 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.6e-06     0.013       4     123 ..     509     612 ..     506     613 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-06
                                    EEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHH CS
                Transketolase_C   4 eilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaa 83 
                                     ++ e +d++l+++Gs+v+ + e+ ++L    +++++v+ ++ + + ++  +       +  ++++ v+r++i++  +  
  gene772|gene772|rna771|rna771 509 LVEVEDPDLILLSTGSEVQLCYEVTKALP--DLRISIVSFFSWELFEEQEEE------YKKHILKD-VPRVSIEALSTFG 579
                                    67899***********************7..788899999999999988877......33334444.5557774444444 PP

                                    HHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHH CS
                Transketolase_C  84 laeeafdgldapvkrvggpdviepgsaeelekafgldaek 123
                                    +++  + +l+  v ++     +++g+ ++++++fgl++++
  gene772|gene772|rna771|rna771 580 WTK--YSDLQIGVDTF-----GVSGPCKDVYNYFGLNCKE 612
                                    444..44444444444.....4557777777777777665 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   9.7e-05      0.35       3      24 ..     371     392 ..     370     393 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.7e-05
                        zf-tcix   3 grktlRGvrkCpkCGtyNGtRg 24 
                                    gr ++ G+r    CGt+NG+++
  gene772|gene772|rna771|rna771 371 GRYINFGIREHCMCGTINGIAS 392
                                    688999*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4082.53
//
Query:       gene773|gene773|rna772|rna772  [L=418]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-11   43.9   4.7      8e-11   42.1   4.7    2.1  1  zf-RING_2     Ring finger domain
    9.5e-10   38.2   4.4    4.2e-09   36.1   4.4    2.2  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    8.5e-09   35.3   5.1    1.6e-08   34.4   3.3    2.5  2  zf-RING_UBOX  RING-type zinc-finger
    5.4e-07   29.3   5.1    1.8e-06   27.6   5.1    2.0  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
      2e-06   27.6   4.5      2e-06   27.6   4.5    2.2  2  zf-RING_5     zinc-RING finger domain
    3.6e-06   27.0   1.8    1.3e-05   25.3   1.8    2.1  1  zf-C3HC4_4    zinc finger of C3HC4-type, RING
    8.2e-06   26.0   5.9    8.2e-06   26.0   5.9    2.5  2  zf-rbx1       RING-H2 zinc finger domain
    1.1e-05   25.2   3.1    3.5e-05   23.6   3.1    1.9  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
     0.0004   20.1   3.1     0.0009   18.9   2.0    2.3  2  zf-RING_11    RING-like zinc finger
    0.00097   19.1   7.3      0.002   18.1   4.8    2.4  2  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
     0.0016   18.3   3.1     0.0039   17.0   3.1    1.7  1  zf-Nse        Zinc-finger of the MIZ type in Nse subunit
  ------ inclusion threshold ------
      0.011   15.6   1.9          2    8.3   0.3    3.0  3  eIF2A         Eukaryotic translation initiation factor eIF2A
      0.014   15.3   7.0      0.014   15.3   7.0    2.9  2  Prok-RING_4   Prokaryotic RING finger family 4
       0.27   10.9   6.2       0.32   10.7   3.7    2.5  2  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
       0.97    9.6   7.6       0.38   10.9   3.2    2.6  2  RINGv         RING-variant domain
        1.3    9.3   3.7        2.3    8.5   3.7    1.3  1  DUF755        Domain of unknown function (DUF755)
        2.3    8.4  11.2       0.51   10.6   2.9    3.2  3  FANCL_C       FANCL C-terminal domain
        3.5    7.8   7.0         12    6.1   7.0    2.0  1  FYVE          FYVE zinc finger


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   4.7     8e-14     8e-11       2      43 ..       6      51 ..       5      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 8e-14
                      zf-RING_2  2 eCpICleel.ssads.vlllpCgHvfhreClerwlrssst..CPlC 43
                                    CpIC++e+ +++++ v+ l+CgH f+ +C+++w+ ++s+  CPlC
  gene773|gene773|rna772|rna772  6 ICPICFSEYtTKGNHrVVSLQCGHLFGSQCIQKWVGKKSKmqCPLC 51
                                   5*******9644444477779*************99999999**** PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   4.4   4.2e-12   4.2e-09       1      41 []       7      51 ..       7      51 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 4.2e-12
                                   -TTT-S--SS-E.....E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4  1 CpiCleeakepn....elleCkHsfCskCirkilksrkkvkCPlC 41
                                   CpiC++e++++      +l+C+H f s+Ci+k++ +++k +CPlC
  gene773|gene773|rna772|rna772  7 CPICFSEYTTKGnhrvVSLQCGHLFGSQCIQKWVGKKSKMQCPLC 51
                                   ***********99999*******************999999**** PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   3.3   1.6e-11   1.6e-08       1      39 []       7      49 ..       7      49 .. 0.88
   2 ?   -1.5   0.0       2.7   2.7e+03      18      25 ..     272     279 ..     271     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.6e-11
                   zf-RING_UBOX  1 CpIClelft...dP.lv.lpCGHtFCreClwelskslegafkCP 39
                                   CpIC++++t   +  +v l CGH F ++C+ +++ +++ + +CP
  gene773|gene773|rna772|rna772  7 CPICFSEYTtkgNHrVVsLQCGHLFGSQCI-QKWVGKKSKMQCP 49
                                   *********77733667679**********.7999999999999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                   zf-RING_UBOX  18 HtFCreCl 25 
                                    H++C++ l
  gene773|gene773|rna772|rna772 272 HSICKKGL 279
                                    99999766 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   5.1   1.8e-09   1.8e-06       2      40 .]       7      51 ..       6      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.8e-09
                     zf-C3HC4_2  2 CpiCldmlkdp....svvtpCgHvfCqkCilrsLeekn..eCPlC 40
                                   CpiC+ ++ +     +v+ +CgH f ++Ci+++  +k+  +CPlC
  gene773|gene773|rna772|rna772  7 CPICFSEYTTKgnhrVVSLQCGHLFGSQCIQKWVGKKSkmQCPLC 51
                                   *******986422224556**************9988779***** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   4.5     2e-09     2e-06       2      43 ..       7      52 ..       6      53 .. 0.95
   2 ?   -3.2   0.0       8.7   8.7e+03      22      27 ..     272     277 ..     272     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2e-09
                      zf-RING_5  2 CnkCfekl..skeekfyltsCgHifCekClkkll..ekeavCpiCr 43
                                   C++Cf+++  +++++++ ++CgH f ++C++k    +++ +Cp+C+
  gene773|gene773|rna772|rna772  7 CPICFSEYttKGNHRVVSLQCGHLFGSQCIQKWVgkKSKMQCPLCS 52
                                   ********9889999*****************9999*********6 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.7
                      zf-RING_5  22 HifCek 27 
                                    H++C+k
  gene773|gene773|rna772|rna772 272 HSICKK 277
                                    899986 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.8   1.3e-08   1.3e-05       1      42 []       7      51 ..       7      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.3e-08
                     zf-C3HC4_4  1 CPiC.ldYLekP....vsleCGhsfClsCisslqkepdgeqllCplC 42
                                   CPiC ++Y +k     vsl+CGh f  +Ci+++  ++++  ++CplC
  gene773|gene773|rna772|rna772  7 CPICfSEYTTKGnhrvVSLQCGHLFGSQCIQKWVGKKSK--MQCPLC 51
                                   99995579876444449*****************99966..7***** PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   5.9   8.3e-09   8.2e-06      14      54 ..       7      51 ..       2      52 .. 0.75
   2 ?   -2.9   0.1       9.1     9e+03       5      18 ..     223     236 ..     222     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 8.3e-09
                        zf-rbx1 14 cieckapgdee..cpvvlGeCgHaFHlhCiskWlkt..rkvCPlc 54
                                   c+ c ++ +++    vv  +CgH F  +Ci+kW+ +  + +CPlc
  gene773|gene773|rna772|rna772  7 CPICFSEYTTKgnHRVVSLQCGHLFGSQCIQKWVGKksKMQCPLC 51
                                   55555555554445666679**************8866889**** PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.1
                        zf-rbx1   5 iCrneleeacieck 18 
                                    i  n++e++c + +
  gene773|gene773|rna772|rna772 223 IAHNQIESTCFDKD 236
                                    77899999998765 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   3.1   3.5e-08   3.5e-05       4      46 ..       6      54 ..       4      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.5e-08
                                   B-TTTSSS.....BS-EEETTEEEEEE-HHHHHHHHH..TT-B-TTT--B CS
                     zf-C3HC4_3  4 eCviCler.....prnvvllpCgHlvlCeeCaekllk..rkkkCpiCrrp 46
                                   +C+iC+++     +  vv l+CgHl + ++C +k+    +k +Cp+C  +
  gene773|gene773|rna772|rna772  6 ICPICFSEyttkgNHRVVSLQCGHL-FGSQCIQKWVGkkSKMQCPLCSVQ 54
                                   7******6656567789999*****.*********86789*******866 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   2.0   9.1e-07    0.0009       2      29 .]       7      36 ..       7      36 .. 0.81
   2 ?   -3.5   0.0       9.7   9.6e+03       3       8 ..     309     314 ..     309     321 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.1e-07
                     zf-RING_11  2 CsICLeefk.pgq.alfilpCsHtFHfkCI 29
                                   C IC +e++ +g+ +++ l C+H+F ++CI
  gene773|gene773|rna772|rna772  7 CPICFSEYTtKGNhRVVSLQCGHLFGSQCI 36
                                   *********54443556667*********9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.7
                     zf-RING_11   3 sICLee 8  
                                    sIC + 
  gene773|gene773|rna772|rna772 309 SICTNM 314
                                    799875 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   4.8   2.1e-06     0.002      35      79 ..       7      53 ..       2      59 .. 0.73
   2 ?    0.4   0.0      0.69   6.9e+02       2      44 ..     265     307 ..     264     329 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.1e-06
                                   -TTC...STTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSS CS
                     zf-ANAPC11 35 cpsc...kfpGddcplvlGkckhnfhlhcilkwletetskglcpmcrq 79
                                   cp c    +   +  +v  +c h f   ci+kw+ + +sk +cp+c  
  gene773|gene773|rna772|rna772  7 CPICfseYTTKGNHRVVSLQCGHLFGSQCIQKWVGK-KSKMQCPLCSV 53
                                   66662211223456788889*************975.689******74 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.69
                                    -EEEEEEEE--B--B.-SSSSB-TTT-SBTTS--TTCSTTTTT CS
                     zf-ANAPC11   2 kvkikevksvatwswdvasddvcGicrvsfdGtcpsckfpGdd 44 
                                    kv   +++s+++   +v    +    r+ f G c  c++  + 
  gene773|gene773|rna772|rna772 265 KVSDISIHSICKKGLEVFASTIYQTYRIIFSGDCIPCNLEMEP 307
                                    5666667888888888888888888999******999876554 PP

>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   3.1   3.9e-06    0.0039      14      57 .]       7      52 ..       3      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.9e-06
                                   -TTTSSB-S....SEEEESSS--EEEHHHHHHHCTTTS-EE-SCCC-S CS
                         zf-Nse 14 CPltlqpfe....ePvtskkCpHvFEreaIlelikrkktvkCPvagCs 57
                                   CP+ +++++    + v s +C H F  + I++ + +k +++CP+  Cs
  gene773|gene773|rna772|rna772  7 CPICFSEYTtkgnHRVVSLQCGHLFGSQCIQKWVGKKSKMQCPL--CS 52
                                   7777777751111346677*************************..86 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3     0.002         2      89     147 ..     106     163 ..      87     173 .. 0.85
   2 ?    4.0   0.0     0.041        41      54     163 ..     179     286 ..     168     293 .. 0.73
   3 ?    1.0   0.0      0.35   3.4e+02      20      78 ..     342     400 ..     325     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                                    ECSCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEEEETTTTEEEEEEE-TT-- CS
                          eIF2A  89 dlkvkviskleeqkrNtiffspkgklvllaGfgnlaGeleiwdvkkkkkiakaeaanat 147
                                     lk+++++  ee+ +Nt + +++ k+ + aGf n+a ++  +d+++++ i + ++ + +
  gene773|gene773|rna772|rna772 106 ALKMELLHAKEEKTENTFLIHKHKKFSINAGF-NTANSIIWYDESNCTMIVTRKSGKNV 163
                                    5678999999**********************.56689999********9998876655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.041
                                    CCEESSS.EEEEEE-TTSS-EEEE.ESSSSCEEEEEECSCEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEEEET CS
                          eIF2A  54 velkkegpihdvaWspkskefavi.yGkmpakvslfdlkvkviskleeqkrNtiffspkgklvllaGfgnlaGeleiwdv 132
                                    + l +  pi+ ++ sp ++++ ++  G++ + v++++ +v +++  ++q + t  f++ ++  + +G  + +G++ + + 
  gene773|gene773|rna772|rna772 179 IVLGEGPPIKNMSLSPFNEDLGLLpIGNVLNIVNIYNGNVVAKYIAHNQIEST-CFDKDDRNTIYCG--DDKGSVYFINI 255
                                    55555556888888888888877635999999****99988877666665555.5666666666664..7789******* PP

                                    TTTEEEEEEE-TT--EEEE-TTSSEEEEEE- CS
                          eIF2A 133 kkkkkiakaeaanatlvewspdgryvlTatt 163
                                    ++++ ++ ++ ++ +    + +g  v  +t 
  gene773|gene773|rna772|rna772 256 SSCEPLKILKVSDISIHSICKKGLEVFASTI 286
                                    ***9999999999888877777766666665 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.35
                                    EEEEEE.E--TT-CEEEEEEEEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEEEE CS
                          eIF2A  20 llvlvstevdktnksyygetelyliklkkkksevvelkkegpihdvaWspkskefaviy 78 
                                    +++    +  k+++      ++y+++ + +++ v++l+    i+  + +++  +f v+ 
  gene773|gene773|rna772|rna772 342 VCLSLGIKQAKKHRDRIHRDHIYIVDDERSSIRVLKLHSLEVIYTYTFKERVLDFFVCD 400
                                    555566667888888999999******************999****9999999999986 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   7.0   1.4e-05     0.014       1      39 [.       7      54 ..       7      60 .. 0.71
   2 ?   -2.4   0.1       4.6   4.5e+03      23      31 ..     231     239 ..     228     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.4e-05
                    Prok-RING_4  1 CvlCgeq.....ekkailepCgHlvCkeCfdsk..dls..sCPlCqrr 39
                                   C +C ++     ++ ++   CgHl+  +C +++  + s  +CPlC  +
  gene773|gene773|rna772|rna772  7 CPICFSEyttkgNHRVVSLQCGHLFGSQCIQKWvgKKSkmQCPLCSVQ 54
                                   55666555554355555567***********998855569*****855 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                    Prok-RING_4  23 eCfdskdls 31 
                                    +Cfd+ d +
  gene773|gene773|rna772|rna772 231 TCFDKDDRN 239
                                    7**999877 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.7   0.00032      0.32      18      47 ..      21      50 ..       5      60 .. 0.79
   2 ?   -2.3   0.0       3.6   3.6e+03      25      41 ..     221     237 ..     217     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00032
                   Zn_ribbon_17 18 vvlcgvCeHvlHasCarewfenddlaeCps 47
                                    v+  +C+H   ++C+++w  ++ + +Cp 
  gene773|gene773|rna772|rna772 21 RVVSLQCGHLFGSQCIQKWVGKKSKMQCPL 50
                                   478899*****************999**95 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                   Zn_ribbon_17  25 eHvlHasCarewfendd 41 
                                    + ++H++  +  f++dd
  gene773|gene773|rna772|rna772 221 KYIAHNQIESTCFDKDD 237
                                    57899998888999998 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.2   0.00038      0.38       1      48 []       7      51 ..       7      51 .. 0.72
   2 ?   -1.0   0.1       1.9   1.9e+03       4      18 ..      83      97 ..      82     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                                   ETTTTEE-SSSS.--B-SS--STCCCSB-HHHHHHHHHHTCT-SB-TTT CS
                          RINGv  1 CriCleeeeese.plispCkCrGslklvHesClekWldekeantqCeiC 48
                                   C iC+ e + +  + +   +C    +l+  +C++kW+ + +++ qC +C
  gene773|gene773|rna772|rna772  7 CPICFSEYTTKGnHRVVSLQCG---HLFGSQCIQKWVGK-KSKMQCPLC 51
                                   6677766666554344444553...57889*********.********* PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
                                   TTEE-SSSS--B-SS CS
                          RINGv  4 CleeeeeseplispC 18
                                   Cl+ee+e+++ i+ C
  gene773|gene773|rna772|rna772 83 CLREEKEKNEYIEIC 97
                                   999999999999998 PP

>> DUF755  Domain of unknown function (DUF755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.7    0.0023       2.3       2      95 ..      42     129 ..      41     135 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
                         DUF755   2 nktnmpcPitskkqyklrtqkqkkqkqssttgttdgalLqkqLlkEcqktsqLiqlsqqlqqkk........qkkrkeqk 73 
                                    +k +m cP++s +  k +++   + k + +   ++++lL++ L+ E +  ++ i+++  l+ +         + k+++++
  gene773|gene773|rna772|rna772  42 KKSKMQCPLCSVQSTKRQIRPVYASKIVAIDTENEQKLLERCLREE-KEKNEYIEICTGLKAQIealkmellHAKEEKTE 120
                                    5789********************6666666666666666666655.555667788888833333344444433333333 PP

                         DUF755  74 kssqthkkkkkksrnvssrsak 95 
                                    ++             +  ++ k
  gene773|gene773|rna772|rna772 121 NT-------------FLIHKHK 129
                                    33.............3333333 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.9   0.00051      0.51       5      47 ..       7      46 ..       4      52 .. 0.86
   2 ?    3.1   0.3      0.11   1.1e+02       2      55 ..      45      98 ..      44     100 .. 0.73
   3 ?   -1.1   0.4       2.2   2.2e+03      31      62 ..     270     302 ..     233     306 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                                   -SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSS CS
                        FANCL_C  5 CgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrslkes 47
                                   C+iC+++   +g+  ++s    +C++ f s+C++ W+ + +++
  gene773|gene773|rna772|rna772  7 CPICFSEYTTKGNHRVVS---LQCGHLFGSQCIQKWVGKKSKM 46
                                   ********9888888776...79*************9887766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.11
                                   --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--E CS
                        FANCL_C  2 eveCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrslkesrqsfdvlf 55
                                   +++C++C ++  + + +p+++        +  ++ L+  lr+ ke  +++++  
  gene773|gene773|rna772|rna772 45 KMQCPLCSVQSTKRQIRPVYASKIVAIDTENEQKLLERCLREEKEKNEYIEICT 98
                                   689******999999999888777766666666666666777776666666665 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.2
                                    -B-SGGGHHHHHHHHSSS-TTT--E.EE-TTT- CS
                        FANCL_C  31 kfHsaCLkeWlrslkesrqsfdvlf.GeCPyCk 62 
                                    ++Hs C k      ++  q + ++f G+C  C+
  gene773|gene773|rna772|rna772 270 SIHSICKKGLEVFASTIYQTYRIIFsGDCIPCN 302
                                    456666655444455566777776658887776 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.0     0.012        12      11      48 ..       6      54 ..       2     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                                   B-TTT--B--SS.S--EE-TTT--EE-STTS-EEE.EE..........G CS
                           FYVE 11 kCeiCakkFsll.rrrhhCrlCGkvvCekCssklvall..........e 48
                                    C+iC +++++  + r     CG+++ ++C +k v +           +
  gene773|gene773|rna772|rna772  6 ICPICFSEYTTKgNHRVVSLQCGHLFGSQCIQKWVGKKskmqcplcsvQ 54
                                   6********665599999*************998876644455555440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2691.11
//
Query:       gene774|gene774|rna773|rna773  [L=620]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0028   17.7   0.0      0.015   15.4   0.0    2.2  2  BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
     0.0036   18.1   0.1      0.084   13.8   0.0    3.3  3  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> BBS2_Mid  Ciliary BBSome complex subunit 2, middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.76   6.8e+03      18      32 ..      20      34 ..       9      39 .. 0.69
   2 !   15.4   0.0   1.6e-06     0.015      12      69 ..     145     203 ..     137     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.76
                       BBS2_Mid 18 gsddfeirvfkeeel 32
                                   +s++ +i +f++++ 
  gene774|gene774|rna773|rna773 20 SSNNSTIVLFRKDRT 34
                                   566666777776654 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.6e-06
                       BBS2_Mid  12 eneLvvgsddfeirvfkeeelvaeitete.kvvslarlekerfayaleNGtvgvyekke 69 
                                    +++Lv+g  d +i++ k +++++e++ ++ k+ ++++++++ ++   e G+   ++ + 
  gene774|gene774|rna773|rna773 145 DQSLVIGDADGKIKIIKSGKMTSELQLSSgKINMICHITGSTYVSVCEDGSFSYFDTDV 203
                                    479**********************9776388899**********99**9999888765 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   9.4e-06     0.084       6      36 ..     130     159 ..     127     161 .. 0.91
   2 ?   -1.2   0.0      0.52   4.6e+03      20      36 ..     265     280 ..     237     282 .. 0.60
   3 ?   -1.8   0.0      0.78     7e+03       9      16 ..     474     482 ..     470     504 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-06
                                    EEESSSSEEEEEEETTSSEEEEEETTSEEEE CS
                           WD40   6 tltGHssvtslafspdgawlasGsdDgtvri 36 
                                    +++G s +tsl  spd+++++ G+ Dg+++i
  gene774|gene774|rna773|rna773 130 VYRGYSAITSLLLSPDQSLVI-GDADGKIKI 159
                                    6889988************98.*99*****9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.52
                                    TTSSEEEEEETTSEEEE CS
                           WD40  20 pdgawlasGsdDgtvri 36 
                                    ++g+ l ++++D  + i
  gene774|gene774|rna773|rna773 265 DNGRIL-TSGEDTILSI 280
                                    244445.5555877765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.78
                                    SS.SSEEEE CS
                           WD40   9 GH.ssvtsl 16 
                                    GH + ++s+
  gene774|gene774|rna773|rna773 474 GHsKTIYSI 482
                                    997779998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (620 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3857.63
//
Query:       gene775|gene775|rna774|rna774  [L=460]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-08   32.4   8.3      0.051   13.4   0.0    5.6  5  TPR_1     Tetratricopeptide repeat
    6.5e-05   23.1   2.4       0.56   10.5   0.0    4.6  3  TPR_12    Tetratricopeptide repeat
    0.00029   20.4   0.0       0.31   10.7   0.0    3.6  3  TPR_11    TPR repeat
    0.00052   20.0  13.4       0.15   12.3   0.0    6.4  7  TPR_8     Tetratricopeptide repeat
     0.0012   19.0  19.0     0.0066   16.7   0.8    4.8  5  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
     0.0019   18.1  19.7       0.26   11.5   0.1    5.9  8  TPR_2     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.017   15.6   1.9         10    6.7   0.0    4.3  5  TPR_19    Tetratricopeptide repeat
      0.036   14.9   0.1       0.92   10.5   0.0    3.3  4  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.74   1.7e+03      22      29 ..      48      55 ..      47      56 .. 0.85
   2 !   13.4   0.0   2.3e-05     0.051       7      33 ..     232     258 ..     228     259 .. 0.90
   3 ?    0.5   0.1      0.27   6.1e+02       3      15 ..     262     274 ..     260     286 .. 0.76
   4 !   12.3   0.1   5.2e-05      0.12       6      32 ..     299     325 ..     297     326 .. 0.92
   5 !    5.7   0.1    0.0063        14      13      28 ..     398     413 ..     397     414 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.74
                                   HHHHHHHH CS
                          TPR_1 22 eyyekALe 29
                                    +ye+++e
  gene775|gene775|rna774|rna774 48 SCYERCIE 55
                                   69****98 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.3e-05
                                    HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                    lG+ ++   +y eA  ++ kA+++n +
  gene775|gene775|rna774|rna774 232 LGLFFLMSSNYSEARRCFYKAVQINND 258
                                    899999999***************976 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.27
                                    HHHHHHHHHHHTT CS
                          TPR_1   3 alynlGnayfklg 15 
                                     +  lG+ay   +
  gene775|gene775|rna774|rna774 262 GWLYLGMAYSGIK 274
                                    7999*****8665 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 5.2e-05
                                    HHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   6 nlGnayfklgkydeAleyyekALelnP 32 
                                     l+  y+++++++ A  +y+ AL +n 
  gene775|gene775|rna774|rna774 299 YLAKEYHRMNNFERASFFYKHALGINS 325
                                    6999*******************9985 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0063
                                    HTT-HHHHHHHHHHHH CS
                          TPR_1  13 klgkydeAleyyekAL 28 
                                     l+++d A + y+kAL
  gene775|gene775|rna774|rna774 398 LLNNLDSAADNYNKAL 413
                                    689************9 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00025      0.56       7      51 ..     230     273 ..     225     281 .. 0.84
   2 !    6.5   0.1    0.0046        10      49      74 ..     298     323 ..     262     326 .. 0.72
   3 ?    2.9   0.2     0.061   1.4e+02      47      72 ..     388     413 ..     353     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                         TPR_12   7 nnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnL 51 
                                    + l+++ +   +y eA++++ ka++i +  +G  ++++  ++ ++
  gene775|gene775|rna774|rna774 230 VALGLFFLMSSNYSEARRCFYKAVQINND-YGRGWLYLGMAYSGI 273
                                    57899999999****************55.599999999999877 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0046
                         TPR_12  49 rnLgrlyralgryeeAlelleealai 74 
                                    + L+  y++++++e A  ++++al i
  gene775|gene775|rna774|rna774 298 FYLAKEYHRMNNFERASFFYKHALGI 323
                                    679999*****************965 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.061
                         TPR_12  47 tlrnLgrlyralgryeeAlelleeal 72 
                                    ++ + g + ++l++++ A + +++al
  gene775|gene775|rna774|rna774 388 YYATAGFIDHLLNNLDSAADNYNKAL 413
                                    45566666677888888888888876 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00014      0.31       9      38 ..     241     270 ..     236     272 .. 0.94
   2 ?   -1.4   0.0      0.87     2e+03       2      24 ..     302     324 ..     301     326 .. 0.81
   3 !    5.1   0.0    0.0082        18       5      21 ..     397     413 ..     393     415 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                         TPR_11   9 kyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                    +y eA  ++ kA+++++d+ + ++ LG ay
  gene775|gene775|rna774|rna774 241 NYSEARRCFYKAVQINNDYGRGWLYLGMAY 270
                                    79*************************999 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.87
                         TPR_11   2 dayyeqGkyeeAieaYkkAlkld 24 
                                    ++y+  +++e A   Yk Al ++
  gene775|gene775|rna774|rna774 302 KEYHRMNNFERASFFYKHALGIN 324
                                    68999999999998899888776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0082
                         TPR_11   5 yeqGkyeeAieaYkkAl 21 
                                    + +++++ A  +Y+kAl
  gene775|gene775|rna774|rna774 397 HLLNNLDSAADNYNKAL 413
                                    56899***********8 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1         2   4.5e+03      22      29 ..      48      55 ..      47      56 .. 0.87
   2 ?   -3.5   0.1       7.8   1.7e+04      19      25 ..     198     204 ..     197     205 .. 0.81
   3 !    5.9   0.0    0.0078        18      15      33 ..     240     258 ..     227     259 .. 0.82
   4 ?    0.8   0.1      0.35   7.8e+02       4      25 ..     263     284 ..     260     288 .. 0.84
   5 !   12.3   0.0   6.7e-05      0.15       7      32 ..     300     325 ..     298     327 .. 0.93
   6 ?    1.0   0.0      0.29   6.5e+02      11      27 ..     366     382 ..     360     384 .. 0.80
   7 ?    3.3   0.2     0.054   1.2e+02       3      28 ..     388     413 ..     387     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                                   HHHHHHHH CS
                          TPR_8 22 eyyekale 29
                                   ++ye+++e
  gene775|gene775|rna774|rna774 48 SCYERCIE 55
                                   69****98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 7.8
                                    HHHHHHH CS
                          TPR_8  19 eAkeyye 25 
                                     Ak+yy+
  gene775|gene775|rna774|rna774 198 LAKQYYK 204
                                    5999997 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0078
                                    T-HHHHHHHHHHHHHHHHH CS
                          TPR_8  15 gdyeeAkeyyekaleldpd 33 
                                     +y eA  ++ ka++++ d
  gene775|gene775|rna774|rna774 240 SNYSEARRCFYKAVQINND 258
                                    5899************987 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.35
                                    HHHHHHHHHHTT-HHHHHHHHH CS
                          TPR_8   4 yynlgsiylklgdyeeAkeyye 25 
                                    ++ lg++y+  ++ e+++++++
  gene775|gene775|rna774|rna774 263 WLYLGMAYSGIKECESSIACLN 284
                                    6669******999999999986 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 6.7e-05
                                    HHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   7 lgsiylklgdyeeAkeyyekaleldp 32 
                                    l++ y+ ++++e A  +y++al ++ 
  gene775|gene775|rna774|rna774 300 LAKEYHRMNNFERASFFYKHALGINS 325
                                    7899*******************986 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.29
                                    HHHTT-HHHHHHHHHHH CS
                          TPR_8  11 ylklgdyeeAkeyyeka 27 
                                     l lg+  eA++y+  +
  gene775|gene775|rna774|rna774 366 NLFLGKVTEAQKYLSSC 382
                                    5789*********9665 PP

  == domain 7  score: 3.3 bits;  conditional E-value: 0.054
                                    HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekal 28 
                                    +y   g i + l+++++A   y+kal
  gene775|gene775|rna774|rna774 388 YYATAGFIDHLLNNLDSAADNYNKAL 413
                                    677778888889*************8 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.8   2.9e-06    0.0066       7      76 ..      19      87 ..      16      91 .. 0.93
   2 ?    0.7   0.1      0.27   6.1e+02      48      79 ..     217     249 ..     194     258 .. 0.53
   3 !    9.6   2.0   0.00048       1.1       9      79 ..     280     350 ..     274     353 .. 0.76
   4 ?    0.6   0.1      0.31   6.9e+02      63      81 ..     363     381 ..     343     382 .. 0.72
   5 ?   -0.9   0.1      0.85   1.9e+03       4      36 ..     413     450 ..     410     452 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                                   HHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHH CS
                         ANAPC3  7 nAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAi 76
                                   +A+ l+e ++ +e++ +  ++ll +++y+++ y+r++e ++ + +  + +++r+++ +c l  +k ++++
  gene775|gene775|rna774|rna774 19 SALALSEYVY-REKKTDATIMLLLKSMYKLSCYERCIETIELNSSVMRIHEARIIYYRCKLLTGKKNKGL 87
                                   59999*****.********************************8999999***********999988875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                                    CT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                         ANAPC3  48 ka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                    ++ kl+++s+ + + ++   l  ++y eA++++
  gene775|gene775|rna774|rna774 217 TMvKLYPNSEHSFVALGLFFLMSSNYSEARRCF 249
                                    444444444444333333333335555555554 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00048
                                    HHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-H.HHHHHHHHHHHHTT-HHHHHHHH CS
                         ANAPC3   9 iflaerllaaetespedayllAlclylngqykrAyellrka.klnsksl.gcrylfAqcllkLkkyeeAiaaL 79 
                                    i +++ +++ +  s++ a++lA+ + ++++++rA  +++ a ++ns+ + + ry+    l+ ++ y eA++ L
  gene775|gene775|rna774|rna774 280 IACLNIAYKVMIGSYKPAFYLAKEYHRMNNFERASFFYKHAlGINSSVKvQERYI--SLLIYYEYYPEALSYL 350
                                    56677778888889999************************66665554444554..5555555588887766 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.31
                                    HHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  63 AqcllkLkkyeeAiaaLek 81 
                                      c l L+k+ eA + L++
  gene775|gene775|rna774|rna774 363 VYCNLFLGKVTEAQKYLSS 381
                                    4689999999999888865 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 0.85
                                    -HHHHHHHHHHHH......HHH--HHHHHHHHHHHHHT CS
                         ANAPC3   4 nyknAiflaerll.....aaetespedayllAlclyln 36 
                                     +k+ + l e ll     ++  + ++++y +A  l+ n
  gene775|gene775|rna774|rna774 413 LLKTHVNLVEELLglaveNMTCKQNNNVYDYATDLFDN 450
                                    56788888888887766447778889999999999876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.3   1.4e+04      22      29 ..      48      55 ..      46      56 .. 0.80
   2 ?   -2.8   0.1       4.4   9.9e+03       7      16 ..     198     207 ..     197     207 .. 0.75
   3 !    9.5   0.0   0.00052       1.2       6      33 ..     231     258 ..     228     259 .. 0.89
   4 ?   -0.1   0.1       0.6   1.3e+03       3      13 ..     262     272 ..     260     288 .. 0.75
   5 !   11.5   0.1   0.00012      0.26       5      30 ..     298     323 ..     295     326 .. 0.91
   6 ?   -3.9   0.2         8   1.8e+04      17      23 ..     343     349 ..     339     351 .. 0.64
   7 ?   -2.0   0.0       2.4   5.5e+03      14      24 ..     369     379 ..     364     380 .. 0.81
   8 !    7.6   0.3    0.0021       4.7       2      28 ..     387     413 ..     386     416 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.3
                          TPR_2 22 eafekAle 29
                                    ++e+++e
  gene775|gene775|rna774|rna774 48 SCYERCIE 55
                                   69999986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.4
                          TPR_2   7 lGlayyklgd 16 
                                    l++ yyk+g+
  gene775|gene775|rna774|rna774 198 LAKQYYKSGK 207
                                    7888888885 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00052
                          TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                    +lGl  + + +y eA+++f kA++++ +
  gene775|gene775|rna774|rna774 231 ALGLFFLMSSNYSEARRCFYKAVQINND 258
                                    6888899999***************987 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.6
                          TPR_2   3 alynlGlayyk 13 
                                    ++ +lG+ay  
  gene775|gene775|rna774|rna774 262 GWLYLGMAYSG 272
                                    799****9965 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00012
                          TPR_2   5 ynlGlayyklgdyeeAleafekAlel 30 
                                    ++l++ y +++++e+A  +++ Al +
  gene775|gene775|rna774|rna774 298 FYLAKEYHRMNNFERASFFYKHALGI 323
                                    89*********************955 PP

  == domain 6  score: -3.9 bits;  conditional E-value: 8
                          TPR_2  17 yeeAlea 23 
                                    y eAl +
  gene775|gene775|rna774|rna774 343 YPEALSY 349
                                    5666665 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 2.4
                          TPR_2  14 lgdyeeAleaf 24 
                                    lg+  eA +++
  gene775|gene775|rna774|rna774 369 LGKVTEAQKYL 379
                                    89999**9996 PP

  == domain 8  score: 7.6 bits;  conditional E-value: 0.0021
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAl 28 
                                    +++   G +   l++++ A++ ++kAl
  gene775|gene775|rna774|rna774 387 RYYATAGFIDHLLNNLDSAADNYNKAL 413
                                    57888999999***************9 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.7     6e+03      10      31 ..      20      41 ..      19      48 .. 0.84
   2 ?   -1.2   0.1       1.3     3e+03      13      31 ..     127     145 ..     125     147 .. 0.81
   3 ?    6.7   0.0    0.0046        10       2      48 ..     237     283 ..     236     286 .. 0.84
   4 ?   -0.7   0.0      0.94   2.1e+03      29      47 ..     299     316 ..     292     325 .. 0.75
   5 ?    4.1   0.1     0.029        66      16      49 ..     345     380 ..     340     384 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.7
                         TPR_19 10 AlalleqalqedpknaearllL 31
                                   Alal e+++ e+  +a + llL
  gene775|gene775|rna774|rna774 20 ALALSEYVYREKKTDATIMLLL 41
                                   8899999999999999999976 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                         TPR_19  13 lleqalqedpknaearllL 31 
                                    +l +a+  d++n+ea+l++
  gene775|gene775|rna774|rna774 127 ILLEAYRSDNNNLEALLRM 145
                                    56678889999*9999986 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0046
                         TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealL 48 
                                    l++ +y eA + + +a q ++++++ +l+L  a+   ++ +  +a+L
  gene775|gene775|rna774|rna774 237 LMSSNYSEARRCFYKAVQINNDYGRGWLYLGMAYSGIKECESSIACL 283
                                    67789*************************99998766666666665 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.94
                         TPR_19  29 llLAeallalgqldeAeal 47 
                                    + LA+ +  +++++ A   
  gene775|gene775|rna774|rna774 299 Y-LAKEYHRMNNFERASFF 316
                                    4.88889999999999765 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.029
                         TPR_19  16 qalqedpk..naearllLAeallalgqldeAealLd 49 
                                    +al++ +   n+ + ll + + l lg ++eA++ L+
  gene775|gene775|rna774|rna774 345 EALSYLAAqkNSLLGLLRVYCNLFLGKVTEAQKYLS 380
                                    4555544401555555557777777*******9886 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00041      0.92       6      42 ..     231     267 ..     227     269 .. 0.93
   2 ?   -1.8   0.0       3.6     8e+03       6      27 ..     299     320 ..     297     324 .. 0.79
   3 ?   -1.4   0.0       2.7   6.1e+03       7      27 ..     360     382 ..     355     393 .. 0.67
   4 ?   -2.1   0.0       4.4     1e+04      14      28 ..     399     413 ..     385     417 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                         TPR_14   6 alaeallalGdpdeAiallrralalaPddaeawllla 42 
                                    al+ ++l + ++ eA++++ +a++ + d  + wl+l+
  gene775|gene775|rna774|rna774 231 ALGLFFLMSSNYSEARRCFYKAVQINNDYGRGWLYLG 267
                                    899999****************************997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                         TPR_14   6 alaeallalGdpdeAiallrra 27 
                                     la+ + +  ++++A   ++ a
  gene775|gene775|rna774|rna774 299 YLAKEYHRMNNFERASFFYKHA 320
                                    5888999999999997777666 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.7
                         TPR_14   7 laeal..lalGdpdeAiallrra 27 
                                    l++++  l lG+  eA ++l  +
  gene775|gene775|rna774|rna774 360 LLRVYcnLFLGKVTEAQKYLSSC 382
                                    55666224478999999998766 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.4
                         TPR_14  14 lGdpdeAiallrral 28 
                                    l ++d A++ +++al
  gene775|gene775|rna774|rna774 399 LNNLDSAADNYNKAL 413
                                    567888888777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2618.00
//
Query:       gene776|gene776|rna775|rna775  [L=168]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0003   21.1   4.1    0.00034   20.9   3.6    1.4  1  Mis14        Kinetochore protein Mis14 like
  ------ inclusion threshold ------
      0.027   14.4   1.4      0.096   12.6   0.1    2.4  2  ApoC-I       Apolipoprotein C-I (ApoC-1)
      0.049   13.7   1.8       0.27   11.3   0.1    2.5  2  Med9         RNA polymerase II transcription mediator complex
      0.052   13.9   1.4       0.15   12.3   1.4    1.8  1  DUF349       Domain of Unknown Function (DUF349)
      0.058   13.0   0.0      0.068   12.8   0.0    1.2  1  CobT_C       Cobalamin biosynthesis protein CobT VWA domain
       0.08   12.5   0.2       0.17   11.5   0.1    1.5  1  CAMP_factor  CAMP factor (Cfa)
      0.099   12.9   0.6       0.37   11.1   0.1    2.1  2  TcdB_N       TcdB toxin N-terminal helical domain
       0.37   11.1   3.7        3.5    8.0   0.3    2.4  2  Tup_N        Tup N-terminal
        0.4   11.0   2.6       0.79   10.0   1.3    2.0  2  Mrpl_C       54S ribosomal protein L8 C-terminal domain
       0.96    9.7   4.1        5.3    7.3   0.4    2.6  3  DUF5082      Domain of unknown function (DUF5082)


Domain annotation for each model (and alignments):
>> Mis14  Kinetochore protein Mis14 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   3.6   1.9e-07   0.00034      36     132 ..      50     144 ..      19     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCT--HHHHH--....------SSSHHHHHHHH CS
                          Mis14  36 lelnekvrslyqelEdltvevAqlRreaPrkiaeayakelkaeleeldeyleainelek..qekkdpeeddededekerl 113
                                    ++l+ek +    + +  +  +A lR+++P k++e++++ +++  e+++ ++++ ++ e   + +k  e  ++ ++e +r+
  gene776|gene776|rna775|rna775  50 EKLAEKTE----QRDFKVLSLALLRKDLPVKAREEFNEHIRRVKEKIEGLRKIGAQKEGviDYEKRVERPNRIIEEINRI 125
                                    44444444....448889999****************************8877777777999999999999********* PP

                                    HHHHHHHHHHHHHHHHHHH CS
                          Mis14 114 eelvkqyeeslkslkelke 132
                                    ee v + ++ +k+  +l+e
  gene776|gene776|rna775|rna775 126 EESVPDVQKKIKKARDLIE 144
                                    ***********99988875 PP

>> ApoC-I  Apolipoprotein C-I (ApoC-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.4e-05     0.096      35      58 ..      70      93 ..      49      94 .. 0.89
   2 ?   -0.1   0.1      0.52   9.3e+02      18      32 ..     132     145 ..     117     150 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                                   TTSSSSCCHHHHHHHHHHHHHHSS CS
                         ApoC-I 35 qSelpaktrnWfsetfekvkeklk 58
                                   +++lp k r+ f+e +++vkek++
  gene776|gene776|rna775|rna775 70 RKDLPVKAREEFNEHIRRVKEKIE 93
                                   689*******************85 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.52
                                    HHHHHHHHHCCHCCC CS
                         ApoC-I  18 fgktledKaraaiee 32 
                                    + k++  Kar +iee
  gene776|gene776|rna775|rna775 132 VQKKI-KKARDLIEE 145
                                    33333.355555555 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.16   2.9e+02      22      47 ..      79     104 ..      49     118 .. 0.71
   2 ?   11.3   0.1   0.00015      0.27      19      44 ..     120     145 ..     105     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.16
                           Med9  22 kdletktgelrhkLkkarelirelpg 47 
                                    +++  ++  ++ k++  r+  ++ +g
  gene776|gene776|rna775|rna775  79 EEFNEHIRRVKEKIEGLRKIGAQKEG 104
                                    45566666666666666665555555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00015
                           Med9  19 lsskdletktgelrhkLkkarelire 44 
                                     +++ +e ++ ++++k+kkar li+e
  gene776|gene776|rna775|rna775 120 EEINRIEESVPDVQKKIKKARDLIEE 145
                                    578999******************98 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.4   8.6e-05      0.15       4      65 ..      79     145 ..      76     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.6e-05
                         DUF349   4 krFraacdafferrkahfeeqdaer.....eenlekKealieeaealaksttdwksatkrlkelqee 65 
                                    ++F++++ +++e+ +  ++   +++     e+  e+ + +iee++ +++s  d+++++k++++l ee
  gene776|gene776|rna775|rna775  79 EEFNEHIRRVKEKIEGLRKIGAQKEgvidyEKRVERPNRIIEEINRIEESVPDVQKKIKKARDLIEE 145
                                    455555555555555555555555588888*****************99988************986 PP

>> CobT_C  Cobalamin biosynthesis protein CobT VWA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.8e-05     0.068     152     213 ..      72     136 ..      26     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                         CobT_C 152 tlsvaaGdylerhlrtvikeietlsdveliaiGvltdvtryyk...ravlvvdveelGgavvekl 213
                                     l v+a + +++h+r+v ++ie l ++     Gv     r  +       ++ +ee  + v +k+
  gene776|gene776|rna775|rna775  72 DLPVKAREEFNEHIRRVKEKIEGLRKIGAQKEGVIDYEKRVERpnrIIEEINRIEESVPDVQKKI 136
                                    57899**********************99999998766665441004455666777766666655 PP

>> CAMP_factor  CAMP factor (Cfa)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   9.2e-05      0.17      32      98 ..      74     140 ..      48     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.2e-05
                    CAMP_factor  32 kadyekeiekllktakelkealeaiakgkvtlydlksIlaRvellvdivdtiktaattLqdKvqkAh 98 
                                    +++  +e+++ +  +ke  e l++i + k+ ++d +  + R + +++ ++ i+++  + q+K++kA 
  gene776|gene776|rna775|rna775  74 PVKAREEFNEHIRRVKEKIEGLRKIGAQKEGVIDYEKRVERPNRIIEEINRIEESVPDVQKKIKKAR 140
                                    47788999999999999999999*9999*********9*************************9995 PP

>> TcdB_N  TcdB toxin N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.3   2.3e+03      12      36 ..      13      37 ..       8      39 .. 0.75
   2 ?   11.1   0.1   0.00021      0.37       6      38 ..     114     145 ..     109     153 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                                   HHHHTTTTS-HHHHHHHHHHHHHHH CS
                         TcdB_N 12 eklnklseeqskkkyellkklkkei 36
                                   e ++ l  +++k++ + l+ l k+i
  gene776|gene776|rna775|rna775 13 EQIARLAPPSQKEDHKFLNLLRKAI 37
                                   6677788888888888888888888 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00021
                                    HHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHH CS
                         TcdB_N   6 ilenleeklnklseeqskkkyellkklkkeidn 38 
                                    +++ + e++ +  ee+++++++++kk+ ++i +
  gene776|gene776|rna775|rna775 114 RPNRIIEEI-NRIEESVPDVQKKIKKARDLIEE 145
                                    688999***.*******************9976 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3      0.04        72      57      74 ..      76      93 ..      73      96 .. 0.90
   2 ?    8.0   0.3     0.002       3.5      29      64 ..     107     145 ..      95     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.04
                          Tup_N 57 kikqqYEeeiarLkaeLe 74
                                   k +++++e i+r k+++e
  gene776|gene776|rna775|rna775 76 KAREEFNEHIRRVKEKIE 93
                                   789************998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.002
                          Tup_N  29 eyelki...qsqiqElqqirqtlyeLeeahrkikqqYEe 64 
                                    +ye+++   +  i+E+++i +++ + +++ +k ++  Ee
  gene776|gene776|rna775|rna775 107 DYEKRVerpNRIIEEINRIEESVPDVQKKIKKARDLIEE 145
                                    7888762225679*******************9987776 PP

>> Mrpl_C  54S ribosomal protein L8 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.74   1.3e+03      60      89 ..       7      37 ..       1      45 [. 0.53
   2 ?   10.0   1.3   0.00044      0.79      25      69 ..      52      96 ..      49     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.74
                         Mrpl_C 60 avrkflkeeqele.wdeeeekeavkalldqv 89
                                    v +++ + + l+   ++e++++++ l +++
  gene776|gene776|rna775|rna775  7 DVDEVMEQIARLApPSQKEDHKFLNLLRKAI 37
                                   4555555544444344555556666665555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00044
                         Mrpl_C 25 ladeskakayaplTlqnLkKmlkfkskeqllkeilavrkflkeeq 69
                                   la+++++++++ l l  L+K l  k++e++++ i+ v++ +   +
  gene776|gene776|rna775|rna775 52 LAEKTEQRDFKVLSLALLRKDLPVKAREEFNEHIRRVKEKIEGLR 96
                                   6788999*******************************9887654 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.7     3e+03      19      30 ..       8      19 ..       5      42 .. 0.69
   2 ?    3.1   0.1     0.061   1.1e+02      86     113 ..      81     108 ..      75     114 .. 0.65
   3 ?    7.3   0.4     0.003       5.3      92     118 ..     117     143 ..     107     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.7
                        DUF5082 19 iaaleekIerLk 30
                                   ++ + e+I+rL 
  gene776|gene776|rna775|rna775  8 VDEVMEQIARLA 19
                                   455556677664 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.061
                        DUF5082  86 ldelidaieeEIerLenqiseaqgvldt 113
                                      e i++++e+Ie L++   +++gv+d+
  gene776|gene776|rna775|rna775  81 FNEHIRRVKEKIEGLRKIGAQKEGVIDY 108
                                    4455666777777777766666666666 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.003
                        DUF5082  92 aieeEIerLenqiseaqgvldtlqsql 118
                                    +i eEI+r+e+++ + q+++++    +
  gene776|gene776|rna775|rna775 117 RIIEEINRIEESVPDVQKKIKKARDLI 143
                                    7899****************9876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1432  (0.0798706); expected 358.6 (0.02)
Passed bias filter:                      873  (0.0486921); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1249.01
//
Query:       gene777|gene777|rna776|rna776  [L=447]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0003   20.3   0.1          4    7.3   0.0    4.2  4  PUF       Pumilio-family RNA binding repeat


Domain annotation for each model (and alignments):
>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.1    0.0034        61       1      31 [.      28      58 ..      28      62 .. 0.86
   2 ?   -2.1   0.0      0.22     4e+03      10      20 ..      71      81 ..      67      81 .. 0.76
   3 !    3.9   0.0    0.0026        47      11      25 ..     116     130 ..     115     139 .. 0.82
   4 !    7.3   0.0   0.00022         4       2      19 ..     229     246 ..     228     247 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0034
                                   HHGGGHHHHHTSTTHHHHHHHHHHHSCHHHH CS
                            PUF  1 sikgnlvqLstdqyGnyvvQkllehateeqk 31
                                   +i+gn  +L+ d   ++ +++l+ ++ + q+
  gene777|gene777|rna776|rna776 28 EIQGNEKELMLDTETTHQIETLIRKSNSRQI 58
                                   589999******************9777765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.22
                                   HTSTTHHHHHH CS
                            PUF 10 stdqyGnyvvQ 20
                                   ++ + G++v++
  gene777|gene777|rna776|rna776 71 MSKKLGSRVIE 81
                                   55578****97 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0026
                                    TSTTHHHHHHHHHHH CS
                            PUF  11 tdqyGnyvvQklleh 25 
                                    +d +++++++kl++ 
  gene777|gene777|rna776|rna776 116 SDTNATHIIRKLFQL 130
                                    599*********985 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.00022
                                    HGGGHHHHHTSTTHHHHH CS
                            PUF   2 ikgnlvqLstdqyGnyvv 19 
                                    ik+++ +L++ +yGny++
  gene777|gene777|rna776|rna776 229 IKDKVMELCKEKYGNYFI 246
                                    789999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2862.02
//
Query:       gene778|gene778|rna777|rna777  [L=74]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-10   39.6   0.1    4.7e-10   39.1   0.1    1.3  1  DUF1242    Protein of unknown function (DUF1242)
  ------ inclusion threshold ------
      0.063   12.9   0.0      0.075   12.7   0.0    1.2  1  SET_assoc  Histone lysine methyltransferase SET associated


Domain annotation for each model (and alignments):
>> DUF1242  Protein of unknown function (DUF1242)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.1   5.3e-14   4.7e-10       5      34 ..      14      43 ..      10      44 .. 0.94

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 5.3e-14
                        DUF1242  5 lLLlICTCTYvravfPslldrnksgfrGvf 34
                                   l+L ICT TY+++ fPsl+ +nk+gf +vf
  gene778|gene778|rna777|rna777 14 LILAICTATYLKQHFPSLVSKNKKGFYSVF 43
                                   89*************************998 PP

>> SET_assoc  Histone lysine methyltransferase SET associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.4e-06     0.075      21      44 ..      24      47 ..      21      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.4e-06
                      SET_assoc 21 LkkyeweriledktGyYivFndsk 44
                                   Lk++ ++ + ++k+G+Y vF++++
  gene778|gene778|rna777|rna777 24 LKQHFPSLVSKNKKGFYSVFHKLS 47
                                   99999***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 526.10
//
Query:       gene779|gene779|rna778|rna778  [L=779]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.014   16.0   0.6      0.014   16.0   0.6    7.2  7  SlyX           SlyX
        2.7    8.0   8.8       0.61   10.1   0.4    3.9  4  Prp19          Prp19/Pso4-like


Domain annotation for each model (and alignments):
>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.6   1.6e-06     0.014       2      46 ..      39      82 ..      38      99 .. 0.81
   2 ?    4.0   0.2    0.0085        76       1      39 [.     136     174 ..     134     177 .. 0.84
   3 ?   -1.6   0.1      0.47   4.2e+03      36      56 ..     187     207 ..     182     214 .. 0.66
   4 ?    0.3   0.3      0.12   1.1e+03      20      47 ..     258     285 ..     245     300 .. 0.74
   5 ?    6.3   0.2    0.0016        15      18      53 ..     308     343 ..     302     353 .. 0.90
   6 ?   -1.0   0.0      0.31   2.8e+03      22      58 ..     352     388 ..     344     393 .. 0.76
   7 ?    0.1   0.1      0.14   1.3e+03      18      52 ..     521     554 ..     512     575 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           SlyX  2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaer 46
                                   ++r++eLE k+   e+ i++Ln+ +++q  ++++++  +  laer
  gene779|gene779|rna778|rna778 39 KNRVKELEKKVELCEEIINDLNKKLVKQSVEMTEIKSSFT-LAER 82
                                   68******************************99987765.4444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0085
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX   1 leerleeLEiklafqedtieeLndvvaeqqqqidrlqrq 39 
                                    le+r+e+L+ k   +e+  ++L + v +q  q++ l r+
  gene779|gene779|rna778|rna778 136 LENRMEALQKKCVELERCNKKLVEKVLDQKNQVSYLLRK 174
                                    588999999999999999999999999999998877665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.47
                                    HHHHHHHHHHT-XXXXXXXXX CS
                           SlyX  36 lqrqlrllaerlkeleessga 56 
                                    l + +++l ++ +ele++ g+
  gene779|gene779|rna778|rna778 187 LVKLVQKLSKKNEELEQALGS 207
                                    556666777777777776654 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                           SlyX  20 eeLndvvaeqqqqidrlqrqlrllaerl 47 
                                    +eL +++++  ++ + +qr++++++e++
  gene779|gene779|rna778|rna778 258 NELYNQLIRNSEEKKVMQRHIDEMKEEI 285
                                    5777888888888888888888888776 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.0016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                           SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                     + e+n+++++ +  i+  + ++r+l+ +l+e ee+
  gene779|gene779|rna778|rna778 308 KLGEMNNEIIRSNFIIKDSRNKIRELKAQLAESEER 343
                                    5779**************************999987 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                           SlyX  22 Lndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                                      +vva   ++i+ ++r+l+   +++ ++e+  +++ 
  gene779|gene779|rna778|rna778 352 RTNVVAVIGREIEGIKRKLDTNFKQIYDIEDGFKKAM 388
                                    5678999999********9999999988887766544 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                           SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                      + L ++ +  + +i+ l    +ll e++++lee
  gene779|gene779|rna778|rna778 521 ERDILKQENIFLRNKIESLGDSSDLL-EKISNLEE 554
                                    44444444444444444444333322.33333333 PP

>> Prp19  Prp19/Pso4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4     0.084   7.5e+02      21      41 ..     185     205 ..     183     209 .. 0.92
   2 ?   -2.9   0.0       0.8   7.2e+03      22      37 ..     221     236 ..     215     240 .. 0.74
   3 ?   -3.4   0.0       1.1   9.8e+03      53      65 ..     494     506 ..     492     508 .. 0.79
   4 ?   10.1   0.4   6.8e-05      0.61      11      60 ..     593     642 ..     591     647 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.084
                                    HHHHHHHHHHHHHHHHHHHHH CS
                          Prp19  21 letfelrkqleqtrqeLsqaL 41 
                                    le+ +l ++l +  +eL qaL
  gene779|gene779|rna778|rna778 185 LELVKLVQKLSKKNEELEQAL 205
                                    7999999**********9998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.8
                                    HHHHHHHHHHHHHHHH CS
                          Prp19  22 etfelrkqleqtrqeL 37 
                                    e+ e  k+++ +r+eL
  gene779|gene779|rna778|rna778 221 ENIEAEKEYKRMREEL 236
                                    7777778888888887 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHH CS
                          Prp19  53 rllkerdeareal 65 
                                    +ll+erd+  + l
  gene779|gene779|rna778|rna778 494 KLLEERDQVLHSL 506
                                    8999**9988766 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 6.8e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Prp19  11 tlqnEWDalmletfelrkqleqtrqeLsqaLYqnDAAvrViArllkerde 60 
                                     lq++ D+++ ++ +l+++l+ +r+e s+     D  + +i +l k +d+
  gene779|gene779|rna778|rna778 593 LLQSDVDQVLQDNLSLKNELQMARKEISNNYAAIDKYKIIIEKLKKIKDA 642
                                    69**************************9988888888888888776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2374  (0.132411); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.29u 0.38s 00:00:01.67 Elapsed: 00:00:00.54
# Mc/sec: 4357.40
//
Query:       gene780|gene780|rna779|rna779  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-13   49.5  20.3    3.8e-07   30.3   4.2    2.1  2  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   4.2   2.1e-11   3.8e-07       1      59 [.      33      91 ..      33      92 .. 0.97
   2 !   25.3   8.2   8.1e-10   1.4e-05       2      60 .]     110     168 ..     109     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.1e-11
                                   HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivali 59
                                   +g+ ++++ls +g+  g   +g  +i+a+ + p++ t++l++++++ea + ++L+++ +
  gene780|gene780|rna779|rna779 33 FGIVMCIALSSFGTSKGYQAIGRYMIGASIKTPRVGTRALLGIVICEANFFFCLVMSNL 91
                                   699****************************************************9966 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 8.1e-10
                                    HHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C   2 gaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                                     ag+  G +   s ++ G++++a+  + a++p lf k++ + +++  i+++gL+ +l+l
  gene780|gene780|rna779|rna779 110 TAGFIAGACSYCSSLASGIICAAITMMDAKDPTLFYKLVFLEVIPAGIGILGLVLGLVL 168
                                    69****************************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1124.02
//
Query:       gene78|gene78|rna78|rna78  [L=414]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-07   31.3   1.2    2.3e-07   30.5   1.2    1.5  1  LisH      LisH
      6e-07   30.1  12.1      0.067   14.1   0.8    6.2  6  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> LisH  LisH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   1.2   2.6e-11   2.3e-07       1      27 []       7      33 ..       7      33 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.6e-11
                               HHHHHHHHHHHHHCT-HHHHHHHHHHT CS
                       LisH  1 eeLNrLIydYLvkeGyeetAeaFekEa 27
                               +eLN+L+y YL  eGy  t ++F++Ea
  gene78|gene78|rna78|rna78  7 DELNQLVYKYLEDEGYIYTLFTFKNEA 33
                               69************************8 PP

>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.25   2.2e+03      13      22 ..     154     163 ..     148     173 .. 0.82
   2 ?    3.4   0.1     0.018   1.6e+02       5      34 ..     184     212 ..     180     214 .. 0.68
   3 !    8.0   0.1   0.00062       5.5       9      38 .]     264     292 ..     255     292 .. 0.75
   4 !   14.1   0.8   7.5e-06     0.067      10      38 .]     304     331 ..     299     331 .. 0.77
   5 !    5.2   0.0    0.0047        42       5      34 ..     339     366 ..     336     368 .. 0.71
   6 ?    0.2   0.0      0.18   1.7e+03      11      28 ..     383     400 ..     374     404 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.25
                                EEEEEEETTS CS
                       WD40  13 vtslafspdg 22 
                                vt+l++s+d+
  gene78|gene78|rna78|rna78 154 VTALSWSDDN 163
                                99**999997 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.018
                                EEEESS.SSEEEEEEETTSSE....EEEEETTSEE CS
                       WD40   5 rtltGH.ssvtslafspdgaw....lasGsdDgtv 34 
                                r+ t H + vt +      +     ++s+++Dg +
  gene78|gene78|rna78|rna78 184 RSHTCHsKAVTKV------KQrgmgILSSGRDGRI 212
                                5667897779999......4444554566779988 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00062
                                SS.SSEEEEEEETTSSEEEEEETTSEEEEEE CS
                       WD40   9 GH.ssvtslafspdgawlasGsdDgtvriWd 38 
                                +H + ++ +   ++   l+++s Dgt+ +Wd
  gene78|gene78|rna78|rna78 264 THeDKISNI--EHNEEILSTSSHDGTLGLWD 292
                                564447766..677777999988*******9 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 7.5e-06
                                S.SSEEEEEEETTSSE.....EEEEETTSEEEEEE CS
                       WD40  10 H.ssvtslafspdgaw.....lasGsdDgtvriWd 38 
                                H + v++       +w     +++Gs D+ v++Wd
  gene78|gene78|rna78|rna78 304 HdGRVNCH------KWmngriVTCGS-DRFVKVWD 331
                                84559999......888888455667.*******9 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0047
                                EEEESS.SSEEEEEEETTSSEEEEEETTSEE CS
                       WD40   5 rtltGH.ssvtslafspdgawlasGsdDgtv 34 
                                ++l  H + v s+  + +++++asGs Dg v
  gene78|gene78|rna78|rna78 339 HEL-NHeDEVISV--DCSSRLVASGSLDGRV 366
                                555.364445466..669999********98 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.18
                                SSEEEEEEETTSSEEEEE CS
                       WD40  11 ssvtslafspdgawlasG 28 
                                +s++ + fs +g++l+ +
  gene78|gene78|rna78|rna78 383 GSISKVLFSESGSYLCIC 400
                                4588899******98643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2635.59
//
Query:       gene781|gene781|rna780|rna780  [L=743]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-47  161.2   0.1      7e-46  156.5   0.0    2.3  2  Helicase_C_2  Helicase C-terminal domain
    4.4e-47  160.0   1.3    4.7e-47  159.9   0.2    1.6  2  DEAD_2        DEAD_2
    3.1e-12   46.6   0.4    8.9e-09   35.3   0.1    2.4  2  HBB           Helical and beta-bridge domain
    1.6e-06   28.2   0.0    0.00063   19.8   0.0    2.4  2  ResIII        Type III restriction enzyme, res subunit
      0.003   17.4   0.0        0.2   11.4   0.0    2.5  2  DEAD          DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.01   15.3   0.0       0.74    9.2   0.0    2.5  2  PhoH          PhoH-like protein
       0.02   15.2   0.0        4.2    7.7   0.0    3.0  3  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.073   1.9e+02      20      85 ..     310     372 ..     296     378 .. 0.72
   2 !  156.5   0.0   2.7e-49     7e-46       2     170 ..     521     695 ..     520     696 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.073
                   Helicase_C_2  20 klleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcr.GklsEGidfsddll 85 
                                    + l++++e++k++l+    ++ +e ++es+ k ++e +   +k+a+ +++ r G ls  + + d+ +
  gene781|gene781|rna780|rna780 310 SALKRITEFFKTKLK--TTHLTTE-STESFCKSIKELSF-IGKKALRFCSQRlGMLSQSLGLDDEDM 372
                                    456677777777763..4455555.66666666666666.999999999999999999988888876 PP

  == domain 2  score: 156.5 bits;  conditional E-value: 2.7e-49
                   Helicase_C_2   2 lellevvpggvlvffpSyklleevverlkeel....eskkieifvee.keesrekvleeykek..kkkgaillavcrGkl 74 
                                    +el++vvp+g+++ffpSy ++ee+v+ ++e+      +k++ +fve+ + +++e  l++y+++  +++g +l++v+rGk+
  gene781|gene781|rna780|rna780 521 IELSRVVPDGIVCFFPSYMYMEEIVSLWAETNiineINKNKLVFVETpDGRETEMALSNYRRAcdNGRGGMLFSVARGKV 600
                                    57899*************************87666666777888887688899*********556*************** PP

                   Helicase_C_2  75 sEGidfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygaivllDeR 154
                                    sEG+df+d ++r+v++ g+Pf+ +++ +++ + ++l+e+ +  +  ++ + +a+r   Q++GR++R+k+Dyg ++l DeR
  gene781|gene781|rna780|rna780 601 SEGVDFEDGYGRCVVMLGVPFQYTESVRLRKRLDFLREEYG-IKEYDFLTFDAMRHAAQCLGRVLRNKNDYGLMILADER 679
                                    *****************************************.99************************************ PP

                   Helicase_C_2 155 fakeeireklpkwlre 170
                                    f++++ + klpkw+++
  gene781|gene781|rna780|rna780 680 FERNDKKGKLPKWIQN 695
                                    **************97 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.9   0.2   1.8e-50   4.7e-47       1     175 [.      74     240 ..      74     241 .. 0.93
   2 ?   -3.5   0.1       2.7   6.8e+03      15      41 ..     311     337 ..     307     355 .. 0.52

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 1.8e-50
                                    EEESSHHHHHHHHHHHHHHHHHCHH..HS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTTTTT-S CS
                         DEAD_2   1 ycsRThsqleqvvkelkklesykkk..kekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeekeekCsffe 78 
                                    ycsRT+ ++e++++el+ ++sy kk    +++ ++L++RknlCin+ + k   + +v+ aC++l++   e   ++C+f+e
  gene781|gene781|rna780|rna780  74 YCSRTVPEVEKALRELDGVVSYIKKhrPIEFLGLGLTGRKNLCINKVAFK---SFNVDVACRRLVNRLGE---SRCDFYE 147
                                    9*********************998778899999***********77766...899***********975...5*****9 PP

                                    CCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHHT..GCGCEEEECTCCC CS
                         DEAD_2  79 nleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslkgislknsivilDEAhN 158
                                    nl++++    +++  v+d+  l+e+gek+++CPYyl+r+ ++ +d+ii+pY+yL+d++i + +++    ns+vi+DEAhN
  gene781|gene781|rna780|rna780 148 NLNNFN----EVPVAVYDFSRLKEIGEKKGICPYYLVRRSIPVCDCIIYPYNYLIDPRIYSIVSKELGPNSVVIFDEAHN 223
                                    996555....59***************************************************966689*********** PP

                                    HHHHHHHCC-EEEECHH CS
                         DEAD_2 159 iedvceeaasveisees 175
                                    i+++c+e++s+ei+++ 
  gene781|gene781|rna780|rna780 224 IDSHCIEVLSIEIKRNI 240
                                    *************9875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.7
                                    HHHHHHHHCHHHS---EEEE--CCCC- CS
                         DEAD_2  15 elkklesykkkkekvkvviLgSRknlC 41 
                                     lk+++++ k+k k+ +++  S + +C
  gene781|gene781|rna780|rna780 311 ALKRITEFFKTKLKTTHLTTESTESFC 337
                                    556655544433333333334444455 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.1   3.5e-12   8.9e-09      49     189 ..     295     390 ..     265     391 .. 0.89
   2 !   10.1   0.1   0.00018      0.47     117     160 ..     407     451 ..     372     465 .. 0.67

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.5e-12
                                    HCHCHHHCHHHHHHHHHHHHHHHHHHHCCHHCCCTCC-SHHHHHHHHHHHHHHHTS.TTTEEEEEE.STT.EECCCCS-T CS
                            HBB  49 eeavpglirsaehflsllkrlveygkarreekieksesPrsflsrlaefllawlssdeedYvrlvskeegesLeavcldP 128
                                     e +pg+ r++ hf+s lkr++e+ k+ ++ ++  +es  sf+++++                          e++++  
  gene781|gene781|rna780|rna780 295 YEFIPGNLRNSYHFISALKRITEFFKTKLKTTHLTTESTESFCKSIK--------------------------ELSFIG- 347
                                    6899*******************************************..........................******. PP

                                    CCHHHHHHHCHCCCCCCTS-SSHHHHHHHHT....EEE.S..S.GGHCCCCCCCCCSHTCC CS
                            HBB 129 skalrflkerlssllmsgtltpleeysdiiGleaklkkfpspfpkEnlivlfatdVsTkyk 189
                                    +kalrf+++rl +l++s+ l++ e+ +++                 + ++ f t Vs+++k
  gene781|gene781|rna780|rna780 348 KKALRFCSQRLGMLSQSLGLDD-EDMTHL-----------------KTVADFSTMVSMYSK 390
                                    ********************98.888888.................788888888888776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00018
                                    TT.EECCCCS-TCCHHH.HHHHCHCCCCCCTS-SSHHHHHHHHT. CS
                            HBB 117 egesLeavcldPskalr.flkerlssllmsgtltpleeysdiiGl 160
                                     ++ L ++cld s a++ + +  + ++++sgt++p++ y +i+ +
  gene781|gene781|rna780|rna780 407 FNPTLRLACLDSSIAMSsVFARFRNVIITSGTMSPIDMYPKILNF 451
                                    3689*******6666651557778999*************99443 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.5e-07   0.00063       4      66 ..      17      79 ..      15     119 .. 0.83
   2 !    5.8   0.0    0.0049        13     133     147 ..     213     227 ..     199     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.5e-07
                                   E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH..HHHHHHH-S.....-EEEEESSHHH CS
                         ResIII  4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva..aklierllkkgkeekflflvprksl 66
                                   +++ Q + +++++ +l+  ++ + l++m+ GtGKT+ +  + + ++l+ k+k+++f ++  ++++
  gene781|gene781|rna780|rna780 17 VYPEQLKYMREIKRSLD--NRGHCLLEMPSGTGKTVALlsMTISYQLHMKAKNDHFKIVYCSRTV 79
                                   57889999999999995..999*************977447888999999999988777665555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0049
                                    -SEEEEETGGGTTS. CS
                         ResIII 133 fdviiiDEaHrlgak 147
                                    + v+i+DEaH++ + 
  gene781|gene781|rna780|rna780 213 NSVVIFDEAHNIDSH 227
                                    569********9884 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   7.7e-05       0.2      12      75 ..      32      97 ..      18     125 .. 0.73
   2 ?    3.2   0.0     0.026        66     119     136 ..     210     227 ..     187     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.7e-05
                                   H.TTCEEEEEESTTSSHHHHHHHHHHHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                   x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 12 l.gggdvlvaaeTGsGKTlaflipvlqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyid 75
                                   l + g++l++++ G+GKT a l   ++  +++  ++++ k+++ + t   +e+ l++l  + +yi+
  gene781|gene781|rna780|rna780 32 LdNRGHCLLEMPSGTGKTVALLSMTISYQLHMkAKNDHFKIVYCSRTVPEVEKALRELDGVVSYIK 97
                                   236689**************9988887666664577788888887777777777777766666655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.026
                                    CTTEEEEEEETHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxx RF
                           DEAD 119 lsqvrflVlDEadrlldq 136
                                    l   +++++DEa+++ + 
  gene781|gene781|rna780|rna780 210 LGPNSVVIFDEAHNIDSH 227
                                    566689********9987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00029      0.74       8      70 ..      20      91 ..      16     101 .. 0.70
   2 ?    3.2   0.0      0.02        51     120     141 ..     213     234 ..     212     265 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00029
                                   HHHHHHHHHH....H-SEEEEE--TTSSTTH....HHHHHHHHHHHTTS-SEEEEEE-S-.-TT----SS-- CS
                           PhoH  8 eQkeylealk....kndivfaiGpaGtGKty....lavalavealkkkkvkriiltrpav.eageelGflpg 70
                                   eQ +y++ +k    +   +    p+GtGKt     +++++ +++  k++  +i++   +v e+++ l  l+g
  gene781|gene781|rna780|rna780 20 EQLKYMREIKrsldNRGHCLLEMPSGTGKTVallsMTISYQLHMKAKNDHFKIVYCSRTVpEVEKALRELDG 91
                                   78999999987765666899999*******733222333344444556677999987777577888877766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                                    SEEEEE-SGGG--HHHHHHHHT CS
                           PhoH 120 dafvilDEAQnttkeqmkmflt 141
                                    +++vi+DEA n+ ++ ++++ +
  gene781|gene781|rna780|rna780 213 NSVVIFDEAHNIDSHCIEVLSI 234
                                    89**********9998877655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0016       4.2       4      51 ..      34      81 ..      29      94 .. 0.80
   2 ?    3.7   0.0     0.027        70      92     106 ..     213     229 ..     197     260 .. 0.70
   3 ?   -2.0   0.0       1.5   3.9e+03      46      75 ..     433     468 ..     422     490 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51
                                   ++g++++  +sGtGKT+ l  ++ +++ + ka++ + ++v++  ++++
  gene781|gene781|rna780|rna780 34 NRGHCLLEMPSGTGKTVALLSMTISYQLHMKAKNDHFKIVYCSRTVPE 81
                                   678888888*****************9999999977777766555554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.027
                         AAA_22  92 ielliiDEaqhlr.s.e 106
                                     +++i DEa++++ +  
  gene781|gene781|rna780|rna780 213 NSVVIFDEAHNIDsHcI 229
                                    689*********64132 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.5
                         AAA_22  46 tlpsst.sskdllrellralglelka.....erlss 75 
                                     ++s+t s+ d++ ++l+++ +++ +     er+s 
  gene781|gene781|rna780|rna780 433 IITSGTmSPIDMYPKILNFVPSRTAEigatlERNSI 468
                                    56677779999******9999888777766544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (743 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 5376.15
//
Query:       gene782|gene782|rna781|rna781  [L=203]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-27   95.3   0.2    3.1e-27   94.8   0.2    1.2  1  eIF-5_eIF-2B  Domain found in IF2B/IF5
  ------ inclusion threshold ------
       0.04   13.4   0.9       0.09   12.3   0.9    1.6  1  TF_Zn_Ribbon  TFIIB zinc-binding


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.2   3.4e-31   3.1e-27       8     115 ..      72     177 ..      65     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 3.4e-31
                                    SS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHHHH CS
                   eIF-5_eIF-2B   8 kerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyieey 87 
                                    + r+k+p l+vk+e + kt  vN++e+++ Lnr+ +h++++l +el t+gs++++g+l+l+g f +++++++l++yie++
  gene782|gene782|rna781|rna781  72 SARIKLP-LDVKREAR-KTS-VNISEVSEILNRPVDHLVSFLCNELMTTGSVNKDGKLLLKGMFIRSEIQEVLRRYIEHF 148
                                    5677877.89999999.776.5********************************************************** PP

                                    TSTSSSTS.TCEEECCSSSCEEEEESSST CS
                   eIF-5_eIF-2B  88 VlCkeCks.petelekeerllvlkCkaCg 115
                                    V+Ck C+s  +t++++++rl++lkC++Cg
  gene782|gene782|rna781|rna781 149 VVCKICESvEDTDIVRDKRLYFLKCSKCG 177
                                    *******9679*****************9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.9     1e-05      0.09       2      26 ..     150     177 ..     149     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                                    EETTTTCEE.C..HEETSTTCEEESSSS CS
                   TF_Zn_Ribbon   2 kCPnCgstn.l..veDpergelvCtdCG 26 
                                    +C++C s + +  v+D     l C++CG
  gene782|gene782|rna781|rna781 150 VCKICESVEdTdiVRDKRLYFLKCSKCG 177
                                    8******653366999888888*****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1612.25
//
Query:       gene783|gene783|rna782|rna782  [L=808]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.3   11.7   4.2        8.8    7.0   0.1    3.7  5  Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region


Domain annotation for each model (and alignments):
>> Vac14_Fab1_bd  Vacuolar 14 Fab1-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00049       8.8      20      65 ..     165     211 ..     154     222 .. 0.79
   2 ?   -3.6   0.1         1   1.8e+04      46      71 ..     335     361 ..     332     372 .. 0.58
   3 ?   -2.0   0.0      0.32   5.7e+03      10      38 ..     549     577 ..     546     593 .. 0.80
   4 ?    1.6   0.1     0.025   4.4e+02      23      67 ..     694     738 ..     687     752 .. 0.81
   5 ?    3.2   0.3    0.0076   1.4e+02      23      77 ..     724     779 ..     712     793 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00049
                  Vac14_Fab1_bd  20 kikeyleeivkpvlkcfsDkdsrvRyyacEslyniakvakg.evlkl 65 
                                     +++ +++++k  +++++++dsr+ ++ c s+  ++k +++ +v++ 
  gene783|gene783|rna782|rna782 165 MSNNPTDNVLKCFFEMLNERDSRLGWTLCKSFLKVIKYVETgSVVSA 211
                                    46778899*****************************8765145555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1
                  Vac14_Fab1_bd  46 yacEslyniakvakgev.lkllneifd 71 
                                    +++  l n +k++k  + + + +e+f+
  gene783|gene783|rna782|rna782 335 HSVKRLRNCSKAVKRVLeILKCEEVFE 361
                                    556666677776654321334456665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.32
                  Vac14_Fab1_bd  10 LaavaialekkikeyleeivkpvlkcfsD 38 
                                     a  ai l+ +i++y ++i+  + ++ +D
  gene783|gene783|rna782|rna782 549 YAMKAIRLSGDIEKYKDHILGGLENYHTD 577
                                    5788999*********9999776666555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.025
                  Vac14_Fab1_bd  23 eyleeivkpvlkcfsDkdsrvRyyacEslyniakvakgevlklln 67 
                                    ey ee+ + vl ++  +d+ +R + +E ++      ++ +++++ 
  gene783|gene783|rna782|rna782 694 EYQEEFFRGVLGTIGSSDASLRSFIIEEVFKARERFEKLIITMFY 738
                                    677888899999999999999999999999988888888877775 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.0076
                  Vac14_Fab1_bd  23 eyleeivkpvlkcfsDkdsrvRyyacEslyniakv.akgevlkllneifdalvklv 77 
                                    +  e++ k ++++f  + +rv y a+E +  +++  +++++l  + + +++l +l+
  gene783|gene783|rna782|rna782 724 KARERFEKLIITMFYKSCKRVMYPAIEVVCEMIRLeTEEDCLVIFGNNHEILNRLS 779
                                    5667777899********************99987256779999998888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 5485.64
//
Query:       gene784|gene784|rna783|rna783  [L=217]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   43.9   0.1    2.3e-11   43.3   0.1    1.3  1  RRM_1     RNA recognition motif. (a.k.a. RRM, RBD, or RNP dom


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.1   1.3e-15   2.3e-11       3      70 .]     140     211 ..     138     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.3e-15
                                    EESETTTSSHHHHHHHHHT.TSCEEEEEEEEE...TTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                          RRM_1   3 VgnLppdvteeeLkelFsk.fGpiksiklvrd...etgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                    V +L  ++te+++k ++++ + +i++ k+v       g skg++f++F++ +dA  A+++l g++++g+e++
  gene784|gene784|rna783|rna783 140 VFGLGAYITEDDVKNFLKErISGITNYKVVIVydkYSGLSKGYGFIQFDTLDDAITAKNKLLGQTIKGKEIR 211
                                    7789999*****************99888877769***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1446.34
//
Query:       gene785|gene785|rna784|rna784  [L=274]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-38  132.4   6.1    2.2e-38  132.1   6.1    1.0  1  PTP2      Polar tube protein 2 from Microsporidia


Domain annotation for each model (and alignments):
>> PTP2  Polar tube protein 2 from Microsporidia
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.1   6.1   1.2e-42   2.2e-38       1     214 [.      45     245 ..      45     251 .. 0.90

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 1.2e-42
                           PTP2   1 CnnqfieGkkilgangvnanllkkeqpeeClkekkekkkaiealakelikkavkkkask...nkqkkeCikkvskksqaC 77 
                                    C+n+ +eG +i + n+ +           Clk+++e+++a+ ++ak+ + +  +k++sk   +k++ +Ci+++ + +++C
  gene785|gene785|rna784|rna784  45 CANKQVEGVQIFQGNMAE-----------CLKRNSEAANAMFQRAKQRALEIYNKEVSKgptPKDSGQCIERAVQGTDRC 113
                                    99*******999999999...........*************************************************** PP

                           PTP2  78 ilkkvlkelinepeyavkvhgNvvelekkdklvamivneqiky..lvkkkkkkakfafvkkpnaevkfNelGdvlskege 155
                                    il+k++++++n  +y+++ +gN++ l++++kl+ +i+n+++++       kkk   + v  +  e +fN +G+++  +g+
  gene785|gene785|rna784|rna784 114 ILAKIIDKAVNMLKYRISKVGNATALFRGNKLISLILNVDYGLkpFFTVVKKKT--KRVFPSGDELNFNGIGQLIGVKGT 191
                                    ******************************************988455555555..345678899*************** PP

                           PTP2 156 ppqrkkknpcaeClkslkekaqtvEgeldkCeneCd..nssiltsisnnttkkesksekkk 214
                                    +pq  ++++c++C +++k    tvE+ +++C+ +C+  ++  l  is++++kk++k+ +k+
  gene785|gene785|rna784|rna784 192 FPQD-NNDECKPCDSPKK----TVETVAEECNLGCQlkGTPGL--ISKAIQKKDTKESSKD 245
                                    **99.*************....**************7766666..7777777777766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1570.98
//
Query:       gene786|gene786|rna785|rna785  [L=380]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.55
# Mc/sec: 2095.36
//
Query:       gene787|gene787|rna786|rna786  [L=211]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.1e-14   51.6   1.3    1.2e-13   50.9   0.1    1.9  2  E2F_TDP    E2F/DP family winged-helix DNA-binding domain
    1.7e-10   40.9   2.8    3.3e-10   40.0   2.8    1.5  1  DP         Transcription factor DP
  ------ inclusion threshold ------
       0.11   12.8   0.2       0.18   12.2   0.2    1.3  1  PBP_dimer  Penicillin-binding Protein dimerisation domain


Domain annotation for each model (and alignments):
>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   1.9e-17   1.2e-13       2      67 ..      14      76 ..      13      78 .. 0.94
   2 ?   -2.1   0.1      0.71   4.2e+03      20      42 ..      91     115 ..      86     120 .. 0.50

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.9e-17
                        E2F_TDP  2 dksLgvltkkfvellkesakgtlslneaakeLvdkkdekvkkRRiYDilNVLealglieKesknei 67
                                   +++L+++t+ +++ll+e  ++ ++++ ++k++v   ++++ +RRiYD+lNV++a+gli+K+ k ++
  gene787|gene787|rna786|rna786 14 REGLRYITQAVFQLLRE--NRACTYSFICKNIV-FPNTETLNRRIYDVLNVMKAVGLISKRGKRYF 76
                                   789************88..999***********.99999**********************99765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.71
                        E2F_TDP  20 akgtlslneaakeLv..dkkdekvk 42 
                                    ak+ ++++++ k +v  ++++e ++
  gene787|gene787|rna786|rna786  91 AKKLMEMKKVFKFIVdrNSAAEDTH 115
                                    4445555555555554444444455 PP

>> DP  Transcription factor DP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   2.8   5.5e-14   3.3e-10      19     107 ..      86     169 ..      79     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.5e-14
                             DP  19 kkkeqlqeLilqqvalknLvqrNreleekkgapsensviqLPFiivnTskktvidcsiseDkseylfnFdktFeihdDie 98 
                                    ++ke+ + L++ +  +k +v rN ++e+++      + + LPF++v+Tskk+ i c+  e+++ ++f+  k  ++ +D++
  gene787|gene787|rna786|rna786  86 RRKEEAKKLMEMKKVFKFIVDRNSAAEDTHL-----ERLYLPFMVVSTSKKADIHCETNEERNFFVFKSTKPLKVNEDLD 160
                                    567788889999999*********9988543.....3489**************************************** PP

                             DP  99 vLkrmglal 107
                                    +L+++    
  gene787|gene787|rna786|rna786 161 ILREIYEKA 169
                                    ***875544 PP

>> PBP_dimer  Penicillin-binding Protein dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2     3e-05      0.18      41     101 ..      91     203 ..      67     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                                    H.....HHHHHHHC.HHHTTS-HHHHHH..............................................HHCCCC CS
                      PBP_dimer  41 k.....ikklakll.eseenldderlee..............................................lalkkn 68 
                                          +kk++k + + ++  +d+ le                                               ++ k  
  gene787|gene787|rna786|rna786  91 AkklmeMKKVFKFIvDRNSAAEDTHLERlylpfmvvstskkadihcetneernffvfkstkplkvnedldilreIYEKAH 170
                                    12356699999999777777777888889999999999999999999999999999999999999999999999999*** PP

                                    TSSTTSCECCCCCEECHHHCCCHHHHHCSTT-E CS
                      PBP_dimer  69 sykaykpvviaediseeevarikenakdlpGin 101
                                    s+++ + + i + +s+e +++++en+++  G++
  gene787|gene787|rna786|rna786 171 SKEKTTDFSIVDRLSNERFEYFEENNYQREGLD 203
                                    ***************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1440.43
//
Query:       gene788|gene788|rna787|rna787  [L=123]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-19   67.9   0.2    1.1e-18   67.5   0.2    1.1  1  Sybindin  Sybindin-like family
    1.7e-05   24.9   0.1    2.3e-05   24.5   0.1    1.2  1  Sedlin_N  Sedlin, N-terminal conserved region


Domain annotation for each model (and alignments):
>> Sybindin  Sybindin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.2   1.3e-22   1.1e-18       2     136 ..       4     119 ..       3     121 .. 0.90

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.3e-22
                       Sybindin   2 fslyiinkaGgliyqkeaneekkearpklstneklllasmlhslkaiasklspvkakeelqgssgievletdtfkLhclq 81 
                                     +l+iink+Gg++++ e +e++       + n  l+l+s l+s++ i sk+         + s  + +++    +++++ 
  gene788|gene788|rna787|rna787   4 EQLFIINKSGGMVFKYEREENT-------DINSFLILTSSLYSVSVILSKVMD------NPASRQVVYFRNR--TISIFR 68 
                                    589***********99988664.......6799****************9988......5777788888876..5899** PP

                       Sybindin  82 tltGiKfvlitdtktnaeadsllrkiyelYsdyvlknPfyslempircelFdekl 136
                                    t tG+ fv ++d+ +    d l +++y  Y  yv ++Pfys+empi+c +F+ +l
  gene788|gene788|rna787|rna787  69 TITGLVFVFVADKPA----DALFERVYSHYCKYVTRDPFYSPEMPIQCSKFRPHL 119
                                    ***********9988....********************************9876 PP

>> Sedlin_N  Sedlin, N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   2.5e-09   2.3e-05      21     122 ..      20     116 ..       4     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.5e-09
                       Sedlin_N  21 eekelkeLnqf.ilhasLDivedlqwk.tnnlylgkvdkfeklsvsayvtnskikflllhesssskkkdekikqffqevh 98 
                                    e++e++ +n+f il +sL  v    +k  +n   ++v  f + ++s + t +++ f+ + +        +    +f++v+
  gene788|gene788|rna787|rna787  20 EREENTDINSFlILTSSLYSVSVILSKvMDNPASRQVVYFRNRTISIFRTITGLVFVFVAD--------KPADALFERVY 91 
                                    344578888873567899999998888566788899***********************99........445579***** PP

                       Sedlin_N  99 elyvktlm.nPFykvneeirSpaFd 122
                                      y k++   PFy+++++i+ ++F+
  gene788|gene788|rna787|rna787  92 SHYCKYVTrDPFYSPEMPIQCSKFR 116
                                    *****97648**********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 809.92
//
Query:       gene789|gene789|rna788|rna788  [L=873]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-24   85.1   0.7    7.5e-14   50.9   0.0    2.9  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    3.8e-23   81.9   0.1    2.2e-10   39.9   0.1    2.8  3  tRNA-synt_1g  tRNA synthetases class I (M)
    8.3e-09   35.2   0.1      7e-08   32.2   0.1    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.024   13.6   0.1       0.13   11.2   0.0    2.1  2  tRNA-synt_1d  tRNA synthetases class I (R)
       0.54   10.6   5.3       0.29   11.4   0.4    2.9  4  DUF4709       Domain of unknown function (DUF4709)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   2.1e-17   7.5e-14      20     167 ..      24     183 ..      15     250 .. 0.85
   2 !   30.4   0.4   3.4e-11   1.2e-07     365     601 ..     350     583 ..     331     584 .. 0.74

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.1e-17
                    tRNA-synt_1  20 kekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea...kvekklgake.....kke 91 
                                     e+k+f ++ + Py +G+lH+Gh +  +  d+   yk+m+G++vl+ + + + G++i a   k+e++l   e     kk 
  gene789|gene789|rna788|rna788  24 SERKKFFVTFPMPYMNGRLHLGHLFSVSKADFFSYYKEMEGYNVLFPFAFHCTGMPISAsakKLEEELNGGEvdlsvKKI 103
                                    56899****************************************************86222566666433322222667 PP

                    tRNA-synt_1  92 rkklgreefrekv..rewkaeyaeeirkqvkrlGvsvDfdreylTld..keleeavkevfvrladkgliyrgkklvnwst 167
                                      +lg e+    +   +w+ ++ +   k++kr+   +D+ r  +T d  k +   v++ f+rl + g +  gk+   +++
  gene789|gene789|rna788|rna788 104 IRDLGFEDVSSFTdpTHWVRTFPNLCIKSLKRFHGNIDWRRSFITTDinKYYDSFVRWQFKRLNELGYLSFGKRHSIFCP 183
                                    77888887766553368****************************763255778899************99999888876 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 3.4e-11
                    tRNA-synt_1 365 cerskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskekryaswleniqdWciSRqrwWGhriplfvsketeev 442
                                     +rs+   i+ +t+qW+++ ++   ++++ + + +  +  + ++   ++ l  i  W +SR+   G+rip + +k   + 
  gene789|gene789|rna788|rna788 350 ISRSGGKCIVALTDQWYINYDDaeWKEKVKECI-DDLICTEDTKIVLKDALSWIGKWGFSRSFGLGTRIP-WDEKYLIDS 427
                                    57999999************9843444444444.555677778888899999999***************.544443333 PP

                    tRNA-synt_1 443 vvreelkelvagreeeeaekkalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypee...dteelkkffpadm 519
                                       +++ +++   + ++   k+   e kd++     + +  +dv    F    ++    ++ e     ++ ++ f+p d+
  gene789|gene789|rna788|rna788 428 LS-DSTVYMAI-CTFKHFLYKD--LEGKDEI-F--PSSKLSDDVWNYIFLNQRITEELKEFEEIlenCRKSFNYFYPVDL 500
                                    33.22222222.3333333333..3345555.2..333446788888898888888777776532226899********* PP

                    tRNA-synt_1 520 lleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgr 597
                                     ++G D ++  +   ++  +al++++ + ++++++g ++  +  KmSKs gN +  ++ ++k g+ + R+ l+   d+ +
  gene789|gene789|rna788|rna788 501 RVSGKDLLKNHLIFFLFNHVALFERKHWpRRIFTNGYLML-NSEKMSKSSGNFLTVDESLDKFGVSSTRMCLAvCGDTNE 579
                                    ***********************99966478999997765.458****************************97788888 PP

                    tRNA-synt_1 598 dinl 601
                                    d n+
  gene789|gene789|rna788|rna788 580 DANF 583
                                    8775 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   1.3e-13   4.6e-10       2      60 ..      30      88 ..      29     157 .. 0.86
   2 ?   -2.0   0.0      0.31   1.1e+03      88     129 ..     146     188 ..     113     193 .. 0.78
   3 !   39.9   0.1     6e-14   2.2e-10     285     368 ..     500     585 ..     462     593 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.3e-13
                                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTT CS
                   tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekeg 60
                                   +vt ++pY+ng+lHlGhl +v +aD f+ yk ++g++vlf  +    G+pi  +A+k +
  gene789|gene789|rna788|rna788 30 FVTFPMPYMNGRLHLGHLFSVSKADFFSYYKEMEGYNVLFPFAFHCTGMPISASAKKLE 88
                                   89*****************************************************9854 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.31
                                    EEETTSHH.HHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEE CS
                   tRNA-synt_1g  88 ygrttsee.hkelvqeifkklkekgliyekeieqlycpkderf 129
                                    +++t+ ++   ++v+  fk+l+e g+++ ++ + ++cp d+++
  gene789|gene789|rna788|rna788 146 FITTDINKyYDSFVRWQFKRLNELGYLSFGKRHSIFCPIDKQT 188
                                    666654431456888999*******************998876 PP

  == domain 3  score: 39.9 bits;  conditional E-value: 6e-14
                                    EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
                   tRNA-synt_1g 285 vhfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                                      + gkd +k H if+     +  ++ + p+++++++yl+++ +K+SkS g++ +++e l+++ +   R  la+ +++++
  gene789|gene789|rna788|rna788 500 LRVSGKDLLKNHLIFFLFNHVAlfERKHWPRRIFTNGYLMLNSEKMSKSSGNFLTVDESLDKFGVSSTRMCLAVCGDTNE 579
                                    4577***********9999888889999**************************************************** PP

                                    -EEE-H CS
                   tRNA-synt_1g 363 Dldfsw 368
                                    D++f++
  gene789|gene789|rna788|rna788 580 DANFME 585
                                    ***986 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.13   4.8e+02      21      50 ..      40      69 ..      25     159 .. 0.91
   2 !   32.2   0.1     2e-11     7e-08     207     282 ..     497     573 ..     488     591 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                   S--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                   tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvqf 50
                                      hlGh  s+   D +  + ++ gY+v f
  gene789|gene789|rna788|rna788 40 GRLHLGHLFSVSKADFFSYYKEMEGYNVLF 69
                                   568************************987 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 2e-11
                                    SEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                   tRNA-synt_1e 207 eidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                                     +d+ + G+DL+  h    l  + a+f+ k++ +  + ng+l+++ ekmsks +nf+t+ + l kf  +  R+ l+ 
  gene789|gene789|rna788|rna788 497 PVDLRVSGKDLLKNHLIFFLFNHVALFErKHWPRRIFTNGYLMLNSEKMSKSSGNFLTVDESLDKFGVSSTRMCLAV 573
                                    5799999*********99**********999**************************************99998864 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.6e-05      0.13      14      61 ..      21      68 ..      10      71 .. 0.90
   2 ?   -1.3   0.1      0.22   7.9e+02     128     181 ..     757     810 ..     732     819 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.6e-05
                                   ---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEE CS
                   tRNA-synt_1d 14 kksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvi 61
                                      +e+kk  v f  P +   +h GhL s    d+ s   e+ Gy+v+
  gene789|gene789|rna788|rna788 21 SDVSERKKFFVTFPMPYMNGRLHLGHLFSVSKADFFSYYKEMEGYNVL 68
                                   56789*****************************************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.22
                                    T-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC--CC.CCCCCHHHHHHHHHCTT CS
                   tRNA-synt_1d 128 gdedirklwkllvditrtelqklydrldvtlierGes.lykeslneivkelkkkg 181
                                    +  ++++    +vd +  e ++l++++   + ++ es ++ + ++ i + lk+ g
  gene789|gene789|rna788|rna788 757 KYSKWKRKCMSIVDQIACECKILNINISEEM-RKNESsFSSKVIDAIREVLKEFG 810
                                    3344777777799999998888888877666.56777477766666655555544 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.5   1.2e+04      53      81 ..     235     263 ..     230     269 .. 0.78
   2 ?   -1.4   0.0      0.78   2.8e+03      73      99 ..     467     493 ..     458     494 .. 0.80
   3 ?   -1.4   0.0      0.81   2.9e+03      36      77 ..     615     656 ..     602     668 .. 0.83
   4 ?   11.4   0.4     8e-05      0.29      22     109 ..     721     805 ..     718     806 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.5
                        DUF4709  53 lkqllqakyeeklkeealelytrlndklk 81 
                                    + ++++++y++k      ++++++n ++ 
  gene789|gene789|rna788|rna788 235 QSDFVEFEYNDKNYFVEKDIFENINAQVC 263
                                    56788999999988888899999998876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.78
                        DUF4709  73 ytrlndklkeleklykekvevvRksfk 99 
                                    y  ln++++e  k ++e  e+ Rksf+
  gene789|gene789|rna788|rna788 467 YIFLNQRITEELKEFEEILENCRKSFN 493
                                    556788888888888999999999986 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.81
                        DUF4709  36 tqkLvkevkslkrdfeflkqllqakyeeklkeealelytrln 77 
                                    + +L+++ ++++   +fl q++ ++  + ++ +  +ly+ + 
  gene789|gene789|rna788|rna788 615 ILSLIRKYDEMSFADKFLLQTISMNITHTIRAHEDMLYRDVV 656
                                    567888999999999999999999999999999999998875 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 8e-05
                        DUF4709  22 dvsEilelkeltevtqkLvkevkslkrdfeflkqllqakyeeklkeealelytrlndklkeleklykekvevvRksfkqQ 101
                                    d+sEi  + +l +++++L+  +++ kr+ ++ k l+ +ky  k k + +++ +++ ++ k l+ +  e++++   sf++ 
  gene789|gene789|rna788|rna788 721 DTSEIDGVSHLKSTLKRLM--IQKRKRKCDTVKILVGVKYS-KWKRKCMSIVDQIACECKILNINISEEMRKNESSFSSK 797
                                    899**************98..5667899999*********6.78************************************ PP

                        DUF4709 102 Ladaiaki 109
                                    + dai ++
  gene789|gene789|rna788|rna788 798 VIDAIREV 805
                                    *****875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (873 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.50
# Mc/sec: 5240.67
//
Query:       gene790|gene790|rna789|rna789  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-20   72.5  11.1      5e-20   71.8  11.1    1.4  1  zf-CCCH_3      Zinc-finger containing family
  ------ inclusion threshold ------
        2.4    8.8  21.6       0.51   10.9   4.7    3.9  4  zf-CCCH_2      RNA-binding, Nab2-type zinc finger
          6    7.4  11.0         13    6.3  10.8    1.6  1  Paramecium_SA  Paramecium surface antigen domain


Domain annotation for each model (and alignments):
>> zf-CCCH_3  Zinc-finger containing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8  11.1   8.4e-24     5e-20       6      90 ..       2      88 ..       1     104 [. 0.90

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 8.4e-24
                      zf-CCCH_3  6 ddcyffyystctkGdscpfrheeaalGsetvctlWqegrclrevckfrhme..idkkrkeipcywenqpaGcqklhcaflhe 85
                                   ddcyff ys c+  d+c++rh+e    + ++c+ W+     +e c +rh +  ++k+r+e  cywe +p+Gc+k +c + h+
  gene790|gene790|rna789|rna789  2 DDCYFFLYSSCKFKDRCTYRHNEGCRNNLVTCKNWESKIPCSEDCPYRHSKfhLKKNRREEMCYWEDKPGGCTKDRCEYRHT 83
                                   8*************************************9999*******753379**************************9 PP

                      zf-CCCH_3 86 kprav 90
                                    p + 
  gene790|gene790|rna789|rna789 84 DPTKD 88
                                   99864 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.7   8.5e-05      0.51       1      17 [.       3      22 ..       3      22 .. 0.95
   2 ?   -4.0   0.1         3   1.8e+04       2       4 ..      26      28 ..      24      29 .. 0.62
   3 ?    2.2   1.3     0.047   2.8e+02      11      17 ..      44      50 ..      32      50 .. 0.82
   4 ?    6.4   0.1    0.0022        13       8      17 ..      73      82 ..      65      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                      zf-CCCH_2  1 pCrffpn..C.tnpkCpFaH 17
                                   +C ff +  C ++++C+++H
  gene790|gene790|rna789|rna789  3 DCYFFLYssCkFKDRCTYRH 22
                                   6999**************** PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3
                      zf-CCCH_2  2 Crf 4 
                                   Cr+
  gene790|gene790|rna789|rna789 26 CRN 28
                                   554 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.047
                      zf-CCCH_2 11 pkCpFaH 17
                                   ++Cp++H
  gene790|gene790|rna789|rna789 44 EDCPYRH 50
                                   58***99 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.0022
                      zf-CCCH_2  8 CtnpkCpFaH 17
                                   Ct+++C ++H
  gene790|gene790|rna789|rna789 73 CTKDRCEYRH 82
                                   *********9 PP

>> Paramecium_SA  Paramecium surface antigen domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  10.8    0.0022        13      10      63 .]      14      79 ..       6      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0022
                  Paramecium_SA 10 ysstCtvnadgtgCvelkaaCssyttqeqCkknk.............tggkClwngsttaCvdktCa 63
                                   ++  Ct ++ ++gC ++  +C++  ++  C+ +               ++ C+w+++   C +  C+
  gene790|gene790|rna789|rna789 14 FKDRCTYRH-NEGCRNNLVTCKNWESKIPCSEDCpyrhskfhlkknrREEMCYWEDKPGGCTKDRCE 79
                                   5667***65.66***********99999998888888899****999999******99*****9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1261  (0.070333); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1454.33
//
Query:       gene79|gene79|rna79|rna79  [L=1231]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.80u 0.35s 00:00:01.14 Elapsed: 00:00:00.51
# Mc/sec: 7208.08
//
Query:       gene791|gene791|rna790|rna790  [L=688]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-17   63.0   0.0    7.7e-17   62.1   0.0    1.5  1  ABC_tran       ABC transporter
     0.0013   18.2  15.0     0.0013   18.2  15.0    2.3  3  ABC2_membrane  ABC-2 type transporter
     0.0025   17.3   0.1     0.0081   15.6   0.1    1.7  1  SMC_N          RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.018   15.3   0.1       0.09   13.0   0.0    2.2  2  SbcCD_C        Putative exonuclease SbcCD, C subunit
       0.14   12.4   0.1       0.14   12.4   0.1    4.1  4  Sigma_reg_N    Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   2.1e-20   7.7e-17       2     137 .]      38     191 ..      37     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 2.1e-20
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                    + ++  ++ g+++a++G +G+ K+t ++++ag       t Geil+d+k+ +     +++ ++++  qe    +eltv e
  gene791|gene791|rna790|rna790  38 NGLDAGFEYGKMYAFMGTSGSSKTTTMEAIAGVIPYgsrTRGEILIDSKERNG---DEWEGKSAYGRQEGYTIEELTVDE 114
                                    5678899**************************987889*****999777666...999**********99999999*99 PP

                                    H...........HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHH......TSSEEEEESTTT CS
                                    x...........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxx RF
                       ABC_tran  79 n...........esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallk......kpkllllDEpta 137
                                                es+e+i+ka++++ ++ l  ++v+++  ++LSgG+k+rv++a +++k      k k+ llDEpt+
  gene791|gene791|rna790|rna790 115 FiyystafslpnESKENIKKAMDEVLNSLLGLENVRNNRmENLSGGEKKRVVIATTFMKmlllegKLKVALLDEPTS 191
                                    9**********97777777777776666655555555445***************9986444444789*******96 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  15.0   3.7e-07    0.0013       5     172 ..     327     492 ..     324     510 .. 0.80
   2 ?   -2.6   0.4      0.81   2.9e+03     130     148 ..     584     602 ..     576     607 .. 0.50
   3 ?   -2.0   0.2      0.54   1.9e+03      26      39 ..     645     658 ..     623     669 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-07
                  ABC2_membrane   5 allkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr....pgllffsvlflafsaltsvapvfererg 80 
                                     l kr+++  wr+++l     +i++++la+ + +v   +   +    +      +l+ +++ l+ ++l+s+ +    + +
  gene791|gene791|rna790|rna790 327 SLAKRQLIIDWRNWNLP--HGFISTIVLAFSCILVEKFIIRPK----YnigeKSFLVYIMFKLFSVLLSSIPNRLLNGVR 400
                                    6899**********877..488888888888888888433344....144559999999999998888888666666666 PP

                  ABC2_membrane  81 vlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rfflflllllltalaasslgllisalapsfe 159
                                       +e + +ly +++  ++ +++e+++s+lq +if+ ++y++ gl  +   f++   +++++la s++ l+i +++  + 
  gene791|gene791|rna790|rna790 401 YTTKEVSRGLYDAATLWFSALVMEILLSILQFAIFFGTIYYF-GLVKKeEAFFLGSRFMMSVLANSTFRLIILSITDPLT 479
                                    66***********************************99998.9988864455566677777777888888889999999 PP

                  ABC2_membrane 160 dasqlaslvllpl 172
                                    +++ +++++++++
  gene791|gene791|rna790|rna790 480 TFGRIIGVFTSLI 492
                                    9999998888764 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.81
                  ABC2_membrane 130 fflflllllltalaasslg 148
                                    +f + ++ll++++a+s lg
  gene791|gene791|rna790|rna790 584 GFVLSAMLLVSLFALSLLG 602
                                    3443444444444444444 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.54
                  ABC2_membrane  26 liqplllalvfgtv 39 
                                    ++ +l+++l++ tv
  gene791|gene791|rna790|rna790 645 FLITLFTILIILTV 658
                                    33333333333322 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.3e-06    0.0081      28     201 ..      51     224 ..      35     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-06
                                    EEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE..SSSSSSC.EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.xxxxxxxx RF
                          SMC_N  28 aivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk..lkiekee.vsisrrvk 104
                                    a +G  GS K+  ++Ai  v+   s      ++ + li +  ++++ ++ e +  +  ++    ++ + +e ++ s+  +
  gene791|gene791|rna790|rna790  51 AFMGTSGSSKTTTMEAIAGVIPYGSR-----TRGEILIDS--KERNGDEWEGKSAYGRQEGYtiEELTVDEfIYYSTAFS 123
                                    56677777777777777666664322.....444455554..34444444444444333333122222233122222222 PP

                                    TTSEEEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHH..HHCCS--SEEEECTTTTTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtkkevsellesagi...skelLSgGektLvalaLlfA..iqkvkpaplyllDeidaaLDeknvkkv 179
                                      +es+   n k++  + +++ll  +++    +e+LSgGek+ v +a  f   +    +  + llDe  ++LD      v
  gene791|gene791|rna790|rna790 124 LPNESKE--NIKKAMDEVLNSLLGLENVrnnRMENLSGGEKKRVVIATTFMkmLLLEGKLKVALLDEPTSELDSGLAMDV 201
                                    2333333..33344444444444444441114569*******999999998766667788899***************** PP

                                    HHHHHHHCTT.SEEEEE-SSHHH CS
                                    xxxxxxxxxx.xxxxxxxxxxxx RF
                          SMC_N 180 aellkekskn.aQfivislreem 201
                                    a++lk    +   +i +++++  
  gene791|gene791|rna790|rna790 202 AKFLKDYARRsGTMILVTIHQPG 224
                                    *****766552566777776654 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.5e-05      0.09      26      89 ..     150     206 ..     134     207 .. 0.85
   2 ?   -1.8   0.0         1   3.7e+03      26      52 ..     571     597 ..     560     600 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     ++++++lSGGek     +++a  +  ++      e +l++ +LDE  s+lD+  +  + ++l+
  gene791|gene791|rna790|rna790 150 RNNRMENLSGGEK---KRVVIATTFMKMLLL----EGKLKVALLDEPTSELDSGLAMDVAKFLK 206
                                    568999*******...677788888888888....458**************998888888776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaa 52 
                                    ls+++++lS   + f+++ +l+ +l a
  gene791|gene791|rna790|rna790 571 LSDETRGLSQSKNGFVLSAMLLVSLFA 597
                                    789999*******99999999999876 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       1.6   5.7e+03      12      12 ..     375     375 ..     346     407 .. 0.49
   2 ?   -1.0   0.5      0.63   2.2e+03      13      38 ..     418     444 ..     414     454 .. 0.68
   3 ?    4.2   1.4     0.015        53      21      65 ..     494     539 ..     478     553 .. 0.71
   4 ?   12.4   0.1     4e-05      0.14       3      51 ..     635     683 ..     634     687 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.6
                    Sigma_reg_N  12 i 12 
                                    +
  gene791|gene791|rna790|rna790 375 F 375
                                    2 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.63
                    Sigma_reg_N  13 lrivlislivlllifvilvvtllyl.a 38 
                                    ++  +  +++ +l f+i++ t+ y+ +
  gene791|gene791|rna790|rna790 418 FSALVMEILLSILQFAIFFGTIYYFgL 444
                                    566666677788888888888888842 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.015
                    Sigma_reg_N  21 ivlllifvilvvtllyl....aekegnklrevlelaveitsPNvyvdsg 65 
                                    +++l+i++i+     +     +++ ++ l +++e++ ++  PNv +d++
  gene791|gene791|rna790|rna790 494 MITLVISIIS---SVKAkvskTSSAPTFLKKFFESLYAMLVPNVVIDGD 539
                                    2334444444...3333345688888999****************9986 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 4e-05
                    Sigma_reg_N   3 ilkkakrksilrivlislivlllifvilvvtllylaekegnklrevlel 51 
                                    +l+k+ +  ++ i+l++++++l++++ l++ +l++++  +++  ev+++
  gene791|gene791|rna790|rna790 635 SLTKGVWFKRFLITLFTILIILTVTFALYKKGLHFETTDSSDNGEVYRS 683
                                    7999*******************************77777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (688 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.72u 0.34s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 4240.56
//
Query:       gene792|gene792|rna791|rna791  [L=527]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3507.39
//
Query:       gene793|gene793|rna792|rna792  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.7e-117  390.5   0.0   7.9e-117  390.3   0.0    1.0  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.3   0.0  4.4e-121  7.9e-117       2     349 ..      15     371 ..      11     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 390.3 bits;  conditional E-value: 4.4e-121
                                    TEEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE CS
                            TGT   2 gaRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltd 81 
                                    +aR++klel++  +e P+fmpvgt+g++kg+   +l    + ++il+ntyhl+        a  +g++kf+++ + +ltd
  gene793|gene793|rna792|rna792  15 NARVSKLELNDVCLELPIFMPVGTYGAMKGIRVSDL----QEKMILANTYHLR--------ALGKGIKKFMKYRGGMLTD 82 
                                    59*********99***********************....4789*********........44679************** PP

                                    -SHHHHHHH.E.EEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHH CS
                            TGT  82 sggfqvfsl.k.kiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcl 159
                                    sggfq+ sl +  +teegv+f     G   l+tpe+s++iq klg+Di+m+lddvv++ ++k+++e +++r++rw+drc+
  gene793|gene793|rna792|rna792  83 SGGFQIGSLpDvVVTEEGVKF-----GA-TLFTPEDSMDIQMKLGADIVMQLDDVVNPCDTKEKIEIAMRRSIRWMDRCI 156
                                    *********64677*******.....88.99************************************************* PP

                                    HHH............................SEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHH CS
                            TGT 160 eah............................qalfgivqGglyedlreesaeelakrdfdgyaigGlsvgeekeellevv 211
                                    +a                             q+lf+i+qGgl+e+lr+es+ e+ kr  +g+aigGls+geek+e+ +vv
  gene793|gene793|rna792|rna792 157 NAInshgvnghnkkvkremnvpqikldekstQILFPIIQGGLDEELRAESIAEVLKRSPKGLAIGGLSGGEEKSEFARVV 236
                                    87778899999*******************999*********************************************** PP

                                    HHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHH CS
                            TGT 212 eavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCk 291
                                    ++++++lpe+ prylmGvg+Ped++++ alG Dm dcvyptrtar+g+al ++g++  + +k ++d + +de+C+Cy+C+
  gene793|gene793|rna792|rna792 237 HFCIQNLPENIPRYLMGVGYPEDIVVCAALGSDMSDCVYPTRTARFGKALSDTGDILFT-SKLKNDKRRIDESCDCYVCS 315
                                    ******************************************************99886.89*****************9 PP

                                    H-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                            TGT 292 nytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                    +y+ra + +++ t +  +++Ll++HNlhy+++l++riRe+I e++++ef+++f+r+++
  gene793|gene793|rna792|rna792 316 KYSRAFIFSIKGTTN--FCMLLSVHNLHYMRNLTRRIRESIMEDKYPEFIKTFMRRRF 371
                                    9**********9999..*************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2453.98
//
Query:       gene794|gene794|rna793|rna793  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-21   77.5   0.0    2.5e-21   76.4   0.0    1.5  1  Rotamase    PPIC-type PPIASE domain
    3.7e-15   56.5   0.0    6.6e-15   55.7   0.0    1.4  1  Rotamase_3  PPIC-type PPIASE domain
    1.9e-06   27.8   0.5      3e-06   27.2   0.5    1.3  1  WW          WW domain
    4.7e-05   24.2   0.0    7.2e-05   23.6   0.0    1.3  1  Rotamase_2  PPIC-type PPIASE domain


Domain annotation for each model (and alignments):
>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   5.5e-25   2.5e-21       1      95 [.     112     213 ..     112     214 .] 0.91

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 5.5e-25
                                    EEEESSCCS..E----HHHHHHHHHHHHCCTCCCH......HHHHHHHCCC-.-CHHHCCTTEEECEETTTS-CCCHHHH CS
                       Rotamase   1 HILlkvkek..asekeraeakakaeeileqlksge......dtFeelArkySddknsakngGdlgwvekgqlppefekaa 72 
                                    HIL+k++++  + + + +ea  ++++i+e+lk++       d F+e+A k+S +++sak+gGdlg+v  +++ +efe+ a
  gene794|gene794|rna793|rna793 112 HILIKHEKSrkPVDVSIDEALSRIKTIYEDLKAKVndknfkDLFKEAAFKHS-QCSSAKRGGDLGFVCGNEMMKEFERPA 190
                                    ********98877788888888888888888877666668888*********.*************************** PP

                                    CCS-CT-B-S-EEETTEEEEEEE CS
                       Rotamase  73 fslkkGeisepvetkfGfhiikl 95 
                                    fsl+kGe+sepv t  Gfhii++
  gene794|gene794|rna793|rna793 191 FSLRKGEMSEPVSTPSGFHIIYR 213
                                    *********************86 PP

>> Rotamase_3  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   1.5e-18   6.6e-15       9     110 ..     101     211 ..      92     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1.5e-18
                     Rotamase_3   9 kksakdsvkvshIlistkg...kesrseeeakakadsllaalk...egad....FaalAkeySdDpaskenGGelgwftk 78 
                                    +k+  +  ++ hIli+ ++    ++ s +ea +++  +++ lk   + ++    F+++A + S+  +s+++GG+lg++  
  gene794|gene794|rna793|rna793 101 EKKPMEGFRLYHILIKHEKsrkPVDVSIDEALSRIKTIYEDLKakvNDKNfkdlFKEAAFKHSQ-CSSAKRGGDLGFVCG 179
                                    34455689999*****988998445555555555555555555322233312236777778888.678************ PP

                     Rotamase_3  79 gqmvkeFedavfslkkgeiskvvktdfGyHii 110
                                    ++m+keFe  +fsl kge+s++v t+ G+Hii
  gene794|gene794|rna793|rna793 180 NEMMKEFERPAFSLRKGEMSEPVSTPSGFHII 211
                                    *******************************9 PP

>> WW  WW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.5   6.8e-10     3e-06       2      25 ..      75      98 ..      74     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.8e-10
                                   -TTEEEEE-TTTT-EEEEETTT-- CS
                             WW  2 PpGWeeqwdpdsGrvYYyNheTge 25
                                   P+ W++ +d+++G++Y+yN+eT+e
  gene794|gene794|rna793|rna793 75 PEMWIKLKDKETGQPYFYNTETRE 98
                                   999*******************99 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.6e-08   7.2e-05      37     104 ..     136     212 ..     116     214 .] 0.68

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-08
                     Rotamase_2  37 eaalalakag.aekdfaalakgnskk.........aadlgifesasnlpeelakaafalkpgevsgpvetdngyyivk 104
                                    +++ + +ka+ ++k+f++l k++++k          +dlg++  ++ + +e++  af+l +ge s+pv t+ g++i++
  gene794|gene794|rna793|rna793 136 KTIYEDLKAKvNDKNFKDLFKEAAFKhsqcssakrGGDLGFVCGNE-MMKEFERPAFSLRKGEMSEPVSTPSGFHIIY 212
                                    4555666666455888888888887733333332233333444444.556**************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1559.26
//
Query:       gene795|gene795|rna794|rna794  [L=696]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-98  326.7   0.1    2.6e-97  324.3   0.0    2.0  2  MCM             MCM P-loop domain
    6.2e-34  116.6   1.6    1.1e-33  115.7   1.6    1.4  1  MCM_OB          MCM OB domain
    8.1e-29   99.9   2.4    1.7e-28   98.9   2.4    1.6  1  MCM_lid         MCM AAA-lid domain
    3.7e-09   37.1   2.3    4.9e-09   36.7   0.7    2.0  2  MCM_N           MCM N-terminal domain
    1.3e-07   31.2   0.0    3.7e-05   23.2   0.0    2.5  2  Mg_chelatase    Magnesium chelatase, subunit ChlI
      2e-05   24.6   0.0    0.00035   20.6   0.0    2.6  2  AAA_5           AAA domain (dynein-related subfamily)
    0.00094   19.1   0.0     0.0039   17.0   0.0    2.1  1  AAA_3           ATPase family associated with various cellula
     0.0033   18.0   0.6       0.01   16.4   0.2    2.1  2  Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.3   0.0  1.2e-100   2.6e-97       2     224 .]     269     488 ..     268     488 .. 0.97
   2 ?   -0.3   0.1       0.2   4.6e+02      13      58 ..     584     628 ..     575     637 .. 0.77

  Alignments for each domain:
  == domain 1  score: 324.3 bits;  conditional E-value: 1.2e-100
                                    HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                            MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla 81 
                                    +e++++l+k+ +i+ek++ksiaps+yghedvkka++++lfgg+++  edk++lrgdinvll+gdpg+aKsqlLk++e ++
  gene795|gene795|rna794|rna794 269 EESFRSLSKT-NIYEKISKSIAPSVYGHEDVKKALACMLFGGTRRVFEDKVTLRGDINVLLLGDPGMAKSQLLKFMELVS 347
                                    5677888877.8******************************************************************** PP

                                    SSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEE CS
                            MCM  82 pravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatL 161
                                    p +vytsgkgssaagLta+v rd+ +gef+le+Galvlad+G+cciDefdkm+e+dr+a+hEamEqqtisiaKaGi+++L
  gene795|gene795|rna794|rna794 348 PVGVYTSGKGSSAAGLTASVIRDS-SGEFYLEGGALVLADNGICCIDEFDKMNEHDRVAIHEAMEQQTISIAKAGITTML 426
                                    **********************98.689**************************************************** PP

                                    E--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                            MCM 162 nartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                    n+rts+laAanp++gryd+ k+  eni++ a++LsrFD if+l+Dk    +D+ la+h++s+h
  gene795|gene795|rna794|rna794 427 NTRTSILAAANPVFGRYDDYKTPDENIEFGATILSRFDCIFILKDKFG-PNDAVLARHVLSVH 488
                                    **********************************************98.579********987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.2
                                    THHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS- CS
                            MCM  13 diieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdi 58 
                                    ++ e+l+k+   +i+ +++v +ai l  +++++  + +++ l g i
  gene795|gene795|rna794|rna794 584 RVGESLAKMELSQIVTEKHVEEAIRLFNVSTMNAVS-QGHMLEGMI 628
                                    566789999999***************999999655.556666665 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   1.6     5e-37   1.1e-33       2     124 ..     116     237 ..     115     239 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 5e-37
                                    XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES----SB-..TTT-HHH-EEE-GGGSEEEEEEEEE CS
                         MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktveveleePrkCeekeCeskdpfkletekskfvdfqklk 81 
                                    +R++++++ +k+vk++Giv++as+v +k k++++ c++c +++ev    Pr C++ eC+ +dp+ + +eks+++d+q +k
  gene795|gene795|rna794|rna794 116 IREINASKTNKIVKIQGIVVSASSVITKPKTLFLVCRNCLNSKEVVDMIPRVCDKAECP-TDPYIVIPEKSRVIDVQYVK 194
                                    8***************************************999865555**********.9******************* PP

                                    EE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                         MCM_OB  82 lQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                    +QE  e++p+Ge+Pr+++++le+ +v+++ PG++v vtGiy++
  gene795|gene795|rna794|rna794 195 IQEFFEDIPVGETPRHFSLVLEKGMVNRLIPGSKVVVTGIYCM 237
                                    *****************************************97 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.9   2.4   7.5e-32   1.7e-28       2      86 ..     524     613 ..     523     614 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.9 bits;  conditional E-value: 7.5e-32
                                    HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHH...TSS..TSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHH CS
                        MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkee...eds..krksipitvRqLesliRLseAlAklrlsevvteedv 76 
                                    ++++Y++ya++k++P+ls++a+ +ls++Yv++Rke    e+s  kr++ipitvRqLe++iR+ e+lAk++ls++vte++v
  gene795|gene795|rna794|rna794 524 VIKRYVQYAKSKVFPTLSDAASRQLSRYYVNTRKEVrefEHStlKRNAIPITVRQLEAIIRVGESLAKMELSQIVTEKHV 603
                                    689*******************************99988434579*********************************** PP

                                    HHHHHHHHHH CS
                        MCM_lid  77 eeairllkes 86 
                                    eeairl++ s
  gene795|gene795|rna794|rna794 604 EEAIRLFNVS 613
                                    *******987 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.7   2.2e-12   4.9e-09       2      72 ..      27      91 ..      26      95 .. 0.95
   2 ?   -2.5   0.0       3.6     8e+03      18      37 ..     546     565 ..     527     575 .. 0.52

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.2e-12
                          MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleeal 72
                                   ++F +F+e+f      + + k Y   l +++++++ +L+v+l++++++++ L++++++ p++ ++++eea+
  gene795|gene795|rna794|rna794 27 HEFIRFIEQF------KTTHKEYSHVLSSNINQNNFSLTVKLEHIYQYSDLLSQELSRRPERAIEWFEEAI 91
                                   78********......45679************************************************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                          MCM_N  18 edgekkYrdqlqemaerekt 37 
                                    ++ +++Y++  +e++e e++
  gene795|gene795|rna794|rna794 546 RQLSRYYVNTRKEVREFEHS 565
                                    22224444444444444444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0046        10      16      45 ..     317     346 ..     307     354 .. 0.85
   2 !   23.2   0.0   1.7e-08   3.7e-05      94     159 ..     374     439 ..     358     458 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0046
                   Mg_chelatase  16 eiaaaGgHnlllvGppGsGKtmlakrlpsl 45 
                                    +++  G  n+ll+G pG  K+ l k ++ +
  gene795|gene795|rna794|rna794 317 KVTLRGDINVLLLGDPGMAKSQLLKFMELV 346
                                    57888999**************99877655 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 1.7e-08
                   Mg_chelatase  94 gskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                        + G++ la nG+  +DE+ +++++   ++ e +e+++++i++a  ++   +r+ ++aa+Np 
  gene795|gene795|rna794|rna794 374 EFYLEGGALVLADNGICCIDEFDKMNEHDRVAIHEAMEQQTISIAKAGITTMLNTRTSILAAANPV 439
                                    4467889**********************************************************6 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.25   5.6e+02      61     106 ..      23      68 ..      13     105 .. 0.74
   2 !   20.6   0.0   1.5e-07   0.00035       1     123 [.     325     439 ..     325     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.25
                                    ----G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE-- CS
                          AAA_5  61 raaregeilvlDEveraesevlnsLlslleerrllleeggelvkak 106
                                    +a+++  i +++ +++ ++e   +L s ++++ ++l    e ++  
  gene795|gene795|rna794|rna794  23 EAVKHEFIRFIEQFKTTHKEYSHVLSSNINQNNFSLTVKLEHIYQY 68 
                                    5677889999*********************999987666666554 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.5e-07
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGGG--H CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEveraes 79 
                                    +vlL+G+pG +Ks+l + +   l ++v ++   ++ +++ l+ ++  + +g+  l+ ++lv       i+++DE+++++ 
  gene795|gene795|rna794|rna794 325 NVLLLGDPGMAKSQLLKFME--LVSPVGVYTSGKGSSAAGLTASVIRDsSGEFYLEGGALV--LADNGICCIDEFDKMNE 400
                                    69************998765..4688999999999*********99778999999999999..77889************ PP

                                    HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS- CS
                          AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpl 123
                                    +   + +  +e++++++++ g  +  +       ++++a+anp+
  gene795|gene795|rna794|rna794 401 HDRVAIHEAMEQQTISIAKAGITTMLNTR-----TSILAAANPV 439
                                    ****************9988877766664.....8999999986 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.8e-06    0.0039      42     113 ..     363     439 ..     325     454 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.8e-06
                          AAA_3  42 lGtevfeekekefefkkGpvf...anllladeinrappktqsalleameerqvtve..gethklpepflvlatqnPi 113
                                    l ++v+++++ ef ++ G+++   + +   de ++ + + + a+ eame+++++++  g t+ l++   +la+ nP+
  gene795|gene795|rna794|rna794 363 LTASVIRDSSGEFYLEGGALVladNGICCIDEFDKMNEHDRVAIHEAMEQQTISIAkaGITTMLNTRTSILAAANPV 439
                                    456788999999****99976332358999**********************99872256899*************8 PP

>> Mg_chelatase_C  Magnesium chelatase, subunit ChlI C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   4.6e-06      0.01      30      91 ..     544     608 ..     524     609 .. 0.79
   2 ?   -3.8   0.0         8   1.8e+04      45      66 ..     671     692 ..     669     692 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.6e-06
                 Mg_chelatase_C  30 sgeelre.vceldeeaeelleeaierlg..lsaRaydrilkvArTiADLegseeieeehlaeAlq 91 
                                     +++l + +++ ++e++e+ ++ ++r    +++R+++ i++v  ++A +e s+ ++e+h++eA++
  gene795|gene795|rna794|rna794 544 ASRQLSRyYVNTRKEVREFEHSTLKRNAipITVRQLEAIIRVGESLAKMELSQIVTEKHVEEAIR 608
                                    44455441588899999999999887652279*******************************97 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8
                 Mg_chelatase_C  45 eelleeaierlglsaRaydril 66 
                                    ++ ++ ++++ +l aR + ril
  gene795|gene795|rna794|rna794 671 RKAIDYMCKQEKLIARDMGRIL 692
                                    5667778899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 4293.95
//
Query:       gene796|gene796|rna795|rna795  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-14   51.9   0.5    1.9e-13   49.9   0.3    2.3  2  TFA2_Winged_2  TFA2 Winged helix domain 2
    4.8e-14   52.4   1.4    4.8e-14   52.4   1.4    2.5  3  TFIIE_beta     TFIIE beta subunit core domain
  ------ inclusion threshold ------
      0.074   13.3   0.0       0.15   12.3   0.0    1.5  1  DUF4777        Domain of unknown function (DUF4777)
       0.11   12.9   0.0       0.24   11.8   0.0    1.5  1  HARE-HTH       HB1, ASXL, restriction endonuclease HTH domain


Domain annotation for each model (and alignments):
>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         1   4.5e+03       7      20 ..      77      88 ..      74      94 .. 0.61
   2 !   49.9   0.3   4.2e-17   1.9e-13       6      61 .]     106     190 ..     101     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1
                  TFA2_Winged_2  7 lalLkkrpkaeGik 20
                                    +lLk+++    + 
  gene796|gene796|rna795|rna795 77 ISLLKQHD--RPVT 88
                                   67999995..4444 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 4.2e-17
                  TFA2_Winged_2   6 LlalLkkrp...............................kaeGikvkdLkdswpdveealeeLeaegeilvlrtkkdg. 53 
                                    Ll+ +kk+p                               ++eG+++++L+ds+++  +++eeL++  ei+vl    d  
  gene796|gene796|rna795|rna795 106 LLQSIKKNPrivathstlmfkplysirgvedlrkvmkeinGEEGLEMSKLMDSPVNITPFVEELKRNDEIIVL---SDId 182
                                    55556666666666666666666655555555555555549********************************...7888 PP

                  TFA2_Winged_2  54 qpkiVfwN 61 
                                    +++iVfwN
  gene796|gene796|rna795|rna795 183 GSEIVFWN 190
                                    *******9 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   1.4   1.1e-17   4.8e-14       2      68 .]      70     131 ..      69     131 .. 0.95
   2 ?   -2.2   0.0       1.1   5.1e+03      39      53 ..     163     177 ..     141     184 .. 0.61
   3 ?    0.4   0.2      0.18   8.1e+02      18      55 ..     210     245 ..     201     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.1e-17
                     TFIIE_beta   2 ftqLakiveylKkkdgplsleeIlsylslqldlsdknwllleaLknnpkieyDpkkgkfsfkPlyni 68 
                                    +t+++ +++ lK++d+p+++eeI +++ +  dl ++n  ll+  k+np+i   +   +++fkPly i
  gene796|gene796|rna795|rna795  70 NTYIHAVISLLKQHDRPVTFEEIKDKTRI--DL-HNNYMLLQSIKKNPRIVATH--STLMFKPLYSI 131
                                    799**************************..99.88****************76..7********98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                     TFIIE_beta  39 wllleaLknnpkiey 53 
                                       +e Lk n+ i +
  gene796|gene796|rna795|rna795 163 TPFVEELKRNDEIIV 177
                                    345666777776655 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.18
                     TFIIE_beta  18 plsleeIlsylslqldlsdknwllleaLknnpkiey..Dp 55 
                                      +++++ ++l++   l++   + +e  k+ p i++  D 
  gene796|gene796|rna795|rna795 210 ISTYHDLIRELNT-AGLKT---EKVENIKKRPTIKIkkDR 245
                                    5688999999996.33333...567888888866554465 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.5e-05      0.15       3      27 ..      70      94 ..      68     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                        DUF4777  3 kqngalvlealkvlnrPaTldEive 27
                                   + +++ v+++lk  +rP+T++Ei +
  gene796|gene796|rna795|rna795 70 NTYIHAVISLLKQHDRPVTFEEIKD 94
                                   6799*******************76 PP

>> HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.4e-05      0.24       2      26 ..      71      95 ..      70      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                                   -HHHHHHHHHHHH-S-EEHHHHHHH CS
                       HARE-HTH  2 tlkeaAkqVLeeegrpltvkeIwek 26
                                   t+++a +  L++++rp t++eI +k
  gene796|gene796|rna795|rna795 71 TYIHAVISLLKQHDRPVTFEEIKDK 95
                                   899*******************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1762.23
//
Query:       gene797|gene797|rna796|rna796  [L=226]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-09   37.6   0.0    2.9e-09   36.8   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0013   19.4   0.0     0.0026   18.4   0.0    1.6  1  RPA_C            Replication protein A C terminal


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   3.3e-13   2.9e-09       1      73 [.      53     124 ..      53     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 3.3e-13
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                    V + G+v+s   r ++  + ++l+Dgtg++ +++++  +  +++ + l+e  + +v G +++++g+  +++v+ +
  gene797|gene797|rna796|rna796  53 VQIIGWVVSS--RISATGSMFVLEDGTGSVDCTFWPsnSYEEEQCKILEEKNLFKVNGSLRTFNGK-RSVSVSHL 124
                                    78********..999999******************99999999999****************999.88888765 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.9e-07    0.0026      46      99 ..     162     216 ..     137     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.9e-07
                                    XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHS..TSXHHHHHHHHHHHHHTTSEEE CS
                          RPA_C  46 gltalaqqvlnlikqspeseeGvhvdeiaqkl..rlsvndvkqavdeLsneGiiYs 99 
                                     l + ++ +l+  ++  ++e+G+h++++ + l  + ++n++++ +d L+ + ++Ys
  gene797|gene797|rna796|rna796 162 RLDRIQEDILECYRK-NQDENGLHINVVIKMLssKYPENEIRENIDVLLRDCHLYS 216
                                    477889999999999.899**********99999*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1477.21
//
Query:       gene798|gene798|rna797|rna797  [L=731]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.091   13.1   0.0        2.8    8.3   0.0    3.3  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
       0.22   11.2   1.5        1.7    8.4   0.3    2.3  2  BRCA2        BRCA2 repeat


Domain annotation for each model (and alignments):
>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00032       2.8      38      87 ..     192     239 ..     167     244 .. 0.80
   2 ?   -0.9   0.0      0.23   2.1e+03      49      85 ..     293     329 ..     245     336 .. 0.61
   3 ?   -2.5   0.0      0.71   6.4e+03      40      80 ..     509     548 ..     500     566 .. 0.66
   4 ?   -1.3   0.0      0.31   2.8e+03      38      66 ..     547     575 ..     516     589 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00032
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtcl 87 
                                    +  ++s++ +p   +  ++ ++g++++++  + k++ s++ ++   v  l
  gene798|gene798|rna797|rna797 192 EAPITSIEQSPVVDVVGIGLENGSIHIFNLRTDKILFSFKLQDA--VGEL 239
                                    56788888889999999**********************99876..5555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.23
                    ANAPC4_WD40  49 dgklLavaysdg.evrlldaesgkvvhslsvksekavt 85 
                                    d++ L+v+++d+ +v  ++ +s ++v+  ++ +++ + 
  gene798|gene798|rna797|rna797 293 DNRSLVVSTKDSlTVYEVENYSLETVKRRRTYNDE-II 329
                                    55666676666655555555666666666666663.55 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.71
                    ANAPC4_WD40  40 evrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvks 80 
                                    e+ + + + d k +a+ ++  +v l+d+ +++++  l  ++
  gene798|gene798|rna797|rna797 509 EIVDYCLSSDSKWIAILCNR-NVFLYDILTTTLLDMLALDN 548
                                    56666667777777777754.46666666666665555444 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.31
                    ANAPC4_WD40  38 dsevrsLaWkpdgklLavaysdgevrlld 66 
                                    d+e + ++++p+  +L v+   + + l++
  gene798|gene798|rna797|rna797 547 DNEAKFIRFSPNLDFLLVVSRGNDLILFS 575
                                    55566666666666666666666555555 PP

>> BRCA2  BRCA2 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.3   0.00019       1.7      11      21 ..     102     112 ..     102     114 .. 0.93
   2 ?    1.4   0.1     0.029   2.6e+02      23      31 ..     163     171 ..     163     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00019
                          BRCA2  11 sGKkIrVSkes 21 
                                    s+K+IrVS+es
  gene798|gene798|rna797|rna797 102 SNKRIRVSEES 112
                                    89********9 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.029
                          BRCA2  23 qKAkklFse 31 
                                    +K++k+F+e
  gene798|gene798|rna797|rna797 163 NKVVKIFKE 171
                                    7*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 4711.13
//
Query:       gene799|gene799|rna798|rna798  [L=553]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.9e-06   25.3   0.0    1.6e-05   24.7   0.0    1.2  1  Reprolysin_4   Metallo-peptidase family M12B Reprolysin-like
    5.1e-05   23.5   0.0     0.0001   22.5   0.0    1.5  1  Reprolysin_5   Metallo-peptidase family M12
    0.00017   22.1   0.0    0.00029   21.3   0.0    1.4  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
    0.00045   20.2   0.0    0.00072   19.5   0.0    1.4  1  Reprolysin_2   Metallo-peptidase family M12B Reprolysin-like
    0.00047   20.1   0.0    0.00092   19.2   0.0    1.5  1  Reprolysin     Reprolysin (M12B) family zinc metalloprotease
     0.0041   17.0   0.0     0.0057   16.5   0.0    1.3  1  Peptidase_M10  Matrixin
  ------ inclusion threshold ------
      0.055   13.4   0.0       0.11   12.5   0.0    1.4  1  Peptidase_M78  IrrE N-terminal-like domain


Domain annotation for each model (and alignments):
>> Reprolysin_4  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   6.2e-09   1.6e-05      96     160 ..     261     326 ..     245     367 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 6.2e-09
                   Reprolysin_4  96 allrdtrasqqnvgvawvgalclsarqnkkasgvaas.rdey....difAHEiGHtfGaaHdlsdegegl 160
                                     ll++t +s + +g+ +vg++++s   + + ++++ s  d y    +++AHEi H +Ga+H+l++++   
  gene799|gene799|rna798|rna798 261 ILLLQT-SSIKVNGLTFVGGIGSS---TRRFGVIRISeSDSYfykgKVLAHEIAHGLGAEHELDEKCLMR 326
                                    566666.677779*********44...445567776654555578899****************999754 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     4e-08    0.0001       3     172 ..     142     333 ..     140     364 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4e-08
                   Reprolysin_5   3 rtvallvaaDcsfvaafgg.daaaqanivnlvnrasnvyeres....nislglanv.tildeedpstase.......... 66 
                                    r++++++  D+  v++  g d  ++   ++++++a nv+e +     +i+l+l+++  ++d++  +++ +          
  gene799|gene799|rna798|rna798 142 RVIKVFLINDYDRVQEI-GpD--INLDTMEIFKNARNVFEGNKwnihGIKLSLNGIlNVVDKPLVQEPFSrlhnlgmtet 218
                                    66677777777777777.437..778888888888888887777777777888854145555555444446777787777 PP

                   Reprolysin_5  67 ......asstgdaselLnefq.......sassalrgqqnddlailflmtnfsggvGlAwlgqlcnsgsagsvstrveksn 133
                                          + ++ d+  +L++f+        + +a  + +  +l  l+ +++ + + Gl  +g++++s+  ++v    e   
  gene799|gene799|rna798|rna798 219 rdfnpeYIEKADSIRVLSAFSrilgsarTDTDAGSFLETSNLILLLQTSSIKVN-GLTFVGGIGSSTRRFGVIRISE--- 294
                                    777777777777788888888877776555555555444444455555555556.********99999665553322... PP

                   Reprolysin_5 134 svvvstatevqvvaHElGHnfGavHDcdsss..esqsCsls 172
                                        s  +  +v+aHE+ H +Ga+H  d ++   + +++l+
  gene799|gene799|rna798|rna798 295 --SDSYFYKGKVLAHEIAHGLGAEHELDEKClmREEESPLE 333
                                    ..25678999***************9998878755555554 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.1e-07   0.00029      63     124 .]     248     318 ..     202     318 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                   Reprolysin_3  63 gyDlvhlftarde........sgvgGlAyvgsvcnsskkagvnsgssvlgk.vgadtvaHEiGHnfganHt 124
                                    + D + ++ +++          +v Gl +vg++ +s++++gv++ s+      + +++aHEi H +ga+H+
  gene799|gene799|rna798|rna798 248 DTDAGSFLETSNLilllqtssIKVNGLTFVGGIGSSTRRFGVIRISESDSYfYKGKVLAHEIAHGLGAEHE 318
                                    4444444545444555555546999**************9998877433331445***************5 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.8e-07   0.00072      78     156 ..     262     330 ..     166     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.8e-07
                   Reprolysin_2  78 vllgtfsggvlGLayvgqicqkeassrktntglsttansgsaveetkeidvvaHEvGHaFGatHdndgs...sasegvee 154
                                    +ll+t s  v GL +vg+i + +  +     g+  + +s+s  +   + +v+aHE+ H  Ga H+ d +   +     ee
  gene799|gene799|rna798|rna798 262 LLLQTSSIKVNGLTFVGGIGSSTRRF-----GVIRISESDSYFY---KGKVLAHEIAHGLGAEHELDEKclmR-----EE 328
                                    44777799999*********888888.....7776777777776...899**************999444331.....22 PP

                   Reprolysin_2 155 na 156
                                    ++
  gene799|gene799|rna798|rna798 329 ES 330
                                    22 PP

>> Reprolysin  Reprolysin (M12B) family zinc metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.6e-07   0.00092      91     160 ..     261     330 ..     228     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.6e-07
                                    EEEESS--STTSSEEE-TT-TTSTSTSEEEEE--S.SSHHHHHHHHHHHHHHHCT---GHHTTS--STTS- CS
                     Reprolysin  91 qLlsgkefekktvGaayvgglCskeksggvaedkk.knlealavilaqeLghnlGlthdeekeCkceekgv 160
                                    +Ll +++   k  G+++vgg+ s+++  gv+  ++ ++      +la+e++h lG +h+ +++C  +e+++
  gene799|gene799|rna798|rna798 261 ILLLQTSSI-KVNGLTFVGGIGSSTRRFGVIRISEsDSYFYKGKVLAHEIAHGLGAEHELDEKCLMREEES 330
                                    344444444.489*****************99998577778899***************998888764444 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.2e-06    0.0057     104     151 ..     296     346 ..     124     351 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                                    SSSEEHHHHHHHHHHHHTTBESXSSTTSTTSSSCT...XTTTXSSXHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                  Peptidase_M10 104 eqgvslflVaaHEiGHalGLeHssdkdalmyplyk...eekkvrlskdDvk 151
                                    ++ +    V aHEi+H lG eH  d++ lm    +   +e++  ls+  +k
  gene799|gene799|rna798|rna798 296 DSYFYKGKVLAHEIAHGLGAEHELDEKCLMREEESpleKEENAVLSHKTIK 346
                                    45555668**********************876555544455556655555 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.2e-05      0.11      26      59 ..     282     318 ..     260     344 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                  Peptidase_M78  26 s...etkvivlnsnhsptrqrftlaHElgHlllhher 59 
                                    s   +  vi +++++s + +  +laHE++H l  +  
  gene799|gene799|rna798|rna798 282 SstrRFGVIRISESDSYFYKGKVLAHEIAHGLGAEHE 318
                                    1444799***********************9965544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 3053.30
//
Query:       gene800|gene800|rna799|rna799  [L=223]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-06   26.2   0.0    0.00049   20.4   0.0    2.2  2  DUF1040   Protein of unknown function (DUF1040)


Domain annotation for each model (and alignments):
>> DUF1040  Protein of unknown function (DUF1040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.7e-08   0.00049       4      72 ..      72     141 ..      69     146 .. 0.91
   2 !    3.7   0.0    0.0044        80      26      67 ..     181     222 ..     167     223 .] 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-08
                        DUF1040   4 hrinellellqpeWkkekdlnllqllqklaeeagf.egeleeltddvliyhlkmresdkeemiPGlkkdy 72 
                                    +r ++ll++l+++++k+k ++l  l  kl ee++f + +l  l+ d  iy l +++ ++  ++ G+k +y
  gene800|gene800|rna799|rna799  72 KRHEKLLNFLHKVYTKQKSIDLESLCVKLNEEVTFiHIDLRILSSDGNIYSLAVKGVNSVLEVLGVKMNY 141
                                    7999*****************************983569******************9999999999877 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0044
                        DUF1040  26 lqllqklaeeagfegeleeltddvliyhlkmresdkeemiPG 67 
                                    + +l+k+ +e+g+e+ le++   +  + +++ e+++ee+  G
  gene800|gene800|rna799|rna799 181 IIFLEKVGKECGIEQVLEAVDRSTGNFAMRIPEIESEEECGG 222
                                    5589**************998888888888877777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1409.78
//
Query:       gene8|gene8|rna8|rna8  [L=239]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-34  116.3   4.8    1.5e-33  115.7   4.8    1.2  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    0.00015   21.7   0.1    0.00015   21.7   0.1    2.1  3  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain
  ------ inclusion threshold ------
       0.16   11.9   0.7        0.4   10.6   0.7    1.6  1  LBP_C           Lacto-N-biose phosphorylase C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   4.8   2.5e-37   1.5e-33       2     123 ..      84     212 ..      83     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 2.5e-37
                            SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B...SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT----STTHH CS
         Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvak..egkkvtvklpSgevrkvssecrAtiGvvsngehkekklgkAgrk 87 
                            +Gn++++kn+peG+ v ++e+  g+gg +  + G+y+ vv++  e++++++k+pSg++ +v+secr+++Gvv++g+ ++k+l+kA+ +
  gene8|gene8|rna8|rna8  84 IGNITKIKNVPEGMAVNSVEVVYGDGGCISMTNGSYSLVVNHrkETNETVIKIPSGKKITVNSECRCIVGVVAGGGIHDKPLLKASVA 171
                            7****************************************975599***************************************99 PP

                            HHT.....TBS----SSSS-TTTSSS--SS....SS--SSSSTEE CS
         Ribosomal_L2_C  88 rwl.....grrpkvrGvamnpvdHphGGGe....Gktksrkapvs 123
                            +++     ++ p+vrGvamnpv+H hGGG+    Gk     + vs
  gene8|gene8|rna8|rna8 172 HYRakargHIFPRVRGVAMNPVEHIHGGGNhqhvGK----PTTVS 212
                            9999999999********************555554....33333 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.5e-08   0.00015       6      76 ..       2      75 ..       1      76 [. 0.82
   2 ?   -3.5   0.0       1.8   1.1e+04       6      16 ..     119     129 ..     114     137 .. 0.54
   3 ?   -4.1   0.3       2.8   1.7e+04      11      19 ..     195     203 ..     193     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.5e-08
                           --BSSTT--------EE-B--S---SS....--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
           Ribosomal_L2  6 gritvrhrggGhkkkyrlidfkrnkek....vkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                           g+it r r+   k++ ++++   ++       +g V++i +   R Ap+A +++++     + a eg+ +G++v+
  gene8|gene8|rna8|rna8  2 GKITRRTREAKKKERQPIVKVSLKYPIvpqvEEGEVIDIVHERSRGAPVAIISFKE-LDCMVPASEGIYTGKKVL 75
                           67777777776666777777765666656656899*********************.999************996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.8
                            --BSSTT---- CS
           Ribosomal_L2   6 gritvrhrggG 16 
                            +   v hr+  
  gene8|gene8|rna8|rna8 119 YSLVVNHRKET 129
                            55555555553 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 2.8
                            TT------- CS
           Ribosomal_L2  11 rhrggGhkk 19 
                            + +ggG+ +
  gene8|gene8|rna8|rna8 195 HIHGGGNHQ 203
                            778888876 PP

>> LBP_C  Lacto-N-biose phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.7   6.7e-05       0.4      20      44 ..     121     145 ..     115     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.7e-05
                  LBP_C  20 vViNNsdeeqtTtvytgdgkrfevt 44 
                             V+N+ +e+ +T+++ ++gk+ +v+
  gene8|gene8|rna8|rna8 121 LVVNHRKETNETVIKIPSGKKITVN 145
                            7*******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1558.81
//
Query:       gene80|gene80|rna80|rna80  [L=189]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-10   42.1   1.3    1.1e-10   42.1   1.3    2.1  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.3   6.2e-15   1.1e-10       1      66 []       8      68 ..       8      68 .. 0.81
   2 ?   -0.6   0.9      0.13   2.4e+03      30      38 ..     140     148 ..      85     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 6.2e-15
                               S-HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHH...HHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
            CDP-OH_P_transf  1 nlPnaiTllrlllsvlailllltyyplvlaillll...iasltDalDGklARrlnqvstlGkllDslaD 66
                               n+Pn+i ++r+ l ++++++         + ++++   ++sl+D++DG+lAR lnq s lG  lD + D
  gene80|gene80|rna80|rna80  8 NVPNTIGYFRIGLLIASTFVS--------GSAFVVlygLSSLLDFFDGHLARMLNQCSLLGSSLDMITD 68
                               68**********977666533........23333335699****************888********98 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.13
                                HHHHHHHHH CS
            CDP-OH_P_transf  30 aillllias 38 
                                 ++++ i++
  gene80|gene80|rna80|rna80 140 EVFFMYIYC 148
                                222222333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1245.48
//
Query:       gene801|gene801|rna800|rna800  [L=197]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.5e-15   55.0   0.0    9.9e-15   54.6   0.0    1.1  1  RIO1         RIO1 family
    1.4e-08   34.3   0.1      4e-08   32.9   0.1    1.7  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
    3.1e-08   33.8   0.0     0.0049   16.8   0.0    2.1  2  APH          Phosphotransferase enzyme family
      3e-06   26.8   0.2    3.8e-06   26.5   0.2    1.1  1  Pkinase      Protein kinase domain
    0.00016   21.4   0.2     0.0002   21.1   0.2    1.2  1  WaaY         Lipopolysaccharide core biosynthesis protein (Wa
  ------ inclusion threshold ------
       0.02   14.2   0.1      0.031   13.6   0.1    1.3  1  Pkinase_Tyr  Protein tyrosine kinase
       0.14   11.4   0.1       0.18   11.1   0.1    1.2  1  EcKinase     Ecdysteroid kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   3.9e-18   9.9e-15      43     152 ..      30     133 ..      14     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.9e-18
                                    -GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGB.HHHCG-HHHHHHHHHHHHHHHHHH CS
                           RIO1  43 sktnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapk.lkdveeeeeaeelyeevleemrkl 121
                                     +    k+++  +++E r+Lk+le  g+p+Pk i+++ + +vme i+  g+++++ ++d +   +++ l++++   + kl
  gene801|gene801|rna800|rna800  30 IEALDTKIINSRTRREARILKKLEVVGIPAPKLIDVHGNTIVMEKID--GMPLKEkIDDSD---DQKALFYDLGVLVSKL 104
                                    345567899**************************************..999875155555...5555555555545555 PP

                                    HHTSTEEESS-STTSEEEETTEEEE--GTTE CS
                           RIO1 122 ykeaglvHaDLSeyNvlvdedkvviIDvsQa 152
                                     + a +vH+DL   N ++ +dk+++ID++ +
  gene801|gene801|rna800|rna800 105 -HLADIVHGDLTTSN-FIFRDKIHVIDFGLS 133
                                    .48************.667889*****9854 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.1   1.6e-11     4e-08      51     184 ..      35     147 ..      14     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.6e-11
                            Kdo  51 fklgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLedllakwaelaeelkrallkavgrl 130
                                     k+ + r +rE r+lk+Le +g+++pk +              +++e+++g+  L++ + +        ++al+ ++g l
  gene801|gene801|rna800|rna800  35 TKIINSRTRREARILKKLEVVGIPAPKLIDVHG--------NTIVMEKIDGM-PLKEKIDD-----SDDQKALFYDLGVL 100
                                    45668899********************97654........479*******8.59999998.....9999********** PP

                            Kdo 131 iaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLa 184
                                    ++klh a++ H+dl   n+ ++ +      i +iD+  ++  + +d ++  dL 
  gene801|gene801|rna800|rna800 101 VSKLHLADIVHGDLTTSNFIFRDK------IHVIDFGLSYVSS-KDEDKAVDLY 147
                                    ********************9976......6999998888777.6666666665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.9e-06    0.0049      36     109 ..      41     108 ..      36     109 .. 0.89
   2 !   15.3   0.1   5.6e-06     0.014     168     199 ..     109     136 ..     107     173 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                                    HHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SS.HHHHHHHHHHHHHHHHHHCCHHCH. CS
                            APH  36 eirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllr.klsaaqlpellealgeflaalhqvd 109
                                    ++rre+++l+ L+  g+p+P++++      ++g    ++e ++g +l +  ++ +++++l+++lg +  +lh +d
  gene801|gene801|rna800|rna800  41 RTRREARILKKLEVVGIPAPKLID------VHG-NTIVMEKIDGMPLKEkIDDSDDQKALFYDLGVLVSKLHLAD 108
                                    589*********************......444.3679999999999999889999****************875 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.6e-06
                                    EE-SS-SGGGEEEC..TTEEEEE---TT-EEE CS
                            APH 168 llHgDlhpgNllvdpddgrvtGviDfedaglg 199
                                    ++HgDl + N++++ d+ +   viDf+++ ++
  gene801|gene801|rna800|rna800 109 IVHGDLTTSNFIFR-DKIH---VIDFGLSYVS 136
                                    79************.5555...9***987665 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   1.5e-09   3.8e-06      41     153 ..      38     141 ..      12     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.5e-09
                                    HHHHHHHHHHHHHHHSCTTB-..-EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTT CS
                        Pkinase  41 kekkvlrEikilkklkhpniv..rlyevfeekdelylvleyveggeladllerkgslseeeakkiakqilegleylHskg 118
                                     +++++rE +ilkkl+   i   +l++v       ++v+e ++g  l++ +      ++++ k +++ +   ++ lH + 
  gene801|gene801|rna800|rna800  38 INSRTRREARILKKLEVVGIPapKLIDVHG----NTIVMEKIDGMPLKEKID-----DSDDQKALFYDLGVLVSKLHLAD 108
                                    337788999999999877775113444433....4689*******9*99998.....689999999***99********* PP

                                    EE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                        Pkinase 119 iiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                    i+H Dl ++N+++   +++ ++DFGl+   +++++
  gene801|gene801|rna800|rna800 109 IVHGDLTTSNFIFR--DKIHVIDFGLSYVSSKDED 141
                                    ************99..89*********98887765 PP

>> WaaY  Lipopolysaccharide core biosynthesis protein (WaaY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   7.7e-08    0.0002     116     208 ..      66     162 ..      33     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 7.7e-08
                           WaaY 116 kvyimiieyiegielvdmpeiddevka...kikqsieklhqlgmvsgdphrgnfivkkdevriid..lsgkrasaerkak 190
                                    +   +++e i+g+ l +  + +d+ ka   ++   + klh  ++v gd    nfi + d++ +id  ls  ++  e ka 
  gene801|gene801|rna800|rna800  66 HGNTIVMEKIDGMPLKEKIDDSDDQKAlfyDLGVLVSKLHLADIVHGDLTTSNFIFR-DKIHVIDfgLSYVSSKDEDKAV 144
                                    5566889******99988888887777333567789******************986.7899999556888888999*** PP

                           WaaY 191 dridlerhygikneirdl 208
                                    d   +e+ +g + + + l
  gene801|gene801|rna800|rna800 145 DLYVFEKAVGCRHDTKLL 162
                                    *********999887755 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05     0.031      77     158 ..      69     141 ..      26     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                    EEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTS CS
                    Pkinase_Tyr  77 livteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekd 156
                                     iv+e ++g  L++ + +++       d   + +++   ++ L+  ++vH dl++ N + +  +++ + DfGL+   +kd
  gene801|gene801|rna800|rna800  69 TIVMEKIDGMPLKEKIDDSD-------DQKALFYDLGVLVSKLHLADIVHGDLTTSNFIFR--DKIHVIDFGLSYVSSKD 139
                                    56666666666666666662.......33334444444556689999***********998..789999*****988666 PP

                                    SE CS
                    Pkinase_Tyr 157 de 158
                                    ++
  gene801|gene801|rna800|rna800 140 ED 141
                                    55 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   6.9e-05      0.18     213     258 ..     105     147 ..      70     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.9e-05
                       EcKinase 213 efnvlnHGDlwvnNimfkydeegepedvilvDFQlsrygSp....alDLl 258
                                    +++ ++HGDl ++N++f+        ++  +DF ls+++S     a+DL+
  gene801|gene801|rna800|rna800 105 HLADIVHGDLTTSNFIFRD-------KIHVIDFGLSYVSSKdedkAVDLY 147
                                    667799***********86.......4889****9999995222255555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1157.96
//
Query:       gene803|gene803|rna802|rna802  [L=235]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-24   86.1   0.4    2.2e-24   85.3   0.4    1.4  1  CAP_GLY    CAP-Gly domain
  ------ inclusion threshold ------
       0.12   11.6   5.7       0.42    9.9   3.5    2.0  2  CorA       CorA-like Mg2+ transporter protein
        1.3    9.5   6.3        3.8    8.0   6.3    1.8  1  FlaC_arch  Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> CAP_GLY  CAP-Gly domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.4   3.6e-28   2.2e-24       1      65 []       6      70 ..       6      70 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 3.6e-28
                        CAP_GLY  1 vgdrvklkegrrGvvryvGpvpfakgewvGveldepnGkndGsvkgkrYFeckpnrGvFvrpekv 65
                                   v+dr  l ++ +G+vry+G++++++g+w+G+eldep+G+n+Gsv+g rYF+ck+++G+F+r ek+
  gene803|gene803|rna802|rna802  6 VNDRLTLGDKFKGTVRYIGKIKSKDGKWIGLELDEPVGANNGSVNGIRYFHCKDKHGIFIRYEKI 70
                                   67888878999**************************************************9986 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.5     7e-05      0.42     131     208 ..      96     171 ..      89     186 .. 0.80
   2 ?    2.2   0.1     0.016        94      99     132 ..     188     221 ..     174     228 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 7e-05
                           CorA 131 eeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlldelerlleml 208
                                    e ++++le+++ +s k  + +e+++lr++  +++r+++ +re +++ +  ++d+++  e ke+ +  + +++ ++  +
  gene803|gene803|rna802|rna802  96 ELKIKKLEETI-ESLKSTEKEEIVELRKENEEIKRIVLSLREGINSKKI-DRDGRIYLELKELVEGSRKHISDMVGLV 171
                                    67899******.888888899***********************55444.8999999999998888888888743333 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.016
                           CorA  99 kdeggkpkspgellyrlldeivdrlfelleklee 132
                                    + ++ +++ +  l+ r++d+++d+++e+ e+ + 
  gene803|gene803|rna802|rna802 188 SVQECERHRVMFLVKRIIDSVLDDNIEAAENFKG 221
                                    256789999999**************99988765 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   6.3   0.00064       3.8       1      37 [.      98     138 ..      98     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00064
                      FlaC_arch   1 ridelEnklsklst....eletvkkeneelsksveelkenV 37 
                                    +i++lE+ +++l++    e+  ++kenee++  v  l e +
  gene803|gene803|rna802|rna802  98 KIKKLEETIESLKStekeEIVELRKENEEIKRIVLSLREGI 138
                                    89**********999999999********999888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1397  (0.0779185); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.56
# Mc/sec: 1274.12
//
Query:       gene804|gene804|rna803|rna803  [L=777]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-67  225.8   1.8    7.4e-67  225.8   1.8    2.3  1  RIBIOP_C         40S ribosome biogenesis protein Tsr1 and BMS
    8.2e-18   64.3   1.2    2.8e-15   56.2   0.6    3.5  2  AARP2CN          AARP2CN (NUC121) domain
    6.7e-05   22.5   0.0      0.026   14.1   0.0    2.8  2  GTP_EFTU         Elongation factor Tu GTP binding domain
     0.0071   16.4   0.0      0.023   14.8   0.0    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0093   15.8   1.9      0.014   15.2   0.0    2.1  2  ATP_bind_1       Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.028   14.6   0.0       0.13   12.5   0.0    2.1  1  Ribosomal_L35Ae  Ribosomal protein L35Ae
      0.048   13.9   0.2       0.77   10.0   0.0    2.7  2  AAA_22           AAA domain
      0.068   13.6   1.5       0.29   11.5   0.0    2.4  2  AAA              ATPase family associated with various cellul
       0.08   13.5   0.4       0.81   10.2   0.0    2.6  2  ABC_tran         ABC transporter
      0.099   12.8   0.7       0.17   12.1   0.0    1.8  1  AAA_33           AAA domain
       0.12   12.7   0.0       0.45   10.9   0.0    2.0  1  RNA_helicase     RNA helicase
       0.15   12.5   0.0       0.38   11.1   0.0    1.6  1  AAA_16           AAA ATPase domain
       0.23   11.1   3.4       0.82    9.3   0.0    2.8  3  Terminase_6      Terminase-like family


Domain annotation for each model (and alignments):
>> RIBIOP_C  40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.8   1.8   5.4e-70   7.4e-67       4     291 ..     331     625 ..     328     626 .. 0.80

  Alignments for each domain:
  == domain 1  score: 225.8 bits;  conditional E-value: 5.4e-70
                       RIBIOP_C   4 pedvearerfakyrglkslrtsewdpken.lpeeyarifefen.fketkkrvlk....eale..........eregveg. 66 
                                    +e++ea+e  +   g ++l++ + d  ++   +e++ i +f++ ++e++k+  +    e  +          e  ++++ 
  gene804|gene804|rna803|rna803 331 KEEEEAEEEDESSLGFEELKKMTSDRFQKeAVTEEELIEKFNKgYEEKEKESSNillrE--KrrleeeikrnE--EMMVp 406
                                    55555566656666666666666655555333333334444331333333333344431..122334444432..33224 PP

                       RIBIOP_C  67 .....Gtyvrleik.nvpeelveeknfdekkplivfgllphEekvsvvnvrikrhreyekpikskdplifsvGfRrfqak 140
                                         G+yv++ ++ +vp    +  + d ++ +i+++ l  E+++ +++ ++kr ++y+k++k+++p+ifsvG+Rrfq+ 
  gene804|gene804|rna803|rna803 407 gviipGKYVKIRLSnHVP----Q--TVDFSNVIILGSFLVAEKEMNIIQGKVKRYKWYKKILKTNEPVIFSVGWRRFQSV 480
                                    57777********82455....3..345688************************************************* PP

                       RIBIOP_C 141 Pifsqedtknnkhklerylkpght.cvatfygpitfpntpvlafkelsskeasfrlvatGsvlevdpsriivkrivLtGh 219
                                    Pifs +d  ++++++ +y+ p+++ c ++fygp+++  t++ +++e    +++f++++ G++ +v+ + ++vk+++L+G+
  gene804|gene804|rna803|rna803 481 PIFSMKD--ATRNRVIKYT-PESMhCNVSFYGPVVPAGTGFSVYSE----KGDFKVLGLGTITDVNGDAKLVKKLKLVGY 553
                                    *******..79********.88888*******************99....478*************************** PP

                       RIBIOP_C 220 pfkihkktaviryMFfnpedvawFkpveLrTksGrrGhIkeslgthGyfkatFddklkqsDiVlmslYkrvf 291
                                    p  i ++t+++++MF+++++v +F++++L+ +sG+rG++k + g++G ++atF++++ +sDi++++++++v+
  gene804|gene804|rna803|rna803 554 PKEIRQNTVFVQDMFTSDLEVLKFQGASLKAVSGLRGQVKAPHGKNGVYRATFEGNMLMSDIITLRCFVPVE 625
                                    ********************************************************************9985 PP

>> AARP2CN  AARP2CN (NUC121) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.6     2e-18   2.8e-15       2      86 .]     185     253 ..     184     253 .. 0.94
   2 ?   -2.2   0.0       3.4   4.7e+03      41      75 ..     388     429 ..     352     430 .. 0.63

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 2e-18
                        AARP2CN   2 ilnllrfisvqkfrplswReqrpyiladrveiltdseskeeeskedrtlsveGyvrGsplsanqlvHipglGDfqiekie 81 
                                     l+l+r i v+k+rp++w++ +p+i++drv+                +  v+GyvrG  ++++  vHipg+GD +i++ie
  gene804|gene804|rna803|rna803 185 LLKLCRSIGVMKYRPIEWKCMHPHIIVDRVD----------------ETFVYGYVRGGLMRKDMEVHIPGVGDSKIADIE 248
                                    689*************************974................3469***************************** PP

                        AARP2CN  82 klpdP 86 
                                     l dP
  gene804|gene804|rna803|rna803 249 VLMDP 253
                                    ***99 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                        AARP2CN  41 e......eeskedrtlsveGyv.rGsplsanqlvHipglGDf 75 
                                    +      ee k +++++v G++  G+ ++     H+p+  Df
  gene804|gene804|rna803|rna803 388 RekrrleEEIKRNEEMMVPGVIiPGKYVKIRLSNHVPQTVDF 429
                                    033333377788888888887514566666667777776666 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.011        16       6      26 ..      42      62 ..      40      71 .. 0.88
   2 !   14.1   0.0   1.9e-05     0.026      91     150 ..     101     163 ..      95     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                                   EEEEESTTSSHHHHHHHHHHH CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrLlyk 26
                                   ++i+g   +GKtTL+ +++++
  gene804|gene804|rna803|rna803 42 VSIVGPPSSGKTTLMRSIVKY 62
                                   7899**************987 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.9e-05
                                    HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST..HHHHHHHHHHHHHHH CS
                       GTP_EFTU  91 lrvlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl..kaelkeiveevkqkl 150
                                     +v D+++l + a +G e+ t e l l++++g+  i ++++ +D +  ++ lk i++ + +++
  gene804|gene804|rna803|rna803 101 SKVSDLVILTINAGSGLEMETFEFLTLLISHGLSkILCIVTNVDSCknQKHLKSIKKRIWEEI 163
                                    5789*****************************9899999******99999999999887766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05     0.023       2      42 ..      42      86 ..      41     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                   EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSE.EEEEEE CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdi.negrvk 42
                                   v ivG p +GK+tL++++++    + i + +  +T+ + + +r++
  gene804|gene804|rna803|rna803 42 VSIVGPPSSGKTTLMRSIVKYfthQLIDNPRGPVTLSPsKSKRIT 86
                                   89*****************94422333344445666663333333 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.8e-06     0.014       1      68 [.      44     115 ..      44     145 .. 0.80
   2 ?   -3.0   2.1       3.6     5e+03     169     214 ..     722     768 ..     717     775 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.8e-06
                     ATP_bind_1   1 vvGpaGsGKttfvgalseil..elrgrsvavvNLDPAa..eelpYeaavdirelitledvmedlglgpngal 68 
                                    +vGp++sGKtt+++++++++  +l+  +   v L P    +++ +e  vdi  ++++ +v++   l  n + 
  gene804|gene804|rna803|rna803  44 IVGPPSSGKTTLMRSIVKYFthQLIDNPRGPVTLSPSKskRITLFESRVDIHQFVDVSKVSDLVILTINAGS 115
                                    79****************9822456788889****9862145789***********9999987766666655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.6
                     ATP_bind_1 169 lkeklekeleffedvealslllekee.ekykklaeaiaelleefalv 214
                                    +ke+ +k+ e  e++++l++++e++  +k k+ +e i++++ + + +
  gene804|gene804|rna803|rna803 722 MKERIKKDREEEENIQRLRRMKEENLrKKEKEREERIKKTIHDNYKH 768
                                    56667777888888888888887766788999999999999987765 PP

>> Ribosomal_L35Ae  Ribosomal protein L35Ae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.1e-05      0.13      59      83 ..     586     610 ..     568     621 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                                    -EEEEEEEEECTTTTEEEEEETT-- CS
                Ribosomal_L35Ae  59 rviwGkvtrahGnsgvvrakFkknL 83 
                                      + G+v  +hG++gv ra F+ n+
  gene804|gene804|rna803|rna803 586 SGLRGQVKAPHGKNGVYRATFEGNM 610
                                    4567******************997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00056      0.77       7      37 ..      41      70 ..      38     145 .. 0.82
   2 ?    0.5   0.2      0.51     7e+02      38      91 ..     694     752 ..     675     774 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee 37
                                   ++ ++G++ +GKTtl+r +++ ++ ++ +++
  gene804|gene804|rna803|rna803 41 FVSIVGPPSSGKTTLMRSIVKYFT-HQLIDN 70
                                   6789*************9998773.444444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.51
                         AAA_22  38 erpevv..fvtlpsstsskdllrellralglelka...erlsseellealeqalrarav 91 
                                    +r +vv  +++lp + + k+  ++  ++++++ k+   e+ + ++l+++ e++lr++ +
  gene804|gene804|rna803|rna803 694 RRISVVseKIELPIPPDYKEKHEMKNNIMKERIKKdreEEENIQRLRRMKEENLRKKEK 752
                                    55555566666666666666655555555555555777899999999999999998876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.29       3      27 ..      44      68 ..      42     112 .. 0.69
   2 ?   -0.9   1.4       1.4     2e+03      55     104 ..     338     386 ..     318     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                   EESSTTSSHHHHHHHHHHHHTHEEE CS
                            AAA  3 lyGppGtGKTllakavakelgvefl 27
                                   ++Gpp  GKT+l+++++k +  +++
  gene804|gene804|rna803|rna803 44 IVGPPSSGKTTLMRSIVKYFTHQLI 68
                                   79***************99865543 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.4
                                    HTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEE CS
                            AAA  55 ekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvi 104
                                    e+   s l ++E+ +++++r ++e   ee++++++ +  ++ +k++s+++
  gene804|gene804|rna803|rna803 338 EED-ESSLGFEELKKMTSDRFQKEAVTEEELIEKFNKGYEEKEKESSNIL 386
                                    443.567889999***9999999999999999999999988888766654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00059      0.81      14      37 ..      42      65 ..      38     104 .. 0.73
   2 ?   -1.1   0.8       1.8   2.5e+03      52      96 ..     687     743 ..     662     772 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                                   EEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagllkp 37
                                   v ivG+  +GK+tL++ + +  + 
  gene804|gene804|rna803|rna803 42 VSIVGPPSSGKTTLMRSIVKYFTH 65
                                   89***************9986554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.8
                                    B-HHHCCHCEEEE-SS......--S-TTSBHHHH......HHHTCHHHHHHHSTTGG CS
                                    xxxxxxxxxxxxxxxx......xxxxxxxxxxxx......xxxxxxxxxxxxxxxxx RF
                       ABC_tran  52 qeleslrkeigvlpqe......pqlfpeltvren......esdeeiekalsklglke 96 
                                    +el++ +++i+v++++      p  ++++++++n      ++d+e e+ +++l+  +
  gene804|gene804|rna803|rna803 687 NELPFDKRRISVVSEKielpipPDYKEKHEMKNNimkeriKKDREEEENIQRLRRMK 743
                                    466777777888888755443333333444444466666644444444444333333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.17       3      32 ..      43      72 ..      41     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                         AAA_33  3 llvGlpGsGKstlaerllkklgavllssdt 32
                                    +vG+p sGK+tl ++++k  + +l++ + 
  gene804|gene804|rna803|rna803 43 SIVGPPSSGKTTLMRSIVKYFTHQLIDNPR 72
                                   589**************9988877777665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00032      0.45       2      61 ..      43     103 ..      42     110 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYt.gqevvvidDfgqv 61 
                                     ++Gp+  GK+tl+++++k ++ +l ++ ++ v   +++++    ++ + +++ + D+++v
  gene804|gene804|rna803|rna803  43 SIVGPPSSGKTTLMRSIVKYFTHQLIDNPRGPVTLSPSKSKRITLFEsRVDIHQFVDVSKV 103
                                    589*******************999777777777777777776666666666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00028      0.38      26      51 ..      41      66 ..      32     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                         AAA_16 26 lvllsGesGvGKsslvrellralekd 51
                                    v ++G++ +GK++l+r++ ++++ +
  gene804|gene804|rna803|rna803 41 FVSIVGPPSSGKTTLMRSIVKYFTHQ 66
                                   6899**************99887766 PP

>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   1.9e+03       2      14 ..      44      56 ..      44      83 .. 0.80
   2 ?    9.3   0.0   0.00059      0.82      24      91 ..     377     447 ..     361     456 .. 0.85
   3 ?    0.2   1.1      0.37   5.1e+02     139     186 ..     714     761 ..     710     770 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                                   EEE-SSS-HHHHH CS
                    Terminase_6  2 ilggrqsGKTfag 14
                                   i+g+++sGKT+++
  gene804|gene804|rna803|rna803 44 IVGPPSSGKTTLM 56
                                   5799******986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00059
                                    SSSS.-EEEEEESSHHHHHHHHH....HHHHHHHTS-TTTS--EEEE-SSEEEETTS-E.EEEES....SHHH CS
                    Terminase_6  24 grgprnqvflsasktqareeggq....fekgigelakeildiefeesaknlvvlsnGas.lhflslesetagg 91 
                                    +++++++ +l ++k+ ++ee+ +    + +g++++ k  ++i+++++ + +v++sn +  ++fl +e+e    
  gene804|gene804|rna803|rna803 377 EKEKESSNILLREKRRLEEEIKRneemMVPGVIIPGKY-VKIRLSNHVPQTVDFSNVIIlGSFLVAEKE-MNI 447
                                    45558999***********9999999999999999888.*************************99996.333 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.37
                                    SSHHHHHHHHHHCTSS-EEEEE-GGGSGB-TTSBB-TTHHHHHHHHHT CS
                    Terminase_6 139 dhgvydfvtgwldeegpqsvtkiqavvevtiedakklgedlieeleae 186
                                    +h+++ ++ ++   +++++ ++iq++ ++  e+++k++++  e++++ 
  gene804|gene804|rna803|rna803 714 KHEMKNNIMKERIKKDREEEENIQRLRRMKEENLRKKEKEREERIKKT 761
                                    567776666555555599999****99988888888888877777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (777 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2279  (0.127112); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.99u 0.35s 00:00:01.34 Elapsed: 00:00:00.55
# Mc/sec: 4252.07
//
Query:       gene805|gene805|rna804|rna804  [L=144]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-29  100.4   0.0    6.5e-29  100.2   0.0    1.0  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   3.6e-33   6.5e-29       2     129 .]      14     142 ..      13     142 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 3.6e-33
                                    TCTBEBESSTT-SSEEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEE.EEEETTBTSEEEEEE CS
                        dUTPase   2 eaeiptrkspesAgyDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvp.gvidsdyrGevkvvl 80 
                                    +a+ip+r+s+++AgyD+ + +  ++ pge++ + t++ +++p+++ +l+++RSgla+k+ + v+ + +    + e+ ++l
  gene805|gene805|rna804|rna804  14 NAKIPKRQSEGAAGYDVHSVESGVILPGERKSIRTGLIWDIPQSIVGLVFGRSGLALKNWMEVVeTCVYPGENKELVITL 93 
                                    689*********************************************************999977777777779***** PP

                                    EE-SSS-EEE-TT-EEEEEEEEEBECGEEEEESSTTTESSBTTXTTTTX CS
                        dUTPase  81 fnltkkdvkikkgdRiAqLifariltaeleevetlkatergeggfgssg 129
                                    +n++k+++++++  RiAqL+f+++l  e+++ve+l++terg  gfgs+g
  gene805|gene805|rna804|rna804  94 INNGKQPFEYEECCRIAQLVFVPVLSCEVNLVESLDSTERGCLGFGSTG 142
                                    **********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 825.37
//
Query:       gene806|gene806|rna805|rna805  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 604.39
//
Query:       gene807|gene807|rna806|rna806  [L=596]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-16   60.6   0.4    4.4e-16   59.0   0.3    1.9  2  Lactamase_B_2  Beta-lactamase superfamily domain
    4.1e-10   39.2   0.1    6.6e-09   35.3   0.0    2.6  2  Lactamase_B_4  tRNase Z endonuclease
    2.9e-07   30.7   0.4    7.2e-07   29.4   0.5    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0018   17.8   0.0     0.0034   16.8   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.2   5.2e+03      48      69 ..      65      86 ..      64     124 .. 0.79
   2 !   59.0   0.3   9.9e-20   4.4e-16       3     201 .]     344     548 ..     343     548 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.2
                                   GCCCCC--EEEEEEEEHHHHHH CS
                  Lactamase_B_2 48 ltlrelrpkklplyapkgvlav 69
                                   ltlr  ++k l++++++++++ 
  gene807|gene807|rna806|rna806 65 LTLRDVKKKALDIVCSPRIQEM 86
                                   6888877777999999998874 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 9.9e-20
                                    EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH.............. CS
                  Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla.............. 68 
                                    i +D+g d++ q +ra   +   + l++++a++++h+H+DH+ g+ +  +   +k++++ap+ +                
  gene807|gene807|rna806|rna806 344 IMLDCGEDTLFQIHRAY--G-GFNVLKKLKAIFVSHSHADHVLGITSALKKISHKIKIFAPAAIKPfvksfdignheyie 420
                                    889*****888867777..3.477889*******************999955567******9988855566555555433 PP

                                    .....HCCTTCGHHHCHTTTTEEEEEE-TTSEEEE......CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEE CS
                  Lactamase_B_2  69 .....vleanfvylaleeepavnvheldwgesfel......gdggleitatparhksgrrldrnagdtlGlriegggkrv 137
                                          +e++f+ +++  + + ++ ++d      +       d+g+e+ +  + h s           +G r+++g+  +
  gene807|gene807|rna806|rna806 421 tnhakAMERKFQDIWKLSQ-RSPLCTVD------VedhilkFDVGFEVGICGVDHCSDS---------CGIRVKDGDTII 484
                                    3333333333333333333.22222222......1222222235566667777777776.........************ PP

                                    EEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 138 yyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                                     y+gD        g +  + d++++++t+  d+e ++ h gH+t+++a++++++ + k+l+l+H+
  gene807|gene807|rna806|rna806 485 TYSGDARPSI-LFGMMSLDSDVMIHEATFALDQEERAmHTGHSTIDGALKVFKASKSKVLLLTHF 548
                                    ******9333.33334446***********99997779**************************7 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   1.5e-12   6.6e-09      14      54 ..      14      53 ..       8      57 .. 0.92
   2 ?    0.4   0.0      0.11   5.1e+02      44      59 ..     366     380 ..     354     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 1.5e-12
                  Lactamase_B_4 14 lllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtg 54
                                   +l+L++d+krYlf ++ Eg QR ++e+ v++sk++ iF++ 
  gene807|gene807|rna806|rna806 14 SLVLTIDNKRYLF-NLFEGFQRYCIESSVSISKISTIFVSS 53
                                   79***********.************************975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                  Lactamase_B_4  44 lsklesiFLtgkvsws 59 
                                    l kl+ iF+++++  +
  gene807|gene807|rna806|rna806 366 LKKLKAIFVSHSH-AD 380
                                    48********998.44 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.5   1.6e-10   7.2e-07       5      87 ..     331     411 ..     328     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.6e-10
                                    SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSG.GGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglk.pkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                    +v+s+l e  + +i+ D+G +t ++  +   a+ g++ +k+++a++++H+H+DH+ g     ++   ++ + a +a ++f
  gene807|gene807|rna806|rna806 331 NVSSILYESHDAAIMLDCGEDTLFQIHR---AYGGFNvLKKLKAIFVSHSHADHVLGITSALKKISHKIKIFAPAAIKPF 407
                                    799************************9...5777773689****************99999998888888888777776 PP

                                    CHHH CS
                    Lactamase_B  84 meea 87 
                                        
  gene807|gene807|rna806|rna806 408 VKSF 411
                                    6555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.7e-07    0.0034       5      78 ..     340     407 ..     336     441 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-07
                  Lactamase_B_6   5 dnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkL 78 
                                     ++ i+lD+G d   +++++a     +v++++ +i +sh+ ++h+ + +    ++ +k+ ++i+++a+ +++  
  gene807|gene807|rna806|rna806 340 HDAAIMLDCGEDTL-FQIHRA-YGGFNVLKKLKAIFVSHSHADHVLGIT----SALKKISHKIKIFAPAAIKPF 407
                                    5789********86.667544.55678*****************99843....445678899*****9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 3431.44
//
Query:       gene808|gene808|rna807|rna807  [L=502]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.77   10.7   2.8         84    4.3   0.0    3.5  3  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.26   4.6e+03       8      35 ..     118     144 ..     111     145 .. 0.66
   2 ?    4.3   0.0    0.0047        84      13      26 ..     163     176 ..     154     187 .. 0.86
   3 ?    3.8   0.5    0.0066   1.2e+02       9      32 ..     392     416 ..     385     421 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.26
                                    ESSSSEEEEEEETTSSEEEEEE.TTSEEE CS
                           WD40   8 tGHssvtslafspdgawlasGs.dDgtvr 35 
                                    +G ++v+ + +s dg ++  +   D t+ 
  gene808|gene808|rna807|rna807 118 SGFNDVRKCMVSNDGVFV--CFlVDSTIE 144
                                    566778666589999996..532577776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0047
                                    EEEEEEETTSSEEE CS
                           WD40  13 vtslafspdgawla 26 
                                    v +++fspd+++++
  gene808|gene808|rna807|rna807 163 VVDVSFSPDNKFIV 176
                                    789*********86 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0066
                                    SSSSEEEEEEETTSSEEEEEET.TS CS
                           WD40   9 GHssvtslafspdgawlasGsd.Dg 32 
                                     H s ts+ +s++g + as+s  D+
  gene808|gene808|rna807|rna807 392 SHPSCTSILWSHSGLYAASASAgDC 416
                                    474489**********987652265 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3392.88
//
Query:       gene809|gene809|rna808|rna808  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-14   53.1   0.0    4.8e-14   52.6   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.3e-12   47.1   0.0    3.5e-12   46.6   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.4e-11   41.7   0.0    1.1e-10   41.5   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    1.5e-07   31.3   0.0    2.5e-07   30.6   0.0    1.3  1  FR47             FR47-like protein
    0.00054   20.1   0.0    0.00066   19.8   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.023   14.2   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase
      0.096   12.8   0.0       0.16   12.1   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.9e-17   4.8e-14      27     117 .]      43     134 ..      17     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.9e-17
                                    HHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHT.TESE..EEEEEET CS
                 Acetyltransf_1  27 sfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeeraree.gikk..ivlavee 103
                                    s+s    + +vae d+++iG+  +       + +++i+s+ V+  +r++G+G++L++  ++ +r e ++++  i l+v++
  gene809|gene809|rna808|rna808  43 SLSMSYTTSFVAETDEKVIGYSEAVFFKS--KMKGHIYSICVDAPFRRSGIGRRLVNLSIDAMRIEsQGRRceIDLHVRA 120
                                    44444457899***********9999999..99****************************999998665523677**** PP

                                    TEHHHHHHHHH.TTE CS
                 Acetyltransf_1 104 dndaairlYek.lGF 117
                                    +n++ai lY +  GF
  gene809|gene809|rna808|rna808 121 SNVGAISLY-RsAGF 134
                                    *********.65**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   1.4e-15   3.5e-12       5      75 ..      51     135 ..      47     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.4e-15
                                    EEEEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH.....TT..SE..EEEE.EEEETHHHHHHHHH CS
                 Acetyltransf_7   5 vfVaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea.....ae..kg..iile.qlelnaekaikfYe 70 
                                     fVae d+k++G+  ++  +    ++i  ++Vd  +r+ GiGr+L+++     ++  +g  +++  +++ ++  ai++Y+
  gene809|gene809|rna808|rna808  51 SFVAETDEKVIGYSEAVFFKskmkGHIYSICVDAPFRRSGIGRRLVNLsidamRIesQGrrCEIDlHVRASNVGAISLYR 130
                                    69**********99888888999778888******************766665225655447656555555569****** PP

                                    HTTEE CS
                 Acetyltransf_7  71 klGFe 75 
                                    + GFe
  gene809|gene809|rna808|rna808 131 SAGFE 135
                                    ****8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   4.4e-14   1.1e-10      29     124 ..      47     154 ..      22     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.4e-14
                Acetyltransf_10  29 gealllvaeeggkivGviel..rdgs....hisllfVdpeyrgqGigkaLleaveee..aekdgikl..eltvnasp.ya 97 
                                    + ++ +vae ++k++G+ e    + s    hi+ ++Vd  +r+ Gig++L++  +++  +e +g +   +l+v+as+  a
  gene809|gene809|rna808|rna808  47 SYTTSFVAETDEKVIGYSEAvfFK-SkmkgHIYSICVDAPFRRSGIGRRLVNLSIDAmrIESQGRRCeiDLHVRASNvGA 125
                                    667889***********9443322.23577*********************9999885455555555889********** PP

                Acetyltransf_10  98 vpfYeklGFkav..geeqeenGirfvpMe 124
                                    +++Y++ GF+    + + +e+G   ++M 
  gene809|gene809|rna808|rna808 126 ISLYRSAGFEIReaNIPYYEAGAAGHRMS 154
                                    *********98765777888888888886 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   9.8e-11   2.5e-07      19      82 ..      71     139 ..      62     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 9.8e-11
                                    -TT.SSEEEEEE-GGG-SSSHHHHHHHHH..HHHHHHS-S..-EEEEEETT-HHHHHHHHHHT-EEEEE CS
                           FR47  19 kdg.gelgalqvlpehrrrGlgsrlvkal..akeiaergk..tvllvvvasNtpsirlyeklGfekiee 82 
                                    +++ g +++++v+  +rr G g+rlv+    a +i  +g   ++ l+v+asN  +i+ly + Gfe +e+
  gene809|gene809|rna808|rna808  71 SKMkGHIYSICVDAPFRRSGIGRRLVNLSidAMRIESQGRrcEIDLHVRASNVGAISLYRSAGFEIREA 139
                                    44559*********************86512345666665226789******************98865 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.6e-07   0.00066      31     137 ..      29     137 ..      13     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.6e-07
                 Acetyltransf_4  31 vssveefe..kflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvl.k 107
                                     +s e f   +fl++l   +   f ++ +++++Gy  ++ fk+  k +  + s+ ++    +  g+gr l+++ ++ +  
  gene809|gene809|rna808|rna808  29 KNSTENFLlgTFLNSLSMSYTTSFVAETDEKVIGYSEAVFFKS--KMKGHIYSICVD-APFRRSGIGRRLVNLSIDAMrI 105
                                    4566665555899998444466666666***************..9**********6.89***************99998 PP

                 Acetyltransf_4 108 eqnienllaeiasp..nensiqfhkalGFelv 137
                                    e   ++ ++ + +   n  +i ++ + GFe+ 
  gene809|gene809|rna808|rna808 106 ESQGRRCEIDLHVRasNVGAISLYRSAGFEIR 137
                                    9888988888866533778**********985 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     9e-06     0.023      74     137 ..      76     135 ..      11     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9e-06
                Acetyltransf_15  74 eiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFr 137
                                     iY+++v+  +r+ G+ ++l++ s+++++   +      + LH+ ++      + +lY+s gF 
  gene809|gene809|rna808|rna808  76 HIYSICVDAPFRRSGIGRRLVNLSIDAMRI-ESQGRRCEIDLHVRASNV---GAISLYRSAGFE 135
                                    8************************99944.444448889999988754...588899999995 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.4e-05      0.16      20      54 ..      70     104 ..      51     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.4e-05
                Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaalddar 54 
                                    + + + +++ + V+  +r+ Gi+++Lv+  +d +r
  gene809|gene809|rna808|rna808  70 KSKMKGHIYSICVDAPFRRSGIGRRLVNLSIDAMR 104
                                    44456789*******************99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.54
# Mc/sec: 904.53
//
Query:       gene810|gene810|rna809|rna809  [L=964]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-17   63.4   0.3    2.6e-17   62.7   0.3    1.2  1  Nucleoporin_N  Nup133 N terminal like
  ------ inclusion threshold ------
      0.045   12.5   1.5        2.3    6.8   0.1    2.8  3  Nucleoporin_C  Non-repetitive/WGA-negative nucleoporin C-term


Domain annotation for each model (and alignments):
>> Nucleoporin_N  Nup133 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.3   2.9e-21   2.6e-17      29     211 ..      89     248 ..      86     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 2.9e-21
                                    EEEEECTTTEEEEEETTEEEEEETTSSSS...EEEEEE----S---EEEEEE---SSSS-SSSCEEEEECTTSEEEEECE CS
                  Nucleoporin_N  29 kgglfpeigrawitvdnklflWnYnstasspstdtipydgeehtilavglLvkpkpgtfveevgllLvvattgeivywev 108
                                     +g+ p  +  w+t++++l++W+Y+s++         +   ++++l+v  + +pk+g+f+e ++++L +at  ++ +++ 
  gene810|gene810|rna809|rna809  89 RCGILPVMSALWFTNGKNLVIWRYESNE------EEEIGTFSSEVLEVI-IFTPKAGIFNERISHCLFIATEKQVMIYG- 160
                                    59*************************7......566666689******.**************************999. PP

                                    CCS--------EEEEEEEE--EETT.TTEEEEEEETTTC-EEEEETTSSEEEEEEC-SSS-CEEEEEEEEE-SSSS-... CS
                  Nucleoporin_N 109 iysaasllstnelslfntdlsvssdgeivtqvinseptgriflagstgrlyeltyrdssgwpslkckkicltkgglssll 188
                                            +++ l l+ntd+  ss    +  + ++  +g++f++ ++g++y++ y++ ++w  +      ++++ ls   
  gene810|gene810|rna809|rna809 161 ---I----EKDTLCLVNTDFVASSP--SCVRCAEAS-NGDVFIGCENGKVYQIVYKSVDSWSFKIMHAYDPSSSILS--- 227
                                    ...4....6678********88887..566666666.899*********************9999999*********... PP

                                    --SSS--G----GG-EEEEEEEC CS
                  Nucleoporin_N 189 silpgvlsgasereeivqlrids 211
                                    s++p+vl+   +r+++ +l  ++
  gene810|gene810|rna809|rna809 228 SLVPSVLK--RKRSAVRALSLGK 248
                                    ********..9999999988776 PP

>> Nucleoporin_C  Non-repetitive/WGA-negative nucleoporin C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.033   2.9e+02     186     241 ..     552     606 ..     492     626 .. 0.71
   2 ?    2.9   0.0    0.0042        37     359     455 ..     718     808 ..     706     818 .. 0.79
   3 ?    6.8   0.1   0.00026       2.3     499     565 ..     815     858 ..     809     862 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.033
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHH CS
                  Nucleoporin_C 186 kdlfapnlssiinrnisrgesieleatllqeicgslcsltdvllfraiErlrwake 241
                                    ++ f++++  +i    ++++s e+  ++l+ +c  +    +v+ +r +E l++  +
  gene810|gene810|rna809|rna809 552 EE-FKKRTLKSILEMFKVNQSVEPLIKTLSARCPLFLPMEEVYYQRGLEMLNKRPS 606
                                    23.33333444444458999*****************************9998755 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0042
                                    XXTTHHHHHHHTX......XHHHHHHTHHHHXXSHHHHHHHHHHHHSSSSXXXHHHHHHHHHHX---HHH.......... CS
                  Nucleoporin_C 359 dtsfilpFLrekp......elakllWiydvkekdfeeAAeiLysLalskeqlvlskrieLSlakLaqLaeleesekekkg 432
                                      +f+ +FL+ek+      ++ +l W y v ++d  +  ++L++La +     l+ +i L +  L    +          
  gene810|gene810|rna809|rna809 718 SVPFLERFLKEKAmsssdpRIFELHWKYCVYRNDKMKGTQSLLELADN-KPVPLETKIDLLRTALSVSVN---------- 786
                                    66899********99***************99999999********88.677888889887776655444.......... PP

                                    ......HGGGHHHHHHHHHHHHH CS
                  Nucleoporin_C 433 lekklekieellevaaiQddlla 455
                                        ++ ++  le+a+iQ d+l+
  gene810|gene810|rna809|rna809 787 -TPLFNEVKLRLELADIQVDILK 808
                                    .3456777777888888888776 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.00026
                                    HHHHS---HHHHHHHTT.........TTTT-HHHHHHHHHHTT---HHH............HHHHHH CS
                  Nucleoporin_C 499 lLkhkildasdLidlltLidtkeeeedplgefelALkvlkvsdlrneeeealekliWRRcvIrddWe 565
                                    +++++ l+a++L+++++            ++ elALk++ +s+++++              Ir+ We
  gene810|gene810|rna809|rna809 815 TISNNLLSADELFNDYA-----------YKYPELALKIIGISSYTDKAV------------IRELWE 858
                                    68999************...........77889**********999888............666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (964 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.78u 0.34s 00:00:01.12 Elapsed: 00:00:00.49
# Mc/sec: 5864.80
//
Query:       gene81|gene81|rna81|rna81  [L=191]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-35  120.0   0.0    6.6e-35  119.8   0.0    1.1  1  UQ_con    Ubiquitin-conjugating enzyme


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.0   3.7e-39   6.6e-35      17     137 ..      31     163 ..       9     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 3.7e-39
                                EEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBETTSBB-CGGGS............T CS
                     UQ_con  17 isaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvdksGevcldiLk............e 88 
                                + +++++++n + w++ ++   d++Y+g + k+ +efp+ YPl+pP++kfv+k+fHPn++++G+ c++iL+            +
  gene81|gene81|rna81|rna81  31 CPRGPKENRNYKVWDIYFTLGGDSLYAGRILKAVMEFPDCYPLQPPTLKFVSKMFHPNIYEDGKMCISILEedapdptgygdsK 114
                                456677789**********99**************************************************9999999999887 PP

                                TT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHH CS
                     UQ_con  89 ekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvk 137
                                +kW p+++++++llsi+++l+ pn++sp+n++a  + ++++eey kkv 
  gene81|gene81|rna81|rna81 115 DKWAPVQNIRTILLSIIVILNAPNTSSPANVDASVMHRDNHEEYAKKVI 163
                                77********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1381.72
//
Query:       gene811|gene811|rna810|rna810  [L=284]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-34  118.9   1.4      3e-34  118.7   1.4    1.0  1  Porin_3   Eukaryotic porin


Domain annotation for each model (and alignments):
>> Porin_3  Eukaryotic porin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   1.4   1.7e-38     3e-34       3     270 .]      22     279 ..      20     279 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.7e-38
                                    --CCCCCHHHHHHHHCCHTTTECEEEEEEEECCECCEEEEEEEETTTS.-ECEEEEEEEEETCCCEEEEEECCCSCCEEE CS
                        Porin_3   3 gtyedlgkeakdllpkdYhfeglkldvtkktslgvaFqvshsfslgsg.kvsysfeakykdkgltltlkgntdndlslta 81 
                                     t++  + ea+++++ + +++g++ +++k  +  +++qvs    l+ + +vs  f+++    +++l +++++d++ s  +
  gene811|gene811|rna810|rna810  22 STFDTYNAEANEIVTSQ-TCSGVRTEISK--TIFPFLQVSRVDILDRNaHVSQMFGTLSL--KNSL-VQVSMDHENSIGV 95 
                                    589999****9999999.9**********..99*************999**********9..6666.999********** PP

                                    EEECCSSTTCEEEEEEEE-TTT--EEEEEEEEEEETTEEEEEEEEC.TC...EEEEEEEEEEECTSTEEEEEEEEEECTT CS
                        Porin_3  82 rvneqlaeglklklsaqltpekgkksakleldykgddftaslklgn.sk...tpvvvasllqsvtpglalGaeavydtas 157
                                    r+ + +  +l +++++ +t +k+ + +++e+++k++  ++ lk++       + v+va+ lq++   l+lGae++   a+
  gene811|gene811|rna810|rna810  96 RAMN-MYGNLATRIHTIITGKKE-VFSQVEMEMKNRISSFGLKMISpAIkstGMVYVANTLQQFG-SLSLGAEII--GAD 170
                                    ****.8**************986.*********************96559999************.********9..666 PP

                                    TCCEEEEEEEEEEECSEEEEEEEEETTTEEEEEEEEECCTTEEEEEEEEEETTEEEEEEEEEEEEEECTCEEEEEEEECT CS
                        Porin_3 158 gkltkyaaalsyaardwiaslqllnnggaltasyyqkvsekvevgaeltlnassqestttlGakydldksttvkakidsn 237
                                    ++++  +++  y +r+ ++s+ l ++++al++syy+k+ + +++gae++     +  ++++G+++++ k  +vka ++s+
  gene811|gene811|rna810|rna810 171 TEVG-ISMCGRYEHRNGVFSVGL-QQFTALSLSYYHKIGKFFDIGAEIQAPRA-NPPSAAIGCRLSTSKT-QVKANVNSD 246
                                    6677.6677788888*******8.78***********************9875.5588************.********* PP

                                    TEEEEEEEEEECTTEEEEEEEEEECCCTEEEEE CS
                        Porin_3 238 gkvgllleqkLrpgvtltlsaelDhkknahkfG 270
                                    +++g++l ++L++g+t+++ ae++    +h fG
  gene811|gene811|rna810|rna810 247 MSLGFYLGERLTEGLTFNVNAEVNKSGCSHGFG 279
                                    **************************99**999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1931.91
//
Query:       gene812|gene812|rna811|rna811  [L=302]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-40  136.5   0.0    1.4e-39  135.8   0.0    1.3  1  MDD_C           Mevalonate 5-diphosphate decarboxylase C-term
    1.8e-08   34.5   0.6    3.5e-08   33.5   0.6    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.026   14.7   0.5       0.58   10.3   0.0    2.9  4  KIP1            KIP1-like protein


Domain annotation for each model (and alignments):
>> MDD_C  Mevalonate 5-diphosphate decarboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.8   0.0   2.3e-43   1.4e-39       2     132 ..     167     294 ..     166     299 .. 0.95

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 2.3e-43
                          MDD_C   2 lilvvsdekkkvsStsGmqrsvetSeLlkhrakevvperieelekAikekdFetfaeitmkdSnqlhavcldtyPpifYl 81 
                                    l ++ s + kk++St+Gm r+  tS+L++ r++  ++e+++++ + i +kdF+ fa++tm++Sn+lh++ +dtyPpi+Y+
  gene812|gene812|rna811|rna811 167 LSIILSGDCKKIGSTEGMIRTRYTSNLYQARLSG-MEEKVKAMAQYITHKDFDGFAHLTMRESNELHSILMDTYPPIRYI 245
                                    55789999************************99.9******************************************** PP

                          MDD_C  82 ndtSraiielvhelNeaagkikvAYtFDAGpNavlyleekdveellsllkk 132
                                     d   +iie+ he+N  ++++k+AYtFDAGpN +l+++e+ ++e+ +++k+
  gene812|gene812|rna811|rna811 246 RDDGFNIIEMCHEFN--RDRVKIAYTFDAGPNPFLITLERYLNEVEDFFKA 294
                                    ***************..899*********************9999887765 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.6   5.9e-12   3.5e-08       3      45 ..      90     135 ..      88     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 5.9e-12
                                    EEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHH CS
                 GHMP_kinases_N   3 vikseiPvgaGLGSSAAlavalvaAllallglslee...aklalea 45 
                                    ++ + +P+++GL+SSA+  +al++Al+++++l+ +e    ++a ++
  gene812|gene812|rna811|rna811  90 KSFNSFPHSCGLASSASGFAALALALNDFYNLETSEeelCRIARVG 135
                                    667899************************8665331234444433 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.7     1e+04      15      34 ..      58      77 ..      49      81 .. 0.70
   2 ?   10.3   0.0   9.7e-05      0.58      12      62 ..     190     238 ..     184     245 .. 0.72
   3 ?   -2.5   0.0      0.97   5.8e+03      55      72 ..     252     269 ..     251     271 .. 0.74
   4 ?    1.0   0.0     0.076   4.5e+02      56      69 ..     285     298 ..     281     302 .] 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                           KIP1 15 wLqetlseldekvkemlkli 34
                                   +L++++  + e++++++++ 
  gene812|gene812|rna811|rna811 58 YLNNEMVTIGERMNRVVEIF 77
                                   67777777778888887775 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9.7e-05
                           KIP1  12 qskwLqetlseldekvkemlkli.eedadsfakraemyykkrpeLielveef 62 
                                     s+  q+ ls ++ekvk+m + i ++d d f   a++ +++ +eL ++++++
  gene812|gene812|rna811|rna811 190 TSNLYQARLSGMEEKVKAMAQYItHKDFDGF---AHLTMRESNELHSILMDT 238
                                    56667899*************9934455555...455566666666666665 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.97
                           KIP1  55 LielveefyrsyrsLaer 72 
                                    +ie+ +ef+r    +a  
  gene812|gene812|rna811|rna811 252 IIEMCHEFNRDRVKIAYT 269
                                    799999999986666655 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.076
                           KIP1  56 ielveefyrsyrsL 69 
                                    ++ ve+f+++y+ +
  gene812|gene812|rna811|rna811 285 LNEVEDFFKAYKLI 298
                                    5779*******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2100.83
//
Query:       gene813|gene813|rna812|rna812  [L=110]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-19   70.1   0.4    1.8e-19   69.3   0.4    1.4  1  Homeodomain  Homeodomain
    4.1e-06   26.6   1.9    7.6e-06   25.7   0.5    2.0  2  Homeobox_KN  Homeobox KN domain
     0.0084   15.9   0.2      0.019   14.7   0.2    1.6  1  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.17   11.8   0.0    1.3  1  Csm4_C       CRISPR Csm4 C-terminal domain


Domain annotation for each model (and alignments):
>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.4     4e-23   1.8e-19       1      56 [.      10      65 ..      10      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 4e-23
                                   ST-SSSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                    Homeodomain  1 rrkRttftkeqleeLeklFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56
                                   +++Rt++t +q+++L ++F+ n+ ps+++reeL++ l ++ r V++WFqN+R++ k
  gene813|gene813|rna812|rna812 10 KKPRTRMTGDQIKALMACFQDNPFPSTSTREELSRILSISPRTVQIWFQNQRQRIK 65
                                   79****************************************************98 PP

>> Homeobox_KN  Homeobox KN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.2   9.1e+02      11      28 ..       5      22 ..       5      30 .. 0.72
   2 !   25.7   0.5   1.7e-09   7.6e-06       7      40 .]      30      63 ..      25      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                    Homeobox_KN 11 PseedKeeLlkeTglsvk 28
                                   P++e K++  + Tg ++k
  gene813|gene813|rna812|rna812  5 PKREGKKPRTRMTGDQIK 22
                                   777888777777777766 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 1.7e-09
                    Homeobox_KN  7 hnPYPseedKeeLlkeTglsvkqitnWFINaRrR 40
                                   +nP+Ps   +eeL +   +s + ++ WF N+R+R
  gene813|gene813|rna812|rna812 30 DNPFPSTSTREELSRILSISPRTVQIWFQNQRQR 63
                                   8*******************************99 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   4.3e-06     0.019      19      40 ..      38      59 ..      36      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.3e-06
                         HTH_23 19 svreIAreLgvsrrTvyrwlkr 40
                                   +++e +r+L +s+rTv+ w + 
  gene813|gene813|rna812|rna812 38 TREELSRILSISPRTVQIWFQN 59
                                   7899***************876 PP

>> Csm4_C  CRISPR Csm4 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.8e-05      0.17      43      65 ..      60      82 ..      52      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
                         Csm4_C 43 aeqlkkkdvymfaeGSvfkkkle 65
                                   ++q+ k++++m++eG vf++++ 
  gene813|gene813|rna812|rna812 60 QRQRIKNQMRMISEGEVFEENVH 82
                                   45799*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 742.20
//
Query:       gene814|gene814|rna813|rna813  [L=343]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      7e-80  269.0   0.0    8.5e-80  268.7   0.0    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
        0.1   13.1   0.1       0.25   11.9   0.1    1.7  1  RtxA        RtxA repeat


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.7   0.0   9.5e-84   8.5e-80       2     302 ..      28     331 ..      27     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 268.7 bits;  conditional E-value: 9.5e-84
                                    HHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   2 adivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekli 81 
                                    + ++++++GP G +K l+++g+++ + +DG+t++ke++++hP+  ++++aa+s+ + +GDG tt++iL++e+ + a+++ 
  gene814|gene814|rna813|rna813  28 SGLFSSSIGPFGSYKALISPGQTLRIAKDGNTLCKEIQFTHPTSIIITRAATSMYTTFGDGATTLIILCCEIFNDAFRHF 107
                                    66789*************************************************************************** PP

                                    HCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCSEEC CS
                     Cpn60_TCP1  82 aagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieenekel 160
                                    ++gv + +i+  ++ +l++++++Lk  ++ ++      ++L k+a++++++k++++ a  ls  +v+Av ++i+++   +
  gene814|gene814|rna813|rna813 108 ENGVPIPRICASLQLCLDDVMRYLKTLERPFEE-----DTLSKMAYSIIRTKVDEDMALSLSMVLVQAVeNAIQSQ--FF 180
                                    ***************************777764.....79*****************************8888655..8* PP

                                    SCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHH CS
                     Cpn60_TCP1 161 dlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekq 240
                                    d+++++v+k+++g+++++  v+Glvld+g ++  mp kle++ +l++++sLe+ek+e+++++++s+ae++e+l+ +e+++
  gene814|gene814|rna813|rna813 181 DINMVEVIKMQEGDVSETMYVDGLVLDHGGRHYAMPDKLEEVCILITNMSLEYEKPEINAEFCYSSAEQREELAGKEREF 260
                                    ******************************************************************************** PP

                                    HHHHHHHHHHTTECE.........EEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGG CS
                     Cpn60_TCP1 241 leellekiiksgvnv.........vvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssle 302
                                    ++++ ++i++ g+++         vv++kgid+++l+++a +gilalrr+k+++lerl++++G+++++ ++
  gene814|gene814|rna813|rna813 261 ILQRSRAIAEFGRKIkekngktlmVVTEKGIDPYSLEVFASSGILALRRAKRRNLERLVRMCGGNVITHVG 331
                                    *******************************************************************9886 PP

>> RtxA  RtxA repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.8e-05      0.25       4      14 ..     323     333 ..     323     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                           RtxA   4 aaNkitrvGsg 14 
                                    ++N+it+vGs+
  gene814|gene814|rna813|rna813 323 GGNVITHVGSS 333
                                    89*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2306.93
//
Query:       gene815|gene815|rna814|rna814  [L=133]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-18   65.4   1.4    8.6e-17   60.9   1.4    2.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   1.4   4.8e-21   8.6e-17     350     490 ..       2     123 ..       1     124 [. 0.95

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 4.8e-21
                                    HHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHH CS
                     Cpn60_TCP1 350 deieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievla 429
                                      +e  i+ Al+++   ++++k++ GG + + +l ++++e+++svs+++ +++++++++++ ++k+L +N+G d +e l+
  gene815|gene815|rna814|rna814   2 SRMESGIRGALKSLYISLKNRKYIEGGYSLYRSLISYIREKMNSVSEKDVVGYKVMENSFLNVVKALLRNSGKDIQEELT 81 
                                    57899*************************************************************************** PP

                                    HHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                     Cpn60_TCP1 430 klraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiikak 490
                                    +++     ge           +     ++vvD+ +v++ +++++t +a+++L +deiika+
  gene815|gene815|rna814|rna814  82 RILR---GGE-----------C-----ERVVDNSCVVSAVISNSTVVATSLLLVDEIIKAG 123
                                    **99...455...........4.....689*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 881.24
//
Query:       gene816|gene816|rna815|rna815  [L=655]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.097   12.3   0.0    2.3  2  AbrB_C    AbrB C-terminal domain
       0.13   12.9   0.8       0.44   11.3   0.5    2.1  2  PMC2NT    PMC2NT (NUC016) domain


Domain annotation for each model (and alignments):
>> AbrB_C  AbrB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05     0.097      13      30 ..      55      72 ..      53      76 .. 0.88
   2 ?   -0.8   0.1      0.14   1.2e+03      11      30 ..     165     184 ..     162     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                         AbrB_C 13 isLanGkivLSkeGAeiL 30
                                   +++ +G i+LSk+GA+i 
  gene816|gene816|rna815|rna815 55 KKFEEGVIYLSKDGARIV 72
                                   89*************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.14
                         AbrB_C  11 eNisLanGkivLSkeGAeiL 30 
                                    ++i   +Gk++L+  ++e +
  gene816|gene816|rna815|rna815 165 KIIVVTEGKLILGDSEIENI 184
                                    6666779*****98887765 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.5   4.9e-05      0.44      30      91 ..     318     381 ..     310     382 .. 0.77
   2 ?   -2.6   0.0       1.1   9.7e+03      64      83 ..     447     464 ..     420     476 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.9e-05
                         PMC2NT  30 deqserllslinsllklaaskseisas..sklededdveekfksvvd.vvDsllEkadtcLDelt 91 
                                    d++++r  +++nsll++a+  +   +s  +k  +  dv  + k  +d  vD l+E++d+ +De+t
  gene816|gene816|rna815|rna815 318 DTEEKRAFASLNSLLDSAKGGNVSVESesKKPSGNKDVL-SRKLTGDsRVDALIERVDSQIDEIT 381
                                    678899999999999999988887776555555666644.5555555269*************98 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                         PMC2NT  64 dveekfksvvdvvDsllEka 83 
                                    +  e+ ++ v  +Ds +E++
  gene816|gene816|rna815|rna815 447 E--ENIRNAVRYIDSAIESI 464
                                    2..46777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (655 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4443.98
//
Query:       gene817|gene817|rna816|rna816  [L=271]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-34  119.8   0.6    3.6e-32  112.0   0.6    2.8  1  Tub       Tub family


Domain annotation for each model (and alignments):
>> Tub  Tub family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.6     2e-36   3.6e-32      62     240 ..     126     265 ..     107     266 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 2e-36
                            Tub  62 srdsesyiGklrsnflgtkftlydkgvspkksaakesakvkkekvrkelaavvYelnvlgtrgprkmkvlipsiekkvev 141
                                    ++++e+ +G l+sn++gtk++ y+ +                    k + ++ Y +++++ rgpr+++v+   i      
  gene817|gene817|rna816|rna816 126 EQNNEEKVGYLKSNLFGTKYIFYQGE--------------------KAVLEIRYATSIFKRRGPRSFSVMFMGIL----- 180
                                    67889999************999876....................346789*******************9994..... PP

                            Tub 142 spedeeeslqeetkkeeesdllvlknksprwneqlqayvLnFrgRvtvaSvKNfqLvaaedeekvilqfGkvgkdvFtmD 221
                                                   ++ ++++v+knk+p +n ++++y LnF+gRvt +SvKNfqL++  +  +v l fGkv++ ++ +D
  gene817|gene817|rna816|rna816 181 --------------GSSLNEPVVMKNKEPYYNAETNSYSLNFNGRVTTPSVKNFQLIHPLEPTYVTLTFGKVSRFKYILD 246
                                    ..............3444579*********************************************************** PP

                            Tub 222 yryPlsalqAFaiclssfd 240
                                    y+yP s +qAFai+l+++d
  gene817|gene817|rna816|rna816 247 YTYPWSGVQAFAIALAALD 265
                                    ****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1956.72
//
Query:       gene818|gene818|rna817|rna817  [L=388]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-27   94.8   6.7    4.3e-05   24.1   0.3    7.3  7  Sel1      Sel1 repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.3   2.4e-09   4.3e-05       2      38 .]      97     132 ..      96     132 .. 0.88
   2 !   15.5   0.0   1.2e-06     0.021       5      37 ..     137     167 ..     133     168 .. 0.93
   3 !    7.2   0.0   0.00047       8.4       3      35 ..     171     202 ..     169     205 .. 0.85
   4 !    9.1   0.1   0.00012       2.2       5      37 ..     213     246 ..     212     247 .. 0.71
   5 !   18.3   0.1   1.5e-07    0.0027       3      37 ..     250     283 ..     248     284 .. 0.90
   6 !    9.9   0.0   6.6e-05       1.2       7      38 .]     291     322 ..     285     322 .. 0.82
   7 !    7.6   0.0   0.00037       6.6       2      32 ..     324     352 ..     323     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.4e-09
                           Sel1   2 eAmyrLGmfylylnGl.gvpkDpekAiewyekAAeqGd 38 
                                    eA   +G  + y++Gl g+ kD ++Ai +y  AA+q++
  gene818|gene818|rna817|rna817  97 EAETYMG--LGYEFGLfGLRKDGRLAISYYSSAARQNH 132
                                    6777777..666****88******************98 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-06
                           Sel1   5 yrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                    +r+G  +++++G g  k+ + A+ +y+ +A++G
  gene818|gene818|rna817|rna817 137 FRMG--QCLEKGVGKTKNHRHALDFYRCSAKLG 167
                                    8***..********999**************99 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.00047
                           Sel1   3 AmyrLGmfylylnGl.gvpkDpekAiewyekAAe 35 
                                     m+++G ++   nG+ g +kD ++++ ++++A +
  gene818|gene818|rna817|rna817 171 GMHAYGSVL--INGDiGSKKDLQSGLFYLKLAVR 202
                                    588999666..9***99**************976 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00012
                           Sel1   5 yrLGmfylylnGl..g.vpkDpekAiewyekAAeqG 37 
                                    y+L+ +y  +  +    + +D e A+++y k Ae++
  gene818|gene818|rna817|rna817 213 YDLAQIY--ESTTapSeIQADDEYAFRLYLKGAELD 246
                                    7777444..33335443677**************97 PP

  == domain 5  score: 18.3 bits;  conditional E-value: 1.5e-07
                           Sel1   3 AmyrLGmfylylnGlg.vpkDpekAiewyekAAeqG 37 
                                    ++yr++   +y+ G    +k   +A+ wy++A  +G
  gene818|gene818|rna817|rna817 250 CQYRVA--RCYELGELkQEKSLPLAVDWYRRASLLG 283
                                    79****..999****778889***********9887 PP

  == domain 6  score: 9.9 bits;  conditional E-value: 6.6e-05
                           Sel1   7 LGmfylylnGl.g.vpkDpekAiewyekAAeqGd 38 
                                    +    ++++G  g v ++ ++ + w  kAA +G+
  gene818|gene818|rna817|rna817 291 YS--RILFTGIeGaVQPNLKESFFWALKAAVKGH 322
                                    55..56699**999****************6665 PP

  == domain 7  score: 7.6 bits;  conditional E-value: 0.00037
                           Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewyek 32 
                                     A++ ++  ++ ++G g pk+  +A+ wy  
  gene818|gene818|rna817|rna817 324 QAAFSVA--EFIETGCGMPKNTFLALWWYTI 352
                                    6889999..66699999************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2858.28
//
Query:       gene819|gene819|rna818|rna818  [L=155]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   12.8   2.7       0.14   12.1   0.8    2.0  2  PX        PX domain
       0.16   12.5   2.8        3.4    8.3   0.5    2.3  2  SKICH     SKICH domain


Domain annotation for each model (and alignments):
>> PX  PX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.058   5.2e+02      58      81 ..      38      69 ..      29      92 .. 0.57
   2 ?   12.1   0.8   1.6e-05      0.14      33      53 ..      93     113 ..      67     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.058
                                   STSTSSSTSGSSSSS........CTTSHHHHH CS
                             PX 58 vkiPplPkkvlfgsv........rkkdeefie 81
                                   v+ P++P+k++ ++         +++++e+++
  gene819|gene819|rna818|rna818 38 VSHPTIPDKKIKYRLcytkssgyESESNEVLR 69
                                   56788888888776577777776333333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.6e-05
                                    SEEEEEEEHHHHHHHHHHHHH CS
                             PX  33 kewtvkRrYsdFeeLhskLlr 53 
                                    k+ +++ +Ys+F +Lh+++++
  gene819|gene819|rna818|rna818  93 KRLKIYVKYSEFLKLHKEIEK 113
                                    6889*************9987 PP

>> SKICH  SKICH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0063        56      62      91 ..      31      58 ..       9      68 .. 0.73
   2 ?    8.3   0.5   0.00038       3.4      41      87 ..      92     143 ..      87     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0063
                          SKICH 62 eeekqvlfkaselpkeekeeeYqlvYvskk 91
                                   e +k v++++ ++p++  + +Y l+Y +++
  gene819|gene819|rna818|rna818 31 EYKKIVYVSHPTIPDK--KIKYRLCYTKSS 58
                                   4445555555555555..479*****9865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00038
                          SKICH  41 fkslkdyvtyvwv.....keeeeeeseeekqvlfkaselpkeekeeeYqlvY 87 
                                    fk lk yv y        + e+ ++   +++++fk s +p++ keeeY+l+Y
  gene819|gene819|rna818|rna818  92 FKRLKIYVKYSEFlklhkEIEKVNNDLFTCNYTFKFSFIPSSYKEEEYVLLY 143
                                    677777888766667665446677777889************667******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1032.98
//
Query:       gene820|gene820|rna819|rna819  [L=246]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.4   0.9      0.039   14.0   0.9    1.1  1  DUF2514   Protein of unknown function (DUF2514)


Domain annotation for each model (and alignments):
>> DUF2514  Protein of unknown function (DUF2514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.9   2.2e-06     0.039      36     117 ..     146     230 ..     123     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-06
                        DUF2514  36 rdaedsqakviaeeaaReeeqrrkaaaekavkdaqekaaaAradavg...aaaaadrLrqeaakLaaaksavaadsaaaa 112
                                     ++ +++ k  a   + + e ++k ++  +v ++ +++++A+++a +   a+ ++d++ ++a++++  +++ ++d   a+
  gene820|gene820|rna819|rna819 146 SKSMEKKNKSKASPSVEDSESKKKLSNIAVVVKSSQEISSAKDGAEDgssAKDTKDSIEKQAEEIEEVAEQCPSDRKPAN 225
                                    5667788888999999999*********9************998865222777899*********999999999999999 PP

                        DUF2514 113 rgkaa 117
                                    +g++ 
  gene820|gene820|rna819|rna819 226 KGNTM 230
                                    99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1877  (0.104691); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1529.28
//
Query:       gene82|gene82|rna82|rna82  [L=261]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.23   12.2   4.5        5.4    7.8   0.0    3.8  3  YccF      Inner membrane component domain


Domain annotation for each model (and alignments):
>> YccF  Inner membrane component domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0003       5.4       5      26 ..      67      88 ..      66     102 .. 0.92
   2 ?    1.0   0.0     0.039     7e+02      13      45 ..     122     155 ..     117     156 .. 0.62
   3 ?    1.3   1.6     0.033   5.8e+02      16      39 ..     194     215 ..     185     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0003
                       YccF  5 lWlllfGwwlaliyllaglllf 26
                               l++l+ G+ +a iy+ ++ l++
  gene82|gene82|rna82|rna82 67 LYFLCYGFTMAAIYVSVSNLCM 88
                               79**************999886 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.039
                       YccF  13 wlaliyllaglllfitii.........gipygrvlfklakyl 45 
                                +la+ ++l+        i         +  yg ++ k+a++l
  gene82|gene82|rna82|rna82 122 FLAVFHFLI--------IhrlmsppieSDDYGQAYKKIAWLL 155
                                344444444........2344444558888999999999986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.033
                       YccF  16 liyllaglllfitiigipygrvlf 39 
                                l +l  +++++     ip+g+ ++
  gene82|gene82|rna82|rna82 194 LSCLSKAIICCSS--LIPIGKSHW 215
                                5677777777754..677777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1540.58
//
Query:       gene821|gene821|rna820|rna820  [L=266]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1629.32
//
Query:       gene822|gene822|rna821|rna821  [L=253]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        1.5    8.1   6.6        0.4   10.0   2.0    2.1  2  DUF3810      Protein of unknown function (DUF3810)


Domain annotation for each model (and alignments):
>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3     0.055   9.9e+02      33      36 ..      85      88 ..      51     138 .. 0.47
   2 ?   10.0   2.0   2.2e-05       0.4      26      90 ..     152     250 ..     132     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.055
                        DUF3810 33 illv 36
                                   ++l 
  gene822|gene822|rna821|rna821 85 AVLG 88
                                   2222 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 2.2e-05
                        DUF3810  26 ellivllillvilylvlaiklkkrkkkkkrllk....................................vllrvllvllv 69 
                                    e ++++ il v+l++v++i l  r ++++rll                                     ++  +++  ++
  gene822|gene822|rna821|rna821 152 ESTLYAGILGVVLFFVYII-L-GRMREDSRLLVsmakadvsslgfaafvnvwgvldlfggmhglnanegLFSGFIIGGII 229
                                    5567778888888888888.2.233333344444778999999999**********************999999****** PP

                        DUF3810  70 vyflftllwglnYyreplser 90 
                                    ++++ft+++ +nY++e  +e+
  gene822|gene822|rna821|rna821 230 ILMVFTIVFVMNYFQEWTEEK 250
                                    **************9987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1364  (0.0760779); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1590.14
//
Query:       gene823|gene823|rna822|rna822  [L=582]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.1   5.0       0.59   10.1   0.8    2.7  3  Suf              Suppressor of forked protein (Suf)
       0.33   10.9   4.6        0.3   11.1   1.9    2.2  2  Coatomer_b_Cpla  Coatomer beta subunit appendage platform


Domain annotation for each model (and alignments):
>> Suf  Suppressor of forked protein (Suf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.53   4.7e+03     146     163 ..     206     223 ..     198     228 .. 0.88
   2 ?    6.1   0.2    0.0011       9.5      67     139 ..     361     435 ..     355     479 .. 0.84
   3 ?   10.1   0.8   6.6e-05      0.59      88     128 ..     526     567 ..     516     581 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.53
                            Suf 146 fvdRYklknldpikkrel 163
                                     ++RYk+ +  ++++re+
  gene823|gene823|rna822|rna822 206 TSNRYKVGDTVECAVREV 223
                                    579***********9996 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0011
                            Suf  67 pedeefvlkYldyLislnddnnaRvlfekvvsklskekeakel...ykkfleyestfgdlssilklekRmeelfpe 139
                                    p +   v+kY++y i++ ++     +f + +  +  e+   +l   +  +l +++ +  l+ i  lek +++ f +
  gene823|gene823|rna822|rna822 361 PGEAMPVIKYIQYKIEIGEEGGPEKVFHEFLPVIEGEE-KDKLcisFVNYLMFAKDMECLKTIRRLEKICSQRFLD 435
                                    56667799**************************9999.55553347788899999999**********9999977 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 6.6e-05
                            Suf  88 naRvlfekvvsklskekeakelykkfleyestfg.dlssilk 128
                                     +R+lf +vv k  k  ++ke yk +leye++ + ++++++ 
  gene823|gene823|rna822|rna822 526 YLRSLFRRVVDKKWKVSDMKEFYKMWLEYEKENNgNVEEVKL 567
                                    68**********999999************976636666654 PP

>> Coatomer_b_Cpla  Coatomer beta subunit appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.29   2.6e+03      52      77 ..     405     430 ..     397     482 .. 0.68
   2 ?   11.1   1.9   3.3e-05       0.3      24      60 ..     543     579 ..     535     581 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.29
                Coatomer_b_Cpla  52 eyleelvkktnmklltpeeeleeeae 77 
                                    ++++ l+ +  m++l+  ++le+ ++
  gene823|gene823|rna822|rna822 405 SFVNYLMFAKDMECLKTIRRLEKICS 430
                                    56777777777777776444444433 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.3e-05
                Coatomer_b_Cpla  24 seeeFremWaefeWEnkiavktkltdlkeyleelvkk 60 
                                    + +eF +mW e+e En+ +v+  +   key+e +++k
  gene823|gene823|rna822|rna822 543 DMKEFYKMWLEYEKENNGNVEEVKLRAKEYVESIKNK 579
                                    5689****************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 3521.05
//
Query:       gene824|gene824|rna823|rna823  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-24   86.7   0.0      2e-24   86.1   0.0    1.3  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    1.5e-13   49.9   0.0    2.2e-13   49.4   0.0    1.3  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0   2.3e-28     2e-24       1     112 []      45     154 ..      45     154 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2.3e-28
                                    EEEEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC....EEGGGCBESSSSC CS
                  RNA_pol_A_bac   1 VeieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge....vtagdlkledadv 76 
                                    Veie+n++vl DEv+aHrlgl+p+ s+ +l+   + +e+  +++ +++e+sv++++++  +++    v a+d+++ d+  
  gene824|gene824|rna823|rna823  45 VEIERNNTVLPDEVLAHRLGLVPIYSKRELK---YKEEC--SCSGFCSECSVVFEIDIVHTEDalrvVSARDIVC-DEGD 118
                                    89***********************888776...*****..8*****************99999***********.9999 PP

                                    EESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                  RNA_pol_A_bac  77 eivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                     +++ + +I kL+ +q l+ +++ +kGiGk hak+s
  gene824|gene824|rna823|rna823 119 VVIKSGPMITKLARDQGLKARCIGRKGIGKIHAKWS 154
                                    99*********************************8 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.0   2.4e-17   2.2e-13       1      68 [.      15     228 ..      15     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 2.4e-17
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                      RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea.................................................. 30 
                                    +f+l++ ++ ++NaLRril+sevp++ai+                                                   
  gene824|gene824|rna823|rna823  15 KFTLSNATVGYANALRRILISEVPTIAIDMveiernntvlpdevlahrlglvpiyskrelkykeecscsgfcsecsvvfe 94 
                                    6999************************************************9999999999999999999999999999 PP

                                    ................................................................................ RF
                      RNA_pol_L  31 ................................................................................ 30 
                                                                                                                    
  gene824|gene824|rna823|rna823  95 idivhtedalrvvsardivcdegdvviksgpmitklardqglkarcigrkgigkihakwspvsaisfeydkdnvrretny 174
                                    99999999999999999999999888888888888888888888888888888888888866666666655555555555 PP

                                    ..............xxxxxx.....xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  31 ..............pvvkvn.....tdkdklilevetd.gslkPeealkeAlkiLkek 68 
                                                             ++ dk+++ ve   g   P  +++e+lkiLkek
  gene824|gene824|rna823|rna823 175 wfeesieeewpgvkQ----GeanpmQKVDKIHMCVEVIeGGAGPIAIVLEGLKILKEK 228
                                    555555555544440....144455899********988999***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1610.47
//
Query:       gene825|gene825|rna824|rna824  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-06   27.6   0.6      5e-06   26.2   0.6    1.6  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.037   14.2   0.0      0.043   13.9   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
       0.12   13.1   0.0       0.26   12.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
       0.51    9.7   2.2       0.82    9.0   2.2    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.6   1.1e-09     5e-06      20     109 ..      10      90 ..       3      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.1e-09
                                    HHHHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS- CS
                            MTS  20 sklLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekk 97 
                                    +  L++ ++ke  + + vlDlG+ +G+l+  l+k++   +v+  d + +Al+         +  +++v  ++l+ +++++
  gene825|gene825|rna824|rna824  10 TYTLMDVMEKEdlEMKIVLDLGTSTGILTECLKKKN---TVVSSDLNIKALQN--------HNGGNLVRANLLDSINQQS 78 
                                    567999999998666679***********9998854...57999****99963........33378999*********** PP

                                    EEEEEE---STT CS
                            MTS  98 fdlivsNPPfha 109
                                    +d++v NPP+  
  gene825|gene825|rna824|rna824  79 VDVVVFNPPYVP 90 
                                    *********865 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.7e-06     0.043      11      80 ..      15      80 ..       9     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                                   HHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..HHHTTEEEECS-CCCSSHHHHHC CS
                           FtsJ 11 eidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..aplpgvttiqgditdpetiekik 80
                                   ++ ek + + + k v+Dlg ++G  +++l ++      vv+ Dl+    ++++g ++++++ +d  +++ + 
  gene825|gene825|rna824|rna824 15 DVMEKED-L-EMKIVLDLGTSTGILTECLKKK----NTVVSSDLNIKalQNHNGGNLVRANLLDSINQQSVD 80
                                   4555555.3.5678***************999....35******6663467799999999999888887664 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.9e-05      0.26       1      38 [.      27      61 ..      27      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-05
                                   EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHH CS
                Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaar 38
                                   vLdlG+ tG lt+ l k+    +v+  D++ ++l++ +
  gene825|gene825|rna824|rna824 27 VLDLGTSTGILTECLKKK---NTVVSSDLNIKALQNHN 61
                                   9**************998...79******998887644 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.2   0.00018      0.82     152     233 ..      14      85 ..       8      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                           PrmA 152 lealeklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadviv 231
                                    + ++ek   e + vlD+Gt +GiL+   +k   ++vv  D++  A++   +    N v+a+l     +++ + +++dv+v
  gene825|gene825|rna824|rna824  14 MDVMEKEDLEMKIVLDLGTSTGILTECLKK--KNTVVSSDLNIKALQ---NHNGGNLVRANL----LDSINQ-QSVDVVV 83 
                                    678899999999************855544..667888888766654...334557777766....244444.7888888 PP

                           PrmA 232 aN 233
                                     N
  gene825|gene825|rna824|rna824  84 FN 85 
                                    77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1016.98
//
Query:       gene826|gene826|rna825|rna825  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-34  119.4   0.0    2.2e-34  119.1   0.0    1.0  1  tRNA-synt_His  Histidyl-tRNA synthetase
    0.00069   19.2   0.0     0.0015   18.1   0.0    1.6  1  tRNA-synt_2d   tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.0   2.5e-38   2.2e-34       1     296 [.       9     309 ..       9     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.5e-38
                                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHHHS-EEE-TTSSEEEE-SSSHHHHHHHHH CS
                  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedldqtfklvDqsgrllglRaDiTpqvaRiaa 80 
                                    g+ d  p++    ee+ +++ ++f  +G  ++s+P++E+   l+++ ged++ ++ l+Dq g+  +lR D+T+  aR+ a
  gene826|gene826|rna825|rna825   9 GTTDESPRQCFLYEEIIEKIRGVFVLYGAVPISTPTFEMKSILTNKYGEDTKLIYDLKDQGGEICALRYDLTVPFARYLA 88 
                                    5678889999999******************************************************************* PP

                                    HHHHTSS-EEEEEEEEEEESS-SS..TT--CCEEEEEEEEESS-.SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHH CS
                  tRNA-synt_His  81 hrlnrerplRlcYaGsvlrtrpdg..lgrsreplQvGaEliGae.gleadlEvlslllealeaaagvkelrldlghvglv 157
                                     +   +++ R+  +G+v+r+ + +   gr re++Q+   + G+   + ad+Ev+s +  +l+  +++ e+++++++ +++
  gene826|gene826|rna825|rna825  89 SNK-IRKMKRY-QIGRVYRRDQPSivKGRLREFMQADFDIAGECiRMMADAEVISCVDRILK-EFEIGEFKIKVNDRRIL 165
                                    974.6666665.69****9888774568**************9989***************7.***************** PP

                                    HHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHH...CCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTH.HHHHHHH CS
                  tRNA-synt_His 158 ralleaaglsesleeallaalarkdlaelkelaa...eaglkealrellkal.elygdaevleealealaaa.palqaal 232
                                    +++lea+g++ +   ++ + +++ +  + k++ +   ++gl+e+++++++++ e++g+++vl+ ++e  a++ +++++ +
  gene826|gene826|rna825|rna825 166 TSILEAVGVPCESYGTVCSTIDKIEKMSWKDISKefiQKGLSEHQVNMIRKYmEMSGKENVLKLLRECPAYEiERCKEGV 245
                                    *****************999887766666655552225799*****************9999998774333236788888 PP

                                    HHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-S.S-SEEEEEECTTTGGGT- CS
                  tRNA-synt_His 233 deleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvg.qaiarGGrYdelgaafgr 296
                                    +++eel + ++ l+  e ++ +D+++ rg++YytG++ +a   g++   + +GGrYd+l +++g+
  gene826|gene826|rna825|rna825 246 HDMEELFKFCRILG-CEGSLVMDVSLARGLDYYTGMILEAEYIGKSvGSVIGGGRYDNLTENLGE 309
                                    99999999999987.7899*******************9955555527***********999875 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.6e-07    0.0015      79     160 ..      71     158 ..      12     163 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-07
                                    ESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST..-SSSB-SEEEEEEEEEEETT--H...HHHHHHHHHHHHHH CS
                   tRNA-synt_2d  79 ekllLRthttavqirtl.ekkkppikiisigrvfRrda..vDathlaeFhqveglvvdenvsl...adlkgvleellkkl 152
                                    e   LR   t   +r+l ++k   +k   igrv+Rrd+  + + +l eF+q+++ +++e +++   a+++ +++ +lk++
  gene826|gene826|rna825|rna825  71 EICALRYDLTVPFARYLaSNKIRKMKRYQIGRVYRRDQpsIVKGRLREFMQADFDIAGECIRMmadAEVISCVDRILKEF 150
                                    4567999999999****65566899*************6666789**************999933334566667777777 PP

                                    CTST.EEEE CS
                   tRNA-synt_2d 153 fgae.vkvr 160
                                     +   +k++
  gene826|gene826|rna825|rna825 151 -EIGeFKIK 158
                                    .44324554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1983.45
//
Query:       gene827|gene827|rna826|rna826  [L=874]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 5574.06
//
Query:       gene828|gene828|rna827|rna827  [L=141]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 866.20
//
Query:       gene829|gene829|rna828|rna828  [L=136]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-21   76.9   0.4      2e-21   76.7   0.4    1.0  1  ADK              Adenylate kinase
    2.2e-07   31.4   0.8    2.9e-07   31.0   0.8    1.2  1  AAA_17           AAA domain
    0.00053   19.7   0.0    0.00092   18.9   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.4   3.3e-25     2e-21      35     150 ..       1     113 [.       1     114 [. 0.96

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 3.3e-25
                                    HHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEESB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  35 vksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllDGfPRtveqaealeelleeekvkldlvleldvpee 114
                                    +k++++  + ++ev++ g+l pde+v+klv +++++    ++++lDG+PR +eqae+l +       ++dlv+ +dv+e+
  gene829|gene829|rna828|rna828   1 MKKNSKEAEIVREVVNSGRLAPDELVNKLVLKKIRSM---DKYILDGYPRRIEQAEMLGD-------DVDLVIFIDVDED 70 
                                    578999999***********************99977...99****************99.......99*********** PP

                                    HHHHHHHT.......GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                    xxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK 115 vlveRltg.......DneetvkkRletykkqtkplidyykkkg 150
                                    v v+R+ g       D ee  +kR e+y  +t+p+++ y+k+g
  gene829|gene829|rna828|rna828  71 VSVRRICGrnqgrddDVEEVARKRHEVYLGETAPVVELYRKQG 113
                                    **************9999999*******************997 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.8   4.9e-11   2.9e-07      43     134 ..      12      90 ..       1      92 [. 0.81

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 4.9e-11
                                    HHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                         AAA_17  43 rdemrklpleekkelqkeaaekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                    r+ ++ + l +++ + k++ +ki+ +   +++++dg+pr  eqa++l        ++  +d++i++++d+++ ++r    
  gene829|gene829|rna828|rna828  12 REVVNSGRLAPDELVNKLVLKKIRSM---DKYILDGYPRRIEQAEMLG-------DD--VDLVIFIDVDEDVSVRRICG- 78 
                                    455567889999***********986...78********999888543.......34..59*********988888877. PP

                                    TTST-TS-SHHH CS
                         AAA_17 123 rtrgrdddnees 134
                                    r++grddd ee+
  gene829|gene829|rna828|rna828  79 RNQGRDDDVEEV 90 
                                    79******9986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.5e-07   0.00092     118     185 .]      59     131 ..      47     131 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.5e-07
                                    -SEEEEEESSHHHHHTSCCTTSS.TTTSHHHHHHHHHHHH....HHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
                Thymidylate_kin 118 PdltflldvdpevalkRlakrde.ldeeeeeqldflrkvr....erylelakederiliidasksieevheeI 185
                                     dl++++dvd++v+++R+  r++ +d+++ee  ++ ++v     +   el+++++++l+++  +s e v +eI
  gene829|gene829|rna828|rna828  59 VDLVIFIDVDEDVSVRRICGRNQgRDDDVEEVARKRHEVYlgetAPVVELYRKQGKLLTVNGHDSPETVFSEI 131
                                    59*********************97777776666666654111145889999999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 946.04
//
Query:       gene830|gene830|rna829|rna829  [L=744]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 4597.87
//
Query:       gene83|gene83|rna83|rna83  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-07   31.7   4.4    3.8e-07   30.3   4.4    1.8  1  EB1             EB1-like C-terminal motif
    4.9e-05   23.1   1.4    0.00011   21.9   1.4    1.7  1  PKcGMP_CC       Coiled-coil N-terminus of cGMP-dependent prot
     0.0032   17.5   0.6     0.0063   16.5   0.6    1.4  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
     0.0055   17.1   2.2     0.0076   16.6   1.1    1.8  2  V-SNARE         Vesicle transport v-SNARE protein N-terminus
      0.008   16.1   0.9      0.014   15.4   0.9    1.4  1  SPATA24         Spermatogenesis-associated protein 24
  ------ inclusion threshold ------
       0.02   15.1   1.3      0.034   14.3   1.3    1.3  1  Fib_alpha       Fibrinogen alpha/beta chain family
        1.5    9.1   5.4       0.17   12.1   1.0    1.8  2  ABC_tran_CTD    ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> EB1  EB1-like C-terminal motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   4.4   1.5e-10   3.8e-07       2      41 .]     197     234 ..     196     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.5e-10
                                HHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHS- CS
                        EB1   2 ekERdFYFsKLRdIEilcqtepeleedlpivkkikkILYa 41 
                                ekERdFYF+KL  +E +    +++  d+++ + + +ILY+
  gene83|gene83|rna83|rna83 197 EKERDFYFKKLFTVEKYFL--EKKGLDESLKNDVLSILYE 234
                                9*****************4..56666999**********5 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.4   4.5e-08   0.00011       2      27 ..     140     165 ..     139     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.5e-08
                  PKcGMP_CC   2 llllKDERIRELEkrlaekdeEIqEL 27 
                                ++ +KD RIRELE  l++ ++ I++ 
  gene83|gene83|rna83|rna83 140 IVDAKDNRIRELESTLSRMEDRITQM 165
                                799********************985 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.6   2.5e-06    0.0063      83     125 ..     135     177 ..     122     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.5e-06
             CENP-F_leu_zip  83 eeLekelqkkqervseLeslnsslenlleekEqekvqmkeesk 125
                                +++++ +  k +r+ eLes+ s +e  + + E ek+ ++e++ 
  gene83|gene83|rna83|rna83 135 KNIKEIVDAKDNRIRELESTLSRMEDRITQMETEKRTIEEQAT 177
                                56677788999****************************9975 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.8   9.8e+03      34      50 ..       6      22 ..       2      24 .. 0.71
   2 !   16.6   1.1     3e-06    0.0076       5      52 ..     127     173 ..     123     179 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.8
                    V-SNARE 34 ldeaeelldqMelEvrn 50
                                 e+ e ++++ +E++ 
  gene83|gene83|rna83|rna83  6 RRELIEWIRSLGIEISA 22
                               56778888888888875 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3e-06
                    V-SNARE   5 laeiksklarlsslageerkaalreiekkldeaeelldqMelEvrnlp 52 
                                +++ +s ++++++   + +   +re+e+ l  +e+ + qMe E r + 
  gene83|gene83|rna83|rna83 127 VNSHCSGCKNIKEI-VDAKDNRIRELESTLSRMEDRITQMETEKRTIE 173
                                55666777777743.68****************************984 PP

>> SPATA24  Spermatogenesis-associated protein 24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.9   5.3e-06     0.014      98     152 ..     103     161 ..      71     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.3e-06
                    SPATA24  98 gsvkekaarEskkadqLkekCs.evese...ierqeDilnakeneikeLkqrlskqkev 152
                                +++ e+  rEs++ + L +  s  v+s+   ++  ++i++ak+n+i+eL+  ls+  + 
  gene83|gene83|rna83|rna83 103 KNMGERKPRESTRDESLGTSASsSVNSHcsgCKNIKEIVDAKDNRIRELESTLSRMEDR 161
                                67889999*********88766467776222578899***************9987664 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.3   1.3e-05     0.034      57     125 ..     101     169 ..      81     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                HHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Fib_alpha  57 lvkeikdslrekqkskkdn..dnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdi 125
                                ++k++ +   +++++ +++  +++ +++++++     ++ke +da+ ++ir+L ++l++ e +i+++e++ 
  gene83|gene83|rna83|rna83 101 YSKNMGERK-PRESTRDESlgTSASSSVNSHCS-GCKNIKEIVDAKDNRIRELESTLSRMEDRITQMETEK 169
                                334443332.22222222234666666677777.7899*****************************9875 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2         4     1e+04      17      29 ..      13      25 ..       3      26 .. 0.59
   2 ?   12.1   1.0   6.8e-05      0.17       8      39 ..     149     186 ..     143     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4
               ABC_tran_CTD 17 IeaLEeeiaelea 29
                               I +L  ei+++e+
  gene83|gene83|rna83|rna83 13 IRSLGIEISAIEE 25
                               5566666666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 6.8e-05
               ABC_tran_CTD   8 rele....eleaeIeaLEeeiaelea..eladpelysd 39 
                                rele    ++e++I ++E+e+ ++e+   ++ p  ++d
  gene83|gene83|rna83|rna83 149 RELEstlsRMEDRITQMETEKRTIEEqaTISGPKGFED 186
                                566633337***************99334555655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1320.73
//
Query:       gene831|gene831|rna830|rna830  [L=272]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-09   35.7   1.9    2.1e-08   34.6   1.9    1.6  1  PH               PH domain
    1.8e-05   25.1   3.5    1.8e-05   25.1   3.5    1.9  2  PH_11            Pleckstrin homology domain
     0.0026   18.0   0.4     0.0062   16.8   0.4    1.7  1  PH_8             Pleckstrin homology domain
  ------ inclusion threshold ------
      0.042   13.6   0.2      0.084   12.6   0.0    1.5  2  Glyco_transf_10  Glycosyltransferase family 10 (fucosyltransf
       0.16   11.9   2.1       0.31   11.0   2.1    1.4  1  Toxin_21         Spider insecticidal peptide
       0.23   11.4   3.2       0.78    9.7   2.4    2.2  2  RsgI_N           Anti-sigma factor N-terminus


Domain annotation for each model (and alignments):
>> PH  PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   1.9   7.2e-12   2.1e-08       2     104 ..     169     267 ..     168     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 7.2e-12
                                    EEEEEEEEETSSSSCSEEEEEEEEETTE.EEEESSTTCTTESSEEEEEESTTEEEEEEEC..TTSSSSTSEEEEEESTSS CS
                             PH   2 vkeGwLlkkgsgkkkswkkrwfvLkdse.llyykndksekdkepkgsislsncevvevva..tedpkrkfcfelrivern 78 
                                    v eGw++kk+  ++  w++++fvL+++  l yyk+d    +   kg  ++++ +  ++ +  +e+ ++++ +++ ++   
  gene831|gene831|rna830|rna830 169 VAEGWIWKKRRIFSCFWHQKYFVLTKDGtLKYYKAD---GRRHAKGNWNMKESTEIRHYNlsSEENTHPCRIMVFFS--- 242
                                    569*******99988**********5555*******...77777888888777777666666779999999999999... PP

                                    STEEEEEEESSHHHHHHHHHHHHHHH CS
                             PH  79 gsrtyllqasseeerkeWikaiqsai 104
                                     ++++ll+++    +  W++ +++ai
  gene831|gene831|rna830|rna830 243 -DHSFLLAFDERNTKDYWVEKLNRAI 267
                                    .68********************997 PP

>> PH_11  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.7     5e+03      63      77 ..      45      59 ..      13      82 .. 0.55
   2 !   25.1   3.5     6e-09   1.8e-05       2     104 ..     171     265 ..     170     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                          PH_11 63 idsirssksddllle 77
                                   +++ ++++ +++++e
  gene831|gene831|rna830|rna830 45 VKEMNGEEDTRIDTE 59
                                   333333333333333 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 6e-09
                          PH_11   2 kGylkkkgsk...aWkrrwfavlkdgvLeyYksekkkvvkhviklSngseaklkadlisaalfkidsirssksddlllei 78 
                                    +G+++kk+      W +++f++ kdg L+yYk+++ +            ++ ++++ +   +   + +  ++   +++ +
  gene831|gene831|rna830|rna830 171 EGWIWKKRRIfscFWHQKYFVLTKDGTLKYYKADGRRH----------AKGNWNMKESTEIRH-YNLSSEENTHPCRIMV 239
                                    79****99889999******99***************9..........788898876655444.3333335555677777 PP

                          PH_11  79 stetkifflkgdsneeteeWvealke 104
                                    + +   f l+ d+++++  Wve+l +
  gene831|gene831|rna830|rna830 240 FFSDHSFLLAFDERNTKDYWVEKLNR 265
                                    77788888***************987 PP

>> PH_8  Pleckstrin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   2.1e-06    0.0062       1      47 [.     172     217 ..     172     266 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                           PH_8   1 gillkkrrkklqgyakRfFvLdlksstlsYyrddnssalrgkiplsl 47 
                                    g++ kkrr     + +++FvL  k +tl+Yy+ d   + +g+  +++
  gene831|gene831|rna830|rna830 172 GWIWKKRRIFSCFWHQKYFVL-TKDGTLKYYKADGRRHAKGNWNMKE 217
                                    7999*****************.9********9876654444444433 PP

>> Glyco_transf_10  Glycosyltransferase family 10 (fucosyltransferase) C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       3.2   9.5e+03      30      47 ..      61      80 ..      54      87 .. 0.59
   2 ?   12.6   0.0   2.8e-05     0.084      44      80 ..     231     267 ..     206     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.2
                Glyco_transf_10 30 evdvyGkcgklkv..eelse 47
                                   +++  G+++++k+  +++++
  gene831|gene831|rna830|rna830 61 KIESTGEAFETKAdeRSHEK 80
                                   67778888877764222223 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.8e-05
                Glyco_transf_10  44 elsekeveelikkykFYLafEnsickDYiTeKlwnal 80 
                                    ++++  ++   +++ F Laf++ + kDY  eKl +a+
  gene831|gene831|rna830|rna830 231 NTHPCRIMVFFSDHSFLLAFDERNTKDYWVEKLNRAI 267
                                    3334445556899********************9776 PP

>> Toxin_21  Spider insecticidal peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.1    0.0001      0.31       4      17 ..      78      91 ..      76      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                       Toxin_21  4 kryPCsNaddCCsG 17
                                       Cs +++CC+G
  gene831|gene831|rna830|rna830 78 HEKECSESKECCGG 91
                                   5667*********9 PP

>> RsgI_N  Anti-sigma factor N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.4   0.00026      0.78       1      23 [.       6      28 ..       6      29 .. 0.93
   2 ?   -0.9   0.0      0.55   1.6e+03      10      25 ..     191     206 ..     187     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00026
                         RsgI_N  1 leikkkkaivlTpdGeFikikrk 23
                                   +++kkk +i+ +++Ge++ + +k
  gene831|gene831|rna830|rna830  6 MRKKKKNIIIINDKGEMLSVTKK 28
                                   89****************99876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.55
                         RsgI_N  10 vlTpdGeFikikrkgg 25 
                                    vlT dG  +  k +g 
  gene831|gene831|rna830|rna830 191 VLTKDGTLKYYKADGR 206
                                    9*****8887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1544.21
//
Query:       gene832|gene832|rna831|rna831  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-51  174.5  12.1    3.9e-51  173.7  12.1    1.3  1  DUF5094   Domain of unknown function (DUF5094)
  ------ inclusion threshold ------
      0.054   13.3   0.2       0.07   13.0   0.2    1.1  1  Bclt      Putative Bcl-2 like protein of testis
      0.056   12.8   1.3      0.078   12.3   0.1    1.7  2  Pkinase   Protein kinase domain
       0.28   11.3   6.4       0.41   10.8   6.4    1.2  1  CRA       Circumsporozoite-related antigen (CRA)


Domain annotation for each model (and alignments):
>> DUF5094  Domain of unknown function (DUF5094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7  12.1   8.8e-55   3.9e-51       1     178 []       5     169 ..       5     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 8.8e-55
                        DUF5094   1 rkrltlrtpkkstkkvskkknklssknlkekenvkvkeaeekkeekvtstkenkenekqdkd....sllkeikdieneli 76 
                                    rk++t++tp+k tk++                 vk+ +a++ ke+k+ +++++ e++  d++    ++l e+k+ e++li
  gene832|gene832|rna831|rna831   5 RKKITFKTPRKGTKTP-----------------VKDGHASDTKENKTPKIENKDEQKGLDSAsrykQILIEMKMKEEDLI 67 
                                    7999*********999.................5566666777777777777777666666667789************* PP

                        DUF5094  77 eaykeeNeyLrslknevlltskllGltiketgdtfivkykvekkeiekslkFeLkeedenYiYkliesknvdlpeyLsee 156
                                    e+yk+eNeyLrslk+++ll++k++G++i e++ +++v++++ +++i+k++ F L +ed++YiYkl+es+n++lp++Lsee
  gene832|gene832|rna831|rna831  68 ESYKKENEYLRSLKTDALLYKKFVGFDIVESNGCYEVTHEIVSNNITKFIRFVLTPEDSSYIYKLVESRNIELPDFLSEE 147
                                    ******************************************************************************** PP

                        DUF5094 157 isFekeqlkkFfykvmqiviek 178
                                    i+F+++q+k+Ff+kvm++vi+k
  gene832|gene832|rna831|rna831 148 ITFDECQIKTFFFKVMEAVITK 169
                                    *******************986 PP

>> Bclt  Putative Bcl-2 like protein of testis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   1.6e-05      0.07       2      45 ..      24      67 ..      23      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
                           Bclt  2 GnnsshkrtkvPkqarkekPPdmdkakrkkqffshlkrkkpslr 45
                                   G  s  k  k+Pk  +k+    +d a r kq++  +k k+  l 
  gene832|gene832|rna831|rna831 24 GHASDTKENKTPKIENKDEQKGLDSASRYKQILIEMKMKEEDLI 67
                                   677899*********************************98754 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.19   8.6e+02      23      55 ..      29      61 ..      15      89 .. 0.48
   2 ?   12.3   0.1   1.7e-05     0.078      51     111 ..     104     166 ..      99     168 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                                   TTEEEEEEEEECHCHCHHHH....HHHHHHHHHHHHH CS
                        Pkinase 23 tgkivAvKkikkekakkkke....kkvlrEikilkkl 55
                                   t++    K+ +k+++k  +     k++l E+k    +
  gene832|gene832|rna831|rna831 29 TKENKTPKIENKDEQKGLDSasryKQILIEMK----M 61
                                   55554555555544444444222222222222....2 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.7e-05
                                    HHHHHSCTTB--EEEEEEESSEEEEEEE--TTEB..HHHHHHHHSS--HHHHHHHHHHHHHHH CS
                        Pkinase  51 ilkklkhpnivrlyevfeekdelylvleyvegge..ladllerkgslseeeakkiakqilegl 111
                                    + +++ ++ni ++++++ ++++   +  +ve  +  l d+l+++ +++e+++k ++ +++e++
  gene832|gene832|rna831|rna831 104 VTHEIVSNNITKFIRFVLTPEDSSYIYKLVESRNieLPDFLSEEITFDECQIKTFFFKVMEAV 166
                                    567778899999999998855555555555555444************************997 PP

>> CRA  Circumsporozoite-related antigen (CRA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   6.4   9.1e-05      0.41      44      93 ..      27      76 ..       6      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                            CRA 44 kykknekevekaeekedeneedridvlkLikelekKeeeliivnKkkkkY 93
                                     +k++k+ + ++++e++  ++ + + +++ e++ Kee+li+  Kk + Y
  gene832|gene832|rna831|rna831 27 SDTKENKTPKIENKDEQKGLDSASRYKQILIEMKMKEEDLIESYKKENEY 76
                                   45677787777888889999*****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1115.65
//
Query:       gene833|gene833|rna832|rna832  [L=439]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.22   11.1   4.6       0.43   10.2   4.6    1.4  1  PTRF_SDPR  PTRF/SDPR family


Domain annotation for each model (and alignments):
>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   4.6   2.4e-05      0.43     130     236 ..     313     427 ..     288     437 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 2.4e-05
                                    .XXXXXXXXXXXXXX.XXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXX CS
                      PTRF_SDPR 130 eleeketeeeelekptidlssdeeeveveeeaeesraerlkrsslkkvdslKkaFs.........kenlektrqniekkv 200
                                    +l++ke +ee+++ +  +ls  +e+ e +e+  +s  +++k    k ++ +K   s           n+   ++  ++++
  gene833|gene833|rna832|rna832 313 KLKKKEDMEESTS-TLSSLSGSDEGREDKENDGDSIVDKMKERIAKYIECFKGSKSksifyaytsVINVMNHKKYCGRNL 391
                                    4556666666666.44888888888999************************9999888888877779999999****** PP

                                    XXXXXXXXXXXXXXX........XXXXX.......XX CS
                      PTRF_SDPR 201 nklgtkivtpErrekikqsk.ekikksltpnhskser 236
                                    + ++ k  ++Er e +k+ + +k k  +  +hsk  r
  gene833|gene833|rna832|rna832 392 EFIRRKASKKERVESMKNGRaDKEKYCG-GKHSKGRR 427
                                    ****************987625544444.66666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3153.26
//
Query:       gene834|gene834|rna833|rna833  [L=423]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2962.40
//
Query:       gene835|gene835|rna834|rna834  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-52  177.3   6.6    5.7e-44  150.8   1.6    3.0  2  PTPA      Phosphotyrosyl phosphate activator (PTPA) protein


Domain annotation for each model (and alignments):
>> PTPA  Phosphotyrosyl phosphate activator (PTPA) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.2     3e-10   5.4e-06      12      90 ..       5      76 ..       1      80 [. 0.87
   2 !  150.8   1.6   3.2e-48   5.7e-44     118     299 ..      80     236 ..      74     238 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3e-10
                                   HHHCCCHHHHHHHHHHHHHHHHHT........T-SS-HHHHHHHHHHHHHCCCTS---SS--SSS-THHHHHHHHHHHH CS
                           PTPA 12 ekfkkSkayadilefisrlneavkgkkleeeeeasesvekllklLdeleelideippeeqpsRfGnkafrtwhdrleer 90
                                    +f++++aya+i +fi  + +++k++k +       + ++  +lL+++ e+i+e++++++p+R+ n a +  ++r+ ++
  gene835|gene835|rna834|rna834  5 IDFTETEAYARIYNFILMVDDSIKSSKQN-------QSRQHRDLLASIAEIIKETEKDQTPQRYANAAAKIVFKRICDE 76
                                   579*********************88775.......3467889*************************99888887665 PP

  == domain 2  score: 150.8 bits;  conditional E-value: 3.2e-48
                                    HHHHTTT-BTTTTEE-HHHHHHHHHHHHHHHHTT-STT....--HHHHHHHHHHHHHHHHHHHHHTT-EES--------S CS
                           PTPA 118 aYlkesfGnatrlDYGtGhElsFlafllcLeklgllkeeeeedeealvlkvfekYlelvrrLqstYtLepAgshGvwGLD 197
                                    +Yl++sfGn+ rlDYGtGhEl+Fl++l+  +  g+++          v++ + +Y+e+vr   ++++LepAgshG+wGLD
  gene835|gene835|rna834|rna834  80 EYLRNSFGNKIRLDYGTGHELNFLCYLYNQYCEGAIT-------IDCVFTTLVEYFEVVRLFVTKFNLEPAGSHGIWGLD 152
                                    8***************************999999884.......4599999***************************** PP

                                    SS-SHHHHHHHHCSSS-G....GGGG-HHHHHHHTTT-HHHHHHHHHHHH--S-HHHH-HHHHHHHCC--HHHHHHHHHH CS
                           PTPA 198 DyqflpflfGsaQlvehkklkpksildaevveeyakeylYlsaiafinevKkgpfrehSpmLydisavktWekvnkGlik 277
                                    DyqflpflfGs+ l++++            ++e  ++  Y+ a++      + ++   S++L++i   k+W+ +n+G+i+
  gene835|gene835|rna834|rna834 153 DYQFLPFLFGSSELCNTRL----------RFDELDDTKCYFVAVK------R-KLGGSSQILKSIMD-KDWATINRGMIR 214
                                    *************888764..........5788888999998764......3.699*********97.55********** PP

                                    HHHHHTTT-HHHHTT--BBSSS CS
                           PTPA 278 mYkaevLskfpvvqhflfGsll 299
                                    mY++ vL+k  v qhf++G++l
  gene835|gene835|rna834|rna834 215 MYDDYVLKKDVVTQHFIYGRYL 236
                                    *******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1401.14
//
Query:       gene836|gene836|rna835|rna835  [L=326]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     3e-109  364.8   2.0   3.5e-109  364.6   2.0    1.0  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.6   2.0    2e-113  3.5e-109       1     279 []      17     283 ..      17     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 364.6 bits;  conditional E-value: 2e-113
                                    TT-TTS-SSHHHHHHHHHHHCT---GGGS-GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBSSHH CS
                 Ribonuc_red_sm   1 rfvlfpikypeiwelykkleanfWtpeevdlskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevqipe 80 
                                    rfvlfpiky++iw+lykk+e++fWt eev+l kD++dw  +L+ +ek+fi++vlaf+a++d+ivn nlver++sev+i e
  gene836|gene836|rna835|rna835  17 RFVLFPIKYDDIWALYKKAESSFWTVEEVSLDKDVEDWG-RLNAKEKHFISHVLAFFAASDGIVNLNLVERFSSEVKILE 95 
                                    79************************************9.7*************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHT.-HHHHHHHHCHHHH-HHHHHHHHHHHHHHCTTTSCHHHHHHHHHHHHHHHCC CS
                 Ribonuc_red_sm  81 arafygfqaamEniHaesYsllletlvkdekekdelfnaieenpalqkkaewikkwyeskkdeekfaerlvafallegil 160
                                    ar fygfq+a+E+iH+e+Ysll+et++++ +e+d lfnai+++p++++ka+w+ kw+e+k++  +fa+rlvafa++egi+
  gene836|gene836|rna835|rna835  96 ARFFYGFQVAIESIHSEMYSLLIETYIRNAEERDFLFNAIKNIPSVKDKADWAIKWIEDKDS--DFATRLVAFACVEGIF 173
                                    **********************************************************9984..5*************** PP

                                    CHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                 Ribonuc_red_sm 161 fysgFaailwlkkrgllpglaeiielilrDeglHtdfagllfkelkeenelenkeleeeveelikeavelEkefitdalp 240
                                    f++ Fa+i+wlkkrgl+pgl++++eli+rDeglH++fa+ l ++ +++         ++++e++ +av++Ek+f+ ++lp
  gene836|gene836|rna835|rna835 174 FSGAFASIFWLKKRGLMPGLTFSNELISRDEGLHCEFACHLHRYHLNN-------KCTRTKEVVMDAVRIEKRFLSESLP 246
                                    *******************************************66555.......47899******************** PP

                                    T.BTTCHHHHHHHHHHHHHHHHHHCTT---SS-TT---C CS
                 Ribonuc_red_sm 241 vellglnkedvkqYieyvadrllmnlgyeklYnveeenP 279
                                    v+l+g+n+e++++Yie+vad ll+nlg ek+Y++   nP
  gene836|gene836|rna835|rna835 247 VNLIGMNCELMCRYIEFVADTLLENLGEEKIYHA--INP 283
                                    *********************************9..887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1998.90
//
Query:       gene837|gene837|rna836|rna836  [L=874]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-35  121.5   0.0    6.4e-35  120.3   0.0    1.6  1  Peptidase_M16    Insulinase (Peptidase family M16)
    7.3e-20   71.4   0.1    1.2e-17   64.2   0.1    2.5  1  Peptidase_M16_M  Middle or third domain of peptidase_M16
      3e-12   46.9   0.1    6.3e-08   32.8   0.0    2.4  2  Peptidase_M16_C  Peptidase M16 inactive domain
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.58   10.1   0.0    1.9  2  DUF4994          Domain of unknown function


Domain annotation for each model (and alignments):
>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   1.4e-38   6.4e-35       3     123 ..      27     141 ..      25     154 .. 0.94

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 1.4e-38
                                    EEEE-TSSSEEEEEEEES-SGGGSCTTTTTHHHHHHHHTTSBBSSSCH.HHHHHHHHHTTCEEEEEEESSEEEEEEEEEG CS
                  Peptidase_M16   3 alesdppaktsavglvvdaGSryepkdlnGlAHllehmafkgTkkyps.nklaeeleklGgslnAttsrentvYyvevls 81 
                                    + +sdp+ +++++++ v++G+++ p+  +GlAH+lehm+f+gT+kyp+ +++ ++l++++g +nAtt  e t+Yy++v++
  gene837|gene837|rna836|rna836  27 LVISDPSLDKCSCAVSVKVGAFDNPESAQGLAHFLEHMLFMGTEKYPDeEGFSKFLARNNGGYNATTYGEVTIYYFDVAP 106
                                    56899*************************************************************************** PP

                                    GGHHHHHHHHHHHHHSBTTSHHHHHHHHHHHHHHHHHHCCHH CS
                  Peptidase_M16  82 kdlekaldvladvfkaplleesevererkvvekeveavdaep 123
                                    k++e+ +d+lad+fkapll+++ ver       ev+av++e 
  gene837|gene837|rna836|rna836 107 KAFEEGVDRLADFFKAPLLKKNSVER-------EVSAVHSEF 141
                                    **************************.......666666654 PP

>> Peptidase_M16_M  Middle or third domain of peptidase_M16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.1   2.7e-21   1.2e-17       1     277 [.     372     639 ..     372     641 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 2.7e-21
                Peptidase_M16_M   1 FrFkekeepsdyvsslaenmqkyppedvlsgpylleeydpelikellssL.tpenarivlvske.t..dekekwygteYs 76 
                                    F+++e+ ep+ +++++a++mq+yp+e+vl ++y++e++d++++k++++++ + ++ +++ v+k+    d  e++yg+++ 
  gene837|gene837|rna836|rna836 372 FKYEENDEPMYQTQKIAKRMQFYPIENVLDKDYCFERFDENEMKRIIKRMgSFSEWLVFHVAKDaGvfDMCEEIYGVRFG 451
                                    9************************************************9889**********6425789*********9 PP

                Peptidase_M16_M  77 vekiseelleewksaeeneeLhLPepNpFiptdfslkkesesepakaPelirdt.elvrlWykkDdtFkvPkasvrlklr 155
                                    + +   ++le  k+++      L +      ++ ++    + ++++   +i+++ +++++ y   dt+kvPk+++   +r
  gene837|gene837|rna836|rna836 452 LGD---KILE-AKDIK---GEPLEKVDSVEWKEGEM----A-SSENGSDIISKEfPGGKINYLFNDTYKVPKVFIGYLIR 519
                                    877...4555.22222...22355666666666666....2.3444455555444************************* PP

                Peptidase_M16_M 156 splasksprn..avltelfvellkdslneylydAelAglsyslssskeglelsvsGYndklpvLlekvleklknfeiked 233
                                    ++++sk  r   + l+e   + + ++   yly     g+++s+  + +g+e++++ +n+   +  +k+++ l   +++++
  gene837|gene837|rna836|rna836 520 TENISKESRVdmMFLAENAKSQFFKKHGGYLYGT---GVDVSVRIEHYGIEIRIECFNHMSVEVSQKFFDILF-GDPDQS 595
                                    ****554443114566666666666666777765...66********************************96.4***** PP

                Peptidase_M16_M 234 rFevikekllrelknfklekpyqqarellsslleekawtleell 277
                                    r + ikek+++el+ +++++py+ ++e ++++    ++  ee++
  gene837|gene837|rna836|rna836 596 RKDLIKEKIRNELEIMRNSSPYRRCDEGMRWMKVPDHMMAEEMM 639
                                    ***************************99999888777777776 PP

>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.4e-11   6.3e-08       5     181 ..     184     366 ..     183     368 .. 0.83
   2 !   11.7   0.1   4.3e-05      0.19     113     180 ..     739     807 ..     651     810 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.4e-11
                                    HHHHHHHHHHSSGGGEEEEEEESS-HHHHHHHHHHHHTTSTHHSH..........CSGSCTSSSSSGGGSSEE.EEEEEE CS
                Peptidase_M16_C   5 edlkefykkfYrpenmvlaivGdvdheelvkliekyfgdlkaska..........ppakptgepltpatlkkp.pvvlkk 73 
                                    e++k+f +k Y+ ++m ++i+G+ ++ el+kl++k+ g  k  ++          + ++ ++++ t  +++ + + v + 
  gene837|gene837|rna836|rna836 184 EEMKDFWRKKYSCDKMCVVIYGNKSPSELKKLLKKFEGVPKGLEEkecsgknmgsELEEGWSVFDT--EYTNRwIRVEPI 261
                                    799*****************************7776666666655********9988899999999..555550555555 PP

                                    SSSSSEEEEEEEEEECTCTHTTHHHHHHHHHHHHSSTTSHHHHHHHTTTTSESEEEEEEEEESSCEEEEEEEEEECTTHH CS
                Peptidase_M16_C  74 ldeeqahlslafegpskendeddlalavlntlLgggmesrLytnlrekeglaysvsafndsyrdsglfgisatadpenve 153
                                     d  + ++ ++  + s ++ +++ + + + ++++      +  +++  +gla +v+++n +y+d++l+ i++ +      
  gene837|gene837|rna836|rna836 262 AD--TKSIVVTITVESGYKVFRNNPYECITEMILRDDPRGFACKVK-DKGLALDVECENANYTDYSLIIITVHLSVVGSK 338
                                    66..555555555555556*****************8888999999.********************9999999988666 PP

                                    HHHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                Peptidase_M16_C 154 evvevilkelrklkkeglteeelerakn 181
                                       +v+l+ ++ ++   +te+e e+ k+
  gene837|gene837|rna836|rna836 339 RPKDVVLELVKYIQGMNITESEYEELKK 366
                                    6678999999999988999***999987 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.3e-05
                                    HHHHHHHTTTTSESEEEEEEEEESSCEEEEEEEEEECT..THHHHHHHHHHHHHHHHHHTS-HHHHHHHH CS
                Peptidase_M16_C 113 rLytnlrekeglaysvsafndsyrdsglfgisatadpe..nveevvevilkelrklkkeglteeelerak 180
                                     +++ lr+ke l+y v + ++   d  ++++ ++++++   +e+++  +++ l+   ke ++ee +e+ k
  gene837|gene837|rna836|rna836 739 MFFDDLRTKEELGYVVASRVMHLDDEQYIVFLVQSEKDvdFLEKRIRKFVEDLDGYYKE-MSEEQFEEFK 807
                                    489****************8888899999999999999989999999999999999999.******9877 PP

>> DUF4994  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.9   8.6e+03      40      64 ..     252     277 ..     251     279 .. 0.77
   2 ?   10.1   0.0   0.00013      0.58       9      75 ..     581     647 ..     575     655 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                        DUF4994  40 kkkWkyiePskgpalikl.tkielGn 64 
                                    +++W  +eP ++++ i +   +e G+
  gene837|gene837|rna836|rna836 252 TNRWIRVEPIADTKSIVVtITVESGY 277
                                    689999***98887776657888887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                        DUF4994   9 SenvlkallGkdkkdReyvieqaanktlsvrkkkWkyiePskgpalikltkielGnskepqLydlkk 75 
                                    S++ ++ l G+ +++R+ +i++ ++++l +++++  y + ++g + +k+++  + +++ ++L+ +++
  gene837|gene837|rna836|rna836 581 SQKFFDILFGDPDQSRKDLIKEKIRNELEIMRNSSPYRRCDEGMRWMKVPDHMMAEEMMEKLHSVDT 647
                                    899999*********************************************9999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.35s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 5545.80
//
Query:       gene838|gene838|rna837|rna837  [L=440]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2777.79
//
Query:       gene839|gene839|rna838|rna838  [L=779]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-16   60.4   3.8    1.6e-16   60.0   2.3    1.8  2  Adaptin_N  Adaptin N terminal region
     0.0044   17.1   0.1      0.016   15.2   0.0    1.9  2  Cnd1       non-SMC mitotic condensation complex subunit 1
  ------ inclusion threshold ------
       0.29   11.3   1.8         14    5.9   0.1    3.2  3  DUF1296    Protein of unknown function (DUF1296)


Domain annotation for each model (and alignments):
>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.0   2.3   2.7e-20   1.6e-16       6     340 ..      28     344 ..      24     358 .. 0.89
   2 ?   -1.4   0.0      0.11   6.3e+02     424     457 ..     404     435 ..     398     475 .. 0.76

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.7e-20
                                    CHHHHHHCCSSS-SCHHHHHHHHHHHHHHHCT---GHHHHHHHCCCCSS-CHHHHHHHHHHHHHCTTSCCHHCCCCHHHH CS
                      Adaptin_N   6 qqelaeilnsnkdddekkkeavkkliylialGedvsflffevvklvaskdfelKrlvYlylellaeesedlalLvtnslq 85 
                                    ++++++  +s   +++k  +a k l+  +  Ged+s+l  +v+k + + d e Kr++ lyl+++++  +   l+ +n++ 
  gene839|gene839|rna838|rna838  28 KSQIVKYISSP--SPKKQMQAAKSLMCRMQCGEDLSDLCNDVIKAIDTRDAEFKRMLNLYLVRYIQGWPAKQLICINTML 105
                                    66777778888..99***************************************************************** PP

                                    HHCCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCC.HHHHHHHCTT-S CS
                      Adaptin_N  86 kDlkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkq.lveeikellsdk 164
                                    kDl d n+ +r  A++  + +++  + +   + +k+  k++ p  r+k a ++   ++kd++l+ +  l + +k+l  d+
  gene839|gene839|rna838|rna838 106 KDLGDGNKEMRYCAIQDSGLLGDGVVIKNYINPLKEHGKSQVPETRRKVADSLQNYFRKDSKLFYDSgLCDLLKDLAFDE 185
                                    ******************************************************************************** PP

                                    SHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCHHHHHHCS-HHHHHHHHHHHCC---SSHHHH..HHHHHHHCGGCGCSS CS
                      Adaptin_N 165 dpgvvlaAvalleeikkndrlllkllpklvrrLcnllteldpwlqvkiiklltrlarqepeerskkellesllnllqssn 244
                                    dp+v ++A++ ++ i+ + ++l+      ++ +++l+   ++ +  +++  l +++r+  e+         l  ll++sn
  gene839|gene839|rna838|rna838 186 DPSVSASALNSIQVIEEETKILS------TEDIYKLFRRNTESGSKEVLGSLLEVMRNRVEDFHD---PSLLVGLLATSN 256
                                    ***************66666633......344444445566777788888888888877777732...356778999*** PP

                                    CHHHHHHHHHCCHCCCCSTHHHCCHHCHHHHHHSSCCTCHHHHHCHHHHHHHHXXTTTTTTTCCCCSXXTTSXHHHHHHH CS
                      Adaptin_N 245 naVlletvnlivelapknelivlavnaLvrllsskdenlryvaLrtllkivkkepkavqhldlkifllktdddvsirlka 324
                                      V + +  l+++++p+ +  + +   L  +lss de   y++L+   +++k       + d   f +  +d  + ++k+
  gene839|gene839|rna838|rna838 257 LRVFYLASSLLISIDPSYK--QMVFDHLKGFLSSYDE-ELYLVLDYAESLLKDV-----SYDNSCFAIYHSDKKYNKIKK 328
                                    *****************99..799*************.779***9999998877.....666677777778889999999 PP

                                    HHHHCCCXXTTTHHHH CS
                      Adaptin_N 325 ldlllklvdesNvkei 340
                                    l ll+k +d++++kei
  gene839|gene839|rna838|rna838 329 LRLLFKRLDATSIKEI 344
                                    9999999999999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.11
                                    CGXXSHHHHHHHHHHHHHTTTTXTT...HHHHHH CS
                      Adaptin_N 424 ekieseearaaaiWllGeygelvsntesasdllr 457
                                     + +  e r+++i+l+G y+ +v+   ++ ++ +
  gene839|gene839|rna838|rna838 404 MNARKVEERQKYIYLCGRYVHEVPL--EIMNIQN 435
                                    555556668999**********998..5545444 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.9   1.1e+04     104     139 ..      35      65 ..      21      74 .. 0.56
   2 !   15.2   0.0   2.7e-06     0.016      19     128 ..     132     236 ..     128     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.9
                           Cnd1 104 lsdalnecsewgqitilefLlsyipkdkqeaeslve 139
                                    +s    + s ++q++  ++L+  ++  +    +l++
  gene839|gene839|rna838|rna838  35 IS----SPSPKKQMQAAKSLMCRMQCGED-LSDLCN 65 
                                    22....44555666666666655555544.555555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.7e-06
                           Cnd1  19 veylvepLrkrLkDedpyVRktaaivvakLilnd..mvkekgflselaklleDenprVvanalaalteiseksenaiynl 96 
                                    + ++++pL++  k + p  R+  a  + + +++d  ++ ++g+ + l++l  De+p+V+a+al++++ i e++ +++   
  gene839|gene839|rna838|rna838 132 IKNYINPLKEHGKSQVPETRRKVADSLQNYFRKDskLFYDSGLCDLLKDLAFDEDPSVSASALNSIQVIEEET-KILS-- 208
                                    6778888888888888888888888888886666448999******************************998.3333.. PP

                           Cnd1  97 lpdiisklsdalnecsewgqitilefLlsyip 128
                                    + di++ +       +e g +++l +Ll+ + 
  gene839|gene839|rna838|rna838 209 TEDIYKLFR----RNTESGSKEVLGSLLEVMR 236
                                    345555444....5689999999999988776 PP

>> DUF1296  Protein of unknown function (DUF1296)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.72   4.3e+03       1      35 [.     147     185 ..     147     191 .. 0.61
   2 ?    2.9   0.1      0.02   1.2e+02       4      28 ..     192     216 ..     189     222 .. 0.85
   3 ?    5.9   0.1    0.0023        14      11      35 ..     340     364 ..     337     370 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.72
                        DUF1296   1 ipasvrkviqsikEivgk....hsdeeIyamLkecnmDp 35 
                                    +p++ rkv +s++ + +k      d+   + Lk+ + D 
  gene839|gene839|rna838|rna838 147 VPETRRKVADSLQNYFRKdsklFYDSGLCDLLKDLAFDE 185
                                    688889999999887764211223555556666666655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.02
                        DUF1296   4 svrkviqsikEivgkhsdeeIyamL 28 
                                    s+   iq i E ++  s e+Iy+ +
  gene839|gene839|rna838|rna838 192 SALNSIQVIEEETKILSTEDIYKLF 216
                                    556679*******99*******987 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0023
                        DUF1296  11 sikEivgkhsdeeIyamLkecnmDp 35 
                                    sikEi +++ dee  +++   + D+
  gene839|gene839|rna838|rna838 340 SIKEIKNQCRDEELLSVILRESLDA 364
                                    8************999876555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.34s 00:00:01.14 Elapsed: 00:00:00.55
# Mc/sec: 4263.71
//
Query:       gene840|gene840|rna839|rna839  [L=592]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.7e-20   71.6   3.6    4.2e-19   69.4   0.7    3.2  2  Symplekin_C  Symplekin tight junction protein C terminal
  ------ inclusion threshold ------
      0.046   13.6   0.2        2.2    8.2   0.0    2.9  3  SPOC         SPOC domain


Domain annotation for each model (and alignments):
>> Symplekin_C  Symplekin tight junction protein C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1     0.086   7.7e+02      15      39 ..     259     283 ..     222     306 .. 0.65
   2 !   69.4   0.7   4.7e-23   4.2e-19      54     184 ..     435     556 ..     400     558 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.086
                    Symplekin_C  15 eevislLpkliklnekvvkevfrrl 39 
                                    +e++++L+++ik     v+++++ +
  gene840|gene840|rna839|rna839 259 DETVEILNHMIKERRVYVEKIVKMI 283
                                    4555666666666555555444444 PP

  == domain 2  score: 69.4 bits;  conditional E-value: 4.7e-23
                    Symplekin_C  54 spltpaellvalhnlekkkkevelkslvealdlclsekevftqevlaaalqqlveeeplpllfmrtviqalkkypslref 133
                                    + +  +ell+  h+++      ++ ++++ l+lc+++++  +++ l + l  l  e++lpll++rt+iq+l k+p+l++f
  gene840|gene840|rna839|rna839 435 RAIECSELLIFAHRIP------DISKAIRILNLCFKSPRFNESDFLFT-LTTL--EKELPLLIVRTLIQTLLKFPNLKNF 505
                                    566779**********......9999**********988777777664.4444..5789********************* PP

                    Symplekin_C 134 vsniLprLikkqvWknkklWkgfircakklkpksfeallqLPeeqleellk 184
                                    v + L+rL+++++Wk++++ +g+++c++ +  +++ +++ L ++ ++++l 
  gene840|gene840|rna839|rna839 506 VVSFLSRLVRRNIWKQEEMVEGVVKCFEIIGAAAVDIIVYLDSDATAKVLG 556
                                    *************************************99998888888775 PP

>> SPOC  SPOC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.097   8.7e+02      75     114 ..      38      78 ..      22      99 .. 0.64
   2 ?    1.0   0.0     0.041   3.7e+02      20      57 ..     208     246 ..     204     277 .. 0.75
   3 ?    8.2   0.0   0.00024       2.2      76     111 ..     336     371 ..     311     395 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.097
                                    E.SSGGGHHHHHHHHHHHHTTTEEEE.....EE-TTS-EEE CS
                           SPOC  75 p.sdesdesgfaelvdYLksKqraGvvnlnksglnqngvly 114
                                      s+  d+ +   l  YL+s q+ G ++   ++   n++++
  gene840|gene840|rna839|rna839  38 TaSKILDRDSAVILLAYLRSAQSKGMICPRYAQRSVNYHVH 78 
                                    2355555555555999****999999544444433335544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.041
                                    EEEEEEEEEE---------.-SEEEE-EEEEHHHHHHHH CS
                           SPOC  20 vssfqvqahllsgdrslvs.pslLritqRlrldqvkkyl 57 
                                    ++sf v a+ll+ d   +    +L+ +q  r+d vk ++
  gene840|gene840|rna839|rna839 208 SHSFFVYAYLLNRDVYDATvELILESKQYFRIDIVKHLV 246
                                    599**********99887667789999999999999543 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00024
                                    SSGGGHHHHHHHHHHHHTTTEEEE.....EE-TTS- CS
                           SPOC  76 sdesdesgfaelvdYLksKqraGvvnlnksglnqng 111
                                    +  + +++++++vd Lk+K+ + v+nl ks  n+++
  gene840|gene840|rna839|rna839 336 DAVDTQESMNSFVDLLKEKEDWAVINLIKSMKNDQR 371
                                    44456677888******************9998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.51
# Mc/sec: 3482.57
//
Query:       gene84|gene84|rna84|rna84  [L=161]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-12   45.3   0.2    1.2e-11   44.8   0.2    1.3  1  NOT2_3_5  NOT2 / NOT3 / NOT5 family


Domain annotation for each model (and alignments):
>> NOT2_3_5  NOT2 / NOT3 / NOT5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.2   6.8e-16   1.2e-11      14     129 ..      40     154 ..      27     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6.8e-16
                   NOT2_3_5  14 kprqyep......klphptsisypqeplyekle...sakklekldedtLFyiFYysqgtleqllAakeLkkrsWryhkelktWf 88 
                                 p++y p       lp+     yp+ p++ +++   +  k+++l+e+tLFyiFY+ +++  q+ A+  + +r++ + + +k+ +
  gene84|gene84|rna84|rna84  40 DPSTYYPqsllsrMLPN----CYPKAPNEGIFKvniEDMKMDNLHEETLFYIFYTFPNDKLQVKAYDNILRRKYIFCRMYKCFV 119
                                44445554322223444....4877774443332156789******************************************** PP

                   NOT2_3_5  89 lreekeepkekteeyekgsYkyFD.yetWlkrrkkdfkleye 129
                                + +          ++ k s ++FD + +W+k++  + +++++
  gene84|gene84|rna84|rna84 120 TFN--A---PPIADHVKRSIVMFDpF-SWSKVS-IEVVFDER 154
                                999..3...333445678899***88.***999.77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1172.65
//
Query:       gene841|gene841|rna840|rna840  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-27   95.0   0.0    4.7e-27   94.9   0.0    1.0  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.0   2.6e-31   4.7e-27     199     313 ..      23     133 ..       2     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 2.6e-31
                                    S--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 199 eknepvfvtdfPaelkpFyarkeeddkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswyleale 278
                                    ++ +++ + d+P  ++pFy+ ++e+ k +t+syD++++g E+++G++R++ ++ l +  +++g++   +++++ yle ++
  gene841|gene841|rna840|rna840  23 HGVDIFVIKDYPICTRPFYTYRDEE-KGVTRSYDFILRGEEILSGAQRVNVYKDLVRYVEEHGIS---PSSLGGYLESFR 98 
                                    556778899****************.9**************************************...************ PP

                                    CT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 279 yGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                    yGapphgG+g+Gl+Rl+    g+ +Ir  ++FP+ 
  gene841|gene841|rna840|rna840  99 YGAPPHGGCGIGLERLMKAYFGMGDIRRFSLFPRD 133
                                    *********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 809.33
//
Query:       gene842|gene842|rna841|rna841  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-36  125.4   0.1    3.1e-36  125.0   0.1    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    8.7e-09   35.3   0.2    1.7e-08   34.3   0.2    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.0   0.1   3.5e-40   3.1e-36       3     150 ..     150     295 ..     148     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 3.5e-40
                                    CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                    tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqs 78 
                                    ++rl+nr +dlrt++ ++++r+   v+  +r yl +ngf+ei+tP L+ s +e+ga+lF v       ++f    +++qs
  gene842|gene842|rna841|rna841 150 HIRLDNRAMDLRTPQARATFRIIDGVMFFFRGYLRRNGFVEIKTPKLIGSSSEGGANLFSV-------DYFkrkaFMAQS 222
                                    689**********************************************************.......555555569*** PP

                                    SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET.-SCHHHHHHHHHHHHHHHHHHHHCSC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  79 pqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsf.ieeedimqvleelikslvkevlessa 150
                                    pqly+++ i++g++rv +i++++RaE+s+ +r l+EF+ +++em++ ++++d++ ++  ++ s+++ ++e+ +
  gene842|gene842|rna841|rna841 223 PQLYKQMAIIGGLKRVCEIGHVYRAEESNINRYLSEFVGLDMEMEIsTDYNDMIAFIHSMFVSIFDSLKEEYQ 295
                                    ********************************************98356667****************66653 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.2   1.9e-12   1.7e-08       3      70 ..      30     111 ..      24     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1.9e-12
                                    EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.........HHHHHHHTTS-TTSEEEEEEEEEECTTS.......SE CS
                tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr.........eeatklaenlkeGdvvrvtGrvkrrpgg.......el 66 
                                    v+G   ++    +gk++fi+lrD+  +iq+++ +          + ++l+++++ +++++v+G+v + +++       ++
  gene842|gene842|rna841|rna841  30 VRGFALKV--SCTGKYVFIVLRDNGCTIQCMCEKpiggkgsltPQEFNLLKKVTHESFIEVKGKVVKQEKEisgcdkkDI 107
                                    66666677..899*******************************************************555555555577 PP

                                    EEEE CS
                tRNA_anti-codon  67 elkv 70 
                                    e+++
  gene842|gene842|rna841|rna841 108 EIHI 111
                                    7776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2170.64
//
Query:       gene843|gene843|rna842|rna842  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.024   15.0   0.7      0.024   15.0   0.7    2.1  2  DUF3852        Protein of unknown function (DUF3852)
      0.038   13.6   4.9      0.064   12.8   4.8    1.5  1  DUF368         Domain of unknown function (DUF368)
       0.29   11.0  11.1       0.47   10.3  10.1    1.9  1  7TMR-DISM_7TM  7TM diverse intracellular signalling


Domain annotation for each model (and alignments):
>> DUF3852  Protein of unknown function (DUF3852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.7     4e-06     0.024      57      99 ..     117     159 ..     105     164 .. 0.89
   2 ?   -2.7   0.2       1.3   7.7e+03      11      24 ..     214     227 ..     208     232 .. 0.45

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                        DUF3852  57 idvilavllfvklatayldYrkhgqlefaapailfagLvfslt 99 
                                    ++v +a ll + ++ a ldY++  + +++   i+f +Lvf ++
  gene843|gene843|rna842|rna842 117 MIVSMASLLGMVISCALLDYKHLPKRNYIDYLIIFSCLVFIVM 159
                                    56678999999****************************9865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                        DUF3852  11 vvlilaallavtal 24 
                                    v+ i++++l++ a+
  gene843|gene843|rna842|rna842 214 VLSIAILALSIAAV 227
                                    33333333333333 PP

>> DUF368  Domain of unknown function (DUF368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.8   1.1e-05     0.064      52     155 ..      88     189 ..      58     255 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
                         DUF368  52 inlkfLlalvlGivvsilvlakllsyllekypillwslffGlilasvvvlikevkkwsvkkiialllglaiallltvlep 131
                                      +  Llal++Gi+  +l++   ++ l  +  i +++ ++G+++  +++ +k++ k ++  +++++  l+++++l++l p
  gene843|gene843|rna842|rna842  88 WMVAYLLALFSGIA--FLFVKPNMTDLKGQAMIVSMASLLGMVISCALLDYKHLPKRNYIDYLIIFSCLVFIVMLASLLP 165
                                    33578999999975..7889999*********************************999999888888888888777766 PP

                         DUF368 132 veteeslvfvflaGaiaicAmilP 155
                                      +++++v  + a    ++++i+P
  gene843|gene843|rna842|rna842 166 PLKKHDMVSKVAAWGSMATGLIIP 189
                                    555555555444444444556665 PP

>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  10.1   7.9e-05      0.47      39     140 ..      88     188 ..      84     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.9e-05
                  7TMR-DISM_7TM  39 lsfllyllslngllfqylwpnappalnnkllyltlllllilfll.Farsflelkkkprllklllllavllsllllllpll 117
                                     +++ +l+ ++g++f ++ pn++  l  ++++++++ ll++++   +  + +l+k++++++l+++ +++++++l++  l 
  gene843|gene843|rna842|rna842  88 WMVAYLLALFSGIAFLFVKPNMT-DLKGQAMIVSMASLLGMVIScALLDYKHLPKRNYIDYLIIFSCLVFIVMLAS-LLP 165
                                    4556666678********99887.********99999998888878888888877668888888888886666666.333 PP

                  7TMR-DISM_7TM 118 pyteslslaqllallvillllli 140
                                    p ++   ++ + a+  + + l+i
  gene843|gene843|rna842|rna842 166 PLKKHDMVSKVAAWGSMATGLII 188
                                    44443333334444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1704.33
//
Query:       gene844|gene844|rna843|rna843  [L=122]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-06   26.0   1.4      0.013   15.2   0.4    2.1  2  DUF4477   Domain of unknown function (DUF4477)


Domain annotation for each model (and alignments):
>> DUF4477  Domain of unknown function (DUF4477)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4     7e-07     0.013      44      80 ..      10      48 ..       3      60 .. 0.85
   2 !   10.0   0.0   2.7e-05      0.49     137     175 ..      64     102 ..      59     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-07
                        DUF4477 44 ke..eleteaallsrllyrlknkfrnhkgfralkkveqa 80
                                   +e  +l +e+++l+ ++y+ kn +r +k fr+l +++++
  gene844|gene844|rna843|rna843 10 EEnlKLMEELEILKLVVYKSKNGHRGSKLFRKLVHLKRL 48
                                   3357899**************************999875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 2.7e-05
                        DUF4477 137 ildlckkafllsvkhlrlgefiklntvllallsrlwvls 175
                                    i+ ++ +   l ++ +  g++i  ++++l+l sr+  l+
  gene844|gene844|rna843|rna843  64 IRRVSEELYILATSNIPEGHLISYTLIILGLCSRIHYLV 102
                                    78889999999************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 789.53
//
Query:       gene845|gene845|rna844|rna844  [L=559]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-22   78.9   0.0      6e-22   77.8   0.0    1.5  1  SNF2_N        SNF2 family N-terminal domain
    1.7e-11   44.4   0.0    3.3e-11   43.5   0.0    1.5  1  Helicase_C    Helicase conserved C-terminal domain
      3e-06   27.3   0.0    9.4e-05   22.5   0.0    2.8  3  ResIII        Type III restriction enzyme, res subunit
     0.0024   17.9   0.0      0.015   15.3   0.0    2.1  2  Hpr_kinase_N  HPr Serine kinase N terminus
  ------ inclusion threshold ------
       0.22   11.9   0.1       0.22   11.9   0.1    2.2  2  PH_2          Plant pleckstrin homology-like region


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   1.7e-25     6e-22      60     302 ..     146     361 ..     135     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 1.7e-25
                                    E---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH----- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  60 LaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkmkkkn 139
                                     aD+mGLGKT+q+la+     +    ++        + p Li++Pasll+ W +  +r++   a+   v+  +       
  gene845|gene845|rna844|rna844 146 VADDMGLGKTIQALAISY---Y---YRS--------EWPLLIIAPASLLEDWADACKRFLGAEAM---VMRRK------- 201
                                    69*************888...3...233........368**********************9986...33322....... PP

                                    ------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH.--.-S-EEEE-S--SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxx RF
                         SNF2_N 140 tkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavsk.Ls.tsnrwiltGTPiq 217
                                        +     + + i++Y+v s++a      ++l + e   v+ DE+h lk+ ++k ++a+   L+   + ++l+GTP  
  gene845|gene845|rna844|rna844 202 ----E--DFGQTIGIVSYEVASSNA------NALLRCEVGVVIADECHYLKSLQTKRTKAIVPlLQrVPRAVLLSGTPAV 269
                                    ....1..235667888******877......9*********************999999988845535677899****** PP

                                    S-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH......HHHHHHHHHHHTT-ST.TEE---GGGT--S---EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 218 nsledlygLlkfLreepfgekqtfdkllqrpie......aqaekgrsrLlqllqr.lmlrrakkdveknlPpkteeiifl 290
                                        +ly++++ +   +f  +  +  ++ +  +       +   ++++L+ +l++ +m+rr+k++v ++lPpk  + + l
  gene845|gene845|rna844|rna844 270 SRPLELYPIIASIDRTIFPRFAEYGARYCNGRKvglwydYKGCSNAEELNYILKKcFMIRRTKDEVLAQLPPKFRRQVVL 349
                                    *******************999988887777777899988899999*******98469*****************99999 PP

                                    E--HHHHHHHH. CS
                                    xxxxxxxxxxxx RF
                         SNF2_N 291 klskverksYnr 302
                                    + + ++    ++
  gene845|gene845|rna844|rna844 350 QCEGKQSDPRKE 361
                                    998888776664 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   9.3e-15   3.3e-11       2     111 .]     382     494 ..     381     494 .. 0.92

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.3e-15
                                    HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH.TTSSS.EEEESGGGTS CS
                     Helicase_C   2 kleallell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfn.kgesd.vLiatdvaer 78 
                                    k+e+++++l ++ e++ k +if++  ++++ ++ ++ ++++ +++++g++p+ +r   +++f+ ++e++  L++ ++ ++
  gene845|gene845|rna844|rna844 382 KMEQVKQYLaTMMEKNMKFVIFCHHSEMMDGIEEFCVERKVPMIRIDGSIPSGNRHLLVKNFQeNDEIRvALLSITACST 461
                                    56677777778889***************99888877888**********************977888899********* PP

                                    SSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                    G++++  + V++ +l +n+  + q+ +R++R+g
  gene845|gene845|rna844|rna844 462 GLTLTAGRAVVFAELYWNPGVLLQAEDRIHRIG 494
                                    *******************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.57   2.1e+03      84     121 ..      55      92 ..      17     127 .. 0.68
   2 !   22.5   0.0   2.6e-08   9.4e-05      23     169 ..     140     267 ..     122     269 .. 0.77
   3 ?    0.8   0.0      0.12   4.4e+02      69     152 ..     330     415 ..     321     446 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.57
                                    .GEEEESSS-B--.......-SEEEEEHHHHHHTH... CS
                         ResIII  84 eigkkvsgdkkkakekdstnkkilvttiqsldadseee 121
                                    + ++++s+ +++ +  +s++++i v  + s++ +++++
  gene845|gene845|rna844|rna844  55 RLCTELSKLEESVYDVKSNEWRISVKDYISVKGELKRN 92 
                                    35555555555557888999999999999888888544 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.6e-08
                                    TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                         ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                                    r+ r++++   G GKT+ a+++ ++++++      l+++   slle + ++ k+fl  ++      v  +k+++      
  gene845|gene845|rna844|rna844 140 RRGRIVVADDMGLGKTIQALAISYYYRSEW----PLLIIAPASLLEDWADACKRFLGAEA-----MVMRRKEDF------ 204
                                    56678888889***********99999973....466666789**************875.....577777777...... PP

                                    .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS...TTTHHHHHT---.SEEEEEESS- CS
                         ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak..kswreilekfke.avllglTATp 169
                                       i +++++ ++++        + llr +  v+i DE+H l++   k  ++i+  +++    + l++Tp
  gene845|gene845|rna844|rna844 205 GQTIGIVSYEVASSNA-------NALLRCEVGVVIADECHYLKSLqtKRTKAIVPLLQRvPRAVLLSGTP 267
                                    6778888888888888.......889****************9975446666644443334445555777 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.12
                                    HHHHHGGGGTGG........GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGT CS
                         ResIII  69 qtleefkkflseayke....igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrl 144
                                    +t++e+   l++++ +    +++ +++d +k+  ++s +++++v   ++++ ++e+ +++  ++ +++ +++i+  +H++
  gene845|gene845|rna844|rna844 330 RTKDEVLAQLPPKFRRqvvlQCEGKQSDPRKEVVGESVDMNVVVQYREAVKLKMEQVKQYLATMMEKNMKFVIF--CHHS 407
                                    56666666666666656666444444444444568999999999999999999966677777777777788888..8999 PP

                                    TS.TTTHH CS
                         ResIII 145 gakkswre 152
                                      ++ ++e
  gene845|gene845|rna844|rna844 408 EMMDGIEE 415
                                    88766655 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.39   1.4e+03      56      73 ..     234     251 ..     228     270 .. 0.75
   2 !   15.3   0.0   4.2e-06     0.015      63     111 ..     380     428 ..     374     438 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.39
                                    HHHHHHHT-HHHHH..HH CS
                   Hpr_kinase_N  56 tElsYleklseeerkerl 73 
                                     E++Yl++l++++ k ++
  gene845|gene845|rna844|rna844 234 DECHYLKSLQTKRTKAIV 251
                                    6999*****988776554 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.2e-06
                                    T-HHHHH..HHHHHHTT--S-EEEETTT---HHHHHHHHHH---EEEES CS
                   Hpr_kinase_N  63 klseeerkerleklfskkipciiltrgleppeellelaeeygvpllrtk 111
                                    kl+ e+ k+ l ++++k++ ++i+++  e+ + + e++ e +vp +r +
  gene845|gene845|rna844|rna844 380 KLKMEQVKQYLATMMEKNMKFVIFCHHSEMMDGIEEFCVERKVPMIRID 428
                                    6889999*************************************99976 PP

>> PH_2  Plant pleckstrin homology-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.1e-05      0.22      15      57 ..      36      75 ..      25     106 .. 0.84
   2 ?   -1.5   0.5      0.89   3.2e+03      18      47 ..     371     402 ..     367     422 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                           PH_2 15 tVsvyinkksqVvlklkskhvggafskkkksvVldvskdipaw 57
                                   +++vy+n++++Vvl+  +k++   +sk ++s V+dv ++  +w
  gene845|gene845|rna844|rna844 36 KIKVYVNEDGKVVLRPSNKRLCTELSKLEES-VYDVKSN--EW 75
                                   689***********************98887.7999844..34 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.89
                           PH_2  18 vyinkksqVvlklks.khvggaf.skkkksvV 47 
                                    v+++ +  V lk+ + k+   ++ +k+ k v+
  gene845|gene845|rna844|rna844 371 VVVQYREAVKLKMEQvKQYLATMmEKNMKFVI 402
                                    66777777888886523333344044444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3501.80
//
Query:       gene846|gene846|rna845|rna845  [L=809]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-11   43.9  15.5    3.2e-11   43.1  15.5    1.4  1  RINGv            RING-variant domain
  ------ inclusion threshold ------
      0.057   13.0   0.5       0.14   11.7   0.5    1.6  1  Cytochrome-c551  Photosystem P840 reaction-centre cytochrome 
       0.95    9.4   8.8       0.14   12.0   3.9    2.2  2  60KD_IMP         60Kd inner membrane protein


Domain annotation for each model (and alignments):
>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1  15.5   5.4e-15   3.2e-11       1      48 []       8      54 ..       8      54 .. 0.99

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.4e-15
                                   ETTTTEE-SSSS--B-SS--STCCCSB-HHHHHHHHHHTCT-SB-TTT CS
                          RINGv  1 CriCleeeeeseplispCkCrGslklvHesClekWldekeantqCeiC 48
                                   C+iC++++   ++l +pC+C+G++k++H++Cl+ W++  ++ ++C+iC
  gene846|gene846|rna845|rna845  8 CKICHMGDVRGDDLCNPCRCSGTIKYIHRECLMSWIEC-SKIKRCDIC 54
                                   **********99**************************.9******** PP

>> Cytochrome-c551  Photosystem P840 reaction-centre cytochrome c-551
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   2.4e-05      0.14      39      95 ..     428     486 ..     420     505 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                Cytochrome-c551  39 nisavltplksfmGwflliffasliilgl..Gklsskisdkwflsfplsilvivavmfv 95 
                                     is +l  + +++G f l + a l+++ l  G +s k s + fl + ls  +  +v++ 
  gene846|gene846|rna845|rna845 428 GISRILLRVMAYLGLFTLFYGAGLMMIRLvcGEMSIKFSIRSFLKLSLSYKAFTMVLYS 486
                                    5899******************998766545***************9998888888774 PP

>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.9   2.4e-05      0.14      96     157 ..     278     355 ..     240     361 .. 0.71
   2 ?   -3.7   0.2       1.6   9.6e+03      69      90 ..     428     449 ..     416     489 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                       60KD_IMP  96 kdLsapd..............lpillavttflqqklsks.kkm.qkmmlyvmplmilffslsfpaglvlYwlvsnlls 157
                                    + Ls+++              + i++++t ++  ++ +s +k    +m + + +m+ +f++++  gl+l ++++ +l+
  gene846|gene846|rna845|rna845 278 EFLSDTNlkelysrlvgfgivFWIVMGCTEYMWRRFKSSsMKYiCIFMKIYLIVMMNIFFMNLTFGLILHYMFGGILN 355
                                    33444334444556677777777999999888877774414446778999999*******************998876 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.6
                       60KD_IMP  69 GclplLiqlpifialyrvlrsl 90 
                                    G+  +L+ +   ++l+++++ +
  gene846|gene846|rna845|rna845 428 GISRILLRVMAYLGLFTLFYGA 449
                                    4555566666666666666552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (809 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.83u 0.35s 00:00:01.18 Elapsed: 00:00:00.58
# Mc/sec: 4193.49
//
Query:       gene847|gene847|rna846|rna846  [L=190]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-61  205.7   0.1    5.6e-61  205.4   0.1    1.0  1  Ssu72     Ssu72-like protein


Domain annotation for each model (and alignments):
>> Ssu72  Ssu72-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.1   3.1e-65   5.6e-61       1     188 [.       1     187 [.       1     189 [. 0.95

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 3.1e-65
                                    SEEEEEESSSSSHHHHHHHHHHHTT-EEEEEE-SSSEEEEESSTTSEEEE-TTS-HHHHHHHHHHHHHHHHHHTSHHHHH CS
                          Ssu72   1 lkfavvcasnqnrsmeahkvLkkagfkvkSfGtgsavrLPgpsidkpnvyeFgtsyeeiyedLkskdkelyeanGllkml 80 
                                    +k+av ca+nqnrsm++h++++k+g+++kSfGt+ +++LPg+++dkpnvy+Fg++y++iy+dL  k++++y++ G+l +l
  gene847|gene847|rna846|rna846   1 MKLAVSCAMNQNRSMQTHDLFAKKGIPIKSFGTNPVIKLPGETMDKPNVYSFGQTYQQIYDDLCMKNEDYYRESGILYLL 80 
                                    589***************************************************************************** PP

                                    HHHHHH-SS--BGGG---.--SEEEESSHHHHHHHHHHHHHS--SS-EEEEEEEE---SSHHHHHHHHHHHHHHHHHHHT CS
                          Ssu72  81 drnrkiKkaPerwqeaeekkfdvvitceervfdavvedllsreselnrpvhvinvdikDnheeAlvgakaileLakalee 160
                                    +rn+++K++Pe++ + +e +fd+vitceervf++++e+    +s+ ++ ++++n+dikD+ ++A++ga++ile+++ + +
  gene847|gene847|rna846|rna846  81 ERNMRVKEKPENFFQRDE-DFDLVITCEERVFTSIFEHYA-DGSSCTKSFFMVNFDIKDTPSDAITGAQEILEFVEDVLS 158
                                    ***************877.******************997.56889999**************************98876 PP

                                    -SS..HHHHHHHHHHHHHHHHT--EEEEE CS
                          Ssu72 161 aede.leeevkeilaefeektkklllytv 188
                                     e++ l  +v++ l+++ e++ ++ll+tv
  gene847|gene847|rna846|rna846 159 LEENgLRYAVDDALRRYFERKGTMLLFTV 187
                                    655559*********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 1141.59
//
Query:       gene848|gene848|rna847|rna847  [L=152]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   10.8   0.1      0.098   10.5   0.1    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   5.4e-06     0.098     459     534 ..       6      92 ..       3     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.4e-06
                       PolC_DP2 459 hPkytylwhdisveelekLaeavaekkkl.......eeeklvleleee....vkeiLekllvehkvkeekivieealall 527
                                    +P    l++d+s+e l+ L+++++++ +        ++e+l +++++      k+ Le+l+++ ++ +e + iee+   +
  gene848|gene848|rna847|rna847   6 YPFMDRLYKDVSEEFLSGLKRYINDEISYselerlsTRESLAFNSHKWneviEKKSLEALGIKRRMYDEILQIEEHIKTM 85 
                                    7888899****************99987788888875555555554335677899******************9999988 PP

                       PolC_DP2 528 kslgldl 534
                                    + l+  +
  gene848|gene848|rna847|rna847  86 EKLEKGE 92 
                                    8887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 919.15
//
Query:       gene849|gene849|rna848|rna848  [L=411]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.9e-05   23.3   0.0    0.00015   22.0   0.0    1.7  1  Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic d
    0.00014   22.1   0.1    0.00036   20.8   0.0    1.7  2  FHA           FHA domain
  ------ inclusion threshold ------
       0.13   13.3  13.1       0.12   13.4   3.2    3.4  3  RNase_J_C     Ribonuclease J C-terminal domain
        2.2    8.9  16.9        6.9    7.3   0.2    4.0  4  FeoB_Cyto     FeoB cytosolic helical domain
        3.8    5.4   5.9        6.2    4.6   5.9    1.3  1  Prominin      Prominin


Domain annotation for each model (and alignments):
>> Yop-YscD_cpl  Inner membrane component of T3SS, cytoplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   4.1e-08   0.00015      15      88 ..      23      95 ..      13      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 4.1e-08
                                   TTEEEEEES-TT-SEE---TTS-TT-EEEEEETTEEEEEE-CESS--EETTEE-S.ECC...--TTSEEEETTEEEEE CS
                   Yop-YscD_cpl 15 eegevviGsdedcDivLsDkevsrkhlkLeveeesvrledlgsrngllvngerve.ele...lrpgdvlelGttelal 88
                                   +e e++iGs+ d+D+ L+ ++++++h+ +++++ ++r+     +n++++n+e  e e +    r gdv+++   ++++
  gene849|gene849|rna848|rna848 23 NESEITIGSGLDSDVRLQQPSIEERHVLVYFDHMKIRVL----GNNVFLNEEALEkE-SmygFRFGDVVKINRYKFVF 95
                                   7889***********************************....9**********954.44789999999998888876 PP

>> FHA  FHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     1e-07   0.00036       1      68 [.      27      88 ..      27      89 .. 0.93
   2 ?   -3.9   0.0         5   1.8e+04      17      28 ..     240     251 ..     236     261 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1e-07
                                   EEEESSTTSSEETTSTTSTTTEEEEEEETTCEEEEEEEESSSSSEEETTEEESTTSEEEE-TTEEEEE CS
                            FHA  1 vtiGRssdcdivlddpsiSrkHalikfdkgsgkvyleDlgSknGtfvNgqrigkgepveLksgdviel 68
                                   +tiG   d+d++l++psi  +H l++fd +     ++ lg  n +f+N++ ++k+  +  + gdv+++
  gene849|gene849|rna848|rna848 27 ITIGSGLDSDVRLQQPSIEERHVLVYFDHM----KIRVLG--NNVFLNEEALEKESMYGFRFGDVVKI 88
                                   59*************************999....888898..************99999999999986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5
                                    TSTTTEEEEEEE CS
                            FHA  17 siSrkHalikfd 28 
                                    ++   Ha i+ +
  gene849|gene849|rna848|rna848 240 KMKEEHAAIDEE 251
                                    567789999755 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.062   2.2e+02      16      44 ..     181     209 ..     174     220 .. 0.79
   2 ?   13.4   3.2   3.5e-05      0.12      15      63 ..     226     274 ..     221     276 .. 0.94
   3 ?    3.7   0.2     0.036   1.3e+02      16      50 ..     273     302 ..     269     312 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.062
                      RNase_J_C  16 eeLieeakkvvretieealeekesdwnel 44 
                                    +++iee k+v+++ i+e++e++ +d+ +l
  gene849|gene849|rna848|rna848 181 KQVIEEQKEVLKKEIKESIETSMVDTPVL 209
                                    57899999999999999998888777665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 3.5e-05
                      RNase_J_C  15 seeLieeakkvvretieealeekesdwnelkrkirealkkflykktkrr 63 
                                    ++e++++a+kvv+e+++e     + + +elk+++++++k+ l++ +kr+
  gene849|gene849|rna848|rna848 226 KKEILDSAEKVVEEKMKEEHAAIDEELDELKQNVKDNIKEELKEDLKRD 274
                                    5799*******************************************96 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.036
                      RNase_J_C  16 eeLieeakkvvretieealeekesdwnelkrkire 50 
                                    ++++e++k+ +r+ ++e l++     +++k++i +
  gene849|gene849|rna848|rna848 273 RDFMEDVKEDIRDEVKEVLSS-----SDMKNAIAT 302
                                    567777888887777777766.....444444444 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.6   9.4e+03      61      82 ..      71      94 ..      68      98 .. 0.77
   2 ?    7.3   0.2    0.0019       6.9      43      77 ..     172     206 ..     165     208 .. 0.89
   3 ?    2.7   8.8     0.053   1.9e+02      39      89 ..     235     290 ..     227     314 .. 0.65
   4 ?   -2.0   0.0       1.6   5.6e+03      24      39 ..     341     356 ..     325     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.6
                      FeoB_Cyto 61 eleae..lgedledvIvdarykfi 82
                                    le+e  +g  + dv+   rykf+
  gene849|gene849|rna848|rna848 71 ALEKEsmYGFRFGDVVKINRYKFV 94
                                   466665588999999999999996 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0019
                      FeoB_Cyto  43 eelkedpelraeveearkeleaelgedledvIvda 77 
                                    ee+++   +++ +ee ++ l++e++e++e+ +vd+
  gene849|gene849|rna848|rna848 172 EEVENVSSVKQVIEEQKEVLKKEIKESIETSMVDT 206
                                    677777889999*******************9996 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.053
                      FeoB_Cyto  39 eelleelked.pelraeveearkeleae....lgedledvIvdarykfiegilrev 89 
                                    + ++e++ke+ +++ +e++e++++++++    l+edl+  + +++ + i++ ++ev
  gene849|gene849|rna848|rna848 235 KVVEEKMKEEhAAIDEELDELKQNVKDNikeeLKEDLKRDFMEDVKEDIRDEVKEV 290
                                    44566666442466666655555544441111666777777777776666666665 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.6
                      FeoB_Cyto  24 klppRwlAlklLegDe 39 
                                       +R  A++lL +D+
  gene849|gene849|rna848|rna848 341 GRRRRSSAMRLLPQDD 356
                                    5567888888887776 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   5.9    0.0017       6.2     274     395 ..     182     301 ..     155     324 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0017
                       Prominin 274 dglrgvkrdlnqalsnlCqseeC.skilssleiekldtskcldqlpnvdevlealeevletnlssivkeglarlneipek 352
                                    + ++++k+ l++ ++++++++   + +l s+ +   ++s++l ++   +e+l++ e+v+e+++++      ++l+e+++ 
  gene849|gene849|rna848|rna848 182 QVIEEQKEVLKKEIKESIETSMVdTPVLPSMGK---KNSRDLGEVMIKKEILDSAEKVVEEKMKEEHAAIDEELDELKQN 258
                                    444444444444444444432220234444444...56666677777777777777777777777766666677777777 PP

                       Prominin 353 vknqtaevvp.dlkka.lakgreqikklakkiprealdavisdle 395
                                    vk++++e ++ dlk++ +++ +e i+++ k++     +++ +++ 
  gene849|gene849|rna848|rna848 259 VKDNIKEELKeDLKRDfMEDVKEDIRDEVKEV--LSSSDMKNAIA 301
                                    77666655544666653455666666666665..22233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2645  (0.147526); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 2702.18
//
Query:       gene850|gene850|rna849|rna849  [L=552]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-07   30.9   0.0    2.6e-07   30.1   0.0    1.4  1  Sec63     Sec63 Brl domain
    2.1e-07   30.9   0.2    4.1e-07   30.0   0.2    1.5  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.9e-11   2.6e-07      13     169 ..     208     374 ..     206     466 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.9e-11
                                    --HHHHHHHHHHS-TT-.-HHHHH.......HHHHTSGGGGGS---TTHHHHHHHHHHTSSS--SSSTTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx.xxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63  13 isyetiklfneslkpnt.tlkdlL.......eilssasEFeeipvReeEkkelkkLlekvpikvkediespeaKvniLlq 84 
                                    ++++t+++f e++   + ++k  L        +++++ EF+e + R + +   +k+ + + +++ +d + +e+K ++ l 
  gene850|gene850|rna849|rna849 208 VNFRTMETFYEKIDVGMnQTKRPLevvmrliVLMTKSVEFSEYRWRSDVEGLRSKIESGFAFPL-KD-CGKENKGYLVLM 285
                                    6899999999999855533333333333444889*************************99998.45.467778888888 PP

                                    HHHTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTS-TT......S--EEE.EEEECE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxx.xxxxxx RF
                          Sec63  85 ayisrlklegsdlvsDlkyilqnairilralveillskgwlslalslleLskmveqrlwds......lPklei.eaevqp 157
                                     ++ r+     +  sD++y+ +   r+++ +  i ++k++  ++ +l+ L  m+ q++ d       +P ++  ++ +q 
  gene850|gene850|rna849|rna849 286 DHLFRIG---QAERSDVEYVQKVSLRLVEGMKAIGIAKRYGGVVRNLVILESMIIQAVFDVkysmlqIPFVKFeDIFIQE 362
                                    8988886...5679*********************************************998999996666665555566 PP

                                    BTTSEEEEEEEE CS
                                    xxxxxxxxxxxx RF
                          Sec63 158 itrsklrvevti 169
                                    ++++k++ve  +
  gene850|gene850|rna849|rna849 363 NSKEKVSVEGYL 374
                                    666666555443 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2   4.5e-11   4.1e-07       4      58 ..      93     149 ..      90     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.5e-11
                                    HHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHH..HHHHHHHHHHHHHHHHTSHHH CS
                           DnaJ   4 eiLgvskdasedeIkkaYrklalkyHPDknpkdp..eaeekFkeineAyevLsdpek 58 
                                    e+Lgv++   e+eIk++ rkl +ky   k p+d   e eek k in+Ay   sd+++
  gene850|gene850|rna849|rna849  93 EVLGVDEGTGEKEIKRKLRKLLMKYNLSKAPEDLrkEYEEKQKIINKAYGLVSDKKR 149
                                    8*****************************8887779*****************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3479.58
//
Query:       gene85|gene85|rna85|rna85  [L=562]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.007   16.2   1.4        1.2    9.1   0.0    3.5  3  SpoOE-like     Spo0E like sporulation regulatory protein
  ------ inclusion threshold ------
      0.032   14.7   6.8        3.3    8.3   1.2    4.1  4  HSCB_C         HSCB C-terminal oligomerisation domain
       0.11   12.2   0.6       0.28   10.9   0.1    1.8  2  Serum_albumin  Serum albumin family
       0.58    9.9   9.6        1.5    8.5   1.0    2.7  2  TACC_C         Transforming acidic coiled-coil-containing pro


Domain annotation for each model (and alignments):
>> SpoOE-like  Spo0E like sporulation regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.3     0.011        49       1      22 [.      27      47 ..      27      56 .. 0.79
   2 !    9.1   0.0   0.00027       1.2       5      39 ..     360     394 ..     359     395 .. 0.89
   3 ?   -3.2   0.0       1.9   8.3e+03      22      32 ..     420     430 ..     411     430 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.011
                               HHHHHHHHHHHHHHHHHHCC-- CS
                 SpoOE-like  1 LlkeIEelRkeLnelaekkglt 22
                               L keIE++ ke++ + +++++ 
  gene85|gene85|rna85|rna85 27 LSKEIERKEKEMMGS-ISQDYM 47
                               789*********988.555555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00027
                                HHHHHHHHHHHHHHC.C--HHHHHHHHHHHHHHHHH CS
                 SpoOE-like   5 IEelRkeLnelaekk.gltdpeVlelSqeLDeLine 39 
                                +E+l+  ++  ++++ g+ +  + + S eLDeL+ +
  gene85|gene85|rna85|rna85 360 MEQLKSSMMTFIDECnGFVS-SIFQFSNELDELLAK 394
                                699************66666.9***********975 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.9
                                -HHHHHHHHHH CS
                 SpoOE-like  22 tdpeVlelSqe 32 
                                t +e+l++S e
  gene85|gene85|rna85|rna85 420 TASEILKYSIE 430
                                67899999976 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.2   0.00074       3.3      14      61 ..       9      62 ..       7      65 .. 0.80
   2 ?   -3.6   0.0       3.6   1.6e+04      49      66 ..     303     320 ..     299     320 .. 0.76
   3 ?    0.9   0.0      0.15   6.5e+02      23      50 ..     355     382 ..     351     439 .. 0.77
   4 ?    5.4   0.1    0.0058        26      35      76 .]     454     503 ..     443     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00074
                               HHHHCG.GGSSSHHHHHHHHHHHHHHHHHHHHHHHHHH.....HTT-HHHHHHH CS
                     HSCB_C 14 Eeleea.eeaadkeeleelkaeveerieeleaeleeaf.....ekkdleaaadl 61
                               E+l e+ ++++++e l el++e+e +++e++ ++++ +     + +dle+ ++ 
  gene85|gene85|rna85|rna85  9 ERLKEVlKSKRKEEVLVELSKEIERKEKEMMGSISQDYmdiisKCSDLEKTKQR 62
                               8899996555666**********************9997766555577777765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                                HHHTT-HHHHHHHHHHHH CS
                     HSCB_C  49 afekkdleaaadllrrlr 66 
                                +fe +++++++++l+ lr
  gene85|gene85|rna85|rna85 303 LFESHNFSQIREALISLR 320
                                566668888999888876 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.15
                                SSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     HSCB_C  23 adkeeleelkaeveerieeleaeleeaf 50 
                                 d++ +e+lk+ +++ i+e+   +++ f
  gene85|gene85|rna85|rna85 355 PDADGMEQLKSSMMTFIDECNGFVSSIF 382
                                4778888888888888888887777777 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.0058
                                HHHHHHHHHHHHHHHH.....HTT....-HHHHHHHHHHHHHHHHHHHHHH CS
                     HSCB_C  35 veerieeleaeleeaf.....ekk....dleaaadllrrlrYlekikeeik 76 
                                +ee i++ e+e++e+f     + +    dl ++   +r l++ ++i+  ik
  gene85|gene85|rna85|rna85 454 MEEVIKQKEKEIDELFkivtkN-DdfgvDLLKVFSMARSLKFPANINTTIK 503
                                5677899999999999998743.347888889999*******999998886 PP

>> Serum_albumin  Serum albumin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   6.2e-05      0.28       7     171 ..      12      58 ..       6      73 .. 0.61
   2 ?   -3.3   0.0       1.5   6.8e+03     134     147 ..     451     464 ..     432     475 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.2e-05
                                HHHHHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHHHHHHHCTTTCHHHHCHHHHHHHHHHHTGTTHTHCCCTHHHHHGS-C CS
              Serum_albumin   7 qklgeekfkallliklsqklpqatfeelsklvkdvtkvaekCckledaleCaedeaslllekiCekqelspksskvkeCCeksl 90 
                                +++ ++k k+ +l++ls+ + + + e++ ++++d +++++kC +l                                       
  gene85|gene85|rna85|rna85  12 KEVLKSKRKEEVLVELSKEIERKEKEMMGSISQDYMDIISKCSDL--------------------------------------- 56 
                                555555555555555555555555555555555555555555555....................................... PP

                                THHHHHHHTT--SSTSS--SCHHHHCTHHHHHHHHHHCHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHHHHHHTTSSS CS
              Serum_albumin  91 lerreCflalkdadpkylppllepftenedlCkayeeekqkflqkflyelsrrhpelteeqllslakeyeellekCCkaen 171
                                                                                                               e+
  gene85|gene85|rna85|rna85  57 -------------------------------------------------------------------------------EK 58 
                                ...............................................................................33 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                                HHHHHHHHHHSTTS CS
              Serum_albumin 134 qkflyelsrrhpel 147
                                +kf+ e+++++ + 
  gene85|gene85|rna85|rna85 451 KKFMEEVIKQKEKE 464
                                33444444444333 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.0    0.0039        17      20      64 ..      20      61 ..       4     126 .. 0.57
   2 ?    8.5   1.0   0.00035       1.5     179     197 ..     454     472 ..     448     474 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0039
                     TACC_C 20 keeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqke 64
                               kee + el+k++e +  e++ m+ i +++  +i++  + + k+k+
  gene85|gene85|rna85|rna85 20 KEEVLVELSKEIERK--EKEMMGSISQDYMDIISKCSDLE-KTKQ 61
                               344444444444432..23345555555555554443322.2221 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00035
                     TACC_C 179 LeksleqKtkeneeLtkiC 197
                                +e+ ++qK+ke++eL ki 
  gene85|gene85|rna85|rna85 454 MEEVIKQKEKEIDELFKIV 472
                                899**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.54
# Mc/sec: 3144.33
//
Query:       gene851|gene851|rna850|rna850  [L=701]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-05   24.6   2.5    0.00013   21.9   2.2    2.5  2  Cullin_Nedd8     Cullin protein neddylation domain
     0.0084   16.5   0.3      0.033   14.5   0.1    2.1  2  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.025   14.8   0.2      0.076   13.3   0.2    1.8  1  MutS_I           MutS domain I


Domain annotation for each model (and alignments):
>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.64   3.8e+03      23      37 ..     242     256 ..     240     264 .. 0.89
   2 !   21.9   2.2   2.2e-08   0.00013       5      58 ..     642     691 ..     640     692 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.64
                   Cullin_Nedd8  23 neLvsevieqlskrf 37 
                                    n+L++e+++ ++ rf
  gene851|gene851|rna850|rna850 242 NKLYKEIVSRVRDRF 256
                                    899******999999 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.2e-08
                   Cullin_Nedd8   5 aiqaaIVRiMKsrktlshneLvsevieqlskrftpsiadikkrIesLiekeYle 58 
                                     ++a I Ri+K+rk+++++++++ +    ++ f  + + + ++I +L ekeY +
  gene851|gene851|rna850|rna850 642 ILEARITRILKKRKRVEISQMIAAI----EEEFGSDEKSVMETIRKLSEKEYCK 691
                                    589*****************99988....8889*******************75 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7     1e+04      73      99 ..     413     439 ..     411     443 .. 0.75
   2 !   14.5   0.1   5.6e-06     0.033       4      51 ..     643     690 ..     641     694 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                Penicillinase_R  73 asavkqlldklfegsvkelvaafveee 99 
                                    ++++ +l++k f+g ++++++ + e++
  gene851|gene851|rna850|rna850 413 EGMLVSLMQKHFGGTINRAISIMYENQ 439
                                    567778899999999999888777773 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.6e-06
                                    S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS- CS
                Penicillinase_R   4 lEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgll 51 
                                    lEa + +il +++++ +++ ++++eee    +++V+ ++r+L +K++ 
  gene851|gene851|rna850|rna850 643 LEARITRILKKRKRVEISQMIAAIEEEFGSDEKSVMETIRKLSEKEYC 690
                                    79*******************************************985 PP

>> MutS_I  MutS domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.3e-05     0.076       7      88 ..     581     665 ..     577     687 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
                                    HHCCCHH-TTCEEEEEETT.....EEEEECHHHHHHHHHCSSSSTT.ESSSSC.EEEEEEEHHHHHHHHHHHHHTT-EEE CS
                         MutS_I   7 ylelkkkykdavlffrvGd.....fYelfgeDAviaareleitltkrkkssekeipmagvPehalekylrkLvekgykVa 81 
                                    y  +++kykd+v + +  +       e   e+A+ +  ++ei + +     + e++++gvP+  le  + ++++k ++V+
  gene851|gene851|rna850|rna850 581 YNYIRNKYKDKVCLLDSEQnlisgRMEKKMEEAEEIVDLFEIEFARVM-A-KREMETVGVPDAILEARITRILKKRKRVE 658
                                    66666666666666665442222245666799**********999443.3.3339************************* PP

                                    EEEE-S- CS
                         MutS_I  82 vveqtet 88 
                                    + +    
  gene851|gene851|rna850|rna850 659 ISQMIAA 665
                                    9876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.33s 00:00:01.06 Elapsed: 00:00:00.53
# Mc/sec: 3960.65
//
Query:       gene852|gene852|rna851|rna851  [L=193]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.078   12.8   0.0       0.11   12.3   0.0    1.2  1  AbiGi     Putative abortive phage resistance protein AbiGi, a


Domain annotation for each model (and alignments):
>> AbiGi  Putative abortive phage resistance protein AbiGi, antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.3e-06      0.11      93     148 ..      48     113 ..      21     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-06
                          AbiGi  93 e........fkesehsklesslelfliyiktfdkse..nksfylerEWRlvpnllsilgekvteee 148
                                    +        +kes+h+ +++++e  ++yik + ++    k++   r W++ ++    +  +++eee
  gene852|gene852|rna851|rna851  48 DlrsrvdavLKESTHKGIKMVMEVIMMYIKGYMEESsrYKTVDIIRGWKSLGKYIREMVGSLSEEE 113
                                    2333444559*********************97665447788889999999987655555777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1143.34
//
Query:       gene853|gene853|rna852|rna852  [L=287]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-71  239.9   0.5    2.1e-71  239.2   0.5    1.4  1  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    3.6e-27   95.1   9.1    3.6e-27   95.1   9.1    2.1  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region
  ------ inclusion threshold ------
       0.15   12.2   0.1       0.33   11.1   0.1    1.6  1  RsbU_N           Phosphoserine phosphatase RsbU, N-terminal d


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.2   0.5   3.5e-75   2.1e-71       1     162 [.      12     172 ..      12     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 3.5e-75
                  Ribosomal_L5e   1 krfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvglt 80 
                                    k+fqvk rrrregktdY++r+++i+qd n y + k+RlvVrvtn+++icqi+ a +egd+v+++a+s+elpkygv++glt
  gene853|gene853|rna852|rna852  12 KNFQVKRRRRREGKTDYKHRTNMIRQDSNSYGSVKHRLVVRVTNSKVICQIVGAYMEGDRVMVYADSSELPKYGVNFGLT 91 
                                    78****************************************************************************** PP

                  Ribosomal_L5e  81 nyaaaYatglllarrllkklgldkiyegqeevtgeeynveeideekrafkaiLdvGLartttgakvfgalkgavdgglsi 160
                                    ny+aaYatg+l++rr+l+ l+ldkiy   +e++g++  ++++d+ek+af+++LdvGLar+t+gakvfga+kga+d+glsi
  gene853|gene853|rna852|rna852  92 NYSAAYATGFLIGRRALTALSLDKIYG-PKEIDGSHSITKDVDGEKKAFRVFLDVGLARSTKGAKVFGAMKGASDAGLSI 170
                                    **************************6.6689************************************************ PP

                  Ribosomal_L5e 161 ph 162
                                    ph
  gene853|gene853|rna852|rna852 171 PH 172
                                    *9 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5      0.67     4e+03      71      94 ..      14      37 ..       3      46 .. 0.65
   2 !   95.1   9.1   6.1e-31   3.6e-27       1      95 []     188     280 ..     188     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.67
                Ribosomal_L18_c 71 vkkeskkykkkkltleqrkarvkq 94
                                    + ++++ ++ k +++ r++ ++q
  gene853|gene853|rna852|rna852 14 FQVKRRRRREGKTDYKHRTNMIRQ 37
                                   333555666777777777666654 PP

  == domain 2  score: 95.1 bits;  conditional E-value: 6.1e-31
                Ribosomal_L18_c   1 AevlrkrIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIredpvkkekkekkevkkeskkykk 80 
                                    A++l++rIfg +++eYm+eL+e+++ekyk qFs+yikkgi+++d+ ++yk+a+++I edp k ekke k+++   kkyk+
  gene853|gene853|rna852|rna852 188 AQELHDRIFGYNISEYMQELRENNPEKYKIQFSDYIKKGIQPEDIPQIYKNAFDKIAEDPIK-EKKEIKDYSG-FKKYKQ 265
                                    78899********************************************************6.7788888888.79**** PP

                Ribosomal_L18_c  81 kkltleqrkarvkqK 95 
                                    ++lt+e+rk+rv++K
  gene853|gene853|rna852|rna852 266 ARLTYEERKERVQAK 280
                                    *************98 PP

>> RsbU_N  Phosphoserine phosphatase RsbU, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   5.5e-05      0.33      28      54 ..     221     247 ..     200     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.5e-05
                                    HHHHTT--HHHHHHHHHHHHHHH-TTS CS
                         RsbU_N  28 ellekgispeeivelHkevleelskdl 54 
                                    + ++kgi+pe+i ++ k++++++++d 
  gene853|gene853|rna852|rna852 221 DYIKKGIQPEDIPQIYKNAFDKIAEDP 247
                                    578********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1995.13
//
Query:       gene855|gene855|rna854|rna854  [L=720]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-43  146.9   1.0    9.9e-43  146.5   1.0    1.2  1  UCH       Ubiquitin carboxyl-terminal hydrolase
    8.2e-11   42.0   0.4    0.00067   19.3   0.0    3.3  2  UCH_1     Ubiquitin carboxyl-terminal hydrolase


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   1.0   1.1e-46   9.9e-43       1     256 [.     224     715 ..     224     716 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 1.1e-46
                                    -EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE--HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH   1 tGlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskavsPkk 80 
                                    +Gl+N GntC+mns lQcL+++ +l++y++s       ++++k+l   +++++   la+a+ dl+++++   +++v+P  
  gene855|gene855|rna854|rna854 224 RGLKNQGNTCFMNSGLQCLMNCWKLTEYFIS-------REYEKHL--VKHKPNYVSLANAYYDLIAQVYDGGHESVTPAG 294
                                    59*****************************.......4444444..222233347*************7789******* PP

                                    HHHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCC..HCCCHHH.HHHCCCTTSHHHHHH-EEEEE............ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.xxxxxxxxxxxxxxxxxxxxx............ RF
                            UCH  81 lkktlsklaksfsgykqqDaqEflaflLdqlhedlnr..evaeekw.kkhlkrndslitdlfegqlks............ 145
                                    +k++l++++++ + ++ qD+ Ef++ +Ld lhe l+   e +++k  k   + n+s+itdlf + lks            
  gene855|gene855|rna854|rna854 295 IKRSLGAIYEEYKRNDEQDTVEFITKILDILHEGLSTqvEFHQKKErKGWWEYNRSIITDLFFFCLKStlscrvcgrskv 374
                                    *************************************44222333345566789************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                            UCH 146 ................................................................................ 145
                                                                                                                    
  gene855|gene855|rna854|rna854 375 smepamclslpvphpmeyknnivlfyessrkqpkriyadssigikelkellyakydvlgkvafiwydsnrnmieasdgai 454
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                            UCH 146 ................................................................................ 145
                                                                                                                    
  gene855|gene855|rna854|rna854 455 lkdisqtlfcyeyfegieycwvhlkikklfmnkslkfnvlikafayneslmlleirralsylvqkgsqdllededispyv 534
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                            UCH 146 ................................................................................ 145
                                                                                                                    
  gene855|gene855|rna854|rna854 535 klelpnqgtkefmanfpvvagmskahegkrlfnalddtldtiqtvspppatldhcldrfleredlhpsellycegcdgkr 614
                                    ******************************************************************************** PP

                                    ....EEEEEEB-SEEEEEEESEEETEE.EEE--SEEB--SEEE-GGGBSS-BTTS-TCS-BEEEEEEEEEES..CTTSEE CS
                                    ....xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                            UCH 146 ....klklkrlPeiLiihlkRfsynss.ksKlntkvefpeeldlssylaeekkkkteekkkYeLiavvvHsG..slssGH 218
                                        k++l++lP++Lii+lkRf+y +s + K++t ve+p    l+++   ++        +Y  +++ +H     +s+GH
  gene855|gene855|rna854|rna854 615 mfskKMDLESLPTYLIIQLKRFQYVNSfPVKISTLVEYP----LNRFHL-GD-------AEYMVMGICNHDSetATSNGH 682
                                    ************************6667***********....555554.22.......23*********99745899** PP

                                    EEEEEECTTTTEEEEEETTEEEEE-HHCCCTT.CEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                            UCH 219 YvayiknekngkWykydDetvkevkeeeevls.sayiLf 256
                                    Yv+y +   +  Wy ++D+++++ ++   v++ + y+Lf
  gene855|gene855|rna854|rna854 683 YVSYLR---KDGWYLCNDQKIEKADR---VDKeHTYVLF 715
                                    ******...567************94...5556999998 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   1.9e-07    0.0017       2     168 ..     225     391 ..     224     419 .. 0.74
   2 !   19.3   0.0   7.5e-08   0.00067     174     320 .]     581     700 ..     526     700 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-07
                                    xxxxxxxxxxxxxxxxxxxxx....xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1   2 GLEnhivnsYlNslLQvlyfi....pplr.nlalshlakeckkehcLlcElgflfdmldkakglncqasnFlralssipe 76 
                                    GL n+ +++++Ns LQ+l  +    + +  + + +hl k+ ++  +L+     l+    ++  +++      r+l+ i  
  gene855|gene855|rna854|rna854 225 GLKNQGNTCFMNSGLQCLMNCwkltEYFIsREYEKHLVKHKPNYVSLANAYYDLIAQVYDGGHESVTPAGIKRSLGAIY- 303
                                    9999999999999999998886666333347788999999999999999999999999999999999999999999887. PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1  77 asalglileeeeetekssaislssliqsfnrflldqlekelketkkns.....seeesaieqllgtkaettirclkCgse 151
                                     ++ +            +++++ + i ++  +l + l+++ +  +k++     + + s+i++l+ + +++t++c+ Cg+ 
  gene855|gene855|rna854|rna854 304 -EEYKRN----------DEQDTVEFITKILDILHEGLSTQVEFHQKKErkgwwEYNRSIITDLFFFCLKSTLSCRVCGRS 372
                                    .444442..........2233445566666666666666555444444567899************************** PP

                                    xxxxxxxxxxxxxxx..xx RF
                          UCH_1 152 ksrksstlvldlkyP..kp 168
                                    k+  +  + l+l  P  ++
  gene855|gene855|rna854|rna854 373 KVSMEPAMCLSLPVPhpME 391
                                    ***9999999996653222 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 7.5e-08
                                    xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 174 eakvtfasilksslerekttra...wCekCkryqpteqrktvknlPpvLalnakleeeeelelwktknwlpleiklslde 250
                                    ++  t++++l ++lere+ +++    Ce C+ + +++++  +++lP  L++++k+++          n +p +i++ ++ 
  gene855|gene855|rna854|rna854 581 PPPATLDHCLDRFLEREDLHPSellYCEGCDGKRMFSKKMDLESLPTYLIIQLKRFQYV--------NSFPVKISTLVEY 652
                                    33479999********8877543449****************************97665........99****9996664 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 251 dknleeklkeerekakaekeikvYeLqsvvvhigdske.sghLvslvkvaekelerdppesqWylFNDflV 320
                                              +r     + + + Y ++++  h +++ + +gh+vs+ +   k        + Wyl ND ++
  gene855|gene855|rna854|rna854 653 PL--------NR----FHLGDAEYMVMGICNHDSETATsNGHYVSYLR---K--------DGWYLCNDQKI 700
                                    32........22....2445679*****99999877556*********...3........79******876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 4335.93
//
Query:       gene856|gene856|rna855|rna855  [L=1480]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-22   78.1   2.6    2.7e-15   56.3   0.1    3.4  3  Sec63          Sec63 Brl domain
      1e-20   74.2   0.0    3.5e-20   72.5   0.0    1.9  1  DEAD           DEAD/DEAH box helicase
    8.1e-11   42.2   0.0    1.6e-10   41.2   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
    3.4e-09   37.0   0.0    1.7e-08   34.8   0.0    2.2  2  Helicase_C     Helicase conserved C-terminal domain
     0.0044   16.1   0.0     0.0086   15.2   0.0    1.4  1  T2SSE          Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.065   13.6   0.1       0.22   11.9   0.1    1.9  1  AAA_19         AAA domain
      0.071   12.8   0.1       0.54   10.0   0.0    2.3  2  IstB_IS21      IstB-like ATP binding protein
      0.078   12.5   0.0       0.17   11.4   0.0    1.5  1  AAA_7          P-loop containing dynein motor region
       0.13   12.2   0.0       0.36   10.8   0.0    1.7  1  Microtub_bd    Microtubule binding
       0.21   11.1   0.0       0.39   10.2   0.0    1.4  1  UvrD-helicase  UvrD/REP helicase N-terminal domain


Domain annotation for each model (and alignments):
>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.1   1.5e-18   2.7e-15       1     213 [.     676     912 ..     676     940 .. 0.92
   2 !   19.6   0.1   2.2e-07    0.0004       2     132 ..    1265    1384 ..    1264    1397 .. 0.75
   3 ?   -3.2   0.0         2   3.6e+03     239     252 ..    1456    1469 ..    1451    1470 .. 0.86

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.5e-18
                                    ECHHHHHHHHHT--HHHHHHHHHHS-TT--HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHTSSS--SSSTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63   1 ptelGriaShYyisyetiklfneslkpnttlkdlLeilssasEFeeipvReeEkkelkkLlekvpikvkediespeaKvn 80 
                                    pt++G+i+S+Yyi y+  k + +++++ + +++l++il +  EF+++++ ++E ++lk+L    pi+     esp     
  gene856|gene856|rna855|rna855 676 PTTIGEISSRYYIHYRDAKRLFDEVSQIMMESSLFRILERTREFSDLKIDQKEMETLKELV---PIPT----ESP---FG 745
                                    799**********************************************999999999997...8884....344...48 PP

                                    HHHHHHHTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHTS-TT............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                          Sec63  81 iLlqayisrlklegsdlvsDlkyilqnairilralveillskgwlslalslleLskmveqrlwds............... 145
                                    iL+q+yi++          D ++  qn +r++r l+ei ++k+     + +l  +k  e+r+ +                
  gene856|gene856|rna855|rna855 746 ILVQCYIANRM--------DSSSLSQNLCRMFRVLFEIGIRKRLGIS-KMILGWCKASEHRIFPYqtplrhfacdkdalr 816
                                    *******8755........888999***************9987655.99*************9899************* PP

                                    ....................................S--EEEEEEECEBTTSEEEEEEEEEESSSS-SCTSSS-CHTSBE CS
                                    ....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63 146 ....................................lPkleieaevqpitrsklrvevtiereeeeskpdfpwdkkgkse 189
                                                                        +Pk++i  ++++ +   + v++ ie       + f  +   +s+
  gene856|gene856|rna855|rna855 817 nlemkeipfgmieilgkegldeigvcgnsiieylkyVPKFNILPSLRVSALGHYIVSIGIE-------KAFDDSM-IHSN 888
                                    *************************************************************.......6666666.899* PP

                                    EEEEEEEETTTTEEEEEEEEEESS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63 190 kfwlvvedsendellaikrvtlek 213
                                    + +l++ ds +++l+ ++ +++e+
  gene856|gene856|rna855|rna855 889 TYYLFITDSMEEKLIVYDAIIFER 912
                                    ******************999976 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.2e-07
                                     CHHHHHHHHHT--HHHHHHHHHHS-TT--HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHTSSS--SSSTTSHHHHH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63    2 telGriaShYyisyetiklfneslkpnttlkdlLeilssasEFeeipvReeEkkelkkLlekvpikvkediespeaKv 79  
                                     t +G++  +Y++ ++ti++fne++k ++ lk++  ++++asE     v + + +e ++L           ++ +  Kv
  gene856|gene856|rna855|rna855 1265 TRYGMVLCKYCVGMDTIEMFNERIKDKMGLKSIQALVCRASE----AVLDMDTDEFEALSRA-------GVDLSAGKV 1331
                                     789**************************************9....5556666666666633.......555666777 PP

                                     HHHHHHHHTT---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Sec63   80 niLlqayisrlklegsdlvsDlkyilqnairilralveillskgwlslalsll 132 
                                     +  +  ++  +  ++  +++   +il  + r+  ++vei+l+k  l++a +++
  gene856|gene856|rna855|rna855 1332 HGVISYVLRMSGGDEWVFQQYEDKILPVMHRLYLCTVEISLEKMCLKTAFNAM 1384
                                     77777766666666666666667777777777777777777777777666665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2
                                     EEEEEESSSSS-EE CS
                                     xxxxxxxxxxxxxx RF
                          Sec63  239 tvrlisdswlgldq 252 
                                     +++++sds+ g+++
  gene856|gene856|rna855|rna855 1456 SCYVMSDSYPGFET 1469
                                     789*******9986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   1.9e-23   3.5e-20       3     171 ..     247     401 ..     245     405 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.9e-23
                                    HHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   3 iQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    iQ+ + + il ++g+vlv+a+TGsGKT + ++ +l+++   +++++ ++ +++P+++La++++++++k ++  d  v  +
  gene856|gene856|rna855|rna855 247 IQSVVQDSILkRNGNVLVCAPTGSGKTVIGIMSILREI---ERRERIRVGYIVPMKALAREMCKTISKALSDHDTVV--V 321
                                    88889999996678*********************999...68****************************877333..3 PP

                                    ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrq 161
                                     + ++  + +++l +++ ++v+tp+++d l+++      q+ ++++DE++ + d  ++  i++i+++++     g    +
  gene856|gene856|rna855|rna855 322 EHTSDVYSGYNHL-EKAGVIVSTPEKFDVLTRNTD---LQFDLMIIDEIHIVGDT-RGGAIEAIVARMS---MGG--GCR 391
                                    3344556788888.99************9885555...48899***********9.************3...333..356 PP

                                    EEEEESSBSH CS
                                    xxxxxxxxxx RF
                           DEAD 162 vivlSATlpk 171
                                    ++ lSATlp+
  gene856|gene856|rna855|rna855 392 IVGLSATLPN 401
                                    ********94 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   9.1e-14   1.6e-10      21     170 ..     252     400 ..     229     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 9.1e-14
                                    ......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS CS
                         ResIII  21 s....krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke....igkkvsgd 92 
                                    +    kr+ ++l+ ++TG+GKT++ +  i r  + +++ ++  +vp k+l   + ++++k ls++++     ++ ++sg 
  gene856|gene856|rna855|rna855 252 QdsilKRNGNVLVCAPTGSGKTVIGIMSILREIERRERIRVGYIVPMKALAREMCKTISKALSDHDTVvvehTSDVYSGY 331
                                    1444489999***************77777777777777************************99876666666667777 PP

                                    -B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T..TTHHHHHT---...SEEEEEES CS
                         ResIII  93 kkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk..swreilekfke...avllglTA 167
                                    ++ +      ++ ++v+t +++d           ++ + +fd++iiDE H +g+    ++++i+  ++    + ++gl+A
  gene856|gene856|rna855|rna855 332 NHLE------KAGVIVSTPEKFDVLT--------RNTDLQFDLMIIDEIHIVGDTRggAIEAIVARMSMgggCRIVGLSA 397
                                    7777......****************........89999***************635688888666666777******** PP

                                    S-S CS
                         ResIII 168 Tpe 170
                                    T++
  gene856|gene856|rna855|rna855 398 TLP 400
                                    *86 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   9.3e-12   1.7e-08      10     110 ..     450     578 ..     442     579 .. 0.75
   2 ?   -2.6   0.1       3.8   6.9e+03      12      35 ..    1112    1136 ..    1104    1150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 9.3e-12
                                    HHHTTTTSEEEEEESSHH...HHHH....HHHH..HHHT..............TSTEEEESTTSTHHHHHHHHHHHHTTS CS
                     Helicase_C  10 lkleeeggkilifvntid...rlek....vkll..lekk..............gikvavlhgelpqnereeileqfnkge 66 
                                    l++ e++g il+fv+++    +        +++                    + +v ++h+ l  + r ++ + +++g+
  gene856|gene856|rna855|rna855 450 LENLESNGPILVFVHSRGealE--VaneiKRYMerM--DspevdvspnvqgllKHRVGIHHAGLDRKTRVAVEDLYRDGK 525
                                    4455888999999999985441..233443444330..1333444555557789************************** PP

                                    SSEEEESGGGTSSSTSTTESEEE....ESSSS..SSH...HHHHHHHTTSSST CS
                     Helicase_C  67 sdvLiatdvaerGidipkvnlVi....nfdlp..rnv...tsyiqriGRtgRa 110
                                    +dv+++t  ++ G+++p+ +++i     +d+   +++    ++iq+ GR+gR+
  gene856|gene856|rna855|rna855 526 IDVMVSTATLAWGVNLPGKTVIIkgteVYDASygWKPvkqIEMIQMFGRAGRF 578
                                    *****************999999776666666555446779***********7 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.8
                                     HTTTTSEEEEEESSHHHHHH.HHHH CS
                     Helicase_C   12 leeeggkilifvntidrlek.vkll 35  
                                     l+ e++ +li++ t + +++  k++
  gene856|gene856|rna855|rna855 1112 LNMEKYSCLIICSTSKVVKHfKKFF 1136
                                     5667889999999999886533444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.8e-06    0.0086     107     160 ..     236     290 ..     219     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.8e-06
                          T2SSE 107 dlgaeealkekiaevlrkav.rerglilvsGgTgsGKttll.yallkeinksderi 160
                                     l  +  + + i++v++ ++ +++g++lv  +TgsGKt++   ++l ei+ + eri
  gene856|gene856|rna855|rna855 236 RLFGNDFMFNYIQSVVQDSIlKRNGNVLVCAPTGSGKTVIGiMSILREIERR-ERI 290
                                    5555566667788888887625669*************98648999999998.766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00012      0.22       9     117 ..     258     372 ..     251     387 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddllteal 88 
                                    +++++lv a+ G+GKT +  +i+++l e+++++  ++  + + +  a+e+ + +++++ + +T+     ++ ++++    
  gene856|gene856|rna855|rna855 258 RNGNVLVCAPTGSGKTVI--GIMSILREIERRERIRVGYIVPMKALAREMCKTISKALSDHDTVV----VEHTSDVYSGY 331
                                    67899**********976..555555565555566788888888888888888866666655553....22222222222 PP

                         AAA_19  89 elle.............eaeeekklqeeellivDEfqdvdel 117
                                    + le               +++++l + +l+i+DE+  v ++
  gene856|gene856|rna855|rna855 332 NHLEkagvivstpekfdVLTRNTDL-QFDLMIIDEIHIVGDT 372
                                    2222233333455555433455566.4559999998777655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0003      0.54      33      67 ..     245     279 ..     228     311 .. 0.78
   2 ?   -0.9   0.1      0.65   1.2e+03      74     120 ..     684     730 ..     678     735 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0003
                      IstB_IS21  33 rkvkeLatlsfiekkenivllGpsGvGKshlaial 67 
                                    + +++++++s ++++ n++++ p+G GK+ + i  
  gene856|gene856|rna855|rna855 245 NYIQSVVQDSILKRNGNVLVCAPTGSGKTVIGIMS 279
                                    56899999*********************987654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.65
                      IstB_IS21  74 aglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgll 120
                                    + + + +  +++L+ e+++   + +l r+l+r  +++ l +D+  ++
  gene856|gene856|rna855|rna855 684 SRYYIHYRDAKRLFDEVSQIMMESSLFRILERTREFSDLKIDQKEME 730
                                    567789999**********************9999987877776555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.5e-05      0.17      23      65 ..     249     292 ..     244     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.5e-05
                          AAA_7  23 syllelllknkkpvllvGptGtGKtvi.ikdllkkldkekylsl 65 
                                    s++ + +lk++ +vl++ ptG+GKtvi i+++l+++++++ + +
  gene856|gene856|rna855|rna855 249 SVVQDSILKRNGNVLVCAPTGSGKTVIgIMSILREIERRERIRV 292
                                    56778999******************944559999987665555 PP

>> Microtub_bd  Microtubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002      0.36      64      98 ..     240     274 ..     217     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                    CCCCCCCCHHHHHHHHTT--EEEEEEES....... CS
                    Microtub_bd  64 qeevfeeisqlvqsaldgynvcifaygqTGsGKty 98 
                                    ++++f+ i+ +vq ++ + n +++ ++ TGsGKt 
  gene856|gene856|rna855|rna855 240 NDFMFNYIQSVVQDSILKRNGNVLVCAPTGSGKTV 274
                                    78999****************************95 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00022      0.39       8      67 ..     254     311 ..     248     358 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                    HHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS.STGGGEEEEESSHHHHHHHHHHHHH CS
                  UvrD-helicase   8 aiaslggpilveAsAGsGKTfvlaerilrlikeee.iepdrilvvTFTnkAaeElkeRiee 67 
                                     i + +g++lv A  GsGKT + +  ilr i+ +e i +  i+     ++ a+E+ + i +
  gene856|gene856|rna855|rna855 254 SILKRNGNVLVCAPTGSGKTVIGIMSILREIERRErIRVGYIVP---MKALAREMCKTISK 311
                                    566779*************************9884344444432...35556666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.88u 0.30s 00:00:01.18 Elapsed: 00:00:00.48
# Mc/sec: 9342.48
//
Query:       gene857|gene857|rna856|rna856  [L=990]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-48  166.1  27.6    3.1e-48  164.7  27.6    1.7  1  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
    2.6e-17   62.3   3.4    2.6e-17   62.3   3.4    2.8  3  PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
    3.5e-12   47.1   0.0    8.5e-11   42.5   0.0    2.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    2.4e-05   24.3   0.0    0.00029   20.9   0.0    2.4  2  Cation_ATPase    Cation transport ATPase (P-type)
    0.00012   21.6   4.4    0.00012   21.6   4.4    2.9  3  E1-E2_ATPase     E1-E2 ATPase
     0.0013   18.5   0.1     0.0055   16.5   0.0    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.046   13.7   0.1        4.9    7.3   0.0    2.5  2  KorB             KorB domain
       0.09   12.5   0.2       0.25   11.1   0.1    1.7  2  ASFV_J13L        African swine fever virus J13L protein


Domain annotation for each model (and alignments):
>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.7  27.6   1.4e-51   3.1e-48       2     242 ..     742     979 ..     741     986 .. 0.90

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 1.4e-51
                PhoLip_ATPase_C   2 raSDyaiaqFrfLkrLLlvhGrwsyrRisklilyffyKnvvftlvqfwfqfyngfsgqslyeswlltlynllftslpviv 81 
                                     ++D+ai++Fr Lk+L+lvhGr++++R sk+ l  f+Kn++f+ +qf+++f+ng+sg ++y++++l  yn+lfts+ ++ 
  gene857|gene857|rna856|rna856 742 LSADFAIPEFRLLKKLILVHGRYNLIRFSKITLNAFFKNIFFISIQFMYNFFNGYSGKPIYNNFFLNYYNVLFTSFVPLS 821
                                    69****************************************************************************** PP

                PhoLip_ATPase_C  82 lgifdqdvsaelllkyPelYklgqknklfnlktfllwileglyqsliifflsylv..lddssfsdgktndlqlfgtlvft 159
                                    +g+fd+d ++++l+++Pe Yk  +  ++f+  +f++ ++  ++ ++++f+ls+ v  ++d+++ +g   ++ l+ ++  +
  gene857|gene857|rna856|rna856 822 IGLFDKDKPENYLMAHPEDYKNAR--RFFSRPSFVFGFIYTILLGIVVFLLSVGVvyIKDMVSRSGLVGGYILLTNYFSI 899
                                    *********************888..7*************************9996444444448999998888887777 PP

                PhoLip_ATPase_C 160 alvlvvnlkvaletktwtliliililgsillyflflllyssllpsssefygvleelfsspsfwlvlllvvvvallpdlli 239
                                    +++lvv+ + + e++++ ++++i+i +si+l f+ l+++++l  +     +++++lfs p f+lv+l+v+  +ll+dl+i
  gene857|gene857|rna856|rna856 900 VVFLVVLSTQIREISFFVIYSWIAIALSIALNFITLFFIQELDVT---ANNAAFNLFSLPVFYLVTLFVLSGTLLVDLVI 976
                                    777777777777*****************************8763...444589**********************9998 PP

                PhoLip_ATPase_C 240 kvl 242
                                      +
  gene857|gene857|rna856|rna856 977 MRM 979
                                    755 PP

>> PhoLip_ATPase_N  Phospholipid-translocating ATPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   3.4   1.2e-20   2.6e-17      16      66 ..       5      55 ..       2      56 .. 0.97
   2 ?   -5.6   5.6         8   1.8e+04      17      41 ..     765     789 ..     761     794 .. 0.50
   3 ?   -3.7   0.3       4.4   9.8e+03      27      43 ..     930     946 ..     929     947 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 1.2e-20
                PhoLip_ATPase_N 16 sNkIsTsKYtlltFlpknLfeqFrrvaNlYFLviailqliPqisplspvtt 66
                                   +NkI TsKYt++tFlp+n+++q++r +Nl+FL+++il  iP+isp+sp+t+
  gene857|gene857|rna856|rna856  5 ENKIVTSKYTAMTFLPQNMYHQLSRPSNLFFLLTLILLSIPAISPFSPFTY 55
                                   7************************************************97 PP

  == domain 2  score: -5.6 bits;  conditional E-value: 8
                PhoLip_ATPase_N  17 NkIsTsKYtlltFlpknLfeqFrrv 41 
                                    N I+ sK tl  F+   +f   + +
  gene857|gene857|rna856|rna856 765 NLIRFSKITLNAFFKNIFFISIQFM 789
                                    4445555555555554444444444 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.4
                PhoLip_ATPase_N  27 ltFlpknLfeqFrrvaN 43 
                                    l+F+ +++++++   aN
  gene857|gene857|rna856|rna856 930 LNFITLFFIQELDVTAN 946
                                    79999999999998888 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   3.8e-14   8.5e-11       2     207 ..     380     724 ..     379     727 .. 0.64

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 3.8e-14
                                    SEEEEESBTTTBCHHHHHHHHHHHH.............CHHHHHHHHHHHHCHHHHHHHHHHHHH............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa.............alalaaaletgsehpigkalvaaakar............... 53 
                                    + ++ Dk+GTLt+ +++ + + v++                            + + l  aa++r               
  gene857|gene857|rna856|rna856 380 EYILTDKTGTLTKNSMVFKYCHVYNspelisredlkehC----------LSIDLLNDLSPAAEKRrsrmmfilallccns 449
                                    56899**********999999999966544444444331..........3333333333333333233333333333332 PP

                                    HHHH.HHHHHETTTE......................HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHH....... CS
                                    xxxx.xxxxxxxxxx......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                      Hydrolase  54 sgal.tgfatfigrg......................ayaigkpewltaldippdlgaaigsaqsqgrtvall....... 103
                                     ++l  +f+ +                          +                                  l       
  gene857|gene857|rna856|rna856 450 IEPLnNNFEGISQDElcivqelrnqgyvlierderyvV----------------------------------Leingrrt 495
                                    22222333332222233333333333222222233330..................................13333333 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                      Hydrolase 104 ................................................................................ 103
                                                                                                                    
  gene857|gene857|rna856|rna856 496 klnimisldftssrqrmsvvmemlgkyilfckgsdqkllgdkkmtfekgdtgtikalinnnseyrslvvgykeldrnale 575
                                    33355555555555555555557777777777777777777777777777777777788888888888888888888888 PP

                                    ...........................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT CS
                                    ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 104 ...........................qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG 156
                                                                  +l+   i+d+  + ++++ ++ sL++agi+++++tgd +eta ++ + +G
  gene857|gene857|rna856|rna856 576 rmreqynrvslknkfleqervfdsveeGMVYLGATFIEDE--LQEGVRGTITSLRDAGIKIWMITGDKKETAISCSEDCG 653
                                    89999999999999999999988887666899999999**..************************************** PP

                                    ...............GGGESEEEEHHCES....STTT.............SHHHHHHHHHHHTSTGGGEEEEESSHHHHH CS
                                    ...............xxxxxxxxxxxxxx....xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 157 ...............ddyfdaviasdiet....vakp.............spegkvaaireLqgkpeevamVGDgvnDaa 204
                                                   +            +      +p              p +k ++++++ + +++++ +GDg nD++
  gene857|gene857|rna856|rna856 654 iiqknneaqslvvdgK------------EflnrLTGPdifeyrsiviyraTPYHKGKIAEKIVELGKNTLSIGDGNNDVP 721
                                    7765544444444322............1333423335555555555555************877999************ PP

                                    HHH CS
                                    xxx RF
                      Hydrolase 205 ala 207
                                    +l 
  gene857|gene857|rna856|rna856 722 MLT 724
                                    *95 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.3e-07   0.00029      39      85 ..     490     534 ..     463     538 .. 0.87
   2 ?    0.1   0.0      0.38   8.5e+02      13      28 ..     631     646 ..     622     667 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
                  Cation_ATPase  39 teelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiil 85 
                                    ++  r + +++  + F+ssr rmsvv++    +k++l++KG+ + +l
  gene857|gene857|rna856|rna856 490 INGRRTKLNIMISLDFTSSRQRMSVVMEML--GKYILFCKGSDQKLL 534
                                    5667788899999***************87..*********988776 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.38
                  Cation_ATPase  13 ekdevkllGnktEsAL 28 
                                      + + ++G+k E+A+
  gene857|gene857|rna856|rna856 631 GIKIWMITGDKKETAI 646
                                    567799*********8 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   4.4   5.5e-08   0.00012       6      97 ..      88     259 ..      83     311 .. 0.85
   2 ?   -4.1   3.6       4.2   9.4e+03     119     154 ..     894     928 ..     882     938 .. 0.48
   3 ?   -2.4   2.5       1.3     3e+03     117     146 ..     914     947 ..     905     972 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.5e-08
                                    EEEEE.-TT...S-EEEEGGG--TTSEEEEETT-B--SEEEEEE............E-SEEE-TTTS---S-EE-..... CS
                   E1-E2_ATPase   6 takvi.rdg...teeeidakelvpGDivllkagdrvpaDgrive............gsaevdesaLTGEslpvek..... 64 
                                     a+v+ r+g    +e+i +++++ GD++++ + + vp D+++++              +  ++s L GE    +k     
  gene857|gene857|rna856|rna856  88 PANVVrRSGddvYVEKIHVEDINAGDLIFIMKDQEVPGDVVLLNsrmetkdgvkckNYCFAETSNLDGETNLKKKtsqhq 167
                                    4555545554446778************************************99866669******************** PP

                                    ..........................................................G-TTEE-TT-EEEE.-EEEEEE CS
                   E1-E2_ATPase  65 ..........................................................ekgdmvfsGtvvvs.geakavV 85 
                                                                                              ++++ +  G+ +++  ++ a V
  gene857|gene857|rna856|rna856 168 vkckeegmevefcgevlnvcscdkyymkntsefivedtgdlfnkfecqvsiegknilcNEKNVLLRGSRIKNtERVLAMV 247
                                    ***********************************************************************977899*** PP

                                    EE-TTTSTTTTT CS
                   E1-E2_ATPase  86 tatgedtelgki 97 
                                    + +g++t+lgk 
  gene857|gene857|rna856|rna856 248 VCVGKQTKLGKS 259
                                    *********985 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 4.2
                                    HHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHH CS
                   E1-E2_ATPase 119 gkvlvpvvlliallvflialllgkslaeallralal 154
                                    ++++++vv+l++l + +  ++ +     ++  al++
  gene857|gene857|rna856|rna856 894 TNYFSIVVFLVVLSTQIREISFFVIY-SWIAIALSI 928
                                    44455555555444444333322222.333333333 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHHHHHHHHHHS-STTTSSTT....H CS
                   E1-E2_ATPase 117 klgkvlvpvvlliallvflialllgksla....e 146
                                    +++ +++++++++++++ +i+l+  ++l     +
  gene857|gene857|rna856|rna856 914 SFFVIYSWIAIALSIALNFITLFFIQELDvtanN 947
                                    5778899999999999998888866555433443 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   3.5e+03      16      52 ..     616     652 ..     613     657 .. 0.79
   2 !   16.5   0.0   2.4e-06    0.0055     203     227 ..     707     731 ..     696     749 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                                    --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHC CS
                    Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleel 52 
                                    ++e  + +i  l+++gik+   TG + +++++  e+ 
  gene857|gene857|rna856|rna856 616 LQEGVRGTITSLRDAGIKIWMITGDKKETAISCSEDC 652
                                    5677788999***********9998888877776665 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.4e-06
                                    GGGEEEEESSGGGHHHHHHSSEEEE CS
                    Hydrolase_3 203 leeviafGDgeNDieMLeaaglgvA 227
                                     ++++++GDg+ND++ML+ + +gv 
  gene857|gene857|rna856|rna856 707 GKNTLSIGDGNNDVPMLTSSHVGVG 731
                                    589**************99988874 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0022       4.9      29      86 ..     111     171 ..     103     173 .. 0.88
   2 ?    3.6   0.0      0.03        66      18      60 ..     394     436 ..     389     446 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0022
                           KorB  29 vpdylrelydseviadirtLyeLrraaekhpaevrafv.....aengeagltrsavrrflksl 86 
                                    + d ++ + d+ev +d+ +L++  r+  k++ ++++++     +  ge +l+++++++++k +
  gene857|gene857|rna856|rna856 111 AGDLIFIMKDQEVPGDVVLLNS--RMETKDGVKCKNYCfaetsNLDGETNLKKKTSQHQVKCK 171
                                    568899999************7..9999***********99888899**********999865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.03
                           KorB  18 sfvslylklldvpdylrelydseviadirtLyeLrraaekhpa 60 
                                    s v  y  ++++p+ +     +e +  i++L++L  aaek   
  gene857|gene857|rna856|rna856 394 SMVFKYCHVYNSPELISREDLKEHCLSIDLLNDLSPAAEKRRS 436
                                    667788899999999977666799**************99765 PP

>> ASFV_J13L  African swine fever virus J13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.5   5.6e+03      20      66 ..      43      87 ..      40     100 .. 0.65
   2 ?   11.1   0.1   0.00011      0.25       9      53 ..     836     881 ..     829     887 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.5
                      ASFV_J13L 20 svsapsffsthmytiliaivvliiiiivliylfssrkkkaaaaieee 66
                                   s++a s fs   +t l+a vv++   ++   +   r++k   ai+e+
  gene857|gene857|rna856|rna856 43 SIPAISPFSP--FTYLLAFVVVVGASMMKDGVEDYRRHKQDKAINEK 87
                                   5666677776..45577777777666666666666666666666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                      ASFV_J13L   9 vyprhygeclssvsapsffsthmytiliaivvliiii.ivliylfs 53 
                                     +p  y +     s psf    +ytil+ ivv+++ + +v i  + 
  gene857|gene857|rna856|rna856 836 AHPEDYKNARRFFSRPSFVFGFIYTILLGIVVFLLSVgVVYIKDMV 881
                                    57888888999999*****************987755255555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (990 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 6256.01
//
Query:       gene858|gene858|rna857|rna857  [L=381]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-62  211.7   0.2      2e-62  210.9   0.0    1.5  2  Thiolase_N     Thiolase, N-terminal domain
    1.2e-42  144.4   0.1    2.5e-42  143.4   0.1    1.5  1  Thiolase_C     Thiolase, C-terminal domain
     0.0004   20.0   0.3     0.0012   18.5   0.2    1.8  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.9   0.0   3.3e-66     2e-62       1     259 [.       7     248 ..       7     249 .. 0.94
   2 ?   -3.1   0.0      0.67     4e+03      30      47 ..     282     299 ..     280     310 .. 0.81

  Alignments for each domain:
  == domain 1  score: 210.9 bits;  conditional E-value: 3.3e-66
                                    EEEEEEEEE--EE.TTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEE CS
                     Thiolase_N   1 vvivsaartpigk.fggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpav 79 
                                    vviv a rtpig+  +g lk+l+ +eL ++a+++++ek+ +dp+ ++ev++G  l+++eg+  ar  al+agip e+p++
  gene858|gene858|rna857|rna857   7 VVIVCALRTPIGRaGKGKLKSLKNDELITAAIQGVIEKTRIDPKLIEEVVLGHCLSSMEGSVAARIGALRAGIPAETPVM 86 
                                    8************99***************************************************************** PP

                                    EEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHH CS
                     Thiolase_N  80 tvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGlta 159
                                    t+n++c+Sg++++ l+a++i++g++++ +agG Esms     ++   + + +  ++ a+d+ +             G  +
  gene858|gene858|rna857|rna857  87 TINRLCASGMESIGLIAEKIKSGRIEIGLAGGFESMSSYGLPQE--YNLSRNETSTDARDCFLSF-----------GEVT 153
                                    *************************************8777776..5556677778899**9888...........**** PP

                                    HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS- CS
                     Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtv 239
                                    e+l k+y+i+R+e de+A  s+++a +a k+g++ +ei+ +kv    g++ ++ de+ir+ + +e ++klkp+F+++G  
  gene858|gene858|rna857|rna857 154 EMLSKTYGITRDEADEYASMSQRRALEAMKKGNLLKEIIQMKV----GDENIKDDEGIRE-TLLEVIKKLKPVFRDDGIC 228
                                    **************************************44444....445699******9.9****************** PP

                                    BTTSB--BEEEEEEEEEEEH CS
                     Thiolase_N 240 tAgnasqisDGaaavllmse 259
                                    t +n+sq+sDGa+a+llm++
  gene858|gene858|rna857|rna857 229 TSANSSQLSDGASAILLMKR 248
                                    ******************96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.67
                                    HHHHHHHHHTS-GGGCCE CS
                     Thiolase_N  30 alkallekagvdpeevde 47 
                                    a+++ll++++++++++++
  gene858|gene858|rna857|rna857 282 AIEKLLDRNNLKKDQISY 299
                                    789999999999999876 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.1   4.2e-46   2.5e-42       3     122 ..     258     378 ..     256     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 4.2e-46
                                    -SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHHH-B-T CS
                     Thiolase_C   3 plakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaialGHPl 82 
                                    ++++++++++vg +p+++glgP+ ai+k+l+++ l+ ++i +fEinEAFa+q+L ++++l++ ++kvN +GGaialGHP+
  gene858|gene858|rna857|rna857 258 VIGEFVDFIVVGLKPRDMGLGPVVAIEKLLDRNNLKKDQISYFEINEAFASQVLCCLRRLGIGEDKVNRYGGAIALGHPI 337
                                    567899************************************************************************** PP

                                    TTHHHHHHHHHHHHHHHCT.TSEEEEEEEETTTEEEEEEEE CS
                     Thiolase_C  83 GasGaRivvtllselkkeg.gklgvaalCigggqgvalvie 122
                                    GasGaRiv tll+ +++e  g++gva+lC g+g+g+a++++
  gene858|gene858|rna857|rna857 338 GASGARIVCTLLNVMENESlGEYGVASLCVGAGHGIAALFK 378
                                    ***************998779****************9987 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2     2e-07    0.0012     146     207 ..      61     124 ..      24     145 .. 0.81
   2 ?   -2.5   0.0      0.52   3.1e+03     237     253 .]     235     251 ..     223     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-07
                                    HHHHSTTHHHHHHHHH...HT--SSEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                  ketoacyl-synt 146 vgavlanviagrisya...lglrGpsvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                    +++ +   +a+ri        ++ p++t+   C+S+   + ++ ++++sg++++ laGG e + +
  gene858|gene858|rna857|rna857  61 LSS-MEGSVAARIGALragIPAETPVMTINRLCASGMESIGLIAEKIKSGRIEIGLAGGFESMSS 124
                                    455.66677888876665555788************99999999****************98765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.52
                                    -BB-EEEEEEEEECHHH CS
                  ketoacyl-synt 237 vlGEGvGavvLkrleda 253
                                     l++G+ a++L+++++a
  gene858|gene858|rna857|rna857 235 QLSDGASAILLMKRRKA 251
                                    57999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2254.98
//
Query:       gene859|gene859|rna858|rna858  [L=602]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0039   16.9   1.1       0.02   14.6   1.1    2.3  1  DUF3953   Protein of unknown function (DUF3953)
     0.0053   16.6   0.0       0.01   15.7   0.0    1.4  1  MIR       MIR domain
  ------ inclusion threshold ------
      0.088   12.7   1.5        0.1   12.5   0.1    1.9  2  PsbJ      PsbJ


Domain annotation for each model (and alignments):
>> DUF3953  Protein of unknown function (DUF3953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.1   3.3e-06      0.02       6      39 ..     145     178 ..     143     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                        DUF3953   6 GlmaltiGieEfkkenkfsGillilaalfvlfVs 39 
                                    ++++l+ Gi ++kk++++++ +li  ++++  +s
  gene859|gene859|rna858|rna858 145 SIYFLVSGIVQLKKNRTTTSGFLIGLSIASSWAS 178
                                    799************************9986665 PP

>> MIR  MIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-06      0.01      41     171 ..     294     417 ..     272     429 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-06
                            MIR  41 adaanssraLWeievvqkd......awrgglikwgkvyRlkHlaTgryLaseeekksplseseddqkevsayglegfegd 114
                                     d+ ++  ++W    v+ +      + +g++i++g++++l  l + + L + +e      ++ed+ k+v  ++ +  e  
  gene859|gene859|rna858|rna858 294 SDQRTE-SSMWMMIKVHPTnstgnvEEEGRYINHGDLVKLVELGSSMCLRVSNE------DTEDKFKKVIGFTQQDNE-- 364
                                    455555.588887777666566766679*************************9......888899999988884443.. PP

                            MIR 115 nDkveifekksttgmksaklvprdsyvrlqHvvtgcwLhstsvk.lkkekfekvqqkv 171
                                     D+++i      +  ++  +v+r+s +r++H++t+  L   + + l++e ++++ +kv
  gene859|gene859|rna858|rna858 365 ADEEDIW-----QIIGDGPVVSRSSLIRFRHYKTAMDLCVRNLRkLEEEAKRNGVEKV 417
                                    4445555.....6899*******************98888887646666544445555 PP

>> PsbJ  PsbJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.8e-05       0.1       3      22 ..     113     132 ..     111     139 .. 0.76
   2 ?   -3.1   0.1       1.2   7.5e+03      34      39 .]     334     339 ..     333     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.8e-05
                                    XTTSS-HHHHHHHHHHHHHH CS
                           PsbJ   3 gtGRIPLWlVatvaGlgvit 22 
                                    +  R+P W+Vatv  +g ++
  gene859|gene859|rna858|rna858 113 TYSRVPSWIVATVHVIGLLV 132
                                    568*********97666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                                    STTS-- CS
                           PsbJ  34 GlGSSL 39 
                                     lGSS+
  gene859|gene859|rna858|rna858 334 ELGSSM 339
                                    59***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3835.27
//
Query:       gene860|gene860|rna859|rna859  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-07   29.8   0.0    6.4e-07   29.2   0.0    1.2  1  Guanylate_cyc  Adenylate and Guanylate cyclase catalytic doma
  ------ inclusion threshold ------
      0.073   13.2   0.0       0.14   12.3   0.0    1.5  1  KHA            KHA, dimerisation domain of potassium ion chan


Domain annotation for each model (and alignments):
>> Guanylate_cyc  Adenylate and Guanylate cyclase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   7.1e-11   6.4e-07      11     151 ..     107     249 ..     102     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.1e-11
                  Guanylate_cyc  11 ilFadIvgftalssahspievvklLnelyarfdelldekkvykvktiGdaymvvsglp.......eekaahaakl..ael 81 
                                    ++ +dIv++t+l++   p ++ + ++ + +  + l++++++ +v+  Gd++  v+            ++    ++  +++
  gene860|gene860|rna859|rna859 107 LVITDIVDSTSLWNCF-PDAMHRTIEVHDEVARGLCKAYGGLEVRNEGDSFFLVFTDIrnaldfsI-RFYREIECisFNF 184
                                    6779*********955.**********************************999988767876632.3333333301344 PP

                  Guanylate_cyc  82 aLdmlealeevaveskeglkvrvGihtGpvvagviGakkprydvwGntvnlAsrmestgkagkiqvseet 151
                                      ++++ ++e ++ ++  lk+r  +++Gp+++ +     +   ++G++v+ +  m s+++ gki +s++ 
  gene860|gene860|rna859|rna859 185 RHAFTKRVREGKETEFLPLKIRMAMNKGPIMLCHN----KFLEIYGDAVTKTFGMLSHSN-GKICISQNC 249
                                    44555666666666689*************99887....7789*********99999986.678888765 PP

>> KHA  KHA, dimerisation domain of potassium ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05      0.14       2      30 ..      54      82 ..      53      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                            KHA  2 RVtifpnhpedskrseGklvllpdsleeL 30
                                   R+++ p+++e+++++++k +llp+++e L
  gene860|gene860|rna859|rna859 54 RCMLVPRSKEKESQEARKAILLPKNMEVL 82
                                   9********9888**************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1808.15
//
Query:       gene86|gene86|rna86|rna86  [L=672]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   6.4e-114  379.3   0.1   1.1e-113  378.6   0.1    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.7e-30  105.7   0.0      3e-30  105.0   0.0    1.4  1  Helicase_C_3   Helicase conserved C-terminal domain
    1.4e-16   61.0   0.0    2.6e-16   60.1   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
    1.1e-11   45.1   0.0    3.6e-11   43.4   0.0    2.0  1  Helicase_C     Helicase conserved C-terminal domain
    5.7e-07   28.6   0.1    9.1e-07   27.9   0.1    1.3  1  SNF2_N         SNF2 family N-terminal domain
    2.7e-06   27.3   0.0    4.6e-06   26.5   0.0    1.4  1  DEAD           DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.6   0.1  3.5e-117  1.1e-113       1     238 [.     390     626 ..     390     639 .. 0.97

  Alignments for each domain:
  == domain 1  score: 378.6 bits;  conditional E-value: 3.5e-117
              ERCC3_RAD25_C   1 LqekgylakvqcaevWcpmtaefykeylkakskkkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpy 84 
                                L++kg++akv c+evWc mt +fy+eyl++ +++++ll +mnp+kf++ce+Li+ he+rgDkiivfsD+v+aLk+ya kl kp+
  gene86|gene86|rna86|rna86 390 LSAKGHIAKVSCVEVWCGMTGDFYREYLSQPTRRRRLLSIMNPTKFQVCEYLINKHESRGDKIIVFSDSVYALKAYALKLGKPF 473
                                6789******************************************************************************** PP

              ERCC3_RAD25_C  85 iyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLv 168
                                iyG t ++er++il++f++np +ntiflskvgDtsiDlPea++liqisshfgsrrqeaqrlGriLrak++ n+ +f+ +fYsLv
  gene86|gene86|rna86|rna86 474 IYGPTGQTERMRILKQFQTNPVINTIFLSKVGDTSIDLPEATCLIQISSHFGSRRQEAQRLGRILRAKRR-NDPDFRVYFYSLV 556
                                **********************************************************************.9************ PP

              ERCC3_RAD25_C 169 skDtkemaystkrqqflvdqGYafkviteleeleeeeelaystkeeqkellqkvlaakdeeaeeeeleke 238
                                skDt+em+ys+krqqfl+dqGY+f ++t++ e++e+e+++y+tk +q+ell+ vl a+++e e+ee  +e
  gene86|gene86|rna86|rna86 557 SKDTDEMFYSSKRQQFLIDQGYTFTILTDIPEVHENEHCVYKTKGQQRELLAGVLLASEKELESEESGSE 626
                                **********************************************************999988876544 PP

>> Helicase_C_3  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   0.0     1e-33     3e-30       1     120 [.      31     151 ..      31     155 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 1e-33
               Helicase_C_3   1 livqaDltillegdsplaeearaaLaafAelesrpehahtyrltplSlrrAldaGltaeeiiefLerlskypvPqaleylirdv 84 
                                ++v+ D+ i+le++ + +++a ++L+a+Ae+ srp  +h++++t++Sl++A+++Glt+ +iie+L+r+sk+++P +++++i+++
  gene86|gene86|rna86|rna86  31 MWVNYDGLIILETFRESSRQASDFLIAIAEPMSRPLRVHEFQITAYSLYAAVSVGLTTGDIIETLDRFSKNHLPRSVKVFITEC 114
                                69********************************************************************************** PP

               Helicase_C_3  85 arryGklrlgl.easlvlrsddpalleelladkkiak 120
                                + +yGk++l+  e+s++l+++++++++ l +d  i++
  gene86|gene86|rna86|rna86 115 TLSYGKVKLVMkENSFFLEAANESVYKILSEDTVIRS 151
                                ***********9******************9999886 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   8.8e-20   2.6e-16       4     169 ..     209     364 ..     206     366 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 8.8e-20
                                E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEE CS
                     ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigk 87 
                                +r+yQe +++++  +    r + g+i++++G+GKT+v + +i  ++k      +l+l+ +   +eq++++ ++f++   +++g 
  gene86|gene86|rna86|rna86 209 IRSYQEICLNKMFGN---GRARSGIIVLPCGSGKTIVGITAISTIKK-----SCLVLCTSAVSVEQWRQQTQQFTNISPDNVGR 284
                                689999999998643...67899***********************9.....5***************8888888887777899 PP

                                EESSS-B--.......-SEEEEEHHHHHHTH...........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEEEEEESS CS
                     ResIII  88 kvsgdkkkakekdstnkkilvttiqsldadseee...eeeseellrdrfdviiiDEaHrlgakkswreilekfkeavllglTAT 168
                                ++s+ k+ +    ++++ i+vtt+ +l    ++    ++  +  ++++  +++ DE+H + a   +r++l  +++ ++lglTAT
  gene86|gene86|rna86|rna86 285 FTSDHKEWP----RDDCGIVVTTYTMLAYTGKRSyeaQKIMDLIRKTEWGLLVLDEVHVVPA-MMFRRVLSLVSHHCKLGLTAT 363
                                998888888....**************98886666667777777788888************.9******************** PP

                                - CS
                     ResIII 169 p 169
                                +
  gene86|gene86|rna86|rna86 364 L 364
                                7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.2e-14   3.6e-11       2     110 ..     434     540 ..     433     541 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.2e-14
                                HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGGTSSSTST CS
                 Helicase_C   2 kleallell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesd.vLiatdvaerGidip 83 
                                k++ + +l+ k+e++g+ki++f+ ++  l+   +   k g  +  ++g + q er +il+qf+ + +   +  ++v+ ++id+p
  gene86|gene86|rna86|rna86 434 KFQVCEYLInKHESRGDKIIVFSDSVYALK--AYA-LKLGKPF--IYGPTGQTERMRILKQFQTNPVInTIFLSKVGDTSIDLP 512
                                56677777799*****************95..454.2445555..99***************9555555*************** PP

                                TESEEEESSSS.SSHHHHHHHHTTSSST CS
                 Helicase_C  84 kvnlVinfdlp.rnvtsyiqriGRtgRa 110
                                +++++i+++    + ++  qr GR+ Ra
  gene86|gene86|rna86|rna86 513 EATCLIQISSHfGSRRQEAQRLGRILRA 540
                                ********9994559************8 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1     3e-10   9.1e-07      44     216 ..     215     365 ..     166     436 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3e-10
                                .....HHHHHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHH.HHHHHHHHHHH-TTS-EEE CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                     SNF2_N  44 vveesaeakqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPasl.ldqWeneierhvsssalrv 126
                                ++ ++++ +   r Gi+    G GKT+  ++ i                 t+++  L+++ +++ ++qW ++ +++++ s  +v
  gene86|gene86|rna86|rna86 215 ICLNKMFGNGRARSGIIVLPCGSGKTIVGITAIS----------------TIKKSCLVLCTSAVsVEQWRQQTQQFTNISPDNV 282
                                5555666666778888888999999998888888................233469******55389*********98887777 PP

                                --SSHHHH-----------------EEEE-HHHHHHHT..........TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH--.- CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                     SNF2_N 127 lvyggqkkmkkkntkvapklladydvvittYdvlsreaelq....kkrsvlkqvewkrvvlDEghtlknstskaaeavskLs.t 205
                                   ++++k+ ++          d ++v+ttY +l+   +++    k+++ + + ew  +vlDE h +       +  v++L+  
  gene86|gene86|rna86|rna86 283 GRFTSDHKEWPR---------DDCGIVVTTYTMLAYTGKRSyeaqKIMDLIRKTEWGLLVLDEVHVVPAM--MFRR-VLSLVsH 354
                                666665544444.........899**********98877778888********************99643..2233.3333314 PP

                                S-EEEE-S--S CS
                                xxxxxxxxxxx RF
                     SNF2_N 206 snrwiltGTPi 216
                                + ++ lt+T +
  gene86|gene86|rna86|rna86 355 HCKLGLTATLV 365
                                44666777655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.5e-09   4.6e-06       4     170 ..     213     365 ..     210     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.5e-09
                                HHHHHHHHHTT...CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETT CS
                                xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DEAD   4 Qaeaiplilgg...gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliigg 84 
                                Q+ +++ + g+   ++ ++  + GsGKT +  i +++++       ++ +l+++ +   +eq  +++++f++  +     +  g
  gene86|gene86|rna86|rna86 213 QEICLNKMFGNgraRSGIIVLPCGSGKTIV-GITAISTI-------KKSCLVLCTSAVSVEQWRQQTQQFTNI-S--PDNV--G 283
                                666666666332335778999*******99.66666455.......679***********************3.3..3322..4 PP

                                SSHHHHHHHHHTTCSEEEEEHHHHHHHH....HCTSSH....CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTS CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       DEAD  85 vaardqlskldngvdivvgtpgrlddll....stgkln....lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqr 160
                                  ++d ++  + ++ ivv+t  +l+       + +k+       +  +lVlDE++ +  + f++ ++ + +++           
  gene86|gene86|rna86|rna86 284 RFTSDHKEWPRDDCGIVVTTYTMLAYTGkrsyEAQKIMdlirKTEWGLLVLDEVHVVPAMMFRRVLSLVSHHC----------- 356
                                4455666666678********999997677774444334522455688******************9999988........... PP

                                EEEEEESSBS CS
                                xxxxxxxxxx RF
                       DEAD 161 qvivlSATlp 170
                                  + l+ATl 
  gene86|gene86|rna86|rna86 357 -KLGLTATLV 365
                                .678888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 4114.68
//
Query:       gene861|gene861|rna860|rna860  [L=298]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.18   11.7   0.1        1.6    8.7   0.1    2.1  2  SSrecog   Structure-specific recognition protein (SSRP1)


Domain annotation for each model (and alignments):
>> SSrecog  Structure-specific recognition protein (SSRP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1   8.7e-05       1.6      14      45 ..     141     172 ..     133     175 .. 0.87
   2 ?    0.3   0.0     0.037   6.7e+02      11      37 ..     191     219 ..     186     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 8.7e-05
                        SSrecog  14 lvfqvdnkpafeiplsevsncnlagknEvale 45 
                                    l ++++n ++f i+ sev n +l + nEv+++
  gene861|gene861|rna860|rna860 141 LFLSFENGKVFSIKESEVMNIVLGKINEVVMD 172
                                    566788999**************999***996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.037
                        SSrecog  11 gselvfqvdnk..pafeiplsevsncnla 37 
                                    g+elv++  nk   + +++ ++vs + l+
  gene861|gene861|rna860|rna860 191 GKELVISLFNKkvLVLDLDTKDVSYTELP 219
                                    66777777766334678999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2095.67
//
Query:       gene862|gene862|rna861|rna861  [L=500]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.074   12.4   0.0    1.9  2  Nrap_D4   Nrap protein nucleotidyltransferase domain 4


Domain annotation for each model (and alignments):
>> Nrap_D4  Nrap protein nucleotidyltransferase domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0     0.099   1.8e+03     149     177 ..      61      89 ..      49     109 .. 0.73
   2 ?   12.4   0.0   4.1e-06     0.074      78     119 ..     193     234 ..     174     272 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.099
                                    EE-TTS-EEEEEEE-TTHHHHHHH.HH... CS
                        Nrap_D4 149 vlkesgfaFrlrilherEltller.qlkdk 177
                                    +l   ++ F +++  ++E++l+ + +lkdk
  gene862|gene862|rna861|rna861  61 ILN-GEYLFDIEVGLNDEKSLYCDkELKDK 89 
                                    555.4899**********999854044444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.1e-06
                                    .....TTSTEEEEEEE---TTS-SSHHHHHHHHHHHHHHHHH CS
                        Nrap_D4  78 ksskeylepidvvlqfEsSgkWPddleAiqkvKaAFllkiae 119
                                    +  ++  +++++ l+  s ++WP+d +A+  +K+A++  i +
  gene862|gene862|rna861|rna861 193 HMATSITNVHECYLHCGSHANWPEDEDALDCAKTALYCLIYK 234
                                    34456777889*************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3035.94
//
Query:       gene863|gene863|rna862|rna862  [L=532]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     6e-152  506.7   3.8   6.9e-152  506.5   3.8    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.5   3.8  3.8e-156  6.9e-152       1     489 [.      40     529 ..      40     531 .. 0.97

  Alignments for each domain:
  == domain 1  score: 506.5 bits;  conditional E-value: 3.8e-156
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXX.XSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkelei.ehPaakllveaaesqdeevGDGTttvviLageLleeaek 79 
                                    +a +++t+lGP+GmdK+l++k +++vvTnDGatilke+e+ e+P+ +l+v+++esqdee+GDGTt+vv+La++Ll++a+ 
  gene863|gene863|rna862|rna862  40 IATFLSTSLGPTGMDKILQSKDDDIVVTNDGATILKEMEMtENPISRLIVQLSESQDEEIGDGTTSVVVLASALLDQAQV 119
                                    6889***********************************9789************************************* PP

                                    HHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCS.E CS
                     Cpn60_TCP1  80 liaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieene.k 158
                                    l+ +g+hp++i eg+e ale a+e+L+ei++eis+    re+++k+artsl+sk++ k+ e+++++++ Av+++ + e k
  gene863|gene863|rna862|rna862 120 LLGQGIHPIKISEGFELALEYAIEHLSEISEEISDL---RETMMKAARTSLGSKIVYKSLEKFAEICTSAVLMVADMErK 196
                                    *****************************9999876...9*******************************77777767* PP

                                    ECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHH CS
                     Cpn60_TCP1 159 eldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaee 238
                                    +ld++ i ++++ g++++d++lv+G+vl+k++++p+m+k++++ +++ll++++e++k +tk+++v+s+++e+++le+ e+
  gene863|gene863|rna862|rna862 197 DLDFELISIESKVGRDISDTTLVKGVVLNKEFSHPQMKKEIKDGRIALLSCPFEPPKLKTKHSLVISNPKEYKELEEYEK 276
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEEC CS
                     Cpn60_TCP1 239 kqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkveee 318
                                    +++ e++e+++ksg+nvv+cq+g+dd+a+++l++n++ a+r+v  ++le la  tG+++++++edl+++++G+a+   ee
  gene863|gene863|rna862|rna862 277 RKFVEMIESVKKSGANVVMCQWGFDDEANSLLMENDLPAVRWVGGHELELLAVHTGGSIIARFEDLEESDIGNAEIR-EE 355
                                    *************************************************************************9865.66 PP

                                    CETT..CCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXC CS
                     Cpn60_TCP1 319 kigs..ekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsg 396
                                    ++g+  +k++++e++++++++til+rga+d v++e++r+++dAl++v+n+++++k+v+GGG++e++++ +l++ a+ +sg
  gene863|gene863|rna862|rna862 356 SLGTenDKIVVVENSEHSRAVTILVRGANDLVIEEAKRSVRDALCAVRNILTNSKIVYGGGSSEMSCSLALEKTAEGYSG 435
                                    77664589************************************************************************ PP

                                    CHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHH.HTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHH CS
                     Cpn60_TCP1 397 eeqlaieafakALevipktLaeNaGldpievlaklraah.nkgekelgidvesgeiidlveagvvDplkvkrqalksAte 475
                                    ee+ a   f++ALe+ip +La+N+G++pie  + lr+ + ++++  lg+d+     +d++e gv+D l+ k + +++At+
  gene863|gene863|rna862|rna862 436 EEREALLGFGRALEEIPLCLARNSGYNPIEYSSGLRKLQmESKNSYLGVDCLGVGEQDMKELGVFDALSSKIRQFQMATQ 515
                                    ************************************96644555599****99999************************ PP

                                    HHHHHHCEEEEEXX CS
                     Cpn60_TCP1 476 aastiLrideiika 489
                                    ++++iL+id++i++
  gene863|gene863|rna862|rna862 516 LVTMILKIDNVISD 529
                                    ************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.50
# Mc/sec: 3221.70
//
Query:       gene864|gene864|rna863|rna863  [L=146]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-13   49.6   0.0    4.9e-13   49.3   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.4e-12   45.7   0.0    7.1e-12   45.4   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.9e-09   36.8   0.4    5.9e-09   36.2   0.4    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.2e-05   25.2   0.0    2.2e-05   24.3   0.0    1.4  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.054   13.2   0.0      0.064   13.0   0.0    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0   1.4e-16   4.9e-13      24     117 .]      40     128 ..      12     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.4e-16
                                    HHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEET CS
                 Acetyltransf_1  24 feesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlavee 103
                                     ++s+ + ++ ++++  ++ ++Gfi+++   d    ++y+ +l+V +e+r  G+G +Ll+++ ++  +  +++ivl+v  
  gene864|gene864|rna863|rna863  40 KAKSLKNKNNNYIFCFVGEVPVGFITFRFSRD----TTYVFELHVEKEHRSLGIGALLLDECKKQYDKV-VRRIVLYVYR 114
                                    34445556677777889999************....8**************************988777.899******* PP

                                    TEHHHHHHHHHTTE CS
                 Acetyltransf_1 104 dndaairlYeklGF 117
                                     n +  ++Ye+ GF
  gene864|gene864|rna863|rna863 115 ENSRGLKFYERNGF 128
                                    *************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0     2e-15   7.1e-12      25     108 ..      43     130 ..      31     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2e-15
                Acetyltransf_10  25 rieegealllvaeeggkivGvi..el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikleltvnasp.yavpf 100
                                     ++++++ ++ +++g+ +vG+i  +  rd+ ++  l V++e+r+ Gig+ Ll++++++++k   ++ l v   +    +f
  gene864|gene864|rna863|rna863  43 SLKNKNNNYIFCFVGEVPVGFItfRFsRDTTYVFELHVEKEHRSLGIGALLLDECKKQYDKVVRRIVLYVYRENsRGLKF 122
                                    446888999*************888888888****************************8887766888888888***** PP

                Acetyltransf_10 101 YeklGFka 108
                                    Ye+ GF+ 
  gene864|gene864|rna863|rna863 123 YERNGFRI 130
                                    ******85 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.4   1.7e-12   5.9e-09       5      75 ..      52     129 ..      47     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.7e-12
                                    EEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH.TT..SEEE....EEEEEE..THHHHHHHHHHTT CS
                 Acetyltransf_7   5 vfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea.ae..kgii....leqlel..naekaikfYeklG 73 
                                    +f +  ++ +vGfi +  +   ++  +l V +e+r  GiG  Ll+  ++     +    ++ l++  ++++ +kfYe++G
  gene864|gene864|rna863|rna863  52 IF-CFVGEVPVGFITFRFSRdtTYVFELHVEKEHRSLGIGALLLDEcKKqyD--KvvrrIV-LYVyrENSRGLKFYERNG 127
                                    34.45567899*99988888777777799***************96322331..0222323.344324458999****** PP

                                    EE CS
                 Acetyltransf_7  74 Fe 75 
                                    F+
  gene864|gene864|rna863|rna863 128 FR 129
                                    *8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   6.1e-09   2.2e-05      13      80 ..      64     131 ..      55     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.1e-09
                                    EEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  13 aawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                    ++ ++ +d ++++ l v++ehr  G g +l  +  k+  +    ++l+v  +N++  ++ye+ Gf+  
  gene864|gene864|rna863|rna863  64 ITFRFSRDTTYVFELHVEKEHRSLGIGALLLDECKKQYDKVVRRIVLYVYRENSRGLKFYERNGFRIN 131
                                    6678899**********************************************************976 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.8e-05     0.064      56      98 ..      67     109 ..      42     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                           PanZ  56 eledkeaelsdlcVRevTRrRGVgsyLleearrqaPevkswvl 98 
                                    +++ ++  + +l V ++ R  G+g  Ll+e+++q  +v +  +
  gene864|gene864|rna863|rna863  67 RFSRDTTYVFELHVEKEHRSLGIGALLLDECKKQYDKVVRRIV 109
                                    56778888999***********************988776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 893.10
//
Query:       gene865|gene865|rna864|rna864  [L=156]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.3e-06   27.5   2.0    8.1e-06   26.3   1.2    2.1  2  TRAUB      Apoptosis-antagonizing transcription factor, C-ter
     0.0016   18.3   0.4     0.0029   17.5   0.4    1.4  1  DASH_Dad4  DASH complex subunit Dad4
  ------ inclusion threshold ------
      0.047   13.9   0.5      0.082   13.1   0.3    1.5  2  BORCS6     BLOC-1-related complex sub-unit 6
       0.11   12.4   0.8       0.38   10.7   0.1    2.0  2  Med10      Transcription factor subunit Med10 of Mediator com


Domain annotation for each model (and alignments):
>> TRAUB  Apoptosis-antagonizing transcription factor, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.24   1.1e+03      58      68 ..      57      67 ..       9      84 .. 0.66
   2 !   26.3   1.2   1.8e-09   8.1e-06       5      84 ..      80     154 ..      46     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.24
                          TRAUB 58 eklqNFmapee 68
                                   +kl + m p++
  gene865|gene865|rna864|rna864 57 DKLNSLMNPMK 67
                                   45555555555 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.8e-09
                          TRAUB   5 LkelvekksaessaaasdsrqllalqklrkkkkkkkkvDtka...SKGRklrYevheklqNFmapeergkweeeqidelf 81 
                                    Lk l e+k+a ++++         ++ l k+k +    ++ka   SKG+ l Ye +ekl  F + +  ++w++e+id+++
  gene865|gene865|rna864|rna864  80 LKYLYERKKAFDENK--------VYTLLAKNKVNVMLSNKKAafkSKGKTLSYEFKEKLTGFLTRRGCASWSDEKIDDFI 151
                                    666666666555533........23334444444223344433339********************************** PP

                          TRAUB  82 asL 84 
                                    +s+
  gene865|gene865|rna864|rna864 152 SSM 154
                                    998 PP

>> DASH_Dad4  DASH complex subunit Dad4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.4   6.5e-07    0.0029      10      67 ..      46     103 ..      43     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.5e-07
                      DASH_Dad4  10 salLsRIiknvekLnesvvelnkeleeinkkNknvelvsqlwenYqrnvqfnLeatge 67 
                                    + lL+R i+ ++kLn+ +  +++++++i +  ++++ + +  + + +n  + L a ++
  gene865|gene865|rna864|rna864  46 QELLRRCIARMDKLNSLMNPMKHTISTIPSIEEQLKYLYERKKAFDENKVYTLLAKNK 103
                                    579*********************************************9999988775 PP

>> BORCS6  BLOC-1-related complex sub-unit 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   1.8e-05     0.082      69     149 ..       5      83 ..       1      86 [. 0.90
   2 ?   -3.4   0.0       2.3     1e+04     115     121 ..      95     101 ..      90     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                         BORCS6  69 aasvdnllenlssklhsisaltvgnietykdavdklgdavDssiksmYqLlAkaEElskamkPveklakqikeikrlldl 148
                                       v +ll++ +s++++i+ l ++  ++  + ++++ d++D+    +   +A+++ l++ m+P+++  + i  i + l+ 
  gene865|gene865|rna864|rna864   5 KITVKELLRKTESQIDKIAFLHANPTQA--REIKRTIDTLDNPQELLRRCIARMDKLNSLMNPMKHTISTIPSIEEQLKY 82 
                                    567999*****************99886..679********************************999999999888876 PP

                         BORCS6 149 l 149
                                    l
  gene865|gene865|rna864|rna864  83 L 83 
                                    5 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.3
                         BORCS6 115 mYqLlAk 121
                                     Y+LlAk
  gene865|gene865|rna864|rna864  95 VYTLLAK 101
                                    6999999 PP

>> Med10  Transcription factor subunit Med10 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   8.6e-05      0.38      44      98 ..      18      71 ..       1      80 [. 0.76
   2 ?   -0.1   0.1      0.19   8.7e+02      85     112 ..     103     130 ..      95     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.6e-05
                                   HHHHHHH..HH--EEEHHHHHHHHTTB-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Med10 44 elsktaskllqdikiPlelieyvenGrNPdiYtrefvelvrrkNqlmkGkmeafk 98
                                   +++k a   ++++    e+ + ++   NP+   r ++ ++ + N lm+   ++++
  gene865|gene865|rna864|rna864 18 QIDKIAFL-HANPTQAREIKRTIDTLDNPQELLRRCIARMDKLNSLMNPMKHTIS 71
                                   33444442.88888899******************************99888776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                          Med10  85 rkNqlmkGkmeafkkfrdvLaeelekal 112
                                    + N ++  k  afk+  ++L  e +++l
  gene865|gene865|rna864|rna864 103 KVNVMLSNKKAAFKSKGKTLSYEFKEKL 130
                                    5588889999999999999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1191  (0.0664287); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 989.51
//
Query:       gene866|gene866|rna865|rna865  [L=257]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-29  101.0   5.4    4.5e-12   46.0   0.1    4.3  4  Myb_DNA-binding  Myb-like DNA-binding domain
    8.8e-26   89.9   4.8    8.8e-12   45.1   0.1    5.0  5  Myb_DNA-bind_6   Myb-like DNA-binding domain
    0.00076   19.3   0.4     0.0033   17.3   0.1    2.2  2  Myb_DNA-bind_7   Myb DNA-binding like
    0.00091   19.2   0.4        0.3   11.1   0.1    2.9  2  SLIDE            SLIDE
  ------ inclusion threshold ------
      0.045   13.9   0.0        0.2   11.9   0.0    2.1  2  DUF2774          Protein of unknown function (DUF2774)
      0.093   12.8   0.1       0.46   10.6   0.0    2.1  2  HTH_7            Helix-turn-helix domain of resolvase
       0.11   12.9   0.3       0.11   12.9   0.3    3.2  5  MADF_DNA_bdg     Alcohol dehydrogenase transcription factor M


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0022       5.7      22      44 ..      78     101 ..      60     102 .. 0.83
   2 ?    2.2   0.0     0.085   2.2e+02      20      31 ..     125     136 ..     117     141 .. 0.86
   3 !   46.0   0.1   1.8e-15   4.5e-12       3      43 ..     157     198 ..     155     200 .. 0.95
   4 !   45.2   0.1   3.1e-15   8.1e-12       1      42 [.     206     248 ..     206     250 .. 0.98

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0022
                                    C..HHHHHHHHTSS-HHHHHHHHHH CS
                Myb_DNA-binding  22 r..WkkIaerlggRtekqcrsrwrn 44 
                                    +  Wk+I+ r+ +  +++c +rw n
  gene866|gene866|rna865|rna865  78 DpfWKEISIRF-NIPRNECFNRWIN 101
                                    466****9999.8**********87 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.085
                                    TTCHHHHHHHHT CS
                Myb_DNA-binding  20 GnrWkkIaerlg 31 
                                    G++W  Ia+++g
  gene866|gene866|rna865|rna865 125 GKDWIQIAKEMG 136
                                    899*******98 PP

  == domain 3  score: 46.0 bits;  conditional E-value: 1.8e-15
                                    SSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHHH CS
                Myb_DNA-binding   3 kWteeEdelLleavkkhG.nrWkkIaerlggRtekqcrsrwr 43 
                                     W+ eEd lL+++v+k+G ++W+ +++ +g+Rt+k+c  r++
  gene866|gene866|rna865|rna865 157 MWSLEEDRLLEKGVEKYGlSKWRYVSKIVGTRTGKECAMRFY 198
                                    6*************************************9997 PP

  == domain 4  score: 45.2 bits;  conditional E-value: 3.1e-15
                                    CSSSBHHHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHH CS
                Myb_DNA-binding   1 rgkWteeEdelLleavkkhG.nrWkkIaerlggRtekqcrsrw 42 
                                    +gkWt++E e+L e+v+ +G ++W+ ++ ++ +R + qcrs++
  gene866|gene866|rna865|rna865 206 KGKWTKDEKERLFEGVEIYGeGDWRGVSTHVMTRNPIQCRSKY 248
                                    79****************************************9 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.25   6.4e+02      14      48 ..      16      47 ..       8      55 .. 0.66
   2 !    8.7   1.1   0.00079         2      19      43 ..      78     103 ..      61     116 .. 0.77
   3 !   15.6   0.0   5.6e-06     0.014      10      45 ..     118     151 ..     107     157 .. 0.83
   4 !   45.1   0.1   3.4e-15   8.8e-12       1      58 [.     158     215 ..     158     216 .. 0.96
   5 !   27.3   0.0   1.2e-09   3.1e-06       1      40 [.     209     249 ..     209     256 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                 Myb_DNA-bind_6 14 ekygndWknIaealnrRtp...kqcfdrwknkLrpkis 48
                                   ++y     +I+++l+ R     kqc +r    ++pki+
  gene866|gene866|rna865|rna865 16 MDY----IEIEKILK-RLRdikKQCSYRSTV-IKPKIK 47
                                   444....67888888.555555888888666.777666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00079
                 Myb_DNA-bind_6  19 d..WknIaealnrRtpkqcfdrwknkL 43 
                                    d  Wk+I+  +n    ++cf+rw+nk+
  gene866|gene866|rna865|rna865  78 DpfWKEISIRFN-IPRNECFNRWINKV 103
                                    344********9.888********965 PP

  == domain 3  score: 15.6 bits;  conditional E-value: 5.6e-06
                 Myb_DNA-bind_6  10 lklvekygndWknIaealnrRtpkqcfdrwknkLrp 45 
                                    +k++++ g+dW +Ia++++   p+ +f ++++ L++
  gene866|gene866|rna865|rna865 118 VKHMSDEGKDWIQIAKEMG-CKPLKVFAEYLR-LNS 151
                                    6899999************.************.864 PP

  == domain 4  score: 45.1 bits;  conditional E-value: 3.4e-15
                 Myb_DNA-bind_6   1 WteeEdeiLlklvekyg.ndWknIaealnrRtpkqcfdrwknkLrpkisrkkwskeedi 58 
                                    W+ eEd++L k+vekyg ++W+ ++++ + Rt k+c +r+   L+ +++++kw+k e++
  gene866|gene866|rna865|rna865 158 WSLEEDRLLEKGVEKYGlSKWRYVSKIVGTRTGKECAMRFYF-LNKNVQKGKWTKDEKE 215
                                    9****************77*********99************.************9986 PP

  == domain 5  score: 27.3 bits;  conditional E-value: 1.2e-09
                 Myb_DNA-bind_6   1 WteeEdeiLlklvekygn.dWknIaealnrRtpkqcfdrwk 40 
                                    Wt++E+e+L ++ve yg  dW+ ++++   R+p qc+ ++ 
  gene866|gene866|rna865|rna865 209 WTKDEKERLFEGVEIYGEgDWRGVSTHVMTRNPIQCRSKYV 249
                                    ****************966********855*********96 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.74   1.9e+03       7      45 ..     154     193 ..     150     199 .. 0.71
   2 !   17.3   0.1   1.3e-06    0.0033       4      55 ..     202     254 ..     198     257 .] 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.74
                 Myb_DNA-bind_7   7 ktkkWskeetekFYkaLsqfGt.DFsliaklfpkrtrrql 45 
                                    ++k Ws ee ++  k+++++G   +  ++k+   rt ++ 
  gene866|gene866|rna865|rna865 154 TPKMWSLEEDRLLEKGVEKYGLsKWRYVSKIVGTRTGKEC 193
                                    5688999999999999999885246667777666666665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.3e-06
                 Myb_DNA-bind_7   4 krkktkkWskeetekFYkaLsqfGt.DFsliaklfpkrtrrqlKlKFkkEerk 55 
                                    k+ ++ kW+k+e e+ +++++ +G  D+  +++    r+  q ++K+  E rk
  gene866|gene866|rna865|rna865 202 KNVQKGKWTKDEKERLFEGVEIYGEgDWRGVSTHVMTRNPIQCRSKYVAETRK 254
                                    555899******************66************************997 PP

>> SLIDE  SLIDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00012       0.3      44      77 ..     151     183 ..      97     189 .. 0.70
   2 !    5.3   0.0    0.0075        19      38      81 ..     195     238 ..     191     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                          SLIDE  44 psnkgkkeyteeeDrfllvllakyGygnyekikk 77 
                                    + ++ k+ ++ eeDr l   ++kyG+++++ + k
  gene866|gene866|rna865|rna865 151 SISTPKM-WSLEEDRLLEKGVEKYGLSKWRYVSK 183
                                    3344555.********************998765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0075
                          SLIDE  38 lkikyppsnkgkkeyteeeDrfllvllakyGygnyekikkeire 81 
                                    +++ + ++n +k ++t++e + l   ++ yG g+++ +   +++
  gene866|gene866|rna865|rna865 195 MRFYFLNKNVQKGKWTKDEKERLFEGVEIYGEGDWRGVSTHVMT 238
                                    66777789999999*********************999888765 PP

>> DUF2774  Protein of unknown function (DUF2774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.3   8.4e+03      17      23 ..      19      25 ..      15      46 .. 0.58
   2 ?   11.9   0.0   7.7e-05       0.2       8      30 ..     120     142 ..     116     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.3
                        DUF2774 17 veIAkkl 23
                                   +eI k l
  gene866|gene866|rna865|rna865 19 IEIEKIL 25
                                   4444432 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.7e-05
                        DUF2774   8 flhesgknFveIAkkldirakdv 30 
                                     + + gk++++IAk+++ ++  v
  gene866|gene866|rna865|rna865 120 HMSDEGKDWIQIAKEMGCKPLKV 142
                                    5899*************998766 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.9   4.8e+03      17      30 ..      14      27 ..      10      29 .. 0.59
   2 ?   10.6   0.0   0.00018      0.46       5      33 ..     109     137 ..     108     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.9
                                   STTTT--STTTSSS CS
                          HTH_7 17 LleeGisiskIAke 30
                                   L+ + i i kI k+
  gene866|gene866|rna865|rna865 14 LYMDYIEIEKILKR 27
                                   44444667777776 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00018
                                    SS-HHHHGGGGSSTTTT--STTTSSSS-- CS
                          HTH_7   5 klskndinrvvkLleeGisiskIAkevni 33 
                                    kl k d+++v+ + +eG    +IAke ++
  gene866|gene866|rna865|rna865 109 KLCKSDMDTVKHMSDEGKDWIQIAKEMGC 137
                                    455569********************987 PP

>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.4   6.2e+03      46      56 ..      25      37 ..      11      49 .. 0.52
   2 ?   12.9   0.3   4.1e-05      0.11      23      65 ..      75     117 ..      64     135 .. 0.79
   3 ?    0.7   0.0      0.26   6.7e+02      20      40 ..     119     137 ..     112     150 .. 0.77
   4 ?   -1.5   0.1       1.3   3.3e+03      28      55 ..     177     203 ..     169     216 .. 0.67
   5 ?   -2.8   0.0       3.3   8.3e+03      52      63 ..     244     255 ..     237     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                   MADF_DNA_bdg 46 kkkwknLR..dry 56
                                    k+++ ++  ++y
  gene866|gene866|rna865|rna865 25 LKRLRDIKkqCSY 37
                                   2222222233334 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.1e-05
                   MADF_DNA_bdg  23 ekrekaweeiaeelnekvdveeckkkwknLRdryrrelrkkk..s 65 
                                    +  +  w+ei+ ++n  ++ +ec ++w n  + + ++l k +   
  gene866|gene866|rna865|rna865  75 DLNDPFWKEISIRFN--IPRNECFNRWINKVEDFDKKLCKSDmdT 117
                                    667899*********..*******************998877442 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.26
                   MADF_DNA_bdg  20 rnkekrekaweeiaeelnekv 40 
                                    ++ +   k w +ia+e++  +
  gene866|gene866|rna865|rna865 119 KHMSDEGKDWIQIAKEMG--C 137
                                    666777899********9..4 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.3
                   MADF_DNA_bdg  28 aweeiaeelnekvdveeckkkwknLRdr 55 
                                     w+ +++ ++ + + +ec  ++  L ++
  gene866|gene866|rna865|rna865 177 KWRYVSKIVG-TRTGKECAMRFYFLNKN 203
                                    5777777777.55666777776655554 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 3.3
                   MADF_DNA_bdg  52 LRdryrrelrkk 63 
                                     R++y  e rk 
  gene866|gene866|rna865|rna865 244 CRSKYVAETRKI 255
                                    699999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1767.91
//
Query:       gene867|gene867|rna866|rna866  [L=341]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-20   73.8   0.0    1.4e-20   73.4   0.0    1.1  1  RTC         RNA 3'-terminal phosphate cyclase
    7.8e-10   39.2   0.0    1.8e-09   38.1   0.0    1.6  2  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.0   1.6e-24   1.4e-20      43     222 .]      42     317 ..      15     317 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 1.6e-24
                                    HHHHHHHHHHT-EEE--STT-SEEEEE------SEEEEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC  43 tavrllakitnaevegaeigsteleFkPgeikageyevdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsv 122
                                    ++ +ll+ki+++++   ++    + F+Pg++k+ge+   i+    i+l+++++l+l++f  +p+++++kG+Tn       
  gene867|gene867|rna866|rna866  42 SFAKLLQKISHGTAY--SLSEGYMAFTPGSLKGGEVA--IQCEEEISLYIEPILVLCPFVIEPLKIKFKGITNG--KLCT 115
                                    67899********44..555556*********99655..555568****************************8..789* PP

                                    HHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEEEEEEE-.-S---EB.............................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                            RTC 123 dylktvllpllkrfgvlelelelkkrGfypkGgGevelevepskklkpie.............................. 172
                                    d ++ + + +lkrfgv e+e+ +kkrGf p G+Gev+++v  + k+++++                              
  gene867|gene867|rna866|rna866 116 DLIRIAHFDVLKRFGVKECEVVVKKRGFGPVGKGEVVFTVDSPGKISTVRlerlekivkirglvlssrvssiptkemter 195
                                    ***************999**********************887789999899999************************* PP

                                    .......................................................................BSS-HHHHH CS
                                    .......................................................................xxxxxxxxx RF
                            RTC 173 .......................................................................acvDehlqd 181
                                                                                                           +++D+ l  
  gene867|gene867|rna866|rna866 196 ikelmgdvsntkvfsnmsnrldsgpspgfqcavfaeskngiyysvmsgegltpketatiackdllrsirhgGVFDKKLLY 275
                                    ******************************************************************************** PP

                                    HHHHHHHHHT..-EEEEESS--HHHHHHHHHHHHHSS-EEEE CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC 182 qlilfmaLak.gksrirvaeltlhtetairvieqflgvkfkv 222
                                    +++ +m L++   +++ v+++++ ++  +++++qf+g ++++
  gene867|gene867|rna866|rna866 276 LALSLMSLSSpSIGSLWVGKVDSDVKIILDLLRQFFGFEYEI 317
                                    *********963468999*******************99886 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   1.1e+04      24      32 ..      37      45 ..       5      59 .. 0.61
   2 !   38.1   0.0     2e-13   1.8e-09       4     102 ..     170     263 ..     167     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                                   HHHHHHHHH CS
                     RTC_insert 24 nrmveaarg 32
                                   ++m+++  +
  gene867|gene867|rna866|rna866 37 QKMAKSFAK 45
                                   233333333 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 2e-13
                                    ---SEEEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-T CS
                     RTC_insert   4 GrvkrirGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgek 83 
                                     ++ +irG ++++rvs+   ++m e++++++ +  ++ ++++    +  +sg spGf ++++ae+++ g+ ++  +++ +
  gene867|gene867|rna866|rna866 170 EKIVKIRGLVLSSRVSSIPTKEMTERIKELMGDV-SNTKVFSN-MSNRLDSGPSPGFQCAVFAESKN-GIYYS--VMSGE 244
                                    589****************************776.99999999.899999***************85.65444..55678 PP

                                    T--HHHHHHHHHHHHHHHH CS
                     RTC_insert  84 gvppedvGeeaaeeLleei 102
                                    g +p++ ++ a++ Ll+ i
  gene867|gene867|rna866|rna866 245 GLTPKETATIACKDLLRSI 263
                                    9***************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2162.52
//
Query:       gene868|gene868|rna867|rna867  [L=210]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-43  148.2   2.4    2.1e-43  148.0   2.4    1.0  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
     0.0023   17.3   0.2     0.0036   16.7   0.2    1.4  1  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.013   15.5   0.2       0.14   12.2   0.1    2.1  2  B12-binding     B12 binding domain


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.0   2.4   3.5e-47   2.1e-43       2     198 .]       6     190 ..       5     190 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 3.5e-47
                                    EEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT- CS
                 Ribul_P_3_epim   2 iapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefaeaga 81 
                                    +  S+l  +fa+l+ee+++++++ga  +H+DvmD+ fv+N+t+gp +++ + ++  + +d+H+mve++  iv +    + 
  gene868|gene868|rna867|rna867   6 VGISILDCNFAKLEEELRELKANGATNIHLDVMDTTFVKNITFGPCIINRILEHD-FVFDIHMMVESPLDIVMQIDLERV 84 
                                    778*************************************************997.9******************99999 PP

                                    SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHH CS
                 Ribul_P_3_epim  82 siisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevlekikkvrklid 161
                                     ++++H E ++++  + + +k+  +  g+++np+t +e +e  +e+ d++l+msv PgfgGQkF +++l ki++++k  +
  gene868|gene868|rna867|rna867  85 FLVTIHHEISNKV-GVREYLKQRNVLFGIAINPETRMEEIE--MEDADFILVMSVRPGFGGQKFQESCLAKIRDIQKHGK 161
                                    9*******77665.678899******************999..7********************************9988 PP

                                    HHT---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
                 Ribul_P_3_epim 162 ekeldlkievDGGvkldnieqiaeagadvlVagsavf 198
                                           i +DGG+ ++nie+++  g+d +V+gs+ f
  gene868|gene868|rna867|rna867 162 I------IGIDGGIGMANIEKVV--GVDYVVIGSGYF 190
                                    6......****************..*********876 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2     6e-07    0.0036      57     175 ..      64     183 ..      12     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-07
                       TMP-TENI  57 gvpliindrvdlalavgadgvHlgq...ddlpvaearellgp.dliiGlSvhsleeaeeaealgadYigvGpifpTdtKk 132
                                    ++ ++++  +d+ ++++ + v l     +  +   +re l++ +++ G+ ++ +  +ee+e++ ad+i v ++ p    +
  gene868|gene868|rna867|rna867  64 DIHMMVESPLDIVMQIDLERVFLVTihhEISNKVGVREYLKQrNVLFGIAINPETRMEEIEMEDADFILVMSVRPGFGGQ 143
                                    67788999999999999999888775544445556777776516777********************************* PP

                       TMP-TENI 133 daeplgleglkelaealeiPvvai.GGitlenvaevleagadgv 175
                                    + +   l+++++++++ +i  + i GGi ++n+++v+  g+d v
  gene868|gene868|rna867|rna867 144 KFQESCLAKIRDIQKHGKI--IGIdGGIGMANIEKVV--GVDYV 183
                                    ***************9984..4444**********98..55555 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.059   3.5e+02      28      59 ..       5      37 ..       1      47 [. 0.62
   2 ?   12.2   0.1   2.4e-05      0.14      23     113 ..     102     188 ..      86     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.059
                    B12-binding 28 gfeVqllganven.edivaairaekpdvvglSa 59
                                   ++ +++l++n+ + e+ +++++a+ +  + l +
  gene868|gene868|rna867|rna867  5 RVGISILDCNFAKlEEELRELKANGATNIHLDV 37
                                   456789999996555555555555555566666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.4e-05
                    B12-binding  23 alrdagfeVqllganvenedivaairaekpdvvgl.Salltsqleavkelvel...lkrirprvkvvvGGahpsldpeet 98 
                                    +l+++  + +l g+ +++e+ +++i+ e++d++++ S++++   ++++e + +     +++ +++ + GG++    ++  
  gene868|gene868|rna867|rna867 102 YLKQR--N-VLFGIAINPETRMEEIEMEDADFILVmSVRPGFGGQKFQESCLAkirDIQKHGKIIGIDGGIGMANIEKV- 177
                                    55552..3.477999999**************776488766666667666666634333444788888**983333333. PP

                    B12-binding  99 leaklgiddvvvgeg 113
                                         g+d+vv+g g
  gene868|gene868|rna867|rna867 178 ----VGVDYVVIGSG 188
                                    ....9********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1423.30
//
Query:       gene869|gene869|rna868|rna868  [L=115]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   15.4   2.0      0.042   14.9   2.0    1.2  1  PLAC8     PLAC8 family
      0.046   14.2   0.0      0.065   13.7   0.0    1.2  1  DUF4790   Domain of unknown function (DUF4790)


Domain annotation for each model (and alignments):
>> PLAC8  PLAC8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.0   4.6e-06     0.042      12      96 ..      14      87 ..       6      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-06
                          PLAC8 12 levcllalfcpcvllgqnaerldsgnlscllllvlllallvllglgllatlllRskiRekyniegssceDclaslcCacCal 93
                                   +  cl +++cpc+l + +  r+ ++   + +   + l+++          +  R+ ++ k + ++s +e  ++  +C+c +l
  gene869|gene869|rna868|rna868 14 PRYCLASTLCPCYLSSIIYARIFKN-KRFSMF-GFFLVPFS--------VYGIRRYVQDKLQYKES-FETSAIKSLCCCNSL 84
                                   467999******9999888886433.333221.12222222........689***********888.777777777778999 PP

                          PLAC8 94 aQe 96
                                   aQ+
  gene869|gene869|rna868|rna868 85 AQD 87
                                   997 PP

>> DUF4790  Domain of unknown function (DUF4790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-06     0.065       8      66 ..      47     108 ..      40     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                        DUF4790   8 lkvpyqvvClerYkeakrkyerqfkr.Eikklidlqssald..avrlvRvlayttlwpplht 66 
                                    + vp++v  ++rY + k +y++ f+   ik+l    s a+d  +++++R+  y+ l+ p++ 
  gene869|gene869|rna868|rna868  47 FLVPFSVYGIRRYVQDKLQYKESFETsAIKSLCCCNSLAQDlhEMKIRRIGVYKFLSEPIPC 108
                                    6799********************86269999999998876447999***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 715.90
//
Query:       gene870|gene870|rna869|rna869  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-09   36.5   2.8      3e-09   36.5   2.8    2.2  3  zf-CCCH        Zinc finger C-x8-C-x5-C-x3-H type (and similar
    1.1e-08   34.8   5.2    2.3e-08   33.7   5.2    1.6  1  zf-C3HC4_2     Zinc finger, C3HC4 type (RING finger)
    7.8e-08   32.1   7.2    1.7e-07   31.1   7.2    1.6  1  zf-RING_5      zinc-RING finger domain
    8.2e-08   32.0   3.8    8.2e-08   32.0   3.8    1.7  2  zf-C3HC4_3     Zinc finger, C3HC4 type (RING finger)
    3.4e-07   30.2   2.0    3.9e-07   30.0   0.8    1.7  1  zf-RING_UBOX   RING-type zinc-finger
    4.7e-07   29.6   6.1    4.7e-07   29.6   6.1    1.6  2  zf-C3HC4       Zinc finger, C3HC4 type (RING finger)
    2.7e-06   27.0   2.2    2.7e-06   27.0   2.2    2.6  3  zf-CCCH_4      CCCH-type zinc finger
      1e-05   25.4   5.8      1e-05   25.4   5.8    2.8  3  zf_CCCH_4      Zinc finger domain
    5.8e-05   23.3   5.0    5.8e-05   23.3   5.0    2.0  2  zf-RING_2      Ring finger domain
    0.00026   21.1   5.8    0.00067   19.8   5.8    1.8  1  zf-C3HC4_4     zinc finger of C3HC4-type, RING
     0.0015   18.4   4.5     0.0015   18.4   4.5    1.6  2  Prok-RING_4    Prokaryotic RING finger family 4
  ------ inclusion threshold ------
      0.015   15.4   4.4      0.015   15.4   4.4    1.7  2  zf-RING_10     zinc RING finger of MSL2
      0.032   14.1   4.1      0.054   13.4   4.1    1.3  1  zf-RING_6      zf-RING of BARD1-type protein
      0.093   13.2   1.3      0.093   13.2   1.3    2.2  2  zf-CCCH_2      RNA-binding, Nab2-type zinc finger
        2.9    7.8  10.3         28    4.7   1.6    3.4  3  C1_1           Phorbol esters/diacylglycerol binding domain (


Domain annotation for each model (and alignments):
>> zf-CCCH  Zinc finger C-x8-C-x5-C-x3-H type (and similar)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   2.8   2.5e-12     3e-09       5      26 ..      14      35 ..      12      36 .. 0.94
   2 ?   -2.5   1.0       4.5   5.4e+03       6      11 ..      56      61 ..      54      74 .. 0.52
   3 ?   -2.4   0.1       4.2     5e+03      17      21 ..      83      87 ..      82      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.5e-12
                                   CBCHHHHHS--TTGGG-SSBSC CS
                        zf-CCCH  5 lCrffmrtGyCkyGdrCkFaHg 26
                                   +C+ f++tGyC yGd+Ck++H+
  gene870|gene870|rna869|rna869 14 ICKSFRETGYCGYGDSCKYSHD 35
                                   7********************7 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.5
                                   BCHHHH CS
                        zf-CCCH  6 Crffmr 11
                                   Cr  ++
  gene870|gene870|rna869|rna869 56 CRKLYK 61
                                   554444 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.2
                                   TGGG- CS
                        zf-CCCH 17 yGdrC 21
                                    Gd C
  gene870|gene870|rna869|rna869 83 NGDEC 87
                                   69999 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   5.2     2e-11   2.3e-08       2      40 .]      53      90 ..      52      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2e-11
                     zf-C3HC4_2  2 CpiCldmlkdpsvvtpCgHvfCqkCilrsLeekneCPlC 40
                                   C iC   +k+  vvt+CgH+fC+ C  r  ++++eC +C
  gene870|gene870|rna869|rna869 53 CGICRKLYKER-VVTECGHSFCSLCAIRKYQNGDECGVC 90
                                   9********96.****************99******999 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   7.2   1.4e-10   1.7e-07       2      44 .]      53      92 ..      52      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.4e-10
                      zf-RING_5  2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44
                                   C +C++ +   ++ ++t+CgH+fC+ C+ ++ ++ ++C +C+k
  gene870|gene870|rna869|rna869 53 CGICRKLY---KERVVTECGHSFCSLCAIRKYQNGDECGVCGK 92
                                   ********...8899*****************9********86 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       2.6   3.1e+03      28      28 ..      17      17 ..      10      33 .. 0.57
   2 !   32.0   3.8   6.9e-11   8.2e-08       3      47 ..      51      94 ..      49      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.6
                                   H CS
                     zf-C3HC4_3 28 e 28
                                   +
  gene870|gene870|rna869|rna869 17 S 17
                                   2 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 6.9e-11
                                   SB-TTTSSSBS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                     zf-C3HC4_3  3 eeCviClerprnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpi 47
                                    +C iC +  ++ v+ +CgH  +C+ Ca +  ++ ++C +C +p+
  gene870|gene870|rna869|rna869 51 LLCGICRKLYKERVVTECGHS-FCSLCAIRKYQNGDECGVCGKPV 94
                                   58*******************.*********9**********998 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.8   3.3e-10   3.9e-07       1      31 [.      53      81 ..      53      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.3e-10
                   zf-RING_UBOX  1 CpIClelftdPlvlpCGHtFCreClwelsks 31
                                   C IC+ l+++ +v++CGH+FC+ C   ++k 
  gene870|gene870|rna869|rna869 53 CGICRKLYKERVVTECGHSFCSLCA--IRKY 81
                                   9*******9994579*********9..3333 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       7.2   8.6e+03       3       6 ..      14      17 ..      13      24 .. 0.62
   2 !   29.6   6.1     4e-10   4.7e-07       1      41 []      53      90 ..      53      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.2
                                   TT-S CS
                       zf-C3HC4  3 iCle 6 
                                   iC++
  gene870|gene870|rna869|rna869 14 ICKS 17
                                   6665 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 4e-10
                                   -TTT-S--SS-E.E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4  1 CpiCleeakepnelleCkHsfCskCirkilksrkkvkCPlC 41
                                   C iC + +ke + ++eC+HsfCs C  + ++  +  +C +C
  gene870|gene870|rna869|rna869 53 CGICRKLYKERV-VTECGHSFCSLCAIRKYQ--NGDECGVC 90
                                   99**********.************888888..67779888 PP

>> zf-CCCH_4  CCCH-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   2.2   2.3e-09   2.7e-06       2      22 .]      14      35 ..      13      35 .. 0.96
   2 ?   -0.3   0.3      0.81   9.7e+02       8      12 ..      53      57 ..      51      58 .. 0.83
   3 ?   -1.7   0.1       2.4   2.8e+03       4      11 ..      79      87 ..      79      88 .. 0.71

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.3e-09
                      zf-CCCH_4  2 lCpyfa.kGsCrfGdnCrFsHd 22
                                   +C++f  +G C +Gd C++sHd
  gene870|gene870|rna869|rna869 14 ICKSFReTGYCGYGDSCKYSHD 35
                                   8********************9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.81
                      zf-CCCH_4  8 kGsCr 12
                                   +G+Cr
  gene870|gene870|rna869|rna869 53 CGICR 57
                                   89998 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.4
                      zf-CCCH_4  4 pyfakG.sC 11
                                   +++++G  C
  gene870|gene870|rna869|rna869 79 RKYQNGdEC 87
                                   578888666 PP

>> zf_CCCH_4  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   5.8   8.4e-09     1e-05       1      19 []      15      34 ..      15      34 .. 0.99
   2 ?   -1.4   0.2       2.2   2.7e+03       7      11 ..      54      58 ..      51      58 .. 0.77
   3 ?   -0.7   0.1       1.4   1.7e+03      11      15 ..      83      87 ..      82      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8.4e-09
                      zf_CCCH_4  1 Ckfflq.GtCkkGdkCrFaH 19
                                   Ck f + G+C +Gd+C+++H
  gene870|gene870|rna869|rna869 15 CKSFREtGYCGYGDSCKYSH 34
                                   ******************** PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                      zf_CCCH_4  7 GtCkk 11
                                   G C+k
  gene870|gene870|rna869|rna869 54 GICRK 58
                                   88997 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.4
                      zf_CCCH_4 11 kGdkC 15
                                   +Gd C
  gene870|gene870|rna869|rna869 83 NGDEC 87
                                   8**** PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2       2.4   2.9e+03      13      13 ..      22      22 ..       7      36 .. 0.54
   2 !   23.3   5.0   4.9e-08   5.8e-05       3      43 ..      53      90 ..      51      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                      zf-RING_2 13 a 13
                                   +
  gene870|gene870|rna869|rna869 22 G 22
                                   1 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 4.9e-08
                      zf-RING_2  3 CpICleelssadsvlllpCgHvfhreClerwlrssstCPlC 43
                                   C+IC + + + ++v+++ CgH+f+  C+ r  ++  +C +C
  gene870|gene870|rna869|rna869 53 CGICRKLY-K-ERVVTE-CGHSFCSLCAIRKYQNGDECGVC 90
                                   ****7555.3.677777.*********9887888888*999 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   5.8   5.6e-07   0.00067       1      34 [.      53      86 ..      53      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.6e-07
                     zf-C3HC4_4  1 CPiCldYLekPvsleCGhsfClsCisslqkepdg 34
                                   C iC+++ ++ v  eCGhsfC  C  +  ++ d+
  gene870|gene870|rna869|rna869 53 CGICRKLYKERVVTECGHSFCSLCAIRKYQNGDE 86
                                   99**********************7666655544 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.1       9.2   1.1e+04      19      22 ..      13      16 ..      11      17 .. 0.62
   2 !   18.4   4.5   1.2e-06    0.0015       1      39 [.      53      93 ..      53      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 9.2
                    Prok-RING_4 19 lvCk 22
                                   ++Ck
  gene870|gene870|rna869|rna869 13 IICK 16
                                   5776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.2e-06
                    Prok-RING_4  1 CvlCgeqekkailepCgHlvCkeCfdskdls..sCPlCqrr 39
                                   C +C++  k++++  CgH +C  C   k  +   C +C + 
  gene870|gene870|rna869|rna869 53 CGICRKLYKERVVTECGHSFCSLCAIRKYQNgdECGVCGKP 93
                                   99**********************9999666679****886 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.3   3.9e+03      13      13 ..      22      22 ..       9      39 .. 0.55
   2 ?   15.4   4.4   1.3e-05     0.015       1      44 [.      51      91 ..      51      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.3
                     zf-RING_10 13 P 13
                                    
  gene870|gene870|rna869|rna869 22 G 22
                                   1 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                     zf-RING_10  1 lsCvvCckLLvdPlepkekeCqHyvCrlCvgkkkklkpsCsqCk 44
                                   l C +C kL ++ +    +eC+H+ C lC  +k +   +C  C 
  gene870|gene870|rna869|rna869 51 LLCGICRKLYKERVV---TECGHSFCSLCAIRKYQNGDECGVCG 91
                                   68********99776...59***********************7 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.1   4.5e-05     0.054       8      51 ..      51      95 ..      47      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                      zf-RING_6  8 lrcsrctdilrepvclggcehifcsncisdcf..gsgcpvcytpaw 51
                                   l c  c  + +e v    c h fcs c    +  g  c vc  p +
  gene870|gene870|rna869|rna869 51 LLCGICRKLYKERVV-TECGHSFCSLCAIRKYqnGDECGVCGKPVY 95
                                   67999*******995.68*********8877633666****99875 PP

>> zf-CCCH_2  RNA-binding, Nab2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.3   7.8e-05     0.093       1      17 [.      14      34 ..      14      34 .. 0.88
   2 ?   -2.8   0.2       8.9   1.1e+04      10      13 ..      84      87 ..      83      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                      zf-CCCH_2  1 pCrffpn...C.tnpkCpFaH 17
                                   +C+ f     C ++++C+++H
  gene870|gene870|rna869|rna869 14 ICKSFREtgyCgYGDSCKYSH 34
                                   6888888888*********** PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.9
                      zf-CCCH_2 10 npkC 13
                                   +++C
  gene870|gene870|rna869|rna869 84 GDEC 87
                                   7899 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.6     0.024        28       1      38 [.      11      60 ..      11      71 .. 0.70
   2 ?   -0.8   3.7       1.2   1.5e+03      11      16 ..      70      75 ..      47      79 .. 0.47
   3 ?    4.0   3.2     0.039        47       6      25 ..      79      98 ..      63     101 .] 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.024
                                   --EEEE--SS--B-TTT-SB-...........-S.SSS-EEEETTT--EE CS
                           C1_1  1 HhwvhrnfkqptfCkhCgefl...........wg.kekqglkCswCkllv 38
                                   H++  ++f+++++C + +++            +   + +gl C  C+ l+
  gene870|gene870|rna869|rna869 11 HKIICKSFRETGYCGYGDSCKyshdrsmgyseSPvVSDTGLLCGICRKLY 60
                                   88899999999999875554455577777766555667777777776655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                                   --B-TT CS
                           C1_1 11 ptfCkh 16
                                    +fC+ 
  gene870|gene870|rna869|rna869 70 HSFCSL 75
                                   233333 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.039
                                   E--SS--B-TTT-SB--SSS CS
                           C1_1  6 rnfkqptfCkhCgeflwgke 25
                                   r++++   C  Cg++++gk+
  gene870|gene870|rna869|rna869 79 RKYQNGDECGVCGKPVYGKF 98
                                   67888999999999997754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 703.81
//
Query:       gene87|gene87|rna87|rna87  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.047   13.3   0.1      0.047   13.3   0.1    1.4  2  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.6e-06     0.047     203     280 ..      95     193 ..      61     270 .. 0.62
   2 ?   -3.9   0.1      0.42   7.6e+03     313     321 ..     370     378 ..     348     389 .. 0.42

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-06
                  Cas_DxTHG 203 lkklkklkeklkkeleefskalelir..............p.lellekaekleke...........................iv 244
                                ++k ++lk++l+++l++f+++le +r              + l+ll        +                           i 
  gene87|gene87|rna87|rna87  95 SEKKEQLKKCLADQLNKFKNILENCRktlgenakeccidqKcLDLL--------NggntscneedngkdckdkncrdkiadeI- 169
                                344459********************55555555555554344444........04444333345444433333333333333. PP

                  Cas_DxTHG 245 eklkeeleeiesleeeesakplel......lldeikkklekf 280
                                                  +k l+l      lld++k  l+k+
  gene87|gene87|rna87|rna87 170 ------------------VKNLNLdqlkksLLDSLKGSLKKI 193
                                ..................333333333335455554444444 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.42
                  Cas_DxTHG 313 edilnkkkr 321
                                +  ++k+++
  gene87|gene87|rna87|rna87 370 DTKKSKDEE 378
                                111122222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1296  (0.0722851); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2915.50
//
Query:       gene871|gene871|rna870|rna870  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.001   18.8   1.7     0.0023   17.7   1.7    1.7  1  DUF21            Cyclin M transmembrane N-terminal domain
  ------ inclusion threshold ------
       0.17   10.1   9.5       0.23    9.6   9.5    1.2  1  YfhO             Bacterial membrane protein YfhO
          1   10.1   3.5        2.6    8.9   1.0    2.7  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
        2.3    8.2   9.0       0.12   12.3   2.2    2.1  2  Colicin_V        Colicin V production protein


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.7   5.1e-07    0.0023      52     169 ..     138     271 ..      62     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.1e-07
                          DUF21  52 lLstlligntlvnillsalatalfvellae..galavviatvivtllilvfgEilPkslalkyaekialalapplrvlmv 129
                                    ++s +++   ++ i+ +a +t++ +  ++   +++a v+ +++  + + v g ++ ks+++++  ++ +a+  +  +   
  gene871|gene871|rna870|rna870 138 YWSKMIFSTVIILIIGVAAVTDFSDGGVEGpySEIAYVVGVILAICELAVEGRVVKKSVFKHRRFSVFMAFLLICAISFP 217
                                    55666666677777777788888777776688889999999888************************************ PP

                          DUF21 130 llyPlv.....wllskllnlil.........esesepavseeelkklveeseee 169
                                     +yP+v      ++++l++ i+          +++  av++e+++++++  +++
  gene871|gene871|rna870|rna870 218 AMYPIVnkwknLFVKWLTERIViwikprmikVKDKILAVTKEQIRAFISDYTRK 271
                                    ******98877667777777778888*****99**************9877665 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   9.5   5.2e-05      0.23     282     445 ..      14     191 ..       9     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 5.2e-05
                           YfhO 282 iyvgllpllllilyFvlkkiklkeklafallllllilsfllpplnlvwhgfqaPvgfpyRfsfilsflllllaaealk.. 359
                                    i+  ll l+ l+++++ +      k+++ ++ ll+++ fl  +   +w  f++ +    R sf+  ++ +  ++e ++  
  gene871|gene871|rna870|rna870  14 IFAELLTLVSLFFMITVQFGDINGKVINHIIKLLMFINFLYHVGSCIWRIFTSIQ---ERMSFLNGMFNVRNIVELVTmc 90 
                                    7888999************************************************...******9999888888877777 PP

                           YfhO 360 ....elkql......kklkllaailllvlllliilllknkksynfltssqlllgllllllalllllllll........kk 421
                                        ++k++      +k+++ + +++l++++l++     + + ++ t+++++ ++++ ++++l+++++++          
  gene871|gene871|rna870|rna870  91 iltlYFKEVvttfdpDKRRMDRCVIVLSMGYLLSK---VNEVLDYSTTQSYWSKMIFSTVIILIIGVAAVtdfsdggvEG 167
                                    77787777777777667788777777777777665...334456777777777888888877777765556777788878 PP

                           YfhO 422 kkkklvllllllvlvlelggnayl 445
                                    +++ + +++ ++++++el++ + +
  gene871|gene871|rna870|rna870 168 PYSEIAYVVGVILAICELAVEGRV 191
                                    888888888888888888777655 PP

>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.0   0.00059       2.6       5      45 ..      18     163 ..      14     165 .. 0.68
   2 ?   -2.0   0.1       1.4   6.4e+03      15      31 ..     205     214 ..     197     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00059
                                    HHHHHHHHHHHHHHHGGGS-H........................................................... CS
                CDP-OH_P_transf   5 aiTllrlllsvlailllltyyp.......................................................... 26 
                                    ++Tl++l++    ++++ + +                                                           
  gene871|gene871|rna870|rna870  18 LLTLVSLFF----MITVQFGDIngkvinhiikllmfinflyhvgsciwriftsiqermsflngmfnvrnivelvtmcilt 93 
                                    666666666....3333333335566777777666666666677777777777777777777777777777777666777 PP

                                    ...................................................HHHHHHHH.HHHHHTTHHH CS
                CDP-OH_P_transf  27 ..................................................lvlaillll.iasltDalDG 45 
                                                                                      + + i+l++ +a++tD+ DG
  gene871|gene871|rna870|rna870  94 lyfkevvttfdpdkrrmdrcvivlsmgyllskvnevldysttqsywskmiFSTVIILIIgVAAVTDFSDG 163
                                    7777777777778888888887777777788888888888888888887655555555589********9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                    HHHHHGGGS-H..HHHH CS
                CDP-OH_P_transf  15 vlailllltyyplvlai 31 
                                    ++a+ll+       +ai
  gene871|gene871|rna870|rna870 205 FMAFLLI-------CAI 214
                                    4444333.......222 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.7      0.27   1.2e+03      20      51 ..      13      42 ..      11      95 .. 0.60
   2 ?   12.3   2.2   2.8e-05      0.12       1      74 [.     144     218 ..     144     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                      Colicin_V 20 Gfvrevlsllgwvvafvvasllypslaellae 51
                                   G++ e+l+l++++  f++++++++  ++ +++
  gene871|gene871|rna870|rna870 13 GIFAELLTLVSLF--FMITVQFGDINGKVINH 42
                                   5555555555555..34444444444444444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.8e-05
                      Colicin_V   1 lDliillilllsallGlrrGfvrevlsllgwvvafvvasllypslaellae.lilspalaaiiaflllfllvlli 74 
                                    ++ +i+li++++a++ ++ G v    s +++vv++++a+      +  +++ +++++++  ++afll+  +++ +
  gene871|gene871|rna870|rna870 144 FSTVIILIIGVAAVTDFSDGGVEGPYSEIAYVVGVILAICELAVEGRVVKKsVFKHRRFSVFMAFLLICAISFPA 218
                                    5789***********************************9999999999999999**********9988777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1137  (0.0634168); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2107.26
//
Query:       gene872|gene872|rna871|rna871  [L=171]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-53  178.7  12.4      8e-53  178.4  12.4    1.1  1  Ribosomal_L19e  Ribosomal protein L19e
    7.8e-05   22.3   0.0    0.00031   20.4   0.0    2.1  1  SHOCT           Short C-terminal domain
  ------ inclusion threshold ------
       0.29   10.9   3.5        3.7    7.3   0.6    2.5  3  SAND            SAND domain
        1.9    8.8   7.8       0.37   11.0   1.4    2.7  2  GFD1            GFD1 mRNA transport factor


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.4  12.4   1.8e-56     8e-53       4     143 ..       6     145 ..       3     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 1.8e-56
                                    HHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG--S-H CS
                 Ribosomal_L19e   4 lqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrkGtk 83 
                                      +rla+++l++Gkn++wld++e+e++++A++re+ir+likd++Ii k++k +sr+r+rer ++krkgr++g+Gkr Gt 
  gene872|gene872|rna871|rna871   6 RIRRLASEILNCGKNKLWLDNNEIERLNSATSREQIRQLIKDNVIIMKQDKHTSRGRFRERLRAKRKGRHMGPGKRFGTT 85 
                                    679***************************************************************************** PP

                                    HHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                 Ribosomal_L19e  84 eaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                    +aR+p+kelW+k+iRa+R++Lke+r++++i+k+ +r +Y++akG  fk++ ++k+ i k+
  gene872|gene872|rna871|rna871  86 NARMPKKELWMKKIRAMRKMLKEMRASGEITKEDFRVFYKQAKGHLFKHRFHMKDCIVKR 145
                                    *******************************************************99876 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     7e-08   0.00031       5      21 ..     105     121 ..     103     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 7e-08
                          SHOCT   5 kLkeLyarGeIteEEFe 21 
                                     Lke++a+GeIt+E+F+
  gene872|gene872|rna871|rna871 105 MLKEMRASGEITKEDFR 121
                                    69*************95 PP

>> SAND  SAND domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.6   7.1e+03      11      21 ..      17      27 ..      15      42 .. 0.65
   2 ?    7.3   0.6   0.00083       3.7      48      74 ..      86     112 ..      70     115 .. 0.83
   3 ?    4.0   0.1    0.0088        39       7      34 ..     120     144 ..     114     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                                   ETTEEEEEEHH CS
                           SAND 11 CgdakGlLykk 21
                                   Cg++k +L  +
  gene872|gene872|rna871|rna871 17 CGKNKLWLDNN 27
                                   77766665544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00083
                                    HHT-TT-S-HHHH-EETTEEHHHHHHT CS
                           SAND  48 eagkasskdWKksIrlggktLkeliek 74 
                                    +a + +++ W k+Ir  +k+Lke+  +
  gene872|gene872|rna871|rna871  86 NARMPKKELWMKKIRAMRKMLKEMRAS 112
                                    577888888*************98665 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0088
                                    EEEEETTEEEEEEHHHHHS-TTS--EE- CS
                           SAND   7 lpVtCgdakGlLykkklkqgisekCiqt 34 
                                    + V  ++akG L+k+++     ++Ci  
  gene872|gene872|rna871|rna871 120 FRVFYKQAKGHLFKHRFHM---KDCIVK 144
                                    6677799**********98...999855 PP

>> GFD1  GFD1 mRNA transport factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.6      0.21   9.2e+02      13      20 ..      97     104 ..      97     104 .. 0.91
   2 ?   11.0   1.4   8.3e-05      0.37       6      13 ..     144     151 ..     142     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.21
                           GFD1  13 rkIleekq 20 
                                    +kI+++++
  gene872|gene872|rna871|rna871  97 KKIRAMRK 104
                                    8*****97 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.3e-05
                           GFD1   6 KKKIEEQr 13 
                                    K+KIEEQr
  gene872|gene872|rna871|rna871 144 KRKIEEQR 151
                                    9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1038.69
//
Query:       gene873|gene873|rna872|rna872  [L=164]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-26   92.3   0.3    3.3e-26   91.7   0.3    1.3  1  Evr1_Alr  Erv1 / Alr family
  ------ inclusion threshold ------
      0.085   12.1   0.0       0.12   11.6   0.0    1.2  1  Innexin   Innexin
      0.085   13.1   0.1       0.26   11.5   0.0    1.7  2  APOBEC1   APOBEC1


Domain annotation for each model (and alignments):
>> Evr1_Alr  Erv1 / Alr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.7   0.3   5.5e-30   3.3e-26       1      99 [.      67     158 ..      67     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 5.5e-30
                                    HHHHHHHHHHHHCSHSS..HHHHHHH-CHHHHHHHHHHHSSCHHHHHHHHHHHHHCH.CCCGSSHHHHHHHHHHHHHHHH CS
                       Evr1_Alr   1 cslWtllHtlaaevpekpteeqqkelavlkaflkliakfypCeeCaehfekvlaenppekevesrdelvlWlweaHNeVn 80 
                                    +s+WtllHt+  ++p  pt +q+k++    +f++l+++++pC +C +hf+k+l+++pp+  v s++e+  Wl+e+HN Vn
  gene873|gene873|rna872|rna872  67 RSTWTLLHTMGSRYPAFPTFQQKKDT---LTFIHLLSSVFPCGDCTKHFQKLLRDHPPR--VGSNEEFKAWLCEVHNVVN 141
                                    79*************99*****9999...9***************************88..******************* PP

                                    HHTT...T-HHCHHHCCCC CS
                       Evr1_Alr  81 krlakeefdcsedkvkerw 99 
                                    +rl+k  +dc+  +v++ w
  gene873|gene873|rna872|rna872 142 ERLGKAVVDCK--TVDNIW 158
                                    ***********..777777 PP

>> Innexin  Innexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05      0.12     266     334 ..      10      79 ..       7      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
                        Innexin 266 flliltiisllywllrlllpslrerfikkylkiakvlkskeekq.kalkkfveeylrpdgvfllrliakn 334
                                    +l+il +  +ly+++ l+++s++e++   +l+ +++   ++ ++ k++kk ++e+l++  + ll+ +++ 
  gene873|gene873|rna872|rna872  10 ILIILVAAWVLYRCYGLIVRSREEKISTAFLRDTTMDGVENFQTrKMSKKEIRERLGRSTWTLLHTMGSR 79 
                                    6788889999******9999999998888886555444333333259******************99876 PP

>> APOBEC1  APOBEC1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   6.4e+03      22      22 ..      50      50 ..      32      76 .. 0.55
   2 ?   11.5   0.0   4.4e-05      0.26      37      65 ..      92     120 ..      83     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                        APOBEC1 22 n 22
                                   n
  gene873|gene873|rna872|rna872 50 N 50
                                   3 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.4e-05
                        APOBEC1  37 vscsitwflstspcgkcskaileflsqhp 65 
                                    +  +i  + s+ pcg+c+k+ +++l+ hp
  gene873|gene873|rna872|rna872  92 TLTFIHLLSSVFPCGDCTKHFQKLLRDHP 120
                                    556677778899****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1213.57
//
Query:       gene874|gene874|rna873|rna873  [L=312]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-40  136.7   4.6    2.4e-21   75.6   0.6    2.2  2  TFIIB         Transcription factor TFIIB repeat
    1.9e-13   49.7   3.0    5.2e-13   48.3   3.0    1.8  1  TF_Zn_Ribbon  TFIIB zinc-binding
    6.4e-06   25.9   0.4    2.7e-05   23.9   0.2    2.0  2  Cyclin_N      Cyclin, N-terminal domain
      4e-05   23.7   0.1      0.063   13.4   0.0    2.3  2  Cyclin_C      Cyclin, C-terminal domain
    0.00016   21.7   1.0     0.0015   18.6   1.0    2.2  1  RB_B          Retinoblastoma-associated protein B domain
     0.0058   16.5   0.2      0.072   13.0   0.0    2.0  2  DUF4370       Domain of unknown function (DUF4370)
  ------ inclusion threshold ------
      0.078   13.0   0.1        0.2   11.7   0.1    1.7  1  TFIIB_C_1     Transcription factor IIB C-terminal module 1


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.6   9.2e-25   2.4e-21       1      71 []     117     187 ..     117     187 .. 0.98
   2 !   63.0   0.2     8e-21     2e-17       1      71 []     210     281 ..     210     281 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 9.2e-25
                                    HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    i++f+++ +L+ ++ d+A +++k+  e+k+lkG+  +gi+AAc+yiAcr+ee  rt+keis ++ V++ +i
  gene874|gene874|rna873|rna873 117 ITAFCERSNLSRTIIDRAHYIFKNIEERKLLKGKNVEGIVAACMYIACRQEECPRTFKEISVMTAVQKREI 187
                                    899****************************************************************9987 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 8e-21
                                    HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTT.TSS--HHHHHHHSS--SHHH CS
                          TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrke.evkrtqkeissvlqVsekti 71 
                                    i rf++ l+L+ k+++ A+e+ak a+e + l+G+sp++iaAA++y+ + ++ e+k+ qk+i+ v++V+e+ti
  gene874|gene874|rna873|rna873 210 IARFCSDLNLSIKIQKIATEIAKAAHELGCLAGKSPDSIAAAVIYMVTNLFpEEKKIQKDIQFVTNVTEVTI 281
                                    78********************************************9988648899**************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   3.0     2e-16   5.2e-13       3      43 .]      14      55 ..      12      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2e-16
                                   ETTTTCEE.CHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                   TF_Zn_Ribbon  3 CPnCgstn.lveDpergelvCtdCGlVlednsidegpewref 43
                                   C +Cg t+ ++eD+++g +vC++CG+++ +++ideg+ewr f
  gene874|gene874|rna873|rna873 14 CSDCGETQnIIEDYKNGYHVCGRCGCIVGNRIIDEGSEWRSF 55
                                   ******999*******************************87 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2     1e-08   2.7e-05      32     110 ..     111     186 ..      89     199 .. 0.80
   2 ?   -0.7   0.0      0.44   1.1e+03      47      67 ..     198     218 ..     191     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1e-08
                                    HHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHH CS
                       Cyclin_N  32 ailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteee 110
                                    +  ++ ++  +e+ +l++ ++  a+ ++    ++k ++ ++++ ++a+c+++A++ ee+ p + +++ ++t   ++++e
  gene874|gene874|rna873|rna873 111 KHGMNLITAFCERSNLSRTIIDRAHYIFKNIEERKLLKGKNVEGIVAACMYIACRQEEC-PRTFKEISVMTA--VQKRE 186
                                    445778999***********************************************999.999999999964..45555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.44
                                    --TTHHHHHHHHHHHHHHHS- CS
                       Cyclin_N  47 ltpetlflavnyldRflskks 67 
                                    l++   + + n++ Rf+s  +
  gene874|gene874|rna873|rna873 198 LERMATMSTENIIARFCSDLN 218
                                    556667788999*****9433 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0012         3      48     101 ..     156     209 ..     153     228 .. 0.79
   2 !   13.4   0.0   2.5e-05     0.063      43      89 ..     244     291 ..     238     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0012
                                    HHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHHHHHHGSS--HH CS
                       Cyclin_C  48 Aaaalllarstlnspewtetlehytgyskedlkpcvelilellssapssklqav 101
                                     aa++++a+++ + p   +++   t ++k ++  c +li ++l + ++ +++++
  gene874|gene874|rna873|rna873 156 VAACMYIACRQEECPRTFKEISVMTAVQKREIGRCFKLISPHLERMATMSTENI 209
                                    589999999994445555666666677****************88888777666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.5e-05
                                    -HHHHHHHHHHHCCHHH.HS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                       Cyclin_C  43 ppSliAaaalllarstl.nspewtetlehytgyskedlkpcvelilel 89 
                                    +p  iAaa+++++++   ++++ ++ ++++t +++  +k+ ++ ++ +
  gene874|gene874|rna873|rna873 244 SPDSIAAAVIYMVTNLFpEEKKIQKDIQFVTNVTEVTIKNTYKELVAF 291
                                    6889*************99999*********************99876 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.0   5.8e-07    0.0015      14      91 ..     114     189 ..     107     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.8e-07
                           RB_B  14 avrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqassk 91 
                                    +  +   cer +ls+++ ++++ +f+++  ee++llk ++++ i+ +++Y+ ++ ++  ++Fkei  +   q+ +  +
  gene874|gene874|rna873|rna873 114 MNLITAFCERSNLSRTIIDRAHYIFKNI--EERKLLKGKNVEGIVAACMYIACRQEECPRTFKEISVMTAVQKREIGR 189
                                    5567889999999999999999999985..999*******************************97766666655555 PP

>> DUF4370  Domain of unknown function (DUF4370)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.082   2.1e+02       8      89 ..     114     192 ..     107     198 .. 0.77
   2 !   13.0   0.0   2.8e-05     0.072      36     105 ..     233     302 ..     198     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.082
                        DUF4370   8 rsllrsaaaassrlsaaaaasaalekhlssrslfavlsasskavlsdlrsplalslGsvrsfsedvshlPeikdsevkka 87 
                                     +l+ + +++s   ++ + +++ + k++ +r+l++    + + +++ + +  + +    r+f  ++s + +++  e+ + 
  gene874|gene874|rna873|rna873 114 MNLITAFCERSNLSRTIIDRAHYIFKNIEERKLLK--GKNVEGIVAACMYIACRQEECPRTFK-EISVMTAVQKREIGRC 190
                                    57888999999999999999999999999999994..55666667777776666666777775.5888999999999998 PP

                        DUF4370  88 fk 89 
                                    fk
  gene874|gene874|rna873|rna873 191 FK 192
                                    88 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.8e-05
                        DUF4370  36 ssrslfavlsasskavlsdlrsplalslGsvrsfsedvshlPeikdsevkkafkdllaaswdelPdavve 105
                                    +  +l  ++  s+ ++ + + + ++  + + ++  +d++ + ++ +  +k+++k+l+a ++d +P+ +v+
  gene874|gene874|rna873|rna873 233 AAHELGCLAGKSPDSIAAAVIYMVTNLFPEEKKIQKDIQFVTNVTEVTIKNTYKELVAFKYDIIPENMVN 302
                                    45666677788888889999999999999999**********************************9997 PP

>> TFIIB_C_1  Transcription factor IIB C-terminal module 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.8e-05       0.2       7      76 ..     115     181 ..     110     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
                      TFIIB_C_1   7 nalevllklsrrdeavleealelakrfvGkrrergervekqeevaaaclmlaaerlrqPvPLaelrvldp 76 
                                    n + +++++s+   +++++a  + k+   ++  +g+ ve    ++aac+ +a+ + + P  ++e+ v+ +
  gene874|gene874|rna873|rna873 115 NLITAFCERSNLSRTIIDRAHYIFKNIEERKLLKGKNVE---GIVAACMYIACRQEECPRTFKEISVMTA 181
                                    67899*******************998887778888887...689**************99999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1965.61
//
Query:       gene875|gene875|rna874|rna874  [L=153]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-35  121.9   3.4    2.3e-35  121.8   3.4    1.0  1  Ribosomal_S13  Ribosomal protein S13/S18
     0.0075   15.1   0.0      0.009   14.8   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   3.4   2.6e-39   2.3e-35       1     128 []      15     143 ..      15     143 .. 0.98

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 2.6e-39
                  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdG 79 
                                    Ri +t+idg+k++++alt i+G+G r +++i+k++++d +kr+ge++ee++++i + +  +a+  ip+ + n+qkd++dG
  gene875|gene875|rna874|rna874  15 RIHNTNIDGTKRIAFALTGIRGVGIRISTAICKRLGIDLKKRAGEMSEEDMKRIGDAILDPASVGIPESYmNHQKDVIDG 94 
                                    99**************************************************************9998777********* PP

                  Ribosomal_S13  80 kdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                     +sh++ ++l+  lr+ ieR kk +  r  R   GlkvRGQrTk++gR+
  gene875|gene875|rna874|rna874  95 TTSHLIGTKLDADLRMMIERGKKNKLIRACRLDVGLKVRGQRTKSNGRR 143
                                    ************************************************7 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     1e-06     0.009     185     235 ..      23      72 ..       3      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-06
                                    S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHH CS
                           FbpA 185 kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyeal 235
                                     +k+++ aL + ++G++  ++  +++r+g+d +++a e+seed++r+ +a+
  gene875|gene875|rna874|rna874  23 GTKRIAFAL-TGIRGVGIRISTAICKRLGIDLKKRAGEMSEEDMKRIGDAI 72 
                                    555565555.4569********************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 936.28
//
Query:       gene876|gene876|rna875|rna875  [L=94]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.7e-11   42.3   4.9    7.6e-11   42.1   4.9    1.1  1  Ribosomal_L36e  Ribosomal protein L36e


Domain annotation for each model (and alignments):
>> Ribosomal_L36e  Ribosomal protein L36e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   4.9   4.2e-15   7.6e-11      14      92 ..      14      92 ..       4      94 .] 0.92

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4.2e-15
                 Ribosomal_L36e 14 vtknvsklrpsrrkgrltkrtkfvrdiirevaGfapyerrvmellkvskdKralKfaKkrlgthirakrKreelsnvla 92
                                   v++   k +p++ +++  k   +  ++  e+ G++p e++v+ l+  +++ +a K++K rlg+h+ra  ++e+l++++ 
  gene876|gene876|rna875|rna875 14 VKRPDVKRKPKKLSEEFRKARMLAASVAEEIGGLSPLEKKVVSLIEAKNNNKAQKILKVRLGSHKRAGIRIEKLTKMIL 92
                                   5556678899999999999999****************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 651.99
//
Query:       gene877|gene877|rna876|rna876  [L=863]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (863 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 5093.37
//
Query:       gene878|gene878|rna877|rna877  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-08   34.6   0.0    1.1e-08   34.6   0.0    1.0  1  LSM         LSM domain
      0.006   16.7   0.0     0.0067   16.5   0.0    1.1  1  SM-ATX      Ataxin 2 SM domain
  ------ inclusion threshold ------
       0.02   15.1   0.0      0.024   14.8   0.0    1.1  1  FLgD_tudor  FlgD Tudor-like domain
       0.14   12.3   0.0       0.21   11.7   0.0    1.3  1  DUF150_C    RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   2.6e-12   1.1e-08       5      62 ..       8      64 ..       4      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.6e-12
                                   HTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGE CS
                            LSM  5 klinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnni 62
                                    +i++ v v+  +  e+rGt +++D ++N+ Le v+ ++ ++ e r+++ ++i+G+ i
  gene878|gene878|rna877|rna877  8 AFIGRVVKVKICDSSEFRGTSVAVDAYLNISLESVSYIQSGQ-EPRHYSSLFIKGSYI 64
                                   689999*********************************999.************977 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.5e-06    0.0067       7      58 ..       5      52 ..       3      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-06
                                   HHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS....... CS
                         SM-ATX  7 lltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkansksss 58
                                   l+t+++G++v+v++ + + ++G   +v+    ++++L+ +  +++  +++  
  gene878|gene878|rna877|rna877  5 LYTAFIGRVVKVKICDSSEFRGTSVAVDA--YLNISLESVSYIQS--GQEPR 52
                                   79***************************..**********9999..33333 PP

>> FLgD_tudor  FlgD Tudor-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.4e-06     0.024       7      42 ..       7      51 ..       3      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.4e-06
                                   TCTTTSEEEEE........TEEEEE-EEEEEEEEEEEE..ETTEE CS
                                   xxxxxxxxxxx........xxxxxxxxxxxxxxxxxxx.xxxxxx RF
                     FLgD_tudor  7 asLiGkeVlvp........GtsvaattlvygtVdsVsl.stgggl 42
                                   +++iG+ V v         Gtsva++++ +   +sVs+ ++g+++
  gene878|gene878|rna877|rna877  7 TAFIGRVVKVKicdssefrGTSVAVDAYLNISLESVSYiQSGQEP 51
                                   689***********************************8888765 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.7e-05      0.21       7      38 ..       6      33 ..       5      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.7e-05
                       DUF150_C  7 FarflGelVkvklklpvegrkkftGkivevde 38
                                   ++ f+G+ Vkvk +    ++ +f+G+ v+vd+
  gene878|gene878|rna877|rna877  6 YTAFIGRVVKVKIC----DSSEFRGTSVAVDA 33
                                   789*********99....*******9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 465.14
//
Query:       gene879|gene879|rna878|rna878  [L=145]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-07   31.0   0.5    2.2e-07   31.0   0.5    2.7  3  zf-H2C2_2  Zinc-finger double domain
    0.00011   22.5   2.0    0.00011   22.5   2.0    3.7  3  zf-C2H2    Zinc finger, C2H2 type
    0.00021   21.9  10.1    0.00032   21.3   1.2    3.3  3  zf-C2H2_4  C2H2-type zinc finger
     0.0028   18.3   5.8        1.3    9.7   0.2    3.3  3  FOXP-CC    FOXP coiled-coil domain
  ------ inclusion threshold ------
       0.13   12.3   0.4       0.13   12.3   0.4    2.2  2  zf-BED     BED zinc finger
        5.1    7.6   8.6        4.6    7.8   6.2    2.2  3  zf-C2HE    C2HE / C2H2 / C2HC zinc-binding finger


Domain annotation for each model (and alignments):
>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.79   2.4e+03       2      13 ..      16      27 ..      15      32 .. 0.69
   2 !   31.0   0.5   7.3e-11   2.2e-07       1      25 [.      49      73 ..      49      74 .. 0.91
   3 ?   -0.1   0.1      0.51   1.5e+03       2      10 ..      78      86 ..      78      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.79
                      zf-H2C2_2  2 LrrHirkHtgek 13
                                    r H+ +H  ++
  gene879|gene879|rna878|rna878 16 VRDHLLSHIEKN 27
                                   678999998665 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 7.3e-11
                      zf-H2C2_2  1 nLrrHirkHtgekpyeCplCdkaFk 25
                                   +L  H r Htge+p+eC lC+k ++
  gene879|gene879|rna878|rna878 49 ALLAHARRHTGERPFECHLCGKDYT 73
                                   5778******************997 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.51
                      zf-H2C2_2  2 LrrHirkHt 10
                                   L++H+  H 
  gene879|gene879|rna878|rna878 78 LKKHLLRHE 86
                                   789998886 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   2.0      0.87   2.6e+03      13      20 ..      17      24 ..       1      26 [. 0.65
   2 ?    2.0   1.0      0.11   3.3e+02      12      23 .]      46      57 ..      45      57 .. 0.88
   3 !   22.5   2.0   3.5e-08   0.00011       1      23 []      63      85 ..      63      85 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.87
                                   HHHHHHHH CS
                        zf-C2H2 13 ksnLkrHi 20
                                   +++L +Hi
  gene879|gene879|rna878|rna878 17 RDHLLSHI 24
                                   35566665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                   SHHHHHHHHHCC CS
                        zf-C2H2 12 rksnLkrHirtH 23
                                   +k+ L +H r+H
  gene879|gene879|rna878|rna878 46 SKHALLAHARRH 57
                                   67899******9 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 3.5e-08
                                   EEETTTTEEESSHHHHHHHHHCC CS
                        zf-C2H2  1 ykCpdCgksFkrksnLkrHirtH 23
                                   ++C+ Cgk ++r++ Lk+H+ +H
  gene879|gene879|rna878|rna878 63 FECHLCGKDYTRSDPLKKHLLRH 85
                                   89********************9 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.22   6.5e+02      15      23 ..      15      23 ..       2      26 .. 0.57
   2 ?    3.5   0.3     0.057   1.7e+02      12      23 ..      46      57 ..      42      58 .. 0.90
   3 !   21.3   1.2   1.1e-07   0.00032       1      23 [.      63      85 ..      63      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
                      zf-C2H2_4 15 aLlrHlkth 23
                                   ++++Hl++h
  gene879|gene879|rna878|rna878 15 NVRDHLLSH 23
                                   356677666 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.057
                      zf-C2H2_4 12 skkaLlrHlkth 23
                                   sk+aLl H ++h
  gene879|gene879|rna878|rna878 46 SKHALLAHARRH 57
                                   8899******99 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 1.1e-07
                      zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkth 23
                                   f+C++Cgk +++++ L++Hl++h
  gene879|gene879|rna878|rna878 63 FECHLCGKDYTRSDPLKKHLLRH 85
                                   89********************9 PP

>> FOXP-CC  FOXP coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00045       1.3       6      29 ..       2      27 ..       1      31 [. 0.82
   2 ?    4.2   0.2     0.023        68       5      26 ..      30      54 ..      27      61 .. 0.61
   3 !    6.6   0.1     0.004        12      12      61 ..      68     116 ..      64     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00045
                        FOXP-CC  6 vCkWPgCekvledv..eeflkhlnse 29
                                    C+W gC+k +ed   +++l+h++++
  gene879|gene879|rna878|rna878  2 KCEWEGCQKDIEDNvrDHLLSHIEKN 27
                                   5**********996346899999876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.023
                        FOXP-CC  5 gvCkWPgCekvle...dveeflkhl 26
                                     C W gC++  e   + +++l+h+
  gene879|gene879|rna878|rna878 30 AKCLWRGCQRYGEaqvSKHALLAHA 54
                                   57******87665111334444444 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.004
                        FOXP-CC  12 CekvledveeflkhlnseHalddkstaqlrvqmqvvqqlekqlvkEkerL 61 
                                    C k  + ++ + khl   H++ d   + l ++++++  l +++++E+ r+
  gene879|gene879|rna878|rna878  68 CGKDYTRSDPLKKHLL-RHEVADSKNENLMMKIEYLGLLLTEYRRESLRI 116
                                    6777777888889985.699999999*******************99876 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.26   7.8e+02       5      18 ..      18      31 ..       3      38 .. 0.56
   2 ?   12.3   0.4   4.5e-05      0.13       5      41 ..      52      84 ..      48      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.26
                                   SSS----GGSS--E CS
                         zf-BED  5 kyftpvslkeqkav 18
                                   ++   + +k+  a+
  gene879|gene879|rna878|rna878 18 DHLLSHIEKNDEAK 31
                                   33333333333444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.5e-05
                                   SSS----GGSS--EETTTTEE----SSTHHHHHHHHH CS
                         zf-BED  5 kyftpvslkeqkavCryCgkilsrgggttnLkrHLrr 41
                                    ++++++  e   +C  Cgk ++r+     Lk+HL r
  gene879|gene879|rna878|rna878 52 AHARRHT-GERPFECHLCGKDYTRS---DPLKKHLLR 84
                                   6777787.777889**********8...888888854 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.71   2.1e+03      55      64 .]      17      26 ..      14      26 .. 0.85
   2 ?    7.8   6.2    0.0016       4.6      34      61 ..      59      85 ..      17      87 .. 0.71
   3 ?   -3.0   0.0       3.5     1e+04      22      35 ..     128     141 ..     112     143 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.71
                        zf-C2HE 55 KeHLeeefek 64
                                   ++HL +++ek
  gene879|gene879|rna878|rna878 17 RDHLLSHIEK 26
                                   68*****986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0016
                        zf-C2HE 34 lktpLkCtrCganfgnkfpkLKeHLeee 61
                                    ++p++C+ Cg +       LK+HL  +
  gene879|gene879|rna878|rna878 59 GERPFECHLCG-KDYTRSDPLKKHLLRH 85
                                   689********.55555588*****887 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.5
                        zf-C2HE  22 eslseeqskelilk 35 
                                    ++++++ ++e+ ++
  gene879|gene879|rna878|rna878 128 QTMNRKIAYEIKRN 141
                                    66777777777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 853.97
//
Query:       gene880|gene880|rna879|rna879  [L=305]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.097   12.2   0.0       0.14   11.7   0.0    1.2  1  Mu-like_Pro  Mu-like prophage I protein


Domain annotation for each model (and alignments):
>> Mu-like_Pro  Mu-like prophage I protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.7e-06      0.14     299     325 .]      95     121 ..      81     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-06
                    Mu-like_Pro 299 akkeaaLsaeekavakqlGiseeefaK 325
                                    a+++  Ls+e+k+++++ Giseeef K
  gene880|gene880|rna879|rna879  95 AENKYLLSDEDKKICRERGISEEEFYK 121
                                    566789*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1826.82
//
Query:       gene88|gene88|rna88|rna88  [L=306]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-66  223.0   0.0    4.9e-66  222.2   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    4.5e-11   43.1   0.0    1.2e-10   41.7   0.0    1.7  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    9.5e-08   32.3   0.0    1.6e-07   31.6   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
    1.8e-06   27.8   0.0    2.8e-06   27.3   0.0    1.2  1  Met_10           Met-10+ like-protein
     0.0023   17.1   0.0     0.0036   16.5   0.0    1.3  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
       0.03   13.9   0.0      0.056   13.0   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.032   14.0   0.0       0.05   13.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      0.043   13.1   0.2      0.087   12.1   0.2    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.047   14.4   0.1        0.1   13.3   0.1    1.6  1  Methyltransf_25  Methyltransferase domain
      0.047   12.9   0.0      0.058   12.6   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
       0.14   11.8   0.0       0.22   11.2   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.0     3e-69   4.9e-66       4     199 ..     103     302 ..     100     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 3e-69
                                H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEEE CS
            Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlDa 87 
                                ++++e+ t++DlcaaPGgKTthia+lm+n+g ++A+d+n+ R+  +++n++r+gv+n iv+++D+rk+   +g+  +Dr+LlDa
  gene88|gene88|rna88|rna88 103 MELKEGLTVVDLCAAPGGKTTHIAALMENTGIIYANDVNEDRMAGLKSNIQRMGVRNCIVMNMDGRKV--NVGK--VDRVLLDA 182
                                67889999***********************************************************9..6786..******** PP

                                --CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEEESSBSTTST CS
            Methyltr_RsmB-F  88 PCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvetelsepk 171
                                PCsgtgvi++dp+vk++r+ ++i ++a+lqkel+   +++l++gG+l+YsTCsvlv+Eneev++++L k + +++ + e+  +k
  gene88|gene88|rna88|rna88 183 PCSGTGVISKDPSVKTTRTRSEIDRMATLQKELILHGFEMLRPGGILMYSTCSVLVKENEEVVNYLLTKCPSAKMAQCEVDIGK 266
                                **************************************************************************9999876555 PP

                                TSSECEEC........TSEEE-TTTTSS-SEEEEEE CS
            Methyltr_RsmB-F 172 glklgeea........gtlrllPhtenkdgffiakl 199
                                   ++ +          ++r++Ph +n+dgff+ak+
  gene88|gene88|rna88|rna88 267 DGFMSFKGrnyngslkMARRIYPHVHNMDGFFYAKI 302
                                444444435678888899****************96 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   7.5e-14   1.2e-10       5      90 .]       8      97 ..       5      97 .. 0.92
   2 ?   -2.9   0.0       6.3     1e+04      20      39 ..     136     155 ..     123     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 7.5e-14
                               HHHHHHHHHGG.GHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---....TTSHHHHTTS-EE-- CS
            Methyltr_RsmF_N  5 Fiekmkellge.eaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerp.gkhplheaGlyYiQE 86
                                +ek+ el+++ eae f++  e++r++ +R+Ntl  ++++++kl +  +++l+   w+++G+++ +++ p g +p++ aG+y +Q 
  gene88|gene88|rna88|rna88  8 LLEKICELFPRkEAEVFIEESEKQRPTTIRINTLLKHRKDVSKLLRgrGVDLDDLSWTDSGCVVFKSSVPiGATPEYLAGYYCLQG 93
                               578888999888*********************9999******999999************9998887777*************** PP

                               TTTH CS
            Methyltr_RsmF_N 87 pSam 90
                               +++m
  gene88|gene88|rna88|rna88 94 AASM 97
                               ***9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.3
                                HHHHHH-----EEE--TTS. CS
            Methyltr_RsmF_N  20 flaaleeprkkglRvNtlKi 39 
                                + + ++e+r  gl+ N  ++
  gene88|gene88|rna88|rna88 136 YANDVNEDRMAGLKSNIQRM 155
                                45556777777888777665 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   9.5e-11   1.6e-07      19     138 ..     105     238 ..      92     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 9.5e-11
                                S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHH.....SSEEEEEE--S- CS
                       FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealse.....rkvdlvvsDgap 97 
                                +k+g tvvDl+aaPGg +  ++  ++++g ++a D+++     ++  ++ +i+++ +++ i   +++      kvd v+ D   
  gene88|gene88|rna88|rna88 105 LKEGLTVVDLCAAPGGKTTHIAALMENTGIIYANDVNED----RMAGLKSNIQRMGVRNCIVMNMDGrkvnvGKVDRVLLDAPC 184
                                67899********************999*********94....55666666666666666665555544444667778877655 PP

                                SS-CHHHHHHHHH..........C.CCCHHHHCCHCCCCECCCEEEECCCH..C CS
                       FtsJ  98 dvsgvhdldeylq..........s.qLllaalelalkllkpggtfvlkifr..g 138
                                + +gv ++d  ++          +  L +  +  ++++l+pgg+++  ++    
  gene88|gene88|rna88|rna88 185 SGTGVISKDPSVKttrtrseidrMaTLQKELILHGFEMLRPGGILMYSTCSvlV 238
                                444444444444444445555555488899999999********9876665552 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.7e-09   2.8e-06      97     181 ..     103     187 ..      88     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.7e-09
                                T.--TT-EEEETT-TTTCCHHHCCH.HTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE--TT CS
                     Met_10  97 l.veegevVvdvfAGiGpfaipiak.yskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmnlpk 178
                                +  +eg +Vvd+ A  G  +  ia  + +  +++a+d+n + +  lk+ni++  v + + ++++Dgr+v    ++drv++++p 
  gene88|gene88|rna88|rna88 103 MeLKEGLTVVDLCAAPGGKTTHIAAlMENTGIIYANDVNEDRMAGLKSNIQRMGVRNCI-VMNMDGRKVN-VGKVDRVLLDAPC 184
                                4479999******9988777666551567889***************************.9********7.99*******9997 PP

                                TGG CS
                     Met_10 179 sai 181
                                s +
  gene88|gene88|rna88|rna88 185 SGT 187
                                765 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.2e-06    0.0036      58     110 ..      95     147 ..      90     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                                HHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHH CS
                Fibrillarin  58 ailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlre 110
                                a +  + ++ +k+g  v+ l aa G    H++ +++++g++ya ++ +  +  
  gene88|gene88|rna88|rna88  95 ASMLPVLNMELKEGLTVVDLCAAPGGKTTHIAALMENTGIIYANDVNEDRMAG 147
                                455567789**********************************9887766655 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.4e-05     0.056       4      54 ..     111     164 ..     109     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
            Methyltransf_15   4 ilDlfsGaGGnviqfalvfek...viaieinleklacaqhNaevYgvsdkitlv 54 
                                ++Dl++  GG++ ++a   e+   ++a ++n++++a  + N +  gv + i + 
  gene88|gene88|rna88|rna88 111 VVDLCAAPGGKTTHIAALMENtgiIYANDVNEDRMAGLKSNIQRMGVRNCIVMN 164
                                89*************99855423389*********************9988764 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.1e-05      0.05       2     127 ..     106     243 ..     105     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.1e-05
            Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevl. 84 
                                ++gl+v+Dl ++ G +t  +a ++   + ++  D +e+     ++n q+ g+ n+ +   d  + +  +   k+D +l ++++ 
  gene88|gene88|rna88|rna88 106 KEGLTVVDLCAAPGGKTTHIAALMENTGIIYANDVNEDRMAGLKSNIQRMGVRNCIVMNMDGRKVN--V--GKVDRVLLDAPCs 185
                                6799**********999999988888899****************************999999988..4..68***99996666 PP

            Methyltransf_31  85 ......................naladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                                      +a+  ++ il + ++ l+pggil+ ++++        v+e+++
  gene88|gene88|rna88|rna88 186 gtgviskdpsvkttrtrseidrMATLQKELILHG-FEMLRPGGILMYSTCS------VLVKENEE 243
                                6666677777778888888888888888888888.99**************......33333333 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   5.3e-05     0.087      44     109 ..     104     169 ..     100     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
                                -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT CS
            Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaee 109
                                  k+g +v+D+++  g  + +++  ++++g +   D+ne+ +   +  +++ g+ n   ++ ++ +
  gene88|gene88|rna88|rna88 104 ELKEGLTVVDLCAAPGGKTTHIAALMENTGIIYANDVNEDRMAGLKSNIQRMGVRNCIVMNMDGRK 169
                                5689************************************99999999999999887666666655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   6.3e-05       0.1       1      69 [.     111     179 ..     111     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                                EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEE CS
            Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvv 69 
                                v+dl++ +G  t ++a+ + + + +++ D++e+ ++  ++++++ g+ n+ ++++d ++++   g++D v+
  gene88|gene88|rna88|rna88 111 VVDLCAAPGGKTTHIAALMeNTGIIYANDVNEDRMAGLKSNIQRMGVrNCIVMNMDGRKVNV--GKVDRVL 179
                                89***************996699********************9999999999999998874..4466665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05     0.058      42     109 ..     100     166 ..      34     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                                HHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S- CS
                        TRM  42 llkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvinedd 109
                                +l+ +l+e ++v+d  +a G ++   a  ++++  ++aND++e  ++ +k N++   v + +v+n  d
  gene88|gene88|rna88|rna88 100 VLNMELKEGLTVVDLCAAPGGKTTHIAALMENTGIIYANDVNEDRMAGLKSNIQRMGVRNCIVMNM-D 166
                                5566777789*****************9999*****************************999887.4 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.22      33     128 ..     100     189 ..      94     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                      GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkvDa 116
                                + ++elk+G  vv+  +  g  ++ ia  ++ tG +++ +  e+r+   + + ++ ++ + + ++      +G + +v gkvD 
  gene88|gene88|rna88|rna88 100 VLNMELKEGLTVVDLCAAPGGKTTHIAALMENTGIIYANDVNEDRMAGLKSNIQRMGVRNCIVMN-----MDGRKVNV-GKVDR 177
                                5689*****************************************************99988654.....45777778.99*** PP

                      GCD14 117 vfLDlPaPweai 128
                                v+LD P     +
  gene88|gene88|rna88|rna88 178 VLLDAPCSGTGV 189
                                ****99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1981.59
//
Query:       gene881|gene881|rna880|rna880  [L=215]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.17   11.9   0.0    1.3  1  PP2       Phloem protein 2


Domain annotation for each model (and alignments):
>> PP2  Phloem protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.6e-06      0.17      80     117 ..     150     200 ..     122     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.6e-06
                            PP2  80 pvevsvkv.gs......eskrkvcl.vpkkredgWleielgefvv.....e 117
                                    pv++ + + g+      ++k+ v++   kkr dgW e +  +f+      e
  gene881|gene881|rna880|rna880 150 PVKIYLVCtGKsheikdKEKKFVMMyLAKKRGDGWCEAHTNQFYEemsngE 200
                                    555555553335666554555555557899*************55665431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1343.59
//
Query:       gene882|gene882|rna881|rna881  [L=322]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1874.82
//
Query:       gene883|gene883|rna882|rna882  [L=370]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-36  122.2   1.8    7.9e-36  122.1   0.2    1.9  2  YchF-GTPase_C  Protein of unknown function (DUF933)
    3.2e-22   78.8   0.0    1.4e-21   76.7   0.0    1.9  2  MMR_HSR1       50S ribosome-binding GTPase
    1.5e-08   34.3   0.0    2.9e-08   33.4   0.0    1.4  1  FeoB_N         Ferrous iron transport protein B
     0.0067   16.5   0.0       0.15   12.0   0.0    2.9  2  AAA_14         AAA domain
  ------ inclusion threshold ------
      0.041   14.4   0.2       0.14   12.7   0.2    2.1  1  ABC_tran       ABC transporter
      0.048   12.6   0.0       0.28   10.1   0.0    2.0  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
       0.07   13.8   0.1       0.11   13.2   0.1    1.3  1  DUF4247        Domain of unknown function (DUF4247)


Domain annotation for each model (and alignments):
>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.2   8.2e+03      46      69 ..     149     173 ..     142     177 .. 0.60
   2 !  122.1   0.2   3.1e-39   7.9e-36       1      84 []     278     361 ..     278     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.2
                  YchF-GTPase_C  46 yedlvel.gseaaakeagklrlegk 69 
                                    ++d+ +l ++e+++ + +k +  +k
  gene883|gene883|rna882|rna882 149 LKDYETLvRHEEKMSKDMKSKPSDK 173
                                    5566666333667777666665555 PP

  == domain 2  score: 122.1 bits;  conditional E-value: 3.1e-39
                  YchF-GTPase_C   1 LitffTaGekevraWtikkgttapqaAgviHsDfekgFiraevikyedlvelgseaaakeagklrlegkdyvvqdgDiil 80 
                                    Li+ffT+G++evr+Wti++g++ap+a  viHsDf+k F++aev+++ed++++gsea++k+agk++++gk+yvv+dgDiil
  gene883|gene883|rna882|rna882 278 LINFFTVGKDEVRSWTIRRGINAPSAGAVIHSDFKKYFVMAEVMSFEDFKAYGSEAEVKRAGKYHQRGKTYVVNDGDIIL 357
                                    89****************************************************************************** PP

                  YchF-GTPase_C  81 fkfN 84 
                                    fk+N
  gene883|gene883|rna882|rna882 358 FKVN 361
                                    **98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   5.5e-25   1.4e-21       2      95 ..      20     138 ..      19     162 .. 0.84
   2 ?   -1.1   0.0      0.76   1.9e+03      71      90 ..     210     229 ..     161     256 .. 0.60

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 5.5e-25
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.................EEEEECGGCSSHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.................ielvDtpGliegaseek 64 
                                    ++ivG pNvGKStL+n lt++++ ++++p++T+d+ egrv++++++                 + ++D++Gl++gas++ 
  gene883|gene883|rna882|rna882  20 MGIVGLPNVGKSTLFNFLTRNNVPAENYPFCTIDPSEGRVEIQDERvealaekymphnvvrayLSVTDIAGLVKGASTGV 99 
                                    69***************************************8875578889999999999999***************** PP

                                    HHHHHHHHHHC.TSEEEEEEETT........TTCSHHHHH CS
                       MMR_HSR1  65 glgkaflalee.adlillvvdas........eeklkplde 95 
                                    glg++fl++++ +d i++vv++         e++++p+ +
  gene883|gene883|rna882|rna882 100 GLGNHFLDNIRnVDGIFHVVRCFedpevahfEDGVDPI-R 138
                                    ********99879********99665555553344444.4 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.76
                                    HHHHCTSEEEEEEETTTTCS CS
                       MMR_HSR1  71 laleeadlillvvdaseekl 90 
                                    l+l  ++ ++++ ++se+++
  gene883|gene883|rna882|rna882 210 LNLLTVKNVVYLANISEKDY 229
                                    22333566666666663322 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.1e-11   2.9e-08       3      50 ..      20      67 ..      18      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.1e-11
                                   EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEE CS
                         FeoB_N  3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeve 50
                                   + +vG pnvGk+tlfn lt  +    N+p  t++ +eg++++++++ve
  gene883|gene883|rna882|rna882 20 MGIVGLPNVGKSTLFNFLTRNNVPAENYPFCTIDPSEGRVEIQDERVE 67
                                   568**************************************9998876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0     6e-05      0.15       5      84 ..      20     120 ..      16     130 .. 0.60
   2 ?    0.5   0.2      0.22   5.6e+02      28      71 ..     213     266 ..     197     279 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke...................... 62 
                                    + i+G+  vGK+tl + l +++  ++e++ + ++d  + + + +  +  e++ ek+++                      
  gene883|gene883|rna882|rna882  20 MGIVGLPNVGKSTLFNFLTRNNV-PAENYPFCTIDPSEGRVEIQD-ERVEALAEKYMPhnvvraylsvtdiaglvkgast 97 
                                    6799**********777776666.899999888887666433222.2233333333222233334444455667766665 PP

                         AAA_14  63 ...ekktylflDEiqevpewekalk 84 
                                             flD i +v++++++++
  gene883|gene883|rna882|rna882  98 gvgL--GNHFLDNIRNVDGIFHVVR 120
                                    5321..2267777777777777776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.22
                         AAA_14  28 vkkesilyinldderdkkladpekllelileklke..........ekktylflD 71 
                                     + ++++y++  +e+d++++  +k l+++++   +          ++++ +flD
  gene883|gene883|rna882|rna882 213 LTVKNVVYLANISEKDYEMRRANKHLRAVMKYSDDvivfsaayesNHESKVFLD 266
                                    456789999888888888887766777777742223344444444444445555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.4e-05      0.14      14      51 ..      20      68 ..      13     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.4e-05
                                   EEEEESTTSSHHHHHHHHTTSS--...........SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx RF
                       ABC_tran 14 vaivGenGaGKStLlkllagllkp...........teGeilldgkdlke 51
                                   ++ivG    GKStL++ l+++  p            eG+++++++ ++ 
  gene883|gene883|rna882|rna882 20 MGIVGLPNVGKSTLFNFLTRNNVPaenypfctidpSEGRVEIQDERVEA 68
                                   79*******************9995555555555555555555555444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00011      0.28      27      54 ..      15      42 ..       5      60 .. 0.72
   2 ?   -0.2   0.1      0.15   3.9e+02     129     183 ..      98     153 ..      77     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                                   S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                           MeaB 27 GraqvvGltGvPGaGkstlvealglelr 54
                                    +   +G+ G+P +Gkstl + l+ + +
  gene883|gene883|rna882|rna882 15 SNNLSMGIVGLPNVGKSTLFNFLTRNNV 42
                                   456789*************999887654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.15
                                    EESSTTHHHHHHTT-SEEEEEEESSTTTTTTT--CCCHHH-SEEEEE---.HHHHH CS
                           MeaB 129 tvGvGqsevdvaevvdtfvvlllpeaGDelqgikkGileiaDiivvnkaD.kkeae 183
                                     vG G    d ++ vd +  ++      e+  +  G+  i Di +vn +  +k+ e
  gene883|gene883|rna882|rna882  98 GVGLGNHFLDNIRNVDGIFHVVRCFEDPEVAHFEDGVDPIRDIEIVNEELrLKDYE 153
                                    57888888888888888888888888889999999999999999999875333333 PP

>> DUF4247  Domain of unknown function (DUF4247)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.3e-05      0.11      33     112 ..     204     299 ..     188     354 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                        DUF4247  33 dstvYraanksvpeVa..keiaaqeePedkspeddetmyLvYeddivtvqkddtkgsdvlveidsk..ggYrgYs..... 103
                                     +++++ +  +v++V+  ++i++++    ++ ++  +++++Y+dd+++ + + + + +++v +d    +gY +       
  gene883|gene883|rna882|rna882 204 IEYISTLNLLTVKNVVylANISEKDYEMRRA-NKHLRAVMKYSDDVIVFSAAYESNHESKVFLDKLvkKGYESLDlinff 282
                                    5666666777888888334555555544444.8899**************************987444333331133344 PP

                        DUF4247 104 ........Gsiirrgkg 112
                                             + irrg +
  gene883|gene883|rna882|rna882 283 tvgkdevrSWTIRRGIN 299
                                    44444444344444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.66u 0.36s 00:00:01.02 Elapsed: 00:00:00.55
# Mc/sec: 2032.53
//
Query:       gene884|gene884|rna883|rna883  [L=537]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   40.6   0.0    4.6e-10   39.0   0.1    1.8  2  SAP       SAP domain
  ------ inclusion threshold ------
        0.1   12.7   0.3        0.1   12.7   0.3    2.2  2  DUF4460   Domain of unknown function (DUF4460)
       0.13   11.6   1.1       0.34   10.2   0.1    2.0  2  LETM1     LETM1-like protein


Domain annotation for each model (and alignments):
>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.59   3.5e+03       6      22 ..     156     172 ..     155     173 .. 0.86
   2 !   39.0   0.1   7.7e-14   4.6e-10       1      33 [.     473     505 ..     473     507 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.59
                                    HHHHHHHHHHTT--TTS CS
                            SAP   6 VaeLKeeLkkrGLptsG 22 
                                     +eL ++L+++   t G
  gene884|gene884|rna883|rna883 156 ISELSSFLQEFKAETGG 172
                                    589999****9999998 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 7.7e-14
                                    HTT--HHHHHHHHHHTT--TTS-HHHHHHHHHH CS
                            SAP   1 lskltVaeLKeeLkkrGLptsGkKaeLieRLke 33 
                                    +++ tV++LK+++k++GL  +GkK+eLieRL++
  gene884|gene884|rna883|rna883 473 FNNVTVQQLKSLMKEFGLNHTGKKNELIERLRD 505
                                    5788***************************86 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.7e-05       0.1      27      54 ..     143     170 ..     138     183 .. 0.86
   2 ?   -1.6   0.3      0.44   2.7e+03      73      90 ..     463     480 ..     443     511 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                        DUF4460  27 gqyPkekkvNeeSLklLnsyleelkkee 54 
                                    ++yP+ k+ Ne++++ L+s+l e+k e 
  gene884|gene884|rna883|rna883 143 SSYPNRKNRNEQNISELSSFLQEFKAET 170
                                    78*********************99874 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.44
                        DUF4460  73 nseekekkgefkevsiql 90 
                                    n  +++++  f++v++q 
  gene884|gene884|rna883|rna883 463 NFRNSINELDFNNVTVQQ 480
                                    344455555555555532 PP

>> LETM1  LETM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.16   9.4e+02     122     158 ..     147     181 ..     138     195 .. 0.52
   2 ?   10.2   0.1   5.6e-05      0.34     153     206 ..     455     511 ..     429     524 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.16
                          LETM1 122 kkkkekkekaeelkeflkkvrsggepeevsneeilkv 158
                                    ++k++++++ +el++fl++ + ++    ++ + + +v
  gene884|gene884|rna883|rna883 147 NRKNRNEQNISELSSFLQEFKAET--GGPQDNSLSEV 181
                                    334555556666666666655554..22344444433 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.6e-05
                          LETM1 153 eeilkvaklFkde...ltLdnlsrkqlkalckllslqpfgtdnllryrlrkklreik 206
                                    +e  +v + F++    l ++n++ +qlk+l+k ++l++ g++n l  rlr  l++i 
  gene884|gene884|rna883|rna883 455 DEFKEVVQNFRNSineLDFNNVTVQQLKSLMKEFGLNHTGKKNELIERLRDILKKID 511
                                    5555666666665545999*******************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3406.04
//
Query:       gene885|gene885|rna884|rna884  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1059.54
//
Query:       gene886|gene886|rna885|rna885  [L=106]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.024   15.1   0.3       0.05   14.1   0.3    1.5  1  Ribosomal_L14e  Ribosomal protein L14


Domain annotation for each model (and alignments):
>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   2.8e-06      0.05      57      72 ..      79      94 ..      72      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-06
                 Ribosomal_L14e 57 aaltDFdRFkvmvakk 72
                                     ++DFdRFk+++ k+
  gene886|gene886|rna885|rna885 79 DTTNDFDRFKLRLRKR 94
                                   579********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 739.38
//
Query:       gene887|gene887|rna886|rna886  [L=99]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0057   16.9   0.8      0.027   14.7   0.3    1.8  2  Med21        Subunit 21 of Mediator complex
  ------ inclusion threshold ------
      0.047   13.4   1.3      0.084   12.6   0.9    1.5  2  DUF4423      Domain of unknown function (DUF4423)
        0.1   13.0   0.6        1.2    9.6   0.6    2.2  1  FlaC_arch    Flagella accessory protein C (FlaC)
       0.13   12.2   0.5        3.8    7.5   0.0    2.3  2  Shugoshin_N  Shugoshin N-terminal coiled-coil region


Domain annotation for each model (and alignments):
>> Med21  Subunit 21 of Mediator complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.3   6.1e-06     0.027       4      40 ..       2      38 ..       1      49 [. 0.85
   2 ?    2.5   0.3     0.036   1.6e+02     105     129 ..      35      59 ..      31      74 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.1e-06
                          Med21  4 rLTqLQdcldqLaeqfyatlgylntshdpsplseqdp 40
                                    +T LQ++++ L+  +++++g++++++ +s + e+ +
  gene887|gene887|rna886|rna886  2 KITDLQNEVNHLLFLYFTSIGVIQRDAGLSDVYEKME 38
                                   58*************************9998875555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.036
                          Med21 105 erikeLeeelreveeereekvkeke 129
                                    e+++eL++e+++ +++    +   e
  gene887|gene887|rna886|rna886  35 EKMEELKKEIEDCRKRIIRLIDSEE 59 
                                    5677777777777777766666555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.9   1.9e-05     0.084     129     154 ..      35      60 ..      33      66 .. 0.89
   2 ?   -2.0   0.0      0.55   2.5e+03     129     149 ..      66      86 ..      65      89 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                        DUF4423 129 edyekikkeirefrkkilaiaeeske 154
                                    e++e++kkei+++rk+i++++++++ 
  gene887|gene887|rna886|rna886  35 EKMEELKKEIEDCRKRIIRLIDSEEA 60 
                                    789*****************999887 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.55
                        DUF4423 129 edyekikkeirefrkkilaia 149
                                    +dy +i  e +ef+k+ ++++
  gene887|gene887|rna886|rna886  66 SDYREIISEGKEFVKDGVSFL 86 
                                    578888888888888766655 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.6   0.00027       1.2      15      41 ..      29      55 ..       2      57 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00027
                      FlaC_arch 15 eletvkkeneelsksveelkenVkdll 41
                                    l+ v +++eel+k++e+  +++ +l+
  gene887|gene887|rna886|rna886 29 GLSDVYEKMEELKKEIEDCRKRIIRLI 55
                                   778888899999999999999888887 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00084       3.8      21      34 ..       1      14 [.       1      15 [. 0.95
   2 ?    2.7   0.3     0.026   1.2e+02      22      34 ..      43      55 ..      35      58 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00084
                    Shugoshin_N 21 lkirelekevseLl 34
                                   +ki +l +ev++Ll
  gene887|gene887|rna886|rna886  1 MKITDLQNEVNHLL 14
                                   8***********97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.026
                    Shugoshin_N 22 kirelekevseLl 34
                                    i +++k++ +L+
  gene887|gene887|rna886|rna886 43 EIEDCRKRIIRLI 55
                                   4667777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1255  (0.0699983); expected 358.6 (0.02)
Passed bias filter:                      982  (0.0547716); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 639.51
//
Query:       gene888|gene888|rna887|rna887  [L=679]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-12   45.7  11.7      0.017   15.2   0.2    8.0  7  TPR_2         Tetratricopeptide repeat
    1.6e-10   40.4  11.8    1.4e-05   24.9   0.3    6.9  6  TPR_8         Tetratricopeptide repeat
    6.2e-08   33.0   3.5        1.6    9.3   0.0    6.2  5  TPR_19        Tetratricopeptide repeat
    6.9e-08   32.0  16.3     0.0045   16.7   0.2    6.8  8  TPR_1         Tetratricopeptide repeat
    4.3e-05   23.7   1.7        2.7    8.4   0.0    5.2  6  TPR_12        Tetratricopeptide repeat
    0.00022   21.8   0.2         19    6.0   0.0    5.3  5  TPR_16        Tetratricopeptide repeat
    0.00035   21.2   4.5       0.68   10.9   0.0    6.8  7  TPR_14        Tetratricopeptide repeat
     0.0075   16.8   0.3         14    6.6   0.0    5.1  4  TPR_6         Tetratricopeptide repeat
     0.0087   16.4   0.8         17    6.1   0.0    4.9  4  TPR_17        Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.016   13.7   0.1       0.13   10.7   0.0    2.0  2  Cohesin_load  Cohesin loading factor
       0.04   14.1   1.4         72    3.7   0.1    4.9  6  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
       0.16   11.7   3.1          1    9.0   0.0    2.7  3  TPR_21        Tetratricopeptide repeat-like domain
        0.2   11.4   2.6         70    3.2   0.1    4.8  5  TPR_11        TPR repeat
        1.4    8.9   6.9         10    6.1   0.0    4.8  6  TPR_10        Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.15   1.9e+02       7      27 ..     108     128 ..     106     129 .. 0.91
   2 !   15.2   0.2   1.3e-05     0.017       1      28 [.     231     258 ..     231     263 .. 0.92
   3 !    7.2   0.1    0.0047         6      15      33 ..     401     419 ..     398     420 .. 0.90
   4 ?    4.2   0.0     0.043        55       5      26 ..     466     487 ..     462     488 .. 0.87
   5 ?    5.2   0.0      0.02        26       8      25 ..     535     552 ..     532     555 .. 0.87
   6 !   10.9   0.0   0.00032      0.41       3      26 ..     561     584 ..     559     585 .. 0.91
   7 ?   -1.0   0.1       2.1   2.7e+03      11      22 ..     627     638 ..     625     639 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                          TPR_2   7 lGlayyklgdyeeAleafekA 27 
                                     G a ++++ y+ Al +f kA
  gene888|gene888|rna887|rna887 108 KGFASLRKKSYDGALFLFGKA 128
                                    689999************998 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.3e-05
                          TPR_2   1 aealynlGlayyklgdyeeAleafekAl 28 
                                    ae+ly +G++  k+gd+e A++++ ++l
  gene888|gene888|rna887|rna887 231 AEVLYLRGKIEHKKGDLENAKKYYMESL 258
                                    79**********************9887 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0047
                          TPR_2  15 gdyeeAleafekAleldPn 33 
                                    ++ +eA++++ +Al  +P+
  gene888|gene888|rna887|rna887 401 DRVKEAEKYLLRALDECPD 419
                                    6889************997 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.043
                          TPR_2   5 ynlGlayyklgdyeeAleafek 26 
                                       G  ++k+++++ A++ f+k
  gene888|gene888|rna887|rna887 466 ELVGFYHMKRKEFKLAKKIFQK 487
                                    56799***************98 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.02
                          TPR_2   8 GlayyklgdyeeAleafe 25 
                                    G +++ +g++eeA++ f+
  gene888|gene888|rna887|rna887 535 GICLALKGRLEEAINIFN 552
                                    99************9887 PP

  == domain 6  score: 10.9 bits;  conditional E-value: 0.00032
                          TPR_2   3 alynlGlayyklgdyeeAleafek 26 
                                    ++ nlG+a++  ++y+eA + f k
  gene888|gene888|rna887|rna887 561 GYVNLGNALILCKRYKEAMDVFSK 584
                                    799****************99976 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 2.1
                          TPR_2  11 yyklgdyeeAle 22 
                                    + +++++eeA++
  gene888|gene888|rna887|rna887 627 LVEQNRLEEAEK 638
                                    6689******98 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.3   1.1e-08   1.4e-05       1      33 [.     231     263 ..     231     264 .. 0.94
   2 ?    3.0   0.1      0.11   1.4e+02      16      33 ..     402     419 ..     398     420 .. 0.84
   3 ?    1.7   0.1      0.29   3.7e+02      10      30 ..     471     491 ..     467     494 .. 0.83
   4 ?    1.9   0.0      0.26   3.3e+02      13      25 ..     540     552 ..     534     554 .. 0.83
   5 !    9.9   0.0   0.00072      0.93       3      26 ..     561     584 ..     559     589 .. 0.90
   6 ?   -2.5   0.0       6.8   8.8e+03      10      22 ..     626     638 ..     625     638 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    ae++y+ g+i +k+gd+e+Ak+yy++ l +d++
  gene888|gene888|rna887|rna887 231 AEVLYLRGKIEHKKGDLENAKKYYMESLGYDRS 263
                                    799*************************99975 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                    -HHHHHHHHHHHHHHHHH CS
                          TPR_8  16 dyeeAkeyyekaleldpd 33 
                                    + +eA++y+ +al+  pd
  gene888|gene888|rna887|rna887 402 RVKEAEKYLLRALDECPD 419
                                    678**********97776 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.29
                                    HHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8  10 iylklgdyeeAkeyyekalel 30 
                                     ++k ++++ Ak+ ++k  +l
  gene888|gene888|rna887|rna887 471 YHMKRKEFKLAKKIFQKLDTL 491
                                    578999**********98665 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.26
                                    HTT-HHHHHHHHH CS
                          TPR_8  13 klgdyeeAkeyye 25 
                                     +g++eeA+  ++
  gene888|gene888|rna887|rna887 540 LKGRLEEAINIFN 552
                                    68*******9997 PP

  == domain 5  score: 9.9 bits;  conditional E-value: 0.00072
                                    HHHHHHHHHHHTT-HHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyek 26 
                                     y+nlg++++  ++y+eA+ ++ k
  gene888|gene888|rna887|rna887 561 GYVNLGNALILCKRYKEAMDVFSK 584
                                    69*****************99977 PP

  == domain 6  score: -2.5 bits;  conditional E-value: 6.8
                                    HHHHTT-HHHHHH CS
                          TPR_8  10 iylklgdyeeAke 22 
                                    ++ +++++eeA++
  gene888|gene888|rna887|rna887 626 LLVEQNRLEEAEK 638
                                    567899*****86 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.023        29       8      39 ..      55      86 ..      50      87 .. 0.83
   2 ?    5.7   0.0     0.017        22       2      46 ..     212     252 ..     167     262 .. 0.83
   3 ?    1.5   0.0      0.34   4.3e+02      40      61 ..     402     421 ..     398     434 .. 0.59
   4 !    9.3   0.0    0.0013       1.6       4      55 ..     541     589 ..     538     598 .. 0.80
   5 ?    5.6   0.1     0.018        23      27      47 ..     619     639 ..     610     640 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                         TPR_19  8 aeAlalleqalqedpknaearllLAeallalg 39
                                   + A+++l q+   d k+ + +llL  + l++g
  gene888|gene888|rna887|rna887 55 ELAMKILDQLSRMDDKDYNTLLLLLACKLQAG 86
                                   56899999999999999999999999998887 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                         TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                    ++++ +  A++++e      pk ae+++l  ++  + g+l+ A++
  gene888|gene888|rna887|rna887 212 VDREEFSKAQEMMET----MPKCAEVLYLRGKIEHKKGDLENAKK 252
                                    455566666666666....58888888888888888888888876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.34
                         TPR_19  40 qldeAealLdalpeedpddary 61 
                                    +++eAe+ L ++++e pd  +y
  gene888|gene888|rna887|rna887 402 RVKEAEKYLLRALDECPD--EY 421
                                    455566666555555555..33 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0013
                         TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeed 55 
                                     g+++eA++++ ++ +   + a    +L +al+  ++++eA+++ +++ ++ 
  gene888|gene888|rna887|rna887 541 KGRLEEAINIFNNV-AI--DWAGGYVNLGNALILCKRYKEAMDVFSKISLMR 589
                                    5999*********7.33..33444456699***************9998765 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.018
                         TPR_19  27 arllLAeallalgqldeAeal 47 
                                    a+  L e+l+++++l+eAe+l
  gene888|gene888|rna887|rna887 619 AKEKLFELLVEQNRLEEAEKL 639
                                    555689************985 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.8   3.6e+03       8      27 ..     109     128 ..     107     128 .. 0.82
   2 !   16.7   0.2   3.5e-06    0.0045       1      32 [.     231     262 ..     231     264 .. 0.90
   3 ?    3.3   0.2     0.063        81      17      33 ..     403     419 ..     399     420 .. 0.89
   4 ?   -0.6   0.1       1.1   1.4e+03      10      26 ..     471     487 ..     468     487 .. 0.86
   5 ?   -2.9   0.0       5.8   7.4e+03      19      29 ..     516     526 ..     515     526 .. 0.88
   6 ?    4.8   0.0      0.02        26       8      25 ..     535     552 ..     532     554 .. 0.85
   7 !   12.6   0.1   7.2e-05     0.092       3      26 ..     561     584 ..     559     585 .. 0.91
   8 ?   -2.2   0.0       3.5   4.5e+03      13      22 ..     629     638 ..     626     639 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.8
                                    HHHHHHTT-HHHHHHHHHHH CS
                          TPR_1   8 GnayfklgkydeAleyyekA 27 
                                    G a ++++ yd Al  + kA
  gene888|gene888|rna887|rna887 109 GFASLRKKSYDGALFLFGKA 128
                                    666678899*****999887 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.5e-06
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   1 akalynlGnayfklgkydeAleyyekALelnP 32 
                                    a++ly +G + +k+g+++ A +yy + L  + 
  gene888|gene888|rna887|rna887 231 AEVLYLRGKIEHKKGDLENAKKYYMESLGYDR 262
                                    799*********************99987665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.063
                                    HHHHHHHHHHHHHHSTT CS
                          TPR_1  17 ydeAleyyekALelnPn 33 
                                     +eA++y  +AL  +P+
  gene888|gene888|rna887|rna887 403 VKEAEKYLLRALDECPD 419
                                    589*********99997 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.1
                                    HHHHTT-HHHHHHHHHH CS
                          TPR_1  10 ayfklgkydeAleyyek 26 
                                     ++k ++++ A + ++k
  gene888|gene888|rna887|rna887 471 YHMKRKEFKLAKKIFQK 487
                                    589********999987 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 5.8
                                    HHHHHHHHHHH CS
                          TPR_1  19 eAleyyekALe 29 
                                    +A +++++ L+
  gene888|gene888|rna887|rna887 516 KAMKAFSRGLK 526
                                    899***99986 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.02
                                    HHHHHHTT-HHHHHHHHH CS
                          TPR_1   8 GnayfklgkydeAleyye 25 
                                    G ++  +g+++eA+  ++
  gene888|gene888|rna887|rna887 535 GICLALKGRLEEAINIFN 552
                                    99************8665 PP

  == domain 7  score: 12.6 bits;  conditional E-value: 7.2e-05
                                    HHHHHHHHHHHTT-HHHHHHHHHH CS
                          TPR_1   3 alynlGnayfklgkydeAleyyek 26 
                                     + nlGna+   ++y+eA + ++k
  gene888|gene888|rna887|rna887 561 GYVNLGNALILCKRYKEAMDVFSK 584
                                    599****************99987 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 3.5
                                    HTT-HHHHHH CS
                          TPR_1  13 klgkydeAle 22 
                                    ++++++eA++
  gene888|gene888|rna887|rna887 629 EQNRLEEAEK 638
                                    799*****97 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0021       2.7       3      37 ..     231     265 ..     229     283 .. 0.78
   2 ?    0.8   0.0      0.48   6.2e+02      18      31 ..     402     415 ..     394     432 .. 0.80
   3 ?   -2.9   0.0       6.6   8.5e+03       9      29 ..     468     488 ..     465     499 .. 0.77
   4 ?    5.6   0.0     0.015        19       9      27 ..     534     552 ..     527     561 .. 0.72
   5 ?    2.5   0.0      0.14   1.8e+02       6      28 ..     562     584 ..     557     592 .. 0.84
   6 ?   -2.1   0.0       3.7   4.8e+03      55      66 ..     627     638 ..     625     639 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrll 37 
                                    a +l+ ++ ++++ g+++ A +++ ++l   r+ +
  gene888|gene888|rna887|rna887 231 AEVLYLRGKIEHKKGDLENAKKYYMESLGYDRSFF 265
                                    56788999999999999999999999987666655 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.48
                         TPR_12  18 rydeAlellekale 31 
                                    r  eA+++l +al+
  gene888|gene888|rna887|rna887 402 RVKEAEKYLLRALD 415
                                    66788888888886 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 6.6
                         TPR_12   9 laavlrrlgrydeAlelleka 29 
                                    ++  +++++++  A ++++k 
  gene888|gene888|rna887|rna887 468 VGFYHMKRKEFKLAKKIFQKL 488
                                    567778899999999999885 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.015
                         TPR_12   9 laavlrrlgrydeAlelle 27 
                                    ++ +l+  gr++eA+ +++
  gene888|gene888|rna887|rna887 534 VGICLALKGRLEEAINIFN 552
                                    5667777777777776665 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 0.14
                         TPR_12   6 lnnlaavlrrlgrydeAlellek 28 
                                    ++nl+++l   +ry eA + + k
  gene888|gene888|rna887|rna887 562 YVNLGNALILCKRYKEAMDVFSK 584
                                    78999999999999999777766 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 3.7
                         TPR_12  55 yralgryeeAle 66 
                                    + +++r+eeA++
  gene888|gene888|rna887|rna887 627 LVEQNRLEEAEK 638
                                    556777777775 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.7   6.1e+03      40      57 ..     108     126 ..     106     129 .. 0.76
   2 ?    4.7   0.0     0.038        49      31      53 ..     228     250 ..     208     258 .. 0.90
   3 ?    3.1   0.0      0.12   1.6e+02      49      67 ..     402     420 ..     399     421 .. 0.90
   4 ?    6.0   0.0     0.015        19      38      61 ..     532     556 ..     514     562 .. 0.84
   5 ?   -0.2   0.0       1.2   1.6e+03       4      18 ..     624     638 ..     622     639 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.7
                         TPR_16  40 lgdaalrqgrlaeAa.aly 57 
                                    +g a lr++ +++A+  + 
  gene888|gene888|rna887|rna887 108 KGFASLRKKSYDGALfLFG 126
                                    6788899999999986665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.038
                         TPR_16  31 PdaaeAllllgdaalrqgrlaeA 53 
                                    P +ae l+l+g +  ++g+l+ A
  gene888|gene888|rna887|rna887 228 PKCAEVLYLRGKIEHKKGDLENA 250
                                    889*****************998 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.12
                         TPR_16  49 rlaeAaalyraalraapda 67 
                                    r++eA+ ++++al++ pd+
  gene888|gene888|rna887|rna887 402 RVKEAEKYLLRALDECPDE 420
                                    789*************996 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.015
                         TPR_16  38 lllgdaalrqgrlaeAa.alyraal 61 
                                    ++ g +++ +grl+eA+  + + a+
  gene888|gene888|rna887|rna887 532 NGVGICLALKGRLEEAInIFNNVAI 556
                                    57899************99988876 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 1.2
                         TPR_16   4 araalragdyddAaa 18 
                                      +++++++ ++A++
  gene888|gene888|rna887|rna887 624 FELLVEQNRLEEAEK 638
                                    567899999999987 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       5.6   7.2e+03      16      41 ..      53      79 ..      50      80 .. 0.66
   2 ?    0.9   0.1      0.89   1.1e+03       9      27 ..     162     180 ..     158     186 .. 0.76
   3 ?    0.6   0.0       1.1   1.4e+03       2      24 ..     232     254 ..     231     258 .. 0.89
   4 !   10.9   0.0   0.00053      0.68       4      40 ..     390     428 ..     387     432 .. 0.78
   5 ?   -0.8   0.0         3   3.8e+03      13      26 ..     540     553 ..     535     558 .. 0.79
   6 ?   -0.2   0.0         2   2.5e+03       7      26 ..     565     584 ..     560     587 .. 0.86
   7 ?    0.2   0.0       1.5   1.9e+03       5      23 ..     621     639 ..     617     639 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.6
                         TPR_14 16 dpdeAiallrralalaPdda.eawlll 41
                                    p+ A+++l+++ + + +d  +++lll
  gene888|gene888|rna887|rna887 53 HPELAMKILDQLSRMDDKDYnTLLLLL 79
                                   688899999999886555541444554 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.89
                         TPR_14   9 eallalGdpdeAiallrra 27 
                                    +    ++d+de ++l+r+a
  gene888|gene888|rna887|rna887 162 REAKGNEDLDEVRRLFRDA 180
                                    55556789*********99 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.1
                         TPR_14   2 eallalaeallalGdpdeAiall 24 
                                    e+l+++++++   Gd++ A +++
  gene888|gene888|rna887|rna887 232 EVLYLRGKIEHKKGDLENAKKYY 254
                                    78999**************9998 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00053
                         TPR_14   4 llalaeallalGdpdeAiallrralalaPdd..aeawll 40 
                                    +++l +  +  ++ +eA+++l ral+ +Pd+  +++++ 
  gene888|gene888|rna887|rna887 390 RRCLIDGKMIEDRVKEAEKYLLRALDECPDEykEVIRYN 428
                                    6778888888999****************9844455555 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 3
                         TPR_14  13 alGdpdeAiallrr 26 
                                      G+++eAi++++ 
  gene888|gene888|rna887|rna887 540 LKGRLEEAINIFNN 553
                                    469******99975 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 2
                         TPR_14   7 laeallalGdpdeAiallrr 26 
                                    l+ al    +++eA++++ +
  gene888|gene888|rna887|rna887 565 LGNALILCKRYKEAMDVFSK 584
                                    788999999*******9976 PP

  == domain 7  score: 0.2 bits;  conditional E-value: 1.5
                         TPR_14   5 lalaeallalGdpdeAial 23 
                                     +l e+l ++ +++eA++l
  gene888|gene888|rna887|rna887 621 EKLFELLVEQNRLEEAEKL 639
                                    578999**********986 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.011        14       1      23 [.     232     254 ..     232     258 .. 0.91
   2 ?    0.6   0.0      0.86   1.1e+03      13      30 ..     475     492 ..     468     494 .. 0.76
   3 ?    1.8   0.0      0.36   4.6e+02       7      26 ..     535     554 ..     533     556 .. 0.86
   4 ?   -1.4   0.0       3.9     5e+03       4      25 ..     563     584 ..     561     585 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   1 dAlyklalsyrklgdtdkAleal 23 
                                    ++ly++++   k gd ++A++++
  gene888|gene888|rna887|rna887 232 EVLYLRGKIEHKKGDLENAKKYY 254
                                    68**********99*******98 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.86
                                    HHHHHHHHHHHHHHHHH- CS
                          TPR_6  13 lgdtdkAlealerlikeY 30 
                                     ++   A++++++l + Y
  gene888|gene888|rna887|rna887 475 RKEFKLAKKIFQKLDTLY 492
                                    457779*******96666 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.36
                                    HHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   7 alsyrklgdtdkAlealerl 26 
                                    + ++   g+ ++A+ +++++
  gene888|gene888|rna887|rna887 535 GICLALKGRLEEAINIFNNV 554
                                    67888878*********987 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 3.9
                                    HHHHHHHHH.HHHHHHHHHHHHH CS
                          TPR_6   4 yklalsyrk.lgdtdkAlealer 25 
                                     +l+ +++    ++ +A++ + +
  gene888|gene888|rna887|rna887 563 VNLGNALILcK-RYKEAMDVFSK 584
                                    57788888777.999***99976 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.013        17      13      33 ..     231     251 ..     228     252 .. 0.92
   2 ?    1.8   0.0      0.31     4e+02      12      26 ..     347     361 ..     341     371 .. 0.91
   3 ?   -0.3   0.0       1.4   1.9e+03       2      24 ..     410     434 ..     409     448 .. 0.77
   4 ?    1.4   0.1      0.41   5.3e+02      15      32 ..     561     578 ..     557     580 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                         TPR_17  13 adaynnLAelllknGdlmtAr 33 
                                    a+++++++++ +k+Gdl+ A+
  gene888|gene888|rna887|rna887 231 AEVLYLRGKIEHKKGDLENAK 251
                                    89****************997 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.31
                         TPR_17  12 nadaynnLAelllkn 26 
                                    n++++nn ++ l++n
  gene888|gene888|rna887|rna887 347 NFVVMNNIGYSLCRN 361
                                    89********99976 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                         TPR_17   2 ylkaleldPnn..adaynnLAelll 24 
                                    +l+al+ +P+    +  +nL+++++
  gene888|gene888|rna887|rna887 410 LLRALDECPDEykEVIRYNLGYVME 434
                                    5788888888656778899998765 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.41
                         TPR_17  15 aynnLAelllknGdlmtA 32 
                                     y nL+++l   +++++A
  gene888|gene888|rna887|rna887 561 GYVNLGNALILCKRYKEA 578
                                    599*******99999998 PP

>> Cohesin_load  Cohesin loading factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0001      0.13     404     431 ..     232     259 ..     209     277 .. 0.83
   2 ?    0.3   0.0      0.14   1.8e+02     406     427 ..     465     486 ..     439     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                   Cohesin_load 404 lllyLeglyaqskgdlkaAlaqyketaa 431
                                     +lyL g + ++kgdl++A+++y+e++ 
  gene888|gene888|rna887|rna887 232 EVLYLRGKIEHKKGDLENAKKYYMESLG 259
                                    579********************97654 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                   Cohesin_load 406 lyLeglyaqskgdlkaAlaqyk 427
                                    l L g y++++ ++k A+++++
  gene888|gene888|rna887|rna887 465 LELVGFYHMKRKEFKLAKKIFQ 486
                                    56889****************9 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.1   2.7e+03      40      69 ..      55      85 ..      51      94 .. 0.81
   2 ?    2.6   0.0      0.12   1.6e+02       2      38 ..     115     165 ..     112     180 .. 0.85
   3 ?   -2.1   0.0       3.7   4.8e+03      30      39 ..     231     240 ..     211     270 .. 0.63
   4 ?    0.8   0.0      0.46   5.9e+02      29      55 ..     468     494 ..     457     509 .. 0.71
   5 ?    1.1   0.0      0.36   4.6e+02      65      81 ..     536     553 ..     512     554 .. 0.84
   6 ?    3.7   0.1     0.057        72      32      81 ..     537     584 ..     534     585 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
                                   HHHHHHHHCT.SHHHC-HHHHHHHHHHHHHT CS
                         ANAPC3 40 krAyellrka.klnskslgcrylfAqcllkL 69
                                   + A+++l+++ + ++k+ + ++l+  c l+ 
  gene888|gene888|rna887|rna887 55 ELAMKILDQLsRMDDKDYNTLLLLLACKLQA 85
                                   5688999999888888888888888888875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                                    TT-HHHHHHHHHHHH...............HHH--HHHHHHHHHHHHHTT- CS
                         ANAPC3   2 qnnyknAiflaerll.............a.aetespedayllAlclylngq 38 
                                    ++ y+ A+fl+ ++              +  e+++ +d  l+++cl++  +
  gene888|gene888|rna887|rna887 115 KKSYDGALFLFGKARfslgiqicnyylgSiGEAKRFDDKVLKGYCLLREAK 165
                                    578999999999999999999988877636899999999999999999765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.7
                                    HHHHHHTT-H CS
                         ANAPC3  30 Alclylngqy 39 
                                    A++lyl+g+ 
  gene888|gene888|rna887|rna887 231 AEVLYLRGKI 240
                                    4444444443 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.46
                                    HHHHHHHTT-HHHHHHHHHCTSHHHC- CS
                         ANAPC3  29 lAlclylngqykrAyellrkaklnsks 55 
                                     +  + +++++k A ++++k+++  +s
  gene888|gene888|rna887|rna887 468 VGFYHMKRKEFKLAKKIFQKLDTLYSS 494
                                    5667999*************9444444 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.36
                                    HHHHT.T-HHHHHHHH-S CS
                         ANAPC3  65 cllkL.kkyeeAiaaLek 81 
                                     +l+L +++eeAi+++ +
  gene888|gene888|rna887|rna887 536 ICLALkGRLEEAINIFNN 553
                                    589999999999999876 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.057
                                    HHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  32 clylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    cl l g+ ++A++++++   +    g  + ++ +l+  k+y+eA ++++k
  gene888|gene888|rna887|rna887 537 CLALKGRLEEAINIFNNV--AIDWAGGYVNLGNALILCKRYKEAMDVFSK 584
                                    666666777777777777..556666666677777888888888888876 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00081         1     115     174 ..     203     259 ..     193     279 .. 0.87
   2 ?    2.4   0.0     0.088   1.1e+02      90     127 ..     401     437 ..     395     457 .. 0.87
   3 ?   -2.8   0.4       3.3   4.3e+03     118     149 ..     622     655 ..     619     663 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00081
                         TPR_21 115 arlRLarvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                    +++RL   l++ +++ +A +++e+ ++    a+v  lrG i  ++g+l++A++ Y ++l 
  gene888|gene888|rna887|rna887 203 VKMRLVGELVDREEFSKAQEMMETMPKC---AEVLYLRGKIEHKKGDLENAKKYYMESLG 259
                                    689*****************99988774...79999*******************99875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.088
                         TPR_21  90 gdlaaAkaqLewvlekakdeelkalarlRLarvllaek 127
                                    + +++A++ L ++l++ +de +k+++r  L  v+ + +
  gene888|gene888|rna887|rna887 401 DRVKEAEKYLLRALDECPDE-YKEVIRYNLGYVMEDRE 437
                                    6789*************999.*********99987655 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.3
                         TPR_21 118 RLarvllaekkydeA..lktLeakkeeafaalva 149
                                    +L ++l++++ ++eA  l+ L++   + ++ + +
  gene888|gene888|rna887|rna887 622 KLFELLVEQNRLEEAekLRVLDQRLMKMYDEKKE 655
                                    6777788888888873334566666666665555 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.055        70       1      27 [.     238     264 ..     232     271 .. 0.79
   2 ?   -0.6   0.0      0.84   1.1e+03      30      38 ..     425     433 ..     419     435 .. 0.83
   3 ?    2.1   0.0      0.13   1.6e+02       7      15 ..     541     549 ..     538     554 .. 0.83
   4 ?    0.2   0.0       0.5   6.4e+02       1      17 [.     566     582 ..     562     584 .. 0.82
   5 ?   -0.8   0.0         1   1.3e+03       4      13 ..     627     636 ..     625     637 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.055
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdn 27 
                                    G++ +++G++e+A + Y + l +d ++
  gene888|gene888|rna887|rna887 238 GKIEHKKGDLENAKKYYMESLGYDRSF 264
                                    899**********88887777666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.84
                         TPR_11  30 ayynLGlay 38 
                                    + ynLG+++
  gene888|gene888|rna887|rna887 425 IRYNLGYVM 433
                                    689999986 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.13
                         TPR_11   7 qGkyeeAie 15 
                                    +G++eeAi+
  gene888|gene888|rna887|rna887 541 KGRLEEAIN 549
                                    8*******8 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.5
                         TPR_11   1 GdayyeqGkyeeAieaY 17 
                                    G+a+    +y+eA+ ++
  gene888|gene888|rna887|rna887 566 GNALILCKRYKEAMDVF 582
                                    89999999999998776 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 1
                         TPR_11   4 yyeqGkyeeA 13 
                                    ++eq+++eeA
  gene888|gene888|rna887|rna887 627 LVEQNRLEEA 636
                                    79*******9 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.3   5.6e+03      13      29 ..     242     258 ..     238     259 .. 0.83
   2 ?   -3.7   0.1       9.8   1.3e+04       5      13 ..     351     359 ..     350     360 .. 0.80
   3 ?    0.9   0.1      0.37   4.7e+02      17      30 ..     402     415 ..     401     417 .. 0.88
   4 ?   -2.1   0.0       3.1     4e+03      16      25 ..     542     551 ..     535     552 .. 0.81
   5 ?    6.1   0.0    0.0081        10       1      23 [.     558     580 ..     558     582 .. 0.88
   6 ?    1.2   0.1      0.28   3.5e+02      12      24 ..     627     639 ..     625     640 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.3
                         TPR_10  13 rqrgrydeAealleeal 29 
                                    ++ g+++ A +++ e+l
  gene888|gene888|rna887|rna887 242 HKKGDLENAKKYYMESL 258
                                    66799*******99887 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.8
                         TPR_10   5 lnNLanalr 13 
                                    +nN++  l+
  gene888|gene888|rna887|rna887 351 MNNIGYSLC 359
                                    9***98775 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.37
                         TPR_10  17 rydeAealleeala 30 
                                    r +eAe++l +al+
  gene888|gene888|rna887|rna887 402 RVKEAEKYLLRALD 415
                                    789*********95 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 3.1
                         TPR_10  16 grydeAeall 25 
                                    gr++eA +++
  gene888|gene888|rna887|rna887 542 GRLEEAINIF 551
                                    8999998875 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.0081
                         TPR_10   1 tAsslnNLanalrqrgrydeAea 23 
                                    +A  + NL+nal   +ry+eA++
  gene888|gene888|rna887|rna887 558 WAGGYVNLGNALILCKRYKEAMD 580
                                    677789***************85 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.28
                         TPR_10  12 lrqrgrydeAeal 24 
                                    l +++r++eAe+l
  gene888|gene888|rna887|rna887 627 LVEQNRLEEAEKL 639
                                    668********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1374  (0.0766356); expected 358.6 (0.02)
Passed bias filter:                      752  (0.0419432); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 4486.00
//
Query:       gene889|gene889|rna888|rna888  [L=487]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-38  130.1   8.1      2e-20   73.0   1.4    5.7  5  TruD           tRNA pseudouridine synthase D (TruD)
  ------ inclusion threshold ------
      0.087   13.0   3.3       0.95    9.7   0.1    2.9  3  baeRF_family5  Bacterial archaeo-eukaryotic release factor fa


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.3   0.0    0.0033        30      12      33 ..      18      39 ..       8      53 .. 0.82
   2 !   28.9   0.0   5.4e-11   4.8e-07      44      93 ..     105     154 ..      88     170 .. 0.85
   3 ?    0.2   0.1     0.029   2.6e+02     335     365 ..     182     212 ..     175     221 .. 0.83
   4 !   73.0   1.4   2.2e-24     2e-20     120     300 ..     255     407 ..     234     421 .. 0.77
   5 !   21.3   0.0   1.1e-08    0.0001     371     416 .]     431     476 ..     412     476 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0033
                           TruD 12 egigGrlrespeDFiVeEieef 33
                                   e  ++ l++++ DF+V+Ei++ 
  gene889|gene889|rna888|rna888 18 ENAECVLKQEAFDFVVQEITDS 39
                                   567899*************654 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 5.4e-11
                           TruD  44 ylvlrvekrnwdtldlvrelaralgisrkrvgfaGtKDkrAvTtQlisir 93 
                                     + + ++k   +t+d+ r + r+lg+ +++++faG KDkrAvT Q ++ir
  gene889|gene889|rna888|rna888 105 VYSFVLQKVMFNTIDAGRWICRRLGVPENAFQFAGNKDKRAVTFQEVTIR 154
                                    4667899999***********************************99985 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.029
                           TruD 335 vGtetelaegevgeierevleeegleledFk 365
                                     G++ e  e e++ ie+e+l   g++ e++k
  gene889|gene889|rna888|rna888 182 EGYTRERIENENKMIEKEILMTVGISFEEWK 212
                                    5888888999999999999999999988876 PP

  == domain 4  score: 73.0 bits;  conditional E-value: 2.2e-24
                           TruD 120 lrlGdLaGNkFeirvrdvaeeeeaakraeeileeleekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkp 199
                                     +lGdL+GN+F i +++    +      + ++++le+  g+ NyfG+QRFG+ +  +h++G  i+ + +eeA+++++   
  gene889|gene889|rna888|rna888 255 KNLGDLKGNRFSIALKGFR--D------QGLVKNLER--GFLNYFGQQRFGN-KLRNHEIGYDILTRRYEEAIDKIMKGG 323
                                    379**************62..2......578899997..6***********9.799******************998665 PP

                           TruD 200 feeesedtreareavaetgdleealeelpkslryErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseR 279
                                    + +         e++  +g +eea+ +     ++E+ +lk   + + + k  +  l ++L++l++h+yqS  FN+++++R
  gene889|gene889|rna888|rna888 324 KCH---------ELY-ISGKYEEAMGLGD---SVEKYILKCKSK-GMKEKDMVYGLRRELRMLYLHSYQSLKFNEAINSR 389
                                    544.........444.3555555544433...346666665555.5555566666777********************** PP

                           TruD 280 lerglpldepveGDvvifaee 300
                                    +e g   +++veGD+v+ + +
  gene889|gene889|rna888|rna888 390 MELG---TDVVEGDMVYVNGD 407
                                    ****...579******98865 PP

  == domain 5  score: 21.3 bits;  conditional E-value: 1.1e-08
                           TruD 371 elsskGtrRaillrvedlelsaeedeltleFsLpkGsYATvvlrEi 416
                                    +   kG +R+++ + +d+ +s+ +d+++++FsL++ +YAT+ lrE+
  gene889|gene889|rna888|rna888 431 NKMLKGGYRKVVEKADDVVISDAKDGIVVRFSLNSSCYATMALREV 476
                                    44579****************************************6 PP

>> baeRF_family5  Bacterial archaeo-eukaryotic release factor family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.018   1.6e+02      73     110 ..     162     200 ..     157     209 .. 0.83
   2 ?   -1.6   0.1      0.31   2.8e+03      53      67 ..     216     230 ..     209     232 .. 0.80
   3 ?    9.7   0.1   0.00011      0.95      75     121 ..     313     359 ..     308     362 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.018
                  baeRF_family5  73 slaskleklakereweeiylvGekeeakeleeel.nkkv 110
                                    +la +l+++a+  ewe +++ G + e  e e+++ +k++
  gene889|gene889|rna888|rna888 162 KLAVELNEEANCFEWEDFIVEGYTRERIENENKMiEKEI 200
                                    58999*****************98887777777746665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.31
                  baeRF_family5  53 sgskdefeerfeenq 67 
                                    +g++de++er e+n+
  gene889|gene889|rna888|rna888 216 KGKEDEVKERCEKNR 230
                                    567999****99997 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00011
                  baeRF_family5  75 askleklakereweeiylvGekeeakeleeelnkkvkevieknllnk 121
                                     + ++k +k  + +e+y+ G+ eea  l ++++k + ++  k + +k
  gene889|gene889|rna888|rna888 313 EEAIDKIMKGGKCHELYISGKYEEAMGLGDSVEKYILKCKSKGMKEK 359
                                    6789***********************************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2904.34
//
Query:       gene890|gene890|rna889|rna889  [L=409]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2625.95
//
Query:       gene89|gene89|rna89|rna89  [L=589]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-12   46.3   1.9    0.00019   21.6   0.0    4.1  4  Myb_DNA-binding  Myb-like DNA-binding domain
    0.00029   21.0   1.7       0.55   10.5   0.0    3.3  3  Myb_DNA-bind_6   Myb-like DNA-binding domain
  ------ inclusion threshold ------
      0.079   12.9   8.6       0.32   10.9   0.2    3.8  3  Myb_DNA-bind_7   Myb DNA-binding like


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.52   3.1e+03      36      42 ..     287     293 ..     286     294 .. 0.89
   2 !   21.6   0.0   3.1e-08   0.00019       4      43 ..     357     396 ..     355     399 .. 0.85
   3 !    9.0   0.1   0.00027       1.6       2      45 ..     424     466 ..     423     467 .. 0.85
   4 !   12.5   0.0   2.2e-05      0.13       2      45 ..     497     540 ..     496     541 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.52
                                HHHHHHH CS
            Myb_DNA-binding  36 kqcrsrw 42 
                                ++cr+r+
  gene89|gene89|rna89|rna89 287 NDCRYRY 293
                                89****9 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 3.1e-08
                                SBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHH CS
            Myb_DNA-binding   4 WteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwr 43 
                                +t+eEd+l  e++ k+Gn++kkI e  + +  + c ++++
  gene89|gene89|rna89|rna89 357 FTKEEDKLASELIYKYGNNFKKIRELAPHLRTEKCVLKYY 396
                                8***************************655555666665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00027
                                SSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHHH CS
            Myb_DNA-binding   2 gkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrny 45 
                                + W+e E + +++ ++ +G++W+k    + +++e + + ++r y
  gene89|gene89|rna89|rna89 424 STWSEYERNVFIQHFRIFGKSWAKYQPLI-NKSERDLKMFFRYY 466
                                68********************9976666.78888888888877 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 2.2e-05
                                SSSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHHH CS
            Myb_DNA-binding   2 gkWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrny 45 
                                +kWt +E + ++ ++  + ++W + a +++ +t  + r ++++y
  gene89|gene89|rna89|rna89 497 KKWTIDERQVFAIYFPYYNKNWVLMAAYFPAKTSGDLRQYYNRY 540
                                69****************************************98 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   9.2e-05      0.55       1      40 [.     357     396 ..     357     411 .. 0.84
   2 ?   -0.1   0.0       0.2   1.2e+03       1      40 [.     426     464 ..     426     493 .. 0.77
   3 !    7.5   0.1   0.00083         5       1      42 [.     499     540 ..     499     553 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.2e-05
             Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwk 40 
                                +t+eEd++  +l  kygn++k+I e  ++ + + c  ++ 
  gene89|gene89|rna89|rna89 357 FTKEEDKLASELIYKYGNNFKKIRELAPHLRTEKCVLKYY 396
                                79*********************99987555566766664 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.2
             Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwk 40 
                                W+e E    +++ + +g+ W + +  +n ++  ++++ ++
  gene89|gene89|rna89|rna89 426 WSEYERNVFIQHFRIFGKSWAKYQPLIN-KSERDLKMFFR 464
                                9999999999999999****99999998.66644433333 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00083
             Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwknk 42 
                                Wt +E +  + +   y+++W + a  ++ +t+ ++++++++ 
  gene89|gene89|rna89|rna89 499 WTIDERQVFAIYFPYYNKNWVLMAAYFPAKTSGDLRQYYNRY 540
                                888888888888888999*********77***********94 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.033     2e+02      13      45 ..     359     392 ..     353     406 .. 0.76
   2 ?    2.3   0.7     0.027   1.6e+02       9      49 ..     424     463 ..     419     468 .. 0.83
   3 ?   10.9   0.2   5.3e-05      0.32       4      51 ..     492     539 ..     489     559 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.033
             Myb_DNA-bind_7  13 keetekFYkaLsqfGtDFsliaklfpk.rtrrql 45 
                                kee ++  + + ++G +F+ i++l p+ rt + +
  gene89|gene89|rna89|rna89 359 KEEDKLASELIYKYGNNFKKIRELAPHlRTEKCV 392
                                5666666678899*************96665544 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.027
             Myb_DNA-bind_7   9 kkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKF 49 
                                ++Ws+ e + F +  + fG  +   + l + ++ r+lK+ F
  gene89|gene89|rna89|rna89 424 STWSEYERNVFIQHFRIFGKSWAKYQPLIN-KSERDLKMFF 463
                                68******************9998888764.5666777655 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 5.3e-05
             Myb_DNA-bind_7   4 krkktkkWskeetekFYkaLsqfGtDFsliaklfpkrtrrqlKlKFkk 51 
                                k+   kkW+ +e + F      +  ++ l+a++fp +t  +l++ +++
  gene89|gene89|rna89|rna89 492 KEDVLKKWTIDERQVFAIYFPYYNKNWVLMAAYFPAKTSGDLRQYYNR 539
                                566779*********************************999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3610.21
//
Query:       gene891|gene891|rna890|rna890  [L=465]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.4e-24   84.3   0.6    7.5e-17   61.6   0.0    2.5  3  DEAD        DEAD/DEAH box helicase
      2e-21   76.4   0.6    1.9e-20   73.3   0.0    2.5  3  Helicase_C  Helicase conserved C-terminal domain
    9.9e-07   28.9   1.4    0.00023   21.2   0.0    3.0  4  ResIII      Type III restriction enzyme, res subunit
     0.0024   17.9   0.2       0.25   11.3   0.2    3.3  4  Flavi_DEAD  Flavivirus DEAD domain
     0.0094   15.7   0.0      0.016   14.9   0.0    1.3  1  AAA_30      AAA domain
  ------ inclusion threshold ------
      0.044   13.1   0.5       0.29   10.4   0.0    2.2  2  SecA_DEAD   SecA DEAD-like domain
      0.054   13.0   0.0       0.11   11.9   0.0    1.5  1  PhoH        PhoH-like protein
       0.54   10.5   3.3         29    4.9   3.3    2.8  1  AAA_22      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   3.4e-20   7.5e-17       1      74 [.      31      99 ..      31     112 .. 0.91
   2 !   20.8   0.0   1.2e-07   0.00026     115     171 ..     112     160 ..     101     165 .. 0.75
   3 ?   -3.3   0.0       2.9   6.5e+03      50      56 ..     204     210 ..     191     258 .. 0.53

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 3.4e-20
                                   -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyi 74
                                   t+iQ+++ipl+l+ +++++ ++TGsGKTl++lip++q+ +e     g ++l+++Pt+eL+ q+ + lkk+   +
  gene891|gene891|rna890|rna890 31 TPIQRKTIPLVLERRSLMGVGRTGSGKTLCYLIPAVQRAIE-----GERTLVIVPTKELTTQVRRVLKKLSRGM 99
                                   89***********************************9965.....8899*******************98764 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.2e-07
                                    TSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSH CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 115 gklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqitcdgklqrqvivlSATlpk 171
                                    g+++  +  +lV+DE+dr+l++ + +   +++ ++l         + q i++SATlp+
  gene891|gene891|rna890|rna890 112 GNIQSTNADLLVVDEIDRILEEpSLRSVFDKVSEEL---------TCQKIFFSATLPD 160
                                    567778899************955666666666666.........3459*******94 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.9
                                    EEEEESS CS
                                    xxxxxxx RF
                           DEAD  50 alivePt 56 
                                    +++ + t
  gene891|gene891|rna890|rna890 204 TIVFVAT 210
                                    2222222 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.42   9.5e+02       8      35 ..      61      92 ..      57     114 .. 0.69
   2 !   73.3   0.0   8.3e-24   1.9e-20       2     107 ..     190     291 ..     189     294 .. 0.91
   3 ?   -3.2   0.0       4.7   1.1e+04      18      38 ..     358     375 ..     350     399 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.42
                                   HHH...HHTTTTSEEEEEESSHHHHHH.HHHH CS
                     Helicase_C  8 ell...kleeeggkilifvntidrlek.vkll 35
                                   +l+   ++  eg+++l++v+t++   +  ++l
  gene891|gene891|rna890|rna890 61 YLIpavQRAIEGERTLVIVPTKELTTQvRRVL 92
                                   4445556777999*********9443322333 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 8.3e-24
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                    k +all++l    + +k+++fv t+  +e  +++l +k+++++  +++++  + r+  +++fn+ ++ +L+ tdva+rG+
  gene891|gene891|rna890|rna890 190 KEAALLQIL---DKSKKTIVFVATKYAVELlLEIL-NKNNFESHGIYSSMDDEARRSNFRDFNASKTGILVVTDVAARGL 265
                                    556788888...89************997656666.7778**************************99************ PP

                                    TSTTESEEEESSSSSSHHHHHHHHTTS CS
                     Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRt 107
                                    dip++++V+n+dl+++ +++ +r+GR+
  gene891|gene891|rna890|rna890 266 DIPCLDTVVNYDLCDE-RTFLHRVGRV 291
                                    **************66.889******8 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.7
                                    EEEEEESSHHHHHHHHHHHHH CS
                     Helicase_C  18 kilifvntidrlekvklllek 38 
                                    k+ + ++++dr+   kl++++
  gene891|gene891|rna890|rna890 358 KVSVPAEYKDRI---KLFKTH 375
                                    555555555555...343222 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     1e-07   0.00023      30      81 ..      50      99 ..      31     118 .. 0.79
   2 !    5.5   0.0    0.0071        16     130     170 ..     116     159 ..     109     160 .. 0.89
   3 ?   -3.5   0.0       4.1   9.2e+03      55      64 ..     202     211 ..     191     243 .. 0.58
   4 ?   -1.6   0.1         1   2.3e+03      62      72 ..     380     392 ..     336     459 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1e-07
                                   EESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                         ResIII 30 kmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflsea 81
                                   +  TG+GKTl++ + +++r  +    e++l++vp+k+l+ q ++ +kk++   
  gene891|gene891|rna890|rna890 50 VGRTGSGKTLCYlIPAVQRAIE---GERTLVIVPTKELTTQVRRVLKKLSRGM 99
                                   567*********6667777776...359***************9998887665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0071
                                    TTT-SEEEEETGGGTTS.TTTHHHHHT---...SEEEEEESS-S CS
                         ResIII 130 rdrfdviiiDEaHrlgakkswreilekfke...avllglTATpe 170
                                    +++ d++++DE  r+ ++ s r++ +k++e   + ++ ++AT++
  gene891|gene891|rna890|rna890 116 STNADLLVVDEIDRILEEPSLRSVFDKVSEeltCQKIFFSATLP 159
                                    56789************99******9999988899999****86 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.1
                                    .-EEEEESSH CS
                         ResIII  55 ekflflvprk 64 
                                    +k++++v +k
  gene891|gene891|rna890|rna890 202 KKTIVFVATK 211
                                    2333333333 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1
                                    SSHHHHHHHH..H CS
                         ResIII  62 prkslleqtl..e 72 
                                    +r++ll++++  +
  gene891|gene891|rna890|rna890 380 HRETLLDKLKkmN 392
                                    4444444444221 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00011      0.25      13      56 ..      53      95 ..      45     102 .. 0.90
   2 ?    1.2   0.0      0.15   3.3e+02      93     139 ..     116     161 ..     108     165 .. 0.74
   3 ?    0.1   0.0      0.33   7.3e+02      28      61 ..     196     229 ..     190     245 .. 0.82
   4 ?   -3.6   0.0       4.5     1e+04     106     119 ..     338     351 ..     330     359 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                   TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS CS
                     Flavi_DEAD 13 PGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkgl 56
                                    G+Gkt  +l   v++aie   rtlv++Pt+   + + + lk+l
  gene891|gene891|rna890|rna890 53 TGSGKTLCYLIPAVQRAIE-GERTLVIVPTKELTTQVRRVLKKL 95
                                   59***************97.579*********999999999875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                                    ----SEEEEETTT--.SHHHHHHHHHHHHHHHTTS-EEEEEESS-TT- CS
                     Flavi_DEAD  93 kknyeliimDeahfl.DPasiaarGyletkaeegeaalilltatPPGt 139
                                    ++n +l+++De   + +  s   r   ++ +ee +++ i+++at P +
  gene891|gene891|rna890|rna890 116 STNADLLVVDEIDRIlEEPS--LRSVFDKVSEELTCQKIFFSATLPDH 161
                                    56777777777653313333..5888999999999*********9865 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.33
                                    HHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE- CS
                     Flavi_DEAD  28 eaierrlrtlvLaPtrvvlaemeealkglevryk 61 
                                    + +++ ++t+v + t+  ++ + e l++ + +++
  gene891|gene891|rna890|rna890 196 QILDKSKKTIVFVATKYAVELLLEILNKNNFESH 229
                                    5678999*********999999999998887766 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 4.5
                                    --SHHHHHHHHHHH CS
                     Flavi_DEAD 106 flDPasiaarGyle 119
                                    f    s+a rG+ +
  gene891|gene891|rna890|rna890 338 FEHLRSVANRGHQK 351
                                    66668999999976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.3e-06     0.016       6     111 ..      34     142 ..      31     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.3e-06
                         AAA_30   6 QaaavealltsgdrvavltGpAGtGKt..talkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.. 81 
                                    Q++ +  +l+ +    + +G+ G+GKt  +++ a+++a+e  g+r +++ pt++   ++++ l   ++ ++ ++k  +  
  gene891|gene891|rna890|rna890  34 QRKTIPLVLERR--SLMGVGRTGSGKTlcYLIPAVQRAIE--GERTLVIVPTKELTTQVRRVLKKLSRGMEDVWKFIEis 109
                                    555565555444..58899********4446788888888..77899999999999999987777666666666555666 PP

                         AAA_30  82 ..grarlepgtllivDEagmv.dtkqlaallka 111
                                      g  + ++++ll+vDE+  +    +l++++++
  gene891|gene891|rna890|rna890 110 tpGNIQSTNADLLVVDEIDRIlEEPSLRSVFDK 142
                                    7977888999*******9765455566666555 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.29      98     127 ..      52      81 ..      40     110 .. 0.84
   2 ?   -0.1   0.1       0.2   4.4e+02     196     210 ..     117     131 ..     105     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SecA_DEAD  98 kTGEGKtlvatlpaylnaltgkgvhvvtvn 127
                                    +TG GKtl+  +pa+  a++g+   v+   
  gene891|gene891|rna890|rna890  52 RTGSGKTLCYLIPAVQRAIEGERTLVIVPT 81 
                                    6********************999888654 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.2
                                    xxxxxxxxxxxxxxx RF
                      SecA_DEAD 196 rglnfaivDEvDsvL 210
                                     + ++ +vDE+D +L
  gene891|gene891|rna890|rna890 117 TNADLLVVDEIDRIL 131
                                    677889*******98 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     5e-05      0.11       6      54 ..      31      79 ..      27      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
                                   SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE CS
                           PhoH  6 tkeQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriil 54
                                   t  Q++++  + +   ++++G++G+GKt+  +  av+   +++ + +i+
  gene891|gene891|rna890|rna890 31 TPIQRKTIPLVLERRSLMGVGRTGSGKTLCYLIPAVQRAIEGERTLVIV 79
                                   5679999999999999********************9988877665554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.3     0.013        29       7     103 ..      46     131 ..      42     168 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst.sskdllrellralglelkaerlsseell.eale 83 
                                    +l+ +G +G+GKT+++   + q  +e      + +++  v  +++t   + +l++l r +++           ++     
  gene891|gene891|rna890|rna890  46 SLMGVGRTGSGKTLCYLIPAVQRAIE------GERTLvIVPTKELTtQVRRVLKKLSRGMEDVW--------KFIeISTP 111
                                    55667888888888876655555332......33333133333333334444444444444221........22212222 PP

                         AAA_22  84 qalraravielliiDEaqh.l 103
                                     +++++ +  ll++DE+++ l
  gene891|gene891|rna890|rna890 112 GNIQSTNA-DLLVVDEIDRiL 131
                                    33444444.788888888844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3117.64
//
Query:       gene893|gene893|rna892|rna892  [L=201]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-09   37.6   4.9    9.3e-05   22.8   0.5    3.4  3  HMG_box    HMG (high mobility group) box
    2.3e-05   24.9   5.0     0.0014   19.1   1.0    2.5  2  HMG_box_2  HMG-box domain
     0.0021   18.4   1.3        0.6   10.5   0.0    2.2  2  FAM195     FAM195 family
      0.004   17.2   3.7        1.8    8.6   1.8    2.7  3  Erp_C      Erp protein C-terminus
  ------ inclusion threshold ------
      0.031   13.5   3.1       0.93    8.6   0.3    2.3  2  N1221      N1221-like protein
      0.037   14.3   0.0        4.7    7.6   0.0    2.4  2  DUF4806    Domain of unknown function (DUF4806)
      0.045   13.8   0.5      0.077   13.0   0.1    1.6  2  Crl        Sigma factor-binding transcriptional regulator Crl


Domain annotation for each model (and alignments):
>> HMG_box  HMG (high mobility group) box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.5   3.6e-08   9.3e-05       2      57 ..      15      68 ..      14      75 .. 0.89
   2 ?    1.9   0.1      0.12     3e+02      43      69 .]      79     105 ..      77     105 .. 0.87
   3 !   13.3   0.0   3.2e-05     0.082      32      54 ..     133     155 ..     110     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.6e-08
                                   -SS--HHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHHSHHHHHHHHHHHHHHH CS
                        HMG_box  2 kRplsafflfskeqraklkaenPelknaeiskklgekWkalseeeKkkYeekaeke 57
                                    +  s + +f++e  ++ k e ++    +++k l ++W+++++eeK  Y ek +k 
  gene893|gene893|rna892|rna892 15 TKQRSPYSVFAREFFRNNKHEYTS--HVDLAKALVKTWNEMQDEEKSTYVEKCNKS 68
                                   577899***********9999975..68***********************99885 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HMG_box  43 seeeKkkYeekaekekaryekekpeyk 69 
                                    see   +Y+++  k  ++y k+ p y+
  gene893|gene893|rna892|rna892  79 SEESPIPYDKDNLKKLKKYIKAGPTYR 105
                                    6677789**************999996 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHSHHHHHHHHHHHH CS
                        HMG_box  32 skklgekWkalseeeKkkYeeka 54 
                                    +++ +e+W +l++e++ kY++ka
  gene893|gene893|rna892|rna892 133 VRMFAEMWESLEDEVQNKYRNKA 155
                                    6899****************998 PP

>> HMG_box_2  HMG-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.0   5.6e-07    0.0014       5      61 ..      15      68 ..      12      78 .. 0.87
   2 !    7.1   0.2    0.0032       8.1      29      59 ..     126     156 ..     105     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.6e-07
                                   -SS--HHHHHHHTTHHHHHHHT---SSHHHHTGGGHHHHHHS-HHHHHHHHHHHHHH CS
                      HMG_box_2  5 kaarnAYalfvqemipelkrkGnpviglaevsklcsekWkalseeeKekYeekAked 61
                                     +r+ Y +f++e   + k +        +  k++ + W  +++eeK+ Y ek ++ 
  gene893|gene893|rna892|rna892 15 TKQRSPYSVFAREFFRNNKHE---YTSHVDLAKALVKTWNEMQDEEKSTYVEKCNKS 68
                                   567899*******99999988...788899**********************98876 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0032
                                    -SSHHHHTGGGHHHHHHS-HHHHHHHHHHHH CS
                      HMG_box_2  29 viglaevsklcsekWkalseeeKekYeekAk 59 
                                    ++  +e ++   e W +l++e ++kY +kA 
  gene893|gene893|rna892|rna892 126 TVSPEENVRMFAEMWESLEDEVQNKYRNKAL 156
                                    666678889999****************994 PP

>> FAM195  FAM195 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.4    0.0033       8.4      31      74 ..      36      87 ..       6      99 .. 0.65
   2 !   10.5   0.0   0.00023       0.6      30      62 ..     125     157 ..     123     185 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0033
                         FAM195 31 tpqheElikyindsWnevvaelesdekgeaea........stssstsvvvYk 74
                                     +h +l k +  +Wne++ e++s+  ++ ++         + s++s++ Y 
  gene893|gene893|rna892|rna892 36 YTSHVDLAKALVKTWNEMQDEEKSTYVEKCNKsledaselAVASEESPIPYD 87
                                   45799**************999998555444423333332233355555554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00023
                         FAM195  30 itpqheElikyindsWnevvaelesdekgeaea 62 
                                    +t + eE++++  + W++++ e +++ +++a +
  gene893|gene893|rna892|rna892 125 MTVSPEENVRMFAEMWESLEDEVQNKYRNKALG 157
                                    67788*****************99998777655 PP

>> Erp_C  Erp protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   1.8   0.00072       1.8      38      74 ..      36      73 ..      30      99 .. 0.79
   2 ?   -0.0   0.1      0.32   8.1e+02     114     126 ..      88     100 ..      73     114 .. 0.68
   3 !    7.1   0.0     0.002       5.1      46      96 ..     134     190 ..     116     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00072
                          Erp_C 38 yddftdgnkaiyktwgdledeede.glgkllkelsdtr 74
                                   y    d  ka+ ktw++++dee+   + k  k l d+ 
  gene893|gene893|rna892|rna892 36 YTSHVDLAKALVKTWNEMQDEEKStYVEKCNKSLEDAS 73
                                   66677889************976515788999998875 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.32
                          Erp_C 114 kskleevkkylkd 126
                                    k +l+++kky+k 
  gene893|gene893|rna892|rna892  88 KDNLKKLKKYIKA 100
                                    5566666666665 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.002
                          Erp_C  46 kaiyktwgdlede.....edeglgkllkelsdtrdelrtklnegnkayivlek.epk 96 
                                    +   + w+ lede      ++ lg l  +    + ++   l + +k y++ e  ep+
  gene893|gene893|rna892|rna892 134 RMFAEMWESLEDEvqnkyRNKALGSLAAKKKPRKRNMGNALRKSDKIYTTSEGlEPS 190
                                    667899******963222234567777666677789999999999999998866775 PP

>> N1221  N1221-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3   0.00036      0.93      28      72 ..      28      72 ..      20      82 .. 0.83
   2 ?    5.2   0.2    0.0039        10       2      77 ..     103     167 ..     102     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00036
                          N1221 28 lllkakkaFeskweevseeeeeWedvdederkkfverllesless 72
                                    ++++k+ + s+++ ++   ++W +++++e++++ve++ +sle+ 
  gene893|gene893|rna892|rna892 28 FFRNNKHEYTSHVDLAKALVKTWNEMQDEEKSTYVEKCNKSLEDA 72
                                   5778889999999988888999********************965 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0039
                          N1221   2 aydFeykdsdsleeEldeWFsys.dv.vlllkakkaFeskweevseeeeeWedvdederkkfverlleslessdkaRl 77 
                                    +y +ey+ + s+ +E+   F+   d+ v  +++ ++F + we+           +++ ++k+ ++ l sl+ ++k R 
  gene893|gene893|rna892|rna892 103 TYRWEYSGYLSFVNEI---FDICgDMtVSPEENVRMFAEMWESL----------EDEVQNKYRNKALGSLAAKKKPRK 167
                                    6778888888887777...5555566555556666666666665..........555555555555555555444444 PP

>> DUF4806  Domain of unknown function (DUF4806)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.017        43      11      40 ..      87     116 ..      76     134 .. 0.81
   2 ?    7.6   0.0    0.0018       4.7      16      53 ..     141     180 ..     135     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.017
                        DUF4806  11 seeelerLEaavrtdekirqqyvnyLrkik 40 
                                    + + l++L + ++  +++r +y  yL++  
  gene893|gene893|rna892|rna892  87 DKDNLKKLKKYIKAGPTYRWEYSGYLSFVN 116
                                    6799**********************9976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0018
                        DUF4806  16 erLEaavrtdekirqqyvnyLrkikgk.kadlkkvf...dkl 53 
                                    e LE++v+  +k+r++ + +L+++k   k ++ +++   dk+
  gene893|gene893|rna892|rna892 141 ESLEDEVQ--NKYRNKALGSLAAKKKPrKRNMGNALrksDKI 180
                                    78******..789*********99988558888887555555 PP

>> Crl  Sigma factor-binding transcriptional regulator Crl
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   4.7e+03      95      99 ..      56      60 ..      30      80 .. 0.53
   2 ?   13.0   0.1     3e-05     0.077       7      95 ..      91     182 ..      86     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                                   HHHHH CS
                            Crl 95 ktlee 99
                                   +  ++
  gene893|gene893|rna892|rna892 56 EEKST 60
                                   22222 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3e-05
                                    HHHHHHHHCT-TTB-GGG-BTTEEEEEEEEEES-TTS-GGG..--EEEEEEEEEEETTEEEEEEEEEEE-TTS-EESEEE CS
                            Crl   7 srllkklkalGPYlreeqceedrfffDCLavCvnakkapek..refwGWWleleaeeeefeyeyqlGlydkegeWkaeki 84 
                                     + lkk+ + GP  r e +   +f+ +  ++C ++  +pe+  r f   W +le e ++   + +lG   ++++  ++++
  gene893|gene893|rna892|rna892  91 LKKLKKYIKAGPTYRWEYSGYLSFVNEIFDICGDMTVSPEEnvRMFAEMWESLEDEVQNKYRNKALGSLAAKKKPRKRNM 170
                                    5668999999*****************************976699*********99999888999999988888777776 PP

                                    --H.HHHHHHHH CS
                            Crl  85 kkk.eveeklek 95 
                                     ++ ++++k+ +
  gene893|gene893|rna892|rna892 171 GNAlRKSDKIYT 182
                                    544144455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.52
# Mc/sec: 1166.05
//
Query:       gene894|gene894|rna893|rna893  [L=181]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-23   80.9  14.2      6e-14   52.2   5.4    2.4  2  HMG_box         HMG (high mobility group) box
    9.4e-14   51.8  15.3    3.4e-08   33.9   6.0    2.5  2  HMG_box_2       HMG-box domain
    0.00015   21.6   0.3    0.00061   19.7   0.0    2.1  2  CHDNT           CHDNT (NUC034) domain
  ------ inclusion threshold ------
      0.015   15.8   6.5      0.022   15.3   6.5    1.4  1  YABBY           YABBY protein
      0.029   13.6   2.9       0.03   13.6   2.2    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.033   14.4   8.3       0.14   12.4   0.7    2.3  2  Protamine_like  Protamine and protamine like
       0.07   12.2   6.4       0.77    8.8   0.1    2.1  2  RE_HaeIII       HaeIII restriction endonuclease
        0.3   10.9   2.1         13    5.7   0.3    2.5  2  DUF1289         Protein of unknown function (DUF1289)


Domain annotation for each model (and alignments):
>> HMG_box  HMG (high mobility group) box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   5.4   2.7e-17     6e-14       1      69 []      24      91 ..      24      91 .. 0.98
   2 !   33.7   1.5   1.6e-11   3.6e-08       5      57 ..     120     172 ..     117     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.7e-17
                                   --SS--HHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HMG_box  1 pkRplsafflfskeqraklkaenPelknaeiskklgekWkalseeeKkkYeekaekekaryekekpeyk 69
                                   pk+p+s +f+f +eqr+k  +e ++l +ae ++ ++e+Wk+l++ee+++Y + ++ke++ y+++++eyk
  gene894|gene894|rna893|rna893 24 PKKPMSGYFIFGQEQRKK-NEELSKLPVAEQGRSISEMWKKLTDEEREEYNKISNKERELYQAKVEEYK 91
                                   8***************98.799**********************************************8 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.6e-11
                                    --HHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHHSHHHHHHHHHHHHHHH CS
                        HMG_box   5 lsafflfskeqraklkaenPelknaeiskklgekWkalseeeKkkYeekaeke 57 
                                    ++ ++ f+k  r+ + +enP+ +  e ++ ++++Wk+ls++eK+ Y + ae+ 
  gene894|gene894|rna893|rna893 120 VTGYNEFFKVIRKAVSEENPNFTMMETTSAVAKRWKELSDDEKAVYNKIAEEK 172
                                    578999*****************************************999986 PP

>> HMG_box_2  HMG-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   6.0   1.5e-11   3.4e-08       1      72 [.      21      90 ..      21      97 .. 0.91
   2 !   22.9   1.8   4.3e-08   9.7e-05       3      62 ..     115     173 ..     111     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.5e-11
                                   ---.-SS--HHHHHHHTTHHHHHHHT---SSHHHHTGGGHHHHHHS-HHHHHHHHHHHHHHHHHHHH-SS-- CS
                      HMG_box_2  1 pkkpkaarnAYalfvqemipelkrkGnpviglaevsklcsekWkalseeeKekYeekAkedkkrydrealty 72
                                   p+ pk ++++Y++f qe++++  ++     ++ae  + +se Wk l +ee+e+Y++  ++ ++ y++   +y
  gene894|gene894|rna893|rna893 21 PNAPKKPMSGYFIFGQEQRKKN-EE-LSKLPVAEQGRSISEMWKKLTDEEREEYNKISNKERELYQAKVEEY 90
                                   789*************988765.44.5899*********************************999876665 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 4.3e-08
                                    -.-SS--HHHHHHHTTHHHHHHHT---SSHHHHTGGGHHHHHHS-HHHHHHHHHHHHHHH CS
                      HMG_box_2   3 kpkaarnAYalfvqemipelkrkGnpviglaevsklcsekWkalseeeKekYeekAkedk 62 
                                    k   +  +Y+ f +  ++ + ++ np   + e + ++ ++Wk ls++eK  Y++ A e+ 
  gene894|gene894|rna893|rna893 115 KGVKKVTGYNEFFKVIRKAVSEE-NPNFTMMETTSAVAKRWKELSDDEKAVYNKIAEEKN 173
                                    44567889***************.*******************************99875 PP

>> CHDNT  CHDNT (NUC034) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.3   2.8e+03      40      50 ..      81      91 ..      69      94 .. 0.65
   2 !   19.7   0.0   2.7e-07   0.00061      11      51 ..     119     159 ..     116     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.3
                          CHDNT 40 mLvaakwrEFq 50
                                   +L +ak +E+ 
  gene894|gene894|rna893|rna893 81 ELYQAKVEEYK 91
                                   46677777765 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.7e-07
                          CHDNT  11 nltnyKlFsqhvRPlllkenPkvavsklvmLvaakwrEFqe 51 
                                    ++t y  F +++R  + +enP+ ++  + + va +w+E ++
  gene894|gene894|rna893|rna893 119 KVTGYNEFFKVIRKAVSEENPNFTMMETTSAVAKRWKELSD 159
                                    7899**********************************776 PP

>> YABBY  YABBY protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   6.5     1e-05     0.022      66     154 ..      62     156 ..       3     160 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                          YABBY  66 elksellskelasssksseksk...ksalasssseqeeeeeekvvnrppekrq...RvPsaYnrFikeeiqRikaenPdi 139
                                    ++ ++++++e+++ s++ ++      +++++s++ ++  e+ +  + ++ k++   +    Yn F k   + +  enP+ 
  gene894|gene894|rna893|rna893  62 KKLTDEEREEYNKISNKERELYqakVEEYKKSAEYHDYLEKVAADEEAAGKKKkgvKKVTGYNEFFKVIRKAVSEENPNF 141
                                    2222222222222222222221111222222222233333334444444443311134689******99999******** PP

                          YABBY 140 shreaFsaaaknWah 154
                                    +  e  sa ak W +
  gene894|gene894|rna893|rna893 142 TMMETTSAVAKRWKE 156
                                    *************75 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   2.2   1.3e-05      0.03      54     118 ..      66     131 ..      47     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                    Pyr_redox_3  54 kleipdlnaiseetspafslk.eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevet 118
                                    + e  + n is+++ + ++ k ee+ + +e+ +Yl++va+ +e   k+++ V++v+  +e f+v  
  gene894|gene894|rna893|rna893  66 DEEREEYNKISNKERELYQAKvEEYKKSAEYHDYLEKVAADEEAAGKKKKGVKKVTGYNEFFKVIR 131
                                    4466789999*99999999884669999***********************************975 PP

>> Protamine_like  Protamine and protamine like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.6    0.0069        15      78     130 ..      23      78 ..       2      97 .. 0.67
   2 ?   12.4   0.7   6.1e-05      0.14      74     130 ..     113     171 ..     101     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0069
                 Protamine_like  78 varvtnnaylnfvrefkkkfynlkPrelva...kaakawarlsearkdaykrvack 130
                                      +    +y+ f +e +kk  +l+   + +     +  w +l+ ++++ y +++ k
  gene894|gene894|rna893|rna893  23 APKKPMSGYFIFGQEQRKKNEELSKLPVAEqgrSISEMWKKLTDEEREEYNKISNK 78 
                                    22344579***********9999976555411156889************998765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.1e-05
                 Protamine_like  74 krskvarvtnnaylnfvrefkkkfynlkPr....elvakaakawarlsearkdaykrvack 130
                                    k++ v +v   +y +f +  +k   + +P+    e     ak+w +ls ++k  y ++a +
  gene894|gene894|rna893|rna893 113 KKKGVKKV--TGYNEFFKVIRKAVSEENPNftmmETTSAVAKRWKELSDDEKAVYNKIAEE 171
                                    33334445..4899999999998887777532225566789***************99965 PP

>> RE_HaeIII  HaeIII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.3    0.0053        12     144     211 ..      59     132 ..      48     137 .. 0.66
   2 ?    8.8   0.1   0.00034      0.77     141     173 ..     136     168 ..     131     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0053
                      RE_HaeIII 144 pifdelkeekekkkkwseledkeedvyvPllkafid......elerayekdkd..ipeklveyllGkkdfykiisi 211
                                    +++++l+   e++++++++++ke+++y+  ++ + +       le+  ++++     +k v+ + G ++f+k+i +
  gene894|gene894|rna893|rna893  59 EMWKKLTD--EEREEYNKISNKERELYQAKVEEYKKsaeyhdYLEKVAADEEAagKKKKGVKKVTGYNEFFKVIRK 132
                                    44444443..456789***********9988766541111114444443333312667889999********9975 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00034
                      RE_HaeIII 141 evepifdelkeekekkkkwseledkeedvyvPl 173
                                    e +p f++++++ +  k+w+el+d e+ vy  +
  gene894|gene894|rna893|rna893 136 EENPNFTMMETTSAVAKRWKELSDDEKAVYNKI 168
                                    56899*************************865 PP

>> DUF1289  Protein of unknown function (DUF1289)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3    0.0058        13      28      41 ..      60      73 ..      54      81 .. 0.78
   2 ?    4.5   0.1     0.013        30      27      40 ..     152     165 ..     147     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0058
                        DUF1289 28 aWssmsdeerravl 41
                                    W++++deer++  
  gene894|gene894|rna893|rna893 60 MWKKLTDEEREEYN 73
                                   6*********9875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                        DUF1289  27 aaWssmsdeerrav 40 
                                    ++W+++sd+e++  
  gene894|gene894|rna893|rna893 152 KRWKELSDDEKAVY 165
                                    79********9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2006  (0.111886); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1260.28
//
Query:       gene895|gene895|rna894|rna894  [L=258]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-12   46.8   4.2    2.5e-12   46.8   4.2    1.9  2  SNAP      Soluble NSF attachment protein, SNAP
    4.7e-06   26.8   1.2      0.028   14.7   0.0    3.2  3  TPR_12    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.038   14.0   1.9         16    5.8   0.5    4.4  4  TPR_7     Tetratricopeptide repeat
       0.85    9.9  12.4        7.8    6.9   0.0    5.1  7  TPR_2     Tetratricopeptide repeat
        2.3    8.6  12.0        7.3    7.1   0.0    5.2  7  TPR_8     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   4.2     7e-16   2.5e-12       4     180 ..       7     180 ..       4     188 .. 0.89
   2 ?   -1.5   0.0      0.36   1.3e+03     119     224 ..     211     232 ..     208     243 .. 0.54

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 7e-16
                                    HHHHHHHHHHSS---THHHHH--SHHHHHHHHHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHH.TT-..HHHHHHHHHH CS
                           SNAP   4 eellakAekklksssglfslfgsksskaeeAadlyeqAAnayklakkweeAgeaflkaAecqek.lke..kdeaanayve 80 
                                    +  l++Aek  ++ +  +slf+s   +++  a+++ + +n   ++++++e  + +++aA+++e   +e  + +a++ y +
  gene895|gene895|rna894|rna894   7 NRKLKEAEKLRTKGTFPLSLFSSP--DYDASAEIFMEVGN---MEEDLSERVRYYEEAAKTYEMeEGEygRYQASQVYEK 81 
                                    567899**9999655555***995..59***********9...8****************99863222225689999999 PP

                                    HHHHHHHT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHH CS
                           SNAP  81 AakcykkvspeeAvealekAieiytekgrfrraAklkkeiaelyekelgdlekAieaYekAaelyeqeeakalankcllk 160
                                     a++ + ++p+++++a++++  +  + gr + aA   +   e+++ke gdl+ ++e+ +k ae y + + k +  k++ +
  gene895|gene895|rna894|rna894  82 IAQICEDEHPKKSIAAYKRSGMYSKQCGRESLAAISFQRASEILKKE-GDLNGCLECLQKVAECYCGSNWKHHKRKVMRD 160
                                    9*******************999999*********************.******************************** PP

                                    HHHHHHHTT-HHHHHHHHHH CS
                           SNAP 161 vAelsaelekyekAieiyek 180
                                    +A+++ el+ky  A++++ +
  gene895|gene895|rna894|rna894 161 IADVYIELGKYGLAAKVFLS 180
                                    ****************9965 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.36
                                    HHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-TTTGGGHHHH CS
                           SNAP 119 eiaelyekelgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekvakkslennllkysvkey 198
                                    ei++ +e + ++ +k ie                                                              
  gene895|gene895|rna894|rna894 211 EICDALERDFNEAHKTIEE------------------------------------------------------------- 229
                                    4455555555555555554............................................................. PP

                                    HHHHHHHHHHTT-HHHHHHHHHGGG- CS
                           SNAP 199 flkaglcrLaagDvvaakralekyee 224
                                                           y +
  gene895|gene895|rna894|rna894 230 -----------------------YIT 232
                                    .......................444 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.3    0.0011       4.1      24      71 ..      54     101 ..      46     101 .. 0.90
   2 !   11.3   0.1     9e-05      0.32      21      77 .]      74     127 ..      71     127 .. 0.88
   3 !   14.7   0.0   7.9e-06     0.028      11      67 ..     123     177 ..     114     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                         TPR_12  24 ellekaleiarrllGpdh.pltattlrnLgrlyralgryeeAlelleea 71 
                                    +++e+a   ++   G++  +++++++  +++++ + +++++ +++++++
  gene895|gene895|rna894|rna894  54 RYYEEAAKTYEMEEGEYGrYQASQVYEKIAQIC-EDEHPKKSIAAYKRS 101
                                    79********88888887799***********9.777*********997 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9e-05
                         TPR_12  21 eAlellekaleiarrllGpdhpltattlrnLgrlyral.gryeeAlelleealaiaek 77 
                                    +A + +ek  +i+    +++hp  +++ +  + +y+++ gr   A   +++a +i++k
  gene895|gene895|rna894|rna894  74 QASQVYEKIAQIC----EDEHPKKSIAAYKRSGMYSKQcGRESLAAISFQRASEILKK 127
                                    5666788888888....489****************999****************986 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 7.9e-06
                         TPR_12  11 avlrrlgrydeAlellekaleiarrllGpdh.pltattlrnLgrlyralgryeeAlel 67 
                                    ++l + g++  +le+l+k+ e +    G ++ +    ++r+++++y +lg+y  A + 
  gene895|gene895|rna894|rna894 123 EILKKEGDLNGCLECLQKVAECY---CGSNWkHHKRKVMRDIADVYIELGKYGLAAKV 177
                                    788999*****************...67777677*******************99876 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.42   1.5e+03       3      17 ..      33      47 ..      32      47 .. 0.84
   2 ?    5.8   0.5    0.0045        16      10      24 ..      51      65 ..      43      67 .. 0.87
   3 ?    0.1   0.0      0.29     1e+03       6      24 ..      83     100 ..      73     108 .. 0.63
   4 ?    2.3   0.0      0.06   2.1e+02       5      22 ..     161     178 ..     159     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.42
                          TPR_7  3 lnLarlysrlGdyee 17
                                   ++ a+++ ++G++ee
  gene895|gene895|rna894|rna894 33 DASAEIFMEVGNMEE 47
                                   67799*******996 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0045
                          TPR_7 10 srlGdyeeAielyeq 24
                                   +r+++yeeA++ ye 
  gene895|gene895|rna894|rna894 51 ERVRYYEEAAKTYEM 65
                                   6899*********96 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.29
                          TPR_7   6 arlysrlGdyeeAielyeq 24 
                                    a+++++  + ++ i  y++
  gene895|gene895|rna894|rna894  83 AQICED-EHPKKSIAAYKR 100
                                    455444.666666766766 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.06
                          TPR_7   5 LarlysrlGdyeeAiely 22 
                                    +a++y +lG+y  A++++
  gene895|gene895|rna894|rna894 161 IADVYIELGKYGLAAKVF 178
                                    799********9999877 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1         5   1.8e+04      14      22 ..       7      15 ..       6      16 .. 0.70
   2 ?    0.8   0.2      0.19   6.7e+02      16      25 ..      55      64 ..      50      64 .. 0.70
   3 ?   -1.1   0.0      0.79   2.8e+03      16      26 ..      90     100 ..      75     108 .. 0.66
   4 ?    0.6   0.1      0.23   8.1e+02       3      30 ..      97     124 ..      95     127 .. 0.79
   5 ?    6.3   0.1    0.0035        12       6      29 ..     120     143 ..     115     147 .. 0.85
   6 ?    6.9   0.0    0.0022       7.8       5      24 ..     159     178 ..     156     180 .. 0.87
   7 ?   -1.5   0.1         1   3.6e+03      15      26 ..     218     229 ..     214     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5
                          TPR_2 14 lgdyeeAle 22
                                   + +++eA++
  gene895|gene895|rna894|rna894  7 NRKLKEAEK 15
                                   567888887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.19
                          TPR_2 16 dyeeAleafe 25
                                    yeeA++ +e
  gene895|gene895|rna894|rna894 55 YYEEAAKTYE 64
                                   5778877775 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.79
                          TPR_2  16 dyeeAleafek 26 
                                    ++++ ++a+++
  gene895|gene895|rna894|rna894  90 HPKKSIAAYKR 100
                                    44555666655 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.23
                          TPR_2   3 alynlGlayyklgdyeeAleafekAlel 30 
                                    a+ + G+   + g+   A+  f++A e+
  gene895|gene895|rna894|rna894  97 AYKRSGMYSKQCGRESLAAISFQRASEI 124
                                    6777788888888999999999999776 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.0035
                          TPR_2   6 nlGlayyklgdyeeAleafekAle 29 
                                    +  +++ k gd++ +le+++k+ e
  gene895|gene895|rna894|rna894 120 RASEILKKEGDLNGCLECLQKVAE 143
                                    6678999**************987 PP

  == domain 6  score: 6.9 bits;  conditional E-value: 0.0022
                          TPR_2   5 ynlGlayyklgdyeeAleaf 24 
                                      ++++y++lg+y  A++ f
  gene895|gene895|rna894|rna894 159 RDIADVYIELGKYGLAAKVF 178
                                    6789*************988 PP

  == domain 7  score: -1.5 bits;  conditional E-value: 1
                          TPR_2  15 gdyeeAleafek 26 
                                     d++eA++  e+
  gene895|gene895|rna894|rna894 218 RDFNEAHKTIEE 229
                                    688888886665 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   4.9e+03      16      26 ..      31      41 ..      31      48 .. 0.60
   2 ?    0.8   0.4      0.21   7.6e+02      19      29 ..      51      61 ..      35      64 .. 0.69
   3 ?   -1.0   0.0      0.77   2.8e+03      21      30 ..      76      85 ..      72      89 .. 0.53
   4 ?    1.3   0.1      0.15   5.3e+02       8      30 ..     102     124 ..      95     127 .. 0.81
   5 ?    4.0   0.1     0.019        70       5      28 ..     119     142 ..     115     143 .. 0.85
   6 ?    7.1   0.0     0.002       7.3       7      24 ..     161     178 ..     160     180 .. 0.91
   7 ?   -3.2   0.0       4.2   1.5e+04      16      28 ..     219     231 ..     218     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                                   -HHHHHHHHHH CS
                          TPR_8 16 dyeeAkeyyek 26
                                   dy+++ e +++
  gene895|gene895|rna894|rna894 31 DYDASAEIFME 41
                                   56666666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHH CS
                          TPR_8 19 eAkeyyekale 29
                                   e + yye+a +
  gene895|gene895|rna894|rna894 51 ERVRYYEEAAK 61
                                   55555555543 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.77
                                   HHHHHHHHHH CS
                          TPR_8 21 keyyekalel 30
                                    ++yek  ++
  gene895|gene895|rna894|rna894 76 SQVYEKIAQI 85
                                   4555554444 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.15
                                    HHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   8 gsiylklgdyeeAkeyyekalel 30 
                                    g+  ++ g+   A  ++++a e+
  gene895|gene895|rna894|rna894 102 GMYSKQCGRESLAAISFQRASEI 124
                                    555699999999******99987 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.019
                                    HHHHHHHHHTT-HHHHHHHHHHHH CS
                          TPR_8   5 ynlgsiylklgdyeeAkeyyekal 28 
                                    ++ + i++k gd++   e+++k+ 
  gene895|gene895|rna894|rna894 119 QRASEILKKEGDLNGCLECLQKVA 142
                                    56679****************985 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.002
                                    HHHHHHHTT-HHHHHHHH CS
                          TPR_8   7 lgsiylklgdyeeAkeyy 24 
                                    ++++y++lg+y  A +++
  gene895|gene895|rna894|rna894 161 IADVYIELGKYGLAAKVF 178
                                    89************9988 PP

  == domain 7  score: -3.2 bits;  conditional E-value: 4.2
                                    -HHHHHHHHHHHH CS
                          TPR_8  16 dyeeAkeyyekal 28 
                                    d++eA +++e+++
  gene895|gene895|rna894|rna894 219 DFNEAHKTIEEYI 231
                                    7889988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1115  (0.0621897); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1661.88
//
Query:       gene896|gene896|rna895|rna895  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   61.1  14.1    1.2e-16   61.0  14.1    1.0  1  TPT       Triose-phosphate Transporter family
     0.0055   16.9  33.7     0.0081   16.3  12.2    2.4  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.086   12.3   5.1      0.081   12.4   3.9    1.6  1  DUF1129   Protein of unknown function (DUF1129)


Domain annotation for each model (and alignments):
>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0  14.1     2e-20   1.2e-16       3     290 .]       6     298 ..       4     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 2e-20
                            TPT   3 lgllfllWYllnvvfnilnKkilnvf....pyPltvsavqllvgsvlilvlwalglkkrpkisseflkailplalvktlg 78 
                                    ++ l+l++Y+l+++   l   +l+       +Pl+ +++q l+  + ++ +++l+ +k+pk   +++   +p al+ +  
  gene896|gene896|rna895|rna895   6 VLGLVLMYYILSLSLGYLTSFLLSRKtynfSFPLFKASLQNLIHFLGASTALRLQREKAPK--PNYFGPSFPCALAGATD 83 
                                    5667777888877766666666654322338999999999999998888888777777776..56889999********* PP

                            TPT  79 hvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasvtElsFnligfisAlisnltfs 158
                                      l+ +sl  ++  f  +vK+s P+F  ++   l  e++s++ +l++  i +Gv l+s++  sF++igf +  ++ l++ 
  gene896|gene896|rna895|rna895  84 IGLSSISLRFTTLAFYTMVKSSSPVFILLFGFALGIENPSITFFLTIFTIGVGVFLTSIKNTSFDIIGFGTISLASLMAG 163
                                    ******************************999999******************************************** PP

                            TPT 159 lrnifsKkllkk...lkd...ldalnlfaiitilslllllPvallvegvlktpsllkstkvslkevllllllsgvlfhly 232
                                    +r  f   l+++   +k+   ++  +l   i++l ll++l v  l+e   +t   +++ +++l+++   +ll g l ++ 
  gene896|gene896|rna895|rna895 164 FRWAFVQYLIRNqevRKEgvfVTMRDLCLPISFLLLLISLHVEGLMEI--VTSRFFNTFDAALRNFGY-ILLCGTLSFML 240
                                    **********99554444665566666666666666666666666666..333333333344666665.55566677777 PP

                            TPT 233 nqvaymvLervspvthsvantvKrvvvIvlsvlvfknpvsllnaiGtavaivGvflYs 290
                                        +++++++  v  sva  vK  ++I  +++     +s ln  G  ++i+G+++Y+
  gene896|gene896|rna895|rna895 241 LCAEFSLVSETGVVFLSVAGIVKELIIIFYAIITKDIILSNLNYAGLGISIMGILVYN 298
                                    7889******************************9999*******************8 PP

>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  12.2   1.4e-06    0.0081       5     136 ..      13     141 ..       6     142 .. 0.91
   2 !    6.4  13.5    0.0016       9.7       7     136 ..     155     298 ..     149     299 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                           EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffy 84 
                                    +++l  +l + ++f+ls++++++  pl+ + ++ li ++  +  + l+++k    ++ +++   + ++l+++   +l  +
  gene896|gene896|rna895|rna895  13 YYILSLSLGYLTSFLLSRKTYNFSFPLFKASLQNLIHFLGASTALRLQREKA---PKPNYFGPSFPCALAGATDIGLSSI 89 
                                    5577777778889999999999999999999999999999988888888888...8889999999999************ PP

                           EamA  85 alkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    +l+ t+ ++ +++ s +Pvf+l+++++l  e+++++ +l i+ i +Gv+l++
  gene896|gene896|rna895|rna895  90 SLRFTTLAFYTMVKSSSPVFILLFGFALGIENPSITFFLTIFTIGVGVFLTS 141
                                    **************************************************87 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0016
                           EamA   7 allaalfwaiyfvlskillrkvspl...tltfvr..fliagillliiallkegkl.....aklslkd.....wllllllg 71 
                                    + la+l+ ++ + + ++l+r+ +      ++++r  +l  ++lll+i+l+ eg +     + ++  d     + ++ll g
  gene896|gene896|rna895|rna895 155 ISLASLMAGFRWAFVQYLIRNQEVRkegVFVTMRdlCLPISFLLLLISLHVEGLMeivtsRFFNTFDaalrnFGYILLCG 234
                                    55677777777777777766663333222222231133334444444444444443444433333334333377777777 PP

                           EamA  72 llgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    +l+++l  ++ f+++++t++ + s++  +  +++++++++     l+ + ++g++++++G+l+ +
  gene896|gene896|rna895|rna895 235 TLSFMLL-CAEFSLVSETGVVFLSVAGIVKELIIIFYAIITKDIILSNLNYAGLGISIMGILVYN 298
                                    7777777.788**************************************************9975 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.9   1.3e-05     0.081      87     162 ..     126     201 ..     122     242 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                        DUF1129  87 lllalfallfgilalfskkkqtasiGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlv 162
                                    ++l +f++ +g++    k+++   iG+ t+ l +l++G+   +v++l+ +++ +k+   +  r l+l ++++++l+
  gene896|gene896|rna895|rna895 126 FFLTIFTIGVGVFLTSIKNTSFDIIGFGTISLASLMAGFRWAFVQYLIRNQEVRKEGVFVTMRDLCLPISFLLLLI 201
                                    799999999999887767677777************************9853333222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2011.73
//
Query:       gene898|gene898|rna897|rna897  [L=268]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-33  115.8   0.0    3.3e-33  115.5   0.0    1.1  1  ATP_bind_1    Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
      0.041   13.6   0.0      0.066   12.9   0.0    1.4  1  AAA_24        AAA domain
      0.045   14.0   0.0      0.077   13.3   0.0    1.4  1  AAA_22        AAA domain
       0.06   12.7   0.1      0.093   12.0   0.1    1.2  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
       0.11   12.7   0.0        0.2   11.8   0.0    1.5  1  AAA_33        AAA domain
       0.12   12.3   0.0        0.2   11.6   0.0    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
       0.14   11.9   0.0       0.24   11.2   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
       0.14   12.5   0.4        1.4    9.4   0.4    2.4  1  RNA_helicase  RNA helicase
       0.17   12.0   0.1         22    5.2   0.0    2.5  2  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   1.6e-36   3.3e-33       1     238 [.       7     237 ..       7     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 1.6e-36
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresld 80 
                                    ++Gp+GsGK+t+v +   +l+ r  +++++NLDP++ +   e++  i  +      +e+ ++gpn ++   le + +++d
  gene898|gene898|rna897|rna897   7 IIGPPGSGKSTYVMSKKAWLSHR--NPYIINLDPGNCND-KEFDYSICSISPSLMYQERHNVGPNMSTKCILEEFYTRID 83 
                                    79***********9999999977..**********8642.2444455555555666777999*****************8 PP

                     ATP_bind_1  81 wl.deelekeeddyllfDtPGQielfthseslakiveeLes.efalvvvyLvDsqrltdptkfisgllsalsamlrlelP 158
                                    ++ +e++ +  d y+l+D PGQ+e+f  s+    i+  L+s  +++vvv+LvD  + ++  ++is+ +++   ++ le  
  gene898|gene898|rna897|rna897  84 EFfQENI-EGTDHYILLDFPGQVEFFISSDIPNSIIGYLKSnGYSVVVVNLVDLVFFSNDHSLISSYFISTLCLCLLESA 162
                                    8846666.7799*****************************999************************************ PP

                     ATP_bind_1 159 hvvvlnkfDllkek.lekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllslide 237
                                    +++v++k+D  k+  l++ le +  +e l++++     k kk  e++a+++ + +l     +l+ ++ +s+ +l  +id+
  gene898|gene898|rna897|rna897 163 QINVISKCDNWKKLgLKYSLEDIASLECLEEME-----KKKKIHEEMASFVLNQGLL-AYEVLDYDNPDSVLNLQVAIDK 236
                                    **********99446666666666555555544.....46799************99.9*******************99 PP

                     ATP_bind_1 238 a 238
                                    a
  gene898|gene898|rna897|rna897 237 A 237
                                    7 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.3e-05     0.066       6      71 ..       6     131 ..       1     141 [. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                         AAA_24   6 liyGpsgiGKTtlakel.....gpkplfidtekGlksldadkfpdie.....................swedfldevvel 59 
                                    +i+Gp+g+GK+t + +        +p +i+++ G  + +  ++  ++                      +e+f+  ++e+
  gene898|gene898|rna897|rna897   6 VIIGPPGSGKSTYVMSKkawlsHRNPYIINLDPGNCNDKEFDYSICSispslmyqerhnvgpnmstkcILEEFYTRIDEF 85 
                                    89*********988776679999********9986333333333333556666666666666665444334444444444 PP

                         AAA_24  60 ..................................aaeladyktlvi 71 
                                                                      + + ++y+++v+
  gene898|gene898|rna897|rna897  86 fqeniegtdhyilldfpgqveffissdipnsiigYLKSNGYSVVVV 131
                                    5555555555555555555555555566666655555555666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.077       9      61 ..       6      51 ..       2      95 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                         AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrell 61
                                   v++G++G+GK+t +   + +l         r +++    p+ ++ k++   ++
  gene898|gene898|rna897|rna897  6 VIIGPPGSGKSTYVMSKKAWLSH-------RNPYIINLDPGNCNDKEFDYSIC 51
                                   89***********9999999952.......44433333333335555555555 PP

>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.7e-05     0.093      71     142 ..     148     220 ..     138     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                                    H..HHHHHHHTCHTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHH CS
                   tRNA-synt_1b  71 a..ikaqlakgldpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLq 142
                                    +  i+ +  ++l+  +++v+   + +++l l + l+d+++l  l++m ++k++++++++   ++ g++ Y +L+
  gene898|gene898|rna897|rna897 148 SyfISTLCLCLLESAQINVISKCDNWKKLGLKYSLEDIASLECLEEMEKKKKIHEEMASF-VLNQGLLAYEVLD 220
                                    3456677789999999*******************************************5.79********996 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001       0.2       4      18 ..       7      21 ..       6     102 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                         AAA_33  4 lvGlpGsGKstlaer 18
                                   ++G+pGsGKst++ +
  gene898|gene898|rna897|rna897  7 IIGPPGSGKSTYVMS 21
                                   79*********9875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001       0.2       3      32 ..       6      36 ..       5      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                   EEE--SSSSHHHHHHHGGGGB.S--EEEEE- CS
                          AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvql 32
                                   +++GppG+gKs+ +++ +a l  r+  +++l
  gene898|gene898|rna897|rna897  6 VIIGPPGSGKSTYVMSKKAWLsHRNPYIINL 36
                                   589************9999998666666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.24      26      39 ..       6      19 ..       1      28 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                         AAA_29 26 lltGpsGsGKSTll 39
                                   +++Gp GsGKST +
  gene898|gene898|rna897|rna897  6 VIIGPPGSGKSTYV 19
                                   79**********75 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.4   0.00068       1.4       3      25 ..       7      28 ..       6     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00068
                   RNA_helicase  3 lyGpsgeGKStlakeLakallkk 25
                                   + Gp+g GKSt++ +  ka+l++
  gene898|gene898|rna897|rna897  7 IIGPPGSGKSTYVMS-KKAWLSH 28
                                   89**********998.5555544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.019        39       3      15 ..       6      18 ..       5      24 .. 0.90
   2 ?    5.2   0.0     0.011        22      37      86 ..      84     137 ..      68     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.019
                                   EEEESTTSSHHHH CS
                       MMR_HSR1  3 aivGrpNvGKStL 15
                                   +i+G p +GKSt 
  gene898|gene898|rna897|rna897  6 VIIGPPGSGKSTY 18
                                   69*********95 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                                    EEEEEEETT.EEEEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETT CS
                       MMR_HSR1  37 negrvklkg.keielvDtpGlie...gaseekglgkaflaleeadlillvvdas 86 
                                    ++++ +++g ++++l+D pG +e   +++  +++   ++++  + +++ +vd+ 
  gene898|gene898|rna897|rna897  84 EFFQENIEGtDHYILLDFPGQVEffiSSDIPNSIIGYLKSNGYSVVVVNLVDLV 137
                                    4444445566899*******7655444555555555555555577777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1719.93
//
Query:       gene899|gene899|rna898|rna898  [L=250]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-10   40.8   5.9    2.5e-10   40.3   5.9    1.2  1  RINGv     RING-variant domain
  ------ inclusion threshold ------
        1.6    8.7   6.3        2.6    7.9   5.4    1.8  2  Tmemb_9   TMEM9


Domain annotation for each model (and alignments):
>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   5.9   2.8e-14   2.5e-10       1      48 []      36      89 ..      36      89 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.8e-14
                                   ETTTTEE-SSSS...--B-SS--STCCCSB-HHHHHHHHHH...TCT-SB-TTT CS
                          RINGv  1 CriCleeeeese...plispCkCrGslklvHesClekWlde...keantqCeiC 48
                                   C+iC+   +  +   +lispC+C+Gs++lvH  Cl++W       ++ ++Ce+C
  gene899|gene899|rna898|rna898 36 CKICYSLTNPINmkdDLISPCNCKGSIGLVHGVCLKMWRYRgkrIKDIRKCEQC 89
                                   ******999999999***********************999766666777**** PP

>> Tmemb_9  TMEM9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.39   3.5e+03      26      41 ..      45      59 ..      31      65 .. 0.71
   2 ?    7.9   5.4   0.00029       2.6      30      78 ..      81     129 ..      54     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.39
                        Tmemb_9 26 evkgkelefcprCeCk 41
                                   +++ k+ +++  C+Ck
  gene899|gene899|rna898|rna898 45 PINMKD-DLISPCNCK 59
                                   455554.677778887 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00029
                        Tmemb_9  30 kelefcprCeCkyesRntttikvvviivivvislLviYmlflllldpll 78 
                                    k++  c +C+  y+  n  + + +v+ + +vi lL+iY++  +l  +l+
  gene899|gene899|rna898|rna898  81 KDIRKCEQCSSFYKLDNEIVPHRIVVSLATVIILLLIYLVSTILFKSLI 129
                                    56668***************9*******************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1639.63
//
Query:       gene900|gene900|rna899|rna899  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1159.10
//
Query:       gene9|gene9|rna9|rna9  [L=158]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-05   22.5   1.5    3.6e-05   22.4   1.5    1.0  1  Mpp10     Mpp10 protein


Domain annotation for each model (and alignments):
>> Mpp10  Mpp10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.5     2e-09   3.6e-05      43     152 ..      14     120 ..       3     158 .] 0.57

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2e-09
                  Mpp10  43 kspLeelvvegfDeeqiWqqlelqneavleellkkiskllakkeklklldeeeeeeseeseeeeeeeeeeeeeeeeeeeeeeeeeeek 130
                            k   +el+vegf  eqi+ q+e   ++++e+   +is+l  k +kl+l ++ +    ++se++++e+ ++++ee    e+ e e+   
  gene9|gene9|rna9|rna9  14 KYGYQELYVEGFTPEQIYYQIEDLCNSIVERSDVAISRLYPKYQKLSLQNDGKVCCGKSSEDSQKETIADQDEE-IPPESIEIEKC-- 98 
                            34479*************************************98877655555444444444444444444444.33333333311.. PP

                  Mpp10 131 eeseekeeeeesekeeeeeded 152
                            ++  + +++e++ +++ +++e+
  gene9|gene9|rna9|rna9  99 SSVGRLHKDESLGSSSFDSSEN 120
                            1111222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 950.83
//
Query:       gene90|gene90|rna90|rna90  [L=71]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-22   79.7  13.1    1.7e-22   79.4  13.1    1.1  1  zf-rbx1       RING-H2 zinc finger domain
    6.5e-14   51.8   7.8    7.1e-14   51.6   7.8    1.1  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
    7.9e-08   32.5  14.0    3.6e-06   27.2  14.0    2.1  1  zf-RING_2     Ring finger domain
    3.3e-06   26.8   3.3    3.3e-06   26.8   3.3    2.3  2  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    0.00027   20.8  12.2     0.0023   17.8  12.2    2.1  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
      0.033   13.9  11.9        1.3    8.8  11.9    2.3  1  zf-RING_11    RING-like zinc finger
      0.073   12.7  15.6         12    5.6  15.6    2.2  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
       0.13   12.3   8.2       0.46   10.5   8.2    1.9  1  zf-RING_UBOX  RING-type zinc-finger
       0.28   11.4  10.9       0.46   10.7  10.9    1.5  1  FANCL_C       FANCL C-terminal domain
        0.3   11.0  12.0       0.86    9.5   5.4    2.3  2  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
       0.81    9.7  12.8         14    5.7  12.9    2.3  2  zf-RING_5     zinc-RING finger domain
       0.96    9.8  13.0        7.7    6.9  13.0    2.1  1  zf-RING-like  RING-like domain
        1.7    8.6   9.6        1.9    8.4   7.7    2.1  2  DUF3797       Domain of unknown function (DUF3797)
        5.3    7.2  15.1          1    9.5   6.0    2.1  2  PHD_4         PHD-finger


Domain annotation for each model (and alignments):
>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.4  13.1   1.4e-25   1.7e-22       1      54 [.       4      59 ..       4      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 1.4e-25
                    zf-rbx1  1 dtCaiCrneleeacieckapgdee..cpvvlGeCgHaFHlhCiskWlktrkvCPlc 54
                               +tCaiCrn+++++c+ec++   ++  c+v +G C+HaFH+hCi++Wl++++vCPl+
  gene90|gene90|rna90|rna90  4 ETCAICRNHIMDTCVECQNGVISNdeCKVSWGICNHAFHTHCITRWLSSKNVCPLD 59
                               69****************86544445*****************************9 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   7.8   5.6e-17   7.1e-14      22      82 ..       4      64 ..       1      67 [. 0.89

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 5.6e-17
                               SB-TTT-SBTTS--TTCS...TTTTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB-- CS
                 zf-ANAPC11 22 dvcGicrvsfdGtcpsck...fpGddcplvlGkckhnfhlhcilkwletetskglcpmcrqtfk 82
                               ++c icr +   tc +c+   +  d+c + +G c+h+fh+hci++wl+   sk+ cp++ ++++
  gene90|gene90|rna90|rna90  4 ETCAICRNHIMDTCVECQngvISNDECKVSWGICNHAFHTHCITRWLS---SKNVCPLDTKKWV 64
                               79***************8443579***********************5...8899***999886 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  14.0   2.8e-09   3.6e-06       1      42 [.      15      58 ..       4      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.8e-09
                  zf-RING_2  1 deCpICleelssadsvlll..pCgHvfhreClerwlrssstCPl 42
                               d+C+ C++ + s+d++ +    C+H fh +C++rwl s++ CPl
  gene90|gene90|rna90|rna90 15 DTCVECQNGVISNDECKVSwgICNHAFHTHCITRWLSSKNVCPL 58
                               5799999999888888755435*********************7 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   4.9       0.2   2.5e+02       2      19 ..       6      21 ..       5      34 .. 0.85
   2 !   26.8   3.3   2.5e-09   3.3e-06      18      39 ..      37      58 ..      27      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                 zf-C3HC4_2  2 CpiCldmlkdpsvvtpCg 19
                               C+iC + + d  +  +C+
  gene90|gene90|rna90|rna90  6 CAICRNHIMD--TCVECQ 21
                               9****99999..477776 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 2.5e-09
                 zf-C3HC4_2 18 CgHvfCqkCilrsLeekneCPl 39
                               C+H f+  Ci r+L++kn CPl
  gene90|gene90|rna90|rna90 37 CNHAFHTHCITRWLSSKNVCPL 58
                               *********************7 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8  12.2   1.8e-06    0.0023       1      40 [.       6      58 ..       6      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                               -TTT-S--SS-E................E-TTS--B-CHHHHHHHHCTSSB--TT CS
                   zf-C3HC4  1 CpiCleeakepn...............elleCkHsfCskCirkilksrkkvkCPl 40
                               C+iC + +++++                   C+H+f+++Ci+++l+ +k+v CPl
  gene90|gene90|rna90|rna90  6 CAICRNHIMDTCvecqngvisndeckvSWGICNHAFHTHCITRWLS-SKNV-CPL 58
                               9**********9**********999998899***************.6666.*96 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  11.9     0.001       1.3       5      29 .]      20      46 ..       5      46 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                 zf-RING_11  5 CLeefkpgqalfilp..CsHtFHfkCI 29
                               C + +  +++  +    C+H+FH +CI
  gene90|gene90|rna90|rna90 20 CQNGVISNDECKVSWgiCNHAFHTHCI 46
                               44555544544444378*********9 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  15.6    0.0095        12       5      46 ..      15      57 ..       1      59 [. 0.68

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0095
               Zn_ribbon_17  5 ksCayCelav...kgrvvlcgvCeHvlHasCarewfenddlaeCp 46
                                +C+ C+  v       v  g C+H  H+ C+  w++ ++  +Cp
  gene90|gene90|rna90|rna90 15 DTCVECQNGVisnDECKVSWGICNHAFHTHCITRWLSSKN--VCP 57
                               4455555333110223344468****************99..998 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.2   0.00036      0.46       1      39 []       6      57 ..       6      57 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
               zf-RING_UBOX  1 CpICle.lft............dP.lvlp...CGHtFCreClwelskslegafkCP 39
                               C IC++  ++            d  +v +   C H F+ +C+   +++l+ +  CP
  gene90|gene90|rna90|rna90  6 CAICRNhIMDtcvecqngvisnDEcKV-SwgiCNHAFHTHCI---TRWLSSKNVCP 57
                               778885244466665555555422333.1445**********...88999999998 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  10.9   0.00036      0.46       4      44 ..       5      53 ..       2      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                               S-SSS--SS-......TT-----B--S-T..T----B-SGGGHHHHHHH CS
                    FANCL_C  4 eCgiCyayrl......dsgevpdisCdne..kCnkkfHsaCLkeWlrsl 44
                                C iC ++ +      ++g +++  C      Cn+ fH++C++ Wl s 
  gene90|gene90|rna90|rna90  5 TCAICRNHIMdtcvecQNGVISNDECKVSwgICNHAFHTHCITRWLSSK 53
                               69999998887888888999999999875336**************986 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4    0.0068       8.7      38      48 ..       4      14 ..       1      16 [. 0.77
   2 ?    9.5   5.4   0.00067      0.86       3      42 ..      15      58 ..      13      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0068
                               -B-TTT--B-- CS
                 zf-C3HC4_3 38 kkCpiCrrpie 48
                               ++C iCr +i 
  gene90|gene90|rna90|rna90  4 ETCAICRNHIM 14
                               68999999885 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00067
                               SB-TTTSS.....SBS-EEETTEEEEEE-HHHHHHHHHTT-B-TT CS
                 zf-C3HC4_3  3 eeCviCle.....rprnvvllpCgHlvlCeeCaekllkrkkkCpi 42
                               ++Cv C++      + +v    C+H  +  +C +++l++k+ Cp+
  gene90|gene90|rna90|rna90 15 DTCVECQNgvisnDECKVSWGICNHA-FHTHCITRWLSSKNVCPL 58
                               5899999977764477788888****.99***************8 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.4      0.14   1.9e+02      37      43 ..       4      10 ..       1      11 [. 0.77
   2 ?    5.7  12.9     0.011        14       2      41 ..       6      58 ..       5      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
                  zf-RING_5 37 avCpiCr 43
                                +C iCr
  gene90|gene90|rna90|rna90  4 ETCAICR 10
                               6899998 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                  zf-RING_5  2 CnkCfekl.............skeekfyltsCgHifCekClkkllekeavCpi 41
                               C +C++++             ++e k+    C H f+ +C+++ l +++vCp+
  gene90|gene90|rna90|rna90  6 CAICRNHImdtcvecqngvisNDECKVSWGICNHAFHTHCITRWLSSKNVCPL 58
                               666666666666666666686666669999***************9*****96 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  13.0     0.006       7.7      10      41 ..      16      57 ..       6      58 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.006
               zf-RING-like 10 qGvrC.....snesCn.......vrlHvdCfqhyirthsskkCp 41
                                +v C     sn++C+        ++H +C+++ ++++  + Cp
  gene90|gene90|rna90|rna90 16 TCVECqngviSNDECKvswgicnHAFHTHCITRWLSSK--NVCP 57
                               55555555554555555555555**********99443..3687 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.7    0.0015       1.9      15      42 ..      16      45 ..       3      49 .. 0.92
   2 ?   -1.9   0.0       2.5   3.2e+03       6      13 ..      55      63 ..      52      68 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                    DUF3797 15 qCPeCgNnkvlNsegkv..iieddtfyreC 42
                                C eC+N  + N e kv   i +++f   C
  gene90|gene90|rna90|rna90 16 TCVECQNGVISNDECKVswGICNHAFHTHC 45
                               599**************9999******999 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                    DUF3797  6 ivkLdek.Y 13
                               + +Ld k +
  gene90|gene90|rna90|rna90 55 VCPLDTKkW 63
                               667776653 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.0    0.0008         1      32      62 ..       5      34 ..       1      36 [. 0.83
   2 ?    3.8   1.6     0.048        61      35      48 ..      36      49 ..      35      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
                      PHD_4 32 eCsvCyeivHpeClkekegeg.vvnedlpnsW 62
                               +C++C +++   C++ +  +g + n++   sW
  gene90|gene90|rna90|rna90  5 TCAICRNHIMDTCVECQ--NGvISNDECKVSW 34
                               7*************994..4647888999999 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.048
                      PHD_4 35 vCyeivHpeClkek 48
                               +C+   H +C+++ 
  gene90|gene90|rna90|rna90 36 ICNHAFHTHCITRW 49
                               8**********874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.49u 0.34s 00:00:00.83 Elapsed: 00:00:00.54
# Mc/sec: 397.03
//
Query:       gene901|gene901|rna900|rna900  [L=317]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-11   44.4   0.4    1.5e-10   41.0   0.4    2.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.4   8.3e-15   1.5e-10     173     299 ..     133     252 ..       3     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 8.3e-15
                Diphthamide_syn 173 pvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkeagkksylvlvgelnpa 252
                                     +y+y+  s   + e+ d  ++l+ + ++ ++++d + ++ii+ +     + el++++++ l ++ k++yl++++ l+ +
  gene901|gene901|rna900|rna900 133 YFYKYNAESF-YNLERRDRMEYLSSKCNKGRRIRDLQIFAIIFTSR---AYEELARSIRRALVSRRKNAYLLFLKDLSYE 208
                                    3556666664.6699999*************************886...5999*************************** PP

                Diphthamide_syn 253 kLanfaeidafVlvaCprlsid.dgkeFekPvltpyElevalgerewt 299
                                    ++  ++  ++ V+v Cp      d    + Pv+tp+E+e+a++  ew+
  gene901|gene901|rna900|rna900 209 RMITIEGTECIVVVDCPFFECTlD---LHIPVVTPFEVEYAFS-GEWK 252
                                    *****99**********9988734...57*************9.6664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1882.96
//
Query:       gene902|gene902|rna901|rna901  [L=175]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-08   34.7   0.2    2.8e-08   33.8   0.2    1.5  1  DnaJ      DnaJ domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.2   1.5e-12   2.8e-08       1      63 []      36      94 ..      36      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.5e-12
                                   HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                           DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                   +yYe+ gvs++as + Ikk Y+k+++  HP   p+ ++ e++   ++eAy++L++  k+++YD
  gene902|gene902|rna901|rna901 36 TYYEVFGVSENASIASIKKLYQKMMK--HPSPIPGIEKREDAVALLTEAYNILKN--KKSAYD 94
                                   69*********************876..9**9*9*******************99..777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1101.98
//
Query:       gene903|gene903|rna902|rna902  [L=148]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.4   0.1      0.053   13.3   0.1    1.7  2  EcoRII-N  Restriction endonuclease EcoRII, N-terminal


Domain annotation for each model (and alignments):
>> EcoRII-N  Restriction endonuclease EcoRII, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.9e-06     0.053      36      76 ..      36      76 ..      16      87 .. 0.91
   2 ?   -2.0   0.0      0.15   2.7e+03      99     124 ..     110     135 ..     100     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-06
                       EcoRII-N 36 tlFpsinrteeenpsvslklkisshsveesevraiyYnnrl 76
                                   t F ++n+t+e+n ++s++++  +  +e  +v+ i Yn++ 
  gene903|gene903|rna902|rna902 36 TNFSDVNHTHETNGKCSMSVRDLDECTESVQVKNIEYNSQK 76
                                   5699**********************9***********864 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.15
                       EcoRII-N  99 pentGaLlllafkkskesdsllvevw 124
                                    +   G L l+a   ++ ++s   +++
  gene903|gene903|rna902|rna902 110 TSFCGILKLIATFDYQAANSVAAKIF 135
                                    56677777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 999.40
//
Query:       gene904|gene904|rna903|rna903  [L=6]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (6 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                         8  (0.000446204); expected 358.6 (0.02)
Passed bias filter:                        3  (0.000167327); expected 358.6 (0.02)
Passed Vit filter:                         0  (0); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.42
# Mc/sec: 42.40
//
Query:       gene905|gene905|rna904|rna904  [L=188]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-07   29.0   0.1    1.2e-06   28.4   0.1    1.3  1  DUF4539       Domain of unknown function (DUF4539)
  ------ inclusion threshold ------
       0.14   11.8   0.1        3.6    7.3   0.0    2.1  2  DDE_Tnp_ISL3  Transposase


Domain annotation for each model (and alignments):
>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   1.4e-10   1.2e-06       5      83 ..     115     188 .]     110     188 .] 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.4e-10
                        DUF4539   5 qlvviiksintlnslgdalvtlkDptGeidgtihrkvleeygkdlsvGavllLkqVsvfspsrrahyLnItlsnivkif 83 
                                    ++++iik++++   +  a + l D++G+i g+    v++e+   l+vG+++lL + s+ + +    +LnI+ +ni k++
  gene905|gene905|rna904|rna904 115 VFAGIIKKLSVFGAD-TACLELVDESGSICGSCPLAVVDEF--GLKVGTIVLLSKCSLWKIN--GNHLNIVGANIRKVI 188
                                    45789****555555.8************************..689****************..99**********996 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.011        98     171     210 ..       1      40 [.       1      42 [. 0.93
   2 ?    7.3   0.0    0.0004       3.6      84     114 ..      78     108 ..      73     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.011
                   DDE_Tnp_ISL3 171 lkewiekaersglkefkklaktlknhreeIlnyfdsrlsn 210
                                    ++e+i+++++++ ke ++++ t++++   I n++ ++lsn
  gene905|gene905|rna904|rna904   1 MDELISELRSTQAKEERQIGSTVNTNDLPISNATSKGLSN 40 
                                    57899999***************************99998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0004
                   DDE_Tnp_ISL3  84 FHvvklanealdevRrreqkelreekrkklk 114
                                    FH++kl  +al +v+++ q e+  +k k +k
  gene905|gene905|rna904|rna904  78 FHIMKLDFDALAQVKKENQVEIGIDKIKCCK 108
                                    ******************9998444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1176.67
//
Query:       gene906|gene906|rna905|rna905  [L=174]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-24   84.7   0.1    8.6e-24   84.1   0.1    1.2  1  Ferritin       Ferritin-like domain
    0.00025   21.5   0.4    0.00038   20.9   0.4    1.3  1  Rubrerythrin   Rubrerythrin
  ------ inclusion threshold ------
      0.015   15.5   0.2      0.023   14.9   0.2    1.2  1  Ferritin_2     Ferritin-like domain
       0.11   12.0   0.0       0.25   10.8   0.0    1.5  1  Phenol_Hydrox  Methane/Phenol/Toluene Hydroxylase


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.1   1.9e-27   8.6e-24       3     136 ..      20     152 ..      19     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.9e-27
                                    HHHHHHHHHHHHHHHHHHHHHHHH..STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS..C CS
                       Ferritin   3 aLneqladeltaayqylamawyvk..gpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke..f 78 
                                    +L +ql  e++a y y a+a+++   ++ l+gl  ff+e++ +e eha++++++++++        +e+ +ieap+   +
  gene906|gene906|rna905|rna905  20 LLSSQLLLEYNAFYFYAACAAHFGnpNVCLKGLERFFKESSLDENEHAQRIINFMNMRSL-----NIEFRTIEAPDIkrY 94 
                                    6899********************99999*******************************.....999999999999889 PP

                                    SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  79 gsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleall 136
                                    +++ ++l+a  e e++v +++  + e+a+++gD   ++f+edf++eq++++ e+++l 
  gene906|gene906|rna905|rna905  95 EKTSDILKASKEFEQTVLNNILTVSEIAAKAGDGSIVEFFEDFIAEQVKSISEFNDLY 152
                                    9*****************************************************9875 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.4   8.4e-08   0.00038       7     123 ..      25     138 ..      20     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.4e-08
                                    HHHHHHHHHHHHHHHHCHHTT...-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH..B.SSBBS-------TTGGHH CS
                   Rubrerythrin   7 iagEssarrlYkelaekakeg...ypqiaelFeelAeeEreHakilnklleklepele.levkekvreyaeakpkfltta 82 
                                    +  E+ a+ +Y + a ++ +    ++ ++++F+e + +E eHa++++++++ + ++ e   +++  ++ +e + ++    
  gene906|gene906|rna905|rna905  25 LLLEYNAFYFYAACAAHFGNPnvcLKGLERFFKESSLDENEHAQRIINFMNMRSLNIEfRTIEAPDIKRYEKTSDI---- 100
                                    567999999999999999843112456789**************************99444444444444444444.... PP

                                    HHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHH CS
                   Rubrerythrin  83 knLeeaiegayaeeeemyrfyeelaekegneeakklfkkla 123
                                      L++  e + ++  ++  + +e+a k+g+ ++ ++f++ +
  gene906|gene906|rna905|rna905 101 --LKASKEFEQTVLNNI-LTVSEIAAKAGDGSIVEFFEDFI 138
                                    ..444444444444444.56677777777777777777655 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   5.1e-06     0.023       6      96 ..      21     111 ..      19     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.1e-06
                     Ferritin_2   6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaavakptfdf......afdpf 79 
                                    L+  l lEy +  fY+a ++ ++    +   +   ++++e   +e +H++ + +  +    +++++++f      + + +
  gene906|gene906|rna905|rna905  21 LSSQLLLEYNAFYFYAACAAHFGN--PNVCLKGLERFFKESSLDENEHAQRIINFMN----MRSLNIEFrtieapDIKRY 94 
                                    566799************998876..6888889999*******************95....677888888888888999* PP

                     Ferritin_2  80 adeksflalaavlEdvg 96 
                                    ++  ++l++++ +E++ 
  gene906|gene906|rna905|rna905  95 EKTSDILKASKEFEQTV 111
                                    **************986 PP

>> Phenol_Hydrox  Methane/Phenol/Toluene Hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.7e-05      0.25      62     156 ..       7     107 ..       4     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.7e-05
                                    GGS-HHHHHIIIIHHHHHHHHHHHHHHTTHHHHHH-SSH.....HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTT.-- CS
                  Phenol_Hydrox  62 erldpawrevlkkhlgalrhleygaqmaeaylaryapgt.....airnaalfqalDelrhaqiltylglelakavdgafd 136
                                    ++l+++w++++  +l+    ley a+   a +a+ + ++     +++  +   +lDe  haq++++++ + + +++ +  
  gene906|gene906|rna905|rna905   7 QALTDEWKAEAGLLLSSQLLLEYNAFYFYAACAAHFGNPnvclkGLERFFKESSLDENEHAQRIINFMNMRSLNIEFRTI 86 
                                    67999*********************999999998888622222568888899****************99999887788 PP

                                    --SH.HHHHHH-STTHHHHHH CS
                  Phenol_Hydrox 137 gale.kaawlndpawqglRel 156
                                    +a + k++ +++ ++++ +e+
  gene906|gene906|rna905|rna905  87 EAPDiKRYEKTSDILKASKEF 107
                                    888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1205.37
//
Query:       gene907|gene907|rna906|rna906  [L=648]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-26   93.7   0.1    2.5e-26   92.4   0.1    1.7  1  NFACT-R_1     NFACT protein RNA binding domain
    6.1e-26   91.2   9.4    8.9e-26   90.7   9.4    1.2  1  FbpA          Fibronectin-binding protein A N-terminus (FbpA)
    1.5e-15   57.0   0.0    1.5e-15   57.0   0.0    3.2  4  NFACT-C       NFACT protein C-terminal domain
      0.004   17.3   0.2      0.055   13.7   0.0    2.7  2  NFACT-R_2     NFACT protein RNA binding domain
  ------ inclusion threshold ------
       0.17   11.6   0.1       0.17   11.6   0.1    2.7  3  Hormone_1     Somatotropin hormone family
       0.25   11.4  14.8       0.13   12.3   3.1    3.5  4  P4Ha_N        Prolyl 4-Hydroxylase alpha-subunit, N-terminal 
          5    7.5  11.6       0.63   10.4   1.1    3.5  4  MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/


Domain annotation for each model (and alignments):
>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.4   0.1   9.8e-30   2.5e-26       1     109 []     421     526 ..     421     526 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 9.8e-30
                      NFACT-R_1   1 kvfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gn 79 
                                    k+++F ssdg lvi+Gk++q+ne+l+kk+le +d++fh d+++s++++++       + +++++eeaa +a ++S+  ++
  gene907|gene907|rna906|rna906 421 KFHFFFSSDGILVIGGKNAQQNEILVKKHLEPTDLYFHGDMHGSSSIIVK-------KPTQKTIEEAASMALCMSKCwEA 493
                                    8*************************************************.......44568***************999 PP

                      NFACT-R_1  80 klssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                    ++    v+yv+ +++sktap    l++Gs+++kg
  gene907|gene907|rna906|rna906 494 NV-VSPVWYVYGEQVSKTAPsgeyLTKGSFMIKG 526
                                    99.9****************************97 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   9.4   3.5e-29   8.9e-26       2     410 ..       7     403 ..       6     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 3.5e-29
                                    HHHHHHHHHHHHHHHTTXEEEEEEEEETTEEEEEEEETTEEEE.EEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHH CS
                           FbpA   2 glvlaavvaELqkellggridkiyqpekdelvltlranrgrhk.LllsahpsyarihltekpkenpkeppnFcmlLRkyL 80 
                                     l+++a+v+EL+ +l+g  i++ y   ++ +++++     +++ Ll++    + rihlt+++    ++ ++Fc++LR++ 
  gene907|gene907|rna906|rna906   7 FLDIRATVNELRPRLVGKFIQNFYTTSQRIIYIKFS----NKDiLLVEP---GVRIHLTQEHD---MDISHFCKILRRKA 76 
                                    589*********************************....4444*****...******99988...999*********** PP

                                    TTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXX CS
                           FbpA  81 kgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYel 160
                                    +  ++v+i q gfdR+v l++ ++         ++++E +   +Ni++v e++kI + ++ v+        i++g++Y++
  gene907|gene907|rna906|rna906  77 RRDKVVDIYQCGFDRVVVLELGRQ---------KIVFEFFSG-GNILIV-EDGKISEIFRIVKDL-----DIVKGSEYVF 140
                                    ************************.........9********.******.588*********665.....9********* PP

                                    SXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXS....SSH...............HHHHH CS
                           FbpA 161 PpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeellerag....ldketsakelseedlerlyealq 236
                                          l++  + + +++k+       +l++ Lv+++  l++l ++  ++ +      ++  ++ke  ++ +e+ +++++
  gene907|gene907|rna906|rna906 141 NNVDFDLSIDAFVK-NDLKDF-----LPLDHLLVDKV--LGELGSRIKANPMDmkksAENGIPIKEDVKNVFEEFMKEFK 212
                                    99977777776666.677777.....46788888887..55555554454444000134555555555555555555555 PP

                                    HHHTXXX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX..--SHHHHHHHHHHHHHHHHHH CS
                           FbpA 237 elleeleeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkae..rdrveqkrsdlekrvenelek 314
                                    + +e+++       +++++ kp+++ ++++        + f+++++a + +++++ +  r+  e+k  +++kr en ++ 
  gene907|gene907|rna906|rna906 213 KKMEDIQ---GYGGVIIEKGKPSNLIPFKIDG-----ARDFSTFNDAAEFFFQNRKKfgRNDRESKVDKVRKRQENYMKE 284
                                    5555555...5567788888999999997765.....389************9877622566667888999999999999 PP

                                    HHHHHHHHHHHHHCCGGH.HHHHCCHH-----------------------..--........................-- CS
                           FbpA 315 lekklkklekelekaeka.enyrligelltaylyaikkgmsevelenyyde.ge........................ev 368
                                     e++++ ++k++e  e+  + +++i ++++ +    k++  + + e++ ++ ++                        + 
  gene907|gene907|rna906|rna906 285 MEQERQSYRKKAELLEENaDFVNKILDIFKIVK---KNKVRWTDFEKFREQeNKkgneiskaivktdfishtctialeGE 361
                                    999999999999987765266677777777666...778999999999997644899******************99999 PP

                                    -------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FbpA 369 tIpLdprkspsenAqkyfkkykKlkraveaveeqieetkeel 410
                                    +I++d + s  +n  ++++k kKl++++++    +ee+ +++
  gene907|gene907|rna906|rna906 362 EIQIDFETSLFSNISRFYQKNKKLEEKIKKTRDSLEEVLKKV 403
                                    *********************************999987766 PP

>> NFACT-C  NFACT protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.7      0.77     2e+03      70      92 ..     266     288 ..     245     324 .. 0.61
   2 ?   -2.4   0.1       1.8   4.5e+03      73      92 ..     328     347 ..     291     356 .. 0.52
   3 ?   -3.3   0.1       3.3   8.4e+03      67      89 ..     384     403 ..     371     413 .. 0.48
   4 !   57.0   0.0     6e-19   1.5e-15      15     105 ..     571     646 ..     558     647 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.77
                        NFACT-C  70 ekeedkeklwprekelikalkee 92 
                                    ++e++ +k+++r+++ +k++++e
  gene907|gene907|rna906|rna906 266 DRESKVDKVRKRQENYMKEMEQE 288
                                    33333455666666666665544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.8
                        NFACT-C  73 edkeklwprekelikalkee 92 
                                    + +e+ +++ +e+ ka+ ++
  gene907|gene907|rna906|rna906 328 KFREQENKKGNEISKAIVKT 347
                                    11334444445555555555 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.3
                        NFACT-C  67 kvdekeedkeklwprekelikal 89 
                                    k +e   + +k+++  +e++k++
  gene907|gene907|rna906|rna906 384 KLEE---KIKKTRDSLEEVLKKV 403
                                    2222...2233333344444444 PP

  == domain 4  score: 57.0 bits;  conditional E-value: 6e-19
                        NFACT-C  15 plpeDeileaipvcAPyaaLqkykYkvKlqPGsvKkGkavkeilekflkkkkkvdekeedkeklwprekelikalkeeel 94 
                                    p ++ ei++ +pvc+P++ +++ykYkv+l PG  KkGk ++ei ++f+              ++ ++ek  ++++  ee 
  gene907|gene907|rna906|rna906 571 P-EGMEIVHSMPVCGPWSVISTYKYKVRLVPGREKKGKLIQEISKRFIG-------------QAPDNEKSYVRSISVEEY 636
                                    4.3568999****************************************.............445567777777777777 PP

                        NFACT-C  95 vntlpvgkvkv 105
                                    +n++  g+v++
  gene907|gene907|rna906|rna906 637 INVMF-GNVRI 646
                                    77777.77776 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.4      0.48   1.2e+03      18      85 ..     331     395 ..     330     411 .. 0.58
   2 !   13.7   0.0   2.1e-05     0.055       6      76 ..     427     497 ..     423     514 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.48
                      NFACT-R_2  18 eeEnkflkgllkkdfvslrakshkGplvlidgels.eedlelaarivarYskgkeeeevevkvkkkege 85 
                                    e+Enk+ +++ +k +v+    sh+  ++l  +e++ + +  l ++i   Y k k   ++e k+kk++++
  gene907|gene907|rna906|rna906 331 EQENKKGNEI-SKAIVKTDFISHTCTIALEGEEIQiDFETSLFSNISRFYQKNK---KLEEKIKKTRDS 395
                                    5666666666.7777777777888888877556664556666667766666533...333333344343 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.1e-05
                      NFACT-R_2   6 lsekaklIvgReeeEnkflkgll..kkdfvslrakshkGplvlidgelseedlelaarivarYskgkeeeeve 76 
                                     s+++ +I g++++ n+ l +      d++     +++G+  +i  +++++++e aa++++  sk  e++ v+
  gene907|gene907|rna906|rna906 427 SSDGILVIGGKNAQQNEILVKKHlePTDLY--FHGDMHGSSSIIVKKPTQKTIEEAASMALCMSKCWEANVVS 497
                                    455666788999999*99977755344444..556777777777779*************9999988877765 PP

>> Hormone_1  Somatotropin hormone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.88   2.3e+03     119     153 ..     179     213 ..     165     220 .. 0.60
   2 ?   -1.1   1.0      0.51   1.3e+03     116     149 ..     282     314 ..     270     338 .. 0.47
   3 ?   11.6   0.1   6.7e-05      0.17     122     175 ..     374     428 ..     367     430 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.88
                                    GGSSS------TTTGGGHHHHHHHHHHHHHHHH-- CS
                      Hormone_1 119 mkevsetilskakeieeklkeLlegierilskvev 153
                                    +k+++ ++ ++a++     ++++++ e+ ++  ++
  gene907|gene907|rna906|rna906 179 IKANPMDMKKSAENGIPIKEDVKNVFEEFMKEFKK 213
                                    56666666666666555555555555555554442 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.51
                                    ..GGGSSS------TTTGGGHHHHHHHHHHHHHH CS
                      Hormone_1 116 lssmkevsetilskakeieeklkeLlegierils 149
                                    +++m++  +++++ka+ +ee+  +  + i  i++
  gene907|gene907|rna906|rna906 282 MKEMEQERQSYRKKAELLEEN-ADFVNKILDIFK 314
                                    344444444444444433332.222333333333 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 6.7e-05
                                    SS------TTTGGGHHHHHHHHHHHHHHHH----------------.---..--- CS
                      Hormone_1 122 vsetilskakeieeklkeLlegierilskvevpverkekeekpaws.klssLkss 175
                                    +  ++ +k k++eek+k+ ++ +e++l+kv  +ve k+  +  +w+ k++++ ss
  gene907|gene907|rna906|rna906 374 NISRFYQKNKKLEEKIKKTRDSLEEVLKKVAPKVETKKVTRALYWFeKFHFFFSS 428
                                    55678899***********************999999988888886156666655 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.089   2.3e+02      52     112 ..     150     205 ..     123     219 .. 0.74
   2 ?   12.3   3.1     5e-05      0.13      25      89 ..     266     338 ..     261     351 .. 0.72
   3 ?    3.8   0.4     0.021        53       9      47 ..     365     404 ..     360     420 .. 0.81
   4 ?   -3.8   0.1       4.7   1.2e+04      30      56 ..     547     569 ..     543     571 .. 0.46

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.089
                         P4Ha_N  52 eeylsnPlnaFklikRltsdWeeleklleeseseelieqlealkkrkes.lPteeDlegaak 112
                                    + +++n l+ F+ + +l +d     k+l  + +++ +++ +++kk+ e+ +P +eD++ + +
  gene907|gene907|rna906|rna906 150 DAFVKNDLKDFLPLDHLLVD-----KVLG-ELGSRIKANPMDMKKSAENgIPIKEDVKNVFE 205
                                    66788888888888888888.....2332.23333334445688888899999999987665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5e-05
                         P4Ha_N  25 eeekkleklkrfleeleeehesakedkee..........ylsnPlnaFklikRltsdWeeleklleeseseelie 89 
                                    + e+k++k+++  e++ +e+e+++++ ++          ++++ l+ Fk++k+ ++ W+++ek+ e++++++  +
  gene907|gene907|rna906|rna906 266 DRESKVDKVRKRQENYMKEMEQERQSYRKkaelleenadFVNKILDIFKIVKKNKVRWTDFEKFREQENKKG--N 338
                                    5677777777755555555544444433344456677889999*********************99877766..3 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.021
                         P4Ha_N   9 lklErelveeLesyieeeekkleklkrfleeleeehes.a 47 
                                    +++E  l++++ ++ ++++k  ek+k+  ++lee  ++ a
  gene907|gene907|rna906|rna906 365 IDFETSLFSNISRFYQKNKKLEEKIKKTRDSLEEVLKKvA 404
                                    6889999999999999999999999999999999886633 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 4.7
                         P4Ha_N  30 leklkrfleeleeehesakedkeeyls 56 
                                    l+++++ +e+++  +    ++ ++++s
  gene907|gene907|rna906|rna906 547 LKEIEEEIEDMNIDE----KENHKFVS 569
                                    444555555544433....23344555 PP

>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.3   3.4e+03      44      64 ..     192     215 ..     168     222 .. 0.69
   2 ?    0.5   2.2      0.29   7.5e+02      49      77 ..     271     297 ..     257     308 .. 0.53
   3 ?   10.4   1.1   0.00025      0.63      32      84 ..     375     424 ..     366     425 .. 0.84
   4 ?   -2.0   0.0       1.8   4.5e+03      21      37 ..     601     618 ..     592     631 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                   MADF_DNA_bdg  44 e...ckkkwknLRdryrrelrkkk 64 
                                    +   +k+ +kn  +++ +e++kk 
  gene907|gene907|rna906|rna906 192 NgipIKEDVKNVFEEFMKEFKKKM 215
                                    255688889999999999997765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.29
                   MADF_DNA_bdg  49 wknLRdryrrelrkkksseskekkkskwr 77 
                                    + + R+r ++++++++  ++ +++++k +
  gene907|gene907|rna906|rna906 271 VDKVRKRQENYMKEME--QERQSYRKKAE 297
                                    4444444444444444..33344444433 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00025
                   MADF_DNA_bdg  32 iaeelnekvdveeckkkwknLRdryrrelrkkksseskekkkskwryfeelsF 84 
                                    i++ ++   +++++++k+k+ Rd+ +  l+k+  + +++k ++ +++fe+++F
  gene907|gene907|rna906|rna906 375 ISRFYQ---KNKKLEEKIKKTRDSLEEVLKKVAPKVETKKVTRALYWFEKFHF 424
                                    555555...45689*******************99999999999999***999 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.8
                   MADF_DNA_bdg  21 nkekrekaweeiaeel.n 37 
                                     +ek+ k  +ei++++ +
  gene907|gene907|rna906|rna906 601 GREKKGKLIQEISKRFiG 618
                                    688999999***999853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (648 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2128  (0.11869); expected 358.6 (0.02)
Passed bias filter:                      707  (0.0394333); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 4033.35
//
Query:       gene908|gene908|rna907|rna907  [L=374]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-10   41.2   1.0    0.00032   21.0   0.1    2.6  2  CDT1      DNA replication factor CDT1 like
  ------ inclusion threshold ------
      0.025   15.0   3.2      0.036   14.5   1.6    2.1  2  CDT1_C    DNA replication factor Cdt1 C-terminal domain


Domain annotation for each model (and alignments):
>> CDT1  DNA replication factor CDT1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.6e-08   0.00032       1      68 [.     118     183 ..     118     204 .. 0.89
   2 !   18.4   0.1   2.3e-07     0.002     121     168 ..     205     246 ..     199     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.6e-08
                           CDT1   1 LPskYevLlelFkaldtivsmlenrketitfakvkkaVermsrksfeekhLaqiktvyPeayklkqek 68 
                                    LP +++ L ++F+ l+ti ++  +r+ t++f k    +e++++++    +++++ +++P+ + +k  k
  gene908|gene908|rna907|rna907 118 LPKSLQKLSRIFRVLETIQRFNSARNLTTIFIKSLGCIENLVKQRVVVGDIERMYYIAPDLFRFK--K 183
                                    9***************************************************************9..2 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.3e-07
                           CDT1 121 kkFrrkLleiVkehHekFLeslnppvevpdlekltrwHpeFdldtvpe 168
                                    k F+++L e+Vk+ H +FL++ +    v    + +r+HpeF++++vp 
  gene908|gene908|rna907|rna907 205 KEFNERLEEYVKKCHLEFLNENG-Y--VY---NGNRFHPEFNFEEVPL 246
                                    78*****************7776.3..22...347**********985 PP

>> CDT1_C  DNA replication factor Cdt1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.69   6.2e+03      31      45 ..     122     136 ..     119     152 .. 0.70
   2 ?   14.5   1.6     4e-06     0.036       2      61 ..     286     338 ..     285     341 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.69
                         CDT1_C  31 lgrlpdvarilrllf 45 
                                    l++l++++r+l ++ 
  gene908|gene908|rna907|rna907 122 LQKLSRIFRVLETIQ 136
                                    478888888887664 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4e-06
                         CDT1_C   2 llerIraKearqalaamtreeelerrsallgrlpdvarilrllfvaekksalpmeevvkk 61 
                                    +lerIr+Ke  + ++ m +++e+e    l        + + +l  +e+++a+p+++vv+ 
  gene908|gene908|rna907|rna907 286 ILERIREKERLRREEFMNKSKEEEDNVLL-------SNRIKMLLRSENRRAIPVNKVVDL 338
                                    69***********8887777766666666.......588999999*********999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2559.71
//
Query:       gene909|gene909|rna908|rna908  [L=173]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-15   56.3   0.2    5.5e-15   55.8   0.2    1.2  1  Sld5      GINS complex protein


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.2   3.1e-19   5.5e-15       2     108 ..      43     148 ..      42     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 3.1e-19
                                    EEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS.SSSTTTTTTHHHHHHHHHHHHT....HCHHHHHHHHHHHH CS
                           Sld5   2 eLPlWlaelLkrqrrveieppewlspesleailedetks.sdlpslpphflelavkllelard...ldelkrllrdllev 77 
                                     +Pl+ a+lLk+++ ++i++p +l+ esl+ai + e ++  + + + p+f+ la  lle + +   ++e k ++++++e+
  gene909|gene909|rna908|rna908  43 RIPLYAALLLKKSNMCKIRLPSYLQLESLKAIMDTEVEKiDEYSHIHPYFFPLAGELLECCYNtenIEESKVMIEKIREI 122
                                    69*************************************999999*********999999988889************** PP

                                    HHHHHHHTHCHHHHHHHTS-TCCHCCS-HHH CS
                           Sld5  78 RlakirkfaenledaagggggellsglseeE 108
                                    Rlak  k+ + l++ a     +++++++ +E
  gene909|gene909|rna908|rna908 123 RLAKTLKGIKCLDGRA-----LNMNNITLFE 148
                                    ****************.....9999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1098.19
//
Query:       gene910|gene910|rna909|rna909  [L=611]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-84  282.7   1.9      3e-84  282.7   1.9    1.5  2  VTC       VTC domain
    3.8e-12   46.5   2.6    6.8e-12   45.7   2.6    1.4  1  DUF202    Domain of unknown function (DUF202)
  ------ inclusion threshold ------
      0.027   14.4   0.6      0.027   14.4   0.6    2.8  3  SPX       SPX domain


Domain annotation for each model (and alignments):
>> VTC  VTC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3      0.54   3.2e+03     131     139 ..      68      76 ..      27     130 .. 0.52
   2 !  282.7   1.9   5.1e-88     3e-84       2     275 .]     167     440 ..     166     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.54
                                    HHHHHHHT- CS
                            VTC 131 leklkkkee 139
                                    l++ +kk +
  gene910|gene910|rna909|rna909  68 LKAVEKKPS 76 
                                    222222222 PP

  == domain 2  score: 282.7 bits;  conditional E-value: 5.1e-88
                                    -EEEEEEE-HHHHHHHHHHHHTTS-B----------------..------EEEEEEE-TT-HHHHHHHHT-TT--EEEEE CS
                            VTC   2 rnetKywvhsdnvvevktlilkhlpvlvygaseeeiaaallr..ksadqtitsvYfDnndfelyenrilkmegaekiRlR 79 
                                    r++ Kywvh++n+v+vk +i +hlp+ v++++++e++   ++  +s+d  i+svYfDn +f+ly +r++k +++e iR+R
  gene910|gene910|rna909|rna909 167 RRTDKYWVHKENIVPVKFYITQHLPIYVFSKDNKEKSPYSSWdrESHDTCISSVYFDNVTFDLYGERLKKLHHSEAIRIR 246
                                    899****************************9999987655455************************************ PP

                                    EES-GGG--EEEEEEEE--------EEEEEEEE-GGGHHHHH---HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHH CS
                            VTC  80 wygkldnedvflErktkheswtgesstkerftlkqkfvksyllgrlpaeerleklkkkeeekevekleqlaeeiqntilr 159
                                    wy ++  + vf+Erk +++ wtgess+k rf +++ +v +y++g+    + +++ kk +     e  + l+ee+q  i++
  gene910|gene910|rna909|rna909 247 WYTSKIPDVVFVERKRHEDGWTGESSKKLRFMISESQVLKYINGE----NVWDDVKKLNG---DEDVRALYEEVQTSIVN 319
                                    ******************************************776....55665555554...6889************* PP

                                    TT-EEEEEEEEEEEEE--TT--SEEEEEEEEEEEEE-.---SSSS-SS-T..SS-SSTTSS-TTTT--GGGEEE--SEEE CS
                            VTC 160 nslqPvvrtsYlRaaFqlstdnavRitiDtnlcmvre.dsfeerrkledt..werldedvqqpvkllrkgevvrfpyavl 236
                                    + l+Pvvrt Y+R aFq+++d +vRi++Dt+lcm++e +++e  ++ ++   w+r d +++ p+k + k+e++rfp+a+l
  gene910|gene910|rna909|rna909 320 KGLRPVVRTFYRRNAFQIPNDSSVRISLDTDLCMIKEcSDAEITNPAHPIkrWRRNDVNCEFPFKNIPKNEIIRFPHAIL 399
                                    *************************************9999*****99999***************************** PP

                                    EEEE--..----HHHHHHHTSTT-EE-TT--HHHHHHHHHH CS
                            VTC 237 EvKlqt..skspewiqeLlashlvievpkfSKYqhgvaslh 275
                                    E+K+q+  + +p+wi+eL++  lv++v+kfSKY hg+a+l+
  gene910|gene910|rna909|rna909 400 EIKTQSldETKPKWIEELINGPLVEHVHKFSKYLHGCAALY 440
                                    *******9******************************996 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   2.6   1.1e-15   6.8e-12       1      67 [.     510     571 ..     510     572 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.1e-15
                         DUF202   1 rdglAnERTfLaWlRtslalialglallrffltgepsalgkilglilivlgiltllvglvrylrrqr 67 
                                    ++++AnERTfL+W+ +++ l+++g all +   g+++a  +  gl+li +++++ +++l+ yl+r++
  gene910|gene910|rna909|rna909 510 KVFFANERTFLSWVQFAIFLGGIGSALLGL---GDEKA--SFSGLVLIFVAVIFSFYSLYLYLWRAS 571
                                    689*************************97...77777..799*********************986 PP

>> SPX  SPX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6      0.16   9.4e+02       1      25 [.       1      25 [.       1      28 [. 0.94
   2 ?    5.2   3.2    0.0029        17     181     230 ..      31      86 ..      20      95 .. 0.78
   3 ?   14.4   0.6   4.6e-06     0.027     352     380 ..      95     123 ..      89     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.16
                            SPX  1 MKFakeLeenlvpEWrdaYldYkqL 25
                                   M+F k+L++n     +  YldY  L
  gene910|gene910|rna909|rna909  1 MRFQKYLKRNVYAPYKYNYLDYENL 25
                                   9*********************988 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0029
                            SPX 181 r......aekeFferLdseLnkvetFykakeeefterlesLrkqlealrprrikea 230
                                    +       e+eF+  Ld++ + v  F ++k  ef++rl++ +k  ++ +  +ike 
  gene910|gene910|rna909|rna909  31 KeeftsnDEDEFIIELDADIKRVFGFVESKHSEFVQRLKAVEKKPSKEAKIKIKEM 86 
                                    144445699******************************99998777766666655 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 4.6e-06
                            SPX 352 sYqeLNrtAFrKIlKKfDKvtaltaskry 380
                                     ++++N+++F K+lK +DK t +++ ++y
  gene910|gene910|rna909|rna909  95 EFIRINVIGFKKLLKRHDKHTRYKLLSSY 123
                                    699********************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.55
# Mc/sec: 3319.96
//
Query:       gene91|gene91|rna91|rna91  [L=208]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.013   14.3  14.1      0.017   13.9  14.1    1.1  1  EVC2_like        Ellis van Creveld protein 2 like protein
       0.02   14.6   3.7      0.031   14.0   3.7    1.3  1  DUF5314          Family of unknown function (DUF5314)
      0.047   12.5  13.9      0.067   12.0  13.9    1.4  1  Mitofilin        Mitochondrial inner membrane protein
      0.069   12.0   1.8      0.095   11.5   1.8    1.2  1  UxuA             D-mannonate dehydratase (UxuA)
       0.11   12.6  14.3       0.17   12.0  14.3    1.3  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.29   11.5  19.9       0.44   10.9  18.4    2.1  2  Muted            Organelle biogenesis, Muted-like protein
        0.4   11.5   4.7       0.73   10.7   4.7    1.4  1  Ima1_N           Ima1 N-terminal domain
        0.4   10.6   2.3        1.3    8.9   0.5    2.4  2  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
       0.51    8.2   5.6       0.69    7.8   5.6    1.1  1  Prominin         Prominin
       0.53   10.1  10.6        2.1    8.2  10.6    1.9  1  SICA_alpha       SICA extracellular alpha domain
        0.6    9.9  11.3        1.5    8.7   3.0    2.5  2  SKA2             Spindle and kinetochore-associated protein 2
       0.71   10.5  11.1       0.62   10.7   1.9    1.9  2  ING              Inhibitor of growth proteins N-terminal hist
       0.85    9.1   7.5          1    8.9   7.5    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
        4.2    6.5   9.3        5.7    6.1   9.3    1.2  1  TMPIT            TMPIT-like protein
        4.5    7.6  14.6        3.5    8.0  12.7    1.8  1  DUF641           Plant protein of unknown function (DUF641)
        4.5    7.4  11.1         16    5.6   8.6    2.1  2  Fib_alpha        Fibrinogen alpha/beta chain family


Domain annotation for each model (and alignments):
>> EVC2_like  Ellis van Creveld protein 2 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9  14.1   1.5e-05     0.017     199     281 ..     116     198 ..      93     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                  EVC2_like 199 svfkkqllalekelkeeyerkmvaLaaecnletrekleaehkkeeaekeeaeellkkasekellelssLLdklhkleqeeLqr 281
                                + +++++l++ ++l +  e++m++L+++++++++ ++e+++++ +++++e++e +k++ ++++le+++ Ld+  +++  eL++
  gene91|gene91|rna91|rna91 116 KEMHRKALGARRKLIKTMEKEMSELKQRMEAKQKVEMENLKRQYDEKLREKQEAYKRICKEKILEYKRKLDEAYRVKVMELKE 198
                                4589999****************************************************************999988888875 PP

>> DUF5314  Family of unknown function (DUF5314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.7   2.7e-05     0.031     122     192 ..     102     170 ..      97     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                    DUF5314 122 rkkvsstaeifselqsmsnkslkekelwakklvktilddaeelelsdklsdpelaavkneisklkdsiaAl 192
                                +  vs +++ f+el++m+ k+l  +++ +k + k++ + ++ +e ++k++ ++l  ++++ +kl+++ +A+
  gene91|gene91|rna91|rna91 102 DSVVSRIQKEFEELKEMHRKALGARRKLIKTMEKEMSELKQRMEAKQKVEMENL--KRQYDEKLREKQEAY 170
                                56789999*****************************************99997..999999999998886 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  13.9     6e-05     0.067     317     386 ..     109     178 ..      72     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6e-05
                  Mitofilin 317 kkieralekqkeelekqeealsarleeerakeerqlrlelereleeireeyeekLrteLerqaeaheehL 386
                                +k  ++l++ + +   ++++l++ +e+e+++ +++++++++ e+e ++++y+ekLr+++e  + + +e++
  gene91|gene91|rna91|rna91 109 QKEFEELKEMHRKALGARRKLIKTMEKEMSELKQRMEAKQKVEMENLKRQYDEKLREKQEAYKRICKEKI 178
                                3444566666666666899*************************************88877766666553 PP

>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.8   8.5e-05     0.095     127     182 ..     122     180 ..     103     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.5e-05
                                EEEE-HHHHHHHHHH...TT--TTGGGGS--TT-S---HHHHHHHHGCCTT--HHHHHH CS
                       UxuA 127 alrfdkkeiealelk...ilrrkeaekeytlPgaeeerldelrelleaykkideeklre 182
                                al   +k i+ +e +   +++r ea++++++   ++++ ++lre+ eayk+i +ek+ e
  gene91|gene91|rna91|rna91 122 ALGARRKLIKTMEKEmseLKQRMEAKQKVEMENLKRQYDEKLREKQEAYKRICKEKILE 180
                                555566666655554446999*********************************99875 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  14.3   0.00015      0.17      75     167 ..      92     187 ..      73     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                    UPF0242  75 aklteldeglktkeealeelqeeeeeLkee....ldakeeelerlkeenqqLqekleaiae.dfeelkleleeqLaekqellqe 153
                                +k  ++++g +     +   q+e eeLke     l a+ ++++ +++e  +L++++ea ++ ++e+lk++++e+L+ekqe  + 
  gene91|gene91|rna91|rna91  92 RKAESKENGSDS---VVSRIQKEFEELKEMhrkaLGARRKLIKTMEKEMSELKQRMEAKQKvEMENLKRQYDEKLREKQEAYKR 172
                                444444433333...444555555666555555799**********************9989******************9987 PP

                    UPF0242 154 y.qetieeqrsvlek 167
                                  +e+i e +  l++
  gene91|gene91|rna91|rna91 173 IcKEKILEYKRKLDE 187
                                526678888877775 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.5   6.2e+03      32      52 ..      15      35 ..      11      45 .. 0.54
   2 ?   10.9  18.4   0.00039      0.44      33     145 ..     107     206 ..      92     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.5
                      Muted 32 kRgdrevelLenikklvnelk 52
                               +   r  ++L+ni+++  +++
  gene91|gene91|rna91|rna91 15 RVRVRKRNVLSNITNKSGDIS 35
                               444444555555555554444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00039
                      Muted  33 RgdrevelLenikklvnelkeqllpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaeweeflke 116
                                R ++e e L+++++++   + +    ++++m++++sel+++     e  ++++ ++l++++  +e+l ek+e++k+  +e    
  gene91|gene91|rna91|rna91 107 RIQKEFEELKEMHRKALGARRK----LIKTMEKEMSELKQR----MEAKQKVEMENLKRQY--DEKLREKQEAYKRICKEK--- 177
                                4556666666666666665555....566677778888888....5667778888777787..888999888888887765... PP

                      Muted 117 lqekkeevDeefeekveelkekYselekk 145
                                + e k+++De ++ kv elke+Y  l kk
  gene91|gene91|rna91|rna91 178 ILEYKRKLDEAYRVKVMELKERYGALRKK 206
                                7788899****************999886 PP

>> Ima1_N  Ima1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.7   0.00065      0.73      46     125 ..     110     190 ..      77     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00065
                     Ima1_N  46 eeslneaakkaaasksksks...............eeaessssssllCskClknqelkvsklaeylpke.deddpeyeekeea. 112
                                +e                 +                 ++ +++ s l ++ + +q++ +++l++  +++ +e+++ y++  ++ 
  gene91|gene91|rna91|rna91 110 KEF----------------EelkemhrkalgarrkLIKTMEKEMSELKQRMEAKQKVEMENLKRQYDEKlREKQEAYKRICKEk 177
                                222................12333344444444444567888999999**************9888888788888888876555 PP

                     Ima1_N 113 leeykkeleerYp 125
                                + eyk++l+e Y+
  gene91|gene91|rna91|rna91 178 ILEYKRKLDEAYR 190
                                ************8 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.66   7.4e+02      16      31 ..     102     117 ..      94     119 .. 0.84
   2 ?    8.9   0.5    0.0012       1.3      20      44 ..     131     155 ..     126     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.66
            HU-CCDC81_bac_2  16 eeAlqkiekeveelkq 31 
                                ++++++i+ke eelk+
  gene91|gene91|rna91|rna91 102 DSVVSRIQKEFEELKE 117
                                567899*******997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
            HU-CCDC81_bac_2  20 qkiekeveelkqeLeeegrveleni 44 
                                +  eke++elkq++e +++ve+en+
  gene91|gene91|rna91|rna91 131 KTMEKEMSELKQRMEAKQKVEMENL 155
                                788********************96 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.6   0.00061      0.69     634     734 ..      91     200 ..      80     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00061
                   Prominin 634 eelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkklde........ensdlqesikkllaa.veraenfl 708
                                e +a++ +ng++++ +++++e ++l++++++     ++++k+++k++ +l++        e ++l+++ ++ l++  e+ + + 
  gene91|gene91|rna91|rna91  91 ERKAESKENGSDSVVSRIQKEFEELKEMHRKALGARRKLIKTMEKEMSELKQrmeakqkvEMENLKRQYDEKLREkQEAYKRIC 174
                                567888888889999***********************************9998777777777788877655544044445556 PP

                   Prominin 709 kkngseiinneskklldrileqfeeY 734
                                k+++ e+ +++ + +   ++e  e+Y
  gene91|gene91|rna91|rna91 175 KEKILEYKRKLDEAYRVKVMELKERY 200
                                67777777777777777777776666 PP

>> SICA_alpha  SICA extracellular alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  10.6    0.0019       2.1      16      77 ..     116     175 ..      75     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                 SICA_alpha  16 katgtkakeitekLkkelekmfeeLkkrLkkqeskeiaklCadvkeevekkkkeeymkelCk 77 
                                k+ + ka  +  kL k +ek+  eLk+r++ +++ e+++l ++++e+ ++k++    k++Ck
  gene91|gene91|rna91|rna91 116 KEMHRKALGARRKLIKTMEKEMSELKQRMEAKQKVEMENLKRQYDEKLREKQE--AYKRICK 175
                                444447777889***********************************987544..699***9 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.0    0.0013       1.5      47      86 ..     105     144 ..     103     150 .. 0.83
   2 ?    4.1   3.9     0.035        39      51      77 ..     149     175 ..     139     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                       SKA2  47 lkkvkeelqaLkeqceellaekkelidkirttlvanrell 86 
                                ++++++e+++Lke +++ l ++++li+++++ +++ ++ +
  gene91|gene91|rna91|rna91 105 VSRIQKEFEELKEMHRKALGARRKLIKTMEKEMSELKQRM 144
                                5799*************************99997666554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.035
                       SKA2  51 keelqaLkeqceellaekkelidkirt 77 
                                k e+++Lk+q +e l ek+e  ++i++
  gene91|gene91|rna91|rna91 149 KVEMENLKRQYDEKLREKQEAYKRICK 175
                                669*******************99987 PP

>> ING  Inhibitor of growth proteins N-terminal histone-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.9   0.00055      0.62      47      99 ..      93     145 ..      76     147 .. 0.85
   2 ?    9.4  10.4    0.0013       1.5      15      77 ..     107     178 ..     101     191 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00055
                                S..S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTX CS
                        ING  47 ngslqknekeeelsriqeelkeaqelldeKiqlaqqaldlvdkhlrrLdqdle 99 
                                + + ++n +++++sriq+e++e++e+ ++ +    ++ ++++k++++L+q +e
  gene91|gene91|rna91|rna91  93 KAESKENGSDSVVSRIQKEFEELKEMHRKALGARRKLIKTMEKEMSELKQRME 145
                                55777888888999**********************************99987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH........TS..S-HHHHHHHHH.HHHHHHHHHHHHHHHHH CS
                        ING  15 elqrnltelreiDakvqellkeidskiekfl........kngslqknekeeels.riqeelkeaqelldeKi 77 
                                 +q+ ++el+e+  k   +++++ + +ek +        ++++ + ++ ++++  +++e++++ +++ +eKi
  gene91|gene91|rna91|rna91 107 RIQKEFEELKEMHRKALGARRKLIKTMEKEMselkqrmeAKQKVEMENLKRQYDeKLREKQEAYKRICKEKI 178
                                799********************99999999999999987778888888888889****************8 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.5   0.00091         1     155     233 ..      99     186 ..      67     208 .] 0.47

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00091
               Exonuc_VII_L 155 rlekaikrlleekkqrleklasrl.kspeellerkrqrldeleerleralkkqlkkkrerleelkerlk........ekleekk 229
                                + ++++ ++++++ ++l++++++     ++l+++ +++++el++r+e+++k ++++ +++++e  ++ +        ek+ e k
  gene91|gene91|rna91|rna91  99 NGSDSVVSRIQKEFEELKEMHRKAlGARRKLIKTMEKEMSELKQRMEAKQKVEMENLKRQYDEKLREKQeaykrickEKILEYK 182
                                334444455555555555554433135556666666666666666666444333322222222221111111112222222233 PP

               Exonuc_VII_L 230 erlk 233
                                ++l+
  gene91|gene91|rna91|rna91 183 RKLD 186
                                2322 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   9.3    0.0051       5.7       4      83 ..     105     186 ..     102     201 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0051
                      TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkel.ksslkklkksvk...eeeeeeveel.keelkerkkvl 82 
                                +++++kef+el+e +++         kl++++ ke+++ k+r+++  k ++++lk++ +   +e++e+++++ ke++ e k+ l
  gene91|gene91|rna91|rna91 105 VSRIQKEFEELKEMHRKAL---GARRKLIKTMEKEMSELKQRMEAKqKVEMENLKRQYDeklREKQEAYKRIcKEKILEYKRKL 185
                                5789999999999996555...55555556666666666666654313456666666443334444444444256666666666 PP

                      TMPIT  83 k 83 
                                +
  gene91|gene91|rna91|rna91 186 D 186
                                5 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  12.7    0.0031       3.5      71     128 .]     114     172 ..      85     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                     DUF641  71 aeeseleaeiqeqrsllktyeitvkkleaelkakd.seieeLkekLeeaeksnkklekr 128
                                + +++ ++ +  +r+l+kt+e+ +++l++ ++ak+ +e+e+Lk++ +e  +++++  kr
  gene91|gene91|rna91|rna91 114 ELKEMHRKALGARRKLIKTMEKEMSELKQRMEAKQkVEMENLKRQYDEKLREKQEAYKR 172
                                2333334444559******************998537***********99999887665 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   8.6     0.014        16      76     135 ..     109     169 ..      85     177 .. 0.56
   2 ?    5.6   9.7     0.015        17      42     111 ..     121     189 ..     107     206 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.014
                                HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHTTSB CS
                  Fib_alpha  76 dnvikksskeleeeilrlketidaqesnirvLqnvle.sneqkiqkLeqdidqkerkCkep 135
                                ++ +++++++ ++     ++ i++ e+++ +L++ +e ++++++++L+ + d+k r+ +e 
  gene91|gene91|rna91|rna91 109 QKEFEELKEMHRKALGARRKLIKTMEKEMSELKQRMEaKQKVEMENLKRQYDEKLREKQEA 169
                                3334444444444444445556666688888877765256678888888877777665554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
                                CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHH CS
                  Fib_alpha  42 neleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnvl 111
                                + l   ++  k++e+ ++e+k+ +++kqk +   +n+ +++ ++l+e+++ +k+  ++++ +  r+L + +
  gene91|gene91|rna91|rna91 121 KALGARRKLIKTMEKEMSELKQRMEAKQKVEM--ENLKRQYDEKLREKQEAYKRICKEKIlEYKRKLDEAY 189
                                33444455555555555666666555555555..4555555555655555555555444433333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3310  (0.184617); expected 358.6 (0.02)
Passed bias filter:                      887  (0.0494729); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 1218.77
//
Query:       gene911|gene911|rna910|rna910  [L=463]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-32  109.3   6.3    2.6e-06   27.0   0.0    7.5  7  TPR_1     Tetratricopeptide repeat
    8.8e-28   94.2   2.7     0.0002   21.2   0.0    7.4  7  TPR_2     Tetratricopeptide repeat
    1.2e-25   87.5  14.8    0.00049   20.1   0.4    7.3  7  TPR_8     Tetratricopeptide repeat
    2.7e-13   49.9   8.9    3.6e-05   23.9   0.0    5.2  5  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
    2.5e-12   46.6   3.0      0.032   14.9   0.1    6.5  7  TPR_6     Tetratricopeptide repeat
    5.9e-12   45.1   0.2    1.3e-05   24.8   0.0    4.9  5  TPR_11    TPR repeat
    2.4e-11   43.8   1.0      0.066   13.5   0.0    6.0  6  TPR_12    Tetratricopeptide repeat
    4.2e-10   39.6   0.0        2.3    9.2   0.0    5.9  6  TPR_14    Tetratricopeptide repeat
    2.3e-09   36.6   0.7     0.0096   15.9   0.0    5.4  5  TPR_7     Tetratricopeptide repeat
    5.6e-09   35.8  10.8    0.00059   20.0   0.0    7.1  7  TPR_17    Tetratricopeptide repeat
    3.4e-07   30.8   0.0      0.075   13.7   0.0    3.7  4  TPR_16    Tetratricopeptide repeat
    4.2e-07   29.3   1.1    0.00082   18.5   0.4    2.6  3  ChAPs     ChAPs (Chs5p-Arf1p-binding proteins)
    7.9e-07   29.5   0.0     0.0006   20.3   0.0    4.0  5  TPR_19    Tetratricopeptide repeat
    4.8e-05   23.1   0.2        9.2    6.3   0.0    4.8  5  TPR_10    Tetratricopeptide repeat
    4.9e-05   22.7   0.0     0.0017   17.6   0.0    3.0  4  TPR_15    Tetratricopeptide repeat
     0.0036   17.4   0.0        3.5    7.8   0.0    3.2  4  TPR_9     Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.13   12.3   7.7         38    4.4   0.0    4.7  4  TPR_3     Tetratricopeptide repeat
       0.23   11.8  10.8       0.35   11.2   0.1    4.7  4  PPR       PPR repeat


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.3      0.18   1.8e+02      10      22 ..      40      52 ..      39      54 .. 0.86
   2 ?    6.1   0.0      0.01        10       8      27 ..     205     224 ..     202     226 .. 0.93
   3 !   23.4   0.0   3.7e-08   3.6e-05       3      33 ..     268     298 ..     266     299 .. 0.92
   4 !   10.9   0.0   0.00032      0.32       3      32 ..     302     331 ..     300     333 .. 0.91
   5 !   15.2   0.5   1.4e-05     0.014       2      30 ..     335     363 ..     334     367 .. 0.92
   6 !   27.0   0.0   2.6e-09   2.6e-06       3      31 ..     370     398 ..     368     399 .. 0.95
   7 !   19.8   0.2     5e-07    0.0005       2      29 ..     401     428 ..     400     433 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                                   HHHHTT-HHHHHH CS
                          TPR_1 10 ayfklgkydeAle 22
                                   +y++l++y +A +
  gene911|gene911|rna910|rna910 40 TYQNLKEYRKAYA 52
                                   7**********75 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.01
                                    HHHHHHTT-HHHHHHHHHHH CS
                          TPR_1   8 GnayfklgkydeAleyyekA 27 
                                    G+++++++++d ++e +ek+
  gene911|gene911|rna910|rna910 205 GAVLYHQKDFDGCIEIFEKV 224
                                    899**************996 PP

  == domain 3  score: 23.4 bits;  conditional E-value: 3.7e-08
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALelnPn 33 
                                    + + ++n y  ++++++A+ey++ +++lnP+
  gene911|gene911|rna910|rna910 268 TMCCIANYYSMKKEHEKAIEYFRLCVKLNPS 298
                                    66899*************************7 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00032
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                    ++  +G+ y++++  ++A+  y+ AL+ +P
  gene911|gene911|rna910|rna910 302 VHTLIGHEYLEMKSMEKAVSSYNVALKMCP 331
                                    68899******************9999998 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALel 30 
                                    +a+y +G+ay  + +y+ Al + +kALe 
  gene911|gene911|rna910|rna910 335 RAWYSIGQAYVTMTMYEYALFFIKKALEC 363
                                    8**************************96 PP

  == domain 6  score: 27.0 bits;  conditional E-value: 2.6e-09
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                          TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                    ++  lG++y++l++ d+A+ +++ ++eln
  gene911|gene911|rna910|rna910 370 VWTTLGQCYMNLNRMDDAIGCFKNVIELN 398
                                    899*************************9 PP

  == domain 7  score: 19.8 bits;  conditional E-value: 5e-07
                                    HHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                          TPR_1   2 kalynlGnayfklgkydeAleyyekALe 29 
                                    + +  +G ay ++++y eA+ yyek +e
  gene911|gene911|rna910|rna910 401 DGYLYIGDAYKNMKMYTEAVVYYEKYVE 428
                                    7899********************9665 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4      0.18   1.8e+02       6      22 ..      36      52 ..      34      55 .. 0.87
   2 !    8.7   0.0     0.002         2       7      27 ..     204     224 ..     202     228 .. 0.89
   3 !   19.4   0.0   7.5e-07   0.00075       3      33 ..     268     298 ..     266     299 .. 0.92
   4 !    7.2   0.0    0.0063       6.3       3      32 ..     302     331 ..     300     333 .. 0.91
   5 !   12.5   0.2   0.00012      0.12       2      33 ..     335     366 ..     334     367 .. 0.92
   6 !   21.2   0.0     2e-07    0.0002       3      32 ..     370     399 ..     368     401 .. 0.93
   7 !   15.0   0.2     2e-05      0.02       2      29 ..     401     428 ..     400     433 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.18
                          TPR_2  6 nlGlayyklgdyeeAle 22
                                   +l l y +l++y +A +
  gene911|gene911|rna910|rna910 36 YLSLTYQNLKEYRKAYA 52
                                   78999**********76 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                          TPR_2   7 lGlayyklgdyeeAleafekA 27 
                                     G ++y+++d++ ++e fek+
  gene911|gene911|rna910|rna910 204 AGAVLYHQKDFDGCIEIFEKV 224
                                    699****************97 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 7.5e-07
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                      +++++ y  ++++e+A+e+f+ +++l+P 
  gene911|gene911|rna910|rna910 268 TMCCIANYYSMKKEHEKAIEYFRLCVKLNPS 298
                                    67899*************************6 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0063
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                    ++  +G  y++++  e+A+  ++ Al+ +P
  gene911|gene911|rna910|rna910 302 VHTLIGHEYLEMKSMEKAVSSYNVALKMCP 331
                                    677899*********************999 PP

  == domain 5  score: 12.5 bits;  conditional E-value: 0.00012
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                    +a+y +G+ay  +  ye Al + +kAle   n
  gene911|gene911|rna910|rna910 335 RAWYSIGQAYVTMTMYEYALFFIKKALECKNN 366
                                    69*************************97666 PP

  == domain 6  score: 21.2 bits;  conditional E-value: 2e-07
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldP 32 
                                    ++  lG++y++l++ ++A+ +f+ ++el+ 
  gene911|gene911|rna910|rna910 370 VWTTLGQCYMNLNRMDDAIGCFKNVIELND 399
                                    7999************************95 PP

  == domain 7  score: 15.0 bits;  conditional E-value: 2e-05
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAle 29 
                                    +++ ++G+ay +++ y eA+ ++ek +e
  gene911|gene911|rna910|rna910 401 DGYLYIGDAYKNMKMYTEAVVYYEKYVE 428
                                    7899********************9877 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3      0.15   1.5e+02       7      24 ..      37      54 ..      37      55 .. 0.88
   2 ?    2.6   0.0       0.2     2e+02       8      28 ..     205     225 ..     202     228 .. 0.83
   3 !   19.1   0.1     1e-06     0.001       7      33 ..     272     298 ..     266     299 .. 0.90
   4 !   14.7   0.0   2.7e-05     0.026       5      32 ..     304     331 ..     302     332 .. 0.92
   5 !   14.1   0.4   4.1e-05     0.041       1      30 [.     334     363 ..     334     367 .. 0.91
   6 !   17.3   0.0     4e-06    0.0039       3      31 ..     370     398 ..     369     401 .. 0.94
   7 !   20.1   0.4     5e-07   0.00049       4      33 ..     403     432 ..     400     433 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.15
                                   HHHHHHHTT-HHHHHHHH CS
                          TPR_8  7 lgsiylklgdyeeAkeyy 24
                                   l+++y++l++y +A +++
  gene911|gene911|rna910|rna910 37 LSLTYQNLKEYRKAYASL 54
                                   6789**********8876 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
                                    HHHHHHTT-HHHHHHHHHHHH CS
                          TPR_8   8 gsiylklgdyeeAkeyyekal 28 
                                    g ++  ++d++  +e +ek++
  gene911|gene911|rna910|rna910 205 GAVLYHQKDFDGCIEIFEKVT 225
                                    56677899***********97 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 1e-06
                                    HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                    +++ y+ ++++e+A+ey++ +++l+p+
  gene911|gene911|rna910|rna910 272 IANYYSMKKEHEKAIEYFRLCVKLNPS 298
                                    7889999******************96 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 2.7e-05
                                    HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                          TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                     ++g+ yl+++ +e+A+++y+ al++ p
  gene911|gene911|rna910|rna910 304 TLIGHEYLEMKSMEKAVSSYNVALKMCP 331
                                    68*********************99977 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 4.1e-05
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                    ++a+y +g++y ++  ye A  +++kale 
  gene911|gene911|rna910|rna910 334 YRAWYSIGQAYVTMTMYEYALFFIKKALEC 363
                                    59**************************95 PP

  == domain 6  score: 17.3 bits;  conditional E-value: 4e-06
                                    HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                    ++  lg++y++l++++ A+ +++ ++el+
  gene911|gene911|rna910|rna910 370 VWTTLGQCYMNLNRMDDAIGCFKNVIELN 398
                                    6999***********************98 PP

  == domain 7  score: 20.1 bits;  conditional E-value: 5e-07
                                    HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                    y+ +g++y++++ y eA+ yyek++e ++d
  gene911|gene911|rna910|rna910 403 YLYIGDAYKNMKMYTEAVVYYEKYVETSKD 432
                                    5559*********************98887 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.039        39      23      46 ..      31      54 ..       3      75 .. 0.78
   2 ?    4.3   0.0     0.047        47      46      81 ..     188     223 ..     182     228 .. 0.60
   3 !   15.5   0.5   1.5e-05     0.015       8      78 ..     251     322 ..     246     326 .. 0.93
   4 !   23.9   0.0   3.6e-08   3.6e-05      15      81 ..     329     393 ..     322     394 .. 0.91
   5 ?    2.9   0.1      0.13   1.2e+02       2      33 ..     413     444 ..     412     451 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                                   HHHHHHHHHHHHHTT-HHHHHHHH CS
                         ANAPC3 23 pedayllAlclylngqykrAyell 46
                                   ++++ +l+l++ ++++y +Ay  l
  gene911|gene911|rna910|rna910 31 LSSREYLSLTYQNLKEYRKAYASL 54
                                   56677899************9866 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.047
                                    HHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  46 lrkaklnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                     ++++  + ++++  l++ +l+ +k ++ +i ++ek
  gene911|gene911|rna910|rna910 188 MKSSDGLCVNMKYPNLAGAVLYHQKDFDGCIEIFEK 223
                                    555555566666666666666666666666666655 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                         ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                     i+lae  l+ +++++e     A  +   +++++A+e++r + kln++s  ++ l+++ +l++k++e+A++ 
  gene911|gene911|rna910|rna910 251 VILLAENTLNINKYRSETMCCIANYYSMKKEHEKAIEYFRLCvKLNPSSSIVHTLIGHEYLEMKSMEKAVSS 322
                                    58999****999********************************************************9876 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 3.6e-08
                                    HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                         ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                    ++   + ++ + y  ++++  +  y+ A+ +++ka + +++++ ++ +++qc+  L+++++Ai ++++
  gene911|gene911|rna910|rna910 329 MC---PMDYRAWYSIGQAYVTMTMYEYALFFIKKAlECKNNDPVVWTTLGQCYMNLNRMDDAIGCFKN 393
                                    44...7788888999*************************************************9986 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.13
                                    TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHH CS
                         ANAPC3   2 qnnyknAiflaerllaaetespedayllAlcl 33 
                                    +++y +A+ ++e+++++++++   + l+ + +
  gene911|gene911|rna910|rna910 413 MKMYTEAVVYYEKYVETSKDDTRKICLFLEEY 444
                                    689************98888888777765555 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.8   2.8e+03       6      21 ..      37      52 ..      36      54 .. 0.78
   2 ?    5.7   0.0     0.027        27       8      29 ..     206     227 ..     203     228 .. 0.83
   3 !    8.8   0.0    0.0028       2.8      10      33 .]     275     299 ..     272     299 .. 0.85
   4 ?   -0.5   0.0       2.6   2.6e+03      10      28 ..     310     328 ..     305     331 .. 0.81
   5 ?   -0.6   0.2       2.8   2.7e+03       2      19 ..     336     353 ..     335     361 .. 0.83
   6 !    9.5   0.0    0.0016       1.6       6      28 ..     374     396 ..     373     400 .. 0.94
   7 !   14.9   0.1   3.2e-05     0.032       1      28 [.     401     428 ..     401     432 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.8
                                   HHHHHHHHHHHHHHHH CS
                          TPR_6  6 lalsyrklgdtdkAle 21
                                   l l y++l++++kA +
  gene911|gene911|rna910|rna910 37 LSLTYQNLKEYRKAYA 52
                                   6688999999999976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.027
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   8 lsyrklgdtdkAlealerlike 29 
                                      ++ ++d d  +e++e++ ++
  gene911|gene911|rna910|rna910 206 AVLYHQKDFDGCIEIFEKVTRN 227
                                    5667788************986 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0028
                                    HHH.HHHHHHHHHHHHHHHHH-TT- CS
                          TPR_6  10 yrk.lgdtdkAlealerlikeYPdS 33 
                                    y++  ++++kA+e+++ ++k  P S
  gene911|gene911|rna910|rna910 275 YYSmKKEHEKAIEYFRLCVKLNPSS 299
                                    6663469**************9987 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.6
                                    HHHHHHHHHHHHHHHHHHH CS
                          TPR_6  10 yrklgdtdkAlealerlik 28 
                                    y++++  +kA+  ++  +k
  gene911|gene911|rna910|rna910 310 YLEMKSMEKAVSSYNVALK 328
                                    78888999***99998775 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 2.8
                                    HHHHHHHHHHHHHHHHHH CS
                          TPR_6   2 AlyklalsyrklgdtdkA 19 
                                    A y ++++y  ++ ++ A
  gene911|gene911|rna910|rna910 336 AWYSIGQAYVTMTMYEYA 353
                                    88999***9988888766 PP

  == domain 6  score: 9.5 bits;  conditional E-value: 0.0016
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                    l+++y +l++ d+A+  ++++i+
  gene911|gene911|rna910|rna910 374 LGQCYMNLNRMDDAIGCFKNVIE 396
                                    79*****99************98 PP

  == domain 7  score: 14.9 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          TPR_6   1 dAlyklalsyrklgdtdkAlealerlik 28 
                                    d +++++ +y++++ +++A+ ++e+ ++
  gene911|gene911|rna910|rna910 401 DGYLYIGDAYKNMKMYTEAVVYYEKYVE 428
                                    5799*********************987 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       6.2   6.2e+03      15      26 ..     237     248 ..     236     249 .. 0.75
   2 ?    3.1   0.0     0.076        76       8      40 ..     280     312 ..     274     314 .. 0.86
   3 !   24.8   0.0   1.3e-08   1.3e-05       1      39 [.     307     345 ..     307     347 .. 0.96
   4 ?    3.4   0.0     0.063        63      18      41 ..     358     381 ..     358     382 .. 0.92
   5 !   12.3   0.0    0.0001       0.1       1      41 [.     375     413 ..     375     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.2
                         TPR_11  15 eaYkkAlkldPd 26 
                                      Y++Al +++d
  gene911|gene911|rna910|rna910 237 DLYSNALYIKND 248
                                    679999988877 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.076
                         TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGlayyk 40 
                                     + e+Aie ++  +kl+P++  ++  +G+ y++
  gene911|gene911|rna910|rna910 280 KEHEKAIEYFRLCVKLNPSSSIVHTLIGHEYLE 312
                                    6889*******************9999987765 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.3e-08
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                    G++y e    e+A+ +Y+ Alk +P + +a+y +G+ay 
  gene911|gene911|rna910|rna910 307 GHEYLEMKSMEKAVSSYNVALKMCPMDYRAWYSIGQAYV 345
                                    899***********************************7 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.063
                         TPR_11  18 kkAlkldPdnaeayynLGlayykq 41 
                                    kkAl+ +++++ ++  LG+ y+++
  gene911|gene911|rna910|rna910 358 KKALECKNNDPVVWTTLGQCYMNL 381
                                    79*****************99875 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.0001
                         TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                    G+ y+ +++ ++Ai ++k+ ++l  ++++ y+ +G+ay ++
  gene911|gene911|rna910|rna910 375 GQCYMNLNRMDDAIGCFKNVIEL--NDPDGYLYIGDAYKNM 413
                                    6679999****************..5************876 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       4.3   4.3e+03       9      22 ..      37      50 ..      30      54 .. 0.61
   2 !    7.8   0.0     0.004       3.9       8      29 ..     203     224 ..     197     241 .. 0.89
   3 !   10.0   0.0    0.0008       0.8      27      73 ..     249     294 ..     245     298 .. 0.84
   4 !   10.9   0.0   0.00042      0.42       4      75 ..     267     330 ..     264     332 .. 0.84
   5 ?    0.5   0.0      0.78   7.8e+02      47      75 ..     336     364 ..     335     366 .. 0.86
   6 !   13.5   0.0   6.6e-05     0.066       6      74 ..     371     429 ..     368     432 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.3
                         TPR_12  9 laavlrrlgrydeA 22
                                   l ++++ l++y +A
  gene911|gene911|rna910|rna910 37 LSLTYQNLKEYRKA 50
                                   55667777777666 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.004
                         TPR_12   8 nlaavlrrlgrydeAlelleka 29 
                                      +avl++++++d ++e++ek+
  gene911|gene911|rna910|rna910 203 LAGAVLYHQKDFDGCIEIFEKV 224
                                    4799****************97 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0008
                         TPR_12  27 ekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                     +++ +a+++l+ ++ + ++t++ ++ +y++ +++e+A+e+++ +++
  gene911|gene911|rna910|rna910 249 SRVILLAENTLNINK-YRSETMCCIANYYSMKKEHEKAIEYFRLCVK 294
                                    677888999999988.89999999*****************997765 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00042
                         TPR_12   4 talnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                     ++  +a+ +   +++++A+e+++ ++ +      p     +++   +g  y++++  e+A++ ++ al+++
  gene911|gene911|rna910|rna910 267 ETMCCIANYYSMKKEHEKAIEYFRLCVKLN-----P---SSSIVHTLIGHEYLEMKSMEKAVSSYNVALKMC 330
                                    566678999999999999999999996665.....5...469999999999999999999999999999998 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.78
                         TPR_12  47 tlrnLgrlyralgryeeAlelleealaia 75 
                                    + + +g++y  +  ye Al + ++al+ +
  gene911|gene911|rna910|rna910 336 AWYSIGQAYVTMTMYEYALFFIKKALECK 364
                                    66789****9999*******999999975 PP

  == domain 6  score: 13.5 bits;  conditional E-value: 6.6e-05
                         TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                    ++ l+++++ l r+d+A+ +++ ++e+     +pd       +  +g++y  ++ y eA+ ++e+ ++ 
  gene911|gene911|rna910|rna910 371 WTTLGQCYMNLNRMDDAIGCFKNVIELN----DPDG------YLYIGDAYKNMKMYTEAVVYYEKYVET 429
                                    667*********************9999....4998......677999999999999999999998875 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.72   7.2e+02      22      44 .]     117     139 ..     116     139 .. 0.88
   2 ?    4.6   0.0      0.07        70       7      28 ..     204     225 ..     203     228 .. 0.88
   3 !    9.1   0.0    0.0025       2.5       7      39 ..     272     304 ..     268     308 .. 0.87
   4 ?   -2.0   0.0       9.2   9.2e+03      15      39 ..     314     338 ..     305     345 .. 0.63
   5 ?    7.0   0.0     0.012        12       3      31 ..     370     398 ..     368     401 .. 0.87
   6 !    9.2   0.0    0.0023       2.3       2      35 ..     401     434 ..     400     441 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.72
                         TPR_14  22 allrralalaPddaeawlllaql 44 
                                    ++l +++  +P+++ea+  la+l
  gene911|gene911|rna910|rna910 117 RILSDVVVINPWFWEAYSDLAEL 139
                                    67899999*********999986 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.07
                         TPR_14   7 laeallalGdpdeAiallrral 28 
                                    ++++l+++ d+d+ i++++++ 
  gene911|gene911|rna910|rna910 204 AGAVLYHQKDFDGCIEIFEKVT 225
                                    5789***************986 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0025
                         TPR_14   7 laeallalGdpdeAiallrralalaPddaeawl 39 
                                    +a ++    ++++Ai+++r +++l+P++  +++
  gene911|gene911|rna910|rna910 272 IANYYSMKKEHEKAIEYFRLCVKLNPSSSIVHT 304
                                    678888999*****************9987765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 9.2
                         TPR_14  15 GdpdeAiallrralalaPddaeawl 39 
                                       ++A+  ++ al+ +P d +aw+
  gene911|gene911|rna910|rna910 314 KSMEKAVSSYNVALKMCPMDYRAWY 338
                                    5556777777777777776666665 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.012
                         TPR_14   3 allalaeallalGdpdeAiallrralala 31 
                                    ++  l++ +++l + d+Ai +++ +++l+
  gene911|gene911|rna910|rna910 370 VWTTLGQCYMNLNRMDDAIGCFKNVIELN 398
                                    68899********************9975 PP

  == domain 6  score: 9.2 bits;  conditional E-value: 0.0023
                         TPR_14   2 eallalaeallalGdpdeAiallrralalaPdda 35 
                                    + +l +++a+ +   + eA+ ++++++++  dd 
  gene911|gene911|rna910|rna910 401 DGYLYIGDAYKNMKMYTEAVVYYEKYVETSKDDT 434
                                    678999***********************99985 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       1.1   1.1e+03       5      18 ..      37      50 ..      35      54 .. 0.84
   2 ?    3.4   0.0     0.091        91      14      24 ..     281     291 ..     272     301 .. 0.75
   3 ?   -1.9   0.0       4.8   4.8e+03       1      17 [.     336     352 ..     336     363 .. 0.72
   4 !   15.9   0.0   9.6e-06    0.0096       4      28 ..     373     397 ..     370     402 .. 0.83
   5 !    9.7   0.1   0.00092      0.92       2      24 ..     403     425 ..     403     436 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.1
                          TPR_7  5 LarlysrlGdyeeA 18
                                   L  +y++l +y++A
  gene911|gene911|rna910|rna910 37 LSLTYQNLKEYRKA 50
                                   6679*********9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.091
                          TPR_7  14 dyeeAielyeq 24 
                                    ++e+Aie+++ 
  gene911|gene911|rna910|rna910 281 EHEKAIEYFRL 291
                                    89*******97 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.8
                          TPR_7   1 aLlnLarlysrlGdyee 17 
                                    a++ ++++y+ +  ye 
  gene911|gene911|rna910|rna910 336 AWYSIGQAYVTMTMYEY 352
                                    67889999988777765 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 9.6e-06
                          TPR_7   4 nLarlysrlGdyeeAielyeqsLal 28 
                                     L+++y +l+++++Ai++++ +++l
  gene911|gene911|rna910|rna910 373 TLGQCYMNLNRMDDAIGCFKNVIEL 397
                                    69******************96555 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00092
                          TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                    +l+++++y ++  y eA+ +ye+
  gene911|gene911|rna910|rna910 403 YLYIGDAYKNMKMYTEAVVYYEK 425
                                    789*******************9 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       4.7   4.7e+03      18      32 ..      36      50 ..      33      52 .. 0.84
   2 ?    2.1   0.0      0.32   3.2e+02       8      22 ..     125     139 ..     121     141 .. 0.89
   3 ?    5.2   0.1     0.032        32       2      34 .]     255     287 ..     254     287 .. 0.87
   4 ?    3.3   0.0      0.13   1.3e+02       3      24 ..     290     311 ..     288     319 .. 0.82
   5 ?    2.6   0.1      0.22   2.2e+02       2      23 ..     323     344 ..     322     354 .. 0.88
   6 !   20.0   0.0   5.9e-07   0.00059       2      33 ..     357     388 ..     356     389 .. 0.92
   7 ?    2.5   0.0      0.23   2.3e+02      11      32 ..     398     419 ..     390     420 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.7
                         TPR_17 18 nLAelllknGdlmtA 32
                                   +L  ++ +++++++A
  gene911|gene911|rna910|rna910 36 YLSLTYQNLKEYRKA 50
                                   788899999999998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.32
                         TPR_17   8 ldPnnadaynnLAel 22 
                                    ++P  ++ay  LAel
  gene911|gene911|rna910|rna910 125 INPWFWEAYSDLAEL 139
                                    79***********97 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.032
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtArq 34 
                                     ++ l +++  ++ ++  A+++++++++++A++
  gene911|gene911|rna910|rna910 255 AENTLNINKYRSETMCCIANYYSMKKEHEKAIE 287
                                    567778888889******************986 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.13
                         TPR_17   3 lkaleldPnnadaynnLAelll 24 
                                    + +++l+P+++ ++++ +  +l
  gene911|gene911|rna910|rna910 290 RLCVKLNPSSSIVHTLIGHEYL 311
                                    5699**********99987555 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.22
                         TPR_17   2 ylkaleldPnnadaynnLAell 23 
                                    y  al+ +P +  a++  ++++
  gene911|gene911|rna910|rna910 323 YNVALKMCPMDYRAWYSIGQAY 344
                                    667999**************99 PP

  == domain 6  score: 20.0 bits;  conditional E-value: 5.9e-07
                         TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                     +kale+  n++++++ L++++ ++++ ++A+
  gene911|gene911|rna910|rna910 357 IKKALECKNNDPVVWTTLGQCYMNLNRMDDAI 388
                                    58************************988885 PP

  == domain 7  score: 2.5 bits;  conditional E-value: 0.23
                         TPR_17  11 nnadaynnLAelllknGdlmtA 32 
                                    n++d y + + ++++ + + +A
  gene911|gene911|rna910|rna910 398 NDPDGYLYIGDAYKNMKMYTEA 419
                                    79999*********99998887 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.4   5.4e+03      40      52 ..     204     216 ..     202     225 .. 0.82
   2 ?    1.4   0.0      0.53   5.3e+02      42      66 ..     274     298 ..     272     300 .. 0.80
   3 !   11.0   0.0   0.00052      0.52       3      44 ..     306     344 ..     304     346 .. 0.95
   4 !   13.7   0.0   7.6e-05     0.075       3      66 ..     374     432 ..     372     434 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.4
                         TPR_16  40 lgdaalrqgrlae 52 
                                     g ++++q+++++
  gene911|gene911|rna910|rna910 204 AGAVLYHQKDFDG 216
                                    689999**99986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.53
                         TPR_16  42 daalrqgrlaeAaalyraalraapd 66 
                                    + +  ++++++A++++r  ++  p+
  gene911|gene911|rna910|rna910 274 NYYSMKKEHEKAIEYFRLCVKLNPS 298
                                    5677899*********987777776 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00052
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaa 44 
                                     ++++l+ +  ++A+  ++ alk+    P +++A++  g+a+
  gene911|gene911|rna910|rna910 306 IGHEYLEMKSMEKAVSSYNVALKMC---PMDYRAWYSIGQAY 344
                                    599**********************...************98 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 7.6e-05
                         TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                    l++ ++++++ ddA+  ++ +++++     +++ +l+ gda+   + ++eA+ +y+++++ + d
  gene911|gene911|rna910|rna910 374 LGQCYMNLNRMDDAIGCFKNVIELN-----DPDGYLYIGDAYKNMKMYTEAVVYYEKYVETSKD 432
                                    5666999******************.....999************************9987765 PP

>> ChAPs  ChAPs (Chs5p-Arf1p-binding proteins)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   8.3e-07   0.00082     183     297 ..     212     333 ..     206     346 .. 0.78
   2 !    6.2   0.0    0.0044       4.4     259     289 ..     325     355 ..     319     359 .. 0.89
   3 !    8.5   0.0   0.00088      0.87     249     288 ..     349     388 ..     340     395 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.3e-07
                                    T-HHHHHHHHHHHHTT-..GGGHHH.HHHHHHHTT-HHHHHHHHHHHH-SSS-HHHHHHHHHHHHHHSS--HHHHHHHHH CS
                          ChAPs 183 krydralellekLkeee..pevvil.larvllladeEvdavkllneeleeeekdaelLllqaefllskkkeelAlevakr 259
                                    k +d ++e++ek+++++   +   + l    l   ++ + + l +++l+ ++  +e +++ a++   kk++e A+e  + 
  gene911|gene911|rna910|rna910 212 KDFDGCIEIFEKVTRNSfyYDLDYIdLYSNALYIKNDSRVILLAENTLNINKYRSETMCCIANYYSMKKEHEKAIEYFRL 291
                                    566777777777776653322222223344455555566788999999999999************************** PP

                                    HHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHH....T---- CS
                          ChAPs 260 avksaPsefktWalLvkvYikledienALltLN....scPmf 297
                                     vk+ Ps +   +l+ + Y++++ +e+A+ + N     cPm 
  gene911|gene911|rna910|rna910 292 CVKLNPSSSIVHTLIGHEYLEMKSMEKAVSSYNvalkMCPMD 333
                                    ****************************97655222279995 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                                    HHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                          ChAPs 259 ravksaPsefktWalLvkvYikledienALl 289
                                     a k+ P +++ W+ + + Y+++  +e AL+
  gene911|gene911|rna910|rna910 325 VALKMCPMDYRAWYSIGQAYVTMTMYEYALF 355
                                    58899************************97 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00088
                                    --HHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHH CS
                          ChAPs 249 keelAlevakravksaPsefktWalLvkvYikledienAL 288
                                     +e Al   k+a ++  ++   W++L ++Y++l+ +++A+
  gene911|gene911|rna910|rna910 349 MYEYALFFIKKALECKNNDPVVWTTLGQCYMNLNRMDDAI 388
                                    568899999****************************997 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.4   9.4e+03       2      17 ..     209     224 ..     207     240 .. 0.65
   2 ?   -0.6   0.0         2     2e+03       7      53 ..     282     328 ..     278     344 .. 0.67
   3 !    9.9   0.0     0.001         1       2      68 .]     311     377 ..     310     377 .. 0.94
   4 !   20.3   0.0   6.1e-07    0.0006       7      56 ..     350     399 ..     345     404 .. 0.88
   5 ?    4.7   0.0     0.045        45      23      58 ..     398     433 ..     391     435 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.4
                         TPR_19   2 laegdyaeAlalleqa 17 
                                    + ++d++  ++++e++
  gene911|gene911|rna910|rna910 209 YHQKDFDGCIEIFEKV 224
                                    4466666666666664 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2
                         TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                    ++ A+++++   + +p ++ +  l    +l+++  ++A    + +++
  gene911|gene911|rna910|rna910 282 HEKAIEYFRLCVKLNPSSSIVHTLIGHEYLEMKSMEKAVSSYNVALK 328
                                    66777777777777777777777777777777777777766666655 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.001
                         TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLlAkl 68 
                                    l+++  + A++ +  al+  p + +a++   +a++ +  ++ A   +++++e + +d+ +++ l+++
  gene911|gene911|rna910|rna910 311 LEMKSMEKAVSSYNVALKMCPMDYRAWYSIGQAYVTMTMYEYALFFIKKALECKNNDPVVWTTLGQC 377
                                    778888999999999**********************************************988886 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 6.1e-07
                         TPR_19   7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedp 56 
                                    y+ Al + ++al+ +++++ ++  L +++++l++ d+A+ + + + e + 
  gene911|gene911|rna910|rna910 350 YEYALFFIKKALECKNNDPVVWTTLGQCYMNLNRMDDAIGCFKNVIELND 399
                                    566999*********************************99988777665 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.045
                         TPR_19  23 knaearllLAeallalgqldeAealLdalpeedpdd 58 
                                    ++++  l+  +a+ +++ ++eA    +++ e  +dd
  gene911|gene911|rna910|rna910 398 NDPDGYLYIGDAYKNMKMYTEAVVYYEKYVETSKDD 433
                                    578888888**************9999999998887 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.076        76       1      21 [.      30      50 ..      30      50 .. 0.93
   2 ?    3.3   0.0     0.083        82       9      28 ..     205     224 ..     202     226 .. 0.90
   3 !    6.3   0.0    0.0093       9.2       4      30 ..     268     294 ..     266     296 .. 0.89
   4 ?   -2.0   0.0       3.7   3.7e+03       8      29 ..     374     395 ..     372     397 .. 0.75
   5 ?    3.8   0.0     0.057        57       8      31 ..     406     429 ..     403     432 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.076
                         TPR_10  1 tAsslnNLanalrqrgrydeA 21
                                   t+ss+  L+ +++++++y +A
  gene911|gene911|rna910|rna910 30 TLSSREYLSLTYQNLKEYRKA 50
                                   899999************987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.083
                         TPR_10   9 analrqrgrydeAealleea 28 
                                    +++l++++++d+  +++e++
  gene911|gene911|rna910|rna910 205 GAVLYHQKDFDGCIEIFEKV 224
                                    7899*************996 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0093
                         TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                    ++  +an+++  +++++A ++++ ++ 
  gene911|gene911|rna910|rna910 268 TMCCIANYYSMKKEHEKAIEYFRLCVK 294
                                    67779*****************99986 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.7
                         TPR_10   8 LanalrqrgrydeAealleeal 29 
                                    L+  + +++r d+A   ++ ++
  gene911|gene911|rna910|rna910 374 LGQCYMNLNRMDDAIGCFKNVI 395
                                    7777999999999977666655 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.057
                         TPR_10   8 LanalrqrgrydeAealleealai 31 
                                    ++ a+ +++ y+eA+ ++e+ +++
  gene911|gene911|rna910|rna910 406 IGDAYKNMKMYTEAVVYYEKYVET 429
                                    6889***************96666 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.22   2.2e+02      18      56 ..     106     139 ..     104     143 .. 0.74
   2 !   17.6   0.0   1.7e-06    0.0017     144     251 ..     265     371 ..     217     388 .. 0.79
   3 ?    2.3   0.0     0.078        78     144     177 ..     366     399 ..     363     405 .. 0.85
   4 ?   -2.9   0.0       3.2   3.2e+03     223     247 ..     409     433 ..     403     436 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.22
                         TPR_15  18 lykqgdvkkAlevLkeaaqkaapskdteyWrtladLAwa 56 
                                    ly +g+vk+ +++L +++  +    +  +W+ ++dLA  
  gene911|gene911|rna910|rna910 106 LYIEGKVKRDFRIL-SDVVVI----NPWFWEAYSDLAEL 139
                                    67777888888888.444444....689*********75 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.7e-06
                         TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellkawkara...esdasLwgpl 220
                                    +s+  +   a++y+ + ++++A++ +r  ++l+p ss +   +   ++++++ +   ++++ ++ +      d + w   
  gene911|gene911|rna910|rna910 265 RSE-TMCCIANYYSMKKEHEKAIEYFRLCVKLNPSSSIVHTLIGHEYLEMKSME---KAVSSYNVALkmcPMDYRAWYSI 340
                                    343.446789*************************7777777779999999888...599999877677899******** PP

                         TPR_15 221 aaAlllLgrpkkALeylrkqakenrkdplwl 251
                                    + A++++  ++ AL +++k ++ +++dp + 
  gene911|gene911|rna910|rna910 341 GQAYVTMTMYEYALFFIKKALECKNNDPVVW 371
                                    ***************************9875 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.078
                         TPR_15 144 qsaafllaraelyrqegqtdaAlrdyreAlalap 177
                                    +++ ++  +++ y + ++ d+A+ +++++++l++
  gene911|gene911|rna910|rna910 366 NDPVVWTTLGQCYMNLNRMDDAIGCFKNVIELND 399
                                    6899999999999999999999999999988765 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.2
                         TPR_15 223 AlllLgrpkkALeylrkqakenrkd 247
                                    A+  ++ +++A  y++k+ +  ++d
  gene911|gene911|rna910|rna910 409 AYKNMKMYTEAVVYYEKYVETSKDD 433
                                    6777778888888888888877777 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.6   2.6e+03       6      27 ..     277     298 ..     272     304 .. 0.74
   2 !    7.8   0.0    0.0035       3.5       5      56 ..     310     361 ..     306     370 .. 0.86
   3 !    6.7   0.0    0.0078       7.8      20      59 ..     359     398 ..     350     405 .. 0.84
   4 ?    3.3   0.0     0.092        92       2      62 ..     375     433 ..     374     435 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.6
                          TPR_9   6 ireedweralavverllllaPd 27 
                                      ++++e+a+++  + + l+P 
  gene911|gene911|rna910|rna910 277 SMKKEHEKAIEYFRLCVKLNPS 298
                                    5567788888888888888875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0035
                          TPR_9   5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayl 56 
                                    +++ + +e+a   ++  l + P d + ++  G++++ +  ++ Al+    +l
  gene911|gene911|rna910|rna910 310 YLEMKSMEKAVSSYNVALKMCPMDYRAWYSIGQAYVTMTMYEYALFFIKKAL 361
                                    7788899*******************************99999997666666 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0078
                          TPR_9  20 rllllaPddpeerrdRGlllaqlGclsaAladLeaylala 59 
                                      l  + +dp  +   G++++ l+++  A+ ++   ++l+
  gene911|gene911|rna910|rna910 359 KALECKNNDPVVWTTLGQCYMNLNRMDDAIGCFKNVIELN 398
                                    56778999************************99998765 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.092
                          TPR_9   2 kaiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapda 62 
                                     +++++ ++++ a+ +   ++ l+  dp+ ++  G ++  +  + +A+   e y++ + d+
  gene911|gene911|rna910|rna910 375 GQCYMNLNRMDDAIGCFKNVIELN--DPDGYLYIGDAYKNMKMYTEAVVYYEKYVETSKDD 433
                                    567888888999999998888885..55566667888888888888888888888877665 PP

>> TPR_3  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.093        93      10      21 ..      40      51 ..      37      57 .. 0.87
   2 ?    3.0   0.0      0.11   1.1e+02       7      23 ..     200     220 ..     198     225 .. 0.77
   3 ?    4.4   0.0     0.038        38      13      30 ..     278     293 ..     273     298 .. 0.80
   4 ?    2.4   0.4      0.16   1.6e+02      13      26 ..     412     423 ..     409     425 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.093
                                   HHHHTT-HHHHH CS
                          TPR_3 10 efynkkkyqeAr 21
                                   +++n k+y +A+
  gene911|gene911|rna910|rna910 40 TYQNLKEYRKAY 51
                                   8**********8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                    H....HHHHHHTT-HHHHHHH CS
                          TPR_3   7 y....AaefynkkkyqeArel 23 
                                    y    +a++y +k+++  +e 
  gene911|gene911|rna910|rna910 200 YpnlaGAVLYHQKDFDGCIEI 220
                                    555569*********987776 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.038
                                    HTT-HHHHHHH..HHHHH CS
                          TPR_3  13 nkkkyqeArelfsYalla 30 
                                    +kk+ ++A+e+  ++l  
  gene911|gene911|rna910|rna910 278 MKKEHEKAIEY--FRLCV 293
                                    78999******..87855 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.16
                                    HTT-HHHHHHH..H CS
                          TPR_3  13 nkkkyqeArelfsY 26 
                                    n+k y+eA+ +  Y
  gene911|gene911|rna910|rna910 412 NMKMYTEAVVY--Y 423
                                    7999*******..6 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.71   7.1e+02      13      29 ..     211     227 ..     207     229 .. 0.81
   2 ?    3.2   0.3      0.13   1.3e+02       7      26 ..     273     292 ..     267     296 .. 0.80
   3 ?   11.2   0.1   0.00035      0.35       1      28 [.     369     396 ..     369     398 .. 0.91
   4 ?   -1.3   0.1       3.6   3.5e+03       8      25 ..     408     425 ..     407     428 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.71
                            PPR  13 nGkleeAlelfkeMkek 29 
                                      +++ ++e+f++  ++
  gene911|gene911|rna910|rna910 211 QKDFDGCIEIFEKVTRN 227
                                    6799********98776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                            PPR   7 IsgycknGkleeAlelfkeM 26 
                                     + y+ + ++e+A+e+f+  
  gene911|gene911|rna910|rna910 273 ANYYSMKKEHEKAIEYFRLC 292
                                    5679999**********875 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00035
                            PPR   1 vtynslIsgycknGkleeAlelfkeMke 28 
                                    v++++l ++y   +++++A+ +fk  +e
  gene911|gene911|rna910|rna910 369 VVWTTLGQCYMNLNRMDDAIGCFKNVIE 396
                                    79*********************97665 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.6
                            PPR   8 sgycknGkleeAlelfke 25 
                                    ++y    ++ eA+ ++++
  gene911|gene911|rna910|rna910 408 DAYKNMKMYTEAVVYYEK 425
                                    6899999999**999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.53
# Mc/sec: 2653.24
//
Query:       gene912|gene912|rna911|rna911  [L=424]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-38  130.9   0.0    4.9e-38  130.6   0.0    1.2  1  GTP_EFTU         Elongation factor Tu GTP binding domain
      6e-13   49.1   0.1    1.4e-12   47.9   0.1    1.7  1  GTP_EFTU_D3      Elongation factor Tu C-terminal domain
    0.00014   22.0   0.0    0.00057   19.9   0.0    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0023   18.3   0.4      0.011   16.1   0.2    2.3  2  GTP_EFTU_D2      Elongation factor Tu domain 2
     0.0063   15.9   0.0      0.031   13.6   0.0    1.9  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
  ------ inclusion threshold ------
      0.021   14.0   0.0      0.037   13.2   0.0    1.4  1  G-alpha          G-protein alpha subunit
      0.079   13.3   0.2         17    5.8   0.2    2.5  2  Peptidase_U32_C  Peptidase family U32 C-terminal domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   0.0   1.9e-41   4.9e-38       1     182 [.      11     205 ..      11     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 1.9e-41
                                    TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST.............HCHSHHHHHHTSCSSCEEEEEETTC CS
                       GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv.............lDtlkeErergiTiksaaisleket 67 
                                    k+++ni+++ghvD+GK+T+++++l + g ++ ++ ++ +++              lD ++eErerg T ++ ++s+e   
  gene912|gene912|rna911|rna911  11 KKVINIVFVGHVDAGKSTICGQILVQMGLVDPRTLEKYKQMSreqnreswylswcLDINPEERERGKTTEVGTASFE--L 88 
                                    5899*****************************999954444568899*****************************..* PP

                                    SSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETT.....TB..STHHHHHHHHHHHHTTTE.EEEEEESCGST.... CS
                       GTP_EFTU  68 kkylinliDtPGHvdFskevirglrvlDgavlvvdav.....eG..vepqteevlrlalkegvp.iivfiNKmDrl.... 135
                                     +++in++D+PGH +F+ e+i+g++ +D+ vlv++a+      G     qt+e++ l+++  v+ +iv++NKmD      
  gene912|gene912|rna911|rna911  89 PHRRINILDAPGHNQFVFEMINGANRADVGVLVISARinefeAGfeKGGQTREHIFLLKAGSVQrLIVLVNKMDDSsvew 168
                                    *************************************655554466789***************9**********99999 PP

                                    .HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH CS
                       GTP_EFTU 136 .kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk 182
                                     k++++ei+++v + +       + +  +      ++++S+++ge +k
  gene912|gene912|rna911|rna911 169 sKKRFDEIKDKVGSFV-------KRMFPSP----VFIPVSGFTGEYIK 205
                                    9999999999998444.......3332222....47888888887666 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.1   5.5e-16   1.4e-12       3     111 ..     323     422 ..     321     423 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 5.5e-16
                                    EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE CS
                    GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpial 82 
                                    k++++f++ + il     t+i +gY+++l++  ++v++k++e+     +  +   +kk +f ++G +v +++ + +pi++
  gene912|gene912|rna911|rna911 323 KSTQEFTCGLNILDS--DTIISSGYTCILHVGIVTVQCKIKEI-----RDIN---NKKIRFCRHGSRVLAKIVTPSPICV 392
                                    7789***********..**************************.....2222...3467********************* PP

                                    --TT.THCCCCEEEEECTTCEEEEEEEEEE CS
                    GTP_EFTU_D3  83 ekgs.eypqlGrFaiReggrTvaaGvvtei 111
                                      gs + ++  rFa+R + +T+a+Gv+  i
  gene912|gene912|rna911|rna911 393 FYGSrDEEERQRFALRLESKTIAVGVIRAI 422
                                    87763567889****************988 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.2e-07   0.00057       1      87 [.      15     134 ..      15     160 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.2e-07
                                    EEEEEESTTSSHHHHHHHHHTS.....TEEESSSTTSSSSEEEEEEEET..........................TEEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge.....kaivsdkpgtTrdinegrvklk..........................gkeie 49 
                                    ++++vG+  +GKSt+  +++ +         +++++  r+ n++ + l+                          +++i+
  gene912|gene912|rna911|rna911  15 NIVFVGHVDAGKSTICGQILVQmglvdPRTLEKYKQMSREQNRESWYLSwcldinpeerergkttevgtasfelpHRRIN 94 
                                    589****************86545442346699999999999999983333444444444444444444444443455** PP

                                    EEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT........T CS
                       MMR_HSR1  50 lvDtpGliegaseekglgkaflaleeadlillvvdas........e 87 
                                    ++D pG  +    ++ + + +   ++ad+ +lv++a+        e
  gene912|gene912|rna911|rna911  95 ILDAPG--H----NQFVFEMINGANRADVGVLVISARinefeagfE 134
                                    ******..3....233444455566799999999977544433321 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         2   5.1e+03      19      45 ..      16      40 ..      15      41 .. 0.79
   2 !   16.1   0.2   4.4e-06     0.011       3      70 ..     250     311 ..     248     315 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2
                                   EEEEC.TCTTSEEEEEEEEEEEEETEEE CS
                    GTP_EFTU_D2 19 vrilg.ndtskkeivtrissletfhede 45
                                   ++++g +d +k+   t  +++++ ++ +
  gene912|gene912|rna911|rna911 16 IVFVGhVDAGKS---TICGQILVQMGLV 40
                                   667788999999...9999999998866 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.4e-06
                                    EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS..GSSTT CS
                    GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgled..aiivG 70 
                                    v +g+++ G++ +G+ v+il++        tr   l  + e e+ +++++  G+ v++k  e+  +++vG
  gene912|gene912|rna911|rna911 250 VLFGKIECGKVVPGMPVKILPQN-------TRNVILSIMDE-EEVEIEEGEPGDVVKLKLKEEadDVLVG 311
                                    88*****************7733.......44455555533.5555555566666655554443357777 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   1.2e-05     0.031       2     146 ..      16     186 ..      15     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                      Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylardtlrlgati..............................dveksevrflgnltln 51 
                                    ++++G+  +GK++++  i  ++   d ++l+                                 +v   ++  l +  +n
  gene912|gene912|rna911|rna911  16 IVFVGHVDAGKSTICGQILVQMGLVDPRTLEKYKqmsreqnreswylswcldinpeerergkttEVGTASF-ELPHRRIN 94 
                                    56788888888888888888888888888888777888888888888888888888888766445555555.3556699* PP

                      Gtr1_RagA  52 lwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealr..qyspeakvfvlihKmDliqeder 129
                                    ++D +G ++fv e+++        +vgvl+    ++  e+e  +e+  ++ e++   +     ++ vl++KmD  + +  
  gene912|gene912|rna911|rna911  95 ILDAPGHNQFVFEMIN---GANRADVGVLVISARIN--EFEAGFEKGGQTREHIFllKAGSVQRLIVLVNKMDDSSVEWS 169
                                    ***********99755...45567999997665555..8888888777777765511444556899************** PP

                      Gtr1_RagA 130 eeifeerkeeireeiek 146
                                    ++ f+e+k+++ + +++
  gene912|gene912|rna911|rna911 170 KKRFDEIKDKVGSFVKR 186
                                    ********999887765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.037      15      44 ..       5      34 ..       1      65 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                   XXXXXE..EEEEEEEESTTSSHHHHHHHHH CS
                        G-alpha 15 rkarkkkrevkllllGqseSGKsTilkqlk 44
                                   +++ ++k+ ++++++G+ + GKsTi+ q+ 
  gene912|gene912|rna911|rna911  5 EMRISRKKVINIVFVGHVDAGKSTICGQIL 34
                                   45555667*****************99986 PP

>> Peptidase_U32_C  Peptidase family U32 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2    0.0066        17      33      74 ..     267     304 ..     258     309 .. 0.75
   2 ?    4.6   0.0     0.015        38      38      68 ..     352     381 ..     347     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0066
                Peptidase_U32_C  33 EvltPkgenveftveelydedgeeievaphpgqkvkiklpve 74 
                                     +l     n++ ++ +++de++ eie+   pg  vk+kl++e
  gene912|gene912|rna911|rna911 267 KILPQ---NTRNVILSIMDEEEVEIEEG-EPGDVVKLKLKEE 304
                                    55533...4555577999**********.999*****98755 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
                Peptidase_U32_C  38 kgenveftveelydedgeeievaphpgqkvk 68 
                                    +   v+ +++e++d ++++i  ++h   +v 
  gene912|gene912|rna911|rna911 352 GIVTVQCKIKEIRDINNKKIRFCRHG-SRVL 381
                                    5667899****************994.5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2558.42
//
Query:       gene913|gene913|rna912|rna912  [L=107]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-38  131.3   6.5    1.8e-38  131.3   6.5    1.0  1  Ribosomal_S26e  Ribosomal protein S26e


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   6.5     1e-42   1.8e-38       1      97 [.       1      99 [.       1     107 [] 0.95

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 1e-42
                                   X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHHHTT CS
                 Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscaihsk 82
                                   mt+KRrn+gr+kk+rg+vk+++C++c+r++pkdKaikrf +++++e+a+  dl+e+++ye +++P++ +k+++cvsca h+k
  gene913|gene913|rna912|rna912  1 MTVKRRNHGRSKKNRGSVKPIQCDKCGRVTPKDKAIKRFRIQSLIEQASFDDLKEKTIYEVFEVPRMGYKSQFCVSCACHAK 82
                                   9********************************************************************************* PP

                                   SS----TTTTS--S..- CS
                 Ribosomal_S26e 83 vvrvRsredrknre..p 97
                                   +vrvRs+++rk+r   +
  gene913|gene913|rna912|rna912 83 IVRVRSSQARKIRYgfN 99
                                   ************97434 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 719.58
//
Query:       gene914|gene914|rna913|rna913  [L=270]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.1e-37  127.2   0.0    1.3e-36  126.6   0.0    1.3  1  CDC50        LEM3 (ligand-effect modulator 3) family / CDC50 
     0.0092   15.7   0.0      0.015   15.0   0.0    1.3  1  ISK_Channel  Slow voltage-gated potassium channel
  ------ inclusion threshold ------
       0.15   11.8   0.4        1.2    8.9   0.0    2.0  2  DUF2157      Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> CDC50  LEM3 (ligand-effect modulator 3) family / CDC50 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.0   2.2e-40   1.3e-36      39     268 ..      60     265 ..      50     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 2.2e-40
                          CDC50  39 qftvpedl.......kapvyvyYeLtnfyQnhrryvkSrddsqlkgkaksslksssssdCepletakekkekkkiiyPCG 111
                                    ++  ++d+       k++ y++ e+++fyQ + ry kS++++ql+g+  +sl     ++ +pl++++      kiiyP G
  gene914|gene914|rna913|rna913  60 TIPYTNDMstdvylpKGRTYLFLEMKDFYQTNLRYSKSISYDQLRGERPKSL-----NSAKPLSYDDG-----KIIYPAG 129
                                    55556666555566678899****************************4233.....3589**76333.....79***** PP

                          CDC50 112 liAnslFNDtfslveessskltkvnltkkgIawksdkekkfknktkyealeevvkPpnWakkpeeteipelkenedfivW 191
                                    + +ns+  D++     +      v+++++gI+w+s++ +  k + +y+  +evv+Pp W   p+ +eip+l+ +e+fi+W
  gene914|gene914|rna913|rna913 130 MLPNSFPHDSY-----RI---DGVDIETEGISWESER-NAIK-PSSYTR-DEVVSPPLW---PDYDEIPNLSLDERFINW 195
                                    ***********.....42...4699************.7888.466766.9********...66799************* PP

                          CDC50 192 mrtAalptFrKlyrrindeedLkagtyevdiennfpvksFkGtKsivlsttswlGgknpflgiaYlvvGgiclvlai 268
                                    +  A +p+FrKl++ ++     ++g y+++i++ fp     G+K++ ++++s++G kn+fl i  ++vG  +++l++
  gene914|gene914|rna913|rna913 196 IYIAPFPSFRKLWGVVDV---ETEGMYTLNITSMFPY----GKKYVSFAQSSIIGPKNYFLSIGLMLVGLAMILLSL 265
                                    ***************887...56799**********5....9******************************99986 PP

>> ISK_Channel  Slow voltage-gated potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.5e-06     0.015      35     101 ..      26      90 ..       3     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-06
                    ISK_Channel  35 ddklevlyillllgffgfftlGimlsyirskklehshdPynvyiesdaWqkkdkaefqarvlesyka 101
                                    +++ + + il++lg+   ftlGim + + s  +e    Py   + +d++  k ++++  ++ + y++
  gene914|gene914|rna913|rna913  26 ESNRNFMAILFILGLIN-FTLGIMATLVYSSLME-VTIPYTNDMSTDVYLPKGRTYLFLEMKDFYQT 90 
                                    34445667888899987.5**********98776.567***********999999987777766665 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0002       1.2      17      52 ..      19      49 ..      11      56 .. 0.79
   2 ?    0.8   0.1     0.065   3.9e+02      36      53 ..     246     263 ..     230     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0002
                        DUF2157 17 llaryeaeeresarrrsfleallvlGalllglGlil 52
                                   l   y+ e     ++r+f+ +l++lG + ++lG++ 
  gene914|gene914|rna913|rna913 19 LPGTYRSE-----SNRNFMAILFILGLINFTLGIMA 49
                                   55556655.....56789***************985 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.065
                        DUF2157  36 eallvlGalllglGlilf 53 
                                    + +l +G +l+gl++il+
  gene914|gene914|rna913|rna913 246 NYFLSIGLMLVGLAMILL 263
                                    567888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2132.64
//
Query:       gene915|gene915|rna914|rna914  [L=489]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-49  169.6   7.9    3.7e-49  168.4   7.9    1.5  1  Sec1         Sec1 family
  ------ inclusion threshold ------
      0.062   13.2   0.1       0.17   11.8   0.0    1.7  1  GyrB_insert  DNA gyrase B subunit insert domain


Domain annotation for each model (and alignments):
>> Sec1  Sec1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.4   7.9   4.1e-53   3.7e-49       1     573 [.      21     486 ..      21     487 .. 0.77

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 4.1e-53
                                    EEEEE-HHHHHHHHTT--HHHHHTTTEEETT..T..--S-.....BTTSEEEEEE-S-HHHHHHHHH....HHHSS-SBS CS
                           Sec1   1 KvLvlDkelskilssvlkvsdlleegVtkieklk..krepskrealphlkaiyflrptkenidrlak....dfisarryk 74 
                                    K+L++D++++ ils v+ +s  le+  + ++++   +re     +++ + +++++rp   ni+ l++    +      y 
  gene915|gene915|rna914|rna914  21 KALLCDEDTKIILSNVIPHSKFLENDYFLFDNIMnrRRE-----KIQGITCVVVIRPE--NIRWLIEevasP-----FYE 88 
                                    89*********************9966645544324555.....5************9..******755444.....6** PP

                                    -EEEEESS---HHHHHHHHH..S.G.GGGEEEEE----SEEEETTEEE-S..TTHHHHSTTG.....GG.......--HH CS
                           Sec1  75 eyhifftprlseslleglakade.evvkkvklkelnldfvplesdlfsln..pelplsfrdlyldndnsaleeeieslld 151
                                    +y ++ft+++++ +le la +d   v+++v+  e+++df+  ++ l++++  +      +d            ++ s+ +
  gene915|gene915|rna914|rna914  89 RYIVLFTNQIDSLMLEILATSDVyCVISEVH--EIYMDFFKQDDFLYTFHraK-----TSD-----------FTSPSMRK 150
                                    *******************999668999999..*******9999999994211.....112...........23567778 PP

                                    HHHHHHHHHHHHH-..--EEEE-TT-HHHHHHHH...........HHHHTTT--SS--EEEEE-GGG-SSTTTS---BHH CS
                           Sec1 152 riakgLlsvllslekkiPiirykgsaasmvakkladelkekids.kknfesessrqrpvLiIlDRsvDlvtpllhqwTYq 230
                                    r+ +g++s+++ l + iP+ir +    +++ +   d l+++++  +        +q  +Li lDRs+Dl+tpll +w Yq
  gene915|gene915|rna914|rna914 151 RALDGIFSLIMNL-GGIPTIRVQTG-DKYLLEDS-DVLNTRLTGlN-------LEQGGTLIMLDRSFDLYTPLLYEWRYQ 220
                                    9*******88888.78******763.55444444.55565555433.......457899********************* PP

                                    HHHHHHS--BTEEEEEE--SSSEEEEEE--TT..-TTHHHHTTSBHHHHHHHHHHHHHHHHHHHHTTT...-TTHHHHHH CS
                           Sec1 231 aliddllgglnnnnvvleeepkeekeaelvesssDeffaelrhlnfgevgeklkkeakeyqeenekkrngakesiadlkk 310
                                    +l+++  +  ++n vv +      k+++ v++  D+ff+  +++ + ev+e++k  +k+      +k+       + l++
  gene915|gene915|rna914|rna914 221 SLLHEHAD--YENGVVRIG-----KKSYSVLD--DSFFNASKFKDIYEVSEDIKGLIKKAE----FKK-------KRLHE 280
                                    *******9..777777776.....8*******..***********************9876....344.......3599* PP

                                    HH.HH-GGGHHHHHHHHHHHHHHHHHHHHS-HHH.HHHHHHHHHHHHSS--.B--..-HHHHHHHH-TTS-H.HHHHHHH CS
                           Sec1 311 fv.aklpelqeekkklskHtnlaeellkevkkrkldellelEqdlatgesdkkikekkvieeliaddeptseledklRLl 389
                                    f+ + l e + ++++l+ H++  ++++k     +l +l+e+E +++ +  +k     + i+e + + +++s + ++ +Ll
  gene915|gene915|rna914|rna914 281 FIfDDLEENTRLSRQLEAHLSQHGHVMKACL--RLKDLSEMEMNILKN--NKVGR--EEIDEYLVR-KDVS-IIERSKLL 352
                                    *9555***********************998..599*********953..33333..347777777.4444.56****** PP

                                    HHHHH...-B.-HT--GG....GGHHHHGGGGG.........---.BGGG-------.......---------S...TT- CS
                           Sec1 390 llyslvegglkekelkellrelvqsalygleylktlrslek.lgllkkrkgkksskkksslklikeeedeesnydlsgvs 468
                                    ++ysl++++ +++e+k +  +l++++ + +         +k   l  +                 + +d+++      ++
  gene915|gene915|rna914|rna914 353 IIYSLRNKKNPNDEVKRYP-DLIDEV-ESF---------TKrYPLGMPIWR-----Y-----YGYRFDDDVD------IK 405
                                    ******7554555666662.333334.332.........332333222333.....1.....1233333333......55 PP

                                    .----HHHHHHHHHTTT-S-TTTS-BSS-GGGS--------------------------S-EEEEEEEEEE-HHHHHHH. CS
                           Sec1 469 .ryaPllvrlvealikgkklssespslskkdpsqeesssslrsakktnsaskesaekkkkqrviVffvGGvTysEiral. 546
                                      y+P+++r++ +    ++l+ ++ s+                       +++ +     + +iV++  G+TysE+ral 
  gene915|gene915|rna914|rna914 406 lGYQPAVKRVLRHWWT-NRLDGKYFST----------------------VRESENPM---NYIIVYVRNGITYSEYRALc 459
                                    57**************.6666666643......................34455555...78*****************9 PP

                                    HHHT...TSSSEEEEEEEEE--HHHHH CS
                           Sec1 547 rllskqekknkeiiigttsilnpksfl 573
                                    ++++   k+  + +++++s++++k+++
  gene915|gene915|rna914|rna914 460 EYYNIAMKGRSRLYVVGDSMVSYKNIM 486
                                    999976545566**********99987 PP

>> GyrB_insert  DNA gyrase B subunit insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17     106     140 ..     236     270 ..     218     277 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                    GyrB_insert 106 hGnekesvldadffesadYralaelaeklkgLiee 140
                                     G ++ svld +ff+ + ++ + e++e +kgLi++
  gene915|gene915|rna914|rna914 236 IGKKSYSVLDDSFFNASKFKDIYEVSEDIKGLIKK 270
                                    688999***************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2762.50
//
Query:       gene916|gene916|rna915|rna915  [L=598]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-19   69.4   8.3    4.2e-10   39.3   0.2    4.3  4  KH_1         KH domain
  ------ inclusion threshold ------
      0.016   15.1   0.6      0.042   13.7   0.6    1.7  1  HATPase_c_5  GHKL domain
      0.018   14.8   0.1      0.071   13.0   0.1    2.0  1  KH_2         KH domain
      0.098   13.1   2.7         17    5.9   0.1    3.1  3  BRCT_2       BRCT domain, a BRCA1 C-terminus domain
       0.13   11.2   0.2       0.19   10.6   0.2    1.2  1  DUF4553      Domain of unknown function (DUF4553)


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0013       4.5      20      64 ..     111     150 ..     110     152 .. 0.84
   2 ?    3.2   0.0     0.023        81      22      65 ..     231     272 ..     223     273 .. 0.76
   3 !   21.9   0.4   3.2e-08   0.00011       3      66 .]     329     390 ..     328     390 .. 0.89
   4 !   39.3   0.2   1.2e-13   4.2e-10       2      60 ..     396     456 ..     395     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
                                    HHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                           KH_1  20 snIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                    ++IkeI++ t ++I +  ++    +  e  i G+++++ +A+ ++
  gene916|gene916|rna915|rna915 111 EKIKEIMDATDTSICIK-ID----GKVEAFICGKRKSCLDARMKV 150
                                    68******9*****976.65....46899999*999999998766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.023
                                    HHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHHHHHHHHHHH CS
                           KH_1  22 IkeIreetgakIkvpksedegsderevtisG.speavekAkelie 65 
                                    + +I ++t+ +I    +e + +d +ev ++G + + v +Ak++i+
  gene916|gene916|rna915|rna915 231 VEDILADTQSYIA-T-REIC-EDYTEVILKGfDLYEVRRAKNKIN 272
                                    5555566666666.5.4444.7899*****************996 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 3.2e-08
                                    EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT...T.-EEEEEESHHHHHHHHHHHHH CS
                           KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sedegsderevtisGspeavekAkeliee 66 
                                    ++ + ++ v ++ Gk++ +I +I+++  + I++ k +e+   +    tisGs ea + A+ +ie+
  gene916|gene916|rna915|rna915 329 EMDIETETVEFLCGKKNGKITRIMRDVCCGITIHKkPES---TRIHMTISGSSEAFKSALGMIED 390
                                    57889999*****************77*****9975554...8999*****9999*******985 PP

  == domain 4  score: 39.3 bits;  conditional E-value: 1.2e-13
                                    EEEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT......T.-EEEEEESHHHHHHH CS
                           KH_1   2 lrilvPsslvgriIGkgGsnIkeIreetgakIkvpksedeg...sderevtisGspeavekA 60 
                                    l++ ++ +++ riIG gG+nI++I+++ g++Ik+++ e e+      + v+i+ ++++ve+ 
  gene916|gene916|rna915|rna915 396 LTFYIDEKHHKRIIGYGGKNIQKIMKKHGVYIKFMN-ERERkrfAYKDNVVIKTPRKNVENL 456
                                    57899*********************88*******5.444446*999999999999999875 PP

>> HATPase_c_5  GHKL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   1.2e-05     0.042      27      92 ..     366     434 ..     357     447 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                    HATPase_c_5  27 ekrfIrltvrekk...ksliisieNsyegekkklesskskkeehGiGlksireivkkykgnlsieaedg 92 
                                    e+  I++t++ ++   ks + +ie ++ +e   + ++k++k+  G+G k+i++i+kk++  +++ +e +
  gene916|gene916|rna915|rna915 366 ESTRIHMTISGSSeafKSALGMIEDEFPEELTFYIDEKHHKRIIGYGGKNIQKIMKKHGVYIKFMNERE 434
                                    46778888885552335578899999999999999************************9999876654 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     2e-05     0.071      24      55 ..     393     424 ..     378     454 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                                    SCEEEEEEEESCHHHHHTGGGHHHHHHHHHHH CS
                           KH_2  24 anrviiviresqpgivIGkgGsnikkigkelr 55 
                                    ++ +++ i e + +++IG gG+ni+ki k+ +
  gene916|gene916|rna915|rna915 393 PEELTFYIDEKHHKRIIGYGGKNIQKIMKKHG 424
                                    5789999********************98766 PP

>> BRCT_2  BRCT domain, a BRCA1 C-terminus domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.88   3.1e+03      28      50 ..     174     197 ..     166     221 .. 0.69
   2 ?    5.9   0.1    0.0048        17      20      46 ..     311     337 ..     303     370 .. 0.75
   3 ?    5.6   0.2    0.0057        20       5      52 ..     392     432 ..     381     459 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.88
                         BRCT_2  28 IeknGGev.vetitsavyiviaes 50 
                                    +  nGG++ +++  +++ ++i+++
  gene916|gene916|rna915|rna915 174 VVRNGGRIfYHSRINSDKCLISHN 197
                                    678999995333333355555544 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0048
                         BRCT_2  20 sreklkklIeknGGevvetitsavyiv 46 
                                    ++++l k++e+nGG v+ +++ ++ +v
  gene916|gene916|rna915|rna915 311 EKRTLLKIVEENGGYVEGEMDIETETV 337
                                    7899************87775543332 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0057
                         BRCT_2   5 F.eglrFYindaepspsreklkklIeknGGevvetitsavyiviaesne 52 
                                    F e+l+FYi        +ek +k I+ +GG+  ++i +++ + i   ne
  gene916|gene916|rna915|rna915 392 FpEELTFYI--------DEKHHKRIIGYGGKNIQKIMKKHGVYIKFMNE 432
                                    557899***........56778889999999988887664444443333 PP

>> DUF4553  Domain of unknown function (DUF4553)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   5.4e-05      0.19      89     109 ..     527     547 ..     525     552 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.4e-05
                        DUF4553  89 kfdlseiCkWFleTTETkSLv 109
                                    +f+l +  +WF++TTET SL 
  gene916|gene916|rna915|rna915 527 AFKLKNSGQWFIKTTETLSLE 547
                                    79*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 3435.85
//
Query:       gene917|gene917|rna916|rna916  [L=394]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-28   99.4  35.6    2.9e-27   95.6  35.6    1.9  1  AA_permease_2  Amino acid permease
    2.7e-20   72.4  40.2    2.4e-19   69.3  40.2    1.9  1  AA_permease    Amino acid permease
     0.0077   16.2   0.1      0.019   15.0   0.1    1.6  1  TAP35_44       Tapetum specific protein TAP35/TAP44


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6  35.6   4.9e-31   2.9e-27       1     390 [.       5     380 ..       5     393 .. 0.76

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 4.9e-31
                  AA_permease_2   1 lsllsafalvigsvigsgifvkn.....laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                    +++l++++l+i  ++g+g+f        ++++   +++l+v  a+++  + ++l+yaEl+s+ p  gG+ +y+++a+ k 
  gene917|gene917|rna916|rna916   5 IEMLDLLFLSICNMVGIGVFSLAhyvlsQTGTCASSIFLIVASAIIA--TVFGLCYAELGSTYPYAGGDLNYLSRAYTK- 81 
                                    67899**************9988887544444444444444444444..589*******777***************87. PP

                  AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillp 155
                                      +l ++++++++++ l+++++++   +   + +d+ g ++++ +    +l l++++ ++g k + +   il+ lk++ +
  gene917|gene917|rna916|rna916  82 --HLGTIYSVVSILLILPLSCAIMSIKIHECFEEDI-GRDYCIAM----LLGLCTIFLSFGGKLVTWTMRILFFLKVVTV 154
                                    ..7778899999999999**************9999.55645444....999999999*******************877 PP

                  AA_permease_2 156 liiliilglitvdgggfssl.stetdtffpngwpg.vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivl 231
                                      +l+i  + ++ ++ ++++   ++ +++ ++  + ++ gl+ +++sfdG+++ +++++++ +  k +pkai+ ++ +v+
  gene917|gene917|rna916|rna916 155 ASLLVISSISFIVARNAPNPaILDKRNSTVEIDATsIVKGLCFTQFSFDGWNCGNYIANRIHNpgKSFPKAIVGSIWVVT 234
                                    777777777777777777666667777888866653799*********************6666699************* PP

                  AA_permease_2 232 vlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrf 311
                                    ++y+l++++++ vvp d i   +n+  ++  +f+avg ++  +++++++     ++ +  ++ +s ++   + +   P  
  gene917|gene917|rna916|rna916 235 FIYILISLSMMCVVPYDDIV--GNVF-FIDEYFRAVGIPITPRMLSVMV----TLIPTFGSLVCSLIVGTGIIESLVPAK 307
                                    *******************9..5765.5666666666555555555444....444455555555555555666667877 PP

                  AA_permease_2 312 fakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrpgk....ilv 387
                                    f+k  +  s  +  +++++++            +++n+++s  ++g+ ++y l   g+++l+ k p  +rp      +++
  gene917|gene917|rna916|rna916 308 FSKKLEVISLAAFSFIVFVFA----------KLESINWMVSKIAFGISLFYSLSCMGLVVLKLKHPSIERPFNlplaVPL 377
                                    777766655555555555555..........33689******************************99995442222322 PP

                  AA_permease_2 388 aii 390
                                    a+ 
  gene917|gene917|rna916|rna916 378 AAS 380
                                    222 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3  40.2   4.1e-23   2.4e-19       2     390 ..      10     358 ..       9     392 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 4.1e-23
                    AA_permease   2 vlvialggviGtglfvglgvvlsqaGplga.llayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                    +l+ ++ +++G+g+f    +vlsq G  +  +  ++ + ++ + ++l+ +e+ + +p +gg+ +y sr   ++lG   + 
  gene917|gene917|rna916|rna916  10 LLFLSICNMVGIGVFSLAHYVLSQTGTCASsIFLIVASAIIATVFGLCYAELGSTYPYAGGDLNYLSRAYTKHLGTIYSV 89 
                                    7899**********************9887688888888999999*******************************9999 PP

                    AA_permease  81 nylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivg.ii 159
                                        s ++ l+l ++++si i+ +  +++ +  ++ +a +l++ +i+  +g k+   +  il+++k+++++++++++ i+
  gene917|gene917|rna916|rna916  90 V---SILLILPLSCAIMSIKIHEC--FEEDIGRDYCIAMLLGLCTIFLSFGGKLVTWTMRILFFLKVVTVASLLVISsIS 164
                                    9...55555666655555555555..999999*********************************************655 PP

                    AA_permease 160 llaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqv 239
                                    +++  +  +    + l       k n      +  e   ++++ ++ +  f+f+G   + +ia ++ +P ks Pkai   
  gene917|gene917|rna916|rna916 165 FIVARNAPNP---AILD------KRN------STVEIDATSIVKGLCFTQFSFDGWNCGNYIANRIHNPGKSFPKAIVGS 229
                                    5555555555...1222......222......233456899*************************************** PP

                    AA_permease 240 viritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlapli.naviltaalssansslysasRvlysl 318
                                    ++ +t++Y+l++l+++ +vp++d  ++  +      +  +++  g+++ +  + ++v+l+ +++s++ sl++++ ++ sl
  gene917|gene917|rna916|rna916 230 IWVVTFIYILISLSMMCVVPYDD--IVGNVF----FIDEYFRAVGIPITPRMLsVMVTLIPTFGSLVCSLIVGTGIIESL 303
                                    **********************9..555333....6788**********9988345789**************9999887 PP

                    AA_permease 319 akdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrf 390
                                          P k+ kk++        ++  +++s+++++ a+l ++     n++++  a+ + + + l+++ ++++
  gene917|gene917|rna916|rna916 304 -----VPaKFSKKLE--------VISLAAFSFIVFVFAKLESI-----NWMVSKIAFGISLFYSLSCMGLVVL 358
                                    .....3445555544........67777777777777777777.....5555555555555555555555544 PP

>> TAP35_44  Tapetum specific protein TAP35/TAP44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.1e-06     0.019      13      89 ..     145     218 ..     136     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-06
                       TAP35_44  13 llilltflssqlvlslrspklqseaaaseqtkvddsssmakidedaaksaiagffrhkfPlkgWPfpkyppftmvnP 89 
                                    +l +l +++    l ++s    +++ a++ +++d+  s ++i   +a s++ g+   +f + gW    y + ++ nP
  gene917|gene917|rna916|rna916 145 ILFFLKVVTVASLLVISSISFIVARNAPNPAILDKRNSTVEI---DATSIVKGLCFTQFSFDGWNCGNYIANRIHNP 218
                                    4555555555555566666666677778999***********...688*********************99999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2415.16
//
Query:       gene918|gene918|rna917|rna917  [L=285]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-20   73.7   0.0    6.2e-10   39.3   0.0    3.1  3  HEAT_2    HEAT repeats
    4.7e-17   60.9   0.0     0.0012   19.3   0.0    5.6  5  HEAT_PBS  PBS lyase HEAT-like repeat
    2.2e-05   24.3   0.0       0.28   11.6   0.0    4.3  4  HEAT      HEAT repeat
     0.0017   18.8   0.0         12    6.5   0.0    4.2  5  HEAT_EZ   HEAT-like repeat


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0     1e-10   4.5e-07      12      74 ..      46     111 ..      36     116 .. 0.86
   2 !    7.5   0.0    0.0012       5.2       8      47 ..     156     196 ..     151     201 .. 0.79
   3 !   39.3   0.0   1.4e-13   6.2e-10       3      82 ..     184     263 ..     182     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1e-10
                         HEAT_2  12 pdpevrraairaLgrignpealpaLvellededpa..vRraaaeaLgaigd.pealpaLkellddd 74 
                                    ++  ++++a+ +Lg++  +e++  L+++l+de+++  vR++a eaLg ++  +e ++ Lk++++++
  gene918|gene918|rna917|rna917  46 KSILLKHEAAYVLGQMCMEESVHVLLSILSDENEDeiVRHEAGEALGNFKPtKEIVEGLKKYANHP 111
                                    5667899**********************99765445************95499999999998875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                         HEAT_2   8 lendpdpevrr.aairaLgrignpealpaLvellededpav 47 
                                    l +++++  rr +a   L ++ + +a+ aL +++ede++  
  gene918|gene918|rna917|rna917 156 LLDSSECLYRRyQAMFYLRDLETSDAIHALGKAMEDESSLF 196
                                    445555555444************************99876 PP

  == domain 3  score: 39.3 bits;  conditional E-value: 1.4e-13
                         HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvelled..edpavRraaaeaLgaigdpealpaLkellddddddvvR 80 
                                    aL +a+ +d++   ++++  + g++++ e++p+L++ +ed  e+ +vR++ aeaLgaig++++l+aL ++l d+ d + R
  gene918|gene918|rna917|rna917 184 ALGKAM-EDESSLFKHEISFVFGQMRSIESIPYLIKGMEDvkEHGMVRHECAEALGAIGNDKSLEALVKYLYDPCDIL-R 261
                                    799999.9******************************99889999*************************9876654.6 PP

                         HEAT_2  81 ea 82 
                                    e+
  gene918|gene918|rna917|rna917 262 ES 263
                                    54 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   9.7e-05      0.44       2      27 .]      51      76 ..      50      76 .. 0.92
   2 !    9.6   0.0   0.00036       1.6       1      24 [.      83     107 ..      83     110 .. 0.91
   3 !    8.9   0.0   0.00061       2.8       2      27 .]     166     191 ..     166     191 .. 0.96
   4 ?    4.5   0.0     0.017        74       9      27 .]     204     222 ..     198     222 .. 0.88
   5 !   19.3   0.0   2.6e-07    0.0012       1      26 [.     229     254 ..     229     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.7e-05
                                   HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS  2 RraAakaLgqlgdeeaipaLleaLqd 27
                                    ++Aa+ Lgq+  ee++ +Ll  L d
  gene918|gene918|rna917|rna917 51 KHEAAYVLGQMCMEESVHVLLSILSD 76
                                   589******************99986 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00036
                                    HHHHHHHHHHHCTS.GGGHHHHHHH CS
                       HEAT_PBS   1 vRraAakaLgqlgd.eeaipaLlea 24 
                                    vR++A +aLg+++  +e+++ L++ 
  gene918|gene918|rna917|rna917  83 VRHEAGEALGNFKPtKEIVEGLKKY 107
                                    9******************999986 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00061
                                    HHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLqd 27 
                                    R+ A++ L  l + +ai aL +a +d
  gene918|gene918|rna917|rna917 166 RYQAMFYLRDLETSDAIHALGKAMED 191
                                    9********************99987 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.017
                                    HHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS   9 LgqlgdeeaipaLleaLqd 27 
                                     gq+++ e+ip L++  +d
  gene918|gene918|rna917|rna917 204 FGQMRSIESIPYLIKGMED 222
                                    59************98876 PP

  == domain 5  score: 19.3 bits;  conditional E-value: 2.6e-07
                                    HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                    vR+++a+aLg++g + +++aL++ L 
  gene918|gene918|rna917|rna917 229 VRHECAEALGAIGNDKSLEALVKYLY 254
                                    9********************99885 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.15   6.8e+02       5      28 ..      39      62 ..      36      63 .. 0.78
   2 !    5.4   0.0    0.0059        26       4      27 ..      69      94 ..      67      96 .. 0.85
   3 !   11.6   0.0   6.2e-05      0.28       2      28 ..     213     241 ..     213     243 .. 0.94
   4 ?   -0.5   0.0      0.46   2.1e+03       2      19 ..     246     263 ..     246     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.15
                                   HHHHHT-SSHHHHHHHHHHHHHHH CS
                           HEAT  5 llkllsDpspeVReaAakaLgala 28
                                   ++ +  ++s      Aa+ Lg+++
  gene918|gene918|rna917|rna917 39 IVGAFGSKSILLKHEAAYVLGQMC 62
                                   666667777778888*******98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0059
                                   HHHHHHT-..SSHHHHHHHHHHHHHH CS
                           HEAT  4 lllkllsD..pspeVReaAakaLgal 27
                                   +ll+ lsD  ++  VR  A +aLg++
  gene918|gene918|rna917|rna917 69 VLLSILSDenEDEIVRHEAGEALGNF 94
                                   688889998788889*********87 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 6.2e-05
                                    HHHHHHHHT-..SSHHHHHHHHHHHHHHH CS
                           HEAT   2 lPlllkllsD..pspeVReaAakaLgala 28 
                                    +P l+k ++D  ++  VR  +a+aLga+ 
  gene918|gene918|rna917|rna917 213 IPYLIKGMEDvkEHGMVRHECAEALGAIG 241
                                    799************************95 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.46
                                    HHHHHHHHT-SSHHHHHH CS
                           HEAT   2 lPlllkllsDpspeVRea 19 
                                    l +l+k l Dp+   Re+
  gene918|gene918|rna917|rna917 246 LEALVKYLYDPCDILRES 263
                                    5689999****9988886 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.15   6.9e+02      26      55 .]      36      61 ..      29      62 .. 0.78
   2 ?    4.5   0.0     0.012        52      30      54 ..      67      93 ..      63      94 .. 0.83
   3 ?    0.0   0.0      0.29   1.3e+03      25      42 ..     177     194 ..     172     197 .. 0.83
   4 !    6.5   0.0    0.0027        12      30      55 .]     213     240 ..     210     240 .. 0.89
   5 ?   -2.2   0.0       1.5   6.6e+03      30      46 ..     246     262 ..     243     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                        HEAT_EZ 26 vpeilpaLlalLnddsd.eVRaaAagaLgnl 55
                                   v +i+ a++     +++ + +  Aa+ Lg++
  gene918|gene918|rna917|rna917 36 VNAIVGAFG-----SKSiLLKHEAAYVLGQM 61
                                   567888888.....77768899999999997 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                        HEAT_EZ 30 lpaLlalLnddsd.eV.RaaAagaLgn 54
                                   +  Ll+ L+d++  e+ R  A  aLgn
  gene918|gene918|rna917|rna917 67 VHVLLSILSDENEdEIvRHEAGEALGN 93
                                   77899*****7777666*********9 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.29
                        HEAT_EZ  25 lvpeilpaLlalLnddsd 42 
                                    + ++++ aL+++++d+s+
  gene918|gene918|rna917|rna917 177 ETSDAIHALGKAMEDESS 194
                                    66889999****999875 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0027
                        HEAT_EZ  30 lpaLlalLnd.dsd.eVRaaAagaLgnl 55 
                                    +p+L+++++d ++  +VR  +a aLg++
  gene918|gene918|rna917|rna917 213 IPYLIKGMEDvKEHgMVRHECAEALGAI 240
                                    8*********96667***********87 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 1.5
                        HEAT_EZ  30 lpaLlalLnddsdeVRa 46 
                                    l aL++ L d++d  R+
  gene918|gene918|rna917|rna917 246 LEALVKYLYDPCDILRE 262
                                    56888889999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1629.14
//
Query:       gene919|gene919|rna918|rna918  [L=218]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-34  118.5  18.1    3.8e-34  118.4  18.1    1.0  1  HlyIII    Haemolysin-III related


Domain annotation for each model (and alignments):
>> HlyIII  Haemolysin-III related
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.4  18.1   2.1e-38   3.8e-34       4     223 ..       4     203 ..       1     204 [. 0.92

  Alignments for each domain:
  == domain 1  score: 118.4 bits;  conditional E-value: 2.1e-38
                         HlyIII   4 hnEtlniwtHllgailfivlailllslaevkensklakvvvlvfllgallcllcSalyHtlsihseeklrkffaklDysg 83 
                                    ++++l++ +H ++++l i+ ++++ +++ + +     ++ ++++l++ l+++++S++yH+ s++ e k++++f++lD+++
  gene919|gene919|rna918|rna918   4 QKPILRGRIHQVAFYLTIAKTFMYAICCIHRK----GNFGIMIYLMSQLVLFGVSSTYHVTSWKDE-KTKSLFQRLDHIS 78 
                                    688999***********998877777765444....489************************999.************* PP

                         HlyIII  84 Islliagsylplilyalakapkagllylslilalgvlgiisklvplfsrpearplravlfillgllgvipllhlllvltq 163
                                    I+lli g+ +++il  + +++ ++  +l++++++ ++gi+  ++++   + ++ +  +++il g++ v ++  ++  ++ 
  gene919|gene919|rna918|rna918  79 IFLLISGTQTSVILNLV-PTGMYTKYILMMTWTISLAGILKIILMK---KLHMHFDLMVYILHGVSIVPFFRIIMNSIPI 154
                                    **************999.5599******************999999...***************9988888887777886 PP

                         HlyIII 164 lgeaaelalvllvlggvlylvGavfYalrvPErlkpgkfdivghsHqiFHvfvvlgalfh 223
                                     +      l l++lgg++y++G+++Y+++     +p++++ v+++H+iFHv++vl+ +++
  gene919|gene919|rna918|rna918 155 SD------LSLFILGGAIYIIGGLIYGME-----RPNPYPQVFGYHEIFHVMTVLANWCF 203
                                    66......*********************.....**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1348.61
//
Query:       gene920|gene920|rna919|rna919  [L=227]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-34  118.4   9.4    3.1e-34  117.9   9.4    1.2  1  NOT2_3_5  NOT2 / NOT3 / NOT5 family


Domain annotation for each model (and alignments):
>> NOT2_3_5  NOT2 / NOT3 / NOT5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   9.4   1.7e-38   3.1e-34       2     131 .]      97     222 ..      96     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 1.7e-38
                       NOT2_3_5   2 sllnspdsedaekprqyepklphptsisypqeplyeklesakklekldedtLFyiFYysqgtleqllAakeLkkrsWryh 81 
                                    sl++ p+  d ek+  y+p+ p +t++++p+  l   +es+++++kld dtLF+iFY++ gt++q++Aa +Lk  sWr+h
  gene920|gene920|rna919|rna919  97 SLVHIPNFRDLEKN--YTPRTPVETPSFFPKVAL-YVFESQDIFKKLDIDTLFFIFYSQLGTIQQYYAAVQLKTYSWRFH 173
                                    67889999999888..*************99997.5599***************************************** PP

                       NOT2_3_5  82 kelktWflreekeepkekteeyekgsYkyFDye.tWlkrrkkdfkleyekL 131
                                    +++ tWf+r    epk +t +ye+g++ +FDy+ tW+  +k+df++ey++L
  gene920|gene920|rna919|rna919 174 TKYFTWFQRL--DEPKLITADYERGDFLFFDYDvTWSFMKKSDFTFEYKYL 222
                                    **********..99**********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1351.84
//
Query:       gene92|gene92|rna92|rna92  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-05   24.0   0.0    6.4e-05   22.9   0.0    1.5  1  DUF5092   Domain of unknown function (DUF5092)


Domain annotation for each model (and alignments):
>> DUF5092  Domain of unknown function (DUF5092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.5e-09   6.4e-05      40     148 ..      47     151 ..      19     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.5e-09
                    DUF5092  40 ynvyYdAeelnkvlFevvieserrllhrkkvkdPlnnmkIkqvyyYkltveeld.ralveyffkeaksksevkedsiaaveela 122
                                ++ +Y A+ +  ++++v       ++++ k+kdP +  ++k+++y+++  + l  r+ +++ +++  +++  + ds  +++   
  gene92|gene92|rna92|rna92  47 TRHVYLASSIVSMRYTV-----SGAIRIYKLKDPSTRNEVKDILYFEVVRNPLYlRIFKDIQKSNPLRRKGNTMDSLGSSAGDF 125
                                5679************9.....789***********************999986256666666666666677778888888888 PP

                    DUF5092 123 kekklilkaeyfasdddFLeksevre 148
                                ++   ++ka +++++ d   ++++++
  gene92|gene92|rna92|rna92 126 SQVGPVVKAVFIGNELDLVYNTDLQK 151
                                999999***********999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1332.42
//
Query:       gene921|gene921|rna920|rna920  [L=355]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-08   33.0   0.0    1.2e-07   31.9   0.0    1.6  1  NTP_transf_2     Nucleotidyltransferase domain
    3.9e-06   27.0   1.2    3.9e-06   27.0   1.2    2.9  2  PAP_assoc        Cid1 family poly A polymerase
    0.00067   19.9   0.0     0.0019   18.4   0.0    1.8  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    0.00083   19.4   0.0     0.0021   18.1   0.0    1.7  1  Polbeta          Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.6e-11   1.2e-07       3      94 ..      69     184 ..      67     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.6e-11
                                    HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH......................HHHEHHHHHHHHC CS
                   NTP_transf_2   3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre......................kkeegleklaeii 60 
                                    ++++ + +++p+a+v  fGS  +G+  + SDiD+ + l  ++++e                      + + +++ +++i 
  gene921|gene921|rna920|rna920  69 RIKKVIVREFPNADVMPFGSHTTGLIIPSSDIDINIQLGTNTDKEysnkylskirslmmgvsfikkeTLFHIKKCKIPIL 148
                                    799999999*********************************999*******************99988899999***** PP

                                    CCEEECTTEEEEEECEEECCC..CTEEEEEECEEEH CS
                   NTP_transf_2  61 kfleellglevdlvtrekled..pllvksileerpl 94 
                                    kf ++++g ++d++++++ +    + v+++l+e+p+
  gene921|gene921|rna920|rna920 149 KFRDRIFGFRIDISVNQPNGVeaAKFVRYTLKEYPY 184
                                    ***************999998888888888888876 PP

>> PAP_assoc  Cid1 family poly A polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   1.2         4   1.8e+04       5      12 ..     217     224 ..     217     224 .. 0.88
   2 !   27.0   1.2   8.7e-10   3.9e-06       1      59 [.     238     283 ..     238     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 4
                                    HHHHHHHH CS
                      PAP_assoc   5 LLigFFey 12 
                                    LL+ FF++
  gene921|gene921|rna920|rna920 217 LLLSFFQL 224
                                    89****86 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 8.7e-10
                                    -HHHHHHHHHHHHHHT--TTTEEEECSST-EEEHHHHCGCS-SSEECESSSSEBEETTC CS
                      PAP_assoc   1 sLGeLLigFFeyYgreFdyenvvisirtggiltkkekgwesaeskernrfllaIeDPfe 59 
                                    ++G+L+++FF+yYg  F y+   is+++ g+++ ++             ++l+IeDP +
  gene921|gene921|rna920|rna920 238 NIGVLFMDFFQYYGCSFPYKIARISVNKVGYVKNNT-------------KTLSIEDPTD 283
                                    79*************************988654443.............4555666655 PP

>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.3e-07    0.0019       5      94 ..     191     298 ..     189     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.3e-07
                                    HHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHH............TT--TTEEEE............... CS
                tRNA_NucTransf2   5 llKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaa............akwkpkvvid..............l 58 
                                    llK+fl+  +   s+  + G+  Y   ll l++ +++ ++++             +        d               
  gene921|gene921|rna920|rna920 191 LLKHFLTIRNQ--SDAATGGLNSYSQFLLLLSFFQLHPLVQEGqvsplknigvlfM--------DffqyygcsfpykiaR 260
                                    78888887774..99999********************999874444333333330........3333333333333331 PP

                                    ...........EEE..-SS-EEEETTEEEEETTTTS-HHHHH CS
                tRNA_NucTransf2  59 eekea......llkkfdeplvviDPvDpkRNvaaalslekla 94 
                                                +k+ ++ l + DP+Dp+  vaa++ +++l 
  gene921|gene921|rna920|rna920 261 ----IsvnkvgYVKNNTKTLSIEDPTDPECDVAAVCRNSQLI 298
                                    ....03333446888899******************999875 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.6e-07    0.0021      16      58 ..      83     125 ..      68     155 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.6e-07
                                    TTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH CS
                        Polbeta  16 aylFGSrakgkareeSDiDlavllkekldleeelelaaeledi 58 
                                    ++ FGS  +g + ++SDiD+ + l ++ d+e+  ++ +++ ++
  gene921|gene921|rna920|rna920  83 VMPFGSHTTGLIIPSSDIDINIQLGTNTDKEYSNKYLSKIRSL 125
                                    677***********************97777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2480.22
//
Query:       gene922|gene922|rna921|rna921  [L=147]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-50  168.1   0.0    1.1e-49  167.9   0.0    1.0  1  NDK       Nucleoside diphosphate kinase
  ------ inclusion threshold ------
       0.15   11.9   0.0       0.28   11.0   0.0    1.4  1  HTH_23    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   0.0   1.3e-53   1.1e-49       1     131 [.       2     132 ..       2     135 .. 0.99

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 1.3e-53
                                    EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHH CS
                            NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedai 80 
                                    ert+++iKPd++kr+li +ii+r+eekgl ++a k +  +++ +e+hY++ ++kpff+e+ve m+sg v+a+v+ g++a+
  gene922|gene922|rna921|rna921   2 ERTFIMIKPDGIKRRLISRIIQRFEEKGLYLAASKCVIPKRDVLEQHYSHLSSKPFFNEIVESMMSGMVLAMVWVGKNAV 81 
                                    89****************************************************************************** PP

                                    HHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHST CS
                            NDK  81 ekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFk 131
                                    ++ r+liG+t+p+ a+ gtiR+d+g+++g+N++HgSd+ e+aereikl+  
  gene922|gene922|rna921|rna921  82 STGRKLIGETDPQAASIGTIRGDYGITVGKNIIHGSDTVENAEREIKLWIG 132
                                    *************************************************86 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.1e-05      0.28      28      46 ..      12      30 ..      12      34 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.1e-05
                         HTH_23 28 gvsrrTvyrwlkryreeGl 46
                                   g+ rr ++r+++r++e+Gl
  gene922|gene922|rna921|rna921 12 GIKRRLISRIIQRFEEKGL 30
                                   899***********99**8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1023.84
//
Query:       gene923|gene923|rna922|rna922  [L=495]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3588.87
//
Query:       gene924|gene924|rna923|rna923  [L=318]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-16   58.7   4.8    1.9e-05   25.3   0.2    5.4  6  WD40         WD domain, G-beta repeat
    4.2e-08   33.4   0.1          2    8.8   0.0    4.5  4  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
  ------ inclusion threshold ------
      0.016   15.7   3.7        4.5    7.9   0.3    4.5  5  PQQ_3        PQQ-like domain


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   4.1e-05      0.24      13      38 .]      19      44 ..       9      44 .. 0.87
   2 ?    3.2   0.0     0.032   1.9e+02      15      36 ..      64      86 ..      50      88 .. 0.79
   3 !   25.3   0.2   3.2e-09   1.9e-05       3      38 .]      93     127 ..      91     127 .. 0.83
   4 ?   -2.7   0.0       2.2   1.3e+04      10      23 ..     176     194 ..     171     207 .. 0.63
   5 !   14.5   0.0   8.1e-06     0.049       5      38 .]     217     257 ..     213     257 .. 0.77
   6 ?   -0.3   0.0      0.39   2.3e+03       7      28 ..     265     290 ..     261     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                                   EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40 13 vtslafspdgawlasGsdDgtvriWd 38
                                   v+ +afs+ ++++a++s+Dgt+r +d
  gene924|gene924|rna923|rna923 19 VSEIAFSQMHSLMAASSWDGTIRTYD 44
                                   88999*****************9766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.032
                                   EEEEETTSSEEE.EEETTSEEEE CS
                           WD40 15 slafspdgawla.sGsdDgtvri 36
                                    ++fs++ + la +G  Dg++ +
  gene924|gene924|rna923|rna923 64 TCCFSKETPSLAfAGAADGSLQV 86
                                   45599999999779989**9976 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 3.2e-09
                                    EEEEEESS.SS...EEEEEEETTSSEEEEEETTSEEEEEE CS
                           WD40   3 clrtltGH.ss...vtslafspdgawlasGsdDgtvriWd 38 
                                    ++ ++ +H  +   v+++     +++la+Gs+D+tv++Wd
  gene924|gene924|rna923|rna923  93 QVSSFQAHnAGvksVRCF-----SNMLATGSWDKTVKFWD 127
                                    578999**6335558888.....899*************9 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 2.2
                                    S.SS....EEEEEEETTSS CS
                           WD40  10 H.ss....vtslafspdga 23 
                                    H s     ++s+a  +d+ 
  gene924|gene924|rna923|rna923 176 HaSKlnwmIRSIACAQDNE 194
                                    6322455677776555554 PP

  == domain 5  score: 14.5 bits;  conditional E-value: 8.1e-06
                                    EEEESS.SS.....EEEEEEETTSSEEE..EEETTSEEEEEE CS
                           WD40   5 rtltGH.ss.....vtslafspdgawla..sGsdDgtvriWd 38 
                                     +++ H  +     v+s++f p ++ ++  +G+ Dgt+ ++d
  gene924|gene924|rna923|rna923 217 MIFRCHrVDnkvyaVNSVSFLPTNHNILvtAGG-DGTIVFFD 257
                                    578999844478889999999998885333678.****9987 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 0.39
                                    EESS..SSEEEEEEETTSSE.E.EEE CS
                           WD40   7 ltGH..ssvtslafspdgaw.l.asG 28 
                                    +t    +++t+ +f+ +g++ + a+G
  gene924|gene924|rna923|rna923 265 FTQTesQPITCGRFNTNGNYyVyATG 290
                                    55444345999999999999642345 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0     0.001         6      38      69 ..      16      47 ..       6      66 .. 0.87
   2 !    4.9   0.0    0.0053        32      14      78 ..      79     139 ..      66     149 .. 0.76
   3 !    8.8   0.0   0.00034         2       7      69 ..     150     212 ..     145     225 .. 0.85
   4 !    7.1   0.0    0.0011       6.6      35      87 ..     225     276 ..     214     281 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                    ANAPC4_WD40 38 dsevrsLaWkpdgklLavaysdgevrlldaes 69
                                   + +v+++a+++  +l+a +  dg++r +d e+
  gene924|gene924|rna923|rna923 16 SDTVSEIAFSQMHSLMAASSWDGTIRTYDLEN 47
                                   5689*************************998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0053
                    ANAPC4_WD40  14 tedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsv 78 
                                     +dg+l+v  l+  +v ++  ++++  v+s++     ++La +  d +v++ d  s k+v sl+ 
  gene924|gene924|rna923|rna923  79 AADGSLQVVDLQTSQVSSF--QAHNAGVKSVR--CFSNMLATGSWDKTVKFWDTRSSKLVFSLDL 139
                                    4677778888888888888..56666666664..3457999999999999999999999998865 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00034
                    ANAPC4_WD40   7 mDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaes 69 
                                    ++L+A+  + +e++ + ln  +  +++++k +  +rs+a  +d++ +a +  +g+ ++++++s
  gene924|gene924|rna923|rna923 150 KELLAISLSGNEVVTYNLNDINQKKTHASKLNWMIRSIACAQDNETFALGGIEGKAEIFNINS 212
                                    68999999999999999988666666779999**************************99987 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0011
                    ANAPC4_WD40  35 dkedsevrsLaWkp.dgklLavaysdgevrlldaesgkvvhslsvksekavtcl 87 
                                    d++   v+s+++ p + ++L+ a  dg++ ++da+    + + + ++   +tc 
  gene924|gene924|rna923|rna923 225 DNKVYAVNSVSFLPtNHNILVTAGGDGTIVFFDAQARMKIFTQTESQP--ITCG 276
                                    56667889999987245689999***********98877766655555..7775 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.25   1.5e+03      26      39 ..      33      46 ..      28      47 .. 0.82
   2 ?    4.1   0.0     0.012        70      23      40 .]      74      91 ..      72      91 .. 0.92
   3 ?   -0.9   0.0      0.44   2.6e+03      30      38 ..     140     148 ..     112     150 .. 0.71
   4 ?    7.9   0.3   0.00075       4.5      20      39 ..     240     259 ..     223     259 .. 0.85
   5 ?   -2.9   0.0       1.8   1.1e+04      20      28 ..     281     290 ..     267     294 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
                          PQQ_3 26 vgtgdGtlyAlDae 39
                                   ++++dGt++ +D e
  gene924|gene924|rna923|rna923 33 ASSWDGTIRTYDLE 46
                                   4678****999987 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                          PQQ_3 23 lvyvgtgdGtlyAlDaet 40
                                   l ++g+ dG+l  +D +t
  gene924|gene924|rna923|rna923 74 LAFAGAADGSLQVVDLQT 91
                                   689************988 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.44
                          PQQ_3  30 dGtlyAlDa 38 
                                     G++yA D 
  gene924|gene924|rna923|rna923 140 PGKVYAMDL 148
                                    477777775 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.00075
                          PQQ_3  20 dgglvyvgtgdGtlyAlDae 39 
                                      +++++++gdGt++ +Da+
  gene924|gene924|rna923|rna923 240 NHNILVTAGGDGTIVFFDAQ 259
                                    56789999**********95 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 1.8
                          PQQ_3  20 dggl.vyvgt 28 
                                     g++ vy+++
  gene924|gene924|rna923|rna923 281 NGNYyVYATG 290
                                    3443255544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1973.50
//
Query:       gene925|gene925|rna924|rna924  [L=692]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3971.84
//
Query:       gene926|gene926|rna925|rna925  [L=238]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-45  155.9  11.0    1.2e-45  155.9  11.0    1.5  2  ER_lumen_recept  ER lumen protein retaining receptor
    0.00053   19.7   8.4      0.076   12.8   0.2    3.5  4  PQ-loop          PQ loop repeat


Domain annotation for each model (and alignments):
>> ER_lumen_recept  ER lumen protein retaining receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.9  11.0   1.3e-49   1.2e-45       1     147 []      35     185 ..      35     185 .. 0.98
   2 ?   -3.5   0.2       1.9   1.7e+04      15      29 ..     202     217 ..     198     223 .. 0.56

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 1.3e-49
                ER_lumen_recept   1 svaGlSlktqilyalvfltryldlf.lylreeislyntlmkialillsiyiiylilvkfketyekekDtfklellivpsl 79 
                                    s++GlSlktq+lya+vf++ry+dlf +y++  + +yn++mki++i ++i+i++++++k+ +ty+k+ D+f++ +livp++
  gene926|gene926|rna925|rna925  35 SCSGLSLKTQFLYAMVFIFRYVDLFdFYIKGSLGVYNFIMKILFIGFQILILFMMRFKYFSTYDKKWDKFNVLVLIVPCF 114
                                    8************************999988************************************************* PP

                ER_lumen_recept  80 llallfhpg...ssktllevlwtfsiiLesvAilPQlillqktgevesltshyvfalglyRalyllnWivr 147
                                    +++l+f +g      ++ +vl + s++LesvAilPQl++lq+ ge e++ts+y+++lglyRa y +++iv+
  gene926|gene926|rna925|rna925 115 AFSLFFARGgggVYRYTSNVLYISSLFLESVAILPQLVQLQEAGESETMTSKYILLLGLYRASYTIYFIVK 185
                                    ********9**999999***************************************************985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.9
                ER_lumen_recept  15 lvfltryldlf.lylr 29 
                                    +v +  y+d+f +y+r
  gene926|gene926|rna925|rna925 202 IVQTLLYMDFFaIYYR 217
                                    5555556666555554 PP

>> PQ-loop  PQ loop repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.32   2.8e+03      38      51 ..       2      15 ..       1      23 [. 0.59
   2 !   12.8   0.2   8.5e-06     0.076      21      49 ..      27      55 ..      27      59 .. 0.90
   3 !   10.5   0.3   4.4e-05      0.39       2      55 ..     132     185 ..     131     189 .. 0.88
   4 ?   -3.7   0.0       1.2   1.1e+04       5      16 ..     193     204 ..     192     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.32
                        PQ-loop 38 lllwllGdilslly 51
                                   +l  +++d++++ +
  gene926|gene926|rna925|rna925  2 FLSTIIADTFRFCG 15
                                   66666667666644 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.5e-06
                        PQ-loop 21 iikNykrkSteGlSilflllwllGdilsl 49
                                   i k+ +++S++GlS+ + +l  + +i++ 
  gene926|gene926|rna925|rna925 27 ITKIARTRSCSGLSLKTQFLYAMVFIFRY 55
                                   67999*****************9999985 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 4.4e-05
                        PQ-loop   2 seilgyislvlwlvsyiPQiikNykrkSteGlSilflllwllGdilsllyliln 55 
                                    s++l + sl+l++v+ +PQ+++       e +   ++ll  l    +++y+i++
  gene926|gene926|rna925|rna925 132 SNVLYISSLFLESVAILPQLVQLQEAGESETMTSKYILLLGLYRASYTIYFIVK 185
                                    899******************999999999999999999888888888888876 PP

  == domain 4  score: -3.7 bits;  conditional E-value: 1.2
                        PQ-loop   5 lgyislvlwlvs 16 
                                    +g i +++ +v+
  gene926|gene926|rna925|rna925 193 IGNIPIACGIVQ 204
                                    577777887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1541.28
//
Query:       gene928|gene928|rna927|rna927  [L=230]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-29  102.2   5.3    2.1e-29  101.6   5.3    1.2  1  PSP1      PSP1 C-terminal conserved region


Domain annotation for each model (and alignments):
>> PSP1  PSP1 C-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   5.3   1.2e-33   2.1e-29       1      85 [.     132     216 ..     132     216 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 1.2e-33
                           PSP1   1 kqvlrlatpedvstnlenkqdeekalhiaqeklkelnlnmklldaefqfdrkkltfyYvaeervDFreLvkeLfkfyktR 80 
                                    k++lr+a+++d+s++++ k+ e + l+ ++e +++ nlnm++l++e+q+d kk+tfy+ +++r+DFr+L+keLfk++k+R
  gene928|gene928|rna927|rna927 132 KKILRKASADDLSKLKQRKKIEIESLRQCKELVSARNLNMEILSCEYQWDMKKITFYFKSDKRIDFRDLLKELFKIFKVR 211
                                    79****************************************************************************** PP

                           PSP1  81 IwLca 85 
                                    Iw+ca
  gene928|gene928|rna927|rna927 212 IWMCA 216
                                    ****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1333.58
//
Query:       gene929|gene929|rna928|rna928  [L=520]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3323.17
//
Query:       gene930|gene930|rna929|rna929  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.13   12.5   5.0        0.1   12.9   1.4    2.5  2  DUF4383      Domain of unknown function (DUF4383)


Domain annotation for each model (and alignments):
>> DUF4383  Domain of unknown function (DUF4383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.5     0.064   1.2e+03      71      96 ..     107     132 ..      43     157 .. 0.47
   2 ?   12.9   1.4   5.6e-06       0.1      15     105 ..     148     244 ..     138     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.064
                        DUF4383  71 garlyllllgvvylllailgllvldk 96 
                                    g+  y++ +  + +  +++++lv + 
  gene930|gene930|rna929|rna929 107 GGWSYGVDARSLIATQTLYMFLVSQS 132
                                    34444444444445555555555333 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.6e-06
                        DUF4383  15 GvlGfiPgltseydelalageasgakllglfqvnllhnlvhllvGvlgla.........aa.rsasgarlyllllgvvyl 84 
                                    GvlGf   +++    ++   +++++kll  +++ ++++++  ++G +  +         ++  +++ a+++ ++++v++ 
  gene930|gene930|rna929|rna929 148 GVLGFY-EIVT---LSSIKNDKDYGKLLD-LTYPMIFSFLPFVLGEASSLiskwlfqnkLSeYTPRVAKAITVIAAVMCT 222
                                    666666.4443...344444566666666.5666666666666664432212222223323367899************* PP

                        DUF4383  85 llailgllvldkt.anllplng 105
                                    +++i+g++v+ +  +n+ p+++
  gene930|gene930|rna929|rna929 223 VVGIYGVFVMLNVmGNITPVEV 244
                                    *********9999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1877.93
//
Query:       gene93|gene93|rna93|rna93  [L=93]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-21   75.9   0.0    2.2e-21   75.8   0.0    1.1  1  Cyt-b5    Cytochrome b5-like Heme/Steroid binding domain


Domain annotation for each model (and alignments):
>> Cyt-b5  Cytochrome b5-like Heme/Steroid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   1.2e-25   2.2e-21       1      68 [.      20      85 ..      20      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.2e-25
                               EHHHHTTTECTTEEEEEETTEEEECTTTCCCSTTCSHHHHTTTTSBBHHHHHHTTGGCHHHHHHHHGG CS
                     Cyt-b5  1 tleelskhngkndlwvairgkVYDvskflskhpGgesailkyaGkDateafksvvhsekdaekllkky 68
                               t+ee+s+hn+ +d+w++++g VYDv++fl+ hpGg ++i+ky GkD+t+af+   h   + ++ll + 
  gene93|gene93|rna93|rna93 20 TAEEVSRHNKADDCWIIMDGMVYDVTDFLNLHPGGMDVIMKYGGKDCTDAFNEA-HGYVN-KELLLNS 85
                               78***************************************************9.54443.5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 640.78
//
Query:       gene931|gene931|rna930|rna930  [L=419]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-06   28.0   0.1      5e-06   26.6   0.1    1.7  1  Mur_ligase_M  Mur ligase middle domain
  ------ inclusion threshold ------
      0.047   13.9   0.0       0.12   12.6   0.0    1.8  1  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   5.5e-10     5e-06       1     121 [.      70     228 ..      70     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.5e-10
                                    EESSS-HHHHHHHHHHHHHCTEEEEETTC...........................................SS-THHHH CS
                   Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvg...........................................ttnneigl 37 
                                    v+Gt+GK +t  ++ +il++ g  +g+                                              +  e  +
  gene931|gene931|rna930|rna930  70 VAGTKGKGSTCAMVDSILRNYGIRTGLYTsphlidprerirvggrliphskfaqylnevyykiqeaesangmPFFFEFMT 149
                                    89******************955555555556********************************6666655533333334 PP

                                    HHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETTCEEEEET CS
                   Mur_ligase_M  38 pktlaemekkeaeyavlEvsshglge.krlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkeegiavina 115
                                     ++++ +++++++ a++Ev+  gl +   +    +p v+ it+++ dH++ +  t+e++a  Ka +f+       a++ +
  gene931|gene931|rna930|rna930 150 ILAFYVFVHEKVNGAIIEVGLGGLYDcTNIIR--NPVVVGITSLGFDHIEVLgNTIEEIA--KAGIFKPGV---QAFTTH 222
                                    4444455559************9988777766..8***************996899**97..567777333...577777 PP

                                    TSC... CS
                   Mur_ligase_M 116 ddpyak 121
                                    d+p+++
  gene931|gene931|rna930|rna930 223 DNPISA 228
                                    777544 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.4e-05      0.12       1      74 [.     328     401 ..     328     409 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.4e-05
                                    CTTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSS..SSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSE CS
                   Mur_ligase_C   1 vkgRlevvgeadgvtvidDyahnpdslsaalkalreiap..dkrlilvfgpggelgertrtfhdefgrlasalads 74 
                                    ++gR++++   +gv+++ D ah+ +s+    + ++   +  +  ++ +f ++   + ++  +  +  +++s+l+ +
  gene931|gene931|rna930|rna930 328 WPGRFQMIFH-NGVHLYLDGAHTAESIFLCANWFKSRSKlkKVDKHKCFRALLY-YCKGPRDCRDHVKILSKLDFD 401
                                    79*******8.99************99766666666555443344555554333.555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2767.48
//
Query:       gene932|gene932|rna931|rna931  [L=256]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-22   78.7   6.9    2.5e-22   78.7   6.9    2.1  2  U3_assoc_6   U3 small nucleolar RNA-associated protein 6
     0.0054   17.3   0.2     0.0086   16.6   0.2    1.3  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.099   13.1   0.0       0.18   12.3   0.0    1.4  1  KinB_sensor  Sensor domain of alginate biosynthesis sensor pr


Domain annotation for each model (and alignments):
>> U3_assoc_6  U3 small nucleolar RNA-associated protein 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   6.9   4.2e-26   2.5e-22       1      81 [.       9      87 ..       9      89 .. 0.95
   2 ?   -0.8   0.3      0.27   1.6e+03      17      26 ..     225     234 ..     217     255 .. 0.57

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 4.2e-26
                     U3_assoc_6  1 LEqmlpeledleekglFtkeEikeIvkkrrkfEyklqrrgkkkedflkYieyElnLeklrkkRrkrlklkkkksksdysiv 81
                                   +E+m+ eled++++g+F+ +E+++Iv++rrk+E +lqr++kk+ df++Yi+ E+ Lek+r kR+++ ++  ++s++d+ i 
  gene932|gene932|rna931|rna931  9 MERMISELEDYKNRGIFSSDELRKIVETRRKYELRLQRPEKKLLDFVRYIKSECMLEKIRDKRLREKNV--NASLHDMIIP 87
                                   8******************************************************************99..8888886665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.27
                     U3_assoc_6  17 FtkeEikeIv 26 
                                    Ft++Ei e++
  gene932|gene932|rna931|rna931 225 FTEKEIIEVL 234
                                    5555554443 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   1.4e-06    0.0086      70     199 ..      35     254 ..       6     255 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-06
                         AAA_23  70 kvkayveltfenkdgry...trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqer.fee 145
                                    ++++ +el++++  ++                                                      ++++e   e+
  gene932|gene932|rna931|rna931  35 ETRRKYELRLQRPEKKLldfV------------------------------------------------RYIKSECmLEK 66 
                                    333334444433333333332................................................33333322111 PP

                         AAA_23 146 felkdkke........................................................................ 153
                                    +++k+  e                                                                        
  gene932|gene932|rna931|rna931  67 IRDKRLREknvnaslhdmiipkkvvelyrsalyrfndpkiisqftayviekkmygemknvfaecctrnpmdvdlwiycgf 146
                                    11111111222233333333333333333333333333333334444444444444444444444444555555555555 PP

                         AAA_23 154 .........................................rleelekeleeledekkllekl................. 175
                                                                             ++e+l+ke+   e++++++e+                  
  gene932|gene932|rna931|rna931 147 klfevgdiessramflkgirmngkntririeffrmevmyveKIEALNKEIGLDEEDRDEIERGevafaifsdclndssft 226
                                    55555555558888888888888889999999999999999********************99***************99 PP

                         AAA_23 176 ....eqekekekeleeleeeleeilkel 199
                                        ++ +e  k ++el+e++ee++k+ 
  gene932|gene932|rna931|rna931 227 ekeiIEVLEISKSIKELRERIEEYIKDK 254
                                    999989999999************9986 PP

>> KinB_sensor  Sensor domain of alginate biosynthesis sensor protein KinB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05      0.18      59     109 ..     198     248 ..     187     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                    -SHHHHHHHHHHHHHHHHH..HHHHHHHHHS-SSSSHHHHHHHHHHHHHHH CS
                    KinB_sensor  59 vdeaerqaleqiasayrqflqalespatsrrelldnddlseafdklRnrLl 109
                                    +de++r+ +e+ ++a++ f++ l+++  +++e+ +  ++s+++++lR+r+ 
  gene932|gene932|rna931|rna931 198 LDEEDRDEIERGEVAFAIFSDCLNDSSFTEKEIIEVLEISKSIKELRERIE 248
                                    5899*******************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1095  (0.0610742); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1731.54
//
Query:       gene933|gene933|rna932|rna932  [L=1315]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-85  284.4   0.2    1.8e-84  283.3   0.2    1.6  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    3.2e-76  256.6   2.0    6.3e-76  255.7   0.3    2.1  2  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    1.8e-70  236.5   0.0    3.1e-70  235.7   0.0    1.4  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    1.2e-33  116.3   0.1    3.7e-33  114.7   0.1    2.0  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    9.1e-29   99.6   0.1    2.4e-28   98.2   0.1    1.8  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.3   0.2   5.1e-88   1.8e-84       1     266 [.     805    1262 ..     805    1263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 283.3 bits;  conditional E-value: 5.1e-88
                                     B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS............ CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                 RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg............ 66  
                                     GL++ efffh+  gReGL+DtAvkTae+GY+qRrl+kaled+ ++yd++vrns++e+vqf++ged+            
  gene933|gene933|rna932|rna932  805 GLTSPEFFFHAVSGREGLVDTAVKTAETGYMQRRLMKALEDLSIQYDGSVRNSSMEVVQFAFGEDQidpvmsegddpi 882 
                                     9***************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                 RNA_pol_Rpb1_5   67 .............................................................................. 66  
                                                                                                                   
  gene933|gene933|rna932|rna932  883 nlervflqtkskflrslnsgqgpclfqleewdsidnlkrsipkgypverivnkrfietllgfieskrgdkfplngtfy 960 
                                     ****************************************************************************** PP

                                     .......................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS- CS
                                     .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   67 .......................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskni 121 
                                                            ++epG+ vG+ia QSiGePgTQ+tl+TFHfaGvas+n+tlGvprlkei+n+  ni
  gene933|gene933|rna932|rna932  961 syfscndfakiffsaisqkmidlIIEPGTTVGAIAGQSIGEPGTQMTLKTFHFAGVASMNITLGVPRLKEIINAVCNI 1038
                                     ****************************************************************************** PP

                                     SS-EEEEEB-SSSSSCHHHCHHHHHHHSE................................................. CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                 RNA_pol_Rpb1_5  122 ksksltvllvdeeakelekakkvkkaiek................................................. 150 
                                     +++ +++ l d +  +l +a  +k++i k                                                 
  gene933|gene933|rna932|rna932 1039 STPIINAELSDPN--DLFRAEVIKGRIDKislkdicclitevigkdeiflditidleslsrlklnldiykiekslsih 1114
                                     ************9..88888999999999999********************************************** PP

                                     .......................................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTST CS
                                     .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  151 .......................................gikkikrilvkeaekgkeeekelvletegvnlsevlkve 189 
                                                                            g ++++r+++++ ++      ++ l +eg  l +v++++
  gene933|gene933|rna932|rna932 1115 dqtevigenslrihvkkindqsyfnlqkikkkllgtkicGAPQVSRVIINS-NR-----GHYSLVIEGRGLLNVINTD 1186
                                     *************99999999999888888888877777777777777772.22.....467799************* PP

                                     TTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSHH CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  190 evvdageilsndiaeileilgieaarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaelsa 266 
                                     + ++ ++++sn++ e+ e+lgieaar+ +++ei+ +++++g++++ rH++l++d+mt +ge+  ++r Gi k++ s+
  gene933|gene933|rna932|rna932 1187 G-IKSSTTTSNSVTEVEEVLGIEAARAQIIHEIEYTISNHGIKIDPRHIMLLADTMTYRGEVFGITRFGISKMSRST 1262
                                     *.**********************************************************************99875 PP

>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.7   0.3   1.8e-79   6.3e-76       3     312 .]      13     331 ..      11     331 .. 0.95
   2 ?   -0.5   0.1      0.17     6e+02     156     197 ..     695     733 ..     612     753 .. 0.67

  Alignments for each domain:
  == domain 1  score: 255.7 bits;  conditional E-value: 1.8e-79
                                    ---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   3 kikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvfh 82 
                                    +i +i+fg++sp+ei ++Sv e++++++++ +++ P ++G lD rlg+ +k+ +C+tCg+  + C ghfG ++La P+f+
  gene933|gene933|rna932|rna932  13 RIRRISFGLLSPREISSLSVHEISSKDLYDISTRIPLPNGPLDLRLGVGNKKDKCATCGEGLATCIGHFGEVRLALPIFN 92 
                                    799***************************************************************************** PP

                                    HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHH..HHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-EEE.EEETTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                 RNA_pol_Rpb1_1  83 igffklilkilecvckecskllldeekkkllsklk..krekleelkkrlkaieelckkinlcekCgavqpkl.eeegekl 159
                                    +g +k +++ l+c ck c+++ll e+kk +++k k  + +  ++++  l+++ + ckk n+c  C  +++++ +  g ++
  gene933|gene933|rna932|rna932  93 VGLIKNTISTLNCLCKSCGSILLGEKKK-IYFKRKlrESTGGNDTRLILRKVIAECKKANMCFVCSSRNGQVkKTFGFRI 171
                                    *************************988.66666623555667888999**********************94456789* PP

                                    EEEESSSST..............SCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESS CS
                                    xxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 160 kaalkkske..............eekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqld 225
                                     +++++s+                ++e++++  +++++k ++++d e+lgf++    P+ li++++ VpP++iRPsv++d
  gene933|gene933|rna932|rna932 172 AHEIEDSERkkrdkdgkgpggyfPHHEEMNPLMALNIFKMMKEDDYELLGFSE---SPDRLIIQNVIVPPSCIRPSVSMD 248
                                    ****9999999************999*************************99...6*********************** PP

                                    SSSEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 226 ggrrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKe 305
                                     + ++edD+t k+++i+++N+ Lk+ +e+g p ++i+e++++LQ+++a l+++e ++        ++p++++ qrLkGK+
  gene933|gene933|rna932|rna932 249 DEGTNEDDITIKISEIVHTNKILKEGIEKGNPLNLINEDWDHLQLQCALLINSELPQ----VGIPGQPVRGIVQRLKGKN 324
                                    *******************************************************88....667**************** PP

                                    SCCCCCT CS
                                    xxxxxxx RF
                 RNA_pol_Rpb1_1 306 GrfRgnL 312
                                    GrfR+nL
  gene933|gene933|rna932|rna932 325 GRFRCNL 331
                                    ******9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.17
                                    TTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 156 geklkaalkkskeeekeklsaekvkkllkriededvevlgfk 197
                                     +k+ +  kks+  ++e++ + +++++l+ri+ e++  + +k
  gene933|gene933|rna932|rna932 695 ESKILEYSKKSE--SNEEVLEMEISSILNRIR-EECGSICIK 733
                                    334444333333..367777777888888887.555444444 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.7   0.0   8.7e-74   3.1e-70       1     166 []     333     495 ..     333     495 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.7 bits;  conditional E-value: 8.7e-74
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SC CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkrk 80 
                                    Gkrvd+s+R+vispdpnl+++evg+P ++ak+lt+ e+vt++n++kl++lv ngpe+yPga+yv  e+  ++ l + k  
  gene933|gene933|rna932|rna932 333 GKRVDFSGRTVISPDPNLSIEEVGIPERMAKILTISEKVTRFNKEKLQSLVLNGPEKYPGANYVVGEKF-KRFLMYGK-- 409
                                    9***************************************************************98765.55666664.. PP

                                    HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHH CS
                 RNA_pol_Rpb1_2  81 lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEa 160
                                     + el++g++verh+ dgd++l+NRqPsLh++sim+h+vk+ ++ktlr+n++v+t+yNaDFDGDemn+h+pq+e+araEa
  gene933|gene933|rna932|rna932 410 RDAELKYGEVVERHLLDGDMILFNRQPSLHRMSIMSHKVKIHNNKTLRFNECVCTPYNADFDGDEMNVHVPQTEKARAEA 489
                                    499***************************************************************************** PP

                                    HHCSBT CS
                 RNA_pol_Rpb1_2 161 eelllv 166
                                    + l++v
  gene933|gene933|rna932|rna932 490 SILMSV 495
                                    ***986 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.1     1e-36   3.7e-33       1     157 []     498     673 ..     498     673 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 1e-36
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHC... CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpn... 77 
                                    ni++p++g+P+i+++QD+++G+yl+T +d+f+dre + ql+++ +g+    v+++pai +p+el+tgkq++  ++ +   
  gene933|gene933|rna932|rna932 498 NIVTPRHGEPIIAPTQDFITGLYLITGKDTFFDRERFGQLVSYFSGT---RVNIKPAIRRPVELFTGKQLIEALIKDsfg 574
                                    9*******************************************887...799***********************9877 PP

                                    ............CCCEEEESSSS................STSEEECSSEEEES--SHHHHS.SSSTTSHHHHHHHHCHHH CS
                 RNA_pol_Rpb1_3  78 ............einyerkneek................dgkvlikngelikGvidkkvvg.kksqgslihvlakeygik 128
                                                                           dg+v+i ++  + G++dk+++g +++++sli+ ++k    k
  gene933|gene933|rna932|rna932 575 gikersteyqdkS---------IsligknrsfksrndpnDGNVIILDNSYYFGRLDKSIIGgENKKNSLIYAIMKVS-NK 644
                                    7777655555553.........03444445556677788*********************9878889********99.9* PP

                                    HHHHHHHHHHHHHHHHHHHHCEB-TGGGG CS
                 RNA_pol_Rpb1_3 129 etvrfldslqrlgfkyllqsgftigigDt 157
                                    ++vr+++s+++l+ +yl   gf+ig++D+
  gene933|gene933|rna932|rna932 645 AAVRVMNSITKLCSRYLGEVGFSIGLDDV 673
                                    ****************************6 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.1   6.8e-32   2.4e-28      12     108 .]     702     798 ..     692     798 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 6.8e-32
                                    HHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS--SSTSCS CS
                 RNA_pol_Rpb1_4  12 dlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkripkgfsgrt 91 
                                    ++ ++s+ee++e++i++iln++r+++g+i+ k+l+++Ns  +M  +G+KGs+in+sq+++c+Gqq v+g rip+g+++r 
  gene933|gene933|rna932|rna932 702 SKKSESNEEVLEMEISSILNRIREECGSICIKELSIRNSPNTMQACGSKGSKINVSQMVACVGQQIVSGTRIPNGMDDRC 781
                                    67899******************************88******************************************* PP

                                    STTSSSSESSTTTSSEE CS
                 RNA_pol_Rpb1_4  92 lphfkkidespesrGFv 108
                                    lphf +   +pes+GFv
  gene933|gene933|rna932|rna932 782 LPHFPRGCRTPESKGFV 798
                                    ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.96u 0.29s 00:00:01.25 Elapsed: 00:00:00.51
# Mc/sec: 7741.51
//
Query:       gene934|gene934|rna933|rna933  [L=242]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-35  122.3   0.3      1e-33  117.0   0.3    2.0  1  NIF3            NIF3 (NGG1p interacting factor 3)
  ------ inclusion threshold ------
      0.095   11.9   0.1       0.42    9.8   0.0    1.8  2  DS              Deoxyhypusine synthase
       0.13   12.7   0.1       0.93    9.9   0.0    2.1  2  Linker_histone  linker histone H1 and H5 family


Domain annotation for each model (and alignments):
>> NIF3  NIF3 (NGG1p interacting factor 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.3   1.7e-37     1e-33       3     243 ..       7     225 ..       5     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.7e-37
                           NIF3   3 vevleelaplelae.swDnvGlqvgdpekevkkvllaldlteevleeAiekgadliithHPlifkplkrlteddykkrll 81 
                                     +++ ++a l+ a+ +wDnvG+ v d+ ++ +kvll++dlte vlee ie g+  i+++HP+ifk +k+l ++   ++++
  gene934|gene934|rna933|rna933   7 GKAIGRFASLRRAKtDWDNVGVIV-DSGTQDNKVLLTIDLTEPVLEECIELGIKNIVAYHPIIFKAIKKLGSK---ESIV 82 
                                    5788999******99*********.688899**************************************9998...9*** PP

                           NIF3  82 kkliknnislysaHtnlDaapgGvndwlakalglekieplepskeekkeeeeglgrigeleepvsleelakklkkklgle 161
                                    +++ikn+i+++++Ht+lD   +   + l++   +   ++ +p                   +  ++++ +  lk+k g++
  gene934|gene934|rna933|rna933  83 IECIKNGINVFTPHTALDPLMNNYVYSLVNSGAFLYKKNCGP-------------------NFSTIRNAITILKEKSGIK 143
                                    ******************996444444444443333333332...................2357888999999****** PP

                           NIF3 162 kvrva...g.dldkkvkkvaicaGsGaslieeakakgaDlliTGelkhhealdakekgiavidvgHyatErvflealael 237
                                    ++r++   g ++++  +++ +  G+    +      +  + +TGe+ hh+ l   +++ +vi+++H+++Er+ l+++  +
  gene934|gene934|rna933|rna933 144 NFRIClarGhTMESIPESMHVGVGATFRNV----PLKDSIVVTGEMHHHDLLLCIANNASVILMEHSNSERICLKHISSK 219
                                    *99997665456666666666555554333....45556***************************************** PP

                           NIF3 238 Lkeklk 243
                                    L+e+l+
  gene934|gene934|rna933|rna933 220 LQEELP 225
                                    ***986 PP

>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0     7e-05      0.42     132     166 ..      61      95 ..      29     109 .. 0.77
   2 ?   -0.2   0.0     0.079   4.7e+02      59      81 ..     175     197 ..     119     212 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 7e-05
                             DS 132 vwspselikelGkeindeeSilywAykndipvfcp 166
                                    + + + +i +  k++ ++eSi+  + kn+i vf+p
  gene934|gene934|rna933|rna933  61 IVAYHPIIFKAIKKLGSKESIVIECIKNGINVFTP 95 
                                    44666677777788889*****************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.079
                             DS  59 lvdvivtTaggieeDlikalgkk 81 
                                    l d iv T+   ++Dl+ +++++
  gene934|gene934|rna933|rna933 175 LKDSIVVTGEMHHHDLLLCIANN 197
                                    45889999999999999999875 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00016      0.93       4      68 ..      64     125 ..      62     128 .. 0.92
   2 ?    0.2   0.0      0.16   9.7e+02       8      21 ..     129     142 ..     125     147 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00016
                 Linker_histone   4 ykdMikeAIkalkerkGsSrqaIkkyikakykvvdvskfksllkkalkkgvekgelvqpkgkGas 68 
                                    y+ +i +AIk+l ++  + +  Ik+ i    +    ++++ l+++ + ++v++g++   k+ G++
  gene934|gene934|rna933|rna933  64 YHPIIFKAIKKLGSKESIVIECIKNGINVFTPH---TALDPLMNNYVYSLVNSGAFLYKKNCGPN 125
                                    7789***********************998885...789*******************9999986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.16
                 Linker_histone   8 ikeAIkalkerkGs 21 
                                    i +AI+ lke++G+
  gene934|gene934|rna933|rna933 129 IRNAITILKEKSGI 142
                                    789*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1555.55
//
Query:       gene935|gene935|rna934|rna934  [L=105]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-10   41.1   4.9    2.4e-10   40.8   4.9    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
      0.061   13.7   0.1      0.098   13.0   0.1    1.4  1  DUF1456        Protein of unknown function (DUF1456)


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   4.9   2.7e-14   2.4e-10       2      80 ..      17      98 ..      16     105 .] 0.80

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.7e-14
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX- CS
                  Ribosomal_60s  2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaakla....aaaaaaaaaaaaaaaaaaaeekkkeeeeeEee 79
                                    ++++i+++++a g+e+e++++ l+++ + +k++ee++ +g++ +a    ++a  +a++++a+a+a+ +  + kee+e Eee
  gene935|gene935|rna934|rna934 17 LNEKSITELFNAIGAEIEPETMRLFLSKVSNKSMEEIMLKGKELMAslaiSSARESAPTQTADASAPSQTTENKEEKE-EEE 97
                                   5799***************************************999*9885656666666666666666666666665.344 PP

                                   - CS
                  Ribosomal_60s 80 d 80
                                   d
  gene935|gene935|rna934|rna934 98 D 98
                                   4 PP

>> DUF1456  Protein of unknown function (DUF1456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.1e-05     0.098      13      50 ..      16      53 ..      12      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                        DUF1456 13 dlkdedmveifklggvevtkeelsalLkkedeegyeec 50
                                   +l+++ + e+f++ g e+++e+++ +L k +++ +ee+
  gene935|gene935|rna934|rna934 16 ELNEKSITELFNAIGAEIEPETMRLFLSKVSNKSMEEI 53
                                   58999************************999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 741.53
//
Query:       gene936|gene936|rna935|rna935  [L=219]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-33  113.5  21.3    7.3e-33  112.9  21.3    1.3  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
  ------ inclusion threshold ------
       0.51   10.4  13.1       0.52   10.3   3.3    2.3  2  zinc-ribbons_6   zinc-ribbons
        5.3    7.6  13.1    1.8e+02    2.7  13.1    2.7  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain


Domain annotation for each model (and alignments):
>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9  21.3   1.2e-36   7.3e-33       1     107 [.       1     107 [.       1     108 [. 0.99

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 1.2e-36
                     zf-RRPl_C4   1 mkkCkyClskklknlnetvyCeaCeiyfkvknekqkvelvpikelekislrdkLCtkCkeknekekeircetfeeylkkl 80 
                                    m++C+yC+s ++  l+ ++yCe+Ceiy+ +k++kq+++++pi++++++ + d+LC  Ck+k+ ++k+i c+tf+ey++kl
  gene936|gene936|rna935|rna935   1 MSECEYCKSTNMLPLSGKYYCEECEIYYIYKDKKQEYSNLPIEDVNQMCVGDHLCGRCKSKYYEKKTIVCTTFREYFRKL 80 
                                    789***************************************************************************** PP

                     zf-RRPl_C4  81 klCkeCkervekvlkndfvknfllykk 107
                                     lCk+Ck+++ek++kn+f++nf+lyk+
  gene936|gene936|rna935|rna935  81 PLCKKCKKSNEKSIKNAFFRNFILYKM 107
                                    *************************96 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.6     0.012        70       2      56 ..       3      59 ..       2      60 .. 0.68
   2 ?   10.3   3.3   8.7e-05      0.52       2      40 ..      54      91 ..      53      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
                                   --SSS-S--E.E-SSEEE-TTT--EEEEEEE-.SSS-S---EEEETTEEEE--TTTT CS
                 zinc-ribbons_6  2 kCpeCqqele.krgeqyhCeaCqedlkkealC.peCeqelevlkaCgavdyfCnkcn 56
                                   +C+ C++      + +y Ce+C+  +  +    +  + ++e +++ +  d++C +c+
  gene936|gene936|rna935|rna935  3 ECEYCKSTNMlPLSGKYYCEECEIYYIYKDKKqEYSNLPIEDVNQMCVGDHLCGRCK 59
                                   699998765558899999****99665444440445567776665555688888886 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.7e-05
                                   --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S--- CS
                 zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqele 40
                                    C +C+++  +++ ++ C + +e ++k +lC +C+++ e
  gene936|gene936|rna935|rna935 54 LCGRCKSKYYEKK-TIVCTTFREYFRKLPLCKKCKKSNE 91
                                   599****999877.8*******************98755 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  13.1     0.031   1.8e+02       1      47 [.      14      66 ..      14     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.031
                Zn_ribbon_recom  1 lLsGllrCgeCGspmtrrkrkgkr.......hyYrCstyrrkgkkCsnhsiree 47
                                   +LsG+ +C eC   ++++ +k ++          +C + +  g +C+++++ ++
  gene936|gene936|rna935|rna935 14 PLSGKYYCEECEIYYIYKDKKQEYsnlpiedVNQMCVGDHLCG-RCKSKYYEKK 66
                                   69*****************999999999999777888877777.7887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1558.07
//
Query:       gene937|gene937|rna936|rna936  [L=292]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-29  103.5   0.1    2.1e-29  102.5   0.1    1.5  1  ASF1_hist_chap  ASF1 like histone chaperone


Domain annotation for each model (and alignments):
>> ASF1_hist_chap  ASF1 like histone chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.1   1.2e-33   2.1e-29       1     119 [.       1     119 [.       1     142 [. 0.92

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 1.2e-33
                                    X-SEEEEEEEESS-SEETTS-EEEEEEEEESS--SS-EEEEEEEESSSSSGGGEEEEEEEEEES--SEEEEEEEEE---- CS
                 ASF1_hist_chap   1 mslvnvtnvkvlnnpakfsdpfkfeitfeclekLeedlewkliyvgsaeseeedqeLdsvlvGPikvGvnkFvfeadppd 80 
                                    m  +++++vkv + + k+ dp+kf+ +f c +++++ +e++++y    +s+e+dq+L +v + Pi++G+ +F ++ad+pd
  gene937|gene937|rna936|rna936   1 MGYLKLKSVKVDSTTKKLVDPLKFNFRFACSNEIKSGVEFTVLYNMDVHSDENDQVLAEVEIAPIPKGKIEFSIDADAPD 80 
                                    677899************************************************************************** PP

                                    GGGSSSGGGSEEEEEEEEEEETTEEEEEEEEEEEEEETT CS
                 ASF1_hist_chap  81 vskipkedvlgvtvilltasYkeqeFvrvGYyvnneyed 119
                                    v+kip +d++g+t il+   Yk+q+F+r+GY v   y +
  gene937|gene937|rna936|rna936  81 VNKIPLDDIFGLTSILIIGRYKGQQFIRIGYIVDVGYPG 119
                                    *********************************999966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1738.39
//
Query:       gene938|gene938|rna937|rna937  [L=1319]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.83u 0.29s 00:00:01.11 Elapsed: 00:00:00.47
# Mc/sec: 8426.62
//
Query:       gene939|gene939|rna938|rna938  [L=299]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-05   25.1   0.1      0.034   14.4   0.0    2.7  3  ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
      0.001   18.5   0.1       0.93    8.9   0.0    2.8  3  BBS1         Ciliary BBSome complex subunit 1
     0.0016   17.8   5.5        0.2   11.0   0.3    3.1  3  WD40_like    WD40-like domain
  ------ inclusion threshold ------
      0.035   13.2   0.0       0.14   11.2   0.0    1.8  2  VID27        VID27 C-terminal WD40-like domain


Domain annotation for each model (and alignments):
>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00093       4.2       5      72 ..     105     170 ..     102     185 .. 0.86
   2 !   14.4   0.0   7.5e-06     0.034      49      90 ..     187     226 ..     183     228 .. 0.94
   3 ?   -2.4   0.0       1.4   6.2e+03      46      62 ..     254     270 ..     237     273 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00093
                    ANAPC4_WD40   5 ptmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkv 72 
                                    ++   i ++t++g++lv   n+ +vw++   ++ s v +L+ +  gk+ ++   d +vr++d ++ +v
  gene939|gene939|rna938|rna938 105 QSSGHIVIGTNKGKILVLTQNF-EVWKT-FYETPSGVIDLSISGLGKIACIYEIDPTVRIFDLKHSEV 170
                                    555568999********99888.59999.678889999************************998775 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.5e-06
                    ANAPC4_WD40  49 dgklLavaysdgevrlldaesgkvvhslsvksekavtclgWg 90 
                                    +g+ La++ + ge++lld    k+ hs+++ +   +t+l+W 
  gene939|gene939|rna938|rna938 187 NGTHLAIGNDAGEIHLLDTTVMKIQHSSTIPQA--ITTLTWR 226
                                    899*************************99988..******7 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                    ANAPC4_WD40  46 WkpdgklLavaysdgev 62 
                                    +k +g + av  +d+++
  gene939|gene939|rna938|rna938 254 YKCNGFVNAVCLNDNHI 270
                                    45555555666666655 PP

>> BBS1  Ciliary BBSome complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00021      0.93     192     234 ..     105     147 ..      92     157 .. 0.84
   2 !    6.3   0.0    0.0013       5.7     195     229 ..     189     223 ..     184     230 .. 0.88
   3 ?   -2.2   0.0      0.49   2.2e+03      24      37 ..     285     298 ..     283     299 .] 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00021
                           BBS1 192 daisclvigtEskeiyildseaftvlkkvklpsvpvfisatGl 234
                                    +++ ++vigt++++i++l ++     + ++ ps  + +s++Gl
  gene939|gene939|rna938|rna938 105 QSSGHIVIGTNKGKILVLTQNFEVWKTFYETPSGVIDLSISGL 147
                                    57789*************9887777788999999998888887 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
                           BBS1 195 sclvigtEskeiyildseaftvlkkvklpsvpvfi 229
                                    ++l ig +++ei++ld++ ++++++ ++p++ +++
  gene939|gene939|rna938|rna938 189 THLAIGNDAGEIHLLDTTVMKIQHSSTIPQAITTL 223
                                    5799***********************99876665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.49
                           BBS1  24 lkgdgdvkLvvadl 37 
                                    +k+dg++kL++  +
  gene939|gene939|rna938|rna938 285 VKKDGEHKLIILRM 298
                                    899*******9665 PP

>> WD40_like  WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.15   6.6e+02     130     184 ..      27      81 ..      18      88 .. 0.72
   2 !   11.0   0.3   4.4e-05       0.2      91     130 ..     106     145 ..      99     175 .. 0.82
   3 !    7.5   0.4   0.00049       2.2      64     167 ..     159     265 ..     149     280 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
                      WD40_like 130 ennkiysLsesafivfdlfsqnieykisvkdiktfeiienkdilligtegeilil 184
                                    +++kiy   ++++++   ++  ++++i vk+   + +  +++i+l + +g + i+
  gene939|gene939|rna938|rna938  27 TESKIYVSLKKKYVIETGYNALKLRRIPVKENIRVMVGCEENIFLFSDKGGFYIF 81 
                                    6778887777778887788888888888886555555558888888888777664 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.4e-05
                      WD40_like  91 iddklliGtnkGsiyvfskdlqleevllgqsseIkeikie 130
                                      ++++iGtnkG+i v+ +++++ +++    s + +++i+
  gene939|gene939|rna938|rna938 106 SSGHIVIGTNKGKILVLTQNFEVWKTFYETPSGVIDLSIS 145
                                    5689**********************99999999998876 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00049
                      WD40_like  64 tillslleneeevenekieedi..stvkviddklliGtnkGsiyvfskdlqleevllgqsseIkeikiennkiysLsesa 141
                                    t+   +l+++e v++ ki      +++ v + +l+iG + G+i++++  ++  +  +     I  ++  ++ ++   e+ 
  gene939|gene939|rna938|rna938 159 TVRIFDLKHSE-VKSIKIPSGFpqAVAFVNGTHLAIGNDAGEIHLLDTTVMKIQHSSTIPQAITTLTWRDGLLFIGGEDS 237
                                    55555555555.44444443321122234567899999999999998885555555555566677777777777777777 PP

                      WD40_like 142 fivfdlfsqnieykisvk..diktfeii 167
                                    +    +  ++i    s+k  ++ +  ++
  gene939|gene939|rna938|rna938 238 LYLSSIAENGIDIMNSYKcnGFVNAVCL 265
                                    6666666665555444431144444444 PP

>> VID27  VID27 C-terminal WD40-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.16     7e+02     157     171 ..     106     120 ..      94     128 .. 0.81
   2 ?   11.2   0.0   3.1e-05      0.14     123     185 ..     152     217 ..     141     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.16
                          VID27 157 ekGyiavasekGdir 171
                                     +G+i ++ +kG i 
  gene939|gene939|rna938|rna938 106 SSGHIVIGTNKGKIL 120
                                    689999999999985 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.1e-05
                          VID27 123 alfriDPrlsgnklvdselkqyaskndfs.avattekGyiavasekGdirlfdr..lginaktalP 185
                                     ++ iDP ++   l +se+k+ +    f  ava  +  ++a++ + G+i+l d+  + i+  +++P
  gene939|gene939|rna938|rna938 152 CIYEIDPTVRIFDLKHSEVKSIKIPSGFPqAVAFVNGTHLAIGNDAGEIHLLDTtvMKIQHSSTIP 217
                                    59**************************62677777789**************8223444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2125.91
//
Query:       gene940|gene940|rna939|rna939  [L=63]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-11   43.3   0.0    2.9e-11   43.3   0.0    1.0  1  PNK3P     Polynucleotide kinase 3 phosphatase
  ------ inclusion threshold ------
       0.14   12.2   0.1        2.4    8.2   0.0    2.0  2  Rsbr_N    Rsbr N terminal


Domain annotation for each model (and alignments):
>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   3.2e-15   2.9e-11      52     112 ..       3      60 ..       1      63 [] 0.90

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 3.2e-15
                          PNK3P  52 sNqggvvekktkkslekfkekieallkeldvpllvyaatkkdkyRKPetGmweelkkdlee 112
                                    s q++v++    ++le f++ki+++l +ldvp++++aa+kk+kyRKP+tG++e+ ++++ +
  gene940|gene940|rna939|rna939   3 SDQSQVIR---LNTLEVFVKKICNILVDLDVPIMLLAALKKNKYRKPSTGIYEYTCREYVD 60 
                                    67777777...7899***************************************9998765 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.018   1.6e+02     100     123 ..       4      27 ..       1      29 [. 0.77
   2 ?    8.2   0.0   0.00027       2.4      20      43 ..      39      61 ..      32      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.018
                                    T--HHHHHHHHHHHHHHHHHHHHH CS
                         Rsbr_N 100 eeqslelleeieewidpivnelvn 123
                                    ++ ++  l+ +e ++++i n lv+
  gene940|gene940|rna939|rna939   4 DQSQVIRLNTLEVFVKKICNILVD 27 
                                    445566688999999999999996 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00027
                                   HTTSSS-.--HHHHHHHHHHHHHH CS
                         Rsbr_N 20 rkeeslqtisdevyektskefvdl 43
                                   + ++++++ s  +ye t++e+vd 
  gene940|gene940|rna939|rna939 39 K-KNKYRKPSTGIYEYTCREYVDR 61
                                   4.4555668899**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 450.49
//
Query:       gene94|gene94|rna94|rna94  [L=477]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.1e-131  437.4   0.0   6.9e-131  437.2   0.0    1.0  1  RtcB      tRNA-splicing ligase RtcB


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.2   0.0  3.9e-135  6.9e-131       1     412 []      52     477 .]      52     477 .] 0.97

  Alignments for each domain:
  == domain 1  score: 437.2 bits;  conditional E-value: 3.9e-135
                                HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-.....-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHHHS CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk.....gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkelekav 78 
                                q+ +v slpg++ +v+ +PD+H+G+g+piG+V+a++      v++P+++G+DI CGvr+l+tnl+ + ++ek ++l++el+  +
  gene94|gene94|rna94|rna94  52 QISDVCSLPGLIGNVIGLPDIHTGYGFPIGCVAAFDinnpeSVVSPGGIGYDInCGVRALRTNLDISCFKEKAESLADELFGII 135
                                7999************************************99****************************************** PP

                                -------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EEEEEEEE CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       RtcB  79 pvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFiEvqlve 162
                                p+g+gs+k+ +++  +l+++l++g ++ ++ +   +ed e++e++g++++ d++ v +kak r+ +qlGtlGsGNH++Evq+v+
  gene94|gene94|rna94|rna94 136 PTGMGSDKRSNVDLGALDSILDQGLDYLLKLKEIPDEDAEYCESNGRMTG-DSRLVGQKAKGRGLNQLGTLGSGNHYLEVQYVD 218
                                *****999999999**************9999999999**********99.7999***************************** PP

                                EES-HHHHHHHT--TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHHHHHHHHHHHHH CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       RtcB 163 eildeeaakalgleegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlkamqaaanyAkaN 246
                                e++d+e a+ +g++++q+v+m+HsGSRglGh+i++d l  + +       ++   +La+ p +s+e q+Yl  m +aan+A++N
  gene94|gene94|rna94|rna94 219 EVYDTEKAEVMGIRKKQIVLMIHSGSRGLGHRICHDSLMRMARM------STGYGQLACSPYNSKESQEYLLSMGCAANFAFVN 296
                                **********************************9999888833......34568***************************** PP

                                HHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-.............TT--EEEE--S CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx.............xxxxxxxxxxx RF
                       RtcB 247 RqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA.............kvgqpviipGs 313
                                R++it+++r+++e+v+     + +l+l++dv+HNiak E+h+ +    + +VhRKGA rA             ++gqpv++ Gs
  gene94|gene94|rna94|rna94 297 RAMITKKARQAFERVFP----EARLDLIYDVCHNIAKIESHKiNgmeYDAIVHRKGASRAfppghrdipwkykEMGQPVVVGGS 376
                                ****************6....456799***************9457799*********************************** PP

                                TTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE------------------HHHHHHHHC CS
                                xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       RtcB 314 mgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvleEapeaYKdideVveaqaea 395
                                mgt Syi+ G ++++  sfgS++HGAGR++sR k+k  f++++v + l++q i+ ++ ++ g++eE p+ YKdi++Vv+  ++ 
  gene94|gene94|rna94|rna94 377 MGTYSYILCGSEKSMelSFGSSCHGAGRVLSRGKSKDLFTHKNVCDLLRDQDIVFRCPSDPGMVEESPGCYKDINRVVDLSDRI 460
                                ************************************************************************************ PP

                                TS-EEEEEEEEEEEEE- CS
                                xxxxxxxxxxxxxxxxx RF
                       RtcB 396 glvevvarlkpvlvvkg 412
                                gl+++v+rlkp+lv+kg
  gene94|gene94|rna94|rna94 461 GLTKKVCRLKPCLVIKG 477
                                ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 2837.68
//
Query:       gene941|gene941|rna940|rna940  [L=101]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 653.12
//
Query:       gene942|gene942|rna941|rna941  [L=395]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-16   61.0   0.1    5.5e-11   42.4   0.0    3.1  2  His_Phos_2  Histidine phosphatase superfamily (branch 2)
  ------ inclusion threshold ------
       0.21   11.9   4.1        2.4    8.6   1.0    2.4  2  VWC         von Willebrand factor type C domain


Domain annotation for each model (and alignments):
>> His_Phos_2  Histidine phosphatase superfamily (branch 2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   6.2e-15   5.5e-11       2     147 ..      49     172 ..      48     207 .. 0.77
   2 !   13.2   0.0   4.6e-06     0.041     312     383 .]     279     332 ..     241     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 6.2e-15
                                    EEEEEEEEE--SBB-SHHHHHHHHHHHHHHHH.........HHCHHTGCCGGGGT.........--SSSTTS.B-HHHHH CS
                     His_Phos_2   2 LksvvvviRHGdRtPkqkvkksvtspiflsllkkhkeKlkqlktalekkghfpgtyrkveveklqlilkwggelthaGrk 81 
                                    L+++ v+ RHG+RtP+ + + + +s+ ++  +             l      +  +          ++  g+ lth+G +
  gene942|gene942|rna941|rna941  49 LEKLFVIFRHGARTPTRNLTRTWDSQECMPCS-------------LNN-TTISDCK--------RKECSEGD-LTHRGFM 105
                                    88999**************7555555554444.............322.2233333........34777888.******* PP

                                    HHHHHHHHHHHHCHTCCHTTSS--TTEEEEEESSHHHHHHHHHHHHHHCHCCC---.S-TTSTTGGG CS
                     His_Phos_2  82 qaeelGrqfrqrYplgLlrlhltykdlkirassegRviaSAaafakGllglegelt.dllskdkdll 147
                                    q+ +lG+ ++++Y+ +L++++  +k++++ra++  R+  S a +++Gl g    ++ +  ++d++ll
  gene942|gene942|rna941|rna941 106 QMITLGKFIKNNYNSLLFDKKIEQKNIEMRATKIPRTHSSLAGVVRGLTGDTVVENvEIPKSDDTLL 172
                                    **************9999999999*************************655543364445554444 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.6e-06
                                    CS-SEEEEEE-HHHHHHHHHHC..TTTTTBTTB.SSS.TTT..HCCCS-CT-EEEEEEEEETCTTTEEEEEEEC CS
                     His_Phos_2 312 rhvrlrlyfthdshiysllnaL..glpeelagedslaaldrlsaspelpymsqivfelyedssekkfyvrllls 383
                                    + + ++ly++hds i ++l+ +  g+                  s+++ y+s +++e +   ++ k+yvr++++
  gene942|gene942|rna941|rna941 279 KEKHIFLYSAHDSSIGAILTGFdtGI------------------SEWPSYASALFIEIWC--NTGKQYVRMIFN 332
                                    455899*******9999888653333..................669************9..78889*****98 PP

>> VWC  von Willebrand factor type C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.0   0.00026       2.4      10      38 ..      67      96 ..      61     107 .. 0.83
   2 ?    3.7   0.1    0.0086        77      24      42 ..     220     238 ..     198     250 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00026
                            VWC 10 ngeewkpdlCkkCtCkdskv.nCdkikCpe 38
                                      +w ++ C  C+ ++  +  C++++C+e
  gene942|gene942|rna941|rna941 67 LTRTWDSQECMPCSLNNTTIsDCKRKECSE 96
                                   5789***********9966627******97 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0086
                            VWC  24 CkdskvnCdkikCpeskCe 42 
                                    C +  v C++++C+ ++ e
  gene942|gene942|rna941|rna941 220 CSRVPVDCRELNCDIKSVE 238
                                    8888999999999876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2429.21
//
Query:       gene943|gene943|rna942|rna942  [L=391]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-44  151.5   0.0    2.6e-44  150.8   0.0    1.4  1  AAA              ATPase family associated with various cellul
    6.9e-13   48.2   0.1    1.5e-12   47.1   0.1    1.6  1  AAA_lid_3        AAA+ lid domain
      3e-09   36.7   0.1    7.8e-09   35.4   0.1    1.8  1  Prot_ATP_ID_OB   Proteasomal ATPase OB C-terminal domain
    2.6e-08   34.1   0.0    7.4e-08   32.7   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
    2.8e-07   30.4   0.0      6e-07   29.3   0.0    1.5  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.6e-06   26.7   0.1    2.8e-05   24.1   0.1    2.3  1  AAA_5            AAA domain (dynein-related subfamily)
    7.3e-06   26.5   0.0     0.0025   18.2   0.0    2.5  2  AAA_16           AAA ATPase domain
    9.5e-05   22.7   2.2      0.038   14.3   0.4    2.8  2  AAA_22           AAA domain
     0.0029   18.2   1.2      0.019   15.5   0.1    2.7  2  AAA_18           AAA domain
     0.0039   16.7   0.0     0.0074   15.8   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
     0.0045   17.0   0.0     0.0088   16.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0094   15.4   0.0      0.017   14.5   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.015   14.6   0.1       0.22   10.8   0.0    2.4  2  Zeta_toxin       Zeta toxin
      0.017   15.0   0.0      0.031   14.1   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.019   14.1   0.0      0.036   13.2   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
      0.021   14.6   0.4      0.085   12.6   0.1    2.3  2  AAA_24           AAA domain
      0.025   13.8   0.8      0.041   13.1   0.0    1.7  2  TIP49            TIP49 P-loop domain
      0.068   12.9   0.5       0.76    9.5   0.0    2.2  2  AAA_30           AAA domain
      0.069   12.6   0.0       0.16   11.4   0.0    1.6  1  PhoH             PhoH-like protein
      0.075   13.4   0.0       0.15   12.4   0.0    1.6  1  RNA_helicase     RNA helicase
      0.089   12.5   0.0       0.19   11.4   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
       0.09   12.5   0.0       0.28   10.9   0.0    1.9  1  Sigma54_activat  Sigma-54 interaction domain
       0.13   12.4   0.0        0.3   11.2   0.0    1.7  1  AAA_33           AAA domain
       0.13   12.4   0.0       0.44   10.8   0.0    1.8  1  AAA_28           AAA domain
       0.16   11.5   0.0       0.33   10.5   0.0    1.5  1  AAA_25           AAA domain
       0.35   10.6   1.6       0.62    9.8   0.0    1.9  3  AAA_11           AAA domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.8   0.0   3.8e-47   2.6e-44       1     132 []     172     305 ..     172     305 .. 0.96

  Alignments for each domain:
  == domain 1  score: 150.8 bits;  conditional E-value: 3.8e-47
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgs 77 
                                    vllyGppGtGKTlla+ va +++v+fl++  s l++ky+ges++ ire+f+ a++ka p+i+f+DEida++++r   s+s
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATMDVNFLKVVSSALIEKYIGESSRMIREMFAYARRKA-PCIIFMDEIDAIGGKRsreSSS 250
                                    79******************************************************9.****************887777 PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETTS CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieiel 132
                                    +++e +r++ +Ll++ldg+++ ++ v vi+atnrpd ldpallr gR+drkiei+l
  gene943|gene943|rna942|rna942 251 SDREVQRTLMELLNQLDGFNELDN-VKVIMATNRPDILDPALLRpGRLDRKIEIPL 305
                                    88899999999**********755.****************************985 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   2.2e-15   1.5e-12       2      44 ..     328     370 ..     327     371 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 2.2e-15
                      AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                                    +d++ L+++T+G+ GADl ++c eA++ Al++ ++ ++ edf 
  gene943|gene943|rna942|rna942 328 IDYDSLVKLTAGFNGADLRNVCTEAGMIALKDERDYVKHEDFV 370
                                    89***************************************96 PP

>> Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.1   1.1e-11   7.8e-09       1      57 []      58     113 ..      58     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.1e-11
                                    EEEEEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST--TTEEEEEETTTTEEEEEE- CS
                 Prot_ATP_ID_OB   1 VatVsEvlddteraiVktssdeevvvslagavpremLrpgDlVavdkdtgfifEkLP 57 
                                    +++V E l d e+ iVk+s +  +vv + +a++r+ +  g++Va+d +t  i+ +LP
  gene943|gene943|rna942|rna942  58 IGEVLEKLSD-EKFIVKSSQGPRYVVGCMKAIDRKNITTGTRVALDITTLTIMVVLP 113
                                    799*******.******************************************9998 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.1e-10   7.4e-08       6     104 ..     172     264 ..     169     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.1e-10
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG------ CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihpkes 85 
                                    +ll gp g+Gkt+la+ +a +++v    ++  +  s+l+e  +     sr i +  +y +++   i+++DEid i  k+s
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATMDV----NFLKVVSSALIE--KYIGESSRMIREMFAYARRKAPCIIFMDEIDAIGGKRS 245
                                    5789*******************8....999999999999..444456899999999*********************99 PP

                                    -------HHHHHHHHHHHH CS
                          AAA_2  86 sgadvSregVqrdLLqile 104
                                     ++  S  +Vqr L+ +l 
  gene943|gene943|rna942|rna942 246 RESSSSDREVQRTLMELLN 264
                                    999************9986 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   8.7e-10     6e-07      34      94 ..     170     238 ..     161     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8.7e-10
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvk.lkitsgPvleka.gdlaalltnl......eekdvlfideih 94 
                                      vllyGpPG Gkt la+i+a+ ++v+ lk+ s+  +ek  g+ + ++ ++      ++  ++f+dei 
  gene943|gene943|rna942|rna942 170 KGVLLYGPPGTGKTLLARIVAATMDVNfLKVVSSALIEKYiGESSRMIREMfayarrKAPCIIFMDEID 238
                                    569***********************9458999999998524444444444222111233477777775 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   4.1e-08   2.8e-05       1     135 [.     171     292 ..     171     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.1e-08
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--.H CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEverae.s 79 
                                    +vlL GppGtgK+ la+ +aa +  +++ v  ++      l+ ++   ++ +  ++  ++   + ++i+++DE++ +  +
  gene943|gene943|rna942|rna942 171 GVLLYGPPGTGKTLLARIVAATMDVNFLKVVSSA------LIEKYIG-ESSRMIREMFAYARRKAPCIIFMDEIDAIGgK 243
                                    59*********************99999888777......4444441.2222244444444445999********99967 PP

                                    HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       +s  s  e +r l+e +++l ++++   l ++ vi+++n++d     l+pal+
  gene943|gene943|rna942|rna942 244 RSRESSSSDREVQRTLMELLNQLDGFNE---LDNVKVIMATNRPD----ILDPALL 292
                                    7777777777777777666777777766...44699999999999....6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.7e-06    0.0025      16      45 ..     161     190 ..     139     209 .. 0.83
   2 ?    5.9   0.0     0.022        15     123     163 ..     217     264 ..     211     278 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-06
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrell 45 
                                    ++r+    p  vll+G++G+GK+ l+r ++
  gene943|gene943|rna942|rna942 161 FKRIGVRAPKGVLLYGPPGTGKTLLARIVA 190
                                    45555556799**************99776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.022
                         AAA_16 123 lkrllallsrderplvlvlDdlq........wadeaslqllaaLlrlle 163
                                    +++++a+++r + p ++++D+++           ++++++ ++L++ll+
  gene943|gene943|rna942|rna942 217 IREMFAYARR-KAPCIIFMDEIDaiggkrsrESSSSDREVQRTLMELLN 264
                                    5677799999.778*********88888777444444444445554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       6.1   4.2e+03      56      87 ..       9      38 ..       4      71 .. 0.50
   2 !   14.3   0.4   5.5e-05     0.038       8      29 ..     172     193 ..     167     288 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.1
                         AAA_22 56 llrellralglelka..erlsseellealeqalr 87
                                   l++e ++al ++ ka  + + ++e++    ++ +
  gene943|gene943|rna942|rna942  9 LYEEYAQALLSNEKAyqALKMEQEVY----RQTH 38
                                   55555555555444433222222222....2222 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.5e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G++GtGKT+l+r ++ + 
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATM 193
                                    689************9998876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   2.7e-05     0.019       1      68 [.     172     270 ..     172     292 .. 0.58
   2 ?   -0.8   0.0         3   2.1e+03      18      45 ..     333     365 ..     330     385 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.7e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe............... 44 
                                    +ll G+pG+GKt la+ ++  + +                             +e   +  + ++               
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATMDVnflkvvssaliekyigessrmI-------REMFAYARRKAPciifmdeidaiggkr 244
                                    799***************9987334577777666666644443331.......222222222222333344455556664 PP

                         AAA_18  45 ..aldeskrldedkldklldaleens 68 
                                      + ++s+r+++  l++ll++l++ +
  gene943|gene943|rna942|rna942 245 srESSSSDREVQRTLMELLNQLDGFN 270
                                    44444555555555555555555544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3
                         AAA_18  18 Lskrl.gf.gvnlrdvakenglllevdpe...a 45 
                                    L k++ gf g  lr v++e g+    d+    +
  gene943|gene943|rna942|rna942 333 LVKLTaGFnGADLRNVCTEAGMIALKDERdyvK 365
                                    667777778999999999999999999884331 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05    0.0074      30     110 ..     166     238 ..     159     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDl 109
                                    +++ k vll+Gp GtGKt++++ +  ++d        +nf +  s++ + + i ++    r+    +  +  +++F+D++
  gene943|gene943|rna942|rna942 166 VRAPKGVLLYGPPGTGKTLLARIVAATMD--------VNFLKVVSSALIEKYIGESSRMIREMFAYARRKAPCIIFMDEI 237
                                    567789***************99999999........9999999999999999999999998888899999999999988 PP

                          AAA_7 110 n 110
                                    +
  gene943|gene943|rna942|rna942 238 D 238
                                    6 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-05    0.0088      18      60 ..     168     210 ..     144     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                    HTEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEE CS
                           TsaE  18 lgdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYe 60 
                                    + + +lL+G+ G+GKT l+r +a++++v+  +v S   +l+e+Y 
  gene943|gene943|rna942|rna942 168 APKGVLLYGPPGTGKTLLARIVAATMDVNflKVVSS--ALIEKYI 210
                                    34569***********************98877665..5777775 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.5e-05     0.017      24      44 ..     171     191 ..     163     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlps 44 
                                     +ll+GppG+GKt+la+ +++
  gene943|gene943|rna942|rna942 171 GVLLYGPPGTGKTLLARIVAA 191
                                    589*************97765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.32   2.2e+02      42      89 ..      22      67 ..      10      71 .. 0.75
   2 ?   10.8   0.0   0.00031      0.22      13      46 ..     166     197 ..     157     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.32
                     Zeta_toxin 42 rqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllq 89
                                   ++ +++++++  +R+ h +y +   +++ ka + +   ++e+ ekl +
  gene943|gene943|rna942|rna942 22 KAYQALKMEQEVYRQTHKHYLK--SENDVKALQTVGHIIGEVLEKLSD 67
                                   466788899999********99..566777777777777777777655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00031
                     Zeta_toxin  13 qerPklillgGqpGAGKselaellkdelerqgnv 46 
                                     + Pk +ll G pG GK+ la+ +++ +  + n+
  gene943|gene943|rna942|rna942 166 VRAPKGVLLYGPPGTGKTLLARIVAATM--DVNF 197
                                    478**********************999..4555 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.5e-05     0.031       2      31 ..     172     201 ..     171     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-05
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    vll g PG++ktll++ +a ++d++f ++ 
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATMDVNFLKVV 201
                                    7999**********************8874 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.2e-05     0.036      54     116 ..     170     237 ..     130     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrlie..vekedlkelpklvellr...erperfilfvDDL 116
                                    + vLL+G  GtGK  l + + +++  + L+++   + ++ + e +++++++    +r+  +i+f+D +
  gene943|gene943|rna942|rna942 170 KGVLLYGPPGTGKTLLARIVAATMDVNFLKVVSsaLIEKYIGESSRMIREMFayaRRKAPCIIFMDEI 237
                                    679****************************9744445667777777666542336677799999975 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.5   2.4e+03      82     120 ..      30      67 ..      25     102 .. 0.78
   2 ?   12.6   0.1   0.00012     0.085       4      22 ..     171     189 ..     168     289 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.5
                         AAA_24  82 laevirqnekaeskedkgdgkGygelaeefrrllkklqe 120
                                     +ev+rq++k++  ++ +d+k+ + +++ ++++l+kl++
  gene943|gene943|rna942|rna942  30 EQEVYRQTHKHYL-KSENDVKALQTVGHIIGEVLEKLSD 67 
                                    5677888888555.4778888888888888888887765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00012
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     +l+yGp+g+GKT la+  
  gene943|gene943|rna942|rna942 171 GVLLYGPPGTGKTLLARIV 189
                                    589***********99866 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.2       3.2   2.2e+03     142     177 ..      13      48 ..       4      69 .. 0.69
   2 ?   13.1   0.0     6e-05     0.041      49      93 ..     168     210 ..     160     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.2
                                    -EEEEEE-SS-EEEEEE-HHHHHHHHHHT--TT-EE CS
                          TIP49 142 evkitlktakeekklklgskiaeellkekvkegDvi 177
                                    +++  l  +k  + lk++++++ + +k+ +k+++ +
  gene943|gene943|rna942|rna942  13 YAQALLSNEKAYQALKMEQEVYRQTHKHYLKSENDV 48 
                                    455567777888888888888888888887654333 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                    a ++vLl Gp+gtGkt la  ++  +   v f ++++s +    +
  gene943|gene943|rna942|rna942 168 APKGVLLYGPPGTGKTLLARIVAATMD--VNFLKVVSSALIEKYI 210
                                    5689***************99998875..9999999987755444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.38   2.6e+02     144     190 ..      22      74 ..      13      76 .. 0.64
   2 ?    9.5   0.0    0.0011      0.76      21      51 ..     172     202 ..     162     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.38
                         AAA_30 144 agigtaeLt.evvRqkeseeraaalalr....egdae.ealealadrgriheg 190
                                    ++ ++ +++ ev+Rq+++++ +  ++++     g++  e+le+l+d+++i  +
  gene943|gene943|rna942|rna942  22 KAYQALKMEqEVYRQTHKHYLKSENDVKalqtVGHIIgEVLEKLSDEKFIVKS 74 
                                    455566664279***88766555555551112566558999999999998765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                         AAA_30  21 avltGpAGtGKttalkalreaweaaggrvig 51 
                                    ++l Gp+GtGKt + + ++++++ +  +v+ 
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATMDVNFLKVVS 202
                                    5789*********999999888766666665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.16      22      43 ..     172     193 ..     162     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                    EEEE--TTSSTTHHHHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                    v   Gp GtGKt+la  +a+++
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATM 193
                                    7789***********9999875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00022      0.15       1      23 [.     172     194 ..     172     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                    ++lyGp+g+GK++la+ +a+++ 
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATMD 194
                                    689*************9887765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00028      0.19      45      68 ..     167     190 ..     161     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialg 68 
                                    ++ ++++l Gp+G+GK+ la  ++
  gene943|gene943|rna942|rna942 167 RAPKGVLLYGPPGTGKTLLARIVA 190
                                    566789*************97554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00041      0.28      21      47 ..     168     194 ..     159     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                                    SSS-EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat  21 tdlsvlitGesGtGKellaraiheask 47 
                                     +  vl+ G  GtGK+llar + ++ +
  gene943|gene943|rna942|rna942 168 APKGVLLYGPPGTGKTLLARIVAATMD 194
                                    55779***************9876554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00044       0.3       2      24 ..     172     194 ..     172     270 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                         AAA_33   2 vllvGlpGsGKstlaerllkklg 24 
                                    vll G+pG+GK+ la+ +++  +
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATMD 194
                                    7899***********99886655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00064      0.44       2      25 ..     172     196 ..     171     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
                         AAA_28   2 ivitGgestGKTtlleaLaar.gyp 25 
                                    + + G+++tGKT l++  aa+ +++
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAATmDVN 196
                                    6799**************9976333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00048      0.33      36      55 ..     172     191 ..     143     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                         AAA_25  36 allaGapgtGKttlaldlal 55 
                                    +ll+G+pgtGKt la  +a+
  gene943|gene943|rna942|rna942 172 VLLYGPPGTGKTLLARIVAA 191
                                    79************976666 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       8.4   5.8e+03     111     115 ..      31      35 ..       4      70 .. 0.48
   2 ?    9.8   0.0    0.0009      0.62      18      35 ..     170     189 ..     154     231 .. 0.76
   3 ?   -1.8   0.0       3.1   2.1e+03     170     203 ..     248     282 ..     235     284 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.4
                         AAA_11 111 ekvek 115
                                    ++v +
  gene943|gene943|rna942|rna942  31 QEVYR 35 
                                    11111 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0009
                         AAA_11  18 eitliqGPPGtgKT..ktiv 35 
                                    + +l+ GPPGtgKT    iv
  gene943|gene943|rna942|rna942 170 KGVLLYGPPGTGKTllARIV 189
                                    55799*********553333 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.1
                         AAA_11 170 lkkerkelskeleeaeesle.eevldeaeivltTl 203
                                    ++++ +e++++l e  ++l   + ld+++++++T+
  gene943|gene943|rna942|rna942 248 SSSSDREVQRTLMELLNQLDgFNELDNVKVIMATN 282
                                    33333333333333333332467899999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      703  (0.0392102); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 2243.49
//
Query:       gene944|gene944|rna943|rna943  [L=602]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-67  227.2   2.6    2.8e-67  226.0   2.6    1.6  1  DUF5088   Domain of unknown function (DUF5088)


Domain annotation for each model (and alignments):
>> DUF5088  Domain of unknown function (DUF5088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.0   2.6   1.6e-71   2.8e-67       2     186 .]     192     374 ..     191     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 226.0 bits;  conditional E-value: 1.6e-71
                        DUF5088   2 kvilktrlstvsssgslplfffiilstsaglvkvvvWkealrkysslkvGDiivikkfrkkkkiealskidrntfsetky 81 
                                     v++ktr+s+v++++++p++ffi+l++s +++kv+vW e+l +yss+kvGD i+++k rkk  ie+ +++++n+f+e++y
  gene944|gene944|rna943|rna943 192 WVVYKTRMSSVTYTRKYPYYFFILLTSSLDFIKVFVWGEDL-PYSSMKVGDGICLTKCRKKSIIEGPPVVEHNRFTEARY 270
                                    699**************************************.************************************** PP

                        DUF5088  82 fdvkEisvkeilkiellkkkekvkeiFttvvGkveYlsvllrksangkyeeYvllkvsgikvvLlansdkelydievgks 161
                                    f++kE+s+ke+++i+l + +e+   +F +++G++eYlsvl+r++ +g++eeY+l+++++ kv+L++ns++e+y++evgk+
  gene944|gene944|rna943|rna943 271 FRCKEVSAKEMFRINLDRCQEMPASVFAEAFGRIEYLSVLNRRN-AGYLEEYYLVRMGEYKVLLFYNSSREFYEMEVGKY 349
                                    ********************************************.9********************************** PP

                        DUF5088 162 ieitelRkikrgefefyistiytqf 186
                                    ++it+lR ++rg++efy+stiytq+
  gene944|gene944|rna943|rna943 350 VRITNLRTSRRGRSEFYVSTIYTQI 374
                                    ************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 3557.72
//
Query:       gene945|gene945|rna944|rna944  [L=150]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.3e-08   32.7   0.0    6.6e-07   29.2   0.0    2.3  2  Nup35_RRM  Nup53/35/40-type RNA recognition motif


Domain annotation for each model (and alignments):
>> Nup35_RRM  Nup53/35/40-type RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   3.7e-11   6.6e-07       2      89 ..      50     122 ..      49     131 .. 0.91
   2 !    2.5   0.0    0.0078   1.4e+02      22      46 ..     115     139 ..     114     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.7e-11
                                    XXXXXXX-EEEE-S-GGGHHHHHHHHHTTS-BSS--CCC------------EETTEEEEEBS-HHHHHHHHTTTTEEETT CS
                      Nup35_RRM   2 eketsdtsvivFGfpesianevlehFskfGeiledvqvlklgkglnpkpiptgenwvkltYksessaskAlqengtilng 81 
                                    +++ +++ v+++Gf +   + v+   + +G +le                  g+nw+++ +++e s ++ l+ n t++++
  gene945|gene945|rna944|rna944  50 QHRVKKKYVTIYGFTPRNLDAVIDAVKSCGDVLEVE---------------YGKNWINVLFDNEESIKRCLRLNTTMIED 114
                                    57778899*************************985...............89*************************** PP

                                    EEEEEEE- CS
                      Nup35_RRM  82 slivgvsy 89 
                                    ++i++  +
  gene945|gene945|rna944|rna944 115 EIIGAFRQ 122
                                    ***98765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0078
                                    HHHHHHHTTS-BSS--CCC------ CS
                      Nup35_RRM  22 evlehFskfGeiledvqvlklgkgl 46 
                                    e++  F + G i+ed  +    kg+
  gene945|gene945|rna944|rna944 115 EIIGAFRQGGGIIEDHDIFVRKKGV 139
                                    7999***********9988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 1001.78
//
Query:       gene946|gene946|rna945|rna945  [L=291]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-16   60.7  10.1    2.9e-16   59.2  10.1    1.8  1  TFIIE_alpha      TFIIE alpha subunit
  ------ inclusion threshold ------
      0.045   12.9   5.7      0.052   12.7   5.7    1.1  1  Mitovir_RNA_pol  Mitovirus RNA-dependent RNA polymerase
      0.046   14.0   7.2       0.12   12.7   7.2    1.8  1  TFIIE-A_C        C-terminal general transcription factor TFII
      0.076   13.7   1.1      0.076   13.7   1.1    2.6  2  E1_UFD           Ubiquitin fold domain
        4.3    7.5   6.9        7.1    6.8   3.9    2.5  3  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2  10.1     8e-20   2.9e-16       1     101 [.       9     112 ..       9     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 8e-20
                                    HHHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE...TTTEEEEEEEEEE CS
                    TFIIE_alpha   1 ellkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrd...eekswykyywrin 77 
                                    +l+k vvrkfy+ ++v + d+Ll+k  + + +l + +k+  +e+ +l+ rL+e++++ky  +++   ++ ++ +  ++in
  gene946|gene946|rna945|rna945   9 KLIKKVVRKFYEPHHVVITDILLKKILLYDTELCERMKMLSKEVNRLVIRLKEDKIIKYETKVEnkeDNGQILRTVYYIN 88 
                                    599********************************************************9998877799999******** PP

                                    CCCHCCCHHHHHHHHHHHHHHHHC CS
                    TFIIE_alpha  78 yeklvdvvkrkleevvkkLeekle 101
                                    y ++ dv+k+k+ ++ k+Le+ ++
  gene946|gene946|rna945|rna945  89 YAEVRDVIKYKIFKMTKNLENSIK 112
                                    ********************9987 PP

>> Mitovir_RNA_pol  Mitovirus RNA-dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   5.7   1.5e-05     0.052     302     478 ..      10     182 ..       1     207 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                Mitovir_RNA_pol 302 gilenlrk.ieivvallldllekglkeseesllqllssllklskqylllikkklklknelklslkdlklalryskklvtl 380
                                     i + +rk +e   +++ d+l k++ ++  +l +++ +l+k +++ ++ +k+ +++k e k+ +k+ + ++ ++ +++++
  gene946|gene946|rna945|rna945  10 LIKKVVRKfYEPHHVVITDILLKKILLYDTELCERMKMLSKEVNRLVIRLKEDKIIKYETKVENKEDNGQILRTVYYINY 89 
                                    555556663444566788999999999************************999******999999999*********** PP

                Mitovir_RNA_pol 381 eellsllkkkieevvlslnrvsdl..lkeilkkslakklkalvledkkelllfekevetlkillesendlvkesselali 458
                                     e++ ++k ki +++++l++  ++  +  +++ ++ k++++l  ++  e ++f+ e  +  + +e+++d ++     +++
  gene946|gene946|rna945|rna945  90 AEVRDVIKYKIFKMTKNLENSIKMaqTEGYMCMECGKEYSSLDAQSLMENYVFKCEDCKGDL-VENKKDRSAD---CMMY 165
                                    **********9777777766655511567999*********************999888888.8888888877...3233 PP

                Mitovir_RNA_pol 459 ksilnkvkklkdaiaallee 478
                                    ++    +++l+d +  l e+
  gene946|gene946|rna945|rna945 166 SN---LMSELDDIVLLLKET 182
                                    33...333333333333333 PP

>> TFIIE-A_C  C-terminal general transcription factor TFIIE alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   7.2   3.4e-05      0.12      25      84 ..     217     289 ..     197     290 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                      TFIIE-A_C  25 e...............veeeeeeeeeee.....addptvmVaGrpvslsevsqrpelvsqmtpeEkeaYikvgqelfsdl 84 
                                    +               v+     ++ ++     + d  v+V+G +  +s++++  e  + m ++E e+Y +++ ++++dl
  gene946|gene946|rna945|rna945 217 SiafptveefdvgkgyVT-----DDGSDrrkdiKIDEYVTVNGAKKLFSDITE--EDKEMMNETEYEEYYEIYSRYHEDL 289
                                    223566666665544222.....2222223446899****************9..77899*****************987 PP

>> E1_UFD  Ubiquitin fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   2.1e-05     0.076      11      71 ..      10      68 ..       2      81 .. 0.86
   2 ?   -1.0   0.3      0.84     3e+03      67      67 ..     187     187 ..     159     211 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                         E1_UFD 11 tlkelldyfkekkklevsmislgvsllYasflpkkkdkerlklklselveevtkkkipphq 71
                                    +k+++++f e++++ ++ i+l++ llY + l   ++ + l++++  lv +++++ki + +
  gene946|gene946|rna945|rna945 10 LIKKVVRKFYEPHHVVITDILLKKILLYDTELC--ERMKMLSKEVNRLVIRLKEDKIIKYE 68
                                   5899**************************999..888899********999999865544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.84
                         E1_UFD  67 i 67 
                                    i
  gene946|gene946|rna945|rna945 187 I 187
                                    2 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   3.9     0.002       7.1       6      36 ..     119     151 ..     118     153 .. 0.71
   2 ?    6.2   0.5    0.0032        12       3      13 ..     139     149 ..     137     162 .. 0.81
   3 ?   -3.2   0.0       2.8   9.9e+03      15      25 ..     193     203 ..     192     206 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.002
                    Zn-ribbon_8   6 YrCeeCghefevlqsis..dapltaCPeCgsev 36 
                                    Y C eCg+e+  l + s  ++   +C +C++++
  gene946|gene946|rna945|rna945 119 YMCMECGKEYSSLDAQSlmENYVFKCEDCKGDL 151
                                    89999**99996555555255555599999865 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0032
                    Zn-ribbon_8   3 iYeYrCeeCgh 13 
                                     Y ++Ce+C+ 
  gene946|gene946|rna945|rna945 139 NYVFKCEDCKG 149
                                    6********85 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                    Zn-ribbon_8  15 fevlqsisdap 25 
                                    f vlq  ++++
  gene946|gene946|rna945|rna945 193 FQVLQMKKEKE 203
                                    88999544655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 1704.50
//
Query:       gene947|gene947|rna946|rna946  [L=888]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 5456.97
//
Query:       gene949|gene949|rna948|rna948  [L=139]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-09   36.1   1.8    1.8e-07   31.5   1.8    2.2  1  Tim17     Tim17/Tim22/Tim23/Pmp24 family
  ------ inclusion threshold ------
      0.051   12.0   0.1      0.052   12.0   0.1    1.0  1  SP2       Structural protein 2


Domain annotation for each model (and alignments):
>> Tim17  Tim17/Tim22/Tim23/Pmp24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   1.8     2e-11   1.8e-07      46     109 ..      60     125 ..      31     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2e-11
                          Tim17  46 gkrgpslGknfgvvgglysgiecaleklRgkediwnsvaAGaltGal.lr.agpqaaavgaiggaa 109
                                     ++   +Gk+f+++ ++ys++e+ l+ +   + ++ns+++G+++G+l ++ ++ ++ + ga+ +++
  gene949|gene949|rna948|rna948  60 LSSIHESGKSFAKISLVYSTTESSLQLYGSENAPLNSFISGVVAGGLgVNdKSKRTIFAGAASFGL 125
                                    4455678*********************7799999***********97776778888888888765 PP

>> SP2  Structural protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.8e-06     0.052     443     514 ..      32     104 ..      12     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-06
                            SP2 443 fagtatdsmltpgpgsitvtfllqlrGkls.fteltqtkiaasstydttdsdleraasqrvevdtylsslips 514
                                    f  +a+d++   + g+++ +f +  +  ls   e +++ +  s  y tt+s+l+   s++  +++++s+++  
  gene949|gene949|rna948|rna948  32 FLKVASDTLQGYAFGCMVGVFSSSKKPTLSsIHESGKSFAKISLVYSTTESSLQLYGSENAPLNSFISGVVAG 104
                                    67789999999999999999**9999999725799**********************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 910.80
//
Query:       gene950|gene950|rna949|rna949  [L=240]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-36  124.3   1.4    1.9e-30  106.3   0.0    2.1  2  Gti1_Pac2  Gti1/Pac2 family
     0.0083   15.8   0.1      0.025   14.2   0.1    1.8  2  DUF5053    Domain of unknown function (DUF5053)


Domain annotation for each model (and alignments):
>> Gti1_Pac2  Gti1/Pac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   2.1e-34   1.9e-30       4      95 ..       6      96 ..       4     117 .. 0.89
   2 !   17.0   0.6   5.3e-07    0.0048     159     180 ..     119     140 ..     100     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2.1e-34
                                   S---SHHHHHHHHHHHHTTSS---SS---HHHHHHHSSTTEEEEEEHHHH--SS---S--B---EEETTEEEEEB------- CS
                      Gti1_Pac2  4 gyiettkdalllieavlegilkrvtrRlkekErkeliksGsvFvfeeeesgikRWTDGvsWSpSrilgnfLvYreldkkrak 85
                                   gyi+t ++a l+++ v+ g l+ ++ Rl+ +Er+  i+sG++F+f e+ +gi+RWTDG +WSpS+i g+fL+Y+e+ k+ +k
  gene950|gene950|rna949|rna949  6 GYIKTYEEACLIVHSVRLGYLNAIQGRLTPEERE-NIRSGDIFCFVESPNGIRRWTDGKTWSPSKIHGQFLLYQEVPKHMNK 86
                                   9*********************************.*****************************************999888 PP

                                   ---------- CS
                      Gti1_Pac2 86 kkkkkkkkks 95
                                   ++  k+++++
  gene950|gene950|rna949|rna949 87 SAIGKRNRQK 96
                                   7766655444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.3e-07
                                    --EEEEEEEEEETTTEEEEEEE CS
                      Gti1_Pac2 159 gLvKkTisvtlkgkelhlisYy 180
                                     L KkTis+ l++k++h+i+Y+
  gene950|gene950|rna949|rna949 119 SLNKKTISILLQNKTYHVIAYF 140
                                    599******************9 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.82   7.4e+03      37      49 ..      30      42 ..      27      43 .. 0.77
   2 !   14.2   0.1   2.8e-06     0.025      22      42 ..     216     236 ..     213     239 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.82
                        DUF5053 37 vatFteeeletLk 49
                                   ++++t+ee e ++
  gene950|gene950|rna949|rna949 30 QGRLTPEERENIR 42
                                   5689999998765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.8e-06
                        DUF5053  22 sWlyqrlnGidvngkvatFte 42 
                                     W+ q++ G+dv +k  +F +
  gene950|gene950|rna949|rna949 216 EWMRQKMKGNDVGKKYICFYD 236
                                    7****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1385.32
//
Query:       gene95|gene95|rna95|rna95  [L=464]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-30  107.1   2.2    2.6e-29  102.4   2.2    2.4  1  Peptidase_S8  Subtilase family
      2e-06   28.4   0.0    6.3e-06   26.8   0.0    1.9  1  Inhibitor_I9  Peptidase inhibitor I9


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.4   2.2   2.9e-33   2.6e-29       1     288 [.     139     424 ..     139     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 2.9e-33
                                -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSSSSB- CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeegekng 84 
                                g+gv v vlDtG++ shp+++                  g ++  ++   ++ ++d++g    HGth+AG+++++      + g
  gene95|gene95|rna95|rna95 139 GEGVDVYVLDTGIEVSHPEFE------------------GRARWGANFVAESLNEDEHG----HGTHCAGVIGGK------NFG 194
                                78999**************99..................34555556666666677777....************......889 PP

                                SSTTSEEEEEE-SSTTSB-HH..HHHHHH...........HHHHHHCT-S.................................. CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxx.................................. RF
               Peptidase_S8  85 vapgakilsvkvldtsggsmetgtelira...........ieeaaedkvd.................................. 123
                                +  + +i++vkvld  g+ m+  + l+++                    d                                  
  gene95|gene95|rna95|rna95 195 ISKKSSIIAVKVLDRYGSGMT--SRLLQGldfvikehekkK--------Delynaaaneyldstrssdidieiddsesfsflqs 268
                                999**************9998..688888444444444440........26666666666667777777788888888888888 PP

                                .....................EEEE-EESCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTT CS
                                .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Peptidase_S8 124 .....................vinmslgestslpktgrsiealainravnkkgvlvviSaGNngktgsslqagspvgtpstskn 186
                                                     +in+s+g ++ +p         ai++a  + g+ + ++aGN++       + +++ +p++sk 
  gene95|gene95|rna95|rna95 269 kvpsvqrlvdtisekalepktIINLSVG-GFRNPALNF-----AIEYAS-RLGIHFSTAAGNEH------EDACDF-SPGSSKA 338
                                888888888888888888888*******.999998885.....788999.99************......888887.6999*** PP

                                CEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHHHHTT--H CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
               Peptidase_S8 187 vitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAlllsalpkltp 270
                                +it ga t ++ +a fS+ G +++      i apG++i+s+w   +         + +sGTSmA+P+ +g++A  l +++ + p
  gene95|gene95|rna95|rna95 339 SITTGASTYKDTVAFFSNFGECVN------IFAPGVDILSSWIGGT--------QKIVSGTSMAAPHTTGVMAAYLTYYD-YDP 407
                                **********************95......****************........689*******************9999.*** PP

                                HHHHHHHHCCS-EE.... CS
                                xxxxxxxxxxxxxxxxxx RF
               Peptidase_S8 271 etvraallntAqdlgkad 288
                                +t+++ ++n A+++ +++
  gene95|gene95|rna95|rna95 408 HTLKKRIINDARIV-EES 424
                                ***********987.332 PP

>> Inhibitor_I9  Peptidase inhibitor I9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0     7e-10   6.3e-06       2      79 ..      19      90 ..      18      93 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7e-10
                               EEEEE-TTS-HHHHHHHHHHHHH....HHHHTT..--EEEEEEESS.SSSEEEEEE-GGGHHHHHTSTTEEEEEEEEEE CS
               Inhibitor_I9  2 YIVtfkeaakaakkassheswhqsllksvlkgedsakagilysYki.lfnGfavklteeqaeklrkrpeVesVepDqsv 79
                               YIV f+++  +++k s  +  + ++lk     +  +  +   s +i   nGf +++t+++aek++++p V+ V++D++v
  gene95|gene95|rna95|rna95 19 YIVMFDQD-PSMDKGSMNALYSMNILKA----Q--SILEPDESIEIkITNGFVARMTKSTAEKMKRHPNVKMVVRDTPV 90
                               77777774.3333233333333333333....2..12223334444467****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.50
# Mc/sec: 2816.18
//
Query:       gene951|gene951|rna950|rna950  [L=709]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-10   39.5   0.3    1.3e-09   38.1   0.3    1.9  1  Sec8_exocyst    Sec8 exocyst complex component specific domai
  ------ inclusion threshold ------
      0.015   14.8   1.2      0.015   14.8   1.2    3.2  3  DegS            Sensor protein DegS
        0.1   12.8   0.1        0.1   12.8   0.1    2.3  3  RFC1            Replication factor RFC1 C terminal domain
       0.18   12.1   0.3         29    5.0   0.0    2.5  2  HK_sensor       Sensor domain of 2-component histidine kinase
       0.23   11.5   2.2        8.3    6.4   0.1    2.8  3  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
        4.1    8.1  10.4      0.096   13.3   0.5    3.3  5  Com_YlbF        Control of competence regulator ComK, YlbF/Ym


Domain annotation for each model (and alignments):
>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.3   4.4e-13   1.3e-09       4     104 ..       6     104 ..       3     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 4.4e-13
                   Sec8_exocyst   4 evlnkikeeWpavlsddanpvelalsllDdssvGlahrlkefkqlkkqieeaLqevvnehhqaFnssiasYskilssiqe 83 
                                    + l++i+ +W+ ++++d+np++ al+    s      + ++f++l +++e++++ ++++++++F++s+ sY +  +    
  gene951|gene951|rna950|rna950   6 ALLREIRIDWETLITEDFNPLKQALKNRNSSV-----EASNFRNLFHKVEKVMEGIIEKNYKGFSDSVLSYMESYRLNRR 80 
                                    6799*********************9875544.....7899*********************************999999 PP

                   Sec8_exocyst  84 sqekvsel...Kesleeakkklst 104
                                    ++++++e+    ++l+e k ++++
  gene951|gene951|rna950|rna950  81 CHDSIQEIfraTKELSEMKIEVKD 104
                                    999999882112333333333333 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   1.2   5.1e-06     0.015      25      74 ..      84     135 ..      76     166 .. 0.88
   2 ?    1.6   0.3     0.056   1.7e+02      16      71 ..     243     304 ..     236     315 .. 0.57
   3 ?   -1.7   0.1      0.62   1.8e+03      73     114 ..     415     456 ..     407     483 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                           DegS  25 arkeverlkkeleelkeevsevikevdklekkerkark..rLaeVskdFkky 74 
                                    + +e+ r +kel+e+k ev+++ike d+++  + k++    L+e+ ++F+++
  gene951|gene951|rna950|rna950  84 SIQEIFRATKELSEMKIEVKDMIKEYDDVKVFKAKEKIclALLEIRRNFDEF 135
                                    668999*********************99987777775226789*****987 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.056
                           DegS  16 eeifeIaEsarkeverlkke......leelkeevsevikevdklekkerkarkrLaeVskdF 71 
                                    +e f++ Es+ +ever k+e       + +  +++++i++  +l +    +   L e sk+F
  gene951|gene951|rna950|rna950 243 REYFKVVESVIEEVERSKEEnqaemlAKMVMGRTRTIIRNFKTLFEMADASFDGLCEKSKNF 304
                                    56677777777777776665211111123445556666666666666666666666666665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.62
                           DegS  73 kyseeeikeaYeeakelqvelallrekEkqlrerRdelerrL 114
                                    ky  + + e Y + ke q+e ++      +  +r d l+rrL
  gene951|gene951|rna950|rna950 415 KYLRKILDERYIKEKENQIEKQIICLLNGEEWHRNDYLNRRL 456
                                    555555556666666666655554444444445555555555 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.4e-05       0.1      90     133 ..      50      94 ..      21     109 .. 0.73
   2 ?   -3.6   0.0       3.8   1.1e+04      92     130 ..     237     255 ..     222     272 .. 0.51
   3 ?   -3.8   0.1       4.2   1.3e+04     108     127 ..     401     420 ..     390     436 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                                    HHHHS---------.HHHHHHTTT--SHHHHHHHHHH-X...XXX CS
                           RFC1  90 kklvkpLkeegkdg.veevielmdeysLtkedvdslvelslvkge 133
                                    +k+++ + e++ +g  ++v+++m++y+L++   ds++e+   ++e
  gene951|gene951|rna950|rna950  50 EKVMEGIIEKNYKGfSDSVLSYMESYRLNRRCHDSIQEIFRATKE 94 
                                    5566667777777789***********************655333 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.8
                                    HHS---------HHHHHHTTT--SHHHHHHHHHH-X... CS
                           RFC1  92 lvkpLkeegkdgveevielmdeysLtkedvdslvelslv 130
                                    ++++                    L +e++  + ++   
  gene951|gene951|rna950|rna950 237 QIDN--------------------LEREYFKVVESVIEE 255
                                    3333....................344444444444333 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 4.2
                                    HHTTT--SHHHHHHHHHH-X CS
                           RFC1 108 ielmdeysLtkedvdslvel 127
                                    + +m++y ++  +   l ++
  gene951|gene951|rna950|rna950 401 VIYMEKYAINNGMKKYLRKI 420
                                    55788888876665555555 PP

>> HK_sensor  Sensor domain of 2-component histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.013        40      22      81 ..      32      89 ..      27     108 .. 0.81
   2 ?    5.0   0.0    0.0098        29      32      82 ..     211     261 ..     199     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHTS-EEEE-TTS-BSSSS---HHHHGGGSS-B-TTS---STT CS
                      HK_sensor 22 eeggeealaewlaeleqreqtwvavvdselqslssrplteefeekltflRkvdwklsrrv 81
                                   +++++ + +++++ +++ e++   +++++ +++s++ l+  ++e +++ R+ + ++++ +
  gene951|gene951|rna950|rna950 32 NRNSSVEASNFRNLFHKVEKVMEGIIEKNYKGFSDSVLS--YMESYRLNRRCHDSIQEIF 89
                                   6677888999*9**************************9..7777888888888887655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0098
                                    HHHHHHHHHTS-EEEE-TTS-BSSSS---HHHHGGGSS-B-TTS---STTT CS
                      HK_sensor  32 wlaeleqreqtwvavvdselqslssrplteefeekltflRkvdwklsrrvq 82 
                                    + +e e +++++ +v+ + lqsl + ++++ + e ++++ +v ++++r  +
  gene951|gene951|rna950|rna950 211 FYNECEYQDDFRCVVILNGLQSLEKYQIDNLEREYFKVVESVIEEVERSKE 261
                                    77899999*****************************99999888887655 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0028       8.3      13      55 ..      87     129 ..      79     134 .. 0.88
   2 ?    3.7   0.1      0.02        59       3      42 ..     141     180 ..     139     199 .. 0.88
   3 ?   -3.0   0.0       2.3   6.8e+03       9      30 ..     667     688 ..     652     691 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                                    SSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHH CS
                 Succ_DH_flav_C  13 gvfRteegLkealkelkelrerlknvkvtdkskvaNqelveal 55 
                                    ++fR  ++L+e   e+k++ +++++vkv + ++ +  +l+e++
  gene951|gene951|rna950|rna950  87 EIFRATKELSEMKIEVKDMIKEYDDVKVFKAKEKICLALLEIR 129
                                    69**************************999988887777765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
                                    HHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S- CS
                 Succ_DH_flav_C   3 eLgkimqkkvgvfRteegLkealkelkelrerlknvkvtd 42 
                                     +++ m+++v++   +++L +a k+++++++ +++ +++d
  gene951|gene951|rna950|rna950 141 GIQNDMKRNVEIRQMSSKLLKASKRIRAIYDLIDENGLAD 180
                                    68999************************99888777766 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.3
                                    HHHSSSSB-HHHHHHHHHHHHH CS
                 Succ_DH_flav_C   9 qkkvgvfRteegLkealkelke 30 
                                    ++  g   +e++Lkea+k +++
  gene951|gene951|rna950|rna950 667 DEILGFINEEDSLKEAVKFIED 688
                                    5556677789999999998775 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.016        47      20     102 ..      25     108 ..      20     109 .. 0.69
   2 ?   13.3   0.5   3.2e-05     0.096       7      76 ..     101     176 ..      95     206 .. 0.85
   3 ?   -2.3   0.3       2.2   6.7e+03      69      91 ..     249     271 ..     229     283 .. 0.47
   4 ?   -3.3   0.0       4.9   1.5e+04      18      36 ..     459     477 ..     456     479 .. 0.81
   5 ?   -3.5   0.1       5.2   1.6e+04      71      99 ..     661     689 ..     649     691 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.016
                                    HHHHHHHHHHCSHHHHHHHHHHHHHHHHHHH.HHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHH CS
                       Com_YlbF  20 eykeaeealeedeelqklikefkklqkelqe.kqmkgeelkeeekkelqelkeeldknplvkeyleaeqelnellqevnk 98 
                                     +k+a ++ ++  e+ +  + f+k +k ++   +++++ ++++  + +++   + + ++ ++e + a +el+e+  ev++
  gene951|gene951|rna950|rna950  25 PLKQALKNRNSSVEASNFRNLFHKVEKVMEGiIEKNYKGFSDSVLSYMESYRLNRRCHDSIQEIFRATKELSEMKIEVKD 104
                                    56666666666666666666666666655553444446666666656666666668899********************* PP

                                    HHHH CS
                       Com_YlbF  99 iiae 102
                                    +i e
  gene951|gene951|rna950|rna950 105 MIKE 108
                                    *976 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.2e-05
                                    HHHHHHHHSHHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHH......HHHHHHHHHHTS CS
                       Com_YlbF   7 eLaeaIkeseeykeykeaeealeedeelqklikefkklqkelqekqmkgeelkeeekk......elqelkeeldkn 76 
                                    e +++Ike + +k +k+ e+   +  e+++ ++ef  +++ +q+ +++  e+++ + k      +++++++ +d+n
  gene951|gene951|rna950|rna950 101 EVKDMIKEYDDVKVFKAKEKICLALLEIRRNFDEFCVIRDGIQNDMKRNVEIRQMSSKllkaskRIRAIYDLIDEN 176
                                    7899****************************************88888677776664444555777777777776 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.2
                                    HHHHHHTSHHHHHHHHHHHHHHH CS
                       Com_YlbF  69 lkeeldknplvkeyleaeqelne 91 
                                    +++ +++ +  ke ++ae+  ++
  gene951|gene951|rna950|rna950 249 VESVIEEVERSKEENQAEMLAKM 271
                                    22223444444444444444444 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4.9
                                    HHHHHHHHHHHHCSHHHHH CS
                       Com_YlbF  18 ykeykeaeealeedeelqk 36 
                                    y +yk++ e + +++el +
  gene951|gene951|rna950|rna950 459 YSRYKNLVEDFSSHPELCN 477
                                    7889999999999998866 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 5.2
                                    HHHHTSHHHHHHHHHHHHHHHHHHHHHHH CS
                       Com_YlbF  71 eeldknplvkeyleaeqelnellqevnki 99 
                                    e+++  +++  +++ e+ l+e ++ + ++
  gene951|gene951|rna950|rna950 661 EKIKLLDEILGFINEEDSLKEAVKFIEDT 689
                                    44444555555566666666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (709 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       991  (0.0552736); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 4363.70
//
Query:       gene952|gene952|rna951|rna951  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-10   39.5   0.4    1.1e-09   38.8   0.4    1.5  1  RasGEF        RasGEF domain
  ------ inclusion threshold ------
      0.066   12.3   0.0      0.094   11.7   0.0    1.1  1  FA_synthesis  Fatty acid synthesis protein


Domain annotation for each model (and alignments):
>> RasGEF  RasGEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.4   1.2e-13   1.1e-09       2     139 ..      89     206 ..      88     271 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.2e-13
                         RasGEF   2 lAeqltlieaelfskikpeellgsawskedrspnveaviarfnrlsnwvaseilseeslkkRakviekfikiakecrkln 81 
                                    l + lt+i+  ++++i+p el+++    ++++ n++++ ++   l+n+v++e+l       R +  ++f k+ k++++++
  gene952|gene952|rna951|rna951  89 LSKALTFIDLSILQRITPNELVDYDGPGNTKCRNIRHMRSKNVGLTNFVSNELL-------REQNYKYFFKLLKHLERIG 161
                                    6789*******************76333335699****999999**********.......556799************* PP

                         RasGEF  82 NfnslmailsaLqsspvs..rLkktweavskkslktleeleelmspennfknyrealkss 139
                                    N+ns+++i+ a+q ++    rL+   ++++               ++ ++  +r+ l++ 
  gene952|gene952|rna951|rna951 162 NYNSFYCIIKAFQMQKLDlkRLNTLSRHME---------------KSTSYFDMRQFLDDL 206
                                    *************99754226666555555...............344444444444444 PP

>> FA_synthesis  Fatty acid synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.1e-05     0.094     117     209 ..      72     162 ..      63     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                                    B-TT-SS-EEE-EE--TTS.-EEEE-SSS-TT--HHHHHHHHHHHHHHHHHTS--SS-EEEEEESSSSTT-SSHHHHHHH CS
                   FA_synthesis 117 rikgierpalavllPtvsg.ktvlLDvganvdckpkeLvqfalmGsvyaesvlgvdsprvglLniGeeevkgndlvkqtf 195
                                    +ik  e++ +  + P + + +   +D+       p+eLv++  +G +  ++++++ s  vgl n  ++e   ++  k  f
  gene952|gene952|rna951|rna951  72 KIKKAEAKDIYHMTPRKLSkALTFIDLSILQRITPNELVDYDGPGNTKCRNIRHMRSKNVGLTNFVSNELLREQNYKYFF 151
                                    688899999999***9996478899******************************************************* PP

                                    HHHHT-TTSEEEEE CS
                   FA_synthesis 196 ellkaiesieflGn 209
                                    +llk     e +Gn
  gene952|gene952|rna951|rna951 152 KLLKHL---ERIGN 162
                                    **9985...55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1956.62
//
Query:       gene953|gene953|rna952|rna952  [L=279]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0039   17.6   0.1         34    5.1   0.0    4.5  5  PQQ_3          PQQ-like domain
  ------ inclusion threshold ------
      0.049   13.0   0.0        2.8    7.3   0.0    2.7  3  Glu_cyclase_2  Glutamine cyclotransferase


Domain annotation for each model (and alignments):
>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.1     9e+02      15      25 ..      17      27 ..      16      42 .. 0.86
   2 ?   -3.2   0.2       1.5   1.4e+04      21      31 ..      99     109 ..      94     114 .. 0.55
   3 !    5.1   0.0    0.0037        34      20      40 .]     137     157 ..     124     157 .. 0.83
   4 ?    1.0   0.0     0.071   6.4e+02      23      31 ..     179     187 ..     178     195 .. 0.82
   5 !    4.1   0.0    0.0077        69      12      37 ..     245     271 ..     240     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.1
                          PQQ_3 15 sspavdgglvy 25
                                   ss++v+gg+++
  gene953|gene953|rna952|rna952 17 SSALVAGGYLF 27
                                   78999999987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                          PQQ_3  21 gglvyvgtgdG 31 
                                    g  v+v +  G
  gene953|gene953|rna952|rna952  99 GSNVFVFDVGG 109
                                    44555544444 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0037
                          PQQ_3  20 dgglvyvgtgdGtlyAlDaet 40 
                                    ++  + +g++dG l+ +D++t
  gene953|gene953|rna952|rna952 137 SDKELICGSEDGMLRFVDTRT 157
                                    5556889***********998 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.071
                          PQQ_3  23 lvyvgtgdG 31 
                                    ++yvg++d 
  gene953|gene953|rna952|rna952 179 YLYVGSYDE 187
                                    69*****85 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.0077
                          PQQ_3  12 pvnsspavdgglvyvgtg.dGtlyAlD 37 
                                     + ++++v + +v++++  d ++y ++
  gene953|gene953|rna952|rna952 245 SIAYGLTVKDSKVFFTSFyDKKIYKFE 271
                                    577899********99999*****987 PP

>> Glu_cyclase_2  Glutamine cyclotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00031       2.8     128     164 ..     132     168 ..     108     184 .. 0.81
   2 ?    2.6   0.0    0.0082        74     104     150 ..     186     232 ..     168     244 .. 0.79
   3 ?   -0.6   0.0     0.081   7.2e+02      79     113 ..     239     273 ..     228     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00031
                  Glu_cyclase_2 128 WGlttdgkrlvmsdGsstltfldpktfaetksvevtk 164
                                    W+l + +k+l+       l+f+d +tf+e+++++ t+
  gene953|gene953|rna952|rna952 132 WALKASDKELICGSEDGMLRFVDTRTFSEHHTMKRTS 168
                                    ************99999**************998665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0082
                  Glu_cyclase_2 104 egvafvydaetleeigrvsyegeGWGlttdgkrlvmsdGsstltfld 150
                                    ++ + + d++++e i++v++ g  W ++++g+ ++ s   + l++ d
  gene953|gene953|rna952|rna952 186 DECIEIIDKRKYEIIKKVRVGGGIWRICKEGEMFYLSCMYEGLKVCD 232
                                    4566789*************************999886555555555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.081
                  Glu_cyclase_2  79 aeldeelFgEGitvlgdklyqltwkegvafvydae 113
                                    ++++++  + G+tv ++k++   + ++++++++++
  gene953|gene953|rna952|rna952 239 EKFPTNSIAYGLTVKDSKVFFTSFYDKKIYKFERH 273
                                    57788888889999999999999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1677.00
//
Query:       gene954|gene954|rna953|rna953  [L=351]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-08   33.4   0.1      3e-08   33.4   0.1    1.8  2  UBA              UBA/TS-N domain
    7.8e-07   28.8   1.1    1.3e-06   28.0   1.1    1.3  1  ubiquitin        Ubiquitin family
  ------ inclusion threshold ------
      0.014   15.5   0.4      0.035   14.2   0.2    1.8  2  DnaGprimase_HBD  DnaG-primase C-terminal, helicase-binding do
      0.017   13.6   0.1      0.024   13.1   0.1    1.1  1  Head-tail_con    Bacteriophage head to tail connecting protei
      0.033   14.6   0.1       0.08   13.4   0.1    1.8  1  Ubiquitin_2      Ubiquitin-like domain
      0.047   13.7   0.6      0.047   13.7   0.6    2.8  4  RRF              Ribosome recycling factor
      0.053   13.6   0.9      0.053   13.6   0.9    2.4  2  DUF1542          Domain of Unknown Function (DUF1542)
      0.082   12.7   1.3       0.17   11.7   1.3    1.5  1  partial_CstF     Partial cleavage stimulation factor domain
       0.23   11.9   1.1        3.6    8.0   0.1    2.6  3  LIAS_N           N-terminal domain of lipoyl synthase of Radi
       0.51   10.6   3.0        0.6   10.3   0.4    2.3  2  DUF3213          Protein of unknown function (DUF3213)


Domain annotation for each model (and alignments):
>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   1.5       8.5   1.5e+04       2      12 ..     178     188 ..     177     188 .. 0.84
   2 !   33.4   0.1   1.7e-11     3e-08       5      37 .]     301     333 ..     297     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8.5
                                    CHHHHHHHHHT CS
                            UBA   2 deeaiqrLveM 12 
                                     +++ q++ +M
  gene954|gene954|rna953|rna953 178 SNAMMQQMEQM 188
                                    57899**9998 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 1.7e-11
                                    HHHHHHHTTS-HHHHHHHHHHTTTSHHHHHHHH CS
                            UBA   5 aiqrLveMGFdreevveALratgnNeErAveyL 37 
                                    ++++L++MGF++e++ +AL  + ++++rA+++L
  gene954|gene954|rna953|rna953 301 QLEQLKAMGFEDEDATKALKEARGDINRALDIL 333
                                    89*****************************98 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   1.1   7.3e-10   1.3e-06       8      65 ..       9      71 ..       3      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 7.3e-10
                                   SEEEEEEEETTS.BHHHHHHHHHHHHT....SSGGGEEEEETTEEE-TTSBHGGHTTSTTEEE CS
                      ubiquitin  8 gkkitleveesd.tveelKekiaekeg....ipaeqqrLiysGkvLedertleeygiqdgstl 65
                                   ++k+ +eve  d t+eelK+k++e  g    ipa+ q Li++ + L+d ++l++y   +   +
  gene954|gene954|rna953|rna953  9 KNKFVVEVENLDiTIEELKKKLEEAMGesvrIPASDQTLIFEREKLDDGKKLSDYVKGSTEEI 71
                                   5679999987666*************99***************************55444555 PP

>> DnaGprimase_HBD  DnaG-primase C-terminal, helicase-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2     2e-05     0.035      10      46 ..     187     223 ..     181     242 .. 0.87
   2 ?   -3.6   0.0       6.2   1.1e+04       9      28 ..     317     336 ..     316     343 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                    HHHH-CHHHHHHTTT--GGG-SS-HHHHHHHHTT-TT CS
                DnaGprimase_HBD  10 tllekpelldsvldyidaslfkykkeefelllqgeld 46 
                                     +l++p lld+vl++ ++++ +++kee +++l++ l+
  gene954|gene954|rna953|rna953 187 QMLNNPTLLDQVLNIQNPNMTSEQKEEQKKMLKEALN 223
                                    69****************************9998776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.2
                                    HHHHH-CHHHHHHTTT--GG CS
                DnaGprimase_HBD   9 ktllekpelldsvldyidas 28 
                                    k+l e +  ++ +ld+++ +
  gene954|gene954|rna953|rna953 317 KALKEARGDINRALDILHEN 336
                                    56667777788888888765 PP

>> Head-tail_con  Bacteriophage head to tail connecting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.3e-05     0.024     330     414 ..     176     265 ..     161     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                  Head-tail_con 330 avlqeviqdlrerIrraffadllanqrraevTAtEvlera...eEklrlLGpvlerlqsellsPliervfgilrr..agk 404
                                    a +++++q++++ ++   + d++ n++++++T ++  e++   +E l+++ +  + +q+ l    + ++++ ++   +g+
  gene954|gene954|rna953|rna953 176 AFSNAMMQQMEQMLNNPTLLDQVLNIQNPNMTSEQKEEQKkmlKEALNMMKANPSLFQQALTPERLSWALNTMNGghGGM 255
                                    67889***************************986666552227*****************************96558** PP

                  Head-tail_con 405 lppppeeLeg 414
                                    +p+ p+ + g
  gene954|gene954|rna953|rna953 256 FPSYPPNMGG 265
                                    *****98865 PP

>> Ubiquitin_2  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.5e-05      0.08      21      48 ..      18      49 ..       1      81 [. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                                   ETTSBHHHHHHHHHHHH-....--TTCEEEEE CS
                    Ubiquitin_2 21 sksltieelKekLelitG....tspasmrLql 48
                                   ++++tieelK+kLe  +G    +++++++L +
  gene954|gene954|rna953|rna953 18 NLDITIEELKKKLEEAMGesvrIPASDQTLIF 49
                                   789**************944444555666655 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       1.3   2.3e+03      98     103 ..      26      31 ..       2      81 .. 0.55
   2 ?   -3.2   0.0         4   7.2e+03      51      74 ..      63      86 ..      54      92 .. 0.64
   3 ?   13.7   0.6   2.6e-05     0.047      69     106 ..     189     226 ..     173     231 .. 0.82
   4 ?    1.0   0.3      0.21   3.8e+02     100     125 ..     310     335 ..     301     346 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.3
                                    HHHHHH CS
                            RRF  98 akkaae 103
                                    +kk+ e
  gene954|gene954|rna953|rna953  26 LKKKLE 31 
                                    222222 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4
                                   SSCCHHHHHHHHHHHSCC-SEEEE CS
                            RRF 51 fdkslvkaiekaIlksdlglnpqq 74
                                   + k ++++i+  ++k++ + np +
  gene954|gene954|rna953|rna953 63 YVKGSTEEIKLFVIKQNKNPNPIS 86
                                   445666677777777777766654 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.6e-05
                                    -SEEEEESSEEEEE--SSSHHHHHHHHHHHHHHHHHHH CS
                            RRF  69 glnpqqdgevlrvpipplTeErrkelvkeakkaaekak 106
                                      np+  ++vl+++ p++T E+++e  k +k+a + +k
  gene954|gene954|rna953|rna953 189 LNNPTLLDQVLNIQNPNMTSEQKEEQKKMLKEALNMMK 226
                                    347777899***********************998776 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.21
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            RRF 100 kaaekakvairniRrdankklkklek 125
                                     + e+a +a++++R d+n +l  l++
  gene954|gene954|rna953|rna953 310 FEDEDATKALKEARGDINRALDILHE 335
                                    55699999*********999954333 PP

>> DUF1542  Domain of Unknown Function (DUF1542)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.9     3e-05     0.053      20      47 ..     201     227 ..     195     228 .. 0.87
   2 ?   -1.1   0.4       1.2   2.2e+03      38      52 ..     315     329 ..     312     343 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3e-05
                        DUF1542  20 InnnpnaTdeEKqaainkvnaalneaik 47 
                                    I +npn T e+K+++++ +++aln  ++
  gene954|gene954|rna953|rna953 201 I-QNPNMTSEQKEEQKKMLKEALNMMKA 227
                                    4.79*******************97665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                        DUF1542  38 vnaalneaiknInqa 52 
                                    +++al+ea  +In a
  gene954|gene954|rna953|rna953 315 ATKALKEARGDINRA 329
                                    566777777777766 PP

>> partial_CstF  Partial cleavage stimulation factor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.3   9.6e-05      0.17      16      51 ..     183     218 ..     170     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.6e-05
                   partial_CstF  16 aLVdeViknkdiLqnilkskpedmtsWpsEqkqqVL 51 
                                    +  +  ++n+ +L  +l+++  +mts  +E++ + L
  gene954|gene954|rna953|rna953 183 QQMEQMLNNPTLLDQVLNIQNPNMTSEQKEEQKKML 218
                                    5568899*******************9999999887 PP

>> LIAS_N  N-terminal domain of lipoyl synthase of Radical_SAM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.46   8.2e+02      45      79 ..      12      46 ..      10      49 .. 0.78
   2 ?    8.0   0.1     0.002       3.6      11      53 ..      31      71 ..      19      85 .. 0.72
   3 ?    1.7   0.1      0.19   3.5e+02      29      68 ..     181     219 ..     172     230 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.46
                         LIAS_N 45 FvsgdkedkseweeykgnlkrekgerlrLPswlkt 79
                                   Fv + ++   + ee+k++l++  ge +r+P   +t
  gene954|gene954|rna953|rna953 12 FVVEVENLDITIEELKKKLEEAMGESVRIPASDQT 46
                                   55555556668899***************986665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.002
                         LIAS_N 11 krvlgsaltkaastsssltdekkelleeGPdlqDFvsgdkedk 53
                                   ++++g++++ +as+++      +e l++G +l+D+v+g +e+ 
  gene954|gene954|rna953|rna953 31 EEAMGESVRIPASDQTLI--FEREKLDDGKKLSDYVKGSTEEI 71
                                   455566666666665555..56999*************98875 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.19
                         LIAS_N  29 tdekkelleeGPdlqDFvsgdkedkseweeykgnlkrekg 68 
                                    + ++ e + + P+l D v + ++ + + e+ +++ k   +
  gene954|gene954|rna953|rna953 181 MMQQMEQMLNNPTLLDQVLNIQNPNMTSEQKEEQKK-MLK 219
                                    445556666778888888888888755555444433.333 PP

>> DUF3213  Protein of unknown function (DUF3213)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.4   0.00034       0.6      35      63 ..       9      38 ..       2      51 .. 0.81
   2 ?   -0.9   0.1         1   1.9e+03      48      80 ..     211     243 ..     205     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                                   S--EEE.--B-S-SHHHHHHHT...TT-SS CS
                        DUF3213 35 kvaevv.ideekvnieelkkkleelkgevv 63
                                   k+ +vv +++  + ieelkkklee  ge v
  gene954|gene954|rna953|rna953  9 KNKFVVeVENLDITIEELKKKLEEAMGESV 38
                                   7788883555679************99987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                    HHHHHHHT...TT-SS-------SS--XXXXXX CS
                        DUF3213  48 ieelkkkleelkgevveekeltlqelieeslsw 80 
                                    +ee kk l+e    +  +  l  q l  e lsw
  gene954|gene954|rna953|rna953 211 KEEQKKMLKEALNMMKANPSLFQQALTPERLSW 243
                                    577777777766666677788888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1305  (0.0727871); expected 358.6 (0.02)
Passed bias filter:                      650  (0.0362541); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 2157.59
//
Query:       gene955|gene955|rna954|rna954  [L=241]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.017   15.5   0.0    1.2  1  Cyclin    Cyclin


Domain annotation for each model (and alignments):
>> Cyclin  Cyclin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   9.8e-07     0.017      77     161 .]     126     206 ..      16     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.8e-07
                                    TT--HHHHHHHHHHHHHHHH..H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-HHHHHHHHHHHHHH CS
                         Cyclin  77 gesaplvllgtliYldrivkrcvsealvvtsanihRllivallvatKflvDlsysnekfakvggislkELnkLEidFlfl 156
                                    ++  plvl++ +iYl++ vk   +  ++ +   + ++     l+ +Kf+ D+  +++ f    gis +E+ ++E + l  
  gene955|gene955|rna954|rna954 126 AKELPLVLISGYIYLEKYVK--KAGIVFYDCKKLIKFFFGCCLIGSKFIYDTRHPDDLF--FVGISPAEIFRIEGSILSA 201
                                    566799**************..899999***************************9999..479**************** PP

                                    TTT-- CS
                         Cyclin 157 vdFdl 161
                                    +d+dl
  gene955|gene955|rna954|rna954 202 IDYDL 206
                                    ***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1546.90
//
Query:       gene956|gene956|rna955|rna955  [L=725]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-07   30.6   0.0    2.9e-07   30.1   0.0    1.3  1  Metalloenzyme  Metalloenzyme superfamily
    1.5e-06   28.1   0.8    3.9e-06   26.7   0.2    1.8  2  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
       0.15   12.9   0.0        2.4    9.0   0.0    2.2  2  DUF1911        Domain of unknown function (DUF1911)


Domain annotation for each model (and alignments):
>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   4.8e-11   2.9e-07     111     190 ..     162     241 ..      56     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 4.8e-11
                                    STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHH...TT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 111 qpemkavevaekaldailsgkfdlvvvniknaDmvGH...tgdleatiaaieaaDeavkeildaieqvdgilvvtADHgn 187
                                    + + ++ +++ek+l+ i  +++d+++ ++ n D++GH   t d e+  + +  +D+ ++ i ++++++  ++v+++DHg 
  gene956|gene956|rna955|rna955 162 EIRKQEDDLIEKMLQSI--NNYDVIIAHLINLDSYGHiyeTIDHEEMEHQLVIYDNLINGIYKKMSEDT-LFVICSDHGV 238
                                    5567788999*******..56****************7777899********************99988.*********9 PP

                                    -TT CS
                                    xxx RF
                  Metalloenzyme 188 aed 190
                                    +++
  gene956|gene956|rna955|rna955 239 DNN 241
                                    876 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.16   9.7e+02       2      56 ..      42     100 ..      41     103 .. 0.76
   2 !   26.7   0.2   6.6e-10   3.9e-06     165     237 ..     170     241 ..     119     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.16
                                    EEEEETT-BTTHHHHHG.S..TSHHHHHHHHHSEEESE.EE-SSS-SHHHHHHHHHHSS CS
                   Phosphodiest   2 lvislDGlradlldrla.e..llpnlaaLakegvsapn.lrpvfPtlTfpnhaslvTGl 56 
                                    + +++DGlr+d   + + +      +++L +  ++++    + +Pt+T +    l TG+
  gene956|gene956|rna955|rna955  42 VYLLIDGLRFDSSIKTSkKghIFNKMKHLESIDSKFHAlSVSGIPTETGSRVIGLTTGT 100
                                    6689*****99877766556777778888777777776678889999999888888886 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 6.6e-10
                                    HHHHCT...SSESEEEEEECCCHHHHHHH-T.TSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEE CS
                   Phosphodiest 165 vlekel...ekpdlllvyleetDtvgHkfGp.dspevedalrrvDkaigdLlealderglsaetniilvSDHGmadv 237
                                     +ek l    ++d+++ +l ++D+ gH +   d++e+e +l  +D+ i+ +++ + e+     t +++ SDHG+  +
  gene956|gene956|rna955|rna955 170 LIEKMLqsiNNYDVIIAHLINLDSYGHIYETiDHEEMEHQLVIYDNLINGIYKKMSED-----TLFVICSDHGVDNN 241
                                    344444667999*****************7548*************************.....**********9876 PP

>> DUF1911  Domain of unknown function (DUF1911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0004       2.4       2      94 ..     167     262 ..     166     269 .. 0.79
   2 ?    1.2   0.0      0.11   6.4e+02      32      81 ..     346     394 ..     322     413 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0004
                                    --HHHHHHHHHHHT-SS--S--S-HHHHGGGHHHH.HH--SS-GGGGHHHH.HHHTHHHHTS-...HHHHHHT----TTT CS
                        DUF1911   2 eDvLldfllasrqekreikeellhpkpyqkllevieeedkeeaskaLkkYl.keWYkgakela...wheahkereegayf 77 
                                    eD L++++l+s ++ + i  +l++ + y ++ e i ++++ e++  + + l +  Yk+++e        +h  +++ga+ 
  gene956|gene956|rna955|rna955 167 EDDLIEKMLQSINNYDVIIAHLINLDSYGHIYETI-DHEEMEHQLVIYDNLiNGIYKKMSEDTlfvICSDHGVDNNGAHG 245
                                    799********************************.4555555555555566*****99875412245667679999999 PP

                                    TT--HHHHHHHHHH--- CS
                        DUF1911  78 GyWafEaaavakllglD 94 
                                    G   +E +av   ++ D
  gene956|gene956|rna955|rna955 246 GVSTLEMSAVGIFISKD 262
                                    99999999998776655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                                    GHHHH.HH--SS-GGGGHHHHHHHTHHHHTS-HHHHHHT----TTTTT-- CS
                        DUF1911  32 llevieeedkeeaskaLkkYlkeWYkgakelawheahkereegayfGyWa 81 
                                      +v+ + + e+++++L++Y+k  Yk ++e++ + a+ ++ + +  G  +
  gene956|gene956|rna955|rna955 346 KCDVL-NIPFEDSHRELNEYIKLNYKLSEEISNRFAGRDHFRLVVSGILS 394
                                    34555.677889999***********999887766665444445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (725 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4453.45
//
Query:       gene957|gene957|rna956|rna956  [L=365]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-29  101.0   0.0    9.8e-29  100.4   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0015   18.7   0.0     0.0027   17.9   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
     0.0024   17.0   0.0     0.0039   16.3   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0028   17.4   0.0     0.0047   16.7   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0046   16.1   0.6       0.45    9.6   0.1    2.6  2  DREV             DREV methyltransferase
     0.0089   15.8   0.0      0.017   15.0   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.011   15.0   0.0       0.02   14.2   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.019   14.6   0.0      0.036   13.7   0.0    1.4  1  GCD14            tRNA methyltransferase complex GCD14 subunit
      0.026   13.6   0.1       0.36    9.9   0.0    2.3  2  Fibrillarin      Fibrillarin
      0.087   12.4   0.0       0.18   11.3   0.0    1.5  1  HMGL-like        HMGL-like
       0.11   12.0   0.0       0.38   10.2   0.0    1.8  2  Methyltransf_4   Putative methyltransferase


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.4   0.0     6e-32   9.8e-29       1     199 [.     169     360 ..     169     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.4 bits;  conditional E-value: 6e-32
                                    HHHH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..E CS
                Methyltr_RsmB-F   1 allLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelf 80 
                                    a++L+p+e  +++D c+aPG KT+ ++ +mkn+g+++A +++++R+k +++ l+rLgv n+ v+e D  k + +  +  +
  gene957|gene957|rna956|rna956 169 AYILNPKECSRVIDTCSAPGNKTSQLSMIMKNTGRIYAFERSETRAKTLQDQLERLGVSNVEVIENDFMKASPDDFK-DI 247
                                    589****************************************************************9887655553.59 PP

                                    EEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTE CS
                Methyltr_RsmB-F  81 DriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredv 160
                                      iL D  Csg g+      + ++ +ek i +l+  q ++++ a+   k++  lvYs Cs + eE eev++e+Lk+  d 
  gene957|gene957|rna956|rna956 248 QYILCDPSCSGSGMH-----LGYKMDEKRIESLKLFQIAIVEHALRF-KPE-RLVYSVCSDHKEEGEEVVDEVLKNS-DY 319
                                    99***********74.....5567799**************998864.555.7*********************998.88 PP

                                    EEESSBSTTSTTSSECEEC..TSEEE-TTTTSS-SEEEEEE CS
                Methyltr_RsmB-F 161 elvetelsepkglklgeea..gtlrllPhtenkdgffiakl 199
                                    el++++++ ++   ++     + +r   + +   gffia +
  gene957|gene957|rna956|rna956 320 ELEDISTFWSSSCPFEFPFshKVIRCKRNDNGATGFFIALF 360
                                    88887766555554444441156667777778899999976 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.6e-06    0.0027      21     105 ..     176     264 ..     137     334 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-06
                                    TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHH..TTEEEECS-CCCSSHHHHHCHCHHHSSEE CS
                           FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........apl..pgvttiqgditdpetiekikealserkvd 89 
                                    +  +v+D ++aPG+ +  l+  ++++g+++a+   +          + l  ++v++i+ d+++ +  + +k+      ++
  gene957|gene957|rna956|rna956 176 ECSRVIDTCSAPGNKTSQLSMIMKNTGRIYAFERSETraktlqdqlERLgvSNVEVIENDFMKASPDD-FKD------IQ 248
                                    4578*****************99989999999999988877775443336689999999999998888.443......9* PP

                                    EEEE--S-SS-CHHHH CS
                           FtsJ  90 lvvsDgapdvsgvhdl 105
                                     +++D + + sg+h  
  gene957|gene957|rna956|rna956 249 YILCDPSCSGSGMHLG 264
                                    *****99888887743 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.4e-06    0.0039       8      90 ..     149     241 ..     143     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                                    CG--EE--HHHHHHHHHH.....H-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT..TCCC CS
                         RrnaAD   8 ygqnflknkkvineIldk.....lnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls..kdek 77 
                                    ++q++   k vi++I +      ln++e   v++  + +G+ T +L  ++       ++E  e  ak lq++l+    ++
  gene957|gene957|rna956|rna956 149 FSQEYKDGKFVIQNISSClpayiLNPKECSRVIDTCSAPGNKTSQLSMIMkntGRIYAFERSETRAKTLQDQLErlGVSN 228
                                    677777778888888654111115778*******************988833345789****************9999** PP

                                    EEEE-S-CCGHHH CS
                         RrnaAD  78 lkvvhqDflkfet 90 
                                    ++v+++Df+k++ 
  gene957|gene957|rna956|rna956 229 VEVIENDFMKASP 241
                                    **********986 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.9e-06    0.0047      71     132 ..     174     235 ..     154     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                                    --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                           PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                     k+ +rv++  s  G +t  l+++++++gr+ + er++  +++ + +l++l+++nv v++ D
  gene957|gene957|rna956|rna956 174 PKECSRVIDTCSAPGNKTSQLSMIMKNTGRIYAFERSETRAKTLQDQLERLGVSNVEVIEND 235
                                    57789******************************************************998 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1   0.00028      0.45     136     179 ..      56      99 ..      16     112 .. 0.76
   2 ?    4.3   0.1     0.011        18      93     136 ..     175     221 ..     131     327 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                           DREV 136 kynvlsalelqetdvkldlilclnlldrcfdplklledirsale 179
                                      +v+ + ++ e d +l ++ c+++ldr     ++ +   +al+
  gene957|gene957|rna956|rna956  56 LLEVIKKCKYMEDDRELGVVRCFEILDRRIRNTRMYKKFMKALD 99 
                                    3468888999********************99999998888876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                           DREV  93 qedkklldlGaGdGeitkrvaptfee...vyatelsetmrdrlkkkk 136
                                    +e  +++d  +  G+ t +++  +++   +ya e set  + l+ + 
  gene957|gene957|rna956|rna956 175 KECSRVIDTCSAPGNKTSQLSMIMKNtgrIYAFERSETRAKTLQDQL 221
                                    566789999999999998888888777779**999998776666432 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     1e-05     0.017       5      81 ..     178     253 ..     174     333 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-05
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsn 81 
                                     rv+D  ++ G++t +l   +   ++++ +++se+  +  +  +++lg++nve+ + d+ +++ + ++d  + +il++
  gene957|gene957|rna956|rna956 178 SRVIDTCSAPGNKTSQLSMIMKNTGRIYAFERSETRAKTLQDQLERLGVSNVEVIENDFMKASPDdFKD--IQYILCD 253
                                    589***************87778999***********************************66566887..8888887 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.2e-05      0.02      43     117 ..     172     245 ..     157     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                    --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-E CS
                Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsf 117
                                     ++k+ ++v+D ++  g+ + +ls  ++++g++   + +e+  k+ +++l++ g++n+e +  + ++    dd +
  gene957|gene957|rna956|rna956 172 LNPKECSRVIDTCSAPGNKTSQLSMIMKNTGRIYAFERSETRAKTLQDQLERLGVSNVEVIENDFMKAS-PDDFK 245
                                    678999*****************************************************9998887754.44444 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.2e-05     0.036      36     103 ..     172     238 ..     159     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.2e-05
                          GCD14  36 LelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvck 103
                                    L+ k+ s+v+++    g  +++++  ++ tG++++fe  e+ra++ ++++++ ++s +v v + D  k
  gene957|gene957|rna956|rna956 172 LNPKECSRVIDTCSAPGNKTSQLSMIMKNTGRIYAFERSETRAKTLQDQLERLGVS-NVEVIENDFMK 238
                                    6668899****************************************999999986.56666666654 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.1   1.6e+02     105     141 ..      13      49 ..       9      56 .. 0.82
   2 ?    9.9   0.0   0.00022      0.36      69     112 ..     175     218 ..     135     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                                    HHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--E CS
                    Fibrillarin 105 prvlrelievakkRknivPileDArkPekYralvekv 141
                                     r++  + +v + R+ i   +   r+P+ Y+ lv++v
  gene957|gene957|rna956|rna956  13 RRCVEMVRNVLEGRSTIKGEVYKTRNPKMYHRLVHMV 49 
                                    55555566889999999999999***********998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                                    -TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH CS
                    Fibrillarin  69 kkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlreli 112
                                    k+ s+v+   +a G   s +s i++++g++ya e s++  + l 
  gene957|gene957|rna956|rna956 175 KECSRVIDTCSAPGNKTSQLSMIMKNTGRIYAFERSETRAKTLQ 218
                                    566788888999************************99988876 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.18      25      59 ..     214     251 ..     206     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHT-SEE--...TSGGGT.THHHHHHHS- CS
                      HMGL-like  25 klaiakaLdeagvdeiEv...gfpaaseddfevvraia 59 
                                     +++ ++L+++gv+ +Ev    f  as+ddf+++++i 
  gene957|gene957|rna956|rna956 214 AKTLQDQLERLGVSNVEVienDFMKASPDDFKDIQYIL 251
                                    567889*********9999999*************996 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00023      0.38       5      70 ..     180     246 ..     177     254 .. 0.85
   2 ?   -2.0   0.0       1.3   2.1e+03     114     140 ..     297     323 ..     269     335 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00023
                                    EEEET-TTSHHHHHHHHH.STTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-T CS
                 Methyltransf_4   5 vleiGcGkGeflvalAkk.nPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelled 70 
                                    v++ +++ G+ +++l+   + +  + + E ++++ +++ ++ e+l+++N++++++d +k  ++ ++d
  gene957|gene957|rna956|rna956 180 VIDTCSAPGNKTSQLSMImKNTGRIYAFERSETRAKTLQDQLERLGVSNVEVIENDFMKASPDDFKD 246
                                    688899999999999975145557789*****************************99998888876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                    EEEESHHHHHHHHHHHHHCSTTEEESS CS
                 Methyltransf_4 114 elaTDveeyaeemlkvleeeplferls 140
                                     + +D++e  ee+++++ ++ ++e  +
  gene957|gene957|rna956|rna956 297 SVCSDHKEEGEEVVDEVLKNSDYELED 323
                                    466888888899999998888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2348.00
//
Query:       gene958|gene958|rna957|rna957  [L=307]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-12   47.8  10.1    2.1e-12   47.2  10.1    1.3  1  zf-RING_2     Ring finger domain
    2.1e-10   40.1   2.5    4.3e-10   39.2   2.5    1.6  1  zf-RING_11    RING-like zinc finger
    1.1e-08   34.8   7.3    1.9e-08   34.0   7.3    1.4  1  zf-C3HC4_2    Zinc finger, C3HC4 type (RING finger)
    4.4e-08   32.9   6.2    7.8e-08   32.1   6.2    1.4  1  zf-C3HC4      Zinc finger, C3HC4 type (RING finger)
    1.9e-06   27.7   5.9    3.4e-06   26.9   5.9    1.4  1  zf-RING_5     zinc-RING finger domain
    1.6e-05   25.1   9.2    4.4e-05   23.7   9.2    1.7  1  zf-rbx1       RING-H2 zinc finger domain
     0.0001   22.1   6.3    0.00017   21.4   6.3    1.4  1  Prok-RING_4   Prokaryotic RING finger family 4
    0.00013   21.7   8.3     0.0002   21.1   8.3    1.3  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
    0.00021   21.2   1.5    0.00021   21.2   1.5    1.7  1  zf-RING_UBOX  RING-type zinc-finger
     0.0078   16.2   5.4      0.016   15.3   5.4    1.5  1  zf-ANAPC11    Anaphase-promoting complex subunit 11 RING-H2 f
  ------ inclusion threshold ------
      0.087   13.0   3.2       0.23   11.6   3.2    1.7  1  RINGv         RING-variant domain
       0.16   12.2   7.1       0.51   10.6   7.1    1.9  1  FANCL_C       FANCL C-terminal domain
       0.16   12.2   6.1       0.37   11.1   6.1    1.6  1  zf-HC5HC2H    PHD-like zinc-binding domain
       0.18   11.6   6.6       0.38   10.6   6.6    1.6  1  zf-RING_4     RING/Ubox like zinc-binding domain
       0.28   11.1   5.9       0.56   10.1   5.9    1.5  1  zf-C3HC4_5    Zinc finger, C3HC4 type (RING finger)
       0.39   11.1   5.7       0.77   10.1   5.7    1.5  1  zf-RING-like  RING-like domain
          1    9.1   7.4        1.6    8.4   7.4    1.3  1  Zn_ribbon_17  Zinc-ribbon, C4HC2 type
        9.8    6.4   9.1         29    4.9   6.8    2.3  2  zf-C3HC4_4    zinc finger of C3HC4-type, RING


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2  10.1   2.1e-15   2.1e-12       2      44 .]     261     304 ..     260     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2.1e-15
                      zf-RING_2   2 eCpICleelssadsvlllpCgHvfhreClerw.lrssstCPlCr 44 
                                    eC+IC++++s ++++++lpC H fh  C+++w l +s++CP+Cr
  gene958|gene958|rna957|rna957 261 ECTICMSNFSMNQKLRVLPCDHKFHTGCVDKWlLGHSNKCPVCR 304
                                    8*******************************7778888****9 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   2.5   4.3e-13   4.3e-10       1      29 []     261     289 ..     261     289 .. 0.98

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 4.3e-13
                     zf-RING_11   1 eCsICLeefkpgqalfilpCsHtFHfkCI 29 
                                    eC+IC+++f  +q+l++lpC H FH  C+
  gene958|gene958|rna957|rna957 261 ECTICMSNFSMNQKLRVLPCDHKFHTGCV 289
                                    9***************************7 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   7.3   1.9e-11   1.9e-08       1      40 []     261     303 ..     261     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.9e-11
                     zf-C3HC4_2   1 kCpiCldmlkdpsvvt..pCgHvfCqkCilr.sLeekneCPlC 40 
                                    +C+iC+  +++   +   pC H+f+  C+++  L ++n+CP+C
  gene958|gene958|rna957|rna957 261 ECTICMSNFSMNQKLRvlPCDHKFHTGCVDKwLLGHSNKCPVC 303
                                    6******99987554455*************4457777***** PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   6.2   7.8e-11   7.8e-08       1      41 []     262     303 ..     262     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 7.8e-11
                                    -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                       zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                    C iC+++++ ++  ++l+C+H+f++ C++k+l    ++kCP+C
  gene958|gene958|rna957|rna957 262 CTICMSNFSMNQklRVLPCDHKFHTGCVDKWLL-GHSNKCPVC 303
                                    ********9999899******************.89999**** PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   5.9   3.4e-09   3.4e-06       1      44 []     261     305 ..     261     305 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.4e-09
                      zf-RING_5   1 hCnkCfeklskeekfyltsCgHifCekClkkll.ekeavCpiCrk 44 
                                    +C +C++++s ++k  +++C H f+  C++k l + +++Cp+Crk
  gene958|gene958|rna957|rna957 261 ECTICMSNFSMNQKLRVLPCDHKFHTGCVDKWLlGHSNKCPVCRK 305
                                    6******************************************97 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   9.2   4.4e-08   4.4e-05      13      55 .]     261     304 ..     254     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.4e-08
                        zf-rbx1  13 acieckapgdeecpvvlGeCgHaFHlhCiskWlkt.rkvCPlcr 55 
                                    +c+ c ++ + + ++ +  C H+FH+ C++kWl   +++CP+cr
  gene958|gene958|rna957|rna957 261 ECTICMSNFSMNQKLRVLPCDHKFHTGCVDKWLLGhSNKCPVCR 304
                                    4666766666666666679*************9876999****8 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   6.3   1.7e-07   0.00017       1      40 [.     262     307 .]     262     307 .] 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                    Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk...dlssCPlCqrri 40 
                                    C +C ++   ++k ++ pC H +   C d++    ++ CP+C++ i
  gene958|gene958|rna957|rna957 262 CTICMSNfsmNQKLRVLPCDHKFHTGCVDKWllgHSNKCPVCRKII 307
                                    9999999999*********************997777******975 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   8.3     2e-07    0.0002       3      46 ..     260     306 ..     258     307 .] 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                                    SB-TTTSSS...BS-EEETTEEEEEE-HHHHHHHHH.TT-B-TTT--B CS
                     zf-C3HC4_3   3 eeCviCler...prnvvllpCgHlvlCeeCaekllk.rkkkCpiCrrp 46 
                                     eC iC+++   +++  +lpC H  +   C++k+l  +++kCp+Cr+ 
  gene958|gene958|rna957|rna957 260 CECTICMSNfsmNQKLRVLPCDHK-FHTGCVDKWLLgHSNKCPVCRKI 306
                                    68******9877889*********.9********989*********86 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.5   2.1e-07   0.00021       1      39 []     262     301 ..     262     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.1e-07
                   zf-RING_UBOX   1 CpIClelft.dP.lv.lpCGHtFCreClwelskslegafkCP 39 
                                    C+IC++ f+ +  l  lpC H F+  C+   +  l+ + kCP
  gene958|gene958|rna957|rna957 262 CTICMSNFSmNQkLRvLPCDHKFHTGCV--DKWLLGHSNKCP 301
                                    ********964453436***********..677889999998 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.4   1.6e-05     0.016      48      80 ..     276     306 ..     246     307 .] 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                                    EEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB CS
                     zf-ANAPC11  48 vlGkckhnfhlhcilkwletetskglcpmcrqt 80 
                                     +  c+h+fh+ c+ kwl  ++  ++cp+cr++
  gene958|gene958|rna957|rna957 276 RVLPCDHKFHTGCVDKWLLGHS--NKCPVCRKI 306
                                    4456**************8776..57*****86 PP

>> RINGv  RING-variant domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.2   0.00023      0.23       1      48 []     262     303 ..     262     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                    ETTTTEE-SSSS--.B-SS--STCCCSB-HHHHHHHHHHTCT-SB-TTT CS
                          RINGv   1 CriCleeeeesepl.ispCkCrGslklvHesClekWldekeantqCeiC 48 
                                    C iC+ + + +++l + pC      + +H  C++kWl    ++++C +C
  gene958|gene958|rna957|rna957 262 CTICMSNFSMNQKLrVLPCD-----HKFHTGCVDKWLLG--HSNKCPVC 303
                                    99999998888855367887.....679*********99..8899***9 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   7.1   0.00051      0.51       2      44 ..     259     296 ..     258     307 .] 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                                    --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHH CS
                        FANCL_C   2 eveCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrsl 44 
                                    + eC iC++++  ++++ +  Cd     +kfH+ C+  Wl + 
  gene958|gene958|rna957|rna957 259 TCECTICMSNFSMNQKLRVLPCD-----HKFHTGCVDKWLLGH 296
                                    579*********99999999887.....58*********9765 PP

>> zf-HC5HC2H  PHD-like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.1   0.00037      0.37      21      68 ..     244     291 ..     232     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                     zf-HC5HC2H  21 meeiedvekikkerkklkCylCkkkvGaciqCskkkCkkafHvtCake 68 
                                      + +dv k+ k+ ++ +C++C+++ +++ + +   C ++fH+ C  +
  gene958|gene958|rna957|rna957 244 SLKKTDVVKATKDDETCECTICMSNFSMNQKLRVLPCDHKFHTGCVDK 291
                                    56778999999**********************************865 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   6.6   0.00038      0.38       1      45 [.     262     305 ..     259     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                      zf-RING_4   1 cplCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaCre 45 
                                    c +C++++   +++l+  +C++++   C ++ l  ++++CP Cr+
  gene958|gene958|rna957|rna957 262 CTICMSNF-SMNQKLRVLPCDHKFHTGCVDKWLLGHSNKCPVCRK 305
                                    88999999.567889999999************99*********7 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.9   0.00056      0.56       4      48 ..     262     303 ..     257     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                     zf-C3HC4_5   4 CPvCkssrYlnpdleflinpeCYhkmCesCvdRlFsdGPnqCPva 48 
                                    C +C s+  +n++l++l    C hk  + Cvd+      n+CPv 
  gene958|gene958|rna957|rna957 262 CTICMSNFSMNQKLRVL---PCDHKFHTGCVDKWLLGHSNKCPVC 303
                                    89*************99...6***************99*****85 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.7   0.00077      0.77       1      43 []     262     303 ..     262     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00077
                   zf-RING-like   1 CeaCkeivtqGvrCsnesCnvrlHvdCfqhyirthsskkCpkC 43 
                                    C++C +   + ++     C  ++H  C+++ +  hs+ kCp C
  gene958|gene958|rna957|rna957 262 CTICMSNFSMNQKLRVLPCDHKFHTGCVDKWLLGHSN-KCPVC 303
                                    777777777777777788**************88888.***** PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.4    0.0016       1.6       4      47 ..     259     302 ..     256     304 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                   Zn_ribbon_17   4 lksCayCelavkgrvvl.cgvCeHvlHasCarewfenddlaeCps 47 
                                    + +C++C  +   +  l    C H  H+ C+++w+     ++Cp+
  gene958|gene958|rna957|rna957 259 TCECTICMSNFSMNQKLrVLPCDHKFHTGCVDKWLLGHS-NKCPV 302
                                    568999987766554441457*************75555.79997 PP

>> zf-C3HC4_4  zinc finger of C3HC4-type, RING
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.3      0.21   2.1e+02      16      25 ..     260     269 ..     258     276 .. 0.74
   2 ?    4.9   6.8     0.029        29       1      42 []     262     303 ..     262     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                     zf-C3HC4_4  16 CGhsfClsCi 25 
                                    C++++C+s  
  gene958|gene958|rna957|rna957 260 CECTICMSNF 269
                                    9999999855 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.029
                     zf-C3HC4_4   1 CPiCldYL...ekPvsleCGhsfClsCisslqkepdgeqllCplC 42 
                                    C iC++ +   +k   l+C+h f   C++++    ++    Cp+C
  gene958|gene958|rna957|rna957 262 CTICMSNFsmnQKLRVLPCDHKFHTGCVDKWLLGHSN---KCPVC 303
                                    778887773333445689************9998877...5**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1764.69
//
Query:       gene959|gene959|rna958|rna958  [L=333]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-25   87.7   2.3    5.3e-14   51.8   0.0    3.6  4  RRM_1          RNA recognition motif. (a.k.a. RRM, RBD, or RN
    0.00013   21.6   0.0      0.012   15.2   0.0    2.6  3  RRM_5          RNA recognition motif. (a.k.a. RRM, RBD, or RN
     0.0019   18.2   1.6        1.6    8.8   0.0    3.4  4  RRM_3          RNA binding motif
  ------ inclusion threshold ------
      0.058   13.2   0.0       0.39   10.6   0.0    2.2  2  DUF1866        Domain of unknown function (DUF1866)
      0.073   13.2   0.0        0.2   11.8   0.0    1.8  1  DNA_ligase_IV  DNA ligase IV


Domain annotation for each model (and alignments):
>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7     6e+03      11      24 ..       5      18 ..       4      26 .. 0.64
   2 !   19.0   0.0   2.5e-07   0.00089       1      69 [.      60     120 ..      60     121 .. 0.88
   3 !   51.8   0.0   1.5e-17   5.3e-14       1      70 []     144     213 ..     144     213 .. 0.97
   4 !   14.9   0.2     5e-06     0.018      12      70 .]     269     323 ..     268     323 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                   SHHHHHHHHHTTSC CS
                          RRM_1 11 teeeLkelFskfGp 24
                                   ++e+Lk+  +++  
  gene959|gene959|rna958|rna958  5 NDEDLKKTIEEVAN 18
                                   67788877776655 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 2.5e-07
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrel 69 
                                    +++gn++  +++  +k+l+s fGp+ s++ ++      k +af +F+++ +A  ++e+ ng+  +g+ l
  gene959|gene959|rna958|rna958  60 VYIGNIT--ASKGSIKDLLSVFGPV-SVTYISG-----KECAFADFDNPHAAYLCMEEINGMAHDGKIL 120
                                    5777775..67889***********.8998886.....***********************98888765 PP

  == domain 3  score: 51.8 bits;  conditional E-value: 1.5e-17
                                    EEEESETTTSSHHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                          RRM_1   1 lfVgnLppdvteeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                    ++V+n+  d+ ee+Lk++F+k G+ik+++lv++e   +kg+++V+F  + dA++Al   n+  l g++++
  gene959|gene959|rna958|rna958 144 VYVSNIDLDIEEEQLKDVFGKMGEIKDVRLVYEESFVHKGYGYVQFSRPGDARRALGYSNKISLYGKRIR 213
                                    8********************************************************9999999999986 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 5e-06
                                    HHHHHHHHHTTSCEEEEEEEEETTTSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE CS
                          RRM_1  12 eeeLkelFskfGpiksiklvrdetgkskgfafVeFeskedAekAlealngkklggrelk 70 
                                    ++e++  ++k+G ++++ ++++       + ++ + ++++A++  + lng+ +ggr+++
  gene959|gene959|rna958|rna958 269 DQEIENEMRKYGNVERFGISKE----GEVVVYCLYSTEDEAKHSFNILNGRFFGGRRIR 323
                                    5899999**************6....999***************************996 PP

>> RRM_5  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.91   3.3e+03      62      94 ..      88     120 ..      71     126 .. 0.69
   2 !   15.2   0.0   3.3e-06     0.012      18      99 ..     133     217 ..     121     240 .. 0.85
   3 ?    3.3   0.0     0.016        58      50      99 ..     278     327 ..     265     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.91
                          RRM_5  62 tkketalvqmgdasaveravqHLnnaklfgkrl 94 
                                    + ke a+ +  +  a+ ++++ +n+    gk l
  gene959|gene959|rna958|rna958  88 SGKECAFADFDNPHAAYLCMEEINGMAHDGKIL 120
                                    446778888888888999999998887666655 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 3.3e-06
                          RRM_5  18 pgaagvaegsVllVyglepdkvnldklFnlfclYgnvervkfl....ktkketalvqmgdasaveravqHLnnaklfgkr 93 
                                    p   g ++++++ V++++ d +  ++l  +f+  g+++ v+++    +  k++  vq +   ++ ra+   n ++l+gkr
  gene959|gene959|rna958|rna958 133 PKDLGPPDETIVYVSNIDLD-IEEEQLKDVFGKMGEIKDVRLVyeesFVHKGYGYVQFSRPGDARRALGYSNKISLYGKR 211
                                    456788999********987.78899****************944334579***************************** PP

                          RRM_5  94 levalS 99 
                                    +++ +S
  gene959|gene959|rna958|rna958 212 IRIGPS 217
                                    ***998 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.016
                          RRM_5  50 lYgnvervkflktkketalvqmgdasaveravqHLnnaklfgkrlevalS 99 
                                     Ygnver  + k  +       + + +++ + + Ln+    g+r+++ +S
  gene959|gene959|rna958|rna958 278 KYGNVERFGISKEGEVVVYCLYSTEDEAKHSFNILNGRFFGGRRIRAEMS 327
                                    69999998775544444444567888899999999999888889998887 PP

>> RRM_3  RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         1   3.7e+03      74      95 ..       4      25 ..       2      29 .. 0.62
   2 !    6.2   0.0     0.003        11      13      56 ..      67     109 ..      61     123 .. 0.83
   3 !    8.8   0.0   0.00045       1.6       3      58 ..     143     203 ..     142     223 .. 0.78
   4 ?   -0.8   0.1      0.44   1.6e+03      17      54 ..     271     309 ..     260     314 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                                   --HHHHHHHHHHHHHHHHHCC- CS
                          RRM_3 74 LeGeeEkeywkkiledkqkkkn 95
                                   +++e  k+  ++++++k ++++
  gene959|gene959|rna958|rna958  4 VNDEDLKKTIEEVANAKRNELK 25
                                   5566666666777666666654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.003
                                    --HHHHHHHCHCCS-ECEEEE-TTSSEEEEEESSHHHHHHHHHH CS
                          RRM_3  13 lsredikellsklgevayvdyekgdkegevrFkedeeakkalek 56 
                                     s+ +ik+lls +g+v  v y +g++ +   F+++++a   +e+
  gene959|gene959|rna958|rna958  67 ASKGSIKDLLSVFGPVS-VTYISGKECAFADFDNPHAAYLCMEE 109
                                    4689**********997.88999999999999999888766665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00045
                                    EEEEEE-SSS--HHHHHHHCHCCS-ECEEEE-TTSS.....EEEEEESSHHHHHHHHHHHH CS
                          RRM_3   3 ilklsGlnkelsredikellsklgevayvdyekgdk.....egevrFkedeeakkalekat 58 
                                    i+ +s ++ ++  e++k+++ k+ge++ v +  +++      g+v+F  + +a++al    
  gene959|gene959|rna958|rna958 143 IVYVSNIDLDIEEEQLKDVFGKMGEIKDVRLVYEESfvhkgYGYVQFSRPGDARRALGYSN 203
                                    788888899999************99988776655422222799*********99987655 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.44
                                    HHHHHCHCCS-ECEEEE.-TTSSEEEEEESSHHHHHHHH CS
                          RRM_3  17 dikellsklgevayvdy.ekgdkegevrFkedeeakkal 54 
                                    +i + ++k+g+v+  +  ++g+   + ++ +++eak+ +
  gene959|gene959|rna958|rna958 271 EIENEMRKYGNVERFGIsKEGEVVVYCLYSTEDEAKHSF 309
                                    677777888888766551456777888999999998765 PP

>> DUF1866  Domain of unknown function (DUF1866)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.39      17      75 ..     130     180 ..     118     207 .. 0.77
   2 ?   -0.6   0.0      0.31   1.1e+03     101     119 ..     261     278 ..     247     309 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                    XXXS-----TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETTCEEE CS
                        DUF1866  17 keviallGPpDgtilvslksgdedeknifdenlideLlqeltslGeviLvRfvedkmwv 75 
                                     e+ ++lGPpD ti+  + + d+d +   +e    +L + ++++Ge+  vR+v ++ +v
  gene959|gene959|rna958|rna958 130 SEIPKDLGPPDETIVY-VSNIDLDIE---EE----QLKDVFGKMGEIKDVRLVYEESFV 180
                                    68889********974.333345444...33....455678999999999999888776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.31
                                    EEEXXXXXXXXXXXXXXXX CS
                        DUF1866 101 iklkskdWlksleeeillk 119
                                    i    +d+ +++e+e+  k
  gene959|gene959|rna958|rna958 261 IDDADDDFDQEIENEMR-K 278
                                    55555555555555552.2 PP

>> DNA_ligase_IV  DNA ligase IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.7e-05       0.2      19      33 ..     152     166 ..     151     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                  DNA_ligase_IV  19 DtdeeqLKevFnrId 33 
                                    D+ eeqLK+vF +++
  gene959|gene959|rna958|rna958 152 DIEEEQLKDVFGKMG 166
                                    999*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.38s 00:00:01.06 Elapsed: 00:00:00.57
# Mc/sec: 1762.13
//
Query:       gene960|gene960|rna959|rna959  [L=774]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-47  162.6   0.5    2.7e-40  138.7   0.0    2.3  2  Peptidase_C50  Peptidase family C50


Domain annotation for each model (and alignments):
>> Peptidase_C50  Peptidase family C50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.4     5e-09   8.9e-05      39      94 ..     507     560 ..     496     565 .. 0.90
   2 !  138.7   0.0   1.5e-44   2.7e-40     215     395 .]     566     729 ..     559     729 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 5e-09
                                    HHHHHHHHHHHHHHHHHHHHCHCCHHCCTHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                  Peptidase_C50  39 feevkeelkeiieesnestksakdvktkeakkeWWkeReeLDkrLkeLleniekvw 94 
                                    f++vk+++++i+ es++++k+  +v++  +k++WW +R eLD++L e+l+++ + +
  gene960|gene960|rna959|rna959 507 FRDVKARISRILIESRNILKE--NVHNDVDKARWWMQRIELDTKLGEVLHSVSTKF 560
                                    8899***************99..889999*********************998765 PP

  == domain 2  score: 138.7 bits;  conditional E-value: 1.5e-44
                                    .SEEEEEE-TTCTTS-GGGSTTTTTS-EEEES-HHHHHHHHHHHCTTGCSEEEESTSTEEEEE-TTS-SHHHHHHHHHHH CS
                  Peptidase_C50 215 kehtiLvldkelqalPWEslpiLrgqsvsRvpSleslrellekskekeegekvsksskgtyiLnPsgDLksTqetfeewl 294
                                    ++ +iLvld++ + +P+Es+pi+rg++v+RvpSle+l e+  ++        +s s + +y+L+P+++L +Tq+++++ l
  gene960|gene960|rna959|rna959 566 RKDIILVLDETTTEFPFESMPIFRGKAVYRVPSLEYLEETSGAN--------ISGS-SFFYLLDPENNLPKTQDRMTKFL 636
                                    6789*********************************9988444........5666.89********************* PP

                                    HHHCCT-EEEESS---HHHHHHHHHHSSEEEEESSTTSTTTS-HHHHTT.S--SEEEEESTTTT--ECTTTCECCSHHHH CS
                  Peptidase_C50 295 eklekgwkgivgraPteeeleeaLkssdlflYfGHGsGaqYirsreirklercaatlLmGCSSgalkeaGefepsGtvln 374
                                    +++    +g++gr+ ++ e +ea  + d++lYfGHGsG +Y++ +   k     + lL+GCSS++l    +++++G++l+
  gene960|gene960|rna959|rna959 637 KSFG-ITNGVTGRSLSDLECREA-DKCDILLYFGHGSGLKYLKISGEGK-----IMLLFGCSSAKLLCIENYKRNGAILK 709
                                    *985.99*************998.89****************9887555.....67************************ PP

                                    HHHTT-SEEEEESS--BHHHH CS
                  Peptidase_C50 375 YllagcpavvanLWDVTDkDI 395
                                    +l  +  +vv++LW+VTDkDI
  gene960|gene960|rna959|rna959 710 HLRKN-STVVGCLWEVTDKDI 729
                                    *9865.589***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (774 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.80u 0.33s 00:00:01.13 Elapsed: 00:00:00.54
# Mc/sec: 4324.79
//
Query:       gene96|gene96|rna96|rna96  [L=375]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00013   22.1   0.1    0.00066   19.8   0.0    2.3  2  Myb_DNA-binding  Myb-like DNA-binding domain
  ------ inclusion threshold ------
      0.037   14.3   0.0      0.037   14.3   0.0    2.6  4  Myb_DNA-bind_6   Myb-like DNA-binding domain
        0.1   12.3   0.0       0.25   11.0   0.0    1.7  1  Sigma70_r4_2     Sigma-70, region 4
       0.21   11.6   2.7        5.7    7.0   0.0    4.1  5  HTH_19           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.5e-07   0.00066       3      44 ..     113     153 ..     111     155 .. 0.91
   2 ?   -2.7   0.0       1.6   7.2e+03      25      44 ..     307     326 ..     301     327 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-07
                                SSBHHHHHHHHHHHHHHTTCHHHHHHHHTSS-HHHHHHHHHH CS
            Myb_DNA-binding   3 kWteeEdelLleavkkhGnrWkkIaerlggRtekqcrsrwrn 44 
                                kW +e + +Ll++v+ +G +Wk+I   + ++t   c+s +++
  gene96|gene96|rna96|rna96 113 KWEPENEIQLLNLVRVLGFKWKEICGIM-NKTSRKCISMYYR 153
                                8***********************9999.7999999987765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.6
                                HHHHHHTSS-HHHHHHHHHH CS
            Myb_DNA-binding  25 kIaerlggRtekqcrsrwrn 44 
                                 I + +g Rt k+ ++ +rn
  gene96|gene96|rna96|rna96 307 QITKVYGIRTFKDLIEVFRN 326
                                46666666777777766666 PP

>> Myb_DNA-bind_6  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.4   1.1e+04      23      34 ..      86      97 ..      85      99 .. 0.81
   2 ?   14.3   0.0   8.3e-06     0.037       1      41 [.     114     153 ..     114     170 .. 0.88
   3 ?   -3.2   0.1       2.4   1.1e+04       2       9 ..     175     182 ..     175     187 .. 0.81
   4 ?   -2.4   0.0       1.3   5.8e+03      21      41 ..     306     326 ..     287     338 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.4
             Myb_DNA-bind_6 23 IaealnrRtpkq 34
                               I++al +Rt+++
  gene96|gene96|rna96|rna96 86 ISNALRQRTMNS 97
                               999998899987 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 8.3e-06
             Myb_DNA-bind_6   1 WteeEdeiLlklvekygndWknIaealnrRtpkqcfdrwkn 41 
                                W +e +  Ll+lv+  g++Wk+I  ++n +t+  c   + +
  gene96|gene96|rna96|rna96 114 WEPENEIQLLNLVRVLGFKWKEICGIMN-KTSRKCISMYYR 153
                                88999999********************.***999877766 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.4
             Myb_DNA-bind_6   2 teeEdeiL 9  
                                t+eE+e L
  gene96|gene96|rna96|rna96 175 TDEEWEGL 182
                                89999877 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.3
             Myb_DNA-bind_6  21 knIaealnrRtpkqcfdrwkn 41 
                                 +I + ++ Rt k++ + ++n
  gene96|gene96|rna96|rna96 306 IQITKVYGIRTFKDLIEVFRN 326
                                344455544555555555555 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.6e-05      0.25      15      50 ..     119     154 ..     116     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.6e-05
                                HHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHH CS
               Sigma70_r4_2  15 qreifllryleglsykEIAellgisegtVksrlsRA 50 
                                + + + l ++ g++ kEI+ +++ +++ + s+++R 
  gene96|gene96|rna96|rna96 119 EIQLLNLVRVLGFKWKEICGIMNKTSRKCISMYYRI 154
                                557899*********************999999985 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.58   2.6e+03      36      54 ..      15      33 ..      10      37 .. 0.84
   2 ?   -0.4   0.2      0.27   1.2e+03       2      16 ..      50      64 ..      50      68 .. 0.85
   3 ?    0.2   0.0      0.17   7.6e+02      11      32 ..     129     151 ..     123     153 .. 0.90
   4 ?    7.0   0.0    0.0013       5.7      18      43 ..     182     204 ..     180     225 .. 0.84
   5 ?   -3.0   0.0       1.8   7.9e+03      17      33 ..     253     268 ..     252     276 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.58
                     HTH_19 36 kkdvpsaelllkiaealgi 54
                               +++ ++a++++++ e  gi
  gene96|gene96|rna96|rna96 15 RTKFTDAHEVKDLIERHGI 33
                               566899********99998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                     HTH_19  2 erLkeaReelgltqe 16
                               e ++++ ee+g+ ++
  gene96|gene96|rna96|rna96 50 EAIRRFLEERGMEMK 64
                               689********9776 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.17
                     HTH_19  11 lgltqeelae.rlgisrskisai 32 
                                lg++ +e+++ ++++sr+ is++
  gene96|gene96|rna96|rna96 129 LGFKWKEICGiMNKTSRKCISMY 151
                                688889999999*********98 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0013
                     HTH_19  18 laerlgisrskisaiEngkkdvpsae 43 
                                l++rl+++r+++s+++ng   ++s++
  gene96|gene96|rna96|rna96 182 LCDRLRTNRKRLSHLING---YISSK 204
                                6789**************...55544 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 1.8
                     HTH_19  17 elaerlgisrskisaiE 33 
                                e+++r +i +  is+++
  gene96|gene96|rna96|rna96 253 EIVGREKI-KEEISKLI 268
                                78888888.88888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2267.36
//
Query:       gene961|gene961|rna960|rna960  [L=100]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-23   81.6   1.2    4.1e-23   81.3   1.2    1.1  1  DUF167    Uncharacterised ACR, YggU family COG1872


Domain annotation for each model (and alignments):
>> DUF167  Uncharacterised ACR, YggU family COG1872
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   1.2   2.3e-27   4.1e-23       2      76 ..      11      81 ..      10      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 2.3e-27
                                   EEEEEES---SSS----...--TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                         DUF167  2 vilavrvkPgakkdaigleedaegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                   ++l+vr++P a+ + i     ++++ ++ v+v+appv++kANk+l++f++k+l+vpks+++iv G++s +K+v++
  gene961|gene961|rna960|rna960 11 LRLSVRARPSARSTGIR----EISGTEIVVNVNAPPVENKANKELVRFISKMLRVPKSSIKIVIGTTSMQKTVEV 81
                                   79***************....788899**********************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 589.21
//
Query:       gene962|gene962|rna961|rna961  [L=272]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-71  240.8   0.0    1.7e-71  240.7   0.0    1.0  1  Pkinase          Protein kinase domain
    5.4e-40  137.3   0.0    6.7e-40  137.0   0.0    1.1  1  Pkinase_Tyr      Protein tyrosine kinase
      1e-05   25.0   0.0    6.2e-05   22.4   0.0    1.9  2  Kinase-like      Kinase-like
     0.0005   19.0   0.0    0.00086   18.2   0.0    1.3  1  Pkinase_fungal   Fungal protein kinase
     0.0065   15.5   0.1       0.02   13.9   0.1    1.8  2  Pox_ser-thr_kin  Poxvirus serine/threonine protein kinase
  ------ inclusion threshold ------
      0.022   14.4   0.0       0.07   12.7   0.0    1.8  2  RIO1             RIO1 family
      0.049   13.2   0.1       0.11   12.1   0.0    1.6  2  Choline_kinase   Choline/ethanolamine kinase
      0.092   11.7   0.1       0.43    9.5   0.1    1.9  1  Haspin_kinase    Haspin like kinase domain
       0.12   12.3   0.1        1.1    9.1   0.0    2.0  2  APH              Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.7   0.0   8.7e-75   1.7e-71       1     264 []      10     263 ..      10     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: 240.7 bits;  conditional E-value: 8.7e-75
                                    EEEEEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE- CS
                        Pkinase   1 yekleklGeGsfGkVykaveketgkivAvKkikkekakkkke.kkvlrEikilkklkhpnivrlyevfeekdelylvley 79 
                                    +e  + lG+G+fG+V  a+eke+g ivA+K+i  ++++  ++ ++++rE++i+ +lkhpni+r+y+ f++kd++yl+ley
  gene962|gene962|rna961|rna961  10 FEIGRLLGRGKFGQVWLAREKEKGFIVALKIIPIKEIQTVETaRQIRREVEIHSNLKHPNILRMYGHFHDKDHIYLILEY 89 
                                    577899******************************99999989************************************ PP

                                    -TTEBHHHHHHHHSS.--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBCTTT CS
                        Pkinase  80 veggeladllerkgs.lseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskltsfv 158
                                    + +ge++++l++kg  + e+ea+ +++q++ +l y+ + ++iHrD+KpeN+L+ ++++lKi+DFG a     +   ++f+
  gene962|gene962|rna961|rna961  90 AGKGEFFKFLSEKGGrFGEKEASLYIRQVILALIYMKECNVIHRDIKPENLLLGSDNQLKIADFGWAVYNADKR-RMTFC 168
                                    ***********76666**************************************************98766655.9**** PP

                                    SCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHHH CS
                        Pkinase 159 gtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseeak 238
                                    gt eYlAPE++++  +++ +D+W lG++ ye+l gk+pf+++++      ++++    +k  + +++k+  +++is++a 
  gene962|gene962|rna961|rna961 169 GTMEYLAPEMVNNDIHDSGIDLWCLGILTYEFLIGKTPFESKNR------NMRE---AYK--RINSLKYSIPETISSNAS 237
                                    ****************************************3333......3344...111..24578999********** PP

                                    HHHHHHT-SSGCCSTTHHHHHTSGGG CS
                        Pkinase 239 dllkkllkkdpkkRltaeellqhpyl 264
                                    d+++kll  + ++R+  +e+l+hp++
  gene962|gene962|rna961|rna961 238 DFISKLLVLNSNDRMELTEALNHPFI 263
                                    ************************97 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   0.0   3.4e-43   6.7e-40       2     254 ..      11     256 ..      10     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 3.4e-43
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEE..STTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtl..keeateeekeelleeakimkklkhpnivkllgvctkeeplliv 79 
                                    e+g+ lG+G+fG+V+ ++ k    +k   Va+K++  ke +t e+ +++ +e++i ++lkhpni++++g   ++++++++
  gene962|gene962|rna961|rna961  11 EIGRLLGRGKFGQVWLAREK----EKGFIVALKIIpiKEIQTVETARQIRREVEIHSNLKHPNILRMYGHFHDKDHIYLI 86 
                                    67899************999....999*******977888999999********************************** PP

                                    EE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSEE CS
                    Pkinase_Tyr  80 teyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekddey 159
                                    +ey+ +G++ kfL +k   ++  k+   ++ qv  ++ y+++ +++Hrd+   N Ll ++++ ki+DfG a         
  gene962|gene962|rna961|rna961  87 LEYAGKGEFFKFLSEK-GGRFGEKEASLYIRQVILALIYMKECNVIHRDIKPENLLLGSDNQLKIADFGWAVYN----AD 161
                                    ***************9.*****************************************************9877....33 PP

                                    EETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTS.HHH.HHHHHHHTTEES-BBTTSBHHHHHH CS
                    Pkinase_Tyr 160 vkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypgl.kne.evleklkegkrlekpekcpeelyel 237
                                    +++ +    ++++apE++++    s  D W+ G+l++E +  g++p+++  +n+ e++++  ++ + + pe+++++  ++
  gene962|gene962|rna961|rna961 162 KRRMTFCGTMEYLAPEMVNNDIHDSGIDLWCLGILTYEFLI-GKTPFESKnRNMrEAYKR-INSLKYSIPETISSNASDF 239
                                    4455566789****************************998.*****8764333033444.45567889*********** PP

                                    HHHHT-SSGGGS--HHH CS
                    Pkinase_Tyr 238 mkkcweedpeeRptfse 254
                                    ++k +  + ++R +++e
  gene962|gene962|rna961|rna961 240 ISKLLVLNSNDRMELTE 256
                                    *****999999999876 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.18   3.7e+02      17      62 ..      13      58 ..       9      86 .. 0.82
   2 !   22.4   0.0   3.1e-08   6.2e-05     145     288 .]     111     251 ..      93     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.18
                    Kinase-like 17 gellkkgdrsvvfevkdqetgeplavkvfllpseaskkdlerlkeq 62
                                   g ll++g+++ v++++++e+g  +a+k+  +++    ++  +++++
  gene962|gene962|rna961|rna961 13 GRLLGRGKFGQVWLAREKEKGFIVALKIIPIKEIQTVETARQIRRE 58
                                   67999**************999999998888876666666666665 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.1e-08
                    Kinase-like 145 arlllTlqlirlaanLqakglvhgkftvdnllldekgglmlggftaLvragtkvvlseve..kgfaPpEllgsrggytrk 222
                                    a l++  q+i    ++++  ++h +++++nlll  + +l++ +f+  v   +k ++ + +    +  pE++++       
  gene962|gene962|rna961|rna961 111 ASLYI-RQVILALIYMKECNVIHRDIKPENLLLGSDNQLKIADFGWAVYNADKRRM-TFCgtMEYLAPEMVNN------- 181
                                    55566.57787888999***************************987777777773.4442345666777766....... PP

                    Kinase-like 223 nktkmthkldaWqlGlviyriwclklPltlateeakeew......kfklckkipekvkaLlkkfLqlsqedR 288
                                           ++d W lG+  y     k P++ +  ++ e++      k++  + i+ +    + k+L l+++dR
  gene962|gene962|rna961|rna961 182 --DIHDSGIDLWCLGILTYEFLIGKTPFESKNRNMREAYkrinslKYSIPETISSNASDFISKLLVLNSNDR 251
                                    ..334579*******************************99999999999999999999********99998 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.3e-07   0.00086     312     396 ..     115     189 ..     105     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.3e-07
                 Pkinase_fungal 312 lrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkgeeH 391
                                    +r++I ++  +  +++++HrDi  +N+l+      ++++  ++D+ +a+  +d+ ++    +  GT+e++a e++++  H
  gene962|gene962|rna961|rna961 115 IRQVILALIYMK-ECNVIHRDIKPENLLLG-----SDNQLKIADFGWAVYNADK-RR---MTFCGTMEYLAPEMVNNDIH 184
                                    577788887777.9****************.....789999********99973.33...4589************7669 PP

                 Pkinase_fungal 392 syrhD 396
                                        D
  gene962|gene962|rna961|rna961 185 DSGID 189
                                    76666 PP

>> Pox_ser-thr_kin  Poxvirus serine/threonine protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   9.9e-06      0.02     268     321 ..     106     150 ..      97     167 .. 0.79
   2 ?   -2.1   0.0      0.69   1.4e+03     108     135 ..     157     184 ..     148     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.9e-06
                Pox_ser-thr_kin 268 lGfaslveyikfifLqiaLLyikiyelpdcenflhvDlkPdniLifdskeklii 321
                                    +G +  + yi+ ++L  aL+y+k      c n +h D+kP+n+L+  s+++l+i
  gene962|gene962|rna961|rna961 106 FGEKEASLYIRQVIL--ALIYMKE-----C-NVIHRDIKPENLLL-GSDNQLKI 150
                                    566677789999998..8888775.....3.789********987.45566665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.69
                Pox_ser-thr_kin 108 vfepnkkyspldataefviPrfLynnlk 135
                                    v++++k+   +  t e++ P ++ n ++
  gene962|gene962|rna961|rna961 157 VYNADKRRMTFCGTMEYLAPEMVNNDIH 184
                                    6666666666667788888888877765 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.5e-05      0.07     104     159 ..     108     163 ..      78     169 .. 0.72
   2 ?   -3.3   0.0       2.9   5.8e+03      61      80 ..     217     236 ..     210     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                    HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEEETTSTT CS
                           RIO1 104 eeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQaveldhpn 159
                                    e+ea+ + ++v+    + +ke++++H D+   N+l+ +d ++ i D++ av  ++++
  gene962|gene962|rna961|rna961 108 EKEASLYIRQVIL-ALIYMKECNVIHRDIKPENLLLGSDnQLKIADFGWAVYNADKR 163
                                    5556655666666.567778****************99989*******999877665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                                    HHHHHHHTT--S--EEEEET CS
                           RIO1  61 nLkrleeagvpvPkpielkr 80 
                                    + kr+++ + ++P+ i  + 
  gene962|gene962|rna961|rna961 217 AYKRINSLKYSIPETISSNA 236
                                    56777777778888776665 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.6   5.1e+03     153     159 ..      66      72 ..      47      91 .. 0.54
   2 ?   12.1   0.0   5.4e-05      0.11     145     178 ..     128     160 ..     109     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.6
                                    SGGGEEE CS
                 Choline_kinase 153 qegNill 159
                                     + Nil 
  gene962|gene962|rna961|rna961  66 KHPNILR 72 
                                    3333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.4e-05
                                    EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEE CS
                 Choline_kinase 145 vvfcHnDlqegNillnkeekklvlIDFEYagyny 178
                                     +  H D+ ++N+ll  ++++l + DF +a yn 
  gene962|gene962|rna961|rna961 128 CNVIHRDIKPENLLL-GSDNQLKIADFGWAVYNA 160
                                    5667***********.9***************96 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00022      0.43     109     266 ..      17     168 ..       6     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00022
                  Haspin_kinase 109 seklssevyqtkekdk..evvlKviplevledvtiskelslkelkslklvkgtypglllllqdkvlkekpdfyseqqlfl 186
                                    +++ +++v+ ++ek+k   v+lK+ip+  ++ v++ + ++    +++++      +++ +l+ +       f ++++++l
  gene962|gene962|rna961|rna961  17 GRGKFGQVWLAREKEKgfIVALKIIPIKEIQTVETARQIR----REVEIHSNL--KHPNILRMYGH-----FHDKDHIYL 85 
                                    5667889999999555115789999995555555543332....445555554..55555554433.....444667777 PP

                  Haspin_kinase 187 vlllkdkGtdLeev.....klkswkqalsifwqivkiLyvaEtkfeFEHRdLhldniLvdknlnvtlidlklsRlesseg 261
                                    +l+   kG+  + +     ++ + +  l i   i++ +y+ E +    HRd++ +n L+ +  +  + d+  + +++++ 
  gene962|gene962|rna961|rna961  86 ILEYAGKGEFFKFLsekggRFGEKEASLYIRQVILALIYMKECN--VIHRDIKPENLLLGSDNQLKIADFGWAVYNADKR 163
                                    77777777654444332556667777777777788888888876..5699999999999999999999999888887777 PP

                  Haspin_kinase 262 kvlyt 266
                                     + ++
  gene962|gene962|rna961|rna961 164 RMTFC 168
                                    77665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.2   3.9e+02      28      69 ..      46      85 ..      14     105 .. 0.68
   2 ?    9.1   0.0   0.00057       1.1     168     198 ..     130     158 ..     125     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                                   E-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTE CS
                            APH 28 npparaaeeirrevallrlLakagvpvPevlagdtddeeigl 69
                                   + + ++a++irrev++  +L   ++   +++    d ++i+l
  gene962|gene962|rna961|rna961 46 IQTVETARQIRREVEIHSNLKHPNI--LRMYGHFHDKDHIYL 85
                                   3344899999999999988875544..666666666666664 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00057
                                    EE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 168 llHgDlhpgNllvdpddgrvtGviDfedagl 198
                                    ++H+D++p Nll+ +d +++  + Df+ a++
  gene962|gene962|rna961|rna961 130 VIHRDIKPENLLLGSD-NQL-KIADFGWAVY 158
                                    69************55.555.4888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1755.22
//
Query:       gene963|gene963|rna962|rna962  [L=234]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-11   44.0   0.0      3e-11   43.8   0.0    1.1  1  GPP34     Golgi phosphoprotein 3 (GPP34)


Domain annotation for each model (and alignments):
>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   1.7e-15     3e-11      13     182 ..      33     206 ..      23     220 .. 0.72

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.7e-15
                          GPP34  13 ekgrlsfandnlsyaLaGAiLiELalrgriavdkeggrvvvidsrptgdplldealklik.aserprsvktwvdlls... 88 
                                    ++ ++ f  +++s+  +++i++ELal g+i +  ++grvv  d +  +  ll ea++ i   +     +++++ +l    
  gene963|gene963|rna962|rna962  33 TRSEIKFLCNRVSLSIRACIVVELALCGAIGL--KEGRVVGKDNT-LNSSLLLEAMSKIYqTQ---LPPDELMYRLNgek 106
                                    34445444446799******************..89*99977774.55555555555454044...55667775555577 PP

                          GPP34  89 .......ksvrervakgLvdkGilrtekrr.flglfdmtthpvadtaakeavrrrvraaltsgepadprtaaLvallaaa 160
                                           ++vr rv+k L++k++ + e r+ ++     ++ + +d +++ ++ + +++ lts++  d r+ aLv++l  +
  gene963|gene963|rna962|rna962 107 rggsiymRNVRLRVYKDLEEKRVCKVESRSlIF-----NKITMNDYNIRIELINYIKEYLTSSKGVDYRAEALVVCLIFC 181
                                    99*************************999444.....577899******************999998888888877555 PP

                          GPP34 161 gllenllpdl...eareaaarakel 182
                                       + +l      ea +++a+++ +
  gene963|gene963|rna962|rna962 182 SAIDSILICMtekEAAASSAHINRI 206
                                    5555555544322333333555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1495.63
//
Query:       gene964|gene964|rna963|rna963  [L=370]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.7e-06   26.7   0.0    1.8e-05   25.3   0.0    1.8  1  RNase_T   Exonuclease


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0     1e-09   1.8e-05      33     164 ..     173     290 ..     150     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1e-09
                                    EEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHHHHHHHHTCCCETTTCEEEESSHHHHHHHHHHHHH CS
                        RNase_T  33 igetfhfyvkptelakltdecteftgitqemldeapsfkevleefkellrklallvahnaafdvgflraadkrilkkevp 112
                                    ++  +++  kp+++  + d++t+++g t+e +de   ++ + +e++ ++++++++v+h+        + +d   l ++  
  gene964|gene964|rna963|rna963 173 GKTIYDKILKPEDP--VIDYLTKYSGLTKEIIDEGVDIDLAKNEIFNFIGTNTVIVGHG--------VENDLDSLRLY-- 240
                                    455678999*****..**********************************887777766........44444444553.. PP

                                    HHHHCSEHCECHHHHHHHHHCHHHHHHHHHTTCHSSSS.TSSHHHHHHHHHHH CS
                        RNase_T 113 krnqfldtlildkatlkelartsldklaeklgleedgr.aHrAldDaeatakl 164
                                     +++++dt++l+ + l +    sl++l ++++ + +    H++  Da+++++l
  gene964|gene964|rna963|rna963 241 -HEKIIDTAHLFSSPLGRKI--SLAQLSRTYLSKDIHLeTHDSRIDALTCLEL 290
                                    .3478899999888875555..5999999988888888889999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2246.16
//
Query:       gene965|gene965|rna964|rna964  [L=980]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-14   53.3   6.9      5e-14   53.3   6.9    5.5  1  AAA_23        AAA domain
    5.4e-11   42.4  32.7    5.6e-10   39.0  32.7    2.6  1  SMC_N         RecF/RecN/SMC N terminal domain
    3.5e-07   30.5   0.2    1.9e-06   28.2   0.1    2.4  2  SMC_hinge     SMC proteins Flexible Hinge Domain
  ------ inclusion threshold ------
      0.013   15.9   3.0      0.013   15.9   3.0    6.3  5  DUF4140       N-terminal domain of unknown function (DUF4140)
      0.053   13.8   0.4        8.3    6.7   0.0    3.4  3  AAA_22        AAA domain
        0.1   12.7   0.7         18    5.6   0.2    2.9  2  DUF739        Protein of unknown function (DUF739)
       0.21   11.4   0.0       0.44   10.3   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
       0.31   10.8   4.4          2    8.2   0.1    3.0  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
       0.59    9.9  18.7       0.24   11.2   0.2    4.0  3  Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
        5.5    7.0   0.0        5.5    7.0   0.0    4.4  4  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
        8.6    6.0   8.8       0.58    9.8   0.3    3.2  3  DUF4988       Domain of unknown function


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   6.9   3.1e-17     5e-14       1     198 [.      12     261 ..      12     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.1e-17
                         AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfe 80 
                                    ++++  f+++++  i++ k+lt+++G NG+GK++++  i l+L+ +++ l+r+s   ++k+ ++   +g+ +a+v++ +e
  gene965|gene965|rna964|rna964  12 SIELIKFMCHDHLLINLRKPLTIVSGCNGSGKSAVMVGIGLVLGQRAHSLERGS---SFKDLIK---SGESSAIVRVVLE 85 
                                    689999******************************************999954...4788887...67999******** PP

                         AAA_23  81 nkdgrytrsiererelskkkgkttkkaklellei........deleqfisellgskki....il.nlilflgqerfeefe 147
                                    n +g     ++re+++ +   +++ +     ++i        + +++ ++  l    +    ++ n + fl qe+ ++f+
  gene965|gene965|rna964|rna964  86 NHKG-----FKREFFKERIIIEKRLGMRSATISImngerkiwSMRREDLELVL----EffslRFeNPLNFLSQEQSKRFL 156
                                    ****.....99999999999988877766666665446444422233333222....23335453667788888888999 PP

                         AAA_23 148 lkdkke......................................rleelekeleeledekkllekl.............. 175
                                    ++  +e                                      +lee+ek+++++e + + ++++              
  gene965|gene965|rna964|rna964 157 NMMNPEmlyelfmqgtemaeicrlndesmgnvrmmrerislvgkELEEIEKQIKDEESRLEIINNVkamenaivdledem 236
                                    988888899999999999999***************************************99999988888888887777 PP

                         AAA_23 176 ..................eqekekekeleeleeeleeilke 198
                                                                       ++ ++e
  gene965|gene965|rna964|rna964 237 awakvnerkmemdklferF----------------QSKQEE 261
                                    7755554444444444330................333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0  32.7   3.4e-13   5.6e-10       4     196 ..      12     952 ..       9     957 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.4e-13
                                    EEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   4 rleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitf 83 
                                    ++e+ +F     ++  +++ k +t++ G NGSGKs ++  i  vLG+r+ +  r ++++dli++       ++a v +++
  gene965|gene965|rna964|rna964  12 SIELIKFMCH--DHLLINLRKPLTIVSGCNGSGKSAVMVGIGLVLGQRAHSLERGSSFKDLIKS-----GESSAIVRVVL 84 
                                    5666666665..799999****************************999977799********8.....56788899988 PP

                                    EETTEE.SSSSSSCEEEEEEEETTSEEEEEETTEE....E-HHHHHHHHHCTT-STT....................... CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx....................... RF
                          SMC_N  84 dnedkk.lkiekeevsisrrvkrkgeseykingke....vtkkevsellesagiske....................... 135
                                    +n++    +  ke++ i++r+     +   +ng++    +++++++ +le   +  e                       
  gene965|gene965|rna964|rna964  85 ENHKGFkREFFKERIIIEKRLGMRSATISIMNGERkiwsMRREDLELVLEFFSLRFEnplnflsqeqskrflnmmnpeml 164
                                    77776535667888999999999999999999985333378999******9999999*********************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 165 yelfmqgtemaeicrlndesmgnvrmmrerislvgkeleeiekqikdeesrleiinnvkamenaivdledemawakvner 244
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 245 kmemdklferfqskqeemdkdhgrleelsqmikeareklvmieseeverkrsrdrrreeidgaisklrmkyreiendcse 324
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 325 lketedfksriamdfenqdgivrnllpqleerhrkvsseiealnammerlaveseecrkkareeeeilserqsrilhlkk 404
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 405 qiefyskndqnsffgpnfgsvineisrtrfnekvvgpiafeiklkeqkwgkavsivlnntlstfivmnkldkdillrifr 484
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 485 kykvdfpistlstrvpeiikykrneryktvldvleiqssfvtnyliittsieqtilieerkeayeiirsrpgfvecaytk 564
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 565 ngdrirlvggsmsdfvtrgvdrfffentheklerckaemkrlmkekaekswgkkleeirsevgkvneeiehrrrvcksle 644
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 645 vemeqekqihdaqmeiinsdeiyeeiknlkrqisllkkkqdeinqeiealeiekreikeykasgtenlrqeickskaeas 724
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 725 rierkidlcridalklkeehakytevynterrmlaedgrkeivtrsedeirrdiihikaqidmckeaedekktlavvehl 804
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gene965|gene965|rna964|rna964 805 rkmkkmkedlldeykekienalsdvrlriikrdgmrneiarnatlefsrltrirgyegilefdhegkrldvkmkvhgqte 884
                                    ******************************************************************************** PP

                                    .....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE- CS
                                    .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                          SMC_N 136 .....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivis 196
                                         +LSgGe++ ++++L++++      p+ +lDe+d  +D+ n+k+  +ll e  k+  +Q i i+
  gene965|gene965|rna964|rna964 885 agsrsMLSGGERSFASVSLILSLWPSLSCPIKILDEFDVFMDNLNRKQAIRLLLEFFKEngTQGILIT 952
                                    **********************************************9999988876655458888776 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.2   5.2e+03      25      77 ..     366     415 ..     365     429 .. 0.61
   2 !   28.2   0.1   1.2e-09   1.9e-06       2     116 ..     436     550 ..     435     551 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.2
                      SMC_hinge  25 algnrlqalvvedeetakkii...eflkkknagratflpldrikqknkadgandkn 77 
                                    al + ++ l ve+ee+ kk+    e l ++   +  +l l   k++ ++ ++nd+n
  gene965|gene965|rna964|rna964 366 ALNAMMERLAVESEECRKKAReeeEILSER---QSRILHL---KKQIEFYSKNDQN 415
                                    677778889999999999987443333333...3444444...5555555555555 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.2e-09
                      SMC_hinge   2 kgvlGrladlievd.egyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsga 80 
                                    ++v+G++a  i+++ +++ kAv+++l n l++++v ++ +   +++ ++k        +p+++++++ ++  ++++n+++
  gene965|gene965|rna964|rna964 436 EKVVGPIAFEIKLKeQKWGKAVSIVLNNTLSTFIVMNKLDKDILLRIFRKY----KVDFPISTLSTRVPEIIKYKRNERY 511
                                    469************************************************....6777********************* PP

                      SMC_hinge  81 vplidlvevdde.lrkal..ryllgdtlvvdsldeAeel 116
                                    + ++d++e +++ + + l     + +t++ +  +eA e+
  gene965|gene965|rna964|rna964 512 KTVLDVLEIQSSfVTNYLiiTTSIEQTILIEERKEAYEI 550
                                    ***********9888877667999999999998888876 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.4       0.2   3.3e+02      70      97 ..     191     218 ..     170     240 .. 0.64
   2 ?   -1.6   0.1       2.3   3.8e+03      67      89 ..     612     634 ..     590     641 .. 0.57
   3 ?   15.9   3.0   8.2e-06     0.013      37      94 ..     641     697 ..     637     701 .. 0.94
   4 ?   -0.7   0.1       1.2     2e+03      54      90 ..     696     732 ..     693     737 .. 0.77
   5 ?   -2.1   0.5       3.4   5.6e+03      59      86 ..     788     820 ..     755     830 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.2
                        DUF4140  70 lraeleeledelaaledelaaaearlaf 97 
                                    +r+++  + +el+++e++++  e+rl++
  gene965|gene965|rna964|rna964 191 MRERISLVGKELEEIEKQIKDEESRLEI 218
                                    4444444444555555555444444443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.3
                        DUF4140  67 lkalraeleeledelaaledela 89 
                                     k+  ++lee++ e  ++++e++
  gene965|gene965|rna964|rna964 612 EKSWGKKLEEIRSEVGKVNEEIE 634
                                    34455555555555555555554 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 8.2e-06
                        DUF4140  37 dSlrVegagaatildvqvervpnreaeeeelkalraeleeledelaaledelaaaear 94 
                                    +Sl Ve +++ +i+d q e    +e+ ee +k l++++  l+++++++++e++a+e +
  gene965|gene965|rna964|rna964 641 KSLEVEMEQEKQIHDAQMEIINSDEIYEE-IKNLKRQISLLKKKQDEINQEIEALEIE 697
                                    69******************999999997.************************9976 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.2
                        DUF4140  54 vervpnreaeeeelkalraeleeledelaaledelaa 90 
                                    +e+++ +e +++  + lr+e+ + ++e +++e++++ 
  gene965|gene965|rna964|rna964 696 IEKREIKEYKASGTENLRQEICKSKAEASRIERKIDL 732
                                    5566666666666899999999999999999999876 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 3.4
                        DUF4140  59 nreaeee....e.lkalraeleeledelaaled 86 
                                     +eae+e    + +++lr+  +  ed l+++++
  gene965|gene965|rna964|rna964 788 CKEAEDEkktlAvVEHLRKMKKMKEDLLDEYKE 820
                                    333333333443344555555555555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0051       8.3       5      32 ..      30      57 ..      27      97 .. 0.73
   2 ?   -3.2   0.0       5.6   9.1e+03      52      84 ..     341     373 ..     327     385 .. 0.66
   3 ?    3.1   0.0     0.064     1e+02      89     137 .]     911     960 ..     873     960 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0051
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldee 32
                                   + +++v G+ G+GK+ ++  +   l ++
  gene965|gene965|rna964|rna964 30 KPLTIVSGCNGSGKSAVMVGIGLVLGQR 57
                                   56899***********987666655555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.6
                         AAA_22  52 sskdllrellralglelkaerlsseellealeq 84 
                                    +++ + r+ll +l++++ +   + e+l +++e+
  gene965|gene965|rna964|rna964 341 NQDGIVRNLLPQLEERHRKVSSEIEALNAMMER 373
                                    667788889999998888833333333344433 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.064
                         AAA_22  89 ravielliiDEaqhlr....seealeeLrsllnlsrkgvqliLvGtpelrkll 137
                                     +  ++ i+DE++ ++    +++a++ L ++++  + g+q iL+   ++++l+
  gene965|gene965|rna964|rna964 911 LSC-PIKILDEFDVFMdnlnRKQAIRLLLEFFK--ENGTQGILITPLGVEDLF 960
                                    555.67799****97656655999999999999..*******99877887765 PP

>> DUF739  Protein of unknown function (DUF739)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.028        46      32      66 ..     494     529 ..     488     531 .. 0.89
   2 ?    5.6   0.2     0.011        18      44      65 ..     683     704 ..     672     707 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.028
                         DUF739  32 slslkLndkvsWkddeilkav.dlLdldrekiakyf 66 
                                    +ls ++ + + +k +e +k v d+L+++ + +++y+
  gene965|gene965|rna964|rna964 494 TLSTRVPEIIKYKRNERYKTVlDVLEIQSSFVTNYL 529
                                    799999999*******9997549********99996 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                         DUF739  44 kddeilkavdlLdldrekiaky 65 
                                    k+dei + ++ L++++++i++y
  gene965|gene965|rna964|rna964 683 KQDEINQEIEALEIEKREIKEY 704
                                    99*******************9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027      0.44      19      41 ..      26      49 ..      11      59 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                         AAA_29 19 idlkg.atlltGpsGsGKSTllDA 41
                                   i+l+   t+++G +GsGKS+++  
  gene965|gene965|rna964|rna964 26 INLRKpLTIVSGCNGSGKSAVMVG 49
                                   4455668************99855 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.044        71       2      23 ..      33      54 ..      32     106 .. 0.80
   2 ?   -2.8   0.1       2.7   4.3e+03     134     142 ..     404     412 ..     331     493 .. 0.63
   3 ?    8.2   0.1    0.0012         2     233     286 ..     887     945 ..     791     953 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.044
                         AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                   +++ G NgsGKS ++  + l+ 
  gene965|gene965|rna964|rna964 33 TIVSGCNGSGKSAVMVGIGLVL 54
                                   777799********98887774 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.7
                         AAA_21 134 epndlqfgk 142
                                    ++++ +++ 
  gene965|gene965|rna964|rna964 404 KQIEFYSKN 412
                                    222222222 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0012
                         AAA_21 233 parelSdGtkrll..alltallralkkgsllliDEpEngLHP....kllrrllellkels 286
                                    + + lS G ++++   l+++l+  l+  ++ ++DE++ +++     +++r lle++ke+ 
  gene965|gene965|rna964|rna964 887 SRSMLSGGERSFAsvSLILSLWPSLSC-PIKILDEFDVFMDNlnrkQAIRLLLEFFKENG 945
                                    33445*******999*******99999.**************999899999999997763 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   1.0      0.28   4.6e+02     104     136 ..     245     277 ..     198     284 .. 0.56
   2 ?   11.2   0.2   0.00015      0.24     110     172 ..     349     411 ..     340     416 .. 0.90
   3 ?    5.6   4.9     0.008        13      88     175 ..     600     692 ..     589     694 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.28
                   Bacillus_HBL 104 lellekLqeeiqqnqkevkqlikeLkklklkla 136
                                    +  + kL e  q++q+e++++ + L++l + ++
  gene965|gene965|rna964|rna964 245 KMEMDKLFERFQSKQEEMDKDHGRLEELSQMIK 277
                                    334455555555555555555555555554443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                   Bacillus_HBL 110 LqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqg 172
                                    L  ++ +   +v + i++L+++ ++la +s++  +++ e ++il+  +  i +l+++ie + +
  gene965|gene965|rna964|rna964 349 LLPQLEERHRKVSSEIEALNAMMERLAVESEECRKKAREEEEILSERQSRILHLKKQIEFYSK 411
                                    55577788999***********************************************98766 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.008
                   Bacillus_HBL  88 yktlveavdkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv.....deltsilagdsgvisq 162
                                    + +++ + ++k+ +++ ++le++++e+ + ++e+++     k+l+++++++++  ++++     de+ + +++ + +is 
  gene965|gene965|rna964|rna964 600 KAEMKRLMKEKAEKSWGKKLEEIRSEVGKVNEEIEHRRRVCKSLEVEMEQEKQIHDAQMeiinsDEIYEEIKNLKRQISL 679
                                    567899999******************************************99999988777778888899999999999 PP

                   Bacillus_HBL 163 lqneiedlqgkik 175
                                    l+++  +++++i+
  gene965|gene965|rna964|rna964 680 LKKKQDEINQEIE 692
                                    9999999999886 PP

>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0034       5.5      31     102 ..      29      99 ..      13     126 .. 0.86
   2 ?   -3.8   3.5       7.5   1.2e+04      88     110 ..     246     268 ..     192     317 .. 0.61
   3 ?   -3.8   0.3       7.7   1.3e+04      90     101 ..     378     389 ..     353     412 .. 0.49
   4 ?   -3.6   0.0       6.8   1.1e+04      72      87 ..     447     462 ..     443     477 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0034
                                    SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEETTT-EEEEEEE-CCTHHHHHHHCCT-- CS
                           FmdE  31 deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkkrktgkavrlklkeelpelreklakgka 102
                                    +++l +++ ++++   A++v  g  lG++++ ++   +++ ++k+ ++   vr++l  +++ ++++++k++ 
  gene965|gene965|rna964|rna964  29 RKPLTIVSGCNGSGKSAVMVGIGLVLGQRAHSLERGSSFKDLIKSGESSAIVRVVLE-NHKGFKREFFKERI 99 
                                    6899******************************99999999988899999999999.88888888888765 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.5
                                    CCTHHHHHHHCCT--GGGS-HHH CS
                           FmdE  88 eelpelreklakgkakeekeeee 110
                                     e+++l+e++ +++++ +k++ +
  gene965|gene965|rna964|rna964 246 MEMDKLFERFQSKQEEMDKDHGR 268
                                    34444444444444433333333 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 7.7
                                    THHHHHHHCCT- CS
                           FmdE  90 lpelreklakgk 101
                                     +e r+k  +++
  gene965|gene965|rna964|rna964 378 SEECRKKAREEE 389
                                    222222222222 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 6.8
                                    EEEETTT-EEEEEEE- CS
                           FmdE  72 tfkkrktgkavrlklk 87 
                                     +k++k gkav ++l+
  gene965|gene965|rna964|rna964 447 KLKEQKWGKAVSIVLN 462
                                    5677788999999998 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.6         1   1.7e+03       3      42 ..     193     232 ..     187     240 .. 0.61
   2 ?   -0.7   0.1       0.6   9.7e+02      14      40 ..     352     377 ..     346     405 .. 0.78
   3 ?    9.8   0.3   0.00036      0.58       3      30 ..     668     695 ..     666     767 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                        DUF4988   3 ddvndlkdrvaaleeqvkelndniealkklleegkvitev 42 
                                    ++++ + ++ + +e+q+k+ ++ +e ++++   +++i+++
  gene965|gene965|rna964|rna964 193 ERISLVGKELEEIEKQIKDEESRLEIINNVKAMENAIVDL 232
                                    4555555666666666666666666666666555555554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.6
                        DUF4988  14 aleeqvkelndniealkklleegkvit 40 
                                     lee+ +++ ++ieal++++ e+ ++ 
  gene965|gene965|rna964|rna964 352 QLEERHRKVSSEIEALNAMM-ERLAVE 377
                                    58888899999999999988.555554 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00036
                        DUF4988   3 ddvndlkdrvaaleeqvkelndniealk 30 
                                    +++ +lk +++ l+++ +e+n++ieal+
  gene965|gene965|rna964|rna964 668 EEIKNLKRQISLLKKKQDEINQEIEALE 695
                                    79************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (980 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2468  (0.137654); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        47  (0.00262145); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 1.46u 0.37s 00:00:01.83 Elapsed: 00:00:00.57
# Mc/sec: 5180.51
//
Query:       gene966|gene966|rna965|rna965  [L=272]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
          2    8.2  13.3        3.2    7.5  13.3    1.2  1  SpoIIIAH  SpoIIIAH-like protein


Domain annotation for each model (and alignments):
>> SpoIIIAH  SpoIIIAH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  13.3   0.00018       3.2      17     103 ..     170     255 ..     167     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00018
                                    XXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXX CS
                       SpoIIIAH  17 gYlnftedsgk.kaaetaeteqeesekaeigddkekdessaasaeaesssetesesseksdiassdedeade.ltsetas 94 
                                    gY  +++++++ ka+et+++++++s+k++ g+    ++ s++s++++ s+ te+ ++e++  +++d++++ + +ts  ++
  gene966|gene966|rna965|rna965 170 GYNKMSKQKNEtKATETNSASSVDSTKSNSGK---GEKGSTTSDDEKVSNGTEGGKTEDGSLENQDQNDQGNnITSDGET 246
                                    78778887766788899999999999999999...455555555555566666666666666655555555467888787 PP

                                    XXXXX--HH CS
                       SpoIIIAH  95 aaasasdyf 103
                                    +++++s +f
  gene966|gene966|rna965|rna965 247 KTSDKSGFF 255
                                    788888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1046  (0.0583412); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1630.18
//
Query:       gene967|gene967|rna966|rna966  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-33  114.4   1.3      1e-32  113.6   1.3    1.4  1  UCH             Ubiquitin carboxyl-terminal hydrolase
    2.3e-05   24.1   3.2    0.00044   19.9   3.2    2.1  1  UCH_1           Ubiquitin carboxyl-terminal hydrolase
  ------ inclusion threshold ------
      0.089   12.7   0.1        3.1    7.7   0.0    2.6  2  ADD_ATRX        Cysteine Rich ADD domain
       0.11   12.2   0.8        3.7    7.2   0.0    2.4  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.11   12.4   0.3       0.41   10.6   0.0    2.0  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.44   10.1   3.1        1.7    8.3   0.3    2.3  2  PHD_2           PHD-finger
        6.4    6.7   7.8        4.6    7.2   0.2    2.4  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> UCH  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.6   1.3     4e-36     1e-32       2     257 .]      14     294 ..      13     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 4e-36
                                    EES-SSSTHHHHHHHHHHHTSHHHHHHHHTCHHCCSSTCCCCC-.TT.TTS.TTHHHHHHHHHHHHHHSH-CCEE--HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH   2 GlsNlGntCymnsvlQcLfsipelrdyllsleevkkesrnkkelnesnplgkkgelakalkdlfkellkskskavsPkkl 81 
                                    Gl+N GntC+ ns++Qc++si el  + +++                  l+k++ +++alk++++   + + +++ P++l
  gene967|gene967|rna966|rna966  14 GLKNKGNTCFFNSAMQCILSISELNAFYRDT------L-----------LPKEKVISNALKQFISGYEN-SPQSYDPRNL 75 
                                    9***********************9988882......1...........22334489999999988875.799******* PP

                                    HHHHHHHSGGGTSSSTCEHHHHHHHHHHHHHHHHCCHCCCHHH...HHHCCCTTSHHHHHH-EEEEE............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx............. RF
                            UCH  82 kktlsklaksfsgykqqDaqEflaflLdqlhedlnrevaeekw...kkhlkrndslitdlfegqlks............. 145
                                    +++ls+  k f+ ++qqD++Efl + +d l  +++ + +++ +   + ++ r ++li + +  + ++             
  gene967|gene967|rna966|rna966  76 ISVLSTKMKLFN-GMQQDSHEFLIQFIDLLYTEFDWN-KDMFTsmdEFEEARRKNLIAKTLLSMDRQvlicerckhsstt 153
                                    ***********6.89*******************994.444444666666777777777776666668************ PP

                                    ...............................................EEEEEEB-SEEEEEEESEEETEEEEE--SEEB- CS
                                    ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 146 ...............................................klklkrlPeiLiihlkRfsynssksKlntkvef 178
                                                                                   +++    Pe+L++h++Rf    s  K   +v++
  gene967|gene967|rna966|rna966 154 ivinstiliepytsvqegidryyeevilekengwkcdrcgkgmgaikRMENLIHPEVLTVHISRFHPRGS--KDTASVDV 231
                                    ********************************************9987777778*************877..99999999 PP

                                    -SEEE-GGGBSS-BTTS-TCS-BEEEEEEEEEESCTTSEEEEEEEECTTTTEEEEEETTEEEEE-HHCCCTTCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UCH 179 peeldlssylaeekkkkteekkkYeLiavvvHsGslssGHYvayiknekngkWykydDetvkevkeeeevlssayiLfY 257
                                      +l  ++             +kY+L++vv+H+G+ls+GHY+a +k  ++g W  y+De+v++  ++    s++y+ fY
  gene967|gene967|rna966|rna966 232 NTTLFFNN-------------RKYNLFGVVCHTGTLSGGHYFAEAK--RSGTWNVYNDEQVTKGFQT-YSGSHPYLAFY 294
                                    98888873.............24********************999..89************99865.45559999998 PP

>> UCH_1  Ubiquitin carboxyl-terminal hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   3.2   1.7e-07   0.00044       2     319 ..      14     276 ..      13     277 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.7e-07
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1   2 GLEnhivnsYlNslLQvlyfipplrnlalshlakeckkehcLlcElgflfdmldkakglncqasnFlralssipeasalg 81 
                                    GL n+ ++++ Ns +Q+   i +l +++   l    +ke+ ++  l   ++  +++  ++    n+   ls+    + ++
  gene967|gene967|rna966|rna966  14 GLKNKGNTCFFNSAMQCILSISELNAFYRDTL---LPKEKVISNALKQFISGYENSP-QSYDPRNLISVLSTKM--KLFN 87 
                                    89999999999999999999999999999999...7777666666666666666655.7889999999999655..5555 PP

                                    xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1  82 lileeeeetekssaislssliqs...fnrflldqlekelketkknsseeesaieqllgtkaettirclkCgseksrksst 158
                                     ++++++e      i++  l  +   +n+ ++  + + ++        +++ i++ l     +++ c +C++ ++   + 
  gene967|gene967|rna966|rna966  88 GMQQDSHE----FLIQFIDLLYTefdWNKDMFTSMDEFEEAR------RKNLIAKTLLSMDRQVLICERCKHSSTTIVIN 157
                                    55444333....344444444434559999999987766664......45788888756666677777777766544443 PP

                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 159 lvldlkyP.kpsnekkeakvtfasilksslerekttrawCekCkryqpteqrktvknlPpvLalnakleeeeelelwktk 237
                                     ++ l+ P +      + +  ++ + ++ + + k++   C++C +     +r      P+vL+++ ++++ +       k
  gene967|gene967|rna966|rna966 158 STI-LIEPyT------SVQEGIDRYYEEVILE-KENGWKCDRCGKGMGAIKRMENLIHPEVLTVHISRFHPR-----GSK 224
                                    333.344422......2344567777766665.666677999966555555555556699999999987665.....112 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          UCH_1 238 nwlpleiklsldedknleeklkeerekakaekeikvYeLqsvvvhigdskesghLvslvkvaekelerdppesqWylFND 317
                                    +  + ++++                   +   + ++Y+L++vv+h g + + gh+ + +k            + W + ND
  gene967|gene967|rna966|rna966 225 DTASVDVNT-------------------TLFFNNRKYNLFGVVCHTG-TLSGGHYFAEAKR----------SGTWNVYND 274
                                    222222222...................33345679***********.666*****99993..........356888887 PP

                                    xx RF
                          UCH_1 318 fl 319
                                     +
  gene967|gene967|rna966|rna966 275 EQ 276
                                    65 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.079     2e+02      36      44 ..     140     148 ..     124     153 .. 0.89
   2 ?    7.7   0.0    0.0012       3.1      11      39 ..     186     215 ..     180     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.079
                       ADD_ATRX  36 kVLiCksCf 44 
                                    +VLiC  C 
  gene967|gene967|rna966|rna966 140 QVLICERCK 148
                                    69******5 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                       ADD_ATRX  11 ivsCtaCgqqvnhfqkdslykHP.vLkVLi 39 
                                      +C  Cg+ +  ++++   +HP vL V i
  gene967|gene967|rna966|rna966 186 GWKCDRCGKGMGAIKRMENLIHPeVLTVHI 215
                                    469********************7788866 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.027        70       4      11 ..     143     150 ..     141     153 .. 0.86
   2 ?    7.2   0.0    0.0014       3.7       2      12 ..     186     196 ..     185     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                         zf_UBZ   4 lCerCgke 11 
                                    +CerC+++
  gene967|gene967|rna966|rna966 143 ICERCKHS 150
                                    7****986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0014
                         zf_UBZ   2 tylCerCgkei 12 
                                     + C+rCgk +
  gene967|gene967|rna966|rna966 186 GWKCDRCGKGM 196
                                    689*****976 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.41      16      27 ..     138     149 ..     128     150 .. 0.89
   2 ?   -1.1   0.1      0.77     2e+03      20      26 ..     187     193 ..     178     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                 PhnA_Zn_Ribbon  16 dgallvCpeCah 27 
                                    d+++l+C+ C+h
  gene967|gene967|rna966|rna966 138 DRQVLICERCKH 149
                                    99*********9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.77
                 PhnA_Zn_Ribbon  20 lvCpeCa 26 
                                    + C+ C+
  gene967|gene967|rna966|rna966 187 WKCDRCG 193
                                    6688887 PP

>> PHD_2  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.062   1.6e+02       4      35 ..     141     147 ..     136     149 .. 0.60
   2 ?    8.3   0.3   0.00065       1.7      25      35 ..     182     192 ..     176     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.062
                          PHD_2   4 llsCdkCsvaVHasCYGvskesdgeeWlCrrC 35 
                                    +l                         +C+rC
  gene967|gene967|rna966|rna966 141 VL-------------------------ICERC 147
                                    44.........................55555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00065
                          PHD_2  25 sdgeeWlCrrC 35 
                                    +++++W+C+rC
  gene967|gene967|rna966|rna966 182 EKENGWKCDRC 192
                                    45568****** PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2    0.0018       4.6       4      17 ..     144     157 ..     143     159 .. 0.91
   2 ?    2.0   2.5     0.074   1.9e+02       3       8 ..     188     193 ..     186     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                                    -TTT--BBEEEECT CS
                   zf-FPG_IleRS   4 CpRCwryiervgqa 17 
                                    C+RC++  ++++++
  gene967|gene967|rna966|rna966 144 CERCKHSSTTIVIN 157
                                    ************96 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.074
                                    B-TTT- CS
                   zf-FPG_IleRS   3 pCpRCw 8  
                                    +C+RC+
  gene967|gene967|rna966|rna966 188 KCDRCG 193
                                    9****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.52
# Mc/sec: 1732.95
//
Query:       gene968|gene968|rna967|rna967  [L=267]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.85    8.5   9.7        0.6    9.0   8.3    1.4  1  DUF3435      Protein of unknown function (DUF3435)


Domain annotation for each model (and alignments):
>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   8.3   3.3e-05       0.6     226     353 ..      22     149 ..      14     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 3.3e-05
                        DUF3435 226 assrtFlkhYlsqkvdkdvqavvlglppqealir..aassmsrsiDprrPkeLtdeqkasveedpelqelkrkreelkke 303
                                      ++t+lk Y + + ++d +++v +   +e+l +  + ++ sr  +++ P+++   + as+ ++ ++ e+k++  + ++ 
  gene968|gene968|rna967|rna967  22 VMKSTYLKTYETLQSEDDSNSLVDNDGMDEMLTKdsFRGMKSRGSERKMPRKI--RKGASMSSEVKIDERKKQTTKSNSM 99 
                                    5679*****************************97788999************..8899999**********99999995 PP

                        DUF3435 304 leakygqvakakgtelyeelekakrelrnerqrlrrelkkkireeFkeeq 353
                                     ++     ++ ++t ++ e++  ++e r++r r  ++  +  r  F+e+ 
  gene968|gene968|rna967|rna967 100 TNSDDSWSDSYEDTFEKTEFRSSSKEKRKNRERYDKKESRSSRRVFSEDS 149
                                    55555555666667799999999999999999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2044  (0.114005); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 1927.55
//
Query:       gene969|gene969|rna968|rna968  [L=297]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   13.5   0.0       0.13   12.3   0.0    1.5  1  HHH_2     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.5e-06      0.13       8      29 ..     229     250 ..     225     254 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-06
                          HHH_2   8 IrhVGektAklLakrFksldaL 29 
                                    I+ +G+ +A+ L  +Fks+ +L
  gene969|gene969|rna968|rna968 229 IPGIGKDAARSLSLHFKSISRL 250
                                    99*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1876.99
//
Query:       gene970|gene970|rna969|rna969  [L=487]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-18   66.6   0.0    8.1e-18   64.5   0.0    2.1  1  BRCA-2_OB1  BRCA2, oligonucleotide/oligosaccharide-binding, d
    8.2e-06   25.4   0.1    3.3e-05   23.4   0.1    2.2  1  BRCA2       BRCA2 repeat


Domain annotation for each model (and alignments):
>> BRCA-2_OB1  BRCA2, oligonucleotide/oligosaccharide-binding, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.0   9.1e-22   8.1e-18       1     122 [.     253     355 ..     253     356 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 9.1e-22
                                    -HHHHHHTTSSTT--SEEEEEEE----------------------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEE CS
                     BRCA-2_OB1   1 salkkilerDdsaskpmvLcVsaiekkesekeekekekeksekaeleltDGWYsikavlDaalsrllkrgkikvGqKlvv 80 
                                    s+l++i+e+D+++ + m+L+V +i k+                 ++e+ DG+Ys+ a  D++l+r +++++i+vG Kl +
  gene970|gene970|rna969|rna969 253 SILRRIVEGDEVPWRYMILLVIGIDKE-----------------RIEVFDGYYSLYALYDEPLRRKIEKKEIRVGLKLKI 315
                                    89**********************664.................69********************************** PP

                                    S--EEES--S---GGG--SS-EEE--TTTEEE--SSS-SEE- CS
                     BRCA-2_OB1  81 agaelvgseeavspleaseklllkisaNstrrarwnakLGfq 122
                                    +gael g  e +s ++ +e+  l+++ N+++ ++   +LG++
  gene970|gene970|rna969|rna969 316 FGAEL-GGGEFMSIFD-PESAFLRLHHNGVQVVHSRRRLGYR 355
                                    *****.9999999999.***********************86 PP

>> BRCA2  BRCA2 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   3.7e-09   3.3e-05       4      25 ..     141     162 ..     138     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.7e-09
                          BRCA2   4 fsgFkTAsGKkIrVSkesLqKA 25 
                                    fsgF T+s KkI+V+kes + A
  gene970|gene970|rna969|rna969 141 FSGFTTGSRKKIQVRKESMDSA 162
                                    9*****************6655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2933.29
//
Query:       gene97|gene97|rna97|rna97  [L=195]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0044   16.8   0.2     0.0068   16.1   0.2    1.3  1  Cyclin_N  Cyclin, N-terminal domain


Domain annotation for each model (and alignments):
>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   3.8e-07    0.0068      66     126 ..      43     108 ..      13     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.8e-07
                                S---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHT......TTSS-HHHHHHHHHHHHHHTTT-- CS
                   Cyclin_N  66 ksvpkdklqlvgatcLllAaKveeisppkledlvyit......deafteeeilemErliLetLnfdl 126
                                k ++k+  + v++++++lA+K++e+   kl+ +  ++      +++  +e i+ +E +++e ++f+ 
  gene97|gene97|rna97|rna97  43 KLFKKESYNIVALVSVYLASKINET-LIKLDTILEAMakvthmGSVPPRERIIAIECKVIELIEFQF 108
                                34556699**************999.56666665555455555669999**********99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1274.76
//
Query:       gene971|gene971|rna970|rna970  [L=728]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-53  179.4  22.8    1.4e-52  178.7  22.8    1.4  1  RSN1_7TM      Calcium-dependent channel, 7TM region, putative
    1.2e-16   61.4   0.3    1.1e-07   32.2   0.0    2.6  2  PHM7_cyt      Cytosolic domain of 10TM putative phosphate tra
    0.00057   19.7   1.7      0.033   14.0   0.0    2.5  2  DUF648        Family of unknown function (DUF648)
  ------ inclusion threshold ------
      0.019   14.7   1.2      0.037   13.8   1.2    1.4  1  DUF4303       Domain of unknown function (DUF4303)
      0.037   13.9   0.3       0.16   11.8   0.0    2.2  3  Lig_chan      Ligand-gated ion channel
       0.24   11.3   5.7        0.4   10.6   5.7    1.3  1  Phage_Mu_Gam  Bacteriophage Mu Gam like protein
          5    5.8  18.4       0.13   11.1  10.6    2.0  2  Anoctamin     Calcium-activated chloride channel


Domain annotation for each model (and alignments):
>> RSN1_7TM  Calcium-dependent channel, 7TM region, putative phosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.7  22.8   5.7e-56   1.4e-52       3     271 ..     319     590 ..     317     593 .. 0.92

  Alignments for each domain:
  == domain 1  score: 178.7 bits;  conditional E-value: 5.7e-56
                       RSN1_7TM   3 livtlllvlliifwiipvafv.gllsnletltkvlpflkkilelskkllsvvtgllPtlllslllallpiilrllsklqG 81 
                                    +++ ++++++i++++  va + +ll++ e +++  + ++ +l++++++++ ++g+l +l+++ +++++p+i++ l +++G
  gene971|gene971|rna970|rna970 319 VFGAVFFIVFIVLFSSIVANIvTLLVSSEMFRES-KLISSFLDKHETITDSLRGILFPLIYNSMMLFVPTIITALVNMEG 397
                                    6778888888888888877664888888888885.6666666************************************** PP

                       RSN1_7TM  82 alsrselelsvvskyfaFlvvnvFlvftlagtalslleeiidnptsipkllaeslp...kasnFfityillqglagaale 158
                                    ++s s+ ++++++k++ Fl++n F+ + +a+++++l+++++ +++ i++ +  +     ++s Ff + i++++l+g+al+
  gene971|gene971|rna970|rna970 398 IYSYSNFQQKLMEKLCNFLFFNGFVSVFFATSFYRLFSDVLFRNERIYNVIRAFSNeslESSVFFANTIIQRSLVGTALT 477
                                    ******************************************999888888777744459******************** PP

                       RSN1_7TM 159 Llqlvklilflikrkfls.ktprdlaerytkppsfdygteypkvllifvialiYsviaPlilpfaliyfllgylvykyql 237
                                    Ll+ ++l++++i   f++ kt r++ ++  +pp fd+gt +p +l++f++ ++Y vi+P il++++++++++yl++k ++
  gene971|gene971|rna970|rna970 478 LLKPAPLLINYIIFPFTGrKTRRERLDAEFSPP-FDFGTIFPSCLTVFSMSIVYTVICPPILLLGAFFYFCNYLAFKSEF 556
                                    ******************9********996555.********************************************** PP

                       RSN1_7TM 238 lyvydtkyesgGklwpralnrllvglvlfqllli 271
                                    ly  +++yesgG +w  a+++++++l++fq+  +
  gene971|gene971|rna970|rna970 557 LYSSRNEYESGGGYWDSACQNIMFSLIFFQVATF 590
                                    ******************************9877 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   4.4e-11   1.1e-07       2     121 ..      53     209 ..      52     226 .. 0.83
   2 !   26.6   0.0   2.3e-09   5.8e-06     121     176 .]     262     306 ..     255     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4.4e-11
                       PHM7_cyt   2 rTvlvtgiPkelrseeklkeffeelypgkvvesvqivrdvkkldklveerekavrkleaals.kykkngkklpkkr.... 76 
                                    rT++++ +P+ ++++ +l+ef+++l  g+  +++ +v+d+++l++l+ e++ ++ ++e+ ++ k  + ++ ++k++    
  gene971|gene971|rna970|rna970  53 RTLILSRLPSYVSNDADLSEFINSLGVGEI-DDCVLVYDTNTLQSLYSEKDSYIYNIEKEINeKFARMNEWSEKNQeeck 131
                                    9*************************9985.*************************999876155555554455558999 PP

                       PHM7_cyt  77 .......................................pthklgflglkligkkvdaidyyrekleeldeeieeerekv 117
                                                                           +      ++ kl ++ v  + +y ekl++++ +i++e+e +
  gene971|gene971|rna970|rna970 132 ksisgfkedilktveeaeiegvfdnsqkrqlivlflngaN-----QFENKL-KEDVPKVSFYLEKLNNVNGRISKEKEVI 205
                                    *************************987777777543221.....223343.6889*********************998 PP

                       PHM7_cyt 118 kkkp 121
                                    ++++
  gene971|gene971|rna970|rna970 206 RNEE 209
                                    7765 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 2.3e-09
                       PHM7_cyt 121 plgaaFvtfesersaaavakqakcaaqiqqssnptlkpkkwtvelAPePrDviWeN 176
                                    ++  +Fvtf+++rsa+ v k    ++qi +         ++t+e AP+P+DviWeN
  gene971|gene971|rna970|rna970 262 KTKRGFVTFKDQRSANIV-K----QSQIGSRI------FSVTAEDAPAPNDVIWEN 306
                                    56679**********988.3....34444333......369**************9 PP

>> DUF648  Family of unknown function (DUF648)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.013        32      12      30 ..     402     420 ..     398     421 .. 0.92
   2 !   14.0   0.0   1.3e-05     0.033      65     108 ..     601     641 ..     600     702 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.013
                         DUF648  12 tsfserllakLdsYfflGG 30 
                                     +f+++l++kL +++f+ G
  gene971|gene971|rna970|rna970 402 SNFQQKLMEKLCNFLFFNG 420
                                    58***************98 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.3e-05
                         DUF648  65 LSylliPiViialllrylLHskfhnkvlkiklLdsaepeavrvd 108
                                    LS ll+Pi++i ++ r  L + f +       L+++e+e++  d
  gene971|gene971|rna970|rna970 601 LSMLLFPIILITFIFRSSLRKMFYKSCHFY-PLNIKEEEYL--D 641
                                    99**********************997766.7899999999..3 PP

>> DUF4303  Domain of unknown function (DUF4303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.2   1.4e-05     0.037      78     143 ..     110     175 ..      89     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                        DUF4303  78 edvnkllaardnefeleekefeafrdklleamvkAlkeldkeglfgkgqdrefivifvvvepedea 143
                                    +++n+++a+ ++ +e++++e ++    + e ++k ++e++ eg+f++ q+r+ iv+f     ++e+
  gene971|gene971|rna970|rna970 110 KEINEKFARMNEWSEKNQEECKKSISGFKEDILKTVEEAEIEGVFDNSQKRQLIVLFLNGANQFEN 175
                                    5899999999999999999**************************************998887765 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   3.4e+03     116     125 ..      54     135 ..       6     154 .. 0.47
   2 ?   11.8   0.0   6.3e-05      0.16      73     113 ..     319     359 ..     306     576 .. 0.83
   3 ?   -1.5   0.1      0.77     2e+03      50      88 ..     576     614 ..     525     624 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                                    S........................................................................SSXSXXX CS
                                    x........................................................................xxxxxxx RF
                       Lig_chan 116 t........................................................................kaeCsse 123
                                    t                                                                        ++eC+++
  gene971|gene971|rna970|rna970  54 TlilsrlpsyvsndadlsefinslgvgeiddcvlvydtntlqslysekdsyiyniekeinekfarmnewseknQEECKKS 133
                                    14444444444444444444444444444444444444444444444444444444444444444444444445566665 PP

                                    XX CS
                                    xx RF
                       Lig_chan 124 ks 125
                                     s
  gene971|gene971|rna970|rna970 134 IS 135
                                    55 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.3e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXS-SSCCHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lig_chan  73 ivvavWwffvlillssYtAnLaafltvermqtpiksledLa 113
                                    +  av++++ ++l+ss +An++ +l++++m  + k ++++ 
  gene971|gene971|rna970|rna970 319 VFGAVFFIVFIVLFSSIVANIVTLLVSSEMFRESKLISSFL 359
                                    67899*************************99877777754 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.77
                                    HHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lig_chan  50 lwfslgalvqqGcdesprsvsgRivvavWwffvlillss 88 
                                     +++++ +++q +  +  s   R+  ++ +f +++++  
  gene971|gene971|rna970|rna970 576 QNIMFSLIFFQVATFAKMSSDKRFYLSMLLFPIILITFI 614
                                    456677777777777777777777766666666555555 PP

>> Phage_Mu_Gam  Bacteriophage Mu Gam like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.7   0.00016       0.4      11     105 ..      98     192 ..      92     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCTHHH..H-..----.-EE-SS-EE------ CS
                   Phage_Mu_Gam  11 iaelkreleeieaeaneeiaaikekleaeleplkkeieylesllkqYaeankde..LfkdgktK.slklpfGkvgfrkst 87 
                                    + e +  +  ie+e+ne+ a+++e+ e++ e+ kk+i+ +++ + + +e+ + e  +++ +k++  + + +G  +f ++ 
  gene971|gene971|rna970|rna970  98 YSEKDSYIYNIEKEINEKFARMNEWSEKNQEECKKSISGFKEDILKTVEEAEIEgvFDNSQKRQlIVLFLNGANQFENKL 177
                                    5677788899**********************************999998765443888888888899999999999888 PP

                                    ---.--TT--HHHHHHHH CS
                   Phage_Mu_Gam  88 pkvkkrdkekeelLealk 105
                                    ++ +++  +    Le+l+
  gene971|gene971|rna970|rna970 178 KEDVPKVSFY---LEKLN 192
                                    8777777664...55554 PP

>> Anoctamin  Calcium-activated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  10.6     5e-05      0.13     128     228 ..     323     436 ..     293     504 .. 0.70
   2 ?   -1.4   0.8       0.3   7.7e+02     151     151 ..     591     591 ..     493     656 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5e-05
                      Anoctamin 128 vllliclavvgvlilrcla............l.qelvssvkellsflptvlnlvlililnevykklaiwltdlEnhrtqs 194
                                    v+++++++++  ++  ++             l ++++ + +++++ l  +l  ++   +  ++  + + l+++E     s
  gene971|gene971|rna970|rna970 323 VFFIVFIVLFSSIVANIVTllvssemfreskLiSSFLDKHETITDSLRGILFPLIYNSMMLFVPTIITALVNMEGIYSYS 402
                                    22333333333333322222222222223333244444444466688888888888888889999*************** PP

                      Anoctamin 195 eyekslilKvflfqfvnsylslfyiaFvkgkflk 228
                                    +++++l+ K+  f f+n ++s+f+   +++ f +
  gene971|gene971|rna970|rna970 403 NFQQKLMEKLCNFLFFNGFVSVFFATSFYRLFSD 436
                                    **********************998888775554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.3
                      Anoctamin 151 v 151
                                    +
  gene971|gene971|rna970|rna970 591 A 591
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 4638.59
//
Query:       gene972|gene972|rna971|rna971  [L=166]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-22   79.3   4.7    3.1e-22   79.0   4.7    1.1  1  RSN1_TM      Late exocytosis, associated with Golgi transport
  ------ inclusion threshold ------
        4.3    7.5   9.7        1.5    9.0   0.3    3.1  4  Insulin_TMD  Insulin receptor trans-membrane segment


Domain annotation for each model (and alignments):
>> RSN1_TM  Late exocytosis, associated with Golgi transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   4.7   3.4e-26   3.1e-22       2     110 ..      60     165 ..      59     166 .] 0.96

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 3.4e-26
                        RSN1_TM   2 lltslvinlvlalvflllFlilRkknkrvYaprtylkgeeertpplpqkglfgWipallkisdeeilekaGLDayvflrf 81 
                                    +lt++v + ++++++l++++i+Rk+ k +Y+p+ +    + ++p+ ++ g+++Wi++++++sd+ +l+ +GLDa+++l+ 
  gene972|gene972|rna971|rna971  60 VLTNIVSQGLITFCILIVYIIFRKRAKWLYSPNVKD---RPSHPCYNYAGFLSWIIPVVTVSDTVLLSIIGLDAFMMLQT 136
                                    899******************************995...89999************************************ PP

                        RSN1_TM  82 lkmlikiflvlavlalivLlPvnatggeg 110
                                    lkml++i+++l++++++ L  + +t++++
  gene972|gene972|rna971|rna971 137 LKMLYRILFILSFFVIPSLGYLFWTNQRE 165
                                    ************************99876 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   1.1e+04       5      16 ..      36      46 ..      36      48 .. 0.77
   2 ?    9.0   0.3   0.00017       1.5      19      42 ..      61      84 ..      57      86 .. 0.87
   3 ?    3.8   0.3    0.0067        60      21      39 ..     113     134 ..     105     136 .. 0.75
   4 ?   -1.8   0.1      0.38   3.4e+03      23      35 ..     143     155 ..     143     165 .. 0.60

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                    Insulin_TMD  5 vadyldpsnivk 16
                                   +ad +d+ ni+k
  gene972|gene972|rna971|rna971 36 MAD-VDRDNIAK 46
                                   678.78889987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00017
                    Insulin_TMD 19 igPviciillllvigavfvvvkKr 42
                                      ++   l+ + i +v+++++Kr
  gene972|gene972|rna971|rna971 61 LTNIVSQGLITFCILIVYIIFRKR 84
                                   566888889**************9 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0067
                    Insulin_TMD  21 Pvici...illllvigavfvvv 39 
                                    Pv+ +   +ll++++  +f+++
  gene972|gene972|rna971|rna971 113 PVVTVsdtVLLSIIGLDAFMML 134
                                    555433339***********98 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 0.38
                    Insulin_TMD  23 iciillllvigav 35 
                                    i++il  +vi ++
  gene972|gene972|rna971|rna971 143 ILFILSFFVIPSL 155
                                    5667766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1092.68
//
Query:       gene973|gene973|rna972|rna972  [L=120]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-23   82.1   0.1    2.1e-23   81.9   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.048   13.7   0.3    1.9  1  UPF0147         Uncharacterised protein family (UPF0147)


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.1   2.3e-27   2.1e-23       2      92 ..      17     107 ..      16     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2.3e-27
                                    HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECS CS
                 Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvs 81 
                                    +i +++++a +++++++G++e+tk l++g+a lv++A d+ep+e++++l+++c++k+vp+v+v+sk +LG ++g +rp +
  gene973|gene973|rna972|rna972  17 NILRLIQNATRSRNIRKGINESTKCLNKGRALLVVIACDAEPQEITAFLPIICEDKGVPFVHVPSKSALGVACGIHRPIA 96 
                                    677899************************************************************************99 PP

                                    EEEEEESTTTH CS
                 Ribosomal_L7Ae  82 alaikdegdsk 92 
                                    a++i  +++++
  gene973|gene973|rna972|rna972  97 ACTIYLPKEAE 107
                                    99998777766 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   5.3e-06     0.048      11      47 ..      17      53 ..      10      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.3e-06
                                   HHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHH CS
                        UPF0147 11 lLeeiiedtsvPrniRraakeakekLkdekeslavra 47
                                    + ++i++ +  rniR+ ++e+++ L++ +  l v a
  gene973|gene973|rna972|rna972 17 NILRLIQNATRSRNIRKGINESTKCLNKGRALLVVIA 53
                                   455799999*****************99887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 809.80
//
Query:       gene974|gene974|rna973|rna973  [L=128]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-35  120.7   3.4    3.6e-35  120.6   3.4    1.0  1  DUF5100   Domain of unknown function (DUF5100)


Domain annotation for each model (and alignments):
>> DUF5100  Domain of unknown function (DUF5100)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.6   3.4     2e-39   3.6e-35       1     125 [.       1     124 [.       1     125 [. 0.97

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 2e-39
                        DUF5100   1 MsiesklekiekiLsikkd.lenilesleslelileq.kedeeeiflvPqeANfQLPnvFLrtkqlpecekfikskakki 78 
                                    Msi+sk++k+ k+L+i+++ l+ +++ +++le+++++ + ++eei++vP eANfQLPn+FL+t  +pe++k+i+ +    
  gene974|gene974|rna973|rna973   1 MSIKSKYNKVMKALTIRQNdLWLLPKLITPLENSFQSeAINDEEICIVPCEANFQLPNIFLKTGLNPEYQKLIDTSGC-- 78 
                                    9***************9999*****************9***********************************99887.. PP

                        DUF5100  79 sveewneaidevldiLeeieleevefeeskkkipidqevleelvkkv 125
                                     +e+wn+ i+e ++ Leei+l++++ ++  kk+ +dq++l++lv+++
  gene974|gene974|rna973|rna973  79 -SEDWNDIIEEAIEALEEIDLSSINHNIMTKKCLVDQDTLNRLVFER 124
                                    .79*****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 904.88
//
Query:       gene975|gene975|rna974|rna974  [L=444]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.2e-06   25.1   0.1      0.046   13.4   0.0    3.7  4  PUF       Pumilio-family RNA binding repeat


Domain annotation for each model (and alignments):
>> PUF  Pumilio-family RNA binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.41   7.3e+03       5      21 ..     295     311 ..     293     314 .. 0.69
   2 !    6.3   0.0   0.00047       8.4      11      35 .]     337     361 ..     334     361 .. 0.89
   3 !   13.4   0.0   2.5e-06     0.046       9      27 ..     372     389 ..     372     397 .. 0.83
   4 ?    0.0   0.0     0.047   8.4e+02      17      27 ..     412     422 ..     400     428 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.41
                                    GHHHHHTSTTHHHHHHH CS
                            PUF   5 nlvqLstdqyGnyvvQk 21 
                                    n  +L++    n v+Q 
  gene975|gene975|rna974|rna974 295 NTKELAVGNQSNKVMQE 311
                                    55667766667999995 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00047
                                    TSTTHHHHHHHHHHHSCHHHHHHHH CS
                            PUF  11 tdqyGnyvvQkllehateeqkklil 35 
                                     +++G+y +Q l+ +++++ ++++l
  gene975|gene975|rna974|rna974 337 ANKHGAYTIQMLISVSKTPLTQNLL 361
                                    59****************9999876 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 2.5e-06
                                    HHTSTTHHHHHHHHHHHSC CS
                            PUF   9 LstdqyGnyvvQkllehat 27 
                                    L+t+  Gny++Qk+l  ++
  gene975|gene975|rna974|rna974 372 LITHEIGNYAIQKILR-FD 389
                                    89*************8.44 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.047
                                    HHHHHHHHHSC CS
                            PUF  17 yvvQkllehat 27 
                                     v++++le ++
  gene975|gene975|rna974|rna974 412 KVLRRCLEFFP 422
                                    59******644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.58
# Mc/sec: 2312.42
//
Query:       gene976|gene976|rna975|rna975  [L=556]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-67  227.2   0.0      2e-67  226.6   0.0    1.3  1  MCM              MCM P-loop domain
    1.3e-14   54.4   0.1    2.3e-14   53.6   0.1    1.4  1  MCM_lid          MCM AAA-lid domain
    1.3e-10   41.2   0.4    2.4e-10   40.3   0.4    1.3  1  MCM_OB           MCM OB domain
      3e-06   26.7   0.5      0.011   15.1   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.8e-05   24.5   0.1      0.082   12.6   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
    0.00025   21.1   0.0    0.00055   20.0   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00053   20.4   0.2     0.0018   18.7   0.3    1.8  2  AAA_16           AAA ATPase domain
     0.0019   18.7   0.3     0.0071   16.9   0.2    2.0  2  ABC_tran         ABC transporter
      0.002   18.4   0.2     0.0077   16.5   0.2    2.0  1  AAA_22           AAA domain
     0.0021   17.8   0.2     0.0076   16.0   0.2    2.0  1  AAA_29           P-loop containing region of AAA domain
     0.0082   15.7   0.2      0.019   14.5   0.2    1.5  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.018   15.4   0.2          5    7.4   0.1    2.7  2  AAA_19           AAA domain
      0.025   14.7   0.1      0.051   13.7   0.1    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
      0.032   13.4   0.1      0.054   12.6   0.1    1.3  1  DUF815           Protein of unknown function (DUF815)
      0.044   12.7   0.1        0.1   11.5   0.0    1.5  2  AAA_10           AAA-like domain
      0.063   13.0   0.1       0.84    9.3   0.1    2.2  1  AAA_30           AAA domain
       0.14   11.9   0.1       0.32   10.7   0.1    1.5  1  IstB_IS21        IstB-like ATP binding protein


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.6   0.0   1.9e-70     2e-67      18     222 ..     222     421 ..     208     423 .. 0.94

  Alignments for each domain:
  == domain 1  score: 226.6 bits;  conditional E-value: 1.9e-70
                                    HHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHS CS
                            MCM  18 lvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssaagL 97 
                                    l+ s+ ++i g e+vk ++ll+l +g++   e+k  +r++ ++llvgd+gt+Ks+lLk++++l++ ++ t+g g+++agL
  gene976|gene976|rna975|rna975 222 LIGSFGEEIQGLENVKLGLLLALASGSHT--EQKGGVRSNSHILLVGDSGTGKSHLLKTCTRLLSPSILTNGVGTTQAGL 299
                                    7889999*********************5..556699******************************************* PP

                                    SSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSS CS
                            MCM  98 taavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagr 177
                                    t+  vr  + +e+vleaGalvlad+G+cciDef k k ++++ l+EamEqqt+siaKaGiv +L++r+sv+aA+ ++ +r
  gene976|gene976|rna975|rna975 300 TTCAVR--QGKEWVLEAGALVLADTGLCCIDEFSKLKINEKNGLLEAMEQQTLSIAKAGIVSSLSTRCSVIAAVSTR-RR 376
                                    988886..5689************************************************************99876.5* PP

                                    CCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHH CS
                            MCM 178 ydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivs 222
                                    y+ +ks++eni ++++l+srFDlif l D+ ++e+D  ++++i++
  gene976|gene976|rna975|rna975 377 YNFNKSISENIMIPTPLISRFDLIFGLFDDGSSENDLLVVDKILN 421
                                    ****************************************99987 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.1   2.2e-17   2.3e-14       2      86 ..     442     521 ..     441     522 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.2e-17
                                    HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                        MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                    +lr+Yi++ar k + ++ ++ + +l ++Y+  Rk+e  +   s   tvR+Lesl RL+e+++kl     vte+dv  ai 
  gene976|gene976|rna975|rna975 442 VLRNYISVAR-KRSSTIPDDLNSILLSYYHYRRKTEG-A---SELNTVRMLESLARLAESHSKLLNAGKVTENDVYGAIL 516
                                    69********.99*********************884.3...4567********************************** PP

                                    HHHHH CS
                        MCM_lid  82 llkes 86 
                                    l++++
  gene976|gene976|rna975|rna975 517 LMETT 521
                                    **976 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.4   2.3e-13   2.4e-10       5     123 ..      51     167 ..      47     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 2.3e-13
                                    --GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEES----S.....B-..TTT-HHH-EEE-GGGS..EEEEE CS
                         MCM_OB   5 lrsehigklvkveGivtrasevkpklkkavfeckkcgktveveleePr.....kCeekeCeskdpfkleteks..kfvdf 77 
                                     +s++i+k+++v+G+v+ra e+  + +++ + c kc+ +  ++++  +      C  ++C+   +  l+ +++  + +  
  gene976|gene976|rna975|rna975  51 CNSKDINKIITVSGTVIRAYETLIRNVTSELICLKCNVK-AYRCSPGKrrnkmLC--ESCG---SSLLKDRRCfgEAIPS 124
                                    5899*********************************74.444444332222255..5565...555665555338999* PP

                                    EEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEE CS
                         MCM_OB  78 qklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyr 123
                                    qk+++Q+  +   + +++++lev+le+dl  k  PGd+  +tG++ 
  gene976|gene976|rna975|rna975 125 QKIRIQDIGN---PNSMSETLEVVLEEDLAGKFFPGDKLLITGTIL 167
                                    ******9875...6899**************************975 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00055      0.58      23      50 ..     260     287 ..     228     298 .. 0.84
   2 !   15.1   0.0   1.1e-05     0.011      96     158 ..     311     373 ..     297     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00055
                   Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllppls 50 
                                     ++llvG +G+GK+ l k  + ll+p  
  gene976|gene976|rna975|rna975 260 SHILLVGDSGTGKSHLLKTCTRLLSPSI 287
                                    589*******************999865 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                   Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                      + G++ la +G+  +DE++++k +  + L e +e+++++i++a    +  +r+ ++aa+  
  gene976|gene976|rna975|rna975 311 VLEAGALVLADTGLCCIDEFSKLKINEKNGLLEAMEQQTLSIAKAGIVSSLSTRCSVIAAVST 373
                                    5678*******************************************************9876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00068      0.71      19      41 ..     256     278 ..     246     289 .. 0.83
   2 !   12.6   0.0   7.8e-05     0.082      86     144 ..     314     374 ..     301     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00068
                                    CTSSS-EEEECSTTSSHHHHHHH CS
                Sigma54_activat  19 aktdlsvlitGesGtGKellara 41 
                                    +++++++l++G+sGtGK+ l ++
  gene976|gene976|rna975|rna975 256 VRSNSHILLVGDSGTGKSHLLKT 278
                                    67899************998765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.8e-05
                                    EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS- CS
                Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatned 144
                                    +G++  ad G   +De ++l+++  + Ll+++++++  + + G  ++ ++ + +iaa ++ 
  gene976|gene976|rna975|rna975 314 AGALVLADTGLCCIDEFSKLKINEKNGLLEAMEQQTlsIAKAGIVSSLSTRCSVIAAVSTR 374
                                    69999***************************9996336799*99***********98765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   5.2e-07   0.00055       1     124 [.     261     375 ..     261     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 5.2e-07
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HH CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraese 80 
                                    ++lLvG++GtgKs l +   ++l  +++   +  +tt++ l+     ++++ +l+ ++lv       ++++DE+ +++ +
  gene976|gene976|rna975|rna975 261 HILLVGDSGTGKSHLLKTCTRLLSPSIL--TNGVGTTQAGLTTCAVRQGKEWVLEAGALV--LADTGLCCIDEFSKLKIN 336
                                    79*********************66655..456677777777766655666688999999..778889************ PP

                                    HHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS-- CS
                          AAA_5  81 vlnsLlslleerrllleeggelvkaknddllerfrviatanpld 124
                                      n Ll  +e+++l++++ g + + +        +via+  +++
  gene976|gene976|rna975|rna975 337 EKNGLLEAMEQQTLSIAKAGIVSSLSTR-----CSVIAAVSTRR 375
                                    9**************8888777766654.....77777776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       9.6     1e+04      63      91 ..      40      65 ..      21      90 .. 0.70
   2 !   18.7   0.3   1.7e-06    0.0018      25      53 ..     260     292 ..     241     320 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.6
                         AAA_16 63 lesaipysalaqalareellrqlldeaes 91
                                       ipy+ +++ + +++ ++++ + + +
  gene976|gene976|rna975|rna975 40 K---IPYALFTNKACNSKDINKIITVSGT 65
                                   2...7888888888888888888887655 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.7e-06
                         AAA_16  25 elvllsGesGvGKsslvrellralekd....gg 53 
                                    + +ll+G+sG+GKs l++++ r l+ +    g+
  gene976|gene976|rna975|rna975 260 SHILLVGDSGTGKSHLLKTCTRLLSPSiltnGV 292
                                    79******************9977777333333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   6.7e-06    0.0071       8      37 ..     256     285 ..     251     321 .. 0.86
   2 ?   -2.0   0.0       4.5   4.8e+03      35      68 ..     429     461 ..     418     506 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.7e-06
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkp 37 
                                    ++ ++ + +vG++G+GKS Llk+ ++ll+p
  gene976|gene976|rna975|rna975 256 VRSNSHILLVGDSGTGKSHLLKTCTRLLSP 285
                                    6778999********************998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                                    S--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  35 lkpteGeilldgkdlkeqeleslrkeigvlpqep 68 
                                    +++++G++++d   l++  ++++rk+++++p + 
  gene976|gene976|rna975|rna975 429 TDKKQGSMHWDAGVLRN-YISVARKRSSTIPDDL 461
                                    55678888888555554.6788888888888772 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   7.3e-06    0.0077       4      30 ..     258     284 ..     256     358 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.3e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqld 30 
                                    + ++++++G sGtGK++ll++ ++ l 
  gene976|gene976|rna975|rna975 258 SNSHILLVGDSGTGKSHLLKTCTRLLS 284
                                    6799*****************999884 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   7.2e-06    0.0076      21      49 ..     258     286 ..     247     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.2e-06
                         AAA_29  21 lkgatlltGpsGsGKSTllDAiqalLvpa 49 
                                     ++ +ll+G+sG+GKS ll   + lL p+
  gene976|gene976|rna975|rna975 258 SNSHILLVGDSGTGKSHLLKTCTRLLSPS 286
                                    44579*********************997 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   1.8e-05     0.019      30      59 ..     256     285 ..     253     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldk 59 
                                    ++++ ++llvG++GtGK+ ++k++++ l++
  gene976|gene976|rna975|rna975 256 VRSNSHILLVGDSGTGKSHLLKTCTRLLSP 285
                                    67899*****************99988774 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0048         5       9      35 ..     258     284 ..     252     311 .. 0.85
   2 ?    5.2   0.0     0.024        25     102     129 ..     321     349 ..     288     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0048
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallv 35 
                                    +++++l+++  GtGK+++lk+  +ll 
  gene976|gene976|rna975|rna975 258 SNSHILLVGDSGTGKSHLLKTCTRLLS 284
                                    57889***************9988775 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.024
                         AAA_19 102 eeellivDEfqdvd.elqyrLlkallgek 129
                                    ++ l  +DEf+ ++    + Ll+a+ +++
  gene976|gene976|rna975|rna975 321 DTGLCCIDEFSKLKiNEKNGLLEAMEQQT 349
                                    344889******************99654 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.8e-05     0.051       2      54 ..     262     323 ..     261     389 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-05
                                    EEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEEEETTEE.......EEEEECG CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrvklkgke.......ielvDtp 54 
                                    +++vG + +GKS L+++ t+    +i ++  gtT+   +     +gke       ++l+Dt 
  gene976|gene976|rna975|rna975 262 ILLVGDSGTGKSHLLKTCTRLlsPSILTNGVGTTQAGLTTCAVRQGKEwvleagaLVLADTG 323
                                    89*****************9543789999999999885554432333333333337777773 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.1e-05     0.054      52      77 ..     258     283 ..     231     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                         DUF815  52 pannvLLwGarGtGKSslvkallney 77 
                                    + +++LL+G+ GtGKS l+k++++ +
  gene976|gene976|rna975|rna975 258 SNSHILLVGDSGTGKSHLLKTCTRLL 283
                                    5679****************987655 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.7   3.9e+03     266     302 ..     173     209 ..     168     224 .. 0.73
   2 ?   11.5   0.0   9.5e-05       0.1      13      41 ..     251     279 ..     240     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.7
                         AAA_10 266 vRiGRsynaavylvtqsadDvlkeelknniglklaFr 302
                                     +iG ++   +y+ + +++  ++e++++ +g +++ +
  gene976|gene976|rna975|rna975 173 FKIGEQMASSIYMHALAVHKQDEESMNDSLGRAFMSK 209
                                    6678888888888888888888888888888888765 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.5e-05
                         AAA_10  13 evkgsktnasasliiGdlGnGKSvlakll 41 
                                    e kg +  +s+ l++Gd G GKS l k+ 
  gene976|gene976|rna975|rna975 251 EQKGGVRSNSHILLVGDSGTGKSHLLKTC 279
                                    557889999*****************997 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0008      0.84      20     115 ..     261     348 ..     255     356 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0008
                         AAA_30  20 vavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEag 98 
                                      +l+G  GtGK+++lk+ ++++  +   + +g +  g    +++++        ++++ +  g+  l++  l  +DE +
  gene976|gene976|rna975|rna975 261 HILLVGDSGTGKSHLLKTCTRLLSPSiLTNGVGTTQAGLTTCAVRQG--------KEWVLEA-GALVLADTGLCCIDEFS 331
                                    5789**************99988755323333333333222222222........3333222.22334445667777777 PP

                         AAA_30  99 mvdtkqlaallkaaeka 115
                                     + +++ + ll+a+e++
  gene976|gene976|rna975|rna975 332 KLKINEKNGLLEAMEQQ 348
                                    77777777777777665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00031      0.32      44      64 ..     256     276 ..     242     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                      IstB_IS21  44 iekkenivllGpsGvGKshla 64 
                                    ++++  i+l+G sG+GKshl 
  gene976|gene976|rna975|rna975 256 VRSNSHILLVGDSGTGKSHLL 276
                                    5678899************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.75u 0.35s 00:00:01.10 Elapsed: 00:00:00.55
# Mc/sec: 3039.05
//
Query:       gene977|gene977|rna976|rna976  [L=187]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-49  168.0   6.1    2.4e-49  167.9   6.1    1.0  1  DUF5090   Domain of unknown function (DUF5090)
  ------ inclusion threshold ------
       0.16   11.9   0.0       0.26   11.2   0.0    1.3  1  ApoC-I    Apolipoprotein C-I (ApoC-1)
        2.1    6.6  11.1        2.4    6.3  11.1    1.1  1  DUF2070   Predicted membrane protein (DUF2070)
        5.5    6.3   5.5        7.9    5.8   5.5    1.2  1  TMEM43    Transmembrane protein 43


Domain annotation for each model (and alignments):
>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.9   6.1   5.3e-53   2.4e-49       4     187 ..       4     179 ..       1     180 [. 0.95

  Alignments for each domain:
  == domain 1  score: 167.9 bits;  conditional E-value: 5.3e-53
                        DUF5090   4 entenskekaleekvkkveekvkeqiekieeSklGkklPtevknlklkdiikitlllkavllipiyllviaengnk...l 80 
                                         ++ek+l+ +++ ve+k++  i+++e+S+lG+++P+ev +l l++++k+++l++++ +ip+yl++  ++gnk   l
  gene977|gene977|rna976|rna976   4 G----QQEKVLD-AANVVEAKAMSAIDNVEKSSLGNSIPLEV-SLPLRELTKYLMLFTIFESIPVYLIF--CEGNKnefL 75 
                                    3....4899999.*****************************.**************************..666666699 PP

                        DUF5090  81 dflksksriifltlikivlsilvdlvvyfselsslfkvflllkiikllitlivllalsistglfilvlsliylllcliid 160
                                    +++++++++ifl++  ++++ ++dlv++++++++l+k+++ +++ k+ + ++v+++++is ++++++++++y l+++++d
  gene977|gene977|rna976|rna976  76 HWISKGTGLIFLVI--AIIAGILDLVTFYGKMFNLYKFVVPATLAKTALSFLVVVFSNIS-SMYVVFIAILYSLRIALFD 152
                                    **************..99******************************************.******************* PP

                        DUF5090 161 llflyYlaiylkrlesdeyddngkklk 187
                                     lflyYlai l+r+esd+yd+ng++l 
  gene977|gene977|rna976|rna976 153 ALFLYYLAILLRRIESDDYDNNGERLR 179
                                    ***********************9875 PP

>> ApoC-I  Apolipoprotein C-I (ApoC-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.8e-05      0.26       9      39 ..       3      33 ..       1      36 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.8e-05
                                   ....HHHCHHHHHHHHHHCCHCCCHCTTSSS CS
                         ApoC-I  9 eslpdklkEfgktledKaraaieeIkqSelp 39
                                   e  ++k+   ++ +e Ka+ ai ++++S l 
  gene977|gene977|rna976|rna976  3 EGQQEKVLDAANVVEAKAMSAIDNVEKSSLG 33
                                   6668999999******************986 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  11.1   0.00054       2.4     107     181 ..      80     165 ..      22     168 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00054
                        DUF2070 107 s........lalvfalrllvlvavsdesllkavlpaliqpllailllvly...fspesfllllllslifalavylfivvv 175
                                    +        +a+++++  lv++     +l k v+pa++   ++ +l+v++   +s++ +++++l+sl +al+ +lf++++
  gene977|gene977|rna976|rna976  80 KgtgliflvIAIIAGILDLVTFYGKMFNLYKFVVPATLAKTALSFLVVVFsniSSMYVVFIAILYSLRIALFDALFLYYL 159
                                    13444444466666666666666667777777777777766666666666666666666666777777777777777777 PP

                        DUF2070 176 drplkr 181
                                     + l+r
  gene977|gene977|rna976|rna976 160 AILLRR 165
                                    666665 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.5    0.0018       7.9     180     248 ..      70     144 ..      64     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0018
                         TMEM43 180 senklltwllRllGfllmfl....glllllsplsvlvslipll..gelvglglalvalllslslsllvialawll 248
                                    ++n++l w+ +  G++ +++    g+l l++    +++l +++  ++l++++l+++ +++s + s+ v+ +a l+
  gene977|gene977|rna976|rna976  70 NKNEFLHWISKGTGLIFLVIaiiaGILDLVTFYGKMFNLYKFVvpATLAKTALSFLVVVFSNISSMYVVFIAILY 144
                                    7899**********8888883333444444444445555555588999999999999999999999888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1067.08
//
Query:       gene978|gene978|rna977|rna977  [L=399]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-33  114.9  13.8    1.4e-07   31.9   0.1    7.4  7  Sel1      Sel1 repeat
    0.00067   20.1   5.9        5.7    7.8   0.0    5.3  5  TPR_6     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Sel1  Sel1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.4     1e-07   0.00094       2      38 .]      99     134 ..      98     134 .. 0.89
   2 !   11.9   0.0   3.2e-05      0.29       5      37 ..     139     169 ..     135     170 .. 0.94
   3 ?    3.8   0.0     0.011     1e+02       2      36 ..     172     205 ..     171     206 .. 0.81
   4 !   21.6   0.1   2.9e-08   0.00026       1      36 [.     211     247 ..     211     249 .. 0.89
   5 !   31.9   0.1   1.6e-11   1.4e-07       3      37 ..     252     285 ..     250     286 .. 0.94
   6 !   14.7   0.0   4.1e-06     0.036       1      35 [.     287     321 ..     287     324 .. 0.92
   7 !   14.7   0.1   4.2e-06     0.038       2      31 ..     326     353 ..     325     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-07
                           Sel1   2 eAmyrLGmfylylnGl.gvpkDpekAiewyekAAeqGd 38 
                                    e  y LG  + y++Gl g  +D++kA+ +y  +A++G+
  gene978|gene978|rna977|rna977  99 EMHYYLG--LSYEKGLfGMRRDYRKAFGHYLTSAQLGS 134
                                    668****..666****88****************9996 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.2e-05
                           Sel1   5 yrLGmfylylnGlgvpkDpekAiewyekAAeqG 37 
                                    ++++  ++y++G g ++ ++ A+ +y+ AA++G
  gene978|gene978|rna977|rna977 139 FKVA--QCYEKGIGKKRSIKNALCFYRCAAKLG 169
                                    7899..*************************99 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.011
                           Sel1   2 eAmyrLGmfylylnGlgvpk..DpekAiewyekAAeq 36 
                                    +Am+ +G   + l+G  ++   D e ++ ++++AA++
  gene978|gene978|rna977|rna977 172 DAMHTYG--VIILFGN-IENdcDLETGYFYLRLAARK 205
                                    5788888..6669997.999667999*********85 PP

  == domain 4  score: 21.6 bits;  conditional E-value: 2.9e-08
                           Sel1   1 aeAmyrLGmfylylnGl..g.vpkDpekAiewyekAAeq 36 
                                    ++A+y+L+   +y+ G+  + v +D + A+++y +  ++
  gene978|gene978|rna977|rna977 211 PYALYDLA--RCYERGKgpDiVSPDDSYAFKLYLRGGSL 247
                                    68******..999****8878999*********997666 PP

  == domain 5  score: 31.9 bits;  conditional E-value: 1.6e-11
                           Sel1   3 AmyrLGmfylylnGl.gvpkDpekAiewyekAAeqG 37 
                                    +++r G   +++nG+ g +kD  kA+ewy kAA++G
  gene978|gene978|rna977|rna977 252 CQFRIG--KCFENGDmGQEKDMVKALEWYAKAADLG 285
                                    79****..*******77*****************99 PP

  == domain 6  score: 14.7 bits;  conditional E-value: 4.1e-06
                           Sel1   1 aeAmyrLGmfylylnGl.g.vpkDpekAiewyekAAe 35 
                                    ++A+ rL    l+lnG  + v+++  +A+++  kAA 
  gene978|gene978|rna977|rna977 287 PDAQLRLS--ALFLNGFeDiVKRNHGLAFKLGLKAAT 321
                                    68******..888****988***************97 PP

  == domain 7  score: 14.7 bits;  conditional E-value: 4.2e-06
                           Sel1   2 eAmyrLGmfylylnGlgvpkDpekAiewye 31 
                                    +A+y +   ++y+ G g++++  +A+ w +
  gene978|gene978|rna977|rna977 326 SAAYLVS--ECYEQGIGIKRNALLALWWGR 353
                                    8******..*******************65 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.1    0.0036        33       3      19 ..     101     122 ..      99     128 .. 0.77
   2 ?    0.8   0.0      0.11   9.5e+02       4      17 ..     139     153 ..     138     159 .. 0.74
   3 !    7.8   0.0   0.00064       5.7       1      14 [.     212     225 ..     212     229 .. 0.85
   4 ?    4.0   0.0      0.01        90       3      23 ..     253     275 ..     251     283 .. 0.77
   5 ?   -1.3   0.1      0.51   4.6e+03       2      20 ..     327     346 ..     326     349 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0036
                                    HHHHHHHHHHH.....HHHHHH CS
                          TPR_6   3 lyklalsyrkl.....gdtdkA 19 
                                     y+l+lsy+k+      d++kA
  gene978|gene978|rna977|rna977 101 HYYLGLSYEKGlfgmrRDYRKA 122
                                    59********669666666666 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                                    HHHHHHHHH.HHHHH CS
                          TPR_6   4 yklalsyrk.lgdtd 17 
                                    +k a++y+k  g+++
  gene978|gene978|rna977|rna977 139 FKVAQCYEKgIGKKR 153
                                    799*****9556655 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00064
                                    HHHHHHHHHHHHHH CS
                          TPR_6   1 dAlyklalsyrklg 14 
                                    +Aly la++y++++
  gene978|gene978|rna977|rna977 212 YALYDLARCYERGK 225
                                    8**********975 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.01
                                    HHHHHHHHHHH..HHHHHHHHHH CS
                          TPR_6   3 lyklalsyrkl..gdtdkAleal 23 
                                    +++++++++++  g+  + ++al
  gene978|gene978|rna977|rna977 253 QFRIGKCFENGdmGQEKDMVKAL 275
                                    89*******98786666666655 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 0.51
                                    HHHHHHHHHHH.HHHHHHHH CS
                          TPR_6   2 Alyklalsyrk.lgdtdkAl 20 
                                    A y+  ++y++  g +++Al
  gene978|gene978|rna977|rna977 327 AAYLVSECYEQgIGIKRNAL 346
                                    6789999**99557777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2748.84
//
Query:       gene979|gene979|rna978|rna978  [L=324]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-59  200.7   0.0    3.3e-59  200.4   0.0    1.1  1  Pkinase         Protein kinase domain
    2.8e-30  105.5   0.0    3.3e-30  105.2   0.0    1.1  1  Pkinase_Tyr     Protein tyrosine kinase
    5.2e-05   22.7   0.0    7.7e-05   22.1   0.0    1.3  1  Kinase-like     Kinase-like
    0.00043   20.3   0.0       0.01   15.8   0.0    2.1  2  APH             Phosphotransferase enzyme family
     0.0062   16.2   0.1        3.7    7.1   0.1    2.2  2  FTA2            Kinetochore Sim4 complex subunit FTA2
  ------ inclusion threshold ------
      0.013   14.3   0.0      0.018   13.8   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase
      0.048   13.0   0.0      0.081   12.3   0.0    1.3  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.067   12.1   0.0       0.11   11.4   0.0    1.2  1  Haspin_kinase   Haspin like kinase domain
       0.11   12.1   0.0       0.23   11.0   0.0    1.5  1  Choline_kinase  Choline/ethanolamine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.4   0.0   1.6e-62   3.3e-59       1     264 []       7     261 ..       7     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 1.6e-62
                                    EEEEEEEEEESSEEEEEEEETTT.TEEEEEEEEECHCHCHHHH.HHHHHHHHHHHHHS.CTTB--EEEEEEESSEEEEEE CS
                        Pkinase   1 yekleklGeGsfGkVykaveket.gkivAvKkikkekakkkke.kkvlrEikilkklk.hpnivrlyevfeekdelylvl 77 
                                    +e ++ +GeG+fGkVy ++ k++ + ++A+K+++ +++ k++  +++ +Ei+ilk+l  +p+i +ly++  +  ++ l+l
  gene979|gene979|rna978|rna978   7 FEFVKVVGEGAFGKVYLVKLKNNpSSMFAMKMLDFDEILKQRLaDQLESEISILKRLYgCPFIAKLYSTDFHCGKIGLIL 86 
                                    577899***********9876652789***********9998889************99********************* PP

                                    E--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCSBCTT CS
                        Pkinase  78 eyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakelessskltsf 157
                                    eyv ggel+ +l++ g ++e+ ++++a++i+++l+++H kgi++rDlKpeNiLi ++g++K++DFG+a   ++s     +
  gene979|gene979|rna978|rna978  87 EYVGGGELFYWLKKCGRFDEKMTRFYAAEIVSALRFIHGKGILYRDLKPENILITSSGHIKLIDFGFAVYENES--IYMI 164
                                    **************9****************************************************9766654..799* PP

                                    TSCGGGS-HHHHTTSCBSHHHHHHHHHHHHHHHHHSS-STTTSSHHHHHHHHHHTHHHHHHHCTSHH...HHHTTS-HHH CS
                        Pkinase 158 vgtseYlAPEvlkeneyskkvDvWslGvilyelltgkppfsgekgkekvekeldqlekilkilgetkeklpeaseiseea 237
                                     gt+eY++PE l++++ ++++D+W+lGvi+ye+l+g ppf++ + ++ ++k+l+              ++  +s +s+ a
  gene979|gene979|rna978|rna978 165 SGTPEYMSPEKLRSEDDGRASDYWGLGVIIYEMLCGDPPFYDASADTIYHKILE-------------SQVTFPSYVSPIA 231
                                    *****************************************6666654444444.............478999******* PP

                                    HHHHHHHT-SSGCCSTT...HHHHHTSGGG CS
                        Pkinase 238 kdllkkllkkdpkkRlt...aeellqhpyl 264
                                    ++l+  ll+k + +Rl+   + e++ hp++
  gene979|gene979|rna978|rna978 232 RSLIAGLLDKSRATRLGakgICEIMGHPFF 261
                                    *****************6666678888887 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   1.6e-33   3.3e-30       2     244 ..       8     241 ..       7     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 1.6e-33
                                    EEEEEEEEESSEEEEEEEEETTTTSSEEEEEEEEE..STTSSHHHHHHHHHHHHHHHTS.-BTTB--EEEEEESSSSEEE CS
                    Pkinase_Tyr   2 elgkklGeGafGkVvegtlkgekekkevkVavKtl..keeateeekeelleeakimkkl.khpnivkllgvctkeeplli 78 
                                    e+ k +GeGafGkV+  +lk   ++ +   a+K+l  +e  +++  ++l +e++i+k+l   p i kl+    + +++ +
  gene979|gene979|rna978|rna978   8 EFVKVVGEGAFGKVYLVKLK---NNPSSMFAMKMLdfDEILKQRLADQLESEISILKRLyGCPFIAKLYSTDFHCGKIGL 84 
                                    67899***************...888999******5446666666899999********99******************* PP

                                    EEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEETTTSSE CS
                    Pkinase_Tyr  79 vteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLardiekdde 158
                                    ++eyv gG+L   L+k    +++ k +  +a+++ +++++++ k ++ rdl   N+L++++ ++k+ DfG a    +++ 
  gene979|gene979|rna978|rna978  85 ILEYVGGGELFYWLKKC--GRFDEKMTRFYAAEIVSALRFIHGKGILYRDLKPENILITSSGHIKLIDFGFAVYE-NESI 161
                                    ****************8..999999999********************************************977.4444 PP

                                    EEETTSSTSGGGGS-HHHHHHSEEEHHHHHHHHHHHHHHHHTTSSGTTTTSHHHHHHHHHHTTEES-BBTTSBHHHHHHH CS
                    Pkinase_Tyr 159 yvkkeeaklpvkWmapEslkekkftsksDvWsfGvllwEiftlgespypglkneevleklkegkrlekpekcpeelyelm 238
                                    y  +       ++m+pE l+++    +sD W  Gv+++E+++ g+ p+ + ++ ++++k+ e+ +++ p+++++   +l+
  gene979|gene979|rna978|rna978 162 YMIS----GTPEYMSPEKLRSEDDGRASDYWGLGVIIYEMLC-GDPPFYDASADTIYHKILES-QVTFPSYVSPIARSLI 235
                                    4433....3579*****************************9.***************99764.4556666666555555 PP

                                    HHHT-S CS
                    Pkinase_Tyr 239 kkcwee 244
                                       +++
  gene979|gene979|rna978|rna978 236 AGLLDK 241
                                    555555 PP

>> Kinase-like  Kinase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.9e-08   7.7e-05     155     286 ..     118     244 ..      99     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.9e-08
                    Kinase-like 155 rlaanLqakglvhgkftvdnllldekgglmlggft.aLvragtkvvlsevekgfaPpEllgsrggytrknktkmthklda 233
                                         ++ kg++  +++++n+l    g ++l +f+ a +     + +s +++  +P  l+++  g           + d 
  gene979|gene979|rna978|rna978 118 SALRFIHGKGILYRDLKPENILITSSGHIKLIDFGfAVYENESIYMISGTPEYMSPEKLRSEDDG----------RASDY 187
                                    555567889*************************9455666666777*********999999766..........467** PP

                    Kinase-like 234 WqlGlviyriwclklPltlateeakeewkfklckkipekv....kaLlkkfLqlsqe 286
                                    W+lG+ iy + c + P+  a  + +   +++  +  p  v    + L++++L  s+ 
  gene979|gene979|rna978|rna978 188 WGLGVIIYEMLCGDPPFYDASADTIYHKILESQVTFPSYVspiaRSLIAGLLDKSRA 244
                                    ****************98877776666566555566665533335677777776665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.055   1.1e+02      28      82 ..      44      94 ..      10     115 .. 0.72
   2 !   15.8   0.0   5.1e-06      0.01     166     198 ..     126     156 ..      96     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.055
                                   E-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE- CS
                            APH 28 npparaaeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsl 82
                                   + ++r+a ++++e  +l+ L + ++ +++++ +d  ++ ig   +++eyv+g  l
  gene979|gene979|rna978|rna978 44 ILKQRLADQLESEISILKRLYGCPF-IAKLYSTDFHCGKIG---LILEYVGGGEL 94
                                   56668999***************99.99****777777777...69999988765 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 5.1e-06
                                    EEEE-SS-SGGGEEEC..TTEEEEE---TT-EE CS
                            APH 166 tvllHgDlhpgNllvdpddgrvtGviDfedagl 198
                                    +++l +Dl+p N+l++   g++  +iDf++a++
  gene979|gene979|rna978|rna978 126 KGILYRDLKPENILIT-SSGHI-KLIDFGFAVY 156
                                    68999***********.44555.59******98 PP

>> FTA2  Kinetochore Sim4 complex subunit FTA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0019       3.7      22      56 ..       5      42 ..       2      73 .. 0.78
   2 !    6.9   0.0    0.0021       4.2     171     214 ..     106     154 ..      98     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0019
                           FTA2 22 kdiefleyLgkglhsiVlkvkirgk...eYALKlFrfl 56
                                   +d+ef++++g+g+ + V+ vk +++    +A+K+  f 
  gene979|gene979|rna978|rna978  5 RDFEFVKVVGEGAFGKVYLVKLKNNpssMFAMKMLDFD 42
                                   589********************988889****96555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0021
                           FTA2 171 eelevsqlpkllrdlkklhklgIvvrDlkeenyi...dg..kLvDlsaa 214
                                    e+++  ++ ++++ l+ +h  gI+ rDlk+en++   +g  kL+D++ a
  gene979|gene979|rna978|rna978 106 EKMTRFYAAEIVSALRFIHGKGILYRDLKPENILitsSGhiKLIDFGFA 154
                                    56666778999*********************98444223378888876 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.1e-06     0.018     315     388 ..     116     178 ..     105     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.1e-06
                 Pkinase_fungal 315 aIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddssesgarertGTleFmaievlkg 388
                                     + ++r  +  +giL rD   +Nilit     ++ +  LiD+ +a+ +++     +     GT+e+m+ e l+ 
  gene979|gene979|rna978|rna978 116 IVSALRFIH-GKGILYRDLKPENILIT-----SSGHIKLIDFGFAVYENE-----SIYMISGTPEYMSPEKLRS 178
                                    577888888.99***************.....778899********9995.....335689******9988875 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.1e-05     0.081     105     166 ..      94     151 ..      84     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                            Kdo 105 LedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDl 166
                                    L  +l+k  +++e+++r    ++  + + +h  g+  +dl + nil+   +    +i liD+
  gene979|gene979|rna978|rna978  94 LFYWLKKCGRFDEKMTRFYAAEIVSALRFIHGKGILYRDLKPENILITSSG----HIKLIDF 151
                                    566888877899**************************************9....******9 PP

>> Haspin_kinase  Haspin like kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.6e-05      0.11     231     257 ..     131     157 ..     120     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.6e-05
                  Haspin_kinase 231 RdLhldniLvdknlnvtlidlklsRle 257
                                    RdL+ +niL+ +++++ lid+  + +e
  gene979|gene979|rna978|rna978 131 RDLKPENILITSSGHIKLIDFGFAVYE 157
                                    9********************988765 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.23     150     177 ..     131     157 ..     101     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                    S--SGGGEEE.-CTTEEEE--GTT-EEE CS
                 Choline_kinase 150 nDlqegNillnkeekklvlIDFEYagyn 177
                                     Dl ++Nil  ++ +++ lIDF +a y 
  gene979|gene979|rna978|rna978 131 RDLKPENILI-TSSGHIKLIDFGFAVYE 157
                                    59********.99************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1830.26
//
Query:       gene980|gene980|rna979|rna979  [L=385]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.035   14.5   0.5       0.47   10.9   0.1    2.6  2  S-antigen    S-antigen protein
       0.17   12.5   4.0         12    6.6   0.2    3.1  3  SPT6_acidic  Acidic N-terminal SPT6


Domain annotation for each model (and alignments):
>> S-antigen  S-antigen protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.082   7.4e+02      36      73 ..      47      84 ..      30      96 .. 0.78
   2 ?   10.9   0.1   5.2e-05      0.47      22      69 ..     264     311 ..     258     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.082
                      S-antigen 36 ygikyy.lrnglldkkngkgqkyedleeeenddeedsns 73
                                   yg  +y  r  ++dk   +g +y+ ++++e  d ed ++
  gene980|gene980|rna979|rna979 47 YGSYFYaWRVNFADKLMTHG-RYKLIKKNEHPDTEDRKR 84
                                   77766635778888887777.699999999999888765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.2e-05
                      S-antigen  22 ygkvkntdqelsniygikyylrnglldkkngkgqkyedleee.enddee 69 
                                     gkv  t  e    y   yyl n l+ + + k qk  +l+ e   dd+e
  gene980|gene980|rna979|rna979 264 NGKVSATPYET-FAYSRAYYLFNFLTAGIEFKSQKLAELRSEsSSDDNE 311
                                    68999999885.579************************9884556665 PP

>> SPT6_acidic  Acidic N-terminal SPT6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.83   7.4e+03      62      83 ..      68      88 ..      67      92 .. 0.65
   2 ?    6.6   0.2    0.0013        12      11      46 ..     122     157 ..     120     161 .. 0.63
   3 ?    5.8   0.0    0.0024        21      52      68 ..     360     376 ..     333     382 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.83
                    SPT6_acidic 62 ldLieentgvkvkrkkkkfkRl 83
                                   ++Li+ n   +++ + k+f R+
  gene980|gene980|rna979|rna979 68 YKLIKKNEHPDTEDR-KRFYRI 88
                                   567777777666665.477665 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0013
                    SPT6_acidic  11 eeerkvregFIvddd..eeeeeeeeseeeeekkrrkkk 46 
                                    e+  k+re FIv+ +  ee+ + ++s+    ++ +kkk
  gene980|gene980|rna979|rna979 122 EDFLKIRERFIVETEglEEDMNLSHSD--LMERMKKKK 157
                                    566799*******98666655555554..223333333 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0024
                    SPT6_acidic  52 eeedaLdedDldLieen 68 
                                    +e++++de Dl+Li+  
  gene980|gene980|rna979|rna979 360 DEKKEVDEADLELIQKS 376
                                    56689*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 2350.59
//
Query:       gene98|gene98|rna98|rna98  [L=1001]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-57  194.2   0.3    8.3e-57  192.1   0.3    2.3  1  SMC_N           RecF/RecN/SMC N terminal domain
    6.2e-16   58.8   0.0    2.1e-15   57.1   0.0    2.0  2  SMC_hinge       SMC proteins Flexible Hinge Domain
    5.2e-10   39.6   0.7    1.8e-05   24.8   0.0    4.0  5  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      9e-09   36.1  55.8    2.2e-07   31.6  26.7    5.3  4  AAA_23          AAA domain
     0.0011   18.7   0.0     0.0023   17.6   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.21   12.1  11.0        6.2    7.3   0.0    4.5  4  ABC_tran        ABC transporter


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.1   0.3   2.8e-60   8.3e-57       1     216 [.       2     993 ..       2     996 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.1 bits;  conditional E-value: 2.8e-60
                                EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEE CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfd 84 
                                ++k++++++Fk y++k +  +++ksf+ai+G NGSGKsn+ld ilF LG +s+k+lr++++ +l++      +  +++v++++ 
  gene98|gene98|rna98|rna98   2 FIKEIILDGFKCYEEKVTMANLDKSFNAITGMNGSGKSNVLDGILFALGLESTKALRASNIGELVNT-----NRRECRVSLVLC 80 
                                69************999*************************************************8.....7789*******9 PP

                                ETTEE....SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............................. CS
                                xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                      SMC_N  85 nedkk....lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske............................. 135
                                n +k+      ++ +e+ +sr++  +g+++ +in++ ++++ +s+l  s+g+ +                              
  gene98|gene98|rna98|rna98  81 NREKSrsppGYEHYDEICVSRTIDPEGRTKCYINNHLCSFSTLSKLCVSMGLGSRgtfssivmqghitkvlsmkssdlreliee 164
                                99988788888999********************************************************************** PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 165 tagtrsyekekeramamiekkeerlkdvqemlkrrispfydklrqertrfletrdlhekkrelehrereirkrlalheigeevd 248
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 249 tlgkclknyaaemksleaiekrieeisgikeevdvvwiktsidgerlrldelksknleeelrlkkeemdviknlkpnleldkla 332
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 333 ererllveslrridsgendvlkkieeitslkfqrsrvefefnsipevgfsqerldeieklkvsedeieelrkkarmlrskisyp 416
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 417 fvegvfgtveenieicnrkyleavytvmgqrskyvitsdekvggflvstmersvsviplskirvfylspnvlreieskggvsmv 500
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 501 sllkfdsnvrkaiefvfnnffvfeskemarkvcfeqkvmcvtvdgtvydpkgtlsggktnfrvntvrrkdvedieraieslean 584
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 585 krrfdgvkqeyngllrsktlherreklkeemesldtrisilsdlcengmnikeelravrekmvegmreknevdglmerrkklen 668
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 669 rikeieseilsskeeirmceerilsyekmlgkhniendsrrmsekemdgleakhrdlirstgklhnramkiyndverklkqvpq 752
                                ************************************************************************************ PP

                                .................................................................................... CS
                                .................................................................................... RF
                      SMC_N 136 .................................................................................... 135
                                                                                                                    
  gene98|gene98|rna98|rna98 753 ndveqervcmvdeevhkiaesvgisprcllirkqcmaeeeknglkrelemitnemerlrcmkrstmdpanfdllernelmieel 836
                                ************************************************************************************ PP

                                ............................................................................CS-HHHHH CS
                                ............................................................................xxxxxxxx RF
                      SMC_N 136 ............................................................................lLSgGekt 143
                                                                                                            +LSgG+++
  gene98|gene98|rna98|rna98 837 kekidklekdrfaigqsisrfddlgykenlkafkhingrlgrflryfipgsdaridekngeyalkvkvgswkeslnELSGGQRS 920
                                ************************************************************************************ PP

                                HHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEET CS
                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SMC_N 144 LvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkven 216
                                Lval L+f++  ++p+++y++Deid+aLD ++++ + e++k++ ++aQfiv+sl+++m+ +a+++++v+ ++ 
  gene98|gene98|rna98|rna98 921 LVALCLIFSMLTYRPSSFYIFDEIDSALDLSYTQGIGEIIKKEFDSAQFIVVSLKSGMFDNANNIFKVYLQDG 993
                                *********************************************************************9554 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0     7e-19   2.1e-15       2     116 ..     419     532 ..     418     533 .. 0.97
   2 ?   -3.8   0.0       5.1   1.5e+04      36      52 ..     569     585 ..     563     630 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 7e-19
                  SMC_hinge   2 kgvlGrladlievd.egyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns..gavp 82 
                                +gv+G++ ++ie+  ++y  Av +++g+r ++++++de++   +++ +++     ++++pl++i+ +  ++ +  + +  g v+
  gene98|gene98|rna98|rna98 419 EGVFGTVEENIEICnRKYLEAVYTVMGQRSKYVITSDEKVGGFLVSTMERS----VSVIPLSKIRVFYLSPNVLREIEskGGVS 498
                                79*************************************************....*************999998887799**** PP

                  SMC_hinge  83 lidlvevddelrkalryllgdtlvvdsldeAeel 116
                                +++l+++d+++rka+++++ +++v +s + A+++
  gene98|gene98|rna98|rna98 499 MVSLLKFDSNVRKAIEFVFNNFFVFESKEMARKV 532
                                *******************************997 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.1
                  SMC_hinge  36 edeetakkiieflkkkn 52 
                                +d e+ +++ie l++++
  gene98|gene98|rna98|rna98 569 KDVEDIERAIESLEANK 585
                                67777788888887773 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.8e-08   8.5e-05       1      35 [.      27      63 ..      27      87 .. 0.74
   2 ?   -3.2   0.6       1.9   5.6e+03      84     133 ..     186     235 ..     171     243 .. 0.72
   3 ?    0.6   0.9      0.14   4.1e+02      76     168 ..     320     410 ..     276     420 .. 0.69
   4 ?   -3.2   0.0       1.9   5.8e+03     185     214 ..     663     692 ..     642     756 .. 0.64
   5 !   24.8   0.0   5.9e-09   1.8e-05     232     296 ..     909     973 ..     825     973 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.8e-08
                     AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..drdvegltde 35
                               +n+++G NgsGKSn+Ld + ++ +l   + ++ +++ 
  gene98|gene98|rna98|rna98 27 FNAITGMNGSGKSNVLDGILFALGLesTKALRASNIG 63
                               8********************9887764444444433 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.9
                     AAA_21  84 eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvs 133
                                ee+l++v + l++++  +++ l++e   + e r+ ++ +++ +++e ++ 
  gene98|gene98|rna98|rna98 186 EERLKDVQEMLKRRISPFYDKLRQERTRFLETRDLHEKKRELEHREREIR 235
                                45777777777888888888888888888888888888888777776665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.14
                     AAA_21  76 lrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllld 159
                                 +l+ +     l  + ++++    + +r++  e+++  + ++i ++++ +s+ e++ ++  +  f++ ++d ++ +  ++++ +
  gene98|gene98|rna98|rna98 320 KNLKPNLE---LDKLAERERLLVESLRRIDSGENDVLKKIEEITSLKFQRSRVEFEFNSIPEVGFSQERLDEIEKLKVSEDEIE 400
                                33333333...4444447777777778888888888888888888888888888888888888888888888888888888888 PP

                     AAA_21 160 glrke.rigl 168
                                +lrk+ r+++
  gene98|gene98|rna98|rna98 401 ELRKKaRMLR 410
                                8877665554 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.9
                     AAA_21 185 lqrlvrslklveielsdlgegeeliasvde 214
                                +++l++++k++e+e+  ++e +++ +++++
  gene98|gene98|rna98|rna98 663 RKKLENRIKEIESEILSSKEEIRMCEERIL 692
                                444444444444444444444444444433 PP

  == domain 5  score: 24.8 bits;  conditional E-value: 5.9e-09
                     AAA_21 232 lparelSdGtkrll..alltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltT 296
                                 +++elS G+++l   +l+ ++l  +++ s++++DE+++ L+ + +  + e++ ke  +  aQ+i+++
  gene98|gene98|rna98|rna98 909 ESLNELSGGQRSLValCLIFSMLTYRPS-SFYIFDEIDSALDLSYTQGIGEIIkKEFDS--AQFIVVS 973
                                46788********546999999999999.************************666655..9**9976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6  26.7   7.5e-11   2.2e-07       2     192 ..       6     316 ..       5     415 .. 0.74
   2 !    5.8  11.1    0.0057        17      86     198 ..     530     683 ..     489     715 .. 0.71
   3 ?    2.6   4.3     0.056   1.7e+02      86     190 ..     732     845 ..     690     872 .. 0.65
   4 ?   -2.6   0.0       2.2   6.6e+03      79     133 ..     869     929 ..     853     949 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.5e-11
                     AAA_23   2 Lkienfrsf.rdqe.idFskgltlItGpNGaGKTTildAiklaLygetprlsrks....grgfeksdveiese........... 68 
                                + + +f+++ ++++  +++k +++ItG+NG+GK+ +ld i +aL+ e+++  r s      + ++++++++             
  gene98|gene98|rna98|rna98   6 IILDGFKCYeEKVTmANLDKSFNAITGMNGSGKSNVLDGILFALGLESTKALRASnigeLVNTNRRECRVSLVlcnreksrspp 89 
                                889******5556657*****************************998777776645432255566666555566667777777 PP

                     AAA_23  69 ...gkvkayveltfenkdgry............................................trsiererelskkkgkttk 105
                                   + ++ +v++t+  +++++                                               +++ +e++ +  ++ k
  gene98|gene98|rna98|rna98  90 gyeHYDEICVSRTIDPEGRTKcyinnhlcsfstlsklcvsmglgsrgtfssivmqghitkvlsmkSSDLRELIEETAGTRSYEK 173
                                775333333666655554444888888888888888999999999999999999889888886542222222222222222223 PP

                     AAA_23 106 kaklelleideleqfisellgskki.ilnlilflgqer...........feefelkdkke........................ 153
                                ++++    i+++e+++++  +  k+ i+++++ l qer           +         +                        
  gene98|gene98|rna98|rna98 174 EKERAMAMIEKKEERLKDVQEMLKRrISPFYDKLRQERtrfletrdlheK---------Krelehrereirkrlalheigeevd 248
                                33333333355566666655543333779999999999554444333321.........1234456666778888888888888 PP

                     AAA_23 154 ..............rleelekeleeledekkllekl...............eqekekekeleeleeel 192
                                               le++ek +ee++ +k++++ +               ++ k+ e+el  ++ee+
  gene98|gene98|rna98|rna98 249 tlgkclknyaaemkSLEAIEKRIEEISGIKEEVDVVwiktsidgerlrldeLKSKNLEEELRLKKEEM 316
                                88888888888888888888888888888888777788888999888877766777777776666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0057
                     AAA_23  86 y.......trsiererelskkkgkttkkaklellei..deleqfisellgskkiilnlilflgqerfeefelkdkkerleelek 160
                                +        ++++ + ++++ kg    +++ + +++  ++  + i++ ++s +++ ++++  +qe +  ++ k+  er e+l++
  gene98|gene98|rna98|rna98 530 RkvcfeqkVMCVTVDGTVYDPKGTLSGGKTNFRVNTvrRKDVEDIERAIESLEANKRRFDGVKQEYNGLLRSKTLHERREKLKE 613
                                144444445778888888888888887777777777777777888888888888888888888888777777777788888888 PP

                     AAA_23 161 eleeledekkllekl................................eqekekekeleeleeeleeilke 198
                                e+e l ++++ l +l                                e++k+ e++++e+e+e+ + ++e
  gene98|gene98|rna98|rna98 614 EMESLDTRISILSDLcengmnikeelravrekmvegmreknevdglmERRKKLENRIKEIESEILSSKEE 683
                                8888888888877777777766666666676667666666666666666666666666666666555555 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.056
                     AAA_23  86 y...trsiererelskkkgkttkkaklelleideleqfisellgskki.ilnlilflgqer.......feefel..kdkkerle 156
                                     ++i ++ e++ k+  + + ++++ + +de   +i e++g++ +  l + +++++e+            +   ++ erl+
  gene98|gene98|rna98|rna98 732 LhnrAMKIYNDVERKLKQVPQNDVEQERVCMVDEEVHKIAESVGISPRcLLIRKQCMAEEEknglkreL----EmiTNEMERLR 811
                                144457888999999999999999999999999999999999999988656888888888855533220....22233333444 PP

                     AAA_23 157 elekeleeledekkllekleqekekekeleelee 190
                                 +++++ +  +++ l ++++ ++e ++++++le+
  gene98|gene98|rna98|rna98 812 CMKRSTMDPANFDLLERNELMIEELKEKIDKLEK 845
                                4444444444444444444444444444444443 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.2
                     AAA_23  79 fenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskki......iln 133
                                f++++gr  r++++ ++ s+   ++++++   ++++   ++ ++el g + +      i++
  gene98|gene98|rna98|rna98 869 FKHINGRLGRFLRYFIPGSDARIDEKNGEYALKVKVGSWKESLNELSGGQRSlvalclIFS 929
                                8999999988888888999999999999999999998889999988887776555555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.6e-07    0.0023      19      46 ..      21      49 ..      11      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.6e-07
                     AAA_29 19 idlkg.atlltGpsGsGKSTllDAiqalL 46
                                +l+  +  +tG +GsGKS +lD i + L
  gene98|gene98|rna98|rna98 21 ANLDKsFNAITGMNGSGKSNVLDGILFAL 49
                               444445899***************98776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0021       6.2      14      31 ..      28      45 ..      17      85 .. 0.87
   2 ?   -3.1   0.1       3.5     1e+04      60      60 ..     199     199 ..     148     254 .. 0.49
   3 ?   -3.3   0.0       3.9   1.2e+04      46      67 ..     391     412 ..     379     453 .. 0.66
   4 ?    6.3   2.6    0.0042        13      71     123 ..     857     928 ..     509     945 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                               EEEEESTTSSHHHHHHHH CS
                               xxxxxxxxxxxxxxxxxx RF
                   ABC_tran 14 vaivGenGaGKStLlkll 31
                                ai+G nG+GKS +l  +
  gene98|gene98|rna98|rna98 28 NAITGMNGSGKSNVLDGI 45
                               59**********999766 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.5
                                C CS
                                x RF
                   ABC_tran  60 e 60 
                                +
  gene98|gene98|rna98|rna98 199 R 199
                                1 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.9
                                TCEGGGB-HHHCCHCEEEE-SS CS
                                xxxxxxxxxxxxxxxxxxxxxx RF
                   ABC_tran  46 gkdlkeqeleslrkeigvlpqe 67 
                                + +++e+e+e+lrk+ ++l  +
  gene98|gene98|rna98|rna98 391 KLKVSEDEIEELRKKARMLRSK 412
                                4445556666666666666554 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0042
                                -TTSBHHHH....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHH CS
                                xxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   ABC_tran  71 fpeltvren....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalaral 123
                                f++l  +en                     sd++i++   ++ lk  k   +k+s ++LSgGq++ val+ ++
  gene98|gene98|rna98|rna98 857 FDDLGYKENlkafkhingrlgrflryfipGSDARIDEKNGEYALKV-KVGSWKESLNELSGGQRSLVALCLIF 928
                                4444444446666666666666666666655555555555555554.4444566669**********998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1001 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1803  (0.100563); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 1.08u 0.33s 00:00:01.41 Elapsed: 00:00:00.54
# Mc/sec: 5617.51
//
Query:       gene981|gene981|rna980|rna980  [L=252]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-61  208.1   0.0    1.9e-61  207.9   0.0    1.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    2.2e-05   24.3   0.0     0.0093   15.8   0.0    2.2  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
    3.2e-05   24.5   0.0    6.5e-05   23.5   0.0    1.6  1  AAA_18           AAA domain
    0.00021   20.7   0.0      0.027   13.8   0.0    2.5  3  Gtr1_RagA        Gtr1/RagA G protein conserved region
     0.0014   18.9   0.0     0.0021   18.4   0.0    1.5  1  AAA_22           AAA domain
     0.0046   16.7   0.0        0.7    9.6   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
     0.0047   16.7   0.0     0.0064   16.2   0.0    1.3  1  AAA_24           AAA domain
     0.0067   16.8   0.0      0.061   13.7   0.0    2.4  2  RNA_helicase     RNA helicase
     0.0077   15.4   0.0      0.013   14.7   0.0    1.2  1  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.032   14.1   0.0    1.7  2  ATPase_2         ATPase domain predominantly from Archaea
      0.028   14.1   0.0      0.039   13.7   0.0    1.2  1  AAA_30           AAA domain
      0.041   13.8   0.0        7.7    6.4   0.0    2.4  2  RsgA_GTPase      RsgA GTPase
      0.046   13.9   0.0      0.071   13.3   0.0    1.2  1  AAA_33           AAA domain
      0.049   13.7   0.1       0.16   12.0   0.1    1.9  1  MMR_HSR1_Xtn     C-terminal region of MMR_HSR1 domain
      0.065   13.0   0.0        0.1   12.3   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
       0.11   12.1   0.0        3.7    7.0   0.0    2.4  2  GTP_EFTU         Elongation factor Tu GTP binding domain
       0.13   12.0   0.0       0.18   11.5   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.14   12.5   0.0       0.22   11.9   0.0    1.3  1  AAA_16           AAA ATPase domain
       0.15   12.5   0.0       0.28   11.6   0.0    1.4  1  AAA_17           AAA domain
       0.17   12.0   0.0       0.45   10.6   0.0    1.8  1  MMR_HSR1         50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.9   0.0   2.1e-64   1.9e-61       1     241 []       7     240 ..       7     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 207.9 bits;  conditional E-value: 2.1e-64
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresld 80 
                                    v GpaGsGK+tf+++++e+ e++grs++v+NLDPA  +++ + a+d r++it+ dvme++g+gpng+l vale l e++ 
  gene981|gene981|rna980|rna980   7 VFGPAGSGKSTFCRNIQEHGESIGRSYRVINLDPAQISTSDNYALDLRDFITVGDVMEEYGYGPNGGLLVALEELYENIS 86 
                                    89*****************************************************************************5 PP

                     ATP_bind_1  81 wldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhv 160
                                    +l  ele+ e ++l+fD+PGQielf hse + ki++  ++ f+ ++vy+++sq+l d  k+i+g++ al  m+r+++P +
  gene981|gene981|rna980|rna980  87 EL--ELEDLEGSFLIFDCPGQIELFVHSEIMPKIIDYVSRYFRCGIVYVMESQYLVDINKYINGCFCALISMARMNVPCI 164
                                    44..4444488********************************************************************* PP

                     ATP_bind_1 161 vvlnkfDllkeklekeleffedv.ealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllslideal 239
                                    +v++k+Dl+k   +++l++f  + e+ls+l+   +++y+ l + + +++ e ++  +f+pl+ +kee ie+l+ +id+a+
  gene981|gene981|rna980|rna980 165 NVISKMDLIK---NEDLDMFYTPnEDLSALIG--TGRYSGLCKRMLSFVAENNML-NFYPLDWNKEEYIEELIYCIDNAV 238
                                    ********99...5566666544144444443..3789*****************.***********************9 PP

                     ATP_bind_1 240 qe 241
                                    q+
  gene981|gene981|rna980|rna980 239 QY 240
                                    96 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     1e-05    0.0093       1      37 [.       9      45 ..       9      53 .. 0.91
   2 !    6.4   0.0    0.0079       7.1      83     142 ..      77     139 ..      72     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqsei 37
                                   Gp  sGKST++r++ +   + gr+  +++lD+ q + 
  gene981|gene981|rna980|rna980  9 GPAGSGKSTFCRNIQEHGESIGRSYRVINLDPAQIST 45
                                   899*****************************99765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0079
                         CLP1_P  83 lvkelareveekleenkkakasgliIntpGwvk.....glgaellleliealepdvvvvldqeel 142
                                    +++el+++++e le  ++ + s+li ++pG ++     ++  +++ ++ +++++ +v+v++++ l
  gene981|gene981|rna980|rna980  77 ALEELYENISE-LEL-EDLEGSFLIFDCPGQIElfvhsEIMPKIIDYVSRYFRCGIVYVMESQYL 139
                                    67888888884.444.479***********99854444556678888899999999999998654 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   7.2e-08   6.5e-05       1      25 [.       5      32 ..       5      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.2e-08
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf...g 25
                                   I++ G++G+GK+t+++++++++++   +
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQEHGESigrS 32
                                   99*******************8444552 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.027        24       2      65 ..       5      66 ..       4      74 .. 0.84
   2 !   13.8   0.0     3e-05     0.027      50     131 ..      97     180 ..      84     196 .. 0.70
   3 ?   -2.6   0.0       3.1   2.8e+03      76      91 ..     226     241 ..     219     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.027
                      Gtr1_RagA  2 vLLmGksgsGKtsmrsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveey 65
                                   ++  G+ gsGK++ ++ i +    + + r    i+++  ++ +++n  l+l D+    +++eey
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQEH--GESIGRSYRVINLDPAQISTSDNYALDLRDFITVGDVMEEY 66
                                   5678*********99999765..55677778889999999999999999999998888888887 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3e-05
                      Gtr1_RagA  50 lnlwDcgGqeafveeylssqkeeifrnvg.....vliyVfDvesreleedletlkeilealrqysp.eakvfvlihKmDl 123
                                    + ++Dc+Gq +++ ++  +   +i   v+      ++yV+ ++   l +  ++++ +++al  + + ++     i KmDl
  gene981|gene981|rna980|rna980  97 FLIFDCPGQIELFVHS--EIMPKIIDYVSryfrcGIVYVMESQ--YLVDINKYINGCFCALISMARmNVPCINVISKMDL 172
                                    6689*****9998774..445555555555555779****999..444444555778888877655244445579***** PP

                      Gtr1_RagA 124 iqederee 131
                                    i+++  + 
  gene981|gene981|rna980|rna980 173 IKNEDLDM 180
                                    *8765443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.1
                      Gtr1_RagA  76 nvgvliyVfDvesrel 91 
                                     ++ liy +D   + +
  gene981|gene981|rna980|rna980 226 YIEELIYCIDNAVQYY 241
                                    5677888888764434 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.3e-06    0.0021       7      58 ..       4      51 ..       2     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.3e-06
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllr 58
                                    ++v+G++G+GK+t +r+++e  +       ++ +v+  ++++ ++s++ + 
  gene981|gene981|rna980|rna980  4 AIFVFGPAGSGKSTFCRNIQEHGE----SIGRSYRVINLDPAQISTSDNYAL 51
                                   689****************99752....333566666666665555555555 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00078       0.7       4      47 ..       5      49 ..       2      59 .. 0.75
   2 ?    4.6   0.0     0.028        25      85     108 ..     156     178 ..      93     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00078
                      PduV-EutP  4 illiGkvgsGKttLtqalkge.elkYkktqaiefsdeviDtPGey 47
                                   i+++G+ gsGK t +++++++ e + ++   i++ ++ i t  +y
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQEHgESIGRSYRVINLDPAQISTSDNY 49
                                   899***************984134445666777777777777666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.028
                      PduV-EutP  85 asvfnkeviGiitkidlaedeeni 108
                                    ++ +n ++i +i k+dl  ++e++
  gene981|gene981|rna980|rna980 156 MARMNVPCINVISKMDLI-KNEDL 178
                                    356889***********9.55555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.2e-06    0.0064       1      44 [.       1      51 [.       1     114 [. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-06
                         AAA_24  1 kklkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfp 44
                                   +++ i+++Gp+g+GK+t+++++       g +  +i+++    s+ ++   
  gene981|gene981|rna980|rna980  1 MGYAIFVFGPAGSGKSTFCRNIqehgesiGRSYRVINLDPAQISTSDNYAL 51
                                   5789*****************988777776666666666544444444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.8e-05     0.061       1      22 [.       5      25 ..       5      65 .. 0.79
   2 ?    0.0   0.1       1.2   1.1e+03      70      92 ..     147     169 ..     115     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-05
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakal 22
                                   i+++Gp+g GKSt+++++ ++ 
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNI-QEH 25
                                   789*************94.443 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                   RNA_helicase  70 laelirlvsstpyplnmasleek 92 
                                       ++ l+s++ +++++ ++ +k
  gene981|gene981|rna980|rna980 147 NGCFCALISMARMNVPCINVISK 169
                                    55689999999999999998776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.4e-05     0.013      23      54 ..       5      36 ..       2      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                   EEEEESTTSSHHHHHHHHCCSHCCCCCCBTEE CS
                         NB-ARC 23 valvGmgGvGKttlakqilnksdevegrFdsv 54
                                   +++ G +G+GK+t  ++i ++ +++ + + ++
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQEHGESIGRSYRVI 36
                                   89*******************99999999765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.6e-05     0.032      23      57 ..       5      41 ..       2      67 .. 0.73
   2 ?   -2.1   0.0       3.2   2.9e+03     138     154 ..     223     239 ..     211     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                       ATPase_2 23 yfiYGpegsGKtaLlkeiienledkdk..yviyyial 57
                                   +f++Gp gsGK+++ ++i e  e+ +   +vi +++ 
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQEHGESIGRsyRVINLDPA 41
                                   8****************99988776542244444433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.2
                       ATPase_2 138 aellvkeLlnliesltk 154
                                    +e++++eL+++i++  +
  gene981|gene981|rna980|rna980 223 KEEYIEELIYCIDNAVQ 239
                                    78999999999998766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.4e-05     0.039      22      53 ..       6      39 ..       2      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                         AAA_30 22 vltGpAGtGKttalkalreaweaag..grviglA 53
                                   ++ GpAG+GK+t  + ++e+ e+ g  +rvi l 
  gene981|gene981|rna980|rna980  6 FVFGPAGSGKSTFCRNIQEHGESIGrsYRVINLD 39
                                   578******************9998677887665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0086       7.7     103     122 ..       6      25 ..       2      71 .. 0.83
   2 ?    5.0   0.0     0.024        21      38      66 ..     152     179 ..     142     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0086
                                    EEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 103 vlvGqSGvGKStLinallpe 122
                                    ++ G+ G GKSt+  +++++
  gene981|gene981|rna980|rna980   6 FVFGPAGSGKSTFCRNIQEH 25 
                                    678***********999876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.024
                                    HHHHHHHTT-EEEEEEE-GGG--HHHHHH CS
                    RsgA_GTPase  38 fLvlaeekgiepvivlnKiDlleeeeele 66 
                                    +L+ + + +++ + v++K+Dl+++e+ l+
  gene981|gene981|rna980|rna980 152 ALISMARMNVPCINVISKMDLIKNED-LD 179
                                    5888999999*************998.44 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     8e-05     0.071       2      25 ..       5      33 ..       5      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg......a 25
                                   +++ G++GsGKst+ +++  ++g      +
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQ-EHGesigrsY 33
                                   6889************965.4444555554 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00018      0.16      48      78 ..     153     183 ..     139     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                   MMR_HSR1_Xtn  48 viegnrvYipclyvlNKiDlisleeldelar 78 
                                     i+  r+ +pc+ v+ K+Dli++e+ld +++
  gene981|gene981|rna980|rna980 153 LISMARMNVPCINVISKMDLIKNEDLDMFYT 183
                                    57778899******************98876 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011       0.1       3      21 ..       7      25 ..       5      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                   EE-STTSSHHHHHHHHHHH CS
                 Cytidylate_kin  3 iDGPagsGKssvaralaek 21
                                   + GPagsGKs+ +r + e+
  gene981|gene981|rna980|rna980  7 VFGPAGSGKSTFCRNIQEH 25
                                   56************99765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.072        65       6      35 ..       5      34 ..       3     114 .. 0.74
   2 ?    7.0   0.0    0.0042       3.7     118     140 ..     156     179 ..     139     239 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.072
                                   EEEEESTTSSHHHHHHHHHHHTTSSCHHHH CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkge 35
                                   i + g   +GK+T++ ++ ++ + i ++ +
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQEHGESIGRSYR 34
                                   678899999****99999888777776554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
                                    HHHTTTEEEEEEESCGST.HHHHH CS
                       GTP_EFTU 118 alkegvpiivfiNKmDrl.kaelk 140
                                    + +++vp i +i KmD + +++l+
  gene981|gene981|rna980|rna980 156 MARMNVPCINVISKMDLIkNEDLD 179
                                    6679**************533333 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.18       2      24 ..       6      29 ..       5      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                Viral_helicase1  2 vvhGvpGcGKStlirkllrts.li 24
                                    v G +G+GKSt +r++ ++   i
  gene981|gene981|rna980|rna980  6 FVFGPAGSGKSTFCRNIQEHGeSI 29
                                   68999************9986533 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.22      27      47 ..       5      25 ..       2      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                         AAA_16 27 vllsGesGvGKsslvrellra 47
                                   +++ G++G+GKs+  r ++++
  gene981|gene981|rna980|rna980  5 IFVFGPAGSGKSTFCRNIQEH 25
                                   89**************99973 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.28       1      18 [.       8      25 ..       8      38 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                                   EE-TTSSHHHHHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklvek 18
                                   +G+ GsGK+t c++++e+
  gene981|gene981|rna980|rna980  8 FGPAGSGKSTFCRNIQEH 25
                                   699************986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0005      0.45       2      58 ..       5     107 ..       4     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                    EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE................................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke................................. 47 
                                    + ++G   +GKSt+ + + +  ++i  ++    +d+ ++  + +                                    
  gene981|gene981|rna980|rna980   5 IFVFGPAGSGKSTFCRNIQEHgESIGRSYRVINLDPAQISTSDN-YAldlrdfitvgdvmeeygygpnggllvaleelye 83 
                                    6799**************99877888888888888888877622.22445556666666677777777777777777777 PP

                                    .............EEEEECGGCSS CS
                       MMR_HSR1  48 .............ielvDtpGlie 58 
                                                 + + D+pG ie
  gene981|gene981|rna980|rna980  84 niseleledlegsFLIFDCPGQIE 107
                                    777777777777788999999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1644.75
//
Query:       gene982|gene982|rna981|rna981  [L=167]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1033.36
//
Query:       gene983|gene983|rna982|rna982  [L=583]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-30  105.3  24.5    2.7e-30  105.3  24.5    1.8  2  ABC2_membrane    ABC-2 type transporter
      3e-20   73.1   0.0    4.5e-20   72.6   0.0    1.3  1  ABC_tran         ABC transporter
    5.3e-06   25.8  25.9      7e-06   25.4  25.9    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    6.3e-05   22.5   0.0       0.28   10.6   0.0    2.3  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00023   21.1   0.8       0.14   12.0   0.1    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    0.00047   20.1   0.0    0.00088   19.2   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
     0.0013   19.0   0.3       0.72   10.1   0.1    2.4  2  AAA_22           AAA domain
     0.0021   17.7   0.1     0.0049   16.6   0.1    1.6  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.014   15.1   0.4      0.029   14.1   0.4    1.5  1  AAA_30           AAA domain
      0.016   14.8   0.3      0.026   14.1   0.3    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.043   14.3   0.1      0.078   13.5   0.1    1.3  1  AAA_23           AAA domain
      0.064   13.4   0.1       0.11   12.7   0.1    1.4  1  AAA_33           AAA domain
       0.07   13.2   0.1       0.16   12.1   0.1    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
       0.13   12.3   0.1       0.23   11.5   0.1    1.4  1  Dynamin_N        Dynamin family
       0.19   12.1   0.1       0.39   11.1   0.1    1.5  1  AAA_16           AAA ATPase domain
       0.39   11.0   1.2        1.5    9.1   1.2    1.9  1  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3  24.5   2.4e-33   2.7e-30       2     209 ..     310     519 ..     309     520 .. 0.96
   2 ?   -1.4   0.4       1.2   1.3e+03     129     148 ..     555     574 ..     541     578 .. 0.52

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 2.4e-33
                  ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg.nsedglnrpgllffsvlflafsaltsvapvfererg 80 
                                     +++++ r++  + r+  l      iq + ++ ++ +v+++l+ +++++++r g+l f+v+  +  a++ +++++ + ++
  gene983|gene983|rna982|rna982 310 SFFLVFERNLSDFSRSHGLM-KILSIQKFTTLSFLVFVYYRLDyTQKGIQDRFGILSFIVMSSFEKAAFISIIFISSHKK 388
                                    688999***********999.88999*****************8888888*************98888877799999999 PP

                  ABC2_membrane  81 vlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls..rfflflllllltalaasslgllisalapsf 158
                                     l+re  +++y + + ++a++++ l+vs + ++++++ vy++vgl+++  rf++f++++ +++l+++s+g+++s +++++
  gene983|gene983|rna982|rna982 389 ALKREVCAGMYGAITSYFANMASTLCVSGVPSILYIAGVYWIVGLNPDlfRFAFFVFIFAVVVLFSTSFGIIVSLYTKTL 468
                                    9******************************************************************************* PP

                  ABC2_membrane 159 edasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                      a++las +++ +++l+G f+++ s+p++++w  +++P++ya+e +++++
  gene983|gene983|rna982|rna982 469 IHAQILASTIVMTFTMLGGTFVNPGSIPGFIRWAIWISPVYYAFETVLQTQ 519
                                    **********************************************99987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                  ABC2_membrane 129 rfflflllllltalaasslg 148
                                     ++l+l++++++al a+s+ 
  gene983|gene983|rna982|rna982 555 TGILLLITIIFIALGAISMN 574
                                    34455555555555555554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0   4.1e-23   4.5e-20       3     137 .]      30     175 ..      28     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 4.1e-23
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                    + + k+k++e++++vG +GaGK+t+l+++ g+  +     Geill+g+ +++   +++++ +g++ ++ +  ++ tv+e+
  gene983|gene983|rna982|rna982  30 RAQGKVKPSEMTVLVGVSGAGKTTMLNAIVGKPMDglrVTGEILLNGHLVNT---KVWERAVGFVGEHLHSYETQTVEET 106
                                    66789***************************9999999*********9999...*************99999999**** PP

                                    ...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                   +  ee++ ++++lgl+ ++ t++    ss+S G+++r++l  +l+k+p++l++DE t+
  gene983|gene983|rna982|rna982 107 lrfavmisrglspgmAVGEEVSGLIRSLGLSRVAYTPI----SSISTGERVRLSLGITLAKRPSILIIDEVTN 175
                                    *************9999999******************....****************************997 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4  25.9   6.3e-09     7e-06     163     344 ..     361     570 ..     291     571 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.3e-09
                ABC2_membrane_3 163 lvgliliilifit..asfiavsiveEkesrik.elqlvsgvsplqywlskilgdflvyllqlllill..l.afglgipfg 236
                                    + +l +i++++    a+fi+  +++ +++ +k e+   +   +++ +++++ +++ v+ ++++l+++  + ++g  ++ +
  gene983|gene983|rna982|rna982 361 FGILSFIVMSS-FekAAFISIIFISSHKKALKrEVCAGM-YGAITSYFANMASTLCVSGVPSILYIAgvYwIVG--LNPD 436
                                    44422222222.234666776666666665551444444.89************************99536999..9888 PP

                ABC2_membrane_3 237 ..nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp.ledlpsalkwifsiiPffapglgl 313
                                       + ++++ f +  l ++++g  +s  +k+   aqil++ + +++ ++ gg+f+   ++p++++w+ +i P ++ ++  
  gene983|gene983|rna982|rna982 437 lfRFAFFVFIFAVVVLFSTSFGIIVSLYTKTLIHAQILASTIVMTFTML-GGTFVnPGSIPGFIRWAIWISPVYYAFETV 515
                                    66777777888889***********************988888845555.55555599********************** PP

                ABC2_membrane_3 314 lrlitgdplwe........................illsliilalfavvylllal 344
                                    l+      ++e                        +  s +il+l+++++++l++
  gene983|gene983|rna982|rna982 516 LQTQLEGLIFEckdsercisngkealnmygfkrvrYTVSTGILLLITIIFIALGA 570
                                    ***96666888999999999999999999999999999*************9987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00048      0.54      10      44 ..      23      58 ..      13      74 .. 0.77
   2 !   10.6   0.0   0.00025      0.28     138     199 ..     148     205 ..      93     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00048
                                   ETTEECEEEEEETTS.SEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 10 Fksyagktvilpfsk.sftaivGpNGSGKsnlldAi 44
                                   Fk    k++++++++ ++t++vG  G+GK+ +l+Ai
  gene983|gene983|rna982|rna982 23 FKEAIVKRAQGKVKPsEMTVLVGVSGAGKTTMLNAI 58
                                   555555666666665269*****************9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                                    -HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 138 SgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                    S Ge+      L + i  +k+ ++ ++De+   LD  n+  + ++l   +++   i+is+++
  gene983|gene983|rna982|rna982 148 STGERV----RLSLGITLAKRPSILIIDEVTNDLDSFNIIHILKILMDLKHRGKGIMISFQR 205
                                    556653....45556666788999************************99999999999875 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1     0.003       3.4       1      19 [.      40      58 ..      40      69 .. 0.93
   2 !   12.0   0.1   0.00012      0.14     231     287 ..     141     195 ..     105     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.003
                         AAA_21  1 lnvliGpNgsGKSnLLdal 19
                                   ++vl+G  g+GK++ L a+
  gene983|gene983|rna982|rna982 40 MTVLVGVSGAGKTTMLNAI 58
                                   69**************999 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00012
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsr 287
                                     +p++++S G +  l l   l+ ++   s+l+iDE+ n L+   + ++l++l ++++r
  gene983|gene983|rna982|rna982 141 YTPISSISTGERVRLSLGITLAKRP---SILIIDEVTNDLDSFNIIHILKILmDLKHR 195
                                    5788999999998888888888888...*********************999455444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.9e-07   0.00088      96     122 ..      34      61 ..       6     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.9e-07
                                    HCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpe 122
                                    ++k  +++vlvG SG+GK+t++na++++
  gene983|gene983|rna982|rna982  34 KVKPsEMTVLVGVSGAGKTTMLNAIVGK 61 
                                    4555589******************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00065      0.72       6      26 ..      39      59 ..      34      68 .. 0.87
   2 !    6.5   0.0    0.0085       9.5      90     119 ..     164     195 ..     130     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00065
                         AAA_22  6 gilvvtGesGtGKTtllrrll 26
                                    ++v++G sG+GKTt l+ ++
  gene983|gene983|rna982|rna982 39 EMTVLVGVSGAGKTTMLNAIV 59
                                   689*************98765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0085
                         AAA_22  90 avielliiDEaqh.lrseealeeLrsllnl..s 119
                                    + +++liiDE+ + l+s +++  L++l++l  +
  gene983|gene983|rna982|rna982 164 R-PSILIIDEVTNdLDSFNIIHILKILMDLkhR 195
                                    2.479********99889999999999998643 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.4e-06    0.0049      18      42 ..      34      58 ..      27      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.4e-06
                         AAA_29 18 eidlkgatlltGpsGsGKSTllDAi 42
                                   +++++++t+l+G sG+GK+T+l Ai
  gene983|gene983|rna982|rna982 34 KVKPSEMTVLVGVSGAGKTTMLNAI 58
                                   678899****************998 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   2.6e-05     0.029      18      40 ..      38      60 ..      30     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                         AAA_30 18 drvavltGpAGtGKttalkalre 40
                                     ++vl+G+ G+GKtt+l+a++ 
  gene983|gene983|rna982|rna982 38 SEMTVLVGVSGAGKTTMLNAIVG 60
                                   4589***************9975 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   2.3e-05     0.026       2      28 ..      40      67 ..      39      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                                   EEEEEESTTCCHHHHHHHHH.CT--SS- CS
                           cobW  2 vtvltGflGsGKTtLlnhll.enraglk 28
                                   +tvl+G  G+GKTt+ln+++ +  +gl+
  gene983|gene983|rna982|rna982 40 MTVLVGVSGAGKTTMLNAIVgKPMDGLR 67
                                   69*****************965555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     7e-05     0.078      20      39 ..      39      58 ..      33      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                         AAA_23 20 gltlItGpNGaGKTTildAi 39
                                    +t+++G  GaGKTT l+Ai
  gene983|gene983|rna982|rna982 39 EMTVLVGVSGAGKTTMLNAI 58
                                   58*****************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.7e-05      0.11       2      35 ..      41      75 ..      40     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg.avllssdtlrr 35
                                   ++lvG++G+GK+t +  ++ k   + +++  +l++
  gene983|gene983|rna982|rna982 41 TVLVGVSGAGKTTMLNAIVGKPMdGLRVTGEILLN 75
                                   789*************9997776788888877766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00014      0.16       3      22 ..      42      61 ..      40      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                   EEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                   ++vG + +GK+t++na++g+
  gene983|gene983|rna982|rna982 42 VLVGVSGAGKTTMLNAIVGK 61
                                   79****************97 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0002      0.23       2      22 ..      42      62 ..      41      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                   EEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N  2 avvGsqSsGKSSvlnaLlged 22
                                   ++vG   +GK+++lna++g++
  gene983|gene983|rna982|rna982 42 VLVGVSGAGKTTMLNAIVGKP 62
                                   689****************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00035      0.39      24      44 ..      37      58 ..      24      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                         AAA_16 24 p.elvllsGesGvGKsslvrel 44
                                   p e+++l+G sG GK+++++++
  gene983|gene983|rna982|rna982 37 PsEMTVLVGVSGAGKTTMLNAI 58
                                   25899*************9986 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.2    0.0014       1.5       7      78 ..      35     139 ..      28     201 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                         AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkp.....eeillvaftgrAakelrerlaalgaeatTiHrlal.... 77 
                                      ++++ ++++  G GKT++l++iv    +  +v        +++   + +rA+  + e l++++ +  T+ +  l    
  gene983|gene983|rna982|rna982  35 VKPSEMTVLVGVSGAGKTTMLNAIVGKPMDGLRVTGeillnGHLVNTKVWERAVGFVGEHLHSYETQ--TVEET-Lrfav 111
                                    5578899999**************9887776666433333222222334567777777776444333..33322.11222 PP

                         AAA_19  78 ...........................l 78 
                                                               +
  gene983|gene983|rna982|rna982 112 misrglspgmavgeevsglirslglsrV 139
                                    4555555555555555555555444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (583 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.52
# Mc/sec: 3405.35
//
Query:       gene984|gene984|rna983|rna983  [L=509]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3643.05
//
Query:       gene985|gene985|rna984|rna984  [L=286]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1874.01
//
Query:       gene986|gene986|rna985|rna985  [L=389]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-13   51.7   0.5    3.7e-13   49.9   0.2    2.0  2  PCI       PCI domain
    1.7e-09   38.1   0.8    1.6e-08   34.9   0.1    2.3  2  RPN6_N    26S proteasome regulatory subunit RPN6 N-terminal d
     0.0049   16.6   0.1        0.5   10.1   0.2    2.8  2  RPN7      26S proteasome subunit RPN7


Domain annotation for each model (and alignments):
>> PCI  PCI domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.56   3.3e+03      38      72 ..      49      85 ..      29      99 .. 0.74
   2 !   49.9   0.2   6.2e-17   3.7e-13       6     104 ..     264     362 ..     259     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.56
                                   HHHHHHHHHHHHHHHHHHH..CESEEEHHHHHHHHTS CS
                            PCI 38 llesLekkvrerllrqvsk..iyssislerlaklldl 72
                                   ++e+     +++ +r++++  +ys+  +e++ kll +
  gene986|gene986|rna985|rna985 49 VWEDITTPRITKIIRRLFEmiPYSQDNFEHVLKLLTV 85
                                   5666666667777778877778888888887777766 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 6.2e-17
                                    HHHHHHHTSHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHCESEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                            PCI   6 llkalrsgnlsgfseelkdleeelladdglaqllesLekkvrerllrqvskiyssislerlaklldlsvdevEkilvklI 85 
                                    +  ++ +++l ++s  l+ + e+l  d ++  +l++L++++  r++++++++ys +++  +a+ l++  d +Ek l k+I
  gene986|gene986|rna985|rna985 264 VSDSFGNRDLRSYSDVLQRYAEQLRCDSFVWSHLQYLYDVLLDRNIIKIIEPYSVVRINFIADVLGFEADIIEKKLRKMI 343
                                    567888999*********************************************************************** PP

                                    HTTSSSEEEETTTTEEEEC CS
                            PCI  86 rdgeirakidqesgivvfk 104
                                     d+ +++++d+ +++++++
  gene986|gene986|rna985|rna985 344 LDKVVDGTLDHIDECLILH 362
                                    ****************976 PP

>> RPN6_N  26S proteasome regulatory subunit RPN6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   2.7e-12   1.6e-08      24     116 ..       9     101 ..       2     102 .. 0.94
   2 ?    1.2   0.1     0.078   4.6e+02      33      98 ..     115     186 ..     110     189 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.7e-12
                         RPN6_N  24 skedeealreqeqalleLgelyrdqkkaeeLaelikesrsflssiaKaKtaKlvrtLldlfskipnslelqievlkesie 103
                                      ++e++l+e+e+a+le+ +++ ++++ +e+  +i + + + + i+  + +K++r+L++++   ++  e  +++l+  +e
  gene986|gene986|rna985|rna985   9 VGSKEATLEEKEEAVLEIFRVLISKGDYHEIGCVIMSLKGVWEDITTPRITKIIRRLFEMIPYSQDNFEHVLKLLTVLVE 88 
                                    4678899************************************************************************* PP

                         RPN6_N 104 wakeekriFLrqs 116
                                    wa +e++  Lr +
  gene986|gene986|rna985|rna985  89 WADKENKKMLRLD 101
                                    **********976 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.078
                         RPN6_N  33 eqeqalleLgelyrdqkkaeeLaelik....esrsf..lssiaKaKtaKlvrtLldlfskipnslelqievl 98 
                                    ++ +al ++g + ++ kk ++  +li+    es++f  ++si+K+K++    ++l + + +p  l+ qi++l
  gene986|gene986|rna985|rna985 115 KYSEALAQIGPVAHELKKYDDKINLITlyvyESKAFyeIKSISKSKSSLTSARVLAVSAYCPPQLQAQIDLL 186
                                    566788888887777777776666654332367776446899999998877777777777887777777765 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   8.3e-05       0.5     108     171 ..     168     240 ..      11     243 .. 0.73
   2 ?   -2.6   0.0      0.66   3.9e+03     131     154 ..     256     279 ..     255     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.3e-05
                                    .........HHHHHHHHHHHHHHHHHTT-HHHHHHHHCTS-GGGT.TTT--HHHHHH.HHHHHHHHH--HHHH CS
                           RPN7 108 d........werknrlkvyeGlallairkfkeAaellldilstftskellsyedlav.yavlcalatldRkdL 171
                                              + ++++   +G++ +  r++  A++ ++++l+ ft +++ s   + + y +l+ +++ +R+++
  gene986|gene986|rna985|rna985 168 VlavsaycpPQLQAQIDLLSGIYICDERNYGVASSYFIEALEGFTLGKMPSEACVSLrYLILSKIMAGKREEI 240
                                    24444444567788899999************************99777666666533666666666666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.66
                                    HHHHHHCTS-GGGT.TTT--HHHH CS
                           RPN7 131 eAaellldilstftskellsyedl 154
                                    e+ + ll +  +f++  l sy+d+
  gene986|gene986|rna985|rna985 256 EVIKVLLRVSDSFGNRDLRSYSDV 279
                                    677889999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2532.11
//
Query:       gene987|gene987|rna986|rna986  [L=157]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-09   36.4   0.1    4.7e-09   36.1   0.1    1.1  1  Fer2         2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
        0.1   12.2   0.1       0.19   11.4   0.1    1.4  1  MCR          Magnetochrome domain
       0.14   12.5   0.0       0.25   11.7   0.0    1.3  1  Pas_Saposin  Pas factor saposin fold


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.1   7.8e-13   4.7e-09       7      77 ..      53     129 ..      47     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 7.8e-13
                                    EEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSS.SSTTEEEEEESCE.CTT.SSSSTHHHHHTTEE.....EEGGGSEE CS
                           Fer2   7 evevevadgettlldaaeenggidipysCgggg.CgtClvevlegev.qsd.etelegeeldegkl.....rlaCqtiv 77 
                                     v v ++ g+t +l+ a +n g+ ++ +C+g+  C+tC+v ++e  + + + ++++e +  d+++      rl Cq +v
  gene987|gene987|rna986|rna986  53 MVPVKAVYGDT-VLETAHKN-GVNLEGACEGNLaCSTCHVILEESLYkRLGePSDKEYDLIDQAFGgtstsRLGCQLKV 129
                                    56677778999.88888889.**********99*******8888877855568888888888877799********998 PP

>> MCR  Magnetochrome domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.1e-05      0.19      17      27 ..      82      92 ..      81      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                   -S-GGGT--BS CS
                            MCR 17 nmnCtkCHqIi 27
                                   n +C++CH+I+
  gene987|gene987|rna986|rna986 82 NLACSTCHVIL 92
                                   679*******8 PP

>> Pas_Saposin  Pas factor saposin fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.1e-05      0.25      20      67 ..      89     136 ..      82     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.1e-05
                    Pas_Saposin  20 hakiRqnLYeqLdLsfdkqlaLYssvLGPassGkleddqalnnavesa 67 
                                    h  + + LY++L+ + dk++ L  ++ G +s+ +l  +  +++  e+a
  gene987|gene987|rna986|rna986  89 HVILEESLYKRLGEPSDKEYDLIDQAFGGTSTSRLGCQLKVDKNFENA 136
                                    5667789*************************9997665555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1026.94
//
Query:       gene988|gene988|rna987|rna987  [L=1249]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-25   90.0   0.0    2.9e-25   90.0   0.0    6.8  1  AAA_23         AAA domain
    6.1e-09   35.6  27.8    8.8e-07   28.6   0.0    3.0  2  SMC_N          RecF/RecN/SMC N terminal domain
    0.00016   21.5  70.7       0.47   10.1  26.0    4.6  2  AAA_15         AAA ATPase domain
    0.00046   20.4   0.0     0.0017   18.6   0.0    2.0  1  SbcCD_C        Putative exonuclease SbcCD, C subunit
    0.00063   19.6  22.9      0.001   19.0   0.0    4.5  3  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0014   18.4  10.7     0.0022   17.8   0.2    5.7  3  Rad50_zn_hook  Rad50 zinc hook motif
      0.002   17.9   0.0     0.0047   16.6   0.0    1.5  1  AAA_29         P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.038   13.7   0.0       0.17   11.6   0.0    2.1  2  AAA_30         AAA domain
      0.043   12.5   0.0      0.043   12.5   0.0    6.2  3  AAA_13         AAA domain
       0.24   11.8   0.7        3.1    8.1   0.0    2.8  2  AAA_19         AAA domain
       0.25   11.7   0.0       0.25   11.7   0.0    3.7  3  AAA_16         AAA ATPase domain
        6.4    7.0  14.0       0.42   10.8   0.1    3.8  4  AAA_28         AAA domain


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.0   1.9e-28   2.9e-25       1     194 [.       6     221 ..       6     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.9e-28
                         AAA_23   1 kLkienfrsf..rdqe.idFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                    kL ++++rsf  ++ + ++F ++ltlI+G NG+GKTTi++ +k++ +g  p++sr   +g++  d++++  ++v+++v+l
  gene988|gene988|rna987|rna987   6 KLMMRGIRSFshKESNiLEFYSPLTLIVGANGTGKTTIIESLKYVSTGSLPPNSR---GGAFIYDPRVAGLAEVQGQVKL 82 
                                    7899******65444567******************************8766555...79******************** PP

                         AAA_23  78 tfenkdgrytrsiererelskkkgkttkkaklellei...........deleqfisellgskkiilnlilflgqer.fee 145
                                     f n +g+ t+ ++r+ +ls+  gk+ +k+ ++ +              + + ++++++g++ + l++i+f++qe+ +++
  gene988|gene988|rna987|rna987  83 LFINVHGE-TMVCSRSLQLSQRRGKREQKTLESVVWAerdgggvsgrsGDVDIEMPQHFGVSSSVLENIIFCHQEEsTWP 161
                                    *******9.6********************87766553466666555555555566689999999966666666665555 PP

                         AAA_23 146 fel....kdkke...rleelekeleeledekkllekl....eqekekekeleeleeelee 194
                                    + +    k+k++   + e++ k+l+ l+  kk+         qe+e   + +e +e le 
  gene988|gene988|rna987|rna987 162 LGEpvvvKKKLDeifASEKYGKALDSLKSSKKECSSDikmkMQELEFLRKVKERKESLEA 221
                                    555544444444444444555555555555554333332222333333333333333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   5.9e-10   8.8e-07       1      48 [.       3      51 ..       3     113 .. 0.74
   2 !    5.8  25.7    0.0055       8.2      84     204 ..     394    1208 ..     350    1226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.9e-10
                                   EEEEEEEESETTEECEE.EEEETTSSEEEEEESTTSSHHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  1 vlkrleienFksyagkt.vilpfsksftaivGpNGSGKsnlldAilFvL 48
                                   +lk+l++++ +s+ +k+  il+f + +t ivG+NG GK+ +++++++v 
  gene988|gene988|rna987|rna987  3 FLKKLMMRGIRSFSHKEsNILEFYSPLTLIVGANGTGKTTIIESLKYVS 51
                                   699**********876516789*************************95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0055
                                     EETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......................... CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                          SMC_N   84 dnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.......................... 135 
                                     d +++++ +ek e +  r + ++++   ++ +k+    e+++l++++ i+ +                          
  gene988|gene988|rna987|rna987  394 DIKGRREYVEKLEEEFLRLKREDNDKMKTLSEKKRIVDEYKDLVNDESIDVSisheeeverlrtevgrdkemealeer 471 
                                     555555555555555555555555555556666666666666666666666666666666666666666666666666 PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987  472 ledyqrrlnnaysiaernfmvnqarnrkkeiekmlkevnvselrtrlerqrmelrekekkmkeiekevnlrkaemiqr 549 
                                     666666666666666666666666666666666666666666699999999999999999999999999999999999 PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987  550 ermndrirkdirmkatelrtmmqranistveglritrfydrsrynvkeakeivskngaffgedivafgvemldfegly 627 
                                     999999999999999999999999999999************************************************ PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987  628 dnnegqvvsneteglyreriyreiledgskshgcpvcnrsfsmeeeagfkrrlemeiekvldgkensvrnlervddva 705 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987  706 kevervnegimnrnkireeiielllryepdsdgvdseileemeldildevegikktefyielvselfsingklrdeee 783 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987  784 gesvqelksmidgvrkiyedkkrevkrkkemieylegkqekiraekeirrkinfreeakraieqiersnmrarindis 861 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987  862 eeicrrkgkvdkifekfsrkrvelemnmeifyqkekevvqlekeveelnvkakkllqvehceeardeakfdsvrndll 939 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987  940 ekknevlevgqrirmmhemrslaeesiryynkqkrieeiekelsetdfeylatlkekkrlleekkmnlisqkslllge 1017
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene988|gene988|rna987|rna987 1018 ckqialgiksckqelqkdhsrtvekynkcfielkalemacldldkciqaldkaiidfhtskleeinatlkdlwehtyr 1095
                                     ****************************************************************************** PP

                                     ....................................CS-HHHHHHHHHHHHHHHHC.CS--S.EEEECTTTTTS-HHH CS
                                     ....................................xxxxxxxxxxxxxxxxxxxx.xxxxx.xxxxxxxxxxxxxxx RF
                          SMC_N  136 ....................................lLSgGektLvalaLlfAiqk.vkpap.lyllDeidaaLDekn 175 
                                                                           S G+k ++++ +++A+ + +  ++ +  lDe   +LD  n
  gene988|gene988|rna987|rna987 1096 gddvdwieikteslgqktysykvvfikggvelemrgRSSAGQKMIASILIRLALSNsFASNCnILALDEPTTNLDRDN 1173
                                     *********************************99999***************7652444443899************ PP

                                     HHHHHHHHH....HHCTT..SEEEEE-SSHHHCCC CS
                                     xxxxxxxxx....xxxxx..xxxxxxxxxxxxxxx RF
                          SMC_N  176 vkkvaellk....ekskn..aQfivislreemlek 204 
                                     ++ +a  l     ++++n  +Q+ivi+++e++++ 
  gene988|gene988|rna987|rna987 1174 IESLAFTLSrvisRHKENsgFQLIVITHDEDFVQL 1208
                                     **9986554333266666569*********99875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1  26.0   0.00031      0.47      17     208 ..      21     481 ..       4     568 .. 0.55
   2 ?    3.7  36.7     0.029        43      73     369 .]     827    1206 ..     684    1206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00031
                         AAA_15  17 veidlseeltvliGkNnsGKSsilealdlFlnnkekkn.......................................... 54 
                                      +++ + lt+++G+N++GK++i+e l++  + + + n                                          
  gene988|gene988|rna987|rna987  21 NILEFYSPLTLIVGANGTGKTTIIESLKYVSTGSLPPNsrggafiydprvaglaevqgqvkllfinvhgetmvcsrslql 100
                                    44566666**************************8888999999999*********999999999999999999999999 PP

                         AAA_15  55 ................................................................................ 54 
                                                                                                                    
  gene988|gene988|rna987|rna987 101 sqrrgkreqktlesvvwaerdgggvsgrsgdvdiempqhfgvsssvleniifchqeestwplgepvvvkkkldeifasek 180
                                    99999998888877777777777777777777777777777766666666666666666666666666555555555544 PP

                         AAA_15  55 ..........................kkvikiekedleifeniseskdikIdvef......................... 83 
                                                              +                           f                         
  gene988|gene988|rna987|rna987 181 ygkaldslksskkecssdikmkmqelE---------------------------Flrkvkerkeslearikngcmsiern 233
                                    444444444444444443333332220...........................02222222222222222222333333 PP

                         AAA_15  84 ................................................................................ 83 
                                                                                                                    
  gene988|gene988|rna987|rna987 234 emklevydnevrrcesvieeidvellnneeaerkayvlrneyeelmsfvggfkerrlgleeardilrgesladaekryer 313
                                    34444444444444444444444445555555555555555566666666666666666666666666655555555555 PP

                         AAA_15  84 ................................aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknel 131
                                                                        ++++  ++l +++k+++   + ++es+l  t+  ++++l++ ++
  gene988|gene988|rna987|rna987 314 ikieseesetrfrylsekrsaylknkveldgvF---SEISVKSSLLDEAKRQKMEAFRNLESELLVTKDFRETALEAFRK 390
                                    555555555555555555555554443333221...12222222222222222223445555555555555555554444 PP

                         AAA_15 132 sdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee................elknvlksaii 195
                                      e i+   + +++e  +e+   l+ e+++  ++ +++k++ ++++  ++ e+                e++   + ++ 
  gene988|gene988|rna987|rna987 391 VEEDIK--GRREYVEKLEEEFLRLKREDNDKMKTLSEKKRIVDEYKDLVNDESidvsisheeeverlrtEVGRDKEMEAL 468
                                    444433..333344444444444444444444445555555555555555555555556666666666644444444444 PP

                         AAA_15 196 klllisakRnvsd 208
                                    + +l   +R  ++
  gene988|gene988|rna987|rna987 469 EERLEDYQRRLNN 481
                                    4444444444444 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.029
                         AAA_15   73 eskdikIdvef....................................aek.ekakeyektlkskekkkadl..llkkk 111 
                                      +                                             + k + +k++ek+++++ + ++++   ++k+
  gene988|gene988|rna987|rna987  827 AE--------KeirrkinfreeakraieqiersnmrarindiseeicRRKgKVDKIFEKFSRKRVELEMNMeiFYQKE 896 
                                     22........22222222233444444444444444444443333331122344444444444444333321033333 PP

                         AAA_15  112 esdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid.....kedlkklikkleeslkkee 184 
                                     ++  +  +++++l++k+++l +  ++ e + ++ ++++ +++ lek++e l++        ++++l ++ + + +k++
  gene988|gene988|rna987|rna987  897 KEVVQLEKEVEELNVKAKKLLQVEHCEEARDEA-KFDSVRNDLLEKKNEVLEVGqrirmMHEMRSLAEESIRYYNKQK 973 
                                     333344444444444444444444443333333.33334455555555555555444555555555555555555555 PP

                         AAA_15  185 elknvlksaiiklllisakRnvsdedsekkssllgklkek..ileealqekl.......................... 234 
                                                         ++++e+se   ++l +lkek  +lee+                               
  gene988|gene988|rna987|rna987  974 -----------------RIEEIEKELSETDFEYLATLKEKkrLLEEK----Kmnlisqkslllgeckqialgiksckq 1030
                                     .................333333333333333333332220022221....112234444444444444457666644 PP

                         AAA_15  235 ...................eeelteklkeiqeklkeidkklaeelk...kilkkkidkikkfnykgkkneeieik... 287 
                                                         + l+++  ++++ ++ +dk + +  +   ++++  ++++    y g ++  ieik   
  gene988|gene988|rna987|rna987 1031 elqkdhsrtvekynkcfieLKALEMACLDLDKCIQALDKAIIDFHTsklEEINATLKDLWEHTYRGDDVDWIEIKtes 1108
                                     445555555556555555534444444444444444444443333355555555555555666666666666666999 PP

                         AAA_15  288 ..............ddeelplnknGs.GvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllke 350 
                                                    ++el++  ++s G++ + ++++ ++  +      ++ +il+++EP ++L  ++ ++l+ +l +
  gene988|gene988|rna987|rna987 1109 lgqktysykvvfikGGVELEMRGRSSaGQKMIASILIRLALSNSF---ASNCNILALDEPTTNLDRDNIESLAFTLSR 1183
                                     99999999999999*******988774777777777777777777...999*************************** PP

                         AAA_15  351 landnkt....QviitTHSphii 369 
                                     +++ +k     Q+i+ TH + ++
  gene988|gene988|rna987|rna987 1184 VISRHKEnsgfQLIVITHDEDFV 1206
                                     ******9***********98875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0017      27      85 ..    1127    1178 ..    1111    1183 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                        SbcCD_C   27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatll 85  
                                      +++g+ S G+k ++a++ + +al+  + s      ++ +++LDE   +lD ++i++l 
  gene988|gene988|rna987|rna987 1127 LEMRGRSSAGQK-MIASILIRLALSNSFAS------NCNILALDEPTTNLDRDNIESLA 1178
                                     5688999*****.*****************......59*****************9986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.7e-07     0.001       1      34 [.      29      56 ..      29     114 .. 0.74
   2 ?   -1.4   0.1       1.1   1.6e+03      96     172 ..     256     331 ..     228     370 .. 0.75
   3 !   13.5   1.9     3e-05     0.045     220     299 ..    1115    1203 ..     724    1207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.7e-07
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltd 34
                                   l++++G+Ng+GK+++++ l++++      +g+ +
  gene988|gene988|rna987|rna987 29 LTLIVGANGTGKTTIIESLKYVS------TGSLP 56
                                   69*****************8884......34444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                         AAA_21  96 sgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnif 172
                                      ll +++++++  v  +e+++  + v +f+++ l ++e+ d  +g+ l d  +r+++++ +++++   r+++l+  
  gene988|gene988|rna987|rna987 256 VELLNNEEAERKAYVLRNEYEELMSFVGGFKERRLGLEEARDILRGESLADAEKRYERIKIESEESET-RFRYLSEK 331
                                    46677888888888888888888888888888888888888888888888888888888888887765.44444433 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 3e-05
                         AAA_21  220 gvvflengdgqelparel.SdGtkrllalltallralkkg...sllliDEpEngLHPkllrrll....ell.kelsrn 288 
                                      +  +  ++g el +r   S G+k ++ +l  l+  ++ +    +l++DEp ++L+   +++l+    +++ + +++ 
  gene988|gene988|rna987|rna987 1115 SYKVVFIKGGVELEMRGRsSAGQKMIASILIRLALSNSFAsncNILALDEPTTNLDRDNIESLAftlsRVIsRHKENS 1192
                                     55666667777777777755566666666666666666669999*************999999987778887666669 PP

                         AAA_21  289 gaQviltTHSp 299 
                                     g Q+i+ TH+ 
  gene988|gene988|rna987|rna987 1193 GFQLIVITHDE 1203
                                     9********95 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.6      0.41   6.1e+02       6      22 ..     179     195 ..     177     222 .. 0.79
   2 !   17.8   0.2   1.5e-06    0.0022       7      47 ..     647     686 ..     644     688 .. 0.85
   3 ?    1.2   0.5      0.22   3.3e+02       1      21 [.     902     922 ..     902     922 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.41
                                    HHHHHHHHHHTT-SEE- CS
                  Rad50_zn_hook   6 eelnkkieelkeakgcC 22 
                                    e + k+++ lk++k  C
  gene988|gene988|rna987|rna987 179 EKYGKALDSLKSSKKEC 195
                                    78999999999999876 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.5e-06
                                    HHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHHHH CS
                  Rad50_zn_hook   7 elnkkieelkeakgcCPlCgReldeehrseLikelqskler 47 
                                     +++++e  ++++  CP+C R+++ e+ + + ++l+ ++e+
  gene988|gene988|rna987|rna987 647 IYREILEDGSKSH-GCPVCNRSFSMEEEAGFKRRLEMEIEK 686
                                    5777777777777.9********************999986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHHHHHTT-SEE CS
                  Rad50_zn_hook   1 lhqeteelnkkieelkeakgc 21 
                                    l++e eeln k+++l ++++c
  gene988|gene988|rna987|rna987 902 LEKEVEELNVKAKKLLQVEHC 922
                                    6899***************77 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.1e-06    0.0047      24      48 ..      29      53 ..      14      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.1e-06
                         AAA_29 24 atlltGpsGsGKSTllDAiqalLvp 48
                                    tl++G++G+GK+T++ +++++ ++
  gene988|gene988|rna987|rna987 29 LTLIVGANGTGKTTIIESLKYVSTG 53
                                   69****************9998765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.17      20      77 ..      29      98 ..      21     118 .. 0.73
   2 ?   -3.4   0.0       4.3   6.5e+03     146     169 ..     351     374 ..     340     392 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                         AAA_30 20 vavltGpAGtGKttalkalreaweaa.g...........grviglAptgkaAkvLaeelgieastiakll 77
                                   +++++G+ GtGKtt++++l+ + + +              rv+glA  + + k L  ++  e++   + l
  gene988|gene988|rna987|rna987 29 LTLIVGANGTGKTTIIESLKYVSTGSlPpnsrggafiydPRVAGLAEVQGQVKLLFINVHGETMVCSRSL 98
                                   789****************998887644777778888777788888777777666655555555555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.3
                         AAA_30 146 igtaeLtevvRqkeseeraaalal 169
                                     ++  L+e  Rqk +++r++  +l
  gene988|gene988|rna987|rna987 351 VKSSLLDEAKRQKMEAFRNLESEL 374
                                    577889999999998888875554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05     0.043      15      55 ..      26      66 ..      11      87 .. 0.78
   2 ?    0.8   4.0     0.099   1.5e+02     380     456 ..     180     254 ..     165     280 .. 0.65
   3 ?    4.4  11.4    0.0081        12     335     597 ..     929    1222 ..     921    1237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                         AAA_13 15 fkriNliYGwNGaGKTtLSrllrslelgetepkfangsiei 55
                                    +   li G+NG+GKTt+ + l+ +++g+  p+   g++++
  gene988|gene988|rna987|rna987 26 YSPLTLIVGANGTGKTTIIESLKYVSTGSLPPNSRGGAFIY 66
                                   4667899**********************999999888855 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.099
                         AAA_13 380 khNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrde 456
                                    k+ +  ++l+++k+e+ ++++  + e l + l + k+ +++le+ i++   +++ +e +l+ +++e++  e  ++++
  gene988|gene988|rna987|rna987 180 KYGKALDSLKSSKKECSSDIKMKMQE-L-EFLRKVKERKESLEARIKNGCMSIERNEMKLEVYDNEVRRCESVIEEI 254
                                    44455666777777777777664443.3.445566677777777777777777777777777777777766666544 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0081
                         AAA_13  335 eqLkglqraleaKrkepfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv........ 404 
                                     ++++++++ l +K++e+ +      v ++i  + +  + ++e+i+ +N++    e eke  ++++e+           
  gene988|gene988|rna987|rna987  929 AKFDSVRNDLLEKKNEVLE------VGQRIRMMHEMRSLAEESIRYYNKQKRIEEIEKELSETDFEYLATlkekkrll 1000
                                     5677777778788776666......78888888888888999999999888888888888888888877678888888 PP

                         AAA_13  405 .........................eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd.e 456 
                                                              +++++el+   k+ +++ ++ +k   elk+ e +   l++ i++L k + d +
  gene988|gene988|rna987|rna987 1001 eekkmnlisqkslllgeckqialgiKSCKQELQ---KDHSRTVEKYNKCFIELKALEMACLDLDKCIQALDKAIIDfH 1075
                                     888889999999999999888888788888876...666777779999999**********************99857 PP

                         AAA_13  457 kpaaeeinkeLka.....f.GlgeleLkfeee.....kkgYriv.rkggsqaa..etLSeGEktaIaflYFlkslked 520 
                                     +   eein  Lk+     + G   + +++  e     +  Y++v +kgg + +  +  S G k +  +l  l++ ++ 
  gene988|gene988|rna987|rna987 1076 TSKLEEINATLKDlwehtYrGDDVDWIEIKTEslgqkTYSYKVVfIKGGVELEmrGRSSAGQKMIASILIRLALSNSF 1153
                                     788********8544444889999999999989996666677652445433332377888988888888777777744 PP

                         AAA_13  521 dseigkdkivviDDPvSSLDsnsl.fivfsliksrll.kkkkakQlfiLTHnleffkevkkntkrkrkkkeesfyllk 596 
                                      s   +  i  +D P   LD + +  ++f+l +   + k+++  Ql++ TH  +f + +++          e+fy+l+
  gene988|gene988|rna987|rna987 1154 AS---NCNILALDEPTTNLDRDNIeSLAFTLSRVISRhKENSGFQLIVITHDEDFVQLLSRD-------GPEHFYRLN 1221
                                     44...559************755515666666555576788889***********9998775.......235666666 PP

                         AAA_13  597 k 597 
                                     +
  gene988|gene988|rna987|rna987 1222 R 1222
                                     5 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0021       3.1       8      29 ..      25      46 ..      19      58 .. 0.84
   2 ?    0.2   0.2      0.59   8.9e+02      88     115 ..     407     437 ..     354     450 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                         AAA_19  8 lkekvllvtaGpGtGKTrvlkh 29
                                   + +++ l+++  GtGKT++++ 
  gene988|gene988|rna987|rna987 25 FYSPLTLIVGANGTGKTTIIES 46
                                   6678899************985 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.59
                         AAA_19  88 lelle....eaeeekklqeeellivDEfqdvd 115
                                     e+l+    ++++ k+l +e+  ivDE+ d+ 
  gene988|gene988|rna987|rna987 407 EEFLRlkreDNDKMKTL-SEKKRIVDEYKDLV 437
                                    33444556444445555.77788899998874 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.25      25      45 ..      28      48 ..      19      79 .. 0.81
   2 ?   -0.6   0.1         1   1.5e+03      51     120 ..     266     326 ..     256     416 .. 0.59
   3 ?   -1.5   0.1       1.9   2.9e+03       3      18 ..     459     474 ..     457     486 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                         AAA_16 25 elvllsGesGvGKsslvrell 45
                                   +l+l++G+ G+GK++++++l+
  gene988|gene988|rna987|rna987 28 PLTLIVGANGTGKTTIIESLK 48
                                   789**************9998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                         AAA_16  51 dggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleealaavpelagaeasrll 120
                                    +++++lr ++++l       + ++  +++++l  +++++    e  a++ek  e+++     + ++++r++
  gene988|gene988|rna987|rna987 266 RKAYVLRNEYEEL-------MsFVGGFKERRLGLEEARDILRGESLADAEKRYERIK---IESEESETRFR 326
                                    3488888888888.......3377777443333333333333333333333333333...11111112222 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.9
                         AAA_16   3 vGReeeleqLlsaler 18 
                                    vGR++e+e+L++ le+
  gene988|gene988|rna987|rna987 459 VGRDKEMEALEERLED 474
                                    8*********999885 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00028      0.42       3      20 ..      31      48 ..      29      69 .. 0.90
   2 ?   -2.4   0.1       3.4     5e+03      98      98 ..     264     264 ..     189     323 .. 0.53
   3 ?    1.2   4.2      0.27     4e+02      58     144 ..     466     559 ..     420     575 .. 0.76
   4 ?   -3.5   0.0       7.2   1.1e+04      28      65 ..     645     685 ..     642     694 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                         AAA_28  3 vitGgestGKTtlleaLa 20
                                    i+G+ +tGKTt++e L+
  gene988|gene988|rna987|rna987 31 LIVGANGTGKTTIIESLK 48
                                   699************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.4
                         AAA_28  98 a 98 
                                    a
  gene988|gene988|rna987|rna987 264 A 264
                                    1 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.27
                         AAA_28  58 rvleeqleeeaaaaankvlfcDrglldtlaYaraygge.aeaeleaaar..ekrydlvfllppap...ei.dddgeRred 130
                                    + lee+le+++++ +n + + +r+++ + a  r  ++e   +e++  +   + + +++ l + ++   ei ++ + R+ +
  gene988|gene988|rna987|rna987 466 EALEERLEDYQRRLNNAYSIAERNFMVNQARNRKKEIEkMLKEVNVSELrtRLERQRMELREKEKkmkEIeKEVNLRKAE 545
                                    4589999999********************9999988854445443333013333333333333344488999999**99 PP

                         AAA_28 131 leereaiderlrea 144
                                    + +re++++r+r+ 
  gene988|gene988|rna987|rna987 546 MIQRERMNDRIRKD 559
                                    *********99975 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 7.2
                         AAA_28  28 pEaareileeklakgedalpwv.e...dllafaervleeqle 65 
                                    ++++reile++++++++  +   +   +   f +r+le+++e
  gene988|gene988|rna987|rna987 645 ERIYREILEDGSKSHGCPVCNRsFsmeEEAGF-KRRLEMEIE 685
                                    56788999988888875444322222122233.344556555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2691  (0.150092); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 1.38u 0.35s 00:00:01.73 Elapsed: 00:00:00.56
# Mc/sec: 6737.46
//
Query:       gene989|gene989|rna988|rna988  [L=214]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-05   23.1   0.6       0.17   11.9   0.3    2.8  2  Mis12     Mis12 protein
  ------ inclusion threshold ------
       0.16   11.8   0.1         24    4.8   0.0    2.3  2  RFX5_N    RFX5 N-terminal domain


Domain annotation for each model (and alignments):
>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00019       1.7       3      33 ..       7      37 ..       6      53 .. 0.84
   2 !   11.9   0.3   1.9e-05      0.17      70     120 ..      53     124 ..      41     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00019
                                   HHHHCTHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Mis12  3 tehlgftPqsliddiinavndllyravdave 33
                                    e++gf P++l+ +    ++ +l ++v+++ 
  gene989|gene989|rna988|rna988  7 IEFFGFVPVTLVAELQSEIEGILRDGVEQLS 37
                                   69*********************99998864 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHHHHHHHHHHCTS---HHHHCCCHCCHH...CCTTS.........................HHHHHHHHHHHH CS
                          Mis12  70 asvDknfdkfElyvlrniltipeelvewvrLphd...eglel.........................eerldeeieelr 120
                                    +s+ +n+  f  +vlrnil+ p+     +rL+ +       +                           rl+e+i+  r
  gene989|gene989|rna988|rna988  53 ESFRRNYFIFSNFVLRNILRFPP----SFRLERKandA---VvtidlqsitdelvnvlgeedyyeaeVLRLKESIDIER 124
                                    677788889999***********....*****995440...33444444555555566554443322111444444444 PP

>> RFX5_N  RFX5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0027        24      14      34 ..      20      41 ..      15      43 .. 0.82
   2 ?    4.5   0.0    0.0033        29      12      49 ..     137     174 ..     133     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0027
                         RFX5_N 14 avqsKvdgiLqd.veKFtDleK 34
                                     qs ++giL d ve+ + l+K
  gene989|gene989|rna988|rna988 20 ELQSEIEGILRDgVEQLSFLDK 41
                                   57********997898887776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0033
                         RFX5_N  12 cKavqsKvdgiLqdveKFtDleKLYLYLqLPsGpssgd 49 
                                    +K v s +++i+       ++ KLY  + + sG+   d
  gene989|gene989|rna988|rna988 137 SKPVNSLIESIMEAYSELENVTKLYDKMSMISGMDDED 174
                                    899**********************9999999986555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1313.33
//
Query:       gene990|gene990|rna989|rna989  [L=376]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.7e-117  392.1   8.3   8.2e-117  390.5   8.3    1.6  1  Actin_micro     Putative actin-like family
  ------ inclusion threshold ------
      0.023   14.6   0.5      0.045   13.6   0.5    1.5  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.5   8.3  9.2e-121  8.2e-117       1     369 []      15     376 .]      15     376 .] 0.99

  Alignments for each domain:
  == domain 1  score: 390.5 bits;  conditional E-value: 9.2e-121
                    Actin_micro   1 ieqIttanKnitsffmrsdnSyfvkekeryaaYrkdedrvlivvvedkliisekevetddyfykselnkeeeeglieegk 80 
                                    i+qItt+nKni+sffmrsd+Sy+++ek+r+a+Yr+de++++i+v+++kl ++ ++++++d+fy + +n            
  gene990|gene990|rna989|rna989  15 IDQITTPNKNIQSFFMRSDASYYADEKHRMANYRTDEQIIHILVWNNKLLVESESIDLGDFFYLTGMN------------ 82 
                                    89******************************************************************............ PP

                    Actin_micro  81 iaknikkvsldklfktikeivysLesevl...lkeelkpkdiFvslvfkdtlnrseilalvdlflnisgfkGilllPesL 157
                                              +k f +++e+v++L+++++    k ++kp  +Fvslvf+d+lnr+e+lal++lf+n+++fkGil++P+sL
  gene990|gene990|rna989|rna989  83 ----------TKRFGSLEECVGWLGNQISdvlRKLKIKPGSSFVSLVFQDLLNRTEVLALCNLFINVLSFKGILITPRSL 152
                                    ..........789**************99988999********************************************* PP

                    Actin_micro 158 alclglgiqsaiviseyekhttvslveDyvlldsftvkrekstnlsladeedfvdefrkleelkekkefsCkvCdvkfev 237
                                    ++++g+   +++v++ ye+ tt+++veD+++ld ++v+re +++++l+d+ dfvdef+k+++++ek+ fsC++Cd+k+e+
  gene990|gene990|rna989|rna989 153 SQAIGTLSPNCVVVNLYEQYTTICFVEDFWMLDGICVSRECNKGFELIDSVDFVDEFNKIKVFEEKNIFSCDKCDYKDET 232
                                    ******************************************************************************** PP

                    Actin_micro 238 .ekiseHllkkHii..........kehvkehiteyknkhkdviekigkrlraklsklerlkkinskvifidldnvtisel 306
                                      k+++H+l+ H            +eh+k+h + y  ++ d++e i+kr  ++lsk e+ kki skvi++++  + +se+
  gene990|gene990|rna989|rna989 233 eAKMEAHFLSLHQEesvchtdvgqSEHFKMHFRVYDGEEGDIHELIAKRTIHVLSK-EKAKKIGSKVIVFNYGGMGLSEE 311
                                    99******************************************************.*********************** PP

                    Actin_micro 307 keklafetanvvpeii..eeakessilrgakvlkelevsKelWlTDkEWnsvrlRvLKeKvLFyl 369
                                    +   afe++ + pei+  ee++es+i +++ +++ l++ Ke+W+TDkEWn ++lRvLKeKvLF++
  gene990|gene990|rna989|rna989 312 CLGRAFEEYGINPEISmhEEPNESMITNVMVAFSGLDCVKEIWMTDKEWNGAGLRVLKEKVLFII 376
                                    ***************9989999*****************************************97 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5     5e-06     0.045      17      35 ..     216     234 ..     212     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-06
                                    SCCCEEEESSSS-EEESSC CS
                 RNA_POL_M_15KD  17 kegknfeCrqCgYeepadq 35 
                                    +e+++f C++C+Y+ ++++
  gene990|gene990|rna989|rna989 216 EEKNIFSCDKCDYKDETEA 234
                                    56666***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2372.78
//
Query:       gene99|gene99|rna99|rna99  [L=627]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-15   56.2   2.6    6.9e-15   55.1   2.6    1.5  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.013   14.7   0.2      0.013   14.7   0.2    1.8  2  Zip         ZIP Zinc transporter
      0.068   13.2   3.9      0.095   12.8   0.1    2.5  2  DUF4501     Domain of unknown function (DUF4501)
       0.12   12.5   0.8       0.42   10.7   0.1    2.2  2  DUF2973     Protein of unknown function (DUF2973)
       0.46   10.4   2.4          8    6.4   0.0    3.0  2  DUF2970     Protein of unknown function (DUF2970)


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   2.6   1.9e-18   6.9e-15      27     195 ..     428     598 ..     404     615 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.9e-18
                                HHHHHHHHHHHHH..HHHCHHHHHHHHHHHHHTT-.SS-TT-EEESS....SEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHT CS
                 MS_channel  27 llavlGalglalg..lalkdlisnlvaGiillfek.pfkiGDlveig....dieGtVediglrttkirtfdgrivtiPnsslvt 103
                                 ++  G++++  g  + + +  ++++++ii+lf   p++iGD+v +     +    V +++ ++t + ++dg ++ti n  l++
  gene99|gene99|rna99|rna99 428 GVTTIGMISAFFGtqFISNSFSASVISSIIFLFFIhPYDIGDRVFVTlegiEENLVVSELNVFSTVFYRWDGVYITILNTVLAQ 511
                                3444555555444337778888999***99998755**********999666667899************************** PP

                                S-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHH CS
                 MS_channel 104 snieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefgdsslnfevrvfvktvvpeeylsv 187
                                ++i+Nl+r sg +    +i+++  +++kkl ++ e + +++k++pe+ ++  +l++    ++s l ++v++ +k+    +++++
  gene99|gene99|rna99|rna99 512 KAIKNLRR-SGIMAESHKIQINSRTNQKKLIRLKELIEDFVKSNPEDYTEYIMLNHEYIEDASKLHMKVYMQYKS----NWQNF 590
                                ********.****************************************88888888888888888888888888....77777 PP

                                HHHHHHHH CS
                 MS_channel 188 qseinlri 195
                                + +++++ 
  gene99|gene99|rna99|rna99 591 ELYLRRKT 598
                                77777773 PP

>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   3.8e-06     0.013     244     331 ..      76     174 ..      69     176 .. 0.83
   2 ?   -3.6   0.3       1.4   4.8e+03     256     285 ..     430     460 ..     429     460 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-06
                        Zip 244 kavllnllfaltaplGiliGilvrsisessgaeivsgillalsaGtflYvalvellp.hEllnek..........gssslkqsl 316
                                +++l  + ++++a+++  i + v   +es ++  +  +l+ +s G+f+ +al  +++ + +l  k           +++l++++
  gene99|gene99|rna99|rna99  76 WILLVGISLSILAVCCWNIQVDVKDRNESIYSIRARDVLFTCSLGVFIFIALNFVISkMSFLGLKrsnslntlfyYTNELSEHI 159
                                55567777777777777777777778899999999*********************8655555447779******889****** PP

                        Zip 317 lqllglllGfalmll 331
                                ++ ++++lGf lmll
  gene99|gene99|rna99|rna99 160 SAGIIFTLGFSLMLL 174
                                *************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
                        Zip 256 aplGiliGilvrs.isessgaeivsgillal 285
                                + +G++ +++ ++ is+s  a+++s+i++ +
  gene99|gene99|rna99|rna99 430 TTIGMISAFFGTQfISNSFSASVISSIIFLF 460
                                6789999988555899999999999988865 PP

>> DUF4501  Domain of unknown function (DUF4501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.7e-05     0.095      90     126 ..     117     154 ..      87     160 .. 0.83
   2 ?    0.3   0.8      0.18   6.6e+02      87     108 ..     434     455 ..     419     464 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                    DUF4501  90 lllgtl.fislfLilsvasffylkrssklPkvfYrrnk 126
                                  lg++ fi+l  ++s  sf+ lkrs+ l ++fY +n 
  gene99|gene99|rna99|rna99 117 CSLGVFiFIALNFVISKMSFLGLKRSNSLNTLFYYTNE 154
                                45676548**************************9985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
                    DUF4501  87 aaslllgtlfislfLilsvasf 108
                                 +s ++gt fis     sv s 
  gene99|gene99|rna99|rna99 434 MISAFFGTQFISNSFSASVISS 455
                                5799*******98776666442 PP

>> DUF2973  Protein of unknown function (DUF2973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.74   2.7e+03       4      34 ..     113     143 ..     112     158 .. 0.75
   2 ?   10.7   0.1   0.00012      0.42       5      35 ..     500     534 ..     499     548 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.74
                    DUF2973   4 llYilaftvlaflAvanLirslitlsadsqr 34 
                                +l+   + v  f+A++  i  +  l+ ++++
  gene99|gene99|rna99|rna99 113 VLFTCSLGVFIFIALNFVISKMSFLGLKRSN 143
                                5788888899999999999888887777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                    DUF2973   5 lYilaf.tvlaflAvanLirslitlsadsqr...k 35 
                                +Yi+++ tvla  A++nL rs i++++++ +   +
  gene99|gene99|rna99|rna99 500 VYITILnTVLAQKAIKNLRRSGIMAESHKIQinsR 534
                                577766599***************98887763321 PP

>> DUF2970  Protein of unknown function (DUF2970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0022         8      11      49 ..     135     174 ..     130     175 .. 0.90
   2 ?    2.1   0.7     0.051   1.8e+02      32      44 ..     409     421 ..     407     424 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0022
                    DUF2970  11 affGVrkgknrerDfaqls.plhviivGlilaalfvllLi 49 
                                +f+G++++  ++  f  ++ ++  i +G+i+++ f l+L+
  gene99|gene99|rna99|rna99 135 SFLGLKRSNSLNTLFYYTNeLSEHISAGIIFTLGFSLMLL 174
                                89999999999999998888999************98885 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.051
                    DUF2970  32 hviivGlilaalf 44 
                                 vii+Glila+l 
  gene99|gene99|rna99|rna99 409 KVIIAGLILAMLY 421
                                79********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.52
# Mc/sec: 3645.56
//
Query:       gene991|gene991|rna990|rna990  [L=213]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-07   32.1   8.8    1.8e-07   32.1   8.8    2.2  2  CDC37_N     Cdc37 N terminal kinase binding
  ------ inclusion threshold ------
       0.21   11.5   0.3       0.45   10.4   0.0    1.8  1  bacHORMA_1  Bacterial HORMA domain family 1


Domain annotation for each model (and alignments):
>> CDC37_N  Cdc37 N terminal kinase binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   8.8     2e-11   1.8e-07       5     125 ..       3     137 ..       2     141 .. 0.67
   2 ?    0.4   0.1      0.13   1.2e+03      89     119 ..     169     199 ..     147     210 .. 0.48

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2e-11
                        CDC37_N   5 skWDklELSDDsDievHPNVDkrsfirwKqrdihekreqrkaeikklklereindkllkridkllealkekeveeeevvf 84 
                                    sk+  ++L +D++ e HPN+D +s   wK+r+  +kr + +++++++++ ++  ++++++ +++   lk + v  ++ +f
  gene991|gene991|rna990|rna990   3 SKYSGINLDSDEEEEIHPNIDEKSYKEWKRRQREQKRRELEQRLQEINSINDPGEEMIEEKNEIERILKPSYVCLDTESF 82 
                                    89999*********************************999999999999999999999999999988888777755555 PP

                        CDC37_N  85 kalnesleekkekedkpkae.....k.........eeeqptydem.leklldqvkk 125
                                    +  +e+  ek+  ++ +        +         + ++++++ + l++l +q+k+
  gene991|gene991|rna990|rna990  83 RIPSEDS-EKDYIQELEYLIvhnelDnfielmnqsKINMEKFEVVvLHNLAEQIKE 137
                                    5444444.222222221111222220222232222344455554446666666665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.13
                        CDC37_N  89 esleekkekedkpkaekeeeqptydemlekl 119
                                    ++l++k++k++ ++  +++ ++t + +le+ 
  gene991|gene991|rna990|rna990 169 AQLTNKEKKKQFEEDCRKDFEETKRMFLEEF 199
                                    3332333333333222222233333334444 PP

>> bacHORMA_1  Bacterial HORMA domain family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     5e-05      0.45      35      96 ..      83     144 ..      75     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5e-05
                     bacHORMA_1  35 gkpsdeeiedyeedievllkagyLdtvdlgfksngkwievtavryavdldgssltddrpGkv 96 
                                      ps+ + +dy +++e+l+ ++ Ld +     +   + e+ +v +  +l+ ++ + +++G++
  gene991|gene991|rna990|rna990  83 RIPSEDSEKDYIQELEYLIVHNELDNFIELMNQSKINMEKFEVVVLHNLAEQIKEGNDAGGL 144
                                    55899999******************98888888888999999999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1631  (0.0909699); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1327.83
//
Query:       gene992|gene992|rna991|rna991  [L=142]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-16   61.1   0.7    1.3e-16   60.9   0.7    1.0  1  TMEM208_SND2    SRP-independent targeting protein 2/TMEM208
  ------ inclusion threshold ------
      0.023   13.1   0.3      0.023   13.1   0.3    1.6  2  SID-1_RNA_chan  dsRNA-gated channel SID-1


Domain annotation for each model (and alignments):
>> TMEM208_SND2  SRP-independent targeting protein 2/TMEM208
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.7   1.4e-20   1.3e-16       3     131 ..       4     130 ..       2     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.4e-20
                   TMEM208_SND2   3 kksaKkiaeeNkatLknlrlislavnalylllrlllrsslrprslllylllslpalllyyvlekmgrpkydedg...elv 79 
                                    +k++ +  eeN+ t + l + +++ n+ +l++ l+     + rs+ +yl+ s+p++l++y+l +++ p+++++g   +lv
  gene992|gene992|rna991|rna991   4 SKAQMRVFEENRVTRRLLLRSMILYNVCTLAMYLVN----KERSISTYLVRSIPEALAIYYLYRISAPTITSEGnttTLV 79 
                                    789999999**9999999999999999888877766....9999***************************888788*** PP

                   TMEM208_SND2  80 dsGeDLsegGlteymfDviyltwivqvlsilfgnkfWllylviPayalYklw 131
                                    + G  Ls +G ++ +fD+++++++v++l + +  k Wllyl   +  +Y l 
  gene992|gene992|rna991|rna991  80 NPGAALSGKGHVSVAFDLLFISMLVKLLLLYSR-KSWLLYLFFVISCCYELL 130
                                    ****************************99999.*********999999874 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   2.6e-06     0.023     453     509 ..      10      66 ..       2      80 .. 0.85
   2 ?   -1.7   0.5      0.08   7.2e+02     385     414 ..      95     124 ..      88     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-06
                 SID-1_RNA_chan 453 csrplyksrmvllvlgnlvnvslavlglvlkpkdfasylLaifivnlllYlvfYiim 509
                                    ++++    r +ll  ++l+nv+ ++++lv k++++++yl++ +   l +Y ++ i  
  gene992|gene992|rna991|rna991  10 VFEENRVTRRLLLRSMILYNVCTLAMYLVNKERSISTYLVRSIPEALAIYYLYRISA 66 
                                    56666778999*******************************999*****9997765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.08
                 SID-1_RNA_chan 385 fallavvillgvigvlegknkfwilfsiih 414
                                    f ll + +l+ ++ +++ k+++++lf +i 
  gene992|gene992|rna991|rna991  95 FDLLFISMLVKLLLLYSRKSWLLYLFFVIS 124
                                    555555555555656666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 934.12
//
Query:       gene993|gene993|rna992|rna992  [L=103]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-14   53.8   0.0    1.5e-14   53.5   0.0    1.1  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
    1.7e-05   24.4   0.0    2.3e-05   24.1   0.0    1.1  1  ubiquitin    Ubiquitin family
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.15   12.5   0.0    1.2  1  Ubiquitin_5  Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.0   2.6e-18   1.5e-14       1      71 [.      25      94 ..      25      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 2.6e-18
                                   EEEEEEESSS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEEEEEE CS
                      Rad60-SLD  1 ikiilkgkdgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdtidvv 71
                                   + ++l+++dg  + ++Vk +tt++k+++a+ + +g    +++rL+F+G+ +dp +t++d ++e +++++vv
  gene993|gene993|rna992|rna992 25 MPLKLVDQDGTMLVFNVKVNTTFKKILDAFSRNVGKNS-SEFRLLFNGKNIDPGKTPNDFGFEGNEELEVV 94
                                   679***********************************.*******************************8 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   3.8e-09   2.3e-05       6      71 ..      32      97 ..      27      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.8e-09
                                   TTSEEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEESS CS
                      ubiquitin  6 ldgkkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlvlrl 71
                                   +dg+ + + v+ ++t +++ ++ ++  g   +++rL+++Gk ++  +t+ + g + +  l++v ++
  gene993|gene993|rna992|rna992 32 QDGTMLVFNVKVNTTFKKILDAFSRNVGKNSSEFRLLFNGKNIDPGKTPNDFGFEGNEELEVVTSQ 97
                                   88999999******************************************************9987 PP

>> Ubiquitin_5  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.4e-05      0.15      33      85 ..      36      88 ..       7      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.4e-05
                    Ubiquitin_5 33 kklletkLdvtgkelvskiaeefglkensiKlilngklleldktLeeQgvknn 85
                                     ++++k + t k+++++ + + g + ++ +l+ ngk ++++kt ++ g + n
  gene993|gene993|rna992|rna992 36 MLVFNVKVNTTFKKILDAFSRNVGKNSSEFRLLFNGKNIDPGKTPNDFGFEGN 88
                                   345688999999*******************************9888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 768.43
//
Query:       gene994|gene994|rna993|rna993  [L=277]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-05   22.1   2.8      0.013   14.6   0.3    2.1  2  Paf1      Paf1
  ------ inclusion threshold ------
      0.034   14.6   1.4         10    6.7   0.1    2.4  2  DUF234    Archaea bacterial proteins of unknown function
       0.11   12.8   0.0       0.19   12.0   0.0    1.4  1  Pro_CA    Carbonic anhydrase


Domain annotation for each model (and alignments):
>> Paf1  Paf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   2.1e-06     0.013     154     194 ..     114     152 ..      74     179 .. 0.74
   2 !    7.9   0.1   0.00023       1.4     291     326 ..     197     232 ..     190     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-06
                           Paf1 154 qika.iektFedakkplkdlkHpskknlkaVealpllPDfel 194
                                      ++ i+++Fed+ +++    Hp +k++++ e+++l+P f+ 
  gene994|gene994|rna993|rna993 114 DYQKyIQESFEDVDSTII---HPVDKDIQVEETYNLFPGFDE 152
                                    235569***********8...*****************9874 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00023
                           Paf1 291 gyeenlllvfrddkkkavyYneletrveLrkrRkk...e 326
                                    + ++ l+++++++    +yYne+ t  +L+  Rkk    
  gene994|gene994|rna993|rna993 197 RVDDFLVFHIKNG---NAYYNEVSTLYRLQEPRKKkkqT 232
                                    5666666666666...9************9888883430 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0018        11       8      45 ..      96     132 ..      93     147 .. 0.82
   2 ?    6.7   0.1    0.0017        10      44      74 ..     219     249 ..     204     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0018
                         DUF234   8 nrseielgeseevlekikeelneyvgkvFEelvrelll 45 
                                    + + +e+++ +e +++i  ++++y+++ FE++   ++ 
  gene994|gene994|rna993|rna993  96 RAEVLERERIKESVNRIF-DYQKYIQESFEDVDSTIIH 132
                                    567899999999999998.99**********9887776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0017
                         DUF234  44 llelnkagklpfrftkvGrwWkkeeeiDiva 74 
                                    l++l++ +k + +  k G+wW +++ i ++ 
  gene994|gene994|rna993|rna993 219 LYRLQEPRKKKKQTGKKGSWWSRRSKISVIQ 249
                                    55556666667778999**********9986 PP

>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.19      81     142 ..      63     128 ..      48     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                                    SSHHHHHHHHHHHHHHHCHHHHHTTS....SHHHHHHHHHHHHHHHHHHHHHCS.HHHHHHHHTTS- CS
                         Pro_CA  81 agaidkwlekirealekveeelesek....ekearerlleeenVaeqlenLlek.pvvreavekgkl 142
                                     ++++ ++++i+ +++++++  ++++    ++e+r+++le+e ++e+++++ ++ + ++e++e+ + 
  gene994|gene994|rna993|rna993  63 IDFMGMVINHIEGSVQNTKNL-DHPSevlkDSERRAEVLERERIKESVNRIFDYqKYIQESFEDVDS 128
                                    567888999999999996553.3333356699999*******************999*999987664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1589.28
//
Query:       gene995|gene995|rna994|rna994  [L=1104]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-65  219.0   1.0    7.6e-65  218.4   1.0    1.3  1  SMC_N         RecF/RecN/SMC N terminal domain
    9.2e-24   84.0   0.1    3.4e-23   82.2   0.0    2.0  2  SMC_hinge     SMC proteins Flexible Hinge Domain
    1.1e-13   51.7   6.2      4e-06   26.9   0.0    3.5  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.6e-12   47.8   4.4    1.6e-12   47.8   4.4    4.2  2  AAA_15        AAA ATPase domain
    1.2e-06   28.2   0.0    2.2e-06   27.3   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.099   12.9   0.0        0.5   10.6   0.0    2.3  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.24   10.7   2.7        1.6    8.0   0.0    3.3  3  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.36   11.3  17.9       0.36   11.3   0.0    4.7  4  ABC_tran      ABC transporter


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.4   1.0   3.4e-68   7.6e-65       2     216 ..       5    1089 ..       4    1093 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.4 bits;  conditional E-value: 3.4e-68
                                     EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEE CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaev 79  
                                     l++++i+nFksy+g++vi  ++++ftaivG+NGSGKsn++d+ilFvLG+r+  k+r+++++ li+k       + ++v
  gene995|gene995|rna994|rna994    5 LESITIHNFKSYKGTHVIQGLDPKFTAIVGANGSGKSNVIDSILFVLGFRAR-KMRHSSMEGLIYK--GDGTESMCYV 79  
                                     799*********************************************9655.************8..7777889*** PP

                                     EEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...................... CS
                                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                          SMC_N   80 eitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske...................... 135 
                                     e+ f+           ++ i+r+v    +s+y+++g+e++++ v++ll+s+g+++e                      
  gene995|gene995|rna994|rna994   80 ELGFN-----------KFRIKREVCLPRRSRYFVDGEEASSAVVMSLLNSEGVDMEhnrflilqgeieniamikpmgd 146 
                                     **653...........489*********************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  147 glleyledvigtneykeeiekeerehqrvaeeyegksaalkfyekeyehierkkeenlriakrkaeclyldvdlqllc 224 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  225 sswnrkklerlvserkeieekletivrknkenggkveilerkgvkarekargseerflearreyqraerrrkmleeek 302 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  303 ekelrrmeelsreieeikcgedrrqkmrtkykeeidqntkeisrcnvlgeklrleidkdqrrvdkearekveeilree 380 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  381 ermmkllerkgeigerqrdtesklgglisrkseivrriedienkllridgkktvpgrseeaveneikeiekdlaetrr 458 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  459 emgrrmqrveeykeneeknskeseilkrvghvkgvygklsdlgevesrydkafrvagkglnsivvdttctaeecisli 536 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  537 ksqglgratfiildrisevpnlpkesvpyiyslvkcspefqkcfyfalkdtlvcdelevakklafgrqrkrvvtidgk 614 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  615 lieksgvmsggkisgriksveelekaclkmtelkkmkveelevirslkergslcktleglrselecvvkdievvskki 692 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  693 nkeeiekvemelgeirkkvsslrsivesltdietrrkkenllnlneriemfekrnlelrlqiegcvetglkdkekele 770 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  771 errkrfsritiedisgirsrmveceseyredagnlkeilneiasiksilgndyhmeidlknrlddvddkgdecrrqic 848 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  849 esernigilesevrryagicndvhskvraedmdeeemeemmkkinatiaklrkeeegeidmnvfgdyekakieyekvk 926 
                                     ****************************************************************************** PP

                                     .............................................................................. CS
                                     .............................................................................. RF
                          SMC_N  136 .............................................................................. 135 
                                                                                                                   
  gene995|gene995|rna994|rna994  927 eehkwlesrlkkigasveclkkrrhdefmkgflqisenlkeiykaityggnaelelvdhldpfsegvilsvmppkksw 1004
                                     ****************************************************************************** PP

                                     ....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                                     ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  136 ....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209 
                                         +LSgGektL++laL+fA++++kp+p+y++DeidaaLD +nv+ +++++ke s++aQf+vislr++m+e +++l+
  gene995|gene995|rna994|rna994 1005 ksvgNLSGGEKTLSSLALIFALHRYKPSPFYVMDEIDAALDYRNVSVISNFIKEMSETAQFLVISLRSDMFELSETLL 1082
                                     ****************************************************************************** PP

                                     EEEEEET CS
                                     xxxxxxx RF
                          SMC_N  210 gvtkven 216 
                                     gv+k++n
  gene995|gene995|rna994|rna994 1083 GVYKTDN 1089
                                     ****665 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.9   6.6e+03      34      71 ..     236     275 ..     230     280 .. 0.58
   2 !   82.2   0.0   1.5e-26   3.4e-23       2     117 .]     491     600 ..     490     600 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.9
                      SMC_hinge  34 vvedeetakkiieflkkk..nagratflpldrikqknkad 71 
                                    v e +e+ +k+   ++k+  n+g++++l  + +k ++ka 
  gene995|gene995|rna994|rna994 236 VSERKEIEEKLETIVRKNkeNGGKVEILERKGVKAREKAR 275
                                    5555555555554555443348888888777777666655 PP

  == domain 2  score: 82.2 bits;  conditional E-value: 1.5e-26
                      SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandknsgav 81 
                                    kgv+G l dl ev+++y+kA+  ++g+ l+++vv++  ta+++i+ +k++ +gratf+ ldri+  ++ +++      + 
  gene995|gene995|rna994|rna994 491 KGVYGKLSDLGEVESRYDKAF-RVAGKGLNSIVVDTTCTAEECISLIKSQGLGRATFIILDRISEVPNLPKE-----SVP 564
                                    89*******************.678999*************************************9888887.....79* PP

                      SMC_hinge  82 plidlvevddelrkalryllgdtlvvdsldeAeela 117
                                    +  +lv++ +e++k+++++l+dtlv+d l++A++la
  gene995|gene995|rna994|rna994 565 YIYSLVKCSPEFQKCFYFALKDTLVCDELEVAKKLA 600
                                    *********************************986 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.9e-09   6.5e-06       1      38 [.      29      70 ..      29      97 .. 0.77
   2 ?   -3.1   1.3       2.4   5.3e+03     112     209 ..     316     414 ..     247     482 .. 0.62
   3 ?   -0.8   0.1      0.47   1.1e+03      93     203 ..     682     788 ..     672     815 .. 0.74
   4 !   26.9   0.0   1.8e-09     4e-06     235     296 ..    1008    1069 ..     970    1069 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.9e-09
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarl....drdvegltdelsg 38
                                   +++++G+NgsGKSn++d + ++ ++    +r++ +++ +  g
  gene995|gene995|rna994|rna994 29 FTAIVGANGSGKSNVIDSILFVLGFrarkMRHSSMEGLIYKG 70
                                   89********************99887776666665555555 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                         AAA_21 112 npeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke.rigllnifadyfgfakekrllqrlvr 190
                                    + e ++  + ++  + k ++ +++n+++ ++ +++  +   ++ ++++   ke r  + +i +++   +k++++ ++   
  gene995|gene995|rna994|rna994 316 IEEIKCGEDRRQKMRTKYKEEIDQNTKEISRCNVLGEKLRLEIDKDQRRVDKEaREKVEEILREEERMMKLLERKGEIGE 395
                                    44444555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                         AAA_21 191 slklveielsdlgegeeli 209
                                    + ++ e++l  l  ++ +i
  gene995|gene995|rna994|rna994 396 RQRDTESKLGGLISRKSEI 414
                                    5555555555555444444 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.47
                         AAA_21  93 llesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnif 172
                                    ++ +   ++k ++ee+ ++  e  +ir+ vs+ +++  s+ + +++ ++++l+++ +r++ +++ + +      ++ +  
  gene995|gene995|rna994|rna994 682 VKDIEVVSKKINKEEIEKVEMELGEIRKKVSSLRSIVESLTDIETRRKKENLLNLNERIEMFEKRNLE----LRLQIEGC 757
                                    56667778888899999999999999999999999999999999999999999999998877766655....55666666 PP

                         AAA_21 173 adyfgfakekrllqrlvrslklveielsdlg 203
                                     ++  ++kek+l +r+ r ++     +s ++
  gene995|gene995|rna994|rna994 758 VETGLKDKEKELEERRKRFSRITIEDISGIR 788
                                    6666666666666666666666665555555 PP

  == domain 4  score: 26.9 bits;  conditional E-value: 1.8e-09
                         AAA_21  235 relSdGtkrll..alltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                      +lS G k l   al+ al+r  ++ ++++ DE+++ L+++ ++ +  ++ke s+  aQ+++ +
  gene995|gene995|rna994|rna994 1008 GNLSGGEKTLSslALIFALHRYKPS-PFYVMDEIDAALDYRNVSVISNFIKEMSE-TAQFLVIS 1069
                                     6789999999656**********99.*****************************.****9876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   4.4   7.1e-16   1.6e-12       3     262 ..       5     352 ..       1     548 [. 0.55
   2 ?  -13.0  20.5         8   1.8e+04     118     284 ..     728     930 ..     626    1068 .. 0.55

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 7.1e-16
                         AAA_15   3 IkkikikNFRslkdvei..dlseeltvliGkNnsGKSsilealdlFlnnkekkn....................kkviki 60 
                                    +++i+i NF+s+k +++   l++++t ++G+N+sGKS++++ + + l    +k                     +     
  gene995|gene995|rna994|rna994   5 LESITIHNFKSYKGTHViqGLDPKFTAIVGANGSGKSNVIDSILFVLGFRARKMrhssmegliykgdgtesmcyV----- 79 
                                    78***********97774469999*******************99999886666888995555555555555550..... PP

                         AAA_15  61 ekedleifeniseskdikIdvef......................................................... 83 
                                              +  +++++I+ e                                                          
  gene995|gene995|rna994|rna994  80 ----------ELGFNKFRIKREVclprrsryfvdgeeassavvmsllnsegvdmehnrflilqgeieniamikpmgdgll 149
                                    ..........5555555555555555555555555555555555555555555555666666666666666666666666 PP

                         AAA_15  84 ................................aekekakeyektlkskekkkadlllkkkesdlkktikdkklklkkne. 130
                                                                    +             s + k+++++++++e+++ + ++  k k ++ + 
  gene995|gene995|rna994|rna994 150 eyledvigtneykeeiekeerehqrvaeeyegK-------------SAALKFYEKEYEHIERKKEENLRIAKRKAECLYl 216
                                    666666555444443332222222111111110.............1111222222222222222222222222222210 PP

                         AAA_15 131 ..lsdekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkee...elknvlksaiiklllisakRn 205
                                      + +  +s +++k+   l +e++e +ek ++ + ++ke+  k+    ++ +k  e     ++ + +a ++++  + +R+
  gene995|gene995|rna994|rna994 217 dvDLQLLCSSWNRKKLERLVSERKEIEEKLETIVRKNKENGGKVEILERKGVKAREkarGSEERFLEARREYQRAERRRK 296
                                    00222233334444444444444444444444444444444444333333333333555444444444444444444444 PP

                         AAA_15 206 vsdedsekkssllgklkekileealqekl....eeelteklkeiqeklkeidkklaeelk......k 262
                                      +e++ek+   +++l ++i e +  e      + + +e++++  +++           +      +
  gene995|gene995|rna994|rna994 297 MLEEEKEKELRRMEELSREIEEIKCGEDRrqkmRTKYKEEIDQNTKEI-----------SrcnvlgE 352
                                    444555555555555444444422111112222111111111111111...........12222221 PP

  == domain 2  score: -13.0 bits;  conditional E-value: 8
                         AAA_15 118 tikdkklklkknelsdekisvekkks...........kkelpkekeeklekekeelkidkedlkklikkleeslkkee.. 184
                                    ++k++ l+       +e+i+ ++k +           +  l+++++e +e +k    i+ ed+  + +++ e+ +++   
  gene995|gene995|rna994|rna994 728 RKKENLLN------LNERIEMFEKRNlelrlqiegcvETGLKDKEKELEERRKRFSRITIEDISGIRSRMVECESEYRed 801
                                    12222222......233333333333555555777776777777777777777777777777777777777777777766 PP

                         AAA_15 185 .........elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl..................... 234
                                             e+ ++ + +  ++    + +n  d+ ++k     +++ ++i e+                           
  gene995|gene995|rna994|rna994 802 agnlkeilnEIASIKSILGNDYHMEIDLKNRLDDVDDKG----DECRRQICES-----Ernigilesevrryagicndvh 872
                                    665555555333333333333333333333333333332....2222222222.....0223444455566667777777 PP

                         AAA_15 235 .....eeelteklkeiqeklkeidkklaeelk....kilkkkidkikkfnykgkkneei 284
                                         e++++e+ +e+ +k++ ++ kl +e++     +++ + +k  k++y ++k+e +
  gene995|gene995|rna994|rna994 873 skvraEDMDEEEMEEMMKKINATIAKLRKEEEgeidMNVFGDYEK-AKIEYEKVKEEHK 930
                                    777776666666666666666666666665555443333333333.2444444444443 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   9.7e-10   2.2e-06       1      46 [.       5      51 ..       5      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.7e-10
                         AAA_29  1 LkrlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                   L+++ + N  +++g h+i+     +t ++G++GsGKS ++D+i ++L
  gene995|gene995|rna994|rna994  5 LESITIHNFKSYKGtHVIQGLDPKFTAIVGANGSGKSNVIDSILFVL 51
                                   78999*********99887543338*******************998 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       7.7   1.7e+04      23      36 ..     612     625 ..     598     626 .. 0.78
   2 ?   10.6   0.0   0.00022       0.5      28      52 ..    1005    1028 ..     996    1057 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.7
                        SbcCD_C  23 ekelsrssgtlSGG 36 
                                    +++l ++sg +SGG
  gene995|gene995|rna994|rna994 612 DGKLIEKSGVMSGG 625
                                    45688999999999 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                        SbcCD_C   28 rssgtlSGGekqflaylalaaalaa 52  
                                     +s+g+lSGGek +l +lal +al+ 
  gene995|gene995|rna994|rna994 1005 KSVGNLSGGEK-TLSSLALIFALHR 1028
                                     789********.**********975 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00073       1.6      42      61 ..      30      49 ..       7      56 .. 0.84
   2 ?    0.4   0.2      0.15   3.3e+02      82     163 ..     650     732 ..     641     754 .. 0.72
   3 ?   -2.3   0.0      0.99   2.2e+03     113     145 ..     766     798 ..     750     817 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00073
                                   EEEE--TTSSHHHHHHHHHH CS
                   FtsK_SpoIIIE 42 llvaGatgsGKStalntLil 61
                                   + ++Ga gsGKS+++ +++ 
  gene995|gene995|rna994|rna994 30 TAIVGANGSGKSNVIDSILF 49
                                   68************998876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.15
                                    SSCGGGTT-TTBSS..S-B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-....... CS
                   FtsK_SpoIIIE  82 velsalediphlls.vavatdperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflvlDnyddla 160
                                    ++ ++le i  l +  +  +  e  ++ le +vk +e + ++++++ ++++++  gei ++   ++ +v  + D     +
  gene995|gene995|rna994|rna994 650 MKVEELEVIRSLKErGSLCKTLEGLRSELECVVKDIEVVSKKINKEEIEKVEMELGEIRKKVSSLRSIVESLTDIETRRK 729
                                    44444444444444444778889999999************************999999988888888877776554444 PP

                                    ... CS
                   FtsK_SpoIIIE 161 aen 163
                                    +en
  gene995|gene995|rna994|rna994 730 KEN 732
                                    444 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.99
                                    HHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT CS
                   FtsK_SpoIIIE 113 vkemeeryalfreagvrsiaaydgeiaedpldi 145
                                    +ke+eer + f+   +++i++ ++ + e + + 
  gene995|gene995|rna994|rna994 766 EKELEERRKRFSRITIEDISGIRSRMVECESEY 798
                                    577788888888777777777666655555444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.36      13      31 ..      29      47 ..      26      52 .. 0.88
   2 ?   -7.1   7.6         8   1.8e+04      99      99 ..     334     334 ..     180     492 .. 0.64
   3 ?   -0.8   0.2      0.89     2e+03      53      91 ..     670     710 ..     641     783 .. 0.61
   4 ?   10.2   0.0   0.00036      0.81      29     125 ..     894    1026 ..     834    1041 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkll 31
                                    +aivG nG+GKS ++  +
  gene995|gene995|rna994|rna994 29 FTAIVGANGSGKSNVIDSI 47
                                   589***********99887 PP

  == domain 2  score: -7.1 bits;  conditional E-value: 8
                                    C CS
                                    x RF
                       ABC_tran  99 d 99 
                                    +
  gene995|gene995|rna994|rna994 334 K 334
                                    1 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.89
                                    -HHHCCHCEEEE-SS--S-TTSBHHHH............HHHTCHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxx RF
                       ABC_tran  53 eleslrkeigvlpqepqlfpeltvren............esdeeiekalsk 91 
                                    +le lr+e++++ ++ ++ +++ ++e+            +          k
  gene995|gene995|rna994|rna994 670 TLEGLRSELECVVKDIEVVSKKINKEEiekvemelgeirK----------K 710
                                    4555566666666665555555455544433333333321..........1 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.00036
                                     HHHTTSS--SEEEE...........EETTCEGGG......B-HHHCCHCEEEE-SS...--S-TTSBHHHH....... CS
                                     xxxxxxxxxxxxxx...........xxxxxxxxx......xxxxxxxxxxxxxxxx...xxxxxxxxxxxx....... RF
                       ABC_tran   29 kllagllkpteGei...........lldgkdlke......qeleslrkeigvlpqe...pqlfpeltvren....... 79  
                                     +++a+l k +eGei           +++ +++ke       +l++  +++++l++    +                  
  gene995|gene995|rna994|rna994  894 ATIAKLRKEEEGEIdmnvfgdyekaKIEYEKVKEehkwleSRLKKIGASVECLKKRrhdE----------Fmkgflqi 961 
                                     578999999999997777775555533333333322222244444444444444443323..........24445544 PP

                                     ...................HHHTCHHHHHHHSTTGG.............TTCBGESTTSGGS-HHHHHHHHHHHHHHH CS
                                     ...................xxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   80 ...................esdeeiekalsklglke.............lkdtvvksspssLSgGqkqrvalarallk 125 
                                                        e               +             ++ ++  +s  +LSgG+k   +la +++ 
  gene995|gene995|rna994|rna994  962 senlkeiykaityggnaelELV-------------DhldpfsegvilsvMPPKKSWKSVGNLSGGEKTLSSLALIFAL 1026
                                     4226665554444444333333.............255555555555556666666888**********999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2143  (0.119527); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 1.41u 0.39s 00:00:01.79 Elapsed: 00:00:00.62
# Mc/sec: 5323.84
//
Query:       gene996|gene996|rna995|rna995  [L=349]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-12   48.6   0.1    3.1e-12   47.2   0.0    1.7  2  2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
    1.6e-12   47.9   0.0    9.9e-12   45.4   0.0    2.1  2  2OG-FeII_Oxy_4  2OG-Fe(II) oxygenase superfamily


Domain annotation for each model (and alignments):
>> 2OG-FeII_Oxy_3  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.8   1.6e+04      62      72 ..      52      62 ..      33      66 .. 0.60
   2 !   47.2   0.0   3.4e-16   3.1e-12       5      95 ..      84     166 ..      80     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.8
                                   -TT-EEEEE-. CS
                 2OG-FeII_Oxy_3 62 kkgrlvlFesd 72
                                   ++ +l++F+s+
  gene996|gene996|rna995|rna995 52 EREDLAFFKSS 62
                                   45566666665 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 3.4e-16
                                    EE-TT-EEEEE-SS----TT.-.EEEEEEEEE....ET-B--EEE............---TT-EEEEE-..B-TEEE--B CS
                 2OG-FeII_Oxy_3   5 rygegqeykpHvDnfekeegsgqrrltvllyLnekeseeGGelelyekdk..eavkikpkkgrlvlFesdellpHevlpv 82 
                                     y++g+++ +H+D+      +g+rr+++ +yL   e+++ Gel lye+d    +++++ k++rlv+Fe+++++ Hev   
  gene996|gene996|rna995|rna995  84 YYRKGDYLLCHDDK------TGSRRFAFSYYL---EDYDSGELILYENDCmtVSKRVEVKANRLVVFEVSDISFHEVGYC 154
                                    68999********5......479*********...689**********99999999999**********99999*****9 PP

                                    .-SS-EEEEEEEE CS
                 2OG-FeII_Oxy_3  83 tkggeRlsltgwi 95 
                                    +k+  R ++tgw+
  gene996|gene996|rna995|rna995 155 EKD-GRRAFTGWL 166
                                    776.9*******8 PP

>> 2OG-FeII_Oxy_4  2OG-Fe(II) oxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.1e-15   9.9e-12       4      92 ..      83     166 ..      80     167 .. 0.86
   2 ?   -0.3   0.0       0.2   1.8e+03      33      47 ..     242     256 ..     225     286 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.1e-15
                 2OG-FeII_Oxy_4   4 ssYekgdvllnHdDvlegeRrvayilyleeeWkeddGGaLllsdde.gdvtksivPkwnqlvlFevkeshsvaevasvae 82 
                                    s Y+kgd+ll+HdD+ +g+Rr+a+ +yle+     d G+L l++++  +v+k++  k n+lv+Fev ++ s++ev   ++
  gene996|gene996|rna995|rna995  83 SYYRKGDYLLCHDDK-TGSRRFAFSYYLED----YDSGELILYENDcMTVSKRVEVKANRLVVFEV-SDISFHEVGYCEK 156
                                    78*************.89**********75....4678886655551689****************.5578999988889 PP

                 2OG-FeII_Oxy_4  83 keRlsisgWf 92 
                                      R + +gW+
  gene996|gene996|rna995|rna995 157 DGRRAFTGWL 166
                                    99*******8 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.2
                 2OG-FeII_Oxy_4  33 eeWkeddGGaLllsd 47 
                                    e Wk +dGG  +++ 
  gene996|gene996|rna995|rna995 242 EGWKLKDGGFYHFRV 256
                                    789*****9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2384.57
//
Query:       gene997|gene997|rna996|rna996  [L=198]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      9e-34  116.9   0.7    9.4e-34  116.8   0.7    1.1  1  Sec62     Translocation protein Sec62
  ------ inclusion threshold ------
      0.068   13.2   0.0       0.11   12.6   0.0    1.3  1  DEP       Domain found in Dishevelled, Egl-10, and Pleckstrin
       0.17   10.6   0.6       0.17   10.6   0.6    1.1  1  DUF2207   Predicted membrane protein (DUF2207)
       0.64   10.4   5.7        1.2    9.5   5.7    1.5  1  DUF4149   Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> Sec62  Translocation protein Sec62
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   0.7   2.1e-37   9.4e-34      77     202 ..      70     193 ..      16     198 .] 0.85

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 2.1e-37
                          Sec62  77 kkkkvkleieeeqefvddnevYvWiYepkqlktlligllvvvailavvlFPLWPaelrkgvy.YLSiaalgllglilala 155
                                    k++  + ++  +q f +++++Yv   e+++  +l++  + v++++++vlF +WP+ +++  + Y+   + g++ +i++la
  gene997|gene997|rna996|rna996  70 KRNIRECDVVLDQRF-QEDHHYVFANEKTSNISLVLCGVFVLVTFTIVLFRMWPRNIQQRLFsYMVYPLGGFITFIIVLA 148
                                    444445778889***.************99999999999999***************998877***************** PP

                          Sec62 156 ivRlilflivllvtkgklhlWlfPnlfeDvGfldSFrPlYeyeekdk 202
                                    i+Rlilf i++++ +++  +WlfPnlfeDvGf++SF Pl+ey+ ++k
  gene997|gene997|rna996|rna996 149 IIRLILFSITYILYSPG--IWLFPNLFEDVGFFESFVPLWEYHGSKK 193
                                    *****************..************************4222 PP

>> DEP  Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.4e-05      0.11      17      69 ..      30      91 ..      15      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                                   E-HHHHHHHHHHHHTSSSSHHHHHHHHHHHHHCTSCECSSSSHCC...........--SSSSS- CS
                            DEP 17 cftGseavdWLldnldiedreeAvalgqlLldqgliehvedkhqe...........Frdskqaf 69
                                   +f Gs+a   L ++    d ++A +++q+Ll++ ++  v+  +++           F+++++++
  gene997|gene997|rna996|rna996 30 VFKGSDALVLLTKKG--LDSSQARSVMQELLNESILFKVSINKRNirecdvvldqrFQEDHHYV 91
                                   799**********99..5669******************8888888899999999999996554 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   3.8e-05      0.17     366     431 ..      70     156 ..       4     186 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.8e-05
                        DUF2207 366 k........kergyfdkkg...kkklkklsalglgliilglilillallllvll............lvfllilllillli 422
                                    k        +  + f+++     ++ k++++ ++++++++l+ +  +++l+ ++            +++l+ ++++++++
  gene997|gene997|rna996|rna996  70 KrnirecdvVLDQRFQEDHhyvFANEKTSNISLVLCGVFVLVTF--TIVLFRMWprniqqrlfsymVYPLGGFITFIIVL 147
                                    24555566633333333331111222333334444433333333..3333344466999**9877744444444444444 PP

                        DUF2207 423 aiivlllfs 431
                                    aii l+lfs
  gene997|gene997|rna996|rna996 148 AIIRLILFS 156
                                    444444443 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.7   0.00027       1.2       7      59 ..     105     151 ..     100     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00027
                        DUF4149   7 lGsqlwvtfvvapvlfrsLprhqfgelqsklFplyfglglalsvlllltevav 59 
                                    +G+ + vt   ++vlfr  pr+    +q++lF+++ +  +++ ++++++ +++
  gene997|gene997|rna996|rna996 105 CGVFVLVT--FTIVLFRMWPRN----IQQRLFSYMVYPLGGFITFIIVLAIIR 151
                                    44444454..69**********....***********7777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1222.65
//
Query:       gene998|gene998|rna997|rna997  [L=170]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00024   21.4   0.1    0.00043   20.6   0.1    1.4  1  Med27     Mediator complex subunit 27


Domain annotation for each model (and alignments):
>> Med27  Mediator complex subunit 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.4e-08   0.00043      20      85 ..      97     163 ..      95     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.4e-08
                          Med27  20 ekallhflnsrqrelallsllewissYsnlfskpCkkCkkllssdkqlPpvirdvr.dsleayHesC 85 
                                    ++++l+++ s ++++ l    +++ +Y     +pC+ C+++     +l p+ r+++ d + + H++C
  gene998|gene998|rna997|rna997  97 DNHILCSIRSEPTDKHLGLANDMLMMYIGYERAPCDVCGSYATIPGFLTPTCRSIEeDFILVHHSQC 163
                                    6899999999*********************************999999999999944455666788 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1431.34
//
Query:       gene999|gene999|rna998|rna998  [L=169]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00075   19.4   0.0    0.00094   19.1   0.0    1.2  1  Med18     Med18 protein


Domain annotation for each model (and alignments):
>> Med18  Med18 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.2e-08   0.00094     110     239 ..      53     164 ..      21     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.2e-08
                                    EEEE----SS-SSS-EEEEEEEEEE..ESS-HTHHHHHTTEEEEEEEEEEEEEEEETTEEEEEEEEE.EESSTTB...-T CS
                          Med18 110 LqisDiPeagknqkvlvrtiyestlverkdsllqfledlGysvineYivkGvrFfhgdivielfkvfkrddekqeelpdk 189
                                    L  ++ P+  kn+  l  ++++s++ ++ ++l  fl +lG++++++  v+ + F ++   ie++k  + +++k++     
  gene999|gene999|rna998|rna998  53 LISRGAPDRNKNRMSLCSKVQRSRV-RTLGTLKVFLFSLGFELVRQGKVELITFEKEPGHIEISKHVSEESSKHK----- 126
                                    556799******************7.999************************************9976666555..... PP

                                    STEEESSTT--EEEEEEEEES-TTSHHHHHHHHHHHHHHHHHHCTTS-EB CS
                          Med18 190 iklklldesntflikayinvnkstdiesinqgvkeLlklkeeLkglvkLe 239
                                          ++ + +l+k+++  +++ d e++ ++v       eeL+g v+L 
  gene999|gene999|rna998|rna998 127 ------ETDDYYLVKVFVISENAHDGERMLSRV------IEELEGQVQLV 164
                                    ......799999999999988888887776555......66777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1085.01
//
Query:       gene1000|gene1000|rna999|rna999  [L=330]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2072.73
//
[ok]
